AutoCloner

Multiple sequence alignment - TraesCS3D01G076800

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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	TraesCS3D01G076800	chr3D	100.000	2913	0	0	1	2913	37452791	37449879	0.000000e+00	5380
1	TraesCS3D01G076800	chr3D	94.006	2836	140	13	1	2813	37268701	37271529	0.000000e+00	4268
2	TraesCS3D01G076800	chr3D	94.134	2131	98	13	702	2813	37246892	37249014	0.000000e+00	3217
3	TraesCS3D01G076800	chr3D	93.620	2069	100	8	1	2037	37287842	37289910	0.000000e+00	3061
4	TraesCS3D01G076800	chr3D	95.579	1787	60	8	1	1781	37545890	37544117	0.000000e+00	2844
5	TraesCS3D01G076800	chr3D	94.656	786	41	1	2028	2813	37442307	37441523	0.000000e+00	1218
6	TraesCS3D01G076800	chr3D	92.697	712	49	3	5	715	37246162	37246871	0.000000e+00	1024
7	TraesCS3D01G076800	chr3D	95.034	584	28	1	1847	2429	37532843	37532260	0.000000e+00	917
8	TraesCS3D01G076800	chr3D	93.316	389	25	1	2425	2813	37526991	37526604	9.050000e-160	573
9	TraesCS3D01G076800	chr3D	93.316	389	25	1	2425	2813	37540860	37540473	9.050000e-160	573
10	TraesCS3D01G076800	chr3D	97.842	139	3	0	1724	1862	37532995	37532857	1.040000e-59	241
11	TraesCS3D01G076800	chr3D	97.115	104	1	2	2812	2913	581123515	581123412	1.070000e-39	174
12	TraesCS3D01G076800	chr3A	94.865	2824	132	7	1	2813	47554117	47556938	0.000000e+00	4399
13	TraesCS3D01G076800	chr3A	94.366	2822	147	8	1	2813	47526425	47529243	0.000000e+00	4320
14	TraesCS3D01G076800	chr3A	95.491	2107	86	4	715	2813	47583521	47585626	0.000000e+00	3356
15	TraesCS3D01G076800	chr3A	94.483	725	37	2	1	722	47582631	47583355	0.000000e+00	1114
16	TraesCS3D01G076800	chr3A	95.238	105	3	2	2811	2913	700603346	700603242	6.460000e-37	165
17	TraesCS3D01G076800	chr3A	89.231	130	11	3	2786	2913	30403732	30403860	3.000000e-35	159
18	TraesCS3D01G076800	chr3B	94.340	2827	128	12	1	2813	59751810	59754618	0.000000e+00	4305
19	TraesCS3D01G076800	chr3B	95.620	1347	51	8	1	1344	59996517	59995176	0.000000e+00	2154
20	TraesCS3D01G076800	chr3B	95.365	1014	41	3	1526	2534	59968849	59967837	0.000000e+00	1607
21	TraesCS3D01G076800	chr4A	99.029	103	1	0	2811	2913	739618065	739618167	4.960000e-43	185
22	TraesCS3D01G076800	chr7B	98.058	103	1	1	2812	2913	7529513	7529411	8.300000e-41	178
23	TraesCS3D01G076800	chr5D	94.783	115	4	2	2801	2913	387660968	387660854	8.300000e-41	178
24	TraesCS3D01G076800	chr6B	96.262	107	2	2	2809	2913	95353248	95353354	1.070000e-39	174
25	TraesCS3D01G076800	chr2D	95.455	110	3	2	2806	2913	489590639	489590530	1.070000e-39	174
26	TraesCS3D01G076800	chr7D	91.736	121	7	3	2795	2913	574851249	574851130	6.460000e-37	165

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	TraesCS3D01G076800	chr3D	37449879	37452791	2912	True	5380.0	5380	100.0000	1	2913	1	chr3D.!!$R2	2912
1	TraesCS3D01G076800	chr3D	37268701	37271529	2828	False	4268.0	4268	94.0060	1	2813	1	chr3D.!!$F1	2812
2	TraesCS3D01G076800	chr3D	37287842	37289910	2068	False	3061.0	3061	93.6200	1	2037	1	chr3D.!!$F2	2036
3	TraesCS3D01G076800	chr3D	37246162	37249014	2852	False	2120.5	3217	93.4155	5	2813	2	chr3D.!!$F3	2808
4	TraesCS3D01G076800	chr3D	37540473	37545890	5417	True	1708.5	2844	94.4475	1	2813	2	chr3D.!!$R6	2812
5	TraesCS3D01G076800	chr3D	37441523	37442307	784	True	1218.0	1218	94.6560	2028	2813	1	chr3D.!!$R1	785
6	TraesCS3D01G076800	chr3D	37532260	37532995	735	True	579.0	917	96.4380	1724	2429	2	chr3D.!!$R5	705
7	TraesCS3D01G076800	chr3A	47554117	47556938	2821	False	4399.0	4399	94.8650	1	2813	1	chr3A.!!$F3	2812
8	TraesCS3D01G076800	chr3A	47526425	47529243	2818	False	4320.0	4320	94.3660	1	2813	1	chr3A.!!$F2	2812
9	TraesCS3D01G076800	chr3A	47582631	47585626	2995	False	2235.0	3356	94.9870	1	2813	2	chr3A.!!$F4	2812
10	TraesCS3D01G076800	chr3B	59751810	59754618	2808	False	4305.0	4305	94.3400	1	2813	1	chr3B.!!$F1	2812
11	TraesCS3D01G076800	chr3B	59995176	59996517	1341	True	2154.0	2154	95.6200	1	1344	1	chr3B.!!$R2	1343
12	TraesCS3D01G076800	chr3B	59967837	59968849	1012	True	1607.0	1607	95.3650	1526	2534	1	chr3B.!!$R1	1008

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
87	89	2.418368	TGCATGGTGTAAGACATCCC	57.582	50.000	0.00	0.0	0.0	3.85	F
1381	1645	1.820519	GGGAATCAGAATGTGCTGCAA	59.179	47.619	2.77	0.0	37.4	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1800	2065	0.819582	GTCAACTGGATGCATTGGGG	59.180	55.0	0.00	0.00	0.00	4.96	R
2829	5831	0.111061	CTGCTATTGGCTGGCCCATA	59.889	55.0	9.28	7.14	44.89	2.74	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
46	47	7.872113	AAGTAGAGCTTCAATTTCCTTATGG	57.128	36.000	0.00	0.00	30.06	2.74
86	88	2.620115	CCATGCATGGTGTAAGACATCC	59.380	50.000	33.68	0.00	43.05	3.51
87	89	2.418368	TGCATGGTGTAAGACATCCC	57.582	50.000	0.00	0.00	0.00	3.85
511	533	4.613925	AGATTGTATGATCACGATGGCT	57.386	40.909	0.00	0.00	0.00	4.75
632	654	5.185454	TGGATATTAGCTTTGCATATCGGG	58.815	41.667	0.00	0.00	0.00	5.14
636	658	2.566833	AGCTTTGCATATCGGGCATA	57.433	45.000	0.00	0.00	41.58	3.14
909	1150	5.992217	GGAAGCATATCCGAGTTATGTTCTT	59.008	40.000	0.00	0.00	31.13	2.52
1202	1462	2.511218	AGGAGAGGCAGCCAAATATCAA	59.489	45.455	15.80	0.00	0.00	2.57
1381	1645	1.820519	GGGAATCAGAATGTGCTGCAA	59.179	47.619	2.77	0.00	37.40	4.08
1553	1817	9.566530	CAATCTATACGTGAAGAATCTAGATGG	57.433	37.037	5.86	0.00	0.00	3.51
1650	1914	9.539825	CTCTCTTTATTTGCTAGCTAATTCTGA	57.460	33.333	25.64	18.87	0.00	3.27
1800	2065	5.098218	TGGTTTAGTTGTATGCAAACGTC	57.902	39.130	0.00	0.00	36.22	4.34
1886	3359	5.779241	TGGGATGAACAGGAAGATAGTTT	57.221	39.130	0.00	0.00	0.00	2.66
1888	3361	5.014123	TGGGATGAACAGGAAGATAGTTTGT	59.986	40.000	0.00	0.00	0.00	2.83
1899	3373	8.306761	CAGGAAGATAGTTTGTAAAAGCCATTT	58.693	33.333	0.00	0.00	34.92	2.32
1934	3460	2.218603	TCAACGCAAAGAGGAAAGACC	58.781	47.619	0.00	0.00	39.35	3.85
2007	3543	5.007136	GTGCCTTCTGCTGATAAGTGATAAC	59.993	44.000	0.00	0.00	42.00	1.89
2430	5430	1.276421	ACAACGCAGGAGTTCTAGCAT	59.724	47.619	0.00	0.00	30.96	3.79
2517	5517	2.113774	CACAGGTTCCTGCAGGCA	59.886	61.111	28.91	15.88	37.57	4.75
2521	5521	2.045926	GGTTCCTGCAGGCATCGT	60.046	61.111	28.91	0.00	34.44	3.73
2541	5541	3.378112	CGTGTATCAGCAATTCCCACAAT	59.622	43.478	0.00	0.00	0.00	2.71
2555	5555	2.689983	CCCACAATAGCATTTCACTCCC	59.310	50.000	0.00	0.00	0.00	4.30
2575	5575	1.344953	TGGGTTCCTAGCGGCATGAT	61.345	55.000	1.45	0.00	0.00	2.45
2643	5643	4.624024	GTGGTGTGCATCAAGAAATCAATG	59.376	41.667	0.00	0.00	0.00	2.82
2650	5650	5.476254	TGCATCAAGAAATCAATGTACACCA	59.524	36.000	0.00	0.00	0.00	4.17
2671	5671	5.163055	ACCAACAGGTATTATGGCATGAGAT	60.163	40.000	10.98	4.27	36.37	2.75
2781	5782	5.029807	TGTCACAAGTAGTCAATTCACCA	57.970	39.130	0.00	0.00	0.00	4.17
2824	5826	3.947910	CAGATGGTGCTGGAATTTTGT	57.052	42.857	0.00	0.00	32.26	2.83
2825	5827	3.841643	CAGATGGTGCTGGAATTTTGTC	58.158	45.455	0.00	0.00	32.26	3.18
2826	5828	3.508793	CAGATGGTGCTGGAATTTTGTCT	59.491	43.478	0.00	0.00	32.26	3.41
2827	5829	4.701651	CAGATGGTGCTGGAATTTTGTCTA	59.298	41.667	0.00	0.00	32.26	2.59
2828	5830	5.359009	CAGATGGTGCTGGAATTTTGTCTAT	59.641	40.000	0.00	0.00	32.26	1.98
2829	5831	5.954150	AGATGGTGCTGGAATTTTGTCTATT	59.046	36.000	0.00	0.00	0.00	1.73
2830	5832	7.067372	CAGATGGTGCTGGAATTTTGTCTATTA	59.933	37.037	0.00	0.00	32.26	0.98
2831	5833	7.781693	AGATGGTGCTGGAATTTTGTCTATTAT	59.218	33.333	0.00	0.00	0.00	1.28
2832	5834	7.099266	TGGTGCTGGAATTTTGTCTATTATG	57.901	36.000	0.00	0.00	0.00	1.90
2833	5835	6.096705	TGGTGCTGGAATTTTGTCTATTATGG	59.903	38.462	0.00	0.00	0.00	2.74
2834	5836	6.461509	GGTGCTGGAATTTTGTCTATTATGGG	60.462	42.308	0.00	0.00	0.00	4.00
2835	5837	5.068987	TGCTGGAATTTTGTCTATTATGGGC	59.931	40.000	0.00	0.00	0.00	5.36
2836	5838	5.509670	GCTGGAATTTTGTCTATTATGGGCC	60.510	44.000	0.00	0.00	0.00	5.80
2837	5839	5.523588	TGGAATTTTGTCTATTATGGGCCA	58.476	37.500	9.61	9.61	0.00	5.36
2838	5840	5.598005	TGGAATTTTGTCTATTATGGGCCAG	59.402	40.000	13.78	0.00	0.00	4.85
2839	5841	5.509670	GGAATTTTGTCTATTATGGGCCAGC	60.510	44.000	13.78	0.00	0.00	4.85
2840	5842	2.656947	TTGTCTATTATGGGCCAGCC	57.343	50.000	13.78	0.00	0.00	4.85
2841	5843	1.517238	TGTCTATTATGGGCCAGCCA	58.483	50.000	13.78	0.00	37.98	4.75
2842	5844	1.849692	TGTCTATTATGGGCCAGCCAA	59.150	47.619	13.78	6.41	37.98	4.52
2843	5845	2.446666	TGTCTATTATGGGCCAGCCAAT	59.553	45.455	13.78	13.53	37.98	3.16
2844	5846	3.655291	TGTCTATTATGGGCCAGCCAATA	59.345	43.478	13.78	13.93	37.98	1.90
2845	5847	4.263462	TGTCTATTATGGGCCAGCCAATAG	60.263	45.833	25.21	25.21	33.81	1.73
2846	5848	1.928868	ATTATGGGCCAGCCAATAGC	58.071	50.000	13.78	0.00	44.25	2.97
2861	5863	5.105063	GCCAATAGCAGTTTCAGAAATTCC	58.895	41.667	0.00	0.00	42.97	3.01
2862	5864	5.105595	GCCAATAGCAGTTTCAGAAATTCCT	60.106	40.000	0.00	0.00	42.97	3.36
2863	5865	6.095440	GCCAATAGCAGTTTCAGAAATTCCTA	59.905	38.462	0.00	0.00	42.97	2.94
2864	5866	7.362920	GCCAATAGCAGTTTCAGAAATTCCTAA	60.363	37.037	0.00	0.00	42.97	2.69
2865	5867	8.689972	CCAATAGCAGTTTCAGAAATTCCTAAT	58.310	33.333	0.00	0.00	0.00	1.73
2871	5873	9.521503	GCAGTTTCAGAAATTCCTAATAAATCC	57.478	33.333	0.00	0.00	0.00	3.01
2878	5880	9.225436	CAGAAATTCCTAATAAATCCTAGAGGC	57.775	37.037	0.00	0.00	34.44	4.70
2879	5881	8.387039	AGAAATTCCTAATAAATCCTAGAGGCC	58.613	37.037	0.00	0.00	34.44	5.19
2880	5882	6.644308	ATTCCTAATAAATCCTAGAGGCCC	57.356	41.667	0.00	0.00	34.44	5.80
2881	5883	5.101254	TCCTAATAAATCCTAGAGGCCCA	57.899	43.478	0.00	0.00	34.44	5.36
2882	5884	4.844655	TCCTAATAAATCCTAGAGGCCCAC	59.155	45.833	0.00	0.00	34.44	4.61
2883	5885	3.771577	AATAAATCCTAGAGGCCCACG	57.228	47.619	0.00	0.00	34.44	4.94
2884	5886	0.756903	TAAATCCTAGAGGCCCACGC	59.243	55.000	0.00	0.00	34.44	5.34
2885	5887	1.271840	AAATCCTAGAGGCCCACGCA	61.272	55.000	0.00	0.00	36.38	5.24
2886	5888	1.690219	AATCCTAGAGGCCCACGCAG	61.690	60.000	0.00	0.00	36.38	5.18
2887	5889	4.537433	CCTAGAGGCCCACGCAGC	62.537	72.222	0.00	0.00	36.38	5.25
2905	5907	2.887360	CCATTCGGGCAAGGCAAG	59.113	61.111	0.00	0.00	0.00	4.01
2906	5908	1.678635	CCATTCGGGCAAGGCAAGA	60.679	57.895	0.00	0.00	0.00	3.02
2907	5909	1.660560	CCATTCGGGCAAGGCAAGAG	61.661	60.000	0.00	0.00	0.00	2.85
2908	5910	1.379044	ATTCGGGCAAGGCAAGAGG	60.379	57.895	0.00	0.00	0.00	3.69
2909	5911	2.142292	ATTCGGGCAAGGCAAGAGGT	62.142	55.000	0.00	0.00	0.00	3.85
2910	5912	3.058160	CGGGCAAGGCAAGAGGTG	61.058	66.667	0.00	0.00	0.00	4.00
2911	5913	2.677875	GGGCAAGGCAAGAGGTGG	60.678	66.667	0.00	0.00	0.00	4.61
2912	5914	2.436109	GGCAAGGCAAGAGGTGGA	59.564	61.111	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	4.764679	TGGTGCACAATCTACATGAAAC	57.235	40.909	20.43	0.00	0.00	2.78
86	88	3.058501	GTGACAATGTTAACTTCCACGGG	60.059	47.826	7.22	0.00	0.00	5.28
87	89	3.562141	TGTGACAATGTTAACTTCCACGG	59.438	43.478	7.22	0.00	0.00	4.94
167	185	9.772973	AGAACATAGACACACAGTAATTGTAAA	57.227	29.630	0.00	0.00	38.16	2.01
222	240	8.157476	AGATAGACAACACCAATAACAGAAACT	58.843	33.333	0.00	0.00	0.00	2.66
300	319	3.821033	ACAAACTGCATGGACTAACCTTC	59.179	43.478	0.00	0.00	39.86	3.46
369	389	2.437281	TCCAAATTGCCACACCAACATT	59.563	40.909	0.00	0.00	0.00	2.71
371	391	1.489481	TCCAAATTGCCACACCAACA	58.511	45.000	0.00	0.00	0.00	3.33
511	533	8.331931	ACTAGGTTAACTATGAAATCCATGGA	57.668	34.615	18.88	18.88	37.22	3.41
632	654	5.883328	TCGAACAGACAATTATCGTATGC	57.117	39.130	0.00	0.00	35.20	3.14
636	658	5.867174	TGTTCATCGAACAGACAATTATCGT	59.133	36.000	5.47	0.00	45.88	3.73
909	1150	0.251916	CAGCGTTGGGTCCCTATTCA	59.748	55.000	10.00	0.00	0.00	2.57
1239	1503	5.241506	GTCATTGTGAGTGAATTCCTTTGGA	59.758	40.000	2.27	0.00	0.00	3.53
1344	1608	7.073598	TCTGATTCCCCATAGTTAATGAATCCA	59.926	37.037	0.00	0.00	37.86	3.41
1351	1615	6.491403	GCACATTCTGATTCCCCATAGTTAAT	59.509	38.462	0.00	0.00	0.00	1.40
1381	1645	6.715347	ACCATTAAGACTTTTCACAGCTTT	57.285	33.333	0.00	0.00	0.00	3.51
1420	1684	6.489700	TGAGCTCTTCCAACATACAAAATTGA	59.510	34.615	16.19	0.00	0.00	2.57
1595	1859	4.316645	CTTGCATGATCCTATCTCACCAG	58.683	47.826	0.00	0.00	0.00	4.00
1650	1914	6.328672	AGAAGGTGAGCCATGATACTAAGAAT	59.671	38.462	0.00	0.00	37.19	2.40
1800	2065	0.819582	GTCAACTGGATGCATTGGGG	59.180	55.000	0.00	0.00	0.00	4.96
1839	2727	9.941664	CATCAATCTACCACATTGATTAAAGAC	57.058	33.333	5.36	0.00	44.96	3.01
1886	3359	6.821388	ACACCAACATAAAATGGCTTTTACA	58.179	32.000	0.00	0.00	39.10	2.41
1888	3361	7.039363	AGCTACACCAACATAAAATGGCTTTTA	60.039	33.333	0.00	2.24	40.51	1.52
1899	3373	2.739913	GCGTTGAGCTACACCAACATAA	59.260	45.455	14.29	0.00	41.85	1.90
1934	3460	2.035193	AGACATACCACTAGCATCGCTG	59.965	50.000	0.00	0.00	40.10	5.18
2377	4353	5.591099	CAAAGTGTGCCTAGAAACAATGTT	58.409	37.500	0.00	0.00	0.00	2.71
2411	4387	1.929836	GATGCTAGAACTCCTGCGTTG	59.070	52.381	0.00	0.00	0.00	4.10
2430	5430	3.797184	GCAAAATTTTGTGGTACTGCGGA	60.797	43.478	27.13	0.00	40.24	5.54
2517	5517	3.206150	GTGGGAATTGCTGATACACGAT	58.794	45.455	0.00	0.00	0.00	3.73
2521	5521	4.580167	GCTATTGTGGGAATTGCTGATACA	59.420	41.667	0.00	0.00	0.00	2.29
2541	5541	1.668826	ACCCAGGGAGTGAAATGCTA	58.331	50.000	14.54	0.00	0.00	3.49
2555	5555	1.524621	CATGCCGCTAGGAACCCAG	60.525	63.158	0.00	0.00	41.02	4.45
2575	5575	5.983540	TCGGCATGTTATATGTATATGGCA	58.016	37.500	16.73	0.00	42.39	4.92
2650	5650	7.826252	GTCATATCTCATGCCATAATACCTGTT	59.174	37.037	0.00	0.00	0.00	3.16
2733	5734	4.722700	ACATGGGCACGGCTGGAC	62.723	66.667	0.00	0.00	0.00	4.02
2781	5782	5.534654	TGCATAGTAAAAGCACCAAAGTCTT	59.465	36.000	0.00	0.00	32.55	3.01
2813	5815	5.598005	TGGCCCATAATAGACAAAATTCCAG	59.402	40.000	0.00	0.00	0.00	3.86
2814	5816	5.523588	TGGCCCATAATAGACAAAATTCCA	58.476	37.500	0.00	0.00	0.00	3.53
2815	5817	5.509670	GCTGGCCCATAATAGACAAAATTCC	60.510	44.000	0.00	0.00	0.00	3.01
2816	5818	5.509670	GGCTGGCCCATAATAGACAAAATTC	60.510	44.000	0.00	0.00	0.00	2.17
2817	5819	4.344968	GGCTGGCCCATAATAGACAAAATT	59.655	41.667	0.00	0.00	0.00	1.82
2818	5820	3.897505	GGCTGGCCCATAATAGACAAAAT	59.102	43.478	0.00	0.00	0.00	1.82
2819	5821	3.295973	GGCTGGCCCATAATAGACAAAA	58.704	45.455	0.00	0.00	0.00	2.44
2820	5822	2.243478	TGGCTGGCCCATAATAGACAAA	59.757	45.455	9.28	0.00	39.18	2.83
2821	5823	1.849692	TGGCTGGCCCATAATAGACAA	59.150	47.619	9.28	0.00	39.18	3.18
2822	5824	1.517238	TGGCTGGCCCATAATAGACA	58.483	50.000	9.28	0.00	39.18	3.41
2823	5825	2.656947	TTGGCTGGCCCATAATAGAC	57.343	50.000	9.28	0.00	44.89	2.59
2824	5826	3.308402	GCTATTGGCTGGCCCATAATAGA	60.308	47.826	22.94	1.49	44.89	1.98
2825	5827	3.019564	GCTATTGGCTGGCCCATAATAG	58.980	50.000	18.14	18.14	44.89	1.73
2826	5828	2.378208	TGCTATTGGCTGGCCCATAATA	59.622	45.455	9.28	6.03	44.89	0.98
2827	5829	1.147608	TGCTATTGGCTGGCCCATAAT	59.852	47.619	9.28	5.20	44.89	1.28
2828	5830	0.555280	TGCTATTGGCTGGCCCATAA	59.445	50.000	9.28	0.00	44.89	1.90
2829	5831	0.111061	CTGCTATTGGCTGGCCCATA	59.889	55.000	9.28	7.14	44.89	2.74
2830	5832	1.152610	CTGCTATTGGCTGGCCCAT	60.153	57.895	9.28	6.30	44.89	4.00
2831	5833	2.153898	AACTGCTATTGGCTGGCCCA	62.154	55.000	9.28	0.00	42.95	5.36
2832	5834	0.972471	AAACTGCTATTGGCTGGCCC	60.972	55.000	9.28	0.00	42.95	5.80
2833	5835	0.457443	GAAACTGCTATTGGCTGGCC	59.543	55.000	4.43	4.43	42.95	5.36
2834	5836	1.133790	CTGAAACTGCTATTGGCTGGC	59.866	52.381	4.06	0.00	42.95	4.85
2835	5837	2.715046	TCTGAAACTGCTATTGGCTGG	58.285	47.619	4.06	0.00	42.95	4.85
2836	5838	4.771590	TTTCTGAAACTGCTATTGGCTG	57.228	40.909	0.00	0.00	44.00	4.85
2837	5839	5.105595	GGAATTTCTGAAACTGCTATTGGCT	60.106	40.000	4.73	0.00	42.39	4.75
2838	5840	5.105063	GGAATTTCTGAAACTGCTATTGGC	58.895	41.667	4.73	0.00	42.22	4.52
2839	5841	6.521151	AGGAATTTCTGAAACTGCTATTGG	57.479	37.500	3.77	0.00	0.00	3.16
2845	5847	9.521503	GGATTTATTAGGAATTTCTGAAACTGC	57.478	33.333	4.73	0.00	0.00	4.40
2852	5854	9.225436	GCCTCTAGGATTTATTAGGAATTTCTG	57.775	37.037	0.00	0.00	37.39	3.02
2853	5855	8.387039	GGCCTCTAGGATTTATTAGGAATTTCT	58.613	37.037	0.00	0.00	37.39	2.52
2854	5856	7.612244	GGGCCTCTAGGATTTATTAGGAATTTC	59.388	40.741	0.84	0.00	37.39	2.17
2855	5857	7.075009	TGGGCCTCTAGGATTTATTAGGAATTT	59.925	37.037	4.53	0.00	37.39	1.82
2856	5858	6.566480	TGGGCCTCTAGGATTTATTAGGAATT	59.434	38.462	4.53	0.00	37.39	2.17
2857	5859	6.012421	GTGGGCCTCTAGGATTTATTAGGAAT	60.012	42.308	4.53	0.00	37.39	3.01
2858	5860	5.309806	GTGGGCCTCTAGGATTTATTAGGAA	59.690	44.000	4.53	0.00	37.39	3.36
2859	5861	4.844655	GTGGGCCTCTAGGATTTATTAGGA	59.155	45.833	4.53	0.00	37.39	2.94
2860	5862	4.322801	CGTGGGCCTCTAGGATTTATTAGG	60.323	50.000	4.53	0.00	37.39	2.69
2861	5863	4.822026	CGTGGGCCTCTAGGATTTATTAG	58.178	47.826	4.53	0.00	37.39	1.73
2862	5864	3.007614	GCGTGGGCCTCTAGGATTTATTA	59.992	47.826	4.53	0.00	37.39	0.98
2863	5865	2.224548	GCGTGGGCCTCTAGGATTTATT	60.225	50.000	4.53	0.00	37.39	1.40
2864	5866	1.348036	GCGTGGGCCTCTAGGATTTAT	59.652	52.381	4.53	0.00	37.39	1.40
2865	5867	0.756903	GCGTGGGCCTCTAGGATTTA	59.243	55.000	4.53	0.00	37.39	1.40
2866	5868	1.271840	TGCGTGGGCCTCTAGGATTT	61.272	55.000	4.53	0.00	38.85	2.17
2867	5869	1.689233	TGCGTGGGCCTCTAGGATT	60.689	57.895	4.53	0.00	38.85	3.01
2868	5870	2.041922	TGCGTGGGCCTCTAGGAT	60.042	61.111	4.53	0.00	38.85	3.24
2869	5871	2.759973	CTGCGTGGGCCTCTAGGA	60.760	66.667	4.53	0.00	38.85	2.94
2870	5872	4.537433	GCTGCGTGGGCCTCTAGG	62.537	72.222	4.53	0.00	38.85	3.02
2871	5873	4.537433	GGCTGCGTGGGCCTCTAG	62.537	72.222	4.53	3.75	45.57	2.43
2888	5890	1.660560	CTCTTGCCTTGCCCGAATGG	61.661	60.000	0.00	0.00	37.09	3.16
2889	5891	1.660560	CCTCTTGCCTTGCCCGAATG	61.661	60.000	0.00	0.00	0.00	2.67
2890	5892	1.379044	CCTCTTGCCTTGCCCGAAT	60.379	57.895	0.00	0.00	0.00	3.34
2891	5893	2.034066	CCTCTTGCCTTGCCCGAA	59.966	61.111	0.00	0.00	0.00	4.30
2892	5894	3.249189	ACCTCTTGCCTTGCCCGA	61.249	61.111	0.00	0.00	0.00	5.14
2893	5895	3.058160	CACCTCTTGCCTTGCCCG	61.058	66.667	0.00	0.00	0.00	6.13
2894	5896	2.677875	CCACCTCTTGCCTTGCCC	60.678	66.667	0.00	0.00	0.00	5.36
2895	5897	2.436109	TCCACCTCTTGCCTTGCC	59.564	61.111	0.00	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.