One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/dyads_test_vs_ctrl_m1/peak-motifs_dyads_test_vs_ctrl_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/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/dyads_test_vs_ctrl_m1/peak-motifs_dyads_test_vs_ctrl_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift0 ; 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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| dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1) |
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; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; ssCtGCCCtssGGCCaggGCCcsg
; Alignment reference
a 40 26 6 29 1 5 7 3 16 23 50 7 5 11 11 82 13 19 8 14 8 13 28 34
c 76 82 141 38 18 173 169 191 43 70 54 26 28 166 167 50 49 32 26 153 145 139 68 50
g 57 64 46 36 172 20 22 13 28 110 94 169 163 18 16 51 137 138 157 26 35 33 77 91
t 34 35 14 104 16 9 9 0 120 4 9 5 11 12 13 24 8 18 16 14 19 22 34 32
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| MA0003.2_rc_shift3 (TFAP2A_rc) |
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0.818 |
0.511 |
0.828 |
-0.130 |
0.939 |
1.701 |
0.943 |
1 |
1 |
3 |
3 |
1 |
1 |
1 |
1.571 |
1 |
; dyads_test_vs_ctrl_m1 versus MA0003.2_rc (TFAP2A_rc); m=1/4; ncol2=15; w=15; offset=3; strand=R; shift=3; score= 1.5714; ---tGsCCTsrGGCwrtk------
; cor=0.818; Ncor=0.511; logoDP=0.828; NIcor=-0.130; NsEucl=0.939; SSD=1.701; NSW=0.943; rcor=1; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=1
a 0 0 0 1094 510 84 0 0 204 308 3215 336 0 131 2077 1981 1105 1230 0 0 0 0 0 0
c 0 0 0 168 465 3455 5098 4638 920 1715 85 0 0 3712 985 884 792 851 0 0 0 0 0 0
g 0 0 0 690 3672 1443 0 0 236 2729 1736 4762 5098 1199 519 1506 1060 1630 0 0 0 0 0 0
t 0 0 0 3146 451 116 0 460 3738 346 62 0 0 56 1517 727 2141 1387 0 0 0 0 0 0
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| MA0146.1_rc_shift9 (Zfx_rc) |
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0.770 |
0.449 |
2.691 |
0.383 |
0.928 |
2.012 |
0.928 |
3 |
3 |
2 |
1 |
3 |
3 |
3 |
2.571 |
2 |
; dyads_test_vs_ctrl_m1 versus MA0146.1_rc (Zfx_rc); m=2/4; ncol2=14; w=14; offset=9; strand=R; shift=9; score= 2.5714; ---------sAGGCCbvGscsss-
; cor=0.770; Ncor=0.449; logoDP=2.691; NIcor=0.383; NsEucl=0.928; SSD=2.012; NSW=0.928; rcor=3; rNcor=3; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.571; match_rank=2
a 0 0 0 0 0 0 0 0 0 56 479 1 0 1 1 15 144 111 30 60 37 75 70 0
c 0 0 0 0 0 0 0 0 0 219 0 0 0 477 469 121 182 2 144 298 199 172 179 0
g 0 0 0 0 0 0 0 0 0 122 2 480 480 3 2 154 125 362 297 49 151 170 177 0
t 0 0 0 0 0 0 0 0 0 84 0 0 1 0 9 191 30 6 10 72 91 60 50 0
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| MA0524.1_rc_shift3 (TFAP2C_rc) |
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0.809 |
0.506 |
0.734 |
-0.143 |
0.938 |
1.755 |
0.941 |
2 |
2 |
4 |
4 |
2 |
2 |
2 |
2.571 |
3 |
; dyads_test_vs_ctrl_m1 versus MA0524.1_rc (TFAP2C_rc); m=3/4; ncol2=15; w=15; offset=3; strand=R; shift=3; score= 2.5714; ---tgsCCTGrGGshrkd------
; cor=0.809; Ncor=0.506; logoDP=0.734; NIcor=-0.143; NsEucl=0.938; SSD=1.755; NSW=0.941; rcor=2; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.571; match_rank=3
a 0 0 0 3726 3060 11 0 0 789 786 7872 3609 0 932 5401 8290 3909 4750 0 0 0 0 0 0
c 0 0 0 2536 1788 10222 18426 18235 1195 1768 1237 0 0 11033 6098 2643 3347 2123 0 0 0 0 0 0
g 0 0 0 3259 9235 7908 0 0 0 14790 9317 14817 18426 6040 2009 4943 4693 6752 0 0 0 0 0 0
t 0 0 0 8905 4343 285 0 191 16442 1082 0 0 0 421 4918 2550 6477 4801 0 0 0 0 0 0
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| MA0146.2_rc_shift9 (Zfx_rc) |
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0.769 |
0.449 |
2.697 |
0.383 |
0.928 |
2.021 |
0.928 |
4 |
4 |
1 |
2 |
4 |
4 |
4 |
3.286 |
4 |
; dyads_test_vs_ctrl_m1 versus MA0146.2_rc (Zfx_rc); m=4/4; ncol2=14; w=14; offset=9; strand=R; shift=9; score= 3.2857; ---------sAGGCCbvGscsss-
; cor=0.769; Ncor=0.449; logoDP=2.697; NIcor=0.383; NsEucl=0.928; SSD=2.021; NSW=0.928; rcor=4; rNcor=4; rlogoDP=1; rNIcor=2; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=3.286; match_rank=4
a 0 0 0 0 0 0 0 0 0 56 480 1 0 1 1 15 144 112 30 61 37 75 70 0
c 0 0 0 0 0 0 0 0 0 218 0 0 0 477 470 122 183 2 144 297 199 173 179 0
g 0 0 0 0 0 0 0 0 0 122 1 480 481 3 2 153 124 361 297 49 151 170 178 0
t 0 0 0 0 0 0 0 0 0 84 0 0 0 0 8 191 30 6 10 72 91 59 50 0
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