AutoCloner

Multiple sequence alignment - TraesCS3D01G120500

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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	TraesCS3D01G120500	chr3D	100.000	7238	0	0	1	7238	75983648	75990885	0.000000e+00	13367.0
1	TraesCS3D01G120500	chr3D	89.831	59	5	1	6577	6634	581512145	581512087	2.800000e-09	75.0
2	TraesCS3D01G120500	chr3D	89.655	58	5	1	6571	6628	581402666	581402610	1.010000e-08	73.1
3	TraesCS3D01G120500	chr3B	94.978	4042	138	20	942	4955	123121523	123125527	0.000000e+00	6279.0
4	TraesCS3D01G120500	chr3B	92.998	1571	70	21	4952	6507	123125875	123127420	0.000000e+00	2255.0
5	TraesCS3D01G120500	chr3B	84.879	701	79	8	6544	7238	123147202	123147881	0.000000e+00	682.0
6	TraesCS3D01G120500	chr3A	97.940	3593	56	7	1515	5103	90790897	90794475	0.000000e+00	6209.0
7	TraesCS3D01G120500	chr3A	95.630	1991	45	10	5257	7238	90795118	90797075	0.000000e+00	3157.0
8	TraesCS3D01G120500	chr3A	94.485	544	19	7	908	1450	90790364	90790897	0.000000e+00	828.0
9	TraesCS3D01G120500	chr3A	100.000	54	0	0	5090	5143	90794494	90794547	4.620000e-17	100.0
10	TraesCS3D01G120500	chr3A	90.769	65	6	0	5100	5164	476142916	476142980	3.600000e-13	87.9
11	TraesCS3D01G120500	chr3A	90.323	62	5	1	6571	6631	716589610	716589671	6.020000e-11	80.5
12	TraesCS3D01G120500	chr1D	98.405	878	10	3	1	876	54177074	54177949	0.000000e+00	1541.0
13	TraesCS3D01G120500	chr1D	97.836	878	15	3	1	876	18319992	18319117	0.000000e+00	1513.0
14	TraesCS3D01G120500	chr1D	87.805	82	8	1	4487	4566	267794565	267794484	2.150000e-15	95.3
15	TraesCS3D01G120500	chr5B	94.994	879	38	5	1	876	297125671	297124796	0.000000e+00	1375.0
16	TraesCS3D01G120500	chr5B	93.699	857	46	6	26	876	28220868	28220014	0.000000e+00	1277.0
17	TraesCS3D01G120500	chr5B	81.982	222	33	6	4484	4700	323708742	323708523	1.600000e-41	182.0
18	TraesCS3D01G120500	chr4A	95.000	880	36	6	1	876	567325088	567324213	0.000000e+00	1375.0
19	TraesCS3D01G120500	chr1A	94.785	882	38	7	1	879	548993754	548992878	0.000000e+00	1367.0
20	TraesCS3D01G120500	chr1A	87.805	82	8	1	4487	4566	335028624	335028705	2.150000e-15	95.3
21	TraesCS3D01G120500	chr1A	86.905	84	7	3	4487	4567	335028465	335028547	2.780000e-14	91.6
22	TraesCS3D01G120500	chr7A	94.470	886	38	8	1	884	465793475	465794351	0.000000e+00	1354.0
23	TraesCS3D01G120500	chr7A	98.113	53	1	0	5100	5152	395270267	395270319	7.730000e-15	93.5
24	TraesCS3D01G120500	chrUn	92.474	877	61	5	1	875	275050079	275049206	0.000000e+00	1249.0
25	TraesCS3D01G120500	chrUn	92.474	877	61	5	1	875	275057742	275056869	0.000000e+00	1249.0
26	TraesCS3D01G120500	chr4D	80.000	210	38	4	4558	4766	482704237	482704443	1.260000e-32	152.0
27	TraesCS3D01G120500	chr4B	80.000	210	38	4	4558	4766	612274954	612275160	1.260000e-32	152.0
28	TraesCS3D01G120500	chr6B	87.952	83	6	3	4487	4566	642971434	642971353	2.150000e-15	95.3
29	TraesCS3D01G120500	chr1B	86.905	84	7	3	4487	4567	345320369	345320451	2.780000e-14	91.6
30	TraesCS3D01G120500	chr1B	86.585	82	9	1	4487	4566	345320529	345320610	1.000000e-13	89.8
31	TraesCS3D01G120500	chr2B	94.545	55	3	0	5102	5156	401140448	401140502	1.290000e-12	86.1
32	TraesCS3D01G120500	chr6D	78.947	114	10	8	6507	6611	1404593	1404701	1.690000e-06	65.8

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	TraesCS3D01G120500	chr3D	75983648	75990885	7237	False	13367.0	13367	100.00000	1	7238	1	chr3D.!!$F1	7237
1	TraesCS3D01G120500	chr3B	123121523	123127420	5897	False	4267.0	6279	93.98800	942	6507	2	chr3B.!!$F2	5565
2	TraesCS3D01G120500	chr3B	123147202	123147881	679	False	682.0	682	84.87900	6544	7238	1	chr3B.!!$F1	694
3	TraesCS3D01G120500	chr3A	90790364	90797075	6711	False	2573.5	6209	97.01375	908	7238	4	chr3A.!!$F3	6330
4	TraesCS3D01G120500	chr1D	54177074	54177949	875	False	1541.0	1541	98.40500	1	876	1	chr1D.!!$F1	875
5	TraesCS3D01G120500	chr1D	18319117	18319992	875	True	1513.0	1513	97.83600	1	876	1	chr1D.!!$R1	875
6	TraesCS3D01G120500	chr5B	297124796	297125671	875	True	1375.0	1375	94.99400	1	876	1	chr5B.!!$R2	875
7	TraesCS3D01G120500	chr5B	28220014	28220868	854	True	1277.0	1277	93.69900	26	876	1	chr5B.!!$R1	850
8	TraesCS3D01G120500	chr4A	567324213	567325088	875	True	1375.0	1375	95.00000	1	876	1	chr4A.!!$R1	875
9	TraesCS3D01G120500	chr1A	548992878	548993754	876	True	1367.0	1367	94.78500	1	879	1	chr1A.!!$R1	878
10	TraesCS3D01G120500	chr7A	465793475	465794351	876	False	1354.0	1354	94.47000	1	884	1	chr7A.!!$F2	883
11	TraesCS3D01G120500	chrUn	275049206	275050079	873	True	1249.0	1249	92.47400	1	875	1	chrUn.!!$R1	874
12	TraesCS3D01G120500	chrUn	275056869	275057742	873	True	1249.0	1249	92.47400	1	875	1	chrUn.!!$R2	874

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
931	949	1.073923	ACAAACTCTTCCTTCCCGCAT	59.926	47.619	0.00	0.00	0.00	4.73	F
1484	1504	0.536915	GGAATCTGGATGCAGGAGCC	60.537	60.000	14.84	9.11	41.13	4.70	F
1489	1509	1.614525	TGGATGCAGGAGCCACTCT	60.615	57.895	0.00	0.00	34.19	3.24	F
3597	3645	0.819582	CATTCCTGATGGTTGGTGCC	59.180	55.000	0.00	0.00	31.83	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2724	2767	0.664166	CACCACGCAATGCCTGAAAC	60.664	55.000	5.81	0.00	2.78	R
2998	3041	1.348036	AGGTGAACACTGCCTAACTCC	59.652	52.381	4.96	0.00	3.85	R
4629	4678	2.222445	TCTCGGCTTTCGCAGTTAAAAC	59.778	45.455	0.00	39.05	2.43	R
6623	7533	0.919710	GGCCCTTGGAACCTAGACAT	59.080	55.000	0.00	0.00	3.06	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
202	206	2.092429	TGGTCAAGATAAGGGGCACATC	60.092	50.000	0.00	0.00	0.00	3.06
307	311	3.280295	CCTACGCCTTCAGAGAGAACTA	58.720	50.000	0.00	0.00	31.61	2.24
690	700	4.079500	GGGAAAGGAAGGATGAGGAGAATT	60.080	45.833	0.00	0.00	0.00	2.17
800	812	4.678256	ACCAGTCCTATCATATCCGACAT	58.322	43.478	0.00	0.00	0.00	3.06
805	817	7.421599	CAGTCCTATCATATCCGACATACATC	58.578	42.308	0.00	0.00	0.00	3.06
876	894	1.470979	CGTACGGGCATTCAGCTAGTT	60.471	52.381	7.57	0.00	44.79	2.24
880	898	3.270877	ACGGGCATTCAGCTAGTTTAAG	58.729	45.455	0.00	0.00	44.79	1.85
884	902	5.006746	CGGGCATTCAGCTAGTTTAAGTAAG	59.993	44.000	0.00	0.00	44.79	2.34
885	903	6.113411	GGGCATTCAGCTAGTTTAAGTAAGA	58.887	40.000	0.00	0.00	44.79	2.10
886	904	6.598064	GGGCATTCAGCTAGTTTAAGTAAGAA	59.402	38.462	0.00	0.00	44.79	2.52
887	905	7.120726	GGGCATTCAGCTAGTTTAAGTAAGAAA	59.879	37.037	0.00	0.00	44.79	2.52
888	906	8.178313	GGCATTCAGCTAGTTTAAGTAAGAAAG	58.822	37.037	0.00	0.00	44.79	2.62
889	907	8.936864	GCATTCAGCTAGTTTAAGTAAGAAAGA	58.063	33.333	0.00	0.00	41.15	2.52
893	911	9.804758	TCAGCTAGTTTAAGTAAGAAAGATAGC	57.195	33.333	0.00	0.00	34.98	2.97
894	912	9.587772	CAGCTAGTTTAAGTAAGAAAGATAGCA	57.412	33.333	0.00	0.00	36.08	3.49
895	913	9.810545	AGCTAGTTTAAGTAAGAAAGATAGCAG	57.189	33.333	0.00	0.00	36.08	4.24
896	914	9.589111	GCTAGTTTAAGTAAGAAAGATAGCAGT	57.411	33.333	0.00	0.00	34.93	4.40
898	916	8.779354	AGTTTAAGTAAGAAAGATAGCAGTGG	57.221	34.615	0.00	0.00	0.00	4.00
899	917	8.376270	AGTTTAAGTAAGAAAGATAGCAGTGGT	58.624	33.333	0.00	0.00	0.00	4.16
900	918	8.443937	GTTTAAGTAAGAAAGATAGCAGTGGTG	58.556	37.037	4.76	0.00	0.00	4.17
901	919	5.746990	AGTAAGAAAGATAGCAGTGGTGT	57.253	39.130	4.76	0.00	0.00	4.16
902	920	5.482908	AGTAAGAAAGATAGCAGTGGTGTG	58.517	41.667	4.76	0.00	0.00	3.82
903	921	3.340814	AGAAAGATAGCAGTGGTGTGG	57.659	47.619	4.76	0.00	0.00	4.17
904	922	2.639839	AGAAAGATAGCAGTGGTGTGGT	59.360	45.455	4.76	0.00	0.00	4.16
905	923	3.073062	AGAAAGATAGCAGTGGTGTGGTT	59.927	43.478	4.76	0.00	0.00	3.67
906	924	2.479566	AGATAGCAGTGGTGTGGTTG	57.520	50.000	4.76	0.00	0.00	3.77
922	940	4.338118	TGTGGTTGATGAACAAACTCTTCC	59.662	41.667	0.00	0.00	45.48	3.46
927	945	4.398319	TGATGAACAAACTCTTCCTTCCC	58.602	43.478	0.00	0.00	0.00	3.97
928	946	2.846193	TGAACAAACTCTTCCTTCCCG	58.154	47.619	0.00	0.00	0.00	5.14
931	949	1.073923	ACAAACTCTTCCTTCCCGCAT	59.926	47.619	0.00	0.00	0.00	4.73
940	958	5.261216	TCTTCCTTCCCGCATAAAAAGAAT	58.739	37.500	0.00	0.00	0.00	2.40
974	992	1.197036	GCTACTGCCGGAGAACAAAAC	59.803	52.381	5.05	0.00	0.00	2.43
982	1001	3.202906	CCGGAGAACAAAACTGAGAACA	58.797	45.455	0.00	0.00	0.00	3.18
1020	1039	0.757561	TGGAAGACGACCACCTCACA	60.758	55.000	0.00	0.00	32.03	3.58
1139	1158	3.676324	CGCTCCAAACTCTATCCTTCGTT	60.676	47.826	0.00	0.00	0.00	3.85
1252	1271	2.283676	TTCGCCGGAGAAGGAGGT	60.284	61.111	17.34	0.00	0.00	3.85
1316	1335	1.625818	GAGTTCTTCTCCAAGGGCAGA	59.374	52.381	0.00	0.00	37.22	4.26
1327	1346	1.066858	CAAGGGCAGAGTAAGCGAAGA	60.067	52.381	0.00	0.00	0.00	2.87
1331	1350	1.261097	GCAGAGTAAGCGAAGACGAC	58.739	55.000	0.00	0.00	42.66	4.34
1450	1470	7.938563	ATTCGTTAGCTCTTCAAGATGATAC	57.061	36.000	0.00	0.00	0.00	2.24
1451	1471	6.451064	TCGTTAGCTCTTCAAGATGATACA	57.549	37.500	0.00	0.00	0.00	2.29
1454	1474	8.797438	TCGTTAGCTCTTCAAGATGATACATAT	58.203	33.333	0.00	0.00	0.00	1.78
1484	1504	0.536915	GGAATCTGGATGCAGGAGCC	60.537	60.000	14.84	9.11	41.13	4.70
1489	1509	1.614525	TGGATGCAGGAGCCACTCT	60.615	57.895	0.00	0.00	34.19	3.24
1529	1555	8.940768	AGTATTTAGCAGCTTTTGTTTTTGAA	57.059	26.923	0.00	0.00	0.00	2.69
1536	1571	5.555069	GCAGCTTTTGTTTTTGAACGAGATG	60.555	40.000	0.00	0.00	0.00	2.90
1608	1643	7.500720	TCACTCTATGTTATCCATTGCATTG	57.499	36.000	1.49	1.49	34.86	2.82
1642	1677	6.818644	GTGATCTTAAGTGAGTTAATGCCAGA	59.181	38.462	1.63	0.00	29.97	3.86
1782	1817	4.410400	GGCTACCAGCGGTGCCTT	62.410	66.667	21.63	0.00	43.62	4.35
1811	1846	3.199727	TGGTGTTGAGCAGGCATAAGATA	59.800	43.478	0.00	0.00	0.00	1.98
1812	1847	4.199310	GGTGTTGAGCAGGCATAAGATAA	58.801	43.478	0.00	0.00	0.00	1.75
1864	1899	8.408601	AGGTTCATACTGTGATTGAATTAATGC	58.591	33.333	0.00	0.00	36.54	3.56
1988	2024	3.691702	CGAATCGTCGTAATGCAGC	57.308	52.632	0.00	0.00	42.53	5.25
2008	2044	4.272991	CAGCAGTATCTTCAAGCATTCTCC	59.727	45.833	0.00	0.00	0.00	3.71
2713	2756	8.674263	ATGTCAGAGATTTGATCCTTTACATC	57.326	34.615	0.00	0.00	0.00	3.06
2998	3041	3.318839	TCCTCAAAGAATGGTGTTGCAAG	59.681	43.478	0.00	0.00	0.00	4.01
3506	3554	3.283684	CACGCTCCACCGCCAAAA	61.284	61.111	0.00	0.00	0.00	2.44
3595	3643	3.156293	TGTTCATTCCTGATGGTTGGTG	58.844	45.455	0.00	0.00	36.37	4.17
3597	3645	0.819582	CATTCCTGATGGTTGGTGCC	59.180	55.000	0.00	0.00	31.83	5.01
3650	3698	5.301835	AGGATATCTTGGTGACCATCTTG	57.698	43.478	4.56	0.00	31.53	3.02
4613	4661	4.583073	GGCCTAAAAGTGGACAAAAAGAGA	59.417	41.667	0.00	0.00	31.53	3.10
5011	5413	6.205784	ACCATTTCAACATAAGACAACAACG	58.794	36.000	0.00	0.00	0.00	4.10
5309	6200	7.510549	TCTTAGCATTATAAATGCACCTTCC	57.489	36.000	22.58	0.00	46.77	3.46
5504	6395	5.861787	TGTAGTTGTGTATGAACATCTGACG	59.138	40.000	0.00	0.00	38.08	4.35
6143	7051	6.428159	TCAATGTAGCTTCTTTTCAGTTCTCC	59.572	38.462	0.00	0.00	0.00	3.71
6358	7268	8.700051	TGGTTATCCAAAAGTTCTGAATTTTGA	58.300	29.630	23.90	14.89	45.13	2.69
6547	7457	8.928733	GTCGACTATGTATGTTACAAGGAAAAA	58.071	33.333	8.70	0.00	42.76	1.94
6623	7533	2.562298	GGAACCATGTTCAGCAAATCCA	59.438	45.455	9.01	0.00	0.00	3.41
6669	7579	9.064706	CAAACATTGCATCTCTCTTCCTAATAT	57.935	33.333	0.00	0.00	0.00	1.28
6721	7631	2.891580	GAGATACTTGGCGGTAGGATCA	59.108	50.000	8.45	0.00	35.74	2.92
6791	7701	2.890311	CACTAGCAAAATCCAACCACCA	59.110	45.455	0.00	0.00	0.00	4.17
6855	7765	2.005537	CGCGTGACTTTGCAACTGC	61.006	57.895	0.00	0.00	42.50	4.40
6938	7854	5.971202	ACTTGTCGCAAACTATGAGTTTTTG	59.029	36.000	1.85	0.00	45.38	2.44
6954	7870	7.563906	TGAGTTTTTGAGTGATTTTTCCCAAT	58.436	30.769	0.00	0.00	0.00	3.16
6995	7911	8.087750	TGAGTTTGTTCTTCATTTGTTCTGTTT	58.912	29.630	0.00	0.00	0.00	2.83
6996	7912	8.831715	AGTTTGTTCTTCATTTGTTCTGTTTT	57.168	26.923	0.00	0.00	0.00	2.43
6997	7913	8.711457	AGTTTGTTCTTCATTTGTTCTGTTTTG	58.289	29.630	0.00	0.00	0.00	2.44
6998	7914	8.707839	GTTTGTTCTTCATTTGTTCTGTTTTGA	58.292	29.630	0.00	0.00	0.00	2.69
6999	7915	8.824159	TTGTTCTTCATTTGTTCTGTTTTGAA	57.176	26.923	0.00	0.00	0.00	2.69
7000	7916	8.824159	TGTTCTTCATTTGTTCTGTTTTGAAA	57.176	26.923	0.00	0.00	0.00	2.69
7001	7917	9.265901	TGTTCTTCATTTGTTCTGTTTTGAAAA	57.734	25.926	0.00	0.00	0.00	2.29
7002	7918	9.745323	GTTCTTCATTTGTTCTGTTTTGAAAAG	57.255	29.630	0.00	0.00	0.00	2.27
7003	7919	9.487790	TTCTTCATTTGTTCTGTTTTGAAAAGT	57.512	25.926	0.00	0.00	0.00	2.66
7004	7920	9.487790	TCTTCATTTGTTCTGTTTTGAAAAGTT	57.512	25.926	0.00	0.00	0.00	2.66
7082	7998	2.535984	CCGTTGCACGTATCAAGATCTC	59.464	50.000	0.00	0.00	40.58	2.75
7180	8097	5.133941	TGCACTCCCAACAACAATAAACTA	58.866	37.500	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
690	700	6.318913	TCAAAAACTCCCCCTTCATCATTTA	58.681	36.000	0.00	0.00	0.00	1.40
876	894	7.602644	CACACCACTGCTATCTTTCTTACTTAA	59.397	37.037	0.00	0.00	0.00	1.85
880	898	4.631813	CCACACCACTGCTATCTTTCTTAC	59.368	45.833	0.00	0.00	0.00	2.34
884	902	3.059352	ACCACACCACTGCTATCTTTC	57.941	47.619	0.00	0.00	0.00	2.62
885	903	3.149196	CAACCACACCACTGCTATCTTT	58.851	45.455	0.00	0.00	0.00	2.52
886	904	2.371841	TCAACCACACCACTGCTATCTT	59.628	45.455	0.00	0.00	0.00	2.40
887	905	1.977854	TCAACCACACCACTGCTATCT	59.022	47.619	0.00	0.00	0.00	1.98
888	906	2.472695	TCAACCACACCACTGCTATC	57.527	50.000	0.00	0.00	0.00	2.08
889	907	2.305635	TCATCAACCACACCACTGCTAT	59.694	45.455	0.00	0.00	0.00	2.97
890	908	1.696884	TCATCAACCACACCACTGCTA	59.303	47.619	0.00	0.00	0.00	3.49
891	909	0.473755	TCATCAACCACACCACTGCT	59.526	50.000	0.00	0.00	0.00	4.24
892	910	1.001378	GTTCATCAACCACACCACTGC	60.001	52.381	0.00	0.00	0.00	4.40
893	911	2.296792	TGTTCATCAACCACACCACTG	58.703	47.619	0.00	0.00	0.00	3.66
894	912	2.727123	TGTTCATCAACCACACCACT	57.273	45.000	0.00	0.00	0.00	4.00
895	913	3.130340	AGTTTGTTCATCAACCACACCAC	59.870	43.478	0.00	0.00	35.61	4.16
896	914	3.360867	AGTTTGTTCATCAACCACACCA	58.639	40.909	0.00	0.00	35.61	4.17
897	915	3.632145	AGAGTTTGTTCATCAACCACACC	59.368	43.478	0.00	0.00	35.61	4.16
898	916	4.900635	AGAGTTTGTTCATCAACCACAC	57.099	40.909	0.00	0.00	35.61	3.82
899	917	4.338118	GGAAGAGTTTGTTCATCAACCACA	59.662	41.667	0.00	0.00	35.61	4.17
900	918	4.580580	AGGAAGAGTTTGTTCATCAACCAC	59.419	41.667	0.00	0.00	35.61	4.16
901	919	4.792068	AGGAAGAGTTTGTTCATCAACCA	58.208	39.130	0.00	0.00	35.61	3.67
902	920	5.278512	GGAAGGAAGAGTTTGTTCATCAACC	60.279	44.000	0.00	0.00	35.61	3.77
903	921	5.278512	GGGAAGGAAGAGTTTGTTCATCAAC	60.279	44.000	0.00	0.00	35.61	3.18
904	922	4.827284	GGGAAGGAAGAGTTTGTTCATCAA	59.173	41.667	0.00	0.00	0.00	2.57
905	923	4.398319	GGGAAGGAAGAGTTTGTTCATCA	58.602	43.478	0.00	0.00	0.00	3.07
906	924	3.437049	CGGGAAGGAAGAGTTTGTTCATC	59.563	47.826	0.00	0.00	0.00	2.92
922	940	5.102313	GTGGAATTCTTTTTATGCGGGAAG	58.898	41.667	5.23	0.00	0.00	3.46
927	945	3.300590	GCACGTGGAATTCTTTTTATGCG	59.699	43.478	18.88	2.07	0.00	4.73
928	946	4.089923	GTGCACGTGGAATTCTTTTTATGC	59.910	41.667	18.88	8.77	0.00	3.14
931	949	4.602995	GTGTGCACGTGGAATTCTTTTTA	58.397	39.130	18.88	0.00	0.00	1.52
974	992	1.409412	CTGACGACGGTTGTTCTCAG	58.591	55.000	1.88	2.20	0.00	3.35
982	1001	0.883833	ACGTTATCCTGACGACGGTT	59.116	50.000	0.00	0.00	42.82	4.44
1020	1039	2.643551	CATTGCCAGTACGGAGGAATT	58.356	47.619	7.77	0.00	36.56	2.17
1316	1335	1.531423	TGGAGTCGTCTTCGCTTACT	58.469	50.000	0.00	0.00	36.96	2.24
1327	1346	0.889186	AAAATGCGCCTTGGAGTCGT	60.889	50.000	4.18	0.00	0.00	4.34
1430	1450	9.703892	ACATATGTATCATCTTGAAGAGCTAAC	57.296	33.333	6.56	0.00	0.00	2.34
1450	1470	5.882000	TCCAGATTCCAAACTGACACATATG	59.118	40.000	0.00	0.00	36.38	1.78
1451	1471	6.065976	TCCAGATTCCAAACTGACACATAT	57.934	37.500	0.00	0.00	36.38	1.78
1454	1474	3.855255	TCCAGATTCCAAACTGACACA	57.145	42.857	0.00	0.00	36.38	3.72
1484	1504	8.994429	AATACTTTCACATCTTCACTAGAGTG	57.006	34.615	3.12	3.12	46.91	3.51
1489	1509	9.371136	CTGCTAAATACTTTCACATCTTCACTA	57.629	33.333	0.00	0.00	0.00	2.74
1502	1528	9.377312	TCAAAAACAAAAGCTGCTAAATACTTT	57.623	25.926	0.90	0.00	33.92	2.66
1529	1555	3.190874	GCTAAAAGCTGCTACATCTCGT	58.809	45.455	0.90	0.00	38.45	4.18
1536	1571	1.668237	GCTCTGGCTAAAAGCTGCTAC	59.332	52.381	0.90	0.00	41.99	3.58
1608	1643	4.843728	TCACTTAAGATCACCCCAATCAC	58.156	43.478	10.09	0.00	0.00	3.06
1642	1677	7.678171	AGAGAAACCCAATTTATACACCCAAAT	59.322	33.333	0.00	0.00	0.00	2.32
1739	1774	6.599356	TTAAGGTGACAGCTCAATACTACA	57.401	37.500	7.78	0.00	0.00	2.74
1782	1817	1.543208	CCTGCTCAACACCAAGCTACA	60.543	52.381	0.00	0.00	39.31	2.74
1817	1852	4.202440	CCTCCATTGTTAGCAGAGGATGAT	60.202	45.833	7.37	0.00	45.83	2.45
1988	2024	4.437239	ACGGAGAATGCTTGAAGATACTG	58.563	43.478	0.00	0.00	0.00	2.74
2030	2066	2.612972	CCCTCACCTGTGACATGTACAC	60.613	54.545	16.70	16.70	38.55	2.90
2484	2527	2.416547	TCGCAAAGCTATTCTCAAGCAC	59.583	45.455	0.00	0.00	42.62	4.40
2568	2611	6.575162	TCTTGAAGTTCCTTAAATTCTGGC	57.425	37.500	0.00	0.00	39.75	4.85
2713	2756	5.287035	GCAATGCCTGAAACGAAATTAGAAG	59.713	40.000	0.00	0.00	0.00	2.85
2724	2767	0.664166	CACCACGCAATGCCTGAAAC	60.664	55.000	5.81	0.00	0.00	2.78
2998	3041	1.348036	AGGTGAACACTGCCTAACTCC	59.652	52.381	4.96	0.00	0.00	3.85
4629	4678	2.222445	TCTCGGCTTTCGCAGTTAAAAC	59.778	45.455	0.00	0.00	39.05	2.43
4759	4808	9.515226	TGTACTATCAAAAAGATAAAGGTGCTT	57.485	29.630	0.00	0.00	38.69	3.91
5210	5644	7.888021	TGACTCCACCACTAATTTTAATCATGT	59.112	33.333	0.00	0.00	0.00	3.21
5222	5656	3.791320	AGAATCCTGACTCCACCACTAA	58.209	45.455	0.00	0.00	0.00	2.24
5504	6395	5.993106	ACAACAAAGACAAGCTCTAACTC	57.007	39.130	0.00	0.00	0.00	3.01
6143	7051	2.228822	ACCTTGGTTTTCGCATAGCAAG	59.771	45.455	9.67	9.67	45.00	4.01
6494	7404	8.989653	TGTATACTCGTGTAAATGACATCAAA	57.010	30.769	4.17	0.00	41.14	2.69
6495	7405	8.989653	TTGTATACTCGTGTAAATGACATCAA	57.010	30.769	4.17	0.00	41.14	2.57
6623	7533	0.919710	GGCCCTTGGAACCTAGACAT	59.080	55.000	0.00	0.00	0.00	3.06
6721	7631	2.444388	TGATCCAAGCCATCCTTAGCAT	59.556	45.455	0.00	0.00	31.00	3.79
6791	7701	2.534990	GAGGCAGCCTGATATAGACCT	58.465	52.381	22.26	0.00	31.76	3.85
6797	7707	0.399454	AATGCGAGGCAGCCTGATAT	59.601	50.000	22.26	6.90	43.65	1.63
6855	7765	2.517402	CGAGGGAGAGGGGAGACG	60.517	72.222	0.00	0.00	0.00	4.18
6954	7870	3.973973	CAAACTCACCTATCCCTCCCATA	59.026	47.826	0.00	0.00	0.00	2.74
7005	7921	8.764524	TCAAAAGATCTTTCGTTTTGGAAAAA	57.235	26.923	20.71	0.00	40.20	1.94
7082	7998	8.824159	AATTATCAACATGAGATCTAGTTCGG	57.176	34.615	0.00	0.00	0.00	4.30
7180	8097	1.374343	CTTCACCAGCGCATGAGCAT	61.374	55.000	23.73	5.63	42.27	3.79
7216	8133	2.472909	GCATGGGTGCGCTTCCTAC	61.473	63.158	9.73	0.00	42.28	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.