AutoCloner

Multiple sequence alignment - TraesCS5A01G463900

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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	TraesCS5A01G463900	chr5A	100.000	3527	0	0	1	3527	643736063	643732537	0.000000e+00	6514.0
1	TraesCS5A01G463900	chr5A	88.882	1619	140	23	1043	2639	643855482	643853882	0.000000e+00	1956.0
2	TraesCS5A01G463900	chr5A	82.114	984	152	17	1519	2493	643626922	643625954	0.000000e+00	821.0
3	TraesCS5A01G463900	chr5A	79.551	1247	175	42	786	2004	643652956	643651762	0.000000e+00	817.0
4	TraesCS5A01G463900	chr5A	80.400	1000	166	17	1517	2501	643578077	643577093	0.000000e+00	734.0
5	TraesCS5A01G463900	chr5A	82.388	829	131	12	1667	2492	643453173	643452357	0.000000e+00	708.0
6	TraesCS5A01G463900	chr5A	89.953	428	40	3	997	1423	643453876	643453451	1.850000e-152	549.0
7	TraesCS5A01G463900	chr5A	97.396	192	4	1	568	758	643665866	643665675	3.400000e-85	326.0
8	TraesCS5A01G463900	chr5A	100.000	44	0	0	748	791	643664475	643664432	8.110000e-12	82.4
9	TraesCS5A01G463900	chr5D	88.831	2507	215	29	1043	3527	515466194	515463731	0.000000e+00	3018.0
10	TraesCS5A01G463900	chr5D	91.104	1956	149	12	1595	3527	551243519	551241566	0.000000e+00	2625.0
11	TraesCS5A01G463900	chr5D	85.946	1416	148	24	812	2205	515425165	515423779	0.000000e+00	1465.0
12	TraesCS5A01G463900	chr5D	92.842	922	66	0	1595	2516	515568290	515567369	0.000000e+00	1338.0
13	TraesCS5A01G463900	chr5D	83.353	841	131	5	1653	2493	515411817	515410986	0.000000e+00	769.0
14	TraesCS5A01G463900	chr5D	87.759	580	59	7	986	1561	515568865	515568294	0.000000e+00	667.0
15	TraesCS5A01G463900	chr5D	87.241	580	63	6	986	1561	551244095	551243523	0.000000e+00	651.0
16	TraesCS5A01G463900	chr5D	87.166	187	21	1	612	798	515426152	515425969	3.570000e-50	209.0
17	TraesCS5A01G463900	chr5D	77.866	253	47	8	294	542	531904275	531904028	7.890000e-32	148.0
18	TraesCS5A01G463900	chr5D	76.136	264	53	9	1517	1778	515338597	515338342	2.860000e-26	130.0
19	TraesCS5A01G463900	chr5B	85.393	1910	216	29	598	2483	648181254	648179384	0.000000e+00	1923.0
20	TraesCS5A01G463900	chr5B	89.080	1456	136	14	1043	2479	648260525	648259074	0.000000e+00	1786.0
21	TraesCS5A01G463900	chr5B	81.992	994	156	15	1517	2501	648135550	648134571	0.000000e+00	822.0
22	TraesCS5A01G463900	chr5B	89.165	443	45	3	986	1426	647994573	647994132	1.850000e-152	549.0
23	TraesCS5A01G463900	chr5B	90.323	186	16	2	2897	3080	648258833	648258648	3.520000e-60	243.0
24	TraesCS5A01G463900	chr5B	91.525	59	5	0	2832	2890	648258930	648258872	8.110000e-12	82.4
25	TraesCS5A01G463900	chr7B	90.764	563	50	2	2	564	137540948	137541508	0.000000e+00	750.0
26	TraesCS5A01G463900	chr6A	79.401	568	110	7	1	565	370607959	370608522	9.180000e-106	394.0
27	TraesCS5A01G463900	chr2B	88.382	241	25	3	326	565	717494383	717494145	1.600000e-73	287.0
28	TraesCS5A01G463900	chr2B	73.580	352	81	11	220	565	798733673	798733328	1.330000e-24	124.0
29	TraesCS5A01G463900	chr7D	80.165	242	40	7	328	568	169042060	169041826	1.300000e-39	174.0
30	TraesCS5A01G463900	chr7D	78.067	269	50	9	302	565	9992439	9992703	1.010000e-35	161.0
31	TraesCS5A01G463900	chr4D	76.173	277	59	7	294	566	347507292	347507565	4.750000e-29	139.0
32	TraesCS5A01G463900	chr1D	73.239	355	85	10	216	565	209735873	209735524	1.720000e-23	121.0
33	TraesCS5A01G463900	chr7A	95.833	48	0	2	2758	2803	690204348	690204395	3.780000e-10	76.8
34	TraesCS5A01G463900	chr6D	76.429	140	17	11	2676	2803	443850696	443850831	1.060000e-05	62.1

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	TraesCS5A01G463900	chr5A	643732537	643736063	3526	True	6514.0	6514	100.000000	1	3527	1	chr5A.!!$R4	3526
1	TraesCS5A01G463900	chr5A	643853882	643855482	1600	True	1956.0	1956	88.882000	1043	2639	1	chr5A.!!$R5	1596
2	TraesCS5A01G463900	chr5A	643625954	643626922	968	True	821.0	821	82.114000	1519	2493	1	chr5A.!!$R2	974
3	TraesCS5A01G463900	chr5A	643651762	643652956	1194	True	817.0	817	79.551000	786	2004	1	chr5A.!!$R3	1218
4	TraesCS5A01G463900	chr5A	643577093	643578077	984	True	734.0	734	80.400000	1517	2501	1	chr5A.!!$R1	984
5	TraesCS5A01G463900	chr5A	643452357	643453876	1519	True	628.5	708	86.170500	997	2492	2	chr5A.!!$R6	1495
6	TraesCS5A01G463900	chr5A	643664432	643665866	1434	True	204.2	326	98.698000	568	791	2	chr5A.!!$R7	223
7	TraesCS5A01G463900	chr5D	515463731	515466194	2463	True	3018.0	3018	88.831000	1043	3527	1	chr5D.!!$R3	2484
8	TraesCS5A01G463900	chr5D	551241566	551244095	2529	True	1638.0	2625	89.172500	986	3527	2	chr5D.!!$R7	2541
9	TraesCS5A01G463900	chr5D	515567369	515568865	1496	True	1002.5	1338	90.300500	986	2516	2	chr5D.!!$R6	1530
10	TraesCS5A01G463900	chr5D	515423779	515426152	2373	True	837.0	1465	86.556000	612	2205	2	chr5D.!!$R5	1593
11	TraesCS5A01G463900	chr5D	515410986	515411817	831	True	769.0	769	83.353000	1653	2493	1	chr5D.!!$R2	840
12	TraesCS5A01G463900	chr5B	648179384	648181254	1870	True	1923.0	1923	85.393000	598	2483	1	chr5B.!!$R3	1885
13	TraesCS5A01G463900	chr5B	648134571	648135550	979	True	822.0	822	81.992000	1517	2501	1	chr5B.!!$R2	984
14	TraesCS5A01G463900	chr5B	648258648	648260525	1877	True	703.8	1786	90.309333	1043	3080	3	chr5B.!!$R4	2037
15	TraesCS5A01G463900	chr7B	137540948	137541508	560	False	750.0	750	90.764000	2	564	1	chr7B.!!$F1	562
16	TraesCS5A01G463900	chr6A	370607959	370608522	563	False	394.0	394	79.401000	1	565	1	chr6A.!!$F1	564

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
514	516	0.691332	GGAAACCTTCCTTCCGTCCT	59.309	55.0	0.0	0.0	46.57	3.85	F
847	1640	1.071605	CGCTCCTGTTTGACTAGCAC	58.928	55.0	0.0	0.0	32.69	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2511	3962	0.388649	CTGTTCACGAAGTAGCGGCT	60.389	55.0	7.98	7.98	41.61	5.52	R
2634	4088	5.063817	TCTGAGCGAAAACATACATCACATG	59.936	40.0	0.00	0.00	0.00	3.21	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
26	27	1.061546	TTCAAACGCTCCTAAGGGGT	58.938	50.000	0.00	0.00	39.68	4.95
38	39	1.766496	CTAAGGGGTCGGCTAATGGAA	59.234	52.381	0.00	0.00	0.00	3.53
50	51	3.282021	GCTAATGGAAGACAGCCAATGA	58.718	45.455	0.00	0.00	39.21	2.57
170	171	4.398319	GGACCAAACAGGAGAATTCTTGA	58.602	43.478	9.87	0.00	41.22	3.02
180	181	2.682352	GAGAATTCTTGAGGGCTTCAGC	59.318	50.000	9.87	0.00	37.07	4.26
189	190	0.886490	AGGGCTTCAGCTTTCGTGTG	60.886	55.000	0.00	0.00	41.70	3.82
194	195	0.937304	TTCAGCTTTCGTGTGCAGAC	59.063	50.000	3.38	3.38	0.00	3.51
223	224	4.284490	TCAGATCCTACAACACTTGAAGCT	59.716	41.667	0.00	0.00	0.00	3.74
264	265	4.069300	TGGCTCTAGCAGATGATCTTTG	57.931	45.455	4.07	0.00	44.36	2.77
268	269	4.270566	GCTCTAGCAGATGATCTTTGTGTG	59.729	45.833	0.00	0.00	41.59	3.82
291	292	7.174772	TGTGCAAAGTATTCATATTGTGTCAGT	59.825	33.333	0.00	0.00	0.00	3.41
307	308	0.823460	CAGTTTGCAAGGTGGTGGTT	59.177	50.000	0.00	0.00	0.00	3.67
340	341	8.601047	TCCAGAAGCATAATATGTCTAGCTAT	57.399	34.615	1.92	0.00	0.00	2.97
412	414	9.838975	TTTTCGTAACATAGTCTATGAACGTAA	57.161	29.630	29.76	26.64	43.08	3.18
443	445	3.815856	TTTGAAGCTCACAATTTGGCA	57.184	38.095	7.04	0.00	0.00	4.92
491	493	1.883275	CGCCATGTTTGGTTAGGTCAA	59.117	47.619	0.00	0.00	45.57	3.18
514	516	0.691332	GGAAACCTTCCTTCCGTCCT	59.309	55.000	0.00	0.00	46.57	3.85
761	764	7.095313	GGATCAAATATGTCGTCTCTCTACGTA	60.095	40.741	0.00	0.00	43.31	3.57
762	765	7.175073	TCAAATATGTCGTCTCTCTACGTAG	57.825	40.000	16.73	16.73	43.31	3.51
802	1586	7.857404	TCCAAATCCCAAAACCTAAACAATA	57.143	32.000	0.00	0.00	0.00	1.90
847	1640	1.071605	CGCTCCTGTTTGACTAGCAC	58.928	55.000	0.00	0.00	32.69	4.40
981	1787	2.169352	GCTCCTGATCAAGACCTTGCTA	59.831	50.000	4.94	0.00	40.24	3.49
982	1788	3.740764	GCTCCTGATCAAGACCTTGCTAG	60.741	52.174	4.94	3.67	40.24	3.42
983	1789	3.445008	TCCTGATCAAGACCTTGCTAGT	58.555	45.455	4.94	0.00	40.24	2.57
984	1790	3.840666	TCCTGATCAAGACCTTGCTAGTT	59.159	43.478	4.94	0.00	40.24	2.24
1266	2240	3.677648	AACGACGTCCCCGACCAG	61.678	66.667	10.58	0.00	37.88	4.00
1481	2505	2.226200	TCCATTAATTCCATCGCATGCG	59.774	45.455	33.61	33.61	41.35	4.73
1486	2519	1.859427	ATTCCATCGCATGCGCATCC	61.859	55.000	34.45	11.53	38.40	3.51
1487	2520	2.946172	TTCCATCGCATGCGCATCCT	62.946	55.000	34.45	13.46	38.40	3.24
1499	2536	4.607293	TGCGCATCCTAAATGATCTAGT	57.393	40.909	5.66	0.00	0.00	2.57
1504	2541	5.343593	CGCATCCTAAATGATCTAGTTCGAC	59.656	44.000	0.00	0.00	0.00	4.20
1545	2582	2.496817	GCGATGCTTCTCCCGACT	59.503	61.111	0.00	0.00	0.00	4.18
1698	2814	3.730761	CAGCGCTGGCAGTTGACC	61.731	66.667	29.88	0.00	43.41	4.02
1713	2829	3.885814	ACCAAAGAGAGGTCCGCA	58.114	55.556	0.00	0.00	32.90	5.69
1773	2889	3.850098	CTTCCCGCTGGTGCCAACT	62.850	63.158	0.00	0.00	35.36	3.16
2074	3512	1.241990	GCTTCCTCCCGGTTTCCAAC	61.242	60.000	0.00	0.00	0.00	3.77
2378	3824	2.364317	CGGAGAGGCCAGGAGGAA	60.364	66.667	5.01	0.00	36.89	3.36
2530	3981	0.388649	AGCCGCTACTTCGTGAACAG	60.389	55.000	0.00	0.00	0.00	3.16
2537	3988	2.833631	ACTTCGTGAACAGTAAGGGG	57.166	50.000	0.00	0.00	0.00	4.79
2634	4088	4.875544	TGAAACACTGAAACTGTAGCAC	57.124	40.909	0.00	0.00	0.00	4.40
2640	4094	3.809279	CACTGAAACTGTAGCACATGTGA	59.191	43.478	29.80	6.58	0.00	3.58
2646	4100	6.092533	TGAAACTGTAGCACATGTGATGTATG	59.907	38.462	29.80	16.32	42.70	2.39
2669	4124	7.202016	TGTTTTCGCTCAGAATTGTAGAAAT	57.798	32.000	0.00	0.00	38.86	2.17
2672	4127	7.433708	TTTCGCTCAGAATTGTAGAAATGAA	57.566	32.000	0.00	0.00	38.86	2.57
2673	4128	7.615582	TTCGCTCAGAATTGTAGAAATGAAT	57.384	32.000	0.00	0.00	33.14	2.57
2674	4129	7.615582	TCGCTCAGAATTGTAGAAATGAATT	57.384	32.000	0.00	0.00	0.00	2.17
2697	4152	6.091441	ATTTTGCTAAATCTCAGTCGACTGAC	59.909	38.462	37.87	27.20	46.39	3.51
2713	4172	2.887783	ACTGACAAGTCTCAGTCGATGT	59.112	45.455	1.53	0.00	46.65	3.06
2810	4294	3.887110	TGACTTAGACTTGGTCGACTGAA	59.113	43.478	16.46	7.88	37.67	3.02
2836	4320	6.157994	ACTTAGCCATACCCTTGTAGAAATGA	59.842	38.462	0.00	0.00	0.00	2.57
2842	4326	6.409695	CCATACCCTTGTAGAAATGATCCAGT	60.410	42.308	0.00	0.00	0.00	4.00
2875	4359	0.747255	CTCGCTAGGTGGTGCTACAT	59.253	55.000	0.00	0.00	0.00	2.29
2906	4423	0.823356	GGTGCACACATGACCAACCT	60.823	55.000	20.43	0.00	0.00	3.50
2935	4453	0.384309	TCGACGAGTGTGCTGAACTT	59.616	50.000	0.00	0.00	0.00	2.66
3062	4581	6.732154	CAAGATCAAGACACACACAAAGAAT	58.268	36.000	0.00	0.00	0.00	2.40
3113	4632	4.698583	ACTCACGCTCGAAGTAAACTAT	57.301	40.909	0.00	0.00	0.00	2.12
3138	4657	1.202510	TGCAGCAAAATCAACCACCAC	60.203	47.619	0.00	0.00	0.00	4.16
3161	4680	4.641541	CCAATGACAGCAACCAGATTATGA	59.358	41.667	0.00	0.00	0.00	2.15
3176	4695	8.470002	ACCAGATTATGAGGAAAATGCTTTAAC	58.530	33.333	0.00	0.00	0.00	2.01
3182	4701	6.137794	TGAGGAAAATGCTTTAACAACGAA	57.862	33.333	0.00	0.00	0.00	3.85
3188	4707	2.846193	TGCTTTAACAACGAAGCCTCT	58.154	42.857	5.72	0.00	37.46	3.69
3207	4726	4.259292	CCTCTAATAAAGAAACGACGCACG	60.259	45.833	0.00	1.21	40.00	5.34
3261	4780	7.289084	GGAGACTAGATCTTAGAATTTCACCCT	59.711	40.741	0.00	0.00	38.00	4.34
3274	4793	7.851228	AGAATTTCACCCTCAAAAGAAAGTTT	58.149	30.769	0.00	0.00	33.96	2.66
3316	4835	4.228210	GCCTCCAATAAGGGGATGATATGA	59.772	45.833	0.00	0.00	42.25	2.15
3323	4842	4.713792	AAGGGGATGATATGAAGACACC	57.286	45.455	0.00	0.00	0.00	4.16
3331	4850	6.349115	GGATGATATGAAGACACCATCATTGC	60.349	42.308	0.00	0.00	39.48	3.56
3344	4863	1.240256	TCATTGCCGGGTACAACAAC	58.760	50.000	2.18	0.00	0.00	3.32
3362	4881	4.460263	ACAACTGCATGACAAACCTAGAA	58.540	39.130	0.00	0.00	0.00	2.10
3371	4890	7.147976	GCATGACAAACCTAGAATTTTCACTT	58.852	34.615	0.00	0.00	0.00	3.16
3374	4893	6.764085	TGACAAACCTAGAATTTTCACTTCGA	59.236	34.615	0.00	0.00	0.00	3.71
3394	4913	1.444553	GCTCGAGACCCTGTGTTCG	60.445	63.158	18.75	0.00	34.56	3.95
3417	4936	2.218603	AGCACCACCAAACTTAAGTCG	58.781	47.619	8.95	3.31	0.00	4.18
3437	4956	0.109412	CCTTGTACCGTCGTCTCCAC	60.109	60.000	0.00	0.00	0.00	4.02
3443	4962	0.314302	ACCGTCGTCTCCACTTTCAG	59.686	55.000	0.00	0.00	0.00	3.02
3452	4971	4.698575	GTCTCCACTTTCAGTGAAGAAGT	58.301	43.478	5.56	5.06	41.31	3.01
3460	4979	6.291377	ACTTTCAGTGAAGAAGTCATTGCTA	58.709	36.000	5.56	0.00	42.28	3.49
3466	4985	5.239525	AGTGAAGAAGTCATTGCTACAAACC	59.760	40.000	0.00	0.00	38.90	3.27
3477	4996	4.284829	TGCTACAAACCAGATCATCACA	57.715	40.909	0.00	0.00	0.00	3.58
3480	4999	3.795688	ACAAACCAGATCATCACACCT	57.204	42.857	0.00	0.00	0.00	4.00
3481	5000	4.104383	ACAAACCAGATCATCACACCTT	57.896	40.909	0.00	0.00	0.00	3.50
3484	5003	4.371624	AACCAGATCATCACACCTTGAA	57.628	40.909	0.00	0.00	37.92	2.69
3506	5025	1.889829	GTCATACGAGCTCATAGCCCT	59.110	52.381	15.40	0.00	43.77	5.19
3507	5026	3.082548	GTCATACGAGCTCATAGCCCTA	58.917	50.000	15.40	0.00	43.77	3.53
3523	5042	4.781934	AGCCCTAAAGTGGACATCAATAC	58.218	43.478	0.00	0.00	0.00	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	4.222847	GCCGACCCCTTAGGAGCG	62.223	72.222	0.00	0.00	39.89	5.03
26	27	0.178068	GGCTGTCTTCCATTAGCCGA	59.822	55.000	0.00	0.00	45.33	5.54
38	39	1.133823	TGTTGTGGTCATTGGCTGTCT	60.134	47.619	0.00	0.00	0.00	3.41
69	70	0.821301	TTTCACGCTGCCATCCACAA	60.821	50.000	0.00	0.00	0.00	3.33
170	171	0.886490	CACACGAAAGCTGAAGCCCT	60.886	55.000	0.00	0.00	43.38	5.19
189	190	4.507710	TGTAGGATCTGAAATGTGTCTGC	58.492	43.478	0.00	0.00	0.00	4.26
194	195	6.427853	TCAAGTGTTGTAGGATCTGAAATGTG	59.572	38.462	0.00	0.00	0.00	3.21
196	197	7.439157	TTCAAGTGTTGTAGGATCTGAAATG	57.561	36.000	0.00	0.00	0.00	2.32
223	224	0.109913	TAGCTTCCCGGATAGCGAGA	59.890	55.000	18.23	8.39	42.18	4.04
264	265	7.304735	TGACACAATATGAATACTTTGCACAC	58.695	34.615	0.00	0.00	0.00	3.82
268	269	8.853345	CAAACTGACACAATATGAATACTTTGC	58.147	33.333	0.00	0.00	0.00	3.68
274	275	7.176515	ACCTTGCAAACTGACACAATATGAATA	59.823	33.333	0.00	0.00	0.00	1.75
291	292	1.411977	CATCAACCACCACCTTGCAAA	59.588	47.619	0.00	0.00	0.00	3.68
307	308	7.455891	ACATATTATGCTTCTGGATGTCATCA	58.544	34.615	14.72	0.67	0.00	3.07
340	341	6.899393	AAATCTCTTGAACTATTGCACCAA	57.101	33.333	0.00	0.00	0.00	3.67
390	392	7.320797	GCTCTTACGTTCATAGACTATGTTACG	59.679	40.741	29.64	29.64	43.62	3.18
443	445	2.268298	CCGAGCGTAAGTACATGCTTT	58.732	47.619	1.79	0.00	37.91	3.51
514	516	0.973632	AGCCGTCACCACATTGACTA	59.026	50.000	2.06	0.00	43.30	2.59
565	567	6.201226	TGACAATTACACTTTTGCACTTCA	57.799	33.333	0.00	0.00	0.00	3.02
566	568	7.518731	TTTGACAATTACACTTTTGCACTTC	57.481	32.000	0.00	0.00	0.00	3.01
761	764	3.819877	GAAACACCCACGCCGACCT	62.820	63.158	0.00	0.00	0.00	3.85
762	765	3.351416	GAAACACCCACGCCGACC	61.351	66.667	0.00	0.00	0.00	4.79
802	1586	4.240881	ACTTGCTATCCACCATGTGAAT	57.759	40.909	0.00	0.00	35.23	2.57
847	1640	5.332355	GCTATCCACGCACGAAGTATTTTAG	60.332	44.000	0.00	0.00	41.61	1.85
891	1684	0.975040	CTAGGTGGTGCTCAGGCTCT	60.975	60.000	0.00	0.00	39.59	4.09
981	1787	2.510238	GCGCGATCAGGAGCAACT	60.510	61.111	12.10	0.00	32.60	3.16
982	1788	3.567797	GGCGCGATCAGGAGCAAC	61.568	66.667	12.10	0.00	34.13	4.17
983	1789	3.390183	ATGGCGCGATCAGGAGCAA	62.390	57.895	12.10	0.00	34.13	3.91
984	1790	3.853487	ATGGCGCGATCAGGAGCA	61.853	61.111	12.10	0.00	34.13	4.26
1011	1821	3.219928	AGCGACGAGGATGCCGAT	61.220	61.111	0.00	0.00	0.00	4.18
1310	2284	1.741770	GCCATGAACTCCGCGAAGT	60.742	57.895	8.23	0.00	0.00	3.01
1402	2376	4.717629	CTTGTGCTCGACGGCGGA	62.718	66.667	12.58	0.00	38.28	5.54
1481	2505	5.343593	CGTCGAACTAGATCATTTAGGATGC	59.656	44.000	0.00	0.00	0.00	3.91
1486	2519	5.511571	TGAGCGTCGAACTAGATCATTTAG	58.488	41.667	0.00	0.00	0.00	1.85
1487	2520	5.494632	TGAGCGTCGAACTAGATCATTTA	57.505	39.130	0.00	0.00	0.00	1.40
1499	2536	1.471501	CCTGATGGATTGAGCGTCGAA	60.472	52.381	0.00	0.00	34.57	3.71
1504	2541	1.442526	GGCACCTGATGGATTGAGCG	61.443	60.000	0.00	0.00	37.04	5.03
1545	2582	3.122971	GCAGCGATCACAGCAGCA	61.123	61.111	0.00	0.00	44.79	4.41
1646	2756	3.982372	GATGCGCCTTGGTCGTCGA	62.982	63.158	4.18	0.00	0.00	4.20
1698	2814	0.734253	CGAGTGCGGACCTCTCTTTG	60.734	60.000	2.38	0.00	33.06	2.77
1773	2889	2.362503	ACCGGCATGTCGAGGAGA	60.363	61.111	23.62	0.00	0.00	3.71
1846	3275	1.063174	GTGCTCTGATGATTCGTTGGC	59.937	52.381	0.00	0.00	0.00	4.52
2074	3512	3.108289	CTGGTCACGAGTGCGCTG	61.108	66.667	3.44	0.00	42.48	5.18
2378	3824	2.281070	CTGCACCTGCCACGAAGT	60.281	61.111	0.00	0.00	41.18	3.01
2408	3854	3.002656	CCGTTCCGAATTAGCTACGACTA	59.997	47.826	3.97	0.00	0.00	2.59
2409	3855	2.223433	CCGTTCCGAATTAGCTACGACT	60.223	50.000	3.97	0.00	0.00	4.18
2436	3882	1.267806	ACAAACTCGTCGATGTACCGT	59.732	47.619	4.21	0.00	0.00	4.83
2511	3962	0.388649	CTGTTCACGAAGTAGCGGCT	60.389	55.000	7.98	7.98	41.61	5.52
2530	3981	8.364894	AGTATCAAACACAAAAATTCCCCTTAC	58.635	33.333	0.00	0.00	0.00	2.34
2537	3988	9.584839	GCATGAAAGTATCAAACACAAAAATTC	57.415	29.630	0.00	0.00	42.54	2.17
2634	4088	5.063817	TCTGAGCGAAAACATACATCACATG	59.936	40.000	0.00	0.00	0.00	3.21
2640	4094	6.500684	ACAATTCTGAGCGAAAACATACAT	57.499	33.333	0.00	0.00	34.79	2.29
2646	4100	7.298122	TCATTTCTACAATTCTGAGCGAAAAC	58.702	34.615	0.00	0.00	34.79	2.43
2669	4124	6.650807	AGTCGACTGAGATTTAGCAAAATTCA	59.349	34.615	19.30	0.00	35.41	2.57
2672	4127	6.414408	CAGTCGACTGAGATTTAGCAAAAT	57.586	37.500	36.73	0.00	46.59	1.82
2673	4128	5.845985	CAGTCGACTGAGATTTAGCAAAA	57.154	39.130	36.73	0.00	46.59	2.44
2697	4152	8.809159	ATGAATATAACATCGACTGAGACTTG	57.191	34.615	0.00	0.00	0.00	3.16
2810	4294	6.382919	TTTCTACAAGGGTATGGCTAAGTT	57.617	37.500	0.00	0.00	0.00	2.66
2836	4320	7.275920	AGCGAGAAAGAAAATATACACTGGAT	58.724	34.615	0.00	0.00	0.00	3.41
2842	4326	6.984474	CCACCTAGCGAGAAAGAAAATATACA	59.016	38.462	0.00	0.00	0.00	2.29
2875	4359	2.612604	GTGTGCACCACGTCACATATA	58.387	47.619	15.69	0.00	43.94	0.86
2900	4417	2.666508	CGTCGACACTTTGATAGGTTGG	59.333	50.000	17.16	0.00	0.00	3.77
2906	4423	3.561503	CACACTCGTCGACACTTTGATA	58.438	45.455	17.16	0.00	0.00	2.15
3022	4540	5.062528	TGATCTTGCCGATGTGCATTATAA	58.937	37.500	0.00	0.00	41.70	0.98
3035	4553	1.195448	GTGTGTGTCTTGATCTTGCCG	59.805	52.381	0.00	0.00	0.00	5.69
3062	4581	5.193728	AGGCCACTGATTTTTCCCTTCTATA	59.806	40.000	5.01	0.00	0.00	1.31
3099	4618	6.255670	TGCTGCATGTTATAGTTTACTTCGAG	59.744	38.462	0.00	0.00	0.00	4.04
3113	4632	4.305769	GTGGTTGATTTTGCTGCATGTTA	58.694	39.130	1.84	0.00	0.00	2.41
3138	4657	4.641541	TCATAATCTGGTTGCTGTCATTGG	59.358	41.667	0.00	0.00	0.00	3.16
3161	4680	4.982295	GCTTCGTTGTTAAAGCATTTTCCT	59.018	37.500	2.41	0.00	45.67	3.36
3176	4695	6.090358	TCGTTTCTTTATTAGAGGCTTCGTTG	59.910	38.462	0.00	0.00	33.51	4.10
3182	4701	3.864003	GCGTCGTTTCTTTATTAGAGGCT	59.136	43.478	0.00	0.00	36.81	4.58
3243	4762	8.567285	TCTTTTGAGGGTGAAATTCTAAGATC	57.433	34.615	0.00	0.00	0.00	2.75
3274	4793	2.739913	GGCAATGTACGTAGTTTGCTCA	59.260	45.455	27.92	10.98	46.99	4.26
3293	4812	4.228210	TCATATCATCCCCTTATTGGAGGC	59.772	45.833	0.00	0.00	38.35	4.70
3316	4835	0.680921	CCCGGCAATGATGGTGTCTT	60.681	55.000	0.00	0.00	0.00	3.01
3323	4842	1.458398	TGTTGTACCCGGCAATGATG	58.542	50.000	0.00	0.00	0.00	3.07
3331	4850	0.521291	CATGCAGTTGTTGTACCCGG	59.479	55.000	0.00	0.00	0.00	5.73
3344	4863	6.583806	GTGAAAATTCTAGGTTTGTCATGCAG	59.416	38.462	0.00	0.00	0.00	4.41
3374	4893	0.318762	GAACACAGGGTCTCGAGCTT	59.681	55.000	7.81	0.00	0.00	3.74
3394	4913	3.477530	ACTTAAGTTTGGTGGTGCTCTC	58.522	45.455	1.12	0.00	0.00	3.20
3417	4936	1.153881	GGAGACGACGGTACAAGGC	60.154	63.158	0.00	0.00	0.00	4.35
3437	4956	5.686159	AGCAATGACTTCTTCACTGAAAG	57.314	39.130	0.00	0.00	32.93	2.62
3443	4962	5.008613	TGGTTTGTAGCAATGACTTCTTCAC	59.991	40.000	0.00	0.00	36.92	3.18
3452	4971	5.355071	GTGATGATCTGGTTTGTAGCAATGA	59.645	40.000	0.00	0.00	0.00	2.57
3460	4979	3.795688	AGGTGTGATGATCTGGTTTGT	57.204	42.857	0.00	0.00	0.00	2.83
3466	4985	4.999311	TGACTTTCAAGGTGTGATGATCTG	59.001	41.667	0.00	0.00	35.70	2.90
3477	4996	3.258372	TGAGCTCGTATGACTTTCAAGGT	59.742	43.478	9.64	0.00	0.00	3.50
3480	4999	5.043903	GCTATGAGCTCGTATGACTTTCAA	58.956	41.667	15.95	0.00	38.45	2.69
3481	5000	4.499865	GGCTATGAGCTCGTATGACTTTCA	60.500	45.833	15.95	0.00	41.99	2.69
3484	5003	2.297597	GGGCTATGAGCTCGTATGACTT	59.702	50.000	15.95	0.00	41.99	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.