AutoCloner

Multiple sequence alignment - TraesCS4D01G066000

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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	TraesCS4D01G066000	chr4D	100.000	2360	0	0	1	2360	40823447	40825806	0.000000e+00	4359.0
1	TraesCS4D01G066000	chr4A	92.527	1686	102	7	678	2360	558676680	558675016	0.000000e+00	2394.0
2	TraesCS4D01G066000	chr4A	93.369	377	20	4	1	373	558677565	558677190	9.530000e-154	553.0
3	TraesCS4D01G066000	chr4A	97.987	149	2	1	512	660	558677167	558677020	8.370000e-65	257.0
4	TraesCS4D01G066000	chr4B	93.362	919	47	4	890	1804	59866217	59867125	0.000000e+00	1347.0
5	TraesCS4D01G066000	chr4B	96.689	151	5	0	510	660	59865030	59865180	3.890000e-63	252.0
6	TraesCS4D01G066000	chr4B	88.177	203	5	3	5	207	59864618	59864801	8.490000e-55	224.0
7	TraesCS4D01G066000	chr4B	95.652	115	4	1	737	850	59865216	59865330	1.440000e-42	183.0
8	TraesCS4D01G066000	chr4B	86.207	87	4	4	328	406	59864941	59865027	1.160000e-13	87.9
9	TraesCS4D01G066000	chr3B	84.352	409	50	5	1929	2324	546181199	546180792	2.840000e-104	388.0
10	TraesCS4D01G066000	chr2B	79.322	590	93	17	872	1433	114431230	114430642	1.020000e-103	387.0
11	TraesCS4D01G066000	chr2D	82.207	444	57	13	943	1368	74986589	74986150	1.720000e-96	363.0
12	TraesCS4D01G066000	chr2D	85.308	211	30	1	1722	1932	346076678	346076469	1.420000e-52	217.0
13	TraesCS4D01G066000	chr2D	75.831	451	87	18	1926	2360	142477003	142476559	2.380000e-50	209.0
14	TraesCS4D01G066000	chr2A	83.636	385	51	6	996	1368	74562115	74561731	3.730000e-93	351.0
15	TraesCS4D01G066000	chr2A	89.899	99	9	1	408	506	773486940	773487037	2.460000e-25	126.0
16	TraesCS4D01G066000	chr2A	85.366	123	5	4	408	518	2797368	2797489	5.330000e-22	115.0
17	TraesCS4D01G066000	chrUn	83.898	354	47	9	1727	2073	83954322	83954672	1.750000e-86	329.0
18	TraesCS4D01G066000	chrUn	75.954	524	89	24	1830	2323	26526182	26526698	3.920000e-58	235.0
19	TraesCS4D01G066000	chr5D	78.035	519	85	12	1723	2215	423247885	423247370	1.370000e-77	300.0
20	TraesCS4D01G066000	chr5D	94.382	89	4	1	418	506	529823881	529823794	4.090000e-28	135.0
21	TraesCS4D01G066000	chr5D	90.000	100	9	1	408	507	29485199	29485101	6.850000e-26	128.0
22	TraesCS4D01G066000	chr5D	92.941	85	4	2	408	492	462033622	462033540	3.190000e-24	122.0
23	TraesCS4D01G066000	chr5D	84.000	75	10	2	307	379	48778411	48778485	1.170000e-08	71.3
24	TraesCS4D01G066000	chr5D	82.278	79	5	8	307	379	48767762	48767837	2.530000e-05	60.2
25	TraesCS4D01G066000	chr5D	80.723	83	6	9	307	383	48770554	48770632	3.280000e-04	56.5
26	TraesCS4D01G066000	chr5D	80.723	83	6	9	307	383	48772522	48772600	3.280000e-04	56.5
27	TraesCS4D01G066000	chr5D	81.013	79	6	8	307	379	48768591	48768666	1.000000e-03	54.7
28	TraesCS4D01G066000	chr5D	82.812	64	6	5	307	367	48774489	48774550	4.000000e-03	52.8
29	TraesCS4D01G066000	chr5D	83.077	65	4	6	307	367	48780362	48780423	4.000000e-03	52.8
30	TraesCS4D01G066000	chr3D	88.626	211	22	2	1723	1932	419562627	419562836	3.010000e-64	255.0
31	TraesCS4D01G066000	chr3D	85.782	211	30	0	1722	1932	385432127	385432337	8.490000e-55	224.0
32	TraesCS4D01G066000	chr3D	75.885	452	83	20	1926	2360	13292881	13293323	8.550000e-50	207.0
33	TraesCS4D01G066000	chr3A	89.109	202	17	3	1723	1924	747410907	747411103	1.810000e-61	246.0
34	TraesCS4D01G066000	chr3A	76.094	297	64	6	1917	2212	36082086	36082376	5.260000e-32	148.0
35	TraesCS4D01G066000	chr7A	87.619	210	24	2	1723	1932	523725	523932	2.340000e-60	243.0
36	TraesCS4D01G066000	chr7A	73.745	518	90	33	1741	2221	139416968	139417476	6.750000e-36	161.0
37	TraesCS4D01G066000	chr5B	85.308	211	27	4	1722	1931	530963496	530963289	5.110000e-52	215.0
38	TraesCS4D01G066000	chr5B	93.000	100	5	2	408	506	456498054	456498152	6.800000e-31	145.0
39	TraesCS4D01G066000	chr5B	75.159	314	46	25	525	823	5433723	5433427	4.120000e-23	119.0
40	TraesCS4D01G066000	chr6D	75.245	408	83	14	1926	2320	448819894	448820296	6.700000e-41	178.0
41	TraesCS4D01G066000	chr6D	89.899	99	6	2	408	506	237426248	237426154	8.860000e-25	124.0
42	TraesCS4D01G066000	chr7B	74.402	418	83	19	1920	2320	66883912	66884322	8.730000e-35	158.0
43	TraesCS4D01G066000	chr7D	91.176	102	6	2	408	506	20298834	20298935	4.090000e-28	135.0
44	TraesCS4D01G066000	chr6A	89.899	99	9	1	408	506	100670800	100670703	2.460000e-25	126.0
45	TraesCS4D01G066000	chr6B	89.000	100	9	2	408	507	599532286	599532383	3.190000e-24	122.0
46	TraesCS4D01G066000	chr5A	87.234	94	11	1	694	786	435247664	435247757	3.210000e-19	106.0

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	TraesCS4D01G066000	chr4D	40823447	40825806	2359	False	4359.00	4359	100.000000	1	2360	1	chr4D.!!$F1	2359
1	TraesCS4D01G066000	chr4A	558675016	558677565	2549	True	1068.00	2394	94.627667	1	2360	3	chr4A.!!$R1	2359
2	TraesCS4D01G066000	chr4B	59864618	59867125	2507	False	418.78	1347	92.017400	5	1804	5	chr4B.!!$F1	1799
3	TraesCS4D01G066000	chr2B	114430642	114431230	588	True	387.00	387	79.322000	872	1433	1	chr2B.!!$R1	561
4	TraesCS4D01G066000	chrUn	26526182	26526698	516	False	235.00	235	75.954000	1830	2323	1	chrUn.!!$F1	493
5	TraesCS4D01G066000	chr5D	423247370	423247885	515	True	300.00	300	78.035000	1723	2215	1	chr5D.!!$R2	492

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
851	1220	0.611714	ACCACGATGTACCAACTCCC	59.388	55.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2202	3486	1.066858	ACCTCATGCACCGTAGACAAG	60.067	52.381	0.0	0.0	0.0	3.16	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
54	55	0.847670	TACGTCTGTTGTTTCGCACG	59.152	50.000	0.00	0.00	0.00	5.34
217	218	2.301009	ACTGTTAAGGGGAGTTGGTACG	59.699	50.000	0.00	0.00	0.00	3.67
406	451	6.814076	CGTAGCAACTCTCCTTTAATAGTG	57.186	41.667	0.00	0.00	0.00	2.74
407	452	6.561614	CGTAGCAACTCTCCTTTAATAGTGA	58.438	40.000	0.00	0.00	0.00	3.41
409	454	7.544566	CGTAGCAACTCTCCTTTAATAGTGAAA	59.455	37.037	0.00	0.00	0.00	2.69
410	455	9.384764	GTAGCAACTCTCCTTTAATAGTGAAAT	57.615	33.333	0.00	0.00	0.00	2.17
412	457	8.103305	AGCAACTCTCCTTTAATAGTGAAATCA	58.897	33.333	0.00	0.00	0.00	2.57
413	458	8.394121	GCAACTCTCCTTTAATAGTGAAATCAG	58.606	37.037	0.00	0.00	0.00	2.90
414	459	8.887717	CAACTCTCCTTTAATAGTGAAATCAGG	58.112	37.037	0.00	0.00	0.00	3.86
415	460	7.569240	ACTCTCCTTTAATAGTGAAATCAGGG	58.431	38.462	0.00	0.00	0.00	4.45
416	461	6.900194	TCTCCTTTAATAGTGAAATCAGGGG	58.100	40.000	0.00	0.00	0.00	4.79
417	462	6.013554	TCCTTTAATAGTGAAATCAGGGGG	57.986	41.667	0.00	0.00	0.00	5.40
439	484	6.716284	GGGGGAGATGATTAGATTAGAAAGG	58.284	44.000	0.00	0.00	0.00	3.11
440	485	6.502158	GGGGGAGATGATTAGATTAGAAAGGA	59.498	42.308	0.00	0.00	0.00	3.36
441	486	7.017651	GGGGGAGATGATTAGATTAGAAAGGAA	59.982	40.741	0.00	0.00	0.00	3.36
442	487	8.440771	GGGGAGATGATTAGATTAGAAAGGAAA	58.559	37.037	0.00	0.00	0.00	3.13
443	488	9.853177	GGGAGATGATTAGATTAGAAAGGAAAA	57.147	33.333	0.00	0.00	0.00	2.29
477	522	1.742768	CGTAGGATGAGGTGGGAGC	59.257	63.158	0.00	0.00	0.00	4.70
478	523	1.043116	CGTAGGATGAGGTGGGAGCA	61.043	60.000	0.00	0.00	0.00	4.26
479	524	1.428869	GTAGGATGAGGTGGGAGCAT	58.571	55.000	0.00	0.00	0.00	3.79
480	525	1.071385	GTAGGATGAGGTGGGAGCATG	59.929	57.143	0.00	0.00	0.00	4.06
481	526	1.150081	GGATGAGGTGGGAGCATGG	59.850	63.158	0.00	0.00	0.00	3.66
482	527	1.150081	GATGAGGTGGGAGCATGGG	59.850	63.158	0.00	0.00	0.00	4.00
483	528	2.349100	GATGAGGTGGGAGCATGGGG	62.349	65.000	0.00	0.00	0.00	4.96
484	529	2.692368	GAGGTGGGAGCATGGGGA	60.692	66.667	0.00	0.00	0.00	4.81
485	530	2.693864	AGGTGGGAGCATGGGGAG	60.694	66.667	0.00	0.00	0.00	4.30
486	531	3.813724	GGTGGGAGCATGGGGAGG	61.814	72.222	0.00	0.00	0.00	4.30
487	532	3.813724	GTGGGAGCATGGGGAGGG	61.814	72.222	0.00	0.00	0.00	4.30
488	533	4.037413	TGGGAGCATGGGGAGGGA	62.037	66.667	0.00	0.00	0.00	4.20
489	534	3.174265	GGGAGCATGGGGAGGGAG	61.174	72.222	0.00	0.00	0.00	4.30
490	535	3.883549	GGAGCATGGGGAGGGAGC	61.884	72.222	0.00	0.00	0.00	4.70
491	536	3.092511	GAGCATGGGGAGGGAGCA	61.093	66.667	0.00	0.00	0.00	4.26
492	537	3.095163	AGCATGGGGAGGGAGCAG	61.095	66.667	0.00	0.00	0.00	4.24
493	538	4.201122	GCATGGGGAGGGAGCAGG	62.201	72.222	0.00	0.00	0.00	4.85
494	539	4.201122	CATGGGGAGGGAGCAGGC	62.201	72.222	0.00	0.00	0.00	4.85
495	540	4.765970	ATGGGGAGGGAGCAGGCA	62.766	66.667	0.00	0.00	0.00	4.75
497	542	4.120755	GGGGAGGGAGCAGGCAAG	62.121	72.222	0.00	0.00	0.00	4.01
498	543	4.811364	GGGAGGGAGCAGGCAAGC	62.811	72.222	0.00	0.00	0.00	4.01
499	544	4.811364	GGAGGGAGCAGGCAAGCC	62.811	72.222	2.02	2.02	34.23	4.35
500	545	4.039092	GAGGGAGCAGGCAAGCCA	62.039	66.667	14.40	0.00	38.92	4.75
501	546	3.991725	GAGGGAGCAGGCAAGCCAG	62.992	68.421	14.40	6.48	38.92	4.85
502	547	4.039092	GGGAGCAGGCAAGCCAGA	62.039	66.667	14.40	0.00	38.92	3.86
503	548	2.274760	GGAGCAGGCAAGCCAGAT	59.725	61.111	14.40	3.44	38.92	2.90
504	549	1.823041	GGAGCAGGCAAGCCAGATC	60.823	63.158	14.40	13.41	37.30	2.75
505	550	1.823041	GAGCAGGCAAGCCAGATCC	60.823	63.158	14.40	0.00	38.92	3.36
506	551	2.832201	GCAGGCAAGCCAGATCCC	60.832	66.667	14.40	0.00	38.92	3.85
507	552	2.123982	CAGGCAAGCCAGATCCCC	60.124	66.667	14.40	0.00	38.92	4.81
508	553	2.614969	AGGCAAGCCAGATCCCCA	60.615	61.111	14.40	0.00	38.92	4.96
509	554	2.240918	AGGCAAGCCAGATCCCCAA	61.241	57.895	14.40	0.00	38.92	4.12
510	555	1.755783	GGCAAGCCAGATCCCCAAG	60.756	63.158	6.14	0.00	35.81	3.61
660	706	8.417176	CGTTCTCCAAATTGTTTTTCGATTAAG	58.583	33.333	0.00	0.00	30.61	1.85
662	708	7.947282	TCTCCAAATTGTTTTTCGATTAAGGT	58.053	30.769	0.00	0.00	32.07	3.50
697	1065	7.142680	CCTTTTAATAGACTTGGTGCGAAAAA	58.857	34.615	0.00	0.00	0.00	1.94
833	1202	5.457140	TGCATTAATGACTTTGTCCGAAAC	58.543	37.500	19.73	0.00	0.00	2.78
834	1203	4.857037	GCATTAATGACTTTGTCCGAAACC	59.143	41.667	19.73	0.00	0.00	3.27
850	1219	2.467566	AACCACGATGTACCAACTCC	57.532	50.000	0.00	0.00	0.00	3.85
851	1220	0.611714	ACCACGATGTACCAACTCCC	59.388	55.000	0.00	0.00	0.00	4.30
852	1221	0.902531	CCACGATGTACCAACTCCCT	59.097	55.000	0.00	0.00	0.00	4.20
853	1222	1.278127	CCACGATGTACCAACTCCCTT	59.722	52.381	0.00	0.00	0.00	3.95
854	1223	2.290071	CCACGATGTACCAACTCCCTTT	60.290	50.000	0.00	0.00	0.00	3.11
855	1224	3.408634	CACGATGTACCAACTCCCTTTT	58.591	45.455	0.00	0.00	0.00	2.27
856	1225	4.563993	CCACGATGTACCAACTCCCTTTTA	60.564	45.833	0.00	0.00	0.00	1.52
857	1226	4.998672	CACGATGTACCAACTCCCTTTTAA	59.001	41.667	0.00	0.00	0.00	1.52
858	1227	5.470777	CACGATGTACCAACTCCCTTTTAAA	59.529	40.000	0.00	0.00	0.00	1.52
859	1228	5.471116	ACGATGTACCAACTCCCTTTTAAAC	59.529	40.000	0.00	0.00	0.00	2.01
860	1229	5.470777	CGATGTACCAACTCCCTTTTAAACA	59.529	40.000	0.00	0.00	0.00	2.83
861	1230	6.348213	CGATGTACCAACTCCCTTTTAAACAG	60.348	42.308	0.00	0.00	0.00	3.16
965	2205	4.530857	GCAGATCCACCGTCCCCG	62.531	72.222	0.00	0.00	0.00	5.73
1073	2320	4.680237	CTCAGCGGTGTTGGGCGA	62.680	66.667	15.22	0.00	0.00	5.54
1474	2728	7.230913	TGAGTAGAATATTACTCCCTCTTTCCG	59.769	40.741	13.44	0.00	45.77	4.30
1498	2752	7.797123	CCGTAATATAAGATTGTTTTTCGCTCC	59.203	37.037	0.00	0.00	0.00	4.70
1597	2851	0.948623	TGGTTTGATCGTGACGCCTG	60.949	55.000	0.00	0.00	0.00	4.85
1602	2856	4.796231	ATCGTGACGCCTGCGGTC	62.796	66.667	16.63	11.06	44.69	4.79
1710	2968	0.113972	TGTGATGGCCCATGGTTCAA	59.886	50.000	11.73	0.00	0.00	2.69
1725	2983	7.083858	CCATGGTTCAAAGTTAATGTGTACTG	58.916	38.462	2.57	0.00	0.00	2.74
1731	2989	8.617809	GTTCAAAGTTAATGTGTACTGGAAGAA	58.382	33.333	0.00	0.00	37.43	2.52
1737	2995	4.657814	ATGTGTACTGGAAGAATTGGGT	57.342	40.909	0.00	0.00	37.43	4.51
2091	3375	0.620556	TTTTTGGTGGGCCTTTTGCA	59.379	45.000	4.53	0.00	43.89	4.08
2135	3419	6.597562	GGTAATCAACCCATACTTATGTGGA	58.402	40.000	9.49	0.00	43.16	4.02
2162	3446	8.922058	AAAATTTCTACATCAATGACTGCATC	57.078	30.769	0.00	0.00	32.35	3.91
2165	3449	9.570468	AATTTCTACATCAATGACTGCATCTAT	57.430	29.630	0.00	0.00	32.35	1.98
2202	3486	2.095567	ACATCACATGTTTGCGCTTCTC	60.096	45.455	9.73	0.00	41.63	2.87
2205	3489	2.031769	TCACATGTTTGCGCTTCTCTTG	60.032	45.455	9.73	7.71	0.00	3.02
2252	3548	7.043961	TGTTTTTATATGCCTGTTGTTGTCA	57.956	32.000	0.00	0.00	0.00	3.58
2253	3549	7.144661	TGTTTTTATATGCCTGTTGTTGTCAG	58.855	34.615	0.00	0.00	0.00	3.51
2332	3630	1.362237	TCAATGAAATGGGGGAGCCTT	59.638	47.619	0.00	0.00	0.00	4.35
2340	3638	6.026186	TGAAATGGGGGAGCCTTAAAATTAA	58.974	36.000	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	5.079643	ACAGACGTACTAACTCCCCTTTAA	58.920	41.667	0.00	0.00	0.00	1.52
54	55	0.318275	TTTCGTGCCAAATCAACCGC	60.318	50.000	0.00	0.00	0.00	5.68
217	218	4.041049	TCAATTGCATGTGAAACGACAAC	58.959	39.130	0.00	0.00	42.39	3.32
228	229	2.029200	TCGTGCCAAATCAATTGCATGT	60.029	40.909	0.00	0.00	37.73	3.21
304	305	7.428020	TCAAGTCATTAATGCCATGAATTAGC	58.572	34.615	10.76	0.00	36.95	3.09
364	401	6.183360	TGCTACGCATGCAGTAATTAATGAAA	60.183	34.615	19.57	4.35	35.31	2.69
415	460	6.502158	TCCTTTCTAATCTAATCATCTCCCCC	59.498	42.308	0.00	0.00	0.00	5.40
416	461	7.560796	TCCTTTCTAATCTAATCATCTCCCC	57.439	40.000	0.00	0.00	0.00	4.81
417	462	9.853177	TTTTCCTTTCTAATCTAATCATCTCCC	57.147	33.333	0.00	0.00	0.00	4.30
448	493	3.600388	CTCATCCTACGGCTGTCTTTTT	58.400	45.455	0.00	0.00	0.00	1.94
449	494	2.093447	CCTCATCCTACGGCTGTCTTTT	60.093	50.000	0.00	0.00	0.00	2.27
450	495	1.482593	CCTCATCCTACGGCTGTCTTT	59.517	52.381	0.00	0.00	0.00	2.52
451	496	1.115467	CCTCATCCTACGGCTGTCTT	58.885	55.000	0.00	0.00	0.00	3.01
452	497	0.033011	ACCTCATCCTACGGCTGTCT	60.033	55.000	0.00	0.00	0.00	3.41
453	498	0.103208	CACCTCATCCTACGGCTGTC	59.897	60.000	0.00	0.00	0.00	3.51
454	499	1.330655	CCACCTCATCCTACGGCTGT	61.331	60.000	2.42	2.42	0.00	4.40
455	500	1.443407	CCACCTCATCCTACGGCTG	59.557	63.158	0.00	0.00	0.00	4.85
456	501	1.762460	CCCACCTCATCCTACGGCT	60.762	63.158	0.00	0.00	0.00	5.52
457	502	1.749334	CTCCCACCTCATCCTACGGC	61.749	65.000	0.00	0.00	0.00	5.68
458	503	1.749334	GCTCCCACCTCATCCTACGG	61.749	65.000	0.00	0.00	0.00	4.02
459	504	1.043116	TGCTCCCACCTCATCCTACG	61.043	60.000	0.00	0.00	0.00	3.51
460	505	1.071385	CATGCTCCCACCTCATCCTAC	59.929	57.143	0.00	0.00	0.00	3.18
461	506	1.427809	CATGCTCCCACCTCATCCTA	58.572	55.000	0.00	0.00	0.00	2.94
462	507	1.351080	CCATGCTCCCACCTCATCCT	61.351	60.000	0.00	0.00	0.00	3.24
463	508	1.150081	CCATGCTCCCACCTCATCC	59.850	63.158	0.00	0.00	0.00	3.51
464	509	1.150081	CCCATGCTCCCACCTCATC	59.850	63.158	0.00	0.00	0.00	2.92
465	510	2.389449	CCCCATGCTCCCACCTCAT	61.389	63.158	0.00	0.00	0.00	2.90
466	511	3.016971	CCCCATGCTCCCACCTCA	61.017	66.667	0.00	0.00	0.00	3.86
467	512	2.692368	TCCCCATGCTCCCACCTC	60.692	66.667	0.00	0.00	0.00	3.85
468	513	2.693864	CTCCCCATGCTCCCACCT	60.694	66.667	0.00	0.00	0.00	4.00
469	514	3.813724	CCTCCCCATGCTCCCACC	61.814	72.222	0.00	0.00	0.00	4.61
470	515	3.813724	CCCTCCCCATGCTCCCAC	61.814	72.222	0.00	0.00	0.00	4.61
471	516	4.037413	TCCCTCCCCATGCTCCCA	62.037	66.667	0.00	0.00	0.00	4.37
472	517	3.174265	CTCCCTCCCCATGCTCCC	61.174	72.222	0.00	0.00	0.00	4.30
473	518	3.883549	GCTCCCTCCCCATGCTCC	61.884	72.222	0.00	0.00	0.00	4.70
474	519	3.092511	TGCTCCCTCCCCATGCTC	61.093	66.667	0.00	0.00	0.00	4.26
475	520	3.095163	CTGCTCCCTCCCCATGCT	61.095	66.667	0.00	0.00	0.00	3.79
476	521	4.201122	CCTGCTCCCTCCCCATGC	62.201	72.222	0.00	0.00	0.00	4.06
477	522	4.201122	GCCTGCTCCCTCCCCATG	62.201	72.222	0.00	0.00	0.00	3.66
478	523	4.765970	TGCCTGCTCCCTCCCCAT	62.766	66.667	0.00	0.00	0.00	4.00
480	525	4.120755	CTTGCCTGCTCCCTCCCC	62.121	72.222	0.00	0.00	0.00	4.81
481	526	4.811364	GCTTGCCTGCTCCCTCCC	62.811	72.222	0.00	0.00	0.00	4.30
482	527	4.811364	GGCTTGCCTGCTCCCTCC	62.811	72.222	4.11	0.00	0.00	4.30
483	528	3.991725	CTGGCTTGCCTGCTCCCTC	62.992	68.421	13.18	0.00	0.00	4.30
484	529	4.044439	CTGGCTTGCCTGCTCCCT	62.044	66.667	13.18	0.00	0.00	4.20
485	530	3.355957	ATCTGGCTTGCCTGCTCCC	62.356	63.158	13.18	0.00	0.00	4.30
486	531	1.823041	GATCTGGCTTGCCTGCTCC	60.823	63.158	13.18	1.95	0.00	4.70
487	532	1.823041	GGATCTGGCTTGCCTGCTC	60.823	63.158	13.18	12.53	0.00	4.26
488	533	2.274760	GGATCTGGCTTGCCTGCT	59.725	61.111	13.18	3.90	0.00	4.24
489	534	2.832201	GGGATCTGGCTTGCCTGC	60.832	66.667	13.18	0.00	0.00	4.85
490	535	2.123982	GGGGATCTGGCTTGCCTG	60.124	66.667	13.18	12.33	0.00	4.85
491	536	2.220786	CTTGGGGATCTGGCTTGCCT	62.221	60.000	13.18	0.00	0.00	4.75
492	537	1.755783	CTTGGGGATCTGGCTTGCC	60.756	63.158	4.43	4.43	0.00	4.52
493	538	1.034292	GTCTTGGGGATCTGGCTTGC	61.034	60.000	0.00	0.00	0.00	4.01
494	539	0.622665	AGTCTTGGGGATCTGGCTTG	59.377	55.000	0.00	0.00	0.00	4.01
495	540	1.840635	GTAGTCTTGGGGATCTGGCTT	59.159	52.381	0.00	0.00	0.00	4.35
496	541	1.501582	GTAGTCTTGGGGATCTGGCT	58.498	55.000	0.00	0.00	0.00	4.75
497	542	0.470341	GGTAGTCTTGGGGATCTGGC	59.530	60.000	0.00	0.00	0.00	4.85
498	543	1.879575	TGGTAGTCTTGGGGATCTGG	58.120	55.000	0.00	0.00	0.00	3.86
499	544	3.370953	CCTTTGGTAGTCTTGGGGATCTG	60.371	52.174	0.00	0.00	0.00	2.90
500	545	2.846827	CCTTTGGTAGTCTTGGGGATCT	59.153	50.000	0.00	0.00	0.00	2.75
501	546	2.576648	ACCTTTGGTAGTCTTGGGGATC	59.423	50.000	0.00	0.00	32.11	3.36
502	547	2.644151	ACCTTTGGTAGTCTTGGGGAT	58.356	47.619	0.00	0.00	32.11	3.85
503	548	2.127651	ACCTTTGGTAGTCTTGGGGA	57.872	50.000	0.00	0.00	32.11	4.81
504	549	2.890945	CAAACCTTTGGTAGTCTTGGGG	59.109	50.000	0.00	0.00	33.12	4.96
505	550	3.827722	TCAAACCTTTGGTAGTCTTGGG	58.172	45.455	0.00	0.00	38.66	4.12
506	551	6.215845	CAAATCAAACCTTTGGTAGTCTTGG	58.784	40.000	0.00	0.00	38.66	3.61
507	552	6.215845	CCAAATCAAACCTTTGGTAGTCTTG	58.784	40.000	6.64	0.00	44.95	3.02
508	553	6.405278	CCAAATCAAACCTTTGGTAGTCTT	57.595	37.500	6.64	0.00	44.95	3.01
660	706	7.054751	AGTCTATTAAAAGGGATTGCTACACC	58.945	38.462	0.00	0.00	0.00	4.16
662	708	7.556275	CCAAGTCTATTAAAAGGGATTGCTACA	59.444	37.037	0.00	0.00	0.00	2.74
729	1097	8.394877	TGAATTAGCCAGACAATTAATTACGTG	58.605	33.333	0.00	0.00	0.00	4.49
730	1098	8.500753	TGAATTAGCCAGACAATTAATTACGT	57.499	30.769	0.00	0.00	0.00	3.57
731	1099	9.950680	AATGAATTAGCCAGACAATTAATTACG	57.049	29.630	0.00	0.00	27.82	3.18
833	1202	0.902531	AGGGAGTTGGTACATCGTGG	59.097	55.000	0.00	0.00	39.30	4.94
834	1203	2.762535	AAGGGAGTTGGTACATCGTG	57.237	50.000	0.00	0.00	39.30	4.35
850	1219	5.501156	AGGCTAGATGACCTGTTTAAAAGG	58.499	41.667	0.00	0.00	40.93	3.11
851	1220	7.308435	CAAAGGCTAGATGACCTGTTTAAAAG	58.692	38.462	0.00	0.00	36.07	2.27
852	1221	6.294508	GCAAAGGCTAGATGACCTGTTTAAAA	60.295	38.462	0.00	0.00	36.07	1.52
853	1222	5.183140	GCAAAGGCTAGATGACCTGTTTAAA	59.817	40.000	0.00	0.00	36.07	1.52
854	1223	4.700213	GCAAAGGCTAGATGACCTGTTTAA	59.300	41.667	0.00	0.00	36.07	1.52
855	1224	4.261801	GCAAAGGCTAGATGACCTGTTTA	58.738	43.478	0.00	0.00	36.07	2.01
856	1225	3.084786	GCAAAGGCTAGATGACCTGTTT	58.915	45.455	0.00	0.00	36.07	2.83
857	1226	2.040278	TGCAAAGGCTAGATGACCTGTT	59.960	45.455	0.00	0.00	41.91	3.16
858	1227	1.630369	TGCAAAGGCTAGATGACCTGT	59.370	47.619	0.00	0.00	41.91	4.00
859	1228	2.012673	GTGCAAAGGCTAGATGACCTG	58.987	52.381	0.00	0.00	41.91	4.00
860	1229	1.065126	GGTGCAAAGGCTAGATGACCT	60.065	52.381	0.00	0.00	41.91	3.85
861	1230	1.340017	TGGTGCAAAGGCTAGATGACC	60.340	52.381	0.00	0.00	41.91	4.02
965	2205	0.902984	GGAATTGGGTGTTGGGGGTC	60.903	60.000	0.00	0.00	0.00	4.46
1066	2313	2.099652	CTCTCACTGTGGTCGCCCAA	62.100	60.000	8.11	0.00	44.15	4.12
1073	2320	2.279069	CCGAGCCTCTCACTGTGGT	61.279	63.158	8.11	0.00	0.00	4.16
1114	2361	2.032634	GGATGTGCGCGTCCTTCAA	61.033	57.895	27.81	0.00	45.23	2.69
1469	2723	9.493206	GCGAAAAACAATCTTATATTACGGAAA	57.507	29.630	0.00	0.00	0.00	3.13
1474	2728	8.545420	TCGGAGCGAAAAACAATCTTATATTAC	58.455	33.333	0.00	0.00	31.06	1.89
1494	2748	6.222038	TGATCTTATATTATGGGTCGGAGC	57.778	41.667	0.00	0.00	0.00	4.70
1536	2790	1.201647	CGTCCCACAGTACAAGATCGT	59.798	52.381	0.00	0.00	0.00	3.73
1544	2798	0.611340	ACTCCCTCGTCCCACAGTAC	60.611	60.000	0.00	0.00	0.00	2.73
1547	2801	0.323542	AGTACTCCCTCGTCCCACAG	60.324	60.000	0.00	0.00	0.00	3.66
1597	2851	0.103208	CACTAGTGAGGATGGACCGC	59.897	60.000	18.45	0.00	44.74	5.68
1602	2856	5.686753	AGTAGTAGTCACTAGTGAGGATGG	58.313	45.833	25.81	0.00	39.09	3.51
1689	2943	1.273154	TGAACCATGGGCCATCACAAT	60.273	47.619	18.16	0.91	0.00	2.71
1710	2968	7.176690	CCCAATTCTTCCAGTACACATTAACTT	59.823	37.037	0.00	0.00	0.00	2.66
1725	2983	2.867647	GCAAAGCACACCCAATTCTTCC	60.868	50.000	0.00	0.00	0.00	3.46
1731	2989	1.368579	GCAGCAAAGCACACCCAAT	59.631	52.632	0.00	0.00	0.00	3.16
1751	3009	5.692613	TGAAAACCCAATAACACTAACGG	57.307	39.130	0.00	0.00	0.00	4.44
1879	3138	7.402811	TCGAATGACACCGATTTGATATTAC	57.597	36.000	0.00	0.00	0.00	1.89
2068	3352	1.578897	AAAGGCCCACCAAAAACACT	58.421	45.000	0.00	0.00	39.06	3.55
2091	3375	3.961408	ACCAGATAACCTAGAATCGCACT	59.039	43.478	0.00	0.00	0.00	4.40
2140	3424	9.570468	AATAGATGCAGTCATTGATGTAGAAAT	57.430	29.630	0.00	0.00	31.96	2.17
2202	3486	1.066858	ACCTCATGCACCGTAGACAAG	60.067	52.381	0.00	0.00	0.00	3.16
2205	3489	1.067142	TCAACCTCATGCACCGTAGAC	60.067	52.381	0.00	0.00	0.00	2.59
2285	3582	8.179615	GGTATTAAATTTGGACTTAGTTCACGG	58.820	37.037	0.00	0.00	0.00	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.