AutoCloner

Multiple sequence alignment - TraesCS2D01G518300

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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	TraesCS2D01G518300	chr2D	100.000	3533	0	0	1	3533	608579408	608575876	0.000000e+00	6525
1	TraesCS2D01G518300	chr2D	87.922	2310	170	47	603	2827	608559828	608557543	0.000000e+00	2619
2	TraesCS2D01G518300	chr2B	93.711	2433	77	29	506	2910	742173242	742170858	0.000000e+00	3576
3	TraesCS2D01G518300	chr2B	89.291	1905	151	29	676	2535	742110633	742108737	0.000000e+00	2338
4	TraesCS2D01G518300	chr2B	92.760	442	21	5	3053	3490	742170773	742170339	2.310000e-176	628
5	TraesCS2D01G518300	chr2A	90.367	2398	165	33	496	2853	740143558	740141187	0.000000e+00	3088
6	TraesCS2D01G518300	chr2A	90.158	2398	170	33	496	2853	740119370	740116999	0.000000e+00	3061
7	TraesCS2D01G518300	chr2A	89.370	2192	165	35	496	2650	740079526	740077366	0.000000e+00	2695
8	TraesCS2D01G518300	chr2A	85.714	238	16	1	3065	3302	740116888	740116669	5.900000e-58	235
9	TraesCS2D01G518300	chr2A	86.147	231	13	2	3065	3294	740141076	740140864	7.630000e-57	231
10	TraesCS2D01G518300	chr7B	85.016	2209	247	45	679	2837	525598818	525596644	0.000000e+00	2169
11	TraesCS2D01G518300	chr7B	86.207	174	23	1	2895	3067	641152378	641152205	1.670000e-43	187
12	TraesCS2D01G518300	chr7A	86.215	2053	195	41	676	2670	563247162	563245140	0.000000e+00	2143
13	TraesCS2D01G518300	chr7A	84.713	2211	234	49	698	2836	563293695	563291517	0.000000e+00	2115
14	TraesCS2D01G518300	chr7A	89.308	159	17	0	2902	3060	734604070	734604228	2.150000e-47	200
15	TraesCS2D01G518300	chr1B	86.133	1875	208	30	685	2536	50950265	50952110	0.000000e+00	1975
16	TraesCS2D01G518300	chr1B	86.011	1880	212	27	681	2536	50900359	50902211	0.000000e+00	1967
17	TraesCS2D01G518300	chr1B	86.207	174	22	2	2900	3071	402233260	402233433	1.670000e-43	187
18	TraesCS2D01G518300	chr1B	86.826	167	21	1	2895	3060	427602935	427603101	6.020000e-43	185
19	TraesCS2D01G518300	chr7D	96.593	499	15	2	1	499	212817437	212817933	0.000000e+00	826
20	TraesCS2D01G518300	chr7D	96.386	498	16	2	1	497	42198826	42199322	0.000000e+00	819
21	TraesCS2D01G518300	chr7D	96.378	497	17	1	1	497	601070108	601070603	0.000000e+00	817
22	TraesCS2D01G518300	chr7D	95.030	503	24	1	1	503	603274610	603274109	0.000000e+00	789
23	TraesCS2D01G518300	chr7D	88.571	175	19	1	2901	3075	49173038	49173211	9.940000e-51	211
24	TraesCS2D01G518300	chr3D	96.573	496	16	1	1	496	463677618	463678112	0.000000e+00	821
25	TraesCS2D01G518300	chr3D	95.565	496	20	2	1	495	81850270	81849776	0.000000e+00	793
26	TraesCS2D01G518300	chr3D	95.565	496	20	2	1	495	81853428	81852934	0.000000e+00	793
27	TraesCS2D01G518300	chr3D	86.391	169	22	1	2900	3067	160889345	160889513	2.170000e-42	183
28	TraesCS2D01G518300	chr6D	95.976	497	19	1	1	497	100478171	100477676	0.000000e+00	806
29	TraesCS2D01G518300	chr6D	89.241	158	16	1	2903	3059	6319373	6319216	2.780000e-46	196
30	TraesCS2D01G518300	chr5D	95.758	495	20	1	1	495	421092986	421093479	0.000000e+00	797
31	TraesCS2D01G518300	chr5D	87.195	164	20	1	2898	3060	479153979	479154142	6.020000e-43	185
32	TraesCS2D01G518300	chr5B	87.879	165	19	1	2903	3066	12846525	12846361	3.600000e-45	193

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	TraesCS2D01G518300	chr2D	608575876	608579408	3532	True	6525.0	6525	100.0000	1	3533	1	chr2D.!!$R2	3532
1	TraesCS2D01G518300	chr2D	608557543	608559828	2285	True	2619.0	2619	87.9220	603	2827	1	chr2D.!!$R1	2224
2	TraesCS2D01G518300	chr2B	742108737	742110633	1896	True	2338.0	2338	89.2910	676	2535	1	chr2B.!!$R1	1859
3	TraesCS2D01G518300	chr2B	742170339	742173242	2903	True	2102.0	3576	93.2355	506	3490	2	chr2B.!!$R2	2984
4	TraesCS2D01G518300	chr2A	740077366	740079526	2160	True	2695.0	2695	89.3700	496	2650	1	chr2A.!!$R1	2154
5	TraesCS2D01G518300	chr2A	740140864	740143558	2694	True	1659.5	3088	88.2570	496	3294	2	chr2A.!!$R3	2798
6	TraesCS2D01G518300	chr2A	740116669	740119370	2701	True	1648.0	3061	87.9360	496	3302	2	chr2A.!!$R2	2806
7	TraesCS2D01G518300	chr7B	525596644	525598818	2174	True	2169.0	2169	85.0160	679	2837	1	chr7B.!!$R1	2158
8	TraesCS2D01G518300	chr7A	563245140	563247162	2022	True	2143.0	2143	86.2150	676	2670	1	chr7A.!!$R1	1994
9	TraesCS2D01G518300	chr7A	563291517	563293695	2178	True	2115.0	2115	84.7130	698	2836	1	chr7A.!!$R2	2138
10	TraesCS2D01G518300	chr1B	50950265	50952110	1845	False	1975.0	1975	86.1330	685	2536	1	chr1B.!!$F2	1851
11	TraesCS2D01G518300	chr1B	50900359	50902211	1852	False	1967.0	1967	86.0110	681	2536	1	chr1B.!!$F1	1855
12	TraesCS2D01G518300	chr7D	603274109	603274610	501	True	789.0	789	95.0300	1	503	1	chr7D.!!$R1	502
13	TraesCS2D01G518300	chr3D	81849776	81853428	3652	True	793.0	793	95.5650	1	495	2	chr3D.!!$R1	494

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
571	606	0.678395	AAAAACCATCCATGCACGCA	59.322	45.0	0.00	0.0	0.0	5.24	F
707	1281	0.944386	AAGCACGTGTTGACCATCAC	59.056	50.0	18.38	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2449	3955	0.327924	TCCTGCAATGACGACCCAAT	59.672	50.000	0.0	0.0	0.0	3.16	R
2557	4063	4.113354	GGATTTGTGTAGCTCCTAGAACG	58.887	47.826	0.0	0.0	0.0	3.95	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
183	184	0.824595	ATGGCAACTGCAGTTCAGCA	60.825	50.000	31.28	21.79	46.76	4.41
247	248	1.966901	ATAGCAATCACGGCGGGACA	61.967	55.000	16.93	0.00	36.08	4.02
249	250	2.358125	CAATCACGGCGGGACACA	60.358	61.111	16.93	0.00	0.00	3.72
443	445	3.716195	TGTCGATGCCACAGGGGG	61.716	66.667	0.00	0.00	37.04	5.40
505	520	7.592533	GCAGTTATCGACGTCCTTGTATTATTA	59.407	37.037	10.58	0.00	0.00	0.98
506	521	9.622004	CAGTTATCGACGTCCTTGTATTATTAT	57.378	33.333	10.58	0.00	0.00	1.28
508	523	6.946229	ATCGACGTCCTTGTATTATTATGC	57.054	37.500	10.58	0.00	0.00	3.14
509	524	5.834169	TCGACGTCCTTGTATTATTATGCA	58.166	37.500	10.58	0.00	0.00	3.96
510	525	5.918576	TCGACGTCCTTGTATTATTATGCAG	59.081	40.000	10.58	0.00	0.00	4.41
511	526	5.690409	CGACGTCCTTGTATTATTATGCAGT	59.310	40.000	10.58	0.00	0.00	4.40
512	527	6.200286	CGACGTCCTTGTATTATTATGCAGTT	59.800	38.462	10.58	0.00	0.00	3.16
513	528	7.380333	CGACGTCCTTGTATTATTATGCAGTTA	59.620	37.037	10.58	0.00	0.00	2.24
514	529	8.951787	ACGTCCTTGTATTATTATGCAGTTAA	57.048	30.769	0.00	0.00	0.00	2.01
542	577	8.889849	ATAATACGAACAGGAAACGATTTTTG	57.110	30.769	0.00	0.00	0.00	2.44
569	604	1.068610	ACGAAAAACCATCCATGCACG	60.069	47.619	0.00	0.00	0.00	5.34
570	605	1.349234	GAAAAACCATCCATGCACGC	58.651	50.000	0.00	0.00	0.00	5.34
571	606	0.678395	AAAAACCATCCATGCACGCA	59.322	45.000	0.00	0.00	0.00	5.24
574	609	2.827190	CCATCCATGCACGCAGCT	60.827	61.111	0.00	0.00	45.94	4.24
592	627	1.419387	GCTCCCTAGTAGTCCGGAGTA	59.581	57.143	15.28	15.28	43.28	2.59
672	728	2.223876	GCACCATAACGGGTCTATTCGA	60.224	50.000	0.00	0.00	39.79	3.71
707	1281	0.944386	AAGCACGTGTTGACCATCAC	59.056	50.000	18.38	0.00	0.00	3.06
1036	1711	2.504274	AACGCCACGTCCTTCTCCA	61.504	57.895	0.00	0.00	39.99	3.86
1242	1993	2.164219	GCCATTTGACGTCACCATGAAT	59.836	45.455	27.51	18.41	0.00	2.57
1746	2497	2.680913	CGACCCGGCAAAGCTTCTG	61.681	63.158	0.00	1.71	0.00	3.02
1749	2500	1.603455	CCCGGCAAAGCTTCTGGAA	60.603	57.895	13.41	0.00	0.00	3.53
2557	4063	2.776659	GGACCTATCGGTGCCAAAC	58.223	57.895	0.00	0.00	45.73	2.93
2744	4298	9.309224	AGACTGTAAAAGGTAAAATGGCTTATT	57.691	29.630	0.00	0.00	0.00	1.40
2870	4494	9.116067	CCATTTCTGTAAATAAGTAATTCGGGA	57.884	33.333	0.00	0.00	33.45	5.14
2910	4534	3.579151	ACTCAGTTGGTTTCTACTCCCTC	59.421	47.826	0.00	0.00	0.00	4.30
2911	4535	3.835395	CTCAGTTGGTTTCTACTCCCTCT	59.165	47.826	0.00	0.00	0.00	3.69
2912	4536	3.578716	TCAGTTGGTTTCTACTCCCTCTG	59.421	47.826	0.00	0.00	0.00	3.35
2915	4539	4.040584	AGTTGGTTTCTACTCCCTCTGTTC	59.959	45.833	0.00	0.00	0.00	3.18
2916	4540	2.904434	TGGTTTCTACTCCCTCTGTTCC	59.096	50.000	0.00	0.00	0.00	3.62
2917	4541	3.174779	GGTTTCTACTCCCTCTGTTCCT	58.825	50.000	0.00	0.00	0.00	3.36
2920	4544	5.247792	GGTTTCTACTCCCTCTGTTCCTAAA	59.752	44.000	0.00	0.00	0.00	1.85
2923	4547	8.706521	GTTTCTACTCCCTCTGTTCCTAAATAT	58.293	37.037	0.00	0.00	0.00	1.28
2924	4548	9.947189	TTTCTACTCCCTCTGTTCCTAAATATA	57.053	33.333	0.00	0.00	0.00	0.86
2925	4549	9.589461	TTCTACTCCCTCTGTTCCTAAATATAG	57.411	37.037	0.00	0.00	0.00	1.31
2950	4574	9.586435	AGGTTTTTCTAAAGATTTCAACAAGTG	57.414	29.630	0.00	0.00	0.00	3.16
2951	4575	9.581099	GGTTTTTCTAAAGATTTCAACAAGTGA	57.419	29.630	0.00	0.00	0.00	3.41
2956	4580	9.607988	TTCTAAAGATTTCAACAAGTGACTACA	57.392	29.630	0.00	0.00	35.39	2.74
2957	4581	9.778741	TCTAAAGATTTCAACAAGTGACTACAT	57.221	29.630	0.00	0.00	35.39	2.29
2960	4584	8.902540	AAGATTTCAACAAGTGACTACATACA	57.097	30.769	0.00	0.00	35.39	2.29
2961	4585	8.902540	AGATTTCAACAAGTGACTACATACAA	57.097	30.769	0.00	0.00	35.39	2.41
2962	4586	9.337396	AGATTTCAACAAGTGACTACATACAAA	57.663	29.630	0.00	0.00	35.39	2.83
2963	4587	9.944663	GATTTCAACAAGTGACTACATACAAAA	57.055	29.630	0.00	0.00	35.39	2.44
2964	4588	9.730420	ATTTCAACAAGTGACTACATACAAAAC	57.270	29.630	0.00	0.00	35.39	2.43
2965	4589	7.851387	TCAACAAGTGACTACATACAAAACA	57.149	32.000	0.00	0.00	0.00	2.83
2966	4590	8.270080	TCAACAAGTGACTACATACAAAACAA	57.730	30.769	0.00	0.00	0.00	2.83
2967	4591	8.731605	TCAACAAGTGACTACATACAAAACAAA	58.268	29.630	0.00	0.00	0.00	2.83
2968	4592	9.515020	CAACAAGTGACTACATACAAAACAAAT	57.485	29.630	0.00	0.00	0.00	2.32
3057	4681	9.303537	CTCTAAAAGACTTAGATTTAGGAACGG	57.696	37.037	12.79	0.00	37.29	4.44
3058	4682	9.028284	TCTAAAAGACTTAGATTTAGGAACGGA	57.972	33.333	12.79	0.00	37.29	4.69
3059	4683	9.303537	CTAAAAGACTTAGATTTAGGAACGGAG	57.696	37.037	0.00	0.00	34.51	4.63
3060	4684	7.477945	AAAGACTTAGATTTAGGAACGGAGA	57.522	36.000	0.00	0.00	0.00	3.71
3061	4685	6.702716	AGACTTAGATTTAGGAACGGAGAG	57.297	41.667	0.00	0.00	0.00	3.20
3062	4686	5.595133	AGACTTAGATTTAGGAACGGAGAGG	59.405	44.000	0.00	0.00	0.00	3.69
3145	4769	3.906720	TTGGTCCTATCTAACTGCCAC	57.093	47.619	0.00	0.00	0.00	5.01
3205	4829	3.974401	CAGCATTAACACAGGAAAACACG	59.026	43.478	0.00	0.00	0.00	4.49
3218	4842	3.069016	GGAAAACACGGGGTCAAAGATTT	59.931	43.478	0.00	0.00	0.00	2.17
3219	4843	3.726291	AAACACGGGGTCAAAGATTTG	57.274	42.857	0.00	0.00	39.48	2.32
3220	4844	1.616159	ACACGGGGTCAAAGATTTGG	58.384	50.000	5.52	0.00	38.66	3.28
3221	4845	0.243636	CACGGGGTCAAAGATTTGGC	59.756	55.000	5.52	3.46	41.84	4.52
3222	4846	0.178975	ACGGGGTCAAAGATTTGGCA	60.179	50.000	11.64	0.00	44.25	4.92
3223	4847	0.965439	CGGGGTCAAAGATTTGGCAA	59.035	50.000	11.64	0.00	44.25	4.52
3224	4848	1.067635	CGGGGTCAAAGATTTGGCAAG	60.068	52.381	11.64	0.00	44.25	4.01
3225	4849	1.276138	GGGGTCAAAGATTTGGCAAGG	59.724	52.381	11.64	0.00	44.25	3.61
3226	4850	2.247358	GGGTCAAAGATTTGGCAAGGA	58.753	47.619	11.64	0.00	44.25	3.36
3227	4851	2.029020	GGGTCAAAGATTTGGCAAGGAC	60.029	50.000	11.64	3.31	44.25	3.85
3228	4852	2.351738	GGTCAAAGATTTGGCAAGGACG	60.352	50.000	11.64	0.00	44.25	4.79
3229	4853	2.293399	GTCAAAGATTTGGCAAGGACGT	59.707	45.455	5.07	0.00	42.14	4.34
3230	4854	3.500680	GTCAAAGATTTGGCAAGGACGTA	59.499	43.478	5.07	0.00	42.14	3.57
3231	4855	4.023536	GTCAAAGATTTGGCAAGGACGTAA	60.024	41.667	5.07	0.00	42.14	3.18
3232	4856	4.764823	TCAAAGATTTGGCAAGGACGTAAT	59.235	37.500	0.00	0.00	38.66	1.89
3233	4857	5.941058	TCAAAGATTTGGCAAGGACGTAATA	59.059	36.000	0.00	0.00	38.66	0.98
3234	4858	6.431543	TCAAAGATTTGGCAAGGACGTAATAA	59.568	34.615	0.00	0.00	38.66	1.40
3235	4859	6.827586	AAGATTTGGCAAGGACGTAATAAA	57.172	33.333	0.00	0.00	0.00	1.40
3274	4916	3.471495	AATTTGCGTCCAACTTCGATC	57.529	42.857	0.00	0.00	0.00	3.69
3302	4944	2.280628	GCAAAGGAAGGAACGATCGAT	58.719	47.619	24.34	10.66	0.00	3.59
3310	4952	3.972950	AGGAACGATCGATCTGTGTAG	57.027	47.619	24.34	8.80	0.00	2.74
3315	4957	4.030134	ACGATCGATCTGTGTAGTTTCC	57.970	45.455	24.34	0.00	0.00	3.13
3329	4971	7.276658	TGTGTAGTTTCCTGTTTGAGTATGAA	58.723	34.615	0.00	0.00	0.00	2.57
3376	5018	1.646189	CAGGAGCGCTTAAGTTCCTC	58.354	55.000	13.26	13.31	46.84	3.71
3395	5037	5.116180	TCCTCGAGGCAATATTTTGTACAG	58.884	41.667	27.39	0.00	35.17	2.74
3401	5043	6.866248	CGAGGCAATATTTTGTACAGGTTTTT	59.134	34.615	0.00	0.00	35.17	1.94
3421	5063	3.921119	TTAAGCGTCCGACTACTTGAA	57.079	42.857	11.84	3.27	0.00	2.69
3422	5064	2.061740	AAGCGTCCGACTACTTGAAC	57.938	50.000	0.00	0.00	0.00	3.18
3424	5066	0.110056	GCGTCCGACTACTTGAACGA	60.110	55.000	0.00	0.00	0.00	3.85
3453	5098	5.848036	CACTCGAAAAGTATCAAAACAGCTG	59.152	40.000	13.48	13.48	36.07	4.24
3461	5106	6.272822	AGTATCAAAACAGCTGGGATTTTC	57.727	37.500	19.93	4.34	0.00	2.29
3473	6200	1.453928	GATTTTCCCCGGAGCCCAG	60.454	63.158	0.73	0.00	0.00	4.45
3478	6205	4.475444	CCCCGGAGCCCAGACCTA	62.475	72.222	0.73	0.00	0.00	3.08
3497	6224	4.740235	GAGCATCTACGGCTGGAC	57.260	61.111	0.00	0.00	42.78	4.02
3498	6225	1.816537	GAGCATCTACGGCTGGACA	59.183	57.895	0.00	0.00	42.78	4.02
3499	6226	0.390860	GAGCATCTACGGCTGGACAT	59.609	55.000	0.00	0.00	42.78	3.06
3500	6227	0.390860	AGCATCTACGGCTGGACATC	59.609	55.000	0.00	0.00	40.80	3.06
3501	6228	0.390860	GCATCTACGGCTGGACATCT	59.609	55.000	0.00	0.00	0.00	2.90
3503	6230	2.748605	CATCTACGGCTGGACATCTTC	58.251	52.381	0.00	0.00	0.00	2.87
3504	6231	1.112113	TCTACGGCTGGACATCTTCC	58.888	55.000	0.00	0.00	46.13	3.46
3505	6232	0.105039	CTACGGCTGGACATCTTCCC	59.895	60.000	0.00	0.00	45.17	3.97
3506	6233	1.672854	TACGGCTGGACATCTTCCCG	61.673	60.000	0.00	0.00	45.17	5.14
3507	6234	2.190578	GGCTGGACATCTTCCCGG	59.809	66.667	0.00	0.00	45.17	5.73
3508	6235	2.190578	GCTGGACATCTTCCCGGG	59.809	66.667	16.85	16.85	45.17	5.73
3509	6236	2.190578	CTGGACATCTTCCCGGGC	59.809	66.667	18.49	0.00	45.17	6.13
3510	6237	3.740128	CTGGACATCTTCCCGGGCG	62.740	68.421	18.49	9.76	45.17	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
183	184	2.884639	GTGTAACTCCAGTTGCCATGTT	59.115	45.455	2.01	0.00	39.42	2.71
237	238	2.585341	TAACCATGTGTCCCGCCGT	61.585	57.895	0.00	0.00	0.00	5.68
247	248	2.032634	CGCGTGGCAGTAACCATGT	61.033	57.895	0.00	0.00	46.65	3.21
249	250	2.435938	CCGCGTGGCAGTAACCAT	60.436	61.111	0.00	0.00	43.01	3.55
363	365	4.986531	CGCAACGTTCGGTGTGCG	62.987	66.667	14.67	14.67	43.81	5.34
505	520	9.772973	TCCTGTTCGTATTATTATTAACTGCAT	57.227	29.630	0.00	0.00	0.00	3.96
506	521	9.602568	TTCCTGTTCGTATTATTATTAACTGCA	57.397	29.630	0.00	0.00	0.00	4.41
529	544	3.377439	GTCACCACCAAAAATCGTTTCC	58.623	45.455	0.00	0.00	0.00	3.13
542	577	1.268625	GGATGGTTTTTCGTCACCACC	59.731	52.381	0.00	0.00	46.01	4.61
569	604	1.457009	CCGGACTACTAGGGAGCTGC	61.457	65.000	0.00	0.00	0.00	5.25
570	605	0.183014	TCCGGACTACTAGGGAGCTG	59.817	60.000	0.00	0.00	0.00	4.24
571	606	0.475044	CTCCGGACTACTAGGGAGCT	59.525	60.000	0.00	0.00	39.60	4.09
574	609	6.409005	GCATATATACTCCGGACTACTAGGGA	60.409	46.154	0.00	0.00	0.00	4.20
616	651	1.670083	ACCGTCCGGCTGCTAAAAC	60.670	57.895	5.47	0.00	39.32	2.43
617	652	1.669760	CACCGTCCGGCTGCTAAAA	60.670	57.895	5.47	0.00	39.32	1.52
941	1594	4.322273	AAAGAAGGCTTGGCTTAATGAAGC	60.322	41.667	3.46	6.20	44.64	3.86
1036	1711	2.580601	CCTTGTCGTCGGGGAAGGT	61.581	63.158	8.76	0.00	31.88	3.50
1746	2497	0.379669	CATCGGCTTGCATGACTTCC	59.620	55.000	3.33	0.00	0.00	3.46
1749	2500	1.086067	CGACATCGGCTTGCATGACT	61.086	55.000	3.33	0.00	35.37	3.41
2400	3868	1.066858	ACCACCGTGTGAGCAAGATAG	60.067	52.381	5.71	0.00	35.23	2.08
2449	3955	0.327924	TCCTGCAATGACGACCCAAT	59.672	50.000	0.00	0.00	0.00	3.16
2557	4063	4.113354	GGATTTGTGTAGCTCCTAGAACG	58.887	47.826	0.00	0.00	0.00	3.95
2704	4251	9.014297	CCTTTTACAGTCTACAATCAATTTCCT	57.986	33.333	0.00	0.00	0.00	3.36
2705	4252	8.793592	ACCTTTTACAGTCTACAATCAATTTCC	58.206	33.333	0.00	0.00	0.00	3.13
2854	4417	9.916360	ACTCCTTTTATCCCGAATTACTTATTT	57.084	29.630	0.00	0.00	0.00	1.40
2862	4425	6.039382	GCAACATACTCCTTTTATCCCGAATT	59.961	38.462	0.00	0.00	0.00	2.17
2870	4494	6.476378	ACTGAGTGCAACATACTCCTTTTAT	58.524	36.000	0.00	0.00	43.00	1.40
2871	4495	5.865085	ACTGAGTGCAACATACTCCTTTTA	58.135	37.500	0.00	0.00	43.00	1.52
2924	4548	9.586435	CACTTGTTGAAATCTTTAGAAAAACCT	57.414	29.630	0.00	0.00	0.00	3.50
2925	4549	9.581099	TCACTTGTTGAAATCTTTAGAAAAACC	57.419	29.630	0.00	0.00	0.00	3.27
2931	4555	9.778741	ATGTAGTCACTTGTTGAAATCTTTAGA	57.221	29.630	0.00	0.00	35.39	2.10
2936	4560	8.902540	TTGTATGTAGTCACTTGTTGAAATCT	57.097	30.769	0.00	0.00	35.39	2.40
2937	4561	9.944663	TTTTGTATGTAGTCACTTGTTGAAATC	57.055	29.630	0.00	0.00	35.39	2.17
2939	4563	8.731605	TGTTTTGTATGTAGTCACTTGTTGAAA	58.268	29.630	0.00	0.00	35.39	2.69
2941	4565	7.851387	TGTTTTGTATGTAGTCACTTGTTGA	57.149	32.000	0.00	0.00	0.00	3.18
2942	4566	8.903570	TTTGTTTTGTATGTAGTCACTTGTTG	57.096	30.769	0.00	0.00	0.00	3.33
3032	4656	9.028284	TCCGTTCCTAAATCTAAGTCTTTTAGA	57.972	33.333	0.00	0.00	35.79	2.10
3033	4657	9.303537	CTCCGTTCCTAAATCTAAGTCTTTTAG	57.696	37.037	0.00	0.00	34.30	1.85
3034	4658	9.028284	TCTCCGTTCCTAAATCTAAGTCTTTTA	57.972	33.333	0.00	0.00	0.00	1.52
3035	4659	7.904205	TCTCCGTTCCTAAATCTAAGTCTTTT	58.096	34.615	0.00	0.00	0.00	2.27
3036	4660	7.363968	CCTCTCCGTTCCTAAATCTAAGTCTTT	60.364	40.741	0.00	0.00	0.00	2.52
3037	4661	6.097129	CCTCTCCGTTCCTAAATCTAAGTCTT	59.903	42.308	0.00	0.00	0.00	3.01
3039	4663	5.221283	CCCTCTCCGTTCCTAAATCTAAGTC	60.221	48.000	0.00	0.00	0.00	3.01
3040	4664	4.650131	CCCTCTCCGTTCCTAAATCTAAGT	59.350	45.833	0.00	0.00	0.00	2.24
3041	4665	4.650131	ACCCTCTCCGTTCCTAAATCTAAG	59.350	45.833	0.00	0.00	0.00	2.18
3042	4666	4.617593	ACCCTCTCCGTTCCTAAATCTAA	58.382	43.478	0.00	0.00	0.00	2.10
3043	4667	4.261411	ACCCTCTCCGTTCCTAAATCTA	57.739	45.455	0.00	0.00	0.00	1.98
3044	4668	3.117552	ACCCTCTCCGTTCCTAAATCT	57.882	47.619	0.00	0.00	0.00	2.40
3045	4669	3.321396	CCTACCCTCTCCGTTCCTAAATC	59.679	52.174	0.00	0.00	0.00	2.17
3046	4670	3.306613	CCTACCCTCTCCGTTCCTAAAT	58.693	50.000	0.00	0.00	0.00	1.40
3047	4671	2.043526	ACCTACCCTCTCCGTTCCTAAA	59.956	50.000	0.00	0.00	0.00	1.85
3048	4672	1.642762	ACCTACCCTCTCCGTTCCTAA	59.357	52.381	0.00	0.00	0.00	2.69
3049	4673	1.302907	ACCTACCCTCTCCGTTCCTA	58.697	55.000	0.00	0.00	0.00	2.94
3050	4674	0.412640	AACCTACCCTCTCCGTTCCT	59.587	55.000	0.00	0.00	0.00	3.36
3051	4675	1.206610	GAAACCTACCCTCTCCGTTCC	59.793	57.143	0.00	0.00	0.00	3.62
3052	4676	1.897802	TGAAACCTACCCTCTCCGTTC	59.102	52.381	0.00	0.00	0.00	3.95
3053	4677	2.019807	TGAAACCTACCCTCTCCGTT	57.980	50.000	0.00	0.00	0.00	4.44
3054	4678	1.900486	CTTGAAACCTACCCTCTCCGT	59.100	52.381	0.00	0.00	0.00	4.69
3055	4679	2.176889	TCTTGAAACCTACCCTCTCCG	58.823	52.381	0.00	0.00	0.00	4.63
3056	4680	3.118223	CCATCTTGAAACCTACCCTCTCC	60.118	52.174	0.00	0.00	0.00	3.71
3057	4681	3.682999	GCCATCTTGAAACCTACCCTCTC	60.683	52.174	0.00	0.00	0.00	3.20
3058	4682	2.239907	GCCATCTTGAAACCTACCCTCT	59.760	50.000	0.00	0.00	0.00	3.69
3059	4683	2.026262	TGCCATCTTGAAACCTACCCTC	60.026	50.000	0.00	0.00	0.00	4.30
3060	4684	1.992557	TGCCATCTTGAAACCTACCCT	59.007	47.619	0.00	0.00	0.00	4.34
3061	4685	2.026262	TCTGCCATCTTGAAACCTACCC	60.026	50.000	0.00	0.00	0.00	3.69
3062	4686	3.010420	GTCTGCCATCTTGAAACCTACC	58.990	50.000	0.00	0.00	0.00	3.18
3145	4769	8.680001	TCATTAATTCAGACAGATGGAATTGTG	58.320	33.333	8.61	7.68	40.41	3.33
3205	4829	1.276138	CCTTGCCAAATCTTTGACCCC	59.724	52.381	4.25	0.00	40.55	4.95
3218	4842	9.398538	ACTTAATTATTTATTACGTCCTTGCCA	57.601	29.630	0.00	0.00	28.13	4.92
3219	4843	9.659830	CACTTAATTATTTATTACGTCCTTGCC	57.340	33.333	0.00	0.00	31.04	4.52
3274	4916	1.544724	TCCTTCCTTTGCAAATCCGG	58.455	50.000	13.23	10.90	0.00	5.14
3302	4944	5.353394	ACTCAAACAGGAAACTACACAGA	57.647	39.130	0.00	0.00	40.21	3.41
3310	4952	5.440685	CACGTTCATACTCAAACAGGAAAC	58.559	41.667	0.00	0.00	0.00	2.78
3315	4957	3.067106	AGCCACGTTCATACTCAAACAG	58.933	45.455	0.00	0.00	0.00	3.16
3329	4971	2.172717	AGATGCCCTAATTAAGCCACGT	59.827	45.455	5.04	0.00	0.00	4.49
3376	5018	5.560966	AACCTGTACAAAATATTGCCTCG	57.439	39.130	0.00	0.00	40.34	4.63
3401	5043	3.568538	GTTCAAGTAGTCGGACGCTTAA	58.431	45.455	16.41	4.57	0.00	1.85
3424	5066	4.884668	TTGATACTTTTCGAGTGGACCT	57.115	40.909	0.00	0.00	39.48	3.85
3461	5106	3.995809	TTAGGTCTGGGCTCCGGGG	62.996	68.421	0.00	0.00	0.00	5.73
3464	6191	2.022240	GCTCTTAGGTCTGGGCTCCG	62.022	65.000	0.00	0.00	0.00	4.63
3473	6200	1.957877	AGCCGTAGATGCTCTTAGGTC	59.042	52.381	0.00	0.00	32.41	3.85
3476	6203	1.957177	TCCAGCCGTAGATGCTCTTAG	59.043	52.381	0.00	0.00	36.81	2.18
3478	6205	0.461961	GTCCAGCCGTAGATGCTCTT	59.538	55.000	0.00	0.00	36.81	2.85
3509	6236	3.939837	ATCAGTGCCTGTGGACGCG	62.940	63.158	3.53	3.53	32.61	6.01
3510	6237	2.046892	ATCAGTGCCTGTGGACGC	60.047	61.111	2.68	0.00	32.61	5.19
3511	6238	1.807165	CGATCAGTGCCTGTGGACG	60.807	63.158	0.00	0.00	32.61	4.79
3512	6239	1.448540	CCGATCAGTGCCTGTGGAC	60.449	63.158	0.00	0.00	32.61	4.02
3513	6240	2.659063	CCCGATCAGTGCCTGTGGA	61.659	63.158	0.00	0.00	32.61	4.02
3514	6241	2.124983	CCCGATCAGTGCCTGTGG	60.125	66.667	0.00	3.99	32.61	4.17
3515	6242	2.821366	GCCCGATCAGTGCCTGTG	60.821	66.667	0.00	0.00	32.61	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.