One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/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/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift8 ; 17 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_6nt_test_vs_ctrl_m5_shift8 (oligos_6nt_test_vs_ctrl_m5)                                
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=8; ncol=20; --------cmAAGGTCAGrr
; Alignment reference
a	0	0	0	0	0	0	0	0	139	297	715	715	0	0	0	0	715	0	220	200
c	0	0	0	0	0	0	0	0	264	201	0	0	0	0	0	715	0	0	145	133
g	0	0	0	0	0	0	0	0	154	130	0	0	715	715	0	0	0	715	200	212
t	0	0	0	0	0	0	0	0	158	87	0	0	0	0	715	0	0	0	150	170
MA0141.2_shift5 (Esrrb) 0.957 0.574 10.632 0.573 0.947 0.453 0.975 1 9 5 5 1 1 1 3.286 1
; oligos_6nt_test_vs_ctrl_m5 versus MA0141.2 (Esrrb); m=1/16; ncol2=12; w=9; offset=-3; strand=D; shift=5; score= 3.2857; -----rgsyCAAGGTCA---
; cor=0.957; Ncor=0.574; logoDP=10.632; NIcor=0.573; NsEucl=0.947; SSD=0.453; NSW=0.975; rcor=1; rNcor=9; rlogoDP=5; rNIcor=5; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=3.286; match_rank=1
a	0	0	0	0	0	1055	673	403	260	312	3347	3590	33	12	180	9	3478	0	0	0
c	0	0	0	0	0	801	832	1212	1230	2653	32	2	2	11	43	3394	21	0	0	0
g	0	0	0	0	0	984	1352	1212	449	630	248	60	3597	3622	243	167	128	0	0	0
t	0	0	0	0	0	773	767	807	1702	51	27	6	29	16	3192	85	26	0	0	0
MA0071.1_shift7 (RORA_1) 0.913 0.632 10.808 0.628 0.926 0.886 0.951 3 5 4 4 5 3 3 3.857 2
; oligos_6nt_test_vs_ctrl_m5 versus MA0071.1 (RORA_1); m=2/16; ncol2=10; w=9; offset=-1; strand=D; shift=7; score= 3.8571; -------wwcwAGGTCA---
; cor=0.913; Ncor=0.632; logoDP=10.808; NIcor=0.628; NsEucl=0.926; SSD=0.886; NSW=0.951; rcor=3; rNcor=5; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=3; rNSW=3; rank_mean=3.857; match_rank=2
a	0	0	0	0	0	0	0	15	9	6	11	21	0	0	0	0	25	0	0	0
c	0	0	0	0	0	0	0	1	1	12	2	0	0	0	0	25	0	0	0	0
g	0	0	0	0	0	0	0	2	0	4	5	4	25	25	0	0	0	0	0	0
t	0	0	0	0	0	0	0	7	15	3	7	0	0	0	25	0	0	0	0	0
MA0141.1_shift5 (Esrrb) 0.956 0.574 10.474 0.573 0.947 0.455 0.975 2 10 7 6 2 2 2 4.429 3
; oligos_6nt_test_vs_ctrl_m5 versus MA0141.1 (Esrrb); m=3/16; ncol2=12; w=9; offset=-3; strand=D; shift=5; score= 4.4286; -----rgsyCAAGGTCA---
; cor=0.956; Ncor=0.574; logoDP=10.474; NIcor=0.573; NsEucl=0.947; SSD=0.455; NSW=0.975; rcor=2; rNcor=10; rlogoDP=7; rNIcor=6; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=4.429; match_rank=3
a	0	0	0	0	0	1054	673	420	259	310	3326	3567	32	21	182	9	3458	0	0	0
c	0	0	0	0	0	800	829	1211	1250	2664	32	2	5	12	46	3376	20	0	0	0
g	0	0	0	0	0	985	1370	1209	448	627	248	60	3586	3602	244	170	129	0	0	0
t	0	0	0	0	0	793	767	805	1693	52	50	27	31	17	3175	85	27	0	0	0
MA0592.1_shift8 (ESRRA) 0.870 0.797 11.273 0.783 0.921 1.511 0.931 6 1 2 1 9 10 6 5.000 4
; oligos_6nt_test_vs_ctrl_m5 versus MA0592.1 (ESRRA); m=4/16; ncol2=11; w=11; offset=0; strand=D; shift=8; score=      5; --------yCAAGGTCAcm-
; cor=0.870; Ncor=0.797; logoDP=11.273; NIcor=0.783; NsEucl=0.921; SSD=1.511; NSW=0.931; rcor=6; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=9; rSSD=10; rNSW=6; rank_mean=5.000; match_rank=4
a	0	0	0	0	0	0	0	0	17	18	200	198	0	0	6	0	197	23	70	0
c	0	0	0	0	0	0	0	0	118	174	2	0	0	0	0	205	1	108	54	0
g	0	0	0	0	0	0	0	0	11	15	6	10	203	207	22	3	10	44	40	0
t	0	0	0	0	0	0	0	0	62	1	0	0	5	1	180	0	0	33	44	0
MA0512.1_shift8 (Rxra) 0.853 0.782 9.135 0.742 0.917 1.660 0.925 13 2 13 2 12 14 11 9.571 5
; oligos_6nt_test_vs_ctrl_m5 versus MA0512.1 (Rxra); m=5/16; ncol2=11; w=11; offset=0; strand=D; shift=8; score= 9.5714; --------CArAGKTCAgd-
; cor=0.853; Ncor=0.782; logoDP=9.135; NIcor=0.742; NsEucl=0.917; SSD=1.660; NSW=0.925; rcor=13; rNcor=2; rlogoDP=13; rNIcor=2; rNsEucl=12; rSSD=14; rNSW=11; rank_mean=9.571; match_rank=5
a	0	0	0	0	0	0	0	0	278	4154	2623	4877	0	0	0	0	5348	1150	1640	0
c	0	0	0	0	0	0	0	0	4521	418	252	0	0	0	583	5348	0	1070	742	0
g	0	0	0	0	0	0	0	0	305	9	2473	471	5348	3882	643	0	0	2336	1569	0
t	0	0	0	0	0	0	0	0	244	767	0	0	0	1466	4122	0	0	792	1397	0
MA0258.2_shift11 (ESR2) 0.896 0.448 7.773 0.442 0.919 1.075 0.940 5 38 18 23 11 4 4 14.714 10
; oligos_6nt_test_vs_ctrl_m5 versus MA0258.2 (ESR2); m=6/16; ncol2=15; w=9; offset=3; strand=D; shift=11; score=14.7143; -----------rGGTCAsms
; cor=0.896; Ncor=0.448; logoDP=7.773; NIcor=0.442; NsEucl=0.919; SSD=1.075; NSW=0.940; rcor=5; rNcor=38; rlogoDP=18; rNIcor=23; rNsEucl=11; rSSD=4; rNSW=4; rank_mean=14.714; match_rank=10
a	0	0	0	0	0	0	0	0	0	0	0	5410	429	59	74	0	8098	502	2092	1808
c	0	0	0	0	0	0	0	0	0	0	0	96	0	0	147	7621	1	4202	3235	2510
g	0	0	0	0	0	0	0	0	0	0	0	2563	7170	8143	989	533	57	2738	1688	2173
t	0	0	0	0	0	0	0	0	0	0	0	174	644	41	7033	89	87	801	1228	1752
MA0505.1_shift4 (Nr5a2) 0.833 0.573 9.942 0.545 0.911 1.909 0.913 22 11 11 9 23 18 18 16.000 11
; oligos_6nt_test_vs_ctrl_m5 versus MA0505.1 (Nr5a2); m=7/16; ncol2=15; w=11; offset=-4; strand=D; shift=4; score=     16; ----ragtTCAAGGyCAgs-
; cor=0.833; Ncor=0.573; logoDP=9.942; NIcor=0.545; NsEucl=0.911; SSD=1.909; NSW=0.913; rcor=22; rNcor=11; rlogoDP=11; rNIcor=9; rNsEucl=23; rSSD=18; rNSW=18; rank_mean=16.000; match_rank=11
a	0	0	0	0	645	985	276	122	71	8	1685	1679	39	0	169	0	1437	271	249	0
c	0	0	0	0	224	170	198	378	351	1616	14	0	0	0	584	1568	20	345	693	0
g	0	0	0	0	634	336	990	366	23	74	0	23	1663	1702	61	12	90	740	454	0
t	0	0	0	0	199	211	238	836	1257	4	3	0	0	0	888	122	155	346	306	0
MA0065.1_shift0 (PPARG::RXRA) 0.831 0.498 11.103 0.484 0.916 2.048 0.915 24 23 3 15 14 20 16 16.429 12
; oligos_6nt_test_vs_ctrl_m5 versus MA0065.1 (PPARG::RXRA); m=8/16; ncol2=20; w=12; offset=-8; strand=D; shift=0; score=16.4286; yywrrGGTCAAAGGTCAymk
; cor=0.831; Ncor=0.498; logoDP=11.103; NIcor=0.484; NsEucl=0.916; SSD=2.048; NSW=0.915; rcor=24; rNcor=23; rlogoDP=3; rNIcor=15; rNsEucl=14; rSSD=20; rNSW=16; rank_mean=16.429; match_rank=12
a	10	7	19	13	17	0	0	0	2	41	41	39	0	0	0	2	38	10	13	7
c	12	13	4	1	0	0	0	2	37	0	0	0	0	0	2	36	1	12	15	10
g	7	8	6	27	24	41	39	0	2	0	0	2	41	39	0	1	2	4	9	12
t	12	13	12	0	0	0	2	39	0	0	0	0	0	2	39	2	0	15	4	12
MA0258.1_shift9 (ESR2) 0.849 0.491 6.707 0.476 0.914 1.786 0.919 14 27 23 18 18 17 13 18.571 13
; oligos_6nt_test_vs_ctrl_m5 versus MA0258.1 (ESR2); m=9/16; ncol2=18; w=11; offset=1; strand=D; shift=9; score=18.5714; ---------cwrGGTCAsgk
; cor=0.849; Ncor=0.491; logoDP=6.707; NIcor=0.476; NsEucl=0.914; SSD=1.786; NSW=0.919; rcor=14; rNcor=27; rlogoDP=23; rNIcor=18; rNsEucl=18; rSSD=17; rNSW=13; rank_mean=18.571; match_rank=13
a	0	0	0	0	0	0	0	0	0	78	158	186	27	18	13	0	337	49	64	52
c	0	0	0	0	0	0	0	0	0	161	51	15	0	20	19	357	1	123	63	61
g	0	0	0	0	0	0	0	0	0	63	41	154	275	319	33	0	0	113	149	147
t	0	0	0	0	0	0	0	0	0	55	107	2	55	0	292	0	19	72	81	97
MA0160.1_shift10 (NR4A2) 0.859 0.573 8.211 0.562 0.888 1.606 0.900 9 12 16 8 47 13 26 18.714 14
; oligos_6nt_test_vs_ctrl_m5 versus MA0160.1 (NR4A2); m=10/16; ncol2=8; w=8; offset=2; strand=D; shift=10; score=18.7143; ----------aAGGTCAc--
; cor=0.859; Ncor=0.573; logoDP=8.211; NIcor=0.562; NsEucl=0.888; SSD=1.606; NSW=0.900; rcor=9; rNcor=12; rlogoDP=16; rNIcor=8; rNsEucl=47; rSSD=13; rNSW=26; rank_mean=18.714; match_rank=14
a	0	0	0	0	0	0	0	0	0	0	8	13	0	3	2	0	14	3	0	0
c	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	13	0	8	0	0
g	0	0	0	0	0	0	0	0	0	0	3	1	13	11	0	0	0	2	0	0
t	0	0	0	0	0	0	0	0	0	0	1	0	1	0	10	1	0	0	0	0
MA0065.2_shift2 (PPARG::RXRA) 0.858 0.429 4.750 0.402 0.906 1.432 0.920 10 43 34 31 29 7 12 23.714 20
; oligos_6nt_test_vs_ctrl_m5 versus MA0065.2 (PPARG::RXRA); m=11/16; ncol2=15; w=9; offset=-6; strand=D; shift=2; score=23.7143; --strGGgcArAGGkcA---
; cor=0.858; Ncor=0.429; logoDP=4.750; NIcor=0.402; NsEucl=0.906; SSD=1.432; NSW=0.920; rcor=10; rNcor=43; rlogoDP=34; rNIcor=31; rNsEucl=29; rSSD=7; rNSW=12; rank_mean=23.714; match_rank=20
a	0	0	94	101	390	100	139	145	71	819	522	713	82	41	22	54	676	0	0	0
c	0	0	317	166	23	3	15	129	547	21	48	5	2	9	99	555	58	0	0	0
g	0	0	320	127	368	671	674	395	179	15	270	137	767	693	263	144	47	0	0	0
t	0	0	126	464	79	87	34	193	66	8	23	9	12	120	479	109	81	0	0	0
MA0017.1_rc_shift3 (NR2F1_rc) 0.868 0.460 0.751 -0.135 0.909 1.339 0.926 7 35 46 48 24 5 10 25.000 23
; oligos_6nt_test_vs_ctrl_m5 versus MA0017.1_rc (NR2F1_rc); m=12/16; ncol2=14; w=9; offset=-5; strand=R; shift=3; score=     25; ---arGkkCAAAGkTCA---
; cor=0.868; Ncor=0.460; logoDP=0.751; NIcor=-0.135; NsEucl=0.909; SSD=1.339; NSW=0.926; rcor=7; rNcor=35; rlogoDP=46; rNIcor=48; rNsEucl=24; rSSD=5; rNSW=10; rank_mean=25.000; match_rank=23
a	0	0	0	7	4	1	1	0	0	12	11	10	0	0	0	0	11	0	0	0
c	0	0	0	3	0	1	1	3	11	0	0	0	0	0	1	12	2	0	0	0
g	0	0	0	3	6	10	5	4	0	0	2	3	13	7	0	0	0	0	0	0
t	0	0	0	0	3	1	6	6	2	1	0	0	0	6	12	1	0	0	0	0
MA0504.1_shift2 (NR2C2) 0.845 0.423 6.396 0.402 0.903 1.517 0.916 17 44 27 30 33 11 15 25.286 24
; oligos_6nt_test_vs_ctrl_m5 versus MA0504.1 (NR2C2); m=13/16; ncol2=15; w=9; offset=-6; strand=D; shift=2; score=25.2857; --mgrGGTCArAGGTCA---
; cor=0.845; Ncor=0.423; logoDP=6.396; NIcor=0.402; NsEucl=0.903; SSD=1.517; NSW=0.916; rcor=17; rNcor=44; rlogoDP=27; rNIcor=30; rNsEucl=33; rSSD=11; rNSW=15; rank_mean=25.286; match_rank=24
a	0	0	129	82	193	0	10	3	6	343	187	324	10	11	0	9	290	0	0	0
c	0	0	126	70	6	8	3	0	309	0	0	0	0	0	27	315	0	0	0	0
g	0	0	90	221	195	366	355	79	54	48	208	71	385	336	89	35	92	0	0	0
t	0	0	50	22	1	21	27	313	26	4	0	0	0	48	279	36	13	0	0	0
MA0115.1_shift2 (NR1H2::RXRA) 0.797 0.487 13.304 0.469 0.893 2.754 0.875 35 29 1 20 42 33 40 28.571 27
; oligos_6nt_test_vs_ctrl_m5 versus MA0115.1 (NR1H2::RXRA); m=14/16; ncol2=17; w=11; offset=-6; strand=D; shift=2; score=28.5714; --AAAGGTCAAAGGTCAAc-
; cor=0.797; Ncor=0.487; logoDP=13.304; NIcor=0.469; NsEucl=0.893; SSD=2.754; NSW=0.875; rcor=35; rNcor=29; rlogoDP=1; rNIcor=20; rNsEucl=42; rSSD=33; rNSW=40; rank_mean=28.571; match_rank=27
a	0	0	17	17	20	0	0	0	0	25	24	25	0	0	0	0	25	20	0	0
c	0	0	5	1	0	0	0	0	25	0	0	0	0	0	0	25	0	1	15	0
g	0	0	0	5	5	25	24	0	0	0	0	0	25	25	0	0	0	2	6	0
t	0	0	3	2	0	0	1	25	0	0	1	0	0	0	25	0	0	2	4	0
MA0114.1_shift4 (HNF4A) 0.818 0.460 3.992 0.424 0.895 1.782 0.901 28 34 38 27 40 15 23 29.286 29
; oligos_6nt_test_vs_ctrl_m5 versus MA0114.1 (HNF4A); m=15/16; ncol2=13; w=9; offset=-4; strand=D; shift=4; score=29.2857; ----rGgbCAAAGkyCa---
; cor=0.818; Ncor=0.460; logoDP=3.992; NIcor=0.424; NsEucl=0.895; SSD=1.782; NSW=0.901; rcor=28; rNcor=34; rlogoDP=38; rNIcor=27; rNsEucl=40; rSSD=15; rNSW=23; rank_mean=29.286; match_rank=29
a	0	0	0	0	28	2	12	5	3	59	53	56	4	6	3	4	42	0	0	0
c	0	0	0	0	7	2	4	23	51	1	2	1	4	2	22	49	7	0	0	0
g	0	0	0	0	27	56	35	20	4	3	10	8	58	33	11	5	10	0	0	0
t	0	0	0	0	5	7	16	19	9	4	2	2	1	26	31	9	8	0	0	0
MA0112.2_shift6 (ESR1) 0.751 0.451 4.613 0.445 0.904 2.672 0.889 47 37 36 22 32 32 34 34.286 41
; oligos_6nt_test_vs_ctrl_m5 versus MA0112.2 (ESR1); m=16/16; ncol2=20; w=12; offset=-2; strand=D; shift=6; score=34.2857; ------vkscmaGGtCAccc
; cor=0.751; Ncor=0.451; logoDP=4.613; NIcor=0.445; NsEucl=0.904; SSD=2.672; NSW=0.889; rcor=47; rNcor=37; rlogoDP=36; rNIcor=22; rNsEucl=32; rSSD=32; rNSW=34; rank_mean=34.286; match_rank=41
a	0	0	0	0	0	0	122	107	64	83	134	308	36	19	33	4	398	58	63	64
c	0	0	0	0	0	0	120	80	173	229	232	28	8	18	41	394	13	250	276	258
g	0	0	0	0	0	0	154	164	149	65	47	89	387	420	91	53	27	107	53	97
t	0	0	0	0	0	0	71	117	82	93	57	48	43	18	310	24	37	60	83	56

One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m4_shift0 ; 5 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_8nt_test_vs_ctrl_m4_shift0 (oligos_8nt_test_vs_ctrl_m4)                                
; oligos_8nt_test_vs_ctrl_m4; m=0 (reference); ncol1=20; shift=0; ncol=20; hyCCCTGGACTTTGCCCTvb
; Alignment reference
a	12	8	4	4	0	3	0	1	37	0	1	0	0	1	0	1	0	6	11	6
c	15	12	28	30	34	1	0	2	2	39	1	4	0	3	33	38	37	0	11	10
g	3	8	3	2	0	0	40	36	0	0	0	1	2	34	3	0	0	1	13	10
t	10	12	5	4	6	36	0	1	1	1	38	35	38	2	4	1	3	33	5	14
MA0114.2_shift4 (HNF4A) 0.856 0.642 8.481 0.631 0.930 2.224 0.926 11 3 15 3 4 24 9 9.857 6
; oligos_8nt_test_vs_ctrl_m4 versus MA0114.2 (HNF4A); m=1/4; ncol2=15; w=15; offset=4; strand=D; shift=4; score= 9.8571; ----cTGrmCTTTGrmCyy-
; cor=0.856; Ncor=0.642; logoDP=8.481; NIcor=0.631; NsEucl=0.930; SSD=2.224; NSW=0.926; rcor=11; rNcor=3; rlogoDP=15; rNIcor=3; rNsEucl=4; rSSD=24; rNSW=9; rank_mean=9.857; match_rank=6
a	0	0	0	0	2766	1731	837	6075	11026	117	26	178	0	864	5270	6119	1156	1870	2070	0
c	0	0	0	0	5971	720	51	1846	4425	16535	1630	2637	173	35	3745	5653	13491	6498	6450	0
g	0	0	0	0	3974	907	15810	8370	329	67	0	367	407	15741	5340	1662	352	415	3001	0
t	0	0	0	0	4057	13410	70	477	988	49	15112	13586	16188	128	2413	3334	1769	7985	5247	0
MA0484.1_rc_shift5 (HNF4G_rc) 0.853 0.640 0.743 -0.132 0.931 2.114 0.930 12 4 47 47 3 21 8 20.286 17
; oligos_8nt_test_vs_ctrl_m4 versus MA0484.1_rc (HNF4G_rc); m=2/4; ncol2=15; w=15; offset=5; strand=R; shift=5; score=20.2857; -----TGrmCTTTGrmCyyt
; cor=0.853; Ncor=0.640; logoDP=0.743; NIcor=-0.132; NsEucl=0.931; SSD=2.114; NSW=0.930; rcor=12; rNcor=4; rlogoDP=47; rNIcor=47; rNsEucl=3; rSSD=21; rNSW=8; rank_mean=20.286; match_rank=17
a	0	0	0	0	0	1317	831	3782	5361	249	50	0	0	404	2792	3494	668	843	832	2063
c	0	0	0	0	0	556	85	1107	3624	9098	938	1481	54	221	2279	3301	7480	3811	3830	2011
g	0	0	0	0	0	794	8377	4338	143	6	0	82	55	8827	2870	713	201	102	1531	1864
t	0	0	0	0	0	6785	159	225	324	99	8464	7889	9343	0	1511	1944	1103	4696	3259	3514
MA0114.1_rc_shift5 (HNF4A_rc) 0.846 0.550 2.854 0.172 0.917 2.353 0.910 16 15 44 36 13 25 19 24.000 21
; oligos_8nt_test_vs_ctrl_m4 versus MA0114.1_rc (HNF4A_rc); m=3/4; ncol2=13; w=13; offset=5; strand=R; shift=5; score=     24; -----tGrmCTTTGvcCy--
; cor=0.846; Ncor=0.550; logoDP=2.854; NIcor=0.172; NsEucl=0.917; SSD=2.353; NSW=0.910; rcor=16; rNcor=15; rlogoDP=44; rNIcor=36; rNsEucl=13; rSSD=25; rNSW=19; rank_mean=24.000; match_rank=21
a	0	0	0	0	0	8	9	31	26	1	2	2	4	9	19	16	7	5	0	0
c	0	0	0	0	0	10	5	11	33	58	8	10	3	4	20	35	56	27	0	0
g	0	0	0	0	0	7	49	22	2	4	1	2	1	51	23	4	2	7	0	0
t	0	0	0	0	0	42	4	3	6	4	56	53	59	3	5	12	2	28	0	0
MA0065.2_rc_shift5 (PPARG::RXRA_rc) 0.751 0.563 0.673 -0.122 0.913 3.368 0.888 48 14 48 46 20 39 36 35.857 43
; oligos_8nt_test_vs_ctrl_m4 versus MA0065.2_rc (PPARG::RXRA_rc); m=4/4; ncol2=15; w=15; offset=5; strand=R; shift=5; score=35.8571; -----TgmCCTyTgcCCyas
; cor=0.751; Ncor=0.563; logoDP=0.673; NIcor=-0.122; NsEucl=0.913; SSD=3.368; NSW=0.888; rcor=48; rNcor=14; rlogoDP=48; rNIcor=46; rNsEucl=20; rSSD=39; rNSW=36; rank_mean=35.857; match_rank=43
a	0	0	0	0	0	81	109	479	120	12	9	23	8	66	193	34	87	79	464	126
c	0	0	0	0	0	47	144	263	693	767	137	270	15	179	395	674	671	368	127	320
g	0	0	0	0	0	58	555	99	9	2	5	48	21	547	129	15	3	23	166	317
t	0	0	0	0	0	676	54	22	41	82	713	522	819	71	145	139	100	390	101	94

One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m2_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
oligos_8nt_test_vs_ctrl_m2_shift0 (oligos_8nt_test_vs_ctrl_m2)                                
; oligos_8nt_test_vs_ctrl_m2; m=0 (reference); ncol1=23; shift=0; ncol=23; myTCCArrGmCCAAAGGkCAGvh
; Alignment reference
a	2	0	0	0	0	3	2	2	0	2	0	0	3	3	3	0	0	0	0	3	0	1	1
c	1	2	0	3	3	0	0	0	0	1	3	3	0	0	0	0	0	0	3	0	0	1	1
g	0	0	0	0	0	0	1	1	3	0	0	0	0	0	0	3	3	1	0	0	3	1	0
t	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	1
MA0512.1_shift11 (Rxra) 0.905 0.433 10.330 0.424 0.925 1.352 0.939 4 41 8 28 7 6 5 14.143 7
; oligos_8nt_test_vs_ctrl_m2 versus MA0512.1 (Rxra); m=1/5; ncol2=11; w=11; offset=11; strand=D; shift=11; score=14.1429; -----------CArAGKTCAgd-
; cor=0.905; Ncor=0.433; logoDP=10.330; NIcor=0.424; NsEucl=0.925; SSD=1.352; NSW=0.939; rcor=4; rNcor=41; rlogoDP=8; rNIcor=28; rNsEucl=7; rSSD=6; rNSW=5; rank_mean=14.143; match_rank=7
a	0	0	0	0	0	0	0	0	0	0	0	278	4154	2623	4877	0	0	0	0	5348	1150	1640	0
c	0	0	0	0	0	0	0	0	0	0	0	4521	418	252	0	0	0	583	5348	0	1070	742	0
g	0	0	0	0	0	0	0	0	0	0	0	305	9	2473	471	5348	3882	643	0	0	2336	1569	0
t	0	0	0	0	0	0	0	0	0	0	0	244	767	0	0	0	1466	4122	0	0	792	1397	0
MA0114.1_shift7 (HNF4A) 0.862 0.487 6.666 0.497 0.914 2.491 0.904 8 30 24 14 17 27 22 20.286 16
; oligos_8nt_test_vs_ctrl_m2 versus MA0114.1 (HNF4A); m=2/5; ncol2=13; w=13; offset=7; strand=D; shift=7; score=20.2857; -------rGgbCAAAGkyCa---
; cor=0.862; Ncor=0.487; logoDP=6.666; NIcor=0.497; NsEucl=0.914; SSD=2.491; NSW=0.904; rcor=8; rNcor=30; rlogoDP=24; rNIcor=14; rNsEucl=17; rSSD=27; rNSW=22; rank_mean=20.286; match_rank=16
a	0	0	0	0	0	0	0	28	2	12	5	3	59	53	56	4	6	3	4	42	0	0	0
c	0	0	0	0	0	0	0	7	2	4	23	51	1	2	1	4	2	22	49	7	0	0	0
g	0	0	0	0	0	0	0	27	56	35	20	4	3	10	8	58	33	11	5	10	0	0	0
t	0	0	0	0	0	0	0	5	7	16	19	9	4	2	2	1	26	31	9	8	0	0	0
MA0484.1_shift5 (HNF4G) 0.818 0.534 10.149 0.530 0.916 3.212 0.893 27 17 10 11 15 37 30 21.000 18
; oligos_8nt_test_vs_ctrl_m2 versus MA0484.1 (HNF4G); m=3/5; ncol2=15; w=15; offset=5; strand=D; shift=5; score=     21; -----arrGkyCAAAGkyCA---
; cor=0.818; Ncor=0.534; logoDP=10.149; NIcor=0.530; NsEucl=0.916; SSD=3.212; NSW=0.893; rcor=27; rNcor=17; rlogoDP=10; rNIcor=11; rNsEucl=15; rSSD=37; rNSW=30; rank_mean=21.000; match_rank=18
a	0	0	0	0	0	3514	3259	4696	1103	1944	1511	0	9343	7889	8464	99	324	225	159	6785	0	0	0
c	0	0	0	0	0	1864	1531	102	201	713	2870	8827	55	82	0	6	143	4338	8377	794	0	0	0
g	0	0	0	0	0	2011	3830	3811	7480	3301	2279	221	54	1481	938	9098	3624	1107	85	556	0	0	0
t	0	0	0	0	0	2063	832	843	668	3494	2792	404	0	0	50	249	5361	3782	831	1317	0	0	0
MA0017.1_rc_shift6 (NR2F1_rc) 0.817 0.497 3.603 -0.066 0.914 2.905 0.896 29 24 41 44 19 34 28 31.286 37
; oligos_8nt_test_vs_ctrl_m2 versus MA0017.1_rc (NR2F1_rc); m=4/5; ncol2=14; w=14; offset=6; strand=R; shift=6; score=31.2857; ------arGkkCAAAGkTCA---
; cor=0.817; Ncor=0.497; logoDP=3.603; NIcor=-0.066; NsEucl=0.914; SSD=2.905; NSW=0.896; rcor=29; rNcor=24; rlogoDP=41; rNIcor=44; rNsEucl=19; rSSD=34; rNSW=28; rank_mean=31.286; match_rank=37
a	0	0	0	0	0	0	7	4	1	1	0	0	12	11	10	0	0	0	0	11	0	0	0
c	0	0	0	0	0	0	3	0	1	1	3	11	0	0	0	0	0	1	12	2	0	0	0
g	0	0	0	0	0	0	3	6	10	5	4	0	0	2	3	13	7	0	0	0	0	0	0
t	0	0	0	0	0	0	0	3	1	6	6	2	1	0	0	0	6	12	1	0	0	0	0
MA0114.2_rc_shift6 (HNF4A_rc) 0.795 0.519 5.945 0.175 0.912 3.514 0.883 36 19 32 35 22 40 38 31.714 38
; oligos_8nt_test_vs_ctrl_m2 versus MA0114.2_rc (HNF4A_rc); m=5/5; ncol2=15; w=15; offset=6; strand=R; shift=6; score=31.7143; ------rrGkyCAAAGkyCAg--
; cor=0.795; Ncor=0.519; logoDP=5.945; NIcor=0.175; NsEucl=0.912; SSD=3.514; NSW=0.883; rcor=36; rNcor=19; rlogoDP=32; rNIcor=35; rNsEucl=22; rSSD=40; rNSW=38; rank_mean=31.714; match_rank=38
a	0	0	0	0	0	0	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0
c	0	0	0	0	0	0	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0
g	0	0	0	0	0	0	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0
t	0	0	0	0	0	0	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0

One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_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
oligos_8nt_test_vs_ctrl_m1_shift0 (oligos_8nt_test_vs_ctrl_m1)                                
; oligos_8nt_test_vs_ctrl_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; ymAAGTCCAAAGTCCAGGGrw
; Alignment reference
a	3	5	15	18	0	1	0	0	18	17	16	0	0	0	2	15	1	3	0	6	6
c	6	7	0	0	0	1	18	18	0	0	0	2	1	18	16	0	1	0	0	3	4
g	3	4	2	0	17	1	0	0	0	1	2	15	3	0	0	0	14	14	15	7	3
t	6	2	1	0	1	15	0	0	0	0	0	1	14	0	0	3	2	1	3	2	5
MA0484.1_shift1 (HNF4G) 0.841 0.600 8.171 0.570 0.925 2.513 0.916 19 8 17 7 6 28 14 14.143 8
; oligos_8nt_test_vs_ctrl_m1 versus MA0484.1 (HNF4G); m=1/3; ncol2=15; w=15; offset=1; strand=D; shift=1; score=14.1429; -arrGkyCAAAGkyCA-----
; cor=0.841; Ncor=0.600; logoDP=8.171; NIcor=0.570; NsEucl=0.925; SSD=2.513; NSW=0.916; rcor=19; rNcor=8; rlogoDP=17; rNIcor=7; rNsEucl=6; rSSD=28; rNSW=14; rank_mean=14.143; match_rank=8
a	0	3514	3259	4696	1103	1944	1511	0	9343	7889	8464	99	324	225	159	6785	0	0	0	0	0
c	0	1864	1531	102	201	713	2870	8827	55	82	0	6	143	4338	8377	794	0	0	0	0	0
g	0	2011	3830	3811	7480	3301	2279	221	54	1481	938	9098	3624	1107	85	556	0	0	0	0	0
t	0	2063	832	843	668	3494	2792	404	0	0	50	249	5361	3782	831	1317	0	0	0	0	0
MA0114.2_rc_shift2 (HNF4A_rc) 0.843 0.602 4.672 0.155 0.924 2.580 0.914 18 7 35 39 8 30 17 22.000 19
; oligos_8nt_test_vs_ctrl_m1 versus MA0114.2_rc (HNF4A_rc); m=2/3; ncol2=15; w=15; offset=2; strand=R; shift=2; score=     22; --rrGkyCAAAGkyCAg----
; cor=0.843; Ncor=0.602; logoDP=4.672; NIcor=0.155; NsEucl=0.924; SSD=2.580; NSW=0.914; rcor=18; rNcor=7; rlogoDP=35; rNIcor=39; rNsEucl=8; rSSD=30; rNSW=17; rank_mean=22.000; match_rank=19
a	0	0	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0	0	0
c	0	0	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0	0	0
g	0	0	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0	0	0
t	0	0	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0	0	0
MA0114.1_shift3 (HNF4A) 0.799 0.495 5.209 0.470 0.906 2.964 0.886 33 25 33 19 28 36 37 30.143 33
; oligos_8nt_test_vs_ctrl_m1 versus MA0114.1 (HNF4A); m=3/3; ncol2=13; w=13; offset=3; strand=D; shift=3; score=30.1429; ---rGgbCAAAGkyCa-----
; cor=0.799; Ncor=0.495; logoDP=5.209; NIcor=0.470; NsEucl=0.906; SSD=2.964; NSW=0.886; rcor=33; rNcor=25; rlogoDP=33; rNIcor=19; rNsEucl=28; rSSD=36; rNSW=37; rank_mean=30.143; match_rank=33
a	0	0	0	28	2	12	5	3	59	53	56	4	6	3	4	42	0	0	0	0	0
c	0	0	0	7	2	4	23	51	1	2	1	4	2	22	49	7	0	0	0	0	0
g	0	0	0	27	56	35	20	4	3	10	8	58	33	11	5	10	0	0	0	0	0
t	0	0	0	5	7	16	19	9	4	2	2	1	26	31	9	8	0	0	0	0	0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift2 ; 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
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)                                
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=2; ncol=18; --mdGGGTCAGrr-----
; Alignment reference
a	0	0	425	502	0	0	0	0	0	1513	0	452	396	0	0	0	0	0
c	0	0	446	86	0	0	0	0	1513	0	0	285	256	0	0	0	0	0
g	0	0	284	466	1513	1513	1513	0	0	0	1513	477	526	0	0	0	0	0
t	0	0	358	459	0	0	0	1513	0	0	0	299	335	0	0	0	0	0
MA0258.1_shift2 (ESR2) 0.848 0.518 6.561 0.507 0.920 1.531 0.930 15 20 26 12 10 12 7 14.571 9
; oligos_6nt_test_vs_ctrl_m3 versus MA0258.1 (ESR2); m=1/5; ncol2=18; w=11; offset=0; strand=D; shift=2; score=14.5714; --cwrGGTCAsgkTGmCC
; cor=0.848; Ncor=0.518; logoDP=6.561; NIcor=0.507; NsEucl=0.920; SSD=1.531; NSW=0.930; rcor=15; rNcor=20; rlogoDP=26; rNIcor=12; rNsEucl=10; rSSD=12; rNSW=7; rank_mean=14.571; match_rank=9
a	0	0	78	158	186	27	18	13	0	337	49	64	52	21	63	178	34	46
c	0	0	161	51	15	0	20	19	357	1	123	63	61	33	25	99	268	289
g	0	0	63	41	154	275	319	33	0	0	113	149	147	24	265	19	2	0
t	0	0	55	107	2	55	0	292	0	19	72	81	97	279	4	61	53	22
MA0071.1_shift0 (RORA_1) 0.834 0.513 9.825 0.504 0.892 1.486 0.907 21 21 12 13 43 8 20 19.714 15
; oligos_6nt_test_vs_ctrl_m3 versus MA0071.1 (RORA_1); m=2/5; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=19.7143; wwcwAGGTCA--------
; cor=0.834; Ncor=0.513; logoDP=9.825; NIcor=0.504; NsEucl=0.892; SSD=1.486; NSW=0.907; rcor=21; rNcor=21; rlogoDP=12; rNIcor=13; rNsEucl=43; rSSD=8; rNSW=20; rank_mean=19.714; match_rank=15
a	15	9	6	11	21	0	0	0	0	25	0	0	0	0	0	0	0	0
c	1	1	12	2	0	0	0	0	25	0	0	0	0	0	0	0	0	0
g	2	0	4	5	4	25	25	0	0	0	0	0	0	0	0	0	0	0
t	7	15	3	7	0	0	0	25	0	0	0	0	0	0	0	0	0	0
MA0504.1_shift2 (NR2C2) 0.775 0.568 6.381 0.530 0.904 2.216 0.899 43 13 28 10 30 23 27 24.857 22
; oligos_6nt_test_vs_ctrl_m3 versus MA0504.1 (NR2C2); m=3/5; ncol2=15; w=11; offset=0; strand=D; shift=2; score=24.8571; --mgrGGTCArAGGTCA-
; cor=0.775; Ncor=0.568; logoDP=6.381; NIcor=0.530; NsEucl=0.904; SSD=2.216; NSW=0.899; rcor=43; rNcor=13; rlogoDP=28; rNIcor=10; rNsEucl=30; rSSD=23; rNSW=27; rank_mean=24.857; match_rank=22
a	0	0	129	82	193	0	10	3	6	343	187	324	10	11	0	9	290	0
c	0	0	126	70	6	8	3	0	309	0	0	0	0	0	27	315	0	0
g	0	0	90	221	195	366	355	79	54	48	208	71	385	336	89	35	92	0
t	0	0	50	22	1	21	27	313	26	4	0	0	0	48	279	36	13	0
MA0258.2_shift4 (ESR2) 0.814 0.431 7.479 0.420 0.895 1.783 0.901 30 42 19 29 41 16 24 28.714 28
; oligos_6nt_test_vs_ctrl_m3 versus MA0258.2 (ESR2); m=4/5; ncol2=15; w=9; offset=2; strand=D; shift=4; score=28.7143; ----rGGTCAsmstGaCC
; cor=0.814; Ncor=0.431; logoDP=7.479; NIcor=0.420; NsEucl=0.895; SSD=1.783; NSW=0.901; rcor=30; rNcor=42; rlogoDP=19; rNIcor=29; rNsEucl=41; rSSD=16; rNSW=24; rank_mean=28.714; match_rank=28
a	0	0	0	0	5410	429	59	74	0	8098	502	2092	1808	1602	1121	3278	434	1111
c	0	0	0	0	96	0	0	147	7621	1	4202	3235	2510	975	398	2056	6469	5854
g	0	0	0	0	2563	7170	8143	989	533	57	2738	1688	2173	533	6658	1391	363	0
t	0	0	0	0	174	644	41	7033	89	87	801	1228	1752	5133	66	1518	977	1278
MA0074.1_shift4 (RXRA::VDR) 0.798 0.423 8.578 0.442 0.890 1.954 0.891 34 45 14 24 46 19 31 30.429 34
; oligos_6nt_test_vs_ctrl_m3 versus MA0074.1 (RXRA::VDR); m=5/5; ncol2=15; w=9; offset=2; strand=D; shift=4; score=30.4286; ----RGGTCAwcGrGTTC
; cor=0.798; Ncor=0.423; logoDP=8.578; NIcor=0.442; NsEucl=0.890; SSD=1.954; NSW=0.891; rcor=34; rNcor=45; rlogoDP=14; rNIcor=24; rNsEucl=46; rSSD=19; rNSW=31; rank_mean=30.429; match_rank=34
a	0	0	0	0	3	0	0	0	0	9	4	2	2	5	0	0	1	0
c	0	0	0	0	0	0	0	0	9	0	2	4	0	0	0	0	0	9
g	0	0	0	0	7	10	9	0	0	1	0	2	8	5	10	0	0	0
t	0	0	0	0	0	0	1	10	1	0	4	2	0	0	0	10	9	1

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_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_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)                                
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; TmGGkCCAGkCCAAAGwCCAArwk
; Alignment reference
a	0	1	0	0	0	0	0	2	0	0	0	0	2	2	2	0	1	0	0	2	2	1	1	0
c	0	1	0	0	0	2	2	0	0	0	2	2	0	0	0	0	0	2	2	0	0	0	0	0
g	0	0	2	2	1	0	0	0	2	1	0	0	0	0	0	2	0	0	0	0	0	1	0	1
t	2	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1
MA0114.1_shift7 (HNF4A) 0.838 0.454 6.625 0.452 0.907 2.909 0.888 20 36 25 21 26 35 35 28.286 25
; oligos_7nt_test_vs_ctrl_m4 versus MA0114.1 (HNF4A); m=1/3; ncol2=13; w=13; offset=7; strand=D; shift=7; score=28.2857; -------rGgbCAAAGkyCa----
; cor=0.838; Ncor=0.454; logoDP=6.625; NIcor=0.452; NsEucl=0.907; SSD=2.909; NSW=0.888; rcor=20; rNcor=36; rlogoDP=25; rNIcor=21; rNsEucl=26; rSSD=35; rNSW=35; rank_mean=28.286; match_rank=25
a	0	0	0	0	0	0	0	28	2	12	5	3	59	53	56	4	6	3	4	42	0	0	0	0
c	0	0	0	0	0	0	0	7	2	4	23	51	1	2	1	4	2	22	49	7	0	0	0	0
g	0	0	0	0	0	0	0	27	56	35	20	4	3	10	8	58	33	11	5	10	0	0	0	0
t	0	0	0	0	0	0	0	5	7	16	19	9	4	2	2	1	26	31	9	8	0	0	0	0
MA0484.1_shift5 (HNF4G) 0.776 0.485 10.252 0.478 0.904 4.147 0.862 41 31 9 17 31 45 44 31.143 36
; oligos_7nt_test_vs_ctrl_m4 versus MA0484.1 (HNF4G); m=2/3; ncol2=15; w=15; offset=5; strand=D; shift=5; score=31.1429; -----arrGkyCAAAGkyCA----
; cor=0.776; Ncor=0.485; logoDP=10.252; NIcor=0.478; NsEucl=0.904; SSD=4.147; NSW=0.862; rcor=41; rNcor=31; rlogoDP=9; rNIcor=17; rNsEucl=31; rSSD=45; rNSW=44; rank_mean=31.143; match_rank=36
a	0	0	0	0	0	3514	3259	4696	1103	1944	1511	0	9343	7889	8464	99	324	225	159	6785	0	0	0	0
c	0	0	0	0	0	1864	1531	102	201	713	2870	8827	55	82	0	6	143	4338	8377	794	0	0	0	0
g	0	0	0	0	0	2011	3830	3811	7480	3301	2279	221	54	1481	938	9098	3624	1107	85	556	0	0	0	0
t	0	0	0	0	0	2063	832	843	668	3494	2792	404	0	0	50	249	5361	3782	831	1317	0	0	0	0
MA0114.2_rc_shift6 (HNF4A_rc) 0.800 0.500 6.018 0.161 0.908 3.775 0.874 32 22 30 37 25 43 41 32.857 40
; oligos_7nt_test_vs_ctrl_m4 versus MA0114.2_rc (HNF4A_rc); m=3/3; ncol2=15; w=15; offset=6; strand=R; shift=6; score=32.8571; ------rrGkyCAAAGkyCAg---
; cor=0.800; Ncor=0.500; logoDP=6.018; NIcor=0.161; NsEucl=0.908; SSD=3.775; NSW=0.874; rcor=32; rNcor=22; rlogoDP=30; rNIcor=37; rNsEucl=25; rSSD=43; rNSW=41; rank_mean=32.857; match_rank=40
a	0	0	0	0	0	0	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0	0
c	0	0	0	0	0	0	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0	0
g	0	0	0	0	0	0	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0	0
t	0	0	0	0	0	0	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0	0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_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
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)                                
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; TykGGCCAGyCCAAAGTCCArGAy
; Alignment reference
a	0	0	0	0	0	0	0	2	0	0	0	0	2	2	2	0	0	0	0	2	1	0	2	0
c	0	1	0	0	0	2	2	0	0	1	2	2	0	0	0	0	0	2	2	0	0	0	0	1
g	0	0	1	2	2	0	0	0	2	0	0	0	0	0	0	2	0	0	0	0	1	2	0	0
t	2	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	2	0	0	0	0	0	0	1
MA0114.2_rc_shift6 (HNF4A_rc) 0.832 0.520 5.970 0.153 0.914 3.300 0.890 23 18 31 40 16 38 33 28.429 26
; oligos_7nt_test_vs_ctrl_m1 versus MA0114.2_rc (HNF4A_rc); m=1/3; ncol2=15; w=15; offset=6; strand=R; shift=6; score=28.4286; ------rrGkyCAAAGkyCAg---
; cor=0.832; Ncor=0.520; logoDP=5.970; NIcor=0.153; NsEucl=0.914; SSD=3.300; NSW=0.890; rcor=23; rNcor=18; rlogoDP=31; rNIcor=40; rNsEucl=16; rSSD=38; rNSW=33; rank_mean=28.429; match_rank=26
a	0	0	0	0	0	0	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0	0
c	0	0	0	0	0	0	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0	0
g	0	0	0	0	0	0	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0	0
t	0	0	0	0	0	0	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0	0
MA0484.1_shift5 (HNF4G) 0.775 0.484 10.539 0.478 0.901 4.388 0.854 42 32 6 16 35 47 46 32.000 39
; oligos_7nt_test_vs_ctrl_m1 versus MA0484.1 (HNF4G); m=2/3; ncol2=15; w=15; offset=5; strand=D; shift=5; score=     32; -----arrGkyCAAAGkyCA----
; cor=0.775; Ncor=0.484; logoDP=10.539; NIcor=0.478; NsEucl=0.901; SSD=4.388; NSW=0.854; rcor=42; rNcor=32; rlogoDP=6; rNIcor=16; rNsEucl=35; rSSD=47; rNSW=46; rank_mean=32.000; match_rank=39
a	0	0	0	0	0	3514	3259	4696	1103	1944	1511	0	9343	7889	8464	99	324	225	159	6785	0	0	0	0
c	0	0	0	0	0	1864	1531	102	201	713	2870	8827	55	82	0	6	143	4338	8377	794	0	0	0	0
g	0	0	0	0	0	2011	3830	3811	7480	3301	2279	221	54	1481	938	9098	3624	1107	85	556	0	0	0	0
t	0	0	0	0	0	2063	832	843	668	3494	2792	404	0	0	50	249	5361	3782	831	1317	0	0	0	0
MA0114.1_shift7 (HNF4A) 0.801 0.434 6.718 0.434 0.897 3.573 0.863 31 40 22 26 39 42 43 34.714 42
; oligos_7nt_test_vs_ctrl_m1 versus MA0114.1 (HNF4A); m=3/3; ncol2=13; w=13; offset=7; strand=D; shift=7; score=34.7143; -------rGgbCAAAGkyCa----
; cor=0.801; Ncor=0.434; logoDP=6.718; NIcor=0.434; NsEucl=0.897; SSD=3.573; NSW=0.863; rcor=31; rNcor=40; rlogoDP=22; rNIcor=26; rNsEucl=39; rSSD=42; rNSW=43; rank_mean=34.714; match_rank=42
a	0	0	0	0	0	0	0	28	2	12	5	3	59	53	56	4	6	3	4	42	0	0	0	0
c	0	0	0	0	0	0	0	7	2	4	23	51	1	2	1	4	2	22	49	7	0	0	0	0
g	0	0	0	0	0	0	0	27	56	35	20	4	3	10	8	58	33	11	5	10	0	0	0	0
t	0	0	0	0	0	0	0	5	7	16	19	9	4	2	2	1	26	31	9	8	0	0	0	0

One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m5_shift4 ; 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_8nt_test_vs_ctrl_m5_shift4 (oligos_8nt_test_vs_ctrl_m5)                                
; oligos_8nt_test_vs_ctrl_m5; m=0 (reference); ncol1=13; shift=4; ncol=17; ----aaAAATCAATAww
; Alignment reference
a	0	0	0	0	185	190	438	449	466	1	13	425	465	0	467	139	167
c	0	0	0	0	92	81	4	0	0	0	452	0	1	1	2	93	76
g	0	0	0	0	94	90	8	4	2	0	0	29	1	0	0	102	81
t	0	0	0	0	98	108	19	16	1	468	4	15	2	468	0	135	145
MA0594.1_shift1 (Hoxa9) 0.826 0.413 6.314 0.388 0.891 1.508 0.906 25 46 29 33 45 9 21 29.714 31
; oligos_8nt_test_vs_ctrl_m5 versus MA0594.1 (Hoxa9); m=1/3; ncol2=11; w=8; offset=-3; strand=D; shift=1; score=29.7143; -syCATmAATCA-----
; cor=0.826; Ncor=0.413; logoDP=6.314; NIcor=0.388; NsEucl=0.891; SSD=1.508; NSW=0.906; rcor=25; rNcor=46; rlogoDP=29; rNIcor=33; rNsEucl=45; rSSD=9; rNSW=21; rank_mean=29.714; match_rank=31
a	0	34	12	38	161	0	101	157	171	5	7	131	0	0	0	0	0
c	0	53	110	117	3	0	58	6	1	0	154	11	0	0	0	0	0
g	0	81	5	0	8	0	8	0	0	1	0	0	0	0	0	0	0
t	0	4	45	17	0	172	5	9	0	166	11	30	0	0	0	0	0
MA0047.1_rc_shift6 (Foxa2_rc) 0.787 0.618 3.193 0.211 0.900 2.399 0.891 38 6 43 34 36 26 32 30.714 35
; oligos_8nt_test_vs_ctrl_m5 versus MA0047.1_rc (Foxa2_rc); m=2/3; ncol2=12; w=11; offset=2; strand=R; shift=6; score=30.7143; ------RArymAAyAwt
; cor=0.787; Ncor=0.618; logoDP=3.193; NIcor=0.211; NsEucl=0.900; SSD=2.399; NSW=0.891; rcor=38; rNcor=6; rlogoDP=43; rNIcor=34; rNsEucl=36; rSSD=26; rNSW=32; rank_mean=30.714; match_rank=35
a	0	0	0	0	0	0	12	14	8	0	11	16	16	0	16	5	2
c	0	0	0	0	0	0	0	1	0	8	6	0	0	6	0	1	1
g	0	0	0	0	0	0	5	1	9	0	0	1	1	0	1	3	3
t	0	0	0	0	0	0	0	1	0	9	0	0	0	11	0	8	11
MA0485.1_shift0 (Hoxc9) 0.770 0.407 6.798 0.388 0.885 2.142 0.881 46 47 21 32 48 22 39 36.429 44
; oligos_8nt_test_vs_ctrl_m5 versus MA0485.1 (Hoxc9); m=3/3; ncol2=13; w=9; offset=-4; strand=D; shift=0; score=36.4286; rgCmATAAATCwy----
; cor=0.770; Ncor=0.407; logoDP=6.798; NIcor=0.388; NsEucl=0.885; SSD=2.142; NSW=0.881; rcor=46; rNcor=47; rlogoDP=21; rNIcor=32; rNsEucl=48; rSSD=22; rNSW=39; rank_mean=36.429; match_rank=44
a	235	112	88	224	661	0	745	881	879	18	48	567	141	0	0	0	0
c	110	171	605	468	3	9	84	0	6	0	715	72	329	0	0	0	0
g	401	536	40	1	205	0	35	0	0	0	5	6	160	0	0	0	0
t	139	66	152	192	16	876	21	4	0	867	117	240	255	0	0	0	0

One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m3_shift3 ; 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
oligos_8nt_test_vs_ctrl_m3_shift3 (oligos_8nt_test_vs_ctrl_m3)                                
; oligos_8nt_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=3; ncol=20; ---ksCCAGAGTCCAGGGwt
; Alignment reference
a	0	0	0	17	13	6	0	84	5	84	0	0	0	0	74	4	4	9	31	19
c	0	0	0	13	28	68	88	3	2	2	1	1	87	88	3	4	6	4	19	18
g	0	0	0	32	30	9	0	1	82	2	88	4	0	1	5	77	77	72	15	17
t	0	0	0	28	19	7	2	2	1	2	1	85	3	1	8	5	3	5	25	36
MA0484.1_shift0 (HNF4G) 0.774 0.464 6.915 0.438 0.906 2.521 0.895 45 33 20 25 27 29 29 29.714 30
; oligos_8nt_test_vs_ctrl_m3 versus MA0484.1 (HNF4G); m=1/2; ncol2=15; w=12; offset=-3; strand=D; shift=0; score=29.7143; arrGkyCAAAGkyCA-----
; cor=0.774; Ncor=0.464; logoDP=6.915; NIcor=0.438; NsEucl=0.906; SSD=2.521; NSW=0.895; rcor=45; rNcor=33; rlogoDP=20; rNIcor=25; rNsEucl=27; rSSD=29; rNSW=29; rank_mean=29.714; match_rank=30
a	3514	3259	4696	1103	1944	1511	0	9343	7889	8464	99	324	225	159	6785	0	0	0	0	0
c	1864	1531	102	201	713	2870	8827	55	82	0	6	143	4338	8377	794	0	0	0	0	0
g	2011	3830	3811	7480	3301	2279	221	54	1481	938	9098	3624	1107	85	556	0	0	0	0	0
t	2063	832	843	668	3494	2792	404	0	0	50	249	5361	3782	831	1317	0	0	0	0	0
MA0114.2_rc_shift1 (HNF4A_rc) 0.784 0.537 3.897 0.157 0.913 2.587 0.900 39 16 39 38 21 31 25 29.857 32
; oligos_8nt_test_vs_ctrl_m3 versus MA0114.2_rc (HNF4A_rc); m=2/2; ncol2=15; w=13; offset=-2; strand=R; shift=1; score=29.8571; -rrGkyCAAAGkyCAg----
; cor=0.784; Ncor=0.537; logoDP=3.897; NIcor=0.157; NsEucl=0.913; SSD=2.587; NSW=0.900; rcor=39; rNcor=16; rlogoDP=39; rNIcor=38; rNsEucl=21; rSSD=31; rNSW=25; rank_mean=29.857; match_rank=32
a	0	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0	0	0
c	0	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0	0	0
g	0	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0	0	0
t	0	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0	0	0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_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_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)                                
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; CACCTGCCCTTTGACCTGGCCACG
; Alignment reference
a	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0
c	1	0	1	1	0	0	1	1	1	0	0	0	0	0	1	1	0	0	0	1	1	0	1	0
g	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	1	1	0	0	0	0	1
t	0	0	0	0	1	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0
MA0114.1_rc_shift4 (HNF4A_rc) 0.822 0.445 3.550 0.112 0.897 3.566 0.863 26 39 42 41 38 41 42 38.429 45
; oligos_7nt_test_vs_ctrl_m2 versus MA0114.1_rc (HNF4A_rc); m=1/3; ncol2=13; w=13; offset=4; strand=R; shift=4; score=38.4286; ----tGrmCTTTGvcCy-------
; cor=0.822; Ncor=0.445; logoDP=3.550; NIcor=0.112; NsEucl=0.897; SSD=3.566; NSW=0.863; rcor=26; rNcor=39; rlogoDP=42; rNIcor=41; rNsEucl=38; rSSD=41; rNSW=42; rank_mean=38.429; match_rank=45
a	0	0	0	0	8	9	31	26	1	2	2	4	9	19	16	7	5	0	0	0	0	0	0	0
c	0	0	0	0	10	5	11	33	58	8	10	3	4	20	35	56	27	0	0	0	0	0	0	0
g	0	0	0	0	7	49	22	2	4	1	2	1	51	23	4	2	7	0	0	0	0	0	0	0
t	0	0	0	0	42	4	3	6	4	56	53	59	3	5	12	2	28	0	0	0	0	0	0	0
MA0504.1_rc_shift4 (NR2C2_rc) 0.787 0.492 3.742 0.013 0.902 4.336 0.855 37 26 40 43 34 46 45 38.714 46
; oligos_7nt_test_vs_ctrl_m2 versus MA0504.1_rc (NR2C2_rc); m=2/3; ncol2=15; w=15; offset=4; strand=R; shift=4; score=38.7143; ----TGACCTyTGACCyck-----
; cor=0.787; Ncor=0.492; logoDP=3.742; NIcor=0.013; NsEucl=0.902; SSD=4.336; NSW=0.855; rcor=37; rNcor=26; rlogoDP=40; rNIcor=43; rNsEucl=34; rSSD=46; rNSW=45; rank_mean=38.714; match_rank=46
a	0	0	0	0	13	36	279	48	0	0	0	4	26	313	27	21	1	22	50	0	0	0	0	0
c	0	0	0	0	92	35	89	336	385	71	208	48	54	79	355	366	195	221	90	0	0	0	0	0
g	0	0	0	0	0	315	27	0	0	0	0	0	309	0	3	8	6	70	126	0	0	0	0	0
t	0	0	0	0	290	9	0	11	10	324	187	343	6	3	10	0	193	82	129	0	0	0	0	0
MA0065.2_rc_shift4 (PPARG::RXRA_rc) 0.779 0.487 1.791 -0.076 0.898 4.682 0.844 40 28 45 45 37 48 48 41.571 47
; oligos_7nt_test_vs_ctrl_m2 versus MA0065.2_rc (PPARG::RXRA_rc); m=3/3; ncol2=15; w=15; offset=4; strand=R; shift=4; score=41.5714; ----TgmCCTyTgcCCyas-----
; cor=0.779; Ncor=0.487; logoDP=1.791; NIcor=-0.076; NsEucl=0.898; SSD=4.682; NSW=0.844; rcor=40; rNcor=28; rlogoDP=45; rNIcor=45; rNsEucl=37; rSSD=48; rNSW=48; rank_mean=41.571; match_rank=47
a	0	0	0	0	81	109	479	120	12	9	23	8	66	193	34	87	79	464	126	0	0	0	0	0
c	0	0	0	0	47	144	263	693	767	137	270	15	179	395	674	671	368	127	320	0	0	0	0	0
g	0	0	0	0	58	555	99	9	2	5	48	21	547	129	15	3	23	166	317	0	0	0	0	0
t	0	0	0	0	676	54	22	41	82	713	522	819	71	145	139	100	390	101	94	0	0	0	0	0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift2 ; 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
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)                                
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=23; shift=2; ncol=25; --ATCCAAAGTCCAGAGCAGGGAAT
; Alignment reference
a	0	0	1	0	0	0	1	1	1	0	0	0	0	1	0	1	0	0	1	0	0	0	1	1	0
c	0	0	0	0	1	1	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0
g	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	1	1	1	0	0	0
t	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1
MA0114.2_rc_shift0 (HNF4A_rc) 0.774 0.402 4.452 0.058 0.892 3.946 0.848 44 48 37 42 44 44 47 43.714 48
; oligos_6nt_test_vs_ctrl_m2 versus MA0114.2_rc (HNF4A_rc); m=1/1; ncol2=15; w=13; offset=-2; strand=R; shift=0; score=43.7143; rrGkyCAAAGkyCAg----------
; cor=0.774; Ncor=0.402; logoDP=4.452; NIcor=0.058; NsEucl=0.892; SSD=3.946; NSW=0.848; rcor=44; rNcor=48; rlogoDP=37; rNIcor=42; rNsEucl=44; rSSD=44; rNSW=47; rank_mean=43.714; match_rank=48
a	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0	0	0	0	0	0	0	0	0
c	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0	0	0	0	0	0	0	0	0
g	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0	0	0	0	0	0	0	0	0
t	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0	0	0	0	0	0	0	0	0