One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_6nt_mkv3_m40/peak-motifs_oligos_6nt_mkv3_m40.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_6nt_mkv3_m40/peak-motifs_oligos_6nt_mkv3_m40_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m40_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m40_shift0 (oligos_6nt_mkv3_m40oligos_6nt_mkv3_m40)
; oligos_6nt_mkv3_m40 (oligos_6nt_mkv3_m40oligos_6nt_mkv3_m40); m=0 (reference); ncol1=16; shift=0; ncol=17; sssCGGCGGGGCGGss- ; Alignment reference a 17 10 6 5 3 4 3 1 2 2 4 1 1 2 11 7 0 c 32 29 52 70 6 9 88 5 14 8 5 92 8 7 32 25 0 g 36 47 35 19 83 81 4 90 81 87 86 3 87 88 46 60 0 t 12 11 4 3 5 3 2 1 0 0 2 1 1 0 8 5 0

MA1513.1_rc_shift1 (KLF15_rc)
; oligos_6nt_mkv3_m40 versus MA1513.1_rc (KLF15_rc); m=1/3; ncol2=11; w=11; offset=1; strand=R; shift=1; score=0.564006; -sgGGGCGGGgs----- ; cor=; Ncor= a 0 2165.0 1602.0 3.0 1.0 11.0 0.0 0.0 3.0 9.0 1809.0 1744.0 0 0 0 0 0 c 0 3124.0 1934.0 100.0 359.0 2.0 11369.0 1.0 333.0 86.0 2117.0 5538.0 0 0 0 0 0 g 0 5013.0 6267.0 11254.0 10954.0 11345.0 0.0 11368.0 10940.0 11234.0 6506.0 2903.0 0 0 0 0 0 t 0 1067.0 1566.0 12.0 55.0 11.0 0.0 0.0 93.0 40.0 937.0 1184.0 0 0 0 0 0

MA0599.1_rc_shift2 (KLF5_rc)
; oligos_6nt_mkv3_m40 versus MA0599.1_rc (KLF5_rc); m=2/3; ncol2=10; w=10; offset=2; strand=R; shift=2; score=0.467837; --dGGGyGKGGc----- ; cor=; Ncor= a 0 0 4101.0 476.0 0.0 0.0 3378.0 0.0 565.0 1603.0 1711.0 2587.0 0 0 0 0 0 c 0 0 0.0 0.0 0.0 0.0 5182.0 0.0 0.0 0.0 0.0 7572.0 0 0 0 0 0 g 0 0 5595.0 13135.0 13611.0 13611.0 0.0 13611.0 9569.0 12008.0 11900.0 2023.0 0 0 0 0 0 t 0 0 3915.0 0.0 0.0 0.0 5051.0 0.0 3477.0 0.0 0.0 1429.0 0 0 0 0 0

MA1564.1_rc_shift5 (SP9_rc)
; oligos_6nt_mkv3_m40 versus MA1564.1_rc (SP9_rc); m=3/3; ncol2=12; w=11; offset=5; strand=R; shift=5; score=0.45802; -----rgkGGGCGkGgy ; cor=; Ncor= a 0 0 0 0 0 660.0 588.0 353.0 412.0 30.0 14.0 173.0 9.0 96.0 284.0 518.0 226.0 c 0 0 0 0 0 204.0 191.0 38.0 24.0 0.0 0.0 2451.0 17.0 56.0 113.0 309.0 952.0 g 0 0 0 0 0 1167.0 1863.0 1259.0 2451.0 2451.0 2451.0 200.0 2451.0 1127.0 2451.0 2451.0 440.0 t 0 0 0 0 0 420.0 188.0 1192.0 39.0 0.0 22.0 211.0 2.0 2451.0 321.0 566.0 834.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m40_shift0 (oligos_6nt_mkv3_m40oligos_6nt_mkv3_m40)				; oligos_6nt_mkv3_m40 (oligos_6nt_mkv3_m40oligos_6nt_mkv3_m40); m=0 (reference); ncol1=16; shift=0; ncol=17; sssCGGCGGGGCGGss- ; Alignment reference a 17 10 6 5 3 4 3 1 2 2 4 1 1 2 11 7 0 c 32 29 52 70 6 9 88 5 14 8 5 92 8 7 32 25 0 g 36 47 35 19 83 81 4 90 81 87 86 3 87 88 46 60 0 t 12 11 4 3 5 3 2 1 0 0 2 1 1 0 8 5 0
MA1513.1_rc_shift1 (KLF15_rc)				; oligos_6nt_mkv3_m40 versus MA1513.1_rc (KLF15_rc); m=1/3; ncol2=11; w=11; offset=1; strand=R; shift=1; score=0.564006; -sgGGGCGGGgs----- ; cor=; Ncor= a 0 2165.0 1602.0 3.0 1.0 11.0 0.0 0.0 3.0 9.0 1809.0 1744.0 0 0 0 0 0 c 0 3124.0 1934.0 100.0 359.0 2.0 11369.0 1.0 333.0 86.0 2117.0 5538.0 0 0 0 0 0 g 0 5013.0 6267.0 11254.0 10954.0 11345.0 0.0 11368.0 10940.0 11234.0 6506.0 2903.0 0 0 0 0 0 t 0 1067.0 1566.0 12.0 55.0 11.0 0.0 0.0 93.0 40.0 937.0 1184.0 0 0 0 0 0
MA0599.1_rc_shift2 (KLF5_rc)				; oligos_6nt_mkv3_m40 versus MA0599.1_rc (KLF5_rc); m=2/3; ncol2=10; w=10; offset=2; strand=R; shift=2; score=0.467837; --dGGGyGKGGc----- ; cor=; Ncor= a 0 0 4101.0 476.0 0.0 0.0 3378.0 0.0 565.0 1603.0 1711.0 2587.0 0 0 0 0 0 c 0 0 0.0 0.0 0.0 0.0 5182.0 0.0 0.0 0.0 0.0 7572.0 0 0 0 0 0 g 0 0 5595.0 13135.0 13611.0 13611.0 0.0 13611.0 9569.0 12008.0 11900.0 2023.0 0 0 0 0 0 t 0 0 3915.0 0.0 0.0 0.0 5051.0 0.0 3477.0 0.0 0.0 1429.0 0 0 0 0 0
MA1564.1_rc_shift5 (SP9_rc)				; oligos_6nt_mkv3_m40 versus MA1564.1_rc (SP9_rc); m=3/3; ncol2=12; w=11; offset=5; strand=R; shift=5; score=0.45802; -----rgkGGGCGkGgy ; cor=; Ncor= a 0 0 0 0 0 660.0 588.0 353.0 412.0 30.0 14.0 173.0 9.0 96.0 284.0 518.0 226.0 c 0 0 0 0 0 204.0 191.0 38.0 24.0 0.0 0.0 2451.0 17.0 56.0 113.0 309.0 952.0 g 0 0 0 0 0 1167.0 1863.0 1259.0 2451.0 2451.0 2451.0 200.0 2451.0 1127.0 2451.0 2451.0 440.0 t 0 0 0 0 0 420.0 188.0 1192.0 39.0 0.0 22.0 211.0 2.0 2451.0 321.0 566.0 834.0