AutoCloner

Multiple sequence alignment - TraesCS5D01G470500

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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	TraesCS5D01G470500	chr5D	100.000	2375	0	0	1	2375	511890072	511887698	0.000000e+00	4386.0
1	TraesCS5D01G470500	chr5D	97.826	46	1	0	961	1006	511889245	511889200	1.960000e-11	80.5
2	TraesCS5D01G470500	chr4A	96.197	973	34	3	1	970	486299481	486298509	0.000000e+00	1589.0
3	TraesCS5D01G470500	chr4A	94.805	385	20	0	1014	1398	486298512	486298128	3.380000e-168	601.0
4	TraesCS5D01G470500	chr4A	95.455	330	15	0	1014	1343	722378259	722378588	5.810000e-146	527.0
5	TraesCS5D01G470500	chr4A	97.826	46	1	0	961	1006	486298651	486298606	1.960000e-11	80.5
6	TraesCS5D01G470500	chr4A	97.826	46	1	0	961	1006	722378120	722378165	1.960000e-11	80.5
7	TraesCS5D01G470500	chr6D	95.773	970	35	4	1	967	128082674	128083640	0.000000e+00	1559.0
8	TraesCS5D01G470500	chr6D	92.487	386	26	3	1014	1398	128083640	128084023	1.240000e-152	549.0
9	TraesCS5D01G470500	chr6D	100.000	46	0	0	961	1006	128083501	128083546	4.210000e-13	86.1
10	TraesCS5D01G470500	chr4B	94.861	973	47	3	1	970	591234890	591233918	0.000000e+00	1517.0
11	TraesCS5D01G470500	chr4B	83.116	995	145	12	1397	2373	244467695	244468684	0.000000e+00	885.0
12	TraesCS5D01G470500	chr4B	92.448	384	29	0	1014	1397	591233921	591233538	1.240000e-152	549.0
13	TraesCS5D01G470500	chr4B	95.652	46	2	0	961	1006	591234060	591234015	9.100000e-10	75.0
14	TraesCS5D01G470500	chr2D	93.320	973	62	3	1	970	531631033	531630061	0.000000e+00	1434.0
15	TraesCS5D01G470500	chr2D	89.533	984	95	5	1397	2375	422606183	422607163	0.000000e+00	1240.0
16	TraesCS5D01G470500	chr2D	88.980	980	102	4	1397	2372	422611125	422612102	0.000000e+00	1206.0
17	TraesCS5D01G470500	chr2D	88.618	984	104	5	1397	2375	422608653	422609633	0.000000e+00	1190.0
18	TraesCS5D01G470500	chr2D	82.618	909	108	16	1397	2296	191052517	191053384	0.000000e+00	758.0
19	TraesCS5D01G470500	chr2D	90.674	386	35	1	1014	1398	110633004	110632619	1.630000e-141	512.0
20	TraesCS5D01G470500	chr2D	90.649	385	36	0	1014	1398	531630064	531629680	1.630000e-141	512.0
21	TraesCS5D01G470500	chr6A	92.923	975	61	8	1	970	180929412	180928441	0.000000e+00	1411.0
22	TraesCS5D01G470500	chr5A	92.466	969	70	3	2	967	122126622	122127590	0.000000e+00	1382.0
23	TraesCS5D01G470500	chr5A	87.256	973	120	4	1	970	584030476	584031447	0.000000e+00	1107.0
24	TraesCS5D01G470500	chr5A	89.844	384	36	3	1014	1396	693613941	693614322	7.630000e-135	490.0
25	TraesCS5D01G470500	chr6B	91.795	975	75	4	1	970	546087569	546086595	0.000000e+00	1352.0
26	TraesCS5D01G470500	chr1D	95.871	775	29	3	195	967	74292546	74293319	0.000000e+00	1251.0
27	TraesCS5D01G470500	chr1D	100.000	46	0	0	961	1006	74293180	74293225	4.210000e-13	86.1
28	TraesCS5D01G470500	chr7A	88.629	985	99	8	1397	2375	580491508	580492485	0.000000e+00	1186.0
29	TraesCS5D01G470500	chr3B	88.674	671	69	3	1396	2060	805490643	805489974	0.000000e+00	811.0
30	TraesCS5D01G470500	chr3B	90.123	162	11	3	2217	2375	5533397	5533238	3.090000e-49	206.0
31	TraesCS5D01G470500	chr5B	81.659	916	115	25	1397	2297	436747982	436748859	0.000000e+00	712.0
32	TraesCS5D01G470500	chr1B	94.301	386	21	1	1014	1398	685662507	685662892	7.310000e-165	590.0
33	TraesCS5D01G470500	chr1B	100.000	46	0	0	961	1006	685662370	685662415	4.210000e-13	86.1
34	TraesCS5D01G470500	chr1B	97.727	44	1	0	961	1004	289096467	289096424	2.530000e-10	76.8
35	TraesCS5D01G470500	chr4D	90.390	385	34	3	1014	1397	508248425	508248807	9.800000e-139	503.0
36	TraesCS5D01G470500	chr3D	86.436	376	33	11	2012	2373	142867738	142868109	1.710000e-106	396.0
37	TraesCS5D01G470500	chrUn	86.624	314	25	9	2062	2375	475106273	475105977	4.890000e-87	331.0
38	TraesCS5D01G470500	chr2B	92.157	51	3	1	956	1006	183307911	183307960	1.180000e-08	71.3

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	TraesCS5D01G470500	chr5D	511887698	511890072	2374	True	2233.250000	4386	98.913000	1	2375	2	chr5D.!!$R1	2374
1	TraesCS5D01G470500	chr4A	486298128	486299481	1353	True	756.833333	1589	96.276000	1	1398	3	chr4A.!!$R1	1397
2	TraesCS5D01G470500	chr6D	128082674	128084023	1349	False	731.366667	1559	96.086667	1	1398	3	chr6D.!!$F1	1397
3	TraesCS5D01G470500	chr4B	244467695	244468684	989	False	885.000000	885	83.116000	1397	2373	1	chr4B.!!$F1	976
4	TraesCS5D01G470500	chr4B	591233538	591234890	1352	True	713.666667	1517	94.320333	1	1397	3	chr4B.!!$R1	1396
5	TraesCS5D01G470500	chr2D	422606183	422612102	5919	False	1212.000000	1240	89.043667	1397	2375	3	chr2D.!!$F2	978
6	TraesCS5D01G470500	chr2D	531629680	531631033	1353	True	973.000000	1434	91.984500	1	1398	2	chr2D.!!$R2	1397
7	TraesCS5D01G470500	chr2D	191052517	191053384	867	False	758.000000	758	82.618000	1397	2296	1	chr2D.!!$F1	899
8	TraesCS5D01G470500	chr6A	180928441	180929412	971	True	1411.000000	1411	92.923000	1	970	1	chr6A.!!$R1	969
9	TraesCS5D01G470500	chr5A	122126622	122127590	968	False	1382.000000	1382	92.466000	2	967	1	chr5A.!!$F1	965
10	TraesCS5D01G470500	chr5A	584030476	584031447	971	False	1107.000000	1107	87.256000	1	970	1	chr5A.!!$F2	969
11	TraesCS5D01G470500	chr6B	546086595	546087569	974	True	1352.000000	1352	91.795000	1	970	1	chr6B.!!$R1	969
12	TraesCS5D01G470500	chr1D	74292546	74293319	773	False	668.550000	1251	97.935500	195	1006	2	chr1D.!!$F1	811
13	TraesCS5D01G470500	chr7A	580491508	580492485	977	False	1186.000000	1186	88.629000	1397	2375	1	chr7A.!!$F1	978
14	TraesCS5D01G470500	chr3B	805489974	805490643	669	True	811.000000	811	88.674000	1396	2060	1	chr3B.!!$R2	664
15	TraesCS5D01G470500	chr5B	436747982	436748859	877	False	712.000000	712	81.659000	1397	2297	1	chr5B.!!$F1	900
16	TraesCS5D01G470500	chr1B	685662370	685662892	522	False	338.050000	590	97.150500	961	1398	2	chr1B.!!$F1	437

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
465	470	0.304705	GCACATGAAACTATCGCCCG	59.695	55.000	0.0	0.0	0.00	6.13	F
986	992	1.080498	TGGACAAGACCTCCTATGGGT	59.920	52.381	0.0	0.0	40.13	4.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1315	1322	0.036765	TGTACAATGTCCCTCACGGC	60.037	55.0	0.00	0.0	0.00	5.68	R
1841	1859	1.700042	GGGATCTTGGGCGGATCAGT	61.700	60.0	13.04	0.0	40.74	3.41	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
161	163	2.124122	GAATCAAACGTTGTGGCCAAC	58.876	47.619	7.24	1.01	46.09	3.77
278	283	4.526970	GGTCAGCTTATTTGGAGGAATGA	58.473	43.478	0.00	0.00	0.00	2.57
339	344	6.331572	TGGTATGGGAAGAATCAAGGCTAATA	59.668	38.462	0.00	0.00	0.00	0.98
456	461	3.429085	CTTGCGAATAGGCACATGAAAC	58.571	45.455	0.00	0.00	43.82	2.78
465	470	0.304705	GCACATGAAACTATCGCCCG	59.695	55.000	0.00	0.00	0.00	6.13
528	534	6.915300	CACGTTTTATTCATGTGTCAAAAGGA	59.085	34.615	16.37	0.00	31.74	3.36
620	626	4.600062	AGAGGCGGTTTTGGAATTCTTAT	58.400	39.130	5.23	0.00	0.00	1.73
651	657	5.064707	TGCCAGAACAAGAATTAGCGATAAC	59.935	40.000	0.00	0.00	0.00	1.89
717	723	2.972713	ACTTATGGTGGGATAGACGCAT	59.027	45.455	0.00	0.00	43.03	4.73
936	942	3.431572	GCTGTTCTCGGAGATGATAATGC	59.568	47.826	8.81	3.71	33.89	3.56
970	976	1.340114	GGTGGAAACTGGAGGATGGAC	60.340	57.143	0.00	0.00	0.00	4.02
971	977	1.351017	GTGGAAACTGGAGGATGGACA	59.649	52.381	0.00	0.00	0.00	4.02
972	978	2.061848	TGGAAACTGGAGGATGGACAA	58.938	47.619	0.00	0.00	0.00	3.18
973	979	2.040278	TGGAAACTGGAGGATGGACAAG	59.960	50.000	0.00	0.00	0.00	3.16
974	980	2.305927	GGAAACTGGAGGATGGACAAGA	59.694	50.000	0.00	0.00	0.00	3.02
975	981	3.339141	GAAACTGGAGGATGGACAAGAC	58.661	50.000	0.00	0.00	0.00	3.01
976	982	1.280457	ACTGGAGGATGGACAAGACC	58.720	55.000	0.00	0.00	0.00	3.85
977	983	1.203364	ACTGGAGGATGGACAAGACCT	60.203	52.381	0.00	0.00	35.29	3.85
978	984	1.484240	CTGGAGGATGGACAAGACCTC	59.516	57.143	0.00	0.00	45.50	3.85
980	986	1.872773	GAGGATGGACAAGACCTCCT	58.127	55.000	0.00	8.44	41.89	3.69
981	987	3.033659	GAGGATGGACAAGACCTCCTA	57.966	52.381	0.00	0.00	41.89	2.94
982	988	3.582164	GAGGATGGACAAGACCTCCTAT	58.418	50.000	0.00	0.00	41.89	2.57
983	989	3.312890	AGGATGGACAAGACCTCCTATG	58.687	50.000	0.00	0.00	36.53	2.23
984	990	2.370189	GGATGGACAAGACCTCCTATGG	59.630	54.545	0.00	0.00	0.00	2.74
985	991	1.879575	TGGACAAGACCTCCTATGGG	58.120	55.000	0.00	0.00	0.00	4.00
986	992	1.080498	TGGACAAGACCTCCTATGGGT	59.920	52.381	0.00	0.00	40.13	4.51
987	993	2.197465	GGACAAGACCTCCTATGGGTT	58.803	52.381	0.00	0.00	37.17	4.11
988	994	2.576648	GGACAAGACCTCCTATGGGTTT	59.423	50.000	0.00	0.00	37.17	3.27
989	995	3.010250	GGACAAGACCTCCTATGGGTTTT	59.990	47.826	0.00	0.00	37.17	2.43
991	997	4.034285	CAAGACCTCCTATGGGTTTTGT	57.966	45.455	7.65	0.00	41.25	2.83
992	998	4.407365	CAAGACCTCCTATGGGTTTTGTT	58.593	43.478	7.65	0.00	41.25	2.83
993	999	5.566469	CAAGACCTCCTATGGGTTTTGTTA	58.434	41.667	7.65	0.00	41.25	2.41
994	1000	5.853572	AGACCTCCTATGGGTTTTGTTAA	57.146	39.130	0.00	0.00	37.17	2.01
995	1001	5.816682	AGACCTCCTATGGGTTTTGTTAAG	58.183	41.667	0.00	0.00	37.17	1.85
996	1002	4.341487	ACCTCCTATGGGTTTTGTTAAGC	58.659	43.478	0.00	0.00	32.46	3.09
997	1003	4.044191	ACCTCCTATGGGTTTTGTTAAGCT	59.956	41.667	0.00	0.00	32.46	3.74
998	1004	5.016831	CCTCCTATGGGTTTTGTTAAGCTT	58.983	41.667	3.48	3.48	0.00	3.74
999	1005	6.184789	CCTCCTATGGGTTTTGTTAAGCTTA	58.815	40.000	0.86	0.86	0.00	3.09
1000	1006	6.661805	CCTCCTATGGGTTTTGTTAAGCTTAA	59.338	38.462	14.96	14.96	0.00	1.85
1001	1007	7.342026	CCTCCTATGGGTTTTGTTAAGCTTAAT	59.658	37.037	21.28	5.43	0.00	1.40
1002	1008	8.062065	TCCTATGGGTTTTGTTAAGCTTAATG	57.938	34.615	21.28	2.19	0.00	1.90
1003	1009	7.672239	TCCTATGGGTTTTGTTAAGCTTAATGT	59.328	33.333	21.28	4.05	0.00	2.71
1004	1010	8.311109	CCTATGGGTTTTGTTAAGCTTAATGTT	58.689	33.333	21.28	3.50	0.00	2.71
1005	1011	7.961325	ATGGGTTTTGTTAAGCTTAATGTTG	57.039	32.000	21.28	0.00	0.00	3.33
1006	1012	5.755861	TGGGTTTTGTTAAGCTTAATGTTGC	59.244	36.000	21.28	9.18	0.00	4.17
1007	1013	5.989168	GGGTTTTGTTAAGCTTAATGTTGCT	59.011	36.000	21.28	0.00	41.82	3.91
1009	1015	7.654116	GGGTTTTGTTAAGCTTAATGTTGCTTA	59.346	33.333	21.28	3.68	46.19	3.09
1051	1057	7.372714	TGACGTATTAACAGTAGAAGCTTTGA	58.627	34.615	0.00	0.00	0.00	2.69
1315	1322	4.608948	ACTACTGACTTGTTTGAGGAGG	57.391	45.455	0.00	0.00	0.00	4.30
1317	1324	1.202818	ACTGACTTGTTTGAGGAGGCC	60.203	52.381	0.00	0.00	0.00	5.19
1347	1354	9.920946	AGGGACATTGTACATTTACTTATTGAT	57.079	29.630	0.57	0.00	0.00	2.57
1427	1434	5.163499	CCCAACCTAAGCTACACAAAACAAA	60.163	40.000	0.00	0.00	0.00	2.83
1430	1438	6.518208	ACCTAAGCTACACAAAACAAAACA	57.482	33.333	0.00	0.00	0.00	2.83
1492	1500	5.752892	TCTGACCGCTAAGATTACACTAG	57.247	43.478	0.00	0.00	0.00	2.57
1539	1548	1.540267	TTTCATGGGCGGACGAAAAT	58.460	45.000	0.00	0.00	0.00	1.82
1552	1561	1.094785	CGAAAATTCTGCCGTCCCAT	58.905	50.000	0.00	0.00	0.00	4.00
1565	1574	1.065764	TCCCATGTTCGCGATCTCG	59.934	57.895	10.88	0.00	43.27	4.04
1572	1581	2.392974	TTCGCGATCTCGACGACCA	61.393	57.895	10.88	0.00	43.29	4.02
1573	1582	1.712018	TTCGCGATCTCGACGACCAT	61.712	55.000	10.88	0.00	43.29	3.55
1582	1591	4.100707	TCTCGACGACCATACGAAAATT	57.899	40.909	0.00	0.00	35.70	1.82
1601	1610	5.389859	AATTGGAAACTGATCGCAATCAA	57.610	34.783	0.00	0.00	41.33	2.57
1623	1632	2.778299	TCTCCTTAATTTGTGCGCTGT	58.222	42.857	9.73	0.00	0.00	4.40
1685	1694	4.210304	GCACGAGACGCGAATGGC	62.210	66.667	15.93	4.66	44.57	4.40
1761	1778	1.753078	CCATGGGAGAGGACGTCGA	60.753	63.158	9.92	0.00	0.00	4.20
1841	1859	1.795768	GGGATATCATTGCGCGAAGA	58.204	50.000	12.10	4.82	0.00	2.87
1861	1879	1.692395	TGATCCGCCCAAGATCCCA	60.692	57.895	0.00	0.00	39.56	4.37
2034	2059	1.376812	GTTCAAGCCCACCTACCCG	60.377	63.158	0.00	0.00	0.00	5.28
2138	7109	2.325761	CCGTCGACGAGAAAGAAACAT	58.674	47.619	37.65	0.00	43.02	2.71
2210	7182	3.910627	ACAAGTTCCTGGGTTAGTGATCT	59.089	43.478	0.00	0.00	0.00	2.75
2211	7183	5.091552	ACAAGTTCCTGGGTTAGTGATCTA	58.908	41.667	0.00	0.00	0.00	1.98
2279	7269	2.012673	CAAGGATACCAGCAGCTGTTC	58.987	52.381	21.26	13.86	37.17	3.18
2297	7287	3.133901	TGTTCGAGCTAATGGCCTAATGA	59.866	43.478	3.32	0.00	43.05	2.57
2340	7337	5.303845	ACGTAAGAGGAAGACCAACTACTTT	59.696	40.000	0.00	0.00	43.62	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
255	259	3.366052	TTCCTCCAAATAAGCTGACCC	57.634	47.619	0.00	0.00	0.00	4.46
278	283	6.553524	CAATTTTGTTCCATGTTGCTTGTTT	58.446	32.000	0.00	0.00	0.00	2.83
339	344	5.342361	TTCCAAACCTTACCCCAAATAGT	57.658	39.130	0.00	0.00	0.00	2.12
465	470	1.266175	CCTTCGAGCATGATGGCAATC	59.734	52.381	0.00	0.00	35.83	2.67
528	534	5.893824	CCTAACTTGCCCCATATCTCTTTTT	59.106	40.000	0.00	0.00	0.00	1.94
620	626	7.201609	CGCTAATTCTTGTTCTGGCATAAGTAA	60.202	37.037	0.00	0.00	0.00	2.24
651	657	1.164041	ACGTGCTTTTGGAGAACCCG	61.164	55.000	0.00	0.00	37.93	5.28
717	723	6.361433	TGAAACTTTCCTTCATGAACCAGTA	58.639	36.000	3.38	0.00	0.00	2.74
936	942	5.693104	CAGTTTCCACCAACAATGAATCTTG	59.307	40.000	0.00	0.00	0.00	3.02
970	976	4.034285	ACAAAACCCATAGGAGGTCTTG	57.966	45.455	0.00	0.00	36.27	3.02
971	977	4.741928	AACAAAACCCATAGGAGGTCTT	57.258	40.909	0.00	0.00	36.27	3.01
972	978	5.806734	GCTTAACAAAACCCATAGGAGGTCT	60.807	44.000	0.00	0.00	36.27	3.85
973	979	4.398358	GCTTAACAAAACCCATAGGAGGTC	59.602	45.833	0.00	0.00	36.27	3.85
974	980	4.044191	AGCTTAACAAAACCCATAGGAGGT	59.956	41.667	0.00	0.00	40.14	3.85
975	981	4.600062	AGCTTAACAAAACCCATAGGAGG	58.400	43.478	0.00	0.00	36.73	4.30
976	982	7.696992	TTAAGCTTAACAAAACCCATAGGAG	57.303	36.000	14.96	0.00	36.73	3.69
977	983	7.672239	ACATTAAGCTTAACAAAACCCATAGGA	59.328	33.333	20.85	0.00	36.73	2.94
978	984	7.836842	ACATTAAGCTTAACAAAACCCATAGG	58.163	34.615	20.85	0.00	40.04	2.57
979	985	9.139174	CAACATTAAGCTTAACAAAACCCATAG	57.861	33.333	20.85	3.03	0.00	2.23
980	986	7.600752	GCAACATTAAGCTTAACAAAACCCATA	59.399	33.333	20.85	0.00	0.00	2.74
981	987	6.426633	GCAACATTAAGCTTAACAAAACCCAT	59.573	34.615	20.85	0.00	0.00	4.00
982	988	5.755861	GCAACATTAAGCTTAACAAAACCCA	59.244	36.000	20.85	0.00	0.00	4.51
983	989	5.989168	AGCAACATTAAGCTTAACAAAACCC	59.011	36.000	20.85	6.96	38.01	4.11
994	1000	7.086376	CACTCAACATTAAGCAACATTAAGCT	58.914	34.615	0.00	0.00	44.31	3.74
995	1001	6.308766	CCACTCAACATTAAGCAACATTAAGC	59.691	38.462	0.00	0.00	0.00	3.09
996	1002	7.326789	CACCACTCAACATTAAGCAACATTAAG	59.673	37.037	0.00	0.00	0.00	1.85
997	1003	7.144661	CACCACTCAACATTAAGCAACATTAA	58.855	34.615	0.00	0.00	0.00	1.40
998	1004	6.264292	ACACCACTCAACATTAAGCAACATTA	59.736	34.615	0.00	0.00	0.00	1.90
999	1005	5.068987	ACACCACTCAACATTAAGCAACATT	59.931	36.000	0.00	0.00	0.00	2.71
1000	1006	4.584325	ACACCACTCAACATTAAGCAACAT	59.416	37.500	0.00	0.00	0.00	2.71
1001	1007	3.951037	ACACCACTCAACATTAAGCAACA	59.049	39.130	0.00	0.00	0.00	3.33
1002	1008	4.290155	CACACCACTCAACATTAAGCAAC	58.710	43.478	0.00	0.00	0.00	4.17
1003	1009	3.243367	GCACACCACTCAACATTAAGCAA	60.243	43.478	0.00	0.00	0.00	3.91
1004	1010	2.293122	GCACACCACTCAACATTAAGCA	59.707	45.455	0.00	0.00	0.00	3.91
1005	1011	2.554032	AGCACACCACTCAACATTAAGC	59.446	45.455	0.00	0.00	0.00	3.09
1006	1012	3.814842	TCAGCACACCACTCAACATTAAG	59.185	43.478	0.00	0.00	0.00	1.85
1007	1013	3.563808	GTCAGCACACCACTCAACATTAA	59.436	43.478	0.00	0.00	0.00	1.40
1008	1014	3.138304	GTCAGCACACCACTCAACATTA	58.862	45.455	0.00	0.00	0.00	1.90
1009	1015	1.949525	GTCAGCACACCACTCAACATT	59.050	47.619	0.00	0.00	0.00	2.71
1010	1016	1.597742	GTCAGCACACCACTCAACAT	58.402	50.000	0.00	0.00	0.00	2.71
1011	1017	0.809636	CGTCAGCACACCACTCAACA	60.810	55.000	0.00	0.00	0.00	3.33
1012	1018	0.810031	ACGTCAGCACACCACTCAAC	60.810	55.000	0.00	0.00	0.00	3.18
1013	1019	0.747852	TACGTCAGCACACCACTCAA	59.252	50.000	0.00	0.00	0.00	3.02
1051	1057	4.484912	AGGAATAGGCCGAATCTAAGAGT	58.515	43.478	0.00	0.00	0.00	3.24
1304	1311	1.371183	CTCACGGCCTCCTCAAACA	59.629	57.895	0.00	0.00	0.00	2.83
1315	1322	0.036765	TGTACAATGTCCCTCACGGC	60.037	55.000	0.00	0.00	0.00	5.68
1317	1324	5.175859	AGTAAATGTACAATGTCCCTCACG	58.824	41.667	0.00	0.00	32.12	4.35
1407	1414	6.376018	TCTGTTTTGTTTTGTGTAGCTTAGGT	59.624	34.615	0.00	0.00	0.00	3.08
1427	1434	7.994911	TGATCATGAGGCTGTAATTAATCTGTT	59.005	33.333	0.09	0.00	0.00	3.16
1430	1438	7.016957	TCCTGATCATGAGGCTGTAATTAATCT	59.983	37.037	0.09	0.00	0.00	2.40
1473	1481	3.552478	GGGCTAGTGTAATCTTAGCGGTC	60.552	52.174	0.00	0.00	34.82	4.79
1492	1500	2.653115	GCAGTTTTGGCTGAGGGC	59.347	61.111	0.00	0.00	38.70	5.19
1518	1527	1.319541	TTTCGTCCGCCCATGAAAAA	58.680	45.000	0.00	0.00	29.97	1.94
1524	1533	1.094785	CAGAATTTTCGTCCGCCCAT	58.905	50.000	0.00	0.00	0.00	4.00
1539	1548	1.375396	CGAACATGGGACGGCAGAA	60.375	57.895	0.00	0.00	0.00	3.02
1552	1561	1.225936	GTCGTCGAGATCGCGAACA	60.226	57.895	23.21	9.84	44.32	3.18
1565	1574	4.932268	TTCCAATTTTCGTATGGTCGTC	57.068	40.909	0.00	0.00	35.66	4.20
1572	1581	5.123186	TGCGATCAGTTTCCAATTTTCGTAT	59.877	36.000	0.00	0.00	0.00	3.06
1573	1582	4.452795	TGCGATCAGTTTCCAATTTTCGTA	59.547	37.500	0.00	0.00	0.00	3.43
1582	1591	4.701651	AGATTTGATTGCGATCAGTTTCCA	59.298	37.500	16.16	0.00	42.90	3.53
1601	1610	3.758554	ACAGCGCACAAATTAAGGAGATT	59.241	39.130	11.47	0.00	0.00	2.40
1623	1632	0.249955	TGAGCGAGCACCATCAATCA	59.750	50.000	0.00	0.00	0.00	2.57
1685	1694	2.693591	TGTTAGATAGGAAGGCACTCGG	59.306	50.000	0.00	0.00	38.49	4.63
1698	1707	7.094975	CCGATCTTTGTTGTGGTTTGTTAGATA	60.095	37.037	0.00	0.00	0.00	1.98
1738	1748	2.041922	TCCTCTCCCATGGGTCGG	60.042	66.667	30.28	25.44	36.47	4.79
1751	1767	2.583593	GCCAGCATCGACGTCCTC	60.584	66.667	10.58	0.00	0.00	3.71
1761	1778	1.822613	CGAGGAGCATTGCCAGCAT	60.823	57.895	4.70	0.00	0.00	3.79
1841	1859	1.700042	GGGATCTTGGGCGGATCAGT	61.700	60.000	13.04	0.00	40.74	3.41
2124	7095	3.660865	ACCGCTTATGTTTCTTTCTCGT	58.339	40.909	0.00	0.00	0.00	4.18
2138	7109	1.741706	CGAGTCTTGTAGGACCGCTTA	59.258	52.381	0.00	0.00	36.95	3.09
2187	7159	3.764237	TCACTAACCCAGGAACTTGTC	57.236	47.619	0.00	0.00	34.60	3.18
2279	7269	3.995199	TCTTCATTAGGCCATTAGCTCG	58.005	45.455	5.01	0.00	43.05	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.