AutoCloner

Multiple sequence alignment - TraesCS5D01G075400

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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	TraesCS5D01G075400	chr5D	100.000	2396	0	0	1	2396	74471742	74474137	0.000000e+00	4425
1	TraesCS5D01G075400	chr5D	83.778	1424	224	7	1	1421	453122480	453121061	0.000000e+00	1343
2	TraesCS5D01G075400	chr5D	83.636	1430	228	6	1	1427	350304884	350306310	0.000000e+00	1339
3	TraesCS5D01G075400	chr5D	99.095	663	4	1	1731	2393	9443398	9444058	0.000000e+00	1190
4	TraesCS5D01G075400	chr5D	84.247	292	35	10	1456	1739	62515773	62515485	8.440000e-70	274
5	TraesCS5D01G075400	chr7A	96.011	1429	56	1	1	1428	709984356	709985784	0.000000e+00	2322
6	TraesCS5D01G075400	chr3A	95.621	1416	61	1	1	1415	466478231	466476816	0.000000e+00	2270
7	TraesCS5D01G075400	chr1A	95.394	1433	50	10	1	1429	307483025	307481605	0.000000e+00	2266
8	TraesCS5D01G075400	chr6A	95.551	1416	61	2	1	1415	521475419	521476833	0.000000e+00	2265
9	TraesCS5D01G075400	chr6A	94.128	1158	67	1	1	1158	171568781	171569937	0.000000e+00	1760
10	TraesCS5D01G075400	chr4A	95.913	1199	47	2	1	1198	542489758	542490955	0.000000e+00	1941
11	TraesCS5D01G075400	chr4A	95.968	248	8	1	1182	1429	542491587	542491832	3.710000e-108	401
12	TraesCS5D01G075400	chr7D	98.949	666	5	1	1728	2393	43374288	43374951	0.000000e+00	1190
13	TraesCS5D01G075400	chr6D	99.095	663	4	1	1731	2393	178803591	178804251	0.000000e+00	1190
14	TraesCS5D01G075400	chr6D	99.095	663	4	1	1731	2393	178813449	178814109	0.000000e+00	1190
15	TraesCS5D01G075400	chr6D	98.514	673	8	1	1724	2396	327556903	327556233	0.000000e+00	1186
16	TraesCS5D01G075400	chr3D	99.095	663	4	1	1731	2393	17106881	17107541	0.000000e+00	1190
17	TraesCS5D01G075400	chr1D	99.095	663	4	1	1731	2393	364074449	364075109	0.000000e+00	1190
18	TraesCS5D01G075400	chr1D	98.227	677	10	1	1720	2396	277405743	277405069	0.000000e+00	1182
19	TraesCS5D01G075400	chr2A	87.552	964	101	13	1441	2393	542745326	542746281	0.000000e+00	1098
20	TraesCS5D01G075400	chr5B	83.688	1128	179	5	303	1428	662648727	662647603	0.000000e+00	1059
21	TraesCS5D01G075400	chr5A	88.963	299	25	4	1448	1739	69869170	69869467	1.750000e-96	363
22	TraesCS5D01G075400	chr1B	85.174	344	51	0	1059	1402	327315490	327315147	1.050000e-93	353
23	TraesCS5D01G075400	chr1B	86.007	293	30	8	1444	1729	536698925	536698637	1.080000e-78	303
24	TraesCS5D01G075400	chr1B	85.050	301	36	7	1446	1739	7073445	7073147	5.010000e-77	298
25	TraesCS5D01G075400	chr2D	86.333	300	32	7	1448	1739	606191857	606191559	3.840000e-83	318
26	TraesCS5D01G075400	chr4D	85.859	297	35	4	1441	1731	43459546	43459841	2.310000e-80	309
27	TraesCS5D01G075400	chrUn	84.053	301	39	7	1446	1739	331240292	331240590	5.040000e-72	281
28	TraesCS5D01G075400	chrUn	84.053	301	39	7	1446	1739	338785706	338786004	5.040000e-72	281
29	TraesCS5D01G075400	chr2B	94.815	135	7	0	1	135	699116002	699116136	6.710000e-51	211

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	TraesCS5D01G075400	chr5D	74471742	74474137	2395	False	4425	4425	100.0000	1	2396	1	chr5D.!!$F2	2395
1	TraesCS5D01G075400	chr5D	453121061	453122480	1419	True	1343	1343	83.7780	1	1421	1	chr5D.!!$R2	1420
2	TraesCS5D01G075400	chr5D	350304884	350306310	1426	False	1339	1339	83.6360	1	1427	1	chr5D.!!$F3	1426
3	TraesCS5D01G075400	chr5D	9443398	9444058	660	False	1190	1190	99.0950	1731	2393	1	chr5D.!!$F1	662
4	TraesCS5D01G075400	chr7A	709984356	709985784	1428	False	2322	2322	96.0110	1	1428	1	chr7A.!!$F1	1427
5	TraesCS5D01G075400	chr3A	466476816	466478231	1415	True	2270	2270	95.6210	1	1415	1	chr3A.!!$R1	1414
6	TraesCS5D01G075400	chr1A	307481605	307483025	1420	True	2266	2266	95.3940	1	1429	1	chr1A.!!$R1	1428
7	TraesCS5D01G075400	chr6A	521475419	521476833	1414	False	2265	2265	95.5510	1	1415	1	chr6A.!!$F2	1414
8	TraesCS5D01G075400	chr6A	171568781	171569937	1156	False	1760	1760	94.1280	1	1158	1	chr6A.!!$F1	1157
9	TraesCS5D01G075400	chr4A	542489758	542491832	2074	False	1171	1941	95.9405	1	1429	2	chr4A.!!$F1	1428
10	TraesCS5D01G075400	chr7D	43374288	43374951	663	False	1190	1190	98.9490	1728	2393	1	chr7D.!!$F1	665
11	TraesCS5D01G075400	chr6D	178803591	178804251	660	False	1190	1190	99.0950	1731	2393	1	chr6D.!!$F1	662
12	TraesCS5D01G075400	chr6D	178813449	178814109	660	False	1190	1190	99.0950	1731	2393	1	chr6D.!!$F2	662
13	TraesCS5D01G075400	chr6D	327556233	327556903	670	True	1186	1186	98.5140	1724	2396	1	chr6D.!!$R1	672
14	TraesCS5D01G075400	chr3D	17106881	17107541	660	False	1190	1190	99.0950	1731	2393	1	chr3D.!!$F1	662
15	TraesCS5D01G075400	chr1D	364074449	364075109	660	False	1190	1190	99.0950	1731	2393	1	chr1D.!!$F1	662
16	TraesCS5D01G075400	chr1D	277405069	277405743	674	True	1182	1182	98.2270	1720	2396	1	chr1D.!!$R1	676
17	TraesCS5D01G075400	chr2A	542745326	542746281	955	False	1098	1098	87.5520	1441	2393	1	chr2A.!!$F1	952
18	TraesCS5D01G075400	chr5B	662647603	662648727	1124	True	1059	1059	83.6880	303	1428	1	chr5B.!!$R1	1125

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
78	79	0.413434	TGGAGAGTGGGAGATGGACA	59.587	55.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1613	2272	0.030638	ATTTGCTTCGTGCCACACAC	59.969	50.0	0.0	0.0	46.45	3.82	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
37	38	6.016276	GGAGAAGCATTTTGAAAGGAGTACAA	60.016	38.462	0.00	0.00	0.00	2.41
67	68	5.008415	GCAAAGTGGAATCATATGGAGAGTG	59.992	44.000	2.13	0.00	0.00	3.51
78	79	0.413434	TGGAGAGTGGGAGATGGACA	59.587	55.000	0.00	0.00	0.00	4.02
98	99	7.412627	TGGACACAATATCAATATATGGGCAT	58.587	34.615	0.00	0.00	0.00	4.40
146	147	4.464069	AGGAGAGTAACATCTCAGCAAC	57.536	45.455	6.12	0.00	46.31	4.17
171	172	5.540911	CAGCCATGTTATCACAAAGGTTTT	58.459	37.500	0.00	0.00	36.16	2.43
240	241	9.305925	GATTGATCAAACTTTCAACAAAGAAGT	57.694	29.630	13.09	0.00	41.60	3.01
371	373	2.039418	GGAAAACCAAGCCAGGAACTT	58.961	47.619	0.00	0.00	34.60	2.66
386	388	1.956477	GAACTTTGCACATGGTGGAGT	59.044	47.619	0.00	0.00	34.96	3.85
388	390	1.682854	ACTTTGCACATGGTGGAGTTG	59.317	47.619	0.00	0.00	34.96	3.16
390	392	0.754587	TTGCACATGGTGGAGTTGCA	60.755	50.000	0.00	0.00	34.96	4.08
444	446	7.595819	AACATTTTGGAAGAAACTATGGACA	57.404	32.000	0.00	0.00	0.00	4.02
487	489	1.275010	TGCACTTTCTATGGCGACTGA	59.725	47.619	0.00	0.00	0.00	3.41
500	502	2.561419	GGCGACTGACCCATTATAGCTA	59.439	50.000	0.00	0.00	0.00	3.32
588	590	4.387598	GAATGGATGAAGATGGAGGTCAG	58.612	47.826	0.00	0.00	0.00	3.51
600	602	7.510675	AGATGGAGGTCAGTATTTCCTAAAA	57.489	36.000	0.00	0.00	0.00	1.52
608	610	8.470002	AGGTCAGTATTTCCTAAAATGCAAATC	58.530	33.333	0.00	0.00	39.23	2.17
619	621	5.726980	AAAATGCAAATCTGTCAAGGCTA	57.273	34.783	0.00	0.00	0.00	3.93
838	840	1.402968	CAGTTCAGCTGCACTTGTTGT	59.597	47.619	16.79	0.00	38.52	3.32
925	927	5.400653	CCTCCCCCTGATGATTTCCTTAAAT	60.401	44.000	0.00	0.00	38.03	1.40
1098	1103	0.508641	CTGTGAACGAAGCGTCAAGG	59.491	55.000	0.00	0.00	39.99	3.61
1186	1839	3.693085	CCTGTACGACTACTCAAGCCTAA	59.307	47.826	0.00	0.00	0.00	2.69
1404	2057	3.243068	GCTTGCCTTGGTAATGGAATACG	60.243	47.826	0.00	0.00	0.00	3.06
1418	2071	7.696992	AATGGAATACGTTTGTGTTTCCTAT	57.303	32.000	0.00	0.00	40.06	2.57
1419	2072	6.730960	TGGAATACGTTTGTGTTTCCTATC	57.269	37.500	0.00	0.00	40.06	2.08
1451	2104	0.182775	AAAGGAAAGGGCGCCGATAT	59.817	50.000	22.54	6.32	0.00	1.63
1453	2106	1.122019	AGGAAAGGGCGCCGATATCT	61.122	55.000	22.54	12.31	0.00	1.98
1454	2107	0.951040	GGAAAGGGCGCCGATATCTG	60.951	60.000	22.54	0.00	0.00	2.90
1460	2113	2.598632	GCGCCGATATCTGCCACAC	61.599	63.158	12.83	0.00	0.00	3.82
1480	2133	5.294306	CACACGTGTGGCATATTAGAAATCT	59.706	40.000	35.65	0.00	42.10	2.40
1486	2139	4.773323	GGCATATTAGAAATCTGCCCAC	57.227	45.455	14.78	0.00	45.26	4.61
1489	2142	4.319766	GCATATTAGAAATCTGCCCACACG	60.320	45.833	0.00	0.00	0.00	4.49
1490	2143	1.448985	TTAGAAATCTGCCCACACGC	58.551	50.000	0.00	0.00	0.00	5.34
1492	2145	2.676471	AAATCTGCCCACACGCCC	60.676	61.111	0.00	0.00	0.00	6.13
1493	2146	4.740822	AATCTGCCCACACGCCCC	62.741	66.667	0.00	0.00	0.00	5.80
1512	2165	1.586422	CGTGTGGCATAATCAGGAGG	58.414	55.000	0.00	0.00	0.00	4.30
1513	2166	1.312815	GTGTGGCATAATCAGGAGGC	58.687	55.000	0.00	0.00	0.00	4.70
1515	2168	1.284491	TGTGGCATAATCAGGAGGCAA	59.716	47.619	0.00	0.00	38.31	4.52
1541	2194	2.997986	CACGGGTTATGTGTGGTAGAAC	59.002	50.000	0.00	0.00	32.68	3.01
1552	2205	6.494893	TGTGTGGTAGAACATTAGAATTGC	57.505	37.500	0.00	0.00	31.49	3.56
1554	2207	4.947388	TGTGGTAGAACATTAGAATTGCCC	59.053	41.667	0.00	0.00	0.00	5.36
1563	2216	3.404224	TTAGAATTGCCCACACGTGTA	57.596	42.857	22.90	5.59	0.00	2.90
1565	2218	0.802494	GAATTGCCCACACGTGTAGG	59.198	55.000	26.41	26.41	0.00	3.18
1566	2219	0.608035	AATTGCCCACACGTGTAGGG	60.608	55.000	33.88	33.88	45.68	3.53
1571	2224	3.112075	CACACGTGTAGGGCGCAG	61.112	66.667	22.90	2.01	0.00	5.18
1588	2241	0.599991	CAGCTACTTCGTGCCACACA	60.600	55.000	0.00	0.00	33.40	3.72
1600	2253	1.133637	TGCCACACACCCAACAAGTAT	60.134	47.619	0.00	0.00	0.00	2.12
1607	2266	6.152661	CCACACACCCAACAAGTATTATTCAT	59.847	38.462	0.00	0.00	0.00	2.57
1613	2272	4.319477	CCAACAAGTATTATTCATCCCGCG	60.319	45.833	0.00	0.00	0.00	6.46
1614	2273	4.067972	ACAAGTATTATTCATCCCGCGT	57.932	40.909	4.92	0.00	0.00	6.01
1649	2308	3.202906	CAAATATACCCACACGTCCTGG	58.797	50.000	2.19	2.19	0.00	4.45
1650	2309	2.170012	ATATACCCACACGTCCTGGT	57.830	50.000	7.80	6.38	34.85	4.00
1654	2313	2.666190	CCACACGTCCTGGTGCAG	60.666	66.667	0.00	0.00	41.65	4.41
1664	2323	0.246635	CCTGGTGCAGCTACGTTAGT	59.753	55.000	18.08	0.00	0.00	2.24
1668	2327	2.559668	TGGTGCAGCTACGTTAGTTACT	59.440	45.455	18.08	0.00	0.00	2.24
1680	2340	1.753930	TAGTTACTCGCGGGATGACA	58.246	50.000	15.95	0.00	0.00	3.58
1681	2341	0.172803	AGTTACTCGCGGGATGACAC	59.827	55.000	15.95	0.82	0.00	3.67
1689	2349	2.492881	TCGCGGGATGACACTTTAGTTA	59.507	45.455	6.13	0.00	0.00	2.24
1692	2352	3.528532	CGGGATGACACTTTAGTTACCC	58.471	50.000	0.00	0.00	0.00	3.69
1693	2353	3.680754	CGGGATGACACTTTAGTTACCCC	60.681	52.174	0.00	0.00	0.00	4.95
1694	2354	3.528532	GGATGACACTTTAGTTACCCCG	58.471	50.000	0.00	0.00	0.00	5.73
1697	2358	0.986527	ACACTTTAGTTACCCCGGGG	59.013	55.000	39.18	39.18	42.03	5.73
1704	2365	2.614331	TTACCCCGGGGATGGCAA	60.614	61.111	46.68	25.55	38.96	4.52
1705	2366	2.986355	TTACCCCGGGGATGGCAAC	61.986	63.158	46.68	0.00	38.96	4.17
1707	2368	4.060667	CCCCGGGGATGGCAACTT	62.061	66.667	38.41	0.00	37.50	2.66
1715	2376	3.951680	CGGGGATGGCAACTTTAGTTATT	59.048	43.478	0.00	0.00	36.32	1.40
1751	2412	4.473196	TGTGTTGGAAATATGCCCTAGAGA	59.527	41.667	0.00	0.00	0.00	3.10
1752	2413	5.059833	GTGTTGGAAATATGCCCTAGAGAG	58.940	45.833	0.00	0.00	0.00	3.20
1899	2560	6.133356	AGTAAGCCTCTAATTGACTAGCTCT	58.867	40.000	0.00	0.00	0.00	4.09
2090	2753	2.996249	AGACCATGAGATCGTGCAAT	57.004	45.000	0.00	0.00	0.00	3.56
2280	2943	6.598457	GGTAATGCATCATCATAATGAGCTCT	59.402	38.462	16.19	0.00	44.90	4.09
2393	3056	1.552348	CGATCGAATCTCGGGCAAGC	61.552	60.000	10.26	0.00	40.88	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	5.105635	CCATATGATTCCACTTTGCAACACT	60.106	40.000	3.65	0.00	0.00	3.55
67	68	9.334947	CATATATTGATATTGTGTCCATCTCCC	57.665	37.037	0.00	0.00	0.00	4.30
146	147	2.478370	CCTTTGTGATAACATGGCTGCG	60.478	50.000	0.00	0.00	0.00	5.18
171	172	5.366768	CCAGAGGTAGGGTCAATCAAATCTA	59.633	44.000	0.00	0.00	0.00	1.98
240	241	6.373216	CGGAATTTGGACAATTACCTCTACAA	59.627	38.462	0.00	0.00	0.00	2.41
371	373	0.754587	TGCAACTCCACCATGTGCAA	60.755	50.000	2.71	0.00	31.34	4.08
386	388	7.451501	TGAACATTCTTACTTGATGATGCAA	57.548	32.000	0.00	0.00	0.00	4.08
388	390	5.970023	GCTGAACATTCTTACTTGATGATGC	59.030	40.000	0.00	0.00	0.00	3.91
390	392	7.876936	ATGCTGAACATTCTTACTTGATGAT	57.123	32.000	0.00	0.00	34.40	2.45
444	446	4.309879	TTGTTGGGCAAGGGCAAT	57.690	50.000	0.00	0.00	43.71	3.56
487	489	8.598041	CATTCTTAGAGGTTAGCTATAATGGGT	58.402	37.037	0.00	0.00	0.00	4.51
532	534	3.265791	GACAGCTTGTATCCACTTCCAG	58.734	50.000	0.00	0.00	0.00	3.86
549	551	2.602257	TTCGATGGCATACTGGACAG	57.398	50.000	0.00	0.00	0.00	3.51
588	590	9.638239	TTGACAGATTTGCATTTTAGGAAATAC	57.362	29.630	0.00	0.00	39.25	1.89
600	602	5.394883	CCAAATAGCCTTGACAGATTTGCAT	60.395	40.000	0.00	0.00	36.57	3.96
608	610	4.394300	CAGTTCTCCAAATAGCCTTGACAG	59.606	45.833	0.00	0.00	0.00	3.51
619	621	3.896888	TCCAACAATGCAGTTCTCCAAAT	59.103	39.130	0.00	0.00	0.00	2.32
1029	1034	4.887071	TGTAGTGGTTCAGCAACATTTTCT	59.113	37.500	0.00	0.00	33.70	2.52
1098	1103	1.337118	TGACTTTTTGGCACCCCATC	58.663	50.000	0.00	0.00	41.78	3.51
1186	1839	5.479306	TCTTATCTCTTTAAACAGCACGCT	58.521	37.500	0.00	0.00	0.00	5.07
1263	1916	8.020819	GCTAAACAGTGTGCAGAAATATTACAA	58.979	33.333	0.00	0.00	0.00	2.41
1428	2081	1.292223	GGCGCCCTTTCCTTTTTCC	59.708	57.895	18.11	0.00	0.00	3.13
1429	2082	1.080772	CGGCGCCCTTTCCTTTTTC	60.081	57.895	23.46	0.00	0.00	2.29
1430	2083	0.898326	ATCGGCGCCCTTTCCTTTTT	60.898	50.000	23.46	0.00	0.00	1.94
1431	2084	0.034863	TATCGGCGCCCTTTCCTTTT	60.035	50.000	23.46	0.00	0.00	2.27
1432	2085	0.182775	ATATCGGCGCCCTTTCCTTT	59.817	50.000	23.46	0.00	0.00	3.11
1433	2086	0.250338	GATATCGGCGCCCTTTCCTT	60.250	55.000	23.46	0.00	0.00	3.36
1434	2087	1.122019	AGATATCGGCGCCCTTTCCT	61.122	55.000	23.46	10.26	0.00	3.36
1435	2088	0.951040	CAGATATCGGCGCCCTTTCC	60.951	60.000	23.46	7.82	0.00	3.13
1436	2089	1.569479	GCAGATATCGGCGCCCTTTC	61.569	60.000	23.46	13.06	0.00	2.62
1437	2090	1.598130	GCAGATATCGGCGCCCTTT	60.598	57.895	23.46	8.38	0.00	3.11
1438	2091	2.031163	GCAGATATCGGCGCCCTT	59.969	61.111	23.46	11.31	0.00	3.95
1439	2092	4.008933	GGCAGATATCGGCGCCCT	62.009	66.667	23.46	11.53	38.67	5.19
1442	2095	2.280119	TGTGGCAGATATCGGCGC	60.280	61.111	19.53	19.75	37.94	6.53
1460	2113	4.776743	GCAGATTTCTAATATGCCACACG	58.223	43.478	7.58	0.00	0.00	4.49
1476	2129	4.740822	GGGGCGTGTGGGCAGATT	62.741	66.667	0.00	0.00	44.56	2.40
1490	2143	0.819259	CCTGATTATGCCACACGGGG	60.819	60.000	0.00	0.00	37.04	5.73
1492	2145	1.586422	CTCCTGATTATGCCACACGG	58.414	55.000	0.00	0.00	0.00	4.94
1493	2146	1.586422	CCTCCTGATTATGCCACACG	58.414	55.000	0.00	0.00	0.00	4.49
1500	2153	2.301346	GTGGGTTGCCTCCTGATTATG	58.699	52.381	0.00	0.00	0.00	1.90
1501	2154	1.922447	TGTGGGTTGCCTCCTGATTAT	59.078	47.619	0.00	0.00	0.00	1.28
1503	2156	0.251341	GTGTGGGTTGCCTCCTGATT	60.251	55.000	0.00	0.00	0.00	2.57
1505	2158	2.836154	GTGTGGGTTGCCTCCTGA	59.164	61.111	0.00	0.00	0.00	3.86
1506	2159	2.669569	CGTGTGGGTTGCCTCCTG	60.670	66.667	0.00	0.00	0.00	3.86
1526	2179	8.673711	GCAATTCTAATGTTCTACCACACATAA	58.326	33.333	0.00	0.00	33.11	1.90
1528	2181	6.095440	GGCAATTCTAATGTTCTACCACACAT	59.905	38.462	0.00	0.00	35.00	3.21
1536	2189	4.634004	CGTGTGGGCAATTCTAATGTTCTA	59.366	41.667	0.00	0.00	0.00	2.10
1537	2190	3.440173	CGTGTGGGCAATTCTAATGTTCT	59.560	43.478	0.00	0.00	0.00	3.01
1541	2194	2.487762	ACACGTGTGGGCAATTCTAATG	59.512	45.455	22.71	0.00	34.19	1.90
1554	2207	3.112075	CTGCGCCCTACACGTGTG	61.112	66.667	30.83	19.25	0.00	3.82
1563	2216	3.382832	ACGAAGTAGCTGCGCCCT	61.383	61.111	4.18	3.54	41.94	5.19
1565	2218	3.854459	GCACGAAGTAGCTGCGCC	61.854	66.667	4.18	0.00	41.61	6.53
1566	2219	3.854459	GGCACGAAGTAGCTGCGC	61.854	66.667	0.00	0.00	41.61	6.09
1567	2220	2.432456	TGGCACGAAGTAGCTGCG	60.432	61.111	0.00	0.00	41.61	5.18
1568	2221	1.667830	TGTGGCACGAAGTAGCTGC	60.668	57.895	13.77	0.00	41.61	5.25
1569	2222	0.599991	TGTGTGGCACGAAGTAGCTG	60.600	55.000	13.77	0.00	41.61	4.24
1571	2224	1.860078	GTGTGTGGCACGAAGTAGC	59.140	57.895	13.77	0.00	41.61	3.58
1579	2232	1.319614	ACTTGTTGGGTGTGTGGCAC	61.320	55.000	11.55	11.55	46.97	5.01
1588	2241	5.130350	CGGGATGAATAATACTTGTTGGGT	58.870	41.667	0.00	0.00	0.00	4.51
1600	2253	1.364721	CACACACGCGGGATGAATAA	58.635	50.000	19.19	0.00	0.00	1.40
1613	2272	0.030638	ATTTGCTTCGTGCCACACAC	59.969	50.000	0.00	0.00	46.45	3.82
1614	2273	1.598882	TATTTGCTTCGTGCCACACA	58.401	45.000	0.00	0.00	42.00	3.72
1632	2291	1.187974	CACCAGGACGTGTGGGTATA	58.812	55.000	16.15	0.00	39.65	1.47
1635	2294	4.250305	GCACCAGGACGTGTGGGT	62.250	66.667	16.15	7.08	39.65	4.51
1649	2308	2.844804	CGAGTAACTAACGTAGCTGCAC	59.155	50.000	1.02	0.00	0.00	4.57
1650	2309	2.730090	GCGAGTAACTAACGTAGCTGCA	60.730	50.000	1.02	0.00	0.00	4.41
1654	2313	1.460766	CCGCGAGTAACTAACGTAGC	58.539	55.000	8.23	0.00	0.00	3.58
1664	2323	0.892755	AAGTGTCATCCCGCGAGTAA	59.107	50.000	8.23	0.00	0.00	2.24
1668	2327	0.892755	ACTAAAGTGTCATCCCGCGA	59.107	50.000	8.23	0.00	0.00	5.87
1680	2340	1.841919	CATCCCCGGGGTAACTAAAGT	59.158	52.381	38.73	11.74	36.47	2.66
1681	2341	1.142262	CCATCCCCGGGGTAACTAAAG	59.858	57.143	38.73	15.59	36.47	1.85
1692	2352	0.034477	ACTAAAGTTGCCATCCCCGG	60.034	55.000	0.00	0.00	0.00	5.73
1693	2353	1.834188	AACTAAAGTTGCCATCCCCG	58.166	50.000	0.00	0.00	36.80	5.73
1694	2354	4.036380	CGAATAACTAAAGTTGCCATCCCC	59.964	45.833	5.62	0.00	38.90	4.81
1697	2358	4.879545	TCCCGAATAACTAAAGTTGCCATC	59.120	41.667	5.62	0.00	38.90	3.51
1704	2365	8.050930	ACATTTACCATCCCGAATAACTAAAGT	58.949	33.333	0.00	0.00	0.00	2.66
1705	2366	8.342634	CACATTTACCATCCCGAATAACTAAAG	58.657	37.037	0.00	0.00	0.00	1.85
1707	2368	7.340256	ACACATTTACCATCCCGAATAACTAA	58.660	34.615	0.00	0.00	0.00	2.24
1715	2376	2.306219	TCCAACACATTTACCATCCCGA	59.694	45.455	0.00	0.00	0.00	5.14
1899	2560	7.121168	GGAAACCATGACTATCTGTTGATCAAA	59.879	37.037	10.35	0.00	34.32	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.