One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift3 ; 11 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m3_shift3 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=3; ncol=15; ---wrCAGGTAra-- ; Alignment reference a | 0 0 0 1036 986 0 3557 0 0 0 3557 1228 1214 0 0 c | 0 0 0 764 745 3557 0 0 0 0 0 538 770 0 0 g | 0 0 0 860 1059 0 0 3557 3557 0 0 1249 762 0 0 t | 0 0 0 897 767 0 0 0 0 3557 0 542 811 0 0

vfl_SANGER_5_FBgn0259789_shift4 (vfl_SANGER_5_FBgn0259789) 0.955 0.764 11.552 0.761 0.940 0.455 0.972 3 4 1 1 6 5 6 3.714 1
; positions_6nt_m3 versus vfl_SANGER_5_FBgn0259789; m=1/10; ncol2=8; w=8; offset=1; strand=D; shift=4; score= 3.7143; ----gCAGGTAG--- ; cor=0.955; Ncor=0.764; logoDP=11.552; NIcor=0.761; NsEucl=0.940; SSD=0.455; NSW=0.972; rcor=3; rNcor=4; rlogoDP=1; rNIcor=1; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=3.714; match_rank=1 a | 0 0 0 0 1 0 18 0 0 0 18 3 0 0 0 c | 0 0 0 0 1 18 0 0 0 0 0 1 0 0 0 g | 0 0 0 0 12 0 0 18 18 0 0 14 0 0 0 t | 0 0 0 0 4 0 0 0 0 18 0 0 0 0 0

vfl_SOLEXA_5_FBgn0259789_shift0 (vfl_SOLEXA_5_FBgn0259789) 0.948 0.632 10.716 0.637 0.950 0.494 0.975 8 16 2 6 1 9 3 6.429 3
; positions_6nt_m3 versus vfl_SOLEXA_5_FBgn0259789; m=2/10; ncol2=15; w=10; offset=-3; strand=D; shift=0; score= 6.4286; kkkbkCAGGTAGsyg ; cor=0.948; Ncor=0.632; logoDP=10.716; NIcor=0.637; NsEucl=0.950; SSD=0.494; NSW=0.975; rcor=8; rNcor=16; rlogoDP=2; rNIcor=6; rNsEucl=1; rSSD=9; rNSW=3; rank_mean=6.429; match_rank=3 a | 110 149 144 116 54 7 756 0 1 4 756 76 145 140 169 c | 150 123 119 212 0 749 1 0 0 0 5 75 203 227 99 g | 196 254 234 237 478 0 1 731 750 3 0 566 230 167 277 t | 229 235 264 196 229 5 3 30 10 754 0 44 183 217 160

wor_SOLEXA_2.5_FBgn0001983_rc_shift4 (wor_SOLEXA_2.5_FBgn0001983_rc) 0.781 0.624 4.606 0.271 0.876 1.959 0.878 40 17 25 28 43 45 46 34.857 38
; positions_6nt_m3 versus wor_SOLEXA_2.5_FBgn0001983_rc; m=3/10; ncol2=8; w=8; offset=1; strand=R; shift=4; score=34.8571; ----rCAGGTGk--- ; cor=0.781; Ncor=0.624; logoDP=4.606; NIcor=0.271; NsEucl=0.876; SSD=1.959; NSW=0.878; rcor=40; rNcor=17; rlogoDP=25; rNIcor=28; rNsEucl=43; rSSD=45; rNSW=46; rank_mean=34.857; match_rank=38 a | 0 0 0 0 548 20 1786 29 24 51 78 150 0 0 0 c | 0 0 0 0 5 1759 8 0 0 0 5 383 0 0 0 g | 0 0 0 0 1085 1 0 1743 1770 19 1499 645 0 0 0 t | 0 0 0 0 86 9 0 22 0 1724 127 428 0 0 0

l(1)sc_da_SANGER_5_FBgn0000413_shift4 (l(1)sc_da_SANGER_5_FBgn0000413) 0.754 0.528 8.426 0.513 0.849 2.229 0.841 52 31 5 8 55 50 55 36.571 42
; positions_6nt_m3 versus l(1)sc_da_SANGER_5_FBgn0000413; m=4/10; ncol2=7; w=7; offset=1; strand=D; shift=4; score=36.5714; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=52; rNcor=31; rlogoDP=5; rNIcor=8; rNsEucl=55; rSSD=50; rNSW=55; rank_mean=36.571; match_rank=42 a | 0 0 0 0 4 0 21 1 0 0 1 0 0 0 0 c | 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 g | 0 0 0 0 19 0 1 22 22 0 22 0 0 0 0 t | 0 0 0 0 0 0 1 0 1 23 0 0 0 0 0

l(1)sc_da_SANGER_5_FBgn0002561_shift4 (l(1)sc_da_SANGER_5_FBgn0002561) 0.754 0.528 8.426 0.513 0.849 2.229 0.841 53 32 6 9 56 51 56 37.571 43
; positions_6nt_m3 versus l(1)sc_da_SANGER_5_FBgn0002561; m=5/10; ncol2=7; w=7; offset=1; strand=D; shift=4; score=37.5714; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=53; rNcor=32; rlogoDP=6; rNIcor=9; rNsEucl=56; rSSD=51; rNSW=56; rank_mean=37.571; match_rank=43 a | 0 0 0 0 4 0 21 1 0 0 1 0 0 0 0 c | 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 g | 0 0 0 0 19 0 1 22 22 0 22 0 0 0 0 t | 0 0 0 0 0 0 1 0 1 23 0 0 0 0 0

nau_da_SANGER_5_FBgn0000413_rc_shift3 (nau_da_SANGER_5_FBgn0000413_rc) 0.754 0.603 4.460 0.175 0.865 2.318 0.855 50 20 26 31 48 54 51 40.000 51
; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0000413_rc; m=6/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 40; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=50; rNcor=20; rlogoDP=26; rNIcor=31; rNsEucl=48; rSSD=54; rNSW=51; rank_mean=40.000; match_rank=51 a | 0 0 0 6 13 0 22 0 0 0 0 0 0 0 0 c | 0 0 0 1 0 22 0 0 0 0 1 0 0 0 0 g | 0 0 0 14 9 0 0 22 22 0 16 0 0 0 0 t | 0 0 0 1 0 0 0 0 0 22 0 0 0 0 0

nau_da_SANGER_5_FBgn0002922_rc_shift3 (nau_da_SANGER_5_FBgn0002922_rc) 0.754 0.603 4.460 0.175 0.865 2.318 0.855 51 21 27 32 49 55 52 41.000 52
; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0002922_rc; m=7/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 41; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=51; rNcor=21; rlogoDP=27; rNIcor=32; rNsEucl=49; rSSD=55; rNSW=52; rank_mean=41.000; match_rank=52 a | 0 0 0 6 13 0 22 0 0 0 0 0 0 0 0 c | 0 0 0 1 0 22 0 0 0 0 1 0 0 0 0 g | 0 0 0 14 9 0 0 22 22 0 16 0 0 0 0 t | 0 0 0 1 0 0 0 0 0 22 0 0 0 0 0

CG12605_SANGER_10_FBgn0035481_rc_shift2 (CG12605_SANGER_10_FBgn0035481_rc) 0.753 0.548 3.837 0.142 0.866 2.295 0.857 54 26 29 34 47 53 50 41.857 53
; positions_6nt_m3 versus CG12605_SANGER_10_FBgn0035481_rc; m=8/10; ncol2=9; w=8; offset=-1; strand=R; shift=2; score=41.8571; --CaACAGGTG---- ; cor=0.753; Ncor=0.548; logoDP=3.837; NIcor=0.142; NsEucl=0.866; SSD=2.295; NSW=0.857; rcor=54; rNcor=26; rlogoDP=29; rNIcor=34; rNsEucl=47; rSSD=53; rNSW=50; rank_mean=41.857; match_rank=53 a | 0 0 0 14 21 0 22 2 0 0 1 0 0 0 0 c | 0 0 19 5 0 22 0 0 0 0 2 0 0 0 0 g | 0 0 1 0 0 0 0 20 22 0 16 0 0 0 0 t | 0 0 2 3 1 0 0 0 0 22 3 0 0 0 0

wor_SANGER_2.5_FBgn0001983_rc_shift4 (wor_SANGER_2.5_FBgn0001983_rc) 0.761 0.533 0.045 -0.215 0.851 2.188 0.844 45 29 56 54 53 48 53 48.286 54
; positions_6nt_m3 versus wor_SANGER_2.5_FBgn0001983_rc; m=9/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score=48.2857; ----rCAGGTG---- ; cor=0.761; Ncor=0.533; logoDP=0.045; NIcor=-0.215; NsEucl=0.851; SSD=2.188; NSW=0.844; rcor=45; rNcor=29; rlogoDP=56; rNIcor=54; rNsEucl=53; rSSD=48; rNSW=53; rank_mean=48.286; match_rank=54 a | 0 0 0 0 6 0 21 0 0 1 0 0 0 0 0 c | 0 0 0 0 0 21 0 0 0 0 0 0 0 0 0 g | 0 0 0 0 12 0 0 21 21 0 21 0 0 0 0 t | 0 0 0 0 1 0 0 0 0 20 0 0 0 0 0

esg_SANGER_2.5_FBgn0001981_rc_shift4 (esg_SANGER_2.5_FBgn0001981_rc) 0.757 0.530 0.124 -0.209 0.850 2.204 0.843 48 30 51 53 54 49 54 48.429 55
; positions_6nt_m3 versus esg_SANGER_2.5_FBgn0001981_rc; m=10/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score=48.4286; ----aCAGGTG---- ; cor=0.757; Ncor=0.530; logoDP=0.124; NIcor=-0.209; NsEucl=0.850; SSD=2.204; NSW=0.843; rcor=48; rNcor=30; rlogoDP=51; rNIcor=53; rNsEucl=54; rSSD=49; rNSW=54; rank_mean=48.429; match_rank=55 a | 0 0 0 0 7 0 11 1 0 0 0 0 0 0 0 c | 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 g | 0 0 0 0 2 0 0 10 11 0 11 0 0 0 0 t | 0 0 0 0 2 0 0 0 0 11 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m3_shift3 (positions_6nt_m3)																	; positions_6nt_m3; m=0 (reference); ncol1=10; shift=3; ncol=15; ---wrCAGGTAra-- ; Alignment reference a \| 0 0 0 1036 986 0 3557 0 0 0 3557 1228 1214 0 0 c \| 0 0 0 764 745 3557 0 0 0 0 0 538 770 0 0 g \| 0 0 0 860 1059 0 0 3557 3557 0 0 1249 762 0 0 t \| 0 0 0 897 767 0 0 0 0 3557 0 542 811 0 0
vfl_SANGER_5_FBgn0259789_shift4 (vfl_SANGER_5_FBgn0259789)	0.955	0.764	11.552	0.761	0.940	0.455	0.972	3	4	1	1	6	5	6	3.714	1	; positions_6nt_m3 versus vfl_SANGER_5_FBgn0259789; m=1/10; ncol2=8; w=8; offset=1; strand=D; shift=4; score= 3.7143; ----gCAGGTAG--- ; cor=0.955; Ncor=0.764; logoDP=11.552; NIcor=0.761; NsEucl=0.940; SSD=0.455; NSW=0.972; rcor=3; rNcor=4; rlogoDP=1; rNIcor=1; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=3.714; match_rank=1 a \| 0 0 0 0 1 0 18 0 0 0 18 3 0 0 0 c \| 0 0 0 0 1 18 0 0 0 0 0 1 0 0 0 g \| 0 0 0 0 12 0 0 18 18 0 0 14 0 0 0 t \| 0 0 0 0 4 0 0 0 0 18 0 0 0 0 0
vfl_SOLEXA_5_FBgn0259789_shift0 (vfl_SOLEXA_5_FBgn0259789)	0.948	0.632	10.716	0.637	0.950	0.494	0.975	8	16	2	6	1	9	3	6.429	3	; positions_6nt_m3 versus vfl_SOLEXA_5_FBgn0259789; m=2/10; ncol2=15; w=10; offset=-3; strand=D; shift=0; score= 6.4286; kkkbkCAGGTAGsyg ; cor=0.948; Ncor=0.632; logoDP=10.716; NIcor=0.637; NsEucl=0.950; SSD=0.494; NSW=0.975; rcor=8; rNcor=16; rlogoDP=2; rNIcor=6; rNsEucl=1; rSSD=9; rNSW=3; rank_mean=6.429; match_rank=3 a \| 110 149 144 116 54 7 756 0 1 4 756 76 145 140 169 c \| 150 123 119 212 0 749 1 0 0 0 5 75 203 227 99 g \| 196 254 234 237 478 0 1 731 750 3 0 566 230 167 277 t \| 229 235 264 196 229 5 3 30 10 754 0 44 183 217 160
wor_SOLEXA_2.5_FBgn0001983_rc_shift4 (wor_SOLEXA_2.5_FBgn0001983_rc)	0.781	0.624	4.606	0.271	0.876	1.959	0.878	40	17	25	28	43	45	46	34.857	38	; positions_6nt_m3 versus wor_SOLEXA_2.5_FBgn0001983_rc; m=3/10; ncol2=8; w=8; offset=1; strand=R; shift=4; score=34.8571; ----rCAGGTGk--- ; cor=0.781; Ncor=0.624; logoDP=4.606; NIcor=0.271; NsEucl=0.876; SSD=1.959; NSW=0.878; rcor=40; rNcor=17; rlogoDP=25; rNIcor=28; rNsEucl=43; rSSD=45; rNSW=46; rank_mean=34.857; match_rank=38 a \| 0 0 0 0 548 20 1786 29 24 51 78 150 0 0 0 c \| 0 0 0 0 5 1759 8 0 0 0 5 383 0 0 0 g \| 0 0 0 0 1085 1 0 1743 1770 19 1499 645 0 0 0 t \| 0 0 0 0 86 9 0 22 0 1724 127 428 0 0 0
l(1)sc_da_SANGER_5_FBgn0000413_shift4 (l(1)sc_da_SANGER_5_FBgn0000413)	0.754	0.528	8.426	0.513	0.849	2.229	0.841	52	31	5	8	55	50	55	36.571	42	; positions_6nt_m3 versus l(1)sc_da_SANGER_5_FBgn0000413; m=4/10; ncol2=7; w=7; offset=1; strand=D; shift=4; score=36.5714; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=52; rNcor=31; rlogoDP=5; rNIcor=8; rNsEucl=55; rSSD=50; rNSW=55; rank_mean=36.571; match_rank=42 a \| 0 0 0 0 4 0 21 1 0 0 1 0 0 0 0 c \| 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 g \| 0 0 0 0 19 0 1 22 22 0 22 0 0 0 0 t \| 0 0 0 0 0 0 1 0 1 23 0 0 0 0 0
l(1)sc_da_SANGER_5_FBgn0002561_shift4 (l(1)sc_da_SANGER_5_FBgn0002561)	0.754	0.528	8.426	0.513	0.849	2.229	0.841	53	32	6	9	56	51	56	37.571	43	; positions_6nt_m3 versus l(1)sc_da_SANGER_5_FBgn0002561; m=5/10; ncol2=7; w=7; offset=1; strand=D; shift=4; score=37.5714; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=53; rNcor=32; rlogoDP=6; rNIcor=9; rNsEucl=56; rSSD=51; rNSW=56; rank_mean=37.571; match_rank=43 a \| 0 0 0 0 4 0 21 1 0 0 1 0 0 0 0 c \| 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 g \| 0 0 0 0 19 0 1 22 22 0 22 0 0 0 0 t \| 0 0 0 0 0 0 1 0 1 23 0 0 0 0 0
nau_da_SANGER_5_FBgn0000413_rc_shift3 (nau_da_SANGER_5_FBgn0000413_rc)	0.754	0.603	4.460	0.175	0.865	2.318	0.855	50	20	26	31	48	54	51	40.000	51	; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0000413_rc; m=6/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 40; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=50; rNcor=20; rlogoDP=26; rNIcor=31; rNsEucl=48; rSSD=54; rNSW=51; rank_mean=40.000; match_rank=51 a \| 0 0 0 6 13 0 22 0 0 0 0 0 0 0 0 c \| 0 0 0 1 0 22 0 0 0 0 1 0 0 0 0 g \| 0 0 0 14 9 0 0 22 22 0 16 0 0 0 0 t \| 0 0 0 1 0 0 0 0 0 22 0 0 0 0 0
nau_da_SANGER_5_FBgn0002922_rc_shift3 (nau_da_SANGER_5_FBgn0002922_rc)	0.754	0.603	4.460	0.175	0.865	2.318	0.855	51	21	27	32	49	55	52	41.000	52	; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0002922_rc; m=7/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 41; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=51; rNcor=21; rlogoDP=27; rNIcor=32; rNsEucl=49; rSSD=55; rNSW=52; rank_mean=41.000; match_rank=52 a \| 0 0 0 6 13 0 22 0 0 0 0 0 0 0 0 c \| 0 0 0 1 0 22 0 0 0 0 1 0 0 0 0 g \| 0 0 0 14 9 0 0 22 22 0 16 0 0 0 0 t \| 0 0 0 1 0 0 0 0 0 22 0 0 0 0 0
CG12605_SANGER_10_FBgn0035481_rc_shift2 (CG12605_SANGER_10_FBgn0035481_rc)	0.753	0.548	3.837	0.142	0.866	2.295	0.857	54	26	29	34	47	53	50	41.857	53	; positions_6nt_m3 versus CG12605_SANGER_10_FBgn0035481_rc; m=8/10; ncol2=9; w=8; offset=-1; strand=R; shift=2; score=41.8571; --CaACAGGTG---- ; cor=0.753; Ncor=0.548; logoDP=3.837; NIcor=0.142; NsEucl=0.866; SSD=2.295; NSW=0.857; rcor=54; rNcor=26; rlogoDP=29; rNIcor=34; rNsEucl=47; rSSD=53; rNSW=50; rank_mean=41.857; match_rank=53 a \| 0 0 0 14 21 0 22 2 0 0 1 0 0 0 0 c \| 0 0 19 5 0 22 0 0 0 0 2 0 0 0 0 g \| 0 0 1 0 0 0 0 20 22 0 16 0 0 0 0 t \| 0 0 2 3 1 0 0 0 0 22 3 0 0 0 0
wor_SANGER_2.5_FBgn0001983_rc_shift4 (wor_SANGER_2.5_FBgn0001983_rc)	0.761	0.533	0.045	-0.215	0.851	2.188	0.844	45	29	56	54	53	48	53	48.286	54	; positions_6nt_m3 versus wor_SANGER_2.5_FBgn0001983_rc; m=9/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score=48.2857; ----rCAGGTG---- ; cor=0.761; Ncor=0.533; logoDP=0.045; NIcor=-0.215; NsEucl=0.851; SSD=2.188; NSW=0.844; rcor=45; rNcor=29; rlogoDP=56; rNIcor=54; rNsEucl=53; rSSD=48; rNSW=53; rank_mean=48.286; match_rank=54 a \| 0 0 0 0 6 0 21 0 0 1 0 0 0 0 0 c \| 0 0 0 0 0 21 0 0 0 0 0 0 0 0 0 g \| 0 0 0 0 12 0 0 21 21 0 21 0 0 0 0 t \| 0 0 0 0 1 0 0 0 0 20 0 0 0 0 0
esg_SANGER_2.5_FBgn0001981_rc_shift4 (esg_SANGER_2.5_FBgn0001981_rc)	0.757	0.530	0.124	-0.209	0.850	2.204	0.843	48	30	51	53	54	49	54	48.429	55	; positions_6nt_m3 versus esg_SANGER_2.5_FBgn0001981_rc; m=10/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score=48.4286; ----aCAGGTG---- ; cor=0.757; Ncor=0.530; logoDP=0.124; NIcor=-0.209; NsEucl=0.850; SSD=2.204; NSW=0.843; rcor=48; rNcor=30; rlogoDP=51; rNIcor=53; rNsEucl=54; rSSD=49; rNSW=54; rank_mean=48.429; match_rank=55 a \| 0 0 0 0 7 0 11 1 0 0 0 0 0 0 0 c \| 0 0 0 0 0 11 0 0 0 0 0 0 0 0 0 g \| 0 0 0 0 2 0 0 10 11 0 11 0 0 0 0 t \| 0 0 0 0 2 0 0 0 0 11 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd ; Alignment reference a | 338 299 421 1039 1054 828 0 0 0 3 8 840 779 305 274 c | 216 265 122 1 2 15 1 0 0 0 4 1 89 195 240 g | 316 275 453 11 13 223 1073 1071 1074 27 1 232 103 393 287 t | 204 235 78 23 5 8 0 3 0 1044 1061 1 103 181 273

Kr_NAR_FBgn0001325_shift1 (Kr_NAR_FBgn0001325) 0.953 0.699 8.659 0.701 0.950 0.608 0.972 4 10 4 3 2 13 4 5.714 2
; positions_6nt_m1 versus Kr_NAR_FBgn0001325; m=1/2; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 5.7143; -crAAaGGGTTa--- ; cor=0.953; Ncor=0.699; logoDP=8.659; NIcor=0.701; NsEucl=0.950; SSD=0.608; NSW=0.972; rcor=4; rNcor=10; rlogoDP=4; rNIcor=3; rNsEucl=2; rSSD=13; rNSW=4; rank_mean=5.714; match_rank=2 a | 0 3 11 24 30 18 0 2 2 0 4 20 0 0 0 c | 0 17 4 0 0 6 0 0 0 1 0 4 0 0 0 g | 0 5 10 7 0 7 31 29 29 7 5 3 0 0 0 t | 0 6 6 0 1 0 0 0 0 23 22 4 0 0 0

Kr_FlyReg_FBgn0001325_shift3 (Kr_FlyReg_FBgn0001325) 0.958 0.639 5.639 0.639 0.935 0.845 0.958 2 13 16 5 8 17 14 10.714 5
; positions_6nt_m1 versus Kr_FlyReg_FBgn0001325; m=2/2; ncol2=10; w=10; offset=3; strand=D; shift=3; score=10.7143; ---AAmGGGTtaw-- ; cor=0.958; Ncor=0.639; logoDP=5.639; NIcor=0.639; NsEucl=0.935; SSD=0.845; NSW=0.958; rcor=2; rNcor=13; rlogoDP=16; rNIcor=5; rNsEucl=8; rSSD=17; rNSW=14; rank_mean=10.714; match_rank=5 a | 0 0 0 37 33 20 2 4 6 1 8 28 16 0 0 c | 0 0 0 0 6 11 0 1 3 3 4 6 8 0 0 g | 0 0 0 4 1 9 40 37 35 4 4 5 5 0 0 t | 0 0 0 3 4 4 2 2 0 36 28 5 15 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)																	; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd ; Alignment reference a \| 338 299 421 1039 1054 828 0 0 0 3 8 840 779 305 274 c \| 216 265 122 1 2 15 1 0 0 0 4 1 89 195 240 g \| 316 275 453 11 13 223 1073 1071 1074 27 1 232 103 393 287 t \| 204 235 78 23 5 8 0 3 0 1044 1061 1 103 181 273
Kr_NAR_FBgn0001325_shift1 (Kr_NAR_FBgn0001325)	0.953	0.699	8.659	0.701	0.950	0.608	0.972	4	10	4	3	2	13	4	5.714	2	; positions_6nt_m1 versus Kr_NAR_FBgn0001325; m=1/2; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 5.7143; -crAAaGGGTTa--- ; cor=0.953; Ncor=0.699; logoDP=8.659; NIcor=0.701; NsEucl=0.950; SSD=0.608; NSW=0.972; rcor=4; rNcor=10; rlogoDP=4; rNIcor=3; rNsEucl=2; rSSD=13; rNSW=4; rank_mean=5.714; match_rank=2 a \| 0 3 11 24 30 18 0 2 2 0 4 20 0 0 0 c \| 0 17 4 0 0 6 0 0 0 1 0 4 0 0 0 g \| 0 5 10 7 0 7 31 29 29 7 5 3 0 0 0 t \| 0 6 6 0 1 0 0 0 0 23 22 4 0 0 0
Kr_FlyReg_FBgn0001325_shift3 (Kr_FlyReg_FBgn0001325)	0.958	0.639	5.639	0.639	0.935	0.845	0.958	2	13	16	5	8	17	14	10.714	5	; positions_6nt_m1 versus Kr_FlyReg_FBgn0001325; m=2/2; ncol2=10; w=10; offset=3; strand=D; shift=3; score=10.7143; ---AAmGGGTtaw-- ; cor=0.958; Ncor=0.639; logoDP=5.639; NIcor=0.639; NsEucl=0.935; SSD=0.845; NSW=0.958; rcor=2; rNcor=13; rlogoDP=16; rNIcor=5; rNsEucl=8; rSSD=17; rNSW=14; rank_mean=10.714; match_rank=5 a \| 0 0 0 37 33 20 2 4 6 1 8 28 16 0 0 c \| 0 0 0 0 6 11 0 1 3 3 4 6 8 0 0 g \| 0 0 0 4 1 9 40 37 35 4 4 5 5 0 0 t \| 0 0 0 3 4 4 2 2 0 36 28 5 15 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd ; Alignment reference a | 325 287 388 918 991 801 0 0 0 1 1 821 814 317 252 c | 201 244 235 0 1 5 0 0 0 0 0 0 49 162 228 g | 288 256 319 72 12 200 1008 1008 1008 10 0 187 73 370 271 t | 194 221 66 18 4 2 0 0 0 997 1007 0 72 159 257

Kr_NAR_FBgn0001325_shift1 (Kr_NAR_FBgn0001325) 0.953 0.699 8.685 0.699 0.950 0.614 0.972 5 11 3 4 3 14 5 6.429 4
; positions_7nt_m1 versus Kr_NAR_FBgn0001325; m=1/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 6.4286; -crAAaGGGTTa--- ; cor=0.953; Ncor=0.699; logoDP=8.685; NIcor=0.699; NsEucl=0.950; SSD=0.614; NSW=0.972; rcor=5; rNcor=11; rlogoDP=3; rNIcor=4; rNsEucl=3; rSSD=14; rNSW=5; rank_mean=6.429; match_rank=4 a | 0 3 11 24 30 18 0 2 2 0 4 20 0 0 0 c | 0 17 4 0 0 6 0 0 0 1 0 4 0 0 0 g | 0 5 10 7 0 7 31 29 29 7 5 3 0 0 0 t | 0 6 6 0 1 0 0 0 0 23 22 4 0 0 0

Kr_FlyReg_FBgn0001325_shift3 (Kr_FlyReg_FBgn0001325) 0.950 0.634 5.608 0.630 0.931 0.965 0.952 7 15 17 7 12 20 16 13.429 6
; positions_7nt_m1 versus Kr_FlyReg_FBgn0001325; m=2/3; ncol2=10; w=10; offset=3; strand=D; shift=3; score=13.4286; ---AAmGGGTtaw-- ; cor=0.950; Ncor=0.634; logoDP=5.608; NIcor=0.630; NsEucl=0.931; SSD=0.965; NSW=0.952; rcor=7; rNcor=15; rlogoDP=17; rNIcor=7; rNsEucl=12; rSSD=20; rNSW=16; rank_mean=13.429; match_rank=6 a | 0 0 0 37 33 20 2 4 6 1 8 28 16 0 0 c | 0 0 0 0 6 11 0 1 3 3 4 6 8 0 0 g | 0 0 0 4 1 9 40 37 35 4 4 5 5 0 0 t | 0 0 0 3 4 4 2 2 0 36 28 5 15 0 0

Ptx1_SOLEXA_FBgn0020912_rc_shift6 (Ptx1_SOLEXA_FBgn0020912_rc) 0.751 0.400 0.103 -0.128 0.868 2.230 0.861 56 56 53 47 46 52 49 51.286 56
; positions_7nt_m1 versus Ptx1_SOLEXA_FBgn0020912_rc; m=3/3; ncol2=8; w=8; offset=6; strand=R; shift=6; score=51.2857; ------GGATTArc- ; cor=0.751; Ncor=0.400; logoDP=0.103; NIcor=-0.128; NsEucl=0.868; SSD=2.230; NSW=0.861; rcor=56; rNcor=56; rlogoDP=53; rNIcor=47; rNsEucl=46; rSSD=52; rNSW=49; rank_mean=51.286; match_rank=56 a | 0 0 0 0 0 0 23 1 355 0 0 348 186 65 0 c | 0 0 0 0 0 0 6 0 3 6 3 0 14 139 0 g | 0 0 0 0 0 0 329 361 4 4 0 11 110 87 0 t | 0 0 0 0 0 0 4 0 0 352 359 3 52 71 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)																	; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd ; Alignment reference a \| 325 287 388 918 991 801 0 0 0 1 1 821 814 317 252 c \| 201 244 235 0 1 5 0 0 0 0 0 0 49 162 228 g \| 288 256 319 72 12 200 1008 1008 1008 10 0 187 73 370 271 t \| 194 221 66 18 4 2 0 0 0 997 1007 0 72 159 257
Kr_NAR_FBgn0001325_shift1 (Kr_NAR_FBgn0001325)	0.953	0.699	8.685	0.699	0.950	0.614	0.972	5	11	3	4	3	14	5	6.429	4	; positions_7nt_m1 versus Kr_NAR_FBgn0001325; m=1/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 6.4286; -crAAaGGGTTa--- ; cor=0.953; Ncor=0.699; logoDP=8.685; NIcor=0.699; NsEucl=0.950; SSD=0.614; NSW=0.972; rcor=5; rNcor=11; rlogoDP=3; rNIcor=4; rNsEucl=3; rSSD=14; rNSW=5; rank_mean=6.429; match_rank=4 a \| 0 3 11 24 30 18 0 2 2 0 4 20 0 0 0 c \| 0 17 4 0 0 6 0 0 0 1 0 4 0 0 0 g \| 0 5 10 7 0 7 31 29 29 7 5 3 0 0 0 t \| 0 6 6 0 1 0 0 0 0 23 22 4 0 0 0
Kr_FlyReg_FBgn0001325_shift3 (Kr_FlyReg_FBgn0001325)	0.950	0.634	5.608	0.630	0.931	0.965	0.952	7	15	17	7	12	20	16	13.429	6	; positions_7nt_m1 versus Kr_FlyReg_FBgn0001325; m=2/3; ncol2=10; w=10; offset=3; strand=D; shift=3; score=13.4286; ---AAmGGGTtaw-- ; cor=0.950; Ncor=0.634; logoDP=5.608; NIcor=0.630; NsEucl=0.931; SSD=0.965; NSW=0.952; rcor=7; rNcor=15; rlogoDP=17; rNIcor=7; rNsEucl=12; rSSD=20; rNSW=16; rank_mean=13.429; match_rank=6 a \| 0 0 0 37 33 20 2 4 6 1 8 28 16 0 0 c \| 0 0 0 0 6 11 0 1 3 3 4 6 8 0 0 g \| 0 0 0 4 1 9 40 37 35 4 4 5 5 0 0 t \| 0 0 0 3 4 4 2 2 0 36 28 5 15 0 0
Ptx1_SOLEXA_FBgn0020912_rc_shift6 (Ptx1_SOLEXA_FBgn0020912_rc)	0.751	0.400	0.103	-0.128	0.868	2.230	0.861	56	56	53	47	46	52	49	51.286	56	; positions_7nt_m1 versus Ptx1_SOLEXA_FBgn0020912_rc; m=3/3; ncol2=8; w=8; offset=6; strand=R; shift=6; score=51.2857; ------GGATTArc- ; cor=0.751; Ncor=0.400; logoDP=0.103; NIcor=-0.128; NsEucl=0.868; SSD=2.230; NSW=0.861; rcor=56; rNcor=56; rlogoDP=53; rNIcor=47; rNsEucl=46; rSSD=52; rNSW=49; rank_mean=51.286; match_rank=56 a \| 0 0 0 0 0 0 23 1 355 0 0 348 186 65 0 c \| 0 0 0 0 0 0 6 0 3 6 3 0 14 139 0 g \| 0 0 0 0 0 0 329 361 4 4 0 11 110 87 0 t \| 0 0 0 0 0 0 4 0 0 352 359 3 52 71 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 8 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=12; wkCTTATsArw- ; Alignment reference a | 474 394 0 0 0 1796 0 0 1796 611 473 0 c | 435 355 1796 0 0 0 0 1203 0 347 443 0 g | 342 496 0 0 0 0 0 593 0 458 295 0 t | 545 551 0 1796 1796 0 1796 0 0 380 585 0

So_Cell_FBgn0003460_rc_shift4 (So_Cell_FBgn0003460_rc) 0.939 0.598 4.152 0.234 0.932 0.448 0.968 9 22 28 29 9 4 7 15.429 7
; oligos_6nt_mkv4_m1 versus So_Cell_FBgn0003460_rc; m=1/7; ncol2=7; w=7; offset=4; strand=R; shift=4; score=15.4286; ----TATCAyt- ; cor=0.939; Ncor=0.598; logoDP=4.152; NIcor=0.234; NsEucl=0.932; SSD=0.448; NSW=0.968; rcor=9; rNcor=22; rlogoDP=28; rNIcor=29; rNsEucl=9; rSSD=4; rNSW=7; rank_mean=15.429; match_rank=7 a | 0 0 0 0 0 26 0 0 26 3 6 0 c | 0 0 0 0 0 1 0 27 1 10 5 0 g | 0 0 0 0 0 0 0 0 0 1 4 0 t | 0 0 0 0 27 0 27 0 0 13 12 0

So_SOLEXA_FBgn0003460_rc_shift4 (So_SOLEXA_FBgn0003460_rc) 0.959 0.559 0.152 -0.080 0.947 0.278 0.980 1 24 48 43 4 1 1 17.429 9
; oligos_6nt_mkv4_m1 versus So_SOLEXA_FBgn0003460_rc; m=2/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=17.4286; ----TATCAyww ; cor=0.959; Ncor=0.559; logoDP=0.152; NIcor=-0.080; NsEucl=0.947; SSD=0.278; NSW=0.980; rcor=1; rNcor=24; rlogoDP=48; rNIcor=43; rNsEucl=4; rSSD=1; rNSW=1; rank_mean=17.429; match_rank=9 a | 0 0 0 0 0 509 0 0 467 122 165 166 c | 0 0 0 0 0 14 0 519 4 151 117 95 g | 0 0 0 0 0 8 0 0 58 87 92 102 t | 0 0 0 0 531 0 531 12 2 171 157 168

Optix_SOLEXA_FBgn0025360_rc_shift4 (Optix_SOLEXA_FBgn0025360_rc) 0.951 0.555 0.123 -0.085 0.942 0.330 0.976 6 25 52 44 5 2 2 19.429 14
; oligos_6nt_mkv4_m1 versus Optix_SOLEXA_FBgn0025360_rc; m=3/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=19.4286; ----TATCAcww ; cor=0.951; Ncor=0.555; logoDP=0.123; NIcor=-0.085; NsEucl=0.942; SSD=0.330; NSW=0.976; rcor=6; rNcor=25; rlogoDP=52; rNIcor=44; rNsEucl=5; rSSD=2; rNSW=2; rank_mean=19.429; match_rank=14 a | 0 0 0 0 0 564 0 0 497 116 151 143 c | 0 0 0 0 17 0 0 564 0 216 119 126 g | 0 0 0 0 43 0 0 0 67 93 111 91 t | 0 0 0 0 504 0 564 0 0 139 183 204

Six4_SOLEXA_FBgn0027364_rc_shift4 (Six4_SOLEXA_FBgn0027364_rc) 0.928 0.541 0.246 -0.054 0.931 0.465 0.967 10 27 45 38 10 6 8 20.571 15
; oligos_6nt_mkv4_m1 versus Six4_SOLEXA_FBgn0027364_rc; m=4/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=20.5714; ----TaTCAhww ; cor=0.928; Ncor=0.541; logoDP=0.246; NIcor=-0.054; NsEucl=0.931; SSD=0.465; NSW=0.967; rcor=10; rNcor=27; rlogoDP=45; rNIcor=38; rNsEucl=10; rSSD=6; rNSW=8; rank_mean=20.571; match_rank=15 a | 0 0 0 0 0 383 0 38 599 194 203 181 c | 0 0 0 0 0 126 0 556 0 167 83 116 g | 0 0 0 0 40 128 0 0 38 84 91 93 t | 0 0 0 0 597 0 637 43 0 192 260 247

Optix_Cell_FBgn0025360_rc_shift4 (Optix_Cell_FBgn0025360_rc) 0.920 0.537 0.340 -0.056 0.924 0.560 0.960 12 28 43 39 17 11 11 23.000 18
; oligos_6nt_mkv4_m1 versus Optix_Cell_FBgn0025360_rc; m=5/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 23; ----TATCAcww ; cor=0.920; Ncor=0.537; logoDP=0.340; NIcor=-0.056; NsEucl=0.924; SSD=0.560; NSW=0.960; rcor=12; rNcor=28; rlogoDP=43; rNIcor=39; rNsEucl=17; rSSD=11; rNSW=11; rank_mean=23.000; match_rank=18 a | 0 0 0 0 0 27 0 0 22 3 7 9 c | 0 0 0 0 1 0 0 27 0 16 3 2 g | 0 0 0 0 0 0 0 0 5 4 4 4 t | 0 0 0 0 26 0 27 0 0 4 13 12

exd_SOLEXA_2_FBgn0000611_rc_shift3 (exd_SOLEXA_2_FBgn0000611_rc) 0.770 0.560 0.192 -0.070 0.886 1.674 0.895 43 23 47 40 38 38 42 38.714 46
; oligos_6nt_mkv4_m1 versus exd_SOLEXA_2_FBgn0000611_rc; m=6/7; ncol2=8; w=8; offset=3; strand=R; shift=3; score=38.7143; ---wyrTCAaa- ; cor=0.770; Ncor=0.560; logoDP=0.192; NIcor=-0.070; NsEucl=0.886; SSD=1.674; NSW=0.895; rcor=43; rNcor=23; rlogoDP=47; rNIcor=40; rNsEucl=38; rSSD=38; rNSW=42; rank_mean=38.714; match_rank=46 a | 0 0 0 483 259 1228 0 0 2672 1314 1025 0 c | 0 0 0 145 914 86 0 2672 0 598 458 0 g | 0 0 0 91 14 1169 0 0 0 204 568 0 t | 0 0 0 474 1470 189 2672 0 0 539 587 0

Exd_SOLEXA_FBgn0000611_rc_shift4 (Exd_SOLEXA_FBgn0000611_rc) 0.777 0.453 0.344 -0.025 0.880 1.404 0.900 41 41 42 36 41 34 39 39.143 47
; oligos_6nt_mkv4_m1 versus Exd_SOLEXA_FBgn0000611_rc; m=7/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=39.1429; ----yrTCAaaw ; cor=0.777; Ncor=0.453; logoDP=0.344; NIcor=-0.025; NsEucl=0.880; SSD=1.404; NSW=0.900; rcor=41; rNcor=41; rlogoDP=42; rNIcor=36; rNsEucl=41; rSSD=34; rNSW=39; rank_mean=39.143; match_rank=47 a | 0 0 0 0 77 323 0 0 883 541 408 266 c | 0 0 0 0 259 0 0 883 0 168 143 207 g | 0 0 0 0 26 505 0 0 0 40 172 152 t | 0 0 0 0 521 55 883 0 0 134 160 258

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)																	; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=12; wkCTTATsArw- ; Alignment reference a \| 474 394 0 0 0 1796 0 0 1796 611 473 0 c \| 435 355 1796 0 0 0 0 1203 0 347 443 0 g \| 342 496 0 0 0 0 0 593 0 458 295 0 t \| 545 551 0 1796 1796 0 1796 0 0 380 585 0
So_Cell_FBgn0003460_rc_shift4 (So_Cell_FBgn0003460_rc)	0.939	0.598	4.152	0.234	0.932	0.448	0.968	9	22	28	29	9	4	7	15.429	7	; oligos_6nt_mkv4_m1 versus So_Cell_FBgn0003460_rc; m=1/7; ncol2=7; w=7; offset=4; strand=R; shift=4; score=15.4286; ----TATCAyt- ; cor=0.939; Ncor=0.598; logoDP=4.152; NIcor=0.234; NsEucl=0.932; SSD=0.448; NSW=0.968; rcor=9; rNcor=22; rlogoDP=28; rNIcor=29; rNsEucl=9; rSSD=4; rNSW=7; rank_mean=15.429; match_rank=7 a \| 0 0 0 0 0 26 0 0 26 3 6 0 c \| 0 0 0 0 0 1 0 27 1 10 5 0 g \| 0 0 0 0 0 0 0 0 0 1 4 0 t \| 0 0 0 0 27 0 27 0 0 13 12 0
So_SOLEXA_FBgn0003460_rc_shift4 (So_SOLEXA_FBgn0003460_rc)	0.959	0.559	0.152	-0.080	0.947	0.278	0.980	1	24	48	43	4	1	1	17.429	9	; oligos_6nt_mkv4_m1 versus So_SOLEXA_FBgn0003460_rc; m=2/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=17.4286; ----TATCAyww ; cor=0.959; Ncor=0.559; logoDP=0.152; NIcor=-0.080; NsEucl=0.947; SSD=0.278; NSW=0.980; rcor=1; rNcor=24; rlogoDP=48; rNIcor=43; rNsEucl=4; rSSD=1; rNSW=1; rank_mean=17.429; match_rank=9 a \| 0 0 0 0 0 509 0 0 467 122 165 166 c \| 0 0 0 0 0 14 0 519 4 151 117 95 g \| 0 0 0 0 0 8 0 0 58 87 92 102 t \| 0 0 0 0 531 0 531 12 2 171 157 168
Optix_SOLEXA_FBgn0025360_rc_shift4 (Optix_SOLEXA_FBgn0025360_rc)	0.951	0.555	0.123	-0.085	0.942	0.330	0.976	6	25	52	44	5	2	2	19.429	14	; oligos_6nt_mkv4_m1 versus Optix_SOLEXA_FBgn0025360_rc; m=3/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=19.4286; ----TATCAcww ; cor=0.951; Ncor=0.555; logoDP=0.123; NIcor=-0.085; NsEucl=0.942; SSD=0.330; NSW=0.976; rcor=6; rNcor=25; rlogoDP=52; rNIcor=44; rNsEucl=5; rSSD=2; rNSW=2; rank_mean=19.429; match_rank=14 a \| 0 0 0 0 0 564 0 0 497 116 151 143 c \| 0 0 0 0 17 0 0 564 0 216 119 126 g \| 0 0 0 0 43 0 0 0 67 93 111 91 t \| 0 0 0 0 504 0 564 0 0 139 183 204
Six4_SOLEXA_FBgn0027364_rc_shift4 (Six4_SOLEXA_FBgn0027364_rc)	0.928	0.541	0.246	-0.054	0.931	0.465	0.967	10	27	45	38	10	6	8	20.571	15	; oligos_6nt_mkv4_m1 versus Six4_SOLEXA_FBgn0027364_rc; m=4/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=20.5714; ----TaTCAhww ; cor=0.928; Ncor=0.541; logoDP=0.246; NIcor=-0.054; NsEucl=0.931; SSD=0.465; NSW=0.967; rcor=10; rNcor=27; rlogoDP=45; rNIcor=38; rNsEucl=10; rSSD=6; rNSW=8; rank_mean=20.571; match_rank=15 a \| 0 0 0 0 0 383 0 38 599 194 203 181 c \| 0 0 0 0 0 126 0 556 0 167 83 116 g \| 0 0 0 0 40 128 0 0 38 84 91 93 t \| 0 0 0 0 597 0 637 43 0 192 260 247
Optix_Cell_FBgn0025360_rc_shift4 (Optix_Cell_FBgn0025360_rc)	0.920	0.537	0.340	-0.056	0.924	0.560	0.960	12	28	43	39	17	11	11	23.000	18	; oligos_6nt_mkv4_m1 versus Optix_Cell_FBgn0025360_rc; m=5/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 23; ----TATCAcww ; cor=0.920; Ncor=0.537; logoDP=0.340; NIcor=-0.056; NsEucl=0.924; SSD=0.560; NSW=0.960; rcor=12; rNcor=28; rlogoDP=43; rNIcor=39; rNsEucl=17; rSSD=11; rNSW=11; rank_mean=23.000; match_rank=18 a \| 0 0 0 0 0 27 0 0 22 3 7 9 c \| 0 0 0 0 1 0 0 27 0 16 3 2 g \| 0 0 0 0 0 0 0 0 5 4 4 4 t \| 0 0 0 0 26 0 27 0 0 4 13 12
exd_SOLEXA_2_FBgn0000611_rc_shift3 (exd_SOLEXA_2_FBgn0000611_rc)	0.770	0.560	0.192	-0.070	0.886	1.674	0.895	43	23	47	40	38	38	42	38.714	46	; oligos_6nt_mkv4_m1 versus exd_SOLEXA_2_FBgn0000611_rc; m=6/7; ncol2=8; w=8; offset=3; strand=R; shift=3; score=38.7143; ---wyrTCAaa- ; cor=0.770; Ncor=0.560; logoDP=0.192; NIcor=-0.070; NsEucl=0.886; SSD=1.674; NSW=0.895; rcor=43; rNcor=23; rlogoDP=47; rNIcor=40; rNsEucl=38; rSSD=38; rNSW=42; rank_mean=38.714; match_rank=46 a \| 0 0 0 483 259 1228 0 0 2672 1314 1025 0 c \| 0 0 0 145 914 86 0 2672 0 598 458 0 g \| 0 0 0 91 14 1169 0 0 0 204 568 0 t \| 0 0 0 474 1470 189 2672 0 0 539 587 0
Exd_SOLEXA_FBgn0000611_rc_shift4 (Exd_SOLEXA_FBgn0000611_rc)	0.777	0.453	0.344	-0.025	0.880	1.404	0.900	41	41	42	36	41	34	39	39.143	47	; oligos_6nt_mkv4_m1 versus Exd_SOLEXA_FBgn0000611_rc; m=7/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score=39.1429; ----yrTCAaaw ; cor=0.777; Ncor=0.453; logoDP=0.344; NIcor=-0.025; NsEucl=0.880; SSD=1.404; NSW=0.900; rcor=41; rNcor=41; rlogoDP=42; rNIcor=36; rNsEucl=41; rSSD=34; rNSW=39; rank_mean=39.143; match_rank=47 a \| 0 0 0 0 77 323 0 0 883 541 408 266 c \| 0 0 0 0 259 0 0 883 0 168 143 207 g \| 0 0 0 0 26 505 0 0 0 40 172 152 t \| 0 0 0 0 521 55 883 0 0 134 160 258

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; yckCTCkCKCtc ; Alignment reference a | 576 599 23 0 0 0 0 0 0 0 798 520 c | 1281 2822 4 5043 0 5043 0 5043 0 5043 816 2766 g | 950 581 1788 0 0 0 1653 0 1290 0 972 752 t | 2236 1041 3228 0 5043 0 3390 0 3753 0 2457 1005

Trl_FlyReg_FBgn0013263_shift0 (Trl_FlyReg_FBgn0013263) 0.893 0.744 4.967 0.731 0.927 1.071 0.946 18 6 24 2 14 24 21 15.571 8
; positions_7nt_m3 versus Trl_FlyReg_FBgn0013263; m=1/1; ncol2=10; w=10; offset=0; strand=D; shift=0; score=15.5714; yykCTCTCty-- ; cor=0.893; Ncor=0.744; logoDP=4.967; NIcor=0.731; NsEucl=0.927; SSD=1.071; NSW=0.946; rcor=18; rNcor=6; rlogoDP=24; rNIcor=2; rNsEucl=14; rSSD=24; rNSW=21; rank_mean=15.571; match_rank=8 a | 4 6 12 0 3 1 13 5 7 9 0 0 c | 22 23 6 64 0 70 0 54 13 33 0 0 g | 9 11 30 3 14 0 2 7 11 10 0 0 t | 36 31 23 4 54 0 56 5 40 19 0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)																		; positions_7nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; yckCTCkCKCtc ; Alignment reference a \| 576 599 23 0 0 0 0 0 0 0 798 520 c \| 1281 2822 4 5043 0 5043 0 5043 0 5043 816 2766 g \| 950 581 1788 0 0 0 1653 0 1290 0 972 752 t \| 2236 1041 3228 0 5043 0 3390 0 3753 0 2457 1005
Trl_FlyReg_FBgn0013263_shift0 (Trl_FlyReg_FBgn0013263)		0.893	0.744	4.967	0.731	0.927	1.071	0.946	18	6	24	2	14	24	21	15.571	8	; positions_7nt_m3 versus Trl_FlyReg_FBgn0013263; m=1/1; ncol2=10; w=10; offset=0; strand=D; shift=0; score=15.5714; yykCTCTCty-- ; cor=0.893; Ncor=0.744; logoDP=4.967; NIcor=0.731; NsEucl=0.927; SSD=1.071; NSW=0.946; rcor=18; rNcor=6; rlogoDP=24; rNIcor=2; rNsEucl=14; rSSD=24; rNSW=21; rank_mean=15.571; match_rank=8 a \| 4 6 12 0 3 1 13 5 7 9 0 0 c \| 22 23 6 64 0 70 0 54 13 33 0 0 g \| 9 11 30 3 14 0 2 7 11 10 0 0 t \| 36 31 23 4 54 0 56 5 40 19 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift4 ; 12 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----waAACAyAAww ; Alignment reference a | 0 0 0 0 2194 2297 6636 6636 0 6636 0 6636 6636 2283 2203 c | 0 0 0 0 1355 1342 0 0 5129 0 3468 0 0 1367 1387 g | 0 0 0 0 1234 1358 0 0 0 0 1211 0 0 1096 1135 t | 0 0 0 0 1853 1639 0 0 1507 0 1957 0 0 1890 1911

Mirr_Cell_FBgn0014343_shift2 (Mirr_Cell_FBgn0014343) 0.921 0.425 5.397 0.422 0.921 0.444 0.963 11 45 20 18 20 3 9 18.000 10
; oligos_7nt_mkv5_m2 versus Mirr_Cell_FBgn0014343; m=1/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score= 18; --waawAACA----- ; cor=0.921; Ncor=0.425; logoDP=5.397; NIcor=0.422; NsEucl=0.921; SSD=0.444; NSW=0.963; rcor=11; rNcor=45; rlogoDP=20; rNIcor=18; rNsEucl=20; rSSD=3; rNSW=9; rank_mean=18.000; match_rank=10 a | 0 0 18 18 22 20 29 41 0 41 0 0 0 0 0 c | 0 0 6 4 7 1 0 0 41 0 0 0 0 0 0 g | 0 0 6 10 6 1 2 0 0 0 0 0 0 0 0 t | 0 0 11 9 6 19 10 0 0 0 0 0 0 0 0

Mirr_SOLEXA_FBgn0014343_shift4 (Mirr_SOLEXA_FBgn0014343) 0.906 0.494 5.077 0.481 0.917 0.491 0.959 15 37 22 13 22 8 12 18.429 11
; oligos_7nt_mkv5_m2 versus Mirr_SOLEXA_FBgn0014343; m=2/11; ncol2=6; w=6; offset=0; strand=D; shift=4; score=18.4286; ----wwwACA----- ; cor=0.906; Ncor=0.494; logoDP=5.077; NIcor=0.481; NsEucl=0.917; SSD=0.491; NSW=0.959; rcor=15; rNcor=37; rlogoDP=22; rNIcor=13; rNsEucl=22; rSSD=8; rNSW=12; rank_mean=18.429; match_rank=11 a | 0 0 0 0 550 410 782 1415 0 1415 0 0 0 0 0 c | 0 0 0 0 158 93 0 0 1415 0 0 0 0 0 0 g | 0 0 0 0 327 282 204 0 0 0 0 0 0 0 0 t | 0 0 0 0 380 630 429 0 0 0 0 0 0 0 0

Ara_SOLEXA_FBgn0015904_shift4 (Ara_SOLEXA_FBgn0015904) 0.906 0.494 5.171 0.484 0.916 0.507 0.958 14 36 21 12 23 10 13 18.429 12
; oligos_7nt_mkv5_m2 versus Ara_SOLEXA_FBgn0015904; m=3/11; ncol2=6; w=6; offset=0; strand=D; shift=4; score=18.4286; ----awwACA----- ; cor=0.906; Ncor=0.494; logoDP=5.171; NIcor=0.484; NsEucl=0.916; SSD=0.507; NSW=0.958; rcor=14; rNcor=36; rlogoDP=21; rNIcor=12; rNsEucl=23; rSSD=10; rNSW=13; rank_mean=18.429; match_rank=12 a | 0 0 0 0 155 97 193 313 0 313 0 0 0 0 0 c | 0 0 0 0 36 0 0 0 313 0 0 0 0 0 0 g | 0 0 0 0 44 45 38 0 0 0 0 0 0 0 0 t | 0 0 0 0 78 171 82 0 0 0 0 0 0 0 0

Caup_Cell_FBgn0015919_shift2 (Caup_Cell_FBgn0015919) 0.917 0.423 5.406 0.419 0.920 0.465 0.961 13 46 19 20 21 7 10 19.429 13
; oligos_7nt_mkv5_m2 versus Caup_Cell_FBgn0015919; m=4/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score=19.4286; --cwwtAACA----- ; cor=0.917; Ncor=0.423; logoDP=5.406; NIcor=0.419; NsEucl=0.920; SSD=0.465; NSW=0.961; rcor=13; rNcor=46; rlogoDP=19; rNIcor=20; rNsEucl=21; rSSD=7; rNSW=10; rank_mean=19.429; match_rank=13 a | 0 0 4 9 8 4 14 19 0 19 0 0 0 0 0 c | 0 0 9 0 0 1 0 0 19 0 0 0 0 0 0 g | 0 0 2 3 4 2 2 0 0 0 0 0 0 0 0 t | 0 0 4 7 7 12 3 0 0 0 0 0 0 0 0

Caup_SOLEXA_FBgn0015919_shift4 (Caup_SOLEXA_FBgn0015919) 0.880 0.480 4.998 0.465 0.907 0.623 0.948 21 39 23 16 28 15 18 22.857 17
; oligos_7nt_mkv5_m2 versus Caup_SOLEXA_FBgn0015919; m=5/11; ncol2=6; w=6; offset=0; strand=D; shift=4; score=22.8571; ----wtwACA----- ; cor=0.880; Ncor=0.480; logoDP=4.998; NIcor=0.465; NsEucl=0.907; SSD=0.623; NSW=0.948; rcor=21; rNcor=39; rlogoDP=23; rNIcor=16; rNsEucl=28; rSSD=15; rNSW=18; rank_mean=22.857; match_rank=17 a | 0 0 0 0 999 577 1415 2904 2 2904 0 0 0 0 0 c | 0 0 0 0 460 201 0 0 2902 0 0 0 0 0 0 g | 0 0 0 0 626 639 511 0 0 0 0 0 0 0 0 t | 0 0 0 0 819 1487 978 0 0 0 0 0 0 0 0

Ara_Cell_FBgn0015904_shift2 (Ara_Cell_FBgn0015904) 0.896 0.414 5.472 0.409 0.909 0.597 0.950 16 49 18 23 26 12 17 23.000 19
; oligos_7nt_mkv5_m2 versus Ara_Cell_FBgn0015904; m=6/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score= 23; --raAwwACA----- ; cor=0.896; Ncor=0.414; logoDP=5.472; NIcor=0.409; NsEucl=0.909; SSD=0.597; NSW=0.950; rcor=16; rNcor=49; rlogoDP=18; rNIcor=23; rNsEucl=26; rSSD=12; rNSW=17; rank_mean=23.000; match_rank=19 a | 0 0 12 16 24 14 23 34 0 34 0 0 0 0 0 c | 0 0 5 7 1 0 0 0 34 0 0 0 0 0 0 g | 0 0 10 6 1 5 0 0 0 0 0 0 0 0 0 t | 0 0 7 5 8 15 11 0 0 0 0 0 0 0 0

fd64A_SANGER_5_FBgn0004895_shift2 (fd64A_SANGER_5_FBgn0004895) 0.887 0.409 5.990 0.393 0.896 0.780 0.935 19 51 10 25 32 16 23 25.143 23
; oligos_7nt_mkv5_m2 versus fd64A_SANGER_5_FBgn0004895; m=7/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score=25.1429; --tvtAAACA----- ; cor=0.887; Ncor=0.409; logoDP=5.990; NIcor=0.393; NsEucl=0.896; SSD=0.780; NSW=0.935; rcor=19; rNcor=51; rlogoDP=10; rNIcor=25; rNsEucl=32; rSSD=16; rNSW=23; rank_mean=25.143; match_rank=23 a | 0 0 3 7 4 20 19 20 0 20 0 0 0 0 0 c | 0 0 0 5 3 0 1 0 17 0 0 0 0 0 0 g | 0 0 4 6 0 0 0 0 0 0 0 0 0 0 0 t | 0 0 13 2 13 0 0 0 3 0 0 0 0 0 0

slp1_NAR_FBgn0003430_rc_shift0 (slp1_NAR_FBgn0003430_rc) 0.866 0.404 0.606 -0.012 0.902 0.945 0.932 23 54 40 35 30 19 26 32.429 31
; oligos_7nt_mkv5_m2 versus slp1_NAR_FBgn0003430_rc; m=8/11; ncol2=11; w=7; offset=-4; strand=R; shift=0; score=32.4286; wryrtAAACAm---- ; cor=0.866; Ncor=0.404; logoDP=0.606; NIcor=-0.012; NsEucl=0.902; SSD=0.945; NSW=0.932; rcor=23; rNcor=54; rlogoDP=40; rNIcor=35; rNsEucl=30; rSSD=19; rNSW=26; rank_mean=32.429; match_rank=31 a | 19 21 1 11 10 39 40 41 0 41 16 0 0 0 0 c | 4 3 15 7 4 2 1 0 38 0 14 0 0 0 0 g | 3 13 8 22 0 0 0 0 0 0 3 0 0 0 0 t | 15 4 17 1 27 0 0 0 3 0 8 0 0 0 0

bin_SANGER_5_FBgn0045759_shift3 (bin_SANGER_5_FBgn0045759) 0.830 0.415 6.342 0.388 0.861 1.385 0.885 31 48 8 26 52 32 44 34.429 36
; oligos_7nt_mkv5_m2 versus bin_SANGER_5_FBgn0045759; m=9/11; ncol2=7; w=6; offset=-1; strand=D; shift=3; score=34.4286; ---rTAAACA----- ; cor=0.830; Ncor=0.415; logoDP=6.342; NIcor=0.388; NsEucl=0.861; SSD=1.385; NSW=0.885; rcor=31; rNcor=48; rlogoDP=8; rNIcor=26; rNsEucl=52; rSSD=32; rNSW=44; rank_mean=34.429; match_rank=36 a | 0 0 0 9 0 20 20 20 0 19 0 0 0 0 0 c | 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 g | 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 t | 0 0 0 1 20 0 0 0 0 1 0 0 0 0 0

slp2_SANGER_5_FBgn0004567_shift3 (slp2_SANGER_5_FBgn0004567) 0.773 0.451 6.714 0.451 0.863 1.841 0.869 42 42 7 17 51 42 48 35.571 39
; oligos_7nt_mkv5_m2 versus slp2_SANGER_5_FBgn0004567; m=10/11; ncol2=8; w=7; offset=-1; strand=D; shift=3; score=35.5714; ---rTAAACAa---- ; cor=0.773; Ncor=0.451; logoDP=6.714; NIcor=0.451; NsEucl=0.863; SSD=1.841; NSW=0.869; rcor=42; rNcor=42; rlogoDP=7; rNIcor=17; rNsEucl=51; rSSD=42; rNSW=48; rank_mean=35.571; match_rank=39 a | 0 0 0 6 0 18 18 18 0 18 11 0 0 0 0 c | 0 0 0 0 1 0 0 0 18 0 3 0 0 0 0 g | 0 0 0 12 0 0 0 0 0 0 3 0 0 0 0 t | 0 0 0 0 17 0 0 0 0 0 1 0 0 0 0

CG16899_SANGER_5_FBgn0037735_shift2 (CG16899_SANGER_5_FBgn0037735) 0.761 0.410 6.041 0.412 0.865 1.788 0.872 46 50 9 22 50 41 47 37.857 44
; oligos_7nt_mkv5_m2 versus CG16899_SANGER_5_FBgn0037735; m=11/11; ncol2=9; w=7; offset=-2; strand=D; shift=2; score=37.8571; --vrTAAACAA---- ; cor=0.761; Ncor=0.410; logoDP=6.041; NIcor=0.412; NsEucl=0.865; SSD=1.788; NSW=0.872; rcor=46; rNcor=50; rlogoDP=9; rNIcor=22; rNsEucl=50; rSSD=41; rNSW=47; rank_mean=37.857; match_rank=44 a | 0 0 6 10 1 21 20 21 0 21 15 0 0 0 0 c | 0 0 5 2 2 0 0 0 18 0 2 0 0 0 0 g | 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 t | 0 0 0 0 18 0 1 0 3 0 4 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2)																	; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----waAACAyAAww ; Alignment reference a \| 0 0 0 0 2194 2297 6636 6636 0 6636 0 6636 6636 2283 2203 c \| 0 0 0 0 1355 1342 0 0 5129 0 3468 0 0 1367 1387 g \| 0 0 0 0 1234 1358 0 0 0 0 1211 0 0 1096 1135 t \| 0 0 0 0 1853 1639 0 0 1507 0 1957 0 0 1890 1911
Mirr_Cell_FBgn0014343_shift2 (Mirr_Cell_FBgn0014343)	0.921	0.425	5.397	0.422	0.921	0.444	0.963	11	45	20	18	20	3	9	18.000	10	; oligos_7nt_mkv5_m2 versus Mirr_Cell_FBgn0014343; m=1/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score= 18; --waawAACA----- ; cor=0.921; Ncor=0.425; logoDP=5.397; NIcor=0.422; NsEucl=0.921; SSD=0.444; NSW=0.963; rcor=11; rNcor=45; rlogoDP=20; rNIcor=18; rNsEucl=20; rSSD=3; rNSW=9; rank_mean=18.000; match_rank=10 a \| 0 0 18 18 22 20 29 41 0 41 0 0 0 0 0 c \| 0 0 6 4 7 1 0 0 41 0 0 0 0 0 0 g \| 0 0 6 10 6 1 2 0 0 0 0 0 0 0 0 t \| 0 0 11 9 6 19 10 0 0 0 0 0 0 0 0
Mirr_SOLEXA_FBgn0014343_shift4 (Mirr_SOLEXA_FBgn0014343)	0.906	0.494	5.077	0.481	0.917	0.491	0.959	15	37	22	13	22	8	12	18.429	11	; oligos_7nt_mkv5_m2 versus Mirr_SOLEXA_FBgn0014343; m=2/11; ncol2=6; w=6; offset=0; strand=D; shift=4; score=18.4286; ----wwwACA----- ; cor=0.906; Ncor=0.494; logoDP=5.077; NIcor=0.481; NsEucl=0.917; SSD=0.491; NSW=0.959; rcor=15; rNcor=37; rlogoDP=22; rNIcor=13; rNsEucl=22; rSSD=8; rNSW=12; rank_mean=18.429; match_rank=11 a \| 0 0 0 0 550 410 782 1415 0 1415 0 0 0 0 0 c \| 0 0 0 0 158 93 0 0 1415 0 0 0 0 0 0 g \| 0 0 0 0 327 282 204 0 0 0 0 0 0 0 0 t \| 0 0 0 0 380 630 429 0 0 0 0 0 0 0 0
Ara_SOLEXA_FBgn0015904_shift4 (Ara_SOLEXA_FBgn0015904)	0.906	0.494	5.171	0.484	0.916	0.507	0.958	14	36	21	12	23	10	13	18.429	12	; oligos_7nt_mkv5_m2 versus Ara_SOLEXA_FBgn0015904; m=3/11; ncol2=6; w=6; offset=0; strand=D; shift=4; score=18.4286; ----awwACA----- ; cor=0.906; Ncor=0.494; logoDP=5.171; NIcor=0.484; NsEucl=0.916; SSD=0.507; NSW=0.958; rcor=14; rNcor=36; rlogoDP=21; rNIcor=12; rNsEucl=23; rSSD=10; rNSW=13; rank_mean=18.429; match_rank=12 a \| 0 0 0 0 155 97 193 313 0 313 0 0 0 0 0 c \| 0 0 0 0 36 0 0 0 313 0 0 0 0 0 0 g \| 0 0 0 0 44 45 38 0 0 0 0 0 0 0 0 t \| 0 0 0 0 78 171 82 0 0 0 0 0 0 0 0
Caup_Cell_FBgn0015919_shift2 (Caup_Cell_FBgn0015919)	0.917	0.423	5.406	0.419	0.920	0.465	0.961	13	46	19	20	21	7	10	19.429	13	; oligos_7nt_mkv5_m2 versus Caup_Cell_FBgn0015919; m=4/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score=19.4286; --cwwtAACA----- ; cor=0.917; Ncor=0.423; logoDP=5.406; NIcor=0.419; NsEucl=0.920; SSD=0.465; NSW=0.961; rcor=13; rNcor=46; rlogoDP=19; rNIcor=20; rNsEucl=21; rSSD=7; rNSW=10; rank_mean=19.429; match_rank=13 a \| 0 0 4 9 8 4 14 19 0 19 0 0 0 0 0 c \| 0 0 9 0 0 1 0 0 19 0 0 0 0 0 0 g \| 0 0 2 3 4 2 2 0 0 0 0 0 0 0 0 t \| 0 0 4 7 7 12 3 0 0 0 0 0 0 0 0
Caup_SOLEXA_FBgn0015919_shift4 (Caup_SOLEXA_FBgn0015919)	0.880	0.480	4.998	0.465	0.907	0.623	0.948	21	39	23	16	28	15	18	22.857	17	; oligos_7nt_mkv5_m2 versus Caup_SOLEXA_FBgn0015919; m=5/11; ncol2=6; w=6; offset=0; strand=D; shift=4; score=22.8571; ----wtwACA----- ; cor=0.880; Ncor=0.480; logoDP=4.998; NIcor=0.465; NsEucl=0.907; SSD=0.623; NSW=0.948; rcor=21; rNcor=39; rlogoDP=23; rNIcor=16; rNsEucl=28; rSSD=15; rNSW=18; rank_mean=22.857; match_rank=17 a \| 0 0 0 0 999 577 1415 2904 2 2904 0 0 0 0 0 c \| 0 0 0 0 460 201 0 0 2902 0 0 0 0 0 0 g \| 0 0 0 0 626 639 511 0 0 0 0 0 0 0 0 t \| 0 0 0 0 819 1487 978 0 0 0 0 0 0 0 0
Ara_Cell_FBgn0015904_shift2 (Ara_Cell_FBgn0015904)	0.896	0.414	5.472	0.409	0.909	0.597	0.950	16	49	18	23	26	12	17	23.000	19	; oligos_7nt_mkv5_m2 versus Ara_Cell_FBgn0015904; m=6/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score= 23; --raAwwACA----- ; cor=0.896; Ncor=0.414; logoDP=5.472; NIcor=0.409; NsEucl=0.909; SSD=0.597; NSW=0.950; rcor=16; rNcor=49; rlogoDP=18; rNIcor=23; rNsEucl=26; rSSD=12; rNSW=17; rank_mean=23.000; match_rank=19 a \| 0 0 12 16 24 14 23 34 0 34 0 0 0 0 0 c \| 0 0 5 7 1 0 0 0 34 0 0 0 0 0 0 g \| 0 0 10 6 1 5 0 0 0 0 0 0 0 0 0 t \| 0 0 7 5 8 15 11 0 0 0 0 0 0 0 0
fd64A_SANGER_5_FBgn0004895_shift2 (fd64A_SANGER_5_FBgn0004895)	0.887	0.409	5.990	0.393	0.896	0.780	0.935	19	51	10	25	32	16	23	25.143	23	; oligos_7nt_mkv5_m2 versus fd64A_SANGER_5_FBgn0004895; m=7/11; ncol2=8; w=6; offset=-2; strand=D; shift=2; score=25.1429; --tvtAAACA----- ; cor=0.887; Ncor=0.409; logoDP=5.990; NIcor=0.393; NsEucl=0.896; SSD=0.780; NSW=0.935; rcor=19; rNcor=51; rlogoDP=10; rNIcor=25; rNsEucl=32; rSSD=16; rNSW=23; rank_mean=25.143; match_rank=23 a \| 0 0 3 7 4 20 19 20 0 20 0 0 0 0 0 c \| 0 0 0 5 3 0 1 0 17 0 0 0 0 0 0 g \| 0 0 4 6 0 0 0 0 0 0 0 0 0 0 0 t \| 0 0 13 2 13 0 0 0 3 0 0 0 0 0 0
slp1_NAR_FBgn0003430_rc_shift0 (slp1_NAR_FBgn0003430_rc)	0.866	0.404	0.606	-0.012	0.902	0.945	0.932	23	54	40	35	30	19	26	32.429	31	; oligos_7nt_mkv5_m2 versus slp1_NAR_FBgn0003430_rc; m=8/11; ncol2=11; w=7; offset=-4; strand=R; shift=0; score=32.4286; wryrtAAACAm---- ; cor=0.866; Ncor=0.404; logoDP=0.606; NIcor=-0.012; NsEucl=0.902; SSD=0.945; NSW=0.932; rcor=23; rNcor=54; rlogoDP=40; rNIcor=35; rNsEucl=30; rSSD=19; rNSW=26; rank_mean=32.429; match_rank=31 a \| 19 21 1 11 10 39 40 41 0 41 16 0 0 0 0 c \| 4 3 15 7 4 2 1 0 38 0 14 0 0 0 0 g \| 3 13 8 22 0 0 0 0 0 0 3 0 0 0 0 t \| 15 4 17 1 27 0 0 0 3 0 8 0 0 0 0
bin_SANGER_5_FBgn0045759_shift3 (bin_SANGER_5_FBgn0045759)	0.830	0.415	6.342	0.388	0.861	1.385	0.885	31	48	8	26	52	32	44	34.429	36	; oligos_7nt_mkv5_m2 versus bin_SANGER_5_FBgn0045759; m=9/11; ncol2=7; w=6; offset=-1; strand=D; shift=3; score=34.4286; ---rTAAACA----- ; cor=0.830; Ncor=0.415; logoDP=6.342; NIcor=0.388; NsEucl=0.861; SSD=1.385; NSW=0.885; rcor=31; rNcor=48; rlogoDP=8; rNIcor=26; rNsEucl=52; rSSD=32; rNSW=44; rank_mean=34.429; match_rank=36 a \| 0 0 0 9 0 20 20 20 0 19 0 0 0 0 0 c \| 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 g \| 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 t \| 0 0 0 1 20 0 0 0 0 1 0 0 0 0 0
slp2_SANGER_5_FBgn0004567_shift3 (slp2_SANGER_5_FBgn0004567)	0.773	0.451	6.714	0.451	0.863	1.841	0.869	42	42	7	17	51	42	48	35.571	39	; oligos_7nt_mkv5_m2 versus slp2_SANGER_5_FBgn0004567; m=10/11; ncol2=8; w=7; offset=-1; strand=D; shift=3; score=35.5714; ---rTAAACAa---- ; cor=0.773; Ncor=0.451; logoDP=6.714; NIcor=0.451; NsEucl=0.863; SSD=1.841; NSW=0.869; rcor=42; rNcor=42; rlogoDP=7; rNIcor=17; rNsEucl=51; rSSD=42; rNSW=48; rank_mean=35.571; match_rank=39 a \| 0 0 0 6 0 18 18 18 0 18 11 0 0 0 0 c \| 0 0 0 0 1 0 0 0 18 0 3 0 0 0 0 g \| 0 0 0 12 0 0 0 0 0 0 3 0 0 0 0 t \| 0 0 0 0 17 0 0 0 0 0 1 0 0 0 0
CG16899_SANGER_5_FBgn0037735_shift2 (CG16899_SANGER_5_FBgn0037735)	0.761	0.410	6.041	0.412	0.865	1.788	0.872	46	50	9	22	50	41	47	37.857	44	; oligos_7nt_mkv5_m2 versus CG16899_SANGER_5_FBgn0037735; m=11/11; ncol2=9; w=7; offset=-2; strand=D; shift=2; score=37.8571; --vrTAAACAA---- ; cor=0.761; Ncor=0.410; logoDP=6.041; NIcor=0.412; NsEucl=0.865; SSD=1.788; NSW=0.872; rcor=46; rNcor=50; rlogoDP=9; rNIcor=22; rNsEucl=50; rSSD=41; rNSW=47; rank_mean=37.857; match_rank=44 a \| 0 0 6 10 1 21 20 21 0 21 15 0 0 0 0 c \| 0 0 5 2 2 0 0 0 18 0 2 0 0 0 0 g \| 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 t \| 0 0 0 0 18 0 1 0 3 0 4 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift4 ; 13 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----wsCCACdCmCac ; Alignment reference a | 0 0 0 0 700 493 0 0 2679 0 1110 0 1408 0 1227 463 c | 0 0 0 0 641 905 2679 2679 0 2679 0 2679 1271 2679 662 1262 g | 0 0 0 0 571 804 0 0 0 0 862 0 0 0 311 365 t | 0 0 0 0 767 477 0 0 0 0 707 0 0 0 479 589

CG12029_SOLEXA_5_FBgn0035454_rc_shift2 (CG12029_SOLEXA_5_FBgn0035454_rc) 0.896 0.716 0.880 -0.075 0.939 1.064 0.956 17 9 39 41 7 23 15 21.571 16
; oligos_7nt_mkv5_m3 versus CG12029_SOLEXA_5_FBgn0035454_rc; m=1/12; ncol2=15; w=12; offset=-2; strand=R; shift=2; score=21.5714; --mvrRCCACACCCay ; cor=0.896; Ncor=0.716; logoDP=0.880; NIcor=-0.075; NsEucl=0.939; SSD=1.064; NSW=0.956; rcor=17; rNcor=9; rlogoDP=39; rNIcor=41; rNsEucl=7; rSSD=23; rNSW=15; rank_mean=21.571; match_rank=16 a | 0 0 311 274 360 291 135 12 912 9 742 4 33 34 595 198 c | 0 0 334 331 174 0 911 1052 109 1058 0 1062 1031 980 203 377 g | 0 0 170 278 328 767 21 0 44 0 237 0 3 2 19 147 t | 0 0 175 164 214 18 9 12 11 9 97 10 9 60 259 248

CG9895_SANGER_10_FBgn0034810_rc_shift5 (CG9895_SANGER_10_FBgn0034810_rc) 0.881 0.746 1.008 -0.170 0.931 1.149 0.948 20 5 38 51 11 26 19 24.286 21
; oligos_7nt_mkv5_m3 versus CG9895_SANGER_10_FBgn0034810_rc; m=2/12; ncol2=12; w=11; offset=1; strand=R; shift=5; score=24.2857; -----rCCACrCCCwh ; cor=0.881; Ncor=0.746; logoDP=1.008; NIcor=-0.170; NsEucl=0.931; SSD=1.149; NSW=0.948; rcor=20; rNcor=5; rlogoDP=38; rNIcor=51; rNsEucl=11; rSSD=26; rNSW=19; rank_mean=24.286; match_rank=21 a | 0 0 0 0 0 11 3 2 20 1 10 1 0 0 14 7 c | 0 0 0 0 0 0 20 21 4 23 0 22 22 22 2 7 g | 0 0 0 0 0 13 1 0 0 0 14 0 2 0 2 3 t | 0 0 0 0 0 0 0 1 0 0 0 1 0 2 6 7

CG9895_SOLEXA_5_FBgn0034810_rc_shift4 (CG9895_SOLEXA_5_FBgn0034810_rc) 0.876 0.803 0.412 -0.142 0.930 1.178 0.946 22 1 41 48 13 27 20 24.571 22
; oligos_7nt_mkv5_m3 versus CG9895_SOLEXA_5_FBgn0034810_rc; m=3/12; ncol2=11; w=11; offset=0; strand=R; shift=4; score=24.5714; ----rrCCACrCCCa- ; cor=0.876; Ncor=0.803; logoDP=0.412; NIcor=-0.142; NsEucl=0.930; SSD=1.178; NSW=0.946; rcor=22; rNcor=1; rlogoDP=41; rNIcor=48; rNsEucl=13; rSSD=27; rNSW=20; rank_mean=24.571; match_rank=22 a | 0 0 0 0 274 376 101 86 760 27 327 31 31 24 494 0 c | 0 0 0 0 126 29 781 818 212 961 0 959 957 921 200 0 g | 0 0 0 0 425 503 45 18 15 0 644 0 0 0 52 0 t | 0 0 0 0 109 73 63 68 3 2 19 0 2 44 239 0

CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc_shift3 (CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc) 0.850 0.728 1.503 -0.035 0.927 1.543 0.936 26 7 35 37 15 36 22 25.429 24
; oligos_7nt_mkv5_m3 versus CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc; m=4/12; ncol2=14; w=12; offset=-1; strand=R; shift=3; score=25.4286; ---crrCCACGCCCmc ; cor=0.850; Ncor=0.728; logoDP=1.503; NIcor=-0.035; NsEucl=0.927; SSD=1.543; NSW=0.936; rcor=26; rNcor=7; rlogoDP=35; rNIcor=37; rNsEucl=15; rSSD=36; rNSW=22; rank_mean=25.429; match_rank=24 a | 0 0 0 308 363 440 154 25 1086 19 54 53 32 24 593 146 c | 0 0 0 435 296 39 1022 1265 199 1290 9 1263 1276 1125 610 856 g | 0 0 0 291 384 766 62 0 27 0 1205 0 0 1 20 78 t | 0 0 0 218 276 74 81 29 7 10 51 3 11 169 96 219

luna_SOLEXA_5_FBgn0040765_rc_shift4 (luna_SOLEXA_5_FBgn0040765_rc) 0.837 0.717 1.085 -0.079 0.926 1.563 0.935 29 8 37 42 16 37 24 27.571 26
; oligos_7nt_mkv5_m3 versus luna_SOLEXA_5_FBgn0040765_rc; m=5/12; ncol2=14; w=12; offset=0; strand=R; shift=4; score=27.5714; ----grCCACGCCCwt ; cor=0.837; Ncor=0.717; logoDP=1.085; NIcor=-0.079; NsEucl=0.926; SSD=1.563; NSW=0.935; rcor=29; rNcor=8; rlogoDP=37; rNIcor=42; rNsEucl=16; rSSD=37; rNSW=24; rank_mean=27.571; match_rank=26 a | 0 0 0 0 132 155 85 73 434 5 126 18 29 18 276 111 c | 0 0 0 0 68 26 463 462 149 607 1 588 579 558 120 121 g | 0 0 0 0 283 396 27 18 24 0 468 5 0 0 36 111 t | 0 0 0 0 84 35 37 59 5 0 17 1 4 36 180 269

CG12029_SANGER_10_FBgn0035454_rc_shift5 (CG12029_SANGER_10_FBgn0035454_rc) 0.865 0.793 0.144 -0.192 0.922 1.465 0.933 24 2 49 52 19 35 25 29.429 27
; oligos_7nt_mkv5_m3 versus CG12029_SANGER_10_FBgn0035454_rc; m=6/12; ncol2=11; w=11; offset=1; strand=R; shift=5; score=29.4286; -----RCCACACCCac ; cor=0.865; Ncor=0.793; logoDP=0.144; NIcor=-0.192; NsEucl=0.922; SSD=1.465; NSW=0.933; rcor=24; rNcor=2; rlogoDP=49; rNIcor=52; rNsEucl=19; rSSD=35; rNSW=25; rank_mean=29.429; match_rank=27 a | 0 0 0 0 0 5 4 0 16 0 17 0 0 0 13 4 c | 0 0 0 0 0 0 14 20 2 20 0 20 20 20 3 11 g | 0 0 0 0 0 15 2 0 2 0 2 0 0 0 0 1 t | 0 0 0 0 0 0 0 0 0 0 1 0 0 0 4 4

CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc_shift3 (CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc) 0.844 0.675 0.051 -0.153 0.924 1.680 0.930 27 12 55 49 18 39 27 32.429 30
; oligos_7nt_mkv5_m3 versus CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc; m=7/12; ncol2=15; w=12; offset=-1; strand=R; shift=3; score=32.4286; ---carCCACGCCCmC ; cor=0.844; Ncor=0.675; logoDP=0.051; NIcor=-0.153; NsEucl=0.924; SSD=1.680; NSW=0.930; rcor=27; rNcor=12; rlogoDP=55; rNIcor=49; rNsEucl=18; rSSD=39; rNSW=27; rank_mean=32.429; match_rank=30 a | 0 0 0 47 105 85 40 1 234 11 4 9 10 13 171 38 c | 0 0 0 110 52 7 211 260 29 249 0 253 253 217 77 181 g | 0 0 0 53 59 166 8 0 0 0 255 0 0 0 1 10 t | 0 0 0 47 44 5 4 2 0 3 4 1 0 33 14 34

CG3065_F1-3_SANGER_2.5_FBgn0034946_rc_shift5 (CG3065_F1-3_SANGER_2.5_FBgn0034946_rc) 0.855 0.784 0.079 -0.218 0.916 1.714 0.922 25 3 54 55 24 40 30 33.000 33
; oligos_7nt_mkv5_m3 versus CG3065_F1-3_SANGER_2.5_FBgn0034946_rc; m=8/12; ncol2=11; w=11; offset=1; strand=R; shift=5; score= 33; -----rCCACGCCCmC ; cor=0.855; Ncor=0.784; logoDP=0.079; NIcor=-0.218; NsEucl=0.916; SSD=1.714; NSW=0.922; rcor=25; rNcor=3; rlogoDP=54; rNIcor=55; rNsEucl=24; rSSD=40; rNSW=30; rank_mean=33.000; match_rank=33 a | 0 0 0 0 0 7 2 0 20 0 0 0 0 0 12 0 c | 0 0 0 0 0 0 18 21 1 21 0 21 21 20 6 15 g | 0 0 0 0 0 13 1 0 0 0 21 0 0 0 1 1 t | 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 5

klu_SOLEXA_5_FBgn0013469_rc_shift2 (klu_SOLEXA_5_FBgn0013469_rc) 0.793 0.634 0.139 -0.165 0.916 2.046 0.915 36 14 50 50 25 46 32 36.143 41
; oligos_7nt_mkv5_m3 versus klu_SOLEXA_5_FBgn0013469_rc; m=9/12; ncol2=15; w=12; offset=-2; strand=R; shift=2; score=36.1429; --mmmmmCACCCmCrC ; cor=0.793; Ncor=0.634; logoDP=0.139; NIcor=-0.165; NsEucl=0.916; SSD=2.046; NSW=0.915; rcor=36; rNcor=14; rlogoDP=50; rNIcor=50; rNsEucl=25; rSSD=46; rNSW=32; rank_mean=36.143; match_rank=41 a | 0 0 132 156 135 134 155 9 378 3 3 5 315 2 226 54 c | 0 0 152 168 188 204 298 491 6 491 485 472 168 493 10 360 g | 0 0 82 90 85 64 24 0 48 0 5 0 6 1 230 5 t | 0 0 91 79 95 101 26 3 71 9 10 26 14 7 37 33

CG5669_SANGER_10_FBgn0039169_rc_shift2 (CG5669_SANGER_10_FBgn0039169_rc) 0.768 0.614 1.132 -0.092 0.908 2.428 0.899 44 18 36 45 27 56 40 38.000 45
; oligos_7nt_mkv5_m3 versus CG5669_SANGER_10_FBgn0039169_rc; m=10/12; ncol2=15; w=12; offset=-2; strand=R; shift=2; score= 38; --kwgRCCmCGCCCmy ; cor=0.768; Ncor=0.614; logoDP=1.132; NIcor=-0.092; NsEucl=0.908; SSD=2.428; NSW=0.899; rcor=44; rNcor=18; rlogoDP=36; rNIcor=45; rNsEucl=27; rSSD=56; rNSW=40; rank_mean=38.000; match_rank=45 a | 0 0 1 6 5 6 0 0 10 0 1 0 0 0 8 1 c | 0 0 1 3 2 0 21 20 14 24 1 24 24 23 14 11 g | 0 0 7 2 13 18 0 1 0 0 20 0 0 0 1 4 t | 0 0 15 13 4 0 3 3 0 0 2 0 0 1 1 7

sr_SOLEXA_5_FBgn0003499_rc_shift0 (sr_SOLEXA_5_FBgn0003499_rc) 0.782 0.489 0.322 -0.101 0.902 1.906 0.905 39 38 44 46 29 43 37 39.429 48
; oligos_7nt_mkv5_m3 versus sr_SOLEXA_5_FBgn0003499_rc; m=11/12; ncol2=14; w=10; offset=-4; strand=R; shift=0; score=39.4286; mcmCrCCCmCrcmm-- ; cor=0.782; Ncor=0.489; logoDP=0.322; NIcor=-0.101; NsEucl=0.902; SSD=1.906; NSW=0.905; rcor=39; rNcor=38; rlogoDP=44; rNIcor=46; rNsEucl=29; rSSD=43; rNSW=37; rank_mean=39.429; match_rank=48 a | 605 561 853 199 766 38 0 39 1576 8 722 366 933 560 0 0 c | 716 874 1114 1915 91 2300 2338 1947 697 2330 320 1380 588 851 0 0 g | 461 351 163 90 1194 0 0 0 6 0 1078 230 483 340 0 0 t | 424 552 208 134 287 0 0 352 59 0 218 362 309 436 0 0

klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc) 0.793 0.610 0.211 -0.227 0.896 2.151 0.892 35 19 46 56 31 47 43 39.571 50
; oligos_7nt_mkv5_m3 versus klu_SANGER_10_FBgn0013469_rc; m=12/12; ncol2=11; w=10; offset=2; strand=R; shift=6; score=39.5714; ------mCACCCmCrC ; cor=0.793; Ncor=0.610; logoDP=0.211; NIcor=-0.227; NsEucl=0.896; SSD=2.151; NSW=0.892; rcor=35; rNcor=19; rlogoDP=46; rNIcor=56; rNsEucl=31; rSSD=47; rNSW=43; rank_mean=39.571; match_rank=50 a | 0 0 0 0 0 0 7 0 18 0 0 0 13 0 9 0 c | 0 0 0 0 0 0 11 20 0 20 20 19 7 20 0 16 g | 0 0 0 0 0 0 2 0 0 0 0 0 0 0 10 0 t | 0 0 0 0 0 0 0 0 2 0 0 1 0 0 1 3

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m3_shift4 (oligos_7nt_mkv5_m3)																	; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----wsCCACdCmCac ; Alignment reference a \| 0 0 0 0 700 493 0 0 2679 0 1110 0 1408 0 1227 463 c \| 0 0 0 0 641 905 2679 2679 0 2679 0 2679 1271 2679 662 1262 g \| 0 0 0 0 571 804 0 0 0 0 862 0 0 0 311 365 t \| 0 0 0 0 767 477 0 0 0 0 707 0 0 0 479 589
CG12029_SOLEXA_5_FBgn0035454_rc_shift2 (CG12029_SOLEXA_5_FBgn0035454_rc)	0.896	0.716	0.880	-0.075	0.939	1.064	0.956	17	9	39	41	7	23	15	21.571	16	; oligos_7nt_mkv5_m3 versus CG12029_SOLEXA_5_FBgn0035454_rc; m=1/12; ncol2=15; w=12; offset=-2; strand=R; shift=2; score=21.5714; --mvrRCCACACCCay ; cor=0.896; Ncor=0.716; logoDP=0.880; NIcor=-0.075; NsEucl=0.939; SSD=1.064; NSW=0.956; rcor=17; rNcor=9; rlogoDP=39; rNIcor=41; rNsEucl=7; rSSD=23; rNSW=15; rank_mean=21.571; match_rank=16 a \| 0 0 311 274 360 291 135 12 912 9 742 4 33 34 595 198 c \| 0 0 334 331 174 0 911 1052 109 1058 0 1062 1031 980 203 377 g \| 0 0 170 278 328 767 21 0 44 0 237 0 3 2 19 147 t \| 0 0 175 164 214 18 9 12 11 9 97 10 9 60 259 248
CG9895_SANGER_10_FBgn0034810_rc_shift5 (CG9895_SANGER_10_FBgn0034810_rc)	0.881	0.746	1.008	-0.170	0.931	1.149	0.948	20	5	38	51	11	26	19	24.286	21	; oligos_7nt_mkv5_m3 versus CG9895_SANGER_10_FBgn0034810_rc; m=2/12; ncol2=12; w=11; offset=1; strand=R; shift=5; score=24.2857; -----rCCACrCCCwh ; cor=0.881; Ncor=0.746; logoDP=1.008; NIcor=-0.170; NsEucl=0.931; SSD=1.149; NSW=0.948; rcor=20; rNcor=5; rlogoDP=38; rNIcor=51; rNsEucl=11; rSSD=26; rNSW=19; rank_mean=24.286; match_rank=21 a \| 0 0 0 0 0 11 3 2 20 1 10 1 0 0 14 7 c \| 0 0 0 0 0 0 20 21 4 23 0 22 22 22 2 7 g \| 0 0 0 0 0 13 1 0 0 0 14 0 2 0 2 3 t \| 0 0 0 0 0 0 0 1 0 0 0 1 0 2 6 7
CG9895_SOLEXA_5_FBgn0034810_rc_shift4 (CG9895_SOLEXA_5_FBgn0034810_rc)	0.876	0.803	0.412	-0.142	0.930	1.178	0.946	22	1	41	48	13	27	20	24.571	22	; oligos_7nt_mkv5_m3 versus CG9895_SOLEXA_5_FBgn0034810_rc; m=3/12; ncol2=11; w=11; offset=0; strand=R; shift=4; score=24.5714; ----rrCCACrCCCa- ; cor=0.876; Ncor=0.803; logoDP=0.412; NIcor=-0.142; NsEucl=0.930; SSD=1.178; NSW=0.946; rcor=22; rNcor=1; rlogoDP=41; rNIcor=48; rNsEucl=13; rSSD=27; rNSW=20; rank_mean=24.571; match_rank=22 a \| 0 0 0 0 274 376 101 86 760 27 327 31 31 24 494 0 c \| 0 0 0 0 126 29 781 818 212 961 0 959 957 921 200 0 g \| 0 0 0 0 425 503 45 18 15 0 644 0 0 0 52 0 t \| 0 0 0 0 109 73 63 68 3 2 19 0 2 44 239 0
CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc_shift3 (CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc)	0.850	0.728	1.503	-0.035	0.927	1.543	0.936	26	7	35	37	15	36	22	25.429	24	; oligos_7nt_mkv5_m3 versus CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc; m=4/12; ncol2=14; w=12; offset=-1; strand=R; shift=3; score=25.4286; ---crrCCACGCCCmc ; cor=0.850; Ncor=0.728; logoDP=1.503; NIcor=-0.035; NsEucl=0.927; SSD=1.543; NSW=0.936; rcor=26; rNcor=7; rlogoDP=35; rNIcor=37; rNsEucl=15; rSSD=36; rNSW=22; rank_mean=25.429; match_rank=24 a \| 0 0 0 308 363 440 154 25 1086 19 54 53 32 24 593 146 c \| 0 0 0 435 296 39 1022 1265 199 1290 9 1263 1276 1125 610 856 g \| 0 0 0 291 384 766 62 0 27 0 1205 0 0 1 20 78 t \| 0 0 0 218 276 74 81 29 7 10 51 3 11 169 96 219
luna_SOLEXA_5_FBgn0040765_rc_shift4 (luna_SOLEXA_5_FBgn0040765_rc)	0.837	0.717	1.085	-0.079	0.926	1.563	0.935	29	8	37	42	16	37	24	27.571	26	; oligos_7nt_mkv5_m3 versus luna_SOLEXA_5_FBgn0040765_rc; m=5/12; ncol2=14; w=12; offset=0; strand=R; shift=4; score=27.5714; ----grCCACGCCCwt ; cor=0.837; Ncor=0.717; logoDP=1.085; NIcor=-0.079; NsEucl=0.926; SSD=1.563; NSW=0.935; rcor=29; rNcor=8; rlogoDP=37; rNIcor=42; rNsEucl=16; rSSD=37; rNSW=24; rank_mean=27.571; match_rank=26 a \| 0 0 0 0 132 155 85 73 434 5 126 18 29 18 276 111 c \| 0 0 0 0 68 26 463 462 149 607 1 588 579 558 120 121 g \| 0 0 0 0 283 396 27 18 24 0 468 5 0 0 36 111 t \| 0 0 0 0 84 35 37 59 5 0 17 1 4 36 180 269
CG12029_SANGER_10_FBgn0035454_rc_shift5 (CG12029_SANGER_10_FBgn0035454_rc)	0.865	0.793	0.144	-0.192	0.922	1.465	0.933	24	2	49	52	19	35	25	29.429	27	; oligos_7nt_mkv5_m3 versus CG12029_SANGER_10_FBgn0035454_rc; m=6/12; ncol2=11; w=11; offset=1; strand=R; shift=5; score=29.4286; -----RCCACACCCac ; cor=0.865; Ncor=0.793; logoDP=0.144; NIcor=-0.192; NsEucl=0.922; SSD=1.465; NSW=0.933; rcor=24; rNcor=2; rlogoDP=49; rNIcor=52; rNsEucl=19; rSSD=35; rNSW=25; rank_mean=29.429; match_rank=27 a \| 0 0 0 0 0 5 4 0 16 0 17 0 0 0 13 4 c \| 0 0 0 0 0 0 14 20 2 20 0 20 20 20 3 11 g \| 0 0 0 0 0 15 2 0 2 0 2 0 0 0 0 1 t \| 0 0 0 0 0 0 0 0 0 0 1 0 0 0 4 4
CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc_shift3 (CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc)	0.844	0.675	0.051	-0.153	0.924	1.680	0.930	27	12	55	49	18	39	27	32.429	30	; oligos_7nt_mkv5_m3 versus CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc; m=7/12; ncol2=15; w=12; offset=-1; strand=R; shift=3; score=32.4286; ---carCCACGCCCmC ; cor=0.844; Ncor=0.675; logoDP=0.051; NIcor=-0.153; NsEucl=0.924; SSD=1.680; NSW=0.930; rcor=27; rNcor=12; rlogoDP=55; rNIcor=49; rNsEucl=18; rSSD=39; rNSW=27; rank_mean=32.429; match_rank=30 a \| 0 0 0 47 105 85 40 1 234 11 4 9 10 13 171 38 c \| 0 0 0 110 52 7 211 260 29 249 0 253 253 217 77 181 g \| 0 0 0 53 59 166 8 0 0 0 255 0 0 0 1 10 t \| 0 0 0 47 44 5 4 2 0 3 4 1 0 33 14 34
CG3065_F1-3_SANGER_2.5_FBgn0034946_rc_shift5 (CG3065_F1-3_SANGER_2.5_FBgn0034946_rc)	0.855	0.784	0.079	-0.218	0.916	1.714	0.922	25	3	54	55	24	40	30	33.000	33	; oligos_7nt_mkv5_m3 versus CG3065_F1-3_SANGER_2.5_FBgn0034946_rc; m=8/12; ncol2=11; w=11; offset=1; strand=R; shift=5; score= 33; -----rCCACGCCCmC ; cor=0.855; Ncor=0.784; logoDP=0.079; NIcor=-0.218; NsEucl=0.916; SSD=1.714; NSW=0.922; rcor=25; rNcor=3; rlogoDP=54; rNIcor=55; rNsEucl=24; rSSD=40; rNSW=30; rank_mean=33.000; match_rank=33 a \| 0 0 0 0 0 7 2 0 20 0 0 0 0 0 12 0 c \| 0 0 0 0 0 0 18 21 1 21 0 21 21 20 6 15 g \| 0 0 0 0 0 13 1 0 0 0 21 0 0 0 1 1 t \| 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 5
klu_SOLEXA_5_FBgn0013469_rc_shift2 (klu_SOLEXA_5_FBgn0013469_rc)	0.793	0.634	0.139	-0.165	0.916	2.046	0.915	36	14	50	50	25	46	32	36.143	41	; oligos_7nt_mkv5_m3 versus klu_SOLEXA_5_FBgn0013469_rc; m=9/12; ncol2=15; w=12; offset=-2; strand=R; shift=2; score=36.1429; --mmmmmCACCCmCrC ; cor=0.793; Ncor=0.634; logoDP=0.139; NIcor=-0.165; NsEucl=0.916; SSD=2.046; NSW=0.915; rcor=36; rNcor=14; rlogoDP=50; rNIcor=50; rNsEucl=25; rSSD=46; rNSW=32; rank_mean=36.143; match_rank=41 a \| 0 0 132 156 135 134 155 9 378 3 3 5 315 2 226 54 c \| 0 0 152 168 188 204 298 491 6 491 485 472 168 493 10 360 g \| 0 0 82 90 85 64 24 0 48 0 5 0 6 1 230 5 t \| 0 0 91 79 95 101 26 3 71 9 10 26 14 7 37 33
CG5669_SANGER_10_FBgn0039169_rc_shift2 (CG5669_SANGER_10_FBgn0039169_rc)	0.768	0.614	1.132	-0.092	0.908	2.428	0.899	44	18	36	45	27	56	40	38.000	45	; oligos_7nt_mkv5_m3 versus CG5669_SANGER_10_FBgn0039169_rc; m=10/12; ncol2=15; w=12; offset=-2; strand=R; shift=2; score= 38; --kwgRCCmCGCCCmy ; cor=0.768; Ncor=0.614; logoDP=1.132; NIcor=-0.092; NsEucl=0.908; SSD=2.428; NSW=0.899; rcor=44; rNcor=18; rlogoDP=36; rNIcor=45; rNsEucl=27; rSSD=56; rNSW=40; rank_mean=38.000; match_rank=45 a \| 0 0 1 6 5 6 0 0 10 0 1 0 0 0 8 1 c \| 0 0 1 3 2 0 21 20 14 24 1 24 24 23 14 11 g \| 0 0 7 2 13 18 0 1 0 0 20 0 0 0 1 4 t \| 0 0 15 13 4 0 3 3 0 0 2 0 0 1 1 7
sr_SOLEXA_5_FBgn0003499_rc_shift0 (sr_SOLEXA_5_FBgn0003499_rc)	0.782	0.489	0.322	-0.101	0.902	1.906	0.905	39	38	44	46	29	43	37	39.429	48	; oligos_7nt_mkv5_m3 versus sr_SOLEXA_5_FBgn0003499_rc; m=11/12; ncol2=14; w=10; offset=-4; strand=R; shift=0; score=39.4286; mcmCrCCCmCrcmm-- ; cor=0.782; Ncor=0.489; logoDP=0.322; NIcor=-0.101; NsEucl=0.902; SSD=1.906; NSW=0.905; rcor=39; rNcor=38; rlogoDP=44; rNIcor=46; rNsEucl=29; rSSD=43; rNSW=37; rank_mean=39.429; match_rank=48 a \| 605 561 853 199 766 38 0 39 1576 8 722 366 933 560 0 0 c \| 716 874 1114 1915 91 2300 2338 1947 697 2330 320 1380 588 851 0 0 g \| 461 351 163 90 1194 0 0 0 6 0 1078 230 483 340 0 0 t \| 424 552 208 134 287 0 0 352 59 0 218 362 309 436 0 0
klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc)	0.793	0.610	0.211	-0.227	0.896	2.151	0.892	35	19	46	56	31	47	43	39.571	50	; oligos_7nt_mkv5_m3 versus klu_SANGER_10_FBgn0013469_rc; m=12/12; ncol2=11; w=10; offset=2; strand=R; shift=6; score=39.5714; ------mCACCCmCrC ; cor=0.793; Ncor=0.610; logoDP=0.211; NIcor=-0.227; NsEucl=0.896; SSD=2.151; NSW=0.892; rcor=35; rNcor=19; rlogoDP=46; rNIcor=56; rNsEucl=31; rSSD=47; rNSW=43; rank_mean=39.571; match_rank=50 a \| 0 0 0 0 0 0 7 0 18 0 0 0 13 0 9 0 c \| 0 0 0 0 0 0 11 20 0 20 20 19 7 20 0 16 g \| 0 0 0 0 0 0 2 0 0 0 0 0 0 0 10 0 t \| 0 0 0 0 0 0 0 0 2 0 0 1 0 0 1 3

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift2 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --yaTACATAta ; Alignment reference a | 0 0 1566 3368 0 7443 0 7443 0 7443 1588 3283 c | 0 0 1981 835 0 0 7443 0 0 0 1762 858 g | 0 0 900 1799 0 0 0 0 0 0 757 1698 t | 0 0 2996 1441 7443 0 0 0 7443 0 3336 1604

Caup_SOLEXA_FBgn0015919_shift2 (Caup_SOLEXA_FBgn0015919) 0.839 0.503 5.933 0.497 0.886 0.929 0.923 28 34 13 10 37 18 29 24.143 20
; oligos_6nt_mkv4_m3 versus Caup_SOLEXA_FBgn0015919; m=1/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score=24.1429; --wtwACA---- ; cor=0.839; Ncor=0.503; logoDP=5.933; NIcor=0.497; NsEucl=0.886; SSD=0.929; NSW=0.923; rcor=28; rNcor=34; rlogoDP=13; rNIcor=10; rNsEucl=37; rSSD=18; rNSW=29; rank_mean=24.143; match_rank=20 a | 0 0 999 577 1415 2904 2 2904 0 0 0 0 c | 0 0 460 201 0 0 2902 0 0 0 0 0 g | 0 0 626 639 511 0 0 0 0 0 0 0 t | 0 0 819 1487 978 0 0 0 0 0 0 0

Mirr_SOLEXA_FBgn0014343_shift2 (Mirr_SOLEXA_FBgn0014343) 0.828 0.497 5.948 0.491 0.883 0.991 0.917 32 35 12 11 39 21 31 25.857 25
; oligos_6nt_mkv4_m3 versus Mirr_SOLEXA_FBgn0014343; m=2/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score=25.8571; --wwwACA---- ; cor=0.828; Ncor=0.497; logoDP=5.948; NIcor=0.491; NsEucl=0.883; SSD=0.991; NSW=0.917; rcor=32; rNcor=35; rlogoDP=12; rNIcor=11; rNsEucl=39; rSSD=21; rNSW=31; rank_mean=25.857; match_rank=25 a | 0 0 550 410 782 1415 0 1415 0 0 0 0 c | 0 0 158 93 0 0 1415 0 0 0 0 0 g | 0 0 327 282 204 0 0 0 0 0 0 0 t | 0 0 380 630 429 0 0 0 0 0 0 0

Ara_SOLEXA_FBgn0015904_shift2 (Ara_SOLEXA_FBgn0015904) 0.790 0.474 5.958 0.466 0.869 1.234 0.897 37 40 11 15 45 31 41 31.429 28
; oligos_6nt_mkv4_m3 versus Ara_SOLEXA_FBgn0015904; m=3/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score=31.4286; --awwACA---- ; cor=0.790; Ncor=0.474; logoDP=5.958; NIcor=0.466; NsEucl=0.869; SSD=1.234; NSW=0.897; rcor=37; rNcor=40; rlogoDP=11; rNIcor=15; rNsEucl=45; rSSD=31; rNSW=41; rank_mean=31.429; match_rank=28 a | 0 0 155 97 193 313 0 313 0 0 0 0 c | 0 0 36 0 0 0 313 0 0 0 0 0 g | 0 0 44 45 38 0 0 0 0 0 0 0 t | 0 0 78 171 82 0 0 0 0 0 0 0

CG11617_SOLEXA_FBgn0031232_shift0 (CG11617_SOLEXA_FBgn0031232) 0.805 0.402 5.767 0.396 0.874 1.140 0.905 34 55 14 24 44 25 36 33.143 34
; oligos_6nt_mkv4_m3 versus CG11617_SOLEXA_FBgn0031232; m=4/4; ncol2=8; w=6; offset=-2; strand=D; shift=0; score=33.1429; wtwTwACA---- ; cor=0.805; Ncor=0.402; logoDP=5.767; NIcor=0.396; NsEucl=0.874; SSD=1.140; NSW=0.905; rcor=34; rNcor=55; rlogoDP=14; rNIcor=24; rNsEucl=44; rSSD=25; rNSW=36; rank_mean=33.143; match_rank=34 a | 370 281 352 133 483 1159 7 1148 0 0 0 0 c | 201 262 176 167 0 0 1152 2 0 0 0 0 g | 211 257 176 20 283 0 0 9 0 0 0 0 t | 377 359 455 839 393 0 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3)																	; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --yaTACATAta ; Alignment reference a \| 0 0 1566 3368 0 7443 0 7443 0 7443 1588 3283 c \| 0 0 1981 835 0 0 7443 0 0 0 1762 858 g \| 0 0 900 1799 0 0 0 0 0 0 757 1698 t \| 0 0 2996 1441 7443 0 0 0 7443 0 3336 1604
Caup_SOLEXA_FBgn0015919_shift2 (Caup_SOLEXA_FBgn0015919)	0.839	0.503	5.933	0.497	0.886	0.929	0.923	28	34	13	10	37	18	29	24.143	20	; oligos_6nt_mkv4_m3 versus Caup_SOLEXA_FBgn0015919; m=1/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score=24.1429; --wtwACA---- ; cor=0.839; Ncor=0.503; logoDP=5.933; NIcor=0.497; NsEucl=0.886; SSD=0.929; NSW=0.923; rcor=28; rNcor=34; rlogoDP=13; rNIcor=10; rNsEucl=37; rSSD=18; rNSW=29; rank_mean=24.143; match_rank=20 a \| 0 0 999 577 1415 2904 2 2904 0 0 0 0 c \| 0 0 460 201 0 0 2902 0 0 0 0 0 g \| 0 0 626 639 511 0 0 0 0 0 0 0 t \| 0 0 819 1487 978 0 0 0 0 0 0 0
Mirr_SOLEXA_FBgn0014343_shift2 (Mirr_SOLEXA_FBgn0014343)	0.828	0.497	5.948	0.491	0.883	0.991	0.917	32	35	12	11	39	21	31	25.857	25	; oligos_6nt_mkv4_m3 versus Mirr_SOLEXA_FBgn0014343; m=2/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score=25.8571; --wwwACA---- ; cor=0.828; Ncor=0.497; logoDP=5.948; NIcor=0.491; NsEucl=0.883; SSD=0.991; NSW=0.917; rcor=32; rNcor=35; rlogoDP=12; rNIcor=11; rNsEucl=39; rSSD=21; rNSW=31; rank_mean=25.857; match_rank=25 a \| 0 0 550 410 782 1415 0 1415 0 0 0 0 c \| 0 0 158 93 0 0 1415 0 0 0 0 0 g \| 0 0 327 282 204 0 0 0 0 0 0 0 t \| 0 0 380 630 429 0 0 0 0 0 0 0
Ara_SOLEXA_FBgn0015904_shift2 (Ara_SOLEXA_FBgn0015904)	0.790	0.474	5.958	0.466	0.869	1.234	0.897	37	40	11	15	45	31	41	31.429	28	; oligos_6nt_mkv4_m3 versus Ara_SOLEXA_FBgn0015904; m=3/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score=31.4286; --awwACA---- ; cor=0.790; Ncor=0.474; logoDP=5.958; NIcor=0.466; NsEucl=0.869; SSD=1.234; NSW=0.897; rcor=37; rNcor=40; rlogoDP=11; rNIcor=15; rNsEucl=45; rSSD=31; rNSW=41; rank_mean=31.429; match_rank=28 a \| 0 0 155 97 193 313 0 313 0 0 0 0 c \| 0 0 36 0 0 0 313 0 0 0 0 0 g \| 0 0 44 45 38 0 0 0 0 0 0 0 t \| 0 0 78 171 82 0 0 0 0 0 0 0
CG11617_SOLEXA_FBgn0031232_shift0 (CG11617_SOLEXA_FBgn0031232)	0.805	0.402	5.767	0.396	0.874	1.140	0.905	34	55	14	24	44	25	36	33.143	34	; oligos_6nt_mkv4_m3 versus CG11617_SOLEXA_FBgn0031232; m=4/4; ncol2=8; w=6; offset=-2; strand=D; shift=0; score=33.1429; wtwTwACA---- ; cor=0.805; Ncor=0.402; logoDP=5.767; NIcor=0.396; NsEucl=0.874; SSD=1.140; NSW=0.905; rcor=34; rNcor=55; rlogoDP=14; rNIcor=24; rNsEucl=44; rSSD=25; rNSW=36; rank_mean=33.143; match_rank=34 a \| 370 281 352 133 483 1159 7 1148 0 0 0 0 c \| 201 262 176 167 0 0 1152 2 0 0 0 0 g \| 211 257 176 20 283 0 0 9 0 0 0 0 t \| 377 359 455 839 393 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift1 ; 7 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATYTkKAww ; Alignment reference a | 0 1274 1387 0 4484 0 0 0 0 0 4484 1227 1330 c | 0 685 584 0 0 0 1204 0 0 0 0 707 1019 g | 0 685 1071 0 0 0 0 0 1682 1241 0 715 758 t | 0 1840 1442 4484 0 4484 3280 4484 2802 3243 0 1835 1377

br-Z1_FlyReg_FBgn0000210_rc_shift0 (br-Z1_FlyReg_FBgn0000210_rc) 0.832 0.448 2.082 0.158 0.896 1.063 0.924 30 43 34 33 33 22 28 31.857 29
; oligos_7nt_mkv5_m1 versus br-Z1_FlyReg_FBgn0000210_rc; m=1/6; ncol2=8; w=7; offset=-1; strand=R; shift=0; score=31.8571; TtcTAwTT----- ; cor=0.832; Ncor=0.448; logoDP=2.082; NIcor=0.158; NsEucl=0.896; SSD=1.063; NSW=0.924; rcor=30; rNcor=43; rlogoDP=34; rNIcor=33; rNsEucl=33; rSSD=22; rNSW=28; rank_mean=31.857; match_rank=29 a | 0 1 3 1 14 8 0 3 0 0 0 0 0 c | 0 2 9 2 0 0 3 2 0 0 0 0 0 g | 1 3 4 0 3 0 2 0 0 0 0 0 0 t | 16 11 1 14 0 9 12 12 0 0 0 0 0

CG12361_Cell_FBgn0250756_shift6 (CG12361_Cell_FBgn0250756) 0.784 0.422 3.808 0.419 0.889 1.216 0.913 38 47 30 19 34 28 33 32.714 32
; oligos_7nt_mkv5_m1 versus CG12361_Cell_FBgn0250756; m=2/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score=32.7143; ------tTTwATk ; cor=0.784; Ncor=0.422; logoDP=3.808; NIcor=0.419; NsEucl=0.889; SSD=1.216; NSW=0.913; rcor=38; rNcor=47; rlogoDP=30; rNIcor=19; rNsEucl=34; rSSD=28; rNSW=33; rank_mean=32.714; match_rank=32 a | 0 0 0 0 0 0 2 2 2 6 16 0 0 c | 0 0 0 0 0 0 2 0 0 0 0 0 2 g | 0 0 0 0 0 0 3 0 0 2 0 0 6 t | 0 0 0 0 0 0 9 14 14 8 0 16 8

hb_FlyReg_FBgn0001180_shift4 (hb_FlyReg_FBgn0001180) 0.759 0.506 5.738 0.469 0.878 1.919 0.880 47 33 15 14 42 44 45 34.286 35
; oligos_7nt_mkv5_m1 versus hb_FlyReg_FBgn0001180; m=3/6; ncol2=8; w=8; offset=3; strand=D; shift=4; score=34.2857; ----tTTTTTrt- ; cor=0.759; Ncor=0.506; logoDP=5.738; NIcor=0.469; NsEucl=0.878; SSD=1.919; NSW=0.880; rcor=47; rNcor=33; rlogoDP=15; rNIcor=14; rNsEucl=42; rSSD=44; rNSW=45; rank_mean=34.286; match_rank=35 a | 0 0 0 0 17 0 1 0 0 1 59 20 0 c | 0 0 0 0 13 0 5 1 0 4 7 17 0 g | 0 0 0 0 7 3 1 0 0 0 29 14 0 t | 0 0 0 0 66 100 96 102 103 98 8 52 0

Abd-B_FlyReg_FBgn0000015_rc_shift6 (Abd-B_FlyReg_FBgn0000015_rc) 0.825 0.444 2.968 0.202 0.888 1.232 0.912 33 44 33 30 36 30 35 34.429 37
; oligos_7nt_mkv5_m1 versus Abd-B_FlyReg_FBgn0000015_rc; m=4/6; ncol2=8; w=7; offset=5; strand=R; shift=6; score=34.4286; ------TTTTATG ; cor=0.825; Ncor=0.444; logoDP=2.968; NIcor=0.202; NsEucl=0.888; SSD=1.232; NSW=0.912; rcor=33; rNcor=44; rlogoDP=33; rNIcor=30; rNsEucl=36; rSSD=30; rNSW=35; rank_mean=34.429; match_rank=37 a | 0 0 0 0 0 0 1 1 0 0 7 0 0 c | 0 0 0 0 0 0 1 0 0 0 0 1 1 g | 0 0 0 0 0 0 0 0 0 0 0 0 5 t | 0 0 0 0 0 0 5 6 7 7 0 6 1

AbdB_SOLEXA_FBgn0000015_shift6 (AbdB_SOLEXA_FBgn0000015) 0.756 0.407 3.160 0.413 0.889 1.217 0.913 49 52 32 21 35 29 34 36.000 40
; oligos_7nt_mkv5_m1 versus AbdB_SOLEXA_FBgn0000015; m=5/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 36; ------tTTwATk ; cor=0.756; Ncor=0.407; logoDP=3.160; NIcor=0.413; NsEucl=0.889; SSD=1.217; NSW=0.913; rcor=49; rNcor=52; rlogoDP=32; rNIcor=21; rNsEucl=35; rSSD=29; rNSW=34; rank_mean=36.000; match_rank=40 a | 0 0 0 0 0 0 619 344 61 1124 2704 55 449 c | 0 0 0 0 0 0 519 201 0 33 0 630 62 g | 0 0 0 0 0 0 545 252 0 38 0 71 1301 t | 0 0 0 0 0 0 1021 1907 2643 1509 0 1948 892

Cad_Cell_FBgn0000251_shift6 (Cad_Cell_FBgn0000251) 0.751 0.404 3.263 0.386 0.880 1.403 0.900 55 53 31 27 40 33 38 39.571 49
; oligos_7nt_mkv5_m1 versus Cad_Cell_FBgn0000251; m=6/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score=39.5714; ------wTTwATT ; cor=0.751; Ncor=0.404; logoDP=3.263; NIcor=0.386; NsEucl=0.880; SSD=1.403; NSW=0.900; rcor=55; rNcor=53; rlogoDP=31; rNIcor=27; rNsEucl=40; rSSD=33; rNSW=38; rank_mean=39.571; match_rank=49 a | 0 0 0 0 0 0 12 3 4 12 38 0 4 c | 0 0 0 0 0 0 6 3 0 0 0 0 0 g | 0 0 0 0 0 0 4 3 0 2 0 0 7 t | 0 0 0 0 0 0 16 29 34 24 0 38 27

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)																	; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATYTkKAww ; Alignment reference a \| 0 1274 1387 0 4484 0 0 0 0 0 4484 1227 1330 c \| 0 685 584 0 0 0 1204 0 0 0 0 707 1019 g \| 0 685 1071 0 0 0 0 0 1682 1241 0 715 758 t \| 0 1840 1442 4484 0 4484 3280 4484 2802 3243 0 1835 1377
br-Z1_FlyReg_FBgn0000210_rc_shift0 (br-Z1_FlyReg_FBgn0000210_rc)	0.832	0.448	2.082	0.158	0.896	1.063	0.924	30	43	34	33	33	22	28	31.857	29	; oligos_7nt_mkv5_m1 versus br-Z1_FlyReg_FBgn0000210_rc; m=1/6; ncol2=8; w=7; offset=-1; strand=R; shift=0; score=31.8571; TtcTAwTT----- ; cor=0.832; Ncor=0.448; logoDP=2.082; NIcor=0.158; NsEucl=0.896; SSD=1.063; NSW=0.924; rcor=30; rNcor=43; rlogoDP=34; rNIcor=33; rNsEucl=33; rSSD=22; rNSW=28; rank_mean=31.857; match_rank=29 a \| 0 1 3 1 14 8 0 3 0 0 0 0 0 c \| 0 2 9 2 0 0 3 2 0 0 0 0 0 g \| 1 3 4 0 3 0 2 0 0 0 0 0 0 t \| 16 11 1 14 0 9 12 12 0 0 0 0 0
CG12361_Cell_FBgn0250756_shift6 (CG12361_Cell_FBgn0250756)	0.784	0.422	3.808	0.419	0.889	1.216	0.913	38	47	30	19	34	28	33	32.714	32	; oligos_7nt_mkv5_m1 versus CG12361_Cell_FBgn0250756; m=2/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score=32.7143; ------tTTwATk ; cor=0.784; Ncor=0.422; logoDP=3.808; NIcor=0.419; NsEucl=0.889; SSD=1.216; NSW=0.913; rcor=38; rNcor=47; rlogoDP=30; rNIcor=19; rNsEucl=34; rSSD=28; rNSW=33; rank_mean=32.714; match_rank=32 a \| 0 0 0 0 0 0 2 2 2 6 16 0 0 c \| 0 0 0 0 0 0 2 0 0 0 0 0 2 g \| 0 0 0 0 0 0 3 0 0 2 0 0 6 t \| 0 0 0 0 0 0 9 14 14 8 0 16 8
hb_FlyReg_FBgn0001180_shift4 (hb_FlyReg_FBgn0001180)	0.759	0.506	5.738	0.469	0.878	1.919	0.880	47	33	15	14	42	44	45	34.286	35	; oligos_7nt_mkv5_m1 versus hb_FlyReg_FBgn0001180; m=3/6; ncol2=8; w=8; offset=3; strand=D; shift=4; score=34.2857; ----tTTTTTrt- ; cor=0.759; Ncor=0.506; logoDP=5.738; NIcor=0.469; NsEucl=0.878; SSD=1.919; NSW=0.880; rcor=47; rNcor=33; rlogoDP=15; rNIcor=14; rNsEucl=42; rSSD=44; rNSW=45; rank_mean=34.286; match_rank=35 a \| 0 0 0 0 17 0 1 0 0 1 59 20 0 c \| 0 0 0 0 13 0 5 1 0 4 7 17 0 g \| 0 0 0 0 7 3 1 0 0 0 29 14 0 t \| 0 0 0 0 66 100 96 102 103 98 8 52 0
Abd-B_FlyReg_FBgn0000015_rc_shift6 (Abd-B_FlyReg_FBgn0000015_rc)	0.825	0.444	2.968	0.202	0.888	1.232	0.912	33	44	33	30	36	30	35	34.429	37	; oligos_7nt_mkv5_m1 versus Abd-B_FlyReg_FBgn0000015_rc; m=4/6; ncol2=8; w=7; offset=5; strand=R; shift=6; score=34.4286; ------TTTTATG ; cor=0.825; Ncor=0.444; logoDP=2.968; NIcor=0.202; NsEucl=0.888; SSD=1.232; NSW=0.912; rcor=33; rNcor=44; rlogoDP=33; rNIcor=30; rNsEucl=36; rSSD=30; rNSW=35; rank_mean=34.429; match_rank=37 a \| 0 0 0 0 0 0 1 1 0 0 7 0 0 c \| 0 0 0 0 0 0 1 0 0 0 0 1 1 g \| 0 0 0 0 0 0 0 0 0 0 0 0 5 t \| 0 0 0 0 0 0 5 6 7 7 0 6 1
AbdB_SOLEXA_FBgn0000015_shift6 (AbdB_SOLEXA_FBgn0000015)	0.756	0.407	3.160	0.413	0.889	1.217	0.913	49	52	32	21	35	29	34	36.000	40	; oligos_7nt_mkv5_m1 versus AbdB_SOLEXA_FBgn0000015; m=5/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 36; ------tTTwATk ; cor=0.756; Ncor=0.407; logoDP=3.160; NIcor=0.413; NsEucl=0.889; SSD=1.217; NSW=0.913; rcor=49; rNcor=52; rlogoDP=32; rNIcor=21; rNsEucl=35; rSSD=29; rNSW=34; rank_mean=36.000; match_rank=40 a \| 0 0 0 0 0 0 619 344 61 1124 2704 55 449 c \| 0 0 0 0 0 0 519 201 0 33 0 630 62 g \| 0 0 0 0 0 0 545 252 0 38 0 71 1301 t \| 0 0 0 0 0 0 1021 1907 2643 1509 0 1948 892
Cad_Cell_FBgn0000251_shift6 (Cad_Cell_FBgn0000251)	0.751	0.404	3.263	0.386	0.880	1.403	0.900	55	53	31	27	40	33	38	39.571	49	; oligos_7nt_mkv5_m1 versus Cad_Cell_FBgn0000251; m=6/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score=39.5714; ------wTTwATT ; cor=0.751; Ncor=0.404; logoDP=3.263; NIcor=0.386; NsEucl=0.880; SSD=1.403; NSW=0.900; rcor=55; rNcor=53; rlogoDP=31; rNIcor=27; rNsEucl=40; rSSD=33; rNSW=38; rank_mean=39.571; match_rank=49 a \| 0 0 0 0 0 0 12 3 4 12 38 0 4 c \| 0 0 0 0 0 0 6 3 0 0 0 0 0 g \| 0 0 0 0 0 0 4 3 0 2 0 0 7 t \| 0 0 0 0 0 0 16 29 34 24 0 38 27