AutoCloner

Multiple sequence alignment - TraesCS1D01G371500

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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	TraesCS1D01G371500	chr1D	100.000	3339	0	0	1	3339	449673526	449676864	0.000000e+00	6167.0
1	TraesCS1D01G371500	chr1D	88.181	1506	107	30	832	2287	449660090	449661574	0.000000e+00	1729.0
2	TraesCS1D01G371500	chr1D	87.206	1274	95	37	1097	2335	449752614	449753854	0.000000e+00	1387.0
3	TraesCS1D01G371500	chr1D	87.137	1205	104	27	831	1992	449846544	449847740	0.000000e+00	1319.0
4	TraesCS1D01G371500	chr1D	81.872	1346	171	54	881	2198	449923838	449922538	0.000000e+00	1066.0
5	TraesCS1D01G371500	chr1D	83.773	1023	94	33	2336	3339	449754137	449755106	0.000000e+00	904.0
6	TraesCS1D01G371500	chr1D	89.146	562	26	15	1	553	449656568	449657103	0.000000e+00	667.0
7	TraesCS1D01G371500	chr1D	83.425	543	61	20	894	1422	449983659	449983132	8.380000e-131	477.0
8	TraesCS1D01G371500	chr1D	88.770	374	36	4	2354	2722	449661812	449662184	1.410000e-123	453.0
9	TraesCS1D01G371500	chr1D	88.889	279	23	4	235	513	449749829	449750099	1.480000e-88	337.0
10	TraesCS1D01G371500	chr1D	81.853	259	23	16	3017	3268	449666339	449666098	2.630000e-46	196.0
11	TraesCS1D01G371500	chr1D	91.729	133	10	1	875	1006	449750999	449751131	2.050000e-42	183.0
12	TraesCS1D01G371500	chr1D	84.127	126	12	7	9	129	449972934	449972812	7.570000e-22	115.0
13	TraesCS1D01G371500	chr1D	88.043	92	1	2	551	632	449659631	449659722	2.120000e-17	100.0
14	TraesCS1D01G371500	chr1D	88.750	80	5	1	551	630	449750220	449750295	9.860000e-16	95.3
15	TraesCS1D01G371500	chr1D	80.741	135	14	5	582	714	449845807	449845931	9.860000e-16	95.3
16	TraesCS1D01G371500	chr1D	92.857	56	4	0	79	134	449845231	449845286	7.680000e-12	82.4
17	TraesCS1D01G371500	chr1B	86.972	1658	114	43	961	2545	615581590	615583218	0.000000e+00	1772.0
18	TraesCS1D01G371500	chr1B	86.865	1241	99	32	770	1992	615731821	615733015	0.000000e+00	1330.0
19	TraesCS1D01G371500	chr1B	88.814	885	58	14	2395	3269	615627111	615627964	0.000000e+00	1048.0
20	TraesCS1D01G371500	chr1B	91.549	568	45	1	1491	2058	615626000	615626564	0.000000e+00	780.0
21	TraesCS1D01G371500	chr1B	85.764	569	49	16	7	553	615580478	615581036	1.040000e-159	573.0
22	TraesCS1D01G371500	chr1B	83.305	593	40	30	844	1392	615625319	615625896	2.990000e-135	492.0
23	TraesCS1D01G371500	chr1B	89.101	367	24	9	187	551	615624537	615624889	3.060000e-120	442.0
24	TraesCS1D01G371500	chr1B	88.258	264	17	5	235	498	615731173	615731422	1.510000e-78	303.0
25	TraesCS1D01G371500	chr1B	91.327	196	8	7	1	189	615624059	615624252	3.300000e-65	259.0
26	TraesCS1D01G371500	chr1B	81.481	135	12	6	582	714	615731667	615731790	7.620000e-17	99.0
27	TraesCS1D01G371500	chr1A	90.978	1186	68	23	1093	2256	544748269	544749437	0.000000e+00	1561.0
28	TraesCS1D01G371500	chr1A	82.672	1512	134	70	551	1992	544999631	545001084	0.000000e+00	1223.0
29	TraesCS1D01G371500	chr1A	90.652	920	54	20	1249	2167	544927966	544928854	0.000000e+00	1194.0
30	TraesCS1D01G371500	chr1A	80.999	1342	162	63	902	2200	545009712	545008421	0.000000e+00	979.0
31	TraesCS1D01G371500	chr1A	85.027	935	82	20	2166	3092	544933988	544934872	0.000000e+00	898.0
32	TraesCS1D01G371500	chr1A	81.998	1011	118	25	2262	3265	544749631	544750584	0.000000e+00	800.0
33	TraesCS1D01G371500	chr1A	84.464	560	29	27	1	553	544747164	544747672	1.790000e-137	499.0
34	TraesCS1D01G371500	chr1A	80.943	488	49	23	79	553	544765504	544765048	2.470000e-91	346.0
35	TraesCS1D01G371500	chr1A	82.308	390	37	17	831	1194	544927579	544927962	3.240000e-80	309.0
36	TraesCS1D01G371500	chr1A	82.943	299	18	12	19	317	544998795	544999060	4.310000e-59	239.0
37	TraesCS1D01G371500	chr1A	92.216	167	12	1	342	507	544999317	544999483	5.570000e-58	235.0
38	TraesCS1D01G371500	chr1A	76.122	490	52	38	79	553	544923981	544924420	2.630000e-46	196.0
39	TraesCS1D01G371500	chr1A	85.714	91	4	1	551	632	544747767	544747857	1.650000e-13	87.9
40	TraesCS1D01G371500	chr1A	86.076	79	4	3	582	660	544764897	544764826	9.930000e-11	78.7

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	TraesCS1D01G371500	chr1D	449673526	449676864	3338	False	6167.000000	6167	100.000000	1	3339	1	chr1D.!!$F1	3338
1	TraesCS1D01G371500	chr1D	449922538	449923838	1300	True	1066.000000	1066	81.872000	881	2198	1	chr1D.!!$R2	1317
2	TraesCS1D01G371500	chr1D	449656568	449662184	5616	False	737.250000	1729	88.535000	1	2722	4	chr1D.!!$F2	2721
3	TraesCS1D01G371500	chr1D	449749829	449755106	5277	False	581.260000	1387	88.069400	235	3339	5	chr1D.!!$F3	3104
4	TraesCS1D01G371500	chr1D	449845231	449847740	2509	False	498.900000	1319	86.911667	79	1992	3	chr1D.!!$F4	1913
5	TraesCS1D01G371500	chr1D	449983132	449983659	527	True	477.000000	477	83.425000	894	1422	1	chr1D.!!$R4	528
6	TraesCS1D01G371500	chr1B	615580478	615583218	2740	False	1172.500000	1772	86.368000	7	2545	2	chr1B.!!$F1	2538
7	TraesCS1D01G371500	chr1B	615624059	615627964	3905	False	604.200000	1048	88.819200	1	3269	5	chr1B.!!$F2	3268
8	TraesCS1D01G371500	chr1B	615731173	615733015	1842	False	577.333333	1330	85.534667	235	1992	3	chr1B.!!$F3	1757
9	TraesCS1D01G371500	chr1A	545008421	545009712	1291	True	979.000000	979	80.999000	902	2200	1	chr1A.!!$R1	1298
10	TraesCS1D01G371500	chr1A	544933988	544934872	884	False	898.000000	898	85.027000	2166	3092	1	chr1A.!!$F1	926
11	TraesCS1D01G371500	chr1A	544747164	544750584	3420	False	736.975000	1561	85.788500	1	3265	4	chr1A.!!$F2	3264
12	TraesCS1D01G371500	chr1A	544923981	544928854	4873	False	566.333333	1194	83.027333	79	2167	3	chr1A.!!$F3	2088
13	TraesCS1D01G371500	chr1A	544998795	545001084	2289	False	565.666667	1223	85.943667	19	1992	3	chr1A.!!$F4	1973
14	TraesCS1D01G371500	chr1A	544764826	544765504	678	True	212.350000	346	83.509500	79	660	2	chr1A.!!$R2	581

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
784	7543	0.178921	TGGCCACACCTTCTCTCTCT	60.179	55.0	0.0	0.0	40.22	3.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2360	11814	0.322456	ATGCGCAACTGCCCTAGAAA	60.322	50.0	17.11	0.0	37.91	2.52	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
163	188	0.945265	GAGCAGCATCCATCGAGCTC	60.945	60.000	2.73	2.73	41.21	4.09
175	200	4.220821	TCCATCGAGCTCAGTAAAAAGACT	59.779	41.667	15.40	0.00	0.00	3.24
213	542	2.768253	CACTGGTGCCAAGTGATAGA	57.232	50.000	12.34	0.00	35.75	1.98
406	1032	4.451150	GGCGCACCGAGTCCATCA	62.451	66.667	10.83	0.00	0.00	3.07
426	1052	6.350780	CCATCAATCGATCCATCTCTGTATCA	60.351	42.308	0.00	0.00	0.00	2.15
437	1063	1.153842	CTGTATCAGGACGCGCACA	60.154	57.895	5.73	0.00	0.00	4.57
438	1064	1.413767	CTGTATCAGGACGCGCACAC	61.414	60.000	5.73	0.00	0.00	3.82
577	5134	2.014093	CTGCCGTGACGCGATTCTTC	62.014	60.000	15.93	0.00	44.77	2.87
660	5897	3.612860	GTGTCGCACTTAATCTACAGTGG	59.387	47.826	0.00	0.00	40.77	4.00
663	5900	2.418746	CGCACTTAATCTACAGTGGCCT	60.419	50.000	3.32	0.00	40.77	5.19
666	5903	2.092914	ACTTAATCTACAGTGGCCTGCC	60.093	50.000	3.32	0.00	42.81	4.85
694	5945	4.016944	AGCTAGTAGAGAGGAAAGAAGGGT	60.017	45.833	0.00	0.00	0.00	4.34
719	5970	4.307443	CTTCTTGTGAAGGAAACAACCC	57.693	45.455	0.00	0.00	44.33	4.11
720	5971	2.661718	TCTTGTGAAGGAAACAACCCC	58.338	47.619	0.00	0.00	34.02	4.95
721	5972	2.024846	TCTTGTGAAGGAAACAACCCCA	60.025	45.455	0.00	0.00	34.02	4.96
722	5973	2.765689	TGTGAAGGAAACAACCCCAT	57.234	45.000	0.00	0.00	0.00	4.00
723	5974	2.315176	TGTGAAGGAAACAACCCCATG	58.685	47.619	0.00	0.00	0.00	3.66
730	7489	2.028130	GAAACAACCCCATGACACACA	58.972	47.619	0.00	0.00	0.00	3.72
765	7524	3.252284	CCCTGACACAGTGCCCCT	61.252	66.667	0.00	0.00	0.00	4.79
767	7526	2.033141	CTGACACAGTGCCCCTGG	59.967	66.667	0.00	0.00	46.06	4.45
778	7537	3.260100	CCCCTGGCCACACCTTCT	61.260	66.667	0.00	0.00	40.22	2.85
779	7538	2.352805	CCCTGGCCACACCTTCTC	59.647	66.667	0.00	0.00	40.22	2.87
780	7539	2.227036	CCCTGGCCACACCTTCTCT	61.227	63.158	0.00	0.00	40.22	3.10
781	7540	1.298014	CCTGGCCACACCTTCTCTC	59.702	63.158	0.00	0.00	40.22	3.20
782	7541	1.197430	CCTGGCCACACCTTCTCTCT	61.197	60.000	0.00	0.00	40.22	3.10
783	7542	0.248843	CTGGCCACACCTTCTCTCTC	59.751	60.000	0.00	0.00	40.22	3.20
784	7543	0.178921	TGGCCACACCTTCTCTCTCT	60.179	55.000	0.00	0.00	40.22	3.10
785	7544	0.248843	GGCCACACCTTCTCTCTCTG	59.751	60.000	0.00	0.00	34.51	3.35
786	7545	1.261480	GCCACACCTTCTCTCTCTGA	58.739	55.000	0.00	0.00	0.00	3.27
787	7546	1.067213	GCCACACCTTCTCTCTCTGAC	60.067	57.143	0.00	0.00	0.00	3.51
788	7547	2.242926	CCACACCTTCTCTCTCTGACA	58.757	52.381	0.00	0.00	0.00	3.58
789	7548	2.029470	CCACACCTTCTCTCTCTGACAC	60.029	54.545	0.00	0.00	0.00	3.67
790	7549	2.625314	CACACCTTCTCTCTCTGACACA	59.375	50.000	0.00	0.00	0.00	3.72
791	7550	2.890311	ACACCTTCTCTCTCTGACACAG	59.110	50.000	0.00	0.00	0.00	3.66
792	7551	2.890311	CACCTTCTCTCTCTGACACAGT	59.110	50.000	0.00	0.00	32.61	3.55
793	7552	2.890311	ACCTTCTCTCTCTGACACAGTG	59.110	50.000	0.00	0.00	32.61	3.66
794	7553	2.230992	CCTTCTCTCTCTGACACAGTGG	59.769	54.545	5.31	0.00	32.61	4.00
795	7554	1.252175	TCTCTCTCTGACACAGTGGC	58.748	55.000	5.31	1.32	32.61	5.01
796	7555	0.246086	CTCTCTCTGACACAGTGGCC	59.754	60.000	3.17	0.00	32.61	5.36
797	7556	1.188219	TCTCTCTGACACAGTGGCCC	61.188	60.000	3.17	0.00	32.61	5.80
798	7557	1.152247	TCTCTGACACAGTGGCCCT	60.152	57.895	3.17	0.00	32.61	5.19
862	7810	1.668294	CGCAGGTGTCTTGACCTCT	59.332	57.895	0.00	0.00	45.15	3.69
954	7932	1.589716	GAGCTTGCGGTTCTTGCCAT	61.590	55.000	0.00	0.00	0.00	4.40
1008	7993	1.303236	CCACCAGGCAACCATCGAA	60.303	57.895	0.00	0.00	37.17	3.71
1009	9367	0.893270	CCACCAGGCAACCATCGAAA	60.893	55.000	0.00	0.00	37.17	3.46
1018	9376	2.790433	CAACCATCGAAAGGGAGGAAA	58.210	47.619	11.44	0.00	0.00	3.13
1055	9422	3.070446	TCATTACCGATCGCCATTACCTT	59.930	43.478	10.32	0.00	0.00	3.50
1078	9451	0.464036	CCATCCACGTTGCCTAGCTA	59.536	55.000	0.00	0.00	0.00	3.32
1080	9453	0.105039	ATCCACGTTGCCTAGCTAGC	59.895	55.000	15.74	6.62	0.00	3.42
1081	9454	0.970937	TCCACGTTGCCTAGCTAGCT	60.971	55.000	23.12	23.12	0.00	3.32
1082	9455	0.528684	CCACGTTGCCTAGCTAGCTC	60.529	60.000	23.26	7.84	0.00	4.09
1084	9457	1.115467	ACGTTGCCTAGCTAGCTCAT	58.885	50.000	23.26	0.00	0.00	2.90
1085	9458	1.067821	ACGTTGCCTAGCTAGCTCATC	59.932	52.381	23.26	11.28	0.00	2.92
1086	9459	1.777101	GTTGCCTAGCTAGCTCATCG	58.223	55.000	23.26	8.18	0.00	3.84
1087	9460	1.067821	GTTGCCTAGCTAGCTCATCGT	59.932	52.381	23.26	0.00	0.00	3.73
1129	9545	1.017387	GGATCAACAGAATGGGACGC	58.983	55.000	0.00	0.00	43.62	5.19
1222	9644	0.543277	ACAGTCACATCATCCGGCAT	59.457	50.000	0.00	0.00	0.00	4.40
1436	9894	4.679197	GTGCAATGCAATTTTTCAGTACGA	59.321	37.500	10.44	0.00	41.47	3.43
1437	9895	5.345741	GTGCAATGCAATTTTTCAGTACGAT	59.654	36.000	10.44	0.00	41.47	3.73
1438	9896	5.925397	TGCAATGCAATTTTTCAGTACGATT	59.075	32.000	5.01	0.00	34.76	3.34
1439	9897	6.423302	TGCAATGCAATTTTTCAGTACGATTT	59.577	30.769	5.01	0.00	34.76	2.17
1441	9899	7.266756	GCAATGCAATTTTTCAGTACGATTTTG	59.733	33.333	0.00	0.00	31.22	2.44
1442	9900	6.209129	TGCAATTTTTCAGTACGATTTTGC	57.791	33.333	0.00	0.00	37.90	3.68
1443	9901	5.750547	TGCAATTTTTCAGTACGATTTTGCA	59.249	32.000	12.92	12.92	43.07	4.08
1444	9902	6.074409	TGCAATTTTTCAGTACGATTTTGCAG	60.074	34.615	12.92	0.00	41.17	4.41
1445	9903	6.074356	GCAATTTTTCAGTACGATTTTGCAGT	60.074	34.615	0.00	0.00	37.47	4.40
1447	9905	3.536158	TTCAGTACGATTTTGCAGTGC	57.464	42.857	8.58	8.58	0.00	4.40
1556	10040	2.609491	CCGGACAGACAACGAGATCAAA	60.609	50.000	0.00	0.00	0.00	2.69
1561	10045	5.694910	GGACAGACAACGAGATCAAAAACTA	59.305	40.000	0.00	0.00	0.00	2.24
1562	10046	6.369065	GGACAGACAACGAGATCAAAAACTAT	59.631	38.462	0.00	0.00	0.00	2.12
1844	10345	0.401395	TCTGTGGTGGAAAGGAGGGT	60.401	55.000	0.00	0.00	0.00	4.34
1914	10418	4.332543	TCCCGGAGAACCTGGGCT	62.333	66.667	0.73	0.00	44.08	5.19
1915	10419	2.365105	CCCGGAGAACCTGGGCTA	60.365	66.667	0.73	0.00	40.79	3.93
1916	10420	2.732619	CCCGGAGAACCTGGGCTAC	61.733	68.421	0.73	0.00	40.79	3.58
2104	10659	2.021208	GCAGAGCCTCCTCCCAAATTC	61.021	57.143	0.00	0.00	38.96	2.17
2133	10693	5.984725	TCAACTTGGAACAGTACTTCTGAA	58.015	37.500	0.00	0.00	46.27	3.02
2256	11057	7.976135	ACTTCAGGTCATTTATAGCATCATC	57.024	36.000	0.00	0.00	0.00	2.92
2258	11059	6.692849	TCAGGTCATTTATAGCATCATCCT	57.307	37.500	0.00	0.00	0.00	3.24
2287	11276	3.233684	AGGCGAGTTAGCTTACTTCAC	57.766	47.619	6.86	0.68	37.29	3.18
2289	11437	2.269172	GCGAGTTAGCTTACTTCACCC	58.731	52.381	6.86	0.00	0.00	4.61
2308	11456	3.770933	ACCCTGCATGCTGAACAAATTAT	59.229	39.130	24.53	0.00	0.00	1.28
2310	11458	5.068198	ACCCTGCATGCTGAACAAATTATAG	59.932	40.000	24.53	6.04	0.00	1.31
2312	11484	6.183360	CCCTGCATGCTGAACAAATTATAGAA	60.183	38.462	24.53	0.00	0.00	2.10
2360	11814	7.977789	TGTCAAATTACACAGATGTACACAT	57.022	32.000	0.00	0.00	41.12	3.21
2399	11853	4.082026	GCATCATAGCCAAGAAACCAAACT	60.082	41.667	0.00	0.00	0.00	2.66
2487	11948	9.941325	AGATTTATATCAGATTCATGACACCTC	57.059	33.333	0.00	0.00	32.95	3.85
2555	12016	3.198635	TCAAGTCCCTAGCAATTCCTGAG	59.801	47.826	0.00	0.00	0.00	3.35
2573	12034	0.392336	AGAGCATGCTTCGGAGGATC	59.608	55.000	23.61	5.62	30.71	3.36
2668	12132	3.432326	GCTCTGGAGTTATCCCGACAAAT	60.432	47.826	0.00	0.00	46.04	2.32
2694	12161	8.240682	TGTTACCGCTAAAAGTAAATACGTCTA	58.759	33.333	0.00	0.00	30.64	2.59
2703	12170	8.732746	AAAAGTAAATACGTCTATGAGCCAAT	57.267	30.769	0.00	0.00	0.00	3.16
2739	12206	0.110486	AGCCCATTTTCAGGTGACGT	59.890	50.000	0.00	0.00	0.00	4.34
2761	12228	4.650972	ACTATCAAACTGCAACCCCTAA	57.349	40.909	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	2.274437	CAATCACGATCCACACTCCAG	58.726	52.381	0.00	0.00	0.00	3.86
175	200	8.946085	CACCAGTGCTTATTACTGATCTAAAAA	58.054	33.333	6.70	0.00	46.52	1.94
211	540	2.740447	GGAGAAATTAACGCGGTGTTCT	59.260	45.455	16.42	16.42	42.09	3.01
212	541	2.740447	AGGAGAAATTAACGCGGTGTTC	59.260	45.455	7.07	8.00	42.09	3.18
213	542	2.740447	GAGGAGAAATTAACGCGGTGTT	59.260	45.455	7.07	12.06	44.78	3.32
288	635	1.673400	CCGTCGATCTGACTGACTGAT	59.327	52.381	13.30	0.00	45.87	2.90
311	664	1.287730	CCGCTGCTGTCTGTCTGTTC	61.288	60.000	0.00	0.00	0.00	3.18
312	665	1.301244	CCGCTGCTGTCTGTCTGTT	60.301	57.895	0.00	0.00	0.00	3.16
406	1032	5.184864	GTCCTGATACAGAGATGGATCGATT	59.815	44.000	0.00	0.00	32.44	3.34
437	1063	4.664677	GTCCCGTCTGCTGTGCGT	62.665	66.667	8.69	0.00	0.00	5.24
631	5226	4.566004	AGATTAAGTGCGACACTGCTAAA	58.434	39.130	12.22	6.55	44.62	1.85
663	5900	0.683179	TCTCTACTAGCTTGCCGGCA	60.683	55.000	29.03	29.03	34.17	5.69
666	5903	1.681538	TCCTCTCTACTAGCTTGCCG	58.318	55.000	0.00	0.00	0.00	5.69
714	5965	2.091541	GGTATGTGTGTCATGGGGTTG	58.908	52.381	0.00	0.00	37.91	3.77
715	5966	1.992557	AGGTATGTGTGTCATGGGGTT	59.007	47.619	0.00	0.00	37.91	4.11
716	5967	1.668826	AGGTATGTGTGTCATGGGGT	58.331	50.000	0.00	0.00	37.91	4.95
717	5968	2.239654	AGAAGGTATGTGTGTCATGGGG	59.760	50.000	0.00	0.00	37.91	4.96
719	5970	3.273434	CCAGAAGGTATGTGTGTCATGG	58.727	50.000	0.00	0.00	37.91	3.66
720	5971	2.679837	GCCAGAAGGTATGTGTGTCATG	59.320	50.000	0.00	0.00	35.21	3.07
721	5972	2.573462	AGCCAGAAGGTATGTGTGTCAT	59.427	45.455	0.00	0.00	36.62	3.06
722	5973	1.977854	AGCCAGAAGGTATGTGTGTCA	59.022	47.619	0.00	0.00	37.19	3.58
723	5974	2.770164	AGCCAGAAGGTATGTGTGTC	57.230	50.000	0.00	0.00	37.19	3.67
730	7489	2.022527	AGGGAGAGAAGCCAGAAGGTAT	60.023	50.000	0.00	0.00	37.19	2.73
765	7524	0.178921	AGAGAGAGAAGGTGTGGCCA	60.179	55.000	0.00	0.00	40.61	5.36
766	7525	0.248843	CAGAGAGAGAAGGTGTGGCC	59.751	60.000	0.00	0.00	37.58	5.36
767	7526	1.067213	GTCAGAGAGAGAAGGTGTGGC	60.067	57.143	0.00	0.00	0.00	5.01
768	7527	2.029470	GTGTCAGAGAGAGAAGGTGTGG	60.029	54.545	0.00	0.00	0.00	4.17
769	7528	2.625314	TGTGTCAGAGAGAGAAGGTGTG	59.375	50.000	0.00	0.00	0.00	3.82
770	7529	2.890311	CTGTGTCAGAGAGAGAAGGTGT	59.110	50.000	0.00	0.00	32.44	4.16
771	7530	2.890311	ACTGTGTCAGAGAGAGAAGGTG	59.110	50.000	3.59	0.00	35.18	4.00
772	7531	2.890311	CACTGTGTCAGAGAGAGAAGGT	59.110	50.000	3.59	0.00	35.18	3.50
773	7532	2.230992	CCACTGTGTCAGAGAGAGAAGG	59.769	54.545	3.59	0.00	35.18	3.46
774	7533	2.352617	GCCACTGTGTCAGAGAGAGAAG	60.353	54.545	3.59	0.00	35.18	2.85
775	7534	1.615883	GCCACTGTGTCAGAGAGAGAA	59.384	52.381	3.59	0.00	35.18	2.87
776	7535	1.252175	GCCACTGTGTCAGAGAGAGA	58.748	55.000	3.59	0.00	35.18	3.10
777	7536	0.246086	GGCCACTGTGTCAGAGAGAG	59.754	60.000	3.59	0.00	35.18	3.20
778	7537	1.188219	GGGCCACTGTGTCAGAGAGA	61.188	60.000	4.39	0.00	35.18	3.10
779	7538	1.190833	AGGGCCACTGTGTCAGAGAG	61.191	60.000	6.18	0.00	35.18	3.20
780	7539	1.152247	AGGGCCACTGTGTCAGAGA	60.152	57.895	6.18	0.00	35.18	3.10
781	7540	1.004080	CAGGGCCACTGTGTCAGAG	60.004	63.158	6.18	0.00	42.42	3.35
782	7541	3.150949	CAGGGCCACTGTGTCAGA	58.849	61.111	6.18	0.00	42.42	3.27
794	7553	3.678951	GAGCAGAGACAGGCAGGGC	62.679	68.421	0.00	0.00	0.00	5.19
795	7554	2.583520	GAGCAGAGACAGGCAGGG	59.416	66.667	0.00	0.00	0.00	4.45
796	7555	2.583520	GGAGCAGAGACAGGCAGG	59.416	66.667	0.00	0.00	0.00	4.85
797	7556	1.958902	GAGGGAGCAGAGACAGGCAG	61.959	65.000	0.00	0.00	0.00	4.85
798	7557	1.986757	GAGGGAGCAGAGACAGGCA	60.987	63.158	0.00	0.00	0.00	4.75
862	7810	2.159393	GCAACGCAGAAGCAATGGATTA	60.159	45.455	0.00	0.00	42.27	1.75
954	7932	1.933021	ATATATCGGGGAGGCGTGAA	58.067	50.000	0.00	0.00	0.00	3.18
967	7946	8.964772	GTGGGTATATATGGTCGGGTATATATC	58.035	40.741	0.00	0.00	35.31	1.63
1008	7993	0.250166	CGACGGTTGTTTCCTCCCTT	60.250	55.000	0.00	0.00	0.00	3.95
1009	9367	1.370064	CGACGGTTGTTTCCTCCCT	59.630	57.895	0.00	0.00	0.00	4.20
1018	9376	0.323629	AATGATGGACCGACGGTTGT	59.676	50.000	22.69	10.21	35.25	3.32
1055	9422	1.138859	CTAGGCAACGTGGATGGATGA	59.861	52.381	0.00	0.00	46.39	2.92
1078	9451	0.684479	TGGCTACTCCACGATGAGCT	60.684	55.000	5.98	0.00	40.72	4.09
1080	9453	0.249238	GCTGGCTACTCCACGATGAG	60.249	60.000	0.00	0.00	40.72	2.90
1081	9454	0.684479	AGCTGGCTACTCCACGATGA	60.684	55.000	0.00	0.00	40.72	2.92
1082	9455	0.529337	CAGCTGGCTACTCCACGATG	60.529	60.000	5.57	0.00	40.72	3.84
1084	9457	3.006756	GCAGCTGGCTACTCCACGA	62.007	63.158	17.12	0.00	40.72	4.35
1085	9458	2.510238	GCAGCTGGCTACTCCACG	60.510	66.667	17.12	0.00	40.72	4.94
1086	9459	2.124942	GGCAGCTGGCTACTCCAC	60.125	66.667	31.40	3.23	40.72	4.02
1087	9460	3.774528	CGGCAGCTGGCTACTCCA	61.775	66.667	34.13	0.00	44.18	3.86
1194	9616	3.494045	TGATGTGACTGTAGAGCTTCG	57.506	47.619	0.00	0.00	0.00	3.79
1207	9629	1.526686	GCCATGCCGGATGATGTGA	60.527	57.895	5.05	0.00	36.56	3.58
1441	9899	1.958205	AGTTCACTCAGCGCACTGC	60.958	57.895	11.47	0.00	44.10	4.40
1442	9900	0.598419	TCAGTTCACTCAGCGCACTG	60.598	55.000	11.47	12.95	45.95	3.66
1443	9901	0.104855	TTCAGTTCACTCAGCGCACT	59.895	50.000	11.47	0.00	0.00	4.40
1444	9902	0.937304	TTTCAGTTCACTCAGCGCAC	59.063	50.000	11.47	0.00	0.00	5.34
1445	9903	1.882912	ATTTCAGTTCACTCAGCGCA	58.117	45.000	11.47	0.00	0.00	6.09
1447	9905	5.327091	CCAAATATTTCAGTTCACTCAGCG	58.673	41.667	0.00	0.00	0.00	5.18
1541	10025	6.934645	TCCAATAGTTTTTGATCTCGTTGTCT	59.065	34.615	0.00	0.00	0.00	3.41
1556	10040	6.830324	TCTTGATGCAGCTATTCCAATAGTTT	59.170	34.615	2.53	0.00	40.37	2.66
1561	10045	5.443283	TCTTCTTGATGCAGCTATTCCAAT	58.557	37.500	2.53	0.00	0.00	3.16
1562	10046	4.847198	TCTTCTTGATGCAGCTATTCCAA	58.153	39.130	2.53	0.00	0.00	3.53
2104	10659	2.561569	ACTGTTCCAAGTTGAACTCGG	58.438	47.619	3.87	0.00	43.96	4.63
2256	11057	7.964604	AAGCTAACTCGCCTATAAAATTAGG	57.035	36.000	0.00	0.00	41.54	2.69
2287	11276	2.754946	AATTTGTTCAGCATGCAGGG	57.245	45.000	21.98	9.12	34.76	4.45
2289	11437	7.972277	AGTTTCTATAATTTGTTCAGCATGCAG	59.028	33.333	21.98	12.90	34.76	4.41
2338	11792	9.283768	AGAAATGTGTACATCTGTGTAATTTGA	57.716	29.630	0.00	0.00	42.18	2.69
2360	11814	0.322456	ATGCGCAACTGCCCTAGAAA	60.322	50.000	17.11	0.00	37.91	2.52
2399	11853	7.377397	GGTCAATATATTAAACAAATTCGCGCA	59.623	33.333	8.75	0.00	0.00	6.09
2429	11883	5.712004	TCCATGTTCATGCACAAAGTAATG	58.288	37.500	1.37	0.00	0.00	1.90
2506	11967	2.225019	CACAGAAGCACAGAACCATGAC	59.775	50.000	0.00	0.00	0.00	3.06
2555	12016	0.943359	CGATCCTCCGAAGCATGCTC	60.943	60.000	22.93	13.44	0.00	4.26
2668	12132	7.090173	AGACGTATTTACTTTTAGCGGTAACA	58.910	34.615	6.56	0.00	0.00	2.41
2739	12206	5.765576	TTAGGGGTTGCAGTTTGATAGTA	57.234	39.130	0.00	0.00	0.00	1.82
2938	12415	8.954950	ATGAAATCCTAGAGATGTTGTAGTTG	57.045	34.615	0.00	0.00	34.56	3.16
2971	12448	8.882415	TTATTTATTTTGTGTTTTGGCCGTAA	57.118	26.923	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.