AutoCloner

Multiple sequence alignment - TraesCS4A01G490100

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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	TraesCS4A01G490100	chr4A	100.000	2369	0	0	1	2369	740458249	740455881	0.000000e+00	4375.0
1	TraesCS4A01G490100	chr4A	95.151	928	42	1	1445	2369	741795905	741794978	0.000000e+00	1461.0
2	TraesCS4A01G490100	chr4A	95.043	928	43	1	1445	2369	741589050	741589977	0.000000e+00	1456.0
3	TraesCS4A01G490100	chr4A	94.967	914	43	1	1445	2355	740022105	740021192	0.000000e+00	1430.0
4	TraesCS4A01G490100	chr4A	93.959	927	53	1	1446	2369	739650677	739651603	0.000000e+00	1399.0
5	TraesCS4A01G490100	chr4A	93.851	927	54	1	1446	2369	741485579	741484653	0.000000e+00	1393.0
6	TraesCS4A01G490100	chr4A	93.420	927	58	1	1446	2369	742055956	742056882	0.000000e+00	1371.0
7	TraesCS4A01G490100	chr4A	91.581	487	35	1	876	1356	740022713	740022227	0.000000e+00	667.0
8	TraesCS4A01G490100	chr4A	89.571	489	45	1	878	1360	740268916	740269404	1.200000e-172	616.0
9	TraesCS4A01G490100	chr4A	89.474	494	43	3	876	1360	740926846	740927339	1.200000e-172	616.0
10	TraesCS4A01G490100	chr4A	89.366	489	46	1	878	1360	740346321	740346809	5.600000e-171	610.0
11	TraesCS4A01G490100	chr4A	89.366	489	43	3	878	1360	740303069	740303554	7.240000e-170	606.0
12	TraesCS4A01G490100	chr4A	89.139	488	48	3	876	1359	739860786	739861272	9.370000e-169	603.0
13	TraesCS4A01G490100	chr4A	76.800	625	81	40	527	1109	739920984	739920382	2.300000e-75	292.0
14	TraesCS4A01G490100	chr4A	84.663	163	18	5	360	518	739921829	739921670	3.150000e-34	156.0
15	TraesCS4A01G490100	chr4A	85.124	121	9	7	1305	1425	739861434	739861545	5.350000e-22	115.0
16	TraesCS4A01G490100	chr4A	85.124	121	9	7	1305	1425	740567424	740567535	5.350000e-22	115.0
17	TraesCS4A01G490100	chr7D	95.356	926	40	1	1447	2369	2611249	2610324	0.000000e+00	1469.0
18	TraesCS4A01G490100	chr7D	91.991	924	71	1	1446	2369	3788305	3787385	0.000000e+00	1293.0
19	TraesCS4A01G490100	chr7D	92.057	919	70	1	1451	2369	2358996	2358081	0.000000e+00	1290.0
20	TraesCS4A01G490100	chr7D	81.538	975	104	47	428	1366	2612361	2611427	0.000000e+00	734.0
21	TraesCS4A01G490100	chr7D	85.783	415	47	6	207	612	3896699	3897110	1.680000e-116	429.0
22	TraesCS4A01G490100	chr7D	87.578	161	10	3	49	209	3896363	3896513	6.730000e-41	178.0
23	TraesCS4A01G490100	chr7D	95.588	68	2	1	1368	1435	2611400	2611334	8.950000e-20	108.0
24	TraesCS4A01G490100	chr7D	95.833	48	1	1	1	48	3896331	3896377	2.520000e-10	76.8
25	TraesCS4A01G490100	chr7A	89.958	478	48	0	880	1357	3285340	3285817	3.350000e-173	617.0
26	TraesCS4A01G490100	chr7A	88.668	503	50	3	863	1359	3634709	3634208	7.240000e-170	606.0
27	TraesCS4A01G490100	chr7A	81.134	811	91	35	235	1021	3215215	3214443	5.640000e-166	593.0
28	TraesCS4A01G490100	chr7A	90.385	208	11	3	1	208	3215651	3215453	5.020000e-67	265.0
29	TraesCS4A01G490100	chr7A	93.805	113	5	2	58	170	2003604	2003494	4.050000e-38	169.0
30	TraesCS4A01G490100	chr7A	100.000	41	0	0	207	247	3215267	3215227	2.520000e-10	76.8
31	TraesCS4A01G490100	chr7B	95.238	42	2	0	404	445	708487069	708487028	1.520000e-07	67.6

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	TraesCS4A01G490100	chr4A	740455881	740458249	2368	True	4375.000000	4375	100.000000	1	2369	1	chr4A.!!$R1	2368
1	TraesCS4A01G490100	chr4A	741794978	741795905	927	True	1461.000000	1461	95.151000	1445	2369	1	chr4A.!!$R3	924
2	TraesCS4A01G490100	chr4A	741589050	741589977	927	False	1456.000000	1456	95.043000	1445	2369	1	chr4A.!!$F7	924
3	TraesCS4A01G490100	chr4A	739650677	739651603	926	False	1399.000000	1399	93.959000	1446	2369	1	chr4A.!!$F1	923
4	TraesCS4A01G490100	chr4A	741484653	741485579	926	True	1393.000000	1393	93.851000	1446	2369	1	chr4A.!!$R2	923
5	TraesCS4A01G490100	chr4A	742055956	742056882	926	False	1371.000000	1371	93.420000	1446	2369	1	chr4A.!!$F8	923
6	TraesCS4A01G490100	chr4A	740021192	740022713	1521	True	1048.500000	1430	93.274000	876	2355	2	chr4A.!!$R5	1479
7	TraesCS4A01G490100	chr4A	739860786	739861545	759	False	359.000000	603	87.131500	876	1425	2	chr4A.!!$F9	549
8	TraesCS4A01G490100	chr4A	739920382	739921829	1447	True	224.000000	292	80.731500	360	1109	2	chr4A.!!$R4	749
9	TraesCS4A01G490100	chr7D	3787385	3788305	920	True	1293.000000	1293	91.991000	1446	2369	1	chr7D.!!$R2	923
10	TraesCS4A01G490100	chr7D	2358081	2358996	915	True	1290.000000	1290	92.057000	1451	2369	1	chr7D.!!$R1	918
11	TraesCS4A01G490100	chr7D	2610324	2612361	2037	True	770.333333	1469	90.827333	428	2369	3	chr7D.!!$R3	1941
12	TraesCS4A01G490100	chr7D	3896331	3897110	779	False	227.933333	429	89.731333	1	612	3	chr7D.!!$F1	611
13	TraesCS4A01G490100	chr7A	3634208	3634709	501	True	606.000000	606	88.668000	863	1359	1	chr7A.!!$R2	496
14	TraesCS4A01G490100	chr7A	3214443	3215651	1208	True	311.600000	593	90.506333	1	1021	3	chr7A.!!$R3	1020

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
284	684	0.038599	TAGTACCGTGGCAGTCCTCA	59.961	55.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1937	3488	0.036875	GCTGGTACCACTTGAGCCTT	59.963	55.0	11.6	0.0	0.0	4.35	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
35	36	3.710722	CTCTGGCCCTGGAAGCGT	61.711	66.667	0.00	0.00	0.00	5.07
75	76	3.125316	GCGGTGACCTAGTCAGATTTTTG	59.875	47.826	0.00	0.00	43.57	2.44
82	83	9.654663	GTGACCTAGTCAGATTTTTGTATAGTT	57.345	33.333	0.00	0.00	43.57	2.24
166	167	1.662629	CTAGCCAAGACATCAAGCGTG	59.337	52.381	0.00	0.00	0.00	5.34
167	168	1.154150	GCCAAGACATCAAGCGTGC	60.154	57.895	0.00	0.00	0.00	5.34
168	169	1.855213	GCCAAGACATCAAGCGTGCA	61.855	55.000	0.00	0.00	0.00	4.57
169	170	0.110056	CCAAGACATCAAGCGTGCAC	60.110	55.000	6.82	6.82	0.00	4.57
170	171	0.587768	CAAGACATCAAGCGTGCACA	59.412	50.000	18.64	0.00	0.00	4.57
171	172	1.002576	CAAGACATCAAGCGTGCACAA	60.003	47.619	18.64	0.00	0.00	3.33
172	173	0.588252	AGACATCAAGCGTGCACAAC	59.412	50.000	18.64	8.30	0.00	3.32
173	174	0.588252	GACATCAAGCGTGCACAACT	59.412	50.000	18.64	10.75	0.00	3.16
284	684	0.038599	TAGTACCGTGGCAGTCCTCA	59.961	55.000	0.00	0.00	0.00	3.86
289	689	0.804989	CCGTGGCAGTCCTCATTTTC	59.195	55.000	0.00	0.00	0.00	2.29
380	784	2.441532	GCTCCATGTGCATGCCCT	60.442	61.111	16.68	0.00	37.49	5.19
451	856	7.279750	AGAGTCTCCTCGAAAGTAATAATCC	57.720	40.000	0.00	0.00	42.86	3.01
455	860	7.342284	AGTCTCCTCGAAAGTAATAATCCAAGA	59.658	37.037	0.00	0.00	0.00	3.02
458	863	7.046033	TCCTCGAAAGTAATAATCCAAGAACC	58.954	38.462	0.00	0.00	0.00	3.62
473	878	6.108015	TCCAAGAACCTACGCGTATTTTAAT	58.892	36.000	20.91	5.55	0.00	1.40
524	959	8.958506	GTACTACTACTCTTTCAAATCCAGAGA	58.041	37.037	2.46	0.00	37.97	3.10
550	1635	7.230027	AGATAAGAATCCAATGAGATTGTCCC	58.770	38.462	2.50	0.00	36.60	4.46
554	1639	3.198409	TCCAATGAGATTGTCCCATCG	57.802	47.619	0.00	0.00	38.59	3.84
577	1662	5.181245	CGGATTCCAGTGTTTGAAACTATGT	59.819	40.000	9.69	0.00	0.00	2.29
579	1664	7.065803	CGGATTCCAGTGTTTGAAACTATGTAT	59.934	37.037	9.69	4.30	0.00	2.29
614	1704	2.159296	GGCCAAGGTAATTAACAAGGCG	60.159	50.000	22.34	0.98	40.02	5.52
644	1735	2.748605	CCTAGCTAGGCAATCGACAAG	58.251	52.381	26.62	0.00	36.53	3.16
655	1746	0.459899	ATCGACAAGGACGCATAGCA	59.540	50.000	0.00	0.00	0.00	3.49
657	1748	1.679153	TCGACAAGGACGCATAGCATA	59.321	47.619	0.00	0.00	0.00	3.14
673	1774	6.347725	GCATAGCATACGAGGAATTAACAAGG	60.348	42.308	0.00	0.00	0.00	3.61
674	1775	5.353394	AGCATACGAGGAATTAACAAGGA	57.647	39.130	0.00	0.00	0.00	3.36
676	1777	5.128827	AGCATACGAGGAATTAACAAGGAGA	59.871	40.000	0.00	0.00	0.00	3.71
677	1778	5.992217	GCATACGAGGAATTAACAAGGAGAT	59.008	40.000	0.00	0.00	0.00	2.75
678	1779	6.073548	GCATACGAGGAATTAACAAGGAGATG	60.074	42.308	0.00	0.00	0.00	2.90
679	1780	5.422214	ACGAGGAATTAACAAGGAGATGT	57.578	39.130	0.00	0.00	34.24	3.06
680	1781	5.178797	ACGAGGAATTAACAAGGAGATGTG	58.821	41.667	0.00	0.00	32.81	3.21
681	1782	5.046591	ACGAGGAATTAACAAGGAGATGTGA	60.047	40.000	0.00	0.00	32.81	3.58
682	1783	5.292101	CGAGGAATTAACAAGGAGATGTGAC	59.708	44.000	0.00	0.00	32.81	3.67
683	1784	5.178797	AGGAATTAACAAGGAGATGTGACG	58.821	41.667	0.00	0.00	32.81	4.35
724	1825	1.980232	CCCACAGTGCCATGCATGT	60.980	57.895	24.58	4.09	41.91	3.21
725	1826	1.214325	CCACAGTGCCATGCATGTG	59.786	57.895	24.58	17.95	41.91	3.21
726	1827	1.245376	CCACAGTGCCATGCATGTGA	61.245	55.000	24.58	8.31	43.53	3.58
727	1828	0.815095	CACAGTGCCATGCATGTGAT	59.185	50.000	24.58	5.59	43.53	3.06
728	1829	0.815095	ACAGTGCCATGCATGTGATG	59.185	50.000	24.58	18.30	41.91	3.07
729	1830	0.815095	CAGTGCCATGCATGTGATGT	59.185	50.000	24.58	3.15	41.91	3.06
730	1831	0.815095	AGTGCCATGCATGTGATGTG	59.185	50.000	24.58	9.73	41.91	3.21
731	1832	0.812549	GTGCCATGCATGTGATGTGA	59.187	50.000	24.58	0.00	41.91	3.58
732	1833	1.407618	GTGCCATGCATGTGATGTGAT	59.592	47.619	24.58	0.00	41.91	3.06
733	1834	1.407258	TGCCATGCATGTGATGTGATG	59.593	47.619	24.58	7.60	31.71	3.07
734	1835	1.407618	GCCATGCATGTGATGTGATGT	59.592	47.619	24.58	0.00	0.00	3.06
735	1836	2.798145	GCCATGCATGTGATGTGATGTG	60.798	50.000	24.58	6.39	0.00	3.21
736	1837	2.685897	CCATGCATGTGATGTGATGTGA	59.314	45.455	24.58	0.00	0.00	3.58
737	1838	3.317993	CCATGCATGTGATGTGATGTGAT	59.682	43.478	24.58	0.00	0.00	3.06
738	1839	4.290155	CATGCATGTGATGTGATGTGATG	58.710	43.478	18.91	0.00	0.00	3.07
793	1927	0.455005	TGAGAGAGAGACGCATGCAG	59.545	55.000	19.57	12.98	0.00	4.41
812	1946	1.752198	CACTTGTCCCCGTCTCCAA	59.248	57.895	0.00	0.00	0.00	3.53
813	1947	0.107831	CACTTGTCCCCGTCTCCAAA	59.892	55.000	0.00	0.00	0.00	3.28
814	1948	0.108019	ACTTGTCCCCGTCTCCAAAC	59.892	55.000	0.00	0.00	0.00	2.93
815	1949	0.107831	CTTGTCCCCGTCTCCAAACA	59.892	55.000	0.00	0.00	0.00	2.83
1003	2202	2.897350	GCTACGGCCTGACCATGC	60.897	66.667	0.00	0.00	39.03	4.06
1028	2227	2.048222	CGACGTGTCCACCAGCAT	60.048	61.111	0.00	0.00	0.00	3.79
1062	2261	0.533755	AGCTCAAGTCGTTGCTTGCT	60.534	50.000	10.59	0.00	43.92	3.91
1218	2419	2.669569	TTCGTCTGCCAAGCCTGC	60.670	61.111	0.00	0.00	0.00	4.85
1371	2846	6.436027	TCTCTCCTTCCTAATTGCTTAGAGA	58.564	40.000	0.00	0.00	37.16	3.10
1373	2848	6.198639	TCTCCTTCCTAATTGCTTAGAGACT	58.801	40.000	0.00	0.00	37.16	3.24
1374	2849	6.097554	TCTCCTTCCTAATTGCTTAGAGACTG	59.902	42.308	0.00	0.00	37.16	3.51
1375	2850	5.958380	TCCTTCCTAATTGCTTAGAGACTGA	59.042	40.000	0.00	0.00	37.16	3.41
1376	2851	6.440647	TCCTTCCTAATTGCTTAGAGACTGAA	59.559	38.462	0.00	0.00	37.16	3.02
1377	2852	6.536941	CCTTCCTAATTGCTTAGAGACTGAAC	59.463	42.308	0.00	0.00	37.16	3.18
1378	2853	6.859112	TCCTAATTGCTTAGAGACTGAACT	57.141	37.500	0.00	0.00	37.16	3.01
1379	2854	7.246171	TCCTAATTGCTTAGAGACTGAACTT	57.754	36.000	0.00	0.00	37.16	2.66
1380	2855	7.099764	TCCTAATTGCTTAGAGACTGAACTTG	58.900	38.462	0.00	0.00	37.16	3.16
1381	2856	5.619625	AATTGCTTAGAGACTGAACTTGC	57.380	39.130	0.00	0.00	0.00	4.01
1382	2857	4.342862	TTGCTTAGAGACTGAACTTGCT	57.657	40.909	0.00	0.00	0.00	3.91
1383	2858	4.342862	TGCTTAGAGACTGAACTTGCTT	57.657	40.909	0.00	0.00	0.00	3.91
1384	2859	5.468540	TGCTTAGAGACTGAACTTGCTTA	57.531	39.130	0.00	0.00	0.00	3.09
1385	2860	5.473931	TGCTTAGAGACTGAACTTGCTTAG	58.526	41.667	0.00	0.00	0.00	2.18
1386	2861	5.243954	TGCTTAGAGACTGAACTTGCTTAGA	59.756	40.000	0.00	0.00	0.00	2.10
1387	2862	5.804979	GCTTAGAGACTGAACTTGCTTAGAG	59.195	44.000	0.00	0.00	0.00	2.43
1388	2863	6.349777	GCTTAGAGACTGAACTTGCTTAGAGA	60.350	42.308	0.00	0.00	0.00	3.10
1389	2864	5.643379	AGAGACTGAACTTGCTTAGAGAG	57.357	43.478	0.00	0.00	0.00	3.20
1683	3231	3.118112	AGCCACATACCTTGAAGATCTGG	60.118	47.826	0.00	0.00	0.00	3.86
1804	3355	3.937706	CCTGAGTCTCTTGGCTACAAATG	59.062	47.826	0.65	0.00	35.89	2.32
1867	3418	4.778534	AGTGGCAGAAACAGATTGAATG	57.221	40.909	0.00	0.00	0.00	2.67
1908	3459	4.094887	CAGGACATGTTATCTCCAAAACCG	59.905	45.833	0.00	0.00	0.00	4.44
1937	3488	4.299586	TGATGTAATTTGTGCTCCCAGA	57.700	40.909	0.00	0.00	0.00	3.86
2007	3558	1.080638	TTATGCCCAGGAGGTGGTTT	58.919	50.000	0.00	0.00	46.37	3.27
2042	3593	1.802553	ACCAGGTCCACTGTTGTAGT	58.197	50.000	0.00	0.00	46.06	2.73
2065	3616	3.081804	CCTCGGTGGCAAGTAGATTTTT	58.918	45.455	0.00	0.00	0.00	1.94
2112	3663	1.244019	GCCACCGCCTTGTGAGAAAT	61.244	55.000	0.00	0.00	38.55	2.17
2187	3738	3.805108	GCTGGCTAATGATGAGAATCGGT	60.805	47.826	0.00	0.00	38.61	4.69
2313	3864	0.250989	CCGGGTGTCCAAAAAGCCTA	60.251	55.000	0.00	0.00	0.00	3.93
2324	3875	6.095440	TGTCCAAAAAGCCTAATATGAAGAGC	59.905	38.462	0.00	0.00	0.00	4.09
2335	3886	2.568623	ATGAAGAGCCTTTTCCGTGT	57.431	45.000	0.00	0.00	0.00	4.49
2359	3910	2.158769	TGCTATCACAATTCCAGCGGAT	60.159	45.455	0.00	0.00	34.96	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	0.456221	AATCTGACTAGGTCACCGCG	59.544	55.000	0.00	0.00	37.67	6.46
167	168	0.751277	TTGGGAGGTGTGCAGTTGTG	60.751	55.000	0.00	0.00	0.00	3.33
168	169	0.185901	ATTGGGAGGTGTGCAGTTGT	59.814	50.000	0.00	0.00	0.00	3.32
169	170	1.331214	AATTGGGAGGTGTGCAGTTG	58.669	50.000	0.00	0.00	0.00	3.16
170	171	2.969821	TAATTGGGAGGTGTGCAGTT	57.030	45.000	0.00	0.00	0.00	3.16
171	172	3.456380	AATAATTGGGAGGTGTGCAGT	57.544	42.857	0.00	0.00	0.00	4.40
172	173	7.502226	TCTTATTAATAATTGGGAGGTGTGCAG	59.498	37.037	8.34	0.00	0.00	4.41
173	174	7.350382	TCTTATTAATAATTGGGAGGTGTGCA	58.650	34.615	8.34	0.00	0.00	4.57
284	684	4.157289	GTGACATGCACATGAGGAGAAAAT	59.843	41.667	17.19	0.00	46.91	1.82
289	689	3.810006	CACGTGACATGCACATGAGGAG	61.810	54.545	10.90	8.12	43.03	3.69
308	708	3.808466	TGCTCTCTATCACCACATCAC	57.192	47.619	0.00	0.00	0.00	3.06
320	720	3.956848	AGCACTCATGTGTATGCTCTCTA	59.043	43.478	6.97	0.00	45.11	2.43
402	806	2.260743	GAACGTCGACAGGGTCCC	59.739	66.667	17.16	0.00	0.00	4.46
451	856	8.663771	AAAATTAAAATACGCGTAGGTTCTTG	57.336	30.769	24.78	0.00	0.00	3.02
455	860	7.809665	ACTGAAAATTAAAATACGCGTAGGTT	58.190	30.769	24.78	20.83	0.00	3.50
524	959	7.723172	GGGACAATCTCATTGGATTCTTATCTT	59.277	37.037	1.50	0.00	44.42	2.40
550	1635	4.216257	AGTTTCAAACACTGGAATCCGATG	59.784	41.667	2.41	0.00	0.00	3.84
554	1639	6.575162	ACATAGTTTCAAACACTGGAATCC	57.425	37.500	2.41	0.00	0.00	3.01
577	1662	1.204146	GGCCTCTCCCACTCACAATA	58.796	55.000	0.00	0.00	0.00	1.90
579	1664	1.059584	TTGGCCTCTCCCACTCACAA	61.060	55.000	3.32	0.00	33.82	3.33
627	1717	1.134670	GTCCTTGTCGATTGCCTAGCT	60.135	52.381	0.00	0.00	0.00	3.32
628	1718	1.291132	GTCCTTGTCGATTGCCTAGC	58.709	55.000	0.00	0.00	0.00	3.42
629	1719	1.560923	CGTCCTTGTCGATTGCCTAG	58.439	55.000	0.00	0.00	0.00	3.02
630	1720	0.459585	GCGTCCTTGTCGATTGCCTA	60.460	55.000	0.00	0.00	0.00	3.93
644	1735	0.596577	TCCTCGTATGCTATGCGTCC	59.403	55.000	6.54	0.00	39.45	4.79
655	1746	6.986817	CACATCTCCTTGTTAATTCCTCGTAT	59.013	38.462	0.00	0.00	0.00	3.06
657	1748	5.046591	TCACATCTCCTTGTTAATTCCTCGT	60.047	40.000	0.00	0.00	0.00	4.18
673	1774	0.248296	GTCGAGCCTCGTCACATCTC	60.248	60.000	14.64	0.00	41.35	2.75
674	1775	0.960861	TGTCGAGCCTCGTCACATCT	60.961	55.000	14.64	0.00	41.35	2.90
676	1777	1.244697	ACTGTCGAGCCTCGTCACAT	61.245	55.000	14.64	0.96	41.35	3.21
677	1778	0.604511	TACTGTCGAGCCTCGTCACA	60.605	55.000	14.64	10.99	41.35	3.58
678	1779	0.097325	CTACTGTCGAGCCTCGTCAC	59.903	60.000	14.64	6.50	41.35	3.67
679	1780	0.036671	TCTACTGTCGAGCCTCGTCA	60.037	55.000	14.64	13.81	41.35	4.35
680	1781	0.653636	CTCTACTGTCGAGCCTCGTC	59.346	60.000	14.64	9.34	41.35	4.20
681	1782	0.745128	CCTCTACTGTCGAGCCTCGT	60.745	60.000	14.64	0.00	41.35	4.18
682	1783	2.018544	CCTCTACTGTCGAGCCTCG	58.981	63.158	8.05	8.05	42.10	4.63
683	1784	1.032657	TGCCTCTACTGTCGAGCCTC	61.033	60.000	3.94	0.00	0.00	4.70
724	1825	4.632688	GTCACATCACATCACATCACATCA	59.367	41.667	0.00	0.00	0.00	3.07
725	1826	4.632688	TGTCACATCACATCACATCACATC	59.367	41.667	0.00	0.00	0.00	3.06
726	1827	4.581868	TGTCACATCACATCACATCACAT	58.418	39.130	0.00	0.00	0.00	3.21
727	1828	3.998341	CTGTCACATCACATCACATCACA	59.002	43.478	0.00	0.00	0.00	3.58
728	1829	3.999001	ACTGTCACATCACATCACATCAC	59.001	43.478	0.00	0.00	0.00	3.06
729	1830	4.276058	ACTGTCACATCACATCACATCA	57.724	40.909	0.00	0.00	0.00	3.07
730	1831	5.654497	TCTACTGTCACATCACATCACATC	58.346	41.667	0.00	0.00	0.00	3.06
731	1832	5.394993	CCTCTACTGTCACATCACATCACAT	60.395	44.000	0.00	0.00	0.00	3.21
732	1833	4.082026	CCTCTACTGTCACATCACATCACA	60.082	45.833	0.00	0.00	0.00	3.58
733	1834	4.158579	TCCTCTACTGTCACATCACATCAC	59.841	45.833	0.00	0.00	0.00	3.06
734	1835	4.344104	TCCTCTACTGTCACATCACATCA	58.656	43.478	0.00	0.00	0.00	3.07
735	1836	4.642437	TCTCCTCTACTGTCACATCACATC	59.358	45.833	0.00	0.00	0.00	3.06
736	1837	4.604156	TCTCCTCTACTGTCACATCACAT	58.396	43.478	0.00	0.00	0.00	3.21
737	1838	4.034285	TCTCCTCTACTGTCACATCACA	57.966	45.455	0.00	0.00	0.00	3.58
738	1839	4.642437	TCATCTCCTCTACTGTCACATCAC	59.358	45.833	0.00	0.00	0.00	3.06
793	1927	2.047179	GGAGACGGGGACAAGTGC	60.047	66.667	0.00	0.00	0.00	4.40
812	1946	4.082679	CCGAAGAAGAGTGTAGCTAGTGTT	60.083	45.833	0.00	0.00	0.00	3.32
813	1947	3.440872	CCGAAGAAGAGTGTAGCTAGTGT	59.559	47.826	0.00	0.00	0.00	3.55
814	1948	3.440872	ACCGAAGAAGAGTGTAGCTAGTG	59.559	47.826	0.00	0.00	0.00	2.74
815	1949	3.440872	CACCGAAGAAGAGTGTAGCTAGT	59.559	47.826	0.00	0.00	0.00	2.57
870	2043	3.356639	CTCCTTGGCGTGCGAGCTA	62.357	63.158	3.26	0.00	37.29	3.32
907	2092	0.798771	GCTGACGCCGTGTAGAGAAG	60.799	60.000	0.00	0.00	0.00	2.85
945	2144	2.124403	TAGAGGTCGGCGGAGGAC	60.124	66.667	7.21	0.00	0.00	3.85
946	2145	2.124403	GTAGAGGTCGGCGGAGGA	60.124	66.667	7.21	0.00	0.00	3.71
1114	2313	3.809013	ATCTTTGGGGCCGCCGAT	61.809	61.111	18.45	13.19	0.00	4.18
1197	2398	2.669569	GCTTGGCAGACGAAGGCA	60.670	61.111	0.00	0.00	40.01	4.75
1218	2419	3.068691	TCGGAGCCGACCCTCTTG	61.069	66.667	7.66	0.00	44.01	3.02
1329	2749	1.412710	AGAAGCGAAGTGTCACCTTGA	59.587	47.619	0.00	0.00	0.00	3.02
1381	2856	4.998033	AGAAAAGGAAAACGGCTCTCTAAG	59.002	41.667	0.00	0.00	0.00	2.18
1382	2857	4.969484	AGAAAAGGAAAACGGCTCTCTAA	58.031	39.130	0.00	0.00	0.00	2.10
1383	2858	4.618920	AGAAAAGGAAAACGGCTCTCTA	57.381	40.909	0.00	0.00	0.00	2.43
1384	2859	3.493767	AGAAAAGGAAAACGGCTCTCT	57.506	42.857	0.00	0.00	0.00	3.10
1385	2860	3.564225	TCAAGAAAAGGAAAACGGCTCTC	59.436	43.478	0.00	0.00	0.00	3.20
1386	2861	3.551846	TCAAGAAAAGGAAAACGGCTCT	58.448	40.909	0.00	0.00	0.00	4.09
1387	2862	3.982576	TCAAGAAAAGGAAAACGGCTC	57.017	42.857	0.00	0.00	0.00	4.70
1388	2863	3.552890	GCATCAAGAAAAGGAAAACGGCT	60.553	43.478	0.00	0.00	0.00	5.52
1389	2864	2.731451	GCATCAAGAAAAGGAAAACGGC	59.269	45.455	0.00	0.00	0.00	5.68
1390	2865	3.983344	CAGCATCAAGAAAAGGAAAACGG	59.017	43.478	0.00	0.00	0.00	4.44
1391	2866	4.676924	GTCAGCATCAAGAAAAGGAAAACG	59.323	41.667	0.00	0.00	0.00	3.60
1392	2867	5.591099	TGTCAGCATCAAGAAAAGGAAAAC	58.409	37.500	0.00	0.00	0.00	2.43
1393	2868	5.850557	TGTCAGCATCAAGAAAAGGAAAA	57.149	34.783	0.00	0.00	0.00	2.29
1726	3274	6.644592	GTCATAAGATAACTCATGTGCCTCTC	59.355	42.308	0.00	0.00	0.00	3.20
1804	3355	3.668447	ACATGAGTCATCTTGTGGTCAC	58.332	45.455	1.56	0.00	41.04	3.67
1867	3418	0.321034	TGACACATCAGGAGCTGCAC	60.321	55.000	8.35	0.00	0.00	4.57
1908	3459	3.911964	GCACAAATTACATCAACACGGAC	59.088	43.478	0.00	0.00	0.00	4.79
1937	3488	0.036875	GCTGGTACCACTTGAGCCTT	59.963	55.000	11.60	0.00	0.00	4.35
2007	3558	2.011947	CTGGTATCTGTCGTACCGTCA	58.988	52.381	0.00	0.00	43.65	4.35
2042	3593	2.154567	ATCTACTTGCCACCGAGGTA	57.845	50.000	0.00	0.00	40.61	3.08
2112	3663	3.516300	TCAATTACTAGGCCGGAACAAGA	59.484	43.478	5.05	0.00	0.00	3.02
2187	3738	2.848678	ATAGACACCACCCTGAGCTA	57.151	50.000	0.00	0.00	0.00	3.32
2313	3864	4.589908	ACACGGAAAAGGCTCTTCATATT	58.410	39.130	2.55	0.00	0.00	1.28
2324	3875	3.063997	GTGATAGCATGACACGGAAAAGG	59.936	47.826	0.00	0.00	0.00	3.11
2335	3886	2.874086	CGCTGGAATTGTGATAGCATGA	59.126	45.455	0.00	0.00	34.16	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.