One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift3 ; 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_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3) |
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; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=3; ncol=15; ---wtATTTTTAww-
; Alignment reference
a 0 0 0 185 133 557 0 6 5 7 1 557 196 213 0
c 0 0 0 88 130 0 0 0 1 1 0 0 95 90 0
g 0 0 0 103 105 0 0 2 1 1 0 0 81 94 0
t 0 0 0 181 189 0 557 549 550 548 556 0 185 160 0
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| MA0465.1_rc_shift7 (CDX2_rc) |
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0.864 |
0.403 |
0.857 |
-0.052 |
0.895 |
1.083 |
0.923 |
1 |
4 |
3 |
3 |
3 |
1 |
1 |
2.286 |
1 |
; oligos_7nt_mkv5_m3 versus MA0465.1_rc (CDX2_rc); m=1/4; ncol2=11; w=7; offset=4; strand=R; shift=7; score= 2.2857; -------tTTTATkr
; cor=0.864; Ncor=0.403; logoDP=0.857; NIcor=-0.052; NsEucl=0.895; SSD=1.083; NSW=0.923; rcor=1; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=1; rank_mean=2.286; match_rank=1
a 0 0 0 0 0 0 0 121 0 0 0 1597 0 68 549
c 0 0 0 0 0 0 0 313 0 0 0 0 0 0 0
g 0 0 0 0 0 0 0 150 0 0 0 0 0 832 1048
t 0 0 0 0 0 0 0 1013 1597 1597 1597 0 1597 697 0
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| MA0497.1_rc_shift1 (MEF2C_rc) |
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0.803 |
0.589 |
0.422 |
-0.185 |
0.909 |
2.017 |
0.908 |
2 |
1 |
4 |
4 |
1 |
3 |
2 |
2.429 |
2 |
; oligos_7nt_mkv5_m3 versus MA0497.1_rc (MEF2C_rc); m=2/4; ncol2=15; w=11; offset=-2; strand=R; shift=1; score= 2.4286; -wkCTATTTTTrgmh
; cor=0.803; Ncor=0.589; logoDP=0.422; NIcor=-0.185; NsEucl=0.909; SSD=2.017; NSW=0.908; rcor=2; rNcor=1; rlogoDP=4; rNIcor=4; rNsEucl=1; rSSD=3; rNSW=2; rank_mean=2.429; match_rank=2
a 0 624 250 29 0 2091 70 76 15 230 263 1224 337 760 752
c 0 126 148 1671 32 0 4 2 87 241 74 0 78 822 573
g 0 450 836 120 0 62 0 0 0 32 256 985 1412 196 151
t 0 1009 975 389 2177 56 2135 2131 2107 1706 1616 0 382 431 733
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| MA0052.2_rc_shift0 (MEF2A_rc) |
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0.792 |
0.581 |
2.732 |
0.021 |
0.905 |
2.206 |
0.900 |
3 |
2 |
2 |
2 |
2 |
4 |
3 |
2.571 |
3 |
; oligos_7nt_mkv5_m3 versus MA0052.2_rc (MEF2A_rc); m=3/4; ncol2=15; w=11; offset=-3; strand=R; shift=0; score= 2.5714; rdkCTATTTTTrGmh
; cor=0.792; Ncor=0.581; logoDP=2.732; NIcor=0.021; NsEucl=0.905; SSD=2.206; NSW=0.900; rcor=3; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=3; rank_mean=2.571; match_rank=3
a 476 424 142 33 1 1467 83 116 51 346 119 1000 146 530 465
c 203 110 112 1160 0 0 0 0 39 119 14 0 32 625 379
g 449 409 632 49 0 0 0 5 0 0 68 473 1179 149 148
t 345 530 587 231 1472 6 1390 1352 1383 1008 1272 0 116 169 481
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| MA0151.1_rc_shift8 (ARID3A_rc) |
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0.754 |
0.411 |
4.276 |
0.275 |
0.849 |
1.647 |
0.863 |
4 |
3 |
1 |
1 |
4 |
2 |
4 |
2.714 |
4 |
; oligos_7nt_mkv5_m3 versus MA0151.1_rc (ARID3A_rc); m=4/4; ncol2=6; w=6; offset=5; strand=R; shift=8; score= 2.7143; --------TTTrAT-
; cor=0.754; Ncor=0.411; logoDP=4.276; NIcor=0.275; NsEucl=0.849; SSD=1.647; NSW=0.863; rcor=4; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=2.714; match_rank=4
a 0 0 0 0 0 0 0 0 6 0 0 17 27 0 0
c 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
g 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0
t 0 0 0 0 0 0 0 0 20 27 27 1 0 27 0
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