AutoCloner

Multiple sequence alignment - TraesCS7A01G542100

Loading Multiple Alignment...

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	TraesCS7A01G542100	chr7A	100.000	2333	0	0	1	2333	718428149	718425817	0.000000e+00	4309
1	TraesCS7A01G542100	chr7A	83.686	803	91	19	561	1339	718344310	718343524	0.000000e+00	721
2	TraesCS7A01G542100	chr7A	89.738	458	41	4	1	455	718266545	718266091	4.320000e-162	580
3	TraesCS7A01G542100	chr7A	84.466	515	64	5	843	1357	718440851	718440353	5.790000e-136	494
4	TraesCS7A01G542100	chr7A	87.119	427	40	6	127	550	718344768	718344354	9.760000e-129	470
5	TraesCS7A01G542100	chr7A	74.686	557	98	27	891	1421	718312952	718312413	8.450000e-50	207
6	TraesCS7A01G542100	chr7A	84.375	128	8	5	561	686	718265641	718265524	5.270000e-22	115
7	TraesCS7A01G542100	chr7A	86.813	91	11	1	461	550	718265775	718265685	1.480000e-17	100
8	TraesCS7A01G542100	chr7B	94.236	1041	41	9	552	1575	720933026	720931988	0.000000e+00	1572
9	TraesCS7A01G542100	chr7B	95.612	752	33	0	1582	2333	720931799	720931048	0.000000e+00	1206
10	TraesCS7A01G542100	chr7B	93.431	548	28	7	3	546	720933604	720933061	0.000000e+00	806
11	TraesCS7A01G542100	chr7B	82.935	879	103	23	561	1420	720829429	720828579	0.000000e+00	749
12	TraesCS7A01G542100	chr7B	86.000	600	57	12	769	1357	720948744	720948161	3.290000e-173	617
13	TraesCS7A01G542100	chr7B	86.450	524	37	10	1	515	720874354	720873856	5.670000e-151	544
14	TraesCS7A01G542100	chr7B	85.379	554	45	12	1	544	720830004	720829477	2.040000e-150	542
15	TraesCS7A01G542100	chr7D	83.910	752	92	16	671	1420	623358961	623359685	0.000000e+00	691
16	TraesCS7A01G542100	chr7D	88.428	458	45	6	1	455	623357901	623358353	1.580000e-151	545
17	TraesCS7A01G542100	chr7D	83.019	530	62	19	769	1286	622995222	622995735	2.730000e-124	455
18	TraesCS7A01G542100	chr7D	80.068	296	37	11	878	1158	623390240	623390528	1.410000e-47	200
19	TraesCS7A01G542100	chr7D	84.921	126	9	4	561	686	623358807	623358922	4.070000e-23	119

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	TraesCS7A01G542100	chr7A	718425817	718428149	2332	True	4309.000000	4309	100.000000	1	2333	1	chr7A.!!$R2	2332
1	TraesCS7A01G542100	chr7A	718343524	718344768	1244	True	595.500000	721	85.402500	127	1339	2	chr7A.!!$R5	1212
2	TraesCS7A01G542100	chr7A	718265524	718266545	1021	True	265.000000	580	86.975333	1	686	3	chr7A.!!$R4	685
3	TraesCS7A01G542100	chr7A	718312413	718312952	539	True	207.000000	207	74.686000	891	1421	1	chr7A.!!$R1	530
4	TraesCS7A01G542100	chr7B	720931048	720933604	2556	True	1194.666667	1572	94.426333	3	2333	3	chr7B.!!$R4	2330
5	TraesCS7A01G542100	chr7B	720828579	720830004	1425	True	645.500000	749	84.157000	1	1420	2	chr7B.!!$R3	1419
6	TraesCS7A01G542100	chr7B	720948161	720948744	583	True	617.000000	617	86.000000	769	1357	1	chr7B.!!$R2	588
7	TraesCS7A01G542100	chr7D	622995222	622995735	513	False	455.000000	455	83.019000	769	1286	1	chr7D.!!$F1	517
8	TraesCS7A01G542100	chr7D	623357901	623359685	1784	False	451.666667	691	85.753000	1	1420	3	chr7D.!!$F3	1419

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
507	845	0.178961	GGCCTGGTGAACCCTCTTTT	60.179	55.0	0.0	0.0	34.29	2.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1442	1982	0.24858	GCGCCGATGAATCAAATGCA	60.249	50.0	0.0	0.0	0.0	3.96	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
44	45	4.283978	TCCAGGAATCAACAACATTTGCAT	59.716	37.500	0.00	0.00	0.00	3.96
308	331	4.234550	ACTAGGAATCCATGCATCCACTA	58.765	43.478	0.61	0.00	35.62	2.74
372	398	4.012374	ACAATGACTGCTTAATGTGGGAG	58.988	43.478	0.00	0.00	0.00	4.30
373	399	4.012374	CAATGACTGCTTAATGTGGGAGT	58.988	43.478	0.00	0.00	36.86	3.85
383	409	6.072175	TGCTTAATGTGGGAGTACATTTTGTC	60.072	38.462	9.12	0.00	46.18	3.18
507	845	0.178961	GGCCTGGTGAACCCTCTTTT	60.179	55.000	0.00	0.00	34.29	2.27
515	853	7.472240	GCCTGGTGAACCCTCTTTTAAAATTAA	60.472	37.037	0.09	0.00	34.29	1.40
547	885	6.489127	TTAAACCTGTTCATCCACATTACG	57.511	37.500	0.00	0.00	0.00	3.18
549	887	4.487714	ACCTGTTCATCCACATTACGAT	57.512	40.909	0.00	0.00	0.00	3.73
550	888	5.607939	ACCTGTTCATCCACATTACGATA	57.392	39.130	0.00	0.00	0.00	2.92
582	960	2.170166	AGGACACTGCAAGAGAGAGAG	58.830	52.381	0.00	0.00	37.43	3.20
614	995	2.580322	TCCCACAGAAAATATGGCCTCA	59.420	45.455	3.32	0.00	31.66	3.86
695	1136	2.294479	GTGTGTGTGTGAACATACGC	57.706	50.000	14.65	14.65	44.98	4.42
773	1227	2.854076	CAGAAAACCAGGGCCCCT	59.146	61.111	21.43	0.00	0.00	4.79
906	1382	4.584688	GCTTGGCCATTTGTGCTC	57.415	55.556	6.09	0.00	0.00	4.26
907	1383	1.079612	GCTTGGCCATTTGTGCTCC	60.080	57.895	6.09	0.00	0.00	4.70
908	1384	1.593265	CTTGGCCATTTGTGCTCCC	59.407	57.895	6.09	0.00	0.00	4.30
909	1385	1.891722	CTTGGCCATTTGTGCTCCCC	61.892	60.000	6.09	0.00	0.00	4.81
910	1386	2.283821	GGCCATTTGTGCTCCCCA	60.284	61.111	0.00	0.00	0.00	4.96
911	1387	2.353610	GGCCATTTGTGCTCCCCAG	61.354	63.158	0.00	0.00	0.00	4.45
912	1388	1.304381	GCCATTTGTGCTCCCCAGA	60.304	57.895	0.00	0.00	0.00	3.86
913	1389	0.685458	GCCATTTGTGCTCCCCAGAT	60.685	55.000	0.00	0.00	0.00	2.90
914	1390	1.856629	CCATTTGTGCTCCCCAGATT	58.143	50.000	0.00	0.00	0.00	2.40
915	1391	2.181975	CCATTTGTGCTCCCCAGATTT	58.818	47.619	0.00	0.00	0.00	2.17
916	1392	2.093869	CCATTTGTGCTCCCCAGATTTG	60.094	50.000	0.00	0.00	0.00	2.32
950	1449	1.302033	CAGCTCACAGTCACCCACC	60.302	63.158	0.00	0.00	0.00	4.61
970	1476	5.336929	CCACCCATCCATATACGAATACGAA	60.337	44.000	0.00	0.00	42.66	3.85
971	1477	5.575606	CACCCATCCATATACGAATACGAAC	59.424	44.000	0.00	0.00	42.66	3.95
976	1482	5.765176	TCCATATACGAATACGAACCACAG	58.235	41.667	0.00	0.00	42.66	3.66
982	1488	4.121317	ACGAATACGAACCACAGAACAAA	58.879	39.130	0.00	0.00	42.66	2.83
1094	1615	0.384309	TTCCTATGCGTCTACTGCCG	59.616	55.000	0.00	0.00	0.00	5.69
1302	1838	3.200887	GATCTCGTGGGAGCGCGAT	62.201	63.158	12.10	1.23	40.26	4.58
1432	1972	4.627900	GTCTAGCTACTTGTTTCAAGCTCC	59.372	45.833	9.06	0.00	43.96	4.70
1439	1979	4.747810	ACTTGTTTCAAGCTCCTGTTTTG	58.252	39.130	9.06	0.00	0.00	2.44
1442	1982	3.132646	TGTTTCAAGCTCCTGTTTTGCAT	59.867	39.130	0.00	0.00	0.00	3.96
1491	2031	8.662255	TCTAGTTAGTTGGAATTGGTTAAAGGA	58.338	33.333	0.00	0.00	0.00	3.36
1503	2043	4.422984	TGGTTAAAGGACTAGGTACAGCT	58.577	43.478	0.00	0.00	0.00	4.24
1565	2105	6.410942	AAAATTTCCCTTTTCTCCAGACTG	57.589	37.500	0.00	0.00	0.00	3.51
1566	2106	4.731313	ATTTCCCTTTTCTCCAGACTGT	57.269	40.909	0.93	0.00	0.00	3.55
1567	2107	5.843019	ATTTCCCTTTTCTCCAGACTGTA	57.157	39.130	0.93	0.00	0.00	2.74
1575	2115	4.743057	TTCTCCAGACTGTATGACCATG	57.257	45.455	3.59	0.00	0.00	3.66
1576	2116	3.033909	TCTCCAGACTGTATGACCATGG	58.966	50.000	11.19	11.19	0.00	3.66
1577	2117	1.486310	TCCAGACTGTATGACCATGGC	59.514	52.381	13.04	5.35	0.00	4.40
1578	2118	1.210234	CCAGACTGTATGACCATGGCA	59.790	52.381	13.04	11.62	0.00	4.92
1579	2119	2.558378	CAGACTGTATGACCATGGCAG	58.442	52.381	13.04	13.06	34.02	4.85
1584	2306	1.103398	GTATGACCATGGCAGGTGGC	61.103	60.000	13.04	0.27	43.38	5.01
1613	2335	7.396540	TCCTGAAAAATCTGAATCTTTAGGC	57.603	36.000	0.00	0.00	0.00	3.93
1634	2356	5.827797	AGGCAAGTCTAAATGTTCAAGTTGA	59.172	36.000	0.08	0.08	0.00	3.18
1667	2389	3.435671	GGACACTGAAAATAGGGACGTTG	59.564	47.826	0.00	0.00	0.00	4.10
1675	2397	4.823790	AAATAGGGACGTTGTTCAACAC	57.176	40.909	14.60	8.33	0.00	3.32
1725	2447	5.484998	ACCCTACGTAAGATAGGTTTTTGGA	59.515	40.000	0.00	0.00	38.03	3.53
1741	2463	6.238676	GGTTTTTGGACTCTGACCTTTAAGAC	60.239	42.308	0.00	0.00	0.00	3.01
1890	2612	3.153919	TGTTTCCATTGGCAGGTTACTC	58.846	45.455	0.00	0.00	0.00	2.59
1910	2632	6.319048	ACTCAATATTGATGGGAGAACTGT	57.681	37.500	18.26	6.26	36.46	3.55
1934	2656	3.375699	TGGTGAATTCCTCCCTCTCTAC	58.624	50.000	2.27	0.00	0.00	2.59
1947	2669	6.072563	CCTCCCTCTCTACTTTACGCTTATAC	60.073	46.154	0.00	0.00	0.00	1.47
1948	2670	6.359804	TCCCTCTCTACTTTACGCTTATACA	58.640	40.000	0.00	0.00	0.00	2.29
1954	2676	8.288208	TCTCTACTTTACGCTTATACATGCTAC	58.712	37.037	0.00	0.00	0.00	3.58
2019	2741	2.025887	ACCAAGGGCTAGATTTCTGTGG	60.026	50.000	0.00	0.00	0.00	4.17
2065	2787	3.834489	ATCACCTAGTCTCTTGGCATG	57.166	47.619	0.00	0.00	29.74	4.06
2066	2788	1.208052	TCACCTAGTCTCTTGGCATGC	59.792	52.381	9.90	9.90	29.74	4.06
2083	2805	9.616634	CTTGGCATGCAGTATATTTACATAAAG	57.383	33.333	21.36	0.00	0.00	1.85
2113	2835	0.031616	TTTGGGGGTGCTTGACCTTT	60.032	50.000	0.00	0.00	45.33	3.11
2126	2848	5.992829	TGCTTGACCTTTAGTTAATGAACGA	59.007	36.000	0.00	0.00	40.76	3.85
2150	2872	4.774200	AGCTCTTTTATCCAAATGGCTTGT	59.226	37.500	0.00	0.00	32.65	3.16
2151	2873	5.246883	AGCTCTTTTATCCAAATGGCTTGTT	59.753	36.000	0.00	0.00	32.65	2.83
2169	2891	3.831323	TGTTGCAGAATCTTCTTTGGGA	58.169	40.909	0.00	0.00	34.74	4.37
2174	2896	4.648762	TGCAGAATCTTCTTTGGGACAAAA	59.351	37.500	0.00	0.00	38.66	2.44
2201	2923	0.555769	TGGGAAAACTTGAGGCCTGT	59.444	50.000	12.00	0.00	0.00	4.00
2202	2924	1.248486	GGGAAAACTTGAGGCCTGTC	58.752	55.000	12.00	0.00	0.00	3.51
2301	3023	4.935352	TCTGTGTTGGAAATGGGAAAAG	57.065	40.909	0.00	0.00	0.00	2.27
2305	3027	4.467795	TGTGTTGGAAATGGGAAAAGAACA	59.532	37.500	0.00	0.00	0.00	3.18
2325	3047	8.461249	AGAACATGATTTTGGGAAGATAGATG	57.539	34.615	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	3.992643	TGCAAATGTTGTTGATTCCTGG	58.007	40.909	0.00	0.00	0.00	4.45
44	45	2.580322	TCCCAATGTATCTTGAAGCCCA	59.420	45.455	0.00	0.00	0.00	5.36
308	331	5.068460	CGAGGAGAGGATTCACTTATCTTGT	59.932	44.000	0.00	0.00	0.00	3.16
530	868	6.019559	CACACTATCGTAATGTGGATGAACAG	60.020	42.308	0.00	0.00	40.05	3.16
532	870	5.276868	GCACACTATCGTAATGTGGATGAAC	60.277	44.000	5.81	0.00	43.22	3.18
546	884	4.335874	AGTGTCCTACTAAGCACACTATCG	59.664	45.833	0.29	0.00	46.04	2.92
547	885	5.583495	CAGTGTCCTACTAAGCACACTATC	58.417	45.833	1.97	0.00	46.13	2.08
549	887	3.192844	GCAGTGTCCTACTAAGCACACTA	59.807	47.826	1.97	0.00	46.13	2.74
568	946	3.680937	CAGCTTTTCTCTCTCTCTTGCAG	59.319	47.826	0.00	0.00	0.00	4.41
721	1167	1.901159	TGGCCCAACAAAGATTCCATG	59.099	47.619	0.00	0.00	0.00	3.66
732	1178	2.603776	TGCATGCATGGCCCAACA	60.604	55.556	27.34	13.03	0.00	3.33
902	1378	1.075601	AGGTTCAAATCTGGGGAGCA	58.924	50.000	0.00	0.00	0.00	4.26
903	1379	3.584733	ATAGGTTCAAATCTGGGGAGC	57.415	47.619	0.00	0.00	0.00	4.70
904	1380	4.349342	AGCTATAGGTTCAAATCTGGGGAG	59.651	45.833	0.00	0.00	0.00	4.30
905	1381	4.307259	AGCTATAGGTTCAAATCTGGGGA	58.693	43.478	0.00	0.00	0.00	4.81
906	1382	4.713792	AGCTATAGGTTCAAATCTGGGG	57.286	45.455	0.00	0.00	0.00	4.96
907	1383	5.012561	AGCTAGCTATAGGTTCAAATCTGGG	59.987	44.000	17.69	0.00	36.31	4.45
908	1384	6.107901	AGCTAGCTATAGGTTCAAATCTGG	57.892	41.667	17.69	0.00	36.31	3.86
909	1385	6.753180	TGAGCTAGCTATAGGTTCAAATCTG	58.247	40.000	19.38	0.00	39.82	2.90
910	1386	6.985653	TGAGCTAGCTATAGGTTCAAATCT	57.014	37.500	19.38	0.00	39.82	2.40
950	1449	5.575606	GTGGTTCGTATTCGTATATGGATGG	59.424	44.000	0.00	0.00	38.33	3.51
970	1476	0.732571	CGTGCTGTTTGTTCTGTGGT	59.267	50.000	0.00	0.00	0.00	4.16
971	1477	1.003545	CTCGTGCTGTTTGTTCTGTGG	60.004	52.381	0.00	0.00	0.00	4.17
976	1482	0.111089	CTCGCTCGTGCTGTTTGTTC	60.111	55.000	7.97	0.00	36.97	3.18
982	1488	3.790334	TTGTGCTCGCTCGTGCTGT	62.790	57.895	15.65	0.00	36.97	4.40
1140	1661	2.327940	GCGCGTTCTTGCTTGTGT	59.672	55.556	8.43	0.00	0.00	3.72
1192	1716	2.114670	CCGGATTCCAAGCATGCGT	61.115	57.895	13.01	6.07	33.95	5.24
1270	1806	0.179100	GAGATCCTGCTGCGCTTGTA	60.179	55.000	9.73	0.00	0.00	2.41
1432	1972	5.599359	TGAATCAAATGCATGCAAAACAG	57.401	34.783	26.68	13.02	0.00	3.16
1439	1979	1.790623	GCCGATGAATCAAATGCATGC	59.209	47.619	11.82	11.82	0.00	4.06
1442	1982	0.248580	GCGCCGATGAATCAAATGCA	60.249	50.000	0.00	0.00	0.00	3.96
1491	2031	5.767670	TCTAGGAATTCAGCTGTACCTAGT	58.232	41.667	31.06	14.42	43.98	2.57
1503	2043	6.445139	AGACCAGGAAAATCTCTAGGAATTCA	59.555	38.462	7.93	0.00	0.00	2.57
1565	2105	1.103398	GCCACCTGCCATGGTCATAC	61.103	60.000	14.67	0.00	38.45	2.39
1566	2106	1.227102	GCCACCTGCCATGGTCATA	59.773	57.895	14.67	0.00	38.45	2.15
1567	2107	2.043652	GCCACCTGCCATGGTCAT	60.044	61.111	14.67	0.00	38.45	3.06
1575	2115	2.116125	AGGAAAGTGCCACCTGCC	59.884	61.111	0.00	0.00	40.16	4.85
1576	2116	3.359002	CAGGAAAGTGCCACCTGC	58.641	61.111	0.00	0.00	43.32	4.85
1578	2118	2.452600	TTTTCAGGAAAGTGCCACCT	57.547	45.000	0.00	0.00	34.02	4.00
1579	2119	3.321968	AGATTTTTCAGGAAAGTGCCACC	59.678	43.478	0.00	0.00	0.00	4.61
1667	2389	5.464389	ACTTAATCTACACCGTGTGTTGAAC	59.536	40.000	14.66	0.00	46.83	3.18
1675	2397	3.585862	AGTGCACTTAATCTACACCGTG	58.414	45.455	15.25	0.00	31.58	4.94
1725	2447	7.067496	TGAGAAATGTCTTAAAGGTCAGAGT	57.933	36.000	0.00	0.00	32.80	3.24
1741	2463	9.910511	CAAGTTTCTGAATTGTTTTGAGAAATG	57.089	29.630	3.87	0.00	35.65	2.32
1876	2598	6.266103	CCATCAATATTGAGTAACCTGCCAAT	59.734	38.462	21.97	0.00	41.08	3.16
1890	2612	6.039047	CCAAGACAGTTCTCCCATCAATATTG	59.961	42.308	9.29	9.29	0.00	1.90
1910	2632	2.840651	GAGAGGGAGGAATTCACCAAGA	59.159	50.000	18.21	0.00	0.00	3.02
1934	2656	7.478520	AAAGGTAGCATGTATAAGCGTAAAG	57.521	36.000	0.00	0.00	35.48	1.85
1947	2669	5.757850	GGAGACCATAAAAAGGTAGCATG	57.242	43.478	0.00	0.00	40.09	4.06
1990	2712	7.019388	AGAAATCTAGCCCTTGGTCTATCATA	58.981	38.462	0.00	0.00	0.00	2.15
2004	2726	2.420687	CCCACTCCACAGAAATCTAGCC	60.421	54.545	0.00	0.00	0.00	3.93
2019	2741	7.712204	TTTCTATTTGGTTTTATCCCCACTC	57.288	36.000	0.00	0.00	0.00	3.51
2055	2777	6.866010	TGTAAATATACTGCATGCCAAGAG	57.134	37.500	16.68	8.31	32.98	2.85
2065	2787	9.726438	ACCCTGATCTTTATGTAAATATACTGC	57.274	33.333	0.00	0.00	32.98	4.40
2083	2805	1.000359	CCCCCAAACCACCCTGATC	60.000	63.158	0.00	0.00	0.00	2.92
2113	2835	9.095065	GGATAAAAGAGCTTCGTTCATTAACTA	57.905	33.333	0.00	0.00	33.15	2.24
2126	2848	5.246883	ACAAGCCATTTGGATAAAAGAGCTT	59.753	36.000	0.00	0.00	44.63	3.74
2150	2872	3.831323	TGTCCCAAAGAAGATTCTGCAA	58.169	40.909	0.00	0.00	37.65	4.08
2151	2873	3.507162	TGTCCCAAAGAAGATTCTGCA	57.493	42.857	0.00	0.00	37.65	4.41
2169	2891	7.108847	TCAAGTTTTCCCATTGACATTTTTGT	58.891	30.769	0.00	0.00	0.00	2.83
2174	2896	4.262592	GCCTCAAGTTTTCCCATTGACATT	60.263	41.667	0.00	0.00	0.00	2.71
2201	2923	4.458989	GGAATCCAACTGCTTATGTTGTGA	59.541	41.667	0.00	0.00	42.09	3.58
2202	2924	4.380867	GGGAATCCAACTGCTTATGTTGTG	60.381	45.833	0.09	0.00	42.09	3.33
2281	3003	4.935352	TCTTTTCCCATTTCCAACACAG	57.065	40.909	0.00	0.00	0.00	3.66
2301	3023	7.286316	ACCATCTATCTTCCCAAAATCATGTTC	59.714	37.037	0.00	0.00	0.00	3.18
2305	3027	7.946776	CCTAACCATCTATCTTCCCAAAATCAT	59.053	37.037	0.00	0.00	0.00	2.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.