One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/cisBP2/cisBP_Caenorhabditis_elegans_2019.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/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/results/discovered_vs_db/peak-motifs_motifs_vs_db_cisBP_Caenorhabditis_elegans.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --hwATACTAaw ; Alignment reference a 0 0 24 37 76 0 76 0 0 76 44 38 c 0 0 21 11 0 0 0 76 0 0 6 1 g 0 0 3 4 0 0 0 0 0 0 12 9 t 0 0 28 24 0 76 0 0 76 0 14 28

M00651_2.00_rc_shift2 (mex-6_rc)
; oligos_6nt_mkv2_m1 versus M00651_2.00_rc (mex-6_rc); m=1/11; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.742289; --waATAATAAr ; cor=; Ncor= a 0 0 29.2863 66.3373 79.0552 17.5069 99.9633 99.9633 12.0422 99.9633 76.2969 39.2485 c 0 0 20.5145 8.16601 12.1974 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 4.49775 16.8462 g 0 0 20.5145 8.16601 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 14.7076 27.0591 t 0 0 29.6848 17.3306 8.73512 82.4686 0.0122303 0.0122303 87.9333 0.0122303 4.49775 16.8462

M02210_2.00_shift2 (ceh-9,mls-2)
; oligos_6nt_mkv2_m1 versus M02210_2.00 (ceh-9,mls-2); m=2/11; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.70568; --rrvTACTtaa ; cor=; Ncor= a 0 0 37.1512 37.7943 27.6907 0.0797675 83.0278 0.000257885 16.5124 16.5252 65.3553 47.008 c 0 0 19.0106 20.129 30.9105 14.1733 0.00659908 78.8071 5.6639 11.9998 4.22002 11.9451 g 0 0 26.9773 31.5685 41.3097 0.00331719 14.7195 21.0522 0.0258386 5.12887 21.7549 19.4981 t 0 0 16.8609 10.5082 0.0890193 85.7436 2.24606 0.140437 77.7978 66.3462 8.66974 21.5488

M00669_2.00_shift1 (med-1,med-2)
; oligos_6nt_mkv2_m1 versus M00669_2.00 (med-1,med-2); m=3/11; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.585037; -tGkATACyhy- ; cor=; Ncor= a 0 22.8085 16.6426 4.0068 85.4876 4.36638 93.3654 5.60155 10.6833 26.1435 23.8028 0 c 0 24.9564 5.32262 4.65524 2.55581 12.7297 1.51668 79.2845 28.1819 25.8834 25.2747 0 g 0 22.3568 71.6624 34.0556 5.14678 1.13194 0.279856 4.27611 8.74673 19.3676 16.1159 0 t 0 29.8783 6.37234 57.2824 6.80985 81.772 4.83809 10.8378 52.3881 28.6055 34.8065 0

M00367_2.00_rc_shift0 (nhr-23,nhr-41,nhr-91_rc)
; oligos_6nt_mkv2_m1 versus M00367_2.00_rc (nhr-23,nhr-41,nhr-91_rc); m=4/11; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.546661; tkwtATAAtAws ; cor=; Ncor= a 22.5715 20.2323 39.2195 24.5374 73.073 0.0270709 99.9188 80.4586 21.9158 76.0942 25.5241 19.8486 c 22.5715 20.2323 10.4805 16.4668 2.43408 9.94694 0.0270709 10.1305 2.4556 14.3162 14.5466 30.8261 g 22.5715 29.9464 20.1946 5.17847 12.5375 0.0270709 0.0270709 0.0270709 13.4331 4.7948 14.5466 29.4767 t 32.2856 29.5891 30.1053 53.8173 11.9555 89.9989 0.0270709 9.38387 62.1955 4.7948 45.3828 19.8486

M00169_2.00_shift2 (ceh-32)
; oligos_6nt_mkv2_m1 versus M00169_2.00 (ceh-32); m=5/11; ncol2=7; w=0; offset=0; strand=D; shift=2; score=0.506474; --tgAtmyc--- ; cor=; Ncor= a 0 0 18.9564 17.1082 73.6823 11.9808 54.4071 13.072 20.5555 0 0 0 c 0 0 24.8322 16.4374 17.2837 19.3619 33.6662 45.6257 33.5531 0 0 0 g 0 0 16.4799 43.3608 0.011218 3.075 0.0272281 14.4468 22.9457 0 0 0 t 0 0 39.7314 23.0936 9.02287 65.5823 11.8995 26.8555 22.9457 0 0 0

M00056_2.00_shift5 (alr-1,ceh-10,ceh-16,ceh-17,ceh-8,unc-4,unc-42,vab-15)
; oligos_6nt_mkv2_m1 versus M00056_2.00 (alr-1,ceh-10,ceh-16,ceh-17,ceh-8,unc-4,unc-42,vab-15); m=6/11; ncol2=8; w=0; offset=3; strand=D; shift=5; score=0.462147; -----TAATAwa ; cor=; Ncor= a 0 0 0 0 0 7.09225 86.6502 87.326 0.00620964 75.1428 63.5123 66.9102 c 0 0 0 0 0 7.09225 1.33964 1.27183 0.00620964 3.11103 5.03647 6.15964 g 0 0 0 0 0 0.795025 1.33964 1.90458 0.00620964 1.8691 0.63506 3.08367 t 0 0 0 0 0 85.0205 10.6705 9.4976 99.9814 19.877 30.8161 23.8465

M06497_2.00_shift2 (ceh-33,unc-39)
; oligos_6nt_mkv2_m1 versus M06497_2.00 (ceh-33,unc-39); m=7/11; ncol2=6; w=0; offset=0; strand=D; shift=2; score=0.444614; --TGATAC---- ; cor=; Ncor= a 0 0 0 0 100 0 100 0 0 0 0 0 c 0 0 0 0 0 0 0 76.9231 0 0 0 0 g 0 0 3.7037 100 0 3.7037 0 0 0 0 0 0 t 0 0 96.2963 0 0 96.2963 0 23.0769 0 0 0 0

M00483_2.00_shift1 (ceh-32)
; oligos_6nt_mkv2_m1 versus M00483_2.00 (ceh-32); m=8/11; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.444235; -gtgAtmy---- ; cor=; Ncor= a 0 24.7356 18.7686 20.6531 81.8609 12.6658 53.9508 14.6793 0 0 0 0 c 0 24.2458 24.5862 14.554 11.19 17.097 33.7193 41.9484 0 0 0 0 g 0 26.5291 20.3318 43.7226 3.37036 9.96323 4.34086 17.9294 0 0 0 0 t 0 24.4895 36.3134 21.0703 3.57878 60.274 7.98905 25.443 0 0 0 0

M02745_2.00_shift5 (mef-2)
; oligos_6nt_mkv2_m1 versus M02745_2.00 (mef-2); m=9/11; ncol2=12; w=0; offset=3; strand=D; shift=5; score=0.429554; -----TaCTAwA ; cor=; Ncor= a 0 0 0 0 0 2.00391 61.8663 0.100301 0.100301 99.5994 62.6062 97.5478 c 0 0 0 0 0 0.342131 0.870918 99.7492 0.0501505 0.0500751 0.125905 0 g 0 0 0 0 0 0.439883 12.4106 0.100301 0.100301 0.2003 0.283286 0.147131 t 0 0 0 0 0 97.2141 24.8523 0.0501505 99.7492 0.150225 36.9846 2.30505

M00326_2.00_shift1 (ceh-32)
; oligos_6nt_mkv2_m1 versus M00326_2.00 (ceh-32); m=10/11; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.428616; -dtgATmy---- ; cor=; Ncor= a 0 27.3376 16.6014 15.991 91.3679 4.59768 64.8564 7.762 0 0 0 0 c 0 19.8512 21.1045 7.11373 3.11084 13.2706 29.1419 45.1161 0 0 0 0 g 0 27.0656 15.325 61.6841 5.39188 6.52442 1.97818 16.2687 0 0 0 0 t 0 25.7456 46.969 15.2111 0.129367 75.6073 4.02359 30.8532 0 0 0 0

M06329_2.00_shift5 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15)
; oligos_6nt_mkv2_m1 versus M06329_2.00 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15); m=11/11; ncol2=9; w=0; offset=3; strand=D; shift=5; score=0.413423; -----yryTAAT ; cor=; Ncor= a 0 0 0 0 0 4.7619 42.8571 0 0 100 100 0 c 0 0 0 0 0 42.8571 19.0476 57.1429 0 0 0 0 g 0 0 0 0 0 9.52381 28.5714 0 0 0 0 4.7619 t 0 0 0 0 0 42.8571 9.52381 42.8571 100 0 0 95.2381

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wAATACTAAwa ; Alignment reference a 48 118 138 2 162 0 16 169 141 73 86 c 37 17 0 0 0 173 2 2 6 6 35 g 3 6 5 27 0 0 0 2 12 9 25 t 85 32 30 144 11 0 155 0 14 85 27

M00651_2.00_rc_shift0 (mex-6_rc)
; oligos_7nt_mkv2_m1 versus M00651_2.00_rc (mex-6_rc); m=1/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.667066; waATAATAAr- ; cor=; Ncor= a 29.2863 66.3373 79.0552 17.5069 99.9633 99.9633 12.0422 99.9633 76.2969 39.2485 0 c 20.5145 8.16601 12.1974 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 4.49775 16.8462 0 g 20.5145 8.16601 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 14.7076 27.0591 0 t 29.6848 17.3306 8.73512 82.4686 0.0122303 0.0122303 87.9333 0.0122303 4.49775 16.8462 0

M06329_2.00_shift3 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15)
; oligos_7nt_mkv2_m1 versus M06329_2.00 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15); m=2/5; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.477299; ---yryTAATk ; cor=; Ncor= a 0 0 0 4.7619 42.8571 0 0 100 100 0 0 c 0 0 0 42.8571 19.0476 57.1429 0 0 0 0 0 g 0 0 0 9.52381 28.5714 0 0 0 0 4.7619 38.0952 t 0 0 0 42.8571 9.52381 42.8571 100 0 0 95.2381 61.9048

M02745_2.00_shift3 (mef-2)
; oligos_7nt_mkv2_m1 versus M02745_2.00 (mef-2); m=3/5; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.464342; ---TaCTAwAA ; cor=; Ncor= a 0 0 0 2.00391 61.8663 0.100301 0.100301 99.5994 62.6062 97.5478 96.6942 c 0 0 0 0.342131 0.870918 99.7492 0.0501505 0.0500751 0.125905 0 0.194458 g 0 0 0 0.439883 12.4106 0.100301 0.100301 0.2003 0.283286 0.147131 0.0486145 t 0 0 0 97.2141 24.8523 0.0501505 99.7492 0.150225 36.9846 2.30505 3.06271

M00282_2.00_rc_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc)
; oligos_7nt_mkv2_m1 versus M00282_2.00_rc (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc); m=4/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.425346; ----acYAATT ; cor=; Ncor= a 0 0 0 0 57.8256 10.7347 0.0285388 99.919 99.919 0.0269978 0.0269978 c 0 0 0 0 10.5567 64.2297 25.7135 0.0269978 0.0269978 0.0269978 2.72678 g 0 0 0 0 21.0609 10.7347 0.0285388 0.0269978 0.0269978 0.0269978 0.0269978 t 0 0 0 0 10.5567 14.301 74.2295 0.0269978 0.0269978 99.919 97.2192

M06350_2.00_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15)
; oligos_7nt_mkv2_m1 versus M06350_2.00 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15); m=5/5; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.410441; ----ayTAATT ; cor=; Ncor= a 0 0 0 0 55 10 0 90 100 0 0 c 0 0 0 0 10 45 0 0 0 0 0 g 0 0 0 0 20 15 0 0 0 0 5 t 0 0 0 0 15 30 100 10 0 100 95

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --hwATACTAaw ; Alignment reference a 0 0 24 37 76 0 76 0 0 76 44 38 c 0 0 21 11 0 0 0 76 0 0 6 1 g 0 0 3 4 0 0 0 0 0 0 12 9 t 0 0 28 24 0 76 0 0 76 0 14 28
M00651_2.00_rc_shift2 (mex-6_rc)				; oligos_6nt_mkv2_m1 versus M00651_2.00_rc (mex-6_rc); m=1/11; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.742289; --waATAATAAr ; cor=; Ncor= a 0 0 29.2863 66.3373 79.0552 17.5069 99.9633 99.9633 12.0422 99.9633 76.2969 39.2485 c 0 0 20.5145 8.16601 12.1974 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 4.49775 16.8462 g 0 0 20.5145 8.16601 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 14.7076 27.0591 t 0 0 29.6848 17.3306 8.73512 82.4686 0.0122303 0.0122303 87.9333 0.0122303 4.49775 16.8462
M02210_2.00_shift2 (ceh-9,mls-2)				; oligos_6nt_mkv2_m1 versus M02210_2.00 (ceh-9,mls-2); m=2/11; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.70568; --rrvTACTtaa ; cor=; Ncor= a 0 0 37.1512 37.7943 27.6907 0.0797675 83.0278 0.000257885 16.5124 16.5252 65.3553 47.008 c 0 0 19.0106 20.129 30.9105 14.1733 0.00659908 78.8071 5.6639 11.9998 4.22002 11.9451 g 0 0 26.9773 31.5685 41.3097 0.00331719 14.7195 21.0522 0.0258386 5.12887 21.7549 19.4981 t 0 0 16.8609 10.5082 0.0890193 85.7436 2.24606 0.140437 77.7978 66.3462 8.66974 21.5488
M00669_2.00_shift1 (med-1,med-2)				; oligos_6nt_mkv2_m1 versus M00669_2.00 (med-1,med-2); m=3/11; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.585037; -tGkATACyhy- ; cor=; Ncor= a 0 22.8085 16.6426 4.0068 85.4876 4.36638 93.3654 5.60155 10.6833 26.1435 23.8028 0 c 0 24.9564 5.32262 4.65524 2.55581 12.7297 1.51668 79.2845 28.1819 25.8834 25.2747 0 g 0 22.3568 71.6624 34.0556 5.14678 1.13194 0.279856 4.27611 8.74673 19.3676 16.1159 0 t 0 29.8783 6.37234 57.2824 6.80985 81.772 4.83809 10.8378 52.3881 28.6055 34.8065 0
M00367_2.00_rc_shift0 (nhr-23,nhr-41,nhr-91_rc)				; oligos_6nt_mkv2_m1 versus M00367_2.00_rc (nhr-23,nhr-41,nhr-91_rc); m=4/11; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.546661; tkwtATAAtAws ; cor=; Ncor= a 22.5715 20.2323 39.2195 24.5374 73.073 0.0270709 99.9188 80.4586 21.9158 76.0942 25.5241 19.8486 c 22.5715 20.2323 10.4805 16.4668 2.43408 9.94694 0.0270709 10.1305 2.4556 14.3162 14.5466 30.8261 g 22.5715 29.9464 20.1946 5.17847 12.5375 0.0270709 0.0270709 0.0270709 13.4331 4.7948 14.5466 29.4767 t 32.2856 29.5891 30.1053 53.8173 11.9555 89.9989 0.0270709 9.38387 62.1955 4.7948 45.3828 19.8486
M00169_2.00_shift2 (ceh-32)				; oligos_6nt_mkv2_m1 versus M00169_2.00 (ceh-32); m=5/11; ncol2=7; w=0; offset=0; strand=D; shift=2; score=0.506474; --tgAtmyc--- ; cor=; Ncor= a 0 0 18.9564 17.1082 73.6823 11.9808 54.4071 13.072 20.5555 0 0 0 c 0 0 24.8322 16.4374 17.2837 19.3619 33.6662 45.6257 33.5531 0 0 0 g 0 0 16.4799 43.3608 0.011218 3.075 0.0272281 14.4468 22.9457 0 0 0 t 0 0 39.7314 23.0936 9.02287 65.5823 11.8995 26.8555 22.9457 0 0 0
M00056_2.00_shift5 (alr-1,ceh-10,ceh-16,ceh-17,ceh-8,unc-4,unc-42,vab-15)				; oligos_6nt_mkv2_m1 versus M00056_2.00 (alr-1,ceh-10,ceh-16,ceh-17,ceh-8,unc-4,unc-42,vab-15); m=6/11; ncol2=8; w=0; offset=3; strand=D; shift=5; score=0.462147; -----TAATAwa ; cor=; Ncor= a 0 0 0 0 0 7.09225 86.6502 87.326 0.00620964 75.1428 63.5123 66.9102 c 0 0 0 0 0 7.09225 1.33964 1.27183 0.00620964 3.11103 5.03647 6.15964 g 0 0 0 0 0 0.795025 1.33964 1.90458 0.00620964 1.8691 0.63506 3.08367 t 0 0 0 0 0 85.0205 10.6705 9.4976 99.9814 19.877 30.8161 23.8465
M06497_2.00_shift2 (ceh-33,unc-39)				; oligos_6nt_mkv2_m1 versus M06497_2.00 (ceh-33,unc-39); m=7/11; ncol2=6; w=0; offset=0; strand=D; shift=2; score=0.444614; --TGATAC---- ; cor=; Ncor= a 0 0 0 0 100 0 100 0 0 0 0 0 c 0 0 0 0 0 0 0 76.9231 0 0 0 0 g 0 0 3.7037 100 0 3.7037 0 0 0 0 0 0 t 0 0 96.2963 0 0 96.2963 0 23.0769 0 0 0 0
M00483_2.00_shift1 (ceh-32)				; oligos_6nt_mkv2_m1 versus M00483_2.00 (ceh-32); m=8/11; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.444235; -gtgAtmy---- ; cor=; Ncor= a 0 24.7356 18.7686 20.6531 81.8609 12.6658 53.9508 14.6793 0 0 0 0 c 0 24.2458 24.5862 14.554 11.19 17.097 33.7193 41.9484 0 0 0 0 g 0 26.5291 20.3318 43.7226 3.37036 9.96323 4.34086 17.9294 0 0 0 0 t 0 24.4895 36.3134 21.0703 3.57878 60.274 7.98905 25.443 0 0 0 0
M02745_2.00_shift5 (mef-2)				; oligos_6nt_mkv2_m1 versus M02745_2.00 (mef-2); m=9/11; ncol2=12; w=0; offset=3; strand=D; shift=5; score=0.429554; -----TaCTAwA ; cor=; Ncor= a 0 0 0 0 0 2.00391 61.8663 0.100301 0.100301 99.5994 62.6062 97.5478 c 0 0 0 0 0 0.342131 0.870918 99.7492 0.0501505 0.0500751 0.125905 0 g 0 0 0 0 0 0.439883 12.4106 0.100301 0.100301 0.2003 0.283286 0.147131 t 0 0 0 0 0 97.2141 24.8523 0.0501505 99.7492 0.150225 36.9846 2.30505
M00326_2.00_shift1 (ceh-32)				; oligos_6nt_mkv2_m1 versus M00326_2.00 (ceh-32); m=10/11; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.428616; -dtgATmy---- ; cor=; Ncor= a 0 27.3376 16.6014 15.991 91.3679 4.59768 64.8564 7.762 0 0 0 0 c 0 19.8512 21.1045 7.11373 3.11084 13.2706 29.1419 45.1161 0 0 0 0 g 0 27.0656 15.325 61.6841 5.39188 6.52442 1.97818 16.2687 0 0 0 0 t 0 25.7456 46.969 15.2111 0.129367 75.6073 4.02359 30.8532 0 0 0 0
M06329_2.00_shift5 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15)				; oligos_6nt_mkv2_m1 versus M06329_2.00 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15); m=11/11; ncol2=9; w=0; offset=3; strand=D; shift=5; score=0.413423; -----yryTAAT ; cor=; Ncor= a 0 0 0 0 0 4.7619 42.8571 0 0 100 100 0 c 0 0 0 0 0 42.8571 19.0476 57.1429 0 0 0 0 g 0 0 0 0 0 9.52381 28.5714 0 0 0 0 4.7619 t 0 0 0 0 0 42.8571 9.52381 42.8571 100 0 0 95.2381

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wAATACTAAwa ; Alignment reference a 48 118 138 2 162 0 16 169 141 73 86 c 37 17 0 0 0 173 2 2 6 6 35 g 3 6 5 27 0 0 0 2 12 9 25 t 85 32 30 144 11 0 155 0 14 85 27
M00651_2.00_rc_shift0 (mex-6_rc)				; oligos_7nt_mkv2_m1 versus M00651_2.00_rc (mex-6_rc); m=1/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.667066; waATAATAAr- ; cor=; Ncor= a 29.2863 66.3373 79.0552 17.5069 99.9633 99.9633 12.0422 99.9633 76.2969 39.2485 0 c 20.5145 8.16601 12.1974 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 4.49775 16.8462 0 g 20.5145 8.16601 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 14.7076 27.0591 0 t 29.6848 17.3306 8.73512 82.4686 0.0122303 0.0122303 87.9333 0.0122303 4.49775 16.8462 0
M06329_2.00_shift3 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15)				; oligos_7nt_mkv2_m1 versus M06329_2.00 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15); m=2/5; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.477299; ---yryTAATk ; cor=; Ncor= a 0 0 0 4.7619 42.8571 0 0 100 100 0 0 c 0 0 0 42.8571 19.0476 57.1429 0 0 0 0 0 g 0 0 0 9.52381 28.5714 0 0 0 0 4.7619 38.0952 t 0 0 0 42.8571 9.52381 42.8571 100 0 0 95.2381 61.9048
M02745_2.00_shift3 (mef-2)				; oligos_7nt_mkv2_m1 versus M02745_2.00 (mef-2); m=3/5; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.464342; ---TaCTAwAA ; cor=; Ncor= a 0 0 0 2.00391 61.8663 0.100301 0.100301 99.5994 62.6062 97.5478 96.6942 c 0 0 0 0.342131 0.870918 99.7492 0.0501505 0.0500751 0.125905 0 0.194458 g 0 0 0 0.439883 12.4106 0.100301 0.100301 0.2003 0.283286 0.147131 0.0486145 t 0 0 0 97.2141 24.8523 0.0501505 99.7492 0.150225 36.9846 2.30505 3.06271
M00282_2.00_rc_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc)				; oligos_7nt_mkv2_m1 versus M00282_2.00_rc (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc); m=4/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.425346; ----acYAATT ; cor=; Ncor= a 0 0 0 0 57.8256 10.7347 0.0285388 99.919 99.919 0.0269978 0.0269978 c 0 0 0 0 10.5567 64.2297 25.7135 0.0269978 0.0269978 0.0269978 2.72678 g 0 0 0 0 21.0609 10.7347 0.0285388 0.0269978 0.0269978 0.0269978 0.0269978 t 0 0 0 0 10.5567 14.301 74.2295 0.0269978 0.0269978 99.919 97.2192
M06350_2.00_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15)				; oligos_7nt_mkv2_m1 versus M06350_2.00 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15); m=5/5; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.410441; ----ayTAATT ; cor=; Ncor= a 0 0 0 0 55 10 0 90 100 0 0 c 0 0 0 0 10 45 0 0 0 0 0 g 0 0 0 0 20 15 0 0 0 0 5 t 0 0 0 0 15 30 100 10 0 100 95