One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m30/peak-motifs_dyads_m30.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_Rep3_motifs50/results/discovered_motifs/dyads_m30/peak-motifs_dyads_m30_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m30_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m30_shift3 (dyads_m30dyads_m30)
; dyads_m30 (dyads_m30dyads_m30); m=0 (reference); ncol1=11; shift=3; ncol=17; ---ymCCCMGCCyr--- ; Alignment reference a 0 0 0 2 4 0 0 0 8 0 0 0 2 3 0 0 0 c 0 0 0 3 3 11 11 11 3 0 11 11 4 2 0 0 0 g 0 0 0 2 2 0 0 0 0 11 0 0 2 4 0 0 0 t 0 0 0 4 2 0 0 0 0 0 0 0 3 2 0 0 0

MA0039.4_shift2 (KLF4)
; dyads_m30 versus MA0039.4 (KLF4); m=1/4; ncol2=12; w=11; offset=-1; strand=D; shift=2; score=0.656938; --ssCCCCACCChs--- ; cor=; Ncor= a 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 0 0 0 c 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 0 0 0 g 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 0 0 0 t 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 0 0 0

MA1513.1_shift4 (KLF15)
; dyads_m30 versus MA1513.1 (KLF15); m=2/4; ncol2=11; w=10; offset=1; strand=D; shift=4; score=0.656888; ----scCCCGCCCcs-- ; cor=; Ncor= a 0 0 0 0 1184.0 937.0 40.0 93.0 0.0 0.0 11.0 55.0 12.0 1566.0 1067.0 0 0 c 0 0 0 0 2903.0 6506.0 11234.0 10940.0 11368.0 0.0 11345.0 10954.0 11254.0 6267.0 5013.0 0 0 g 0 0 0 0 5538.0 2117.0 86.0 333.0 1.0 11369.0 2.0 359.0 100.0 1934.0 3124.0 0 0 t 0 0 0 0 1744.0 1809.0 9.0 3.0 0.0 0.0 11.0 1.0 3.0 1602.0 2165.0 0 0

MA0599.1_shift4 (KLF5)
; dyads_m30 versus MA0599.1 (KLF5); m=3/4; ncol2=10; w=10; offset=1; strand=D; shift=4; score=0.646609; ----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 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 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 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 0 0

MA0516.2_shift0 (SP2)
; dyads_m30 versus MA0516.2 (SP2); m=4/4; ncol2=17; w=11; offset=-3; strand=D; shift=0; score=0.457029; mTAAGyCCCGCCCmCyy ; cor=; Ncor= a 256.0 53.0 613.0 753.0 54.0 34.0 14.0 16.0 4.0 82.0 0.0 5.0 23.0 402.0 22.0 109.0 150.0 c 308.0 171.0 76.0 84.0 127.0 456.0 774.0 786.0 788.0 52.0 795.0 793.0 774.0 390.0 679.0 221.0 203.0 g 123.0 57.0 0.0 33.0 791.0 8.0 1.0 13.0 22.0 780.0 0.0 26.0 0.0 22.0 1.0 0.0 88.0 t 106.0 608.0 180.0 67.0 43.0 327.0 0.0 8.0 12.0 45.0 18.0 7.0 27.0 17.0 101.0 503.0 352.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m30_shift3 (dyads_m30dyads_m30)				; dyads_m30 (dyads_m30dyads_m30); m=0 (reference); ncol1=11; shift=3; ncol=17; ---ymCCCMGCCyr--- ; Alignment reference a 0 0 0 2 4 0 0 0 8 0 0 0 2 3 0 0 0 c 0 0 0 3 3 11 11 11 3 0 11 11 4 2 0 0 0 g 0 0 0 2 2 0 0 0 0 11 0 0 2 4 0 0 0 t 0 0 0 4 2 0 0 0 0 0 0 0 3 2 0 0 0
MA0039.4_shift2 (KLF4)				; dyads_m30 versus MA0039.4 (KLF4); m=1/4; ncol2=12; w=11; offset=-1; strand=D; shift=2; score=0.656938; --ssCCCCACCChs--- ; cor=; Ncor= a 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 0 0 0 c 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 0 0 0 g 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 0 0 0 t 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 0 0 0
MA1513.1_shift4 (KLF15)				; dyads_m30 versus MA1513.1 (KLF15); m=2/4; ncol2=11; w=10; offset=1; strand=D; shift=4; score=0.656888; ----scCCCGCCCcs-- ; cor=; Ncor= a 0 0 0 0 1184.0 937.0 40.0 93.0 0.0 0.0 11.0 55.0 12.0 1566.0 1067.0 0 0 c 0 0 0 0 2903.0 6506.0 11234.0 10940.0 11368.0 0.0 11345.0 10954.0 11254.0 6267.0 5013.0 0 0 g 0 0 0 0 5538.0 2117.0 86.0 333.0 1.0 11369.0 2.0 359.0 100.0 1934.0 3124.0 0 0 t 0 0 0 0 1744.0 1809.0 9.0 3.0 0.0 0.0 11.0 1.0 3.0 1602.0 2165.0 0 0
MA0599.1_shift4 (KLF5)				; dyads_m30 versus MA0599.1 (KLF5); m=3/4; ncol2=10; w=10; offset=1; strand=D; shift=4; score=0.646609; ----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 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 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 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 0 0
MA0516.2_shift0 (SP2)				; dyads_m30 versus MA0516.2 (SP2); m=4/4; ncol2=17; w=11; offset=-3; strand=D; shift=0; score=0.457029; mTAAGyCCCGCCCmCyy ; cor=; Ncor= a 256.0 53.0 613.0 753.0 54.0 34.0 14.0 16.0 4.0 82.0 0.0 5.0 23.0 402.0 22.0 109.0 150.0 c 308.0 171.0 76.0 84.0 127.0 456.0 774.0 786.0 788.0 52.0 795.0 793.0 774.0 390.0 679.0 221.0 203.0 g 123.0 57.0 0.0 33.0 791.0 8.0 1.0 13.0 22.0 780.0 0.0 26.0 0.0 22.0 1.0 0.0 88.0 t 106.0 608.0 180.0 67.0 43.0 327.0 0.0 8.0 12.0 45.0 18.0 7.0 27.0 17.0 101.0 503.0 352.0