AutoCloner

Multiple sequence alignment - TraesCS2D01G479200

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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	TraesCS2D01G479200	chr2D	100.000	2597	0	0	1	2597	580132997	580130401	0.000000e+00	4796
1	TraesCS2D01G479200	chr2D	96.448	366	11	2	236	600	207477311	207476947	1.030000e-168	603
2	TraesCS2D01G479200	chr2D	98.516	337	5	0	264	600	524463028	524462692	1.720000e-166	595
3	TraesCS2D01G479200	chr2D	95.902	366	12	3	236	600	598325505	598325142	8.000000e-165	590
4	TraesCS2D01G479200	chr2D	95.502	289	12	1	1	288	524463325	524463037	6.550000e-126	460
5	TraesCS2D01G479200	chr2D	96.350	137	4	1	599	734	207477002	207476866	9.350000e-55	224
6	TraesCS2D01G479200	chr2D	88.235	187	22	0	1276	1462	580131647	580131461	9.350000e-55	224
7	TraesCS2D01G479200	chr2D	88.235	187	22	0	1351	1537	580131722	580131536	9.350000e-55	224
8	TraesCS2D01G479200	chr2B	91.234	1232	68	21	739	1963	699073991	699072793	0.000000e+00	1640
9	TraesCS2D01G479200	chr2B	93.506	231	15	0	2367	2597	699072199	699071969	6.880000e-91	344
10	TraesCS2D01G479200	chr2B	84.454	238	26	5	2052	2289	699072425	699072199	9.350000e-55	224
11	TraesCS2D01G479200	chr2B	86.087	115	16	0	1273	1387	699073318	699073204	9.760000e-25	124
12	TraesCS2D01G479200	chr1D	95.016	622	9	1	1	600	477487620	477486999	0.000000e+00	957
13	TraesCS2D01G479200	chr1D	82.875	327	42	10	2052	2376	71637421	71637107	5.470000e-72	281
14	TraesCS2D01G479200	chr1D	79.683	379	62	9	2052	2427	4117686	4117320	2.560000e-65	259
15	TraesCS2D01G479200	chr1D	97.080	137	3	1	599	734	477487054	477486918	2.010000e-56	230
16	TraesCS2D01G479200	chr1D	95.620	137	5	1	599	734	41896741	41896605	4.350000e-53	219
17	TraesCS2D01G479200	chr2A	85.580	957	74	23	738	1672	717956140	717955226	0.000000e+00	944
18	TraesCS2D01G479200	chr2A	80.990	384	49	15	2052	2427	707204160	707204527	1.520000e-72	283
19	TraesCS2D01G479200	chr2A	85.455	220	29	2	1351	1567	717955617	717955398	2.600000e-55	226
20	TraesCS2D01G479200	chr6D	95.902	366	13	2	236	600	328580344	328579980	2.230000e-165	592
21	TraesCS2D01G479200	chr6D	95.368	367	13	4	236	601	336220940	336220577	4.820000e-162	580
22	TraesCS2D01G479200	chr6D	95.502	289	12	1	1	288	328580613	328580325	6.550000e-126	460
23	TraesCS2D01G479200	chr6D	97.080	137	3	1	599	734	328580035	328579899	2.010000e-56	230
24	TraesCS2D01G479200	chr7D	97.329	337	8	1	264	600	602148332	602147997	2.900000e-159	571
25	TraesCS2D01G479200	chr7D	93.448	290	17	2	1	288	602148630	602148341	1.850000e-116	429
26	TraesCS2D01G479200	chr7D	80.392	459	60	13	2052	2507	495280166	495280597	3.220000e-84	322
27	TraesCS2D01G479200	chr7D	96.350	137	4	1	599	734	479121096	479121232	9.350000e-55	224
28	TraesCS2D01G479200	chr7D	96.350	137	3	2	599	734	503630196	503630331	9.350000e-55	224
29	TraesCS2D01G479200	chr7D	96.350	137	4	1	599	734	519190317	519190181	9.350000e-55	224
30	TraesCS2D01G479200	chr7D	96.350	137	3	2	599	734	554677061	554676926	9.350000e-55	224
31	TraesCS2D01G479200	chr1B	91.184	397	28	6	207	600	429217537	429217145	1.370000e-147	532
32	TraesCS2D01G479200	chr1B	91.601	381	28	4	220	600	397798223	397797847	8.230000e-145	523
33	TraesCS2D01G479200	chr1B	95.062	243	11	1	1	242	678041313	678041071	5.240000e-102	381
34	TraesCS2D01G479200	chr4A	94.118	289	15	2	2	288	698263811	698263523	3.070000e-119	438
35	TraesCS2D01G479200	chr7B	96.400	250	8	1	1	249	45845919	45845670	6.690000e-111	411
36	TraesCS2D01G479200	chr7B	80.579	484	61	11	2052	2528	445660938	445660481	2.470000e-90	342
37	TraesCS2D01G479200	chr3A	92.069	290	21	2	1	288	675327820	675327531	8.650000e-110	407
38	TraesCS2D01G479200	chr5A	92.042	289	21	2	2	288	29910245	29909957	3.110000e-109	405
39	TraesCS2D01G479200	chr5A	81.984	383	54	9	2052	2429	60523666	60524038	6.980000e-81	311
40	TraesCS2D01G479200	chr6B	79.562	548	70	17	2052	2597	130164619	130164112	1.140000e-93	353
41	TraesCS2D01G479200	chr3D	95.000	140	6	1	599	737	15994848	15994709	4.350000e-53	219

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	TraesCS2D01G479200	chr2D	580130401	580132997	2596	True	1748.000000	4796	92.156667	1	2597	3	chr2D.!!$R4	2596
1	TraesCS2D01G479200	chr2D	524462692	524463325	633	True	527.500000	595	97.009000	1	600	2	chr2D.!!$R3	599
2	TraesCS2D01G479200	chr2B	699071969	699073991	2022	True	583.000000	1640	88.820250	739	2597	4	chr2B.!!$R1	1858
3	TraesCS2D01G479200	chr1D	477486918	477487620	702	True	593.500000	957	96.048000	1	734	2	chr1D.!!$R4	733
4	TraesCS2D01G479200	chr2A	717955226	717956140	914	True	585.000000	944	85.517500	738	1672	2	chr2A.!!$R1	934
5	TraesCS2D01G479200	chr6D	328579899	328580613	714	True	427.333333	592	96.161333	1	734	3	chr6D.!!$R2	733
6	TraesCS2D01G479200	chr7D	602147997	602148630	633	True	500.000000	571	95.388500	1	600	2	chr7D.!!$R3	599
7	TraesCS2D01G479200	chr6B	130164112	130164619	507	True	353.000000	353	79.562000	2052	2597	1	chr6B.!!$R1	545

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
600	636	0.261696	AACAGCCAACCCCTGACTTT	59.738	50.0	0.0	0.0	34.47	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2120	2470	0.033504	CGTAGACCTGTTGTGTGGCT	59.966	55.0	0.0	0.0	0.0	4.75	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
485	521	1.871039	CCCACAAGTCAGTTAACGGTG	59.129	52.381	5.64	6.22	32.56	4.94
600	636	0.261696	AACAGCCAACCCCTGACTTT	59.738	50.000	0.00	0.00	34.47	2.66
601	637	1.145571	ACAGCCAACCCCTGACTTTA	58.854	50.000	0.00	0.00	34.47	1.85
602	638	1.497286	ACAGCCAACCCCTGACTTTAA	59.503	47.619	0.00	0.00	34.47	1.52
603	639	2.110011	ACAGCCAACCCCTGACTTTAAT	59.890	45.455	0.00	0.00	34.47	1.40
604	640	3.165071	CAGCCAACCCCTGACTTTAATT	58.835	45.455	0.00	0.00	32.03	1.40
605	641	3.578282	CAGCCAACCCCTGACTTTAATTT	59.422	43.478	0.00	0.00	32.03	1.82
606	642	4.040339	CAGCCAACCCCTGACTTTAATTTT	59.960	41.667	0.00	0.00	32.03	1.82
607	643	4.658435	AGCCAACCCCTGACTTTAATTTTT	59.342	37.500	0.00	0.00	0.00	1.94
630	666	9.521841	TTTTTAACAAAGAGAATTTGGGGTTTT	57.478	25.926	5.43	0.00	33.92	2.43
631	667	9.521841	TTTTAACAAAGAGAATTTGGGGTTTTT	57.478	25.926	5.43	0.00	33.92	1.94
648	684	2.977772	TTTTGAAACAGCCAACCCTG	57.022	45.000	0.00	0.00	38.78	4.45
649	685	2.151502	TTTGAAACAGCCAACCCTGA	57.848	45.000	0.00	0.00	36.67	3.86
650	686	1.398692	TTGAAACAGCCAACCCTGAC	58.601	50.000	0.00	0.00	36.67	3.51
651	687	0.550914	TGAAACAGCCAACCCTGACT	59.449	50.000	0.00	0.00	36.67	3.41
652	688	1.064017	TGAAACAGCCAACCCTGACTT	60.064	47.619	0.00	0.00	36.67	3.01
653	689	1.338020	GAAACAGCCAACCCTGACTTG	59.662	52.381	0.00	0.00	36.67	3.16
654	690	0.550914	AACAGCCAACCCTGACTTGA	59.449	50.000	0.00	0.00	36.67	3.02
784	828	4.767255	GGGTGCTGGAGCCGACAG	62.767	72.222	0.54	0.00	41.18	3.51
812	856	1.194098	CAGCACTGAAAACAGAGCGAG	59.806	52.381	12.18	7.16	42.28	5.03
835	879	4.785453	CGAGCCAAGTGCCCCCTC	62.785	72.222	0.00	0.00	42.71	4.30
845	889	2.445654	GCCCCCTCCTCTCCTCTG	60.446	72.222	0.00	0.00	0.00	3.35
846	890	2.445654	CCCCCTCCTCTCCTCTGC	60.446	72.222	0.00	0.00	0.00	4.26
862	906	1.152030	TGCACTGGACCCCTTCTCT	60.152	57.895	0.00	0.00	0.00	3.10
865	909	1.202940	GCACTGGACCCCTTCTCTTTT	60.203	52.381	0.00	0.00	0.00	2.27
866	910	2.784347	CACTGGACCCCTTCTCTTTTC	58.216	52.381	0.00	0.00	0.00	2.29
867	911	2.373502	CACTGGACCCCTTCTCTTTTCT	59.626	50.000	0.00	0.00	0.00	2.52
868	912	2.640332	ACTGGACCCCTTCTCTTTTCTC	59.360	50.000	0.00	0.00	0.00	2.87
869	913	2.909662	CTGGACCCCTTCTCTTTTCTCT	59.090	50.000	0.00	0.00	0.00	3.10
870	914	2.907042	TGGACCCCTTCTCTTTTCTCTC	59.093	50.000	0.00	0.00	0.00	3.20
871	915	3.178046	GGACCCCTTCTCTTTTCTCTCT	58.822	50.000	0.00	0.00	0.00	3.10
872	916	3.196901	GGACCCCTTCTCTTTTCTCTCTC	59.803	52.174	0.00	0.00	0.00	3.20
889	933	2.713167	CTCTCTCTCTCTCTCTCCCCAT	59.287	54.545	0.00	0.00	0.00	4.00
916	970	0.459585	CCATTGCTGCATGTTCCTGC	60.460	55.000	1.84	0.00	42.62	4.85
1371	1434	4.452733	GGGGTCGCTTCCTCCACG	62.453	72.222	0.00	0.00	0.00	4.94
1407	1470	3.777925	CCGAGCGTGCCGAACTTG	61.778	66.667	4.65	0.00	0.00	3.16
1629	1699	4.202161	TGGTTGATTATTCTCTCTCGAGGC	60.202	45.833	13.56	0.00	37.86	4.70
1644	1714	1.656095	CGAGGCTGAGAAATTGTCGTC	59.344	52.381	0.00	0.00	0.00	4.20
1780	1851	9.236006	CCCTCTTTCTGAAATCTGAGAAATAAA	57.764	33.333	15.50	0.00	37.52	1.40
1838	1909	2.262211	GAGGCTTTAATTTTGCTGCGG	58.738	47.619	0.00	0.00	0.00	5.69
1840	1911	1.358877	GCTTTAATTTTGCTGCGGGG	58.641	50.000	0.00	0.00	0.00	5.73
1842	1913	2.606108	CTTTAATTTTGCTGCGGGGTC	58.394	47.619	0.00	0.00	0.00	4.46
1899	1970	5.581874	GTCGTCGGGTGAATTAATTAAAGGA	59.418	40.000	1.21	0.00	0.00	3.36
1903	1974	7.971722	CGTCGGGTGAATTAATTAAAGGAAAAT	59.028	33.333	1.21	0.00	0.00	1.82
1932	2003	5.447624	TTTTCGTTCCTCAATTTTCTCCC	57.552	39.130	0.00	0.00	0.00	4.30
1936	2007	3.821033	CGTTCCTCAATTTTCTCCCAAGT	59.179	43.478	0.00	0.00	0.00	3.16
1938	2009	5.106673	CGTTCCTCAATTTTCTCCCAAGTAC	60.107	44.000	0.00	0.00	0.00	2.73
1940	2011	6.139679	TCCTCAATTTTCTCCCAAGTACAT	57.860	37.500	0.00	0.00	0.00	2.29
1942	2013	7.695055	TCCTCAATTTTCTCCCAAGTACATAA	58.305	34.615	0.00	0.00	0.00	1.90
1946	2017	8.748412	TCAATTTTCTCCCAAGTACATAAATGG	58.252	33.333	0.00	0.00	0.00	3.16
1949	2020	6.381498	TTCTCCCAAGTACATAAATGGTCA	57.619	37.500	0.00	0.00	0.00	4.02
1967	2038	6.500684	TGGTCATTCAACTCTAAAATCAGC	57.499	37.500	0.00	0.00	0.00	4.26
1969	2040	6.660521	TGGTCATTCAACTCTAAAATCAGCAT	59.339	34.615	0.00	0.00	0.00	3.79
1970	2041	7.177216	TGGTCATTCAACTCTAAAATCAGCATT	59.823	33.333	0.00	0.00	0.00	3.56
1972	2043	9.415544	GTCATTCAACTCTAAAATCAGCATTTT	57.584	29.630	1.00	1.00	43.39	1.82
2005	2333	9.710900	AAAAACCCTAAAATCAGCAAATCTTAG	57.289	29.630	0.00	0.00	0.00	2.18
2009	2337	8.548877	ACCCTAAAATCAGCAAATCTTAGTCTA	58.451	33.333	0.00	0.00	0.00	2.59
2024	2353	9.804758	AATCTTAGTCTATCACTTCTTAAACCG	57.195	33.333	0.00	0.00	36.43	4.44
2032	2361	8.755977	TCTATCACTTCTTAAACCGGATAACTT	58.244	33.333	9.46	0.00	0.00	2.66
2033	2362	9.379791	CTATCACTTCTTAAACCGGATAACTTT	57.620	33.333	9.46	0.00	0.00	2.66
2035	2364	9.729281	ATCACTTCTTAAACCGGATAACTTTAA	57.271	29.630	9.46	7.62	0.00	1.52
2036	2365	9.729281	TCACTTCTTAAACCGGATAACTTTAAT	57.271	29.630	9.46	0.00	0.00	1.40
2040	2369	9.743581	TTCTTAAACCGGATAACTTTAATTCCT	57.256	29.630	9.46	0.00	0.00	3.36
2042	2371	8.510243	TTAAACCGGATAACTTTAATTCCTCC	57.490	34.615	9.46	0.00	0.00	4.30
2043	2372	4.700700	ACCGGATAACTTTAATTCCTCCG	58.299	43.478	9.46	0.00	42.79	4.63
2045	2374	5.363580	ACCGGATAACTTTAATTCCTCCGTA	59.636	40.000	9.46	0.00	41.87	4.02
2046	2375	5.693555	CCGGATAACTTTAATTCCTCCGTAC	59.306	44.000	0.00	0.00	41.87	3.67
2047	2376	5.693555	CGGATAACTTTAATTCCTCCGTACC	59.306	44.000	0.00	0.00	39.36	3.34
2049	2378	6.481313	GGATAACTTTAATTCCTCCGTACCAC	59.519	42.308	0.00	0.00	0.00	4.16
2095	2445	2.670934	CCTATCATGCGCCTGCCC	60.671	66.667	4.18	0.00	41.78	5.36
2103	2453	4.496927	GCGCCTGCCCCATTTTCG	62.497	66.667	0.00	0.00	33.98	3.46
2129	2479	2.355837	GCGTCGAGAGCCACACAA	60.356	61.111	0.00	0.00	0.00	3.33
2140	2490	0.949105	GCCACACAACAGGTCTACGG	60.949	60.000	0.00	0.00	0.00	4.02
2201	2551	2.359850	GCGTCTTGCACCCATCCA	60.360	61.111	0.00	0.00	45.45	3.41
2202	2552	2.690778	GCGTCTTGCACCCATCCAC	61.691	63.158	0.00	0.00	45.45	4.02
2203	2553	1.003355	CGTCTTGCACCCATCCACT	60.003	57.895	0.00	0.00	0.00	4.00
2204	2554	1.300971	CGTCTTGCACCCATCCACTG	61.301	60.000	0.00	0.00	0.00	3.66
2205	2555	1.303561	TCTTGCACCCATCCACTGC	60.304	57.895	0.00	0.00	0.00	4.40
2206	2556	2.283101	TTGCACCCATCCACTGCC	60.283	61.111	0.00	0.00	0.00	4.85
2207	2557	2.776370	CTTGCACCCATCCACTGCCT	62.776	60.000	0.00	0.00	0.00	4.75
2208	2558	2.439156	GCACCCATCCACTGCCTC	60.439	66.667	0.00	0.00	0.00	4.70
2209	2559	2.273449	CACCCATCCACTGCCTCC	59.727	66.667	0.00	0.00	0.00	4.30
2257	2607	2.036556	AAAAGACGCGTTGCAGATTG	57.963	45.000	15.53	0.00	0.00	2.67
2266	2616	1.073025	TTGCAGATTGTGGCCGTCT	59.927	52.632	0.00	0.00	0.00	4.18
2318	2669	2.111878	GGAGGATGTCCATGGGCG	59.888	66.667	12.67	0.00	46.10	6.13
2319	2670	2.443394	GGAGGATGTCCATGGGCGA	61.443	63.158	12.67	0.95	46.10	5.54
2320	2671	1.227674	GAGGATGTCCATGGGCGAC	60.228	63.158	12.67	7.96	38.89	5.19
2321	2672	2.203209	GGATGTCCATGGGCGACC	60.203	66.667	12.67	13.61	43.75	4.79
2494	2845	3.768922	GGCTGAGGCACGAGCTCT	61.769	66.667	12.85	0.00	41.70	4.09
2511	2862	0.241213	TCTTCTCCAAGCGAGTGTCG	59.759	55.000	0.00	0.00	43.89	4.35
2516	2867	2.049156	CAAGCGAGTGTCGAGGCA	60.049	61.111	0.00	0.00	43.74	4.75
2528	2879	2.359850	GAGGCATGCCGGACAACA	60.360	61.111	30.50	0.00	41.95	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
485	521	3.553917	CCGTTTGGTTGACCATTTGTTTC	59.446	43.478	3.28	0.00	46.97	2.78
579	615	0.261696	AGTCAGGGGTTGGCTGTTTT	59.738	50.000	0.00	0.00	41.13	2.43
604	640	9.521841	AAAACCCCAAATTCTCTTTGTTAAAAA	57.478	25.926	0.00	0.00	0.00	1.94
605	641	9.521841	AAAAACCCCAAATTCTCTTTGTTAAAA	57.478	25.926	0.00	0.00	0.00	1.52
628	664	2.834549	TCAGGGTTGGCTGTTTCAAAAA	59.165	40.909	0.00	0.00	0.00	1.94
629	665	2.167487	GTCAGGGTTGGCTGTTTCAAAA	59.833	45.455	0.00	0.00	0.00	2.44
630	666	1.754226	GTCAGGGTTGGCTGTTTCAAA	59.246	47.619	0.00	0.00	0.00	2.69
631	667	1.064017	AGTCAGGGTTGGCTGTTTCAA	60.064	47.619	0.00	0.00	38.00	2.69
632	668	0.550914	AGTCAGGGTTGGCTGTTTCA	59.449	50.000	0.00	0.00	38.00	2.69
633	669	1.338020	CAAGTCAGGGTTGGCTGTTTC	59.662	52.381	0.00	0.00	38.62	2.78
634	670	1.064017	TCAAGTCAGGGTTGGCTGTTT	60.064	47.619	0.00	0.00	38.62	2.83
635	671	0.550914	TCAAGTCAGGGTTGGCTGTT	59.449	50.000	0.00	0.00	38.62	3.16
636	672	0.773644	ATCAAGTCAGGGTTGGCTGT	59.226	50.000	0.00	0.00	38.62	4.40
637	673	2.026822	ACTATCAAGTCAGGGTTGGCTG	60.027	50.000	0.00	0.00	38.62	4.85
638	674	2.269940	ACTATCAAGTCAGGGTTGGCT	58.730	47.619	0.00	0.00	42.21	4.75
639	675	2.789409	ACTATCAAGTCAGGGTTGGC	57.211	50.000	0.00	0.00	0.00	4.52
640	676	6.051717	CAGATAACTATCAAGTCAGGGTTGG	58.948	44.000	0.00	0.00	33.75	3.77
641	677	6.878317	TCAGATAACTATCAAGTCAGGGTTG	58.122	40.000	0.00	0.00	33.75	3.77
642	678	6.897966	TCTCAGATAACTATCAAGTCAGGGTT	59.102	38.462	0.00	0.00	33.75	4.11
643	679	6.436027	TCTCAGATAACTATCAAGTCAGGGT	58.564	40.000	0.00	0.00	33.75	4.34
644	680	6.968263	TCTCAGATAACTATCAAGTCAGGG	57.032	41.667	0.00	0.00	33.75	4.45
645	681	9.658799	TTTTTCTCAGATAACTATCAAGTCAGG	57.341	33.333	0.00	0.00	33.75	3.86
734	770	1.202154	ACGTGCACACTAGCGAGATAC	60.202	52.381	18.64	0.00	37.31	2.24
735	771	1.092348	ACGTGCACACTAGCGAGATA	58.908	50.000	18.64	0.00	37.31	1.98
736	772	0.456824	CACGTGCACACTAGCGAGAT	60.457	55.000	18.64	0.00	37.31	2.75
784	828	1.737355	TTTTCAGTGCTGGTGCTGCC	61.737	55.000	0.00	0.00	40.48	4.85
835	879	1.612395	GGTCCAGTGCAGAGGAGAGG	61.612	65.000	7.29	0.00	33.85	3.69
845	889	0.402121	AAAGAGAAGGGGTCCAGTGC	59.598	55.000	0.00	0.00	0.00	4.40
846	890	2.373502	AGAAAAGAGAAGGGGTCCAGTG	59.626	50.000	0.00	0.00	0.00	3.66
862	906	5.339200	GGGAGAGAGAGAGAGAGAGAGAAAA	60.339	48.000	0.00	0.00	0.00	2.29
865	909	3.309296	GGGAGAGAGAGAGAGAGAGAGA	58.691	54.545	0.00	0.00	0.00	3.10
866	910	2.370189	GGGGAGAGAGAGAGAGAGAGAG	59.630	59.091	0.00	0.00	0.00	3.20
867	911	2.293519	TGGGGAGAGAGAGAGAGAGAGA	60.294	54.545	0.00	0.00	0.00	3.10
868	912	2.126882	TGGGGAGAGAGAGAGAGAGAG	58.873	57.143	0.00	0.00	0.00	3.20
869	913	2.278657	TGGGGAGAGAGAGAGAGAGA	57.721	55.000	0.00	0.00	0.00	3.10
870	914	2.867624	CATGGGGAGAGAGAGAGAGAG	58.132	57.143	0.00	0.00	0.00	3.20
871	915	1.133513	GCATGGGGAGAGAGAGAGAGA	60.134	57.143	0.00	0.00	0.00	3.10
872	916	1.331214	GCATGGGGAGAGAGAGAGAG	58.669	60.000	0.00	0.00	0.00	3.20
916	970	1.021202	CTCCAGCTACCACTCTCTCG	58.979	60.000	0.00	0.00	0.00	4.04
958	1014	0.179113	CTGCTCTTCTTCCTCTCGGC	60.179	60.000	0.00	0.00	0.00	5.54
959	1015	1.405105	CTCTGCTCTTCTTCCTCTCGG	59.595	57.143	0.00	0.00	0.00	4.63
1422	1485	3.090532	GAGGCGACCCCTGGGAAT	61.091	66.667	16.20	0.78	46.60	3.01
1587	1650	5.334724	ACCAAAAATCTTCTCATGGATGC	57.665	39.130	0.00	0.00	0.00	3.91
1780	1851	4.020485	ACAAATACTCCTCCGTTTGCTAGT	60.020	41.667	0.00	0.00	35.53	2.57
1838	1909	1.521681	GCTCACAGCATACGGACCC	60.522	63.158	0.00	0.00	41.89	4.46
1840	1911	1.661112	GAAAGCTCACAGCATACGGAC	59.339	52.381	0.00	0.00	45.56	4.79
1842	1913	1.725641	TGAAAGCTCACAGCATACGG	58.274	50.000	0.00	0.00	45.56	4.02
1844	1915	3.937706	ACAGATGAAAGCTCACAGCATAC	59.062	43.478	10.14	0.00	45.56	2.39
1880	1951	8.996024	ACATTTTCCTTTAATTAATTCACCCG	57.004	30.769	3.39	0.00	0.00	5.28
1913	1984	3.780804	TGGGAGAAAATTGAGGAACGA	57.219	42.857	0.00	0.00	0.00	3.85
1914	1985	3.821033	ACTTGGGAGAAAATTGAGGAACG	59.179	43.478	0.00	0.00	0.00	3.95
1915	1986	5.768164	TGTACTTGGGAGAAAATTGAGGAAC	59.232	40.000	0.00	0.00	0.00	3.62
1916	1987	5.947663	TGTACTTGGGAGAAAATTGAGGAA	58.052	37.500	0.00	0.00	0.00	3.36
1917	1988	5.576563	TGTACTTGGGAGAAAATTGAGGA	57.423	39.130	0.00	0.00	0.00	3.71
1930	2001	7.122650	AGTTGAATGACCATTTATGTACTTGGG	59.877	37.037	0.00	0.00	33.39	4.12
1932	2003	8.950210	AGAGTTGAATGACCATTTATGTACTTG	58.050	33.333	0.00	0.00	0.00	3.16
1942	2013	7.177216	TGCTGATTTTAGAGTTGAATGACCATT	59.823	33.333	0.00	0.00	0.00	3.16
1946	2017	8.976986	AAATGCTGATTTTAGAGTTGAATGAC	57.023	30.769	0.00	0.00	0.00	3.06
1992	2320	8.072321	AGAAGTGATAGACTAAGATTTGCTGA	57.928	34.615	0.00	0.00	33.09	4.26
2005	2333	8.196103	AGTTATCCGGTTTAAGAAGTGATAGAC	58.804	37.037	0.00	0.00	0.00	2.59
2009	2337	9.729281	TTAAAGTTATCCGGTTTAAGAAGTGAT	57.271	29.630	0.00	0.00	0.00	3.06
2024	2353	6.481313	GTGGTACGGAGGAATTAAAGTTATCC	59.519	42.308	0.00	0.00	0.00	2.59
2032	2361	4.210724	CCAAGTGGTACGGAGGAATTAA	57.789	45.455	0.00	0.00	0.00	1.40
2033	2362	3.899052	CCAAGTGGTACGGAGGAATTA	57.101	47.619	0.00	0.00	0.00	1.40
2034	2363	2.781681	CCAAGTGGTACGGAGGAATT	57.218	50.000	0.00	0.00	0.00	2.17
2046	2375	0.457851	TGCCAACGAAAACCAAGTGG	59.542	50.000	0.00	0.00	42.17	4.00
2047	2376	2.507339	ATGCCAACGAAAACCAAGTG	57.493	45.000	0.00	0.00	0.00	3.16
2049	2378	5.694006	TGATAAAATGCCAACGAAAACCAAG	59.306	36.000	0.00	0.00	0.00	3.61
2095	2445	2.696759	GCCACCGGTCCGAAAATGG	61.697	63.158	14.39	15.12	0.00	3.16
2120	2470	0.033504	CGTAGACCTGTTGTGTGGCT	59.966	55.000	0.00	0.00	0.00	4.75
2129	2479	3.066814	GGGACGCCGTAGACCTGT	61.067	66.667	0.00	0.00	0.00	4.00
2140	2490	2.506438	CGTCGAAGAAGGGGACGC	60.506	66.667	0.00	0.00	45.55	5.19
2180	2530	3.925630	ATGGGTGCAAGACGCTGGG	62.926	63.158	0.00	0.00	43.06	4.45
2189	2539	2.283101	GGCAGTGGATGGGTGCAA	60.283	61.111	0.00	0.00	39.05	4.08
2193	2543	3.402681	CGGAGGCAGTGGATGGGT	61.403	66.667	0.00	0.00	0.00	4.51
2194	2544	2.446848	ATCGGAGGCAGTGGATGGG	61.447	63.158	0.00	0.00	0.00	4.00
2197	2547	2.037620	GCTCATCGGAGGCAGTGGAT	62.038	60.000	0.00	0.00	41.67	3.41
2200	2550	2.584418	CGCTCATCGGAGGCAGTG	60.584	66.667	0.00	0.00	41.67	3.66
2239	2589	0.944386	ACAATCTGCAACGCGTCTTT	59.056	45.000	14.44	0.00	0.00	2.52
2266	2616	2.675423	CGGTGACCCTCGAGTGGA	60.675	66.667	22.16	2.86	0.00	4.02
2312	2663	4.760047	GTGCACGAGGTCGCCCAT	62.760	66.667	0.00	0.00	44.43	4.00
2494	2845	0.241213	CTCGACACTCGCTTGGAGAA	59.759	55.000	0.00	0.00	46.23	2.87
2511	2862	2.359850	TGTTGTCCGGCATGCCTC	60.360	61.111	33.07	22.38	0.00	4.70
2516	2867	2.742372	GTCGCTGTTGTCCGGCAT	60.742	61.111	0.00	0.00	46.47	4.40
2528	2879	0.110328	CTGTTGTAGTCGTCGTCGCT	60.110	55.000	0.00	0.97	36.96	4.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.