One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.174600_2025-05-16.174600_au3zWU/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2025/05/16/peak-motifs.2025-05-16.174600_2025-05-16.174600_au3zWU/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --mtCCCAGCAas ; Alignment reference a 0 0 17 8 5 1 0 40 1 0 44 19 8 c 0 0 13 8 40 40 41 2 1 41 0 8 12 g 0 0 8 7 0 1 0 1 41 2 0 8 17 t 0 0 7 22 0 3 4 2 2 2 1 10 8

MA2125.1_shift2 (Zfp809)
; oligos_7nt_mkv2_m1 versus MA2125.1 (Zfp809); m=1/8; ncol2=9; w=0; offset=0; strand=D; shift=2; score=0.661382; --wTCCCAGCc-- ; cor=; Ncor= a 0 0 828.0 23.0 15.0 20.0 10.0 1529.0 32.0 287.0 217.0 0 0 c 0 0 66.0 41.0 1607.0 1610.0 1621.0 26.0 35.0 1218.0 1091.0 0 0 g 0 0 81.0 23.0 18.0 14.0 16.0 73.0 1572.0 99.0 115.0 0 0 t 0 0 690.0 1578.0 25.0 21.0 18.0 37.0 26.0 61.0 242.0 0 0

MA1724.2_shift4 (Rfx6)
; oligos_7nt_mkv2_m1 versus MA1724.2 (Rfx6); m=2/8; ncol2=9; w=0; offset=2; strand=D; shift=4; score=0.639745; ----CCTAGCAAC ; cor=; Ncor= a 0 0 0 0 187.0 1093.0 344.0 7215.0 179.0 378.0 8085.0 7740.0 552.0 c 0 0 0 0 7859.0 6405.0 1066.0 64.0 102.0 7474.0 117.0 258.0 6811.0 g 0 0 0 0 232.0 242.0 146.0 1205.0 8215.0 359.0 132.0 339.0 552.0 t 0 0 0 0 272.0 810.0 6994.0 66.0 54.0 339.0 216.0 213.0 635.0

MA1629.2_shift4 (Zic2)
; oligos_7nt_mkv2_m1 versus MA1629.2 (Zic2); m=3/8; ncol2=9; w=0; offset=2; strand=D; shift=4; score=0.628515; ----CaCAGCAGG ; cor=; Ncor= a 0 0 0 0 1161.0 6888.0 135.0 11074.0 140.0 80.0 10625.0 192.0 96.0 c 0 0 0 0 9933.0 1765.0 11476.0 391.0 228.0 11272.0 118.0 133.0 204.0 g 0 0 0 0 585.0 829.0 188.0 186.0 11484.0 269.0 735.0 11184.0 11465.0 t 0 0 0 0 240.0 2437.0 120.0 268.0 67.0 298.0 441.0 410.0 154.0

MA0697.3_shift6 (Zic3)
; oligos_7nt_mkv2_m1 versus MA0697.3 (Zic3); m=4/8; ncol2=7; w=0; offset=4; strand=D; shift=6; score=0.537437; ------CAGCAGG ; cor=; Ncor= a 0 0 0 0 0 0 345.0 23947.0 331.0 354.0 22980.0 393.0 347.0 c 0 0 0 0 0 0 25035.0 872.0 670.0 24272.0 568.0 500.0 955.0 g 0 0 0 0 0 0 460.0 759.0 24907.0 756.0 1768.0 24314.0 24340.0 t 0 0 0 0 0 0 334.0 596.0 266.0 792.0 858.0 967.0 532.0

MA1628.2_shift6 (Zic1::Zic2)
; oligos_7nt_mkv2_m1 versus MA1628.2 (Zic1::Zic2); m=5/8; ncol2=7; w=0; offset=4; strand=D; shift=6; score=0.535437; ------CAGCAGG ; cor=; Ncor= a 0 0 0 0 0 0 29.0 9238.0 96.0 75.0 8950.0 11.0 46.0 c 0 0 0 0 0 0 9594.0 384.0 195.0 9293.0 311.0 512.0 91.0 g 0 0 0 0 0 0 106.0 266.0 9527.0 96.0 627.0 9279.0 9631.0 t 0 0 0 0 0 0 163.0 4.0 74.0 428.0 4.0 90.0 124.0

MA2341.1_shift4 (FEZF2)
; oligos_7nt_mkv2_m1 versus MA2341.1 (FEZF2); m=6/8; ncol2=8; w=0; offset=2; strand=D; shift=4; score=0.512765; ----CCCAGCCT- ; cor=; Ncor= a 0 0 0 0 17.0 5.0 4.0 231.0 6.0 8.0 7.0 14.0 0 c 0 0 0 0 202.0 206.0 258.0 15.0 8.0 224.0 247.0 10.0 0 g 0 0 0 0 10.0 9.0 0.0 14.0 251.0 28.0 2.0 8.0 0 t 0 0 0 0 36.0 45.0 3.0 5.0 0.0 5.0 9.0 233.0 0

MA1116.2_rc_shift2 (RBPJ_rc)
; oligos_7nt_mkv2_m1 versus MA1116.2_rc (RBPJ_rc); m=7/8; ncol2=6; w=0; offset=0; strand=R; shift=2; score=0.454872; --TTCCCA----- ; cor=; Ncor= a 0 0 4.0 29.0 78.0 60.0 1.0 2386.0 0 0 0 0 0 c 0 0 1.0 4.0 2309.0 2313.0 2341.0 2.0 0 0 0 0 0 g 0 0 15.0 0.0 8.0 20.0 25.0 12.0 0 0 0 0 0 t 0 0 2382.0 2369.0 7.0 9.0 35.0 2.0 0 0 0 0 0

MA0483.2_shift0 (Gfi1B)
; oligos_7nt_mkv2_m1 versus MA0483.2 (Gfi1B); m=8/8; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.431551; aAATCwCwGC--- ; cor=; Ncor= a 1124.0 1761.0 1759.0 0.0 0.0 1033.0 61.0 1116.0 57.0 142.0 0 0 0 c 438.0 0.0 0.0 338.0 1761.0 21.0 1312.0 0.0 1.0 1328.0 0 0 0 g 104.0 0.0 2.0 28.0 0.0 0.0 388.0 1.0 1676.0 76.0 0 0 0 t 95.0 0.0 0.0 1395.0 0.0 707.0 0.0 644.0 27.0 215.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --mtCCCAGCAas ; Alignment reference a 0 0 17 8 5 1 0 40 1 0 44 19 8 c 0 0 13 8 40 40 41 2 1 41 0 8 12 g 0 0 8 7 0 1 0 1 41 2 0 8 17 t 0 0 7 22 0 3 4 2 2 2 1 10 8
MA2125.1_shift2 (Zfp809)				; oligos_7nt_mkv2_m1 versus MA2125.1 (Zfp809); m=1/8; ncol2=9; w=0; offset=0; strand=D; shift=2; score=0.661382; --wTCCCAGCc-- ; cor=; Ncor= a 0 0 828.0 23.0 15.0 20.0 10.0 1529.0 32.0 287.0 217.0 0 0 c 0 0 66.0 41.0 1607.0 1610.0 1621.0 26.0 35.0 1218.0 1091.0 0 0 g 0 0 81.0 23.0 18.0 14.0 16.0 73.0 1572.0 99.0 115.0 0 0 t 0 0 690.0 1578.0 25.0 21.0 18.0 37.0 26.0 61.0 242.0 0 0
MA1724.2_shift4 (Rfx6)				; oligos_7nt_mkv2_m1 versus MA1724.2 (Rfx6); m=2/8; ncol2=9; w=0; offset=2; strand=D; shift=4; score=0.639745; ----CCTAGCAAC ; cor=; Ncor= a 0 0 0 0 187.0 1093.0 344.0 7215.0 179.0 378.0 8085.0 7740.0 552.0 c 0 0 0 0 7859.0 6405.0 1066.0 64.0 102.0 7474.0 117.0 258.0 6811.0 g 0 0 0 0 232.0 242.0 146.0 1205.0 8215.0 359.0 132.0 339.0 552.0 t 0 0 0 0 272.0 810.0 6994.0 66.0 54.0 339.0 216.0 213.0 635.0
MA1629.2_shift4 (Zic2)				; oligos_7nt_mkv2_m1 versus MA1629.2 (Zic2); m=3/8; ncol2=9; w=0; offset=2; strand=D; shift=4; score=0.628515; ----CaCAGCAGG ; cor=; Ncor= a 0 0 0 0 1161.0 6888.0 135.0 11074.0 140.0 80.0 10625.0 192.0 96.0 c 0 0 0 0 9933.0 1765.0 11476.0 391.0 228.0 11272.0 118.0 133.0 204.0 g 0 0 0 0 585.0 829.0 188.0 186.0 11484.0 269.0 735.0 11184.0 11465.0 t 0 0 0 0 240.0 2437.0 120.0 268.0 67.0 298.0 441.0 410.0 154.0
MA0697.3_shift6 (Zic3)				; oligos_7nt_mkv2_m1 versus MA0697.3 (Zic3); m=4/8; ncol2=7; w=0; offset=4; strand=D; shift=6; score=0.537437; ------CAGCAGG ; cor=; Ncor= a 0 0 0 0 0 0 345.0 23947.0 331.0 354.0 22980.0 393.0 347.0 c 0 0 0 0 0 0 25035.0 872.0 670.0 24272.0 568.0 500.0 955.0 g 0 0 0 0 0 0 460.0 759.0 24907.0 756.0 1768.0 24314.0 24340.0 t 0 0 0 0 0 0 334.0 596.0 266.0 792.0 858.0 967.0 532.0
MA1628.2_shift6 (Zic1::Zic2)				; oligos_7nt_mkv2_m1 versus MA1628.2 (Zic1::Zic2); m=5/8; ncol2=7; w=0; offset=4; strand=D; shift=6; score=0.535437; ------CAGCAGG ; cor=; Ncor= a 0 0 0 0 0 0 29.0 9238.0 96.0 75.0 8950.0 11.0 46.0 c 0 0 0 0 0 0 9594.0 384.0 195.0 9293.0 311.0 512.0 91.0 g 0 0 0 0 0 0 106.0 266.0 9527.0 96.0 627.0 9279.0 9631.0 t 0 0 0 0 0 0 163.0 4.0 74.0 428.0 4.0 90.0 124.0
MA2341.1_shift4 (FEZF2)				; oligos_7nt_mkv2_m1 versus MA2341.1 (FEZF2); m=6/8; ncol2=8; w=0; offset=2; strand=D; shift=4; score=0.512765; ----CCCAGCCT- ; cor=; Ncor= a 0 0 0 0 17.0 5.0 4.0 231.0 6.0 8.0 7.0 14.0 0 c 0 0 0 0 202.0 206.0 258.0 15.0 8.0 224.0 247.0 10.0 0 g 0 0 0 0 10.0 9.0 0.0 14.0 251.0 28.0 2.0 8.0 0 t 0 0 0 0 36.0 45.0 3.0 5.0 0.0 5.0 9.0 233.0 0
MA1116.2_rc_shift2 (RBPJ_rc)				; oligos_7nt_mkv2_m1 versus MA1116.2_rc (RBPJ_rc); m=7/8; ncol2=6; w=0; offset=0; strand=R; shift=2; score=0.454872; --TTCCCA----- ; cor=; Ncor= a 0 0 4.0 29.0 78.0 60.0 1.0 2386.0 0 0 0 0 0 c 0 0 1.0 4.0 2309.0 2313.0 2341.0 2.0 0 0 0 0 0 g 0 0 15.0 0.0 8.0 20.0 25.0 12.0 0 0 0 0 0 t 0 0 2382.0 2369.0 7.0 9.0 35.0 2.0 0 0 0 0 0
MA0483.2_shift0 (Gfi1B)				; oligos_7nt_mkv2_m1 versus MA0483.2 (Gfi1B); m=8/8; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.431551; aAATCwCwGC--- ; cor=; Ncor= a 1124.0 1761.0 1759.0 0.0 0.0 1033.0 61.0 1116.0 57.0 142.0 0 0 0 c 438.0 0.0 0.0 338.0 1761.0 21.0 1312.0 0.0 1.0 1328.0 0 0 0 g 104.0 0.0 2.0 28.0 0.0 0.0 388.0 1.0 1676.0 76.0 0 0 0 t 95.0 0.0 0.0 1395.0 0.0 707.0 0.0 644.0 27.0 215.0 0 0 0