AutoCloner

Multiple sequence alignment - TraesCS7A01G166400

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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	TraesCS7A01G166400	chr7A	100.000	2222	0	0	1	2222	121912003	121914224	0.000000e+00	4104.0
1	TraesCS7A01G166400	chr7A	98.367	796	12	1	1	796	13137507	13136713	0.000000e+00	1397.0
2	TraesCS7A01G166400	chr7A	97.362	796	21	0	1	796	220115258	220114463	0.000000e+00	1354.0
3	TraesCS7A01G166400	chr7A	96.231	796	30	0	1	796	59391601	59390806	0.000000e+00	1304.0
4	TraesCS7A01G166400	chr7A	80.093	432	78	7	1562	1991	734925943	734925518	4.610000e-82	315.0
5	TraesCS7A01G166400	chr3B	98.367	796	13	0	1	796	310864357	310863562	0.000000e+00	1399.0
6	TraesCS7A01G166400	chr3A	97.625	800	18	1	1	800	23266974	23267772	0.000000e+00	1371.0
7	TraesCS7A01G166400	chr6A	97.491	797	19	1	1	796	410321364	410320568	0.000000e+00	1360.0
8	TraesCS7A01G166400	chr6A	100.000	28	0	0	1196	1223	35929124	35929097	4.000000e-03	52.8
9	TraesCS7A01G166400	chr1A	97.362	796	20	1	1	796	292580282	292579488	0.000000e+00	1352.0
10	TraesCS7A01G166400	chr5A	97.118	798	22	1	1	797	184235805	184235008	0.000000e+00	1345.0
11	TraesCS7A01G166400	chr2A	96.992	798	22	2	1	796	695650874	695651671	0.000000e+00	1339.0
12	TraesCS7A01G166400	chr7D	93.822	696	31	8	806	1500	117522955	117523639	0.000000e+00	1037.0
13	TraesCS7A01G166400	chr7D	82.215	641	108	6	1585	2222	19282349	19281712	4.170000e-152	547.0
14	TraesCS7A01G166400	chr7D	79.190	716	117	16	1513	2222	62255605	62256294	3.340000e-128	468.0
15	TraesCS7A01G166400	chr7D	79.213	712	117	17	1513	2219	62232709	62233394	1.200000e-127	466.0
16	TraesCS7A01G166400	chr7D	80.615	423	79	3	1513	1933	170560357	170560778	7.650000e-85	324.0
17	TraesCS7A01G166400	chr7B	88.525	427	37	11	913	1332	78062972	78063393	7.080000e-140	507.0
18	TraesCS7A01G166400	chr1D	81.655	556	96	4	1513	2063	17018922	17019476	7.230000e-125	457.0
19	TraesCS7A01G166400	chr4A	78.242	694	133	18	1512	2197	688515799	688516482	1.580000e-116	429.0
20	TraesCS7A01G166400	chr4A	79.713	488	85	11	1513	1994	72971895	72972374	7.600000e-90	340.0
21	TraesCS7A01G166400	chr5B	79.500	600	112	8	1514	2105	89304130	89303534	1.230000e-112	416.0
22	TraesCS7A01G166400	chr5D	81.579	380	68	2	1834	2212	23651439	23651817	1.660000e-81	313.0
23	TraesCS7A01G166400	chr6D	78.689	488	83	13	1513	1995	356601554	356602025	2.770000e-79	305.0
24	TraesCS7A01G166400	chr6D	97.674	43	1	0	1288	1330	33434437	33434479	8.510000e-10	75.0
25	TraesCS7A01G166400	chr6B	77.672	524	90	22	1505	2014	45547047	45546537	6.000000e-76	294.0
26	TraesCS7A01G166400	chrUn	94.118	34	2	0	1190	1223	100575727	100575760	4.000000e-03	52.8
27	TraesCS7A01G166400	chrUn	94.118	34	2	0	1190	1223	100705829	100705862	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	TraesCS7A01G166400	chr7A	121912003	121914224	2221	False	4104	4104	100.000	1	2222	1	chr7A.!!$F1	2221
1	TraesCS7A01G166400	chr7A	13136713	13137507	794	True	1397	1397	98.367	1	796	1	chr7A.!!$R1	795
2	TraesCS7A01G166400	chr7A	220114463	220115258	795	True	1354	1354	97.362	1	796	1	chr7A.!!$R3	795
3	TraesCS7A01G166400	chr7A	59390806	59391601	795	True	1304	1304	96.231	1	796	1	chr7A.!!$R2	795
4	TraesCS7A01G166400	chr3B	310863562	310864357	795	True	1399	1399	98.367	1	796	1	chr3B.!!$R1	795
5	TraesCS7A01G166400	chr3A	23266974	23267772	798	False	1371	1371	97.625	1	800	1	chr3A.!!$F1	799
6	TraesCS7A01G166400	chr6A	410320568	410321364	796	True	1360	1360	97.491	1	796	1	chr6A.!!$R2	795
7	TraesCS7A01G166400	chr1A	292579488	292580282	794	True	1352	1352	97.362	1	796	1	chr1A.!!$R1	795
8	TraesCS7A01G166400	chr5A	184235008	184235805	797	True	1345	1345	97.118	1	797	1	chr5A.!!$R1	796
9	TraesCS7A01G166400	chr2A	695650874	695651671	797	False	1339	1339	96.992	1	796	1	chr2A.!!$F1	795
10	TraesCS7A01G166400	chr7D	117522955	117523639	684	False	1037	1037	93.822	806	1500	1	chr7D.!!$F3	694
11	TraesCS7A01G166400	chr7D	19281712	19282349	637	True	547	547	82.215	1585	2222	1	chr7D.!!$R1	637
12	TraesCS7A01G166400	chr7D	62255605	62256294	689	False	468	468	79.190	1513	2222	1	chr7D.!!$F2	709
13	TraesCS7A01G166400	chr7D	62232709	62233394	685	False	466	466	79.213	1513	2219	1	chr7D.!!$F1	706
14	TraesCS7A01G166400	chr1D	17018922	17019476	554	False	457	457	81.655	1513	2063	1	chr1D.!!$F1	550
15	TraesCS7A01G166400	chr4A	688515799	688516482	683	False	429	429	78.242	1512	2197	1	chr4A.!!$F2	685
16	TraesCS7A01G166400	chr5B	89303534	89304130	596	True	416	416	79.500	1514	2105	1	chr5B.!!$R1	591
17	TraesCS7A01G166400	chr6B	45546537	45547047	510	True	294	294	77.672	1505	2014	1	chr6B.!!$R1	509

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
988	994	0.317103	CACTGACCGTCCGATCGATC	60.317	60.0	18.66	15.68	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1969	1988	0.593618	GACGACAGTGAGTCTCTGCA	59.406	55.0	19.62	0.0	45.32	4.41	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
132	134	2.742348	TGAATTCATGCTCCAGCCAAT	58.258	42.857	3.38	0.00	41.18	3.16
224	227	7.063780	TCACGTTTAGGCTTATTTAGTGCTTAC	59.936	37.037	0.00	0.00	0.00	2.34
238	241	5.262588	AGTGCTTACATGTGTGATCGATA	57.737	39.130	9.11	0.00	0.00	2.92
287	290	0.893727	GCGTTGGTGGGGTCTTGAAT	60.894	55.000	0.00	0.00	0.00	2.57
800	806	3.635373	CACGGGCATTCTACTAGTTCCTA	59.365	47.826	0.00	0.00	0.00	2.94
801	807	4.281182	CACGGGCATTCTACTAGTTCCTAT	59.719	45.833	0.00	0.00	0.00	2.57
802	808	4.281182	ACGGGCATTCTACTAGTTCCTATG	59.719	45.833	0.00	1.90	0.00	2.23
803	809	4.523173	CGGGCATTCTACTAGTTCCTATGA	59.477	45.833	0.00	0.00	0.00	2.15
804	810	5.186021	CGGGCATTCTACTAGTTCCTATGAT	59.814	44.000	0.00	0.00	0.00	2.45
805	811	6.295349	CGGGCATTCTACTAGTTCCTATGATT	60.295	42.308	0.00	0.00	0.00	2.57
806	812	7.454225	GGGCATTCTACTAGTTCCTATGATTT	58.546	38.462	0.00	0.00	0.00	2.17
807	813	7.939588	GGGCATTCTACTAGTTCCTATGATTTT	59.060	37.037	0.00	0.00	0.00	1.82
808	814	9.998106	GGCATTCTACTAGTTCCTATGATTTTA	57.002	33.333	0.00	0.00	0.00	1.52
822	828	9.976511	TCCTATGATTTTATACTACAACGGAAG	57.023	33.333	0.00	0.00	0.00	3.46
867	873	2.582436	GGGCGACAAATCCGAGGA	59.418	61.111	0.00	0.00	0.00	3.71
925	931	2.054232	AGCAAGCATCCATCAGAAGG	57.946	50.000	0.00	0.00	0.00	3.46
964	970	2.093973	TCCGAGATTCAAGCACTCCTTC	60.094	50.000	0.00	0.00	0.00	3.46
965	971	2.275318	CGAGATTCAAGCACTCCTTCC	58.725	52.381	0.00	0.00	0.00	3.46
966	972	2.093764	CGAGATTCAAGCACTCCTTCCT	60.094	50.000	0.00	0.00	0.00	3.36
967	973	3.618507	CGAGATTCAAGCACTCCTTCCTT	60.619	47.826	0.00	0.00	0.00	3.36
988	994	0.317103	CACTGACCGTCCGATCGATC	60.317	60.000	18.66	15.68	0.00	3.69
990	996	1.153025	TGACCGTCCGATCGATCCT	60.153	57.895	18.66	0.00	0.00	3.24
993	999	0.384669	ACCGTCCGATCGATCCTTTC	59.615	55.000	18.66	7.07	0.00	2.62
1098	1104	2.428569	CACGACAGGTCCGACGTG	60.429	66.667	17.60	17.60	46.78	4.49
1110	1116	2.202756	GACGTGGCCATCGAGGTC	60.203	66.667	27.07	17.42	44.53	3.85
1198	1204	4.316823	AGTCCCAGGGCCTCGTCA	62.317	66.667	0.95	0.00	0.00	4.35
1276	1282	4.702831	TGCCGATCTGAATAATGTTGCTA	58.297	39.130	0.00	0.00	0.00	3.49
1279	1285	4.452455	CCGATCTGAATAATGTTGCTACCC	59.548	45.833	0.00	0.00	0.00	3.69
1283	1289	6.061022	TCTGAATAATGTTGCTACCCTTCA	57.939	37.500	0.00	0.00	0.00	3.02
1303	1309	2.485426	CAGTTGTGTTCCCTAGTGCATG	59.515	50.000	0.00	0.00	0.00	4.06
1338	1344	1.608590	ACCGTCTTCCATGCTTTGTTG	59.391	47.619	0.00	0.00	0.00	3.33
1365	1371	3.193479	GCTTAACTGGCTTGCCTATGTTT	59.807	43.478	13.18	1.98	0.00	2.83
1406	1412	4.789095	GCGAATCAGCGATAAACCTTTA	57.211	40.909	0.00	0.00	0.00	1.85
1410	1416	6.411652	CGAATCAGCGATAAACCTTTACTTC	58.588	40.000	0.00	0.00	0.00	3.01
1412	1418	4.178540	TCAGCGATAAACCTTTACTTCCG	58.821	43.478	0.00	0.00	0.00	4.30
1420	1426	7.970614	CGATAAACCTTTACTTCCGTAACTACT	59.029	37.037	0.00	0.00	35.44	2.57
1421	1427	9.295214	GATAAACCTTTACTTCCGTAACTACTC	57.705	37.037	0.00	0.00	35.44	2.59
1422	1428	5.651387	ACCTTTACTTCCGTAACTACTCC	57.349	43.478	0.00	0.00	35.44	3.85
1423	1429	5.079643	ACCTTTACTTCCGTAACTACTCCA	58.920	41.667	0.00	0.00	35.44	3.86
1424	1430	5.047731	ACCTTTACTTCCGTAACTACTCCAC	60.048	44.000	0.00	0.00	35.44	4.02
1425	1431	5.047802	CCTTTACTTCCGTAACTACTCCACA	60.048	44.000	0.00	0.00	35.44	4.17
1426	1432	5.633830	TTACTTCCGTAACTACTCCACAG	57.366	43.478	0.00	0.00	30.92	3.66
1429	1435	2.440409	TCCGTAACTACTCCACAGACC	58.560	52.381	0.00	0.00	0.00	3.85
1430	1436	2.165167	CCGTAACTACTCCACAGACCA	58.835	52.381	0.00	0.00	0.00	4.02
1431	1437	2.094854	CCGTAACTACTCCACAGACCAC	60.095	54.545	0.00	0.00	0.00	4.16
1432	1438	2.555325	CGTAACTACTCCACAGACCACA	59.445	50.000	0.00	0.00	0.00	4.17
1433	1439	3.366070	CGTAACTACTCCACAGACCACAG	60.366	52.174	0.00	0.00	0.00	3.66
1434	1440	2.383442	ACTACTCCACAGACCACAGT	57.617	50.000	0.00	0.00	0.00	3.55
1435	1441	3.520691	ACTACTCCACAGACCACAGTA	57.479	47.619	0.00	0.00	0.00	2.74
1465	1471	5.963004	CGTGAGTTGAAAGTTGAAATTCGAA	59.037	36.000	0.00	0.00	0.00	3.71
1483	1489	8.452989	AATTCGAAATGTAGTTGAAAGAATGC	57.547	30.769	0.00	0.00	0.00	3.56
1492	1498	7.161404	TGTAGTTGAAAGAATGCAGTGTAGAT	58.839	34.615	0.00	0.00	0.00	1.98
1500	1506	6.090483	AGAATGCAGTGTAGATACGCTATT	57.910	37.500	5.78	4.02	44.53	1.73
1501	1507	6.516718	AGAATGCAGTGTAGATACGCTATTT	58.483	36.000	5.78	1.37	44.53	1.40
1502	1508	6.986817	AGAATGCAGTGTAGATACGCTATTTT	59.013	34.615	5.78	1.07	44.53	1.82
1503	1509	7.495934	AGAATGCAGTGTAGATACGCTATTTTT	59.504	33.333	5.78	0.00	44.53	1.94
1543	1549	2.844362	CCCCGGCCTCTGCATCTA	60.844	66.667	0.00	0.00	40.13	1.98
1549	1555	0.031449	GGCCTCTGCATCTAGACGAC	59.969	60.000	0.00	0.00	40.13	4.34
1554	1560	2.218603	TCTGCATCTAGACGACGCATA	58.781	47.619	0.00	0.00	31.10	3.14
1555	1561	2.814336	TCTGCATCTAGACGACGCATAT	59.186	45.455	0.00	0.00	31.10	1.78
1661	1670	9.988815	ATCGCTACTCTTATTTACTTGATGAAT	57.011	29.630	0.00	0.00	0.00	2.57
1663	1672	9.249457	CGCTACTCTTATTTACTTGATGAATGA	57.751	33.333	0.00	0.00	0.00	2.57
1677	1686	4.874396	TGATGAATGAGTGCAGATTGTCTC	59.126	41.667	0.00	0.00	0.00	3.36
1691	1703	1.855295	TGTCTCAGCCGTATACCCAA	58.145	50.000	0.00	0.00	0.00	4.12
1700	1712	2.420967	GCCGTATACCCAAACCTCACAT	60.421	50.000	0.00	0.00	0.00	3.21
1719	1732	9.003658	CCTCACATCAAAGACTAACATTAAAGT	57.996	33.333	0.00	0.00	0.00	2.66
1737	1750	3.966543	CGGAGGCCCCAACCAAGT	61.967	66.667	0.00	0.00	34.14	3.16
1810	1823	3.763356	ATGCGTCCGCTGCAGAGA	61.763	61.111	20.43	10.62	46.98	3.10
1820	1833	1.593787	CTGCAGAGACCGTCACCAT	59.406	57.895	8.42	0.00	0.00	3.55
1828	1841	0.526662	GACCGTCACCATCGTCTTCT	59.473	55.000	0.00	0.00	0.00	2.85
1836	1849	2.357952	CACCATCGTCTTCTACCGATCA	59.642	50.000	0.00	0.00	41.54	2.92
1869	1885	5.247564	AGCAGGTACTAACACATCAACCTTA	59.752	40.000	0.00	0.00	36.02	2.69
1884	1902	2.925706	TTACCAGGCCTGCCGTCA	60.926	61.111	28.39	9.58	41.95	4.35
1899	1917	1.959226	GTCAACGCCACCATGACGT	60.959	57.895	0.00	0.00	42.81	4.34
1902	1920	1.227704	AACGCCACCATGACGTCAA	60.228	52.632	24.13	6.23	39.49	3.18
1933	1952	1.448540	CCCTGTGCGAGTCCATCAC	60.449	63.158	0.00	0.00	0.00	3.06
1939	1958	1.153549	GCGAGTCCATCACCTCACC	60.154	63.158	0.00	0.00	0.00	4.02
1956	1975	3.812019	CTCCGTCACCGAGACCCG	61.812	72.222	2.96	0.00	44.66	5.28
1969	1988	4.096003	ACCCGGCTACGCAATGCT	62.096	61.111	2.94	0.00	39.22	3.79
2058	2078	1.345415	CTGCTCCAAAACAATGCCCTT	59.655	47.619	0.00	0.00	0.00	3.95
2076	2096	2.028130	CTTATGAGGGAGAGCGACACT	58.972	52.381	0.00	0.00	0.00	3.55
2099	2119	3.202001	CGCCGCCATCGTCCAATT	61.202	61.111	0.00	0.00	0.00	2.32
2126	2146	1.203492	ACCCAGATCTGAGGTTTCCCT	60.203	52.381	24.62	3.97	46.66	4.20
2144	2164	4.717629	CGGAACAGCGCGAGTGGA	62.718	66.667	12.10	0.00	0.00	4.02
2151	2171	0.382158	CAGCGCGAGTGGATAGAAGA	59.618	55.000	12.10	0.00	0.00	2.87
2197	2218	0.179145	AAGTAACGCGCGTAGATGCT	60.179	50.000	37.93	25.95	0.00	3.79
2204	2225	2.105128	GCGTAGATGCTGCCGTCT	59.895	61.111	9.20	9.20	40.38	4.18
2206	2227	1.730487	CGTAGATGCTGCCGTCTCT	59.270	57.895	7.77	2.91	38.30	3.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
224	227	6.743172	CCTACGTTCTATATCGATCACACATG	59.257	42.308	0.00	0.00	0.00	3.21
287	290	3.631250	ACAAGCCAAGAGGTCTTTTGAA	58.369	40.909	8.83	0.00	37.19	2.69
701	707	6.594159	GGTCATCTTTTATCTTCTCCACGAAA	59.406	38.462	0.00	0.00	0.00	3.46
800	806	8.500753	TTGCTTCCGTTGTAGTATAAAATCAT	57.499	30.769	0.00	0.00	0.00	2.45
801	807	7.908827	TTGCTTCCGTTGTAGTATAAAATCA	57.091	32.000	0.00	0.00	0.00	2.57
802	808	8.231837	TGTTTGCTTCCGTTGTAGTATAAAATC	58.768	33.333	0.00	0.00	0.00	2.17
803	809	8.101654	TGTTTGCTTCCGTTGTAGTATAAAAT	57.898	30.769	0.00	0.00	0.00	1.82
804	810	7.493743	TGTTTGCTTCCGTTGTAGTATAAAA	57.506	32.000	0.00	0.00	0.00	1.52
805	811	7.493743	TTGTTTGCTTCCGTTGTAGTATAAA	57.506	32.000	0.00	0.00	0.00	1.40
806	812	6.347888	GCTTGTTTGCTTCCGTTGTAGTATAA	60.348	38.462	0.00	0.00	0.00	0.98
807	813	5.121142	GCTTGTTTGCTTCCGTTGTAGTATA	59.879	40.000	0.00	0.00	0.00	1.47
808	814	4.083484	GCTTGTTTGCTTCCGTTGTAGTAT	60.083	41.667	0.00	0.00	0.00	2.12
809	815	3.249080	GCTTGTTTGCTTCCGTTGTAGTA	59.751	43.478	0.00	0.00	0.00	1.82
810	816	2.032924	GCTTGTTTGCTTCCGTTGTAGT	59.967	45.455	0.00	0.00	0.00	2.73
811	817	2.032799	TGCTTGTTTGCTTCCGTTGTAG	59.967	45.455	0.00	0.00	0.00	2.74
822	828	0.240411	CTCAGGAGCTGCTTGTTTGC	59.760	55.000	4.36	0.00	0.00	3.68
849	855	2.890474	CCTCGGATTTGTCGCCCG	60.890	66.667	0.00	0.00	44.22	6.13
886	892	3.531538	CTTATATACGAATGCGGCCCAT	58.468	45.455	0.00	0.00	43.17	4.00
895	901	7.105588	TGATGGATGCTTGCTTATATACGAAT	58.894	34.615	0.00	0.00	0.00	3.34
925	931	2.739932	CGGAGATGGATGTGGTTCTGAC	60.740	54.545	0.00	0.00	0.00	3.51
964	970	0.246635	ATCGGACGGTCAGTGAAAGG	59.753	55.000	10.76	0.00	0.00	3.11
965	971	1.630148	GATCGGACGGTCAGTGAAAG	58.370	55.000	10.76	0.00	0.00	2.62
966	972	0.109458	CGATCGGACGGTCAGTGAAA	60.109	55.000	7.38	0.00	0.00	2.69
967	973	0.956902	TCGATCGGACGGTCAGTGAA	60.957	55.000	16.41	0.00	0.00	3.18
988	994	1.137404	CGGCCATTTCAGCGAAAGG	59.863	57.895	2.24	8.60	34.92	3.11
990	996	2.988688	GCCGGCCATTTCAGCGAAA	61.989	57.895	18.11	6.26	35.94	3.46
1098	1104	3.551407	GGGAGGACCTCGATGGCC	61.551	72.222	15.46	4.04	40.22	5.36
1198	1204	2.758737	GACGACGGGGGTCCTGAT	60.759	66.667	0.00	0.00	33.36	2.90
1260	1266	6.061022	TGAAGGGTAGCAACATTATTCAGA	57.939	37.500	0.00	0.00	0.00	3.27
1276	1282	1.222567	AGGGAACACAACTGAAGGGT	58.777	50.000	0.00	0.00	0.00	4.34
1279	1285	2.808543	GCACTAGGGAACACAACTGAAG	59.191	50.000	0.00	0.00	0.00	3.02
1283	1289	2.783135	CATGCACTAGGGAACACAACT	58.217	47.619	0.00	0.00	0.00	3.16
1303	1309	1.661112	GACGGTACTTCTGCATCAAGC	59.339	52.381	5.63	0.00	45.96	4.01
1320	1326	2.350772	GGTCAACAAAGCATGGAAGACG	60.351	50.000	0.00	0.00	32.39	4.18
1357	1363	5.862924	AACACAATCGAGACAAACATAGG	57.137	39.130	0.00	0.00	0.00	2.57
1365	1371	2.131972	CGTCCAAACACAATCGAGACA	58.868	47.619	0.00	0.00	0.00	3.41
1410	1416	2.094854	GTGGTCTGTGGAGTAGTTACGG	60.095	54.545	0.00	0.00	0.00	4.02
1412	1418	3.573110	ACTGTGGTCTGTGGAGTAGTTAC	59.427	47.826	0.00	0.00	0.00	2.50
1420	1426	3.554129	CGTCATTTACTGTGGTCTGTGGA	60.554	47.826	0.00	0.00	0.00	4.02
1421	1427	2.736721	CGTCATTTACTGTGGTCTGTGG	59.263	50.000	0.00	0.00	0.00	4.17
1422	1428	3.184379	CACGTCATTTACTGTGGTCTGTG	59.816	47.826	0.00	0.00	32.50	3.66
1423	1429	3.069016	TCACGTCATTTACTGTGGTCTGT	59.931	43.478	0.00	0.00	35.04	3.41
1424	1430	3.649073	TCACGTCATTTACTGTGGTCTG	58.351	45.455	0.00	0.00	35.04	3.51
1425	1431	3.321111	ACTCACGTCATTTACTGTGGTCT	59.679	43.478	0.00	0.00	35.04	3.85
1426	1432	3.650139	ACTCACGTCATTTACTGTGGTC	58.350	45.455	0.00	0.00	35.04	4.02
1429	1435	5.651172	TTCAACTCACGTCATTTACTGTG	57.349	39.130	0.00	0.00	35.38	3.66
1430	1436	5.815740	ACTTTCAACTCACGTCATTTACTGT	59.184	36.000	0.00	0.00	0.00	3.55
1431	1437	6.287107	ACTTTCAACTCACGTCATTTACTG	57.713	37.500	0.00	0.00	0.00	2.74
1432	1438	6.537301	TCAACTTTCAACTCACGTCATTTACT	59.463	34.615	0.00	0.00	0.00	2.24
1433	1439	6.711579	TCAACTTTCAACTCACGTCATTTAC	58.288	36.000	0.00	0.00	0.00	2.01
1434	1440	6.912203	TCAACTTTCAACTCACGTCATTTA	57.088	33.333	0.00	0.00	0.00	1.40
1435	1441	5.811399	TCAACTTTCAACTCACGTCATTT	57.189	34.783	0.00	0.00	0.00	2.32
1460	1466	6.964908	TGCATTCTTTCAACTACATTTCGAA	58.035	32.000	0.00	0.00	0.00	3.71
1465	1471	6.639632	ACACTGCATTCTTTCAACTACATT	57.360	33.333	0.00	0.00	0.00	2.71
1543	1549	0.666913	AACGGCTATATGCGTCGTCT	59.333	50.000	6.90	0.00	44.05	4.18
1615	1623	7.834803	AGCGATAGATGTTATCAAGATGATGA	58.165	34.615	3.17	0.00	36.35	2.92
1635	1644	9.988815	ATTCATCAAGTAAATAAGAGTAGCGAT	57.011	29.630	0.00	0.00	0.00	4.58
1649	1658	6.656270	ACAATCTGCACTCATTCATCAAGTAA	59.344	34.615	0.00	0.00	0.00	2.24
1677	1686	1.208535	TGAGGTTTGGGTATACGGCTG	59.791	52.381	0.00	0.00	0.00	4.85
1691	1703	8.918202	TTAATGTTAGTCTTTGATGTGAGGTT	57.082	30.769	0.00	0.00	0.00	3.50
1700	1712	6.872020	CCTCCGACTTTAATGTTAGTCTTTGA	59.128	38.462	0.00	0.00	38.86	2.69
1719	1732	3.646715	CTTGGTTGGGGCCTCCGA	61.647	66.667	0.00	0.00	38.76	4.55
1737	1750	0.325933	CCTCAGACCTGGCATTGTGA	59.674	55.000	0.00	0.00	0.00	3.58
1798	1811	3.749064	GACGGTCTCTGCAGCGGA	61.749	66.667	9.47	3.23	41.63	5.54
1810	1823	1.471684	GTAGAAGACGATGGTGACGGT	59.528	52.381	0.00	0.00	34.93	4.83
1820	1833	4.638865	TGAAGATTGATCGGTAGAAGACGA	59.361	41.667	0.00	0.00	43.85	4.20
1828	1841	3.068732	CCTGCTCTGAAGATTGATCGGTA	59.931	47.826	0.00	0.00	0.00	4.02
1836	1849	5.246203	TGTGTTAGTACCTGCTCTGAAGATT	59.754	40.000	0.00	0.00	0.00	2.40
1869	1885	4.643387	GTTGACGGCAGGCCTGGT	62.643	66.667	33.46	23.54	0.00	4.00
1964	1983	1.347050	ACAGTGAGTCTCTGCAGCATT	59.653	47.619	19.62	0.00	36.50	3.56
1969	1988	0.593618	GACGACAGTGAGTCTCTGCA	59.406	55.000	19.62	0.00	45.32	4.41
1972	1991	1.735018	CATCGACGACAGTGAGTCTCT	59.265	52.381	16.84	0.00	45.32	3.10
2058	2078	1.064685	TCAGTGTCGCTCTCCCTCATA	60.065	52.381	0.00	0.00	0.00	2.15
2126	2146	4.717629	CCACTCGCGCTGTTCCGA	62.718	66.667	5.56	0.00	0.00	4.55
2144	2164	2.236766	GCCATTGCAGCCATCTTCTAT	58.763	47.619	0.00	0.00	37.47	1.98
2151	2171	3.125607	CATCGCCATTGCAGCCAT	58.874	55.556	0.00	0.00	37.32	4.40
2179	2199	0.866061	CAGCATCTACGCGCGTTACT	60.866	55.000	42.10	25.84	36.85	2.24
2197	2218	1.375908	GTCATGGCAAGAGACGGCA	60.376	57.895	0.00	0.00	43.74	5.69
2201	2222	1.204941	ACTACGGTCATGGCAAGAGAC	59.795	52.381	0.00	8.92	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.