One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m45/peak-motifs_dyads_m45.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_m45/peak-motifs_dyads_m45_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m45_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m45_shift1 (dyads_m45dyads_m45)
; dyads_m45 (dyads_m45dyads_m45); m=0 (reference); ncol1=14; shift=1; ncol=15; -srGGGGCAGGGAgg ; Alignment reference a 0 39 66 9 9 5 8 9 188 3 4 10 182 39 56 c 0 62 24 2 4 2 3 200 4 1 2 10 25 48 46 g 0 85 82 207 205 214 210 15 22 218 214 203 10 97 90 t 0 39 53 7 7 4 4 1 11 3 5 2 8 41 33

MA1513.1_rc_shift2 (KLF15_rc)
; dyads_m45 versus MA1513.1_rc (KLF15_rc); m=1/4; ncol2=11; w=11; offset=1; strand=R; shift=2; score=0.607643; --sgGGGCGGGgs-- ; cor=; Ncor= a 0 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 c 0 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 g 0 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 t 0 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

MA0599.1_rc_shift3 (KLF5_rc)
; dyads_m45 versus MA0599.1_rc (KLF5_rc); m=2/4; ncol2=10; w=10; offset=2; strand=R; shift=3; score=0.50423; ---dGGGyGKGGc-- ; cor=; Ncor= a 0 0 0 4101.0 476.0 0.0 0.0 3378.0 0.0 565.0 1603.0 1711.0 2587.0 0 0 c 0 0 0 0.0 0.0 0.0 0.0 5182.0 0.0 0.0 0.0 0.0 7572.0 0 0 g 0 0 0 5595.0 13135.0 13611.0 13611.0 0.0 13611.0 9569.0 12008.0 11900.0 2023.0 0 0 t 0 0 0 3915.0 0.0 0.0 0.0 5051.0 0.0 3477.0 0.0 0.0 1429.0 0 0

MA1630.1_shift0 (Znf281)
; dyads_m45 versus MA1630.1 (Znf281); m=3/4; ncol2=11; w=10; offset=-1; strand=D; shift=0; score=0.503905; ggTGGGGGAgG---- ; cor=; Ncor= a 1197.0 996.0 8.0 19.0 25.0 36.0 22.0 18.0 6504.0 735.0 374.0 0 0 0 0 c 878.0 1076.0 233.0 88.0 163.0 131.0 115.0 41.0 45.0 418.0 356.0 0 0 0 0 g 3539.0 3751.0 29.0 6449.0 6356.0 6378.0 6402.0 6457.0 8.0 4312.0 5523.0 0 0 0 0 t 954.0 745.0 6298.0 12.0 24.0 23.0 29.0 52.0 11.0 1103.0 315.0 0 0 0 0

MA0597.1_rc_shift1 (THAP1_rc)
; dyads_m45 versus MA0597.1_rc (THAP1_rc); m=4/4; ncol2=9; w=9; offset=0; strand=R; shift=1; score=0.482841; -trmKGGCar----- ; cor=; Ncor= a 0 32.0 57.0 58.0 4.0 1.0 10.0 42.0 125.0 61.0 0 0 0 0 0 c 0 17.0 41.0 77.0 1.0 0.0 0.0 137.0 12.0 27.0 0 0 0 0 0 g 0 34.0 71.0 17.0 136.0 195.0 182.0 0.0 47.0 93.0 0 0 0 0 0 t 0 116.0 30.0 47.0 58.0 3.0 7.0 20.0 15.0 18.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m45_shift1 (dyads_m45dyads_m45)				; dyads_m45 (dyads_m45dyads_m45); m=0 (reference); ncol1=14; shift=1; ncol=15; -srGGGGCAGGGAgg ; Alignment reference a 0 39 66 9 9 5 8 9 188 3 4 10 182 39 56 c 0 62 24 2 4 2 3 200 4 1 2 10 25 48 46 g 0 85 82 207 205 214 210 15 22 218 214 203 10 97 90 t 0 39 53 7 7 4 4 1 11 3 5 2 8 41 33
MA1513.1_rc_shift2 (KLF15_rc)				; dyads_m45 versus MA1513.1_rc (KLF15_rc); m=1/4; ncol2=11; w=11; offset=1; strand=R; shift=2; score=0.607643; --sgGGGCGGGgs-- ; cor=; Ncor= a 0 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 c 0 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 g 0 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 t 0 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
MA0599.1_rc_shift3 (KLF5_rc)				; dyads_m45 versus MA0599.1_rc (KLF5_rc); m=2/4; ncol2=10; w=10; offset=2; strand=R; shift=3; score=0.50423; ---dGGGyGKGGc-- ; cor=; Ncor= a 0 0 0 4101.0 476.0 0.0 0.0 3378.0 0.0 565.0 1603.0 1711.0 2587.0 0 0 c 0 0 0 0.0 0.0 0.0 0.0 5182.0 0.0 0.0 0.0 0.0 7572.0 0 0 g 0 0 0 5595.0 13135.0 13611.0 13611.0 0.0 13611.0 9569.0 12008.0 11900.0 2023.0 0 0 t 0 0 0 3915.0 0.0 0.0 0.0 5051.0 0.0 3477.0 0.0 0.0 1429.0 0 0
MA1630.1_shift0 (Znf281)				; dyads_m45 versus MA1630.1 (Znf281); m=3/4; ncol2=11; w=10; offset=-1; strand=D; shift=0; score=0.503905; ggTGGGGGAgG---- ; cor=; Ncor= a 1197.0 996.0 8.0 19.0 25.0 36.0 22.0 18.0 6504.0 735.0 374.0 0 0 0 0 c 878.0 1076.0 233.0 88.0 163.0 131.0 115.0 41.0 45.0 418.0 356.0 0 0 0 0 g 3539.0 3751.0 29.0 6449.0 6356.0 6378.0 6402.0 6457.0 8.0 4312.0 5523.0 0 0 0 0 t 954.0 745.0 6298.0 12.0 24.0 23.0 29.0 52.0 11.0 1103.0 315.0 0 0 0 0
MA0597.1_rc_shift1 (THAP1_rc)				; dyads_m45 versus MA0597.1_rc (THAP1_rc); m=4/4; ncol2=9; w=9; offset=0; strand=R; shift=1; score=0.482841; -trmKGGCar----- ; cor=; Ncor= a 0 32.0 57.0 58.0 4.0 1.0 10.0 42.0 125.0 61.0 0 0 0 0 0 c 0 17.0 41.0 77.0 1.0 0.0 0.0 137.0 12.0 27.0 0 0 0 0 0 g 0 34.0 71.0 17.0 136.0 195.0 182.0 0.0 47.0 93.0 0 0 0 0 0 t 0 116.0 30.0 47.0 58.0 3.0 7.0 20.0 15.0 18.0 0 0 0 0 0