AutoCloner

Multiple sequence alignment - TraesCS6D01G268300

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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	TraesCS6D01G268300	chr6D	100.000	2786	0	0	1	2786	378264925	378262140	0.000000e+00	5145.0
1	TraesCS6D01G268300	chr6D	98.113	53	1	0	687	739	454578483	454578431	2.950000e-15	93.5
2	TraesCS6D01G268300	chr6D	96.226	53	2	0	687	739	42418825	42418877	1.370000e-13	87.9
3	TraesCS6D01G268300	chr6B	93.114	1612	68	13	726	2314	564660986	564659395	0.000000e+00	2322.0
4	TraesCS6D01G268300	chr6B	85.714	427	20	14	2314	2731	564659326	564658932	2.000000e-111	412.0
5	TraesCS6D01G268300	chr6A	93.538	1563	56	12	776	2314	520052028	520050487	0.000000e+00	2285.0
6	TraesCS6D01G268300	chr6A	88.150	481	37	7	2318	2786	520050452	520049980	3.140000e-154	555.0
7	TraesCS6D01G268300	chr6A	76.471	340	62	11	1074	1403	84060500	84060169	4.770000e-38	169.0
8	TraesCS6D01G268300	chr7A	93.237	695	41	4	1	689	607613726	607613032	0.000000e+00	1018.0
9	TraesCS6D01G268300	chr2B	92.219	694	48	4	1	690	405268151	405268842	0.000000e+00	977.0
10	TraesCS6D01G268300	chr5D	91.775	693	52	3	1	688	273065581	273064889	0.000000e+00	959.0
11	TraesCS6D01G268300	chr5D	90.300	701	55	4	1	696	491292837	491292145	0.000000e+00	905.0
12	TraesCS6D01G268300	chr5D	84.299	656	87	8	54	697	410505817	410505166	6.550000e-176	627.0
13	TraesCS6D01G268300	chr5D	96.226	53	2	0	687	739	284962863	284962915	1.370000e-13	87.9
14	TraesCS6D01G268300	chr3D	91.424	688	49	5	8	690	531454664	531453982	0.000000e+00	935.0
15	TraesCS6D01G268300	chr2D	90.585	701	61	3	1	696	496332253	496331553	0.000000e+00	924.0
16	TraesCS6D01G268300	chr2D	98.077	52	1	0	688	739	582676754	582676703	1.060000e-14	91.6
17	TraesCS6D01G268300	chr2D	100.000	47	0	0	693	739	637960728	637960682	1.370000e-13	87.9
18	TraesCS6D01G268300	chr1B	90.171	702	62	6	1	696	35392072	35391372	0.000000e+00	907.0
19	TraesCS6D01G268300	chr1B	89.049	694	70	4	2	690	582523884	582524576	0.000000e+00	856.0
20	TraesCS6D01G268300	chr5B	90.014	701	62	4	1	696	681382180	681382877	0.000000e+00	900.0
21	TraesCS6D01G268300	chr3A	89.915	704	58	11	1	696	82445474	82444776	0.000000e+00	894.0
22	TraesCS6D01G268300	chr2A	89.038	447	42	5	256	696	506590634	506590189	5.250000e-152	547.0
23	TraesCS6D01G268300	chr4B	98.182	55	1	0	687	741	640463517	640463463	2.280000e-16	97.1
24	TraesCS6D01G268300	chr4B	96.364	55	2	0	687	741	7881982	7882036	1.060000e-14	91.6
25	TraesCS6D01G268300	chr4D	98.113	53	1	0	687	739	467211581	467211633	2.950000e-15	93.5
26	TraesCS6D01G268300	chr7D	94.643	56	3	0	687	742	123743607	123743552	1.370000e-13	87.9

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	TraesCS6D01G268300	chr6D	378262140	378264925	2785	True	5145	5145	100.000	1	2786	1	chr6D.!!$R1	2785
1	TraesCS6D01G268300	chr6B	564658932	564660986	2054	True	1367	2322	89.414	726	2731	2	chr6B.!!$R1	2005
2	TraesCS6D01G268300	chr6A	520049980	520052028	2048	True	1420	2285	90.844	776	2786	2	chr6A.!!$R2	2010
3	TraesCS6D01G268300	chr7A	607613032	607613726	694	True	1018	1018	93.237	1	689	1	chr7A.!!$R1	688
4	TraesCS6D01G268300	chr2B	405268151	405268842	691	False	977	977	92.219	1	690	1	chr2B.!!$F1	689
5	TraesCS6D01G268300	chr5D	273064889	273065581	692	True	959	959	91.775	1	688	1	chr5D.!!$R1	687
6	TraesCS6D01G268300	chr5D	491292145	491292837	692	True	905	905	90.300	1	696	1	chr5D.!!$R3	695
7	TraesCS6D01G268300	chr5D	410505166	410505817	651	True	627	627	84.299	54	697	1	chr5D.!!$R2	643
8	TraesCS6D01G268300	chr3D	531453982	531454664	682	True	935	935	91.424	8	690	1	chr3D.!!$R1	682
9	TraesCS6D01G268300	chr2D	496331553	496332253	700	True	924	924	90.585	1	696	1	chr2D.!!$R1	695
10	TraesCS6D01G268300	chr1B	35391372	35392072	700	True	907	907	90.171	1	696	1	chr1B.!!$R1	695
11	TraesCS6D01G268300	chr1B	582523884	582524576	692	False	856	856	89.049	2	690	1	chr1B.!!$F1	688
12	TraesCS6D01G268300	chr5B	681382180	681382877	697	False	900	900	90.014	1	696	1	chr5B.!!$F1	695
13	TraesCS6D01G268300	chr3A	82444776	82445474	698	True	894	894	89.915	1	696	1	chr3A.!!$R1	695

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
701	719	0.111089	GACTCTGCAGACGCGTTTTG	60.111	55.0	15.53	16.62	42.97	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2470	2604	0.837272	TCCGGGCAAAGCTAGCTAAT	59.163	50.0	19.7	7.46	0.0	1.73	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
30	31	2.930826	AAGAGTTGGCCGAGAAGAAA	57.069	45.000	0.00	0.00	0.00	2.52
97	99	2.751436	GCAAGGCGGCCATTGAGA	60.751	61.111	25.39	0.00	0.00	3.27
103	105	0.813210	GGCGGCCATTGAGAAGAGAG	60.813	60.000	15.62	0.00	0.00	3.20
197	200	2.615447	GCAATGACATGGACGACATCAT	59.385	45.455	0.00	0.00	37.84	2.45
316	319	1.818674	GATTTGGAACCAACATCGCCT	59.181	47.619	5.73	0.00	35.46	5.52
481	490	3.509575	TGCAAGTCCTTTTGTGTTTGTCT	59.490	39.130	0.00	0.00	0.00	3.41
512	521	1.405469	GCTTTCATTTGCGCGCGAAT	61.405	50.000	35.16	35.16	0.00	3.34
557	567	0.726827	TCATTTGTCGGAATCGCTGC	59.273	50.000	0.00	0.00	36.13	5.25
692	710	1.979155	CGGGGTCTGACTCTGCAGA	60.979	63.158	17.19	17.19	42.31	4.26
696	714	2.563427	TCTGACTCTGCAGACGCG	59.437	61.111	13.74	3.53	39.84	6.01
697	715	2.256764	CTGACTCTGCAGACGCGT	59.743	61.111	13.85	13.85	42.97	6.01
698	716	1.372251	CTGACTCTGCAGACGCGTT	60.372	57.895	15.53	0.00	42.97	4.84
699	717	0.941463	CTGACTCTGCAGACGCGTTT	60.941	55.000	15.53	4.14	42.97	3.60
700	718	0.529773	TGACTCTGCAGACGCGTTTT	60.530	50.000	15.53	1.39	42.97	2.43
701	719	0.111089	GACTCTGCAGACGCGTTTTG	60.111	55.000	15.53	16.62	42.97	2.44
702	720	1.439365	CTCTGCAGACGCGTTTTGC	60.439	57.895	30.69	30.69	42.97	3.68
713	731	3.956317	GTTTTGCGGGTCGGCGTT	61.956	61.111	6.85	0.00	35.06	4.84
714	732	2.280660	TTTTGCGGGTCGGCGTTA	60.281	55.556	6.85	0.00	35.06	3.18
715	733	1.671704	TTTTGCGGGTCGGCGTTAT	60.672	52.632	6.85	0.00	35.06	1.89
716	734	0.390866	TTTTGCGGGTCGGCGTTATA	60.391	50.000	6.85	0.00	35.06	0.98
717	735	1.083242	TTTGCGGGTCGGCGTTATAC	61.083	55.000	6.85	0.00	35.06	1.47
718	736	3.026311	GCGGGTCGGCGTTATACG	61.026	66.667	6.85	7.29	45.88	3.06
719	737	2.353839	CGGGTCGGCGTTATACGG	60.354	66.667	6.85	0.00	42.82	4.02
720	738	2.028043	GGGTCGGCGTTATACGGG	59.972	66.667	6.85	0.00	42.82	5.28
721	739	2.028043	GGTCGGCGTTATACGGGG	59.972	66.667	6.85	0.00	42.82	5.73
722	740	2.785425	GGTCGGCGTTATACGGGGT	61.785	63.158	6.85	0.00	42.82	4.95
723	741	1.299392	GTCGGCGTTATACGGGGTC	60.299	63.158	6.85	0.00	42.82	4.46
724	742	1.453745	TCGGCGTTATACGGGGTCT	60.454	57.895	6.85	0.00	42.82	3.85
729	747	1.335689	GCGTTATACGGGGTCTGCTAG	60.336	57.143	1.14	0.00	42.82	3.42
755	774	4.763073	TGCTCTTACACATCTCATTCAGG	58.237	43.478	0.00	0.00	0.00	3.86
756	775	4.467438	TGCTCTTACACATCTCATTCAGGA	59.533	41.667	0.00	0.00	0.00	3.86
765	784	4.713814	ACATCTCATTCAGGAGCAGTAGAA	59.286	41.667	0.00	0.00	34.84	2.10
834	853	3.140623	GTGGCCAATTTCAGCACAAAAT	58.859	40.909	7.24	0.00	0.00	1.82
849	868	4.712763	CACAAAATAGACTTTGCTCGTCC	58.287	43.478	0.00	0.00	39.46	4.79
863	882	3.443045	GTCCGGCAAGCCACCATG	61.443	66.667	12.19	0.00	35.37	3.66
935	954	1.079405	TCGTCGCCCTGTTTCATCC	60.079	57.895	0.00	0.00	0.00	3.51
968	987	2.640316	ACTTCCCAAGAACACCAGAC	57.360	50.000	0.00	0.00	0.00	3.51
993	1012	0.653636	CCACACGTACGTTGCAACTT	59.346	50.000	26.09	20.00	0.00	2.66
1149	1180	4.052229	CTCACGACGACGGGCCTT	62.052	66.667	12.58	0.00	43.22	4.35
1392	1423	1.689243	CCGGCATGGTGGAGATCTCA	61.689	60.000	23.85	7.82	0.00	3.27
1687	1718	2.037136	GGGGACGACGAACGAGAGA	61.037	63.158	0.00	0.00	45.77	3.10
1782	1819	2.874780	AAGATCGTCGTGCGCGTC	60.875	61.111	20.50	13.51	41.07	5.19
1794	1831	0.245266	TGCGCGTCTGAAGGTTGATA	59.755	50.000	8.43	0.00	0.00	2.15
1795	1832	1.337354	TGCGCGTCTGAAGGTTGATAA	60.337	47.619	8.43	0.00	0.00	1.75
1796	1833	1.730064	GCGCGTCTGAAGGTTGATAAA	59.270	47.619	8.43	0.00	0.00	1.40
1918	1958	1.263217	GTCGTTGATGCGTTGGAAACT	59.737	47.619	0.00	0.00	46.99	2.66
1961	2001	1.611673	GCCAAGAGAGCTTTGCAGGTA	60.612	52.381	0.00	0.00	41.17	3.08
2007	2047	1.484038	AGTCCAGACTCCAGATCTGC	58.516	55.000	17.76	3.53	41.97	4.26
2033	2073	6.165577	GGTGTTATAAACTGGTCTACCGAAA	58.834	40.000	0.00	0.00	39.43	3.46
2034	2074	6.820152	GGTGTTATAAACTGGTCTACCGAAAT	59.180	38.462	0.00	0.00	39.43	2.17
2035	2075	7.201582	GGTGTTATAAACTGGTCTACCGAAATG	60.202	40.741	0.00	0.00	39.43	2.32
2036	2076	6.314400	TGTTATAAACTGGTCTACCGAAATGC	59.686	38.462	0.00	0.00	39.43	3.56
2037	2077	2.851263	AACTGGTCTACCGAAATGCA	57.149	45.000	0.00	0.00	39.43	3.96
2038	2078	3.350219	AACTGGTCTACCGAAATGCAT	57.650	42.857	0.00	0.00	39.43	3.96
2039	2079	3.350219	ACTGGTCTACCGAAATGCATT	57.650	42.857	5.99	5.99	39.43	3.56
2104	2149	7.455008	TGATAAATCTTCAGGGGTATACTCTCC	59.545	40.741	2.03	2.85	0.00	3.71
2137	2185	3.122948	GCTGCATACGTACATTAATCGGG	59.877	47.826	0.00	0.00	0.00	5.14
2138	2186	3.655486	TGCATACGTACATTAATCGGGG	58.345	45.455	0.00	0.00	0.00	5.73
2169	2219	6.250819	CAAGCTACAAGTTCATTCGGTTATG	58.749	40.000	0.00	0.00	0.00	1.90
2202	2253	7.658167	TGTCGTCTTATTCCAATTTGTCTTGTA	59.342	33.333	0.00	0.00	0.00	2.41
2314	2366	8.347035	CGAAAATAACAACTTTTAGAGGACCAA	58.653	33.333	0.00	0.00	0.00	3.67
2347	2465	3.040147	TCTTTCTTCCTACCAAGTGCG	57.960	47.619	0.00	0.00	0.00	5.34
2354	2472	2.432456	TACCAAGTGCGAGCGCTG	60.432	61.111	18.48	8.79	42.51	5.18
2380	2502	3.614150	CGAGTATGCCCGTAATGCACTAT	60.614	47.826	0.00	0.00	42.38	2.12
2391	2513	5.447279	CCGTAATGCACTATGAGTTTCCAAC	60.447	44.000	0.00	0.00	0.00	3.77
2399	2533	6.034683	GCACTATGAGTTTCCAACTACGTAAG	59.965	42.308	0.00	0.00	43.03	2.34
2420	2554	3.826236	CAAGATGCCTTGTCTTGTCAG	57.174	47.619	7.51	0.00	44.67	3.51
2421	2555	3.144506	CAAGATGCCTTGTCTTGTCAGT	58.855	45.455	7.51	0.00	44.67	3.41
2422	2556	3.051081	AGATGCCTTGTCTTGTCAGTC	57.949	47.619	0.00	0.00	0.00	3.51
2470	2604	0.238553	CTGAGCGCGGAATCTATCGA	59.761	55.000	8.83	0.00	0.00	3.59
2533	2667	2.359107	CTCTGCGCCCTCTTTGCA	60.359	61.111	4.18	0.00	37.07	4.08
2612	2746	2.112898	GGAGTACGATCCGCTCCAA	58.887	57.895	15.81	0.00	45.93	3.53
2625	2759	1.153628	CTCCAACCCGACGTGATCC	60.154	63.158	0.00	0.00	0.00	3.36
2658	2792	1.425428	GCACTGCTTACACGCATCC	59.575	57.895	0.00	0.00	39.52	3.51
2659	2793	1.021390	GCACTGCTTACACGCATCCT	61.021	55.000	0.00	0.00	39.52	3.24
2660	2794	1.442769	CACTGCTTACACGCATCCTT	58.557	50.000	0.00	0.00	39.52	3.36
2661	2795	1.129251	CACTGCTTACACGCATCCTTG	59.871	52.381	0.00	0.00	39.52	3.61
2662	2796	0.097674	CTGCTTACACGCATCCTTGC	59.902	55.000	0.00	0.00	45.78	4.01
2742	2876	1.188863	GTGTCTAGGGTTTAGGCCGA	58.811	55.000	0.00	0.00	0.00	5.54
2747	2881	2.897969	TCTAGGGTTTAGGCCGATCATC	59.102	50.000	0.00	0.00	0.00	2.92
2749	2883	0.250770	GGGTTTAGGCCGATCATCCC	60.251	60.000	0.00	2.35	0.00	3.85
2765	2899	6.555463	ATCATCCCGAGTTCCTAGTAAAAA	57.445	37.500	0.00	0.00	0.00	1.94
2769	2903	4.221482	TCCCGAGTTCCTAGTAAAAACTCC	59.779	45.833	14.32	3.24	43.77	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	1.188219	TCTCTTGCTTCTCCCGTGCT	61.188	55.000	0.00	0.00	0.00	4.40
97	99	2.659610	GGCACGTGCTCCTCTCTT	59.340	61.111	36.84	0.00	41.70	2.85
197	200	3.216800	GCCATATCATGCCACTCTTTGA	58.783	45.455	0.00	0.00	0.00	2.69
333	336	2.569354	GGCACCAAAATCACCGGCA	61.569	57.895	0.00	0.00	0.00	5.69
481	490	6.128956	GCGCAAATGAAAGCATAGTTTTGTAA	60.129	34.615	0.30	0.00	33.44	2.41
498	507	1.465837	ACATAATTCGCGCGCAAATG	58.534	45.000	32.61	24.88	0.00	2.32
557	567	2.107366	ACCCCCAATAAGCGAATTTGG	58.893	47.619	0.00	4.40	39.69	3.28
640	654	9.569167	CGTATAAAAGGATATTCGCAGAAGATA	57.431	33.333	0.00	0.00	45.90	1.98
696	714	1.914531	ATAACGCCGACCCGCAAAAC	61.915	55.000	0.00	0.00	0.00	2.43
697	715	0.390866	TATAACGCCGACCCGCAAAA	60.391	50.000	0.00	0.00	0.00	2.44
698	716	1.083242	GTATAACGCCGACCCGCAAA	61.083	55.000	0.00	0.00	0.00	3.68
699	717	1.519013	GTATAACGCCGACCCGCAA	60.519	57.895	0.00	0.00	0.00	4.85
700	718	2.104729	GTATAACGCCGACCCGCA	59.895	61.111	0.00	0.00	0.00	5.69
701	719	3.026311	CGTATAACGCCGACCCGC	61.026	66.667	0.00	0.00	33.65	6.13
702	720	2.353839	CCGTATAACGCCGACCCG	60.354	66.667	0.00	0.00	40.91	5.28
703	721	2.028043	CCCGTATAACGCCGACCC	59.972	66.667	0.00	0.00	40.91	4.46
704	722	2.028043	CCCCGTATAACGCCGACC	59.972	66.667	0.00	0.00	40.91	4.79
705	723	1.299392	GACCCCGTATAACGCCGAC	60.299	63.158	0.00	0.00	40.91	4.79
706	724	1.453745	AGACCCCGTATAACGCCGA	60.454	57.895	0.00	0.00	40.91	5.54
707	725	1.299620	CAGACCCCGTATAACGCCG	60.300	63.158	0.00	0.00	40.91	6.46
708	726	1.593479	GCAGACCCCGTATAACGCC	60.593	63.158	0.00	0.00	40.91	5.68
709	727	0.670162	TAGCAGACCCCGTATAACGC	59.330	55.000	0.00	0.00	40.91	4.84
710	728	2.224606	TCTAGCAGACCCCGTATAACG	58.775	52.381	0.00	0.00	42.11	3.18
711	729	3.484407	TCTCTAGCAGACCCCGTATAAC	58.516	50.000	0.00	0.00	0.00	1.89
712	730	3.870538	TCTCTAGCAGACCCCGTATAA	57.129	47.619	0.00	0.00	0.00	0.98
713	731	3.687125	CATCTCTAGCAGACCCCGTATA	58.313	50.000	0.00	0.00	32.26	1.47
714	732	2.520069	CATCTCTAGCAGACCCCGTAT	58.480	52.381	0.00	0.00	32.26	3.06
715	733	1.982660	CATCTCTAGCAGACCCCGTA	58.017	55.000	0.00	0.00	32.26	4.02
716	734	1.395826	GCATCTCTAGCAGACCCCGT	61.396	60.000	0.00	0.00	32.26	5.28
717	735	1.112315	AGCATCTCTAGCAGACCCCG	61.112	60.000	0.00	0.00	32.26	5.73
718	736	0.678950	GAGCATCTCTAGCAGACCCC	59.321	60.000	0.00	0.00	32.26	4.95
755	774	7.486870	GCTTTCTAGTTTCTAGTTCTACTGCTC	59.513	40.741	4.13	0.00	0.00	4.26
756	775	7.317390	GCTTTCTAGTTTCTAGTTCTACTGCT	58.683	38.462	4.13	0.00	0.00	4.24
834	853	1.214589	GCCGGACGAGCAAAGTCTA	59.785	57.895	5.05	0.00	38.58	2.59
849	868	4.424566	GCACATGGTGGCTTGCCG	62.425	66.667	7.18	0.00	33.64	5.69
863	882	0.972883	TGCCCTTGGTTTTATGGCAC	59.027	50.000	0.00	0.00	46.57	5.01
903	922	3.476181	GGCGACGAGTGTTTAATCAAAC	58.524	45.455	0.00	0.00	43.67	2.93
935	954	1.067582	GAAGTATGGCTCGTCCGGG	59.932	63.158	0.00	0.00	37.80	5.73
968	987	3.562779	AACGTACGTGTGGCTCCCG	62.563	63.158	23.57	0.00	0.00	5.14
993	1012	0.943673	CGGTGAGTGACATTGTTGCA	59.056	50.000	0.00	0.00	0.00	4.08
1029	1060	0.917333	AGAGGACGAGGAGGAGGAGT	60.917	60.000	0.00	0.00	0.00	3.85
1149	1180	1.623081	GCTCGTTGATTTCGTCCGCA	61.623	55.000	0.00	0.00	0.00	5.69
1251	1282	3.233980	TGCAGGGAGAGCACGTGT	61.234	61.111	18.38	3.69	37.02	4.49
1326	1357	1.663702	GAACAGGGTGGACACGTCG	60.664	63.158	0.00	0.00	0.00	5.12
1450	1481	2.743928	GAAGAGCACGCTGGTGGG	60.744	66.667	0.00	0.00	44.54	4.61
1687	1718	1.156736	CCGTTCTTCTTCGCATGGTT	58.843	50.000	0.00	0.00	0.00	3.67
1782	1819	4.074970	ACACAGCCTTTATCAACCTTCAG	58.925	43.478	0.00	0.00	0.00	3.02
1794	1831	2.128771	ACTCACAACACACAGCCTTT	57.871	45.000	0.00	0.00	0.00	3.11
1795	1832	1.745087	CAACTCACAACACACAGCCTT	59.255	47.619	0.00	0.00	0.00	4.35
1796	1833	1.382522	CAACTCACAACACACAGCCT	58.617	50.000	0.00	0.00	0.00	4.58
1918	1958	7.604164	TGGCAAACAAAATGAAACTACAAGAAA	59.396	29.630	0.00	0.00	0.00	2.52
1961	2001	5.188555	ACACACTAGATGAATCAGGACACAT	59.811	40.000	0.00	0.00	0.00	3.21
2007	2047	5.105635	TCGGTAGACCAGTTTATAACACCAG	60.106	44.000	0.00	0.00	35.14	4.00
2033	2073	6.906157	AAGCTAGGCAAATGTATAATGCAT	57.094	33.333	0.00	0.00	41.80	3.96
2034	2074	6.713762	AAAGCTAGGCAAATGTATAATGCA	57.286	33.333	0.00	0.00	41.80	3.96
2035	2075	6.803807	GCTAAAGCTAGGCAAATGTATAATGC	59.196	38.462	0.00	0.00	37.43	3.56
2068	2108	7.930865	CCCCTGAAGATTTATCAAAACAAAACA	59.069	33.333	0.00	0.00	0.00	2.83
2090	2135	6.800223	ATTACTACAGGAGAGTATACCCCT	57.200	41.667	0.00	1.33	29.68	4.79
2104	2149	5.746721	TGTACGTATGCAGCAATTACTACAG	59.253	40.000	0.00	0.00	0.00	2.74
2137	2185	3.181480	TGAACTTGTAGCTTGCAAAACCC	60.181	43.478	0.00	0.00	0.00	4.11
2138	2186	4.040445	TGAACTTGTAGCTTGCAAAACC	57.960	40.909	0.00	0.00	0.00	3.27
2169	2219	9.490663	CAAATTGGAATAAGACGACAGATTTAC	57.509	33.333	0.00	0.00	0.00	2.01
2284	2336	8.553696	TCCTCTAAAAGTTGTTATTTTCGACAC	58.446	33.333	0.00	0.00	32.38	3.67
2314	2366	5.885465	AGGAAGAAAGAACACCTTGATCAT	58.115	37.500	0.00	0.00	34.79	2.45
2315	2367	5.310409	AGGAAGAAAGAACACCTTGATCA	57.690	39.130	0.00	0.00	34.79	2.92
2347	2465	1.332178	GCATACTCGTATCAGCGCTC	58.668	55.000	7.13	0.00	0.00	5.03
2354	2472	2.921754	GCATTACGGGCATACTCGTATC	59.078	50.000	0.00	0.00	40.77	2.24
2391	2513	3.933155	CAAGGCATCTTGCTTACGTAG	57.067	47.619	0.00	0.00	44.28	3.51
2414	2548	1.887242	GGTGCGTGCTGACTGACAA	60.887	57.895	0.00	0.00	0.00	3.18
2415	2549	2.280119	GGTGCGTGCTGACTGACA	60.280	61.111	0.00	0.00	0.00	3.58
2416	2550	3.406361	CGGTGCGTGCTGACTGAC	61.406	66.667	0.00	0.00	0.00	3.51
2440	2574	2.901292	GCGCTCAGTTGCAAGCACT	61.901	57.895	0.00	0.00	38.45	4.40
2444	2578	1.915614	ATTCCGCGCTCAGTTGCAAG	61.916	55.000	5.56	0.00	0.00	4.01
2470	2604	0.837272	TCCGGGCAAAGCTAGCTAAT	59.163	50.000	19.70	7.46	0.00	1.73
2533	2667	3.805108	GCTGTCCCAAATATGCTCGAGAT	60.805	47.826	18.75	9.48	0.00	2.75
2607	2741	1.153628	GGATCACGTCGGGTTGGAG	60.154	63.158	0.00	0.00	0.00	3.86
2608	2742	1.601419	GAGGATCACGTCGGGTTGGA	61.601	60.000	0.00	0.00	33.17	3.53
2612	2746	2.758737	GGGAGGATCACGTCGGGT	60.759	66.667	0.00	0.00	36.25	5.28
2742	2876	6.156429	AGTTTTTACTAGGAACTCGGGATGAT	59.844	38.462	0.00	0.00	41.75	2.45
2747	2881	4.502016	GGAGTTTTTACTAGGAACTCGGG	58.498	47.826	17.00	0.00	46.33	5.14
2749	2883	5.143376	TGGGAGTTTTTACTAGGAACTCG	57.857	43.478	17.00	0.00	46.33	4.18
2765	2899	1.988107	TCAGCCTGAAGAAATGGGAGT	59.012	47.619	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.