AutoCloner

Multiple sequence alignment - TraesCS2D01G464400

Loading Multiple Alignment...

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	TraesCS2D01G464400	chr2D	100.000	2088	0	0	1	2088	570064043	570061956	0.000000e+00	3856.0
1	TraesCS2D01G464400	chr2D	90.341	1056	70	9	883	1919	570089973	570088931	0.000000e+00	1356.0
2	TraesCS2D01G464400	chr2D	88.049	1071	84	22	882	1924	569854291	569853237	0.000000e+00	1229.0
3	TraesCS2D01G464400	chr2D	100.000	413	0	0	2380	2792	570061664	570061252	0.000000e+00	763.0
4	TraesCS2D01G464400	chr2D	82.373	295	49	2	600	891	569854602	569854308	1.280000e-63	254.0
5	TraesCS2D01G464400	chr2B	92.621	1030	53	10	883	1902	682573643	682572627	0.000000e+00	1459.0
6	TraesCS2D01G464400	chr2B	91.031	1048	64	16	883	1924	682227433	682226410	0.000000e+00	1387.0
7	TraesCS2D01G464400	chr2B	95.455	352	8	4	2444	2792	607264231	607263885	3.140000e-154	555.0
8	TraesCS2D01G464400	chr2B	92.082	341	25	2	553	891	682227791	682227451	1.950000e-131	479.0
9	TraesCS2D01G464400	chr2B	95.374	281	10	1	2515	2792	775736895	775736615	7.100000e-121	444.0
10	TraesCS2D01G464400	chr2B	84.076	314	27	15	249	543	682228297	682227988	5.890000e-72	281.0
11	TraesCS2D01G464400	chr2B	96.104	154	6	0	1935	2088	607264479	607264326	4.620000e-63	252.0
12	TraesCS2D01G464400	chr2B	90.104	192	14	3	1	191	682228571	682228384	7.720000e-61	244.0
13	TraesCS2D01G464400	chr2B	94.656	131	7	0	1935	2065	775737212	775737082	1.310000e-48	204.0
14	TraesCS2D01G464400	chr2B	100.000	36	0	0	2470	2505	775736925	775736890	1.790000e-07	67.6
15	TraesCS2D01G464400	chr2A	91.280	1078	57	9	883	1936	709185842	709184778	0.000000e+00	1435.0
16	TraesCS2D01G464400	chr2A	87.725	611	56	9	1138	1736	709126695	709126092	0.000000e+00	695.0
17	TraesCS2D01G464400	chr2A	85.380	684	56	24	249	891	709154005	709153325	0.000000e+00	669.0
18	TraesCS2D01G464400	chr2A	91.791	268	15	4	882	1148	709153303	709153042	1.580000e-97	366.0
19	TraesCS2D01G464400	chr2A	85.992	257	25	4	1	256	709154290	709154044	5.930000e-67	265.0
20	TraesCS2D01G464400	chr5D	95.092	326	13	2	2470	2792	537642927	537642602	6.900000e-141	510.0
21	TraesCS2D01G464400	chr5D	83.030	165	28	0	1313	1477	556423703	556423867	1.730000e-32	150.0
22	TraesCS2D01G464400	chr5D	94.737	57	3	0	2029	2085	537643098	537643042	3.830000e-14	89.8
23	TraesCS2D01G464400	chr1A	94.479	326	15	2	2470	2792	413324221	413323896	1.490000e-137	499.0
24	TraesCS2D01G464400	chr1A	84.024	169	27	0	1313	1481	517520086	517520254	2.230000e-36	163.0
25	TraesCS2D01G464400	chr1A	90.566	106	10	0	1936	2041	413716461	413716356	1.040000e-29	141.0
26	TraesCS2D01G464400	chr1A	88.679	106	12	0	1936	2041	413759220	413759115	2.260000e-26	130.0
27	TraesCS2D01G464400	chr1A	98.077	52	1	0	2037	2088	413324378	413324327	1.060000e-14	91.6
28	TraesCS2D01G464400	chr1A	88.000	75	6	2	251	324	536636743	536636815	4.950000e-13	86.1
29	TraesCS2D01G464400	chr4B	89.939	328	18	5	2470	2792	248865216	248865533	2.590000e-110	409.0
30	TraesCS2D01G464400	chr4B	82.274	299	47	5	1299	1591	1102327	1102625	1.280000e-63	254.0
31	TraesCS2D01G464400	chr4B	93.464	153	8	2	1934	2086	248864909	248865059	2.800000e-55	226.0
32	TraesCS2D01G464400	chr4B	94.286	35	1	1	1936	1970	574006547	574006514	5.000000e-03	52.8
33	TraesCS2D01G464400	chr7B	87.179	78	7	2	251	327	667475830	667475755	4.950000e-13	86.1
34	TraesCS2D01G464400	chr7B	84.615	78	9	2	251	327	332258890	332258815	1.070000e-09	75.0
35	TraesCS2D01G464400	chr1B	85.185	81	9	2	251	330	355814445	355814367	2.310000e-11	80.5
36	TraesCS2D01G464400	chr1B	95.000	40	2	0	1935	1974	6501118	6501079	2.320000e-06	63.9
37	TraesCS2D01G464400	chr1B	97.297	37	1	0	1934	1970	357445353	357445317	2.320000e-06	63.9
38	TraesCS2D01G464400	chr6B	85.333	75	8	2	251	324	520547309	520547237	1.070000e-09	75.0
39	TraesCS2D01G464400	chr3B	85.333	75	8	2	251	324	65199714	65199786	1.070000e-09	75.0

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	TraesCS2D01G464400	chr2D	570061252	570064043	2791	True	2309.500000	3856	100.000000	1	2792	2	chr2D.!!$R3	2791
1	TraesCS2D01G464400	chr2D	570088931	570089973	1042	True	1356.000000	1356	90.341000	883	1919	1	chr2D.!!$R1	1036
2	TraesCS2D01G464400	chr2D	569853237	569854602	1365	True	741.500000	1229	85.211000	600	1924	2	chr2D.!!$R2	1324
3	TraesCS2D01G464400	chr2B	682572627	682573643	1016	True	1459.000000	1459	92.621000	883	1902	1	chr2B.!!$R1	1019
4	TraesCS2D01G464400	chr2B	682226410	682228571	2161	True	597.750000	1387	89.323250	1	1924	4	chr2B.!!$R3	1923
5	TraesCS2D01G464400	chr2B	607263885	607264479	594	True	403.500000	555	95.779500	1935	2792	2	chr2B.!!$R2	857
6	TraesCS2D01G464400	chr2B	775736615	775737212	597	True	238.533333	444	96.676667	1935	2792	3	chr2B.!!$R4	857
7	TraesCS2D01G464400	chr2A	709184778	709185842	1064	True	1435.000000	1435	91.280000	883	1936	1	chr2A.!!$R2	1053
8	TraesCS2D01G464400	chr2A	709126092	709126695	603	True	695.000000	695	87.725000	1138	1736	1	chr2A.!!$R1	598
9	TraesCS2D01G464400	chr2A	709153042	709154290	1248	True	433.333333	669	87.721000	1	1148	3	chr2A.!!$R3	1147
10	TraesCS2D01G464400	chr4B	248864909	248865533	624	False	317.500000	409	91.701500	1934	2792	2	chr4B.!!$F2	858

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
195	197	0.044702	AGGGAGGGGTGATGATGTGA	59.955	55.0	0.0	0.0	0.0	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1892	2247	1.519408	GAAGCTGTTTCCTGGCGTAA	58.481	50.0	0.0	0.0	0.0	3.18	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
38	40	6.655078	ACAATTTGAGGTGTATGAGCTTTT	57.345	33.333	2.79	0.00	30.42	2.27
47	49	6.567050	AGGTGTATGAGCTTTTAAATGCATG	58.433	36.000	23.38	0.00	0.00	4.06
48	50	5.232838	GGTGTATGAGCTTTTAAATGCATGC	59.767	40.000	23.38	11.82	0.00	4.06
60	62	8.519492	TTTTAAATGCATGCTACTCAAAAGAC	57.481	30.769	20.33	0.00	0.00	3.01
66	68	4.082571	GCATGCTACTCAAAAGACCAACAT	60.083	41.667	11.37	0.00	0.00	2.71
78	80	2.401766	CCAACATGCTCGTGCCCTC	61.402	63.158	7.05	0.00	38.71	4.30
81	83	0.957395	AACATGCTCGTGCCCTCTTG	60.957	55.000	7.05	0.23	38.71	3.02
82	84	1.376424	CATGCTCGTGCCCTCTTGT	60.376	57.895	7.05	0.00	38.71	3.16
83	85	1.376424	ATGCTCGTGCCCTCTTGTG	60.376	57.895	7.05	0.00	38.71	3.33
84	86	2.031163	GCTCGTGCCCTCTTGTGT	59.969	61.111	0.00	0.00	0.00	3.72
85	87	2.320587	GCTCGTGCCCTCTTGTGTG	61.321	63.158	0.00	0.00	0.00	3.82
86	88	1.367471	CTCGTGCCCTCTTGTGTGA	59.633	57.895	0.00	0.00	0.00	3.58
88	90	0.179234	TCGTGCCCTCTTGTGTGAAA	59.821	50.000	0.00	0.00	0.00	2.69
89	91	1.021202	CGTGCCCTCTTGTGTGAAAA	58.979	50.000	0.00	0.00	0.00	2.29
90	92	1.268539	CGTGCCCTCTTGTGTGAAAAC	60.269	52.381	0.00	0.00	0.00	2.43
139	141	2.607750	ACATGGGTCCACGCCTCT	60.608	61.111	0.00	0.00	0.00	3.69
155	157	0.467384	CTCTATGGCCAGGTCACCAG	59.533	60.000	13.05	0.00	39.88	4.00
193	195	2.127708	GTAAGGGAGGGGTGATGATGT	58.872	52.381	0.00	0.00	0.00	3.06
194	196	0.921896	AAGGGAGGGGTGATGATGTG	59.078	55.000	0.00	0.00	0.00	3.21
195	197	0.044702	AGGGAGGGGTGATGATGTGA	59.955	55.000	0.00	0.00	0.00	3.58
196	198	0.181350	GGGAGGGGTGATGATGTGAC	59.819	60.000	0.00	0.00	0.00	3.67
197	199	0.179073	GGAGGGGTGATGATGTGACG	60.179	60.000	0.00	0.00	0.00	4.35
200	202	2.173669	GGGTGATGATGTGACGGCG	61.174	63.158	4.80	4.80	0.00	6.46
201	203	2.703409	GTGATGATGTGACGGCGC	59.297	61.111	6.90	0.00	0.00	6.53
202	204	2.885164	TGATGATGTGACGGCGCG	60.885	61.111	6.90	0.00	0.00	6.86
273	321	7.564793	GGATGGGCCTTAAAAATCAACTAATT	58.435	34.615	4.53	0.00	0.00	1.40
347	399	1.536922	CGCTAGGTATGCCACTGACTG	60.537	57.143	1.54	0.00	37.19	3.51
365	417	2.492088	ACTGCAGTGCTTATAGTCGTCA	59.508	45.455	20.97	0.00	0.00	4.35
369	421	4.338400	TGCAGTGCTTATAGTCGTCAGTAT	59.662	41.667	17.60	0.00	0.00	2.12
549	624	7.388437	TGTGTCCTATACTTGAAATTTACGGT	58.612	34.615	0.00	0.00	0.00	4.83
550	625	7.879160	TGTGTCCTATACTTGAAATTTACGGTT	59.121	33.333	0.00	0.00	0.00	4.44
551	626	9.369904	GTGTCCTATACTTGAAATTTACGGTTA	57.630	33.333	0.00	0.00	0.00	2.85
642	904	1.344953	ACCATAGCGGAAGGGCATGA	61.345	55.000	0.00	0.00	38.63	3.07
843	1109	2.295909	GGTTAGATCATCGCTGAGCTCT	59.704	50.000	10.71	4.03	44.70	4.09
850	1116	1.675483	CATCGCTGAGCTCTGTAGTCT	59.325	52.381	20.24	6.42	0.00	3.24
854	1120	2.352225	CGCTGAGCTCTGTAGTCTGTTT	60.352	50.000	20.24	0.00	0.00	2.83
966	1286	2.331132	GGAAGCAGCAGCCACTGTC	61.331	63.158	0.00	0.00	43.56	3.51
1060	1381	1.605058	CTACCAGCACCACCGCTACT	61.605	60.000	0.00	0.00	41.38	2.57
1311	1644	3.962718	CCATTATGGCCAAGGACTTCATT	59.037	43.478	10.96	0.00	0.00	2.57
1736	2075	1.624336	CCGCCCATGGATCATTTCAT	58.376	50.000	15.22	0.00	0.00	2.57
1737	2076	1.542915	CCGCCCATGGATCATTTCATC	59.457	52.381	15.22	0.00	0.00	2.92
1779	2118	1.416030	TCCTCACACTGCAAGCTTGTA	59.584	47.619	26.55	21.76	37.60	2.41
1840	2185	8.338259	CAAATTAATCGCATGCTACTTCTTAGT	58.662	33.333	17.13	0.00	38.44	2.24
1841	2186	8.438676	AATTAATCGCATGCTACTTCTTAGTT	57.561	30.769	17.13	1.20	35.78	2.24
1842	2187	5.975410	AATCGCATGCTACTTCTTAGTTC	57.025	39.130	17.13	0.00	35.78	3.01
1843	2188	4.720649	TCGCATGCTACTTCTTAGTTCT	57.279	40.909	17.13	0.00	35.78	3.01
1844	2189	5.073311	TCGCATGCTACTTCTTAGTTCTT	57.927	39.130	17.13	0.00	35.78	2.52
1845	2190	6.203808	TCGCATGCTACTTCTTAGTTCTTA	57.796	37.500	17.13	0.00	35.78	2.10
1846	2191	6.034591	TCGCATGCTACTTCTTAGTTCTTAC	58.965	40.000	17.13	0.00	35.78	2.34
1876	2231	5.505173	AGAAAATGCATGTGTATACAGCC	57.495	39.130	5.62	0.00	40.79	4.85
1892	2247	3.686016	ACAGCCCATGAGTAAATTCGTT	58.314	40.909	0.00	0.00	0.00	3.85
1924	2279	2.614259	ACAGCTTCCCTTCTCTTCTCA	58.386	47.619	0.00	0.00	0.00	3.27
1925	2280	2.975489	ACAGCTTCCCTTCTCTTCTCAA	59.025	45.455	0.00	0.00	0.00	3.02
1926	2281	3.392616	ACAGCTTCCCTTCTCTTCTCAAA	59.607	43.478	0.00	0.00	0.00	2.69
1927	2282	3.750652	CAGCTTCCCTTCTCTTCTCAAAC	59.249	47.826	0.00	0.00	0.00	2.93
1928	2283	3.650461	AGCTTCCCTTCTCTTCTCAAACT	59.350	43.478	0.00	0.00	0.00	2.66
1929	2284	4.103943	AGCTTCCCTTCTCTTCTCAAACTT	59.896	41.667	0.00	0.00	0.00	2.66
1930	2285	4.824537	GCTTCCCTTCTCTTCTCAAACTTT	59.175	41.667	0.00	0.00	0.00	2.66
1931	2286	5.998363	GCTTCCCTTCTCTTCTCAAACTTTA	59.002	40.000	0.00	0.00	0.00	1.85
1932	2287	6.486993	GCTTCCCTTCTCTTCTCAAACTTTAA	59.513	38.462	0.00	0.00	0.00	1.52
1933	2288	7.013369	GCTTCCCTTCTCTTCTCAAACTTTAAA	59.987	37.037	0.00	0.00	0.00	1.52
2433	2805	5.242795	ACTGAGTGCTAACATACCCTTTT	57.757	39.130	0.00	0.00	0.00	2.27
2434	2806	5.003804	ACTGAGTGCTAACATACCCTTTTG	58.996	41.667	0.00	0.00	0.00	2.44
2438	2810	6.322712	TGAGTGCTAACATACCCTTTTGTTTT	59.677	34.615	0.00	0.00	37.29	2.43
2439	2811	7.119709	AGTGCTAACATACCCTTTTGTTTTT	57.880	32.000	0.00	0.00	37.29	1.94
2440	2812	7.207383	AGTGCTAACATACCCTTTTGTTTTTC	58.793	34.615	0.00	0.00	37.29	2.29
2441	2813	7.069455	AGTGCTAACATACCCTTTTGTTTTTCT	59.931	33.333	0.00	0.00	37.29	2.52
2442	2814	7.709182	GTGCTAACATACCCTTTTGTTTTTCTT	59.291	33.333	0.00	0.00	37.29	2.52
2443	2815	7.708752	TGCTAACATACCCTTTTGTTTTTCTTG	59.291	33.333	0.00	0.00	37.29	3.02
2444	2816	6.918892	AACATACCCTTTTGTTTTTCTTGC	57.081	33.333	0.00	0.00	32.28	4.01
2445	2817	6.233905	ACATACCCTTTTGTTTTTCTTGCT	57.766	33.333	0.00	0.00	0.00	3.91
2446	2818	6.649155	ACATACCCTTTTGTTTTTCTTGCTT	58.351	32.000	0.00	0.00	0.00	3.91
2447	2819	6.761242	ACATACCCTTTTGTTTTTCTTGCTTC	59.239	34.615	0.00	0.00	0.00	3.86
2448	2820	5.420725	ACCCTTTTGTTTTTCTTGCTTCT	57.579	34.783	0.00	0.00	0.00	2.85
2449	2821	5.178061	ACCCTTTTGTTTTTCTTGCTTCTG	58.822	37.500	0.00	0.00	0.00	3.02
2453	2825	7.495606	CCCTTTTGTTTTTCTTGCTTCTGTAAT	59.504	33.333	0.00	0.00	0.00	1.89
2578	2958	4.000325	CTCAACCGAATGGATGTTGTACA	59.000	43.478	0.00	0.00	39.03	2.90
2579	2959	4.584874	TCAACCGAATGGATGTTGTACAT	58.415	39.130	0.00	0.00	42.43	2.29
2580	2960	5.735766	TCAACCGAATGGATGTTGTACATA	58.264	37.500	0.00	0.00	39.27	2.29
2581	2961	6.353323	TCAACCGAATGGATGTTGTACATAT	58.647	36.000	0.00	0.00	39.27	1.78
2582	2962	6.259829	TCAACCGAATGGATGTTGTACATATG	59.740	38.462	0.00	0.00	39.27	1.78
2583	2963	5.680619	ACCGAATGGATGTTGTACATATGT	58.319	37.500	13.93	13.93	39.27	2.29
2584	2964	6.822442	ACCGAATGGATGTTGTACATATGTA	58.178	36.000	11.62	11.62	39.27	2.29
2585	2965	6.704493	ACCGAATGGATGTTGTACATATGTAC	59.296	38.462	30.81	30.81	39.27	2.90
2761	3144	9.429359	ACATAACTAATGTCATAGATTAGCAGC	57.571	33.333	0.00	0.00	46.15	5.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	40	5.709631	TGGTCTTTTGAGTAGCATGCATTTA	59.290	36.000	21.98	0.00	0.00	1.40
47	49	3.503748	AGCATGTTGGTCTTTTGAGTAGC	59.496	43.478	0.00	0.00	0.00	3.58
48	50	4.143030	CGAGCATGTTGGTCTTTTGAGTAG	60.143	45.833	5.31	0.00	42.30	2.57
60	62	2.360350	AGGGCACGAGCATGTTGG	60.360	61.111	7.26	0.00	44.61	3.77
66	68	2.031012	CACAAGAGGGCACGAGCA	59.969	61.111	7.26	0.00	44.61	4.26
78	80	0.248866	GGGCACCGTTTTCACACAAG	60.249	55.000	0.00	0.00	40.86	3.16
139	141	2.998097	GCTGGTGACCTGGCCATA	59.002	61.111	5.51	0.00	33.84	2.74
155	157	3.069318	AGAAGAGGGGGTCGTCGC	61.069	66.667	0.00	0.00	38.60	5.19
201	203	3.669036	CTGGAGTGAGCCGACGACG	62.669	68.421	0.00	0.00	39.43	5.12
202	204	2.179517	CTGGAGTGAGCCGACGAC	59.820	66.667	0.00	0.00	0.00	4.34
204	206	2.179517	GACTGGAGTGAGCCGACG	59.820	66.667	0.00	0.00	0.00	5.12
205	207	1.214062	CTGACTGGAGTGAGCCGAC	59.786	63.158	0.00	0.00	0.00	4.79
215	217	2.217038	GGGTCTGCCACTGACTGGA	61.217	63.158	4.88	0.00	43.95	3.86
347	399	3.152261	ACTGACGACTATAAGCACTGC	57.848	47.619	0.00	0.00	0.00	4.40
469	543	4.695217	AACACGAATTGAACGGCATAAT	57.305	36.364	0.00	0.00	34.93	1.28
471	545	5.608676	TTTAACACGAATTGAACGGCATA	57.391	34.783	0.00	0.00	34.93	3.14
472	546	4.491234	TTTAACACGAATTGAACGGCAT	57.509	36.364	0.00	0.00	34.93	4.40
473	547	3.965292	TTTAACACGAATTGAACGGCA	57.035	38.095	0.00	0.00	34.93	5.69
474	548	3.116700	CGTTTTAACACGAATTGAACGGC	59.883	43.478	8.45	0.00	43.15	5.68
543	618	8.715998	TGCGTCATTTTAACTTTATAACCGTAA	58.284	29.630	0.00	0.00	0.00	3.18
545	620	7.131498	TGCGTCATTTTAACTTTATAACCGT	57.869	32.000	0.00	0.00	0.00	4.83
546	621	8.437443	TTTGCGTCATTTTAACTTTATAACCG	57.563	30.769	0.00	0.00	0.00	4.44
547	622	9.998381	GTTTTGCGTCATTTTAACTTTATAACC	57.002	29.630	0.00	0.00	0.00	2.85
549	624	9.661187	TCGTTTTGCGTCATTTTAACTTTATAA	57.339	25.926	0.00	0.00	42.13	0.98
550	625	9.661187	TTCGTTTTGCGTCATTTTAACTTTATA	57.339	25.926	0.00	0.00	42.13	0.98
551	626	8.563289	TTCGTTTTGCGTCATTTTAACTTTAT	57.437	26.923	0.00	0.00	42.13	1.40
574	836	1.134371	CCTCCGATGGGGTTCTTCTTC	60.134	57.143	0.00	0.00	37.00	2.87
642	904	1.617947	GGTGTTCGGAGGAGCCTGAT	61.618	60.000	0.00	0.00	0.00	2.90
676	939	2.280524	CGAAACACCAGGCCGTCA	60.281	61.111	0.00	0.00	0.00	4.35
681	944	0.997196	GATACGACGAAACACCAGGC	59.003	55.000	0.00	0.00	0.00	4.85
729	993	1.569479	GACACAGGAAGCGGCAGAAC	61.569	60.000	1.45	0.00	0.00	3.01
850	1116	8.624367	TGATCGGACTAATTTAAAAGGAAACA	57.376	30.769	0.00	0.00	0.00	2.83
854	1120	9.456147	TGATTTGATCGGACTAATTTAAAAGGA	57.544	29.630	0.00	0.00	0.00	3.36
966	1286	0.831288	AGGCTGATCGATGGGGAGAG	60.831	60.000	0.54	0.00	0.00	3.20
999	1319	1.358046	GGCGAAATGCTGCTCCATC	59.642	57.895	0.00	0.00	45.43	3.51
1083	1404	2.353889	GTCGCTCATGTCGTAGTAGGAA	59.646	50.000	9.23	0.00	0.00	3.36
1086	1407	3.292423	CATGTCGCTCATGTCGTAGTAG	58.708	50.000	10.71	0.00	46.18	2.57
1087	1408	3.334272	CATGTCGCTCATGTCGTAGTA	57.666	47.619	10.71	0.00	46.18	1.82
1736	2075	4.351938	CCGTCGCCGTTGAGTGGA	62.352	66.667	0.00	0.00	0.00	4.02
1763	2102	1.538512	AGCATACAAGCTTGCAGTGTG	59.461	47.619	26.27	15.76	43.70	3.82
1840	2185	7.229306	ACATGCATTTTCTTCAGACAGTAAGAA	59.771	33.333	0.00	0.00	39.36	2.52
1841	2186	6.712095	ACATGCATTTTCTTCAGACAGTAAGA	59.288	34.615	0.00	0.00	0.00	2.10
1842	2187	6.800408	CACATGCATTTTCTTCAGACAGTAAG	59.200	38.462	0.00	0.00	0.00	2.34
1843	2188	6.262944	ACACATGCATTTTCTTCAGACAGTAA	59.737	34.615	0.00	0.00	0.00	2.24
1844	2189	5.764686	ACACATGCATTTTCTTCAGACAGTA	59.235	36.000	0.00	0.00	0.00	2.74
1845	2190	4.581824	ACACATGCATTTTCTTCAGACAGT	59.418	37.500	0.00	0.00	0.00	3.55
1846	2191	5.117355	ACACATGCATTTTCTTCAGACAG	57.883	39.130	0.00	0.00	0.00	3.51
1876	2231	4.093703	TGGCGTAAACGAATTTACTCATGG	59.906	41.667	6.71	0.00	45.46	3.66
1892	2247	1.519408	GAAGCTGTTTCCTGGCGTAA	58.481	50.000	0.00	0.00	0.00	3.18
1924	2279	8.570488	CGGGGTATTGTCTAGTTTTTAAAGTTT	58.430	33.333	0.00	0.00	0.00	2.66
1925	2280	7.308770	GCGGGGTATTGTCTAGTTTTTAAAGTT	60.309	37.037	0.00	0.00	0.00	2.66
1926	2281	6.149973	GCGGGGTATTGTCTAGTTTTTAAAGT	59.850	38.462	0.00	0.00	0.00	2.66
1927	2282	6.549061	GCGGGGTATTGTCTAGTTTTTAAAG	58.451	40.000	0.00	0.00	0.00	1.85
1928	2283	5.122082	CGCGGGGTATTGTCTAGTTTTTAAA	59.878	40.000	0.00	0.00	0.00	1.52
1929	2284	4.630940	CGCGGGGTATTGTCTAGTTTTTAA	59.369	41.667	0.00	0.00	0.00	1.52
1930	2285	4.183101	CGCGGGGTATTGTCTAGTTTTTA	58.817	43.478	0.00	0.00	0.00	1.52
1931	2286	3.004862	CGCGGGGTATTGTCTAGTTTTT	58.995	45.455	0.00	0.00	0.00	1.94
1932	2287	2.624636	CGCGGGGTATTGTCTAGTTTT	58.375	47.619	0.00	0.00	0.00	2.43
1933	2288	1.741394	GCGCGGGGTATTGTCTAGTTT	60.741	52.381	8.83	0.00	0.00	2.66
2013	2368	4.217754	TCGTTGGTGCTAAATTTCACAC	57.782	40.909	12.76	12.76	35.04	3.82
2017	2372	3.831715	AGCTCGTTGGTGCTAAATTTC	57.168	42.857	0.00	0.00	40.95	2.17
2032	2387	8.723777	TTAATTCATTACGTGATAGTAGCTCG	57.276	34.615	8.21	8.21	36.54	5.03
2411	2782	4.910458	AAAGGGTATGTTAGCACTCAGT	57.090	40.909	0.00	0.00	0.00	3.41
2460	2832	6.910536	ATTACAGAAGCAAGACTTTATCGG	57.089	37.500	0.00	0.00	39.29	4.18
2578	2958	4.904251	AGAGGTCTGCATCAAGGTACATAT	59.096	41.667	0.00	0.00	0.00	1.78
2579	2959	4.290093	AGAGGTCTGCATCAAGGTACATA	58.710	43.478	0.00	0.00	0.00	2.29
2580	2960	3.110705	AGAGGTCTGCATCAAGGTACAT	58.889	45.455	0.00	0.00	0.00	2.29
2581	2961	2.497675	GAGAGGTCTGCATCAAGGTACA	59.502	50.000	0.00	0.00	0.00	2.90
2582	2962	2.763448	AGAGAGGTCTGCATCAAGGTAC	59.237	50.000	0.00	0.00	0.00	3.34
2583	2963	3.107402	AGAGAGGTCTGCATCAAGGTA	57.893	47.619	0.00	0.00	0.00	3.08
2584	2964	1.949799	AGAGAGGTCTGCATCAAGGT	58.050	50.000	0.00	0.00	0.00	3.50
2585	2965	3.640498	TCATAGAGAGGTCTGCATCAAGG	59.360	47.826	0.00	0.00	33.84	3.61
2588	2968	3.635836	CAGTCATAGAGAGGTCTGCATCA	59.364	47.826	0.00	0.00	33.84	3.07
2761	3144	3.797039	TCTTAATCGATCCAACTGCCAG	58.203	45.455	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.