AutoCloner

Multiple sequence alignment - TraesCS5B01G145500

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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	TraesCS5B01G145500	chr5B	100.000	3206	0	0	1	3206	272676300	272679505	0.000000e+00	5921
1	TraesCS5B01G145500	chr5B	87.145	809	90	11	2392	3190	265435648	265436452	0.000000e+00	905
2	TraesCS5B01G145500	chr5B	85.226	643	77	9	2274	2904	287429328	287428692	0.000000e+00	645
3	TraesCS5B01G145500	chr5A	94.880	1582	57	10	58	1622	323369646	323371220	0.000000e+00	2451
4	TraesCS5B01G145500	chr5A	94.369	586	30	1	1621	2203	323371255	323371840	0.000000e+00	896
5	TraesCS5B01G145500	chr5A	85.816	141	19	1	2274	2413	32158676	32158536	7.170000e-32	148
6	TraesCS5B01G145500	chr5D	94.295	1595	72	11	58	1639	232404652	232403064	0.000000e+00	2423
7	TraesCS5B01G145500	chr5D	94.817	656	32	2	1621	2275	232403047	232402393	0.000000e+00	1022
8	TraesCS5B01G145500	chr5D	86.724	934	98	19	2275	3191	442673206	442674130	0.000000e+00	1014
9	TraesCS5B01G145500	chr1B	88.116	934	90	14	2273	3190	216104497	216105425	0.000000e+00	1090
10	TraesCS5B01G145500	chr1D	87.834	937	91	14	2273	3194	289773958	289773030	0.000000e+00	1077
11	TraesCS5B01G145500	chr1D	86.809	940	94	20	2274	3191	37440914	37439983	0.000000e+00	1022
12	TraesCS5B01G145500	chr4D	87.849	930	93	16	2274	3191	375118618	375117697	0.000000e+00	1074
13	TraesCS5B01G145500	chr4D	85.486	937	93	20	2269	3190	335890570	335889662	0.000000e+00	937
14	TraesCS5B01G145500	chr3D	87.781	933	84	14	2274	3191	491992069	491992986	0.000000e+00	1064
15	TraesCS5B01G145500	chr3D	88.346	635	61	7	2273	2897	495167307	495167938	0.000000e+00	750
16	TraesCS5B01G145500	chr3D	80.505	277	35	13	2255	2517	50876306	50876035	9.070000e-46	195
17	TraesCS5B01G145500	chr3B	87.259	934	98	11	2274	3191	548053398	548054326	0.000000e+00	1046
18	TraesCS5B01G145500	chr3B	86.780	938	96	14	2274	3191	652963052	652963981	0.000000e+00	1020
19	TraesCS5B01G145500	chr3B	83.313	809	81	23	2280	3069	668111721	668110948	0.000000e+00	697
20	TraesCS5B01G145500	chr3B	93.939	99	6	0	309	407	182420298	182420200	1.990000e-32	150
21	TraesCS5B01G145500	chr7D	86.887	938	97	20	2272	3191	506498643	506499572	0.000000e+00	1027
22	TraesCS5B01G145500	chr7D	84.854	515	59	7	2274	2780	395294055	395293552	4.770000e-138	501
23	TraesCS5B01G145500	chr7A	87.417	906	83	17	2283	3166	46963651	46962755	0.000000e+00	1013
24	TraesCS5B01G145500	chr7A	85.134	935	99	20	2274	3190	608327067	608326155	0.000000e+00	920
25	TraesCS5B01G145500	chr3A	86.403	934	97	19	2274	3190	523610017	523610937	0.000000e+00	994
26	TraesCS5B01G145500	chr6B	88.608	237	24	3	1064	1300	227837925	227837692	5.230000e-73	285
27	TraesCS5B01G145500	chr6D	88.710	186	19	2	1115	1300	377542240	377542423	3.220000e-55	226

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	TraesCS5B01G145500	chr5B	272676300	272679505	3205	False	5921.0	5921	100.0000	1	3206	1	chr5B.!!$F2	3205
1	TraesCS5B01G145500	chr5B	265435648	265436452	804	False	905.0	905	87.1450	2392	3190	1	chr5B.!!$F1	798
2	TraesCS5B01G145500	chr5B	287428692	287429328	636	True	645.0	645	85.2260	2274	2904	1	chr5B.!!$R1	630
3	TraesCS5B01G145500	chr5A	323369646	323371840	2194	False	1673.5	2451	94.6245	58	2203	2	chr5A.!!$F1	2145
4	TraesCS5B01G145500	chr5D	232402393	232404652	2259	True	1722.5	2423	94.5560	58	2275	2	chr5D.!!$R1	2217
5	TraesCS5B01G145500	chr5D	442673206	442674130	924	False	1014.0	1014	86.7240	2275	3191	1	chr5D.!!$F1	916
6	TraesCS5B01G145500	chr1B	216104497	216105425	928	False	1090.0	1090	88.1160	2273	3190	1	chr1B.!!$F1	917
7	TraesCS5B01G145500	chr1D	289773030	289773958	928	True	1077.0	1077	87.8340	2273	3194	1	chr1D.!!$R2	921
8	TraesCS5B01G145500	chr1D	37439983	37440914	931	True	1022.0	1022	86.8090	2274	3191	1	chr1D.!!$R1	917
9	TraesCS5B01G145500	chr4D	375117697	375118618	921	True	1074.0	1074	87.8490	2274	3191	1	chr4D.!!$R2	917
10	TraesCS5B01G145500	chr4D	335889662	335890570	908	True	937.0	937	85.4860	2269	3190	1	chr4D.!!$R1	921
11	TraesCS5B01G145500	chr3D	491992069	491992986	917	False	1064.0	1064	87.7810	2274	3191	1	chr3D.!!$F1	917
12	TraesCS5B01G145500	chr3D	495167307	495167938	631	False	750.0	750	88.3460	2273	2897	1	chr3D.!!$F2	624
13	TraesCS5B01G145500	chr3B	548053398	548054326	928	False	1046.0	1046	87.2590	2274	3191	1	chr3B.!!$F1	917
14	TraesCS5B01G145500	chr3B	652963052	652963981	929	False	1020.0	1020	86.7800	2274	3191	1	chr3B.!!$F2	917
15	TraesCS5B01G145500	chr3B	668110948	668111721	773	True	697.0	697	83.3130	2280	3069	1	chr3B.!!$R2	789
16	TraesCS5B01G145500	chr7D	506498643	506499572	929	False	1027.0	1027	86.8870	2272	3191	1	chr7D.!!$F1	919
17	TraesCS5B01G145500	chr7D	395293552	395294055	503	True	501.0	501	84.8540	2274	2780	1	chr7D.!!$R1	506
18	TraesCS5B01G145500	chr7A	46962755	46963651	896	True	1013.0	1013	87.4170	2283	3166	1	chr7A.!!$R1	883
19	TraesCS5B01G145500	chr7A	608326155	608327067	912	True	920.0	920	85.1340	2274	3190	1	chr7A.!!$R2	916
20	TraesCS5B01G145500	chr3A	523610017	523610937	920	False	994.0	994	86.4030	2274	3190	1	chr3A.!!$F1	916

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
183	197	0.251165	TCTTTTGCGAAAGGGGGAGG	60.251	55.000	23.38	0.39	42.05	4.30	F
1110	1130	0.671472	CAGGCTTGTCTGCGATGACA	60.671	55.000	6.80	6.80	44.17	3.58	F
1807	1901	1.524961	GATGACCCCGCCATGTACA	59.475	57.895	0.00	0.00	0.00	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1966	2060	0.034896	GTCTGGTGGTGGTCAACGAT	59.965	55.000	35.35	3.73	R
2173	2270	0.382873	CCATCGACGTGACCCGAATA	59.617	55.000	40.70	1.75	R
2829	2957	3.606687	AGACGATGGGGTGTTTTATGTC	58.393	45.455	0.00	3.06	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
18	19	3.384816	TATGATTGTGCTCGCAGGG	57.615	52.632	0.00	0.00	0.00	4.45
19	20	0.815213	TATGATTGTGCTCGCAGGGC	60.815	55.000	0.00	0.00	0.00	5.19
20	21	2.437359	GATTGTGCTCGCAGGGCT	60.437	61.111	2.27	0.00	0.00	5.19
21	22	1.153369	GATTGTGCTCGCAGGGCTA	60.153	57.895	2.27	0.00	0.00	3.93
22	23	1.153289	ATTGTGCTCGCAGGGCTAG	60.153	57.895	2.27	0.00	0.00	3.42
23	24	3.958147	TTGTGCTCGCAGGGCTAGC	62.958	63.158	6.04	6.04	45.59	3.42
24	25	4.154347	GTGCTCGCAGGGCTAGCT	62.154	66.667	15.72	0.00	45.59	3.32
25	26	2.442087	TGCTCGCAGGGCTAGCTA	60.442	61.111	15.72	0.00	45.59	3.32
26	27	2.338257	GCTCGCAGGGCTAGCTAG	59.662	66.667	16.84	16.84	42.76	3.42
27	28	3.857109	GCTCGCAGGGCTAGCTAGC	62.857	68.421	33.40	33.40	42.76	3.42
36	37	2.051105	GCTAGCTAGCTACCCCACC	58.949	63.158	33.71	6.02	45.62	4.61
37	38	0.759436	GCTAGCTAGCTACCCCACCA	60.759	60.000	33.71	0.00	45.62	4.17
38	39	1.789523	CTAGCTAGCTACCCCACCAA	58.210	55.000	20.67	0.00	0.00	3.67
39	40	2.330216	CTAGCTAGCTACCCCACCAAT	58.670	52.381	20.67	0.00	0.00	3.16
40	41	2.489528	AGCTAGCTACCCCACCAATA	57.510	50.000	17.69	0.00	0.00	1.90
41	42	2.991580	AGCTAGCTACCCCACCAATAT	58.008	47.619	17.69	0.00	0.00	1.28
42	43	3.327439	AGCTAGCTACCCCACCAATATT	58.673	45.455	17.69	0.00	0.00	1.28
43	44	3.722101	AGCTAGCTACCCCACCAATATTT	59.278	43.478	17.69	0.00	0.00	1.40
44	45	4.072839	GCTAGCTACCCCACCAATATTTC	58.927	47.826	7.70	0.00	0.00	2.17
45	46	3.208747	AGCTACCCCACCAATATTTCG	57.791	47.619	0.00	0.00	0.00	3.46
46	47	1.607148	GCTACCCCACCAATATTTCGC	59.393	52.381	0.00	0.00	0.00	4.70
47	48	2.227194	CTACCCCACCAATATTTCGCC	58.773	52.381	0.00	0.00	0.00	5.54
48	49	0.333312	ACCCCACCAATATTTCGCCA	59.667	50.000	0.00	0.00	0.00	5.69
49	50	1.272760	ACCCCACCAATATTTCGCCAA	60.273	47.619	0.00	0.00	0.00	4.52
50	51	1.827969	CCCCACCAATATTTCGCCAAA	59.172	47.619	0.00	0.00	0.00	3.28
51	52	2.234908	CCCCACCAATATTTCGCCAAAA	59.765	45.455	0.00	0.00	0.00	2.44
52	53	3.307059	CCCCACCAATATTTCGCCAAAAA	60.307	43.478	0.00	0.00	0.00	1.94
75	76	2.282110	TGTCCCACCCAATGCACG	60.282	61.111	0.00	0.00	0.00	5.34
182	196	1.616159	TTCTTTTGCGAAAGGGGGAG	58.384	50.000	23.38	0.76	42.05	4.30
183	197	0.251165	TCTTTTGCGAAAGGGGGAGG	60.251	55.000	23.38	0.39	42.05	4.30
204	218	1.529244	GGCAGGTATCCCATGGTGC	60.529	63.158	11.73	12.48	0.00	5.01
223	237	1.369625	CTATCCACGGTGTTTGCTCC	58.630	55.000	7.45	0.00	0.00	4.70
240	254	9.982651	TGTTTGCTCCTTCATATAGTACTATTC	57.017	33.333	20.21	1.28	0.00	1.75
263	278	6.540995	TCTATACCGACTTATTGCTAGTCCT	58.459	40.000	0.00	0.00	39.03	3.85
268	283	1.831736	ACTTATTGCTAGTCCTGGCGT	59.168	47.619	0.00	0.00	40.17	5.68
363	378	1.084289	GGCTCGCAGTTTAATCCGTT	58.916	50.000	0.00	0.00	0.00	4.44
529	544	1.393539	CTTACATTTGGCACGACCGAG	59.606	52.381	0.00	0.00	43.94	4.63
583	598	0.845337	TGGAGCATGGCCACATATGA	59.155	50.000	8.16	0.00	34.99	2.15
652	667	1.014044	ACTAACGTGCGTGCATGAGG	61.014	55.000	20.13	11.25	36.80	3.86
653	668	2.296692	CTAACGTGCGTGCATGAGGC	62.297	60.000	20.13	2.41	45.13	4.70
763	782	4.597404	TGACCATGCACTCATAGAGATC	57.403	45.455	0.31	0.00	33.32	2.75
790	809	2.890474	CCGTGCTGCCGATGTACC	60.890	66.667	11.24	0.00	0.00	3.34
817	836	4.269123	TGTGTATGTGTCAGTCGTTTTGTC	59.731	41.667	0.00	0.00	0.00	3.18
818	837	3.805422	TGTATGTGTCAGTCGTTTTGTCC	59.195	43.478	0.00	0.00	0.00	4.02
830	849	2.605338	CGTTTTGTCCAGTTGCCATCTG	60.605	50.000	0.00	0.00	0.00	2.90
914	933	9.845740	TGCAGCTGATTTTATAACTTATAAGGA	57.154	29.630	20.43	4.75	32.67	3.36
971	990	1.035139	CGCGGTTACATAGGGGTACT	58.965	55.000	0.00	0.00	0.00	2.73
1002	1022	1.287815	CCGTGGACGCACAGTTAGA	59.712	57.895	0.00	0.00	38.18	2.10
1106	1126	1.078848	GTCCAGGCTTGTCTGCGAT	60.079	57.895	0.00	0.00	33.64	4.58
1110	1130	0.671472	CAGGCTTGTCTGCGATGACA	60.671	55.000	6.80	6.80	44.17	3.58
1151	1171	2.683465	GGAGATGGCCAGGGAGCAA	61.683	63.158	13.05	0.00	0.00	3.91
1319	1339	5.007332	CGATCATTCTCAAGTTGATGATGCA	59.993	40.000	20.11	11.43	30.48	3.96
1373	1393	2.750166	GAGAGTCAGGAAGATCGTCACA	59.250	50.000	10.88	0.00	0.00	3.58
1395	1415	2.282958	ACGGAGAGAAGGACGGCA	60.283	61.111	0.00	0.00	0.00	5.69
1457	1477	3.273434	GTGAGGAGCACTGCATATTTGA	58.727	45.455	3.30	0.00	44.27	2.69
1586	1610	2.301346	CACCAATGGAGGAAGTATGGC	58.699	52.381	6.16	0.00	0.00	4.40
1625	1649	3.009723	CACAAAGCACCCTAGGTACATG	58.990	50.000	8.29	1.69	32.11	3.21
1807	1901	1.524961	GATGACCCCGCCATGTACA	59.475	57.895	0.00	0.00	0.00	2.90
1935	2029	2.281070	CGGAGCAACAGCCAGTGT	60.281	61.111	0.00	0.00	43.24	3.55
1966	2060	4.459337	TCTCAGTGACTTGCTCTTCGATTA	59.541	41.667	0.00	0.00	0.00	1.75
1987	2081	1.597027	GTTGACCACCACCAGACGG	60.597	63.158	0.00	0.00	38.77	4.79
2167	2264	4.243007	CAAAAGTTTGGAGGCTGGTAAG	57.757	45.455	0.00	0.00	34.59	2.34
2172	2269	4.844884	AGTTTGGAGGCTGGTAAGAATAC	58.155	43.478	0.00	0.00	0.00	1.89
2173	2270	4.536489	AGTTTGGAGGCTGGTAAGAATACT	59.464	41.667	0.00	0.00	32.36	2.12
2180	2277	4.283722	AGGCTGGTAAGAATACTATTCGGG	59.716	45.833	3.58	0.00	32.36	5.14
2309	2407	0.844660	GCTCCCTAGGGGTAAAAGGG	59.155	60.000	28.19	0.62	44.74	3.95
2314	2412	2.136026	CCTAGGGGTAAAAGGGCTCAT	58.864	52.381	0.00	0.00	0.00	2.90
2331	2429	5.827797	GGGCTCATAATCAATTGAGGTGTTA	59.172	40.000	14.54	7.87	39.79	2.41
2381	2480	6.097554	TGGCCAAGTTAACAATTTCTCAAAGA	59.902	34.615	0.61	0.00	0.00	2.52
2393	2502	9.075678	ACAATTTCTCAAAGATCTCACTCAATT	57.924	29.630	0.00	0.00	0.00	2.32
2396	2507	8.915057	TTTCTCAAAGATCTCACTCAATTCTT	57.085	30.769	0.00	0.00	0.00	2.52
2425	2536	8.956426	CACTATGCTTCCTAATTTTTAAGTCCA	58.044	33.333	0.00	0.00	0.00	4.02
2493	2606	7.880160	TTTGATCGGGTCAATAATTTCTCAT	57.120	32.000	4.24	0.00	45.77	2.90
2517	2631	6.346477	GGAGCCCTCCCATTTAATTATTTC	57.654	41.667	2.81	0.00	43.94	2.17
2599	2715	8.682128	TGAATTTGGTTTACTATTTTGATCGC	57.318	30.769	0.00	0.00	0.00	4.58
2635	2752	4.522405	TCAAATCAATCAACACCAACCGAT	59.478	37.500	0.00	0.00	0.00	4.18
2777	2903	6.092122	TCACAAAAGTATGAGTTGATTAGCGG	59.908	38.462	0.00	0.00	0.00	5.52
2792	2918	7.015226	TGATTAGCGGATAACACAAAATCAG	57.985	36.000	0.00	0.00	30.79	2.90
2806	2932	5.047092	CACAAAATCAGACCATAAAAGGCCT	60.047	40.000	0.00	0.00	0.00	5.19
2818	2945	6.900743	ACCATAAAAGGCCTACAAATAACCAT	59.099	34.615	5.16	0.00	0.00	3.55
2847	2976	6.693315	AAATAGACATAAAACACCCCATCG	57.307	37.500	0.00	0.00	0.00	3.84
2848	2977	3.713826	AGACATAAAACACCCCATCGT	57.286	42.857	0.00	0.00	0.00	3.73
2849	2978	3.606687	AGACATAAAACACCCCATCGTC	58.393	45.455	0.00	0.00	0.00	4.20
2882	3012	4.513692	CCGCCAAACTAAATATTCCATCGA	59.486	41.667	0.00	0.00	0.00	3.59
2945	3085	9.581099	GTCAAATTTCTTTAACTTTGACCAAGA	57.419	29.630	16.82	0.00	45.88	3.02
3040	3188	7.892445	AATAACACAAATTCGATATTGCGAC	57.108	32.000	9.81	0.00	40.42	5.19
3098	3249	4.406648	AAGAGGTTGGGCTTTTCAAAAG	57.593	40.909	5.43	5.43	0.00	2.27
3109	3262	6.775629	TGGGCTTTTCAAAAGAGTAATACACT	59.224	34.615	14.39	0.00	41.47	3.55
3193	3356	2.682858	GCGCCCAACCCTTCTAGTATTT	60.683	50.000	0.00	0.00	0.00	1.40
3194	3357	3.617284	CGCCCAACCCTTCTAGTATTTT	58.383	45.455	0.00	0.00	0.00	1.82
3195	3358	4.773013	CGCCCAACCCTTCTAGTATTTTA	58.227	43.478	0.00	0.00	0.00	1.52
3196	3359	4.814771	CGCCCAACCCTTCTAGTATTTTAG	59.185	45.833	0.00	0.00	0.00	1.85
3197	3360	5.628433	CGCCCAACCCTTCTAGTATTTTAGT	60.628	44.000	0.00	0.00	0.00	2.24
3198	3361	6.407299	CGCCCAACCCTTCTAGTATTTTAGTA	60.407	42.308	0.00	0.00	0.00	1.82
3199	3362	7.515586	GCCCAACCCTTCTAGTATTTTAGTAT	58.484	38.462	0.00	0.00	0.00	2.12
3200	3363	7.444487	GCCCAACCCTTCTAGTATTTTAGTATG	59.556	40.741	0.00	0.00	0.00	2.39
3201	3364	7.937394	CCCAACCCTTCTAGTATTTTAGTATGG	59.063	40.741	0.00	0.00	0.00	2.74
3202	3365	8.711170	CCAACCCTTCTAGTATTTTAGTATGGA	58.289	37.037	0.00	0.00	0.00	3.41
3203	3366	9.543783	CAACCCTTCTAGTATTTTAGTATGGAC	57.456	37.037	0.00	0.00	0.00	4.02
3204	3367	8.260099	ACCCTTCTAGTATTTTAGTATGGACC	57.740	38.462	0.00	0.00	0.00	4.46
3205	3368	7.847848	ACCCTTCTAGTATTTTAGTATGGACCA	59.152	37.037	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.815213	GCCCTGCGAGCACAATCATA	60.815	55.000	0.00	0.00	0.00	2.15
1	2	2.117156	GCCCTGCGAGCACAATCAT	61.117	57.895	0.00	0.00	0.00	2.45
2	3	1.898330	TAGCCCTGCGAGCACAATCA	61.898	55.000	0.00	0.00	0.00	2.57
3	4	1.153369	TAGCCCTGCGAGCACAATC	60.153	57.895	0.00	0.00	0.00	2.67
4	5	1.153289	CTAGCCCTGCGAGCACAAT	60.153	57.895	0.00	0.00	0.00	2.71
5	6	2.265739	CTAGCCCTGCGAGCACAA	59.734	61.111	0.00	0.00	0.00	3.33
10	11	2.338257	GCTAGCTAGCCCTGCGAG	59.662	66.667	31.67	1.95	43.39	5.03
19	20	1.789523	TTGGTGGGGTAGCTAGCTAG	58.210	55.000	24.78	16.84	0.00	3.42
20	21	2.489528	ATTGGTGGGGTAGCTAGCTA	57.510	50.000	20.67	20.67	0.00	3.32
21	22	2.489528	TATTGGTGGGGTAGCTAGCT	57.510	50.000	23.12	23.12	0.00	3.32
22	23	3.790089	AATATTGGTGGGGTAGCTAGC	57.210	47.619	14.67	14.67	0.00	3.42
23	24	4.315803	CGAAATATTGGTGGGGTAGCTAG	58.684	47.826	0.00	0.00	0.00	3.42
24	25	3.495453	GCGAAATATTGGTGGGGTAGCTA	60.495	47.826	0.00	0.00	0.00	3.32
25	26	2.748465	GCGAAATATTGGTGGGGTAGCT	60.748	50.000	0.00	0.00	0.00	3.32
26	27	1.607148	GCGAAATATTGGTGGGGTAGC	59.393	52.381	0.00	0.00	0.00	3.58
27	28	2.227194	GGCGAAATATTGGTGGGGTAG	58.773	52.381	0.00	0.00	0.00	3.18
28	29	1.564818	TGGCGAAATATTGGTGGGGTA	59.435	47.619	0.00	0.00	0.00	3.69
29	30	0.333312	TGGCGAAATATTGGTGGGGT	59.667	50.000	0.00	0.00	0.00	4.95
30	31	1.479709	TTGGCGAAATATTGGTGGGG	58.520	50.000	0.00	0.00	0.00	4.96
31	32	3.601443	TTTTGGCGAAATATTGGTGGG	57.399	42.857	0.00	0.00	0.00	4.61
52	53	1.416030	GCATTGGGTGGGACAGTTTTT	59.584	47.619	0.00	0.00	41.80	1.94
53	54	1.047801	GCATTGGGTGGGACAGTTTT	58.952	50.000	0.00	0.00	41.80	2.43
54	55	0.105760	TGCATTGGGTGGGACAGTTT	60.106	50.000	0.00	0.00	41.80	2.66
55	56	0.827507	GTGCATTGGGTGGGACAGTT	60.828	55.000	0.00	0.00	41.80	3.16
56	57	1.228552	GTGCATTGGGTGGGACAGT	60.229	57.895	0.00	0.00	41.80	3.55
69	70	0.314935	CTTTTTCACCTGGCGTGCAT	59.685	50.000	0.00	0.00	42.69	3.96
75	76	3.219281	TGTAGGTTCTTTTTCACCTGGC	58.781	45.455	0.89	0.00	43.68	4.85
198	212	0.618458	AACACCGTGGATAGCACCAT	59.382	50.000	3.03	0.00	42.17	3.55
204	218	1.066143	AGGAGCAAACACCGTGGATAG	60.066	52.381	3.03	0.00	0.00	2.08
240	254	6.349445	CCAGGACTAGCAATAAGTCGGTATAG	60.349	46.154	0.00	0.00	43.55	1.31
251	265	2.621998	GACTACGCCAGGACTAGCAATA	59.378	50.000	0.00	0.00	0.00	1.90
263	278	5.847111	ATCTAAGTACATTGACTACGCCA	57.153	39.130	0.00	0.00	0.00	5.69
349	364	4.270084	TGATCGATCAACGGATTAAACTGC	59.730	41.667	25.44	0.00	42.82	4.40
384	399	6.056428	ACACGTTTACATGTTCCTTCTTTC	57.944	37.500	2.30	0.00	0.00	2.62
529	544	3.394635	TAAAGTCCCATCGGCGCCC	62.395	63.158	23.46	4.36	0.00	6.13
534	549	4.337274	GGTAAAATGGTAAAGTCCCATCGG	59.663	45.833	0.00	0.00	41.87	4.18
583	598	1.623311	TCACCACAATCTCGTCACCAT	59.377	47.619	0.00	0.00	0.00	3.55
652	667	6.074005	GTGCTCAAGAGTTAATTATATGCGC	58.926	40.000	0.00	0.00	0.00	6.09
653	668	6.143919	TCGTGCTCAAGAGTTAATTATATGCG	59.856	38.462	0.00	0.00	0.00	4.73
763	782	1.139163	GGCAGCACGGTTTTGATTTG	58.861	50.000	0.00	0.00	0.00	2.32
790	809	2.185262	CGACTGACACATACACATCGG	58.815	52.381	0.00	0.00	0.00	4.18
817	836	3.304257	GCGATAATTCAGATGGCAACTGG	60.304	47.826	22.46	7.58	36.22	4.00
818	837	3.313249	TGCGATAATTCAGATGGCAACTG	59.687	43.478	17.76	17.76	35.43	3.16
830	849	3.185188	ACATCGAGCACATGCGATAATTC	59.815	43.478	5.76	0.00	44.56	2.17
914	933	3.328505	GCCACTTGCACATAAAATTGCT	58.671	40.909	0.00	0.00	39.62	3.91
971	990	6.206438	TGTGCGTCCACGGTTTAGTATATATA	59.794	38.462	0.55	0.00	45.04	0.86
1002	1022	5.534278	TCGATCTCAGAGTCAGATTAAGCAT	59.466	40.000	0.00	0.00	30.30	3.79
1151	1171	3.005539	AGCTGCGTCACCAGGGAT	61.006	61.111	0.00	0.00	33.44	3.85
1373	1393	0.961358	CGTCCTTCTCTCCGTCACCT	60.961	60.000	0.00	0.00	0.00	4.00
1395	1415	0.258774	AGGGGCTTGGCATTATCGTT	59.741	50.000	0.00	0.00	0.00	3.85
1400	1420	1.752694	GCGAAGGGGCTTGGCATTA	60.753	57.895	0.00	0.00	43.04	1.90
1586	1610	3.678289	TGTGTGGTTGATGATCTTCTGG	58.322	45.455	9.75	0.00	0.00	3.86
1625	1649	8.673626	TTTTGCATTTCGATTTGTAATCTCTC	57.326	30.769	0.00	0.00	0.00	3.20
1740	1834	3.786809	CACCGTCTTCGTTGCTCTA	57.213	52.632	0.00	0.00	35.01	2.43
1966	2060	0.034896	GTCTGGTGGTGGTCAACGAT	59.965	55.000	0.00	0.00	35.35	3.73
2124	2221	1.149174	CCCATGCCCGCTTACATCT	59.851	57.895	0.00	0.00	0.00	2.90
2167	2264	3.002656	TCGACGTGACCCGAATAGTATTC	59.997	47.826	12.18	12.18	40.70	1.75
2172	2269	1.599667	CCATCGACGTGACCCGAATAG	60.600	57.143	0.00	0.00	40.70	1.73
2173	2270	0.382873	CCATCGACGTGACCCGAATA	59.617	55.000	0.00	0.00	40.70	1.75
2180	2277	2.279582	AACTCATCCATCGACGTGAC	57.720	50.000	0.00	0.00	0.00	3.67
2309	2407	9.807649	AATTTAACACCTCAATTGATTATGAGC	57.192	29.630	8.96	0.00	41.36	4.26
2358	2457	8.084684	AGATCTTTGAGAAATTGTTAACTTGGC	58.915	33.333	7.22	0.00	0.00	4.52
2365	2464	9.559732	TTGAGTGAGATCTTTGAGAAATTGTTA	57.440	29.630	0.00	0.00	0.00	2.41
2381	2480	8.263640	AGCATAGTGTAAAGAATTGAGTGAGAT	58.736	33.333	0.00	0.00	0.00	2.75
2387	2486	7.856145	AGGAAGCATAGTGTAAAGAATTGAG	57.144	36.000	0.00	0.00	0.00	3.02
2425	2536	7.696992	AACCGAATACCTCAATTAATTGTGT	57.303	32.000	23.95	22.40	38.84	3.72
2535	2650	9.559958	TCAATCGAATAAAAGAGCTTCAAAATC	57.440	29.630	0.00	0.00	0.00	2.17
2599	2715	7.319227	TGATTGATTTGAAAAATCGTTGACG	57.681	32.000	7.90	0.00	41.45	4.35
2635	2752	6.708949	GCACGGGGTTGATATATTTTTCTAGA	59.291	38.462	0.00	0.00	0.00	2.43
2689	2813	7.251281	GTGCTATAGTATCATCACATAGCGAA	58.749	38.462	0.84	0.00	44.48	4.70
2777	2903	9.573133	CCTTTTATGGTCTGATTTTGTGTTATC	57.427	33.333	0.00	0.00	0.00	1.75
2792	2918	6.378848	TGGTTATTTGTAGGCCTTTTATGGTC	59.621	38.462	12.58	0.00	0.00	4.02
2829	2957	3.606687	AGACGATGGGGTGTTTTATGTC	58.393	45.455	0.00	0.00	0.00	3.06
2945	3085	5.769662	TGGATGCGATATTTTTGGCTCTAAT	59.230	36.000	0.00	0.00	0.00	1.73
3066	3215	4.524328	AGCCCAACCTCTTTAAGTTTCATG	59.476	41.667	0.00	0.00	0.00	3.07
3069	3218	5.531122	AAAGCCCAACCTCTTTAAGTTTC	57.469	39.130	0.00	0.00	31.39	2.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.