One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_8nt_mkv6_m8/peak-motifs_oligos_8nt_mkv6_m8.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_m8/peak-motifs_oligos_8nt_mkv6_m8_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m8_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv6_m8_shift2 (oligos_8nt_mkv6_m8oligos_8nt_mkv6_m8)
; oligos_8nt_mkv6_m8 (oligos_8nt_mkv6_m8oligos_8nt_mkv6_m8); m=0 (reference); ncol1=12; shift=2; ncol=18; --ssCGCmGCCGcs---- ; Alignment reference a 0 0 624 495 10 8 103 2488 71 94 0 4 475 765 0 0 0 0 c 0 0 1758 2117 4899 29 4360 1570 165 4507 4808 68 2783 1896 0 0 0 0 g 0 0 1915 1804 54 4929 437 828 4653 300 164 4888 1219 1706 0 0 0 0 t 0 0 675 556 9 6 72 86 83 71 0 12 495 605 0 0 0 0

MA0506.1_rc_shift2 (NRF1_rc)
; oligos_8nt_mkv6_m8 versus MA0506.1_rc (NRF1_rc); m=1/3; ncol2=11; w=11; offset=0; strand=R; shift=2; score=0.670349; --yGCGCAkGCGC----- ; cor=; Ncor= a 0 0 0.0 0.0 0.0 286.0 0.0 3693.0 313.0 140.0 0.0 0.0 0.0 0 0 0 0 0 c 0 0 1575.0 0.0 4275.0 0.0 4624.0 528.0 935.0 468.0 4239.0 0.0 3647.0 0 0 0 0 0 g 0 0 804.0 4550.0 349.0 4338.0 0.0 403.0 1862.0 4016.0 189.0 4001.0 375.0 0 0 0 0 0 t 0 0 2245.0 74.0 0.0 0.0 0.0 0.0 1514.0 0.0 196.0 623.0 602.0 0 0 0 0 0

MA0048.2_shift4 (NHLH1)
; oligos_8nt_mkv6_m8 versus MA0048.2 (NHLH1); m=2/3; ncol2=10; w=10; offset=2; strand=D; shift=4; score=0.59965; ----cGCAGCTGCk---- ; cor=; Ncor= a 0 0 0 0 788.0 461.0 3.0 2166.0 0.0 96.0 0.0 2.0 296.0 308.0 0 0 0 0 c 0 0 0 0 2166.0 179.0 2166.0 3.0 301.0 2166.0 4.0 4.0 2166.0 736.0 0 0 0 0 g 0 0 0 0 181.0 2166.0 0.0 1.0 2166.0 124.0 4.0 2166.0 102.0 2166.0 0 0 0 0 t 0 0 0 0 111.0 142.0 0.0 0.0 114.0 0.0 2166.0 1.0 350.0 1489.0 0 0 0 0

MA1529.1_rc_shift0 (NHLH2_rc)
; oligos_8nt_mkv6_m8 versus MA1529.1_rc (NHLH2_rc); m=3/3; ncol2=18; w=12; offset=-2; strand=R; shift=0; score=0.477902; gkGrCGCAGCTGCKrCcc ; cor=; Ncor= a 4228.0 3330.0 2533.0 13503.0 740.0 1230.0 0.0 21358.0 0.0 1054.0 1.0 5.0 2634.0 151.0 5394.0 2763.0 5198.0 4143.0 c 2264.0 1579.0 1183.0 1520.0 20977.0 275.0 21363.0 3.0 2266.0 20096.0 26.0 2.0 18930.0 671.0 4908.0 18450.0 13903.0 9732.0 g 11271.0 13462.0 18351.0 7207.0 204.0 20611.0 2.0 14.0 20268.0 2459.0 0.0 21359.0 2324.0 15451.0 6141.0 1065.0 2219.0 2655.0 t 3601.0 6392.0 3766.0 1184.0 210.0 693.0 0.0 0.0 525.0 6.0 21364.0 2.0 2378.0 5603.0 4921.0 3741.0 4312.0 4834.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv6_m8_shift2 (oligos_8nt_mkv6_m8oligos_8nt_mkv6_m8)				; oligos_8nt_mkv6_m8 (oligos_8nt_mkv6_m8oligos_8nt_mkv6_m8); m=0 (reference); ncol1=12; shift=2; ncol=18; --ssCGCmGCCGcs---- ; Alignment reference a 0 0 624 495 10 8 103 2488 71 94 0 4 475 765 0 0 0 0 c 0 0 1758 2117 4899 29 4360 1570 165 4507 4808 68 2783 1896 0 0 0 0 g 0 0 1915 1804 54 4929 437 828 4653 300 164 4888 1219 1706 0 0 0 0 t 0 0 675 556 9 6 72 86 83 71 0 12 495 605 0 0 0 0
MA0506.1_rc_shift2 (NRF1_rc)				; oligos_8nt_mkv6_m8 versus MA0506.1_rc (NRF1_rc); m=1/3; ncol2=11; w=11; offset=0; strand=R; shift=2; score=0.670349; --yGCGCAkGCGC----- ; cor=; Ncor= a 0 0 0.0 0.0 0.0 286.0 0.0 3693.0 313.0 140.0 0.0 0.0 0.0 0 0 0 0 0 c 0 0 1575.0 0.0 4275.0 0.0 4624.0 528.0 935.0 468.0 4239.0 0.0 3647.0 0 0 0 0 0 g 0 0 804.0 4550.0 349.0 4338.0 0.0 403.0 1862.0 4016.0 189.0 4001.0 375.0 0 0 0 0 0 t 0 0 2245.0 74.0 0.0 0.0 0.0 0.0 1514.0 0.0 196.0 623.0 602.0 0 0 0 0 0
MA0048.2_shift4 (NHLH1)				; oligos_8nt_mkv6_m8 versus MA0048.2 (NHLH1); m=2/3; ncol2=10; w=10; offset=2; strand=D; shift=4; score=0.59965; ----cGCAGCTGCk---- ; cor=; Ncor= a 0 0 0 0 788.0 461.0 3.0 2166.0 0.0 96.0 0.0 2.0 296.0 308.0 0 0 0 0 c 0 0 0 0 2166.0 179.0 2166.0 3.0 301.0 2166.0 4.0 4.0 2166.0 736.0 0 0 0 0 g 0 0 0 0 181.0 2166.0 0.0 1.0 2166.0 124.0 4.0 2166.0 102.0 2166.0 0 0 0 0 t 0 0 0 0 111.0 142.0 0.0 0.0 114.0 0.0 2166.0 1.0 350.0 1489.0 0 0 0 0
MA1529.1_rc_shift0 (NHLH2_rc)				; oligos_8nt_mkv6_m8 versus MA1529.1_rc (NHLH2_rc); m=3/3; ncol2=18; w=12; offset=-2; strand=R; shift=0; score=0.477902; gkGrCGCAGCTGCKrCcc ; cor=; Ncor= a 4228.0 3330.0 2533.0 13503.0 740.0 1230.0 0.0 21358.0 0.0 1054.0 1.0 5.0 2634.0 151.0 5394.0 2763.0 5198.0 4143.0 c 2264.0 1579.0 1183.0 1520.0 20977.0 275.0 21363.0 3.0 2266.0 20096.0 26.0 2.0 18930.0 671.0 4908.0 18450.0 13903.0 9732.0 g 11271.0 13462.0 18351.0 7207.0 204.0 20611.0 2.0 14.0 20268.0 2459.0 0.0 21359.0 2324.0 15451.0 6141.0 1065.0 2219.0 2655.0 t 3601.0 6392.0 3766.0 1184.0 210.0 693.0 0.0 0.0 525.0 6.0 21364.0 2.0 2378.0 5603.0 4921.0 3741.0 4312.0 4834.0