AutoCloner

Multiple sequence alignment - TraesCS1A01G337100

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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	TraesCS1A01G337100	chr1A	100.000	3565	0	0	1	3565	526620885	526624449	0.000000e+00	6584.0
1	TraesCS1A01G337100	chr1A	96.891	965	27	3	2263	3225	524611360	524612323	0.000000e+00	1613.0
2	TraesCS1A01G337100	chr1A	89.956	1145	70	20	573	1690	524700051	524701177	0.000000e+00	1435.0
3	TraesCS1A01G337100	chr1A	95.221	858	25	7	570	1412	524285953	524286809	0.000000e+00	1343.0
4	TraesCS1A01G337100	chr1A	95.058	688	34	0	1886	2573	524287056	524287743	0.000000e+00	1083.0
5	TraesCS1A01G337100	chr1A	94.236	694	29	4	1886	2573	522972899	522973587	0.000000e+00	1050.0
6	TraesCS1A01G337100	chr1A	93.948	694	31	4	1886	2573	524701176	524701864	0.000000e+00	1038.0
7	TraesCS1A01G337100	chr1A	86.752	936	86	12	764	1666	524599123	524600053	0.000000e+00	1007.0
8	TraesCS1A01G337100	chr1A	90.091	767	55	10	944	1690	522972135	522972900	0.000000e+00	976.0
9	TraesCS1A01G337100	chr1A	95.547	247	10	1	1445	1690	524286811	524287057	9.280000e-106	394.0
10	TraesCS1A01G337100	chr1A	86.818	220	22	4	683	902	522971921	522972133	4.600000e-59	239.0
11	TraesCS1A01G337100	chr1A	100.000	29	0	0	3067	3095	522970106	522970134	2.000000e-03	54.7
12	TraesCS1A01G337100	chr1B	90.648	1080	65	13	625	1686	579943439	579944500	0.000000e+00	1402.0
13	TraesCS1A01G337100	chr1B	90.302	959	58	11	764	1690	580211408	580212363	0.000000e+00	1223.0
14	TraesCS1A01G337100	chr1B	96.444	703	25	0	1886	2588	580212362	580213064	0.000000e+00	1160.0
15	TraesCS1A01G337100	chr1B	94.860	642	33	0	1886	2527	579944503	579945144	0.000000e+00	1003.0
16	TraesCS1A01G337100	chr1B	93.166	439	26	4	3128	3565	580213877	580214312	3.000000e-180	641.0
17	TraesCS1A01G337100	chr1B	92.500	440	29	4	3128	3565	580227719	580228156	8.400000e-176	627.0
18	TraesCS1A01G337100	chr1B	87.336	458	50	6	2571	3025	580213078	580213530	5.280000e-143	518.0
19	TraesCS1A01G337100	chr1B	77.336	503	78	20	2574	3066	579941518	579941994	7.590000e-67	265.0
20	TraesCS1A01G337100	chr1B	96.512	86	3	0	3025	3110	580227644	580227729	3.710000e-30	143.0
21	TraesCS1A01G337100	chr1B	93.023	86	6	0	3025	3110	580213802	580213887	3.740000e-25	126.0
22	TraesCS1A01G337100	chr1D	95.930	688	28	0	1886	2573	427634476	427635163	0.000000e+00	1116.0
23	TraesCS1A01G337100	chr1D	87.313	804	51	18	620	1405	427633113	427633883	0.000000e+00	872.0
24	TraesCS1A01G337100	chr1D	90.444	293	25	3	1401	1690	427634185	427634477	2.010000e-102	383.0
25	TraesCS1A01G337100	chr1D	76.817	509	74	24	2571	3066	427631574	427632051	2.750000e-61	246.0
26	TraesCS1A01G337100	chr5D	88.552	594	45	11	1	580	497021359	497021943	0.000000e+00	699.0
27	TraesCS1A01G337100	chr3D	87.648	591	55	14	1	579	589878613	589878029	0.000000e+00	671.0
28	TraesCS1A01G337100	chr3D	93.382	136	9	0	1689	1824	158288961	158288826	6.030000e-48	202.0
29	TraesCS1A01G337100	chr7D	89.943	527	41	8	3	517	461087527	461087001	0.000000e+00	669.0
30	TraesCS1A01G337100	chr7D	87.031	586	46	15	1	577	575591139	575590575	5.020000e-178	634.0
31	TraesCS1A01G337100	chr7D	94.118	136	8	0	1689	1824	140313281	140313146	1.300000e-49	207.0
32	TraesCS1A01G337100	chr7D	94.118	136	8	0	1689	1824	140314572	140314437	1.300000e-49	207.0
33	TraesCS1A01G337100	chr7D	93.382	136	9	0	1689	1824	140312766	140312631	6.030000e-48	202.0
34	TraesCS1A01G337100	chr6D	92.840	419	22	6	2	413	438097355	438096938	5.090000e-168	601.0
35	TraesCS1A01G337100	chr6D	82.283	587	77	16	1	577	396462117	396461548	1.920000e-132	483.0
36	TraesCS1A01G337100	chr3A	84.175	594	69	19	1	579	43033900	43033317	1.450000e-153	553.0
37	TraesCS1A01G337100	chr3A	84.175	594	69	19	1	579	43645286	43644703	1.450000e-153	553.0
38	TraesCS1A01G337100	chr4D	83.221	596	72	20	1	579	66957388	66957972	4.080000e-144	521.0
39	TraesCS1A01G337100	chr7B	82.747	597	75	20	1	579	720342484	720341898	1.140000e-139	507.0
40	TraesCS1A01G337100	chr5A	94.161	137	8	0	1688	1824	513872997	513872861	3.610000e-50	209.0
41	TraesCS1A01G337100	chrUn	94.118	136	8	0	1689	1824	47323727	47323592	1.300000e-49	207.0
42	TraesCS1A01G337100	chr7A	94.118	136	8	0	1680	1815	571941201	571941336	1.300000e-49	207.0
43	TraesCS1A01G337100	chr3B	95.312	128	6	0	1688	1815	825529970	825530097	1.680000e-48	204.0
44	TraesCS1A01G337100	chr2A	93.382	136	9	0	1689	1824	43530715	43530580	6.030000e-48	202.0

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	TraesCS1A01G337100	chr1A	526620885	526624449	3564	False	6584.000000	6584	100.000000	1	3565	1	chr1A.!!$F3	3564
1	TraesCS1A01G337100	chr1A	524611360	524612323	963	False	1613.000000	1613	96.891000	2263	3225	1	chr1A.!!$F2	962
2	TraesCS1A01G337100	chr1A	524700051	524701864	1813	False	1236.500000	1435	91.952000	573	2573	2	chr1A.!!$F6	2000
3	TraesCS1A01G337100	chr1A	524599123	524600053	930	False	1007.000000	1007	86.752000	764	1666	1	chr1A.!!$F1	902
4	TraesCS1A01G337100	chr1A	524285953	524287743	1790	False	940.000000	1343	95.275333	570	2573	3	chr1A.!!$F5	2003
5	TraesCS1A01G337100	chr1A	522970106	522973587	3481	False	579.925000	1050	92.786250	683	3095	4	chr1A.!!$F4	2412
6	TraesCS1A01G337100	chr1B	579941518	579945144	3626	False	890.000000	1402	87.614667	625	3066	3	chr1B.!!$F1	2441
7	TraesCS1A01G337100	chr1B	580211408	580214312	2904	False	733.600000	1223	92.054200	764	3565	5	chr1B.!!$F2	2801
8	TraesCS1A01G337100	chr1B	580227644	580228156	512	False	385.000000	627	94.506000	3025	3565	2	chr1B.!!$F3	540
9	TraesCS1A01G337100	chr1D	427631574	427635163	3589	False	654.250000	1116	87.626000	620	3066	4	chr1D.!!$F1	2446
10	TraesCS1A01G337100	chr5D	497021359	497021943	584	False	699.000000	699	88.552000	1	580	1	chr5D.!!$F1	579
11	TraesCS1A01G337100	chr3D	589878029	589878613	584	True	671.000000	671	87.648000	1	579	1	chr3D.!!$R2	578
12	TraesCS1A01G337100	chr7D	461087001	461087527	526	True	669.000000	669	89.943000	3	517	1	chr7D.!!$R1	514
13	TraesCS1A01G337100	chr7D	575590575	575591139	564	True	634.000000	634	87.031000	1	577	1	chr7D.!!$R2	576
14	TraesCS1A01G337100	chr7D	140312631	140314572	1941	True	205.333333	207	93.872667	1689	1824	3	chr7D.!!$R3	135
15	TraesCS1A01G337100	chr6D	396461548	396462117	569	True	483.000000	483	82.283000	1	577	1	chr6D.!!$R1	576
16	TraesCS1A01G337100	chr3A	43033317	43033900	583	True	553.000000	553	84.175000	1	579	1	chr3A.!!$R1	578
17	TraesCS1A01G337100	chr3A	43644703	43645286	583	True	553.000000	553	84.175000	1	579	1	chr3A.!!$R2	578
18	TraesCS1A01G337100	chr4D	66957388	66957972	584	False	521.000000	521	83.221000	1	579	1	chr4D.!!$F1	578
19	TraesCS1A01G337100	chr7B	720341898	720342484	586	True	507.000000	507	82.747000	1	579	1	chr7B.!!$R1	578

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
616	670	0.602905	CGCCGGGTGAAGAAGAGTTT	60.603	55.0	2.18	0.0	0.0	2.66	F
1331	2761	1.182667	CTACCGTGTCACCCTGATCA	58.817	55.0	0.00	0.0	0.0	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1447	3207	0.032952	CACTCCGACTTTGGGTTCGA	59.967	55.0	0.0	0.0	0.0	3.71	R
2755	4610	0.465097	CAGGGATCGATGCTTGGCTT	60.465	55.0	19.4	0.0	0.0	4.35	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
210	213	2.342279	CGGTCCGCCTTGAAGACA	59.658	61.111	0.00	0.00	31.99	3.41
274	301	4.493747	GAAGGCCGACGACGAGGG	62.494	72.222	9.28	2.93	42.66	4.30
328	355	2.199236	CAACTTCTTCGCCCCGTATAC	58.801	52.381	0.00	0.00	0.00	1.47
490	540	3.077556	ACGAGCGGCTGGGAATCT	61.078	61.111	16.46	0.00	0.00	2.40
518	569	2.788581	CGCCGATTTTAGCGCCAA	59.211	55.556	2.29	0.00	46.50	4.52
580	634	1.137872	ACGGCTGAAGATGCTCTAAGG	59.862	52.381	0.00	0.00	0.00	2.69
581	635	1.137872	CGGCTGAAGATGCTCTAAGGT	59.862	52.381	0.00	0.00	0.00	3.50
582	636	2.419297	CGGCTGAAGATGCTCTAAGGTT	60.419	50.000	0.00	0.00	0.00	3.50
583	637	3.202097	GGCTGAAGATGCTCTAAGGTTC	58.798	50.000	0.00	0.00	0.00	3.62
585	639	3.870419	GCTGAAGATGCTCTAAGGTTCTG	59.130	47.826	0.00	0.00	0.00	3.02
588	642	3.988976	AGATGCTCTAAGGTTCTGCAA	57.011	42.857	0.00	0.00	37.20	4.08
589	643	3.604582	AGATGCTCTAAGGTTCTGCAAC	58.395	45.455	0.00	0.00	37.20	4.17
590	644	1.795768	TGCTCTAAGGTTCTGCAACG	58.204	50.000	0.00	0.00	32.68	4.10
591	645	1.079503	GCTCTAAGGTTCTGCAACGG	58.920	55.000	0.00	0.00	32.68	4.44
592	646	1.726853	CTCTAAGGTTCTGCAACGGG	58.273	55.000	0.00	0.00	32.68	5.28
594	648	1.275291	TCTAAGGTTCTGCAACGGGAG	59.725	52.381	0.00	0.00	32.68	4.30
597	651	1.671379	GGTTCTGCAACGGGAGGTC	60.671	63.158	0.00	0.00	32.68	3.85
598	652	2.027625	GTTCTGCAACGGGAGGTCG	61.028	63.158	0.00	0.00	32.55	4.79
599	653	3.876589	TTCTGCAACGGGAGGTCGC	62.877	63.158	0.00	0.00	32.55	5.19
611	665	2.434359	GGTCGCCGGGTGAAGAAG	60.434	66.667	12.67	0.00	0.00	2.85
613	667	1.446272	GTCGCCGGGTGAAGAAGAG	60.446	63.158	12.67	0.00	0.00	2.85
614	668	1.906824	TCGCCGGGTGAAGAAGAGT	60.907	57.895	8.05	0.00	0.00	3.24
615	669	1.004918	CGCCGGGTGAAGAAGAGTT	60.005	57.895	2.18	0.00	0.00	3.01
616	670	0.602905	CGCCGGGTGAAGAAGAGTTT	60.603	55.000	2.18	0.00	0.00	2.66
617	671	1.605753	GCCGGGTGAAGAAGAGTTTT	58.394	50.000	2.18	0.00	0.00	2.43
620	674	2.949644	CCGGGTGAAGAAGAGTTTTTGT	59.050	45.455	0.00	0.00	0.00	2.83
622	676	4.577283	CCGGGTGAAGAAGAGTTTTTGTTA	59.423	41.667	0.00	0.00	0.00	2.41
624	678	6.199393	CGGGTGAAGAAGAGTTTTTGTTAAG	58.801	40.000	0.00	0.00	0.00	1.85
626	680	7.418408	GGGTGAAGAAGAGTTTTTGTTAAGAG	58.582	38.462	0.00	0.00	0.00	2.85
627	681	7.067129	GGGTGAAGAAGAGTTTTTGTTAAGAGT	59.933	37.037	0.00	0.00	0.00	3.24
628	682	7.910683	GGTGAAGAAGAGTTTTTGTTAAGAGTG	59.089	37.037	0.00	0.00	0.00	3.51
924	2342	1.898574	CCTGTTCCTTTGCACCGCT	60.899	57.895	0.00	0.00	0.00	5.52
1114	2544	4.113815	CCCTGGCCGGCATCTTCA	62.114	66.667	30.85	15.73	0.00	3.02
1331	2761	1.182667	CTACCGTGTCACCCTGATCA	58.817	55.000	0.00	0.00	0.00	2.92
1392	2834	1.272490	CTCTCGCCACACTTTGAGGTA	59.728	52.381	0.00	0.00	30.35	3.08
1458	3218	1.375523	CGACCCCTCGAACCCAAAG	60.376	63.158	0.00	0.00	43.06	2.77
1557	3317	2.367202	GGAAGGGATGCCTCCACGA	61.367	63.158	6.10	0.00	44.08	4.35
1603	3366	4.328536	ACTCATGAGAGACGTGTACTCTT	58.671	43.478	29.27	0.00	44.98	2.85
1641	3404	0.824759	GGGGACGTCTCTATGTGCTT	59.175	55.000	16.48	0.00	33.71	3.91
1723	3490	6.037830	GTCACAGTTTAGAAGGCACAGTTAAA	59.962	38.462	0.00	0.00	0.00	1.52
1733	3500	3.120041	GGCACAGTTAAATTTGCGTGTT	58.880	40.909	7.84	0.00	35.74	3.32
1740	3507	6.181944	CAGTTAAATTTGCGTGTTTTTCCAC	58.818	36.000	0.00	0.00	0.00	4.02
1756	3523	8.919145	TGTTTTTCCACAATAGACAAGGTTTAT	58.081	29.630	0.00	0.00	0.00	1.40
1758	3525	8.698973	TTTTCCACAATAGACAAGGTTTATGA	57.301	30.769	0.00	0.00	0.00	2.15
1838	3655	6.906901	TGTATACCTAGGTCCCAGAGAATTTT	59.093	38.462	20.32	0.00	0.00	1.82
1843	3660	4.731313	AGGTCCCAGAGAATTTTCAAGT	57.269	40.909	0.00	0.00	0.00	3.16
1845	3662	4.141158	AGGTCCCAGAGAATTTTCAAGTGT	60.141	41.667	0.00	0.00	0.00	3.55
1856	3673	7.428826	AGAATTTTCAAGTGTGCCTTCTAAAG	58.571	34.615	0.00	0.00	0.00	1.85
1873	3690	1.313812	AAGCGTGACGGAGGGAGTAG	61.314	60.000	7.25	0.00	0.00	2.57
1876	3693	1.171308	CGTGACGGAGGGAGTAGAAA	58.829	55.000	0.00	0.00	0.00	2.52
1877	3694	1.542915	CGTGACGGAGGGAGTAGAAAA	59.457	52.381	0.00	0.00	0.00	2.29
1878	3695	2.415625	CGTGACGGAGGGAGTAGAAAAG	60.416	54.545	0.00	0.00	0.00	2.27
1879	3696	2.094130	GTGACGGAGGGAGTAGAAAAGG	60.094	54.545	0.00	0.00	0.00	3.11
1880	3697	2.225192	TGACGGAGGGAGTAGAAAAGGA	60.225	50.000	0.00	0.00	0.00	3.36
1881	3698	2.427812	GACGGAGGGAGTAGAAAAGGAG	59.572	54.545	0.00	0.00	0.00	3.69
1882	3699	1.757699	CGGAGGGAGTAGAAAAGGAGG	59.242	57.143	0.00	0.00	0.00	4.30
1883	3700	2.623502	CGGAGGGAGTAGAAAAGGAGGA	60.624	54.545	0.00	0.00	0.00	3.71
1884	3701	3.035363	GGAGGGAGTAGAAAAGGAGGAG	58.965	54.545	0.00	0.00	0.00	3.69
1885	3702	3.566997	GGAGGGAGTAGAAAAGGAGGAGT	60.567	52.174	0.00	0.00	0.00	3.85
1886	3703	4.325974	GGAGGGAGTAGAAAAGGAGGAGTA	60.326	50.000	0.00	0.00	0.00	2.59
1930	3747	2.422479	CACGGTGACTAGCTAGCTAACA	59.578	50.000	24.20	21.96	0.00	2.41
1947	3764	7.447374	AGCTAACATTGTGCAGTAAATAACA	57.553	32.000	0.00	0.00	0.00	2.41
2031	3848	1.332028	CGATTAATGAAGCACGCGGAC	60.332	52.381	12.47	0.68	0.00	4.79
2113	3936	5.689068	GCAAACTTCAGATTTGGTTTCTCAG	59.311	40.000	0.00	0.00	37.49	3.35
2114	3937	6.460123	GCAAACTTCAGATTTGGTTTCTCAGA	60.460	38.462	0.00	0.00	37.49	3.27
2147	3970	2.811431	TCACACCGAATGGATGTTGAAC	59.189	45.455	0.00	0.00	39.21	3.18
2589	4412	9.675464	AGAATGTATTTACGTTGGATTCCTTAA	57.325	29.630	3.95	0.00	35.69	1.85
2590	4413	9.712359	GAATGTATTTACGTTGGATTCCTTAAC	57.288	33.333	3.95	0.18	35.69	2.01
2591	4414	8.795842	ATGTATTTACGTTGGATTCCTTAACA	57.204	30.769	3.95	0.00	0.00	2.41
2614	4468	9.480053	AACATCCATATGCAAGCATATTAAAAC	57.520	29.630	21.47	0.00	44.49	2.43
2647	4502	1.902508	CCTGAGTGGAGCTTTACAGGA	59.097	52.381	16.00	0.00	45.02	3.86
2648	4503	2.503356	CCTGAGTGGAGCTTTACAGGAT	59.497	50.000	16.00	0.00	45.02	3.24
2866	4721	3.998341	GACCAATTTTGTACGGCTACTCA	59.002	43.478	0.00	0.00	0.00	3.41
3032	5536	2.030007	CGTTGGAGCCAAACATGTGATT	60.030	45.455	0.00	0.00	37.70	2.57
3298	6094	1.447140	TACGATGTCCGGTGCTTGC	60.447	57.895	0.00	0.00	43.93	4.01
3469	6266	2.147958	GTGTTTGCCGTGGTGAAGATA	58.852	47.619	0.00	0.00	0.00	1.98
3558	6355	0.251165	CCTCGGGTTGGTTGTGGAAT	60.251	55.000	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
535	587	1.664151	CCCTCAGACGGCGATTTTAAC	59.336	52.381	16.62	0.00	0.00	2.01
580	634	2.027625	CGACCTCCCGTTGCAGAAC	61.028	63.158	0.00	0.00	0.00	3.01
581	635	2.342279	CGACCTCCCGTTGCAGAA	59.658	61.111	0.00	0.00	0.00	3.02
591	645	4.452733	CTTCACCCGGCGACCTCC	62.453	72.222	9.30	0.00	0.00	4.30
592	646	2.837371	CTTCTTCACCCGGCGACCTC	62.837	65.000	9.30	0.00	0.00	3.85
594	648	2.434359	CTTCTTCACCCGGCGACC	60.434	66.667	9.30	0.00	0.00	4.79
597	651	0.602905	AAACTCTTCTTCACCCGGCG	60.603	55.000	0.00	0.00	0.00	6.46
598	652	1.605753	AAAACTCTTCTTCACCCGGC	58.394	50.000	0.00	0.00	0.00	6.13
599	653	2.949644	ACAAAAACTCTTCTTCACCCGG	59.050	45.455	0.00	0.00	0.00	5.73
601	655	7.067129	ACTCTTAACAAAAACTCTTCTTCACCC	59.933	37.037	0.00	0.00	0.00	4.61
602	656	7.910683	CACTCTTAACAAAAACTCTTCTTCACC	59.089	37.037	0.00	0.00	0.00	4.02
603	657	7.910683	CCACTCTTAACAAAAACTCTTCTTCAC	59.089	37.037	0.00	0.00	0.00	3.18
605	659	6.913132	GCCACTCTTAACAAAAACTCTTCTTC	59.087	38.462	0.00	0.00	0.00	2.87
606	660	6.183360	GGCCACTCTTAACAAAAACTCTTCTT	60.183	38.462	0.00	0.00	0.00	2.52
607	661	5.299531	GGCCACTCTTAACAAAAACTCTTCT	59.700	40.000	0.00	0.00	0.00	2.85
611	665	3.304458	CGGGCCACTCTTAACAAAAACTC	60.304	47.826	4.39	0.00	0.00	3.01
613	667	2.287970	CCGGGCCACTCTTAACAAAAAC	60.288	50.000	4.39	0.00	0.00	2.43
614	668	1.957877	CCGGGCCACTCTTAACAAAAA	59.042	47.619	4.39	0.00	0.00	1.94
615	669	1.143277	TCCGGGCCACTCTTAACAAAA	59.857	47.619	4.39	0.00	0.00	2.44
616	670	0.766131	TCCGGGCCACTCTTAACAAA	59.234	50.000	4.39	0.00	0.00	2.83
617	671	0.323629	CTCCGGGCCACTCTTAACAA	59.676	55.000	4.39	0.00	0.00	2.83
620	674	2.987125	GCTCCGGGCCACTCTTAA	59.013	61.111	4.39	0.00	34.27	1.85
1331	2761	3.393089	AGTCGTGTTTGATGAAGCTCT	57.607	42.857	0.00	0.00	0.00	4.09
1359	2801	3.847621	CGAGAGCGTTGGATCGTAT	57.152	52.632	0.00	0.00	32.66	3.06
1392	2834	2.744202	GCGAACACACTCCATGAAGAAT	59.256	45.455	0.00	0.00	0.00	2.40
1447	3207	0.032952	CACTCCGACTTTGGGTTCGA	59.967	55.000	0.00	0.00	0.00	3.71
1557	3317	5.558818	AGTAGTATGTTAGGGTCGATCGAT	58.441	41.667	22.50	8.10	0.00	3.59
1573	3333	6.584488	ACACGTCTCTCATGAGTAGTAGTAT	58.416	40.000	21.92	9.22	40.98	2.12
1603	3366	3.495983	CCCCGCCAATACACAGATTCATA	60.496	47.826	0.00	0.00	0.00	2.15
1608	3371	0.180406	GTCCCCGCCAATACACAGAT	59.820	55.000	0.00	0.00	0.00	2.90
1723	3490	5.689961	GTCTATTGTGGAAAAACACGCAAAT	59.310	36.000	0.00	0.00	44.21	2.32
1733	3500	8.573035	GTCATAAACCTTGTCTATTGTGGAAAA	58.427	33.333	0.00	0.00	0.00	2.29
1740	3507	5.794687	TGCGTCATAAACCTTGTCTATTG	57.205	39.130	0.00	0.00	0.00	1.90
1756	3523	6.435430	ACTAGAAATAAATGCAATGCGTCA	57.565	33.333	0.00	0.00	0.00	4.35
1758	3525	6.260936	AGCTACTAGAAATAAATGCAATGCGT	59.739	34.615	0.00	0.00	0.00	5.24
1804	3571	9.543231	CTGGGACCTAGGTATACATATAGAAAA	57.457	37.037	16.29	0.00	0.00	2.29
1815	3582	7.136885	TGAAAATTCTCTGGGACCTAGGTATA	58.863	38.462	16.29	3.11	0.00	1.47
1838	3655	2.143122	CGCTTTAGAAGGCACACTTGA	58.857	47.619	0.00	0.00	40.21	3.02
1843	3660	1.508632	GTCACGCTTTAGAAGGCACA	58.491	50.000	0.00	0.00	0.00	4.57
1845	3662	0.669318	CCGTCACGCTTTAGAAGGCA	60.669	55.000	0.00	0.00	0.00	4.75
1856	3673	1.310933	TTCTACTCCCTCCGTCACGC	61.311	60.000	0.00	0.00	0.00	5.34
1873	3690	5.701750	GTGACCTTTTCTACTCCTCCTTTTC	59.298	44.000	0.00	0.00	0.00	2.29
1876	3693	3.583526	GGTGACCTTTTCTACTCCTCCTT	59.416	47.826	0.00	0.00	0.00	3.36
1877	3694	3.174779	GGTGACCTTTTCTACTCCTCCT	58.825	50.000	0.00	0.00	0.00	3.69
1878	3695	3.613494	GGTGACCTTTTCTACTCCTCC	57.387	52.381	0.00	0.00	0.00	4.30
2031	3848	9.683069	CTTCTCCGATTTTCCCAAATTAATATG	57.317	33.333	0.00	0.00	32.35	1.78
2113	3936	5.801350	TTCGGTGTGATCAATTGATTCTC	57.199	39.130	21.57	16.51	34.37	2.87
2114	3937	5.066893	CCATTCGGTGTGATCAATTGATTCT	59.933	40.000	21.57	0.57	34.37	2.40
2147	3970	1.030457	GCTTGAGGCCAATCTCATGG	58.970	55.000	5.01	0.00	42.57	3.66
2377	4200	8.623903	TGTCTGATATGTGCAAAAAGATAATCC	58.376	33.333	0.00	0.00	0.00	3.01
2589	4412	8.640651	TGTTTTAATATGCTTGCATATGGATGT	58.359	29.630	23.52	13.06	35.30	3.06
2590	4413	9.647797	ATGTTTTAATATGCTTGCATATGGATG	57.352	29.630	23.52	5.27	36.02	3.51
2633	4488	2.356125	GCTTCCATCCTGTAAAGCTCCA	60.356	50.000	0.00	0.00	40.68	3.86
2755	4610	0.465097	CAGGGATCGATGCTTGGCTT	60.465	55.000	19.40	0.00	0.00	4.35
2792	4647	2.677199	TGTCAACGAGCAATGAGAGTC	58.323	47.619	0.00	0.00	0.00	3.36
2794	4649	2.606725	GGATGTCAACGAGCAATGAGAG	59.393	50.000	0.00	0.00	0.00	3.20
2866	4721	4.949856	CCAAACACTATGTATCCCAAAGCT	59.050	41.667	0.00	0.00	0.00	3.74
2874	4729	4.941263	TGCCAGAACCAAACACTATGTATC	59.059	41.667	0.00	0.00	0.00	2.24
2876	4731	4.359434	TGCCAGAACCAAACACTATGTA	57.641	40.909	0.00	0.00	0.00	2.29
3032	5536	7.994425	TCCATAAAACAAATTCACTCTAGCA	57.006	32.000	0.00	0.00	0.00	3.49
3126	5632	4.789012	AAGTGTCCAATAAACTGCATGG	57.211	40.909	0.00	0.00	0.00	3.66
3152	5658	8.920665	TGATTAAAATTTGCTTCAACATAACCG	58.079	29.630	0.00	0.00	0.00	4.44
3261	6057	5.950883	TCGTACAACTTTGACTAGATCTGG	58.049	41.667	5.18	4.69	0.00	3.86
3270	6066	2.410730	CCGGACATCGTACAACTTTGAC	59.589	50.000	0.00	0.00	37.11	3.18
3298	6094	4.790962	AGCCCAGACATGCTGCGG	62.791	66.667	10.54	12.80	43.50	5.69
3303	6099	2.037620	ATCGAGGAGCCCAGACATGC	62.038	60.000	0.00	0.00	0.00	4.06
3456	6253	3.736252	CGCTATCTTTATCTTCACCACGG	59.264	47.826	0.00	0.00	0.00	4.94
3469	6266	9.973450	ATATATGATCGCTAATTCGCTATCTTT	57.027	29.630	14.81	7.47	34.34	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.