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/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_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/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_FlyFactorSurvey
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 |
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| oligos_6nt_mkv4_m3_shift2 (oligos_6nt_mkv4_m3) |
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; 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
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| Caup_SOLEXA_FBgn0015919_shift2 (Caup_SOLEXA_FBgn0015919) |
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0.839 |
0.503 |
5.933 |
0.497 |
0.886 |
0.929 |
0.923 |
1 |
1 |
3 |
1 |
1 |
1 |
1 |
1.286 |
1 |
; oligos_6nt_mkv4_m3 versus Caup_SOLEXA_FBgn0015919; m=1/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 1.2857; --wtwACA----
; cor=0.839; Ncor=0.503; logoDP=5.933; NIcor=0.497; NsEucl=0.886; SSD=0.929; NSW=0.923; rcor=1; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
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
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| Mirr_SOLEXA_FBgn0014343_shift2 (Mirr_SOLEXA_FBgn0014343) |
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0.828 |
0.497 |
5.948 |
0.491 |
0.883 |
0.991 |
0.917 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; oligos_6nt_mkv4_m3 versus Mirr_SOLEXA_FBgn0014343; m=2/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 2; --wwwACA----
; cor=0.828; Ncor=0.497; logoDP=5.948; NIcor=0.491; NsEucl=0.883; SSD=0.991; NSW=0.917; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
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
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| Ara_SOLEXA_FBgn0015904_shift2 (Ara_SOLEXA_FBgn0015904) |
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0.790 |
0.474 |
5.958 |
0.466 |
0.869 |
1.234 |
0.897 |
4 |
3 |
1 |
3 |
4 |
4 |
4 |
3.286 |
3 |
; oligos_6nt_mkv4_m3 versus Ara_SOLEXA_FBgn0015904; m=3/4; ncol2=6; w=6; offset=0; strand=D; shift=2; score= 3.2857; --awwACA----
; cor=0.790; Ncor=0.474; logoDP=5.958; NIcor=0.466; NsEucl=0.869; SSD=1.234; NSW=0.897; rcor=4; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=3.286; match_rank=3
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
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| CG11617_SOLEXA_FBgn0031232_shift0 (CG11617_SOLEXA_FBgn0031232) |
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0.805 |
0.402 |
5.767 |
0.396 |
0.874 |
1.140 |
0.905 |
3 |
4 |
4 |
4 |
3 |
3 |
3 |
3.429 |
4 |
; oligos_6nt_mkv4_m3 versus CG11617_SOLEXA_FBgn0031232; m=4/4; ncol2=8; w=6; offset=-2; strand=D; shift=0; score= 3.4286; wtwTwACA----
; cor=0.805; Ncor=0.402; logoDP=5.767; NIcor=0.396; NsEucl=0.874; SSD=1.140; NSW=0.905; rcor=3; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.429; match_rank=4
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
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