AutoCloner

Multiple sequence alignment - TraesCS3D01G486700

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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	TraesCS3D01G486700	chr3D	100.000	2528	0	0	1	2528	582612214	582609687	0.000000e+00	4669
1	TraesCS3D01G486700	chr3D	85.580	1172	109	29	392	1539	582536141	582535006	0.000000e+00	1173
2	TraesCS3D01G486700	chr3D	88.333	720	71	9	861	1575	582250579	582249868	0.000000e+00	852
3	TraesCS3D01G486700	chr3D	86.822	129	17	0	233	361	26231205	26231077	7.290000e-31	145
4	TraesCS3D01G486700	chr3D	80.882	204	19	10	347	543	582271343	582271153	2.620000e-30	143
5	TraesCS3D01G486700	chr3B	87.300	1811	141	38	756	2525	778678849	778680611	0.000000e+00	1988
6	TraesCS3D01G486700	chr3B	90.220	910	77	7	762	1668	778793012	778793912	0.000000e+00	1177
7	TraesCS3D01G486700	chr3B	88.011	734	58	17	2	726	778791565	778792277	0.000000e+00	841
8	TraesCS3D01G486700	chr3B	90.202	643	59	2	960	1598	779135326	779135968	0.000000e+00	835
9	TraesCS3D01G486700	chr3B	87.015	670	72	11	866	1521	779139045	779139713	0.000000e+00	741
10	TraesCS3D01G486700	chr3B	89.588	413	37	4	2033	2441	778794301	778794711	1.040000e-143	520
11	TraesCS3D01G486700	chr3B	90.361	332	22	1	1683	2004	778793899	778794230	6.460000e-116	427
12	TraesCS3D01G486700	chr3B	84.975	406	44	12	358	761	778678432	778678822	1.820000e-106	396
13	TraesCS3D01G486700	chr3B	85.602	382	39	12	347	726	778678069	778678436	1.100000e-103	387
14	TraesCS3D01G486700	chr3B	83.439	314	38	9	358	671	778792273	778792572	1.920000e-71	279
15	TraesCS3D01G486700	chr3B	87.083	240	23	4	2	234	778677833	778678071	5.360000e-67	265
16	TraesCS3D01G486700	chrUn	88.143	953	69	7	1064	2001	382449215	382450138	0.000000e+00	1094
17	TraesCS3D01G486700	chrUn	87.174	499	58	5	2033	2528	382450212	382450707	1.700000e-156	562
18	TraesCS3D01G486700	chrUn	84.597	409	41	14	1683	2074	41591308	41591711	1.100000e-103	387
19	TraesCS3D01G486700	chrUn	85.032	314	35	8	358	671	41422242	41422543	2.440000e-80	309
20	TraesCS3D01G486700	chrUn	85.032	314	34	9	358	671	321841592	321841892	8.780000e-80	307
21	TraesCS3D01G486700	chrUn	85.522	297	33	6	762	1057	41431435	41431722	4.090000e-78	302
22	TraesCS3D01G486700	chrUn	85.522	297	33	6	762	1057	330746884	330747171	4.090000e-78	302
23	TraesCS3D01G486700	chrUn	85.522	297	33	6	762	1057	330758356	330758643	4.090000e-78	302
24	TraesCS3D01G486700	chrUn	90.047	211	21	0	1395	1605	403590996	403590786	8.910000e-70	274
25	TraesCS3D01G486700	chrUn	86.458	192	23	3	481	671	41418527	41418716	9.170000e-50	207
26	TraesCS3D01G486700	chrUn	86.458	192	23	3	484	674	292828570	292828381	9.170000e-50	207
27	TraesCS3D01G486700	chrUn	87.413	143	11	1	48	183	41589014	41589156	9.360000e-35	158
28	TraesCS3D01G486700	chrUn	87.413	143	11	1	48	183	346207153	346207011	9.360000e-35	158
29	TraesCS3D01G486700	chrUn	88.983	118	12	1	233	349	311697997	311697880	7.290000e-31	145
30	TraesCS3D01G486700	chr4A	88.983	118	13	0	233	350	702148793	702148910	2.030000e-31	147
31	TraesCS3D01G486700	chr1B	88.983	118	13	0	232	349	3240088	3239971	2.030000e-31	147
32	TraesCS3D01G486700	chr4B	88.889	117	13	0	233	349	22280391	22280275	7.290000e-31	145
33	TraesCS3D01G486700	chr5D	88.235	119	14	0	232	350	352456282	352456400	2.620000e-30	143
34	TraesCS3D01G486700	chr2D	87.097	124	16	0	232	355	441085884	441085761	9.430000e-30	141
35	TraesCS3D01G486700	chr2B	87.200	125	14	2	233	356	648067297	648067174	9.430000e-30	141

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	TraesCS3D01G486700	chr3D	582609687	582612214	2527	True	4669.0	4669	100.0000	1	2528	1	chr3D.!!$R5	2527
1	TraesCS3D01G486700	chr3D	582535006	582536141	1135	True	1173.0	1173	85.5800	392	1539	1	chr3D.!!$R4	1147
2	TraesCS3D01G486700	chr3D	582249868	582250579	711	True	852.0	852	88.3330	861	1575	1	chr3D.!!$R2	714
3	TraesCS3D01G486700	chr3B	779135326	779139713	4387	False	788.0	835	88.6085	866	1598	2	chr3B.!!$F3	732
4	TraesCS3D01G486700	chr3B	778677833	778680611	2778	False	759.0	1988	86.2400	2	2525	4	chr3B.!!$F1	2523
5	TraesCS3D01G486700	chr3B	778791565	778794711	3146	False	648.8	1177	88.3238	2	2441	5	chr3B.!!$F2	2439
6	TraesCS3D01G486700	chrUn	382449215	382450707	1492	False	828.0	1094	87.6585	1064	2528	2	chrUn.!!$F7	1464
7	TraesCS3D01G486700	chrUn	41589014	41591711	2697	False	272.5	387	86.0050	48	2074	2	chrUn.!!$F6	2026
8	TraesCS3D01G486700	chrUn	41418527	41422543	4016	False	258.0	309	85.7450	358	671	2	chrUn.!!$F5	313

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
432	3791	0.03831	TCAGCAAGGGAGAGAGTCGA	59.962	55.0	0.0	0.0	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1606	6986	0.169672	CACGGAAAGCAGCTCCATTG	59.83	55.0	0.0	0.0	32.77	2.82	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
35	36	5.233988	CGTTTCTCTTTGTCTCTCCATCTT	58.766	41.667	0.00	0.00	0.00	2.40
120	121	4.075682	TGCATAAATGAGGGTCAAAACGA	58.924	39.130	0.00	0.00	0.00	3.85
155	163	4.973055	CGTCCGTGGGCGTTTGGA	62.973	66.667	4.40	0.00	36.15	3.53
158	166	3.047877	CCGTGGGCGTTTGGAGAC	61.048	66.667	0.00	0.00	36.15	3.36
235	243	1.999648	TACCACCACCAAGTCGTACT	58.000	50.000	0.00	0.00	0.00	2.73
236	244	1.125633	ACCACCACCAAGTCGTACTT	58.874	50.000	0.00	0.00	39.39	2.24
245	253	2.094649	CCAAGTCGTACTTCCTCTGTCC	60.095	54.545	0.00	0.00	36.03	4.02
268	276	6.647481	TCCGAAAATACTTGTCGAAGAAATGA	59.353	34.615	1.13	0.00	39.69	2.57
272	280	9.612620	GAAAATACTTGTCGAAGAAATGAATGT	57.387	29.630	0.00	0.00	39.69	2.71
282	290	9.395707	GTCGAAGAAATGAATGTATATAGACGT	57.604	33.333	0.00	0.00	39.69	4.34
359	367	1.066358	GGTGGGAGTAGGTGTTAGTGC	60.066	57.143	0.00	0.00	0.00	4.40
430	3789	1.620819	TGTTCAGCAAGGGAGAGAGTC	59.379	52.381	0.00	0.00	0.00	3.36
431	3790	0.891373	TTCAGCAAGGGAGAGAGTCG	59.109	55.000	0.00	0.00	0.00	4.18
432	3791	0.038310	TCAGCAAGGGAGAGAGTCGA	59.962	55.000	0.00	0.00	0.00	4.20
433	3792	1.110442	CAGCAAGGGAGAGAGTCGAT	58.890	55.000	0.00	0.00	0.00	3.59
434	3793	1.066908	CAGCAAGGGAGAGAGTCGATC	59.933	57.143	0.00	0.00	0.00	3.69
445	3804	5.452776	GGAGAGAGTCGATCTAGAACAGAGA	60.453	48.000	0.00	0.00	38.84	3.10
447	3806	5.815740	AGAGAGTCGATCTAGAACAGAGAAC	59.184	44.000	0.00	0.00	38.84	3.01
509	4213	1.208052	CATCACCTCACATTCCTCCGT	59.792	52.381	0.00	0.00	0.00	4.69
510	4214	2.225382	TCACCTCACATTCCTCCGTA	57.775	50.000	0.00	0.00	0.00	4.02
542	4246	2.209273	TCACATTCACTCACACAACCG	58.791	47.619	0.00	0.00	0.00	4.44
580	4284	6.997239	TCTATAGACGTACATGACACAACT	57.003	37.500	0.00	2.18	0.00	3.16
615	4319	2.484065	CCAACTTTCCCTCACACGTACA	60.484	50.000	0.00	0.00	0.00	2.90
630	4334	6.092533	TCACACGTACAATATCGACTTCACTA	59.907	38.462	0.00	0.00	0.00	2.74
646	5571	2.890945	TCACTACAGCACTGCTACAAGA	59.109	45.455	2.39	0.00	36.40	3.02
653	5578	1.630148	CACTGCTACAAGAGTACGGC	58.370	55.000	0.00	0.00	0.00	5.68
678	5684	7.196637	TCTCTAGAGACACCACTCTAATACA	57.803	40.000	18.76	0.00	45.12	2.29
714	5720	3.763897	GCTACAGGAAATGAAACCACCAT	59.236	43.478	0.00	0.00	0.00	3.55
749	5755	4.508124	GCTAGAAAGATACGGACCACAATG	59.492	45.833	0.00	0.00	0.00	2.82
760	5798	2.435938	CACAATGTACGCCGCCCT	60.436	61.111	0.00	0.00	0.00	5.19
777	6051	4.980805	TGCGAGGACGGTGGTTGC	62.981	66.667	0.00	0.00	40.15	4.17
816	6090	2.162208	CCGTTGTACCTACTGCGAAGTA	59.838	50.000	2.54	2.54	0.00	2.24
819	6093	4.614535	CGTTGTACCTACTGCGAAGTAACT	60.615	45.833	4.45	0.00	0.00	2.24
820	6094	5.225642	GTTGTACCTACTGCGAAGTAACTT	58.774	41.667	4.45	0.00	0.00	2.66
821	6095	5.051891	TGTACCTACTGCGAAGTAACTTC	57.948	43.478	4.45	0.00	37.16	3.01
822	6096	4.763793	TGTACCTACTGCGAAGTAACTTCT	59.236	41.667	4.45	0.00	38.24	2.85
823	6097	5.939883	TGTACCTACTGCGAAGTAACTTCTA	59.060	40.000	4.45	0.00	38.24	2.10
824	6098	5.564048	ACCTACTGCGAAGTAACTTCTAG	57.436	43.478	4.45	0.00	38.24	2.43
831	6105	5.947443	TGCGAAGTAACTTCTAGTAGTTCC	58.053	41.667	16.98	7.31	38.24	3.62
858	6132	2.470286	GCAACGAGCCGACTTTCG	59.530	61.111	1.50	0.00	42.26	3.46
955	6327	2.690778	GCGTTACAGCCAAGCCCAG	61.691	63.158	0.00	0.00	0.00	4.45
976	6348	4.208460	CAGAAAAGCATCACAACAGCAAAG	59.792	41.667	0.00	0.00	0.00	2.77
1106	6482	2.431942	GTACTGGCACGACGTGGG	60.432	66.667	27.86	5.51	33.64	4.61
1188	6564	2.586357	GCCTTCGGCCTCGTGATC	60.586	66.667	0.00	0.00	44.06	2.92
1209	6585	2.750637	ATCGACGACCCGCTCACT	60.751	61.111	0.00	0.00	0.00	3.41
1212	6588	2.126424	GACGACCCGCTCACTGAC	60.126	66.667	0.00	0.00	0.00	3.51
1311	6687	2.163815	GCTGCTCATGCTCATGAACTTT	59.836	45.455	12.92	0.00	46.10	2.66
1527	6903	4.308458	CACTTGTCCCGGCCGTGA	62.308	66.667	26.12	17.03	0.00	4.35
1606	6986	8.699749	GCTGTTTAACTTGGTTTCATTTCATAC	58.300	33.333	0.00	0.00	0.00	2.39
1622	7002	3.282021	TCATACAATGGAGCTGCTTTCC	58.718	45.455	6.82	1.74	35.20	3.13
1638	7018	1.310904	TTCCGTGAACCTTTTTCCCG	58.689	50.000	0.00	0.00	0.00	5.14
1669	7049	6.864685	GTGTGATGTCAATGACAATGAAATGT	59.135	34.615	20.64	0.46	45.96	2.71
1670	7050	7.383029	GTGTGATGTCAATGACAATGAAATGTT	59.617	33.333	20.64	0.00	45.96	2.71
1671	7051	7.927092	TGTGATGTCAATGACAATGAAATGTTT	59.073	29.630	20.64	0.00	45.96	2.83
1672	7052	8.430063	GTGATGTCAATGACAATGAAATGTTTC	58.570	33.333	20.64	9.43	45.96	2.78
1673	7053	7.599621	TGATGTCAATGACAATGAAATGTTTCC	59.400	33.333	20.64	0.00	45.96	3.13
1674	7054	5.919707	TGTCAATGACAATGAAATGTTTCCG	59.080	36.000	14.37	0.00	39.78	4.30
1675	7055	4.922692	TCAATGACAATGAAATGTTTCCGC	59.077	37.500	3.26	0.00	36.36	5.54
1676	7056	3.998099	TGACAATGAAATGTTTCCGCA	57.002	38.095	3.26	0.00	36.36	5.69
1677	7057	4.313277	TGACAATGAAATGTTTCCGCAA	57.687	36.364	3.26	0.00	36.36	4.85
1678	7058	4.686972	TGACAATGAAATGTTTCCGCAAA	58.313	34.783	3.26	0.00	36.36	3.68
1679	7059	5.111989	TGACAATGAAATGTTTCCGCAAAA	58.888	33.333	3.26	0.00	36.36	2.44
1680	7060	5.582269	TGACAATGAAATGTTTCCGCAAAAA	59.418	32.000	3.26	0.00	36.36	1.94
1681	7061	6.046885	ACAATGAAATGTTTCCGCAAAAAG	57.953	33.333	3.26	0.00	36.36	2.27
1682	7062	5.814705	ACAATGAAATGTTTCCGCAAAAAGA	59.185	32.000	3.26	0.00	36.36	2.52
1683	7063	6.314896	ACAATGAAATGTTTCCGCAAAAAGAA	59.685	30.769	3.26	0.00	36.36	2.52
1684	7064	7.012232	ACAATGAAATGTTTCCGCAAAAAGAAT	59.988	29.630	3.26	0.00	36.36	2.40
1685	7065	6.284475	TGAAATGTTTCCGCAAAAAGAATG	57.716	33.333	3.26	0.00	36.36	2.67
1686	7066	6.045318	TGAAATGTTTCCGCAAAAAGAATGA	58.955	32.000	3.26	0.00	36.36	2.57
1687	7067	5.905480	AATGTTTCCGCAAAAAGAATGAC	57.095	34.783	0.00	0.00	0.00	3.06
1688	7068	4.377839	TGTTTCCGCAAAAAGAATGACA	57.622	36.364	0.00	0.00	0.00	3.58
1689	7069	4.748892	TGTTTCCGCAAAAAGAATGACAA	58.251	34.783	0.00	0.00	0.00	3.18
1690	7070	5.355596	TGTTTCCGCAAAAAGAATGACAAT	58.644	33.333	0.00	0.00	0.00	2.71
1691	7071	5.233902	TGTTTCCGCAAAAAGAATGACAATG	59.766	36.000	0.00	0.00	0.00	2.82
1692	7072	4.844998	TCCGCAAAAAGAATGACAATGA	57.155	36.364	0.00	0.00	0.00	2.57
1693	7073	5.193663	TCCGCAAAAAGAATGACAATGAA	57.806	34.783	0.00	0.00	0.00	2.57
1694	7074	5.595885	TCCGCAAAAAGAATGACAATGAAA	58.404	33.333	0.00	0.00	0.00	2.69
1695	7075	6.222389	TCCGCAAAAAGAATGACAATGAAAT	58.778	32.000	0.00	0.00	0.00	2.17
1696	7076	6.145858	TCCGCAAAAAGAATGACAATGAAATG	59.854	34.615	0.00	0.00	0.00	2.32
1742	7128	7.960738	TGTTACAAGTCGTTCTTCTTCTTTTTG	59.039	33.333	0.00	0.00	33.63	2.44
1776	7166	3.499918	GGCTGTGTGCATAGTTGATATCC	59.500	47.826	0.00	0.00	45.15	2.59
2083	7553	2.034179	AGATCAATGATGGCGCATGTTG	59.966	45.455	10.83	6.81	0.00	3.33
2086	7556	1.135344	CAATGATGGCGCATGTTGTCA	60.135	47.619	10.83	3.87	0.00	3.58
2099	7767	2.150390	TGTTGTCACGTCCATCCATTG	58.850	47.619	0.00	0.00	0.00	2.82
2118	7786	9.620259	ATCCATTGTTTCTATTAAAGGAGAGTC	57.380	33.333	0.00	0.00	0.00	3.36
2127	7795	8.306680	TCTATTAAAGGAGAGTCAAAACGTTG	57.693	34.615	0.00	0.00	35.95	4.10
2215	8255	5.923733	TTTTCTACTCACCCATCTCTCTC	57.076	43.478	0.00	0.00	0.00	3.20
2249	8289	2.875933	CTCGCTCTTTCTATCTCCGACT	59.124	50.000	0.00	0.00	0.00	4.18
2321	10355	1.133181	TCCCAACCATGTCTGCTCCA	61.133	55.000	0.00	0.00	0.00	3.86
2324	10358	1.012086	CAACCATGTCTGCTCCATCG	58.988	55.000	0.00	0.00	0.00	3.84
2352	10388	2.737830	GCTATCCACTCCCGCTCC	59.262	66.667	0.00	0.00	0.00	4.70
2470	10614	1.422531	GAGAGGAGGCATGACCATCT	58.577	55.000	4.19	4.19	43.14	2.90
2482	10626	3.198409	TGACCATCTGACATACATGGC	57.802	47.619	0.00	0.00	33.35	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.173390	AGACAAAGAGAAACGGAAGAATAAAGG	59.827	37.037	0.00	0.00	0.00	3.11
120	121	1.822186	GTTGCCGGTCAGGTGTGTT	60.822	57.895	1.90	0.00	43.70	3.32
235	243	5.223449	ACAAGTATTTTCGGACAGAGGAA	57.777	39.130	0.00	0.00	0.00	3.36
236	244	4.617530	CGACAAGTATTTTCGGACAGAGGA	60.618	45.833	0.00	0.00	0.00	3.71
245	253	8.779561	CATTCATTTCTTCGACAAGTATTTTCG	58.220	33.333	0.00	0.00	0.00	3.46
312	320	4.335594	GGGAAATACTTGTCGGAGAAATGG	59.664	45.833	0.00	0.00	39.69	3.16
359	367	2.624838	ACAAGGTGAAAATGTCCTGCAG	59.375	45.455	6.78	6.78	0.00	4.41
430	3789	5.062809	GCTTTTGGTTCTCTGTTCTAGATCG	59.937	44.000	0.00	0.00	34.21	3.69
431	3790	5.934625	TGCTTTTGGTTCTCTGTTCTAGATC	59.065	40.000	0.00	0.00	34.21	2.75
432	3791	5.703130	GTGCTTTTGGTTCTCTGTTCTAGAT	59.297	40.000	0.00	0.00	34.21	1.98
433	3792	5.057149	GTGCTTTTGGTTCTCTGTTCTAGA	58.943	41.667	0.00	0.00	0.00	2.43
434	3793	5.059833	AGTGCTTTTGGTTCTCTGTTCTAG	58.940	41.667	0.00	0.00	0.00	2.43
445	3804	2.577449	CCAAACGAGTGCTTTTGGTT	57.423	45.000	5.14	0.00	44.22	3.67
509	4213	6.065976	AGTGAATGTGAGGTGATGGAAATA	57.934	37.500	0.00	0.00	0.00	1.40
510	4214	4.927049	AGTGAATGTGAGGTGATGGAAAT	58.073	39.130	0.00	0.00	0.00	2.17
542	4246	8.951787	ACGTCTATAGATATGATACACTCCTC	57.048	38.462	5.57	0.00	0.00	3.71
568	4272	6.291377	ACTTGTTAGATCAGTTGTGTCATGT	58.709	36.000	0.00	0.00	0.00	3.21
580	4284	6.043938	AGGGAAAGTTGGTACTTGTTAGATCA	59.956	38.462	0.00	0.00	43.74	2.92
615	4319	5.344066	CAGTGCTGTAGTGAAGTCGATATT	58.656	41.667	0.00	0.00	30.94	1.28
630	4334	2.351835	CGTACTCTTGTAGCAGTGCTGT	60.352	50.000	27.97	17.26	40.10	4.40
646	5571	2.420408	GGTGTCTCTAGAGAGCCGTACT	60.420	54.545	22.95	0.00	41.80	2.73
653	5578	7.276658	TGTATTAGAGTGGTGTCTCTAGAGAG	58.723	42.308	22.95	0.00	44.46	3.20
678	5684	9.696917	CATTTCCTGTAGCACTTTAGAAAATTT	57.303	29.630	0.00	0.00	0.00	1.82
714	5720	1.681793	CTTTCTAGCTAGCAGGCGGTA	59.318	52.381	18.83	0.00	37.29	4.02
760	5798	4.980805	GCAACCACCGTCCTCGCA	62.981	66.667	0.00	0.00	35.54	5.10
816	6090	4.838986	TCAGCAAGGGAACTACTAGAAGTT	59.161	41.667	0.00	0.00	42.68	2.66
819	6093	4.322801	GCTTCAGCAAGGGAACTACTAGAA	60.323	45.833	0.00	0.00	42.68	2.10
820	6094	3.195825	GCTTCAGCAAGGGAACTACTAGA	59.804	47.826	0.00	0.00	42.68	2.43
821	6095	3.526534	GCTTCAGCAAGGGAACTACTAG	58.473	50.000	0.00	0.00	42.68	2.57
822	6096	3.611766	GCTTCAGCAAGGGAACTACTA	57.388	47.619	0.00	0.00	42.68	1.82
823	6097	2.481289	GCTTCAGCAAGGGAACTACT	57.519	50.000	0.00	0.00	42.68	2.57
858	6132	0.854062	TACATTACGCGGCGCATTAC	59.146	50.000	32.61	1.39	0.00	1.89
859	6133	0.854062	GTACATTACGCGGCGCATTA	59.146	50.000	32.61	19.03	0.00	1.90
898	6270	1.144969	GTATTTATGCGCTGCGGCTA	58.855	50.000	24.61	4.74	36.09	3.93
955	6327	3.060070	GCTTTGCTGTTGTGATGCTTTTC	60.060	43.478	0.00	0.00	0.00	2.29
976	6348	0.606604	TTCCCTTGAGTAGTCGGTGC	59.393	55.000	0.00	0.00	0.00	5.01
1152	6528	0.670162	CTGCCTTGGAAGTGTTGGTG	59.330	55.000	0.00	0.00	0.00	4.17
1161	6537	2.034066	CCGAAGGCTGCCTTGGAA	59.966	61.111	35.64	0.00	44.82	3.53
1311	6687	4.243008	TTGCCGGCGGTGAAGACA	62.243	61.111	28.82	12.94	0.00	3.41
1504	6880	2.690778	GCCGGGACAAGTGCATGAC	61.691	63.158	2.18	0.00	0.00	3.06
1514	6890	2.191786	ATTTGATCACGGCCGGGACA	62.192	55.000	36.43	28.35	0.00	4.02
1606	6986	0.169672	CACGGAAAGCAGCTCCATTG	59.830	55.000	0.00	0.00	32.77	2.82
1622	7002	3.561503	GAATTCGGGAAAAAGGTTCACG	58.438	45.455	4.39	4.39	45.86	4.35
1638	7018	5.281693	TGTCATTGACATCACACGAATTC	57.718	39.130	15.41	0.00	37.67	2.17
1669	7049	5.595885	TCATTGTCATTCTTTTTGCGGAAA	58.404	33.333	0.00	0.00	0.00	3.13
1670	7050	5.193663	TCATTGTCATTCTTTTTGCGGAA	57.806	34.783	0.00	0.00	0.00	4.30
1671	7051	4.844998	TCATTGTCATTCTTTTTGCGGA	57.155	36.364	0.00	0.00	0.00	5.54
1672	7052	5.903764	TTTCATTGTCATTCTTTTTGCGG	57.096	34.783	0.00	0.00	0.00	5.69
1673	7053	7.107834	TCATTTCATTGTCATTCTTTTTGCG	57.892	32.000	0.00	0.00	0.00	4.85
1674	7054	9.325150	CATTCATTTCATTGTCATTCTTTTTGC	57.675	29.630	0.00	0.00	0.00	3.68
1675	7055	9.820229	CCATTCATTTCATTGTCATTCTTTTTG	57.180	29.630	0.00	0.00	0.00	2.44
1676	7056	9.563748	ACCATTCATTTCATTGTCATTCTTTTT	57.436	25.926	0.00	0.00	0.00	1.94
1677	7057	8.995220	CACCATTCATTTCATTGTCATTCTTTT	58.005	29.630	0.00	0.00	0.00	2.27
1678	7058	8.152246	ACACCATTCATTTCATTGTCATTCTTT	58.848	29.630	0.00	0.00	0.00	2.52
1679	7059	7.673180	ACACCATTCATTTCATTGTCATTCTT	58.327	30.769	0.00	0.00	0.00	2.52
1680	7060	7.235935	ACACCATTCATTTCATTGTCATTCT	57.764	32.000	0.00	0.00	0.00	2.40
1681	7061	7.385752	ACAACACCATTCATTTCATTGTCATTC	59.614	33.333	0.00	0.00	0.00	2.67
1682	7062	7.218614	ACAACACCATTCATTTCATTGTCATT	58.781	30.769	0.00	0.00	0.00	2.57
1683	7063	6.761312	ACAACACCATTCATTTCATTGTCAT	58.239	32.000	0.00	0.00	0.00	3.06
1684	7064	6.159299	ACAACACCATTCATTTCATTGTCA	57.841	33.333	0.00	0.00	0.00	3.58
1685	7065	6.479660	ACAACAACACCATTCATTTCATTGTC	59.520	34.615	0.00	0.00	0.00	3.18
1686	7066	6.347696	ACAACAACACCATTCATTTCATTGT	58.652	32.000	0.00	0.00	0.00	2.71
1687	7067	6.847956	ACAACAACACCATTCATTTCATTG	57.152	33.333	0.00	0.00	0.00	2.82
1688	7068	7.862512	AAACAACAACACCATTCATTTCATT	57.137	28.000	0.00	0.00	0.00	2.57
1689	7069	8.991026	CATAAACAACAACACCATTCATTTCAT	58.009	29.630	0.00	0.00	0.00	2.57
1690	7070	7.984050	ACATAAACAACAACACCATTCATTTCA	59.016	29.630	0.00	0.00	0.00	2.69
1691	7071	8.274939	CACATAAACAACAACACCATTCATTTC	58.725	33.333	0.00	0.00	0.00	2.17
1692	7072	7.768120	ACACATAAACAACAACACCATTCATTT	59.232	29.630	0.00	0.00	0.00	2.32
1693	7073	7.271511	ACACATAAACAACAACACCATTCATT	58.728	30.769	0.00	0.00	0.00	2.57
1694	7074	6.815089	ACACATAAACAACAACACCATTCAT	58.185	32.000	0.00	0.00	0.00	2.57
1695	7075	6.214191	ACACATAAACAACAACACCATTCA	57.786	33.333	0.00	0.00	0.00	2.57
1696	7076	7.702772	TGTAACACATAAACAACAACACCATTC	59.297	33.333	0.00	0.00	0.00	2.67
1742	7128	5.818136	TGCACACAGCCTAATAAAAGATC	57.182	39.130	0.00	0.00	44.83	2.75
1776	7166	9.698309	AATGATACAATATCAAGACTAAGTCGG	57.302	33.333	2.79	0.00	37.67	4.79
2083	7553	3.074412	AGAAACAATGGATGGACGTGAC	58.926	45.455	0.00	0.00	0.00	3.67
2086	7556	7.067008	CCTTTAATAGAAACAATGGATGGACGT	59.933	37.037	0.00	0.00	0.00	4.34
2099	7767	8.771766	ACGTTTTGACTCTCCTTTAATAGAAAC	58.228	33.333	0.00	0.00	0.00	2.78
2118	7786	2.111162	TGGTGAGGCCAACGTTTTG	58.889	52.632	5.01	0.00	45.94	2.44
2127	7795	2.048603	GGCAGAATGTGGTGAGGCC	61.049	63.158	0.00	0.00	39.31	5.19
2215	8255	7.352719	AGAAAGAGCGAGTTTTACTTATGTG	57.647	36.000	0.00	0.00	0.00	3.21
2249	8289	3.990092	ACACATGAGAAAACTAGACGCA	58.010	40.909	0.00	0.00	0.00	5.24
2352	10388	0.535102	GGACCATGGCGGAGGTATTG	60.535	60.000	13.04	0.00	38.50	1.90
2433	10577	4.742201	CTCCACCACCGACGCCAG	62.742	72.222	0.00	0.00	0.00	4.85
2443	10587	2.039624	GCCTCCTCTCCTCCACCA	59.960	66.667	0.00	0.00	0.00	4.17
2470	10614	3.609853	GTTCTTCAGGCCATGTATGTCA	58.390	45.455	5.01	0.00	0.00	3.58
2482	10626	2.048222	TCGCTGCGGTTCTTCAGG	60.048	61.111	23.03	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.