AutoCloner

Multiple sequence alignment - TraesCS5A01G546900

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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	TraesCS5A01G546900	chr5A	100.000	3447	0	0	1	3447	700787681	700784235	0.000000e+00	6366.0
1	TraesCS5A01G546900	chr5A	84.660	1030	100	25	999	2004	700696297	700695302	0.000000e+00	974.0
2	TraesCS5A01G546900	chr5A	84.772	591	40	18	2045	2607	700695300	700694732	6.500000e-152	547.0
3	TraesCS5A01G546900	chr4B	90.457	1991	139	20	1	1976	660517569	660519523	0.000000e+00	2577.0
4	TraesCS5A01G546900	chr4B	91.001	1578	96	19	143	1692	660685813	660684254	0.000000e+00	2085.0
5	TraesCS5A01G546900	chr4B	93.009	844	48	7	2607	3445	599369075	599368238	0.000000e+00	1221.0
6	TraesCS5A01G546900	chr4B	88.534	846	74	17	2602	3444	57802293	57803118	0.000000e+00	1003.0
7	TraesCS5A01G546900	chr4B	90.891	494	38	6	1673	2165	660684243	660683756	0.000000e+00	656.0
8	TraesCS5A01G546900	chr4B	83.611	720	89	11	1011	1703	660677574	660676857	0.000000e+00	649.0
9	TraesCS5A01G546900	chr4B	88.727	479	32	5	2149	2607	660683739	660683263	1.800000e-157	566.0
10	TraesCS5A01G546900	chr4B	88.496	452	26	6	2170	2595	660519519	660519970	1.100000e-144	523.0
11	TraesCS5A01G546900	chr4B	84.783	460	35	18	2186	2610	660535829	660536288	2.460000e-116	429.0
12	TraesCS5A01G546900	chr4B	89.815	324	26	3	2141	2458	660676555	660676233	3.200000e-110	409.0
13	TraesCS5A01G546900	chr4B	82.386	352	48	9	1350	1695	660535423	660535766	9.360000e-76	294.0
14	TraesCS5A01G546900	chr4B	91.667	48	1	2	2004	2050	646651702	646651657	2.870000e-06	63.9
15	TraesCS5A01G546900	chrUn	88.391	1740	162	25	1	1717	110702423	110700701	0.000000e+00	2058.0
16	TraesCS5A01G546900	chrUn	83.835	798	103	18	1001	1781	110688709	110687921	0.000000e+00	736.0
17	TraesCS5A01G546900	chrUn	80.083	959	105	35	569	1492	110692774	110691867	4.850000e-178	634.0
18	TraesCS5A01G546900	chrUn	90.930	430	16	4	2198	2607	110700126	110699700	1.080000e-154	556.0
19	TraesCS5A01G546900	chrUn	92.375	341	17	4	2121	2458	110690952	110690618	8.650000e-131	477.0
20	TraesCS5A01G546900	chrUn	86.771	446	28	11	2141	2555	110687934	110687489	5.210000e-128	468.0
21	TraesCS5A01G546900	chrUn	81.081	296	40	8	904	1190	110697413	110697125	4.480000e-54	222.0
22	TraesCS5A01G546900	chr4D	93.206	839	53	4	2607	3445	329140655	329141489	0.000000e+00	1230.0
23	TraesCS5A01G546900	chr3D	93.042	848	46	11	2602	3447	10705949	10706785	0.000000e+00	1227.0
24	TraesCS5A01G546900	chr7A	92.553	846	53	7	2601	3445	698746055	698746891	0.000000e+00	1205.0
25	TraesCS5A01G546900	chr1A	92.619	840	52	9	2607	3443	292528012	292528844	0.000000e+00	1199.0
26	TraesCS5A01G546900	chr1A	76.765	1558	249	63	226	1717	528067266	528065756	0.000000e+00	767.0
27	TraesCS5A01G546900	chr1A	88.591	298	31	1	2181	2475	528065320	528065023	3.270000e-95	359.0
28	TraesCS5A01G546900	chr6A	91.985	786	52	8	2661	3444	454482311	454481535	0.000000e+00	1092.0
29	TraesCS5A01G546900	chr6A	90.000	50	3	2	1996	2045	19600626	19600673	2.870000e-06	63.9
30	TraesCS5A01G546900	chr7B	89.655	841	75	9	2606	3445	43563532	43564361	0.000000e+00	1061.0
31	TraesCS5A01G546900	chr6D	90.220	818	63	12	2606	3423	455252945	455253745	0.000000e+00	1051.0
32	TraesCS5A01G546900	chr6D	97.561	41	1	0	2004	2044	368363625	368363665	1.720000e-08	71.3
33	TraesCS5A01G546900	chr1D	80.978	736	116	15	996	1717	430469340	430468615	2.320000e-156	562.0
34	TraesCS5A01G546900	chr1D	93.478	46	2	1	2004	2049	198283021	198282977	2.220000e-07	67.6
35	TraesCS5A01G546900	chr2A	90.964	332	23	4	2586	2914	42784420	42784093	1.140000e-119	440.0
36	TraesCS5A01G546900	chr2B	90.462	325	29	2	2586	2910	20668817	20669139	8.840000e-116	427.0
37	TraesCS5A01G546900	chr1B	86.111	360	36	3	2119	2475	581413881	581413533	3.250000e-100	375.0
38	TraesCS5A01G546900	chr1B	74.795	611	108	27	348	935	581415644	581415057	2.070000e-57	233.0
39	TraesCS5A01G546900	chr1B	97.674	43	1	0	2003	2045	202010492	202010450	1.330000e-09	75.0
40	TraesCS5A01G546900	chr1B	90.000	50	3	2	2004	2052	51601851	51601803	2.870000e-06	63.9
41	TraesCS5A01G546900	chr3B	93.333	60	4	0	1800	1859	146152208	146152149	4.740000e-14	89.8
42	TraesCS5A01G546900	chr2D	95.238	42	2	0	2004	2045	312020477	312020518	2.220000e-07	67.6
43	TraesCS5A01G546900	chr3A	88.679	53	5	1	2004	2055	661647681	661647733	2.870000e-06	63.9

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	TraesCS5A01G546900	chr5A	700784235	700787681	3446	True	6366.000000	6366	100.000000	1	3447	1	chr5A.!!$R1	3446
1	TraesCS5A01G546900	chr5A	700694732	700696297	1565	True	760.500000	974	84.716000	999	2607	2	chr5A.!!$R2	1608
2	TraesCS5A01G546900	chr4B	660517569	660519970	2401	False	1550.000000	2577	89.476500	1	2595	2	chr4B.!!$F2	2594
3	TraesCS5A01G546900	chr4B	599368238	599369075	837	True	1221.000000	1221	93.009000	2607	3445	1	chr4B.!!$R1	838
4	TraesCS5A01G546900	chr4B	660683263	660685813	2550	True	1102.333333	2085	90.206333	143	2607	3	chr4B.!!$R4	2464
5	TraesCS5A01G546900	chr4B	57802293	57803118	825	False	1003.000000	1003	88.534000	2602	3444	1	chr4B.!!$F1	842
6	TraesCS5A01G546900	chr4B	660676233	660677574	1341	True	529.000000	649	86.713000	1011	2458	2	chr4B.!!$R3	1447
7	TraesCS5A01G546900	chr4B	660535423	660536288	865	False	361.500000	429	83.584500	1350	2610	2	chr4B.!!$F3	1260
8	TraesCS5A01G546900	chrUn	110697125	110702423	5298	True	945.333333	2058	86.800667	1	2607	3	chrUn.!!$R2	2606
9	TraesCS5A01G546900	chrUn	110687489	110692774	5285	True	578.750000	736	85.766000	569	2555	4	chrUn.!!$R1	1986
10	TraesCS5A01G546900	chr4D	329140655	329141489	834	False	1230.000000	1230	93.206000	2607	3445	1	chr4D.!!$F1	838
11	TraesCS5A01G546900	chr3D	10705949	10706785	836	False	1227.000000	1227	93.042000	2602	3447	1	chr3D.!!$F1	845
12	TraesCS5A01G546900	chr7A	698746055	698746891	836	False	1205.000000	1205	92.553000	2601	3445	1	chr7A.!!$F1	844
13	TraesCS5A01G546900	chr1A	292528012	292528844	832	False	1199.000000	1199	92.619000	2607	3443	1	chr1A.!!$F1	836
14	TraesCS5A01G546900	chr1A	528065023	528067266	2243	True	563.000000	767	82.678000	226	2475	2	chr1A.!!$R1	2249
15	TraesCS5A01G546900	chr6A	454481535	454482311	776	True	1092.000000	1092	91.985000	2661	3444	1	chr6A.!!$R1	783
16	TraesCS5A01G546900	chr7B	43563532	43564361	829	False	1061.000000	1061	89.655000	2606	3445	1	chr7B.!!$F1	839
17	TraesCS5A01G546900	chr6D	455252945	455253745	800	False	1051.000000	1051	90.220000	2606	3423	1	chr6D.!!$F2	817
18	TraesCS5A01G546900	chr1D	430468615	430469340	725	True	562.000000	562	80.978000	996	1717	1	chr1D.!!$R2	721
19	TraesCS5A01G546900	chr1B	581413533	581415644	2111	True	304.000000	375	80.453000	348	2475	2	chr1B.!!$R3	2127

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
99	100	1.069049	GCCAACAACACAGGAGCAAAT	59.931	47.619	0.0	0.0	0.0	2.32	F
1430	1539	0.038744	CAAGCCCAAGTCACCCATCT	59.961	55.000	0.0	0.0	0.0	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1573	5364	0.104304	CCTGCCACCATCCTACGTAC	59.896	60.0	0.0	0.0	0.0	3.67	R
2839	7431	0.996762	GGAGAGGGAGGAGAGAGGGA	60.997	65.0	0.0	0.0	0.0	4.20	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
38	39	9.178758	CTCTTATAGAGCACTACCCAAAAATTT	57.821	33.333	0.00	0.00	35.30	1.82
52	53	8.669946	ACCCAAAAATTTACTAAAACACATGG	57.330	30.769	0.00	0.00	0.00	3.66
99	100	1.069049	GCCAACAACACAGGAGCAAAT	59.931	47.619	0.00	0.00	0.00	2.32
101	102	3.612479	GCCAACAACACAGGAGCAAATAG	60.612	47.826	0.00	0.00	0.00	1.73
240	241	1.883638	GCAACAGAAGAGTGATGGCCA	60.884	52.381	8.56	8.56	0.00	5.36
367	374	2.279741	GCGATTAAGTGGATGCAGTCA	58.720	47.619	0.00	0.00	0.00	3.41
373	380	6.347969	CGATTAAGTGGATGCAGTCAATATGG	60.348	42.308	0.00	0.00	0.00	2.74
381	388	5.645497	GGATGCAGTCAATATGGTTCCTATC	59.355	44.000	0.00	0.00	0.00	2.08
475	483	6.648879	TTTCAGAAGGGGTAAAATCTGTTG	57.351	37.500	0.00	0.00	0.00	3.33
484	492	5.944007	GGGGTAAAATCTGTTGACACTATGT	59.056	40.000	0.00	0.00	0.00	2.29
529	545	9.880064	CAATATCAGCAGATGTCTTAGAAATTG	57.120	33.333	1.18	0.00	35.67	2.32
712	753	2.158534	TGATTACCCACAGTTTGCAGGT	60.159	45.455	0.00	0.00	31.86	4.00
726	767	2.571212	TGCAGGTTTGTTCCAGTACAG	58.429	47.619	0.00	0.00	0.00	2.74
727	768	2.092646	TGCAGGTTTGTTCCAGTACAGT	60.093	45.455	0.00	0.00	0.00	3.55
728	769	2.290641	GCAGGTTTGTTCCAGTACAGTG	59.709	50.000	0.00	0.00	0.00	3.66
734	775	1.151668	GTTCCAGTACAGTGCAGCAG	58.848	55.000	0.00	0.00	0.00	4.24
792	836	1.123861	AACAGCCTGAGAGCCTGACA	61.124	55.000	0.00	0.00	0.00	3.58
868	916	1.302351	TGACGCATGGCATGACACA	60.302	52.632	30.69	20.83	0.00	3.72
959	1019	2.564062	ACACAATTTCTTCAGGGCCATG	59.436	45.455	12.23	12.23	0.00	3.66
1086	1172	4.346709	TCAACTGTTCCACTCACAATAGGA	59.653	41.667	0.00	0.00	0.00	2.94
1116	1202	2.509336	CTAGTTCGGCCAGGTGCG	60.509	66.667	2.24	0.00	42.61	5.34
1306	1406	8.221965	AGAATTTCGTAGAAACAAAAGGTCTT	57.778	30.769	0.00	0.00	45.90	3.01
1380	1489	9.581099	GTTAACTTGGTTGAATTTCTCTTTCAA	57.419	29.630	0.00	0.00	39.96	2.69
1430	1539	0.038744	CAAGCCCAAGTCACCCATCT	59.961	55.000	0.00	0.00	0.00	2.90
1505	5283	4.105697	TCAATATGACCCCCTACCCATTTC	59.894	45.833	0.00	0.00	0.00	2.17
1509	5287	2.310647	TGACCCCCTACCCATTTCTTTC	59.689	50.000	0.00	0.00	0.00	2.62
1576	5367	9.347934	CTCATTTTCATATATCTCCACTCGTAC	57.652	37.037	0.00	0.00	0.00	3.67
1592	5383	0.104304	GTACGTAGGATGGTGGCAGG	59.896	60.000	0.00	0.00	0.00	4.85
1625	5416	2.256117	ACTGGTGTCAGCTTTGGTAC	57.744	50.000	3.30	0.00	44.59	3.34
1633	5424	2.415512	GTCAGCTTTGGTACGATGTTCC	59.584	50.000	0.00	0.00	0.00	3.62
1634	5425	2.301870	TCAGCTTTGGTACGATGTTCCT	59.698	45.455	0.00	0.00	0.00	3.36
1670	5461	3.124466	GCCATTTGATTTTGCGGGTTTAC	59.876	43.478	0.00	0.00	0.00	2.01
1682	5474	2.924880	GCGGGTTTACCTGAATTTGTGC	60.925	50.000	11.93	0.00	45.36	4.57
1717	5538	8.911918	TTATCACTTGTTAAGTTCTTTGCCTA	57.088	30.769	0.00	0.00	40.46	3.93
1724	5545	7.575414	TGTTAAGTTCTTTGCCTAACATTCA	57.425	32.000	0.00	0.00	0.00	2.57
1728	5549	5.831997	AGTTCTTTGCCTAACATTCACAAC	58.168	37.500	0.00	0.00	0.00	3.32
1734	5555	4.677584	TGCCTAACATTCACAACAACAAC	58.322	39.130	0.00	0.00	0.00	3.32
1737	5558	5.005299	GCCTAACATTCACAACAACAACAAC	59.995	40.000	0.00	0.00	0.00	3.32
1740	5561	6.851222	AACATTCACAACAACAACAACAAA	57.149	29.167	0.00	0.00	0.00	2.83
1741	5562	6.464895	ACATTCACAACAACAACAACAAAG	57.535	33.333	0.00	0.00	0.00	2.77
1743	5564	6.873076	ACATTCACAACAACAACAACAAAGAT	59.127	30.769	0.00	0.00	0.00	2.40
1744	5565	7.387397	ACATTCACAACAACAACAACAAAGATT	59.613	29.630	0.00	0.00	0.00	2.40
1745	5566	7.721286	TTCACAACAACAACAACAAAGATTT	57.279	28.000	0.00	0.00	0.00	2.17
1746	5567	7.721286	TCACAACAACAACAACAAAGATTTT	57.279	28.000	0.00	0.00	0.00	1.82
1747	5568	8.147642	TCACAACAACAACAACAAAGATTTTT	57.852	26.923	0.00	0.00	0.00	1.94
1898	5961	4.532276	TCAACGTGTAAAATGACATGCAC	58.468	39.130	0.00	0.00	39.53	4.57
1922	5985	8.812329	CACGTGTTTTAAAGATTTTGGAAATCA	58.188	29.630	7.58	0.00	0.00	2.57
1958	6022	5.299279	CCATTGTACAGCCTAAAATACAGGG	59.701	44.000	0.00	0.00	33.44	4.45
1959	6023	5.765576	TTGTACAGCCTAAAATACAGGGA	57.234	39.130	0.00	0.00	33.44	4.20
1976	6040	4.103311	ACAGGGAGATCCTAAAATAGTGGC	59.897	45.833	0.00	0.00	46.12	5.01
1999	6063	2.572290	ACTTCAGAAACACCTTTCCCG	58.428	47.619	0.00	0.00	37.12	5.14
2015	6079	5.358160	CCTTTCCCGATCTAGCTTGAAAAAT	59.642	40.000	0.99	0.00	0.00	1.82
2034	6098	8.620416	TGAAAAATGATCTTATATTGTGGGACG	58.380	33.333	0.00	0.00	0.00	4.79
2035	6099	8.746052	AAAAATGATCTTATATTGTGGGACGA	57.254	30.769	0.00	0.00	0.00	4.20
2038	6102	5.853936	TGATCTTATATTGTGGGACGAAGG	58.146	41.667	0.00	0.00	0.00	3.46
2091	6161	1.067565	TGCACAAAACCAAACTTGCGA	60.068	42.857	0.00	0.00	32.49	5.10
2511	6934	8.371571	TCACAATATAGGATGCTCTGTATCAT	57.628	34.615	0.00	0.00	0.00	2.45
2538	6969	7.712639	CCATATATGCAGGGTATGTATCTTCAC	59.287	40.741	7.24	0.00	35.63	3.18
2581	7170	4.837896	TGTATCTTCAGCTATGACGAGG	57.162	45.455	0.00	0.00	37.16	4.63
2596	7185	6.857437	ATGACGAGGATGATGGAATATACA	57.143	37.500	0.00	0.00	0.00	2.29
2687	7276	3.795688	ACAACCATCACTCAAGACCAT	57.204	42.857	0.00	0.00	0.00	3.55
2763	7355	3.382832	CTTCTCACCCTCGCCGGT	61.383	66.667	1.90	0.00	36.18	5.28
2820	7412	9.535878	AAAAACGTGTGTTGAATATGGTTAATT	57.464	25.926	0.00	0.00	38.62	1.40
2829	7421	8.609176	TGTTGAATATGGTTAATTCTAAGACGC	58.391	33.333	0.00	0.00	34.95	5.19
2839	7431	3.637911	TTCTAAGACGCCTCTCTCTCT	57.362	47.619	0.00	0.00	0.00	3.10
2860	7452	1.292941	CCTCTCTCCTCCCTCTCCCA	61.293	65.000	0.00	0.00	0.00	4.37
2981	7663	1.028905	CTGTTGTTTTCCCCTGCGAA	58.971	50.000	0.00	0.00	0.00	4.70
2999	7681	4.458989	TGCGAAATTTTTCAGAGGTATGCT	59.541	37.500	4.12	0.00	37.01	3.79
3059	7741	3.744238	AGTGGGGTGTTTATTTGCAAC	57.256	42.857	0.00	0.00	0.00	4.17
3079	7761	3.986006	GGATCGCCGCCGGTATGA	61.986	66.667	4.45	0.54	34.56	2.15
3080	7762	2.028484	GATCGCCGCCGGTATGAA	59.972	61.111	4.45	0.00	34.56	2.57
3385	9719	9.051679	TCATATATAACATGTTCAAAACGGAGG	57.948	33.333	15.85	0.00	0.00	4.30
3404	10023	5.050567	CGGAGGTACGGTTTAAAAGATATGC	60.051	44.000	0.00	0.00	0.00	3.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	6.460781	CACCAGTCTACCATGTGTTTTAGTA	58.539	40.000	0.00	0.00	0.00	1.82
52	53	7.422399	TGATTTTAAACAAAGCACCAGTCTAC	58.578	34.615	0.00	0.00	0.00	2.59
56	57	5.523552	GCTTGATTTTAAACAAAGCACCAGT	59.476	36.000	17.54	0.00	0.00	4.00
159	160	5.928839	GCAAAGACTAACTTGATCTGTCTCA	59.071	40.000	0.00	0.00	38.98	3.27
216	217	2.551721	CCATCACTCTTCTGTTGCCACT	60.552	50.000	0.00	0.00	0.00	4.00
221	222	2.189594	TGGCCATCACTCTTCTGTTG	57.810	50.000	0.00	0.00	0.00	3.33
318	322	1.098050	GAGCCTGGCCACATTAACTG	58.902	55.000	16.57	0.00	0.00	3.16
319	323	0.034089	GGAGCCTGGCCACATTAACT	60.034	55.000	16.57	0.00	0.00	2.24
320	324	0.034089	AGGAGCCTGGCCACATTAAC	60.034	55.000	16.57	0.00	0.00	2.01
321	325	0.034186	CAGGAGCCTGGCCACATTAA	60.034	55.000	16.57	0.00	40.17	1.40
322	326	1.609239	CAGGAGCCTGGCCACATTA	59.391	57.895	16.57	0.00	40.17	1.90
323	327	2.357836	CAGGAGCCTGGCCACATT	59.642	61.111	16.57	0.00	40.17	2.71
367	374	7.190501	GGACTAGTAGGGATAGGAACCATATT	58.809	42.308	0.00	0.00	0.00	1.28
373	380	5.481122	GGAATGGACTAGTAGGGATAGGAAC	59.519	48.000	0.00	0.00	0.00	3.62
381	388	2.398588	TGCAGGAATGGACTAGTAGGG	58.601	52.381	0.00	0.00	0.00	3.53
561	589	3.572255	TGTTTGGGTTCTCATTAACTGCC	59.428	43.478	0.00	0.00	0.00	4.85
688	725	4.487948	CTGCAAACTGTGGGTAATCATTG	58.512	43.478	0.00	0.00	0.00	2.82
691	728	2.158534	ACCTGCAAACTGTGGGTAATCA	60.159	45.455	0.00	0.00	0.00	2.57
712	753	1.946768	GCTGCACTGTACTGGAACAAA	59.053	47.619	4.66	0.00	38.70	2.83
726	767	3.750130	CCATCCTATTATCACTGCTGCAC	59.250	47.826	0.00	0.00	0.00	4.57
727	768	3.808265	GCCATCCTATTATCACTGCTGCA	60.808	47.826	0.88	0.88	0.00	4.41
728	769	2.746362	GCCATCCTATTATCACTGCTGC	59.254	50.000	0.00	0.00	0.00	5.25
734	775	6.881065	TCATGCTTAAGCCATCCTATTATCAC	59.119	38.462	24.30	0.00	41.18	3.06
792	836	6.814954	TTAGATCCTGAGCTTTATGGAGTT	57.185	37.500	0.00	0.00	31.59	3.01
959	1019	7.123847	TCTGTTATTCTGTTAACCTACCTCTCC	59.876	40.741	2.48	0.00	32.24	3.71
991	1051	2.102420	CCACTGCCGACATATACTGGAA	59.898	50.000	0.00	0.00	0.00	3.53
1086	1172	4.377897	GCCGAACTAGCCTATTGTTGTAT	58.622	43.478	0.00	0.00	0.00	2.29
1116	1202	2.716217	ACTGCAGATGGTTTTAGCTCC	58.284	47.619	23.35	0.00	0.00	4.70
1306	1406	7.109501	TGCTAAGAGTAAATTATTCACCTGCA	58.890	34.615	0.00	0.00	0.00	4.41
1380	1489	5.085920	TGGATCCACCAACATCTTTTCAAT	58.914	37.500	11.44	0.00	46.75	2.57
1430	1539	2.832129	CCAGTGCAAGTACTCCCTTAGA	59.168	50.000	0.00	0.00	0.00	2.10
1556	5344	6.592994	CCTACGTACGAGTGGAGATATATGAA	59.407	42.308	24.41	0.00	0.00	2.57
1558	5346	6.104665	TCCTACGTACGAGTGGAGATATATG	58.895	44.000	24.41	0.00	0.00	1.78
1573	5364	0.104304	CCTGCCACCATCCTACGTAC	59.896	60.000	0.00	0.00	0.00	3.67
1576	5367	2.203070	GCCTGCCACCATCCTACG	60.203	66.667	0.00	0.00	0.00	3.51
1592	5383	0.251341	ACCAGTTGTTCCAGGGATGC	60.251	55.000	0.00	0.00	0.00	3.91
1625	5416	5.512788	GCACAAATTGTTATGAGGAACATCG	59.487	40.000	0.00	0.00	39.04	3.84
1670	5461	3.663995	TTCCACATGCACAAATTCAGG	57.336	42.857	0.00	0.00	0.00	3.86
1682	5474	9.912634	AACTTAACAAGTGATAATTTCCACATG	57.087	29.630	11.02	11.11	41.91	3.21
1717	5538	6.703607	TCTTTGTTGTTGTTGTTGTGAATGTT	59.296	30.769	0.00	0.00	0.00	2.71
1746	5567	2.626840	GCAACAGGTTTGAGGCAAAAA	58.373	42.857	0.00	0.00	35.03	1.94
1747	5568	1.134551	GGCAACAGGTTTGAGGCAAAA	60.135	47.619	0.00	0.00	35.03	2.44
1882	5944	4.560136	AACACGTGCATGTCATTTTACA	57.440	36.364	17.22	0.00	30.55	2.41
1922	5985	5.648092	GGCTGTACAATGGACTTGTCTTAAT	59.352	40.000	0.00	0.00	44.99	1.40
1958	6022	8.150945	TGAAGTATGCCACTATTTTAGGATCTC	58.849	37.037	0.00	0.00	36.04	2.75
1959	6023	8.034313	TGAAGTATGCCACTATTTTAGGATCT	57.966	34.615	0.00	0.00	36.04	2.75
1976	6040	4.154195	CGGGAAAGGTGTTTCTGAAGTATG	59.846	45.833	0.00	0.00	41.72	2.39
2015	6079	5.221641	CCCTTCGTCCCACAATATAAGATCA	60.222	44.000	0.00	0.00	0.00	2.92
2034	6098	9.588096	AAATCAAGTATAAATGATACCCCCTTC	57.412	33.333	2.80	0.00	41.36	3.46
2178	6575	4.796606	AGCACCATGGCATTAATTAGTCT	58.203	39.130	13.04	0.00	35.83	3.24
2511	6934	7.623278	TGAAGATACATACCCTGCATATATGGA	59.377	37.037	14.51	10.73	31.75	3.41
2555	6986	7.135089	TCGTCATAGCTGAAGATACATAGTC	57.865	40.000	0.00	0.00	35.37	2.59
2596	7185	7.440198	GGGCTCTTTTACTAGTAATAACCGAT	58.560	38.462	15.92	0.00	0.00	4.18
2611	7200	1.847890	GCAACGCACGGGCTCTTTTA	61.848	55.000	8.62	0.00	38.10	1.52
2707	7298	4.863689	CACAAATATGATGCCTCGCAAAAA	59.136	37.500	0.00	0.00	43.62	1.94
2763	7355	1.044611	TGTGAACACCGAGACCATCA	58.955	50.000	2.46	0.00	0.00	3.07
2820	7412	2.158871	GGAGAGAGAGAGGCGTCTTAGA	60.159	54.545	10.79	0.00	30.97	2.10
2826	7418	1.226262	GAGGGAGAGAGAGAGGCGT	59.774	63.158	0.00	0.00	0.00	5.68
2829	7421	1.421646	GGAGAGAGGGAGAGAGAGAGG	59.578	61.905	0.00	0.00	0.00	3.69
2839	7431	0.996762	GGAGAGGGAGGAGAGAGGGA	60.997	65.000	0.00	0.00	0.00	4.20
2860	7452	4.877773	AGAGAGAGAGAGAGAGAGAGAGT	58.122	47.826	0.00	0.00	0.00	3.24
2981	7663	6.655078	ACACAAGCATACCTCTGAAAAATT	57.345	33.333	0.00	0.00	0.00	1.82
2999	7681	9.872757	GAAAAGAAAACATCGATAACTACACAA	57.127	29.630	0.00	0.00	0.00	3.33
3379	9713	4.541973	ATCTTTTAAACCGTACCTCCGT	57.458	40.909	0.00	0.00	0.00	4.69
3385	9719	9.730420	AAATCATGCATATCTTTTAAACCGTAC	57.270	29.630	0.00	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.