AutoCloner

Multiple sequence alignment - TraesCS3B01G599900

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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	TraesCS3B01G599900	chr3B	100.000	3317	0	0	1	3317	820763829	820760513	0.000000e+00	6126.0
1	TraesCS3B01G599900	chr3B	90.205	3369	220	42	1	3317	820798089	820794779	0.000000e+00	4292.0
2	TraesCS3B01G599900	chr3B	90.509	1612	108	22	1741	3317	820599643	820598042	0.000000e+00	2087.0
3	TraesCS3B01G599900	chr3B	91.232	1437	94	15	1757	3174	820677010	820675587	0.000000e+00	1927.0
4	TraesCS3B01G599900	chr3B	87.280	1250	132	19	981	2209	820775270	820774027	0.000000e+00	1402.0
5	TraesCS3B01G599900	chr3B	85.872	1359	130	27	641	1975	820719921	820718601	0.000000e+00	1389.0
6	TraesCS3B01G599900	chr3B	92.422	739	50	4	1741	2474	820506721	820505984	0.000000e+00	1050.0
7	TraesCS3B01G599900	chr3B	94.640	653	29	1	1	653	820720755	820720109	0.000000e+00	1007.0
8	TraesCS3B01G599900	chr3B	85.035	989	124	18	1003	1978	820507527	820506550	0.000000e+00	985.0
9	TraesCS3B01G599900	chr3B	84.350	1016	133	14	981	1978	820677862	820676855	0.000000e+00	972.0
10	TraesCS3B01G599900	chr3B	87.128	839	87	12	1741	2570	820718703	820717877	0.000000e+00	931.0
11	TraesCS3B01G599900	chr3B	92.691	643	39	7	2680	3317	820505847	820505208	0.000000e+00	920.0
12	TraesCS3B01G599900	chr3B	91.020	657	47	6	1741	2388	820772694	820772041	0.000000e+00	876.0
13	TraesCS3B01G599900	chr3B	88.814	590	37	13	2680	3265	820717851	820717287	0.000000e+00	697.0
14	TraesCS3B01G599900	chr3B	91.124	507	37	4	1720	2219	820555028	820554523	0.000000e+00	680.0
15	TraesCS3B01G599900	chr3B	88.501	487	51	3	1003	1489	820561010	820560529	4.770000e-163	584.0
16	TraesCS3B01G599900	chr3B	84.069	521	57	14	246	757	820514475	820513972	2.310000e-131	479.0
17	TraesCS3B01G599900	chr3B	78.756	579	94	15	1439	1995	820599990	820599419	8.750000e-96	361.0
18	TraesCS3B01G599900	chr3B	86.916	214	18	5	2333	2544	820554394	820554189	7.160000e-57	231.0
19	TraesCS3B01G599900	chr3B	91.453	117	6	2	3204	3317	820675592	820675477	1.230000e-34	158.0
20	TraesCS3B01G599900	chr3B	85.517	145	18	3	2680	2824	820554100	820553959	7.410000e-32	148.0
21	TraesCS3B01G599900	chr3B	92.308	104	5	1	2422	2522	820772044	820771941	9.590000e-31	145.0
22	TraesCS3B01G599900	chr3B	100.000	42	0	0	2293	2334	820554512	820554471	9.870000e-11	78.7
23	TraesCS3B01G599900	chr3B	87.234	47	6	0	1010	1056	820571769	820571723	2.000000e-03	54.7
24	TraesCS3B01G599900	chr3D	91.869	1562	85	14	1757	3286	609627787	609626236	0.000000e+00	2143.0
25	TraesCS3B01G599900	chr3D	86.050	1190	123	22	815	1978	609628801	609627629	0.000000e+00	1238.0
26	TraesCS3B01G599900	chr3D	84.449	463	47	13	230	673	609630327	609629871	1.830000e-117	433.0
27	TraesCS3B01G599900	chr3D	78.344	157	28	5	236	389	572571875	572571722	2.720000e-16	97.1
28	TraesCS3B01G599900	chr3D	85.333	75	5	5	2509	2581	474436169	474436099	4.590000e-09	73.1
29	TraesCS3B01G599900	chr3A	84.464	1622	172	29	1629	3212	743193926	743192347	0.000000e+00	1526.0
30	TraesCS3B01G599900	chr3A	84.447	1048	133	19	975	2001	743194622	743193584	0.000000e+00	1005.0
31	TraesCS3B01G599900	chr3A	82.883	555	67	15	230	767	743230007	743229464	1.080000e-129	473.0
32	TraesCS3B01G599900	chr3A	90.551	127	9	3	815	939	743194751	743194626	7.360000e-37	165.0
33	TraesCS3B01G599900	chr3A	88.000	75	3	5	2509	2581	616715156	616715086	2.120000e-12	84.2
34	TraesCS3B01G599900	chr5A	82.394	426	69	4	2767	3190	626249983	626250404	1.880000e-97	366.0
35	TraesCS3B01G599900	chr7A	91.189	227	20	0	1	227	6799267	6799041	3.210000e-80	309.0
36	TraesCS3B01G599900	chr2D	91.228	228	18	2	1	227	596575832	596575606	3.210000e-80	309.0
37	TraesCS3B01G599900	chr2D	87.500	64	8	0	364	427	10324793	10324730	1.280000e-09	75.0
38	TraesCS3B01G599900	chr1D	90.749	227	21	0	1	227	375353133	375353359	1.500000e-78	303.0
39	TraesCS3B01G599900	chr2A	89.427	227	24	0	1	227	105681532	105681306	1.510000e-73	287.0
40	TraesCS3B01G599900	chr2A	89.091	55	6	0	364	418	10588377	10588323	5.940000e-08	69.4
41	TraesCS3B01G599900	chr2A	89.091	55	6	0	364	418	10589240	10589186	5.940000e-08	69.4
42	TraesCS3B01G599900	chr1A	89.427	227	24	0	1	227	584525819	584525593	1.510000e-73	287.0
43	TraesCS3B01G599900	chr7D	89.035	228	25	0	1	228	610839482	610839255	1.950000e-72	283.0
44	TraesCS3B01G599900	chr7D	79.787	188	26	7	235	419	2220498	2220676	3.470000e-25	126.0
45	TraesCS3B01G599900	chr1B	89.035	228	23	2	1	227	678205178	678204952	7.010000e-72	281.0
46	TraesCS3B01G599900	chr7B	82.353	136	18	5	242	373	726135384	726135517	2.700000e-21	113.0
47	TraesCS3B01G599900	chr2B	83.333	120	16	4	271	388	422965757	422965640	1.260000e-19	108.0

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	TraesCS3B01G599900	chr3B	820760513	820763829	3316	True	6126.000000	6126	100.000000	1	3317	1	chr3B.!!$R4	3316
1	TraesCS3B01G599900	chr3B	820794779	820798089	3310	True	4292.000000	4292	90.205000	1	3317	1	chr3B.!!$R5	3316
2	TraesCS3B01G599900	chr3B	820598042	820599990	1948	True	1224.000000	2087	84.632500	1439	3317	2	chr3B.!!$R8	1878
3	TraesCS3B01G599900	chr3B	820675477	820677862	2385	True	1019.000000	1927	89.011667	981	3317	3	chr3B.!!$R9	2336
4	TraesCS3B01G599900	chr3B	820717287	820720755	3468	True	1006.000000	1389	89.113500	1	3265	4	chr3B.!!$R10	3264
5	TraesCS3B01G599900	chr3B	820505208	820507527	2319	True	985.000000	1050	90.049333	1003	3317	3	chr3B.!!$R6	2314
6	TraesCS3B01G599900	chr3B	820771941	820775270	3329	True	807.666667	1402	90.202667	981	2522	3	chr3B.!!$R11	1541
7	TraesCS3B01G599900	chr3B	820513972	820514475	503	True	479.000000	479	84.069000	246	757	1	chr3B.!!$R1	511
8	TraesCS3B01G599900	chr3B	820553959	820555028	1069	True	284.425000	680	90.889250	1720	2824	4	chr3B.!!$R7	1104
9	TraesCS3B01G599900	chr3D	609626236	609630327	4091	True	1271.333333	2143	87.456000	230	3286	3	chr3D.!!$R3	3056
10	TraesCS3B01G599900	chr3A	743192347	743194751	2404	True	898.666667	1526	86.487333	815	3212	3	chr3A.!!$R3	2397
11	TraesCS3B01G599900	chr3A	743229464	743230007	543	True	473.000000	473	82.883000	230	767	1	chr3A.!!$R2	537

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
160	164	0.039764	ACAGGAGACGTGGGAGATCA	59.960	55.0	0.00	0.0	0.0	2.92	F
1827	4847	0.395311	CATGGCCACTGGAGATGCTT	60.395	55.0	8.16	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1829	4849	0.823356	TGGCAGTGGGAAGTTCTTGC	60.823	55.0	2.25	7.98	0.0	4.01	R
3085	6418	0.031043	TACAGACCACAACACCGACG	59.969	55.0	0.00	0.00	0.0	5.12	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
24	25	1.446907	CATCTTCAAGAAGCTGCCGT	58.553	50.000	4.95	0.00	38.28	5.68
36	37	1.081376	CTGCCGTCGTCTCGTCTTT	60.081	57.895	0.00	0.00	0.00	2.52
53	54	4.498009	CGTCTTTTTGAGCAGGACACAAAT	60.498	41.667	0.00	0.00	38.41	2.32
68	72	6.569780	GGACACAAATCCTAACAAAACTTGT	58.430	36.000	0.00	0.00	39.69	3.16
79	83	6.708949	CCTAACAAAACTTGTAGAAGCACCTA	59.291	38.462	0.00	0.00	44.59	3.08
84	88	8.474831	ACAAAACTTGTAGAAGCACCTAAAAAT	58.525	29.630	0.00	0.00	43.27	1.82
86	90	7.817418	AACTTGTAGAAGCACCTAAAAATGA	57.183	32.000	0.00	0.00	31.68	2.57
160	164	0.039764	ACAGGAGACGTGGGAGATCA	59.960	55.000	0.00	0.00	0.00	2.92
189	193	2.747686	GACGGGAGGCAGAAACCA	59.252	61.111	0.00	0.00	38.26	3.67
244	248	5.451520	GGAGGAGCCATGATTTTTCATTCTG	60.452	44.000	0.00	0.00	36.34	3.02
399	413	9.590451	AAGATATATTGCAACCAATTTTCACAG	57.410	29.630	0.00	0.00	41.68	3.66
523	539	2.232298	GAGCCAGTCGGTCTGAAGGG	62.232	65.000	3.76	0.62	46.27	3.95
796	1930	3.129287	AGGTCGGTTGCAATTGATCAATC	59.871	43.478	20.95	10.40	0.00	2.67
854	2008	1.299165	CGTCCTCCTCCAATACGCG	60.299	63.158	3.53	3.53	0.00	6.01
883	2037	2.046217	GCCGGTCTCCAAACCCTC	60.046	66.667	1.90	0.00	35.79	4.30
890	2048	1.145119	GTCTCCAAACCCTCAAACCCT	59.855	52.381	0.00	0.00	0.00	4.34
891	2049	1.144913	TCTCCAAACCCTCAAACCCTG	59.855	52.381	0.00	0.00	0.00	4.45
900	2059	2.283173	CAAACCCTGCCACCTCCC	60.283	66.667	0.00	0.00	0.00	4.30
901	2060	2.452491	AAACCCTGCCACCTCCCT	60.452	61.111	0.00	0.00	0.00	4.20
902	2061	2.539081	AAACCCTGCCACCTCCCTC	61.539	63.158	0.00	0.00	0.00	4.30
971	2130	2.158295	GCCTCCCTACTCCTGAATCCTA	60.158	54.545	0.00	0.00	0.00	2.94
977	2136	4.530161	CCCTACTCCTGAATCCTAATCCTG	59.470	50.000	0.00	0.00	0.00	3.86
1080	2240	1.890552	TCCTCTACTACCTCGACCCT	58.109	55.000	0.00	0.00	0.00	4.34
1089	2249	3.322466	CTCGACCCTTGGGTGGCT	61.322	66.667	17.10	0.00	0.00	4.75
1485	2645	2.363795	AGGACGGCGGAGGATGAA	60.364	61.111	13.24	0.00	0.00	2.57
1527	2696	1.035932	CCGCCCGGTCTTCTAAGAGA	61.036	60.000	0.00	0.00	35.32	3.10
1530	2699	1.747709	CCCGGTCTTCTAAGAGACGA	58.252	55.000	14.71	0.00	45.53	4.20
1555	2724	2.190313	GGGAGCATGACATCGCCA	59.810	61.111	0.00	0.00	0.00	5.69
1558	2727	1.709147	GGAGCATGACATCGCCACAC	61.709	60.000	0.00	0.00	0.00	3.82
1559	2728	2.028766	GAGCATGACATCGCCACACG	62.029	60.000	0.00	0.00	45.62	4.49
1565	2734	1.911293	GACATCGCCACACGTGCAAT	61.911	55.000	17.22	0.00	44.19	3.56
1566	2735	0.672091	ACATCGCCACACGTGCAATA	60.672	50.000	17.22	0.00	44.19	1.90
1696	4614	2.641815	GAGCCATGGGAGATGATAACCT	59.358	50.000	15.13	0.00	0.00	3.50
1752	4673	1.067295	TGGACAAGCCATCTCCACTT	58.933	50.000	0.00	0.00	43.33	3.16
1761	4682	3.054139	AGCCATCTCCACTTCAAATGCTA	60.054	43.478	0.00	0.00	0.00	3.49
1771	4692	5.347342	CACTTCAAATGCTAACCAACAACA	58.653	37.500	0.00	0.00	0.00	3.33
1784	4804	2.622470	CCAACAACATGACATGTCCACA	59.378	45.455	22.85	5.75	44.07	4.17
1794	4814	1.950828	CATGTCCACAGGAGATGCTC	58.049	55.000	9.82	0.00	44.41	4.26
1827	4847	0.395311	CATGGCCACTGGAGATGCTT	60.395	55.000	8.16	0.00	0.00	3.91
1829	4849	0.543277	TGGCCACTGGAGATGCTTAG	59.457	55.000	0.00	0.00	0.00	2.18
1833	4853	2.286872	CCACTGGAGATGCTTAGCAAG	58.713	52.381	12.08	6.13	43.62	4.01
1839	4892	4.256920	TGGAGATGCTTAGCAAGAACTTC	58.743	43.478	12.08	2.78	43.62	3.01
1963	5091	1.297968	TCCATTGGAGATCCTTGGCA	58.702	50.000	0.00	0.00	38.82	4.92
1964	5092	1.640149	TCCATTGGAGATCCTTGGCAA	59.360	47.619	0.00	0.00	38.82	4.52
1965	5093	2.029623	CCATTGGAGATCCTTGGCAAG	58.970	52.381	20.31	20.31	34.74	4.01
1966	5094	2.357465	CCATTGGAGATCCTTGGCAAGA	60.357	50.000	28.18	14.44	34.74	3.02
1967	5095	3.359033	CATTGGAGATCCTTGGCAAGAA	58.641	45.455	28.18	9.18	36.82	2.52
1968	5096	2.496899	TGGAGATCCTTGGCAAGAAC	57.503	50.000	28.18	17.19	36.82	3.01
1969	5097	1.988107	TGGAGATCCTTGGCAAGAACT	59.012	47.619	28.18	21.12	36.82	3.01
1970	5098	2.376518	TGGAGATCCTTGGCAAGAACTT	59.623	45.455	28.18	10.96	36.82	2.66
1971	5099	2.751806	GGAGATCCTTGGCAAGAACTTG	59.248	50.000	28.18	11.21	43.14	3.16
2115	5306	1.228124	GTGGCACTTGCACTACCCA	60.228	57.895	11.13	0.00	44.36	4.51
2234	5431	3.119096	GGTCCAAGAACTCGGCGC	61.119	66.667	0.00	0.00	0.00	6.53
2525	5835	4.289245	CCTGGAATTTATTGGTCCCACAT	58.711	43.478	0.00	0.00	0.00	3.21
2608	5919	1.856012	GTGCTATCGCGGATTCTGC	59.144	57.895	6.13	7.45	39.65	4.26
2633	5944	3.923461	TGCACTTTGTAACAACAGCAAAC	59.077	39.130	0.00	0.00	0.00	2.93
2815	6148	1.834263	AGTGCCCCTTCACTCTATGAC	59.166	52.381	0.00	0.00	43.28	3.06
2816	6149	0.824109	TGCCCCTTCACTCTATGACG	59.176	55.000	0.00	0.00	36.92	4.35
2936	6269	1.668826	TAGTGATCAGGCAGGGGTTT	58.331	50.000	0.00	0.00	0.00	3.27
3047	6380	1.546923	TGAACATTGGCATTGCTGAGG	59.453	47.619	8.82	2.03	0.00	3.86
3085	6418	4.223255	AGTTTGGGCTACTAGAAGGTTCTC	59.777	45.833	0.00	0.00	38.70	2.87
3086	6446	2.376109	TGGGCTACTAGAAGGTTCTCG	58.624	52.381	0.00	0.00	38.70	4.04
3092	6452	1.811359	ACTAGAAGGTTCTCGTCGGTG	59.189	52.381	0.00	0.00	38.70	4.94
3093	6453	1.811359	CTAGAAGGTTCTCGTCGGTGT	59.189	52.381	0.00	0.00	38.70	4.16
3094	6454	1.038280	AGAAGGTTCTCGTCGGTGTT	58.962	50.000	0.00	0.00	29.94	3.32
3095	6455	1.137513	GAAGGTTCTCGTCGGTGTTG	58.862	55.000	0.00	0.00	0.00	3.33
3096	6456	0.462789	AAGGTTCTCGTCGGTGTTGT	59.537	50.000	0.00	0.00	0.00	3.32
3097	6457	0.249322	AGGTTCTCGTCGGTGTTGTG	60.249	55.000	0.00	0.00	0.00	3.33
3098	6458	1.219522	GGTTCTCGTCGGTGTTGTGG	61.220	60.000	0.00	0.00	0.00	4.17
3099	6459	0.529119	GTTCTCGTCGGTGTTGTGGT	60.529	55.000	0.00	0.00	0.00	4.16
3100	6460	0.249155	TTCTCGTCGGTGTTGTGGTC	60.249	55.000	0.00	0.00	0.00	4.02
3101	6461	1.105167	TCTCGTCGGTGTTGTGGTCT	61.105	55.000	0.00	0.00	0.00	3.85
3102	6462	0.939577	CTCGTCGGTGTTGTGGTCTG	60.940	60.000	0.00	0.00	0.00	3.51
3103	6463	1.227147	CGTCGGTGTTGTGGTCTGT	60.227	57.895	0.00	0.00	0.00	3.41
3104	6464	0.031043	CGTCGGTGTTGTGGTCTGTA	59.969	55.000	0.00	0.00	0.00	2.74
3105	6465	1.494824	GTCGGTGTTGTGGTCTGTAC	58.505	55.000	0.00	0.00	0.00	2.90
3106	6466	1.068127	GTCGGTGTTGTGGTCTGTACT	59.932	52.381	0.00	0.00	0.00	2.73
3107	6467	1.338973	TCGGTGTTGTGGTCTGTACTC	59.661	52.381	0.00	0.00	0.00	2.59
3108	6468	1.340248	CGGTGTTGTGGTCTGTACTCT	59.660	52.381	0.00	0.00	0.00	3.24
3109	6469	2.607282	CGGTGTTGTGGTCTGTACTCTC	60.607	54.545	0.00	0.00	0.00	3.20
3110	6470	2.628657	GGTGTTGTGGTCTGTACTCTCT	59.371	50.000	0.00	0.00	0.00	3.10
3111	6471	3.069729	GGTGTTGTGGTCTGTACTCTCTT	59.930	47.826	0.00	0.00	0.00	2.85
3112	6472	4.051922	GTGTTGTGGTCTGTACTCTCTTG	58.948	47.826	0.00	0.00	0.00	3.02
3113	6473	3.069586	TGTTGTGGTCTGTACTCTCTTGG	59.930	47.826	0.00	0.00	0.00	3.61
3114	6474	2.958818	TGTGGTCTGTACTCTCTTGGT	58.041	47.619	0.00	0.00	0.00	3.67
3115	6475	3.305720	TGTGGTCTGTACTCTCTTGGTT	58.694	45.455	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	2.394708	CTGCTCAAAAAGACGAGACGA	58.605	47.619	0.00	0.00	0.00	4.20
36	37	3.228188	AGGATTTGTGTCCTGCTCAAA	57.772	42.857	0.00	0.00	46.76	2.69
53	54	5.529800	GGTGCTTCTACAAGTTTTGTTAGGA	59.470	40.000	0.00	0.00	42.22	2.94
59	63	8.755018	CATTTTTAGGTGCTTCTACAAGTTTTG	58.245	33.333	0.00	0.00	31.45	2.44
60	64	8.691797	TCATTTTTAGGTGCTTCTACAAGTTTT	58.308	29.630	0.00	0.00	31.45	2.43
61	65	8.232913	TCATTTTTAGGTGCTTCTACAAGTTT	57.767	30.769	0.00	0.00	31.45	2.66
68	72	4.705023	GGGCTTCATTTTTAGGTGCTTCTA	59.295	41.667	0.00	0.00	0.00	2.10
79	83	1.257750	GGCGGGAGGGCTTCATTTTT	61.258	55.000	0.00	0.00	38.40	1.94
394	408	0.320050	TATCCTGTGCGTTGCTGTGA	59.680	50.000	0.00	0.00	0.00	3.58
399	413	2.212652	TGATGATATCCTGTGCGTTGC	58.787	47.619	0.00	0.00	0.00	4.17
523	539	1.131218	GCCGGCTCGTTTACGTTTC	59.869	57.895	22.15	0.00	40.80	2.78
655	881	5.284079	GTCAACATTTTCTCACATTGCAGT	58.716	37.500	0.00	0.00	0.00	4.40
796	1930	1.018148	AGATGCTGAGTCGGTCTACG	58.982	55.000	0.00	0.00	46.11	3.51
883	2037	2.283173	GGGAGGTGGCAGGGTTTG	60.283	66.667	0.00	0.00	0.00	2.93
953	2112	4.423960	AGGATTAGGATTCAGGAGTAGGGA	59.576	45.833	0.00	0.00	0.00	4.20
971	2130	7.086685	TGAGGGTACTTCTTTTTACAGGATT	57.913	36.000	0.00	0.00	0.00	3.01
977	2136	5.067954	TGGCTTGAGGGTACTTCTTTTTAC	58.932	41.667	0.00	0.00	0.00	2.01
1089	2249	4.011517	GGCGTCTTTCCCGGGTCA	62.012	66.667	22.86	5.57	0.00	4.02
1233	2393	2.124860	GCGCGGTTACCCTTCCAT	60.125	61.111	8.83	0.00	0.00	3.41
1387	2547	2.979649	GGTCCCGAACTCCTCCAC	59.020	66.667	0.00	0.00	0.00	4.02
1431	2591	2.125106	CAGAGCACCCTAACGCCC	60.125	66.667	0.00	0.00	0.00	6.13
1437	2597	2.122729	ACCCTGCAGAGCACCCTA	59.877	61.111	17.39	0.00	33.79	3.53
1478	2638	1.306141	TCCCCACGCTCTTCATCCT	60.306	57.895	0.00	0.00	0.00	3.24
1485	2645	2.681778	CTGGACTCCCCACGCTCT	60.682	66.667	0.00	0.00	40.82	4.09
1545	2714	3.041351	GCACGTGTGGCGATGTCA	61.041	61.111	18.38	0.00	44.77	3.58
1555	2724	2.352617	CCAATGGCTTTATTGCACGTGT	60.353	45.455	18.38	0.00	36.86	4.49
1558	2727	2.423185	TCTCCAATGGCTTTATTGCACG	59.577	45.455	0.00	0.00	36.86	5.34
1559	2728	4.142093	ACATCTCCAATGGCTTTATTGCAC	60.142	41.667	0.00	0.00	36.86	4.57
1565	2734	3.195396	GGCAAACATCTCCAATGGCTTTA	59.805	43.478	0.00	0.00	34.14	1.85
1566	2735	2.027837	GGCAAACATCTCCAATGGCTTT	60.028	45.455	0.00	0.00	34.14	3.51
1606	2790	1.905922	GCGAAGACTTGCTCCAGTGC	61.906	60.000	0.00	0.00	0.00	4.40
1617	2801	2.046938	TTCGTCCTTGGCGAAGACT	58.953	52.632	10.40	0.00	44.69	3.24
1696	4614	1.183549	GGCTCTAGTTCGTCCTCCAA	58.816	55.000	0.00	0.00	0.00	3.53
1752	4673	5.068329	TGTCATGTTGTTGGTTAGCATTTGA	59.932	36.000	0.00	0.00	0.00	2.69
1761	4682	3.068024	GTGGACATGTCATGTTGTTGGTT	59.932	43.478	26.47	0.00	45.03	3.67
1771	4692	2.421107	GCATCTCCTGTGGACATGTCAT	60.421	50.000	26.47	6.70	32.02	3.06
1794	4814	1.667151	CCATGGCAGGTTGTTGGTG	59.333	57.895	0.00	0.00	0.00	4.17
1827	4847	1.271379	GGCAGTGGGAAGTTCTTGCTA	60.271	52.381	16.04	0.00	0.00	3.49
1829	4849	0.823356	TGGCAGTGGGAAGTTCTTGC	60.823	55.000	2.25	7.98	0.00	4.01
1833	4853	0.890996	CCAGTGGCAGTGGGAAGTTC	60.891	60.000	30.04	0.00	35.02	3.01
1839	4892	1.077930	CATCTCCAGTGGCAGTGGG	60.078	63.158	34.80	26.05	39.21	4.61
1972	5100	7.418760	TCTTTGGTAAGGATGTCCAACTTTGG	61.419	42.308	1.13	1.13	40.32	3.28
1973	5101	5.534654	TCTTTGGTAAGGATGTCCAACTTTG	59.465	40.000	1.30	0.00	40.32	2.77
1974	5102	5.701224	TCTTTGGTAAGGATGTCCAACTTT	58.299	37.500	1.30	0.00	40.32	2.66
1975	5103	5.316987	CTCTTTGGTAAGGATGTCCAACTT	58.683	41.667	1.30	0.00	40.32	2.66
1976	5104	4.263506	CCTCTTTGGTAAGGATGTCCAACT	60.264	45.833	1.30	0.00	40.32	3.16
1977	5105	4.010349	CCTCTTTGGTAAGGATGTCCAAC	58.990	47.826	1.30	0.00	40.32	3.77
1978	5106	3.913799	TCCTCTTTGGTAAGGATGTCCAA	59.086	43.478	1.30	0.00	36.75	3.53
1979	5107	3.526899	TCCTCTTTGGTAAGGATGTCCA	58.473	45.455	1.30	0.00	36.75	4.02
1980	5108	4.262617	GTTCCTCTTTGGTAAGGATGTCC	58.737	47.826	0.00	0.00	41.26	4.02
1981	5109	4.262617	GGTTCCTCTTTGGTAAGGATGTC	58.737	47.826	0.00	0.00	41.26	3.06
1982	5110	3.010250	GGGTTCCTCTTTGGTAAGGATGT	59.990	47.826	0.00	0.00	41.26	3.06
1983	5111	3.010138	TGGGTTCCTCTTTGGTAAGGATG	59.990	47.826	0.00	0.00	41.26	3.51
1984	5112	3.010250	GTGGGTTCCTCTTTGGTAAGGAT	59.990	47.826	0.00	0.00	41.26	3.24
1985	5113	2.374170	GTGGGTTCCTCTTTGGTAAGGA	59.626	50.000	0.00	0.00	39.94	3.36
1986	5114	2.791655	GTGGGTTCCTCTTTGGTAAGG	58.208	52.381	0.00	0.00	37.07	2.69
1987	5115	2.038033	TCGTGGGTTCCTCTTTGGTAAG	59.962	50.000	0.00	0.00	37.07	2.34
1988	5116	2.048601	TCGTGGGTTCCTCTTTGGTAA	58.951	47.619	0.00	0.00	37.07	2.85
2094	5285	1.291877	GGTAGTGCAAGTGCCACTCG	61.292	60.000	0.00	0.00	42.25	4.18
2105	5296	1.270094	CGAACAGTTCTGGGTAGTGCA	60.270	52.381	11.60	0.00	0.00	4.57
2115	5306	1.069204	TCTTGCTGCTCGAACAGTTCT	59.931	47.619	16.69	0.00	39.96	3.01
2215	5409	2.342648	GCCGAGTTCTTGGACCGT	59.657	61.111	10.05	0.00	0.00	4.83
2363	5648	4.240096	GCACACAATGATTTTCCTTCCAG	58.760	43.478	0.00	0.00	0.00	3.86
2491	5801	7.971722	CCAATAAATTCCAGGGTTTTAACTACG	59.028	37.037	0.00	0.00	0.00	3.51
2503	5813	3.707316	TGTGGGACCAATAAATTCCAGG	58.293	45.455	0.00	0.00	0.00	4.45
2608	5919	2.715268	CTGTTGTTACAAAGTGCACGG	58.285	47.619	12.01	7.93	32.92	4.94
2633	5944	0.178975	TGGGTAAACTGGTGGCAAGG	60.179	55.000	0.00	0.00	0.00	3.61
2693	6025	4.568760	GCTTAGAGTAACCTGACAGATTGC	59.431	45.833	3.32	0.00	0.00	3.56
2815	6148	1.284982	CCTGAACAGAGTCGTTGCCG	61.285	60.000	3.19	0.00	0.00	5.69
2816	6149	0.033504	TCCTGAACAGAGTCGTTGCC	59.966	55.000	3.19	0.00	0.00	4.52
2892	6225	3.152400	GGACGGGCATACCTCGGT	61.152	66.667	0.00	0.00	36.97	4.69
2936	6269	0.174389	GCGAGATCCTGAGCACTTCA	59.826	55.000	0.00	0.00	0.00	3.02
3047	6380	2.092838	CCAAACTCTCGCATCGAAAGTC	59.907	50.000	0.00	0.00	36.08	3.01
3085	6418	0.031043	TACAGACCACAACACCGACG	59.969	55.000	0.00	0.00	0.00	5.12
3086	6446	1.068127	AGTACAGACCACAACACCGAC	59.932	52.381	0.00	0.00	0.00	4.79
3092	6452	3.069729	ACCAAGAGAGTACAGACCACAAC	59.930	47.826	0.00	0.00	0.00	3.32
3093	6453	3.305720	ACCAAGAGAGTACAGACCACAA	58.694	45.455	0.00	0.00	0.00	3.33
3094	6454	2.958818	ACCAAGAGAGTACAGACCACA	58.041	47.619	0.00	0.00	0.00	4.17
3095	6455	3.574826	AGAACCAAGAGAGTACAGACCAC	59.425	47.826	0.00	0.00	0.00	4.16
3096	6456	3.574396	CAGAACCAAGAGAGTACAGACCA	59.426	47.826	0.00	0.00	0.00	4.02
3097	6457	3.615351	GCAGAACCAAGAGAGTACAGACC	60.615	52.174	0.00	0.00	0.00	3.85
3098	6458	3.257127	AGCAGAACCAAGAGAGTACAGAC	59.743	47.826	0.00	0.00	0.00	3.51
3099	6459	3.501349	AGCAGAACCAAGAGAGTACAGA	58.499	45.455	0.00	0.00	0.00	3.41
3100	6460	3.671971	CGAGCAGAACCAAGAGAGTACAG	60.672	52.174	0.00	0.00	0.00	2.74
3101	6461	2.229062	CGAGCAGAACCAAGAGAGTACA	59.771	50.000	0.00	0.00	0.00	2.90
3102	6462	2.229302	ACGAGCAGAACCAAGAGAGTAC	59.771	50.000	0.00	0.00	0.00	2.73
3103	6463	2.229062	CACGAGCAGAACCAAGAGAGTA	59.771	50.000	0.00	0.00	0.00	2.59
3104	6464	1.000283	CACGAGCAGAACCAAGAGAGT	60.000	52.381	0.00	0.00	0.00	3.24
3105	6465	1.707632	CACGAGCAGAACCAAGAGAG	58.292	55.000	0.00	0.00	0.00	3.20
3106	6466	0.319900	GCACGAGCAGAACCAAGAGA	60.320	55.000	0.00	0.00	41.58	3.10
3107	6467	0.320247	AGCACGAGCAGAACCAAGAG	60.320	55.000	7.77	0.00	45.49	2.85
3108	6468	0.106708	AAGCACGAGCAGAACCAAGA	59.893	50.000	7.77	0.00	45.49	3.02
3109	6469	0.947244	AAAGCACGAGCAGAACCAAG	59.053	50.000	7.77	0.00	45.49	3.61
3110	6470	1.065401	CAAAAGCACGAGCAGAACCAA	59.935	47.619	7.77	0.00	45.49	3.67
3111	6471	0.662619	CAAAAGCACGAGCAGAACCA	59.337	50.000	7.77	0.00	45.49	3.67
3112	6472	0.944386	TCAAAAGCACGAGCAGAACC	59.056	50.000	7.77	0.00	45.49	3.62
3113	6473	2.287915	TCTTCAAAAGCACGAGCAGAAC	59.712	45.455	7.77	0.00	45.49	3.01
3114	6474	2.560504	TCTTCAAAAGCACGAGCAGAA	58.439	42.857	7.77	4.94	45.49	3.02
3115	6475	2.238942	TCTTCAAAAGCACGAGCAGA	57.761	45.000	7.77	0.00	45.49	4.26
3243	6607	5.364778	TGATTGTTCGTCCCCACTATAATG	58.635	41.667	0.00	0.00	0.00	1.90
3249	6613	1.348064	TCTGATTGTTCGTCCCCACT	58.652	50.000	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.