One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/dyads_m13/peak-motifs_dyads_m13.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/dyads_m13/peak-motifs_dyads_m13_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m13_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m13_shift0 (dyads_m13dyads_m13)
; dyads_m13 (dyads_m13dyads_m13); m=0 (reference); ncol1=10; shift=0; ncol=21; ssCCTGGChs----------- ; Alignment reference a 2532 1749 0 0 0 0 0 0 3641 2131 0 0 0 0 0 0 0 0 0 0 0 c 3440 3647 13044 13044 0 0 0 13044 4037 3774 0 0 0 0 0 0 0 0 0 0 0 g 3973 4737 0 0 0 13044 13044 0 1482 4139 0 0 0 0 0 0 0 0 0 0 0 t 3099 2911 0 0 13044 0 0 0 3884 3000 0 0 0 0 0 0 0 0 0 0 0

MA0092.1_shift0 (Hand1::Tcf3)
; dyads_m13 versus MA0092.1 (Hand1::Tcf3); m=1/4; ncol2=10; w=10; offset=0; strand=D; shift=0; score=0.705495; srTCTGGmwt----------- ; cor=; Ncor= a 4.0 10.0 2.0 0.0 0.0 0.0 0.0 9.0 16.0 5.0 0 0 0 0 0 0 0 0 0 0 0 c 8.0 0.0 2.0 28.0 0.0 0.0 3.0 14.0 0.0 4.0 0 0 0 0 0 0 0 0 0 0 0 g 10.0 15.0 1.0 0.0 0.0 29.0 25.0 1.0 3.0 4.0 0 0 0 0 0 0 0 0 0 0 0 t 7.0 4.0 24.0 1.0 29.0 0.0 1.0 5.0 10.0 16.0 0 0 0 0 0 0 0 0 0 0 0

MA0161.2_shift0 (NFIC)
; dyads_m13 versus MA0161.2 (NFIC); m=2/4; ncol2=11; w=10; offset=0; strand=D; shift=0; score=0.656432; twCTTGGCAsa---------- ; cor=; Ncor= a 2615.0 3896.0 412.0 154.0 352.0 310.0 223.0 264.0 10158.0 2626.0 3344.0 0 0 0 0 0 0 0 0 0 0 c 2647.0 2137.0 10542.0 303.0 333.0 129.0 121.0 10725.0 397.0 2951.0 2712.0 0 0 0 0 0 0 0 0 0 0 g 2478.0 2086.0 329.0 369.0 177.0 11087.0 10973.0 88.0 478.0 3186.0 2760.0 0 0 0 0 0 0 0 0 0 0 t 3867.0 3488.0 324.0 10781.0 10745.0 81.0 290.0 530.0 574.0 2844.0 2791.0 0 0 0 0 0 0 0 0 0 0

MA0671.1_rc_shift2 (NFIX_rc)
; dyads_m13 versus MA0671.1_rc (NFIX_rc); m=3/4; ncol2=9; w=8; offset=2; strand=R; shift=2; score=0.556267; --byTGGCacs---------- ; cor=; Ncor= a 0 0 6439.0 2399.0 110.0 0.0 29.0 2539.0 32864.0 8043.0 7378.0 0 0 0 0 0 0 0 0 0 0 c 0 0 9135.0 12688.0 180.0 0.0 3257.0 32864.0 5911.0 10855.0 8725.0 0 0 0 0 0 0 0 0 0 0 g 0 0 9039.0 1356.0 2230.0 32864.0 32864.0 186.0 9695.0 6134.0 8810.0 0 0 0 0 0 0 0 0 0 0 t 0 0 8251.0 32864.0 32864.0 0.0 3.0 132.0 11279.0 7832.0 7951.0 0 0 0 0 0 0 0 0 0 0

MA1643.1_shift0 (NFIB)
; dyads_m13 versus MA1643.1 (NFIB); m=4/4; ncol2=21; w=10; offset=0; strand=D; shift=0; score=0.437934; trcCTGGCAykgTGCCAagha ; cor=; Ncor= a 1055.0 1181.0 424.0 273.0 133.0 5.0 16.0 148.0 3178.0 443.0 1087.0 594.0 701.0 14.0 16.0 8.0 3937.0 2989.0 552.0 1156.0 1367.0 c 946.0 839.0 2911.0 3142.0 20.0 11.0 12.0 4223.0 519.0 1190.0 792.0 532.0 181.0 31.0 4357.0 4382.0 373.0 161.0 467.0 1193.0 1015.0 g 1023.0 1298.0 526.0 193.0 162.0 4389.0 4372.0 27.0 175.0 608.0 1149.0 2822.0 451.0 4191.0 23.0 11.0 36.0 1055.0 2969.0 874.0 984.0 t 1392.0 1098.0 555.0 808.0 4101.0 11.0 16.0 18.0 544.0 2175.0 1388.0 468.0 3083.0 180.0 20.0 15.0 70.0 211.0 428.0 1193.0 1050.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m13_shift0 (dyads_m13dyads_m13)				; dyads_m13 (dyads_m13dyads_m13); m=0 (reference); ncol1=10; shift=0; ncol=21; ssCCTGGChs----------- ; Alignment reference a 2532 1749 0 0 0 0 0 0 3641 2131 0 0 0 0 0 0 0 0 0 0 0 c 3440 3647 13044 13044 0 0 0 13044 4037 3774 0 0 0 0 0 0 0 0 0 0 0 g 3973 4737 0 0 0 13044 13044 0 1482 4139 0 0 0 0 0 0 0 0 0 0 0 t 3099 2911 0 0 13044 0 0 0 3884 3000 0 0 0 0 0 0 0 0 0 0 0
MA0092.1_shift0 (Hand1::Tcf3)				; dyads_m13 versus MA0092.1 (Hand1::Tcf3); m=1/4; ncol2=10; w=10; offset=0; strand=D; shift=0; score=0.705495; srTCTGGmwt----------- ; cor=; Ncor= a 4.0 10.0 2.0 0.0 0.0 0.0 0.0 9.0 16.0 5.0 0 0 0 0 0 0 0 0 0 0 0 c 8.0 0.0 2.0 28.0 0.0 0.0 3.0 14.0 0.0 4.0 0 0 0 0 0 0 0 0 0 0 0 g 10.0 15.0 1.0 0.0 0.0 29.0 25.0 1.0 3.0 4.0 0 0 0 0 0 0 0 0 0 0 0 t 7.0 4.0 24.0 1.0 29.0 0.0 1.0 5.0 10.0 16.0 0 0 0 0 0 0 0 0 0 0 0
MA0161.2_shift0 (NFIC)				; dyads_m13 versus MA0161.2 (NFIC); m=2/4; ncol2=11; w=10; offset=0; strand=D; shift=0; score=0.656432; twCTTGGCAsa---------- ; cor=; Ncor= a 2615.0 3896.0 412.0 154.0 352.0 310.0 223.0 264.0 10158.0 2626.0 3344.0 0 0 0 0 0 0 0 0 0 0 c 2647.0 2137.0 10542.0 303.0 333.0 129.0 121.0 10725.0 397.0 2951.0 2712.0 0 0 0 0 0 0 0 0 0 0 g 2478.0 2086.0 329.0 369.0 177.0 11087.0 10973.0 88.0 478.0 3186.0 2760.0 0 0 0 0 0 0 0 0 0 0 t 3867.0 3488.0 324.0 10781.0 10745.0 81.0 290.0 530.0 574.0 2844.0 2791.0 0 0 0 0 0 0 0 0 0 0
MA0671.1_rc_shift2 (NFIX_rc)				; dyads_m13 versus MA0671.1_rc (NFIX_rc); m=3/4; ncol2=9; w=8; offset=2; strand=R; shift=2; score=0.556267; --byTGGCacs---------- ; cor=; Ncor= a 0 0 6439.0 2399.0 110.0 0.0 29.0 2539.0 32864.0 8043.0 7378.0 0 0 0 0 0 0 0 0 0 0 c 0 0 9135.0 12688.0 180.0 0.0 3257.0 32864.0 5911.0 10855.0 8725.0 0 0 0 0 0 0 0 0 0 0 g 0 0 9039.0 1356.0 2230.0 32864.0 32864.0 186.0 9695.0 6134.0 8810.0 0 0 0 0 0 0 0 0 0 0 t 0 0 8251.0 32864.0 32864.0 0.0 3.0 132.0 11279.0 7832.0 7951.0 0 0 0 0 0 0 0 0 0 0
MA1643.1_shift0 (NFIB)				; dyads_m13 versus MA1643.1 (NFIB); m=4/4; ncol2=21; w=10; offset=0; strand=D; shift=0; score=0.437934; trcCTGGCAykgTGCCAagha ; cor=; Ncor= a 1055.0 1181.0 424.0 273.0 133.0 5.0 16.0 148.0 3178.0 443.0 1087.0 594.0 701.0 14.0 16.0 8.0 3937.0 2989.0 552.0 1156.0 1367.0 c 946.0 839.0 2911.0 3142.0 20.0 11.0 12.0 4223.0 519.0 1190.0 792.0 532.0 181.0 31.0 4357.0 4382.0 373.0 161.0 467.0 1193.0 1015.0 g 1023.0 1298.0 526.0 193.0 162.0 4389.0 4372.0 27.0 175.0 608.0 1149.0 2822.0 451.0 4191.0 23.0 11.0 36.0 1055.0 2969.0 874.0 984.0 t 1392.0 1098.0 555.0 808.0 4101.0 11.0 16.0 18.0 544.0 2175.0 1388.0 468.0 3083.0 180.0 20.0 15.0 70.0 211.0 428.0 1193.0 1050.0