AutoCloner

Multiple sequence alignment - TraesCS3D01G227700

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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	TraesCS3D01G227700	chr3D	100.000	2213	0	0	1	2213	309695993	309698205	0.000000e+00	4087
1	TraesCS3D01G227700	chr5D	82.060	1466	148	51	52	1468	38275761	38277160	0.000000e+00	1144
2	TraesCS3D01G227700	chr1D	89.434	918	69	15	581	1480	9256201	9255294	0.000000e+00	1133
3	TraesCS3D01G227700	chr1D	85.714	455	32	8	39	486	9256618	9256190	1.210000e-122	449
4	TraesCS3D01G227700	chr1D	88.056	360	35	4	1857	2213	9253915	9253561	9.450000e-114	420
5	TraesCS3D01G227700	chr6B	81.305	1471	155	51	49	1468	711364479	711365880	0.000000e+00	1083
6	TraesCS3D01G227700	chr6B	84.133	750	96	16	1474	2211	709008706	709007968	0.000000e+00	704
7	TraesCS3D01G227700	chr6B	83.979	749	101	14	1474	2211	14019748	14019008	0.000000e+00	701
8	TraesCS3D01G227700	chr6B	78.862	369	50	16	42	393	709011084	709010727	7.950000e-55	224
9	TraesCS3D01G227700	chr1A	80.722	1468	162	53	52	1468	551193624	551192227	0.000000e+00	1031
10	TraesCS3D01G227700	chr2D	83.704	675	93	14	804	1471	595527780	595527116	2.410000e-174	621
11	TraesCS3D01G227700	chr2D	77.305	282	38	15	97	364	595528223	595527954	2.290000e-30	143
12	TraesCS3D01G227700	chr2A	83.284	676	96	14	804	1471	47355906	47356572	6.760000e-170	606
13	TraesCS3D01G227700	chr2A	82.047	674	103	15	811	1472	779329396	779328729	1.920000e-155	558
14	TraesCS3D01G227700	chr2A	79.737	760	114	31	1474	2213	126654430	126655169	4.210000e-142	514
15	TraesCS3D01G227700	chr6D	82.815	675	96	15	804	1471	455456911	455456250	8.800000e-164	586
16	TraesCS3D01G227700	chr6D	81.524	617	94	15	1605	2211	94936362	94936968	7.100000e-135	490
17	TraesCS3D01G227700	chr6D	78.905	621	94	25	97	694	455457688	455457082	9.580000e-104	387
18	TraesCS3D01G227700	chr2B	83.471	605	86	9	1615	2213	453862369	453862965	3.210000e-153	551
19	TraesCS3D01G227700	chr2B	82.505	463	66	12	1465	1926	750113126	750112678	2.060000e-105	392
20	TraesCS3D01G227700	chr3A	81.575	673	105	15	811	1472	735228574	735227910	2.500000e-149	538
21	TraesCS3D01G227700	chr3A	82.410	614	83	16	1605	2211	732086704	732087299	1.520000e-141	512
22	TraesCS3D01G227700	chr3A	88.136	118	11	3	39	154	508522624	508522740	1.070000e-28	137
23	TraesCS3D01G227700	chr7A	81.892	613	89	12	1605	2211	321658681	321658085	4.240000e-137	497
24	TraesCS3D01G227700	chr3B	79.238	761	113	35	1474	2213	750877187	750876451	2.550000e-134	488
25	TraesCS3D01G227700	chr3B	86.087	115	13	3	42	154	750895309	750895196	1.070000e-23	121
26	TraesCS3D01G227700	chr6A	76.248	661	126	25	42	681	615378596	615377946	2.740000e-84	322
27	TraesCS3D01G227700	chr7D	82.237	304	42	10	1478	1772	20433451	20433751	3.650000e-63	252
28	TraesCS3D01G227700	chr5A	86.538	208	26	2	2004	2211	396485207	396485412	6.150000e-56	228
29	TraesCS3D01G227700	chr7B	77.512	418	63	20	42	438	201268136	201267729	2.860000e-54	222
30	TraesCS3D01G227700	chr7B	89.888	89	8	1	67	154	265361432	265361520	1.800000e-21	113

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	TraesCS3D01G227700	chr3D	309695993	309698205	2212	False	4087.000000	4087	100.000000	1	2213	1	chr3D.!!$F1	2212
1	TraesCS3D01G227700	chr5D	38275761	38277160	1399	False	1144.000000	1144	82.060000	52	1468	1	chr5D.!!$F1	1416
2	TraesCS3D01G227700	chr1D	9253561	9256618	3057	True	667.333333	1133	87.734667	39	2213	3	chr1D.!!$R1	2174
3	TraesCS3D01G227700	chr6B	711364479	711365880	1401	False	1083.000000	1083	81.305000	49	1468	1	chr6B.!!$F1	1419
4	TraesCS3D01G227700	chr6B	14019008	14019748	740	True	701.000000	701	83.979000	1474	2211	1	chr6B.!!$R1	737
5	TraesCS3D01G227700	chr6B	709007968	709011084	3116	True	464.000000	704	81.497500	42	2211	2	chr6B.!!$R2	2169
6	TraesCS3D01G227700	chr1A	551192227	551193624	1397	True	1031.000000	1031	80.722000	52	1468	1	chr1A.!!$R1	1416
7	TraesCS3D01G227700	chr2D	595527116	595528223	1107	True	382.000000	621	80.504500	97	1471	2	chr2D.!!$R1	1374
8	TraesCS3D01G227700	chr2A	47355906	47356572	666	False	606.000000	606	83.284000	804	1471	1	chr2A.!!$F1	667
9	TraesCS3D01G227700	chr2A	779328729	779329396	667	True	558.000000	558	82.047000	811	1472	1	chr2A.!!$R1	661
10	TraesCS3D01G227700	chr2A	126654430	126655169	739	False	514.000000	514	79.737000	1474	2213	1	chr2A.!!$F2	739
11	TraesCS3D01G227700	chr6D	94936362	94936968	606	False	490.000000	490	81.524000	1605	2211	1	chr6D.!!$F1	606
12	TraesCS3D01G227700	chr6D	455456250	455457688	1438	True	486.500000	586	80.860000	97	1471	2	chr6D.!!$R1	1374
13	TraesCS3D01G227700	chr2B	453862369	453862965	596	False	551.000000	551	83.471000	1615	2213	1	chr2B.!!$F1	598
14	TraesCS3D01G227700	chr3A	735227910	735228574	664	True	538.000000	538	81.575000	811	1472	1	chr3A.!!$R1	661
15	TraesCS3D01G227700	chr3A	732086704	732087299	595	False	512.000000	512	82.410000	1605	2211	1	chr3A.!!$F2	606
16	TraesCS3D01G227700	chr7A	321658085	321658681	596	True	497.000000	497	81.892000	1605	2211	1	chr7A.!!$R1	606
17	TraesCS3D01G227700	chr3B	750876451	750877187	736	True	488.000000	488	79.238000	1474	2213	1	chr3B.!!$R1	739
18	TraesCS3D01G227700	chr6A	615377946	615378596	650	True	322.000000	322	76.248000	42	681	1	chr6A.!!$R1	639

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
609	674	0.032952	TCGTCGACAACTCAAAGGGG	59.967	55.0	17.16	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1640	2885	0.321671	TAGGTTCTGAGCCAGCACAC	59.678	55.0	13.26	0.0	29.69	3.82	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
37	38	2.045045	CACCGGATGTGGGCATGT	60.045	61.111	9.46	0.00	41.52	3.21
91	93	1.671742	CTTCCCGTGGTAGCTGTGT	59.328	57.895	0.00	0.00	0.00	3.72
99	101	0.611062	TGGTAGCTGTGTAGAGCGGT	60.611	55.000	0.00	0.00	44.24	5.68
172	175	3.530910	AACGAACCTGCCGTCCCTG	62.531	63.158	0.00	0.00	39.57	4.45
200	206	3.350219	TGCCCTTGATTAGTCCAGAAC	57.650	47.619	0.00	0.00	0.00	3.01
201	207	2.912956	TGCCCTTGATTAGTCCAGAACT	59.087	45.455	0.00	0.00	42.33	3.01
202	208	3.055094	TGCCCTTGATTAGTCCAGAACTC	60.055	47.826	0.00	0.00	39.55	3.01
203	209	3.682999	GCCCTTGATTAGTCCAGAACTCC	60.683	52.174	0.00	0.00	39.55	3.85
204	210	3.519510	CCCTTGATTAGTCCAGAACTCCA	59.480	47.826	0.00	0.00	39.55	3.86
205	211	4.383552	CCCTTGATTAGTCCAGAACTCCAG	60.384	50.000	0.00	0.00	39.55	3.86
206	212	4.467795	CCTTGATTAGTCCAGAACTCCAGA	59.532	45.833	0.00	0.00	39.55	3.86
248	254	2.348411	ATTATGCTCCTTGGTTCCCG	57.652	50.000	0.00	0.00	0.00	5.14
313	344	2.279741	TCTTGTATGTGCCGCAGATTC	58.720	47.619	8.50	4.25	0.00	2.52
334	365	4.256180	CCTAGGGTGGATGCGGGC	62.256	72.222	0.00	0.00	0.00	6.13
341	372	2.513666	TGGATGCGGGCGATGTTC	60.514	61.111	0.00	0.00	0.00	3.18
358	389	2.511600	CTGGGTGGCGGAATCGAC	60.512	66.667	0.00	0.00	46.45	4.20
402	434	2.874648	ATCAATGAAGCTCGCGGGCA	62.875	55.000	35.41	13.95	34.17	5.36
410	442	2.187946	CTCGCGGGCAATCCTCTT	59.812	61.111	6.13	0.00	0.00	2.85
478	537	4.201951	CGAGGGGTTGACGGAATG	57.798	61.111	0.00	0.00	0.00	2.67
480	539	1.683441	GAGGGGTTGACGGAATGGT	59.317	57.895	0.00	0.00	0.00	3.55
481	540	0.676782	GAGGGGTTGACGGAATGGTG	60.677	60.000	0.00	0.00	0.00	4.17
482	541	2.340328	GGGGTTGACGGAATGGTGC	61.340	63.158	0.00	0.00	0.00	5.01
483	542	2.340328	GGGTTGACGGAATGGTGCC	61.340	63.158	0.00	0.00	0.00	5.01
484	543	1.303317	GGTTGACGGAATGGTGCCT	60.303	57.895	0.00	0.00	0.00	4.75
485	544	1.305930	GGTTGACGGAATGGTGCCTC	61.306	60.000	0.00	0.00	0.00	4.70
486	545	0.605319	GTTGACGGAATGGTGCCTCA	60.605	55.000	0.00	0.00	0.00	3.86
487	546	0.327924	TTGACGGAATGGTGCCTCAT	59.672	50.000	0.00	0.00	0.00	2.90
488	547	1.199615	TGACGGAATGGTGCCTCATA	58.800	50.000	0.00	0.00	0.00	2.15
489	548	1.134521	TGACGGAATGGTGCCTCATAC	60.135	52.381	0.00	0.00	0.00	2.39
490	549	0.180406	ACGGAATGGTGCCTCATACC	59.820	55.000	0.00	0.00	38.71	2.73
495	554	3.642938	TGGTGCCTCATACCACAAC	57.357	52.632	0.00	0.00	43.00	3.32
496	555	0.321210	TGGTGCCTCATACCACAACG	60.321	55.000	0.00	0.00	43.00	4.10
497	556	1.024579	GGTGCCTCATACCACAACGG	61.025	60.000	0.00	0.00	38.12	4.44
534	593	1.940613	GGTGACTCAAACGATATGGCC	59.059	52.381	0.00	0.00	0.00	5.36
547	606	1.324383	TATGGCCGCTCAGAATACGA	58.676	50.000	0.00	0.00	0.00	3.43
579	644	2.851588	GGAGAGGAGGGGGATGCC	60.852	72.222	0.00	0.00	0.00	4.40
609	674	0.032952	TCGTCGACAACTCAAAGGGG	59.967	55.000	17.16	0.00	0.00	4.79
648	715	5.585445	ACGGTAACAAACACACACTCATTTA	59.415	36.000	0.00	0.00	0.00	1.40
708	861	1.333619	GGACTCGCACAAAACACACAT	59.666	47.619	0.00	0.00	0.00	3.21
981	1167	0.178953	ATGCCAACCCAAGCAGAGTT	60.179	50.000	0.00	0.00	43.38	3.01
1006	1192	2.091541	CCCTTGAGGCTTTAATGCGAA	58.908	47.619	7.20	0.50	0.00	4.70
1011	1197	4.939509	TGAGGCTTTAATGCGAACTTAC	57.060	40.909	7.20	0.00	0.00	2.34
1047	1233	0.878416	GCACTGTTGTTAATCCGGCA	59.122	50.000	0.00	0.00	0.00	5.69
1076	1262	3.561725	ACTAGCTTTGACACAGTTGAAGC	59.438	43.478	0.00	9.14	42.17	3.86
1099	1285	6.884295	AGCAGCATATGAGTTTTACAACCTAA	59.116	34.615	6.97	0.00	32.70	2.69
1133	1319	0.676782	GGCTTTGGCGTCAGGTATGT	60.677	55.000	0.00	0.00	39.81	2.29
1146	1332	3.263170	TCAGGTATGTCAAAAGCAGGCTA	59.737	43.478	0.00	0.00	0.00	3.93
1365	1561	2.316108	TGCGGGTGCTTAGATCTGATA	58.684	47.619	5.18	0.00	43.34	2.15
1368	1564	3.681897	GCGGGTGCTTAGATCTGATAATG	59.318	47.826	5.18	0.00	38.39	1.90
1445	1641	5.102953	ACTATATGGAAAAGCTGCACTGA	57.897	39.130	1.02	0.00	0.00	3.41
1453	1649	3.464111	AAAGCTGCACTGAAAATTGCT	57.536	38.095	1.02	0.00	39.62	3.91
1475	1671	8.753497	TGCTCCGACACATAGATAGATATATT	57.247	34.615	0.00	0.00	0.00	1.28
1574	2813	9.166126	CAATTTATCTTGTCATGAATCATGTCG	57.834	33.333	21.13	9.48	41.98	4.35
1610	2853	5.890424	AAACGATAGGTAAAACCACATGG	57.110	39.130	0.00	0.00	41.95	3.66
1636	2881	0.918799	TATGTCCCCACATGCAGGGT	60.919	55.000	19.45	6.51	43.54	4.34
1639	2884	4.371417	CCCCACATGCAGGGTGCT	62.371	66.667	19.45	0.00	45.31	4.40
1640	2885	3.066190	CCCACATGCAGGGTGCTG	61.066	66.667	14.31	5.53	45.31	4.41
1706	2951	2.684001	TACACGAGGGCTATGTTTGG	57.316	50.000	0.00	0.00	0.00	3.28
1711	2956	3.254657	CACGAGGGCTATGTTTGGAAAAA	59.745	43.478	0.00	0.00	0.00	1.94
1777	3022	2.089887	TTGTGCCTCGCCGTGAGTAA	62.090	55.000	8.14	0.00	43.64	2.24
1785	3030	0.928229	CGCCGTGAGTAAATAGCCAC	59.072	55.000	0.00	0.00	0.00	5.01
1790	3035	2.607635	CGTGAGTAAATAGCCACGCATT	59.392	45.455	0.00	0.00	44.24	3.56
1805	3050	3.848019	CACGCATTTGAAGAAAGATTCCG	59.152	43.478	0.00	0.00	0.00	4.30
1843	3088	3.721087	AATGAATTCCTCGTCCAGGTT	57.279	42.857	2.27	0.00	43.95	3.50
1856	3101	3.741075	CGTCCAGGTTAATGAGCATGCTA	60.741	47.826	22.74	9.75	0.00	3.49
1966	3217	5.574891	TGTTCTGTTGTACATGCAAAACT	57.425	34.783	14.25	0.00	0.00	2.66
1967	3218	5.960113	TGTTCTGTTGTACATGCAAAACTT	58.040	33.333	14.25	0.00	0.00	2.66
1968	3219	6.393990	TGTTCTGTTGTACATGCAAAACTTT	58.606	32.000	14.25	0.00	0.00	2.66
1969	3220	6.870965	TGTTCTGTTGTACATGCAAAACTTTT	59.129	30.769	14.25	0.00	0.00	2.27
1970	3221	7.386299	TGTTCTGTTGTACATGCAAAACTTTTT	59.614	29.630	14.25	0.00	0.00	1.94
2015	3269	2.301870	AGCGGAGATTTTGACACTGGTA	59.698	45.455	0.00	0.00	0.00	3.25
2077	3341	2.842462	TCCCAGCCAGACACGTGT	60.842	61.111	23.64	23.64	0.00	4.49
2096	3360	0.821711	TTGAAGCGTTGGACAAGGGG	60.822	55.000	6.84	0.00	0.00	4.79
2136	3404	4.142138	CCTCTAGAGTTTCTGCGTTACCAT	60.142	45.833	18.42	0.00	0.00	3.55
2200	3468	1.624336	TCTGCATCTGCTTTGCCTTT	58.376	45.000	3.53	0.00	42.66	3.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	0.757188	TGCCCACATCCGGTGTTTTT	60.757	50.000	0.00	0.00	46.44	1.94
16	17	0.541764	ATGCCCACATCCGGTGTTTT	60.542	50.000	0.00	0.00	46.44	2.43
17	18	1.076549	ATGCCCACATCCGGTGTTT	59.923	52.632	0.00	0.00	46.44	2.83
18	19	1.678635	CATGCCCACATCCGGTGTT	60.679	57.895	0.00	0.00	46.44	3.32
19	20	2.045045	CATGCCCACATCCGGTGT	60.045	61.111	0.00	2.11	46.44	4.16
21	22	2.045045	CACATGCCCACATCCGGT	60.045	61.111	0.00	0.00	32.87	5.28
22	23	2.829914	CCACATGCCCACATCCGG	60.830	66.667	0.00	0.00	32.87	5.14
23	24	3.520862	GCCACATGCCCACATCCG	61.521	66.667	0.00	0.00	32.87	4.18
24	25	3.520862	CGCCACATGCCCACATCC	61.521	66.667	0.00	0.00	32.87	3.51
25	26	4.197498	GCGCCACATGCCCACATC	62.197	66.667	0.00	0.00	32.87	3.06
26	27	4.746309	AGCGCCACATGCCCACAT	62.746	61.111	2.29	0.00	36.79	3.21
27	28	4.972733	AAGCGCCACATGCCCACA	62.973	61.111	2.29	0.00	36.24	4.17
28	29	3.225069	AAAAGCGCCACATGCCCAC	62.225	57.895	2.29	0.00	36.24	4.61
29	30	2.916703	AAAAGCGCCACATGCCCA	60.917	55.556	2.29	0.00	36.24	5.36
30	31	2.125952	GAAAAGCGCCACATGCCC	60.126	61.111	2.29	0.00	36.24	5.36
31	32	0.319813	AAAGAAAAGCGCCACATGCC	60.320	50.000	2.29	0.00	36.24	4.40
32	33	1.063031	GAAAGAAAAGCGCCACATGC	58.937	50.000	2.29	0.00	0.00	4.06
33	34	1.669795	GGGAAAGAAAAGCGCCACATG	60.670	52.381	2.29	0.00	0.00	3.21
34	35	0.603065	GGGAAAGAAAAGCGCCACAT	59.397	50.000	2.29	0.00	0.00	3.21
35	36	0.467290	AGGGAAAGAAAAGCGCCACA	60.467	50.000	2.29	0.00	0.00	4.17
36	37	0.241213	GAGGGAAAGAAAAGCGCCAC	59.759	55.000	2.29	0.00	0.00	5.01
37	38	1.234615	CGAGGGAAAGAAAAGCGCCA	61.235	55.000	2.29	0.00	0.00	5.69
42	43	1.807142	GGCTGACGAGGGAAAGAAAAG	59.193	52.381	0.00	0.00	0.00	2.27
172	175	4.396478	GGACTAATCAAGGGCAAGAGAAAC	59.604	45.833	0.00	0.00	0.00	2.78
248	254	4.562552	CCAACAGAGGGAGAAGAAGAACTC	60.563	50.000	0.00	0.00	0.00	3.01
313	344	1.227263	CGCATCCACCCTAGGAACG	60.227	63.158	11.48	0.00	41.92	3.95
334	365	2.796483	TTCCGCCACCCAGAACATCG	62.796	60.000	0.00	0.00	0.00	3.84
338	369	2.106683	CGATTCCGCCACCCAGAAC	61.107	63.158	0.00	0.00	0.00	3.01
341	372	2.511600	GTCGATTCCGCCACCCAG	60.512	66.667	0.00	0.00	35.37	4.45
358	389	0.937304	CAACCACAGACTCCACAACG	59.063	55.000	0.00	0.00	0.00	4.10
402	434	8.641541	GTTCAGAAGAGATCAGATAAGAGGATT	58.358	37.037	0.00	0.00	0.00	3.01
410	442	5.306419	CCATGGGTTCAGAAGAGATCAGATA	59.694	44.000	2.85	0.00	0.00	1.98
477	536	0.321210	CGTTGTGGTATGAGGCACCA	60.321	55.000	0.00	0.00	43.82	4.17
478	537	1.024579	CCGTTGTGGTATGAGGCACC	61.025	60.000	0.00	0.00	36.54	5.01
490	549	2.650196	CCCATTGCCACCGTTGTG	59.350	61.111	0.00	0.00	42.39	3.33
491	550	2.600173	CCCCATTGCCACCGTTGT	60.600	61.111	0.00	0.00	0.00	3.32
492	551	2.600173	ACCCCATTGCCACCGTTG	60.600	61.111	0.00	0.00	0.00	4.10
493	552	2.282887	GACCCCATTGCCACCGTT	60.283	61.111	0.00	0.00	0.00	4.44
494	553	4.715523	CGACCCCATTGCCACCGT	62.716	66.667	0.00	0.00	0.00	4.83
495	554	4.715523	ACGACCCCATTGCCACCG	62.716	66.667	0.00	0.00	0.00	4.94
496	555	2.282887	AACGACCCCATTGCCACC	60.283	61.111	0.00	0.00	0.00	4.61
497	556	2.635443	CCAACGACCCCATTGCCAC	61.635	63.158	0.00	0.00	0.00	5.01
498	557	2.282816	CCAACGACCCCATTGCCA	60.283	61.111	0.00	0.00	0.00	4.92
499	558	2.282887	ACCAACGACCCCATTGCC	60.283	61.111	0.00	0.00	0.00	4.52
500	559	1.602323	TCACCAACGACCCCATTGC	60.602	57.895	0.00	0.00	0.00	3.56
501	560	0.250727	AGTCACCAACGACCCCATTG	60.251	55.000	0.00	0.00	36.52	2.82
502	561	0.036306	GAGTCACCAACGACCCCATT	59.964	55.000	0.00	0.00	36.52	3.16
503	562	1.125093	TGAGTCACCAACGACCCCAT	61.125	55.000	0.00	0.00	36.52	4.00
504	563	1.338890	TTGAGTCACCAACGACCCCA	61.339	55.000	0.00	0.00	36.52	4.96
505	564	0.179040	TTTGAGTCACCAACGACCCC	60.179	55.000	0.00	0.00	36.52	4.95
506	565	0.942252	GTTTGAGTCACCAACGACCC	59.058	55.000	0.00	0.00	36.52	4.46
534	593	1.550065	CAGTGGTCGTATTCTGAGCG	58.450	55.000	0.00	0.00	36.66	5.03
547	606	2.045524	CTCTCCCATAGATGCAGTGGT	58.954	52.381	0.00	0.00	32.41	4.16
587	652	0.776451	CTTTGAGTTGTCGACGACGG	59.224	55.000	26.30	13.54	40.21	4.79
595	660	1.143073	ACAGGACCCCTTTGAGTTGTC	59.857	52.381	0.00	0.00	0.00	3.18
708	861	7.675161	TCATCCATAGGTGAACTCTTCAATA	57.325	36.000	0.00	0.00	42.15	1.90
748	910	7.687388	AGATAGCATCAAATGATATGACAGGT	58.313	34.615	2.67	0.00	41.51	4.00
853	1028	6.238925	GGGATGAACCGGGTAAATATCAAAAG	60.239	42.308	6.32	0.00	40.11	2.27
1006	1192	0.602905	GCCTTGGTGTCTGCGTAAGT	60.603	55.000	0.00	0.00	41.68	2.24
1047	1233	2.364324	TGTGTCAAAGCTAGTTCCGAGT	59.636	45.455	0.00	0.00	0.00	4.18
1076	1262	8.730680	AGTTTAGGTTGTAAAACTCATATGCTG	58.269	33.333	0.00	0.00	43.11	4.41
1099	1285	0.474660	AAGCCAGTCTCCCAGGAGTT	60.475	55.000	13.36	1.08	42.49	3.01
1133	1319	1.877443	GGACGTTTAGCCTGCTTTTGA	59.123	47.619	0.00	0.00	0.00	2.69
1223	1410	8.634475	AAAGTACTTGCAAGAGAAACATTTTC	57.366	30.769	32.50	5.04	0.00	2.29
1289	1483	5.221126	GCTGTTTGATTGGAATGGTATCCTC	60.221	44.000	0.00	0.00	40.35	3.71
1293	1487	3.381272	CGGCTGTTTGATTGGAATGGTAT	59.619	43.478	0.00	0.00	0.00	2.73
1301	1497	1.135315	CGAGCGGCTGTTTGATTGG	59.865	57.895	7.50	0.00	0.00	3.16
1365	1561	4.044308	TCACATATGTACCACCCCTCATT	58.956	43.478	8.32	0.00	0.00	2.57
1368	1564	3.199071	TGTTCACATATGTACCACCCCTC	59.801	47.826	8.32	0.00	0.00	4.30
1445	1641	6.582636	TCTATCTATGTGTCGGAGCAATTTT	58.417	36.000	0.00	0.00	0.00	1.82
1514	2751	9.979578	TCTGACAAGCACATAAAATTTGTATTT	57.020	25.926	0.00	0.00	35.49	1.40
1532	2771	1.376543	ATTGCTCGCCATCTGACAAG	58.623	50.000	0.00	0.00	0.00	3.16
1538	2777	4.202441	ACAAGATAAATTGCTCGCCATCT	58.798	39.130	0.00	0.00	33.28	2.90
1574	2813	6.824557	ACCTATCGTTTTCGTTGACATTTAC	58.175	36.000	0.00	0.00	44.46	2.01
1610	2853	4.397420	TGCATGTGGGGACATATCATTAC	58.603	43.478	0.00	0.00	46.14	1.89
1639	2884	1.227943	GGTTCTGAGCCAGCACACA	60.228	57.895	5.59	0.00	29.69	3.72
1640	2885	0.321671	TAGGTTCTGAGCCAGCACAC	59.678	55.000	13.26	0.00	29.69	3.82
1711	2956	5.311649	ACCCTCATATAGCATCTCACCAATT	59.688	40.000	0.00	0.00	0.00	2.32
1712	2957	4.848660	ACCCTCATATAGCATCTCACCAAT	59.151	41.667	0.00	0.00	0.00	3.16
1777	3022	4.458989	TCTTTCTTCAAATGCGTGGCTATT	59.541	37.500	0.00	0.00	0.00	1.73
1785	3030	3.429085	CCGGAATCTTTCTTCAAATGCG	58.571	45.455	0.00	0.00	0.00	4.73
1790	3035	2.373836	TGTCCCCGGAATCTTTCTTCAA	59.626	45.455	0.73	0.00	0.00	2.69
1805	3050	5.476091	TCATTTTTACACCATTTGTCCCC	57.524	39.130	0.00	0.00	39.91	4.81
1843	3088	6.316140	ACTTGAATTCGTTAGCATGCTCATTA	59.684	34.615	26.57	2.95	0.00	1.90
2077	3341	0.821711	CCCCTTGTCCAACGCTTCAA	60.822	55.000	0.00	0.00	0.00	2.69
2117	3385	5.419788	TCCTTATGGTAACGCAGAAACTCTA	59.580	40.000	0.00	0.00	42.51	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.