AutoCloner

Multiple sequence alignment - TraesCS1A01G310900

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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	TraesCS1A01G310900	chr1A	100.000	2381	0	0	1	2381	501993403	501995783	0.000000e+00	4397
1	TraesCS1A01G310900	chr1A	95.411	1264	33	8	1131	2381	365615349	365616600	0.000000e+00	1989
2	TraesCS1A01G310900	chr1A	96.571	700	15	2	1	694	501887483	501888179	0.000000e+00	1151
3	TraesCS1A01G310900	chr1A	95.652	253	9	2	690	941	365615073	365615324	2.850000e-109	405
4	TraesCS1A01G310900	chr5A	97.773	1706	14	2	687	2381	603052090	603053782	0.000000e+00	2918
5	TraesCS1A01G310900	chr4A	94.886	1271	33	6	1131	2381	624742728	624741470	0.000000e+00	1958
6	TraesCS1A01G310900	chr4A	93.200	250	14	1	695	941	624743002	624742753	4.840000e-97	364
7	TraesCS1A01G310900	chr4A	87.791	172	10	3	2125	2296	624741615	624741455	8.690000e-45	191
8	TraesCS1A01G310900	chr5D	91.945	869	57	12	695	1551	362066952	362067819	0.000000e+00	1205
9	TraesCS1A01G310900	chr2B	91.387	894	54	11	678	1553	733826122	733827010	0.000000e+00	1203
10	TraesCS1A01G310900	chr2B	87.472	894	67	20	684	1558	84533011	84533878	0.000000e+00	989
11	TraesCS1A01G310900	chr2B	86.471	850	57	31	1576	2378	733837140	733837978	0.000000e+00	880
12	TraesCS1A01G310900	chr2B	85.987	785	77	22	1576	2341	637753980	637754750	0.000000e+00	809
13	TraesCS1A01G310900	chr2B	85.366	369	42	8	695	1058	637707742	637708103	2.890000e-99	372
14	TraesCS1A01G310900	chr2B	88.991	218	16	3	1323	1533	733826881	733827097	1.810000e-66	263
15	TraesCS1A01G310900	chr2B	80.781	333	34	16	1087	1396	637708102	637708427	1.420000e-57	233
16	TraesCS1A01G310900	chr2B	85.987	157	15	4	2137	2293	733837844	733837993	6.810000e-36	161
17	TraesCS1A01G310900	chr2B	89.189	111	6	3	1323	1427	733826987	733827097	1.480000e-27	134
18	TraesCS1A01G310900	chr2B	84.000	125	9	5	2190	2305	733837837	733837959	2.500000e-20	110
19	TraesCS1A01G310900	chr1B	96.830	694	19	1	1	694	546967178	546967868	0.000000e+00	1157
20	TraesCS1A01G310900	chr1B	95.965	694	25	1	1	694	546860212	546860902	0.000000e+00	1123
21	TraesCS1A01G310900	chr1B	95.389	694	29	1	1	694	547177774	547178464	0.000000e+00	1101
22	TraesCS1A01G310900	chr1B	95.294	425	17	1	270	694	546701791	546702212	0.000000e+00	671
23	TraesCS1A01G310900	chr1D	95.965	694	25	1	1	694	406676359	406677049	0.000000e+00	1123
24	TraesCS1A01G310900	chr1D	76.675	836	135	32	695	1512	431424203	431423410	2.200000e-110	409
25	TraesCS1A01G310900	chr7B	88.090	890	61	19	687	1558	328571101	328570239	0.000000e+00	1014
26	TraesCS1A01G310900	chr6A	98.098	368	7	0	2014	2381	39135457	39135090	2.000000e-180	641
27	TraesCS1A01G310900	chr6A	86.946	406	32	11	1576	1961	573126600	573127004	1.010000e-118	436
28	TraesCS1A01G310900	chr6A	86.600	403	36	10	1576	1961	27202417	27202016	1.690000e-116	429
29	TraesCS1A01G310900	chr5B	86.946	406	32	11	1576	1961	551419004	551418600	1.010000e-118	436
30	TraesCS1A01G310900	chr4B	86.946	406	32	11	1576	1961	347576751	347577155	1.010000e-118	436
31	TraesCS1A01G310900	chr7D	77.500	720	122	27	696	1398	587289197	587288501	1.720000e-106	396

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	TraesCS1A01G310900	chr1A	501993403	501995783	2380	False	4397.000000	4397	100.000000	1	2381	1	chr1A.!!$F2	2380
1	TraesCS1A01G310900	chr1A	365615073	365616600	1527	False	1197.000000	1989	95.531500	690	2381	2	chr1A.!!$F3	1691
2	TraesCS1A01G310900	chr1A	501887483	501888179	696	False	1151.000000	1151	96.571000	1	694	1	chr1A.!!$F1	693
3	TraesCS1A01G310900	chr5A	603052090	603053782	1692	False	2918.000000	2918	97.773000	687	2381	1	chr5A.!!$F1	1694
4	TraesCS1A01G310900	chr4A	624741455	624743002	1547	True	837.666667	1958	91.959000	695	2381	3	chr4A.!!$R1	1686
5	TraesCS1A01G310900	chr5D	362066952	362067819	867	False	1205.000000	1205	91.945000	695	1551	1	chr5D.!!$F1	856
6	TraesCS1A01G310900	chr2B	84533011	84533878	867	False	989.000000	989	87.472000	684	1558	1	chr2B.!!$F1	874
7	TraesCS1A01G310900	chr2B	637753980	637754750	770	False	809.000000	809	85.987000	1576	2341	1	chr2B.!!$F2	765
8	TraesCS1A01G310900	chr2B	733826122	733827097	975	False	533.333333	1203	89.855667	678	1553	3	chr2B.!!$F4	875
9	TraesCS1A01G310900	chr2B	733837140	733837993	853	False	383.666667	880	85.486000	1576	2378	3	chr2B.!!$F5	802
10	TraesCS1A01G310900	chr2B	637707742	637708427	685	False	302.500000	372	83.073500	695	1396	2	chr2B.!!$F3	701
11	TraesCS1A01G310900	chr1B	546967178	546967868	690	False	1157.000000	1157	96.830000	1	694	1	chr1B.!!$F3	693
12	TraesCS1A01G310900	chr1B	546860212	546860902	690	False	1123.000000	1123	95.965000	1	694	1	chr1B.!!$F2	693
13	TraesCS1A01G310900	chr1B	547177774	547178464	690	False	1101.000000	1101	95.389000	1	694	1	chr1B.!!$F4	693
14	TraesCS1A01G310900	chr1D	406676359	406677049	690	False	1123.000000	1123	95.965000	1	694	1	chr1D.!!$F1	693
15	TraesCS1A01G310900	chr1D	431423410	431424203	793	True	409.000000	409	76.675000	695	1512	1	chr1D.!!$R1	817
16	TraesCS1A01G310900	chr7B	328570239	328571101	862	True	1014.000000	1014	88.090000	687	1558	1	chr7B.!!$R1	871
17	TraesCS1A01G310900	chr7D	587288501	587289197	696	True	396.000000	396	77.500000	696	1398	1	chr7D.!!$R1	702

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
670	677	0.038618	CCACCCTAAAACCTTTGCGC	60.039	55.0	0.0	0.0	0.0	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2275	2463	7.062605	CAGTGATATTTCCAGTGCAATTTCAAC	59.937	37.037	0.0	4.56	0.0	3.18	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
359	366	2.096713	GCTCGTTGTACTTCTGTTGCAG	60.097	50.000	0.00	0.00	0.00	4.41
360	367	1.864711	TCGTTGTACTTCTGTTGCAGC	59.135	47.619	0.00	0.00	0.00	5.25
361	368	1.867233	CGTTGTACTTCTGTTGCAGCT	59.133	47.619	1.17	0.00	0.00	4.24
567	574	4.056125	GCCTTGCGAAACAGCCCC	62.056	66.667	0.00	0.00	36.02	5.80
568	575	2.282462	CCTTGCGAAACAGCCCCT	60.282	61.111	0.00	0.00	36.02	4.79
569	576	2.629656	CCTTGCGAAACAGCCCCTG	61.630	63.158	0.00	0.00	37.52	4.45
570	577	3.273080	CTTGCGAAACAGCCCCTGC	62.273	63.158	0.00	0.00	34.37	4.85
595	602	2.035530	CTTGGAGAAGCAGATGTCCC	57.964	55.000	0.00	0.00	31.86	4.46
596	603	0.250234	TTGGAGAAGCAGATGTCCCG	59.750	55.000	0.00	0.00	31.86	5.14
597	604	0.904865	TGGAGAAGCAGATGTCCCGT	60.905	55.000	0.00	0.00	31.86	5.28
598	605	0.460987	GGAGAAGCAGATGTCCCGTG	60.461	60.000	0.00	0.00	0.00	4.94
599	606	1.078848	AGAAGCAGATGTCCCGTGC	60.079	57.895	0.00	0.00	37.48	5.34
600	607	1.375908	GAAGCAGATGTCCCGTGCA	60.376	57.895	0.00	0.00	39.80	4.57
601	608	1.364626	GAAGCAGATGTCCCGTGCAG	61.365	60.000	0.00	0.00	39.80	4.41
602	609	3.503363	GCAGATGTCCCGTGCAGC	61.503	66.667	0.00	0.00	37.16	5.25
603	610	2.821366	CAGATGTCCCGTGCAGCC	60.821	66.667	0.00	0.00	0.00	4.85
604	611	3.005539	AGATGTCCCGTGCAGCCT	61.006	61.111	0.00	0.00	0.00	4.58
605	612	2.045926	GATGTCCCGTGCAGCCTT	60.046	61.111	0.00	0.00	0.00	4.35
606	613	2.360350	ATGTCCCGTGCAGCCTTG	60.360	61.111	0.00	0.00	0.00	3.61
607	614	3.196207	ATGTCCCGTGCAGCCTTGT	62.196	57.895	0.00	0.00	0.00	3.16
608	615	2.594592	GTCCCGTGCAGCCTTGTT	60.595	61.111	0.00	0.00	0.00	2.83
609	616	2.281484	TCCCGTGCAGCCTTGTTC	60.281	61.111	0.00	0.00	0.00	3.18
610	617	2.281761	CCCGTGCAGCCTTGTTCT	60.282	61.111	0.00	0.00	0.00	3.01
611	618	2.328099	CCCGTGCAGCCTTGTTCTC	61.328	63.158	0.00	0.00	0.00	2.87
612	619	2.671177	CCGTGCAGCCTTGTTCTCG	61.671	63.158	0.00	0.00	0.00	4.04
613	620	1.664649	CGTGCAGCCTTGTTCTCGA	60.665	57.895	0.00	0.00	0.00	4.04
614	621	1.016130	CGTGCAGCCTTGTTCTCGAT	61.016	55.000	0.00	0.00	0.00	3.59
615	622	0.445436	GTGCAGCCTTGTTCTCGATG	59.555	55.000	0.00	0.00	0.00	3.84
616	623	1.300971	TGCAGCCTTGTTCTCGATGC	61.301	55.000	0.00	0.00	0.00	3.91
617	624	1.712081	CAGCCTTGTTCTCGATGCG	59.288	57.895	0.00	0.00	0.00	4.73
618	625	2.103042	AGCCTTGTTCTCGATGCGC	61.103	57.895	0.00	0.00	0.00	6.09
619	626	3.093278	CCTTGTTCTCGATGCGCC	58.907	61.111	4.18	0.00	0.00	6.53
620	627	2.697425	CTTGTTCTCGATGCGCCG	59.303	61.111	4.18	1.29	0.00	6.46
621	628	2.802667	CTTGTTCTCGATGCGCCGG	61.803	63.158	4.18	0.00	0.00	6.13
622	629	3.289704	TTGTTCTCGATGCGCCGGA	62.290	57.895	5.05	0.00	0.00	5.14
623	630	2.279517	GTTCTCGATGCGCCGGAT	60.280	61.111	5.05	0.00	0.00	4.18
624	631	1.883084	GTTCTCGATGCGCCGGATT	60.883	57.895	5.05	0.00	0.00	3.01
625	632	0.596600	GTTCTCGATGCGCCGGATTA	60.597	55.000	5.05	0.00	0.00	1.75
626	633	0.596600	TTCTCGATGCGCCGGATTAC	60.597	55.000	5.05	0.00	0.00	1.89
627	634	2.354188	TCGATGCGCCGGATTACG	60.354	61.111	5.05	0.00	43.80	3.18
640	647	2.405172	GGATTACGATCTTCTTCCGCC	58.595	52.381	0.00	0.00	32.66	6.13
641	648	2.405172	GATTACGATCTTCTTCCGCCC	58.595	52.381	0.00	0.00	0.00	6.13
642	649	0.462789	TTACGATCTTCTTCCGCCCC	59.537	55.000	0.00	0.00	0.00	5.80
643	650	0.685131	TACGATCTTCTTCCGCCCCA	60.685	55.000	0.00	0.00	0.00	4.96
644	651	1.338136	ACGATCTTCTTCCGCCCCAT	61.338	55.000	0.00	0.00	0.00	4.00
645	652	0.179045	CGATCTTCTTCCGCCCCATT	60.179	55.000	0.00	0.00	0.00	3.16
646	653	1.312815	GATCTTCTTCCGCCCCATTG	58.687	55.000	0.00	0.00	0.00	2.82
647	654	0.753111	ATCTTCTTCCGCCCCATTGC	60.753	55.000	0.00	0.00	0.00	3.56
648	655	1.678635	CTTCTTCCGCCCCATTGCA	60.679	57.895	0.00	0.00	0.00	4.08
649	656	1.228706	TTCTTCCGCCCCATTGCAA	60.229	52.632	0.00	0.00	0.00	4.08
650	657	1.531739	TTCTTCCGCCCCATTGCAAC	61.532	55.000	0.00	0.00	0.00	4.17
651	658	2.994417	TTCCGCCCCATTGCAACC	60.994	61.111	0.00	0.00	0.00	3.77
654	661	4.067913	CGCCCCATTGCAACCCAC	62.068	66.667	0.00	0.00	0.00	4.61
655	662	3.705289	GCCCCATTGCAACCCACC	61.705	66.667	0.00	0.00	0.00	4.61
656	663	3.002583	CCCCATTGCAACCCACCC	61.003	66.667	0.00	0.00	0.00	4.61
657	664	2.120274	CCCATTGCAACCCACCCT	59.880	61.111	0.00	0.00	0.00	4.34
658	665	1.386155	CCCATTGCAACCCACCCTA	59.614	57.895	0.00	0.00	0.00	3.53
659	666	0.252012	CCCATTGCAACCCACCCTAA	60.252	55.000	0.00	0.00	0.00	2.69
660	667	1.638529	CCATTGCAACCCACCCTAAA	58.361	50.000	0.00	0.00	0.00	1.85
661	668	1.974236	CCATTGCAACCCACCCTAAAA	59.026	47.619	0.00	0.00	0.00	1.52
662	669	2.289382	CCATTGCAACCCACCCTAAAAC	60.289	50.000	0.00	0.00	0.00	2.43
663	670	1.415200	TTGCAACCCACCCTAAAACC	58.585	50.000	0.00	0.00	0.00	3.27
664	671	0.558712	TGCAACCCACCCTAAAACCT	59.441	50.000	0.00	0.00	0.00	3.50
665	672	1.062810	TGCAACCCACCCTAAAACCTT	60.063	47.619	0.00	0.00	0.00	3.50
666	673	2.043992	GCAACCCACCCTAAAACCTTT	58.956	47.619	0.00	0.00	0.00	3.11
667	674	2.224185	GCAACCCACCCTAAAACCTTTG	60.224	50.000	0.00	0.00	0.00	2.77
668	675	1.712056	ACCCACCCTAAAACCTTTGC	58.288	50.000	0.00	0.00	0.00	3.68
669	676	0.601057	CCCACCCTAAAACCTTTGCG	59.399	55.000	0.00	0.00	0.00	4.85
670	677	0.038618	CCACCCTAAAACCTTTGCGC	60.039	55.000	0.00	0.00	0.00	6.09
671	678	0.038618	CACCCTAAAACCTTTGCGCC	60.039	55.000	4.18	0.00	0.00	6.53
672	679	1.183030	ACCCTAAAACCTTTGCGCCC	61.183	55.000	4.18	0.00	0.00	6.13
673	680	0.898326	CCCTAAAACCTTTGCGCCCT	60.898	55.000	4.18	0.00	0.00	5.19
674	681	0.526211	CCTAAAACCTTTGCGCCCTC	59.474	55.000	4.18	0.00	0.00	4.30
675	682	1.534729	CTAAAACCTTTGCGCCCTCT	58.465	50.000	4.18	0.00	0.00	3.69
676	683	1.468914	CTAAAACCTTTGCGCCCTCTC	59.531	52.381	4.18	0.00	0.00	3.20
677	684	0.178990	AAAACCTTTGCGCCCTCTCT	60.179	50.000	4.18	0.00	0.00	3.10
678	685	0.606673	AAACCTTTGCGCCCTCTCTC	60.607	55.000	4.18	0.00	0.00	3.20
679	686	1.768684	AACCTTTGCGCCCTCTCTCA	61.769	55.000	4.18	0.00	0.00	3.27
680	687	1.449246	CCTTTGCGCCCTCTCTCAG	60.449	63.158	4.18	0.00	0.00	3.35
681	688	1.593787	CTTTGCGCCCTCTCTCAGA	59.406	57.895	4.18	0.00	0.00	3.27
682	689	0.459934	CTTTGCGCCCTCTCTCAGAG	60.460	60.000	4.18	0.00	41.96	3.35
683	690	1.188219	TTTGCGCCCTCTCTCAGAGT	61.188	55.000	4.18	0.00	40.72	3.24
684	691	1.881903	TTGCGCCCTCTCTCAGAGTG	61.882	60.000	4.18	0.00	40.72	3.51
685	692	2.347322	GCGCCCTCTCTCAGAGTGT	61.347	63.158	0.36	0.00	40.72	3.55
686	693	1.882989	GCGCCCTCTCTCAGAGTGTT	61.883	60.000	0.36	0.00	40.72	3.32
687	694	0.605589	CGCCCTCTCTCAGAGTGTTT	59.394	55.000	0.36	0.00	40.72	2.83
688	695	1.671261	CGCCCTCTCTCAGAGTGTTTG	60.671	57.143	0.36	0.00	40.72	2.93
689	696	1.620819	GCCCTCTCTCAGAGTGTTTGA	59.379	52.381	0.36	0.00	40.72	2.69
692	699	4.081420	GCCCTCTCTCAGAGTGTTTGATTA	60.081	45.833	0.36	0.00	40.72	1.75
729	737	6.773976	TTGACATCTGACTGTTTTCCTTTT	57.226	33.333	0.00	0.00	0.00	2.27
820	831	3.924686	GGAGAAAATCAAGACGCTAACGA	59.075	43.478	0.00	0.00	43.93	3.85
913	933	1.999648	TCTGGAAGCTTGCAAACCAT	58.000	45.000	21.68	0.00	0.00	3.55
1892	2030	6.155221	ACCAACTGAATCTGCACTCTCTAATA	59.845	38.462	0.00	0.00	0.00	0.98
2296	2484	6.996509	ACAGTTGAAATTGCACTGGAAATAT	58.003	32.000	15.96	0.00	33.15	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
212	219	3.857854	CAGACCAGCGCGACATGC	61.858	66.667	12.10	0.00	41.47	4.06
341	348	1.867233	AGCTGCAACAGAAGTACAACG	59.133	47.619	1.02	0.00	32.44	4.10
576	583	1.741732	CGGGACATCTGCTTCTCCAAG	60.742	57.143	0.00	0.00	0.00	3.61
577	584	0.250234	CGGGACATCTGCTTCTCCAA	59.750	55.000	0.00	0.00	0.00	3.53
578	585	0.904865	ACGGGACATCTGCTTCTCCA	60.905	55.000	0.00	0.00	0.00	3.86
579	586	0.460987	CACGGGACATCTGCTTCTCC	60.461	60.000	0.00	0.00	0.00	3.71
580	587	1.086634	GCACGGGACATCTGCTTCTC	61.087	60.000	0.00	0.00	0.00	2.87
581	588	1.078848	GCACGGGACATCTGCTTCT	60.079	57.895	0.00	0.00	0.00	2.85
582	589	1.364626	CTGCACGGGACATCTGCTTC	61.365	60.000	0.00	0.00	0.00	3.86
583	590	1.376424	CTGCACGGGACATCTGCTT	60.376	57.895	0.00	0.00	0.00	3.91
584	591	2.267006	CTGCACGGGACATCTGCT	59.733	61.111	0.00	0.00	0.00	4.24
585	592	3.503363	GCTGCACGGGACATCTGC	61.503	66.667	0.00	0.00	0.00	4.26
586	593	2.809861	AAGGCTGCACGGGACATCTG	62.810	60.000	0.50	0.00	0.00	2.90
587	594	2.596851	AAGGCTGCACGGGACATCT	61.597	57.895	0.50	0.00	0.00	2.90
588	595	2.045926	AAGGCTGCACGGGACATC	60.046	61.111	0.50	0.00	0.00	3.06
589	596	2.360350	CAAGGCTGCACGGGACAT	60.360	61.111	0.50	0.00	0.00	3.06
590	597	3.414136	AACAAGGCTGCACGGGACA	62.414	57.895	0.50	0.00	0.00	4.02
591	598	2.594592	AACAAGGCTGCACGGGAC	60.595	61.111	0.50	0.00	0.00	4.46
592	599	2.281484	GAACAAGGCTGCACGGGA	60.281	61.111	0.50	0.00	0.00	5.14
593	600	2.281761	AGAACAAGGCTGCACGGG	60.282	61.111	0.50	0.00	0.00	5.28
594	601	2.671177	CGAGAACAAGGCTGCACGG	61.671	63.158	0.50	0.00	0.00	4.94
595	602	1.016130	ATCGAGAACAAGGCTGCACG	61.016	55.000	0.50	0.00	0.00	5.34
596	603	0.445436	CATCGAGAACAAGGCTGCAC	59.555	55.000	0.50	0.00	0.00	4.57
597	604	1.300971	GCATCGAGAACAAGGCTGCA	61.301	55.000	0.50	0.00	0.00	4.41
598	605	1.427020	GCATCGAGAACAAGGCTGC	59.573	57.895	0.00	0.00	0.00	5.25
599	606	1.712081	CGCATCGAGAACAAGGCTG	59.288	57.895	0.00	0.00	0.00	4.85
600	607	2.103042	GCGCATCGAGAACAAGGCT	61.103	57.895	0.30	0.00	0.00	4.58
601	608	2.401195	GCGCATCGAGAACAAGGC	59.599	61.111	0.30	0.00	0.00	4.35
602	609	2.802667	CGGCGCATCGAGAACAAGG	61.803	63.158	10.83	0.00	0.00	3.61
603	610	2.697425	CGGCGCATCGAGAACAAG	59.303	61.111	10.83	0.00	0.00	3.16
604	611	2.572095	ATCCGGCGCATCGAGAACAA	62.572	55.000	10.83	0.00	0.00	2.83
605	612	2.572095	AATCCGGCGCATCGAGAACA	62.572	55.000	10.83	0.00	0.00	3.18
606	613	0.596600	TAATCCGGCGCATCGAGAAC	60.597	55.000	10.83	0.00	0.00	3.01
607	614	0.596600	GTAATCCGGCGCATCGAGAA	60.597	55.000	10.83	0.00	0.00	2.87
608	615	1.007734	GTAATCCGGCGCATCGAGA	60.008	57.895	10.83	4.76	0.00	4.04
609	616	2.365068	CGTAATCCGGCGCATCGAG	61.365	63.158	10.83	0.00	0.00	4.04
610	617	2.137425	ATCGTAATCCGGCGCATCGA	62.137	55.000	10.83	8.37	37.11	3.59
611	618	1.674611	GATCGTAATCCGGCGCATCG	61.675	60.000	10.83	3.98	37.11	3.84
612	619	0.388649	AGATCGTAATCCGGCGCATC	60.389	55.000	10.83	0.00	37.11	3.91
613	620	0.033504	AAGATCGTAATCCGGCGCAT	59.966	50.000	10.83	0.00	37.11	4.73
614	621	0.596600	GAAGATCGTAATCCGGCGCA	60.597	55.000	10.83	0.00	37.11	6.09
615	622	0.318784	AGAAGATCGTAATCCGGCGC	60.319	55.000	0.00	0.00	37.11	6.53
616	623	2.052157	GAAGAAGATCGTAATCCGGCG	58.948	52.381	0.00	0.00	37.11	6.46
617	624	2.405172	GGAAGAAGATCGTAATCCGGC	58.595	52.381	0.00	0.00	37.11	6.13
618	625	2.662700	CGGAAGAAGATCGTAATCCGG	58.337	52.381	19.95	0.00	44.47	5.14
620	627	2.405172	GGCGGAAGAAGATCGTAATCC	58.595	52.381	3.09	3.09	31.78	3.01
621	628	2.405172	GGGCGGAAGAAGATCGTAATC	58.595	52.381	0.00	0.00	0.00	1.75
622	629	1.070289	GGGGCGGAAGAAGATCGTAAT	59.930	52.381	0.00	0.00	0.00	1.89
623	630	0.462789	GGGGCGGAAGAAGATCGTAA	59.537	55.000	0.00	0.00	0.00	3.18
624	631	0.685131	TGGGGCGGAAGAAGATCGTA	60.685	55.000	0.00	0.00	0.00	3.43
625	632	1.338136	ATGGGGCGGAAGAAGATCGT	61.338	55.000	0.00	0.00	0.00	3.73
626	633	0.179045	AATGGGGCGGAAGAAGATCG	60.179	55.000	0.00	0.00	0.00	3.69
627	634	1.312815	CAATGGGGCGGAAGAAGATC	58.687	55.000	0.00	0.00	0.00	2.75
628	635	0.753111	GCAATGGGGCGGAAGAAGAT	60.753	55.000	0.00	0.00	0.00	2.40
629	636	1.378514	GCAATGGGGCGGAAGAAGA	60.379	57.895	0.00	0.00	0.00	2.87
630	637	1.250154	TTGCAATGGGGCGGAAGAAG	61.250	55.000	0.00	0.00	36.28	2.85
631	638	1.228706	TTGCAATGGGGCGGAAGAA	60.229	52.632	0.00	0.00	36.28	2.52
632	639	1.976474	GTTGCAATGGGGCGGAAGA	60.976	57.895	0.59	0.00	36.28	2.87
633	640	2.573340	GTTGCAATGGGGCGGAAG	59.427	61.111	0.59	0.00	36.28	3.46
634	641	2.994417	GGTTGCAATGGGGCGGAA	60.994	61.111	0.59	0.00	36.28	4.30
637	644	4.067913	GTGGGTTGCAATGGGGCG	62.068	66.667	0.59	0.00	36.28	6.13
638	645	3.705289	GGTGGGTTGCAATGGGGC	61.705	66.667	0.59	0.00	0.00	5.80
639	646	2.161713	TAGGGTGGGTTGCAATGGGG	62.162	60.000	0.59	0.00	0.00	4.96
640	647	0.252012	TTAGGGTGGGTTGCAATGGG	60.252	55.000	0.59	0.00	0.00	4.00
641	648	1.638529	TTTAGGGTGGGTTGCAATGG	58.361	50.000	0.59	0.00	0.00	3.16
642	649	2.289382	GGTTTTAGGGTGGGTTGCAATG	60.289	50.000	0.59	0.00	0.00	2.82
643	650	1.974957	GGTTTTAGGGTGGGTTGCAAT	59.025	47.619	0.59	0.00	0.00	3.56
644	651	1.062810	AGGTTTTAGGGTGGGTTGCAA	60.063	47.619	0.00	0.00	0.00	4.08
645	652	0.558712	AGGTTTTAGGGTGGGTTGCA	59.441	50.000	0.00	0.00	0.00	4.08
646	653	1.712056	AAGGTTTTAGGGTGGGTTGC	58.288	50.000	0.00	0.00	0.00	4.17
647	654	2.224185	GCAAAGGTTTTAGGGTGGGTTG	60.224	50.000	0.00	0.00	0.00	3.77
648	655	2.043992	GCAAAGGTTTTAGGGTGGGTT	58.956	47.619	0.00	0.00	0.00	4.11
649	656	1.712056	GCAAAGGTTTTAGGGTGGGT	58.288	50.000	0.00	0.00	0.00	4.51
650	657	0.601057	CGCAAAGGTTTTAGGGTGGG	59.399	55.000	0.00	0.00	0.00	4.61
651	658	0.038618	GCGCAAAGGTTTTAGGGTGG	60.039	55.000	0.30	0.00	0.00	4.61
652	659	0.038618	GGCGCAAAGGTTTTAGGGTG	60.039	55.000	10.83	0.00	0.00	4.61
653	660	1.183030	GGGCGCAAAGGTTTTAGGGT	61.183	55.000	10.83	0.00	0.00	4.34
654	661	0.898326	AGGGCGCAAAGGTTTTAGGG	60.898	55.000	10.83	0.00	0.00	3.53
655	662	0.526211	GAGGGCGCAAAGGTTTTAGG	59.474	55.000	10.83	0.00	0.00	2.69
656	663	1.468914	GAGAGGGCGCAAAGGTTTTAG	59.531	52.381	10.83	0.00	0.00	1.85
657	664	1.073284	AGAGAGGGCGCAAAGGTTTTA	59.927	47.619	10.83	0.00	0.00	1.52
658	665	0.178990	AGAGAGGGCGCAAAGGTTTT	60.179	50.000	10.83	0.00	0.00	2.43
659	666	0.606673	GAGAGAGGGCGCAAAGGTTT	60.607	55.000	10.83	0.00	0.00	3.27
660	667	1.003233	GAGAGAGGGCGCAAAGGTT	60.003	57.895	10.83	0.00	0.00	3.50
661	668	2.177594	CTGAGAGAGGGCGCAAAGGT	62.178	60.000	10.83	0.00	0.00	3.50
662	669	1.449246	CTGAGAGAGGGCGCAAAGG	60.449	63.158	10.83	0.00	0.00	3.11
663	670	0.459934	CTCTGAGAGAGGGCGCAAAG	60.460	60.000	10.83	0.00	38.67	2.77
664	671	1.188219	ACTCTGAGAGAGGGCGCAAA	61.188	55.000	17.71	0.00	46.45	3.68
665	672	1.607756	ACTCTGAGAGAGGGCGCAA	60.608	57.895	17.71	0.00	46.45	4.85
666	673	2.036414	ACTCTGAGAGAGGGCGCA	59.964	61.111	17.71	0.00	46.45	6.09
667	674	2.493973	CACTCTGAGAGAGGGCGC	59.506	66.667	17.71	0.00	46.45	6.53
671	678	6.047870	CCATAATCAAACACTCTGAGAGAGG	58.952	44.000	17.71	10.20	46.45	3.69
673	680	5.721480	TCCCATAATCAAACACTCTGAGAGA	59.279	40.000	17.71	0.00	33.32	3.10
674	681	5.982356	TCCCATAATCAAACACTCTGAGAG	58.018	41.667	12.44	8.15	35.52	3.20
675	682	6.373005	TTCCCATAATCAAACACTCTGAGA	57.627	37.500	12.44	0.00	0.00	3.27
676	683	6.600822	ACATTCCCATAATCAAACACTCTGAG	59.399	38.462	2.45	2.45	0.00	3.35
677	684	6.484288	ACATTCCCATAATCAAACACTCTGA	58.516	36.000	0.00	0.00	0.00	3.27
678	685	6.600822	AGACATTCCCATAATCAAACACTCTG	59.399	38.462	0.00	0.00	0.00	3.35
679	686	6.725364	AGACATTCCCATAATCAAACACTCT	58.275	36.000	0.00	0.00	0.00	3.24
680	687	8.506168	TTAGACATTCCCATAATCAAACACTC	57.494	34.615	0.00	0.00	0.00	3.51
681	688	9.479549	AATTAGACATTCCCATAATCAAACACT	57.520	29.630	0.00	0.00	0.00	3.55
682	689	9.520204	CAATTAGACATTCCCATAATCAAACAC	57.480	33.333	0.00	0.00	0.00	3.32
683	690	9.473007	TCAATTAGACATTCCCATAATCAAACA	57.527	29.630	0.00	0.00	0.00	2.83
684	691	9.736023	GTCAATTAGACATTCCCATAATCAAAC	57.264	33.333	0.00	0.00	46.77	2.93
729	737	7.382110	TGGACAAGAAATTTGACTGTTTTCAA	58.618	30.769	0.00	0.00	32.94	2.69
820	831	1.296715	GCTGGATGGTTGTCCGACT	59.703	57.895	0.00	0.00	41.35	4.18
2275	2463	7.062605	CAGTGATATTTCCAGTGCAATTTCAAC	59.937	37.037	0.00	4.56	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.