AutoCloner

Multiple sequence alignment - TraesCS2A01G580500

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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	TraesCS2A01G580500	chr2A	100.000	6923	0	0	1	6923	772736518	772743440	0.000000e+00	12785.0
1	TraesCS2A01G580500	chr2A	87.008	1601	169	21	5049	6625	772688751	772690336	0.000000e+00	1768.0
2	TraesCS2A01G580500	chr2A	82.319	2087	297	36	2983	5054	772686700	772688729	0.000000e+00	1744.0
3	TraesCS2A01G580500	chr2A	88.870	1204	110	12	532	1732	772685152	772686334	0.000000e+00	1459.0
4	TraesCS2A01G580500	chr2A	88.192	271	17	2	129	384	772684605	772684875	6.740000e-80	309.0
5	TraesCS2A01G580500	chr2A	81.383	188	35	0	1875	2062	772738341	772738528	3.340000e-33	154.0
6	TraesCS2A01G580500	chr2A	81.383	188	35	0	1824	2011	772738392	772738579	3.340000e-33	154.0
7	TraesCS2A01G580500	chr2B	94.749	6818	267	35	129	6877	788014902	788021697	0.000000e+00	10523.0
8	TraesCS2A01G580500	chr2B	86.579	1967	204	32	4695	6625	788029823	788031765	0.000000e+00	2115.0
9	TraesCS2A01G580500	chr2B	87.951	1220	135	7	3340	4557	788028634	788029843	0.000000e+00	1428.0
10	TraesCS2A01G580500	chr2B	86.036	1153	138	16	3410	4556	787869781	787868646	0.000000e+00	1216.0
11	TraesCS2A01G580500	chr2B	83.053	655	80	20	937	1575	794101908	794102547	3.620000e-157	566.0
12	TraesCS2A01G580500	chr2B	83.053	655	80	20	937	1575	794110508	794111147	3.620000e-157	566.0
13	TraesCS2A01G580500	chr2B	85.494	324	43	3	4729	5051	787860918	787860598	1.110000e-87	335.0
14	TraesCS2A01G580500	chr2B	77.985	268	41	6	1875	2124	788016612	788016879	1.200000e-32	152.0
15	TraesCS2A01G580500	chr2B	81.739	115	10	5	546	649	788026258	788026372	1.240000e-12	86.1
16	TraesCS2A01G580500	chr2D	90.753	1752	105	31	1	1725	647807916	647806195	0.000000e+00	2285.0
17	TraesCS2A01G580500	chr2D	83.327	2537	351	40	3127	5627	647805573	647803073	0.000000e+00	2276.0
18	TraesCS2A01G580500	chr2D	80.801	1922	294	44	2670	4558	636066608	636068487	0.000000e+00	1435.0
19	TraesCS2A01G580500	chr2D	84.400	750	84	16	5866	6595	647802918	647802182	0.000000e+00	706.0
20	TraesCS2A01G580500	chr2D	78.615	1155	154	51	545	1655	636064659	636065764	0.000000e+00	678.0
21	TraesCS2A01G580500	chr2D	83.507	673	100	5	4672	5334	636068532	636069203	9.870000e-173	617.0
22	TraesCS2A01G580500	chr2D	75.341	880	185	21	3634	4491	528323206	528324075	1.810000e-105	394.0
23	TraesCS2A01G580500	chr2D	81.962	316	38	14	6600	6902	647801788	647801479	4.150000e-62	250.0
24	TraesCS2A01G580500	chr2D	75.000	496	99	15	2670	3154	647806063	647805582	9.100000e-49	206.0
25	TraesCS2A01G580500	chr3B	75.391	959	187	28	3634	4560	721039635	721040576	1.070000e-112	418.0
26	TraesCS2A01G580500	chr3B	74.332	935	196	31	3641	4546	721046787	721047706	2.370000e-94	357.0
27	TraesCS2A01G580500	chr3B	76.606	436	81	14	996	1416	721044066	721044495	3.250000e-53	220.0
28	TraesCS2A01G580500	chr3D	76.989	465	87	14	967	1417	544822007	544822465	1.490000e-61	248.0
29	TraesCS2A01G580500	chr7A	77.641	407	80	8	1001	1397	36553169	36552764	3.230000e-58	237.0
30	TraesCS2A01G580500	chrUn	77.088	419	79	10	999	1404	91005182	91004768	6.990000e-55	226.0
31	TraesCS2A01G580500	chr3A	76.659	437	77	17	996	1416	681661491	681661918	1.170000e-52	219.0
32	TraesCS2A01G580500	chr7D	75.917	436	94	9	972	1397	36750409	36749975	5.440000e-51	213.0

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	TraesCS2A01G580500	chr2A	772736518	772743440	6922	False	12785.000000	12785	100.000000	1	6923	1	chr2A.!!$F1	6922
1	TraesCS2A01G580500	chr2A	772684605	772690336	5731	False	1320.000000	1768	86.597250	129	6625	4	chr2A.!!$F2	6496
2	TraesCS2A01G580500	chr2B	788014902	788021697	6795	False	10523.000000	10523	94.749000	129	6877	1	chr2B.!!$F1	6748
3	TraesCS2A01G580500	chr2B	787868646	787869781	1135	True	1216.000000	1216	86.036000	3410	4556	1	chr2B.!!$R2	1146
4	TraesCS2A01G580500	chr2B	788026258	788031765	5507	False	1209.700000	2115	85.423000	546	6625	3	chr2B.!!$F5	6079
5	TraesCS2A01G580500	chr2B	794101908	794102547	639	False	566.000000	566	83.053000	937	1575	1	chr2B.!!$F3	638
6	TraesCS2A01G580500	chr2B	794110508	794111147	639	False	566.000000	566	83.053000	937	1575	1	chr2B.!!$F4	638
7	TraesCS2A01G580500	chr2D	647801479	647807916	6437	True	1144.600000	2285	83.088400	1	6902	5	chr2D.!!$R1	6901
8	TraesCS2A01G580500	chr2D	636064659	636069203	4544	False	910.000000	1435	80.974333	545	5334	3	chr2D.!!$F2	4789
9	TraesCS2A01G580500	chr2D	528323206	528324075	869	False	394.000000	394	75.341000	3634	4491	1	chr2D.!!$F1	857
10	TraesCS2A01G580500	chr3B	721039635	721047706	8071	False	331.666667	418	75.443000	996	4560	3	chr3B.!!$F1	3564

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
590	1010	1.453762	GAAGGATCTGCATGCAGCCC	61.454	60.000	37.48	35.11	44.83	5.19	F
2031	2666	0.233332	GTGCTCTTGCGTGTGAAGAC	59.767	55.000	0.00	0.00	43.34	3.01	F
2529	3404	0.249120	CCCTTGTGCACGGAGATACA	59.751	55.000	18.51	0.00	0.00	2.29	F
2697	3572	0.614979	ACGTCCCTGAGGTGCACTAT	60.615	55.000	17.98	5.74	29.20	2.12	F
3156	4082	1.516892	CTCAGAGCAGCTGGAGGAC	59.483	63.158	17.12	0.00	44.98	3.85	F
4571	5584	0.670162	GCTGGTCAAAAGCTGAAGCA	59.330	50.000	4.90	0.00	45.16	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2364	2999	0.111061	TGCACAAGAGCCTCATTGGT	59.889	50.000	0.00	0.00	38.35	3.67	R
3080	3970	2.602878	CTGTTTGCTTGATGATGGCAC	58.397	47.619	0.00	0.00	35.62	5.01	R
3349	4305	5.302568	TCTGCTGTCTGGTTTCATCAAAATT	59.697	36.000	0.00	0.00	0.00	1.82	R
4571	5584	1.676916	CGACATGACCAGCCAAGACAT	60.677	52.381	0.00	0.00	0.00	3.06	R
4982	6103	0.337773	ACTCAGCTCTGATGGAGGGA	59.662	55.000	0.00	0.00	42.08	4.20	R
6398	7714	0.031449	CGCACTAGCTAGGGAGAAGC	59.969	60.000	27.47	16.41	40.40	3.86	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
44	45	3.343617	CGCTTGGAGGAAGAACCAAATA	58.656	45.455	0.00	0.00	44.03	1.40
70	71	1.687563	CCTTCCAAACGACCAAGGTT	58.312	50.000	0.00	0.00	32.17	3.50
74	75	4.098196	CCTTCCAAACGACCAAGGTTTAAA	59.902	41.667	0.00	0.00	35.93	1.52
465	493	6.477688	CAGAATGTGAAAAATGTTGAGCACTT	59.522	34.615	0.00	0.00	0.00	3.16
487	515	3.057104	TCATCCTGCTTGCAACTGATTTG	60.057	43.478	0.00	0.00	38.37	2.32
496	524	3.703556	TTGCAACTGATTTGGAAAGACCA	59.296	39.130	0.00	0.00	42.09	4.02
540	570	4.458397	TCCCGTCTATTACACTACTCCAG	58.542	47.826	0.00	0.00	0.00	3.86
590	1010	1.453762	GAAGGATCTGCATGCAGCCC	61.454	60.000	37.48	35.11	44.83	5.19
634	1058	7.121168	TGACAGAAAAGAAAAAGAAGAAGCTGA	59.879	33.333	0.00	0.00	0.00	4.26
649	1073	3.287867	AGCTGAGTAATGGGTTCATGG	57.712	47.619	0.00	0.00	33.18	3.66
675	1112	4.094476	TCCTGGAAGAGTAGGAAAATCGT	58.906	43.478	0.00	0.00	40.03	3.73
957	1432	5.168526	TCAATCAAACTCTTGAAACACCG	57.831	39.130	0.00	0.00	44.64	4.94
1359	1854	4.344865	GCCGGCCAACTGAGGGAA	62.345	66.667	18.11	0.00	0.00	3.97
1670	2195	2.276201	CATAAAGTCGAATGTGGCGGA	58.724	47.619	0.00	0.00	0.00	5.54
1737	2262	2.940410	CGCCTTTGTGGTAACGGATAAT	59.060	45.455	0.00	0.00	42.51	1.28
1868	2393	3.518068	GCATGCGGGTGCCCTTAC	61.518	66.667	0.00	0.00	41.78	2.34
2031	2666	0.233332	GTGCTCTTGCGTGTGAAGAC	59.767	55.000	0.00	0.00	43.34	3.01
2067	2702	1.228228	GATCAAGGATGCCAGCCCA	59.772	57.895	0.00	0.00	0.00	5.36
2100	2735	1.228228	GATCAAGGATGCCAGCCCA	59.772	57.895	0.00	0.00	0.00	5.36
2107	2742	1.604593	GATGCCAGCCCAGTTGTGT	60.605	57.895	0.00	0.00	0.00	3.72
2130	2765	1.752833	GGAGACCAAGGACAACGGT	59.247	57.895	0.00	0.00	35.12	4.83
2151	2786	3.382546	GTGCCCTTGTGCATGAAGATATT	59.617	43.478	9.44	0.00	44.30	1.28
2208	2843	1.547372	GTGCATGAAGACAAGGCCATT	59.453	47.619	5.01	0.00	32.15	3.16
2257	2892	2.772077	TACGCATAAAGACAAGGCCA	57.228	45.000	5.01	0.00	0.00	5.36
2277	2912	2.905415	TGCCACCAAAGATCAAGGAT	57.095	45.000	0.00	0.00	0.00	3.24
2306	2941	4.225942	TGCTCTTGTGGATGAAGATAAGGT	59.774	41.667	0.00	0.00	0.00	3.50
2529	3404	0.249120	CCCTTGTGCACGGAGATACA	59.751	55.000	18.51	0.00	0.00	2.29
2532	3407	0.735978	TTGTGCACGGAGATACAGCG	60.736	55.000	13.13	0.00	0.00	5.18
2583	3458	4.439289	GCTCTTGAACACAAAGATATGCCC	60.439	45.833	0.00	0.00	0.00	5.36
2697	3572	0.614979	ACGTCCCTGAGGTGCACTAT	60.615	55.000	17.98	5.74	29.20	2.12
3080	3970	4.717877	TCCATGGTAGCAGAATTGTATGG	58.282	43.478	12.58	0.53	36.13	2.74
3132	4025	5.163550	GCTTAAATGGAAAATAGAAGGCGGT	60.164	40.000	0.00	0.00	0.00	5.68
3156	4082	1.516892	CTCAGAGCAGCTGGAGGAC	59.483	63.158	17.12	0.00	44.98	3.85
3329	4267	7.310052	GGAATTAGAAAAATCTGCCAAGAACCT	60.310	37.037	0.00	0.00	35.59	3.50
3349	4305	3.245300	CCTAGAGGTGATCCCGGAAGATA	60.245	52.174	0.73	0.00	38.74	1.98
4571	5584	0.670162	GCTGGTCAAAAGCTGAAGCA	59.330	50.000	4.90	0.00	45.16	3.91
4711	5727	3.604875	ATCGTTGGAACCGTCTATTGT	57.395	42.857	0.00	0.00	0.00	2.71
4806	5921	2.105134	TGTGGAGGTATTGTCCAACGTT	59.895	45.455	0.00	0.00	45.85	3.99
4812	5927	3.075884	GGTATTGTCCAACGTTAAGCCA	58.924	45.455	0.00	0.00	0.00	4.75
5073	6230	1.327303	CTAGCACACAAAAGGGGCAA	58.673	50.000	0.00	0.00	0.00	4.52
5097	6254	9.846248	CAACTTCTTAAGATATTGGTTGGAAAG	57.154	33.333	5.89	0.00	32.12	2.62
5157	6323	3.269178	CTTGAGCCAGGAAGATCTGAAC	58.731	50.000	0.00	0.00	36.93	3.18
5175	6341	1.999648	ACATCCTTGCCAAGCTTGAA	58.000	45.000	28.05	13.75	0.00	2.69
5589	6761	4.226427	TGGCAGTCAGCTTATCTTCAAT	57.774	40.909	0.00	0.00	44.79	2.57
5614	6786	6.661304	AAGATGAATTCCAAAAGCTCAACT	57.339	33.333	2.27	0.00	0.00	3.16
5634	6812	2.981859	TTCTTATTGTCGGCTCCTCC	57.018	50.000	0.00	0.00	0.00	4.30
5712	6893	8.514594	GTCTGGTCATTCAAGAATATTGTTTCA	58.485	33.333	0.00	0.00	0.00	2.69
5713	6894	9.076781	TCTGGTCATTCAAGAATATTGTTTCAA	57.923	29.630	0.00	0.00	0.00	2.69
5883	7088	2.825836	GGTCCTGCAAGATGCCCG	60.826	66.667	0.00	0.00	44.23	6.13
5933	7138	1.073923	GAGGAACTGAAGGCTTTCCCA	59.926	52.381	11.23	0.02	41.55	4.37
5975	7180	2.363038	CAATTCCTGCCATGGTATGTGG	59.637	50.000	14.67	6.95	39.80	4.17
6170	7398	1.962807	CTGGATTTGTGTGGCTTTCCA	59.037	47.619	0.00	0.00	40.85	3.53
6222	7471	3.485711	CGATGCTTGTACGCACATTTGAT	60.486	43.478	0.00	0.00	43.61	2.57
6261	7510	3.393800	ACGGTTGTGAGCTATATCATGC	58.606	45.455	0.00	0.00	0.00	4.06
6280	7539	0.109597	CGCTTGGGTTCTGCAATGAC	60.110	55.000	0.00	0.00	0.00	3.06
6298	7557	3.845178	TGACGAACTGGTGTATGTCATC	58.155	45.455	0.00	0.00	36.32	2.92
6299	7558	3.257127	TGACGAACTGGTGTATGTCATCA	59.743	43.478	0.00	0.00	36.32	3.07
6347	7622	6.042093	AGCTACCAGCAGCAGTTAATTATAGA	59.958	38.462	0.00	0.00	45.56	1.98
6398	7714	8.202811	TCAGAGATTTCTCAGATATTTGTCCAG	58.797	37.037	10.07	0.00	45.21	3.86
6483	7809	7.337938	TGATCTAATGACAAATAGCAAGGTCA	58.662	34.615	0.00	0.00	43.61	4.02
6512	7838	4.096984	GTCATTGGCCAAATAGACAGAAGG	59.903	45.833	29.32	7.85	31.77	3.46
6577	7903	3.777106	AACAGACTCACACATGACCAT	57.223	42.857	0.00	0.00	0.00	3.55
6595	8457	3.263170	ACCATACACCTATGTTCAGTGCA	59.737	43.478	0.00	0.00	40.48	4.57
6613	8475	2.887783	TGCACGGAAATTTCCTAAAGCA	59.112	40.909	29.85	27.34	45.33	3.91
6633	8932	4.280677	AGCAGTTCATAGAGAGATACCAGC	59.719	45.833	0.00	0.00	0.00	4.85
6649	8948	1.338105	CCAGCTTACTGCAGCAGTACA	60.338	52.381	31.15	21.02	45.13	2.90
6653	8952	2.535984	GCTTACTGCAGCAGTACATACG	59.464	50.000	31.15	18.44	45.13	3.06
6659	10468	1.933181	GCAGCAGTACATACGCATTGA	59.067	47.619	0.00	0.00	0.00	2.57
6760	10584	8.910351	ATCTCAGAAATAGCCAAGTTATTACC	57.090	34.615	0.00	0.00	0.00	2.85
6804	10643	7.219484	TCCAGATTTCATTTTTCAGAGAACC	57.781	36.000	0.00	0.00	0.00	3.62
6807	10646	6.798959	CAGATTTCATTTTTCAGAGAACCGAC	59.201	38.462	0.00	0.00	0.00	4.79
6811	10650	2.144482	TTTTCAGAGAACCGACGGAC	57.856	50.000	23.38	13.97	0.00	4.79
6818	10657	2.522436	AACCGACGGACCTCCACA	60.522	61.111	23.38	0.00	35.14	4.17
6824	10663	2.046892	CGGACCTCCACAGCCAAG	60.047	66.667	0.00	0.00	35.14	3.61
6830	10669	1.494721	ACCTCCACAGCCAAGAGAAAA	59.505	47.619	0.00	0.00	0.00	2.29
6892	11804	3.758300	ACTTTGCAAAACTGAGAACACG	58.242	40.909	13.84	0.00	0.00	4.49
6896	11808	2.744741	TGCAAAACTGAGAACACGACAA	59.255	40.909	0.00	0.00	0.00	3.18
6902	11814	3.448686	ACTGAGAACACGACAAAGTGAG	58.551	45.455	4.00	0.00	44.43	3.51
6903	11815	2.797156	CTGAGAACACGACAAAGTGAGG	59.203	50.000	4.00	0.00	44.43	3.86
6904	11816	1.527311	GAGAACACGACAAAGTGAGGC	59.473	52.381	4.00	0.00	44.43	4.70
6905	11817	1.134521	AGAACACGACAAAGTGAGGCA	60.135	47.619	4.00	0.00	44.43	4.75
6906	11818	1.003866	GAACACGACAAAGTGAGGCAC	60.004	52.381	4.00	0.00	44.43	5.01
6918	11830	4.364318	AGGCACTCGTATCCTGCT	57.636	55.556	0.00	0.00	0.00	4.24
6919	11831	3.515059	AGGCACTCGTATCCTGCTA	57.485	52.632	0.00	0.00	0.00	3.49
6921	11833	2.320781	AGGCACTCGTATCCTGCTATT	58.679	47.619	0.00	0.00	0.00	1.73
6922	11834	2.700897	AGGCACTCGTATCCTGCTATTT	59.299	45.455	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	1.558294	GGTCGTTTGGAAGGGGATAGT	59.442	52.381	0.00	0.00	0.00	2.12
70	71	5.617252	ACTCCAGACCTTGATTTCGTTTAA	58.383	37.500	0.00	0.00	0.00	1.52
74	75	3.181454	ACAACTCCAGACCTTGATTTCGT	60.181	43.478	0.00	0.00	0.00	3.85
391	419	5.841783	GGCAAGGGTATTTTTATTATCCCCA	59.158	40.000	0.00	0.00	35.90	4.96
465	493	2.502142	ATCAGTTGCAAGCAGGATGA	57.498	45.000	0.00	7.90	39.69	2.92
487	515	0.387239	GCGTGCAACATGGTCTTTCC	60.387	55.000	0.00	0.00	35.74	3.13
496	524	0.454285	GCATTACACGCGTGCAACAT	60.454	50.000	37.35	20.98	38.68	2.71
515	545	4.217983	GGAGTAGTGTAATAGACGGGATGG	59.782	50.000	0.00	0.00	0.00	3.51
540	570	9.007252	CGATTTCTCATTTCATCTTTGATTGAC	57.993	33.333	0.00	0.00	0.00	3.18
590	1010	6.658831	TCTGTCATTTCTTTACTTTTCAGCG	58.341	36.000	0.00	0.00	0.00	5.18
634	1058	3.852578	AGGAAGACCATGAACCCATTACT	59.147	43.478	0.00	0.00	38.94	2.24
957	1432	2.357517	CGGCCTGGTCTGTGTGAC	60.358	66.667	0.00	0.00	44.63	3.67
983	1458	0.607489	CATGGATCAATCCCTCCGCC	60.607	60.000	6.57	0.00	46.59	6.13
984	1459	0.607489	CCATGGATCAATCCCTCCGC	60.607	60.000	5.56	0.00	46.59	5.54
985	1460	0.607489	GCCATGGATCAATCCCTCCG	60.607	60.000	18.40	0.00	46.59	4.63
986	1461	0.607489	CGCCATGGATCAATCCCTCC	60.607	60.000	18.40	0.00	46.59	4.30
1191	1686	1.762460	ATTGGCGAGGATCCGGACT	60.762	57.895	6.12	0.00	0.00	3.85
1359	1854	2.397413	CTTGTGCCCGGTCCTTGAGT	62.397	60.000	0.00	0.00	0.00	3.41
1670	2195	1.260544	GGCTGCCAGTTTCCTTGATT	58.739	50.000	15.17	0.00	0.00	2.57
1737	2262	4.243008	TTGGCGTTGGCGTCCTCA	62.243	61.111	0.00	0.00	42.91	3.86
1868	2393	1.518572	ACCGCCTTATCTTCACGCG	60.519	57.895	3.53	3.53	42.37	6.01
2045	2680	0.473326	GCTGGCATCCTTGATCTCCT	59.527	55.000	0.00	0.00	0.00	3.69
2100	2735	1.046472	TGGTCTCCGGTGACACAACT	61.046	55.000	31.48	0.00	38.61	3.16
2107	2742	0.761323	TTGTCCTTGGTCTCCGGTGA	60.761	55.000	0.00	0.06	0.00	4.02
2167	2802	2.700773	GGGCGTTGGCATCCTTGAC	61.701	63.158	0.00	0.00	42.47	3.18
2208	2843	1.195115	CTTCCCTTGTCTCCGATGGA	58.805	55.000	0.00	0.00	0.00	3.41
2257	2892	2.905415	TCCTTGATCTTTGGTGGCAT	57.095	45.000	0.00	0.00	0.00	4.40
2266	2901	1.142465	AGCATCGGCATCCTTGATCTT	59.858	47.619	0.00	0.00	44.61	2.40
2277	2912	0.745486	CATCCACAAGAGCATCGGCA	60.745	55.000	0.00	0.00	44.61	5.69
2364	2999	0.111061	TGCACAAGAGCCTCATTGGT	59.889	50.000	0.00	0.00	38.35	3.67
2563	3438	3.731867	GCGGGCATATCTTTGTGTTCAAG	60.732	47.826	0.00	0.00	34.88	3.02
2697	3572	6.108015	GTGGGGTCGTAGTGTTATAAAATCA	58.892	40.000	0.00	0.00	0.00	2.57
3080	3970	2.602878	CTGTTTGCTTGATGATGGCAC	58.397	47.619	0.00	0.00	35.62	5.01
3106	3996	6.202226	CGCCTTCTATTTTCCATTTAAGCTC	58.798	40.000	0.00	0.00	0.00	4.09
3156	4082	3.668447	CAGGATGTCTTCATATTCGGGG	58.332	50.000	0.00	0.00	34.06	5.73
3329	4267	4.464652	TTATCTTCCGGGATCACCTCTA	57.535	45.455	0.00	0.00	36.97	2.43
3349	4305	5.302568	TCTGCTGTCTGGTTTCATCAAAATT	59.697	36.000	0.00	0.00	0.00	1.82
4571	5584	1.676916	CGACATGACCAGCCAAGACAT	60.677	52.381	0.00	0.00	0.00	3.06
4619	5632	2.273449	GCATCTGGACACTGGGGG	59.727	66.667	0.00	0.00	0.00	5.40
4711	5727	4.042062	AGGACTTGAATCAACATGACCAGA	59.958	41.667	0.00	0.00	34.37	3.86
4806	5921	7.950512	TCAAATCTTGTTCATTCTTTGGCTTA	58.049	30.769	0.00	0.00	0.00	3.09
4982	6103	0.337773	ACTCAGCTCTGATGGAGGGA	59.662	55.000	0.00	0.00	42.08	4.20
5073	6230	7.615757	CCCTTTCCAACCAATATCTTAAGAAGT	59.384	37.037	9.71	0.00	0.00	3.01
5097	6254	1.970640	ACCTTGGCAAGTTGATTTCCC	59.029	47.619	24.57	0.00	0.00	3.97
5157	6323	3.062042	GTTTTCAAGCTTGGCAAGGATG	58.938	45.455	27.25	4.57	0.00	3.51
5175	6341	4.034048	CGAAGCTTGACACAGTGTAAGTTT	59.966	41.667	2.10	13.63	0.00	2.66
5446	6612	4.262377	CCTGGTTATGTGTTTGGCATTGAA	60.262	41.667	0.00	0.00	0.00	2.69
5547	6713	4.760204	CCATTGTAAAACTTCCCGAAGAGT	59.240	41.667	11.35	0.00	40.79	3.24
5589	6761	8.181904	AGTTGAGCTTTTGGAATTCATCTTTA	57.818	30.769	7.93	0.00	0.00	1.85
5614	6786	2.838202	AGGAGGAGCCGACAATAAGAAA	59.162	45.455	0.00	0.00	43.43	2.52
5634	6812	4.563184	GTGAAGCTTAACTCGGTGATGTAG	59.437	45.833	6.71	0.00	0.00	2.74
5712	6893	4.455877	GGAAGTTTGTCGATTCCAGACATT	59.544	41.667	9.39	0.00	46.44	2.71
5713	6894	4.003648	GGAAGTTTGTCGATTCCAGACAT	58.996	43.478	9.39	0.00	46.44	3.06
5718	6899	2.151202	GCAGGAAGTTTGTCGATTCCA	58.849	47.619	15.30	0.00	44.11	3.53
5933	7138	5.160607	TGGTGATGAACGGAAGAAGTAAT	57.839	39.130	0.00	0.00	0.00	1.89
5975	7180	1.024271	ACCACATGAGCACACACAAC	58.976	50.000	0.00	0.00	0.00	3.32
6170	7398	3.575805	ACATGGAACCATTTTGTCCAGT	58.424	40.909	3.35	0.00	33.90	4.00
6239	7488	4.556233	GCATGATATAGCTCACAACCGTA	58.444	43.478	0.00	0.00	0.00	4.02
6241	7490	2.409715	CGCATGATATAGCTCACAACCG	59.590	50.000	0.00	0.00	0.00	4.44
6242	7491	2.158449	GCGCATGATATAGCTCACAACC	59.842	50.000	0.30	0.00	0.00	3.77
6261	7510	0.109597	GTCATTGCAGAACCCAAGCG	60.110	55.000	0.00	0.00	0.00	4.68
6280	7539	8.650714	CATATATTGATGACATACACCAGTTCG	58.349	37.037	0.00	0.00	0.00	3.95
6309	7572	4.220382	TGCTGGTAGCTGCATTGTTATTTT	59.780	37.500	20.75	0.00	42.97	1.82
6311	7574	3.355378	TGCTGGTAGCTGCATTGTTATT	58.645	40.909	20.75	0.00	42.97	1.40
6347	7622	4.469657	TGCATAAAACTCCACTTCAAGGT	58.530	39.130	0.00	0.00	0.00	3.50
6398	7714	0.031449	CGCACTAGCTAGGGAGAAGC	59.969	60.000	27.47	16.41	40.40	3.86
6483	7809	6.245408	TGTCTATTTGGCCAATGACTTTACT	58.755	36.000	29.78	6.61	30.35	2.24
6512	7838	7.703197	GCCTCTACTGAAACTTAGTCTATGAAC	59.297	40.741	0.00	0.00	0.00	3.18
6577	7903	2.353307	CCGTGCACTGAACATAGGTGTA	60.353	50.000	16.19	0.00	37.67	2.90
6613	8475	7.230510	CAGTAAGCTGGTATCTCTCTATGAACT	59.769	40.741	0.00	0.00	39.01	3.01
6633	8932	2.535984	GCGTATGTACTGCTGCAGTAAG	59.464	50.000	36.15	25.58	46.55	2.34
6649	8948	9.769093	GTTCAGTAGTAAATTTTCAATGCGTAT	57.231	29.630	0.00	0.00	0.00	3.06
6653	8952	8.810652	TTGGTTCAGTAGTAAATTTTCAATGC	57.189	30.769	0.00	0.00	0.00	3.56
6659	10468	6.549736	ACAGCCTTGGTTCAGTAGTAAATTTT	59.450	34.615	0.00	0.00	0.00	1.82
6760	10584	3.548818	GGATGGCACTTTTTATGCTAGCG	60.549	47.826	10.77	0.00	40.46	4.26
6804	10643	4.436998	GGCTGTGGAGGTCCGTCG	62.437	72.222	0.00	0.00	39.43	5.12
6807	10646	2.046892	CTTGGCTGTGGAGGTCCG	60.047	66.667	0.00	0.00	39.43	4.79
6811	10650	2.276732	TTTTCTCTTGGCTGTGGAGG	57.723	50.000	0.00	0.00	0.00	4.30
6818	10657	6.469782	TCAACAGAAAATTTTCTCTTGGCT	57.530	33.333	31.48	14.16	45.23	4.75
6824	10663	9.741647	ACAAGAGATTCAACAGAAAATTTTCTC	57.258	29.630	26.87	15.73	45.23	2.87
6892	11804	2.433868	TACGAGTGCCTCACTTTGTC	57.566	50.000	0.66	0.00	45.44	3.18
6896	11808	1.478510	CAGGATACGAGTGCCTCACTT	59.521	52.381	0.66	0.00	45.44	3.16
6902	11814	2.821991	AATAGCAGGATACGAGTGCC	57.178	50.000	0.00	0.00	46.39	5.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.