One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_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/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m1/peak-motifs_oligos_7nt_test_vs_ctrl_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift2 ; 4 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_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1) |
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; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwcTTTATCTGATAww
; Alignment reference
a 0 0 133 133 102 42 41 28 405 14 20 37 33 381 26 326 150 146
c 0 0 69 94 230 28 29 16 14 15 379 6 25 29 16 40 75 105
g 0 0 89 72 44 31 29 14 18 16 19 2 357 16 18 35 69 78
t 0 0 161 153 76 351 353 394 15 407 34 407 37 26 392 51 158 123
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| MA0037.2_rc_shift4 (GATA3_rc) |
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0.877 |
0.438 |
2.500 |
0.052 |
0.904 |
1.178 |
0.926 |
1 |
3 |
2 |
2 |
3 |
1 |
1 |
1.857 |
1 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0037.2_rc (GATA3_rc); m=1/3; ncol2=8; w=8; offset=2; strand=R; shift=4; score= 1.8571; ----tYTTATCT------
; cor=0.877; Ncor=0.438; logoDP=2.500; NIcor=0.052; NsEucl=0.904; SSD=1.178; NSW=0.926; rcor=1; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=1; rNSW=1; rank_mean=1.857; match_rank=1
a 0 0 0 0 0 0 0 0 4628 0 0 0 0 0 0 0 0 0
c 0 0 0 0 1120 3338 0 0 0 0 4628 0 0 0 0 0 0 0
g 0 0 0 0 712 0 0 0 0 0 0 0 0 0 0 0 0 0
t 0 0 0 0 2796 1290 4628 4628 0 4628 0 4628 0 0 0 0 0 0
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| MA0035.2_rc_shift3 (Gata1_rc) |
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0.797 |
0.548 |
0.468 |
-0.135 |
0.916 |
1.718 |
0.922 |
2 |
1 |
3 |
3 |
1 |
2 |
2 |
2.000 |
2 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0035.2_rc (Gata1_rc); m=2/3; ncol2=11; w=11; offset=1; strand=R; shift=3; score= 2; ---yycTTATCWsy----
; cor=0.797; Ncor=0.548; logoDP=0.468; NIcor=-0.135; NsEucl=0.916; SSD=1.718; NSW=0.922; rcor=2; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 0 585 311 224 63 107 3835 0 0 1177 424 775 0 0 0 0
c 0 0 0 1099 1360 2296 383 6 109 0 4000 10 1235 1242 0 0 0 0
g 0 0 0 829 897 681 4 0 29 0 0 31 1633 560 0 0 0 0
t 0 0 0 1487 1432 799 3550 3887 27 4000 0 2782 708 1423 0 0 0 0
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| MA0036.2_shift0 (GATA2) |
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0.765 |
0.510 |
5.523 |
0.505 |
0.913 |
2.162 |
0.910 |
3 |
2 |
1 |
1 |
2 |
3 |
3 |
2.143 |
3 |
; oligos_7nt_test_vs_ctrl_m1 versus MA0036.2 (GATA2); m=3/3; ncol2=14; w=12; offset=-2; strand=D; shift=0; score= 2.1429; wrrttCTTATCWsh----
; cor=0.765; Ncor=0.510; logoDP=5.523; NIcor=0.505; NsEucl=0.913; SSD=2.162; NSW=0.910; rcor=3; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.143; match_rank=3
a 1569 1125 1555 1051 32 9 0 51 4380 0 0 1225 104 1256 0 0 0 0
c 567 768 729 525 1057 3015 192 0 0 0 4380 0 1765 1185 0 0 0 0
g 754 1709 1220 427 765 914 0 0 0 0 0 0 1967 224 0 0 0 0
t 1490 778 876 2377 2526 442 4188 4329 0 4380 0 3155 544 1715 0 0 0 0
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