One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m22/peak-motifs_local_words_8nt_m22.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_m22/peak-motifs_local_words_8nt_m22_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m22_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m22_shift0 (local_words_8nt_m22local_words_8nt_m22)
; local_words_8nt_m22 (local_words_8nt_m22local_words_8nt_m22); m=0 (reference); ncol1=24; shift=0; ncol=24; ysACAGCTGCAGCAGCTGTGGCys ; Alignment reference a 13 15 48 2 65 2 3 8 2 2 56 4 0 59 0 3 2 1 2 4 11 4 17 11 c 27 23 4 62 1 3 64 3 3 60 3 2 65 1 0 64 2 4 7 6 6 52 25 27 g 10 27 13 4 2 65 2 5 63 4 3 62 3 3 68 2 4 63 4 53 51 7 9 19 t 20 5 5 2 2 0 1 54 2 4 8 2 2 7 2 1 62 2 57 7 2 7 19 13

MA1485.1_shift8 (FERD3L)
; local_words_8nt_m22 versus MA1485.1 (FERD3L); m=1/4; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.472921; --------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2158.0 450.0 14384.0 15390.0 36.0 29605.0 0.0 3649.0 81.0 0.0 1268.0 103.0 29605.0 0.0 0 0 c 0 0 0 0 0 0 0 0 68.0 20049.0 2443.0 9363.0 29605.0 126.0 841.0 29605.0 129.0 0.0 3878.0 8664.0 809.0 29605.0 0 0 g 0 0 0 0 0 0 0 0 29605.0 348.0 12703.0 3142.0 0.0 118.0 29605.0 471.0 210.0 29605.0 3395.0 5920.0 9815.0 0.0 0 0 t 0 0 0 0 0 0 0 0 225.0 9557.0 74.0 1710.0 0.0 144.0 4691.0 0.0 29605.0 0.0 21065.0 14919.0 958.0 48.0 0 0

MA0832.1_rc_shift8 (Tcf21_rc)
; local_words_8nt_m22 versus MA0832.1_rc (Tcf21_rc); m=2/4; ncol2=14; w=14; offset=8; strand=R; shift=8; score=0.424824; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 60.0 19.0 171.0 171.0 0.0 171.0 1.0 2.0 0.0 0.0 0.0 3.0 46.0 17.0 0 0 c 0 0 0 0 0 0 0 0 32.0 80.0 0.0 20.0 171.0 0.0 1.0 171.0 0.0 0.0 0.0 23.0 22.0 70.0 0 0 g 0 0 0 0 0 0 0 0 49.0 23.0 23.0 4.0 0.0 0.0 171.0 0.0 1.0 171.0 10.0 1.0 76.0 29.0 0 0 t 0 0 0 0 0 0 0 0 30.0 50.0 5.0 0.0 0.0 0.0 0.0 0.0 171.0 0.0 171.0 171.0 28.0 55.0 0 0

MA0500.2_rc_shift0 (MYOG_rc)
; local_words_8nt_m22 versus MA0500.2_rc (MYOG_rc); m=3/4; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.416816; sarCAGCTGyts------------ ; cor=; Ncor= a 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 0 0 0 0 0 0 0 0 0 0 c 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 0 0 0 0 0 0 0 0 0 0 g 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 0 0 0 0 0 0 0 0 0 0 t 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0 0 0 0 0 0 0 0 0 0 0

MA0521.1_shift1 (Tcf12)
; local_words_8nt_m22 versus MA0521.1 (Tcf12); m=4/4; ncol2=11; w=11; offset=1; strand=D; shift=1; score=0.401711; -rRCAGCTGswg------------ ; cor=; Ncor= a 0 6170.0 8820.0 0.0 12895.0 8.0 184.0 0.0 0.0 1875.0 3912.0 2863.0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 1585.0 124.0 12895.0 0.0 0.0 10822.0 0.0 0.0 5527.0 2416.0 3005.0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 5123.0 3951.0 0.0 0.0 12887.0 1889.0 0.0 12895.0 3811.0 2925.0 4836.0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 17.0 0.0 0.0 0.0 0.0 0.0 12895.0 0.0 1682.0 3642.0 2191.0 0 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m22_shift0 (local_words_8nt_m22local_words_8nt_m22)				; local_words_8nt_m22 (local_words_8nt_m22local_words_8nt_m22); m=0 (reference); ncol1=24; shift=0; ncol=24; ysACAGCTGCAGCAGCTGTGGCys ; Alignment reference a 13 15 48 2 65 2 3 8 2 2 56 4 0 59 0 3 2 1 2 4 11 4 17 11 c 27 23 4 62 1 3 64 3 3 60 3 2 65 1 0 64 2 4 7 6 6 52 25 27 g 10 27 13 4 2 65 2 5 63 4 3 62 3 3 68 2 4 63 4 53 51 7 9 19 t 20 5 5 2 2 0 1 54 2 4 8 2 2 7 2 1 62 2 57 7 2 7 19 13
MA1485.1_shift8 (FERD3L)				; local_words_8nt_m22 versus MA1485.1 (FERD3L); m=1/4; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.472921; --------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2158.0 450.0 14384.0 15390.0 36.0 29605.0 0.0 3649.0 81.0 0.0 1268.0 103.0 29605.0 0.0 0 0 c 0 0 0 0 0 0 0 0 68.0 20049.0 2443.0 9363.0 29605.0 126.0 841.0 29605.0 129.0 0.0 3878.0 8664.0 809.0 29605.0 0 0 g 0 0 0 0 0 0 0 0 29605.0 348.0 12703.0 3142.0 0.0 118.0 29605.0 471.0 210.0 29605.0 3395.0 5920.0 9815.0 0.0 0 0 t 0 0 0 0 0 0 0 0 225.0 9557.0 74.0 1710.0 0.0 144.0 4691.0 0.0 29605.0 0.0 21065.0 14919.0 958.0 48.0 0 0
MA0832.1_rc_shift8 (Tcf21_rc)				; local_words_8nt_m22 versus MA0832.1_rc (Tcf21_rc); m=2/4; ncol2=14; w=14; offset=8; strand=R; shift=8; score=0.424824; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 60.0 19.0 171.0 171.0 0.0 171.0 1.0 2.0 0.0 0.0 0.0 3.0 46.0 17.0 0 0 c 0 0 0 0 0 0 0 0 32.0 80.0 0.0 20.0 171.0 0.0 1.0 171.0 0.0 0.0 0.0 23.0 22.0 70.0 0 0 g 0 0 0 0 0 0 0 0 49.0 23.0 23.0 4.0 0.0 0.0 171.0 0.0 1.0 171.0 10.0 1.0 76.0 29.0 0 0 t 0 0 0 0 0 0 0 0 30.0 50.0 5.0 0.0 0.0 0.0 0.0 0.0 171.0 0.0 171.0 171.0 28.0 55.0 0 0
MA0500.2_rc_shift0 (MYOG_rc)				; local_words_8nt_m22 versus MA0500.2_rc (MYOG_rc); m=3/4; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.416816; sarCAGCTGyts------------ ; cor=; Ncor= a 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 0 0 0 0 0 0 0 0 0 0 c 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 0 0 0 0 0 0 0 0 0 0 g 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 0 0 0 0 0 0 0 0 0 0 t 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0 0 0 0 0 0 0 0 0 0 0
MA0521.1_shift1 (Tcf12)				; local_words_8nt_m22 versus MA0521.1 (Tcf12); m=4/4; ncol2=11; w=11; offset=1; strand=D; shift=1; score=0.401711; -rRCAGCTGswg------------ ; cor=; Ncor= a 0 6170.0 8820.0 0.0 12895.0 8.0 184.0 0.0 0.0 1875.0 3912.0 2863.0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 1585.0 124.0 12895.0 0.0 0.0 10822.0 0.0 0.0 5527.0 2416.0 3005.0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 5123.0 3951.0 0.0 0.0 12887.0 1889.0 0.0 12895.0 3811.0 2925.0 4836.0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 17.0 0.0 0.0 0.0 0.0 0.0 12895.0 0.0 1682.0 3642.0 2191.0 0 0 0 0 0 0 0 0 0 0 0 0