AutoCloner

Multiple sequence alignment - TraesCS1A01G112900

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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	TraesCS1A01G112900	chr1A	100.000	3195	0	0	1	3195	115891171	115887977	0	5901
1	TraesCS1A01G112900	chr1A	96.046	1669	53	7	598	2256	94598363	94596698	0	2704
2	TraesCS1A01G112900	chr1A	95.743	1668	59	8	598	2256	94708669	94710333	0	2676
3	TraesCS1A01G112900	chr1A	97.162	599	17	0	1	599	381983309	381983907	0	1013
4	TraesCS1A01G112900	chr1A	97.162	599	14	3	1	598	99275110	99275706	0	1009
5	TraesCS1A01G112900	chr1A	96.990	598	18	0	1	598	105866858	105866261	0	1005
6	TraesCS1A01G112900	chr1A	96.990	598	18	0	1	598	458368033	458368630	0	1005
7	TraesCS1A01G112900	chr1A	92.807	570	35	4	2630	3195	278509245	278509812	0	821
8	TraesCS1A01G112900	chr3A	95.664	1845	69	7	598	2433	51886620	51884778	0	2953
9	TraesCS1A01G112900	chr3A	96.376	607	21	1	1	607	630712359	630711754	0	998
10	TraesCS1A01G112900	chr5A	96.396	1665	51	5	598	2255	667732083	667730421	0	2734
11	TraesCS1A01G112900	chr5A	97.185	604	15	2	1	604	327193562	327192961	0	1020
12	TraesCS1A01G112900	chr5A	97.157	598	17	0	1	598	10244145	10243548	0	1011
13	TraesCS1A01G112900	chr7D	96.905	1583	42	6	598	2174	381881412	381879831	0	2645
14	TraesCS1A01G112900	chr7D	93.299	582	30	7	2617	3195	382036788	382037363	0	850
15	TraesCS1A01G112900	chr7D	93.127	582	33	5	2617	3195	203566846	203566269	0	846
16	TraesCS1A01G112900	chr7D	92.955	582	33	6	2617	3195	579008575	579007999	0	841
17	TraesCS1A01G112900	chr7D	92.642	530	29	6	2198	2721	382090419	382090944	0	754
18	TraesCS1A01G112900	chr7D	92.264	530	31	6	2198	2721	626710575	626710050	0	743
19	TraesCS1A01G112900	chr7D	91.794	524	31	9	2198	2717	307163536	307164051	0	719
20	TraesCS1A01G112900	chr5B	96.225	1616	50	9	598	2207	127797675	127796065	0	2636
21	TraesCS1A01G112900	chrUn	96.719	1585	43	7	598	2174	223716144	223717727	0	2630
22	TraesCS1A01G112900	chrUn	93.299	582	30	7	2617	3195	267898988	267898413	0	850
23	TraesCS1A01G112900	chrUn	92.467	531	29	7	2198	2721	369464892	369464366	0	749
24	TraesCS1A01G112900	chr2B	95.926	1620	54	7	598	2207	760924287	760925904	0	2615
25	TraesCS1A01G112900	chr4A	94.554	1671	78	7	598	2256	295169128	295167459	0	2569
26	TraesCS1A01G112900	chr7A	97.492	598	15	0	1	598	657862457	657863054	0	1022
27	TraesCS1A01G112900	chr7A	97.157	598	17	0	1	598	702416182	702415585	0	1011
28	TraesCS1A01G112900	chr4D	93.299	582	32	5	2617	3195	123671343	123671920	0	852
29	TraesCS1A01G112900	chr4D	92.075	530	30	8	2198	2721	123402138	123402661	0	736
30	TraesCS1A01G112900	chr4D	92.366	524	29	7	2198	2715	134963633	134964151	0	736
31	TraesCS1A01G112900	chr2D	92.784	582	33	7	2617	3195	200905282	200904707	0	833
32	TraesCS1A01G112900	chr6D	92.612	582	32	8	2617	3195	102355988	102356561	0	826
33	TraesCS1A01G112900	chr3D	92.427	581	36	7	2617	3195	154778134	154777560	0	822
34	TraesCS1A01G112900	chr3D	91.619	525	31	9	2198	2717	602859561	602859045	0	713
35	TraesCS1A01G112900	chr1D	92.642	530	28	7	2198	2721	212444097	212443573	0	752
36	TraesCS1A01G112900	chr1D	92.000	525	30	8	2198	2717	275785969	275785452	0	726

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	TraesCS1A01G112900	chr1A	115887977	115891171	3194	True	5901	5901	100.000	1	3195	1	chr1A.!!$R3	3194
1	TraesCS1A01G112900	chr1A	94596698	94598363	1665	True	2704	2704	96.046	598	2256	1	chr1A.!!$R1	1658
2	TraesCS1A01G112900	chr1A	94708669	94710333	1664	False	2676	2676	95.743	598	2256	1	chr1A.!!$F1	1658
3	TraesCS1A01G112900	chr1A	381983309	381983907	598	False	1013	1013	97.162	1	599	1	chr1A.!!$F4	598
4	TraesCS1A01G112900	chr1A	99275110	99275706	596	False	1009	1009	97.162	1	598	1	chr1A.!!$F2	597
5	TraesCS1A01G112900	chr1A	105866261	105866858	597	True	1005	1005	96.990	1	598	1	chr1A.!!$R2	597
6	TraesCS1A01G112900	chr1A	458368033	458368630	597	False	1005	1005	96.990	1	598	1	chr1A.!!$F5	597
7	TraesCS1A01G112900	chr1A	278509245	278509812	567	False	821	821	92.807	2630	3195	1	chr1A.!!$F3	565
8	TraesCS1A01G112900	chr3A	51884778	51886620	1842	True	2953	2953	95.664	598	2433	1	chr3A.!!$R1	1835
9	TraesCS1A01G112900	chr3A	630711754	630712359	605	True	998	998	96.376	1	607	1	chr3A.!!$R2	606
10	TraesCS1A01G112900	chr5A	667730421	667732083	1662	True	2734	2734	96.396	598	2255	1	chr5A.!!$R3	1657
11	TraesCS1A01G112900	chr5A	327192961	327193562	601	True	1020	1020	97.185	1	604	1	chr5A.!!$R2	603
12	TraesCS1A01G112900	chr5A	10243548	10244145	597	True	1011	1011	97.157	1	598	1	chr5A.!!$R1	597
13	TraesCS1A01G112900	chr7D	381879831	381881412	1581	True	2645	2645	96.905	598	2174	1	chr7D.!!$R2	1576
14	TraesCS1A01G112900	chr7D	382036788	382037363	575	False	850	850	93.299	2617	3195	1	chr7D.!!$F2	578
15	TraesCS1A01G112900	chr7D	203566269	203566846	577	True	846	846	93.127	2617	3195	1	chr7D.!!$R1	578
16	TraesCS1A01G112900	chr7D	579007999	579008575	576	True	841	841	92.955	2617	3195	1	chr7D.!!$R3	578
17	TraesCS1A01G112900	chr7D	382090419	382090944	525	False	754	754	92.642	2198	2721	1	chr7D.!!$F3	523
18	TraesCS1A01G112900	chr7D	626710050	626710575	525	True	743	743	92.264	2198	2721	1	chr7D.!!$R4	523
19	TraesCS1A01G112900	chr7D	307163536	307164051	515	False	719	719	91.794	2198	2717	1	chr7D.!!$F1	519
20	TraesCS1A01G112900	chr5B	127796065	127797675	1610	True	2636	2636	96.225	598	2207	1	chr5B.!!$R1	1609
21	TraesCS1A01G112900	chrUn	223716144	223717727	1583	False	2630	2630	96.719	598	2174	1	chrUn.!!$F1	1576
22	TraesCS1A01G112900	chrUn	267898413	267898988	575	True	850	850	93.299	2617	3195	1	chrUn.!!$R1	578
23	TraesCS1A01G112900	chrUn	369464366	369464892	526	True	749	749	92.467	2198	2721	1	chrUn.!!$R2	523
24	TraesCS1A01G112900	chr2B	760924287	760925904	1617	False	2615	2615	95.926	598	2207	1	chr2B.!!$F1	1609
25	TraesCS1A01G112900	chr4A	295167459	295169128	1669	True	2569	2569	94.554	598	2256	1	chr4A.!!$R1	1658
26	TraesCS1A01G112900	chr7A	657862457	657863054	597	False	1022	1022	97.492	1	598	1	chr7A.!!$F1	597
27	TraesCS1A01G112900	chr7A	702415585	702416182	597	True	1011	1011	97.157	1	598	1	chr7A.!!$R1	597
28	TraesCS1A01G112900	chr4D	123671343	123671920	577	False	852	852	93.299	2617	3195	1	chr4D.!!$F2	578
29	TraesCS1A01G112900	chr4D	123402138	123402661	523	False	736	736	92.075	2198	2721	1	chr4D.!!$F1	523
30	TraesCS1A01G112900	chr4D	134963633	134964151	518	False	736	736	92.366	2198	2715	1	chr4D.!!$F3	517
31	TraesCS1A01G112900	chr2D	200904707	200905282	575	True	833	833	92.784	2617	3195	1	chr2D.!!$R1	578
32	TraesCS1A01G112900	chr6D	102355988	102356561	573	False	826	826	92.612	2617	3195	1	chr6D.!!$F1	578
33	TraesCS1A01G112900	chr3D	154777560	154778134	574	True	822	822	92.427	2617	3195	1	chr3D.!!$R1	578
34	TraesCS1A01G112900	chr3D	602859045	602859561	516	True	713	713	91.619	2198	2717	1	chr3D.!!$R2	519
35	TraesCS1A01G112900	chr1D	212443573	212444097	524	True	752	752	92.642	2198	2721	1	chr1D.!!$R1	523
36	TraesCS1A01G112900	chr1D	275785452	275785969	517	True	726	726	92.000	2198	2717	1	chr1D.!!$R2	519

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
855	860	0.179056	CCGACAAATCCGTAGCCCAT	60.179	55.0	0.0	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2476	2498	0.163146	GTTTTCTTCCTTCGCCGTCG	59.837	55.0	0.0	0.0	0.0	5.12	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
465	466	5.990996	AGGATTTATTTGTTTTGTGCAGGTG	59.009	36.000	0.00	0.00	0.00	4.00
535	536	8.391075	CTCAAAAACTGAGGGAAATACTTACA	57.609	34.615	0.00	0.00	46.89	2.41
591	592	0.463654	ACCAACGCAGTGCTCAAGAA	60.464	50.000	14.33	0.00	45.00	2.52
666	667	4.625742	TGAGATGGAAATCGACGTTCTTTC	59.374	41.667	9.79	5.49	0.00	2.62
692	693	1.810030	GCTAGGTAGTTTGCGCGCT	60.810	57.895	33.29	14.83	0.00	5.92
786	787	1.883926	GAAGCCTTAAGAAACCGGCAA	59.116	47.619	0.00	0.00	44.85	4.52
794	795	1.398692	AGAAACCGGCAAAGAAAGCA	58.601	45.000	0.00	0.00	0.00	3.91
797	798	1.109323	AACCGGCAAAGAAAGCAGCT	61.109	50.000	0.00	0.00	0.00	4.24
802	805	2.130395	GGCAAAGAAAGCAGCTGTTTC	58.870	47.619	23.15	23.15	34.64	2.78
809	814	2.781945	AAGCAGCTGTTTCTTTTCGG	57.218	45.000	16.64	0.00	0.00	4.30
855	860	0.179056	CCGACAAATCCGTAGCCCAT	60.179	55.000	0.00	0.00	0.00	4.00
860	865	1.942657	CAAATCCGTAGCCCATGTGAG	59.057	52.381	0.00	0.00	0.00	3.51
903	908	6.097839	CCAAAATGGGATGAATCTTCTCATGT	59.902	38.462	11.59	4.28	36.15	3.21
978	983	3.988186	GGGTAAATAAGGGGGAAGAGGAT	59.012	47.826	0.00	0.00	0.00	3.24
1019	1024	5.690865	AGAAATGACTACAAGGAACCAACA	58.309	37.500	0.00	0.00	0.00	3.33
1034	1039	7.164803	AGGAACCAACAATTCTCTCTTCTTAG	58.835	38.462	0.00	0.00	0.00	2.18
1146	1151	7.759489	AGCAGGTATTTGTTTAGTCATTCAA	57.241	32.000	0.00	0.00	0.00	2.69
1365	1371	2.105821	AGGGAATTTGTTCGGTGTCTCA	59.894	45.455	0.00	0.00	0.00	3.27
1434	1440	0.772124	ACCACCTTGGGGTCAGATGT	60.772	55.000	0.00	0.00	45.41	3.06
1591	1598	8.500238	CATTTACTCCCCCTTATTTTAGTAGGT	58.500	37.037	0.00	0.00	0.00	3.08
1800	1812	6.634805	ACAATGATATACCTGCTAATCCGAG	58.365	40.000	0.00	0.00	0.00	4.63
1808	1820	2.742116	GCTAATCCGAGGCCCACCA	61.742	63.158	0.00	0.00	39.06	4.17
1872	1884	4.130118	GCCATTCTTCACAGTATACCTGG	58.870	47.826	0.00	0.00	46.06	4.45
2018	2032	3.487544	GCTTTTGGCGGATTGCTTACTAG	60.488	47.826	0.00	0.00	45.43	2.57
2082	2096	7.335924	TGTTACTATTGGACAAATTCCTACTGC	59.664	37.037	0.00	0.00	46.10	4.40
2086	2100	3.686016	TGGACAAATTCCTACTGCCTTC	58.314	45.455	0.00	0.00	46.10	3.46
2249	2268	4.899502	GCCATAGCCATAGAAGAAGCTTA	58.100	43.478	0.00	0.00	36.79	3.09
2260	2279	5.770685	AGAAGAAGCTTATCCTCCAAAGT	57.229	39.130	0.00	0.00	0.00	2.66
2364	2385	5.424757	TGGTACCAAATCTGGATAAACTCG	58.575	41.667	13.60	0.00	46.92	4.18
2368	2389	6.894339	ACCAAATCTGGATAAACTCGTTTT	57.106	33.333	0.00	0.00	46.92	2.43
2439	2461	3.230355	GACGCGAACATGTTTAATTGCA	58.770	40.909	15.93	0.00	0.00	4.08
2475	2497	8.937634	ATTCCAAAATATGATTCAAGAAGCAC	57.062	30.769	2.55	0.00	39.70	4.40
2476	2498	6.866480	TCCAAAATATGATTCAAGAAGCACC	58.134	36.000	2.55	0.00	39.70	5.01
2478	2500	6.404623	CCAAAATATGATTCAAGAAGCACCGA	60.405	38.462	2.55	0.00	39.70	4.69
2480	2502	1.428448	TGATTCAAGAAGCACCGACG	58.572	50.000	0.00	0.00	31.05	5.12
2481	2503	0.721718	GATTCAAGAAGCACCGACGG	59.278	55.000	13.61	13.61	0.00	4.79
2482	2504	1.298859	ATTCAAGAAGCACCGACGGC	61.299	55.000	15.39	0.00	0.00	5.68
2483	2505	3.777925	CAAGAAGCACCGACGGCG	61.778	66.667	15.39	1.94	36.08	6.46
2484	2506	3.986006	AAGAAGCACCGACGGCGA	61.986	61.111	15.16	0.00	40.82	5.54
2542	2564	3.439129	TGTGAAGATCGTCGTATGACTGT	59.561	43.478	13.11	1.48	43.21	3.55
2564	2586	5.726980	TGGAGGAAAGTCCAAAAATGATG	57.273	39.130	0.00	0.00	44.01	3.07
2691	2721	2.325484	GTTGGTTTGGTGGGGAAAGAT	58.675	47.619	0.00	0.00	0.00	2.40
2762	2794	3.530910	AACTCAACGGCTCCCACGG	62.531	63.158	0.00	0.00	35.23	4.94
2796	2828	3.630769	AGCGAATTCATACGAGGACTACA	59.369	43.478	6.22	0.00	0.00	2.74
2836	2868	4.056125	CAGGAGGTCGAGCGCACA	62.056	66.667	19.80	0.00	0.00	4.57
2850	2882	1.504359	CGCACACTTTCCTCGGTTTA	58.496	50.000	0.00	0.00	0.00	2.01
2882	2914	5.246429	GGGACAAAGATAGATCCTCGGTAAT	59.754	44.000	0.00	0.00	0.00	1.89
2914	2946	5.482006	GGATAGCCTTGCTTTTGAACATTT	58.518	37.500	0.00	0.00	40.44	2.32
3069	3101	5.008118	GGCGAGTAACTACTACGAAAGGTAT	59.992	44.000	10.76	0.00	36.50	2.73
3076	3108	9.591792	GTAACTACTACGAAAGGTATGGAAAAT	57.408	33.333	0.00	0.00	0.00	1.82
3094	3126	4.953940	AAATAGGAAAGGCAAAGCACAA	57.046	36.364	0.00	0.00	0.00	3.33
3103	3135	2.363359	AGGCAAAGCACAAGAAAGAAGG	59.637	45.455	0.00	0.00	0.00	3.46
3135	3167	6.834168	AATAATGTCATCCTTGTTTCCGTT	57.166	33.333	0.00	0.00	0.00	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
425	426	0.320858	TCCTTGCAACCAACGCGATA	60.321	50.000	15.93	0.00	0.00	2.92
426	427	0.960364	ATCCTTGCAACCAACGCGAT	60.960	50.000	15.93	0.00	0.00	4.58
535	536	2.240667	AGGGATGATGCAGCAAAGTAGT	59.759	45.455	9.54	0.00	0.00	2.73
591	592	6.595682	AGCAATATTGTTGTCCTATGCTACT	58.404	36.000	16.61	0.00	0.00	2.57
666	667	2.418976	GCAAACTACCTAGCCCTTTTCG	59.581	50.000	0.00	0.00	0.00	3.46
692	693	4.405358	ACCTTTCATGAAGAAGTTTTGCCA	59.595	37.500	8.41	0.00	37.57	4.92
786	787	4.354587	CGAAAAGAAACAGCTGCTTTCTT	58.645	39.130	30.46	30.46	45.68	2.52
794	795	2.814336	GGTCATCCGAAAAGAAACAGCT	59.186	45.455	0.00	0.00	0.00	4.24
797	798	7.519032	AAATAAGGTCATCCGAAAAGAAACA	57.481	32.000	0.00	0.00	39.05	2.83
802	805	5.810587	TCTCGAAATAAGGTCATCCGAAAAG	59.189	40.000	0.00	0.00	39.05	2.27
809	814	7.778470	AGTTGATTCTCGAAATAAGGTCATC	57.222	36.000	0.00	0.00	0.00	2.92
855	860	3.695606	GGGAGGCAGCGACTCACA	61.696	66.667	12.43	0.00	41.55	3.58
860	865	3.071206	TGAGAGGGAGGCAGCGAC	61.071	66.667	0.00	0.00	0.00	5.19
903	908	4.202010	GCGCCCTGAATAATCAAAAAGCTA	60.202	41.667	0.00	0.00	34.49	3.32
958	963	6.432581	ACAAATCCTCTTCCCCCTTATTTAC	58.567	40.000	0.00	0.00	0.00	2.01
1007	1012	5.767168	AGAAGAGAGAATTGTTGGTTCCTTG	59.233	40.000	0.00	0.00	0.00	3.61
1034	1039	7.924947	GGTTAAGTGTGGAGTATATAGGTTGTC	59.075	40.741	0.00	0.00	0.00	3.18
1078	1083	1.906574	ACTAAGATTGCTCGGGGTTGA	59.093	47.619	0.00	0.00	0.00	3.18
1311	1317	4.937201	AACTCGCATGATATAGACCACA	57.063	40.909	0.00	0.00	0.00	4.17
1557	1564	3.747852	AGGGGGAGTAAATGATGGAGAA	58.252	45.455	0.00	0.00	0.00	2.87
1591	1598	2.775911	CCAGATGAAGAAGACTGGCA	57.224	50.000	0.00	0.00	42.30	4.92
1781	1793	3.181474	GGCCTCGGATTAGCAGGTATATC	60.181	52.174	0.00	0.00	0.00	1.63
1813	1825	1.691196	ACCATTCCGGCACAATATGG	58.309	50.000	0.00	5.35	41.18	2.74
1872	1884	2.399356	GCTACACCTCCCGCTTTGC	61.399	63.158	0.00	0.00	0.00	3.68
2018	2032	3.195661	GTTGACATCCGATCCAACCTAC	58.804	50.000	10.16	0.00	34.46	3.18
2078	2092	4.429854	AGAACAAGAAGAAGAAGGCAGT	57.570	40.909	0.00	0.00	0.00	4.40
2082	2096	4.339247	TGGCAAAGAACAAGAAGAAGAAGG	59.661	41.667	0.00	0.00	0.00	3.46
2086	2100	5.853282	CGTTATGGCAAAGAACAAGAAGAAG	59.147	40.000	0.00	0.00	0.00	2.85
2260	2279	1.001631	TGAGATTCCGCTCCCTCCA	59.998	57.895	0.00	0.00	33.95	3.86
2381	2402	7.148171	CGAAAAGCCAGAAATAGAATTTCCTCT	60.148	37.037	8.40	2.24	0.00	3.69
2420	2441	2.341168	GGTGCAATTAAACATGTTCGCG	59.659	45.455	12.39	0.00	0.00	5.87
2451	2473	7.322664	GGTGCTTCTTGAATCATATTTTGGAA	58.677	34.615	0.00	0.00	0.00	3.53
2466	2488	3.777925	CGCCGTCGGTGCTTCTTG	61.778	66.667	12.67	0.00	0.00	3.02
2475	2497	0.947180	TTTTCTTCCTTCGCCGTCGG	60.947	55.000	6.99	6.99	36.13	4.79
2476	2498	0.163146	GTTTTCTTCCTTCGCCGTCG	59.837	55.000	0.00	0.00	0.00	5.12
2478	2500	1.202604	TCTGTTTTCTTCCTTCGCCGT	60.203	47.619	0.00	0.00	0.00	5.68
2480	2502	3.066203	TGTTTCTGTTTTCTTCCTTCGCC	59.934	43.478	0.00	0.00	0.00	5.54
2481	2503	4.287238	TGTTTCTGTTTTCTTCCTTCGC	57.713	40.909	0.00	0.00	0.00	4.70
2482	2504	4.735338	GCTTGTTTCTGTTTTCTTCCTTCG	59.265	41.667	0.00	0.00	0.00	3.79
2483	2505	5.043903	GGCTTGTTTCTGTTTTCTTCCTTC	58.956	41.667	0.00	0.00	0.00	3.46
2484	2506	4.711846	AGGCTTGTTTCTGTTTTCTTCCTT	59.288	37.500	0.00	0.00	0.00	3.36
2542	2564	4.527816	CCATCATTTTTGGACTTTCCTCCA	59.472	41.667	0.00	0.00	38.66	3.86
2559	2581	7.201974	CCATAGGAAAGAAAATGCTTCCATCAT	60.202	37.037	3.12	0.00	0.00	2.45
2562	2584	5.364735	CCCATAGGAAAGAAAATGCTTCCAT	59.635	40.000	3.12	0.00	33.47	3.41
2564	2586	4.956075	TCCCATAGGAAAGAAAATGCTTCC	59.044	41.667	0.00	0.00	40.08	3.46
2691	2721	3.582647	TGAAAGAAGCCCTCATACACTCA	59.417	43.478	0.00	0.00	0.00	3.41
2762	2794	1.452399	GAATTCGCTATCGCTCCGAAC	59.548	52.381	0.00	0.00	42.76	3.95
2796	2828	5.105392	TGGAAGGAATGCAATTATTCGCTTT	60.105	36.000	0.00	0.00	36.07	3.51
2836	2868	5.246307	CCTTGATTCTAAACCGAGGAAAGT	58.754	41.667	0.00	0.00	34.13	2.66
2850	2882	6.619023	AGGATCTATCTTTGTCCCTTGATTCT	59.381	38.462	0.00	0.00	0.00	2.40
2935	2967	4.571984	TCCTACTGATTTCGATTGCACATG	59.428	41.667	0.00	0.00	0.00	3.21
3069	3101	3.900601	TGCTTTGCCTTTCCTATTTTCCA	59.099	39.130	0.00	0.00	0.00	3.53
3076	3108	3.222173	TCTTGTGCTTTGCCTTTCCTA	57.778	42.857	0.00	0.00	0.00	2.94
3077	3109	2.071778	TCTTGTGCTTTGCCTTTCCT	57.928	45.000	0.00	0.00	0.00	3.36
3111	3143	7.066525	GGAACGGAAACAAGGATGACATTATTA	59.933	37.037	0.00	0.00	0.00	0.98
3132	3164	3.057019	TCGACAAGTTGAATCTGGAACG	58.943	45.455	10.54	1.81	0.00	3.95
3135	3167	2.612972	GCCTCGACAAGTTGAATCTGGA	60.613	50.000	10.54	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.