AutoCloner

Multiple sequence alignment - TraesCS6D01G208600

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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	TraesCS6D01G208600	chr6D	100.000	2243	0	0	1	2243	294410116	294412358	0.000000e+00	4143.0
1	TraesCS6D01G208600	chr6D	83.721	129	15	5	1429	1555	143411189	143411313	1.410000e-22	117.0
2	TraesCS6D01G208600	chr5B	93.483	1335	78	6	1	1331	273883989	273885318	0.000000e+00	1975.0
3	TraesCS6D01G208600	chr1B	82.349	1354	221	15	1	1348	359905718	359904377	0.000000e+00	1160.0
4	TraesCS6D01G208600	chr1B	94.569	313	15	2	1037	1348	644361412	644361101	1.200000e-132	483.0
5	TraesCS6D01G208600	chr1B	92.135	267	17	4	1431	1694	658534575	658534840	7.560000e-100	374.0
6	TraesCS6D01G208600	chr1B	90.417	240	17	3	1782	2021	658534982	658535215	6.020000e-81	311.0
7	TraesCS6D01G208600	chr1B	94.203	138	8	0	2074	2211	658535213	658535350	6.280000e-51	211.0
8	TraesCS6D01G208600	chr2B	82.169	1346	221	18	11	1349	395736558	395735225	0.000000e+00	1138.0
9	TraesCS6D01G208600	chr2B	83.465	127	15	5	1431	1555	30626616	30626738	1.820000e-21	113.0
10	TraesCS6D01G208600	chr1A	81.278	1346	234	15	11	1348	372114452	372115787	0.000000e+00	1074.0
11	TraesCS6D01G208600	chr1A	92.398	342	23	3	999	1340	16439312	16438974	3.350000e-133	484.0
12	TraesCS6D01G208600	chr1A	96.875	32	0	1	2094	2124	271848310	271848279	4.000000e-03	52.8
13	TraesCS6D01G208600	chr5A	81.797	1269	218	6	2	1258	444045270	444046537	0.000000e+00	1051.0
14	TraesCS6D01G208600	chr5A	82.132	319	36	9	1431	1733	641526700	641527013	1.030000e-63	254.0
15	TraesCS6D01G208600	chr5A	80.982	326	38	9	1426	1733	553466559	553466240	1.040000e-58	237.0
16	TraesCS6D01G208600	chr4A	80.343	1343	237	14	11	1348	88498803	88500123	0.000000e+00	992.0
17	TraesCS6D01G208600	chr4A	82.203	708	109	16	647	1348	547981492	547980796	5.330000e-166	593.0
18	TraesCS6D01G208600	chr3D	79.399	1131	214	14	223	1349	590085859	590084744	0.000000e+00	780.0
19	TraesCS6D01G208600	chr3B	79.373	1149	192	24	209	1348	414839641	414840753	0.000000e+00	767.0
20	TraesCS6D01G208600	chr3B	83.465	127	14	6	1431	1555	214032742	214032621	6.550000e-21	111.0
21	TraesCS6D01G208600	chr3A	81.859	893	146	14	11	897	171226527	171225645	0.000000e+00	737.0
22	TraesCS6D01G208600	chr7A	81.525	682	126	0	11	692	109369498	109368817	1.500000e-156	562.0
23	TraesCS6D01G208600	chr7B	96.393	305	8	2	1728	2029	727666408	727666104	1.200000e-137	499.0
24	TraesCS6D01G208600	chr7B	94.389	303	16	1	1431	1733	727666802	727666501	4.360000e-127	464.0
25	TraesCS6D01G208600	chr7B	82.249	338	58	2	1008	1345	67810745	67811080	7.840000e-75	291.0
26	TraesCS6D01G208600	chr7B	96.154	156	6	0	2057	2212	727666112	727665957	2.860000e-64	255.0
27	TraesCS6D01G208600	chr7B	74.370	476	83	21	904	1348	297375928	297376395	1.380000e-37	167.0
28	TraesCS6D01G208600	chr4D	82.194	556	90	9	797	1348	384968740	384968190	9.380000e-129	470.0
29	TraesCS6D01G208600	chr4D	80.417	240	29	13	1115	1352	416072525	416072302	1.380000e-37	167.0
30	TraesCS6D01G208600	chrUn	94.194	155	9	0	2057	2211	28289774	28289928	1.040000e-58	237.0
31	TraesCS6D01G208600	chrUn	87.963	108	4	6	1728	1827	28289510	28289616	3.910000e-23	119.0
32	TraesCS6D01G208600	chr6B	80.878	319	39	10	1431	1733	25991216	25990904	4.820000e-57	231.0
33	TraesCS6D01G208600	chr6B	86.207	116	10	2	1429	1542	682536287	682536176	1.090000e-23	121.0
34	TraesCS6D01G208600	chr5D	76.140	285	34	21	1428	1686	291767300	291767576	3.910000e-23	119.0
35	TraesCS6D01G208600	chr6A	94.444	72	4	0	1359	1430	455646971	455646900	6.550000e-21	111.0
36	TraesCS6D01G208600	chr6A	94.444	72	4	0	1359	1430	455654119	455654048	6.550000e-21	111.0
37	TraesCS6D01G208600	chr6A	96.875	32	1	0	2212	2243	455646907	455646876	1.000000e-03	54.7
38	TraesCS6D01G208600	chr6A	96.875	32	1	0	2212	2243	455654055	455654024	1.000000e-03	54.7

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	TraesCS6D01G208600	chr6D	294410116	294412358	2242	False	4143.000000	4143	100.000000	1	2243	1	chr6D.!!$F2	2242
1	TraesCS6D01G208600	chr5B	273883989	273885318	1329	False	1975.000000	1975	93.483000	1	1331	1	chr5B.!!$F1	1330
2	TraesCS6D01G208600	chr1B	359904377	359905718	1341	True	1160.000000	1160	82.349000	1	1348	1	chr1B.!!$R1	1347
3	TraesCS6D01G208600	chr1B	658534575	658535350	775	False	298.666667	374	92.251667	1431	2211	3	chr1B.!!$F1	780
4	TraesCS6D01G208600	chr2B	395735225	395736558	1333	True	1138.000000	1138	82.169000	11	1349	1	chr2B.!!$R1	1338
5	TraesCS6D01G208600	chr1A	372114452	372115787	1335	False	1074.000000	1074	81.278000	11	1348	1	chr1A.!!$F1	1337
6	TraesCS6D01G208600	chr5A	444045270	444046537	1267	False	1051.000000	1051	81.797000	2	1258	1	chr5A.!!$F1	1256
7	TraesCS6D01G208600	chr4A	88498803	88500123	1320	False	992.000000	992	80.343000	11	1348	1	chr4A.!!$F1	1337
8	TraesCS6D01G208600	chr4A	547980796	547981492	696	True	593.000000	593	82.203000	647	1348	1	chr4A.!!$R1	701
9	TraesCS6D01G208600	chr3D	590084744	590085859	1115	True	780.000000	780	79.399000	223	1349	1	chr3D.!!$R1	1126
10	TraesCS6D01G208600	chr3B	414839641	414840753	1112	False	767.000000	767	79.373000	209	1348	1	chr3B.!!$F1	1139
11	TraesCS6D01G208600	chr3A	171225645	171226527	882	True	737.000000	737	81.859000	11	897	1	chr3A.!!$R1	886
12	TraesCS6D01G208600	chr7A	109368817	109369498	681	True	562.000000	562	81.525000	11	692	1	chr7A.!!$R1	681
13	TraesCS6D01G208600	chr7B	727665957	727666802	845	True	406.000000	499	95.645333	1431	2212	3	chr7B.!!$R1	781
14	TraesCS6D01G208600	chr4D	384968190	384968740	550	True	470.000000	470	82.194000	797	1348	1	chr4D.!!$R1	551

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
265	266	0.031616	AAAACAGTTTGGGGGCCTCA	60.032	50.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1272	1291	0.095762	GTTTTAACGACATCCCCGCG	59.904	55.0	0.0	0.0	0.0	6.46	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
174	175	0.767375	TTGACAGGCTGAGGAAAGCT	59.233	50.000	23.66	0.00	43.06	3.74
182	183	3.587506	AGGCTGAGGAAAGCTTACCTTTA	59.412	43.478	0.00	0.00	43.64	1.85
189	190	2.130272	AAGCTTACCTTTAGGCTGGC	57.870	50.000	0.00	0.00	39.65	4.85
265	266	0.031616	AAAACAGTTTGGGGGCCTCA	60.032	50.000	0.00	0.00	0.00	3.86
394	395	4.009675	CAAGGAAGATCGGGACATTTTCA	58.990	43.478	0.00	0.00	0.00	2.69
449	450	2.573009	CCAAGGCCAAATTCTGGGAATT	59.427	45.455	5.01	0.31	46.54	2.17
521	522	5.048013	TCGAGCTATCAAGAAAGAAGTGTGA	60.048	40.000	0.00	0.00	0.00	3.58
643	645	4.433615	GAACAGGCTCTCGAATGTCAATA	58.566	43.478	0.00	0.00	0.00	1.90
731	733	3.828451	ACAGCCTACTTGATGCAATTTGT	59.172	39.130	0.00	0.00	0.00	2.83
751	753	1.265236	TGGCCATGTTCAATCCAACC	58.735	50.000	0.00	0.00	0.00	3.77
819	836	0.669619	TTGCATGCTTGGTCACACAG	59.330	50.000	20.33	0.00	0.00	3.66
1052	1069	0.112412	GGGGTCCTCACCAACAATGT	59.888	55.000	0.00	0.00	45.94	2.71
1234	1251	4.493547	ACATTTGTGTAATTTGATGCCGG	58.506	39.130	0.00	0.00	0.00	6.13
1251	1268	2.957006	GCCGGGAGAGTAGATCTTTGTA	59.043	50.000	2.18	0.00	38.84	2.41
1259	1276	9.674068	GGGAGAGTAGATCTTTGTAAATTTTCT	57.326	33.333	0.00	0.00	38.84	2.52
1272	1291	5.974751	TGTAAATTTTCTCAGTTTTCACGGC	59.025	36.000	0.00	0.00	0.00	5.68
1332	1352	7.804843	TCAATGAAAATGGCAAATCTTTTGT	57.195	28.000	1.54	0.00	0.00	2.83
1340	1360	5.759506	TGGCAAATCTTTTGTCTCGTTTA	57.240	34.783	6.20	0.00	0.00	2.01
1365	1385	5.367945	AAAAACTCTACCTGTCCTTGTCA	57.632	39.130	0.00	0.00	0.00	3.58
1366	1386	4.608948	AAACTCTACCTGTCCTTGTCAG	57.391	45.455	0.00	0.00	0.00	3.51
1367	1387	3.246416	ACTCTACCTGTCCTTGTCAGT	57.754	47.619	0.00	0.00	0.00	3.41
1368	1388	2.894126	ACTCTACCTGTCCTTGTCAGTG	59.106	50.000	0.00	0.00	0.00	3.66
1369	1389	1.618837	TCTACCTGTCCTTGTCAGTGC	59.381	52.381	0.00	0.00	0.00	4.40
1370	1390	0.317160	TACCTGTCCTTGTCAGTGCG	59.683	55.000	0.00	0.00	0.00	5.34
1371	1391	1.069765	CCTGTCCTTGTCAGTGCGT	59.930	57.895	0.00	0.00	0.00	5.24
1372	1392	0.317160	CCTGTCCTTGTCAGTGCGTA	59.683	55.000	0.00	0.00	0.00	4.42
1373	1393	1.419374	CTGTCCTTGTCAGTGCGTAC	58.581	55.000	0.00	0.00	0.00	3.67
1374	1394	0.747852	TGTCCTTGTCAGTGCGTACA	59.252	50.000	6.38	0.00	0.00	2.90
1375	1395	1.137282	TGTCCTTGTCAGTGCGTACAA	59.863	47.619	6.38	0.00	34.57	2.41
1380	1400	3.897325	CTTGTCAGTGCGTACAAGTAGA	58.103	45.455	6.38	0.00	44.83	2.59
1381	1401	3.994204	TGTCAGTGCGTACAAGTAGAA	57.006	42.857	6.38	0.00	0.00	2.10
1382	1402	3.635331	TGTCAGTGCGTACAAGTAGAAC	58.365	45.455	6.38	0.00	0.00	3.01
1383	1403	3.067040	TGTCAGTGCGTACAAGTAGAACA	59.933	43.478	6.38	0.00	0.00	3.18
1384	1404	4.046462	GTCAGTGCGTACAAGTAGAACAA	58.954	43.478	6.38	0.00	0.00	2.83
1385	1405	4.046462	TCAGTGCGTACAAGTAGAACAAC	58.954	43.478	6.38	0.00	0.00	3.32
1386	1406	3.183775	CAGTGCGTACAAGTAGAACAACC	59.816	47.826	6.38	0.00	0.00	3.77
1387	1407	2.154389	GTGCGTACAAGTAGAACAACCG	59.846	50.000	0.00	0.00	0.00	4.44
1388	1408	1.125566	GCGTACAAGTAGAACAACCGC	59.874	52.381	0.00	0.00	0.00	5.68
1389	1409	2.396601	CGTACAAGTAGAACAACCGCA	58.603	47.619	0.00	0.00	0.00	5.69
1390	1410	2.154389	CGTACAAGTAGAACAACCGCAC	59.846	50.000	0.00	0.00	0.00	5.34
1391	1411	2.319136	ACAAGTAGAACAACCGCACA	57.681	45.000	0.00	0.00	0.00	4.57
1392	1412	2.846193	ACAAGTAGAACAACCGCACAT	58.154	42.857	0.00	0.00	0.00	3.21
1393	1413	2.548057	ACAAGTAGAACAACCGCACATG	59.452	45.455	0.00	0.00	0.00	3.21
1394	1414	1.156736	AGTAGAACAACCGCACATGC	58.843	50.000	0.00	0.00	37.78	4.06
1395	1415	0.871722	GTAGAACAACCGCACATGCA	59.128	50.000	4.49	0.00	42.21	3.96
1396	1416	0.871722	TAGAACAACCGCACATGCAC	59.128	50.000	4.49	0.00	42.21	4.57
1397	1417	1.371635	GAACAACCGCACATGCACC	60.372	57.895	4.49	0.00	42.21	5.01
1398	1418	3.192954	AACAACCGCACATGCACCG	62.193	57.895	4.49	0.00	42.21	4.94
1399	1419	4.403137	CAACCGCACATGCACCGG	62.403	66.667	15.22	15.22	46.97	5.28
1400	1420	4.634703	AACCGCACATGCACCGGA	62.635	61.111	21.45	0.00	44.55	5.14
1401	1421	4.634703	ACCGCACATGCACCGGAA	62.635	61.111	21.45	0.00	44.55	4.30
1402	1422	3.361158	CCGCACATGCACCGGAAA	61.361	61.111	9.46	0.00	44.55	3.13
1403	1423	2.126888	CGCACATGCACCGGAAAC	60.127	61.111	9.46	0.00	42.21	2.78
1404	1424	2.902419	CGCACATGCACCGGAAACA	61.902	57.895	9.46	2.78	42.21	2.83
1405	1425	1.586028	GCACATGCACCGGAAACAT	59.414	52.632	9.46	5.52	41.59	2.71
1406	1426	0.456653	GCACATGCACCGGAAACATC	60.457	55.000	9.46	0.00	41.59	3.06
1407	1427	0.880441	CACATGCACCGGAAACATCA	59.120	50.000	9.46	0.00	0.00	3.07
1408	1428	0.881118	ACATGCACCGGAAACATCAC	59.119	50.000	9.46	0.00	0.00	3.06
1409	1429	0.880441	CATGCACCGGAAACATCACA	59.120	50.000	9.46	0.00	0.00	3.58
1410	1430	1.269174	CATGCACCGGAAACATCACAA	59.731	47.619	9.46	0.00	0.00	3.33
1411	1431	0.950836	TGCACCGGAAACATCACAAG	59.049	50.000	9.46	0.00	0.00	3.16
1412	1432	0.387239	GCACCGGAAACATCACAAGC	60.387	55.000	9.46	0.00	0.00	4.01
1413	1433	1.238439	CACCGGAAACATCACAAGCT	58.762	50.000	9.46	0.00	0.00	3.74
1414	1434	1.069022	CACCGGAAACATCACAAGCTG	60.069	52.381	9.46	0.00	0.00	4.24
1415	1435	1.238439	CCGGAAACATCACAAGCTGT	58.762	50.000	0.00	0.00	0.00	4.40
1416	1436	2.224426	ACCGGAAACATCACAAGCTGTA	60.224	45.455	9.46	0.00	0.00	2.74
1417	1437	3.009723	CCGGAAACATCACAAGCTGTAT	58.990	45.455	0.00	0.00	0.00	2.29
1418	1438	4.188462	CCGGAAACATCACAAGCTGTATA	58.812	43.478	0.00	0.00	0.00	1.47
1419	1439	4.271049	CCGGAAACATCACAAGCTGTATAG	59.729	45.833	0.00	0.00	0.00	1.31
1515	1535	0.250901	CACACCTACTGCTTTGGCCT	60.251	55.000	3.32	0.00	37.74	5.19
1603	1625	8.891720	CAAGAGGAAGATAAATTGAGGAAAGAG	58.108	37.037	0.00	0.00	0.00	2.85
1613	1635	4.514781	TTGAGGAAAGAGAACGATTCGA	57.485	40.909	13.95	0.00	34.02	3.71
1706	1728	0.317160	TCGATCGCAATCCCGCTATT	59.683	50.000	11.09	0.00	0.00	1.73
1982	2105	3.979347	ACAGATCTGGGGATAAAGCAGAT	59.021	43.478	26.08	0.00	35.57	2.90
2121	2244	7.826918	ACTACTTGGCCAGTTAATTTTGTTA	57.173	32.000	5.11	0.00	36.88	2.41
2160	2283	2.409152	TCGTGGTTTGGATTTTTCGC	57.591	45.000	0.00	0.00	0.00	4.70
2178	2301	2.429610	TCGCTTCCTTTATAAGTCCGCT	59.570	45.455	0.00	0.00	0.00	5.52
2195	2318	2.081462	CGCTCCGGGTAACTTCAAATT	58.919	47.619	0.00	0.00	0.00	1.82
2203	2326	5.186198	CGGGTAACTTCAAATTCTGGATCT	58.814	41.667	0.00	0.00	0.00	2.75
2212	2335	3.726557	AATTCTGGATCTGCCACTGAA	57.273	42.857	0.00	0.00	43.33	3.02
2213	2336	3.947612	ATTCTGGATCTGCCACTGAAT	57.052	42.857	0.00	0.00	43.33	2.57
2214	2337	5.378230	AATTCTGGATCTGCCACTGAATA	57.622	39.130	0.00	0.00	43.33	1.75
2215	2338	3.827008	TCTGGATCTGCCACTGAATAC	57.173	47.619	0.00	0.00	43.33	1.89
2216	2339	3.378512	TCTGGATCTGCCACTGAATACT	58.621	45.455	0.00	0.00	43.33	2.12
2217	2340	3.386078	TCTGGATCTGCCACTGAATACTC	59.614	47.826	0.00	0.00	43.33	2.59
2218	2341	2.435805	TGGATCTGCCACTGAATACTCC	59.564	50.000	0.00	0.00	43.33	3.85
2219	2342	2.703007	GGATCTGCCACTGAATACTCCT	59.297	50.000	0.00	0.00	36.34	3.69
2220	2343	3.898123	GGATCTGCCACTGAATACTCCTA	59.102	47.826	0.00	0.00	36.34	2.94
2221	2344	4.262249	GGATCTGCCACTGAATACTCCTAC	60.262	50.000	0.00	0.00	36.34	3.18
2222	2345	3.031736	TCTGCCACTGAATACTCCTACC	58.968	50.000	0.00	0.00	0.00	3.18
2223	2346	2.766263	CTGCCACTGAATACTCCTACCA	59.234	50.000	0.00	0.00	0.00	3.25
2224	2347	3.178046	TGCCACTGAATACTCCTACCAA	58.822	45.455	0.00	0.00	0.00	3.67
2225	2348	3.780294	TGCCACTGAATACTCCTACCAAT	59.220	43.478	0.00	0.00	0.00	3.16
2226	2349	4.141711	TGCCACTGAATACTCCTACCAATC	60.142	45.833	0.00	0.00	0.00	2.67
2227	2350	4.141711	GCCACTGAATACTCCTACCAATCA	60.142	45.833	0.00	0.00	0.00	2.57
2228	2351	5.455326	GCCACTGAATACTCCTACCAATCAT	60.455	44.000	0.00	0.00	0.00	2.45
2229	2352	6.239600	GCCACTGAATACTCCTACCAATCATA	60.240	42.308	0.00	0.00	0.00	2.15
2230	2353	7.527868	GCCACTGAATACTCCTACCAATCATAT	60.528	40.741	0.00	0.00	0.00	1.78
2231	2354	8.037758	CCACTGAATACTCCTACCAATCATATC	58.962	40.741	0.00	0.00	0.00	1.63
2232	2355	8.811017	CACTGAATACTCCTACCAATCATATCT	58.189	37.037	0.00	0.00	0.00	1.98
2233	2356	8.811017	ACTGAATACTCCTACCAATCATATCTG	58.189	37.037	0.00	0.00	0.00	2.90
2234	2357	8.956446	TGAATACTCCTACCAATCATATCTGA	57.044	34.615	0.00	0.00	35.41	3.27
2235	2358	9.552695	TGAATACTCCTACCAATCATATCTGAT	57.447	33.333	0.00	0.00	44.14	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
174	175	1.982226	TCAGTGCCAGCCTAAAGGTAA	59.018	47.619	0.00	0.00	37.57	2.85
182	183	4.320456	CGGTGTCAGTGCCAGCCT	62.320	66.667	0.00	0.00	0.00	4.58
265	266	6.105333	CGAACTTCTTCAGATTGAGGATTCT	58.895	40.000	0.00	0.00	32.38	2.40
394	395	4.643387	GACCTTGGTGGCAGCCGT	62.643	66.667	14.97	7.54	40.22	5.68
449	450	0.676184	GATGCCATCTAGCCACGAGA	59.324	55.000	0.00	0.00	0.00	4.04
521	522	1.228245	ATGGCCGAAGCAACAGTGT	60.228	52.632	0.00	0.00	42.56	3.55
657	659	2.286826	CCAGAGAATGGTGTCCGGA	58.713	57.895	0.00	0.00	44.91	5.14
731	733	1.622811	GGTTGGATTGAACATGGCCAA	59.377	47.619	10.96	0.74	36.35	4.52
807	824	5.114780	CAGATCCTATTCTGTGTGACCAAG	58.885	45.833	0.00	0.00	38.64	3.61
819	836	0.038159	CCGCCGTCCAGATCCTATTC	60.038	60.000	0.00	0.00	0.00	1.75
966	983	0.807667	CGACATCTAGGTGCAGCCAC	60.808	60.000	13.29	0.00	40.61	5.01
1172	1189	4.283212	CCCATAGAGAAGCCTCCTCTTTAG	59.717	50.000	5.60	0.00	41.00	1.85
1176	1193	1.761009	GCCCATAGAGAAGCCTCCTCT	60.761	57.143	0.00	0.00	42.97	3.69
1251	1268	4.041723	CGCCGTGAAAACTGAGAAAATTT	58.958	39.130	0.00	0.00	0.00	1.82
1259	1276	3.342627	CCGCGCCGTGAAAACTGA	61.343	61.111	0.00	0.00	0.00	3.41
1272	1291	0.095762	GTTTTAACGACATCCCCGCG	59.904	55.000	0.00	0.00	0.00	6.46
1349	1369	1.618837	GCACTGACAAGGACAGGTAGA	59.381	52.381	0.00	0.00	39.38	2.59
1351	1371	0.317160	CGCACTGACAAGGACAGGTA	59.683	55.000	0.00	0.00	39.38	3.08
1352	1372	1.069765	CGCACTGACAAGGACAGGT	59.930	57.895	0.00	0.00	39.38	4.00
1353	1373	0.317160	TACGCACTGACAAGGACAGG	59.683	55.000	0.00	0.00	39.38	4.00
1354	1374	1.269569	TGTACGCACTGACAAGGACAG	60.270	52.381	0.00	0.00	40.68	3.51
1355	1375	0.747852	TGTACGCACTGACAAGGACA	59.252	50.000	0.00	0.00	0.00	4.02
1356	1376	1.792949	CTTGTACGCACTGACAAGGAC	59.207	52.381	6.83	0.00	45.76	3.85
1357	1377	2.148916	CTTGTACGCACTGACAAGGA	57.851	50.000	6.83	0.00	45.76	3.36
1360	1380	3.994204	TCTACTTGTACGCACTGACAA	57.006	42.857	0.00	0.00	34.49	3.18
1361	1381	3.067040	TGTTCTACTTGTACGCACTGACA	59.933	43.478	0.00	0.00	0.00	3.58
1362	1382	3.635331	TGTTCTACTTGTACGCACTGAC	58.365	45.455	0.00	0.00	0.00	3.51
1363	1383	3.994204	TGTTCTACTTGTACGCACTGA	57.006	42.857	0.00	0.00	0.00	3.41
1364	1384	3.183775	GGTTGTTCTACTTGTACGCACTG	59.816	47.826	0.00	0.00	0.00	3.66
1365	1385	3.387397	GGTTGTTCTACTTGTACGCACT	58.613	45.455	0.00	0.00	0.00	4.40
1366	1386	2.154389	CGGTTGTTCTACTTGTACGCAC	59.846	50.000	0.00	0.00	0.00	5.34
1367	1387	2.396601	CGGTTGTTCTACTTGTACGCA	58.603	47.619	0.00	0.00	0.00	5.24
1368	1388	1.125566	GCGGTTGTTCTACTTGTACGC	59.874	52.381	0.00	0.00	37.66	4.42
1369	1389	2.154389	GTGCGGTTGTTCTACTTGTACG	59.846	50.000	0.00	0.00	0.00	3.67
1370	1390	3.125316	TGTGCGGTTGTTCTACTTGTAC	58.875	45.455	0.00	0.00	0.00	2.90
1371	1391	3.455990	TGTGCGGTTGTTCTACTTGTA	57.544	42.857	0.00	0.00	0.00	2.41
1372	1392	2.319136	TGTGCGGTTGTTCTACTTGT	57.681	45.000	0.00	0.00	0.00	3.16
1373	1393	2.665519	GCATGTGCGGTTGTTCTACTTG	60.666	50.000	0.00	0.00	0.00	3.16
1374	1394	1.535462	GCATGTGCGGTTGTTCTACTT	59.465	47.619	0.00	0.00	0.00	2.24
1375	1395	1.156736	GCATGTGCGGTTGTTCTACT	58.843	50.000	0.00	0.00	0.00	2.57
1376	1396	0.871722	TGCATGTGCGGTTGTTCTAC	59.128	50.000	0.01	0.00	45.83	2.59
1377	1397	0.871722	GTGCATGTGCGGTTGTTCTA	59.128	50.000	0.00	0.00	45.83	2.10
1378	1398	1.654220	GTGCATGTGCGGTTGTTCT	59.346	52.632	0.00	0.00	45.83	3.01
1379	1399	1.371635	GGTGCATGTGCGGTTGTTC	60.372	57.895	0.00	0.00	45.83	3.18
1380	1400	2.727544	GGTGCATGTGCGGTTGTT	59.272	55.556	0.00	0.00	45.83	2.83
1381	1401	3.659092	CGGTGCATGTGCGGTTGT	61.659	61.111	0.00	0.00	45.83	3.32
1382	1402	4.403137	CCGGTGCATGTGCGGTTG	62.403	66.667	0.00	0.00	45.83	3.77
1383	1403	4.634703	TCCGGTGCATGTGCGGTT	62.635	61.111	0.00	0.00	45.83	4.44
1384	1404	4.634703	TTCCGGTGCATGTGCGGT	62.635	61.111	0.00	0.00	45.83	5.68
1385	1405	3.361158	TTTCCGGTGCATGTGCGG	61.361	61.111	0.00	0.00	45.83	5.69
1386	1406	2.126888	GTTTCCGGTGCATGTGCG	60.127	61.111	0.00	0.00	45.83	5.34
1387	1407	0.456653	GATGTTTCCGGTGCATGTGC	60.457	55.000	0.00	0.00	42.50	4.57
1388	1408	0.880441	TGATGTTTCCGGTGCATGTG	59.120	50.000	0.00	0.00	0.00	3.21
1389	1409	0.881118	GTGATGTTTCCGGTGCATGT	59.119	50.000	0.00	0.00	0.00	3.21
1390	1410	0.880441	TGTGATGTTTCCGGTGCATG	59.120	50.000	0.00	0.00	0.00	4.06
1391	1411	1.541147	CTTGTGATGTTTCCGGTGCAT	59.459	47.619	0.00	4.51	0.00	3.96
1392	1412	0.950836	CTTGTGATGTTTCCGGTGCA	59.049	50.000	0.00	0.00	0.00	4.57
1393	1413	0.387239	GCTTGTGATGTTTCCGGTGC	60.387	55.000	0.00	0.00	0.00	5.01
1394	1414	1.069022	CAGCTTGTGATGTTTCCGGTG	60.069	52.381	0.00	0.00	0.00	4.94
1395	1415	1.238439	CAGCTTGTGATGTTTCCGGT	58.762	50.000	0.00	0.00	0.00	5.28
1396	1416	1.238439	ACAGCTTGTGATGTTTCCGG	58.762	50.000	0.00	0.00	40.18	5.14
1397	1417	4.260375	GCTATACAGCTTGTGATGTTTCCG	60.260	45.833	0.00	0.00	40.18	4.30
1398	1418	5.162000	GCTATACAGCTTGTGATGTTTCC	57.838	43.478	0.00	0.00	40.18	3.13
1411	1431	7.775600	CCCCTGGGAGTATTTGCTATACAGC	62.776	52.000	16.20	0.00	42.46	4.40
1412	1432	4.263068	CCCCTGGGAGTATTTGCTATACAG	60.263	50.000	16.20	0.00	37.50	2.74
1413	1433	3.650942	CCCCTGGGAGTATTTGCTATACA	59.349	47.826	16.20	0.00	37.50	2.29
1414	1434	3.559384	GCCCCTGGGAGTATTTGCTATAC	60.559	52.174	16.20	2.47	37.50	1.47
1415	1435	2.642807	GCCCCTGGGAGTATTTGCTATA	59.357	50.000	16.20	0.00	37.50	1.31
1416	1436	1.425448	GCCCCTGGGAGTATTTGCTAT	59.575	52.381	16.20	0.00	37.50	2.97
1417	1437	0.843984	GCCCCTGGGAGTATTTGCTA	59.156	55.000	16.20	0.00	37.50	3.49
1418	1438	1.615262	GCCCCTGGGAGTATTTGCT	59.385	57.895	16.20	0.00	37.50	3.91
1419	1439	1.823899	CGCCCCTGGGAGTATTTGC	60.824	63.158	16.20	6.02	37.50	3.68
1420	1440	1.152963	CCGCCCCTGGGAGTATTTG	60.153	63.158	16.20	0.00	37.50	2.32
1421	1441	3.056754	GCCGCCCCTGGGAGTATTT	62.057	63.158	16.20	0.00	37.50	1.40
1422	1442	3.489513	GCCGCCCCTGGGAGTATT	61.490	66.667	16.20	0.00	37.50	1.89
1574	1596	7.502060	TCCTCAATTTATCTTCCTCTTGACT	57.498	36.000	0.00	0.00	0.00	3.41
1589	1611	5.932303	TCGAATCGTTCTCTTTCCTCAATTT	59.068	36.000	1.52	0.00	0.00	1.82
1603	1625	4.681942	CCATCTGACCTTATCGAATCGTTC	59.318	45.833	1.52	0.00	0.00	3.95
1613	1635	2.785269	TGATTGGCCCATCTGACCTTAT	59.215	45.455	17.19	0.00	0.00	1.73
1947	2070	5.130145	CCCCAGATCTGTAATCTTCAAGTCT	59.870	44.000	21.11	0.00	0.00	3.24
2121	2244	6.753279	CCACGATGCAATCAAAGAATACAATT	59.247	34.615	0.00	0.00	45.97	2.32
2160	2283	3.381949	CGGAGCGGACTTATAAAGGAAG	58.618	50.000	0.00	0.00	0.00	3.46
2178	2301	3.328343	TCCAGAATTTGAAGTTACCCGGA	59.672	43.478	0.73	0.00	0.00	5.14
2203	2326	2.827755	TGGTAGGAGTATTCAGTGGCA	58.172	47.619	0.00	0.00	0.00	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.