One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift3 ; 19 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift3 (oligos_7nt_mkv5_m2)     
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---hhCCACACCmm
; Alignment reference
a	0	0	0	610	665	56	47	1899	120	1884	31	37	665	597
c	0	0	0	779	651	2175	2075	185	2039	272	2139	2175	670	740
g	0	0	0	352	414	33	72	129	81	56	70	39	560	463
t	0	0	0	597	608	74	144	125	98	126	98	87	443	538
CG9895_SOLEXA_5_FBgn0034810_rc_shift3 (CG9895_SOLEXA_5_FBgn0034810_rc) 
; oligos_7nt_mkv5_m2 versus CG9895_SOLEXA_5_FBgn0034810_rc; m=1/18; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.793245; ---rrCCACrCCCa
; cor=; Ncor=
a	0	0	0	274	376	101	86	760	27	327	31	31	24	494
c	0	0	0	126	29	781	818	212	961	0	959	957	921	200
g	0	0	0	425	503	45	18	15	0	644	0	0	0	52
t	0	0	0	109	73	63	68	3	2	19	0	2	44	239
CG12029_SANGER_10_FBgn0035454_rc_shift4 (CG12029_SANGER_10_FBgn0035454_rc) 
; oligos_7nt_mkv5_m2 versus CG12029_SANGER_10_FBgn0035454_rc; m=2/18; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.707066; ----RCCACACCCa
; cor=; Ncor=
a	0	0	0	0	5	4	0	16	0	17	0	0	0	13
c	0	0	0	0	0	14	20	2	20	0	20	20	20	3
g	0	0	0	0	15	2	0	2	0	2	0	0	0	0
t	0	0	0	0	0	0	0	0	0	1	0	0	0	4
CG12029_SOLEXA_5_FBgn0035454_rc_shift1 (CG12029_SOLEXA_5_FBgn0035454_rc) 
; oligos_7nt_mkv5_m2 versus CG12029_SOLEXA_5_FBgn0035454_rc; m=3/18; ncol2=15; w=-2; offset=-2; strand=R; shift=1; score=0.635932; -mvrRCCACACCCa
; cor=; Ncor=
a	0	311	274	360	291	135	12	912	9	742	4	33	34	595
c	0	334	331	174	0	911	1052	109	1058	0	1062	1031	980	203
g	0	170	278	328	767	21	0	44	0	237	0	3	2	19
t	0	175	164	214	18	9	12	11	9	97	10	9	60	259
CG9895_SANGER_10_FBgn0034810_rc_shift4 (CG9895_SANGER_10_FBgn0034810_rc) 
; oligos_7nt_mkv5_m2 versus CG9895_SANGER_10_FBgn0034810_rc; m=4/18; ncol2=12; w=0; offset=1; strand=R; shift=4; score=0.627766; ----rCCACrCCCw
; cor=; Ncor=
a	0	0	0	0	11	3	2	20	1	10	1	0	0	14
c	0	0	0	0	0	20	21	4	23	0	22	22	22	2
g	0	0	0	0	13	1	0	0	0	14	0	2	0	2
t	0	0	0	0	0	0	1	0	0	0	1	0	2	6
CG3065_F1-3_SANGER_2.5_FBgn0034946_rc_shift4 (CG3065_F1-3_SANGER_2.5_FBgn0034946_rc) 
; oligos_7nt_mkv5_m2 versus CG3065_F1-3_SANGER_2.5_FBgn0034946_rc; m=5/18; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.608842; ----rCCACGCCCm
; cor=; Ncor=
a	0	0	0	0	7	2	0	20	0	0	0	0	0	12
c	0	0	0	0	0	18	21	1	21	0	21	21	20	6
g	0	0	0	0	13	1	0	0	0	21	0	0	0	1
t	0	0	0	0	0	0	0	0	0	0	0	0	1	2
CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc_shift2 (CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc) 
; oligos_7nt_mkv5_m2 versus CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc; m=6/18; ncol2=14; w=-1; offset=-1; strand=R; shift=2; score=0.582618; --crrCCACGCCCm
; cor=; Ncor=
a	0	0	308	363	440	154	25	1086	19	54	53	32	24	593
c	0	0	435	296	39	1022	1265	199	1290	9	1263	1276	1125	610
g	0	0	291	384	766	62	0	27	0	1205	0	0	1	20
t	0	0	218	276	74	81	29	7	10	51	3	11	169	96
luna_SOLEXA_5_FBgn0040765_rc_shift3 (luna_SOLEXA_5_FBgn0040765_rc) 
; oligos_7nt_mkv5_m2 versus luna_SOLEXA_5_FBgn0040765_rc; m=7/18; ncol2=14; w=0; offset=0; strand=R; shift=3; score=0.579885; ---grCCACGCCCw
; cor=; Ncor=
a	0	0	0	132	155	85	73	434	5	126	18	29	18	276
c	0	0	0	68	26	463	462	149	607	1	588	579	558	120
g	0	0	0	283	396	27	18	24	0	468	5	0	0	36
t	0	0	0	84	35	37	59	5	0	17	1	4	36	180
CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc_shift2 (CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc) 
; oligos_7nt_mkv5_m2 versus CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc; m=8/18; ncol2=15; w=-1; offset=-1; strand=R; shift=2; score=0.531519; --carCCACGCCCm
; cor=; Ncor=
a	0	0	47	105	85	40	1	234	11	4	9	10	13	171
c	0	0	110	52	7	211	260	29	249	0	253	253	217	77
g	0	0	53	59	166	8	0	0	0	255	0	0	0	1
t	0	0	47	44	5	4	2	0	3	4	1	0	33	14
klu_SOLEXA_5_FBgn0013469_rc_shift3 (klu_SOLEXA_5_FBgn0013469_rc) 
; oligos_7nt_mkv5_m2 versus klu_SOLEXA_5_FBgn0013469_rc; m=9/18; ncol2=15; w=0; offset=0; strand=R; shift=3; score=0.523494; ---mmmmmCACCCm
; cor=; Ncor=
a	0	0	0	132	156	135	134	155	9	378	3	3	5	315
c	0	0	0	152	168	188	204	298	491	6	491	485	472	168
g	0	0	0	82	90	85	64	24	0	48	0	5	0	6
t	0	0	0	91	79	95	101	26	3	71	9	10	26	14
Opa_SANGER_5_FBgn0003002_shift0 (Opa_SANGER_5_FBgn0003002) 
; oligos_7nt_mkv5_m2 versus Opa_SANGER_5_FBgn0003002; m=10/18; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.501186; mkmmMCCCCmCyR-
; cor=; Ncor=
a	7	2	4	4	3	1	0	0	0	8	0	0	3	0
c	3	0	5	7	9	9	12	11	12	3	11	8	0	0
g	1	5	2	1	0	2	0	1	0	1	1	0	9	0
t	1	5	1	0	0	0	0	0	0	0	0	4	0	0
lola-PL_SANGER_2.5_FBgn0005630_rc_shift1 (lola-PL_SANGER_2.5_FBgn0005630_rc) 
; oligos_7nt_mkv5_m2 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=11/18; ncol2=9; w=-2; offset=-2; strand=R; shift=1; score=0.48165; -TGmcCCACm----
; cor=; Ncor=
a	0	2	0	4	2	0	0	11	0	4	0	0	0	0
c	0	0	0	7	5	11	11	0	11	6	0	0	0	0
g	0	0	9	0	2	0	0	0	0	0	0	0	0	0
t	0	8	2	0	2	0	0	0	0	1	0	0	0	0
CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift6 (CG31782-F9-11_SOLEXA_FBgn0051782_rc) 
; oligos_7nt_mkv5_m2 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=12/18; ncol2=11; w=0; offset=3; strand=R; shift=6; score=0.464156; ------ctCACCac
; cor=; Ncor=
a	0	0	0	0	0	0	269	617	42	2023	0	0	1676	407
c	0	0	0	0	0	0	1324	287	1979	143	2554	2552	582	1464
g	0	0	0	0	0	0	584	195	25	0	0	0	27	305
t	0	0	0	0	0	0	375	1453	506	386	0	1	269	377
ac_da_SANGER_5_FBgn0000022_shift7 (ac_da_SANGER_5_FBgn0000022) 
; oligos_7nt_mkv5_m2 versus ac_da_SANGER_5_FBgn0000022; m=13/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.436854; -------rCACCTG
; cor=; Ncor=
a	0	0	0	0	0	0	0	10	0	19	0	0	0	0
c	0	0	0	0	0	0	0	1	19	0	18	19	0	0
g	0	0	0	0	0	0	0	7	0	0	1	0	0	19
t	0	0	0	0	0	0	0	1	0	0	0	0	19	0
ac_da_SANGER_5_FBgn0000413_shift7 (ac_da_SANGER_5_FBgn0000413) 
; oligos_7nt_mkv5_m2 versus ac_da_SANGER_5_FBgn0000413; m=14/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.436854; -------rCACCTG
; cor=; Ncor=
a	0	0	0	0	0	0	0	10	0	19	0	0	0	0
c	0	0	0	0	0	0	0	1	19	0	18	19	0	0
g	0	0	0	0	0	0	0	7	0	0	1	0	0	19
t	0	0	0	0	0	0	0	1	0	0	0	0	19	0
sc_da_SANGER_10_FBgn0000413_shift7 (sc_da_SANGER_10_FBgn0000413) 
; oligos_7nt_mkv5_m2 versus sc_da_SANGER_10_FBgn0000413; m=15/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.428959; -------rCACCTG
; cor=; Ncor=
a	0	0	0	0	0	0	0	11	0	24	0	0	0	0
c	0	0	0	0	0	0	0	5	23	0	21	24	0	0
g	0	0	0	0	0	0	0	7	0	0	1	0	0	24
t	0	0	0	0	0	0	0	0	0	0	2	0	24	0
sc_da_SANGER_10_FBgn0004170_shift7 (sc_da_SANGER_10_FBgn0004170) 
; oligos_7nt_mkv5_m2 versus sc_da_SANGER_10_FBgn0004170; m=16/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.428959; -------rCACCTG
; cor=; Ncor=
a	0	0	0	0	0	0	0	11	0	24	0	0	0	0
c	0	0	0	0	0	0	0	5	23	0	21	24	0	0
g	0	0	0	0	0	0	0	7	0	0	1	0	0	24
t	0	0	0	0	0	0	0	0	0	0	2	0	24	0
HLH54F_da_SANGER_5_FBgn0022740_shift6 (HLH54F_da_SANGER_5_FBgn0022740) 
; oligos_7nt_mkv5_m2 versus HLH54F_da_SANGER_5_FBgn0022740; m=17/18; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.409233; ------mmCACCTG
; cor=; Ncor=
a	0	0	0	0	0	0	12	12	0	24	0	0	0	0
c	0	0	0	0	0	0	10	10	23	0	24	23	1	0
g	0	0	0	0	0	0	1	2	0	0	0	0	2	24
t	0	0	0	0	0	0	1	0	1	0	0	1	21	0
HLH54F_da_SANGER_5_FBgn0000413_shift6 (HLH54F_da_SANGER_5_FBgn0000413) 
; oligos_7nt_mkv5_m2 versus HLH54F_da_SANGER_5_FBgn0000413; m=18/18; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.409233; ------mmCACCTG
; cor=; Ncor=
a	0	0	0	0	0	0	12	12	0	24	0	0	0	0
c	0	0	0	0	0	0	10	10	23	0	24	23	1	0
g	0	0	0	0	0	0	1	2	0	0	0	0	2	24
t	0	0	0	0	0	0	1	0	1	0	0	1	21	0