AutoCloner

Multiple sequence alignment - TraesCS6B01G458700

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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	TraesCS6B01G458700	chr6B	100.000	3023	0	0	1	3023	713720551	713723573	0.000000e+00	5583.0
1	TraesCS6B01G458700	chr6B	84.737	2398	316	28	5	2365	713146542	713148926	0.000000e+00	2355.0
2	TraesCS6B01G458700	chr6B	77.789	986	175	27	1414	2372	713939986	713939018	4.370000e-158	568.0
3	TraesCS6B01G458700	chr6B	78.425	876	147	25	1414	2263	713453496	713452637	1.600000e-147	532.0
4	TraesCS6B01G458700	chr6B	78.501	507	61	22	2390	2870	713148996	713149480	3.810000e-74	289.0
5	TraesCS6B01G458700	chr6A	86.607	2897	348	17	1	2875	613950194	613953072	0.000000e+00	3164.0
6	TraesCS6B01G458700	chr6A	83.983	1386	214	8	987	2365	613894593	613893209	0.000000e+00	1323.0
7	TraesCS6B01G458700	chr6A	85.656	976	138	2	1	975	613895606	613894632	0.000000e+00	1026.0
8	TraesCS6B01G458700	chr6A	88.038	209	23	2	2816	3023	613953070	613953277	2.330000e-61	246.0
9	TraesCS6B01G458700	chr6D	83.101	3089	417	62	5	3023	467787203	467784150	0.000000e+00	2715.0
10	TraesCS6B01G458700	chr6D	85.054	2335	313	28	5	2309	467829430	467831758	0.000000e+00	2346.0
11	TraesCS6B01G458700	chr6D	83.720	2371	328	34	1	2322	467801502	467799141	0.000000e+00	2187.0
12	TraesCS6B01G458700	chr6D	83.812	661	79	10	2390	3023	467799029	467798370	1.200000e-168	603.0
13	TraesCS6B01G458700	chr6D	77.976	672	98	16	2390	3023	467831866	467832525	2.850000e-100	375.0
14	TraesCS6B01G458700	chr5A	83.504	2734	371	46	6	2669	482355067	482357790	0.000000e+00	2477.0
15	TraesCS6B01G458700	chr5A	84.889	1939	283	7	6	1936	482369151	482371087	0.000000e+00	1949.0
16	TraesCS6B01G458700	chr5A	77.587	1981	341	65	1047	2963	482366282	482368223	0.000000e+00	1103.0
17	TraesCS6B01G458700	chr5A	77.244	1749	302	57	1338	3023	482423071	482424786	0.000000e+00	937.0
18	TraesCS6B01G458700	chr5A	78.346	1076	154	38	1997	3023	482371122	482372167	9.200000e-175	623.0
19	TraesCS6B01G458700	chr5A	78.220	955	183	16	1054	1999	482381248	482382186	3.360000e-164	588.0
20	TraesCS6B01G458700	chr5A	77.861	664	121	17	1546	2187	482398179	482397520	3.650000e-104	388.0
21	TraesCS6B01G458700	chr7D	75.990	2349	508	38	5	2316	5009458	5011787	0.000000e+00	1162.0
22	TraesCS6B01G458700	chr7D	78.095	210	40	6	2661	2867	631069104	631069310	8.800000e-26	128.0
23	TraesCS6B01G458700	chr7D	75.393	191	39	8	2673	2859	5012242	5012428	5.370000e-13	86.1
24	TraesCS6B01G458700	chr7D	92.683	41	2	1	2424	2464	5011928	5011967	1.170000e-04	58.4
25	TraesCS6B01G458700	chr7A	77.830	212	42	5	2661	2870	726729263	726729055	3.160000e-25	126.0
26	TraesCS6B01G458700	chr7A	75.393	191	39	8	2673	2859	6168127	6168313	5.370000e-13	86.1
27	TraesCS6B01G458700	chr3A	79.167	120	25	0	2736	2855	691712561	691712442	1.930000e-12	84.2

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	TraesCS6B01G458700	chr6B	713720551	713723573	3022	False	5583.0	5583	100.000000	1	3023	1	chr6B.!!$F1	3022
1	TraesCS6B01G458700	chr6B	713146542	713149480	2938	False	1322.0	2355	81.619000	5	2870	2	chr6B.!!$F2	2865
2	TraesCS6B01G458700	chr6B	713939018	713939986	968	True	568.0	568	77.789000	1414	2372	1	chr6B.!!$R2	958
3	TraesCS6B01G458700	chr6B	713452637	713453496	859	True	532.0	532	78.425000	1414	2263	1	chr6B.!!$R1	849
4	TraesCS6B01G458700	chr6A	613950194	613953277	3083	False	1705.0	3164	87.322500	1	3023	2	chr6A.!!$F1	3022
5	TraesCS6B01G458700	chr6A	613893209	613895606	2397	True	1174.5	1323	84.819500	1	2365	2	chr6A.!!$R1	2364
6	TraesCS6B01G458700	chr6D	467784150	467787203	3053	True	2715.0	2715	83.101000	5	3023	1	chr6D.!!$R1	3018
7	TraesCS6B01G458700	chr6D	467798370	467801502	3132	True	1395.0	2187	83.766000	1	3023	2	chr6D.!!$R2	3022
8	TraesCS6B01G458700	chr6D	467829430	467832525	3095	False	1360.5	2346	81.515000	5	3023	2	chr6D.!!$F1	3018
9	TraesCS6B01G458700	chr5A	482355067	482357790	2723	False	2477.0	2477	83.504000	6	2669	1	chr5A.!!$F1	2663
10	TraesCS6B01G458700	chr5A	482366282	482372167	5885	False	1225.0	1949	80.274000	6	3023	3	chr5A.!!$F4	3017
11	TraesCS6B01G458700	chr5A	482423071	482424786	1715	False	937.0	937	77.244000	1338	3023	1	chr5A.!!$F3	1685
12	TraesCS6B01G458700	chr5A	482381248	482382186	938	False	588.0	588	78.220000	1054	1999	1	chr5A.!!$F2	945
13	TraesCS6B01G458700	chr5A	482397520	482398179	659	True	388.0	388	77.861000	1546	2187	1	chr5A.!!$R1	641
14	TraesCS6B01G458700	chr7D	5009458	5012428	2970	False	435.5	1162	81.355333	5	2859	3	chr7D.!!$F2	2854

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
55	2920	0.392336	GTATGGGAGAGCTGCAGAGG	59.608	60.0	20.43	0.0	0.0	3.69	F
1072	4007	0.319405	AGCTTTGGATGGTTTGCAGC	59.681	50.0	0.00	0.0	0.0	5.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1801	4741	0.671472	TGCAGATGAGGACAGTTGCG	60.671	55.000	0.0	0.0	40.05	4.85	R
2484	5600	1.137282	GGAGGAGACATCTTCCGTTCC	59.863	57.143	0.0	0.0	41.40	3.62	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
24	2889	5.050972	ACGACGAAGAACATCAAGTCTTTTC	60.051	40.000	0.00	0.00	0.00	2.29
55	2920	0.392336	GTATGGGAGAGCTGCAGAGG	59.608	60.000	20.43	0.00	0.00	3.69
156	3022	1.471829	TTGGGAAGACAGCTCTCGCA	61.472	55.000	0.00	0.00	39.10	5.10
165	3031	1.667191	AGCTCTCGCACAGCTTGTG	60.667	57.895	10.75	10.75	45.34	3.33
190	3056	5.535333	ACAATGATCCAGCTTTGAAAAGTG	58.465	37.500	4.80	2.60	38.28	3.16
218	3084	5.387788	TGATCACAAGATATGGATTTGGGG	58.612	41.667	0.00	0.00	33.72	4.96
220	3086	2.629617	CACAAGATATGGATTTGGGGGC	59.370	50.000	0.00	0.00	0.00	5.80
228	3094	1.364328	TGGATTTGGGGGCCTAACAAT	59.636	47.619	0.84	0.00	0.00	2.71
289	3155	4.520492	GTGTCTCCCAAGAAACACATGATT	59.480	41.667	0.00	0.00	39.28	2.57
393	3259	1.526887	GGAAGGCATGGATGACGGA	59.473	57.895	0.00	0.00	41.91	4.69
508	3374	4.351111	AGAGAGGTACAACTGGACCAATTT	59.649	41.667	13.68	0.00	38.27	1.82
579	3445	6.198650	TGTGCATTTGGTGATGAGAATTAG	57.801	37.500	0.00	0.00	0.00	1.73
591	3457	3.525537	TGAGAATTAGGAAGAGCAAGCG	58.474	45.455	0.00	0.00	0.00	4.68
627	3493	7.593825	ACATAGGACAGAAAATAGCACAAAAC	58.406	34.615	0.00	0.00	0.00	2.43
681	3547	5.425217	TGCTGGGTCACTATTAAGAGATCAA	59.575	40.000	3.65	0.00	0.00	2.57
709	3575	6.248433	ACTGTGGATCATTGGAGTAACATTT	58.752	36.000	0.00	0.00	0.00	2.32
743	3609	4.529377	AGATTGGAAATCCTTGCAACACAT	59.471	37.500	0.00	0.00	44.45	3.21
777	3643	6.428159	TCATGTCTTCTTTGAAGCTTTCCTAC	59.572	38.462	0.00	0.00	0.00	3.18
783	3649	4.929808	TCTTTGAAGCTTTCCTACGATGAC	59.070	41.667	0.00	0.00	0.00	3.06
786	3652	4.021229	TGAAGCTTTCCTACGATGACCTA	58.979	43.478	0.00	0.00	0.00	3.08
856	3722	7.981789	CCTACAACTATCAATTTACTGCTGAGA	59.018	37.037	0.00	0.00	0.00	3.27
865	3731	7.611770	TCAATTTACTGCTGAGAAGCTAGTTA	58.388	34.615	0.00	0.00	35.49	2.24
929	3795	2.553028	GCAACAGTTTGGAGGAGATGGA	60.553	50.000	0.00	0.00	32.81	3.41
996	3931	9.874215	CAGCAGGTTAAAAGTTAAACTTACTAC	57.126	33.333	0.00	0.00	37.47	2.73
1052	3987	4.212214	GCTAGTTTCAAGAACTGAGTGTGG	59.788	45.833	1.89	0.00	34.81	4.17
1072	4007	0.319405	AGCTTTGGATGGTTTGCAGC	59.681	50.000	0.00	0.00	0.00	5.25
1104	4039	5.854010	TTTTGCCAACTGTACACCATTTA	57.146	34.783	0.00	0.00	0.00	1.40
1148	4083	1.690633	GGAGGGATGGCCAGACTGA	60.691	63.158	13.05	0.00	35.15	3.41
1230	4165	4.339247	AGAAAGTTGAGGACATTGGTGTTG	59.661	41.667	0.00	0.00	39.09	3.33
1260	4195	8.029522	GGGAAATATGACTCCTTTTTCTTCAAC	58.970	37.037	0.00	0.00	31.88	3.18
1261	4196	8.576442	GGAAATATGACTCCTTTTTCTTCAACA	58.424	33.333	0.00	0.00	0.00	3.33
1394	4329	5.659525	TCCGGTATCTAAAACTTGAGGATGA	59.340	40.000	0.00	0.00	0.00	2.92
1396	4331	7.507956	TCCGGTATCTAAAACTTGAGGATGATA	59.492	37.037	0.00	0.00	0.00	2.15
1497	4432	6.758416	TGTCATTGCATACAGTTCATCTAGAC	59.242	38.462	0.00	0.00	0.00	2.59
1510	4445	3.003793	TCATCTAGACGATTGCGGAGAAG	59.996	47.826	0.00	0.00	43.17	2.85
1514	4449	1.956629	GACGATTGCGGAGAAGGGGA	61.957	60.000	0.00	0.00	43.17	4.81
1548	4483	2.813754	TCTGGAAATGCTTCGGTTTCTG	59.186	45.455	0.00	0.00	35.29	3.02
1553	4488	5.221422	TGGAAATGCTTCGGTTTCTGAAAAT	60.221	36.000	4.09	0.00	35.29	1.82
1554	4489	6.015856	TGGAAATGCTTCGGTTTCTGAAAATA	60.016	34.615	4.09	0.00	35.29	1.40
1577	4512	2.548057	TGAAGTTGAGAAACATGCGGAC	59.452	45.455	0.00	0.00	0.00	4.79
1580	4515	0.874390	TTGAGAAACATGCGGACTGC	59.126	50.000	0.00	0.00	46.70	4.40
1624	4559	9.288576	CATCATTGGAGGAGCTTGTTTTATATA	57.711	33.333	0.00	0.00	0.00	0.86
1664	4599	3.576982	AGATGTTCTTGTACTTCCGTGGA	59.423	43.478	0.00	0.00	0.00	4.02
1742	4680	7.939039	TGAGGTGTTTGATCTATTTCAGAAAGT	59.061	33.333	1.28	0.00	36.67	2.66
1762	4700	7.934120	AGAAAGTTCATAGCTACAAAAGTGAGT	59.066	33.333	0.00	0.00	0.00	3.41
1794	4734	2.893489	GTTGCCCAATCTGAGGAAACTT	59.107	45.455	0.00	0.00	44.43	2.66
1801	4741	6.515696	GCCCAATCTGAGGAAACTTATTATGC	60.516	42.308	0.00	0.00	44.43	3.14
1806	4746	5.064707	TCTGAGGAAACTTATTATGCGCAAC	59.935	40.000	17.11	0.00	44.43	4.17
1856	4796	4.142093	CCTTCCACCTTCAGCCATATTTTG	60.142	45.833	0.00	0.00	0.00	2.44
1882	4828	9.750882	GTAAACTATCAATTAACGAGGTTTCAC	57.249	33.333	0.00	7.27	0.00	3.18
1924	4870	6.836007	GGGATCTTCCATGGAAAAATTAGAGT	59.164	38.462	26.87	10.15	38.64	3.24
2139	5130	1.276859	TGCCAGAGCAGACCCATGAT	61.277	55.000	0.00	0.00	46.52	2.45
2160	5151	6.788243	TGATGACATGATAACTGCAAATGAC	58.212	36.000	0.00	0.00	0.00	3.06
2170	5161	2.061773	CTGCAAATGACGACGTTCTCT	58.938	47.619	0.13	0.00	0.00	3.10
2264	5255	2.747446	CACCGACCCTAAAGGAATTGTG	59.253	50.000	0.00	0.00	39.89	3.33
2339	5330	4.165372	TGTTCAACCAAACCTTCTCCTAGT	59.835	41.667	0.00	0.00	0.00	2.57
2351	5381	4.563786	CCTTCTCCTAGTTTTCGAGGCTTT	60.564	45.833	0.00	0.00	41.52	3.51
2388	5469	0.740868	ATGGAGTCGTGCACATTCCG	60.741	55.000	18.64	1.94	0.00	4.30
2389	5470	1.080093	GGAGTCGTGCACATTCCGA	60.080	57.895	18.64	4.78	0.00	4.55
2390	5471	0.460284	GGAGTCGTGCACATTCCGAT	60.460	55.000	18.64	0.00	32.68	4.18
2391	5472	1.359848	GAGTCGTGCACATTCCGATT	58.640	50.000	18.64	4.39	32.68	3.34
2392	5473	1.324736	GAGTCGTGCACATTCCGATTC	59.675	52.381	18.64	10.30	32.68	2.52
2393	5474	0.373716	GTCGTGCACATTCCGATTCC	59.626	55.000	18.64	0.00	32.68	3.01
2479	5580	1.612726	GCTTTGCTGGAGTCCTCACAT	60.613	52.381	11.33	0.00	0.00	3.21
2484	5600	1.137872	GCTGGAGTCCTCACATGTAGG	59.862	57.143	11.33	6.53	35.26	3.18
2505	5654	0.818296	AACGGAAGATGTCTCCTCCG	59.182	55.000	17.30	17.30	46.42	4.63
2655	5831	7.065683	GGCATTGGACGATTTGGAAATTAAATT	59.934	33.333	0.00	0.00	0.00	1.82
2706	5882	1.745087	GCAATCGCTTGGAATCCTCAA	59.255	47.619	0.00	0.00	32.72	3.02
2778	5958	2.544359	CACGTCGCTGGAACGTTG	59.456	61.111	5.00	0.00	38.07	4.10
2803	5983	6.404734	GGGAAATTGATGATTGTAGTTCGCTT	60.405	38.462	0.00	0.00	0.00	4.68
2810	5990	4.123506	TGATTGTAGTTCGCTTGTCACAA	58.876	39.130	0.00	0.00	0.00	3.33
2843	6080	1.825474	GATCCCTCGTGAACCTCAAGA	59.175	52.381	0.00	0.00	33.97	3.02
2883	6120	0.631212	CCTGCCTTGGGTTCCCTTAT	59.369	55.000	9.43	0.00	0.00	1.73
2890	6127	4.871822	CCTTGGGTTCCCTTATCTCATTT	58.128	43.478	9.43	0.00	0.00	2.32
2893	6130	4.855340	TGGGTTCCCTTATCTCATTTGAC	58.145	43.478	9.43	0.00	0.00	3.18
2918	6155	6.112058	AGTTATGAGCCAACTGAGAGATTTC	58.888	40.000	0.00	0.00	34.96	2.17
2950	6187	4.164988	AGCTATGAGTTATTCCCTGCACTT	59.835	41.667	0.00	0.00	0.00	3.16
2970	6207	6.953167	CACTTGAAAGTCTCGAGATCGATGC	61.953	48.000	19.90	4.24	41.79	3.91
3003	6240	4.701651	CCTTAACATGTCATTCTGCAAGGA	59.298	41.667	0.00	0.00	33.11	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	5.123227	TGGAAAAGACTTGATGTTCTTCGT	58.877	37.500	0.00	0.00	0.00	3.85
24	2889	2.576191	TCTCCCATACACTTTCCCTTGG	59.424	50.000	0.00	0.00	0.00	3.61
78	2943	4.869297	CCTGCAGTTGATTTGTGTTTTTCA	59.131	37.500	13.81	0.00	0.00	2.69
156	3022	4.005650	CTGGATCATTGTACACAAGCTGT	58.994	43.478	0.00	0.00	39.47	4.40
165	3031	6.583806	CACTTTTCAAAGCTGGATCATTGTAC	59.416	38.462	0.00	0.00	39.63	2.90
190	3056	9.472361	CCAAATCCATATCTTGTGATCAAATTC	57.528	33.333	0.00	0.00	34.32	2.17
218	3084	7.276438	GTCTCATTTCATCAAAATTGTTAGGCC	59.724	37.037	0.00	0.00	35.32	5.19
220	3086	9.565213	GAGTCTCATTTCATCAAAATTGTTAGG	57.435	33.333	0.00	0.00	35.32	2.69
228	3094	6.016024	CCCTTGTGAGTCTCATTTCATCAAAA	60.016	38.462	5.68	0.00	0.00	2.44
315	3181	7.510675	TTTAATATGACCCTTCAAGACCTCT	57.489	36.000	0.00	0.00	34.61	3.69
393	3259	2.627699	AGCCAACAATTTGTTCCATCGT	59.372	40.909	11.78	0.00	38.77	3.73
450	3316	8.460428	ACAAACGGTTTTCTAGTTGTCAAAATA	58.540	29.630	2.79	0.00	0.00	1.40
454	3320	5.883503	ACAAACGGTTTTCTAGTTGTCAA	57.116	34.783	2.79	0.00	0.00	3.18
552	3418	1.205179	TCATCACCAAATGCACATGCC	59.795	47.619	0.49	0.00	41.18	4.40
579	3445	2.094442	ACTTAGACTCGCTTGCTCTTCC	60.094	50.000	0.00	0.00	0.00	3.46
627	3493	5.047377	TGCTGCTAATGGGTTTCCTTTTAAG	60.047	40.000	0.00	0.00	33.22	1.85
681	3547	6.013725	TGTTACTCCAATGATCCACAGTAAGT	60.014	38.462	0.00	0.00	0.00	2.24
709	3575	6.546484	AGGATTTCCAATCTTCAGTCTTCAA	58.454	36.000	0.00	0.00	38.89	2.69
743	3609	2.885135	AGAAGACATGATGCCACCAA	57.115	45.000	0.00	0.00	0.00	3.67
777	3643	2.317040	ACAGGGTATGGTAGGTCATCG	58.683	52.381	0.00	0.00	0.00	3.84
783	3649	4.829872	TTGTTGTACAGGGTATGGTAGG	57.170	45.455	0.00	0.00	0.00	3.18
786	3652	4.650972	ACATTGTTGTACAGGGTATGGT	57.349	40.909	0.00	0.00	33.16	3.55
856	3722	7.224297	TGTGAAATCCAAAGACTAACTAGCTT	58.776	34.615	0.00	0.00	0.00	3.74
865	3731	6.324770	ACAAATCCTTGTGAAATCCAAAGACT	59.675	34.615	0.00	0.00	44.28	3.24
909	3775	3.423539	TCCATCTCCTCCAAACTGTTG	57.576	47.619	0.00	0.00	34.25	3.33
912	3778	3.423539	TGTTCCATCTCCTCCAAACTG	57.576	47.619	0.00	0.00	0.00	3.16
929	3795	9.685276	TCACCAAATCATTCAGATAGTATTGTT	57.315	29.630	0.00	0.00	35.39	2.83
932	3798	9.125026	GGTTCACCAAATCATTCAGATAGTATT	57.875	33.333	0.00	0.00	34.29	1.89
944	3810	1.077663	AGCCCAGGTTCACCAAATCAT	59.922	47.619	0.00	0.00	38.89	2.45
948	3814	0.032615	ACAAGCCCAGGTTCACCAAA	60.033	50.000	0.00	0.00	38.89	3.28
996	3931	2.025898	TGCATCAGGCCACACATAATG	58.974	47.619	5.01	0.00	43.89	1.90
1027	3962	3.430218	CACTCAGTTCTTGAAACTAGCCG	59.570	47.826	0.00	0.00	34.81	5.52
1052	3987	1.670967	GCTGCAAACCATCCAAAGCTC	60.671	52.381	0.00	0.00	0.00	4.09
1072	4007	4.121317	ACAGTTGGCAAAATGTCATTGTG	58.879	39.130	10.93	10.93	40.41	3.33
1129	4064	1.692042	CAGTCTGGCCATCCCTCCT	60.692	63.158	5.51	0.00	0.00	3.69
1148	4083	5.254901	ACTTCTCACTACGAGGTATGTTCT	58.745	41.667	0.00	0.00	42.55	3.01
1230	4165	8.298729	AGAAAAAGGAGTCATATTTCCCAATC	57.701	34.615	9.04	0.00	33.83	2.67
1261	4196	7.986320	TGATTTTTCAAACACATCTTGGAATGT	59.014	29.630	0.00	0.00	40.49	2.71
1275	4210	7.538678	AGACGCAGATTATGTGATTTTTCAAAC	59.461	33.333	0.00	0.00	42.31	2.93
1285	4220	2.543641	CAGCAGACGCAGATTATGTGA	58.456	47.619	0.00	0.00	42.31	3.58
1335	4270	9.343539	GGATTTACCAAGCTACATAAGAAAGAT	57.656	33.333	0.00	0.00	38.79	2.40
1344	4279	5.105064	ACGTGTAGGATTTACCAAGCTACAT	60.105	40.000	0.00	0.00	42.04	2.29
1408	4343	4.057406	TCAAAACATGAGGCAAAGGTTG	57.943	40.909	0.00	0.00	33.04	3.77
1497	4432	1.227380	CTCCCCTTCTCCGCAATCG	60.227	63.158	0.00	0.00	0.00	3.34
1514	4449	6.897986	AGCATTTCCAGAGATGAAAGTATCT	58.102	36.000	2.54	0.00	40.02	1.98
1548	4483	8.368126	CGCATGTTTCTCAACTTCAATATTTTC	58.632	33.333	0.00	0.00	33.58	2.29
1553	4488	5.000591	TCCGCATGTTTCTCAACTTCAATA	58.999	37.500	0.00	0.00	33.58	1.90
1554	4489	3.820467	TCCGCATGTTTCTCAACTTCAAT	59.180	39.130	0.00	0.00	33.58	2.57
1577	4512	4.854399	TGGAAACGATACTTTTGTTGCAG	58.146	39.130	0.00	0.00	31.98	4.41
1580	4515	7.941865	CAATGATGGAAACGATACTTTTGTTG	58.058	34.615	0.00	0.00	31.98	3.33
1624	4559	7.607991	AGAACATCTCCGTAAATCTGACATTTT	59.392	33.333	0.00	0.00	0.00	1.82
1664	4599	9.289782	GCACCCTTAAACTAGATTTCATATCAT	57.710	33.333	0.00	0.00	0.00	2.45
1794	4734	3.535280	TGAGGACAGTTGCGCATAATA	57.465	42.857	12.75	0.00	0.00	0.98
1801	4741	0.671472	TGCAGATGAGGACAGTTGCG	60.671	55.000	0.00	0.00	40.05	4.85
1806	4746	3.519579	CTGTACTTGCAGATGAGGACAG	58.480	50.000	12.90	12.90	45.51	3.51
1856	4796	9.750882	GTGAAACCTCGTTAATTGATAGTTTAC	57.249	33.333	0.00	0.00	0.00	2.01
1882	4828	5.638133	AGATCCCTCCATTGTCATAATTGG	58.362	41.667	0.00	0.00	0.00	3.16
1924	4870	8.325421	TCACACAAAAGTTTATATCCGCTAAA	57.675	30.769	0.00	0.00	0.00	1.85
1957	4921	5.943706	TGGAATGCCAAAATTTTGTCATG	57.056	34.783	23.77	12.78	42.49	3.07
2139	5130	4.934602	TCGTCATTTGCAGTTATCATGTCA	59.065	37.500	0.00	0.00	0.00	3.58
2170	5161	7.602753	TCAATATCAAGACTTTCAAGAGACGA	58.397	34.615	0.00	0.00	0.00	4.20
2264	5255	4.393680	TCAACTGTGGGCAATCGTATAAAC	59.606	41.667	0.00	0.00	0.00	2.01
2339	5330	4.199310	CCCTGATGATAAAGCCTCGAAAA	58.801	43.478	0.00	0.00	0.00	2.29
2351	5381	4.428570	TCCATCTGCATACCCTGATGATA	58.571	43.478	11.74	0.00	41.14	2.15
2479	5580	2.758979	GAGACATCTTCCGTTCCCTACA	59.241	50.000	0.00	0.00	0.00	2.74
2484	5600	1.137282	GGAGGAGACATCTTCCGTTCC	59.863	57.143	0.00	0.00	41.40	3.62
2505	5654	3.119137	AGACCAAACAAGTTGTTCAAGCC	60.119	43.478	21.10	10.01	40.14	4.35
2590	5760	8.299570	AGTTGTAGATATTCCAAACTTTTGCTG	58.700	33.333	0.00	0.00	36.86	4.41
2595	5768	9.533831	AATCCAGTTGTAGATATTCCAAACTTT	57.466	29.630	0.00	0.00	0.00	2.66
2655	5831	2.456000	GCGACGAGCTGATTGGAAA	58.544	52.632	0.00	0.00	44.04	3.13
2778	5958	5.066505	AGCGAACTACAATCATCAATTTCCC	59.933	40.000	0.00	0.00	0.00	3.97
2803	5983	1.675714	CGCAAGCCCTCTATTGTGACA	60.676	52.381	0.00	0.00	38.83	3.58
2810	5990	2.062070	GGGATCGCAAGCCCTCTAT	58.938	57.895	4.64	0.00	41.31	1.98
2843	6080	6.405842	GCAGGGGAATCGACTATTTTCAAATT	60.406	38.462	0.00	0.00	0.00	1.82
2883	6120	5.164620	TGGCTCATAACTGTCAAATGAGA	57.835	39.130	21.98	7.82	46.22	3.27
2912	6149	7.372260	ACTCATAGCTATGACTTGGAAATCT	57.628	36.000	28.69	4.13	37.76	2.40
2915	6152	9.547753	GAATAACTCATAGCTATGACTTGGAAA	57.452	33.333	28.69	13.37	37.76	3.13
2918	6155	6.876257	GGGAATAACTCATAGCTATGACTTGG	59.124	42.308	28.69	21.51	37.76	3.61
2970	6207	3.009033	TGACATGTTAAGGGGAGACAAGG	59.991	47.826	0.00	0.00	0.00	3.61
3003	6240	2.203788	TTCGGAGGCAGGTGAGGT	60.204	61.111	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.