AutoCloner

Multiple sequence alignment - TraesCS1B01G111900

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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	TraesCS1B01G111900	chr1B	100.000	3047	0	0	1	3047	130009109	130012155	0.000000e+00	5627.0
1	TraesCS1B01G111900	chr1B	85.769	780	80	17	1	763	430611092	430611857	0.000000e+00	797.0
2	TraesCS1B01G111900	chr1B	76.060	1061	231	19	1017	2067	621947455	621946408	5.780000e-147	531.0
3	TraesCS1B01G111900	chr1A	90.004	2301	154	35	745	3019	97792551	97794801	0.000000e+00	2905.0
4	TraesCS1B01G111900	chr1D	91.917	1695	83	20	764	2434	79115546	79117210	0.000000e+00	2322.0
5	TraesCS1B01G111900	chr1D	90.851	623	38	7	2426	3047	79118053	79118657	0.000000e+00	817.0
6	TraesCS1B01G111900	chr1D	77.207	1031	223	9	1046	2071	451941122	451940099	2.620000e-165	592.0
7	TraesCS1B01G111900	chr4B	87.906	769	82	7	1	763	631062840	631062077	0.000000e+00	894.0
8	TraesCS1B01G111900	chr7B	87.612	783	72	13	1	763	696195941	696195164	0.000000e+00	885.0
9	TraesCS1B01G111900	chr7B	86.100	777	79	18	1	761	514063946	514063183	0.000000e+00	809.0
10	TraesCS1B01G111900	chr5B	86.185	789	68	28	1	766	558689677	558688907	0.000000e+00	815.0
11	TraesCS1B01G111900	chr5B	84.117	787	76	23	1	763	659735177	659735938	0.000000e+00	715.0
12	TraesCS1B01G111900	chr2B	85.967	791	70	13	4	761	770279247	770278465	0.000000e+00	808.0
13	TraesCS1B01G111900	chr2B	84.817	764	87	13	6	761	92552058	92552800	0.000000e+00	741.0
14	TraesCS1B01G111900	chr6B	85.385	780	84	15	1	763	476733809	476733043	0.000000e+00	782.0
15	TraesCS1B01G111900	chr6B	85.944	747	84	11	1	737	673022145	673022880	0.000000e+00	778.0
16	TraesCS1B01G111900	chr3B	85.438	776	81	16	6	761	119407017	119406254	0.000000e+00	778.0
17	TraesCS1B01G111900	chr3B	86.677	653	72	11	116	762	39582839	39582196	0.000000e+00	710.0
18	TraesCS1B01G111900	chr7D	74.635	548	115	16	1460	2001	11261491	11262020	1.420000e-53	220.0
19	TraesCS1B01G111900	chr7A	74.354	542	117	12	1460	1996	10380944	10381468	8.560000e-51	211.0
20	TraesCS1B01G111900	chr7A	74.223	547	121	10	1454	1996	10831308	10831838	8.560000e-51	211.0
21	TraesCS1B01G111900	chr6D	90.196	51	4	1	1678	1728	473059683	473059732	7.050000e-07	65.8

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	TraesCS1B01G111900	chr1B	130009109	130012155	3046	False	5627.0	5627	100.000	1	3047	1	chr1B.!!$F1	3046
1	TraesCS1B01G111900	chr1B	430611092	430611857	765	False	797.0	797	85.769	1	763	1	chr1B.!!$F2	762
2	TraesCS1B01G111900	chr1B	621946408	621947455	1047	True	531.0	531	76.060	1017	2067	1	chr1B.!!$R1	1050
3	TraesCS1B01G111900	chr1A	97792551	97794801	2250	False	2905.0	2905	90.004	745	3019	1	chr1A.!!$F1	2274
4	TraesCS1B01G111900	chr1D	79115546	79118657	3111	False	1569.5	2322	91.384	764	3047	2	chr1D.!!$F1	2283
5	TraesCS1B01G111900	chr1D	451940099	451941122	1023	True	592.0	592	77.207	1046	2071	1	chr1D.!!$R1	1025
6	TraesCS1B01G111900	chr4B	631062077	631062840	763	True	894.0	894	87.906	1	763	1	chr4B.!!$R1	762
7	TraesCS1B01G111900	chr7B	696195164	696195941	777	True	885.0	885	87.612	1	763	1	chr7B.!!$R2	762
8	TraesCS1B01G111900	chr7B	514063183	514063946	763	True	809.0	809	86.100	1	761	1	chr7B.!!$R1	760
9	TraesCS1B01G111900	chr5B	558688907	558689677	770	True	815.0	815	86.185	1	766	1	chr5B.!!$R1	765
10	TraesCS1B01G111900	chr5B	659735177	659735938	761	False	715.0	715	84.117	1	763	1	chr5B.!!$F1	762
11	TraesCS1B01G111900	chr2B	770278465	770279247	782	True	808.0	808	85.967	4	761	1	chr2B.!!$R1	757
12	TraesCS1B01G111900	chr2B	92552058	92552800	742	False	741.0	741	84.817	6	761	1	chr2B.!!$F1	755
13	TraesCS1B01G111900	chr6B	476733043	476733809	766	True	782.0	782	85.385	1	763	1	chr6B.!!$R1	762
14	TraesCS1B01G111900	chr6B	673022145	673022880	735	False	778.0	778	85.944	1	737	1	chr6B.!!$F1	736
15	TraesCS1B01G111900	chr3B	119406254	119407017	763	True	778.0	778	85.438	6	761	1	chr3B.!!$R2	755
16	TraesCS1B01G111900	chr3B	39582196	39582839	643	True	710.0	710	86.677	116	762	1	chr3B.!!$R1	646
17	TraesCS1B01G111900	chr7D	11261491	11262020	529	False	220.0	220	74.635	1460	2001	1	chr7D.!!$F1	541
18	TraesCS1B01G111900	chr7A	10380944	10381468	524	False	211.0	211	74.354	1460	1996	1	chr7A.!!$F1	536
19	TraesCS1B01G111900	chr7A	10831308	10831838	530	False	211.0	211	74.223	1454	1996	1	chr7A.!!$F2	542

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
913	1056	0.179034	CCCTACTGGCCTGCTTGATC	60.179	60.0	9.95	0.0	0.0	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2430	2583	0.106708	TTCATAGCTCGCCATGGACC	59.893	55.0	18.4	0.0	0.0	4.46	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
229	249	3.507009	GGACTACGTCCGCGAGCT	61.507	66.667	8.23	0.00	43.14	4.09
259	279	4.910585	GCGTCGGGCATACCTGGG	62.911	72.222	0.00	0.00	43.29	4.45
472	533	0.452184	CGCTTCTACAGGCTTCTCGA	59.548	55.000	0.00	0.00	0.00	4.04
490	563	2.278596	CATGTAGACGACGGCGGG	60.279	66.667	18.49	5.08	43.17	6.13
537	644	9.961265	GTTTGTTTTTAAGTTATTAGGCAGAGT	57.039	29.630	0.00	0.00	0.00	3.24
558	665	7.168135	CAGAGTTTCTGGCATGTTTTTAAGTTC	59.832	37.037	0.00	0.00	40.71	3.01
583	690	9.047371	TCTTGTACAAATTTCGACAAAGTATGA	57.953	29.630	10.03	6.33	31.76	2.15
591	698	4.247267	TCGACAAAGTATGACCGAGTTT	57.753	40.909	0.00	0.00	34.59	2.66
592	699	4.624015	TCGACAAAGTATGACCGAGTTTT	58.376	39.130	0.00	0.00	34.59	2.43
595	702	5.277154	CGACAAAGTATGACCGAGTTTTTGT	60.277	40.000	0.00	0.00	39.25	2.83
731	848	0.370273	CATCTCTTTTTCGACGCCCG	59.630	55.000	0.00	0.00	40.25	6.13
913	1056	0.179034	CCCTACTGGCCTGCTTGATC	60.179	60.000	9.95	0.00	0.00	2.92
937	1080	2.348472	TGAGATCACTTTTCCCCACCT	58.652	47.619	0.00	0.00	0.00	4.00
1067	1216	2.100631	CGTTCAAGATCGCCGGCTT	61.101	57.895	26.68	12.25	0.00	4.35
1151	1300	1.246056	TACCTCTGGCGCGTACTGTT	61.246	55.000	8.43	0.00	0.00	3.16
1373	1522	1.068333	CGACTTCTTGCAACCATTGGG	60.068	52.381	7.78	0.00	41.29	4.12
1416	1565	1.284297	TGCTTGAGTGCGATGTCACG	61.284	55.000	0.00	0.00	41.61	4.35
1534	1683	0.467804	GGAGGAGGAAGCAGATGTCC	59.532	60.000	0.00	0.00	0.00	4.02
1553	1702	3.641436	GTCCTTTTTGATGTTGAAGGGGT	59.359	43.478	0.00	0.00	39.27	4.95
1572	1721	1.227002	GGTTTTTCCCGCGCACAAA	60.227	52.632	8.75	0.00	0.00	2.83
1671	1820	2.590821	ACCATTGAAGATATGCAGCCC	58.409	47.619	0.00	0.00	0.00	5.19
1759	1908	3.010472	TGGAGATGAGGGCAAAGAAATGA	59.990	43.478	0.00	0.00	0.00	2.57
1856	2005	5.118203	GCAAAAGTCTTGATGTTGAGAATGC	59.882	40.000	0.00	0.00	0.00	3.56
2020	2169	7.208225	TCTATTGTCATAGATGTCTTCGAGG	57.792	40.000	0.00	0.00	37.13	4.63
2043	2192	1.798223	GCAAAAAGGTCCCGCAAAATC	59.202	47.619	0.00	0.00	0.00	2.17
2060	2209	7.348201	CGCAAAATCTAGTATGTTCATCCTTC	58.652	38.462	0.00	0.00	0.00	3.46
2104	2253	8.440059	TGAATAGTTTGTTTAGTTGACGCATAG	58.560	33.333	0.00	0.00	0.00	2.23
2131	2281	2.777832	AGATGAAGTTGGGCTCTCAC	57.222	50.000	0.00	0.00	0.00	3.51
2165	2317	3.755378	CAGTGATCTTTTGGAGAAGGGTG	59.245	47.826	0.00	0.00	38.06	4.61
2166	2318	3.652869	AGTGATCTTTTGGAGAAGGGTGA	59.347	43.478	0.00	0.00	38.06	4.02
2179	2331	5.243954	GGAGAAGGGTGAGCTTTTGTAAAAT	59.756	40.000	0.00	0.00	0.00	1.82
2180	2332	6.239317	GGAGAAGGGTGAGCTTTTGTAAAATT	60.239	38.462	0.00	0.00	0.00	1.82
2181	2333	7.039993	GGAGAAGGGTGAGCTTTTGTAAAATTA	60.040	37.037	0.00	0.00	0.00	1.40
2182	2334	8.422577	AGAAGGGTGAGCTTTTGTAAAATTAT	57.577	30.769	0.00	0.00	0.00	1.28
2183	2335	8.523658	AGAAGGGTGAGCTTTTGTAAAATTATC	58.476	33.333	0.00	0.00	0.00	1.75
2184	2336	8.422577	AAGGGTGAGCTTTTGTAAAATTATCT	57.577	30.769	0.00	0.00	0.00	1.98
2185	2337	8.056407	AGGGTGAGCTTTTGTAAAATTATCTC	57.944	34.615	0.00	0.00	0.00	2.75
2186	2338	7.890655	AGGGTGAGCTTTTGTAAAATTATCTCT	59.109	33.333	0.00	0.00	0.00	3.10
2187	2339	7.970614	GGGTGAGCTTTTGTAAAATTATCTCTG	59.029	37.037	0.00	0.00	0.00	3.35
2188	2340	7.486232	GGTGAGCTTTTGTAAAATTATCTCTGC	59.514	37.037	0.00	0.00	0.00	4.26
2189	2341	8.023128	GTGAGCTTTTGTAAAATTATCTCTGCA	58.977	33.333	0.00	0.00	0.00	4.41
2190	2342	8.742777	TGAGCTTTTGTAAAATTATCTCTGCAT	58.257	29.630	0.00	0.00	0.00	3.96
2191	2343	8.922058	AGCTTTTGTAAAATTATCTCTGCATG	57.078	30.769	0.00	0.00	0.00	4.06
2192	2344	8.526147	AGCTTTTGTAAAATTATCTCTGCATGT	58.474	29.630	0.00	0.00	0.00	3.21
2193	2345	8.589629	GCTTTTGTAAAATTATCTCTGCATGTG	58.410	33.333	0.00	0.00	0.00	3.21
2194	2346	9.844790	CTTTTGTAAAATTATCTCTGCATGTGA	57.155	29.630	0.00	0.00	0.00	3.58
2196	2348	9.791820	TTTGTAAAATTATCTCTGCATGTGATG	57.208	29.630	0.00	0.00	32.05	3.07
2197	2349	8.510243	TGTAAAATTATCTCTGCATGTGATGT	57.490	30.769	0.00	0.00	32.05	3.06
2198	2350	9.612066	TGTAAAATTATCTCTGCATGTGATGTA	57.388	29.630	0.00	0.00	32.05	2.29
2207	2359	8.969260	TCTCTGCATGTGATGTAAAATTATCT	57.031	30.769	0.00	0.00	0.00	1.98
2208	2360	9.049523	TCTCTGCATGTGATGTAAAATTATCTC	57.950	33.333	0.00	0.00	0.00	2.75
2318	2470	2.094545	GCGTTCTTGAAAATGCCCTGAT	60.095	45.455	0.00	0.00	35.55	2.90
2320	2472	3.428045	CGTTCTTGAAAATGCCCTGATCC	60.428	47.826	0.00	0.00	0.00	3.36
2336	2488	4.952335	CCTGATCCTCTGGCTAAACAATTT	59.048	41.667	0.00	0.00	0.00	1.82
2418	2571	5.068198	TGCCATTCTCATTATTGGAAAGAGC	59.932	40.000	0.00	0.00	0.00	4.09
2498	3502	3.314635	GCTAGCAAGTTATTGAGCAGCAT	59.685	43.478	10.63	0.00	38.83	3.79
2499	3503	3.777465	AGCAAGTTATTGAGCAGCATG	57.223	42.857	0.00	0.00	38.83	4.06
2502	3506	5.128205	AGCAAGTTATTGAGCAGCATGATA	58.872	37.500	0.00	0.00	29.75	2.15
2529	3533	6.366877	GTGCAGTATTTTGAGATTGCATTGTT	59.633	34.615	0.03	0.00	42.64	2.83
2531	3535	6.035327	GCAGTATTTTGAGATTGCATTGTTCC	59.965	38.462	0.00	0.00	0.00	3.62
2608	3612	1.316651	GAGGCAGAGGCATTTGGATC	58.683	55.000	0.00	0.00	43.71	3.36
2610	3614	0.106318	GGCAGAGGCATTTGGATCCT	60.106	55.000	14.23	0.00	43.71	3.24
2619	3623	3.471680	GCATTTGGATCCTCTGTAGTCC	58.528	50.000	14.23	0.00	0.00	3.85
2626	3630	3.071312	GGATCCTCTGTAGTCCGTAGAGA	59.929	52.174	3.84	0.00	40.21	3.10
2627	3631	4.444591	GGATCCTCTGTAGTCCGTAGAGAA	60.445	50.000	3.84	0.00	40.21	2.87
2628	3632	4.564782	TCCTCTGTAGTCCGTAGAGAAA	57.435	45.455	0.00	0.00	40.21	2.52
2748	3752	7.646922	GGTGATAAGCAAAGCTGAAATGATTAG	59.353	37.037	0.00	0.00	39.62	1.73
2776	3780	7.039722	ACTTTCCTTAATTGACCAAGGGATA	57.960	36.000	5.14	0.00	41.47	2.59
2780	3784	4.580580	CCTTAATTGACCAAGGGATACTGC	59.419	45.833	0.00	0.00	38.12	4.40
2785	3789	6.763715	ATTGACCAAGGGATACTGCTATAA	57.236	37.500	0.00	0.00	0.00	0.98
2787	3791	7.865530	TTGACCAAGGGATACTGCTATAATA	57.134	36.000	0.00	0.00	0.00	0.98
2908	3920	8.044060	TCATAGTGTTTTGTGAATCTGAATCC	57.956	34.615	0.00	0.00	0.00	3.01
2958	3970	9.224267	AGTGATTTATCTTATGGCATGATGTAC	57.776	33.333	10.98	2.92	0.00	2.90
3019	4031	2.072298	GAACTGAAGCAGGCTGTACTG	58.928	52.381	17.16	13.12	41.41	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
472	533	2.488355	CCGCCGTCGTCTACATGT	59.512	61.111	2.69	2.69	0.00	3.21
490	563	4.803908	AAAGCCTAGCCGCAGCCC	62.804	66.667	0.00	0.00	41.25	5.19
527	634	2.040278	ACATGCCAGAAACTCTGCCTAA	59.960	45.455	0.00	0.00	42.98	2.69
528	635	1.630369	ACATGCCAGAAACTCTGCCTA	59.370	47.619	0.00	0.00	42.98	3.93
529	636	0.403271	ACATGCCAGAAACTCTGCCT	59.597	50.000	0.00	0.00	42.98	4.75
531	638	3.375782	AAAACATGCCAGAAACTCTGC	57.624	42.857	0.00	0.00	42.98	4.26
532	639	6.507023	ACTTAAAAACATGCCAGAAACTCTG	58.493	36.000	0.00	0.00	43.91	3.35
533	640	6.715347	ACTTAAAAACATGCCAGAAACTCT	57.285	33.333	0.00	0.00	0.00	3.24
534	641	7.203218	AGAACTTAAAAACATGCCAGAAACTC	58.797	34.615	0.00	0.00	0.00	3.01
535	642	7.112452	AGAACTTAAAAACATGCCAGAAACT	57.888	32.000	0.00	0.00	0.00	2.66
536	643	7.277760	ACAAGAACTTAAAAACATGCCAGAAAC	59.722	33.333	0.00	0.00	0.00	2.78
537	644	7.327214	ACAAGAACTTAAAAACATGCCAGAAA	58.673	30.769	0.00	0.00	0.00	2.52
542	649	7.995463	TTGTACAAGAACTTAAAAACATGCC	57.005	32.000	3.59	0.00	0.00	4.40
558	665	9.103048	GTCATACTTTGTCGAAATTTGTACAAG	57.897	33.333	8.56	0.00	33.70	3.16
583	690	4.292599	GGCGATTTTTACAAAAACTCGGT	58.707	39.130	19.56	0.00	40.33	4.69
591	698	4.922719	ACAAACTCGGCGATTTTTACAAA	58.077	34.783	20.55	0.00	0.00	2.83
592	699	4.555348	ACAAACTCGGCGATTTTTACAA	57.445	36.364	20.55	0.00	0.00	2.41
652	764	2.449518	TCCCAGTCACAGGCCCAA	60.450	61.111	0.00	0.00	0.00	4.12
699	811	1.817099	GAGATGCAGGCGAACCAGG	60.817	63.158	0.00	0.00	39.06	4.45
701	813	0.036732	AAAGAGATGCAGGCGAACCA	59.963	50.000	0.00	0.00	39.06	3.67
711	824	0.097150	GGGCGTCGAAAAAGAGATGC	59.903	55.000	0.00	1.42	45.73	3.91
738	857	4.514577	ATCTCCAGCCGCCGTTCG	62.515	66.667	0.00	0.00	38.08	3.95
739	858	2.892425	CATCTCCAGCCGCCGTTC	60.892	66.667	0.00	0.00	0.00	3.95
859	978	0.693767	AAGCTGGGGAGGAGGATGAG	60.694	60.000	0.00	0.00	0.00	2.90
913	1056	2.041620	TGGGGAAAAGTGATCTCAAGGG	59.958	50.000	0.00	0.00	0.00	3.95
1328	1477	3.005554	CCCACAGAGTTGCTATGTTCAG	58.994	50.000	0.00	0.00	33.39	3.02
1338	1487	2.022129	GTCGTCGCCCACAGAGTTG	61.022	63.158	0.00	0.00	0.00	3.16
1373	1522	1.014564	GCTGTCGTCAAGCAGGTACC	61.015	60.000	2.73	2.73	33.62	3.34
1416	1565	1.003233	ACCTTGGATTCCGTCAGAACC	59.997	52.381	0.00	0.00	37.29	3.62
1534	1683	3.387699	ACCACCCCTTCAACATCAAAAAG	59.612	43.478	0.00	0.00	0.00	2.27
1553	1702	1.945354	TTTGTGCGCGGGAAAAACCA	61.945	50.000	8.83	0.00	41.20	3.67
1572	1721	3.050339	CGCCCTGCAACCACAATT	58.950	55.556	0.00	0.00	0.00	2.32
1623	1772	0.674895	GCCTTGTCCTGTCGCTCATT	60.675	55.000	0.00	0.00	0.00	2.57
2020	2169	3.691342	GCGGGACCTTTTTGCCCC	61.691	66.667	0.00	0.00	38.69	5.80
2104	2253	2.280628	CCCAACTTCATCTTACGAGGC	58.719	52.381	0.00	0.00	0.00	4.70
2124	2274	6.398918	TCACTGGAAACTAATAAGTGAGAGC	58.601	40.000	0.00	0.00	41.63	4.09
2131	2281	9.231297	TCCAAAAGATCACTGGAAACTAATAAG	57.769	33.333	7.72	0.00	36.30	1.73
2165	2317	9.017669	CATGCAGAGATAATTTTACAAAAGCTC	57.982	33.333	0.00	0.00	0.00	4.09
2166	2318	8.526147	ACATGCAGAGATAATTTTACAAAAGCT	58.474	29.630	0.00	0.00	0.00	3.74
2181	2333	9.570468	AGATAATTTTACATCACATGCAGAGAT	57.430	29.630	0.00	0.00	0.00	2.75
2182	2334	8.969260	AGATAATTTTACATCACATGCAGAGA	57.031	30.769	0.00	0.00	0.00	3.10
2183	2335	9.053840	AGAGATAATTTTACATCACATGCAGAG	57.946	33.333	0.00	0.00	0.00	3.35
2184	2336	8.833493	CAGAGATAATTTTACATCACATGCAGA	58.167	33.333	0.00	0.00	0.00	4.26
2185	2337	7.590322	GCAGAGATAATTTTACATCACATGCAG	59.410	37.037	0.00	0.00	0.00	4.41
2186	2338	7.067251	TGCAGAGATAATTTTACATCACATGCA	59.933	33.333	0.00	0.00	31.12	3.96
2187	2339	7.420002	TGCAGAGATAATTTTACATCACATGC	58.580	34.615	0.00	0.00	0.00	4.06
2188	2340	9.394477	CATGCAGAGATAATTTTACATCACATG	57.606	33.333	0.00	0.00	0.00	3.21
2189	2341	9.128404	ACATGCAGAGATAATTTTACATCACAT	57.872	29.630	0.00	0.00	0.00	3.21
2190	2342	8.400186	CACATGCAGAGATAATTTTACATCACA	58.600	33.333	0.00	0.00	0.00	3.58
2191	2343	8.615211	TCACATGCAGAGATAATTTTACATCAC	58.385	33.333	0.00	0.00	0.00	3.06
2192	2344	8.735692	TCACATGCAGAGATAATTTTACATCA	57.264	30.769	0.00	0.00	0.00	3.07
2193	2345	9.608617	CATCACATGCAGAGATAATTTTACATC	57.391	33.333	0.00	0.00	0.00	3.06
2194	2346	8.573885	CCATCACATGCAGAGATAATTTTACAT	58.426	33.333	0.00	0.00	0.00	2.29
2195	2347	7.774625	TCCATCACATGCAGAGATAATTTTACA	59.225	33.333	0.00	0.00	0.00	2.41
2196	2348	8.158169	TCCATCACATGCAGAGATAATTTTAC	57.842	34.615	0.00	0.00	0.00	2.01
2197	2349	7.446319	CCTCCATCACATGCAGAGATAATTTTA	59.554	37.037	0.00	0.00	0.00	1.52
2198	2350	6.264744	CCTCCATCACATGCAGAGATAATTTT	59.735	38.462	0.00	0.00	0.00	1.82
2199	2351	5.768662	CCTCCATCACATGCAGAGATAATTT	59.231	40.000	0.00	0.00	0.00	1.82
2200	2352	5.314529	CCTCCATCACATGCAGAGATAATT	58.685	41.667	0.00	0.00	0.00	1.40
2201	2353	4.806625	GCCTCCATCACATGCAGAGATAAT	60.807	45.833	0.00	0.00	0.00	1.28
2202	2354	3.495629	GCCTCCATCACATGCAGAGATAA	60.496	47.826	0.00	0.00	0.00	1.75
2203	2355	2.038164	GCCTCCATCACATGCAGAGATA	59.962	50.000	0.00	0.00	0.00	1.98
2204	2356	1.202782	GCCTCCATCACATGCAGAGAT	60.203	52.381	0.00	0.00	0.00	2.75
2205	2357	0.179702	GCCTCCATCACATGCAGAGA	59.820	55.000	0.00	0.00	0.00	3.10
2206	2358	0.180642	AGCCTCCATCACATGCAGAG	59.819	55.000	0.00	0.00	0.00	3.35
2207	2359	0.179702	GAGCCTCCATCACATGCAGA	59.820	55.000	0.00	0.00	0.00	4.26
2208	2360	0.818445	GGAGCCTCCATCACATGCAG	60.818	60.000	5.69	0.00	36.28	4.41
2283	2435	2.245714	GAACGCTAGCAAGCTGCCAC	62.246	60.000	16.45	0.00	46.52	5.01
2298	2450	3.428045	GGATCAGGGCATTTTCAAGAACG	60.428	47.826	0.00	0.00	0.00	3.95
2304	2456	2.357465	CCAGAGGATCAGGGCATTTTCA	60.357	50.000	0.00	0.00	38.26	2.69
2318	2470	4.112634	ACCAAATTGTTTAGCCAGAGGA	57.887	40.909	0.00	0.00	0.00	3.71
2320	2472	6.016276	ACAGTAACCAAATTGTTTAGCCAGAG	60.016	38.462	0.00	0.00	0.00	3.35
2336	2488	7.721409	AAAAGGGAAGTTTTAACAGTAACCA	57.279	32.000	0.00	0.00	0.00	3.67
2430	2583	0.106708	TTCATAGCTCGCCATGGACC	59.893	55.000	18.40	0.00	0.00	4.46
2477	3481	4.573607	TCATGCTGCTCAATAACTTGCTAG	59.426	41.667	0.00	0.00	32.11	3.42
2498	3502	7.121020	TGCAATCTCAAAATACTGCACTTATCA	59.879	33.333	0.00	0.00	35.02	2.15
2499	3503	7.475015	TGCAATCTCAAAATACTGCACTTATC	58.525	34.615	0.00	0.00	35.02	1.75
2502	3506	5.710513	TGCAATCTCAAAATACTGCACTT	57.289	34.783	0.00	0.00	35.02	3.16
2529	3533	7.385267	CCAATCCAAAATTGAACATAGTTGGA	58.615	34.615	5.47	5.47	46.22	3.53
2531	3535	6.649973	TGCCAATCCAAAATTGAACATAGTTG	59.350	34.615	0.00	0.00	0.00	3.16
2608	3612	5.640189	TTTTTCTCTACGGACTACAGAGG	57.360	43.478	0.00	0.00	37.10	3.69
2710	3714	8.773645	GCTTTGCTTATCACCAAGTAAAATTTT	58.226	29.630	8.75	8.75	38.89	1.82
2748	3752	7.231925	TCCCTTGGTCAATTAAGGAAAGTAAAC	59.768	37.037	6.33	0.00	44.98	2.01
2776	3780	8.449423	TGATTACCAATCCCTATTATAGCAGT	57.551	34.615	0.00	0.00	37.09	4.40
2785	3789	7.758609	TGACATTCATGATTACCAATCCCTAT	58.241	34.615	0.00	0.00	37.09	2.57
2787	3791	6.017211	TGACATTCATGATTACCAATCCCT	57.983	37.500	0.00	0.00	37.09	4.20
2885	3890	6.094048	CCGGATTCAGATTCACAAAACACTAT	59.906	38.462	0.00	0.00	0.00	2.12
2908	3920	0.249784	CTCCATGATCTGACTGCCCG	60.250	60.000	0.00	0.00	0.00	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.