One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m16/peak-motifs_local_words_8nt_m16.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_m16/peak-motifs_local_words_8nt_m16_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m16_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m16_shift0 (local_words_8nt_m16local_words_8nt_m16)
; local_words_8nt_m16 (local_words_8nt_m16local_words_8nt_m16); m=0 (reference); ncol1=24; shift=0; ncol=24; vscaGACAGCTGCTGCAGCTGTsd ; Alignment reference a 15 7 11 31 2 45 4 53 0 0 8 1 0 6 2 1 48 1 1 1 1 1 11 18 c 17 23 34 9 4 4 54 3 3 53 1 0 54 1 5 53 2 1 52 2 4 8 24 10 g 17 18 8 10 53 7 1 0 54 3 2 56 2 2 50 4 4 55 2 1 52 4 18 16 t 10 11 6 9 0 3 0 3 2 3 48 2 3 50 2 1 5 2 4 55 2 46 6 15

MA0499.2_rc_shift2 (MYOD1_rc)
; local_words_8nt_m16 versus MA0499.2_rc (MYOD1_rc); m=1/3; ncol2=13; w=13; offset=2; strand=R; shift=2; score=0.425256; --rkrACAGGTGcwg--------- ; cor=; Ncor= a 0 0 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 0 0 0 0 0 0 0 0 0 c 0 0 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 0 0 0 0 0 0 0 0 0 g 0 0 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 0 0 0 0 0 0 0 0 0 t 0 0 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0 0 0 0 0 0 0 0 0 0

MA1485.1_rc_shift2 (FERD3L_rc)
; local_words_8nt_m16 versus MA1485.1_rc (FERD3L_rc); m=2/3; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.41507; --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

MA0500.2_shift12 (MYOG)
; local_words_8nt_m16 versus MA0500.2 (MYOG); m=3/3; ncol2=12; w=12; offset=12; strand=D; shift=12; score=0.406715; ------------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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m16_shift0 (local_words_8nt_m16local_words_8nt_m16)				; local_words_8nt_m16 (local_words_8nt_m16local_words_8nt_m16); m=0 (reference); ncol1=24; shift=0; ncol=24; vscaGACAGCTGCTGCAGCTGTsd ; Alignment reference a 15 7 11 31 2 45 4 53 0 0 8 1 0 6 2 1 48 1 1 1 1 1 11 18 c 17 23 34 9 4 4 54 3 3 53 1 0 54 1 5 53 2 1 52 2 4 8 24 10 g 17 18 8 10 53 7 1 0 54 3 2 56 2 2 50 4 4 55 2 1 52 4 18 16 t 10 11 6 9 0 3 0 3 2 3 48 2 3 50 2 1 5 2 4 55 2 46 6 15
MA0499.2_rc_shift2 (MYOD1_rc)				; local_words_8nt_m16 versus MA0499.2_rc (MYOD1_rc); m=1/3; ncol2=13; w=13; offset=2; strand=R; shift=2; score=0.425256; --rkrACAGGTGcwg--------- ; cor=; Ncor= a 0 0 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 0 0 0 0 0 0 0 0 0 c 0 0 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 0 0 0 0 0 0 0 0 0 g 0 0 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 0 0 0 0 0 0 0 0 0 t 0 0 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0 0 0 0 0 0 0 0 0 0
MA1485.1_rc_shift2 (FERD3L_rc)				; local_words_8nt_m16 versus MA1485.1_rc (FERD3L_rc); m=2/3; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.41507; --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
MA0500.2_shift12 (MYOG)				; local_words_8nt_m16 versus MA0500.2 (MYOG); m=3/3; ncol2=12; w=12; offset=12; strand=D; shift=12; score=0.406715; ------------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