AutoCloner

Multiple sequence alignment - TraesCS2B01G028200

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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	TraesCS2B01G028200	chr2B	100.000	2303	0	0	1	2303	13183327	13185629	0.000000e+00	4253
1	TraesCS2B01G028200	chr1D	94.472	1628	81	6	677	2298	235547575	235545951	0.000000e+00	2499
2	TraesCS2B01G028200	chr5D	94.161	1627	81	8	680	2300	462907869	462909487	0.000000e+00	2466
3	TraesCS2B01G028200	chr7A	92.905	1635	93	14	677	2298	439031072	439032696	0.000000e+00	2355
4	TraesCS2B01G028200	chr7A	91.841	1336	79	13	677	1989	639884909	639883581	0.000000e+00	1836
5	TraesCS2B01G028200	chr7A	95.263	190	7	1	63	250	639885130	639884941	1.340000e-77	300
6	TraesCS2B01G028200	chr7A	95.858	169	5	1	63	229	439030649	439030817	2.920000e-69	272
7	TraesCS2B01G028200	chr1B	92.617	1639	82	19	677	2298	253825459	253823843	0.000000e+00	2320
8	TraesCS2B01G028200	chr7D	94.630	1434	68	7	868	2299	635929327	635927901	0.000000e+00	2213
9	TraesCS2B01G028200	chr2A	94.171	1441	76	4	865	2300	441110111	441111548	0.000000e+00	2189
10	TraesCS2B01G028200	chr5B	93.398	1439	82	8	865	2298	89745418	89746848	0.000000e+00	2119
11	TraesCS2B01G028200	chr4A	93.036	1436	86	5	868	2297	281593802	281592375	0.000000e+00	2085
12	TraesCS2B01G028200	chr3D	94.094	1270	61	8	677	1937	143483348	143482084	0.000000e+00	1917
13	TraesCS2B01G028200	chr3D	95.481	509	19	3	55	561	143484604	143484098	0.000000e+00	809
14	TraesCS2B01G028200	chr3D	92.517	294	19	2	271	561	43023417	43023124	3.540000e-113	418
15	TraesCS2B01G028200	chr3D	89.888	178	8	5	58	226	43023605	43023429	1.070000e-53	220
16	TraesCS2B01G028200	chr3D	98.374	123	2	0	556	678	143483734	143483612	1.390000e-52	217
17	TraesCS2B01G028200	chr3D	92.800	125	8	1	556	679	43022761	43022637	1.820000e-41	180
18	TraesCS2B01G028200	chr7B	92.787	1012	50	11	1297	2298	634824607	634825605	0.000000e+00	1443
19	TraesCS2B01G028200	chr7B	97.500	120	3	0	556	675	634824171	634824290	3.000000e-49	206
20	TraesCS2B01G028200	chr6D	92.111	938	58	8	1243	2179	298130733	298129811	0.000000e+00	1308
21	TraesCS2B01G028200	chr6D	95.874	509	17	3	55	561	298141148	298140642	0.000000e+00	821
22	TraesCS2B01G028200	chr6D	95.122	123	6	0	556	678	298140278	298140156	6.490000e-46	195
23	TraesCS2B01G028200	chr3B	93.542	511	27	4	55	561	66955551	66955043	0.000000e+00	756
24	TraesCS2B01G028200	chr3B	92.063	126	8	2	556	679	66954679	66954554	2.350000e-40	176
25	TraesCS2B01G028200	chr3A	90.944	519	33	9	55	561	55047598	55047082	0.000000e+00	686
26	TraesCS2B01G028200	chr3A	92.742	124	8	1	556	678	55046717	55046594	6.540000e-41	178

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	TraesCS2B01G028200	chr2B	13183327	13185629	2302	False	4253.000000	4253	100.0000	1	2303	1	chr2B.!!$F1	2302
1	TraesCS2B01G028200	chr1D	235545951	235547575	1624	True	2499.000000	2499	94.4720	677	2298	1	chr1D.!!$R1	1621
2	TraesCS2B01G028200	chr5D	462907869	462909487	1618	False	2466.000000	2466	94.1610	680	2300	1	chr5D.!!$F1	1620
3	TraesCS2B01G028200	chr7A	439030649	439032696	2047	False	1313.500000	2355	94.3815	63	2298	2	chr7A.!!$F1	2235
4	TraesCS2B01G028200	chr7A	639883581	639885130	1549	True	1068.000000	1836	93.5520	63	1989	2	chr7A.!!$R1	1926
5	TraesCS2B01G028200	chr1B	253823843	253825459	1616	True	2320.000000	2320	92.6170	677	2298	1	chr1B.!!$R1	1621
6	TraesCS2B01G028200	chr7D	635927901	635929327	1426	True	2213.000000	2213	94.6300	868	2299	1	chr7D.!!$R1	1431
7	TraesCS2B01G028200	chr2A	441110111	441111548	1437	False	2189.000000	2189	94.1710	865	2300	1	chr2A.!!$F1	1435
8	TraesCS2B01G028200	chr5B	89745418	89746848	1430	False	2119.000000	2119	93.3980	865	2298	1	chr5B.!!$F1	1433
9	TraesCS2B01G028200	chr4A	281592375	281593802	1427	True	2085.000000	2085	93.0360	868	2297	1	chr4A.!!$R1	1429
10	TraesCS2B01G028200	chr3D	143482084	143484604	2520	True	981.000000	1917	95.9830	55	1937	3	chr3D.!!$R2	1882
11	TraesCS2B01G028200	chr3D	43022637	43023605	968	True	272.666667	418	91.7350	58	679	3	chr3D.!!$R1	621
12	TraesCS2B01G028200	chr7B	634824171	634825605	1434	False	824.500000	1443	95.1435	556	2298	2	chr7B.!!$F1	1742
13	TraesCS2B01G028200	chr6D	298129811	298130733	922	True	1308.000000	1308	92.1110	1243	2179	1	chr6D.!!$R1	936
14	TraesCS2B01G028200	chr6D	298140156	298141148	992	True	508.000000	821	95.4980	55	678	2	chr6D.!!$R2	623
15	TraesCS2B01G028200	chr3B	66954554	66955551	997	True	466.000000	756	92.8025	55	679	2	chr3B.!!$R1	624
16	TraesCS2B01G028200	chr3A	55046594	55047598	1004	True	432.000000	686	91.8430	55	678	2	chr3A.!!$R1	623

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
35	36	0.400213	ACCTGAATGTTTGCTCGGGA	59.6	50.0	3.96	0.0	40.09	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1304	1971	0.237498	GGGCGTCCTTCAAAAGTTCG	59.763	55.0	0.0	0.0	0.0	3.95	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
25	26	3.418684	AGGCGAAGTTAACCTGAATGT	57.581	42.857	0.88	0.00	30.82	2.71
26	27	3.751518	AGGCGAAGTTAACCTGAATGTT	58.248	40.909	0.88	0.00	30.82	2.71
27	28	4.142038	AGGCGAAGTTAACCTGAATGTTT	58.858	39.130	0.88	0.00	30.82	2.83
28	29	4.023193	AGGCGAAGTTAACCTGAATGTTTG	60.023	41.667	0.88	0.00	30.82	2.93
29	30	3.668656	GCGAAGTTAACCTGAATGTTTGC	59.331	43.478	0.88	0.20	0.00	3.68
30	31	4.556699	GCGAAGTTAACCTGAATGTTTGCT	60.557	41.667	0.88	0.00	0.00	3.91
31	32	5.147162	CGAAGTTAACCTGAATGTTTGCTC	58.853	41.667	0.88	0.00	0.00	4.26
32	33	4.749245	AGTTAACCTGAATGTTTGCTCG	57.251	40.909	0.88	0.00	0.00	5.03
33	34	3.502211	AGTTAACCTGAATGTTTGCTCGG	59.498	43.478	0.88	0.00	0.00	4.63
34	35	1.247567	AACCTGAATGTTTGCTCGGG	58.752	50.000	0.00	0.00	42.88	5.14
35	36	0.400213	ACCTGAATGTTTGCTCGGGA	59.600	50.000	3.96	0.00	40.09	5.14
36	37	1.004745	ACCTGAATGTTTGCTCGGGAT	59.995	47.619	3.96	0.00	40.09	3.85
37	38	2.094675	CCTGAATGTTTGCTCGGGATT	58.905	47.619	0.00	0.00	40.09	3.01
38	39	3.278574	CCTGAATGTTTGCTCGGGATTA	58.721	45.455	0.00	0.00	40.09	1.75
39	40	3.065371	CCTGAATGTTTGCTCGGGATTAC	59.935	47.826	0.00	0.00	40.09	1.89
40	41	3.941483	CTGAATGTTTGCTCGGGATTACT	59.059	43.478	0.00	0.00	0.00	2.24
41	42	4.331968	TGAATGTTTGCTCGGGATTACTT	58.668	39.130	0.00	0.00	0.00	2.24
42	43	4.155826	TGAATGTTTGCTCGGGATTACTTG	59.844	41.667	0.00	0.00	0.00	3.16
43	44	3.410631	TGTTTGCTCGGGATTACTTGA	57.589	42.857	0.00	0.00	0.00	3.02
44	45	3.071479	TGTTTGCTCGGGATTACTTGAC	58.929	45.455	0.00	0.00	0.00	3.18
45	46	3.244422	TGTTTGCTCGGGATTACTTGACT	60.244	43.478	0.00	0.00	0.00	3.41
46	47	3.695830	TTGCTCGGGATTACTTGACTT	57.304	42.857	0.00	0.00	0.00	3.01
47	48	2.972625	TGCTCGGGATTACTTGACTTG	58.027	47.619	0.00	0.00	0.00	3.16
48	49	2.565391	TGCTCGGGATTACTTGACTTGA	59.435	45.455	0.00	0.00	0.00	3.02
49	50	2.930682	GCTCGGGATTACTTGACTTGAC	59.069	50.000	0.00	0.00	0.00	3.18
50	51	3.179830	CTCGGGATTACTTGACTTGACG	58.820	50.000	0.00	0.00	0.00	4.35
51	52	2.559668	TCGGGATTACTTGACTTGACGT	59.440	45.455	0.00	0.00	0.00	4.34
52	53	3.758023	TCGGGATTACTTGACTTGACGTA	59.242	43.478	0.00	0.00	0.00	3.57
53	54	3.855950	CGGGATTACTTGACTTGACGTAC	59.144	47.826	0.00	0.00	0.00	3.67
177	178	4.142425	GCACTCTGGTAAGTAGTGGAGTAC	60.142	50.000	0.00	0.00	40.76	2.73
292	310	8.325046	ACTAAATCTCTTACTCTTTTGCAGGAT	58.675	33.333	0.00	0.00	0.00	3.24
387	406	6.423182	AGATTATGTGTTGCTAGCCCTTTTA	58.577	36.000	13.29	0.00	0.00	1.52
471	491	0.984230	TGGATCGGAGTCCAAAAGCT	59.016	50.000	10.49	0.00	45.03	3.74
519	541	7.750769	AGAATATCTCGTACCTTATTCGCTAC	58.249	38.462	0.00	0.00	36.58	3.58
547	569	4.754114	TGCTTGTTTTATTGTGGCCATTTC	59.246	37.500	9.72	0.00	0.00	2.17
583	977	3.260128	CAGCCATATCAGCATCAGGACTA	59.740	47.826	0.00	0.00	0.00	2.59
675	1071	6.911250	TCTTCTTATGGTCTGTTGACACTA	57.089	37.500	0.00	0.00	44.61	2.74
679	1075	7.482169	TCTTATGGTCTGTTGACACTATCTT	57.518	36.000	0.00	0.00	44.61	2.40
680	1076	8.589701	TCTTATGGTCTGTTGACACTATCTTA	57.410	34.615	0.00	0.00	44.61	2.10
682	1078	9.254133	CTTATGGTCTGTTGACACTATCTTATG	57.746	37.037	0.00	0.00	44.61	1.90
684	1080	5.483937	TGGTCTGTTGACACTATCTTATGGT	59.516	40.000	0.00	0.00	44.61	3.55
816	1477	6.235231	GAGTATCTTGGTGTATTCAAGGGA	57.765	41.667	0.00	0.00	41.23	4.20
817	1478	6.636454	AGTATCTTGGTGTATTCAAGGGAA	57.364	37.500	0.00	0.00	41.23	3.97
837	1498	8.491045	AGGGAAGTTTTTGAAATCCTATTGAA	57.509	30.769	0.00	0.00	0.00	2.69
915	1580	7.259290	TGAAGAAGTTGTCTAACCATTTGAC	57.741	36.000	0.00	0.00	37.52	3.18
1030	1695	8.891671	TCTTGCTTCAGCTTTTATTTTTGAAT	57.108	26.923	0.00	0.00	42.66	2.57
1123	1790	3.855255	TTGGTTTCAGACATCTGGACA	57.145	42.857	8.99	1.33	43.91	4.02
1145	1812	5.185828	ACAAGAAGAAAAAGAAGTGCAAGGT	59.814	36.000	0.00	0.00	0.00	3.50
1175	1842	4.142049	GGTCGAGACTCATCTTGAATTCCT	60.142	45.833	2.27	0.00	45.36	3.36
1247	1914	1.631405	TCATTCCCAAAGGTGCCTTG	58.369	50.000	4.00	0.00	36.26	3.61
1263	1930	3.882888	TGCCTTGTCTACTCAAAACCTTG	59.117	43.478	0.00	0.00	0.00	3.61
1268	1935	6.348540	CCTTGTCTACTCAAAACCTTGTATGC	60.349	42.308	0.00	0.00	33.94	3.14
1283	1950	6.998673	ACCTTGTATGCTATTAGATTTGGTCC	59.001	38.462	0.00	0.00	0.00	4.46
1288	1955	8.590204	TGTATGCTATTAGATTTGGTCCGATTA	58.410	33.333	0.00	0.00	0.00	1.75
1289	1956	9.088512	GTATGCTATTAGATTTGGTCCGATTAG	57.911	37.037	0.00	0.00	0.00	1.73
1303	1970	5.221661	GGTCCGATTAGTATGAAGGGTTGAT	60.222	44.000	0.00	0.00	0.00	2.57
1304	1971	5.927115	GTCCGATTAGTATGAAGGGTTGATC	59.073	44.000	0.00	0.00	0.00	2.92
1492	2163	6.916360	ATTTGGTGTACAGGATTTGACAAT	57.084	33.333	0.00	0.00	0.00	2.71
1493	2164	5.703978	TTGGTGTACAGGATTTGACAATG	57.296	39.130	0.00	0.00	0.00	2.82
1642	2319	6.037391	CGTACTAACAAGTTTTCACTTTCCCA	59.963	38.462	0.00	0.00	40.66	4.37
1643	2320	7.255001	CGTACTAACAAGTTTTCACTTTCCCAT	60.255	37.037	0.00	0.00	40.66	4.00
1671	2360	0.960861	TGAGGTGATCGACGCTGACT	60.961	55.000	0.00	0.00	0.00	3.41
1700	2389	3.782244	GTGGCGCTGTGCTCTTCG	61.782	66.667	13.46	0.00	45.43	3.79
1708	2397	0.730834	CTGTGCTCTTCGACCACTCG	60.731	60.000	0.00	0.00	41.65	4.18
1745	2434	3.454587	AAGCTCGGTTGCCACGTCA	62.455	57.895	0.00	0.00	0.00	4.35
1769	2458	2.760374	GGATGATCGTCCAGGTGATTC	58.240	52.381	26.27	0.00	38.20	2.52
1878	2567	6.428465	CGAGCCTTGTAGATACATCTAGAGAA	59.572	42.308	0.00	0.00	39.87	2.87
1963	2663	6.319911	TGTGTGTGTCTGATGTTAAATGGAAA	59.680	34.615	0.00	0.00	0.00	3.13
1982	2682	5.006386	GGAAACTTGAGATGGTTCTGTGAT	58.994	41.667	0.00	0.00	30.30	3.06
2021	2721	5.815222	CACTGGACGTATTACCATTCATGAA	59.185	40.000	11.26	11.26	35.54	2.57
2095	2798	2.224793	GGGTCAAAAGTGAGGGCTACTT	60.225	50.000	0.00	0.00	39.92	2.24
2179	2882	8.800332	ACTACTACTAACTTTTTAGCTGTAGCA	58.200	33.333	6.65	0.00	41.82	3.49
2190	2894	3.669939	AGCTGTAGCATGGGGTAAAAT	57.330	42.857	6.65	0.00	45.16	1.82
2258	2963	3.886123	GGAACCCATGCTACTTGTATGT	58.114	45.455	0.00	0.00	37.11	2.29
2300	3009	5.868258	GGTAGTGTTTTTCCTAGTAGTGCTC	59.132	44.000	0.00	0.00	0.00	4.26
2301	3010	5.546621	AGTGTTTTTCCTAGTAGTGCTCA	57.453	39.130	0.00	0.00	0.00	4.26
2302	3011	5.298347	AGTGTTTTTCCTAGTAGTGCTCAC	58.702	41.667	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.229936	ACATTCAGGTTAACTTCGCCTATA	57.770	37.500	5.42	0.00	0.00	1.31
3	4	5.099042	ACATTCAGGTTAACTTCGCCTAT	57.901	39.130	5.42	0.00	0.00	2.57
4	5	4.546829	ACATTCAGGTTAACTTCGCCTA	57.453	40.909	5.42	0.00	0.00	3.93
5	6	3.418684	ACATTCAGGTTAACTTCGCCT	57.581	42.857	5.42	0.00	0.00	5.52
6	7	4.226761	CAAACATTCAGGTTAACTTCGCC	58.773	43.478	5.42	0.00	0.00	5.54
7	8	3.668656	GCAAACATTCAGGTTAACTTCGC	59.331	43.478	5.42	0.00	0.00	4.70
8	9	5.108385	AGCAAACATTCAGGTTAACTTCG	57.892	39.130	5.42	0.00	0.00	3.79
9	10	5.147162	CGAGCAAACATTCAGGTTAACTTC	58.853	41.667	5.42	0.00	0.00	3.01
10	11	4.023193	CCGAGCAAACATTCAGGTTAACTT	60.023	41.667	5.42	0.00	0.00	2.66
11	12	3.502211	CCGAGCAAACATTCAGGTTAACT	59.498	43.478	5.42	0.00	0.00	2.24
12	13	3.365969	CCCGAGCAAACATTCAGGTTAAC	60.366	47.826	0.00	0.00	0.00	2.01
13	14	2.817258	CCCGAGCAAACATTCAGGTTAA	59.183	45.455	0.00	0.00	0.00	2.01
14	15	2.039216	TCCCGAGCAAACATTCAGGTTA	59.961	45.455	0.00	0.00	0.00	2.85
15	16	1.202879	TCCCGAGCAAACATTCAGGTT	60.203	47.619	0.00	0.00	0.00	3.50
16	17	0.400213	TCCCGAGCAAACATTCAGGT	59.600	50.000	0.00	0.00	0.00	4.00
17	18	1.755179	ATCCCGAGCAAACATTCAGG	58.245	50.000	0.00	0.00	0.00	3.86
18	19	3.941483	AGTAATCCCGAGCAAACATTCAG	59.059	43.478	0.00	0.00	0.00	3.02
19	20	3.950397	AGTAATCCCGAGCAAACATTCA	58.050	40.909	0.00	0.00	0.00	2.57
20	21	4.394920	TCAAGTAATCCCGAGCAAACATTC	59.605	41.667	0.00	0.00	0.00	2.67
21	22	4.156008	GTCAAGTAATCCCGAGCAAACATT	59.844	41.667	0.00	0.00	0.00	2.71
22	23	3.689649	GTCAAGTAATCCCGAGCAAACAT	59.310	43.478	0.00	0.00	0.00	2.71
23	24	3.071479	GTCAAGTAATCCCGAGCAAACA	58.929	45.455	0.00	0.00	0.00	2.83
24	25	3.335579	AGTCAAGTAATCCCGAGCAAAC	58.664	45.455	0.00	0.00	0.00	2.93
25	26	3.695830	AGTCAAGTAATCCCGAGCAAA	57.304	42.857	0.00	0.00	0.00	3.68
26	27	3.007506	TCAAGTCAAGTAATCCCGAGCAA	59.992	43.478	0.00	0.00	0.00	3.91
27	28	2.565391	TCAAGTCAAGTAATCCCGAGCA	59.435	45.455	0.00	0.00	0.00	4.26
28	29	2.930682	GTCAAGTCAAGTAATCCCGAGC	59.069	50.000	0.00	0.00	0.00	5.03
29	30	3.179830	CGTCAAGTCAAGTAATCCCGAG	58.820	50.000	0.00	0.00	0.00	4.63
30	31	2.559668	ACGTCAAGTCAAGTAATCCCGA	59.440	45.455	0.00	0.00	0.00	5.14
31	32	2.955614	ACGTCAAGTCAAGTAATCCCG	58.044	47.619	0.00	0.00	0.00	5.14
32	33	4.813027	TGTACGTCAAGTCAAGTAATCCC	58.187	43.478	0.00	0.00	0.00	3.85
33	34	5.220416	GCATGTACGTCAAGTCAAGTAATCC	60.220	44.000	0.00	0.00	0.00	3.01
34	35	5.577164	AGCATGTACGTCAAGTCAAGTAATC	59.423	40.000	0.00	0.00	0.00	1.75
35	36	5.348724	CAGCATGTACGTCAAGTCAAGTAAT	59.651	40.000	0.00	0.00	0.00	1.89
36	37	4.684242	CAGCATGTACGTCAAGTCAAGTAA	59.316	41.667	0.00	0.00	0.00	2.24
37	38	4.022676	TCAGCATGTACGTCAAGTCAAGTA	60.023	41.667	0.00	0.00	37.40	2.24
38	39	3.059884	CAGCATGTACGTCAAGTCAAGT	58.940	45.455	0.00	0.00	0.00	3.16
39	40	3.317150	TCAGCATGTACGTCAAGTCAAG	58.683	45.455	0.00	0.00	37.40	3.02
40	41	3.378911	TCAGCATGTACGTCAAGTCAA	57.621	42.857	0.00	0.00	37.40	3.18
41	42	3.592898	ATCAGCATGTACGTCAAGTCA	57.407	42.857	0.00	0.00	37.40	3.41
42	43	3.484229	GCAATCAGCATGTACGTCAAGTC	60.484	47.826	0.00	0.00	44.79	3.01
43	44	2.416547	GCAATCAGCATGTACGTCAAGT	59.583	45.455	0.00	0.00	44.79	3.16
44	45	3.043635	GCAATCAGCATGTACGTCAAG	57.956	47.619	0.00	0.00	44.79	3.02
92	93	7.573710	AGGCACTTAGATTTCCATGTATAACA	58.426	34.615	0.00	0.00	27.25	2.41
292	310	1.234821	CAAGGCGTCCAAGCTTTGTA	58.765	50.000	0.00	0.00	45.38	2.41
341	359	9.574516	AATCTCTATAGAAAAACAAACTGTGGT	57.425	29.630	3.57	0.00	34.73	4.16
379	397	8.747538	TCCTAAGATATTTCAGTTAAAAGGGC	57.252	34.615	0.00	0.00	0.00	5.19
387	406	9.167311	GTTGTGTGATCCTAAGATATTTCAGTT	57.833	33.333	0.00	0.00	30.90	3.16
468	488	4.141824	GGACTTGCCTTAAGAGTATCAGCT	60.142	45.833	3.36	0.00	39.76	4.24
471	491	3.132289	CGGGACTTGCCTTAAGAGTATCA	59.868	47.826	3.36	0.00	39.76	2.15
519	541	3.490526	GCCACAATAAAACAAGCACACTG	59.509	43.478	0.00	0.00	0.00	3.66
547	569	0.179076	TGGCTGTAGACGCATCATGG	60.179	55.000	0.00	0.00	0.00	3.66
583	977	5.363868	TGATGTAGTTCCAGCTAGCATACTT	59.636	40.000	18.83	7.68	0.00	2.24
675	1071	4.935808	GTCAAAGTTCCACGACCATAAGAT	59.064	41.667	0.00	0.00	0.00	2.40
679	1075	3.048337	GGTCAAAGTTCCACGACCATA	57.952	47.619	0.00	0.00	45.96	2.74
680	1076	1.892209	GGTCAAAGTTCCACGACCAT	58.108	50.000	0.00	0.00	45.96	3.55
682	1078	0.108019	AGGGTCAAAGTTCCACGACC	59.892	55.000	0.00	0.00	45.95	4.79
684	1080	0.534203	GCAGGGTCAAAGTTCCACGA	60.534	55.000	0.00	0.00	0.00	4.35
811	1472	8.491045	TCAATAGGATTTCAAAAACTTCCCTT	57.509	30.769	0.00	0.00	0.00	3.95
837	1498	6.621613	GCCTCGAGTTCCTTGAAAAATATTT	58.378	36.000	12.31	0.00	0.00	1.40
915	1580	2.291741	GAGTCAAGCAAACCAAGACAGG	59.708	50.000	0.00	0.00	0.00	4.00
967	1632	1.003580	ACACGAGGCAACATTGGATCT	59.996	47.619	0.00	0.00	41.41	2.75
1030	1695	9.807921	AAGTTCTCTTAGAATATTTTGTCCCAA	57.192	29.630	0.00	0.00	36.50	4.12
1123	1790	5.921962	ACCTTGCACTTCTTTTTCTTCTT	57.078	34.783	0.00	0.00	0.00	2.52
1145	1812	3.698289	AGATGAGTCTCGACCTTACCAA	58.302	45.455	0.00	0.00	0.00	3.67
1175	1842	6.043411	CCAAATTTAACCTTTTCACGTCCAA	58.957	36.000	0.00	0.00	0.00	3.53
1247	1914	8.494016	AATAGCATACAAGGTTTTGAGTAGAC	57.506	34.615	0.00	0.00	37.73	2.59
1263	1930	7.907214	AATCGGACCAAATCTAATAGCATAC	57.093	36.000	0.00	0.00	0.00	2.39
1283	1950	5.769367	TCGATCAACCCTTCATACTAATCG	58.231	41.667	0.00	0.00	35.92	3.34
1288	1955	5.422214	AAGTTCGATCAACCCTTCATACT	57.578	39.130	0.00	0.00	35.28	2.12
1289	1956	6.148811	TCAAAAGTTCGATCAACCCTTCATAC	59.851	38.462	0.00	0.00	35.28	2.39
1303	1970	1.223187	GGCGTCCTTCAAAAGTTCGA	58.777	50.000	0.00	0.00	0.00	3.71
1304	1971	0.237498	GGGCGTCCTTCAAAAGTTCG	59.763	55.000	0.00	0.00	0.00	3.95
1605	2282	6.212955	ACTTGTTAGTACGCAAATTGCATTT	58.787	32.000	18.65	3.97	36.53	2.32
1642	2319	2.599645	GATCACCTCAGCGCCCACAT	62.600	60.000	2.29	0.00	0.00	3.21
1643	2320	3.315142	GATCACCTCAGCGCCCACA	62.315	63.158	2.29	0.00	0.00	4.17
1652	2330	0.960861	AGTCAGCGTCGATCACCTCA	60.961	55.000	0.00	0.00	0.00	3.86
1681	2370	4.254709	AAGAGCACAGCGCCACCA	62.255	61.111	2.29	0.00	44.04	4.17
1700	2389	4.131088	GTCCGCCTCCGAGTGGTC	62.131	72.222	4.35	0.00	38.61	4.02
1731	2420	2.586635	GTGTGACGTGGCAACCGA	60.587	61.111	4.40	0.00	34.83	4.69
1736	2425	2.166130	ATCATCCGTGTGACGTGGCA	62.166	55.000	0.00	0.00	40.58	4.92
1745	2434	0.970937	ACCTGGACGATCATCCGTGT	60.971	55.000	2.91	0.00	43.49	4.49
1749	2438	2.548920	GGAATCACCTGGACGATCATCC	60.549	54.545	0.00	0.00	39.45	3.51
1816	2505	1.229529	ACACGAATCCACCCTCCCT	60.230	57.895	0.00	0.00	0.00	4.20
1818	2507	1.221021	GGACACGAATCCACCCTCC	59.779	63.158	5.04	0.00	38.77	4.30
1854	2543	7.447238	ACTTCTCTAGATGTATCTACAAGGCTC	59.553	40.741	0.00	0.00	39.99	4.70
1878	2567	2.158667	CCACCAACCTAAACAGACCACT	60.159	50.000	0.00	0.00	0.00	4.00
1963	2663	4.630644	ACATCACAGAACCATCTCAAGT	57.369	40.909	0.00	0.00	32.03	3.16
1982	2682	2.300152	TCCAGTGCAAACAAAACCAACA	59.700	40.909	0.00	0.00	0.00	3.33
2095	2798	6.548622	CCCATGCTACTACTAACCTAACTACA	59.451	42.308	0.00	0.00	0.00	2.74
2179	2882	2.103601	AGTAGCGCGTATTTTACCCCAT	59.896	45.455	8.43	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.