AutoCloner

Multiple sequence alignment - TraesCS5A01G484900

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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	TraesCS5A01G484900	chr5A	100.000	2645	0	0	1	2645	656211728	656209084	0.000000e+00	4885.0
1	TraesCS5A01G484900	chr5D	87.568	1842	138	44	55	1851	528231575	528229780	0.000000e+00	2049.0
2	TraesCS5A01G484900	chr5D	89.074	540	57	1	2106	2645	434347102	434346565	0.000000e+00	669.0
3	TraesCS5A01G484900	chr5D	78.065	620	97	25	44	635	371058304	371057696	3.240000e-94	355.0
4	TraesCS5A01G484900	chr5D	82.949	217	25	8	1891	2095	528229309	528229093	4.500000e-43	185.0
5	TraesCS5A01G484900	chr5D	75.298	336	73	9	1202	1532	212627472	212627802	4.560000e-33	152.0
6	TraesCS5A01G484900	chr5B	88.880	1214	86	25	645	1851	664999086	664997915	0.000000e+00	1448.0
7	TraesCS5A01G484900	chr5B	82.888	187	24	5	1921	2100	664996136	664995951	7.580000e-36	161.0
8	TraesCS5A01G484900	chr2B	87.888	677	70	8	979	1650	230594629	230593960	0.000000e+00	785.0
9	TraesCS5A01G484900	chr2B	89.239	539	57	1	2107	2645	87539973	87540510	0.000000e+00	673.0
10	TraesCS5A01G484900	chr2B	79.941	339	68	0	1202	1540	449120461	449120123	1.570000e-62	250.0
11	TraesCS5A01G484900	chr2B	97.297	37	1	0	748	784	230594808	230594772	2.200000e-06	63.9
12	TraesCS5A01G484900	chr2D	86.835	714	79	11	945	1650	167428168	167428874	0.000000e+00	784.0
13	TraesCS5A01G484900	chr2D	89.687	543	50	4	2104	2645	310712034	310711497	0.000000e+00	688.0
14	TraesCS5A01G484900	chr2D	86.029	272	33	5	371	639	636126966	636127235	1.200000e-73	287.0
15	TraesCS5A01G484900	chr2D	84.170	259	35	6	383	637	35203193	35203449	2.030000e-61	246.0
16	TraesCS5A01G484900	chr2D	79.646	339	69	0	1202	1540	377503398	377503060	7.310000e-61	244.0
17	TraesCS5A01G484900	chr2D	81.111	90	10	3	701	784	167427975	167428063	6.110000e-07	65.8
18	TraesCS5A01G484900	chr2A	86.695	714	80	11	945	1650	183208153	183207447	0.000000e+00	778.0
19	TraesCS5A01G484900	chr2A	80.352	341	67	0	1200	1540	511922961	511922621	2.610000e-65	259.0
20	TraesCS5A01G484900	chr2A	80.952	84	13	2	701	784	183208338	183208258	2.200000e-06	63.9
21	TraesCS5A01G484900	chr1D	90.130	537	50	1	2109	2645	399776805	399776272	0.000000e+00	695.0
22	TraesCS5A01G484900	chr1D	89.074	540	53	4	2107	2645	477864861	477865395	0.000000e+00	665.0
23	TraesCS5A01G484900	chr1D	88.725	541	61	0	2105	2645	201650856	201651396	0.000000e+00	662.0
24	TraesCS5A01G484900	chr1D	77.091	550	84	19	45	571	288793858	288794388	2.000000e-71	279.0
25	TraesCS5A01G484900	chr3D	89.981	529	53	0	2109	2637	561766937	561766409	0.000000e+00	684.0
26	TraesCS5A01G484900	chr4D	89.444	540	53	3	2107	2645	37496767	37497303	0.000000e+00	678.0
27	TraesCS5A01G484900	chr4D	77.484	644	104	27	15	638	487799503	487798881	5.420000e-92	348.0
28	TraesCS5A01G484900	chr6A	89.405	538	55	2	2109	2645	513753772	513754308	0.000000e+00	676.0
29	TraesCS5A01G484900	chr7D	81.174	579	78	15	43	598	490439884	490439314	1.120000e-118	436.0
30	TraesCS5A01G484900	chr7D	78.454	608	101	24	44	635	586408918	586409511	1.160000e-98	370.0
31	TraesCS5A01G484900	chr7D	76.548	533	80	26	9	536	262337	262829	1.570000e-62	250.0
32	TraesCS5A01G484900	chr6D	77.990	577	84	20	80	618	57032053	57032624	3.280000e-84	322.0
33	TraesCS5A01G484900	chr3B	75.856	526	83	19	144	635	380867542	380868057	7.370000e-56	228.0

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	TraesCS5A01G484900	chr5A	656209084	656211728	2644	True	4885.00	4885	100.0000	1	2645	1	chr5A.!!$R1	2644
1	TraesCS5A01G484900	chr5D	528229093	528231575	2482	True	1117.00	2049	85.2585	55	2095	2	chr5D.!!$R3	2040
2	TraesCS5A01G484900	chr5D	434346565	434347102	537	True	669.00	669	89.0740	2106	2645	1	chr5D.!!$R2	539
3	TraesCS5A01G484900	chr5D	371057696	371058304	608	True	355.00	355	78.0650	44	635	1	chr5D.!!$R1	591
4	TraesCS5A01G484900	chr5B	664995951	664999086	3135	True	804.50	1448	85.8840	645	2100	2	chr5B.!!$R1	1455
5	TraesCS5A01G484900	chr2B	87539973	87540510	537	False	673.00	673	89.2390	2107	2645	1	chr2B.!!$F1	538
6	TraesCS5A01G484900	chr2B	230593960	230594808	848	True	424.45	785	92.5925	748	1650	2	chr2B.!!$R2	902
7	TraesCS5A01G484900	chr2D	310711497	310712034	537	True	688.00	688	89.6870	2104	2645	1	chr2D.!!$R1	541
8	TraesCS5A01G484900	chr2D	167427975	167428874	899	False	424.90	784	83.9730	701	1650	2	chr2D.!!$F3	949
9	TraesCS5A01G484900	chr2A	183207447	183208338	891	True	420.95	778	83.8235	701	1650	2	chr2A.!!$R2	949
10	TraesCS5A01G484900	chr1D	399776272	399776805	533	True	695.00	695	90.1300	2109	2645	1	chr1D.!!$R1	536
11	TraesCS5A01G484900	chr1D	477864861	477865395	534	False	665.00	665	89.0740	2107	2645	1	chr1D.!!$F3	538
12	TraesCS5A01G484900	chr1D	201650856	201651396	540	False	662.00	662	88.7250	2105	2645	1	chr1D.!!$F1	540
13	TraesCS5A01G484900	chr1D	288793858	288794388	530	False	279.00	279	77.0910	45	571	1	chr1D.!!$F2	526
14	TraesCS5A01G484900	chr3D	561766409	561766937	528	True	684.00	684	89.9810	2109	2637	1	chr3D.!!$R1	528
15	TraesCS5A01G484900	chr4D	37496767	37497303	536	False	678.00	678	89.4440	2107	2645	1	chr4D.!!$F1	538
16	TraesCS5A01G484900	chr4D	487798881	487799503	622	True	348.00	348	77.4840	15	638	1	chr4D.!!$R1	623
17	TraesCS5A01G484900	chr6A	513753772	513754308	536	False	676.00	676	89.4050	2109	2645	1	chr6A.!!$F1	536
18	TraesCS5A01G484900	chr7D	490439314	490439884	570	True	436.00	436	81.1740	43	598	1	chr7D.!!$R1	555
19	TraesCS5A01G484900	chr7D	586408918	586409511	593	False	370.00	370	78.4540	44	635	1	chr7D.!!$F2	591
20	TraesCS5A01G484900	chr6D	57032053	57032624	571	False	322.00	322	77.9900	80	618	1	chr6D.!!$F1	538
21	TraesCS5A01G484900	chr3B	380867542	380868057	515	False	228.00	228	75.8560	144	635	1	chr3B.!!$F1	491

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
639	738	0.242555	ACGGGCGTTTTGCTAATTGG	59.757	50.0	0.0	0.0	45.43	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2011	4105	0.249573	CCTGTTGCCTGCCACTTTTG	60.25	55.0	0.0	0.0	0.0	2.44	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
111	113	6.944557	AAAAGTTCGCCTATTAAACAATGC	57.055	33.333	0.00	0.00	0.00	3.56
121	123	9.891828	CGCCTATTAAACAATGCTAATGAAATA	57.108	29.630	0.00	0.00	0.00	1.40
454	540	7.703328	TCTGTAAAAAGGTTCACAGATTTGAC	58.297	34.615	0.00	0.00	41.76	3.18
460	546	4.874970	AGGTTCACAGATTTGACAAATGC	58.125	39.130	18.00	9.56	0.00	3.56
486	572	7.491682	TCATGATTTCAGATATGTTCACGAGA	58.508	34.615	0.00	0.00	0.00	4.04
545	634	6.207417	ACGATTTCATGAAAATGAGAGTGGTT	59.793	34.615	23.91	3.70	37.70	3.67
586	681	4.900652	AGCAAAATATGGTCATGGCCATTA	59.099	37.500	35.42	21.15	46.33	1.90
635	734	1.532007	CAAGTACGGGCGTTTTGCTAA	59.468	47.619	0.00	0.00	45.43	3.09
638	737	2.160813	AGTACGGGCGTTTTGCTAATTG	59.839	45.455	0.00	0.00	45.43	2.32
639	738	0.242555	ACGGGCGTTTTGCTAATTGG	59.757	50.000	0.00	0.00	45.43	3.16
640	739	0.242555	CGGGCGTTTTGCTAATTGGT	59.757	50.000	0.00	0.00	45.43	3.67
650	749	6.400940	CGTTTTGCTAATTGGTTGCTAATTGG	60.401	38.462	1.58	0.15	0.00	3.16
658	757	2.024414	GGTTGCTAATTGGGGCTACAG	58.976	52.381	12.90	0.00	36.30	2.74
660	759	2.418368	TGCTAATTGGGGCTACAGTG	57.582	50.000	0.00	0.00	0.00	3.66
888	1026	0.316196	GATTTCAAAGCGCCCGATCG	60.316	55.000	8.51	8.51	0.00	3.69
912	1050	1.164411	CTCGCTCACTCACTCACTCT	58.836	55.000	0.00	0.00	0.00	3.24
958	1097	1.303317	CTAAGCCACACACCCACCC	60.303	63.158	0.00	0.00	0.00	4.61
977	1116	1.647545	CCACAGCCATACCAAGCACG	61.648	60.000	0.00	0.00	0.00	5.34
1308	1456	3.708734	GTGACGGTGCCGGTTTCG	61.709	66.667	15.44	7.13	44.69	3.46
1518	1666	1.115930	ACCACCTCTTCGTCAGCTGT	61.116	55.000	14.67	0.00	0.00	4.40
1581	1729	2.345991	GCTGGCCTCAACGGTACA	59.654	61.111	3.32	0.00	34.25	2.90
1585	1733	2.345991	GCCTCAACGGTACAGCCA	59.654	61.111	0.00	0.00	36.97	4.75
1657	1805	3.694734	GGCACATGATGGAAATTACGTG	58.305	45.455	0.00	0.00	0.00	4.49
1659	1807	3.694734	CACATGATGGAAATTACGTGCC	58.305	45.455	0.00	0.00	0.00	5.01
1661	1809	3.953612	ACATGATGGAAATTACGTGCCAT	59.046	39.130	0.00	3.32	43.46	4.40
1685	1833	3.061697	CGTGCCTACGTGGAAGAAATTAC	59.938	47.826	0.00	0.00	44.99	1.89
1691	1846	4.184079	ACGTGGAAGAAATTACGTAGCT	57.816	40.909	0.17	0.00	46.50	3.32
1692	1847	4.563061	ACGTGGAAGAAATTACGTAGCTT	58.437	39.130	0.00	0.00	46.50	3.74
1695	1850	5.788531	CGTGGAAGAAATTACGTAGCTTTTG	59.211	40.000	0.00	0.00	0.00	2.44
1697	1852	7.527457	GTGGAAGAAATTACGTAGCTTTTGAT	58.473	34.615	0.00	0.00	0.00	2.57
1715	1870	7.596248	GCTTTTGATTTTTCTGCTTATGTCTCA	59.404	33.333	0.00	0.00	0.00	3.27
1723	1887	4.112634	TCTGCTTATGTCTCATGTAACGC	58.887	43.478	0.00	0.00	0.00	4.84
1740	1904	8.748582	CATGTAACGCGAGAATAAAATGTACTA	58.251	33.333	15.93	0.00	0.00	1.82
1741	1905	8.331539	TGTAACGCGAGAATAAAATGTACTAG	57.668	34.615	15.93	0.00	0.00	2.57
1742	1906	7.970061	TGTAACGCGAGAATAAAATGTACTAGT	59.030	33.333	15.93	0.00	0.00	2.57
1743	1907	7.823149	AACGCGAGAATAAAATGTACTAGTT	57.177	32.000	15.93	0.00	0.00	2.24
1744	1908	7.447243	ACGCGAGAATAAAATGTACTAGTTC	57.553	36.000	15.93	0.00	0.00	3.01
1745	1909	7.031372	ACGCGAGAATAAAATGTACTAGTTCA	58.969	34.615	15.93	1.74	0.00	3.18
1794	1958	1.623081	TTTCTTCGCCGTCGCATCAC	61.623	55.000	0.00	0.00	35.26	3.06
1811	3653	5.566189	GCATCACGATCTATGCATGGAACA	61.566	45.833	17.30	0.00	46.19	3.18
1825	3667	2.088423	TGGAACAACAACGGGCATATC	58.912	47.619	0.00	0.00	31.92	1.63
1826	3668	2.290641	TGGAACAACAACGGGCATATCT	60.291	45.455	0.00	0.00	31.92	1.98
1836	3678	5.104900	ACAACGGGCATATCTAAGTTCTTCT	60.105	40.000	0.00	0.00	0.00	2.85
1842	3684	7.220030	GGGCATATCTAAGTTCTTCTGAATGA	58.780	38.462	0.00	0.00	34.40	2.57
1859	3704	7.466805	TCTGAATGATTTAAAATCTGAGTGCG	58.533	34.615	0.00	0.00	0.00	5.34
1860	3705	6.554419	TGAATGATTTAAAATCTGAGTGCGG	58.446	36.000	0.00	0.00	0.00	5.69
1865	3710	5.888691	TTTAAAATCTGAGTGCGGCATAA	57.111	34.783	5.72	0.00	0.00	1.90
1867	3712	4.782019	AAAATCTGAGTGCGGCATAAAA	57.218	36.364	5.72	0.00	0.00	1.52
1873	3718	3.000041	TGAGTGCGGCATAAAAGTGTAG	59.000	45.455	5.72	0.00	0.00	2.74
1874	3719	3.000727	GAGTGCGGCATAAAAGTGTAGT	58.999	45.455	5.72	0.00	0.00	2.73
1876	3721	3.930848	AGTGCGGCATAAAAGTGTAGTAC	59.069	43.478	5.72	0.00	0.00	2.73
1877	3722	2.924926	TGCGGCATAAAAGTGTAGTACG	59.075	45.455	0.00	0.00	0.00	3.67
1878	3723	2.283351	GCGGCATAAAAGTGTAGTACGG	59.717	50.000	0.00	0.00	0.00	4.02
1880	3735	3.795101	CGGCATAAAAGTGTAGTACGGAG	59.205	47.826	0.00	0.00	0.00	4.63
1901	3990	5.266733	AGTACTGTGTAGTTTTTCCACGA	57.733	39.130	0.00	0.00	38.36	4.35
1902	3991	5.287226	AGTACTGTGTAGTTTTTCCACGAG	58.713	41.667	0.00	0.00	38.36	4.18
1939	4033	0.040246	TCGCACGTACGATCACACAA	60.040	50.000	24.41	0.00	37.09	3.33
1949	4043	3.706698	ACGATCACACAACCGATAGATG	58.293	45.455	0.00	0.00	39.76	2.90
1950	4044	3.052745	CGATCACACAACCGATAGATGG	58.947	50.000	0.00	0.00	39.76	3.51
1998	4092	2.041216	AGTTGATAGGGAACAACCACCC	59.959	50.000	0.00	0.00	44.79	4.61
2003	4097	2.903404	GGGAACAACCACCCAACAA	58.097	52.632	0.00	0.00	44.96	2.83
2005	4099	1.187087	GGAACAACCACCCAACAACA	58.813	50.000	0.00	0.00	38.79	3.33
2006	4100	1.134936	GGAACAACCACCCAACAACAC	60.135	52.381	0.00	0.00	38.79	3.32
2007	4101	1.546476	GAACAACCACCCAACAACACA	59.454	47.619	0.00	0.00	0.00	3.72
2008	4102	1.859302	ACAACCACCCAACAACACAT	58.141	45.000	0.00	0.00	0.00	3.21
2010	4104	3.366396	ACAACCACCCAACAACACATAA	58.634	40.909	0.00	0.00	0.00	1.90
2011	4105	3.131400	ACAACCACCCAACAACACATAAC	59.869	43.478	0.00	0.00	0.00	1.89
2012	4106	3.019799	ACCACCCAACAACACATAACA	57.980	42.857	0.00	0.00	0.00	2.41
2013	4107	3.366396	ACCACCCAACAACACATAACAA	58.634	40.909	0.00	0.00	0.00	2.83
2017	4111	5.415221	CACCCAACAACACATAACAAAAGT	58.585	37.500	0.00	0.00	0.00	2.66
2018	4112	5.290643	CACCCAACAACACATAACAAAAGTG	59.709	40.000	0.00	0.00	39.12	3.16
2019	4113	4.808364	CCCAACAACACATAACAAAAGTGG	59.192	41.667	0.00	0.00	37.58	4.00
2020	4114	4.269844	CCAACAACACATAACAAAAGTGGC	59.730	41.667	0.00	0.00	37.58	5.01
2026	4127	2.697751	ACATAACAAAAGTGGCAGGCAA	59.302	40.909	0.00	0.00	0.00	4.52
2030	4131	0.249573	CAAAAGTGGCAGGCAACAGG	60.250	55.000	0.00	0.00	41.41	4.00
2042	4143	1.218316	CAACAGGGCGGTCTAGTCC	59.782	63.158	0.00	0.00	35.78	3.85
2045	4146	2.042843	AGGGCGGTCTAGTCCTGG	60.043	66.667	4.46	0.00	45.94	4.45
2054	4155	3.566322	CGGTCTAGTCCTGGTCATTCTAG	59.434	52.174	4.46	0.00	0.00	2.43
2057	4158	1.115467	AGTCCTGGTCATTCTAGCCG	58.885	55.000	0.00	0.00	0.00	5.52
2061	4162	0.461548	CTGGTCATTCTAGCCGCTCA	59.538	55.000	0.00	0.00	0.00	4.26
2072	4173	1.060937	GCCGCTCAATGCAACGTAG	59.939	57.895	0.00	0.00	43.06	3.51
2083	4184	1.206578	CAACGTAGTGCAAAGGCCG	59.793	57.895	0.00	0.00	45.00	6.13
2125	4226	8.189119	ACAAATTAAGAGCAACTTTAATGGGA	57.811	30.769	1.81	0.00	39.72	4.37
2191	4292	4.778143	GCCGCCAACCCGATGTCT	62.778	66.667	0.00	0.00	0.00	3.41
2201	4302	1.026718	CCCGATGTCTGCCCTGTTTC	61.027	60.000	0.00	0.00	0.00	2.78
2252	4353	0.031585	GACTCATATGTGCCGGCGTA	59.968	55.000	23.90	14.00	0.00	4.42
2423	4527	0.469705	TTGGTTGCCAACATGAGCCT	60.470	50.000	10.18	0.00	38.75	4.58
2490	4594	4.093850	TCAATCACGCATGTCTTGATGAAG	59.906	41.667	8.94	0.00	34.38	3.02
2532	4637	2.021068	GCCGCTACTCCATGCTCAGA	62.021	60.000	0.00	0.00	0.00	3.27
2538	4643	3.681034	GCTACTCCATGCTCAGACACAAT	60.681	47.826	0.00	0.00	0.00	2.71
2542	4647	4.880120	ACTCCATGCTCAGACACAATATTG	59.120	41.667	14.01	14.01	0.00	1.90
2565	4670	3.460340	TCACCCTGAAACTGAAACCCTTA	59.540	43.478	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	8.583765	GCTTTCGCGAATACTTATTTTCATTTT	58.416	29.630	24.05	0.00	0.00	1.82
39	40	7.753132	TGCTTTCGCGAATACTTATTTTCATTT	59.247	29.630	24.05	0.00	39.65	2.32
40	41	7.247728	TGCTTTCGCGAATACTTATTTTCATT	58.752	30.769	24.05	0.00	39.65	2.57
41	42	6.781138	TGCTTTCGCGAATACTTATTTTCAT	58.219	32.000	24.05	0.00	39.65	2.57
111	113	9.352784	TGGCGAATTGTTTTTCTATTTCATTAG	57.647	29.630	0.00	0.00	0.00	1.73
121	123	6.917217	TTTGAATTGGCGAATTGTTTTTCT	57.083	29.167	11.72	0.00	31.58	2.52
171	175	9.662545	AAGTCACAAACAGTTTTTGAATTTTTG	57.337	25.926	17.89	0.00	33.83	2.44
439	523	4.874970	AGCATTTGTCAAATCTGTGAACC	58.125	39.130	7.87	0.00	0.00	3.62
454	540	9.181805	GAACATATCTGAAATCATGAGCATTTG	57.818	33.333	0.09	0.00	0.00	2.32
460	546	7.650903	TCTCGTGAACATATCTGAAATCATGAG	59.349	37.037	18.30	18.30	41.66	2.90
545	634	6.538945	TTTGCTACATCACCTAGATACACA	57.461	37.500	0.00	0.00	34.43	3.72
618	715	2.511879	CAATTAGCAAAACGCCCGTAC	58.488	47.619	0.00	0.00	44.04	3.67
619	716	1.469308	CCAATTAGCAAAACGCCCGTA	59.531	47.619	0.00	0.00	44.04	4.02
624	723	2.403259	AGCAACCAATTAGCAAAACGC	58.597	42.857	0.00	0.00	42.91	4.84
635	734	2.252535	AGCCCCAATTAGCAACCAAT	57.747	45.000	0.00	0.00	0.00	3.16
638	737	2.024414	CTGTAGCCCCAATTAGCAACC	58.976	52.381	0.00	0.00	0.00	3.77
639	738	2.423538	CACTGTAGCCCCAATTAGCAAC	59.576	50.000	0.00	0.00	0.00	4.17
640	739	2.722094	CACTGTAGCCCCAATTAGCAA	58.278	47.619	0.00	0.00	0.00	3.91
650	749	1.084289	CCTTTTACGCACTGTAGCCC	58.916	55.000	0.00	0.00	33.75	5.19
658	757	0.517316	CTGGTGAGCCTTTTACGCAC	59.483	55.000	0.00	0.00	37.14	5.34
660	759	1.234615	TGCTGGTGAGCCTTTTACGC	61.235	55.000	0.00	0.00	45.57	4.42
692	791	2.652172	GCGCTTTGAGATTCGTGTTTTC	59.348	45.455	0.00	0.00	0.00	2.29
888	1026	2.878520	GTGAGTGAGCGAGCGAGC	60.879	66.667	0.00	0.00	37.41	5.03
892	1030	0.455972	GAGTGAGTGAGTGAGCGAGC	60.456	60.000	0.00	0.00	0.00	5.03
893	1031	1.130373	GAGAGTGAGTGAGTGAGCGAG	59.870	57.143	0.00	0.00	0.00	5.03
894	1032	1.160989	GAGAGTGAGTGAGTGAGCGA	58.839	55.000	0.00	0.00	0.00	4.93
895	1033	1.135717	CAGAGAGTGAGTGAGTGAGCG	60.136	57.143	0.00	0.00	0.00	5.03
896	1034	2.158559	TCAGAGAGTGAGTGAGTGAGC	58.841	52.381	0.00	0.00	0.00	4.26
897	1035	3.191162	CCTTCAGAGAGTGAGTGAGTGAG	59.809	52.174	0.00	0.00	36.21	3.51
958	1097	1.647545	CGTGCTTGGTATGGCTGTGG	61.648	60.000	0.00	0.00	0.00	4.17
977	1116	2.409651	CGCTCCGCTCTCTGTACC	59.590	66.667	0.00	0.00	0.00	3.34
1437	1585	1.367840	GTCGACCTTGACCTGCAGT	59.632	57.895	13.81	0.11	32.61	4.40
1497	1645	1.272490	CAGCTGACGAAGAGGTGGTAA	59.728	52.381	8.42	0.00	35.68	2.85
1562	1710	4.752879	TACCGTTGAGGCCAGCGC	62.753	66.667	5.01	0.00	44.10	5.92
1563	1711	2.813908	GTACCGTTGAGGCCAGCG	60.814	66.667	5.01	0.00	46.52	5.18
1565	1713	1.741770	GCTGTACCGTTGAGGCCAG	60.742	63.158	5.01	0.00	46.52	4.85
1571	1719	2.345991	GGCTGGCTGTACCGTTGA	59.654	61.111	0.00	0.00	43.94	3.18
1605	1753	2.162921	CTGTCGGCTGCGTGAACTTG	62.163	60.000	0.00	0.00	0.00	3.16
1685	1833	7.538678	ACATAAGCAGAAAAATCAAAAGCTACG	59.461	33.333	0.00	0.00	0.00	3.51
1691	1846	9.414295	CATGAGACATAAGCAGAAAAATCAAAA	57.586	29.630	0.00	0.00	0.00	2.44
1692	1847	8.579006	ACATGAGACATAAGCAGAAAAATCAAA	58.421	29.630	0.00	0.00	0.00	2.69
1695	1850	9.495754	GTTACATGAGACATAAGCAGAAAAATC	57.504	33.333	0.00	0.00	0.00	2.17
1697	1852	7.518161	CGTTACATGAGACATAAGCAGAAAAA	58.482	34.615	0.00	0.00	0.00	1.94
1715	1870	7.766219	AGTACATTTTATTCTCGCGTTACAT	57.234	32.000	5.77	0.00	0.00	2.29
1760	1924	6.252441	CGGCGAAGAAATACAAATTGCAATAA	59.748	34.615	13.39	0.00	0.00	1.40
1761	1925	5.741510	CGGCGAAGAAATACAAATTGCAATA	59.258	36.000	13.39	0.00	0.00	1.90
1794	1958	4.591202	GTTGTTGTTCCATGCATAGATCG	58.409	43.478	0.00	0.00	0.00	3.69
1806	3648	2.365582	AGATATGCCCGTTGTTGTTCC	58.634	47.619	0.00	0.00	0.00	3.62
1811	3653	5.099042	AGAACTTAGATATGCCCGTTGTT	57.901	39.130	0.00	0.00	0.00	2.83
1836	3678	6.554419	CCGCACTCAGATTTTAAATCATTCA	58.446	36.000	18.37	0.40	0.00	2.57
1842	3684	4.989279	ATGCCGCACTCAGATTTTAAAT	57.011	36.364	0.00	0.00	0.00	1.40
1851	3693	1.806542	ACACTTTTATGCCGCACTCAG	59.193	47.619	0.00	0.00	0.00	3.35
1853	3695	3.000727	ACTACACTTTTATGCCGCACTC	58.999	45.455	0.00	0.00	0.00	3.51
1855	3697	3.241868	CGTACTACACTTTTATGCCGCAC	60.242	47.826	0.00	0.00	0.00	5.34
1859	3704	4.752146	ACTCCGTACTACACTTTTATGCC	58.248	43.478	0.00	0.00	0.00	4.40
1860	3705	6.471519	CAGTACTCCGTACTACACTTTTATGC	59.528	42.308	6.38	0.00	46.08	3.14
1865	3710	4.823989	ACACAGTACTCCGTACTACACTTT	59.176	41.667	6.38	0.00	46.08	2.66
1867	3712	4.013267	ACACAGTACTCCGTACTACACT	57.987	45.455	6.38	0.00	46.08	3.55
1873	3718	5.631096	GGAAAAACTACACAGTACTCCGTAC	59.369	44.000	0.00	0.00	39.10	3.67
1874	3719	5.301551	TGGAAAAACTACACAGTACTCCGTA	59.698	40.000	0.00	0.00	32.96	4.02
1876	3721	4.446719	GTGGAAAAACTACACAGTACTCCG	59.553	45.833	0.00	0.00	32.96	4.63
1877	3722	4.446719	CGTGGAAAAACTACACAGTACTCC	59.553	45.833	0.00	0.00	33.48	3.85
1878	3723	5.284079	TCGTGGAAAAACTACACAGTACTC	58.716	41.667	0.00	0.00	33.48	2.59
1880	3735	4.446719	CCTCGTGGAAAAACTACACAGTAC	59.553	45.833	0.00	0.00	34.91	2.73
1885	3740	2.473984	CGACCTCGTGGAAAAACTACAC	59.526	50.000	11.17	0.00	37.04	2.90
1939	4033	2.287977	TCGTCCATCCATCTATCGGT	57.712	50.000	0.00	0.00	0.00	4.69
1949	4043	2.096248	CTCCCTAGCTATCGTCCATCC	58.904	57.143	0.00	0.00	0.00	3.51
1950	4044	3.074675	TCTCCCTAGCTATCGTCCATC	57.925	52.381	0.00	0.00	0.00	3.51
1998	4092	4.867047	TGCCACTTTTGTTATGTGTTGTTG	59.133	37.500	0.00	0.00	31.69	3.33
2003	4097	2.035832	GCCTGCCACTTTTGTTATGTGT	59.964	45.455	0.00	0.00	31.69	3.72
2005	4099	2.315176	TGCCTGCCACTTTTGTTATGT	58.685	42.857	0.00	0.00	0.00	2.29
2006	4100	3.059166	GTTGCCTGCCACTTTTGTTATG	58.941	45.455	0.00	0.00	0.00	1.90
2007	4101	2.697751	TGTTGCCTGCCACTTTTGTTAT	59.302	40.909	0.00	0.00	0.00	1.89
2008	4102	2.100584	CTGTTGCCTGCCACTTTTGTTA	59.899	45.455	0.00	0.00	0.00	2.41
2010	4104	0.461135	CTGTTGCCTGCCACTTTTGT	59.539	50.000	0.00	0.00	0.00	2.83
2011	4105	0.249573	CCTGTTGCCTGCCACTTTTG	60.250	55.000	0.00	0.00	0.00	2.44
2012	4106	1.402107	CCCTGTTGCCTGCCACTTTT	61.402	55.000	0.00	0.00	0.00	2.27
2013	4107	1.833934	CCCTGTTGCCTGCCACTTT	60.834	57.895	0.00	0.00	0.00	2.66
2020	4114	2.859273	CTAGACCGCCCTGTTGCCTG	62.859	65.000	0.00	0.00	0.00	4.85
2026	4127	1.682684	CAGGACTAGACCGCCCTGT	60.683	63.158	5.57	0.00	40.84	4.00
2030	4131	1.043673	ATGACCAGGACTAGACCGCC	61.044	60.000	5.57	0.00	34.73	6.13
2033	4134	3.319689	GCTAGAATGACCAGGACTAGACC	59.680	52.174	2.68	2.68	34.36	3.85
2037	4138	2.307768	CGGCTAGAATGACCAGGACTA	58.692	52.381	0.00	0.00	0.00	2.59
2038	4139	1.115467	CGGCTAGAATGACCAGGACT	58.885	55.000	0.00	0.00	0.00	3.85
2042	4143	0.461548	TGAGCGGCTAGAATGACCAG	59.538	55.000	0.60	0.00	0.00	4.00
2045	4146	1.262683	GCATTGAGCGGCTAGAATGAC	59.737	52.381	26.58	17.96	0.00	3.06
2057	4158	3.296516	GCACTACGTTGCATTGAGC	57.703	52.632	7.34	0.00	42.49	4.26
2072	4173	0.321298	TCTTCCTACGGCCTTTGCAC	60.321	55.000	0.00	0.00	40.13	4.57
2100	4201	8.189119	TCCCATTAAAGTTGCTCTTAATTTGT	57.811	30.769	0.00	0.00	35.02	2.83
2101	4202	9.090692	CATCCCATTAAAGTTGCTCTTAATTTG	57.909	33.333	0.00	0.00	35.02	2.32
2102	4203	9.034800	TCATCCCATTAAAGTTGCTCTTAATTT	57.965	29.630	0.00	0.00	35.02	1.82
2103	4204	8.470002	GTCATCCCATTAAAGTTGCTCTTAATT	58.530	33.333	0.00	0.00	35.02	1.40
2125	4226	1.671054	CGCCGTCTGTTTGGGTCAT	60.671	57.895	0.00	0.00	0.00	3.06
2191	4292	1.922447	ACCCATATCAGAAACAGGGCA	59.078	47.619	0.00	0.00	39.97	5.36
2201	4302	1.665916	CGCTGCCGACCCATATCAG	60.666	63.158	0.00	0.00	36.29	2.90
2236	4337	0.531090	GGTTACGCCGGCACATATGA	60.531	55.000	28.98	0.97	0.00	2.15
2334	4438	9.930693	TTTTTATTTGTATCCGGCTTGTAAAAT	57.069	25.926	0.00	0.88	0.00	1.82
2401	4505	2.431782	GGCTCATGTTGGCAACCAATAT	59.568	45.455	26.31	11.19	45.80	1.28
2423	4527	9.311916	GCAAAATAATTTGGTTGAGCATATGTA	57.688	29.630	4.29	0.00	44.93	2.29
2461	4565	3.554524	AGACATGCGTGATTGAAAAACG	58.445	40.909	14.17	0.00	40.22	3.60
2490	4594	3.859411	TGTTTGAACAGTTCACCCAAC	57.141	42.857	15.93	16.76	39.87	3.77
2532	4637	5.241506	CAGTTTCAGGGTGACAATATTGTGT	59.758	40.000	25.42	2.33	42.43	3.72
2538	4643	4.825085	GGTTTCAGTTTCAGGGTGACAATA	59.175	41.667	0.00	0.00	0.00	1.90
2542	4647	1.954382	GGGTTTCAGTTTCAGGGTGAC	59.046	52.381	0.00	0.00	0.00	3.67
2620	4727	0.807496	GGAAGGTGATGACTGCTTGC	59.193	55.000	0.00	0.00	0.00	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.