AutoCloner

Multiple sequence alignment - TraesCS6A01G073000

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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	TraesCS6A01G073000	chr6A	100.000	2393	0	0	1	2393	39878363	39875971	0.000000e+00	4420.0
1	TraesCS6A01G073000	chr6A	78.731	1434	218	61	352	1761	39670773	39669403	0.000000e+00	878.0
2	TraesCS6A01G073000	chr6A	78.358	1437	221	59	352	1761	39628984	39627611	0.000000e+00	848.0
3	TraesCS6A01G073000	chr6A	72.670	633	126	37	362	978	45066223	45065622	1.470000e-37	167.0
4	TraesCS6A01G073000	chr6D	95.019	2309	70	14	61	2351	36106388	36104107	0.000000e+00	3585.0
5	TraesCS6A01G073000	chr6D	80.967	1634	227	48	361	1973	35667512	35665942	0.000000e+00	1218.0
6	TraesCS6A01G073000	chr6D	88.812	867	83	10	1490	2350	36073835	36072977	0.000000e+00	1051.0
7	TraesCS6A01G073000	chr6D	78.958	1036	145	45	743	1761	36084580	36083601	2.590000e-179	638.0
8	TraesCS6A01G073000	chr6D	83.277	592	80	18	1776	2363	35716006	35715430	5.860000e-146	527.0
9	TraesCS6A01G073000	chr6D	79.287	729	111	24	1037	1754	35717377	35716678	7.740000e-130	473.0
10	TraesCS6A01G073000	chr6D	86.557	305	32	8	363	664	36074173	36073875	6.380000e-86	327.0
11	TraesCS6A01G073000	chr6D	83.696	92	13	2	2147	2237	27847194	27847284	4.240000e-13	86.1
12	TraesCS6A01G073000	chr6D	97.436	39	1	0	1529	1567	36073772	36073734	1.540000e-07	67.6
13	TraesCS6A01G073000	chr6B	79.192	2004	298	64	361	2321	75268456	75266529	0.000000e+00	1280.0
14	TraesCS6A01G073000	chr6B	81.177	1546	205	58	362	1876	75514585	75513095	0.000000e+00	1164.0
15	TraesCS6A01G073000	chr6B	80.670	1283	200	29	358	1629	75510369	75509124	0.000000e+00	952.0
16	TraesCS6A01G073000	chr6B	79.391	1446	197	65	345	1761	75526328	75524955	0.000000e+00	926.0
17	TraesCS6A01G073000	chr6B	83.614	653	82	17	338	984	75423508	75422875	7.370000e-165	590.0
18	TraesCS6A01G073000	chr6B	81.283	561	93	12	1814	2369	75044723	75044170	6.070000e-121	444.0
19	TraesCS6A01G073000	chr6B	79.876	646	86	24	355	997	76153366	76152762	1.310000e-117	433.0
20	TraesCS6A01G073000	chr6B	80.750	587	82	17	1780	2363	75421459	75420901	1.700000e-116	429.0
21	TraesCS6A01G073000	chr6B	80.000	530	80	15	1838	2363	75524595	75524088	3.760000e-98	368.0
22	TraesCS6A01G073000	chr6B	76.398	644	101	33	361	991	75990630	75990025	1.390000e-77	300.0
23	TraesCS6A01G073000	chr6B	72.828	633	134	27	363	978	77764764	77764153	5.250000e-42	182.0
24	TraesCS6A01G073000	chr6B	79.651	172	25	9	1526	1691	51560351	51560518	5.410000e-22	115.0
25	TraesCS6A01G073000	chr1D	82.638	599	74	22	364	958	37880021	37880593	9.870000e-139	503.0
26	TraesCS6A01G073000	chr1D	81.198	601	96	12	1775	2363	37883025	37883620	3.600000e-128	468.0
27	TraesCS6A01G073000	chr1A	84.545	330	40	7	330	655	36785342	36785664	1.380000e-82	316.0
28	TraesCS6A01G073000	chr1A	78.623	276	41	8	691	958	36789149	36789414	1.470000e-37	167.0

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	TraesCS6A01G073000	chr6A	39875971	39878363	2392	True	4420.000000	4420	100.0000	1	2393	1	chr6A.!!$R3	2392
1	TraesCS6A01G073000	chr6A	39669403	39670773	1370	True	878.000000	878	78.7310	352	1761	1	chr6A.!!$R2	1409
2	TraesCS6A01G073000	chr6A	39627611	39628984	1373	True	848.000000	848	78.3580	352	1761	1	chr6A.!!$R1	1409
3	TraesCS6A01G073000	chr6D	36104107	36106388	2281	True	3585.000000	3585	95.0190	61	2351	1	chr6D.!!$R3	2290
4	TraesCS6A01G073000	chr6D	35665942	35667512	1570	True	1218.000000	1218	80.9670	361	1973	1	chr6D.!!$R1	1612
5	TraesCS6A01G073000	chr6D	36083601	36084580	979	True	638.000000	638	78.9580	743	1761	1	chr6D.!!$R2	1018
6	TraesCS6A01G073000	chr6D	35715430	35717377	1947	True	500.000000	527	81.2820	1037	2363	2	chr6D.!!$R4	1326
7	TraesCS6A01G073000	chr6D	36072977	36074173	1196	True	481.866667	1051	90.9350	363	2350	3	chr6D.!!$R5	1987
8	TraesCS6A01G073000	chr6B	75266529	75268456	1927	True	1280.000000	1280	79.1920	361	2321	1	chr6B.!!$R2	1960
9	TraesCS6A01G073000	chr6B	75509124	75514585	5461	True	1058.000000	1164	80.9235	358	1876	2	chr6B.!!$R7	1518
10	TraesCS6A01G073000	chr6B	75524088	75526328	2240	True	647.000000	926	79.6955	345	2363	2	chr6B.!!$R8	2018
11	TraesCS6A01G073000	chr6B	75420901	75423508	2607	True	509.500000	590	82.1820	338	2363	2	chr6B.!!$R6	2025
12	TraesCS6A01G073000	chr6B	75044170	75044723	553	True	444.000000	444	81.2830	1814	2369	1	chr6B.!!$R1	555
13	TraesCS6A01G073000	chr6B	76152762	76153366	604	True	433.000000	433	79.8760	355	997	1	chr6B.!!$R4	642
14	TraesCS6A01G073000	chr6B	75990025	75990630	605	True	300.000000	300	76.3980	361	991	1	chr6B.!!$R3	630
15	TraesCS6A01G073000	chr1D	37880021	37883620	3599	False	485.500000	503	81.9180	364	2363	2	chr1D.!!$F1	1999
16	TraesCS6A01G073000	chr1A	36785342	36789414	4072	False	241.500000	316	81.5840	330	958	2	chr1A.!!$F1	628

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
291	295	0.108424	AGCCGTGACTCTGCAATCTC	60.108	55.0	0.0	0.0	0.0	2.75	F
810	8528	0.253044	TCGATTTGGAGAAGGCCCTG	59.747	55.0	0.0	0.0	0.0	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1194	8921	1.376609	CTGCCCGCATAACCTGGAAC	61.377	60.000	0.0	0.0	0.0	3.62	R
2363	12546	1.771854	TGGAGGGAGTACTTGTTGCAA	59.228	47.619	0.0	0.0	0.0	4.08	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
21	22	3.754965	CTCATCCAACAACCAGGAAAGA	58.245	45.455	0.00	0.00	37.48	2.52
22	23	3.486383	TCATCCAACAACCAGGAAAGAC	58.514	45.455	0.00	0.00	37.48	3.01
23	24	1.961793	TCCAACAACCAGGAAAGACG	58.038	50.000	0.00	0.00	0.00	4.18
24	25	1.210967	TCCAACAACCAGGAAAGACGT	59.789	47.619	0.00	0.00	0.00	4.34
25	26	2.435069	TCCAACAACCAGGAAAGACGTA	59.565	45.455	0.00	0.00	0.00	3.57
26	27	3.071892	TCCAACAACCAGGAAAGACGTAT	59.928	43.478	0.00	0.00	0.00	3.06
27	28	3.435671	CCAACAACCAGGAAAGACGTATC	59.564	47.826	0.00	0.00	0.00	2.24
28	29	3.329929	ACAACCAGGAAAGACGTATCC	57.670	47.619	0.00	6.44	35.88	2.59
29	30	2.268298	CAACCAGGAAAGACGTATCCG	58.732	52.381	0.00	4.83	40.78	4.18
30	31	1.843368	ACCAGGAAAGACGTATCCGA	58.157	50.000	0.00	0.00	40.78	4.55
31	32	1.475682	ACCAGGAAAGACGTATCCGAC	59.524	52.381	0.00	0.00	40.78	4.79
42	43	1.849097	GTATCCGACGGTTCATGACC	58.151	55.000	14.79	0.00	45.55	4.02
43	44	0.748450	TATCCGACGGTTCATGACCC	59.252	55.000	14.79	0.00	46.35	4.46
44	45	2.292794	ATCCGACGGTTCATGACCCG	62.293	60.000	27.94	27.94	46.35	5.28
48	49	2.819595	CGGTTCATGACCCGGCTG	60.820	66.667	22.93	0.00	46.35	4.85
49	50	2.668632	GGTTCATGACCCGGCTGA	59.331	61.111	0.00	0.00	43.06	4.26
50	51	1.224592	GGTTCATGACCCGGCTGAT	59.775	57.895	0.00	0.00	43.06	2.90
51	52	0.394352	GGTTCATGACCCGGCTGATT	60.394	55.000	0.00	0.00	43.06	2.57
52	53	1.463674	GTTCATGACCCGGCTGATTT	58.536	50.000	0.00	0.00	0.00	2.17
53	54	1.401905	GTTCATGACCCGGCTGATTTC	59.598	52.381	0.00	0.00	0.00	2.17
54	55	0.911769	TCATGACCCGGCTGATTTCT	59.088	50.000	0.00	0.00	0.00	2.52
55	56	1.281867	TCATGACCCGGCTGATTTCTT	59.718	47.619	0.00	0.00	0.00	2.52
56	57	1.672881	CATGACCCGGCTGATTTCTTC	59.327	52.381	0.00	0.00	0.00	2.87
57	58	0.690192	TGACCCGGCTGATTTCTTCA	59.310	50.000	0.00	0.00	0.00	3.02
78	79	2.589540	AATCGGCCGGCTGATTCA	59.410	55.556	44.10	24.90	45.79	2.57
120	121	8.729805	AAAATGACCATTTTTGTTAGCTTCAA	57.270	26.923	13.26	0.00	45.67	2.69
236	240	1.063867	TCTCTCCCGAAGTAGGAAGGG	60.064	57.143	0.00	0.00	45.10	3.95
240	244	1.626825	TCCCGAAGTAGGAAGGGTTTG	59.373	52.381	0.00	0.00	44.13	2.93
281	285	3.231889	CTCAGTGGCAGCCGTGACT	62.232	63.158	11.56	4.73	30.05	3.41
282	286	2.740055	CAGTGGCAGCCGTGACTC	60.740	66.667	7.03	0.00	30.05	3.36
283	287	2.919856	AGTGGCAGCCGTGACTCT	60.920	61.111	7.03	0.00	30.18	3.24
284	288	2.740055	GTGGCAGCCGTGACTCTG	60.740	66.667	7.03	0.00	30.05	3.35
288	292	4.291047	CAGCCGTGACTCTGCAAT	57.709	55.556	0.00	0.00	0.00	3.56
289	293	2.084844	CAGCCGTGACTCTGCAATC	58.915	57.895	0.00	0.00	0.00	2.67
290	294	0.390866	CAGCCGTGACTCTGCAATCT	60.391	55.000	0.00	0.00	0.00	2.40
291	295	0.108424	AGCCGTGACTCTGCAATCTC	60.108	55.000	0.00	0.00	0.00	2.75
292	296	0.390340	GCCGTGACTCTGCAATCTCA	60.390	55.000	0.00	0.00	0.00	3.27
293	297	1.354040	CCGTGACTCTGCAATCTCAC	58.646	55.000	7.08	7.08	0.00	3.51
294	298	1.337167	CCGTGACTCTGCAATCTCACA	60.337	52.381	14.42	0.00	33.94	3.58
295	299	1.723542	CGTGACTCTGCAATCTCACAC	59.276	52.381	14.42	7.75	33.94	3.82
302	306	2.827921	TCTGCAATCTCACACTCTGCTA	59.172	45.455	0.00	0.00	34.10	3.49
303	307	3.450096	TCTGCAATCTCACACTCTGCTAT	59.550	43.478	0.00	0.00	34.10	2.97
676	4923	2.880879	CGACGACCGCATCTGGTG	60.881	66.667	0.00	0.00	44.01	4.17
677	4924	2.571757	GACGACCGCATCTGGTGA	59.428	61.111	0.00	0.00	44.01	4.02
807	8525	2.010497	GAGTTCGATTTGGAGAAGGCC	58.990	52.381	0.00	0.00	0.00	5.19
808	8526	1.095600	GTTCGATTTGGAGAAGGCCC	58.904	55.000	0.00	0.00	0.00	5.80
809	8527	0.991920	TTCGATTTGGAGAAGGCCCT	59.008	50.000	0.00	0.00	0.00	5.19
810	8528	0.253044	TCGATTTGGAGAAGGCCCTG	59.747	55.000	0.00	0.00	0.00	4.45
811	8529	0.749454	CGATTTGGAGAAGGCCCTGG	60.749	60.000	0.00	0.00	0.00	4.45
812	8530	0.332972	GATTTGGAGAAGGCCCTGGT	59.667	55.000	0.00	0.00	0.00	4.00
813	8531	0.332972	ATTTGGAGAAGGCCCTGGTC	59.667	55.000	0.00	0.00	0.00	4.02
814	8532	1.065410	TTTGGAGAAGGCCCTGGTCA	61.065	55.000	0.00	0.00	0.00	4.02
815	8533	1.492133	TTGGAGAAGGCCCTGGTCAG	61.492	60.000	0.00	0.00	0.00	3.51
1012	8739	7.120923	TCTAGTTCTACTATGGGCGAATTTT	57.879	36.000	0.00	0.00	29.08	1.82
1033	8760	5.559427	TTCCACCATGATTACAATGTTCG	57.441	39.130	0.00	0.00	0.00	3.95
1167	8894	0.821517	CTGTGATACCGGTGCCAGTA	59.178	55.000	19.93	0.00	0.00	2.74
1194	8921	4.623932	TGCCAATAATAGTCTAGCCCAG	57.376	45.455	0.00	0.00	0.00	4.45
1328	9055	6.409704	TGCTGCAAAGAACTATCAATCTAGT	58.590	36.000	0.00	0.00	33.34	2.57
1454	9231	0.247460	CACGATCCAGCTTGAGTCCA	59.753	55.000	0.00	0.00	0.00	4.02
1678	9493	5.105063	TCTTGCTACTTGATGATCTTGTCG	58.895	41.667	0.00	0.00	0.00	4.35
1757	9572	5.940617	TCCTGTGATGGTTATGATTTAGGG	58.059	41.667	0.00	0.00	0.00	3.53
1842	11980	4.912187	GCGAGCTTAAGCATAATTTTAGGC	59.088	41.667	28.39	11.90	45.16	3.93
2061	12239	1.419374	GATGCGCCCTTGTATCTACG	58.581	55.000	4.18	0.00	0.00	3.51
2145	12324	4.229718	ACCTAATGGCTAGAATACCCCT	57.770	45.455	0.00	0.00	36.63	4.79
2238	12418	5.878669	TCAGATGGATATGCTATTGTGATGC	59.121	40.000	0.00	0.00	0.00	3.91
2363	12546	7.945033	CAACATTGCATTACTTTTTAGTGGT	57.055	32.000	0.00	0.00	0.00	4.16
2365	12548	7.945033	ACATTGCATTACTTTTTAGTGGTTG	57.055	32.000	0.00	0.00	0.00	3.77
2369	12552	5.751028	TGCATTACTTTTTAGTGGTTGCAAC	59.249	36.000	21.59	21.59	33.05	4.17
2370	12553	5.751028	GCATTACTTTTTAGTGGTTGCAACA	59.249	36.000	29.55	13.95	0.00	3.33
2371	12554	6.256757	GCATTACTTTTTAGTGGTTGCAACAA	59.743	34.615	29.55	17.93	0.00	2.83
2372	12555	7.516627	GCATTACTTTTTAGTGGTTGCAACAAG	60.517	37.037	29.55	22.61	0.00	3.16
2373	12556	5.400066	ACTTTTTAGTGGTTGCAACAAGT	57.600	34.783	29.55	23.88	0.00	3.16
2374	12557	6.518208	ACTTTTTAGTGGTTGCAACAAGTA	57.482	33.333	29.55	22.80	0.00	2.24
2375	12558	6.327154	ACTTTTTAGTGGTTGCAACAAGTAC	58.673	36.000	29.55	20.69	0.00	2.73
2376	12559	6.152154	ACTTTTTAGTGGTTGCAACAAGTACT	59.848	34.615	29.55	25.34	0.00	2.73
2377	12560	5.744666	TTTAGTGGTTGCAACAAGTACTC	57.255	39.130	29.55	13.13	0.00	2.59
2378	12561	2.572290	AGTGGTTGCAACAAGTACTCC	58.428	47.619	29.55	11.42	0.00	3.85
2379	12562	1.607148	GTGGTTGCAACAAGTACTCCC	59.393	52.381	29.55	10.69	0.00	4.30
2380	12563	1.493022	TGGTTGCAACAAGTACTCCCT	59.507	47.619	29.55	0.00	0.00	4.20
2381	12564	2.152016	GGTTGCAACAAGTACTCCCTC	58.848	52.381	29.55	5.18	0.00	4.30
2382	12565	2.152016	GTTGCAACAAGTACTCCCTCC	58.848	52.381	24.52	0.00	0.00	4.30
2383	12566	1.429930	TGCAACAAGTACTCCCTCCA	58.570	50.000	0.00	0.00	0.00	3.86
2384	12567	1.985159	TGCAACAAGTACTCCCTCCAT	59.015	47.619	0.00	0.00	0.00	3.41
2385	12568	2.027192	TGCAACAAGTACTCCCTCCATC	60.027	50.000	0.00	0.00	0.00	3.51
2386	12569	2.237392	GCAACAAGTACTCCCTCCATCT	59.763	50.000	0.00	0.00	0.00	2.90
2387	12570	3.866651	CAACAAGTACTCCCTCCATCTG	58.133	50.000	0.00	0.00	0.00	2.90
2388	12571	2.472029	ACAAGTACTCCCTCCATCTGG	58.528	52.381	0.00	0.00	0.00	3.86
2389	12572	2.044492	ACAAGTACTCCCTCCATCTGGA	59.956	50.000	0.00	0.00	43.08	3.86
2390	12573	3.107601	CAAGTACTCCCTCCATCTGGAA	58.892	50.000	0.00	0.00	44.91	3.53
2391	12574	3.491766	AGTACTCCCTCCATCTGGAAA	57.508	47.619	0.00	0.00	44.91	3.13
2392	12575	4.014273	AGTACTCCCTCCATCTGGAAAT	57.986	45.455	0.00	0.00	44.91	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	3.486383	GTCTTTCCTGGTTGTTGGATGA	58.514	45.455	0.00	0.00	31.76	2.92
3	4	2.158667	ACGTCTTTCCTGGTTGTTGGAT	60.159	45.455	0.00	0.00	31.76	3.41
4	5	1.210967	ACGTCTTTCCTGGTTGTTGGA	59.789	47.619	0.00	0.00	0.00	3.53
8	9	3.329929	GGATACGTCTTTCCTGGTTGT	57.670	47.619	0.00	0.00	0.00	3.32
23	24	1.849097	GGTCATGAACCGTCGGATAC	58.151	55.000	20.51	9.07	38.58	2.24
33	34	1.401905	GAAATCAGCCGGGTCATGAAC	59.598	52.381	1.27	0.73	0.00	3.18
34	35	1.281867	AGAAATCAGCCGGGTCATGAA	59.718	47.619	1.27	0.00	0.00	2.57
35	36	0.911769	AGAAATCAGCCGGGTCATGA	59.088	50.000	1.27	0.00	0.00	3.07
36	37	1.672881	GAAGAAATCAGCCGGGTCATG	59.327	52.381	1.27	0.00	0.00	3.07
37	38	1.281867	TGAAGAAATCAGCCGGGTCAT	59.718	47.619	1.27	0.00	33.04	3.06
38	39	0.690192	TGAAGAAATCAGCCGGGTCA	59.310	50.000	1.27	0.00	33.04	4.02
39	40	3.551259	TGAAGAAATCAGCCGGGTC	57.449	52.632	1.27	0.00	33.04	4.46
47	48	3.126858	CGGCCGATTTTCTGAAGAAATCA	59.873	43.478	24.07	0.00	42.83	2.57
48	49	3.487544	CCGGCCGATTTTCTGAAGAAATC	60.488	47.826	30.73	5.21	42.83	2.17
49	50	2.423538	CCGGCCGATTTTCTGAAGAAAT	59.576	45.455	30.73	0.00	42.83	2.17
50	51	1.810151	CCGGCCGATTTTCTGAAGAAA	59.190	47.619	30.73	1.31	41.77	2.52
51	52	1.448985	CCGGCCGATTTTCTGAAGAA	58.551	50.000	30.73	0.00	0.00	2.52
52	53	1.024579	GCCGGCCGATTTTCTGAAGA	61.025	55.000	30.73	0.00	0.00	2.87
53	54	1.026718	AGCCGGCCGATTTTCTGAAG	61.027	55.000	30.73	6.52	0.00	3.02
54	55	1.002624	AGCCGGCCGATTTTCTGAA	60.003	52.632	30.73	0.00	0.00	3.02
55	56	1.745115	CAGCCGGCCGATTTTCTGA	60.745	57.895	30.73	0.00	0.00	3.27
56	57	1.097547	ATCAGCCGGCCGATTTTCTG	61.098	55.000	30.73	22.70	0.00	3.02
57	58	0.394352	AATCAGCCGGCCGATTTTCT	60.394	50.000	28.39	10.19	0.00	2.52
58	59	0.029433	GAATCAGCCGGCCGATTTTC	59.971	55.000	32.76	21.38	32.05	2.29
59	60	0.679640	TGAATCAGCCGGCCGATTTT	60.680	50.000	32.76	17.55	32.05	1.82
65	66	1.227943	TGCTATGAATCAGCCGGCC	60.228	57.895	26.15	7.94	38.29	6.13
99	100	7.106439	TCTTTGAAGCTAACAAAAATGGTCA	57.894	32.000	16.10	0.00	36.91	4.02
103	104	8.872845	ACTGTTTCTTTGAAGCTAACAAAAATG	58.127	29.630	16.10	8.26	36.91	2.32
104	105	9.435688	AACTGTTTCTTTGAAGCTAACAAAAAT	57.564	25.926	16.10	0.00	36.91	1.82
106	107	9.567848	CTAACTGTTTCTTTGAAGCTAACAAAA	57.432	29.630	16.10	8.00	36.91	2.44
120	121	7.027778	ACGCAGAATTTTCTAACTGTTTCTT	57.972	32.000	0.00	0.00	35.34	2.52
159	160	4.754618	CAGTATACGCAGTCTCTCTCTCAT	59.245	45.833	0.00	0.00	43.93	2.90
172	176	5.583061	CCCTCAAATACAAACAGTATACGCA	59.417	40.000	0.00	0.00	42.56	5.24
174	178	7.039882	ACTCCCTCAAATACAAACAGTATACG	58.960	38.462	0.00	0.00	42.56	3.06
281	285	1.622312	AGCAGAGTGTGAGATTGCAGA	59.378	47.619	0.00	0.00	37.24	4.26
282	286	2.096220	AGCAGAGTGTGAGATTGCAG	57.904	50.000	0.00	0.00	37.24	4.41
283	287	3.431346	GGATAGCAGAGTGTGAGATTGCA	60.431	47.826	0.00	0.00	37.24	4.08
284	288	3.129871	GGATAGCAGAGTGTGAGATTGC	58.870	50.000	0.00	0.00	35.09	3.56
285	289	4.099113	TGAGGATAGCAGAGTGTGAGATTG	59.901	45.833	0.00	0.00	0.00	2.67
286	290	4.099266	GTGAGGATAGCAGAGTGTGAGATT	59.901	45.833	0.00	0.00	0.00	2.40
287	291	3.636300	GTGAGGATAGCAGAGTGTGAGAT	59.364	47.826	0.00	0.00	0.00	2.75
288	292	3.020274	GTGAGGATAGCAGAGTGTGAGA	58.980	50.000	0.00	0.00	0.00	3.27
289	293	2.757314	TGTGAGGATAGCAGAGTGTGAG	59.243	50.000	0.00	0.00	0.00	3.51
290	294	2.807676	TGTGAGGATAGCAGAGTGTGA	58.192	47.619	0.00	0.00	0.00	3.58
291	295	3.715495	GATGTGAGGATAGCAGAGTGTG	58.285	50.000	0.00	0.00	0.00	3.82
292	296	2.360483	CGATGTGAGGATAGCAGAGTGT	59.640	50.000	0.00	0.00	0.00	3.55
293	297	2.360483	ACGATGTGAGGATAGCAGAGTG	59.640	50.000	0.00	0.00	0.00	3.51
294	298	2.360483	CACGATGTGAGGATAGCAGAGT	59.640	50.000	0.00	0.00	35.23	3.24
295	299	2.288091	CCACGATGTGAGGATAGCAGAG	60.288	54.545	0.00	0.00	35.23	3.35
302	306	0.392998	GCAACCCACGATGTGAGGAT	60.393	55.000	10.21	0.00	35.23	3.24
303	307	1.003839	GCAACCCACGATGTGAGGA	60.004	57.895	10.21	0.00	35.23	3.71
676	4923	2.595754	GCGGGATCCAAGGGCATC	60.596	66.667	15.23	0.00	0.00	3.91
677	4924	4.209866	GGCGGGATCCAAGGGCAT	62.210	66.667	15.23	0.00	0.00	4.40
679	4926	4.209866	ATGGCGGGATCCAAGGGC	62.210	66.667	15.23	14.51	39.96	5.19
807	8525	4.421515	CTGGCCCAGCTGACCAGG	62.422	72.222	32.48	20.60	45.97	4.45
854	8572	1.152756	ACCACCTGGAAGTGTTGGC	60.153	57.895	0.00	0.00	38.94	4.52
1012	8739	4.584874	ACGAACATTGTAATCATGGTGGA	58.415	39.130	0.00	0.00	0.00	4.02
1167	8894	7.182749	TGGGCTAGACTATTATTGGCAATATCT	59.817	37.037	19.88	19.63	0.00	1.98
1194	8921	1.376609	CTGCCCGCATAACCTGGAAC	61.377	60.000	0.00	0.00	0.00	3.62
1328	9055	6.761312	TCTGAATCCGTGGAAAGTAGTTTAA	58.239	36.000	0.00	0.00	0.00	1.52
1454	9231	5.596836	TTGGAAACTTTCTTGAACTGCAT	57.403	34.783	1.57	0.00	0.00	3.96
1678	9493	8.077836	ACGCTAGAAGAAAATTGCTATATGTC	57.922	34.615	0.00	0.00	0.00	3.06
1842	11980	4.133078	AGCTGAACTGAAGGAAGAAGTTG	58.867	43.478	0.00	0.00	34.37	3.16
2145	12324	2.486203	CACCAATACGCTTGCCTACAAA	59.514	45.455	0.00	0.00	34.74	2.83
2351	12532	5.400066	ACTTGTTGCAACCACTAAAAAGT	57.600	34.783	26.14	21.63	0.00	2.66
2352	12533	6.560711	AGTACTTGTTGCAACCACTAAAAAG	58.439	36.000	26.14	21.03	0.00	2.27
2353	12534	6.404954	GGAGTACTTGTTGCAACCACTAAAAA	60.405	38.462	26.14	11.12	0.00	1.94
2358	12541	2.572290	GGAGTACTTGTTGCAACCACT	58.428	47.619	26.14	21.27	0.00	4.00
2363	12546	1.771854	TGGAGGGAGTACTTGTTGCAA	59.228	47.619	0.00	0.00	0.00	4.08
2365	12548	2.237392	AGATGGAGGGAGTACTTGTTGC	59.763	50.000	0.00	0.00	0.00	4.17
2369	12552	2.752030	TCCAGATGGAGGGAGTACTTG	58.248	52.381	0.00	0.00	39.78	3.16
2370	12553	3.491766	TTCCAGATGGAGGGAGTACTT	57.508	47.619	0.00	0.00	46.36	2.24
2371	12554	3.491766	TTTCCAGATGGAGGGAGTACT	57.508	47.619	0.00	0.00	46.36	2.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.