One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_8nt_mkv6_m40/peak-motifs_oligos_8nt_mkv6_m40.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_8nt_mkv6_m40/peak-motifs_oligos_8nt_mkv6_m40_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m40_shift3 ; 4 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_8nt_mkv6_m40_shift3 (oligos_8nt_mkv6_m40oligos_8nt_mkv6_m40) |
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; oligos_8nt_mkv6_m40 (oligos_8nt_mkv6_m40oligos_8nt_mkv6_m40); m=0 (reference); ncol1=12; shift=3; ncol=15; ---mcCCCAACCCbv
; Alignment reference
a 0 0 0 678 280 26 19 35 1661 1831 41 23 13 232 624
c 0 0 0 526 833 1801 1793 1346 29 24 1815 1804 1809 544 496
g 0 0 0 372 459 36 64 106 143 1 9 54 52 522 537
t 0 0 0 313 317 26 13 402 56 33 24 8 15 591 232
|
| MA0039.4_shift3 (KLF4) |
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; oligos_8nt_mkv6_m40 versus MA0039.4 (KLF4); m=1/3; ncol2=12; w=12; offset=0; strand=D; shift=3; score=0.798446; ---ssCCCCACCChs
; cor=; Ncor=
a 0 0 0 12570.0 11487.0 2465.0 2105.0 7021.0 1173.0 45602.0 852.0 1617.0 1202.0 16264.0 9959.0
c 0 0 0 17520.0 14038.0 49209.0 47865.0 45405.0 52875.0 161.0 52366.0 51112.0 51045.0 18249.0 19217.0
g 0 0 0 14243.0 18473.0 1583.0 1214.0 1422.0 793.0 6598.0 1470.0 1870.0 1005.0 6292.0 14422.0
t 0 0 0 11484.0 11819.0 2560.0 4633.0 1969.0 976.0 3456.0 1129.0 1218.0 2565.0 15012.0 12219.0
|
| MA0599.1_shift4 (KLF5) |
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; oligos_8nt_mkv6_m40 versus MA0599.1 (KLF5); m=2/3; ncol2=10; w=10; offset=1; strand=D; shift=4; score=0.594288; ----gCCMCrCCCh-
; cor=; Ncor=
a 0 0 0 0 1429.0 0.0 0.0 3477.0 0.0 5051.0 0.0 0.0 0.0 3915.0 0
c 0 0 0 0 2023.0 11900.0 12008.0 9569.0 13611.0 0.0 13611.0 13611.0 13135.0 5595.0 0
g 0 0 0 0 7572.0 0.0 0.0 0.0 0.0 5182.0 0.0 0.0 0.0 0.0 0
t 0 0 0 0 2587.0 1711.0 1603.0 565.0 0.0 3378.0 0.0 0.0 476.0 4101.0 0
|
| MA1656.1_shift0 (ZNF449) |
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; oligos_8nt_mkv6_m40 versus MA1656.1 (ZNF449); m=3/3; ncol2=14; w=11; offset=-3; strand=D; shift=0; score=0.586411; cvaAGCCCAACcas-
; cor=; Ncor=
a 1809.0 2104.0 4135.0 6239.0 108.0 139.0 64.0 68.0 6851.0 6620.0 184.0 1143.0 2595.0 1670.0 0
c 2716.0 2320.0 1759.0 582.0 92.0 7088.0 7540.0 7479.0 300.0 96.0 7244.0 5029.0 1875.0 2195.0 0
g 1566.0 1921.0 1463.0 224.0 7368.0 322.0 28.0 54.0 182.0 829.0 167.0 473.0 1585.0 2237.0 0
t 1569.0 1315.0 303.0 615.0 92.0 111.0 28.0 59.0 327.0 115.0 65.0 1015.0 1605.0 1558.0 0
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