AutoCloner

Multiple sequence alignment - TraesCS6B01G003700

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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	TraesCS6B01G003700	chr6B	100.000	3638	0	0	1	3638	2662202	2658565	0.000000e+00	6719.0
1	TraesCS6B01G003700	chr6B	91.832	3330	232	24	98	3405	5305888	5309199	0.000000e+00	4606.0
2	TraesCS6B01G003700	chr6B	92.341	2781	180	15	880	3638	2827150	2824381	0.000000e+00	3925.0
3	TraesCS6B01G003700	chr6B	95.771	1797	58	3	971	2766	5807244	5809023	0.000000e+00	2881.0
4	TraesCS6B01G003700	chr6B	91.993	612	41	6	96	701	2838046	2837437	0.000000e+00	852.0
5	TraesCS6B01G003700	chr6B	86.317	782	77	7	1015	1789	5822318	5823076	0.000000e+00	824.0
6	TraesCS6B01G003700	chr6B	87.796	549	60	2	1426	1974	5564999	5564458	1.420000e-178	636.0
7	TraesCS6B01G003700	chr6B	83.726	467	65	7	2177	2641	5844388	5843931	7.220000e-117	431.0
8	TraesCS6B01G003700	chr6B	84.766	256	36	1	1159	1414	5573994	5573742	1.680000e-63	254.0
9	TraesCS6B01G003700	chr6B	78.385	384	72	7	446	825	5845144	5844768	4.690000e-59	239.0
10	TraesCS6B01G003700	chr6B	83.182	220	30	7	3409	3625	51303212	51303427	1.030000e-45	195.0
11	TraesCS6B01G003700	chr6B	91.071	112	6	3	1	112	21562707	21562600	8.140000e-32	148.0
12	TraesCS6B01G003700	chr6B	90.179	112	7	3	1	112	21534211	21534104	3.790000e-30	143.0
13	TraesCS6B01G003700	chr6B	89.000	100	4	1	1013	1105	5807148	5807247	2.300000e-22	117.0
14	TraesCS6B01G003700	chr6A	96.701	3546	106	5	96	3638	55794	59331	0.000000e+00	5890.0
15	TraesCS6B01G003700	chr6D	86.562	1972	152	48	1026	2971	451854101	451852217	0.000000e+00	2069.0
16	TraesCS6B01G003700	chr6D	87.647	340	29	6	3035	3373	451852215	451851888	2.050000e-102	383.0
17	TraesCS6B01G003700	chr6D	84.595	370	49	6	3045	3408	11758205	11757838	9.600000e-96	361.0
18	TraesCS6B01G003700	chr6D	85.909	220	25	4	3408	3627	306299989	306299776	2.830000e-56	230.0
19	TraesCS6B01G003700	chr2B	84.528	2120	227	49	997	3098	755718888	755716852	0.000000e+00	2004.0
20	TraesCS6B01G003700	chr2B	86.563	707	75	11	159	853	755719730	755719032	0.000000e+00	761.0
21	TraesCS6B01G003700	chr2B	82.129	263	41	6	99	357	799580745	799581005	1.700000e-53	220.0
22	TraesCS6B01G003700	chr2B	93.939	99	6	0	1	99	690746356	690746454	2.260000e-32	150.0
23	TraesCS6B01G003700	chrUn	87.316	1695	172	13	1129	2819	295591991	295590336	0.000000e+00	1899.0
24	TraesCS6B01G003700	chrUn	88.100	1521	137	19	1002	2507	278071617	278073108	0.000000e+00	1766.0
25	TraesCS6B01G003700	chrUn	84.115	768	99	16	98	853	278070737	278071493	0.000000e+00	721.0
26	TraesCS6B01G003700	chrUn	87.771	507	40	4	2551	3052	278073108	278073597	1.130000e-159	573.0
27	TraesCS6B01G003700	chrUn	89.431	123	12	1	3287	3408	259667487	259667365	1.750000e-33	154.0
28	TraesCS6B01G003700	chr3A	82.927	287	41	8	3060	3343	537495890	537496171	6.030000e-63	252.0
29	TraesCS6B01G003700	chr3A	78.344	314	54	14	3024	3329	740899041	740899348	1.330000e-44	191.0
30	TraesCS6B01G003700	chr3A	81.319	91	17	0	455	545	33132386	33132476	1.400000e-09	75.0
31	TraesCS6B01G003700	chr1B	87.215	219	28	0	3407	3625	369613861	369614079	2.170000e-62	250.0
32	TraesCS6B01G003700	chr7D	80.374	321	58	5	3025	3343	460518700	460518383	4.690000e-59	239.0
33	TraesCS6B01G003700	chr7B	82.879	257	41	3	98	352	110879773	110880028	1.020000e-55	228.0
34	TraesCS6B01G003700	chr7B	82.171	258	43	3	98	353	40184665	40184409	6.120000e-53	219.0
35	TraesCS6B01G003700	chr7B	95.833	96	4	0	1	96	253616624	253616529	4.860000e-34	156.0
36	TraesCS6B01G003700	chr7B	95.789	95	4	0	1	95	656906100	656906006	1.750000e-33	154.0
37	TraesCS6B01G003700	chr7B	94.949	99	4	1	1	99	704516403	704516306	1.750000e-33	154.0
38	TraesCS6B01G003700	chr7B	94.000	100	6	0	1	100	72757432	72757333	6.290000e-33	152.0
39	TraesCS6B01G003700	chr3B	83.071	254	40	3	102	353	417373925	417374177	1.020000e-55	228.0
40	TraesCS6B01G003700	chr3B	80.969	289	48	4	3061	3343	539667758	539667471	4.730000e-54	222.0
41	TraesCS6B01G003700	chr3B	94.845	97	5	0	1	97	743848063	743847967	6.290000e-33	152.0
42	TraesCS6B01G003700	chr3B	73.793	290	65	9	458	744	786114661	786114942	1.790000e-18	104.0
43	TraesCS6B01G003700	chr1D	82.625	259	41	4	98	353	461344843	461344586	3.660000e-55	226.0
44	TraesCS6B01G003700	chr4A	84.416	231	33	3	3409	3638	151315687	151315459	1.310000e-54	224.0
45	TraesCS6B01G003700	chr2D	83.043	230	36	2	3409	3638	218385202	218384976	4.760000e-49	206.0
46	TraesCS6B01G003700	chr1A	81.197	234	34	9	3409	3638	373585359	373585132	2.890000e-41	180.0
47	TraesCS6B01G003700	chr1A	94.737	38	2	0	2885	2922	351005374	351005337	3.920000e-05	60.2
48	TraesCS6B01G003700	chr7A	82.292	192	28	6	3418	3607	21984130	21983943	1.050000e-35	161.0
49	TraesCS6B01G003700	chr5B	95.833	96	4	0	1	96	477875446	477875351	4.860000e-34	156.0
50	TraesCS6B01G003700	chr5A	76.779	267	59	1	478	744	91553568	91553305	2.930000e-31	147.0
51	TraesCS6B01G003700	chr5D	74.386	285	60	9	461	740	521086833	521086557	3.840000e-20	110.0

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	TraesCS6B01G003700	chr6B	2658565	2662202	3637	True	6719.0	6719	100.0000	1	3638	1	chr6B.!!$R1	3637
1	TraesCS6B01G003700	chr6B	5305888	5309199	3311	False	4606.0	4606	91.8320	98	3405	1	chr6B.!!$F1	3307
2	TraesCS6B01G003700	chr6B	2824381	2827150	2769	True	3925.0	3925	92.3410	880	3638	1	chr6B.!!$R2	2758
3	TraesCS6B01G003700	chr6B	5807148	5809023	1875	False	1499.0	2881	92.3855	971	2766	2	chr6B.!!$F4	1795
4	TraesCS6B01G003700	chr6B	2837437	2838046	609	True	852.0	852	91.9930	96	701	1	chr6B.!!$R3	605
5	TraesCS6B01G003700	chr6B	5822318	5823076	758	False	824.0	824	86.3170	1015	1789	1	chr6B.!!$F2	774
6	TraesCS6B01G003700	chr6B	5564458	5564999	541	True	636.0	636	87.7960	1426	1974	1	chr6B.!!$R4	548
7	TraesCS6B01G003700	chr6B	5843931	5845144	1213	True	335.0	431	81.0555	446	2641	2	chr6B.!!$R8	2195
8	TraesCS6B01G003700	chr6A	55794	59331	3537	False	5890.0	5890	96.7010	96	3638	1	chr6A.!!$F1	3542
9	TraesCS6B01G003700	chr6D	451851888	451854101	2213	True	1226.0	2069	87.1045	1026	3373	2	chr6D.!!$R3	2347
10	TraesCS6B01G003700	chr2B	755716852	755719730	2878	True	1382.5	2004	85.5455	159	3098	2	chr2B.!!$R1	2939
11	TraesCS6B01G003700	chrUn	295590336	295591991	1655	True	1899.0	1899	87.3160	1129	2819	1	chrUn.!!$R2	1690
12	TraesCS6B01G003700	chrUn	278070737	278073597	2860	False	1020.0	1766	86.6620	98	3052	3	chrUn.!!$F1	2954

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	0.248621	GTGCCGGCTCATATGCAAAC	60.249	55.0	29.7	9.41	35.16	2.93	F
1013	1321	0.179171	AAGTCTCGGATACACGCACG	60.179	55.0	0.0	0.00	0.00	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1886	2220	0.478072	ACCTCCACATCCTGTGCAAA	59.522	50.0	1.71	0.0	46.51	3.68	R
2687	3039	1.085893	TGTGTGCATCGCTTGGTATG	58.914	50.0	0.00	0.0	0.00	2.39	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	4.695455	AGTCATTTGAACCGACACTAATGG	59.305	41.667	0.00	0.00	32.98	3.16
25	26	4.693566	GTCATTTGAACCGACACTAATGGA	59.306	41.667	0.00	0.00	32.98	3.41
26	27	4.693566	TCATTTGAACCGACACTAATGGAC	59.306	41.667	0.00	0.00	32.98	4.02
27	28	3.755112	TTGAACCGACACTAATGGACA	57.245	42.857	0.00	0.00	0.00	4.02
28	29	3.034721	TGAACCGACACTAATGGACAC	57.965	47.619	0.00	0.00	0.00	3.67
30	31	3.007506	TGAACCGACACTAATGGACACAT	59.992	43.478	0.00	0.00	39.54	3.21
32	33	4.811969	ACCGACACTAATGGACACATTA	57.188	40.909	0.00	0.00	45.17	1.90
43	44	4.615901	CACATTAGTGCCGGCTCA	57.384	55.556	29.70	9.72	39.21	4.26
47	48	2.481568	CACATTAGTGCCGGCTCATATG	59.518	50.000	29.70	28.10	39.21	1.78
48	49	1.466167	CATTAGTGCCGGCTCATATGC	59.534	52.381	29.70	8.72	0.00	3.14
50	51	0.467804	TAGTGCCGGCTCATATGCAA	59.532	50.000	29.70	0.00	35.16	4.08
51	52	0.394216	AGTGCCGGCTCATATGCAAA	60.394	50.000	29.70	0.00	35.16	3.68
52	53	0.248621	GTGCCGGCTCATATGCAAAC	60.249	55.000	29.70	9.41	35.16	2.93
54	55	1.648720	CCGGCTCATATGCAAACCG	59.351	57.895	14.68	14.68	40.30	4.44
57	58	1.808512	CGGCTCATATGCAAACCGGTA	60.809	52.381	8.00	0.00	37.04	4.02
59	60	2.561569	GCTCATATGCAAACCGGTACT	58.438	47.619	8.00	0.00	0.00	2.73
60	61	3.493699	GGCTCATATGCAAACCGGTACTA	60.494	47.826	8.00	0.00	34.04	1.82
61	62	4.124238	GCTCATATGCAAACCGGTACTAA	58.876	43.478	8.00	0.00	0.00	2.24
63	64	5.334105	GCTCATATGCAAACCGGTACTAATG	60.334	44.000	8.00	7.84	0.00	1.90
64	65	5.676552	TCATATGCAAACCGGTACTAATGT	58.323	37.500	8.00	0.00	0.00	2.71
65	66	5.525745	TCATATGCAAACCGGTACTAATGTG	59.474	40.000	8.00	8.95	0.00	3.21
67	68	3.068560	TGCAAACCGGTACTAATGTGTC	58.931	45.455	8.00	0.00	0.00	3.67
68	69	3.244284	TGCAAACCGGTACTAATGTGTCT	60.244	43.478	8.00	0.00	0.00	3.41
69	70	3.749609	GCAAACCGGTACTAATGTGTCTT	59.250	43.478	8.00	0.00	0.00	3.01
70	71	4.931002	GCAAACCGGTACTAATGTGTCTTA	59.069	41.667	8.00	0.00	0.00	2.10
71	72	5.063060	GCAAACCGGTACTAATGTGTCTTAG	59.937	44.000	8.00	0.00	35.31	2.18
72	73	6.392354	CAAACCGGTACTAATGTGTCTTAGA	58.608	40.000	8.00	0.00	33.73	2.10
73	74	6.786967	AACCGGTACTAATGTGTCTTAGAT	57.213	37.500	8.00	0.00	33.73	1.98
74	75	6.786967	ACCGGTACTAATGTGTCTTAGATT	57.213	37.500	4.49	0.00	33.73	2.40
75	76	7.179076	ACCGGTACTAATGTGTCTTAGATTT	57.821	36.000	4.49	0.00	33.73	2.17
77	78	7.093640	ACCGGTACTAATGTGTCTTAGATTTGA	60.094	37.037	4.49	0.00	33.73	2.69
79	80	7.222224	CGGTACTAATGTGTCTTAGATTTGACC	59.778	40.741	0.00	0.00	33.73	4.02
81	82	9.088512	GTACTAATGTGTCTTAGATTTGACCTG	57.911	37.037	0.00	0.00	33.73	4.00
83	84	8.157476	ACTAATGTGTCTTAGATTTGACCTGTT	58.843	33.333	0.00	0.00	33.73	3.16
84	85	7.823745	AATGTGTCTTAGATTTGACCTGTTT	57.176	32.000	0.00	0.00	32.67	2.83
85	86	7.823745	ATGTGTCTTAGATTTGACCTGTTTT	57.176	32.000	0.00	0.00	32.67	2.43
86	87	7.259290	TGTGTCTTAGATTTGACCTGTTTTC	57.741	36.000	0.00	0.00	32.67	2.29
88	89	8.208224	TGTGTCTTAGATTTGACCTGTTTTCTA	58.792	33.333	0.00	0.00	32.67	2.10
89	90	8.496751	GTGTCTTAGATTTGACCTGTTTTCTAC	58.503	37.037	0.00	0.00	32.67	2.59
91	92	9.924650	GTCTTAGATTTGACCTGTTTTCTACTA	57.075	33.333	0.00	0.00	0.00	1.82
93	94	9.930693	CTTAGATTTGACCTGTTTTCTACTAGT	57.069	33.333	0.00	0.00	0.00	2.57
94	95	9.706691	TTAGATTTGACCTGTTTTCTACTAGTG	57.293	33.333	5.39	0.00	0.00	2.74
182	183	0.613292	AGGTCAGTGATGGAGACGCT	60.613	55.000	0.00	0.00	33.18	5.07
195	196	2.749044	ACGCTTCGAGCTCGGGTA	60.749	61.111	33.98	19.05	39.60	3.69
198	199	0.734942	CGCTTCGAGCTCGGGTAAAA	60.735	55.000	33.98	19.90	39.60	1.52
237	239	3.256704	TCCTTGGTTTAGAGGGACATGT	58.743	45.455	0.00	0.00	33.73	3.21
282	284	7.856145	ATGCTATCTTTTTCAGTCCTGTAAG	57.144	36.000	0.00	0.00	0.00	2.34
283	285	7.004555	TGCTATCTTTTTCAGTCCTGTAAGA	57.995	36.000	9.75	9.75	34.07	2.10
425	436	0.323957	GTCTTGGGTTTCGGCTAGGT	59.676	55.000	0.00	0.00	0.00	3.08
547	562	1.628846	GTTCTTCCTGCCTTGTCCCTA	59.371	52.381	0.00	0.00	0.00	3.53
571	586	7.798596	ATCTTGGTGATGTTTCTAGCATTAG	57.201	36.000	0.00	0.00	33.43	1.73
616	631	1.097547	CAGCGGATCTTGCGGGATTT	61.098	55.000	5.11	0.00	37.44	2.17
751	766	7.762615	GGCGGTTGCTGTTCTAATGTATATATA	59.237	37.037	0.00	0.00	42.25	0.86
805	1021	0.808125	ACAATAAGATTTGCGCGGCA	59.192	45.000	8.83	3.20	36.47	5.69
843	1059	2.796425	CTGCATGTGAGCTCGCGAC	61.796	63.158	21.66	13.77	34.99	5.19
910	1171	2.636830	CCACATAGTCTCCTGGCTTTG	58.363	52.381	0.00	0.00	0.00	2.77
941	1224	1.407618	CGATGGATAACAGGGACGTGA	59.592	52.381	0.00	0.00	0.00	4.35
995	1303	3.350612	GCCAACGCCACGCAGTAA	61.351	61.111	0.00	0.00	41.61	2.24
1004	1312	0.456221	CCACGCAGTAAGTCTCGGAT	59.544	55.000	0.00	0.00	41.61	4.18
1013	1321	0.179171	AAGTCTCGGATACACGCACG	60.179	55.000	0.00	0.00	0.00	5.34
1643	1977	2.250939	CGCCTCTTCGCCAACAACA	61.251	57.895	0.00	0.00	0.00	3.33
1883	2217	5.530915	CCTTATTTGAGGATCGGTGCATTTA	59.469	40.000	0.00	0.00	39.25	1.40
1884	2218	6.039270	CCTTATTTGAGGATCGGTGCATTTAA	59.961	38.462	0.00	0.00	39.25	1.52
1885	2219	5.913137	ATTTGAGGATCGGTGCATTTAAA	57.087	34.783	0.00	0.00	38.61	1.52
1886	2220	5.913137	TTTGAGGATCGGTGCATTTAAAT	57.087	34.783	0.00	0.00	38.61	1.40
1887	2221	5.913137	TTGAGGATCGGTGCATTTAAATT	57.087	34.783	0.00	0.00	38.61	1.82
2582	2933	4.517952	TGGTGCAATGACCAAATACAAG	57.482	40.909	0.00	0.00	43.31	3.16
2687	3039	2.420466	GGATAACGTCCGGCCTCC	59.580	66.667	0.00	0.00	37.23	4.30
2717	3069	3.747193	CGATGCACACAACCATCTTTAC	58.253	45.455	0.00	0.00	36.55	2.01
2999	3373	6.641169	TTGCATACAAGAACAAATGGTGTA	57.359	33.333	0.00	0.00	40.60	2.90
3470	3847	2.788589	GGAAGGAGGGAGGAGGGT	59.211	66.667	0.00	0.00	0.00	4.34
3529	3906	2.923035	CACGGTGGAGGAGGTGGT	60.923	66.667	0.00	0.00	0.00	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	4.695455	CCATTAGTGTCGGTTCAAATGACT	59.305	41.667	0.00	0.00	33.81	3.41
2	3	4.693566	TCCATTAGTGTCGGTTCAAATGAC	59.306	41.667	0.00	0.00	0.00	3.06
3	4	4.693566	GTCCATTAGTGTCGGTTCAAATGA	59.306	41.667	0.00	0.00	0.00	2.57
4	5	4.454161	TGTCCATTAGTGTCGGTTCAAATG	59.546	41.667	0.00	0.00	0.00	2.32
5	6	4.454504	GTGTCCATTAGTGTCGGTTCAAAT	59.545	41.667	0.00	0.00	0.00	2.32
6	7	3.810941	GTGTCCATTAGTGTCGGTTCAAA	59.189	43.478	0.00	0.00	0.00	2.69
9	10	3.034721	TGTGTCCATTAGTGTCGGTTC	57.965	47.619	0.00	0.00	0.00	3.62
10	11	3.695830	ATGTGTCCATTAGTGTCGGTT	57.304	42.857	0.00	0.00	0.00	4.44
19	20	2.912771	CCGGCACTAATGTGTCCATTA	58.087	47.619	0.00	0.00	45.29	1.90
20	21	1.750193	CCGGCACTAATGTGTCCATT	58.250	50.000	0.00	0.00	45.29	3.16
21	22	0.748005	GCCGGCACTAATGTGTCCAT	60.748	55.000	24.80	0.00	45.29	3.41
22	23	1.376683	GCCGGCACTAATGTGTCCA	60.377	57.895	24.80	0.00	45.29	4.02
24	25	0.391130	TGAGCCGGCACTAATGTGTC	60.391	55.000	31.54	14.56	45.44	3.67
25	26	0.253044	ATGAGCCGGCACTAATGTGT	59.747	50.000	31.54	3.33	45.44	3.72
26	27	2.238942	TATGAGCCGGCACTAATGTG	57.761	50.000	31.54	0.00	46.37	3.21
27	28	2.771089	CATATGAGCCGGCACTAATGT	58.229	47.619	31.54	11.46	0.00	2.71
28	29	1.466167	GCATATGAGCCGGCACTAATG	59.534	52.381	31.54	26.80	0.00	1.90
30	31	0.467804	TGCATATGAGCCGGCACTAA	59.532	50.000	31.54	15.12	0.00	2.24
32	33	0.394216	TTTGCATATGAGCCGGCACT	60.394	50.000	31.54	15.07	35.74	4.40
33	34	0.248621	GTTTGCATATGAGCCGGCAC	60.249	55.000	31.54	24.60	35.74	5.01
34	35	1.383456	GGTTTGCATATGAGCCGGCA	61.383	55.000	31.54	9.64	0.00	5.69
35	36	1.360192	GGTTTGCATATGAGCCGGC	59.640	57.895	21.89	21.89	0.00	6.13
36	37	1.648720	CGGTTTGCATATGAGCCGG	59.351	57.895	6.97	0.00	36.05	6.13
38	39	1.602377	GTACCGGTTTGCATATGAGCC	59.398	52.381	15.04	0.00	0.00	4.70
39	40	2.561569	AGTACCGGTTTGCATATGAGC	58.438	47.619	15.04	0.00	0.00	4.26
43	44	5.433526	ACACATTAGTACCGGTTTGCATAT	58.566	37.500	15.04	0.00	0.00	1.78
47	48	3.332034	AGACACATTAGTACCGGTTTGC	58.668	45.455	15.04	3.55	0.00	3.68
48	49	6.392354	TCTAAGACACATTAGTACCGGTTTG	58.608	40.000	15.04	6.01	34.87	2.93
50	51	6.786967	ATCTAAGACACATTAGTACCGGTT	57.213	37.500	15.04	0.00	34.87	4.44
51	52	6.786967	AATCTAAGACACATTAGTACCGGT	57.213	37.500	13.98	13.98	34.87	5.28
52	53	7.222224	GTCAAATCTAAGACACATTAGTACCGG	59.778	40.741	0.00	0.00	34.87	5.28
54	55	8.258708	AGGTCAAATCTAAGACACATTAGTACC	58.741	37.037	0.00	0.00	36.50	3.34
57	58	7.680730	ACAGGTCAAATCTAAGACACATTAGT	58.319	34.615	0.00	0.00	36.50	2.24
59	60	8.918202	AAACAGGTCAAATCTAAGACACATTA	57.082	30.769	0.00	0.00	36.50	1.90
60	61	7.823745	AAACAGGTCAAATCTAAGACACATT	57.176	32.000	0.00	0.00	36.50	2.71
61	62	7.721399	AGAAAACAGGTCAAATCTAAGACACAT	59.279	33.333	0.00	0.00	36.50	3.21
63	64	7.497925	AGAAAACAGGTCAAATCTAAGACAC	57.502	36.000	0.00	0.00	36.50	3.67
64	65	8.429641	AGTAGAAAACAGGTCAAATCTAAGACA	58.570	33.333	0.00	0.00	36.50	3.41
65	66	8.834749	AGTAGAAAACAGGTCAAATCTAAGAC	57.165	34.615	0.00	0.00	0.00	3.01
67	68	9.930693	ACTAGTAGAAAACAGGTCAAATCTAAG	57.069	33.333	3.59	0.00	0.00	2.18
68	69	9.706691	CACTAGTAGAAAACAGGTCAAATCTAA	57.293	33.333	3.59	0.00	0.00	2.10
69	70	8.867097	ACACTAGTAGAAAACAGGTCAAATCTA	58.133	33.333	3.59	0.00	0.00	1.98
70	71	7.736893	ACACTAGTAGAAAACAGGTCAAATCT	58.263	34.615	3.59	0.00	0.00	2.40
71	72	7.964604	ACACTAGTAGAAAACAGGTCAAATC	57.035	36.000	3.59	0.00	0.00	2.17
91	92	9.201989	TGTCATCTAAAGAATCATACCTACACT	57.798	33.333	0.00	0.00	0.00	3.55
92	93	9.817809	TTGTCATCTAAAGAATCATACCTACAC	57.182	33.333	0.00	0.00	0.00	2.90
182	183	1.345415	ACCTTTTTACCCGAGCTCGAA	59.655	47.619	36.59	20.47	43.02	3.71
195	196	7.703058	AGGAAAATGATACGATCACCTTTTT	57.297	32.000	0.00	0.00	43.01	1.94
198	199	5.590259	CCAAGGAAAATGATACGATCACCTT	59.410	40.000	0.00	0.00	43.01	3.50
237	239	6.373216	AGCATAATCCTACGCAAAAACAAGTA	59.627	34.615	0.00	0.00	0.00	2.24
282	284	1.852067	AAGCCACGCAAACACCGATC	61.852	55.000	0.00	0.00	0.00	3.69
283	285	1.896660	AAGCCACGCAAACACCGAT	60.897	52.632	0.00	0.00	0.00	4.18
425	436	0.391597	ACGAAGGAGGCACGAGAAAA	59.608	50.000	0.00	0.00	0.00	2.29
470	485	3.258622	CCTCTCCGAGTAGGACAAAAACT	59.741	47.826	7.71	0.00	45.98	2.66
535	550	1.281867	CACCAAGATAGGGACAAGGCA	59.718	52.381	0.00	0.00	0.00	4.75
547	562	6.261826	GCTAATGCTAGAAACATCACCAAGAT	59.738	38.462	0.00	0.00	35.00	2.40
571	586	0.320771	AACCTCCACATGTCGTCTGC	60.321	55.000	0.00	0.00	0.00	4.26
616	631	0.606944	AATAAGACAAACGCCGGCCA	60.607	50.000	23.46	0.00	0.00	5.36
663	678	9.692749	CCTGTAGACATATAAACACGAACATAT	57.307	33.333	0.00	0.00	0.00	1.78
706	721	1.135972	CCGCCGATGAACAAAAGAGTG	60.136	52.381	0.00	0.00	0.00	3.51
751	766	7.667557	TCGGAAAATCGACATTATAAGATCCT	58.332	34.615	0.00	0.00	33.92	3.24
805	1021	1.279271	GACTTAGGTGGACTGCATGGT	59.721	52.381	0.00	0.00	0.00	3.55
910	1171	2.872858	GTTATCCATCGGTGCTCCTTTC	59.127	50.000	2.85	0.00	0.00	2.62
941	1224	2.357517	CGTGGCTCCTGCTTCGTT	60.358	61.111	0.00	0.00	39.59	3.85
995	1303	1.303799	ACGTGCGTGTATCCGAGACT	61.304	55.000	0.00	0.00	0.00	3.24
1013	1321	5.526115	TCGGGTTCAATATCATAAGACGAC	58.474	41.667	0.00	0.00	0.00	4.34
1500	1832	0.788391	GATTTCGTCGCCAAACTCGT	59.212	50.000	0.00	0.00	0.00	4.18
1595	1927	3.519579	CATGGATGATATCAGAGGCGAC	58.480	50.000	11.78	0.00	0.00	5.19
1643	1977	0.824109	ACATCATCGTCGTGGATGGT	59.176	50.000	22.99	8.08	43.18	3.55
1883	2217	2.564062	CCTCCACATCCTGTGCAAATTT	59.436	45.455	1.71	0.00	46.51	1.82
1884	2218	2.173519	CCTCCACATCCTGTGCAAATT	58.826	47.619	1.71	0.00	46.51	1.82
1885	2219	1.076024	ACCTCCACATCCTGTGCAAAT	59.924	47.619	1.71	0.00	46.51	2.32
1886	2220	0.478072	ACCTCCACATCCTGTGCAAA	59.522	50.000	1.71	0.00	46.51	3.68
1887	2221	0.478072	AACCTCCACATCCTGTGCAA	59.522	50.000	1.71	0.00	46.51	4.08
2330	2681	3.198635	TCTCTCCAATCTTCTTGCGGAAT	59.801	43.478	0.00	0.00	33.01	3.01
2687	3039	1.085893	TGTGTGCATCGCTTGGTATG	58.914	50.000	0.00	0.00	0.00	2.39
2851	3213	4.440250	GGTGACTGTATGAGCATCTACGTT	60.440	45.833	0.00	0.00	34.92	3.99
2981	3355	7.625395	GCATCGATTACACCATTTGTTCTTGTA	60.625	37.037	0.00	0.00	39.91	2.41
2999	3373	6.481313	TGTACGTAGACTACTAAGCATCGATT	59.519	38.462	10.82	0.00	32.78	3.34
3506	3883	2.284625	TCCTCCACCGTGCAGGAT	60.285	61.111	7.14	0.00	45.00	3.24
3513	3890	2.923035	CACCACCTCCTCCACCGT	60.923	66.667	0.00	0.00	0.00	4.83
3529	3906	2.659063	CCGCCTCCTGTCATCACCA	61.659	63.158	0.00	0.00	0.00	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.