One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4.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 $RSAT/public_html/tmp/www-data/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/results/discovered_motifs/positions_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; rywywyaTgcAwATGCATATgcay ; Alignment reference a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258

MA0507.1_rc_shift10 (POU2F2_rc)
; positions_6nt_m4 versus MA0507.1_rc (POU2F2_rc); m=1/3; ncol2=13; w=13; offset=10; strand=R; shift=10; score=0.470354; ----------wyATGCAAATkmr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1225.0 476.0 2285.0 0.0 16.0 132.0 2287.0 2029.0 2287.0 251.0 442.0 898.0 835.0 0 c 0 0 0 0 0 0 0 0 0 0 107.0 613.0 0.0 0.0 0.0 1997.0 0.0 0.0 0.0 1.0 415.0 593.0 402.0 0 g 0 0 0 0 0 0 0 0 0 0 361.0 39.0 2.0 30.0 2271.0 0.0 0.0 2.0 0.0 19.0 825.0 266.0 635.0 0 t 0 0 0 0 0 0 0 0 0 0 594.0 1159.0 0.0 2257.0 0.0 158.0 0.0 256.0 0.0 2016.0 605.0 530.0 415.0 0

MA0142.1_shift5 (Pou5f1::Sox2)
; positions_6nt_m4 versus MA0142.1 (Pou5f1::Sox2); m=2/3; ncol2=15; w=15; offset=5; strand=D; shift=5; score=0.464113; -----ywTTswyATGCAaAt---- ; cor=; Ncor= a 0 0 0 0 0 63.0 579.0 11.0 47.0 118.0 415.0 206.0 1235.0 17.0 10.0 14.0 1050.0 887.0 1200.0 198.0 0 0 0 0 c 0 0 0 0 0 846.0 58.0 50.0 12.0 363.0 18.0 365.0 30.0 5.0 16.0 1029.0 16.0 68.0 33.0 119.0 0 0 0 0 g 0 0 0 0 0 66.0 28.0 36.0 79.0 825.0 29.0 186.0 24.0 15.0 1239.0 129.0 30.0 315.0 75.0 207.0 0 0 0 0 t 0 0 0 0 0 389.0 701.0 1270.0 1231.0 63.0 907.0 612.0 80.0 1332.0 104.0 196.0 269.0 92.0 53.0 837.0 0 0 0 0

MA0627.2_shift9 (POU2F3)
; positions_6nt_m4 versus MA0627.2 (POU2F3); m=3/3; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.442804; ---------watATGCAAATww-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 17399.0 26660.0 8522.0 54550.0 1090.0 980.0 946.0 54915.0 51382.0 55302.0 5115.0 16288.0 18907.0 0 0 c 0 0 0 0 0 0 0 0 0 11383.0 6824.0 6885.0 194.0 322.0 251.0 50288.0 80.0 567.0 164.0 3478.0 10595.0 11936.0 0 0 g 0 0 0 0 0 0 0 0 0 10722.0 8770.0 3029.0 354.0 1251.0 51971.0 1079.0 138.0 804.0 233.0 4098.0 13237.0 7941.0 0 0 t 0 0 0 0 0 0 0 0 0 16525.0 13775.0 37593.0 931.0 53366.0 2827.0 3716.0 896.0 3276.0 330.0 43338.0 15909.0 17245.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; rywywyaTgcAwATGCATATgcay ; Alignment reference a 218 144 208 145 193 105 459 61 122 88 542 245 539 11 41 42 682 117 597 88 137 149 349 159 c 165 208 158 209 141 349 85 107 56 440 50 132 57 49 9 646 13 70 24 90 80 370 105 197 g 208 160 183 168 187 99 110 58 390 86 72 50 79 13 669 24 41 51 89 60 419 74 181 140 t 163 242 205 232 233 201 100 528 186 140 90 327 79 681 35 42 18 516 44 516 118 161 119 258
MA0507.1_rc_shift10 (POU2F2_rc)				; positions_6nt_m4 versus MA0507.1_rc (POU2F2_rc); m=1/3; ncol2=13; w=13; offset=10; strand=R; shift=10; score=0.470354; ----------wyATGCAAATkmr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1225.0 476.0 2285.0 0.0 16.0 132.0 2287.0 2029.0 2287.0 251.0 442.0 898.0 835.0 0 c 0 0 0 0 0 0 0 0 0 0 107.0 613.0 0.0 0.0 0.0 1997.0 0.0 0.0 0.0 1.0 415.0 593.0 402.0 0 g 0 0 0 0 0 0 0 0 0 0 361.0 39.0 2.0 30.0 2271.0 0.0 0.0 2.0 0.0 19.0 825.0 266.0 635.0 0 t 0 0 0 0 0 0 0 0 0 0 594.0 1159.0 0.0 2257.0 0.0 158.0 0.0 256.0 0.0 2016.0 605.0 530.0 415.0 0
MA0142.1_shift5 (Pou5f1::Sox2)				; positions_6nt_m4 versus MA0142.1 (Pou5f1::Sox2); m=2/3; ncol2=15; w=15; offset=5; strand=D; shift=5; score=0.464113; -----ywTTswyATGCAaAt---- ; cor=; Ncor= a 0 0 0 0 0 63.0 579.0 11.0 47.0 118.0 415.0 206.0 1235.0 17.0 10.0 14.0 1050.0 887.0 1200.0 198.0 0 0 0 0 c 0 0 0 0 0 846.0 58.0 50.0 12.0 363.0 18.0 365.0 30.0 5.0 16.0 1029.0 16.0 68.0 33.0 119.0 0 0 0 0 g 0 0 0 0 0 66.0 28.0 36.0 79.0 825.0 29.0 186.0 24.0 15.0 1239.0 129.0 30.0 315.0 75.0 207.0 0 0 0 0 t 0 0 0 0 0 389.0 701.0 1270.0 1231.0 63.0 907.0 612.0 80.0 1332.0 104.0 196.0 269.0 92.0 53.0 837.0 0 0 0 0
MA0627.2_shift9 (POU2F3)				; positions_6nt_m4 versus MA0627.2 (POU2F3); m=3/3; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.442804; ---------watATGCAAATww-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 17399.0 26660.0 8522.0 54550.0 1090.0 980.0 946.0 54915.0 51382.0 55302.0 5115.0 16288.0 18907.0 0 0 c 0 0 0 0 0 0 0 0 0 11383.0 6824.0 6885.0 194.0 322.0 251.0 50288.0 80.0 567.0 164.0 3478.0 10595.0 11936.0 0 0 g 0 0 0 0 0 0 0 0 0 10722.0 8770.0 3029.0 354.0 1251.0 51971.0 1079.0 138.0 804.0 233.0 4098.0 13237.0 7941.0 0 0 t 0 0 0 0 0 0 0 0 0 16525.0 13775.0 37593.0 931.0 53366.0 2827.0 3716.0 896.0 3276.0 330.0 43338.0 15909.0 17245.0 0 0