AutoCloner

Multiple sequence alignment - TraesCS6A01G101500

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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	TraesCS6A01G101500	chr6A	100.000	2384	0	0	1	2384	70187088	70184705	0.000000e+00	4403.0
1	TraesCS6A01G101500	chr6A	95.124	1210	50	4	1	1209	70153074	70151873	0.000000e+00	1899.0
2	TraesCS6A01G101500	chr6A	91.060	604	53	1	906	1509	384926892	384926290	0.000000e+00	815.0
3	TraesCS6A01G101500	chr6A	96.569	408	14	0	1518	1925	70169487	70169080	0.000000e+00	676.0
4	TraesCS6A01G101500	chr6A	90.000	260	24	2	1259	1516	71615606	71615347	3.800000e-88	335.0
5	TraesCS6A01G101500	chr6A	89.231	260	26	2	1259	1516	71630822	71630563	8.220000e-85	324.0
6	TraesCS6A01G101500	chr3D	93.426	1369	87	1	148	1516	249668809	249667444	0.000000e+00	2026.0
7	TraesCS6A01G101500	chr3D	93.280	1369	89	1	148	1516	249653452	249652087	0.000000e+00	2015.0
8	TraesCS6A01G101500	chr3D	93.538	1300	84	0	148	1447	249281136	249279837	0.000000e+00	1936.0
9	TraesCS6A01G101500	chr3D	89.736	643	62	3	874	1516	99848265	99848903	0.000000e+00	819.0
10	TraesCS6A01G101500	chr3D	83.544	869	98	36	1517	2366	173535117	173535959	0.000000e+00	771.0
11	TraesCS6A01G101500	chr3D	83.077	260	38	4	1216	1473	249668147	249667892	5.120000e-57	231.0
12	TraesCS6A01G101500	chr3D	81.164	292	47	6	1213	1502	249652793	249652508	6.630000e-56	228.0
13	TraesCS6A01G101500	chr3D	89.744	156	14	1	1361	1516	99837908	99838061	5.200000e-47	198.0
14	TraesCS6A01G101500	chr3B	85.304	871	88	33	1515	2366	50216945	50217794	0.000000e+00	863.0
15	TraesCS6A01G101500	chr7B	90.297	639	61	1	876	1514	246764721	246764084	0.000000e+00	835.0
16	TraesCS6A01G101500	chr7B	88.475	564	57	5	226	789	654080796	654081351	0.000000e+00	675.0
17	TraesCS6A01G101500	chr7B	86.567	67	6	3	46	111	611022942	611022878	1.180000e-08	71.3
18	TraesCS6A01G101500	chr3A	89.580	643	65	2	874	1516	666048294	666048934	0.000000e+00	815.0
19	TraesCS6A01G101500	chr3A	97.297	407	8	3	1517	1922	334028192	334028596	0.000000e+00	688.0
20	TraesCS6A01G101500	chr3A	96.126	413	15	1	1513	1925	686237116	686236705	0.000000e+00	673.0
21	TraesCS6A01G101500	chr4A	89.392	641	65	3	876	1516	258966938	258966301	0.000000e+00	804.0
22	TraesCS6A01G101500	chr4A	95.000	460	21	2	1926	2383	236509696	236510155	0.000000e+00	721.0
23	TraesCS6A01G101500	chr4A	96.577	409	13	1	1517	1925	628337350	628337757	0.000000e+00	676.0
24	TraesCS6A01G101500	chr4A	96.319	163	6	0	1	163	299980805	299980967	3.910000e-68	268.0
25	TraesCS6A01G101500	chr4A	89.231	130	11	3	34	163	302239927	302239801	2.450000e-35	159.0
26	TraesCS6A01G101500	chr7A	86.188	724	79	14	1651	2365	614674472	614675183	0.000000e+00	763.0
27	TraesCS6A01G101500	chr7A	94.828	464	22	2	1922	2383	713908831	713909294	0.000000e+00	723.0
28	TraesCS6A01G101500	chr7A	96.117	412	13	3	1517	1927	648799980	648800389	0.000000e+00	669.0
29	TraesCS6A01G101500	chr5D	95.415	458	18	3	1926	2382	46825146	46825601	0.000000e+00	726.0
30	TraesCS6A01G101500	chr2A	95.217	460	19	3	1924	2382	125798447	125798904	0.000000e+00	725.0
31	TraesCS6A01G101500	chr2A	94.978	458	21	2	1926	2382	468600352	468600808	0.000000e+00	717.0
32	TraesCS6A01G101500	chr1D	94.794	461	20	3	1926	2383	412010694	412011153	0.000000e+00	715.0
33	TraesCS6A01G101500	chr1D	88.908	577	50	12	227	789	403575681	403576257	0.000000e+00	699.0
34	TraesCS6A01G101500	chr1D	96.970	165	4	1	1	165	34715832	34715995	2.330000e-70	276.0
35	TraesCS6A01G101500	chr1D	85.039	254	32	4	666	916	403596850	403597100	1.090000e-63	254.0
36	TraesCS6A01G101500	chr1D	84.646	254	32	5	666	916	403576421	403576670	1.830000e-61	246.0
37	TraesCS6A01G101500	chr1D	84.252	254	34	4	666	916	386532148	386532398	2.370000e-60	243.0
38	TraesCS6A01G101500	chr1D	84.190	253	33	5	666	914	386588997	386589246	3.060000e-59	239.0
39	TraesCS6A01G101500	chr1D	96.154	130	3	2	34	163	34792555	34792682	6.680000e-51	211.0
40	TraesCS6A01G101500	chr5A	95.476	420	17	2	1508	1926	354335185	354335603	0.000000e+00	669.0
41	TraesCS6A01G101500	chr6D	87.889	578	54	9	227	789	328150268	328150844	0.000000e+00	665.0
42	TraesCS6A01G101500	chr6D	87.681	138	15	2	1259	1394	328151119	328151256	2.450000e-35	159.0
43	TraesCS6A01G101500	chrUn	86.802	591	63	8	217	792	316384481	316383891	0.000000e+00	645.0
44	TraesCS6A01G101500	chrUn	86.923	260	25	5	1259	1516	318969163	318969415	1.390000e-72	283.0
45	TraesCS6A01G101500	chrUn	85.950	242	25	5	1260	1499	237030124	237030358	1.410000e-62	250.0
46	TraesCS6A01G101500	chrUn	85.714	238	26	4	1280	1516	55591579	55591349	6.580000e-61	244.0
47	TraesCS6A01G101500	chrUn	83.465	254	30	9	1267	1516	55580891	55580646	2.380000e-55	226.0
48	TraesCS6A01G101500	chrUn	84.091	176	21	1	1300	1475	472895712	472895880	1.900000e-36	163.0
49	TraesCS6A01G101500	chr1B	91.613	465	38	1	217	680	514379495	514379959	2.000000e-180	641.0
50	TraesCS6A01G101500	chr4B	85.167	209	24	1	1309	1517	142546991	142546790	8.640000e-50	207.0
51	TraesCS6A01G101500	chr4B	85.167	209	24	1	1309	1517	142555615	142555414	8.640000e-50	207.0
52	TraesCS6A01G101500	chr4B	85.075	67	7	3	46	111	425366786	425366850	5.500000e-07	65.8
53	TraesCS6A01G101500	chr4B	85.075	67	7	3	46	111	425385491	425385555	5.500000e-07	65.8
54	TraesCS6A01G101500	chr4D	82.160	213	35	3	1259	1469	11282738	11282527	1.880000e-41	180.0

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	TraesCS6A01G101500	chr6A	70184705	70187088	2383	True	4403.0	4403	100.0000	1	2384	1	chr6A.!!$R3	2383
1	TraesCS6A01G101500	chr6A	70151873	70153074	1201	True	1899.0	1899	95.1240	1	1209	1	chr6A.!!$R1	1208
2	TraesCS6A01G101500	chr6A	384926290	384926892	602	True	815.0	815	91.0600	906	1509	1	chr6A.!!$R6	603
3	TraesCS6A01G101500	chr3D	249279837	249281136	1299	True	1936.0	1936	93.5380	148	1447	1	chr3D.!!$R1	1299
4	TraesCS6A01G101500	chr3D	249667444	249668809	1365	True	1128.5	2026	88.2515	148	1516	2	chr3D.!!$R3	1368
5	TraesCS6A01G101500	chr3D	249652087	249653452	1365	True	1121.5	2015	87.2220	148	1516	2	chr3D.!!$R2	1368
6	TraesCS6A01G101500	chr3D	99848265	99848903	638	False	819.0	819	89.7360	874	1516	1	chr3D.!!$F2	642
7	TraesCS6A01G101500	chr3D	173535117	173535959	842	False	771.0	771	83.5440	1517	2366	1	chr3D.!!$F3	849
8	TraesCS6A01G101500	chr3B	50216945	50217794	849	False	863.0	863	85.3040	1515	2366	1	chr3B.!!$F1	851
9	TraesCS6A01G101500	chr7B	246764084	246764721	637	True	835.0	835	90.2970	876	1514	1	chr7B.!!$R1	638
10	TraesCS6A01G101500	chr7B	654080796	654081351	555	False	675.0	675	88.4750	226	789	1	chr7B.!!$F1	563
11	TraesCS6A01G101500	chr3A	666048294	666048934	640	False	815.0	815	89.5800	874	1516	1	chr3A.!!$F2	642
12	TraesCS6A01G101500	chr4A	258966301	258966938	637	True	804.0	804	89.3920	876	1516	1	chr4A.!!$R1	640
13	TraesCS6A01G101500	chr7A	614674472	614675183	711	False	763.0	763	86.1880	1651	2365	1	chr7A.!!$F1	714
14	TraesCS6A01G101500	chr1D	403575681	403576670	989	False	472.5	699	86.7770	227	916	2	chr1D.!!$F7	689
15	TraesCS6A01G101500	chr6D	328150268	328151256	988	False	412.0	665	87.7850	227	1394	2	chr6D.!!$F1	1167
16	TraesCS6A01G101500	chrUn	316383891	316384481	590	True	645.0	645	86.8020	217	792	1	chrUn.!!$R3	575

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
769	793	0.389817	CGGAGTTCGCCAAGATGACA	60.39	55.0	0.0	0.0	0.0	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2046	2498	0.179225	CTACATCAACCGCGTTGTGC	60.179	55.0	16.97	0.0	43.23	4.57	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	4.498520	CCGACGCGCCTCTGACAT	62.499	66.667	5.73	0.00	0.00	3.06
46	47	2.930887	GCGCCTCTGACATCAACAGTTA	60.931	50.000	0.00	0.00	36.81	2.24
85	86	9.959749	TGTCTTATTGTTTTATCAGGTTTTCAC	57.040	29.630	0.00	0.00	0.00	3.18
164	166	1.417890	CCGAGGATAGAACCCAAGCAT	59.582	52.381	0.00	0.00	0.00	3.79
244	246	2.094752	CACCAAAAATCCATCGACCACC	60.095	50.000	0.00	0.00	0.00	4.61
413	415	1.202582	AGTCGATCTTCCTGAACGGTG	59.797	52.381	0.00	0.00	40.63	4.94
476	478	4.264638	GCACAACACGTGGTGGCC	62.265	66.667	35.00	21.97	46.45	5.36
543	545	5.190528	TCATCTTCCTCAAGCTAACCAAGAT	59.809	40.000	0.00	0.00	30.84	2.40
553	555	2.544685	CTAACCAAGATGACGAGGCTG	58.455	52.381	0.00	0.00	0.00	4.85
570	572	0.617413	CTGCTCCTGGACTTCACCAT	59.383	55.000	0.00	0.00	39.34	3.55
623	625	4.681978	GACTCGCAGCCCGTTGGT	62.682	66.667	0.00	0.00	38.35	3.67
629	631	2.046892	CAGCCCGTTGGTCTCCTG	60.047	66.667	0.00	0.00	0.00	3.86
768	792	0.389948	ACGGAGTTCGCCAAGATGAC	60.390	55.000	0.00	0.00	37.78	3.06
769	793	0.389817	CGGAGTTCGCCAAGATGACA	60.390	55.000	0.00	0.00	0.00	3.58
773	797	1.202758	AGTTCGCCAAGATGACACCAA	60.203	47.619	0.00	0.00	0.00	3.67
826	850	1.152943	TGACGGAGCTCGCTAGGAT	60.153	57.895	7.83	0.00	43.89	3.24
868	892	2.439156	GCTGGTGCCATGGAGGAC	60.439	66.667	18.40	8.22	41.22	3.85
870	894	3.687321	CTGGTGCCATGGAGGACGG	62.687	68.421	18.40	3.14	41.22	4.79
871	895	3.399181	GGTGCCATGGAGGACGGA	61.399	66.667	18.40	0.00	41.22	4.69
872	896	2.187946	GTGCCATGGAGGACGGAG	59.812	66.667	18.40	0.00	41.22	4.63
967	1226	4.778143	GAGGATGCCGTGGCCGTT	62.778	66.667	8.69	0.00	41.09	4.44
1233	1668	2.113433	GGAGCTCGCTAGGACGACA	61.113	63.158	7.83	0.00	37.09	4.35
1238	1673	4.189188	CGCTAGGACGACACCCGG	62.189	72.222	0.00	0.00	43.93	5.73
1277	1712	1.383109	TGCCATGGAGGACGGAGAT	60.383	57.895	18.40	0.00	41.22	2.75
1278	1713	0.105709	TGCCATGGAGGACGGAGATA	60.106	55.000	18.40	0.00	41.22	1.98
1284	1719	1.215673	TGGAGGACGGAGATAGAGCTT	59.784	52.381	0.00	0.00	0.00	3.74
1298	1733	2.182030	GCTTGCTAGGACGACGCT	59.818	61.111	0.00	0.00	0.00	5.07
1396	1831	2.049063	GATAGCGGCGCGGAGATT	60.049	61.111	27.59	10.56	0.00	2.40
1423	1858	4.344865	ACGCCCCTCGCCAACATT	62.345	61.111	0.00	0.00	43.23	2.71
1433	1868	1.511318	CGCCAACATTGTCAACCCGA	61.511	55.000	0.00	0.00	0.00	5.14
1537	1972	2.224670	TGTTGGGGAACGTAGCAGAAAT	60.225	45.455	0.00	0.00	0.00	2.17
1539	1974	3.149005	TGGGGAACGTAGCAGAAATTT	57.851	42.857	0.00	0.00	0.00	1.82
1544	1979	6.209788	TGGGGAACGTAGCAGAAATTTAAAAT	59.790	34.615	0.00	0.00	0.00	1.82
1574	2011	6.060136	ACACATCACCAAGATCAATCTATGG	58.940	40.000	14.46	14.46	39.18	2.74
1575	2012	6.126681	ACACATCACCAAGATCAATCTATGGA	60.127	38.462	19.34	6.96	37.92	3.41
1576	2013	6.427242	CACATCACCAAGATCAATCTATGGAG	59.573	42.308	19.34	14.57	37.92	3.86
1594	2031	2.034053	GGAGTCATCTAGCAACGAGAGG	59.966	54.545	0.00	0.00	0.00	3.69
1629	2066	2.795175	ACATACCCTTGTAGATCGCG	57.205	50.000	0.00	0.00	0.00	5.87
1703	2145	3.914426	AATCACCAAAGATCCTAGCGT	57.086	42.857	0.00	0.00	0.00	5.07
1754	2197	2.104859	TACGGAGCGAGGACGTCTG	61.105	63.158	16.46	7.06	41.53	3.51
1757	2200	4.838486	GAGCGAGGACGTCTGCCG	62.838	72.222	16.46	16.31	41.98	5.69
1787	2230	0.617249	CAGCAAGGAGGAGGGAGAGT	60.617	60.000	0.00	0.00	0.00	3.24
1896	2339	0.252284	GAGGAGAGGTGTTGGGGAGA	60.252	60.000	0.00	0.00	0.00	3.71
1927	2376	0.537143	GCCTTGGATGGTGTGTGTGA	60.537	55.000	0.00	0.00	0.00	3.58
1978	2427	2.168326	ACGCACACACAAGATCATGA	57.832	45.000	4.68	0.00	0.00	3.07
2077	2529	4.479619	GGTTGATGTAGTCGTACGTCTTT	58.520	43.478	19.61	6.23	43.23	2.52
2079	2531	6.261118	GGTTGATGTAGTCGTACGTCTTTAT	58.739	40.000	19.61	13.84	43.23	1.40
2151	2604	2.266376	TTCAGCTCGATGACGTCCCG	62.266	60.000	14.12	16.31	40.69	5.14
2152	2605	2.750637	AGCTCGATGACGTCCCGT	60.751	61.111	21.31	6.19	45.10	5.28
2176	2629	0.972471	TCCGATCCAGCAGAGCTTCA	60.972	55.000	0.00	0.00	36.40	3.02
2177	2630	0.809241	CCGATCCAGCAGAGCTTCAC	60.809	60.000	0.00	0.00	36.40	3.18
2259	2712	1.877165	GCCTAAGCACCGCTACGAC	60.877	63.158	0.00	0.00	38.25	4.34
2313	2777	2.483877	CTGCACACGGCTAAAAGATCAA	59.516	45.455	0.00	0.00	45.15	2.57
2314	2778	2.483877	TGCACACGGCTAAAAGATCAAG	59.516	45.455	0.00	0.00	45.15	3.02
2366	2834	2.904434	CTGCCCCCGTATATAAAGGAGT	59.096	50.000	7.00	0.00	0.00	3.85
2367	2835	2.635915	TGCCCCCGTATATAAAGGAGTG	59.364	50.000	7.00	0.00	0.00	3.51
2368	2836	2.027469	GCCCCCGTATATAAAGGAGTGG	60.027	54.545	7.00	5.98	0.00	4.00
2369	2837	3.513517	CCCCCGTATATAAAGGAGTGGA	58.486	50.000	7.00	0.00	0.00	4.02
2370	2838	3.514309	CCCCCGTATATAAAGGAGTGGAG	59.486	52.174	7.00	0.00	0.00	3.86
2371	2839	3.514309	CCCCGTATATAAAGGAGTGGAGG	59.486	52.174	7.00	0.00	0.00	4.30
2372	2840	4.413760	CCCGTATATAAAGGAGTGGAGGA	58.586	47.826	7.00	0.00	0.00	3.71
2373	2841	4.463186	CCCGTATATAAAGGAGTGGAGGAG	59.537	50.000	7.00	0.00	0.00	3.69
2374	2842	4.463186	CCGTATATAAAGGAGTGGAGGAGG	59.537	50.000	0.37	0.00	0.00	4.30
2375	2843	4.463186	CGTATATAAAGGAGTGGAGGAGGG	59.537	50.000	0.00	0.00	0.00	4.30
2376	2844	2.198334	ATAAAGGAGTGGAGGAGGGG	57.802	55.000	0.00	0.00	0.00	4.79
2377	2845	0.044244	TAAAGGAGTGGAGGAGGGGG	59.956	60.000	0.00	0.00	0.00	5.40
2378	2846	1.761780	AAAGGAGTGGAGGAGGGGGA	61.762	60.000	0.00	0.00	0.00	4.81
2379	2847	2.041405	GGAGTGGAGGAGGGGGAG	60.041	72.222	0.00	0.00	0.00	4.30
2380	2848	2.041405	GAGTGGAGGAGGGGGAGG	60.041	72.222	0.00	0.00	0.00	4.30
2381	2849	3.700350	AGTGGAGGAGGGGGAGGG	61.700	72.222	0.00	0.00	0.00	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	9.921637	AGACAAAGAAACAAAAATAACTGTTGA	57.078	25.926	2.69	0.00	35.95	3.18
146	147	2.548920	CGGATGCTTGGGTTCTATCCTC	60.549	54.545	0.00	0.00	36.11	3.71
164	166	3.667087	GCAAGGTGATGTTGCGGA	58.333	55.556	0.00	0.00	40.87	5.54
244	246	0.319211	TGTTTCTGCGTACCGTGGAG	60.319	55.000	0.00	0.00	0.00	3.86
413	415	9.995003	ATGAAGGAGTGATTAGATGATAACTTC	57.005	33.333	0.00	0.00	0.00	3.01
543	545	3.385384	CCAGGAGCAGCCTCGTCA	61.385	66.667	0.00	0.00	46.97	4.35
553	555	0.393537	CCATGGTGAAGTCCAGGAGC	60.394	60.000	2.57	0.00	41.12	4.70
570	572	2.989639	CCCTCATCTTCCACGCCA	59.010	61.111	0.00	0.00	0.00	5.69
607	609	4.681978	GACCAACGGGCTGCGAGT	62.682	66.667	0.00	0.00	37.90	4.18
609	611	4.373116	GAGACCAACGGGCTGCGA	62.373	66.667	0.00	0.00	43.92	5.10
623	625	1.192146	GGTAGCCACCACACAGGAGA	61.192	60.000	0.00	0.00	45.04	3.71
768	792	4.487948	GGTTGATGATGTTGACATTGGTG	58.512	43.478	0.00	0.00	36.57	4.17
769	793	3.511146	GGGTTGATGATGTTGACATTGGT	59.489	43.478	0.00	0.00	36.57	3.67
773	797	3.760151	CACTGGGTTGATGATGTTGACAT	59.240	43.478	0.00	0.00	39.70	3.06
780	804	0.729116	GCGACACTGGGTTGATGATG	59.271	55.000	0.26	0.00	32.07	3.07
826	850	1.686587	TGAAGAAGAAGTCAGGCGTCA	59.313	47.619	0.00	0.00	0.00	4.35
996	1431	3.669536	TGTTGACATTGGCGTCATCTTA	58.330	40.909	0.00	0.00	45.03	2.10
1202	1637	4.856607	GCTCCGTCTCGCCTTCCG	62.857	72.222	0.00	0.00	38.61	4.30
1233	1668	0.911769	TGATGAAGAAGATGCCGGGT	59.088	50.000	2.18	0.00	0.00	5.28
1238	1673	4.730657	CACCAACTTGATGAAGAAGATGC	58.269	43.478	0.00	0.00	32.98	3.91
1240	1675	3.760684	GGCACCAACTTGATGAAGAAGAT	59.239	43.478	0.00	0.00	32.98	2.40
1277	1712	1.015109	CGTCGTCCTAGCAAGCTCTA	58.985	55.000	0.00	0.00	0.00	2.43
1278	1713	1.803943	CGTCGTCCTAGCAAGCTCT	59.196	57.895	0.00	0.00	0.00	4.09
1298	1733	2.596452	GCTTGATGAAGAAGACGACGA	58.404	47.619	0.00	0.00	0.00	4.20
1394	1829	2.746277	GGGCGTCGTCTTGGCAAT	60.746	61.111	0.00	0.00	0.00	3.56
1423	1858	1.484653	CTCCATGGTATCGGGTTGACA	59.515	52.381	12.58	0.00	0.00	3.58
1433	1868	1.270305	CGCCACGATTCTCCATGGTAT	60.270	52.381	12.58	4.04	34.50	2.73
1461	1896	1.352622	TTGGTGGTGTCCTCCTTGCT	61.353	55.000	8.11	0.00	37.97	3.91
1509	1944	0.036306	ACGTTCCCCAACACTCCATC	59.964	55.000	0.00	0.00	32.14	3.51
1544	1979	7.884877	AGATTGATCTTGGTGATGTGTAGAAAA	59.115	33.333	0.00	0.00	35.14	2.29
1550	1985	6.060136	CCATAGATTGATCTTGGTGATGTGT	58.940	40.000	0.00	0.00	38.32	3.72
1551	1986	6.293698	TCCATAGATTGATCTTGGTGATGTG	58.706	40.000	15.48	4.13	38.32	3.21
1552	1987	6.100859	ACTCCATAGATTGATCTTGGTGATGT	59.899	38.462	19.38	12.78	38.32	3.06
1553	1988	6.531923	ACTCCATAGATTGATCTTGGTGATG	58.468	40.000	19.38	10.22	38.32	3.07
1554	1989	6.328410	TGACTCCATAGATTGATCTTGGTGAT	59.672	38.462	19.38	10.95	38.32	3.06
1574	2011	2.034053	CCCTCTCGTTGCTAGATGACTC	59.966	54.545	0.00	0.00	0.00	3.36
1575	2012	2.028130	CCCTCTCGTTGCTAGATGACT	58.972	52.381	0.00	0.00	0.00	3.41
1576	2013	2.025155	TCCCTCTCGTTGCTAGATGAC	58.975	52.381	0.00	0.00	0.00	3.06
1594	2031	3.257127	GGTATGTAGATGCACTCCTCTCC	59.743	52.174	0.00	0.00	0.00	3.71
1629	2066	0.388649	TCTCTTGAACGCTTCCGCTC	60.389	55.000	0.00	0.00	38.22	5.03
1655	2093	1.598132	CGACGAGTACGACTCCATCAT	59.402	52.381	8.73	0.00	42.12	2.45
1690	2128	1.202268	CCGTTCGACGCTAGGATCTTT	60.202	52.381	0.00	0.00	40.91	2.52
1703	2145	4.047059	GAGGTGCCGTCCGTTCGA	62.047	66.667	0.00	0.00	0.00	3.71
1757	2200	2.796651	CTTGCTGGATCAAGGCGC	59.203	61.111	0.00	0.00	39.68	6.53
1787	2230	1.073923	GTTGGAGCCCTCTTCCTCAAA	59.926	52.381	0.00	0.00	0.00	2.69
1927	2376	7.527568	TTTTTGAAATTACTACGTTCCCCAT	57.472	32.000	0.00	0.00	0.00	4.00
1954	2403	2.233676	TGATCTTGTGTGTGCGTAGGAT	59.766	45.455	0.00	0.00	0.00	3.24
1967	2416	5.313712	TGCTATGCATCATCATGATCTTGT	58.686	37.500	4.86	0.00	34.28	3.16
1978	2427	2.549563	CCCTCTCGTTGCTATGCATCAT	60.550	50.000	0.19	0.00	38.76	2.45
2035	2487	1.495951	CGTTGTGCTAACGCTTCCC	59.504	57.895	12.46	0.00	36.82	3.97
2046	2498	0.179225	CTACATCAACCGCGTTGTGC	60.179	55.000	16.97	0.00	43.23	4.57
2151	2604	0.532573	TCTGCTGGATCGGAGTTCAC	59.467	55.000	0.00	0.00	0.00	3.18
2152	2605	0.820226	CTCTGCTGGATCGGAGTTCA	59.180	55.000	0.00	0.00	35.32	3.18
2259	2712	4.874396	CCACCATAATCCATCTCGATCATG	59.126	45.833	0.00	0.00	0.00	3.07
2269	2725	1.460218	CCCCCTCCACCATAATCCAT	58.540	55.000	0.00	0.00	0.00	3.41
2270	2726	2.959201	CCCCCTCCACCATAATCCA	58.041	57.895	0.00	0.00	0.00	3.41
2293	2752	2.177394	TGATCTTTTAGCCGTGTGCA	57.823	45.000	0.00	0.00	44.83	4.57
2313	2777	6.118170	CCCATAGACACAACAATTGATCTCT	58.882	40.000	13.59	6.76	33.73	3.10
2314	2778	5.297776	CCCCATAGACACAACAATTGATCTC	59.702	44.000	13.59	0.00	33.73	2.75
2322	2786	1.546773	GGCACCCCATAGACACAACAA	60.547	52.381	0.00	0.00	0.00	2.83
2324	2788	2.868253	GGCACCCCATAGACACAAC	58.132	57.895	0.00	0.00	0.00	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.