AutoCloner

Multiple sequence alignment - TraesCS4A01G196400

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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	TraesCS4A01G196400	chr4A	100.000	3678	0	0	1	3678	478341040	478337363	0.000000e+00	6793.0
1	TraesCS4A01G196400	chr4A	94.281	1224	30	16	543	1752	478303189	478301992	0.000000e+00	1836.0
2	TraesCS4A01G196400	chr4A	85.586	1006	73	37	710	1681	478220000	478219033	0.000000e+00	989.0
3	TraesCS4A01G196400	chr4A	88.496	791	63	10	2178	2942	478301062	478300274	0.000000e+00	931.0
4	TraesCS4A01G196400	chr4A	81.142	578	71	27	3114	3678	478298335	478297783	2.620000e-116	429.0
5	TraesCS4A01G196400	chr4A	82.569	327	14	11	1876	2190	478301886	478301591	7.890000e-62	248.0
6	TraesCS4A01G196400	chr4A	86.066	122	11	6	1933	2049	478218764	478218644	3.860000e-25	126.0
7	TraesCS4A01G196400	chr4D	92.916	1821	79	26	1876	3650	97509603	97511419	0.000000e+00	2603.0
8	TraesCS4A01G196400	chr4D	92.501	1787	85	22	1909	3650	97606291	97608073	0.000000e+00	2512.0
9	TraesCS4A01G196400	chr4D	91.135	1004	34	15	864	1846	97508470	97509439	0.000000e+00	1310.0
10	TraesCS4A01G196400	chr4D	92.281	868	25	9	990	1846	97605241	97606077	0.000000e+00	1194.0
11	TraesCS4A01G196400	chr4D	91.768	826	56	7	1935	2753	97761011	97760191	0.000000e+00	1138.0
12	TraesCS4A01G196400	chr4D	93.534	696	29	4	990	1681	97720614	97721297	0.000000e+00	1022.0
13	TraesCS4A01G196400	chr4D	85.458	1004	78	37	711	1681	97957629	97958597	0.000000e+00	983.0
14	TraesCS4A01G196400	chr4D	94.701	585	25	2	210	791	97507855	97508436	0.000000e+00	904.0
15	TraesCS4A01G196400	chr4D	86.895	496	53	8	2186	2680	97959183	97959667	2.500000e-151	545.0
16	TraesCS4A01G196400	chr4D	82.918	562	68	18	3114	3660	97759804	97759256	7.140000e-132	481.0
17	TraesCS4A01G196400	chr4D	85.786	401	22	18	577	966	97604875	97605251	3.440000e-105	392.0
18	TraesCS4A01G196400	chr4D	85.100	349	23	16	577	916	97718304	97718632	2.740000e-86	329.0
19	TraesCS4A01G196400	chr4D	83.152	184	21	6	1933	2113	97958895	97959071	3.800000e-35	159.0
20	TraesCS4A01G196400	chr4D	91.892	111	4	3	87	197	97504910	97505015	2.290000e-32	150.0
21	TraesCS4A01G196400	chr4D	94.545	55	2	1	1876	1929	97606238	97606292	2.350000e-12	84.2
22	TraesCS4A01G196400	chr4B	90.684	1814	82	48	88	1868	139398200	139399959	0.000000e+00	2333.0
23	TraesCS4A01G196400	chr4B	89.447	1772	107	20	1963	3678	139516070	139517817	0.000000e+00	2163.0
24	TraesCS4A01G196400	chr4B	87.816	1346	82	53	543	1868	139471820	139473103	0.000000e+00	1502.0
25	TraesCS4A01G196400	chr4B	87.893	1305	77	52	543	1827	139510268	139511511	0.000000e+00	1459.0
26	TraesCS4A01G196400	chr4B	86.504	1104	99	25	1876	2942	139473140	139474230	0.000000e+00	1168.0
27	TraesCS4A01G196400	chr4B	86.413	1104	100	22	1876	2942	139399996	139401086	0.000000e+00	1162.0
28	TraesCS4A01G196400	chr4B	90.949	685	49	8	1935	2613	139531997	139532674	0.000000e+00	909.0
29	TraesCS4A01G196400	chr4B	88.957	489	26	17	1187	1673	139511506	139511968	2.460000e-161	579.0
30	TraesCS4A01G196400	chr4B	79.735	829	96	42	1878	2680	139545566	139546348	5.410000e-148	534.0
31	TraesCS4A01G196400	chr4B	84.375	320	46	3	3155	3471	139418193	139418511	9.920000e-81	311.0
32	TraesCS4A01G196400	chr4B	84.375	320	46	3	3155	3471	139449778	139450096	9.920000e-81	311.0
33	TraesCS4A01G196400	chr4B	84.375	320	46	3	3155	3471	139492099	139492417	9.920000e-81	311.0
34	TraesCS4A01G196400	chr4B	93.137	102	4	3	1876	1976	139515850	139515949	2.960000e-31	147.0
35	TraesCS4A01G196400	chr4B	94.915	59	3	0	1739	1797	139515620	139515678	3.910000e-15	93.5
36	TraesCS4A01G196400	chrUn	84.375	320	46	3	3155	3471	298309490	298309172	9.920000e-81	311.0
37	TraesCS4A01G196400	chrUn	84.062	320	47	3	3155	3471	202753122	202753440	4.610000e-79	305.0
38	TraesCS4A01G196400	chr6A	98.889	90	1	0	1	90	558902896	558902807	1.060000e-35	161.0
39	TraesCS4A01G196400	chr6A	97.826	92	2	0	1	92	31466151	31466242	3.800000e-35	159.0
40	TraesCS4A01G196400	chr3A	97.849	93	2	0	1	93	571169543	571169451	1.060000e-35	161.0
41	TraesCS4A01G196400	chr3A	96.739	92	3	0	1	92	432782329	432782238	1.770000e-33	154.0
42	TraesCS4A01G196400	chr3A	94.949	99	4	1	1	99	474832649	474832552	1.770000e-33	154.0
43	TraesCS4A01G196400	chr7A	97.826	92	2	0	1	92	292994052	292994143	3.800000e-35	159.0
44	TraesCS4A01G196400	chr7A	97.778	90	2	0	1	90	535618758	535618669	4.920000e-34	156.0
45	TraesCS4A01G196400	chr2A	97.778	90	2	0	1	90	595390904	595390993	4.920000e-34	156.0
46	TraesCS4A01G196400	chr5A	91.589	107	7	2	1	107	83333761	83333865	2.960000e-31	147.0

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	TraesCS4A01G196400	chr4A	478337363	478341040	3677	True	6793.000000	6793	100.000000	1	3678	1	chr4A.!!$R1	3677
1	TraesCS4A01G196400	chr4A	478297783	478303189	5406	True	861.000000	1836	86.622000	543	3678	4	chr4A.!!$R3	3135
2	TraesCS4A01G196400	chr4A	478218644	478220000	1356	True	557.500000	989	85.826000	710	2049	2	chr4A.!!$R2	1339
3	TraesCS4A01G196400	chr4D	97504910	97511419	6509	False	1241.750000	2603	92.661000	87	3650	4	chr4D.!!$F1	3563
4	TraesCS4A01G196400	chr4D	97604875	97608073	3198	False	1045.550000	2512	91.278250	577	3650	4	chr4D.!!$F2	3073
5	TraesCS4A01G196400	chr4D	97759256	97761011	1755	True	809.500000	1138	87.343000	1935	3660	2	chr4D.!!$R1	1725
6	TraesCS4A01G196400	chr4D	97718304	97721297	2993	False	675.500000	1022	89.317000	577	1681	2	chr4D.!!$F3	1104
7	TraesCS4A01G196400	chr4D	97957629	97959667	2038	False	562.333333	983	85.168333	711	2680	3	chr4D.!!$F4	1969
8	TraesCS4A01G196400	chr4B	139398200	139401086	2886	False	1747.500000	2333	88.548500	88	2942	2	chr4B.!!$F6	2854
9	TraesCS4A01G196400	chr4B	139471820	139474230	2410	False	1335.000000	1502	87.160000	543	2942	2	chr4B.!!$F7	2399
10	TraesCS4A01G196400	chr4B	139531997	139532674	677	False	909.000000	909	90.949000	1935	2613	1	chr4B.!!$F4	678
11	TraesCS4A01G196400	chr4B	139510268	139517817	7549	False	888.300000	2163	90.869800	543	3678	5	chr4B.!!$F8	3135
12	TraesCS4A01G196400	chr4B	139545566	139546348	782	False	534.000000	534	79.735000	1878	2680	1	chr4B.!!$F5	802

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
658	3499	0.171903	ATCGGCATGCAACAGCTTTC	59.828	50.0	21.36	0.0	0.00	2.62	F
1684	6537	0.328592	TCGCACTCTCAGGTAGGAGT	59.671	55.0	0.00	0.0	42.67	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2279	12349	0.038744	ATTGTGTGGGCTCCTGGAAG	59.961	55.0	0.0	0.0	0.00	3.46	R
3256	15168	0.677731	TGCCAGTGCATAGTTCAGCC	60.678	55.0	0.0	0.0	44.23	4.85	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
63	64	9.928236	GTTTGACTTCAGAGAATTCTAATATGC	57.072	33.333	8.25	0.00	30.73	3.14
64	65	9.671279	TTTGACTTCAGAGAATTCTAATATGCA	57.329	29.630	8.25	0.00	30.73	3.96
65	66	8.883954	TGACTTCAGAGAATTCTAATATGCAG	57.116	34.615	8.25	7.58	30.73	4.41
66	67	8.699130	TGACTTCAGAGAATTCTAATATGCAGA	58.301	33.333	8.25	0.00	30.73	4.26
67	68	9.195411	GACTTCAGAGAATTCTAATATGCAGAG	57.805	37.037	8.25	6.79	30.73	3.35
68	69	8.703743	ACTTCAGAGAATTCTAATATGCAGAGT	58.296	33.333	8.25	7.29	30.73	3.24
79	80	8.818141	TCTAATATGCAGAGTAAAAAGGATCG	57.182	34.615	0.00	0.00	0.00	3.69
80	81	6.867662	AATATGCAGAGTAAAAAGGATCGG	57.132	37.500	0.00	0.00	0.00	4.18
81	82	3.973206	TGCAGAGTAAAAAGGATCGGA	57.027	42.857	0.00	0.00	0.00	4.55
82	83	3.861840	TGCAGAGTAAAAAGGATCGGAG	58.138	45.455	0.00	0.00	0.00	4.63
83	84	3.198872	GCAGAGTAAAAAGGATCGGAGG	58.801	50.000	0.00	0.00	0.00	4.30
84	85	3.798202	CAGAGTAAAAAGGATCGGAGGG	58.202	50.000	0.00	0.00	0.00	4.30
85	86	3.451178	CAGAGTAAAAAGGATCGGAGGGA	59.549	47.826	0.00	0.00	0.00	4.20
140	141	5.134725	AGAATTGTCCCTGCCAAAGATAT	57.865	39.130	0.00	0.00	0.00	1.63
141	142	6.266131	AGAATTGTCCCTGCCAAAGATATA	57.734	37.500	0.00	0.00	0.00	0.86
142	143	6.064717	AGAATTGTCCCTGCCAAAGATATAC	58.935	40.000	0.00	0.00	0.00	1.47
143	144	5.653255	ATTGTCCCTGCCAAAGATATACT	57.347	39.130	0.00	0.00	0.00	2.12
144	145	4.422073	TGTCCCTGCCAAAGATATACTG	57.578	45.455	0.00	0.00	0.00	2.74
151	152	7.039011	TCCCTGCCAAAGATATACTGTACTATG	60.039	40.741	0.00	0.00	0.00	2.23
169	170	5.018809	ACTATGAATGTTTTGGCCATGACT	58.981	37.500	6.09	0.00	0.00	3.41
372	3200	3.045601	ACCTTGACATTTCTCGTGGAG	57.954	47.619	0.00	0.00	0.00	3.86
382	3210	6.149633	ACATTTCTCGTGGAGCAAAATAAAC	58.850	36.000	0.00	0.00	0.00	2.01
447	3275	5.001232	TCAACTACCTTTAAGTCCACATGC	58.999	41.667	0.00	0.00	0.00	4.06
492	3320	5.479124	AATTTGACGTAGGGTACAGAGTT	57.521	39.130	0.00	0.00	0.00	3.01
570	3398	2.611224	CCAAGGAAAGCAACATGAAGGC	60.611	50.000	0.00	0.00	0.00	4.35
571	3399	1.260544	AGGAAAGCAACATGAAGGCC	58.739	50.000	0.00	0.00	0.00	5.19
574	3402	0.539438	AAAGCAACATGAAGGCCGGA	60.539	50.000	5.05	0.00	0.00	5.14
658	3499	0.171903	ATCGGCATGCAACAGCTTTC	59.828	50.000	21.36	0.00	0.00	2.62
1356	6191	4.941309	GGGTGTTGTCCCGGCGTT	62.941	66.667	6.01	0.00	37.93	4.84
1485	6327	5.751990	ACCGTTCAACAAAGTCTAACACTAG	59.248	40.000	0.00	0.00	32.30	2.57
1682	6535	0.680280	GGTCGCACTCTCAGGTAGGA	60.680	60.000	0.00	0.00	0.00	2.94
1683	6536	0.736053	GTCGCACTCTCAGGTAGGAG	59.264	60.000	0.00	0.00	36.21	3.69
1684	6537	0.328592	TCGCACTCTCAGGTAGGAGT	59.671	55.000	0.00	0.00	42.67	3.85
1686	6539	1.944024	CGCACTCTCAGGTAGGAGTAG	59.056	57.143	0.00	0.00	40.33	2.57
1708	6561	9.645059	AGTAGTACATACATACATATACGACGT	57.355	33.333	5.52	5.52	36.79	4.34
1770	6674	4.711355	ACATAATCCCAAATCAACCACTGG	59.289	41.667	0.00	0.00	0.00	4.00
1853	11122	6.544197	TCAGGTAGTACAATTTTGCAGTTTGA	59.456	34.615	11.02	0.00	0.00	2.69
1855	11124	7.704472	CAGGTAGTACAATTTTGCAGTTTGAAA	59.296	33.333	11.02	0.00	0.00	2.69
1868	11137	4.677584	CAGTTTGAAATCCGAACCAACAA	58.322	39.130	0.00	0.00	39.49	2.83
1869	11138	4.502645	CAGTTTGAAATCCGAACCAACAAC	59.497	41.667	0.00	0.00	39.49	3.32
1871	11140	4.720649	TTGAAATCCGAACCAACAACAA	57.279	36.364	0.00	0.00	0.00	2.83
1872	11141	4.720649	TGAAATCCGAACCAACAACAAA	57.279	36.364	0.00	0.00	0.00	2.83
1873	11142	5.073311	TGAAATCCGAACCAACAACAAAA	57.927	34.783	0.00	0.00	0.00	2.44
1874	11143	5.479306	TGAAATCCGAACCAACAACAAAAA	58.521	33.333	0.00	0.00	0.00	1.94
2279	12349	4.106029	TGAGCTGACGGTATAACTTGTC	57.894	45.455	0.00	0.00	0.00	3.18
2394	12464	3.324930	CCAGTCAGGCTGCCCTCA	61.325	66.667	16.57	0.00	43.71	3.86
2445	12515	1.677552	CGCTGGACCTACAAACCCT	59.322	57.895	0.00	0.00	0.00	4.34
2462	12532	0.109226	CCTGACCGTCTTCGAGAACC	60.109	60.000	0.00	0.00	39.71	3.62
2582	12652	1.961180	TAGCCAGAGCGCCTTCTTCC	61.961	60.000	2.29	0.00	46.67	3.46
2593	12663	2.289444	CGCCTTCTTCCAGGACTTTGTA	60.289	50.000	0.00	0.00	35.71	2.41
2607	12677	5.669447	AGGACTTTGTAGAGGGAATGATCAT	59.331	40.000	1.18	1.18	0.00	2.45
2711	12788	1.573829	TTCCGCAGCAACAATCCGAC	61.574	55.000	0.00	0.00	0.00	4.79
2735	12812	5.863397	CGTTGTTACCATGCTTGAATTCATT	59.137	36.000	9.40	0.00	0.00	2.57
2755	12865	6.642430	TCATTATGATTTGCCCCTTTTCTTG	58.358	36.000	0.00	0.00	0.00	3.02
2801	12912	3.237268	ACAATACTGCCCTTTTGTGGA	57.763	42.857	0.00	0.00	31.45	4.02
2901	13017	7.473735	TTTCAATGTATGGAGTGGCAAATAA	57.526	32.000	0.00	0.00	0.00	1.40
2946	13062	6.248433	GGGCTAAAGATCAAATCCCATATGA	58.752	40.000	3.65	0.00	32.68	2.15
2965	13081	9.123902	CCATATGATTGGAACTCAAGTTATGAA	57.876	33.333	3.65	0.00	39.25	2.57
2998	14875	1.074395	TCCCCACCACACACTACCA	60.074	57.895	0.00	0.00	0.00	3.25
3025	14906	2.391972	CCCATGGGTTACCCTCCCC	61.392	68.421	23.93	0.00	45.70	4.81
3055	14956	5.478407	GCCACTTATAAAAACACTTGGCAT	58.522	37.500	4.42	0.00	46.23	4.40
3111	15013	8.737168	AAGTATGATATGCAGCAGAGTTTAAA	57.263	30.769	0.00	0.00	0.00	1.52
3127	15030	7.637519	CAGAGTTTAAACATGATATCGCACAAG	59.362	37.037	20.06	0.00	0.00	3.16
3133	15036	7.750229	AAACATGATATCGCACAAGGAATAT	57.250	32.000	0.00	0.00	0.00	1.28
3189	15097	3.878086	CGCAAGTCTTGTAACACACAT	57.122	42.857	14.03	0.00	36.90	3.21
3194	15102	7.173419	CGCAAGTCTTGTAACACACATTATAG	58.827	38.462	14.03	0.00	36.90	1.31
3238	15150	6.684686	CATCAAAGACACCAAAATGTGAGAT	58.315	36.000	0.00	0.00	39.57	2.75
3256	15168	6.127814	TGTGAGATAAGTTAACTACCCAGTCG	60.128	42.308	8.92	0.00	32.29	4.18
3257	15169	5.359009	TGAGATAAGTTAACTACCCAGTCGG	59.641	44.000	8.92	0.00	32.29	4.79
3296	15208	4.732784	CAGAAGAAGGAGAACTCTCTTCG	58.267	47.826	18.85	13.71	42.14	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	9.928236	GCATATTAGAATTCTCTGAAGTCAAAC	57.072	33.333	12.24	0.00	32.70	2.93
38	39	9.671279	TGCATATTAGAATTCTCTGAAGTCAAA	57.329	29.630	12.24	0.00	32.70	2.69
39	40	9.322773	CTGCATATTAGAATTCTCTGAAGTCAA	57.677	33.333	12.24	0.00	32.70	3.18
40	41	8.699130	TCTGCATATTAGAATTCTCTGAAGTCA	58.301	33.333	12.24	3.02	32.70	3.41
41	42	9.195411	CTCTGCATATTAGAATTCTCTGAAGTC	57.805	37.037	12.24	0.25	32.70	3.01
42	43	8.703743	ACTCTGCATATTAGAATTCTCTGAAGT	58.296	33.333	12.24	7.56	32.70	3.01
53	54	9.261180	CGATCCTTTTTACTCTGCATATTAGAA	57.739	33.333	0.00	0.00	0.00	2.10
54	55	7.872993	CCGATCCTTTTTACTCTGCATATTAGA	59.127	37.037	0.00	0.00	0.00	2.10
55	56	7.872993	TCCGATCCTTTTTACTCTGCATATTAG	59.127	37.037	0.00	0.00	0.00	1.73
56	57	7.732025	TCCGATCCTTTTTACTCTGCATATTA	58.268	34.615	0.00	0.00	0.00	0.98
57	58	6.591935	TCCGATCCTTTTTACTCTGCATATT	58.408	36.000	0.00	0.00	0.00	1.28
58	59	6.174720	TCCGATCCTTTTTACTCTGCATAT	57.825	37.500	0.00	0.00	0.00	1.78
59	60	5.453339	CCTCCGATCCTTTTTACTCTGCATA	60.453	44.000	0.00	0.00	0.00	3.14
60	61	4.446371	CTCCGATCCTTTTTACTCTGCAT	58.554	43.478	0.00	0.00	0.00	3.96
61	62	3.369471	CCTCCGATCCTTTTTACTCTGCA	60.369	47.826	0.00	0.00	0.00	4.41
62	63	3.198872	CCTCCGATCCTTTTTACTCTGC	58.801	50.000	0.00	0.00	0.00	4.26
63	64	3.451178	TCCCTCCGATCCTTTTTACTCTG	59.549	47.826	0.00	0.00	0.00	3.35
64	65	3.707102	CTCCCTCCGATCCTTTTTACTCT	59.293	47.826	0.00	0.00	0.00	3.24
65	66	3.451540	ACTCCCTCCGATCCTTTTTACTC	59.548	47.826	0.00	0.00	0.00	2.59
66	67	3.451890	ACTCCCTCCGATCCTTTTTACT	58.548	45.455	0.00	0.00	0.00	2.24
67	68	3.908643	ACTCCCTCCGATCCTTTTTAC	57.091	47.619	0.00	0.00	0.00	2.01
68	69	4.355549	TGTACTCCCTCCGATCCTTTTTA	58.644	43.478	0.00	0.00	0.00	1.52
69	70	3.178865	TGTACTCCCTCCGATCCTTTTT	58.821	45.455	0.00	0.00	0.00	1.94
70	71	2.829023	TGTACTCCCTCCGATCCTTTT	58.171	47.619	0.00	0.00	0.00	2.27
71	72	2.544844	TGTACTCCCTCCGATCCTTT	57.455	50.000	0.00	0.00	0.00	3.11
72	73	2.320781	CATGTACTCCCTCCGATCCTT	58.679	52.381	0.00	0.00	0.00	3.36
73	74	2.002505	CATGTACTCCCTCCGATCCT	57.997	55.000	0.00	0.00	0.00	3.24
74	75	0.318762	GCATGTACTCCCTCCGATCC	59.681	60.000	0.00	0.00	0.00	3.36
75	76	1.333177	AGCATGTACTCCCTCCGATC	58.667	55.000	0.00	0.00	0.00	3.69
76	77	2.240279	GTAGCATGTACTCCCTCCGAT	58.760	52.381	0.00	0.00	0.00	4.18
77	78	1.688772	GTAGCATGTACTCCCTCCGA	58.311	55.000	0.00	0.00	0.00	4.55
78	79	0.674534	GGTAGCATGTACTCCCTCCG	59.325	60.000	0.00	0.00	0.00	4.63
79	80	1.689273	CAGGTAGCATGTACTCCCTCC	59.311	57.143	0.00	0.00	0.00	4.30
80	81	1.689273	CCAGGTAGCATGTACTCCCTC	59.311	57.143	0.00	0.00	0.00	4.30
81	82	1.291033	TCCAGGTAGCATGTACTCCCT	59.709	52.381	0.00	0.00	0.00	4.20
82	83	1.689273	CTCCAGGTAGCATGTACTCCC	59.311	57.143	0.00	0.00	0.00	4.30
83	84	1.689273	CCTCCAGGTAGCATGTACTCC	59.311	57.143	0.00	0.00	0.00	3.85
84	85	2.625790	CTCCTCCAGGTAGCATGTACTC	59.374	54.545	0.00	0.00	36.34	2.59
85	86	2.245028	TCTCCTCCAGGTAGCATGTACT	59.755	50.000	0.00	0.00	36.34	2.73
140	141	6.477253	TGGCCAAAACATTCATAGTACAGTA	58.523	36.000	0.61	0.00	0.00	2.74
141	142	5.321102	TGGCCAAAACATTCATAGTACAGT	58.679	37.500	0.61	0.00	0.00	3.55
142	143	5.895636	TGGCCAAAACATTCATAGTACAG	57.104	39.130	0.61	0.00	0.00	2.74
143	144	5.948758	TCATGGCCAAAACATTCATAGTACA	59.051	36.000	10.96	0.00	0.00	2.90
144	145	6.095440	AGTCATGGCCAAAACATTCATAGTAC	59.905	38.462	10.96	0.00	0.00	2.73
151	152	4.114794	GCATAGTCATGGCCAAAACATTC	58.885	43.478	10.96	0.00	32.36	2.67
169	170	2.076100	CAGAAACTGAAGGCACGCATA	58.924	47.619	0.00	0.00	32.44	3.14
200	201	1.818060	CGGCACCATTTCATTTCTCCA	59.182	47.619	0.00	0.00	0.00	3.86
201	202	1.469767	GCGGCACCATTTCATTTCTCC	60.470	52.381	0.00	0.00	0.00	3.71
202	203	1.469767	GGCGGCACCATTTCATTTCTC	60.470	52.381	3.07	0.00	38.86	2.87
203	204	0.532115	GGCGGCACCATTTCATTTCT	59.468	50.000	3.07	0.00	38.86	2.52
204	205	0.801836	CGGCGGCACCATTTCATTTC	60.802	55.000	10.53	0.00	39.03	2.17
205	206	1.215117	CGGCGGCACCATTTCATTT	59.785	52.632	10.53	0.00	39.03	2.32
207	208	3.140141	CCGGCGGCACCATTTCAT	61.140	61.111	15.42	0.00	39.03	2.57
208	209	4.337177	TCCGGCGGCACCATTTCA	62.337	61.111	23.83	0.00	39.03	2.69
239	3067	3.223435	TCTCAAGTTTCGAGGACAGACT	58.777	45.455	4.19	0.00	0.00	3.24
372	3200	5.404066	ACATTAACACGCTGGTTTATTTTGC	59.596	36.000	0.00	0.00	32.29	3.68
382	3210	4.945246	AGAGGTATACATTAACACGCTGG	58.055	43.478	5.01	0.00	0.00	4.85
459	3287	6.014327	ACCCTACGTCAAATTTAGGTCACTAA	60.014	38.462	0.00	0.00	37.40	2.24
462	3290	4.572909	ACCCTACGTCAAATTTAGGTCAC	58.427	43.478	0.00	0.00	31.85	3.67
479	3307	3.024547	CTGCTAGCAACTCTGTACCCTA	58.975	50.000	19.86	0.00	0.00	3.53
492	3320	0.679505	ACCGACAGTTTCTGCTAGCA	59.320	50.000	18.22	18.22	34.37	3.49
529	3357	4.585879	TGGCTTCGGAAAATTACTAGCTT	58.414	39.130	0.00	0.00	0.00	3.74
570	3398	2.802792	CTTGCATGCATGGTCCGG	59.197	61.111	27.34	0.00	0.00	5.14
571	3399	2.103538	GCTTGCATGCATGGTCCG	59.896	61.111	28.66	12.59	0.00	4.79
601	3441	2.223876	ACGACACGGTTAAGCAAAGAGA	60.224	45.455	5.38	0.00	0.00	3.10
658	3499	1.142870	TGAACAGTTCTGTTCTGGGGG	59.857	52.381	31.73	0.00	45.98	5.40
1485	6327	2.223144	ACGTACACAATGCATGTCACAC	59.777	45.455	0.00	0.00	41.46	3.82
1612	6465	1.373748	GAGCGACGTAAGGTTGGCA	60.374	57.895	0.00	0.00	46.39	4.92
1682	6535	9.645059	ACGTCGTATATGTATGTATGTACTACT	57.355	33.333	0.00	0.00	0.00	2.57
1707	6560	6.306117	GGTTTATTTTGCATGTACCGTGTAAC	59.694	38.462	0.00	0.00	0.00	2.50
1708	6561	6.380190	GGTTTATTTTGCATGTACCGTGTAA	58.620	36.000	0.00	0.00	0.00	2.41
1770	6674	4.268359	AGAAGAAGGTTGATGGAAGATGC	58.732	43.478	0.00	0.00	0.00	3.91
1827	10990	5.941948	ACTGCAAAATTGTACTACCTGAC	57.058	39.130	0.00	0.00	0.00	3.51
1872	11141	6.920210	GCACAGAATCTTACTTGCTTCTTTTT	59.080	34.615	0.00	0.00	0.00	1.94
1873	11142	6.264067	AGCACAGAATCTTACTTGCTTCTTTT	59.736	34.615	0.97	0.00	36.97	2.27
1874	11143	5.767168	AGCACAGAATCTTACTTGCTTCTTT	59.233	36.000	0.97	0.00	36.97	2.52
1888	11193	5.576384	CAGTCTGAGAAAGTAGCACAGAATC	59.424	44.000	0.00	0.00	38.90	2.52
2050	11529	7.657761	ACTTTGTAACTCATCACCTGTAAAGAG	59.342	37.037	0.00	0.00	0.00	2.85
2051	11530	7.506114	ACTTTGTAACTCATCACCTGTAAAGA	58.494	34.615	0.00	0.00	0.00	2.52
2279	12349	0.038744	ATTGTGTGGGCTCCTGGAAG	59.961	55.000	0.00	0.00	0.00	3.46
2408	12478	4.368808	CGCCAGGTTGTTGTCGCG	62.369	66.667	0.00	0.00	0.00	5.87
2437	12507	0.249741	CGAAGACGGTCAGGGTTTGT	60.250	55.000	11.27	0.00	35.72	2.83
2445	12515	0.313043	GTGGTTCTCGAAGACGGTCA	59.687	55.000	11.27	0.00	40.21	4.02
2462	12532	5.354513	TCTGGACGAGATTCTTGTAGTAGTG	59.645	44.000	6.54	0.00	0.00	2.74
2551	12621	2.577700	CTCTGGCTACCGACATACTCT	58.422	52.381	0.00	0.00	0.00	3.24
2582	12652	4.826274	TCATTCCCTCTACAAAGTCCTG	57.174	45.455	0.00	0.00	0.00	3.86
2593	12663	2.648304	CCCCATCATGATCATTCCCTCT	59.352	50.000	5.16	0.00	0.00	3.69
2735	12812	6.154363	CCTTACAAGAAAAGGGGCAAATCATA	59.846	38.462	0.00	0.00	39.94	2.15
2946	13062	7.721399	AGAGTTGTTCATAACTTGAGTTCCAAT	59.279	33.333	0.00	0.00	40.78	3.16
2965	13081	3.009143	GGTGGGGACTTTATCAGAGTTGT	59.991	47.826	0.00	0.00	0.00	3.32
3025	14906	0.748729	TTTTATAAGTGGCGGGCGGG	60.749	55.000	0.00	0.00	0.00	6.13
3111	15013	7.615403	ACTATATTCCTTGTGCGATATCATGT	58.385	34.615	3.12	0.00	0.00	3.21
3194	15102	8.430805	TTTGATGCCAATGGATGACAAAAAGTC	61.431	37.037	2.05	0.00	38.73	3.01
3238	15150	3.194116	CAGCCGACTGGGTAGTTAACTTA	59.806	47.826	14.49	0.00	46.57	2.24
3256	15168	0.677731	TGCCAGTGCATAGTTCAGCC	60.678	55.000	0.00	0.00	44.23	4.85
3257	15169	2.858622	TGCCAGTGCATAGTTCAGC	58.141	52.632	0.00	0.00	44.23	4.26
3296	15208	6.153000	TGAGAAGTTACTGGAGGTCATAAGAC	59.847	42.308	0.00	0.00	44.21	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.