AutoCloner

Multiple sequence alignment - TraesCS1D01G357900

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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	TraesCS1D01G357900	chr1D	100.000	2318	0	0	1	2318	441643275	441645592	0.000000e+00	4281.0
1	TraesCS1D01G357900	chr1D	91.551	1373	80	27	962	2318	441740495	441741847	0.000000e+00	1860.0
2	TraesCS1D01G357900	chr1D	97.364	607	16	0	356	962	188324966	188325572	0.000000e+00	1033.0
3	TraesCS1D01G357900	chr1D	97.364	607	16	0	356	962	410644869	410645475	0.000000e+00	1033.0
4	TraesCS1D01G357900	chr1D	97.360	606	16	0	356	961	188336207	188336812	0.000000e+00	1031.0
5	TraesCS1D01G357900	chr1D	96.399	361	8	4	1	356	348042449	348042089	7.130000e-165	590.0
6	TraesCS1D01G357900	chr1D	95.787	356	15	0	1	356	123598533	123598178	2.000000e-160	575.0
7	TraesCS1D01G357900	chr1B	87.372	1362	104	33	962	2315	599636570	599637871	0.000000e+00	1500.0
8	TraesCS1D01G357900	chr1B	87.170	1364	108	34	962	2318	599577964	599579267	0.000000e+00	1487.0
9	TraesCS1D01G357900	chr1B	87.132	1360	110	32	962	2315	599707778	599709078	0.000000e+00	1482.0
10	TraesCS1D01G357900	chr1B	87.097	1364	109	37	962	2318	599983283	599984586	0.000000e+00	1482.0
11	TraesCS1D01G357900	chr1B	86.941	1363	110	33	962	2318	599926095	599927395	0.000000e+00	1469.0
12	TraesCS1D01G357900	chr1B	86.867	1363	109	34	962	2318	599837280	599838578	0.000000e+00	1461.0
13	TraesCS1D01G357900	chr1B	89.053	950	84	9	962	1906	599765739	599766673	0.000000e+00	1160.0
14	TraesCS1D01G357900	chr1B	87.923	414	36	11	1908	2318	599766791	599767193	2.080000e-130	475.0
15	TraesCS1D01G357900	chr1A	86.452	1240	102	36	996	2224	536629864	536628680	0.000000e+00	1299.0
16	TraesCS1D01G357900	chr5D	98.353	607	10	0	356	962	506106167	506105561	0.000000e+00	1066.0
17	TraesCS1D01G357900	chr5D	95.787	356	13	1	1	356	506101081	506100728	7.180000e-160	573.0
18	TraesCS1D01G357900	chr5D	95.506	356	16	0	1	356	479118963	479119318	9.290000e-159	569.0
19	TraesCS1D01G357900	chr7A	97.858	607	13	0	356	962	127155009	127154403	0.000000e+00	1050.0
20	TraesCS1D01G357900	chrUn	97.855	606	13	0	357	962	99721978	99721373	0.000000e+00	1048.0
21	TraesCS1D01G357900	chr7D	97.529	607	15	0	356	962	29754018	29754624	0.000000e+00	1038.0
22	TraesCS1D01G357900	chr7D	97.533	608	13	2	356	962	139853923	139853317	0.000000e+00	1038.0
23	TraesCS1D01G357900	chr7D	97.529	607	14	1	356	962	523430517	523429912	0.000000e+00	1037.0
24	TraesCS1D01G357900	chr5B	85.044	916	109	14	53	962	546967366	546966473	0.000000e+00	907.0
25	TraesCS1D01G357900	chr5B	81.408	710	90	23	53	750	243378633	243379312	2.030000e-150	542.0
26	TraesCS1D01G357900	chr2A	96.359	357	12	1	1	356	10576410	10576766	9.230000e-164	586.0
27	TraesCS1D01G357900	chr4B	96.089	358	11	3	1	356	5595808	5595452	4.290000e-162	580.0
28	TraesCS1D01G357900	chr4A	91.924	421	23	6	1	414	648958189	648958605	1.540000e-161	579.0
29	TraesCS1D01G357900	chr4D	100.000	30	0	0	2065	2094	383793389	383793418	3.220000e-04	56.5
30	TraesCS1D01G357900	chr2D	100.000	30	0	0	1683	1712	603185113	603185142	3.220000e-04	56.5
31	TraesCS1D01G357900	chr3B	100.000	28	0	0	1543	1570	414369542	414369515	4.000000e-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	TraesCS1D01G357900	chr1D	441643275	441645592	2317	False	4281.0	4281	100.000	1	2318	1	chr1D.!!$F4	2317
1	TraesCS1D01G357900	chr1D	441740495	441741847	1352	False	1860.0	1860	91.551	962	2318	1	chr1D.!!$F5	1356
2	TraesCS1D01G357900	chr1D	188324966	188325572	606	False	1033.0	1033	97.364	356	962	1	chr1D.!!$F1	606
3	TraesCS1D01G357900	chr1D	410644869	410645475	606	False	1033.0	1033	97.364	356	962	1	chr1D.!!$F3	606
4	TraesCS1D01G357900	chr1D	188336207	188336812	605	False	1031.0	1031	97.360	356	961	1	chr1D.!!$F2	605
5	TraesCS1D01G357900	chr1B	599636570	599637871	1301	False	1500.0	1500	87.372	962	2315	1	chr1B.!!$F2	1353
6	TraesCS1D01G357900	chr1B	599577964	599579267	1303	False	1487.0	1487	87.170	962	2318	1	chr1B.!!$F1	1356
7	TraesCS1D01G357900	chr1B	599707778	599709078	1300	False	1482.0	1482	87.132	962	2315	1	chr1B.!!$F3	1353
8	TraesCS1D01G357900	chr1B	599983283	599984586	1303	False	1482.0	1482	87.097	962	2318	1	chr1B.!!$F6	1356
9	TraesCS1D01G357900	chr1B	599926095	599927395	1300	False	1469.0	1469	86.941	962	2318	1	chr1B.!!$F5	1356
10	TraesCS1D01G357900	chr1B	599837280	599838578	1298	False	1461.0	1461	86.867	962	2318	1	chr1B.!!$F4	1356
11	TraesCS1D01G357900	chr1B	599765739	599767193	1454	False	817.5	1160	88.488	962	2318	2	chr1B.!!$F7	1356
12	TraesCS1D01G357900	chr1A	536628680	536629864	1184	True	1299.0	1299	86.452	996	2224	1	chr1A.!!$R1	1228
13	TraesCS1D01G357900	chr5D	506105561	506106167	606	True	1066.0	1066	98.353	356	962	1	chr5D.!!$R2	606
14	TraesCS1D01G357900	chr7A	127154403	127155009	606	True	1050.0	1050	97.858	356	962	1	chr7A.!!$R1	606
15	TraesCS1D01G357900	chrUn	99721373	99721978	605	True	1048.0	1048	97.855	357	962	1	chrUn.!!$R1	605
16	TraesCS1D01G357900	chr7D	29754018	29754624	606	False	1038.0	1038	97.529	356	962	1	chr7D.!!$F1	606
17	TraesCS1D01G357900	chr7D	139853317	139853923	606	True	1038.0	1038	97.533	356	962	1	chr7D.!!$R1	606
18	TraesCS1D01G357900	chr7D	523429912	523430517	605	True	1037.0	1037	97.529	356	962	1	chr7D.!!$R2	606
19	TraesCS1D01G357900	chr5B	546966473	546967366	893	True	907.0	907	85.044	53	962	1	chr5B.!!$R1	909
20	TraesCS1D01G357900	chr5B	243378633	243379312	679	False	542.0	542	81.408	53	750	1	chr5B.!!$F1	697

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
42	43	0.325933	TTGTGTGCCTCTGGGATCTG	59.674	55.0	0.0	0.0	33.58	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1376	1386	0.458543	ACATCACGTAAGCCGCTCAG	60.459	55.0	0.0	0.0	45.62	3.35	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	3.703001	TGTTTTGGAACCAAAGGCAAA	57.297	38.095	16.72	2.09	45.15	3.68
21	22	4.227864	TGTTTTGGAACCAAAGGCAAAT	57.772	36.364	16.72	0.00	45.15	2.32
22	23	4.593956	TGTTTTGGAACCAAAGGCAAATT	58.406	34.783	16.72	0.00	45.15	1.82
23	24	5.012893	TGTTTTGGAACCAAAGGCAAATTT	58.987	33.333	16.72	0.00	45.15	1.82
24	25	5.478332	TGTTTTGGAACCAAAGGCAAATTTT	59.522	32.000	16.72	0.00	45.15	1.82
25	26	5.573337	TTTGGAACCAAAGGCAAATTTTG	57.427	34.783	14.02	4.72	40.51	2.44
26	27	4.227864	TGGAACCAAAGGCAAATTTTGT	57.772	36.364	10.65	0.00	34.51	2.83
27	28	3.944015	TGGAACCAAAGGCAAATTTTGTG	59.056	39.130	10.65	1.47	34.51	3.33
28	29	3.944650	GGAACCAAAGGCAAATTTTGTGT	59.055	39.130	10.65	0.00	34.51	3.72
29	30	4.201901	GGAACCAAAGGCAAATTTTGTGTG	60.202	41.667	10.65	4.38	34.51	3.82
30	31	2.682352	ACCAAAGGCAAATTTTGTGTGC	59.318	40.909	10.65	0.00	34.51	4.57
36	37	2.137523	GCAAATTTTGTGTGCCTCTGG	58.862	47.619	10.65	0.00	31.94	3.86
37	38	2.758009	CAAATTTTGTGTGCCTCTGGG	58.242	47.619	0.78	0.00	0.00	4.45
38	39	2.364970	CAAATTTTGTGTGCCTCTGGGA	59.635	45.455	0.78	0.00	33.58	4.37
39	40	2.610438	ATTTTGTGTGCCTCTGGGAT	57.390	45.000	0.00	0.00	33.58	3.85
40	41	1.909700	TTTTGTGTGCCTCTGGGATC	58.090	50.000	0.00	0.00	33.58	3.36
41	42	1.067295	TTTGTGTGCCTCTGGGATCT	58.933	50.000	0.00	0.00	33.58	2.75
42	43	0.325933	TTGTGTGCCTCTGGGATCTG	59.674	55.000	0.00	0.00	33.58	2.90
43	44	1.222936	GTGTGCCTCTGGGATCTGG	59.777	63.158	0.00	0.00	33.58	3.86
44	45	1.229625	TGTGCCTCTGGGATCTGGT	60.230	57.895	0.00	0.00	33.58	4.00
45	46	1.222936	GTGCCTCTGGGATCTGGTG	59.777	63.158	0.00	0.00	33.58	4.17
46	47	1.997311	TGCCTCTGGGATCTGGTGG	60.997	63.158	0.00	0.00	33.58	4.61
47	48	2.750657	GCCTCTGGGATCTGGTGGG	61.751	68.421	0.00	0.00	33.58	4.61
48	49	2.074948	CCTCTGGGATCTGGTGGGG	61.075	68.421	0.00	0.00	33.58	4.96
49	50	2.042762	TCTGGGATCTGGTGGGGG	59.957	66.667	0.00	0.00	0.00	5.40
50	51	2.042762	CTGGGATCTGGTGGGGGA	59.957	66.667	0.00	0.00	0.00	4.81
51	52	1.386485	CTGGGATCTGGTGGGGGAT	60.386	63.158	0.00	0.00	0.00	3.85
63	64	1.908619	GTGGGGGATTGCTGGAATTTT	59.091	47.619	0.00	0.00	0.00	1.82
76	77	4.631377	GCTGGAATTTTGTCTATTTTGGGC	59.369	41.667	0.00	0.00	0.00	5.36
78	79	4.843516	TGGAATTTTGTCTATTTTGGGCCT	59.156	37.500	4.53	0.00	0.00	5.19
91	92	4.809070	GGCCTAGCCCAATAGCAG	57.191	61.111	0.00	0.00	44.06	4.24
126	127	3.771577	AATAAATCCTAGAGGCCCACG	57.228	47.619	0.00	0.00	34.44	4.94
127	128	0.756903	TAAATCCTAGAGGCCCACGC	59.243	55.000	0.00	0.00	34.44	5.34
149	150	0.680618	CCCATTTGTGCAAGGCAAGA	59.319	50.000	0.00	0.00	41.47	3.02
151	152	1.337447	CCATTTGTGCAAGGCAAGAGG	60.337	52.381	0.00	0.00	41.47	3.69
154	155	1.108727	TTGTGCAAGGCAAGAGGTGG	61.109	55.000	0.00	0.00	41.47	4.61
155	156	1.228245	GTGCAAGGCAAGAGGTGGA	60.228	57.895	0.00	0.00	41.47	4.02
187	188	6.614694	TTAGTCCCACATTGCTAGTTTAGA	57.385	37.500	0.00	0.00	0.00	2.10
190	191	3.844211	TCCCACATTGCTAGTTTAGAGGT	59.156	43.478	0.00	0.00	0.00	3.85
264	265	4.451150	GAGGGACATCCACGCGCA	62.451	66.667	5.73	0.00	38.24	6.09
348	349	1.035385	TGAGCCGAGCCGATGTCTAA	61.035	55.000	0.00	0.00	0.00	2.10
352	353	1.940613	GCCGAGCCGATGTCTAAATTT	59.059	47.619	0.00	0.00	0.00	1.82
353	354	2.354821	GCCGAGCCGATGTCTAAATTTT	59.645	45.455	0.00	0.00	0.00	1.82
354	355	3.181500	GCCGAGCCGATGTCTAAATTTTT	60.181	43.478	0.00	0.00	0.00	1.94
1006	1016	0.687354	AGAACTCCAAGCCATGTCGT	59.313	50.000	0.00	0.00	0.00	4.34
1129	1139	0.907230	GGACAAGCTCCAGGTCCTCT	60.907	60.000	15.62	0.00	45.99	3.69
1167	1177	1.214589	GGTGCCTGACGTGACGTAT	59.785	57.895	11.89	0.00	41.37	3.06
1179	1189	3.414343	GACGTATGGCACCGGCGTA	62.414	63.158	6.01	0.00	42.47	4.42
1376	1386	7.830739	TCTTAGGAGGAAATTTTCTGATTTGC	58.169	34.615	2.93	0.00	37.54	3.68
1544	1570	3.199677	CCTTGTTTCTGTTACGGTGACA	58.800	45.455	5.59	5.59	0.00	3.58
1617	1644	0.034477	AAAACTGCCCCCTATGTCGG	60.034	55.000	0.00	0.00	0.00	4.79
1635	1663	2.424302	CCCCGTGGACGACAAACT	59.576	61.111	0.00	0.00	43.02	2.66
1673	1702	3.028098	ACCTCCGCCCCCTCTCTA	61.028	66.667	0.00	0.00	0.00	2.43
1677	1706	2.002018	CTCCGCCCCCTCTCTACTCT	62.002	65.000	0.00	0.00	0.00	3.24
1679	1708	0.406361	CCGCCCCCTCTCTACTCTAT	59.594	60.000	0.00	0.00	0.00	1.98
1684	1713	1.444836	CCCTCTCTACTCTATCGCCG	58.555	60.000	0.00	0.00	0.00	6.46
1732	1761	3.083293	GACTAGTGTTCCTCTCCTTCGT	58.917	50.000	0.00	0.00	0.00	3.85
1745	1774	2.432510	CTCCTTCGTTCTTGGCTATCCT	59.567	50.000	0.00	0.00	0.00	3.24
1751	1780	0.901827	TTCTTGGCTATCCTGCACGA	59.098	50.000	0.00	0.00	34.04	4.35
1755	1784	0.970427	TGGCTATCCTGCACGAGACA	60.970	55.000	0.00	0.00	34.04	3.41
1766	1795	1.300697	ACGAGACAACTTGGACGGC	60.301	57.895	0.00	0.00	32.13	5.68
1804	1836	4.629115	GCTTGGCAGCGTGCGTTT	62.629	61.111	4.33	0.00	46.21	3.60
1826	1888	3.936203	TGGGGTGTGGACGACTGC	61.936	66.667	0.00	0.00	0.00	4.40
1827	1889	3.626924	GGGGTGTGGACGACTGCT	61.627	66.667	0.00	0.00	0.00	4.24
1828	1890	2.357517	GGGTGTGGACGACTGCTG	60.358	66.667	0.00	0.00	0.00	4.41
1829	1891	2.357517	GGTGTGGACGACTGCTGG	60.358	66.667	0.00	0.00	0.00	4.85
1830	1892	2.421739	GTGTGGACGACTGCTGGT	59.578	61.111	0.00	0.00	0.00	4.00
1831	1893	1.956170	GTGTGGACGACTGCTGGTG	60.956	63.158	0.00	0.00	0.00	4.17
1832	1894	2.357517	GTGGACGACTGCTGGTGG	60.358	66.667	0.00	0.00	0.00	4.61
1833	1895	4.314440	TGGACGACTGCTGGTGGC	62.314	66.667	0.00	0.00	42.22	5.01
1835	1897	4.664677	GACGACTGCTGGTGGCGT	62.665	66.667	0.00	0.00	45.43	5.68
1836	1898	4.969196	ACGACTGCTGGTGGCGTG	62.969	66.667	0.00	0.00	45.43	5.34
1838	1900	4.626081	GACTGCTGGTGGCGTGGT	62.626	66.667	0.00	0.00	45.43	4.16
1839	1901	3.234630	GACTGCTGGTGGCGTGGTA	62.235	63.158	0.00	0.00	45.43	3.25
1840	1902	2.434884	CTGCTGGTGGCGTGGTAG	60.435	66.667	0.00	0.00	45.43	3.18
1841	1903	3.958147	CTGCTGGTGGCGTGGTAGG	62.958	68.421	0.00	0.00	45.43	3.18
1842	1904	4.778143	GCTGGTGGCGTGGTAGGG	62.778	72.222	0.00	0.00	0.00	3.53
1843	1905	4.096003	CTGGTGGCGTGGTAGGGG	62.096	72.222	0.00	0.00	0.00	4.79
1849	1911	4.814294	GCGTGGTAGGGGCGTGAG	62.814	72.222	0.00	0.00	0.00	3.51
1850	1912	3.066190	CGTGGTAGGGGCGTGAGA	61.066	66.667	0.00	0.00	0.00	3.27
1851	1913	2.577593	GTGGTAGGGGCGTGAGAC	59.422	66.667	0.00	0.00	39.70	3.36
1867	1929	1.810030	GACCTTGCGTGGATCGGTC	60.810	63.158	1.60	0.00	40.26	4.79
1868	1930	2.264480	CCTTGCGTGGATCGGTCA	59.736	61.111	0.00	0.00	40.26	4.02
1900	1964	2.614057	CTCGGTGTCATTTATTCCCTGC	59.386	50.000	0.00	0.00	0.00	4.85
1974	2156	7.581011	AAACTTGTGTGCTTTTTCTGTTTAG	57.419	32.000	0.00	0.00	0.00	1.85
2219	2409	4.261031	CGGTTTAAAAGGTCCAACAGTCAG	60.261	45.833	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.703001	TTTGCCTTTGGTTCCAAAACA	57.297	38.095	16.25	14.24	37.10	2.83
1	2	5.574891	AAATTTGCCTTTGGTTCCAAAAC	57.425	34.783	16.25	12.26	35.81	2.43
2	3	5.478332	ACAAAATTTGCCTTTGGTTCCAAAA	59.522	32.000	16.25	3.82	37.96	2.44
3	4	5.012893	ACAAAATTTGCCTTTGGTTCCAAA	58.987	33.333	14.99	14.99	37.96	3.28
4	5	4.397417	CACAAAATTTGCCTTTGGTTCCAA	59.603	37.500	5.52	0.00	37.96	3.53
5	6	3.944015	CACAAAATTTGCCTTTGGTTCCA	59.056	39.130	5.52	0.00	37.96	3.53
6	7	3.944650	ACACAAAATTTGCCTTTGGTTCC	59.055	39.130	5.52	0.00	37.96	3.62
7	8	4.730324	GCACACAAAATTTGCCTTTGGTTC	60.730	41.667	5.52	0.00	37.96	3.62
8	9	3.128415	GCACACAAAATTTGCCTTTGGTT	59.872	39.130	5.52	0.00	37.96	3.67
9	10	2.682352	GCACACAAAATTTGCCTTTGGT	59.318	40.909	5.52	0.00	37.96	3.67
10	11	3.337301	GCACACAAAATTTGCCTTTGG	57.663	42.857	5.52	0.00	37.96	3.28
16	17	2.137523	CCAGAGGCACACAAAATTTGC	58.862	47.619	5.52	0.00	35.40	3.68
17	18	2.364970	TCCCAGAGGCACACAAAATTTG	59.635	45.455	3.89	3.89	0.00	2.32
18	19	2.676748	TCCCAGAGGCACACAAAATTT	58.323	42.857	0.00	0.00	0.00	1.82
19	20	2.380064	TCCCAGAGGCACACAAAATT	57.620	45.000	0.00	0.00	0.00	1.82
20	21	2.042162	AGATCCCAGAGGCACACAAAAT	59.958	45.455	0.00	0.00	0.00	1.82
21	22	1.425066	AGATCCCAGAGGCACACAAAA	59.575	47.619	0.00	0.00	0.00	2.44
22	23	1.067295	AGATCCCAGAGGCACACAAA	58.933	50.000	0.00	0.00	0.00	2.83
23	24	0.325933	CAGATCCCAGAGGCACACAA	59.674	55.000	0.00	0.00	0.00	3.33
24	25	1.556373	CCAGATCCCAGAGGCACACA	61.556	60.000	0.00	0.00	0.00	3.72
25	26	1.222936	CCAGATCCCAGAGGCACAC	59.777	63.158	0.00	0.00	0.00	3.82
26	27	1.229625	ACCAGATCCCAGAGGCACA	60.230	57.895	0.00	0.00	0.00	4.57
27	28	1.222936	CACCAGATCCCAGAGGCAC	59.777	63.158	0.00	0.00	0.00	5.01
28	29	1.997311	CCACCAGATCCCAGAGGCA	60.997	63.158	0.00	0.00	0.00	4.75
29	30	2.750657	CCCACCAGATCCCAGAGGC	61.751	68.421	0.00	0.00	0.00	4.70
30	31	2.074948	CCCCACCAGATCCCAGAGG	61.075	68.421	0.00	0.00	0.00	3.69
31	32	2.074948	CCCCCACCAGATCCCAGAG	61.075	68.421	0.00	0.00	0.00	3.35
32	33	1.913321	ATCCCCCACCAGATCCCAGA	61.913	60.000	0.00	0.00	0.00	3.86
33	34	0.995675	AATCCCCCACCAGATCCCAG	60.996	60.000	0.00	0.00	0.00	4.45
34	35	1.086565	AATCCCCCACCAGATCCCA	59.913	57.895	0.00	0.00	0.00	4.37
35	36	1.538666	CAATCCCCCACCAGATCCC	59.461	63.158	0.00	0.00	0.00	3.85
36	37	1.152673	GCAATCCCCCACCAGATCC	60.153	63.158	0.00	0.00	0.00	3.36
37	38	0.466922	CAGCAATCCCCCACCAGATC	60.467	60.000	0.00	0.00	0.00	2.75
38	39	1.616921	CAGCAATCCCCCACCAGAT	59.383	57.895	0.00	0.00	0.00	2.90
39	40	2.615465	CCAGCAATCCCCCACCAGA	61.615	63.158	0.00	0.00	0.00	3.86
40	41	2.043652	CCAGCAATCCCCCACCAG	60.044	66.667	0.00	0.00	0.00	4.00
41	42	1.517538	ATTCCAGCAATCCCCCACCA	61.518	55.000	0.00	0.00	0.00	4.17
42	43	0.325577	AATTCCAGCAATCCCCCACC	60.326	55.000	0.00	0.00	0.00	4.61
43	44	1.571955	AAATTCCAGCAATCCCCCAC	58.428	50.000	0.00	0.00	0.00	4.61
44	45	1.907936	CAAAATTCCAGCAATCCCCCA	59.092	47.619	0.00	0.00	0.00	4.96
45	46	1.908619	ACAAAATTCCAGCAATCCCCC	59.091	47.619	0.00	0.00	0.00	5.40
46	47	2.833943	AGACAAAATTCCAGCAATCCCC	59.166	45.455	0.00	0.00	0.00	4.81
47	48	5.859205	ATAGACAAAATTCCAGCAATCCC	57.141	39.130	0.00	0.00	0.00	3.85
48	49	7.064966	CCAAAATAGACAAAATTCCAGCAATCC	59.935	37.037	0.00	0.00	0.00	3.01
49	50	7.064966	CCCAAAATAGACAAAATTCCAGCAATC	59.935	37.037	0.00	0.00	0.00	2.67
50	51	6.880529	CCCAAAATAGACAAAATTCCAGCAAT	59.119	34.615	0.00	0.00	0.00	3.56
51	52	6.229733	CCCAAAATAGACAAAATTCCAGCAA	58.770	36.000	0.00	0.00	0.00	3.91
63	64	2.729028	GGCTAGGCCCAAAATAGACA	57.271	50.000	4.61	0.00	44.06	3.41
76	77	3.118261	TCTGAAACTGCTATTGGGCTAGG	60.118	47.826	0.00	0.00	0.00	3.02
78	79	4.568072	TTCTGAAACTGCTATTGGGCTA	57.432	40.909	0.00	0.00	0.00	3.93
126	127	1.375013	CCTTGCACAAATGGGCTGC	60.375	57.895	9.34	0.00	46.62	5.25
127	128	1.375013	GCCTTGCACAAATGGGCTG	60.375	57.895	9.34	2.06	46.62	4.85
149	150	4.661709	TGGGACTAAACTTTAGTTCCACCT	59.338	41.667	28.04	2.35	45.69	4.00
154	155	6.206829	AGCAATGTGGGACTAAACTTTAGTTC	59.793	38.462	14.17	12.33	37.25	3.01
155	156	6.068670	AGCAATGTGGGACTAAACTTTAGTT	58.931	36.000	14.17	0.00	40.50	2.24
190	191	5.903589	CCTCCCTTATAAAGAGGTCCAACTA	59.096	44.000	17.61	0.00	41.96	2.24
221	222	3.824133	TCTCATGCTCATACAATTGGGG	58.176	45.455	10.83	0.00	0.00	4.96
226	227	5.821470	CCTCTTGTTCTCATGCTCATACAAT	59.179	40.000	0.00	0.00	0.00	2.71
227	228	5.181009	CCTCTTGTTCTCATGCTCATACAA	58.819	41.667	0.00	0.00	0.00	2.41
587	597	0.606401	TCGTCGGGGAAGTAGTCGTT	60.606	55.000	0.00	0.00	0.00	3.85
949	959	3.055021	TGCCACGAGGTGTTGGAAATATA	60.055	43.478	0.00	0.00	37.19	0.86
1129	1139	2.029369	GTGGTACCACGCGTCCAA	59.971	61.111	28.55	0.00	37.19	3.53
1155	1165	1.080366	GGTGCCATACGTCACGTCA	60.080	57.895	5.85	0.00	41.54	4.35
1167	1177	3.379865	GAGGAATACGCCGGTGCCA	62.380	63.158	16.69	3.16	0.00	4.92
1297	1307	1.444917	TAGTGCGCGGACATCGATCT	61.445	55.000	32.28	12.50	42.43	2.75
1376	1386	0.458543	ACATCACGTAAGCCGCTCAG	60.459	55.000	0.00	0.00	45.62	3.35
1544	1570	1.903877	CTTCACAGCCGACCCTCCAT	61.904	60.000	0.00	0.00	0.00	3.41
1617	1644	3.351416	GTTTGTCGTCCACGGGGC	61.351	66.667	0.00	0.00	40.29	5.80
1673	1702	2.311688	CTTTGCCCCGGCGATAGAGT	62.312	60.000	9.30	0.00	45.51	3.24
1677	1706	4.868116	GGCTTTGCCCCGGCGATA	62.868	66.667	9.30	0.00	44.06	2.92
1703	1732	1.513586	GAACACTAGTCGCCGACCG	60.514	63.158	14.60	8.12	32.18	4.79
1732	1761	0.901827	TCGTGCAGGATAGCCAAGAA	59.098	50.000	4.68	0.00	36.29	2.52
1745	1774	0.874175	CGTCCAAGTTGTCTCGTGCA	60.874	55.000	1.45	0.00	0.00	4.57
1751	1780	2.030562	CGGCCGTCCAAGTTGTCT	59.969	61.111	19.50	0.00	0.00	3.41
1804	1836	4.248842	CGTCCACACCCCACTGCA	62.249	66.667	0.00	0.00	0.00	4.41
1807	1839	2.122989	AGTCGTCCACACCCCACT	60.123	61.111	0.00	0.00	0.00	4.00
1826	1888	4.096003	CCCCTACCACGCCACCAG	62.096	72.222	0.00	0.00	0.00	4.00
1832	1894	4.814294	CTCACGCCCCTACCACGC	62.814	72.222	0.00	0.00	0.00	5.34
1833	1895	3.066190	TCTCACGCCCCTACCACG	61.066	66.667	0.00	0.00	0.00	4.94
1834	1896	2.577593	GTCTCACGCCCCTACCAC	59.422	66.667	0.00	0.00	0.00	4.16
1835	1897	2.682494	GGTCTCACGCCCCTACCA	60.682	66.667	0.00	0.00	0.00	3.25
1836	1898	1.988406	AAGGTCTCACGCCCCTACC	60.988	63.158	0.00	0.00	0.00	3.18
1837	1899	1.218316	CAAGGTCTCACGCCCCTAC	59.782	63.158	0.00	0.00	0.00	3.18
1838	1900	2.656069	GCAAGGTCTCACGCCCCTA	61.656	63.158	0.00	0.00	0.00	3.53
1839	1901	4.021925	GCAAGGTCTCACGCCCCT	62.022	66.667	0.00	0.00	0.00	4.79
1841	1903	4.681978	ACGCAAGGTCTCACGCCC	62.682	66.667	0.00	0.00	46.39	6.13
1842	1904	3.414700	CACGCAAGGTCTCACGCC	61.415	66.667	0.00	0.00	46.39	5.68
1843	1905	3.414700	CCACGCAAGGTCTCACGC	61.415	66.667	0.00	0.00	46.39	5.34
1844	1906	1.078759	GATCCACGCAAGGTCTCACG	61.079	60.000	0.00	0.00	46.39	4.35
1845	1907	1.078759	CGATCCACGCAAGGTCTCAC	61.079	60.000	0.00	0.00	46.39	3.51
1846	1908	1.215382	CGATCCACGCAAGGTCTCA	59.785	57.895	0.00	0.00	46.39	3.27
1847	1909	1.519455	CCGATCCACGCAAGGTCTC	60.519	63.158	0.00	0.00	46.39	3.36
1848	1910	2.227089	GACCGATCCACGCAAGGTCT	62.227	60.000	5.75	0.00	45.68	3.85
1849	1911	1.810030	GACCGATCCACGCAAGGTC	60.810	63.158	0.00	0.00	43.55	3.85
1850	1912	2.264794	GACCGATCCACGCAAGGT	59.735	61.111	0.00	0.00	46.39	3.50
1851	1913	2.100631	GTGACCGATCCACGCAAGG	61.101	63.158	0.00	0.00	46.39	3.61
1852	1914	1.374125	TGTGACCGATCCACGCAAG	60.374	57.895	0.00	0.00	41.07	4.01
1853	1915	1.666553	GTGTGACCGATCCACGCAA	60.667	57.895	8.67	0.00	42.68	4.85
1854	1916	2.048597	GTGTGACCGATCCACGCA	60.049	61.111	8.67	1.18	42.68	5.24
1867	1929	1.371758	CACCGAGTGTCTCCGTGTG	60.372	63.158	9.04	0.00	35.88	3.82
1868	1930	1.826921	ACACCGAGTGTCTCCGTGT	60.827	57.895	14.48	14.48	43.92	4.49
2197	2387	4.643334	ACTGACTGTTGGACCTTTTAAACC	59.357	41.667	0.00	0.00	0.00	3.27
2272	2462	1.835483	GCGCTCAGTCACACAGGTTG	61.835	60.000	0.00	0.00	0.00	3.77
2282	2472	1.153862	CTCACTCTGGCGCTCAGTC	60.154	63.158	20.54	0.03	43.76	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.