One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m37/peak-motifs_local_words_8nt_m37.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/local_words_8nt_m37/peak-motifs_local_words_8nt_m37_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m37_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m37_shift0 (local_words_8nt_m37local_words_8nt_m37)
; local_words_8nt_m37 (local_words_8nt_m37local_words_8nt_m37); m=0 (reference); ncol1=24; shift=0; ncol=24; srGCCACAGCTGCTGCAGCTGTsr ; Alignment reference a 13 19 7 2 7 57 2 62 1 2 7 2 2 8 4 2 54 1 0 2 2 5 5 20 c 19 9 7 51 53 4 63 4 2 68 3 3 62 3 4 63 5 2 65 2 4 13 27 10 g 27 25 52 6 6 7 4 2 64 0 1 65 2 3 60 3 3 64 3 1 62 4 23 27 t 11 17 4 11 4 2 1 2 3 0 59 0 4 56 2 2 8 3 2 65 2 48 15 13

MA1485.1_rc_shift2 (FERD3L_rc)
; local_words_8nt_m37 versus MA1485.1_rc (FERD3L_rc); m=1/4; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.472921; --GTrACAGCTGkyrC-------- ; cor=; Ncor= a 0 0 48.0 958.0 14919.0 21065.0 0.0 29605.0 0.0 4691.0 144.0 0.0 1710.0 74.0 9557.0 225.0 0 0 0 0 0 0 0 0 c 0 0 0.0 9815.0 5920.0 3395.0 29605.0 210.0 471.0 29605.0 118.0 0.0 3142.0 12703.0 348.0 29605.0 0 0 0 0 0 0 0 0 g 0 0 29605.0 809.0 8664.0 3878.0 0.0 129.0 29605.0 841.0 126.0 29605.0 9363.0 2443.0 20049.0 68.0 0 0 0 0 0 0 0 0 t 0 0 0.0 29605.0 103.0 1268.0 0.0 81.0 3649.0 0.0 29605.0 36.0 15390.0 14384.0 450.0 2158.0 0 0 0 0 0 0 0 0

MA0832.1_shift2 (Tcf21)
; local_words_8nt_m37 versus MA0832.1 (Tcf21); m=2/4; ncol2=14; w=14; offset=2; strand=D; shift=2; score=0.424824; --ryAACAGCTGTTry-------- ; cor=; Ncor= a 0 0 55.0 28.0 171.0 171.0 0.0 171.0 0.0 0.0 0.0 0.0 0.0 5.0 50.0 30.0 0 0 0 0 0 0 0 0 c 0 0 29.0 76.0 1.0 10.0 171.0 1.0 0.0 171.0 0.0 0.0 4.0 23.0 23.0 49.0 0 0 0 0 0 0 0 0 g 0 0 70.0 22.0 23.0 0.0 0.0 0.0 171.0 1.0 0.0 171.0 20.0 0.0 80.0 32.0 0 0 0 0 0 0 0 0 t 0 0 17.0 46.0 3.0 0.0 0.0 0.0 2.0 1.0 171.0 0.0 171.0 171.0 19.0 60.0 0 0 0 0 0 0 0 0

MA0500.2_shift12 (MYOG)
; local_words_8nt_m37 versus MA0500.2 (MYOG); m=3/4; ncol2=12; w=12; offset=12; strand=D; shift=12; score=0.416816; ------------sarCAGCTGyts ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 5310.0 8428.0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 4667.0 5018.0 c 0 0 0 0 0 0 0 0 0 0 0 0 6381.0 3754.0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 5497.0 5660.0 g 0 0 0 0 0 0 0 0 0 0 0 0 5596.0 5483.0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 3718.0 6369.0 t 0 0 0 0 0 0 0 0 0 0 0 0 5070.0 4692.0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 8475.0 5310.0

MA0521.1_rc_shift12 (Tcf12_rc)
; local_words_8nt_m37 versus MA0521.1_rc (Tcf12_rc); m=4/4; ncol2=11; w=11; offset=12; strand=R; shift=12; score=0.401711; ------------cwsCAGCTGYy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2191.0 3642.0 1682.0 0.0 12895.0 0.0 0.0 0.0 0.0 0.0 17.0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 4836.0 2925.0 3811.0 12895.0 0.0 1889.0 12887.0 0.0 0.0 3951.0 5123.0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 3005.0 2416.0 5527.0 0.0 0.0 10822.0 0.0 0.0 12895.0 124.0 1585.0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 2863.0 3912.0 1875.0 0.0 0.0 184.0 8.0 12895.0 0.0 8820.0 6170.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m37_shift0 (local_words_8nt_m37local_words_8nt_m37)				; local_words_8nt_m37 (local_words_8nt_m37local_words_8nt_m37); m=0 (reference); ncol1=24; shift=0; ncol=24; srGCCACAGCTGCTGCAGCTGTsr ; Alignment reference a 13 19 7 2 7 57 2 62 1 2 7 2 2 8 4 2 54 1 0 2 2 5 5 20 c 19 9 7 51 53 4 63 4 2 68 3 3 62 3 4 63 5 2 65 2 4 13 27 10 g 27 25 52 6 6 7 4 2 64 0 1 65 2 3 60 3 3 64 3 1 62 4 23 27 t 11 17 4 11 4 2 1 2 3 0 59 0 4 56 2 2 8 3 2 65 2 48 15 13
MA1485.1_rc_shift2 (FERD3L_rc)				; local_words_8nt_m37 versus MA1485.1_rc (FERD3L_rc); m=1/4; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.472921; --GTrACAGCTGkyrC-------- ; cor=; Ncor= a 0 0 48.0 958.0 14919.0 21065.0 0.0 29605.0 0.0 4691.0 144.0 0.0 1710.0 74.0 9557.0 225.0 0 0 0 0 0 0 0 0 c 0 0 0.0 9815.0 5920.0 3395.0 29605.0 210.0 471.0 29605.0 118.0 0.0 3142.0 12703.0 348.0 29605.0 0 0 0 0 0 0 0 0 g 0 0 29605.0 809.0 8664.0 3878.0 0.0 129.0 29605.0 841.0 126.0 29605.0 9363.0 2443.0 20049.0 68.0 0 0 0 0 0 0 0 0 t 0 0 0.0 29605.0 103.0 1268.0 0.0 81.0 3649.0 0.0 29605.0 36.0 15390.0 14384.0 450.0 2158.0 0 0 0 0 0 0 0 0
MA0832.1_shift2 (Tcf21)				; local_words_8nt_m37 versus MA0832.1 (Tcf21); m=2/4; ncol2=14; w=14; offset=2; strand=D; shift=2; score=0.424824; --ryAACAGCTGTTry-------- ; cor=; Ncor= a 0 0 55.0 28.0 171.0 171.0 0.0 171.0 0.0 0.0 0.0 0.0 0.0 5.0 50.0 30.0 0 0 0 0 0 0 0 0 c 0 0 29.0 76.0 1.0 10.0 171.0 1.0 0.0 171.0 0.0 0.0 4.0 23.0 23.0 49.0 0 0 0 0 0 0 0 0 g 0 0 70.0 22.0 23.0 0.0 0.0 0.0 171.0 1.0 0.0 171.0 20.0 0.0 80.0 32.0 0 0 0 0 0 0 0 0 t 0 0 17.0 46.0 3.0 0.0 0.0 0.0 2.0 1.0 171.0 0.0 171.0 171.0 19.0 60.0 0 0 0 0 0 0 0 0
MA0500.2_shift12 (MYOG)				; local_words_8nt_m37 versus MA0500.2 (MYOG); m=3/4; ncol2=12; w=12; offset=12; strand=D; shift=12; score=0.416816; ------------sarCAGCTGyts ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 5310.0 8428.0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 4667.0 5018.0 c 0 0 0 0 0 0 0 0 0 0 0 0 6381.0 3754.0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 5497.0 5660.0 g 0 0 0 0 0 0 0 0 0 0 0 0 5596.0 5483.0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 3718.0 6369.0 t 0 0 0 0 0 0 0 0 0 0 0 0 5070.0 4692.0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 8475.0 5310.0
MA0521.1_rc_shift12 (Tcf12_rc)				; local_words_8nt_m37 versus MA0521.1_rc (Tcf12_rc); m=4/4; ncol2=11; w=11; offset=12; strand=R; shift=12; score=0.401711; ------------cwsCAGCTGYy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2191.0 3642.0 1682.0 0.0 12895.0 0.0 0.0 0.0 0.0 0.0 17.0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 4836.0 2925.0 3811.0 12895.0 0.0 1889.0 12887.0 0.0 0.0 3951.0 5123.0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 3005.0 2416.0 5527.0 0.0 0.0 10822.0 0.0 0.0 12895.0 124.0 1585.0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 2863.0 3912.0 1875.0 0.0 0.0 184.0 8.0 12895.0 0.0 8820.0 6170.0 0