AutoCloner

Multiple sequence alignment - TraesCS6B01G267400

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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	TraesCS6B01G267400	chr6B	100.000	2288	0	0	1	2288	480867541	480865254	0.000000e+00	4226.0
1	TraesCS6B01G267400	chr6B	96.384	968	35	0	1321	2288	394193638	394192671	0.000000e+00	1594.0
2	TraesCS6B01G267400	chr6B	96.178	968	36	1	1321	2288	505729041	505728075	0.000000e+00	1581.0
3	TraesCS6B01G267400	chr6B	96.178	968	36	1	1321	2288	717611346	717612312	0.000000e+00	1581.0
4	TraesCS6B01G267400	chr6B	95.975	969	38	1	1321	2288	170969533	170970501	0.000000e+00	1572.0
5	TraesCS6B01G267400	chr7B	96.388	969	33	2	1321	2288	376450989	376451956	0.000000e+00	1594.0
6	TraesCS6B01G267400	chr7B	96.074	968	38	0	1321	2288	92345876	92344909	0.000000e+00	1578.0
7	TraesCS6B01G267400	chr7B	85.758	1320	179	5	2	1321	581801296	581802606	0.000000e+00	1387.0
8	TraesCS6B01G267400	chr7B	78.512	1331	264	20	2	1322	654488588	654487270	0.000000e+00	854.0
9	TraesCS6B01G267400	chr5B	96.178	968	37	0	1321	2288	466083540	466084507	0.000000e+00	1583.0
10	TraesCS6B01G267400	chr5B	95.971	968	39	0	1321	2288	275638728	275639695	0.000000e+00	1572.0
11	TraesCS6B01G267400	chr5B	93.271	431	28	1	895	1324	692300821	692300391	3.210000e-178	634.0
12	TraesCS6B01G267400	chr1B	96.178	968	36	1	1321	2288	613132752	613131786	0.000000e+00	1581.0
13	TraesCS6B01G267400	chr1B	69.914	1273	320	52	82	1322	514573492	514572251	1.090000e-38	171.0
14	TraesCS6B01G267400	chr4A	79.955	1332	247	18	2	1322	736419236	736420558	0.000000e+00	963.0
15	TraesCS6B01G267400	chrUn	78.512	1331	264	20	2	1322	253078441	253079759	0.000000e+00	854.0
16	TraesCS6B01G267400	chrUn	78.512	1331	264	20	2	1322	332107699	332106381	0.000000e+00	854.0
17	TraesCS6B01G267400	chr1D	97.619	42	1	0	1	42	4812861	4812820	3.150000e-09	73.1

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	TraesCS6B01G267400	chr6B	480865254	480867541	2287	True	4226	4226	100.000	1	2288	1	chr6B.!!$R2	2287
1	TraesCS6B01G267400	chr6B	394192671	394193638	967	True	1594	1594	96.384	1321	2288	1	chr6B.!!$R1	967
2	TraesCS6B01G267400	chr6B	505728075	505729041	966	True	1581	1581	96.178	1321	2288	1	chr6B.!!$R3	967
3	TraesCS6B01G267400	chr6B	717611346	717612312	966	False	1581	1581	96.178	1321	2288	1	chr6B.!!$F2	967
4	TraesCS6B01G267400	chr6B	170969533	170970501	968	False	1572	1572	95.975	1321	2288	1	chr6B.!!$F1	967
5	TraesCS6B01G267400	chr7B	376450989	376451956	967	False	1594	1594	96.388	1321	2288	1	chr7B.!!$F1	967
6	TraesCS6B01G267400	chr7B	92344909	92345876	967	True	1578	1578	96.074	1321	2288	1	chr7B.!!$R1	967
7	TraesCS6B01G267400	chr7B	581801296	581802606	1310	False	1387	1387	85.758	2	1321	1	chr7B.!!$F2	1319
8	TraesCS6B01G267400	chr7B	654487270	654488588	1318	True	854	854	78.512	2	1322	1	chr7B.!!$R2	1320
9	TraesCS6B01G267400	chr5B	466083540	466084507	967	False	1583	1583	96.178	1321	2288	1	chr5B.!!$F2	967
10	TraesCS6B01G267400	chr5B	275638728	275639695	967	False	1572	1572	95.971	1321	2288	1	chr5B.!!$F1	967
11	TraesCS6B01G267400	chr1B	613131786	613132752	966	True	1581	1581	96.178	1321	2288	1	chr1B.!!$R2	967
12	TraesCS6B01G267400	chr4A	736419236	736420558	1322	False	963	963	79.955	2	1322	1	chr4A.!!$F1	1320
13	TraesCS6B01G267400	chrUn	253078441	253079759	1318	False	854	854	78.512	2	1322	1	chrUn.!!$F1	1320
14	TraesCS6B01G267400	chrUn	332106381	332107699	1318	True	854	854	78.512	2	1322	1	chrUn.!!$R1	1320

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
636	638	0.034198	TGCTTGTTGCGTGCCTACTA	59.966	50.0	0.0	0.0	46.63	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1730	1733	1.076777	GCATCCCCAAGCTTAGGCA	60.077	57.895	5.25	0.0	41.7	4.75	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
39	40	1.208165	ATCGGGAAGGGCAAAGGACT	61.208	55.000	0.00	0.00	0.00	3.85
45	46	1.430369	AAGGGCAAAGGACTCCTGCT	61.430	55.000	0.00	0.00	32.13	4.24
50	51	1.280457	CAAAGGACTCCTGCTACCCT	58.720	55.000	0.00	0.00	32.13	4.34
69	70	0.544697	TTCGGGGTAATTGCCTCCTC	59.455	55.000	12.66	0.00	0.00	3.71
76	77	3.161866	GGTAATTGCCTCCTCACCAAAA	58.838	45.455	5.16	0.00	0.00	2.44
99	100	1.019278	GCGAGCTTGTTGATCCGGAA	61.019	55.000	9.01	0.00	0.00	4.30
118	119	4.589908	GGAAACACATACTTGGGATGAGT	58.410	43.478	0.00	0.00	30.59	3.41
135	136	6.211584	GGGATGAGTTGCTGGTAAGAGATATA	59.788	42.308	0.00	0.00	0.00	0.86
192	194	4.088634	CACCAATCAGGGAGGATTTTGAA	58.911	43.478	0.00	0.00	43.89	2.69
252	254	1.689813	TCGGTGAAGTCAGCCTACAAA	59.310	47.619	4.99	0.00	40.99	2.83
257	259	3.495001	GTGAAGTCAGCCTACAAACTGTC	59.505	47.826	0.00	0.00	35.37	3.51
279	281	1.192534	GTGCAAGAGCGTGACTTACAC	59.807	52.381	0.00	0.00	46.23	2.90
301	303	3.411517	CGGGGGCCTCTGAACCAT	61.412	66.667	5.06	0.00	0.00	3.55
308	310	0.329596	GCCTCTGAACCATCCCACTT	59.670	55.000	0.00	0.00	0.00	3.16
311	313	2.040278	CCTCTGAACCATCCCACTTTGA	59.960	50.000	0.00	0.00	0.00	2.69
312	314	3.308688	CCTCTGAACCATCCCACTTTGAT	60.309	47.826	0.00	0.00	0.00	2.57
334	336	4.844349	TGGGACTAGAAAGAGATTTGGG	57.156	45.455	0.00	0.00	0.00	4.12
337	339	2.609916	GACTAGAAAGAGATTTGGGCGC	59.390	50.000	0.00	0.00	0.00	6.53
357	359	1.207570	CTGCCATGCCAGCCAAAAATA	59.792	47.619	0.00	0.00	0.00	1.40
419	421	3.932822	TGAAGAGTAGCATAAAACGGCA	58.067	40.909	0.00	0.00	0.00	5.69
423	425	3.007635	GAGTAGCATAAAACGGCAAGGT	58.992	45.455	0.00	0.00	0.00	3.50
426	428	1.269448	AGCATAAAACGGCAAGGTGTG	59.731	47.619	0.00	0.00	0.00	3.82
427	429	1.268352	GCATAAAACGGCAAGGTGTGA	59.732	47.619	0.00	0.00	0.00	3.58
438	440	2.791158	GCAAGGTGTGAAGTGTGAAACG	60.791	50.000	0.00	0.00	42.39	3.60
459	461	3.181496	CGCTATGTGTCTACTGCAAGAGA	60.181	47.826	0.00	0.00	37.43	3.10
481	483	3.682292	GATGAGGACGGGGCACACC	62.682	68.421	0.00	0.00	39.11	4.16
492	494	1.506262	GGCACACCTGTTTATGCGG	59.494	57.895	0.00	0.00	39.02	5.69
498	500	0.881118	ACCTGTTTATGCGGTGCAAG	59.119	50.000	0.00	0.00	43.62	4.01
537	539	1.152902	AGCACTGCAACTGGAGCAA	60.153	52.632	3.30	0.00	42.17	3.91
538	540	0.538977	AGCACTGCAACTGGAGCAAT	60.539	50.000	3.30	0.00	42.17	3.56
540	542	1.933500	GCACTGCAACTGGAGCAATTG	60.934	52.381	0.00	0.00	42.17	2.32
547	549	1.366319	ACTGGAGCAATTGAGGGAGT	58.634	50.000	10.34	2.30	0.00	3.85
565	567	0.177141	GTGGCTTACCGCATGTAGGA	59.823	55.000	14.83	0.00	46.41	2.94
603	605	2.333926	CATGAAACGCTTCGTCTACCA	58.666	47.619	0.00	0.00	39.99	3.25
636	638	0.034198	TGCTTGTTGCGTGCCTACTA	59.966	50.000	0.00	0.00	46.63	1.82
653	655	3.136641	ACTATGGAGATGGTGGACCTT	57.863	47.619	0.00	0.00	36.82	3.50
656	658	1.133181	TGGAGATGGTGGACCTTGCA	61.133	55.000	0.00	0.00	36.82	4.08
684	686	2.729360	GGTTAATGCAGGCGACAAAAAC	59.271	45.455	0.00	0.00	0.00	2.43
693	695	1.067846	GGCGACAAAAACATTCCCCTC	60.068	52.381	0.00	0.00	0.00	4.30
694	696	1.611491	GCGACAAAAACATTCCCCTCA	59.389	47.619	0.00	0.00	0.00	3.86
698	700	4.261994	CGACAAAAACATTCCCCTCAACAT	60.262	41.667	0.00	0.00	0.00	2.71
707	709	1.080498	TCCCCTCAACATCCTACCTGT	59.920	52.381	0.00	0.00	0.00	4.00
735	737	1.225704	CCATTGGGCCTCAGAGTCC	59.774	63.158	4.53	0.00	0.00	3.85
745	747	0.528033	CTCAGAGTCCATGCAGCTCG	60.528	60.000	0.00	0.00	34.69	5.03
749	751	4.783621	GTCCATGCAGCTCGGCCA	62.784	66.667	2.24	0.00	0.00	5.36
772	774	1.371183	CCTCGAGGCACACAAGGAA	59.629	57.895	20.67	0.00	0.00	3.36
797	799	1.737735	CAGCGCAGATGTGGACGAA	60.738	57.895	11.47	0.00	40.13	3.85
798	800	1.005037	AGCGCAGATGTGGACGAAA	60.005	52.632	11.47	0.00	0.00	3.46
834	836	2.739913	CCTGAAAATTAACTGCGACGGA	59.260	45.455	0.00	0.00	0.00	4.69
837	839	1.803334	AAATTAACTGCGACGGAGCA	58.197	45.000	16.93	1.42	45.96	4.26
845	847	1.227263	GCGACGGAGCATACCATGT	60.227	57.895	0.00	0.00	37.05	3.21
886	888	1.975680	GGGGGTTTGTAGTCAGAGACA	59.024	52.381	0.00	0.00	34.60	3.41
887	889	2.028020	GGGGGTTTGTAGTCAGAGACAG	60.028	54.545	0.00	0.00	34.60	3.51
906	908	2.757099	GCGGGGGACGTAAGAGGA	60.757	66.667	0.00	0.00	46.52	3.71
910	912	1.202855	CGGGGGACGTAAGAGGATCTA	60.203	57.143	0.00	0.00	41.22	1.98
933	935	2.025981	AGCTGGCCATCTGAAACATGTA	60.026	45.455	8.67	0.00	0.00	2.29
936	938	2.290832	TGGCCATCTGAAACATGTAGCA	60.291	45.455	0.00	0.00	0.00	3.49
962	964	3.711937	TGCAAGCTGAAGCAGAAGA	57.288	47.368	4.90	0.00	45.16	2.87
963	965	1.520494	TGCAAGCTGAAGCAGAAGAG	58.480	50.000	4.90	0.00	45.16	2.85
1022	1024	2.846918	GCGTGTGCAAGTCGAGTC	59.153	61.111	9.93	0.00	42.15	3.36
1036	1038	0.039074	CGAGTCGGACAGCAAAGAGT	60.039	55.000	11.27	0.00	0.00	3.24
1070	1072	1.258445	ACTACCAGGGAAGCAGACCG	61.258	60.000	0.00	0.00	0.00	4.79
1073	1075	3.322466	CAGGGAAGCAGACCGGGT	61.322	66.667	6.32	0.00	0.00	5.28
1077	1079	4.021925	GAAGCAGACCGGGTGGCT	62.022	66.667	15.20	15.20	39.70	4.75
1116	1118	2.037251	AGATATATGCGAGTTTGCCCGT	59.963	45.455	0.00	0.00	0.00	5.28
1122	1124	1.298859	GCGAGTTTGCCCGTCTGAAT	61.299	55.000	0.00	0.00	0.00	2.57
1137	1139	5.391523	CCGTCTGAATTTTAGCCGAATTTCA	60.392	40.000	0.00	6.74	31.73	2.69
1167	1169	3.689832	CCCAAGGGGTTGTAATGCT	57.310	52.632	0.00	0.00	38.25	3.79
1173	1175	2.365582	AGGGGTTGTAATGCTTTAGCG	58.634	47.619	0.00	0.00	45.83	4.26
1186	1188	2.159517	GCTTTAGCGCATGTTGTAGCTT	60.160	45.455	11.47	0.00	40.73	3.74
1188	1190	2.672961	TAGCGCATGTTGTAGCTTCT	57.327	45.000	11.47	0.00	40.73	2.85
1192	1194	2.911102	GCGCATGTTGTAGCTTCTTTTC	59.089	45.455	0.30	0.00	0.00	2.29
1199	1201	4.515191	TGTTGTAGCTTCTTTTCGAGCAAT	59.485	37.500	0.00	0.00	0.00	3.56
1221	1223	1.220206	CACTGCTGCTCGGGAGATT	59.780	57.895	0.00	0.00	38.80	2.40
1254	1256	2.417379	CCTCCCAGACGATGTAAGTGTG	60.417	54.545	0.00	0.00	33.33	3.82
1288	1290	1.826385	CTTGGCTGGACCTGGTTAAG	58.174	55.000	0.00	2.94	40.22	1.85
1409	1411	6.595716	AGTTACAGATTGCTACAGATTGTTCC	59.404	38.462	0.00	0.00	0.00	3.62
1457	1460	6.019961	CGTGTGTTGTTTGCTTATTTTGATGT	60.020	34.615	0.00	0.00	0.00	3.06
1586	1589	5.124138	TGGTTTTGCTTTCTTTCACTAACGA	59.876	36.000	0.00	0.00	0.00	3.85
1655	1658	7.610580	AGTTTTGGGTAAAGATTTGATGGAA	57.389	32.000	0.00	0.00	0.00	3.53
1730	1733	7.671398	CCCCAATATATTCAAGAGTAGCCAAAT	59.329	37.037	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.076559	CAGCCATGGATCTGCCCAA	60.077	57.895	18.40	0.00	40.04	4.12
50	51	0.544697	GAGGAGGCAATTACCCCGAA	59.455	55.000	0.00	0.00	0.00	4.30
69	70	3.559238	ACAAGCTCGCTAATTTTGGTG	57.441	42.857	0.00	0.00	0.00	4.17
76	77	2.205074	CGGATCAACAAGCTCGCTAAT	58.795	47.619	0.00	0.00	0.00	1.73
99	100	3.758554	GCAACTCATCCCAAGTATGTGTT	59.241	43.478	0.00	0.00	40.05	3.32
118	119	6.787458	TCCTGGAATATATCTCTTACCAGCAA	59.213	38.462	0.00	0.00	41.09	3.91
135	136	2.376518	TGTGGCTTCTTCTTCCTGGAAT	59.623	45.455	10.03	0.00	0.00	3.01
192	194	6.604396	TGTCATGAAACCATGCATAGAAATCT	59.396	34.615	0.00	0.00	40.83	2.40
252	254	0.877649	CACGCTCTTGCACAGACAGT	60.878	55.000	0.00	0.00	39.64	3.55
257	259	1.457303	GTAAGTCACGCTCTTGCACAG	59.543	52.381	0.00	0.00	39.64	3.66
308	310	6.886459	CCAAATCTCTTTCTAGTCCCAATCAA	59.114	38.462	0.00	0.00	0.00	2.57
311	313	5.760131	CCCAAATCTCTTTCTAGTCCCAAT	58.240	41.667	0.00	0.00	0.00	3.16
312	314	4.567747	GCCCAAATCTCTTTCTAGTCCCAA	60.568	45.833	0.00	0.00	0.00	4.12
318	320	2.611292	CAGCGCCCAAATCTCTTTCTAG	59.389	50.000	2.29	0.00	0.00	2.43
320	322	1.457346	CAGCGCCCAAATCTCTTTCT	58.543	50.000	2.29	0.00	0.00	2.52
337	339	0.035820	ATTTTTGGCTGGCATGGCAG	60.036	50.000	37.54	37.54	43.29	4.85
342	344	4.556592	ATGTTGTATTTTTGGCTGGCAT	57.443	36.364	4.22	0.00	0.00	4.40
357	359	4.236935	CAAAGCGCCATAAGAAATGTTGT	58.763	39.130	2.29	0.00	0.00	3.32
419	421	1.400494	GCGTTTCACACTTCACACCTT	59.600	47.619	0.00	0.00	0.00	3.50
423	425	3.247411	CACATAGCGTTTCACACTTCACA	59.753	43.478	0.00	0.00	0.00	3.58
426	428	3.741344	AGACACATAGCGTTTCACACTTC	59.259	43.478	0.00	0.00	0.00	3.01
427	429	3.728845	AGACACATAGCGTTTCACACTT	58.271	40.909	0.00	0.00	0.00	3.16
438	440	4.109050	GTCTCTTGCAGTAGACACATAGC	58.891	47.826	19.97	0.00	41.46	2.97
447	449	4.159321	TCCTCATCAAGTCTCTTGCAGTAG	59.841	45.833	4.82	0.00	0.00	2.57
449	451	2.902486	TCCTCATCAAGTCTCTTGCAGT	59.098	45.455	4.82	0.00	0.00	4.40
459	461	1.918293	TGCCCCGTCCTCATCAAGT	60.918	57.895	0.00	0.00	0.00	3.16
481	483	0.240678	TGCTTGCACCGCATAAACAG	59.759	50.000	5.80	0.00	38.76	3.16
487	489	1.454572	TTGACTTGCTTGCACCGCAT	61.455	50.000	10.34	0.00	38.76	4.73
492	494	1.678101	ACCTTCTTGACTTGCTTGCAC	59.322	47.619	0.00	0.00	0.00	4.57
498	500	0.312102	GCCACACCTTCTTGACTTGC	59.688	55.000	0.00	0.00	0.00	4.01
537	539	0.541863	CGGTAAGCCACTCCCTCAAT	59.458	55.000	0.00	0.00	34.09	2.57
538	540	1.980052	CGGTAAGCCACTCCCTCAA	59.020	57.895	0.00	0.00	34.09	3.02
540	542	2.187163	GCGGTAAGCCACTCCCTC	59.813	66.667	0.00	0.00	40.81	4.30
565	567	1.276859	TGCATCACCTCCATGGCTCT	61.277	55.000	6.96	0.00	40.22	4.09
616	618	0.606401	AGTAGGCACGCAACAAGCAT	60.606	50.000	0.00	0.00	46.13	3.79
636	638	0.257039	GCAAGGTCCACCATCTCCAT	59.743	55.000	0.00	0.00	38.89	3.41
653	655	2.557924	CCTGCATTAACCTTGTTCTGCA	59.442	45.455	13.22	13.22	37.93	4.41
656	658	1.812571	CGCCTGCATTAACCTTGTTCT	59.187	47.619	0.00	0.00	0.00	3.01
663	665	2.715737	TTTTGTCGCCTGCATTAACC	57.284	45.000	0.00	0.00	0.00	2.85
684	686	2.780010	AGGTAGGATGTTGAGGGGAATG	59.220	50.000	0.00	0.00	0.00	2.67
693	695	5.508825	GCTGATCTCTACAGGTAGGATGTTG	60.509	48.000	6.62	3.43	36.09	3.33
694	696	4.586841	GCTGATCTCTACAGGTAGGATGTT	59.413	45.833	6.62	0.00	36.09	2.71
698	700	2.514160	TGGCTGATCTCTACAGGTAGGA	59.486	50.000	6.62	3.93	36.09	2.94
729	731	2.898738	CCGAGCTGCATGGACTCT	59.101	61.111	1.02	0.80	0.00	3.24
735	737	3.047718	CTGTTGGCCGAGCTGCATG	62.048	63.158	1.02	0.00	0.00	4.06
760	762	1.360192	GCTGTGTTCCTTGTGTGCC	59.640	57.895	0.00	0.00	0.00	5.01
762	764	0.664761	CTGGCTGTGTTCCTTGTGTG	59.335	55.000	0.00	0.00	0.00	3.82
772	774	2.745100	CATCTGCGCTGGCTGTGT	60.745	61.111	14.70	0.00	40.82	3.72
810	812	3.666902	CGTCGCAGTTAATTTTCAGGGTG	60.667	47.826	0.00	0.00	0.00	4.61
812	814	2.159572	CCGTCGCAGTTAATTTTCAGGG	60.160	50.000	0.00	0.00	0.00	4.45
845	847	4.343323	CCCCGGTGCCATGTGTCA	62.343	66.667	0.00	0.00	0.00	3.58
870	872	2.726760	CGCACTGTCTCTGACTACAAAC	59.273	50.000	0.00	0.00	33.15	2.93
873	875	0.881796	CCGCACTGTCTCTGACTACA	59.118	55.000	0.00	0.00	33.15	2.74
886	888	2.283388	TCTTACGTCCCCCGCACT	60.283	61.111	0.00	0.00	41.42	4.40
887	889	2.183555	CTCTTACGTCCCCCGCAC	59.816	66.667	0.00	0.00	41.42	5.34
906	908	2.395336	TCAGATGGCCAGCTCTAGAT	57.605	50.000	23.48	0.00	0.00	1.98
910	912	0.694771	TGTTTCAGATGGCCAGCTCT	59.305	50.000	23.48	12.47	0.00	4.09
933	935	3.812019	GCTTGCAGCGCTGATGCT	61.812	61.111	40.21	0.00	45.80	3.79
993	995	4.408821	ACACGCGTCATGCCCCAT	62.409	61.111	9.86	0.00	42.08	4.00
1011	1013	2.089349	GCTGTCCGACTCGACTTGC	61.089	63.158	0.00	2.91	33.70	4.01
1022	1024	0.588252	CACCAACTCTTTGCTGTCCG	59.412	55.000	0.00	0.00	0.00	4.79
1036	1038	1.071699	GGTAGTCAGTGCCTTCACCAA	59.928	52.381	0.00	0.00	44.16	3.67
1070	1072	0.183492	TATGATGCCTTCAGCCACCC	59.817	55.000	0.00	0.00	42.71	4.61
1073	1075	3.136992	TCTGAATATGATGCCTTCAGCCA	59.863	43.478	6.64	0.00	43.49	4.75
1089	1091	5.641209	GGCAAACTCGCATATATCTCTGAAT	59.359	40.000	0.00	0.00	0.00	2.57
1137	1139	1.553184	CCCCTTGGGGCAAAAGAGAAT	60.553	52.381	12.40	0.00	42.67	2.40
1167	1169	3.334691	AGAAGCTACAACATGCGCTAAA	58.665	40.909	9.73	0.00	29.21	1.85
1173	1175	4.398247	CTCGAAAAGAAGCTACAACATGC	58.602	43.478	0.00	0.00	0.00	4.06
1182	1184	2.161211	GCTCATTGCTCGAAAAGAAGCT	59.839	45.455	0.00	0.00	38.95	3.74
1186	1188	2.481568	CAGTGCTCATTGCTCGAAAAGA	59.518	45.455	0.00	0.00	43.37	2.52
1188	1190	1.069022	GCAGTGCTCATTGCTCGAAAA	60.069	47.619	8.18	0.00	40.37	2.29
1204	1206	0.392193	CAAATCTCCCGAGCAGCAGT	60.392	55.000	0.00	0.00	0.00	4.40
1270	1272	0.404040	CCTTAACCAGGTCCAGCCAA	59.596	55.000	0.00	0.00	37.99	4.52
1409	1411	6.250527	ACGAAAAACAGAATCTGTCAAAAACG	59.749	34.615	17.02	17.61	44.62	3.60
1560	1563	6.330278	GTTAGTGAAAGAAAGCAAAACCACT	58.670	36.000	0.00	0.00	37.40	4.00
1586	1589	6.479884	ACTCAACAGGAAATCTCATAAGCTT	58.520	36.000	3.48	3.48	0.00	3.74
1655	1658	5.302823	GCTTTTGCCACTCCTTATTCCATAT	59.697	40.000	0.00	0.00	40.15	1.78
1730	1733	1.076777	GCATCCCCAAGCTTAGGCA	60.077	57.895	5.25	0.00	41.70	4.75
1882	1885	9.733556	AAAAGGTGTGTACATCAAGTATGATTA	57.266	29.630	0.00	0.00	43.89	1.75
2121	2125	1.802553	TGCCTACCATTCTAGGACCC	58.197	55.000	0.00	0.00	36.10	4.46
2170	2174	5.114764	TCATAGCATCCAATTCACTTCCA	57.885	39.130	0.00	0.00	0.00	3.53
2223	2228	9.212641	CATGACTTTAATATCACTACCTCCATG	57.787	37.037	0.00	0.00	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.