AutoCloner

Multiple sequence alignment - TraesCS7D01G129600

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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	TraesCS7D01G129600	chr7D	100.000	2782	0	0	1	2782	81793917	81791136	0.000000e+00	5138
1	TraesCS7D01G129600	chr7D	96.109	771	16	4	1	768	123459736	123458977	0.000000e+00	1245
2	TraesCS7D01G129600	chr7D	95.478	774	15	9	1	769	156770090	156770848	0.000000e+00	1218
3	TraesCS7D01G129600	chr7D	94.974	776	18	7	1	769	186827651	186826890	0.000000e+00	1197
4	TraesCS7D01G129600	chr7D	95.065	770	20	7	3	769	557193004	557193758	0.000000e+00	1195
5	TraesCS7D01G129600	chr7D	93.429	487	26	4	1872	2355	565209942	565209459	0.000000e+00	717
6	TraesCS7D01G129600	chr7D	91.716	507	29	8	1859	2356	75313920	75313418	0.000000e+00	691
7	TraesCS7D01G129600	chr7D	92.261	491	31	4	1869	2356	562193019	562193505	0.000000e+00	689
8	TraesCS7D01G129600	chr7D	94.553	257	13	1	2436	2692	565207681	565207426	2.010000e-106	396
9	TraesCS7D01G129600	chr7A	93.846	1040	49	7	787	1812	83750453	83749415	0.000000e+00	1552
10	TraesCS7D01G129600	chr7A	91.398	93	6	2	2690	2782	83749409	83749319	2.910000e-25	126
11	TraesCS7D01G129600	chr7B	94.066	910	39	6	917	1812	28945248	28944340	0.000000e+00	1367
12	TraesCS7D01G129600	chr7B	96.774	124	4	0	787	910	28952057	28951934	1.010000e-49	207
13	TraesCS7D01G129600	chr7B	98.413	63	1	0	787	849	28952216	28952278	8.150000e-21	111
14	TraesCS7D01G129600	chr7B	98.413	63	1	0	787	849	28960235	28960173	8.150000e-21	111
15	TraesCS7D01G129600	chr6D	95.343	773	18	7	1	768	20132776	20132017	0.000000e+00	1212
16	TraesCS7D01G129600	chr6D	95.026	784	15	8	1	777	426894409	426895175	0.000000e+00	1210
17	TraesCS7D01G129600	chr6D	94.422	251	14	0	2436	2686	363852475	363852225	1.210000e-103	387
18	TraesCS7D01G129600	chr6D	97.561	82	1	1	2355	2435	433304700	433304781	3.740000e-29	139
19	TraesCS7D01G129600	chr6B	93.023	774	32	17	3	769	509255964	509255206	0.000000e+00	1110
20	TraesCS7D01G129600	chr1B	92.903	775	28	14	3	769	47169122	47168367	0.000000e+00	1101
21	TraesCS7D01G129600	chrUn	92.377	774	35	14	3	769	81989489	81988733	0.000000e+00	1081
22	TraesCS7D01G129600	chr4D	92.929	495	24	7	1869	2356	476862159	476862649	0.000000e+00	710
23	TraesCS7D01G129600	chr5D	92.843	489	26	5	1873	2356	431559421	431559905	0.000000e+00	701
24	TraesCS7D01G129600	chr5D	94.118	255	15	0	2436	2690	487589613	487589867	3.360000e-104	388
25	TraesCS7D01G129600	chr5D	92.917	240	16	1	2432	2671	382504759	382504997	5.700000e-92	348
26	TraesCS7D01G129600	chr5D	97.561	82	1	1	2355	2435	6998700	6998781	3.740000e-29	139
27	TraesCS7D01G129600	chr5D	94.318	88	4	1	2349	2435	382504635	382504722	1.740000e-27	134
28	TraesCS7D01G129600	chr5D	94.318	88	4	1	2349	2435	487589486	487589573	1.740000e-27	134
29	TraesCS7D01G129600	chr2D	92.480	492	25	8	1873	2356	367989443	367988956	0.000000e+00	693
30	TraesCS7D01G129600	chr2D	92.480	492	25	8	1872	2356	586776499	586776013	0.000000e+00	693
31	TraesCS7D01G129600	chr2D	92.089	493	31	5	1869	2356	6862855	6863344	0.000000e+00	688
32	TraesCS7D01G129600	chr2D	92.229	489	28	6	1869	2354	562893175	562893656	0.000000e+00	684
33	TraesCS7D01G129600	chr2D	93.774	257	15	1	2436	2692	386482273	386482018	4.350000e-103	385
34	TraesCS7D01G129600	chr4A	89.846	325	29	1	2368	2692	73446573	73446893	5.540000e-112	414
35	TraesCS7D01G129600	chr5A	94.163	257	15	0	2436	2692	580928048	580927792	2.600000e-105	392
36	TraesCS7D01G129600	chr1D	94.163	257	15	0	2436	2692	457215498	457215242	2.600000e-105	392
37	TraesCS7D01G129600	chr1D	94.118	255	15	0	2436	2690	433907963	433907709	3.360000e-104	388
38	TraesCS7D01G129600	chr1D	79.443	287	48	9	997	1279	86093076	86093355	2.830000e-45	193
39	TraesCS7D01G129600	chr1D	100.000	81	0	0	2355	2435	324703638	324703558	1.730000e-32	150
40	TraesCS7D01G129600	chr1D	94.318	88	4	1	2349	2435	310855783	310855870	1.740000e-27	134
41	TraesCS7D01G129600	chr3A	94.118	255	15	0	2436	2690	123047091	123046837	3.360000e-104	388
42	TraesCS7D01G129600	chr3D	97.590	83	0	2	2355	2435	594816613	594816531	1.040000e-29	141
43	TraesCS7D01G129600	chr3D	96.296	81	3	0	2355	2435	44879425	44879345	1.740000e-27	134

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	TraesCS7D01G129600	chr7D	81791136	81793917	2781	True	5138.0	5138	100.000	1	2782	1	chr7D.!!$R2	2781
1	TraesCS7D01G129600	chr7D	123458977	123459736	759	True	1245.0	1245	96.109	1	768	1	chr7D.!!$R3	767
2	TraesCS7D01G129600	chr7D	156770090	156770848	758	False	1218.0	1218	95.478	1	769	1	chr7D.!!$F1	768
3	TraesCS7D01G129600	chr7D	186826890	186827651	761	True	1197.0	1197	94.974	1	769	1	chr7D.!!$R4	768
4	TraesCS7D01G129600	chr7D	557193004	557193758	754	False	1195.0	1195	95.065	3	769	1	chr7D.!!$F2	766
5	TraesCS7D01G129600	chr7D	75313418	75313920	502	True	691.0	691	91.716	1859	2356	1	chr7D.!!$R1	497
6	TraesCS7D01G129600	chr7D	565207426	565209942	2516	True	556.5	717	93.991	1872	2692	2	chr7D.!!$R5	820
7	TraesCS7D01G129600	chr7A	83749319	83750453	1134	True	839.0	1552	92.622	787	2782	2	chr7A.!!$R1	1995
8	TraesCS7D01G129600	chr7B	28944340	28945248	908	True	1367.0	1367	94.066	917	1812	1	chr7B.!!$R1	895
9	TraesCS7D01G129600	chr6D	20132017	20132776	759	True	1212.0	1212	95.343	1	768	1	chr6D.!!$R1	767
10	TraesCS7D01G129600	chr6D	426894409	426895175	766	False	1210.0	1210	95.026	1	777	1	chr6D.!!$F1	776
11	TraesCS7D01G129600	chr6B	509255206	509255964	758	True	1110.0	1110	93.023	3	769	1	chr6B.!!$R1	766
12	TraesCS7D01G129600	chr1B	47168367	47169122	755	True	1101.0	1101	92.903	3	769	1	chr1B.!!$R1	766
13	TraesCS7D01G129600	chrUn	81988733	81989489	756	True	1081.0	1081	92.377	3	769	1	chrUn.!!$R1	766

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
883	905	0.531974	TGCCGGATTCCATTACGCTC	60.532	55.0	5.05	0.0	0.0	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1832	1875	0.036388	CTGCCCAGTCGCTAAAAGGA	60.036	55.0	0.0	0.0	0.0	3.36	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
511	532	0.822164	AGGTAACAGGTTCGATCCCG	59.178	55.000	8.95	1.38	41.41	5.14
599	621	3.901222	CCAGGGGTTTTTCCACATAAACT	59.099	43.478	0.00	0.00	43.37	2.66
634	656	4.988716	TCGTCAGGGCCGTGGACT	62.989	66.667	24.54	0.00	0.00	3.85
746	768	3.058983	CACATTCGTAGCAAGTTCAAGCA	60.059	43.478	0.00	0.00	0.00	3.91
747	769	3.058914	ACATTCGTAGCAAGTTCAAGCAC	60.059	43.478	0.00	0.00	0.00	4.40
748	770	2.232756	TCGTAGCAAGTTCAAGCACA	57.767	45.000	0.00	0.00	0.00	4.57
769	791	3.604875	ACCAGTGGTGTAATTACCTCG	57.395	47.619	15.86	0.00	41.43	4.63
770	792	2.901839	ACCAGTGGTGTAATTACCTCGT	59.098	45.455	15.86	0.00	41.43	4.18
772	794	4.159135	ACCAGTGGTGTAATTACCTCGTAG	59.841	45.833	15.86	0.07	41.43	3.51
775	797	6.392354	CAGTGGTGTAATTACCTCGTAGAAA	58.608	40.000	13.01	0.00	41.43	2.52
776	798	6.869913	CAGTGGTGTAATTACCTCGTAGAAAA	59.130	38.462	13.01	0.00	41.43	2.29
777	799	7.385752	CAGTGGTGTAATTACCTCGTAGAAAAA	59.614	37.037	13.01	0.00	41.43	1.94
778	800	7.601508	AGTGGTGTAATTACCTCGTAGAAAAAG	59.398	37.037	13.01	0.00	41.43	2.27
779	801	7.599998	GTGGTGTAATTACCTCGTAGAAAAAGA	59.400	37.037	13.01	0.00	41.43	2.52
780	802	8.149647	TGGTGTAATTACCTCGTAGAAAAAGAA	58.850	33.333	13.01	0.00	41.43	2.52
781	803	8.992073	GGTGTAATTACCTCGTAGAAAAAGAAA	58.008	33.333	13.01	0.00	37.74	2.52
783	805	9.211485	TGTAATTACCTCGTAGAAAAAGAAAGG	57.789	33.333	13.01	0.00	34.09	3.11
784	806	9.212641	GTAATTACCTCGTAGAAAAAGAAAGGT	57.787	33.333	4.11	0.00	39.01	3.50
785	807	7.902387	ATTACCTCGTAGAAAAAGAAAGGTC	57.098	36.000	0.00	0.00	36.97	3.85
807	829	2.571216	CCTCGTCAACCCGGTCACT	61.571	63.158	0.00	0.00	0.00	3.41
864	886	3.338126	GACGATCCACGCCGACTGT	62.338	63.158	0.00	0.00	46.94	3.55
883	905	0.531974	TGCCGGATTCCATTACGCTC	60.532	55.000	5.05	0.00	0.00	5.03
915	945	2.664851	TTCGTGCAGGTCCGCTTG	60.665	61.111	6.26	1.07	0.00	4.01
938	968	2.042843	CCCGCACCCTCCTAGTCT	60.043	66.667	0.00	0.00	0.00	3.24
1018	1048	3.243234	CCAGATGCTCCAGTACTTCTACG	60.243	52.174	0.00	0.00	0.00	3.51
1029	1059	0.677842	ACTTCTACGGCAAGGTCGTT	59.322	50.000	0.00	0.00	42.79	3.85
1342	1375	1.135199	GGCTGACGGACAATTACTCGA	60.135	52.381	0.00	0.00	0.00	4.04
1349	1388	2.627945	GGACAATTACTCGATGTGCCA	58.372	47.619	0.00	0.00	30.23	4.92
1452	1492	2.019249	TCCATAAGGTGTACGTCCTCG	58.981	52.381	9.38	3.14	38.48	4.63
1698	1738	2.604686	ACCTCAAGAGCGGCAGGA	60.605	61.111	9.99	0.00	0.00	3.86
1716	1756	1.550976	GGATGAAGAAGGTCAGGTCGT	59.449	52.381	0.00	0.00	0.00	4.34
1782	1825	0.110056	TTCGACGGTCTCAACGTAGC	60.110	55.000	6.57	0.00	45.68	3.58
1783	1826	1.513586	CGACGGTCTCAACGTAGCC	60.514	63.158	6.57	0.00	45.68	3.93
1784	1827	1.582968	GACGGTCTCAACGTAGCCA	59.417	57.895	0.00	0.00	45.68	4.75
1785	1828	0.731855	GACGGTCTCAACGTAGCCAC	60.732	60.000	0.00	0.00	45.68	5.01
1786	1829	1.445582	CGGTCTCAACGTAGCCACC	60.446	63.158	0.00	0.00	0.00	4.61
1787	1830	1.669440	GGTCTCAACGTAGCCACCA	59.331	57.895	0.00	0.00	0.00	4.17
1788	1831	0.389948	GGTCTCAACGTAGCCACCAG	60.390	60.000	0.00	0.00	0.00	4.00
1789	1832	1.014564	GTCTCAACGTAGCCACCAGC	61.015	60.000	0.00	0.00	44.25	4.85
1798	1841	2.727544	GCCACCAGCTTTTCGCAA	59.272	55.556	0.00	0.00	42.61	4.85
1799	1842	1.290009	GCCACCAGCTTTTCGCAAT	59.710	52.632	0.00	0.00	42.61	3.56
1800	1843	0.733909	GCCACCAGCTTTTCGCAATC	60.734	55.000	0.00	0.00	42.61	2.67
1801	1844	0.597568	CCACCAGCTTTTCGCAATCA	59.402	50.000	0.00	0.00	42.61	2.57
1802	1845	1.000385	CCACCAGCTTTTCGCAATCAA	60.000	47.619	0.00	0.00	42.61	2.57
1803	1846	2.353011	CCACCAGCTTTTCGCAATCAAT	60.353	45.455	0.00	0.00	42.61	2.57
1804	1847	2.919229	CACCAGCTTTTCGCAATCAATC	59.081	45.455	0.00	0.00	42.61	2.67
1805	1848	2.821969	ACCAGCTTTTCGCAATCAATCT	59.178	40.909	0.00	0.00	42.61	2.40
1806	1849	3.119708	ACCAGCTTTTCGCAATCAATCTC	60.120	43.478	0.00	0.00	42.61	2.75
1807	1850	3.119743	CCAGCTTTTCGCAATCAATCTCA	60.120	43.478	0.00	0.00	42.61	3.27
1808	1851	4.478699	CAGCTTTTCGCAATCAATCTCAA	58.521	39.130	0.00	0.00	42.61	3.02
1809	1852	4.919168	CAGCTTTTCGCAATCAATCTCAAA	59.081	37.500	0.00	0.00	42.61	2.69
1810	1853	5.575606	CAGCTTTTCGCAATCAATCTCAAAT	59.424	36.000	0.00	0.00	42.61	2.32
1811	1854	6.090358	CAGCTTTTCGCAATCAATCTCAAATT	59.910	34.615	0.00	0.00	42.61	1.82
1812	1855	6.647895	AGCTTTTCGCAATCAATCTCAAATTT	59.352	30.769	0.00	0.00	42.61	1.82
1813	1856	6.952083	GCTTTTCGCAATCAATCTCAAATTTC	59.048	34.615	0.00	0.00	38.92	2.17
1814	1857	7.148689	GCTTTTCGCAATCAATCTCAAATTTCT	60.149	33.333	0.00	0.00	38.92	2.52
1815	1858	7.801547	TTTCGCAATCAATCTCAAATTTCTC	57.198	32.000	0.00	0.00	0.00	2.87
1816	1859	6.499234	TCGCAATCAATCTCAAATTTCTCA	57.501	33.333	0.00	0.00	0.00	3.27
1817	1860	6.912082	TCGCAATCAATCTCAAATTTCTCAA	58.088	32.000	0.00	0.00	0.00	3.02
1818	1861	7.541162	TCGCAATCAATCTCAAATTTCTCAAT	58.459	30.769	0.00	0.00	0.00	2.57
1819	1862	8.676401	TCGCAATCAATCTCAAATTTCTCAATA	58.324	29.630	0.00	0.00	0.00	1.90
1820	1863	8.955002	CGCAATCAATCTCAAATTTCTCAATAG	58.045	33.333	0.00	0.00	0.00	1.73
1821	1864	9.798994	GCAATCAATCTCAAATTTCTCAATAGT	57.201	29.630	0.00	0.00	0.00	2.12
1842	1885	9.620660	AATAGTGTTATTTGTTTCCTTTTAGCG	57.379	29.630	0.00	0.00	0.00	4.26
1843	1886	7.266922	AGTGTTATTTGTTTCCTTTTAGCGA	57.733	32.000	0.00	0.00	0.00	4.93
1844	1887	7.136772	AGTGTTATTTGTTTCCTTTTAGCGAC	58.863	34.615	0.00	0.00	0.00	5.19
1845	1888	7.012989	AGTGTTATTTGTTTCCTTTTAGCGACT	59.987	33.333	0.00	0.00	0.00	4.18
1846	1889	7.112984	GTGTTATTTGTTTCCTTTTAGCGACTG	59.887	37.037	0.00	0.00	0.00	3.51
1847	1890	4.561735	TTTGTTTCCTTTTAGCGACTGG	57.438	40.909	0.00	0.00	0.00	4.00
1848	1891	2.500229	TGTTTCCTTTTAGCGACTGGG	58.500	47.619	0.00	0.00	0.00	4.45
1849	1892	1.199327	GTTTCCTTTTAGCGACTGGGC	59.801	52.381	0.00	0.00	0.00	5.36
1850	1893	0.398696	TTCCTTTTAGCGACTGGGCA	59.601	50.000	0.00	0.00	34.64	5.36
1851	1894	0.036388	TCCTTTTAGCGACTGGGCAG	60.036	55.000	0.00	0.00	34.64	4.85
1852	1895	1.648467	CCTTTTAGCGACTGGGCAGC	61.648	60.000	0.00	0.00	34.64	5.25
1853	1896	1.970917	CTTTTAGCGACTGGGCAGCG	61.971	60.000	0.00	0.00	35.78	5.18
1854	1897	2.443260	TTTTAGCGACTGGGCAGCGA	62.443	55.000	0.00	0.00	35.78	4.93
1855	1898	3.642778	TTAGCGACTGGGCAGCGAC	62.643	63.158	0.00	0.00	35.78	5.19
1864	1907	2.023320	GGCAGCGACGCAATAAGC	59.977	61.111	23.70	16.24	40.87	3.09
1895	1938	2.452767	GGACGACCCGTTTCATCAC	58.547	57.895	0.00	0.00	41.37	3.06
1898	1941	2.098233	CGACCCGTTTCATCACCCG	61.098	63.158	0.00	0.00	0.00	5.28
1899	1942	2.359478	ACCCGTTTCATCACCCGC	60.359	61.111	0.00	0.00	0.00	6.13
1900	1943	3.496131	CCCGTTTCATCACCCGCG	61.496	66.667	0.00	0.00	0.00	6.46
1901	1944	2.740826	CCGTTTCATCACCCGCGT	60.741	61.111	4.92	0.00	0.00	6.01
1902	1945	2.736682	CCGTTTCATCACCCGCGTC	61.737	63.158	4.92	0.00	0.00	5.19
1903	1946	1.736645	CGTTTCATCACCCGCGTCT	60.737	57.895	4.92	0.00	0.00	4.18
1904	1947	1.787847	GTTTCATCACCCGCGTCTG	59.212	57.895	4.92	0.00	0.00	3.51
1907	1952	0.250124	TTCATCACCCGCGTCTGTTT	60.250	50.000	4.92	0.00	0.00	2.83
1913	1958	2.355363	CCGCGTCTGTTTGGTCGA	60.355	61.111	4.92	0.00	0.00	4.20
1933	1978	2.978010	CGGACAAAAGTGGCGGCT	60.978	61.111	11.43	0.00	31.03	5.52
1996	2041	4.115199	GCGACCCATTCCAGGCCT	62.115	66.667	0.00	0.00	0.00	5.19
2096	2147	2.993471	GCAGCCACCAACATTCCCG	61.993	63.158	0.00	0.00	0.00	5.14
2097	2148	2.676471	AGCCACCAACATTCCCGC	60.676	61.111	0.00	0.00	0.00	6.13
2098	2149	3.758931	GCCACCAACATTCCCGCC	61.759	66.667	0.00	0.00	0.00	6.13
2121	2172	2.486370	CCCATTTTCCCCAAAAACGCTT	60.486	45.455	0.00	0.00	39.59	4.68
2300	2352	2.048222	CCGAAGAAGGCGCTGACA	60.048	61.111	7.64	0.00	0.00	3.58
2367	4065	2.181525	CCGCGGGCCATCTTTTTG	59.818	61.111	20.10	0.00	0.00	2.44
2383	4093	0.322906	TTTGTATGCCGGCATGACCA	60.323	50.000	44.59	33.96	39.03	4.02
2449	4198	8.723942	TTTTTGTGTGCAACTATGGTATTTTT	57.276	26.923	0.00	0.00	38.04	1.94
2635	4384	4.668118	GACGGCCGACCCAAACGA	62.668	66.667	35.90	0.00	0.00	3.85
2656	4405	1.202359	ACAAAAAGCGGACAAATGCGT	60.202	42.857	0.00	0.00	42.52	5.24
2657	4406	1.857837	CAAAAAGCGGACAAATGCGTT	59.142	42.857	0.00	0.00	42.52	4.84
2695	4444	2.369394	CATTGGAGTTGCTCTTACCCC	58.631	52.381	0.00	0.00	0.00	4.95
2702	4451	2.716969	AGTTGCTCTTACCCCTCCTTTT	59.283	45.455	0.00	0.00	0.00	2.27
2703	4452	3.082548	GTTGCTCTTACCCCTCCTTTTC	58.917	50.000	0.00	0.00	0.00	2.29
2704	4453	2.632537	TGCTCTTACCCCTCCTTTTCT	58.367	47.619	0.00	0.00	0.00	2.52
2753	4502	5.918576	GCCGTTAAGCAAGACTAAATTTGTT	59.081	36.000	0.00	0.00	0.00	2.83
2762	4511	8.135529	AGCAAGACTAAATTTGTTTTACACTCC	58.864	33.333	0.00	0.00	0.00	3.85
2764	4513	9.965824	CAAGACTAAATTTGTTTTACACTCCAT	57.034	29.630	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
599	621	3.490851	GGCACCCCAAGTGTCCTA	58.509	61.111	0.00	0.00	45.87	2.94
656	678	4.009675	ACTTGACATGGACGTGCAAATAT	58.990	39.130	15.51	0.00	0.00	1.28
733	755	1.406539	CTGGTTGTGCTTGAACTTGCT	59.593	47.619	0.00	0.00	0.00	3.91
746	768	4.648651	GAGGTAATTACACCACTGGTTGT	58.351	43.478	17.16	3.47	41.40	3.32
747	769	3.682858	CGAGGTAATTACACCACTGGTTG	59.317	47.826	17.16	0.00	41.40	3.77
748	770	3.325716	ACGAGGTAATTACACCACTGGTT	59.674	43.478	17.16	0.00	41.40	3.67
769	791	4.143194	GGTGCGACCTTTCTTTTTCTAC	57.857	45.455	0.00	0.00	34.73	2.59
782	804	2.737376	GGTTGACGAGGTGCGACC	60.737	66.667	0.00	0.00	44.57	4.79
783	805	2.737376	GGGTTGACGAGGTGCGAC	60.737	66.667	0.00	0.00	44.57	5.19
784	806	4.351938	CGGGTTGACGAGGTGCGA	62.352	66.667	0.00	0.00	44.57	5.10
831	853	2.046314	GTCCCCATGGTGGTGACG	60.046	66.667	11.73	0.00	35.17	4.35
864	886	0.531974	GAGCGTAATGGAATCCGGCA	60.532	55.000	0.00	0.00	0.00	5.69
919	949	4.400251	ACTAGGAGGGTGCGGGCT	62.400	66.667	0.00	0.00	0.00	5.19
993	1023	2.848678	AGTACTGGAGCATCTGGGTA	57.151	50.000	0.00	0.00	33.73	3.69
1018	1048	1.446272	CCGAGAGAACGACCTTGCC	60.446	63.158	0.00	0.00	35.09	4.52
1279	1312	4.148825	GTCCTGATCCGCCAGCGT	62.149	66.667	11.55	0.00	37.81	5.07
1342	1375	0.771127	ACCAGGTACTTGTGGCACAT	59.229	50.000	22.73	10.27	37.30	3.21
1349	1388	2.747686	CCGCCACCAGGTACTTGT	59.252	61.111	4.10	0.00	34.60	3.16
1504	1544	0.878961	GTTGTTCAGCCCGACGAACT	60.879	55.000	0.00	0.00	41.67	3.01
1641	1681	3.741476	CTGAAAGCCACGCCTGCC	61.741	66.667	0.00	0.00	0.00	4.85
1655	1695	2.125552	CCGATGCACCGCTTCTGA	60.126	61.111	0.00	0.00	31.76	3.27
1698	1738	1.550976	GGACGACCTGACCTTCTTCAT	59.449	52.381	0.00	0.00	0.00	2.57
1789	1832	8.236084	AGAAATTTGAGATTGATTGCGAAAAG	57.764	30.769	0.00	0.00	0.00	2.27
1790	1833	7.866898	TGAGAAATTTGAGATTGATTGCGAAAA	59.133	29.630	0.00	0.00	0.00	2.29
1791	1834	7.369607	TGAGAAATTTGAGATTGATTGCGAAA	58.630	30.769	0.00	0.00	0.00	3.46
1792	1835	6.912082	TGAGAAATTTGAGATTGATTGCGAA	58.088	32.000	0.00	0.00	0.00	4.70
1793	1836	6.499234	TGAGAAATTTGAGATTGATTGCGA	57.501	33.333	0.00	0.00	0.00	5.10
1794	1837	7.751047	ATTGAGAAATTTGAGATTGATTGCG	57.249	32.000	0.00	0.00	0.00	4.85
1795	1838	9.798994	ACTATTGAGAAATTTGAGATTGATTGC	57.201	29.630	0.00	0.00	0.00	3.56
1816	1859	9.620660	CGCTAAAAGGAAACAAATAACACTATT	57.379	29.630	0.00	0.00	0.00	1.73
1817	1860	9.005777	TCGCTAAAAGGAAACAAATAACACTAT	57.994	29.630	0.00	0.00	0.00	2.12
1818	1861	8.284693	GTCGCTAAAAGGAAACAAATAACACTA	58.715	33.333	0.00	0.00	0.00	2.74
1819	1862	7.012989	AGTCGCTAAAAGGAAACAAATAACACT	59.987	33.333	0.00	0.00	0.00	3.55
1820	1863	7.112984	CAGTCGCTAAAAGGAAACAAATAACAC	59.887	37.037	0.00	0.00	0.00	3.32
1821	1864	7.136119	CAGTCGCTAAAAGGAAACAAATAACA	58.864	34.615	0.00	0.00	0.00	2.41
1822	1865	6.581166	CCAGTCGCTAAAAGGAAACAAATAAC	59.419	38.462	0.00	0.00	0.00	1.89
1823	1866	6.294286	CCCAGTCGCTAAAAGGAAACAAATAA	60.294	38.462	0.00	0.00	0.00	1.40
1824	1867	5.182380	CCCAGTCGCTAAAAGGAAACAAATA	59.818	40.000	0.00	0.00	0.00	1.40
1825	1868	4.022329	CCCAGTCGCTAAAAGGAAACAAAT	60.022	41.667	0.00	0.00	0.00	2.32
1826	1869	3.316868	CCCAGTCGCTAAAAGGAAACAAA	59.683	43.478	0.00	0.00	0.00	2.83
1827	1870	2.882137	CCCAGTCGCTAAAAGGAAACAA	59.118	45.455	0.00	0.00	0.00	2.83
1828	1871	2.500229	CCCAGTCGCTAAAAGGAAACA	58.500	47.619	0.00	0.00	0.00	2.83
1829	1872	1.199327	GCCCAGTCGCTAAAAGGAAAC	59.801	52.381	0.00	0.00	0.00	2.78
1830	1873	1.202830	TGCCCAGTCGCTAAAAGGAAA	60.203	47.619	0.00	0.00	0.00	3.13
1831	1874	0.398696	TGCCCAGTCGCTAAAAGGAA	59.601	50.000	0.00	0.00	0.00	3.36
1832	1875	0.036388	CTGCCCAGTCGCTAAAAGGA	60.036	55.000	0.00	0.00	0.00	3.36
1833	1876	1.648467	GCTGCCCAGTCGCTAAAAGG	61.648	60.000	0.00	0.00	0.00	3.11
1834	1877	1.796796	GCTGCCCAGTCGCTAAAAG	59.203	57.895	0.00	0.00	0.00	2.27
1835	1878	2.032634	CGCTGCCCAGTCGCTAAAA	61.033	57.895	0.00	0.00	0.00	1.52
1836	1879	2.434185	CGCTGCCCAGTCGCTAAA	60.434	61.111	0.00	0.00	0.00	1.85
1837	1880	3.378602	TCGCTGCCCAGTCGCTAA	61.379	61.111	0.00	0.00	0.00	3.09
1838	1881	4.129737	GTCGCTGCCCAGTCGCTA	62.130	66.667	0.00	0.00	0.00	4.26
1843	1886	2.796483	TTATTGCGTCGCTGCCCAGT	62.796	55.000	19.50	0.00	0.00	4.00
1844	1887	2.040213	CTTATTGCGTCGCTGCCCAG	62.040	60.000	19.50	4.34	0.00	4.45
1845	1888	2.046796	TTATTGCGTCGCTGCCCA	60.047	55.556	19.50	0.00	0.00	5.36
1846	1889	2.709475	CTTATTGCGTCGCTGCCC	59.291	61.111	19.50	0.00	0.00	5.36
1847	1890	2.023320	GCTTATTGCGTCGCTGCC	59.977	61.111	19.50	0.00	0.00	4.85
1864	1907	3.487202	CGTCCCATTGGCGTCACG	61.487	66.667	0.00	0.00	0.00	4.35
1866	1909	2.047655	GTCGTCCCATTGGCGTCA	60.048	61.111	0.00	0.00	34.26	4.35
1867	1910	2.818274	GGTCGTCCCATTGGCGTC	60.818	66.667	0.00	0.00	34.26	5.19
1879	1922	1.004200	GGGTGATGAAACGGGTCGT	60.004	57.895	0.00	0.00	43.97	4.34
1886	1929	0.949105	ACAGACGCGGGTGATGAAAC	60.949	55.000	10.96	0.00	0.00	2.78
1891	1934	1.671054	CCAAACAGACGCGGGTGAT	60.671	57.895	10.96	0.00	0.00	3.06
1894	1937	2.280592	GACCAAACAGACGCGGGT	60.281	61.111	12.47	4.12	33.78	5.28
1895	1938	3.411351	CGACCAAACAGACGCGGG	61.411	66.667	12.47	1.69	0.00	6.13
1900	1943	2.654912	CCGCGTCGACCAAACAGAC	61.655	63.158	10.58	0.00	0.00	3.51
1901	1944	2.355363	CCGCGTCGACCAAACAGA	60.355	61.111	10.58	0.00	0.00	3.41
1902	1945	2.355363	TCCGCGTCGACCAAACAG	60.355	61.111	10.58	0.00	0.00	3.16
1903	1946	2.659244	GTCCGCGTCGACCAAACA	60.659	61.111	10.58	0.00	0.00	2.83
1904	1947	1.764180	TTTGTCCGCGTCGACCAAAC	61.764	55.000	10.58	4.13	31.35	2.93
1907	1952	1.952133	CTTTTGTCCGCGTCGACCA	60.952	57.895	10.58	0.00	31.35	4.02
1913	1958	3.645975	CGCCACTTTTGTCCGCGT	61.646	61.111	4.92	0.00	40.96	6.01
1933	1978	4.912485	TTTGGGTCGGCGCGTTGA	62.912	61.111	8.43	2.59	0.00	3.18
1996	2041	2.490115	ACGCAAATCCGGCTCAAAATTA	59.510	40.909	0.00	0.00	0.00	1.40
2098	2149	1.271108	CGTTTTTGGGGAAAATGGGGG	60.271	52.381	0.00	0.00	39.50	5.40
2141	2192	3.671410	CCATGGCTGGTTGGGGGA	61.671	66.667	0.00	0.00	37.79	4.81
2367	4065	2.534019	CGTGGTCATGCCGGCATAC	61.534	63.158	39.94	32.19	41.21	2.39
2489	4238	1.447217	CCAGCGGCCATGTCTCATA	59.553	57.895	2.24	0.00	0.00	2.15
2537	4286	5.575606	CCATTTCATGTCTGCATTCAACTTC	59.424	40.000	0.00	0.00	31.99	3.01
2549	4298	0.255890	CCCCGACCCATTTCATGTCT	59.744	55.000	0.00	0.00	0.00	3.41
2575	4324	3.355203	ATTTGGGTCGGCAATGCGC	62.355	57.895	0.00	0.00	41.28	6.09
2581	4330	0.249657	GTTTTGCATTTGGGTCGGCA	60.250	50.000	0.00	0.00	0.00	5.69
2619	4368	4.238654	TTCGTTTGGGTCGGCCGT	62.239	61.111	27.15	0.00	34.97	5.68
2635	4384	1.857837	CGCATTTGTCCGCTTTTTGTT	59.142	42.857	0.00	0.00	0.00	2.83
2656	4405	2.592287	GGCGACCCAAACGGACAA	60.592	61.111	0.00	0.00	34.64	3.18
2695	4444	8.229811	CCAAAACTCAAAACAAAAGAAAAGGAG	58.770	33.333	0.00	0.00	0.00	3.69
2702	4451	4.391523	GCTGCCAAAACTCAAAACAAAAGA	59.608	37.500	0.00	0.00	0.00	2.52
2703	4452	4.153835	TGCTGCCAAAACTCAAAACAAAAG	59.846	37.500	0.00	0.00	0.00	2.27
2704	4453	4.067896	TGCTGCCAAAACTCAAAACAAAA	58.932	34.783	0.00	0.00	0.00	2.44
2762	4511	2.036958	TGCCGAATTGGTACTCCATG	57.963	50.000	0.00	0.00	43.91	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.