AutoCloner

Multiple sequence alignment - TraesCS2A01G207300

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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	TraesCS2A01G207300	chr2A	100.000	2252	0	0	1	2252	187237580	187239831	0.000000e+00	4159.0
1	TraesCS2A01G207300	chr2A	97.833	600	13	0	91	690	187245473	187246072	0.000000e+00	1037.0
2	TraesCS2A01G207300	chr2A	80.351	911	112	37	91	959	605414653	605415538	1.470000e-176	628.0
3	TraesCS2A01G207300	chr6A	94.114	1750	102	1	504	2252	314900742	314902491	0.000000e+00	2660.0
4	TraesCS2A01G207300	chr6A	83.824	136	20	1	2100	2235	275771364	275771231	6.530000e-26	128.0
5	TraesCS2A01G207300	chr6A	83.077	130	20	1	2046	2175	163154472	163154599	1.410000e-22	117.0
6	TraesCS2A01G207300	chr1D	90.668	1243	112	3	924	2163	104447507	104446266	0.000000e+00	1650.0
7	TraesCS2A01G207300	chr1D	90.569	562	52	1	1131	1691	179510674	179510113	0.000000e+00	743.0
8	TraesCS2A01G207300	chr1D	94.382	89	4	1	1	88	124806123	124806035	3.900000e-28	135.0
9	TraesCS2A01G207300	chr1D	94.382	89	3	2	1	88	324152777	324152864	3.900000e-28	135.0
10	TraesCS2A01G207300	chr1D	94.318	88	4	1	1	88	15801887	15801973	1.400000e-27	134.0
11	TraesCS2A01G207300	chr1D	100.000	30	0	0	1687	1716	198774455	198774484	3.120000e-04	56.5
12	TraesCS2A01G207300	chr3D	90.724	1229	110	3	921	2145	404472431	404473659	0.000000e+00	1635.0
13	TraesCS2A01G207300	chr3D	81.683	202	37	0	1929	2130	173762999	173763200	3.850000e-38	169.0
14	TraesCS2A01G207300	chr2D	89.889	1266	121	5	924	2184	624764071	624762808	0.000000e+00	1622.0
15	TraesCS2A01G207300	chr2D	94.382	89	4	1	1	88	341810899	341810987	3.900000e-28	135.0
16	TraesCS2A01G207300	chr2D	93.407	91	6	0	1	91	530449438	530449348	3.900000e-28	135.0
17	TraesCS2A01G207300	chr2D	94.737	38	0	2	1680	1716	160539932	160539896	8.690000e-05	58.4
18	TraesCS2A01G207300	chr2D	97.059	34	0	1	1684	1716	133684776	133684809	3.120000e-04	56.5
19	TraesCS2A01G207300	chr7D	87.900	1281	118	16	924	2201	462064602	462063356	0.000000e+00	1472.0
20	TraesCS2A01G207300	chr7D	87.066	317	37	2	1932	2244	462063579	462063263	2.750000e-94	355.0
21	TraesCS2A01G207300	chr7D	94.505	91	5	0	1	91	497715274	497715184	8.390000e-30	141.0
22	TraesCS2A01G207300	chr7D	93.478	92	4	2	1	91	30781726	30781636	3.900000e-28	135.0
23	TraesCS2A01G207300	chr7D	94.737	38	1	1	1684	1720	169083460	169083423	8.690000e-05	58.4
24	TraesCS2A01G207300	chr7A	85.417	1344	151	30	921	2252	604757339	604758649	0.000000e+00	1354.0
25	TraesCS2A01G207300	chr7A	95.317	662	30	1	91	751	613741985	613742646	0.000000e+00	1050.0
26	TraesCS2A01G207300	chr7A	96.683	603	18	1	91	691	613767345	613767947	0.000000e+00	1002.0
27	TraesCS2A01G207300	chr7A	93.967	663	37	3	91	751	613870598	613871259	0.000000e+00	1000.0
28	TraesCS2A01G207300	chr7A	93.373	664	35	7	86	743	594510802	594510142	0.000000e+00	974.0
29	TraesCS2A01G207300	chr7A	82.963	270	42	4	1925	2193	333456126	333456392	8.040000e-60	241.0
30	TraesCS2A01G207300	chr7B	85.512	1339	134	25	921	2251	558157076	558158362	0.000000e+00	1343.0
31	TraesCS2A01G207300	chr7B	81.846	325	56	3	1715	2037	408644110	408644433	1.030000e-68	270.0
32	TraesCS2A01G207300	chr7B	79.448	326	59	6	1929	2252	12022410	12022091	8.090000e-55	224.0
33	TraesCS2A01G207300	chr3A	94.893	842	37	6	91	927	392498970	392499810	0.000000e+00	1312.0
34	TraesCS2A01G207300	chr3A	96.667	600	19	1	91	689	392506127	392506726	0.000000e+00	996.0
35	TraesCS2A01G207300	chr3A	87.557	876	66	13	87	929	426135032	426134167	0.000000e+00	974.0
36	TraesCS2A01G207300	chr3A	90.909	77	7	0	855	931	583666932	583666856	1.100000e-18	104.0
37	TraesCS2A01G207300	chr4B	90.012	861	61	11	91	927	268588449	268587590	0.000000e+00	1090.0
38	TraesCS2A01G207300	chr4B	87.648	421	49	3	1131	1550	222110490	222110072	9.350000e-134	486.0
39	TraesCS2A01G207300	chr4B	82.323	198	31	2	2049	2244	248125045	248124850	3.850000e-38	169.0
40	TraesCS2A01G207300	chrUn	89.711	865	59	15	91	927	73145173	73144311	0.000000e+00	1077.0
41	TraesCS2A01G207300	chrUn	84.252	127	18	1	2076	2202	464834269	464834393	3.040000e-24	122.0
42	TraesCS2A01G207300	chr3B	82.859	1266	143	35	924	2183	366468568	366467371	0.000000e+00	1068.0
43	TraesCS2A01G207300	chr3B	92.208	77	6	0	855	931	658055047	658054971	2.360000e-20	110.0
44	TraesCS2A01G207300	chr5B	81.995	1133	157	25	1120	2244	240974885	240973792	0.000000e+00	918.0
45	TraesCS2A01G207300	chr5B	85.714	210	27	1	924	1133	240975041	240974835	3.770000e-53	219.0
46	TraesCS2A01G207300	chr5B	79.856	278	50	4	1928	2202	240973878	240973604	4.910000e-47	198.0
47	TraesCS2A01G207300	chr5B	81.609	174	31	1	1925	2097	369143273	369143446	2.330000e-30	143.0
48	TraesCS2A01G207300	chr6B	87.363	546	60	5	1131	1675	536782301	536782838	3.180000e-173	617.0
49	TraesCS2A01G207300	chr1B	87.179	546	61	5	1131	1675	266208992	266209529	1.480000e-171	612.0
50	TraesCS2A01G207300	chr4A	79.298	541	97	13	1715	2252	252212400	252211872	4.570000e-97	364.0
51	TraesCS2A01G207300	chr4D	77.698	556	92	15	1715	2244	219434924	219434375	6.040000e-81	311.0
52	TraesCS2A01G207300	chr4D	97.059	34	0	1	1684	1716	217103012	217102979	3.120000e-04	56.5
53	TraesCS2A01G207300	chr5A	82.188	320	51	5	1928	2244	559915788	559915472	1.030000e-68	270.0
54	TraesCS2A01G207300	chr5A	80.328	244	40	6	2003	2243	26627305	26627067	6.390000e-41	178.0
55	TraesCS2A01G207300	chr6D	94.382	89	4	1	1	88	89441199	89441287	3.900000e-28	135.0
56	TraesCS2A01G207300	chr6D	94.382	89	4	1	1	88	96661876	96661788	3.900000e-28	135.0
57	TraesCS2A01G207300	chr1A	76.142	197	37	6	2032	2225	331183536	331183725	6.620000e-16	95.3
58	TraesCS2A01G207300	chr5D	97.059	34	0	1	1684	1716	21939607	21939640	3.120000e-04	56.5

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	TraesCS2A01G207300	chr2A	187237580	187239831	2251	False	4159.0	4159	100.000000	1	2252	1	chr2A.!!$F1	2251
1	TraesCS2A01G207300	chr2A	187245473	187246072	599	False	1037.0	1037	97.833000	91	690	1	chr2A.!!$F2	599
2	TraesCS2A01G207300	chr2A	605414653	605415538	885	False	628.0	628	80.351000	91	959	1	chr2A.!!$F3	868
3	TraesCS2A01G207300	chr6A	314900742	314902491	1749	False	2660.0	2660	94.114000	504	2252	1	chr6A.!!$F2	1748
4	TraesCS2A01G207300	chr1D	104446266	104447507	1241	True	1650.0	1650	90.668000	924	2163	1	chr1D.!!$R1	1239
5	TraesCS2A01G207300	chr1D	179510113	179510674	561	True	743.0	743	90.569000	1131	1691	1	chr1D.!!$R3	560
6	TraesCS2A01G207300	chr3D	404472431	404473659	1228	False	1635.0	1635	90.724000	921	2145	1	chr3D.!!$F2	1224
7	TraesCS2A01G207300	chr2D	624762808	624764071	1263	True	1622.0	1622	89.889000	924	2184	1	chr2D.!!$R3	1260
8	TraesCS2A01G207300	chr7D	462063263	462064602	1339	True	913.5	1472	87.483000	924	2244	2	chr7D.!!$R4	1320
9	TraesCS2A01G207300	chr7A	604757339	604758649	1310	False	1354.0	1354	85.417000	921	2252	1	chr7A.!!$F2	1331
10	TraesCS2A01G207300	chr7A	613741985	613742646	661	False	1050.0	1050	95.317000	91	751	1	chr7A.!!$F3	660
11	TraesCS2A01G207300	chr7A	613767345	613767947	602	False	1002.0	1002	96.683000	91	691	1	chr7A.!!$F4	600
12	TraesCS2A01G207300	chr7A	613870598	613871259	661	False	1000.0	1000	93.967000	91	751	1	chr7A.!!$F5	660
13	TraesCS2A01G207300	chr7A	594510142	594510802	660	True	974.0	974	93.373000	86	743	1	chr7A.!!$R1	657
14	TraesCS2A01G207300	chr7B	558157076	558158362	1286	False	1343.0	1343	85.512000	921	2251	1	chr7B.!!$F2	1330
15	TraesCS2A01G207300	chr3A	392498970	392499810	840	False	1312.0	1312	94.893000	91	927	1	chr3A.!!$F1	836
16	TraesCS2A01G207300	chr3A	392506127	392506726	599	False	996.0	996	96.667000	91	689	1	chr3A.!!$F2	598
17	TraesCS2A01G207300	chr3A	426134167	426135032	865	True	974.0	974	87.557000	87	929	1	chr3A.!!$R1	842
18	TraesCS2A01G207300	chr4B	268587590	268588449	859	True	1090.0	1090	90.012000	91	927	1	chr4B.!!$R3	836
19	TraesCS2A01G207300	chrUn	73144311	73145173	862	True	1077.0	1077	89.711000	91	927	1	chrUn.!!$R1	836
20	TraesCS2A01G207300	chr3B	366467371	366468568	1197	True	1068.0	1068	82.859000	924	2183	1	chr3B.!!$R1	1259
21	TraesCS2A01G207300	chr5B	240973604	240975041	1437	True	445.0	918	82.521667	924	2244	3	chr5B.!!$R1	1320
22	TraesCS2A01G207300	chr6B	536782301	536782838	537	False	617.0	617	87.363000	1131	1675	1	chr6B.!!$F1	544
23	TraesCS2A01G207300	chr1B	266208992	266209529	537	False	612.0	612	87.179000	1131	1675	1	chr1B.!!$F1	544
24	TraesCS2A01G207300	chr4A	252211872	252212400	528	True	364.0	364	79.298000	1715	2252	1	chr4A.!!$R1	537
25	TraesCS2A01G207300	chr4D	219434375	219434924	549	True	311.0	311	77.698000	1715	2244	1	chr4D.!!$R2	529

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
34	35	0.327924	TATGGCCCACACTCACTTGG	59.672	55.0	0.0	0.0	0.0	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1507	1631	0.312102	GAGGCAGCCAATTAATCCGC	59.688	55.0	15.8	0.0	0.0	5.54	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
22	23	2.290745	AGGACTCCCCTATGGCCC	59.709	66.667	0.00	0.00	45.48	5.80
23	24	2.039831	GGACTCCCCTATGGCCCA	60.040	66.667	0.00	0.00	0.00	5.36
24	25	2.452937	GGACTCCCCTATGGCCCAC	61.453	68.421	0.00	0.00	0.00	4.61
25	26	1.692749	GACTCCCCTATGGCCCACA	60.693	63.158	0.00	0.00	0.00	4.17
26	27	1.984288	GACTCCCCTATGGCCCACAC	61.984	65.000	0.00	0.00	0.00	3.82
27	28	1.694169	CTCCCCTATGGCCCACACT	60.694	63.158	0.00	0.00	0.00	3.55
28	29	1.692749	TCCCCTATGGCCCACACTC	60.693	63.158	0.00	0.00	0.00	3.51
29	30	2.000701	CCCCTATGGCCCACACTCA	61.001	63.158	0.00	0.00	0.00	3.41
30	31	1.224592	CCCTATGGCCCACACTCAC	59.775	63.158	0.00	0.00	0.00	3.51
31	32	1.274703	CCCTATGGCCCACACTCACT	61.275	60.000	0.00	0.00	0.00	3.41
32	33	0.620556	CCTATGGCCCACACTCACTT	59.379	55.000	0.00	0.00	0.00	3.16
33	34	1.679944	CCTATGGCCCACACTCACTTG	60.680	57.143	0.00	0.00	0.00	3.16
34	35	0.327924	TATGGCCCACACTCACTTGG	59.672	55.000	0.00	0.00	0.00	3.61
35	36	2.985847	GGCCCACACTCACTTGGC	60.986	66.667	0.00	0.00	41.42	4.52
36	37	3.357079	GCCCACACTCACTTGGCG	61.357	66.667	0.00	0.00	31.55	5.69
37	38	2.425592	CCCACACTCACTTGGCGA	59.574	61.111	0.00	0.00	0.00	5.54
38	39	1.961277	CCCACACTCACTTGGCGAC	60.961	63.158	0.00	0.00	0.00	5.19
39	40	2.310233	CCACACTCACTTGGCGACG	61.310	63.158	0.00	0.00	0.00	5.12
40	41	2.029073	ACACTCACTTGGCGACGG	59.971	61.111	0.00	0.00	0.00	4.79
41	42	2.029073	CACTCACTTGGCGACGGT	59.971	61.111	0.00	0.00	0.00	4.83
42	43	1.594293	CACTCACTTGGCGACGGTT	60.594	57.895	0.00	0.00	0.00	4.44
43	44	1.300697	ACTCACTTGGCGACGGTTC	60.301	57.895	0.00	0.00	0.00	3.62
44	45	2.027625	CTCACTTGGCGACGGTTCC	61.028	63.158	0.00	0.00	0.00	3.62
45	46	3.411351	CACTTGGCGACGGTTCCG	61.411	66.667	9.81	9.81	0.00	4.30
46	47	3.608662	ACTTGGCGACGGTTCCGA	61.609	61.111	18.28	0.00	0.00	4.55
47	48	2.356553	CTTGGCGACGGTTCCGAA	60.357	61.111	18.28	0.50	0.00	4.30
48	49	1.740296	CTTGGCGACGGTTCCGAAT	60.740	57.895	18.28	0.00	0.00	3.34
49	50	1.966493	CTTGGCGACGGTTCCGAATG	61.966	60.000	18.28	7.81	0.00	2.67
50	51	3.861263	GGCGACGGTTCCGAATGC	61.861	66.667	18.28	16.01	0.00	3.56
51	52	3.861263	GCGACGGTTCCGAATGCC	61.861	66.667	18.28	1.29	0.00	4.40
55	56	3.550992	CGGTTCCGAATGCCGTCG	61.551	66.667	5.19	0.00	40.53	5.12
56	57	3.861263	GGTTCCGAATGCCGTCGC	61.861	66.667	0.79	0.00	39.74	5.19
57	58	4.204891	GTTCCGAATGCCGTCGCG	62.205	66.667	0.00	0.00	39.74	5.87
68	69	4.874534	CGTCGCGGAAAGGAGTTA	57.125	55.556	6.13	0.00	0.00	2.24
69	70	3.111536	CGTCGCGGAAAGGAGTTAA	57.888	52.632	6.13	0.00	0.00	2.01
70	71	1.421382	CGTCGCGGAAAGGAGTTAAA	58.579	50.000	6.13	0.00	0.00	1.52
71	72	1.794116	CGTCGCGGAAAGGAGTTAAAA	59.206	47.619	6.13	0.00	0.00	1.52
72	73	2.410646	CGTCGCGGAAAGGAGTTAAAAC	60.411	50.000	6.13	0.00	0.00	2.43
73	74	2.096069	GTCGCGGAAAGGAGTTAAAACC	60.096	50.000	6.13	0.00	0.00	3.27
74	75	1.136169	CGCGGAAAGGAGTTAAAACCG	60.136	52.381	0.00	0.00	41.44	4.44
75	76	1.875514	GCGGAAAGGAGTTAAAACCGT	59.124	47.619	0.00	0.00	40.76	4.83
76	77	2.291465	GCGGAAAGGAGTTAAAACCGTT	59.709	45.455	0.00	0.00	40.76	4.44
77	78	3.243168	GCGGAAAGGAGTTAAAACCGTTT	60.243	43.478	0.00	0.00	40.76	3.60
78	79	4.024133	GCGGAAAGGAGTTAAAACCGTTTA	60.024	41.667	0.00	0.00	40.76	2.01
79	80	5.335113	GCGGAAAGGAGTTAAAACCGTTTAT	60.335	40.000	0.00	0.00	40.76	1.40
80	81	6.671190	CGGAAAGGAGTTAAAACCGTTTATT	58.329	36.000	0.00	0.00	35.21	1.40
81	82	7.140705	CGGAAAGGAGTTAAAACCGTTTATTT	58.859	34.615	0.00	0.00	35.21	1.40
82	83	8.288913	CGGAAAGGAGTTAAAACCGTTTATTTA	58.711	33.333	0.00	0.00	35.21	1.40
83	84	9.616634	GGAAAGGAGTTAAAACCGTTTATTTAG	57.383	33.333	0.00	0.00	0.00	1.85
84	85	9.616634	GAAAGGAGTTAAAACCGTTTATTTAGG	57.383	33.333	0.00	0.00	0.00	2.69
89	90	9.435688	GAGTTAAAACCGTTTATTTAGGACCTA	57.564	33.333	0.00	0.00	0.00	3.08
118	119	6.792977	GGGATATACATAATAGGTAGGCCCAT	59.207	42.308	0.00	0.00	33.22	4.00
794	903	6.611785	ACAATCATCAATGGAGGATCTGATT	58.388	36.000	0.00	0.00	43.30	2.57
1077	1193	3.923864	TCAACTGCGCCTCCGTGT	61.924	61.111	4.18	0.00	36.67	4.49
1126	1242	2.555123	GTCATGCACGACCACCAAT	58.445	52.632	0.29	0.00	0.00	3.16
1302	1424	2.840102	ATCGCTCCTTCCTCCGGG	60.840	66.667	0.00	0.00	0.00	5.73
1303	1425	3.375443	ATCGCTCCTTCCTCCGGGA	62.375	63.158	0.00	0.00	40.36	5.14
1384	1507	2.045926	GTCCTGCAACCGATGGCT	60.046	61.111	0.00	0.00	0.00	4.75
1553	1677	1.412079	AGCCATTCAAACAAGGTGCA	58.588	45.000	0.00	0.00	0.00	4.57
1677	1814	4.023450	CGGACAAGTACAAGTCTACACTCA	60.023	45.833	14.74	0.00	35.18	3.41
1754	1891	3.310501	CGTTTTCTTGGACACGTTTAGGT	59.689	43.478	0.00	0.00	0.00	3.08
1795	1937	6.721208	ACTTAATCATTCATGTGTTCCCACTT	59.279	34.615	0.00	0.00	42.34	3.16
1880	2039	2.687842	GTCCTCGATACTCGGACGT	58.312	57.895	5.16	0.00	40.88	4.34
2187	2825	3.515316	CTTCACACGGACGCCCTGT	62.515	63.158	0.00	0.00	0.00	4.00
2193	2831	4.758251	CGGACGCCCTGTGCATCA	62.758	66.667	0.00	0.00	39.19	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	1.419720	GGCCATAGGGGAGTCCTTCC	61.420	65.000	9.58	2.36	45.47	3.46
3	4	1.419720	GGGCCATAGGGGAGTCCTTC	61.420	65.000	9.58	1.94	45.47	3.46
4	5	1.386057	GGGCCATAGGGGAGTCCTT	60.386	63.158	9.58	0.30	45.47	3.36
6	7	2.039831	TGGGCCATAGGGGAGTCC	60.040	66.667	0.00	0.00	40.01	3.85
7	8	1.692749	TGTGGGCCATAGGGGAGTC	60.693	63.158	10.70	0.00	40.01	3.36
8	9	2.001269	GTGTGGGCCATAGGGGAGT	61.001	63.158	10.70	0.00	40.01	3.85
9	10	1.694169	AGTGTGGGCCATAGGGGAG	60.694	63.158	10.70	0.00	40.01	4.30
10	11	1.692749	GAGTGTGGGCCATAGGGGA	60.693	63.158	10.70	0.00	40.01	4.81
11	12	2.000701	TGAGTGTGGGCCATAGGGG	61.001	63.158	10.70	0.00	40.85	4.79
12	13	1.224592	GTGAGTGTGGGCCATAGGG	59.775	63.158	10.70	0.00	37.18	3.53
13	14	0.620556	AAGTGAGTGTGGGCCATAGG	59.379	55.000	10.70	0.00	0.00	2.57
14	15	1.679944	CCAAGTGAGTGTGGGCCATAG	60.680	57.143	10.70	0.00	0.00	2.23
15	16	0.327924	CCAAGTGAGTGTGGGCCATA	59.672	55.000	10.70	3.21	0.00	2.74
16	17	1.075482	CCAAGTGAGTGTGGGCCAT	59.925	57.895	10.70	0.00	0.00	4.40
17	18	2.515398	CCAAGTGAGTGTGGGCCA	59.485	61.111	0.00	0.00	0.00	5.36
18	19	2.985847	GCCAAGTGAGTGTGGGCC	60.986	66.667	0.00	0.00	38.70	5.80
19	20	3.357079	CGCCAAGTGAGTGTGGGC	61.357	66.667	0.00	0.00	41.20	5.36
20	21	1.961277	GTCGCCAAGTGAGTGTGGG	60.961	63.158	0.00	0.00	35.28	4.61
21	22	2.310233	CGTCGCCAAGTGAGTGTGG	61.310	63.158	0.00	0.00	38.00	4.17
22	23	2.310233	CCGTCGCCAAGTGAGTGTG	61.310	63.158	0.00	0.00	0.00	3.82
23	24	2.029073	CCGTCGCCAAGTGAGTGT	59.971	61.111	0.00	0.00	0.00	3.55
24	25	1.557443	GAACCGTCGCCAAGTGAGTG	61.557	60.000	0.00	0.00	0.00	3.51
25	26	1.300697	GAACCGTCGCCAAGTGAGT	60.301	57.895	0.00	0.00	0.00	3.41
26	27	2.027625	GGAACCGTCGCCAAGTGAG	61.028	63.158	0.00	0.00	0.00	3.51
27	28	2.029964	GGAACCGTCGCCAAGTGA	59.970	61.111	0.00	0.00	0.00	3.41
28	29	3.411351	CGGAACCGTCGCCAAGTG	61.411	66.667	4.99	0.00	34.35	3.16
29	30	2.444700	ATTCGGAACCGTCGCCAAGT	62.445	55.000	12.93	0.00	40.74	3.16
30	31	1.740296	ATTCGGAACCGTCGCCAAG	60.740	57.895	12.93	0.00	40.74	3.61
31	32	2.030401	CATTCGGAACCGTCGCCAA	61.030	57.895	12.93	0.28	40.74	4.52
32	33	2.433491	CATTCGGAACCGTCGCCA	60.433	61.111	12.93	0.00	40.74	5.69
33	34	3.861263	GCATTCGGAACCGTCGCC	61.861	66.667	12.93	0.00	40.74	5.54
34	35	3.861263	GGCATTCGGAACCGTCGC	61.861	66.667	12.93	12.82	40.74	5.19
35	36	3.550992	CGGCATTCGGAACCGTCG	61.551	66.667	12.93	6.61	42.01	5.12
39	40	3.861263	GCGACGGCATTCGGAACC	61.861	66.667	8.14	0.00	44.45	3.62
40	41	4.204891	CGCGACGGCATTCGGAAC	62.205	66.667	0.00	0.00	44.45	3.62
51	52	1.421382	TTTAACTCCTTTCCGCGACG	58.579	50.000	8.23	0.00	0.00	5.12
52	53	2.096069	GGTTTTAACTCCTTTCCGCGAC	60.096	50.000	8.23	0.00	0.00	5.19
53	54	2.145536	GGTTTTAACTCCTTTCCGCGA	58.854	47.619	8.23	0.00	0.00	5.87
54	55	1.136169	CGGTTTTAACTCCTTTCCGCG	60.136	52.381	0.00	0.00	0.00	6.46
55	56	1.875514	ACGGTTTTAACTCCTTTCCGC	59.124	47.619	0.00	0.00	40.05	5.54
56	57	4.556942	AAACGGTTTTAACTCCTTTCCG	57.443	40.909	0.00	0.00	41.77	4.30
57	58	9.616634	CTAAATAAACGGTTTTAACTCCTTTCC	57.383	33.333	11.87	0.00	30.86	3.13
58	59	9.616634	CCTAAATAAACGGTTTTAACTCCTTTC	57.383	33.333	11.87	0.00	30.86	2.62
59	60	9.353431	TCCTAAATAAACGGTTTTAACTCCTTT	57.647	29.630	11.87	4.17	30.86	3.11
60	61	8.786898	GTCCTAAATAAACGGTTTTAACTCCTT	58.213	33.333	11.87	0.00	30.86	3.36
61	62	7.391554	GGTCCTAAATAAACGGTTTTAACTCCT	59.608	37.037	11.87	0.00	30.86	3.69
62	63	7.391554	AGGTCCTAAATAAACGGTTTTAACTCC	59.608	37.037	11.87	5.34	30.86	3.85
63	64	8.327941	AGGTCCTAAATAAACGGTTTTAACTC	57.672	34.615	11.87	0.00	30.86	3.01
64	65	9.964354	ATAGGTCCTAAATAAACGGTTTTAACT	57.036	29.630	11.87	0.80	30.86	2.24
67	68	9.176460	CCAATAGGTCCTAAATAAACGGTTTTA	57.824	33.333	11.87	0.00	0.00	1.52
68	69	7.123098	CCCAATAGGTCCTAAATAAACGGTTTT	59.877	37.037	11.87	0.00	0.00	2.43
69	70	6.604396	CCCAATAGGTCCTAAATAAACGGTTT	59.396	38.462	11.33	11.33	0.00	3.27
70	71	6.124340	CCCAATAGGTCCTAAATAAACGGTT	58.876	40.000	1.78	0.00	0.00	4.44
71	72	5.398239	CCCCAATAGGTCCTAAATAAACGGT	60.398	44.000	1.78	0.00	0.00	4.83
72	73	5.067954	CCCCAATAGGTCCTAAATAAACGG	58.932	45.833	1.78	0.00	0.00	4.44
73	74	5.932455	TCCCCAATAGGTCCTAAATAAACG	58.068	41.667	1.78	0.00	0.00	3.60
76	77	9.861919	TGTATATCCCCAATAGGTCCTAAATAA	57.138	33.333	1.78	0.00	0.00	1.40
78	79	8.949798	ATGTATATCCCCAATAGGTCCTAAAT	57.050	34.615	1.78	0.00	0.00	1.40
79	80	9.861919	TTATGTATATCCCCAATAGGTCCTAAA	57.138	33.333	1.78	0.00	0.00	1.85
82	83	9.676129	CTATTATGTATATCCCCAATAGGTCCT	57.324	37.037	0.00	0.00	0.00	3.85
83	84	8.881262	CCTATTATGTATATCCCCAATAGGTCC	58.119	40.741	13.21	0.00	39.59	4.46
89	90	7.294958	GGCCTACCTATTATGTATATCCCCAAT	59.705	40.741	0.00	0.00	0.00	3.16
118	119	7.800155	TGCTTTATGATATTTCGACCATTCA	57.200	32.000	0.00	0.00	0.00	2.57
296	374	4.879197	TCACTATGAGAATGATGCCGAT	57.121	40.909	0.00	0.00	0.00	4.18
758	867	2.146342	GATGATTGTTGATCGGCGGAT	58.854	47.619	7.21	6.45	37.60	4.18
961	1077	0.820074	TGGCGTTTGTCCGAATGGTT	60.820	50.000	0.00	0.00	36.30	3.67
995	1111	4.451150	GCGGACTGGCCATGTCGA	62.451	66.667	21.52	0.00	35.45	4.20
1077	1193	0.974010	GGACATCACCGGTGGTCCTA	60.974	60.000	36.61	21.52	44.99	2.94
1126	1242	0.459489	TGATGATGATGCGGACGACA	59.541	50.000	0.00	0.00	0.00	4.35
1280	1402	1.153549	GAGGAAGGAGCGATGCGTT	60.154	57.895	0.00	0.00	0.00	4.84
1409	1532	3.633525	CAGGTTATGCATGCACTTACCAT	59.366	43.478	32.41	21.59	30.91	3.55
1507	1631	0.312102	GAGGCAGCCAATTAATCCGC	59.688	55.000	15.80	0.00	0.00	5.54
1553	1677	3.256631	GGCTGCGGAAAATATGGATCAAT	59.743	43.478	0.00	0.00	0.00	2.57
1651	1788	4.023365	GTGTAGACTTGTACTTGTCCGAGT	60.023	45.833	12.78	0.00	34.02	4.18
1677	1814	3.552684	GCTGGTTGTGTGTTGCATATGTT	60.553	43.478	4.29	0.00	0.00	2.71
1754	1891	4.354155	GTGCCTGCACGTTAGTCA	57.646	55.556	6.50	0.00	37.19	3.41
1870	2029	3.807538	GCGCAGGACGTCCGAGTA	61.808	66.667	28.26	0.00	46.11	2.59
1880	2039	3.749064	GAGTGACGAGGCGCAGGA	61.749	66.667	10.83	0.00	0.00	3.86
2029	2530	2.802792	CGAAGCGTCCGGGTGATA	59.197	61.111	0.00	0.00	0.00	2.15
2050	2551	2.478890	CGTCCCGTAGAGTGGCGAT	61.479	63.158	0.00	0.00	0.00	4.58
2062	2563	1.585521	GTGATGTAGACGCGTCCCG	60.586	63.158	34.08	0.00	44.21	5.14
2096	2597	4.736896	GTCCCGTGGAGTGGCGAC	62.737	72.222	0.00	0.00	29.39	5.19
2107	2608	2.042259	TGATGTAGTCGCGTCCCGT	61.042	57.895	5.77	0.00	38.35	5.28
2187	2825	0.612744	TCCAACGGAGTGATGATGCA	59.387	50.000	0.00	0.00	45.00	3.96
2193	2831	0.460284	GACGCATCCAACGGAGTGAT	60.460	55.000	0.00	0.00	45.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.