AutoCloner

Multiple sequence alignment - TraesCS5D01G291900

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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	TraesCS5D01G291900	chr5D	100.000	2850	0	0	1	2850	389493983	389496832	0.000000e+00	5264.0
1	TraesCS5D01G291900	chr5B	94.099	1542	47	21	1033	2566	469352969	469354474	0.000000e+00	2303.0
2	TraesCS5D01G291900	chr5B	91.842	1667	57	29	925	2566	468639215	468640827	0.000000e+00	2252.0
3	TraesCS5D01G291900	chr5B	93.515	1542	55	22	1033	2566	469211520	469213024	0.000000e+00	2252.0
4	TraesCS5D01G291900	chr5B	92.367	1559	52	25	1033	2566	467948844	467947328	0.000000e+00	2158.0
5	TraesCS5D01G291900	chr5B	92.506	427	25	3	595	1018	469196333	469196755	3.140000e-169	604.0
6	TraesCS5D01G291900	chr5B	88.660	291	19	7	2560	2850	469213076	469213352	2.720000e-90	342.0
7	TraesCS5D01G291900	chr5B	88.660	291	19	7	2560	2850	469354526	469354802	2.720000e-90	342.0
8	TraesCS5D01G291900	chr5B	88.542	288	19	7	2563	2850	467947273	467947000	1.260000e-88	337.0
9	TraesCS5D01G291900	chr5B	94.595	74	4	0	2560	2633	468640879	468640952	6.450000e-22	115.0
10	TraesCS5D01G291900	chr5A	93.409	1502	60	13	895	2372	492682131	492683617	0.000000e+00	2189.0
11	TraesCS5D01G291900	chr5A	91.973	299	18	4	2555	2850	492683808	492684103	5.680000e-112	414.0
12	TraesCS5D01G291900	chr5A	91.065	291	19	4	587	875	492681758	492682043	1.240000e-103	387.0
13	TraesCS5D01G291900	chr7A	91.637	562	30	8	1	546	108882312	108882872	0.000000e+00	761.0
14	TraesCS5D01G291900	chr7B	91.248	537	32	4	1	524	147732503	147731969	0.000000e+00	717.0
15	TraesCS5D01G291900	chr1B	89.123	570	37	17	4	551	557529874	557530440	0.000000e+00	686.0
16	TraesCS5D01G291900	chr4D	90.282	319	29	2	587	904	154924948	154924631	1.580000e-112	416.0
17	TraesCS5D01G291900	chr4D	89.109	303	27	4	587	887	367043135	367042837	3.470000e-99	372.0
18	TraesCS5D01G291900	chr4D	88.060	67	8	0	2635	2701	310709833	310709899	2.350000e-11	80.5
19	TraesCS5D01G291900	chr4A	91.060	302	24	2	587	887	97875110	97875409	3.420000e-109	405.0
20	TraesCS5D01G291900	chr4A	90.909	44	4	0	2591	2634	724789717	724789760	3.070000e-05	60.2
21	TraesCS5D01G291900	chr3A	79.292	565	105	11	1	559	598573107	598572549	4.450000e-103	385.0
22	TraesCS5D01G291900	chr3B	90.335	269	20	4	631	898	320114469	320114732	5.840000e-92	348.0
23	TraesCS5D01G291900	chr6B	89.850	266	22	3	632	896	259709794	259709533	1.260000e-88	337.0
24	TraesCS5D01G291900	chr6B	94.872	39	2	0	2587	2625	16438394	16438432	8.530000e-06	62.1
25	TraesCS5D01G291900	chr2B	89.051	274	25	3	632	904	311671910	311671641	4.550000e-88	335.0
26	TraesCS5D01G291900	chr4B	88.848	269	24	3	632	898	30595016	30595280	2.740000e-85	326.0
27	TraesCS5D01G291900	chr1D	83.041	171	27	2	73	242	489958757	489958588	1.370000e-33	154.0
28	TraesCS5D01G291900	chr6D	88.060	67	8	0	2635	2701	235588518	235588452	2.350000e-11	80.5
29	TraesCS5D01G291900	chr6D	89.655	58	5	1	2635	2692	168298151	168298207	3.940000e-09	73.1
30	TraesCS5D01G291900	chr3D	97.436	39	1	0	2594	2632	585982688	585982650	1.830000e-07	67.6
31	TraesCS5D01G291900	chr2D	100.000	28	0	0	2580	2607	605654851	605654878	5.000000e-03	52.8

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	TraesCS5D01G291900	chr5D	389493983	389496832	2849	False	5264.000000	5264	100.0000	1	2850	1	chr5D.!!$F1	2849
1	TraesCS5D01G291900	chr5B	469352969	469354802	1833	False	1322.500000	2303	91.3795	1033	2850	2	chr5B.!!$F4	1817
2	TraesCS5D01G291900	chr5B	469211520	469213352	1832	False	1297.000000	2252	91.0875	1033	2850	2	chr5B.!!$F3	1817
3	TraesCS5D01G291900	chr5B	467947000	467948844	1844	True	1247.500000	2158	90.4545	1033	2850	2	chr5B.!!$R1	1817
4	TraesCS5D01G291900	chr5B	468639215	468640952	1737	False	1183.500000	2252	93.2185	925	2633	2	chr5B.!!$F2	1708
5	TraesCS5D01G291900	chr5A	492681758	492684103	2345	False	996.666667	2189	92.1490	587	2850	3	chr5A.!!$F1	2263
6	TraesCS5D01G291900	chr7A	108882312	108882872	560	False	761.000000	761	91.6370	1	546	1	chr7A.!!$F1	545
7	TraesCS5D01G291900	chr7B	147731969	147732503	534	True	717.000000	717	91.2480	1	524	1	chr7B.!!$R1	523
8	TraesCS5D01G291900	chr1B	557529874	557530440	566	False	686.000000	686	89.1230	4	551	1	chr1B.!!$F1	547
9	TraesCS5D01G291900	chr3A	598572549	598573107	558	True	385.000000	385	79.2920	1	559	1	chr3A.!!$R1	558

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
603	618	0.391793	CCCCTCGTCTTCTCTTTGCC	60.392	60.0	0.0	0.0	0.00	4.52	F
1701	1800	0.245813	GGTGGACCCTTCACGTCTAC	59.754	60.0	0.0	0.0	40.05	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1742	1841	0.670546	TCGCAGAGCACTGTAAAGGC	60.671	55.000	12.89	0.0	45.04	4.35	R
2527	2658	2.901839	AGAATGAGCCAAACTTGCCAAT	59.098	40.909	0.00	0.0	0.00	3.16	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
59	60	3.384532	GACGGCGGGGTCCAACTA	61.385	66.667	13.24	0.00	0.00	2.24
400	414	4.575973	GCCAGATCCGCCCAGCAT	62.576	66.667	0.00	0.00	0.00	3.79
436	450	4.787280	AGCAGGAGGAGGGACGGG	62.787	72.222	0.00	0.00	0.00	5.28
564	579	4.899239	GCAGTCGCCATCCTCCGG	62.899	72.222	0.00	0.00	0.00	5.14
565	580	3.461773	CAGTCGCCATCCTCCGGT	61.462	66.667	0.00	0.00	0.00	5.28
566	581	2.683933	AGTCGCCATCCTCCGGTT	60.684	61.111	0.00	0.00	0.00	4.44
567	582	1.380785	AGTCGCCATCCTCCGGTTA	60.381	57.895	0.00	0.00	0.00	2.85
568	583	1.227176	GTCGCCATCCTCCGGTTAC	60.227	63.158	0.00	0.00	0.00	2.50
569	584	1.683025	TCGCCATCCTCCGGTTACA	60.683	57.895	0.00	0.00	0.00	2.41
570	585	1.227263	CGCCATCCTCCGGTTACAG	60.227	63.158	0.00	0.00	0.00	2.74
571	586	1.672854	CGCCATCCTCCGGTTACAGA	61.673	60.000	0.00	0.00	0.00	3.41
572	587	0.759346	GCCATCCTCCGGTTACAGAT	59.241	55.000	0.00	0.00	0.00	2.90
573	588	1.968493	GCCATCCTCCGGTTACAGATA	59.032	52.381	0.00	0.00	0.00	1.98
574	589	2.567615	GCCATCCTCCGGTTACAGATAT	59.432	50.000	0.00	0.00	0.00	1.63
575	590	3.008049	GCCATCCTCCGGTTACAGATATT	59.992	47.826	0.00	0.00	0.00	1.28
576	591	4.505039	GCCATCCTCCGGTTACAGATATTT	60.505	45.833	0.00	0.00	0.00	1.40
577	592	5.238583	CCATCCTCCGGTTACAGATATTTC	58.761	45.833	0.00	0.00	0.00	2.17
578	593	5.221641	CCATCCTCCGGTTACAGATATTTCA	60.222	44.000	0.00	0.00	0.00	2.69
579	594	5.272283	TCCTCCGGTTACAGATATTTCAC	57.728	43.478	0.00	0.00	0.00	3.18
580	595	4.712829	TCCTCCGGTTACAGATATTTCACA	59.287	41.667	0.00	0.00	0.00	3.58
581	596	4.809426	CCTCCGGTTACAGATATTTCACAC	59.191	45.833	0.00	0.00	0.00	3.82
582	597	5.408880	TCCGGTTACAGATATTTCACACA	57.591	39.130	0.00	0.00	0.00	3.72
583	598	5.416083	TCCGGTTACAGATATTTCACACAG	58.584	41.667	0.00	0.00	0.00	3.66
584	599	4.034048	CCGGTTACAGATATTTCACACAGC	59.966	45.833	0.00	0.00	0.00	4.40
585	600	4.034048	CGGTTACAGATATTTCACACAGCC	59.966	45.833	0.00	0.00	0.00	4.85
591	606	0.981183	TATTTCACACAGCCCCTCGT	59.019	50.000	0.00	0.00	0.00	4.18
593	608	1.407656	TTTCACACAGCCCCTCGTCT	61.408	55.000	0.00	0.00	0.00	4.18
603	618	0.391793	CCCCTCGTCTTCTCTTTGCC	60.392	60.000	0.00	0.00	0.00	4.52
608	623	1.686587	TCGTCTTCTCTTTGCCTGTGA	59.313	47.619	0.00	0.00	0.00	3.58
653	668	9.243637	TCAATACTTGTGTTTTATGTCAAAAGC	57.756	29.630	0.00	0.00	33.60	3.51
654	669	9.029243	CAATACTTGTGTTTTATGTCAAAAGCA	57.971	29.630	0.00	0.00	33.60	3.91
676	691	8.773033	AGCAAGACTGAATAAATTATTGGGAT	57.227	30.769	2.58	0.00	0.00	3.85
717	732	7.962441	AGTATGGAAAAATAATAATGGTGGGC	58.038	34.615	0.00	0.00	0.00	5.36
718	733	5.269505	TGGAAAAATAATAATGGTGGGCG	57.730	39.130	0.00	0.00	0.00	6.13
761	776	7.029563	GGTAGCATTGTTTCATTCTTAGGTTG	58.970	38.462	0.00	0.00	0.00	3.77
767	782	9.559958	CATTGTTTCATTCTTAGGTTGTGTATC	57.440	33.333	0.00	0.00	0.00	2.24
769	784	8.918202	TGTTTCATTCTTAGGTTGTGTATCTT	57.082	30.769	0.00	0.00	0.00	2.40
773	788	9.567776	TTCATTCTTAGGTTGTGTATCTTTTGA	57.432	29.630	0.00	0.00	0.00	2.69
774	789	9.567776	TCATTCTTAGGTTGTGTATCTTTTGAA	57.432	29.630	0.00	0.00	0.00	2.69
798	814	4.892965	TGCCAAACAGCTGCGGGT	62.893	61.111	15.27	0.00	0.00	5.28
812	828	2.985847	GGGTGTCAACCTGCTGCC	60.986	66.667	0.00	0.00	46.70	4.85
814	830	2.591715	GTGTCAACCTGCTGCCGT	60.592	61.111	0.00	0.00	0.00	5.68
834	850	5.276348	GCCGTGAACAAAATCTTCAAACAAG	60.276	40.000	0.00	0.00	29.44	3.16
857	873	5.709164	AGAAGTGCACTCAAATATTCAGCTT	59.291	36.000	21.95	0.00	0.00	3.74
859	875	4.157289	AGTGCACTCAAATATTCAGCTTGG	59.843	41.667	15.25	0.00	0.00	3.61
875	891	2.355108	GCTTGGAAGGCTCATCTGTACA	60.355	50.000	0.00	0.00	0.00	2.90
876	892	3.683847	GCTTGGAAGGCTCATCTGTACAT	60.684	47.826	0.00	0.00	0.00	2.29
877	893	4.443457	GCTTGGAAGGCTCATCTGTACATA	60.443	45.833	0.00	0.00	0.00	2.29
878	894	5.674525	CTTGGAAGGCTCATCTGTACATAA	58.325	41.667	0.00	0.00	0.00	1.90
880	896	6.994421	TGGAAGGCTCATCTGTACATAATA	57.006	37.500	0.00	0.00	0.00	0.98
881	897	7.373617	TGGAAGGCTCATCTGTACATAATAA	57.626	36.000	0.00	0.00	0.00	1.40
882	898	7.977818	TGGAAGGCTCATCTGTACATAATAAT	58.022	34.615	0.00	0.00	0.00	1.28
886	902	7.977818	AGGCTCATCTGTACATAATAATTCCA	58.022	34.615	0.00	0.00	0.00	3.53
887	903	8.609483	AGGCTCATCTGTACATAATAATTCCAT	58.391	33.333	0.00	0.00	0.00	3.41
888	904	8.671921	GGCTCATCTGTACATAATAATTCCATG	58.328	37.037	0.00	0.00	0.00	3.66
889	905	9.224267	GCTCATCTGTACATAATAATTCCATGT	57.776	33.333	0.00	5.23	36.82	3.21
945	1029	2.628657	AGCCTAAACCAGTCTATAGCGG	59.371	50.000	0.00	0.00	0.00	5.52
1031	1115	3.266376	GCACGCGCGCCCTAATAA	61.266	61.111	32.58	0.00	0.00	1.40
1327	1419	1.518774	GGCCGACGGGTCTATTTGA	59.481	57.895	17.22	0.00	34.09	2.69
1461	1560	4.077822	CTGAGATCTTTCTGCCCTGTTTT	58.922	43.478	0.00	0.00	30.30	2.43
1491	1590	1.552792	GTCCAAGTCTTCCTCTCAGGG	59.447	57.143	0.00	0.00	35.59	4.45
1701	1800	0.245813	GGTGGACCCTTCACGTCTAC	59.754	60.000	0.00	0.00	40.05	2.59
1742	1841	3.414700	GCTTGTCCGGAGCACGTG	61.415	66.667	12.28	12.28	42.24	4.49
1776	1875	4.005472	CGAGCGCGCCATGGATTC	62.005	66.667	30.33	16.04	0.00	2.52
1842	1941	0.171679	TCAATGGCGAATTGCTGCTG	59.828	50.000	0.00	0.00	44.63	4.41
2015	2114	6.525629	CAAAGGACTTTACTATGATCCGGAT	58.474	40.000	19.21	19.21	34.46	4.18
2131	2230	1.456518	CCCGGAGAGCAGATGGAGA	60.457	63.158	0.73	0.00	0.00	3.71
2132	2231	0.831288	CCCGGAGAGCAGATGGAGAT	60.831	60.000	0.73	0.00	0.00	2.75
2133	2232	0.317799	CCGGAGAGCAGATGGAGATG	59.682	60.000	0.00	0.00	0.00	2.90
2134	2233	0.317799	CGGAGAGCAGATGGAGATGG	59.682	60.000	0.00	0.00	0.00	3.51
2135	2234	1.714541	GGAGAGCAGATGGAGATGGA	58.285	55.000	0.00	0.00	0.00	3.41
2136	2235	1.619827	GGAGAGCAGATGGAGATGGAG	59.380	57.143	0.00	0.00	0.00	3.86
2280	2382	1.725641	TCAGTATTGGAGCAGCAACG	58.274	50.000	0.00	0.00	0.00	4.10
2466	2593	5.820947	ACCACCATTGTAAAGTCGGATAATC	59.179	40.000	0.00	0.00	0.00	1.75
2480	2607	3.578716	CGGATAATCCAGTGGACCACTAT	59.421	47.826	26.70	16.06	43.43	2.12
2493	2620	7.065085	CAGTGGACCACTATTTTGTATCTCTTG	59.935	40.741	26.70	5.93	43.43	3.02
2597	2786	1.559682	TGCTTCCAACATACTCCCTCC	59.440	52.381	0.00	0.00	0.00	4.30
2609	2798	0.322546	CTCCCTCCGTCCCAAAAAGG	60.323	60.000	0.00	0.00	37.03	3.11
2633	2822	9.256228	AGGTTGTCTTAGATTTGTCTAGATACA	57.744	33.333	0.00	0.00	0.00	2.29
2763	2953	4.379499	CGGTTAAAGGAGGAGATGCAAAAC	60.379	45.833	0.00	0.00	0.00	2.43
2784	2974	1.900498	GCTGCTGCTGTTGGGAACT	60.900	57.895	8.53	0.00	36.03	3.01
2826	3016	3.420893	CAAGGGAGGTGTTTAATGCAGA	58.579	45.455	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
559	574	5.416083	TGTGTGAAATATCTGTAACCGGAG	58.584	41.667	9.46	0.00	0.00	4.63
560	575	5.408880	TGTGTGAAATATCTGTAACCGGA	57.591	39.130	9.46	0.00	0.00	5.14
561	576	4.034048	GCTGTGTGAAATATCTGTAACCGG	59.966	45.833	0.00	0.00	0.00	5.28
562	577	4.034048	GGCTGTGTGAAATATCTGTAACCG	59.966	45.833	0.00	0.00	0.00	4.44
563	578	4.335594	GGGCTGTGTGAAATATCTGTAACC	59.664	45.833	0.00	0.00	0.00	2.85
564	579	4.335594	GGGGCTGTGTGAAATATCTGTAAC	59.664	45.833	0.00	0.00	0.00	2.50
565	580	4.227300	AGGGGCTGTGTGAAATATCTGTAA	59.773	41.667	0.00	0.00	0.00	2.41
566	581	3.780294	AGGGGCTGTGTGAAATATCTGTA	59.220	43.478	0.00	0.00	0.00	2.74
567	582	2.578021	AGGGGCTGTGTGAAATATCTGT	59.422	45.455	0.00	0.00	0.00	3.41
568	583	3.209410	GAGGGGCTGTGTGAAATATCTG	58.791	50.000	0.00	0.00	0.00	2.90
569	584	2.158900	CGAGGGGCTGTGTGAAATATCT	60.159	50.000	0.00	0.00	0.00	1.98
570	585	2.213499	CGAGGGGCTGTGTGAAATATC	58.787	52.381	0.00	0.00	0.00	1.63
571	586	1.559682	ACGAGGGGCTGTGTGAAATAT	59.440	47.619	0.00	0.00	0.00	1.28
572	587	0.981183	ACGAGGGGCTGTGTGAAATA	59.019	50.000	0.00	0.00	0.00	1.40
573	588	0.321653	GACGAGGGGCTGTGTGAAAT	60.322	55.000	0.00	0.00	0.00	2.17
574	589	1.070786	GACGAGGGGCTGTGTGAAA	59.929	57.895	0.00	0.00	0.00	2.69
575	590	1.407656	AAGACGAGGGGCTGTGTGAA	61.408	55.000	0.00	0.00	0.00	3.18
576	591	1.816863	GAAGACGAGGGGCTGTGTGA	61.817	60.000	0.00	0.00	0.00	3.58
577	592	1.374758	GAAGACGAGGGGCTGTGTG	60.375	63.158	0.00	0.00	0.00	3.82
578	593	1.534235	AGAAGACGAGGGGCTGTGT	60.534	57.895	0.00	0.00	0.00	3.72
579	594	1.216710	GAGAAGACGAGGGGCTGTG	59.783	63.158	0.00	0.00	0.00	3.66
580	595	0.543174	AAGAGAAGACGAGGGGCTGT	60.543	55.000	0.00	0.00	0.00	4.40
581	596	0.610687	AAAGAGAAGACGAGGGGCTG	59.389	55.000	0.00	0.00	0.00	4.85
582	597	0.610687	CAAAGAGAAGACGAGGGGCT	59.389	55.000	0.00	0.00	0.00	5.19
583	598	1.021920	GCAAAGAGAAGACGAGGGGC	61.022	60.000	0.00	0.00	0.00	5.80
584	599	0.391793	GGCAAAGAGAAGACGAGGGG	60.392	60.000	0.00	0.00	0.00	4.79
585	600	0.610687	AGGCAAAGAGAAGACGAGGG	59.389	55.000	0.00	0.00	0.00	4.30
591	606	2.639347	TCCATCACAGGCAAAGAGAAGA	59.361	45.455	0.00	0.00	0.00	2.87
593	608	2.639347	TCTCCATCACAGGCAAAGAGAA	59.361	45.455	0.00	0.00	0.00	2.87
603	618	0.179936	GAGCCCCTTCTCCATCACAG	59.820	60.000	0.00	0.00	0.00	3.66
608	623	1.283321	GACTTTGAGCCCCTTCTCCAT	59.717	52.381	0.00	0.00	32.22	3.41
735	750	6.485171	ACCTAAGAATGAAACAATGCTACCT	58.515	36.000	0.00	0.00	0.00	3.08
736	751	6.759497	ACCTAAGAATGAAACAATGCTACC	57.241	37.500	0.00	0.00	0.00	3.18
737	752	7.538678	CACAACCTAAGAATGAAACAATGCTAC	59.461	37.037	0.00	0.00	0.00	3.58
738	753	7.230510	ACACAACCTAAGAATGAAACAATGCTA	59.769	33.333	0.00	0.00	0.00	3.49
739	754	6.040842	ACACAACCTAAGAATGAAACAATGCT	59.959	34.615	0.00	0.00	0.00	3.79
761	776	7.887996	TGGCATCAAAATTCAAAAGATACAC	57.112	32.000	0.00	0.00	0.00	2.90
767	782	5.910723	GCTGTTTGGCATCAAAATTCAAAAG	59.089	36.000	0.00	0.00	43.56	2.27
769	784	5.007823	CAGCTGTTTGGCATCAAAATTCAAA	59.992	36.000	5.25	0.00	43.56	2.69
772	787	3.120442	GCAGCTGTTTGGCATCAAAATTC	60.120	43.478	16.64	0.00	43.56	2.17
773	788	2.809696	GCAGCTGTTTGGCATCAAAATT	59.190	40.909	16.64	0.00	43.56	1.82
774	789	2.419667	GCAGCTGTTTGGCATCAAAAT	58.580	42.857	16.64	0.00	43.56	1.82
775	790	1.868469	GCAGCTGTTTGGCATCAAAA	58.132	45.000	16.64	0.00	43.56	2.44
798	814	2.591429	CACGGCAGCAGGTTGACA	60.591	61.111	0.00	0.00	0.00	3.58
812	828	7.273381	ACTTCTTGTTTGAAGATTTTGTTCACG	59.727	33.333	10.68	0.00	44.40	4.35
814	830	7.063308	GCACTTCTTGTTTGAAGATTTTGTTCA	59.937	33.333	10.68	0.00	44.40	3.18
834	850	5.557891	AGCTGAATATTTGAGTGCACTTC	57.442	39.130	22.65	13.01	0.00	3.01
857	873	5.894298	ATTATGTACAGATGAGCCTTCCA	57.106	39.130	0.33	0.00	0.00	3.53
859	875	8.940952	GGAATTATTATGTACAGATGAGCCTTC	58.059	37.037	0.33	0.00	0.00	3.46
880	896	7.984050	CACTCTAACAGATCAGTACATGGAATT	59.016	37.037	0.00	0.00	0.00	2.17
881	897	7.495901	CACTCTAACAGATCAGTACATGGAAT	58.504	38.462	0.00	0.00	0.00	3.01
882	898	6.628175	GCACTCTAACAGATCAGTACATGGAA	60.628	42.308	0.00	0.00	0.00	3.53
886	902	5.420421	AGTGCACTCTAACAGATCAGTACAT	59.580	40.000	15.25	0.00	0.00	2.29
887	903	4.767409	AGTGCACTCTAACAGATCAGTACA	59.233	41.667	15.25	0.00	0.00	2.90
888	904	5.317733	AGTGCACTCTAACAGATCAGTAC	57.682	43.478	15.25	0.00	0.00	2.73
889	905	5.105716	GGAAGTGCACTCTAACAGATCAGTA	60.106	44.000	21.95	0.00	0.00	2.74
891	907	4.180057	GGAAGTGCACTCTAACAGATCAG	58.820	47.826	21.95	0.00	0.00	2.90
892	908	3.578282	TGGAAGTGCACTCTAACAGATCA	59.422	43.478	21.95	5.50	0.00	2.92
893	909	4.180057	CTGGAAGTGCACTCTAACAGATC	58.820	47.826	21.95	11.09	0.00	2.75
945	1029	1.877165	GTACGCTGGCTCGGCTTAC	60.877	63.158	6.82	6.82	34.35	2.34
975	1059	4.473520	AGGAACGCTGGCGATGGG	62.474	66.667	21.77	0.00	42.83	4.00
1029	1113	9.589111	GTGTGGTTTCTTGGTCTTTTTATTTTA	57.411	29.630	0.00	0.00	0.00	1.52
1030	1114	8.097662	TGTGTGGTTTCTTGGTCTTTTTATTTT	58.902	29.630	0.00	0.00	0.00	1.82
1031	1115	7.547722	GTGTGTGGTTTCTTGGTCTTTTTATTT	59.452	33.333	0.00	0.00	0.00	1.40
1461	1560	3.524648	GACTTGGACAACGGCGGGA	62.525	63.158	13.24	0.00	0.00	5.14
1742	1841	0.670546	TCGCAGAGCACTGTAAAGGC	60.671	55.000	12.89	0.00	45.04	4.35
1833	1932	1.624336	ACATCACAACCAGCAGCAAT	58.376	45.000	0.00	0.00	0.00	3.56
1842	1941	2.104253	CGCCCGGTACATCACAACC	61.104	63.158	0.00	0.00	0.00	3.77
1926	2025	1.218316	GCCGAGATCCGTGACCTTT	59.782	57.895	0.00	0.00	36.31	3.11
2015	2114	7.115805	CGTGCTCTACAAAGTAGACACAATTTA	59.884	37.037	23.42	1.25	31.83	1.40
2133	2232	4.785453	CTTCTGCCCGTGCCCTCC	62.785	72.222	0.00	0.00	36.33	4.30
2209	2308	4.956700	CAGTGAAGATCTACCTTACTGGGA	59.043	45.833	9.05	0.00	41.11	4.37
2246	2348	6.592607	TCCAATACTGATTCGGTTACTTTCAC	59.407	38.462	2.92	0.00	0.00	3.18
2280	2382	1.200020	CATTCAAACACGGGAAGCTCC	59.800	52.381	0.00	0.00	35.23	4.70
2443	2570	5.238650	GGATTATCCGACTTTACAATGGTGG	59.761	44.000	0.00	0.00	0.00	4.61
2466	2593	5.745227	AGATACAAAATAGTGGTCCACTGG	58.255	41.667	31.23	17.86	45.01	4.00
2527	2658	2.901839	AGAATGAGCCAAACTTGCCAAT	59.098	40.909	0.00	0.00	0.00	3.16
2541	2672	6.076981	AGTGTTGCCAGTAAAAAGAATGAG	57.923	37.500	0.00	0.00	0.00	2.90
2597	2786	4.131596	TCTAAGACAACCTTTTTGGGACG	58.868	43.478	0.00	0.00	41.11	4.79
2646	2835	9.073475	AGCTTGTCTTCGATTTATCTAGATACT	57.927	33.333	12.12	3.02	0.00	2.12
2763	2953	3.371063	CCCAACAGCAGCAGCAGG	61.371	66.667	3.17	0.00	45.49	4.85
2784	2974	3.136809	TGCCACCTACTCCAAACAACTTA	59.863	43.478	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.