AutoCloner

Multiple sequence alignment - TraesCS4B01G026900

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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	TraesCS4B01G026900	chr4B	100.000	2525	0	0	1	2525	20354967	20352443	0.000000e+00	4663.0
1	TraesCS4B01G026900	chr4B	96.347	1670	28	17	867	2525	20326185	20324538	0.000000e+00	2715.0
2	TraesCS4B01G026900	chr4B	88.995	209	8	6	1631	1832	17179578	17179778	6.980000e-61	244.0
3	TraesCS4B01G026900	chr4B	87.793	213	9	6	1631	1834	17216655	17216859	1.510000e-57	233.0
4	TraesCS4B01G026900	chr4A	90.712	1432	70	22	867	2286	591523194	591521814	0.000000e+00	1849.0
5	TraesCS4B01G026900	chr4A	90.343	1429	73	27	867	2283	592521114	592522489	0.000000e+00	1814.0
6	TraesCS4B01G026900	chr4A	90.343	1429	69	22	867	2283	593087672	593089043	0.000000e+00	1810.0
7	TraesCS4B01G026900	chr4A	90.063	1429	71	28	867	2283	592807413	592808782	0.000000e+00	1786.0
8	TraesCS4B01G026900	chr4A	87.557	659	65	12	1	654	591674776	591674130	0.000000e+00	747.0
9	TraesCS4B01G026900	chr4A	87.771	646	64	11	15	654	591293496	591292860	0.000000e+00	741.0
10	TraesCS4B01G026900	chr4A	87.253	659	68	12	1	654	592362171	592362818	0.000000e+00	737.0
11	TraesCS4B01G026900	chr4A	87.253	659	67	12	1	654	592927504	592928150	0.000000e+00	736.0
12	TraesCS4B01G026900	chr4A	87.102	659	68	12	1	654	591284645	591285291	0.000000e+00	730.0
13	TraesCS4B01G026900	chr4A	87.102	659	68	12	1	654	591347272	591346626	0.000000e+00	730.0
14	TraesCS4B01G026900	chr4A	87.102	659	66	13	1	654	591416789	591416145	0.000000e+00	728.0
15	TraesCS4B01G026900	chr4A	86.950	659	68	12	1	654	592309894	592310539	0.000000e+00	725.0
16	TraesCS4B01G026900	chr4A	86.950	659	68	12	1	654	592335851	592336496	0.000000e+00	725.0
17	TraesCS4B01G026900	chr4A	91.429	210	14	2	2316	2525	592523631	592523836	4.110000e-73	285.0
18	TraesCS4B01G026900	chr4A	91.429	210	14	2	2316	2525	593090185	593090390	4.110000e-73	285.0
19	TraesCS4B01G026900	chr4A	87.978	183	15	2	1125	1307	591454973	591454798	2.550000e-50	209.0
20	TraesCS4B01G026900	chr4A	87.978	183	15	2	1125	1307	592599878	592600053	2.550000e-50	209.0
21	TraesCS4B01G026900	chr4D	95.221	1088	35	6	522	1605	10810820	10809746	0.000000e+00	1705.0
22	TraesCS4B01G026900	chr4D	94.902	510	25	1	2016	2525	10809343	10808835	0.000000e+00	797.0
23	TraesCS4B01G026900	chr4D	94.335	406	9	5	1634	2035	10809755	10809360	5.970000e-171	610.0
24	TraesCS4B01G026900	chrUn	94.705	661	24	4	1626	2283	406815682	406816334	0.000000e+00	1016.0
25	TraesCS4B01G026900	chrUn	89.342	760	47	15	867	1617	390753515	390754249	0.000000e+00	924.0
26	TraesCS4B01G026900	chr5B	83.173	208	31	2	2314	2521	399795885	399796088	1.190000e-43	187.0
27	TraesCS4B01G026900	chr5B	84.431	167	22	3	1928	2094	34915540	34915378	7.230000e-36	161.0
28	TraesCS4B01G026900	chr3D	82.857	175	30	0	2109	2283	579316343	579316169	9.350000e-35	158.0
29	TraesCS4B01G026900	chr3D	89.706	68	7	0	2387	2454	9956026	9956093	1.240000e-13	87.9
30	TraesCS4B01G026900	chr5A	82.386	176	29	2	2109	2283	67985567	67985393	4.350000e-33	152.0
31	TraesCS4B01G026900	chr6A	83.688	141	17	2	2314	2454	436850278	436850412	7.330000e-26	128.0
32	TraesCS4B01G026900	chr2B	81.159	69	10	2	2316	2384	440695747	440695812	5.000000e-03	52.8

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	TraesCS4B01G026900	chr4B	20352443	20354967	2524	True	4663.000000	4663	100.000000	1	2525	1	chr4B.!!$R2	2524
1	TraesCS4B01G026900	chr4B	20324538	20326185	1647	True	2715.000000	2715	96.347000	867	2525	1	chr4B.!!$R1	1658
2	TraesCS4B01G026900	chr4A	591521814	591523194	1380	True	1849.000000	1849	90.712000	867	2286	1	chr4A.!!$R5	1419
3	TraesCS4B01G026900	chr4A	592807413	592808782	1369	False	1786.000000	1786	90.063000	867	2283	1	chr4A.!!$F6	1416
4	TraesCS4B01G026900	chr4A	592521114	592523836	2722	False	1049.500000	1814	90.886000	867	2525	2	chr4A.!!$F8	1658
5	TraesCS4B01G026900	chr4A	593087672	593090390	2718	False	1047.500000	1810	90.886000	867	2525	2	chr4A.!!$F9	1658
6	TraesCS4B01G026900	chr4A	591674130	591674776	646	True	747.000000	747	87.557000	1	654	1	chr4A.!!$R6	653
7	TraesCS4B01G026900	chr4A	591292860	591293496	636	True	741.000000	741	87.771000	15	654	1	chr4A.!!$R1	639
8	TraesCS4B01G026900	chr4A	592362171	592362818	647	False	737.000000	737	87.253000	1	654	1	chr4A.!!$F4	653
9	TraesCS4B01G026900	chr4A	592927504	592928150	646	False	736.000000	736	87.253000	1	654	1	chr4A.!!$F7	653
10	TraesCS4B01G026900	chr4A	591284645	591285291	646	False	730.000000	730	87.102000	1	654	1	chr4A.!!$F1	653
11	TraesCS4B01G026900	chr4A	591346626	591347272	646	True	730.000000	730	87.102000	1	654	1	chr4A.!!$R2	653
12	TraesCS4B01G026900	chr4A	591416145	591416789	644	True	728.000000	728	87.102000	1	654	1	chr4A.!!$R3	653
13	TraesCS4B01G026900	chr4A	592309894	592310539	645	False	725.000000	725	86.950000	1	654	1	chr4A.!!$F2	653
14	TraesCS4B01G026900	chr4A	592335851	592336496	645	False	725.000000	725	86.950000	1	654	1	chr4A.!!$F3	653
15	TraesCS4B01G026900	chr4D	10808835	10810820	1985	True	1037.333333	1705	94.819333	522	2525	3	chr4D.!!$R1	2003
16	TraesCS4B01G026900	chrUn	406815682	406816334	652	False	1016.000000	1016	94.705000	1626	2283	1	chrUn.!!$F2	657
17	TraesCS4B01G026900	chrUn	390753515	390754249	734	False	924.000000	924	89.342000	867	1617	1	chrUn.!!$F1	750

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
407	412	0.238289	GATGTTGTGGCCACGTGAAG	59.762	55.0	30.07	1.58	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1609	1646	0.179227	CACACACACACACACACACG	60.179	55.0	0.0	0.0	0.0	4.49	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	2.788807	AGCAATCTCCTCCTCTCCTCTA	59.211	50.000	0.00	0.00	0.00	2.43
32	33	1.423921	CCTCCTCTCCTCTACTCTCCC	59.576	61.905	0.00	0.00	0.00	4.30
38	41	4.161377	CCTCTCCTCTACTCTCCCTTTTTG	59.839	50.000	0.00	0.00	0.00	2.44
52	55	4.656112	TCCCTTTTTGGCCAAACTCATTAA	59.344	37.500	30.43	18.84	0.00	1.40
53	56	5.131142	TCCCTTTTTGGCCAAACTCATTAAA	59.869	36.000	30.43	18.14	0.00	1.52
55	58	6.054941	CCTTTTTGGCCAAACTCATTAAACT	58.945	36.000	30.43	0.00	0.00	2.66
86	89	5.722263	TCTTCATGCCACAAACCAATAATG	58.278	37.500	0.00	0.00	0.00	1.90
104	107	8.393366	CCAATAATGGTAGCATTGATTAGATCG	58.607	37.037	26.41	4.03	42.18	3.69
140	143	1.140252	CCTCGTGGGGTGGGTAATAAG	59.860	57.143	0.00	0.00	0.00	1.73
142	145	2.102588	CTCGTGGGGTGGGTAATAAGAG	59.897	54.545	0.00	0.00	0.00	2.85
143	146	1.835531	CGTGGGGTGGGTAATAAGAGT	59.164	52.381	0.00	0.00	0.00	3.24
145	148	3.451902	CGTGGGGTGGGTAATAAGAGTAA	59.548	47.826	0.00	0.00	0.00	2.24
181	186	3.338249	ACGTTGGAAGATGTGATTGGAG	58.662	45.455	0.00	0.00	0.00	3.86
182	187	3.244561	ACGTTGGAAGATGTGATTGGAGT	60.245	43.478	0.00	0.00	0.00	3.85
216	221	1.675720	GGCCCACCCCATGAAAATCG	61.676	60.000	0.00	0.00	0.00	3.34
239	244	5.883685	GGGGGCATAGTTAGTTAGTTACT	57.116	43.478	0.00	0.00	41.04	2.24
241	246	6.990798	GGGGGCATAGTTAGTTAGTTACTAG	58.009	44.000	0.00	0.00	40.35	2.57
242	247	6.552725	GGGGGCATAGTTAGTTAGTTACTAGT	59.447	42.308	0.00	0.00	40.35	2.57
243	248	7.725844	GGGGGCATAGTTAGTTAGTTACTAGTA	59.274	40.741	0.00	0.00	40.35	1.82
244	249	9.136323	GGGGCATAGTTAGTTAGTTACTAGTAA	57.864	37.037	11.38	11.38	40.35	2.24
278	283	0.461961	CTCTTCTTAGGAGCCCGTGG	59.538	60.000	0.00	0.00	0.00	4.94
284	289	1.760613	CTTAGGAGCCCGTGGATGTAA	59.239	52.381	0.00	0.00	0.00	2.41
294	299	2.477189	CCGTGGATGTAACATTTTCGGC	60.477	50.000	0.00	0.00	0.00	5.54
309	314	3.331478	TTCGGCGTAATAACCTTCCAA	57.669	42.857	6.85	0.00	0.00	3.53
335	340	3.837399	ACTGTATAGGATCCTCTCCCC	57.163	52.381	20.22	3.72	46.27	4.81
350	355	0.689745	TCCCCCTGTACCAATCCTCG	60.690	60.000	0.00	0.00	0.00	4.63
351	356	1.696097	CCCCCTGTACCAATCCTCGG	61.696	65.000	0.00	0.00	0.00	4.63
358	363	5.337330	CCCTGTACCAATCCTCGGAATATAC	60.337	48.000	0.00	0.00	0.00	1.47
367	372	2.609737	CCTCGGAATATACCCACGCTTC	60.610	54.545	0.00	0.00	0.00	3.86
378	383	1.470098	CCCACGCTTCAAGGATGAAAG	59.530	52.381	0.00	0.00	44.64	2.62
380	385	2.160417	CCACGCTTCAAGGATGAAAGAC	59.840	50.000	0.00	0.00	44.64	3.01
407	412	0.238289	GATGTTGTGGCCACGTGAAG	59.762	55.000	30.07	1.58	0.00	3.02
409	414	2.203280	TTGTGGCCACGTGAAGGG	60.203	61.111	30.07	0.05	0.00	3.95
413	418	2.112297	GGCCACGTGAAGGGTGAA	59.888	61.111	19.30	0.00	37.60	3.18
436	441	4.781934	CCTTTCTTAGGGGTAGATTGTGG	58.218	47.826	0.00	0.00	40.67	4.17
437	442	3.926058	TTCTTAGGGGTAGATTGTGGC	57.074	47.619	0.00	0.00	0.00	5.01
448	453	5.233988	GGTAGATTGTGGCAGATCATAGTC	58.766	45.833	11.91	0.00	0.00	2.59
450	455	5.363562	AGATTGTGGCAGATCATAGTCAA	57.636	39.130	11.91	0.00	0.00	3.18
458	463	6.015010	GTGGCAGATCATAGTCAAGGTAGTAT	60.015	42.308	0.00	0.00	0.00	2.12
464	469	6.553953	TCATAGTCAAGGTAGTATTTGGCA	57.446	37.500	5.21	0.00	31.52	4.92
480	485	4.660352	TTGGCATTTAAAATTCTTGCGC	57.340	36.364	0.00	0.00	34.17	6.09
481	486	3.657634	TGGCATTTAAAATTCTTGCGCA	58.342	36.364	5.66	5.66	34.17	6.09
503	508	5.297029	GCAGAACAAATCAGGGTTAGGTATC	59.703	44.000	0.00	0.00	0.00	2.24
512	517	5.205821	TCAGGGTTAGGTATCAATCTCGAA	58.794	41.667	0.00	0.00	0.00	3.71
524	529	2.119801	ATCTCGAACATTGCTTGGCT	57.880	45.000	0.00	0.00	0.00	4.75
663	670	4.202212	GCCACCAAAACTGATTTTAGGTGT	60.202	41.667	20.32	3.64	44.73	4.16
667	674	5.891551	ACCAAAACTGATTTTAGGTGTGTCT	59.108	36.000	0.00	0.00	37.59	3.41
757	764	0.321298	TGAGTTACCTGCTTTCCGGC	60.321	55.000	0.00	0.00	0.00	6.13
777	788	1.745489	GGAAACCGAGCGCTGGAAT	60.745	57.895	26.07	16.32	0.00	3.01
783	794	2.202797	GAGCGCTGGAATGCTCGA	60.203	61.111	18.48	0.00	47.00	4.04
909	920	8.572151	CGCGATCACGAAAATTTAAAACTTTAT	58.428	29.630	0.00	0.00	42.66	1.40
1605	1642	1.931635	AAAGGGGTTTGTGTGTGTGT	58.068	45.000	0.00	0.00	0.00	3.72
1606	1643	1.181786	AAGGGGTTTGTGTGTGTGTG	58.818	50.000	0.00	0.00	0.00	3.82
1607	1644	0.039035	AGGGGTTTGTGTGTGTGTGT	59.961	50.000	0.00	0.00	0.00	3.72
1608	1645	0.172352	GGGGTTTGTGTGTGTGTGTG	59.828	55.000	0.00	0.00	0.00	3.82
1609	1646	0.457681	GGGTTTGTGTGTGTGTGTGC	60.458	55.000	0.00	0.00	0.00	4.57
1610	1647	0.796491	GGTTTGTGTGTGTGTGTGCG	60.796	55.000	0.00	0.00	0.00	5.34
1611	1648	0.109964	GTTTGTGTGTGTGTGTGCGT	60.110	50.000	0.00	0.00	0.00	5.24
1612	1649	0.110010	TTTGTGTGTGTGTGTGCGTG	60.110	50.000	0.00	0.00	0.00	5.34
1613	1650	1.231296	TTGTGTGTGTGTGTGCGTGT	61.231	50.000	0.00	0.00	0.00	4.49
1614	1651	1.225991	GTGTGTGTGTGTGCGTGTG	60.226	57.895	0.00	0.00	0.00	3.82
1615	1652	1.669437	TGTGTGTGTGTGCGTGTGT	60.669	52.632	0.00	0.00	0.00	3.72
1616	1653	1.225991	GTGTGTGTGTGCGTGTGTG	60.226	57.895	0.00	0.00	0.00	3.82
1617	1654	1.669437	TGTGTGTGTGCGTGTGTGT	60.669	52.632	0.00	0.00	0.00	3.72
1618	1655	1.225991	GTGTGTGTGCGTGTGTGTG	60.226	57.895	0.00	0.00	0.00	3.82
1619	1656	1.669437	TGTGTGTGCGTGTGTGTGT	60.669	52.632	0.00	0.00	0.00	3.72
1620	1657	1.225991	GTGTGTGCGTGTGTGTGTG	60.226	57.895	0.00	0.00	0.00	3.82
1621	1658	1.669437	TGTGTGCGTGTGTGTGTGT	60.669	52.632	0.00	0.00	0.00	3.72
1622	1659	1.225991	GTGTGCGTGTGTGTGTGTG	60.226	57.895	0.00	0.00	0.00	3.82
2006	2048	5.295292	CACGGAGCAAAATGAGTGAATCTAT	59.705	40.000	0.00	0.00	0.00	1.98
2256	2335	0.933097	CTCGATGCCAGATTCGTTGG	59.067	55.000	0.00	0.00	38.78	3.77
2293	2482	4.142026	ACTTTTTAAGTGTTGTGAAGGCCC	60.142	41.667	0.00	0.00	41.01	5.80
2354	3544	9.419297	GCTCATATATGTACTTTGTATCCGAAA	57.581	33.333	12.42	0.00	0.00	3.46
2375	3568	7.138736	CGAAACCATTGCTTTAAAGAAGAAGA	58.861	34.615	19.48	0.00	0.00	2.87
2376	3569	7.647715	CGAAACCATTGCTTTAAAGAAGAAGAA	59.352	33.333	19.48	0.00	0.00	2.52
2377	3570	8.648557	AAACCATTGCTTTAAAGAAGAAGAAC	57.351	30.769	19.48	0.00	0.00	3.01
2378	3571	6.438763	ACCATTGCTTTAAAGAAGAAGAACG	58.561	36.000	19.48	0.00	0.00	3.95
2379	3572	5.858581	CCATTGCTTTAAAGAAGAAGAACGG	59.141	40.000	19.48	2.56	0.00	4.44
2380	3573	6.293955	CCATTGCTTTAAAGAAGAAGAACGGA	60.294	38.462	19.48	0.00	0.00	4.69
2381	3574	5.668558	TGCTTTAAAGAAGAAGAACGGAC	57.331	39.130	19.48	0.00	0.00	4.79
2382	3575	5.120399	TGCTTTAAAGAAGAAGAACGGACA	58.880	37.500	19.48	0.00	0.00	4.02
2480	3673	2.509561	GTCGGAGGAAAGGCTCGC	60.510	66.667	0.00	0.00	0.00	5.03
2502	3695	4.770795	CCCCAACAATAGAGAAGAATCGT	58.229	43.478	0.00	0.00	0.00	3.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	3.314693	GAGAGTAGAGGAGAGGAGGAGA	58.685	54.545	0.00	0.00	0.00	3.71
10	11	2.372172	GGAGAGTAGAGGAGAGGAGGAG	59.628	59.091	0.00	0.00	0.00	3.69
11	12	2.414612	GGAGAGTAGAGGAGAGGAGGA	58.585	57.143	0.00	0.00	0.00	3.71
12	13	1.423921	GGGAGAGTAGAGGAGAGGAGG	59.576	61.905	0.00	0.00	0.00	4.30
13	14	2.418669	AGGGAGAGTAGAGGAGAGGAG	58.581	57.143	0.00	0.00	0.00	3.69
25	26	2.039418	GTTTGGCCAAAAAGGGAGAGT	58.961	47.619	31.92	0.00	38.09	3.24
32	33	6.074356	CGAGTTTAATGAGTTTGGCCAAAAAG	60.074	38.462	31.92	6.57	31.33	2.27
38	41	3.500680	TCACGAGTTTAATGAGTTTGGCC	59.499	43.478	0.00	0.00	0.00	5.36
52	55	1.674221	GGCATGAAGAGCTCACGAGTT	60.674	52.381	17.77	0.00	36.69	3.01
53	56	0.108424	GGCATGAAGAGCTCACGAGT	60.108	55.000	17.77	0.00	36.69	4.18
55	58	0.390340	GTGGCATGAAGAGCTCACGA	60.390	55.000	17.77	0.00	36.69	4.35
86	89	6.159988	AGTTAGCGATCTAATCAATGCTACC	58.840	40.000	0.00	0.00	37.16	3.18
87	90	8.024285	AGTAGTTAGCGATCTAATCAATGCTAC	58.976	37.037	0.00	0.00	37.16	3.58
94	97	9.512435	GTTAAACAGTAGTTAGCGATCTAATCA	57.488	33.333	0.00	0.00	36.84	2.57
104	107	4.624452	CCACGAGGTTAAACAGTAGTTAGC	59.376	45.833	0.00	0.00	36.84	3.09
158	163	4.900684	TCCAATCACATCTTCCAACGTTA	58.099	39.130	0.00	0.00	0.00	3.18
164	169	5.500234	CCTTAACTCCAATCACATCTTCCA	58.500	41.667	0.00	0.00	0.00	3.53
165	170	4.884164	CCCTTAACTCCAATCACATCTTCC	59.116	45.833	0.00	0.00	0.00	3.46
181	186	1.613610	GCCCCTCCCTTCCCTTAAC	59.386	63.158	0.00	0.00	0.00	2.01
182	187	1.621514	GGCCCCTCCCTTCCCTTAA	60.622	63.158	0.00	0.00	0.00	1.85
248	253	9.924010	GGGCTCCTAAGAAGAGAATACTATATA	57.076	37.037	0.00	0.00	32.86	0.86
249	254	7.558444	CGGGCTCCTAAGAAGAGAATACTATAT	59.442	40.741	0.00	0.00	32.86	0.86
250	255	6.885376	CGGGCTCCTAAGAAGAGAATACTATA	59.115	42.308	0.00	0.00	32.86	1.31
251	256	5.712917	CGGGCTCCTAAGAAGAGAATACTAT	59.287	44.000	0.00	0.00	32.86	2.12
252	257	5.071370	CGGGCTCCTAAGAAGAGAATACTA	58.929	45.833	0.00	0.00	32.86	1.82
253	258	3.892588	CGGGCTCCTAAGAAGAGAATACT	59.107	47.826	0.00	0.00	32.86	2.12
265	270	1.483415	GTTACATCCACGGGCTCCTAA	59.517	52.381	0.00	0.00	0.00	2.69
278	283	6.630045	GGTTATTACGCCGAAAATGTTACATC	59.370	38.462	0.00	0.00	0.00	3.06
284	289	4.095334	GGAAGGTTATTACGCCGAAAATGT	59.905	41.667	0.00	0.00	0.00	2.71
294	299	5.006358	CAGTTCGGATTGGAAGGTTATTACG	59.994	44.000	0.00	0.00	0.00	3.18
309	314	5.258051	GAGAGGATCCTATACAGTTCGGAT	58.742	45.833	16.16	0.00	38.90	4.18
335	340	4.891992	ATATTCCGAGGATTGGTACAGG	57.108	45.455	0.00	0.00	41.84	4.00
350	355	3.139077	CCTTGAAGCGTGGGTATATTCC	58.861	50.000	0.00	0.00	0.00	3.01
351	356	4.067972	TCCTTGAAGCGTGGGTATATTC	57.932	45.455	0.00	0.00	0.00	1.75
358	363	1.470098	CTTTCATCCTTGAAGCGTGGG	59.530	52.381	0.00	0.00	42.60	4.61
367	372	7.149973	ACATCATGTTTTGTCTTTCATCCTTG	58.850	34.615	0.00	0.00	0.00	3.61
378	383	3.059166	GGCCACAACATCATGTTTTGTC	58.941	45.455	14.23	2.84	38.77	3.18
380	385	2.801679	GTGGCCACAACATCATGTTTTG	59.198	45.455	31.23	9.38	38.77	2.44
407	412	1.709115	ACCCCTAAGAAAGGTTCACCC	59.291	52.381	0.00	0.00	44.90	4.61
409	414	5.695424	ATCTACCCCTAAGAAAGGTTCAC	57.305	43.478	0.00	0.00	44.90	3.18
413	418	4.227527	CCACAATCTACCCCTAAGAAAGGT	59.772	45.833	0.00	0.00	44.90	3.50
423	428	1.490490	TGATCTGCCACAATCTACCCC	59.510	52.381	0.00	0.00	0.00	4.95
435	440	4.946478	ACTACCTTGACTATGATCTGCC	57.054	45.455	0.00	0.00	0.00	4.85
436	441	7.386299	CCAAATACTACCTTGACTATGATCTGC	59.614	40.741	0.00	0.00	0.00	4.26
437	442	7.386299	GCCAAATACTACCTTGACTATGATCTG	59.614	40.741	0.00	0.00	0.00	2.90
458	463	4.512944	TGCGCAAGAATTTTAAATGCCAAA	59.487	33.333	8.16	0.00	43.02	3.28
464	469	7.475771	TTTGTTCTGCGCAAGAATTTTAAAT	57.524	28.000	13.05	0.00	46.53	1.40
480	485	6.414732	TGATACCTAACCCTGATTTGTTCTG	58.585	40.000	0.00	0.00	0.00	3.02
481	486	6.636454	TGATACCTAACCCTGATTTGTTCT	57.364	37.500	0.00	0.00	0.00	3.01
503	508	2.163010	AGCCAAGCAATGTTCGAGATTG	59.837	45.455	12.62	12.62	34.47	2.67
556	563	0.991920	TGAGGGAGGTAAGGGCTTTG	59.008	55.000	0.00	0.00	0.00	2.77
699	706	0.400594	CGGGGTCTCAACCTTCCTTT	59.599	55.000	0.00	0.00	45.66	3.11
770	777	3.934684	GCGCTCGAGCATTCCAGC	61.935	66.667	34.69	24.66	42.21	4.85
771	778	2.510012	TGCGCTCGAGCATTCCAG	60.510	61.111	34.69	19.33	42.92	3.86
777	788	0.524414	TTACTAGTTGCGCTCGAGCA	59.476	50.000	34.69	16.77	46.54	4.26
783	794	1.477295	GGAGGACTTACTAGTTGCGCT	59.523	52.381	9.73	0.00	33.84	5.92
1605	1642	1.669437	ACACACACACACACGCACA	60.669	52.632	0.00	0.00	0.00	4.57
1606	1643	1.225991	CACACACACACACACGCAC	60.226	57.895	0.00	0.00	0.00	5.34
1607	1644	1.669437	ACACACACACACACACGCA	60.669	52.632	0.00	0.00	0.00	5.24
1608	1645	1.225991	CACACACACACACACACGC	60.226	57.895	0.00	0.00	0.00	5.34
1609	1646	0.179227	CACACACACACACACACACG	60.179	55.000	0.00	0.00	0.00	4.49
1610	1647	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1611	1648	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1612	1649	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1613	1650	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1614	1651	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1615	1652	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1616	1653	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1617	1654	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1618	1655	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1619	1656	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1620	1657	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1621	1658	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1622	1659	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
2293	2482	1.625315	TGACATCTTGTGGGAGGTGAG	59.375	52.381	0.00	0.00	32.07	3.51
2354	3544	6.438763	CGTTCTTCTTCTTTAAAGCAATGGT	58.561	36.000	10.51	0.00	0.00	3.55
2480	3673	4.770795	ACGATTCTTCTCTATTGTTGGGG	58.229	43.478	0.00	0.00	0.00	4.96
2502	3695	0.252330	TGTACACCCGGGATCCAAGA	60.252	55.000	32.02	2.90	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.