AutoCloner

Multiple sequence alignment - TraesCS5D01G459900

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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	TraesCS5D01G459900	chr5D	100.000	5466	0	0	1	5466	503668763	503674228	0.000000e+00	10094.0
1	TraesCS5D01G459900	chr5B	95.293	1721	55	10	2522	4239	632154375	632156072	0.000000e+00	2706.0
2	TraesCS5D01G459900	chr5B	99.058	955	8	1	4273	5227	632156066	632157019	0.000000e+00	1712.0
3	TraesCS5D01G459900	chr5B	93.534	897	44	6	986	1870	632152835	632153729	0.000000e+00	1323.0
4	TraesCS5D01G459900	chr5B	87.048	996	61	32	2	961	632151495	632152458	0.000000e+00	1062.0
5	TraesCS5D01G459900	chr5B	88.008	517	45	14	2018	2522	632153812	632154323	3.640000e-166	595.0
6	TraesCS5D01G459900	chr5B	98.785	247	2	1	5220	5466	632157252	632157497	6.500000e-119	438.0
7	TraesCS5D01G459900	chr5B	88.462	52	5	1	1754	1804	134911287	134911338	1.640000e-05	62.1
8	TraesCS5D01G459900	chr3B	93.526	1838	86	18	1862	3692	212888250	212886439	0.000000e+00	2704.0
9	TraesCS5D01G459900	chr3B	89.236	1087	63	24	807	1870	212889363	212888308	0.000000e+00	1310.0
10	TraesCS5D01G459900	chr3B	91.803	122	3	2	3689	3803	212886240	212886119	4.380000e-36	163.0
11	TraesCS5D01G459900	chr5A	86.744	1373	114	42	3726	5050	631667578	631668930	0.000000e+00	1465.0
12	TraesCS5D01G459900	chr5A	94.420	896	39	6	979	1865	631664291	631665184	0.000000e+00	1367.0
13	TraesCS5D01G459900	chr5A	91.462	855	61	10	2520	3374	631665971	631666813	0.000000e+00	1164.0
14	TraesCS5D01G459900	chr5A	88.922	677	51	17	1862	2522	631665253	631665921	0.000000e+00	813.0
15	TraesCS5D01G459900	chr5A	90.000	510	39	8	1	502	631662929	631663434	0.000000e+00	649.0
16	TraesCS5D01G459900	chr5A	91.089	303	22	3	3331	3632	631666813	631667111	6.590000e-109	405.0
17	TraesCS5D01G459900	chr5A	84.778	427	15	19	509	891	631663548	631663968	3.090000e-102	383.0
18	TraesCS5D01G459900	chr1A	82.273	440	30	20	5053	5461	590673612	590674034	2.440000e-88	337.0
19	TraesCS5D01G459900	chr4A	82.584	356	22	6	5058	5389	21047607	21047268	1.500000e-70	278.0
20	TraesCS5D01G459900	chr4A	79.581	191	35	4	1020	1209	15655000	15654813	3.430000e-27	134.0
21	TraesCS5D01G459900	chr1B	82.508	303	24	11	5170	5460	640593728	640593443	7.080000e-59	239.0
22	TraesCS5D01G459900	chr1B	87.931	58	6	1	1754	1810	660959486	660959429	3.530000e-07	67.6
23	TraesCS5D01G459900	chr4B	84.000	225	24	7	5246	5460	247338614	247338836	7.180000e-49	206.0
24	TraesCS5D01G459900	chr4B	79.058	191	36	4	1020	1209	564866512	564866699	1.600000e-25	128.0
25	TraesCS5D01G459900	chr4B	87.931	58	6	1	1754	1810	612342133	612342190	3.530000e-07	67.6
26	TraesCS5D01G459900	chr4D	79.581	191	35	4	1020	1209	451279445	451279632	3.430000e-27	134.0
27	TraesCS5D01G459900	chr2B	87.931	58	6	1	1754	1810	634672739	634672682	3.530000e-07	67.6

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	TraesCS5D01G459900	chr5D	503668763	503674228	5465	False	10094.000000	10094	100.000000	1	5466	1	chr5D.!!$F1	5465
1	TraesCS5D01G459900	chr5B	632151495	632157497	6002	False	1306.000000	2706	93.621000	2	5466	6	chr5B.!!$F2	5464
2	TraesCS5D01G459900	chr3B	212886119	212889363	3244	True	1392.333333	2704	91.521667	807	3803	3	chr3B.!!$R1	2996
3	TraesCS5D01G459900	chr5A	631662929	631668930	6001	False	892.285714	1465	89.630714	1	5050	7	chr5A.!!$F1	5049

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	Hairpin	End Stability	Orientation
29	30	0.387929	TGAACCTCGCCGACATATCC	59.612	55.000	0.00	0.00	2.59	F
506	522	0.550914	ACTCCACACAAGCTTTCCCA	59.449	50.000	0.00	0.00	4.37	F
1367	1913	1.020333	CGGCGGGTTCGTTTGGATTA	61.020	55.000	0.00	38.89	1.75	F
1637	2189	1.043816	CCGGCTCTGGATATCTGTGT	58.956	55.000	2.05	0.00	3.72	F
2221	2859	1.132262	ACTTTGCAACAACACTGGTCG	59.868	47.619	0.00	0.00	4.79	F
3630	4378	0.392998	ATGCTCAAACTACTGGGGCG	60.393	55.000	0.00	0.00	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1362	1908	0.946221	CCGATCGCCAGCAGTAATCC	60.946	60.000	10.32	0.00	0.00	3.01	R
1826	2385	1.069513	TCCGGAAACCTATACCATGCG	59.930	52.381	0.00	0.00	0.00	4.73	R
2221	2859	1.071305	GCATGTGCGACAAAAGCAAAC	60.071	47.619	0.00	0.00	46.97	2.93	R
3320	4024	1.895798	TGTGAGCGGAGATTCTCTGTT	59.104	47.619	20.87	16.41	38.95	3.16	R
4132	5542	3.569250	TTAAGCAATGTTTTCGGCTCC	57.431	42.857	0.00	0.00	35.11	4.70	R
4482	5897	0.798776	GGGCAGTTGAATGTGTCTCG	59.201	55.000	0.00	0.00	0.00	4.04	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
29	30	0.387929	TGAACCTCGCCGACATATCC	59.612	55.000	0.00	0.00	0.00	2.59
210	213	2.438392	AGGGAAACTTCACCGAAACTCT	59.562	45.455	0.00	0.00	0.00	3.24
212	215	3.203716	GGAAACTTCACCGAAACTCTGT	58.796	45.455	0.00	0.00	0.00	3.41
217	220	4.451900	ACTTCACCGAAACTCTGTTGAAT	58.548	39.130	0.00	0.00	0.00	2.57
270	276	9.823647	ACCTCATAACTCAAATGTTAGACTATG	57.176	33.333	0.00	0.00	36.10	2.23
293	299	7.151999	TGGTGTATATTTCGCTGTCAAAAAT	57.848	32.000	0.00	0.00	0.00	1.82
294	300	7.026562	TGGTGTATATTTCGCTGTCAAAAATG	58.973	34.615	0.00	0.00	0.00	2.32
295	301	7.094592	TGGTGTATATTTCGCTGTCAAAAATGA	60.095	33.333	0.00	0.00	0.00	2.57
296	302	7.915397	GGTGTATATTTCGCTGTCAAAAATGAT	59.085	33.333	0.00	0.00	0.00	2.45
297	303	9.929722	GTGTATATTTCGCTGTCAAAAATGATA	57.070	29.630	0.00	0.00	0.00	2.15
301	307	7.801547	ATTTCGCTGTCAAAAATGATAGTTG	57.198	32.000	4.82	0.00	30.98	3.16
354	364	5.713822	ACCGCGTCATAGTCTTATTTTTC	57.286	39.130	4.92	0.00	0.00	2.29
377	387	2.997303	ACAATAAAGCGCGTCACATGTA	59.003	40.909	8.43	0.00	0.00	2.29
459	471	1.228154	ACAAGCTTCGTTGACCCCC	60.228	57.895	0.00	0.00	0.00	5.40
460	472	1.228124	CAAGCTTCGTTGACCCCCA	60.228	57.895	0.00	0.00	0.00	4.96
461	473	1.073199	AAGCTTCGTTGACCCCCAG	59.927	57.895	0.00	0.00	0.00	4.45
489	505	3.146066	ACAATTACGCACCAATCACACT	58.854	40.909	0.00	0.00	0.00	3.55
490	506	3.188460	ACAATTACGCACCAATCACACTC	59.812	43.478	0.00	0.00	0.00	3.51
502	518	2.418368	TCACACTCCACACAAGCTTT	57.582	45.000	0.00	0.00	0.00	3.51
503	519	2.288666	TCACACTCCACACAAGCTTTC	58.711	47.619	0.00	0.00	0.00	2.62
505	521	0.954452	CACTCCACACAAGCTTTCCC	59.046	55.000	0.00	0.00	0.00	3.97
506	522	0.550914	ACTCCACACAAGCTTTCCCA	59.449	50.000	0.00	0.00	0.00	4.37
507	523	1.242076	CTCCACACAAGCTTTCCCAG	58.758	55.000	0.00	0.00	0.00	4.45
697	845	1.835895	TAACCCTGAAGAAACCCCCA	58.164	50.000	0.00	0.00	0.00	4.96
891	1068	2.228480	CGACCTTTCCCCCTTCCCA	61.228	63.158	0.00	0.00	0.00	4.37
1352	1898	1.141591	GATTTGCTGGATTTGCGGCG	61.142	55.000	0.51	0.51	0.00	6.46
1362	1908	2.741116	ATTTGCGGCGGGTTCGTTTG	62.741	55.000	9.78	0.00	38.89	2.93
1367	1913	1.020333	CGGCGGGTTCGTTTGGATTA	61.020	55.000	0.00	0.00	38.89	1.75
1374	1920	2.161609	GGTTCGTTTGGATTACTGCTGG	59.838	50.000	0.00	0.00	0.00	4.85
1433	1979	3.429372	TTGCTCCCGTGGCTTGGTT	62.429	57.895	0.00	0.00	0.00	3.67
1526	2072	8.809159	ATATCGTGCTATGCAGTCAATATATC	57.191	34.615	0.00	0.00	40.08	1.63
1537	2083	4.148871	CAGTCAATATATCGTGGTTGCTCG	59.851	45.833	0.00	0.00	0.00	5.03
1637	2189	1.043816	CCGGCTCTGGATATCTGTGT	58.956	55.000	2.05	0.00	0.00	3.72
1726	2282	9.964303	CACATATTTATGCTAATTTGGCAGTTA	57.036	29.630	13.06	0.00	43.15	2.24
1738	2294	9.202273	CTAATTTGGCAGTTAATTTGTTGCTTA	57.798	29.630	1.34	0.39	36.79	3.09
1744	2303	5.634859	GCAGTTAATTTGTTGCTTACATGCT	59.365	36.000	0.00	0.00	36.44	3.79
1896	2530	7.461749	TCATACCCTTGATCTTTTTGAAGAGT	58.538	34.615	0.00	0.00	31.48	3.24
1897	2531	8.602424	TCATACCCTTGATCTTTTTGAAGAGTA	58.398	33.333	0.00	0.00	31.48	2.59
1984	2618	4.938226	AGTGCTTAGTATGTTTCAGCCTTC	59.062	41.667	0.00	0.00	0.00	3.46
1994	2628	3.008375	TGTTTCAGCCTTCTATGACAGCT	59.992	43.478	0.00	0.00	0.00	4.24
2006	2640	5.847304	TCTATGACAGCTGATCACATTACC	58.153	41.667	23.35	0.00	0.00	2.85
2012	2646	2.511218	AGCTGATCACATTACCATGGGT	59.489	45.455	18.09	0.33	40.16	4.51
2017	2651	4.413189	TGATCACATTACCATGGGTCATCT	59.587	41.667	18.09	0.00	37.09	2.90
2096	2730	4.357142	CATTGATCTGCAAGCACCATAAC	58.643	43.478	0.00	0.00	40.42	1.89
2221	2859	1.132262	ACTTTGCAACAACACTGGTCG	59.868	47.619	0.00	0.00	0.00	4.79
2285	2925	6.600822	ACTGTAGAGATTTGGATTGATGTTGG	59.399	38.462	0.00	0.00	0.00	3.77
2312	2952	9.887629	AACTATAATGCTCTCTCAATCCATATG	57.112	33.333	0.00	0.00	0.00	1.78
2334	2974	3.996150	AGTTGTCACATTTGGCTTCTG	57.004	42.857	0.00	0.00	0.00	3.02
2384	3024	7.754069	TTACTGAACACAGAAGCAATTTTTG	57.246	32.000	0.00	0.00	35.80	2.44
2440	3080	4.755266	ACCGTTCTAGCAATACCATTCT	57.245	40.909	0.00	0.00	0.00	2.40
2570	3272	6.939551	TTTTCGTAGTGCTACTATGTGAAC	57.060	37.500	7.63	0.00	38.51	3.18
2594	3296	5.534207	TCAATGCACAATTCCTTCAAACT	57.466	34.783	0.00	0.00	0.00	2.66
2625	3327	1.672363	ACACATGTCGCATGGCTTATG	59.328	47.619	19.30	12.40	39.88	1.90
2643	3345	5.106157	GCTTATGGCAGTGACAATAGTGTTT	60.106	40.000	0.77	0.00	38.42	2.83
2656	3358	9.474920	TGACAATAGTGTTTGGAAAAATTGATC	57.525	29.630	0.00	0.00	38.41	2.92
2747	3449	7.272084	CGAAGATAATGCTTGTTTCTTTCCTTG	59.728	37.037	0.00	0.00	0.00	3.61
2807	3509	4.339872	TGGCGTTCCTAACTTTGAAGTA	57.660	40.909	0.00	0.00	38.57	2.24
2998	3700	3.005050	CAGAGAGTTTGGGTACGTGTGTA	59.995	47.826	0.00	0.00	0.00	2.90
3293	3997	3.703001	ATTCAGGTTCTTGATCGTGGT	57.297	42.857	0.00	0.00	0.00	4.16
3320	4024	3.633525	AGATTGAGCTGCTTGTTGACAAA	59.366	39.130	2.53	0.00	35.15	2.83
3630	4378	0.392998	ATGCTCAAACTACTGGGGCG	60.393	55.000	0.00	0.00	0.00	6.13
3686	4434	4.578516	TGAAATCAGTTTGGCCGTATATGG	59.421	41.667	6.62	6.62	0.00	2.74
3687	4435	3.857157	ATCAGTTTGGCCGTATATGGT	57.143	42.857	12.66	0.00	0.00	3.55
4232	5644	5.981088	TGAAGTTCCGTACACCTAACATA	57.019	39.130	0.00	0.00	0.00	2.29
4240	5652	4.505191	CCGTACACCTAACATATGTTTCCG	59.495	45.833	25.31	15.03	39.31	4.30
4250	5662	8.567948	CCTAACATATGTTTCCGATTATGCTTT	58.432	33.333	25.31	0.00	39.31	3.51
4251	5663	9.385902	CTAACATATGTTTCCGATTATGCTTTG	57.614	33.333	25.31	0.00	39.31	2.77
4482	5897	1.153997	GAGGACAAGTCGAGGTCGC	60.154	63.158	0.00	0.00	39.60	5.19
4946	6365	0.886043	TGCGTTCTGCTGCATTCACT	60.886	50.000	1.31	0.00	46.63	3.41
4957	6376	3.625764	GCTGCATTCACTCGGGTTATTTA	59.374	43.478	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	7.267857	AGAACTTCTGGAATTTCAAAAGGTTG	58.732	34.615	4.81	0.00	33.88	3.77
72	73	8.986477	ATTTCAAAGAATTTCGGTGGATTTAG	57.014	30.769	3.51	0.00	35.03	1.85
124	126	4.350346	CAAGTTTCGTGTTTGATTCAGCA	58.650	39.130	0.00	0.00	0.00	4.41
157	159	5.262588	AGTTTTGATGGGTTCAGAAACAC	57.737	39.130	0.00	0.00	39.39	3.32
188	190	2.548480	GAGTTTCGGTGAAGTTTCCCTG	59.452	50.000	0.00	0.00	0.00	4.45
195	198	3.536956	TCAACAGAGTTTCGGTGAAGT	57.463	42.857	0.00	0.00	0.00	3.01
244	247	9.823647	CATAGTCTAACATTTGAGTTATGAGGT	57.176	33.333	0.00	0.00	33.82	3.85
270	276	7.247728	TCATTTTTGACAGCGAAATATACACC	58.752	34.615	0.00	0.00	0.00	4.16
293	299	9.084533	ACTAAAAGTTTTTATGGCCAACTATCA	57.915	29.630	10.96	0.00	32.69	2.15
325	335	0.745845	ACTATGACGCGGTAGACGGT	60.746	55.000	12.47	0.00	44.51	4.83
354	364	3.062099	ACATGTGACGCGCTTTATTGTAG	59.938	43.478	5.73	0.00	0.00	2.74
459	471	5.289917	TGGTGCGTAATTGTATGAAACTG	57.710	39.130	0.00	0.00	0.00	3.16
460	472	5.950758	TTGGTGCGTAATTGTATGAAACT	57.049	34.783	0.00	0.00	0.00	2.66
461	473	6.250527	GTGATTGGTGCGTAATTGTATGAAAC	59.749	38.462	0.00	0.00	0.00	2.78
489	505	0.550914	ACTGGGAAAGCTTGTGTGGA	59.449	50.000	0.00	0.00	0.00	4.02
490	506	2.270352	TACTGGGAAAGCTTGTGTGG	57.730	50.000	0.00	0.00	0.00	4.17
502	518	7.672239	ACAAGTTTGGCTATTAAATTACTGGGA	59.328	33.333	0.00	0.00	0.00	4.37
503	519	7.759433	CACAAGTTTGGCTATTAAATTACTGGG	59.241	37.037	0.00	0.00	0.00	4.45
505	521	8.303876	ACCACAAGTTTGGCTATTAAATTACTG	58.696	33.333	4.56	0.00	40.77	2.74
506	522	8.417273	ACCACAAGTTTGGCTATTAAATTACT	57.583	30.769	4.56	0.00	40.77	2.24
588	732	4.741185	CCGTACCGTCGATGATTGATTTAA	59.259	41.667	6.11	0.00	0.00	1.52
652	796	5.174395	CGAGGGATGGATTGATTAGCTTAG	58.826	45.833	0.00	0.00	0.00	2.18
653	797	4.563580	GCGAGGGATGGATTGATTAGCTTA	60.564	45.833	0.00	0.00	0.00	3.09
654	798	3.808618	GCGAGGGATGGATTGATTAGCTT	60.809	47.826	0.00	0.00	0.00	3.74
655	799	2.289945	GCGAGGGATGGATTGATTAGCT	60.290	50.000	0.00	0.00	0.00	3.32
656	800	2.079925	GCGAGGGATGGATTGATTAGC	58.920	52.381	0.00	0.00	0.00	3.09
657	801	3.692257	AGCGAGGGATGGATTGATTAG	57.308	47.619	0.00	0.00	0.00	1.73
697	845	2.031683	CGCTCGTTGGTTCAACTTTTCT	59.968	45.455	8.80	0.00	41.62	2.52
754	922	2.180674	GGAACGGTCCTCCAAATGC	58.819	57.895	13.76	0.00	41.24	3.56
781	949	4.081142	GGGAAATCAAATTTGGTAGGTGGG	60.081	45.833	17.90	0.00	31.47	4.61
891	1068	4.499116	CGGGAGGGGAGGTGGGAT	62.499	72.222	0.00	0.00	0.00	3.85
1352	1898	2.161609	CAGCAGTAATCCAAACGAACCC	59.838	50.000	0.00	0.00	0.00	4.11
1355	1901	1.810151	GCCAGCAGTAATCCAAACGAA	59.190	47.619	0.00	0.00	0.00	3.85
1362	1908	0.946221	CCGATCGCCAGCAGTAATCC	60.946	60.000	10.32	0.00	0.00	3.01
1367	1913	4.087892	AAGCCGATCGCCAGCAGT	62.088	61.111	10.32	0.00	38.78	4.40
1433	1979	5.125097	CGACCAACTAAACTAGAAGCCTAGA	59.875	44.000	0.00	0.00	44.00	2.43
1526	2072	1.278238	GGATAAGACGAGCAACCACG	58.722	55.000	0.00	0.00	0.00	4.94
1537	2083	2.457366	CCATAGGCGTGGGATAAGAC	57.543	55.000	4.29	0.00	35.55	3.01
1651	2203	2.806745	GCCAGCAACTAACAGTCTGTCA	60.807	50.000	5.82	0.00	0.00	3.58
1764	2323	3.379372	CAGCAATGAACCATCTACCCTTG	59.621	47.826	0.00	0.00	0.00	3.61
1826	2385	1.069513	TCCGGAAACCTATACCATGCG	59.930	52.381	0.00	0.00	0.00	4.73
1966	2600	7.847096	TGTCATAGAAGGCTGAAACATACTAA	58.153	34.615	0.00	0.00	0.00	2.24
1984	2618	5.604565	TGGTAATGTGATCAGCTGTCATAG	58.395	41.667	14.67	0.00	0.00	2.23
1994	2628	4.413189	AGATGACCCATGGTAATGTGATCA	59.587	41.667	16.47	0.00	35.25	2.92
2006	2640	8.345565	GCTTATACAAACTTAAGATGACCCATG	58.654	37.037	10.09	0.00	0.00	3.66
2096	2730	5.540400	ACCATGCAAGGGAATATTCATTG	57.460	39.130	20.33	20.33	43.46	2.82
2221	2859	1.071305	GCATGTGCGACAAAAGCAAAC	60.071	47.619	0.00	0.00	46.97	2.93
2242	2880	4.682787	ACAGTTTTTAAAGCTTCCACTGC	58.317	39.130	17.02	2.91	34.72	4.40
2312	2952	4.787598	CAGAAGCCAAATGTGACAACTAC	58.212	43.478	0.00	0.00	0.00	2.73
2334	2974	6.182039	TGCTACAGTTCAACATTCATAAGC	57.818	37.500	0.00	0.00	0.00	3.09
2401	3041	6.827251	AGAACGGTAATGAGATGTACTCTACA	59.173	38.462	0.00	0.00	45.13	2.74
2551	3252	5.637809	TGAAGTTCACATAGTAGCACTACG	58.362	41.667	0.08	0.00	40.80	3.51
2552	3254	7.464710	GCATTGAAGTTCACATAGTAGCACTAC	60.465	40.741	4.68	0.00	32.84	2.73
2570	3272	5.987347	AGTTTGAAGGAATTGTGCATTGAAG	59.013	36.000	0.00	0.00	0.00	3.02
2594	3296	2.226330	CGACATGTGTTGGAAAAGGGA	58.774	47.619	1.15	0.00	0.00	4.20
2625	3327	3.146066	TCCAAACACTATTGTCACTGCC	58.854	45.455	0.00	0.00	33.55	4.85
2643	3345	8.859090	ACAGTAGTTCATTGATCAATTTTTCCA	58.141	29.630	18.41	0.27	0.00	3.53
2747	3449	6.884836	AGTGTTCTGGAGTTATAATTCAACCC	59.115	38.462	9.86	0.00	0.00	4.11
2998	3700	2.086610	AGACCCACACTGGCAAAAAT	57.913	45.000	0.00	0.00	35.79	1.82
3293	3997	3.413846	ACAAGCAGCTCAATCTTCTCA	57.586	42.857	0.00	0.00	0.00	3.27
3320	4024	1.895798	TGTGAGCGGAGATTCTCTGTT	59.104	47.619	20.87	16.41	38.95	3.16
3567	4315	9.444600	CAATAACTATTAAGTGTACCACCAGTT	57.555	33.333	0.00	0.00	35.62	3.16
3630	4378	4.274459	GCCCTCACTAACATCATGATTGAC	59.726	45.833	5.16	0.00	33.85	3.18
4132	5542	3.569250	TTAAGCAATGTTTTCGGCTCC	57.431	42.857	0.00	0.00	35.11	4.70
4232	5644	5.410067	CAACCAAAGCATAATCGGAAACAT	58.590	37.500	0.00	0.00	0.00	2.71
4240	5652	5.357878	TCAGACATCCAACCAAAGCATAATC	59.642	40.000	0.00	0.00	0.00	1.75
4250	5662	2.229792	GCTGTTTCAGACATCCAACCA	58.770	47.619	0.66	0.00	37.69	3.67
4251	5663	2.229792	TGCTGTTTCAGACATCCAACC	58.770	47.619	0.66	0.00	37.69	3.77
4482	5897	0.798776	GGGCAGTTGAATGTGTCTCG	59.201	55.000	0.00	0.00	0.00	4.04
4946	6365	2.942376	TCGAGCTACGTAAATAACCCGA	59.058	45.455	0.00	0.00	43.13	5.14
4957	6376	3.011119	GGGATATGATCTCGAGCTACGT	58.989	50.000	7.81	5.52	43.13	3.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.