AutoCloner

Multiple sequence alignment - TraesCS2A01G447200

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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	TraesCS2A01G447200	chr2A	100.000	3108	0	0	1	3108	696039433	696042540	0.000000e+00	5740.0
1	TraesCS2A01G447200	chr2A	85.670	1926	177	55	700	2547	695998783	696000687	0.000000e+00	1936.0
2	TraesCS2A01G447200	chr2A	91.587	630	36	7	984	1596	696307025	696307654	0.000000e+00	854.0
3	TraesCS2A01G447200	chr2A	84.906	530	58	13	2583	3108	696241050	696241561	1.650000e-142	516.0
4	TraesCS2A01G447200	chr2A	85.477	482	49	9	2038	2505	696001156	696001630	1.680000e-132	483.0
5	TraesCS2A01G447200	chr2A	86.154	390	40	11	2724	3108	696003844	696004224	2.890000e-110	409.0
6	TraesCS2A01G447200	chr2A	83.916	286	30	9	2583	2864	696273253	696273526	3.070000e-65	259.0
7	TraesCS2A01G447200	chr2B	85.523	2314	221	61	383	2617	663828334	663830612	0.000000e+00	2313.0
8	TraesCS2A01G447200	chr2B	83.190	1981	176	78	700	2587	663837680	663839596	0.000000e+00	1668.0
9	TraesCS2A01G447200	chr2B	82.053	1783	176	70	582	2315	663885604	663887291	0.000000e+00	1387.0
10	TraesCS2A01G447200	chr2B	82.187	1207	144	34	999	2152	663898756	663899944	0.000000e+00	972.0
11	TraesCS2A01G447200	chr2B	82.865	1033	140	20	1335	2349	663180861	663179848	0.000000e+00	893.0
12	TraesCS2A01G447200	chr2B	90.181	387	29	8	2725	3108	663831237	663831617	2.150000e-136	496.0
13	TraesCS2A01G447200	chr2D	88.036	1797	154	31	799	2547	556267000	556268783	0.000000e+00	2071.0
14	TraesCS2A01G447200	chr2D	89.508	1525	81	29	1	1490	556317427	556318907	0.000000e+00	1857.0
15	TraesCS2A01G447200	chr2D	90.068	1329	120	8	979	2296	556350527	556351854	0.000000e+00	1712.0
16	TraesCS2A01G447200	chr2D	89.711	1351	106	16	1347	2666	556339260	556340608	0.000000e+00	1694.0
17	TraesCS2A01G447200	chr2D	82.926	1839	177	65	516	2290	556407516	556409281	0.000000e+00	1530.0
18	TraesCS2A01G447200	chr2D	83.313	1654	158	58	700	2290	556618798	556620396	0.000000e+00	1417.0
19	TraesCS2A01G447200	chr2D	82.062	1678	159	82	700	2315	556365163	556366760	0.000000e+00	1301.0
20	TraesCS2A01G447200	chr2D	83.636	1210	125	37	999	2152	556642397	556643589	0.000000e+00	1070.0
21	TraesCS2A01G447200	chr2D	90.647	417	29	4	2698	3108	556340671	556341083	2.110000e-151	545.0
22	TraesCS2A01G447200	chr2D	82.818	582	75	17	2534	3108	556309995	556310558	5.990000e-137	497.0
23	TraesCS2A01G447200	chr2D	86.117	461	53	9	1485	1942	556333284	556333736	1.300000e-133	486.0
24	TraesCS2A01G447200	chr2D	83.624	287	39	6	2342	2624	556351850	556352132	2.380000e-66	263.0
25	TraesCS2A01G447200	chr2D	100.000	33	0	0	640	672	556641980	556642012	9.310000e-06	62.1
26	TraesCS2A01G447200	chr3A	80.443	271	45	7	1	266	506778887	506779154	1.890000e-47	200.0
27	TraesCS2A01G447200	chr1D	79.853	273	47	7	39	310	449971443	449971178	3.160000e-45	193.0
28	TraesCS2A01G447200	chr1D	79.259	270	51	5	45	312	193783736	193783470	1.900000e-42	183.0
29	TraesCS2A01G447200	chr4A	81.579	228	39	2	39	264	617366437	617366211	5.290000e-43	185.0
30	TraesCS2A01G447200	chr6D	77.564	312	59	7	1	312	388217129	388216829	8.860000e-41	178.0
31	TraesCS2A01G447200	chr1B	79.182	269	46	9	1	266	489577295	489577034	8.860000e-41	178.0
32	TraesCS2A01G447200	chr3D	80.711	197	34	4	45	239	427757817	427758011	1.930000e-32	150.0
33	TraesCS2A01G447200	chr1A	76.370	292	59	7	1806	2092	459441787	459441501	6.940000e-32	148.0
34	TraesCS2A01G447200	chr5B	77.778	243	45	7	1	241	466702903	466703138	1.160000e-29	141.0

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	TraesCS2A01G447200	chr2A	696039433	696042540	3107	False	5740.000000	5740	100.000	1	3108	1	chr2A.!!$F1	3107
1	TraesCS2A01G447200	chr2A	695998783	696004224	5441	False	942.666667	1936	85.767	700	3108	3	chr2A.!!$F5	2408
2	TraesCS2A01G447200	chr2A	696307025	696307654	629	False	854.000000	854	91.587	984	1596	1	chr2A.!!$F4	612
3	TraesCS2A01G447200	chr2A	696241050	696241561	511	False	516.000000	516	84.906	2583	3108	1	chr2A.!!$F2	525
4	TraesCS2A01G447200	chr2B	663837680	663839596	1916	False	1668.000000	1668	83.190	700	2587	1	chr2B.!!$F1	1887
5	TraesCS2A01G447200	chr2B	663828334	663831617	3283	False	1404.500000	2313	87.852	383	3108	2	chr2B.!!$F4	2725
6	TraesCS2A01G447200	chr2B	663885604	663887291	1687	False	1387.000000	1387	82.053	582	2315	1	chr2B.!!$F2	1733
7	TraesCS2A01G447200	chr2B	663898756	663899944	1188	False	972.000000	972	82.187	999	2152	1	chr2B.!!$F3	1153
8	TraesCS2A01G447200	chr2B	663179848	663180861	1013	True	893.000000	893	82.865	1335	2349	1	chr2B.!!$R1	1014
9	TraesCS2A01G447200	chr2D	556267000	556268783	1783	False	2071.000000	2071	88.036	799	2547	1	chr2D.!!$F1	1748
10	TraesCS2A01G447200	chr2D	556317427	556318907	1480	False	1857.000000	1857	89.508	1	1490	1	chr2D.!!$F3	1489
11	TraesCS2A01G447200	chr2D	556407516	556409281	1765	False	1530.000000	1530	82.926	516	2290	1	chr2D.!!$F6	1774
12	TraesCS2A01G447200	chr2D	556618798	556620396	1598	False	1417.000000	1417	83.313	700	2290	1	chr2D.!!$F7	1590
13	TraesCS2A01G447200	chr2D	556365163	556366760	1597	False	1301.000000	1301	82.062	700	2315	1	chr2D.!!$F5	1615
14	TraesCS2A01G447200	chr2D	556339260	556341083	1823	False	1119.500000	1694	90.179	1347	3108	2	chr2D.!!$F8	1761
15	TraesCS2A01G447200	chr2D	556350527	556352132	1605	False	987.500000	1712	86.846	979	2624	2	chr2D.!!$F9	1645
16	TraesCS2A01G447200	chr2D	556641980	556643589	1609	False	566.050000	1070	91.818	640	2152	2	chr2D.!!$F10	1512
17	TraesCS2A01G447200	chr2D	556309995	556310558	563	False	497.000000	497	82.818	2534	3108	1	chr2D.!!$F2	574

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
625	649	0.027979	CCACTTGTTGACAGTGCGTG	59.972	55.0	0.00	0.0	32.68	5.34	F
718	783	0.032017	ATCTCCGGAGCAACTACCCT	60.032	55.0	27.39	0.0	0.00	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1964	2255	0.030235	CCCGCAGATGCAACATCATG	59.970	55.000	10.02	6.53	42.21	3.07	R
2600	4620	1.280998	CTGGAAACATAGGGTTCCGGT	59.719	52.381	22.37	0.00	39.29	5.28	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
19	20	2.609427	TCAATTCTCGAGGCTCATGG	57.391	50.000	15.95	3.74	0.00	3.66
31	32	2.606213	TCATGGCTGGACACGGGA	60.606	61.111	0.00	0.00	0.00	5.14
54	55	1.849097	GGGTGCCGTCGACTATTTAG	58.151	55.000	14.70	0.00	0.00	1.85
59	60	4.916249	GGTGCCGTCGACTATTTAGATTAG	59.084	45.833	14.70	0.00	0.00	1.73
87	88	5.906772	AATTATACCTCCAAATCCGGACT	57.093	39.130	6.12	0.00	0.00	3.85
90	91	2.249309	ACCTCCAAATCCGGACTAGT	57.751	50.000	6.12	0.00	0.00	2.57
92	93	3.924922	ACCTCCAAATCCGGACTAGTAT	58.075	45.455	6.12	0.00	0.00	2.12
118	119	8.817100	TCGCTTAGTTGATGTAAATGTAATGAG	58.183	33.333	0.00	0.00	0.00	2.90
186	187	0.312416	CCCGGTTTGCACGAATTTCA	59.688	50.000	0.00	0.00	0.00	2.69
188	189	2.609244	CCCGGTTTGCACGAATTTCATT	60.609	45.455	0.00	0.00	0.00	2.57
237	238	0.748005	TTCGGCTAAGCTTGGATGGC	60.748	55.000	14.82	10.02	0.00	4.40
269	270	1.006102	CATATCCGCGGACTGGTCC	60.006	63.158	33.75	9.55	46.18	4.46
270	271	2.207924	ATATCCGCGGACTGGTCCC	61.208	63.158	33.75	6.26	46.96	4.46
273	274	4.016706	CCGCGGACTGGTCCCTTT	62.017	66.667	24.07	0.00	46.96	3.11
280	281	1.056660	GACTGGTCCCTTTCTGTCCA	58.943	55.000	0.00	0.00	0.00	4.02
281	282	0.765510	ACTGGTCCCTTTCTGTCCAC	59.234	55.000	0.00	0.00	0.00	4.02
304	305	3.491447	GGATGGATGCGGGAGAAAATTTG	60.491	47.826	0.00	0.00	0.00	2.32
310	311	0.601057	CGGGAGAAAATTTGCGGGTT	59.399	50.000	0.00	0.00	0.00	4.11
343	344	8.528643	GGTGCCCTAAGAATTGTAGTTTATTTT	58.471	33.333	0.00	0.00	0.00	1.82
364	366	1.424403	TTCTTGCGTACATGGACGTG	58.576	50.000	30.03	20.04	44.74	4.49
428	430	1.673923	CGATCTGCACTGCAAGGAAGA	60.674	52.381	4.99	0.00	38.41	2.87
429	431	2.641305	GATCTGCACTGCAAGGAAGAT	58.359	47.619	4.99	7.34	38.41	2.40
430	432	2.574006	TCTGCACTGCAAGGAAGATT	57.426	45.000	4.99	0.00	38.41	2.40
470	491	1.470458	GGTCCCGTTACCTCATTCGTC	60.470	57.143	0.00	0.00	36.53	4.20
490	511	2.030540	TCCGTGGCGCTAACTATGTATC	60.031	50.000	7.64	0.00	0.00	2.24
498	522	4.307432	CGCTAACTATGTATCACCCCAAG	58.693	47.826	0.00	0.00	0.00	3.61
502	526	7.524863	CGCTAACTATGTATCACCCCAAGATTA	60.525	40.741	0.00	0.00	0.00	1.75
513	537	5.548056	TCACCCCAAGATTAAGGATCTATCC	59.452	44.000	0.35	0.35	44.41	2.59
598	622	2.849880	TTCATTTTCTATGCGGCAGC	57.150	45.000	9.25	0.31	45.41	5.25
599	623	1.024271	TCATTTTCTATGCGGCAGCC	58.976	50.000	9.25	0.00	44.33	4.85
600	624	1.027357	CATTTTCTATGCGGCAGCCT	58.973	50.000	10.54	0.00	44.33	4.58
601	625	1.027357	ATTTTCTATGCGGCAGCCTG	58.973	50.000	10.54	4.27	44.33	4.85
622	646	0.029834	CTGCCACTTGTTGACAGTGC	59.970	55.000	0.00	0.00	32.68	4.40
623	647	1.009675	GCCACTTGTTGACAGTGCG	60.010	57.895	0.00	0.00	32.68	5.34
624	648	1.714899	GCCACTTGTTGACAGTGCGT	61.715	55.000	0.00	0.00	32.68	5.24
625	649	0.027979	CCACTTGTTGACAGTGCGTG	59.972	55.000	0.00	0.00	32.68	5.34
708	773	4.118410	GCATGCAGAATATATCTCCGGAG	58.882	47.826	26.32	26.32	35.73	4.63
709	774	3.876274	TGCAGAATATATCTCCGGAGC	57.124	47.619	27.39	12.27	35.73	4.70
713	778	4.322349	GCAGAATATATCTCCGGAGCAACT	60.322	45.833	27.39	14.36	35.73	3.16
714	779	5.105716	GCAGAATATATCTCCGGAGCAACTA	60.106	44.000	27.39	14.72	35.73	2.24
717	782	1.700955	TATCTCCGGAGCAACTACCC	58.299	55.000	27.39	0.00	0.00	3.69
718	783	0.032017	ATCTCCGGAGCAACTACCCT	60.032	55.000	27.39	0.00	0.00	4.34
758	833	5.067413	ACACACGATTAGAGTATCCGACATT	59.933	40.000	0.00	0.00	33.66	2.71
759	834	5.977725	CACACGATTAGAGTATCCGACATTT	59.022	40.000	0.00	0.00	33.66	2.32
790	874	5.018539	TCCAATACTAATGGACAAGACGG	57.981	43.478	0.00	0.00	41.98	4.79
791	875	4.712829	TCCAATACTAATGGACAAGACGGA	59.287	41.667	0.00	0.00	41.98	4.69
792	876	5.188163	TCCAATACTAATGGACAAGACGGAA	59.812	40.000	0.00	0.00	41.98	4.30
793	877	5.523916	CCAATACTAATGGACAAGACGGAAG	59.476	44.000	0.00	0.00	40.56	3.46
794	878	6.338146	CAATACTAATGGACAAGACGGAAGA	58.662	40.000	0.00	0.00	0.00	2.87
930	1049	4.573900	AGAGAGGACACAAACATAGCTTG	58.426	43.478	0.00	0.00	0.00	4.01
1353	1559	3.245016	TGCATGGACTGTCAATTTCCTCT	60.245	43.478	10.38	0.00	0.00	3.69
1384	1593	5.473504	ACCTTTTGCCATAGTTGTTAGTCTG	59.526	40.000	0.00	0.00	0.00	3.51
1687	1946	1.151668	CGCAGCTTCTACAACAGCTT	58.848	50.000	0.00	0.00	44.28	3.74
1757	2016	0.748450	AGCTGCAGCAAACACAATGT	59.252	45.000	38.24	12.75	45.16	2.71
1786	2045	1.512926	GCGGTAGCATGATTCCGAAT	58.487	50.000	29.74	0.00	44.86	3.34
1886	2177	0.100682	GCAGCAGCTGACCAATGATG	59.899	55.000	27.39	0.00	37.91	3.07
1888	2179	1.035932	AGCAGCTGACCAATGATGCC	61.036	55.000	20.43	0.00	45.39	4.40
1918	2209	2.623915	AAGCTCCTTTGCAGCAGCG	61.624	57.895	0.00	0.00	46.23	5.18
1956	2247	3.689347	TCTGCAATACCACAGCTTCATT	58.311	40.909	0.00	0.00	33.80	2.57
1957	2248	4.081406	TCTGCAATACCACAGCTTCATTT	58.919	39.130	0.00	0.00	33.80	2.32
1958	2249	4.082625	TCTGCAATACCACAGCTTCATTTG	60.083	41.667	0.00	0.00	33.80	2.32
1959	2250	2.925563	GCAATACCACAGCTTCATTTGC	59.074	45.455	0.00	0.00	0.00	3.68
1960	2251	3.614630	GCAATACCACAGCTTCATTTGCA	60.615	43.478	9.66	0.00	38.40	4.08
1961	2252	4.751060	CAATACCACAGCTTCATTTGCAT	58.249	39.130	0.00	0.00	0.00	3.96
1962	2253	4.644103	ATACCACAGCTTCATTTGCATC	57.356	40.909	0.00	0.00	0.00	3.91
1963	2254	1.200716	ACCACAGCTTCATTTGCATCG	59.799	47.619	0.00	0.00	0.00	3.84
1964	2255	1.265568	CACAGCTTCATTTGCATCGC	58.734	50.000	0.00	0.00	0.00	4.58
2036	2363	1.454976	CTGGAGCCCATGATGGAGG	59.545	63.158	14.26	0.00	40.96	4.30
2155	2513	5.007234	TGTGTATGACAGTTTTGTACAGTGC	59.993	40.000	0.00	0.00	37.76	4.40
2222	2587	9.175060	CGTTGATTTGTTTATGTGTTGATTGTA	57.825	29.630	0.00	0.00	0.00	2.41
2241	2606	8.677300	TGATTGTATTTCTTCCAGTAGATTTGC	58.323	33.333	0.00	0.00	0.00	3.68
2325	2728	9.679661	TTAAGATGTTGCCACTAATTAAGATGA	57.320	29.630	0.00	0.00	0.00	2.92
2326	2729	8.579850	AAGATGTTGCCACTAATTAAGATGAA	57.420	30.769	0.00	0.00	0.00	2.57
2474	2881	1.080025	ACGAACGGAGCTAAGGTGC	60.080	57.895	0.00	0.00	0.00	5.01
2549	4569	5.193679	GCAGGAACACTACCTTTCCATAAT	58.806	41.667	3.32	0.00	43.41	1.28
2620	5193	1.280998	ACCGGAACCCTATGTTTCCAG	59.719	52.381	9.46	0.00	37.29	3.86
2636	5209	7.447374	TGTTTCCAGTAATGTATTCACCTTG	57.553	36.000	0.00	0.00	0.00	3.61
2666	5239	8.066000	ACAGTTTCTTGTAAATACGTTTGTAGC	58.934	33.333	0.00	0.00	33.17	3.58
2668	5241	7.443272	AGTTTCTTGTAAATACGTTTGTAGCCT	59.557	33.333	0.00	0.00	33.17	4.58
2669	5242	7.733402	TTCTTGTAAATACGTTTGTAGCCTT	57.267	32.000	0.00	0.00	33.17	4.35
2670	5243	7.124347	TCTTGTAAATACGTTTGTAGCCTTG	57.876	36.000	0.00	0.00	33.17	3.61
2671	5244	6.707161	TCTTGTAAATACGTTTGTAGCCTTGT	59.293	34.615	0.00	0.00	33.17	3.16
2672	5245	7.871973	TCTTGTAAATACGTTTGTAGCCTTGTA	59.128	33.333	0.00	0.00	33.17	2.41
2673	5246	7.585286	TGTAAATACGTTTGTAGCCTTGTAG	57.415	36.000	0.00	0.00	33.17	2.74
2674	5247	6.591062	TGTAAATACGTTTGTAGCCTTGTAGG	59.409	38.462	0.00	0.00	33.27	3.18
2675	5248	2.467566	ACGTTTGTAGCCTTGTAGGG	57.532	50.000	0.00	0.00	35.37	3.53
2676	5249	1.972795	ACGTTTGTAGCCTTGTAGGGA	59.027	47.619	0.00	0.00	35.37	4.20
2677	5250	2.369532	ACGTTTGTAGCCTTGTAGGGAA	59.630	45.455	0.00	0.00	35.37	3.97
2678	5251	3.008704	ACGTTTGTAGCCTTGTAGGGAAT	59.991	43.478	0.00	0.00	35.37	3.01
2679	5252	3.374058	CGTTTGTAGCCTTGTAGGGAATG	59.626	47.826	0.00	0.00	35.37	2.67
2688	5262	4.770531	GCCTTGTAGGGAATGGTTTTAAGT	59.229	41.667	0.00	0.00	35.37	2.24
2695	5269	4.772100	AGGGAATGGTTTTAAGTGGTGATG	59.228	41.667	0.00	0.00	0.00	3.07
2777	6765	7.903995	TTCTGGATTAAAATTTGGTTCATGC	57.096	32.000	0.00	0.00	0.00	4.06
2778	6766	6.405538	TCTGGATTAAAATTTGGTTCATGCC	58.594	36.000	0.00	0.00	0.00	4.40
2897	6886	8.863049	GCACAATACCATTTTGAATAGAACAAG	58.137	33.333	0.00	0.00	0.00	3.16
2956	6947	0.736636	CAACATGACATGGCGCATCT	59.263	50.000	19.39	0.00	33.60	2.90
3061	7055	6.721571	AATCCATTGTAGTGACTTTACACG	57.278	37.500	0.00	0.00	44.35	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	2.673523	GTGTCCAGCCATGAGCCT	59.326	61.111	0.00	0.00	45.47	4.58
19	20	3.047877	CCGTTTCCCGTGTCCAGC	61.048	66.667	0.00	0.00	33.66	4.85
21	22	3.162858	ACCCGTTTCCCGTGTCCA	61.163	61.111	0.00	0.00	33.66	4.02
38	39	4.581824	ACCTAATCTAAATAGTCGACGGCA	59.418	41.667	10.46	0.00	0.00	5.69
78	79	4.396522	ACTAAGCGATACTAGTCCGGATT	58.603	43.478	7.81	5.90	0.00	3.01
92	93	8.710835	TCATTACATTTACATCAACTAAGCGA	57.289	30.769	0.00	0.00	0.00	4.93
144	145	9.810545	CGGGTGAATTTTAATATAAACATGGTT	57.189	29.630	0.00	0.00	0.00	3.67
186	187	5.514274	ACAACAGTTTGAATCAACCGAAT	57.486	34.783	0.00	0.00	36.48	3.34
188	189	3.001838	CGACAACAGTTTGAATCAACCGA	59.998	43.478	0.00	0.00	36.48	4.69
237	238	0.729116	GATATGAATGCGGGATGCCG	59.271	55.000	22.84	22.84	45.60	5.69
252	253	3.456317	GGACCAGTCCGCGGATAT	58.544	61.111	33.58	20.78	40.36	1.63
280	281	1.622607	TTTCTCCCGCATCCATCCGT	61.623	55.000	0.00	0.00	0.00	4.69
281	282	0.463654	TTTTCTCCCGCATCCATCCG	60.464	55.000	0.00	0.00	0.00	4.18
304	305	3.670377	GCACCTCCAACAACCCGC	61.670	66.667	0.00	0.00	0.00	6.13
343	344	2.222213	CACGTCCATGTACGCAAGAAAA	59.778	45.455	11.06	0.00	46.71	2.29
406	408	0.390340	TCCTTGCAGTGCAGATCGAC	60.390	55.000	18.81	0.00	40.61	4.20
434	436	0.035458	GACCGGGCTATCCATCAAGG	59.965	60.000	6.32	0.00	39.47	3.61
435	437	0.035458	GGACCGGGCTATCCATCAAG	59.965	60.000	7.57	0.00	34.87	3.02
436	438	1.415672	GGGACCGGGCTATCCATCAA	61.416	60.000	7.57	0.00	36.65	2.57
437	439	1.841556	GGGACCGGGCTATCCATCA	60.842	63.158	7.57	0.00	36.65	3.07
438	440	2.943978	CGGGACCGGGCTATCCATC	61.944	68.421	7.57	0.00	36.65	3.51
439	441	2.923035	CGGGACCGGGCTATCCAT	60.923	66.667	7.57	0.00	36.65	3.41
440	442	2.586450	TAACGGGACCGGGCTATCCA	62.586	60.000	7.57	0.00	44.69	3.41
470	491	2.287970	TGATACATAGTTAGCGCCACGG	60.288	50.000	2.29	0.00	0.00	4.94
490	511	5.569630	CGGATAGATCCTTAATCTTGGGGTG	60.570	48.000	6.97	0.00	42.30	4.61
498	522	3.512680	CACGCCGGATAGATCCTTAATC	58.487	50.000	5.05	0.00	44.93	1.75
502	526	1.115930	AGCACGCCGGATAGATCCTT	61.116	55.000	5.05	0.00	44.93	3.36
513	537	2.476619	CAGGATCTATTTAAGCACGCCG	59.523	50.000	0.00	0.00	0.00	6.46
598	622	1.529010	TCAACAAGTGGCAGGCAGG	60.529	57.895	0.00	0.00	0.00	4.85
599	623	1.102809	TGTCAACAAGTGGCAGGCAG	61.103	55.000	0.00	0.00	36.75	4.85
600	624	1.077140	TGTCAACAAGTGGCAGGCA	60.077	52.632	0.00	0.00	36.75	4.75
601	625	3.840437	TGTCAACAAGTGGCAGGC	58.160	55.556	0.00	0.00	36.75	4.85
623	647	3.564225	ACAAGGAGGAAAAACGTGATCAC	59.436	43.478	16.21	16.21	0.00	3.06
624	648	3.815809	ACAAGGAGGAAAAACGTGATCA	58.184	40.909	0.00	0.00	0.00	2.92
625	649	4.537015	CAACAAGGAGGAAAAACGTGATC	58.463	43.478	0.00	0.00	0.00	2.92
631	659	2.803133	GCAGGCAACAAGGAGGAAAAAC	60.803	50.000	0.00	0.00	41.41	2.43
634	662	0.827507	GGCAGGCAACAAGGAGGAAA	60.828	55.000	0.00	0.00	41.41	3.13
693	734	5.394333	GGGTAGTTGCTCCGGAGATATATTC	60.394	48.000	35.69	15.54	0.00	1.75
694	735	4.466726	GGGTAGTTGCTCCGGAGATATATT	59.533	45.833	35.69	15.95	0.00	1.28
698	762	1.217183	AGGGTAGTTGCTCCGGAGATA	59.783	52.381	35.69	19.73	0.00	1.98
708	773	2.360801	TGCAAGTCAAAAGGGTAGTTGC	59.639	45.455	7.07	7.07	45.51	4.17
709	774	4.613622	CGATGCAAGTCAAAAGGGTAGTTG	60.614	45.833	0.00	0.00	0.00	3.16
713	778	3.134574	ACGATGCAAGTCAAAAGGGTA	57.865	42.857	0.00	0.00	0.00	3.69
714	779	1.981256	ACGATGCAAGTCAAAAGGGT	58.019	45.000	0.00	0.00	0.00	4.34
717	782	4.211389	GTGTGTACGATGCAAGTCAAAAG	58.789	43.478	1.25	0.00	0.00	2.27
718	783	4.203950	GTGTGTACGATGCAAGTCAAAA	57.796	40.909	1.25	0.00	0.00	2.44
758	833	6.709281	TCCATTAGTATTGGACGGTTTGTAA	58.291	36.000	9.30	0.00	38.35	2.41
759	834	6.297080	TCCATTAGTATTGGACGGTTTGTA	57.703	37.500	9.30	0.00	38.35	2.41
789	873	6.901081	TTTTCCTTCCATTCTTCTTCTTCC	57.099	37.500	0.00	0.00	0.00	3.46
790	874	7.752686	CGAATTTTCCTTCCATTCTTCTTCTTC	59.247	37.037	0.00	0.00	0.00	2.87
791	875	7.231519	ACGAATTTTCCTTCCATTCTTCTTCTT	59.768	33.333	0.00	0.00	0.00	2.52
792	876	6.717084	ACGAATTTTCCTTCCATTCTTCTTCT	59.283	34.615	0.00	0.00	0.00	2.85
793	877	6.914259	ACGAATTTTCCTTCCATTCTTCTTC	58.086	36.000	0.00	0.00	0.00	2.87
794	878	6.901081	ACGAATTTTCCTTCCATTCTTCTT	57.099	33.333	0.00	0.00	0.00	2.52
1353	1559	2.576191	ACTATGGCAAAAGGTCCAGCTA	59.424	45.455	0.00	0.00	35.57	3.32
1384	1593	8.682936	ATAATTTATCCATGTCAGTCACTTCC	57.317	34.615	0.00	0.00	0.00	3.46
1456	1691	7.699391	CAGTAGTTCTTGATTTCGTTATCCGTA	59.301	37.037	0.00	0.00	37.94	4.02
1468	1703	3.746492	GCGTGTTCCAGTAGTTCTTGATT	59.254	43.478	0.00	0.00	0.00	2.57
1687	1946	1.838846	GGATCCGATGGCCTGGAGA	60.839	63.158	15.56	3.72	37.76	3.71
1757	2016	2.076100	CATGCTACCGCTTGAGTTCAA	58.924	47.619	0.00	0.00	42.19	2.69
1778	2037	2.420687	GGTCCAGCAAGAGATTCGGAAT	60.421	50.000	2.19	2.19	0.00	3.01
1786	2045	1.942776	TCATCTGGTCCAGCAAGAGA	58.057	50.000	14.64	4.47	29.11	3.10
1886	2177	0.392327	GAGCTTGTTCCTGGAGAGGC	60.392	60.000	0.00	0.08	39.57	4.70
1888	2179	1.274712	AGGAGCTTGTTCCTGGAGAG	58.725	55.000	5.23	0.00	45.84	3.20
1963	2254	0.594028	CCGCAGATGCAACATCATGC	60.594	55.000	10.02	13.49	46.58	4.06
1964	2255	0.030235	CCCGCAGATGCAACATCATG	59.970	55.000	10.02	6.53	42.21	3.07
1976	2276	3.680786	CGACCAGTCACCCGCAGA	61.681	66.667	0.00	0.00	0.00	4.26
2036	2363	1.520342	GAGAGCACAGATCGGGCAC	60.520	63.158	13.02	7.61	0.00	5.01
2192	2554	7.363431	TCAACACATAAACAAATCAACGCATA	58.637	30.769	0.00	0.00	0.00	3.14
2222	2587	5.574188	ACTGGCAAATCTACTGGAAGAAAT	58.426	37.500	0.00	0.00	37.43	2.17
2223	2588	4.985538	ACTGGCAAATCTACTGGAAGAAA	58.014	39.130	0.00	0.00	37.43	2.52
2241	2606	3.694072	TGACAACCTTTCAACTTGACTGG	59.306	43.478	7.39	7.39	0.00	4.00
2325	2728	5.856455	CGACAAAAGTGTTTCAGTTGTCTTT	59.144	36.000	11.70	0.00	43.71	2.52
2326	2729	5.390613	CGACAAAAGTGTTTCAGTTGTCTT	58.609	37.500	11.70	0.00	43.71	3.01
2384	2790	2.200373	ATTGCTAAGCTCCAACCGTT	57.800	45.000	0.00	0.00	0.00	4.44
2386	2792	3.179443	TCTATTGCTAAGCTCCAACCG	57.821	47.619	0.00	0.00	0.00	4.44
2518	2925	1.833787	TAGTGTTCCTGCCGGTTCCC	61.834	60.000	1.90	0.00	0.00	3.97
2589	4609	1.551883	GGGTTCCGGTTAGCTCTGTTA	59.448	52.381	0.00	0.00	0.00	2.41
2592	4612	1.481871	TAGGGTTCCGGTTAGCTCTG	58.518	55.000	0.00	0.00	0.00	3.35
2596	4616	2.704464	AACATAGGGTTCCGGTTAGC	57.296	50.000	0.00	0.04	33.35	3.09
2600	4620	1.280998	CTGGAAACATAGGGTTCCGGT	59.719	52.381	22.37	0.00	39.29	5.28
2604	4624	8.747538	AATACATTACTGGAAACATAGGGTTC	57.252	34.615	0.00	0.00	39.29	3.62
2620	5193	7.553881	ACTGTATGCAAGGTGAATACATTAC	57.446	36.000	9.08	0.00	45.23	1.89
2636	5209	8.837059	CAAACGTATTTACAAGAAACTGTATGC	58.163	33.333	0.00	0.00	31.96	3.14
2666	5239	5.185056	CCACTTAAAACCATTCCCTACAAGG	59.815	44.000	0.00	0.00	34.30	3.61
2668	5241	5.536916	CACCACTTAAAACCATTCCCTACAA	59.463	40.000	0.00	0.00	0.00	2.41
2669	5242	5.074115	CACCACTTAAAACCATTCCCTACA	58.926	41.667	0.00	0.00	0.00	2.74
2670	5243	5.318630	TCACCACTTAAAACCATTCCCTAC	58.681	41.667	0.00	0.00	0.00	3.18
2671	5244	5.586155	TCACCACTTAAAACCATTCCCTA	57.414	39.130	0.00	0.00	0.00	3.53
2672	5245	4.463050	TCACCACTTAAAACCATTCCCT	57.537	40.909	0.00	0.00	0.00	4.20
2673	5246	4.526650	ACATCACCACTTAAAACCATTCCC	59.473	41.667	0.00	0.00	0.00	3.97
2674	5247	5.722021	ACATCACCACTTAAAACCATTCC	57.278	39.130	0.00	0.00	0.00	3.01
2675	5248	7.681939	TCTACATCACCACTTAAAACCATTC	57.318	36.000	0.00	0.00	0.00	2.67
2676	5249	9.747898	TTATCTACATCACCACTTAAAACCATT	57.252	29.630	0.00	0.00	0.00	3.16
2677	5250	9.747898	TTTATCTACATCACCACTTAAAACCAT	57.252	29.630	0.00	0.00	0.00	3.55
2678	5251	9.747898	ATTTATCTACATCACCACTTAAAACCA	57.252	29.630	0.00	0.00	0.00	3.67
2727	6715	4.905429	AGTCTTTGCAAAAGGTGGTTTTT	58.095	34.783	13.84	0.00	36.11	1.94
2835	6824	9.393249	CTTCAAAATCGTCAATTAAGTTGCTAA	57.607	29.630	0.00	0.00	37.74	3.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.