One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m10/peak-motifs_local_words_8nt_m10.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_m10/peak-motifs_local_words_8nt_m10_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m10_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m10_shift0 (local_words_8nt_m10local_words_8nt_m10)
; local_words_8nt_m10 (local_words_8nt_m10local_words_8nt_m10); m=0 (reference); ncol1=24; shift=0; ncol=24; csaCAGCTGCAGCAGCTGTCCcss ; Alignment reference a 13 10 38 1 54 3 3 10 4 1 48 2 0 51 3 1 5 0 0 1 10 5 9 10 c 24 22 8 54 1 0 53 5 2 54 3 0 55 2 3 52 2 1 9 51 39 35 20 16 g 6 19 9 2 1 52 1 1 47 2 1 53 1 0 51 4 3 53 4 5 6 6 17 20 t 14 6 2 0 1 2 0 41 4 0 5 2 1 4 0 0 47 3 44 0 2 11 11 11

MA1485.1_shift8 (FERD3L)
; local_words_8nt_m10 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.446352; --------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

MA0499.2_shift9 (MYOD1)
; local_words_8nt_m10 versus MA0499.2 (MYOD1); m=2/3; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.424813; ---------cwgCACCTGTymy-- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0

MA0500.2_rc_shift0 (MYOG_rc)
; local_words_8nt_m10 versus MA0500.2_rc (MYOG_rc); m=3/3; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.402213; 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m10_shift0 (local_words_8nt_m10local_words_8nt_m10)				; local_words_8nt_m10 (local_words_8nt_m10local_words_8nt_m10); m=0 (reference); ncol1=24; shift=0; ncol=24; csaCAGCTGCAGCAGCTGTCCcss ; Alignment reference a 13 10 38 1 54 3 3 10 4 1 48 2 0 51 3 1 5 0 0 1 10 5 9 10 c 24 22 8 54 1 0 53 5 2 54 3 0 55 2 3 52 2 1 9 51 39 35 20 16 g 6 19 9 2 1 52 1 1 47 2 1 53 1 0 51 4 3 53 4 5 6 6 17 20 t 14 6 2 0 1 2 0 41 4 0 5 2 1 4 0 0 47 3 44 0 2 11 11 11
MA1485.1_shift8 (FERD3L)				; local_words_8nt_m10 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.446352; --------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
MA0499.2_shift9 (MYOD1)				; local_words_8nt_m10 versus MA0499.2 (MYOD1); m=2/3; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.424813; ---------cwgCACCTGTymy-- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0
MA0500.2_rc_shift0 (MYOG_rc)				; local_words_8nt_m10 versus MA0500.2_rc (MYOG_rc); m=3/3; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.402213; 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