AutoCloner

Multiple sequence alignment - TraesCS7A01G124800

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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	TraesCS7A01G124800	chr7A	100.000	3094	0	0	1	3094	80538362	80541455	0.000000e+00	5714.0
1	TraesCS7A01G124800	chr7A	94.521	73	4	0	3022	3094	320984995	320984923	2.520000e-21	113.0
2	TraesCS7A01G124800	chr7A	95.161	62	3	0	3022	3083	564272485	564272424	7.060000e-17	99.0
3	TraesCS7A01G124800	chr7A	86.667	75	9	1	3020	3094	263369260	263369187	7.110000e-12	82.4
4	TraesCS7A01G124800	chr7B	94.888	2895	124	12	1	2878	22708840	22711727	0.000000e+00	4505.0
5	TraesCS7A01G124800	chr7B	94.710	2892	123	16	2	2877	22667112	22669989	0.000000e+00	4466.0
6	TraesCS7A01G124800	chr7B	95.832	2399	79	10	1	2385	22962835	22965226	0.000000e+00	3856.0
7	TraesCS7A01G124800	chr7B	94.600	2000	89	9	893	2878	22833418	22835412	0.000000e+00	3077.0
8	TraesCS7A01G124800	chr7B	95.862	1474	49	7	1	1465	22891894	22893364	0.000000e+00	2374.0
9	TraesCS7A01G124800	chr7B	95.316	1473	59	7	1	1465	22770769	22772239	0.000000e+00	2329.0
10	TraesCS7A01G124800	chr7B	93.841	1380	71	7	1507	2878	22893360	22894733	0.000000e+00	2065.0
11	TraesCS7A01G124800	chr7B	93.669	1390	71	8	1507	2885	22772235	22773618	0.000000e+00	2063.0
12	TraesCS7A01G124800	chr7B	95.700	907	33	4	1	903	22832110	22833014	0.000000e+00	1454.0
13	TraesCS7A01G124800	chr7B	95.084	834	36	4	1	833	23008059	23008888	0.000000e+00	1308.0
14	TraesCS7A01G124800	chr7B	84.761	1004	137	13	769	1767	23410815	23411807	0.000000e+00	992.0
15	TraesCS7A01G124800	chr7B	92.211	398	26	4	2486	2878	22968268	22968665	2.690000e-155	558.0
16	TraesCS7A01G124800	chr7B	91.479	399	28	5	2486	2878	22789496	22789894	7.550000e-151	544.0
17	TraesCS7A01G124800	chr7B	91.753	97	7	1	2882	2977	22713298	22713394	1.940000e-27	134.0
18	TraesCS7A01G124800	chr7B	91.753	97	7	1	2882	2977	22773650	22773746	1.940000e-27	134.0
19	TraesCS7A01G124800	chr7B	91.753	97	7	1	2882	2977	22837497	22837593	1.940000e-27	134.0
20	TraesCS7A01G124800	chr7B	90.722	97	8	1	2882	2977	22899353	22899449	9.010000e-26	128.0
21	TraesCS7A01G124800	chr7B	89.691	97	9	1	2882	2977	22835451	22835547	4.190000e-24	122.0
22	TraesCS7A01G124800	chr7B	94.231	52	3	0	2882	2933	22836970	22837021	2.560000e-11	80.5
23	TraesCS7A01G124800	chr7D	94.040	2886	130	16	1	2878	76502325	76505176	0.000000e+00	4338.0
24	TraesCS7A01G124800	chr7D	94.112	1936	76	13	950	2878	76521420	76523324	0.000000e+00	2909.0
25	TraesCS7A01G124800	chr7D	96.406	807	29	0	132	938	76520388	76521194	0.000000e+00	1330.0
26	TraesCS7A01G124800	chr7D	94.225	710	37	4	1931	2639	76482578	76483284	0.000000e+00	1081.0
27	TraesCS7A01G124800	chr7D	82.294	1203	183	25	756	1951	76725783	76726962	0.000000e+00	1014.0
28	TraesCS7A01G124800	chr7D	85.100	953	123	11	826	1763	76628809	76629757	0.000000e+00	955.0
29	TraesCS7A01G124800	chr5A	98.592	71	1	0	3023	3093	430485797	430485867	3.240000e-25	126.0
30	TraesCS7A01G124800	chr2D	90.625	96	8	1	2882	2976	294540995	294541090	3.240000e-25	126.0
31	TraesCS7A01G124800	chr3D	89.691	97	9	1	2882	2977	603305198	603305102	4.190000e-24	122.0
32	TraesCS7A01G124800	chr4D	88.172	93	9	2	2882	2972	488423197	488423289	3.260000e-20	110.0
33	TraesCS7A01G124800	chr2A	93.151	73	5	0	3022	3094	161633761	161633833	1.170000e-19	108.0
34	TraesCS7A01G124800	chr2A	93.548	62	4	0	3022	3083	48345607	48345546	3.290000e-15	93.5
35	TraesCS7A01G124800	chr3B	89.189	74	8	0	3021	3094	436306532	436306605	3.290000e-15	93.5
36	TraesCS7A01G124800	chr6A	89.041	73	8	0	3022	3094	48033033	48032961	1.180000e-14	91.6
37	TraesCS7A01G124800	chr6A	88.889	72	8	0	3023	3094	147298650	147298579	4.250000e-14	89.8

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	TraesCS7A01G124800	chr7A	80538362	80541455	3093	False	5714.000000	5714	100.000000	1	3094	1	chr7A.!!$F1	3093
1	TraesCS7A01G124800	chr7B	22667112	22669989	2877	False	4466.000000	4466	94.710000	2	2877	1	chr7B.!!$F1	2875
2	TraesCS7A01G124800	chr7B	22708840	22713394	4554	False	2319.500000	4505	93.320500	1	2977	2	chr7B.!!$F6	2976
3	TraesCS7A01G124800	chr7B	22891894	22894733	2839	False	2219.500000	2374	94.851500	1	2878	2	chr7B.!!$F9	2877
4	TraesCS7A01G124800	chr7B	22962835	22968665	5830	False	2207.000000	3856	94.021500	1	2878	2	chr7B.!!$F10	2877
5	TraesCS7A01G124800	chr7B	22770769	22773746	2977	False	1508.666667	2329	93.579333	1	2977	3	chr7B.!!$F7	2976
6	TraesCS7A01G124800	chr7B	23008059	23008888	829	False	1308.000000	1308	95.084000	1	833	1	chr7B.!!$F4	832
7	TraesCS7A01G124800	chr7B	23410815	23411807	992	False	992.000000	992	84.761000	769	1767	1	chr7B.!!$F5	998
8	TraesCS7A01G124800	chr7B	22832110	22837593	5483	False	973.500000	3077	93.195000	1	2977	5	chr7B.!!$F8	2976
9	TraesCS7A01G124800	chr7D	76502325	76505176	2851	False	4338.000000	4338	94.040000	1	2878	1	chr7D.!!$F2	2877
10	TraesCS7A01G124800	chr7D	76520388	76523324	2936	False	2119.500000	2909	95.259000	132	2878	2	chr7D.!!$F5	2746
11	TraesCS7A01G124800	chr7D	76482578	76483284	706	False	1081.000000	1081	94.225000	1931	2639	1	chr7D.!!$F1	708
12	TraesCS7A01G124800	chr7D	76725783	76726962	1179	False	1014.000000	1014	82.294000	756	1951	1	chr7D.!!$F4	1195
13	TraesCS7A01G124800	chr7D	76628809	76629757	948	False	955.000000	955	85.100000	826	1763	1	chr7D.!!$F3	937

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
994	1634	0.109597	GCCCTTCTTGCACACAATCG	60.11	55.0	0.0	0.0	34.61	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2580	6286	0.249699	CGTTATGTCATGGCCGCCTA	60.25	55.0	11.61	0.0	0.0	3.93	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
128	131	4.082895	ACCGACGTATCTAAGGCATACATC	60.083	45.833	0.00	0.00	0.00	3.06
136	139	2.240493	AAGGCATACATCTGCGTACC	57.760	50.000	0.00	0.00	43.23	3.34
305	308	9.849166	CCAACTAGCTTTTATTTTTCGGATAAA	57.151	29.630	0.00	0.00	0.00	1.40
617	622	7.295952	ACTATCGCTTGTTAGTTCATTCTTG	57.704	36.000	0.00	0.00	0.00	3.02
634	639	8.529424	TCATTCTTGGATGAGATAAGCATTTT	57.471	30.769	0.00	0.00	32.50	1.82
705	710	6.599244	TGAATTTAGATAGTTGGCTTGTGAGG	59.401	38.462	0.00	0.00	0.00	3.86
716	721	1.952296	GCTTGTGAGGCATCCTTATGG	59.048	52.381	0.00	0.00	31.76	2.74
781	786	7.989741	AGTCATGTTAGATCCTTAGTTGGATTG	59.010	37.037	0.00	0.00	46.00	2.67
927	1349	7.012327	CCTCTTATTCTCTCACAAAACACAACA	59.988	37.037	0.00	0.00	0.00	3.33
957	1595	1.072266	TGCCCCACCATTCAACTAGT	58.928	50.000	0.00	0.00	0.00	2.57
972	1610	6.672266	TCAACTAGTCCATTCAGTTCTCTT	57.328	37.500	0.00	0.00	30.20	2.85
974	1612	7.155328	TCAACTAGTCCATTCAGTTCTCTTTC	58.845	38.462	0.00	0.00	30.20	2.62
975	1613	5.715070	ACTAGTCCATTCAGTTCTCTTTCG	58.285	41.667	0.00	0.00	0.00	3.46
994	1634	0.109597	GCCCTTCTTGCACACAATCG	60.110	55.000	0.00	0.00	34.61	3.34
1030	1670	2.360801	CCATTCGGTGTCTTGGTTTGTT	59.639	45.455	0.00	0.00	0.00	2.83
1035	1675	4.263435	TCGGTGTCTTGGTTTGTTTACTT	58.737	39.130	0.00	0.00	0.00	2.24
1476	2174	6.614087	ACCTGTACTATATTTGTAGCCAAGGA	59.386	38.462	0.00	0.00	0.00	3.36
1556	2254	5.454966	TCTACATGCACTTCTGACCCTATA	58.545	41.667	0.00	0.00	0.00	1.31
1642	2344	0.821711	CGCAGGTTTGGAAAGTGGGA	60.822	55.000	0.00	0.00	0.00	4.37
1644	2346	1.760029	GCAGGTTTGGAAAGTGGGAAA	59.240	47.619	0.00	0.00	0.00	3.13
1793	2495	7.498443	AGGGATATTACACAAGCTGTAAGTAC	58.502	38.462	3.76	0.00	46.37	2.73
1919	2622	3.713858	TTTGTGGACATTCAAGTGCAG	57.286	42.857	0.00	0.00	40.60	4.41
1947	2650	5.655893	TTAACGGAGGTTCTGTTTTAACG	57.344	39.130	8.43	0.00	42.95	3.18
1953	2656	5.449304	GGAGGTTCTGTTTTAACGACATTG	58.551	41.667	0.00	0.00	0.00	2.82
1997	2701	3.999001	TGCTTGTTGAATGTTTTGTGCAA	59.001	34.783	0.00	0.00	0.00	4.08
2065	2769	3.623906	ATGCTTGACATGACACTAGCT	57.376	42.857	18.26	0.00	37.70	3.32
2098	2802	2.282040	GCTGCAGGCTTGAGGTGT	60.282	61.111	17.12	0.00	38.06	4.16
2185	2889	4.081917	TGCTTGTAGTGTGATGGATCGTTA	60.082	41.667	0.00	0.00	0.00	3.18
2346	3058	9.716531	CTATGTAATGTCTTGGATATGATGTGT	57.283	33.333	0.00	0.00	0.00	3.72
2535	6241	1.284785	CAAGGACCATAAGAGCCCCAA	59.715	52.381	0.00	0.00	0.00	4.12
2537	6243	1.496429	AGGACCATAAGAGCCCCAATG	59.504	52.381	0.00	0.00	0.00	2.82
2551	6257	2.159028	CCCCAATGTTTTCCACAACGTT	60.159	45.455	0.00	0.00	39.50	3.99
2580	6286	7.902920	ATAATTGCCAACAAAGATATCACCT	57.097	32.000	5.32	0.00	39.77	4.00
2598	6304	1.512926	CTAGGCGGCCATGACATAAC	58.487	55.000	23.09	0.00	0.00	1.89
2641	6347	3.304659	GCCATGTTATTTGGTAGCATCGG	60.305	47.826	0.00	0.00	32.62	4.18
2673	6379	9.708222	GCATATACATGTCTTGTACTCTTTTTG	57.292	33.333	0.00	0.00	43.46	2.44
2699	6405	9.352784	GCAAATACACAAAAGATTAGTGCATTA	57.647	29.630	0.00	0.00	36.76	1.90
2737	6447	9.546428	GGGGAAAATTTGATGTTATAGAATTGG	57.454	33.333	0.00	0.00	0.00	3.16
2759	6469	2.427506	GCTCTTAACCACAAGGACCTG	58.572	52.381	0.00	0.00	38.69	4.00
2805	6515	1.274447	AGGGCTACAACGGTTGTACTC	59.726	52.381	25.48	21.15	43.27	2.59
2810	6520	1.713297	ACAACGGTTGTACTCCCTCT	58.287	50.000	24.02	0.00	43.27	3.69
2811	6521	1.343465	ACAACGGTTGTACTCCCTCTG	59.657	52.381	24.02	0.00	43.27	3.35
2843	6554	2.249139	AGAGTGTTTAAGGAGAGCGGT	58.751	47.619	0.00	0.00	0.00	5.68
2845	6556	0.796927	GTGTTTAAGGAGAGCGGTGC	59.203	55.000	0.00	0.00	0.00	5.01
2851	6562	0.900647	AAGGAGAGCGGTGCTACTGT	60.901	55.000	0.00	0.00	39.88	3.55
2867	6578	2.124570	GTGATGGGCGGCATCTGT	60.125	61.111	12.47	0.00	0.00	3.41
2878	6589	3.130633	GCGGCATCTGTACATGTTATCA	58.869	45.455	2.30	0.69	0.00	2.15
2880	6591	4.929211	GCGGCATCTGTACATGTTATCATA	59.071	41.667	2.30	0.00	32.47	2.15
2892	8684	5.072193	ACATGTTATCATAGTCCATGGCAGA	59.928	40.000	6.96	0.22	37.74	4.26
2924	8716	3.243602	TGGAAGAAATTGACGTCGACTGA	60.244	43.478	14.70	0.00	0.00	3.41
2934	8726	2.541346	GACGTCGACTGATGGTATACGA	59.459	50.000	14.70	0.00	38.60	3.43
2958	8750	1.343142	TGAACAGTGATGTACGCCAGT	59.657	47.619	0.00	0.00	0.00	4.00
2961	8753	0.390340	CAGTGATGTACGCCAGTGCT	60.390	55.000	8.56	0.00	33.93	4.40
3021	8835	0.615850	GGAGAACCTGACCCAAGGAG	59.384	60.000	0.00	0.00	40.02	3.69
3022	8836	0.615850	GAGAACCTGACCCAAGGAGG	59.384	60.000	0.00	0.00	40.02	4.30
3023	8837	1.002011	GAACCTGACCCAAGGAGGC	60.002	63.158	0.00	0.00	40.02	4.70
3024	8838	1.774217	AACCTGACCCAAGGAGGCA	60.774	57.895	0.00	0.00	40.02	4.75
3028	8842	1.550869	CCTGACCCAAGGAGGCAAAAT	60.551	52.381	0.00	0.00	40.02	1.82
3029	8843	2.250924	CTGACCCAAGGAGGCAAAATT	58.749	47.619	0.00	0.00	35.39	1.82
3031	8845	2.632512	TGACCCAAGGAGGCAAAATTTC	59.367	45.455	0.00	0.00	35.39	2.17
3034	8848	3.008266	ACCCAAGGAGGCAAAATTTCATG	59.992	43.478	0.00	0.00	35.39	3.07
3035	8849	3.008266	CCCAAGGAGGCAAAATTTCATGT	59.992	43.478	0.00	0.00	35.39	3.21
3036	8850	4.505390	CCCAAGGAGGCAAAATTTCATGTT	60.505	41.667	0.00	0.00	35.39	2.71
3037	8851	5.065235	CCAAGGAGGCAAAATTTCATGTTT	58.935	37.500	0.00	0.00	0.00	2.83
3038	8852	5.532032	CCAAGGAGGCAAAATTTCATGTTTT	59.468	36.000	0.00	0.00	0.00	2.43
3039	8853	6.432107	CAAGGAGGCAAAATTTCATGTTTTG	58.568	36.000	13.09	13.09	45.01	2.44
3040	8854	5.927819	AGGAGGCAAAATTTCATGTTTTGA	58.072	33.333	18.93	0.00	45.02	2.69
3050	8955	6.843069	ATTTCATGTTTTGACCCTTTTTCG	57.157	33.333	0.00	0.00	32.84	3.46
3051	8956	5.584253	TTCATGTTTTGACCCTTTTTCGA	57.416	34.783	0.00	0.00	32.84	3.71
3054	8959	5.808030	TCATGTTTTGACCCTTTTTCGAAAC	59.192	36.000	10.79	7.86	43.47	2.78
3055	8960	4.496360	TGTTTTGACCCTTTTTCGAAACC	58.504	39.130	10.79	0.00	42.91	3.27
3058	8963	6.097129	TGTTTTGACCCTTTTTCGAAACCTAT	59.903	34.615	10.79	0.00	42.91	2.57
3059	8964	6.718522	TTTGACCCTTTTTCGAAACCTATT	57.281	33.333	10.79	0.00	0.00	1.73
3060	8965	5.952526	TGACCCTTTTTCGAAACCTATTC	57.047	39.130	10.79	5.66	0.00	1.75
3063	8968	6.016610	TGACCCTTTTTCGAAACCTATTCAAG	60.017	38.462	10.79	9.42	0.00	3.02
3068	8973	7.965107	CCTTTTTCGAAACCTATTCAAGATCTG	59.035	37.037	10.79	0.00	0.00	2.90
3069	8974	8.615878	TTTTTCGAAACCTATTCAAGATCTGA	57.384	30.769	10.79	0.00	0.00	3.27
3070	8975	7.596749	TTTCGAAACCTATTCAAGATCTGAC	57.403	36.000	6.47	0.00	32.21	3.51
3071	8976	5.661458	TCGAAACCTATTCAAGATCTGACC	58.339	41.667	0.00	0.00	32.21	4.02
3072	8977	4.811557	CGAAACCTATTCAAGATCTGACCC	59.188	45.833	0.00	0.00	32.21	4.46
3073	8978	5.395768	CGAAACCTATTCAAGATCTGACCCT	60.396	44.000	0.00	0.00	32.21	4.34
3074	8979	6.183360	CGAAACCTATTCAAGATCTGACCCTA	60.183	42.308	0.00	0.00	32.21	3.53
3075	8980	7.510675	AAACCTATTCAAGATCTGACCCTAA	57.489	36.000	0.00	0.00	32.21	2.69
3076	8981	6.739331	ACCTATTCAAGATCTGACCCTAAG	57.261	41.667	0.00	0.00	32.21	2.18
3077	8982	6.206042	ACCTATTCAAGATCTGACCCTAAGT	58.794	40.000	0.00	0.00	32.21	2.24
3078	8983	6.674419	ACCTATTCAAGATCTGACCCTAAGTT	59.326	38.462	0.00	0.00	32.21	2.66
3079	8984	6.989169	CCTATTCAAGATCTGACCCTAAGTTG	59.011	42.308	0.00	0.00	32.21	3.16
3080	8985	6.627087	ATTCAAGATCTGACCCTAAGTTGA	57.373	37.500	0.00	0.00	32.21	3.18
3081	8986	6.433847	TTCAAGATCTGACCCTAAGTTGAA	57.566	37.500	0.00	0.00	32.21	2.69
3084	8989	7.461749	TCAAGATCTGACCCTAAGTTGAAATT	58.538	34.615	0.00	0.00	0.00	1.82
3085	8990	7.944554	TCAAGATCTGACCCTAAGTTGAAATTT	59.055	33.333	0.00	0.00	0.00	1.82
3086	8991	8.579863	CAAGATCTGACCCTAAGTTGAAATTTT	58.420	33.333	0.00	0.00	0.00	1.82
3087	8992	8.712228	AGATCTGACCCTAAGTTGAAATTTTT	57.288	30.769	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	6.994421	TTCCATGGAGTAGTTGCAGATATA	57.006	37.500	15.53	0.00	0.00	0.86
41	42	5.894298	TTCCATGGAGTAGTTGCAGATAT	57.106	39.130	15.53	0.00	0.00	1.63
136	139	4.271696	TGTGTCAAGTCAGATAGTTGGG	57.728	45.455	0.00	0.00	38.79	4.12
394	397	4.895297	GGATTTCTATTTTCATGCCCCTCA	59.105	41.667	0.00	0.00	0.00	3.86
541	545	4.891627	TTTGGAATATACATGTGCCACG	57.108	40.909	9.11	0.00	0.00	4.94
598	603	5.122239	TCATCCAAGAATGAACTAACAAGCG	59.878	40.000	0.00	0.00	32.80	4.68
727	732	6.448369	TTCCATGTAAGGATTAGGTATGGG	57.552	41.667	0.00	0.00	37.86	4.00
742	747	9.817809	GATCTAACATGACTAGTTTTCCATGTA	57.182	33.333	21.62	11.45	46.00	2.29
781	786	2.092914	ACCCTATGCAACTTAGACCTGC	60.093	50.000	0.00	0.00	36.60	4.85
927	1349	1.427368	TGGTGGGGCAAGTTGTATCTT	59.573	47.619	4.48	0.00	0.00	2.40
939	1361	1.682087	GGACTAGTTGAATGGTGGGGC	60.682	57.143	0.00	0.00	0.00	5.80
957	1595	2.615493	GGGCGAAAGAGAACTGAATGGA	60.615	50.000	0.00	0.00	0.00	3.41
972	1610	0.749818	TTGTGTGCAAGAAGGGCGAA	60.750	50.000	0.00	0.00	0.00	4.70
974	1612	0.109597	GATTGTGTGCAAGAAGGGCG	60.110	55.000	0.00	0.00	38.10	6.13
975	1613	0.109597	CGATTGTGTGCAAGAAGGGC	60.110	55.000	0.00	0.00	38.10	5.19
1030	1670	8.086143	AGGATTTGTGGTAGCACTATAAGTAA	57.914	34.615	24.35	7.08	0.00	2.24
1035	1675	5.104527	AGCAAGGATTTGTGGTAGCACTATA	60.105	40.000	24.35	10.93	36.65	1.31
1476	2174	9.251440	TCTATACACTAGTAAGGTGTGTGAAAT	57.749	33.333	9.35	0.00	45.83	2.17
1642	2344	3.992943	TCCACCGACAATAGACCATTT	57.007	42.857	0.00	0.00	0.00	2.32
1644	2346	2.838202	AGTTCCACCGACAATAGACCAT	59.162	45.455	0.00	0.00	0.00	3.55
1836	2539	5.450412	CGGTACAATCCATTTCCCTTCAATG	60.450	44.000	0.00	0.00	0.00	2.82
1837	2540	4.644685	CGGTACAATCCATTTCCCTTCAAT	59.355	41.667	0.00	0.00	0.00	2.57
1919	2622	3.270877	ACAGAACCTCCGTTAATGCATC	58.729	45.455	0.00	0.00	30.30	3.91
1929	2632	3.125316	TGTCGTTAAAACAGAACCTCCG	58.875	45.455	0.00	0.00	0.00	4.63
1953	2656	9.546428	AAGCATTTGATTTAGTTAAATATGGCC	57.454	29.630	0.00	0.00	36.13	5.36
1997	2701	9.860650	TTGATATGCAACACCCTATAAACTAAT	57.139	29.630	0.00	0.00	0.00	1.73
2039	2743	4.507710	AGTGTCATGTCAAGCATTCGTAT	58.492	39.130	0.00	0.00	35.19	3.06
2065	2769	2.881513	TGCAGCGAAAAGTGAAACCATA	59.118	40.909	0.00	0.00	37.80	2.74
2098	2802	4.201891	GCTAGTCTTTCAACGGACGAGATA	60.202	45.833	0.00	0.00	37.37	1.98
2185	2889	0.473755	TGACACAGGCAGACCACAAT	59.526	50.000	0.00	0.00	39.06	2.71
2346	3058	8.402798	TCTCAAACAAACAAGCTCCATTATTA	57.597	30.769	0.00	0.00	0.00	0.98
2457	3169	5.992829	TGTATGAATAACGGTTGTCTTGTGT	59.007	36.000	3.07	0.00	0.00	3.72
2498	4680	3.070446	TCCTTGAGGTAAACTGCTTTCGA	59.930	43.478	0.00	0.00	36.34	3.71
2535	6241	9.974980	AATTATTCTAAACGTTGTGGAAAACAT	57.025	25.926	0.00	0.00	38.99	2.71
2537	6243	8.211838	GCAATTATTCTAAACGTTGTGGAAAAC	58.788	33.333	0.00	0.00	0.00	2.43
2580	6286	0.249699	CGTTATGTCATGGCCGCCTA	60.250	55.000	11.61	0.00	0.00	3.93
2598	6304	6.598525	TGGCTATCGTTTTTATATGATTGCG	58.401	36.000	0.00	0.00	40.70	4.85
2614	6320	4.754618	TGCTACCAAATAACATGGCTATCG	59.245	41.667	0.00	0.00	41.89	2.92
2641	6347	5.936686	ACAAGACATGTATATGCATCTGC	57.063	39.130	0.19	0.00	41.63	4.26
2673	6379	7.816945	ATGCACTAATCTTTTGTGTATTTGC	57.183	32.000	0.00	0.00	34.34	3.68
2699	6405	6.777782	TCAAATTTTCCCCTTGCAATACATT	58.222	32.000	0.00	0.00	0.00	2.71
2737	6447	1.613520	GGTCCTTGTGGTTAAGAGCCC	60.614	57.143	0.00	0.00	34.23	5.19
2759	6469	1.874345	TTCGAGTCAAGGTCGAGCCC	61.874	60.000	11.73	0.00	46.50	5.19
2843	6554	2.584064	CCGCCCATCACAGTAGCA	59.416	61.111	0.00	0.00	0.00	3.49
2845	6556	1.146930	ATGCCGCCCATCACAGTAG	59.853	57.895	0.00	0.00	0.00	2.57
2867	6578	6.269769	TCTGCCATGGACTATGATAACATGTA	59.730	38.462	18.40	0.00	39.21	2.29
2878	6589	4.389374	CCGTATTTTCTGCCATGGACTAT	58.611	43.478	18.40	1.81	0.00	2.12
2880	6591	2.643551	CCGTATTTTCTGCCATGGACT	58.356	47.619	18.40	0.00	0.00	3.85
2892	8684	5.335348	CGTCAATTTCTTCCACCCGTATTTT	60.335	40.000	0.00	0.00	0.00	1.82
2924	8716	4.893524	TCACTGTTCATCCTCGTATACCAT	59.106	41.667	0.00	0.00	0.00	3.55
2934	8726	2.418746	GGCGTACATCACTGTTCATCCT	60.419	50.000	0.00	0.00	36.79	3.24
2958	8750	1.841663	GCAAAAAGACGAGCCGAGCA	61.842	55.000	1.50	0.00	0.00	4.26
2961	8753	2.950172	GCGCAAAAAGACGAGCCGA	61.950	57.895	0.30	0.00	0.00	5.54
3002	8816	0.615850	CTCCTTGGGTCAGGTTCTCC	59.384	60.000	0.00	0.00	35.15	3.71
3021	8835	4.821260	AGGGTCAAAACATGAAATTTTGCC	59.179	37.500	12.74	14.86	43.62	4.52
3022	8836	6.375945	AAGGGTCAAAACATGAAATTTTGC	57.624	33.333	12.74	9.14	43.62	3.68
3023	8837	9.288124	GAAAAAGGGTCAAAACATGAAATTTTG	57.712	29.630	11.77	11.77	44.74	2.44
3024	8838	8.180920	CGAAAAAGGGTCAAAACATGAAATTTT	58.819	29.630	0.00	0.00	40.50	1.82
3028	8842	5.967088	TCGAAAAAGGGTCAAAACATGAAA	58.033	33.333	0.00	0.00	40.50	2.69
3029	8843	5.584253	TCGAAAAAGGGTCAAAACATGAA	57.416	34.783	0.00	0.00	40.50	2.57
3031	8845	5.006261	GGTTTCGAAAAAGGGTCAAAACATG	59.994	40.000	13.10	0.00	0.00	3.21
3034	8848	4.751060	AGGTTTCGAAAAAGGGTCAAAAC	58.249	39.130	13.10	0.00	0.00	2.43
3035	8849	6.718522	ATAGGTTTCGAAAAAGGGTCAAAA	57.281	33.333	13.10	0.00	0.00	2.44
3036	8850	6.321690	TGAATAGGTTTCGAAAAAGGGTCAAA	59.678	34.615	13.10	0.00	0.00	2.69
3037	8851	5.828859	TGAATAGGTTTCGAAAAAGGGTCAA	59.171	36.000	13.10	0.00	0.00	3.18
3038	8852	5.378332	TGAATAGGTTTCGAAAAAGGGTCA	58.622	37.500	13.10	10.86	0.00	4.02
3039	8853	5.952526	TGAATAGGTTTCGAAAAAGGGTC	57.047	39.130	13.10	8.44	0.00	4.46
3040	8854	6.066032	TCTTGAATAGGTTTCGAAAAAGGGT	58.934	36.000	13.10	0.00	0.00	4.34
3041	8855	6.569179	TCTTGAATAGGTTTCGAAAAAGGG	57.431	37.500	13.10	0.00	0.00	3.95
3050	8955	5.995446	AGGGTCAGATCTTGAATAGGTTTC	58.005	41.667	0.00	0.00	37.61	2.78
3051	8956	7.182930	ACTTAGGGTCAGATCTTGAATAGGTTT	59.817	37.037	0.00	0.00	37.61	3.27
3054	8959	6.739331	ACTTAGGGTCAGATCTTGAATAGG	57.261	41.667	0.00	0.00	37.61	2.57
3055	8960	7.786030	TCAACTTAGGGTCAGATCTTGAATAG	58.214	38.462	0.00	0.00	37.61	1.73
3058	8963	6.433847	TTCAACTTAGGGTCAGATCTTGAA	57.566	37.500	0.00	0.00	37.61	2.69
3059	8964	6.433847	TTTCAACTTAGGGTCAGATCTTGA	57.566	37.500	0.00	0.00	0.00	3.02
3060	8965	7.693969	AATTTCAACTTAGGGTCAGATCTTG	57.306	36.000	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.