One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m42/peak-motifs_dyads_m42.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/dyads_m42/peak-motifs_dyads_m42_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m42_shift4 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m42_shift4 (dyads_m42dyads_m42)
; dyads_m42 (dyads_m42dyads_m42); m=0 (reference); ncol1=10; shift=4; ncol=16; ----caCACACAsa-- ; Alignment reference a 0 0 0 0 164 835 0 1512 0 1512 0 1512 120 813 0 0 c 0 0 0 0 905 304 1512 0 1512 0 1512 0 872 334 0 0 g 0 0 0 0 249 215 0 0 0 0 0 0 390 205 0 0 t 0 0 0 0 194 158 0 0 0 0 0 0 130 160 0 0

MA1523.1_shift3 (MSANTD3)
; dyads_m42 versus MA1523.1 (MSANTD3); m=1/5; ncol2=10; w=9; offset=-1; strand=D; shift=3; score=0.586018; ---stmCACTCAm--- ; cor=; Ncor= a 0 0 0 98.0 111.0 332.0 64.0 980.0 31.0 37.0 47.0 775.0 271.0 0 0 0 c 0 0 0 269.0 211.0 272.0 723.0 0.0 896.0 7.0 862.0 140.0 568.0 0 0 0 g 0 0 0 515.0 220.0 249.0 31.0 2.0 27.0 0.0 29.0 24.0 63.0 0 0 0 t 0 0 0 117.0 456.0 145.0 180.0 16.0 45.0 954.0 60.0 59.0 96.0 0 0 0

MA1155.1_shift4 (ZSCAN4)
; dyads_m42 versus MA1155.1 (ZSCAN4); m=2/5; ncol2=15; w=10; offset=0; strand=D; shift=4; score=0.49631; ----tGCACACmCTGa ; cor=; Ncor= a 0 0 0 0 257.0 290.0 0.0 1292.0 0.0 1281.0 3.0 772.0 7.0 8.0 3.0 1118.0 c 0 0 0 0 383.0 2.0 1676.0 0.0 1665.0 0.0 1702.0 374.0 1684.0 11.0 50.0 107.0 g 0 0 0 0 112.0 1737.0 1.0 0.0 0.0 2.0 0.0 320.0 0.0 75.0 1873.0 230.0 t 0 0 0 0 1373.0 0.0 0.0 2.0 0.0 2.0 73.0 8.0 2.0 1699.0 218.0 362.0

MA1107.2_shift0 (KLF9)
; dyads_m42 versus MA1107.2 (KLF9); m=3/5; ncol2=16; w=10; offset=-4; strand=D; shift=0; score=0.48148; crgCCACACCCAChyc ; cor=; Ncor= a 5359.0 8015.0 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 18837.0 792.0 6948.0 4110.0 5875.0 c 10412.0 5108.0 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 4339.0 20644.0 8797.0 10520.0 9519.0 g 5200.0 7779.0 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 852.0 1778.0 3289.0 4423.0 5681.0 t 4608.0 4677.0 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0 1551.0 2365.0 6545.0 6526.0 4504.0

MA0493.1_shift1 (Klf1)
; dyads_m42 versus MA0493.1 (Klf1); m=4/5; ncol2=11; w=8; offset=-3; strand=D; shift=1; score=0.437298; -rrCCACACCCw---- ; cor=; Ncor= a 0 150.0 167.0 67.0 13.0 404.0 0.0 400.0 0.0 0.0 0.0 280.0 0 0 0 0 c 0 76.0 40.0 396.0 461.0 118.0 526.0 0.0 526.0 526.0 508.0 35.0 0 0 0 0 g 0 202.0 305.0 32.0 0.0 0.0 0.0 97.0 0.0 0.0 0.0 0.0 0 0 0 0 t 0 98.0 14.0 31.0 52.0 4.0 0.0 29.0 0.0 0.0 18.0 211.0 0 0 0 0

MA0006.1_rc_shift6 (Ahr::Arnt_rc)
; dyads_m42 versus MA0006.1_rc (Ahr::Arnt_rc); m=5/5; ncol2=6; w=6; offset=2; strand=R; shift=6; score=0.43454; ------CACGCr---- ; cor=; Ncor= a 0 0 0 0 0 0 0.0 24.0 1.0 1.0 1.0 11.0 0 0 0 0 c 0 0 0 0 0 0 24.0 0.0 23.0 0.0 23.0 2.0 0 0 0 0 g 0 0 0 0 0 0 0.0 0.0 0.0 23.0 0.0 8.0 0 0 0 0 t 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 3.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m42_shift4 (dyads_m42dyads_m42)				; dyads_m42 (dyads_m42dyads_m42); m=0 (reference); ncol1=10; shift=4; ncol=16; ----caCACACAsa-- ; Alignment reference a 0 0 0 0 164 835 0 1512 0 1512 0 1512 120 813 0 0 c 0 0 0 0 905 304 1512 0 1512 0 1512 0 872 334 0 0 g 0 0 0 0 249 215 0 0 0 0 0 0 390 205 0 0 t 0 0 0 0 194 158 0 0 0 0 0 0 130 160 0 0
MA1523.1_shift3 (MSANTD3)				; dyads_m42 versus MA1523.1 (MSANTD3); m=1/5; ncol2=10; w=9; offset=-1; strand=D; shift=3; score=0.586018; ---stmCACTCAm--- ; cor=; Ncor= a 0 0 0 98.0 111.0 332.0 64.0 980.0 31.0 37.0 47.0 775.0 271.0 0 0 0 c 0 0 0 269.0 211.0 272.0 723.0 0.0 896.0 7.0 862.0 140.0 568.0 0 0 0 g 0 0 0 515.0 220.0 249.0 31.0 2.0 27.0 0.0 29.0 24.0 63.0 0 0 0 t 0 0 0 117.0 456.0 145.0 180.0 16.0 45.0 954.0 60.0 59.0 96.0 0 0 0
MA1155.1_shift4 (ZSCAN4)				; dyads_m42 versus MA1155.1 (ZSCAN4); m=2/5; ncol2=15; w=10; offset=0; strand=D; shift=4; score=0.49631; ----tGCACACmCTGa ; cor=; Ncor= a 0 0 0 0 257.0 290.0 0.0 1292.0 0.0 1281.0 3.0 772.0 7.0 8.0 3.0 1118.0 c 0 0 0 0 383.0 2.0 1676.0 0.0 1665.0 0.0 1702.0 374.0 1684.0 11.0 50.0 107.0 g 0 0 0 0 112.0 1737.0 1.0 0.0 0.0 2.0 0.0 320.0 0.0 75.0 1873.0 230.0 t 0 0 0 0 1373.0 0.0 0.0 2.0 0.0 2.0 73.0 8.0 2.0 1699.0 218.0 362.0
MA1107.2_shift0 (KLF9)				; dyads_m42 versus MA1107.2 (KLF9); m=3/5; ncol2=16; w=10; offset=-4; strand=D; shift=0; score=0.48148; crgCCACACCCAChyc ; cor=; Ncor= a 5359.0 8015.0 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 18837.0 792.0 6948.0 4110.0 5875.0 c 10412.0 5108.0 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 4339.0 20644.0 8797.0 10520.0 9519.0 g 5200.0 7779.0 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 852.0 1778.0 3289.0 4423.0 5681.0 t 4608.0 4677.0 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0 1551.0 2365.0 6545.0 6526.0 4504.0
MA0493.1_shift1 (Klf1)				; dyads_m42 versus MA0493.1 (Klf1); m=4/5; ncol2=11; w=8; offset=-3; strand=D; shift=1; score=0.437298; -rrCCACACCCw---- ; cor=; Ncor= a 0 150.0 167.0 67.0 13.0 404.0 0.0 400.0 0.0 0.0 0.0 280.0 0 0 0 0 c 0 76.0 40.0 396.0 461.0 118.0 526.0 0.0 526.0 526.0 508.0 35.0 0 0 0 0 g 0 202.0 305.0 32.0 0.0 0.0 0.0 97.0 0.0 0.0 0.0 0.0 0 0 0 0 t 0 98.0 14.0 31.0 52.0 4.0 0.0 29.0 0.0 0.0 18.0 211.0 0 0 0 0
MA0006.1_rc_shift6 (Ahr::Arnt_rc)				; dyads_m42 versus MA0006.1_rc (Ahr::Arnt_rc); m=5/5; ncol2=6; w=6; offset=2; strand=R; shift=6; score=0.43454; ------CACGCr---- ; cor=; Ncor= a 0 0 0 0 0 0 0.0 24.0 1.0 1.0 1.0 11.0 0 0 0 0 c 0 0 0 0 0 0 24.0 0.0 23.0 0.0 23.0 2.0 0 0 0 0 g 0 0 0 0 0 0 0.0 0.0 0.0 23.0 0.0 8.0 0 0 0 0 t 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 3.0 0 0 0 0