AutoCloner

Multiple sequence alignment - TraesCS2B01G483100

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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	TraesCS2B01G483100	chr2B	100.000	2243	0	0	1	2243	680521059	680523301	0.000000e+00	4143.0
1	TraesCS2B01G483100	chr2B	82.353	510	63	12	1759	2243	410102295	410101788	3.450000e-113	418.0
2	TraesCS2B01G483100	chr2B	89.873	79	4	3	1298	1372	680573137	680573215	5.100000e-17	99.0
3	TraesCS2B01G483100	chr2A	89.813	1443	83	31	1	1405	707234028	707235444	0.000000e+00	1792.0
4	TraesCS2B01G483100	chr2A	89.869	1066	50	19	720	1758	707269282	707270316	0.000000e+00	1317.0
5	TraesCS2B01G483100	chr2A	82.353	510	63	12	1759	2243	33313582	33314089	3.450000e-113	418.0
6	TraesCS2B01G483100	chr2D	86.564	1042	57	33	618	1609	567967072	567968080	0.000000e+00	1072.0
7	TraesCS2B01G483100	chr2D	87.269	432	25	8	723	1135	567787027	567787447	1.210000e-127	466.0
8	TraesCS2B01G483100	chr2D	82.600	500	66	11	1759	2240	106162827	106163323	2.660000e-114	422.0
9	TraesCS2B01G483100	chr2D	82.353	510	61	16	1759	2243	7137010	7137515	1.240000e-112	416.0
10	TraesCS2B01G483100	chr2D	83.650	263	16	12	1181	1418	567787762	567788022	2.900000e-54	222.0
11	TraesCS2B01G483100	chr2D	79.649	285	28	19	1282	1563	568077903	568078160	6.370000e-41	178.0
12	TraesCS2B01G483100	chr2D	78.862	246	25	14	880	1115	568077474	568077702	8.350000e-30	141.0
13	TraesCS2B01G483100	chr2D	85.567	97	12	1	741	837	568076112	568076206	1.420000e-17	100.0
14	TraesCS2B01G483100	chr2D	88.406	69	6	2	990	1056	567051591	567051659	5.130000e-12	82.4
15	TraesCS2B01G483100	chr6A	92.834	628	38	4	1	622	493726555	493725929	0.000000e+00	904.0
16	TraesCS2B01G483100	chr6A	82.353	510	62	11	1759	2243	573652029	573651523	3.450000e-113	418.0
17	TraesCS2B01G483100	chr6A	82.353	510	62	11	1759	2243	573653316	573652810	3.450000e-113	418.0
18	TraesCS2B01G483100	chr4B	93.065	620	36	5	1	614	567184726	567184108	0.000000e+00	900.0
19	TraesCS2B01G483100	chr4B	92.754	621	38	5	1	615	187621875	187621256	0.000000e+00	891.0
20	TraesCS2B01G483100	chr4A	92.628	624	41	4	1	619	667312557	667313180	0.000000e+00	893.0
21	TraesCS2B01G483100	chr4A	81.907	514	59	17	1759	2243	66348875	66349383	9.650000e-109	403.0
22	TraesCS2B01G483100	chr3A	92.742	620	38	5	1	614	234972913	234972295	0.000000e+00	889.0
23	TraesCS2B01G483100	chr3A	92.593	621	39	5	1	615	429486797	429486178	0.000000e+00	885.0
24	TraesCS2B01G483100	chr3A	92.569	619	39	6	1	614	53029806	53029190	0.000000e+00	881.0
25	TraesCS2B01G483100	chr5B	92.432	621	39	6	1	615	197093277	197093895	0.000000e+00	880.0
26	TraesCS2B01G483100	chrUn	84.818	494	61	12	1759	2243	99193689	99193201	3.350000e-133	484.0
27	TraesCS2B01G483100	chr7D	82.157	510	63	11	1759	2243	418639279	418638773	1.600000e-111	412.0
28	TraesCS2B01G483100	chr1D	82.122	509	63	14	1759	2243	67860401	67859897	5.770000e-111	411.0
29	TraesCS2B01G483100	chr1D	88.660	97	10	1	1759	1855	355506727	355506632	1.410000e-22	117.0
30	TraesCS2B01G483100	chr5A	75.195	512	64	33	1759	2243	95857544	95858019	1.370000e-42	183.0
31	TraesCS2B01G483100	chr7A	75.714	280	38	13	1762	2015	277518255	277517980	1.820000e-21	113.0

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	TraesCS2B01G483100	chr2B	680521059	680523301	2242	False	4143	4143	100.0000	1	2243	1	chr2B.!!$F1	2242
1	TraesCS2B01G483100	chr2B	410101788	410102295	507	True	418	418	82.3530	1759	2243	1	chr2B.!!$R1	484
2	TraesCS2B01G483100	chr2A	707234028	707235444	1416	False	1792	1792	89.8130	1	1405	1	chr2A.!!$F2	1404
3	TraesCS2B01G483100	chr2A	707269282	707270316	1034	False	1317	1317	89.8690	720	1758	1	chr2A.!!$F3	1038
4	TraesCS2B01G483100	chr2A	33313582	33314089	507	False	418	418	82.3530	1759	2243	1	chr2A.!!$F1	484
5	TraesCS2B01G483100	chr2D	567967072	567968080	1008	False	1072	1072	86.5640	618	1609	1	chr2D.!!$F4	991
6	TraesCS2B01G483100	chr2D	7137010	7137515	505	False	416	416	82.3530	1759	2243	1	chr2D.!!$F1	484
7	TraesCS2B01G483100	chr2D	567787027	567788022	995	False	344	466	85.4595	723	1418	2	chr2D.!!$F5	695
8	TraesCS2B01G483100	chr6A	493725929	493726555	626	True	904	904	92.8340	1	622	1	chr6A.!!$R1	621
9	TraesCS2B01G483100	chr6A	573651523	573653316	1793	True	418	418	82.3530	1759	2243	2	chr6A.!!$R2	484
10	TraesCS2B01G483100	chr4B	567184108	567184726	618	True	900	900	93.0650	1	614	1	chr4B.!!$R2	613
11	TraesCS2B01G483100	chr4B	187621256	187621875	619	True	891	891	92.7540	1	615	1	chr4B.!!$R1	614
12	TraesCS2B01G483100	chr4A	667312557	667313180	623	False	893	893	92.6280	1	619	1	chr4A.!!$F2	618
13	TraesCS2B01G483100	chr4A	66348875	66349383	508	False	403	403	81.9070	1759	2243	1	chr4A.!!$F1	484
14	TraesCS2B01G483100	chr3A	234972295	234972913	618	True	889	889	92.7420	1	614	1	chr3A.!!$R2	613
15	TraesCS2B01G483100	chr3A	429486178	429486797	619	True	885	885	92.5930	1	615	1	chr3A.!!$R3	614
16	TraesCS2B01G483100	chr3A	53029190	53029806	616	True	881	881	92.5690	1	614	1	chr3A.!!$R1	613
17	TraesCS2B01G483100	chr5B	197093277	197093895	618	False	880	880	92.4320	1	615	1	chr5B.!!$F1	614
18	TraesCS2B01G483100	chr7D	418638773	418639279	506	True	412	412	82.1570	1759	2243	1	chr7D.!!$R1	484
19	TraesCS2B01G483100	chr1D	67859897	67860401	504	True	411	411	82.1220	1759	2243	1	chr1D.!!$R1	484

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
939	973	1.069906	GCTCACGCAAACACAACTAGG	60.07	52.381	0.0	0.0	35.78	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1781	2151	0.835276	GGTATTGTTCTACCCGCCCT	59.165	55.0	0.0	0.0	36.0	5.19	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
37	38	6.064060	TCATGAAGAGACAATCAAACACCTT	58.936	36.000	0.00	0.00	0.00	3.50
97	98	8.681806	TCAATCATCCAAATAGCGTCAAATTTA	58.318	29.630	0.00	0.00	0.00	1.40
114	115	1.961793	TTATATCCGCCCACAAGTGC	58.038	50.000	0.00	0.00	0.00	4.40
183	184	4.881157	AAATGCTAATAAGGGTGGGAGT	57.119	40.909	0.00	0.00	0.00	3.85
276	278	4.135306	TGCAGGTTATTTTCCGTTGTACA	58.865	39.130	0.00	0.00	0.00	2.90
286	288	1.202440	TCCGTTGTACACACTCGCTTT	60.202	47.619	0.00	0.00	0.00	3.51
387	389	4.013728	CGGAGATTTTTACCCAACATGGA	58.986	43.478	0.00	0.00	40.96	3.41
390	392	5.422012	GGAGATTTTTACCCAACATGGATGT	59.578	40.000	0.00	0.00	40.96	3.06
409	411	2.965147	TGTCAGCATAATCTCCGGATCA	59.035	45.455	3.57	0.00	0.00	2.92
440	442	4.652421	ACCCTTTTCGACATAGGCATAGTA	59.348	41.667	0.00	0.00	0.00	1.82
451	453	7.095565	CGACATAGGCATAGTATCGGTCTATAG	60.096	44.444	0.00	0.00	0.00	1.31
456	458	6.386342	AGGCATAGTATCGGTCTATAGGACTA	59.614	42.308	0.00	0.17	43.97	2.59
535	542	8.094548	AGTTGTGTGCATCTTAGTTATACAGAA	58.905	33.333	0.00	0.00	0.00	3.02
543	550	7.685155	GCATCTTAGTTATACAGAAACCGGGTA	60.685	40.741	6.32	0.00	0.00	3.69
585	592	6.749923	ATCCTCTTGATGCTACTTTTTGAC	57.250	37.500	0.00	0.00	30.54	3.18
586	593	4.690748	TCCTCTTGATGCTACTTTTTGACG	59.309	41.667	0.00	0.00	0.00	4.35
599	606	5.754778	ACTTTTTGACGTAATAAAAGCGCT	58.245	33.333	20.37	2.64	40.69	5.92
937	971	1.948104	AGCTCACGCAAACACAACTA	58.052	45.000	0.00	0.00	39.10	2.24
938	972	1.867233	AGCTCACGCAAACACAACTAG	59.133	47.619	0.00	0.00	39.10	2.57
939	973	1.069906	GCTCACGCAAACACAACTAGG	60.070	52.381	0.00	0.00	35.78	3.02
940	974	2.479837	CTCACGCAAACACAACTAGGA	58.520	47.619	0.00	0.00	0.00	2.94
941	975	2.476619	CTCACGCAAACACAACTAGGAG	59.523	50.000	0.00	0.00	0.00	3.69
942	976	2.159014	TCACGCAAACACAACTAGGAGT	60.159	45.455	0.00	0.00	0.00	3.85
968	1002	2.616458	AACATCTCCCCAGTGGCCC	61.616	63.158	2.61	0.00	0.00	5.80
1260	1578	4.214758	CCATGATCGTCTATGGTGTACGTA	59.785	45.833	0.00	0.00	39.18	3.57
1261	1579	4.801147	TGATCGTCTATGGTGTACGTAC	57.199	45.455	18.90	18.90	37.83	3.67
1262	1580	3.245990	TGATCGTCTATGGTGTACGTACG	59.754	47.826	20.18	15.01	37.83	3.67
1263	1581	2.616960	TCGTCTATGGTGTACGTACGT	58.383	47.619	25.98	25.98	37.83	3.57
1359	1716	3.693085	TCTGTACCAACTATCCTGTCGTC	59.307	47.826	0.00	0.00	0.00	4.20
1446	1815	5.337330	CCCTACTTAACGACTTCCTTGATGT	60.337	44.000	0.00	0.00	0.00	3.06
1447	1816	5.577164	CCTACTTAACGACTTCCTTGATGTG	59.423	44.000	0.00	0.00	0.00	3.21
1448	1817	3.746492	ACTTAACGACTTCCTTGATGTGC	59.254	43.478	0.00	0.00	0.00	4.57
1517	1886	4.280436	TCGCCTTCTTTTGGATAGACAA	57.720	40.909	0.00	0.00	0.00	3.18
1518	1887	4.843728	TCGCCTTCTTTTGGATAGACAAT	58.156	39.130	0.00	0.00	0.00	2.71
1519	1888	4.635765	TCGCCTTCTTTTGGATAGACAATG	59.364	41.667	0.00	0.00	0.00	2.82
1527	1897	8.272545	TCTTTTGGATAGACAATGAACAGATG	57.727	34.615	0.00	0.00	0.00	2.90
1544	1914	5.311265	ACAGATGGCATCATTGGTATACTG	58.689	41.667	27.93	15.58	32.98	2.74
1552	1922	5.741425	CATCATTGGTATACTGCTTTGTCG	58.259	41.667	2.25	0.00	0.00	4.35
1563	1933	1.136000	TGCTTTGTCGCATTGATCACG	60.136	47.619	0.00	0.00	34.44	4.35
1575	1945	1.275666	TGATCACGAGTCCCACCAAT	58.724	50.000	0.00	0.00	0.00	3.16
1576	1946	1.628340	TGATCACGAGTCCCACCAATT	59.372	47.619	0.00	0.00	0.00	2.32
1639	2009	7.421613	CGATAGAAAACGAACGGTTAAGATTTG	59.578	37.037	0.00	0.00	36.31	2.32
1641	2011	6.424683	AGAAAACGAACGGTTAAGATTTGTC	58.575	36.000	0.00	0.00	38.08	3.18
1642	2012	5.996669	AAACGAACGGTTAAGATTTGTCT	57.003	34.783	0.00	0.00	38.08	3.41
1650	2020	7.653767	ACGGTTAAGATTTGTCTACAGAAAG	57.346	36.000	0.00	0.00	0.00	2.62
1658	2028	8.545229	AGATTTGTCTACAGAAAGTTCAGATG	57.455	34.615	0.00	0.00	0.00	2.90
1665	2035	9.262358	GTCTACAGAAAGTTCAGATGTTTAACT	57.738	33.333	0.00	0.00	35.01	2.24
1675	2045	9.125026	AGTTCAGATGTTTAACTGTTGAGATTT	57.875	29.630	2.69	0.00	35.84	2.17
1711	2081	1.215647	GACACAGCCAGGTCCTACG	59.784	63.158	0.00	0.00	0.00	3.51
1781	2151	5.299824	AGGATGGCAATAGGTAGGGTATA	57.700	43.478	0.00	0.00	0.00	1.47
1793	2163	0.862554	AGGGTATAGGGCGGGTAGAA	59.137	55.000	0.00	0.00	0.00	2.10
1814	2184	4.717279	ACAATACCATACCCATACCCAC	57.283	45.455	0.00	0.00	0.00	4.61
1866	3554	3.693411	GTACCCGACGGTTACCCA	58.307	61.111	13.94	0.00	40.58	4.51
1867	3555	2.201927	GTACCCGACGGTTACCCAT	58.798	57.895	13.94	0.00	40.58	4.00
1868	3556	0.179103	GTACCCGACGGTTACCCATG	60.179	60.000	13.94	0.00	40.58	3.66
1869	3557	1.958902	TACCCGACGGTTACCCATGC	61.959	60.000	13.94	0.00	40.58	4.06
1870	3558	2.888534	CCGACGGTTACCCATGCG	60.889	66.667	5.48	0.00	0.00	4.73
1912	3600	5.069516	TCCAACGGGTAGATCAAATAGTACC	59.930	44.000	0.00	0.00	35.17	3.34
2031	3724	8.981724	ATCTCAATTCAAGTTGACAATTGATG	57.018	30.769	23.66	18.94	42.69	3.07
2032	3725	8.168790	TCTCAATTCAAGTTGACAATTGATGA	57.831	30.769	23.66	20.17	42.69	2.92
2033	3726	8.294577	TCTCAATTCAAGTTGACAATTGATGAG	58.705	33.333	23.66	20.94	42.69	2.90
2037	3731	6.940831	TCAAGTTGACAATTGATGAGAACA	57.059	33.333	13.59	0.00	30.67	3.18
2076	3771	5.840940	AGCTCACGACATAACTTTAACAC	57.159	39.130	0.00	0.00	0.00	3.32
2077	3772	4.384846	AGCTCACGACATAACTTTAACACG	59.615	41.667	0.00	0.00	0.00	4.49
2081	3776	3.742369	ACGACATAACTTTAACACGGGTG	59.258	43.478	0.00	0.00	0.00	4.61
2089	3784	1.752683	TTAACACGGGTGCACTTGTT	58.247	45.000	24.98	24.98	36.23	2.83
2120	3815	8.480501	ACGGGTAAAGTTCACATGTTAGTATAT	58.519	33.333	0.00	0.00	0.00	0.86
2148	3843	7.725367	ACAGGTAAGGTATGGGTATATCCATA	58.275	38.462	19.15	19.15	45.03	2.74
2155	3850	8.619683	AGGTATGGGTATATCCATAGGTAAAC	57.380	38.462	22.77	13.51	46.81	2.01
2166	3861	3.579586	CCATAGGTAAACGGCTATACCCA	59.420	47.826	6.62	0.00	42.11	4.51
2173	3868	1.003355	CGGCTATACCCATGCCCTG	60.003	63.158	0.00	0.00	43.42	4.45
2174	3869	1.380302	GGCTATACCCATGCCCTGG	59.620	63.158	0.00	0.00	45.51	4.45
2179	3874	0.775682	ATACCCATGCCCTGGCCATA	60.776	55.000	5.51	0.00	44.46	2.74
2191	3886	3.016736	CCTGGCCATAACTTAACTGGTG	58.983	50.000	5.51	0.00	32.42	4.17
2198	3893	5.163174	GCCATAACTTAACTGGTGGGGTATA	60.163	44.000	0.00	0.00	32.42	1.47

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	98	1.152963	GGCACTTGTGGGCGGATAT	60.153	57.895	2.81	0.00	0.00	1.63
114	115	5.719173	ACCAATGACCAAAAATATTGACGG	58.281	37.500	0.00	0.00	33.50	4.79
183	184	1.810031	GCGACCATAGCAAGGCATACA	60.810	52.381	0.00	0.00	34.19	2.29
276	278	2.490903	AGACCACGTATAAAGCGAGTGT	59.509	45.455	0.00	0.00	0.00	3.55
304	306	0.963962	GGTTGGTACTCCACTCGTCA	59.036	55.000	0.00	0.00	44.22	4.35
305	307	0.109412	CGGTTGGTACTCCACTCGTC	60.109	60.000	0.00	0.00	44.22	4.20
370	372	5.337491	GCTGACATCCATGTTGGGTAAAAAT	60.337	40.000	0.00	0.00	41.95	1.82
387	389	3.580022	TGATCCGGAGATTATGCTGACAT	59.420	43.478	11.34	0.00	34.84	3.06
390	392	3.234353	ACTGATCCGGAGATTATGCTGA	58.766	45.455	11.34	0.00	30.90	4.26
409	411	0.108019	GTCGAAAAGGGTGGTGGACT	59.892	55.000	0.00	0.00	0.00	3.85
451	453	1.338769	ACAAATGGGCGACAGTAGTCC	60.339	52.381	0.00	0.00	41.87	3.85
456	458	0.534203	AACGACAAATGGGCGACAGT	60.534	50.000	0.00	0.00	0.00	3.55
485	492	9.700831	ACTAATCACCTAAAGGCTGATAAAAAT	57.299	29.630	11.85	3.16	36.01	1.82
496	503	4.759693	TGCACACAACTAATCACCTAAAGG	59.240	41.667	0.00	0.00	42.17	3.11
509	516	7.611770	TCTGTATAACTAAGATGCACACAACT	58.388	34.615	0.00	0.00	0.00	3.16
565	572	5.597813	ACGTCAAAAAGTAGCATCAAGAG	57.402	39.130	0.00	0.00	0.00	2.85
585	592	6.711579	TCCAATAAAGAGCGCTTTTATTACG	58.288	36.000	29.07	24.53	41.43	3.18
586	593	8.905103	TTTCCAATAAAGAGCGCTTTTATTAC	57.095	30.769	29.07	13.39	41.43	1.89
637	644	0.657840	GATTTCCATGAAGGTCGGCG	59.342	55.000	0.00	0.00	39.02	6.46
678	685	3.008485	GGGAGCTTATTAGGTGGGATCTG	59.992	52.174	0.00	0.00	30.79	2.90
717	724	4.974645	AGGAACGAAGCCCATTGATATA	57.025	40.909	0.00	0.00	0.00	0.86
719	726	3.054728	TGAAGGAACGAAGCCCATTGATA	60.055	43.478	0.00	0.00	0.00	2.15
755	772	4.802563	CGTCGATCGCTACTGTATATAGGA	59.197	45.833	11.09	0.00	0.00	2.94
756	773	4.025896	CCGTCGATCGCTACTGTATATAGG	60.026	50.000	11.09	0.00	38.35	2.57
758	775	3.308053	GCCGTCGATCGCTACTGTATATA	59.692	47.826	11.09	0.00	38.35	0.86
759	776	2.095532	GCCGTCGATCGCTACTGTATAT	59.904	50.000	11.09	0.00	38.35	0.86
937	971	3.008049	GGGAGATGTTGTTGTGTACTCCT	59.992	47.826	0.00	0.00	41.19	3.69
938	972	3.335579	GGGAGATGTTGTTGTGTACTCC	58.664	50.000	0.00	0.00	40.85	3.85
939	973	3.244422	TGGGGAGATGTTGTTGTGTACTC	60.244	47.826	0.00	0.00	0.00	2.59
940	974	2.708861	TGGGGAGATGTTGTTGTGTACT	59.291	45.455	0.00	0.00	0.00	2.73
941	975	3.074412	CTGGGGAGATGTTGTTGTGTAC	58.926	50.000	0.00	0.00	0.00	2.90
942	976	2.708861	ACTGGGGAGATGTTGTTGTGTA	59.291	45.455	0.00	0.00	0.00	2.90
968	1002	2.434359	GGGAGGTTCCGAGTTGCG	60.434	66.667	0.00	0.00	37.43	4.85
1260	1578	0.888736	TTGCATGTAAGCCAGCACGT	60.889	50.000	0.00	0.00	36.62	4.49
1261	1579	0.179181	CTTGCATGTAAGCCAGCACG	60.179	55.000	10.75	0.00	36.62	5.34
1262	1580	3.708195	CTTGCATGTAAGCCAGCAC	57.292	52.632	10.75	0.00	36.62	4.40
1400	1769	4.992951	GGAAAACATACTTACGTGGACTGT	59.007	41.667	0.00	0.00	0.00	3.55
1420	1789	4.834496	TCAAGGAAGTCGTTAAGTAGGGAA	59.166	41.667	0.00	0.00	0.00	3.97
1517	1886	3.638860	ACCAATGATGCCATCTGTTCAT	58.361	40.909	6.21	0.00	31.40	2.57
1518	1887	3.090210	ACCAATGATGCCATCTGTTCA	57.910	42.857	6.21	0.00	31.40	3.18
1519	1888	6.000219	AGTATACCAATGATGCCATCTGTTC	59.000	40.000	6.21	0.00	31.40	3.18
1527	1897	4.339247	ACAAAGCAGTATACCAATGATGCC	59.661	41.667	8.45	0.00	34.24	4.40
1544	1914	1.128507	TCGTGATCAATGCGACAAAGC	59.871	47.619	0.00	0.00	37.71	3.51
1552	1922	1.009829	GTGGGACTCGTGATCAATGC	58.990	55.000	0.00	0.00	0.00	3.56
1563	1933	2.040412	ACTCTGGAAATTGGTGGGACTC	59.960	50.000	0.00	0.00	0.00	3.36
1612	1982	4.324402	TCTTAACCGTTCGTTTTCTATCGC	59.676	41.667	0.00	0.00	35.79	4.58
1627	1997	7.653767	ACTTTCTGTAGACAAATCTTAACCG	57.346	36.000	0.00	0.00	36.29	4.44
1639	2009	9.262358	AGTTAAACATCTGAACTTTCTGTAGAC	57.738	33.333	0.00	0.00	29.02	2.59
1641	2011	9.046296	ACAGTTAAACATCTGAACTTTCTGTAG	57.954	33.333	0.00	0.00	35.84	2.74
1642	2012	8.958119	ACAGTTAAACATCTGAACTTTCTGTA	57.042	30.769	0.00	0.00	35.84	2.74
1650	2020	9.173939	CAAATCTCAACAGTTAAACATCTGAAC	57.826	33.333	0.00	0.00	35.84	3.18
1675	2045	6.917477	GCTGTGTCATGAGTTTTTATTTGACA	59.083	34.615	0.00	0.00	40.64	3.58
1770	2140	1.374644	ACCCGCCCTATACCCTACCT	61.375	60.000	0.00	0.00	0.00	3.08
1781	2151	0.835276	GGTATTGTTCTACCCGCCCT	59.165	55.000	0.00	0.00	36.00	5.19
1793	2163	3.071892	CGTGGGTATGGGTATGGTATTGT	59.928	47.826	0.00	0.00	0.00	2.71
1829	2199	7.495606	CGGGTACGGGTATTAGTAGAAATTTTT	59.504	37.037	0.00	0.00	36.18	1.94
1860	3548	2.832661	GCATGGCCGCATGGGTAA	60.833	61.111	9.14	0.00	38.44	2.85
1888	3576	5.069516	GGTACTATTTGATCTACCCGTTGGA	59.930	44.000	0.00	0.00	34.81	3.53
1912	3600	8.030744	TGAATGCAAAATTGTGAATAACATGG	57.969	30.769	0.00	0.00	38.99	3.66
1931	3619	9.571810	TTTGTCAAATGTGTTATAGATGAATGC	57.428	29.630	0.00	0.00	0.00	3.56
2026	3719	8.946085	GTGAACCTATGTTAATGTTCTCATCAA	58.054	33.333	0.00	0.00	38.29	2.57
2028	3721	8.492673	TGTGAACCTATGTTAATGTTCTCATC	57.507	34.615	0.00	0.00	36.72	2.92
2029	3722	8.862325	TTGTGAACCTATGTTAATGTTCTCAT	57.138	30.769	0.00	0.00	39.49	2.90
2030	3723	7.094805	GCTTGTGAACCTATGTTAATGTTCTCA	60.095	37.037	0.00	0.00	38.61	3.27
2031	3724	7.119846	AGCTTGTGAACCTATGTTAATGTTCTC	59.880	37.037	0.00	0.00	38.29	2.87
2032	3725	6.942576	AGCTTGTGAACCTATGTTAATGTTCT	59.057	34.615	0.00	0.00	38.29	3.01
2033	3726	7.094805	TGAGCTTGTGAACCTATGTTAATGTTC	60.095	37.037	0.00	0.00	38.03	3.18
2037	3731	5.351465	CGTGAGCTTGTGAACCTATGTTAAT	59.649	40.000	0.00	0.00	33.97	1.40
2076	3771	1.136085	CGTGATTAACAAGTGCACCCG	60.136	52.381	14.63	7.46	0.00	5.28
2077	3772	1.199097	CCGTGATTAACAAGTGCACCC	59.801	52.381	14.63	0.00	0.00	4.61
2081	3776	4.214758	ACTTTACCCGTGATTAACAAGTGC	59.785	41.667	0.00	0.00	0.00	4.40
2089	3784	5.553123	ACATGTGAACTTTACCCGTGATTA	58.447	37.500	0.00	0.00	0.00	1.75
2120	3815	8.017850	TGGATATACCCATACCTTACCTGTTTA	58.982	37.037	0.00	0.00	38.00	2.01
2123	3818	5.984827	TGGATATACCCATACCTTACCTGT	58.015	41.667	0.00	0.00	38.00	4.00
2124	3819	7.290248	CCTATGGATATACCCATACCTTACCTG	59.710	44.444	1.15	0.00	44.66	4.00
2125	3820	7.034574	ACCTATGGATATACCCATACCTTACCT	60.035	40.741	1.15	0.00	44.66	3.08
2130	3825	7.343833	CGTTTACCTATGGATATACCCATACCT	59.656	40.741	1.15	0.00	44.66	3.08
2148	3843	2.224450	GCATGGGTATAGCCGTTTACCT	60.224	50.000	13.12	0.00	38.34	3.08
2173	3868	2.375146	CCCACCAGTTAAGTTATGGCC	58.625	52.381	0.00	0.00	37.64	5.36
2174	3869	2.291346	ACCCCACCAGTTAAGTTATGGC	60.291	50.000	2.91	0.00	37.64	4.40
2179	3874	4.441757	ACCTATACCCCACCAGTTAAGTT	58.558	43.478	0.00	0.00	0.00	2.66
2191	3886	5.846868	ACCCACATATAGTACCTATACCCC	58.153	45.833	0.00	0.00	32.62	4.95
2207	3902	8.856103	GGTATTAGCACAATTTTATACCCACAT	58.144	33.333	0.00	0.00	34.20	3.21
2208	3903	8.228035	GGTATTAGCACAATTTTATACCCACA	57.772	34.615	0.00	0.00	34.20	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.