AutoCloner

Multiple sequence alignment - TraesCS7B01G155000

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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	TraesCS7B01G155000	chr7B	100.000	2468	0	0	1	2468	207902239	207899772	0.000000e+00	4558
1	TraesCS7B01G155000	chr7B	93.026	717	23	8	1	692	208140393	208139679	0.000000e+00	1022
2	TraesCS7B01G155000	chr7B	86.829	782	78	19	1	763	550362403	550363178	0.000000e+00	850
3	TraesCS7B01G155000	chr7D	86.126	1629	206	12	836	2452	497902329	497903949	0.000000e+00	1738
4	TraesCS7B01G155000	chr7D	95.536	336	15	0	2133	2468	242751623	242751958	2.790000e-149	538
5	TraesCS7B01G155000	chr5D	81.470	1646	271	26	826	2452	463908733	463910363	0.000000e+00	1319
6	TraesCS7B01G155000	chr5D	90.095	737	52	8	1	719	470064179	470063446	0.000000e+00	937
7	TraesCS7B01G155000	chr5B	85.376	1224	171	5	938	2157	605997897	605999116	0.000000e+00	1262
8	TraesCS7B01G155000	chr5B	88.402	776	72	13	1	763	33621213	33620443	0.000000e+00	918
9	TraesCS7B01G155000	chr5B	91.343	335	29	0	2133	2467	127483442	127483776	2.240000e-125	459
10	TraesCS7B01G155000	chr7A	82.079	1501	238	25	963	2452	634693032	634691552	0.000000e+00	1253
11	TraesCS7B01G155000	chr7A	80.218	1648	275	36	826	2452	128842482	128844099	0.000000e+00	1190
12	TraesCS7B01G155000	chr2A	84.020	1214	174	14	826	2026	90000056	90001262	0.000000e+00	1149
13	TraesCS7B01G155000	chr2A	80.685	818	141	15	988	1796	39892194	39893003	9.700000e-174	619
14	TraesCS7B01G155000	chr2A	79.582	431	79	4	2022	2452	90020746	90021167	1.430000e-77	300
15	TraesCS7B01G155000	chr1B	89.974	778	64	10	1	767	60530028	60530802	0.000000e+00	992
16	TraesCS7B01G155000	chr1B	86.612	732	74	17	1	717	60362176	60361454	0.000000e+00	787
17	TraesCS7B01G155000	chr3B	89.203	778	66	12	1	763	434311756	434312530	0.000000e+00	955
18	TraesCS7B01G155000	chr3B	88.175	778	74	12	1	763	440875072	440875846	0.000000e+00	911
19	TraesCS7B01G155000	chr3B	88.060	670	59	16	1	657	811473877	811474538	0.000000e+00	774
20	TraesCS7B01G155000	chr6D	88.579	788	60	14	1	763	46907375	46908157	0.000000e+00	929
21	TraesCS7B01G155000	chr1D	88.776	784	53	15	1	763	482315274	482316043	0.000000e+00	928
22	TraesCS7B01G155000	chr6B	82.054	1042	163	16	826	1848	75003313	75004349	0.000000e+00	867
23	TraesCS7B01G155000	chr2B	87.226	775	66	18	1	763	24523505	24522752	0.000000e+00	852
24	TraesCS7B01G155000	chr6A	76.509	1524	317	26	955	2452	524351898	524350390	0.000000e+00	793
25	TraesCS7B01G155000	chr3D	94.328	335	19	0	2133	2467	419540744	419540410	4.710000e-142	514
26	TraesCS7B01G155000	chr3D	87.798	336	41	0	2133	2468	603007895	603008230	6.400000e-106	394
27	TraesCS7B01G155000	chr1A	86.944	337	39	5	2135	2468	455020994	455020660	8.330000e-100	374
28	TraesCS7B01G155000	chr4D	85.672	335	47	1	2135	2468	56711896	56712230	3.900000e-93	351
29	TraesCS7B01G155000	chrUn	86.250	320	43	1	2133	2452	286753092	286752774	1.820000e-91	346
30	TraesCS7B01G155000	chrUn	86.250	320	43	1	2133	2452	296179396	296179078	1.820000e-91	346

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	TraesCS7B01G155000	chr7B	207899772	207902239	2467	True	4558	4558	100.000	1	2468	1	chr7B.!!$R1	2467
1	TraesCS7B01G155000	chr7B	208139679	208140393	714	True	1022	1022	93.026	1	692	1	chr7B.!!$R2	691
2	TraesCS7B01G155000	chr7B	550362403	550363178	775	False	850	850	86.829	1	763	1	chr7B.!!$F1	762
3	TraesCS7B01G155000	chr7D	497902329	497903949	1620	False	1738	1738	86.126	836	2452	1	chr7D.!!$F2	1616
4	TraesCS7B01G155000	chr5D	463908733	463910363	1630	False	1319	1319	81.470	826	2452	1	chr5D.!!$F1	1626
5	TraesCS7B01G155000	chr5D	470063446	470064179	733	True	937	937	90.095	1	719	1	chr5D.!!$R1	718
6	TraesCS7B01G155000	chr5B	605997897	605999116	1219	False	1262	1262	85.376	938	2157	1	chr5B.!!$F2	1219
7	TraesCS7B01G155000	chr5B	33620443	33621213	770	True	918	918	88.402	1	763	1	chr5B.!!$R1	762
8	TraesCS7B01G155000	chr7A	634691552	634693032	1480	True	1253	1253	82.079	963	2452	1	chr7A.!!$R1	1489
9	TraesCS7B01G155000	chr7A	128842482	128844099	1617	False	1190	1190	80.218	826	2452	1	chr7A.!!$F1	1626
10	TraesCS7B01G155000	chr2A	90000056	90001262	1206	False	1149	1149	84.020	826	2026	1	chr2A.!!$F2	1200
11	TraesCS7B01G155000	chr2A	39892194	39893003	809	False	619	619	80.685	988	1796	1	chr2A.!!$F1	808
12	TraesCS7B01G155000	chr1B	60530028	60530802	774	False	992	992	89.974	1	767	1	chr1B.!!$F1	766
13	TraesCS7B01G155000	chr1B	60361454	60362176	722	True	787	787	86.612	1	717	1	chr1B.!!$R1	716
14	TraesCS7B01G155000	chr3B	434311756	434312530	774	False	955	955	89.203	1	763	1	chr3B.!!$F1	762
15	TraesCS7B01G155000	chr3B	440875072	440875846	774	False	911	911	88.175	1	763	1	chr3B.!!$F2	762
16	TraesCS7B01G155000	chr3B	811473877	811474538	661	False	774	774	88.060	1	657	1	chr3B.!!$F3	656
17	TraesCS7B01G155000	chr6D	46907375	46908157	782	False	929	929	88.579	1	763	1	chr6D.!!$F1	762
18	TraesCS7B01G155000	chr1D	482315274	482316043	769	False	928	928	88.776	1	763	1	chr1D.!!$F1	762
19	TraesCS7B01G155000	chr6B	75003313	75004349	1036	False	867	867	82.054	826	1848	1	chr6B.!!$F1	1022
20	TraesCS7B01G155000	chr2B	24522752	24523505	753	True	852	852	87.226	1	763	1	chr2B.!!$R1	762
21	TraesCS7B01G155000	chr6A	524350390	524351898	1508	True	793	793	76.509	955	2452	1	chr6A.!!$R1	1497

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
763	877	0.321298	AGGCGCACGTTAGGAAATGT	60.321	50.0	10.83	0.0	35.12	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2237	2408	0.387202	ATGAGATCACGAAGCTCCCG	59.613	55.0	6.89	6.89	0.0	5.14	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
321	327	8.628280	TGTTCATGTTCTCAATAATTGTTCACA	58.372	29.630	0.00	0.00	0.00	3.58
719	833	2.748647	GGGTATGCGCCCGTTTGT	60.749	61.111	4.18	0.00	39.17	2.83
763	877	0.321298	AGGCGCACGTTAGGAAATGT	60.321	50.000	10.83	0.00	35.12	2.71
767	881	1.320555	CGCACGTTAGGAAATGTCGAG	59.679	52.381	0.00	0.00	32.35	4.04
768	882	1.060698	GCACGTTAGGAAATGTCGAGC	59.939	52.381	0.00	0.00	32.35	5.03
769	883	2.333926	CACGTTAGGAAATGTCGAGCA	58.666	47.619	0.00	0.00	32.35	4.26
770	884	2.734606	CACGTTAGGAAATGTCGAGCAA	59.265	45.455	0.00	0.00	32.35	3.91
771	885	2.735134	ACGTTAGGAAATGTCGAGCAAC	59.265	45.455	0.00	0.00	28.24	4.17
772	886	2.993899	CGTTAGGAAATGTCGAGCAACT	59.006	45.455	0.00	0.00	0.00	3.16
773	887	4.171005	CGTTAGGAAATGTCGAGCAACTA	58.829	43.478	0.00	0.00	0.00	2.24
774	888	4.265556	CGTTAGGAAATGTCGAGCAACTAG	59.734	45.833	0.00	0.00	0.00	2.57
775	889	3.963428	AGGAAATGTCGAGCAACTAGT	57.037	42.857	0.00	0.00	0.00	2.57
776	890	4.273148	AGGAAATGTCGAGCAACTAGTT	57.727	40.909	1.12	1.12	0.00	2.24
777	891	5.401531	AGGAAATGTCGAGCAACTAGTTA	57.598	39.130	8.04	0.00	0.00	2.24
778	892	5.790593	AGGAAATGTCGAGCAACTAGTTAA	58.209	37.500	8.04	0.00	0.00	2.01
779	893	5.638234	AGGAAATGTCGAGCAACTAGTTAAC	59.362	40.000	8.04	3.72	0.00	2.01
780	894	5.444218	GGAAATGTCGAGCAACTAGTTAACG	60.444	44.000	8.04	13.58	0.00	3.18
781	895	3.902261	TGTCGAGCAACTAGTTAACGA	57.098	42.857	19.44	19.44	0.00	3.85
782	896	3.818387	TGTCGAGCAACTAGTTAACGAG	58.182	45.455	22.02	13.50	0.00	4.18
783	897	2.593336	GTCGAGCAACTAGTTAACGAGC	59.407	50.000	22.02	15.53	0.00	5.03
784	898	2.486982	TCGAGCAACTAGTTAACGAGCT	59.513	45.455	15.12	15.12	0.00	4.09
785	899	3.057736	TCGAGCAACTAGTTAACGAGCTT	60.058	43.478	16.01	6.67	0.00	3.74
786	900	3.301116	CGAGCAACTAGTTAACGAGCTTC	59.699	47.826	16.01	9.92	0.00	3.86
787	901	3.586892	AGCAACTAGTTAACGAGCTTCC	58.413	45.455	14.82	2.73	0.00	3.46
788	902	2.671888	GCAACTAGTTAACGAGCTTCCC	59.328	50.000	14.82	0.00	0.00	3.97
789	903	3.616802	GCAACTAGTTAACGAGCTTCCCT	60.617	47.826	14.82	0.00	0.00	4.20
790	904	4.174762	CAACTAGTTAACGAGCTTCCCTC	58.825	47.826	14.82	0.00	37.22	4.30
791	905	3.428532	ACTAGTTAACGAGCTTCCCTCA	58.571	45.455	14.82	0.00	40.78	3.86
792	906	3.830755	ACTAGTTAACGAGCTTCCCTCAA	59.169	43.478	14.82	0.00	40.78	3.02
793	907	3.764237	AGTTAACGAGCTTCCCTCAAA	57.236	42.857	0.00	0.00	40.78	2.69
794	908	4.081322	AGTTAACGAGCTTCCCTCAAAA	57.919	40.909	0.00	0.00	40.78	2.44
795	909	4.457466	AGTTAACGAGCTTCCCTCAAAAA	58.543	39.130	0.00	0.00	40.78	1.94
814	928	4.572950	AAAAATAGTTAACGAGCGACCG	57.427	40.909	0.00	0.00	0.00	4.79
815	929	1.553308	AATAGTTAACGAGCGACCGC	58.447	50.000	6.25	6.25	42.33	5.68
906	1031	1.356494	CCAATCTCCCCTCCCTTCCC	61.356	65.000	0.00	0.00	0.00	3.97
920	1047	2.873557	CTTCCCCTCCCCGCTAGTCA	62.874	65.000	0.00	0.00	0.00	3.41
923	1050	2.754658	CCTCCCCGCTAGTCACGT	60.755	66.667	0.00	0.00	0.00	4.49
1014	1141	3.072184	AGAGATTGATGGGTGATACTGCC	59.928	47.826	0.00	0.00	0.00	4.85
1086	1225	2.275318	GGCTTGAAGGAAGACGATCTG	58.725	52.381	0.00	0.00	32.82	2.90
1208	1347	3.779444	TCTATCGGAATATGAGGGCTGT	58.221	45.455	0.00	0.00	0.00	4.40
1234	1373	2.820197	GACTTGGCAAAGGAGGTAAAGG	59.180	50.000	5.66	0.00	37.76	3.11
1399	1542	8.986847	CGTCAATAGAGCTCAATAAGATTGATT	58.013	33.333	17.77	0.00	35.12	2.57
1428	1571	1.274728	CAGATCCATGATCTCCCCGAC	59.725	57.143	3.66	0.00	45.03	4.79
1452	1596	4.081807	GCTTCTTTTCCAAGATCAAGGCAT	60.082	41.667	0.00	0.00	38.89	4.40
1551	1697	5.624509	CGAGTAAGGATTGATGTCACCAAGA	60.625	44.000	0.00	0.00	0.00	3.02
1612	1758	6.899393	AGATGTTCTCCAGAGAGTGATATC	57.101	41.667	0.00	0.00	41.26	1.63
1659	1808	5.105635	CCAGATTGTGCTGTTTGTGGATATT	60.106	40.000	0.00	0.00	34.06	1.28
1686	1835	4.367450	GCATTTGTTTAAAGAGTGTGGCA	58.633	39.130	0.00	0.00	0.00	4.92
1700	1849	0.251341	GTGGCAATGGAGTTCACCCT	60.251	55.000	0.00	0.00	0.00	4.34
1778	1927	0.547954	GTCCAAGGGAGGGAAGAGGT	60.548	60.000	0.00	0.00	35.88	3.85
1790	1939	2.472029	GGAAGAGGTCAAGAGGATGGA	58.528	52.381	0.00	0.00	0.00	3.41
1862	2029	0.611062	GGGGCCCTACAAAGTCCAAC	60.611	60.000	24.38	0.00	0.00	3.77
1905	2072	6.183360	CGAGGAAGATACAACCAACCATACTA	60.183	42.308	0.00	0.00	0.00	1.82
1934	2105	1.936547	GCTATGGACGAGGCAGAAAAG	59.063	52.381	0.00	0.00	0.00	2.27
1949	2120	5.059833	GCAGAAAAGAACAAGAAGAGAGGA	58.940	41.667	0.00	0.00	0.00	3.71
1959	2130	4.216687	ACAAGAAGAGAGGAGTTACGACAG	59.783	45.833	0.00	0.00	0.00	3.51
1964	2135	3.018149	GAGAGGAGTTACGACAGGTGAT	58.982	50.000	0.00	0.00	0.00	3.06
1992	2163	2.016318	CATCTTTGACATTGGCGGCTA	58.984	47.619	11.43	1.99	0.00	3.93
1993	2164	2.418368	TCTTTGACATTGGCGGCTAT	57.582	45.000	11.43	5.04	0.00	2.97
2066	2237	1.143684	AGCCCTTCTTCAGTGCAAGAA	59.856	47.619	13.56	13.56	39.59	2.52
2075	2246	2.575532	TCAGTGCAAGAACCAAAGAGG	58.424	47.619	0.00	0.00	45.67	3.69
2076	2247	1.610522	CAGTGCAAGAACCAAAGAGGG	59.389	52.381	0.00	0.00	43.89	4.30
2100	2271	0.380378	GCAAAGCTCGAACACAACCA	59.620	50.000	0.00	0.00	0.00	3.67
2108	2279	3.426963	GCTCGAACACAACCAACAAGAAA	60.427	43.478	0.00	0.00	0.00	2.52
2109	2280	4.733523	GCTCGAACACAACCAACAAGAAAT	60.734	41.667	0.00	0.00	0.00	2.17
2130	2301	0.251297	TGGGAAGAATGCAGTGGTGG	60.251	55.000	0.00	0.00	0.00	4.61
2158	2329	1.240641	ATTGATGCGTGTTTGGCGGA	61.241	50.000	0.00	0.00	0.00	5.54
2168	2339	0.035739	GTTTGGCGGACTCCCAAGTA	59.964	55.000	0.00	0.00	42.80	2.24
2181	2352	1.514087	CAAGTAGGGTCGCGCCTAA	59.486	57.895	13.23	2.92	37.43	2.69
2200	2371	5.061853	CCTAATGCAATGAGTCTGCTATGT	58.938	41.667	6.00	0.00	40.59	2.29
2216	2387	3.047877	GTTGGAACTGTCGCGGGG	61.048	66.667	6.13	0.00	0.00	5.73
2237	2408	4.379143	GCAAACCCGCGACGGTTC	62.379	66.667	18.28	5.44	45.63	3.62
2238	2409	4.067016	CAAACCCGCGACGGTTCG	62.067	66.667	18.28	5.61	45.63	3.95
2256	2427	0.387202	CGGGAGCTTCGTGATCTCAT	59.613	55.000	0.00	0.00	29.22	2.90
2278	2449	3.596362	GCAACTTGCCCCCTCTATT	57.404	52.632	1.95	0.00	37.42	1.73
2279	2450	1.106285	GCAACTTGCCCCCTCTATTG	58.894	55.000	1.95	0.00	37.42	1.90
2281	2452	2.094675	CAACTTGCCCCCTCTATTGTG	58.905	52.381	0.00	0.00	0.00	3.33
2287	2458	2.849943	TGCCCCCTCTATTGTGTGTATT	59.150	45.455	0.00	0.00	0.00	1.89
2288	2459	3.214328	GCCCCCTCTATTGTGTGTATTG	58.786	50.000	0.00	0.00	0.00	1.90
2302	2473	6.644347	TGTGTGTATTGTTGAAACCCAAATT	58.356	32.000	0.00	0.00	36.36	1.82
2317	2488	2.168521	CCAAATTGAGGGCTCTCGAGTA	59.831	50.000	13.13	0.00	42.79	2.59
2341	2512	9.364653	GTAGAGAATATGGTAGGTTCTTTAGGA	57.635	37.037	0.00	0.00	32.67	2.94
2389	2560	3.403038	CTCTGGTAGAAGTGGTGGTTTG	58.597	50.000	0.00	0.00	0.00	2.93
2437	2608	4.756502	AGCTCGAAGTTATTGGTTACTCC	58.243	43.478	0.00	0.00	0.00	3.85
2438	2609	3.550678	GCTCGAAGTTATTGGTTACTCCG	59.449	47.826	0.00	0.00	39.52	4.63
2440	2611	5.389859	TCGAAGTTATTGGTTACTCCGAA	57.610	39.130	0.00	0.00	39.52	4.30
2452	2623	6.046593	TGGTTACTCCGAATATCACATTGAC	58.953	40.000	0.00	0.00	39.52	3.18
2453	2624	6.127168	TGGTTACTCCGAATATCACATTGACT	60.127	38.462	0.00	0.00	39.52	3.41
2454	2625	6.761714	GGTTACTCCGAATATCACATTGACTT	59.238	38.462	0.00	0.00	0.00	3.01
2455	2626	7.254455	GGTTACTCCGAATATCACATTGACTTG	60.254	40.741	0.00	0.00	0.00	3.16
2456	2627	5.977635	ACTCCGAATATCACATTGACTTGA	58.022	37.500	0.00	0.00	0.00	3.02
2457	2628	5.812642	ACTCCGAATATCACATTGACTTGAC	59.187	40.000	0.00	0.00	0.00	3.18
2458	2629	5.729510	TCCGAATATCACATTGACTTGACA	58.270	37.500	0.00	0.00	0.00	3.58
2459	2630	5.812127	TCCGAATATCACATTGACTTGACAG	59.188	40.000	0.00	0.00	0.00	3.51
2460	2631	5.582269	CCGAATATCACATTGACTTGACAGT	59.418	40.000	0.00	0.00	35.17	3.55
2461	2632	6.092670	CCGAATATCACATTGACTTGACAGTT	59.907	38.462	0.00	0.00	31.22	3.16
2462	2633	6.957635	CGAATATCACATTGACTTGACAGTTG	59.042	38.462	0.00	0.00	31.22	3.16
2463	2634	7.148590	CGAATATCACATTGACTTGACAGTTGA	60.149	37.037	0.00	0.00	31.22	3.18
2464	2635	8.571461	AATATCACATTGACTTGACAGTTGAT	57.429	30.769	0.00	0.00	31.22	2.57
2465	2636	5.678132	TCACATTGACTTGACAGTTGATG	57.322	39.130	0.00	0.00	34.30	3.07
2466	2637	5.367302	TCACATTGACTTGACAGTTGATGA	58.633	37.500	0.00	0.00	33.24	2.92
2467	2638	5.467735	TCACATTGACTTGACAGTTGATGAG	59.532	40.000	0.00	0.76	33.24	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
554	653	2.829720	ACAGACCACCGTAGCAATTCTA	59.170	45.455	0.00	0.00	0.00	2.10
662	769	5.515270	CGGCTCGTTTTCTTCTTTTTCTTTT	59.485	36.000	0.00	0.00	0.00	2.27
719	833	1.675310	CCCGCTTCATCTGTTGCCA	60.675	57.895	0.00	0.00	0.00	4.92
750	864	2.735134	GTTGCTCGACATTTCCTAACGT	59.265	45.455	0.00	0.00	0.00	3.99
763	877	2.486982	AGCTCGTTAACTAGTTGCTCGA	59.513	45.455	18.56	20.16	0.00	4.04
767	881	2.671888	GGGAAGCTCGTTAACTAGTTGC	59.328	50.000	18.56	12.12	0.00	4.17
768	882	4.174762	GAGGGAAGCTCGTTAACTAGTTG	58.825	47.826	18.56	1.62	0.00	3.16
769	883	3.830755	TGAGGGAAGCTCGTTAACTAGTT	59.169	43.478	13.68	13.68	0.00	2.24
770	884	3.428532	TGAGGGAAGCTCGTTAACTAGT	58.571	45.455	8.74	0.00	0.00	2.57
771	885	4.451629	TTGAGGGAAGCTCGTTAACTAG	57.548	45.455	3.71	3.24	0.00	2.57
772	886	4.877378	TTTGAGGGAAGCTCGTTAACTA	57.123	40.909	3.71	0.00	0.00	2.24
773	887	3.764237	TTTGAGGGAAGCTCGTTAACT	57.236	42.857	3.71	0.00	0.00	2.24
774	888	4.823790	TTTTTGAGGGAAGCTCGTTAAC	57.176	40.909	0.00	0.00	0.00	2.01
793	907	3.181527	GCGGTCGCTCGTTAACTATTTTT	60.182	43.478	8.20	0.00	38.26	1.94
794	908	2.346545	GCGGTCGCTCGTTAACTATTTT	59.653	45.455	8.20	0.00	38.26	1.82
795	909	1.922545	GCGGTCGCTCGTTAACTATTT	59.077	47.619	8.20	0.00	38.26	1.40
796	910	1.553308	GCGGTCGCTCGTTAACTATT	58.447	50.000	8.20	0.00	38.26	1.73
797	911	0.590732	CGCGGTCGCTCGTTAACTAT	60.591	55.000	13.51	0.00	39.32	2.12
798	912	1.226101	CGCGGTCGCTCGTTAACTA	60.226	57.895	13.51	0.00	39.32	2.24
799	913	2.503375	CGCGGTCGCTCGTTAACT	60.503	61.111	13.51	0.00	39.32	2.24
809	923	4.130281	GAGTTTTCCGCGCGGTCG	62.130	66.667	44.16	23.07	36.47	4.79
810	924	3.785499	GGAGTTTTCCGCGCGGTC	61.785	66.667	44.16	33.42	32.79	4.79
817	931	0.320697	AACGAGAGGGGAGTTTTCCG	59.679	55.000	0.00	0.00	45.04	4.30
818	932	2.093606	CCTAACGAGAGGGGAGTTTTCC	60.094	54.545	0.00	0.00	43.23	3.13
819	933	3.248495	CCTAACGAGAGGGGAGTTTTC	57.752	52.381	0.00	0.00	32.39	2.29
869	994	3.095912	TGGTTCTCTACGAGGGATGAA	57.904	47.619	0.00	0.00	0.00	2.57
872	997	3.892588	GAGATTGGTTCTCTACGAGGGAT	59.107	47.826	0.00	0.00	46.33	3.85
906	1031	2.754658	ACGTGACTAGCGGGGAGG	60.755	66.667	0.00	0.00	0.00	4.30
979	1106	5.295950	CATCAATCTCTTGCTCGAGGTATT	58.704	41.667	15.58	0.53	32.11	1.89
981	1108	3.068732	CCATCAATCTCTTGCTCGAGGTA	59.931	47.826	15.58	0.00	32.11	3.08
998	1125	1.764723	CTGAGGCAGTATCACCCATCA	59.235	52.381	0.00	0.00	0.00	3.07
1014	1141	2.105128	GACGTGCCCGATCCTGAG	59.895	66.667	0.00	0.00	37.88	3.35
1086	1225	3.494378	TCGATCACGACGTCCTCC	58.506	61.111	10.58	0.00	43.81	4.30
1208	1347	1.703411	CTCCTTTGCCAAGTCCCAAA	58.297	50.000	0.00	0.00	0.00	3.28
1234	1373	0.249398	TTCTCCTCAAGCGGCCTAAC	59.751	55.000	0.00	0.00	0.00	2.34
1428	1571	3.671702	GCCTTGATCTTGGAAAAGAAGCG	60.672	47.826	8.43	0.00	31.77	4.68
1612	1758	4.974888	GGAGCCGTTCGTATTTAACTCTAG	59.025	45.833	0.00	0.00	0.00	2.43
1659	1808	5.814705	CACACTCTTTAAACAAATGCCCAAA	59.185	36.000	0.00	0.00	0.00	3.28
1700	1849	6.462347	GGTCCTTGAAAACTAATGCTTTTGGA	60.462	38.462	0.00	0.00	0.00	3.53
1764	1913	0.793617	TCTTGACCTCTTCCCTCCCT	59.206	55.000	0.00	0.00	0.00	4.20
1778	1927	2.511218	CCCTCCATTTCCATCCTCTTGA	59.489	50.000	0.00	0.00	0.00	3.02
1790	1939	0.990818	GGCCTCCTCTCCCTCCATTT	60.991	60.000	0.00	0.00	0.00	2.32
1824	1976	2.438075	GCTGCAGCCTCTTCCAGG	60.438	66.667	28.76	0.00	46.82	4.45
1839	2006	3.728373	CTTTGTAGGGCCCCGGCT	61.728	66.667	21.43	1.11	41.60	5.52
1877	2044	4.070009	GGTTGGTTGTATCTTCCTCGTTT	58.930	43.478	0.00	0.00	0.00	3.60
1905	2072	1.410517	CTCGTCCATAGCCACATCAGT	59.589	52.381	0.00	0.00	0.00	3.41
1934	2105	5.155643	GTCGTAACTCCTCTCTTCTTGTTC	58.844	45.833	0.00	0.00	0.00	3.18
1949	2120	1.933021	TGGGATCACCTGTCGTAACT	58.067	50.000	0.00	0.00	41.11	2.24
1959	2130	4.706476	TGTCAAAGATGATTTGGGATCACC	59.294	41.667	0.00	0.00	38.01	4.02
1964	2135	4.081531	GCCAATGTCAAAGATGATTTGGGA	60.082	41.667	17.68	0.00	44.18	4.37
1992	2163	2.620251	TTGCTAGCATTACCGCTGAT	57.380	45.000	20.13	0.00	43.68	2.90
1993	2164	2.483876	GATTGCTAGCATTACCGCTGA	58.516	47.619	20.13	0.00	43.68	4.26
2066	2237	0.398381	TTTGCTTGGCCCTCTTTGGT	60.398	50.000	0.00	0.00	0.00	3.67
2075	2246	1.081175	GTTCGAGCTTTGCTTGGCC	60.081	57.895	0.00	0.00	39.88	5.36
2076	2247	0.661483	GTGTTCGAGCTTTGCTTGGC	60.661	55.000	0.00	2.30	39.88	4.52
2100	2271	4.344679	TGCATTCTTCCCACATTTCTTGTT	59.655	37.500	0.00	0.00	36.00	2.83
2108	2279	1.076024	ACCACTGCATTCTTCCCACAT	59.924	47.619	0.00	0.00	0.00	3.21
2109	2280	0.478072	ACCACTGCATTCTTCCCACA	59.522	50.000	0.00	0.00	0.00	4.17
2130	2301	2.134346	ACACGCATCAATGTTTTTGGC	58.866	42.857	0.00	0.00	0.00	4.52
2181	2352	3.630769	CCAACATAGCAGACTCATTGCAT	59.369	43.478	0.00	0.00	43.92	3.96
2233	2404	0.806492	GATCACGAAGCTCCCGAACC	60.806	60.000	14.26	0.00	0.00	3.62
2237	2408	0.387202	ATGAGATCACGAAGCTCCCG	59.613	55.000	6.89	6.89	0.00	5.14
2238	2409	1.410517	TCATGAGATCACGAAGCTCCC	59.589	52.381	0.00	0.00	0.00	4.30
2239	2410	2.545532	CCTCATGAGATCACGAAGCTCC	60.546	54.545	24.62	0.00	0.00	4.70
2276	2447	5.860941	TGGGTTTCAACAATACACACAAT	57.139	34.783	0.00	0.00	0.00	2.71
2278	2449	5.661056	TTTGGGTTTCAACAATACACACA	57.339	34.783	0.00	0.00	34.67	3.72
2279	2450	6.758886	TCAATTTGGGTTTCAACAATACACAC	59.241	34.615	0.00	0.00	34.67	3.82
2281	2452	6.423604	CCTCAATTTGGGTTTCAACAATACAC	59.576	38.462	0.00	0.00	34.67	2.90
2287	2458	2.103941	GCCCTCAATTTGGGTTTCAACA	59.896	45.455	13.21	0.00	46.22	3.33
2288	2459	2.368548	AGCCCTCAATTTGGGTTTCAAC	59.631	45.455	13.21	0.00	46.22	3.18
2302	2473	3.790691	CTCTACTCGAGAGCCCTCA	57.209	57.895	21.68	0.00	45.33	3.86
2312	2483	7.513371	AAGAACCTACCATATTCTCTACTCG	57.487	40.000	0.00	0.00	31.44	4.18
2368	2539	3.403038	CAAACCACCACTTCTACCAGAG	58.597	50.000	0.00	0.00	0.00	3.35
2407	2578	7.085052	ACCAATAACTTCGAGCTTTAATTCC	57.915	36.000	0.00	0.00	0.00	3.01
2411	2582	7.332678	GGAGTAACCAATAACTTCGAGCTTTAA	59.667	37.037	0.00	0.00	38.79	1.52
2419	2590	7.650504	TGATATTCGGAGTAACCAATAACTTCG	59.349	37.037	0.00	0.00	44.43	3.79
2437	2608	6.653273	ACTGTCAAGTCAATGTGATATTCG	57.347	37.500	0.00	0.00	26.77	3.34
2438	2609	8.032952	TCAACTGTCAAGTCAATGTGATATTC	57.967	34.615	0.00	0.00	34.77	1.75
2440	2611	7.825761	TCATCAACTGTCAAGTCAATGTGATAT	59.174	33.333	0.00	0.00	34.77	1.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.