AutoCloner

Multiple sequence alignment - TraesCS3D01G418500

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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	TraesCS3D01G418500	chr3D	100.000	2930	0	0	1	2930	531292559	531289630	0.000000e+00	5411.0
1	TraesCS3D01G418500	chr3D	77.965	1071	209	20	842	1902	94238991	94240044	0.000000e+00	645.0
2	TraesCS3D01G418500	chr7D	91.206	2820	191	24	119	2930	633733724	633736494	0.000000e+00	3781.0
3	TraesCS3D01G418500	chr7D	88.835	824	76	6	2108	2930	73265613	73264805	0.000000e+00	998.0
4	TraesCS3D01G418500	chr7D	79.104	1072	202	20	842	1902	13045002	13046062	0.000000e+00	719.0
5	TraesCS3D01G418500	chr7D	83.494	624	100	3	2307	2929	500937048	500936427	1.960000e-161	579.0
6	TraesCS3D01G418500	chr4A	87.775	2863	308	22	77	2930	596536810	596533981	0.000000e+00	3310.0
7	TraesCS3D01G418500	chr2D	94.551	1670	75	8	63	1728	162491831	162490174	0.000000e+00	2566.0
8	TraesCS3D01G418500	chr2D	92.479	1210	61	5	1721	2930	162482233	162481054	0.000000e+00	1703.0
9	TraesCS3D01G418500	chr6D	88.682	1555	151	12	1379	2930	457560241	457558709	0.000000e+00	1873.0
10	TraesCS3D01G418500	chr6D	88.655	1331	142	7	57	1381	457577338	457576011	0.000000e+00	1613.0
11	TraesCS3D01G418500	chr6B	88.992	645	68	2	2286	2930	42832528	42833169	0.000000e+00	795.0
12	TraesCS3D01G418500	chr6B	77.647	850	173	15	86	927	42830809	42831649	4.360000e-138	501.0
13	TraesCS3D01G418500	chr6B	84.410	449	57	11	1503	1944	42831865	42832307	2.090000e-116	429.0
14	TraesCS3D01G418500	chr6B	87.654	81	10	0	984	1064	42831664	42831744	8.640000e-16	95.3
15	TraesCS3D01G418500	chrUn	83.186	565	93	2	2365	2929	38727507	38728069	1.560000e-142	516.0
16	TraesCS3D01G418500	chr6A	78.968	756	139	18	1157	1902	599929152	599929897	5.640000e-137	497.0
17	TraesCS3D01G418500	chr7B	79.426	627	116	4	2307	2930	194075379	194075995	5.800000e-117	431.0
18	TraesCS3D01G418500	chr1B	76.797	793	167	9	990	1780	439013050	439013827	2.090000e-116	429.0

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	TraesCS3D01G418500	chr3D	531289630	531292559	2929	True	5411.000	5411	100.00000	1	2930	1	chr3D.!!$R1	2929
1	TraesCS3D01G418500	chr3D	94238991	94240044	1053	False	645.000	645	77.96500	842	1902	1	chr3D.!!$F1	1060
2	TraesCS3D01G418500	chr7D	633733724	633736494	2770	False	3781.000	3781	91.20600	119	2930	1	chr7D.!!$F2	2811
3	TraesCS3D01G418500	chr7D	73264805	73265613	808	True	998.000	998	88.83500	2108	2930	1	chr7D.!!$R1	822
4	TraesCS3D01G418500	chr7D	13045002	13046062	1060	False	719.000	719	79.10400	842	1902	1	chr7D.!!$F1	1060
5	TraesCS3D01G418500	chr7D	500936427	500937048	621	True	579.000	579	83.49400	2307	2929	1	chr7D.!!$R2	622
6	TraesCS3D01G418500	chr4A	596533981	596536810	2829	True	3310.000	3310	87.77500	77	2930	1	chr4A.!!$R1	2853
7	TraesCS3D01G418500	chr2D	162490174	162491831	1657	True	2566.000	2566	94.55100	63	1728	1	chr2D.!!$R2	1665
8	TraesCS3D01G418500	chr2D	162481054	162482233	1179	True	1703.000	1703	92.47900	1721	2930	1	chr2D.!!$R1	1209
9	TraesCS3D01G418500	chr6D	457558709	457560241	1532	True	1873.000	1873	88.68200	1379	2930	1	chr6D.!!$R1	1551
10	TraesCS3D01G418500	chr6D	457576011	457577338	1327	True	1613.000	1613	88.65500	57	1381	1	chr6D.!!$R2	1324
11	TraesCS3D01G418500	chr6B	42830809	42833169	2360	False	455.075	795	84.67575	86	2930	4	chr6B.!!$F1	2844
12	TraesCS3D01G418500	chrUn	38727507	38728069	562	False	516.000	516	83.18600	2365	2929	1	chrUn.!!$F1	564
13	TraesCS3D01G418500	chr6A	599929152	599929897	745	False	497.000	497	78.96800	1157	1902	1	chr6A.!!$F1	745
14	TraesCS3D01G418500	chr7B	194075379	194075995	616	False	431.000	431	79.42600	2307	2930	1	chr7B.!!$F1	623
15	TraesCS3D01G418500	chr1B	439013050	439013827	777	False	429.000	429	76.79700	990	1780	1	chr1B.!!$F1	790

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
52	53	0.179225	CGATTCCACGAGCCGTTTTG	60.179	55.0	0.00	0.0	38.32	2.44	F
779	796	0.549902	TCCCATGGGGTGACAGTCAT	60.550	55.0	30.93	0.0	44.74	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1633	1651	0.033796	CCCCATGACAGTGCCTTGAT	60.034	55.0	0.0	0.0	0.0	2.57	R
2168	2200	0.035725	CCAGCAGCATCACCTCAGAA	60.036	55.0	0.0	0.0	0.0	3.02	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
25	26	7.782897	ACCATTCAAGGATCGATTAGATAGA	57.217	36.000	0.00	0.00	40.26	1.98
26	27	7.607250	ACCATTCAAGGATCGATTAGATAGAC	58.393	38.462	0.00	0.00	40.26	2.59
27	28	7.453126	ACCATTCAAGGATCGATTAGATAGACT	59.547	37.037	0.00	0.00	40.26	3.24
28	29	7.758980	CCATTCAAGGATCGATTAGATAGACTG	59.241	40.741	0.00	0.00	40.26	3.51
29	30	8.518702	CATTCAAGGATCGATTAGATAGACTGA	58.481	37.037	0.00	0.00	40.26	3.41
30	31	7.680442	TCAAGGATCGATTAGATAGACTGAG	57.320	40.000	0.00	0.00	40.26	3.35
31	32	7.454225	TCAAGGATCGATTAGATAGACTGAGA	58.546	38.462	0.00	0.00	40.26	3.27
32	33	7.389330	TCAAGGATCGATTAGATAGACTGAGAC	59.611	40.741	0.00	0.00	40.26	3.36
33	34	6.177610	AGGATCGATTAGATAGACTGAGACC	58.822	44.000	0.00	0.00	40.26	3.85
34	35	5.064198	GGATCGATTAGATAGACTGAGACCG	59.936	48.000	0.00	0.00	40.26	4.79
35	36	5.211174	TCGATTAGATAGACTGAGACCGA	57.789	43.478	0.00	0.00	0.00	4.69
36	37	5.795972	TCGATTAGATAGACTGAGACCGAT	58.204	41.667	0.00	0.00	0.00	4.18
37	38	6.231951	TCGATTAGATAGACTGAGACCGATT	58.768	40.000	0.00	0.00	0.00	3.34
38	39	6.369340	TCGATTAGATAGACTGAGACCGATTC	59.631	42.308	0.00	0.00	0.00	2.52
39	40	6.402766	CGATTAGATAGACTGAGACCGATTCC	60.403	46.154	0.00	0.00	0.00	3.01
40	41	4.171878	AGATAGACTGAGACCGATTCCA	57.828	45.455	0.00	0.00	0.00	3.53
41	42	3.886505	AGATAGACTGAGACCGATTCCAC	59.113	47.826	0.00	0.00	0.00	4.02
42	43	0.811915	AGACTGAGACCGATTCCACG	59.188	55.000	0.00	0.00	0.00	4.94
43	44	0.809385	GACTGAGACCGATTCCACGA	59.191	55.000	0.00	0.00	35.09	4.35
44	45	0.811915	ACTGAGACCGATTCCACGAG	59.188	55.000	0.00	0.00	35.09	4.18
45	46	0.526524	CTGAGACCGATTCCACGAGC	60.527	60.000	0.00	0.00	35.09	5.03
46	47	1.227002	GAGACCGATTCCACGAGCC	60.227	63.158	0.00	0.00	35.09	4.70
47	48	2.582498	GACCGATTCCACGAGCCG	60.582	66.667	0.00	0.00	35.09	5.52
48	49	3.352338	GACCGATTCCACGAGCCGT	62.352	63.158	0.00	0.00	42.36	5.68
49	50	2.125673	CCGATTCCACGAGCCGTT	60.126	61.111	0.00	0.00	38.32	4.44
50	51	1.740296	CCGATTCCACGAGCCGTTT	60.740	57.895	0.00	0.00	38.32	3.60
51	52	1.296056	CCGATTCCACGAGCCGTTTT	61.296	55.000	0.00	0.00	38.32	2.43
52	53	0.179225	CGATTCCACGAGCCGTTTTG	60.179	55.000	0.00	0.00	38.32	2.44
53	54	1.153353	GATTCCACGAGCCGTTTTGA	58.847	50.000	0.00	0.00	38.32	2.69
54	55	0.872388	ATTCCACGAGCCGTTTTGAC	59.128	50.000	0.00	0.00	38.32	3.18
55	56	1.161563	TTCCACGAGCCGTTTTGACC	61.162	55.000	0.00	0.00	38.32	4.02
61	62	4.379143	GCCGTTTTGACCGACCGC	62.379	66.667	0.00	0.00	0.00	5.68
316	318	9.924650	CTTTCTTCAATTCTTCTCCAATTCAAT	57.075	29.630	0.00	0.00	0.00	2.57
407	409	3.213506	CCGCATTCAGGGATGTAAATCA	58.786	45.455	0.00	0.00	0.00	2.57
589	591	8.781951	AGATCATAGGGAATTTTCAGAAACCTA	58.218	33.333	10.84	10.84	34.02	3.08
663	670	3.163503	GGGACCAACGAGGGGAAA	58.836	61.111	0.00	0.00	43.89	3.13
726	743	3.921767	CTCGCCGTCTTCTGCTGCA	62.922	63.158	0.88	0.88	0.00	4.41
779	796	0.549902	TCCCATGGGGTGACAGTCAT	60.550	55.000	30.93	0.00	44.74	3.06
887	904	4.719369	GCTCTCCGTCACGCCGTT	62.719	66.667	0.00	0.00	0.00	4.44
890	907	4.657824	CTCCGTCACGCCGTTGGT	62.658	66.667	0.00	0.00	0.00	3.67
930	948	1.152525	GGCGGTGGATCCTCCTCTA	60.153	63.158	26.39	0.00	38.03	2.43
1009	1027	1.342496	TCATCATCGACATGGAGGCTC	59.658	52.381	5.78	5.78	0.00	4.70
1013	1031	2.896677	ATCGACATGGAGGCTCCCCA	62.897	60.000	30.03	14.44	35.03	4.96
1475	1493	2.890961	GCCGCTAAGGAGGAACGC	60.891	66.667	0.00	0.00	45.00	4.84
1633	1651	0.818445	GGCGGTCTACTCCATCGAGA	60.818	60.000	0.00	0.00	38.52	4.04
1643	1661	1.411977	CTCCATCGAGATCAAGGCACT	59.588	52.381	0.00	0.00	38.51	4.40
1821	1839	1.824329	GACTGCGGATCCTCTCGGA	60.824	63.158	10.75	0.00	45.16	4.55
1927	1946	1.610379	GGGTCAAATGGCCAGGCTT	60.610	57.895	13.05	0.99	42.93	4.35
2041	2061	1.740380	CGCTTCCCTCGTCATCAACAT	60.740	52.381	0.00	0.00	0.00	2.71
2061	2081	4.821589	GAACTCCTGAGGCGCCGG	62.822	72.222	23.20	17.22	0.00	6.13
2083	2103	1.436983	GCATTGGCTACCGCTGGTAC	61.437	60.000	3.72	0.00	37.09	3.34
2159	2191	0.324943	GGCCTGTTGAAGCTCCTACA	59.675	55.000	0.00	0.00	0.00	2.74
2160	2192	1.271379	GGCCTGTTGAAGCTCCTACAA	60.271	52.381	0.00	0.00	0.00	2.41
2161	2193	1.807142	GCCTGTTGAAGCTCCTACAAC	59.193	52.381	14.61	14.61	42.51	3.32
2162	2194	2.069273	CCTGTTGAAGCTCCTACAACG	58.931	52.381	15.67	12.04	44.29	4.10
2163	2195	1.461127	CTGTTGAAGCTCCTACAACGC	59.539	52.381	15.67	0.00	44.29	4.84
2164	2196	0.796927	GTTGAAGCTCCTACAACGCC	59.203	55.000	9.15	0.00	35.42	5.68
2165	2197	0.685097	TTGAAGCTCCTACAACGCCT	59.315	50.000	0.00	0.00	0.00	5.52
2166	2198	0.246635	TGAAGCTCCTACAACGCCTC	59.753	55.000	0.00	0.00	0.00	4.70
2167	2199	0.460459	GAAGCTCCTACAACGCCTCC	60.460	60.000	0.00	0.00	0.00	4.30
2168	2200	0.905337	AAGCTCCTACAACGCCTCCT	60.905	55.000	0.00	0.00	0.00	3.69
2169	2201	0.905337	AGCTCCTACAACGCCTCCTT	60.905	55.000	0.00	0.00	0.00	3.36
2170	2202	0.460459	GCTCCTACAACGCCTCCTTC	60.460	60.000	0.00	0.00	0.00	3.46
2245	2279	0.700564	TCTTTGGATGCCCAGCTTCT	59.299	50.000	2.96	0.00	44.60	2.85
2388	2422	1.200020	CAAAGGGCGTGGAGACAATTC	59.800	52.381	0.00	0.00	46.06	2.17
2396	2430	2.267961	GAGACAATTCGGGGCCGT	59.732	61.111	0.00	0.00	40.74	5.68
2435	2469	1.300156	GGAGCGCGATGAGTATGCA	60.300	57.895	12.10	0.00	0.00	3.96
2466	2500	3.027170	GCCGGTGTCAAGCATGTCG	62.027	63.158	1.90	0.00	0.00	4.35
2776	2811	1.381872	TAGGTGAGGGGAGAGCTGC	60.382	63.158	0.00	0.00	0.00	5.25
2825	2860	0.907704	ATGGGGCTGTCGGTCAACTA	60.908	55.000	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	8.091449	GTCTATCTAATCGATCCTTGAATGGTT	58.909	37.037	0.00	0.00	33.48	3.67
1	2	7.453126	AGTCTATCTAATCGATCCTTGAATGGT	59.547	37.037	0.00	0.00	33.48	3.55
2	3	7.758980	CAGTCTATCTAATCGATCCTTGAATGG	59.241	40.741	0.00	0.00	33.48	3.16
3	4	8.518702	TCAGTCTATCTAATCGATCCTTGAATG	58.481	37.037	0.00	3.17	33.48	2.67
4	5	8.642935	TCAGTCTATCTAATCGATCCTTGAAT	57.357	34.615	0.00	0.00	33.48	2.57
5	6	7.939588	TCTCAGTCTATCTAATCGATCCTTGAA	59.060	37.037	0.00	0.00	33.48	2.69
6	7	7.389330	GTCTCAGTCTATCTAATCGATCCTTGA	59.611	40.741	0.00	0.00	33.48	3.02
7	8	7.361713	GGTCTCAGTCTATCTAATCGATCCTTG	60.362	44.444	0.00	0.00	33.48	3.61
8	9	6.657541	GGTCTCAGTCTATCTAATCGATCCTT	59.342	42.308	0.00	0.00	33.48	3.36
9	10	6.177610	GGTCTCAGTCTATCTAATCGATCCT	58.822	44.000	0.00	0.00	33.48	3.24
10	11	5.064198	CGGTCTCAGTCTATCTAATCGATCC	59.936	48.000	0.00	0.00	33.48	3.36
11	12	5.870433	TCGGTCTCAGTCTATCTAATCGATC	59.130	44.000	0.00	0.00	33.48	3.69
12	13	5.795972	TCGGTCTCAGTCTATCTAATCGAT	58.204	41.667	0.00	0.00	36.11	3.59
13	14	5.211174	TCGGTCTCAGTCTATCTAATCGA	57.789	43.478	0.00	0.00	0.00	3.59
14	15	6.402766	GGAATCGGTCTCAGTCTATCTAATCG	60.403	46.154	0.00	0.00	0.00	3.34
15	16	6.431543	TGGAATCGGTCTCAGTCTATCTAATC	59.568	42.308	0.00	0.00	0.00	1.75
16	17	6.207810	GTGGAATCGGTCTCAGTCTATCTAAT	59.792	42.308	0.00	0.00	0.00	1.73
17	18	5.531659	GTGGAATCGGTCTCAGTCTATCTAA	59.468	44.000	0.00	0.00	0.00	2.10
18	19	5.064558	GTGGAATCGGTCTCAGTCTATCTA	58.935	45.833	0.00	0.00	0.00	1.98
19	20	3.886505	GTGGAATCGGTCTCAGTCTATCT	59.113	47.826	0.00	0.00	0.00	1.98
20	21	3.304123	CGTGGAATCGGTCTCAGTCTATC	60.304	52.174	0.00	0.00	0.00	2.08
21	22	2.619177	CGTGGAATCGGTCTCAGTCTAT	59.381	50.000	0.00	0.00	0.00	1.98
22	23	2.014857	CGTGGAATCGGTCTCAGTCTA	58.985	52.381	0.00	0.00	0.00	2.59
23	24	0.811915	CGTGGAATCGGTCTCAGTCT	59.188	55.000	0.00	0.00	0.00	3.24
24	25	0.809385	TCGTGGAATCGGTCTCAGTC	59.191	55.000	0.00	0.00	0.00	3.51
25	26	0.811915	CTCGTGGAATCGGTCTCAGT	59.188	55.000	0.00	0.00	0.00	3.41
26	27	0.526524	GCTCGTGGAATCGGTCTCAG	60.527	60.000	0.00	0.00	0.00	3.35
27	28	1.511305	GCTCGTGGAATCGGTCTCA	59.489	57.895	0.00	0.00	0.00	3.27
28	29	1.227002	GGCTCGTGGAATCGGTCTC	60.227	63.158	0.00	0.00	0.00	3.36
29	30	2.893398	GGCTCGTGGAATCGGTCT	59.107	61.111	0.00	0.00	0.00	3.85
30	31	2.582498	CGGCTCGTGGAATCGGTC	60.582	66.667	0.00	0.00	0.00	4.79
31	32	2.444700	AAACGGCTCGTGGAATCGGT	62.445	55.000	0.94	0.00	39.99	4.69
32	33	1.296056	AAAACGGCTCGTGGAATCGG	61.296	55.000	0.94	0.00	39.99	4.18
33	34	0.179225	CAAAACGGCTCGTGGAATCG	60.179	55.000	0.94	0.00	39.99	3.34
34	35	1.136057	GTCAAAACGGCTCGTGGAATC	60.136	52.381	0.94	0.00	39.99	2.52
35	36	0.872388	GTCAAAACGGCTCGTGGAAT	59.128	50.000	0.94	0.00	39.99	3.01
36	37	1.161563	GGTCAAAACGGCTCGTGGAA	61.162	55.000	0.94	0.00	39.99	3.53
37	38	1.595929	GGTCAAAACGGCTCGTGGA	60.596	57.895	0.94	0.00	39.99	4.02
38	39	2.943653	GGTCAAAACGGCTCGTGG	59.056	61.111	0.94	0.00	39.99	4.94
39	40	1.952133	TCGGTCAAAACGGCTCGTG	60.952	57.895	0.94	0.00	39.99	4.35
40	41	1.952635	GTCGGTCAAAACGGCTCGT	60.953	57.895	0.00	0.00	43.97	4.18
41	42	2.664436	GGTCGGTCAAAACGGCTCG	61.664	63.158	0.00	0.00	36.01	5.03
42	43	2.664436	CGGTCGGTCAAAACGGCTC	61.664	63.158	0.00	0.00	36.01	4.70
43	44	2.663852	CGGTCGGTCAAAACGGCT	60.664	61.111	0.00	0.00	36.01	5.52
44	45	4.379143	GCGGTCGGTCAAAACGGC	62.379	66.667	0.00	0.00	35.11	5.68
45	46	1.778027	AAAGCGGTCGGTCAAAACGG	61.778	55.000	0.00	0.00	0.00	4.44
46	47	0.656205	CAAAGCGGTCGGTCAAAACG	60.656	55.000	0.00	0.00	0.00	3.60
47	48	0.658897	TCAAAGCGGTCGGTCAAAAC	59.341	50.000	0.00	0.00	0.00	2.43
48	49	0.658897	GTCAAAGCGGTCGGTCAAAA	59.341	50.000	0.00	0.00	0.00	2.44
49	50	1.161563	GGTCAAAGCGGTCGGTCAAA	61.162	55.000	0.00	0.00	0.00	2.69
50	51	1.595929	GGTCAAAGCGGTCGGTCAA	60.596	57.895	0.00	0.00	0.00	3.18
51	52	2.029964	GGTCAAAGCGGTCGGTCA	59.970	61.111	0.00	0.00	0.00	4.02
52	53	3.110178	CGGTCAAAGCGGTCGGTC	61.110	66.667	0.00	0.00	35.16	4.79
53	54	3.154584	TTCGGTCAAAGCGGTCGGT	62.155	57.895	0.00	0.00	39.89	4.69
54	55	2.356553	TTCGGTCAAAGCGGTCGG	60.357	61.111	0.00	0.00	39.89	4.79
55	56	3.011760	GCTTCGGTCAAAGCGGTCG	62.012	63.158	0.00	0.00	41.98	4.79
258	260	1.006832	CCTTCATCCGCCGTAAACAG	58.993	55.000	0.00	0.00	0.00	3.16
316	318	4.960332	TCCTCTCCTCCTTTGATTTCCTA	58.040	43.478	0.00	0.00	0.00	2.94
407	409	5.045066	GGACTAAACTGACCTTTATTCCCCT	60.045	44.000	0.00	0.00	32.80	4.79
663	670	2.436417	CCAATGTCGTTCACCTCCATT	58.564	47.619	0.00	0.00	0.00	3.16
779	796	0.339859	ATCAGGGACAGTAGGAGGCA	59.660	55.000	0.00	0.00	0.00	4.75
824	841	0.768221	AGCTCTCCCTTGGACCAACA	60.768	55.000	1.69	0.00	0.00	3.33
887	904	1.896660	GCAAAGCCAACGGAGACCA	60.897	57.895	0.00	0.00	0.00	4.02
930	948	3.249189	TTGCCGGCCCTCTGAAGT	61.249	61.111	26.77	0.00	0.00	3.01
942	960	0.095935	CGAACATCTTGCTCTTGCCG	59.904	55.000	0.00	0.00	38.71	5.69
1104	1122	0.737715	CACTACCTCGCAGCTTCCAC	60.738	60.000	0.00	0.00	0.00	4.02
1475	1493	0.611896	ACCAAAGGGAATGAAGGCGG	60.612	55.000	0.00	0.00	38.05	6.13
1609	1627	1.264749	ATGGAGTAGACCGCCTTGCA	61.265	55.000	0.00	0.00	0.00	4.08
1633	1651	0.033796	CCCCATGACAGTGCCTTGAT	60.034	55.000	0.00	0.00	0.00	2.57
1700	1718	1.827969	CCGTGTCCTCTTCATCTTCCT	59.172	52.381	0.00	0.00	0.00	3.36
1795	1813	3.047718	GATCCGCAGTCACCGTCGA	62.048	63.158	0.00	0.00	0.00	4.20
1821	1839	4.360405	ATGGAACCCGCCGCCTTT	62.360	61.111	0.00	0.00	0.00	3.11
1927	1946	2.284331	TTCGGCCACCTCCTGCTA	60.284	61.111	2.24	0.00	0.00	3.49
2031	2051	3.012518	CAGGAGTTCCCATGTTGATGAC	58.987	50.000	0.00	0.00	37.41	3.06
2041	2061	3.706373	GCGCCTCAGGAGTTCCCA	61.706	66.667	0.00	0.00	37.41	4.37
2083	2103	1.097547	GGAATGCACTCCATGTCCGG	61.098	60.000	9.87	0.00	35.36	5.14
2164	2196	1.743091	GCAGCATCACCTCAGAAGGAG	60.743	57.143	0.00	0.00	46.67	3.69
2165	2197	0.251354	GCAGCATCACCTCAGAAGGA	59.749	55.000	0.00	0.00	46.67	3.36
2167	2199	1.370609	CAGCAGCATCACCTCAGAAG	58.629	55.000	0.00	0.00	0.00	2.85
2168	2200	0.035725	CCAGCAGCATCACCTCAGAA	60.036	55.000	0.00	0.00	0.00	3.02
2169	2201	1.600638	CCAGCAGCATCACCTCAGA	59.399	57.895	0.00	0.00	0.00	3.27
2170	2202	1.451567	CCCAGCAGCATCACCTCAG	60.452	63.158	0.00	0.00	0.00	3.35
2245	2279	0.685785	CTGCACCTCTCCTAGAGCCA	60.686	60.000	0.00	0.00	40.98	4.75
2466	2500	3.194272	GAGTGGGCACGCCAAACAC	62.194	63.158	10.83	8.96	37.98	3.32
2776	2811	0.615331	TTCCTTAGCAGCCTCACCAG	59.385	55.000	0.00	0.00	0.00	4.00
2802	2837	3.256960	ACCGACAGCCCCATGGTT	61.257	61.111	11.73	0.00	0.00	3.67
2825	2860	2.047274	CTCACATCCACGCCCGTT	60.047	61.111	0.00	0.00	0.00	4.44
2856	2891	6.322201	ACAGTTCCAACTCAGAATTTTCATGT	59.678	34.615	0.00	0.00	37.08	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.