AutoCloner

Multiple sequence alignment - TraesCS3B01G333600

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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	TraesCS3B01G333600	chr3B	100.000	5546	0	0	1	5546	540200229	540205774	0.000000e+00	10242.0
1	TraesCS3B01G333600	chr3B	100.000	1641	0	0	5786	7426	540206014	540207654	0.000000e+00	3031.0
2	TraesCS3B01G333600	chr3B	100.000	28	0	0	5828	5855	136479630	136479657	1.300000e-02	52.8
3	TraesCS3B01G333600	chr3D	97.570	2922	34	15	2611	5526	414368788	414371678	0.000000e+00	4968.0
4	TraesCS3B01G333600	chr3D	95.697	2115	55	11	512	2613	414366616	414368707	0.000000e+00	3369.0
5	TraesCS3B01G333600	chr3D	94.329	1587	52	21	5787	7356	414372028	414373593	0.000000e+00	2398.0
6	TraesCS3B01G333600	chr3A	93.096	1941	96	17	3136	5070	536637916	536636008	0.000000e+00	2808.0
7	TraesCS3B01G333600	chr3A	89.310	1637	100	23	1495	3114	536639483	536637905	0.000000e+00	1984.0
8	TraesCS3B01G333600	chr3A	90.999	1111	75	14	6112	7213	536635229	536634135	0.000000e+00	1474.0
9	TraesCS3B01G333600	chr3A	93.092	941	50	12	512	1445	536640414	536639482	0.000000e+00	1363.0
10	TraesCS3B01G333600	chr3A	89.251	521	42	10	1	512	442288818	442289333	2.260000e-179	640.0
11	TraesCS3B01G333600	chr3A	92.517	441	31	2	5107	5546	536636005	536635566	1.360000e-176	630.0
12	TraesCS3B01G333600	chr3A	93.846	195	8	4	1410	1601	419540288	419540095	2.620000e-74	291.0
13	TraesCS3B01G333600	chr3A	93.367	196	10	3	1401	1594	642038743	642038937	3.390000e-73	287.0
14	TraesCS3B01G333600	chr3A	87.719	228	11	10	7215	7426	536634056	536633830	4.450000e-62	250.0
15	TraesCS3B01G333600	chr3A	91.818	110	7	2	5859	5967	536635544	536635436	1.290000e-32	152.0
16	TraesCS3B01G333600	chr3A	90.000	70	7	0	5786	5855	102680760	102680829	2.850000e-14	91.6
17	TraesCS3B01G333600	chr5B	92.577	485	30	5	1	482	536922643	536922162	0.000000e+00	691.0
18	TraesCS3B01G333600	chr5B	91.051	514	43	3	1	513	669163630	669164141	0.000000e+00	691.0
19	TraesCS3B01G333600	chr5B	93.782	193	10	2	1404	1595	631795000	631794809	9.430000e-74	289.0
20	TraesCS3B01G333600	chr7B	90.541	518	43	5	1	515	670032277	670032791	0.000000e+00	680.0
21	TraesCS3B01G333600	chr7B	89.942	517	45	5	1	515	670049394	670049905	0.000000e+00	660.0
22	TraesCS3B01G333600	chr7B	89.749	517	49	3	1	515	79072983	79072469	0.000000e+00	658.0
23	TraesCS3B01G333600	chr6B	90.385	520	36	11	1	516	55438743	55438234	0.000000e+00	671.0
24	TraesCS3B01G333600	chr4A	87.356	522	60	6	1	520	648317066	648317583	1.780000e-165	593.0
25	TraesCS3B01G333600	chr7A	87.597	516	46	14	1	513	306350979	306351479	3.860000e-162	582.0
26	TraesCS3B01G333600	chr5A	95.187	187	7	2	1409	1594	13889429	13889614	2.030000e-75	294.0
27	TraesCS3B01G333600	chr4B	94.271	192	7	4	1409	1597	295687857	295687667	2.620000e-74	291.0
28	TraesCS3B01G333600	chr4B	93.401	197	8	4	1407	1599	455621635	455621440	3.390000e-73	287.0
29	TraesCS3B01G333600	chr6A	94.211	190	9	2	1406	1594	101870131	101869943	9.430000e-74	289.0
30	TraesCS3B01G333600	chr2A	93.814	194	9	3	1403	1595	286445860	286446051	9.430000e-74	289.0
31	TraesCS3B01G333600	chr1D	97.297	37	0	1	5822	5858	433281517	433281482	2.240000e-05	62.1
32	TraesCS3B01G333600	chr1B	100.000	31	0	0	5828	5858	585312951	585312921	2.890000e-04	58.4

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	TraesCS3B01G333600	chr3B	540200229	540207654	7425	False	6636.500000	10242	100.000000	1	7426	2	chr3B.!!$F2	7425
1	TraesCS3B01G333600	chr3D	414366616	414373593	6977	False	3578.333333	4968	95.865333	512	7356	3	chr3D.!!$F1	6844
2	TraesCS3B01G333600	chr3A	536633830	536640414	6584	True	1237.285714	2808	91.221571	512	7426	7	chr3A.!!$R2	6914
3	TraesCS3B01G333600	chr3A	442288818	442289333	515	False	640.000000	640	89.251000	1	512	1	chr3A.!!$F2	511
4	TraesCS3B01G333600	chr5B	669163630	669164141	511	False	691.000000	691	91.051000	1	513	1	chr5B.!!$F1	512
5	TraesCS3B01G333600	chr7B	670032277	670032791	514	False	680.000000	680	90.541000	1	515	1	chr7B.!!$F1	514
6	TraesCS3B01G333600	chr7B	670049394	670049905	511	False	660.000000	660	89.942000	1	515	1	chr7B.!!$F2	514
7	TraesCS3B01G333600	chr7B	79072469	79072983	514	True	658.000000	658	89.749000	1	515	1	chr7B.!!$R1	514
8	TraesCS3B01G333600	chr6B	55438234	55438743	509	True	671.000000	671	90.385000	1	516	1	chr6B.!!$R1	515
9	TraesCS3B01G333600	chr4A	648317066	648317583	517	False	593.000000	593	87.356000	1	520	1	chr4A.!!$F1	519
10	TraesCS3B01G333600	chr7A	306350979	306351479	500	False	582.000000	582	87.597000	1	513	1	chr7A.!!$F1	512

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	Self any TH	Self end TH	Hairpin	End Stability	Orientation
775	800	0.036388	CGGAGTGCAGTACCATTGGT	60.036	55.000	13.94	13.94	40.16	3.67	F
1458	1487	0.038599	TGCTGCCTTGTGACCATGAT	59.961	50.000	0.00	0.00	0.00	2.45	F
1637	1666	0.036388	TCTGTGGTCAAGGGAATCGC	60.036	55.000	0.00	0.00	0.00	4.58	F
1841	1870	0.881118	TGCCATGCCGAGAGTTTTTC	59.119	50.000	0.00	0.00	0.00	2.29	F
2215	2253	1.621317	GGAGGAGGGCAGCTAGATTAC	59.379	57.143	0.00	0.00	0.00	1.89	F
2378	2416	4.211125	TGAACAACAGGTGGCATCTTTTA	58.789	39.130	0.00	0.00	0.00	1.52	F
3972	4104	5.241728	CCGTGATCACATTATCCTCTCTACA	59.758	44.000	24.93	0.00	0.00	2.74	F
5949	6173	2.159128	ACATCTGCATCAGGAACTCTCG	60.159	50.000	0.00	0.00	34.60	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1637	1666	0.889186	ACCTAACAAAGCACTGCCGG	60.889	55.000	0.00	0.00	6.13	R
2378	2416	8.110860	ACGTCCACAGAAAATCATTTAAAGAT	57.889	30.769	0.00	0.00	2.40	R
3507	3637	2.162208	TCTTGGAAATCATGCACGAAGC	59.838	45.455	0.00	45.96	3.86	R
4072	4205	9.686683	ATTACAACACCTATGAGCTTTCTAAAT	57.313	29.630	0.00	0.00	1.40	R
4127	4260	0.476771	GTTGGTGGGAACTGGAAGGA	59.523	55.000	0.00	39.30	3.36	R
4333	4466	5.899120	ATATGCCATCAGATTGCATCTTC	57.101	39.130	22.14	44.15	2.87	R
5951	6175	0.105194	TGAGGACCAGGAGGACACAA	60.105	55.000	0.00	38.69	3.33	R
7156	7482	0.032952	AGCTGACGTTACCGCTGAAA	59.967	50.000	0.00	37.70	2.69	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
25	26	5.516696	CGACGAACTCATCTACAATGTTCAT	59.483	40.000	0.00	0.00	37.46	2.57
165	166	2.649034	GCTGTTCCTCGGACGACA	59.351	61.111	0.00	0.00	0.00	4.35
202	203	2.210711	CGGGACTAGGAGGGGATGC	61.211	68.421	0.00	0.00	0.00	3.91
203	204	1.074471	GGGACTAGGAGGGGATGCA	60.074	63.158	0.00	0.00	0.00	3.96
369	386	2.018727	ATACACCACGCGCGGGATAA	62.019	55.000	37.25	16.52	0.00	1.75
472	489	3.242059	GCGCGCTAAAACGGACTAATTTA	60.242	43.478	26.67	0.00	0.00	1.40
477	494	4.330894	GCTAAAACGGACTAATTTACGGCT	59.669	41.667	0.00	0.00	0.00	5.52
520	537	3.273434	GTTGGAGATGCTCTAATGCACA	58.727	45.455	0.00	0.00	46.33	4.57
603	628	3.857854	GCACGGCTCACATCGCTG	61.858	66.667	0.00	0.00	39.62	5.18
616	641	1.663379	ATCGCTGTCCAACGATCGGA	61.663	55.000	20.98	4.08	45.35	4.55
736	761	3.864789	TCATCCCAAAGAGCTTATCCC	57.135	47.619	0.00	0.00	0.00	3.85
768	793	0.039798	TCAACGTCGGAGTGCAGTAC	60.040	55.000	0.00	0.00	0.00	2.73
770	795	1.457823	AACGTCGGAGTGCAGTACCA	61.458	55.000	0.00	0.00	0.00	3.25
771	796	1.248785	ACGTCGGAGTGCAGTACCAT	61.249	55.000	0.00	0.00	0.00	3.55
775	800	0.036388	CGGAGTGCAGTACCATTGGT	60.036	55.000	13.94	13.94	40.16	3.67
776	801	1.453155	GGAGTGCAGTACCATTGGTG	58.547	55.000	18.83	2.96	36.19	4.17
974	1001	0.539986	GCCTCCCACTGTTATCGGAA	59.460	55.000	0.00	0.00	0.00	4.30
975	1002	1.742750	GCCTCCCACTGTTATCGGAAC	60.743	57.143	0.00	0.00	0.00	3.62
979	1006	0.390603	CCACTGTTATCGGAACCGCA	60.391	55.000	8.48	0.12	39.59	5.69
1033	1060	3.162154	GTAAGCTCCCCTCCCCCG	61.162	72.222	0.00	0.00	0.00	5.73
1181	1209	2.285083	CGGTTGAGCGATAAATTGGGA	58.715	47.619	0.00	0.00	0.00	4.37
1193	1221	1.923356	AATTGGGAAGTGGCGATGTT	58.077	45.000	0.00	0.00	0.00	2.71
1398	1427	3.678056	TTCTGCACTGTTAGTGGTAGG	57.322	47.619	10.62	0.00	46.01	3.18
1413	1442	1.831736	GGTAGGCTGCTAGTTGGAAGA	59.168	52.381	1.79	0.00	0.00	2.87
1458	1487	0.038599	TGCTGCCTTGTGACCATGAT	59.961	50.000	0.00	0.00	0.00	2.45
1469	1498	3.057969	TGACCATGATGTCACAGGTTC	57.942	47.619	9.50	5.35	40.22	3.62
1514	1543	1.838112	CAATGTAGGGAAAGGCTGCA	58.162	50.000	0.50	0.00	0.00	4.41
1548	1577	4.257810	TGGTCGGACCCTTCCCCA	62.258	66.667	23.81	0.69	38.99	4.96
1563	1592	2.113774	CCAGACCCTGTGCAAGCA	59.886	61.111	0.00	0.00	0.00	3.91
1637	1666	0.036388	TCTGTGGTCAAGGGAATCGC	60.036	55.000	0.00	0.00	0.00	4.58
1641	1670	3.202706	GTCAAGGGAATCGCCGGC	61.203	66.667	19.07	19.07	37.63	6.13
1740	1769	1.877680	GCTTGGTTGGGCAAATTGGAC	60.878	52.381	0.00	0.00	0.00	4.02
1825	1854	4.142609	TCCTCAGTTGATATGTTCTGCC	57.857	45.455	0.00	0.00	0.00	4.85
1841	1870	0.881118	TGCCATGCCGAGAGTTTTTC	59.119	50.000	0.00	0.00	0.00	2.29
1942	1971	3.436470	GGGAAGCCCTGGCATTATCTTTA	60.436	47.826	11.38	0.00	44.88	1.85
2012	2041	5.675970	ACAAACTCGATTGTGTGAATTACG	58.324	37.500	3.65	0.00	41.78	3.18
2013	2042	5.464057	ACAAACTCGATTGTGTGAATTACGA	59.536	36.000	3.65	0.00	41.78	3.43
2014	2043	5.763444	AACTCGATTGTGTGAATTACGAG	57.237	39.130	0.00	0.00	46.80	4.18
2016	2045	5.763444	CTCGATTGTGTGAATTACGAGTT	57.237	39.130	0.00	0.00	40.11	3.01
2017	2046	6.153212	CTCGATTGTGTGAATTACGAGTTT	57.847	37.500	0.00	0.00	40.11	2.66
2018	2047	7.273188	CTCGATTGTGTGAATTACGAGTTTA	57.727	36.000	0.00	0.00	40.11	2.01
2215	2253	1.621317	GGAGGAGGGCAGCTAGATTAC	59.379	57.143	0.00	0.00	0.00	1.89
2249	2287	5.621329	CGGTCGCATATATCATGGTTACTCA	60.621	44.000	0.00	0.00	0.00	3.41
2342	2380	7.912250	CACTTATGCTAACTCATTTCCAATCAC	59.088	37.037	0.00	0.00	0.00	3.06
2378	2416	4.211125	TGAACAACAGGTGGCATCTTTTA	58.789	39.130	0.00	0.00	0.00	1.52
3146	3276	8.421002	ACAACAAAGCCTTTAATGTTAACAGAT	58.579	29.630	14.65	8.07	34.45	2.90
3147	3277	9.260002	CAACAAAGCCTTTAATGTTAACAGATT	57.740	29.630	14.65	7.04	34.45	2.40
3148	3278	9.830975	AACAAAGCCTTTAATGTTAACAGATTT	57.169	25.926	14.65	7.46	34.45	2.17
3507	3637	7.012327	TGACTCAAATTTAGGAAGTTGACACTG	59.988	37.037	0.00	0.00	42.80	3.66
3972	4104	5.241728	CCGTGATCACATTATCCTCTCTACA	59.758	44.000	24.93	0.00	0.00	2.74
4072	4205	7.570132	TCAATTCGGAGGGATTCTTATGTTTA	58.430	34.615	0.00	0.00	0.00	2.01
4127	4260	7.963532	TGACTAGTTCTCTGTTCAATAACCTT	58.036	34.615	0.00	0.00	34.49	3.50
4333	4466	9.823647	ACTAACAGAATACATGAACTAATCTGG	57.176	33.333	0.00	0.00	37.67	3.86
4459	4592	2.290514	TGCCTTAGATGCAAGCAGAACT	60.291	45.455	0.00	3.07	35.40	3.01
4759	4892	4.746611	AGCTGTACAATTCAAAAGCTTTGC	59.253	37.500	13.54	7.03	37.74	3.68
5412	5545	8.738199	TTACAATCGTCTAGAGTTACAGTTTG	57.262	34.615	0.00	0.00	0.00	2.93
5508	5642	3.381272	TGCCTTTTTGGTCACTCTGAAAG	59.619	43.478	0.00	0.00	38.35	2.62
5532	5666	7.177878	AGTATGAATCACCAGAAGAACCAATT	58.822	34.615	0.00	0.00	0.00	2.32
5852	6075	6.912951	TCTTATATTTTAGGACGGAGGGAG	57.087	41.667	0.00	0.00	0.00	4.30
5949	6173	2.159128	ACATCTGCATCAGGAACTCTCG	60.159	50.000	0.00	0.00	34.60	4.04
5951	6175	0.534412	CTGCATCAGGAACTCTCGGT	59.466	55.000	0.00	0.00	34.60	4.69
5983	6207	1.180029	GTCCTCACCTTGCAATGCAT	58.820	50.000	9.39	0.00	38.76	3.96
6134	6450	7.441836	ACTACATGTCAACTACAACTTGATGA	58.558	34.615	0.00	0.00	42.70	2.92
6145	6465	7.959175	ACTACAACTTGATGACAGGTAGTTTA	58.041	34.615	0.00	0.00	37.31	2.01
6169	6489	1.535028	CTGGACGCATGTTAAACTGCA	59.465	47.619	10.20	0.00	38.30	4.41
6170	6490	2.158559	TGGACGCATGTTAAACTGCAT	58.841	42.857	10.20	0.00	38.30	3.96
6399	6719	4.201960	GCCTCCTAGTAAAAATTGCTCAGC	60.202	45.833	0.00	0.00	0.00	4.26
6506	6826	3.469008	TGAGTTGACATTTGACGACCT	57.531	42.857	0.00	0.00	0.00	3.85
6728	7048	3.593442	TCAACAATCTCCCAAGTTGGT	57.407	42.857	20.54	0.00	41.14	3.67
6732	7052	1.270550	CAATCTCCCAAGTTGGTGTGC	59.729	52.381	20.54	0.00	35.17	4.57
6735	7055	1.227823	TCCCAAGTTGGTGTGCTCG	60.228	57.895	20.54	3.55	35.17	5.03
6736	7056	2.639286	CCAAGTTGGTGTGCTCGC	59.361	61.111	14.21	0.00	31.35	5.03
6739	7059	0.311790	CAAGTTGGTGTGCTCGCATT	59.688	50.000	1.32	0.00	0.00	3.56
6740	7060	1.535028	CAAGTTGGTGTGCTCGCATTA	59.465	47.619	1.32	0.00	0.00	1.90
6741	7061	2.113860	AGTTGGTGTGCTCGCATTAT	57.886	45.000	1.32	0.00	0.00	1.28
6742	7062	1.739466	AGTTGGTGTGCTCGCATTATG	59.261	47.619	1.32	0.00	0.00	1.90
6744	7064	2.675844	GTTGGTGTGCTCGCATTATGTA	59.324	45.455	1.32	0.00	0.00	2.29
6747	7067	4.893608	TGGTGTGCTCGCATTATGTATAT	58.106	39.130	1.32	0.00	0.00	0.86
6776	7096	5.405269	GGAATTGGTGTTGAAATGCAGTTAC	59.595	40.000	0.00	0.00	0.00	2.50
6777	7097	5.789643	ATTGGTGTTGAAATGCAGTTACT	57.210	34.783	0.00	0.00	0.00	2.24
6782	7102	7.199766	TGGTGTTGAAATGCAGTTACTAAAAG	58.800	34.615	0.00	0.00	0.00	2.27
6784	7104	7.704899	GGTGTTGAAATGCAGTTACTAAAAGTT	59.295	33.333	0.00	0.00	0.00	2.66
6785	7105	9.724839	GTGTTGAAATGCAGTTACTAAAAGTTA	57.275	29.630	0.00	0.00	0.00	2.24
6797	7117	8.610035	AGTTACTAAAAGTTAAGTGTTGACAGC	58.390	33.333	0.00	0.00	0.00	4.40
6862	7182	3.139077	GTGCCTTGTTGTAACTAGCTGT	58.861	45.455	0.00	0.00	31.71	4.40
6915	7235	1.585002	CGTGTGTTTGTTGGTGGCG	60.585	57.895	0.00	0.00	0.00	5.69
6916	7236	1.876263	GTGTGTTTGTTGGTGGCGC	60.876	57.895	0.00	0.00	0.00	6.53
6965	7285	1.897802	TGTAAGGAACCGGTCTTCTCC	59.102	52.381	8.04	11.88	0.00	3.71
6982	7302	3.122480	TCTCCTGGCTTTTGGATGGATA	58.878	45.455	0.00	0.00	0.00	2.59
7002	7322	5.532779	GGATATTTCCCTCACCAATCTCAAC	59.467	44.000	0.00	0.00	35.84	3.18
7161	7487	3.726517	CACCACCGCGCCTTTCAG	61.727	66.667	0.00	0.00	0.00	3.02
7182	7509	2.281140	GGTAACGTCAGCTCTTCTCC	57.719	55.000	0.00	0.00	0.00	3.71
7190	7517	0.175302	CAGCTCTTCTCCGTGCTCAT	59.825	55.000	0.00	0.00	31.96	2.90
7229	7633	5.050431	GCTAAGTACGAGTAGTAGTAGTGGC	60.050	48.000	1.33	4.34	37.98	5.01
7238	7648	5.679601	AGTAGTAGTAGTGGCAGTAGGTAC	58.320	45.833	1.37	7.82	0.00	3.34
7361	7771	4.749310	CGGCTGAGCTGCGTCCTT	62.749	66.667	3.72	0.00	0.00	3.36
7362	7772	2.359230	GGCTGAGCTGCGTCCTTT	60.359	61.111	3.72	0.00	0.00	3.11
7364	7774	1.963338	GCTGAGCTGCGTCCTTTGT	60.963	57.895	0.00	0.00	0.00	2.83
7367	7777	0.391228	TGAGCTGCGTCCTTTGTGTA	59.609	50.000	0.00	0.00	0.00	2.90
7371	7793	2.290641	AGCTGCGTCCTTTGTGTAAAAG	59.709	45.455	0.00	0.00	0.00	2.27
7378	7800	3.066760	GTCCTTTGTGTAAAAGCTGCACT	59.933	43.478	1.02	0.00	40.98	4.40
7389	7811	1.835494	AGCTGCACTGCTCATCAAAT	58.165	45.000	1.02	0.00	39.34	2.32
7393	7815	3.428999	GCTGCACTGCTCATCAAATCAAT	60.429	43.478	1.98	0.00	0.00	2.57
7394	7816	4.104696	TGCACTGCTCATCAAATCAATG	57.895	40.909	1.98	0.00	0.00	2.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
421	438	4.675029	CGGGTCGCTTCAACGGGT	62.675	66.667	0.00	0.00	0.00	5.28
603	628	3.667261	CGTATAACATCCGATCGTTGGAC	59.333	47.826	15.09	7.75	38.60	4.02
736	761	1.856597	GACGTTGACGGAATATTCGGG	59.143	52.381	22.54	13.71	44.95	5.14
761	786	0.251121	CACCCACCAATGGTACTGCA	60.251	55.000	3.85	0.00	45.66	4.41
768	793	4.312443	GACGTATATACACCCACCAATGG	58.688	47.826	13.22	0.00	46.81	3.16
770	795	3.325716	GGGACGTATATACACCCACCAAT	59.674	47.826	26.87	0.88	40.12	3.16
771	796	2.699846	GGGACGTATATACACCCACCAA	59.300	50.000	26.87	0.00	40.12	3.67
1005	1032	1.677637	GGAGCTTACAGAGGGACGGG	61.678	65.000	0.00	0.00	0.00	5.28
1033	1060	0.466124	AAGGCCAGCTAATCGGAGAC	59.534	55.000	5.01	0.00	42.51	3.36
1176	1204	0.109532	TGAACATCGCCACTTCCCAA	59.890	50.000	0.00	0.00	0.00	4.12
1181	1209	1.073025	TGCCTGAACATCGCCACTT	59.927	52.632	0.00	0.00	0.00	3.16
1193	1221	0.684535	TCACCTCAATTCGTGCCTGA	59.315	50.000	0.00	0.00	0.00	3.86
1398	1427	1.742071	GCTCCTCTTCCAACTAGCAGC	60.742	57.143	0.00	0.00	0.00	5.25
1413	1442	4.711949	CACTGCGCCAAGGCTCCT	62.712	66.667	4.18	0.00	39.32	3.69
1458	1487	2.620251	CAGGACTTGAACCTGTGACA	57.380	50.000	0.00	0.00	46.71	3.58
1466	1495	1.609072	GGCTGTTTCCAGGACTTGAAC	59.391	52.381	0.00	0.00	39.22	3.18
1468	1497	1.072331	GAGGCTGTTTCCAGGACTTGA	59.928	52.381	0.00	0.00	39.22	3.02
1469	1498	1.072965	AGAGGCTGTTTCCAGGACTTG	59.927	52.381	0.00	0.00	39.22	3.16
1563	1592	1.910722	CCCAGTGCATGTAGCTCCT	59.089	57.895	0.00	0.00	45.94	3.69
1637	1666	0.889186	ACCTAACAAAGCACTGCCGG	60.889	55.000	0.00	0.00	0.00	6.13
1641	1670	3.648339	AATGCACCTAACAAAGCACTG	57.352	42.857	0.00	0.00	40.14	3.66
1740	1769	4.384056	CAGTCTAAATATGAGCACCCTGG	58.616	47.826	0.00	0.00	0.00	4.45
1825	1854	4.667668	CGAAGAAGAAAAACTCTCGGCATG	60.668	45.833	0.00	0.00	31.02	4.06
1841	1870	2.475187	CGGCATGAAAGAAGCGAAGAAG	60.475	50.000	0.00	0.00	0.00	2.85
2215	2253	2.004583	TATGCGACCGGACAAGAAAG	57.995	50.000	9.46	0.00	0.00	2.62
2378	2416	8.110860	ACGTCCACAGAAAATCATTTAAAGAT	57.889	30.769	0.00	0.00	0.00	2.40
3034	3161	9.357652	GAATTGAGTTTTCTAGCATTTGCAATA	57.642	29.630	0.00	0.00	45.16	1.90
3507	3637	2.162208	TCTTGGAAATCATGCACGAAGC	59.838	45.455	0.00	0.00	45.96	3.86
4072	4205	9.686683	ATTACAACACCTATGAGCTTTCTAAAT	57.313	29.630	0.00	0.00	0.00	1.40
4127	4260	0.476771	GTTGGTGGGAACTGGAAGGA	59.523	55.000	0.00	0.00	39.30	3.36
4333	4466	5.899120	ATATGCCATCAGATTGCATCTTC	57.101	39.130	22.14	0.00	44.15	2.87
4607	4740	8.962884	ATAACCATTTTCATAGCAAATTTCCC	57.037	30.769	0.00	0.00	0.00	3.97
4759	4892	7.441157	TCCGCCTAAGATTGTACTGAATAAATG	59.559	37.037	0.00	0.00	0.00	2.32
5394	5527	4.148348	GTGTGCAAACTGTAACTCTAGACG	59.852	45.833	0.00	0.00	0.00	4.18
5508	5642	7.396540	AATTGGTTCTTCTGGTGATTCATAC	57.603	36.000	0.00	0.00	0.00	2.39
5826	6049	7.014449	TCCCTCCGTCCTAAAATATAAGATGA	58.986	38.462	0.00	0.00	0.00	2.92
5949	6173	1.128188	AGGACCAGGAGGACACAACC	61.128	60.000	0.00	0.00	38.69	3.77
5951	6175	0.105194	TGAGGACCAGGAGGACACAA	60.105	55.000	0.00	0.00	38.69	3.33
5983	6207	3.009723	GAGAGCATTCGTCCCAAATCAA	58.990	45.455	0.00	0.00	0.00	2.57
6072	6302	6.547141	CCATTGGGATCATTTAAAGCAGAGTA	59.453	38.462	0.00	0.00	35.59	2.59
6145	6465	3.938963	CAGTTTAACATGCGTCCAGGTAT	59.061	43.478	0.00	0.00	34.41	2.73
6169	6489	4.156455	ACCTGCAGAAACGATGGAATAT	57.844	40.909	17.39	0.00	0.00	1.28
6170	6490	3.627395	ACCTGCAGAAACGATGGAATA	57.373	42.857	17.39	0.00	0.00	1.75
6321	6641	8.157476	AGATTTCAGTTCTTGGTACTTGTGTAT	58.843	33.333	0.00	0.00	0.00	2.29
6373	6693	3.696548	AGCAATTTTTACTAGGAGGCTGC	59.303	43.478	0.00	0.00	0.00	5.25
6399	6719	1.278172	CCTTCGTATGCCGCGATCAG	61.278	60.000	8.23	0.00	38.21	2.90
6529	6849	5.796350	AACAGCGTAAACCAACATCTATC	57.204	39.130	0.00	0.00	0.00	2.08
6662	6982	9.632638	AGCTATACATCAACCATTACATTTTCT	57.367	29.630	0.00	0.00	0.00	2.52
6728	7048	6.589907	CCACTTATATACATAATGCGAGCACA	59.410	38.462	0.00	0.00	0.00	4.57
6740	7060	9.693739	TTCAACACCAATTCCACTTATATACAT	57.306	29.630	0.00	0.00	0.00	2.29
6741	7061	9.521841	TTTCAACACCAATTCCACTTATATACA	57.478	29.630	0.00	0.00	0.00	2.29
6744	7064	7.981225	GCATTTCAACACCAATTCCACTTATAT	59.019	33.333	0.00	0.00	0.00	0.86
6747	7067	5.069648	TGCATTTCAACACCAATTCCACTTA	59.930	36.000	0.00	0.00	0.00	2.24
6776	7096	7.126398	GTCAGCTGTCAACACTTAACTTTTAG	58.874	38.462	14.67	0.00	0.00	1.85
6777	7097	6.037830	GGTCAGCTGTCAACACTTAACTTTTA	59.962	38.462	14.67	0.00	0.00	1.52
6782	7102	3.248602	CAGGTCAGCTGTCAACACTTAAC	59.751	47.826	14.67	0.00	0.00	2.01
6784	7104	2.434336	ACAGGTCAGCTGTCAACACTTA	59.566	45.455	14.67	0.00	0.00	2.24
6785	7105	1.210478	ACAGGTCAGCTGTCAACACTT	59.790	47.619	14.67	0.00	0.00	3.16
6846	7166	4.682778	AGTGGACAGCTAGTTACAACAA	57.317	40.909	0.00	0.00	0.00	2.83
6862	7182	1.300963	GGCTGCCAGATCAAGTGGA	59.699	57.895	15.17	0.00	37.23	4.02
6915	7235	4.778143	ATTGACAGGGACCGCGGC	62.778	66.667	28.58	18.35	0.00	6.53
6916	7236	2.046314	AATTGACAGGGACCGCGG	60.046	61.111	26.86	26.86	0.00	6.46
6965	7285	5.205759	GGAAATATCCATCCAAAAGCCAG	57.794	43.478	0.00	0.00	45.79	4.85
6982	7302	3.347216	CGTTGAGATTGGTGAGGGAAAT	58.653	45.455	0.00	0.00	0.00	2.17
7002	7322	1.070445	CAGCTTATCCTCCCCTGCG	59.930	63.158	0.00	0.00	0.00	5.18
7156	7482	0.032952	AGCTGACGTTACCGCTGAAA	59.967	50.000	0.00	0.00	37.70	2.69
7157	7483	0.388134	GAGCTGACGTTACCGCTGAA	60.388	55.000	0.00	0.00	37.70	3.02
7161	7487	0.109226	AGAAGAGCTGACGTTACCGC	60.109	55.000	0.00	0.00	37.70	5.68
7170	7496	0.895559	TGAGCACGGAGAAGAGCTGA	60.896	55.000	0.00	0.00	37.48	4.26
7213	7540	3.808726	CCTACTGCCACTACTACTACTCG	59.191	52.174	0.00	0.00	0.00	4.18
7238	7648	6.194463	CACGGCAAAGAATAACATCACATAG	58.806	40.000	0.00	0.00	0.00	2.23
7356	7766	3.066760	AGTGCAGCTTTTACACAAAGGAC	59.933	43.478	8.23	0.00	36.76	3.85
7357	7767	3.066621	CAGTGCAGCTTTTACACAAAGGA	59.933	43.478	8.23	0.00	36.76	3.36
7358	7768	3.374745	CAGTGCAGCTTTTACACAAAGG	58.625	45.455	8.23	0.00	36.76	3.11
7359	7769	2.791004	GCAGTGCAGCTTTTACACAAAG	59.209	45.455	11.09	0.00	36.76	2.77
7360	7770	2.426738	AGCAGTGCAGCTTTTACACAAA	59.573	40.909	19.20	0.00	43.70	2.83
7361	7771	2.023673	AGCAGTGCAGCTTTTACACAA	58.976	42.857	19.20	0.00	43.70	3.33
7362	7772	1.603802	GAGCAGTGCAGCTTTTACACA	59.396	47.619	19.20	0.00	46.75	3.72
7364	7774	1.965935	TGAGCAGTGCAGCTTTTACA	58.034	45.000	19.20	1.50	46.75	2.41
7367	7777	1.612676	TGATGAGCAGTGCAGCTTTT	58.387	45.000	19.20	0.00	46.75	2.27
7371	7793	1.471287	TGATTTGATGAGCAGTGCAGC	59.529	47.619	19.20	9.51	0.00	5.25
7378	7800	7.814107	GGTTTTCTTACATTGATTTGATGAGCA	59.186	33.333	0.00	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.