AutoCloner

Multiple sequence alignment - TraesCS3A01G453000

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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	TraesCS3A01G453000	chr3A	100.000	4573	0	0	1	4573	691044044	691039472	0.000000e+00	8445.0
1	TraesCS3A01G453000	chr3A	76.890	1614	326	32	1506	3091	690999089	690997495	0.000000e+00	870.0
2	TraesCS3A01G453000	chr3A	77.250	611	126	8	2238	2840	691059117	691058512	3.390000e-91	346.0
3	TraesCS3A01G453000	chr3D	95.055	3721	146	19	22	3713	554779384	554775673	0.000000e+00	5818.0
4	TraesCS3A01G453000	chr3D	93.918	2943	128	23	882	3791	554768932	554766008	0.000000e+00	4396.0
5	TraesCS3A01G453000	chr3D	74.730	740	174	10	2120	2849	554731575	554730839	7.380000e-83	318.0
6	TraesCS3A01G453000	chr3D	93.258	178	10	2	3811	3988	554766022	554765847	1.260000e-65	261.0
7	TraesCS3A01G453000	chrUn	94.007	1752	79	5	882	2631	45262280	45264007	0.000000e+00	2630.0
8	TraesCS3A01G453000	chrUn	91.060	783	35	4	3037	3788	406194386	406195164	0.000000e+00	1026.0
9	TraesCS3A01G453000	chr3B	95.107	1349	64	2	882	2229	736713528	736712181	0.000000e+00	2124.0
10	TraesCS3A01G453000	chr3B	92.350	1438	67	17	2389	3791	736712180	736710751	0.000000e+00	2006.0
11	TraesCS3A01G453000	chr3B	93.881	523	23	4	67	582	736714269	736713749	0.000000e+00	780.0
12	TraesCS3A01G453000	chr3B	91.892	222	17	1	620	840	736713749	736713528	4.440000e-80	309.0
13	TraesCS3A01G453000	chr3B	92.405	158	3	3	3830	3986	736695557	736695408	2.770000e-52	217.0
14	TraesCS3A01G453000	chr3B	84.000	100	13	2	662	758	421676224	421676323	4.870000e-15	93.5
15	TraesCS3A01G453000	chr6A	90.847	590	39	10	3986	4567	579003334	579003916	0.000000e+00	776.0
16	TraesCS3A01G453000	chr1A	89.983	589	46	9	3983	4568	535328542	535329120	0.000000e+00	749.0
17	TraesCS3A01G453000	chr2D	89.748	595	41	11	3983	4573	13653474	13654052	0.000000e+00	743.0
18	TraesCS3A01G453000	chr5A	89.661	590	48	10	3987	4573	659177237	659176658	0.000000e+00	739.0
19	TraesCS3A01G453000	chr5A	89.262	596	48	13	3987	4573	670616984	670617572	0.000000e+00	732.0
20	TraesCS3A01G453000	chr4D	90.619	565	39	11	4006	4567	429752220	429752773	0.000000e+00	737.0
21	TraesCS3A01G453000	chr6D	89.274	606	39	18	3982	4573	413984547	413983954	0.000000e+00	736.0
22	TraesCS3A01G453000	chr7D	89.267	587	46	14	3987	4567	126658715	126659290	0.000000e+00	719.0
23	TraesCS3A01G453000	chr1D	88.851	592	49	15	3987	4573	247133354	247133933	0.000000e+00	712.0

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	TraesCS3A01G453000	chr3A	691039472	691044044	4572	True	8445.00	8445	100.0000	1	4573	1	chr3A.!!$R2	4572
1	TraesCS3A01G453000	chr3A	690997495	690999089	1594	True	870.00	870	76.8900	1506	3091	1	chr3A.!!$R1	1585
2	TraesCS3A01G453000	chr3A	691058512	691059117	605	True	346.00	346	77.2500	2238	2840	1	chr3A.!!$R3	602
3	TraesCS3A01G453000	chr3D	554775673	554779384	3711	True	5818.00	5818	95.0550	22	3713	1	chr3D.!!$R2	3691
4	TraesCS3A01G453000	chr3D	554765847	554768932	3085	True	2328.50	4396	93.5880	882	3988	2	chr3D.!!$R3	3106
5	TraesCS3A01G453000	chr3D	554730839	554731575	736	True	318.00	318	74.7300	2120	2849	1	chr3D.!!$R1	729
6	TraesCS3A01G453000	chrUn	45262280	45264007	1727	False	2630.00	2630	94.0070	882	2631	1	chrUn.!!$F1	1749
7	TraesCS3A01G453000	chrUn	406194386	406195164	778	False	1026.00	1026	91.0600	3037	3788	1	chrUn.!!$F2	751
8	TraesCS3A01G453000	chr3B	736710751	736714269	3518	True	1304.75	2124	93.3075	67	3791	4	chr3B.!!$R2	3724
9	TraesCS3A01G453000	chr6A	579003334	579003916	582	False	776.00	776	90.8470	3986	4567	1	chr6A.!!$F1	581
10	TraesCS3A01G453000	chr1A	535328542	535329120	578	False	749.00	749	89.9830	3983	4568	1	chr1A.!!$F1	585
11	TraesCS3A01G453000	chr2D	13653474	13654052	578	False	743.00	743	89.7480	3983	4573	1	chr2D.!!$F1	590
12	TraesCS3A01G453000	chr5A	659176658	659177237	579	True	739.00	739	89.6610	3987	4573	1	chr5A.!!$R1	586
13	TraesCS3A01G453000	chr5A	670616984	670617572	588	False	732.00	732	89.2620	3987	4573	1	chr5A.!!$F1	586
14	TraesCS3A01G453000	chr4D	429752220	429752773	553	False	737.00	737	90.6190	4006	4567	1	chr4D.!!$F1	561
15	TraesCS3A01G453000	chr6D	413983954	413984547	593	True	736.00	736	89.2740	3982	4573	1	chr6D.!!$R1	591
16	TraesCS3A01G453000	chr7D	126658715	126659290	575	False	719.00	719	89.2670	3987	4567	1	chr7D.!!$F1	580
17	TraesCS3A01G453000	chr1D	247133354	247133933	579	False	712.00	712	88.8510	3987	4573	1	chr1D.!!$F1	586

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
528	536	1.067669	ACCATGGATCACACGATCTCG	59.932	52.381	21.47	0.00	46.30	4.04	F
1135	1145	0.094730	GTCGCGGCTGTGTTTATGAC	59.905	55.000	1.90	0.00	0.00	3.06	F
1536	1546	0.107831	TAAAACGGCTGAGCAGTGGT	59.892	50.000	11.65	4.86	37.01	4.16	F
3093	3122	0.179081	GGTATCCTTGAGCGTCCCAC	60.179	60.000	0.00	0.00	0.00	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2156	2169	0.253044	ATACCGACAGTGCAGCCAAT	59.747	50.000	0.00	0.00	3.16	R
2746	2769	1.678101	AGAGCACACTTTGTTTCTGGC	59.322	47.619	0.00	0.00	4.85	R
3402	3492	1.265905	CCCTAGTGCGACCAAAACAAC	59.734	52.381	0.00	0.00	3.32	R
4025	4119	0.739462	CCAAGTGGCGCTGATCGTTA	60.739	55.000	7.64	41.07	3.18	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
65	66	2.377810	ATGCTGGCCGGATTGAGGA	61.378	57.895	18.31	0.00	0.00	3.71
73	74	1.068753	CGGATTGAGGAGCTGCGAT	59.931	57.895	0.00	0.00	0.00	4.58
87	88	2.509336	CGATGACGTCCTGGTGCC	60.509	66.667	14.12	0.00	34.56	5.01
129	130	1.201429	ATGGGGTCAAAGAGCGGACT	61.201	55.000	0.00	0.00	34.49	3.85
188	189	1.134670	AGGAAGCTAATGTGCGAGTCC	60.135	52.381	0.00	0.00	38.13	3.85
414	415	9.810231	CATTGTGCTAATTCCAAACAAAATAAC	57.190	29.630	0.00	0.00	34.67	1.89
528	536	1.067669	ACCATGGATCACACGATCTCG	59.932	52.381	21.47	0.00	46.30	4.04
810	819	3.951769	ATGCCAGTGGAGCCCTTGC	62.952	63.158	15.20	0.00	37.95	4.01
955	965	3.941483	CTCGTATGCATTTCCCTTTGTCT	59.059	43.478	3.54	0.00	0.00	3.41
1135	1145	0.094730	GTCGCGGCTGTGTTTATGAC	59.905	55.000	1.90	0.00	0.00	3.06
1289	1299	2.330440	AAAACGAGTTGTACCCGGTT	57.670	45.000	0.00	0.00	34.40	4.44
1389	1399	6.153510	ACTCATGAAGCTCTACTGTGATTGTA	59.846	38.462	0.00	0.00	0.00	2.41
1504	1514	0.604073	TGCTTGTTCGTCGTGGGATA	59.396	50.000	0.00	0.00	0.00	2.59
1536	1546	0.107831	TAAAACGGCTGAGCAGTGGT	59.892	50.000	11.65	4.86	37.01	4.16
1537	1547	1.166531	AAAACGGCTGAGCAGTGGTC	61.167	55.000	11.65	15.47	37.01	4.02
1569	1579	1.825090	AGCAAGCAAACCATCATCGA	58.175	45.000	0.00	0.00	0.00	3.59
1594	1604	2.357836	CATCAAGTGGCTGGCCCT	59.642	61.111	9.28	3.21	34.56	5.19
1677	1687	5.611374	ACAAGTACCCGATTCTAATCCATG	58.389	41.667	0.00	0.00	31.68	3.66
1683	1693	2.430465	CGATTCTAATCCATGCTGGGG	58.570	52.381	2.86	0.00	38.32	4.96
1685	1695	1.905839	TTCTAATCCATGCTGGGGGA	58.094	50.000	2.86	0.00	38.32	4.81
1806	1819	2.354109	TCTGTGTCTCTCATTCGCAC	57.646	50.000	0.00	0.00	0.00	5.34
1997	2010	6.714810	TCACCAAATATGCCTCCATAATGTAC	59.285	38.462	0.00	0.00	37.47	2.90
1998	2011	6.489700	CACCAAATATGCCTCCATAATGTACA	59.510	38.462	0.00	0.00	37.47	2.90
2118	2131	7.181143	TCTATTTTGGACAGTCGTTTTGTAC	57.819	36.000	0.00	0.00	0.00	2.90
2156	2169	3.726790	TGTCCTGGTTACCCTAATAGCA	58.273	45.455	0.00	0.00	0.00	3.49
2385	2398	1.653151	CTTTAGTTCCAGCTACCGGC	58.347	55.000	0.00	0.00	42.19	6.13
2415	2428	3.710209	AACATCTCCTTCCAACTGAGG	57.290	47.619	0.00	0.00	0.00	3.86
2746	2769	2.979676	TTGCTTCCAGGCAGTGCG	60.980	61.111	9.45	0.00	43.39	5.34
2800	2823	6.218746	AGTAAAAGAAGCCAAAGAAATGCTG	58.781	36.000	0.00	0.00	35.08	4.41
3079	3108	1.601166	TGCTCATGCATGCTGGTATC	58.399	50.000	22.25	0.51	45.31	2.24
3093	3122	0.179081	GGTATCCTTGAGCGTCCCAC	60.179	60.000	0.00	0.00	0.00	4.61
3253	3334	6.341316	TGTCTGAAACTCTATAATCTGGTGC	58.659	40.000	0.00	0.00	0.00	5.01
3277	3358	5.919141	CACGCTTGTACTACTAATGATACCC	59.081	44.000	0.00	0.00	0.00	3.69
3315	3404	1.143889	TGTACCATGGGTCTGTTGCAA	59.856	47.619	18.09	0.00	37.09	4.08
3351	3440	6.705381	CAGGATTTGATTTTGTTGCTTTGGTA	59.295	34.615	0.00	0.00	0.00	3.25
3368	3457	2.942796	TAGCACAGCACCTCGTGGG	61.943	63.158	8.63	2.00	41.89	4.61
3372	3461	2.113139	CAGCACCTCGTGGGGTTT	59.887	61.111	7.74	0.00	39.49	3.27
3374	3463	1.228154	AGCACCTCGTGGGGTTTTC	60.228	57.895	7.74	0.00	39.49	2.29
3402	3492	1.694133	TTGCTTTGTTGGGGGCTTGG	61.694	55.000	0.00	0.00	0.00	3.61
3410	3500	0.543749	TTGGGGGCTTGGTTGTTTTG	59.456	50.000	0.00	0.00	0.00	2.44
3413	3503	0.105964	GGGGCTTGGTTGTTTTGGTC	59.894	55.000	0.00	0.00	0.00	4.02
3428	3518	1.410004	TGGTCGCACTAGGGATAAGG	58.590	55.000	0.00	0.00	39.07	2.69
3488	3578	4.387026	TCCCTGGAATCAGATGTTTTGT	57.613	40.909	0.00	0.00	43.49	2.83
3514	3604	2.041620	AGGCTAGTTGCTCCCATTTTGA	59.958	45.455	0.00	0.00	42.39	2.69
3525	3615	3.486383	TCCCATTTTGAACTCACTCACC	58.514	45.455	0.00	0.00	0.00	4.02
3536	3626	4.527509	ACTCACTCACCATACAGTTGAG	57.472	45.455	0.00	0.00	0.00	3.02
3575	3665	7.663081	AGCAGAGTCATTGTTCTTCATAAAAGA	59.337	33.333	0.00	0.00	0.00	2.52
3599	3689	6.986904	AAAAGAGTACATACAGGCTTAAGC	57.013	37.500	19.53	19.53	41.14	3.09
3602	3692	6.394025	AGAGTACATACAGGCTTAAGCTAC	57.606	41.667	25.88	17.56	41.70	3.58
3603	3693	5.008811	AGAGTACATACAGGCTTAAGCTACG	59.991	44.000	25.88	16.53	41.70	3.51
3618	3708	5.672421	AAGCTACGTTAGGGATGTAAACT	57.328	39.130	0.00	0.00	29.60	2.66
3670	3760	6.889019	ATCGAGCTAGCAAAAACTAACTAC	57.111	37.500	18.83	0.00	0.00	2.73
3677	3767	6.128634	GCTAGCAAAAACTAACTACACGTGAT	60.129	38.462	25.01	9.25	0.00	3.06
3686	3776	3.462483	ACTACACGTGATTTGTGGACA	57.538	42.857	25.01	0.00	41.64	4.02
3788	3882	1.980844	GCACACAATGCGAATGTCTTG	59.019	47.619	0.00	0.00	46.55	3.02
3789	3883	2.350676	GCACACAATGCGAATGTCTTGA	60.351	45.455	0.00	0.00	46.55	3.02
3790	3884	3.671433	GCACACAATGCGAATGTCTTGAT	60.671	43.478	0.00	0.00	46.55	2.57
3791	3885	4.478699	CACACAATGCGAATGTCTTGATT	58.521	39.130	0.00	0.00	0.00	2.57
3792	3886	4.919168	CACACAATGCGAATGTCTTGATTT	59.081	37.500	0.00	0.00	0.00	2.17
3793	3887	5.403166	CACACAATGCGAATGTCTTGATTTT	59.597	36.000	0.00	0.00	0.00	1.82
3794	3888	5.984926	ACACAATGCGAATGTCTTGATTTTT	59.015	32.000	0.00	0.00	0.00	1.94
3821	3915	5.452078	TTTTTGAGGATTGCGAATGTCTT	57.548	34.783	0.00	0.00	0.00	3.01
3822	3916	4.424061	TTTGAGGATTGCGAATGTCTTG	57.576	40.909	0.00	0.00	0.00	3.02
3834	3928	1.167851	ATGTCTTGATGGTTGTGCGG	58.832	50.000	0.00	0.00	0.00	5.69
3860	3954	1.212935	AGGGTAGCAAATCTTGGCGAT	59.787	47.619	0.00	0.00	34.54	4.58
3910	4004	1.472188	AACAGGAGTAGTAGCGGGTC	58.528	55.000	0.00	0.00	0.00	4.46
3914	4008	0.463474	GGAGTAGTAGCGGGTCGACT	60.463	60.000	16.46	0.00	34.88	4.18
3918	4012	1.200948	GTAGTAGCGGGTCGACTGTTT	59.799	52.381	16.46	2.12	32.72	2.83
3966	4060	1.824230	GCTTGGCCCATGTATTGAACA	59.176	47.619	0.00	0.00	43.86	3.18
4097	4193	2.989422	AACGCTCCTTTCGGATTTTG	57.011	45.000	0.00	0.00	39.01	2.44
4136	4235	1.006494	GCACGTGTTTTCGGCTTTTTG	60.006	47.619	18.38	0.00	34.94	2.44
4142	4241	1.855978	GTTTTCGGCTTTTTGAACGGG	59.144	47.619	0.00	0.00	0.00	5.28
4199	4299	2.415512	CCCGGTCTTTCTTAGCTTTTCG	59.584	50.000	0.00	0.00	0.00	3.46
4415	4530	0.249280	TGTGCTTTCGCGAGAGTCAA	60.249	50.000	25.34	9.13	43.69	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	2.954868	GTATCCGGCGAGCACACG	60.955	66.667	9.30	0.00	0.00	4.49
13	14	2.954868	CGTATCCGGCGAGCACAC	60.955	66.667	9.30	0.00	0.00	3.82
65	66	2.182791	CAGGACGTCATCGCAGCT	59.817	61.111	18.91	0.00	41.18	4.24
188	189	5.192927	TGACTAGGCTTAAAATGGATGTGG	58.807	41.667	0.00	0.00	0.00	4.17
370	371	4.248058	CAATGAACTTCCCTTGAATTGGC	58.752	43.478	0.00	0.00	0.00	4.52
446	447	8.272173	AGGACGATGGAAAATCTAGGAATTTTA	58.728	33.333	2.94	0.00	38.59	1.52
568	576	2.332063	ATCAACTGATAAGCACCCCG	57.668	50.000	0.00	0.00	32.01	5.73
810	819	0.327924	TAGGGGACATGCACAACTGG	59.672	55.000	0.00	0.00	0.00	4.00
876	885	9.836864	TCTATGTTGAAGATGCATATTTAGTGT	57.163	29.630	8.18	0.00	0.00	3.55
955	965	7.788026	AGAGTGTGAATTTGATATACCGGTTA	58.212	34.615	15.04	5.61	0.00	2.85
1015	1025	3.694072	GCATACTTGTGCTTCCATGGTTA	59.306	43.478	12.58	0.03	41.82	2.85
1135	1145	1.821332	GAGAGAATGGCAAGGGCGG	60.821	63.158	0.00	0.00	42.47	6.13
1289	1299	0.762082	TGGCCAGAAACATTGCCCAA	60.762	50.000	0.00	0.00	43.35	4.12
1389	1399	2.350522	GGTGCACATCGAGAACAAGAT	58.649	47.619	20.43	0.00	0.00	2.40
1504	1514	6.126409	TCAGCCGTTTTAATTCCCAATAGAT	58.874	36.000	0.00	0.00	0.00	1.98
1569	1579	1.274167	CAGCCACTTGATGCCATTGTT	59.726	47.619	0.00	0.00	0.00	2.83
1594	1604	2.256306	TGTGCTCACCCTTCATGTAGA	58.744	47.619	0.12	0.00	0.00	2.59
1683	1693	4.756135	TGCATTTTCTCCAATTTTTGCTCC	59.244	37.500	0.00	0.00	0.00	4.70
1685	1695	6.487331	TGATTGCATTTTCTCCAATTTTTGCT	59.513	30.769	0.00	0.00	29.96	3.91
1709	1719	5.863397	GTCACACCAAATGTTATCCAATGTG	59.137	40.000	0.00	0.00	40.64	3.21
1713	1723	5.360999	TGTTGTCACACCAAATGTTATCCAA	59.639	36.000	0.00	0.00	40.64	3.53
2118	2131	2.287788	GGACATCTTGTGTGCTGGTTTG	60.288	50.000	0.00	0.00	44.86	2.93
2156	2169	0.253044	ATACCGACAGTGCAGCCAAT	59.747	50.000	0.00	0.00	0.00	3.16
2385	2398	3.375299	GGAAGGAGATGTTTCAACCGATG	59.625	47.826	0.00	0.00	0.00	3.84
2396	2409	2.907892	TCCTCAGTTGGAAGGAGATGT	58.092	47.619	0.00	0.00	32.39	3.06
2415	2428	2.633509	CCACAGGCTTGCCTGCTTC	61.634	63.158	33.78	0.00	41.12	3.86
2611	2628	3.243035	CCGAGATCTCACAGAAGCTAGTG	60.243	52.174	22.31	7.37	37.10	2.74
2746	2769	1.678101	AGAGCACACTTTGTTTCTGGC	59.322	47.619	0.00	0.00	0.00	4.85
2800	2823	3.583806	CCTTGGAGATACGAGATCATGC	58.416	50.000	0.00	0.00	0.00	4.06
3093	3122	7.038941	CCTTGGTCTAGGGGATTATTGTAGTAG	60.039	44.444	0.00	0.00	0.00	2.57
3253	3334	5.919141	GGGTATCATTAGTAGTACAAGCGTG	59.081	44.000	2.52	0.00	0.00	5.34
3277	3358	6.353323	TGGTACATACATAACCAATCCACAG	58.647	40.000	0.00	0.00	40.28	3.66
3315	3404	2.606587	AAATCCTGCTCCAGCCGGT	61.607	57.895	1.90	0.00	44.45	5.28
3351	3440	4.320456	CCCACGAGGTGCTGTGCT	62.320	66.667	0.00	0.00	34.77	4.40
3359	3448	2.574369	TCATATGAAAACCCCACGAGGT	59.426	45.455	1.98	0.00	44.00	3.85
3368	3457	7.307337	CCAACAAAGCAAGTTCATATGAAAACC	60.307	37.037	19.55	7.97	35.58	3.27
3372	3461	5.279406	CCCCAACAAAGCAAGTTCATATGAA	60.279	40.000	14.23	14.23	0.00	2.57
3374	3463	4.497300	CCCCAACAAAGCAAGTTCATATG	58.503	43.478	0.00	0.00	0.00	1.78
3402	3492	1.265905	CCCTAGTGCGACCAAAACAAC	59.734	52.381	0.00	0.00	0.00	3.32
3410	3500	1.411041	ACCTTATCCCTAGTGCGACC	58.589	55.000	0.00	0.00	0.00	4.79
3413	3503	3.821421	AGAAACCTTATCCCTAGTGCG	57.179	47.619	0.00	0.00	0.00	5.34
3428	3518	6.749118	CAGTTTGCCTGCTATATGAAAGAAAC	59.251	38.462	0.00	0.00	33.59	2.78
3441	3531	5.221501	ACAATCATTAAACAGTTTGCCTGCT	60.222	36.000	8.93	0.00	45.68	4.24
3457	3547	6.520021	TCTGATTCCAGGGATACAATCATT	57.480	37.500	1.85	0.00	40.76	2.57
3466	3556	4.708421	CACAAAACATCTGATTCCAGGGAT	59.292	41.667	0.00	0.00	40.76	3.85
3514	3604	4.955811	TCAACTGTATGGTGAGTGAGTT	57.044	40.909	0.00	0.00	37.49	3.01
3525	3615	5.418310	ACCGTTTTGAACTCAACTGTATG	57.582	39.130	0.00	0.00	35.28	2.39
3536	3626	3.558418	TGACTCTGCTTACCGTTTTGAAC	59.442	43.478	0.00	0.00	0.00	3.18
3575	3665	7.168905	AGCTTAAGCCTGTATGTACTCTTTTT	58.831	34.615	23.71	0.00	43.38	1.94
3599	3689	4.161001	ACCCAGTTTACATCCCTAACGTAG	59.839	45.833	0.00	0.00	0.00	3.51
3602	3692	3.528532	GACCCAGTTTACATCCCTAACG	58.471	50.000	0.00	0.00	0.00	3.18
3603	3693	3.522343	AGGACCCAGTTTACATCCCTAAC	59.478	47.826	0.00	0.00	0.00	2.34
3670	3760	0.110688	CGCTGTCCACAAATCACGTG	60.111	55.000	9.94	9.94	0.00	4.49
3677	3767	2.359214	TGCAATAAACGCTGTCCACAAA	59.641	40.909	0.00	0.00	0.00	2.83
3686	3776	6.208644	GGATGTAAATGATGCAATAAACGCT	58.791	36.000	0.00	0.00	0.00	5.07
3799	3893	5.009510	TCAAGACATTCGCAATCCTCAAAAA	59.990	36.000	0.00	0.00	0.00	1.94
3800	3894	4.518590	TCAAGACATTCGCAATCCTCAAAA	59.481	37.500	0.00	0.00	0.00	2.44
3801	3895	4.071423	TCAAGACATTCGCAATCCTCAAA	58.929	39.130	0.00	0.00	0.00	2.69
3802	3896	3.673902	TCAAGACATTCGCAATCCTCAA	58.326	40.909	0.00	0.00	0.00	3.02
3803	3897	3.333029	TCAAGACATTCGCAATCCTCA	57.667	42.857	0.00	0.00	0.00	3.86
3804	3898	3.003068	CCATCAAGACATTCGCAATCCTC	59.997	47.826	0.00	0.00	0.00	3.71
3805	3899	2.947652	CCATCAAGACATTCGCAATCCT	59.052	45.455	0.00	0.00	0.00	3.24
3806	3900	2.684881	ACCATCAAGACATTCGCAATCC	59.315	45.455	0.00	0.00	0.00	3.01
3807	3901	4.100529	CAACCATCAAGACATTCGCAATC	58.899	43.478	0.00	0.00	0.00	2.67
3808	3902	3.507233	ACAACCATCAAGACATTCGCAAT	59.493	39.130	0.00	0.00	0.00	3.56
3809	3903	2.884012	ACAACCATCAAGACATTCGCAA	59.116	40.909	0.00	0.00	0.00	4.85
3810	3904	2.226200	CACAACCATCAAGACATTCGCA	59.774	45.455	0.00	0.00	0.00	5.10
3811	3905	2.855180	CACAACCATCAAGACATTCGC	58.145	47.619	0.00	0.00	0.00	4.70
3812	3906	2.725759	CGCACAACCATCAAGACATTCG	60.726	50.000	0.00	0.00	0.00	3.34
3813	3907	2.414559	CCGCACAACCATCAAGACATTC	60.415	50.000	0.00	0.00	0.00	2.67
3814	3908	1.541147	CCGCACAACCATCAAGACATT	59.459	47.619	0.00	0.00	0.00	2.71
3815	3909	1.167851	CCGCACAACCATCAAGACAT	58.832	50.000	0.00	0.00	0.00	3.06
3816	3910	1.514678	GCCGCACAACCATCAAGACA	61.515	55.000	0.00	0.00	0.00	3.41
3817	3911	1.210155	GCCGCACAACCATCAAGAC	59.790	57.895	0.00	0.00	0.00	3.01
3818	3912	2.324330	CGCCGCACAACCATCAAGA	61.324	57.895	0.00	0.00	0.00	3.02
3819	3913	2.176546	CGCCGCACAACCATCAAG	59.823	61.111	0.00	0.00	0.00	3.02
3820	3914	4.036804	GCGCCGCACAACCATCAA	62.037	61.111	3.15	0.00	0.00	2.57
3822	3916	4.166011	GAGCGCCGCACAACCATC	62.166	66.667	13.36	0.00	0.00	3.51
3834	3928	0.462759	AGATTTGCTACCCTGAGCGC	60.463	55.000	0.00	0.00	45.99	5.92
3860	3954	0.111832	ACCCAGGTCGTGACACTCTA	59.888	55.000	3.68	0.00	0.00	2.43
3898	3992	0.807496	AACAGTCGACCCGCTACTAC	59.193	55.000	13.01	0.00	0.00	2.73
3910	4004	2.133742	CTTGCAGGCCCAAACAGTCG	62.134	60.000	0.00	0.00	0.00	4.18
3914	4008	3.233231	GGCTTGCAGGCCCAAACA	61.233	61.111	28.65	0.00	45.92	2.83
3966	4060	2.551721	CCTCTTCTCAGGCAACACACAT	60.552	50.000	0.00	0.00	41.41	3.21
4025	4119	0.739462	CCAAGTGGCGCTGATCGTTA	60.739	55.000	7.64	0.00	41.07	3.18
4046	4140	1.895238	GTGGCAAATGGCTGAGCAT	59.105	52.632	6.82	0.00	44.01	3.79
4103	4199	6.404712	AAAACACGTGCGGAAAAATAAAAA	57.595	29.167	17.22	0.00	0.00	1.94
4151	4250	1.406180	CCAAAACGTCGAAAAACCCCT	59.594	47.619	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.