AutoCloner

Multiple sequence alignment - TraesCS5D01G533400

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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	TraesCS5D01G533400	chr5D	100.000	3297	0	0	1	3297	547893889	547890593	0.000000e+00	6089.0
1	TraesCS5D01G533400	chr5D	82.784	1638	186	50	977	2558	547884139	547882542	0.000000e+00	1375.0
2	TraesCS5D01G533400	chr5D	90.819	806	66	8	1756	2558	547925571	547924771	0.000000e+00	1072.0
3	TraesCS5D01G533400	chr5D	82.523	1213	142	40	1378	2558	547840840	547839666	0.000000e+00	1002.0
4	TraesCS5D01G533400	chr5D	88.889	630	55	4	2611	3236	547881761	547881143	0.000000e+00	761.0
5	TraesCS5D01G533400	chr5D	80.160	751	84	42	1003	1710	547841225	547840497	4.910000e-138	501.0
6	TraesCS5D01G533400	chr5D	86.842	342	32	7	1380	1708	547925931	547925590	1.450000e-98	370.0
7	TraesCS5D01G533400	chr5D	85.319	361	37	8	1020	1376	547926317	547925969	3.130000e-95	359.0
8	TraesCS5D01G533400	chr5D	97.778	45	1	0	2552	2596	547882470	547882426	9.810000e-11	78.7
9	TraesCS5D01G533400	chr5D	97.436	39	1	0	977	1015	547926381	547926343	2.120000e-07	67.6
10	TraesCS5D01G533400	chr5D	100.000	28	0	0	981	1008	547841265	547841238	6.000000e-03	52.8
11	TraesCS5D01G533400	chr4A	90.894	1790	117	23	788	2558	618464786	618463024	0.000000e+00	2361.0
12	TraesCS5D01G533400	chr4A	86.743	1569	152	38	1020	2558	618529810	618528268	0.000000e+00	1694.0
13	TraesCS5D01G533400	chr4A	84.672	1220	148	27	1371	2558	618418683	618417471	0.000000e+00	1181.0
14	TraesCS5D01G533400	chr4A	94.840	407	13	3	977	1375	618419114	618418708	2.160000e-176	628.0
15	TraesCS5D01G533400	chr4A	91.480	446	38	0	2791	3236	618416295	618415850	6.050000e-172	614.0
16	TraesCS5D01G533400	chr4A	82.043	323	33	12	977	1289	618412965	618412658	5.460000e-63	252.0
17	TraesCS5D01G533400	chr4A	77.941	272	17	18	580	838	618419517	618419276	2.670000e-26	130.0
18	TraesCS5D01G533400	chr5B	87.716	1620	122	38	977	2558	691825388	691823808	0.000000e+00	1818.0
19	TraesCS5D01G533400	chr5B	83.784	1554	186	35	1003	2529	691798513	691796999	0.000000e+00	1413.0
20	TraesCS5D01G533400	chr5B	87.250	1200	120	22	1380	2558	691942610	691941423	0.000000e+00	1338.0
21	TraesCS5D01G533400	chr5B	81.429	1610	183	61	977	2518	691773821	691772260	0.000000e+00	1210.0
22	TraesCS5D01G533400	chr5B	92.818	362	15	3	2946	3296	691806757	691806396	6.310000e-142	514.0
23	TraesCS5D01G533400	chr5B	93.491	338	18	3	1	338	691826521	691826188	1.770000e-137	499.0
24	TraesCS5D01G533400	chr5B	85.714	469	46	15	2771	3236	691796573	691796123	2.980000e-130	475.0
25	TraesCS5D01G533400	chr5B	86.944	360	34	6	1020	1376	691943005	691942656	3.080000e-105	392.0
26	TraesCS5D01G533400	chr5B	84.487	419	20	12	330	730	691826006	691825615	4.020000e-99	372.0
27	TraesCS5D01G533400	chr5B	91.667	228	14	2	2552	2774	691796947	691796720	8.880000e-81	311.0
28	TraesCS5D01G533400	chr5B	87.143	210	15	4	788	989	691825617	691825412	9.200000e-56	228.0
29	TraesCS5D01G533400	chr5B	85.976	164	14	6	2858	3012	691807394	691807231	2.040000e-37	167.0
30	TraesCS5D01G533400	chr5B	87.705	122	14	1	225	346	372564381	372564261	1.230000e-29	141.0
31	TraesCS5D01G533400	chr5B	88.235	102	8	2	535	632	691807783	691807682	5.780000e-23	119.0
32	TraesCS5D01G533400	chr5B	92.500	80	6	0	2577	2656	691941315	691941236	7.480000e-22	115.0
33	TraesCS5D01G533400	chr5B	90.741	54	4	1	734	786	691798787	691798734	1.640000e-08	71.3
34	TraesCS5D01G533400	chr5B	96.970	33	1	0	200	232	372564602	372564570	4.600000e-04	56.5
35	TraesCS5D01G533400	chr5B	96.875	32	1	0	977	1008	691798557	691798526	2.000000e-03	54.7
36	TraesCS5D01G533400	chr4B	81.203	133	21	4	216	346	611311457	611311587	1.620000e-18	104.0

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	TraesCS5D01G533400	chr5D	547890593	547893889	3296	True	6089.000000	6089	100.000000	1	3297	1	chr5D.!!$R1	3296
1	TraesCS5D01G533400	chr5D	547881143	547884139	2996	True	738.233333	1375	89.817000	977	3236	3	chr5D.!!$R3	2259
2	TraesCS5D01G533400	chr5D	547839666	547841265	1599	True	518.600000	1002	87.561000	981	2558	3	chr5D.!!$R2	1577
3	TraesCS5D01G533400	chr5D	547924771	547926381	1610	True	467.150000	1072	90.104000	977	2558	4	chr5D.!!$R4	1581
4	TraesCS5D01G533400	chr4A	618463024	618464786	1762	True	2361.000000	2361	90.894000	788	2558	1	chr4A.!!$R1	1770
5	TraesCS5D01G533400	chr4A	618528268	618529810	1542	True	1694.000000	1694	86.743000	1020	2558	1	chr4A.!!$R2	1538
6	TraesCS5D01G533400	chr4A	618412658	618419517	6859	True	561.000000	1181	86.195200	580	3236	5	chr4A.!!$R3	2656
7	TraesCS5D01G533400	chr5B	691772260	691773821	1561	True	1210.000000	1210	81.429000	977	2518	1	chr5B.!!$R1	1541
8	TraesCS5D01G533400	chr5B	691823808	691826521	2713	True	729.250000	1818	88.209250	1	2558	4	chr5B.!!$R5	2557
9	TraesCS5D01G533400	chr5B	691941236	691943005	1769	True	615.000000	1338	88.898000	1020	2656	3	chr5B.!!$R6	1636
10	TraesCS5D01G533400	chr5B	691796123	691798787	2664	True	465.000000	1413	89.756200	734	3236	5	chr5B.!!$R3	2502
11	TraesCS5D01G533400	chr5B	691806396	691807783	1387	True	266.666667	514	89.009667	535	3296	3	chr5B.!!$R4	2761

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
313	314	0.174845	GTTTTGCCCCTTTATCCCGC	59.825	55.0	0.00	0.00	0.0	6.13	F
752	964	0.179004	TCATCCCGGCGCCATTTATT	60.179	50.0	28.98	2.07	0.0	1.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1350	1675	0.036577	AGAAGCTCAGAGCATGCGTT	60.037	50.0	24.64	9.34	45.56	4.84	R
2691	4742	0.107703	CGGCAGCCTCATGTTAAGGA	60.108	55.0	10.54	0.00	35.83	3.36	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	2.232452	AGTCTCCGAGAAATGTCACCAG	59.768	50.000	0.00	0.00	0.00	4.00
58	59	9.750125	AAATATCCAACAAAGAGAGAAACAAAC	57.250	29.630	0.00	0.00	0.00	2.93
78	79	7.712797	ACAAACCATTACAAGTTTAGACAAGG	58.287	34.615	0.00	0.00	34.52	3.61
84	85	3.131396	ACAAGTTTAGACAAGGCGACAG	58.869	45.455	0.00	0.00	0.00	3.51
86	87	1.968493	AGTTTAGACAAGGCGACAGGA	59.032	47.619	0.00	0.00	0.00	3.86
87	88	2.367567	AGTTTAGACAAGGCGACAGGAA	59.632	45.455	0.00	0.00	0.00	3.36
99	100	2.483876	CGACAGGAACAGCTCAAAAGA	58.516	47.619	0.00	0.00	0.00	2.52
109	110	6.035005	GGAACAGCTCAAAAGAAACAAAAGAC	59.965	38.462	0.00	0.00	0.00	3.01
118	119	6.460664	AAAGAAACAAAAGACAACAAACCG	57.539	33.333	0.00	0.00	0.00	4.44
131	132	3.738830	ACAAACCGAACACTGCTACTA	57.261	42.857	0.00	0.00	0.00	1.82
140	141	4.982916	CGAACACTGCTACTAAGAAACTGT	59.017	41.667	0.00	0.00	0.00	3.55
253	254	4.671377	TGCTTTGTAAACTTCACTTGCTG	58.329	39.130	0.00	0.00	0.00	4.41
310	311	4.041075	TCCTTTTGTTTTGCCCCTTTATCC	59.959	41.667	0.00	0.00	0.00	2.59
311	312	4.323417	CTTTTGTTTTGCCCCTTTATCCC	58.677	43.478	0.00	0.00	0.00	3.85
312	313	1.551452	TGTTTTGCCCCTTTATCCCG	58.449	50.000	0.00	0.00	0.00	5.14
313	314	0.174845	GTTTTGCCCCTTTATCCCGC	59.825	55.000	0.00	0.00	0.00	6.13
314	315	0.251832	TTTTGCCCCTTTATCCCGCA	60.252	50.000	0.00	0.00	0.00	5.69
315	316	0.251832	TTTGCCCCTTTATCCCGCAA	60.252	50.000	0.00	0.00	37.65	4.85
322	323	3.568430	CCCCTTTATCCCGCAAAATAGAC	59.432	47.826	0.00	0.00	0.00	2.59
364	555	4.021632	GTCATGATCCAGGATCGAGATGAA	60.022	45.833	23.47	8.63	41.51	2.57
424	616	7.954788	TTTTGTTCTGTGTTGCTTTAGTTTT	57.045	28.000	0.00	0.00	0.00	2.43
428	620	6.751425	TGTTCTGTGTTGCTTTAGTTTTCATG	59.249	34.615	0.00	0.00	0.00	3.07
430	622	5.003692	TGTGTTGCTTTAGTTTTCATGCA	57.996	34.783	0.00	0.00	0.00	3.96
441	633	4.720902	TCATGCAGCGTGGGGTGG	62.721	66.667	14.86	0.00	41.91	4.61
459	651	2.099427	GTGGGTGCGACCAAGTTTTAAA	59.901	45.455	0.18	0.00	43.34	1.52
461	653	2.359848	GGGTGCGACCAAGTTTTAAACT	59.640	45.455	4.30	4.30	41.02	2.66
512	704	3.203040	AGGGTAGATTTGTTGCATAGCCT	59.797	43.478	6.23	6.23	39.03	4.58
516	708	4.361451	AGATTTGTTGCATAGCCTTTCG	57.639	40.909	0.00	0.00	0.00	3.46
562	754	6.876155	TGTTGCATAGCCATCATAATTTGTT	58.124	32.000	0.00	0.00	0.00	2.83
656	867	5.630061	GCAAGCAGCAAAAGAAAAGAAAAA	58.370	33.333	0.00	0.00	44.79	1.94
712	924	0.535553	TGTTACTTCAACGCCCACCC	60.536	55.000	0.00	0.00	40.26	4.61
729	941	2.197324	CGGAGGAGGAGGAGGAGG	59.803	72.222	0.00	0.00	0.00	4.30
730	942	2.387772	CGGAGGAGGAGGAGGAGGA	61.388	68.421	0.00	0.00	0.00	3.71
731	943	1.541672	GGAGGAGGAGGAGGAGGAG	59.458	68.421	0.00	0.00	0.00	3.69
732	944	1.541672	GAGGAGGAGGAGGAGGAGG	59.458	68.421	0.00	0.00	0.00	4.30
733	945	1.230819	AGGAGGAGGAGGAGGAGGT	60.231	63.158	0.00	0.00	0.00	3.85
734	946	1.231928	GGAGGAGGAGGAGGAGGTC	59.768	68.421	0.00	0.00	0.00	3.85
735	947	1.585651	GGAGGAGGAGGAGGAGGTCA	61.586	65.000	0.00	0.00	0.00	4.02
736	948	0.560688	GAGGAGGAGGAGGAGGTCAT	59.439	60.000	0.00	0.00	0.00	3.06
737	949	0.560688	AGGAGGAGGAGGAGGTCATC	59.439	60.000	0.00	0.00	35.08	2.92
752	964	0.179004	TCATCCCGGCGCCATTTATT	60.179	50.000	28.98	2.07	0.00	1.40
756	968	1.025812	CCCGGCGCCATTTATTTACA	58.974	50.000	28.98	0.00	0.00	2.41
757	969	1.405821	CCCGGCGCCATTTATTTACAA	59.594	47.619	28.98	0.00	0.00	2.41
979	1249	1.483004	GGCCTCTTCTGTTCCTAGTCC	59.517	57.143	0.00	0.00	0.00	3.85
1220	1542	5.053145	TCTGTTTGTCTCTTCTTCTTGCTC	58.947	41.667	0.00	0.00	0.00	4.26
1350	1675	2.610833	CACCTACATGCTAGACGTACGA	59.389	50.000	24.41	0.00	0.00	3.43
1395	1800	1.268539	CGTGTTGCCTTCAAGGTGTTC	60.269	52.381	5.03	0.00	37.80	3.18
1405	1810	2.844946	TCAAGGTGTTCGCTGAAATGA	58.155	42.857	0.00	0.00	0.00	2.57
1457	1866	2.616458	GGCCTTCACCCACCAGGAT	61.616	63.158	0.00	0.00	39.89	3.24
1514	1924	1.103803	TGCAGGTCCGATCTACTCAC	58.896	55.000	0.00	0.00	0.00	3.51
1521	1931	3.458189	GTCCGATCTACTCACCCAATTG	58.542	50.000	0.00	0.00	0.00	2.32
1528	1939	5.762179	TCTACTCACCCAATTGTTCAGAT	57.238	39.130	4.43	0.00	0.00	2.90
1540	1986	7.432869	CCAATTGTTCAGATAAACCACTTGAA	58.567	34.615	4.43	0.00	0.00	2.69
1546	1992	7.069331	TGTTCAGATAAACCACTTGAACCATTT	59.931	33.333	11.69	0.00	34.90	2.32
1735	2226	8.757789	CATGACAATGGTTATTTGCATATGAAC	58.242	33.333	6.97	1.19	0.00	3.18
1786	2277	3.926527	CACTCGCACACTAATTCTGCTTA	59.073	43.478	0.00	0.00	0.00	3.09
1835	2328	4.753662	AGCCGCGGTACCAGGAGA	62.754	66.667	28.70	0.00	0.00	3.71
1837	2330	3.090219	GCCGCGGTACCAGGAGATT	62.090	63.158	28.70	0.00	0.00	2.40
1986	2479	2.925170	AGGTTCGCAGCTCCACCT	60.925	61.111	1.90	1.90	34.60	4.00
2215	2708	1.413767	CCTTCGTCATGAACTCGCGG	61.414	60.000	6.13	0.00	31.87	6.46
2342	2835	1.130613	GATCAACGTCGCAGTGCAC	59.869	57.895	16.83	9.40	0.00	4.57
2515	3021	7.711339	GTGTAATGAGGAGGAAGTTAGTAATGG	59.289	40.741	0.00	0.00	0.00	3.16
2644	4691	6.449635	TTGCTTATTGACGGCATTATTCTT	57.550	33.333	0.00	0.00	35.84	2.52
2656	4703	4.684703	GGCATTATTCTTTCATGATGCAGC	59.315	41.667	13.85	0.00	44.28	5.25
2659	4706	6.379386	CATTATTCTTTCATGATGCAGCGAT	58.621	36.000	0.00	0.00	0.00	4.58
2691	4742	3.413846	TGAAGCAGAGCAGAACAAGAT	57.586	42.857	0.00	0.00	0.00	2.40
2695	4746	2.305343	AGCAGAGCAGAACAAGATCCTT	59.695	45.455	0.00	0.00	0.00	3.36
2712	4763	1.678728	CCTTAACATGAGGCTGCCGAA	60.679	52.381	13.96	5.87	0.00	4.30
2727	4778	1.205893	GCCGAACTCTGAAGTCTGGAT	59.794	52.381	0.00	0.00	33.48	3.41
2739	4790	2.787994	AGTCTGGATTGGAAAGCACTG	58.212	47.619	0.00	0.00	30.69	3.66
2776	4883	7.735326	ACTATGACTCCTAACCTTGTACAAT	57.265	36.000	9.13	0.00	0.00	2.71
2777	4884	7.556844	ACTATGACTCCTAACCTTGTACAATG	58.443	38.462	9.13	9.11	0.00	2.82
2779	4886	5.547465	TGACTCCTAACCTTGTACAATGTG	58.453	41.667	15.98	7.64	0.00	3.21
2780	4887	4.906618	ACTCCTAACCTTGTACAATGTGG	58.093	43.478	15.98	12.95	0.00	4.17
2784	4891	5.013704	TCCTAACCTTGTACAATGTGGATGT	59.986	40.000	15.98	4.28	34.81	3.06
2801	5059	1.968540	GTTGGAGGCTGGCTGTGAC	60.969	63.158	9.06	0.00	0.00	3.67
2818	5076	0.257039	GACCCTGATGCTGTGGGAAT	59.743	55.000	4.11	0.00	43.47	3.01
2966	5233	8.264347	TGTGTACAATGTATGGATCTGTTACAT	58.736	33.333	0.00	8.82	37.99	2.29
3296	6114	0.107017	TATCTTTGAGGCTGGGCTGC	60.107	55.000	0.33	0.00	0.00	5.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.611518	CTGGTGACATTTCTCGGAGAC	58.388	52.381	7.33	0.00	41.51	3.36
25	26	4.757594	TCTTTGTTGGATATTTGCCATGC	58.242	39.130	0.00	0.00	34.90	4.06
38	39	5.323371	TGGTTTGTTTCTCTCTTTGTTGG	57.677	39.130	0.00	0.00	0.00	3.77
42	43	8.190784	ACTTGTAATGGTTTGTTTCTCTCTTTG	58.809	33.333	0.00	0.00	0.00	2.77
58	59	4.693566	TCGCCTTGTCTAAACTTGTAATGG	59.306	41.667	0.00	0.00	0.00	3.16
78	79	0.944386	TTTTGAGCTGTTCCTGTCGC	59.056	50.000	0.00	0.00	0.00	5.19
84	85	6.035005	GTCTTTTGTTTCTTTTGAGCTGTTCC	59.965	38.462	0.00	0.00	0.00	3.62
86	87	6.454795	TGTCTTTTGTTTCTTTTGAGCTGTT	58.545	32.000	0.00	0.00	0.00	3.16
87	88	6.024552	TGTCTTTTGTTTCTTTTGAGCTGT	57.975	33.333	0.00	0.00	0.00	4.40
99	100	5.176039	GTGTTCGGTTTGTTGTCTTTTGTTT	59.824	36.000	0.00	0.00	0.00	2.83
109	110	2.612212	AGTAGCAGTGTTCGGTTTGTTG	59.388	45.455	0.00	0.00	0.00	3.33
118	119	7.569677	CTACAGTTTCTTAGTAGCAGTGTTC	57.430	40.000	0.00	0.00	0.00	3.18
131	132	4.672587	TGTGTCTCTGCTACAGTTTCTT	57.327	40.909	0.00	0.00	32.61	2.52
140	141	1.497991	GTTGCGTTGTGTCTCTGCTA	58.502	50.000	0.00	0.00	0.00	3.49
185	186	0.625849	AAGGCTGGGATGGTGGTAAG	59.374	55.000	0.00	0.00	0.00	2.34
189	190	2.043652	CCAAGGCTGGGATGGTGG	60.044	66.667	0.00	0.00	39.30	4.61
310	311	1.173043	TGGCTTGGTCTATTTTGCGG	58.827	50.000	0.00	0.00	0.00	5.69
311	312	2.423185	TCATGGCTTGGTCTATTTTGCG	59.577	45.455	0.09	0.00	0.00	4.85
312	313	4.500375	GGATCATGGCTTGGTCTATTTTGC	60.500	45.833	12.72	0.00	35.64	3.68
313	314	4.646040	TGGATCATGGCTTGGTCTATTTTG	59.354	41.667	12.72	0.00	35.64	2.44
314	315	4.870636	TGGATCATGGCTTGGTCTATTTT	58.129	39.130	12.72	0.00	35.64	1.82
315	316	4.079558	ACTGGATCATGGCTTGGTCTATTT	60.080	41.667	12.72	0.00	35.64	1.40
322	323	3.144506	GACATACTGGATCATGGCTTGG	58.855	50.000	0.09	0.00	0.00	3.61
364	555	8.604035	CATACTAAAATCATTGCACTACGTCTT	58.396	33.333	0.00	0.00	0.00	3.01
387	578	9.539825	AACACAGAACAAAATTATTGCAACATA	57.460	25.926	0.00	0.00	0.00	2.29
404	595	6.291796	GCATGAAAACTAAAGCAACACAGAAC	60.292	38.462	0.00	0.00	0.00	3.01
424	616	4.720902	CCACCCCACGCTGCATGA	62.721	66.667	0.00	0.00	0.00	3.07
441	633	3.703286	AGTTTAAAACTTGGTCGCACC	57.297	42.857	0.00	0.00	39.04	5.01
484	676	5.860941	TGCAACAAATCTACCCTCAAAAA	57.139	34.783	0.00	0.00	0.00	1.94
485	677	6.350110	GCTATGCAACAAATCTACCCTCAAAA	60.350	38.462	0.00	0.00	0.00	2.44
486	678	5.125417	GCTATGCAACAAATCTACCCTCAAA	59.875	40.000	0.00	0.00	0.00	2.69
487	679	4.640201	GCTATGCAACAAATCTACCCTCAA	59.360	41.667	0.00	0.00	0.00	3.02
488	680	4.199310	GCTATGCAACAAATCTACCCTCA	58.801	43.478	0.00	0.00	0.00	3.86
489	681	3.565902	GGCTATGCAACAAATCTACCCTC	59.434	47.826	0.00	0.00	0.00	4.30
526	718	6.523840	TGGCTATGCAACAAATCTTCTTTTT	58.476	32.000	0.00	0.00	0.00	1.94
527	719	6.100404	TGGCTATGCAACAAATCTTCTTTT	57.900	33.333	0.00	0.00	0.00	2.27
528	720	5.726980	TGGCTATGCAACAAATCTTCTTT	57.273	34.783	0.00	0.00	0.00	2.52
529	721	5.419788	TGATGGCTATGCAACAAATCTTCTT	59.580	36.000	0.00	0.00	0.00	2.52
577	769	3.681835	GTGAGGCGGTCGTCACCT	61.682	66.667	11.54	0.00	46.68	4.00
712	924	2.197324	CCTCCTCCTCCTCCTCCG	59.803	72.222	0.00	0.00	0.00	4.63
731	943	2.951475	TAAATGGCGCCGGGATGACC	62.951	60.000	23.90	0.00	0.00	4.02
732	944	0.889186	ATAAATGGCGCCGGGATGAC	60.889	55.000	23.90	0.00	0.00	3.06
733	945	0.179004	AATAAATGGCGCCGGGATGA	60.179	50.000	23.90	2.33	0.00	2.92
734	946	0.673437	AAATAAATGGCGCCGGGATG	59.327	50.000	23.90	0.00	0.00	3.51
735	947	1.883926	GTAAATAAATGGCGCCGGGAT	59.116	47.619	23.90	6.99	0.00	3.85
736	948	1.310904	GTAAATAAATGGCGCCGGGA	58.689	50.000	23.90	4.21	0.00	5.14
737	949	1.025812	TGTAAATAAATGGCGCCGGG	58.974	50.000	23.90	0.00	0.00	5.73
738	950	2.456010	GTTGTAAATAAATGGCGCCGG	58.544	47.619	23.90	0.00	0.00	6.13
739	951	2.456010	GGTTGTAAATAAATGGCGCCG	58.544	47.619	23.90	0.00	0.00	6.46
740	952	2.796735	CGGGTTGTAAATAAATGGCGCC	60.797	50.000	22.73	22.73	0.00	6.53
741	953	2.456010	CGGGTTGTAAATAAATGGCGC	58.544	47.619	0.00	0.00	0.00	6.53
752	964	0.329931	ATGGTGGATGCGGGTTGTAA	59.670	50.000	0.00	0.00	0.00	2.41
756	968	0.466189	GATCATGGTGGATGCGGGTT	60.466	55.000	0.00	0.00	31.32	4.11
757	969	1.149174	GATCATGGTGGATGCGGGT	59.851	57.895	0.00	0.00	31.32	5.28
818	1038	0.043485	AGGAGAAGAGGGGGAGGTTC	59.957	60.000	0.00	0.00	0.00	3.62
819	1039	0.043485	GAGGAGAAGAGGGGGAGGTT	59.957	60.000	0.00	0.00	0.00	3.50
820	1040	1.707200	GAGGAGAAGAGGGGGAGGT	59.293	63.158	0.00	0.00	0.00	3.85
857	1080	0.633733	CGCGAGCGCCGTATAAATAG	59.366	55.000	17.38	0.00	41.15	1.73
943	1177	2.978018	GCCTGTTGTTGGCGCTACC	61.978	63.158	7.64	0.00	41.03	3.18
979	1249	0.036010	ATCGCTGGTGGGAACAAGAG	60.036	55.000	0.00	0.00	46.06	2.85
1220	1542	1.743252	GGGAGCTCGCAACTGAAGG	60.743	63.158	24.65	0.00	0.00	3.46
1350	1675	0.036577	AGAAGCTCAGAGCATGCGTT	60.037	50.000	24.64	9.34	45.56	4.84
1395	1800	6.647569	CAGAAGACAGAATATCATTTCAGCG	58.352	40.000	0.00	0.00	0.00	5.18
1405	1810	5.578727	GTCAGAAACGCAGAAGACAGAATAT	59.421	40.000	0.00	0.00	0.00	1.28
1457	1866	2.034066	CCCTTGCGGCCAGAGAAA	59.966	61.111	2.24	0.00	0.00	2.52
1514	1924	5.982890	AGTGGTTTATCTGAACAATTGGG	57.017	39.130	10.83	0.00	0.00	4.12
1521	1931	6.575162	ATGGTTCAAGTGGTTTATCTGAAC	57.425	37.500	4.98	4.98	35.01	3.18
1553	1999	7.718334	TCAGATCCATGTTAGTTCTCAAGTA	57.282	36.000	0.00	0.00	0.00	2.24
1735	2226	8.724229	TGATCATTGTCATGTAAAGAAGTTGAG	58.276	33.333	0.00	0.00	0.00	3.02
1786	2277	2.033372	TCGATGAATGGGCATTTGCAT	58.967	42.857	4.74	0.00	44.36	3.96
1835	2328	2.641305	GCTGATGTCCTTGCTCTCAAT	58.359	47.619	0.00	0.00	0.00	2.57
1837	2330	0.251354	GGCTGATGTCCTTGCTCTCA	59.749	55.000	0.00	0.00	0.00	3.27
2215	2708	4.891037	GCCTGCTGGATCTGGGCC	62.891	72.222	14.77	0.00	37.12	5.80
2342	2835	0.662970	CCCAATGTTTCGCACAACGG	60.663	55.000	0.00	0.00	43.89	4.44
2351	2844	2.179427	CCCTTTCCTCCCCAATGTTTC	58.821	52.381	0.00	0.00	0.00	2.78
2399	2895	8.811017	ACTACTACTACACTCTACACAGAAGTA	58.189	37.037	0.00	0.00	0.00	2.24
2400	2896	7.678837	ACTACTACTACACTCTACACAGAAGT	58.321	38.462	0.00	0.00	0.00	3.01
2401	2897	8.036575	AGACTACTACTACACTCTACACAGAAG	58.963	40.741	0.00	0.00	0.00	2.85
2402	2898	7.905265	AGACTACTACTACACTCTACACAGAA	58.095	38.462	0.00	0.00	0.00	3.02
2403	2899	7.479352	AGACTACTACTACACTCTACACAGA	57.521	40.000	0.00	0.00	0.00	3.41
2473	2975	8.246180	CCTCATTACACACTTTTATTGCATCTT	58.754	33.333	0.00	0.00	0.00	2.40
2474	2976	7.611467	TCCTCATTACACACTTTTATTGCATCT	59.389	33.333	0.00	0.00	0.00	2.90
2515	3021	6.315144	AGTTTGCCTTTTTATGACCAAACAAC	59.685	34.615	14.12	0.00	42.48	3.32
2588	3984	2.239681	TCAAACAAAGGGTTGGTGGT	57.760	45.000	0.00	0.00	40.35	4.16
2644	4691	2.841215	TGATCATCGCTGCATCATGAA	58.159	42.857	0.00	0.00	30.43	2.57
2656	4703	3.660865	TGCTTCATCCTCATGATCATCG	58.339	45.455	4.86	2.07	38.89	3.84
2659	4706	3.494573	GCTCTGCTTCATCCTCATGATCA	60.495	47.826	0.00	0.00	38.89	2.92
2691	4742	0.107703	CGGCAGCCTCATGTTAAGGA	60.108	55.000	10.54	0.00	35.83	3.36
2695	4746	0.613260	AGTTCGGCAGCCTCATGTTA	59.387	50.000	10.54	0.00	0.00	2.41
2712	4763	4.805609	GCTTTCCAATCCAGACTTCAGAGT	60.806	45.833	0.00	0.00	39.32	3.24
2739	4790	7.145932	AGGAGTCATAGTTTTTATGTGCAAC	57.854	36.000	0.00	0.00	37.35	4.17
2748	4855	8.434392	TGTACAAGGTTAGGAGTCATAGTTTTT	58.566	33.333	0.00	0.00	0.00	1.94
2776	4883	1.379916	CCAGCCTCCAACATCCACA	59.620	57.895	0.00	0.00	0.00	4.17
2777	4884	2.048603	GCCAGCCTCCAACATCCAC	61.049	63.158	0.00	0.00	0.00	4.02
2779	4886	1.751927	CAGCCAGCCTCCAACATCC	60.752	63.158	0.00	0.00	0.00	3.51
2780	4887	1.001641	ACAGCCAGCCTCCAACATC	60.002	57.895	0.00	0.00	0.00	3.06
2784	4891	2.431683	GTCACAGCCAGCCTCCAA	59.568	61.111	0.00	0.00	0.00	3.53
2801	5059	2.107031	TGATATTCCCACAGCATCAGGG	59.893	50.000	0.00	0.00	44.22	4.45
2818	5076	1.933181	CAAGCATCCGCGAACTTGATA	59.067	47.619	8.23	0.00	45.49	2.15
2900	5165	6.036470	TCTGCGTCTACAATTTCATCACTAG	58.964	40.000	0.00	0.00	0.00	2.57
2919	5186	3.310774	CAGATCCTTTGTAACCATCTGCG	59.689	47.826	0.00	0.00	35.41	5.18
3040	5847	5.499313	TCACAAGATCATGTAATCTGGCAA	58.501	37.500	2.77	0.00	36.14	4.52
3084	5892	7.187480	CACTCTGAATTGCTATCAAACATCTG	58.813	38.462	0.00	0.00	35.56	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.