AutoCloner

Multiple sequence alignment - TraesCS5B01G315800

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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	TraesCS5B01G315800	chr5B	100.000	2289	0	0	1	2289	497933543	497935831	0.000000e+00	4228.0
1	TraesCS5B01G315800	chr5B	90.671	1683	122	10	59	1714	641300554	641298880	0.000000e+00	2206.0
2	TraesCS5B01G315800	chr6D	90.953	1669	125	8	71	1715	450906017	450907683	0.000000e+00	2222.0
3	TraesCS5B01G315800	chr6D	98.276	58	0	1	2	58	329280515	329280458	1.450000e-17	100.0
4	TraesCS5B01G315800	chr6D	96.667	60	0	2	1	58	433726437	433726378	5.200000e-17	99.0
5	TraesCS5B01G315800	chr4B	90.709	1679	128	9	59	1711	551784761	551786437	0.000000e+00	2211.0
6	TraesCS5B01G315800	chr4B	90.131	1682	138	9	56	1711	551730150	551731829	0.000000e+00	2161.0
7	TraesCS5B01G315800	chr6B	90.682	1685	121	12	58	1714	189103606	189105282	0.000000e+00	2209.0
8	TraesCS5B01G315800	chr2B	90.438	1621	134	11	56	1661	755544064	755545678	0.000000e+00	2115.0
9	TraesCS5B01G315800	chr2B	90.191	1621	134	11	71	1669	479889937	479888320	0.000000e+00	2089.0
10	TraesCS5B01G315800	chr2B	93.150	1416	79	8	312	1711	46495423	46494010	0.000000e+00	2061.0
11	TraesCS5B01G315800	chr2B	87.821	312	29	4	59	361	181999354	181999043	7.780000e-95	357.0
12	TraesCS5B01G315800	chr4D	90.006	1621	136	13	59	1660	490089203	490087590	0.000000e+00	2073.0
13	TraesCS5B01G315800	chr4D	90.643	1571	118	14	168	1711	102106757	102105189	0.000000e+00	2060.0
14	TraesCS5B01G315800	chr4D	90.816	1176	90	11	59	1221	418402941	418401771	0.000000e+00	1557.0
15	TraesCS5B01G315800	chr7D	89.001	1691	141	18	56	1716	533932853	533934528	0.000000e+00	2050.0
16	TraesCS5B01G315800	chr5D	89.106	1689	118	24	61	1715	492732748	492731092	0.000000e+00	2039.0
17	TraesCS5B01G315800	chr5D	90.717	474	27	9	1729	2202	413072205	413072661	1.160000e-172	616.0
18	TraesCS5B01G315800	chr2D	88.578	1681	139	24	59	1715	88299526	88301177	0.000000e+00	1991.0
19	TraesCS5B01G315800	chr2D	96.774	62	0	2	1	61	333929264	333929204	4.020000e-18	102.0
20	TraesCS5B01G315800	chr2D	95.161	62	1	2	1	61	333938613	333938553	1.870000e-16	97.1
21	TraesCS5B01G315800	chr4A	90.605	1405	108	10	59	1445	418072927	418071529	0.000000e+00	1842.0
22	TraesCS5B01G315800	chr5A	93.548	341	15	5	1952	2289	525122437	525122773	3.390000e-138	501.0
23	TraesCS5B01G315800	chr5A	94.372	231	13	0	1712	1942	525120722	525120952	2.800000e-94	355.0
24	TraesCS5B01G315800	chr5A	96.667	60	0	2	1	59	392238873	392238815	5.200000e-17	99.0
25	TraesCS5B01G315800	chr3A	86.898	374	37	6	59	421	649855695	649856067	2.120000e-110	409.0
26	TraesCS5B01G315800	chr3A	95.238	63	2	1	1	62	134006256	134006318	5.200000e-17	99.0
27	TraesCS5B01G315800	chr3A	91.429	70	5	1	1	69	87155676	87155607	6.730000e-16	95.3
28	TraesCS5B01G315800	chr3A	95.161	62	0	3	1	61	684274552	684274493	6.730000e-16	95.3
29	TraesCS5B01G315800	chr7A	92.958	71	2	3	1	70	536892606	536892674	1.450000e-17	100.0

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	TraesCS5B01G315800	chr5B	497933543	497935831	2288	False	4228	4228	100.000	1	2289	1	chr5B.!!$F1	2288
1	TraesCS5B01G315800	chr5B	641298880	641300554	1674	True	2206	2206	90.671	59	1714	1	chr5B.!!$R1	1655
2	TraesCS5B01G315800	chr6D	450906017	450907683	1666	False	2222	2222	90.953	71	1715	1	chr6D.!!$F1	1644
3	TraesCS5B01G315800	chr4B	551784761	551786437	1676	False	2211	2211	90.709	59	1711	1	chr4B.!!$F2	1652
4	TraesCS5B01G315800	chr4B	551730150	551731829	1679	False	2161	2161	90.131	56	1711	1	chr4B.!!$F1	1655
5	TraesCS5B01G315800	chr6B	189103606	189105282	1676	False	2209	2209	90.682	58	1714	1	chr6B.!!$F1	1656
6	TraesCS5B01G315800	chr2B	755544064	755545678	1614	False	2115	2115	90.438	56	1661	1	chr2B.!!$F1	1605
7	TraesCS5B01G315800	chr2B	479888320	479889937	1617	True	2089	2089	90.191	71	1669	1	chr2B.!!$R3	1598
8	TraesCS5B01G315800	chr2B	46494010	46495423	1413	True	2061	2061	93.150	312	1711	1	chr2B.!!$R1	1399
9	TraesCS5B01G315800	chr4D	490087590	490089203	1613	True	2073	2073	90.006	59	1660	1	chr4D.!!$R3	1601
10	TraesCS5B01G315800	chr4D	102105189	102106757	1568	True	2060	2060	90.643	168	1711	1	chr4D.!!$R1	1543
11	TraesCS5B01G315800	chr4D	418401771	418402941	1170	True	1557	1557	90.816	59	1221	1	chr4D.!!$R2	1162
12	TraesCS5B01G315800	chr7D	533932853	533934528	1675	False	2050	2050	89.001	56	1716	1	chr7D.!!$F1	1660
13	TraesCS5B01G315800	chr5D	492731092	492732748	1656	True	2039	2039	89.106	61	1715	1	chr5D.!!$R1	1654
14	TraesCS5B01G315800	chr2D	88299526	88301177	1651	False	1991	1991	88.578	59	1715	1	chr2D.!!$F1	1656
15	TraesCS5B01G315800	chr4A	418071529	418072927	1398	True	1842	1842	90.605	59	1445	1	chr4A.!!$R1	1386
16	TraesCS5B01G315800	chr5A	525120722	525122773	2051	False	428	501	93.960	1712	2289	2	chr5A.!!$F1	577

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
374	399	0.24899	CGCCTTCAGCTTTTGTGCAA	60.249	50.0	0.0	0.0	40.39	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1560	1627	0.033601	ACTGCCTGGTGTTTGGTTGA	60.034	50.0	0.0	0.0	0.0	3.18	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
20	21	2.764007	AGGGATGACACTGAGCACA	58.236	52.632	0.00	0.00	0.00	4.57
22	23	0.610174	GGGATGACACTGAGCACAGA	59.390	55.000	18.54	0.00	46.03	3.41
23	24	1.405256	GGGATGACACTGAGCACAGAG	60.405	57.143	18.54	12.52	46.03	3.35
24	25	1.547820	GGATGACACTGAGCACAGAGA	59.452	52.381	18.54	0.00	46.03	3.10
25	26	2.605030	GATGACACTGAGCACAGAGAC	58.395	52.381	18.54	10.78	46.03	3.36
26	27	1.697284	TGACACTGAGCACAGAGACT	58.303	50.000	18.54	0.00	46.03	3.24
27	28	2.034878	TGACACTGAGCACAGAGACTT	58.965	47.619	18.54	0.00	46.03	3.01
28	29	2.223900	TGACACTGAGCACAGAGACTTG	60.224	50.000	18.54	7.59	46.03	3.16
29	30	2.034878	ACACTGAGCACAGAGACTTGA	58.965	47.619	18.54	0.00	46.03	3.02
30	31	2.223923	ACACTGAGCACAGAGACTTGAC	60.224	50.000	18.54	0.00	46.03	3.18
31	32	1.342819	ACTGAGCACAGAGACTTGACC	59.657	52.381	18.54	0.00	46.03	4.02
32	33	0.315251	TGAGCACAGAGACTTGACCG	59.685	55.000	0.00	0.00	0.00	4.79
33	34	0.315568	GAGCACAGAGACTTGACCGT	59.684	55.000	0.00	0.00	0.00	4.83
34	35	0.753262	AGCACAGAGACTTGACCGTT	59.247	50.000	0.00	0.00	0.00	4.44
35	36	1.139058	AGCACAGAGACTTGACCGTTT	59.861	47.619	0.00	0.00	0.00	3.60
36	37	1.261619	GCACAGAGACTTGACCGTTTG	59.738	52.381	0.00	0.00	0.00	2.93
37	38	2.821546	CACAGAGACTTGACCGTTTGA	58.178	47.619	0.00	0.00	0.00	2.69
38	39	2.797156	CACAGAGACTTGACCGTTTGAG	59.203	50.000	0.00	0.00	0.00	3.02
39	40	2.224066	ACAGAGACTTGACCGTTTGAGG	60.224	50.000	0.00	0.00	37.30	3.86
47	48	2.431942	CCGTTTGAGGTCGGGTCG	60.432	66.667	0.00	0.00	42.61	4.79
48	49	3.110178	CGTTTGAGGTCGGGTCGC	61.110	66.667	0.00	0.00	0.00	5.19
49	50	2.342648	GTTTGAGGTCGGGTCGCT	59.657	61.111	0.00	0.00	0.00	4.93
50	51	1.588082	GTTTGAGGTCGGGTCGCTA	59.412	57.895	0.00	0.00	0.00	4.26
51	52	0.735287	GTTTGAGGTCGGGTCGCTAC	60.735	60.000	0.00	0.00	0.00	3.58
52	53	1.180456	TTTGAGGTCGGGTCGCTACA	61.180	55.000	0.00	0.00	0.00	2.74
53	54	1.592400	TTGAGGTCGGGTCGCTACAG	61.592	60.000	0.00	0.00	0.00	2.74
54	55	1.748122	GAGGTCGGGTCGCTACAGA	60.748	63.158	0.00	0.00	0.00	3.41
55	56	1.716826	GAGGTCGGGTCGCTACAGAG	61.717	65.000	0.00	0.00	0.00	3.35
56	57	2.102553	GTCGGGTCGCTACAGAGC	59.897	66.667	0.00	0.00	46.00	4.09
153	154	2.004808	CTCGCTGGTATCTGCACCGA	62.005	60.000	5.65	0.00	41.88	4.69
191	207	3.151710	CCCCACCGATGACCGCTA	61.152	66.667	0.00	0.00	36.84	4.26
260	276	4.732065	AGGATCCTAGTAGCTCTTGTACC	58.268	47.826	14.27	0.00	0.00	3.34
264	280	2.362717	CCTAGTAGCTCTTGTACCTGGC	59.637	54.545	0.00	0.00	0.00	4.85
288	304	5.006386	CCACTTCTTCCTCTGTTTAGCATT	58.994	41.667	0.00	0.00	0.00	3.56
357	382	1.450312	CTGGGTCAGGAATCACCGC	60.450	63.158	0.00	0.00	44.74	5.68
366	391	0.678048	GGAATCACCGCCTTCAGCTT	60.678	55.000	0.00	0.00	40.39	3.74
374	399	0.248990	CGCCTTCAGCTTTTGTGCAA	60.249	50.000	0.00	0.00	40.39	4.08
421	447	2.915349	TCTTTCTGCATCTCAGCCATC	58.085	47.619	0.00	0.00	42.56	3.51
422	448	2.504585	TCTTTCTGCATCTCAGCCATCT	59.495	45.455	0.00	0.00	42.56	2.90
488	515	2.978010	CACCAGCCGACAACCCAC	60.978	66.667	0.00	0.00	0.00	4.61
678	716	3.880490	AGTGACAGTCATGCCGTTTTAAA	59.120	39.130	6.51	0.00	0.00	1.52
679	717	4.024048	AGTGACAGTCATGCCGTTTTAAAG	60.024	41.667	6.51	0.00	0.00	1.85
688	726	2.227865	TGCCGTTTTAAAGACATGCTCC	59.772	45.455	0.00	0.00	0.00	4.70
712	751	4.760530	ATAAGCCATGAACTCTGTGCTA	57.239	40.909	0.00	0.00	0.00	3.49
716	755	2.286294	GCCATGAACTCTGTGCTATTCG	59.714	50.000	0.00	0.00	0.00	3.34
875	927	2.383527	CGAAGACGCCTGAGGTTGC	61.384	63.158	0.00	0.00	0.00	4.17
883	935	2.338620	CTGAGGTTGCCGACGACA	59.661	61.111	0.00	0.00	31.02	4.35
899	954	2.124819	CAAGCGCATGGAGGAGCT	60.125	61.111	11.47	0.00	46.17	4.09
1080	1136	3.249189	ACCGGCTGCTCCTGGAAA	61.249	61.111	0.00	0.00	34.18	3.13
1132	1188	4.169452	CTGGATCAGGGTTGGGGA	57.831	61.111	0.00	0.00	0.00	4.81
1152	1208	1.522355	CCGACGCAGCCATTCATCT	60.522	57.895	0.00	0.00	0.00	2.90
1325	1384	9.504708	CCTCCTTTCTAATTACTATCGAGTCTA	57.495	37.037	0.00	0.00	37.10	2.59
1378	1444	3.670625	TGTTATGAAGTGTGGTACTGCC	58.329	45.455	0.00	0.00	40.26	4.85
1410	1477	9.377312	GAAATATGCTCTTAAGTAGATGATCCC	57.623	37.037	1.63	0.00	30.92	3.85
1457	1524	0.110238	GTGTGCTACATGGTTGTGCG	60.110	55.000	0.00	0.00	36.53	5.34
1535	1602	2.029110	GCATACAACCAAACACCATGCT	60.029	45.455	0.00	0.00	35.56	3.79
1560	1627	2.884639	GGTTTGTCCACTAACATGCAGT	59.115	45.455	6.41	0.00	34.16	4.40
1605	1672	0.543277	CAGCCCATGCAGGTAAGAGA	59.457	55.000	0.00	0.00	41.13	3.10
1719	1800	2.159382	CCAAACACGCCCATAGACTTT	58.841	47.619	0.00	0.00	0.00	2.66
1725	1806	5.099042	ACACGCCCATAGACTTTAGAATT	57.901	39.130	0.00	0.00	0.00	2.17
1726	1807	5.116882	ACACGCCCATAGACTTTAGAATTC	58.883	41.667	0.00	0.00	0.00	2.17
1727	1808	5.116180	CACGCCCATAGACTTTAGAATTCA	58.884	41.667	8.44	0.00	0.00	2.57
1743	1824	0.892755	TTCAGCCGGTACAGTACAGG	59.107	55.000	22.08	22.08	45.31	4.00
1750	1831	1.671850	CGGTACAGTACAGGCCAAGTG	60.672	57.143	12.89	5.75	0.00	3.16
1763	1844	1.442769	CCAAGTGAACCAGATCCACG	58.557	55.000	0.00	0.00	36.06	4.94
1769	1850	1.272490	TGAACCAGATCCACGACTGAC	59.728	52.381	0.00	0.00	36.38	3.51
1784	1865	8.258007	TCCACGACTGACAGAATAATAATTTCT	58.742	33.333	10.08	0.00	33.75	2.52
1801	1882	2.743636	TCTTGTGCTGTAGCCTGTAC	57.256	50.000	0.80	0.00	41.18	2.90
1919	2000	2.301296	CAGATCTCCACTCACAACCTGT	59.699	50.000	0.00	0.00	0.00	4.00
1922	2003	1.412710	TCTCCACTCACAACCTGTCAC	59.587	52.381	0.00	0.00	0.00	3.67
1942	2023	2.932194	AGCCAGCCAGCCTTGAGA	60.932	61.111	0.00	0.00	0.00	3.27
1943	2024	2.274760	GCCAGCCAGCCTTGAGAT	59.725	61.111	0.00	0.00	0.00	2.75
1945	2026	1.153005	CCAGCCAGCCTTGAGATCC	60.153	63.158	0.00	0.00	0.00	3.36
1947	2028	0.464013	CAGCCAGCCTTGAGATCCAG	60.464	60.000	0.00	0.00	0.00	3.86
1948	2029	0.619832	AGCCAGCCTTGAGATCCAGA	60.620	55.000	0.00	0.00	0.00	3.86
1949	2030	0.254178	GCCAGCCTTGAGATCCAGAA	59.746	55.000	0.00	0.00	0.00	3.02
1950	2031	1.746516	GCCAGCCTTGAGATCCAGAAG	60.747	57.143	0.00	0.00	0.00	2.85
1953	3509	2.117865	AGCCTTGAGATCCAGAAGAGG	58.882	52.381	0.00	0.00	0.00	3.69
1971	3527	1.036707	GGAGAGGAGAGGATCGGTTG	58.963	60.000	0.00	0.00	42.67	3.77
2020	3576	2.362736	GTCAGCTGCCAGATCAATGAA	58.637	47.619	9.47	0.00	0.00	2.57
2022	3578	2.949644	TCAGCTGCCAGATCAATGAATG	59.050	45.455	9.47	0.00	0.00	2.67
2050	3606	5.900865	AAAGGTACTAGAAGACGAAGAGG	57.099	43.478	0.00	0.00	38.49	3.69
2051	3607	3.281158	AGGTACTAGAAGACGAAGAGGC	58.719	50.000	0.00	0.00	36.02	4.70
2052	3608	3.015327	GGTACTAGAAGACGAAGAGGCA	58.985	50.000	0.00	0.00	0.00	4.75
2054	3610	2.096248	ACTAGAAGACGAAGAGGCAGG	58.904	52.381	0.00	0.00	0.00	4.85
2055	3611	2.096248	CTAGAAGACGAAGAGGCAGGT	58.904	52.381	0.00	0.00	0.00	4.00
2056	3612	0.605589	AGAAGACGAAGAGGCAGGTG	59.394	55.000	0.00	0.00	0.00	4.00
2064	3620	0.540597	AAGAGGCAGGTGAAAAGGGC	60.541	55.000	0.00	0.00	0.00	5.19
2070	3626	2.034221	GGTGAAAAGGGCGAGGCT	59.966	61.111	0.00	0.00	0.00	4.58
2076	3632	0.323360	AAAAGGGCGAGGCTAATGCA	60.323	50.000	7.95	0.00	41.91	3.96
2079	3635	2.190578	GGCGAGGCTAATGCAGGT	59.809	61.111	7.95	0.00	41.91	4.00
2084	3640	1.539065	CGAGGCTAATGCAGGTACAGG	60.539	57.143	0.00	0.00	41.91	4.00
2247	3803	0.744874	CGGAGCCTGGACGAAAGATA	59.255	55.000	0.00	0.00	0.00	1.98
2266	3822	2.568623	ATGCCGATCCAGGGATAAAC	57.431	50.000	0.00	0.00	40.71	2.01
2273	3829	3.654414	GATCCAGGGATAAACTACGCTG	58.346	50.000	0.00	0.00	43.42	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.392193	GTGCTCAGTGTCATCCCTGG	60.392	60.000	0.00	0.00	0.00	4.45
2	3	0.612229	CTGTGCTCAGTGTCATCCCT	59.388	55.000	7.63	0.00	36.97	4.20
3	4	0.610174	TCTGTGCTCAGTGTCATCCC	59.390	55.000	15.01	0.00	41.91	3.85
4	5	1.547820	TCTCTGTGCTCAGTGTCATCC	59.452	52.381	15.01	0.00	41.91	3.51
6	7	2.246469	AGTCTCTGTGCTCAGTGTCAT	58.754	47.619	15.01	2.07	41.91	3.06
7	8	1.697284	AGTCTCTGTGCTCAGTGTCA	58.303	50.000	15.01	0.00	41.91	3.58
8	9	2.035193	TCAAGTCTCTGTGCTCAGTGTC	59.965	50.000	15.01	10.54	41.91	3.67
9	10	2.034878	TCAAGTCTCTGTGCTCAGTGT	58.965	47.619	15.01	0.00	41.91	3.55
10	11	2.402305	GTCAAGTCTCTGTGCTCAGTG	58.598	52.381	15.01	12.79	41.91	3.66
11	12	1.342819	GGTCAAGTCTCTGTGCTCAGT	59.657	52.381	15.01	0.00	41.91	3.41
12	13	1.668337	CGGTCAAGTCTCTGTGCTCAG	60.668	57.143	9.54	9.54	42.54	3.35
13	14	0.315251	CGGTCAAGTCTCTGTGCTCA	59.685	55.000	0.00	0.00	0.00	4.26
14	15	0.315568	ACGGTCAAGTCTCTGTGCTC	59.684	55.000	0.00	0.00	0.00	4.26
15	16	0.753262	AACGGTCAAGTCTCTGTGCT	59.247	50.000	0.00	0.00	0.00	4.40
16	17	1.261619	CAAACGGTCAAGTCTCTGTGC	59.738	52.381	0.00	0.00	0.00	4.57
17	18	2.797156	CTCAAACGGTCAAGTCTCTGTG	59.203	50.000	0.00	0.00	0.00	3.66
18	19	2.224066	CCTCAAACGGTCAAGTCTCTGT	60.224	50.000	0.00	0.00	0.00	3.41
19	20	2.224066	ACCTCAAACGGTCAAGTCTCTG	60.224	50.000	0.00	0.00	29.14	3.35
20	21	2.040178	ACCTCAAACGGTCAAGTCTCT	58.960	47.619	0.00	0.00	29.14	3.10
21	22	2.528041	ACCTCAAACGGTCAAGTCTC	57.472	50.000	0.00	0.00	29.14	3.36
29	30	2.739132	GACCCGACCTCAAACGGT	59.261	61.111	0.00	0.00	46.53	4.83
31	32	2.203972	TAGCGACCCGACCTCAAACG	62.204	60.000	0.00	0.00	0.00	3.60
32	33	0.735287	GTAGCGACCCGACCTCAAAC	60.735	60.000	0.00	0.00	0.00	2.93
33	34	1.180456	TGTAGCGACCCGACCTCAAA	61.180	55.000	0.00	0.00	0.00	2.69
34	35	1.592400	CTGTAGCGACCCGACCTCAA	61.592	60.000	0.00	0.00	0.00	3.02
35	36	2.034532	TGTAGCGACCCGACCTCA	59.965	61.111	0.00	0.00	0.00	3.86
36	37	1.716826	CTCTGTAGCGACCCGACCTC	61.717	65.000	0.00	0.00	0.00	3.85
37	38	1.749638	CTCTGTAGCGACCCGACCT	60.750	63.158	0.00	0.00	0.00	3.85
38	39	2.799371	CTCTGTAGCGACCCGACC	59.201	66.667	0.00	0.00	0.00	4.79
39	40	2.102553	GCTCTGTAGCGACCCGAC	59.897	66.667	0.00	0.00	39.39	4.79
48	49	4.880537	CGCCGCCCTGCTCTGTAG	62.881	72.222	0.00	0.00	0.00	2.74
131	132	1.381191	TGCAGATACCAGCGAGGGA	60.381	57.895	3.26	0.00	43.89	4.20
142	143	2.365617	GGAGGAAGAATCGGTGCAGATA	59.634	50.000	0.00	0.00	0.00	1.98
153	154	4.552674	GGAGTCTAAGGAGGAGGAAGAAT	58.447	47.826	0.00	0.00	0.00	2.40
260	276	0.035630	CAGAGGAAGAAGTGGGCCAG	60.036	60.000	6.40	0.00	0.00	4.85
264	280	3.244561	TGCTAAACAGAGGAAGAAGTGGG	60.245	47.826	0.00	0.00	0.00	4.61
288	304	1.077285	TATCAGGCCGTCTCCGACA	60.077	57.895	0.00	0.00	35.63	4.35
357	382	2.409975	CCATTGCACAAAAGCTGAAGG	58.590	47.619	0.00	0.00	34.99	3.46
366	391	2.490509	CTCATGAGAGCCATTGCACAAA	59.509	45.455	18.34	0.00	41.13	2.83
421	447	0.109272	TGTGCTCGAACTTCGGCTAG	60.109	55.000	19.00	9.14	40.88	3.42
422	448	0.388134	GTGTGCTCGAACTTCGGCTA	60.388	55.000	19.00	10.07	40.88	3.93
482	509	2.434774	GGCCTTCTTCCGTGGGTT	59.565	61.111	0.00	0.00	0.00	4.11
488	515	2.586792	CTGGAGGGCCTTCTTCCG	59.413	66.667	14.33	0.54	34.31	4.30
678	716	4.349048	TCATGGCTTATTAGGAGCATGTCT	59.651	41.667	0.00	0.00	41.89	3.41
679	717	4.645535	TCATGGCTTATTAGGAGCATGTC	58.354	43.478	0.00	0.00	41.89	3.06
688	726	5.121811	AGCACAGAGTTCATGGCTTATTAG	58.878	41.667	0.00	0.00	0.00	1.73
712	751	4.154737	CACACAATTCATGGAGTCACGAAT	59.845	41.667	0.00	0.00	37.39	3.34
716	755	2.553602	TGCACACAATTCATGGAGTCAC	59.446	45.455	0.00	0.00	0.00	3.67
875	927	3.853330	CCATGCGCTTGTCGTCGG	61.853	66.667	20.40	1.88	41.07	4.79
883	935	2.188994	GAGCTCCTCCATGCGCTT	59.811	61.111	9.73	0.00	31.96	4.68
980	1035	0.322816	GGGGATGCACTCAAGCTTCA	60.323	55.000	0.00	0.00	39.62	3.02
1060	1115	3.390521	CCAGGAGCAGCCGGTGTA	61.391	66.667	1.90	0.00	43.43	2.90
1080	1136	0.036952	CGTCAGCTTCACCATCACCT	60.037	55.000	0.00	0.00	0.00	4.00
1131	1187	1.369091	ATGAATGGCTGCGTCGGTTC	61.369	55.000	0.00	0.00	0.00	3.62
1132	1188	1.369091	GATGAATGGCTGCGTCGGTT	61.369	55.000	0.00	0.00	0.00	4.44
1136	1192	1.530293	GATCAGATGAATGGCTGCGTC	59.470	52.381	0.00	0.00	32.27	5.19
1145	1201	4.620589	AGCCGATCTTGATCAGATGAAT	57.379	40.909	11.03	0.00	42.92	2.57
1152	1208	2.700371	ACCATGTAGCCGATCTTGATCA	59.300	45.455	10.69	0.00	0.00	2.92
1403	1470	4.910304	AGCAGAGTATAAACAGGGGATCAT	59.090	41.667	0.00	0.00	0.00	2.45
1410	1477	4.399004	AGCAGAGCAGAGTATAAACAGG	57.601	45.455	0.00	0.00	0.00	4.00
1457	1524	1.071699	TGAGGTTACCAGCACACTTCC	59.928	52.381	3.51	0.00	0.00	3.46
1535	1602	3.068873	GCATGTTAGTGGACAAACCCAAA	59.931	43.478	0.00	0.00	38.06	3.28
1560	1627	0.033601	ACTGCCTGGTGTTTGGTTGA	60.034	50.000	0.00	0.00	0.00	3.18
1605	1672	0.464870	TGTTTGGTTGCTTGCATGCT	59.535	45.000	23.31	0.00	0.00	3.79
1662	1743	1.481871	AGCTGCATTGCATAGCCTTT	58.518	45.000	12.53	0.00	38.13	3.11
1719	1800	4.018490	TGTACTGTACCGGCTGAATTCTA	58.982	43.478	14.91	0.00	0.00	2.10
1725	1806	2.575108	CCTGTACTGTACCGGCTGA	58.425	57.895	14.25	0.00	0.00	4.26
1743	1824	1.168714	GTGGATCTGGTTCACTTGGC	58.831	55.000	0.00	0.00	0.00	4.52
1750	1831	1.272490	TGTCAGTCGTGGATCTGGTTC	59.728	52.381	0.00	0.00	33.13	3.62
1763	1844	9.495754	GCACAAGAAATTATTATTCTGTCAGTC	57.504	33.333	0.00	0.00	37.22	3.51
1769	1850	9.443283	GCTACAGCACAAGAAATTATTATTCTG	57.557	33.333	0.00	0.00	41.59	3.02
1784	1865	0.677288	ACGTACAGGCTACAGCACAA	59.323	50.000	3.24	0.00	44.36	3.33
1801	1882	8.141909	TCAGAAAATATTATCACTGGGTCTACG	58.858	37.037	0.00	0.00	0.00	3.51
1935	2016	3.638160	CTCTCCTCTTCTGGATCTCAAGG	59.362	52.174	0.00	0.00	35.30	3.61
1942	2023	2.177669	CCTCTCCTCTCCTCTTCTGGAT	59.822	54.545	0.00	0.00	35.30	3.41
1943	2024	1.568597	CCTCTCCTCTCCTCTTCTGGA	59.431	57.143	0.00	0.00	34.52	3.86
1945	2026	3.490348	GATCCTCTCCTCTCCTCTTCTG	58.510	54.545	0.00	0.00	0.00	3.02
1947	2028	2.504367	CGATCCTCTCCTCTCCTCTTC	58.496	57.143	0.00	0.00	0.00	2.87
1948	2029	1.144913	CCGATCCTCTCCTCTCCTCTT	59.855	57.143	0.00	0.00	0.00	2.85
1949	2030	0.771127	CCGATCCTCTCCTCTCCTCT	59.229	60.000	0.00	0.00	0.00	3.69
1950	2031	0.476771	ACCGATCCTCTCCTCTCCTC	59.523	60.000	0.00	0.00	0.00	3.71
1953	3509	2.060050	TCAACCGATCCTCTCCTCTC	57.940	55.000	0.00	0.00	0.00	3.20
1971	3527	7.630924	TCGAGTCATTTCTTTCTCTTGTTTTC	58.369	34.615	0.00	0.00	0.00	2.29
2025	3581	7.228308	GCCTCTTCGTCTTCTAGTACCTTTATA	59.772	40.741	0.00	0.00	0.00	0.98
2027	3583	5.356470	GCCTCTTCGTCTTCTAGTACCTTTA	59.644	44.000	0.00	0.00	0.00	1.85
2028	3584	4.158209	GCCTCTTCGTCTTCTAGTACCTTT	59.842	45.833	0.00	0.00	0.00	3.11
2029	3585	3.695556	GCCTCTTCGTCTTCTAGTACCTT	59.304	47.826	0.00	0.00	0.00	3.50
2030	3586	3.281158	GCCTCTTCGTCTTCTAGTACCT	58.719	50.000	0.00	0.00	0.00	3.08
2031	3587	3.015327	TGCCTCTTCGTCTTCTAGTACC	58.985	50.000	0.00	0.00	0.00	3.34
2032	3588	3.065648	CCTGCCTCTTCGTCTTCTAGTAC	59.934	52.174	0.00	0.00	0.00	2.73
2033	3589	3.280295	CCTGCCTCTTCGTCTTCTAGTA	58.720	50.000	0.00	0.00	0.00	1.82
2048	3604	2.282462	CGCCCTTTTCACCTGCCT	60.282	61.111	0.00	0.00	0.00	4.75
2050	3606	2.335712	CCTCGCCCTTTTCACCTGC	61.336	63.158	0.00	0.00	0.00	4.85
2051	3607	2.335712	GCCTCGCCCTTTTCACCTG	61.336	63.158	0.00	0.00	0.00	4.00
2052	3608	1.198759	TAGCCTCGCCCTTTTCACCT	61.199	55.000	0.00	0.00	0.00	4.00
2054	3610	1.401905	CATTAGCCTCGCCCTTTTCAC	59.598	52.381	0.00	0.00	0.00	3.18
2055	3611	1.750193	CATTAGCCTCGCCCTTTTCA	58.250	50.000	0.00	0.00	0.00	2.69
2056	3612	0.382158	GCATTAGCCTCGCCCTTTTC	59.618	55.000	0.00	0.00	33.58	2.29
2064	3620	1.539065	CCTGTACCTGCATTAGCCTCG	60.539	57.143	0.00	0.00	41.13	4.63
2070	3626	5.889289	GGAAATTTACCCTGTACCTGCATTA	59.111	40.000	0.00	0.00	0.00	1.90
2076	3632	4.264217	CCCTTGGAAATTTACCCTGTACCT	60.264	45.833	0.00	0.00	0.00	3.08
2079	3635	4.569015	GCTCCCTTGGAAATTTACCCTGTA	60.569	45.833	0.00	0.00	0.00	2.74
2084	3640	2.760650	CCTGCTCCCTTGGAAATTTACC	59.239	50.000	0.00	0.00	0.00	2.85
2137	3693	5.993055	TCTGCATGTGGAAGAATGAAGATA	58.007	37.500	0.00	0.00	34.18	1.98
2215	3771	2.165641	CAGGCTCCGTGATTGTAGTGTA	59.834	50.000	0.00	0.00	0.00	2.90
2247	3803	2.057922	AGTTTATCCCTGGATCGGCAT	58.942	47.619	0.99	0.00	36.17	4.40
2266	3822	1.269831	GGGCAGGACTATTCAGCGTAG	60.270	57.143	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.