AutoCloner

Multiple sequence alignment - TraesCS2A01G060400

Loading Multiple Alignment...

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	TraesCS2A01G060400	chr2A	100.000	4379	0	0	1	4379	27128064	27123686	0.000000e+00	8087.0
1	TraesCS2A01G060400	chr2A	87.019	1040	86	23	2650	3659	27276806	27275786	0.000000e+00	1127.0
2	TraesCS2A01G060400	chr2A	92.089	493	34	2	876	1368	27277349	27276862	0.000000e+00	689.0
3	TraesCS2A01G060400	chr2D	97.115	1733	44	5	2646	4376	24878476	24880204	0.000000e+00	2918.0
4	TraesCS2A01G060400	chr2D	92.410	1423	78	9	1	1413	24877081	24878483	0.000000e+00	2002.0
5	TraesCS2A01G060400	chr2D	92.636	1032	57	10	1427	2450	13656846	13655826	0.000000e+00	1467.0
6	TraesCS2A01G060400	chr2D	91.139	474	38	4	1	473	573962843	573963313	1.330000e-179	640.0
7	TraesCS2A01G060400	chr2D	88.041	485	51	4	1	481	16007533	16007052	6.360000e-158	568.0
8	TraesCS2A01G060400	chr2D	88.186	474	42	9	1	474	538950356	538950815	1.780000e-153	553.0
9	TraesCS2A01G060400	chr2D	89.286	224	15	1	2442	2656	13655797	13655574	5.580000e-69	272.0
10	TraesCS2A01G060400	chr2D	92.079	101	8	0	2511	2611	587588101	587588001	4.570000e-30	143.0
11	TraesCS2A01G060400	chr7A	99.352	1234	7	1	1414	2647	14837736	14836504	0.000000e+00	2233.0
12	TraesCS2A01G060400	chr7A	97.808	1232	24	2	1414	2645	120751359	120752587	0.000000e+00	2122.0
13	TraesCS2A01G060400	chr7A	79.894	189	29	5	2461	2648	622947218	622947398	3.550000e-26	130.0
14	TraesCS2A01G060400	chr3D	93.110	1045	53	10	1414	2450	559221609	559220576	0.000000e+00	1513.0
15	TraesCS2A01G060400	chr3D	92.850	1049	54	11	1412	2450	39024468	39023431	0.000000e+00	1502.0
16	TraesCS2A01G060400	chr3D	90.233	215	12	1	2441	2646	559220548	559220334	5.580000e-69	272.0
17	TraesCS2A01G060400	chr3D	90.187	214	11	2	2442	2646	39023402	39023190	2.010000e-68	270.0
18	TraesCS2A01G060400	chr6D	92.830	1046	55	10	1414	2450	312957068	312956034	0.000000e+00	1498.0
19	TraesCS2A01G060400	chr6D	89.030	474	49	3	1	473	141272285	141272756	6.310000e-163	584.0
20	TraesCS2A01G060400	chr6D	90.233	215	12	1	2441	2646	312956009	312955795	5.580000e-69	272.0
21	TraesCS2A01G060400	chr6D	77.480	373	74	7	991	1361	385787088	385786724	9.540000e-52	215.0
22	TraesCS2A01G060400	chr6D	74.603	252	58	5	3100	3348	385786183	385785935	5.990000e-19	106.0
23	TraesCS2A01G060400	chr4D	92.741	1047	58	9	1412	2450	367747892	367748928	0.000000e+00	1496.0
24	TraesCS2A01G060400	chr4D	87.605	476	53	6	1	473	5724538	5725010	8.280000e-152	547.0
25	TraesCS2A01G060400	chr4D	91.038	212	10	1	2443	2645	367748958	367749169	1.200000e-70	278.0
26	TraesCS2A01G060400	chr4D	77.865	384	73	9	981	1361	422548504	422548878	1.230000e-55	228.0
27	TraesCS2A01G060400	chr2B	88.396	767	51	4	2643	3383	39978135	39977381	0.000000e+00	889.0
28	TraesCS2A01G060400	chr2B	93.647	425	25	2	946	1368	39978595	39978171	6.180000e-178	634.0
29	TraesCS2A01G060400	chr2B	84.524	168	19	4	1826	1990	17470691	17470854	4.530000e-35	159.0
30	TraesCS2A01G060400	chr1A	89.121	478	46	4	1	473	553906272	553906748	1.360000e-164	590.0
31	TraesCS2A01G060400	chr1A	88.325	197	22	1	1414	1609	584756340	584756536	7.320000e-58	235.0
32	TraesCS2A01G060400	chr1A	89.130	46	2	2	3597	3640	12311968	12312012	2.000000e-03	54.7
33	TraesCS2A01G060400	chr5D	88.632	475	48	4	1	474	175788502	175788971	1.370000e-159	573.0
34	TraesCS2A01G060400	chr3A	81.404	769	78	25	1656	2396	20360494	20361225	6.360000e-158	568.0
35	TraesCS2A01G060400	chr3A	84.848	165	20	4	1826	1990	26412476	26412317	1.260000e-35	161.0
36	TraesCS2A01G060400	chrUn	85.983	478	58	6	2	473	87111088	87110614	1.820000e-138	503.0
37	TraesCS2A01G060400	chr6B	86.266	466	56	8	1	464	402757683	402758142	2.350000e-137	499.0
38	TraesCS2A01G060400	chr6A	78.133	375	68	10	991	1361	530252933	530252569	4.410000e-55	226.0
39	TraesCS2A01G060400	chr6A	74.409	254	55	9	3100	3348	530252026	530251778	2.790000e-17	100.0

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	TraesCS2A01G060400	chr2A	27123686	27128064	4378	True	8087.0	8087	100.0000	1	4379	1	chr2A.!!$R1	4378
1	TraesCS2A01G060400	chr2A	27275786	27277349	1563	True	908.0	1127	89.5540	876	3659	2	chr2A.!!$R2	2783
2	TraesCS2A01G060400	chr2D	24877081	24880204	3123	False	2460.0	2918	94.7625	1	4376	2	chr2D.!!$F3	4375
3	TraesCS2A01G060400	chr2D	13655574	13656846	1272	True	869.5	1467	90.9610	1427	2656	2	chr2D.!!$R3	1229
4	TraesCS2A01G060400	chr7A	14836504	14837736	1232	True	2233.0	2233	99.3520	1414	2647	1	chr7A.!!$R1	1233
5	TraesCS2A01G060400	chr7A	120751359	120752587	1228	False	2122.0	2122	97.8080	1414	2645	1	chr7A.!!$F1	1231
6	TraesCS2A01G060400	chr3D	559220334	559221609	1275	True	892.5	1513	91.6715	1414	2646	2	chr3D.!!$R2	1232
7	TraesCS2A01G060400	chr3D	39023190	39024468	1278	True	886.0	1502	91.5185	1412	2646	2	chr3D.!!$R1	1234
8	TraesCS2A01G060400	chr6D	312955795	312957068	1273	True	885.0	1498	91.5315	1414	2646	2	chr6D.!!$R1	1232
9	TraesCS2A01G060400	chr4D	367747892	367749169	1277	False	887.0	1496	91.8895	1412	2645	2	chr4D.!!$F3	1233
10	TraesCS2A01G060400	chr2B	39977381	39978595	1214	True	761.5	889	91.0215	946	3383	2	chr2B.!!$R1	2437
11	TraesCS2A01G060400	chr3A	20360494	20361225	731	False	568.0	568	81.4040	1656	2396	1	chr3A.!!$F1	740

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
989	999	1.078426	GAATACCGGCCAGCACTGT	60.078	57.895	0.0	0.0	0.00	3.55	F
2914	3058	0.178068	GACTACGGCATGACCACCAT	59.822	55.000	0.0	0.0	39.03	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2939	3083	1.675801	CTTGAGCTGCACCTCCAGA	59.324	57.895	6.57	0.0	34.77	3.86	R
4348	4545	1.609061	CCACAGACAACGAGGCAGATT	60.609	52.381	0.00	0.0	0.00	2.40	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
76	77	3.788333	AAGTGCATGTATCATGGCAAC	57.212	42.857	10.96	0.00	38.10	4.17
96	97	6.071616	GGCAACTTTAGTTTATGGTTCATGGA	60.072	38.462	0.00	0.00	35.83	3.41
98	99	7.542130	GCAACTTTAGTTTATGGTTCATGGAAG	59.458	37.037	0.00	0.00	35.83	3.46
103	104	5.501156	AGTTTATGGTTCATGGAAGGTCTC	58.499	41.667	0.00	0.00	0.00	3.36
116	117	6.110411	TGGAAGGTCTCGTTTCTTAATTCT	57.890	37.500	0.00	0.00	0.00	2.40
204	205	5.278463	GCAACTTCAGTGTAAACATCATGGT	60.278	40.000	0.00	0.00	0.00	3.55
224	225	7.503230	TCATGGTAATTCATGTGCAATAGACAT	59.497	33.333	6.93	0.00	43.52	3.06
231	232	5.556355	CATGTGCAATAGACATGTCAACT	57.444	39.130	27.02	9.85	43.81	3.16
232	233	5.946298	CATGTGCAATAGACATGTCAACTT	58.054	37.500	27.02	13.95	43.81	2.66
233	234	6.384224	CATGTGCAATAGACATGTCAACTTT	58.616	36.000	27.02	11.78	43.81	2.66
235	236	7.503521	TGTGCAATAGACATGTCAACTTTTA	57.496	32.000	27.02	10.35	0.00	1.52
236	237	7.935520	TGTGCAATAGACATGTCAACTTTTAA	58.064	30.769	27.02	5.00	0.00	1.52
237	238	7.860373	TGTGCAATAGACATGTCAACTTTTAAC	59.140	33.333	27.02	14.84	0.00	2.01
238	239	7.326063	GTGCAATAGACATGTCAACTTTTAACC	59.674	37.037	27.02	5.87	0.00	2.85
239	240	6.806739	GCAATAGACATGTCAACTTTTAACCC	59.193	38.462	27.02	0.00	0.00	4.11
240	241	7.309194	GCAATAGACATGTCAACTTTTAACCCT	60.309	37.037	27.02	4.73	0.00	4.34
329	330	5.469373	TGATGAAAACGGATCTTCAATCG	57.531	39.130	0.00	0.00	35.31	3.34
375	384	9.996554	ATAAAGACGGAAAATCCAAAAAGATTT	57.003	25.926	0.00	0.00	46.04	2.17
428	437	4.049186	GTCTGTATGTTATAGGGCGTGTG	58.951	47.826	0.00	0.00	0.00	3.82
442	451	2.112297	TGTGGGCGGGTTTGACTC	59.888	61.111	0.00	0.00	0.00	3.36
482	491	5.290400	GCGTTAGCGTTATCCTTCTTTTAGT	59.710	40.000	0.00	0.00	40.81	2.24
494	503	5.860182	TCCTTCTTTTAGTGTACGTGATTCG	59.140	40.000	0.00	0.00	46.00	3.34
545	554	4.899502	ACGTGAGATCTGTTTCTTCCATT	58.100	39.130	0.00	0.00	0.00	3.16
562	571	7.344134	TCTTCCATTGAACATGATTCTGAGAT	58.656	34.615	0.00	0.00	0.00	2.75
565	574	6.766467	TCCATTGAACATGATTCTGAGATCTG	59.234	38.462	0.00	0.00	0.00	2.90
566	575	6.542735	CCATTGAACATGATTCTGAGATCTGT	59.457	38.462	0.00	0.00	0.00	3.41
596	605	2.593346	ATGAGGCACGTGAGATCTTC	57.407	50.000	22.23	7.90	0.00	2.87
597	606	1.550327	TGAGGCACGTGAGATCTTCT	58.450	50.000	22.23	3.91	0.00	2.85
598	607	1.895798	TGAGGCACGTGAGATCTTCTT	59.104	47.619	22.23	0.00	0.00	2.52
604	613	5.352569	AGGCACGTGAGATCTTCTTTTTATG	59.647	40.000	22.23	0.00	0.00	1.90
605	614	5.447818	GGCACGTGAGATCTTCTTTTTATGG	60.448	44.000	22.23	0.00	0.00	2.74
626	635	6.166984	TGGCGATGAGATCTCTTCTTTTAT	57.833	37.500	27.03	11.79	33.74	1.40
628	637	6.183360	TGGCGATGAGATCTCTTCTTTTATCA	60.183	38.462	27.03	16.39	33.74	2.15
633	642	9.906660	GATGAGATCTCTTCTTTTATCATACGT	57.093	33.333	24.43	0.00	33.74	3.57
642	651	8.879759	TCTTCTTTTATCATACGTGATTGTTCC	58.120	33.333	0.00	0.00	42.37	3.62
643	652	8.554835	TTCTTTTATCATACGTGATTGTTCCA	57.445	30.769	0.00	0.00	42.37	3.53
650	659	7.915293	TCATACGTGATTGTTCCAAGTTTAT	57.085	32.000	0.00	0.00	0.00	1.40
657	666	9.672086	CGTGATTGTTCCAAGTTTATTTTTCTA	57.328	29.630	0.00	0.00	0.00	2.10
688	697	9.506018	TGTGATCTTGATTCTGAGATTTGTTTA	57.494	29.630	0.00	0.00	32.96	2.01
915	925	5.437289	TCAAGCAACTCACACCAATTAAG	57.563	39.130	0.00	0.00	0.00	1.85
947	957	3.525619	TTCCGATCGAACACCAAGG	57.474	52.632	18.66	0.00	0.00	3.61
989	999	1.078426	GAATACCGGCCAGCACTGT	60.078	57.895	0.00	0.00	0.00	3.55
1213	1223	2.832661	AGGCCAAGCAACGCAACA	60.833	55.556	5.01	0.00	0.00	3.33
1276	1287	2.105128	GCATGGCGTACGAGAGCT	59.895	61.111	21.65	0.00	0.00	4.09
1303	1314	2.283529	AAGGATGTCACCGACGCCT	61.284	57.895	3.35	3.35	40.12	5.52
1682	1710	1.493311	GACGAAGCAAAGCTGACGG	59.507	57.895	17.75	2.11	40.99	4.79
1727	1755	4.587684	GGAATTTCCCTCACGTAGATAGGA	59.412	45.833	3.89	5.36	35.55	2.94
1728	1756	5.509332	GGAATTTCCCTCACGTAGATAGGAC	60.509	48.000	3.89	0.00	35.55	3.85
2633	2777	9.074576	CACTATGTTAGGTAGTATGATGTACCA	57.925	37.037	8.12	0.00	41.19	3.25
2790	2934	1.361271	GGTGTCCGAGACGAACACA	59.639	57.895	14.41	2.22	43.96	3.72
2874	3018	0.670854	GGAGGAGAACACGTCCAAGC	60.671	60.000	0.00	0.00	42.28	4.01
2914	3058	0.178068	GACTACGGCATGACCACCAT	59.822	55.000	0.00	0.00	39.03	3.55
2939	3083	2.743718	CAGCACGAGGTTGAGGGT	59.256	61.111	0.00	0.00	0.00	4.34
3006	3150	2.202570	CGGACACGGTCGTCATCC	60.203	66.667	11.33	11.33	37.66	3.51
3264	3437	2.119655	CCCTCTGGTCTACCGTCCG	61.120	68.421	0.00	0.00	39.43	4.79
3283	3456	1.019673	GTGCGATCCCTACGAGTACA	58.980	55.000	0.00	0.00	0.00	2.90
3318	3491	2.038269	GGACGAAGGCCGCAAATCA	61.038	57.895	0.00	0.00	43.32	2.57
3532	3729	8.956426	TCTTATGTTTTCAGTTTTGTTCAGACT	58.044	29.630	0.00	0.00	0.00	3.24
3664	3861	7.414222	ACCGATGACCTCAAGTTTATACTAA	57.586	36.000	0.00	0.00	33.17	2.24
3705	3902	4.025401	CGCAACCACGAGGGCAAC	62.025	66.667	3.29	0.00	42.05	4.17
3753	3950	3.004839	GCAACATGTAGCGGATCTAGAGA	59.995	47.826	0.00	0.00	0.00	3.10
3779	3976	8.890472	AGGAGCCATGGAATAATTTGTACTATA	58.110	33.333	18.40	0.00	0.00	1.31
3920	4117	6.432403	TCAAAGGATAAAATGGCAGGTTTT	57.568	33.333	4.49	4.46	33.67	2.43
4132	4329	6.681777	AGTATGTGGATTCTTCAAAAGCAAC	58.318	36.000	0.00	0.00	0.00	4.17
4136	4333	4.925646	GTGGATTCTTCAAAAGCAACATCC	59.074	41.667	0.00	0.00	0.00	3.51
4145	4342	0.773644	AAGCAACATCCCCACTCTGT	59.226	50.000	0.00	0.00	0.00	3.41
4243	4440	9.618890	ATTCTCATGTGTGCTATGTTTATTACT	57.381	29.630	0.00	0.00	0.00	2.24
4302	4499	1.528309	AAAACACCTCCTGCCCACG	60.528	57.895	0.00	0.00	0.00	4.94
4307	4504	3.461773	CCTCCTGCCCACGATCGT	61.462	66.667	16.60	16.60	0.00	3.73
4317	4514	1.681793	CCCACGATCGTCTCCAACTAT	59.318	52.381	19.84	0.00	0.00	2.12
4331	4528	2.618045	CCAACTATGGTTTCCCGCTTCT	60.618	50.000	0.00	0.00	42.18	2.85
4359	4556	1.736586	CGCCTCTAATCTGCCTCGT	59.263	57.895	0.00	0.00	0.00	4.18
4360	4557	0.103208	CGCCTCTAATCTGCCTCGTT	59.897	55.000	0.00	0.00	0.00	3.85
4376	4573	0.673644	CGTTGTCTGTGGCCTTAGGG	60.674	60.000	3.32	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	6.238842	GCCATGATACATGCACTTAGAATTGT	60.239	38.462	0.00	0.00	0.00	2.71
54	55	4.577693	AGTTGCCATGATACATGCACTTAG	59.422	41.667	0.00	0.00	32.63	2.18
76	77	7.611855	AGACCTTCCATGAACCATAAACTAAAG	59.388	37.037	0.00	0.00	0.00	1.85
96	97	5.169295	CGGAGAATTAAGAAACGAGACCTT	58.831	41.667	0.00	0.00	0.00	3.50
98	99	4.492611	ACGGAGAATTAAGAAACGAGACC	58.507	43.478	0.00	0.00	0.00	3.85
164	165	8.571336	ACTGAAGTTGCCATGATATATTTTAGC	58.429	33.333	0.00	0.00	0.00	3.09
167	168	8.297470	ACACTGAAGTTGCCATGATATATTTT	57.703	30.769	0.00	0.00	0.00	1.82
175	176	4.203226	TGTTTACACTGAAGTTGCCATGA	58.797	39.130	0.00	0.00	0.00	3.07
299	300	9.177608	TGAAGATCCGTTTTCATCATTAAATCT	57.822	29.630	0.00	0.00	0.00	2.40
309	310	6.683974	ATTCGATTGAAGATCCGTTTTCAT	57.316	33.333	1.10	0.00	37.57	2.57
350	351	9.825109	AAAATCTTTTTGGATTTTCCGTCTTTA	57.175	25.926	8.72	0.00	46.51	1.85
398	407	0.462375	TAACATACAGACCGCGCCAT	59.538	50.000	0.00	0.00	0.00	4.40
428	437	2.112297	TGTGAGTCAAACCCGCCC	59.888	61.111	0.00	0.00	0.00	6.13
457	466	2.953466	AGAAGGATAACGCTAACGCA	57.047	45.000	0.00	0.00	45.53	5.24
469	478	6.530534	CGAATCACGTACACTAAAAGAAGGAT	59.469	38.462	0.00	0.00	37.22	3.24
482	491	4.713824	AGAAATCTCCGAATCACGTACA	57.286	40.909	0.00	0.00	40.78	2.90
545	554	7.991084	AAAACAGATCTCAGAATCATGTTCA	57.009	32.000	0.00	0.00	31.63	3.18
596	605	6.705381	AGAAGAGATCTCATCGCCATAAAAAG	59.295	38.462	24.39	0.00	30.46	2.27
597	606	6.586344	AGAAGAGATCTCATCGCCATAAAAA	58.414	36.000	24.39	0.00	30.46	1.94
598	607	6.166984	AGAAGAGATCTCATCGCCATAAAA	57.833	37.500	24.39	0.00	30.46	1.52
604	613	6.219473	TGATAAAAGAAGAGATCTCATCGCC	58.781	40.000	24.39	8.32	37.42	5.54
605	614	7.887996	ATGATAAAAGAAGAGATCTCATCGC	57.112	36.000	24.39	10.21	37.42	4.58
638	647	8.568794	ACAGCTCTAGAAAAATAAACTTGGAAC	58.431	33.333	0.00	0.00	0.00	3.62
642	651	9.766277	GATCACAGCTCTAGAAAAATAAACTTG	57.234	33.333	0.00	0.00	0.00	3.16
643	652	9.732130	AGATCACAGCTCTAGAAAAATAAACTT	57.268	29.630	0.00	0.00	0.00	2.66
650	659	8.099537	AGAATCAAGATCACAGCTCTAGAAAAA	58.900	33.333	0.00	0.00	0.00	1.94
657	666	4.710865	TCTCAGAATCAAGATCACAGCTCT	59.289	41.667	0.00	0.00	0.00	4.09
774	783	8.846943	ATTAACTAATTGGATGCATCATACGA	57.153	30.769	27.25	11.02	0.00	3.43
848	857	3.731264	GCGTCTCGTCTAATGCTTGTACT	60.731	47.826	0.00	0.00	0.00	2.73
849	858	2.530700	GCGTCTCGTCTAATGCTTGTAC	59.469	50.000	0.00	0.00	0.00	2.90
850	859	2.162809	TGCGTCTCGTCTAATGCTTGTA	59.837	45.455	0.00	0.00	0.00	2.41
851	860	1.067846	TGCGTCTCGTCTAATGCTTGT	60.068	47.619	0.00	0.00	0.00	3.16
852	861	1.321743	GTGCGTCTCGTCTAATGCTTG	59.678	52.381	0.00	0.00	0.00	4.01
853	862	1.067846	TGTGCGTCTCGTCTAATGCTT	60.068	47.619	0.00	0.00	0.00	3.91
854	863	0.526211	TGTGCGTCTCGTCTAATGCT	59.474	50.000	0.00	0.00	0.00	3.79
855	864	0.640768	GTGTGCGTCTCGTCTAATGC	59.359	55.000	0.00	0.00	0.00	3.56
856	865	1.914051	CAGTGTGCGTCTCGTCTAATG	59.086	52.381	0.00	0.00	0.00	1.90
947	957	0.509499	TTTCGTGCGTGAATTCGTCC	59.491	50.000	0.04	0.00	0.00	4.79
989	999	0.179054	GATCTCCATGAGCTGCTGCA	60.179	55.000	18.42	0.88	42.74	4.41
1104	1114	2.514896	TGCTGGACATGCACCACA	59.485	55.556	7.95	8.64	35.31	4.17
1206	1216	1.098869	TGTCATTGTTGGTGTTGCGT	58.901	45.000	0.00	0.00	0.00	5.24
1213	1223	2.483877	CGTACTGCATGTCATTGTTGGT	59.516	45.455	0.00	0.00	0.00	3.67
1276	1287	0.804364	GTGACATCCTTGATGCGCAA	59.196	50.000	17.11	0.00	43.15	4.85
1303	1314	1.737735	CGAAGTCGCTGATGTGGCA	60.738	57.895	0.00	0.00	0.00	4.92
1727	1755	4.127171	AGCTTTTCTACATCGTTGTGTGT	58.873	39.130	9.39	0.00	36.53	3.72
1728	1756	4.377431	GGAGCTTTTCTACATCGTTGTGTG	60.377	45.833	9.39	2.79	36.53	3.82
2647	2791	6.781507	TGGGATCCATATGCATGTCAAAAATA	59.218	34.615	15.23	0.00	0.00	1.40
2650	2794	4.544683	TGGGATCCATATGCATGTCAAAA	58.455	39.130	15.23	0.00	0.00	2.44
2652	2796	3.880168	TGGGATCCATATGCATGTCAA	57.120	42.857	15.23	0.00	0.00	3.18
2656	2800	4.282449	ACAATGTTGGGATCCATATGCATG	59.718	41.667	15.23	6.55	31.53	4.06
2657	2801	4.485875	ACAATGTTGGGATCCATATGCAT	58.514	39.130	15.23	3.79	31.53	3.96
2658	2802	3.913509	ACAATGTTGGGATCCATATGCA	58.086	40.909	15.23	5.19	31.53	3.96
2659	2803	4.099881	ACAACAATGTTGGGATCCATATGC	59.900	41.667	27.15	0.00	35.91	3.14
2660	2804	5.857471	ACAACAATGTTGGGATCCATATG	57.143	39.130	27.15	5.92	35.91	1.78
2868	3012	4.399395	CGGCAGGCTCAGCTTGGA	62.399	66.667	11.30	0.00	36.14	3.53
2939	3083	1.675801	CTTGAGCTGCACCTCCAGA	59.324	57.895	6.57	0.00	34.77	3.86
3264	3437	1.002684	CTGTACTCGTAGGGATCGCAC	60.003	57.143	12.83	7.31	0.00	5.34
3283	3456	2.711922	CCGAGTACTGGAAGGCGCT	61.712	63.158	7.64	0.00	39.30	5.92
3686	3883	3.545124	TTGCCCTCGTGGTTGCGAT	62.545	57.895	2.33	0.00	40.29	4.58
3705	3902	6.136155	ACCTGGGGATAATAAATTGACCAAG	58.864	40.000	0.00	0.00	0.00	3.61
3753	3950	6.018433	AGTACAAATTATTCCATGGCTCCT	57.982	37.500	6.96	0.00	0.00	3.69
3920	4117	5.133941	ACCTAAGCATCGATCACTCTCTAA	58.866	41.667	0.00	0.00	0.00	2.10
4156	4353	6.697019	CCATTGTAATAACCATTTGCTGTAGC	59.303	38.462	0.00	0.00	42.50	3.58
4157	4354	7.995289	TCCATTGTAATAACCATTTGCTGTAG	58.005	34.615	0.00	0.00	0.00	2.74
4158	4355	7.946381	TCCATTGTAATAACCATTTGCTGTA	57.054	32.000	0.00	0.00	0.00	2.74
4159	4356	6.849085	TCCATTGTAATAACCATTTGCTGT	57.151	33.333	0.00	0.00	0.00	4.40
4160	4357	9.814899	TTATTCCATTGTAATAACCATTTGCTG	57.185	29.630	0.00	0.00	0.00	4.41
4243	4440	3.873910	GCCTTTGGCTTCAGTATAGTCA	58.126	45.455	0.73	0.00	46.69	3.41
4273	4470	1.676006	GAGGTGTTTTGGGTGTGACTG	59.324	52.381	0.00	0.00	0.00	3.51
4302	4499	4.120589	GGAAACCATAGTTGGAGACGATC	58.879	47.826	0.00	0.00	46.92	3.69
4344	4541	3.119316	ACAGACAACGAGGCAGATTAGAG	60.119	47.826	0.00	0.00	0.00	2.43
4347	4544	2.353704	CCACAGACAACGAGGCAGATTA	60.354	50.000	0.00	0.00	0.00	1.75
4348	4545	1.609061	CCACAGACAACGAGGCAGATT	60.609	52.381	0.00	0.00	0.00	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.