AutoCloner

Multiple sequence alignment - TraesCS6A01G192500

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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	TraesCS6A01G192500	chr6A	100.000	2699	0	0	1	2699	260131429	260128731	0.000000e+00	4985
1	TraesCS6A01G192500	chr1D	98.065	2015	32	3	689	2698	206075332	206073320	0.000000e+00	3498
2	TraesCS6A01G192500	chr1D	97.915	2014	36	2	689	2698	254500031	254502042	0.000000e+00	3482
3	TraesCS6A01G192500	chr5D	97.916	2015	35	3	689	2698	560874501	560876513	0.000000e+00	3482
4	TraesCS6A01G192500	chr5D	96.524	2014	42	7	689	2698	6199249	6197260	0.000000e+00	3306
5	TraesCS6A01G192500	chr5D	97.102	1691	45	1	1012	2698	329192306	329193996	0.000000e+00	2848
6	TraesCS6A01G192500	chr3B	97.766	2014	38	3	689	2698	201516712	201518722	0.000000e+00	3463
7	TraesCS6A01G192500	chr4D	96.673	2014	56	4	689	2698	19918525	19920531	0.000000e+00	3338
8	TraesCS6A01G192500	chr7B	95.916	2008	59	9	689	2692	102631597	102629609	0.000000e+00	3232
9	TraesCS6A01G192500	chr7B	96.703	182	5	1	889	1070	57815384	57815204	4.370000e-78	302
10	TraesCS6A01G192500	chr7B	87.037	270	26	6	689	953	672838288	672838023	2.030000e-76	296
11	TraesCS6A01G192500	chr7B	85.496	262	28	5	689	944	672820705	672820448	5.730000e-67	265
12	TraesCS6A01G192500	chr7B	93.805	113	6	1	1057	1168	103735713	103735601	4.620000e-38	169
13	TraesCS6A01G192500	chr7B	100.000	67	0	0	972	1038	57835850	57835784	1.010000e-24	124
14	TraesCS6A01G192500	chr7A	95.184	2014	84	6	689	2698	352191993	352189989	0.000000e+00	3169
15	TraesCS6A01G192500	chr6B	93.768	690	42	1	1	690	389271629	389270941	0.000000e+00	1035
16	TraesCS6A01G192500	chr7D	93.043	690	47	1	1	690	262188644	262187956	0.000000e+00	1007
17	TraesCS6A01G192500	chr2D	92.899	690	49	0	1	690	288297721	288297032	0.000000e+00	1003
18	TraesCS6A01G192500	chr4B	92.909	691	45	4	1	690	252984192	252983505	0.000000e+00	1002
19	TraesCS6A01G192500	chrUn	92.754	690	50	0	1	690	106128030	106127341	0.000000e+00	998
20	TraesCS6A01G192500	chr6D	92.754	690	50	0	1	690	138318257	138317568	0.000000e+00	998
21	TraesCS6A01G192500	chr6D	92.754	690	50	0	1	690	206607352	206606663	0.000000e+00	998
22	TraesCS6A01G192500	chr6D	92.982	684	48	0	1	684	338576981	338577664	0.000000e+00	998
23	TraesCS6A01G192500	chr3D	92.982	684	48	0	1	684	240267403	240268086	0.000000e+00	998

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	TraesCS6A01G192500	chr6A	260128731	260131429	2698	True	4985	4985	100.000	1	2699	1	chr6A.!!$R1	2698
1	TraesCS6A01G192500	chr1D	206073320	206075332	2012	True	3498	3498	98.065	689	2698	1	chr1D.!!$R1	2009
2	TraesCS6A01G192500	chr1D	254500031	254502042	2011	False	3482	3482	97.915	689	2698	1	chr1D.!!$F1	2009
3	TraesCS6A01G192500	chr5D	560874501	560876513	2012	False	3482	3482	97.916	689	2698	1	chr5D.!!$F2	2009
4	TraesCS6A01G192500	chr5D	6197260	6199249	1989	True	3306	3306	96.524	689	2698	1	chr5D.!!$R1	2009
5	TraesCS6A01G192500	chr5D	329192306	329193996	1690	False	2848	2848	97.102	1012	2698	1	chr5D.!!$F1	1686
6	TraesCS6A01G192500	chr3B	201516712	201518722	2010	False	3463	3463	97.766	689	2698	1	chr3B.!!$F1	2009
7	TraesCS6A01G192500	chr4D	19918525	19920531	2006	False	3338	3338	96.673	689	2698	1	chr4D.!!$F1	2009
8	TraesCS6A01G192500	chr7B	102629609	102631597	1988	True	3232	3232	95.916	689	2692	1	chr7B.!!$R3	2003
9	TraesCS6A01G192500	chr7A	352189989	352191993	2004	True	3169	3169	95.184	689	2698	1	chr7A.!!$R1	2009
10	TraesCS6A01G192500	chr6B	389270941	389271629	688	True	1035	1035	93.768	1	690	1	chr6B.!!$R1	689
11	TraesCS6A01G192500	chr7D	262187956	262188644	688	True	1007	1007	93.043	1	690	1	chr7D.!!$R1	689
12	TraesCS6A01G192500	chr2D	288297032	288297721	689	True	1003	1003	92.899	1	690	1	chr2D.!!$R1	689
13	TraesCS6A01G192500	chr4B	252983505	252984192	687	True	1002	1002	92.909	1	690	1	chr4B.!!$R1	689
14	TraesCS6A01G192500	chrUn	106127341	106128030	689	True	998	998	92.754	1	690	1	chrUn.!!$R1	689
15	TraesCS6A01G192500	chr6D	138317568	138318257	689	True	998	998	92.754	1	690	1	chr6D.!!$R1	689
16	TraesCS6A01G192500	chr6D	206606663	206607352	689	True	998	998	92.754	1	690	1	chr6D.!!$R2	689
17	TraesCS6A01G192500	chr6D	338576981	338577664	683	False	998	998	92.982	1	684	1	chr6D.!!$F1	683
18	TraesCS6A01G192500	chr3D	240267403	240268086	683	False	998	998	92.982	1	684	1	chr3D.!!$F1	683

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
629	630	0.810648	TGCGCATAAAGCAAGGGAAG	59.189	50.0	5.66	0.0	46.13	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1874	1877	1.141053	ACACTCCCATAATCCGCCTTC	59.859	52.381	0.0	0.0	0.0	3.46	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	2.995939	GTGAGTGCGACATCATCTCAAA	59.004	45.455	0.00	0.00	37.00	2.69
80	81	4.703093	TGTCATCGTCTGTACCTACATCAA	59.297	41.667	0.00	0.00	35.36	2.57
105	106	2.348218	CGTCTTTGCGACAAGGTAACAC	60.348	50.000	0.00	0.00	42.98	3.32
111	112	2.034432	TGCGACAAGGTAACACTAACGA	59.966	45.455	0.00	0.00	41.41	3.85
160	161	6.261826	AGAATGATGCATGCCTAGTTAACTTC	59.738	38.462	16.68	2.36	0.00	3.01
204	205	2.620115	CTGTTGATTTGAGCACACCACT	59.380	45.455	0.00	0.00	0.00	4.00
358	359	5.934781	ACCTCTAATCTTGGTGATGATTCC	58.065	41.667	0.00	0.00	35.21	3.01
441	442	6.079424	TGCAAGTAAGGTTTATTCACCAAC	57.921	37.500	0.00	0.00	39.62	3.77
463	464	4.398044	ACGTTGGGATGGTTTAATGATGAC	59.602	41.667	0.00	0.00	0.00	3.06
519	520	8.840833	TTCACTTATATGTGCAAACTGAGTTA	57.159	30.769	12.71	0.00	37.81	2.24
534	535	9.409312	CAAACTGAGTTACAATATTTTCATGCA	57.591	29.630	0.00	0.00	0.00	3.96
614	615	5.553721	CATGTATACATGTGTCATATGCGC	58.446	41.667	29.91	0.00	46.40	6.09
615	616	4.626042	TGTATACATGTGTCATATGCGCA	58.374	39.130	14.96	14.96	0.00	6.09
616	617	5.237048	TGTATACATGTGTCATATGCGCAT	58.763	37.500	28.23	28.23	37.53	4.73
617	618	6.393990	TGTATACATGTGTCATATGCGCATA	58.606	36.000	30.72	30.72	35.58	3.14
618	619	6.870965	TGTATACATGTGTCATATGCGCATAA	59.129	34.615	32.02	15.65	35.58	1.90
619	620	6.799926	ATACATGTGTCATATGCGCATAAA	57.200	33.333	32.02	20.69	35.58	1.40
620	621	5.099484	ACATGTGTCATATGCGCATAAAG	57.901	39.130	32.02	25.70	35.58	1.85
621	622	3.607422	TGTGTCATATGCGCATAAAGC	57.393	42.857	32.02	22.94	40.87	3.51
627	628	4.732568	TGCGCATAAAGCAAGGGA	57.267	50.000	5.66	0.00	46.13	4.20
628	629	2.954161	TGCGCATAAAGCAAGGGAA	58.046	47.368	5.66	0.00	46.13	3.97
629	630	0.810648	TGCGCATAAAGCAAGGGAAG	59.189	50.000	5.66	0.00	46.13	3.46
630	631	0.811281	GCGCATAAAGCAAGGGAAGT	59.189	50.000	0.30	0.00	46.13	3.01
631	632	2.014128	GCGCATAAAGCAAGGGAAGTA	58.986	47.619	0.30	0.00	46.13	2.24
632	633	2.422127	GCGCATAAAGCAAGGGAAGTAA	59.578	45.455	0.30	0.00	46.13	2.24
633	634	3.119637	GCGCATAAAGCAAGGGAAGTAAA	60.120	43.478	0.30	0.00	46.13	2.01
634	635	4.617298	GCGCATAAAGCAAGGGAAGTAAAA	60.617	41.667	0.30	0.00	46.13	1.52
635	636	5.465935	CGCATAAAGCAAGGGAAGTAAAAA	58.534	37.500	0.00	0.00	46.13	1.94
636	637	6.099341	CGCATAAAGCAAGGGAAGTAAAAAT	58.901	36.000	0.00	0.00	46.13	1.82
637	638	6.034898	CGCATAAAGCAAGGGAAGTAAAAATG	59.965	38.462	0.00	0.00	46.13	2.32
638	639	6.313658	GCATAAAGCAAGGGAAGTAAAAATGG	59.686	38.462	0.00	0.00	44.79	3.16
639	640	7.610865	CATAAAGCAAGGGAAGTAAAAATGGA	58.389	34.615	0.00	0.00	0.00	3.41
640	641	6.686484	AAAGCAAGGGAAGTAAAAATGGAT	57.314	33.333	0.00	0.00	0.00	3.41
641	642	5.665916	AGCAAGGGAAGTAAAAATGGATG	57.334	39.130	0.00	0.00	0.00	3.51
642	643	5.332743	AGCAAGGGAAGTAAAAATGGATGA	58.667	37.500	0.00	0.00	0.00	2.92
643	644	5.185828	AGCAAGGGAAGTAAAAATGGATGAC	59.814	40.000	0.00	0.00	0.00	3.06
644	645	5.047377	GCAAGGGAAGTAAAAATGGATGACA	60.047	40.000	0.00	0.00	0.00	3.58
645	646	6.518200	GCAAGGGAAGTAAAAATGGATGACAA	60.518	38.462	0.00	0.00	0.00	3.18
646	647	7.441017	CAAGGGAAGTAAAAATGGATGACAAA	58.559	34.615	0.00	0.00	0.00	2.83
647	648	7.797121	AGGGAAGTAAAAATGGATGACAAAT	57.203	32.000	0.00	0.00	0.00	2.32
648	649	8.893563	AGGGAAGTAAAAATGGATGACAAATA	57.106	30.769	0.00	0.00	0.00	1.40
649	650	8.749354	AGGGAAGTAAAAATGGATGACAAATAC	58.251	33.333	0.00	0.00	0.00	1.89
650	651	8.527810	GGGAAGTAAAAATGGATGACAAATACA	58.472	33.333	0.00	0.00	0.00	2.29
678	679	6.867662	CAAGATGTACACCTTGTCTCTTTT	57.132	37.500	20.28	0.00	36.08	2.27
679	680	6.662616	CAAGATGTACACCTTGTCTCTTTTG	58.337	40.000	20.28	0.98	36.08	2.44
680	681	5.930135	AGATGTACACCTTGTCTCTTTTGT	58.070	37.500	0.00	0.00	0.00	2.83
681	682	6.357367	AGATGTACACCTTGTCTCTTTTGTT	58.643	36.000	0.00	0.00	0.00	2.83
682	683	7.506114	AGATGTACACCTTGTCTCTTTTGTTA	58.494	34.615	0.00	0.00	0.00	2.41
683	684	7.657761	AGATGTACACCTTGTCTCTTTTGTTAG	59.342	37.037	0.00	0.00	0.00	2.34
684	685	6.880484	TGTACACCTTGTCTCTTTTGTTAGA	58.120	36.000	0.00	0.00	0.00	2.10
685	686	6.759827	TGTACACCTTGTCTCTTTTGTTAGAC	59.240	38.462	0.00	0.00	42.04	2.59
686	687	4.809426	ACACCTTGTCTCTTTTGTTAGACG	59.191	41.667	0.00	0.00	44.14	4.18
687	688	3.808174	ACCTTGTCTCTTTTGTTAGACGC	59.192	43.478	0.00	0.00	44.14	5.19
934	935	1.168714	GACCCAATTCAGTGGCTGAC	58.831	55.000	0.00	0.00	40.46	3.51
1060	1062	9.151177	TCGGGTTAGTTACCTATCTCAATAAAT	57.849	33.333	0.00	0.00	46.86	1.40
1147	1149	3.279434	GTTCCTCCCCATGTCAACATAC	58.721	50.000	0.00	0.00	34.26	2.39
1271	1273	8.746052	TTTTCCTCGGTTCAATACATAATGAT	57.254	30.769	0.00	0.00	0.00	2.45
1370	1372	6.048509	TGCATGTATTTCGTGTGTATCTCAT	58.951	36.000	0.00	0.00	35.64	2.90
1411	1414	3.756434	CCGTGAATTAACTTGGGTCACAT	59.244	43.478	0.00	0.00	38.80	3.21
1584	1587	0.035056	GTGCTAGTGTGGGCCAATCT	60.035	55.000	8.40	12.48	0.00	2.40
1772	1775	6.589907	GGTTTTGGTATTTCATTGCTACAAGG	59.410	38.462	0.00	0.00	0.00	3.61
1920	1923	6.311200	GTGACTTGAATTATTGATTTGGCCAC	59.689	38.462	3.88	0.00	0.00	5.01
1983	1986	0.620556	AGGTGTCTCCGCATCCAATT	59.379	50.000	0.00	0.00	41.99	2.32
2205	2208	3.608796	TCTTTGCATCGATTGTGATCCA	58.391	40.909	0.00	0.00	0.00	3.41
2237	2240	7.619512	ATCGGAGTAAAAGAAGGGATCTAAT	57.380	36.000	0.00	0.00	37.42	1.73
2240	2243	7.290248	TCGGAGTAAAAGAAGGGATCTAATGAT	59.710	37.037	0.00	0.00	37.42	2.45
2315	2323	3.334691	TGGAGGTAAGAAACTTGCGATG	58.665	45.455	0.00	0.00	0.00	3.84
2364	2372	4.829968	AGAGACATGAGACAATCCACAAG	58.170	43.478	0.00	0.00	0.00	3.16
2473	2485	6.016276	GGTGCAACTTTGGAAAAGAGAATCTA	60.016	38.462	6.73	0.00	41.22	1.98
2543	2555	4.401022	TCTATTAAGGATCTTCCGCGGTA	58.599	43.478	27.15	15.91	42.75	4.02
2589	2601	4.999950	AGCCGGATGATGATAAATTCTCAC	59.000	41.667	5.05	0.00	0.00	3.51
2635	2647	3.958798	TCCTAAAGAGTTCACCTATCCCG	59.041	47.826	0.00	0.00	0.00	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.866883	TGATGTCGCACTCACAATCTA	57.133	42.857	0.00	0.00	0.00	1.98
358	359	4.142622	ACATGCAATAGGTCATTTGACACG	60.143	41.667	12.43	0.00	46.47	4.49
441	442	4.202010	GGTCATCATTAAACCATCCCAACG	60.202	45.833	0.00	0.00	33.11	4.10
473	474	9.118300	AGTGAAGCTCTTATTCATATCAAAAGG	57.882	33.333	0.00	0.00	38.81	3.11
599	600	3.910170	GCTTTATGCGCATATGACACATG	59.090	43.478	29.41	16.22	0.00	3.21
600	601	3.565063	TGCTTTATGCGCATATGACACAT	59.435	39.130	29.41	5.18	46.63	3.21
601	602	2.941720	TGCTTTATGCGCATATGACACA	59.058	40.909	29.41	19.47	46.63	3.72
602	603	3.607422	TGCTTTATGCGCATATGACAC	57.393	42.857	29.41	17.39	46.63	3.67
603	604	3.003585	CCTTGCTTTATGCGCATATGACA	59.996	43.478	29.41	22.65	46.63	3.58
604	605	3.558505	CCTTGCTTTATGCGCATATGAC	58.441	45.455	29.41	20.57	46.63	3.06
605	606	2.553602	CCCTTGCTTTATGCGCATATGA	59.446	45.455	29.41	19.60	46.63	2.15
606	607	2.553602	TCCCTTGCTTTATGCGCATATG	59.446	45.455	29.41	23.94	46.63	1.78
607	608	2.862541	TCCCTTGCTTTATGCGCATAT	58.137	42.857	29.41	10.10	46.63	1.78
608	609	2.340210	TCCCTTGCTTTATGCGCATA	57.660	45.000	25.78	25.78	46.63	3.14
609	610	1.406539	CTTCCCTTGCTTTATGCGCAT	59.593	47.619	28.23	28.23	46.63	4.73
610	611	0.810648	CTTCCCTTGCTTTATGCGCA	59.189	50.000	14.96	14.96	46.63	6.09
611	612	0.811281	ACTTCCCTTGCTTTATGCGC	59.189	50.000	0.00	0.00	46.63	6.09
612	613	4.695217	TTTACTTCCCTTGCTTTATGCG	57.305	40.909	0.00	0.00	46.63	4.73
613	614	6.313658	CCATTTTTACTTCCCTTGCTTTATGC	59.686	38.462	0.00	0.00	43.25	3.14
614	615	7.610865	TCCATTTTTACTTCCCTTGCTTTATG	58.389	34.615	0.00	0.00	0.00	1.90
615	616	7.790782	TCCATTTTTACTTCCCTTGCTTTAT	57.209	32.000	0.00	0.00	0.00	1.40
616	617	7.453126	TCATCCATTTTTACTTCCCTTGCTTTA	59.547	33.333	0.00	0.00	0.00	1.85
617	618	6.269769	TCATCCATTTTTACTTCCCTTGCTTT	59.730	34.615	0.00	0.00	0.00	3.51
618	619	5.779771	TCATCCATTTTTACTTCCCTTGCTT	59.220	36.000	0.00	0.00	0.00	3.91
619	620	5.185828	GTCATCCATTTTTACTTCCCTTGCT	59.814	40.000	0.00	0.00	0.00	3.91
620	621	5.047377	TGTCATCCATTTTTACTTCCCTTGC	60.047	40.000	0.00	0.00	0.00	4.01
621	622	6.588719	TGTCATCCATTTTTACTTCCCTTG	57.411	37.500	0.00	0.00	0.00	3.61
622	623	7.610580	TTTGTCATCCATTTTTACTTCCCTT	57.389	32.000	0.00	0.00	0.00	3.95
623	624	7.797121	ATTTGTCATCCATTTTTACTTCCCT	57.203	32.000	0.00	0.00	0.00	4.20
624	625	8.527810	TGTATTTGTCATCCATTTTTACTTCCC	58.472	33.333	0.00	0.00	0.00	3.97
656	657	6.357367	ACAAAAGAGACAAGGTGTACATCTT	58.643	36.000	15.83	15.83	32.54	2.40
657	658	5.930135	ACAAAAGAGACAAGGTGTACATCT	58.070	37.500	1.73	1.73	0.00	2.90
658	659	6.619801	AACAAAAGAGACAAGGTGTACATC	57.380	37.500	0.00	0.00	0.00	3.06
659	660	7.441458	GTCTAACAAAAGAGACAAGGTGTACAT	59.559	37.037	0.00	0.00	41.49	2.29
660	661	6.759827	GTCTAACAAAAGAGACAAGGTGTACA	59.240	38.462	0.00	0.00	41.49	2.90
661	662	6.074463	CGTCTAACAAAAGAGACAAGGTGTAC	60.074	42.308	3.22	0.00	41.87	2.90
662	663	5.981315	CGTCTAACAAAAGAGACAAGGTGTA	59.019	40.000	3.22	0.00	41.87	2.90
663	664	4.809426	CGTCTAACAAAAGAGACAAGGTGT	59.191	41.667	3.22	0.00	41.87	4.16
664	665	4.318831	GCGTCTAACAAAAGAGACAAGGTG	60.319	45.833	3.22	0.00	41.87	4.00
665	666	3.808174	GCGTCTAACAAAAGAGACAAGGT	59.192	43.478	3.22	0.00	41.87	3.50
666	667	3.807622	TGCGTCTAACAAAAGAGACAAGG	59.192	43.478	3.22	0.00	41.87	3.61
667	668	5.406780	AGATGCGTCTAACAAAAGAGACAAG	59.593	40.000	6.67	0.00	41.87	3.16
668	669	5.297547	AGATGCGTCTAACAAAAGAGACAA	58.702	37.500	6.67	0.00	41.87	3.18
669	670	4.883083	AGATGCGTCTAACAAAAGAGACA	58.117	39.130	6.67	0.00	41.87	3.41
670	671	6.035112	CCTTAGATGCGTCTAACAAAAGAGAC	59.965	42.308	21.89	0.00	40.98	3.36
671	672	6.100004	CCTTAGATGCGTCTAACAAAAGAGA	58.900	40.000	21.89	1.72	40.98	3.10
672	673	5.869888	ACCTTAGATGCGTCTAACAAAAGAG	59.130	40.000	21.89	11.76	40.98	2.85
673	674	5.790593	ACCTTAGATGCGTCTAACAAAAGA	58.209	37.500	21.89	3.08	40.98	2.52
674	675	6.481954	AACCTTAGATGCGTCTAACAAAAG	57.518	37.500	21.89	14.55	40.98	2.27
675	676	6.870971	AAACCTTAGATGCGTCTAACAAAA	57.129	33.333	21.89	6.15	40.98	2.44
676	677	6.870971	AAAACCTTAGATGCGTCTAACAAA	57.129	33.333	21.89	6.50	40.98	2.83
677	678	7.966246	TTAAAACCTTAGATGCGTCTAACAA	57.034	32.000	21.89	6.85	40.98	2.83
678	679	8.447833	CAATTAAAACCTTAGATGCGTCTAACA	58.552	33.333	21.89	5.81	40.98	2.41
679	680	8.662141	TCAATTAAAACCTTAGATGCGTCTAAC	58.338	33.333	21.89	0.00	40.98	2.34
680	681	8.780846	TCAATTAAAACCTTAGATGCGTCTAA	57.219	30.769	23.66	23.66	43.02	2.10
681	682	8.662141	GTTCAATTAAAACCTTAGATGCGTCTA	58.338	33.333	11.74	11.74	35.87	2.59
682	683	7.390718	AGTTCAATTAAAACCTTAGATGCGTCT	59.609	33.333	14.07	14.07	38.52	4.18
683	684	7.481798	CAGTTCAATTAAAACCTTAGATGCGTC	59.518	37.037	0.00	0.00	0.00	5.19
684	685	7.174253	TCAGTTCAATTAAAACCTTAGATGCGT	59.826	33.333	0.53	0.00	0.00	5.24
685	686	7.526608	TCAGTTCAATTAAAACCTTAGATGCG	58.473	34.615	0.53	0.00	0.00	4.73
686	687	9.860898	AATCAGTTCAATTAAAACCTTAGATGC	57.139	29.630	0.53	0.00	0.00	3.91
1060	1062	7.335627	AGACGTTCCTCAAACCAATCATATAA	58.664	34.615	0.00	0.00	34.11	0.98
1147	1149	8.589701	AGTGTAATTCCCCCTAAACAATAAAG	57.410	34.615	0.00	0.00	0.00	1.85
1387	1389	2.372504	TGACCCAAGTTAATTCACGGGA	59.627	45.455	9.09	0.00	37.13	5.14
1411	1414	2.300152	TCAAAACAGCCAAAACCACACA	59.700	40.909	0.00	0.00	0.00	3.72
1874	1877	1.141053	ACACTCCCATAATCCGCCTTC	59.859	52.381	0.00	0.00	0.00	3.46
1983	1986	5.196369	TCCTAGGTAGGGGACTTACATGTTA	59.804	44.000	9.08	0.00	43.79	2.41
2205	2208	7.343833	TCCCTTCTTTTACTCCGATAGTATTGT	59.656	37.037	0.00	0.00	40.41	2.71
2315	2323	7.996644	TGATTAGTTGGTATTTATCCCCTCAAC	59.003	37.037	0.00	0.00	34.87	3.18
2473	2485	6.942576	TGACTCTAGGCAAGAAAAGCTTTATT	59.057	34.615	13.10	7.91	33.60	1.40
2543	2555	6.183360	GCTCGAGCAAGAGTGAAAGAAATAAT	60.183	38.462	31.91	0.00	40.26	1.28
2589	2601	2.359478	CCCCAAAGGAACCGGACG	60.359	66.667	9.46	0.00	38.24	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.