AutoCloner

Multiple sequence alignment - TraesCS2A01G046200

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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	TraesCS2A01G046200	chr2A	100.000	2865	0	0	1	2865	18060370	18057506	0.000000e+00	5291
1	TraesCS2A01G046200	chr2A	95.495	910	23	5	1	892	39416493	39417402	0.000000e+00	1437
2	TraesCS2A01G046200	chr2A	97.579	537	11	2	2330	2865	16027610	16027075	0.000000e+00	918
3	TraesCS2A01G046200	chr2A	92.355	654	33	4	254	890	772042298	772042951	0.000000e+00	915
4	TraesCS2A01G046200	chr2A	97.207	537	13	2	2330	2865	19046110	19046645	0.000000e+00	907
5	TraesCS2A01G046200	chr2A	97.020	537	13	3	2330	2865	17634305	17634839	0.000000e+00	900
6	TraesCS2A01G046200	chr2A	97.424	427	8	3	1956	2381	16028035	16027611	0.000000e+00	725
7	TraesCS2A01G046200	chr2A	96.721	427	10	3	1956	2381	17633682	17634105	0.000000e+00	708
8	TraesCS2A01G046200	chr2A	96.253	427	13	3	1956	2381	19045685	19046109	0.000000e+00	697
9	TraesCS2A01G046200	chr2A	90.617	373	11	4	1957	2328	16712370	16712719	9.290000e-130	473
10	TraesCS2A01G046200	chr2A	94.382	267	14	1	1	266	772039854	772040120	2.660000e-110	409
11	TraesCS2A01G046200	chr2A	94.839	155	8	0	2373	2527	18058144	18057990	2.850000e-60	243
12	TraesCS2A01G046200	chr2A	97.273	110	2	1	1954	2063	17448645	17448753	4.870000e-43	185
13	TraesCS2A01G046200	chr3A	94.714	908	30	5	1	890	745756177	745755270	0.000000e+00	1395
14	TraesCS2A01G046200	chr3A	96.828	536	17	0	2330	2865	708563444	708563979	0.000000e+00	896
15	TraesCS2A01G046200	chr3A	90.385	260	3	2	2123	2381	708563205	708563443	3.560000e-84	322
16	TraesCS2A01G046200	chr7A	93.878	931	27	8	1	901	403981765	403980835	0.000000e+00	1376
17	TraesCS2A01G046200	chr1B	94.826	889	28	5	1	871	473288735	473287847	0.000000e+00	1371
18	TraesCS2A01G046200	chr1B	83.134	919	129	15	1	893	633850263	633851181	0.000000e+00	815
19	TraesCS2A01G046200	chr6D	92.588	904	48	6	4	889	444327	443425	0.000000e+00	1280
20	TraesCS2A01G046200	chrUn	85.353	1106	92	36	897	1949	24305100	24304012	0.000000e+00	1081
21	TraesCS2A01G046200	chrUn	96.642	536	17	1	2330	2865	208399318	208399852	0.000000e+00	889
22	TraesCS2A01G046200	chrUn	91.667	432	25	10	1955	2381	208398694	208399119	3.180000e-164	588
23	TraesCS2A01G046200	chrUn	90.347	259	4	1	2123	2381	208399278	208399515	1.280000e-83	320
24	TraesCS2A01G046200	chr2B	83.527	1117	90	48	883	1946	28417201	28416126	0.000000e+00	957
25	TraesCS2A01G046200	chr2B	96.947	393	11	1	2473	2865	796434711	796435102	0.000000e+00	658
26	TraesCS2A01G046200	chr6A	97.761	536	10	2	2330	2865	36394266	36393733	0.000000e+00	922
27	TraesCS2A01G046200	chr6A	96.487	427	11	3	1956	2381	36394889	36394466	0.000000e+00	702
28	TraesCS2A01G046200	chr6A	90.734	259	2	2	2123	2381	36394306	36394070	2.750000e-85	326
29	TraesCS2A01G046200	chr1A	96.828	536	16	1	2330	2865	2546697	2546163	0.000000e+00	894
30	TraesCS2A01G046200	chr1A	93.427	426	10	5	1956	2381	2547105	2546698	1.460000e-172	616
31	TraesCS2A01G046200	chr5B	97.201	393	10	1	2473	2865	144585245	144584854	0.000000e+00	664
32	TraesCS2A01G046200	chr5B	84.926	272	7	8	2123	2381	442369549	442369799	7.930000e-61	244
33	TraesCS2A01G046200	chr5B	82.443	131	23	0	1263	1393	273896038	273896168	6.490000e-22	115
34	TraesCS2A01G046200	chr4A	84.815	270	7	7	2125	2381	716707016	716706768	1.030000e-59	241
35	TraesCS2A01G046200	chr4A	95.364	151	6	1	2325	2474	677785973	677785823	3.690000e-59	239
36	TraesCS2A01G046200	chr4A	89.474	171	9	6	1955	2125	733465350	733465189	1.040000e-49	207

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	TraesCS2A01G046200	chr2A	18057506	18060370	2864	True	2767.0	5291	97.419500	1	2865	2	chr2A.!!$R2	2864
1	TraesCS2A01G046200	chr2A	39416493	39417402	909	False	1437.0	1437	95.495000	1	892	1	chr2A.!!$F3	891
2	TraesCS2A01G046200	chr2A	16027075	16028035	960	True	821.5	918	97.501500	1956	2865	2	chr2A.!!$R1	909
3	TraesCS2A01G046200	chr2A	17633682	17634839	1157	False	804.0	900	96.870500	1956	2865	2	chr2A.!!$F4	909
4	TraesCS2A01G046200	chr2A	19045685	19046645	960	False	802.0	907	96.730000	1956	2865	2	chr2A.!!$F5	909
5	TraesCS2A01G046200	chr2A	772039854	772042951	3097	False	662.0	915	93.368500	1	890	2	chr2A.!!$F6	889
6	TraesCS2A01G046200	chr3A	745755270	745756177	907	True	1395.0	1395	94.714000	1	890	1	chr3A.!!$R1	889
7	TraesCS2A01G046200	chr3A	708563205	708563979	774	False	609.0	896	93.606500	2123	2865	2	chr3A.!!$F1	742
8	TraesCS2A01G046200	chr7A	403980835	403981765	930	True	1376.0	1376	93.878000	1	901	1	chr7A.!!$R1	900
9	TraesCS2A01G046200	chr1B	473287847	473288735	888	True	1371.0	1371	94.826000	1	871	1	chr1B.!!$R1	870
10	TraesCS2A01G046200	chr1B	633850263	633851181	918	False	815.0	815	83.134000	1	893	1	chr1B.!!$F1	892
11	TraesCS2A01G046200	chr6D	443425	444327	902	True	1280.0	1280	92.588000	4	889	1	chr6D.!!$R1	885
12	TraesCS2A01G046200	chrUn	24304012	24305100	1088	True	1081.0	1081	85.353000	897	1949	1	chrUn.!!$R1	1052
13	TraesCS2A01G046200	chrUn	208398694	208399852	1158	False	599.0	889	92.885333	1955	2865	3	chrUn.!!$F1	910
14	TraesCS2A01G046200	chr2B	28416126	28417201	1075	True	957.0	957	83.527000	883	1946	1	chr2B.!!$R1	1063
15	TraesCS2A01G046200	chr6A	36393733	36394889	1156	True	650.0	922	94.994000	1956	2865	3	chr6A.!!$R1	909
16	TraesCS2A01G046200	chr1A	2546163	2547105	942	True	755.0	894	95.127500	1956	2865	2	chr1A.!!$R1	909

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
590	2783	0.03779	GGGGATGAGCGAGCTGTATC	60.038	60.0	0.84	6.37	0.0	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1929	4240	0.038343	ACGCATGGCATGTGAAAACC	60.038	50.0	39.09	16.62	43.24	3.27	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
92	93	5.205759	AGATGAGAAAAGTTTGGGCTTTG	57.794	39.130	0.00	0.00	38.54	2.77
198	199	6.360370	AGCTAATGTTACTGTTCTGGAGAA	57.640	37.500	0.00	0.00	0.00	2.87
342	2534	1.900486	AGGGAAAGGTAGTCTGTTCCG	59.100	52.381	0.00	0.00	40.45	4.30
352	2544	5.826208	AGGTAGTCTGTTCCGTGAAAAATTT	59.174	36.000	0.00	0.00	0.00	1.82
385	2577	1.740585	CAGACTCCGAAGACGATCTGT	59.259	52.381	0.00	0.00	42.66	3.41
436	2629	5.790593	TGGAAACTAAATACAGAAGCGTCT	58.209	37.500	0.00	0.00	32.85	4.18
477	2670	0.320697	ACCTGTCTTGGAACGGTAGC	59.679	55.000	0.00	0.00	0.00	3.58
505	2698	1.352352	CACAGGGGAGATGTGGTCTTT	59.648	52.381	0.00	0.00	43.47	2.52
506	2699	1.352352	ACAGGGGAGATGTGGTCTTTG	59.648	52.381	0.00	0.00	37.29	2.77
588	2781	0.975556	TTGGGGATGAGCGAGCTGTA	60.976	55.000	0.84	0.00	0.00	2.74
589	2782	0.760567	TGGGGATGAGCGAGCTGTAT	60.761	55.000	0.84	0.00	0.00	2.29
590	2783	0.037790	GGGGATGAGCGAGCTGTATC	60.038	60.000	0.84	6.37	0.00	2.24
602	2812	4.624882	GCGAGCTGTATCCTAATCATTGAG	59.375	45.833	0.00	0.00	0.00	3.02
638	2848	4.183865	CCATAGTGAATCGACTGAAAGCA	58.816	43.478	0.00	0.00	37.60	3.91
640	2850	2.693069	AGTGAATCGACTGAAAGCAGG	58.307	47.619	0.00	0.00	46.60	4.85
922	3149	3.608796	GAGGAAAAAGAGAGCAGCAGAT	58.391	45.455	0.00	0.00	0.00	2.90
938	3166	4.594920	CAGCAGATAGATAAGGGGAAGGAA	59.405	45.833	0.00	0.00	0.00	3.36
1010	3251	3.138798	GCAGAGCATGGCACTGGG	61.139	66.667	15.53	0.00	44.91	4.45
1116	3363	1.748122	GAGGAGGACGCGGTCTGTA	60.748	63.158	12.47	0.00	32.47	2.74
1359	3621	2.278013	GACGACATCTCCGGCGAC	60.278	66.667	9.30	0.00	0.00	5.19
1398	3660	2.203728	ACCTGGCACCTCGGTACA	60.204	61.111	0.00	0.00	0.00	2.90
1399	3661	2.283529	ACCTGGCACCTCGGTACAG	61.284	63.158	11.09	11.09	34.31	2.74
1400	3662	2.283529	CCTGGCACCTCGGTACAGT	61.284	63.158	14.82	0.00	33.36	3.55
1406	3668	0.179171	CACCTCGGTACAGTACGCAG	60.179	60.000	4.58	3.05	0.00	5.18
1408	3670	0.098376	CCTCGGTACAGTACGCAGAC	59.902	60.000	4.58	0.00	0.00	3.51
1410	3672	1.226211	CGGTACAGTACGCAGACCG	60.226	63.158	14.33	14.33	46.16	4.79
1414	3676	2.416431	GGTACAGTACGCAGACCGAAAT	60.416	50.000	4.58	0.00	41.02	2.17
1419	3681	1.925185	GTACGCAGACCGAAATCCTTC	59.075	52.381	0.00	0.00	41.02	3.46
1421	3683	1.002087	ACGCAGACCGAAATCCTTCTT	59.998	47.619	0.00	0.00	41.02	2.52
1428	3690	4.775253	AGACCGAAATCCTTCTTCTCTTCT	59.225	41.667	0.00	0.00	0.00	2.85
1429	3691	5.079689	ACCGAAATCCTTCTTCTCTTCTC	57.920	43.478	0.00	0.00	0.00	2.87
1430	3692	4.081365	ACCGAAATCCTTCTTCTCTTCTCC	60.081	45.833	0.00	0.00	0.00	3.71
1432	3694	4.438148	GAAATCCTTCTTCTCTTCTCCCG	58.562	47.826	0.00	0.00	0.00	5.14
1433	3695	1.853963	TCCTTCTTCTCTTCTCCCGG	58.146	55.000	0.00	0.00	0.00	5.73
1434	3696	0.176910	CCTTCTTCTCTTCTCCCGGC	59.823	60.000	0.00	0.00	0.00	6.13
1436	3698	0.898320	TTCTTCTCTTCTCCCGGCTG	59.102	55.000	0.00	0.00	0.00	4.85
1437	3699	0.251832	TCTTCTCTTCTCCCGGCTGT	60.252	55.000	0.00	0.00	0.00	4.40
1438	3700	0.108424	CTTCTCTTCTCCCGGCTGTG	60.108	60.000	0.00	0.00	0.00	3.66
1439	3701	2.125350	CTCTTCTCCCGGCTGTGC	60.125	66.667	0.00	0.00	0.00	4.57
1440	3702	2.922503	TCTTCTCCCGGCTGTGCA	60.923	61.111	0.00	0.00	0.00	4.57
1441	3703	2.249413	CTCTTCTCCCGGCTGTGCAT	62.249	60.000	0.00	0.00	0.00	3.96
1442	3704	1.817099	CTTCTCCCGGCTGTGCATC	60.817	63.158	0.00	0.00	0.00	3.91
1444	3706	2.202987	CTCCCGGCTGTGCATCTC	60.203	66.667	0.00	0.00	0.00	2.75
1445	3707	3.746949	CTCCCGGCTGTGCATCTCC	62.747	68.421	0.00	0.00	0.00	3.71
1447	3709	4.457496	CCGGCTGTGCATCTCCGT	62.457	66.667	17.89	0.00	40.23	4.69
1448	3710	2.887568	CGGCTGTGCATCTCCGTC	60.888	66.667	13.19	0.00	37.33	4.79
1450	3712	1.812922	GGCTGTGCATCTCCGTCTG	60.813	63.158	0.00	0.00	0.00	3.51
1451	3713	1.216444	GCTGTGCATCTCCGTCTGA	59.784	57.895	0.00	0.00	0.00	3.27
1452	3714	0.805322	GCTGTGCATCTCCGTCTGAG	60.805	60.000	0.00	0.00	42.90	3.35
1464	3726	3.165875	TCCGTCTGAGAGGTCTGAATTT	58.834	45.455	1.20	0.00	32.89	1.82
1465	3727	3.578716	TCCGTCTGAGAGGTCTGAATTTT	59.421	43.478	1.20	0.00	32.89	1.82
1467	3729	3.681897	CGTCTGAGAGGTCTGAATTTTGG	59.318	47.826	0.00	0.00	32.89	3.28
1475	3756	4.037222	AGGTCTGAATTTTGGTTTGGGTT	58.963	39.130	0.00	0.00	0.00	4.11
1581	3862	3.394674	TCAGATCGTGTAAGCAACCAA	57.605	42.857	0.00	0.00	0.00	3.67
1582	3863	3.325870	TCAGATCGTGTAAGCAACCAAG	58.674	45.455	0.00	0.00	0.00	3.61
1583	3864	2.076863	AGATCGTGTAAGCAACCAAGC	58.923	47.619	0.00	0.00	0.00	4.01
1584	3865	1.804151	GATCGTGTAAGCAACCAAGCA	59.196	47.619	0.00	0.00	36.85	3.91
1592	3873	3.756933	AAGCAACCAAGCACATTCATT	57.243	38.095	0.00	0.00	36.85	2.57
1608	3889	4.556942	TTCATTCATTCAGCTAATGGCG	57.443	40.909	12.83	0.00	44.42	5.69
1620	3901	3.957468	GCTAATGGCGAAATCTCCAAAG	58.043	45.455	0.00	0.00	34.01	2.77
1623	3904	0.321210	TGGCGAAATCTCCAAAGCGA	60.321	50.000	0.00	0.00	0.00	4.93
1624	3905	0.802494	GGCGAAATCTCCAAAGCGAA	59.198	50.000	0.00	0.00	0.00	4.70
1625	3906	1.401905	GGCGAAATCTCCAAAGCGAAT	59.598	47.619	0.00	0.00	0.00	3.34
1626	3907	2.539750	GGCGAAATCTCCAAAGCGAATC	60.540	50.000	0.00	0.00	0.00	2.52
1627	3908	2.539750	GCGAAATCTCCAAAGCGAATCC	60.540	50.000	0.00	0.00	0.00	3.01
1657	3938	6.545508	TGTATTCAGATTTGTGAGATTTGCG	58.454	36.000	0.00	0.00	0.00	4.85
1658	3939	4.424061	TTCAGATTTGTGAGATTTGCGG	57.576	40.909	0.00	0.00	0.00	5.69
1730	4011	2.357034	CTGGCGCTGGTACGTTGT	60.357	61.111	7.64	0.00	34.88	3.32
1751	4062	7.492669	CGTTGTTGTACCTCTTCTATGATGATT	59.507	37.037	0.00	0.00	0.00	2.57
1752	4063	8.607459	GTTGTTGTACCTCTTCTATGATGATTG	58.393	37.037	0.00	0.00	0.00	2.67
1753	4064	8.078060	TGTTGTACCTCTTCTATGATGATTGA	57.922	34.615	0.00	0.00	0.00	2.57
1754	4065	7.981789	TGTTGTACCTCTTCTATGATGATTGAC	59.018	37.037	0.00	0.00	0.00	3.18
1755	4066	6.739112	TGTACCTCTTCTATGATGATTGACG	58.261	40.000	0.00	0.00	0.00	4.35
1756	4067	6.546034	TGTACCTCTTCTATGATGATTGACGA	59.454	38.462	0.00	0.00	0.00	4.20
1763	4074	9.551734	TCTTCTATGATGATTGACGAATGAATT	57.448	29.630	0.00	0.00	0.00	2.17
1764	4075	9.595357	CTTCTATGATGATTGACGAATGAATTG	57.405	33.333	0.00	0.00	0.00	2.32
1780	4091	4.842574	TGAATTGTTCCTGATGAATCCGA	58.157	39.130	0.00	0.00	34.90	4.55
1874	4185	1.110442	CAGGCTCTGACTCGATCCTT	58.890	55.000	0.00	0.00	32.44	3.36
1890	4201	3.655276	TCCTTACACAACTCGAACCTC	57.345	47.619	0.00	0.00	0.00	3.85
1917	4228	2.088423	TGATTCATGGTTGTAACGGGC	58.912	47.619	0.00	0.00	0.00	6.13
1929	4240	2.230508	TGTAACGGGCTACAACTCTCTG	59.769	50.000	0.00	0.00	0.00	3.35
1932	4243	0.608640	CGGGCTACAACTCTCTGGTT	59.391	55.000	0.00	0.00	0.00	3.67
1935	4246	3.075148	GGGCTACAACTCTCTGGTTTTC	58.925	50.000	0.00	0.00	0.00	2.29
1949	4260	1.201181	GGTTTTCACATGCCATGCGTA	59.799	47.619	4.17	0.00	0.00	4.42
1950	4261	2.159254	GGTTTTCACATGCCATGCGTAT	60.159	45.455	4.17	0.00	0.00	3.06
1951	4262	2.847959	TTTCACATGCCATGCGTATG	57.152	45.000	4.17	6.50	40.20	2.39
1952	4263	0.381445	TTCACATGCCATGCGTATGC	59.619	50.000	8.12	0.00	38.06	3.14
2020	4347	7.115095	CGGTTTATTTTCGCTGGTTTATTTTCA	59.885	33.333	0.00	0.00	0.00	2.69
2039	4366	0.192064	ATCATCCTCCCATCTCCGGT	59.808	55.000	0.00	0.00	0.00	5.28
2471	5449	4.660168	CATAGCTATCCTTTTCCTGCCAT	58.340	43.478	2.34	0.00	0.00	4.40
2717	5697	2.659016	CCTCGTTGCTCTGCCTCA	59.341	61.111	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	3.057245	GCCCAAACTTTTCTCATCTCACC	60.057	47.826	0.00	0.00	0.00	4.02
92	93	2.751806	CCTGAATTCTTTCTCTGTGGGC	59.248	50.000	7.05	0.00	32.78	5.36
198	199	1.544691	AGTCATCGCGTAGGAACAAGT	59.455	47.619	5.77	0.00	0.00	3.16
342	2534	5.163395	TGGGTGGGAGTGTTAAATTTTTCAC	60.163	40.000	13.79	13.79	0.00	3.18
352	2544	1.640917	GAGTCTGGGTGGGAGTGTTA	58.359	55.000	0.00	0.00	0.00	2.41
436	2629	1.001520	TCCTCTGATTTGCCGACGAAA	59.998	47.619	0.00	0.00	0.00	3.46
477	2670	1.693062	CATCTCCCCTGTGATCTCTGG	59.307	57.143	12.41	12.41	0.00	3.86
506	2699	2.008329	CTTGATCTTCCTGCAGACTGC	58.992	52.381	20.86	20.86	45.29	4.40
588	2781	5.454471	GGCAGTCAGACTCAATGATTAGGAT	60.454	44.000	0.00	0.00	0.00	3.24
589	2782	4.141846	GGCAGTCAGACTCAATGATTAGGA	60.142	45.833	0.00	0.00	0.00	2.94
590	2783	4.125703	GGCAGTCAGACTCAATGATTAGG	58.874	47.826	0.00	0.00	0.00	2.69
602	2812	3.447586	TCACTATGGTTAGGCAGTCAGAC	59.552	47.826	0.00	0.00	0.00	3.51
638	2848	2.338809	TGTGATTTGTCCACTCCTCCT	58.661	47.619	0.00	0.00	35.66	3.69
640	2850	5.705441	TGTAATTGTGATTTGTCCACTCCTC	59.295	40.000	0.00	0.00	35.66	3.71
922	3149	4.080751	CGTTGGTTTCCTTCCCCTTATCTA	60.081	45.833	0.00	0.00	0.00	1.98
938	3166	1.295423	CCTCCATCGTCCGTTGGTT	59.705	57.895	14.51	0.00	36.60	3.67
1087	3334	4.787280	CCTCCTCCTCCCGCCACT	62.787	72.222	0.00	0.00	0.00	4.00
1281	3543	2.359975	CCGAAGAAGCCCACCACC	60.360	66.667	0.00	0.00	0.00	4.61
1398	3660	1.183549	AGGATTTCGGTCTGCGTACT	58.816	50.000	0.00	0.00	0.00	2.73
1399	3661	1.925185	GAAGGATTTCGGTCTGCGTAC	59.075	52.381	0.00	0.00	0.00	3.67
1400	3662	1.822990	AGAAGGATTTCGGTCTGCGTA	59.177	47.619	0.00	0.00	38.38	4.42
1406	3668	5.079689	AGAAGAGAAGAAGGATTTCGGTC	57.920	43.478	0.00	0.00	38.38	4.79
1408	3670	4.438148	GGAGAAGAGAAGAAGGATTTCGG	58.562	47.826	0.00	0.00	38.38	4.30
1410	3672	4.438148	CGGGAGAAGAGAAGAAGGATTTC	58.562	47.826	0.00	0.00	0.00	2.17
1414	3676	1.853963	CCGGGAGAAGAGAAGAAGGA	58.146	55.000	0.00	0.00	0.00	3.36
1419	3681	0.108424	CACAGCCGGGAGAAGAGAAG	60.108	60.000	2.18	0.00	0.00	2.85
1421	3683	2.650116	GCACAGCCGGGAGAAGAGA	61.650	63.158	2.18	0.00	0.00	3.10
1428	3690	3.785859	GGAGATGCACAGCCGGGA	61.786	66.667	2.18	0.00	0.00	5.14
1432	3694	1.812922	CAGACGGAGATGCACAGCC	60.813	63.158	0.00	0.00	0.00	4.85
1433	3695	1.216444	TCAGACGGAGATGCACAGC	59.784	57.895	0.00	0.00	0.00	4.40
1442	3704	1.827681	TTCAGACCTCTCAGACGGAG	58.172	55.000	0.00	0.00	45.49	4.63
1444	3706	3.601443	AAATTCAGACCTCTCAGACGG	57.399	47.619	0.00	0.00	0.00	4.79
1445	3707	3.681897	CCAAAATTCAGACCTCTCAGACG	59.318	47.826	0.00	0.00	0.00	4.18
1446	3708	4.646572	ACCAAAATTCAGACCTCTCAGAC	58.353	43.478	0.00	0.00	0.00	3.51
1447	3709	4.982241	ACCAAAATTCAGACCTCTCAGA	57.018	40.909	0.00	0.00	0.00	3.27
1448	3710	5.278660	CCAAACCAAAATTCAGACCTCTCAG	60.279	44.000	0.00	0.00	0.00	3.35
1450	3712	4.021981	CCCAAACCAAAATTCAGACCTCTC	60.022	45.833	0.00	0.00	0.00	3.20
1451	3713	3.897505	CCCAAACCAAAATTCAGACCTCT	59.102	43.478	0.00	0.00	0.00	3.69
1452	3714	3.641436	ACCCAAACCAAAATTCAGACCTC	59.359	43.478	0.00	0.00	0.00	3.85
1453	3715	3.653164	ACCCAAACCAAAATTCAGACCT	58.347	40.909	0.00	0.00	0.00	3.85
1454	3716	4.141824	TGAACCCAAACCAAAATTCAGACC	60.142	41.667	0.00	0.00	0.00	3.85
1455	3717	5.017294	TGAACCCAAACCAAAATTCAGAC	57.983	39.130	0.00	0.00	0.00	3.51
1464	3726	1.566703	TCCACTCTGAACCCAAACCAA	59.433	47.619	0.00	0.00	0.00	3.67
1465	3727	1.217916	TCCACTCTGAACCCAAACCA	58.782	50.000	0.00	0.00	0.00	3.67
1467	3729	2.230660	CCTTCCACTCTGAACCCAAAC	58.769	52.381	0.00	0.00	0.00	2.93
1475	3756	3.003173	CCGCCCCTTCCACTCTGA	61.003	66.667	0.00	0.00	0.00	3.27
1581	3862	6.461092	CCATTAGCTGAATGAATGAATGTGCT	60.461	38.462	13.99	0.00	46.94	4.40
1582	3863	5.690409	CCATTAGCTGAATGAATGAATGTGC	59.310	40.000	13.99	0.00	46.94	4.57
1583	3864	5.690409	GCCATTAGCTGAATGAATGAATGTG	59.310	40.000	13.99	2.64	46.94	3.21
1584	3865	5.506815	CGCCATTAGCTGAATGAATGAATGT	60.507	40.000	13.99	0.00	46.94	2.71
1592	3873	4.454678	AGATTTCGCCATTAGCTGAATGA	58.545	39.130	13.99	0.00	46.94	2.57
1608	3889	4.907879	ATGGATTCGCTTTGGAGATTTC	57.092	40.909	0.00	0.00	0.00	2.17
1657	3938	1.956170	CCATACCTGCGATGCGACC	60.956	63.158	0.00	0.00	0.00	4.79
1658	3939	2.598632	GCCATACCTGCGATGCGAC	61.599	63.158	0.00	0.00	0.00	5.19
1730	4011	7.068226	TCGTCAATCATCATAGAAGAGGTACAA	59.932	37.037	0.00	0.00	0.00	2.41
1751	4062	5.244755	TCATCAGGAACAATTCATTCGTCA	58.755	37.500	0.00	0.00	0.00	4.35
1752	4063	5.801350	TCATCAGGAACAATTCATTCGTC	57.199	39.130	0.00	0.00	0.00	4.20
1753	4064	6.183360	GGATTCATCAGGAACAATTCATTCGT	60.183	38.462	0.00	0.00	38.60	3.85
1754	4065	6.204359	GGATTCATCAGGAACAATTCATTCG	58.796	40.000	0.00	0.00	38.60	3.34
1755	4066	6.038603	TCGGATTCATCAGGAACAATTCATTC	59.961	38.462	0.00	0.00	38.60	2.67
1756	4067	5.887598	TCGGATTCATCAGGAACAATTCATT	59.112	36.000	0.00	0.00	38.60	2.57
1763	4074	2.673893	CGTGTCGGATTCATCAGGAACA	60.674	50.000	0.00	0.00	38.60	3.18
1764	4075	1.927174	CGTGTCGGATTCATCAGGAAC	59.073	52.381	0.00	0.00	38.60	3.62
1780	4091	4.947147	AATGTGGTGCGGCCGTGT	62.947	61.111	28.70	2.00	41.21	4.49
1874	4185	2.005370	AGGGAGGTTCGAGTTGTGTA	57.995	50.000	0.00	0.00	0.00	2.90
1890	4201	5.466728	CGTTACAACCATGAATCATCTAGGG	59.533	44.000	0.00	0.00	0.00	3.53
1917	4228	5.334414	GCATGTGAAAACCAGAGAGTTGTAG	60.334	44.000	0.00	0.00	0.00	2.74
1929	4240	0.038343	ACGCATGGCATGTGAAAACC	60.038	50.000	39.09	16.62	43.24	3.27
1932	4243	1.202279	GCATACGCATGGCATGTGAAA	60.202	47.619	39.09	27.94	43.24	2.69
1935	4246	1.369568	CGCATACGCATGGCATGTG	60.370	57.895	33.07	33.07	45.88	3.21
1949	4260	5.571285	TCCATTAGGAGTAGAGATACGCAT	58.429	41.667	0.00	0.00	39.61	4.73
1950	4261	4.981812	TCCATTAGGAGTAGAGATACGCA	58.018	43.478	0.00	0.00	39.61	5.24
2020	4347	0.192064	ACCGGAGATGGGAGGATGAT	59.808	55.000	9.46	0.00	0.00	2.45
2456	5236	1.009997	TGGGATGGCAGGAAAAGGAT	58.990	50.000	0.00	0.00	0.00	3.24
2608	5587	9.709495	AGTAGAGATGATTGATGATAAGAAAGC	57.291	33.333	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.