AutoCloner

Multiple sequence alignment - TraesCS1D01G017800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1D01G017800	chr1D	100.000	4912	0	0	1	4912	7876418	7881329	0.000000e+00	9071.0
1	TraesCS1D01G017800	chr1D	90.535	1796	118	27	80	1827	7898768	7900559	0.000000e+00	2327.0
2	TraesCS1D01G017800	chr1D	91.277	1605	96	18	2493	4058	7900986	7902585	0.000000e+00	2148.0
3	TraesCS1D01G017800	chr1D	89.680	1376	108	15	2739	4089	7205731	7204365	0.000000e+00	1724.0
4	TraesCS1D01G017800	chr1D	85.966	1646	174	33	2526	4130	7348855	7347226	0.000000e+00	1707.0
5	TraesCS1D01G017800	chr1D	82.382	806	109	16	993	1783	7207642	7206855	0.000000e+00	671.0
6	TraesCS1D01G017800	chr1D	79.475	838	123	22	998	1809	7350862	7350048	2.580000e-152	549.0
7	TraesCS1D01G017800	chr1D	89.578	403	39	1	98	500	7209647	7209248	4.390000e-140	508.0
8	TraesCS1D01G017800	chr1D	89.313	393	39	1	106	498	7351842	7351453	1.590000e-134	490.0
9	TraesCS1D01G017800	chr1D	86.967	399	40	5	187	579	7208458	7208066	5.840000e-119	438.0
10	TraesCS1D01G017800	chr1D	81.858	226	30	6	1881	2103	7900582	7900799	3.910000e-41	180.0
11	TraesCS1D01G017800	chr1D	89.231	65	6	1	4764	4827	7203357	7203293	4.080000e-11	80.5
12	TraesCS1D01G017800	chr1D	80.000	115	8	7	4791	4905	7204113	7204014	2.450000e-08	71.3
13	TraesCS1D01G017800	chr1B	94.057	3971	167	33	986	4912	10072869	10076814	0.000000e+00	5962.0
14	TraesCS1D01G017800	chr1B	92.520	1778	108	10	2241	4010	9595157	9593397	0.000000e+00	2523.0
15	TraesCS1D01G017800	chr1B	92.063	1663	110	11	2493	4140	10084412	10086067	0.000000e+00	2320.0
16	TraesCS1D01G017800	chr1B	85.478	2052	206	47	105	2107	9597583	9595575	0.000000e+00	2054.0
17	TraesCS1D01G017800	chr1B	82.507	1109	142	28	753	1822	10082869	10083964	0.000000e+00	926.0
18	TraesCS1D01G017800	chr1B	89.706	476	45	2	105	579	10081753	10082225	5.440000e-169	604.0
19	TraesCS1D01G017800	chr1B	89.286	476	47	2	105	579	10069818	10070290	1.180000e-165	593.0
20	TraesCS1D01G017800	chr1B	85.903	227	25	5	1881	2103	10083991	10084214	8.220000e-58	235.0
21	TraesCS1D01G017800	chr1B	91.589	107	6	2	572	675	10070807	10070913	1.430000e-30	145.0
22	TraesCS1D01G017800	chr1B	97.333	75	1	1	681	755	10070351	10070424	5.160000e-25	126.0
23	TraesCS1D01G017800	chr1B	97.222	72	1	1	681	752	10082286	10082356	2.400000e-23	121.0
24	TraesCS1D01G017800	chr1B	85.000	120	9	3	2110	2220	10084249	10084368	4.020000e-21	113.0
25	TraesCS1D01G017800	chr1B	85.321	109	7	6	572	675	10082560	10082664	2.420000e-18	104.0
26	TraesCS1D01G017800	chr1A	91.407	2211	126	28	2223	4424	9362084	9364239	0.000000e+00	2972.0
27	TraesCS1D01G017800	chr1A	89.410	1832	135	32	2270	4071	9555288	9557090	0.000000e+00	2254.0
28	TraesCS1D01G017800	chr1A	89.336	1144	77	14	986	2116	9359216	9360327	0.000000e+00	1395.0
29	TraesCS1D01G017800	chr1A	83.390	1174	102	40	993	2116	9553992	9555122	0.000000e+00	1002.0
30	TraesCS1D01G017800	chr1A	93.895	475	29	0	105	579	9551389	9551863	0.000000e+00	717.0
31	TraesCS1D01G017800	chr1A	90.717	474	41	1	100	573	9357607	9358077	3.230000e-176	628.0
32	TraesCS1D01G017800	chr1A	87.320	347	40	2	226	571	9358445	9358788	1.280000e-105	394.0
33	TraesCS1D01G017800	chr1A	87.435	191	15	3	2594	2777	9174542	9174730	1.390000e-50	211.0
34	TraesCS1D01G017800	chr1A	87.435	191	15	3	2594	2777	9201936	9202124	1.390000e-50	211.0
35	TraesCS1D01G017800	chr1A	88.158	76	5	3	677	752	9358139	9358210	2.440000e-13	87.9
36	TraesCS1D01G017800	chr3A	85.529	1078	152	4	2829	3904	10956448	10957523	0.000000e+00	1123.0
37	TraesCS1D01G017800	chr3A	77.660	94	21	0	1490	1583	10955111	10955204	1.910000e-04	58.4
38	TraesCS1D01G017800	chr6B	93.130	262	10	1	4429	4682	715294013	715294274	1.290000e-100	377.0
39	TraesCS1D01G017800	chr6B	91.538	260	14	1	4432	4683	9480616	9480357	7.820000e-93	351.0
40	TraesCS1D01G017800	chr5D	92.395	263	12	1	4428	4682	505431515	505431253	7.770000e-98	368.0
41	TraesCS1D01G017800	chr5D	91.450	269	14	2	4427	4686	491845033	491845301	1.300000e-95	361.0
42	TraesCS1D01G017800	chr5D	91.736	242	12	1	4428	4661	435477734	435477493	3.670000e-86	329.0
43	TraesCS1D01G017800	chr3D	92.692	260	11	1	4432	4683	604126816	604127075	7.770000e-98	368.0
44	TraesCS1D01G017800	chr3D	91.506	259	13	2	4432	4682	565163418	565163675	1.010000e-91	348.0
45	TraesCS1D01G017800	chr2D	90.152	264	17	3	4430	4685	580967974	580967712	7.880000e-88	335.0
46	TraesCS1D01G017800	chr2A	88.679	265	20	3	4433	4689	17031489	17031227	1.030000e-81	315.0
47	TraesCS1D01G017800	chr7B	89.712	243	14	3	4428	4661	104011252	104011012	2.870000e-77	300.0
48	TraesCS1D01G017800	chr2B	85.882	255	32	4	4429	4682	36911533	36911784	8.100000e-68	268.0
49	TraesCS1D01G017800	chr2B	75.221	452	82	26	1551	1987	109288660	109288224	2.330000e-43	187.0
50	TraesCS1D01G017800	chr7D	85.433	254	28	5	4429	4681	618230506	618230751	6.310000e-64	255.0
51	TraesCS1D01G017800	chrUn	86.911	191	16	3	2594	2777	395190862	395190674	6.440000e-49	206.0
52	TraesCS1D01G017800	chr5B	79.245	212	17	12	3883	4074	103634548	103634344	6.680000e-24	122.0

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1D01G017800	chr1D	7876418	7881329	4911	False	9071.000000	9071	100.000000	1	4912	1	chr1D.!!$F1	4911
1	TraesCS1D01G017800	chr1D	7898768	7902585	3817	False	1551.666667	2327	87.890000	80	4058	3	chr1D.!!$F2	3978
2	TraesCS1D01G017800	chr1D	7347226	7351842	4616	True	915.333333	1707	84.918000	106	4130	3	chr1D.!!$R2	4024
3	TraesCS1D01G017800	chr1D	7203293	7209647	6354	True	582.133333	1724	86.306333	98	4905	6	chr1D.!!$R1	4807
4	TraesCS1D01G017800	chr1B	9593397	9597583	4186	True	2288.500000	2523	88.999000	105	4010	2	chr1B.!!$R1	3905
5	TraesCS1D01G017800	chr1B	10069818	10076814	6996	False	1706.500000	5962	93.066250	105	4912	4	chr1B.!!$F1	4807
6	TraesCS1D01G017800	chr1B	10081753	10086067	4314	False	631.857143	2320	88.246000	105	4140	7	chr1B.!!$F2	4035
7	TraesCS1D01G017800	chr1A	9551389	9557090	5701	False	1324.333333	2254	88.898333	105	4071	3	chr1A.!!$F4	3966
8	TraesCS1D01G017800	chr1A	9357607	9364239	6632	False	1095.380000	2972	89.387600	100	4424	5	chr1A.!!$F3	4324
9	TraesCS1D01G017800	chr3A	10955111	10957523	2412	False	590.700000	1123	81.594500	1490	3904	2	chr3A.!!$F1	2414

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
540	545	0.105142	TAAGGAGGGGAAGGGATCGG	60.105	60.000	4.18	F
1335	5008	0.325296	TCATCCCGCTTGTAGACCCT	60.325	55.000	4.34	F
1391	5064	0.469070	AGCTCATCATCTCCACAGGC	59.531	55.000	4.85	F
2307	8683	1.403679	TGAACAAAAGTTGCCCAGTCG	59.596	47.619	4.18	F
3026	9583	2.172851	AGATGGCACGACGGTTTAAA	57.827	45.000	1.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2158	6441	2.339556	GCGGTTGTAGCCATGCCAA	61.340	57.895	0.00	4.52	R
3026	9583	1.636003	CCTCCCTGCCCTACTTTTTCT	59.364	52.381	0.00	2.52	R
3548	10106	1.558294	GATACTCCCCCAAAGTTCCGT	59.442	52.381	0.00	4.69	R
3602	10160	1.406069	CCGCTCACCATTTCTAGCACT	60.406	52.381	34.60	4.40	R
4863	11481	1.192146	TCCCTCCCACAGTTTCGGAG	61.192	60.000	42.48	4.63	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	4.864916	CAAAACATGCTATGTAGTCGCT	57.135	40.909	0.00	0.00	44.07	4.93
23	24	5.221891	CAAAACATGCTATGTAGTCGCTT	57.778	39.130	0.00	0.00	44.07	4.68
24	25	5.631026	CAAAACATGCTATGTAGTCGCTTT	58.369	37.500	0.00	0.00	44.07	3.51
25	26	4.864916	AACATGCTATGTAGTCGCTTTG	57.135	40.909	0.00	0.00	44.07	2.77
26	27	4.123497	ACATGCTATGTAGTCGCTTTGA	57.877	40.909	0.00	0.00	42.78	2.69
27	28	4.115516	ACATGCTATGTAGTCGCTTTGAG	58.884	43.478	0.00	0.00	42.78	3.02
28	29	3.868757	TGCTATGTAGTCGCTTTGAGT	57.131	42.857	0.00	0.00	0.00	3.41
29	30	3.511699	TGCTATGTAGTCGCTTTGAGTG	58.488	45.455	0.00	0.00	0.00	3.51
30	31	2.860735	GCTATGTAGTCGCTTTGAGTGG	59.139	50.000	0.00	0.00	0.00	4.00
31	32	1.726853	ATGTAGTCGCTTTGAGTGGC	58.273	50.000	0.00	0.00	0.00	5.01
32	33	0.320421	TGTAGTCGCTTTGAGTGGCC	60.320	55.000	0.00	0.00	28.82	5.36
33	34	0.320421	GTAGTCGCTTTGAGTGGCCA	60.320	55.000	0.00	0.00	28.82	5.36
34	35	0.394938	TAGTCGCTTTGAGTGGCCAA	59.605	50.000	7.24	0.00	28.82	4.52
35	36	0.465460	AGTCGCTTTGAGTGGCCAAA	60.465	50.000	7.24	0.00	28.82	3.28
36	37	0.598065	GTCGCTTTGAGTGGCCAAAT	59.402	50.000	7.24	0.00	35.72	2.32
37	38	1.810151	GTCGCTTTGAGTGGCCAAATA	59.190	47.619	7.24	0.00	35.72	1.40
38	39	1.810151	TCGCTTTGAGTGGCCAAATAC	59.190	47.619	7.24	0.00	35.72	1.89
39	40	1.812571	CGCTTTGAGTGGCCAAATACT	59.187	47.619	7.24	0.00	35.72	2.12
40	41	2.414559	CGCTTTGAGTGGCCAAATACTG	60.415	50.000	7.24	0.00	35.72	2.74
41	42	2.819608	GCTTTGAGTGGCCAAATACTGA	59.180	45.455	7.24	0.00	35.72	3.41
42	43	3.255642	GCTTTGAGTGGCCAAATACTGAA	59.744	43.478	7.24	0.00	35.72	3.02
43	44	4.261994	GCTTTGAGTGGCCAAATACTGAAA	60.262	41.667	7.24	6.26	35.72	2.69
44	45	5.452078	TTTGAGTGGCCAAATACTGAAAG	57.548	39.130	7.24	0.00	33.59	2.62
45	46	4.365514	TGAGTGGCCAAATACTGAAAGA	57.634	40.909	7.24	0.00	37.43	2.52
46	47	4.072131	TGAGTGGCCAAATACTGAAAGAC	58.928	43.478	7.24	0.00	37.43	3.01
47	48	4.072131	GAGTGGCCAAATACTGAAAGACA	58.928	43.478	7.24	0.00	37.43	3.41
48	49	9.075712	TTTGAGTGGCCAAATACTGAAAGACAG	62.076	40.741	7.24	0.00	40.17	3.51
57	58	1.805869	CTGAAAGACAGGTGAGGCTG	58.194	55.000	0.00	0.00	42.39	4.85
58	59	1.345741	CTGAAAGACAGGTGAGGCTGA	59.654	52.381	0.00	0.00	42.39	4.26
59	60	1.768275	TGAAAGACAGGTGAGGCTGAA	59.232	47.619	0.00	0.00	0.00	3.02
60	61	2.373169	TGAAAGACAGGTGAGGCTGAAT	59.627	45.455	0.00	0.00	0.00	2.57
61	62	2.777832	AAGACAGGTGAGGCTGAATC	57.222	50.000	0.00	0.00	0.00	2.52
62	63	1.649321	AGACAGGTGAGGCTGAATCA	58.351	50.000	0.00	0.00	0.00	2.57
63	64	1.554160	AGACAGGTGAGGCTGAATCAG	59.446	52.381	5.78	5.78	34.12	2.90
64	65	1.277557	GACAGGTGAGGCTGAATCAGT	59.722	52.381	12.29	0.00	33.43	3.41
65	66	1.701847	ACAGGTGAGGCTGAATCAGTT	59.298	47.619	12.29	0.55	33.43	3.16
66	67	2.082231	CAGGTGAGGCTGAATCAGTTG	58.918	52.381	12.29	0.00	33.43	3.16
67	68	1.701847	AGGTGAGGCTGAATCAGTTGT	59.298	47.619	12.29	0.00	33.43	3.32
68	69	1.808945	GGTGAGGCTGAATCAGTTGTG	59.191	52.381	12.29	0.00	33.43	3.33
69	70	1.198637	GTGAGGCTGAATCAGTTGTGC	59.801	52.381	12.29	0.00	33.43	4.57
70	71	0.807496	GAGGCTGAATCAGTTGTGCC	59.193	55.000	12.29	7.22	40.54	5.01
71	72	0.957395	AGGCTGAATCAGTTGTGCCG	60.957	55.000	12.29	0.00	44.42	5.69
72	73	1.237285	GGCTGAATCAGTTGTGCCGT	61.237	55.000	12.29	0.00	33.43	5.68
73	74	0.110056	GCTGAATCAGTTGTGCCGTG	60.110	55.000	12.29	0.00	33.43	4.94
74	75	0.110056	CTGAATCAGTTGTGCCGTGC	60.110	55.000	1.31	0.00	0.00	5.34
75	76	0.534877	TGAATCAGTTGTGCCGTGCT	60.535	50.000	0.00	0.00	0.00	4.40
76	77	0.166814	GAATCAGTTGTGCCGTGCTC	59.833	55.000	0.00	0.00	0.00	4.26
77	78	0.250467	AATCAGTTGTGCCGTGCTCT	60.250	50.000	0.00	0.00	0.00	4.09
78	79	0.671781	ATCAGTTGTGCCGTGCTCTC	60.672	55.000	0.00	0.00	0.00	3.20
89	90	1.066573	CCGTGCTCTCCTGAATCAGTT	60.067	52.381	9.63	0.00	0.00	3.16
90	91	1.998315	CGTGCTCTCCTGAATCAGTTG	59.002	52.381	9.63	1.71	0.00	3.16
91	92	2.611473	CGTGCTCTCCTGAATCAGTTGT	60.611	50.000	9.63	0.00	0.00	3.32
95	96	1.699083	TCTCCTGAATCAGTTGTGCCA	59.301	47.619	9.63	0.00	0.00	4.92
96	97	2.082231	CTCCTGAATCAGTTGTGCCAG	58.918	52.381	9.63	0.00	0.00	4.85
102	106	2.119801	ATCAGTTGTGCCAGATCCAC	57.880	50.000	0.00	0.00	0.00	4.02
137	141	1.059584	TCCACAGTGGAAGAGGGCAA	61.060	55.000	20.84	0.00	45.00	4.52
331	335	9.126151	GAAAGGATATGATATGTCTCGGAGATA	57.874	37.037	11.46	9.10	33.89	1.98
491	495	4.442052	GCTTCACAGATGCACTATGGACTA	60.442	45.833	0.00	0.00	33.71	2.59
513	517	7.106239	ACTAGATATCCTGGTTTGTTCTGTTG	58.894	38.462	0.00	0.00	32.13	3.33
540	545	0.105142	TAAGGAGGGGAAGGGATCGG	60.105	60.000	0.00	0.00	0.00	4.18
604	969	7.102847	TGACTTCATTGGTATATACACGACA	57.897	36.000	14.70	0.70	0.00	4.35
807	1898	5.769484	ATGCAAAATGCCAATCAAAACAA	57.231	30.435	0.00	0.00	44.23	2.83
879	4462	5.702670	CACACTCAAACCACTAGAACATGAT	59.297	40.000	0.00	0.00	0.00	2.45
946	4570	1.569479	GCACAACTCCGACTGCCTTC	61.569	60.000	0.00	0.00	0.00	3.46
1123	4769	3.052082	CGTCCCAGTGCAGCCAAG	61.052	66.667	0.00	0.00	0.00	3.61
1183	4847	1.133598	GCAATACATCAGCAGCAGCAA	59.866	47.619	3.17	0.00	45.49	3.91
1238	4911	0.745845	AAGTTAGCATGCTCTGGGCG	60.746	55.000	26.57	0.00	45.43	6.13
1272	4945	2.672996	CACCCAGTTCTTGGCCCG	60.673	66.667	0.00	0.00	46.32	6.13
1297	4970	2.134201	TGTCAGCGCCATAGATTACG	57.866	50.000	2.29	0.00	0.00	3.18
1335	5008	0.325296	TCATCCCGCTTGTAGACCCT	60.325	55.000	0.00	0.00	0.00	4.34
1341	5014	1.804748	CCGCTTGTAGACCCTTGTTTC	59.195	52.381	0.00	0.00	0.00	2.78
1391	5064	0.469070	AGCTCATCATCTCCACAGGC	59.531	55.000	0.00	0.00	0.00	4.85
1401	5074	4.164796	TCATCTCCACAGGCTGATGTTATT	59.835	41.667	23.66	0.00	36.04	1.40
1405	5078	5.189736	TCTCCACAGGCTGATGTTATTAACT	59.810	40.000	23.66	0.00	0.00	2.24
1690	5399	3.393089	TCAAGGAAAGCACAGAGAGAC	57.607	47.619	0.00	0.00	0.00	3.36
2159	6442	3.690745	GCTTGAGCAGCCACCATT	58.309	55.556	0.00	0.00	43.65	3.16
2262	8448	2.670934	GACTGCCACTGGGTGCAG	60.671	66.667	15.77	15.77	40.60	4.41
2307	8683	1.403679	TGAACAAAAGTTGCCCAGTCG	59.596	47.619	0.00	0.00	0.00	4.18
2339	8715	5.408909	GGCCTTAAGTTGACTCTAACTGTTC	59.591	44.000	0.00	0.00	40.58	3.18
2460	8837	8.778358	GTTGATAAGTTGTGACAGATTTTCTCT	58.222	33.333	0.00	0.00	33.14	3.10
2461	8838	8.539770	TGATAAGTTGTGACAGATTTTCTCTC	57.460	34.615	0.00	0.00	29.16	3.20
2467	8844	6.266168	TGTGACAGATTTTCTCTCTCTCTC	57.734	41.667	0.00	0.00	29.16	3.20
2752	9280	9.442047	ACAAATTCTTATTACTCTGACTCTTGG	57.558	33.333	0.00	0.00	0.00	3.61
3026	9583	2.172851	AGATGGCACGACGGTTTAAA	57.827	45.000	0.00	0.00	0.00	1.52
3548	10106	7.525526	GGCTATATTGCACCAGAGTTATACTCA	60.526	40.741	11.27	0.00	40.11	3.41
3602	10160	2.343101	GTGTACAGTTTCGGCATGCTA	58.657	47.619	18.92	3.12	0.00	3.49
3758	10316	4.001618	AGAAGAGAAAGACAAGGTGAGC	57.998	45.455	0.00	0.00	0.00	4.26
4110	10694	8.630054	ATTGGACTTGTATTTTAACAGCTACA	57.370	30.769	0.00	0.00	0.00	2.74
4430	11041	5.123027	GTGGATCTCCTCTTTGCACTTTAAG	59.877	44.000	0.00	0.00	36.82	1.85
4461	11072	1.734163	ATCGCGGGAGAAACGATTTT	58.266	45.000	6.13	0.00	43.55	1.82
4462	11073	0.793861	TCGCGGGAGAAACGATTTTG	59.206	50.000	6.13	0.00	0.00	2.44
4464	11075	0.793104	GCGGGAGAAACGATTTTGCG	60.793	55.000	0.00	0.00	37.29	4.85
4885	11503	0.905357	CGAAACTGTGGGAGGGATCT	59.095	55.000	0.00	0.00	0.00	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	4.864916	AGCGACTACATAGCATGTTTTG	57.135	40.909	7.02	0.00	41.63	2.44
2	3	5.411361	TCAAAGCGACTACATAGCATGTTTT	59.589	36.000	7.02	0.00	41.63	2.43
3	4	4.935205	TCAAAGCGACTACATAGCATGTTT	59.065	37.500	7.02	0.00	41.63	2.83
4	5	4.503910	TCAAAGCGACTACATAGCATGTT	58.496	39.130	7.02	0.00	41.63	2.71
5	6	4.115516	CTCAAAGCGACTACATAGCATGT	58.884	43.478	6.93	6.93	46.92	3.21
6	7	4.026228	CACTCAAAGCGACTACATAGCATG	60.026	45.833	0.00	0.00	0.00	4.06
7	8	4.115516	CACTCAAAGCGACTACATAGCAT	58.884	43.478	0.00	0.00	0.00	3.79
8	9	3.511699	CACTCAAAGCGACTACATAGCA	58.488	45.455	0.00	0.00	0.00	3.49
9	10	2.860735	CCACTCAAAGCGACTACATAGC	59.139	50.000	0.00	0.00	0.00	2.97
10	11	2.860735	GCCACTCAAAGCGACTACATAG	59.139	50.000	0.00	0.00	0.00	2.23
11	12	2.418197	GGCCACTCAAAGCGACTACATA	60.418	50.000	0.00	0.00	0.00	2.29
12	13	1.676014	GGCCACTCAAAGCGACTACAT	60.676	52.381	0.00	0.00	0.00	2.29
13	14	0.320421	GGCCACTCAAAGCGACTACA	60.320	55.000	0.00	0.00	0.00	2.74
14	15	0.320421	TGGCCACTCAAAGCGACTAC	60.320	55.000	0.00	0.00	0.00	2.73
15	16	0.394938	TTGGCCACTCAAAGCGACTA	59.605	50.000	3.88	0.00	0.00	2.59
16	17	0.465460	TTTGGCCACTCAAAGCGACT	60.465	50.000	3.88	0.00	33.32	4.18
17	18	0.598065	ATTTGGCCACTCAAAGCGAC	59.402	50.000	3.88	0.00	39.59	5.19
18	19	1.810151	GTATTTGGCCACTCAAAGCGA	59.190	47.619	3.88	0.00	39.59	4.93
19	20	1.812571	AGTATTTGGCCACTCAAAGCG	59.187	47.619	3.88	0.00	39.59	4.68
20	21	2.819608	TCAGTATTTGGCCACTCAAAGC	59.180	45.455	3.88	0.00	39.59	3.51
21	22	5.241506	TCTTTCAGTATTTGGCCACTCAAAG	59.758	40.000	3.88	8.12	39.59	2.77
22	23	5.009610	GTCTTTCAGTATTTGGCCACTCAAA	59.990	40.000	3.88	0.00	40.37	2.69
23	24	4.518970	GTCTTTCAGTATTTGGCCACTCAA	59.481	41.667	3.88	0.00	0.00	3.02
24	25	4.072131	GTCTTTCAGTATTTGGCCACTCA	58.928	43.478	3.88	0.00	0.00	3.41
25	26	4.072131	TGTCTTTCAGTATTTGGCCACTC	58.928	43.478	3.88	0.00	0.00	3.51
26	27	4.074970	CTGTCTTTCAGTATTTGGCCACT	58.925	43.478	3.88	0.00	39.17	4.00
27	28	3.191371	CCTGTCTTTCAGTATTTGGCCAC	59.809	47.826	3.88	0.00	42.19	5.01
28	29	3.181434	ACCTGTCTTTCAGTATTTGGCCA	60.181	43.478	0.00	0.00	42.19	5.36
29	30	3.191371	CACCTGTCTTTCAGTATTTGGCC	59.809	47.826	0.00	0.00	42.19	5.36
30	31	4.072131	TCACCTGTCTTTCAGTATTTGGC	58.928	43.478	0.00	0.00	42.19	4.52
31	32	4.697352	CCTCACCTGTCTTTCAGTATTTGG	59.303	45.833	0.00	0.00	42.19	3.28
32	33	4.154918	GCCTCACCTGTCTTTCAGTATTTG	59.845	45.833	0.00	0.00	42.19	2.32
33	34	4.042187	AGCCTCACCTGTCTTTCAGTATTT	59.958	41.667	0.00	0.00	42.19	1.40
34	35	3.584848	AGCCTCACCTGTCTTTCAGTATT	59.415	43.478	0.00	0.00	42.19	1.89
35	36	3.055530	CAGCCTCACCTGTCTTTCAGTAT	60.056	47.826	0.00	0.00	42.19	2.12
36	37	2.300152	CAGCCTCACCTGTCTTTCAGTA	59.700	50.000	0.00	0.00	42.19	2.74
37	38	1.071385	CAGCCTCACCTGTCTTTCAGT	59.929	52.381	0.00	0.00	42.19	3.41
38	39	1.345741	TCAGCCTCACCTGTCTTTCAG	59.654	52.381	0.00	0.00	43.27	3.02
39	40	1.423584	TCAGCCTCACCTGTCTTTCA	58.576	50.000	0.00	0.00	34.47	2.69
40	41	2.550830	TTCAGCCTCACCTGTCTTTC	57.449	50.000	0.00	0.00	34.47	2.62
41	42	2.373169	TGATTCAGCCTCACCTGTCTTT	59.627	45.455	0.00	0.00	34.47	2.52
42	43	1.980765	TGATTCAGCCTCACCTGTCTT	59.019	47.619	0.00	0.00	34.47	3.01
43	44	1.554160	CTGATTCAGCCTCACCTGTCT	59.446	52.381	0.00	0.00	34.47	3.41
44	45	1.277557	ACTGATTCAGCCTCACCTGTC	59.722	52.381	13.64	0.00	34.37	3.51
45	46	1.356124	ACTGATTCAGCCTCACCTGT	58.644	50.000	13.64	0.00	34.37	4.00
46	47	2.082231	CAACTGATTCAGCCTCACCTG	58.918	52.381	13.64	0.00	34.37	4.00
47	48	1.701847	ACAACTGATTCAGCCTCACCT	59.298	47.619	13.64	0.00	34.37	4.00
48	49	1.808945	CACAACTGATTCAGCCTCACC	59.191	52.381	13.64	0.00	34.37	4.02
49	50	1.198637	GCACAACTGATTCAGCCTCAC	59.801	52.381	13.64	0.00	34.37	3.51
50	51	1.527034	GCACAACTGATTCAGCCTCA	58.473	50.000	13.64	0.00	34.37	3.86
51	52	0.807496	GGCACAACTGATTCAGCCTC	59.193	55.000	13.64	0.00	39.02	4.70
52	53	0.957395	CGGCACAACTGATTCAGCCT	60.957	55.000	13.64	0.00	39.91	4.58
53	54	1.237285	ACGGCACAACTGATTCAGCC	61.237	55.000	13.64	8.52	38.73	4.85
54	55	0.110056	CACGGCACAACTGATTCAGC	60.110	55.000	13.64	0.00	34.37	4.26
55	56	0.110056	GCACGGCACAACTGATTCAG	60.110	55.000	12.17	12.17	37.52	3.02
56	57	0.534877	AGCACGGCACAACTGATTCA	60.535	50.000	0.00	0.00	0.00	2.57
57	58	0.166814	GAGCACGGCACAACTGATTC	59.833	55.000	0.00	0.00	0.00	2.52
58	59	0.250467	AGAGCACGGCACAACTGATT	60.250	50.000	0.00	0.00	0.00	2.57
59	60	0.671781	GAGAGCACGGCACAACTGAT	60.672	55.000	0.00	0.00	0.00	2.90
60	61	1.300931	GAGAGCACGGCACAACTGA	60.301	57.895	0.00	0.00	0.00	3.41
61	62	2.320587	GGAGAGCACGGCACAACTG	61.321	63.158	0.00	0.00	0.00	3.16
62	63	2.031163	GGAGAGCACGGCACAACT	59.969	61.111	0.00	0.00	0.00	3.16
63	64	2.031163	AGGAGAGCACGGCACAAC	59.969	61.111	0.00	0.00	0.00	3.32
64	65	2.031012	CAGGAGAGCACGGCACAA	59.969	61.111	0.00	0.00	0.00	3.33
65	66	1.830587	ATTCAGGAGAGCACGGCACA	61.831	55.000	0.00	0.00	0.00	4.57
66	67	1.078848	ATTCAGGAGAGCACGGCAC	60.079	57.895	0.00	0.00	0.00	5.01
67	68	1.219124	GATTCAGGAGAGCACGGCA	59.781	57.895	0.00	0.00	0.00	5.69
68	69	0.809241	CTGATTCAGGAGAGCACGGC	60.809	60.000	5.73	0.00	0.00	5.68
69	70	0.534412	ACTGATTCAGGAGAGCACGG	59.466	55.000	17.66	0.00	35.51	4.94
70	71	1.998315	CAACTGATTCAGGAGAGCACG	59.002	52.381	17.66	0.00	35.51	5.34
71	72	2.740981	CACAACTGATTCAGGAGAGCAC	59.259	50.000	17.66	0.00	35.51	4.40
72	73	2.873245	GCACAACTGATTCAGGAGAGCA	60.873	50.000	17.66	0.00	35.51	4.26
73	74	1.736681	GCACAACTGATTCAGGAGAGC	59.263	52.381	17.66	14.29	35.51	4.09
74	75	2.289882	TGGCACAACTGATTCAGGAGAG	60.290	50.000	17.66	9.08	35.51	3.20
75	76	1.699083	TGGCACAACTGATTCAGGAGA	59.301	47.619	17.66	0.00	35.51	3.71
76	77	2.082231	CTGGCACAACTGATTCAGGAG	58.918	52.381	17.66	11.45	38.70	3.69
77	78	1.699083	TCTGGCACAACTGATTCAGGA	59.301	47.619	17.66	0.33	38.70	3.86
78	79	2.189594	TCTGGCACAACTGATTCAGG	57.810	50.000	17.66	3.74	38.70	3.86
95	96	3.791320	TCACCTTCCTTACAGTGGATCT	58.209	45.455	0.00	0.00	33.09	2.75
96	97	4.762289	ATCACCTTCCTTACAGTGGATC	57.238	45.455	0.00	0.00	33.09	3.36
137	141	4.041691	ACCAACTTCAATACCAGTAGCAGT	59.958	41.667	0.00	0.00	0.00	4.40
331	335	1.277557	GCTCACTGTTCTCCTGTGGAT	59.722	52.381	0.00	0.00	41.79	3.41
491	495	6.013379	TCTCAACAGAACAAACCAGGATATCT	60.013	38.462	2.05	0.00	0.00	1.98
513	517	3.568443	CCTTCCCCTCCTTAGTACTCTC	58.432	54.545	0.00	0.00	0.00	3.20
604	969	8.316497	TGAGAGAATATCTTCCTCTTTCACAT	57.684	34.615	0.00	0.00	38.84	3.21
664	1029	8.658840	ATCTTCCTCTACTTAACAGAAGACTT	57.341	34.615	2.63	0.00	41.63	3.01
807	1898	4.383335	CCCTTGTGGCATGAGCAATAAATT	60.383	41.667	0.00	0.00	44.61	1.82
879	4462	7.769044	GGAGTAGATTTCAAATGCTAACACCTA	59.231	37.037	0.00	0.00	0.00	3.08
1123	4769	1.566298	AACCTGACCTCTGGGCCATC	61.566	60.000	6.72	1.40	39.04	3.51
1238	4911	2.820197	GGGTGAAAAAGGATGGTGTCTC	59.180	50.000	0.00	0.00	0.00	3.36
1272	4945	2.821546	TCTATGGCGCTGACATTGTAC	58.178	47.619	7.64	0.00	31.56	2.90
1297	4970	2.003301	GAGCTTCATGGAAGAACGTCC	58.997	52.381	10.01	0.11	41.71	4.79
1358	5031	3.132467	TGATGAGCTTCTGGAGATGACAG	59.868	47.826	0.00	0.00	37.30	3.51
1359	5032	3.102204	TGATGAGCTTCTGGAGATGACA	58.898	45.455	0.00	0.00	0.00	3.58
1391	5064	8.837788	TGGCATCTCATAGTTAATAACATCAG	57.162	34.615	5.89	0.00	0.00	2.90
1401	5074	5.957771	AAAGACCTGGCATCTCATAGTTA	57.042	39.130	0.00	0.00	0.00	2.24
1405	5078	3.069586	CGGTAAAGACCTGGCATCTCATA	59.930	47.826	0.00	0.00	44.46	2.15
1432	5105	6.710597	TGAACAGCGTACTAGGATAGAATT	57.289	37.500	0.00	0.00	42.77	2.17
1438	5111	4.270834	TCTCTTGAACAGCGTACTAGGAT	58.729	43.478	0.00	0.00	0.00	3.24
1439	5112	3.682696	TCTCTTGAACAGCGTACTAGGA	58.317	45.455	0.00	0.00	0.00	2.94
1908	6062	4.457834	AACACATGGAGCTGTAGACTAC	57.542	45.455	5.62	5.62	0.00	2.73
1909	6063	4.526650	TCAAACACATGGAGCTGTAGACTA	59.473	41.667	0.00	0.00	0.00	2.59
1910	6064	3.324846	TCAAACACATGGAGCTGTAGACT	59.675	43.478	0.00	0.00	0.00	3.24
1911	6065	3.664107	TCAAACACATGGAGCTGTAGAC	58.336	45.455	0.00	0.00	0.00	2.59
2158	6441	2.339556	GCGGTTGTAGCCATGCCAA	61.340	57.895	0.00	0.00	0.00	4.52
2159	6442	2.749839	GCGGTTGTAGCCATGCCA	60.750	61.111	0.00	0.00	0.00	4.92
2166	6449	3.178539	GCTTCCTGCGGTTGTAGC	58.821	61.111	0.00	0.00	0.00	3.58
2307	8683	2.557056	GTCAACTTAAGGCCCTTTGACC	59.443	50.000	18.40	6.94	40.01	4.02
2339	8715	7.830940	TTTCTAACATTTTTGCCATGCATAG	57.169	32.000	0.00	0.00	38.76	2.23
2460	8837	7.733773	TTTCTAGAAGAGAGAGAGAGAGAGA	57.266	40.000	5.12	0.00	34.93	3.10
2461	8838	7.497249	CCTTTTCTAGAAGAGAGAGAGAGAGAG	59.503	44.444	21.50	0.15	34.93	3.20
2467	8844	5.913137	TGCCTTTTCTAGAAGAGAGAGAG	57.087	43.478	21.50	7.91	34.93	3.20
2700	9214	6.918022	ACAACAGAAAGCTTTTATTTTCTCCG	59.082	34.615	14.05	0.00	40.62	4.63
3026	9583	1.636003	CCTCCCTGCCCTACTTTTTCT	59.364	52.381	0.00	0.00	0.00	2.52
3548	10106	1.558294	GATACTCCCCCAAAGTTCCGT	59.442	52.381	0.00	0.00	0.00	4.69
3602	10160	1.406069	CCGCTCACCATTTCTAGCACT	60.406	52.381	0.00	0.00	34.60	4.40
3758	10316	2.517875	GCCACCATAGCCAGCTGG	60.518	66.667	29.34	29.34	38.55	4.85
4110	10694	9.474313	TTGCTACTTTTGAAGATAAATATGGGT	57.526	29.630	0.00	0.00	0.00	4.51
4430	11041	3.994392	TCTCCCGCGATTTTAATCTATGC	59.006	43.478	8.23	0.00	33.24	3.14
4510	11121	5.062558	CCAGAAAAATTTCCGCTATTTGCTG	59.937	40.000	2.37	0.00	37.92	4.41
4632	11250	2.848887	CGCTATAACTGCGCTATAGCTG	59.151	50.000	29.35	22.68	46.44	4.24
4663	11281	6.867662	AAAGTCATAGATTCAAATAGCCCG	57.132	37.500	0.00	0.00	0.00	6.13
4863	11481	1.192146	TCCCTCCCACAGTTTCGGAG	61.192	60.000	0.00	0.00	42.48	4.63
4885	11503	7.113658	GAGGTACATCACTCCTCAGATTTTA	57.886	40.000	1.92	0.00	44.85	1.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.