AutoCloner

Multiple sequence alignment - TraesCS1D01G410400

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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	TraesCS1D01G410400	chr1D	100.000	1681	0	0	944	2624	472183187	472181507	0.000000e+00	3105
1	TraesCS1D01G410400	chr1D	100.000	471	0	0	1	471	472184130	472183660	0.000000e+00	870
2	TraesCS1D01G410400	chr1D	93.056	144	9	1	1648	1791	300031218	300031360	2.650000e-50	209
3	TraesCS1D01G410400	chr1D	90.141	142	10	3	1649	1787	491605667	491605527	5.770000e-42	182
4	TraesCS1D01G410400	chr1B	94.857	700	31	1	944	1643	598380719	598381413	0.000000e+00	1088
5	TraesCS1D01G410400	chr1B	94.857	700	31	1	944	1643	598395978	598396672	0.000000e+00	1088
6	TraesCS1D01G410400	chr1B	94.857	700	31	1	944	1643	598410750	598411444	0.000000e+00	1088
7	TraesCS1D01G410400	chr1B	94.714	700	32	1	944	1643	598427606	598428300	0.000000e+00	1083
8	TraesCS1D01G410400	chr1B	92.613	731	54	0	1894	2624	148888071	148888801	0.000000e+00	1051
9	TraesCS1D01G410400	chr1B	91.358	729	63	0	1896	2624	26238295	26237567	0.000000e+00	998
10	TraesCS1D01G410400	chr1B	95.117	471	18	2	1	471	598380173	598380638	0.000000e+00	737
11	TraesCS1D01G410400	chr1B	94.904	471	19	2	1	471	598395432	598395897	0.000000e+00	732
12	TraesCS1D01G410400	chr1B	94.904	471	19	2	1	471	598410204	598410669	0.000000e+00	732
13	TraesCS1D01G410400	chr1B	94.904	471	19	2	1	471	598427060	598427525	0.000000e+00	732
14	TraesCS1D01G410400	chr1B	82.169	415	73	1	973	1386	656406057	656406471	3.210000e-94	355
15	TraesCS1D01G410400	chr1B	98.020	101	2	0	1787	1887	598381579	598381679	2.680000e-40	176
16	TraesCS1D01G410400	chr1B	98.020	101	2	0	1787	1887	598396838	598396938	2.680000e-40	176
17	TraesCS1D01G410400	chr1B	98.020	101	2	0	1787	1887	598411610	598411710	2.680000e-40	176
18	TraesCS1D01G410400	chr1B	97.030	101	3	0	1787	1887	598428466	598428566	1.250000e-38	171
19	TraesCS1D01G410400	chr4A	91.382	731	63	0	1894	2624	103324019	103324749	0.000000e+00	1002
20	TraesCS1D01G410400	chr4A	97.556	532	12	1	944	1474	598241364	598240833	0.000000e+00	909
21	TraesCS1D01G410400	chr4A	94.480	471	21	3	1	471	598241886	598241421	0.000000e+00	721
22	TraesCS1D01G410400	chr4A	93.333	180	7	1	1464	1643	598240456	598240282	7.200000e-66	261
23	TraesCS1D01G410400	chr2A	91.393	732	61	2	1894	2624	546334119	546334849	0.000000e+00	1002
24	TraesCS1D01G410400	chr3B	90.934	728	65	1	1898	2624	467893175	467893902	0.000000e+00	977
25	TraesCS1D01G410400	chr3B	87.786	131	12	3	1663	1791	741778612	741778484	1.630000e-32	150
26	TraesCS1D01G410400	chr7A	90.759	725	66	1	1901	2624	652343433	652342709	0.000000e+00	966
27	TraesCS1D01G410400	chr3A	90.340	735	68	1	1890	2624	110073402	110074133	0.000000e+00	961
28	TraesCS1D01G410400	chr3D	90.483	725	65	2	1901	2624	43593641	43592920	0.000000e+00	953
29	TraesCS1D01G410400	chr3D	89.051	137	13	2	1652	1787	453100633	453100768	4.490000e-38	169
30	TraesCS1D01G410400	chr4B	89.637	743	73	4	1884	2624	500348279	500349019	0.000000e+00	942
31	TraesCS1D01G410400	chr2D	91.304	161	9	5	1648	1803	536503924	536504084	5.690000e-52	215
32	TraesCS1D01G410400	chr2D	90.977	133	10	2	1647	1778	499714071	499713940	7.460000e-41	178
33	TraesCS1D01G410400	chr6A	79.412	238	43	2	1027	1258	590787	591024	2.090000e-36	163
34	TraesCS1D01G410400	chr6A	86.275	102	10	4	25	124	589741	589840	9.930000e-20	108
35	TraesCS1D01G410400	chr5D	86.429	140	13	5	1654	1789	41430082	41430219	5.850000e-32	148
36	TraesCS1D01G410400	chr1A	86.429	140	14	4	1654	1791	11418373	11418237	5.850000e-32	148
37	TraesCS1D01G410400	chr6D	84.828	145	18	4	1652	1794	53766943	53766801	2.720000e-30	143

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	TraesCS1D01G410400	chr1D	472181507	472184130	2623	True	1987.500000	3105	100.000000	1	2624	2	chr1D.!!$R2	2623
1	TraesCS1D01G410400	chr1B	148888071	148888801	730	False	1051.000000	1051	92.613000	1894	2624	1	chr1B.!!$F1	730
2	TraesCS1D01G410400	chr1B	26237567	26238295	728	True	998.000000	998	91.358000	1896	2624	1	chr1B.!!$R1	728
3	TraesCS1D01G410400	chr1B	598380173	598381679	1506	False	667.000000	1088	95.998000	1	1887	3	chr1B.!!$F3	1886
4	TraesCS1D01G410400	chr1B	598395432	598396938	1506	False	665.333333	1088	95.927000	1	1887	3	chr1B.!!$F4	1886
5	TraesCS1D01G410400	chr1B	598410204	598411710	1506	False	665.333333	1088	95.927000	1	1887	3	chr1B.!!$F5	1886
6	TraesCS1D01G410400	chr1B	598427060	598428566	1506	False	662.000000	1083	95.549333	1	1887	3	chr1B.!!$F6	1886
7	TraesCS1D01G410400	chr4A	103324019	103324749	730	False	1002.000000	1002	91.382000	1894	2624	1	chr4A.!!$F1	730
8	TraesCS1D01G410400	chr4A	598240282	598241886	1604	True	630.333333	909	95.123000	1	1643	3	chr4A.!!$R1	1642
9	TraesCS1D01G410400	chr2A	546334119	546334849	730	False	1002.000000	1002	91.393000	1894	2624	1	chr2A.!!$F1	730
10	TraesCS1D01G410400	chr3B	467893175	467893902	727	False	977.000000	977	90.934000	1898	2624	1	chr3B.!!$F1	726
11	TraesCS1D01G410400	chr7A	652342709	652343433	724	True	966.000000	966	90.759000	1901	2624	1	chr7A.!!$R1	723
12	TraesCS1D01G410400	chr3A	110073402	110074133	731	False	961.000000	961	90.340000	1890	2624	1	chr3A.!!$F1	734
13	TraesCS1D01G410400	chr3D	43592920	43593641	721	True	953.000000	953	90.483000	1901	2624	1	chr3D.!!$R1	723
14	TraesCS1D01G410400	chr4B	500348279	500349019	740	False	942.000000	942	89.637000	1884	2624	1	chr4B.!!$F1	740

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
392	393	0.806102	GCCGCTATGCTGACGAAGAA	60.806	55.0	0.0	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1742	2131	0.179062	GGCCTCTGCATCAGAACGAT	60.179	55.0	0.0	0.0	40.18	3.73	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
71	72	3.816524	CTTCTCGCCGCCTCGACT	61.817	66.667	0.00	0.00	34.46	4.18
247	248	4.318949	GGGTTACGTGGCGGTGGT	62.319	66.667	0.00	0.00	0.00	4.16
392	393	0.806102	GCCGCTATGCTGACGAAGAA	60.806	55.000	0.00	0.00	0.00	2.52
393	394	1.203928	CCGCTATGCTGACGAAGAAG	58.796	55.000	0.00	0.00	0.00	2.85
394	395	1.202302	CCGCTATGCTGACGAAGAAGA	60.202	52.381	0.00	0.00	0.00	2.87
409	410	3.305398	AGAAGAGTACAAGAACGCCAG	57.695	47.619	0.00	0.00	0.00	4.85
416	417	2.281761	AAGAACGCCAGGGTGCAG	60.282	61.111	0.00	0.00	0.00	4.41
460	461	0.852777	CGTCCAGTGACAACAACTCG	59.147	55.000	0.00	0.00	41.85	4.18
467	468	4.299155	CAGTGACAACAACTCGATGTACT	58.701	43.478	0.00	0.00	29.39	2.73
989	990	6.993175	GTGAAATTTGTCTTCACTAAAGGC	57.007	37.500	0.00	0.00	46.01	4.35
1269	1270	2.742372	GCACTCCACGTGGCGAAT	60.742	61.111	30.33	12.32	43.97	3.34
1302	1303	2.972819	GCCACAGAACCCTCCCTCC	61.973	68.421	0.00	0.00	0.00	4.30
1477	1866	2.283388	TAGTGGTTCCCCGCGACT	60.283	61.111	8.23	3.15	46.35	4.18
1590	1979	1.077501	CACCGATGGCCAGTGGAAT	60.078	57.895	27.96	5.28	0.00	3.01
1591	1980	1.077501	ACCGATGGCCAGTGGAATG	60.078	57.895	27.96	8.10	0.00	2.67
1592	1981	1.825191	CCGATGGCCAGTGGAATGG	60.825	63.158	19.04	6.82	43.72	3.16
1593	1982	1.224315	CGATGGCCAGTGGAATGGA	59.776	57.895	15.20	0.00	43.57	3.41
1594	1983	0.394216	CGATGGCCAGTGGAATGGAA	60.394	55.000	15.20	0.00	43.57	3.53
1643	2032	7.542025	AGTTAAGTGGTTAAGACGGTATACAG	58.458	38.462	5.01	2.99	0.00	2.74
1646	2035	4.400567	AGTGGTTAAGACGGTATACAGGAC	59.599	45.833	7.93	1.84	0.00	3.85
1648	2037	5.018809	TGGTTAAGACGGTATACAGGACTT	58.981	41.667	16.45	16.45	0.00	3.01
1650	2039	5.809051	GGTTAAGACGGTATACAGGACTTTG	59.191	44.000	17.05	0.00	0.00	2.77
1651	2040	6.393171	GTTAAGACGGTATACAGGACTTTGT	58.607	40.000	17.05	3.36	35.09	2.83
1652	2041	5.479124	AAGACGGTATACAGGACTTTGTT	57.521	39.130	7.93	0.00	32.56	2.83
1653	2042	5.479124	AGACGGTATACAGGACTTTGTTT	57.521	39.130	7.93	0.00	32.56	2.83
1655	2044	5.699458	AGACGGTATACAGGACTTTGTTTTG	59.301	40.000	7.93	0.00	32.56	2.44
1656	2045	4.214758	ACGGTATACAGGACTTTGTTTTGC	59.785	41.667	7.93	0.00	32.56	3.68
1657	2046	4.454504	CGGTATACAGGACTTTGTTTTGCT	59.545	41.667	5.01	0.00	32.56	3.91
1658	2047	5.048991	CGGTATACAGGACTTTGTTTTGCTT	60.049	40.000	5.01	0.00	32.56	3.91
1659	2048	6.514376	CGGTATACAGGACTTTGTTTTGCTTT	60.514	38.462	5.01	0.00	32.56	3.51
1661	2050	7.169140	GGTATACAGGACTTTGTTTTGCTTTTG	59.831	37.037	5.01	0.00	32.56	2.44
1663	2052	5.337169	TACAGGACTTTGTTTTGCTTTTGCT	60.337	36.000	0.00	0.00	38.17	3.91
1664	2053	7.119226	TACAGGACTTTGTTTTGCTTTTGCTC	61.119	38.462	0.00	0.00	38.17	4.26
1665	2054	9.190210	TACAGGACTTTGTTTTGCTTTTGCTCT	62.190	37.037	0.00	0.00	38.17	4.09
1705	2094	8.693542	ACTTTTTGAGACATGAAGACTTTTTG	57.306	30.769	0.00	0.00	0.00	2.44
1708	2097	8.464770	TTTTGAGACATGAAGACTTTTTGTTG	57.535	30.769	0.00	0.00	0.00	3.33
1709	2098	7.389803	TTGAGACATGAAGACTTTTTGTTGA	57.610	32.000	0.00	0.00	0.00	3.18
1711	2100	7.250569	TGAGACATGAAGACTTTTTGTTGAAC	58.749	34.615	0.00	0.00	0.00	3.18
1712	2101	6.258160	AGACATGAAGACTTTTTGTTGAACG	58.742	36.000	0.00	0.00	0.00	3.95
1714	2103	3.765026	TGAAGACTTTTTGTTGAACGCC	58.235	40.909	0.00	0.00	0.00	5.68
1716	2105	4.082463	TGAAGACTTTTTGTTGAACGCCTT	60.082	37.500	0.00	0.00	0.00	4.35
1717	2106	3.769536	AGACTTTTTGTTGAACGCCTTG	58.230	40.909	0.00	0.00	0.00	3.61
1718	2107	2.267426	ACTTTTTGTTGAACGCCTTGC	58.733	42.857	0.00	0.00	0.00	4.01
1719	2108	2.094234	ACTTTTTGTTGAACGCCTTGCT	60.094	40.909	0.00	0.00	0.00	3.91
1721	2110	3.784701	TTTTGTTGAACGCCTTGCTTA	57.215	38.095	0.00	0.00	0.00	3.09
1722	2111	4.314740	TTTTGTTGAACGCCTTGCTTAT	57.685	36.364	0.00	0.00	0.00	1.73
1723	2112	3.552604	TTGTTGAACGCCTTGCTTATC	57.447	42.857	0.00	0.00	0.00	1.75
1724	2113	2.499197	TGTTGAACGCCTTGCTTATCA	58.501	42.857	0.00	0.00	0.00	2.15
1725	2114	2.881513	TGTTGAACGCCTTGCTTATCAA	59.118	40.909	0.00	0.00	0.00	2.57
1726	2115	3.505680	TGTTGAACGCCTTGCTTATCAAT	59.494	39.130	0.00	0.00	33.57	2.57
1727	2116	3.763097	TGAACGCCTTGCTTATCAATG	57.237	42.857	0.00	0.00	33.57	2.82
1728	2117	3.342719	TGAACGCCTTGCTTATCAATGA	58.657	40.909	0.00	0.00	33.57	2.57
1729	2118	3.947196	TGAACGCCTTGCTTATCAATGAT	59.053	39.130	0.00	0.00	33.57	2.45
1732	2121	5.618056	ACGCCTTGCTTATCAATGATATG	57.382	39.130	3.54	7.68	33.57	1.78
1733	2122	4.456911	ACGCCTTGCTTATCAATGATATGG	59.543	41.667	15.15	8.24	33.57	2.74
1734	2123	4.673580	CGCCTTGCTTATCAATGATATGGC	60.674	45.833	15.15	15.76	33.57	4.40
1735	2124	4.219070	GCCTTGCTTATCAATGATATGGCA	59.781	41.667	19.65	19.65	34.52	4.92
1739	2128	7.338703	CCTTGCTTATCAATGATATGGCAGTAT	59.661	37.037	21.23	0.00	36.18	2.12
1740	2129	7.619964	TGCTTATCAATGATATGGCAGTATG	57.380	36.000	19.65	0.00	32.91	2.39
1761	2150	0.179062	ATCGTTCTGATGCAGAGGCC	60.179	55.000	0.00	0.00	41.75	5.19
1762	2151	2.169789	CGTTCTGATGCAGAGGCCG	61.170	63.158	0.00	0.00	41.75	6.13
1763	2152	1.817099	GTTCTGATGCAGAGGCCGG	60.817	63.158	0.00	0.00	41.75	6.13
1764	2153	3.035173	TTCTGATGCAGAGGCCGGG	62.035	63.158	2.18	0.00	41.75	5.73
1765	2154	4.559063	CTGATGCAGAGGCCGGGG	62.559	72.222	2.18	0.00	40.13	5.73
1768	2157	2.122413	ATGCAGAGGCCGGGGATA	60.122	61.111	2.18	0.00	40.13	2.59
1770	2159	2.056906	ATGCAGAGGCCGGGGATAAC	62.057	60.000	2.18	0.00	40.13	1.89
1771	2160	2.829592	CAGAGGCCGGGGATAACC	59.170	66.667	2.18	0.00	39.11	2.85
1772	2161	1.766461	CAGAGGCCGGGGATAACCT	60.766	63.158	2.18	0.00	40.03	3.50
1775	2164	1.004361	AGGCCGGGGATAACCTTCT	59.996	57.895	2.18	0.00	40.03	2.85
1778	2167	1.491754	GGCCGGGGATAACCTTCTTTA	59.508	52.381	2.18	0.00	40.03	1.85
1779	2168	2.092267	GGCCGGGGATAACCTTCTTTAA	60.092	50.000	2.18	0.00	40.03	1.52
1781	2170	4.018490	GCCGGGGATAACCTTCTTTAAAA	58.982	43.478	2.18	0.00	40.03	1.52
1782	2171	4.463539	GCCGGGGATAACCTTCTTTAAAAA	59.536	41.667	2.18	0.00	40.03	1.94
1826	2237	8.897809	CATTGCTTCATTGCTTTTAAAAATGTG	58.102	29.630	1.66	0.03	33.84	3.21
1888	2299	2.765699	AGTGGCATGTTCTTGGTGTTTT	59.234	40.909	0.00	0.00	0.00	2.43
2036	2449	2.264005	ATCTGTAAAACGCCACACCA	57.736	45.000	0.00	0.00	0.00	4.17
2108	2522	5.246429	ACACACCTAGCCTATTATTAGCTCC	59.754	44.000	0.00	0.00	0.00	4.70
2113	2527	5.430089	CCTAGCCTATTATTAGCTCCCCATT	59.570	44.000	0.00	0.00	0.00	3.16
2146	2560	0.463654	GATAGCCCATGCAACCGTCA	60.464	55.000	0.00	0.00	41.13	4.35
2192	2606	1.068250	GCTCCCTGTAGTCCGCATC	59.932	63.158	0.00	0.00	0.00	3.91
2231	2645	2.755952	TGGATCTAGGCAGTAGCTCA	57.244	50.000	0.00	0.00	41.70	4.26
2235	2649	4.145807	GGATCTAGGCAGTAGCTCAGTAA	58.854	47.826	0.00	0.00	41.70	2.24
2349	2764	5.539582	TCCGAATATGTTTAGTTGTGTGC	57.460	39.130	0.00	0.00	0.00	4.57
2372	2787	3.093814	TGTCTACTCCATTAAGCCACGA	58.906	45.455	0.00	0.00	0.00	4.35
2382	2797	4.340950	CCATTAAGCCACGACCCAAATAAT	59.659	41.667	0.00	0.00	0.00	1.28
2393	2808	7.148222	CCACGACCCAAATAATGTGTTTATACA	60.148	37.037	0.00	0.00	30.11	2.29
2459	2874	8.474025	TCATAACAGTTTTTCAAGTGGACATTT	58.526	29.630	0.00	0.00	37.62	2.32
2565	2980	4.042809	TCTTTGGTCAAGATGGCTCCTTTA	59.957	41.667	0.00	0.00	36.51	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	2.920912	TCCGGGTGGGTCACAGTC	60.921	66.667	0.00	0.00	35.86	3.51
71	72	1.909781	GTACTCCGGGTGGGTCACA	60.910	63.158	0.00	0.00	35.86	3.58
127	128	1.086696	CAACCTCGATGCCGTTGATT	58.913	50.000	8.36	0.00	39.36	2.57
247	248	2.927580	GCAACTCCCTCGTCCGTCA	61.928	63.158	0.00	0.00	0.00	4.35
392	393	0.608640	CCCTGGCGTTCTTGTACTCT	59.391	55.000	0.00	0.00	0.00	3.24
393	394	0.320697	ACCCTGGCGTTCTTGTACTC	59.679	55.000	0.00	0.00	0.00	2.59
394	395	0.034896	CACCCTGGCGTTCTTGTACT	59.965	55.000	0.00	0.00	0.00	2.73
416	417	3.050275	GGACAGGAAGCCACACGC	61.050	66.667	0.00	0.00	37.98	5.34
418	419	1.961277	CACGGACAGGAAGCCACAC	60.961	63.158	0.00	0.00	0.00	3.82
419	420	1.116536	TACACGGACAGGAAGCCACA	61.117	55.000	0.00	0.00	0.00	4.17
1115	1116	4.101790	CGTCGTTGGCCACCATGC	62.102	66.667	3.88	0.00	31.53	4.06
1212	1213	1.219522	CGAAGGCGGACTTGAACGTT	61.220	55.000	0.00	0.00	40.21	3.99
1269	1270	0.388659	GTGGCACAATGTCTTTGGCA	59.611	50.000	13.86	0.00	44.16	4.92
1281	1282	2.829384	GGGAGGGTTCTGTGGCACA	61.829	63.158	20.76	20.76	0.00	4.57
1302	1303	0.645355	CGTACCACATTAGCAGCACG	59.355	55.000	0.00	0.00	0.00	5.34
1477	1866	1.064758	AGTCTTGTTCACCAGTGCCAA	60.065	47.619	0.00	0.00	0.00	4.52
1482	1871	2.035576	GTCGGTAGTCTTGTTCACCAGT	59.964	50.000	0.00	0.00	0.00	4.00
1611	2000	6.370718	CCGTCTTAACCACTTAACTATGCTTT	59.629	38.462	0.00	0.00	0.00	3.51
1643	2032	4.183865	AGAGCAAAAGCAAAACAAAGTCC	58.816	39.130	0.00	0.00	0.00	3.85
1646	2035	5.791480	CACAAAGAGCAAAAGCAAAACAAAG	59.209	36.000	0.00	0.00	0.00	2.77
1648	2037	4.993584	TCACAAAGAGCAAAAGCAAAACAA	59.006	33.333	0.00	0.00	0.00	2.83
1650	2039	5.134978	CTCACAAAGAGCAAAAGCAAAAC	57.865	39.130	0.00	0.00	37.59	2.43
1679	2068	9.787532	CAAAAAGTCTTCATGTCTCAAAAAGTA	57.212	29.630	0.00	0.00	0.00	2.24
1680	2069	8.306761	ACAAAAAGTCTTCATGTCTCAAAAAGT	58.693	29.630	0.00	0.00	0.00	2.66
1681	2070	8.693542	ACAAAAAGTCTTCATGTCTCAAAAAG	57.306	30.769	0.00	0.00	0.00	2.27
1682	2071	8.924691	CAACAAAAAGTCTTCATGTCTCAAAAA	58.075	29.630	4.27	0.00	0.00	1.94
1685	2074	7.389803	TCAACAAAAAGTCTTCATGTCTCAA	57.610	32.000	4.27	0.00	0.00	3.02
1688	2077	6.258160	CGTTCAACAAAAAGTCTTCATGTCT	58.742	36.000	4.27	0.00	0.00	3.41
1689	2078	5.052370	GCGTTCAACAAAAAGTCTTCATGTC	60.052	40.000	4.27	0.00	0.00	3.06
1690	2079	4.798387	GCGTTCAACAAAAAGTCTTCATGT	59.202	37.500	0.00	0.00	0.00	3.21
1691	2080	4.207019	GGCGTTCAACAAAAAGTCTTCATG	59.793	41.667	0.00	0.00	0.00	3.07
1692	2081	4.097892	AGGCGTTCAACAAAAAGTCTTCAT	59.902	37.500	0.00	0.00	0.00	2.57
1694	2083	4.028852	AGGCGTTCAACAAAAAGTCTTC	57.971	40.909	0.00	0.00	0.00	2.87
1695	2084	4.173256	CAAGGCGTTCAACAAAAAGTCTT	58.827	39.130	0.00	0.00	33.73	3.01
1696	2085	3.769536	CAAGGCGTTCAACAAAAAGTCT	58.230	40.909	0.00	0.00	0.00	3.24
1698	2087	2.094234	AGCAAGGCGTTCAACAAAAAGT	60.094	40.909	0.00	0.00	0.00	2.66
1699	2088	2.539476	AGCAAGGCGTTCAACAAAAAG	58.461	42.857	0.00	0.00	0.00	2.27
1703	2092	2.881513	TGATAAGCAAGGCGTTCAACAA	59.118	40.909	0.00	0.00	0.00	2.83
1704	2093	2.499197	TGATAAGCAAGGCGTTCAACA	58.501	42.857	0.00	0.00	0.00	3.33
1705	2094	3.552604	TTGATAAGCAAGGCGTTCAAC	57.447	42.857	0.00	0.00	31.55	3.18
1708	2097	4.558538	ATCATTGATAAGCAAGGCGTTC	57.441	40.909	0.00	0.00	40.42	3.95
1709	2098	5.048504	CCATATCATTGATAAGCAAGGCGTT	60.049	40.000	10.30	0.00	40.42	4.84
1711	2100	4.673580	GCCATATCATTGATAAGCAAGGCG	60.674	45.833	19.48	3.19	40.42	5.52
1712	2101	4.219070	TGCCATATCATTGATAAGCAAGGC	59.781	41.667	22.58	20.96	40.42	4.35
1714	2103	6.570672	ACTGCCATATCATTGATAAGCAAG	57.429	37.500	23.84	20.50	40.42	4.01
1716	2105	6.094464	GCATACTGCCATATCATTGATAAGCA	59.906	38.462	22.98	22.98	37.42	3.91
1717	2106	6.094464	TGCATACTGCCATATCATTGATAAGC	59.906	38.462	18.35	18.35	44.23	3.09
1718	2107	7.619964	TGCATACTGCCATATCATTGATAAG	57.380	36.000	10.30	6.23	44.23	1.73
1719	2108	7.011669	CGATGCATACTGCCATATCATTGATAA	59.988	37.037	10.30	0.00	44.23	1.75
1721	2110	5.296035	CGATGCATACTGCCATATCATTGAT	59.704	40.000	0.00	4.28	44.23	2.57
1722	2111	4.632688	CGATGCATACTGCCATATCATTGA	59.367	41.667	0.00	0.00	44.23	2.57
1723	2112	4.393990	ACGATGCATACTGCCATATCATTG	59.606	41.667	0.00	0.00	44.23	2.82
1724	2113	4.582869	ACGATGCATACTGCCATATCATT	58.417	39.130	0.00	0.00	44.23	2.57
1725	2114	4.212143	ACGATGCATACTGCCATATCAT	57.788	40.909	0.00	0.00	44.23	2.45
1726	2115	3.683365	ACGATGCATACTGCCATATCA	57.317	42.857	0.00	0.00	44.23	2.15
1727	2116	4.092529	CAGAACGATGCATACTGCCATATC	59.907	45.833	0.00	0.00	44.23	1.63
1728	2117	3.999001	CAGAACGATGCATACTGCCATAT	59.001	43.478	0.00	0.00	44.23	1.78
1729	2118	3.069443	TCAGAACGATGCATACTGCCATA	59.931	43.478	0.00	0.00	44.23	2.74
1732	2121	1.939974	TCAGAACGATGCATACTGCC	58.060	50.000	0.00	0.00	44.23	4.85
1733	2122	3.516681	CATCAGAACGATGCATACTGC	57.483	47.619	0.00	0.00	44.95	4.40
1742	2131	0.179062	GGCCTCTGCATCAGAACGAT	60.179	55.000	0.00	0.00	40.18	3.73
1743	2132	1.219124	GGCCTCTGCATCAGAACGA	59.781	57.895	0.00	0.00	40.18	3.85
1744	2133	2.169789	CGGCCTCTGCATCAGAACG	61.170	63.158	0.00	0.63	40.18	3.95
1746	2135	2.586245	CCGGCCTCTGCATCAGAA	59.414	61.111	0.00	0.00	40.18	3.02
1747	2136	3.473647	CCCGGCCTCTGCATCAGA	61.474	66.667	0.00	0.00	38.25	3.27
1748	2137	4.559063	CCCCGGCCTCTGCATCAG	62.559	72.222	0.00	0.00	40.13	2.90
1749	2138	2.963391	TATCCCCGGCCTCTGCATCA	62.963	60.000	0.00	0.00	40.13	3.07
1750	2139	1.768684	TTATCCCCGGCCTCTGCATC	61.769	60.000	0.00	0.00	40.13	3.91
1751	2140	1.770110	TTATCCCCGGCCTCTGCAT	60.770	57.895	0.00	0.00	40.13	3.96
1754	2143	1.345715	AAGGTTATCCCCGGCCTCTG	61.346	60.000	0.00	0.00	0.00	3.35
1755	2144	1.004361	AAGGTTATCCCCGGCCTCT	59.996	57.895	0.00	0.00	0.00	3.69
1756	2145	1.054978	AGAAGGTTATCCCCGGCCTC	61.055	60.000	0.00	0.00	0.00	4.70
1757	2146	0.623617	AAGAAGGTTATCCCCGGCCT	60.624	55.000	0.00	0.00	0.00	5.19
1758	2147	0.257905	AAAGAAGGTTATCCCCGGCC	59.742	55.000	0.00	0.00	0.00	6.13
1759	2148	3.286329	TTAAAGAAGGTTATCCCCGGC	57.714	47.619	0.00	0.00	0.00	6.13
1782	2171	9.090692	GAAGCAATGCATAAGTACATGATTTTT	57.909	29.630	8.35	0.00	0.00	1.94
1783	2172	8.252417	TGAAGCAATGCATAAGTACATGATTTT	58.748	29.630	8.35	0.00	0.00	1.82
1784	2173	7.774134	TGAAGCAATGCATAAGTACATGATTT	58.226	30.769	8.35	0.00	0.00	2.17
1826	2237	7.496747	AGAAGCTCTTTTAGACACTGGATATC	58.503	38.462	0.00	0.00	0.00	1.63
1913	2325	2.625314	CGATTGATGTAGAGGCCAGAGA	59.375	50.000	5.01	0.00	0.00	3.10
1917	2329	3.391506	CATCGATTGATGTAGAGGCCA	57.608	47.619	14.05	0.00	45.69	5.36
1969	2382	5.223449	TGAGTTTCCGTGGAACTTAAGAT	57.777	39.130	10.09	0.00	33.41	2.40
2108	2522	2.368439	TCTTCAGCCGATTTGAATGGG	58.632	47.619	0.87	0.87	37.34	4.00
2135	2549	1.745115	CGATGGGTGACGGTTGCAT	60.745	57.895	0.00	0.00	0.00	3.96
2192	2606	4.112634	CCATATGTGGTCGTTACTCACTG	58.887	47.826	0.00	0.00	40.83	3.66
2218	2632	5.897824	AGGTTATTTACTGAGCTACTGCCTA	59.102	40.000	0.00	0.00	40.80	3.93
2223	2637	5.677319	TGCAGGTTATTTACTGAGCTACT	57.323	39.130	0.00	0.00	36.86	2.57
2349	2764	3.804325	CGTGGCTTAATGGAGTAGACATG	59.196	47.826	0.00	0.00	0.00	3.21
2393	2808	8.366359	AGCTTTTAATGTTAATCCTCCAATGT	57.634	30.769	0.00	0.00	0.00	2.71
2433	2848	7.581213	ATGTCCACTTGAAAAACTGTTATGA	57.419	32.000	0.00	0.00	0.00	2.15
2446	2861	5.065914	CCTCTTTCTCAAATGTCCACTTGA	58.934	41.667	0.00	0.00	0.00	3.02
2459	2874	7.279615	TGAGACAATTAAACACCTCTTTCTCA	58.720	34.615	0.00	0.00	34.76	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.