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/positions_6nt_m3/peak-motifs_positions_6nt_m3.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_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_FlyFactorSurvey

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 1 1 1 1 2 1 2 1.286 1
; positions_6nt_m3 versus vfl_SANGER_5_FBgn0259789; m=1/10; ncol2=8; w=8; offset=1; strand=D; shift=4; score= 1.2857; ----gCAGGTAG--- ; cor=0.955; Ncor=0.764; logoDP=11.552; NIcor=0.761; NsEucl=0.940; SSD=0.455; NSW=0.972; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.286; 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 2 2 2 2 1 2 1 1.714 2
; positions_6nt_m3 versus vfl_SOLEXA_5_FBgn0259789; m=2/10; ncol2=15; w=10; offset=-3; strand=D; shift=0; score= 1.7143; kkkbkCAGGTAGsyg ; cor=0.948; Ncor=0.632; logoDP=10.716; NIcor=0.637; NsEucl=0.950; SSD=0.494; NSW=0.975; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.714; match_rank=2 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 3 3 5 5 3 3 3 3.571 3
; positions_6nt_m3 versus wor_SOLEXA_2.5_FBgn0001983_rc; m=3/10; ncol2=8; w=8; offset=1; strand=R; shift=4; score= 3.5714; ----rCAGGTGk--- ; cor=0.781; Ncor=0.624; logoDP=4.606; NIcor=0.271; NsEucl=0.876; SSD=1.959; NSW=0.878; rcor=3; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=3 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

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 6 4 6 6 5 9 5 5.857 4
; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0000413_rc; m=4/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 5.8571; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=6; rNcor=4; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=9; rNSW=5; rank_mean=5.857; match_rank=4 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

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 8 9 3 3 9 6 9 6.714 5
; 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= 6.7143; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=8; rNcor=9; rlogoDP=3; rNIcor=3; rNsEucl=9; rSSD=6; rNSW=9; rank_mean=6.714; match_rank=5 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_FBgn0002922_rc_shift3 (nau_da_SANGER_5_FBgn0002922_rc) 0.754 0.603 4.460 0.175 0.865 2.318 0.855 7 5 7 7 6 10 6 6.857 6
; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0002922_rc; m=6/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 6.8571; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=7; rNcor=5; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=10; rNSW=6; rank_mean=6.857; match_rank=6 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 10 6 8 8 4 8 4 6.857 7
; positions_6nt_m3 versus CG12605_SANGER_10_FBgn0035481_rc; m=7/10; ncol2=9; w=8; offset=-1; strand=R; shift=2; score= 6.8571; --CaACAGGTG---- ; cor=0.753; Ncor=0.548; logoDP=3.837; NIcor=0.142; NsEucl=0.866; SSD=2.295; NSW=0.857; rcor=10; rNcor=6; rlogoDP=8; rNIcor=8; rNsEucl=4; rSSD=8; rNSW=4; rank_mean=6.857; match_rank=7 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 4 7 10 10 7 4 7 7.000 8
; positions_6nt_m3 versus wor_SANGER_2.5_FBgn0001983_rc; m=8/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score= 7; ----rCAGGTG---- ; cor=0.761; Ncor=0.533; logoDP=0.045; NIcor=-0.215; NsEucl=0.851; SSD=2.188; NSW=0.844; rcor=4; rNcor=7; rlogoDP=10; rNIcor=10; rNsEucl=7; rSSD=4; rNSW=7; rank_mean=7.000; match_rank=8 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 5 8 9 9 8 5 8 7.429 9
; positions_6nt_m3 versus esg_SANGER_2.5_FBgn0001981_rc; m=9/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score= 7.4286; ----aCAGGTG---- ; cor=0.757; Ncor=0.530; logoDP=0.124; NIcor=-0.209; NsEucl=0.850; SSD=2.204; NSW=0.843; rcor=5; rNcor=8; rlogoDP=9; rNIcor=9; rNsEucl=8; rSSD=5; rNSW=8; rank_mean=7.429; match_rank=9 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

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 9 10 4 4 10 7 10 7.714 10
; positions_6nt_m3 versus l(1)sc_da_SANGER_5_FBgn0000413; m=10/10; ncol2=7; w=7; offset=1; strand=D; shift=4; score= 7.7143; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=9; rNcor=10; rlogoDP=4; rNIcor=4; rNsEucl=10; rSSD=7; rNSW=10; rank_mean=7.714; match_rank=10 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

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	1	1	1	1	2	1	2	1.286	1	; positions_6nt_m3 versus vfl_SANGER_5_FBgn0259789; m=1/10; ncol2=8; w=8; offset=1; strand=D; shift=4; score= 1.2857; ----gCAGGTAG--- ; cor=0.955; Ncor=0.764; logoDP=11.552; NIcor=0.761; NsEucl=0.940; SSD=0.455; NSW=0.972; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.286; 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	2	2	2	2	1	2	1	1.714	2	; positions_6nt_m3 versus vfl_SOLEXA_5_FBgn0259789; m=2/10; ncol2=15; w=10; offset=-3; strand=D; shift=0; score= 1.7143; kkkbkCAGGTAGsyg ; cor=0.948; Ncor=0.632; logoDP=10.716; NIcor=0.637; NsEucl=0.950; SSD=0.494; NSW=0.975; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.714; match_rank=2 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	3	3	5	5	3	3	3	3.571	3	; positions_6nt_m3 versus wor_SOLEXA_2.5_FBgn0001983_rc; m=3/10; ncol2=8; w=8; offset=1; strand=R; shift=4; score= 3.5714; ----rCAGGTGk--- ; cor=0.781; Ncor=0.624; logoDP=4.606; NIcor=0.271; NsEucl=0.876; SSD=1.959; NSW=0.878; rcor=3; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=3 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
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	6	4	6	6	5	9	5	5.857	4	; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0000413_rc; m=4/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 5.8571; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=6; rNcor=4; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=9; rNSW=5; rank_mean=5.857; match_rank=4 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
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	8	9	3	3	9	6	9	6.714	5	; 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= 6.7143; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=8; rNcor=9; rlogoDP=3; rNIcor=3; rNsEucl=9; rSSD=6; rNSW=9; rank_mean=6.714; match_rank=5 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_FBgn0002922_rc_shift3 (nau_da_SANGER_5_FBgn0002922_rc)	0.754	0.603	4.460	0.175	0.865	2.318	0.855	7	5	7	7	6	10	6	6.857	6	; positions_6nt_m3 versus nau_da_SANGER_5_FBgn0002922_rc; m=6/10; ncol2=8; w=8; offset=0; strand=R; shift=3; score= 6.8571; ---rrCAGGTG---- ; cor=0.754; Ncor=0.603; logoDP=4.460; NIcor=0.175; NsEucl=0.865; SSD=2.318; NSW=0.855; rcor=7; rNcor=5; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=10; rNSW=6; rank_mean=6.857; match_rank=6 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	10	6	8	8	4	8	4	6.857	7	; positions_6nt_m3 versus CG12605_SANGER_10_FBgn0035481_rc; m=7/10; ncol2=9; w=8; offset=-1; strand=R; shift=2; score= 6.8571; --CaACAGGTG---- ; cor=0.753; Ncor=0.548; logoDP=3.837; NIcor=0.142; NsEucl=0.866; SSD=2.295; NSW=0.857; rcor=10; rNcor=6; rlogoDP=8; rNIcor=8; rNsEucl=4; rSSD=8; rNSW=4; rank_mean=6.857; match_rank=7 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	4	7	10	10	7	4	7	7.000	8	; positions_6nt_m3 versus wor_SANGER_2.5_FBgn0001983_rc; m=8/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score= 7; ----rCAGGTG---- ; cor=0.761; Ncor=0.533; logoDP=0.045; NIcor=-0.215; NsEucl=0.851; SSD=2.188; NSW=0.844; rcor=4; rNcor=7; rlogoDP=10; rNIcor=10; rNsEucl=7; rSSD=4; rNSW=7; rank_mean=7.000; match_rank=8 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	5	8	9	9	8	5	8	7.429	9	; positions_6nt_m3 versus esg_SANGER_2.5_FBgn0001981_rc; m=9/10; ncol2=7; w=7; offset=1; strand=R; shift=4; score= 7.4286; ----aCAGGTG---- ; cor=0.757; Ncor=0.530; logoDP=0.124; NIcor=-0.209; NsEucl=0.850; SSD=2.204; NSW=0.843; rcor=5; rNcor=8; rlogoDP=9; rNIcor=9; rNsEucl=8; rSSD=5; rNSW=8; rank_mean=7.429; match_rank=9 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
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	9	10	4	4	10	7	10	7.714	10	; positions_6nt_m3 versus l(1)sc_da_SANGER_5_FBgn0000413; m=10/10; ncol2=7; w=7; offset=1; strand=D; shift=4; score= 7.7143; ----GCAGGTG---- ; cor=0.754; Ncor=0.528; logoDP=8.426; NIcor=0.513; NsEucl=0.849; SSD=2.229; NSW=0.841; rcor=9; rNcor=10; rlogoDP=4; rNIcor=4; rNsEucl=10; rSSD=7; rNSW=10; rank_mean=7.714; match_rank=10 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