One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m42/peak-motifs_oligos_8nt_mkv5_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/oligos_8nt_mkv5_m42/peak-motifs_oligos_8nt_mkv5_m42_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m42_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m42_shift3 (oligos_8nt_mkv5_m42oligos_8nt_mkv5_m42)
; oligos_8nt_mkv5_m42 (oligos_8nt_mkv5_m42oligos_8nt_mkv5_m42); m=0 (reference); ncol1=12; shift=3; ncol=15; ---vsCACAGCACag ; Alignment reference a 0 0 0 44 29 2 153 1 148 1 3 145 0 64 19 c 0 0 0 46 50 155 1 151 3 5 149 3 157 34 39 g 0 0 0 42 55 0 2 1 6 147 1 8 0 30 65 t 0 0 0 25 23 0 1 4 0 4 4 1 0 29 34

MA1629.1_shift3 (Zic2)
; oligos_8nt_mkv5_m42 versus MA1629.1 (Zic2); m=1/4; ncol2=14; w=12; offset=0; strand=D; shift=3; score=0.612571; ---mkCaCAGCAGGr ; cor=; Ncor= a 0 0 0 3145.0 2450.0 1161.0 6888.0 135.0 11074.0 140.0 80.0 10625.0 192.0 96.0 3060.0 c 0 0 0 3507.0 1755.0 9933.0 1765.0 11476.0 391.0 228.0 11272.0 118.0 133.0 204.0 1476.0 g 0 0 0 2761.0 3821.0 585.0 829.0 188.0 186.0 11484.0 269.0 735.0 11184.0 11465.0 4911.0 t 0 0 0 2506.0 3893.0 240.0 2437.0 120.0 268.0 67.0 298.0 441.0 410.0 154.0 2472.0

MA0483.1_shift1 (Gfi1b)
; oligos_8nt_mkv5_m42 versus MA0483.1 (Gfi1b); m=2/4; ncol2=11; w=9; offset=-2; strand=D; shift=1; score=0.469147; -aAATCwCwGCw--- ; cor=; Ncor= a 0 1124.0 1761.0 1759.0 0.0 0.0 1033.0 61.0 1116.0 57.0 142.0 740.0 0 0 0 c 0 438.0 0.0 0.0 338.0 1761.0 21.0 1312.0 0.0 1.0 1328.0 433.0 0 0 0 g 0 104.0 0.0 2.0 28.0 0.0 0.0 388.0 1.0 1676.0 76.0 130.0 0 0 0 t 0 95.0 0.0 0.0 1395.0 0.0 707.0 0.0 644.0 27.0 215.0 458.0 0 0 0

MA0002.2_rc_shift1 (RUNX1_rc)
; oligos_8nt_mkv5_m42 versus MA0002.2_rc (RUNX1_rc); m=3/4; ncol2=11; w=9; offset=-2; strand=R; shift=1; score=0.464823; -waaCCACAram--- ; cor=; Ncor= a 0 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 0 0 0 c 0 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 0 0 0 g 0 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 0 0 0 t 0 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0 0 0 0

MA0038.2_shift0 (GFI1)
; oligos_8nt_mkv5_m42 versus MA0038.2 (GFI1); m=4/4; ncol2=12; w=9; offset=-3; strand=D; shift=0; score=0.429402; cmAATCACdGCa--- ; cor=; Ncor= a 3668.0 19146.0 30168.0 30150.0 0.0 15.0 29255.0 838.0 7748.0 2294.0 292.0 16713.0 0 0 0 c 11575.0 10155.0 2.0 0.0 0.0 30139.0 0.0 27769.0 54.0 266.0 27891.0 5221.0 0 0 0 g 7376.0 812.0 0.0 0.0 0.0 0.0 0.0 3888.0 8349.0 27514.0 0.0 4079.0 0 0 0 t 7527.0 565.0 0.0 1.0 30161.0 10.0 1594.0 0.0 13996.0 888.0 3702.0 4134.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv5_m42_shift3 (oligos_8nt_mkv5_m42oligos_8nt_mkv5_m42)				; oligos_8nt_mkv5_m42 (oligos_8nt_mkv5_m42oligos_8nt_mkv5_m42); m=0 (reference); ncol1=12; shift=3; ncol=15; ---vsCACAGCACag ; Alignment reference a 0 0 0 44 29 2 153 1 148 1 3 145 0 64 19 c 0 0 0 46 50 155 1 151 3 5 149 3 157 34 39 g 0 0 0 42 55 0 2 1 6 147 1 8 0 30 65 t 0 0 0 25 23 0 1 4 0 4 4 1 0 29 34
MA1629.1_shift3 (Zic2)				; oligos_8nt_mkv5_m42 versus MA1629.1 (Zic2); m=1/4; ncol2=14; w=12; offset=0; strand=D; shift=3; score=0.612571; ---mkCaCAGCAGGr ; cor=; Ncor= a 0 0 0 3145.0 2450.0 1161.0 6888.0 135.0 11074.0 140.0 80.0 10625.0 192.0 96.0 3060.0 c 0 0 0 3507.0 1755.0 9933.0 1765.0 11476.0 391.0 228.0 11272.0 118.0 133.0 204.0 1476.0 g 0 0 0 2761.0 3821.0 585.0 829.0 188.0 186.0 11484.0 269.0 735.0 11184.0 11465.0 4911.0 t 0 0 0 2506.0 3893.0 240.0 2437.0 120.0 268.0 67.0 298.0 441.0 410.0 154.0 2472.0
MA0483.1_shift1 (Gfi1b)				; oligos_8nt_mkv5_m42 versus MA0483.1 (Gfi1b); m=2/4; ncol2=11; w=9; offset=-2; strand=D; shift=1; score=0.469147; -aAATCwCwGCw--- ; cor=; Ncor= a 0 1124.0 1761.0 1759.0 0.0 0.0 1033.0 61.0 1116.0 57.0 142.0 740.0 0 0 0 c 0 438.0 0.0 0.0 338.0 1761.0 21.0 1312.0 0.0 1.0 1328.0 433.0 0 0 0 g 0 104.0 0.0 2.0 28.0 0.0 0.0 388.0 1.0 1676.0 76.0 130.0 0 0 0 t 0 95.0 0.0 0.0 1395.0 0.0 707.0 0.0 644.0 27.0 215.0 458.0 0 0 0
MA0002.2_rc_shift1 (RUNX1_rc)				; oligos_8nt_mkv5_m42 versus MA0002.2_rc (RUNX1_rc); m=3/4; ncol2=11; w=9; offset=-2; strand=R; shift=1; score=0.464823; -waaCCACAram--- ; cor=; Ncor= a 0 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 0 0 0 c 0 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 0 0 0 g 0 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 0 0 0 t 0 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0 0 0 0
MA0038.2_shift0 (GFI1)				; oligos_8nt_mkv5_m42 versus MA0038.2 (GFI1); m=4/4; ncol2=12; w=9; offset=-3; strand=D; shift=0; score=0.429402; cmAATCACdGCa--- ; cor=; Ncor= a 3668.0 19146.0 30168.0 30150.0 0.0 15.0 29255.0 838.0 7748.0 2294.0 292.0 16713.0 0 0 0 c 11575.0 10155.0 2.0 0.0 0.0 30139.0 0.0 27769.0 54.0 266.0 27891.0 5221.0 0 0 0 g 7376.0 812.0 0.0 0.0 0.0 0.0 0.0 3888.0 8349.0 27514.0 0.0 4079.0 0 0 0 t 7527.0 565.0 0.0 1.0 30161.0 10.0 1594.0 0.0 13996.0 888.0 3702.0 4134.0 0 0 0