AutoCloner

Multiple sequence alignment - TraesCS5D01G533300

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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	TraesCS5D01G533300	chr5D	100.000	2753	0	0	1	2753	547890570	547887818	0.000000e+00	5084.0
1	TraesCS5D01G533300	chr5D	96.056	862	32	2	1892	2753	448731212	448730353	0.000000e+00	1402.0
2	TraesCS5D01G533300	chr5D	84.152	1079	117	29	4	1037	547881087	547880018	0.000000e+00	996.0
3	TraesCS5D01G533300	chr5B	91.945	1229	72	12	666	1885	691805731	691804521	0.000000e+00	1696.0
4	TraesCS5D01G533300	chr5B	96.291	647	18	4	1	641	691806372	691805726	0.000000e+00	1057.0
5	TraesCS5D01G533300	chr5B	85.802	972	94	28	4	948	691796027	691795073	0.000000e+00	990.0
6	TraesCS5D01G533300	chr5B	91.369	672	55	3	1098	1768	8878829	8878160	0.000000e+00	917.0
7	TraesCS5D01G533300	chr5B	89.669	484	26	11	1	475	691807227	691806759	1.830000e-166	595.0
8	TraesCS5D01G533300	chr5B	80.702	114	17	4	169	280	691822617	691822507	1.760000e-12	84.2
9	TraesCS5D01G533300	chr2D	95.954	865	33	2	1890	2753	146289315	146288452	0.000000e+00	1402.0
10	TraesCS5D01G533300	chr2D	95.727	866	33	4	1890	2753	486215940	486215077	0.000000e+00	1391.0
11	TraesCS5D01G533300	chr1D	95.940	862	33	2	1893	2753	335652959	335652099	0.000000e+00	1397.0
12	TraesCS5D01G533300	chr4D	95.723	865	35	2	1890	2753	342074589	342075452	0.000000e+00	1391.0
13	TraesCS5D01G533300	chr3D	95.723	865	36	1	1890	2753	32536787	32537651	0.000000e+00	1391.0
14	TraesCS5D01G533300	chr3D	95.819	861	36	0	1893	2753	558203438	558202578	0.000000e+00	1391.0
15	TraesCS5D01G533300	chr3D	95.502	867	35	3	1890	2753	489888870	489889735	0.000000e+00	1382.0
16	TraesCS5D01G533300	chr7D	95.607	865	35	3	1890	2753	229349141	229348279	0.000000e+00	1384.0
17	TraesCS5D01G533300	chr4A	85.378	978	104	23	4	952	618415794	618414827	0.000000e+00	977.0
18	TraesCS5D01G533300	chr4B	92.760	663	47	1	1098	1759	232154324	232154986	0.000000e+00	957.0
19	TraesCS5D01G533300	chr4B	92.609	663	47	2	1098	1759	613000164	613000825	0.000000e+00	952.0
20	TraesCS5D01G533300	chr3B	92.760	663	47	1	1098	1759	456318781	456318119	0.000000e+00	957.0
21	TraesCS5D01G533300	chr2B	92.760	663	44	4	1098	1759	382563312	382562653	0.000000e+00	955.0
22	TraesCS5D01G533300	chr2B	92.030	665	49	4	1098	1759	593651268	593650605	0.000000e+00	931.0
23	TraesCS5D01G533300	chr7B	92.169	664	50	2	1098	1759	609891810	609892473	0.000000e+00	937.0
24	TraesCS5D01G533300	chr7B	90.211	664	60	5	1098	1758	35633744	35633083	0.000000e+00	861.0
25	TraesCS5D01G533300	chr6B	91.837	49	0	4	953	997	76562243	76562291	6.360000e-07	65.8

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	TraesCS5D01G533300	chr5D	547887818	547890570	2752	True	5084	5084	100.000	1	2753	1	chr5D.!!$R3	2752
1	TraesCS5D01G533300	chr5D	448730353	448731212	859	True	1402	1402	96.056	1892	2753	1	chr5D.!!$R1	861
2	TraesCS5D01G533300	chr5D	547880018	547881087	1069	True	996	996	84.152	4	1037	1	chr5D.!!$R2	1033
3	TraesCS5D01G533300	chr5B	691804521	691807227	2706	True	1116	1696	92.635	1	1885	3	chr5B.!!$R4	1884
4	TraesCS5D01G533300	chr5B	691795073	691796027	954	True	990	990	85.802	4	948	1	chr5B.!!$R2	944
5	TraesCS5D01G533300	chr5B	8878160	8878829	669	True	917	917	91.369	1098	1768	1	chr5B.!!$R1	670
6	TraesCS5D01G533300	chr2D	146288452	146289315	863	True	1402	1402	95.954	1890	2753	1	chr2D.!!$R1	863
7	TraesCS5D01G533300	chr2D	486215077	486215940	863	True	1391	1391	95.727	1890	2753	1	chr2D.!!$R2	863
8	TraesCS5D01G533300	chr1D	335652099	335652959	860	True	1397	1397	95.940	1893	2753	1	chr1D.!!$R1	860
9	TraesCS5D01G533300	chr4D	342074589	342075452	863	False	1391	1391	95.723	1890	2753	1	chr4D.!!$F1	863
10	TraesCS5D01G533300	chr3D	32536787	32537651	864	False	1391	1391	95.723	1890	2753	1	chr3D.!!$F1	863
11	TraesCS5D01G533300	chr3D	558202578	558203438	860	True	1391	1391	95.819	1893	2753	1	chr3D.!!$R1	860
12	TraesCS5D01G533300	chr3D	489888870	489889735	865	False	1382	1382	95.502	1890	2753	1	chr3D.!!$F2	863
13	TraesCS5D01G533300	chr7D	229348279	229349141	862	True	1384	1384	95.607	1890	2753	1	chr7D.!!$R1	863
14	TraesCS5D01G533300	chr4A	618414827	618415794	967	True	977	977	85.378	4	952	1	chr4A.!!$R1	948
15	TraesCS5D01G533300	chr4B	232154324	232154986	662	False	957	957	92.760	1098	1759	1	chr4B.!!$F1	661
16	TraesCS5D01G533300	chr4B	613000164	613000825	661	False	952	952	92.609	1098	1759	1	chr4B.!!$F2	661
17	TraesCS5D01G533300	chr3B	456318119	456318781	662	True	957	957	92.760	1098	1759	1	chr3B.!!$R1	661
18	TraesCS5D01G533300	chr2B	382562653	382563312	659	True	955	955	92.760	1098	1759	1	chr2B.!!$R1	661
19	TraesCS5D01G533300	chr2B	593650605	593651268	663	True	931	931	92.030	1098	1759	1	chr2B.!!$R2	661
20	TraesCS5D01G533300	chr7B	609891810	609892473	663	False	937	937	92.169	1098	1759	1	chr7B.!!$F1	661
21	TraesCS5D01G533300	chr7B	35633083	35633744	661	True	861	861	90.211	1098	1758	1	chr7B.!!$R1	660

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
763	1635	0.535102	AGGACCAAGTGAAGCCAACG	60.535	55.0	0.0	0.0	0.0	4.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1868	2841	0.809241	CATGCGAGACTTGGAGGAGC	60.809	60.0	0.0	0.0	0.0	4.7	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
54	55	3.713826	TTACCTGTCCTAAAAGGCTGG	57.286	47.619	0.00	9.90	37.03	4.85
67	68	4.861102	AAAGGCTGGCATATTTCATAGC	57.139	40.909	3.38	0.00	0.00	2.97
162	168	6.934056	AGGATCATCTAGTCATCTTATGCAC	58.066	40.000	0.00	0.00	0.00	4.57
186	192	4.536364	ATTGTGTTGTCTGACTTGAACG	57.464	40.909	9.51	0.00	0.00	3.95
296	1157	0.948623	TTGGACACGCCGATTCTGTG	60.949	55.000	0.00	0.00	40.66	3.66
475	1343	4.439253	AAAAAGACACTAGAGCTTGGGT	57.561	40.909	0.00	0.00	0.00	4.51
517	1385	1.691976	ACACGACCTCAAGGAACATCA	59.308	47.619	2.30	0.00	38.94	3.07
636	1504	9.912634	TCCATCAAACTGAAGATTTCAAATAAC	57.087	29.630	0.00	0.00	39.58	1.89
637	1505	9.143631	CCATCAAACTGAAGATTTCAAATAACC	57.856	33.333	0.00	0.00	39.58	2.85
638	1506	9.143631	CATCAAACTGAAGATTTCAAATAACCC	57.856	33.333	0.00	0.00	39.58	4.11
639	1507	8.243961	TCAAACTGAAGATTTCAAATAACCCA	57.756	30.769	0.00	0.00	39.58	4.51
640	1508	8.869109	TCAAACTGAAGATTTCAAATAACCCAT	58.131	29.630	0.00	0.00	39.58	4.00
644	1512	9.479549	ACTGAAGATTTCAAATAACCCATATGT	57.520	29.630	1.24	0.00	39.58	2.29
652	1520	7.737972	TCAAATAACCCATATGTATTCACGG	57.262	36.000	1.24	0.00	0.00	4.94
653	1521	7.284074	TCAAATAACCCATATGTATTCACGGT	58.716	34.615	1.24	0.00	0.00	4.83
654	1522	8.430431	TCAAATAACCCATATGTATTCACGGTA	58.570	33.333	1.24	0.00	0.00	4.02
655	1523	9.058174	CAAATAACCCATATGTATTCACGGTAA	57.942	33.333	1.24	0.00	0.00	2.85
656	1524	9.629878	AAATAACCCATATGTATTCACGGTAAA	57.370	29.630	1.24	0.00	0.00	2.01
657	1525	8.842358	ATAACCCATATGTATTCACGGTAAAG	57.158	34.615	1.24	0.00	0.00	1.85
658	1526	6.488769	ACCCATATGTATTCACGGTAAAGA	57.511	37.500	1.24	0.00	0.00	2.52
659	1527	6.285990	ACCCATATGTATTCACGGTAAAGAC	58.714	40.000	1.24	0.00	0.00	3.01
660	1528	6.126997	ACCCATATGTATTCACGGTAAAGACA	60.127	38.462	1.24	0.00	32.92	3.41
661	1529	6.202188	CCCATATGTATTCACGGTAAAGACAC	59.798	42.308	1.24	0.00	31.34	3.67
662	1530	6.074516	CCATATGTATTCACGGTAAAGACACG	60.075	42.308	1.24	0.00	31.34	4.49
663	1531	4.502171	TGTATTCACGGTAAAGACACGA	57.498	40.909	0.00	0.00	0.00	4.35
664	1532	4.478699	TGTATTCACGGTAAAGACACGAG	58.521	43.478	0.00	0.00	0.00	4.18
679	1547	2.390599	CGAGCACCATGTTGACCGG	61.391	63.158	0.00	0.00	0.00	5.28
702	1570	0.685097	CACAAACTTCGGAGGAGGGA	59.315	55.000	0.00	0.00	0.00	4.20
707	1575	1.305381	CTTCGGAGGAGGGAGTGGT	60.305	63.158	0.00	0.00	0.00	4.16
731	1599	2.373502	ACACTTCAAAAGAGGGGGAGAG	59.626	50.000	0.00	0.00	0.00	3.20
763	1635	0.535102	AGGACCAAGTGAAGCCAACG	60.535	55.000	0.00	0.00	0.00	4.10
786	1658	7.453393	ACGACATTTGATAGATAACCCATGAT	58.547	34.615	0.00	0.00	0.00	2.45
827	1699	3.623060	CGGTTTTGGATGACGATCATTCT	59.377	43.478	0.00	0.00	37.20	2.40
865	1737	9.814899	CCTATGCCATGTTTAAATGTGAAATTA	57.185	29.630	0.00	0.00	0.00	1.40
907	1779	7.821652	TGAAGTGTGTAAAGTTGAATGAAACA	58.178	30.769	0.00	0.00	32.21	2.83
957	1829	9.658475	TTAACATCAATTAAAGTGTATATGCGC	57.342	29.630	0.00	0.00	0.00	6.09
958	1830	7.258022	ACATCAATTAAAGTGTATATGCGCA	57.742	32.000	14.96	14.96	0.00	6.09
959	1831	7.132213	ACATCAATTAAAGTGTATATGCGCAC	58.868	34.615	14.90	0.00	35.98	5.34
960	1832	5.733299	TCAATTAAAGTGTATATGCGCACG	58.267	37.500	14.90	0.00	40.26	5.34
961	1833	3.579147	TTAAAGTGTATATGCGCACGC	57.421	42.857	14.90	6.73	40.26	5.34
1036	1908	5.902681	AGTTTTTAGGGAAACTCACTTTGC	58.097	37.500	0.00	0.00	44.30	3.68
1058	1930	4.335416	CTGACCATGCCTCTTTTTAGGAA	58.665	43.478	0.00	0.00	39.15	3.36
1065	1937	7.127339	ACCATGCCTCTTTTTAGGAATCTACTA	59.873	37.037	0.00	0.00	39.15	1.82
1071	1943	8.141268	CCTCTTTTTAGGAATCTACTAGAGCTG	58.859	40.741	0.00	0.00	39.15	4.24
1091	1963	6.183347	AGCTGCTCTAAATGTAAAGGACAAT	58.817	36.000	0.00	0.00	42.78	2.71
1094	1966	5.163764	TGCTCTAAATGTAAAGGACAATGCG	60.164	40.000	0.00	0.00	42.78	4.73
1138	2011	5.180492	GGATGACGTAAACTGGTTCATGAAA	59.820	40.000	10.35	0.00	0.00	2.69
1139	2012	5.412526	TGACGTAAACTGGTTCATGAAAC	57.587	39.130	16.88	16.88	37.12	2.78
1210	2083	3.486875	GGCGAACTATGTTAATGCACACC	60.487	47.826	0.00	0.00	0.00	4.16
1211	2084	3.784199	GCGAACTATGTTAATGCACACCG	60.784	47.826	0.00	0.00	0.00	4.94
1310	2276	2.666317	TGATCACGATCTGCTTAGGGA	58.334	47.619	8.43	0.00	38.60	4.20
1397	2363	6.117911	TGAATTGTGTGCCGATGTATTAAG	57.882	37.500	0.00	0.00	0.00	1.85
1411	2377	6.143118	CGATGTATTAAGAGCAGAAGCACTAC	59.857	42.308	0.00	0.00	40.96	2.73
1514	2482	4.280677	TGACACAATGAAAAATGGAGGACC	59.719	41.667	0.00	0.00	0.00	4.46
1550	2519	1.702299	CGGCAGTGTTCGACGATTC	59.298	57.895	0.00	0.00	0.00	2.52
1662	2632	4.330347	GCGAAATTTTCTGAGACTAGGGAC	59.670	45.833	7.50	0.00	0.00	4.46
1677	2647	2.665603	GACTGGTGTGAGGAGCCC	59.334	66.667	0.00	0.00	0.00	5.19
1795	2768	9.856162	ACCAGTTTTAAAGGTTGTCTTATTAGA	57.144	29.630	0.00	0.00	34.78	2.10
1857	2830	2.280797	CCATACATCCACGGCCGG	60.281	66.667	31.76	18.27	0.00	6.13
1858	2831	2.972505	CATACATCCACGGCCGGC	60.973	66.667	31.76	21.18	0.00	6.13
1859	2832	3.475494	ATACATCCACGGCCGGCA	61.475	61.111	31.76	13.20	0.00	5.69
1860	2833	3.037686	ATACATCCACGGCCGGCAA	62.038	57.895	31.76	14.41	0.00	4.52
1861	2834	3.961838	TACATCCACGGCCGGCAAC	62.962	63.158	31.76	11.20	0.00	4.17
1863	2836	4.344865	ATCCACGGCCGGCAACTT	62.345	61.111	31.76	3.35	0.00	2.66
1866	2839	3.591835	CACGGCCGGCAACTTGTT	61.592	61.111	31.76	0.57	0.00	2.83
1868	2841	4.341502	CGGCCGGCAACTTGTTGG	62.342	66.667	30.85	0.93	0.00	3.77
1885	2858	2.650116	GGCTCCTCCAAGTCTCGCA	61.650	63.158	0.00	0.00	34.01	5.10
1886	2859	1.519719	GCTCCTCCAAGTCTCGCAT	59.480	57.895	0.00	0.00	0.00	4.73
1887	2860	0.809241	GCTCCTCCAAGTCTCGCATG	60.809	60.000	0.00	0.00	0.00	4.06
1888	2861	0.534412	CTCCTCCAAGTCTCGCATGT	59.466	55.000	0.00	0.00	0.00	3.21
1913	2886	5.219739	ACTGAAGGAAATATGCCCTAGAGA	58.780	41.667	0.00	0.00	31.36	3.10
2038	3013	7.997773	AGACAAACAGAGTGTCACTAGTATA	57.002	36.000	5.21	0.00	46.44	1.47
2075	3051	4.872691	AGCTCGTTGATCAAAGATGGTTAG	59.127	41.667	21.83	11.77	0.00	2.34
2107	3083	7.701539	AGCCATAAACATGAGTTGTCATTTA	57.298	32.000	0.00	0.00	40.84	1.40
2250	3227	5.221722	TGACTATGAGATTATGCAACTCCCC	60.222	44.000	0.00	0.00	0.00	4.81
2256	3233	5.132648	TGAGATTATGCAACTCCCCAATACT	59.867	40.000	0.00	0.00	0.00	2.12
2361	3339	4.200838	TGTTGAGTTGGCATAGATCGAA	57.799	40.909	0.00	0.00	0.00	3.71
2379	3357	6.477033	AGATCGAAATTAGGATTTGTCACTCG	59.523	38.462	0.00	0.00	35.65	4.18
2496	3476	9.270640	GATGCATTACAGAATGAGTAAAGAGAT	57.729	33.333	0.00	0.00	44.59	2.75
2658	3638	2.514824	GAGCATCCAGGTTCCGCC	60.515	66.667	0.00	0.00	37.58	6.13
2707	3687	5.190677	TCGGTCATGTCTACATAGTTCTCA	58.809	41.667	0.00	0.00	34.26	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	5.689068	GCTCAACTTTGGCTATGAAATATGC	59.311	40.000	0.00	0.00	0.00	3.14
143	144	9.433153	ACAATATGTGCATAAGATGACTAGATG	57.567	33.333	0.00	0.00	0.00	2.90
162	168	6.073369	CGTTCAAGTCAGACAACACAATATG	58.927	40.000	2.66	0.00	0.00	1.78
220	226	6.921857	GCTACAACTTTAGCGAAGATACCATA	59.078	38.462	9.44	0.00	38.77	2.74
222	228	5.107133	GCTACAACTTTAGCGAAGATACCA	58.893	41.667	9.44	0.00	38.77	3.25
223	229	5.638660	GCTACAACTTTAGCGAAGATACC	57.361	43.478	9.44	0.00	38.77	2.73
260	1119	7.757624	GCGTGTCCAATAAATCCATTTTTCTAA	59.242	33.333	0.00	0.00	0.00	2.10
284	1145	2.919666	AAAAATCCACAGAATCGGCG	57.080	45.000	0.00	0.00	0.00	6.46
296	1157	4.956085	ACCCTTGCACTGTTTAAAAATCC	58.044	39.130	0.00	0.00	0.00	3.01
475	1343	5.206587	GTGTGTTTCCTCTAGTCCCCTATA	58.793	45.833	0.00	0.00	0.00	1.31
564	1432	2.346803	GTTTCTCTGGTTCGCTATGCA	58.653	47.619	0.00	0.00	0.00	3.96
572	1440	5.163561	TGTGATTGTTTGGTTTCTCTGGTTC	60.164	40.000	0.00	0.00	0.00	3.62
609	1477	9.912634	TTATTTGAAATCTTCAGTTTGATGGAC	57.087	29.630	0.00	0.00	41.38	4.02
636	1504	6.202188	GTGTCTTTACCGTGAATACATATGGG	59.798	42.308	7.80	0.00	0.00	4.00
637	1505	6.074516	CGTGTCTTTACCGTGAATACATATGG	60.075	42.308	7.80	0.00	0.00	2.74
638	1506	6.693978	TCGTGTCTTTACCGTGAATACATATG	59.306	38.462	0.00	0.00	0.00	1.78
639	1507	6.798482	TCGTGTCTTTACCGTGAATACATAT	58.202	36.000	0.00	0.00	0.00	1.78
640	1508	6.193514	TCGTGTCTTTACCGTGAATACATA	57.806	37.500	0.00	0.00	0.00	2.29
641	1509	5.063180	TCGTGTCTTTACCGTGAATACAT	57.937	39.130	0.00	0.00	0.00	2.29
642	1510	4.478699	CTCGTGTCTTTACCGTGAATACA	58.521	43.478	0.00	0.00	0.00	2.29
643	1511	3.302699	GCTCGTGTCTTTACCGTGAATAC	59.697	47.826	0.00	0.00	0.00	1.89
644	1512	3.057386	TGCTCGTGTCTTTACCGTGAATA	60.057	43.478	0.00	0.00	0.00	1.75
645	1513	2.288579	TGCTCGTGTCTTTACCGTGAAT	60.289	45.455	0.00	0.00	0.00	2.57
646	1514	1.067364	TGCTCGTGTCTTTACCGTGAA	59.933	47.619	0.00	0.00	0.00	3.18
647	1515	0.669619	TGCTCGTGTCTTTACCGTGA	59.330	50.000	0.00	0.00	0.00	4.35
648	1516	0.782384	GTGCTCGTGTCTTTACCGTG	59.218	55.000	0.00	0.00	0.00	4.94
649	1517	0.319297	GGTGCTCGTGTCTTTACCGT	60.319	55.000	0.00	0.00	0.00	4.83
650	1518	0.319211	TGGTGCTCGTGTCTTTACCG	60.319	55.000	0.00	0.00	0.00	4.02
651	1519	1.732259	CATGGTGCTCGTGTCTTTACC	59.268	52.381	0.00	0.00	0.00	2.85
652	1520	2.413837	ACATGGTGCTCGTGTCTTTAC	58.586	47.619	0.00	0.00	41.45	2.01
653	1521	2.805671	CAACATGGTGCTCGTGTCTTTA	59.194	45.455	0.00	0.00	44.25	1.85
654	1522	1.603802	CAACATGGTGCTCGTGTCTTT	59.396	47.619	0.00	0.00	44.25	2.52
655	1523	1.202639	TCAACATGGTGCTCGTGTCTT	60.203	47.619	5.66	0.00	44.25	3.01
656	1524	0.392706	TCAACATGGTGCTCGTGTCT	59.607	50.000	5.66	0.00	44.25	3.41
657	1525	0.512952	GTCAACATGGTGCTCGTGTC	59.487	55.000	5.66	0.00	44.25	3.67
658	1526	0.884704	GGTCAACATGGTGCTCGTGT	60.885	55.000	5.66	0.69	46.77	4.49
659	1527	1.868997	GGTCAACATGGTGCTCGTG	59.131	57.895	5.66	0.00	38.32	4.35
660	1528	1.667830	CGGTCAACATGGTGCTCGT	60.668	57.895	5.66	0.00	0.00	4.18
661	1529	2.390599	CCGGTCAACATGGTGCTCG	61.391	63.158	5.66	11.88	0.00	5.03
662	1530	1.302511	ACCGGTCAACATGGTGCTC	60.303	57.895	5.66	1.34	33.91	4.26
663	1531	1.600636	CACCGGTCAACATGGTGCT	60.601	57.895	2.59	0.00	45.85	4.40
664	1532	2.953821	CACCGGTCAACATGGTGC	59.046	61.111	2.59	0.81	45.85	5.01
679	1547	0.534203	TCCTCCGAAGTTTGTGCCAC	60.534	55.000	0.00	0.00	0.00	5.01
707	1575	1.691196	CCCCTCTTTTGAAGTGTGCA	58.309	50.000	0.00	0.00	0.00	4.57
717	1585	0.772124	TGTGCCTCTCCCCCTCTTTT	60.772	55.000	0.00	0.00	0.00	2.27
731	1599	2.665603	GTCCTCCCTGACTGTGCC	59.334	66.667	0.00	0.00	32.39	5.01
786	1658	4.773013	ACCGAAGTTCTACCAACAGAAAA	58.227	39.130	0.56	0.00	36.34	2.29
865	1737	9.507329	ACACACTTCAATACATTTCAAGTCTAT	57.493	29.630	0.00	0.00	0.00	1.98
868	1740	9.944663	TTTACACACTTCAATACATTTCAAGTC	57.055	29.630	0.00	0.00	0.00	3.01
970	1842	4.160329	TCTTCTATTCCTCCTGTGTGTGT	58.840	43.478	0.00	0.00	0.00	3.72
1036	1908	3.955471	TCCTAAAAAGAGGCATGGTCAG	58.045	45.455	0.00	0.00	36.45	3.51
1058	1930	8.698973	TTACATTTAGAGCAGCTCTAGTAGAT	57.301	34.615	27.42	18.26	42.92	1.98
1065	1937	5.046304	TGTCCTTTACATTTAGAGCAGCTCT	60.046	40.000	28.02	28.02	37.63	4.09
1071	1943	5.064707	TCGCATTGTCCTTTACATTTAGAGC	59.935	40.000	0.00	0.00	38.10	4.09
1091	1963	3.068165	CACCATAGATACCAAGTCTCGCA	59.932	47.826	0.00	0.00	0.00	5.10
1094	1966	4.223953	TCCCACCATAGATACCAAGTCTC	58.776	47.826	0.00	0.00	0.00	3.36
1138	2011	4.392047	TGATGTGCATCTTGAGACTTTGT	58.608	39.130	12.64	0.00	38.60	2.83
1139	2012	5.366829	TTGATGTGCATCTTGAGACTTTG	57.633	39.130	12.64	0.00	38.60	2.77
1397	2363	3.181480	CCTTAGAGGTAGTGCTTCTGCTC	60.181	52.174	3.01	0.00	40.48	4.26
1411	2377	5.117406	AGGATTAAGCCAAACCTTAGAGG	57.883	43.478	13.21	0.00	36.00	3.69
1587	2556	5.811399	TTGCTTCCCTATTACAATGTTCG	57.189	39.130	0.00	0.00	0.00	3.95
1650	2620	1.427753	TCACACCAGTCCCTAGTCTCA	59.572	52.381	0.00	0.00	0.00	3.27
1662	2632	1.077930	CATGGGCTCCTCACACCAG	60.078	63.158	0.00	0.00	36.27	4.00
1761	2734	8.301252	ACAACCTTTAAAACTGGTTACATCTT	57.699	30.769	9.36	0.00	41.57	2.40
1762	2735	7.778382	AGACAACCTTTAAAACTGGTTACATCT	59.222	33.333	9.36	9.74	41.57	2.90
1763	2736	7.937649	AGACAACCTTTAAAACTGGTTACATC	58.062	34.615	9.36	8.17	41.57	3.06
1769	2742	9.856162	TCTAATAAGACAACCTTTAAAACTGGT	57.144	29.630	0.00	0.00	36.34	4.00
1811	2784	5.807730	CGTGTGGCGTCTATAATTTAGAG	57.192	43.478	0.00	0.00	35.54	2.43
1833	2806	1.151777	CGTGGATGTATGGACGGCAC	61.152	60.000	0.00	0.00	0.00	5.01
1836	2809	4.750460	CCGTGGATGTATGGACGG	57.250	61.111	0.00	0.00	44.86	4.79
1857	2830	0.823356	TGGAGGAGCCAACAAGTTGC	60.823	55.000	1.81	3.80	45.87	4.17
1858	2831	3.419793	TGGAGGAGCCAACAAGTTG	57.580	52.632	0.00	0.00	45.87	3.16
1868	2841	0.809241	CATGCGAGACTTGGAGGAGC	60.809	60.000	0.00	0.00	0.00	4.70
1882	2855	4.787563	GCATATTTCCTTCAGTCACATGCG	60.788	45.833	0.00	0.00	0.00	4.73
1885	2858	4.079558	AGGGCATATTTCCTTCAGTCACAT	60.080	41.667	0.00	0.00	0.00	3.21
1886	2859	3.266772	AGGGCATATTTCCTTCAGTCACA	59.733	43.478	0.00	0.00	0.00	3.58
1887	2860	3.891049	AGGGCATATTTCCTTCAGTCAC	58.109	45.455	0.00	0.00	0.00	3.67
1888	2861	4.968719	TCTAGGGCATATTTCCTTCAGTCA	59.031	41.667	0.00	0.00	34.75	3.41
2038	3013	3.353370	ACGAGCTAGTCAAGTAGAGGT	57.647	47.619	0.00	0.00	0.00	3.85
2075	3051	5.193679	ACTCATGTTTATGGCTAGGAAACC	58.806	41.667	7.60	0.00	34.97	3.27
2107	3083	8.672329	TCTCCTAATGATGTGATCCCATTTATT	58.328	33.333	0.00	0.45	33.21	1.40
2113	3089	5.608015	TCATTCTCCTAATGATGTGATCCCA	59.392	40.000	0.00	0.00	32.21	4.37
2250	3227	6.208644	CACAAAAAGTGTTCCTCCAGTATTG	58.791	40.000	0.00	0.00	43.40	1.90
2361	3339	7.687941	ACAATTCGAGTGACAAATCCTAATT	57.312	32.000	5.29	0.00	0.00	1.40
2379	3357	4.261825	CCAGAGATACCTCTCCGACAATTC	60.262	50.000	0.00	0.00	46.38	2.17
2496	3476	2.459060	TCAATCTCGTTACCGGCAAA	57.541	45.000	0.00	0.00	33.95	3.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.