AutoCloner

Multiple sequence alignment - TraesCS4A01G211000

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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	TraesCS4A01G211000	chr4A	100.000	3305	0	0	1	3305	504677842	504674538	0.000000e+00	6104.0
1	TraesCS4A01G211000	chr4A	92.379	433	17	2	1919	2335	658574213	658574645	1.310000e-168	603.0
2	TraesCS4A01G211000	chr4A	94.667	75	4	0	1789	1863	658574117	658574191	2.080000e-22	117.0
3	TraesCS4A01G211000	chr7A	95.121	1865	88	3	1	1863	675750777	675748914	0.000000e+00	2937.0
4	TraesCS4A01G211000	chr7A	97.518	967	19	3	2340	3305	118151822	118150860	0.000000e+00	1648.0
5	TraesCS4A01G211000	chr7A	97.368	418	10	1	1919	2335	675748892	675748475	0.000000e+00	710.0
6	TraesCS4A01G211000	chr3D	94.376	1867	80	7	1	1863	21770835	21768990	0.000000e+00	2843.0
7	TraesCS4A01G211000	chr3D	97.368	418	10	1	1919	2335	21768968	21768551	0.000000e+00	710.0
8	TraesCS4A01G211000	chr3D	90.265	113	9	2	1368	1479	384655942	384656053	2.660000e-31	147.0
9	TraesCS4A01G211000	chr7D	93.906	1444	73	6	429	1863	544156025	544154588	0.000000e+00	2165.0
10	TraesCS4A01G211000	chr7D	93.573	1307	77	4	1	1303	142215309	142214006	0.000000e+00	1941.0
11	TraesCS4A01G211000	chr7D	97.696	434	9	1	1	433	544161750	544161317	0.000000e+00	745.0
12	TraesCS4A01G211000	chr7D	97.368	418	10	1	1919	2335	544154566	544154149	0.000000e+00	710.0
13	TraesCS4A01G211000	chr7D	93.764	433	11	2	1919	2335	142213892	142213460	1.290000e-178	636.0
14	TraesCS4A01G211000	chr7D	93.779	434	10	9	1919	2335	548186120	548185687	1.290000e-178	636.0
15	TraesCS4A01G211000	chr7D	95.000	160	8	0	1079	1238	548186436	548186277	5.470000e-63	252.0
16	TraesCS4A01G211000	chr7D	96.000	75	3	0	1789	1863	548186216	548186142	4.480000e-24	122.0
17	TraesCS4A01G211000	chr4D	92.890	1308	60	10	1	1303	410093574	410094853	0.000000e+00	1869.0
18	TraesCS4A01G211000	chr4D	93.072	433	14	2	1919	2335	410095641	410096073	1.300000e-173	619.0
19	TraesCS4A01G211000	chr4D	93.333	75	5	0	1789	1863	410094869	410094943	9.690000e-21	111.0
20	TraesCS4A01G211000	chr5A	97.725	967	21	1	2340	3305	68818824	68817858	0.000000e+00	1663.0
21	TraesCS4A01G211000	chr5A	97.725	967	21	1	2340	3305	524722877	524723843	0.000000e+00	1663.0
22	TraesCS4A01G211000	chr2A	97.622	967	22	1	2340	3305	179281960	179282926	0.000000e+00	1657.0
23	TraesCS4A01G211000	chr2A	97.622	967	22	1	2340	3305	578391554	578390588	0.000000e+00	1657.0
24	TraesCS4A01G211000	chr2A	84.615	156	20	3	1148	1303	722101983	722101832	5.710000e-33	152.0
25	TraesCS4A01G211000	chr3A	97.518	967	22	2	2340	3305	80425198	80426163	0.000000e+00	1652.0
26	TraesCS4A01G211000	chr3A	97.417	968	23	2	2340	3305	277497612	277498579	0.000000e+00	1648.0
27	TraesCS4A01G211000	chr3A	83.012	259	20	12	1308	1565	507287419	507287654	2.580000e-51	213.0
28	TraesCS4A01G211000	chr3A	90.351	114	8	2	1368	1479	507273828	507273940	2.660000e-31	147.0
29	TraesCS4A01G211000	chr3A	96.970	33	0	1	1872	1904	5908877	5908846	2.000000e-03	54.7
30	TraesCS4A01G211000	chr1A	97.518	967	23	1	2340	3305	477661759	477660793	0.000000e+00	1652.0
31	TraesCS4A01G211000	chr1A	97.415	967	24	1	2340	3305	292062057	292063023	0.000000e+00	1646.0
32	TraesCS4A01G211000	chr1B	93.267	906	52	3	2	898	659196382	659195477	0.000000e+00	1327.0
33	TraesCS4A01G211000	chr1B	90.741	972	81	4	609	1571	659105039	659104068	0.000000e+00	1288.0
34	TraesCS4A01G211000	chr1B	94.951	515	21	2	1	510	659105553	659105039	0.000000e+00	802.0
35	TraesCS4A01G211000	chr1B	93.533	433	12	2	1919	2335	659103914	659103482	6.020000e-177	630.0
36	TraesCS4A01G211000	chr1B	92.610	433	16	2	1919	2335	39265563	39265995	2.820000e-170	608.0
37	TraesCS4A01G211000	chr1B	87.179	156	16	2	1148	1303	121032281	121032432	1.220000e-39	174.0
38	TraesCS4A01G211000	chr2D	92.593	891	57	6	375	1260	291609651	291608765	0.000000e+00	1271.0
39	TraesCS4A01G211000	chr2D	94.667	75	4	0	1789	1863	614385073	614384999	2.080000e-22	117.0
40	TraesCS4A01G211000	chr6D	93.027	588	33	6	665	1246	67658270	67658855	0.000000e+00	852.0
41	TraesCS4A01G211000	chr6D	87.790	647	63	14	1	640	283305119	283304482	0.000000e+00	743.0
42	TraesCS4A01G211000	chr6D	93.303	433	13	2	1919	2335	322698353	322698785	2.800000e-175	625.0
43	TraesCS4A01G211000	chr6D	93.072	433	14	2	1919	2335	384195887	384195455	1.300000e-173	619.0
44	TraesCS4A01G211000	chr6D	94.667	75	4	0	1789	1863	384195982	384195908	2.080000e-22	117.0
45	TraesCS4A01G211000	chr6D	93.333	75	5	0	1789	1863	322698257	322698331	9.690000e-21	111.0
46	TraesCS4A01G211000	chr1D	93.110	566	37	2	673	1237	408917434	408916870	0.000000e+00	828.0
47	TraesCS4A01G211000	chr1D	100.000	29	0	0	1876	1904	429431123	429431095	2.000000e-03	54.7
48	TraesCS4A01G211000	chr3B	93.303	433	14	2	1918	2335	87708546	87708114	2.800000e-175	625.0
49	TraesCS4A01G211000	chr3B	90.000	70	2	3	1308	1374	500308427	500308494	5.880000e-13	86.1
50	TraesCS4A01G211000	chr3B	90.000	70	2	3	1308	1374	500316974	500317041	5.880000e-13	86.1
51	TraesCS4A01G211000	chr6B	83.333	654	84	16	1	640	104303957	104304599	6.150000e-162	580.0
52	TraesCS4A01G211000	chr6B	100.000	29	0	0	1876	1904	464579700	464579672	2.000000e-03	54.7
53	TraesCS4A01G211000	chr6B	100.000	29	0	0	1876	1904	505319628	505319656	2.000000e-03	54.7
54	TraesCS4A01G211000	chr7B	98.283	233	4	0	2103	2335	130902782	130902550	3.070000e-110	409.0
55	TraesCS4A01G211000	chrUn	100.000	29	0	0	1876	1904	37025316	37025344	2.000000e-03	54.7
56	TraesCS4A01G211000	chr5B	100.000	29	0	0	1876	1904	674911317	674911345	2.000000e-03	54.7
57	TraesCS4A01G211000	chr4B	100.000	29	0	0	1876	1904	48077204	48077232	2.000000e-03	54.7
58	TraesCS4A01G211000	chr4B	100.000	29	0	0	1876	1904	216201893	216201921	2.000000e-03	54.7
59	TraesCS4A01G211000	chr2B	96.970	33	0	1	1872	1904	658923675	658923644	2.000000e-03	54.7

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	TraesCS4A01G211000	chr4A	504674538	504677842	3304	True	6104.000000	6104	100.000000	1	3305	1	chr4A.!!$R1	3304
1	TraesCS4A01G211000	chr4A	658574117	658574645	528	False	360.000000	603	93.523000	1789	2335	2	chr4A.!!$F1	546
2	TraesCS4A01G211000	chr7A	675748475	675750777	2302	True	1823.500000	2937	96.244500	1	2335	2	chr7A.!!$R2	2334
3	TraesCS4A01G211000	chr7A	118150860	118151822	962	True	1648.000000	1648	97.518000	2340	3305	1	chr7A.!!$R1	965
4	TraesCS4A01G211000	chr3D	21768551	21770835	2284	True	1776.500000	2843	95.872000	1	2335	2	chr3D.!!$R1	2334
5	TraesCS4A01G211000	chr7D	544154149	544156025	1876	True	1437.500000	2165	95.637000	429	2335	2	chr7D.!!$R3	1906
6	TraesCS4A01G211000	chr7D	142213460	142215309	1849	True	1288.500000	1941	93.668500	1	2335	2	chr7D.!!$R2	2334
7	TraesCS4A01G211000	chr7D	548185687	548186436	749	True	336.666667	636	94.926333	1079	2335	3	chr7D.!!$R4	1256
8	TraesCS4A01G211000	chr4D	410093574	410096073	2499	False	866.333333	1869	93.098333	1	2335	3	chr4D.!!$F1	2334
9	TraesCS4A01G211000	chr5A	68817858	68818824	966	True	1663.000000	1663	97.725000	2340	3305	1	chr5A.!!$R1	965
10	TraesCS4A01G211000	chr5A	524722877	524723843	966	False	1663.000000	1663	97.725000	2340	3305	1	chr5A.!!$F1	965
11	TraesCS4A01G211000	chr2A	179281960	179282926	966	False	1657.000000	1657	97.622000	2340	3305	1	chr2A.!!$F1	965
12	TraesCS4A01G211000	chr2A	578390588	578391554	966	True	1657.000000	1657	97.622000	2340	3305	1	chr2A.!!$R1	965
13	TraesCS4A01G211000	chr3A	80425198	80426163	965	False	1652.000000	1652	97.518000	2340	3305	1	chr3A.!!$F1	965
14	TraesCS4A01G211000	chr3A	277497612	277498579	967	False	1648.000000	1648	97.417000	2340	3305	1	chr3A.!!$F2	965
15	TraesCS4A01G211000	chr1A	477660793	477661759	966	True	1652.000000	1652	97.518000	2340	3305	1	chr1A.!!$R1	965
16	TraesCS4A01G211000	chr1A	292062057	292063023	966	False	1646.000000	1646	97.415000	2340	3305	1	chr1A.!!$F1	965
17	TraesCS4A01G211000	chr1B	659195477	659196382	905	True	1327.000000	1327	93.267000	2	898	1	chr1B.!!$R1	896
18	TraesCS4A01G211000	chr1B	659103482	659105553	2071	True	906.666667	1288	93.075000	1	2335	3	chr1B.!!$R2	2334
19	TraesCS4A01G211000	chr2D	291608765	291609651	886	True	1271.000000	1271	92.593000	375	1260	1	chr2D.!!$R1	885
20	TraesCS4A01G211000	chr6D	67658270	67658855	585	False	852.000000	852	93.027000	665	1246	1	chr6D.!!$F1	581
21	TraesCS4A01G211000	chr6D	283304482	283305119	637	True	743.000000	743	87.790000	1	640	1	chr6D.!!$R1	639
22	TraesCS4A01G211000	chr6D	322698257	322698785	528	False	368.000000	625	93.318000	1789	2335	2	chr6D.!!$F2	546
23	TraesCS4A01G211000	chr6D	384195455	384195982	527	True	368.000000	619	93.869500	1789	2335	2	chr6D.!!$R2	546
24	TraesCS4A01G211000	chr1D	408916870	408917434	564	True	828.000000	828	93.110000	673	1237	1	chr1D.!!$R1	564
25	TraesCS4A01G211000	chr6B	104303957	104304599	642	False	580.000000	580	83.333000	1	640	1	chr6B.!!$F1	639

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
912	941	1.342074	CCCTTGACTCCTCTGTGTCA	58.658	55.0	0.00	0.0	41.77	3.58	F
1617	1666	0.601046	CTCTTGGCGAGTGCTGTGAA	60.601	55.0	0.77	0.0	42.25	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1897	1946	0.035820	GCGTCATACCCCACTTGGAA	60.036	55.0	0.00	0.0	37.39	3.53	R
2834	3544	0.611618	TTGGCGCCACTTCATCCATT	60.612	50.0	32.95	0.0	0.00	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
177	183	3.430473	AAAAACCCGATGGCACTCA	57.570	47.368	0.00	0.00	33.59	3.41
312	319	5.127693	ACATGAGGCTAATATGTCGAGTC	57.872	43.478	0.00	0.00	29.55	3.36
557	571	1.422024	CCTCTCTGTCTCTCCCCGATA	59.578	57.143	0.00	0.00	0.00	2.92
560	574	2.443632	TCTCTGTCTCTCCCCGATACAT	59.556	50.000	0.00	0.00	29.65	2.29
695	713	2.114625	CAGATCCGCCATGCCCAT	59.885	61.111	0.00	0.00	0.00	4.00
732	752	1.767692	CCAAACCCTACCCACAGCT	59.232	57.895	0.00	0.00	0.00	4.24
750	770	4.760047	GCCACCGTGCTCCGTCAT	62.760	66.667	0.00	0.00	33.66	3.06
753	773	3.060000	ACCGTGCTCCGTCATCGA	61.060	61.111	0.00	0.00	39.71	3.59
912	941	1.342074	CCCTTGACTCCTCTGTGTCA	58.658	55.000	0.00	0.00	41.77	3.58
1127	1161	1.146774	CTCCTGGCTCCTCATCCTCTA	59.853	57.143	0.00	0.00	0.00	2.43
1167	1201	3.706373	ATGGCCTGGACGCTCGTT	61.706	61.111	3.32	0.00	0.00	3.85
1175	1209	1.211190	GGACGCTCGTTAACCTCGT	59.789	57.895	12.29	12.29	35.98	4.18
1209	1246	4.439901	GCCTCTCCCCCTCCCCTT	62.440	72.222	0.00	0.00	0.00	3.95
1319	1368	4.260334	GCAGTCAAAATTTTGCCTGTCAAC	60.260	41.667	31.38	20.22	43.77	3.18
1462	1511	6.935771	TGCAATGGTTGATTAGCAAAATTCTT	59.064	30.769	0.00	0.00	38.44	2.52
1587	1636	6.874288	AAATAGATCTGCCTAATGCTTCAC	57.126	37.500	5.18	0.00	42.00	3.18
1617	1666	0.601046	CTCTTGGCGAGTGCTGTGAA	60.601	55.000	0.77	0.00	42.25	3.18
1644	1693	8.498358	CGCAATACTGAATAATCTTGCTGATAA	58.502	33.333	0.00	0.00	37.44	1.75
1748	1797	5.593095	TGTTAGAAGGCGTAGTCATAGATGT	59.407	40.000	0.00	0.00	0.00	3.06
1752	1801	4.368565	AGGCGTAGTCATAGATGTCCTA	57.631	45.455	0.00	0.00	0.00	2.94
1767	1816	4.574674	TGTCCTATGCAACTCCATCTTT	57.425	40.909	0.00	0.00	0.00	2.52
1780	1829	1.238439	CATCTTTGTCGTTGGTGGCT	58.762	50.000	0.00	0.00	0.00	4.75
1781	1830	1.608590	CATCTTTGTCGTTGGTGGCTT	59.391	47.619	0.00	0.00	0.00	4.35
1841	1890	2.534939	GCTACAAATTGCTACGACGCAG	60.535	50.000	0.00	0.00	41.55	5.18
1863	1912	0.668535	GCCAATCCCGCCAACTAATC	59.331	55.000	0.00	0.00	0.00	1.75
1864	1913	0.944386	CCAATCCCGCCAACTAATCG	59.056	55.000	0.00	0.00	0.00	3.34
1866	1915	2.494059	CAATCCCGCCAACTAATCGAT	58.506	47.619	0.00	0.00	0.00	3.59
1868	1917	4.062293	CAATCCCGCCAACTAATCGATTA	58.938	43.478	16.69	16.69	0.00	1.75
1869	1918	3.102052	TCCCGCCAACTAATCGATTAC	57.898	47.619	13.85	3.48	0.00	1.89
1870	1919	1.790623	CCCGCCAACTAATCGATTACG	59.209	52.381	13.85	14.34	41.26	3.18
1874	1923	3.360384	CGCCAACTAATCGATTACGTTCG	60.360	47.826	20.53	18.59	40.69	3.95
1875	1924	3.600909	GCCAACTAATCGATTACGTTCGC	60.601	47.826	21.44	21.44	38.97	4.70
1876	1925	3.548668	CCAACTAATCGATTACGTTCGCA	59.451	43.478	20.53	2.60	38.97	5.10
1877	1926	4.208460	CCAACTAATCGATTACGTTCGCAT	59.792	41.667	20.53	0.00	38.97	4.73
1878	1927	5.276678	CCAACTAATCGATTACGTTCGCATT	60.277	40.000	20.53	8.14	38.97	3.56
1879	1928	6.074729	CCAACTAATCGATTACGTTCGCATTA	60.075	38.462	20.53	8.72	38.97	1.90
1880	1929	6.670990	ACTAATCGATTACGTTCGCATTAG	57.329	37.500	22.82	22.82	40.37	1.73
1881	1930	4.966850	AATCGATTACGTTCGCATTAGG	57.033	40.909	9.39	0.00	38.97	2.69
1882	1931	2.121786	TCGATTACGTTCGCATTAGGC	58.878	47.619	4.78	0.00	38.97	3.93
1883	1932	1.855978	CGATTACGTTCGCATTAGGCA	59.144	47.619	0.00	0.00	37.23	4.75
1884	1933	2.283086	CGATTACGTTCGCATTAGGCAA	59.717	45.455	0.00	0.00	37.23	4.52
1885	1934	3.604392	GATTACGTTCGCATTAGGCAAC	58.396	45.455	0.00	0.00	45.17	4.17
1886	1935	2.081725	TACGTTCGCATTAGGCAACA	57.918	45.000	0.00	0.00	45.17	3.33
1887	1936	1.448985	ACGTTCGCATTAGGCAACAT	58.551	45.000	0.00	0.00	45.17	2.71
1888	1937	1.810151	ACGTTCGCATTAGGCAACATT	59.190	42.857	0.00	0.00	45.17	2.71
1889	1938	2.176369	CGTTCGCATTAGGCAACATTG	58.824	47.619	0.00	0.00	45.17	2.82
1890	1939	2.414029	CGTTCGCATTAGGCAACATTGT	60.414	45.455	0.00	0.00	45.17	2.71
1891	1940	3.574614	GTTCGCATTAGGCAACATTGTT	58.425	40.909	0.00	0.00	45.17	2.83
1892	1941	3.932545	TCGCATTAGGCAACATTGTTT	57.067	38.095	0.00	0.00	45.17	2.83
1893	1942	3.573598	TCGCATTAGGCAACATTGTTTG	58.426	40.909	0.00	0.00	45.17	2.93
1894	1943	2.667481	CGCATTAGGCAACATTGTTTGG	59.333	45.455	0.00	0.00	45.17	3.28
1895	1944	3.613671	CGCATTAGGCAACATTGTTTGGA	60.614	43.478	0.00	0.00	45.17	3.53
1896	1945	4.314121	GCATTAGGCAACATTGTTTGGAA	58.686	39.130	0.00	0.00	43.97	3.53
1897	1946	4.937015	GCATTAGGCAACATTGTTTGGAAT	59.063	37.500	0.00	0.00	43.97	3.01
1899	1948	6.402442	GCATTAGGCAACATTGTTTGGAATTC	60.402	38.462	0.00	0.00	43.97	2.17
1900	1949	4.006780	AGGCAACATTGTTTGGAATTCC	57.993	40.909	18.17	18.17	41.41	3.01
1901	1950	3.390639	AGGCAACATTGTTTGGAATTCCA	59.609	39.130	23.63	23.63	42.24	3.53
1913	1962	2.922955	TGGAATTCCAAGTGGGGTATGA	59.077	45.455	25.13	0.00	44.35	2.15
1914	1963	3.288092	GGAATTCCAAGTGGGGTATGAC	58.712	50.000	20.04	0.00	37.22	3.06
1915	1964	2.710096	ATTCCAAGTGGGGTATGACG	57.290	50.000	0.00	0.00	37.22	4.35
1916	1965	0.035820	TTCCAAGTGGGGTATGACGC	60.036	55.000	0.00	0.00	37.22	5.19
1917	1966	1.195442	TCCAAGTGGGGTATGACGCA	61.195	55.000	0.00	0.00	37.22	5.24
2021	2712	5.649782	AAATTCACGAAATCATTCTGGCT	57.350	34.783	0.00	0.00	33.17	4.75
2062	2753	0.251787	GGCCCAACCTCAATTCTGGT	60.252	55.000	0.00	0.00	38.35	4.00
2425	3133	4.536364	AATGTTGTGACAAGTGTTCGAG	57.464	40.909	0.00	0.00	39.66	4.04
2449	3157	2.822561	AGTGATGTCGACACTGATGACT	59.177	45.455	22.71	11.84	45.19	3.41
2785	3495	2.823154	CGGTATTTGGGGTCAATGTTGT	59.177	45.455	0.00	0.00	32.28	3.32
2834	3544	0.320374	AACCATCGAGTCAAAGCCGA	59.680	50.000	0.00	0.00	36.72	5.54
2886	3596	4.979943	TCTCTATGACAAGAGAGTGCAG	57.020	45.455	14.31	0.00	45.54	4.41
2904	3614	3.069289	GCAGCAAAAGCTAAAAGGCAAT	58.931	40.909	0.00	0.00	34.17	3.56
2918	3628	1.628846	AGGCAATTTCTACAGGACGGT	59.371	47.619	0.00	0.00	0.00	4.83
3136	3846	4.210331	GAGATGGTTTGGGCATATTCAGT	58.790	43.478	0.00	0.00	0.00	3.41
3277	3988	3.706594	TGGAGTATCACCAAAGAGCTAGG	59.293	47.826	0.00	0.00	36.25	3.02
3300	4011	2.847234	ACAGGGGTGCGTGGAAGA	60.847	61.111	0.00	0.00	0.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
370	379	4.749099	CACCAATCAGACTCTAGCTTATGC	59.251	45.833	0.00	0.00	40.05	3.14
557	571	2.279252	GTGGCGGCGTCGATATGT	60.279	61.111	16.53	0.00	39.00	2.29
695	713	1.381872	GGTGGGGCAGAGAGAGCTA	60.382	63.158	0.00	0.00	0.00	3.32
912	941	4.477119	GGAGCCGAGGGGTAGGGT	62.477	72.222	0.00	0.00	41.47	4.34
1009	1042	2.663520	CACCGCCTGCACGTACAA	60.664	61.111	0.00	0.00	0.00	2.41
1127	1161	2.045926	GGGTGCAGCCGAAGATGT	60.046	61.111	20.97	0.00	38.44	3.06
1167	1201	1.210931	CGCGAAGTGGACGAGGTTA	59.789	57.895	0.00	0.00	0.00	2.85
1209	1246	0.324091	GACGTGTAAGGGAGGGAGGA	60.324	60.000	0.00	0.00	0.00	3.71
1303	1352	5.852282	AGTACAGTTGACAGGCAAAATTT	57.148	34.783	0.00	0.00	38.44	1.82
1309	1358	3.258372	CCTCTTAGTACAGTTGACAGGCA	59.742	47.826	0.00	0.00	0.00	4.75
1319	1368	5.241662	AGAAGCAAAAGCCTCTTAGTACAG	58.758	41.667	0.00	0.00	0.00	2.74
1462	1511	5.914898	TGGTTGAGAATTCAGATCTACGA	57.085	39.130	8.44	0.00	34.15	3.43
1587	1636	3.541711	CTCGCCAAGAGTTTTAAACACG	58.458	45.455	10.60	4.32	41.99	4.49
1617	1666	5.817296	TCAGCAAGATTATTCAGTATTGCGT	59.183	36.000	0.00	0.00	45.73	5.24
1748	1797	4.517285	GACAAAGATGGAGTTGCATAGGA	58.483	43.478	0.00	0.00	0.00	2.94
1752	1801	2.783135	ACGACAAAGATGGAGTTGCAT	58.217	42.857	0.00	0.00	0.00	3.96
1767	1816	0.250124	AATCGAAGCCACCAACGACA	60.250	50.000	0.00	0.00	37.58	4.35
1780	1829	1.586578	GCAGATGCGAACGTAATCGAA	59.413	47.619	13.55	3.11	45.48	3.71
1781	1830	1.197055	GCAGATGCGAACGTAATCGA	58.803	50.000	13.55	0.00	45.48	3.59
1817	1866	3.489785	GCGTCGTAGCAATTTGTAGCTAT	59.510	43.478	0.00	0.00	44.32	2.97
1841	1890	2.862674	TAGTTGGCGGGATTGGCGAC	62.863	60.000	0.00	0.00	46.36	5.19
1852	1901	3.360384	CGAACGTAATCGATTAGTTGGCG	60.360	47.826	24.76	21.73	45.48	5.69
1863	1912	1.855978	TGCCTAATGCGAACGTAATCG	59.144	47.619	5.29	5.29	45.60	3.34
1864	1913	3.062909	TGTTGCCTAATGCGAACGTAATC	59.937	43.478	0.00	0.00	45.60	1.75
1866	1915	2.414806	TGTTGCCTAATGCGAACGTAA	58.585	42.857	0.00	0.00	45.60	3.18
1868	1917	1.448985	ATGTTGCCTAATGCGAACGT	58.551	45.000	0.00	0.00	45.60	3.99
1869	1918	2.176369	CAATGTTGCCTAATGCGAACG	58.824	47.619	0.00	0.00	45.60	3.95
1870	1919	3.216147	ACAATGTTGCCTAATGCGAAC	57.784	42.857	0.00	0.00	45.60	3.95
1874	1923	3.924144	TCCAAACAATGTTGCCTAATGC	58.076	40.909	0.00	0.00	41.77	3.56
1875	1924	6.092533	GGAATTCCAAACAATGTTGCCTAATG	59.907	38.462	20.04	0.00	35.64	1.90
1876	1925	6.172630	GGAATTCCAAACAATGTTGCCTAAT	58.827	36.000	20.04	0.00	35.64	1.73
1877	1926	5.070981	TGGAATTCCAAACAATGTTGCCTAA	59.929	36.000	25.13	0.00	44.35	2.69
1878	1927	4.590647	TGGAATTCCAAACAATGTTGCCTA	59.409	37.500	25.13	0.00	44.35	3.93
1879	1928	3.390639	TGGAATTCCAAACAATGTTGCCT	59.609	39.130	25.13	0.00	44.35	4.75
1880	1929	3.737850	TGGAATTCCAAACAATGTTGCC	58.262	40.909	25.13	0.00	44.35	4.52
1892	1941	2.922955	TCATACCCCACTTGGAATTCCA	59.077	45.455	23.63	23.63	45.94	3.53
1893	1942	3.288092	GTCATACCCCACTTGGAATTCC	58.712	50.000	18.17	18.17	37.39	3.01
1894	1943	2.943033	CGTCATACCCCACTTGGAATTC	59.057	50.000	0.00	0.00	37.39	2.17
1895	1944	2.944094	GCGTCATACCCCACTTGGAATT	60.944	50.000	0.00	0.00	37.39	2.17
1896	1945	1.408266	GCGTCATACCCCACTTGGAAT	60.408	52.381	0.00	0.00	37.39	3.01
1897	1946	0.035820	GCGTCATACCCCACTTGGAA	60.036	55.000	0.00	0.00	37.39	3.53
1899	1948	0.744414	CTGCGTCATACCCCACTTGG	60.744	60.000	0.00	0.00	0.00	3.61
1900	1949	0.036388	ACTGCGTCATACCCCACTTG	60.036	55.000	0.00	0.00	0.00	3.16
1901	1950	0.690762	AACTGCGTCATACCCCACTT	59.309	50.000	0.00	0.00	0.00	3.16
1902	1951	0.690762	AAACTGCGTCATACCCCACT	59.309	50.000	0.00	0.00	0.00	4.00
1903	1952	2.004733	GTAAACTGCGTCATACCCCAC	58.995	52.381	0.00	0.00	0.00	4.61
1904	1953	1.903860	AGTAAACTGCGTCATACCCCA	59.096	47.619	0.00	0.00	0.00	4.96
1905	1954	2.277084	CAGTAAACTGCGTCATACCCC	58.723	52.381	0.00	0.00	37.15	4.95
2006	2697	7.128331	CAGTATTTACAGCCAGAATGATTTCG	58.872	38.462	0.00	0.00	39.69	3.46
2021	2712	5.642063	GCCAACTAGAACTGCAGTATTTACA	59.358	40.000	22.01	1.64	0.00	2.41
2343	3051	1.676006	ACTTTGTGTTTCTCCAAGGCG	59.324	47.619	0.00	0.00	0.00	5.52
2425	3133	1.783284	TCAGTGTCGACATCACTTGC	58.217	50.000	23.12	6.75	43.14	4.01
2449	3157	5.607939	TGCAGTCCTATCTTAATCGGAAA	57.392	39.130	0.00	0.00	29.13	3.13
2599	3309	2.723322	AACTTCCTATTTACCCCCGC	57.277	50.000	0.00	0.00	0.00	6.13
2652	3362	8.367156	TCGGTTTTAGTTCTACTAAGCCTAAAA	58.633	33.333	14.49	0.00	41.23	1.52
2785	3495	3.145861	TCATCAATACCCCCATCCTCCTA	59.854	47.826	0.00	0.00	0.00	2.94
2824	3534	2.749621	ACTTCATCCATTCGGCTTTGAC	59.250	45.455	0.00	0.00	0.00	3.18
2834	3544	0.611618	TTGGCGCCACTTCATCCATT	60.612	50.000	32.95	0.00	0.00	3.16
2904	3614	1.000060	CGAACCACCGTCCTGTAGAAA	60.000	52.381	0.00	0.00	0.00	2.52
2918	3628	1.228003	AACATTGCGGGTCGAACCA	60.228	52.632	21.79	0.00	41.02	3.67
3136	3846	2.932194	AGCTTCTGGAGGCCTGCA	60.932	61.111	26.78	26.78	33.44	4.41
3277	3988	1.449601	CACGCACCCCTGTCCATAC	60.450	63.158	0.00	0.00	0.00	2.39

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.