One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift4 ; 8 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv4_m2_shift4 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=4; ncol=15; ----wwAAATTAtw- ; Alignment reference a 0 0 0 0 306 235 792 792 792 0 0 792 152 307 0 c 0 0 0 0 62 44 0 0 0 0 0 0 135 145 0 g 0 0 0 0 126 42 0 0 0 0 0 0 85 79 0 t 0 0 0 0 298 471 0 0 0 792 792 0 420 261 0

MA0075.1_shift7 (Prrx2) 0.998 0.499 8.498 0.498 0.979 0.021 0.998 1 15 4 7 1 1 1 4.286 1
; oligos_6nt_mkv4_m2 versus MA0075.1 (Prrx2); m=1/7; ncol2=5; w=5; offset=3; strand=D; shift=7; score= 4.2857; -------AATTA--- ; cor=0.998; Ncor=0.499; logoDP=8.498; NIcor=0.498; NsEucl=0.979; SSD=0.021; NSW=0.998; rcor=1; rNcor=15; rlogoDP=4; rNIcor=7; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=4.286; match_rank=1 a 0 0 0 0 0 0 0 52 59 0 0 58 0 0 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 4 0 1 0 1 0 0 0 t 0 0 0 0 0 0 0 1 0 58 59 0 0 0 0

MA0132.1_rc_shift7 (Pdx1_rc) 0.897 0.538 0.052 -0.147 0.897 0.762 0.937 3 9 27 26 12 3 5 12.143 7
; oligos_6nt_mkv4_m2 versus MA0132.1_rc (Pdx1_rc); m=2/7; ncol2=6; w=6; offset=3; strand=R; shift=7; score=12.1429; -------mATTAg-- ; cor=0.897; Ncor=0.538; logoDP=0.052; NIcor=-0.147; NsEucl=0.897; SSD=0.762; NSW=0.937; rcor=3; rNcor=9; rlogoDP=27; rNIcor=26; rNsEucl=12; rSSD=3; rNSW=5; rank_mean=12.143; match_rank=7 a 0 0 0 0 0 0 0 19 30 0 0 31 6 0 0 c 0 0 0 0 0 0 0 10 1 0 0 0 5 0 0 g 0 0 0 0 0 0 0 1 0 0 0 0 19 0 0 t 0 0 0 0 0 0 0 1 0 31 31 0 1 0 0

MA0158.1_rc_shift7 (HOXA5_rc) 0.833 0.530 2.201 0.105 0.889 1.205 0.914 9 11 21 20 17 6 13 13.857 15
; oligos_6nt_mkv4_m2 versus MA0158.1_rc (HOXA5_rc); m=3/7; ncol2=8; w=7; offset=3; strand=R; shift=7; score=13.8571; -------mATTwvhG ; cor=0.833; Ncor=0.530; logoDP=2.201; NIcor=0.105; NsEucl=0.889; SSD=1.205; NSW=0.914; rcor=9; rNcor=11; rlogoDP=21; rNIcor=20; rNsEucl=17; rSSD=6; rNSW=13; rank_mean=13.857; match_rank=15 a 0 0 0 0 0 0 0 9 16 0 2 9 4 4 0 c 0 0 0 0 0 0 0 6 0 2 0 1 5 5 0 g 0 0 0 0 0 0 0 1 0 0 0 0 7 0 13 t 0 0 0 0 0 0 0 0 0 14 14 6 0 7 2

MA0151.1_shift8 (ARID3A) 0.795 0.477 6.375 0.451 0.861 1.398 0.883 19 19 13 14 26 9 22 17.429 19
; oligos_6nt_mkv4_m2 versus MA0151.1 (ARID3A); m=4/7; ncol2=6; w=6; offset=4; strand=D; shift=8; score=17.4286; --------ATyAAA- ; cor=0.795; Ncor=0.477; logoDP=6.375; NIcor=0.451; NsEucl=0.861; SSD=1.398; NSW=0.883; rcor=19; rNcor=19; rlogoDP=13; rNIcor=14; rNsEucl=26; rSSD=9; rNSW=22; rank_mean=17.429; match_rank=19 a 0 0 0 0 0 0 0 0 27 0 1 27 27 20 0 c 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 0 0 0 0 27 17 0 0 6 0

MA0135.1_shift6 (Lhx3) 0.798 0.426 8.113 0.399 0.880 1.851 0.884 18 25 7 17 21 17 21 18.000 21
; oligos_6nt_mkv4_m2 versus MA0135.1 (Lhx3); m=5/7; ncol2=13; w=8; offset=2; strand=D; shift=6; score= 18; ------wAATTAATT ; cor=0.798; Ncor=0.426; logoDP=8.113; NIcor=0.399; NsEucl=0.880; SSD=1.851; NSW=0.884; rcor=18; rNcor=25; rlogoDP=7; rNIcor=17; rNsEucl=21; rSSD=17; rNSW=21; rank_mean=18.000; match_rank=21 a 0 0 0 0 0 0 9 16 19 0 0 19 20 2 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 2 1 g 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 0 1 20 20 1 0 16 19

MA0485.1_shift0 (Hoxc9) 0.756 0.486 7.356 0.462 0.881 2.279 0.873 26 16 9 13 20 24 25 19.000 24
; oligos_6nt_mkv4_m2 versus MA0485.1 (Hoxc9); m=6/7; ncol2=13; w=9; offset=-4; strand=D; shift=0; score= 19; rgCmATAAATCwy-- ; cor=0.756; Ncor=0.486; logoDP=7.356; NIcor=0.462; NsEucl=0.881; SSD=2.279; NSW=0.873; rcor=26; rNcor=16; rlogoDP=9; rNIcor=13; rNsEucl=20; rSSD=24; rNSW=25; rank_mean=19.000; match_rank=24 a 235 112 88 224 661 0 745 881 879 18 48 567 141 0 0 c 110 171 605 468 3 9 84 0 6 0 715 72 329 0 0 g 401 536 40 1 205 0 35 0 0 0 5 6 160 0 0 t 139 66 152 192 16 876 21 4 0 867 117 240 255 0 0

MA0063.1_rc_shift6 (Nkx2-5_rc) 0.765 0.536 2.977 0.115 0.860 1.910 0.864 23 10 18 19 27 18 26 20.143 25
; oligos_6nt_mkv4_m2 versus MA0063.1_rc (Nkx2-5_rc); m=7/7; ncol2=7; w=7; offset=2; strand=R; shift=6; score=20.1429; ------camTTAw-- ; cor=0.765; Ncor=0.536; logoDP=2.977; NIcor=0.115; NsEucl=0.860; SSD=1.910; NSW=0.864; rcor=23; rNcor=10; rlogoDP=18; rNIcor=19; rNsEucl=27; rSSD=18; rNSW=26; rank_mean=20.143; match_rank=25 a 0 0 0 0 0 0 3 11 10 0 0 13 9 0 0 c 0 0 0 0 0 0 11 0 7 0 0 0 1 0 0 g 0 0 0 0 0 0 1 2 0 0 0 4 0 0 0 t 0 0 0 0 0 0 2 4 0 17 17 0 7 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m2_shift4 (oligos_6nt_mkv4_m2)																	; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=4; ncol=15; ----wwAAATTAtw- ; Alignment reference a 0 0 0 0 306 235 792 792 792 0 0 792 152 307 0 c 0 0 0 0 62 44 0 0 0 0 0 0 135 145 0 g 0 0 0 0 126 42 0 0 0 0 0 0 85 79 0 t 0 0 0 0 298 471 0 0 0 792 792 0 420 261 0
MA0075.1_shift7 (Prrx2)	0.998	0.499	8.498	0.498	0.979	0.021	0.998	1	15	4	7	1	1	1	4.286	1	; oligos_6nt_mkv4_m2 versus MA0075.1 (Prrx2); m=1/7; ncol2=5; w=5; offset=3; strand=D; shift=7; score= 4.2857; -------AATTA--- ; cor=0.998; Ncor=0.499; logoDP=8.498; NIcor=0.498; NsEucl=0.979; SSD=0.021; NSW=0.998; rcor=1; rNcor=15; rlogoDP=4; rNIcor=7; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=4.286; match_rank=1 a 0 0 0 0 0 0 0 52 59 0 0 58 0 0 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 4 0 1 0 1 0 0 0 t 0 0 0 0 0 0 0 1 0 58 59 0 0 0 0
MA0132.1_rc_shift7 (Pdx1_rc)	0.897	0.538	0.052	-0.147	0.897	0.762	0.937	3	9	27	26	12	3	5	12.143	7	; oligos_6nt_mkv4_m2 versus MA0132.1_rc (Pdx1_rc); m=2/7; ncol2=6; w=6; offset=3; strand=R; shift=7; score=12.1429; -------mATTAg-- ; cor=0.897; Ncor=0.538; logoDP=0.052; NIcor=-0.147; NsEucl=0.897; SSD=0.762; NSW=0.937; rcor=3; rNcor=9; rlogoDP=27; rNIcor=26; rNsEucl=12; rSSD=3; rNSW=5; rank_mean=12.143; match_rank=7 a 0 0 0 0 0 0 0 19 30 0 0 31 6 0 0 c 0 0 0 0 0 0 0 10 1 0 0 0 5 0 0 g 0 0 0 0 0 0 0 1 0 0 0 0 19 0 0 t 0 0 0 0 0 0 0 1 0 31 31 0 1 0 0
MA0158.1_rc_shift7 (HOXA5_rc)	0.833	0.530	2.201	0.105	0.889	1.205	0.914	9	11	21	20	17	6	13	13.857	15	; oligos_6nt_mkv4_m2 versus MA0158.1_rc (HOXA5_rc); m=3/7; ncol2=8; w=7; offset=3; strand=R; shift=7; score=13.8571; -------mATTwvhG ; cor=0.833; Ncor=0.530; logoDP=2.201; NIcor=0.105; NsEucl=0.889; SSD=1.205; NSW=0.914; rcor=9; rNcor=11; rlogoDP=21; rNIcor=20; rNsEucl=17; rSSD=6; rNSW=13; rank_mean=13.857; match_rank=15 a 0 0 0 0 0 0 0 9 16 0 2 9 4 4 0 c 0 0 0 0 0 0 0 6 0 2 0 1 5 5 0 g 0 0 0 0 0 0 0 1 0 0 0 0 7 0 13 t 0 0 0 0 0 0 0 0 0 14 14 6 0 7 2
MA0151.1_shift8 (ARID3A)	0.795	0.477	6.375	0.451	0.861	1.398	0.883	19	19	13	14	26	9	22	17.429	19	; oligos_6nt_mkv4_m2 versus MA0151.1 (ARID3A); m=4/7; ncol2=6; w=6; offset=4; strand=D; shift=8; score=17.4286; --------ATyAAA- ; cor=0.795; Ncor=0.477; logoDP=6.375; NIcor=0.451; NsEucl=0.861; SSD=1.398; NSW=0.883; rcor=19; rNcor=19; rlogoDP=13; rNIcor=14; rNsEucl=26; rSSD=9; rNSW=22; rank_mean=17.429; match_rank=19 a 0 0 0 0 0 0 0 0 27 0 1 27 27 20 0 c 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 0 0 0 0 27 17 0 0 6 0
MA0135.1_shift6 (Lhx3)	0.798	0.426	8.113	0.399	0.880	1.851	0.884	18	25	7	17	21	17	21	18.000	21	; oligos_6nt_mkv4_m2 versus MA0135.1 (Lhx3); m=5/7; ncol2=13; w=8; offset=2; strand=D; shift=6; score= 18; ------wAATTAATT ; cor=0.798; Ncor=0.426; logoDP=8.113; NIcor=0.399; NsEucl=0.880; SSD=1.851; NSW=0.884; rcor=18; rNcor=25; rlogoDP=7; rNIcor=17; rNsEucl=21; rSSD=17; rNSW=21; rank_mean=18.000; match_rank=21 a 0 0 0 0 0 0 9 16 19 0 0 19 20 2 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 2 1 g 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 0 1 20 20 1 0 16 19
MA0485.1_shift0 (Hoxc9)	0.756	0.486	7.356	0.462	0.881	2.279	0.873	26	16	9	13	20	24	25	19.000	24	; oligos_6nt_mkv4_m2 versus MA0485.1 (Hoxc9); m=6/7; ncol2=13; w=9; offset=-4; strand=D; shift=0; score= 19; rgCmATAAATCwy-- ; cor=0.756; Ncor=0.486; logoDP=7.356; NIcor=0.462; NsEucl=0.881; SSD=2.279; NSW=0.873; rcor=26; rNcor=16; rlogoDP=9; rNIcor=13; rNsEucl=20; rSSD=24; rNSW=25; rank_mean=19.000; match_rank=24 a 235 112 88 224 661 0 745 881 879 18 48 567 141 0 0 c 110 171 605 468 3 9 84 0 6 0 715 72 329 0 0 g 401 536 40 1 205 0 35 0 0 0 5 6 160 0 0 t 139 66 152 192 16 876 21 4 0 867 117 240 255 0 0
MA0063.1_rc_shift6 (Nkx2-5_rc)	0.765	0.536	2.977	0.115	0.860	1.910	0.864	23	10	18	19	27	18	26	20.143	25	; oligos_6nt_mkv4_m2 versus MA0063.1_rc (Nkx2-5_rc); m=7/7; ncol2=7; w=7; offset=2; strand=R; shift=6; score=20.1429; ------camTTAw-- ; cor=0.765; Ncor=0.536; logoDP=2.977; NIcor=0.115; NsEucl=0.860; SSD=1.910; NSW=0.864; rcor=23; rNcor=10; rlogoDP=18; rNIcor=19; rNsEucl=27; rSSD=18; rNSW=26; rank_mean=20.143; match_rank=25 a 0 0 0 0 0 0 3 11 10 0 0 13 9 0 0 c 0 0 0 0 0 0 11 0 7 0 0 0 1 0 0 g 0 0 0 0 0 0 1 2 0 0 0 4 0 0 0 t 0 0 0 0 0 0 2 4 0 17 17 0 7 0 0

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 7 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=17; shift=0; ncol=20; cyGCCCCCCCRCCCCsv--- ; Alignment reference a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 0 0 0 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 0 0 0 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 0 0 0 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2 0 0 0

MA0079.3_shift5 (SP1) 0.865 0.560 8.778 0.561 0.922 1.475 0.933 5 7 3 4 3 12 6 5.714 2
; dyads_m4 versus MA0079.3 (SP1); m=1/6; ncol2=11; w=11; offset=5; strand=D; shift=5; score= 5.7143; -----gCCCCkCCCCy---- ; cor=0.865; Ncor=0.560; logoDP=8.778; NIcor=0.561; NsEucl=0.922; SSD=1.475; NSW=0.933; rcor=5; rNcor=7; rlogoDP=3; rNIcor=4; rNsEucl=3; rSSD=12; rNSW=6; rank_mean=5.714; match_rank=2 a 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0

MA0079.2_shift6 (SP1) 0.879 0.517 6.743 0.524 0.921 1.234 0.938 4 12 10 6 4 7 3 6.571 3
; dyads_m4 versus MA0079.2 (SP1); m=2/6; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 6.5714; ------CCCCkCCCCC---- ; cor=0.879; Ncor=0.517; logoDP=6.743; NIcor=0.524; NsEucl=0.921; SSD=1.234; NSW=0.938; rcor=4; rNcor=12; rlogoDP=10; rNIcor=6; rNsEucl=4; rSSD=7; rNSW=3; rank_mean=6.571; match_rank=3 a 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0

MA0599.1_shift5 (KLF5) 0.860 0.506 8.354 0.490 0.913 1.511 0.924 6 14 5 8 9 13 7 8.857 5
; dyads_m4 versus MA0599.1 (KLF5); m=3/6; ncol2=10; w=10; offset=5; strand=D; shift=5; score= 8.8571; -----gCCMCrCCCh----- ; cor=0.860; Ncor=0.506; logoDP=8.354; NIcor=0.490; NsEucl=0.913; SSD=1.511; NSW=0.924; rcor=6; rNcor=14; rlogoDP=5; rNIcor=8; rNsEucl=9; rSSD=13; rNSW=7; rank_mean=8.857; match_rank=5 a 0 0 0 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 0 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 0 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0

MA0162.2_shift5 (EGR1) 0.816 0.515 6.724 0.489 0.917 1.986 0.917 14 13 11 9 6 19 11 11.857 6
; dyads_m4 versus MA0162.2 (EGR1); m=4/6; ncol2=14; w=12; offset=5; strand=D; shift=5; score=11.8571; -----sccCCgCCCMCkCc- ; cor=0.816; Ncor=0.515; logoDP=6.724; NIcor=0.489; NsEucl=0.917; SSD=1.986; NSW=0.917; rcor=14; rNcor=13; rlogoDP=11; rNIcor=9; rNsEucl=6; rSSD=19; rNSW=11; rank_mean=11.857; match_rank=6 a 0 0 0 0 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 0 0 0 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 0 0 0 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 0 0 0 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0

MA0516.1_shift5 (SP2) 0.801 0.481 8.265 0.476 0.913 2.164 0.910 17 18 6 11 8 21 14 13.571 14
; dyads_m4 versus MA0516.1 (SP2); m=5/6; ncol2=15; w=12; offset=5; strand=D; shift=5; score=13.5714; -----gyCCCGCCyCyyccs ; cor=0.801; Ncor=0.481; logoDP=8.265; NIcor=0.476; NsEucl=0.913; SSD=2.164; NSW=0.910; rcor=17; rNcor=18; rlogoDP=6; rNIcor=11; rNsEucl=8; rSSD=21; rNSW=14; rank_mean=13.571; match_rank=14 a 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

MA0039.2_rc_shift5 (Klf4_rc) 0.793 0.466 0.894 -0.092 0.895 2.218 0.889 20 21 24 25 13 22 18 20.429 26
; dyads_m4 versus MA0039.2_rc (Klf4_rc); m=6/6; ncol2=10; w=10; offset=5; strand=R; shift=5; score=20.4286; -----gCCmCrCCCw----- ; cor=0.793; Ncor=0.466; logoDP=0.894; NIcor=-0.092; NsEucl=0.895; SSD=2.218; NSW=0.889; rcor=20; rNcor=21; rlogoDP=24; rNIcor=25; rNsEucl=13; rSSD=22; rNSW=18; rank_mean=20.429; match_rank=26 a 0 0 0 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 0 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 0 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 0 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m4_shift0 (dyads_m4)																	; dyads_m4; m=0 (reference); ncol1=17; shift=0; ncol=20; cyGCCCCCCCRCCCCsv--- ; Alignment reference a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 0 0 0 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 0 0 0 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 0 0 0 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2 0 0 0
MA0079.3_shift5 (SP1)	0.865	0.560	8.778	0.561	0.922	1.475	0.933	5	7	3	4	3	12	6	5.714	2	; dyads_m4 versus MA0079.3 (SP1); m=1/6; ncol2=11; w=11; offset=5; strand=D; shift=5; score= 5.7143; -----gCCCCkCCCCy---- ; cor=0.865; Ncor=0.560; logoDP=8.778; NIcor=0.561; NsEucl=0.922; SSD=1.475; NSW=0.933; rcor=5; rNcor=7; rlogoDP=3; rNIcor=4; rNsEucl=3; rSSD=12; rNSW=6; rank_mean=5.714; match_rank=2 a 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0
MA0079.2_shift6 (SP1)	0.879	0.517	6.743	0.524	0.921	1.234	0.938	4	12	10	6	4	7	3	6.571	3	; dyads_m4 versus MA0079.2 (SP1); m=2/6; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 6.5714; ------CCCCkCCCCC---- ; cor=0.879; Ncor=0.517; logoDP=6.743; NIcor=0.524; NsEucl=0.921; SSD=1.234; NSW=0.938; rcor=4; rNcor=12; rlogoDP=10; rNIcor=6; rNsEucl=4; rSSD=7; rNSW=3; rank_mean=6.571; match_rank=3 a 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0
MA0599.1_shift5 (KLF5)	0.860	0.506	8.354	0.490	0.913	1.511	0.924	6	14	5	8	9	13	7	8.857	5	; dyads_m4 versus MA0599.1 (KLF5); m=3/6; ncol2=10; w=10; offset=5; strand=D; shift=5; score= 8.8571; -----gCCMCrCCCh----- ; cor=0.860; Ncor=0.506; logoDP=8.354; NIcor=0.490; NsEucl=0.913; SSD=1.511; NSW=0.924; rcor=6; rNcor=14; rlogoDP=5; rNIcor=8; rNsEucl=9; rSSD=13; rNSW=7; rank_mean=8.857; match_rank=5 a 0 0 0 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 0 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 0 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0
MA0162.2_shift5 (EGR1)	0.816	0.515	6.724	0.489	0.917	1.986	0.917	14	13	11	9	6	19	11	11.857	6	; dyads_m4 versus MA0162.2 (EGR1); m=4/6; ncol2=14; w=12; offset=5; strand=D; shift=5; score=11.8571; -----sccCCgCCCMCkCc- ; cor=0.816; Ncor=0.515; logoDP=6.724; NIcor=0.489; NsEucl=0.917; SSD=1.986; NSW=0.917; rcor=14; rNcor=13; rlogoDP=11; rNIcor=9; rNsEucl=6; rSSD=19; rNSW=11; rank_mean=11.857; match_rank=6 a 0 0 0 0 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 0 0 0 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 0 0 0 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 0 0 0 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0
MA0516.1_shift5 (SP2)	0.801	0.481	8.265	0.476	0.913	2.164	0.910	17	18	6	11	8	21	14	13.571	14	; dyads_m4 versus MA0516.1 (SP2); m=5/6; ncol2=15; w=12; offset=5; strand=D; shift=5; score=13.5714; -----gyCCCGCCyCyyccs ; cor=0.801; Ncor=0.481; logoDP=8.265; NIcor=0.476; NsEucl=0.913; SSD=2.164; NSW=0.910; rcor=17; rNcor=18; rlogoDP=6; rNIcor=11; rNsEucl=8; rSSD=21; rNSW=14; rank_mean=13.571; match_rank=14 a 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
MA0039.2_rc_shift5 (Klf4_rc)	0.793	0.466	0.894	-0.092	0.895	2.218	0.889	20	21	24	25	13	22	18	20.429	26	; dyads_m4 versus MA0039.2_rc (Klf4_rc); m=6/6; ncol2=10; w=10; offset=5; strand=R; shift=5; score=20.4286; -----gCCmCrCCCw----- ; cor=0.793; Ncor=0.466; logoDP=0.894; NIcor=-0.092; NsEucl=0.895; SSD=2.218; NSW=0.889; rcor=20; rNcor=21; rlogoDP=24; rNIcor=25; rNsEucl=13; rSSD=22; rNSW=18; rank_mean=20.429; match_rank=26 a 0 0 0 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 0 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 0 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 0 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; ccyCCACCTCss ; Alignment reference a 94 140 65 6 3 595 4 5 35 1 150 89 c 361 304 239 718 703 3 722 704 2 729 276 248 g 131 130 122 7 18 130 1 19 60 2 203 234 t 147 159 307 2 9 5 6 5 636 1 104 162

MA0130.1_shift1 (ZNF354C) 0.949 0.474 5.659 0.480 0.932 0.336 0.972 2 20 14 10 2 2 2 7.429 4
; oligos_7nt_mkv5_m4 versus MA0130.1 (ZNF354C); m=1/2; ncol2=6; w=6; offset=1; strand=D; shift=1; score= 7.4286; -mTCCAC----- ; cor=0.949; Ncor=0.474; logoDP=5.659; NIcor=0.480; NsEucl=0.932; SSD=0.336; NSW=0.972; rcor=2; rNcor=20; rlogoDP=14; rNIcor=10; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=7.429; match_rank=4 a 0 7 3 0 0 16 0 0 0 0 0 0 c 0 6 2 16 16 0 15 0 0 0 0 0 g 0 3 0 0 0 0 1 0 0 0 0 0 t 0 0 11 0 0 0 0 0 0 0 0 0

MA0103.1_shift4 (ZEB1) 0.808 0.404 5.190 0.416 0.863 1.351 0.887 16 27 16 15 25 8 20 18.143 22
; oligos_7nt_mkv5_m4 versus MA0103.1 (ZEB1); m=2/2; ncol2=6; w=6; offset=4; strand=D; shift=4; score=18.1429; ----CACCTk-- ; cor=0.808; Ncor=0.404; logoDP=5.190; NIcor=0.416; NsEucl=0.863; SSD=1.351; NSW=0.887; rcor=16; rNcor=27; rlogoDP=16; rNIcor=15; rNsEucl=25; rSSD=8; rNSW=20; rank_mean=18.143; match_rank=22 a 0 0 0 0 1 38 0 0 0 10 0 0 c 0 0 0 0 34 0 40 38 1 1 0 0 g 0 0 0 0 1 2 1 3 0 16 0 0 t 0 0 0 0 5 1 0 0 40 14 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)																	; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; ccyCCACCTCss ; Alignment reference a 94 140 65 6 3 595 4 5 35 1 150 89 c 361 304 239 718 703 3 722 704 2 729 276 248 g 131 130 122 7 18 130 1 19 60 2 203 234 t 147 159 307 2 9 5 6 5 636 1 104 162
MA0130.1_shift1 (ZNF354C)	0.949	0.474	5.659	0.480	0.932	0.336	0.972	2	20	14	10	2	2	2	7.429	4	; oligos_7nt_mkv5_m4 versus MA0130.1 (ZNF354C); m=1/2; ncol2=6; w=6; offset=1; strand=D; shift=1; score= 7.4286; -mTCCAC----- ; cor=0.949; Ncor=0.474; logoDP=5.659; NIcor=0.480; NsEucl=0.932; SSD=0.336; NSW=0.972; rcor=2; rNcor=20; rlogoDP=14; rNIcor=10; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=7.429; match_rank=4 a 0 7 3 0 0 16 0 0 0 0 0 0 c 0 6 2 16 16 0 15 0 0 0 0 0 g 0 3 0 0 0 0 1 0 0 0 0 0 t 0 0 11 0 0 0 0 0 0 0 0 0
MA0103.1_shift4 (ZEB1)	0.808	0.404	5.190	0.416	0.863	1.351	0.887	16	27	16	15	25	8	20	18.143	22	; oligos_7nt_mkv5_m4 versus MA0103.1 (ZEB1); m=2/2; ncol2=6; w=6; offset=4; strand=D; shift=4; score=18.1429; ----CACCTk-- ; cor=0.808; Ncor=0.404; logoDP=5.190; NIcor=0.416; NsEucl=0.863; SSD=1.351; NSW=0.887; rcor=16; rNcor=27; rlogoDP=16; rNIcor=15; rNsEucl=25; rSSD=8; rNSW=20; rank_mean=18.143; match_rank=22 a 0 0 0 0 1 38 0 0 0 10 0 0 c 0 0 0 0 34 0 40 38 1 1 0 0 g 0 0 0 0 1 2 1 3 0 16 0 0 t 0 0 0 0 5 1 0 0 40 14 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift1 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=11; shift=1; ncol=14; -mkCCTCCCrms-- ; Alignment reference a 0 357 263 13 4 11 9 12 0 347 302 241 0 0 c 0 306 166 1095 1099 6 1103 1089 1113 135 333 357 0 0 g 0 192 312 5 12 52 7 15 7 384 260 336 0 0 t 0 265 379 7 5 1051 1 4 0 254 225 186 0 0

MA0154.1_rc_shift5 (EBF1_rc) 0.859 0.430 2.370 0.268 0.905 0.885 0.937 7 24 20 18 11 4 4 12.571 8
; oligos_6nt_mkv4_m5 versus MA0154.1_rc (EBF1_rc); m=1/3; ncol2=10; w=7; offset=4; strand=R; shift=5; score=12.5714; -----TCCCtkGrG ; cor=0.859; Ncor=0.430; logoDP=2.370; NIcor=0.268; NsEucl=0.905; SSD=0.885; NSW=0.937; rcor=7; rNcor=24; rlogoDP=20; rNIcor=18; rNsEucl=11; rSSD=4; rNSW=4; rank_mean=12.571; match_rank=8 a 0 0 0 0 0 0 0 0 0 3 5 3 7 3 c 0 0 0 0 0 4 25 23 25 5 0 0 1 0 g 0 0 0 0 0 0 0 0 0 1 9 20 16 22 t 0 0 0 0 0 21 0 2 0 16 11 2 1 0

MA0079.3_shift0 (SP1) 0.750 0.625 7.812 0.635 0.894 2.249 0.888 27 5 8 2 14 23 19 14.000 16
; oligos_6nt_mkv4_m5 versus MA0079.3 (SP1); m=2/3; ncol2=11; w=10; offset=-1; strand=D; shift=0; score= 14; gCCCCkCCCCy--- ; cor=0.750; Ncor=0.625; logoDP=7.812; NIcor=0.635; NsEucl=0.894; SSD=2.249; NSW=0.888; rcor=27; rNcor=5; rlogoDP=8; rNIcor=2; rNsEucl=14; rSSD=23; rNSW=19; rank_mean=14.000; match_rank=16 a 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 c 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 g 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 t 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0

MA0056.1_rc_shift5 (MZF1_1-4_rc) 0.839 0.458 0.098 -0.083 0.883 0.988 0.918 8 22 26 24 19 5 10 16.286 18
; oligos_6nt_mkv4_m5 versus MA0056.1_rc (MZF1_1-4_rc); m=3/3; ncol2=6; w=6; offset=4; strand=R; shift=5; score=16.2857; -----TCCCCr--- ; cor=0.839; Ncor=0.458; logoDP=0.098; NIcor=-0.083; NsEucl=0.883; SSD=0.988; NSW=0.918; rcor=8; rNcor=22; rlogoDP=26; rNIcor=24; rNsEucl=19; rSSD=5; rNSW=10; rank_mean=16.286; match_rank=18 a 0 0 0 0 0 0 0 1 0 1 8 0 0 0 c 0 0 0 0 0 2 20 19 18 19 4 0 0 0 g 0 0 0 0 0 0 0 0 0 0 5 0 0 0 t 0 0 0 0 0 18 0 0 2 0 3 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)																	; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=11; shift=1; ncol=14; -mkCCTCCCrms-- ; Alignment reference a 0 357 263 13 4 11 9 12 0 347 302 241 0 0 c 0 306 166 1095 1099 6 1103 1089 1113 135 333 357 0 0 g 0 192 312 5 12 52 7 15 7 384 260 336 0 0 t 0 265 379 7 5 1051 1 4 0 254 225 186 0 0
MA0154.1_rc_shift5 (EBF1_rc)	0.859	0.430	2.370	0.268	0.905	0.885	0.937	7	24	20	18	11	4	4	12.571	8	; oligos_6nt_mkv4_m5 versus MA0154.1_rc (EBF1_rc); m=1/3; ncol2=10; w=7; offset=4; strand=R; shift=5; score=12.5714; -----TCCCtkGrG ; cor=0.859; Ncor=0.430; logoDP=2.370; NIcor=0.268; NsEucl=0.905; SSD=0.885; NSW=0.937; rcor=7; rNcor=24; rlogoDP=20; rNIcor=18; rNsEucl=11; rSSD=4; rNSW=4; rank_mean=12.571; match_rank=8 a 0 0 0 0 0 0 0 0 0 3 5 3 7 3 c 0 0 0 0 0 4 25 23 25 5 0 0 1 0 g 0 0 0 0 0 0 0 0 0 1 9 20 16 22 t 0 0 0 0 0 21 0 2 0 16 11 2 1 0
MA0079.3_shift0 (SP1)	0.750	0.625	7.812	0.635	0.894	2.249	0.888	27	5	8	2	14	23	19	14.000	16	; oligos_6nt_mkv4_m5 versus MA0079.3 (SP1); m=2/3; ncol2=11; w=10; offset=-1; strand=D; shift=0; score= 14; gCCCCkCCCCy--- ; cor=0.750; Ncor=0.625; logoDP=7.812; NIcor=0.635; NsEucl=0.894; SSD=2.249; NSW=0.888; rcor=27; rNcor=5; rlogoDP=8; rNIcor=2; rNsEucl=14; rSSD=23; rNSW=19; rank_mean=14.000; match_rank=16 a 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 c 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 g 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 t 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0
MA0056.1_rc_shift5 (MZF1_1-4_rc)	0.839	0.458	0.098	-0.083	0.883	0.988	0.918	8	22	26	24	19	5	10	16.286	18	; oligos_6nt_mkv4_m5 versus MA0056.1_rc (MZF1_1-4_rc); m=3/3; ncol2=6; w=6; offset=4; strand=R; shift=5; score=16.2857; -----TCCCCr--- ; cor=0.839; Ncor=0.458; logoDP=0.098; NIcor=-0.083; NsEucl=0.883; SSD=0.988; NSW=0.918; rcor=8; rNcor=22; rlogoDP=26; rNIcor=24; rNsEucl=19; rSSD=5; rNSW=10; rank_mean=16.286; match_rank=18 a 0 0 0 0 0 0 0 1 0 1 8 0 0 0 c 0 0 0 0 0 2 20 19 18 19 4 0 0 0 g 0 0 0 0 0 0 0 0 0 0 5 0 0 0 t 0 0 0 0 0 18 0 0 2 0 3 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift4 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv4_m1_shift4 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=4; ncol=14; ----wwCTTTTCwh ; Alignment reference a 0 0 0 0 205 230 0 0 0 0 0 0 234 195 c 0 0 0 0 77 61 630 0 0 0 0 630 77 168 g 0 0 0 0 157 51 0 1 0 0 0 0 27 73 t 0 0 0 0 191 288 0 629 630 630 630 0 292 194

MA0152.1_shift7 (NFATC2) 0.811 0.568 6.389 0.551 0.878 1.459 0.896 15 6 12 5 23 11 17 12.714 9
; oligos_6nt_mkv4_m1 versus MA0152.1 (NFATC2); m=1/2; ncol2=7; w=7; offset=3; strand=D; shift=7; score=12.7143; -------TTTTCCA ; cor=0.811; Ncor=0.568; logoDP=6.389; NIcor=0.551; NsEucl=0.878; SSD=1.459; NSW=0.896; rcor=15; rNcor=6; rlogoDP=12; rNIcor=5; rNsEucl=23; rSSD=11; rNSW=17; rank_mean=12.714; match_rank=9 a 0 0 0 0 0 0 0 3 1 1 0 1 0 18 c 0 0 0 0 0 0 0 1 2 1 0 25 26 3 g 0 0 0 0 0 0 0 2 2 0 0 0 0 1 t 0 0 0 0 0 0 0 20 21 24 26 0 0 4

MA0029.1_rc_shift0 (Mecom_rc) 0.758 0.542 1.509 -0.029 0.888 2.506 0.875 25 8 22 23 18 26 24 20.857 27
; oligos_6nt_mkv4_m1 versus MA0029.1_rc (Mecom_rc); m=2/2; ncol2=14; w=10; offset=-4; strand=R; shift=0; score=20.8571; tvTTATCTTrTCTt ; cor=0.758; Ncor=0.542; logoDP=1.509; NIcor=-0.029; NsEucl=0.888; SSD=2.506; NSW=0.875; rcor=25; rNcor=8; rlogoDP=22; rNIcor=23; rNsEucl=18; rSSD=26; rNSW=24; rank_mean=20.857; match_rank=27 a 3 7 0 2 24 0 0 0 0 16 0 1 4 5 c 3 7 4 0 0 0 27 1 0 0 0 25 2 6 g 6 7 0 1 3 0 0 0 0 10 0 1 1 2 t 15 6 23 24 0 27 0 26 27 1 27 0 20 14

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m1_shift4 (oligos_6nt_mkv4_m1)																	; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=4; ncol=14; ----wwCTTTTCwh ; Alignment reference a 0 0 0 0 205 230 0 0 0 0 0 0 234 195 c 0 0 0 0 77 61 630 0 0 0 0 630 77 168 g 0 0 0 0 157 51 0 1 0 0 0 0 27 73 t 0 0 0 0 191 288 0 629 630 630 630 0 292 194
MA0152.1_shift7 (NFATC2)	0.811	0.568	6.389	0.551	0.878	1.459	0.896	15	6	12	5	23	11	17	12.714	9	; oligos_6nt_mkv4_m1 versus MA0152.1 (NFATC2); m=1/2; ncol2=7; w=7; offset=3; strand=D; shift=7; score=12.7143; -------TTTTCCA ; cor=0.811; Ncor=0.568; logoDP=6.389; NIcor=0.551; NsEucl=0.878; SSD=1.459; NSW=0.896; rcor=15; rNcor=6; rlogoDP=12; rNIcor=5; rNsEucl=23; rSSD=11; rNSW=17; rank_mean=12.714; match_rank=9 a 0 0 0 0 0 0 0 3 1 1 0 1 0 18 c 0 0 0 0 0 0 0 1 2 1 0 25 26 3 g 0 0 0 0 0 0 0 2 2 0 0 0 0 1 t 0 0 0 0 0 0 0 20 21 24 26 0 0 4
MA0029.1_rc_shift0 (Mecom_rc)	0.758	0.542	1.509	-0.029	0.888	2.506	0.875	25	8	22	23	18	26	24	20.857	27	; oligos_6nt_mkv4_m1 versus MA0029.1_rc (Mecom_rc); m=2/2; ncol2=14; w=10; offset=-4; strand=R; shift=0; score=20.8571; tvTTATCTTrTCTt ; cor=0.758; Ncor=0.542; logoDP=1.509; NIcor=-0.029; NsEucl=0.888; SSD=2.506; NSW=0.875; rcor=25; rNcor=8; rlogoDP=22; rNIcor=23; rNsEucl=18; rSSD=26; rNSW=24; rank_mean=20.857; match_rank=27 a 3 7 0 2 24 0 0 0 0 16 0 1 4 5 c 3 7 4 0 0 0 27 1 0 0 0 25 2 6 g 6 7 0 1 3 0 0 0 0 10 0 1 1 2 t 15 6 23 24 0 27 0 26 27 1 27 0 20 14

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; ccGCCCCCCAGCCCCss ; Alignment reference a 2 6 3 5 0 2 0 0 0 18 1 0 0 2 1 4 5 c 13 11 0 19 22 23 24 25 24 3 3 24 21 22 25 8 8 g 6 5 23 0 2 1 2 1 2 3 22 1 2 1 0 10 9 t 5 4 0 2 2 0 0 0 0 2 0 1 3 1 0 4 4

MA0079.2_shift6 (SP1) 0.822 0.483 5.411 0.472 0.910 1.631 0.918 11 17 15 12 10 15 9 12.714 10
; dyads_m1 versus MA0079.2 (SP1); m=1/1; ncol2=10; w=10; offset=6; strand=D; shift=6; score=12.7143; ------CCCCkCCCCC- ; cor=0.822; Ncor=0.483; logoDP=5.411; NIcor=0.472; NsEucl=0.910; SSD=1.631; NSW=0.918; rcor=11; rNcor=17; rlogoDP=15; rNIcor=12; rNsEucl=10; rSSD=15; rNSW=9; rank_mean=12.714; match_rank=10 a 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 c 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 g 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 t 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m1_shift0 (dyads_m1)																		; dyads_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; ccGCCCCCCAGCCCCss ; Alignment reference a 2 6 3 5 0 2 0 0 0 18 1 0 0 2 1 4 5 c 13 11 0 19 22 23 24 25 24 3 3 24 21 22 25 8 8 g 6 5 23 0 2 1 2 1 2 3 22 1 2 1 0 10 9 t 5 4 0 2 2 0 0 0 0 2 0 1 3 1 0 4 4
MA0079.2_shift6 (SP1)		0.822	0.483	5.411	0.472	0.910	1.631	0.918	11	17	15	12	10	15	9	12.714	10	; dyads_m1 versus MA0079.2 (SP1); m=1/1; ncol2=10; w=10; offset=6; strand=D; shift=6; score=12.7143; ------CCCCkCCCCC- ; cor=0.822; Ncor=0.483; logoDP=5.411; NIcor=0.472; NsEucl=0.910; SSD=1.631; NSW=0.918; rcor=11; rNcor=17; rlogoDP=15; rNIcor=12; rNsEucl=10; rSSD=15; rNSW=9; rank_mean=12.714; match_rank=10 a 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 c 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 g 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 t 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift3 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv5_m1_shift3 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=3; ncol=15; ---dtATTTTTAdww ; Alignment reference a 0 0 0 325 297 1277 0 0 0 0 0 1277 451 425 527 c 0 0 0 181 246 0 0 0 0 0 0 0 106 113 141 g 0 0 0 350 120 0 0 0 0 0 0 0 339 158 173 t 0 0 0 421 614 0 1277 1277 1277 1277 1277 0 381 581 436

MA0497.1_rc_shift1 (MEF2C_rc) 0.828 0.663 0.437 -0.188 0.920 1.822 0.924 10 2 25 27 5 16 8 13.286 11
; oligos_7nt_mkv5_m1 versus MA0497.1_rc (MEF2C_rc); m=1/4; ncol2=15; w=12; offset=-2; strand=R; shift=1; score=13.2857; -wkCTATTTTTrgmh ; cor=0.828; Ncor=0.663; logoDP=0.437; NIcor=-0.188; NsEucl=0.920; SSD=1.822; NSW=0.924; rcor=10; rNcor=2; rlogoDP=25; rNIcor=27; rNsEucl=5; rSSD=16; rNSW=8; rank_mean=13.286; match_rank=11 a 0 624 250 29 0 2091 70 76 15 230 263 1224 337 760 752 c 0 126 148 1671 32 0 4 2 87 241 74 0 78 822 573 g 0 450 836 120 0 62 0 0 0 32 256 985 1412 196 151 t 0 1009 975 389 2177 56 2135 2131 2107 1706 1616 0 382 431 733

MA0052.1_shift3 (MEF2A) 0.782 0.652 9.521 0.612 0.889 2.451 0.877 21 4 2 3 16 25 23 13.429 12
; oligos_7nt_mkv5_m1 versus MA0052.1 (MEF2A); m=2/4; ncol2=10; w=10; offset=0; strand=D; shift=3; score=13.4286; ---CTATTTwTAG-- ; cor=0.782; Ncor=0.652; logoDP=9.521; NIcor=0.612; NsEucl=0.889; SSD=2.451; NSW=0.877; rcor=21; rNcor=4; rlogoDP=2; rNIcor=3; rNsEucl=16; rSSD=25; rNSW=23; rank_mean=13.429; match_rank=12 a 0 0 0 1 0 57 2 9 6 37 2 56 6 0 0 c 0 0 0 50 0 1 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2 50 0 0 t 0 0 0 7 58 0 55 49 52 21 56 0 2 0 0

MA0052.2_rc_shift0 (MEF2A_rc) 0.816 0.653 2.905 0.033 0.916 2.012 0.916 13 3 19 21 7 20 12 13.571 13
; oligos_7nt_mkv5_m1 versus MA0052.2_rc (MEF2A_rc); m=3/4; ncol2=15; w=12; offset=-3; strand=R; shift=0; score=13.5714; rdkCTATTTTTrGmh ; cor=0.816; Ncor=0.653; logoDP=2.905; NIcor=0.033; NsEucl=0.916; SSD=2.012; NSW=0.916; rcor=13; rNcor=3; rlogoDP=19; rNIcor=21; rNsEucl=7; rSSD=20; rNSW=12; rank_mean=13.571; match_rank=13 a 476 424 142 33 1 1467 83 116 51 346 119 1000 146 530 465 c 203 110 112 1160 0 0 0 0 39 119 14 0 32 625 379 g 449 409 632 49 0 0 0 5 0 0 68 473 1179 149 148 t 345 530 587 231 1472 6 1390 1352 1383 1008 1272 0 116 169 481

MA0465.1_rc_shift7 (CDX2_rc) 0.819 0.437 1.051 -0.020 0.890 1.536 0.904 12 23 23 22 15 14 15 17.714 20
; oligos_7nt_mkv5_m1 versus MA0465.1_rc (CDX2_rc); m=4/4; ncol2=11; w=8; offset=4; strand=R; shift=7; score=17.7143; -------tTTTATkr ; cor=0.819; Ncor=0.437; logoDP=1.051; NIcor=-0.020; NsEucl=0.890; SSD=1.536; NSW=0.904; rcor=12; rNcor=23; rlogoDP=23; rNIcor=22; rNsEucl=15; rSSD=14; rNSW=15; rank_mean=17.714; match_rank=20 a 0 0 0 0 0 0 0 121 0 0 0 1597 0 68 549 c 0 0 0 0 0 0 0 313 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 150 0 0 0 0 0 832 1048 t 0 0 0 0 0 0 0 1013 1597 1597 1597 0 1597 697 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m1_shift3 (oligos_7nt_mkv5_m1)																	; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=3; ncol=15; ---dtATTTTTAdww ; Alignment reference a 0 0 0 325 297 1277 0 0 0 0 0 1277 451 425 527 c 0 0 0 181 246 0 0 0 0 0 0 0 106 113 141 g 0 0 0 350 120 0 0 0 0 0 0 0 339 158 173 t 0 0 0 421 614 0 1277 1277 1277 1277 1277 0 381 581 436
MA0497.1_rc_shift1 (MEF2C_rc)	0.828	0.663	0.437	-0.188	0.920	1.822	0.924	10	2	25	27	5	16	8	13.286	11	; oligos_7nt_mkv5_m1 versus MA0497.1_rc (MEF2C_rc); m=1/4; ncol2=15; w=12; offset=-2; strand=R; shift=1; score=13.2857; -wkCTATTTTTrgmh ; cor=0.828; Ncor=0.663; logoDP=0.437; NIcor=-0.188; NsEucl=0.920; SSD=1.822; NSW=0.924; rcor=10; rNcor=2; rlogoDP=25; rNIcor=27; rNsEucl=5; rSSD=16; rNSW=8; rank_mean=13.286; match_rank=11 a 0 624 250 29 0 2091 70 76 15 230 263 1224 337 760 752 c 0 126 148 1671 32 0 4 2 87 241 74 0 78 822 573 g 0 450 836 120 0 62 0 0 0 32 256 985 1412 196 151 t 0 1009 975 389 2177 56 2135 2131 2107 1706 1616 0 382 431 733
MA0052.1_shift3 (MEF2A)	0.782	0.652	9.521	0.612	0.889	2.451	0.877	21	4	2	3	16	25	23	13.429	12	; oligos_7nt_mkv5_m1 versus MA0052.1 (MEF2A); m=2/4; ncol2=10; w=10; offset=0; strand=D; shift=3; score=13.4286; ---CTATTTwTAG-- ; cor=0.782; Ncor=0.652; logoDP=9.521; NIcor=0.612; NsEucl=0.889; SSD=2.451; NSW=0.877; rcor=21; rNcor=4; rlogoDP=2; rNIcor=3; rNsEucl=16; rSSD=25; rNSW=23; rank_mean=13.429; match_rank=12 a 0 0 0 1 0 57 2 9 6 37 2 56 6 0 0 c 0 0 0 50 0 1 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2 50 0 0 t 0 0 0 7 58 0 55 49 52 21 56 0 2 0 0
MA0052.2_rc_shift0 (MEF2A_rc)	0.816	0.653	2.905	0.033	0.916	2.012	0.916	13	3	19	21	7	20	12	13.571	13	; oligos_7nt_mkv5_m1 versus MA0052.2_rc (MEF2A_rc); m=3/4; ncol2=15; w=12; offset=-3; strand=R; shift=0; score=13.5714; rdkCTATTTTTrGmh ; cor=0.816; Ncor=0.653; logoDP=2.905; NIcor=0.033; NsEucl=0.916; SSD=2.012; NSW=0.916; rcor=13; rNcor=3; rlogoDP=19; rNIcor=21; rNsEucl=7; rSSD=20; rNSW=12; rank_mean=13.571; match_rank=13 a 476 424 142 33 1 1467 83 116 51 346 119 1000 146 530 465 c 203 110 112 1160 0 0 0 0 39 119 14 0 32 625 379 g 449 409 632 49 0 0 0 5 0 0 68 473 1179 149 148 t 345 530 587 231 1472 6 1390 1352 1383 1008 1272 0 116 169 481
MA0465.1_rc_shift7 (CDX2_rc)	0.819	0.437	1.051	-0.020	0.890	1.536	0.904	12	23	23	22	15	14	15	17.714	20	; oligos_7nt_mkv5_m1 versus MA0465.1_rc (CDX2_rc); m=4/4; ncol2=11; w=8; offset=4; strand=R; shift=7; score=17.7143; -------tTTTATkr ; cor=0.819; Ncor=0.437; logoDP=1.051; NIcor=-0.020; NsEucl=0.890; SSD=1.536; NSW=0.904; rcor=12; rNcor=23; rlogoDP=23; rNIcor=22; rNsEucl=15; rSSD=14; rNSW=15; rank_mean=17.714; match_rank=20 a 0 0 0 0 0 0 0 121 0 0 0 1597 0 68 549 c 0 0 0 0 0 0 0 313 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 150 0 0 0 0 0 832 1048 t 0 0 0 0 0 0 0 1013 1597 1597 1597 0 1597 697 0

One-to-n matrix alignment; reference matrix: positions_6nt_shift1 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_shift1 (positions_6nt)
; positions_6nt; m=0 (reference); ncol1=10; shift=1; ncol=11; -CGCGCGCGCG ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 c 0 6 0 6 0 6 0 6 0 6 0 g 0 0 6 0 6 0 6 0 6 0 6 t 0 0 0 0 0 0 0 0 0 0 0

MA0506.1_shift0 (NRF1) 0.760 0.691 10.568 0.669 0.874 3.190 0.840 24 1 1 1 24 27 27 15.000 17
; positions_6nt versus MA0506.1 (NRF1); m=1/1; ncol2=11; w=10; offset=-1; strand=D; shift=0; score= 15; GCGCmTGCGCr ; cor=0.760; Ncor=0.691; logoDP=10.568; NIcor=0.669; NsEucl=0.874; SSD=3.190; NSW=0.840; rcor=24; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=24; rSSD=27; rNSW=27; rank_mean=15.000; match_rank=17 a 602 623 196 0 1514 0 0 0 0 74 2245 c 375 4001 189 4016 1862 403 0 4338 349 4550 804 g 3647 0 4239 468 935 528 4624 0 4275 0 1575 t 0 0 0 140 313 3693 0 286 0 0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_shift1 (positions_6nt)																		; positions_6nt; m=0 (reference); ncol1=10; shift=1; ncol=11; -CGCGCGCGCG ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 c 0 6 0 6 0 6 0 6 0 6 0 g 0 0 6 0 6 0 6 0 6 0 6 t 0 0 0 0 0 0 0 0 0 0 0
MA0506.1_shift0 (NRF1)		0.760	0.691	10.568	0.669	0.874	3.190	0.840	24	1	1	1	24	27	27	15.000	17	; positions_6nt versus MA0506.1 (NRF1); m=1/1; ncol2=11; w=10; offset=-1; strand=D; shift=0; score= 15; GCGCmTGCGCr ; cor=0.760; Ncor=0.691; logoDP=10.568; NIcor=0.669; NsEucl=0.874; SSD=3.190; NSW=0.840; rcor=24; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=24; rSSD=27; rNSW=27; rank_mean=15.000; match_rank=17 a 602 623 196 0 1514 0 0 0 0 74 2245 c 375 4001 189 4016 1862 403 0 4338 349 4550 804 g 3647 0 4239 468 935 528 4624 0 4275 0 1575 t 0 0 0 140 313 3693 0 286 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=13; yyCTGCCTCmg-- ; Alignment reference a 136 100 1 20 14 7 1 13 2 315 114 0 0 c 256 419 890 62 1 865 869 1 890 252 202 0 0 g 133 118 2 27 877 1 21 30 0 162 401 0 0 t 368 256 0 784 1 20 2 849 1 164 176 0 0

MA0003.1_shift4 (TFAP2A) 0.773 0.416 5.145 0.401 0.878 1.454 0.896 22 26 17 16 22 10 16 18.429 23
; oligos_7nt_mkv5_m2 versus MA0003.1 (TFAP2A); m=1/1; ncol2=9; w=7; offset=4; strand=D; shift=4; score=18.4286; ----GCCcbrrGs ; cor=0.773; Ncor=0.416; logoDP=5.145; NIcor=0.401; NsEucl=0.878; SSD=1.454; NSW=0.896; rcor=22; rNcor=26; rlogoDP=17; rNIcor=16; rNsEucl=22; rSSD=10; rNSW=16; rank_mean=18.429; match_rank=23 a 0 0 0 0 0 0 0 22 19 55 53 19 9 c 0 0 0 0 0 185 185 71 57 44 30 16 78 g 0 0 0 0 185 0 0 46 61 67 91 137 79 t 0 0 0 0 0 0 0 46 48 19 11 13 19