AutoCloner

Multiple sequence alignment - TraesCS1A01G103400

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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	TraesCS1A01G103400	chr1A	100.000	2261	0	0	1	2261	99641032	99643292	0.000000e+00	4176.0
1	TraesCS1A01G103400	chr1A	81.861	1268	178	28	129	1390	99749797	99748576	0.000000e+00	1020.0
2	TraesCS1A01G103400	chr1A	84.295	745	103	6	2	739	99726984	99726247	0.000000e+00	715.0
3	TraesCS1A01G103400	chr5B	91.607	1668	102	16	2	1634	11605565	11603901	0.000000e+00	2270.0
4	TraesCS1A01G103400	chr5B	80.563	1564	216	54	98	1634	11477433	11478935	0.000000e+00	1123.0
5	TraesCS1A01G103400	chr5B	98.917	554	6	0	1708	2261	158560155	158559602	0.000000e+00	990.0
6	TraesCS1A01G103400	chr5B	97.822	551	12	0	1708	2258	655057591	655058141	0.000000e+00	952.0
7	TraesCS1A01G103400	chr5B	83.534	747	101	11	2	733	11503168	11503907	0.000000e+00	678.0
8	TraesCS1A01G103400	chr5B	81.003	658	93	20	844	1492	564478391	564479025	5.610000e-136	494.0
9	TraesCS1A01G103400	chr5D	91.761	886	39	3	2	880	11420860	11421718	0.000000e+00	1201.0
10	TraesCS1A01G103400	chr5D	80.222	1532	211	51	129	1634	11614193	11612728	0.000000e+00	1066.0
11	TraesCS1A01G103400	chr5D	83.026	1137	160	25	129	1259	11364877	11365986	0.000000e+00	1000.0
12	TraesCS1A01G103400	chr5D	85.306	735	94	8	12	739	11576894	11576167	0.000000e+00	747.0
13	TraesCS1A01G103400	chr5D	81.307	658	91	19	844	1492	459751038	459751672	2.590000e-139	505.0
14	TraesCS1A01G103400	chr5D	78.191	752	105	35	838	1572	11576095	11575386	2.080000e-115	425.0
15	TraesCS1A01G103400	chr5D	87.255	204	23	3	1432	1634	11421713	11421914	1.750000e-56	230.0
16	TraesCS1A01G103400	chrUn	83.127	1132	168	15	129	1259	312563202	312564311	0.000000e+00	1011.0
17	TraesCS1A01G103400	chrUn	96.988	498	15	0	1764	2261	360747371	360746874	0.000000e+00	837.0
18	TraesCS1A01G103400	chrUn	96.988	498	15	0	1764	2261	360749448	360748951	0.000000e+00	837.0
19	TraesCS1A01G103400	chr4A	99.636	550	2	0	1709	2258	672237251	672237800	0.000000e+00	1005.0
20	TraesCS1A01G103400	chr4A	95.826	551	23	0	1708	2258	619407877	619408427	0.000000e+00	891.0
21	TraesCS1A01G103400	chr7D	95.126	554	27	0	1708	2261	90612741	90612188	0.000000e+00	874.0
22	TraesCS1A01G103400	chr7D	93.273	550	37	0	1706	2255	415410803	415410254	0.000000e+00	811.0
23	TraesCS1A01G103400	chr2D	93.273	550	34	1	1709	2255	9515127	9514578	0.000000e+00	808.0
24	TraesCS1A01G103400	chr5A	77.482	1279	213	45	231	1492	579844240	579843020	0.000000e+00	697.0
25	TraesCS1A01G103400	chr5A	95.556	45	1	1	1663	1707	535733506	535733549	1.120000e-08	71.3
26	TraesCS1A01G103400	chr5A	95.556	45	1	1	1663	1707	658869415	658869458	1.120000e-08	71.3

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	TraesCS1A01G103400	chr1A	99641032	99643292	2260	False	4176.0	4176	100.0000	1	2261	1	chr1A.!!$F1	2260
1	TraesCS1A01G103400	chr1A	99748576	99749797	1221	True	1020.0	1020	81.8610	129	1390	1	chr1A.!!$R2	1261
2	TraesCS1A01G103400	chr1A	99726247	99726984	737	True	715.0	715	84.2950	2	739	1	chr1A.!!$R1	737
3	TraesCS1A01G103400	chr5B	11603901	11605565	1664	True	2270.0	2270	91.6070	2	1634	1	chr5B.!!$R1	1632
4	TraesCS1A01G103400	chr5B	11477433	11478935	1502	False	1123.0	1123	80.5630	98	1634	1	chr5B.!!$F1	1536
5	TraesCS1A01G103400	chr5B	158559602	158560155	553	True	990.0	990	98.9170	1708	2261	1	chr5B.!!$R2	553
6	TraesCS1A01G103400	chr5B	655057591	655058141	550	False	952.0	952	97.8220	1708	2258	1	chr5B.!!$F4	550
7	TraesCS1A01G103400	chr5B	11503168	11503907	739	False	678.0	678	83.5340	2	733	1	chr5B.!!$F2	731
8	TraesCS1A01G103400	chr5B	564478391	564479025	634	False	494.0	494	81.0030	844	1492	1	chr5B.!!$F3	648
9	TraesCS1A01G103400	chr5D	11612728	11614193	1465	True	1066.0	1066	80.2220	129	1634	1	chr5D.!!$R1	1505
10	TraesCS1A01G103400	chr5D	11364877	11365986	1109	False	1000.0	1000	83.0260	129	1259	1	chr5D.!!$F1	1130
11	TraesCS1A01G103400	chr5D	11420860	11421914	1054	False	715.5	1201	89.5080	2	1634	2	chr5D.!!$F3	1632
12	TraesCS1A01G103400	chr5D	11575386	11576894	1508	True	586.0	747	81.7485	12	1572	2	chr5D.!!$R2	1560
13	TraesCS1A01G103400	chr5D	459751038	459751672	634	False	505.0	505	81.3070	844	1492	1	chr5D.!!$F2	648
14	TraesCS1A01G103400	chrUn	312563202	312564311	1109	False	1011.0	1011	83.1270	129	1259	1	chrUn.!!$F1	1130
15	TraesCS1A01G103400	chrUn	360746874	360749448	2574	True	837.0	837	96.9880	1764	2261	2	chrUn.!!$R1	497
16	TraesCS1A01G103400	chr4A	672237251	672237800	549	False	1005.0	1005	99.6360	1709	2258	1	chr4A.!!$F2	549
17	TraesCS1A01G103400	chr4A	619407877	619408427	550	False	891.0	891	95.8260	1708	2258	1	chr4A.!!$F1	550
18	TraesCS1A01G103400	chr7D	90612188	90612741	553	True	874.0	874	95.1260	1708	2261	1	chr7D.!!$R1	553
19	TraesCS1A01G103400	chr7D	415410254	415410803	549	True	811.0	811	93.2730	1706	2255	1	chr7D.!!$R2	549
20	TraesCS1A01G103400	chr2D	9514578	9515127	549	True	808.0	808	93.2730	1709	2255	1	chr2D.!!$R1	546
21	TraesCS1A01G103400	chr5A	579843020	579844240	1220	True	697.0	697	77.4820	231	1492	1	chr5A.!!$R1	1261

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
950	971	1.072505	GGCGGTTCCTGGTCTTCAA	59.927	57.895	0.0	0.0	0.0	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1968	4177	3.109151	TCTCTCCGTCTTCTCTAGTCCT	58.891	50.0	0.0	0.0	0.0	3.85	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
171	186	3.258622	CCCGTATATTCCTCCTCTTGTCC	59.741	52.174	0.00	0.00	0.00	4.02
177	192	1.079543	CCTCCTCTTGTCCTGCGTG	60.080	63.158	0.00	0.00	0.00	5.34
870	891	3.141488	CGCTACGTCCTGCCCTCT	61.141	66.667	0.00	0.00	0.00	3.69
880	901	4.392166	TGCCCTCTGCCTCCGGTA	62.392	66.667	0.00	0.00	40.16	4.02
950	971	1.072505	GGCGGTTCCTGGTCTTCAA	59.927	57.895	0.00	0.00	0.00	2.69
969	999	3.145228	GCTACAGAAGCCACAGGAC	57.855	57.895	0.00	0.00	46.25	3.85
1056	1092	4.699522	AAGGCCTTCGACACGGGC	62.700	66.667	13.78	11.77	45.46	6.13
1089	1125	1.341531	CCGGGCTACATCTACTTCCTG	59.658	57.143	0.00	0.00	0.00	3.86
1119	1164	3.625897	CCTGGTGGTCCGCACAGA	61.626	66.667	17.64	0.00	36.30	3.41
1135	1180	0.972134	CAGAGTCCTCCAGCAGAACA	59.028	55.000	0.00	0.00	0.00	3.18
1174	1219	2.125269	GCGGGTGGCGTTACTCAT	60.125	61.111	0.00	0.00	0.00	2.90
1180	1225	0.746923	GTGGCGTTACTCATTCCCCC	60.747	60.000	0.00	0.00	0.00	5.40
1280	1341	6.884280	ATGAATTTAGCTATACCCAACAGC	57.116	37.500	0.00	0.00	35.49	4.40
1312	1377	3.195182	AGGCATCACATCGATCATAGAGG	59.805	47.826	0.00	0.00	29.21	3.69
1330	1396	7.987458	TCATAGAGGTTTCCATCAGTTCATTAC	59.013	37.037	0.00	0.00	0.00	1.89
1337	1406	7.227512	GGTTTCCATCAGTTCATTACATAGAGG	59.772	40.741	0.00	0.00	0.00	3.69
1341	1410	6.426328	CCATCAGTTCATTACATAGAGGCTTC	59.574	42.308	0.00	0.00	0.00	3.86
1348	1417	6.216569	TCATTACATAGAGGCTTCGTCATTC	58.783	40.000	0.00	0.00	0.00	2.67
1376	1448	4.724399	TGCTCCTGGTCAATGTTTCTTTA	58.276	39.130	0.00	0.00	0.00	1.85
1390	1463	7.908193	ATGTTTCTTTATTGTTGTTGTCGTC	57.092	32.000	0.00	0.00	0.00	4.20
1412	1500	4.083537	TCGATGGTTGTTGTTGTAAGATGC	60.084	41.667	0.00	0.00	0.00	3.91
1467	1590	3.648339	TGTTCTCAATTTGAAGGCTGC	57.352	42.857	0.01	0.00	0.00	5.25
1483	1606	2.589014	GCTGCTTTGGAACTCATTTCG	58.411	47.619	0.00	0.00	34.67	3.46
1537	1660	7.822600	TCCATGCTACCAGCTACCTATATATA	58.177	38.462	0.00	0.00	42.97	0.86
1539	1662	9.755122	CCATGCTACCAGCTACCTATATATATA	57.245	37.037	2.49	2.49	42.97	0.86
1567	1694	7.809331	TGCTTGAATTGTGTGTATGATTTTCTC	59.191	33.333	0.00	0.00	0.00	2.87
1578	1705	8.994170	TGTGTATGATTTTCTCGTGTAAATTCA	58.006	29.630	4.01	5.63	33.33	2.57
1604	1736	9.878599	AACTTCAGATTTTATATATTTTCCGCG	57.121	29.630	0.00	0.00	0.00	6.46
1634	1766	5.122519	TCAGTAGTGCACACAATTTCTGAA	58.877	37.500	21.04	0.00	33.83	3.02
1635	1767	5.588246	TCAGTAGTGCACACAATTTCTGAAA	59.412	36.000	21.04	5.15	33.83	2.69
1636	1768	5.682862	CAGTAGTGCACACAATTTCTGAAAC	59.317	40.000	21.04	0.00	31.23	2.78
1637	1769	4.045636	AGTGCACACAATTTCTGAAACC	57.954	40.909	21.04	0.00	0.00	3.27
1638	1770	3.701040	AGTGCACACAATTTCTGAAACCT	59.299	39.130	21.04	0.00	0.00	3.50
1639	1771	4.160252	AGTGCACACAATTTCTGAAACCTT	59.840	37.500	21.04	0.00	0.00	3.50
1640	1772	4.268405	GTGCACACAATTTCTGAAACCTTG	59.732	41.667	13.17	9.56	0.00	3.61
1641	1773	4.081752	TGCACACAATTTCTGAAACCTTGT	60.082	37.500	13.57	13.57	0.00	3.16
1642	1774	4.869861	GCACACAATTTCTGAAACCTTGTT	59.130	37.500	15.72	8.11	0.00	2.83
1643	1775	5.351189	GCACACAATTTCTGAAACCTTGTTT	59.649	36.000	15.72	9.69	0.00	2.83
1644	1776	6.672836	GCACACAATTTCTGAAACCTTGTTTG	60.673	38.462	20.65	20.65	33.09	2.93
1645	1777	5.351189	ACACAATTTCTGAAACCTTGTTTGC	59.649	36.000	15.72	0.00	0.00	3.68
1646	1778	5.350914	CACAATTTCTGAAACCTTGTTTGCA	59.649	36.000	15.72	0.00	0.00	4.08
1647	1779	6.037391	CACAATTTCTGAAACCTTGTTTGCAT	59.963	34.615	15.72	0.00	0.00	3.96
1648	1780	7.224362	CACAATTTCTGAAACCTTGTTTGCATA	59.776	33.333	15.72	0.00	0.00	3.14
1649	1781	7.768120	ACAATTTCTGAAACCTTGTTTGCATAA	59.232	29.630	13.57	0.00	0.00	1.90
1650	1782	7.713764	ATTTCTGAAACCTTGTTTGCATAAC	57.286	32.000	4.73	0.00	0.00	1.89
1651	1783	5.843673	TCTGAAACCTTGTTTGCATAACA	57.156	34.783	9.46	9.46	0.00	2.41
1652	1784	5.587289	TCTGAAACCTTGTTTGCATAACAC	58.413	37.500	12.14	3.66	0.00	3.32
1653	1785	4.355437	TGAAACCTTGTTTGCATAACACG	58.645	39.130	12.14	10.80	0.00	4.49
1654	1786	4.142359	TGAAACCTTGTTTGCATAACACGT	60.142	37.500	12.14	9.47	0.00	4.49
1655	1787	5.066117	TGAAACCTTGTTTGCATAACACGTA	59.934	36.000	12.14	1.17	0.00	3.57
1656	1788	5.502153	AACCTTGTTTGCATAACACGTAA	57.498	34.783	12.14	0.90	0.00	3.18
1658	1790	4.817464	ACCTTGTTTGCATAACACGTAAGA	59.183	37.500	12.14	0.08	43.62	2.10
1659	1791	5.297278	ACCTTGTTTGCATAACACGTAAGAA	59.703	36.000	12.14	0.00	43.62	2.52
1660	1792	5.851177	CCTTGTTTGCATAACACGTAAGAAG	59.149	40.000	12.14	4.30	43.62	2.85
1661	1793	6.293190	CCTTGTTTGCATAACACGTAAGAAGA	60.293	38.462	12.14	0.00	43.62	2.87
1662	1794	6.606234	TGTTTGCATAACACGTAAGAAGAA	57.394	33.333	9.46	0.00	43.62	2.52
1663	1795	6.423862	TGTTTGCATAACACGTAAGAAGAAC	58.576	36.000	9.46	0.00	43.62	3.01
1664	1796	6.037281	TGTTTGCATAACACGTAAGAAGAACA	59.963	34.615	9.46	0.00	43.62	3.18
1665	1797	5.839262	TGCATAACACGTAAGAAGAACAG	57.161	39.130	0.00	0.00	43.62	3.16
1666	1798	4.688879	TGCATAACACGTAAGAAGAACAGG	59.311	41.667	0.00	0.00	43.62	4.00
1667	1799	4.092968	GCATAACACGTAAGAAGAACAGGG	59.907	45.833	0.00	0.00	43.62	4.45
1668	1800	2.833631	ACACGTAAGAAGAACAGGGG	57.166	50.000	0.00	0.00	43.62	4.79
1669	1801	2.322658	ACACGTAAGAAGAACAGGGGA	58.677	47.619	0.00	0.00	43.62	4.81
1670	1802	2.701951	ACACGTAAGAAGAACAGGGGAA	59.298	45.455	0.00	0.00	43.62	3.97
1671	1803	3.064931	CACGTAAGAAGAACAGGGGAAC	58.935	50.000	0.00	0.00	43.62	3.62
1672	1804	2.970640	ACGTAAGAAGAACAGGGGAACT	59.029	45.455	0.00	0.00	43.62	3.01
1673	1805	3.006644	ACGTAAGAAGAACAGGGGAACTC	59.993	47.826	0.00	0.00	43.62	3.01
1674	1806	3.006537	CGTAAGAAGAACAGGGGAACTCA	59.993	47.826	0.00	0.00	43.02	3.41
1675	1807	4.322801	CGTAAGAAGAACAGGGGAACTCAT	60.323	45.833	0.00	0.00	43.02	2.90
1676	1808	3.990959	AGAAGAACAGGGGAACTCATC	57.009	47.619	0.00	0.00	0.00	2.92
1677	1809	2.234908	AGAAGAACAGGGGAACTCATCG	59.765	50.000	0.00	0.00	0.00	3.84
1678	1810	1.938585	AGAACAGGGGAACTCATCGA	58.061	50.000	0.00	0.00	0.00	3.59
1679	1811	2.257207	AGAACAGGGGAACTCATCGAA	58.743	47.619	0.00	0.00	0.00	3.71
1680	1812	2.234908	AGAACAGGGGAACTCATCGAAG	59.765	50.000	0.00	0.00	0.00	3.79
1681	1813	0.250513	ACAGGGGAACTCATCGAAGC	59.749	55.000	0.00	0.00	0.00	3.86
1682	1814	0.539051	CAGGGGAACTCATCGAAGCT	59.461	55.000	0.00	0.00	0.00	3.74
1683	1815	0.539051	AGGGGAACTCATCGAAGCTG	59.461	55.000	0.00	0.00	0.00	4.24
1684	1816	0.462759	GGGGAACTCATCGAAGCTGG	60.463	60.000	0.00	0.00	0.00	4.85
1685	1817	1.092345	GGGAACTCATCGAAGCTGGC	61.092	60.000	0.00	0.00	0.00	4.85
1686	1818	1.424493	GGAACTCATCGAAGCTGGCG	61.424	60.000	3.05	3.05	0.00	5.69
1687	1819	2.029904	GAACTCATCGAAGCTGGCGC	62.030	60.000	0.00	0.00	0.00	6.53
1688	1820	2.510012	CTCATCGAAGCTGGCGCA	60.510	61.111	10.83	0.00	39.10	6.09
1689	1821	2.806856	CTCATCGAAGCTGGCGCAC	61.807	63.158	10.83	0.00	39.10	5.34
1690	1822	4.214383	CATCGAAGCTGGCGCACG	62.214	66.667	10.83	0.00	39.10	5.34
1691	1823	4.435436	ATCGAAGCTGGCGCACGA	62.435	61.111	10.83	18.14	45.36	4.35
1702	1834	4.504916	CGCACGAGGCTCTCCTGG	62.505	72.222	13.50	0.00	44.46	4.45
1703	1835	3.071206	GCACGAGGCTCTCCTGGA	61.071	66.667	13.50	0.00	44.46	3.86
1704	1836	2.888863	CACGAGGCTCTCCTGGAC	59.111	66.667	13.50	0.00	44.46	4.02
2258	4470	4.194720	GCCGCGAGATCAGGACGT	62.195	66.667	8.23	0.00	0.00	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
834	855	2.913060	GAGACGATCTCCCCGGGG	60.913	72.222	35.80	35.80	37.55	5.73
880	901	0.107993	CACACCATGAGCAGATCGGT	60.108	55.000	0.00	0.00	0.00	4.69
941	962	3.045601	GCTTCTGTAGCTTGAAGACCA	57.954	47.619	20.60	0.00	46.77	4.02
992	1028	2.279517	GCCCGCTCATCTGGTACG	60.280	66.667	0.00	0.00	0.00	3.67
1033	1069	2.217038	TGTCGAAGGCCTTGGAGCT	61.217	57.895	28.42	0.22	0.00	4.09
1089	1125	1.676967	ACCAGGGTAGACGTCGTCC	60.677	63.158	21.40	18.99	32.18	4.79
1119	1164	1.428869	ACTTGTTCTGCTGGAGGACT	58.571	50.000	9.14	0.00	30.24	3.85
1135	1180	0.179045	GCATCGGCACAGGGATACTT	60.179	55.000	0.00	0.00	40.72	2.24
1174	1219	0.106167	ATCTCGATCTCGTGGGGGAA	60.106	55.000	0.00	0.00	40.80	3.97
1264	1315	4.030913	ACTGAAGCTGTTGGGTATAGCTA	58.969	43.478	0.00	0.00	46.34	3.32
1280	1341	2.084610	TGTGATGCCTCGAACTGAAG	57.915	50.000	0.00	0.00	0.00	3.02
1312	1377	7.254932	GCCTCTATGTAATGAACTGATGGAAAC	60.255	40.741	0.00	0.00	0.00	2.78
1330	1396	3.046390	GACGAATGACGAAGCCTCTATG	58.954	50.000	0.00	0.00	45.77	2.23
1337	1406	1.461127	AGCAAAGACGAATGACGAAGC	59.539	47.619	0.00	0.00	45.77	3.86
1348	1417	1.466167	CATTGACCAGGAGCAAAGACG	59.534	52.381	0.00	0.00	0.00	4.18
1376	1448	2.489971	ACCATCGACGACAACAACAAT	58.510	42.857	0.00	0.00	0.00	2.71
1390	1463	4.158384	GCATCTTACAACAACAACCATCG	58.842	43.478	0.00	0.00	0.00	3.84
1412	1500	7.362056	AAACTGGATATGGAACATTCAGTTTCG	60.362	37.037	13.50	0.00	45.11	3.46
1467	1590	8.648557	TCATATAGACGAAATGAGTTCCAAAG	57.351	34.615	0.00	0.00	31.99	2.77
1497	1620	7.071196	TGGTAGCATGGAGTCTAAATAGTTCAT	59.929	37.037	0.00	0.00	0.00	2.57
1539	1662	8.836268	AAAATCATACACACAATTCAAGCAAT	57.164	26.923	0.00	0.00	0.00	3.56
1540	1663	8.143193	AGAAAATCATACACACAATTCAAGCAA	58.857	29.630	0.00	0.00	0.00	3.91
1542	1665	7.007725	CGAGAAAATCATACACACAATTCAAGC	59.992	37.037	0.00	0.00	0.00	4.01
1543	1666	8.017373	ACGAGAAAATCATACACACAATTCAAG	58.983	33.333	0.00	0.00	0.00	3.02
1551	1678	9.262472	GAATTTACACGAGAAAATCATACACAC	57.738	33.333	0.00	0.00	0.00	3.82
1578	1705	9.878599	CGCGGAAAATATATAAAATCTGAAGTT	57.121	29.630	0.00	0.00	0.00	2.66
1592	1719	5.779922	ACTGAGAATAGCGCGGAAAATATA	58.220	37.500	8.83	0.00	0.00	0.86
1604	1736	3.849911	TGTGTGCACTACTGAGAATAGC	58.150	45.455	19.41	0.00	0.00	2.97
1610	1742	4.751600	TCAGAAATTGTGTGCACTACTGAG	59.248	41.667	19.41	0.20	0.00	3.35
1634	1766	5.297278	TCTTACGTGTTATGCAAACAAGGTT	59.703	36.000	21.50	11.17	34.66	3.50
1635	1767	4.817464	TCTTACGTGTTATGCAAACAAGGT	59.183	37.500	21.50	18.78	34.66	3.50
1636	1768	5.351233	TCTTACGTGTTATGCAAACAAGG	57.649	39.130	21.50	15.78	34.66	3.61
1637	1769	6.655062	TCTTCTTACGTGTTATGCAAACAAG	58.345	36.000	18.42	18.42	36.08	3.16
1638	1770	6.606234	TCTTCTTACGTGTTATGCAAACAA	57.394	33.333	13.58	0.00	31.20	2.83
1639	1771	6.037281	TGTTCTTCTTACGTGTTATGCAAACA	59.963	34.615	0.00	9.46	0.00	2.83
1640	1772	6.423862	TGTTCTTCTTACGTGTTATGCAAAC	58.576	36.000	0.00	0.00	0.00	2.93
1641	1773	6.293190	CCTGTTCTTCTTACGTGTTATGCAAA	60.293	38.462	0.00	0.00	0.00	3.68
1642	1774	5.178623	CCTGTTCTTCTTACGTGTTATGCAA	59.821	40.000	0.00	0.00	0.00	4.08
1643	1775	4.688879	CCTGTTCTTCTTACGTGTTATGCA	59.311	41.667	0.00	0.00	0.00	3.96
1644	1776	4.092968	CCCTGTTCTTCTTACGTGTTATGC	59.907	45.833	0.00	0.00	0.00	3.14
1645	1777	4.630069	CCCCTGTTCTTCTTACGTGTTATG	59.370	45.833	0.00	0.00	0.00	1.90
1646	1778	4.529377	TCCCCTGTTCTTCTTACGTGTTAT	59.471	41.667	0.00	0.00	0.00	1.89
1647	1779	3.896888	TCCCCTGTTCTTCTTACGTGTTA	59.103	43.478	0.00	0.00	0.00	2.41
1648	1780	2.701951	TCCCCTGTTCTTCTTACGTGTT	59.298	45.455	0.00	0.00	0.00	3.32
1649	1781	2.322658	TCCCCTGTTCTTCTTACGTGT	58.677	47.619	0.00	0.00	0.00	4.49
1650	1782	3.064931	GTTCCCCTGTTCTTCTTACGTG	58.935	50.000	0.00	0.00	0.00	4.49
1651	1783	2.970640	AGTTCCCCTGTTCTTCTTACGT	59.029	45.455	0.00	0.00	0.00	3.57
1652	1784	3.006537	TGAGTTCCCCTGTTCTTCTTACG	59.993	47.826	0.00	0.00	0.00	3.18
1653	1785	4.618920	TGAGTTCCCCTGTTCTTCTTAC	57.381	45.455	0.00	0.00	0.00	2.34
1654	1786	4.081642	CGATGAGTTCCCCTGTTCTTCTTA	60.082	45.833	0.00	0.00	0.00	2.10
1655	1787	3.307059	CGATGAGTTCCCCTGTTCTTCTT	60.307	47.826	0.00	0.00	0.00	2.52
1656	1788	2.234908	CGATGAGTTCCCCTGTTCTTCT	59.765	50.000	0.00	0.00	0.00	2.85
1657	1789	2.233922	TCGATGAGTTCCCCTGTTCTTC	59.766	50.000	0.00	0.00	0.00	2.87
1658	1790	2.257207	TCGATGAGTTCCCCTGTTCTT	58.743	47.619	0.00	0.00	0.00	2.52
1659	1791	1.938585	TCGATGAGTTCCCCTGTTCT	58.061	50.000	0.00	0.00	0.00	3.01
1660	1792	2.622436	CTTCGATGAGTTCCCCTGTTC	58.378	52.381	0.00	0.00	0.00	3.18
1661	1793	1.339151	GCTTCGATGAGTTCCCCTGTT	60.339	52.381	1.89	0.00	0.00	3.16
1662	1794	0.250513	GCTTCGATGAGTTCCCCTGT	59.749	55.000	1.89	0.00	0.00	4.00
1663	1795	0.539051	AGCTTCGATGAGTTCCCCTG	59.461	55.000	1.89	0.00	0.00	4.45
1664	1796	0.539051	CAGCTTCGATGAGTTCCCCT	59.461	55.000	1.89	0.00	0.00	4.79
1665	1797	0.462759	CCAGCTTCGATGAGTTCCCC	60.463	60.000	1.89	0.00	0.00	4.81
1666	1798	1.092345	GCCAGCTTCGATGAGTTCCC	61.092	60.000	1.89	0.00	0.00	3.97
1667	1799	1.424493	CGCCAGCTTCGATGAGTTCC	61.424	60.000	1.89	0.00	0.00	3.62
1668	1800	2.002127	CGCCAGCTTCGATGAGTTC	58.998	57.895	1.89	0.00	0.00	3.01
1669	1801	2.103042	GCGCCAGCTTCGATGAGTT	61.103	57.895	9.12	0.00	41.01	3.01
1670	1802	2.510238	GCGCCAGCTTCGATGAGT	60.510	61.111	9.12	0.00	41.01	3.41
1671	1803	2.510012	TGCGCCAGCTTCGATGAG	60.510	61.111	4.18	0.00	45.42	2.90
1672	1804	2.815211	GTGCGCCAGCTTCGATGA	60.815	61.111	4.18	0.00	45.42	2.92
1673	1805	4.214383	CGTGCGCCAGCTTCGATG	62.214	66.667	4.18	0.00	45.42	3.84
1674	1806	4.435436	TCGTGCGCCAGCTTCGAT	62.435	61.111	4.18	0.00	45.42	3.59
1685	1817	4.504916	CCAGGAGAGCCTCGTGCG	62.505	72.222	15.32	8.26	44.80	5.34
1686	1818	3.071206	TCCAGGAGAGCCTCGTGC	61.071	66.667	15.32	0.00	44.80	5.34
1687	1819	2.888863	GTCCAGGAGAGCCTCGTG	59.111	66.667	14.33	14.33	44.80	4.35
1688	1820	2.752238	CGTCCAGGAGAGCCTCGT	60.752	66.667	0.00	0.00	44.80	4.18
1689	1821	3.522731	CCGTCCAGGAGAGCCTCG	61.523	72.222	0.00	0.00	44.80	4.63
1690	1822	2.937959	ATCCCGTCCAGGAGAGCCTC	62.938	65.000	0.00	0.00	44.80	4.70
1692	1824	2.444895	ATCCCGTCCAGGAGAGCC	60.445	66.667	0.00	0.00	45.00	4.70
1693	1825	2.801631	CCATCCCGTCCAGGAGAGC	61.802	68.421	0.00	0.00	45.00	4.09
1694	1826	2.136878	CCCATCCCGTCCAGGAGAG	61.137	68.421	0.00	0.00	45.00	3.20
1695	1827	2.041922	CCCATCCCGTCCAGGAGA	60.042	66.667	0.00	0.00	45.00	3.71
1696	1828	3.866582	GCCCATCCCGTCCAGGAG	61.867	72.222	0.00	0.00	45.00	3.69
1967	4176	3.520317	TCTCTCCGTCTTCTCTAGTCCTT	59.480	47.826	0.00	0.00	0.00	3.36
1968	4177	3.109151	TCTCTCCGTCTTCTCTAGTCCT	58.891	50.000	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.