AutoCloner

Multiple sequence alignment - TraesCS6B01G266300

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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	TraesCS6B01G266300	chr6B	100.000	2318	0	0	1	2318	478884230	478881913	0.000000	4281.0
1	TraesCS6B01G266300	chr6B	89.630	810	75	8	1478	2281	706134433	706133627	0.000000	1022.0
2	TraesCS6B01G266300	chr6B	88.698	814	80	11	1476	2282	604708027	604707219	0.000000	983.0
3	TraesCS6B01G266300	chr6B	100.000	31	0	0	1433	1463	638492813	638492843	0.000090	58.4
4	TraesCS6B01G266300	chr6B	96.875	32	0	1	1435	1465	209247332	209247363	0.004000	52.8
5	TraesCS6B01G266300	chr1B	95.257	1286	53	4	1	1281	68936821	68938103	0.000000	2030.0
6	TraesCS6B01G266300	chr1B	92.074	1350	99	6	1	1344	533811575	533812922	0.000000	1893.0
7	TraesCS6B01G266300	chr1B	88.889	1350	139	8	4	1344	510814672	510813325	0.000000	1652.0
8	TraesCS6B01G266300	chr2B	92.719	1346	95	1	1	1343	115905329	115903984	0.000000	1940.0
9	TraesCS6B01G266300	chr2B	90.059	1348	124	9	4	1345	751294003	751292660	0.000000	1738.0
10	TraesCS6B01G266300	chr2B	91.981	823	59	4	1472	2289	801189326	801188506	0.000000	1147.0
11	TraesCS6B01G266300	chr2B	97.222	36	1	0	1433	1468	659027550	659027585	0.000007	62.1
12	TraesCS6B01G266300	chr7B	89.376	1346	136	6	4	1343	74304277	74302933	0.000000	1687.0
13	TraesCS6B01G266300	chr7D	87.829	1331	152	4	5	1331	205159894	205158570	0.000000	1552.0
14	TraesCS6B01G266300	chr7D	92.525	816	53	7	1476	2284	1104823	1105637	0.000000	1162.0
15	TraesCS6B01G266300	chr6A	87.537	1348	158	7	1	1343	511536374	511537716	0.000000	1550.0
16	TraesCS6B01G266300	chr6A	87.092	1348	164	7	1	1343	97342671	97341329	0.000000	1517.0
17	TraesCS6B01G266300	chr5D	90.764	812	69	5	1478	2284	545911614	545912424	0.000000	1079.0
18	TraesCS6B01G266300	chr5D	88.684	813	80	7	1476	2280	230013838	230014646	0.000000	981.0
19	TraesCS6B01G266300	chr3D	90.864	810	65	8	1486	2289	594543354	594542548	0.000000	1077.0
20	TraesCS6B01G266300	chr3D	100.000	31	0	0	1433	1463	530582960	530582930	0.000090	58.4
21	TraesCS6B01G266300	chr3B	89.655	812	74	7	1476	2282	3413080	3413886	0.000000	1026.0
22	TraesCS6B01G266300	chr5A	88.752	809	82	8	1477	2279	489841156	489841961	0.000000	981.0
23	TraesCS6B01G266300	chr2A	100.000	31	0	0	1435	1465	770247784	770247814	0.000090	58.4
24	TraesCS6B01G266300	chr1A	92.683	41	1	2	1435	1474	335992331	335992292	0.000090	58.4
25	TraesCS6B01G266300	chr4A	96.970	33	1	0	1435	1467	713372712	713372680	0.000322	56.5
26	TraesCS6B01G266300	chr5B	100.000	29	0	0	1435	1463	708847297	708847325	0.001000	54.7
27	TraesCS6B01G266300	chr5B	100.000	29	0	0	1435	1463	708859570	708859598	0.001000	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	TraesCS6B01G266300	chr6B	478881913	478884230	2317	True	4281	4281	100.000	1	2318	1	chr6B.!!$R1	2317
1	TraesCS6B01G266300	chr6B	706133627	706134433	806	True	1022	1022	89.630	1478	2281	1	chr6B.!!$R3	803
2	TraesCS6B01G266300	chr6B	604707219	604708027	808	True	983	983	88.698	1476	2282	1	chr6B.!!$R2	806
3	TraesCS6B01G266300	chr1B	68936821	68938103	1282	False	2030	2030	95.257	1	1281	1	chr1B.!!$F1	1280
4	TraesCS6B01G266300	chr1B	533811575	533812922	1347	False	1893	1893	92.074	1	1344	1	chr1B.!!$F2	1343
5	TraesCS6B01G266300	chr1B	510813325	510814672	1347	True	1652	1652	88.889	4	1344	1	chr1B.!!$R1	1340
6	TraesCS6B01G266300	chr2B	115903984	115905329	1345	True	1940	1940	92.719	1	1343	1	chr2B.!!$R1	1342
7	TraesCS6B01G266300	chr2B	751292660	751294003	1343	True	1738	1738	90.059	4	1345	1	chr2B.!!$R2	1341
8	TraesCS6B01G266300	chr2B	801188506	801189326	820	True	1147	1147	91.981	1472	2289	1	chr2B.!!$R3	817
9	TraesCS6B01G266300	chr7B	74302933	74304277	1344	True	1687	1687	89.376	4	1343	1	chr7B.!!$R1	1339
10	TraesCS6B01G266300	chr7D	205158570	205159894	1324	True	1552	1552	87.829	5	1331	1	chr7D.!!$R1	1326
11	TraesCS6B01G266300	chr7D	1104823	1105637	814	False	1162	1162	92.525	1476	2284	1	chr7D.!!$F1	808
12	TraesCS6B01G266300	chr6A	511536374	511537716	1342	False	1550	1550	87.537	1	1343	1	chr6A.!!$F1	1342
13	TraesCS6B01G266300	chr6A	97341329	97342671	1342	True	1517	1517	87.092	1	1343	1	chr6A.!!$R1	1342
14	TraesCS6B01G266300	chr5D	545911614	545912424	810	False	1079	1079	90.764	1478	2284	1	chr5D.!!$F2	806
15	TraesCS6B01G266300	chr5D	230013838	230014646	808	False	981	981	88.684	1476	2280	1	chr5D.!!$F1	804
16	TraesCS6B01G266300	chr3D	594542548	594543354	806	True	1077	1077	90.864	1486	2289	1	chr3D.!!$R2	803
17	TraesCS6B01G266300	chr3B	3413080	3413886	806	False	1026	1026	89.655	1476	2282	1	chr3B.!!$F1	806
18	TraesCS6B01G266300	chr5A	489841156	489841961	805	False	981	981	88.752	1477	2279	1	chr5A.!!$F1	802

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
101	103	0.396695	AATCATGCTTGGCTGAGGGG	60.397	55.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1370	1380	0.174845	TTGAACGCTAGATCCCCACG	59.825	55.0	0.0	0.0	0.0	4.94	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
101	103	0.396695	AATCATGCTTGGCTGAGGGG	60.397	55.000	0.00	0.00	0.00	4.79
252	254	6.038492	TGGCTACACATGATCATAATGTTGTG	59.962	38.462	22.95	20.89	36.10	3.33
264	266	1.750193	ATGTTGTGACGGCTAATGGG	58.250	50.000	0.00	0.00	0.00	4.00
275	277	1.348036	GGCTAATGGGGCTTCGAGTAT	59.652	52.381	0.00	0.00	0.00	2.12
282	284	1.887707	GGCTTCGAGTATTGCCCCG	60.888	63.158	0.00	0.00	39.49	5.73
367	369	0.607620	TGCATGGAGATGTGTGACGA	59.392	50.000	0.00	0.00	31.50	4.20
478	483	4.701651	TCCATGCCTTGATAACTTGTTCAG	59.298	41.667	0.00	0.00	0.00	3.02
1071	1080	1.801178	CAAACGGACTCTTCTGAAGCC	59.199	52.381	12.54	7.41	31.76	4.35
1087	1096	2.758736	AGCCTTGTCTAGCTTGACAG	57.241	50.000	25.99	18.49	46.02	3.51
1258	1267	2.555547	GCTGTTTGGCTTGGCTCGT	61.556	57.895	0.00	0.00	0.00	4.18
1336	1346	0.323957	AACTCCCTTTACCCTCGCAC	59.676	55.000	0.00	0.00	0.00	5.34
1362	1372	5.895636	AAAGACGTTGGAATTATGCATCA	57.104	34.783	0.19	0.00	0.00	3.07
1363	1373	4.882671	AGACGTTGGAATTATGCATCAC	57.117	40.909	0.19	0.00	0.00	3.06
1364	1374	4.260985	AGACGTTGGAATTATGCATCACA	58.739	39.130	0.19	0.00	0.00	3.58
1365	1375	4.094887	AGACGTTGGAATTATGCATCACAC	59.905	41.667	0.19	0.00	0.00	3.82
1366	1376	3.755905	ACGTTGGAATTATGCATCACACA	59.244	39.130	0.19	0.00	0.00	3.72
1367	1377	4.097714	CGTTGGAATTATGCATCACACAC	58.902	43.478	0.19	0.00	0.00	3.82
1368	1378	4.379290	CGTTGGAATTATGCATCACACACA	60.379	41.667	0.19	0.00	0.00	3.72
1369	1379	5.653507	GTTGGAATTATGCATCACACACAT	58.346	37.500	0.19	0.00	0.00	3.21
1370	1380	5.503662	TGGAATTATGCATCACACACATC	57.496	39.130	0.19	0.00	0.00	3.06
1371	1381	4.035441	TGGAATTATGCATCACACACATCG	59.965	41.667	0.19	0.00	0.00	3.84
1372	1382	4.035558	GGAATTATGCATCACACACATCGT	59.964	41.667	0.19	0.00	0.00	3.73
1382	1392	2.515926	CACACATCGTGGGGATCTAG	57.484	55.000	0.00	0.00	42.34	2.43
1383	1393	0.753262	ACACATCGTGGGGATCTAGC	59.247	55.000	0.00	0.00	37.94	3.42
1384	1394	0.319040	CACATCGTGGGGATCTAGCG	60.319	60.000	0.00	0.00	31.28	4.26
1385	1395	0.755698	ACATCGTGGGGATCTAGCGT	60.756	55.000	0.00	0.00	31.28	5.07
1386	1396	0.389391	CATCGTGGGGATCTAGCGTT	59.611	55.000	0.00	0.00	31.28	4.84
1387	1397	0.674534	ATCGTGGGGATCTAGCGTTC	59.325	55.000	0.00	0.00	0.00	3.95
1388	1398	0.681887	TCGTGGGGATCTAGCGTTCA	60.682	55.000	0.00	0.00	0.00	3.18
1389	1399	0.174845	CGTGGGGATCTAGCGTTCAA	59.825	55.000	0.00	0.00	0.00	2.69
1390	1400	1.653151	GTGGGGATCTAGCGTTCAAC	58.347	55.000	0.00	0.00	0.00	3.18
1391	1401	1.066430	GTGGGGATCTAGCGTTCAACA	60.066	52.381	0.00	0.00	0.00	3.33
1392	1402	1.626321	TGGGGATCTAGCGTTCAACAA	59.374	47.619	0.00	0.00	0.00	2.83
1393	1403	2.007608	GGGGATCTAGCGTTCAACAAC	58.992	52.381	0.00	0.00	0.00	3.32
1394	1404	2.614481	GGGGATCTAGCGTTCAACAACA	60.614	50.000	0.00	0.00	32.14	3.33
1395	1405	3.270877	GGGATCTAGCGTTCAACAACAT	58.729	45.455	0.00	0.00	32.14	2.71
1396	1406	4.439057	GGGATCTAGCGTTCAACAACATA	58.561	43.478	0.00	0.00	32.14	2.29
1397	1407	5.057149	GGGATCTAGCGTTCAACAACATAT	58.943	41.667	0.00	0.00	32.14	1.78
1398	1408	6.220930	GGGATCTAGCGTTCAACAACATATA	58.779	40.000	0.00	0.00	32.14	0.86
1399	1409	6.704493	GGGATCTAGCGTTCAACAACATATAA	59.296	38.462	0.00	0.00	32.14	0.98
1400	1410	7.307219	GGGATCTAGCGTTCAACAACATATAAC	60.307	40.741	0.00	0.00	32.14	1.89
1401	1411	7.223971	GGATCTAGCGTTCAACAACATATAACA	59.776	37.037	0.00	0.00	32.14	2.41
1402	1412	7.285783	TCTAGCGTTCAACAACATATAACAC	57.714	36.000	0.00	0.00	32.14	3.32
1403	1413	5.933187	AGCGTTCAACAACATATAACACA	57.067	34.783	0.00	0.00	32.14	3.72
1404	1414	6.494893	AGCGTTCAACAACATATAACACAT	57.505	33.333	0.00	0.00	32.14	3.21
1405	1415	7.603963	AGCGTTCAACAACATATAACACATA	57.396	32.000	0.00	0.00	32.14	2.29
1406	1416	8.035165	AGCGTTCAACAACATATAACACATAA	57.965	30.769	0.00	0.00	32.14	1.90
1407	1417	8.673711	AGCGTTCAACAACATATAACACATAAT	58.326	29.630	0.00	0.00	32.14	1.28
1408	1418	8.733128	GCGTTCAACAACATATAACACATAATG	58.267	33.333	0.00	0.00	32.14	1.90
1409	1419	9.980780	CGTTCAACAACATATAACACATAATGA	57.019	29.630	0.00	0.00	32.14	2.57
1422	1432	9.896645	ATAACACATAATGAGAGATGTCAAAGT	57.103	29.630	0.00	0.00	34.01	2.66
1424	1434	8.939201	ACACATAATGAGAGATGTCAAAGTAG	57.061	34.615	0.00	0.00	34.01	2.57
1425	1435	8.535335	ACACATAATGAGAGATGTCAAAGTAGT	58.465	33.333	0.00	0.00	34.01	2.73
1426	1436	9.376075	CACATAATGAGAGATGTCAAAGTAGTT	57.624	33.333	0.00	0.00	34.01	2.24
1427	1437	9.376075	ACATAATGAGAGATGTCAAAGTAGTTG	57.624	33.333	0.00	0.00	38.71	3.16
1428	1438	9.376075	CATAATGAGAGATGTCAAAGTAGTTGT	57.624	33.333	0.00	0.00	38.47	3.32
1431	1441	9.950496	AATGAGAGATGTCAAAGTAGTTGTAAT	57.050	29.630	0.00	0.00	38.47	1.89
1432	1442	9.950496	ATGAGAGATGTCAAAGTAGTTGTAATT	57.050	29.630	0.00	0.00	38.47	1.40
1433	1443	9.424319	TGAGAGATGTCAAAGTAGTTGTAATTC	57.576	33.333	0.00	0.00	38.47	2.17
1434	1444	9.424319	GAGAGATGTCAAAGTAGTTGTAATTCA	57.576	33.333	0.00	0.00	38.47	2.57
1435	1445	9.950496	AGAGATGTCAAAGTAGTTGTAATTCAT	57.050	29.630	0.00	0.00	38.47	2.57
1438	1448	9.478019	GATGTCAAAGTAGTTGTAATTCATTCG	57.522	33.333	0.00	0.00	38.47	3.34
1439	1449	8.373048	TGTCAAAGTAGTTGTAATTCATTCGT	57.627	30.769	0.00	0.00	38.47	3.85
1440	1450	8.279800	TGTCAAAGTAGTTGTAATTCATTCGTG	58.720	33.333	0.00	0.00	38.47	4.35
1441	1451	7.268447	GTCAAAGTAGTTGTAATTCATTCGTGC	59.732	37.037	0.00	0.00	38.47	5.34
1442	1452	5.450376	AGTAGTTGTAATTCATTCGTGCG	57.550	39.130	0.00	0.00	0.00	5.34
1443	1453	4.927425	AGTAGTTGTAATTCATTCGTGCGT	59.073	37.500	0.00	0.00	0.00	5.24
1444	1454	4.742438	AGTTGTAATTCATTCGTGCGTT	57.258	36.364	0.00	0.00	0.00	4.84
1445	1455	4.463209	AGTTGTAATTCATTCGTGCGTTG	58.537	39.130	0.00	0.00	0.00	4.10
1446	1456	2.845486	TGTAATTCATTCGTGCGTTGC	58.155	42.857	0.00	0.00	0.00	4.17
1447	1457	2.224314	TGTAATTCATTCGTGCGTTGCA	59.776	40.909	0.00	0.00	35.60	4.08
1462	1472	3.850923	GCACGTGCACGCTTACTA	58.149	55.556	37.35	0.00	44.43	1.82
1463	1473	2.146954	GCACGTGCACGCTTACTAA	58.853	52.632	37.35	0.00	44.43	2.24
1464	1474	0.719465	GCACGTGCACGCTTACTAAT	59.281	50.000	37.35	14.16	44.43	1.73
1465	1475	1.526986	GCACGTGCACGCTTACTAATG	60.527	52.381	37.35	25.31	44.43	1.90
1466	1476	1.724623	CACGTGCACGCTTACTAATGT	59.275	47.619	37.35	12.57	44.43	2.71
1467	1477	2.918600	CACGTGCACGCTTACTAATGTA	59.081	45.455	37.35	0.00	44.43	2.29
1468	1478	3.550275	CACGTGCACGCTTACTAATGTAT	59.450	43.478	37.35	11.79	44.43	2.29
1469	1479	4.032445	CACGTGCACGCTTACTAATGTATT	59.968	41.667	37.35	11.31	44.43	1.89
1470	1480	4.628333	ACGTGCACGCTTACTAATGTATTT	59.372	37.500	37.35	10.61	44.43	1.40
1471	1481	5.806502	ACGTGCACGCTTACTAATGTATTTA	59.193	36.000	37.35	0.00	44.43	1.40
1472	1482	6.310956	ACGTGCACGCTTACTAATGTATTTAA	59.689	34.615	37.35	0.00	44.43	1.52
1473	1483	7.148606	ACGTGCACGCTTACTAATGTATTTAAA	60.149	33.333	37.35	0.00	44.43	1.52
1474	1484	7.688989	CGTGCACGCTTACTAATGTATTTAAAA	59.311	33.333	28.16	0.00	0.00	1.52
1528	1538	3.361158	CAAATCCGCCCACACGCA	61.361	61.111	0.00	0.00	0.00	5.24
1545	1556	7.090808	CCACACGCATATAACATACAGACTAT	58.909	38.462	0.00	0.00	0.00	2.12
1582	1594	4.247258	TGCATGCATGTGGAAATCTTTTC	58.753	39.130	26.79	6.83	0.00	2.29
1650	1663	4.083537	CGATTGAAGATCCGTTTTCACCAA	60.084	41.667	0.00	0.00	33.36	3.67
1975	2000	8.845413	TGCCATTATCAAAAACTAAAATTGCT	57.155	26.923	0.00	0.00	0.00	3.91
1999	2024	7.746475	GCTACATGACAACTTTAGTTTAAGCAG	59.254	37.037	0.00	0.00	35.83	4.24
2020	2045	6.151648	AGCAGCATGACAACTACAATGTAAAT	59.848	34.615	0.00	0.00	39.69	1.40
2073	2100	4.749976	TCGTCGAAACATATCAACATGGA	58.250	39.130	0.00	0.00	0.00	3.41
2074	2101	5.172205	TCGTCGAAACATATCAACATGGAA	58.828	37.500	0.00	0.00	0.00	3.53
2076	2103	6.315144	TCGTCGAAACATATCAACATGGAATT	59.685	34.615	0.00	0.00	0.00	2.17
2118	2145	7.390440	TGTCGAGACAGATTTAATGGTGAAAAT	59.610	33.333	1.24	0.00	36.21	1.82
2120	2147	7.390440	TCGAGACAGATTTAATGGTGAAAATGT	59.610	33.333	0.00	0.00	0.00	2.71
2217	2245	7.713073	TGTCATCTATTCATACGTGGCAAAATA	59.287	33.333	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	11	1.374343	CCTTCGGAGTGATCGGACGA	61.374	60.000	0.00	0.00	0.00	4.20
101	103	1.134946	CATCCATCGGCCAAAAGAACC	59.865	52.381	2.24	0.00	0.00	3.62
252	254	1.887707	CGAAGCCCCATTAGCCGTC	60.888	63.158	0.00	0.00	0.00	4.79
264	266	1.887707	CGGGGCAATACTCGAAGCC	60.888	63.158	0.00	0.00	46.28	4.35
282	284	4.091939	CCCGAACGGTTCCCTCCC	62.092	72.222	14.83	0.00	0.00	4.30
367	369	4.357918	AACTCTGTGTTGCCATAGTTCT	57.642	40.909	0.00	0.00	37.52	3.01
478	483	1.446099	TCCAGAGCGTTCGTGCATC	60.446	57.895	0.00	0.00	37.31	3.91
592	597	2.698855	AGCAGCATATCTTGGACGTT	57.301	45.000	0.00	0.00	0.00	3.99
960	965	0.464373	CCAGCGGGTCATTGCAGTAT	60.464	55.000	0.00	0.00	0.00	2.12
1071	1080	4.270566	GCATCATCTGTCAAGCTAGACAAG	59.729	45.833	0.00	0.00	46.90	3.16
1087	1096	2.029728	CCGAACGAAGAAGTGCATCATC	59.970	50.000	0.00	0.00	0.00	2.92
1258	1267	4.837093	AATCCTCGATACAAGGTGGAAA	57.163	40.909	0.00	0.00	35.29	3.13
1345	1355	4.097714	GTGTGTGATGCATAATTCCAACG	58.902	43.478	0.00	0.00	0.00	4.10
1346	1356	5.058149	TGTGTGTGATGCATAATTCCAAC	57.942	39.130	0.00	0.00	0.00	3.77
1347	1357	5.448904	CGATGTGTGTGATGCATAATTCCAA	60.449	40.000	0.00	0.00	0.00	3.53
1348	1358	4.035441	CGATGTGTGTGATGCATAATTCCA	59.965	41.667	0.00	0.00	0.00	3.53
1349	1359	4.035558	ACGATGTGTGTGATGCATAATTCC	59.964	41.667	0.00	0.00	0.00	3.01
1350	1360	4.965762	CACGATGTGTGTGATGCATAATTC	59.034	41.667	0.00	0.00	43.88	2.17
1351	1361	4.912214	CACGATGTGTGTGATGCATAATT	58.088	39.130	0.00	0.00	43.88	1.40
1352	1362	4.541085	CACGATGTGTGTGATGCATAAT	57.459	40.909	0.00	0.00	43.88	1.28
1364	1374	0.753262	GCTAGATCCCCACGATGTGT	59.247	55.000	0.00	0.00	0.00	3.72
1365	1375	0.319040	CGCTAGATCCCCACGATGTG	60.319	60.000	0.00	0.00	0.00	3.21
1366	1376	0.755698	ACGCTAGATCCCCACGATGT	60.756	55.000	0.00	0.00	0.00	3.06
1367	1377	0.389391	AACGCTAGATCCCCACGATG	59.611	55.000	0.00	0.00	0.00	3.84
1368	1378	0.674534	GAACGCTAGATCCCCACGAT	59.325	55.000	0.00	0.00	0.00	3.73
1369	1379	0.681887	TGAACGCTAGATCCCCACGA	60.682	55.000	0.00	0.00	0.00	4.35
1370	1380	0.174845	TTGAACGCTAGATCCCCACG	59.825	55.000	0.00	0.00	0.00	4.94
1371	1381	1.066430	TGTTGAACGCTAGATCCCCAC	60.066	52.381	0.00	0.00	0.00	4.61
1372	1382	1.271856	TGTTGAACGCTAGATCCCCA	58.728	50.000	0.00	0.00	0.00	4.96
1373	1383	2.007608	GTTGTTGAACGCTAGATCCCC	58.992	52.381	0.00	0.00	0.00	4.81
1374	1384	2.695359	TGTTGTTGAACGCTAGATCCC	58.305	47.619	0.00	0.00	34.49	3.85
1375	1385	7.223971	TGTTATATGTTGTTGAACGCTAGATCC	59.776	37.037	0.00	0.00	34.49	3.36
1376	1386	8.056571	GTGTTATATGTTGTTGAACGCTAGATC	58.943	37.037	0.00	0.00	34.49	2.75
1377	1387	7.547722	TGTGTTATATGTTGTTGAACGCTAGAT	59.452	33.333	0.00	0.00	34.49	1.98
1378	1388	6.869388	TGTGTTATATGTTGTTGAACGCTAGA	59.131	34.615	0.00	0.00	34.49	2.43
1379	1389	7.056002	TGTGTTATATGTTGTTGAACGCTAG	57.944	36.000	0.00	0.00	34.49	3.42
1380	1390	7.603963	ATGTGTTATATGTTGTTGAACGCTA	57.396	32.000	0.00	0.00	34.49	4.26
1381	1391	5.933187	TGTGTTATATGTTGTTGAACGCT	57.067	34.783	0.00	0.00	34.49	5.07
1382	1392	8.733128	CATTATGTGTTATATGTTGTTGAACGC	58.267	33.333	0.00	0.00	34.49	4.84
1383	1393	9.980780	TCATTATGTGTTATATGTTGTTGAACG	57.019	29.630	0.00	0.00	34.49	3.95
1396	1406	9.896645	ACTTTGACATCTCTCATTATGTGTTAT	57.103	29.630	0.00	0.00	36.48	1.89
1398	1408	9.376075	CTACTTTGACATCTCTCATTATGTGTT	57.624	33.333	0.00	0.00	36.48	3.32
1399	1409	8.535335	ACTACTTTGACATCTCTCATTATGTGT	58.465	33.333	0.00	0.00	36.48	3.72
1400	1410	8.939201	ACTACTTTGACATCTCTCATTATGTG	57.061	34.615	0.00	0.00	36.48	3.21
1401	1411	9.376075	CAACTACTTTGACATCTCTCATTATGT	57.624	33.333	0.00	0.00	39.00	2.29
1402	1412	9.376075	ACAACTACTTTGACATCTCTCATTATG	57.624	33.333	0.00	0.00	38.73	1.90
1405	1415	9.950496	ATTACAACTACTTTGACATCTCTCATT	57.050	29.630	0.00	0.00	38.73	2.57
1406	1416	9.950496	AATTACAACTACTTTGACATCTCTCAT	57.050	29.630	0.00	0.00	38.73	2.90
1407	1417	9.424319	GAATTACAACTACTTTGACATCTCTCA	57.576	33.333	0.00	0.00	38.73	3.27
1408	1418	9.424319	TGAATTACAACTACTTTGACATCTCTC	57.576	33.333	0.00	0.00	38.73	3.20
1409	1419	9.950496	ATGAATTACAACTACTTTGACATCTCT	57.050	29.630	0.00	0.00	38.73	3.10
1412	1422	9.478019	CGAATGAATTACAACTACTTTGACATC	57.522	33.333	0.00	0.00	38.73	3.06
1413	1423	8.999431	ACGAATGAATTACAACTACTTTGACAT	58.001	29.630	0.00	0.00	38.73	3.06
1414	1424	8.279800	CACGAATGAATTACAACTACTTTGACA	58.720	33.333	0.00	0.00	38.73	3.58
1415	1425	7.268447	GCACGAATGAATTACAACTACTTTGAC	59.732	37.037	0.00	0.00	38.73	3.18
1416	1426	7.295201	GCACGAATGAATTACAACTACTTTGA	58.705	34.615	0.00	0.00	38.73	2.69
1417	1427	6.246332	CGCACGAATGAATTACAACTACTTTG	59.754	38.462	0.00	0.00	41.49	2.77
1418	1428	6.073440	ACGCACGAATGAATTACAACTACTTT	60.073	34.615	0.00	0.00	0.00	2.66
1419	1429	5.407387	ACGCACGAATGAATTACAACTACTT	59.593	36.000	0.00	0.00	0.00	2.24
1420	1430	4.927425	ACGCACGAATGAATTACAACTACT	59.073	37.500	0.00	0.00	0.00	2.57
1421	1431	5.199424	ACGCACGAATGAATTACAACTAC	57.801	39.130	0.00	0.00	0.00	2.73
1422	1432	5.613812	CAACGCACGAATGAATTACAACTA	58.386	37.500	0.00	0.00	0.00	2.24
1423	1433	4.463209	CAACGCACGAATGAATTACAACT	58.537	39.130	0.00	0.00	0.00	3.16
1424	1434	3.057609	GCAACGCACGAATGAATTACAAC	59.942	43.478	0.00	0.00	0.00	3.32
1425	1435	3.230355	GCAACGCACGAATGAATTACAA	58.770	40.909	0.00	0.00	0.00	2.41
1426	1436	2.224314	TGCAACGCACGAATGAATTACA	59.776	40.909	0.00	0.00	31.71	2.41
1427	1437	2.845486	TGCAACGCACGAATGAATTAC	58.155	42.857	0.00	0.00	31.71	1.89
1445	1455	0.719465	ATTAGTAAGCGTGCACGTGC	59.281	50.000	36.80	33.11	42.22	5.34
1446	1456	1.724623	ACATTAGTAAGCGTGCACGTG	59.275	47.619	36.80	26.41	42.22	4.49
1447	1457	2.074547	ACATTAGTAAGCGTGCACGT	57.925	45.000	36.80	22.79	42.22	4.49
1448	1458	4.772046	AATACATTAGTAAGCGTGCACG	57.228	40.909	34.01	34.01	36.71	5.34
1449	1459	8.883789	TTTTAAATACATTAGTAAGCGTGCAC	57.116	30.769	6.82	6.82	33.13	4.57
1464	1474	8.382130	CGTTAGCGTTGTCCTATTTTAAATACA	58.618	33.333	0.00	0.00	0.00	2.29
1465	1475	7.371615	GCGTTAGCGTTGTCCTATTTTAAATAC	59.628	37.037	0.00	0.00	40.81	1.89
1466	1476	7.401080	GCGTTAGCGTTGTCCTATTTTAAATA	58.599	34.615	0.00	0.00	40.81	1.40
1467	1477	6.253013	GCGTTAGCGTTGTCCTATTTTAAAT	58.747	36.000	0.00	0.00	40.81	1.40
1468	1478	5.620467	GCGTTAGCGTTGTCCTATTTTAAA	58.380	37.500	0.00	0.00	40.81	1.52
1469	1479	5.207305	GCGTTAGCGTTGTCCTATTTTAA	57.793	39.130	0.00	0.00	40.81	1.52
1470	1480	4.845621	GCGTTAGCGTTGTCCTATTTTA	57.154	40.909	0.00	0.00	40.81	1.52
1471	1481	3.734776	GCGTTAGCGTTGTCCTATTTT	57.265	42.857	0.00	0.00	40.81	1.82
1528	1538	8.815912	TGACATGGCATAGTCTGTATGTTATAT	58.184	33.333	21.94	0.00	35.97	0.86
1545	1556	3.442167	GCATGCGGTGACATGGCA	61.442	61.111	0.00	0.00	46.14	4.92
1615	1627	6.634436	CGGATCTTCAATCGGATTTTTCATTC	59.366	38.462	0.00	0.00	0.00	2.67
1844	1864	2.362077	GGTGCATGACAAGTCTGGTTTT	59.638	45.455	0.00	0.00	0.00	2.43
1849	1869	4.456911	AGTTTATGGTGCATGACAAGTCTG	59.543	41.667	0.00	0.00	0.00	3.51
1857	1877	6.105333	GGCAATTTTAGTTTATGGTGCATGA	58.895	36.000	0.00	0.00	32.41	3.07
1948	1971	9.328721	GCAATTTTAGTTTTTGATAATGGCAAC	57.671	29.630	0.00	0.00	0.00	4.17
1975	2000	7.227711	TGCTGCTTAAACTAAAGTTGTCATGTA	59.772	33.333	0.00	0.00	38.44	2.29
2020	2045	5.465532	TTTGCTCAAAAGTTGCCATGATA	57.534	34.783	0.00	0.00	0.00	2.15
2049	2076	5.815222	TCCATGTTGATATGTTTCGACGAAT	59.185	36.000	11.71	0.00	33.42	3.34
2073	2100	9.273016	TCTCGACAAGATCTTCAAAACTAAATT	57.727	29.630	4.57	0.00	0.00	1.82
2074	2101	8.713271	GTCTCGACAAGATCTTCAAAACTAAAT	58.287	33.333	4.57	0.00	36.11	1.40
2076	2103	7.207383	TGTCTCGACAAGATCTTCAAAACTAA	58.793	34.615	4.57	0.00	38.56	2.24
2217	2245	1.003355	CACGCCTCCATCACCACTT	60.003	57.895	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.