AutoCloner

Multiple sequence alignment - TraesCS6A01G206400

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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	TraesCS6A01G206400	chr6A	100.000	2347	0	0	1	2347	364043415	364041069	0.000000e+00	4335
1	TraesCS6A01G206400	chr6A	89.979	469	42	5	1881	2347	435195661	435195196	3.340000e-168	601
2	TraesCS6A01G206400	chr5D	93.632	1382	74	6	1	1380	173675811	173677180	0.000000e+00	2052
3	TraesCS6A01G206400	chr4A	87.482	1398	141	19	1	1383	368218799	368220177	0.000000e+00	1581
4	TraesCS6A01G206400	chr4A	90.812	468	40	3	1881	2347	456354425	456354890	7.120000e-175	623
5	TraesCS6A01G206400	chr4A	90.598	468	41	3	1881	2347	495551242	495551707	3.310000e-173	617
6	TraesCS6A01G206400	chr4A	89.957	468	44	3	1881	2347	457593989	457594454	3.340000e-168	601
7	TraesCS6A01G206400	chr4A	89.930	427	41	2	1575	1999	535316815	535316389	1.230000e-152	549
8	TraesCS6A01G206400	chr1B	91.216	1036	75	13	324	1356	522168150	522167128	0.000000e+00	1395
9	TraesCS6A01G206400	chr1B	91.185	329	26	1	1	329	522177243	522176918	5.950000e-121	444
10	TraesCS6A01G206400	chr6D	90.745	832	63	8	1466	2293	427645500	427646321	0.000000e+00	1098
11	TraesCS6A01G206400	chr7D	91.276	768	62	5	1573	2338	594503115	594502351	0.000000e+00	1042
12	TraesCS6A01G206400	chr3D	91.074	773	66	3	1567	2338	315453349	315452579	0.000000e+00	1042
13	TraesCS6A01G206400	chr3D	89.562	479	41	6	1860	2335	85611869	85611397	1.200000e-167	599
14	TraesCS6A01G206400	chr5B	88.918	776	81	5	1572	2345	10953780	10954552	0.000000e+00	952
15	TraesCS6A01G206400	chr3A	91.335	427	35	2	1575	1999	114737690	114737264	1.210000e-162	582
16	TraesCS6A01G206400	chr3A	85.390	308	42	2	220	525	385312721	385313027	1.350000e-82	316
17	TraesCS6A01G206400	chr3A	78.857	175	29	7	1123	1290	125750991	125750818	6.860000e-21	111
18	TraesCS6A01G206400	chr1A	91.101	427	36	2	1575	1999	34052674	34052248	5.620000e-161	577
19	TraesCS6A01G206400	chr1A	90.152	132	11	2	1	130	533538833	533538702	1.120000e-38	171
20	TraesCS6A01G206400	chr7A	89.977	429	39	3	1575	1999	213538988	213538560	3.410000e-153	551
21	TraesCS6A01G206400	chr5A	89.930	427	41	2	1575	1999	138652917	138652491	1.230000e-152	549
22	TraesCS6A01G206400	chr2D	89.437	142	11	3	1466	1607	86470473	86470336	2.400000e-40	176
23	TraesCS6A01G206400	chr4D	88.194	144	10	4	1466	1607	421227062	421226924	5.190000e-37	165
24	TraesCS6A01G206400	chr7B	90.400	125	7	3	1489	1612	467632369	467632249	2.410000e-35	159
25	TraesCS6A01G206400	chr7B	89.600	125	8	3	1489	1612	467610119	467609999	1.120000e-33	154
26	TraesCS6A01G206400	chr7B	88.889	126	8	4	1489	1612	467724840	467724719	1.450000e-32	150
27	TraesCS6A01G206400	chr7B	88.800	125	9	3	1489	1612	467654414	467654294	5.230000e-32	148
28	TraesCS6A01G206400	chr3B	87.302	126	10	5	1489	1612	462006696	462006575	3.150000e-29	139
29	TraesCS6A01G206400	chr2B	84.028	144	17	4	1466	1607	361077273	361077134	1.460000e-27	134

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	TraesCS6A01G206400	chr6A	364041069	364043415	2346	True	4335	4335	100.000	1	2347	1	chr6A.!!$R1	2346
1	TraesCS6A01G206400	chr5D	173675811	173677180	1369	False	2052	2052	93.632	1	1380	1	chr5D.!!$F1	1379
2	TraesCS6A01G206400	chr4A	368218799	368220177	1378	False	1581	1581	87.482	1	1383	1	chr4A.!!$F1	1382
3	TraesCS6A01G206400	chr1B	522167128	522168150	1022	True	1395	1395	91.216	324	1356	1	chr1B.!!$R1	1032
4	TraesCS6A01G206400	chr6D	427645500	427646321	821	False	1098	1098	90.745	1466	2293	1	chr6D.!!$F1	827
5	TraesCS6A01G206400	chr7D	594502351	594503115	764	True	1042	1042	91.276	1573	2338	1	chr7D.!!$R1	765
6	TraesCS6A01G206400	chr3D	315452579	315453349	770	True	1042	1042	91.074	1567	2338	1	chr3D.!!$R2	771
7	TraesCS6A01G206400	chr5B	10953780	10954552	772	False	952	952	88.918	1572	2345	1	chr5B.!!$F1	773

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
982	998	0.601558	GGAGCTAGTCGTGGTGAACA	59.398	55.0	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2091	2114	1.002315	GTAAACAGGGTCGTAAGGGCA	59.998	52.381	0.0	0.0	38.47	5.36	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
127	128	4.992951	TCTCTCATTCATCCATGCGTTATG	59.007	41.667	0.00	0.00	36.50	1.90
131	132	4.639755	TCATTCATCCATGCGTTATGTTGT	59.360	37.500	0.00	0.00	34.87	3.32
201	202	3.009115	AGTAGGCCATGGCGGTGT	61.009	61.111	29.90	16.55	43.06	4.16
214	215	1.675310	CGGTGTGTGGTGGCATGAT	60.675	57.895	0.00	0.00	0.00	2.45
215	216	1.885157	GGTGTGTGGTGGCATGATG	59.115	57.895	0.00	0.00	0.00	3.07
222	223	4.580044	GTGGCATGATGCGTCGCG	62.580	66.667	13.38	0.00	46.21	5.87
240	241	2.893404	GTGGCGTGTGTTGACGGT	60.893	61.111	0.00	0.00	39.81	4.83
253	259	1.906824	GACGGTGACCAGACCAGGA	60.907	63.158	1.11	0.00	35.50	3.86
295	301	3.976704	CAGGTCCCTGCATGGTTAA	57.023	52.632	7.98	0.00	37.24	2.01
298	304	3.099141	CAGGTCCCTGCATGGTTAATTT	58.901	45.455	7.98	0.00	37.24	1.82
326	332	1.526575	AAAACAGCCTGCATGACCCG	61.527	55.000	0.00	0.00	0.00	5.28
334	340	2.274232	CTGCATGACCCGTTGCCATG	62.274	60.000	0.00	0.00	40.29	3.66
408	414	6.790285	ACATTTCCAAAAATAGCAAAGCTG	57.210	33.333	1.04	0.00	40.10	4.24
459	465	7.693952	ACTATCACAATTGTACCAATAAAGCG	58.306	34.615	11.53	0.00	0.00	4.68
526	532	3.260884	GGATGAGGTTGTGGTGTCTTCTA	59.739	47.826	0.00	0.00	0.00	2.10
595	604	7.609146	ACTTGATTGATGAACAGTATCACATGT	59.391	33.333	0.00	0.00	34.50	3.21
715	724	2.286772	GCGTTCCAAAATCAACACTCGT	60.287	45.455	0.00	0.00	0.00	4.18
770	779	1.174783	GAAGTAGTCGGAGCAGTCCA	58.825	55.000	0.00	0.00	44.18	4.02
831	846	3.151022	GAGCAGGAGGGAGGACGG	61.151	72.222	0.00	0.00	0.00	4.79
915	931	1.755783	CCTGGATGGCTGGGCTTTC	60.756	63.158	0.00	0.00	0.00	2.62
937	953	2.846371	GCTGAAGCGGTGAACATCT	58.154	52.632	0.00	0.00	0.00	2.90
969	985	2.263540	GTTGAACGGCCGGAGCTA	59.736	61.111	31.76	12.05	39.73	3.32
982	998	0.601558	GGAGCTAGTCGTGGTGAACA	59.398	55.000	0.00	0.00	0.00	3.18
1135	1152	1.002134	CACCTGGATCCACGGCTTT	60.002	57.895	22.89	7.69	0.00	3.51
1197	1214	0.249398	AATTACAGGAGGCGTCGCTT	59.751	50.000	18.11	9.97	0.00	4.68
1203	1220	0.754217	AGGAGGCGTCGCTTGGTATA	60.754	55.000	18.11	0.00	0.00	1.47
1204	1221	0.103572	GGAGGCGTCGCTTGGTATAA	59.896	55.000	18.11	0.00	0.00	0.98
1205	1222	1.270147	GGAGGCGTCGCTTGGTATAAT	60.270	52.381	18.11	0.00	0.00	1.28
1246	1263	2.124695	GACCAAGGTGGATCGGGC	60.125	66.667	0.18	0.00	40.96	6.13
1260	1277	2.589157	CGGGCCAGAGGTGGTGTTA	61.589	63.158	4.39	0.00	46.96	2.41
1322	1339	4.329545	TGTGGCGGCAGGAGGAAC	62.330	66.667	13.91	0.00	0.00	3.62
1356	1373	2.438434	GGGAGTGATGTTGGGGCG	60.438	66.667	0.00	0.00	0.00	6.13
1431	1448	4.372999	GGGGCAGGCTCAGGCTTT	62.373	66.667	0.00	0.00	35.88	3.51
1432	1449	2.283460	GGGCAGGCTCAGGCTTTT	60.283	61.111	0.00	0.00	35.88	2.27
1433	1450	1.910276	GGGCAGGCTCAGGCTTTTT	60.910	57.895	0.00	0.00	35.88	1.94
1453	1470	5.554437	TTTTAAATGGGTCCAGGAAAACC	57.446	39.130	0.00	0.00	34.64	3.27
1454	1471	4.479156	TTAAATGGGTCCAGGAAAACCT	57.521	40.909	0.00	0.00	35.78	3.50
1455	1472	2.604912	AATGGGTCCAGGAAAACCTC	57.395	50.000	0.00	0.00	35.78	3.85
1456	1473	1.455822	ATGGGTCCAGGAAAACCTCA	58.544	50.000	0.00	0.00	35.78	3.86
1457	1474	1.455822	TGGGTCCAGGAAAACCTCAT	58.544	50.000	0.00	0.00	35.78	2.90
1458	1475	1.354368	TGGGTCCAGGAAAACCTCATC	59.646	52.381	0.00	0.00	35.78	2.92
1459	1476	1.679032	GGGTCCAGGAAAACCTCATCG	60.679	57.143	0.00	0.00	35.78	3.84
1460	1477	1.679032	GGTCCAGGAAAACCTCATCGG	60.679	57.143	0.00	0.00	39.35	4.18
1461	1478	1.278127	GTCCAGGAAAACCTCATCGGA	59.722	52.381	0.00	0.00	36.31	4.55
1462	1479	1.278127	TCCAGGAAAACCTCATCGGAC	59.722	52.381	0.00	0.00	36.31	4.79
1463	1480	1.359848	CAGGAAAACCTCATCGGACG	58.640	55.000	0.00	0.00	36.31	4.79
1464	1481	0.391263	AGGAAAACCTCATCGGACGC	60.391	55.000	0.00	0.00	36.31	5.19
1487	1504	5.835257	CTGAAAGCAAATCAGTCCAAAAGA	58.165	37.500	5.52	0.00	39.54	2.52
1537	1556	2.159627	GTGGCCGTTGTATCAGAAGTTG	59.840	50.000	0.00	0.00	0.00	3.16
1542	1561	4.712763	CCGTTGTATCAGAAGTTGAAAGC	58.287	43.478	0.00	0.00	39.77	3.51
1543	1562	4.213270	CCGTTGTATCAGAAGTTGAAAGCA	59.787	41.667	0.00	0.00	39.77	3.91
1544	1563	5.106555	CCGTTGTATCAGAAGTTGAAAGCAT	60.107	40.000	0.00	0.00	39.77	3.79
1545	1564	6.092122	CCGTTGTATCAGAAGTTGAAAGCATA	59.908	38.462	0.00	0.00	39.77	3.14
1549	1568	8.932945	TGTATCAGAAGTTGAAAGCATACTAG	57.067	34.615	0.00	0.00	39.77	2.57
1550	1569	8.531982	TGTATCAGAAGTTGAAAGCATACTAGT	58.468	33.333	0.00	0.00	39.77	2.57
1563	1582	9.182933	GAAAGCATACTAGTAGTACTATTGCAC	57.817	37.037	24.97	16.23	35.36	4.57
1570	1589	7.605449	ACTAGTAGTACTATTGCACGGAAAAA	58.395	34.615	10.46	0.00	29.08	1.94
1577	1596	2.045561	TTGCACGGAAAAACCAGAGA	57.954	45.000	0.00	0.00	38.90	3.10
1613	1632	2.235650	ACTATCAGCATCCGGATCATGG	59.764	50.000	15.88	4.32	0.00	3.66
1623	1642	2.515523	GATCATGGCAGGCGCTGT	60.516	61.111	7.64	0.00	38.60	4.40
1696	1715	0.902048	CTGAGTCTCCCAGCCTCACA	60.902	60.000	0.00	0.00	32.16	3.58
1716	1735	5.300034	TCACATCAAAGTGTTCAGCTGATTT	59.700	36.000	19.04	12.17	40.37	2.17
1790	1811	1.896660	GGCAAACCTCTGCAACCGA	60.897	57.895	0.00	0.00	44.52	4.69
1795	1816	2.489329	CAAACCTCTGCAACCGATGATT	59.511	45.455	0.00	0.00	0.00	2.57
1876	1897	5.524971	TTACATATGGATCTTCCGACGTT	57.475	39.130	7.80	0.00	40.17	3.99
2066	2089	0.248012	TCGTCCGTGCCACATTACAT	59.752	50.000	0.00	0.00	0.00	2.29
2101	2124	1.080093	CAAGACGCTGCCCTTACGA	60.080	57.895	0.00	0.00	0.00	3.43
2105	2128	3.771160	CGCTGCCCTTACGACCCT	61.771	66.667	0.00	0.00	0.00	4.34
2197	2220	0.108424	GACTCATCTGCTCTTGCCGT	60.108	55.000	0.00	0.00	38.71	5.68
2239	2262	1.360551	CCATCCGTCTCTCGCGATT	59.639	57.895	10.36	0.00	38.35	3.34
2335	2358	2.355818	GGTAGCCCGGTTCTCTTTCAAT	60.356	50.000	0.00	0.00	0.00	2.57
2338	2361	3.344515	AGCCCGGTTCTCTTTCAATAAC	58.655	45.455	0.00	0.00	0.00	1.89
2340	2363	3.374367	GCCCGGTTCTCTTTCAATAACTC	59.626	47.826	0.00	0.00	0.00	3.01
2341	2364	4.833390	CCCGGTTCTCTTTCAATAACTCT	58.167	43.478	0.00	0.00	0.00	3.24
2343	2366	4.631813	CCGGTTCTCTTTCAATAACTCTGG	59.368	45.833	0.00	0.00	0.00	3.86
2344	2367	5.479306	CGGTTCTCTTTCAATAACTCTGGA	58.521	41.667	0.00	0.00	0.00	3.86
2345	2368	5.578727	CGGTTCTCTTTCAATAACTCTGGAG	59.421	44.000	0.00	0.00	0.00	3.86
2346	2369	5.352846	GGTTCTCTTTCAATAACTCTGGAGC	59.647	44.000	0.00	0.00	0.00	4.70

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	4.088634	TGATGGCCTCAAGCTTGTAAAAT	58.911	39.130	25.19	13.70	43.05	1.82
152	153	1.658673	CACGCCGTAGTCCCTATCC	59.341	63.158	0.00	0.00	0.00	2.59
154	155	2.842256	CGCACGCCGTAGTCCCTAT	61.842	63.158	0.00	0.00	0.00	2.57
201	202	2.033911	ACGCATCATGCCACCACA	59.966	55.556	3.38	0.00	41.12	4.17
222	223	3.645975	CCGTCAACACACGCCACC	61.646	66.667	0.00	0.00	38.52	4.61
224	225	2.892914	CACCGTCAACACACGCCA	60.893	61.111	0.00	0.00	38.52	5.69
240	241	2.997315	CCGCTCCTGGTCTGGTCA	60.997	66.667	0.00	0.00	0.00	4.02
253	259	3.118454	CATCGAACCGCAACCGCT	61.118	61.111	0.00	0.00	35.30	5.52
294	300	5.600696	CAGGCTGTTTTGTTACTGGAAATT	58.399	37.500	6.28	0.00	0.00	1.82
295	301	4.501400	GCAGGCTGTTTTGTTACTGGAAAT	60.501	41.667	17.16	0.00	0.00	2.17
298	304	1.953686	GCAGGCTGTTTTGTTACTGGA	59.046	47.619	17.16	0.00	0.00	3.86
326	332	5.240403	AGAAGAAGTTTTCTCTCATGGCAAC	59.760	40.000	0.00	0.00	39.61	4.17
334	340	8.661257	GGCATTAGTAAGAAGAAGTTTTCTCTC	58.339	37.037	0.00	0.00	39.61	3.20
370	376	9.912634	TTTTGGAAATGTTTTGTTTTGCATAAA	57.087	22.222	0.00	0.00	33.95	1.40
459	465	8.135529	AGCTTTTAAGAAAATACACTTGACACC	58.864	33.333	0.00	0.00	0.00	4.16
498	504	1.021390	CCACAACCTCATCCACGAGC	61.021	60.000	0.00	0.00	0.00	5.03
639	648	3.317993	GCAAAGTCAAGCCTTAACCAAGA	59.682	43.478	0.00	0.00	33.20	3.02
770	779	2.672996	GCACCCAGTCGCCAACAT	60.673	61.111	0.00	0.00	0.00	2.71
831	846	0.681243	CTGCCCTAAAGAACTGCCCC	60.681	60.000	0.00	0.00	0.00	5.80
872	887	0.179020	CAGCCAAACTCCACACCTCA	60.179	55.000	0.00	0.00	0.00	3.86
937	953	1.112916	TCAACCACACGGAGCTCTCA	61.113	55.000	14.64	0.00	35.59	3.27
969	985	1.069765	CAGGCTGTTCACCACGACT	59.930	57.895	6.28	0.00	0.00	4.18
1078	1095	3.861797	GATCCCACCGGCCATCGT	61.862	66.667	0.00	0.00	37.11	3.73
1115	1132	2.125106	GCCGTGGATCCAGGTGTC	60.125	66.667	28.00	15.52	0.00	3.67
1116	1133	1.779061	AAAGCCGTGGATCCAGGTGT	61.779	55.000	28.00	14.97	0.00	4.16
1117	1134	1.002134	AAAGCCGTGGATCCAGGTG	60.002	57.895	28.00	20.98	0.00	4.00
1118	1135	1.201429	AGAAAGCCGTGGATCCAGGT	61.201	55.000	28.00	15.51	0.00	4.00
1119	1136	0.462759	GAGAAAGCCGTGGATCCAGG	60.463	60.000	24.66	24.66	0.00	4.45
1120	1137	0.807667	CGAGAAAGCCGTGGATCCAG	60.808	60.000	16.81	5.54	0.00	3.86
1121	1138	1.218047	CGAGAAAGCCGTGGATCCA	59.782	57.895	11.44	11.44	0.00	3.41
1135	1152	0.959372	GTCCCCGACTGAAGACGAGA	60.959	60.000	3.79	0.00	35.37	4.04
1175	1192	1.868519	GCGACGCCTCCTGTAATTAGG	60.869	57.143	9.14	0.00	39.29	2.69
1180	1197	1.080093	CAAGCGACGCCTCCTGTAA	60.080	57.895	17.79	0.00	0.00	2.41
1181	1198	2.571757	CAAGCGACGCCTCCTGTA	59.428	61.111	17.79	0.00	0.00	2.74
1197	1214	1.749665	CCGGCCGTGGATTATACCA	59.250	57.895	26.12	0.00	37.63	3.25
1225	1242	1.221840	CGATCCACCTTGGTCCTGG	59.778	63.158	0.00	0.00	39.03	4.45
1246	1263	1.950484	GCCATGTAACACCACCTCTGG	60.950	57.143	0.00	0.00	44.26	3.86
1260	1277	1.449601	CTTCTAACCGCCGCCATGT	60.450	57.895	0.00	0.00	0.00	3.21
1414	1431	3.893961	AAAAGCCTGAGCCTGCCCC	62.894	63.158	0.00	0.00	41.25	5.80
1415	1432	1.910276	AAAAAGCCTGAGCCTGCCC	60.910	57.895	0.00	0.00	41.25	5.36
1416	1433	3.783165	AAAAAGCCTGAGCCTGCC	58.217	55.556	0.00	0.00	41.25	4.85
1430	1447	5.931294	GGTTTTCCTGGACCCATTTAAAAA	58.069	37.500	0.00	0.00	36.94	1.94
1431	1448	5.554437	GGTTTTCCTGGACCCATTTAAAA	57.446	39.130	0.00	0.00	36.94	1.52
1446	1463	0.391263	AGCGTCCGATGAGGTTTTCC	60.391	55.000	0.00	0.00	41.99	3.13
1447	1464	0.721718	CAGCGTCCGATGAGGTTTTC	59.278	55.000	0.00	0.00	41.99	2.29
1448	1465	0.320374	TCAGCGTCCGATGAGGTTTT	59.680	50.000	3.20	0.00	41.99	2.43
1449	1466	0.320374	TTCAGCGTCCGATGAGGTTT	59.680	50.000	7.72	0.00	41.71	3.27
1450	1467	0.320374	TTTCAGCGTCCGATGAGGTT	59.680	50.000	7.72	0.00	41.71	3.50
1451	1468	0.108615	CTTTCAGCGTCCGATGAGGT	60.109	55.000	7.72	0.00	41.71	3.85
1452	1469	1.424493	GCTTTCAGCGTCCGATGAGG	61.424	60.000	7.72	6.67	41.71	3.86
1453	1470	0.737367	TGCTTTCAGCGTCCGATGAG	60.737	55.000	7.72	0.00	46.26	2.90
1454	1471	0.320334	TTGCTTTCAGCGTCCGATGA	60.320	50.000	3.20	3.20	46.26	2.92
1455	1472	0.516877	TTTGCTTTCAGCGTCCGATG	59.483	50.000	0.00	0.00	46.26	3.84
1456	1473	1.398390	GATTTGCTTTCAGCGTCCGAT	59.602	47.619	0.00	0.00	46.26	4.18
1457	1474	0.796312	GATTTGCTTTCAGCGTCCGA	59.204	50.000	0.00	0.00	46.26	4.55
1458	1475	0.516877	TGATTTGCTTTCAGCGTCCG	59.483	50.000	0.00	0.00	46.26	4.79
1459	1476	1.537202	ACTGATTTGCTTTCAGCGTCC	59.463	47.619	9.95	0.00	46.26	4.79
1460	1477	2.413371	GGACTGATTTGCTTTCAGCGTC	60.413	50.000	9.95	4.05	46.26	5.19
1461	1478	1.537202	GGACTGATTTGCTTTCAGCGT	59.463	47.619	9.95	0.00	46.26	5.07
1462	1479	1.536766	TGGACTGATTTGCTTTCAGCG	59.463	47.619	9.95	0.00	46.26	5.18
1463	1480	3.648339	TTGGACTGATTTGCTTTCAGC	57.352	42.857	9.95	0.00	43.57	4.26
1464	1481	5.835257	TCTTTTGGACTGATTTGCTTTCAG	58.165	37.500	8.85	8.85	44.95	3.02
1487	1504	8.001292	CCCTCCTTATCCTTCACTTTTAATGAT	58.999	37.037	0.00	0.00	0.00	2.45
1537	1556	9.182933	GTGCAATAGTACTACTAGTATGCTTTC	57.817	37.037	18.33	9.07	38.46	2.62
1542	1561	7.430992	TCCGTGCAATAGTACTACTAGTATG	57.569	40.000	4.31	3.53	33.66	2.39
1543	1562	8.455903	TTTCCGTGCAATAGTACTACTAGTAT	57.544	34.615	4.31	0.00	33.66	2.12
1544	1563	7.864108	TTTCCGTGCAATAGTACTACTAGTA	57.136	36.000	4.31	1.89	33.66	1.82
1545	1564	6.764308	TTTCCGTGCAATAGTACTACTAGT	57.236	37.500	4.31	0.00	33.66	2.57
1549	1568	5.409214	TGGTTTTTCCGTGCAATAGTACTAC	59.591	40.000	4.31	0.00	39.52	2.73
1550	1569	5.549347	TGGTTTTTCCGTGCAATAGTACTA	58.451	37.500	4.77	4.77	39.52	1.82
1563	1582	6.743575	AATACATCTTCTCTGGTTTTTCCG	57.256	37.500	0.00	0.00	39.52	4.30
1570	1589	7.682787	AGTGGATAAATACATCTTCTCTGGT	57.317	36.000	0.00	0.00	0.00	4.00
1577	1596	9.664332	GATGCTGATAGTGGATAAATACATCTT	57.336	33.333	0.00	0.00	0.00	2.40
1639	1658	1.578423	GCTTGAACCACAGCAGCTC	59.422	57.895	0.00	0.00	31.78	4.09
1672	1691	1.359474	AGGCTGGGAGACTCAGAACTA	59.641	52.381	4.53	0.00	34.36	2.24
1696	1715	7.934855	ATAGAAATCAGCTGAACACTTTGAT	57.065	32.000	22.50	9.12	0.00	2.57
1751	1771	3.181514	CCGTAGCTCCATTTTTAACACCG	60.182	47.826	0.00	0.00	0.00	4.94
1763	1784	1.192146	AGAGGTTTGCCGTAGCTCCA	61.192	55.000	0.00	0.00	40.18	3.86
1795	1816	9.916360	ATCGGGTGTATACATAATACTCTGATA	57.084	33.333	9.18	0.00	41.05	2.15
1830	1851	8.967664	AATACCCGTCAATAAGCTAACAATAA	57.032	30.769	0.00	0.00	0.00	1.40
1851	1872	6.618811	ACGTCGGAAGATCCATATGTAATAC	58.381	40.000	1.24	0.00	45.19	1.89
1876	1897	3.709141	TGGATATCACCTGATTTGTCCGA	59.291	43.478	4.83	0.00	34.70	4.55
2066	2089	3.047280	GCACGCGTCCATTCACCA	61.047	61.111	9.86	0.00	0.00	4.17
2091	2114	1.002315	GTAAACAGGGTCGTAAGGGCA	59.998	52.381	0.00	0.00	38.47	5.36
2101	2124	2.162681	GCAAGCTGATGTAAACAGGGT	58.837	47.619	0.00	0.00	37.20	4.34
2105	2128	2.161855	CCCAGCAAGCTGATGTAAACA	58.838	47.619	22.76	0.00	46.30	2.83
2132	2155	2.456119	CGGGCGAGTCAATCACAGC	61.456	63.158	0.00	0.00	0.00	4.40
2239	2262	2.736144	GGTGTGTTGATGTAGACCGA	57.264	50.000	0.00	0.00	0.00	4.69
2270	2293	5.191426	ACTCAATAAACAGCTCATGCAGAT	58.809	37.500	0.00	0.00	42.74	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.