AutoCloner

Multiple sequence alignment - TraesCS6A01G377500

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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	TraesCS6A01G377500	chr6A	100.000	4566	0	0	1	4566	598788619	598793184	0.000000e+00	8432
1	TraesCS6A01G377500	chr6A	78.208	2221	381	56	1362	3566	598810401	598812534	0.000000e+00	1325
2	TraesCS6A01G377500	chr6A	83.360	1268	191	12	2309	3569	598925569	598924315	0.000000e+00	1155
3	TraesCS6A01G377500	chr6A	81.038	944	151	21	972	1900	598926820	598925890	0.000000e+00	726
4	TraesCS6A01G377500	chr6A	78.868	866	137	31	1082	1930	598157642	598156806	1.120000e-150	544
5	TraesCS6A01G377500	chr6A	74.201	845	173	31	1097	1914	598189254	598190080	1.230000e-80	311
6	TraesCS6A01G377500	chr6D	96.000	2600	102	1	1969	4566	452841038	452843637	0.000000e+00	4224
7	TraesCS6A01G377500	chr6D	95.009	1162	35	10	780	1941	452839440	452840578	0.000000e+00	1803
8	TraesCS6A01G377500	chr6D	84.076	1256	194	4	2317	3569	452907500	452908752	0.000000e+00	1206
9	TraesCS6A01G377500	chr6D	83.971	1254	184	9	2318	3569	452931169	452929931	0.000000e+00	1186
10	TraesCS6A01G377500	chr6D	78.186	1169	189	42	1082	2219	452485797	452484664	0.000000e+00	686
11	TraesCS6A01G377500	chr6D	94.903	412	18	3	1	409	452834190	452834601	3.850000e-180	641
12	TraesCS6A01G377500	chr6D	80.560	571	93	11	1366	1927	452848799	452849360	1.520000e-114	424
13	TraesCS6A01G377500	chr6D	94.595	185	8	2	603	787	452837745	452837927	7.480000e-73	285
14	TraesCS6A01G377500	chr6D	89.252	214	9	4	400	604	452837202	452837410	5.860000e-64	255
15	TraesCS6A01G377500	chr6B	95.583	1811	80	0	1987	3797	687732623	687734433	0.000000e+00	2902
16	TraesCS6A01G377500	chr6B	94.222	848	46	3	1105	1950	687731782	687732628	0.000000e+00	1291
17	TraesCS6A01G377500	chr6B	84.848	1254	178	6	2320	3565	688033490	688032241	0.000000e+00	1253
18	TraesCS6A01G377500	chr6B	83.109	1261	209	2	2309	3569	688064585	688063329	0.000000e+00	1146
19	TraesCS6A01G377500	chr6B	83.360	1262	178	13	2310	3569	688125227	688123996	0.000000e+00	1138
20	TraesCS6A01G377500	chr6B	84.211	950	149	1	2319	3267	687876236	687877185	0.000000e+00	922
21	TraesCS6A01G377500	chr6B	79.502	844	145	23	1082	1914	687180441	687179615	3.960000e-160	575
22	TraesCS6A01G377500	chr6B	74.584	842	175	29	1100	1917	687135229	687134403	2.630000e-87	333
23	TraesCS6A01G377500	chr6B	88.889	252	16	8	632	878	687731450	687731694	2.670000e-77	300
24	TraesCS6A01G377500	chr6B	92.814	167	12	0	4400	4566	687736339	687736505	4.560000e-60	243
25	TraesCS6A01G377500	chr6B	83.071	254	39	3	2003	2253	687179497	687179245	1.280000e-55	228
26	TraesCS6A01G377500	chr1D	81.333	300	46	5	112	409	1446691	1446982	7.640000e-58	235
27	TraesCS6A01G377500	chr3B	83.051	118	11	6	4169	4279	101678070	101677955	1.050000e-16	99

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	TraesCS6A01G377500	chr6A	598788619	598793184	4565	False	8432.0	8432	100.0000	1	4566	1	chr6A.!!$F2	4565
1	TraesCS6A01G377500	chr6A	598810401	598812534	2133	False	1325.0	1325	78.2080	1362	3566	1	chr6A.!!$F3	2204
2	TraesCS6A01G377500	chr6A	598924315	598926820	2505	True	940.5	1155	82.1990	972	3569	2	chr6A.!!$R2	2597
3	TraesCS6A01G377500	chr6A	598156806	598157642	836	True	544.0	544	78.8680	1082	1930	1	chr6A.!!$R1	848
4	TraesCS6A01G377500	chr6A	598189254	598190080	826	False	311.0	311	74.2010	1097	1914	1	chr6A.!!$F1	817
5	TraesCS6A01G377500	chr6D	452834190	452843637	9447	False	1441.6	4224	93.9518	1	4566	5	chr6D.!!$F3	4565
6	TraesCS6A01G377500	chr6D	452907500	452908752	1252	False	1206.0	1206	84.0760	2317	3569	1	chr6D.!!$F2	1252
7	TraesCS6A01G377500	chr6D	452929931	452931169	1238	True	1186.0	1186	83.9710	2318	3569	1	chr6D.!!$R2	1251
8	TraesCS6A01G377500	chr6D	452484664	452485797	1133	True	686.0	686	78.1860	1082	2219	1	chr6D.!!$R1	1137
9	TraesCS6A01G377500	chr6D	452848799	452849360	561	False	424.0	424	80.5600	1366	1927	1	chr6D.!!$F1	561
10	TraesCS6A01G377500	chr6B	688032241	688033490	1249	True	1253.0	1253	84.8480	2320	3565	1	chr6B.!!$R2	1245
11	TraesCS6A01G377500	chr6B	687731450	687736505	5055	False	1184.0	2902	92.8770	632	4566	4	chr6B.!!$F2	3934
12	TraesCS6A01G377500	chr6B	688063329	688064585	1256	True	1146.0	1146	83.1090	2309	3569	1	chr6B.!!$R3	1260
13	TraesCS6A01G377500	chr6B	688123996	688125227	1231	True	1138.0	1138	83.3600	2310	3569	1	chr6B.!!$R4	1259
14	TraesCS6A01G377500	chr6B	687876236	687877185	949	False	922.0	922	84.2110	2319	3267	1	chr6B.!!$F1	948
15	TraesCS6A01G377500	chr6B	687179245	687180441	1196	True	401.5	575	81.2865	1082	2253	2	chr6B.!!$R5	1171
16	TraesCS6A01G377500	chr6B	687134403	687135229	826	True	333.0	333	74.5840	1100	1917	1	chr6B.!!$R1	817

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	Hairpin	End Stability	Orientation
243	247	0.178533	AACGTCGGGAAGAACACCAA	59.821	50.0	0.00	3.67	F
543	3156	0.391661	GCAGAAACAGGATCAGCGGA	60.392	55.0	0.00	5.54	F
2324	7332	0.036765	TTGGTTCTCCACGGGAATCG	60.037	55.0	44.22	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1634	6127	0.391130	GAGGAACACATAGCGGCACA	60.391	55.000	1.45	0.00	4.57	R
2374	7384	5.049474	GCATGTGAATAGTGACAAGAACACA	60.049	40.000	0.00	40.25	3.72	R
4140	9175	1.374947	CCTTTCAAGACGGCCCTGA	59.625	57.895	0.00	0.00	3.86	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	2.076863	CCGGATGTCAAGAAGTGAACC	58.923	52.381	0.00	0.00	38.23	3.62
43	44	3.253432	GGATGTCAAGAAGTGAACCAACC	59.747	47.826	0.00	0.00	38.23	3.77
48	49	0.249741	AGAAGTGAACCAACCGTCGG	60.250	55.000	10.48	10.48	0.00	4.79
87	90	4.390603	CCGACGTCCAACTGATAAATTTCA	59.609	41.667	10.58	0.00	0.00	2.69
148	151	2.029623	TCGCAAGGAGTATACTGGACC	58.970	52.381	10.90	5.52	38.47	4.46
163	166	1.067060	TGGACCGATATCAAGACTGCG	59.933	52.381	3.12	0.00	0.00	5.18
183	186	2.347490	GACCTTGCCGAGAAGCCA	59.653	61.111	0.00	0.00	0.00	4.75
243	247	0.178533	AACGTCGGGAAGAACACCAA	59.821	50.000	0.00	0.00	0.00	3.67
304	308	1.103803	CTGAAGGACTCCCGATTCGA	58.896	55.000	7.83	0.00	37.58	3.71
409	413	1.004511	AGGAGCAGATTTGAAGCAGCT	59.995	47.619	0.00	0.00	39.92	4.24
410	414	1.132643	GGAGCAGATTTGAAGCAGCTG	59.867	52.381	10.11	10.11	37.29	4.24
415	3028	3.129988	GCAGATTTGAAGCAGCTGGTAAT	59.870	43.478	20.51	15.19	0.00	1.89
430	3043	2.637382	TGGTAATCCACACAGAAGCAGA	59.363	45.455	0.00	0.00	39.03	4.26
489	3102	2.559668	AGACCATCAAACCAGTTGCATG	59.440	45.455	0.00	0.00	37.13	4.06
515	3128	2.901840	CATGGCAAGGGCGCGTAT	60.902	61.111	8.43	0.00	42.47	3.06
516	3129	1.596752	CATGGCAAGGGCGCGTATA	60.597	57.895	8.43	0.00	42.47	1.47
517	3130	0.955428	CATGGCAAGGGCGCGTATAT	60.955	55.000	8.43	0.00	42.47	0.86
518	3131	0.611200	ATGGCAAGGGCGCGTATATA	59.389	50.000	8.43	0.00	42.47	0.86
543	3156	0.391661	GCAGAAACAGGATCAGCGGA	60.392	55.000	0.00	0.00	0.00	5.54
573	3195	0.824109	GGCCAAACCCTAATTGCCTC	59.176	55.000	0.00	0.00	0.00	4.70
576	3198	1.007118	CCAAACCCTAATTGCCTCCCT	59.993	52.381	0.00	0.00	0.00	4.20
586	3208	0.980754	TTGCCTCCCTAATCGCAGGA	60.981	55.000	0.00	0.00	38.00	3.86
695	3653	3.119849	CGGATTTTAGGAGCACAAACAGG	60.120	47.826	0.00	0.00	0.00	4.00
733	3691	9.814899	ATTTATTTTTGAAATGGCGTCATATGA	57.185	25.926	1.27	0.00	32.44	2.15
765	3727	2.620251	TTGAGTATGGATCCGCTTGG	57.380	50.000	7.39	0.00	0.00	3.61
838	5319	3.055458	TGGAGAACGAGCATGGTCAAATA	60.055	43.478	23.68	1.52	0.00	1.40
839	5320	4.130118	GGAGAACGAGCATGGTCAAATAT	58.870	43.478	23.68	7.02	0.00	1.28
846	5327	4.093998	CGAGCATGGTCAAATATATCTGCC	59.906	45.833	23.68	0.00	0.00	4.85
869	5350	2.556766	CTTTCTCCTCCCCTTCCTTCT	58.443	52.381	0.00	0.00	0.00	2.85
870	5351	2.743131	TTCTCCTCCCCTTCCTTCTT	57.257	50.000	0.00	0.00	0.00	2.52
871	5352	2.255770	TCTCCTCCCCTTCCTTCTTC	57.744	55.000	0.00	0.00	0.00	2.87
872	5353	1.208706	CTCCTCCCCTTCCTTCTTCC	58.791	60.000	0.00	0.00	0.00	3.46
873	5354	0.800239	TCCTCCCCTTCCTTCTTCCT	59.200	55.000	0.00	0.00	0.00	3.36
874	5355	1.154434	TCCTCCCCTTCCTTCTTCCTT	59.846	52.381	0.00	0.00	0.00	3.36
875	5356	1.562008	CCTCCCCTTCCTTCTTCCTTC	59.438	57.143	0.00	0.00	0.00	3.46
876	5357	1.562008	CTCCCCTTCCTTCTTCCTTCC	59.438	57.143	0.00	0.00	0.00	3.46
877	5358	1.154434	TCCCCTTCCTTCTTCCTTCCT	59.846	52.381	0.00	0.00	0.00	3.36
878	5359	1.996291	CCCCTTCCTTCTTCCTTCCTT	59.004	52.381	0.00	0.00	0.00	3.36
879	5360	2.025793	CCCCTTCCTTCTTCCTTCCTTC	60.026	54.545	0.00	0.00	0.00	3.46
895	5376	4.642466	TCCTTCCTTCCTTCCTTCTTTC	57.358	45.455	0.00	0.00	0.00	2.62
897	5378	3.562393	CCTTCCTTCCTTCCTTCTTTCCC	60.562	52.174	0.00	0.00	0.00	3.97
941	5422	3.443045	GCATTCGCACCCACCCTG	61.443	66.667	0.00	0.00	38.36	4.45
942	5423	3.443045	CATTCGCACCCACCCTGC	61.443	66.667	0.00	0.00	0.00	4.85
943	5424	4.740822	ATTCGCACCCACCCTGCC	62.741	66.667	0.00	0.00	0.00	4.85
961	5442	1.516161	CCACCCATCATATCAGCGTG	58.484	55.000	0.00	0.00	0.00	5.34
1019	5500	0.394762	ATGTCAAGCATGGCGACCAT	60.395	50.000	5.65	5.65	46.37	3.55
1449	5939	1.352156	GCTACTTCAACGACGGCAGG	61.352	60.000	0.00	0.00	0.00	4.85
1593	6083	1.338769	GCCCTCTTTAACTTCTCGCCA	60.339	52.381	0.00	0.00	0.00	5.69
1634	6127	0.336737	TTCAACACCAACCCCACCTT	59.663	50.000	0.00	0.00	0.00	3.50
1958	6483	7.389330	TCGAGTCACCAACATTTTATTGTATGT	59.611	33.333	0.00	0.00	36.58	2.29
2324	7332	0.036765	TTGGTTCTCCACGGGAATCG	60.037	55.000	0.00	0.00	44.22	3.34
2374	7384	0.683504	ATCCAGGAGTTAGCGTCGGT	60.684	55.000	1.19	1.19	0.00	4.69
2485	7495	2.268920	GGAGGCGTCATCCTGCAA	59.731	61.111	8.91	0.00	43.22	4.08
2513	7525	4.840005	GCTCCTACAGTGGCGCCC	62.840	72.222	26.77	15.80	32.12	6.13
2644	7656	4.896482	GTGTATAGAGGTGTTCTGGAGGAT	59.104	45.833	0.00	0.00	36.61	3.24
2650	7662	4.230964	AGAGGTGTTCTGGAGGATAGTACT	59.769	45.833	0.00	0.00	33.93	2.73
3029	8043	0.966179	GGACTTTGGGGCGTCAAAAT	59.034	50.000	0.00	0.00	36.37	1.82
3152	8167	3.006003	TGACGTGTATAGCTTTGGTGTCA	59.994	43.478	0.00	0.00	0.00	3.58
3268	8283	2.014554	CAACCGACACGACGAGGTG	61.015	63.158	0.00	8.64	43.54	4.00
3368	8383	3.319198	GTGGGGAGGAGCGACCAA	61.319	66.667	5.84	0.00	42.04	3.67
3643	8676	1.214305	TTGGGGTGGCTAGCTGGATT	61.214	55.000	15.72	0.00	0.00	3.01
3721	8754	1.750778	CTGGGGATATGGTGTGTTTGC	59.249	52.381	0.00	0.00	0.00	3.68
3759	8792	9.594936	TTCCTCTAAATTCCCAACTTATCAAAA	57.405	29.630	0.00	0.00	0.00	2.44
3799	8832	4.546570	TGTTGACGAGTGTCTTGATACAG	58.453	43.478	0.00	0.00	45.70	2.74
3815	8848	8.539544	TCTTGATACAGAAATATGTTGAGACCA	58.460	33.333	0.00	0.00	34.56	4.02
3845	8878	1.538075	CGGGGACTTTATTTGTTGCGT	59.462	47.619	0.00	0.00	0.00	5.24
3854	8887	6.326375	ACTTTATTTGTTGCGTTCTGAAACA	58.674	32.000	0.00	0.00	44.70	2.83
3896	8929	1.901591	AGTGCACCTCATCCAAACAG	58.098	50.000	14.63	0.00	0.00	3.16
3950	8985	7.781219	TGGCGCCTATATACATACCTTTCTATA	59.219	37.037	29.70	0.00	0.00	1.31
3996	9031	3.743132	TGGGAACTTATGGGGTAGACAT	58.257	45.455	0.00	0.00	0.00	3.06
4002	9037	7.287810	GGAACTTATGGGGTAGACATTTACAT	58.712	38.462	0.00	0.00	0.00	2.29
4030	9065	5.736813	TGTACATAGGTGTTACCATTGGAC	58.263	41.667	10.37	0.00	41.95	4.02
4031	9066	4.919774	ACATAGGTGTTACCATTGGACA	57.080	40.909	10.37	0.92	41.95	4.02
4033	9068	5.253330	ACATAGGTGTTACCATTGGACAAG	58.747	41.667	10.37	0.00	41.95	3.16
4077	9112	6.424509	CACTTGTTGGTTTGAGTACGGTATTA	59.575	38.462	0.00	0.00	0.00	0.98
4079	9114	8.313292	ACTTGTTGGTTTGAGTACGGTATTATA	58.687	33.333	0.00	0.00	0.00	0.98
4140	9175	7.391148	ACGCAAGATGTACTTCCATAAAAAT	57.609	32.000	5.19	0.00	43.62	1.82
4148	9183	3.023832	ACTTCCATAAAAATCAGGGCCG	58.976	45.455	0.00	0.00	0.00	6.13
4158	9193	0.035056	ATCAGGGCCGTCTTGAAAGG	60.035	55.000	0.00	0.00	0.00	3.11
4328	9363	9.970395	GATATGTTGCAAGATTTGATGGATTTA	57.030	29.630	14.96	0.00	0.00	1.40
4371	9406	2.661866	GCACCACGCAGACGAAGT	60.662	61.111	0.00	0.00	43.54	3.01
4384	9419	1.299648	CGAAGTGCCCCATCTCCAA	59.700	57.895	0.00	0.00	0.00	3.53
4424	11203	1.961277	CGCCTTCAAGTGACGCCTT	60.961	57.895	0.00	0.00	0.00	4.35
4465	11244	4.216257	GCAACACCATCACTACACTTCATT	59.784	41.667	0.00	0.00	0.00	2.57
4468	11247	5.168569	ACACCATCACTACACTTCATTACG	58.831	41.667	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	2.766313	TGGTTCACTTCTTGACATCCG	58.234	47.619	0.00	0.00	32.26	4.18
28	29	1.578583	CGACGGTTGGTTCACTTCTT	58.421	50.000	0.00	0.00	0.00	2.52
58	59	4.324991	GTTGGACGTCGGGGCCTT	62.325	66.667	9.92	0.00	0.00	4.35
68	69	8.450964	ACTACAATGAAATTTATCAGTTGGACG	58.549	33.333	0.00	0.00	31.22	4.79
87	90	5.129485	ACATCTGCTTGGCTAGTACTACAAT	59.871	40.000	0.00	0.00	0.00	2.71
104	107	6.109359	AGTTTAGGTCTGAACATACATCTGC	58.891	40.000	8.07	0.00	32.27	4.26
142	145	2.748605	GCAGTCTTGATATCGGTCCAG	58.251	52.381	0.00	0.00	0.00	3.86
148	151	0.317854	TCCGCGCAGTCTTGATATCG	60.318	55.000	8.75	0.00	0.00	2.92
183	186	1.889105	CTGTCCTGCAGTGCGTGTT	60.889	57.895	13.81	0.00	40.27	3.32
304	308	3.118884	GCATCTGGATTTTGGCTGTTGAT	60.119	43.478	0.00	0.00	0.00	2.57
348	352	2.025418	GGACCACGGTGTTGCTACG	61.025	63.158	7.45	0.00	0.00	3.51
409	413	2.637382	TCTGCTTCTGTGTGGATTACCA	59.363	45.455	0.00	0.00	44.76	3.25
410	414	3.265791	CTCTGCTTCTGTGTGGATTACC	58.734	50.000	0.00	0.00	0.00	2.85
415	3028	1.413118	TGACTCTGCTTCTGTGTGGA	58.587	50.000	0.00	0.00	0.00	4.02
430	3043	3.423539	TTCTGTGCTAGCCAATTGACT	57.576	42.857	13.29	2.59	0.00	3.41
515	3128	1.828595	TCCTGTTTCTGCGCTGGTATA	59.171	47.619	14.70	0.74	0.00	1.47
516	3129	0.613260	TCCTGTTTCTGCGCTGGTAT	59.387	50.000	14.70	0.00	0.00	2.73
517	3130	0.613260	ATCCTGTTTCTGCGCTGGTA	59.387	50.000	14.70	0.19	0.00	3.25
518	3131	0.674895	GATCCTGTTTCTGCGCTGGT	60.675	55.000	14.70	0.00	0.00	4.00
573	3195	1.543802	CTAGAGCTCCTGCGATTAGGG	59.456	57.143	10.93	0.00	45.42	3.53
576	3198	2.231529	GTCCTAGAGCTCCTGCGATTA	58.768	52.381	10.93	0.00	45.42	1.75
586	3208	2.894126	CCCGAATACATGTCCTAGAGCT	59.106	50.000	0.00	0.00	0.00	4.09
695	3653	5.681880	TCAAAAATAAATGTGACGTCGTCC	58.318	37.500	22.05	13.73	0.00	4.79
733	3691	2.584835	TACTCAATTGCACTTGGGCT	57.415	45.000	16.01	6.75	29.17	5.19
765	3727	5.576384	TCGATATTTTTCAATTGCCTGTTGC	59.424	36.000	0.00	0.00	41.77	4.17
838	5319	2.371510	GGAGGAGAAAGCAGGCAGATAT	59.628	50.000	0.00	0.00	0.00	1.63
839	5320	1.765314	GGAGGAGAAAGCAGGCAGATA	59.235	52.381	0.00	0.00	0.00	1.98
846	5327	0.254462	GGAAGGGGAGGAGAAAGCAG	59.746	60.000	0.00	0.00	0.00	4.24
869	5350	3.005529	AGGAAGGAAGGAAGGAAGGAA	57.994	47.619	0.00	0.00	0.00	3.36
870	5351	2.743131	AGGAAGGAAGGAAGGAAGGA	57.257	50.000	0.00	0.00	0.00	3.36
871	5352	2.916269	AGAAGGAAGGAAGGAAGGAAGG	59.084	50.000	0.00	0.00	0.00	3.46
872	5353	4.649267	AAGAAGGAAGGAAGGAAGGAAG	57.351	45.455	0.00	0.00	0.00	3.46
873	5354	4.202577	GGAAAGAAGGAAGGAAGGAAGGAA	60.203	45.833	0.00	0.00	0.00	3.36
874	5355	3.330998	GGAAAGAAGGAAGGAAGGAAGGA	59.669	47.826	0.00	0.00	0.00	3.36
875	5356	3.562393	GGGAAAGAAGGAAGGAAGGAAGG	60.562	52.174	0.00	0.00	0.00	3.46
876	5357	3.332187	AGGGAAAGAAGGAAGGAAGGAAG	59.668	47.826	0.00	0.00	0.00	3.46
877	5358	3.330998	GAGGGAAAGAAGGAAGGAAGGAA	59.669	47.826	0.00	0.00	0.00	3.36
878	5359	2.913617	GAGGGAAAGAAGGAAGGAAGGA	59.086	50.000	0.00	0.00	0.00	3.36
879	5360	2.916269	AGAGGGAAAGAAGGAAGGAAGG	59.084	50.000	0.00	0.00	0.00	3.46
940	5421	0.250424	CGCTGATATGATGGGTGGCA	60.250	55.000	0.00	0.00	0.00	4.92
941	5422	0.250467	ACGCTGATATGATGGGTGGC	60.250	55.000	0.00	0.00	0.00	5.01
942	5423	1.202687	ACACGCTGATATGATGGGTGG	60.203	52.381	15.59	4.31	45.04	4.61
943	5424	1.869132	CACACGCTGATATGATGGGTG	59.131	52.381	0.00	0.00	45.82	4.61
944	5425	1.486310	ACACACGCTGATATGATGGGT	59.514	47.619	0.00	0.00	0.00	4.51
945	5426	2.245159	ACACACGCTGATATGATGGG	57.755	50.000	0.00	0.00	0.00	4.00
946	5427	7.324616	CGATATATACACACGCTGATATGATGG	59.675	40.741	0.00	0.00	0.00	3.51
947	5428	7.324616	CCGATATATACACACGCTGATATGATG	59.675	40.741	0.00	0.00	0.00	3.07
961	5442	4.703645	TGCTCTGCTCCGATATATACAC	57.296	45.455	0.00	0.00	0.00	2.90
1449	5939	2.202756	CCGCTGACGTAGAAGCCC	60.203	66.667	10.72	0.00	37.43	5.19
1573	6063	1.338769	TGGCGAGAAGTTAAAGAGGGC	60.339	52.381	0.00	0.00	0.00	5.19
1578	6068	1.087501	GCCCTGGCGAGAAGTTAAAG	58.912	55.000	0.00	0.00	0.00	1.85
1634	6127	0.391130	GAGGAACACATAGCGGCACA	60.391	55.000	1.45	0.00	0.00	4.57
1960	6485	8.582657	AGTGATAGAAGTACAGAACACTACAT	57.417	34.615	0.00	0.00	35.95	2.29
2324	7332	9.586150	CACATCGCATACTCAATTATTAGTTTC	57.414	33.333	0.00	0.00	0.00	2.78
2374	7384	5.049474	GCATGTGAATAGTGACAAGAACACA	60.049	40.000	0.00	0.00	40.25	3.72
2614	7626	4.225042	AGAACACCTCTATACACAATGCCA	59.775	41.667	0.00	0.00	30.22	4.92
2941	7955	1.819632	ATCGCCGTGAAGGATTGGC	60.820	57.895	0.00	0.00	45.00	4.52
3029	8043	1.080093	CTTCGTCACTAGGCGCCAA	60.080	57.895	31.54	10.52	0.00	4.52
3152	8167	3.558746	CCTGTCAGAAGCTCCAACAGAAT	60.559	47.826	15.94	0.00	39.72	2.40
3368	8383	2.154462	CTCGGCAACTTCCTTCATTGT	58.846	47.619	0.00	0.00	0.00	2.71
3443	8461	1.540115	TGCCCCTCCTCTAGATCTCT	58.460	55.000	0.00	0.00	0.00	3.10
3451	8469	1.381851	CAAGCTTTGCCCCTCCTCT	59.618	57.895	0.00	0.00	0.00	3.69
3643	8676	7.280876	GTGAAGAATATGCACCTCAGTCAAATA	59.719	37.037	0.00	0.00	0.00	1.40
3759	8792	2.511659	ACATCTGCAAGTGAAGCACAT	58.488	42.857	5.11	0.00	37.02	3.21
3815	8848	7.060421	ACAAATAAAGTCCCCGATGATATTGT	58.940	34.615	0.00	0.00	0.00	2.71
3845	8878	9.519191	TTCTCTGGATCATATTTTGTTTCAGAA	57.481	29.630	0.00	0.00	31.08	3.02
3912	8945	8.671028	TGTATATAGGCGCCATGTATATATACG	58.329	37.037	32.02	6.82	41.20	3.06
4114	9149	7.908827	TTTTATGGAAGTACATCTTGCGTTA	57.091	32.000	0.00	0.00	45.47	3.18
4140	9175	1.374947	CCTTTCAAGACGGCCCTGA	59.625	57.895	0.00	0.00	0.00	3.86
4148	9183	5.099042	TGGATACTAAGCCCTTTCAAGAC	57.901	43.478	0.00	0.00	37.61	3.01
4158	9193	5.897377	AAAACACACATGGATACTAAGCC	57.103	39.130	0.00	0.00	37.61	4.35
4258	9293	7.439381	ACTTGCATCAATTCATCCAATATTCC	58.561	34.615	0.00	0.00	0.00	3.01
4328	9363	6.017192	TGGGTCTACTCATTGTCTTTAGTCT	58.983	40.000	0.00	0.00	0.00	3.24
4371	9406	0.616395	TACGAGTTGGAGATGGGGCA	60.616	55.000	0.00	0.00	0.00	5.36
4384	9419	2.032620	CCCTTATGGTGAGCTACGAGT	58.967	52.381	0.00	0.00	0.00	4.18
4465	11244	4.020573	ACCATGTTGATGAAGACCTTCGTA	60.021	41.667	4.61	0.00	42.28	3.43
4468	11247	6.599244	TGAATACCATGTTGATGAAGACCTTC	59.401	38.462	2.94	2.94	39.91	3.46
4520	11299	3.231734	CATCTTGTGGACGAGGCAA	57.768	52.632	0.00	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.