One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m35/peak-motifs_local_words_8nt_m35.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_m35/peak-motifs_local_words_8nt_m35_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m35_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m35_shift0 (local_words_8nt_m35local_words_8nt_m35)
; local_words_8nt_m35 (local_words_8nt_m35local_words_8nt_m35); m=0 (reference); ncol1=24; shift=0; ncol=24; bsarACAGCTGCTGCAGCTGTCms ; Alignment reference a 7 6 21 21 28 1 30 0 0 5 1 0 3 0 2 26 2 0 1 1 1 0 12 7 c 9 14 7 3 0 30 2 3 31 0 1 32 0 2 31 2 0 34 1 3 4 30 10 13 g 9 9 2 10 5 3 0 30 0 1 31 1 1 32 0 1 31 0 1 29 5 3 5 11 t 9 5 4 0 1 0 2 1 3 28 1 1 30 0 1 5 1 0 31 1 24 1 7 3

MA0832.1_shift1 (Tcf21)
; local_words_8nt_m35 versus MA0832.1 (Tcf21); m=1/4; ncol2=14; w=14; offset=1; strand=D; shift=1; score=0.44708; -ryAACAGCTGTTry--------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA1485.1_rc_shift1 (FERD3L_rc)
; local_words_8nt_m35 versus MA1485.1_rc (FERD3L_rc); m=2/4; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.440585; -GTrACAGCTGkyrC--------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA0499.2_shift11 (MYOD1)
; local_words_8nt_m35 versus MA0499.2 (MYOD1); m=3/4; ncol2=13; w=13; offset=11; strand=D; shift=11; score=0.418618; -----------cwgCACCTGTymy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 7175.0 9462.0 4549.0 349.0 32281.0 463.0 534.0 241.0 208.0 402.0 1808.0 9462.0 5687.0 c 0 0 0 0 0 0 0 0 0 0 0 11279.0 7103.0 5622.0 33328.0 583.0 25275.0 32504.0 563.0 386.0 2555.0 19052.0 10485.0 11760.0 g 0 0 0 0 0 0 0 0 0 0 0 8118.0 8444.0 21884.0 354.0 849.0 7336.0 932.0 366.0 33468.0 1699.0 4440.0 6202.0 7495.0 t 0 0 0 0 0 0 0 0 0 0 0 7728.0 9291.0 2245.0 269.0 587.0 1226.0 330.0 33130.0 238.0 29644.0 9000.0 8151.0 9358.0

MA0500.2_rc_shift2 (MYOG_rc)
; local_words_8nt_m35 versus MA0500.2_rc (MYOG_rc); m=4/4; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.406224; --sarCAGCTGyts---------- ; cor=; Ncor= a 0 0 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 c 0 0 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 g 0 0 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 t 0 0 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m35_shift0 (local_words_8nt_m35local_words_8nt_m35)				; local_words_8nt_m35 (local_words_8nt_m35local_words_8nt_m35); m=0 (reference); ncol1=24; shift=0; ncol=24; bsarACAGCTGCTGCAGCTGTCms ; Alignment reference a 7 6 21 21 28 1 30 0 0 5 1 0 3 0 2 26 2 0 1 1 1 0 12 7 c 9 14 7 3 0 30 2 3 31 0 1 32 0 2 31 2 0 34 1 3 4 30 10 13 g 9 9 2 10 5 3 0 30 0 1 31 1 1 32 0 1 31 0 1 29 5 3 5 11 t 9 5 4 0 1 0 2 1 3 28 1 1 30 0 1 5 1 0 31 1 24 1 7 3
MA0832.1_shift1 (Tcf21)				; local_words_8nt_m35 versus MA0832.1 (Tcf21); m=1/4; ncol2=14; w=14; offset=1; strand=D; shift=1; score=0.44708; -ryAACAGCTGTTry--------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA1485.1_rc_shift1 (FERD3L_rc)				; local_words_8nt_m35 versus MA1485.1_rc (FERD3L_rc); m=2/4; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.440585; -GTrACAGCTGkyrC--------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA0499.2_shift11 (MYOD1)				; local_words_8nt_m35 versus MA0499.2 (MYOD1); m=3/4; ncol2=13; w=13; offset=11; strand=D; shift=11; score=0.418618; -----------cwgCACCTGTymy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 7175.0 9462.0 4549.0 349.0 32281.0 463.0 534.0 241.0 208.0 402.0 1808.0 9462.0 5687.0 c 0 0 0 0 0 0 0 0 0 0 0 11279.0 7103.0 5622.0 33328.0 583.0 25275.0 32504.0 563.0 386.0 2555.0 19052.0 10485.0 11760.0 g 0 0 0 0 0 0 0 0 0 0 0 8118.0 8444.0 21884.0 354.0 849.0 7336.0 932.0 366.0 33468.0 1699.0 4440.0 6202.0 7495.0 t 0 0 0 0 0 0 0 0 0 0 0 7728.0 9291.0 2245.0 269.0 587.0 1226.0 330.0 33130.0 238.0 29644.0 9000.0 8151.0 9358.0
MA0500.2_rc_shift2 (MYOG_rc)				; local_words_8nt_m35 versus MA0500.2_rc (MYOG_rc); m=4/4; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.406224; --sarCAGCTGyts---------- ; cor=; Ncor= a 0 0 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 c 0 0 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 g 0 0 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 t 0 0 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