AutoCloner

Multiple sequence alignment - TraesCS1B01G362900

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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	TraesCS1B01G362900	chr1B	100.000	2769	0	0	1	2769	591428284	591425516	0.000000e+00	5114
1	TraesCS1B01G362900	chr1B	88.959	797	73	7	846	1630	593683508	593684301	0.000000e+00	970
2	TraesCS1B01G362900	chr1B	87.190	765	66	10	821	1572	593721487	593722232	0.000000e+00	841
3	TraesCS1B01G362900	chr1B	81.319	455	51	16	2331	2766	593734487	593734926	3.420000e-89	339
4	TraesCS1B01G362900	chr1B	80.440	455	58	18	2331	2769	593688179	593688618	4.450000e-83	318
5	TraesCS1B01G362900	chr1B	92.683	205	14	1	1029	1233	591359707	591359504	7.500000e-76	294
6	TraesCS1B01G362900	chr1B	94.737	133	7	0	2637	2769	591357249	591357117	1.010000e-49	207
7	TraesCS1B01G362900	chr1B	95.276	127	4	2	1955	2080	72765805	72765930	1.680000e-47	200
8	TraesCS1B01G362900	chr1B	94.531	128	6	1	1947	2073	156585471	156585598	2.180000e-46	196
9	TraesCS1B01G362900	chr1B	94.488	127	5	2	1955	2080	72798693	72798818	7.820000e-46	195
10	TraesCS1B01G362900	chr1B	94.488	127	5	2	1955	2080	72876074	72876199	7.820000e-46	195
11	TraesCS1B01G362900	chr1B	90.654	107	9	1	2103	2208	593684737	593684843	1.030000e-29	141
12	TraesCS1B01G362900	chr1B	90.476	105	9	1	2105	2208	593722328	593722432	1.340000e-28	137
13	TraesCS1B01G362900	chr1B	87.288	118	12	3	1219	1336	591358009	591357895	6.220000e-27	132
14	TraesCS1B01G362900	chr1A	91.010	1357	59	25	6	1334	533696679	533695358	0.000000e+00	1772
15	TraesCS1B01G362900	chr1A	96.535	635	13	5	1327	1958	533695202	533694574	0.000000e+00	1042
16	TraesCS1B01G362900	chr1A	87.898	471	21	7	2329	2769	533693980	533693516	3.160000e-144	521
17	TraesCS1B01G362900	chr1A	80.176	454	63	14	2331	2769	534819288	534819729	5.760000e-82	315
18	TraesCS1B01G362900	chr1A	93.889	180	6	2	2148	2322	533694332	533694153	1.630000e-67	267
19	TraesCS1B01G362900	chr1A	81.341	343	38	18	2447	2769	533671528	533671192	3.540000e-64	255
20	TraesCS1B01G362900	chr1A	93.243	74	4	1	2077	2150	533694574	533694502	1.050000e-19	108
21	TraesCS1B01G362900	chr1D	90.254	1262	67	18	706	1959	436615835	436614622	0.000000e+00	1598
22	TraesCS1B01G362900	chr1D	94.979	478	15	2	241	709	436616450	436615973	0.000000e+00	741
23	TraesCS1B01G362900	chr1D	86.131	685	34	25	2124	2769	436614615	436613953	0.000000e+00	682
24	TraesCS1B01G362900	chr1D	78.378	740	74	46	2094	2769	436335075	436334358	4.300000e-108	401
25	TraesCS1B01G362900	chr1D	90.909	231	20	1	6	236	436616860	436616631	2.680000e-80	309
26	TraesCS1B01G362900	chr1D	84.068	295	32	8	943	1235	436377321	436377040	1.260000e-68	270
27	TraesCS1B01G362900	chr1D	92.661	109	8	0	1395	1503	436335560	436335452	1.030000e-34	158
28	TraesCS1B01G362900	chr4A	91.852	405	21	6	268	671	653640731	653640338	3.120000e-154	555
29	TraesCS1B01G362900	chr4A	95.385	260	11	1	412	671	653698255	653698513	1.980000e-111	412
30	TraesCS1B01G362900	chrUn	95.720	257	10	1	415	671	331933763	331933508	1.980000e-111	412
31	TraesCS1B01G362900	chr6B	96.748	123	2	2	1953	2074	653709322	653709201	1.300000e-48	204
32	TraesCS1B01G362900	chr6B	95.238	126	5	1	1949	2073	470914821	470914946	6.050000e-47	198
33	TraesCS1B01G362900	chr6B	95.122	123	4	2	1958	2078	46511993	46512115	2.810000e-45	193
34	TraesCS1B01G362900	chr6B	95.833	120	4	1	1958	2076	179276135	179276016	2.810000e-45	193
35	TraesCS1B01G362900	chr5B	97.458	118	3	0	1956	2073	73989865	73989982	4.680000e-48	202
36	TraesCS1B01G362900	chr2D	95.968	124	4	1	1956	2078	520503935	520503812	1.680000e-47	200
37	TraesCS1B01G362900	chr3B	95.868	121	4	1	1954	2073	457968802	457968682	7.820000e-46	195
38	TraesCS1B01G362900	chr3B	95.868	121	4	1	1958	2077	545060692	545060812	7.820000e-46	195
39	TraesCS1B01G362900	chr3D	96.581	117	3	1	1958	2073	439679488	439679604	2.810000e-45	193
40	TraesCS1B01G362900	chr4B	94.355	124	7	0	1958	2081	636915348	636915225	1.010000e-44	191

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	TraesCS1B01G362900	chr1B	591425516	591428284	2768	True	5114.000000	5114	100.000000	1	2769	1	chr1B.!!$R1	2768
1	TraesCS1B01G362900	chr1B	593721487	593722432	945	False	489.000000	841	88.833000	821	2208	2	chr1B.!!$F7	1387
2	TraesCS1B01G362900	chr1B	593683508	593688618	5110	False	476.333333	970	86.684333	846	2769	3	chr1B.!!$F6	1923
3	TraesCS1B01G362900	chr1B	591357117	591359707	2590	True	211.000000	294	91.569333	1029	2769	3	chr1B.!!$R2	1740
4	TraesCS1B01G362900	chr1A	533693516	533696679	3163	True	742.000000	1772	92.515000	6	2769	5	chr1A.!!$R2	2763
5	TraesCS1B01G362900	chr1D	436613953	436616860	2907	True	832.500000	1598	90.568250	6	2769	4	chr1D.!!$R3	2763
6	TraesCS1B01G362900	chr1D	436334358	436335560	1202	True	279.500000	401	85.519500	1395	2769	2	chr1D.!!$R2	1374

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
21	22	2.900528	CGGATAGTGTCGGATTGGC	58.099	57.895	0.0	0.0	0.0	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1964	4448	1.133025	GGACGAGTAATTCCGAACGGA	59.867	52.381	12.04	12.04	43.52	4.69	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
21	22	2.900528	CGGATAGTGTCGGATTGGC	58.099	57.895	0.00	0.00	0.00	4.52
39	40	4.789012	TGGCTGGAAATGATTCTTTGTC	57.211	40.909	0.00	0.00	35.79	3.18
81	82	2.984471	CAAGCAGATCACACATTTGCAC	59.016	45.455	0.00	0.00	37.24	4.57
178	179	6.762702	TGTCGATTGGAATACAGTACTACA	57.237	37.500	0.00	0.00	0.00	2.74
197	198	5.659971	ACTACACAGTACCCGATCCTATTTT	59.340	40.000	0.00	0.00	31.45	1.82
205	206	3.074412	CCCGATCCTATTTTAGCGCAAT	58.926	45.455	11.47	2.98	0.00	3.56
455	642	8.492673	AGAAATTATGAGTGTAAGCGATTCAA	57.507	30.769	0.00	0.00	0.00	2.69
479	667	7.595819	AAAATAGGTGGAGTCATTCAAAACA	57.404	32.000	0.00	0.00	0.00	2.83
746	1075	5.964958	GTCCATGGACTTTTCATCAGAAA	57.035	39.130	33.47	0.00	40.23	2.52
907	1237	4.687901	TTCATATGCATTCCCTTCTCGA	57.312	40.909	3.54	0.00	0.00	4.04
951	1299	4.219944	TGGCGTGTACTCTGAACTTCTATT	59.780	41.667	0.00	0.00	0.00	1.73
1012	1360	7.633789	ACTTTGATGTTGTGAATATAGGGAGT	58.366	34.615	0.00	0.00	0.00	3.85
1145	1493	7.273164	CGTGTAGAAAAAGCATTGCAATATTCA	59.727	33.333	12.53	1.19	0.00	2.57
1260	3118	9.916397	GTATCTATTTACATTCAAGGTTTGACG	57.084	33.333	0.00	0.00	39.87	4.35
1270	3128	6.384258	TTCAAGGTTTGACGATGAAATGAA	57.616	33.333	0.00	0.00	39.87	2.57
1292	3150	8.883954	TGAAATTTGTTGCATTCTCATGTTAA	57.116	26.923	0.00	0.00	32.28	2.01
1293	3151	9.322773	TGAAATTTGTTGCATTCTCATGTTAAA	57.677	25.926	0.00	0.00	32.28	1.52
1340	3424	8.979574	AGCAGAATACGATAACAAAGTATAAGC	58.020	33.333	0.00	0.00	31.57	3.09
1457	3547	2.941720	GCATGGACTGATGAAGGAGAAC	59.058	50.000	0.00	0.00	0.00	3.01
1867	4351	4.489810	AGCTTTCGTCTGAAGTCATGTAG	58.510	43.478	0.00	0.00	35.06	2.74
1868	4352	4.218635	AGCTTTCGTCTGAAGTCATGTAGA	59.781	41.667	0.00	0.00	35.06	2.59
1880	4364	9.562408	CTGAAGTCATGTAGAGTAGTCCTTATA	57.438	37.037	0.00	0.00	0.00	0.98
1901	4385	0.833287	AGACATGCTGAATAGGCCGT	59.167	50.000	0.00	0.00	0.00	5.68
1918	4402	2.793232	GCCGTACCATCTTGTTATCGAC	59.207	50.000	0.00	0.00	0.00	4.20
1959	4443	2.916111	CCACTGCGTGTTGATTTGTAC	58.084	47.619	7.68	0.00	0.00	2.90
1964	4448	2.224426	TGCGTGTTGATTTGTACTCCCT	60.224	45.455	0.00	0.00	0.00	4.20
1965	4449	2.415512	GCGTGTTGATTTGTACTCCCTC	59.584	50.000	0.00	0.00	0.00	4.30
1966	4450	3.000727	CGTGTTGATTTGTACTCCCTCC	58.999	50.000	0.00	0.00	0.00	4.30
1967	4451	3.000727	GTGTTGATTTGTACTCCCTCCG	58.999	50.000	0.00	0.00	0.00	4.63
1968	4452	2.635915	TGTTGATTTGTACTCCCTCCGT	59.364	45.455	0.00	0.00	0.00	4.69
1969	4453	3.071892	TGTTGATTTGTACTCCCTCCGTT	59.928	43.478	0.00	0.00	0.00	4.44
1970	4454	3.604875	TGATTTGTACTCCCTCCGTTC	57.395	47.619	0.00	0.00	0.00	3.95
1971	4455	2.094390	TGATTTGTACTCCCTCCGTTCG	60.094	50.000	0.00	0.00	0.00	3.95
1972	4456	0.604578	TTTGTACTCCCTCCGTTCGG	59.395	55.000	4.74	4.74	0.00	4.30
1973	4457	0.251297	TTGTACTCCCTCCGTTCGGA	60.251	55.000	13.34	13.34	0.00	4.55
1974	4458	0.251297	TGTACTCCCTCCGTTCGGAA	60.251	55.000	14.79	0.04	33.41	4.30
1975	4459	1.109609	GTACTCCCTCCGTTCGGAAT	58.890	55.000	14.79	2.09	33.41	3.01
1976	4460	1.479730	GTACTCCCTCCGTTCGGAATT	59.520	52.381	14.79	0.00	33.41	2.17
1977	4461	1.856629	ACTCCCTCCGTTCGGAATTA	58.143	50.000	14.79	2.82	33.41	1.40
1978	4462	1.479730	ACTCCCTCCGTTCGGAATTAC	59.520	52.381	14.79	0.00	33.41	1.89
1979	4463	1.755380	CTCCCTCCGTTCGGAATTACT	59.245	52.381	14.79	0.00	33.41	2.24
1980	4464	1.753073	TCCCTCCGTTCGGAATTACTC	59.247	52.381	14.79	0.00	33.41	2.59
1981	4465	1.535437	CCCTCCGTTCGGAATTACTCG	60.535	57.143	14.79	1.97	33.41	4.18
1982	4466	1.133790	CCTCCGTTCGGAATTACTCGT	59.866	52.381	14.79	0.00	33.41	4.18
1983	4467	2.448219	CTCCGTTCGGAATTACTCGTC	58.552	52.381	14.79	0.00	33.41	4.20
1984	4468	1.133025	TCCGTTCGGAATTACTCGTCC	59.867	52.381	11.66	0.00	0.00	4.79
1985	4469	1.135315	CCGTTCGGAATTACTCGTCCA	60.135	52.381	5.19	0.00	33.10	4.02
1986	4470	2.598589	CGTTCGGAATTACTCGTCCAA	58.401	47.619	0.00	0.00	33.10	3.53
1987	4471	2.597305	CGTTCGGAATTACTCGTCCAAG	59.403	50.000	0.00	0.00	33.10	3.61
1988	4472	3.671433	CGTTCGGAATTACTCGTCCAAGA	60.671	47.826	0.00	0.00	33.10	3.02
1989	4473	4.240096	GTTCGGAATTACTCGTCCAAGAA	58.760	43.478	0.00	0.00	33.10	2.52
1990	4474	4.524316	TCGGAATTACTCGTCCAAGAAA	57.476	40.909	0.00	0.00	33.10	2.52
1991	4475	5.080969	TCGGAATTACTCGTCCAAGAAAT	57.919	39.130	0.00	0.00	33.10	2.17
1992	4476	4.868171	TCGGAATTACTCGTCCAAGAAATG	59.132	41.667	0.00	0.00	33.10	2.32
1993	4477	4.868171	CGGAATTACTCGTCCAAGAAATGA	59.132	41.667	0.00	0.00	33.10	2.57
1994	4478	5.350365	CGGAATTACTCGTCCAAGAAATGAA	59.650	40.000	0.00	0.00	33.10	2.57
1995	4479	6.037172	CGGAATTACTCGTCCAAGAAATGAAT	59.963	38.462	0.00	0.00	33.10	2.57
1996	4480	7.189512	GGAATTACTCGTCCAAGAAATGAATG	58.810	38.462	0.00	0.00	33.79	2.67
1997	4481	7.148239	GGAATTACTCGTCCAAGAAATGAATGT	60.148	37.037	0.00	0.00	33.79	2.71
1998	4482	8.786826	AATTACTCGTCCAAGAAATGAATGTA	57.213	30.769	0.00	0.00	0.00	2.29
1999	4483	8.964476	ATTACTCGTCCAAGAAATGAATGTAT	57.036	30.769	0.00	0.00	0.00	2.29
2000	4484	6.910536	ACTCGTCCAAGAAATGAATGTATC	57.089	37.500	0.00	0.00	0.00	2.24
2001	4485	6.644347	ACTCGTCCAAGAAATGAATGTATCT	58.356	36.000	0.00	0.00	0.00	1.98
2002	4486	7.782049	ACTCGTCCAAGAAATGAATGTATCTA	58.218	34.615	0.00	0.00	0.00	1.98
2003	4487	7.923344	ACTCGTCCAAGAAATGAATGTATCTAG	59.077	37.037	0.00	0.00	0.00	2.43
2004	4488	8.007405	TCGTCCAAGAAATGAATGTATCTAGA	57.993	34.615	0.00	0.00	0.00	2.43
2005	4489	8.642432	TCGTCCAAGAAATGAATGTATCTAGAT	58.358	33.333	10.73	10.73	0.00	1.98
2006	4490	8.706936	CGTCCAAGAAATGAATGTATCTAGATG	58.293	37.037	15.79	0.00	0.00	2.90
2007	4491	9.553064	GTCCAAGAAATGAATGTATCTAGATGT	57.447	33.333	15.79	0.00	0.00	3.06
2060	4544	8.746052	ATCCATTTTATGACAAGTAATTCCGA	57.254	30.769	0.00	0.00	0.00	4.55
2061	4545	8.568676	TCCATTTTATGACAAGTAATTCCGAA	57.431	30.769	0.00	0.00	0.00	4.30
2062	4546	8.455682	TCCATTTTATGACAAGTAATTCCGAAC	58.544	33.333	0.00	0.00	0.00	3.95
2063	4547	7.428183	CCATTTTATGACAAGTAATTCCGAACG	59.572	37.037	0.00	0.00	0.00	3.95
2064	4548	6.411630	TTTATGACAAGTAATTCCGAACGG	57.588	37.500	6.94	6.94	0.00	4.44
2065	4549	3.663995	TGACAAGTAATTCCGAACGGA	57.336	42.857	12.04	12.04	43.52	4.69
2066	4550	3.581755	TGACAAGTAATTCCGAACGGAG	58.418	45.455	15.34	5.60	46.06	4.63
2067	4551	2.928116	GACAAGTAATTCCGAACGGAGG	59.072	50.000	15.34	4.52	46.06	4.30
2068	4552	2.277084	CAAGTAATTCCGAACGGAGGG	58.723	52.381	15.34	0.00	46.06	4.30
2069	4553	1.856629	AGTAATTCCGAACGGAGGGA	58.143	50.000	15.34	2.49	46.06	4.20
2070	4554	1.755380	AGTAATTCCGAACGGAGGGAG	59.245	52.381	15.34	0.00	46.06	4.30
2071	4555	1.479730	GTAATTCCGAACGGAGGGAGT	59.520	52.381	15.34	4.12	46.06	3.85
2072	4556	1.856629	AATTCCGAACGGAGGGAGTA	58.143	50.000	15.34	1.05	46.06	2.59
2073	4557	2.083628	ATTCCGAACGGAGGGAGTAT	57.916	50.000	15.34	3.38	46.06	2.12
2074	4558	1.856629	TTCCGAACGGAGGGAGTATT	58.143	50.000	15.34	0.00	46.06	1.89
2075	4559	2.734755	TCCGAACGGAGGGAGTATTA	57.265	50.000	12.04	0.00	39.76	0.98
2076	4560	3.234234	TCCGAACGGAGGGAGTATTAT	57.766	47.619	12.04	0.00	39.76	1.28
2077	4561	2.889045	TCCGAACGGAGGGAGTATTATG	59.111	50.000	12.04	0.00	39.76	1.90
2078	4562	2.626743	CCGAACGGAGGGAGTATTATGT	59.373	50.000	7.53	0.00	37.50	2.29
2079	4563	3.069158	CCGAACGGAGGGAGTATTATGTT	59.931	47.826	7.53	0.00	37.50	2.71
2080	4564	4.049186	CGAACGGAGGGAGTATTATGTTG	58.951	47.826	0.00	0.00	0.00	3.33
2081	4565	3.470645	ACGGAGGGAGTATTATGTTGC	57.529	47.619	0.00	0.00	0.00	4.17
2082	4566	2.769663	ACGGAGGGAGTATTATGTTGCA	59.230	45.455	0.00	0.00	0.00	4.08
2083	4567	3.131396	CGGAGGGAGTATTATGTTGCAC	58.869	50.000	0.00	0.00	0.00	4.57
2084	4568	3.431626	CGGAGGGAGTATTATGTTGCACA	60.432	47.826	0.00	0.00	0.00	4.57
2085	4569	4.523083	GGAGGGAGTATTATGTTGCACAA	58.477	43.478	0.00	0.00	0.00	3.33
2086	4570	4.947388	GGAGGGAGTATTATGTTGCACAAA	59.053	41.667	0.00	0.00	0.00	2.83
2087	4571	5.417580	GGAGGGAGTATTATGTTGCACAAAA	59.582	40.000	0.00	0.00	0.00	2.44
2164	4824	6.899393	TTCATTTACATCCTTATCATGCCC	57.101	37.500	0.00	0.00	0.00	5.36
2245	8189	5.066893	GCAGCCAGATTATTGATCAAACTGA	59.933	40.000	23.71	9.88	37.22	3.41
2509	8671	6.157994	ACAGGTCCATACACACATAAAGGTAT	59.842	38.462	0.00	0.00	0.00	2.73
2514	8676	9.772973	GTCCATACACACATAAAGGTATATCAA	57.227	33.333	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.939577	CAATCCGACACTATCCGGCG	60.940	60.000	0.00	0.00	44.96	6.46
1	2	0.600255	CCAATCCGACACTATCCGGC	60.600	60.000	0.00	0.00	44.96	6.13
2	3	0.600255	GCCAATCCGACACTATCCGG	60.600	60.000	0.00	0.00	46.57	5.14
3	4	0.389391	AGCCAATCCGACACTATCCG	59.611	55.000	0.00	0.00	0.00	4.18
4	5	1.541233	CCAGCCAATCCGACACTATCC	60.541	57.143	0.00	0.00	0.00	2.59
12	13	2.734755	ATCATTTCCAGCCAATCCGA	57.265	45.000	0.00	0.00	0.00	4.55
13	14	2.954318	AGAATCATTTCCAGCCAATCCG	59.046	45.455	0.00	0.00	31.84	4.18
21	22	4.379813	CCACCGACAAAGAATCATTTCCAG	60.380	45.833	0.00	0.00	31.84	3.86
39	40	2.223572	GCTAATTCAAATCCTGCCACCG	60.224	50.000	0.00	0.00	0.00	4.94
174	175	5.786264	AAATAGGATCGGGTACTGTGTAG	57.214	43.478	0.00	0.00	35.30	2.74
177	178	4.989168	GCTAAAATAGGATCGGGTACTGTG	59.011	45.833	0.00	0.00	35.30	3.66
178	179	4.261909	CGCTAAAATAGGATCGGGTACTGT	60.262	45.833	0.00	0.00	35.30	3.55
272	457	1.398390	CTTTCGCCTTTCCCATTCTCG	59.602	52.381	0.00	0.00	0.00	4.04
455	642	7.505585	TCTGTTTTGAATGACTCCACCTATTTT	59.494	33.333	0.00	0.00	0.00	1.82
907	1237	6.260936	CGCCAATACTTCAGACATTTATTCCT	59.739	38.462	0.00	0.00	0.00	3.36
1012	1360	6.070824	TGAGATCTTGGCTCACACAGTATTTA	60.071	38.462	0.00	0.00	37.46	1.40
1145	1493	1.227556	GTTGCGCCGATCCCTGTAT	60.228	57.895	4.18	0.00	0.00	2.29
1260	3118	8.714179	TGAGAATGCAACAAATTTCATTTCATC	58.286	29.630	0.00	5.08	30.19	2.92
1301	3160	4.615912	CGTATTCTGCTTGGTTTCTTTGGG	60.616	45.833	0.00	0.00	0.00	4.12
1340	3424	3.671716	AGCAAAACTAGAAACCCGGTAG	58.328	45.455	0.00	0.00	0.00	3.18
1343	3427	3.435671	CAGTAGCAAAACTAGAAACCCGG	59.564	47.826	0.00	0.00	0.00	5.73
1387	3476	6.036517	GGCAGTAAGTTCAGACAATACATCAG	59.963	42.308	0.00	0.00	0.00	2.90
1457	3547	1.202651	ACCTTCCTGTTGAGTTGGACG	60.203	52.381	0.00	0.00	0.00	4.79
1811	4274	4.220382	TCTGCCCAAAATAACCACATCTTG	59.780	41.667	0.00	0.00	0.00	3.02
1852	4315	5.883673	AGGACTACTCTACATGACTTCAGAC	59.116	44.000	0.00	0.00	0.00	3.51
1867	4351	7.717568	TCAGCATGTCTTTATAAGGACTACTC	58.282	38.462	23.46	12.69	37.40	2.59
1868	4352	7.661536	TCAGCATGTCTTTATAAGGACTACT	57.338	36.000	23.46	16.26	37.40	2.57
1880	4364	2.292267	CGGCCTATTCAGCATGTCTTT	58.708	47.619	0.00	0.00	37.40	2.52
1918	4402	2.360165	GCTATTCAAGGATGGCCTGTTG	59.640	50.000	3.32	2.34	46.28	3.33
1959	4443	1.755380	AGTAATTCCGAACGGAGGGAG	59.245	52.381	15.34	0.00	46.06	4.30
1964	4448	1.133025	GGACGAGTAATTCCGAACGGA	59.867	52.381	12.04	12.04	43.52	4.69
1965	4449	1.135315	TGGACGAGTAATTCCGAACGG	60.135	52.381	6.94	6.94	0.00	4.44
1966	4450	2.267188	TGGACGAGTAATTCCGAACG	57.733	50.000	0.00	0.00	0.00	3.95
1967	4451	3.841643	TCTTGGACGAGTAATTCCGAAC	58.158	45.455	0.00	0.00	0.00	3.95
1968	4452	4.524316	TTCTTGGACGAGTAATTCCGAA	57.476	40.909	0.00	0.00	0.00	4.30
1969	4453	4.524316	TTTCTTGGACGAGTAATTCCGA	57.476	40.909	0.00	0.00	0.00	4.55
1970	4454	4.868171	TCATTTCTTGGACGAGTAATTCCG	59.132	41.667	0.00	0.00	0.00	4.30
1971	4455	6.737254	TTCATTTCTTGGACGAGTAATTCC	57.263	37.500	0.00	0.00	0.00	3.01
1972	4456	7.752695	ACATTCATTTCTTGGACGAGTAATTC	58.247	34.615	0.00	0.00	0.00	2.17
1973	4457	7.687941	ACATTCATTTCTTGGACGAGTAATT	57.312	32.000	0.00	0.00	0.00	1.40
1974	4458	8.964476	ATACATTCATTTCTTGGACGAGTAAT	57.036	30.769	0.00	0.00	0.00	1.89
1975	4459	8.258007	AGATACATTCATTTCTTGGACGAGTAA	58.742	33.333	0.00	0.00	0.00	2.24
1976	4460	7.782049	AGATACATTCATTTCTTGGACGAGTA	58.218	34.615	0.00	0.00	0.00	2.59
1977	4461	6.644347	AGATACATTCATTTCTTGGACGAGT	58.356	36.000	0.00	0.00	0.00	4.18
1978	4462	8.138074	TCTAGATACATTCATTTCTTGGACGAG	58.862	37.037	0.00	0.00	0.00	4.18
1979	4463	8.007405	TCTAGATACATTCATTTCTTGGACGA	57.993	34.615	0.00	0.00	0.00	4.20
1980	4464	8.706936	CATCTAGATACATTCATTTCTTGGACG	58.293	37.037	4.54	0.00	0.00	4.79
1981	4465	9.553064	ACATCTAGATACATTCATTTCTTGGAC	57.447	33.333	4.54	0.00	0.00	4.02
2034	4518	9.839817	TCGGAATTACTTGTCATAAAATGGATA	57.160	29.630	0.00	0.00	0.00	2.59
2035	4519	8.746052	TCGGAATTACTTGTCATAAAATGGAT	57.254	30.769	0.00	0.00	0.00	3.41
2036	4520	8.455682	GTTCGGAATTACTTGTCATAAAATGGA	58.544	33.333	0.00	0.00	0.00	3.41
2037	4521	7.428183	CGTTCGGAATTACTTGTCATAAAATGG	59.572	37.037	0.00	0.00	0.00	3.16
2038	4522	7.428183	CCGTTCGGAATTACTTGTCATAAAATG	59.572	37.037	5.19	0.00	0.00	2.32
2039	4523	7.334921	TCCGTTCGGAATTACTTGTCATAAAAT	59.665	33.333	11.66	0.00	0.00	1.82
2040	4524	6.649973	TCCGTTCGGAATTACTTGTCATAAAA	59.350	34.615	11.66	0.00	0.00	1.52
2041	4525	6.164876	TCCGTTCGGAATTACTTGTCATAAA	58.835	36.000	11.66	0.00	0.00	1.40
2042	4526	5.722263	TCCGTTCGGAATTACTTGTCATAA	58.278	37.500	11.66	0.00	0.00	1.90
2043	4527	5.327616	TCCGTTCGGAATTACTTGTCATA	57.672	39.130	11.66	0.00	0.00	2.15
2044	4528	4.181578	CTCCGTTCGGAATTACTTGTCAT	58.818	43.478	14.79	0.00	33.41	3.06
2045	4529	3.581755	CTCCGTTCGGAATTACTTGTCA	58.418	45.455	14.79	0.00	33.41	3.58
2046	4530	2.928116	CCTCCGTTCGGAATTACTTGTC	59.072	50.000	14.79	0.00	33.41	3.18
2047	4531	2.354403	CCCTCCGTTCGGAATTACTTGT	60.354	50.000	14.79	0.00	33.41	3.16
2048	4532	2.093869	TCCCTCCGTTCGGAATTACTTG	60.094	50.000	14.79	1.97	33.41	3.16
2049	4533	2.167900	CTCCCTCCGTTCGGAATTACTT	59.832	50.000	14.79	0.00	33.41	2.24
2050	4534	1.755380	CTCCCTCCGTTCGGAATTACT	59.245	52.381	14.79	0.00	33.41	2.24
2051	4535	1.479730	ACTCCCTCCGTTCGGAATTAC	59.520	52.381	14.79	0.00	33.41	1.89
2052	4536	1.856629	ACTCCCTCCGTTCGGAATTA	58.143	50.000	14.79	2.82	33.41	1.40
2053	4537	1.856629	TACTCCCTCCGTTCGGAATT	58.143	50.000	14.79	0.00	33.41	2.17
2054	4538	2.083628	ATACTCCCTCCGTTCGGAAT	57.916	50.000	14.79	2.14	33.41	3.01
2055	4539	1.856629	AATACTCCCTCCGTTCGGAA	58.143	50.000	14.79	0.00	33.41	4.30
2056	4540	2.734755	TAATACTCCCTCCGTTCGGA	57.265	50.000	13.34	13.34	0.00	4.55
2057	4541	2.626743	ACATAATACTCCCTCCGTTCGG	59.373	50.000	4.74	4.74	0.00	4.30
2058	4542	4.049186	CAACATAATACTCCCTCCGTTCG	58.951	47.826	0.00	0.00	0.00	3.95
2059	4543	3.808174	GCAACATAATACTCCCTCCGTTC	59.192	47.826	0.00	0.00	0.00	3.95
2060	4544	3.199071	TGCAACATAATACTCCCTCCGTT	59.801	43.478	0.00	0.00	0.00	4.44
2061	4545	2.769663	TGCAACATAATACTCCCTCCGT	59.230	45.455	0.00	0.00	0.00	4.69
2062	4546	3.131396	GTGCAACATAATACTCCCTCCG	58.869	50.000	0.00	0.00	36.32	4.63
2063	4547	4.150897	TGTGCAACATAATACTCCCTCC	57.849	45.455	0.00	0.00	45.67	4.30
2077	4561	1.227527	GGCCAGGGTTTTGTGCAAC	60.228	57.895	0.00	0.00	37.35	4.17
2078	4562	2.439104	GGGCCAGGGTTTTGTGCAA	61.439	57.895	4.39	0.00	0.00	4.08
2079	4563	2.841988	GGGCCAGGGTTTTGTGCA	60.842	61.111	4.39	0.00	0.00	4.57
2080	4564	2.099652	GAAGGGCCAGGGTTTTGTGC	62.100	60.000	6.18	0.00	0.00	4.57
2081	4565	0.469892	AGAAGGGCCAGGGTTTTGTG	60.470	55.000	6.18	0.00	0.00	3.33
2082	4566	0.178961	GAGAAGGGCCAGGGTTTTGT	60.179	55.000	6.18	0.00	0.00	2.83
2083	4567	1.244019	CGAGAAGGGCCAGGGTTTTG	61.244	60.000	6.18	0.00	0.00	2.44
2084	4568	1.074951	CGAGAAGGGCCAGGGTTTT	59.925	57.895	6.18	0.00	0.00	2.43
2085	4569	2.757077	CGAGAAGGGCCAGGGTTT	59.243	61.111	6.18	0.00	0.00	3.27
2086	4570	4.035102	GCGAGAAGGGCCAGGGTT	62.035	66.667	6.18	0.00	0.00	4.11
2109	4593	3.936372	GCAGAGCCATGCATGAAATAT	57.064	42.857	28.31	7.61	45.77	1.28
2156	4815	0.179045	GTTACAGAGGCGGGCATGAT	60.179	55.000	12.59	1.94	0.00	2.45
2164	4824	1.448540	CAGCAGGGTTACAGAGGCG	60.449	63.158	0.00	0.00	0.00	5.52
2245	8189	6.208007	CAGCCACACCATTATCATGATAACAT	59.792	38.462	26.51	12.15	36.24	2.71
2372	8495	9.530633	AGTACAACTTGTTTTAGACTTCAGTAG	57.469	33.333	0.00	0.00	0.00	2.57
2417	8541	2.919228	AGTGTGAGTGAACTTGGAACC	58.081	47.619	0.00	0.00	0.00	3.62
2509	8671	4.337836	TGTGTGCTGAAGTTTGCTTTGATA	59.662	37.500	3.99	0.00	34.61	2.15
2514	8676	2.287188	CGATGTGTGCTGAAGTTTGCTT	60.287	45.455	3.99	0.00	37.71	3.91
2516	8678	1.678360	CGATGTGTGCTGAAGTTTGC	58.322	50.000	0.00	0.00	0.00	3.68
2617	8807	4.322385	GTGACCAACAACGGCGCC	62.322	66.667	19.07	19.07	0.00	6.53
2618	8808	4.322385	GGTGACCAACAACGGCGC	62.322	66.667	6.90	0.00	0.00	6.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.