AutoCloner

Multiple sequence alignment - TraesCS3A01G507900

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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	TraesCS3A01G507900	chr3A	100.000	5107	0	0	1	5107	729181542	729186648	0.000000e+00	9431.0
1	TraesCS3A01G507900	chr3A	94.361	2979	91	32	837	3785	729578945	729576014	0.000000e+00	4499.0
2	TraesCS3A01G507900	chr3A	95.720	1285	42	6	3824	5103	729576008	729574732	0.000000e+00	2056.0
3	TraesCS3A01G507900	chr3A	99.507	1015	5	0	2661	3675	729353231	729354245	0.000000e+00	1847.0
4	TraesCS3A01G507900	chr3A	85.278	557	58	14	3996	4541	599421758	599421215	2.080000e-153	553.0
5	TraesCS3A01G507900	chr3A	77.590	473	64	23	4674	5107	585433461	585432992	1.100000e-61	248.0
6	TraesCS3A01G507900	chr3A	93.913	115	7	0	3671	3785	729356330	729356444	1.890000e-39	174.0
7	TraesCS3A01G507900	chr3A	86.992	123	15	1	4542	4664	369461372	369461251	2.480000e-28	137.0
8	TraesCS3A01G507900	chr3A	86.869	99	12	1	4543	4641	585433561	585433464	5.410000e-20	110.0
9	TraesCS3A01G507900	chr3B	91.780	3017	139	43	816	3785	807078706	807081660	0.000000e+00	4096.0
10	TraesCS3A01G507900	chr3B	96.023	855	28	5	4070	4918	807081973	807082827	0.000000e+00	1386.0
11	TraesCS3A01G507900	chr3B	94.332	247	8	4	3828	4072	807081656	807081898	1.740000e-99	374.0
12	TraesCS3A01G507900	chr3B	97.409	193	5	0	4915	5107	807116032	807116224	3.810000e-86	329.0
13	TraesCS3A01G507900	chr3B	75.610	410	60	18	847	1234	807187209	807186818	3.160000e-37	167.0
14	TraesCS3A01G507900	chr3B	89.011	91	3	3	2314	2397	257512492	257512402	6.990000e-19	106.0
15	TraesCS3A01G507900	chr3D	95.756	919	32	3	2874	3785	599165150	599166068	0.000000e+00	1474.0
16	TraesCS3A01G507900	chr3D	86.966	890	71	23	1446	2318	599164254	599165115	0.000000e+00	959.0
17	TraesCS3A01G507900	chr3D	91.956	547	29	5	824	1369	599163690	599164222	0.000000e+00	752.0
18	TraesCS3A01G507900	chr3D	80.717	809	86	22	7	776	599162897	599163674	2.670000e-157	566.0
19	TraesCS3A01G507900	chr3D	76.923	455	61	18	4674	5103	444536065	444535630	8.610000e-53	219.0
20	TraesCS3A01G507900	chr3D	100.000	28	0	0	1713	1740	599164552	599164579	9.000000e-03	52.8
21	TraesCS3A01G507900	chr5B	82.679	560	68	17	3994	4541	494900795	494900253	2.150000e-128	470.0
22	TraesCS3A01G507900	chr5B	82.129	526	57	13	4042	4534	11149115	11148594	2.840000e-112	416.0
23	TraesCS3A01G507900	chr4A	81.400	500	55	17	4046	4535	662585172	662585643	1.740000e-99	374.0
24	TraesCS3A01G507900	chr4A	76.396	555	101	18	4540	5082	491722979	491723515	6.520000e-69	272.0
25	TraesCS3A01G507900	chr4A	82.743	226	29	8	4882	5103	156619906	156619687	5.220000e-45	193.0
26	TraesCS3A01G507900	chr2D	77.913	575	93	23	4542	5103	12983256	12983809	1.370000e-85	327.0
27	TraesCS3A01G507900	chr2D	76.938	529	73	29	4584	5103	13071769	13072257	6.560000e-64	255.0
28	TraesCS3A01G507900	chr4D	76.271	531	91	28	4584	5102	318239625	318240132	3.050000e-62	250.0
29	TraesCS3A01G507900	chr4D	88.889	90	8	2	2306	2393	43548860	43548949	5.410000e-20	110.0
30	TraesCS3A01G507900	chr2A	83.264	239	30	4	4868	5103	15126457	15126688	1.440000e-50	211.0
31	TraesCS3A01G507900	chr2A	83.333	180	17	9	4007	4180	578905602	578905774	2.460000e-33	154.0
32	TraesCS3A01G507900	chr5D	79.720	286	40	12	4830	5103	381147931	381147652	1.880000e-44	191.0
33	TraesCS3A01G507900	chr5D	97.143	70	0	2	2317	2384	546839010	546838941	3.230000e-22	117.0
34	TraesCS3A01G507900	chr1A	92.405	79	4	2	2313	2390	24740562	24740639	1.500000e-20	111.0
35	TraesCS3A01G507900	chr1A	91.463	82	4	3	2311	2390	24610948	24611028	5.410000e-20	110.0
36	TraesCS3A01G507900	chr1A	90.361	83	5	3	2310	2390	24591517	24591598	6.990000e-19	106.0
37	TraesCS3A01G507900	chr2B	88.764	89	6	4	2305	2390	168852032	168851945	6.990000e-19	106.0
38	TraesCS3A01G507900	chr7D	79.675	123	22	3	4543	4664	524553858	524553978	9.110000e-13	86.1

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	TraesCS3A01G507900	chr3A	729181542	729186648	5106	False	9431.00	9431	100.0000	1	5107	1	chr3A.!!$F1	5106
1	TraesCS3A01G507900	chr3A	729574732	729578945	4213	True	3277.50	4499	95.0405	837	5103	2	chr3A.!!$R4	4266
2	TraesCS3A01G507900	chr3A	729353231	729356444	3213	False	1010.50	1847	96.7100	2661	3785	2	chr3A.!!$F2	1124
3	TraesCS3A01G507900	chr3A	599421215	599421758	543	True	553.00	553	85.2780	3996	4541	1	chr3A.!!$R2	545
4	TraesCS3A01G507900	chr3B	807078706	807082827	4121	False	1952.00	4096	94.0450	816	4918	3	chr3B.!!$F2	4102
5	TraesCS3A01G507900	chr3D	599162897	599166068	3171	False	760.76	1474	91.0790	7	3785	5	chr3D.!!$F1	3778
6	TraesCS3A01G507900	chr5B	494900253	494900795	542	True	470.00	470	82.6790	3994	4541	1	chr5B.!!$R2	547
7	TraesCS3A01G507900	chr5B	11148594	11149115	521	True	416.00	416	82.1290	4042	4534	1	chr5B.!!$R1	492
8	TraesCS3A01G507900	chr4A	491722979	491723515	536	False	272.00	272	76.3960	4540	5082	1	chr4A.!!$F1	542
9	TraesCS3A01G507900	chr2D	12983256	12983809	553	False	327.00	327	77.9130	4542	5103	1	chr2D.!!$F1	561
10	TraesCS3A01G507900	chr4D	318239625	318240132	507	False	250.00	250	76.2710	4584	5102	1	chr4D.!!$F2	518

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
408	433	0.245539	CTGCTCAAAACATGCCCAGG	59.754	55.000	0.00	0.00	0.0	4.45	F
544	569	0.598158	TTAAACGGCGTCTGAAGCGT	60.598	50.000	15.17	8.09	35.0	5.07	F
817	855	2.334977	TCTCTGTTGAAAGGTAGCCCA	58.665	47.619	0.00	0.00	0.0	5.36	F
1685	1778	1.211949	TCAAAAGCTAATCCCCCTCGG	59.788	52.381	0.00	0.00	0.0	4.63	F
3573	3742	3.603158	TGAAGCTATCACGCCAAGTTA	57.397	42.857	0.00	0.00	31.5	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1664	1756	2.158608	CCGAGGGGGATTAGCTTTTGAT	60.159	50.000	0.00	0.00	38.47	2.57	R
1685	1778	4.507879	GGCAACATGGCAATGAGC	57.492	55.556	8.45	11.15	43.14	4.26	R
2567	2723	5.726980	ATTTTCTGCCTCAAACTTGCATA	57.273	34.783	0.00	0.00	33.97	3.14	R
3620	3789	1.420138	TCTTCTTCCTCACCAACACCC	59.580	52.381	0.00	0.00	0.00	4.61	R
4807	7187	0.107165	GGCGCAGAGGGGATTTAGTT	60.107	55.000	10.83	0.00	0.00	2.24	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
130	135	4.664150	AAGTCCGCAGATTTTGGAAAAA	57.336	36.364	0.00	0.00	32.60	1.94
182	187	8.254178	TGTGGATTTGAAAAATATTCATGCAC	57.746	30.769	8.54	8.54	33.36	4.57
233	238	9.921637	TGTATTTGAATAAAGTTCATTGGGTTC	57.078	29.630	0.00	0.00	0.00	3.62
315	340	6.596309	AAAGCAGATAAAGGGAAGAAAAGG	57.404	37.500	0.00	0.00	0.00	3.11
319	344	6.435591	AGCAGATAAAGGGAAGAAAAGGAAAG	59.564	38.462	0.00	0.00	0.00	2.62
325	350	4.878968	AGGGAAGAAAAGGAAAGACCAAA	58.121	39.130	0.00	0.00	42.04	3.28
330	355	6.876789	GGAAGAAAAGGAAAGACCAAACAAAA	59.123	34.615	0.00	0.00	42.04	2.44
365	390	7.843490	AAAAACTAAAAGAGCAGGGAAAAAC	57.157	32.000	0.00	0.00	0.00	2.43
403	428	2.719426	AGAAGCTGCTCAAAACATGC	57.281	45.000	1.00	0.00	0.00	4.06
408	433	0.245539	CTGCTCAAAACATGCCCAGG	59.754	55.000	0.00	0.00	0.00	4.45
418	443	1.379576	ATGCCCAGGAAGCTTCTGC	60.380	57.895	25.05	20.74	40.05	4.26
421	446	1.003355	CCCAGGAAGCTTCTGCGAA	60.003	57.895	25.05	0.00	45.42	4.70
427	452	0.799393	GAAGCTTCTGCGAACTTCCC	59.201	55.000	19.44	0.00	45.42	3.97
434	459	1.133915	TCTGCGAACTTCCCAAAACCT	60.134	47.619	0.00	0.00	0.00	3.50
435	460	1.001378	CTGCGAACTTCCCAAAACCTG	60.001	52.381	0.00	0.00	0.00	4.00
436	461	1.314730	GCGAACTTCCCAAAACCTGA	58.685	50.000	0.00	0.00	0.00	3.86
439	464	3.702330	CGAACTTCCCAAAACCTGAAAC	58.298	45.455	0.00	0.00	0.00	2.78
458	483	3.056328	GGAGCTTCCCGTTGGTGC	61.056	66.667	0.00	0.00	34.20	5.01
464	489	1.094785	CTTCCCGTTGGTGCCTTATG	58.905	55.000	0.00	0.00	0.00	1.90
475	500	1.883084	GCCTTATGCAGACCGTCCG	60.883	63.158	0.00	0.00	40.77	4.79
490	515	5.047943	AGACCGTCCGATAAAGATTCTATGG	60.048	44.000	0.00	0.00	0.00	2.74
520	545	1.015109	TGTGCGGCTTGTACGAAAAA	58.985	45.000	0.00	0.00	35.72	1.94
531	556	5.108518	GCTTGTACGAAAAAGCCTTTAAACG	60.109	40.000	4.68	0.00	42.40	3.60
544	569	0.598158	TTAAACGGCGTCTGAAGCGT	60.598	50.000	15.17	8.09	35.00	5.07
554	579	2.854777	CGTCTGAAGCGTCAAATAGGAG	59.145	50.000	3.39	0.00	31.88	3.69
555	580	2.605366	GTCTGAAGCGTCAAATAGGAGC	59.395	50.000	3.39	0.00	31.88	4.70
601	639	2.723746	CTTGCGTATGCCATGCCC	59.276	61.111	4.05	0.00	41.78	5.36
654	692	4.320348	GCCTATGCATGCAAGAGATTTCTC	60.320	45.833	26.68	0.00	39.27	2.87
665	703	5.006165	GCAAGAGATTTCTCCACTGTATTCG	59.994	44.000	3.97	0.00	43.88	3.34
805	843	7.269477	AGAAAAACCTTTCTCATCTCTGTTG	57.731	36.000	0.00	0.00	46.88	3.33
806	844	7.056635	AGAAAAACCTTTCTCATCTCTGTTGA	58.943	34.615	0.00	0.00	46.88	3.18
807	845	7.557719	AGAAAAACCTTTCTCATCTCTGTTGAA	59.442	33.333	0.00	0.00	46.88	2.69
808	846	7.645058	AAAACCTTTCTCATCTCTGTTGAAA	57.355	32.000	0.00	0.00	0.00	2.69
809	847	6.874288	AACCTTTCTCATCTCTGTTGAAAG	57.126	37.500	0.00	0.00	40.02	2.62
810	848	5.876612	CCTTTCTCATCTCTGTTGAAAGG	57.123	43.478	15.39	15.39	45.52	3.11
811	849	5.312079	CCTTTCTCATCTCTGTTGAAAGGT	58.688	41.667	19.00	0.00	45.58	3.50
812	850	6.467677	CCTTTCTCATCTCTGTTGAAAGGTA	58.532	40.000	19.00	0.00	45.58	3.08
813	851	6.593382	CCTTTCTCATCTCTGTTGAAAGGTAG	59.407	42.308	19.00	1.29	45.58	3.18
814	852	5.078411	TCTCATCTCTGTTGAAAGGTAGC	57.922	43.478	0.00	0.00	0.00	3.58
815	853	4.081420	TCTCATCTCTGTTGAAAGGTAGCC	60.081	45.833	0.00	0.00	0.00	3.93
816	854	3.055094	TCATCTCTGTTGAAAGGTAGCCC	60.055	47.826	0.00	0.00	0.00	5.19
817	855	2.334977	TCTCTGTTGAAAGGTAGCCCA	58.665	47.619	0.00	0.00	0.00	5.36
818	856	2.912956	TCTCTGTTGAAAGGTAGCCCAT	59.087	45.455	0.00	0.00	0.00	4.00
819	857	3.330701	TCTCTGTTGAAAGGTAGCCCATT	59.669	43.478	0.00	0.00	0.00	3.16
820	858	3.686016	TCTGTTGAAAGGTAGCCCATTC	58.314	45.455	0.00	0.00	38.62	2.67
821	859	3.330701	TCTGTTGAAAGGTAGCCCATTCT	59.669	43.478	0.00	0.00	38.87	2.40
822	860	3.686016	TGTTGAAAGGTAGCCCATTCTC	58.314	45.455	0.00	0.00	38.87	2.87
823	861	3.017442	GTTGAAAGGTAGCCCATTCTCC	58.983	50.000	0.00	0.00	38.87	3.71
824	862	2.562296	TGAAAGGTAGCCCATTCTCCT	58.438	47.619	0.00	0.00	38.87	3.69
825	863	2.919602	TGAAAGGTAGCCCATTCTCCTT	59.080	45.455	0.00	0.00	38.87	3.36
826	864	3.333680	TGAAAGGTAGCCCATTCTCCTTT	59.666	43.478	7.13	7.13	46.72	3.11
827	865	3.653835	AAGGTAGCCCATTCTCCTTTC	57.346	47.619	0.00	0.00	35.32	2.62
828	866	2.852130	AGGTAGCCCATTCTCCTTTCT	58.148	47.619	0.00	0.00	0.00	2.52
829	867	2.774809	AGGTAGCCCATTCTCCTTTCTC	59.225	50.000	0.00	0.00	0.00	2.87
830	868	2.774809	GGTAGCCCATTCTCCTTTCTCT	59.225	50.000	0.00	0.00	0.00	3.10
831	869	3.181459	GGTAGCCCATTCTCCTTTCTCTC	60.181	52.174	0.00	0.00	0.00	3.20
956	995	2.785713	TTTGCGCTACCAAAACCTTC	57.214	45.000	9.73	0.00	32.20	3.46
1312	1384	4.411927	AGCCGACAGTATGGATCTTATCT	58.588	43.478	0.00	0.00	43.62	1.98
1567	1656	6.756074	TGTCTTCTGTAAAATTTGCAGGTTTG	59.244	34.615	20.54	10.40	42.68	2.93
1664	1756	8.455682	GCTACAGGCAAAATGTTATTGTACTAA	58.544	33.333	0.00	0.00	41.35	2.24
1684	1777	2.710096	TCAAAAGCTAATCCCCCTCG	57.290	50.000	0.00	0.00	0.00	4.63
1685	1778	1.211949	TCAAAAGCTAATCCCCCTCGG	59.788	52.381	0.00	0.00	0.00	4.63
2522	2677	9.754382	CAGCTTGAATTTGGCTATGTAAAATAT	57.246	29.630	0.00	0.00	34.71	1.28
2567	2723	9.610705	AGATATCGAAGCTATGCATGAATAATT	57.389	29.630	10.16	0.00	0.00	1.40
2601	2757	7.230849	TGAGGCAGAAAATTACAAATGATGT	57.769	32.000	0.00	0.00	46.36	3.06
3573	3742	3.603158	TGAAGCTATCACGCCAAGTTA	57.397	42.857	0.00	0.00	31.50	2.24
3785	6043	5.032846	TGGTGAGGAATAAGACCAAGAGAT	58.967	41.667	0.00	0.00	35.51	2.75
3786	6044	5.104776	TGGTGAGGAATAAGACCAAGAGATG	60.105	44.000	0.00	0.00	35.51	2.90
3789	6047	7.202047	GGTGAGGAATAAGACCAAGAGATGTAT	60.202	40.741	0.00	0.00	0.00	2.29
3791	6049	9.607333	TGAGGAATAAGACCAAGAGATGTATAT	57.393	33.333	0.00	0.00	0.00	0.86
3841	6099	3.386078	TGAGAGAGAGAGAGAGAGAGAGC	59.614	52.174	0.00	0.00	0.00	4.09
3886	6148	1.368641	TGTAATGGCATGCTGACGAC	58.631	50.000	18.92	10.09	0.00	4.34
3887	6149	1.066215	TGTAATGGCATGCTGACGACT	60.066	47.619	18.92	0.00	0.00	4.18
3888	6150	2.009774	GTAATGGCATGCTGACGACTT	58.990	47.619	18.92	3.77	0.00	3.01
3889	6151	0.806868	AATGGCATGCTGACGACTTG	59.193	50.000	18.92	0.00	0.00	3.16
3923	6185	7.749126	CCTATTGTTTGAAGTCGTATTTTGACC	59.251	37.037	0.00	0.00	37.04	4.02
3941	6203	5.918426	TGACCGTGTACCAACTAATGATA	57.082	39.130	0.00	0.00	0.00	2.15
4246	6614	8.186163	TGTAGTTTATATGTACTGAAGGTGTCG	58.814	37.037	0.00	0.00	0.00	4.35
4565	6941	5.186996	AGTTAAATGCACAGAACCACAAG	57.813	39.130	0.00	0.00	0.00	3.16
4772	7152	0.462047	CCGGTCGGAAGATTCCCAAG	60.462	60.000	2.83	0.00	44.67	3.61
4807	7187	1.140052	CCTCTCTCTCCACTCTCGCTA	59.860	57.143	0.00	0.00	0.00	4.26
4823	7203	2.102588	TCGCTAACTAAATCCCCTCTGC	59.897	50.000	0.00	0.00	0.00	4.26
4974	7393	7.041848	GGGTATGTATACATTGGTTTCGGTTAC	60.042	40.741	22.90	10.36	37.76	2.50
5053	7472	1.337823	GCCTCTCGTTTGTGCCTAAGA	60.338	52.381	0.00	0.00	0.00	2.10
5103	7522	6.767902	TGATACAACTATTGATGCTTCCTTCC	59.232	38.462	0.00	0.00	0.00	3.46
5104	7523	4.922206	ACAACTATTGATGCTTCCTTCCA	58.078	39.130	0.00	0.00	0.00	3.53
5105	7524	5.513233	ACAACTATTGATGCTTCCTTCCAT	58.487	37.500	0.00	0.00	0.00	3.41
5106	7525	5.359009	ACAACTATTGATGCTTCCTTCCATG	59.641	40.000	0.00	0.00	0.00	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	8.173542	ACAATTTTCCTAGTTCGTGGTAATTT	57.826	30.769	0.00	0.00	0.00	1.82
1	2	7.754851	ACAATTTTCCTAGTTCGTGGTAATT	57.245	32.000	0.00	0.00	0.00	1.40
2	3	7.446013	TGAACAATTTTCCTAGTTCGTGGTAAT	59.554	33.333	0.00	0.00	42.35	1.89
5	6	5.127491	TGAACAATTTTCCTAGTTCGTGGT	58.873	37.500	0.00	0.00	42.35	4.16
9	10	8.970691	AATTCATGAACAATTTTCCTAGTTCG	57.029	30.769	11.07	0.00	42.35	3.95
78	79	9.685828	CAAAAACGATGAACTATTCCCTTTTTA	57.314	29.630	0.00	0.00	0.00	1.52
81	82	7.519032	TCAAAAACGATGAACTATTCCCTTT	57.481	32.000	0.00	0.00	0.00	3.11
82	83	7.519032	TTCAAAAACGATGAACTATTCCCTT	57.481	32.000	0.00	0.00	32.10	3.95
84	85	8.582433	TTTTTCAAAAACGATGAACTATTCCC	57.418	30.769	0.00	0.00	36.57	3.97
160	165	9.153721	TCAAGTGCATGAATATTTTTCAAATCC	57.846	29.630	0.00	0.00	31.55	3.01
285	290	7.690256	TCTTCCCTTTATCTGCTTTTTCTAGT	58.310	34.615	0.00	0.00	0.00	2.57
286	291	8.567285	TTCTTCCCTTTATCTGCTTTTTCTAG	57.433	34.615	0.00	0.00	0.00	2.43
287	292	8.934023	TTTCTTCCCTTTATCTGCTTTTTCTA	57.066	30.769	0.00	0.00	0.00	2.10
288	293	7.839680	TTTCTTCCCTTTATCTGCTTTTTCT	57.160	32.000	0.00	0.00	0.00	2.52
289	294	7.600375	CCTTTTCTTCCCTTTATCTGCTTTTTC	59.400	37.037	0.00	0.00	0.00	2.29
292	297	6.314917	TCCTTTTCTTCCCTTTATCTGCTTT	58.685	36.000	0.00	0.00	0.00	3.51
296	301	7.094162	GGTCTTTCCTTTTCTTCCCTTTATCTG	60.094	40.741	0.00	0.00	0.00	2.90
298	303	6.719829	TGGTCTTTCCTTTTCTTCCCTTTATC	59.280	38.462	0.00	0.00	37.07	1.75
299	304	6.620429	TGGTCTTTCCTTTTCTTCCCTTTAT	58.380	36.000	0.00	0.00	37.07	1.40
300	305	6.020881	TGGTCTTTCCTTTTCTTCCCTTTA	57.979	37.500	0.00	0.00	37.07	1.85
304	309	4.404394	TGTTTGGTCTTTCCTTTTCTTCCC	59.596	41.667	0.00	0.00	37.07	3.97
305	310	5.592104	TGTTTGGTCTTTCCTTTTCTTCC	57.408	39.130	0.00	0.00	37.07	3.46
344	369	5.531122	GGTTTTTCCCTGCTCTTTTAGTT	57.469	39.130	0.00	0.00	0.00	2.24
383	408	2.489329	GGCATGTTTTGAGCAGCTTCTA	59.511	45.455	0.00	0.00	0.00	2.10
403	428	1.003355	TTCGCAGAAGCTTCCTGGG	60.003	57.895	22.81	23.68	45.90	4.45
408	433	0.799393	GGGAAGTTCGCAGAAGCTTC	59.201	55.000	19.11	19.11	45.90	3.86
418	443	3.702330	GTTTCAGGTTTTGGGAAGTTCG	58.298	45.455	0.00	0.00	0.00	3.95
421	446	2.028876	CCGTTTCAGGTTTTGGGAAGT	58.971	47.619	0.00	0.00	0.00	3.01
427	452	1.318576	AGCTCCCGTTTCAGGTTTTG	58.681	50.000	0.00	0.00	0.00	2.44
458	483	0.389391	ATCGGACGGTCTGCATAAGG	59.611	55.000	12.17	0.00	0.00	2.69
464	489	2.510768	ATCTTTATCGGACGGTCTGC	57.489	50.000	12.17	0.00	0.00	4.26
468	493	4.560919	GCCATAGAATCTTTATCGGACGGT	60.561	45.833	0.00	0.00	0.00	4.83
469	494	3.927142	GCCATAGAATCTTTATCGGACGG	59.073	47.826	0.00	0.00	0.00	4.79
471	496	3.927142	CCGCCATAGAATCTTTATCGGAC	59.073	47.826	7.56	0.00	36.77	4.79
472	497	3.056107	CCCGCCATAGAATCTTTATCGGA	60.056	47.826	12.71	0.00	36.77	4.55
475	500	4.508662	CCTCCCGCCATAGAATCTTTATC	58.491	47.826	0.00	0.00	0.00	1.75
507	532	5.108518	CGTTTAAAGGCTTTTTCGTACAAGC	60.109	40.000	18.93	4.51	44.06	4.01
526	551	1.005294	GACGCTTCAGACGCCGTTTA	61.005	55.000	0.00	0.00	33.63	2.01
531	556	1.324736	CTATTTGACGCTTCAGACGCC	59.675	52.381	0.00	0.00	31.71	5.68
534	559	2.605366	GCTCCTATTTGACGCTTCAGAC	59.395	50.000	0.00	0.00	31.71	3.51
544	569	1.915489	TCAAGGCCAGCTCCTATTTGA	59.085	47.619	5.01	0.00	34.82	2.69
554	579	2.043227	ACCTCTATAGTCAAGGCCAGC	58.957	52.381	5.01	0.00	33.21	4.85
555	580	4.262249	GCTAACCTCTATAGTCAAGGCCAG	60.262	50.000	5.01	0.00	33.21	4.85
585	623	2.832661	GGGGCATGGCATACGCAA	60.833	61.111	22.06	0.00	41.24	4.85
586	624	4.892965	GGGGGCATGGCATACGCA	62.893	66.667	22.06	0.00	41.24	5.24
601	639	1.059913	CATAGGTTCTGGGCTAGGGG	58.940	60.000	0.00	0.00	0.00	4.79
642	680	6.035435	CACGAATACAGTGGAGAAATCTCTTG	59.965	42.308	10.09	8.78	42.48	3.02
731	769	9.778741	GATGATAAGGTGTAAAGATGGTTATCA	57.221	33.333	0.00	0.00	38.87	2.15
782	820	7.264373	TCAACAGAGATGAGAAAGGTTTTTC	57.736	36.000	0.00	0.00	42.44	2.29
784	822	7.645058	TTTCAACAGAGATGAGAAAGGTTTT	57.355	32.000	0.00	0.00	0.00	2.43
786	824	6.874288	CTTTCAACAGAGATGAGAAAGGTT	57.126	37.500	14.35	0.00	40.69	3.50
789	827	6.091986	GCTACCTTTCAACAGAGATGAGAAAG	59.908	42.308	14.82	14.82	42.79	2.62
790	828	5.934625	GCTACCTTTCAACAGAGATGAGAAA	59.065	40.000	0.00	0.00	0.00	2.52
793	831	4.187694	GGCTACCTTTCAACAGAGATGAG	58.812	47.826	0.00	0.00	0.00	2.90
796	834	2.912956	TGGGCTACCTTTCAACAGAGAT	59.087	45.455	0.00	0.00	37.76	2.75
798	836	2.859165	TGGGCTACCTTTCAACAGAG	57.141	50.000	0.00	0.00	37.76	3.35
799	837	3.686016	GAATGGGCTACCTTTCAACAGA	58.314	45.455	7.32	0.00	45.51	3.41
805	843	3.653835	AAGGAGAATGGGCTACCTTTC	57.346	47.619	0.00	4.70	46.18	2.62
807	845	3.193782	AGAAAGGAGAATGGGCTACCTT	58.806	45.455	0.00	0.00	41.83	3.50
808	846	2.774809	GAGAAAGGAGAATGGGCTACCT	59.225	50.000	0.00	0.00	37.76	3.08
809	847	2.774809	AGAGAAAGGAGAATGGGCTACC	59.225	50.000	0.00	0.00	37.24	3.18
810	848	3.709141	AGAGAGAAAGGAGAATGGGCTAC	59.291	47.826	0.00	0.00	0.00	3.58
811	849	3.964031	GAGAGAGAAAGGAGAATGGGCTA	59.036	47.826	0.00	0.00	0.00	3.93
812	850	2.771372	GAGAGAGAAAGGAGAATGGGCT	59.229	50.000	0.00	0.00	0.00	5.19
813	851	2.771372	AGAGAGAGAAAGGAGAATGGGC	59.229	50.000	0.00	0.00	0.00	5.36
814	852	3.774216	ACAGAGAGAGAAAGGAGAATGGG	59.226	47.826	0.00	0.00	0.00	4.00
815	853	5.177326	CAACAGAGAGAGAAAGGAGAATGG	58.823	45.833	0.00	0.00	0.00	3.16
816	854	5.792741	ACAACAGAGAGAGAAAGGAGAATG	58.207	41.667	0.00	0.00	0.00	2.67
817	855	6.042552	TCAACAACAGAGAGAGAAAGGAGAAT	59.957	38.462	0.00	0.00	0.00	2.40
818	856	5.363868	TCAACAACAGAGAGAGAAAGGAGAA	59.636	40.000	0.00	0.00	0.00	2.87
819	857	4.895889	TCAACAACAGAGAGAGAAAGGAGA	59.104	41.667	0.00	0.00	0.00	3.71
820	858	5.207110	TCAACAACAGAGAGAGAAAGGAG	57.793	43.478	0.00	0.00	0.00	3.69
821	859	4.039730	CCTCAACAACAGAGAGAGAAAGGA	59.960	45.833	0.00	0.00	35.09	3.36
822	860	4.202305	ACCTCAACAACAGAGAGAGAAAGG	60.202	45.833	0.00	0.00	35.09	3.11
823	861	4.954875	ACCTCAACAACAGAGAGAGAAAG	58.045	43.478	0.00	0.00	35.09	2.62
824	862	5.509840	GCTACCTCAACAACAGAGAGAGAAA	60.510	44.000	0.00	0.00	35.09	2.52
825	863	4.021894	GCTACCTCAACAACAGAGAGAGAA	60.022	45.833	0.00	0.00	35.09	2.87
826	864	3.508012	GCTACCTCAACAACAGAGAGAGA	59.492	47.826	0.00	0.00	35.09	3.10
827	865	3.367910	GGCTACCTCAACAACAGAGAGAG	60.368	52.174	0.00	0.00	35.09	3.20
828	866	2.563179	GGCTACCTCAACAACAGAGAGA	59.437	50.000	0.00	0.00	35.09	3.10
829	867	2.354203	GGGCTACCTCAACAACAGAGAG	60.354	54.545	0.00	0.00	35.09	3.20
830	868	1.623811	GGGCTACCTCAACAACAGAGA	59.376	52.381	0.00	0.00	35.09	3.10
831	869	1.347707	TGGGCTACCTCAACAACAGAG	59.652	52.381	0.00	0.00	37.76	3.35
1664	1756	2.158608	CCGAGGGGGATTAGCTTTTGAT	60.159	50.000	0.00	0.00	38.47	2.57
1685	1778	4.507879	GGCAACATGGCAATGAGC	57.492	55.556	8.45	11.15	43.14	4.26
2547	2703	7.660735	GCATAATTATTCATGCATAGCTTCG	57.339	36.000	0.00	0.00	45.51	3.79
2567	2723	5.726980	ATTTTCTGCCTCAAACTTGCATA	57.273	34.783	0.00	0.00	33.97	3.14
2618	2774	6.072008	AGCAAACTGTGACATTACATGCAATA	60.072	34.615	0.00	0.00	36.85	1.90
2623	2779	6.207928	TCAAAGCAAACTGTGACATTACATG	58.792	36.000	0.00	0.00	35.09	3.21
3620	3789	1.420138	TCTTCTTCCTCACCAACACCC	59.580	52.381	0.00	0.00	0.00	4.61
3814	6072	9.199645	CTCTCTCTCTCTCTCTCTCTCATATAT	57.800	40.741	0.00	0.00	0.00	0.86
3815	6073	7.123397	GCTCTCTCTCTCTCTCTCTCTCATATA	59.877	44.444	0.00	0.00	0.00	0.86
3816	6074	6.070881	GCTCTCTCTCTCTCTCTCTCTCATAT	60.071	46.154	0.00	0.00	0.00	1.78
3817	6075	5.244851	GCTCTCTCTCTCTCTCTCTCTCATA	59.755	48.000	0.00	0.00	0.00	2.15
3818	6076	4.040217	GCTCTCTCTCTCTCTCTCTCTCAT	59.960	50.000	0.00	0.00	0.00	2.90
3819	6077	3.386078	GCTCTCTCTCTCTCTCTCTCTCA	59.614	52.174	0.00	0.00	0.00	3.27
3822	6080	3.726607	CAGCTCTCTCTCTCTCTCTCTC	58.273	54.545	0.00	0.00	0.00	3.20
3826	6084	1.312815	GGCAGCTCTCTCTCTCTCTC	58.687	60.000	0.00	0.00	0.00	3.20
3886	6148	3.826157	TCAAACAATAGGACAAGGGCAAG	59.174	43.478	0.00	0.00	0.00	4.01
3887	6149	3.838565	TCAAACAATAGGACAAGGGCAA	58.161	40.909	0.00	0.00	0.00	4.52
3888	6150	3.517296	TCAAACAATAGGACAAGGGCA	57.483	42.857	0.00	0.00	0.00	5.36
3889	6151	3.826729	ACTTCAAACAATAGGACAAGGGC	59.173	43.478	0.00	0.00	0.00	5.19
3923	6185	4.506654	GCACCTATCATTAGTTGGTACACG	59.493	45.833	0.00	0.00	39.29	4.49
3941	6203	0.892755	CATTGTCCATGCAAGCACCT	59.107	50.000	0.00	0.00	0.00	4.00
4246	6614	1.068588	GTTTGGTCACCCTTCTTTGGC	59.931	52.381	0.00	0.00	0.00	4.52
4565	6941	0.725784	CGCAAGTCATGGCACGAAAC	60.726	55.000	0.00	0.00	0.00	2.78
4772	7152	1.674651	GAGGGCCACCGTTTCCTTC	60.675	63.158	6.18	0.00	43.47	3.46
4807	7187	0.107165	GGCGCAGAGGGGATTTAGTT	60.107	55.000	10.83	0.00	0.00	2.24
4875	7288	2.419851	CCAGATCTCTCCAAGAAGGCAC	60.420	54.545	0.00	0.00	37.61	5.01
4974	7393	9.677567	CAATTCATAATATTCAAACCCTAACCG	57.322	33.333	0.00	0.00	0.00	4.44
5053	7472	5.125097	GGATTCTCATGCATTGACAAGAAGT	59.875	40.000	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.