One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.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/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)                                
; positions_7nt_m3; m=0 (reference); ncol1=16; shift=0; ncol=17; srTTTCYwGGAArtsr-
; Alignment reference
a	225	433	191	3	3	105	1	380	30	39	1231	1228	634	142	240	404	0
c	372	246	86	4	3	1125	892	153	7	2	2	3	44	216	326	279	0
g	375	329	66	7	2	3	1	306	1196	1157	1	2	411	156	453	317	0
t	265	229	894	1223	1229	4	343	398	4	39	3	4	148	723	218	237	0
MA0137.2_rc_shift0 (STAT1_rc) 0.975 0.914 8.663 0.878 0.974 0.307 0.990 1 1 5 2 1 1 1 1.714 1
; positions_7nt_m3 versus MA0137.2_rc (STAT1_rc); m=1/5; ncol2=15; w=15; offset=0; strand=R; shift=0; score= 1.7143; gryTTCydGGAArtg--
; cor=0.975; Ncor=0.914; logoDP=8.663; NIcor=0.878; NsEucl=0.974; SSD=0.307; NSW=0.990; rcor=1; rNcor=1; rlogoDP=5; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1
a	431	714	315	15	32	302	66	680	155	44	2023	2038	1112	446	378	0	0
c	425	270	552	23	29	1700	1292	115	7	14	38	11	144	279	415	0	0
g	804	760	263	17	124	30	31	762	1900	1921	14	22	574	496	1076	0	0
t	417	336	954	2030	1900	53	696	528	23	106	8	10	251	859	208	0	0
MA0144.1_shift3 (Stat3) 0.963 0.602 9.169 0.595 0.956 0.390 0.980 4 8 2 7 5 5 4 5.000 4
; positions_7nt_m3 versus MA0144.1 (Stat3); m=2/5; ncol2=10; w=10; offset=3; strand=D; shift=3; score=      5; ---TTCCaGGAAr----
; cor=0.963; Ncor=0.602; logoDP=9.169; NIcor=0.595; NsEucl=0.956; SSD=0.390; NSW=0.980; rcor=4; rNcor=8; rlogoDP=2; rNIcor=7; rNsEucl=5; rSSD=5; rNSW=4; rank_mean=5.000; match_rank=4
a	0	0	0	20	13	38	6	321	8	6	585	606	191	0	0	0	0
c	0	0	0	19	10	552	541	21	0	2	21	1	15	0	0	0	0
g	0	0	0	25	129	9	1	148	605	592	7	5	393	0	0	0	0
t	0	0	0	549	461	14	65	123	0	13	0	1	14	0	0	0	0
MA0156.1_shift6 (FEV) 0.925 0.462 6.770 0.460 0.929 0.646 0.960 10 19 11 16 13 11 11 13.000 10
; positions_7nt_m3 versus MA0156.1 (FEV); m=3/5; ncol2=8; w=8; offset=6; strand=D; shift=6; score=     13; ------CAGGAArT---
; cor=0.925; Ncor=0.462; logoDP=6.770; NIcor=0.460; NsEucl=0.929; SSD=0.646; NSW=0.960; rcor=10; rNcor=19; rlogoDP=11; rNIcor=16; rNsEucl=13; rSSD=11; rNSW=11; rank_mean=13.000; match_rank=10
a	0	0	0	0	0	0	2	9	0	0	13	12	7	0	0	0	0
c	0	0	0	0	0	0	9	3	0	0	0	0	0	0	0	0	0
g	0	0	0	0	0	0	1	1	13	13	0	0	6	0	0	0	0
t	0	0	0	0	0	0	1	0	0	0	0	1	0	13	0	0	0
MA0062.2_shift6 (GABPA) 0.822 0.483 7.163 0.488 0.910 1.621 0.919 24 15 10 12 19 26 24 18.571 19
; positions_7nt_m3 versus MA0062.2 (GABPA); m=4/5; ncol2=11; w=10; offset=6; strand=D; shift=6; score=18.5714; ------CCGGAAGygvc
; cor=0.822; Ncor=0.483; logoDP=7.163; NIcor=0.488; NsEucl=0.910; SSD=1.621; NSW=0.919; rcor=24; rNcor=15; rlogoDP=10; rNIcor=12; rNsEucl=19; rSSD=26; rNSW=24; rank_mean=18.571; match_rank=19
a	0	0	0	0	0	0	32	70	0	0	991	989	94	56	154	264	233
c	0	0	0	0	0	0	768	914	0	0	1	2	32	261	137	262	357
g	0	0	0	0	0	0	188	4	990	991	1	0	866	37	603	415	224
t	0	0	0	0	0	0	1	1	1	0	0	2	0	637	96	49	176
MA0136.1_rc_shift6 (ELF5_rc) 0.834 0.469 0.177 -0.102 0.917 1.111 0.938 23 18 28 26 17 19 16 21.000 22
; positions_7nt_m3 versus MA0136.1_rc (ELF5_rc); m=5/5; ncol2=9; w=9; offset=6; strand=R; shift=6; score=     21; ------mmGGAwrtw--
; cor=0.834; Ncor=0.469; logoDP=0.177; NIcor=-0.102; NsEucl=0.917; SSD=1.111; NSW=0.938; rcor=23; rNcor=18; rlogoDP=28; rNIcor=26; rNsEucl=17; rSSD=19; rNSW=16; rank_mean=21.000; match_rank=22
a	0	0	0	0	0	0	21	26	0	0	43	29	17	5	20	0	0
c	0	0	0	0	0	0	11	11	0	0	0	1	5	7	3	0	0
g	0	0	0	0	0	0	8	3	44	44	1	0	20	3	9	0	0
t	0	0	0	0	0	0	4	4	0	0	0	14	2	29	12	0	0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift1 ; 9 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)                                
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=13; shift=1; ncol=16; -ryTTCCmrGAAry--
; Alignment reference
a	0	381	217	0	4	8	1	597	450	1	1213	1217	492	233	0	0
c	0	271	347	0	0	1168	1214	612	1	0	3	2	185	354	0	0
g	0	337	158	3	1	0	4	10	768	1195	0	0	333	244	0	0
t	0	230	497	1216	1214	43	0	0	0	23	3	0	209	388	0	0
MA0137.2_shift0 (STAT1) 0.972 0.842 9.634 0.851 0.969 0.329 0.987 2 3 1 3 3 2 2 2.286 2
; oligos_7nt_mkv4_m3 versus MA0137.2 (STAT1); m=1/8; ncol2=15; w=13; offset=-1; strand=D; shift=0; score= 2.2857; cayTTCChrGAAryc-
; cor=0.972; Ncor=0.842; logoDP=9.634; NIcor=0.851; NsEucl=0.969; SSD=0.329; NSW=0.987; rcor=2; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2
a	208	859	251	10	8	106	23	528	696	53	1900	2030	954	336	417	0
c	1076	496	574	22	14	1921	1900	762	31	30	124	17	263	760	804	0
g	415	279	144	11	38	14	7	115	1292	1700	29	23	552	270	425	0
t	378	446	1112	2038	2023	44	155	680	66	302	32	15	315	714	431	0
MA0144.1_rc_shift2 (Stat3_rc) 0.922 0.709 4.339 0.204 0.934 0.861 0.957 11 4 24 24 9 13 12 13.857 11
; oligos_7nt_mkv4_m3 versus MA0144.1_rc (Stat3_rc); m=2/8; ncol2=10; w=10; offset=1; strand=R; shift=2; score=13.8571; --yTTCCtGGAA----
; cor=0.922; Ncor=0.709; logoDP=4.339; NIcor=0.204; NsEucl=0.934; SSD=0.861; NSW=0.957; rcor=11; rNcor=4; rlogoDP=24; rNIcor=24; rNsEucl=9; rSSD=13; rNSW=12; rank_mean=13.857; match_rank=11
a	0	0	14	1	0	13	0	123	65	14	461	549	0	0	0	0
c	0	0	393	5	7	592	605	148	1	9	129	25	0	0	0	0
g	0	0	15	1	21	2	0	21	541	552	10	19	0	0	0	0
t	0	0	191	606	585	6	8	321	6	38	13	20	0	0	0	0
MA0152.1_shift1 (NFATC2) 0.875 0.471 6.581 0.469 0.904 0.901 0.936 16 17 12 14 22 14 17 16.000 14
; oligos_7nt_mkv4_m3 versus MA0152.1 (NFATC2); m=3/8; ncol2=7; w=7; offset=0; strand=D; shift=1; score=     16; -TTTTCCA--------
; cor=0.875; Ncor=0.471; logoDP=6.581; NIcor=0.469; NsEucl=0.904; SSD=0.901; NSW=0.936; rcor=16; rNcor=17; rlogoDP=12; rNIcor=14; rNsEucl=22; rSSD=14; rNSW=17; rank_mean=16.000; match_rank=14
a	0	3	1	1	0	1	0	18	0	0	0	0	0	0	0	0
c	0	1	2	1	0	25	26	3	0	0	0	0	0	0	0	0
g	0	2	2	0	0	0	0	1	0	0	0	0	0	0	0	0
t	0	20	21	24	26	0	0	4	0	0	0	0	0	0	0	0
MA0156.1_shift6 (FEV) 0.846 0.521 6.282 0.484 0.901 1.264 0.921 20 11 15 13 24 21 22 18.000 16
; oligos_7nt_mkv4_m3 versus MA0156.1 (FEV); m=4/8; ncol2=8; w=8; offset=5; strand=D; shift=6; score=     18; ------CAGGAArT--
; cor=0.846; Ncor=0.521; logoDP=6.282; NIcor=0.484; NsEucl=0.901; SSD=1.264; NSW=0.921; rcor=20; rNcor=11; rlogoDP=15; rNIcor=13; rNsEucl=24; rSSD=21; rNSW=22; rank_mean=18.000; match_rank=16
a	0	0	0	0	0	0	2	9	0	0	13	12	7	0	0	0
c	0	0	0	0	0	0	9	3	0	0	0	0	0	0	0	0
g	0	0	0	0	0	0	1	1	13	13	0	0	6	0	0	0
t	0	0	0	0	0	0	1	0	0	0	0	1	0	13	0	0
MA0080.2_shift7 (SPI1) 0.842 0.453 5.422 0.442 0.895 1.081 0.923 22 21 18 19 29 18 21 21.143 23
; oligos_7nt_mkv4_m3 versus MA0080.2 (SPI1); m=5/8; ncol2=7; w=7; offset=6; strand=D; shift=7; score=21.1429; -------AGGAAGT--
; cor=0.842; Ncor=0.453; logoDP=5.422; NIcor=0.442; NsEucl=0.895; SSD=1.081; NSW=0.923; rcor=22; rNcor=21; rlogoDP=18; rNIcor=19; rNsEucl=29; rSSD=18; rNSW=21; rank_mean=21.143; match_rank=23
a	0	0	0	0	0	0	0	33	4	4	42	41	5	3	0	0
c	0	0	0	0	0	0	0	3	0	0	0	0	3	5	0	0
g	0	0	0	0	0	0	0	6	37	38	0	1	33	2	0	0
t	0	0	0	0	0	0	0	0	1	0	0	0	1	32	0	0
MA0098.1_rc_shift7 (ETS1_rc) 0.876 0.404 0.152 -0.109 0.904 0.662 0.945 15 30 29 28 23 12 15 21.714 25
; oligos_7nt_mkv4_m3 versus MA0098.1_rc (ETS1_rc); m=6/8; ncol2=6; w=6; offset=6; strand=R; shift=7; score=21.7143; -------mGGAwr---
; cor=0.876; Ncor=0.404; logoDP=0.152; NIcor=-0.109; NsEucl=0.904; SSD=0.662; NSW=0.945; rcor=15; rNcor=30; rlogoDP=29; rNIcor=28; rNsEucl=23; rSSD=12; rNSW=15; rank_mean=21.714; match_rank=25
a	0	0	0	0	0	0	0	15	1	0	39	23	16	0	0	0
c	0	0	0	0	0	0	0	17	0	1	0	0	4	0	0	0
g	0	0	0	0	0	0	0	3	39	39	1	0	16	0	0	0
t	0	0	0	0	0	0	0	5	0	0	0	17	4	0	0	0
MA0062.2_shift6 (GABPA) 0.845 0.422 7.243 0.402 0.897 1.360 0.915 21 27 9 21 27 22 26 21.857 26
; oligos_7nt_mkv4_m3 versus MA0062.2 (GABPA); m=7/8; ncol2=11; w=8; offset=5; strand=D; shift=6; score=21.8571; ------CCGGAAGygv
; cor=0.845; Ncor=0.422; logoDP=7.243; NIcor=0.402; NsEucl=0.897; SSD=1.360; NSW=0.915; rcor=21; rNcor=27; rlogoDP=9; rNIcor=21; rNsEucl=27; rSSD=22; rNSW=26; rank_mean=21.857; match_rank=26
a	0	0	0	0	0	0	32	70	0	0	991	989	94	56	154	264
c	0	0	0	0	0	0	768	914	0	0	1	2	32	261	137	262
g	0	0	0	0	0	0	188	4	990	991	1	0	866	37	603	415
t	0	0	0	0	0	0	1	1	1	0	0	2	0	637	96	49
MA0136.1_rc_shift6 (ELF5_rc) 0.758 0.433 0.210 -0.127 0.888 1.608 0.899 30 24 27 29 30 25 30 27.857 30
; oligos_7nt_mkv4_m3 versus MA0136.1_rc (ELF5_rc); m=8/8; ncol2=9; w=8; offset=5; strand=R; shift=6; score=27.8571; ------mmGGAwrtw-
; cor=0.758; Ncor=0.433; logoDP=0.210; NIcor=-0.127; NsEucl=0.888; SSD=1.608; NSW=0.899; rcor=30; rNcor=24; rlogoDP=27; rNIcor=29; rNsEucl=30; rSSD=25; rNSW=30; rank_mean=27.857; match_rank=30
a	0	0	0	0	0	0	21	26	0	0	43	29	17	5	20	0
c	0	0	0	0	0	0	11	11	0	0	0	1	5	7	3	0
g	0	0	0	0	0	0	8	3	44	44	1	0	20	3	9	0
t	0	0	0	0	0	0	4	4	0	0	0	14	2	29	12	0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 7 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)                                
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=14; shift=0; ncol=15; srTTTCCwGGAAay-
; Alignment reference
a	237	426	84	1	1	178	0	456	265	0	1319	1318	550	257	0
c	455	268	57	1	40	1142	1320	266	1	0	0	2	202	358	0
g	349	370	74	0	0	0	0	176	1054	1138	0	0	315	228	0
t	279	256	1105	1318	1279	0	0	422	0	182	1	0	253	477	0
MA0137.2_shift0 (STAT1) 0.967 0.903 9.138 0.901 0.969 0.372 0.987 3 2 3 1 2 4 3 2.571 3
; oligos_7nt_mkv4_m1 versus MA0137.2 (STAT1); m=1/6; ncol2=15; w=14; offset=0; strand=D; shift=0; score= 2.5714; cayTTCChrGAAryc
; cor=0.967; Ncor=0.903; logoDP=9.138; NIcor=0.901; NsEucl=0.969; SSD=0.372; NSW=0.987; rcor=3; rNcor=2; rlogoDP=3; rNIcor=1; rNsEucl=2; rSSD=4; rNSW=3; rank_mean=2.571; match_rank=3
a	208	859	251	10	8	106	23	528	696	53	1900	2030	954	336	417
c	1076	496	574	22	14	1921	1900	762	31	30	124	17	263	760	804
g	415	279	144	11	38	14	7	115	1292	1700	29	23	552	270	425
t	378	446	1112	2038	2023	44	155	680	66	302	32	15	315	714	431
MA0144.1_shift3 (Stat3) 0.948 0.677 8.999 0.673 0.948 0.541 0.973 6 5 4 5 8 8 7 6.143 6
; oligos_7nt_mkv4_m1 versus MA0144.1 (Stat3); m=2/6; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 6.1429; ---TTCCaGGAAr--
; cor=0.948; Ncor=0.677; logoDP=8.999; NIcor=0.673; NsEucl=0.948; SSD=0.541; NSW=0.973; rcor=6; rNcor=5; rlogoDP=4; rNIcor=5; rNsEucl=8; rSSD=8; rNSW=7; rank_mean=6.143; match_rank=6
a	0	0	0	20	13	38	6	321	8	6	585	606	191	0	0
c	0	0	0	19	10	552	541	21	0	2	21	1	15	0	0
g	0	0	0	25	129	9	1	148	605	592	7	5	393	0	0
t	0	0	0	549	461	14	65	123	0	13	0	1	14	0	0
MA0152.1_shift1 (NFATC2) 0.913 0.456 6.329 0.454 0.919 0.639 0.954 13 20 14 17 16 10 13 14.714 12
; oligos_7nt_mkv4_m1 versus MA0152.1 (NFATC2); m=3/6; ncol2=7; w=7; offset=1; strand=D; shift=1; score=14.7143; -TTTTCCA-------
; cor=0.913; Ncor=0.456; logoDP=6.329; NIcor=0.454; NsEucl=0.919; SSD=0.639; NSW=0.954; rcor=13; rNcor=20; rlogoDP=14; rNIcor=17; rNsEucl=16; rSSD=10; rNSW=13; rank_mean=14.714; match_rank=12
a	0	3	1	1	0	1	0	18	0	0	0	0	0	0	0
c	0	1	2	1	0	25	26	3	0	0	0	0	0	0	0
g	0	2	2	0	0	0	0	1	0	0	0	0	0	0	0
t	0	20	21	24	26	0	0	4	0	0	0	0	0	0	0
MA0156.1_shift6 (FEV) 0.858 0.491 5.956 0.468 0.905 1.161 0.927 18 13 17 15 21 20 20 17.714 15
; oligos_7nt_mkv4_m1 versus MA0156.1 (FEV); m=4/6; ncol2=8; w=8; offset=6; strand=D; shift=6; score=17.7143; ------CAGGAArT-
; cor=0.858; Ncor=0.491; logoDP=5.956; NIcor=0.468; NsEucl=0.905; SSD=1.161; NSW=0.927; rcor=18; rNcor=13; rlogoDP=17; rNIcor=15; rNsEucl=21; rSSD=20; rNSW=20; rank_mean=17.714; match_rank=15
a	0	0	0	0	0	0	2	9	0	0	13	12	7	0	0
c	0	0	0	0	0	0	9	3	0	0	0	0	0	0	0
g	0	0	0	0	0	0	1	1	13	13	0	0	6	0	0
t	0	0	0	0	0	0	1	0	0	0	0	1	0	13	0
MA0080.2_shift7 (SPI1) 0.855 0.427 5.088 0.423 0.899 1.000 0.929 19 26 20 20 26 17 19 21.000 21
; oligos_7nt_mkv4_m1 versus MA0080.2 (SPI1); m=5/6; ncol2=7; w=7; offset=7; strand=D; shift=7; score=     21; -------AGGAAGT-
; cor=0.855; Ncor=0.427; logoDP=5.088; NIcor=0.423; NsEucl=0.899; SSD=1.000; NSW=0.929; rcor=19; rNcor=26; rlogoDP=20; rNIcor=20; rNsEucl=26; rSSD=17; rNSW=19; rank_mean=21.000; match_rank=21
a	0	0	0	0	0	0	0	33	4	4	42	41	5	3	0
c	0	0	0	0	0	0	0	3	0	0	0	0	3	5	0
g	0	0	0	0	0	0	0	6	37	38	0	1	33	2	0
t	0	0	0	0	0	0	0	0	1	0	0	0	1	32	0
MA0136.1_shift0 (ELF5) 0.760 0.488 5.328 0.495 0.899 1.651 0.908 29 14 19 11 25 27 29 22.000 27
; oligos_7nt_mkv4_m1 versus MA0136.1 (ELF5); m=6/6; ncol2=9; w=9; offset=0; strand=D; shift=0; score=     22; waywTCCkk------
; cor=0.760; Ncor=0.488; logoDP=5.328; NIcor=0.495; NsEucl=0.899; SSD=1.651; NSW=0.908; rcor=29; rNcor=14; rlogoDP=19; rNIcor=11; rNsEucl=25; rSSD=27; rNSW=29; rank_mean=22.000; match_rank=27
a	12	29	2	14	0	0	0	4	4	0	0	0	0	0	0
c	9	3	20	0	1	44	44	3	8	0	0	0	0	0	0
g	3	7	5	1	0	0	0	11	11	0	0	0	0	0	0
t	20	5	17	29	43	0	0	26	21	0	0	0	0	0	0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)                                
; positions_7nt_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; wsTsrTTTCCwGGAAatsAsa
; Alignment reference
a	124	107	52	35	289	18	1	4	77	11	153	80	33	472	477	287	85	17	330	114	138
c	117	138	39	167	31	113	2	28	401	442	92	2	4	8	3	30	87	196	57	143	117
g	112	148	53	247	137	19	2	6	2	3	97	395	400	2	2	105	23	244	51	131	113
t	131	91	340	35	27	334	479	446	4	28	142	7	47	2	2	62	289	27	46	96	116
MA0137.2_rc_shift3 (STAT1_rc) 0.945 0.675 7.824 0.676 0.963 0.625 0.979 8 6 6 4 4 9 5 6.000 5
; positions_7nt_m1 versus MA0137.2_rc (STAT1_rc); m=1/3; ncol2=15; w=15; offset=3; strand=R; shift=3; score=      6; ---gryTTCydGGAArtg---
; cor=0.945; Ncor=0.675; logoDP=7.824; NIcor=0.676; NsEucl=0.963; SSD=0.625; NSW=0.979; rcor=8; rNcor=6; rlogoDP=6; rNIcor=4; rNsEucl=4; rSSD=9; rNSW=5; rank_mean=6.000; match_rank=5
a	0	0	0	431	714	315	15	32	302	66	680	155	44	2023	2038	1112	446	378	0	0	0
c	0	0	0	425	270	552	23	29	1700	1292	115	7	14	38	11	144	279	415	0	0	0
g	0	0	0	804	760	263	17	124	30	31	762	1900	1921	14	22	574	496	1076	0	0	0
t	0	0	0	417	336	954	2030	1900	53	696	528	23	106	8	10	251	859	208	0	0	0
MA0144.1_shift6 (Stat3) 0.948 0.451 7.793 0.447 0.948 0.531 0.973 7 22 7 18 7 7 6 10.571 9
; positions_7nt_m1 versus MA0144.1 (Stat3); m=2/3; ncol2=10; w=10; offset=6; strand=D; shift=6; score=10.5714; ------TTCCaGGAAr-----
; cor=0.948; Ncor=0.451; logoDP=7.793; NIcor=0.447; NsEucl=0.948; SSD=0.531; NSW=0.973; rcor=7; rNcor=22; rlogoDP=7; rNIcor=18; rNsEucl=7; rSSD=7; rNSW=6; rank_mean=10.571; match_rank=9
a	0	0	0	0	0	0	20	13	38	6	321	8	6	585	606	191	0	0	0	0	0
c	0	0	0	0	0	0	19	10	552	541	21	0	2	21	1	15	0	0	0	0	0
g	0	0	0	0	0	0	25	129	9	1	148	605	592	7	5	393	0	0	0	0	0
t	0	0	0	0	0	0	549	461	14	65	123	0	13	0	1	14	0	0	0	0	0
MA0062.2_shift9 (GABPA) 0.778 0.408 5.981 0.399 0.909 2.004 0.909 26 29 16 22 20 28 28 24.143 28
; positions_7nt_m1 versus MA0062.2 (GABPA); m=3/3; ncol2=11; w=11; offset=9; strand=D; shift=9; score=24.1429; ---------CCGGAAGygvc-
; cor=0.778; Ncor=0.408; logoDP=5.981; NIcor=0.399; NsEucl=0.909; SSD=2.004; NSW=0.909; rcor=26; rNcor=29; rlogoDP=16; rNIcor=22; rNsEucl=20; rSSD=28; rNSW=28; rank_mean=24.143; match_rank=28
a	0	0	0	0	0	0	0	0	0	32	70	0	0	991	989	94	56	154	264	233	0
c	0	0	0	0	0	0	0	0	0	768	914	0	0	1	2	32	261	137	262	357	0
g	0	0	0	0	0	0	0	0	0	188	4	990	991	1	0	866	37	603	415	224	0
t	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	637	96	49	176	0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)                                
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rwrTGAsTCATty
; Alignment reference
a	169	181	354	0	0	602	45	0	87	602	16	139	146
c	139	111	41	0	0	1	263	0	516	0	63	133	174
g	162	146	192	0	603	0	243	1	0	1	41	148	115
t	133	165	16	603	0	0	52	602	0	0	483	183	168
MA0099.2_rc_shift3 (AP1_rc) 0.951 0.512 6.533 0.518 0.933 0.441 0.969 5 12 13 8 10 6 9 9.000 7
; oligos_7nt_mkv4_m2 versus MA0099.2_rc (AP1_rc); m=1/3; ncol2=7; w=7; offset=3; strand=R; shift=3; score=      9; ---TGAkTCA---
; cor=0.951; Ncor=0.512; logoDP=6.533; NIcor=0.518; NsEucl=0.933; SSD=0.441; NSW=0.969; rcor=5; rNcor=12; rlogoDP=13; rNIcor=8; rNsEucl=10; rSSD=6; rNSW=9; rank_mean=9.000; match_rank=7
a	0	0	0	1	0	14	0	0	3	17	0	0	0
c	0	0	0	1	3	1	1	0	15	0	0	0	0
g	0	0	0	0	15	0	12	2	0	1	0	0	0
t	0	0	0	16	0	3	5	16	0	0	0	0	0
MA0089.1_rc_shift6 (NFE2L1::MafG_rc) 0.942 0.435 0.077 -0.104 0.931 0.340 0.972 9 23 30 27 12 3 8 16.000 13
; oligos_7nt_mkv4_m2 versus MA0089.1_rc (NFE2L1::MafG_rc); m=2/3; ncol2=6; w=6; offset=6; strand=R; shift=6; score=     16; ------GTCATs-
; cor=0.942; Ncor=0.435; logoDP=0.077; NIcor=-0.104; NsEucl=0.931; SSD=0.340; NSW=0.972; rcor=9; rNcor=23; rlogoDP=30; rNIcor=27; rNsEucl=12; rSSD=3; rNSW=8; rank_mean=16.000; match_rank=13
a	0	0	0	0	0	0	6	0	1	34	0	6	0
c	0	0	0	0	0	0	2	0	32	0	3	10	0
g	0	0	0	0	0	0	26	0	0	0	2	11	0
t	0	0	0	0	0	0	0	34	1	0	29	7	0
MA0067.1_rc_shift0 (Pax2_rc) 0.767 0.472 0.370 -0.142 0.896 1.379 0.914 28 16 26 30 28 24 27 25.571 29
; oligos_7nt_mkv4_m2 versus MA0067.1_rc (Pax2_rc); m=3/3; ncol2=8; w=8; offset=0; strand=R; shift=0; score=25.5714; vmrTGAcw-----
; cor=0.767; Ncor=0.472; logoDP=0.370; NIcor=-0.142; NsEucl=0.896; SSD=1.379; NSW=0.914; rcor=28; rNcor=16; rlogoDP=26; rNIcor=30; rNsEucl=28; rSSD=24; rNSW=27; rank_mean=25.571; match_rank=29
a	8	10	11	1	2	26	2	9	0	0	0	0	0
c	11	19	1	3	1	0	21	5	0	0	0	0	0
g	11	0	17	1	28	2	1	7	0	0	0	0	0
t	1	2	2	26	0	3	7	10	0	0	0	0	0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)                                
; positions_7nt_m2; m=0 (reference); ncol1=21; shift=0; ncol=21; dsTsatTTCCcrGAAATsAsr
; Alignment reference
a	66	48	25	10	127	13	2	1	10	7	49	122	1	210	255	230	20	7	187	63	71
c	57	72	23	129	41	56	3	0	200	226	143	4	1	4	1	12	24	102	22	72	57
g	68	77	23	105	47	15	1	2	3	2	7	132	241	46	4	8	17	137	29	73	68
t	69	63	189	16	45	176	254	257	47	25	61	2	17	0	0	10	199	14	22	52	64
MA0137.2_shift3 (STAT1) 0.916 0.654 7.464 0.646 0.953 0.973 0.968 12 7 8 6 6 16 10 9.286 8
; positions_7nt_m2 versus MA0137.2 (STAT1); m=1/2; ncol2=15; w=15; offset=3; strand=D; shift=3; score= 9.2857; ---cayTTCChrGAAryc---
; cor=0.916; Ncor=0.654; logoDP=7.464; NIcor=0.646; NsEucl=0.953; SSD=0.973; NSW=0.968; rcor=12; rNcor=7; rlogoDP=8; rNIcor=6; rNsEucl=6; rSSD=16; rNSW=10; rank_mean=9.286; match_rank=8
a	0	0	0	208	859	251	10	8	106	23	528	696	53	1900	2030	954	336	417	0	0	0
c	0	0	0	1076	496	574	22	14	1921	1900	762	31	30	124	17	263	760	804	0	0	0
g	0	0	0	415	279	144	11	38	14	7	115	1292	1700	29	23	552	270	425	0	0	0
t	0	0	0	378	446	1112	2038	2023	44	155	680	66	302	32	15	315	714	431	0	0	0
MA0144.1_rc_shift5 (Stat3_rc) 0.906 0.432 2.935 0.118 0.931 0.939 0.953 14 25 25 25 11 15 14 18.429 17
; positions_7nt_m2 versus MA0144.1_rc (Stat3_rc); m=2/2; ncol2=10; w=10; offset=5; strand=R; shift=5; score=18.4286; -----yTTCCtGGAA------
; cor=0.906; Ncor=0.432; logoDP=2.935; NIcor=0.118; NsEucl=0.931; SSD=0.939; NSW=0.953; rcor=14; rNcor=25; rlogoDP=25; rNIcor=25; rNsEucl=11; rSSD=15; rNSW=14; rank_mean=18.429; match_rank=17
a	0	0	0	0	0	14	1	0	13	0	123	65	14	461	549	0	0	0	0	0	0
c	0	0	0	0	0	393	5	7	592	605	148	1	9	129	25	0	0	0	0	0	0
g	0	0	0	0	0	15	1	21	2	0	21	541	552	10	19	0	0	0	0	0	0
t	0	0	0	0	0	191	606	585	6	8	321	6	38	13	20	0	0	0	0	0	0

One-to-n matrix alignment; reference matrix: local_words_7nt_m3_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
local_words_7nt_m3_shift0 (local_words_7nt_m3)                                
; local_words_7nt_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; kdaCATTTyCmrgaAATGtmw
; Alignment reference
a	38	43	81	8	142	9	3	13	24	22	40	68	25	103	157	154	13	10	36	48	40
c	26	35	15	136	4	5	3	5	85	112	75	13	7	11	0	3	9	11	17	40	36
g	43	41	27	6	6	8	0	10	8	0	10	65	96	34	2	1	9	127	21	37	32
t	53	41	37	10	8	138	154	132	43	26	35	14	32	12	1	2	129	12	86	35	52
MA0137.2_shift3 (STAT1) 0.783 0.559 4.929 0.508 0.927 2.382 0.921 25 9 21 9 14 29 23 18.571 18
; local_words_7nt_m3 versus MA0137.2 (STAT1); m=1/1; ncol2=15; w=15; offset=3; strand=D; shift=3; score=18.5714; ---cayTTCChrGAAryc---
; cor=0.783; Ncor=0.559; logoDP=4.929; NIcor=0.508; NsEucl=0.927; SSD=2.382; NSW=0.921; rcor=25; rNcor=9; rlogoDP=21; rNIcor=9; rNsEucl=14; rSSD=29; rNSW=23; rank_mean=18.571; match_rank=18
a	0	0	0	208	859	251	10	8	106	23	528	696	53	1900	2030	954	336	417	0	0	0
c	0	0	0	1076	496	574	22	14	1921	1900	762	31	30	124	17	263	760	804	0	0	0
g	0	0	0	415	279	144	11	38	14	7	115	1292	1700	29	23	552	270	425	0	0	0
t	0	0	0	378	446	1112	2038	2023	44	155	680	66	302	32	15	315	714	431	0	0	0

One-to-n matrix alignment; reference matrix: local_words_7nt_m1_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
local_words_7nt_m1_shift0 (local_words_7nt_m1)                                
; local_words_7nt_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; wbwCATTTcchgkAAATGtat
; Alignment reference
a	53	36	70	5	143	5	3	14	23	15	40	20	22	116	154	129	8	6	39	46	38
c	28	40	24	139	4	1	1	11	97	108	41	10	8	9	1	1	4	10	24	39	39
g	35	40	22	8	8	2	1	11	7	0	29	100	84	20	1	25	4	137	24	36	33
t	43	43	43	7	4	151	154	123	32	36	49	29	45	14	3	4	143	6	72	38	49
MA0137.2_shift3 (STAT1) 0.778 0.556 4.892 0.505 0.925 2.501 0.917 27 10 22 10 15 30 25 19.857 20
; local_words_7nt_m1 versus MA0137.2 (STAT1); m=1/2; ncol2=15; w=15; offset=3; strand=D; shift=3; score=19.8571; ---cayTTCChrGAAryc---
; cor=0.778; Ncor=0.556; logoDP=4.892; NIcor=0.505; NsEucl=0.925; SSD=2.501; NSW=0.917; rcor=27; rNcor=10; rlogoDP=22; rNIcor=10; rNsEucl=15; rSSD=30; rNSW=25; rank_mean=19.857; match_rank=20
a	0	0	0	208	859	251	10	8	106	23	528	696	53	1900	2030	954	336	417	0	0	0
c	0	0	0	1076	496	574	22	14	1921	1900	762	31	30	124	17	263	760	804	0	0	0
g	0	0	0	415	279	144	11	38	14	7	115	1292	1700	29	23	552	270	425	0	0	0
t	0	0	0	378	446	1112	2038	2023	44	155	680	66	302	32	15	315	714	431	0	0	0
MA0144.1_shift6 (Stat3) 0.860 0.410 4.350 0.385 0.917 1.374 0.931 17 28 23 23 18 23 18 21.429 24
; local_words_7nt_m1 versus MA0144.1 (Stat3); m=2/2; ncol2=10; w=10; offset=6; strand=D; shift=6; score=21.4286; ------TTCCaGGAAr-----
; cor=0.860; Ncor=0.410; logoDP=4.350; NIcor=0.385; NsEucl=0.917; SSD=1.374; NSW=0.931; rcor=17; rNcor=28; rlogoDP=23; rNIcor=23; rNsEucl=18; rSSD=23; rNSW=18; rank_mean=21.429; match_rank=24
a	0	0	0	0	0	0	20	13	38	6	321	8	6	585	606	191	0	0	0	0	0
c	0	0	0	0	0	0	19	10	552	541	21	0	2	21	1	15	0	0	0	0	0
g	0	0	0	0	0	0	25	129	9	1	148	605	592	7	5	393	0	0	0	0	0
t	0	0	0	0	0	0	549	461	14	65	123	0	13	0	1	14	0	0	0	0	0