One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.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/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_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 |
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| oligos_7nt_mkv5_m1_shift3 (oligos_7nt_mkv5_m1) |
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; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=3; ncol=15; ---dtATTTTTAdww
; Alignment reference
a 0 0 0 325 297 1277 0 0 0 0 0 1277 451 425 527
c 0 0 0 181 246 0 0 0 0 0 0 0 106 113 141
g 0 0 0 350 120 0 0 0 0 0 0 0 339 158 173
t 0 0 0 421 614 0 1277 1277 1277 1277 1277 0 381 581 436
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| MA0497.1_rc_shift1 (MEF2C_rc) |
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0.828 |
0.663 |
0.437 |
-0.188 |
0.920 |
1.822 |
0.924 |
1 |
1 |
4 |
4 |
1 |
2 |
1 |
2.000 |
1 |
; oligos_7nt_mkv5_m1 versus MA0497.1_rc (MEF2C_rc); m=1/4; ncol2=15; w=12; offset=-2; strand=R; shift=1; score= 2; -wkCTATTTTTrgmh
; cor=0.828; Ncor=0.663; logoDP=0.437; NIcor=-0.188; NsEucl=0.920; SSD=1.822; NSW=0.924; rcor=1; rNcor=1; rlogoDP=4; rNIcor=4; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=2.000; match_rank=1
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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0.816 |
0.653 |
2.905 |
0.033 |
0.916 |
2.012 |
0.916 |
3 |
2 |
2 |
2 |
2 |
3 |
2 |
2.286 |
2 |
; oligos_7nt_mkv5_m1 versus MA0052.2_rc (MEF2A_rc); m=2/4; ncol2=15; w=12; offset=-3; strand=R; shift=0; score= 2.2857; rdkCTATTTTTrGmh
; cor=0.816; Ncor=0.653; logoDP=2.905; NIcor=0.033; NsEucl=0.916; SSD=2.012; NSW=0.916; rcor=3; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.286; match_rank=2
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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| MA0465.1_rc_shift7 (CDX2_rc) |
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0.819 |
0.437 |
1.051 |
-0.020 |
0.890 |
1.536 |
0.904 |
2 |
4 |
3 |
3 |
3 |
1 |
3 |
2.714 |
3 |
; oligos_7nt_mkv5_m1 versus MA0465.1_rc (CDX2_rc); m=3/4; ncol2=11; w=8; offset=4; strand=R; shift=7; score= 2.7143; -------tTTTATkr
; cor=0.819; Ncor=0.437; logoDP=1.051; NIcor=-0.020; NsEucl=0.890; SSD=1.536; NSW=0.904; rcor=2; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=3; rank_mean=2.714; match_rank=3
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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| MA0052.1_shift3 (MEF2A) |
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0.782 |
0.652 |
9.521 |
0.612 |
0.889 |
2.451 |
0.877 |
4 |
3 |
1 |
1 |
4 |
4 |
4 |
3.000 |
4 |
; oligos_7nt_mkv5_m1 versus MA0052.1 (MEF2A); m=4/4; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 3; ---CTATTTwTAG--
; cor=0.782; Ncor=0.652; logoDP=9.521; NIcor=0.612; NsEucl=0.889; SSD=2.451; NSW=0.877; rcor=4; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=3.000; match_rank=4
a 0 0 0 1 0 57 2 9 6 37 2 56 6 0 0
c 0 0 0 50 0 1 1 0 0 0 0 0 0 0 0
g 0 0 0 0 0 0 0 0 0 0 0 2 50 0 0
t 0 0 0 7 58 0 55 49 52 21 56 0 2 0 0
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