AutoCloner

Multiple sequence alignment - TraesCS2D01G219900

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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	TraesCS2D01G219900	chr2D	100.000	4019	0	0	1	4019	187110673	187106655	0.000000e+00	7422.0
1	TraesCS2D01G219900	chr2D	99.703	673	1	1	188	860	435336418	435335747	0.000000e+00	1230.0
2	TraesCS2D01G219900	chr2D	81.674	693	97	25	185	855	647489209	647489893	2.110000e-152	549.0
3	TraesCS2D01G219900	chr2D	100.000	33	0	0	3971	4003	151986262	151986294	1.210000e-05	62.1
4	TraesCS2D01G219900	chr2A	95.384	3098	102	20	891	3970	199729166	199726092	0.000000e+00	4891.0
5	TraesCS2D01G219900	chr2A	81.322	696	99	26	185	858	772993713	772993027	1.640000e-148	536.0
6	TraesCS2D01G219900	chr2A	70.983	1282	324	39	1406	2662	147538030	147536772	3.080000e-66	263.0
7	TraesCS2D01G219900	chr2A	94.737	38	2	0	3965	4002	514815052	514815089	4.340000e-05	60.2
8	TraesCS2D01G219900	chr2B	89.064	1271	93	20	2722	3970	242992942	242991696	0.000000e+00	1535.0
9	TraesCS2D01G219900	chr2B	93.553	760	22	7	861	1604	243075534	243074786	0.000000e+00	1107.0
10	TraesCS2D01G219900	chr2B	89.898	782	51	6	1673	2445	243004248	243003486	0.000000e+00	981.0
11	TraesCS2D01G219900	chr2B	90.094	747	55	10	2722	3468	242949123	242948396	0.000000e+00	952.0
12	TraesCS2D01G219900	chr2B	90.373	509	42	4	3464	3967	242948371	242947865	0.000000e+00	662.0
13	TraesCS2D01G219900	chr2B	90.295	237	19	2	2443	2675	242949357	242949121	1.400000e-79	307.0
14	TraesCS2D01G219900	chr2B	89.451	237	21	2	2443	2675	242993176	242992940	3.040000e-76	296.0
15	TraesCS2D01G219900	chr2B	70.536	1585	399	55	1071	2619	551637866	551639418	1.100000e-70	278.0
16	TraesCS2D01G219900	chr2B	96.296	81	3	0	1597	1677	243072080	243072000	2.520000e-27	134.0
17	TraesCS2D01G219900	chr2B	92.473	93	7	0	1	93	243075946	243075854	2.520000e-27	134.0
18	TraesCS2D01G219900	chr2B	93.939	66	1	3	119	184	243075588	243075526	3.310000e-16	97.1
19	TraesCS2D01G219900	chr2B	87.879	66	6	2	3942	4005	786758005	786757940	4.310000e-10	76.8
20	TraesCS2D01G219900	chr1D	99.248	665	5	0	194	858	474219635	474220299	0.000000e+00	1201.0
21	TraesCS2D01G219900	chr1D	89.828	698	33	18	187	860	468028393	468027710	0.000000e+00	861.0
22	TraesCS2D01G219900	chr6D	73.537	1965	409	72	1075	2979	86721419	86723332	0.000000e+00	645.0
23	TraesCS2D01G219900	chr6D	74.389	1597	366	35	1085	2658	264178103	264179679	0.000000e+00	643.0
24	TraesCS2D01G219900	chr6B	73.340	1958	413	71	1075	2973	164363013	164364920	1.230000e-174	623.0
25	TraesCS2D01G219900	chr6A	72.875	1965	428	59	1078	2982	104413813	104411894	2.690000e-161	579.0
26	TraesCS2D01G219900	chr4B	87.417	453	30	13	186	619	452707156	452706712	2.790000e-136	496.0
27	TraesCS2D01G219900	chr4B	92.607	257	18	1	604	860	452699137	452698882	6.350000e-98	368.0
28	TraesCS2D01G219900	chrUn	79.087	526	53	17	375	869	154489912	154489413	3.900000e-80	309.0
29	TraesCS2D01G219900	chrUn	79.264	516	52	15	375	860	189533981	189534471	3.900000e-80	309.0
30	TraesCS2D01G219900	chrUn	80.870	345	35	14	522	860	159531200	159531519	4.010000e-60	243.0
31	TraesCS2D01G219900	chr3D	87.879	66	6	2	3942	4005	586182143	586182078	4.310000e-10	76.8
32	TraesCS2D01G219900	chr3D	100.000	33	0	0	3970	4002	4350237	4350205	1.210000e-05	62.1
33	TraesCS2D01G219900	chr3B	97.619	42	0	1	3962	4002	761925624	761925665	2.000000e-08	71.3
34	TraesCS2D01G219900	chr7A	89.796	49	5	0	3954	4002	136777196	136777148	3.350000e-06	63.9
35	TraesCS2D01G219900	chr5A	92.683	41	3	0	3962	4002	301887004	301887044	4.340000e-05	60.2
36	TraesCS2D01G219900	chr7D	90.244	41	4	0	3962	4002	396451305	396451345	2.000000e-03	54.7

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	TraesCS2D01G219900	chr2D	187106655	187110673	4018	True	7422.000000	7422	100.00000	1	4019	1	chr2D.!!$R1	4018
1	TraesCS2D01G219900	chr2D	435335747	435336418	671	True	1230.000000	1230	99.70300	188	860	1	chr2D.!!$R2	672
2	TraesCS2D01G219900	chr2D	647489209	647489893	684	False	549.000000	549	81.67400	185	855	1	chr2D.!!$F2	670
3	TraesCS2D01G219900	chr2A	199726092	199729166	3074	True	4891.000000	4891	95.38400	891	3970	1	chr2A.!!$R2	3079
4	TraesCS2D01G219900	chr2A	772993027	772993713	686	True	536.000000	536	81.32200	185	858	1	chr2A.!!$R3	673
5	TraesCS2D01G219900	chr2A	147536772	147538030	1258	True	263.000000	263	70.98300	1406	2662	1	chr2A.!!$R1	1256
6	TraesCS2D01G219900	chr2B	243003486	243004248	762	True	981.000000	981	89.89800	1673	2445	1	chr2B.!!$R1	772
7	TraesCS2D01G219900	chr2B	242991696	242993176	1480	True	915.500000	1535	89.25750	2443	3970	2	chr2B.!!$R4	1527
8	TraesCS2D01G219900	chr2B	242947865	242949357	1492	True	640.333333	952	90.25400	2443	3967	3	chr2B.!!$R3	1524
9	TraesCS2D01G219900	chr2B	243072000	243075946	3946	True	368.025000	1107	94.06525	1	1677	4	chr2B.!!$R5	1676
10	TraesCS2D01G219900	chr2B	551637866	551639418	1552	False	278.000000	278	70.53600	1071	2619	1	chr2B.!!$F1	1548
11	TraesCS2D01G219900	chr1D	474219635	474220299	664	False	1201.000000	1201	99.24800	194	858	1	chr1D.!!$F1	664
12	TraesCS2D01G219900	chr1D	468027710	468028393	683	True	861.000000	861	89.82800	187	860	1	chr1D.!!$R1	673
13	TraesCS2D01G219900	chr6D	86721419	86723332	1913	False	645.000000	645	73.53700	1075	2979	1	chr6D.!!$F1	1904
14	TraesCS2D01G219900	chr6D	264178103	264179679	1576	False	643.000000	643	74.38900	1085	2658	1	chr6D.!!$F2	1573
15	TraesCS2D01G219900	chr6B	164363013	164364920	1907	False	623.000000	623	73.34000	1075	2973	1	chr6B.!!$F1	1898
16	TraesCS2D01G219900	chr6A	104411894	104413813	1919	True	579.000000	579	72.87500	1078	2982	1	chr6A.!!$R1	1904

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
147	388	0.400213	ACGGCTGATGGGTCAAAGAA	59.600	50.000	33.05	2.52	F
148	389	1.089920	CGGCTGATGGGTCAAAGAAG	58.910	55.000	33.05	2.85	F
149	390	1.611673	CGGCTGATGGGTCAAAGAAGT	60.612	52.381	33.05	3.01	F
1044	1341	1.685355	GCTGCTTCCTCCTCCTCCTC	61.685	65.000	0.00	3.71	F
2321	5387	2.024918	GGCACTTGTATGGCGATGG	58.975	57.895	35.20	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1044	1341	1.078759	CAAGGCTAACAGCGACGAGG	61.079	60.000	0.00	43.62	4.63	R
1300	1603	2.203480	ATGGCCGCAGTTGTTGGT	60.203	55.556	0.00	0.00	3.67	R
1349	1652	3.509137	AACGCGGCGGAGAAGTTGA	62.509	57.895	27.37	0.00	3.18	R
2867	5949	0.038526	CTCCGGTAGTTGCACGTCTT	60.039	55.000	0.00	0.00	3.01	R
3973	7091	0.107165	CCGGGGTCATCCTCCTTTTC	60.107	60.000	0.00	35.33	2.29	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
50	51	4.395231	GGAATACTTCAAGCCCACAAGTAC	59.605	45.833	0.00	0.00	35.86	2.73
59	60	4.532314	AGCCCACAAGTACTACAGTTAC	57.468	45.455	0.00	0.00	0.00	2.50
68	69	7.332678	CACAAGTACTACAGTTACCCCAATTAC	59.667	40.741	0.00	0.00	0.00	1.89
93	94	8.946085	ACTTTCGCAATCACTAATTTTCATCTA	58.054	29.630	0.00	0.00	0.00	1.98
94	95	9.941664	CTTTCGCAATCACTAATTTTCATCTAT	57.058	29.630	0.00	0.00	0.00	1.98
95	96	9.935682	TTTCGCAATCACTAATTTTCATCTATC	57.064	29.630	0.00	0.00	0.00	2.08
96	97	8.087982	TCGCAATCACTAATTTTCATCTATCC	57.912	34.615	0.00	0.00	0.00	2.59
97	98	7.173218	TCGCAATCACTAATTTTCATCTATCCC	59.827	37.037	0.00	0.00	0.00	3.85
98	99	7.173907	CGCAATCACTAATTTTCATCTATCCCT	59.826	37.037	0.00	0.00	0.00	4.20
99	100	9.507329	GCAATCACTAATTTTCATCTATCCCTA	57.493	33.333	0.00	0.00	0.00	3.53
145	386	1.338674	TGTACGGCTGATGGGTCAAAG	60.339	52.381	0.00	0.00	33.05	2.77
147	388	0.400213	ACGGCTGATGGGTCAAAGAA	59.600	50.000	0.00	0.00	33.05	2.52
148	389	1.089920	CGGCTGATGGGTCAAAGAAG	58.910	55.000	0.00	0.00	33.05	2.85
149	390	1.611673	CGGCTGATGGGTCAAAGAAGT	60.612	52.381	0.00	0.00	33.05	3.01
150	391	2.519013	GGCTGATGGGTCAAAGAAGTT	58.481	47.619	0.00	0.00	33.05	2.66
151	392	2.229784	GGCTGATGGGTCAAAGAAGTTG	59.770	50.000	0.00	0.00	38.71	3.16
860	1133	3.979495	CGGTCGTATAGGATTTTCTTCCG	59.021	47.826	0.00	1.70	40.94	4.30
861	1134	4.498682	CGGTCGTATAGGATTTTCTTCCGT	60.499	45.833	9.14	0.00	40.94	4.69
862	1135	4.743644	GGTCGTATAGGATTTTCTTCCGTG	59.256	45.833	0.00	0.00	40.94	4.94
863	1136	4.743644	GTCGTATAGGATTTTCTTCCGTGG	59.256	45.833	0.00	0.00	40.94	4.94
864	1137	4.646040	TCGTATAGGATTTTCTTCCGTGGA	59.354	41.667	0.00	0.00	40.94	4.02
865	1138	4.982916	CGTATAGGATTTTCTTCCGTGGAG	59.017	45.833	0.00	0.00	40.94	3.86
866	1139	2.789409	AGGATTTTCTTCCGTGGAGG	57.211	50.000	0.00	0.00	40.94	4.30
876	1149	4.261888	CGTGGAGGAAACGGTGAG	57.738	61.111	0.00	0.00	37.39	3.51
889	1162	2.034221	GTGAGGAACCACCCCTGC	59.966	66.667	0.00	0.00	40.05	4.85
890	1163	3.256960	TGAGGAACCACCCCTGCC	61.257	66.667	0.00	0.00	40.05	4.85
891	1164	4.048470	GAGGAACCACCCCTGCCC	62.048	72.222	0.00	0.00	40.05	5.36
933	1206	2.006772	CGTAATTGGTCGAGCAGCC	58.993	57.895	17.81	0.00	0.00	4.85
1044	1341	1.685355	GCTGCTTCCTCCTCCTCCTC	61.685	65.000	0.00	0.00	0.00	3.71
1300	1603	3.785859	GCATCCTCTGCCCCGACA	61.786	66.667	0.00	0.00	45.66	4.35
1515	1818	2.028484	GACGTCAACGGGCTCACA	59.972	61.111	11.55	0.00	44.95	3.58
2034	5068	4.322801	CGGTTCTCCTACAAGGATCTGTTT	60.323	45.833	0.00	0.00	44.81	2.83
2321	5387	2.024918	GGCACTTGTATGGCGATGG	58.975	57.895	0.00	0.00	35.20	3.51
2421	5496	7.718334	TGAGGAGTGTGAGAAAGTAATCATA	57.282	36.000	0.00	0.00	0.00	2.15
2433	5508	5.367945	AAGTAATCATACACCGGGACATT	57.632	39.130	6.32	0.00	34.29	2.71
2867	5949	3.446161	CAGGTCGTGAGGTACCTTAATGA	59.554	47.826	17.53	15.19	43.77	2.57
3058	6140	9.826574	GTGTGTGATTTTCCCTATGTACTAATA	57.173	33.333	0.00	0.00	0.00	0.98
3180	6262	6.472016	TCAGAAGCATGTGGATTAAGTTACA	58.528	36.000	0.00	0.00	0.00	2.41
3219	6301	7.155328	GGCTATTTGAGATAGTTAGCAAGCTA	58.845	38.462	0.00	0.00	37.58	3.32
3279	6362	1.305887	CTTCGGTACCTCCCACCCT	60.306	63.158	10.90	0.00	31.96	4.34
3301	6384	2.238942	CCCCCAAAGAAAGTTTGCAC	57.761	50.000	0.00	0.00	0.00	4.57
3356	6439	8.554835	TTTGGACATTCACGATCAACTAATTA	57.445	30.769	0.00	0.00	0.00	1.40
3442	6536	9.646427	GAAGGAGTATCTTATAATCTTCGCATT	57.354	33.333	0.00	0.00	33.73	3.56
3454	6548	6.381481	AATCTTCGCATTTAATCTGCATCA	57.619	33.333	10.18	0.00	39.64	3.07
3455	6549	5.816449	TCTTCGCATTTAATCTGCATCAA	57.184	34.783	10.18	1.15	39.64	2.57
3457	6551	6.619744	TCTTCGCATTTAATCTGCATCAAAA	58.380	32.000	10.18	0.00	39.64	2.44
3459	6553	7.760794	TCTTCGCATTTAATCTGCATCAAAATT	59.239	29.630	10.18	0.00	39.64	1.82
3461	6555	7.677309	TCGCATTTAATCTGCATCAAAATTTG	58.323	30.769	0.00	0.00	39.64	2.32
3462	6556	6.409761	CGCATTTAATCTGCATCAAAATTTGC	59.590	34.615	0.00	0.00	39.64	3.68
3474	6585	8.784994	TGCATCAAAATTTGCAAACTCAAATAT	58.215	25.926	15.41	0.01	45.30	1.28
3567	6678	5.103771	AGAGAGAAGTGGGGCATTTGATAAT	60.104	40.000	0.00	0.00	0.00	1.28
3568	6679	6.101734	AGAGAGAAGTGGGGCATTTGATAATA	59.898	38.462	0.00	0.00	0.00	0.98
3602	6713	8.325046	CCCAAATTTGAGTAATAAAATGGGGAA	58.675	33.333	19.86	0.00	40.39	3.97
3611	6722	7.564793	AGTAATAAAATGGGGAATTTTGAGCC	58.435	34.615	6.35	0.00	45.89	4.70
3612	6723	6.641161	AATAAAATGGGGAATTTTGAGCCT	57.359	33.333	6.35	0.00	45.89	4.58
3613	6724	7.747809	AATAAAATGGGGAATTTTGAGCCTA	57.252	32.000	6.35	0.00	45.89	3.93
3640	6754	2.561478	TGCTTCCACCTTGTACCTTC	57.439	50.000	0.00	0.00	0.00	3.46
3641	6755	1.771854	TGCTTCCACCTTGTACCTTCA	59.228	47.619	0.00	0.00	0.00	3.02
3703	6817	2.259266	TCCCCGTACCTTGTTTTCAC	57.741	50.000	0.00	0.00	0.00	3.18
3756	6871	6.468956	GGTGTTCACTTGTCATATTTATTGCG	59.531	38.462	2.98	0.00	0.00	4.85
3990	7108	4.797912	ATTAGAAAAGGAGGATGACCCC	57.202	45.455	0.00	0.00	36.73	4.95
3991	7109	0.912486	AGAAAAGGAGGATGACCCCG	59.088	55.000	0.00	0.00	36.73	5.73
3992	7110	0.107165	GAAAAGGAGGATGACCCCGG	60.107	60.000	0.00	0.00	36.73	5.73
3993	7111	2.211468	AAAAGGAGGATGACCCCGGC	62.211	60.000	0.00	0.00	36.73	6.13
3996	7114	3.551407	GAGGATGACCCCGGCCTC	61.551	72.222	7.66	7.66	40.04	4.70
3997	7115	4.095400	AGGATGACCCCGGCCTCT	62.095	66.667	0.00	0.00	36.73	3.69
3998	7116	3.866582	GGATGACCCCGGCCTCTG	61.867	72.222	0.00	0.00	0.00	3.35
3999	7117	4.554036	GATGACCCCGGCCTCTGC	62.554	72.222	0.00	0.00	0.00	4.26
4002	7120	3.161450	GACCCCGGCCTCTGCATA	61.161	66.667	0.00	0.00	40.13	3.14
4003	7121	2.448542	ACCCCGGCCTCTGCATAT	60.449	61.111	0.00	0.00	40.13	1.78
4004	7122	1.152118	ACCCCGGCCTCTGCATATA	60.152	57.895	0.00	0.00	40.13	0.86
4005	7123	0.547712	ACCCCGGCCTCTGCATATAT	60.548	55.000	0.00	0.00	40.13	0.86
4006	7124	0.107508	CCCCGGCCTCTGCATATATG	60.108	60.000	8.45	8.45	40.13	1.78
4007	7125	0.615331	CCCGGCCTCTGCATATATGT	59.385	55.000	14.14	0.00	40.13	2.29
4008	7126	1.003580	CCCGGCCTCTGCATATATGTT	59.996	52.381	14.14	0.00	40.13	2.71
4009	7127	2.553028	CCCGGCCTCTGCATATATGTTT	60.553	50.000	14.14	0.00	40.13	2.83
4010	7128	2.744202	CCGGCCTCTGCATATATGTTTC	59.256	50.000	14.14	0.00	40.13	2.78
4011	7129	2.744202	CGGCCTCTGCATATATGTTTCC	59.256	50.000	14.14	6.56	40.13	3.13
4012	7130	3.557898	CGGCCTCTGCATATATGTTTCCT	60.558	47.826	14.14	0.00	40.13	3.36
4013	7131	4.401925	GGCCTCTGCATATATGTTTCCTT	58.598	43.478	14.14	0.00	40.13	3.36
4014	7132	5.560724	GGCCTCTGCATATATGTTTCCTTA	58.439	41.667	14.14	0.00	40.13	2.69
4015	7133	6.183347	GGCCTCTGCATATATGTTTCCTTAT	58.817	40.000	14.14	0.00	40.13	1.73
4016	7134	7.338710	GGCCTCTGCATATATGTTTCCTTATA	58.661	38.462	14.14	0.00	40.13	0.98
4017	7135	7.995488	GGCCTCTGCATATATGTTTCCTTATAT	59.005	37.037	14.14	0.00	40.13	0.86
4018	7136	8.834465	GCCTCTGCATATATGTTTCCTTATATG	58.166	37.037	14.14	9.53	40.85	1.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	7.718448	GAAGTATTCCTTAGCGATTGCTCCAG	61.718	46.154	11.77	8.83	44.10	3.86
20	21	3.431766	GGGCTTGAAGTATTCCTTAGCGA	60.432	47.826	0.00	0.00	46.93	4.93
21	22	2.872858	GGGCTTGAAGTATTCCTTAGCG	59.127	50.000	0.00	0.00	46.93	4.26
50	51	5.064325	GCGAAAGTAATTGGGGTAACTGTAG	59.936	44.000	0.00	0.00	0.00	2.74
59	60	3.443681	AGTGATTGCGAAAGTAATTGGGG	59.556	43.478	0.00	0.00	46.54	4.96
68	69	9.941664	ATAGATGAAAATTAGTGATTGCGAAAG	57.058	29.630	0.00	0.00	0.00	2.62
107	108	8.357402	AGCCGTACAAGATGAAAATTAGTTTTT	58.643	29.630	0.00	0.00	40.25	1.94
108	109	7.807907	CAGCCGTACAAGATGAAAATTAGTTTT	59.192	33.333	0.00	0.00	40.13	2.43
109	110	7.174253	TCAGCCGTACAAGATGAAAATTAGTTT	59.826	33.333	0.00	0.00	0.00	2.66
111	112	6.170506	TCAGCCGTACAAGATGAAAATTAGT	58.829	36.000	0.00	0.00	0.00	2.24
113	114	6.038161	CCATCAGCCGTACAAGATGAAAATTA	59.962	38.462	5.10	0.00	40.10	1.40
114	115	5.163622	CCATCAGCCGTACAAGATGAAAATT	60.164	40.000	5.10	0.00	40.10	1.82
115	116	4.336433	CCATCAGCCGTACAAGATGAAAAT	59.664	41.667	5.10	0.00	40.10	1.82
116	117	3.689161	CCATCAGCCGTACAAGATGAAAA	59.311	43.478	5.10	0.00	40.10	2.29
117	118	3.270027	CCATCAGCCGTACAAGATGAAA	58.730	45.455	5.10	0.00	40.10	2.69
129	370	1.089920	CTTCTTTGACCCATCAGCCG	58.910	55.000	0.00	0.00	35.83	5.52
145	386	7.010023	GTGAGTCGATCAAATTGTACAACTTC	58.990	38.462	11.22	3.12	40.43	3.01
147	388	5.118664	CGTGAGTCGATCAAATTGTACAACT	59.881	40.000	11.22	0.00	40.43	3.16
148	389	5.305812	CGTGAGTCGATCAAATTGTACAAC	58.694	41.667	11.22	0.00	40.43	3.32
149	390	4.387559	CCGTGAGTCGATCAAATTGTACAA	59.612	41.667	11.41	11.41	40.43	2.41
150	391	3.924073	CCGTGAGTCGATCAAATTGTACA	59.076	43.478	0.00	0.00	40.43	2.90
151	392	3.241995	GCCGTGAGTCGATCAAATTGTAC	60.242	47.826	0.00	0.00	40.43	2.90
676	948	3.120385	CATCGCAGCAAGACGGCA	61.120	61.111	0.00	0.00	39.78	5.69
860	1133	0.395312	TTCCTCACCGTTTCCTCCAC	59.605	55.000	0.00	0.00	0.00	4.02
861	1134	0.395312	GTTCCTCACCGTTTCCTCCA	59.605	55.000	0.00	0.00	0.00	3.86
862	1135	0.321387	GGTTCCTCACCGTTTCCTCC	60.321	60.000	0.00	0.00	35.12	4.30
863	1136	3.228499	GGTTCCTCACCGTTTCCTC	57.772	57.895	0.00	0.00	35.12	3.71
894	1167	2.796193	GGAAAATCATGCGGGGGCC	61.796	63.158	0.00	0.00	0.00	5.80
933	1206	1.392853	GAATTGACTGCTGACTGCTCG	59.607	52.381	5.87	0.00	43.37	5.03
1044	1341	1.078759	CAAGGCTAACAGCGACGAGG	61.079	60.000	0.00	0.00	43.62	4.63
1300	1603	2.203480	ATGGCCGCAGTTGTTGGT	60.203	55.556	0.00	0.00	0.00	3.67
1349	1652	3.509137	AACGCGGCGGAGAAGTTGA	62.509	57.895	27.37	0.00	0.00	3.18
1515	1818	3.842923	CTGCTGGACGCGAGGGAT	61.843	66.667	15.93	0.00	43.27	3.85
2321	5387	3.190874	CAATCTAGAACCGGCTTCTCAC	58.809	50.000	18.60	0.00	40.04	3.51
2421	5496	0.402504	TGGCTTTAATGTCCCGGTGT	59.597	50.000	0.00	0.00	0.00	4.16
2433	5508	3.678806	CGAGGAGCACATTACTGGCTTTA	60.679	47.826	0.00	0.00	38.15	1.85
2867	5949	0.038526	CTCCGGTAGTTGCACGTCTT	60.039	55.000	0.00	0.00	0.00	3.01
3073	6155	6.207928	CCATATAATTTCGTGCATTTGCTCA	58.792	36.000	3.94	0.00	42.66	4.26
3132	6214	5.233988	ACAGTGAAGTAAGAGATGCACTTC	58.766	41.667	0.00	6.73	45.41	3.01
3180	6262	7.895759	TCTCAAATAGCCAAGTTTATTTTGCT	58.104	30.769	0.00	0.00	29.45	3.91
3219	6301	9.569122	TTAACAACTCTACATAAAGCCTTTCTT	57.431	29.630	0.00	0.00	36.34	2.52
3356	6439	5.865977	TGCATTGGGAGAATAGGGATTAT	57.134	39.130	0.00	0.00	0.00	1.28
3413	6496	8.917655	GCGAAGATTATAAGATACTCCTTCAAC	58.082	37.037	0.00	0.00	31.75	3.18
3459	6553	9.283768	TGAAGAGAAGTATATTTGAGTTTGCAA	57.716	29.630	0.00	0.00	0.00	4.08
3483	6594	8.204160	TCAACTCTCTGTTATTCTTGAGTTTGA	58.796	33.333	0.00	0.00	41.11	2.69
3573	6684	8.539544	CCCATTTTATTACTCAAATTTGGGTCT	58.460	33.333	26.62	17.24	41.90	3.85
3602	6713	3.897505	AGCAAACAAGGTAGGCTCAAAAT	59.102	39.130	0.00	0.00	0.00	1.82
3606	6717	2.504367	GAAGCAAACAAGGTAGGCTCA	58.496	47.619	0.00	0.00	32.84	4.26
3607	6718	1.813178	GGAAGCAAACAAGGTAGGCTC	59.187	52.381	0.00	0.00	32.84	4.70
3608	6719	1.144913	TGGAAGCAAACAAGGTAGGCT	59.855	47.619	0.00	0.00	36.13	4.58
3609	6720	1.269723	GTGGAAGCAAACAAGGTAGGC	59.730	52.381	0.00	0.00	0.00	3.93
3611	6722	2.863809	AGGTGGAAGCAAACAAGGTAG	58.136	47.619	0.00	0.00	36.26	3.18
3612	6723	2.955660	CAAGGTGGAAGCAAACAAGGTA	59.044	45.455	0.00	0.00	36.26	3.08
3613	6724	1.756538	CAAGGTGGAAGCAAACAAGGT	59.243	47.619	0.00	0.00	36.26	3.50
3640	6754	7.798596	AGCATGTCTTCCACTATAGAAATTG	57.201	36.000	6.78	0.00	0.00	2.32
3641	6755	7.831193	ACAAGCATGTCTTCCACTATAGAAATT	59.169	33.333	6.78	0.00	33.41	1.82
3684	6798	1.540797	CGTGAAAACAAGGTACGGGGA	60.541	52.381	0.00	0.00	0.00	4.81
3690	6804	6.543100	ACAAGGATTTACGTGAAAACAAGGTA	59.457	34.615	0.00	0.00	0.00	3.08
3694	6808	6.094325	AGACACAAGGATTTACGTGAAAACAA	59.906	34.615	0.00	0.00	33.56	2.83
3703	6817	3.611766	AGGGAGACACAAGGATTTACG	57.388	47.619	0.00	0.00	0.00	3.18
3873	6988	7.568199	ACTTGCAAGAACAACTTACTACAAT	57.432	32.000	32.50	0.70	37.03	2.71
3967	7085	5.013183	CGGGGTCATCCTCCTTTTCTAATAT	59.987	44.000	0.00	0.00	35.33	1.28
3970	7088	2.504175	CGGGGTCATCCTCCTTTTCTAA	59.496	50.000	0.00	0.00	35.33	2.10
3971	7089	2.116238	CGGGGTCATCCTCCTTTTCTA	58.884	52.381	0.00	0.00	35.33	2.10
3972	7090	0.912486	CGGGGTCATCCTCCTTTTCT	59.088	55.000	0.00	0.00	35.33	2.52
3973	7091	0.107165	CCGGGGTCATCCTCCTTTTC	60.107	60.000	0.00	0.00	35.33	2.29
3974	7092	1.999346	CCGGGGTCATCCTCCTTTT	59.001	57.895	0.00	0.00	35.33	2.27
3975	7093	2.680370	GCCGGGGTCATCCTCCTTT	61.680	63.158	2.18	0.00	35.33	3.11
3976	7094	3.090532	GCCGGGGTCATCCTCCTT	61.091	66.667	2.18	0.00	35.33	3.36
3979	7097	3.551407	GAGGCCGGGGTCATCCTC	61.551	72.222	2.18	5.59	38.40	3.71
3980	7098	4.095400	AGAGGCCGGGGTCATCCT	62.095	66.667	2.18	0.00	35.33	3.24
3981	7099	3.866582	CAGAGGCCGGGGTCATCC	61.867	72.222	2.18	0.00	0.00	3.51
3982	7100	4.554036	GCAGAGGCCGGGGTCATC	62.554	72.222	2.18	0.00	0.00	2.92
3984	7102	3.858220	TATATGCAGAGGCCGGGGTCA	62.858	57.143	2.18	0.00	40.13	4.02
3985	7103	1.192146	TATATGCAGAGGCCGGGGTC	61.192	60.000	2.18	0.00	40.13	4.46
3986	7104	0.547712	ATATATGCAGAGGCCGGGGT	60.548	55.000	2.18	0.00	40.13	4.95
3987	7105	0.107508	CATATATGCAGAGGCCGGGG	60.108	60.000	2.18	0.00	40.13	5.73
3988	7106	0.615331	ACATATATGCAGAGGCCGGG	59.385	55.000	12.79	0.00	40.13	5.73
3989	7107	2.479566	AACATATATGCAGAGGCCGG	57.520	50.000	12.79	0.00	40.13	6.13
3990	7108	2.744202	GGAAACATATATGCAGAGGCCG	59.256	50.000	12.79	0.00	40.13	6.13
3991	7109	4.026356	AGGAAACATATATGCAGAGGCC	57.974	45.455	12.79	0.00	40.13	5.19
3992	7110	8.834465	CATATAAGGAAACATATATGCAGAGGC	58.166	37.037	12.79	0.00	43.75	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.