One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m44/peak-motifs_oligos_7nt_mkv4_m44.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_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m44/peak-motifs_oligos_7nt_mkv4_m44_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m44_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m44_shift2 (oligos_7nt_mkv4_m44oligos_7nt_mkv4_m44)
; oligos_7nt_mkv4_m44 (oligos_7nt_mkv4_m44oligos_7nt_mkv4_m44); m=0 (reference); ncol1=12; shift=2; ncol=14; --vaAACCACArvc ; Alignment reference a 0 0 89 126 319 306 9 11 312 7 321 182 86 79 c 0 0 100 80 1 12 317 314 8 314 5 43 86 108 g 0 0 84 58 8 6 3 1 8 6 2 88 91 81 t 0 0 60 69 5 9 4 7 5 6 5 20 70 65

MA0684.2_shift2 (RUNX3)
; oligos_7nt_mkv4_m44 versus MA0684.2 (RUNX3); m=1/5; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.875527; --awAACCTCAawh ; cor=; Ncor= a 0 0 7768.0 9558.0 19136.0 26243.0 427.0 495.0 6357.0 611.0 26121.0 16137.0 8778.0 6879.0 c 0 0 6083.0 5007.0 2662.0 315.0 26293.0 26208.0 419.0 26015.0 414.0 3077.0 5994.0 6900.0 g 0 0 6685.0 3547.0 3500.0 431.0 198.0 385.0 1911.0 390.0 338.0 4696.0 5642.0 6372.0 t 0 0 6841.0 9265.0 2079.0 388.0 459.0 289.0 18690.0 361.0 504.0 3467.0 6963.0 7226.0

MA0002.2_rc_shift3 (RUNX1_rc)
; oligos_7nt_mkv4_m44 versus MA0002.2_rc (RUNX1_rc); m=2/5; ncol2=11; w=11; offset=1; strand=R; shift=3; score=0.871324; ---waaCCACAram ; cor=; Ncor= a 0 0 0 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 c 0 0 0 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 g 0 0 0 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 t 0 0 0 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0

MA0511.2_shift3 (RUNX2)
; oligos_7nt_mkv4_m44 versus MA0511.2 (RUNX2); m=3/5; ncol2=9; w=9; offset=1; strand=D; shift=3; score=0.662975; ---wAACCRCAa-- ; cor=; Ncor= a 0 0 0 3872.0 6621.0 6621.0 0.0 0.0 1914.0 0.0 6621.0 4202.0 0 0 c 0 0 0 1092.0 556.0 325.0 6621.0 6621.0 36.0 6621.0 476.0 677.0 0 0 g 0 0 0 326.0 1215.0 0.0 0.0 0.0 4707.0 0.0 458.0 1134.0 0 0 t 0 0 0 2748.0 582.0 0.0 0.0 0.0 120.0 0.0 191.0 607.0 0 0

MA0479.1_shift0 (FOXH1)
; oligos_7nt_mkv4_m44 versus MA0479.1 (FOXH1); m=4/5; ncol2=11; w=9; offset=-2; strand=D; shift=0; score=0.470522; ybsAATMCACA--- ; cor=; Ncor= a 939.0 1578.0 973.0 8211.0 7547.0 0.0 2374.0 1414.0 8211.0 0.0 7138.0 0 0 0 c 2840.0 2333.0 3261.0 0.0 0.0 0.0 5773.0 6797.0 0.0 8211.0 0.0 0 0 0 g 1490.0 2137.0 3156.0 0.0 229.0 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 t 2942.0 2163.0 821.0 0.0 435.0 8211.0 64.0 0.0 0.0 0.0 1073.0 0 0 0

MA0130.1_shift4 (ZNF354C)
; oligos_7nt_mkv4_m44 versus MA0130.1 (ZNF354C); m=5/5; ncol2=6; w=6; offset=2; strand=D; shift=4; score=0.400493; ----mTCCAC---- ; cor=; Ncor= a 0 0 0 0 7.0 3.0 0.0 0.0 16.0 0.0 0 0 0 0 c 0 0 0 0 6.0 2.0 16.0 16.0 0.0 15.0 0 0 0 0 g 0 0 0 0 3.0 0.0 0.0 0.0 0.0 1.0 0 0 0 0 t 0 0 0 0 0.0 11.0 0.0 0.0 0.0 0.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m44_shift2 (oligos_7nt_mkv4_m44oligos_7nt_mkv4_m44)				; oligos_7nt_mkv4_m44 (oligos_7nt_mkv4_m44oligos_7nt_mkv4_m44); m=0 (reference); ncol1=12; shift=2; ncol=14; --vaAACCACArvc ; Alignment reference a 0 0 89 126 319 306 9 11 312 7 321 182 86 79 c 0 0 100 80 1 12 317 314 8 314 5 43 86 108 g 0 0 84 58 8 6 3 1 8 6 2 88 91 81 t 0 0 60 69 5 9 4 7 5 6 5 20 70 65
MA0684.2_shift2 (RUNX3)				; oligos_7nt_mkv4_m44 versus MA0684.2 (RUNX3); m=1/5; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.875527; --awAACCTCAawh ; cor=; Ncor= a 0 0 7768.0 9558.0 19136.0 26243.0 427.0 495.0 6357.0 611.0 26121.0 16137.0 8778.0 6879.0 c 0 0 6083.0 5007.0 2662.0 315.0 26293.0 26208.0 419.0 26015.0 414.0 3077.0 5994.0 6900.0 g 0 0 6685.0 3547.0 3500.0 431.0 198.0 385.0 1911.0 390.0 338.0 4696.0 5642.0 6372.0 t 0 0 6841.0 9265.0 2079.0 388.0 459.0 289.0 18690.0 361.0 504.0 3467.0 6963.0 7226.0
MA0002.2_rc_shift3 (RUNX1_rc)				; oligos_7nt_mkv4_m44 versus MA0002.2_rc (RUNX1_rc); m=2/5; ncol2=11; w=11; offset=1; strand=R; shift=3; score=0.871324; ---waaCCACAram ; cor=; Ncor= a 0 0 0 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 c 0 0 0 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 g 0 0 0 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 t 0 0 0 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0
MA0511.2_shift3 (RUNX2)				; oligos_7nt_mkv4_m44 versus MA0511.2 (RUNX2); m=3/5; ncol2=9; w=9; offset=1; strand=D; shift=3; score=0.662975; ---wAACCRCAa-- ; cor=; Ncor= a 0 0 0 3872.0 6621.0 6621.0 0.0 0.0 1914.0 0.0 6621.0 4202.0 0 0 c 0 0 0 1092.0 556.0 325.0 6621.0 6621.0 36.0 6621.0 476.0 677.0 0 0 g 0 0 0 326.0 1215.0 0.0 0.0 0.0 4707.0 0.0 458.0 1134.0 0 0 t 0 0 0 2748.0 582.0 0.0 0.0 0.0 120.0 0.0 191.0 607.0 0 0
MA0479.1_shift0 (FOXH1)				; oligos_7nt_mkv4_m44 versus MA0479.1 (FOXH1); m=4/5; ncol2=11; w=9; offset=-2; strand=D; shift=0; score=0.470522; ybsAATMCACA--- ; cor=; Ncor= a 939.0 1578.0 973.0 8211.0 7547.0 0.0 2374.0 1414.0 8211.0 0.0 7138.0 0 0 0 c 2840.0 2333.0 3261.0 0.0 0.0 0.0 5773.0 6797.0 0.0 8211.0 0.0 0 0 0 g 1490.0 2137.0 3156.0 0.0 229.0 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 t 2942.0 2163.0 821.0 0.0 435.0 8211.0 64.0 0.0 0.0 0.0 1073.0 0 0 0
MA0130.1_shift4 (ZNF354C)				; oligos_7nt_mkv4_m44 versus MA0130.1 (ZNF354C); m=5/5; ncol2=6; w=6; offset=2; strand=D; shift=4; score=0.400493; ----mTCCAC---- ; cor=; Ncor= a 0 0 0 0 7.0 3.0 0.0 0.0 16.0 0.0 0 0 0 0 c 0 0 0 0 6.0 2.0 16.0 16.0 0.0 15.0 0 0 0 0 g 0 0 0 0 3.0 0.0 0.0 0.0 0.0 1.0 0 0 0 0 t 0 0 0 0 0.0 11.0 0.0 0.0 0.0 0.0 0 0 0 0