AutoCloner

Multiple sequence alignment - TraesCS3D01G125000

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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	TraesCS3D01G125000	chr3D	100.000	3049	0	0	1	3049	83602491	83599443	0.000000e+00	5631.0
1	TraesCS3D01G125000	chr3D	89.396	877	81	8	992	1865	83502656	83501789	0.000000e+00	1094.0
2	TraesCS3D01G125000	chr3D	88.119	707	69	10	1	698	123691149	123690449	0.000000e+00	826.0
3	TraesCS3D01G125000	chr3B	92.600	1419	75	17	695	2098	130187450	130186047	0.000000e+00	2012.0
4	TraesCS3D01G125000	chr3B	90.282	638	49	10	2419	3047	781206898	781207531	0.000000e+00	822.0
5	TraesCS3D01G125000	chr3B	87.662	462	55	2	1001	1462	130130533	130130074	1.240000e-148	536.0
6	TraesCS3D01G125000	chr3B	88.132	455	48	5	2164	2616	781155466	781155916	1.240000e-148	536.0
7	TraesCS3D01G125000	chr3B	91.760	267	16	3	1430	1690	130128753	130128487	1.730000e-97	366.0
8	TraesCS3D01G125000	chr3B	82.239	259	42	4	1842	2098	130128461	130128205	1.420000e-53	220.0
9	TraesCS3D01G125000	chr3B	86.301	73	3	1	2095	2167	130186010	130185945	4.220000e-09	73.1
10	TraesCS3D01G125000	chr3A	91.763	862	64	6	996	1852	99388554	99387695	0.000000e+00	1192.0
11	TraesCS3D01G125000	chr3A	86.347	1106	129	17	1001	2098	99297569	99296478	0.000000e+00	1186.0
12	TraesCS3D01G125000	chr3A	75.000	216	41	9	2447	2661	724080996	724081199	1.510000e-13	87.9
13	TraesCS3D01G125000	chr2D	89.910	892	77	9	2164	3047	385571214	385572100	0.000000e+00	1136.0
14	TraesCS3D01G125000	chr2D	87.972	715	70	11	1	706	79535711	79535004	0.000000e+00	830.0
15	TraesCS3D01G125000	chr2D	81.818	143	14	7	2883	3016	19938593	19938732	3.210000e-20	110.0
16	TraesCS3D01G125000	chr5B	89.013	892	85	9	2162	3047	682224137	682223253	0.000000e+00	1092.0
17	TraesCS3D01G125000	chr1D	89.189	888	69	14	2165	3047	181065553	181066418	0.000000e+00	1083.0
18	TraesCS3D01G125000	chr1D	88.584	657	71	3	2165	2820	65578178	65577525	0.000000e+00	795.0
19	TraesCS3D01G125000	chr1D	87.190	242	21	9	2812	3047	65576884	65576647	1.800000e-67	267.0
20	TraesCS3D01G125000	chr6D	87.514	897	78	21	2165	3047	296669387	296668511	0.000000e+00	1005.0
21	TraesCS3D01G125000	chr6D	89.407	708	59	11	1	699	387057380	387056680	0.000000e+00	878.0
22	TraesCS3D01G125000	chr7A	90.806	707	48	7	1	697	16626717	16627416	0.000000e+00	929.0
23	TraesCS3D01G125000	chr7A	88.260	707	67	11	1	698	720910986	720910287	0.000000e+00	832.0
24	TraesCS3D01G125000	chr7A	83.119	699	86	19	2364	3047	256178927	256179608	2.600000e-170	608.0
25	TraesCS3D01G125000	chr5D	89.645	705	62	7	1	698	487214931	487215631	0.000000e+00	887.0
26	TraesCS3D01G125000	chr5D	88.543	707	68	8	1	700	507922268	507921568	0.000000e+00	845.0
27	TraesCS3D01G125000	chr2B	84.263	896	103	25	2162	3047	23785515	23786382	0.000000e+00	839.0
28	TraesCS3D01G125000	chr2B	76.371	237	37	16	2728	2955	32966898	32967124	3.210000e-20	110.0
29	TraesCS3D01G125000	chr6B	88.369	705	66	10	4	698	92053234	92053932	0.000000e+00	833.0
30	TraesCS3D01G125000	chr2A	88.045	711	66	14	1	701	712585441	712586142	0.000000e+00	824.0
31	TraesCS3D01G125000	chr2A	75.417	480	79	21	1146	1601	87563683	87563219	2.400000e-46	196.0
32	TraesCS3D01G125000	chrUn	85.943	562	70	8	2492	3047	85690062	85690620	2.620000e-165	592.0

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	TraesCS3D01G125000	chr3D	83599443	83602491	3048	True	5631.00	5631	100.000000	1	3049	1	chr3D.!!$R2	3048
1	TraesCS3D01G125000	chr3D	83501789	83502656	867	True	1094.00	1094	89.396000	992	1865	1	chr3D.!!$R1	873
2	TraesCS3D01G125000	chr3D	123690449	123691149	700	True	826.00	826	88.119000	1	698	1	chr3D.!!$R3	697
3	TraesCS3D01G125000	chr3B	130185945	130187450	1505	True	1042.55	2012	89.450500	695	2167	2	chr3B.!!$R2	1472
4	TraesCS3D01G125000	chr3B	781206898	781207531	633	False	822.00	822	90.282000	2419	3047	1	chr3B.!!$F2	628
5	TraesCS3D01G125000	chr3B	130128205	130130533	2328	True	374.00	536	87.220333	1001	2098	3	chr3B.!!$R1	1097
6	TraesCS3D01G125000	chr3A	99387695	99388554	859	True	1192.00	1192	91.763000	996	1852	1	chr3A.!!$R2	856
7	TraesCS3D01G125000	chr3A	99296478	99297569	1091	True	1186.00	1186	86.347000	1001	2098	1	chr3A.!!$R1	1097
8	TraesCS3D01G125000	chr2D	385571214	385572100	886	False	1136.00	1136	89.910000	2164	3047	1	chr2D.!!$F2	883
9	TraesCS3D01G125000	chr2D	79535004	79535711	707	True	830.00	830	87.972000	1	706	1	chr2D.!!$R1	705
10	TraesCS3D01G125000	chr5B	682223253	682224137	884	True	1092.00	1092	89.013000	2162	3047	1	chr5B.!!$R1	885
11	TraesCS3D01G125000	chr1D	181065553	181066418	865	False	1083.00	1083	89.189000	2165	3047	1	chr1D.!!$F1	882
12	TraesCS3D01G125000	chr1D	65576647	65578178	1531	True	531.00	795	87.887000	2165	3047	2	chr1D.!!$R1	882
13	TraesCS3D01G125000	chr6D	296668511	296669387	876	True	1005.00	1005	87.514000	2165	3047	1	chr6D.!!$R1	882
14	TraesCS3D01G125000	chr6D	387056680	387057380	700	True	878.00	878	89.407000	1	699	1	chr6D.!!$R2	698
15	TraesCS3D01G125000	chr7A	16626717	16627416	699	False	929.00	929	90.806000	1	697	1	chr7A.!!$F1	696
16	TraesCS3D01G125000	chr7A	720910287	720910986	699	True	832.00	832	88.260000	1	698	1	chr7A.!!$R1	697
17	TraesCS3D01G125000	chr7A	256178927	256179608	681	False	608.00	608	83.119000	2364	3047	1	chr7A.!!$F2	683
18	TraesCS3D01G125000	chr5D	487214931	487215631	700	False	887.00	887	89.645000	1	698	1	chr5D.!!$F1	697
19	TraesCS3D01G125000	chr5D	507921568	507922268	700	True	845.00	845	88.543000	1	700	1	chr5D.!!$R1	699
20	TraesCS3D01G125000	chr2B	23785515	23786382	867	False	839.00	839	84.263000	2162	3047	1	chr2B.!!$F1	885
21	TraesCS3D01G125000	chr6B	92053234	92053932	698	False	833.00	833	88.369000	4	698	1	chr6B.!!$F1	694
22	TraesCS3D01G125000	chr2A	712585441	712586142	701	False	824.00	824	88.045000	1	701	1	chr2A.!!$F1	700
23	TraesCS3D01G125000	chrUn	85690062	85690620	558	False	592.00	592	85.943000	2492	3047	1	chrUn.!!$F1	555

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
160	166	0.107312	CTGCAGGTGAGGGATTGAGG	60.107	60.0	5.57	0.0	0.0	3.86	F
1014	1029	0.314935	CAACAATGGCGCTTTCACCT	59.685	50.0	7.64	0.0	0.0	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1417	1435	1.153127	CGTCCTCTCTAGGCGAGGT	60.153	63.158	21.13	0.0	46.49	3.85	R
2202	3626	0.101399	CTCTCAGCCGTAACGCTCAT	59.899	55.000	0.00	0.0	36.82	2.90	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
76	82	1.002746	TGTAGATTTGGCAGCGGCA	60.003	52.632	11.88	5.90	43.71	5.69
108	114	2.753029	GTGACCTTGCTGGAGGCT	59.247	61.111	3.40	0.00	40.65	4.58
124	130	2.743928	CTTCGTCAGGGGTGCTGC	60.744	66.667	0.00	0.00	0.00	5.25
160	166	0.107312	CTGCAGGTGAGGGATTGAGG	60.107	60.000	5.57	0.00	0.00	3.86
286	298	3.197766	GTCCACCTTATGATGTGAGGACA	59.802	47.826	0.00	0.00	37.06	4.02
414	427	3.838903	GTTGTTCCCCTTCTTCTCTAGGA	59.161	47.826	0.00	0.00	33.13	2.94
415	428	4.354208	TGTTCCCCTTCTTCTCTAGGAT	57.646	45.455	0.00	0.00	33.13	3.24
430	443	1.302907	AGGATTTCCTGGAGCATGGT	58.697	50.000	0.00	0.00	46.55	3.55
480	493	2.420372	TCTACTGCTCTGTTCTGCTACG	59.580	50.000	0.00	0.00	0.00	3.51
536	549	9.638239	TGCAAGTTGTAATCTTAATTTCCATTC	57.362	29.630	4.48	0.00	0.00	2.67
538	551	9.289303	CAAGTTGTAATCTTAATTTCCATTCCG	57.711	33.333	0.00	0.00	0.00	4.30
571	584	3.560068	GTGGAGGTTGTAGTGAGTGTTTG	59.440	47.826	0.00	0.00	0.00	2.93
572	585	2.548480	GGAGGTTGTAGTGAGTGTTTGC	59.452	50.000	0.00	0.00	0.00	3.68
573	586	3.467803	GAGGTTGTAGTGAGTGTTTGCT	58.532	45.455	0.00	0.00	0.00	3.91
574	587	3.877508	GAGGTTGTAGTGAGTGTTTGCTT	59.122	43.478	0.00	0.00	0.00	3.91
639	654	3.290948	TGTTTGTTGTAACTCCTGGCT	57.709	42.857	0.00	0.00	0.00	4.75
734	749	0.889186	CAGCTACAAGTTTGCCCGGT	60.889	55.000	0.00	0.00	0.00	5.28
760	775	3.678252	GCTATGAGCTATGGCATCGTCAT	60.678	47.826	17.95	17.95	42.35	3.06
777	792	0.532862	CATCGTGCCCATAGACCCAC	60.533	60.000	0.00	0.00	0.00	4.61
778	793	1.696097	ATCGTGCCCATAGACCCACC	61.696	60.000	0.00	0.00	0.00	4.61
779	794	2.189521	GTGCCCATAGACCCACCG	59.810	66.667	0.00	0.00	0.00	4.94
780	795	2.285069	TGCCCATAGACCCACCGT	60.285	61.111	0.00	0.00	0.00	4.83
781	796	2.363975	TGCCCATAGACCCACCGTC	61.364	63.158	0.00	0.00	42.32	4.79
784	799	1.520666	CCATAGACCCACCGTCCAC	59.479	63.158	0.00	0.00	43.08	4.02
785	800	1.261938	CCATAGACCCACCGTCCACA	61.262	60.000	0.00	0.00	43.08	4.17
787	802	1.614241	ATAGACCCACCGTCCACAGC	61.614	60.000	0.00	0.00	43.08	4.40
887	902	6.371825	AGTCTTATTTCGTGAAAGAATCCACC	59.628	38.462	3.18	0.00	32.04	4.61
888	903	5.646360	TCTTATTTCGTGAAAGAATCCACCC	59.354	40.000	3.18	0.00	32.04	4.61
893	908	3.072476	TCGTGAAAGAATCCACCCTCTTT	59.928	43.478	0.00	0.00	43.03	2.52
904	919	1.197721	CACCCTCTTTTGCACATCGTC	59.802	52.381	0.00	0.00	0.00	4.20
912	927	1.859383	TTGCACATCGTCGTTTCTGA	58.141	45.000	0.00	0.00	0.00	3.27
950	965	1.675720	AACACTGCACCAACCAAGCC	61.676	55.000	0.00	0.00	0.00	4.35
953	968	2.521465	TGCACCAACCAAGCCCAG	60.521	61.111	0.00	0.00	0.00	4.45
1012	1027	2.144362	GCAACAATGGCGCTTTCAC	58.856	52.632	7.64	0.00	0.00	3.18
1014	1029	0.314935	CAACAATGGCGCTTTCACCT	59.685	50.000	7.64	0.00	0.00	4.00
1118	1136	1.003355	GCTTGCTCCACTGCTACCA	60.003	57.895	0.00	0.00	0.00	3.25
1120	1138	1.003355	TTGCTCCACTGCTACCAGC	60.003	57.895	0.00	0.00	43.02	4.85
1198	1216	3.347590	TCCGCTCTCTCCCCTCCA	61.348	66.667	0.00	0.00	0.00	3.86
1289	1307	3.423154	CTTCGGCAACTCCACGGC	61.423	66.667	0.00	0.00	34.01	5.68
1417	1435	0.876777	CTACGCCGACACCAACACAA	60.877	55.000	0.00	0.00	0.00	3.33
1428	1446	0.320374	CCAACACAACCTCGCCTAGA	59.680	55.000	0.00	0.00	0.00	2.43
1520	2901	0.040058	TCCTTCTACTACGCCCACCA	59.960	55.000	0.00	0.00	0.00	4.17
1702	3083	3.858868	GACTGCGTCCGGTGCTTGA	62.859	63.158	19.38	2.27	0.00	3.02
1735	3116	4.742201	CCGTGCACTGGGACCTCG	62.742	72.222	16.19	0.00	30.51	4.63
1832	3213	0.804989	GCAGTGGGTGACAACTATGC	59.195	55.000	0.00	0.00	0.00	3.14
1840	3221	3.877508	GGGTGACAACTATGCCACTAATC	59.122	47.826	0.00	0.00	39.60	1.75
1956	3340	6.739331	ATGAGAGAAACTAATACTCCAGGG	57.261	41.667	0.00	0.00	0.00	4.45
2008	3392	1.134401	CCTCGTGCTGGATATGTTGGT	60.134	52.381	0.00	0.00	0.00	3.67
2043	3427	1.753956	GTTTACTTGTGCTGTTGCCG	58.246	50.000	0.00	0.00	38.71	5.69
2101	3525	7.924412	ACATGTACGTTATTTATCGTCCAAGAT	59.076	33.333	0.00	0.00	40.70	2.40
2122	3546	4.963276	TCCGAGATGCAATAAAACCTTG	57.037	40.909	0.00	0.00	0.00	3.61
2123	3547	4.331968	TCCGAGATGCAATAAAACCTTGT	58.668	39.130	0.00	0.00	0.00	3.16
2124	3548	5.492895	TCCGAGATGCAATAAAACCTTGTA	58.507	37.500	0.00	0.00	0.00	2.41
2125	3549	5.353123	TCCGAGATGCAATAAAACCTTGTAC	59.647	40.000	0.00	0.00	0.00	2.90
2126	3550	5.354234	CCGAGATGCAATAAAACCTTGTACT	59.646	40.000	0.00	0.00	0.00	2.73
2127	3551	6.250819	CGAGATGCAATAAAACCTTGTACTG	58.749	40.000	0.00	0.00	0.00	2.74
2128	3552	6.128282	CGAGATGCAATAAAACCTTGTACTGT	60.128	38.462	0.00	0.00	0.00	3.55
2157	3581	7.605410	TCCAATTCATTTTCTTACGTACTCC	57.395	36.000	0.00	0.00	0.00	3.85
2192	3616	4.492791	GAGTATCTAAGCTCCCTCGAAC	57.507	50.000	0.00	0.00	0.00	3.95
2202	3626	0.035725	TCCCTCGAACGTGAGAGCTA	60.036	55.000	13.28	3.05	38.28	3.32
2256	3680	5.467705	ACCACGTCTATTAGTGTTTGACTC	58.532	41.667	0.00	0.00	35.96	3.36
2258	3682	5.573282	CCACGTCTATTAGTGTTTGACTCAG	59.427	44.000	0.00	0.00	35.96	3.35
2281	3705	2.668212	TCTTTGCCGCTTGGGTCG	60.668	61.111	0.00	0.00	38.44	4.79
2299	3723	5.599242	TGGGTCGACCATCTAATAACATGTA	59.401	40.000	34.40	0.00	46.80	2.29
2301	3725	6.590292	GGGTCGACCATCTAATAACATGTATG	59.410	42.308	34.40	0.00	39.85	2.39
2305	3729	7.877612	TCGACCATCTAATAACATGTATGCAAT	59.122	33.333	0.00	0.00	0.00	3.56
2403	3832	0.320374	TAGTACAGGCACAAGCGCTT	59.680	50.000	18.98	18.98	43.41	4.68
2414	3843	3.308595	GCACAAGCGCTTATATACACACA	59.691	43.478	24.55	0.00	0.00	3.72
2416	3845	3.550275	ACAAGCGCTTATATACACACACG	59.450	43.478	24.55	8.05	0.00	4.49
2417	3846	3.431922	AGCGCTTATATACACACACGT	57.568	42.857	2.64	0.00	0.00	4.49
2461	3898	7.952671	TCTATGAACACACATCCTATCCTTAC	58.047	38.462	0.00	0.00	0.00	2.34
2585	4025	5.231991	GCATCGCCGAAAATTGTGAAATAAT	59.768	36.000	0.00	0.00	0.00	1.28
2623	4063	7.685155	GCGAATACCAGTACTTAAACCCTGATA	60.685	40.741	0.00	0.00	0.00	2.15
2689	4129	3.430333	TTCGCAGCTAATGTACATCGA	57.570	42.857	9.23	9.74	0.00	3.59
2715	4155	2.100197	GGGAAAGAATGGGTTACCTGC	58.900	52.381	0.00	0.00	37.76	4.85
2767	4207	7.147742	GGGCATATGAATCCACTTAAGGAAAAA	60.148	37.037	6.97	0.00	41.92	1.94
2838	4931	0.534877	TCATTCTATGGGCGCGCAAT	60.535	50.000	34.42	26.43	0.00	3.56
2839	4932	0.311790	CATTCTATGGGCGCGCAATT	59.688	50.000	34.42	18.26	0.00	2.32
2840	4933	1.032014	ATTCTATGGGCGCGCAATTT	58.968	45.000	34.42	17.49	0.00	1.82
2841	4934	0.814457	TTCTATGGGCGCGCAATTTT	59.186	45.000	34.42	17.11	0.00	1.82
2889	4986	3.993920	AGCCGATGCAAAAAGACAAAAT	58.006	36.364	0.00	0.00	41.13	1.82
2890	4987	5.132897	AGCCGATGCAAAAAGACAAAATA	57.867	34.783	0.00	0.00	41.13	1.40
2940	5039	4.571984	AGCACTGAAATTTGTCTTTTTGCC	59.428	37.500	0.00	0.00	0.00	4.52
3011	5125	8.079203	TGTTGTGAAGATGTATGCGTAATTTTT	58.921	29.630	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	58	1.742411	GCCGCTGCCAAATCTACAGTA	60.742	52.381	0.00	0.00	33.87	2.74
108	114	4.680237	CGCAGCACCCCTGACGAA	62.680	66.667	0.00	0.00	44.64	3.85
160	166	1.480954	TGGAATACGAAGAGGAGGCAC	59.519	52.381	0.00	0.00	0.00	5.01
259	271	5.512060	CCTCACATCATAAGGTGGACATAGG	60.512	48.000	0.00	0.00	37.76	2.57
286	298	3.390639	CACCCTAGAGCTGGAAGAATGAT	59.609	47.826	0.00	0.00	34.07	2.45
414	427	1.002069	TGGACCATGCTCCAGGAAAT	58.998	50.000	5.59	0.00	35.23	2.17
415	428	1.002069	ATGGACCATGCTCCAGGAAA	58.998	50.000	14.94	0.00	43.82	3.13
480	493	3.639094	AGCACTCCACACTAGGATCATAC	59.361	47.826	0.00	0.00	36.99	2.39
536	549	1.021390	CCTCCACAAGCAGCTAACGG	61.021	60.000	0.00	0.00	0.00	4.44
538	551	1.537202	CAACCTCCACAAGCAGCTAAC	59.463	52.381	0.00	0.00	0.00	2.34
571	584	1.273327	CAATGGGGAACACTGGAAAGC	59.727	52.381	0.00	0.00	0.00	3.51
572	585	2.597455	ACAATGGGGAACACTGGAAAG	58.403	47.619	0.00	0.00	0.00	2.62
573	586	2.765689	ACAATGGGGAACACTGGAAA	57.234	45.000	0.00	0.00	0.00	3.13
574	587	3.621214	CGATACAATGGGGAACACTGGAA	60.621	47.826	0.00	0.00	0.00	3.53
639	654	5.798125	TGAATTAACAAAGCCATCAACCA	57.202	34.783	0.00	0.00	0.00	3.67
720	735	1.597027	CTCGACCGGGCAAACTTGT	60.597	57.895	8.76	0.00	0.00	3.16
755	770	0.597637	GGTCTATGGGCACGATGACG	60.598	60.000	0.00	0.00	45.75	4.35
760	775	2.363975	GGTGGGTCTATGGGCACGA	61.364	63.158	0.00	0.00	0.00	4.35
778	793	3.276091	TTTGTGGCGCTGTGGACG	61.276	61.111	7.64	0.00	0.00	4.79
779	794	1.999071	TTGTTTGTGGCGCTGTGGAC	61.999	55.000	7.64	1.92	0.00	4.02
780	795	1.315981	TTTGTTTGTGGCGCTGTGGA	61.316	50.000	7.64	0.00	0.00	4.02
781	796	0.459237	TTTTGTTTGTGGCGCTGTGG	60.459	50.000	7.64	0.00	0.00	4.17
784	799	0.922717	CACTTTTGTTTGTGGCGCTG	59.077	50.000	7.64	0.00	0.00	5.18
785	800	0.814457	TCACTTTTGTTTGTGGCGCT	59.186	45.000	7.64	0.00	35.15	5.92
788	803	0.920664	GCGTCACTTTTGTTTGTGGC	59.079	50.000	0.00	0.00	35.67	5.01
789	804	1.135257	TGGCGTCACTTTTGTTTGTGG	60.135	47.619	0.00	0.00	35.15	4.17
792	807	2.270275	TGTGGCGTCACTTTTGTTTG	57.730	45.000	22.43	0.00	43.94	2.93
887	902	1.148310	ACGACGATGTGCAAAAGAGG	58.852	50.000	0.00	0.00	0.00	3.69
888	903	2.949714	AACGACGATGTGCAAAAGAG	57.050	45.000	0.00	0.00	0.00	2.85
893	908	1.525197	GTCAGAAACGACGATGTGCAA	59.475	47.619	0.00	0.00	0.00	4.08
904	919	2.474196	CGACGAGGACTAGTCAGAAACG	60.474	54.545	23.91	20.12	35.37	3.60
912	927	2.479566	TAACCACGACGAGGACTAGT	57.520	50.000	18.62	0.00	0.00	2.57
950	965	4.083581	GATGTGTCGAACAAATTCCTGG	57.916	45.455	4.87	0.00	43.61	4.45
1024	1039	1.380515	CGAGGAGGGAGAGGAGCAA	60.381	63.158	0.00	0.00	0.00	3.91
1417	1435	1.153127	CGTCCTCTCTAGGCGAGGT	60.153	63.158	21.13	0.00	46.49	3.85
1621	3002	3.807631	TTCTGCTCACCGCGCTGTT	62.808	57.895	5.56	0.00	43.27	3.16
1702	3083	4.021925	GGCCTGCACCGAGTCCTT	62.022	66.667	0.00	0.00	0.00	3.36
1840	3221	6.589523	AGAAAGATTGATCAAGAGAACTCACG	59.410	38.462	14.54	0.00	0.00	4.35
1956	3340	5.225899	AGTACAACTGTCGGAAAACAAAC	57.774	39.130	0.00	0.00	0.00	2.93
1987	3371	1.586422	CAACATATCCAGCACGAGGG	58.414	55.000	0.00	0.00	0.00	4.30
2008	3392	2.953466	AAACGCGCATAAGACTCCTA	57.047	45.000	5.73	0.00	0.00	2.94
2043	3427	3.589988	TCCATCTTTCTCTTCTTCACGC	58.410	45.455	0.00	0.00	0.00	5.34
2101	3525	4.331968	ACAAGGTTTTATTGCATCTCGGA	58.668	39.130	0.00	0.00	0.00	4.55
2125	3549	9.277565	CGTAAGAAAATGAATTGGAACATACAG	57.722	33.333	0.00	0.00	37.87	2.74
2126	3550	8.788806	ACGTAAGAAAATGAATTGGAACATACA	58.211	29.630	0.00	0.00	39.07	2.29
2192	3616	2.376956	GTAACGCTCATAGCTCTCACG	58.623	52.381	0.00	0.00	39.60	4.35
2202	3626	0.101399	CTCTCAGCCGTAACGCTCAT	59.899	55.000	0.00	0.00	36.82	2.90
2209	3633	1.344065	TTTGACCCTCTCAGCCGTAA	58.656	50.000	0.00	0.00	0.00	3.18
2211	3635	0.693049	ATTTTGACCCTCTCAGCCGT	59.307	50.000	0.00	0.00	0.00	5.68
2256	3680	0.321653	AAGCGGCAAAGAGTACCCTG	60.322	55.000	1.45	0.00	0.00	4.45
2258	3682	1.305930	CCAAGCGGCAAAGAGTACCC	61.306	60.000	1.45	0.00	0.00	3.69
2299	3723	7.559533	TGACACATAACCCATAAAGTATTGCAT	59.440	33.333	0.00	0.00	0.00	3.96
2301	3725	7.328277	TGACACATAACCCATAAAGTATTGC	57.672	36.000	0.00	0.00	0.00	3.56
2403	3832	9.498176	AGATGAGTGTATACGTGTGTGTATATA	57.502	33.333	0.00	0.00	38.98	0.86
2414	3843	9.727859	ATAGAGATGTTAGATGAGTGTATACGT	57.272	33.333	0.00	0.00	0.00	3.57
2461	3898	4.244802	GTCTCTCGGAGGCGCTCG	62.245	72.222	7.64	9.72	0.00	5.03
2505	3945	1.071567	GGCGTCTGTAGTGACTTCGC	61.072	60.000	0.00	0.44	38.15	4.70
2585	4025	4.764823	ACTGGTATTCGCATTTTTCTGGAA	59.235	37.500	0.00	0.00	0.00	3.53
2689	4129	6.101296	CAGGTAACCCATTCTTTCCCTATACT	59.899	42.308	0.00	0.00	37.17	2.12
2715	4155	5.221641	TGAGTTCATCCATATAGTTTCCCGG	60.222	44.000	0.00	0.00	0.00	5.73
2767	4207	8.315220	AGATCTTTTTGGCATTTAGGAATGAT	57.685	30.769	3.47	0.00	44.37	2.45
2984	5096	6.925610	ATTACGCATACATCTTCACAACAT	57.074	33.333	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.