AutoCloner

Multiple sequence alignment - TraesCS7D01G292200

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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	TraesCS7D01G292200	chr7D	100.000	2993	0	0	1	2993	355104067	355101075	0.000000e+00	5528
1	TraesCS7D01G292200	chr4D	84.035	2875	379	62	171	2993	163413981	163411135	0.000000e+00	2693
2	TraesCS7D01G292200	chr4B	84.888	2713	359	42	211	2888	376027700	376030396	0.000000e+00	2691
3	TraesCS7D01G292200	chr4B	83.357	2764	387	54	172	2888	230486571	230483834	0.000000e+00	2488
4	TraesCS7D01G292200	chr4B	80.995	442	47	23	1	410	451473084	451473520	1.730000e-82	316
5	TraesCS7D01G292200	chr2A	84.759	2677	332	47	253	2888	82414750	82412109	0.000000e+00	2614
6	TraesCS7D01G292200	chr2A	83.233	2827	411	52	107	2888	266908703	266905895	0.000000e+00	2536
7	TraesCS7D01G292200	chr2A	83.391	2312	336	36	258	2550	140707520	140709802	0.000000e+00	2098
8	TraesCS7D01G292200	chr2A	82.678	1628	248	26	194	1801	187018616	187020229	0.000000e+00	1413
9	TraesCS7D01G292200	chr2A	81.318	1654	259	37	167	1801	267980184	267981806	0.000000e+00	1297
10	TraesCS7D01G292200	chr2A	85.049	1224	152	23	1789	2991	100898509	100897296	0.000000e+00	1218
11	TraesCS7D01G292200	chr2A	82.934	1295	173	41	1728	2993	267981769	267983044	0.000000e+00	1123
12	TraesCS7D01G292200	chr2A	81.522	1288	182	35	1721	2976	679107326	679106063	0.000000e+00	1009
13	TraesCS7D01G292200	chr2A	82.521	1190	155	37	1728	2888	343445226	343444061	0.000000e+00	996
14	TraesCS7D01G292200	chr2A	79.831	1304	187	44	1728	2993	187020192	187021457	0.000000e+00	881
15	TraesCS7D01G292200	chr2A	88.264	409	40	2	2593	2993	743379343	743379751	1.610000e-132	483
16	TraesCS7D01G292200	chr2A	84.348	230	19	9	2594	2810	586826747	586826972	3.020000e-50	209
17	TraesCS7D01G292200	chr3D	83.285	2776	377	50	122	2855	402309401	402306671	0.000000e+00	2475
18	TraesCS7D01G292200	chr3D	82.620	2802	358	66	278	2993	226750825	226748067	0.000000e+00	2357
19	TraesCS7D01G292200	chr3D	95.238	168	8	0	1	168	226751020	226750853	1.770000e-67	267
20	TraesCS7D01G292200	chr3D	94.643	168	9	0	1	168	226746700	226746533	8.230000e-66	261
21	TraesCS7D01G292200	chr3D	96.053	152	6	0	1	152	251248147	251248298	6.410000e-62	248
22	TraesCS7D01G292200	chr3D	95.395	152	7	0	1	152	251242042	251242193	2.980000e-60	243
23	TraesCS7D01G292200	chr2D	85.733	2334	296	31	167	2478	323249180	323246862	0.000000e+00	2431
24	TraesCS7D01G292200	chr1A	82.989	2757	402	53	279	2993	313569746	313567015	0.000000e+00	2431
25	TraesCS7D01G292200	chrUn	82.882	2401	341	57	465	2830	78705223	78702858	0.000000e+00	2093
26	TraesCS7D01G292200	chrUn	83.702	1221	159	28	1796	2993	387048069	387049272	0.000000e+00	1116
27	TraesCS7D01G292200	chrUn	83.470	1222	161	28	1796	2993	358289014	358290218	0.000000e+00	1099
28	TraesCS7D01G292200	chr3B	81.734	1845	261	51	1	1801	565179372	565181184	0.000000e+00	1471
29	TraesCS7D01G292200	chr3B	80.876	434	50	19	1	404	560060786	560060356	8.060000e-81	311
30	TraesCS7D01G292200	chr3B	80.682	352	40	16	1	327	560056327	560055979	6.410000e-62	248
31	TraesCS7D01G292200	chr6D	83.281	1280	164	27	1728	2993	384977218	384978461	0.000000e+00	1133
32	TraesCS7D01G292200	chr2B	83.702	1221	159	28	1796	2993	115617802	115616599	0.000000e+00	1116
33	TraesCS7D01G292200	chr2B	83.620	1221	160	28	1796	2993	115608945	115607742	0.000000e+00	1110
34	TraesCS7D01G292200	chr2B	83.470	1222	161	28	1796	2993	115613357	115612153	0.000000e+00	1099
35	TraesCS7D01G292200	chr2B	82.043	1214	168	33	1809	2993	272452068	272453260	0.000000e+00	989
36	TraesCS7D01G292200	chr2B	83.658	1028	110	31	2013	2993	268755396	268756412	0.000000e+00	915
37	TraesCS7D01G292200	chr7B	81.105	344	37	16	1	319	161602729	161603069	1.780000e-62	250

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	TraesCS7D01G292200	chr7D	355101075	355104067	2992	True	5528.000000	5528	100.000000	1	2993	1	chr7D.!!$R1	2992
1	TraesCS7D01G292200	chr4D	163411135	163413981	2846	True	2693.000000	2693	84.035000	171	2993	1	chr4D.!!$R1	2822
2	TraesCS7D01G292200	chr4B	376027700	376030396	2696	False	2691.000000	2691	84.888000	211	2888	1	chr4B.!!$F1	2677
3	TraesCS7D01G292200	chr4B	230483834	230486571	2737	True	2488.000000	2488	83.357000	172	2888	1	chr4B.!!$R1	2716
4	TraesCS7D01G292200	chr2A	82412109	82414750	2641	True	2614.000000	2614	84.759000	253	2888	1	chr2A.!!$R1	2635
5	TraesCS7D01G292200	chr2A	266905895	266908703	2808	True	2536.000000	2536	83.233000	107	2888	1	chr2A.!!$R3	2781
6	TraesCS7D01G292200	chr2A	140707520	140709802	2282	False	2098.000000	2098	83.391000	258	2550	1	chr2A.!!$F1	2292
7	TraesCS7D01G292200	chr2A	100897296	100898509	1213	True	1218.000000	1218	85.049000	1789	2991	1	chr2A.!!$R2	1202
8	TraesCS7D01G292200	chr2A	267980184	267983044	2860	False	1210.000000	1297	82.126000	167	2993	2	chr2A.!!$F5	2826
9	TraesCS7D01G292200	chr2A	187018616	187021457	2841	False	1147.000000	1413	81.254500	194	2993	2	chr2A.!!$F4	2799
10	TraesCS7D01G292200	chr2A	679106063	679107326	1263	True	1009.000000	1009	81.522000	1721	2976	1	chr2A.!!$R5	1255
11	TraesCS7D01G292200	chr2A	343444061	343445226	1165	True	996.000000	996	82.521000	1728	2888	1	chr2A.!!$R4	1160
12	TraesCS7D01G292200	chr3D	402306671	402309401	2730	True	2475.000000	2475	83.285000	122	2855	1	chr3D.!!$R1	2733
13	TraesCS7D01G292200	chr3D	226746533	226751020	4487	True	961.666667	2357	90.833667	1	2993	3	chr3D.!!$R2	2992
14	TraesCS7D01G292200	chr2D	323246862	323249180	2318	True	2431.000000	2431	85.733000	167	2478	1	chr2D.!!$R1	2311
15	TraesCS7D01G292200	chr1A	313567015	313569746	2731	True	2431.000000	2431	82.989000	279	2993	1	chr1A.!!$R1	2714
16	TraesCS7D01G292200	chrUn	78702858	78705223	2365	True	2093.000000	2093	82.882000	465	2830	1	chrUn.!!$R1	2365
17	TraesCS7D01G292200	chrUn	387048069	387049272	1203	False	1116.000000	1116	83.702000	1796	2993	1	chrUn.!!$F2	1197
18	TraesCS7D01G292200	chrUn	358289014	358290218	1204	False	1099.000000	1099	83.470000	1796	2993	1	chrUn.!!$F1	1197
19	TraesCS7D01G292200	chr3B	565179372	565181184	1812	False	1471.000000	1471	81.734000	1	1801	1	chr3B.!!$F1	1800
20	TraesCS7D01G292200	chr6D	384977218	384978461	1243	False	1133.000000	1133	83.281000	1728	2993	1	chr6D.!!$F1	1265
21	TraesCS7D01G292200	chr2B	115607742	115617802	10060	True	1108.333333	1116	83.597333	1796	2993	3	chr2B.!!$R1	1197
22	TraesCS7D01G292200	chr2B	272452068	272453260	1192	False	989.000000	989	82.043000	1809	2993	1	chr2B.!!$F2	1184
23	TraesCS7D01G292200	chr2B	268755396	268756412	1016	False	915.000000	915	83.658000	2013	2993	1	chr2B.!!$F1	980

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
844	922	0.618458	TTACTCACATGGGTGGCCTC	59.382	55.000	3.32	0.0	45.32	4.7	F
1041	1119	1.075536	GGTCCTCCATTTGGTCAACCT	59.924	52.381	0.10	0.0	36.82	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1764	1937	0.036105	TGATCTCAACGCTGGCATGT	60.036	50.0	0.0	0.0	0.0	3.21	R
2624	2882	1.305219	ACCCGATTTCACATGGCACG	61.305	55.0	0.0	0.0	0.0	5.34	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
33	34	7.667043	TGTAAACCATCTACATTGTGTCTTC	57.333	36.000	0.00	0.00	0.00	2.87
99	100	3.813166	TGTTCACTTCCCTTTTGTCGATC	59.187	43.478	0.00	0.00	0.00	3.69
104	105	4.216257	CACTTCCCTTTTGTCGATCATGTT	59.784	41.667	0.00	0.00	0.00	2.71
182	213	8.807667	AGTAAAATCTGCATTTTCTTTGTCTG	57.192	30.769	1.38	0.00	40.69	3.51
183	214	8.632679	AGTAAAATCTGCATTTTCTTTGTCTGA	58.367	29.630	1.38	0.00	40.69	3.27
184	215	9.248291	GTAAAATCTGCATTTTCTTTGTCTGAA	57.752	29.630	1.38	0.00	40.69	3.02
186	217	5.833406	TCTGCATTTTCTTTGTCTGAACA	57.167	34.783	0.00	0.00	0.00	3.18
197	228	9.528018	TTTCTTTGTCTGAACATTTTATGGAAC	57.472	29.630	0.00	0.00	34.73	3.62
290	327	1.972660	ATTGCTGTCGCCTAGTCCCC	61.973	60.000	0.00	0.00	34.43	4.81
322	362	1.210931	CACTGCAGATTTGGGCGTG	59.789	57.895	23.35	1.01	0.00	5.34
328	374	2.262211	GCAGATTTGGGCGTGAAAATC	58.738	47.619	9.44	9.44	41.20	2.17
404	450	7.916914	TTTTGTTTGGCTATAGACTAGGTTC	57.083	36.000	7.23	0.00	0.00	3.62
406	452	7.966339	TTGTTTGGCTATAGACTAGGTTCTA	57.034	36.000	7.23	0.00	32.56	2.10
525	578	5.726980	TGAATTGTCTTCTTGGAAATGGG	57.273	39.130	0.00	0.00	0.00	4.00
552	605	7.536159	TCTACTCAGATCATCATGCTTATGT	57.464	36.000	0.00	0.00	0.00	2.29
572	625	4.264253	TGTGAGCAATAGCACAAATAGCT	58.736	39.130	0.00	0.00	42.92	3.32
581	634	6.674694	ATAGCACAAATAGCTCAGAAAGTG	57.325	37.500	0.00	0.00	42.32	3.16
679	732	6.673839	AGGCCTAGTTCTTATGATCCTTAC	57.326	41.667	1.29	0.00	0.00	2.34
680	757	5.544562	AGGCCTAGTTCTTATGATCCTTACC	59.455	44.000	1.29	0.00	0.00	2.85
687	764	7.597327	AGTTCTTATGATCCTTACCCTAGAGT	58.403	38.462	0.00	0.00	0.00	3.24
737	815	6.351711	CCATATTTGTGGTTTTCAGGCCATTA	60.352	38.462	5.01	0.00	37.09	1.90
739	817	5.359194	TTTGTGGTTTTCAGGCCATTAAA	57.641	34.783	5.01	0.00	37.09	1.52
796	874	3.575256	AGATTGTTTTGGCATGAGCTTCA	59.425	39.130	0.00	0.00	41.70	3.02
844	922	0.618458	TTACTCACATGGGTGGCCTC	59.382	55.000	3.32	0.00	45.32	4.70
865	943	7.014615	GGCCTCAAAACCAGAATATGTCATATT	59.985	37.037	16.40	16.40	38.12	1.28
903	981	4.837972	AGGTCTCACCATTTTCTTCTAGC	58.162	43.478	0.00	0.00	41.95	3.42
904	982	3.942115	GGTCTCACCATTTTCTTCTAGCC	59.058	47.826	0.00	0.00	38.42	3.93
934	1012	4.227300	TGCAGGGAATTAGGTACAATGAGT	59.773	41.667	0.00	0.00	0.00	3.41
993	1071	6.040955	CAGCTCCTACTCATATACCTCAACAA	59.959	42.308	0.00	0.00	0.00	2.83
1041	1119	1.075536	GGTCCTCCATTTGGTCAACCT	59.924	52.381	0.10	0.00	36.82	3.50
1054	1153	3.942748	TGGTCAACCTACAACTTCAACAC	59.057	43.478	0.10	0.00	36.82	3.32
1055	1154	3.314357	GGTCAACCTACAACTTCAACACC	59.686	47.826	0.00	0.00	0.00	4.16
1056	1155	3.314357	GTCAACCTACAACTTCAACACCC	59.686	47.826	0.00	0.00	0.00	4.61
1057	1156	2.249844	ACCTACAACTTCAACACCCG	57.750	50.000	0.00	0.00	0.00	5.28
1058	1157	1.487558	ACCTACAACTTCAACACCCGT	59.512	47.619	0.00	0.00	0.00	5.28
1059	1158	2.092807	ACCTACAACTTCAACACCCGTT	60.093	45.455	0.00	0.00	35.01	4.44
1069	1168	2.474410	AACACCCGTTGAGGAATCTC	57.526	50.000	0.00	0.00	45.00	2.75
1119	1218	8.862325	AGTTCGATGATATAGAGAAGATCACT	57.138	34.615	0.00	0.00	32.62	3.41
1134	1233	6.365970	AAGATCACTCTTCTTAGCCTTGAA	57.634	37.500	0.00	0.00	37.09	2.69
1148	1247	2.229784	GCCTTGAATTCACTTGGAGTGG	59.770	50.000	19.59	9.26	45.94	4.00
1185	1284	8.902806	CCTATTAGGAAGCTGATACTAGATGAG	58.097	40.741	3.41	0.00	37.67	2.90
1236	1335	6.097696	AGCTAGTGGAAGAAGTAAGGAAGATC	59.902	42.308	0.00	0.00	0.00	2.75
1252	1351	7.841282	AGGAAGATCGAGAGGAACATTAATA	57.159	36.000	0.00	0.00	0.00	0.98
1267	1366	8.368668	GGAACATTAATACTGGCAGTACTATCT	58.631	37.037	28.40	10.60	32.84	1.98
1268	1367	9.413048	GAACATTAATACTGGCAGTACTATCTC	57.587	37.037	28.40	15.05	32.84	2.75
1269	1368	8.478775	ACATTAATACTGGCAGTACTATCTCA	57.521	34.615	28.40	8.48	32.84	3.27
1339	1442	3.383185	GGTTCCAACACCTTCACATTCAA	59.617	43.478	0.00	0.00	33.50	2.69
1489	1592	6.415206	TCTCTCCCGAAGAAGTAAAAGAAA	57.585	37.500	0.00	0.00	32.23	2.52
1517	1620	6.481644	GCTATAGATGAACTTGAAGAACCAGG	59.518	42.308	3.21	0.00	0.00	4.45
1668	1771	9.346725	GACTTGAAAAATTATTTGCTAGGACAG	57.653	33.333	0.00	0.00	32.91	3.51
1707	1810	3.308438	AGTGGCATTTCTCACATTTGC	57.692	42.857	0.00	0.00	36.43	3.68
1711	1848	5.186409	AGTGGCATTTCTCACATTTGCTATT	59.814	36.000	0.00	0.00	36.43	1.73
1717	1854	7.112565	GCATTTCTCACATTTGCTATTATGACG	59.887	37.037	0.00	0.00	0.00	4.35
1738	1911	3.616076	CGCTTATTCTCCCCATGCTAGAG	60.616	52.174	0.00	0.00	0.00	2.43
1754	1927	8.790718	CCATGCTAGAGTTATGCTTAATGAAAT	58.209	33.333	0.00	0.00	0.00	2.17
1780	1953	1.672030	CCACATGCCAGCGTTGAGA	60.672	57.895	0.00	0.00	0.00	3.27
1782	1955	0.376152	CACATGCCAGCGTTGAGATC	59.624	55.000	0.00	0.00	0.00	2.75
1786	1959	1.825090	TGCCAGCGTTGAGATCATTT	58.175	45.000	0.00	0.00	0.00	2.32
1791	1964	4.035558	GCCAGCGTTGAGATCATTTATTCA	59.964	41.667	0.00	0.00	0.00	2.57
1879	2053	5.224821	GGGTATTATCCCTACCACTTGTC	57.775	47.826	2.25	0.00	43.85	3.18
1895	2069	5.106157	CCACTTGTCTTGTCTCTTTTGTTGT	60.106	40.000	0.00	0.00	0.00	3.32
1896	2070	6.093495	CCACTTGTCTTGTCTCTTTTGTTGTA	59.907	38.462	0.00	0.00	0.00	2.41
1904	2078	6.072112	TGTCTCTTTTGTTGTATGCCTTTC	57.928	37.500	0.00	0.00	0.00	2.62
1988	2162	1.071471	CCGGTGGAGTCAAAGCACT	59.929	57.895	0.00	0.00	0.00	4.40
2008	2183	3.008813	ACTGTGATGAGGAGAAGCAATGT	59.991	43.478	0.00	0.00	0.00	2.71
2044	2222	2.105477	AGAGAGAAGTTGGAGCTTGCAA	59.895	45.455	0.00	0.00	0.00	4.08
2052	2236	0.473755	TGGAGCTTGCAAGTGGAAGA	59.526	50.000	26.55	4.81	44.86	2.87
2068	2265	5.308237	AGTGGAAGAAAAAGGAGAAGAGCTA	59.692	40.000	0.00	0.00	0.00	3.32
2069	2266	5.998363	GTGGAAGAAAAAGGAGAAGAGCTAA	59.002	40.000	0.00	0.00	0.00	3.09
2085	2291	8.811994	AGAAGAGCTAAAGTTTAGAGAGTGATT	58.188	33.333	23.89	9.24	0.00	2.57
2087	2293	7.902087	AGAGCTAAAGTTTAGAGAGTGATTGT	58.098	34.615	23.89	0.00	0.00	2.71
2111	2319	5.715279	TGCGAGACCTACATAATATAAGCCT	59.285	40.000	0.00	0.00	0.00	4.58
2148	2359	3.181455	TGACCCCAATCTGAATACCATCG	60.181	47.826	0.00	0.00	0.00	3.84
2149	2360	2.106511	ACCCCAATCTGAATACCATCGG	59.893	50.000	0.00	0.00	0.00	4.18
2186	2398	6.476706	GCTGTAATCAATTGCTATTTGGGTTC	59.523	38.462	0.00	0.00	0.00	3.62
2223	2439	7.432869	TCTTAAATGTTGTCCCACTGAATTTG	58.567	34.615	0.00	0.00	0.00	2.32
2254	2476	6.260714	TGACATATGGTGCTTGATGTGAATAC	59.739	38.462	7.80	0.00	32.75	1.89
2326	2548	3.057946	GCTTTGCTGAAAGTAGTGAAGGG	60.058	47.826	0.00	0.00	40.77	3.95
2366	2588	6.981559	GCTCAAATCCCTAGTACACTAGAAAG	59.018	42.308	16.34	6.41	46.80	2.62
2483	2708	1.417890	ACCACTATGGACTAGCATGCC	59.582	52.381	15.66	0.00	40.96	4.40
2502	2727	1.202651	CCATGTTCCCTGGATCGGTAC	60.203	57.143	0.00	0.00	35.70	3.34
2624	2882	2.579873	CATGTCATGTTCCCTGGATCC	58.420	52.381	4.20	4.20	0.00	3.36
2628	2886	1.097547	CATGTTCCCTGGATCCGTGC	61.098	60.000	7.39	0.00	0.00	5.34
2648	2906	1.676006	CCATGTGAAATCGGGTTAGCC	59.324	52.381	0.00	0.00	0.00	3.93
2799	7545	0.750850	CGGGATCGGTGGTATGTTCT	59.249	55.000	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	9.604626	GAAGAAACAAGATTAGAAGACACAATG	57.395	33.333	0.00	0.00	0.00	2.82
33	34	9.658799	TGTAAGAGATGGAAGAAACAAGATTAG	57.341	33.333	0.00	0.00	0.00	1.73
182	213	8.742554	AACGAAGATTGTTCCATAAAATGTTC	57.257	30.769	0.00	0.00	32.89	3.18
183	214	9.840427	CTAACGAAGATTGTTCCATAAAATGTT	57.160	29.630	0.00	0.00	0.00	2.71
184	215	9.010029	ACTAACGAAGATTGTTCCATAAAATGT	57.990	29.630	0.00	0.00	0.00	2.71
186	217	9.449719	AGACTAACGAAGATTGTTCCATAAAAT	57.550	29.630	0.00	0.00	0.00	1.82
204	235	7.644490	AGCAGACAATTAGATCTAGACTAACG	58.356	38.462	13.54	11.27	33.58	3.18
223	255	8.830201	ACAGAATTTAGATGATGATAGCAGAC	57.170	34.615	0.00	0.00	0.00	3.51
296	333	1.136529	CAAATCTGCAGTGTCGTGTCG	60.137	52.381	14.67	0.00	0.00	4.35
297	334	1.195448	CCAAATCTGCAGTGTCGTGTC	59.805	52.381	14.67	0.00	0.00	3.67
387	433	6.670617	ACAAGTAGAACCTAGTCTATAGCCA	58.329	40.000	0.00	0.00	32.81	4.75
404	450	5.499139	TGGCACAAAGAGAAAACAAGTAG	57.501	39.130	0.00	0.00	31.92	2.57
491	544	7.839680	AGAAGACAATTCAACCTACCAAATT	57.160	32.000	0.00	0.00	0.00	1.82
525	578	9.089601	CATAAGCATGATGATCTGAGTAGAATC	57.910	37.037	0.00	0.00	33.47	2.52
559	612	5.551233	ACACTTTCTGAGCTATTTGTGCTA	58.449	37.500	0.00	0.00	41.30	3.49
561	614	4.756084	ACACTTTCTGAGCTATTTGTGC	57.244	40.909	0.00	0.00	0.00	4.57
562	615	6.304356	TGAACACTTTCTGAGCTATTTGTG	57.696	37.500	0.00	0.00	32.36	3.33
572	625	4.753516	TCAGGTCTTGAACACTTTCTGA	57.246	40.909	0.00	0.00	31.34	3.27
581	634	8.884726	GGAAATCTTACTTATCAGGTCTTGAAC	58.115	37.037	0.00	0.00	39.77	3.18
679	732	4.503991	GCAACATAAGGATGGACTCTAGGG	60.504	50.000	0.00	0.00	37.39	3.53
680	757	4.346418	AGCAACATAAGGATGGACTCTAGG	59.654	45.833	0.00	0.00	37.39	3.02
687	764	4.037222	TGTAGGAGCAACATAAGGATGGA	58.963	43.478	0.00	0.00	37.39	3.41
796	874	5.420725	TGGTATGAGCTATGTTGTTGAGT	57.579	39.130	0.00	0.00	0.00	3.41
844	922	9.520204	GTTCCAATATGACATATTCTGGTTTTG	57.480	33.333	16.26	6.08	33.34	2.44
865	943	0.923358	ACCTCAGGGTTGTTGTTCCA	59.077	50.000	0.00	0.00	44.73	3.53
903	981	4.927049	ACCTAATTCCCTGCATATGATGG	58.073	43.478	6.97	7.15	0.00	3.51
904	982	6.475504	TGTACCTAATTCCCTGCATATGATG	58.524	40.000	6.97	0.00	0.00	3.07
934	1012	1.066502	TGGCGCATAGTTGTTGCTCTA	60.067	47.619	10.83	0.00	37.96	2.43
951	1029	4.627035	GGAGCTGAATAAAATTGTTGTGGC	59.373	41.667	0.00	0.00	0.00	5.01
993	1071	2.238144	CTCCATTGGACACATCTCCTGT	59.762	50.000	0.00	0.00	39.20	4.00
1057	1156	7.823647	GCACTTGCACATGAGATTCCTCAAC	62.824	48.000	0.00	0.00	45.53	3.18
1058	1157	5.871477	GCACTTGCACATGAGATTCCTCAA	61.871	45.833	0.00	0.00	45.53	3.02
1059	1158	4.424792	GCACTTGCACATGAGATTCCTCA	61.425	47.826	0.00	0.00	45.99	3.86
1060	1159	2.097142	GCACTTGCACATGAGATTCCTC	59.903	50.000	0.00	0.00	41.59	3.71
1061	1160	2.089980	GCACTTGCACATGAGATTCCT	58.910	47.619	0.00	0.00	41.59	3.36
1062	1161	1.133790	GGCACTTGCACATGAGATTCC	59.866	52.381	0.00	0.00	44.36	3.01
1063	1162	1.133790	GGGCACTTGCACATGAGATTC	59.866	52.381	0.00	0.00	45.57	2.52
1064	1163	1.180029	GGGCACTTGCACATGAGATT	58.820	50.000	0.00	0.00	45.57	2.40
1065	1164	2.877975	GGGCACTTGCACATGAGAT	58.122	52.632	0.00	0.00	45.57	2.75
1066	1165	4.402851	GGGCACTTGCACATGAGA	57.597	55.556	0.00	0.00	45.57	3.27
1072	1171	0.108424	TTTTGTGTGGGCACTTGCAC	60.108	50.000	3.15	0.00	45.44	4.57
1073	1172	0.829333	ATTTTGTGTGGGCACTTGCA	59.171	45.000	3.15	0.00	45.44	4.08
1074	1173	1.202510	TCATTTTGTGTGGGCACTTGC	60.203	47.619	0.00	0.00	45.44	4.01
1114	1213	6.597280	GTGAATTCAAGGCTAAGAAGAGTGAT	59.403	38.462	10.35	0.00	0.00	3.06
1119	1218	5.707298	CCAAGTGAATTCAAGGCTAAGAAGA	59.293	40.000	10.35	0.00	0.00	2.87
1148	1247	4.679372	GCTTCCTAATAGGATCATCCTCGC	60.679	50.000	10.40	0.00	45.66	5.03
1185	1284	8.043710	TCCTTTCCACTCTTAATCTTCTTCATC	58.956	37.037	0.00	0.00	0.00	2.92
1236	1335	4.693283	TGCCAGTATTAATGTTCCTCTCG	58.307	43.478	0.00	0.00	0.00	4.04
1252	1351	4.281657	TGTGATGAGATAGTACTGCCAGT	58.718	43.478	5.39	1.54	0.00	4.00
1339	1442	3.699038	GGACTCTCACTATCTTGCTCAGT	59.301	47.826	0.00	0.00	0.00	3.41
1391	1494	6.016276	GTCTTGTTCCTTGGCTTTGAGAATTA	60.016	38.462	0.00	0.00	0.00	1.40
1399	1502	2.341846	TCGTCTTGTTCCTTGGCTTT	57.658	45.000	0.00	0.00	0.00	3.51
1489	1592	7.044798	GGTTCTTCAAGTTCATCTATAGCAGT	58.955	38.462	0.00	0.00	0.00	4.40
1517	1620	9.241317	CTTGTATGACAATAGGCAAATGAATTC	57.759	33.333	0.00	0.00	37.48	2.17
1662	1765	4.163427	CAGGGTATGTATGATCCTGTCCT	58.837	47.826	0.00	0.00	39.90	3.85
1668	1771	5.794894	CCACTAACAGGGTATGTATGATCC	58.205	45.833	0.00	0.00	43.00	3.36
1707	1810	6.037786	TGGGGAGAATAAGCGTCATAATAG	57.962	41.667	0.00	0.00	0.00	1.73
1711	1848	3.557054	GCATGGGGAGAATAAGCGTCATA	60.557	47.826	0.00	0.00	0.00	2.15
1717	1854	3.326297	ACTCTAGCATGGGGAGAATAAGC	59.674	47.826	0.00	0.00	0.00	3.09
1754	1927	2.302733	ACGCTGGCATGTGGATGATATA	59.697	45.455	0.00	0.00	0.00	0.86
1764	1937	0.036105	TGATCTCAACGCTGGCATGT	60.036	50.000	0.00	0.00	0.00	3.21
1786	1959	9.797642	AAGCACATGTTTAGGATGATATGAATA	57.202	29.630	0.00	0.00	0.00	1.75
1837	2011	3.193263	CCTCCAAGTCATCAATCGAGTG	58.807	50.000	6.51	6.51	0.00	3.51
1879	2053	5.695851	AGGCATACAACAAAAGAGACAAG	57.304	39.130	0.00	0.00	0.00	3.16
1895	2069	3.238597	AGCAAAAACCTGGAAAGGCATA	58.761	40.909	0.00	0.00	0.00	3.14
1896	2070	2.049372	AGCAAAAACCTGGAAAGGCAT	58.951	42.857	0.00	0.00	0.00	4.40
1988	2162	3.340928	CACATTGCTTCTCCTCATCACA	58.659	45.455	0.00	0.00	0.00	3.58
2008	2183	5.658634	ACTTCTCTCTTCTATATGTGTGCCA	59.341	40.000	0.00	0.00	0.00	4.92
2044	2222	4.103943	AGCTCTTCTCCTTTTTCTTCCACT	59.896	41.667	0.00	0.00	0.00	4.00
2052	2236	9.278978	CTCTAAACTTTAGCTCTTCTCCTTTTT	57.721	33.333	3.91	0.00	0.00	1.94
2068	2265	5.297547	TCGCACAATCACTCTCTAAACTTT	58.702	37.500	0.00	0.00	0.00	2.66
2069	2266	4.883083	TCGCACAATCACTCTCTAAACTT	58.117	39.130	0.00	0.00	0.00	2.66
2085	2291	6.387465	GCTTATATTATGTAGGTCTCGCACA	58.613	40.000	0.00	0.00	0.00	4.57
2087	2293	5.715279	AGGCTTATATTATGTAGGTCTCGCA	59.285	40.000	0.00	0.00	0.00	5.10
2111	2319	2.092429	GGGGTCATGAAATAGCTCACCA	60.092	50.000	0.00	0.00	0.00	4.17
2186	2398	6.458210	ACAACATTTAAGAATTGGCTCAAGG	58.542	36.000	0.00	0.00	0.00	3.61
2196	2412	7.781324	ATTCAGTGGGACAACATTTAAGAAT	57.219	32.000	0.00	0.00	44.16	2.40
2223	2439	4.009675	TCAAGCACCATATGTCAAAGGTC	58.990	43.478	1.24	0.00	30.44	3.85
2254	2476	4.487948	AGGCATTCAACAATCAATTCACG	58.512	39.130	0.00	0.00	0.00	4.35
2366	2588	8.650714	CAAGGTAAAAGCAGAAAATGATTAAGC	58.349	33.333	0.00	0.00	36.22	3.09
2414	2637	7.012704	CACATTAGGCACAAACTAAGCATCTAT	59.987	37.037	0.00	0.00	34.25	1.98
2423	2646	4.076394	GGGAACACATTAGGCACAAACTA	58.924	43.478	0.00	0.00	0.00	2.24
2483	2708	1.762957	AGTACCGATCCAGGGAACATG	59.237	52.381	0.00	0.00	35.02	3.21
2502	2727	5.089970	TCATCCAGGTCTTGTTCACATAG	57.910	43.478	0.00	0.00	0.00	2.23
2598	2856	3.134623	CCAGGGAACATGACATGCTACTA	59.865	47.826	15.49	0.00	0.00	1.82
2624	2882	1.305219	ACCCGATTTCACATGGCACG	61.305	55.000	0.00	0.00	0.00	5.34
2628	2886	1.676006	GGCTAACCCGATTTCACATGG	59.324	52.381	0.00	0.00	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.