AutoCloner

Multiple sequence alignment - TraesCS1D01G129000

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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	TraesCS1D01G129000	chr1D	100.000	5384	0	0	1	5384	142153153	142147770	0.000000e+00	9943.0
1	TraesCS1D01G129000	chr1D	89.638	994	76	11	1519	2510	468030352	468031320	0.000000e+00	1240.0
2	TraesCS1D01G129000	chr1B	96.890	5048	90	24	1	5002	191000941	191005967	0.000000e+00	8390.0
3	TraesCS1D01G129000	chr1B	91.010	723	55	7	1790	2510	590412998	590412284	0.000000e+00	966.0
4	TraesCS1D01G129000	chr1B	95.441	329	14	1	5057	5384	191011886	191012214	1.720000e-144	523.0
5	TraesCS1D01G129000	chr1A	95.606	2367	62	19	3	2352	148266310	148268651	0.000000e+00	3757.0
6	TraesCS1D01G129000	chr1A	97.294	1552	40	2	2382	3932	148268649	148270199	0.000000e+00	2632.0
7	TraesCS1D01G129000	chr1A	96.144	1141	37	5	3921	5057	148270416	148271553	0.000000e+00	1857.0
8	TraesCS1D01G129000	chr1A	95.763	236	8	2	5096	5329	148271651	148271886	3.940000e-101	379.0
9	TraesCS1D01G129000	chr1A	81.818	88	13	2	50	137	14127796	14127712	2.690000e-08	71.3
10	TraesCS1D01G129000	chr7B	88.454	996	88	14	1519	2512	210630008	210629038	0.000000e+00	1177.0
11	TraesCS1D01G129000	chr7B	100.000	32	0	0	3728	3759	458161036	458161005	5.820000e-05	60.2
12	TraesCS1D01G129000	chr5A	91.148	723	54	7	1790	2510	473425986	473426700	0.000000e+00	972.0
13	TraesCS1D01G129000	chr5A	88.333	60	6	1	4997	5056	25890701	25890643	2.690000e-08	71.3
14	TraesCS1D01G129000	chr4A	88.333	780	68	18	1734	2510	638241367	638240608	0.000000e+00	915.0
15	TraesCS1D01G129000	chr4A	92.157	51	4	0	5006	5056	74586931	74586881	7.480000e-09	73.1
16	TraesCS1D01G129000	chr5B	88.205	780	69	18	1734	2510	407322374	407321615	0.000000e+00	909.0
17	TraesCS1D01G129000	chr2A	86.856	738	61	15	1775	2510	448555055	448554352	0.000000e+00	793.0
18	TraesCS1D01G129000	chr2A	88.462	78	6	3	1287	1364	448555532	448555458	2.070000e-14	91.6
19	TraesCS1D01G129000	chr6A	81.395	129	20	3	5196	5323	82298729	82298854	9.540000e-18	102.0
20	TraesCS1D01G129000	chr7D	88.889	81	7	2	1284	1364	573797286	573797364	1.230000e-16	99.0
21	TraesCS1D01G129000	chr3D	92.647	68	3	2	1297	1364	335212475	335212540	4.440000e-16	97.1
22	TraesCS1D01G129000	chr3D	75.127	197	39	8	54	242	120100793	120100987	3.460000e-12	84.2
23	TraesCS1D01G129000	chr6D	76.875	160	33	4	5196	5354	65727349	65727193	2.670000e-13	87.9
24	TraesCS1D01G129000	chr6D	89.474	57	4	2	5002	5057	10116558	10116613	2.690000e-08	71.3
25	TraesCS1D01G129000	chr5D	85.185	81	10	2	1284	1364	69674921	69674999	1.240000e-11	82.4
26	TraesCS1D01G129000	chr5D	92.308	52	4	0	5006	5057	327726529	327726478	2.080000e-09	75.0
27	TraesCS1D01G129000	chr6B	97.500	40	1	0	5018	5057	532146947	532146908	9.680000e-08	69.4
28	TraesCS1D01G129000	chr4D	97.500	40	1	0	5018	5057	497545613	497545574	9.680000e-08	69.4
29	TraesCS1D01G129000	chr2B	97.500	40	1	0	5018	5057	683262194	683262155	9.680000e-08	69.4
30	TraesCS1D01G129000	chr2D	95.238	42	2	0	5016	5057	7664188	7664147	3.480000e-07	67.6

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	TraesCS1D01G129000	chr1D	142147770	142153153	5383	True	9943.00	9943	100.00000	1	5384	1	chr1D.!!$R1	5383
1	TraesCS1D01G129000	chr1D	468030352	468031320	968	False	1240.00	1240	89.63800	1519	2510	1	chr1D.!!$F1	991
2	TraesCS1D01G129000	chr1B	191000941	191005967	5026	False	8390.00	8390	96.89000	1	5002	1	chr1B.!!$F1	5001
3	TraesCS1D01G129000	chr1B	590412284	590412998	714	True	966.00	966	91.01000	1790	2510	1	chr1B.!!$R1	720
4	TraesCS1D01G129000	chr1A	148266310	148271886	5576	False	2156.25	3757	96.20175	3	5329	4	chr1A.!!$F1	5326
5	TraesCS1D01G129000	chr7B	210629038	210630008	970	True	1177.00	1177	88.45400	1519	2512	1	chr7B.!!$R1	993
6	TraesCS1D01G129000	chr5A	473425986	473426700	714	False	972.00	972	91.14800	1790	2510	1	chr5A.!!$F1	720
7	TraesCS1D01G129000	chr4A	638240608	638241367	759	True	915.00	915	88.33300	1734	2510	1	chr4A.!!$R2	776
8	TraesCS1D01G129000	chr5B	407321615	407322374	759	True	909.00	909	88.20500	1734	2510	1	chr5B.!!$R1	776
9	TraesCS1D01G129000	chr2A	448554352	448555532	1180	True	442.30	793	87.65900	1287	2510	2	chr2A.!!$R1	1223

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
886	902	0.111253	CCCTTCACTGGTCAAAGGCT	59.889	55.000	0.00	0.00	38.59	4.58	F
934	958	1.181098	GCCAAGCCAAGCCAGAGAAA	61.181	55.000	0.00	0.00	0.00	2.52	F
1175	1199	2.400896	TTTTCGTTGGGCGCTCTTGC	62.401	55.000	9.62	0.00	41.07	4.01	F
2649	2917	3.128764	TGTCGTGTAGGCTACTCATTCTG	59.871	47.826	24.07	8.79	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1874	2135	0.255890	TCCCTAAACATCAGGCTGGC	59.744	55.000	15.73	0.0	0.00	4.85	R
1935	2197	2.916934	AGTACCTTCTTAATGGCCACCA	59.083	45.455	8.16	0.0	38.19	4.17	R
3167	3436	5.460419	GGTTGCAAAATATGTGAACGAAACA	59.540	36.000	0.00	0.0	0.00	2.83	R
4426	4937	1.852157	ACCACCCTTCTGCCCATGA	60.852	57.895	0.00	0.0	0.00	3.07	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
183	186	1.155424	GCCCGTGTGACAAGTTTCGA	61.155	55.000	0.00	0.00	0.00	3.71
184	187	1.292061	CCCGTGTGACAAGTTTCGAA	58.708	50.000	0.00	0.00	0.00	3.71
231	234	9.535878	TTTTAGGCTAAACAAAACAAAATCGAT	57.464	25.926	18.87	0.00	0.00	3.59
295	298	0.319641	ACGGAAGTCACTTCTTCGCC	60.320	55.000	17.22	0.00	44.19	5.54
307	317	6.198591	GTCACTTCTTCGCCATATACAAGTAC	59.801	42.308	0.00	0.00	0.00	2.73
329	339	5.844004	ACAACACTACAAGATTCTCGTCTT	58.156	37.500	0.00	0.00	38.95	3.01
427	438	5.456186	CCCAAGATCCATTAGGTATTTCCGT	60.456	44.000	0.00	0.00	41.99	4.69
481	495	4.818546	GGTTCTCCTGTATGACATGAATGG	59.181	45.833	0.00	0.00	0.00	3.16
629	643	8.726870	ATATGCCGTAAATATATTTTAGCGGT	57.273	30.769	28.61	20.51	38.88	5.68
687	703	2.277583	GCAATAAATGCGGCACACG	58.722	52.632	4.03	0.00	46.87	4.49
886	902	0.111253	CCCTTCACTGGTCAAAGGCT	59.889	55.000	0.00	0.00	38.59	4.58
934	958	1.181098	GCCAAGCCAAGCCAGAGAAA	61.181	55.000	0.00	0.00	0.00	2.52
1175	1199	2.400896	TTTTCGTTGGGCGCTCTTGC	62.401	55.000	9.62	0.00	41.07	4.01
1484	1508	7.423199	AGATTTTTCTTCGTTTACCAAGAACC	58.577	34.615	2.75	0.00	38.16	3.62
1488	1512	5.488645	TCTTCGTTTACCAAGAACCAAAC	57.511	39.130	0.00	0.00	0.00	2.93
1565	1589	6.094048	TCAGCCTATTTTTGTAGTGCTCATTC	59.906	38.462	0.00	0.00	30.73	2.67
1874	2135	4.433186	TCCTTGTTTGTGTTGTTGACTG	57.567	40.909	0.00	0.00	0.00	3.51
1935	2197	3.741325	CCTGGAAACCGGGGAGAT	58.259	61.111	6.32	0.00	45.99	2.75
2649	2917	3.128764	TGTCGTGTAGGCTACTCATTCTG	59.871	47.826	24.07	8.79	0.00	3.02
3167	3436	3.720002	TCCTTGGTCAGGTTAGTTCCTTT	59.280	43.478	0.00	0.00	44.37	3.11
3905	4184	6.785488	ATGTGTGTAGTGTACATTTGTCAG	57.215	37.500	0.00	0.00	41.34	3.51
3940	4447	7.809546	TCAGTACTAGTCTTCTATGACCATG	57.190	40.000	0.00	0.00	37.66	3.66
4426	4937	6.344500	TCAACATTGCACCTTATTGTTTTGT	58.656	32.000	0.00	0.00	0.00	2.83
4726	5237	7.251994	TGACGTAAATTGTTGCAGTAAACTTT	58.748	30.769	0.00	0.00	0.00	2.66
4738	5249	6.980593	TGCAGTAAACTTTGCTGTTCAATAT	58.019	32.000	17.70	0.00	44.05	1.28
4798	5311	8.604890	GTCATGTAGTCTAGCTGTTTATTTTCC	58.395	37.037	0.00	0.00	0.00	3.13
4839	5359	1.838112	GTGGGATGGCATGACTGAAA	58.162	50.000	3.81	0.00	0.00	2.69
4864	5385	0.033796	TAGGGTTCGTGGGATCGAGT	60.034	55.000	0.00	0.00	40.86	4.18
4927	5448	6.781014	ACAATAGAATCCAATGCTGATTCCAT	59.219	34.615	8.86	0.00	45.96	3.41
4929	5450	8.459635	CAATAGAATCCAATGCTGATTCCATAG	58.540	37.037	8.86	0.00	45.96	2.23
4958	5479	1.141665	GGCTTAAATTGCCCCGCTG	59.858	57.895	0.00	0.00	44.32	5.18
5013	5534	8.554490	AGTGAACTGATACAATAATACTCCCT	57.446	34.615	0.00	0.00	0.00	4.20
5015	5536	9.262358	GTGAACTGATACAATAATACTCCCTTC	57.738	37.037	0.00	0.00	0.00	3.46
5016	5537	8.988060	TGAACTGATACAATAATACTCCCTTCA	58.012	33.333	0.00	0.00	0.00	3.02
5020	5541	9.868277	CTGATACAATAATACTCCCTTCATCTC	57.132	37.037	0.00	0.00	0.00	2.75
5179	5759	9.474920	CTAACTGAATCTTGATGAGGAGTTATC	57.525	37.037	0.00	0.00	30.25	1.75
5181	5761	7.499292	ACTGAATCTTGATGAGGAGTTATCTG	58.501	38.462	0.00	0.00	0.00	2.90
5263	5845	1.227176	GATCGAACCAGCCCCGTAC	60.227	63.158	0.00	0.00	0.00	3.67
5329	5911	2.158711	TGTCTTCCCAGGATGCATCATC	60.159	50.000	27.25	11.66	39.87	2.92
5330	5912	2.106166	GTCTTCCCAGGATGCATCATCT	59.894	50.000	27.25	13.80	40.39	2.90
5331	5913	3.326006	GTCTTCCCAGGATGCATCATCTA	59.674	47.826	27.25	5.91	40.39	1.98
5332	5914	3.581770	TCTTCCCAGGATGCATCATCTAG	59.418	47.826	27.25	15.41	40.39	2.43
5333	5915	2.981921	TCCCAGGATGCATCATCTAGT	58.018	47.619	27.25	2.38	40.39	2.57
5334	5916	2.636403	TCCCAGGATGCATCATCTAGTG	59.364	50.000	27.25	13.46	40.39	2.74
5335	5917	2.290134	CCCAGGATGCATCATCTAGTGG	60.290	54.545	27.25	20.09	40.39	4.00
5336	5918	2.371179	CCAGGATGCATCATCTAGTGGT	59.629	50.000	27.25	0.00	40.39	4.16
5337	5919	3.580022	CCAGGATGCATCATCTAGTGGTA	59.420	47.826	27.25	0.00	40.39	3.25
5338	5920	4.322574	CCAGGATGCATCATCTAGTGGTAG	60.323	50.000	27.25	5.85	40.39	3.18
5339	5921	4.525874	CAGGATGCATCATCTAGTGGTAGA	59.474	45.833	27.25	0.00	40.39	2.59
5340	5922	5.187381	CAGGATGCATCATCTAGTGGTAGAT	59.813	44.000	27.25	0.00	45.47	1.98
5341	5923	5.784390	AGGATGCATCATCTAGTGGTAGATT	59.216	40.000	27.25	0.00	42.48	2.40
5342	5924	6.070881	AGGATGCATCATCTAGTGGTAGATTC	60.071	42.308	27.25	4.46	42.48	2.52
5343	5925	5.126396	TGCATCATCTAGTGGTAGATTCG	57.874	43.478	0.00	0.00	42.48	3.34
5344	5926	3.923461	GCATCATCTAGTGGTAGATTCGC	59.077	47.826	0.00	0.00	42.48	4.70
5345	5927	4.321601	GCATCATCTAGTGGTAGATTCGCT	60.322	45.833	0.00	0.00	42.48	4.93
5346	5928	5.398169	CATCATCTAGTGGTAGATTCGCTC	58.602	45.833	0.00	0.00	42.48	5.03
5347	5929	4.461198	TCATCTAGTGGTAGATTCGCTCA	58.539	43.478	0.00	0.00	42.48	4.26
5348	5930	5.073428	TCATCTAGTGGTAGATTCGCTCAT	58.927	41.667	0.00	0.00	42.48	2.90
5349	5931	5.536538	TCATCTAGTGGTAGATTCGCTCATT	59.463	40.000	0.00	0.00	42.48	2.57
5350	5932	5.188327	TCTAGTGGTAGATTCGCTCATTG	57.812	43.478	0.00	0.00	29.69	2.82
5351	5933	3.185246	AGTGGTAGATTCGCTCATTGG	57.815	47.619	0.00	0.00	0.00	3.16
5352	5934	2.766263	AGTGGTAGATTCGCTCATTGGA	59.234	45.455	0.00	0.00	0.00	3.53
5353	5935	2.866762	GTGGTAGATTCGCTCATTGGAC	59.133	50.000	0.00	0.00	0.00	4.02
5354	5936	2.158957	TGGTAGATTCGCTCATTGGACC	60.159	50.000	0.00	0.00	0.00	4.46
5355	5937	2.158957	GGTAGATTCGCTCATTGGACCA	60.159	50.000	0.00	0.00	0.00	4.02
5356	5938	3.495100	GGTAGATTCGCTCATTGGACCAT	60.495	47.826	0.00	0.00	0.00	3.55
5357	5939	4.262463	GGTAGATTCGCTCATTGGACCATA	60.262	45.833	0.00	0.00	0.00	2.74
5358	5940	4.000331	AGATTCGCTCATTGGACCATAG	58.000	45.455	0.00	0.00	0.00	2.23
5359	5941	2.620251	TTCGCTCATTGGACCATAGG	57.380	50.000	0.00	0.00	0.00	2.57
5360	5942	0.106708	TCGCTCATTGGACCATAGGC	59.893	55.000	0.00	0.00	0.00	3.93
5361	5943	0.179048	CGCTCATTGGACCATAGGCA	60.179	55.000	0.00	0.00	0.00	4.75
5362	5944	1.602311	GCTCATTGGACCATAGGCAG	58.398	55.000	0.00	0.00	0.00	4.85
5363	5945	1.141657	GCTCATTGGACCATAGGCAGA	59.858	52.381	0.00	0.00	0.00	4.26
5364	5946	2.224719	GCTCATTGGACCATAGGCAGAT	60.225	50.000	0.00	0.00	0.00	2.90
5365	5947	3.749954	GCTCATTGGACCATAGGCAGATT	60.750	47.826	0.00	0.00	0.00	2.40
5366	5948	4.505566	GCTCATTGGACCATAGGCAGATTA	60.506	45.833	0.00	0.00	0.00	1.75
5367	5949	5.805751	GCTCATTGGACCATAGGCAGATTAT	60.806	44.000	0.00	0.00	0.00	1.28
5368	5950	6.204852	TCATTGGACCATAGGCAGATTATT	57.795	37.500	0.00	0.00	0.00	1.40
5369	5951	6.005823	TCATTGGACCATAGGCAGATTATTG	58.994	40.000	0.00	0.00	0.00	1.90
5370	5952	3.754965	TGGACCATAGGCAGATTATTGC	58.245	45.455	0.00	0.00	43.34	3.56
5371	5953	3.138098	TGGACCATAGGCAGATTATTGCA	59.862	43.478	0.00	0.00	45.86	4.08
5372	5954	4.144297	GGACCATAGGCAGATTATTGCAA	58.856	43.478	0.00	0.00	45.86	4.08
5373	5955	4.217118	GGACCATAGGCAGATTATTGCAAG	59.783	45.833	4.94	0.00	45.86	4.01
5374	5956	4.147321	ACCATAGGCAGATTATTGCAAGG	58.853	43.478	4.94	0.00	45.86	3.61
5375	5957	4.141181	ACCATAGGCAGATTATTGCAAGGA	60.141	41.667	4.94	0.00	45.86	3.36
5376	5958	4.828939	CCATAGGCAGATTATTGCAAGGAA	59.171	41.667	4.94	1.82	45.86	3.36
5377	5959	5.479375	CCATAGGCAGATTATTGCAAGGAAT	59.521	40.000	4.94	7.18	45.86	3.01
5378	5960	6.014840	CCATAGGCAGATTATTGCAAGGAATT	60.015	38.462	4.94	0.00	45.86	2.17
5379	5961	5.945144	AGGCAGATTATTGCAAGGAATTT	57.055	34.783	4.94	0.00	45.86	1.82
5380	5962	5.667466	AGGCAGATTATTGCAAGGAATTTG	58.333	37.500	16.88	16.88	45.86	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	5.046663	GCCTCCTTATTTTTGGATCAAACCA	60.047	40.000	0.00	0.00	32.79	3.67
252	255	6.262273	GTGGACTCCTTGACATAAACAAAAGA	59.738	38.462	0.00	0.00	0.00	2.52
307	317	5.059832	CGAAGACGAGAATCTTGTAGTGTTG	59.940	44.000	2.61	0.00	39.08	3.33
329	339	8.940768	AGTCAAAAATTCCTGAAAATTTTCGA	57.059	26.923	22.51	13.64	44.17	3.71
379	390	4.578105	TCCCATTGCAACCAATTTGAAAAC	59.422	37.500	0.00	0.00	39.60	2.43
389	400	0.831288	CTTGGGTCCCATTGCAACCA	60.831	55.000	12.68	0.00	34.62	3.67
448	462	7.399191	TGTCATACAGGAGAACCTTATTAGTGT	59.601	37.037	0.00	0.00	45.36	3.55
481	495	0.657840	CGTCGGAGAAATTGATGGCC	59.342	55.000	0.00	0.00	39.69	5.36
588	602	4.869297	CGGCATATTTTCAATTTCTGCCAA	59.131	37.500	10.85	0.00	46.20	4.52
687	703	4.280929	GGGCATCAGGTTGGGTTTTATATC	59.719	45.833	0.00	0.00	0.00	1.63
886	902	1.059584	ACTGTGATGTGGGTGGTGGA	61.060	55.000	0.00	0.00	0.00	4.02
934	958	2.291043	CCACCTACGCCTGGTCCTT	61.291	63.158	0.00	0.00	35.28	3.36
1077	1101	1.002134	CCCAGCACAGATCCGGTTT	60.002	57.895	0.00	0.00	0.00	3.27
1175	1199	0.321387	TCCTGCTGCTTCTGCTCAAG	60.321	55.000	0.00	0.00	40.48	3.02
1488	1512	2.741612	TCAGCCGCTTTGAAACATTTG	58.258	42.857	0.00	0.00	0.00	2.32
1565	1589	4.503007	CCATAGTTACACGAGGATCAAACG	59.497	45.833	0.00	0.00	33.17	3.60
1874	2135	0.255890	TCCCTAAACATCAGGCTGGC	59.744	55.000	15.73	0.00	0.00	4.85
1935	2197	2.916934	AGTACCTTCTTAATGGCCACCA	59.083	45.455	8.16	0.00	38.19	4.17
2674	2942	5.587388	AATCAAAATAGCACAGACCATGG	57.413	39.130	11.19	11.19	0.00	3.66
3167	3436	5.460419	GGTTGCAAAATATGTGAACGAAACA	59.540	36.000	0.00	0.00	0.00	2.83
3224	3493	9.333724	AGCAAAAACAAATGAAAGATCAGAAAT	57.666	25.926	0.00	0.00	39.39	2.17
3940	4447	6.043411	GGCGGTCCTCATAACTATGATTATC	58.957	44.000	0.00	0.00	41.46	1.75
4407	4918	5.933463	CCATGACAAAACAATAAGGTGCAAT	59.067	36.000	0.00	0.00	0.00	3.56
4426	4937	1.852157	ACCACCCTTCTGCCCATGA	60.852	57.895	0.00	0.00	0.00	3.07
4726	5237	5.335819	CCATGACACAACATATTGAACAGCA	60.336	40.000	0.00	0.00	39.30	4.41
4738	5249	1.596603	CACTCTGCCATGACACAACA	58.403	50.000	0.00	0.00	0.00	3.33
4798	5311	3.557824	GGTCGCAACTACCCAACG	58.442	61.111	0.00	0.00	0.00	4.10
4823	5336	2.424956	GTTCCTTTCAGTCATGCCATCC	59.575	50.000	0.00	0.00	0.00	3.51
4864	5385	8.822805	CATACTAAACCTATAGCTTCCCCAATA	58.177	37.037	0.00	0.00	0.00	1.90
4927	5448	5.261216	CAATTTAAGCCTCCCCTGTTTCTA	58.739	41.667	0.00	0.00	0.00	2.10
4929	5450	3.368427	GCAATTTAAGCCTCCCCTGTTTC	60.368	47.826	0.00	0.00	0.00	2.78
4958	5479	3.219281	TGTTTCCTTTCTACCTGTTGCC	58.781	45.455	0.00	0.00	0.00	4.52
5064	5610	8.691661	ACCAATATTTACTATTCGCTCCATTT	57.308	30.769	0.00	0.00	0.00	2.32
5075	5621	9.216117	GCCGTCTATTCAACCAATATTTACTAT	57.784	33.333	0.00	0.00	0.00	2.12
5085	5631	1.274167	ACTCGCCGTCTATTCAACCAA	59.726	47.619	0.00	0.00	0.00	3.67
5110	5690	2.362503	ACAGGATCGGACGGCTCA	60.363	61.111	0.00	0.00	0.00	4.26
5179	5759	0.603707	TCAGGCCGAAACTGCTTCAG	60.604	55.000	0.00	0.00	35.94	3.02
5181	5761	0.884704	TGTCAGGCCGAAACTGCTTC	60.885	55.000	0.00	0.00	35.94	3.86
5233	5814	0.931005	GTTCGATCGCCATCAACTCC	59.069	55.000	11.09	0.00	0.00	3.85
5234	5815	0.931005	GGTTCGATCGCCATCAACTC	59.069	55.000	11.09	0.46	0.00	3.01
5258	5840	3.548014	CCTTGTTCAAGCAAACAGTACGG	60.548	47.826	7.00	0.00	40.08	4.02
5260	5842	3.372060	GCCTTGTTCAAGCAAACAGTAC	58.628	45.455	7.00	0.00	40.08	2.73
5263	5845	1.856802	GGCCTTGTTCAAGCAAACAG	58.143	50.000	0.00	0.00	40.08	3.16
5329	5911	4.038042	TCCAATGAGCGAATCTACCACTAG	59.962	45.833	0.00	0.00	0.00	2.57
5330	5912	3.958147	TCCAATGAGCGAATCTACCACTA	59.042	43.478	0.00	0.00	0.00	2.74
5331	5913	2.766263	TCCAATGAGCGAATCTACCACT	59.234	45.455	0.00	0.00	0.00	4.00
5332	5914	2.866762	GTCCAATGAGCGAATCTACCAC	59.133	50.000	0.00	0.00	0.00	4.16
5333	5915	2.158957	GGTCCAATGAGCGAATCTACCA	60.159	50.000	0.00	0.00	0.00	3.25
5334	5916	2.158957	TGGTCCAATGAGCGAATCTACC	60.159	50.000	0.00	0.00	41.98	3.18
5335	5917	3.179443	TGGTCCAATGAGCGAATCTAC	57.821	47.619	0.00	0.00	41.98	2.59
5336	5918	4.021104	CCTATGGTCCAATGAGCGAATCTA	60.021	45.833	0.00	0.00	41.98	1.98
5337	5919	3.244353	CCTATGGTCCAATGAGCGAATCT	60.244	47.826	0.00	0.00	41.98	2.40
5338	5920	3.070018	CCTATGGTCCAATGAGCGAATC	58.930	50.000	0.00	0.00	41.98	2.52
5339	5921	2.811873	GCCTATGGTCCAATGAGCGAAT	60.812	50.000	0.00	0.00	41.98	3.34
5340	5922	1.475034	GCCTATGGTCCAATGAGCGAA	60.475	52.381	0.00	0.00	41.98	4.70
5341	5923	0.106708	GCCTATGGTCCAATGAGCGA	59.893	55.000	0.00	0.00	41.98	4.93
5342	5924	0.179048	TGCCTATGGTCCAATGAGCG	60.179	55.000	0.00	0.00	41.98	5.03
5343	5925	1.141657	TCTGCCTATGGTCCAATGAGC	59.858	52.381	0.00	0.00	39.48	4.26
5344	5926	3.784511	ATCTGCCTATGGTCCAATGAG	57.215	47.619	0.00	0.00	0.00	2.90
5345	5927	5.848286	ATAATCTGCCTATGGTCCAATGA	57.152	39.130	0.00	0.00	0.00	2.57
5346	5928	5.336213	GCAATAATCTGCCTATGGTCCAATG	60.336	44.000	0.00	0.00	36.25	2.82
5347	5929	4.768968	GCAATAATCTGCCTATGGTCCAAT	59.231	41.667	0.00	0.00	36.25	3.16
5348	5930	4.144297	GCAATAATCTGCCTATGGTCCAA	58.856	43.478	0.00	0.00	36.25	3.53
5349	5931	3.138098	TGCAATAATCTGCCTATGGTCCA	59.862	43.478	0.00	0.00	41.90	4.02
5350	5932	3.754965	TGCAATAATCTGCCTATGGTCC	58.245	45.455	0.00	0.00	41.90	4.46
5351	5933	4.217118	CCTTGCAATAATCTGCCTATGGTC	59.783	45.833	0.00	0.00	41.90	4.02
5352	5934	4.141181	TCCTTGCAATAATCTGCCTATGGT	60.141	41.667	0.00	0.00	41.90	3.55
5353	5935	4.401022	TCCTTGCAATAATCTGCCTATGG	58.599	43.478	0.00	0.00	41.90	2.74
5354	5936	6.585695	ATTCCTTGCAATAATCTGCCTATG	57.414	37.500	0.00	0.00	41.90	2.23
5355	5937	7.439381	CAAATTCCTTGCAATAATCTGCCTAT	58.561	34.615	0.00	0.00	41.90	2.57
5356	5938	6.808829	CAAATTCCTTGCAATAATCTGCCTA	58.191	36.000	0.00	0.00	41.90	3.93
5357	5939	5.667466	CAAATTCCTTGCAATAATCTGCCT	58.333	37.500	0.00	0.00	41.90	4.75
5358	5940	5.978934	CAAATTCCTTGCAATAATCTGCC	57.021	39.130	0.00	0.00	41.90	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.