AutoCloner

Multiple sequence alignment - TraesCS6A01G154900

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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	TraesCS6A01G154900	chr6A	100.000	4228	0	0	1	4228	143701112	143696885	0.000000e+00	7808.0
1	TraesCS6A01G154900	chr6A	87.931	58	7	0	415	472	344180757	344180814	7.590000e-08	69.4
2	TraesCS6A01G154900	chr6D	95.496	3397	94	25	425	3809	115317081	115313732	0.000000e+00	5371.0
3	TraesCS6A01G154900	chr6D	88.021	384	21	5	1	384	115317784	115317426	8.400000e-117	431.0
4	TraesCS6A01G154900	chr6D	78.428	649	83	25	3596	4224	22141306	22141917	1.860000e-98	370.0
5	TraesCS6A01G154900	chr6D	77.559	508	90	19	3596	4086	445059301	445058801	6.920000e-73	285.0
6	TraesCS6A01G154900	chr6D	89.091	55	6	0	418	472	251240182	251240128	7.590000e-08	69.4
7	TraesCS6A01G154900	chr6B	95.446	3096	82	21	621	3684	204604184	204601116	0.000000e+00	4881.0
8	TraesCS6A01G154900	chr6B	88.390	267	25	2	438	704	204605946	204605686	2.450000e-82	316.0
9	TraesCS6A01G154900	chr6B	85.656	244	27	2	388	624	204604505	204604263	2.520000e-62	250.0
10	TraesCS6A01G154900	chr6B	75.764	491	109	9	3593	4077	516473880	516474366	5.460000e-59	239.0
11	TraesCS6A01G154900	chr6B	74.873	394	83	14	3593	3980	73180150	73180533	9.400000e-37	165.0
12	TraesCS6A01G154900	chr6B	87.273	55	7	0	418	472	326971640	326971694	3.530000e-06	63.9
13	TraesCS6A01G154900	chr6B	88.636	44	4	1	408	450	648844598	648844555	8.000000e-03	52.8
14	TraesCS6A01G154900	chr6B	88.636	44	4	1	408	450	648880836	648880793	8.000000e-03	52.8
15	TraesCS6A01G154900	chr3D	81.186	590	93	4	3597	4168	273383324	273382735	3.850000e-125	459.0
16	TraesCS6A01G154900	chr3D	76.029	413	76	18	3596	3990	69664496	69664903	4.310000e-45	193.0
17	TraesCS6A01G154900	chr3D	73.210	433	93	16	3596	4018	595284114	595284533	7.370000e-28	135.0
18	TraesCS6A01G154900	chr2A	79.939	653	96	16	3596	4225	433356071	433356711	8.340000e-122	448.0
19	TraesCS6A01G154900	chr2A	82.661	248	34	6	3751	3990	18904737	18904983	1.190000e-50	211.0
20	TraesCS6A01G154900	chr2A	85.075	134	14	6	73	204	20026877	20027006	9.540000e-27	132.0
21	TraesCS6A01G154900	chr7D	78.812	623	96	12	3592	4194	89289187	89288581	1.840000e-103	387.0
22	TraesCS6A01G154900	chr7D	82.338	385	67	1	1	384	63376153	63375769	2.440000e-87	333.0
23	TraesCS6A01G154900	chr7D	82.500	320	48	5	2194	2509	587156779	587156464	1.500000e-69	274.0
24	TraesCS6A01G154900	chr7D	74.247	299	75	2	1414	1711	587160125	587159828	1.600000e-24	124.0
25	TraesCS6A01G154900	chr7D	81.119	143	23	3	1	141	170732469	170732329	1.240000e-20	111.0
26	TraesCS6A01G154900	chr7B	84.238	387	58	3	1	385	3694145	3693760	1.440000e-99	374.0
27	TraesCS6A01G154900	chr7B	82.390	318	52	2	2194	2509	658282799	658282484	1.500000e-69	274.0
28	TraesCS6A01G154900	chr7B	75.354	495	101	21	3593	4077	683974488	683974971	7.120000e-53	219.0
29	TraesCS6A01G154900	chr7B	75.667	300	69	4	1414	1711	658292878	658292581	3.410000e-31	147.0
30	TraesCS6A01G154900	chr3A	77.686	484	89	19	3596	4068	147811357	147810882	1.160000e-70	278.0
31	TraesCS6A01G154900	chr7A	82.500	320	48	5	2194	2509	679054155	679053840	1.500000e-69	274.0
32	TraesCS6A01G154900	chr7A	74.582	299	74	2	1414	1711	679060542	679060245	3.430000e-26	130.0
33	TraesCS6A01G154900	chr1D	75.732	478	101	14	3596	4064	457045991	457046462	4.250000e-55	226.0
34	TraesCS6A01G154900	chr3B	73.931	491	115	12	3604	4086	755166182	755166667	7.220000e-43	185.0
35	TraesCS6A01G154900	chrUn	85.075	134	14	6	73	204	310917204	310917333	9.540000e-27	132.0
36	TraesCS6A01G154900	chr4D	75.248	202	42	8	1	199	295012037	295011841	5.820000e-14	89.8
37	TraesCS6A01G154900	chr5B	100.000	28	0	0	423	450	272429621	272429594	8.000000e-03	52.8

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	TraesCS6A01G154900	chr6A	143696885	143701112	4227	True	7808.000000	7808	100.000000	1	4228	1	chr6A.!!$R1	4227
1	TraesCS6A01G154900	chr6D	115313732	115317784	4052	True	2901.000000	5371	91.758500	1	3809	2	chr6D.!!$R3	3808
2	TraesCS6A01G154900	chr6D	22141306	22141917	611	False	370.000000	370	78.428000	3596	4224	1	chr6D.!!$F1	628
3	TraesCS6A01G154900	chr6D	445058801	445059301	500	True	285.000000	285	77.559000	3596	4086	1	chr6D.!!$R2	490
4	TraesCS6A01G154900	chr6B	204601116	204605946	4830	True	1815.666667	4881	89.830667	388	3684	3	chr6B.!!$R3	3296
5	TraesCS6A01G154900	chr3D	273382735	273383324	589	True	459.000000	459	81.186000	3597	4168	1	chr3D.!!$R1	571
6	TraesCS6A01G154900	chr2A	433356071	433356711	640	False	448.000000	448	79.939000	3596	4225	1	chr2A.!!$F3	629
7	TraesCS6A01G154900	chr7D	89288581	89289187	606	True	387.000000	387	78.812000	3592	4194	1	chr7D.!!$R2	602

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
275	276	0.759959	ATCAGGGCAGATCAGAGCAG	59.240	55.0	0.00	0.00	0.00	4.24	F
331	332	1.388837	GGAACCACCGCAACACCTTT	61.389	55.0	0.00	0.00	0.00	3.11	F
1761	2931	0.321298	TGTAAAAGGAGCGCCAGACC	60.321	55.0	9.88	2.72	36.29	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1745	2893	0.690762	TTAGGTCTGGCGCTCCTTTT	59.309	50.0	7.64	0.00	33.34	2.27	R
2287	3460	1.403972	GAAGCGTCGCCTTGTACGAG	61.404	60.0	14.86	2.78	41.55	4.18	R
3443	4616	0.397114	GGATTCCATCAACCACCCCC	60.397	60.0	0.00	0.00	0.00	5.40	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
17	18	4.771127	GAAGGAGCACGACACCAA	57.229	55.556	0.00	0.00	0.00	3.67
57	58	3.507162	TTGAGGGAACATCAGCTTTCA	57.493	42.857	0.00	0.00	0.00	2.69
65	66	4.333926	GGAACATCAGCTTTCACCATAGTC	59.666	45.833	0.00	0.00	0.00	2.59
208	209	2.825836	GCCAGATCTGCCAACCGG	60.826	66.667	17.76	0.00	0.00	5.28
232	233	1.568025	GGAAACGACGACAACAGCC	59.432	57.895	0.00	0.00	0.00	4.85
233	234	1.200839	GAAACGACGACAACAGCCG	59.799	57.895	0.00	0.00	0.00	5.52
234	235	2.743871	GAAACGACGACAACAGCCGC	62.744	60.000	0.00	0.00	0.00	6.53
275	276	0.759959	ATCAGGGCAGATCAGAGCAG	59.240	55.000	0.00	0.00	0.00	4.24
331	332	1.388837	GGAACCACCGCAACACCTTT	61.389	55.000	0.00	0.00	0.00	3.11
381	382	3.971702	GGAAGGCTGCCCACCAGT	61.972	66.667	16.57	0.00	43.71	4.00
403	1458	7.220030	CAGTGCTATAAACTGGATAGAACCAT	58.780	38.462	7.16	0.00	41.13	3.55
404	1459	7.172190	CAGTGCTATAAACTGGATAGAACCATG	59.828	40.741	7.16	0.00	41.13	3.66
410	1465	3.118531	ACTGGATAGAACCATGAGCCTT	58.881	45.455	0.00	0.00	39.34	4.35
416	1471	3.446442	AGAACCATGAGCCTTGTTGAT	57.554	42.857	0.00	0.00	0.00	2.57
417	1472	4.574674	AGAACCATGAGCCTTGTTGATA	57.425	40.909	0.00	0.00	0.00	2.15
455	1517	6.490381	TGGTCTCATATGACTTTACTATCGCT	59.510	38.462	0.00	0.00	37.16	4.93
459	1521	7.883833	TCTCATATGACTTTACTATCGCTACCT	59.116	37.037	0.00	0.00	0.00	3.08
503	1565	5.221106	CCGGATGTCATTCATTATGCTTTGT	60.221	40.000	0.00	0.00	36.83	2.83
569	1631	5.112686	AGATAGGCAAAAACGCTAAGAGAG	58.887	41.667	0.00	0.00	0.00	3.20
615	1677	5.395768	CCTGCTCTAGCTTACAAGTAACCAT	60.396	44.000	3.26	0.00	42.66	3.55
751	1895	3.478274	CCCCTCAGGCCTCAGCTC	61.478	72.222	0.00	0.00	39.73	4.09
752	1896	2.686470	CCCTCAGGCCTCAGCTCA	60.686	66.667	0.00	0.00	39.73	4.26
753	1897	2.733669	CCCTCAGGCCTCAGCTCAG	61.734	68.421	0.00	0.00	39.73	3.35
754	1898	2.733669	CCTCAGGCCTCAGCTCAGG	61.734	68.421	0.00	0.00	39.73	3.86
1055	2203	2.943034	CTTCTACGTCGCCGTCGC	60.943	66.667	0.00	0.00	46.28	5.19
1104	2252	4.849329	GTCCTCGTCGCGGCGATT	62.849	66.667	37.30	0.00	40.29	3.34
1125	2273	2.580601	CGGGGACAAGACGGAAGGT	61.581	63.158	0.00	0.00	0.00	3.50
1363	2511	3.362399	CTCCGCGTCATCAGCCTGT	62.362	63.158	4.92	0.00	0.00	4.00
1748	2896	9.932699	CAAATCAGAATGTTTTGCAATGTAAAA	57.067	25.926	5.16	5.16	45.32	1.52
1757	2927	0.525761	GCAATGTAAAAGGAGCGCCA	59.474	50.000	9.88	0.00	36.29	5.69
1761	2931	0.321298	TGTAAAAGGAGCGCCAGACC	60.321	55.000	9.88	2.72	36.29	3.85
1931	3101	1.284491	TGCCCACCTTCATGAGCATTA	59.716	47.619	1.25	0.00	0.00	1.90
2124	3294	2.590007	CATCAGCCAGGCTACCGC	60.590	66.667	15.64	0.00	36.40	5.68
2287	3460	4.699522	AGCGGCAACTTCGGGTCC	62.700	66.667	1.45	0.00	0.00	4.46
2305	3478	1.443872	CTCGTACAAGGCGACGCTT	60.444	57.895	20.77	9.77	38.93	4.68
2479	3652	3.118775	TCCTCATCACCGATTTCGTGATT	60.119	43.478	12.25	1.50	37.71	2.57
2541	3714	6.645790	AAGTCAAATCTTCACTTTCTGCAT	57.354	33.333	0.00	0.00	0.00	3.96
2556	3729	6.717084	ACTTTCTGCATCATCATCATCATCAT	59.283	34.615	0.00	0.00	0.00	2.45
2557	3730	6.743575	TTCTGCATCATCATCATCATCATC	57.256	37.500	0.00	0.00	0.00	2.92
2558	3731	5.804639	TCTGCATCATCATCATCATCATCA	58.195	37.500	0.00	0.00	0.00	3.07
2559	3732	6.418101	TCTGCATCATCATCATCATCATCAT	58.582	36.000	0.00	0.00	0.00	2.45
2560	3733	6.540189	TCTGCATCATCATCATCATCATCATC	59.460	38.462	0.00	0.00	0.00	2.92
2561	3734	6.179756	TGCATCATCATCATCATCATCATCA	58.820	36.000	0.00	0.00	0.00	3.07
2607	3780	6.404074	GGAAGCTGACTGAGATTTTGTTATGG	60.404	42.308	0.00	0.00	27.54	2.74
3252	4425	2.095263	CGATCGGGCAAACAAGTTCAAT	60.095	45.455	7.38	0.00	0.00	2.57
3257	4430	4.279671	TCGGGCAAACAAGTTCAATACAAT	59.720	37.500	0.00	0.00	0.00	2.71
3260	4433	4.929211	GGCAAACAAGTTCAATACAATCCC	59.071	41.667	0.00	0.00	0.00	3.85
3356	4529	0.033796	ATGGCATGGTGGAACTCTGG	60.034	55.000	0.00	0.00	36.74	3.86
3443	4616	5.991328	AGAACATATGTACATTTGAGCCG	57.009	39.130	26.71	6.25	0.00	5.52
3581	4755	6.273071	AGTACATTGGTTCTTGCTTGTTTTC	58.727	36.000	0.00	0.00	0.00	2.29
3650	4830	9.050601	CATTCATTGATAGAAGGAGTTAGAACC	57.949	37.037	0.00	0.00	0.00	3.62
3661	4841	8.877195	AGAAGGAGTTAGAACCAGTACAAATAA	58.123	33.333	0.00	0.00	0.00	1.40
3684	4865	2.353269	GGAACATCACACAACACGAACA	59.647	45.455	0.00	0.00	0.00	3.18
3702	4883	2.991250	ACACAAGGAGGCATGTACATC	58.009	47.619	5.07	1.16	0.00	3.06
3725	4906	3.009723	CACCCGAAGCACAAAGATATGT	58.990	45.455	0.00	0.00	0.00	2.29
3736	4918	3.136763	CAAAGATATGTGATGCTCCGCT	58.863	45.455	0.00	0.00	0.00	5.52
3773	4956	2.428890	CACAACTAAACCCACAAAGCCA	59.571	45.455	0.00	0.00	0.00	4.75
3781	4964	0.248866	CCCACAAAGCCACGAACAAC	60.249	55.000	0.00	0.00	0.00	3.32
3803	4987	2.808543	AGAAGCAGATCGAACCAACAAC	59.191	45.455	0.00	0.00	0.00	3.32
3805	4989	2.783135	AGCAGATCGAACCAACAACAT	58.217	42.857	0.00	0.00	0.00	2.71
3817	5001	2.551887	CCAACAACATGTCCAACATCGA	59.448	45.455	0.00	0.00	36.53	3.59
4005	5191	1.664649	CACATGCGAGTGTCACCGT	60.665	57.895	13.14	0.00	34.83	4.83
4009	5195	2.661866	GCGAGTGTCACCGTTGCT	60.662	61.111	13.14	0.00	0.00	3.91
4032	5218	3.003480	GCACTAGCAAACCAAGTAGAGG	58.997	50.000	0.00	0.00	41.58	3.69
4091	5277	1.528586	CGGATCCGAAATCTGTGATGC	59.471	52.381	30.62	0.00	42.83	3.91
4092	5278	2.564771	GGATCCGAAATCTGTGATGCA	58.435	47.619	0.00	0.00	0.00	3.96
4106	5309	1.589716	GATGCAGAAGCCGCCAAGTT	61.590	55.000	0.00	0.00	41.13	2.66
4116	5321	1.074248	CGCCAAGTTTGTAGGGGGT	59.926	57.895	0.00	0.00	0.00	4.95
4117	5322	0.538746	CGCCAAGTTTGTAGGGGGTT	60.539	55.000	0.00	0.00	0.00	4.11
4160	5365	4.735132	CGCCACCGGACACACGAT	62.735	66.667	9.46	0.00	35.47	3.73
4168	5373	3.005472	CACCGGACACACGATATAGGATT	59.995	47.826	9.46	0.00	35.47	3.01
4178	5383	5.304614	ACACGATATAGGATTTGGCACTAGT	59.695	40.000	0.00	0.00	0.00	2.57
4183	5389	2.269940	AGGATTTGGCACTAGTCAGGT	58.730	47.619	0.00	0.00	0.00	4.00
4189	5395	0.905357	GGCACTAGTCAGGTGTGGAT	59.095	55.000	0.00	0.00	37.07	3.41
4195	5401	1.195115	AGTCAGGTGTGGATGCGTAT	58.805	50.000	0.00	0.00	0.00	3.06
4201	5407	1.146041	TGTGGATGCGTATGAGGGC	59.854	57.895	0.00	0.00	0.00	5.19
4225	5433	4.625800	GGTGAGGCAGCGAGAATT	57.374	55.556	0.00	0.00	0.00	2.17
4226	5434	2.093216	GGTGAGGCAGCGAGAATTG	58.907	57.895	0.00	0.00	0.00	2.32
4227	5435	1.372087	GGTGAGGCAGCGAGAATTGG	61.372	60.000	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	2.480555	GGCGTCGATGGCACTTTG	59.519	61.111	24.90	0.00	0.00	2.77
17	18	3.958147	CTGGGCGTCGATGGCACTT	62.958	63.158	29.61	0.00	34.08	3.16
24	25	1.443407	CCTCAATCTGGGCGTCGAT	59.557	57.895	0.00	0.00	0.00	3.59
57	58	1.233369	CTCCTCCCCGGACTATGGT	59.767	63.158	0.73	0.00	36.69	3.55
131	132	2.046217	GCCTCCCCAAAGTCGACC	60.046	66.667	13.01	0.00	0.00	4.79
172	173	2.338500	GCGAGTTGGTGAGGTTCTAAG	58.662	52.381	0.00	0.00	0.00	2.18
174	175	0.606604	GGCGAGTTGGTGAGGTTCTA	59.393	55.000	0.00	0.00	0.00	2.10
175	176	1.371558	GGCGAGTTGGTGAGGTTCT	59.628	57.895	0.00	0.00	0.00	3.01
208	209	3.408851	GTCGTCGTTTCCCGGTGC	61.409	66.667	0.00	0.00	37.11	5.01
213	214	1.568025	GCTGTTGTCGTCGTTTCCC	59.432	57.895	0.00	0.00	0.00	3.97
214	215	1.568025	GGCTGTTGTCGTCGTTTCC	59.432	57.895	0.00	0.00	0.00	3.13
215	216	1.200839	CGGCTGTTGTCGTCGTTTC	59.799	57.895	0.00	0.00	36.42	2.78
216	217	2.877974	GCGGCTGTTGTCGTCGTTT	61.878	57.895	0.00	0.00	44.07	3.60
217	218	3.335534	GCGGCTGTTGTCGTCGTT	61.336	61.111	0.00	0.00	44.07	3.85
245	246	4.776322	CCCTGATTCGTGCCGGCA	62.776	66.667	29.03	29.03	0.00	5.69
249	250	1.153086	ATCTGCCCTGATTCGTGCC	60.153	57.895	0.00	0.00	0.00	5.01
261	262	1.153208	CACCCTGCTCTGATCTGCC	60.153	63.158	0.00	0.00	0.00	4.85
275	276	0.620556	TCCATGAAGAAGCTCCACCC	59.379	55.000	0.00	0.00	0.00	4.61
359	360	3.267233	TGGGCAGCCTTCCATGGT	61.267	61.111	12.43	0.00	0.00	3.55
381	382	7.373617	TCATGGTTCTATCCAGTTTATAGCA	57.626	36.000	0.00	0.00	41.05	3.49
384	385	6.558775	AGGCTCATGGTTCTATCCAGTTTATA	59.441	38.462	0.00	0.00	41.05	0.98
403	1458	7.603180	ACTATGTCTATATCAACAAGGCTCA	57.397	36.000	0.00	0.00	0.00	4.26
404	1459	8.894768	AAACTATGTCTATATCAACAAGGCTC	57.105	34.615	0.00	0.00	0.00	4.70
410	1465	9.817809	GAGACCAAAACTATGTCTATATCAACA	57.182	33.333	0.00	0.00	39.36	3.33
417	1472	9.988815	GTCATATGAGACCAAAACTATGTCTAT	57.011	33.333	5.42	0.00	39.36	1.98
549	1611	4.495422	CTCTCTCTTAGCGTTTTTGCCTA	58.505	43.478	0.00	0.00	34.65	3.93
569	1631	6.017275	CAGGATGGAAGATGAAACATTAGCTC	60.017	42.308	0.00	0.00	0.00	4.09
615	1677	2.485426	AGACGACGATCCGTTAGTTTGA	59.515	45.455	0.00	0.00	43.49	2.69
674	1818	5.531659	TGAAATGATTTGTTGCTGCCATTTT	59.468	32.000	10.56	0.00	35.26	1.82
773	1917	2.747686	GTGGTCGGGAGCAAAGGA	59.252	61.111	1.65	0.00	40.82	3.36
927	2075	4.394078	CCGTTCGTCCGCTCGACA	62.394	66.667	0.03	0.00	42.07	4.35
1032	2180	2.758089	GGCGACGTAGAAGGCGAGA	61.758	63.158	0.00	0.00	0.00	4.04
1104	2252	1.812686	CTTCCGTCTTGTCCCCGACA	61.813	60.000	0.00	0.00	41.09	4.35
1125	2273	3.825160	GAACGCCACCAGCACCTCA	62.825	63.158	0.00	0.00	44.04	3.86
1363	2511	4.753877	CGAGAGCGCGTTGTCGGA	62.754	66.667	29.90	0.00	37.56	4.55
1733	2881	3.121025	GCGCTCCTTTTACATTGCAAAAC	60.121	43.478	1.71	0.00	0.00	2.43
1745	2893	0.690762	TTAGGTCTGGCGCTCCTTTT	59.309	50.000	7.64	0.00	33.34	2.27
1747	2895	1.789523	TATTAGGTCTGGCGCTCCTT	58.210	50.000	7.64	0.00	33.34	3.36
1748	2896	1.789523	TTATTAGGTCTGGCGCTCCT	58.210	50.000	7.64	12.73	35.60	3.69
1913	3083	3.824133	TGATAATGCTCATGAAGGTGGG	58.176	45.455	0.00	0.00	0.00	4.61
1931	3101	3.819337	CCGAGGATGATGAGCAAAATGAT	59.181	43.478	0.00	0.00	0.00	2.45
2287	3460	1.403972	GAAGCGTCGCCTTGTACGAG	61.404	60.000	14.86	2.78	41.55	4.18
2556	3729	8.983702	TCCATTGTTCATGATCTTTATGATGA	57.016	30.769	0.00	0.00	34.40	2.92
2557	3730	8.297426	CCTCCATTGTTCATGATCTTTATGATG	58.703	37.037	0.00	0.00	34.76	3.07
2558	3731	8.222637	TCCTCCATTGTTCATGATCTTTATGAT	58.777	33.333	0.00	0.00	34.76	2.45
2559	3732	7.576403	TCCTCCATTGTTCATGATCTTTATGA	58.424	34.615	0.00	0.00	34.31	2.15
2560	3733	7.812690	TCCTCCATTGTTCATGATCTTTATG	57.187	36.000	0.00	2.33	34.31	1.90
2561	3734	7.014038	GCTTCCTCCATTGTTCATGATCTTTAT	59.986	37.037	0.00	0.00	34.31	1.40
2607	3780	3.536956	TCCACGATTCCCTGTATCAAC	57.463	47.619	0.00	0.00	0.00	3.18
3252	4425	0.468226	GGATCAGCGTGGGGATTGTA	59.532	55.000	0.00	0.00	0.00	2.41
3257	4430	1.046472	ATTACGGATCAGCGTGGGGA	61.046	55.000	7.20	0.00	0.00	4.81
3260	4433	3.297830	TGATATTACGGATCAGCGTGG	57.702	47.619	7.20	0.00	0.00	4.94
3443	4616	0.397114	GGATTCCATCAACCACCCCC	60.397	60.000	0.00	0.00	0.00	5.40
3581	4755	7.938563	TTCGTGAAAAATAAAAGAACATGGG	57.061	32.000	0.00	0.00	0.00	4.00
3650	4830	7.870826	TGTGTGATGTTCCTTTATTTGTACTG	58.129	34.615	0.00	0.00	0.00	2.74
3661	4841	2.912771	TCGTGTTGTGTGATGTTCCTT	58.087	42.857	0.00	0.00	0.00	3.36
3684	4865	1.743772	GCGATGTACATGCCTCCTTGT	60.744	52.381	14.43	0.00	34.23	3.16
3702	4883	1.577328	ATCTTTGTGCTTCGGGTGCG	61.577	55.000	0.00	0.00	0.00	5.34
3736	4918	5.546621	AGTTGTGTAGTTTCCTCTGCTTA	57.453	39.130	0.00	0.00	0.00	3.09
3773	4956	2.061773	CGATCTGCTTCTGTTGTTCGT	58.938	47.619	0.00	0.00	0.00	3.85
3781	4964	2.416747	TGTTGGTTCGATCTGCTTCTG	58.583	47.619	0.00	0.00	0.00	3.02
3803	4987	2.414559	GGCTTTGTCGATGTTGGACATG	60.415	50.000	0.00	0.00	43.37	3.21
3805	4989	1.234821	GGCTTTGTCGATGTTGGACA	58.765	50.000	0.00	0.00	42.31	4.02
3817	5001	2.281761	CTCCGGTGCTGGCTTTGT	60.282	61.111	0.00	0.00	0.00	2.83
3961	5147	2.046507	CTTCTTGGAGGCGCTGCT	60.047	61.111	7.64	0.00	0.00	4.24
3990	5176	2.317609	GCAACGGTGACACTCGCAT	61.318	57.895	3.55	3.87	0.00	4.73
4009	5195	4.081642	CCTCTACTTGGTTTGCTAGTGCTA	60.082	45.833	0.00	0.00	40.48	3.49
4021	5207	3.325135	CCAGTGAGAAACCTCTACTTGGT	59.675	47.826	0.00	0.00	39.91	3.67
4024	5210	2.303311	GGCCAGTGAGAAACCTCTACTT	59.697	50.000	0.00	0.00	29.54	2.24
4032	5218	3.055819	TCAGTATCAGGCCAGTGAGAAAC	60.056	47.826	5.01	1.33	0.00	2.78
4039	5225	2.461300	TAGCTCAGTATCAGGCCAGT	57.539	50.000	5.01	0.00	0.00	4.00
4068	5254	0.461870	CACAGATTTCGGATCCGGCA	60.462	55.000	32.79	20.23	40.25	5.69
4091	5277	1.197721	CTACAAACTTGGCGGCTTCTG	59.802	52.381	11.43	3.14	0.00	3.02
4092	5278	1.523758	CTACAAACTTGGCGGCTTCT	58.476	50.000	11.43	0.00	0.00	2.85
4106	5309	1.228613	CGGCCAAAACCCCCTACAA	60.229	57.895	2.24	0.00	0.00	2.41
4116	5321	2.197324	ACCTTCCAGCGGCCAAAA	59.803	55.556	2.24	0.00	0.00	2.44
4117	5322	2.597217	CACCTTCCAGCGGCCAAA	60.597	61.111	2.24	0.00	0.00	3.28
4160	5365	5.070446	CACCTGACTAGTGCCAAATCCTATA	59.930	44.000	0.00	0.00	0.00	1.31
4168	5373	0.396435	CCACACCTGACTAGTGCCAA	59.604	55.000	0.00	0.00	38.87	4.52
4178	5383	1.136891	CTCATACGCATCCACACCTGA	59.863	52.381	0.00	0.00	0.00	3.86
4183	5389	1.146041	GCCCTCATACGCATCCACA	59.854	57.895	0.00	0.00	0.00	4.17
4189	5395	4.155733	CACCCGCCCTCATACGCA	62.156	66.667	0.00	0.00	0.00	5.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.