AutoCloner

Multiple sequence alignment - TraesCS3A01G384700

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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	TraesCS3A01G384700	chr3A	100.000	2495	0	0	1	2495	634660382	634657888	0.000000e+00	4608.0
1	TraesCS3A01G384700	chr3A	93.566	373	23	1	172	544	634548100	634547729	2.800000e-154	555.0
2	TraesCS3A01G384700	chr2D	92.405	1975	124	12	543	2495	12544106	12542136	0.000000e+00	2793.0
3	TraesCS3A01G384700	chr2D	90.344	1978	153	18	543	2495	590929804	590927840	0.000000e+00	2560.0
4	TraesCS3A01G384700	chr2D	100.000	33	0	0	1	33	1603291	1603259	7.450000e-06	62.1
5	TraesCS3A01G384700	chr7A	90.775	1973	145	16	545	2495	152034644	152036601	0.000000e+00	2601.0
6	TraesCS3A01G384700	chr7A	100.000	32	0	0	1	32	637172433	637172402	2.680000e-05	60.2
7	TraesCS3A01G384700	chr6A	90.404	1980	162	14	543	2495	574946044	574944066	0.000000e+00	2579.0
8	TraesCS3A01G384700	chr7B	90.061	1982	157	21	539	2495	685254381	685252415	0.000000e+00	2532.0
9	TraesCS3A01G384700	chr7B	100.000	30	0	0	3	32	653132179	653132208	3.470000e-04	56.5
10	TraesCS3A01G384700	chr3B	89.141	1980	182	17	535	2495	124502338	124500373	0.000000e+00	2435.0
11	TraesCS3A01G384700	chr3B	88.754	1983	185	21	535	2495	124560200	124558234	0.000000e+00	2392.0
12	TraesCS3A01G384700	chr3B	90.761	184	16	1	194	376	654173787	654173604	6.890000e-61	244.0
13	TraesCS3A01G384700	chr3B	100.000	32	0	0	1	32	149981151	149981120	2.680000e-05	60.2
14	TraesCS3A01G384700	chr2B	88.647	1973	194	22	536	2495	540525724	540527679	0.000000e+00	2375.0
15	TraesCS3A01G384700	chr5D	91.540	1643	117	10	844	2480	353835317	353833691	0.000000e+00	2244.0
16	TraesCS3A01G384700	chr5D	89.390	377	35	4	545	917	363887964	363888339	1.040000e-128	470.0
17	TraesCS3A01G384700	chr3D	95.174	373	17	1	172	544	494953898	494953527	2.760000e-164	588.0
18	TraesCS3A01G384700	chr3D	91.354	347	29	1	31	376	495231858	495231512	8.080000e-130	473.0
19	TraesCS3A01G384700	chr3D	94.161	137	8	0	408	544	495231417	495231281	2.510000e-50	209.0
20	TraesCS3A01G384700	chr6B	100.000	32	0	0	1	32	623085363	623085332	2.680000e-05	60.2
21	TraesCS3A01G384700	chr4B	100.000	32	0	0	1	32	625017881	625017912	2.680000e-05	60.2
22	TraesCS3A01G384700	chr1B	100.000	32	0	0	1	32	595754866	595754897	2.680000e-05	60.2
23	TraesCS3A01G384700	chr1A	100.000	32	0	0	1	32	505274835	505274804	2.680000e-05	60.2
24	TraesCS3A01G384700	chr7D	100.000	30	0	0	3	32	20298070	20298041	3.470000e-04	56.5

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	TraesCS3A01G384700	chr3A	634657888	634660382	2494	True	4608	4608	100.0000	1	2495	1	chr3A.!!$R2	2494
1	TraesCS3A01G384700	chr2D	12542136	12544106	1970	True	2793	2793	92.4050	543	2495	1	chr2D.!!$R2	1952
2	TraesCS3A01G384700	chr2D	590927840	590929804	1964	True	2560	2560	90.3440	543	2495	1	chr2D.!!$R3	1952
3	TraesCS3A01G384700	chr7A	152034644	152036601	1957	False	2601	2601	90.7750	545	2495	1	chr7A.!!$F1	1950
4	TraesCS3A01G384700	chr6A	574944066	574946044	1978	True	2579	2579	90.4040	543	2495	1	chr6A.!!$R1	1952
5	TraesCS3A01G384700	chr7B	685252415	685254381	1966	True	2532	2532	90.0610	539	2495	1	chr7B.!!$R1	1956
6	TraesCS3A01G384700	chr3B	124500373	124502338	1965	True	2435	2435	89.1410	535	2495	1	chr3B.!!$R1	1960
7	TraesCS3A01G384700	chr3B	124558234	124560200	1966	True	2392	2392	88.7540	535	2495	1	chr3B.!!$R2	1960
8	TraesCS3A01G384700	chr2B	540525724	540527679	1955	False	2375	2375	88.6470	536	2495	1	chr2B.!!$F1	1959
9	TraesCS3A01G384700	chr5D	353833691	353835317	1626	True	2244	2244	91.5400	844	2480	1	chr5D.!!$R1	1636
10	TraesCS3A01G384700	chr3D	495231281	495231858	577	True	341	473	92.7575	31	544	2	chr3D.!!$R2	513

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
625	690	0.250597	ACGTGCTCAGTTTTACCCCC	60.251	55.0	0.0	0.0	0.0	5.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2190	2308	0.400975	TTTGCCCTAGCGGTTACCAA	59.599	50.0	1.13	0.0	44.31	3.67	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
24	25	7.795482	TCTAAGACAAGAATTTTGGAACGAA	57.205	32.000	0.00	0.00	0.00	3.85
25	26	7.861630	TCTAAGACAAGAATTTTGGAACGAAG	58.138	34.615	0.00	0.00	0.00	3.79
26	27	5.438761	AGACAAGAATTTTGGAACGAAGG	57.561	39.130	0.00	0.00	0.00	3.46
27	28	4.278419	AGACAAGAATTTTGGAACGAAGGG	59.722	41.667	0.00	0.00	0.00	3.95
28	29	4.211920	ACAAGAATTTTGGAACGAAGGGA	58.788	39.130	0.00	0.00	0.00	4.20
29	30	4.278419	ACAAGAATTTTGGAACGAAGGGAG	59.722	41.667	0.00	0.00	0.00	4.30
41	42	2.308690	CGAAGGGAGTAGAAGGGTAGG	58.691	57.143	0.00	0.00	0.00	3.18
44	45	2.009165	AGGGAGTAGAAGGGTAGGTGT	58.991	52.381	0.00	0.00	0.00	4.16
49	50	4.095211	GAGTAGAAGGGTAGGTGTCCTTT	58.905	47.826	0.00	0.00	42.85	3.11
54	55	0.984995	GGGTAGGTGTCCTTTGCTCT	59.015	55.000	0.00	0.00	34.61	4.09
57	58	0.324943	TAGGTGTCCTTTGCTCTGCC	59.675	55.000	0.00	0.00	34.61	4.85
67	68	0.948678	TTGCTCTGCCGGTAAACAAC	59.051	50.000	1.90	0.00	0.00	3.32
69	70	0.517316	GCTCTGCCGGTAAACAACAG	59.483	55.000	1.90	0.00	0.00	3.16
91	92	6.891908	ACAGTGAAGAATAAAACATGCCCTAT	59.108	34.615	0.00	0.00	0.00	2.57
120	121	3.244387	GGGCTTTAACCTTTGAATTGCCA	60.244	43.478	0.00	0.00	39.56	4.92
160	161	4.351874	TTCTTAGGTGAGTGACAAAGGG	57.648	45.455	0.00	0.00	0.00	3.95
164	165	6.258354	TCTTAGGTGAGTGACAAAGGGTATA	58.742	40.000	0.00	0.00	0.00	1.47
166	167	7.402071	TCTTAGGTGAGTGACAAAGGGTATAAT	59.598	37.037	0.00	0.00	0.00	1.28
230	231	3.523606	AACAAGAAAGTGTGCATTGCA	57.476	38.095	7.38	7.38	35.60	4.08
255	256	7.754069	TCAAAACAGCTCACAAACATTTTAG	57.246	32.000	0.00	0.00	0.00	1.85
262	263	6.583806	CAGCTCACAAACATTTTAGGACATTC	59.416	38.462	0.00	0.00	0.00	2.67
282	284	9.722056	GACATTCATTATAATCAAAACGCTCTT	57.278	29.630	0.00	0.00	0.00	2.85
293	295	6.130298	TCAAAACGCTCTTGAAATTCTTGA	57.870	33.333	0.00	0.00	29.93	3.02
299	301	4.671250	CGCTCTTGAAATTCTTGAGCCTTC	60.671	45.833	23.47	7.57	44.94	3.46
308	310	1.625315	TCTTGAGCCTTCTAGCTTGCA	59.375	47.619	0.00	0.00	45.15	4.08
319	321	5.049543	CCTTCTAGCTTGCATCTTATTCTGC	60.050	44.000	0.00	0.00	38.87	4.26
342	344	3.932545	AGTGTGCTCACAAACAACAAA	57.067	38.095	20.16	0.00	46.01	2.83
352	354	6.751888	GCTCACAAACAACAAAGTTAGACAAT	59.248	34.615	0.00	0.00	0.00	2.71
365	367	1.786937	AGACAATGGTGGGCAAACAA	58.213	45.000	0.00	0.00	0.00	2.83
376	378	3.494251	GTGGGCAAACAAGCAATACTTTG	59.506	43.478	0.00	0.00	36.04	2.77
391	393	7.144722	CAATACTTTGCAGTCTTGATAACCA	57.855	36.000	0.00	0.00	38.72	3.67
392	394	6.743575	ATACTTTGCAGTCTTGATAACCAC	57.256	37.500	0.00	0.00	34.06	4.16
393	395	4.718961	ACTTTGCAGTCTTGATAACCACT	58.281	39.130	0.00	0.00	0.00	4.00
394	396	5.865085	ACTTTGCAGTCTTGATAACCACTA	58.135	37.500	0.00	0.00	0.00	2.74
397	399	3.260632	TGCAGTCTTGATAACCACTAGCA	59.739	43.478	0.00	0.00	0.00	3.49
398	400	4.253685	GCAGTCTTGATAACCACTAGCAA	58.746	43.478	0.00	0.00	34.75	3.91
399	401	4.695455	GCAGTCTTGATAACCACTAGCAAA	59.305	41.667	0.00	0.00	35.54	3.68
401	403	6.293955	GCAGTCTTGATAACCACTAGCAAAAA	60.294	38.462	0.00	0.00	35.54	1.94
427	492	5.469084	AGTCGGTTCCAAATTCTTTAGTGTC	59.531	40.000	0.00	0.00	0.00	3.67
541	606	4.278419	CAGTTCACCGAAAAGGGAAGAAAT	59.722	41.667	0.00	0.00	46.96	2.17
625	690	0.250597	ACGTGCTCAGTTTTACCCCC	60.251	55.000	0.00	0.00	0.00	5.40
657	722	1.338973	AGCTACTCGTTCCGTGAACAA	59.661	47.619	14.43	0.00	42.05	2.83
729	794	1.506718	CGGCAGAGACACGCTAGAA	59.493	57.895	0.00	0.00	0.00	2.10
856	953	1.660355	GGTGACAGAGAGCACGACA	59.340	57.895	0.00	0.00	35.91	4.35
924	1023	3.607987	GCGACGGCGTTGAGATCG	61.608	66.667	30.34	20.50	40.36	3.69
962	1061	2.290514	CCATGTCTTCTTCAAGCTCCCA	60.291	50.000	0.00	0.00	0.00	4.37
991	1090	0.390860	GCAGATGTAGAGCCCGACAT	59.609	55.000	0.00	0.00	40.55	3.06
1014	1113	3.250280	GCGTGGAGATGTCTATCTTCGTA	59.750	47.826	0.00	0.00	43.63	3.43
1047	1146	4.508128	GCGGGCGTTGATCGGAGA	62.508	66.667	0.00	0.00	45.75	3.71
1079	1178	3.138304	CACCAAAGAACCAGAATCGTCA	58.862	45.455	0.00	0.00	0.00	4.35
1083	1182	4.994852	CCAAAGAACCAGAATCGTCAGTTA	59.005	41.667	0.00	0.00	0.00	2.24
1104	1203	1.737735	CGTGTGCAGCGAGAATGGA	60.738	57.895	4.77	0.00	0.00	3.41
1127	1226	0.323725	AGAATCGGGGCAATTGCACT	60.324	50.000	30.53	12.40	45.56	4.40
1195	1294	3.940209	TCATGCAGGTGAAATGTTTCC	57.060	42.857	0.00	0.00	36.36	3.13
1216	1315	0.976641	TCTTTGGGTCGATGCTCTGT	59.023	50.000	0.00	0.00	0.00	3.41
1230	1329	3.701664	TGCTCTGTCCAAGACTCTGATA	58.298	45.455	0.00	0.00	33.15	2.15
1237	1336	7.855375	TCTGTCCAAGACTCTGATAAATGAAT	58.145	34.615	0.00	0.00	33.15	2.57
1281	1380	3.725459	CGCATGCTGCCACGAACA	61.725	61.111	17.13	0.00	41.12	3.18
1283	1382	2.327343	GCATGCTGCCACGAACAGA	61.327	57.895	11.37	0.00	37.42	3.41
1297	1396	3.429141	CAGAAGTGGCCGCAGCAG	61.429	66.667	20.59	2.59	42.56	4.24
1435	1534	5.559148	ACCCATTTGCAATTACTTTTGGA	57.441	34.783	0.00	0.00	0.00	3.53
1441	1540	8.351461	CCATTTGCAATTACTTTTGGACATTTT	58.649	29.630	0.00	0.00	0.00	1.82
1554	1653	9.965824	GAGAAATTCACCTTGTTTAAATCTTGA	57.034	29.630	0.00	0.00	0.00	3.02
1564	1664	8.490355	CCTTGTTTAAATCTTGATCAAAGTTGC	58.510	33.333	9.88	3.46	37.18	4.17
1643	1746	6.883756	GGGAGAAGAAATGAGAAGTTCAGAAT	59.116	38.462	5.50	0.00	39.68	2.40
1644	1747	7.065683	GGGAGAAGAAATGAGAAGTTCAGAATC	59.934	40.741	5.50	0.00	39.68	2.52
1815	1926	6.970484	AGATCTCTTGCGTGTTTTTATGTTT	58.030	32.000	0.00	0.00	0.00	2.83
1824	1935	7.473366	TGCGTGTTTTTATGTTTTCTGTTCTA	58.527	30.769	0.00	0.00	0.00	2.10
1980	2094	7.982761	TTACTCCAATTTAAATACACCGTGT	57.017	32.000	9.58	9.58	0.00	4.49
2000	2114	7.603024	ACCGTGTTTTAAATCAAAGACCAAAAA	59.397	29.630	0.55	0.00	28.27	1.94
2186	2304	0.677288	GGTTTGTGGTGTTTAGGGCC	59.323	55.000	0.00	0.00	0.00	5.80
2190	2308	3.943691	TGGTGTTTAGGGCCGCGT	61.944	61.111	4.92	0.00	0.00	6.01
2217	2336	0.740737	CGCTAGGGCAAATGGAAAGG	59.259	55.000	0.00	0.00	38.60	3.11
2400	2522	2.744202	CACATGGTTCTGGTTAGAGTGC	59.256	50.000	0.00	0.00	33.70	4.40
2406	2528	3.067833	GTTCTGGTTAGAGTGCCACTTC	58.932	50.000	0.00	0.00	33.70	3.01
2460	2582	6.833041	TGTTAGTTCATGACTTGGTTTAGGA	58.167	36.000	0.00	0.00	39.86	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.041372	CCTTCGTTCCAAAATTCTTGTCTTAGA	60.041	37.037	0.00	0.00	0.00	2.10
1	2	7.078228	CCTTCGTTCCAAAATTCTTGTCTTAG	58.922	38.462	0.00	0.00	0.00	2.18
2	3	6.016610	CCCTTCGTTCCAAAATTCTTGTCTTA	60.017	38.462	0.00	0.00	0.00	2.10
5	6	4.277423	TCCCTTCGTTCCAAAATTCTTGTC	59.723	41.667	0.00	0.00	0.00	3.18
7	8	4.278419	ACTCCCTTCGTTCCAAAATTCTTG	59.722	41.667	0.00	0.00	0.00	3.02
8	9	4.470602	ACTCCCTTCGTTCCAAAATTCTT	58.529	39.130	0.00	0.00	0.00	2.52
9	10	4.100279	ACTCCCTTCGTTCCAAAATTCT	57.900	40.909	0.00	0.00	0.00	2.40
10	11	5.243207	TCTACTCCCTTCGTTCCAAAATTC	58.757	41.667	0.00	0.00	0.00	2.17
11	12	5.237236	TCTACTCCCTTCGTTCCAAAATT	57.763	39.130	0.00	0.00	0.00	1.82
12	13	4.903045	TCTACTCCCTTCGTTCCAAAAT	57.097	40.909	0.00	0.00	0.00	1.82
13	14	4.504340	CCTTCTACTCCCTTCGTTCCAAAA	60.504	45.833	0.00	0.00	0.00	2.44
14	15	3.007614	CCTTCTACTCCCTTCGTTCCAAA	59.992	47.826	0.00	0.00	0.00	3.28
15	16	2.565834	CCTTCTACTCCCTTCGTTCCAA	59.434	50.000	0.00	0.00	0.00	3.53
16	17	2.176889	CCTTCTACTCCCTTCGTTCCA	58.823	52.381	0.00	0.00	0.00	3.53
17	18	1.481363	CCCTTCTACTCCCTTCGTTCC	59.519	57.143	0.00	0.00	0.00	3.62
18	19	2.177734	ACCCTTCTACTCCCTTCGTTC	58.822	52.381	0.00	0.00	0.00	3.95
19	20	2.322339	ACCCTTCTACTCCCTTCGTT	57.678	50.000	0.00	0.00	0.00	3.85
20	21	2.357986	CCTACCCTTCTACTCCCTTCGT	60.358	54.545	0.00	0.00	0.00	3.85
21	22	2.308690	CCTACCCTTCTACTCCCTTCG	58.691	57.143	0.00	0.00	0.00	3.79
22	23	3.032459	CACCTACCCTTCTACTCCCTTC	58.968	54.545	0.00	0.00	0.00	3.46
23	24	2.386113	ACACCTACCCTTCTACTCCCTT	59.614	50.000	0.00	0.00	0.00	3.95
24	25	2.009165	ACACCTACCCTTCTACTCCCT	58.991	52.381	0.00	0.00	0.00	4.20
25	26	2.386779	GACACCTACCCTTCTACTCCC	58.613	57.143	0.00	0.00	0.00	4.30
26	27	2.024177	AGGACACCTACCCTTCTACTCC	60.024	54.545	0.00	0.00	28.47	3.85
27	28	3.385314	AGGACACCTACCCTTCTACTC	57.615	52.381	0.00	0.00	28.47	2.59
28	29	3.838903	CAAAGGACACCTACCCTTCTACT	59.161	47.826	0.00	0.00	41.61	2.57
29	30	3.619242	GCAAAGGACACCTACCCTTCTAC	60.619	52.174	0.00	0.00	41.61	2.59
41	42	2.328099	CCGGCAGAGCAAAGGACAC	61.328	63.158	0.00	0.00	0.00	3.67
44	45	0.398696	TTTACCGGCAGAGCAAAGGA	59.601	50.000	0.00	0.00	0.00	3.36
49	50	0.179043	TGTTGTTTACCGGCAGAGCA	60.179	50.000	0.00	0.00	0.00	4.26
54	55	1.944024	CTTCACTGTTGTTTACCGGCA	59.056	47.619	0.00	0.00	0.00	5.69
57	58	7.911205	TGTTTTATTCTTCACTGTTGTTTACCG	59.089	33.333	0.00	0.00	0.00	4.02
67	68	5.649782	AGGGCATGTTTTATTCTTCACTG	57.350	39.130	0.00	0.00	0.00	3.66
69	70	6.476706	GCAATAGGGCATGTTTTATTCTTCAC	59.523	38.462	0.00	0.00	0.00	3.18
109	110	7.725251	AGACTAAAACTTGATGGCAATTCAAA	58.275	30.769	5.17	0.00	32.98	2.69
110	111	7.288810	AGACTAAAACTTGATGGCAATTCAA	57.711	32.000	3.70	3.70	32.68	2.69
146	147	8.106247	TGAAAATTATACCCTTTGTCACTCAC	57.894	34.615	0.00	0.00	0.00	3.51
200	201	8.572828	TGCACACTTTCTTGTTTTATATGTTG	57.427	30.769	0.00	0.00	0.00	3.33
230	231	7.439056	CCTAAAATGTTTGTGAGCTGTTTTGAT	59.561	33.333	0.00	0.00	0.00	2.57
255	256	8.345565	AGAGCGTTTTGATTATAATGAATGTCC	58.654	33.333	1.78	0.00	0.00	4.02
282	284	5.171339	AGCTAGAAGGCTCAAGAATTTCA	57.829	39.130	0.00	0.00	38.24	2.69
293	295	4.703379	ATAAGATGCAAGCTAGAAGGCT	57.297	40.909	0.00	0.00	45.30	4.58
319	321	3.573598	TGTTGTTTGTGAGCACACTTTG	58.426	40.909	15.43	0.00	46.07	2.77
326	328	5.182190	TGTCTAACTTTGTTGTTTGTGAGCA	59.818	36.000	0.00	0.00	0.00	4.26
342	344	2.890945	GTTTGCCCACCATTGTCTAACT	59.109	45.455	0.00	0.00	0.00	2.24
352	354	1.342819	GTATTGCTTGTTTGCCCACCA	59.657	47.619	0.00	0.00	0.00	4.17
376	378	3.861840	TGCTAGTGGTTATCAAGACTGC	58.138	45.455	0.00	0.00	0.00	4.40
377	379	6.801539	TTTTGCTAGTGGTTATCAAGACTG	57.198	37.500	0.00	0.00	0.00	3.51
399	401	7.704899	CACTAAAGAATTTGGAACCGACTTTTT	59.295	33.333	0.00	0.00	39.07	1.94
401	403	6.320418	ACACTAAAGAATTTGGAACCGACTTT	59.680	34.615	0.00	0.00	39.07	2.66
402	404	5.826208	ACACTAAAGAATTTGGAACCGACTT	59.174	36.000	0.00	0.00	39.07	3.01
403	405	5.374071	ACACTAAAGAATTTGGAACCGACT	58.626	37.500	0.00	0.00	39.07	4.18
405	407	5.617252	AGACACTAAAGAATTTGGAACCGA	58.383	37.500	0.00	0.00	39.07	4.69
406	408	5.941948	AGACACTAAAGAATTTGGAACCG	57.058	39.130	0.00	0.00	39.07	4.44
441	506	7.718753	AGGAAACTTTATGATTGGAGCTCATAG	59.281	37.037	17.19	0.10	37.44	2.23
483	548	7.550196	TGTTGGGATTCGTTTTTCCTACTATAC	59.450	37.037	0.00	0.00	32.34	1.47
488	553	5.441709	TTGTTGGGATTCGTTTTTCCTAC	57.558	39.130	0.00	0.00	32.34	3.18
498	563	2.160615	TGCGTGTATTTGTTGGGATTCG	59.839	45.455	0.00	0.00	0.00	3.34
541	606	6.747931	AGGGCAAAAGGATAATTAACCCTTA	58.252	36.000	17.67	0.00	42.56	2.69
625	690	1.150567	GAGTAGCTGCGCATGGACTG	61.151	60.000	12.24	0.00	0.00	3.51
729	794	1.086067	CGCATGCAACGGTCTGATCT	61.086	55.000	19.57	0.00	0.00	2.75
820	901	4.681978	GTGGTCACCGCCGCTCTT	62.682	66.667	0.00	0.00	36.19	2.85
856	953	2.910479	TCTGTCGCCGTGGTCACT	60.910	61.111	0.00	0.00	0.00	3.41
934	1033	4.321718	CTTGAAGAAGACATGGAGCTTGA	58.678	43.478	0.00	0.00	0.00	3.02
936	1035	3.080319	GCTTGAAGAAGACATGGAGCTT	58.920	45.455	0.00	0.00	0.00	3.74
962	1061	2.284798	CTACATCTGCGAGGTGGCGT	62.285	60.000	6.20	0.00	35.06	5.68
991	1090	2.033424	CGAAGATAGACATCTCCACGCA	59.967	50.000	0.00	0.00	40.81	5.24
1047	1146	3.694566	GGTTCTTTGGTGTGTGAGAAACT	59.305	43.478	0.00	0.00	33.99	2.66
1079	1178	1.471287	TCTCGCTGCACACGTATAACT	59.529	47.619	0.00	0.00	0.00	2.24
1083	1182	1.280982	CATTCTCGCTGCACACGTAT	58.719	50.000	0.00	0.00	0.00	3.06
1104	1203	2.024414	GCAATTGCCCCGATTCTTACT	58.976	47.619	20.06	0.00	34.31	2.24
1127	1226	3.899052	AAGATCCCGACCACGAAAATA	57.101	42.857	0.00	0.00	42.66	1.40
1195	1294	2.005451	CAGAGCATCGACCCAAAGAAG	58.995	52.381	0.00	0.00	42.67	2.85
1216	1315	6.885918	TGCAATTCATTTATCAGAGTCTTGGA	59.114	34.615	0.00	0.00	0.00	3.53
1230	1329	6.032956	TCATGCTCTTCTTGCAATTCATTT	57.967	33.333	0.00	0.00	44.01	2.32
1237	1336	4.082408	CCATTCTTCATGCTCTTCTTGCAA	60.082	41.667	0.00	0.00	44.01	4.08
1281	1380	4.711949	CCTGCTGCGGCCACTTCT	62.712	66.667	16.57	0.00	37.74	2.85
1283	1382	4.711949	CTCCTGCTGCGGCCACTT	62.712	66.667	16.57	0.00	37.74	3.16
1297	1396	1.068434	CATCTCTTCTTCCGGAGCTCC	59.932	57.143	23.79	23.79	0.00	4.70
1550	1649	8.578308	TCAACATTTAAGCAACTTTGATCAAG	57.422	30.769	8.41	5.87	38.64	3.02
1635	1738	9.084164	CATTTCATTGATCAAAGGATTCTGAAC	57.916	33.333	13.09	0.00	32.67	3.18
1643	1746	4.464951	AGCTGCATTTCATTGATCAAAGGA	59.535	37.500	13.09	10.46	0.00	3.36
1644	1747	4.755411	AGCTGCATTTCATTGATCAAAGG	58.245	39.130	13.09	8.14	0.00	3.11
1698	1807	2.731572	CTCTGAATTTGGCCCACAGAT	58.268	47.619	0.00	0.00	37.07	2.90
1730	1839	1.344763	GCCCATTAGTCTAGCCGACAT	59.655	52.381	6.53	0.00	45.32	3.06
2000	2114	3.256631	GCCGAGGCATATTTTCCATGATT	59.743	43.478	9.58	0.00	41.49	2.57
2001	2115	2.821969	GCCGAGGCATATTTTCCATGAT	59.178	45.455	9.58	0.00	41.49	2.45
2013	2127	1.255882	CTCTATCAGAGCCGAGGCAT	58.744	55.000	17.18	3.46	44.88	4.40
2176	2294	2.109517	TACCAACGCGGCCCTAAACA	62.110	55.000	12.47	0.00	39.03	2.83
2190	2308	0.400975	TTTGCCCTAGCGGTTACCAA	59.599	50.000	1.13	0.00	44.31	3.67
2217	2336	2.019984	CTTCCCTAGCCATGTCAAAGC	58.980	52.381	0.00	0.00	0.00	3.51
2400	2522	5.941647	TCCCTTTAAATCCTAAACGAAGTGG	59.058	40.000	0.00	0.00	45.00	4.00
2460	2582	5.184864	TCGTGCCCAAACATATCATTTCTTT	59.815	36.000	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.