AutoCloner

Multiple sequence alignment - TraesCS2D01G024000

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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	TraesCS2D01G024000	chr2D	100.000	1525	0	0	1	1525	10746195	10747719	0.000000e+00	2817
1	TraesCS2D01G024000	chr2D	100.000	418	0	0	1886	2303	10748080	10748497	0.000000e+00	773
2	TraesCS2D01G024000	chr2D	78.600	1014	186	17	1	988	622369658	622368650	1.930000e-180	641
3	TraesCS2D01G024000	chr2D	80.753	478	62	16	877	1325	352197348	352197824	1.690000e-91	346
4	TraesCS2D01G024000	chr2D	85.833	120	15	2	2179	2297	618253417	618253535	2.400000e-25	126
5	TraesCS2D01G024000	chr1D	83.911	1386	158	25	3	1328	286395874	286397254	0.000000e+00	1264
6	TraesCS2D01G024000	chr1D	83.235	340	54	3	989	1326	159952301	159952639	2.220000e-80	309
7	TraesCS2D01G024000	chr1D	87.805	123	15	0	2181	2303	426593483	426593361	6.630000e-31	145
8	TraesCS2D01G024000	chr1D	86.290	124	16	1	2181	2303	484543934	484544057	1.440000e-27	134
9	TraesCS2D01G024000	chr6B	83.829	1379	162	26	3	1328	331069925	331068555	0.000000e+00	1254
10	TraesCS2D01G024000	chr3A	83.024	1349	185	29	3	1317	464916090	464917428	0.000000e+00	1182
11	TraesCS2D01G024000	chr3A	80.473	1014	167	21	1	988	100036002	100034994	0.000000e+00	747
12	TraesCS2D01G024000	chr7D	82.847	1370	173	30	3	1317	472803826	472802464	0.000000e+00	1171
13	TraesCS2D01G024000	chr7D	81.758	1365	197	30	3	1327	509254647	509253295	0.000000e+00	1094
14	TraesCS2D01G024000	chr3D	85.771	1012	119	10	3	992	339845401	339844393	0.000000e+00	1048
15	TraesCS2D01G024000	chr3D	80.928	1379	206	26	1	1325	177015459	177014084	0.000000e+00	1037
16	TraesCS2D01G024000	chr3D	83.954	349	51	5	990	1335	213676748	213676402	1.710000e-86	329
17	TraesCS2D01G024000	chr2A	80.845	1373	201	35	2	1322	470230642	470232004	0.000000e+00	1022
18	TraesCS2D01G024000	chr2A	80.380	632	90	12	730	1328	728086597	728085967	1.250000e-122	449
19	TraesCS2D01G024000	chr2A	86.486	407	26	17	1907	2300	11022915	11023305	9.840000e-114	420
20	TraesCS2D01G024000	chr2A	95.939	197	8	0	1329	1525	11015544	11015740	1.030000e-83	320
21	TraesCS2D01G024000	chr6D	78.107	1384	243	35	1	1329	48683486	48682108	0.000000e+00	822
22	TraesCS2D01G024000	chr5D	78.132	1381	243	36	2	1326	117351119	117352496	0.000000e+00	822
23	TraesCS2D01G024000	chr5D	85.039	127	18	1	2178	2303	484305158	484305032	6.680000e-26	128
24	TraesCS2D01G024000	chr5B	80.655	1008	169	13	2	987	543106839	543107842	0.000000e+00	758
25	TraesCS2D01G024000	chr2B	82.570	677	94	14	2	658	361966600	361967272	1.980000e-160	575
26	TraesCS2D01G024000	chr2B	80.064	622	91	15	741	1330	473337796	473338416	4.550000e-117	431
27	TraesCS2D01G024000	chr2B	82.609	437	36	19	1886	2303	14949648	14950063	1.310000e-92	350
28	TraesCS2D01G024000	chr2B	95.960	198	6	2	1329	1525	14949374	14949570	1.030000e-83	320
29	TraesCS2D01G024000	chr2B	94.924	197	5	2	1329	1525	15004671	15004862	1.030000e-78	303
30	TraesCS2D01G024000	chr2B	89.474	152	15	1	2153	2303	15005381	15005532	8.400000e-45	191
31	TraesCS2D01G024000	chr2B	87.402	127	10	5	2180	2303	342588370	342588493	8.580000e-30	141
32	TraesCS2D01G024000	chr7A	77.067	1016	195	33	2	988	224966375	224965369	3.340000e-153	551
33	TraesCS2D01G024000	chr4D	75.937	1014	209	24	2	988	127148104	127149109	2.660000e-134	488
34	TraesCS2D01G024000	chrUn	82.609	437	36	19	1886	2303	303370391	303369976	1.310000e-92	350
35	TraesCS2D01G024000	chrUn	82.460	439	35	20	1886	2303	303432768	303432351	1.690000e-91	346
36	TraesCS2D01G024000	chrUn	95.960	198	6	2	1329	1525	303370665	303370469	1.030000e-83	320
37	TraesCS2D01G024000	chrUn	95.960	198	6	2	1329	1525	303433036	303432840	1.030000e-83	320
38	TraesCS2D01G024000	chrUn	95.960	198	6	2	1329	1525	472151075	472151271	1.030000e-83	320
39	TraesCS2D01G024000	chr4B	86.614	127	14	3	2178	2303	590011370	590011494	1.110000e-28	137
40	TraesCS2D01G024000	chr7B	85.039	127	18	1	2178	2303	609741340	609741466	6.680000e-26	128
41	TraesCS2D01G024000	chr4A	85.039	127	13	5	2181	2303	612082800	612082676	8.640000e-25	124

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	TraesCS2D01G024000	chr2D	10746195	10748497	2302	False	1795	2817	100.0000	1	2303	2	chr2D.!!$F3	2302
1	TraesCS2D01G024000	chr2D	622368650	622369658	1008	True	641	641	78.6000	1	988	1	chr2D.!!$R1	987
2	TraesCS2D01G024000	chr1D	286395874	286397254	1380	False	1264	1264	83.9110	3	1328	1	chr1D.!!$F2	1325
3	TraesCS2D01G024000	chr6B	331068555	331069925	1370	True	1254	1254	83.8290	3	1328	1	chr6B.!!$R1	1325
4	TraesCS2D01G024000	chr3A	464916090	464917428	1338	False	1182	1182	83.0240	3	1317	1	chr3A.!!$F1	1314
5	TraesCS2D01G024000	chr3A	100034994	100036002	1008	True	747	747	80.4730	1	988	1	chr3A.!!$R1	987
6	TraesCS2D01G024000	chr7D	472802464	472803826	1362	True	1171	1171	82.8470	3	1317	1	chr7D.!!$R1	1314
7	TraesCS2D01G024000	chr7D	509253295	509254647	1352	True	1094	1094	81.7580	3	1327	1	chr7D.!!$R2	1324
8	TraesCS2D01G024000	chr3D	339844393	339845401	1008	True	1048	1048	85.7710	3	992	1	chr3D.!!$R3	989
9	TraesCS2D01G024000	chr3D	177014084	177015459	1375	True	1037	1037	80.9280	1	1325	1	chr3D.!!$R1	1324
10	TraesCS2D01G024000	chr2A	470230642	470232004	1362	False	1022	1022	80.8450	2	1322	1	chr2A.!!$F3	1320
11	TraesCS2D01G024000	chr2A	728085967	728086597	630	True	449	449	80.3800	730	1328	1	chr2A.!!$R1	598
12	TraesCS2D01G024000	chr6D	48682108	48683486	1378	True	822	822	78.1070	1	1329	1	chr6D.!!$R1	1328
13	TraesCS2D01G024000	chr5D	117351119	117352496	1377	False	822	822	78.1320	2	1326	1	chr5D.!!$F1	1324
14	TraesCS2D01G024000	chr5B	543106839	543107842	1003	False	758	758	80.6550	2	987	1	chr5B.!!$F1	985
15	TraesCS2D01G024000	chr2B	361966600	361967272	672	False	575	575	82.5700	2	658	1	chr2B.!!$F2	656
16	TraesCS2D01G024000	chr2B	473337796	473338416	620	False	431	431	80.0640	741	1330	1	chr2B.!!$F3	589
17	TraesCS2D01G024000	chr2B	14949374	14950063	689	False	335	350	89.2845	1329	2303	2	chr2B.!!$F4	974
18	TraesCS2D01G024000	chr2B	15004671	15005532	861	False	247	303	92.1990	1329	2303	2	chr2B.!!$F5	974
19	TraesCS2D01G024000	chr7A	224965369	224966375	1006	True	551	551	77.0670	2	988	1	chr7A.!!$R1	986
20	TraesCS2D01G024000	chr4D	127148104	127149109	1005	False	488	488	75.9370	2	988	1	chr4D.!!$F1	986
21	TraesCS2D01G024000	chrUn	303369976	303370665	689	True	335	350	89.2845	1329	2303	2	chrUn.!!$R1	974
22	TraesCS2D01G024000	chrUn	303432351	303433036	685	True	333	346	89.2100	1329	2303	2	chrUn.!!$R2	974

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
496	523	0.687354	GTCCCTGTTGCTCTGAAGGA	59.313	55.0	0.0	0.0	30.92	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2116	2237	0.318441	ATAGACAGCGTGTGTGTGCT	59.682	50.0	0.0	0.0	40.56	4.4	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
26	27	1.749258	GGCGAGTGGGGAATGAACC	60.749	63.158	0.00	0.00	0.00	3.62
130	132	7.181305	TGTTAACTTAGGTGGGTGATCTCATTA	59.819	37.037	7.22	0.00	0.00	1.90
173	176	7.918076	TGGGATGAAGACTTAGTTAGACAAAT	58.082	34.615	0.00	0.00	0.00	2.32
219	222	4.142071	CGGATTCTCTCAATTCCACTCTCA	60.142	45.833	0.00	0.00	0.00	3.27
227	230	4.074259	TCAATTCCACTCTCACAACATGG	58.926	43.478	0.00	0.00	0.00	3.66
319	323	2.046604	GGAACCACCAGTACGGCC	60.047	66.667	0.00	0.00	39.03	6.13
345	349	9.612620	CGCAAATTAAAATACTCTAATGGGATC	57.387	33.333	0.00	0.00	0.00	3.36
470	482	2.095364	CGGGTTACGCTCGCTAATAGAT	60.095	50.000	0.00	0.00	32.68	1.98
475	487	7.424001	GGGTTACGCTCGCTAATAGATATATT	58.576	38.462	0.00	0.00	0.00	1.28
482	509	7.493367	GCTCGCTAATAGATATATTTGTCCCT	58.507	38.462	0.00	0.00	0.00	4.20
483	510	7.436673	GCTCGCTAATAGATATATTTGTCCCTG	59.563	40.741	0.00	0.00	0.00	4.45
493	520	2.727123	TTTGTCCCTGTTGCTCTGAA	57.273	45.000	0.00	0.00	0.00	3.02
496	523	0.687354	GTCCCTGTTGCTCTGAAGGA	59.313	55.000	0.00	0.00	30.92	3.36
532	559	3.379372	AGCACATGATGTTCCATTGTAGC	59.621	43.478	0.00	0.00	0.00	3.58
547	576	5.349543	CCATTGTAGCAAAGCAGGAAATTTC	59.650	40.000	9.83	9.83	0.00	2.17
548	577	5.789643	TTGTAGCAAAGCAGGAAATTTCT	57.210	34.783	17.42	1.61	0.00	2.52
564	593	2.717639	TTCTGAAAGGCTAGGGATGC	57.282	50.000	0.00	0.00	0.00	3.91
585	614	9.947669	GGATGCATGATATTATTGATAAAGCTC	57.052	33.333	2.46	0.00	0.00	4.09
633	662	7.179694	AGGCAGTGTTGGAGTACTTATTACTTA	59.820	37.037	0.00	0.00	41.48	2.24
664	694	7.290014	GGACCAAAATTGAGGATAATGGGTTAT	59.710	37.037	3.60	0.00	33.26	1.89
688	718	3.693085	ACAATGTGTGAGAGATGATTGCC	59.307	43.478	0.00	0.00	0.00	4.52
698	728	3.820467	AGAGATGATTGCCGTTTCAACAA	59.180	39.130	0.00	0.00	0.00	2.83
766	796	5.776744	ACTCAAAATGCACTTCAGATTTCC	58.223	37.500	0.00	0.00	0.00	3.13
838	882	2.032620	GCTTCTACGAAGGAGGGATGA	58.967	52.381	5.83	0.00	0.00	2.92
847	893	2.575921	AGGAGGGATGATCTTGTCCA	57.424	50.000	12.37	0.00	36.19	4.02
868	914	3.715628	CCCAGAGGTTTTGTGAAACTG	57.284	47.619	2.51	0.00	43.68	3.16
975	1042	3.549794	GAGGGAATGGGAAGATTGACTG	58.450	50.000	0.00	0.00	0.00	3.51
1062	1162	3.688185	CAGACAACATGGAGGTGATTGAG	59.312	47.826	0.00	0.00	36.95	3.02
1067	1167	5.882557	ACAACATGGAGGTGATTGAGATTAC	59.117	40.000	0.00	0.00	36.95	1.89
1118	1218	4.261572	GGCAGCAACACTTTTCAATGACTA	60.262	41.667	0.00	0.00	0.00	2.59
1119	1219	4.676924	GCAGCAACACTTTTCAATGACTAC	59.323	41.667	0.00	0.00	0.00	2.73
1134	1234	7.475015	TCAATGACTACTTTCATTATGCTTGC	58.525	34.615	0.00	0.00	43.08	4.01
1146	1246	7.025485	TCATTATGCTTGCGATTTCATTACA	57.975	32.000	0.00	0.00	0.00	2.41
1154	1254	7.494298	TGCTTGCGATTTCATTACAACTAGATA	59.506	33.333	0.00	0.00	0.00	1.98
1188	1288	9.031360	TGTAATAGAGAAGCAAATAAAGTAGCG	57.969	33.333	0.00	0.00	0.00	4.26
1282	1382	9.899661	TTGTAATGCTCCTTACAAACTATGTAT	57.100	29.630	13.69	0.00	44.45	2.29
1430	1531	1.263217	ACGTTTGCCAGCTAACTTTCG	59.737	47.619	13.57	4.69	31.39	3.46
1456	1557	3.270027	TCTGAAAATGGACTATGCACCG	58.730	45.455	0.00	0.00	0.00	4.94
1491	1592	2.482721	CCCATTCTTAAAACGTCGCTGT	59.517	45.455	0.00	0.00	0.00	4.40
1502	1603	1.009675	GTCGCTGTGTGGTTTGCTG	60.010	57.895	0.00	0.00	0.00	4.41
1921	2026	6.040955	TCTCTCTCTGTCTCTATCTCTCTCAC	59.959	46.154	0.00	0.00	0.00	3.51
1933	2038	7.607250	TCTATCTCTCTCACTTTCCAAGTTTC	58.393	38.462	0.00	0.00	40.46	2.78
1939	2044	6.881065	TCTCTCACTTTCCAAGTTTCCATATG	59.119	38.462	0.00	0.00	40.46	1.78
1942	2047	6.303054	TCACTTTCCAAGTTTCCATATGTGA	58.697	36.000	1.24	0.00	40.46	3.58
1943	2048	6.206634	TCACTTTCCAAGTTTCCATATGTGAC	59.793	38.462	1.24	0.00	40.46	3.67
1997	2116	2.061773	CAACCTTGTACGCACTCTCTG	58.938	52.381	0.00	0.00	0.00	3.35
2013	2132	3.804036	TCTCTGTCAACGACCACAAATT	58.196	40.909	0.00	0.00	0.00	1.82
2015	2134	5.361427	TCTCTGTCAACGACCACAAATTAA	58.639	37.500	0.00	0.00	0.00	1.40
2055	2174	5.329035	ACTGTGTTTGCTTTGAATGTTCT	57.671	34.783	0.00	0.00	0.00	3.01
2061	2180	6.753744	GTGTTTGCTTTGAATGTTCTCTTCTT	59.246	34.615	0.00	0.00	0.00	2.52
2070	2189	5.406780	TGAATGTTCTCTTCTTTTCTCTCGC	59.593	40.000	0.00	0.00	0.00	5.03
2091	2212	0.589729	CACACACACGCTGCTTTGAC	60.590	55.000	0.00	0.00	0.00	3.18
2116	2237	5.163447	TGTTCTCTTTTCTTCTCTCGTCCAA	60.163	40.000	0.00	0.00	0.00	3.53
2117	2238	5.127693	TCTCTTTTCTTCTCTCGTCCAAG	57.872	43.478	0.00	0.00	0.00	3.61
2126	2247	0.529773	TCTCGTCCAAGCACACACAC	60.530	55.000	0.00	0.00	0.00	3.82
2134	2255	0.104120	AAGCACACACACGCTGTCTA	59.896	50.000	0.00	0.00	38.82	2.59
2144	2265	2.159366	ACACGCTGTCTATCTGCTGTAC	60.159	50.000	0.00	0.00	38.56	2.90
2145	2266	2.092323	ACGCTGTCTATCTGCTGTACA	58.908	47.619	0.00	0.00	38.56	2.90
2146	2267	2.690497	ACGCTGTCTATCTGCTGTACAT	59.310	45.455	0.00	0.00	38.56	2.29
2147	2268	3.048501	CGCTGTCTATCTGCTGTACATG	58.951	50.000	0.00	0.00	38.56	3.21
2148	2269	3.243201	CGCTGTCTATCTGCTGTACATGA	60.243	47.826	0.00	0.00	38.56	3.07
2149	2270	4.686972	GCTGTCTATCTGCTGTACATGAA	58.313	43.478	0.00	0.00	37.88	2.57
2150	2271	5.295950	GCTGTCTATCTGCTGTACATGAAT	58.704	41.667	0.00	0.00	37.88	2.57
2151	2272	5.757320	GCTGTCTATCTGCTGTACATGAATT	59.243	40.000	0.00	0.00	37.88	2.17
2241	2362	9.884465	GATTTTAATATGGACTACATGTGAAGC	57.116	33.333	9.11	0.00	40.82	3.86
2255	2376	7.972832	ACATGTGAAGCAAAATGAATGAATT	57.027	28.000	0.00	0.00	0.00	2.17
2285	2406	8.213679	ACTCTAAACTACGTCTATATACACCCA	58.786	37.037	0.00	0.00	0.00	4.51
2290	2411	8.874744	AACTACGTCTATATACACCCATATGT	57.125	34.615	1.24	0.00	36.56	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	9.492973	AGTCATCTTCCCAAATGTTAATTTTTG	57.507	29.630	6.24	6.24	33.59	2.44
50	51	5.700402	AGTAGCACAATTTGGGATCTAGT	57.300	39.130	1.96	0.00	0.00	2.57
53	54	4.721776	TCCTAGTAGCACAATTTGGGATCT	59.278	41.667	1.96	0.00	0.00	2.75
112	114	5.307976	CAGGATTAATGAGATCACCCACCTA	59.692	44.000	0.00	0.00	0.00	3.08
163	166	2.685897	TGGGCCGCATAATTTGTCTAAC	59.314	45.455	0.00	0.00	0.00	2.34
173	176	0.682292	TACATCGATGGGCCGCATAA	59.318	50.000	28.09	0.75	0.00	1.90
178	181	1.487452	CGTTGTACATCGATGGGCCG	61.487	60.000	28.09	17.69	0.00	6.13
227	230	2.017049	AGGCAACGAAATCTGGCATAC	58.983	47.619	0.00	0.00	46.39	2.39
277	281	3.136443	TCCATGGAATAAGCTGACCGAAT	59.864	43.478	13.46	0.00	0.00	3.34
319	323	9.612620	GATCCCATTAGAGTATTTTAATTTGCG	57.387	33.333	0.00	0.00	0.00	4.85
345	349	1.571215	GGTTAACTGTGGTTCGCCCG	61.571	60.000	5.42	0.00	36.92	6.13
373	377	5.729510	ACAAGCTAACTTCCAGATCTTCTC	58.270	41.667	0.00	0.00	32.29	2.87
422	434	3.259876	GGGAGTGTTCCATGTAGTGTACA	59.740	47.826	0.00	0.00	45.98	2.90
470	482	5.692115	TCAGAGCAACAGGGACAAATATA	57.308	39.130	0.00	0.00	0.00	0.86
475	487	1.202806	CCTTCAGAGCAACAGGGACAA	60.203	52.381	0.00	0.00	0.00	3.18
482	509	5.745312	TCTTCTAATCCTTCAGAGCAACA	57.255	39.130	0.00	0.00	0.00	3.33
483	510	6.419413	CGTATCTTCTAATCCTTCAGAGCAAC	59.581	42.308	0.00	0.00	0.00	4.17
493	520	5.854010	TGTGCTTCGTATCTTCTAATCCT	57.146	39.130	0.00	0.00	0.00	3.24
496	523	7.212976	ACATCATGTGCTTCGTATCTTCTAAT	58.787	34.615	0.00	0.00	0.00	1.73
532	559	4.450080	GCCTTTCAGAAATTTCCTGCTTTG	59.550	41.667	14.61	5.63	0.00	2.77
547	576	2.158711	TCATGCATCCCTAGCCTTTCAG	60.159	50.000	0.00	0.00	0.00	3.02
548	577	1.845791	TCATGCATCCCTAGCCTTTCA	59.154	47.619	0.00	0.00	0.00	2.69
585	614	1.354337	CCAGCACGGTCAATCTCACG	61.354	60.000	0.00	0.00	0.00	4.35
633	662	3.449746	TCCTCAATTTTGGTCCGGAAT	57.550	42.857	5.23	0.00	0.00	3.01
688	718	6.090129	CCACCATAAATACCTTGTTGAAACG	58.910	40.000	0.00	0.00	0.00	3.60
698	728	4.472108	TCGTCTTTCCCACCATAAATACCT	59.528	41.667	0.00	0.00	0.00	3.08
766	796	3.214328	GGTAATGGCTAGAACACCCATG	58.786	50.000	0.00	0.00	39.22	3.66
782	814	7.219917	CGATGCATTTACGAAATTTGTGGTAAT	59.780	33.333	0.00	0.00	0.00	1.89
838	882	1.747444	AACCTCTGGGTGGACAAGAT	58.253	50.000	0.00	0.00	46.67	2.40
868	914	3.975035	GGTCAAAAGAAGCATCAACGTTC	59.025	43.478	0.00	0.00	0.00	3.95
975	1042	0.027586	GACCAATACATCCGCGCAAC	59.972	55.000	8.75	0.00	0.00	4.17
1062	1162	3.062763	CTGTCCTCCATCATGCGTAATC	58.937	50.000	0.00	0.00	0.00	1.75
1067	1167	0.176449	TGACTGTCCTCCATCATGCG	59.824	55.000	5.17	0.00	0.00	4.73
1118	1218	5.953183	TGAAATCGCAAGCATAATGAAAGT	58.047	33.333	0.00	0.00	37.18	2.66
1119	1219	7.459394	AATGAAATCGCAAGCATAATGAAAG	57.541	32.000	0.00	0.00	37.18	2.62
1154	1254	8.798859	ATTTGCTTCTCTATTACAGTGTTCAT	57.201	30.769	0.00	0.00	0.00	2.57
1222	1322	3.463944	GTTCCTCGAACCAAACAGAAGA	58.536	45.455	0.00	0.00	36.65	2.87
1248	1348	8.984891	TTGTAAGGAGCATTACAATTTCATTG	57.015	30.769	14.26	0.00	45.85	2.82
1340	1440	5.105997	GGTGGAATTGAATTCTTGACCTCAG	60.106	44.000	16.58	0.00	39.24	3.35
1491	1592	0.681564	AACGTTCCCAGCAAACCACA	60.682	50.000	0.00	0.00	0.00	4.17
1895	1996	6.611236	TGAGAGAGATAGAGACAGAGAGAGAA	59.389	42.308	0.00	0.00	0.00	2.87
1933	2038	4.520874	ACGAGATACCTCTGTCACATATGG	59.479	45.833	7.80	0.00	37.28	2.74
1939	2044	2.747989	TCACACGAGATACCTCTGTCAC	59.252	50.000	0.00	0.00	37.28	3.67
1942	2047	6.296803	TGTATATCACACGAGATACCTCTGT	58.703	40.000	5.14	0.00	42.98	3.41
1943	2048	6.621812	GCTGTATATCACACGAGATACCTCTG	60.622	46.154	5.14	0.00	42.98	3.35
1997	2116	3.607542	CGGGTTAATTTGTGGTCGTTGAC	60.608	47.826	0.00	0.00	0.00	3.18
2013	2132	1.153978	GCACGACGATCACGGGTTA	60.154	57.895	0.00	0.00	44.46	2.85
2015	2134	3.215597	TTGCACGACGATCACGGGT	62.216	57.895	0.00	0.00	44.46	5.28
2055	2174	1.691976	TGTGGGCGAGAGAAAAGAAGA	59.308	47.619	0.00	0.00	0.00	2.87
2061	2180	0.531974	GTGTGTGTGGGCGAGAGAAA	60.532	55.000	0.00	0.00	0.00	2.52
2070	2189	2.480610	AAAGCAGCGTGTGTGTGGG	61.481	57.895	0.00	0.00	0.00	4.61
2091	2212	4.920927	GGACGAGAGAAGAAAAGAGAACAG	59.079	45.833	0.00	0.00	0.00	3.16
2116	2237	0.318441	ATAGACAGCGTGTGTGTGCT	59.682	50.000	0.00	0.00	40.56	4.40
2117	2238	0.716108	GATAGACAGCGTGTGTGTGC	59.284	55.000	0.00	0.00	40.56	4.57
2126	2247	2.851805	TGTACAGCAGATAGACAGCG	57.148	50.000	0.00	0.00	36.14	5.18
2145	2266	6.128553	GGCAATACGTACGATCATGAATTCAT	60.129	38.462	24.41	15.36	36.96	2.57
2146	2267	5.176774	GGCAATACGTACGATCATGAATTCA	59.823	40.000	24.41	11.26	0.00	2.57
2147	2268	5.176774	TGGCAATACGTACGATCATGAATTC	59.823	40.000	24.41	0.00	0.00	2.17
2148	2269	5.050363	GTGGCAATACGTACGATCATGAATT	60.050	40.000	24.41	6.67	0.00	2.17
2149	2270	4.447724	GTGGCAATACGTACGATCATGAAT	59.552	41.667	24.41	0.00	0.00	2.57
2150	2271	3.799963	GTGGCAATACGTACGATCATGAA	59.200	43.478	24.41	4.86	0.00	2.57
2151	2272	3.067601	AGTGGCAATACGTACGATCATGA	59.932	43.478	24.41	0.00	0.00	3.07
2220	2341	8.800370	TTTTGCTTCACATGTAGTCCATATTA	57.200	30.769	0.00	0.00	30.71	0.98
2231	2352	7.972832	AATTCATTCATTTTGCTTCACATGT	57.027	28.000	0.00	0.00	0.00	3.21
2233	2354	9.491675	TGTAAATTCATTCATTTTGCTTCACAT	57.508	25.926	0.00	0.00	0.00	3.21
2235	2356	8.981647	AGTGTAAATTCATTCATTTTGCTTCAC	58.018	29.630	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.