AutoCloner

Multiple sequence alignment - TraesCS4D01G018100

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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	TraesCS4D01G018100	chr4D	100.000	3000	0	0	1	3000	7875058	7872059	0.000000e+00	5541.0
1	TraesCS4D01G018100	chr4A	86.978	2634	152	87	84	2589	595441952	595444522	0.000000e+00	2787.0
2	TraesCS4D01G018100	chr4A	83.421	380	47	10	2623	3000	595444783	595445148	3.700000e-89	339.0
3	TraesCS4D01G018100	chr4B	89.521	1794	112	37	998	2727	14054656	14056437	0.000000e+00	2202.0
4	TraesCS4D01G018100	chr4B	91.228	228	16	3	2774	3000	14078071	14078295	1.040000e-79	307.0
5	TraesCS4D01G018100	chr4B	80.000	440	42	27	1	401	14053637	14054069	1.760000e-72	283.0
6	TraesCS4D01G018100	chr4B	81.795	390	20	19	528	867	14054159	14054547	2.280000e-71	279.0
7	TraesCS4D01G018100	chr3B	87.859	1878	150	27	1169	3000	731095665	731093820	0.000000e+00	2134.0
8	TraesCS4D01G018100	chr3B	79.315	672	61	39	468	1101	731096292	731095661	1.680000e-107	399.0
9	TraesCS4D01G018100	chr3D	86.036	1733	136	48	998	2676	551346275	551344595	0.000000e+00	1762.0
10	TraesCS4D01G018100	chr3D	83.153	1478	134	57	557	2014	551429943	551431325	0.000000e+00	1243.0
11	TraesCS4D01G018100	chr3D	87.109	1024	94	10	2012	3000	551432586	551433606	0.000000e+00	1125.0
12	TraesCS4D01G018100	chr3D	84.877	324	30	7	2694	3000	551303577	551303256	2.900000e-80	309.0
13	TraesCS4D01G018100	chr3D	77.895	570	56	43	574	1094	551346700	551346152	1.050000e-74	291.0
14	TraesCS4D01G018100	chr3D	80.769	390	33	22	148	523	551350777	551350416	1.770000e-67	267.0
15	TraesCS4D01G018100	chr3D	78.109	402	60	19	2165	2556	551433854	551434237	2.330000e-56	230.0
16	TraesCS4D01G018100	chr3A	88.794	1169	87	19	1155	2304	688591850	688590707	0.000000e+00	1393.0
17	TraesCS4D01G018100	chr3A	86.700	609	59	6	2412	3000	688590596	688589990	0.000000e+00	656.0
18	TraesCS4D01G018100	chr3A	90.244	123	9	3	557	678	688592358	688592238	1.110000e-34	158.0
19	TraesCS4D01G018100	chr3A	75.515	388	42	33	740	1103	688592218	688591860	1.120000e-29	141.0
20	TraesCS4D01G018100	chr3A	94.231	52	2	1	998	1049	688591998	688591948	8.920000e-11	78.7
21	TraesCS4D01G018100	chr7D	81.244	997	137	30	1054	2023	550800534	550801507	0.000000e+00	760.0
22	TraesCS4D01G018100	chr7D	84.060	734	92	18	1303	2023	550553393	550554114	0.000000e+00	684.0
23	TraesCS4D01G018100	chr7D	77.734	256	30	14	2068	2305	550801664	550801910	6.750000e-27	132.0
24	TraesCS4D01G018100	chr7D	75.484	310	47	14	1078	1368	550643358	550643657	1.130000e-24	124.0
25	TraesCS4D01G018100	chr7D	78.710	155	21	6	1084	1229	550553192	550553343	3.180000e-15	93.5
26	TraesCS4D01G018100	chr7D	76.684	193	18	13	595	771	550800173	550800354	6.890000e-12	82.4
27	TraesCS4D01G018100	chr7D	100.000	38	0	0	734	771	550462802	550462839	1.490000e-08	71.3
28	TraesCS4D01G018100	chr7D	100.000	38	0	0	734	771	550552890	550552927	1.490000e-08	71.3
29	TraesCS4D01G018100	chr7B	80.392	1071	143	35	998	2023	595080569	595081617	0.000000e+00	752.0
30	TraesCS4D01G018100	chr7B	81.718	908	115	24	1149	2023	595007628	595008517	0.000000e+00	710.0
31	TraesCS4D01G018100	chr7B	78.307	189	17	10	597	771	595007117	595007295	1.900000e-17	100.0
32	TraesCS4D01G018100	chr7B	91.111	45	3	1	1005	1049	595007457	595007500	3.230000e-05	60.2
33	TraesCS4D01G018100	chr7A	82.215	894	117	24	1149	2023	636629234	636630104	0.000000e+00	732.0
34	TraesCS4D01G018100	chr7A	80.909	990	128	42	1070	2023	636126987	636127951	0.000000e+00	725.0
35	TraesCS4D01G018100	chr7A	80.471	891	116	30	1173	2023	635860554	635861426	1.960000e-176	628.0
36	TraesCS4D01G018100	chr7A	91.111	45	3	1	1005	1049	636629060	636629103	3.230000e-05	60.2

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	TraesCS4D01G018100	chr4D	7872059	7875058	2999	True	5541.000000	5541	100.000000	1	3000	1	chr4D.!!$R1	2999
1	TraesCS4D01G018100	chr4A	595441952	595445148	3196	False	1563.000000	2787	85.199500	84	3000	2	chr4A.!!$F1	2916
2	TraesCS4D01G018100	chr4B	14053637	14056437	2800	False	921.333333	2202	83.772000	1	2727	3	chr4B.!!$F2	2726
3	TraesCS4D01G018100	chr3B	731093820	731096292	2472	True	1266.500000	2134	83.587000	468	3000	2	chr3B.!!$R1	2532
4	TraesCS4D01G018100	chr3D	551429943	551434237	4294	False	866.000000	1243	82.790333	557	3000	3	chr3D.!!$F1	2443
5	TraesCS4D01G018100	chr3D	551344595	551350777	6182	True	773.333333	1762	81.566667	148	2676	3	chr3D.!!$R2	2528
6	TraesCS4D01G018100	chr3A	688589990	688592358	2368	True	485.340000	1393	87.096800	557	3000	5	chr3A.!!$R1	2443
7	TraesCS4D01G018100	chr7D	550800173	550801910	1737	False	324.800000	760	78.554000	595	2305	3	chr7D.!!$F4	1710
8	TraesCS4D01G018100	chr7D	550552890	550554114	1224	False	282.933333	684	87.590000	734	2023	3	chr7D.!!$F3	1289
9	TraesCS4D01G018100	chr7B	595080569	595081617	1048	False	752.000000	752	80.392000	998	2023	1	chr7B.!!$F1	1025
10	TraesCS4D01G018100	chr7B	595007117	595008517	1400	False	290.066667	710	83.712000	597	2023	3	chr7B.!!$F2	1426
11	TraesCS4D01G018100	chr7A	636126987	636127951	964	False	725.000000	725	80.909000	1070	2023	1	chr7A.!!$F2	953
12	TraesCS4D01G018100	chr7A	635860554	635861426	872	False	628.000000	628	80.471000	1173	2023	1	chr7A.!!$F1	850
13	TraesCS4D01G018100	chr7A	636629060	636630104	1044	False	396.100000	732	86.663000	1005	2023	2	chr7A.!!$F3	1018

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
27	28	0.035056	ATTTTGAGCCCCCGTCTCTG	60.035	55.0	0.00	0.00	0.00	3.35	F
685	4508	0.238553	TCGTCTGTTGCTCACTCGAG	59.761	55.0	11.84	11.84	42.66	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1505	5578	1.005512	CCACGGTGGACACGATCAA	60.006	57.895	22.77	0.0	40.96	2.57	R
2197	7731	0.465460	TGGTCGCAGCCCAAATATCC	60.465	55.000	0.00	0.0	0.00	2.59	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
19	20	2.967599	CCTTGCTAATTTTGAGCCCC	57.032	50.000	0.00	0.00	39.30	5.80
22	23	0.039035	TGCTAATTTTGAGCCCCCGT	59.961	50.000	0.00	0.00	39.30	5.28
23	24	0.738975	GCTAATTTTGAGCCCCCGTC	59.261	55.000	0.00	0.00	33.60	4.79
27	28	0.035056	ATTTTGAGCCCCCGTCTCTG	60.035	55.000	0.00	0.00	0.00	3.35
28	29	2.748058	TTTTGAGCCCCCGTCTCTGC	62.748	60.000	0.00	0.00	0.00	4.26
33	34	2.279073	CCCCCGTCTCTGCCTCTA	59.721	66.667	0.00	0.00	0.00	2.43
45	46	3.552875	TCTGCCTCTACTACGCTGTAAT	58.447	45.455	0.00	0.00	0.00	1.89
56	57	5.416947	ACTACGCTGTAATTTACTCCCTTG	58.583	41.667	7.99	0.00	0.00	3.61
64	65	9.569167	GCTGTAATTTACTCCCTTGTTATTTTC	57.431	33.333	7.99	0.00	0.00	2.29
66	67	9.816787	TGTAATTTACTCCCTTGTTATTTTCCT	57.183	29.630	7.99	0.00	0.00	3.36
140	163	7.429633	ACGCCTAATATATATCTCAGCACATC	58.570	38.462	0.00	0.00	0.00	3.06
143	166	9.258826	GCCTAATATATATCTCAGCACATCAAG	57.741	37.037	0.00	0.00	0.00	3.02
265	312	2.736682	CGGCGCTTTACCAAGTCCG	61.737	63.158	7.64	0.00	39.86	4.79
293	351	1.602191	GAAGCGCGTGGTAATTTGTG	58.398	50.000	8.43	0.00	0.00	3.33
339	401	2.099062	CAAGATTCGTGCGGCAGC	59.901	61.111	1.18	0.31	45.41	5.25
397	460	2.413796	CGCCACGACATGCTAACTTAAA	59.586	45.455	0.00	0.00	0.00	1.52
398	461	3.723835	CGCCACGACATGCTAACTTAAAC	60.724	47.826	0.00	0.00	0.00	2.01
399	462	3.723835	GCCACGACATGCTAACTTAAACG	60.724	47.826	0.00	0.00	0.00	3.60
400	463	3.676172	CCACGACATGCTAACTTAAACGA	59.324	43.478	0.00	0.00	0.00	3.85
401	464	4.433805	CCACGACATGCTAACTTAAACGAC	60.434	45.833	0.00	0.00	0.00	4.34
402	465	3.362831	ACGACATGCTAACTTAAACGACG	59.637	43.478	0.00	0.00	0.00	5.12
403	466	3.605056	CGACATGCTAACTTAAACGACGA	59.395	43.478	0.00	0.00	0.00	4.20
404	467	4.488258	CGACATGCTAACTTAAACGACGAC	60.488	45.833	0.00	0.00	0.00	4.34
405	468	3.362831	ACATGCTAACTTAAACGACGACG	59.637	43.478	5.58	5.58	45.75	5.12
406	469	3.266541	TGCTAACTTAAACGACGACGA	57.733	42.857	15.32	0.00	42.66	4.20
407	470	2.973224	TGCTAACTTAAACGACGACGAC	59.027	45.455	15.32	0.00	42.66	4.34
408	471	2.024528	GCTAACTTAAACGACGACGACG	59.975	50.000	17.60	17.60	42.66	5.12
409	472	2.383298	AACTTAAACGACGACGACGA	57.617	45.000	25.15	1.01	42.66	4.20
410	473	1.663494	ACTTAAACGACGACGACGAC	58.337	50.000	25.15	7.02	42.66	4.34
436	508	3.507162	TGATCTGGTCTCCTTTTGCAA	57.493	42.857	0.00	0.00	0.00	4.08
438	510	3.072915	TGATCTGGTCTCCTTTTGCAAGA	59.927	43.478	0.00	0.00	30.57	3.02
439	511	3.795688	TCTGGTCTCCTTTTGCAAGAT	57.204	42.857	0.00	0.00	30.57	2.40
440	512	3.679389	TCTGGTCTCCTTTTGCAAGATC	58.321	45.455	0.00	0.00	30.57	2.75
442	514	3.415212	TGGTCTCCTTTTGCAAGATCAG	58.585	45.455	0.00	0.00	30.57	2.90
443	515	2.163211	GGTCTCCTTTTGCAAGATCAGC	59.837	50.000	0.00	0.00	30.57	4.26
444	516	2.816087	GTCTCCTTTTGCAAGATCAGCA	59.184	45.455	8.58	8.58	40.85	4.41
453	525	2.030540	TGCAAGATCAGCAAACAGAAGC	60.031	45.455	10.03	0.00	39.39	3.86
454	526	2.670509	GCAAGATCAGCAAACAGAAGCC	60.671	50.000	5.41	0.00	0.00	4.35
455	527	2.555325	CAAGATCAGCAAACAGAAGCCA	59.445	45.455	0.00	0.00	0.00	4.75
456	528	2.434428	AGATCAGCAAACAGAAGCCAG	58.566	47.619	0.00	0.00	0.00	4.85
458	530	0.466007	TCAGCAAACAGAAGCCAGCA	60.466	50.000	0.00	0.00	0.00	4.41
459	531	0.601558	CAGCAAACAGAAGCCAGCAT	59.398	50.000	0.00	0.00	0.00	3.79
496	592	3.111853	TGGTTGCAGACTCTTGTGTAG	57.888	47.619	0.00	0.00	0.00	2.74
525	623	5.066375	AGGTAACACGCGGCGAATATATATA	59.934	40.000	30.94	7.25	41.41	0.86
553	651	9.830186	ATATATTCTTGGTTTCTAGCTAGGAGA	57.170	33.333	20.58	11.07	0.00	3.71
554	652	5.923733	TTCTTGGTTTCTAGCTAGGAGAG	57.076	43.478	20.58	8.76	0.00	3.20
579	4365	6.846283	GCACTCCGAATTAAGTCGAATTATTG	59.154	38.462	25.41	13.69	43.86	1.90
671	4482	1.123928	GGGGGTCAATCTCATCGTCT	58.876	55.000	0.00	0.00	0.00	4.18
685	4508	0.238553	TCGTCTGTTGCTCACTCGAG	59.761	55.000	11.84	11.84	42.66	4.04
776	4614	4.559063	CTGCCTGCCATCCGAGGG	62.559	72.222	0.00	0.00	0.00	4.30
914	4827	2.914097	GCCTTGGCTGCCTGTGTT	60.914	61.111	21.03	0.00	0.00	3.32
921	4834	4.516698	CCTTGGCTGCCTGTGTTTATATAG	59.483	45.833	21.03	0.53	0.00	1.31
991	4911	3.140814	GTCCCCGGCCTTTGCATC	61.141	66.667	0.00	0.00	40.13	3.91
992	4912	4.794648	TCCCCGGCCTTTGCATCG	62.795	66.667	0.00	0.00	40.13	3.84
996	4916	3.746889	CGGCCTTTGCATCGCCAA	61.747	61.111	16.69	0.00	43.17	4.52
1379	5394	2.029290	ACAGACATGTAAGTCCCGTGAC	60.029	50.000	0.00	0.00	38.09	3.67
1406	5440	2.572095	ATCGCCGCGTTTGATCAGGA	62.572	55.000	13.39	0.00	0.00	3.86
1413	5447	3.419915	CGCGTTTGATCAGGATTTTCTG	58.580	45.455	0.00	0.00	36.17	3.02
1416	5460	3.428045	CGTTTGATCAGGATTTTCTGGCC	60.428	47.826	0.00	0.00	35.58	5.36
1813	5907	4.200283	GTCTGCGCGGAGGAGGAG	62.200	72.222	27.80	1.24	38.98	3.69
2039	7447	4.522722	AGAGTAGGGTCGACTTTTCTTG	57.477	45.455	16.46	0.00	0.00	3.02
2257	7803	3.785859	GAGCGGTGGGAGATGGCA	61.786	66.667	0.00	0.00	0.00	4.92
2346	7945	0.451135	CGAGAAACGAGCGCAAAAGG	60.451	55.000	11.47	0.00	45.77	3.11
2347	7946	0.586802	GAGAAACGAGCGCAAAAGGT	59.413	50.000	11.47	0.00	0.00	3.50
2348	7947	1.796459	GAGAAACGAGCGCAAAAGGTA	59.204	47.619	11.47	0.00	0.00	3.08
2400	8003	1.224003	AGAAATGGGTGGATGGGCCT	61.224	55.000	4.53	0.00	37.63	5.19
2406	8009	3.661648	GTGGATGGGCCTGGTGGT	61.662	66.667	4.53	0.00	37.63	4.16
2413	8016	2.676471	GGCCTGGTGGTGCGATTT	60.676	61.111	0.00	0.00	35.27	2.17
2434	8037	6.524101	TTTAGAAATTGGTGGATTGGCTAC	57.476	37.500	0.00	0.00	0.00	3.58
2437	8040	1.767759	ATTGGTGGATTGGCTACTGC	58.232	50.000	0.00	0.00	38.76	4.40
2468	8072	4.941713	AGAGATCTAGACAACTGGGAAGT	58.058	43.478	0.00	0.00	0.00	3.01
2520	8130	5.156355	CAACGGTCCAAAGATTGATTTGAG	58.844	41.667	0.91	0.00	41.71	3.02
2686	8523	7.123997	GCTAGGTTTAAGGTTTAGAGGTCTAGT	59.876	40.741	0.00	0.00	0.00	2.57
2692	8529	9.716531	TTTAAGGTTTAGAGGTCTAGTAAAAGC	57.283	33.333	0.00	0.00	0.00	3.51
2699	8536	6.622833	AGAGGTCTAGTAAAAGCGAGATAC	57.377	41.667	0.00	0.00	0.00	2.24
2706	8543	5.007385	AGTAAAAGCGAGATACGAACCAT	57.993	39.130	0.00	0.00	45.77	3.55
2727	8564	9.969001	AACCATATTCAGGTTTAAGCTAAGTTA	57.031	29.630	0.00	0.00	46.85	2.24
2851	8705	1.523258	CGCTTGGAGGCATGAGAGG	60.523	63.158	0.00	0.00	0.00	3.69
2879	8733	8.319057	AGGAAATGACATCTACAACTATGGTA	57.681	34.615	0.00	0.00	0.00	3.25
2891	8745	1.761198	ACTATGGTAGAGGGGCGAAAC	59.239	52.381	0.00	0.00	0.00	2.78
2956	8810	3.627577	CGTTTGAGAAATAGGTGGATGGG	59.372	47.826	0.00	0.00	0.00	4.00
2965	8819	6.332901	AGAAATAGGTGGATGGGCTAGTTTAT	59.667	38.462	0.00	0.00	0.00	1.40
2973	8827	5.070685	GGATGGGCTAGTTTATGGTTTAGG	58.929	45.833	0.00	0.00	0.00	2.69
2982	8836	7.660617	GCTAGTTTATGGTTTAGGGATCTAACC	59.339	40.741	10.59	10.59	35.40	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	3.706373	GCAGAGACGGGGGCTCAA	61.706	66.667	0.72	0.00	34.85	3.02
19	20	0.938713	CGTAGTAGAGGCAGAGACGG	59.061	60.000	0.00	0.00	0.00	4.79
22	23	1.065345	ACAGCGTAGTAGAGGCAGAGA	60.065	52.381	0.00	0.00	41.59	3.10
23	24	1.384525	ACAGCGTAGTAGAGGCAGAG	58.615	55.000	0.00	0.00	41.59	3.35
27	28	5.829829	AGTAAATTACAGCGTAGTAGAGGC	58.170	41.667	5.89	0.00	39.33	4.70
28	29	6.437094	GGAGTAAATTACAGCGTAGTAGAGG	58.563	44.000	5.89	0.00	0.00	3.69
29	30	6.262720	AGGGAGTAAATTACAGCGTAGTAGAG	59.737	42.308	5.89	0.00	0.00	2.43
30	31	6.125029	AGGGAGTAAATTACAGCGTAGTAGA	58.875	40.000	5.89	0.00	0.00	2.59
33	34	5.046807	ACAAGGGAGTAAATTACAGCGTAGT	60.047	40.000	5.89	0.00	0.00	2.73
116	135	7.428826	TGATGTGCTGAGATATATATTAGGCG	58.571	38.462	0.00	0.00	0.00	5.52
117	136	9.258826	CTTGATGTGCTGAGATATATATTAGGC	57.741	37.037	0.00	1.29	0.00	3.93
140	163	2.447089	CATCTGCATGCACGTACTTG	57.553	50.000	18.46	5.29	0.00	3.16
164	197	2.394136	CGTACGTTCATGCACGCC	59.606	61.111	17.85	7.84	44.37	5.68
166	199	2.018137	CGCGTACGTTCATGCACG	59.982	61.111	16.39	16.39	46.04	5.34
293	351	1.202325	GGAAACCCACAACCGAACAAC	60.202	52.381	0.00	0.00	0.00	3.32
339	401	1.129998	CGTTGAGGCTGCTTTGATCTG	59.870	52.381	0.00	0.00	0.00	2.90
340	402	1.002430	TCGTTGAGGCTGCTTTGATCT	59.998	47.619	0.00	0.00	0.00	2.75
397	460	4.400776	CGTCGTCGTCGTCGTCGT	62.401	66.667	18.87	0.00	45.27	4.34
398	461	3.397649	ATCGTCGTCGTCGTCGTCG	62.398	63.158	20.39	20.39	45.27	5.12
399	462	1.922220	CATCGTCGTCGTCGTCGTC	60.922	63.158	18.44	5.52	45.27	4.20
400	463	1.690283	ATCATCGTCGTCGTCGTCGT	61.690	55.000	18.44	6.36	45.27	4.34
401	464	0.981076	GATCATCGTCGTCGTCGTCG	60.981	60.000	14.18	14.18	46.06	5.12
402	465	0.301088	AGATCATCGTCGTCGTCGTC	59.699	55.000	11.41	2.48	38.33	4.20
403	466	0.026414	CAGATCATCGTCGTCGTCGT	59.974	55.000	11.41	0.00	38.33	4.34
404	467	0.654760	CCAGATCATCGTCGTCGTCG	60.655	60.000	5.50	5.50	38.33	5.12
405	468	0.377554	ACCAGATCATCGTCGTCGTC	59.622	55.000	1.33	0.00	38.33	4.20
406	469	0.377554	GACCAGATCATCGTCGTCGT	59.622	55.000	1.33	0.00	38.33	4.34
407	470	0.658368	AGACCAGATCATCGTCGTCG	59.342	55.000	0.00	0.00	38.55	5.12
408	471	1.002251	GGAGACCAGATCATCGTCGTC	60.002	57.143	0.00	0.00	0.00	4.20
409	472	1.025812	GGAGACCAGATCATCGTCGT	58.974	55.000	0.00	0.00	0.00	4.34
410	473	1.313772	AGGAGACCAGATCATCGTCG	58.686	55.000	0.00	0.00	0.00	5.12
411	474	3.810310	AAAGGAGACCAGATCATCGTC	57.190	47.619	0.00	0.00	0.00	4.20
436	508	2.434428	CTGGCTTCTGTTTGCTGATCT	58.566	47.619	0.00	0.00	0.00	2.75
438	510	0.886563	GCTGGCTTCTGTTTGCTGAT	59.113	50.000	0.00	0.00	0.00	2.90
439	511	0.466007	TGCTGGCTTCTGTTTGCTGA	60.466	50.000	0.00	0.00	0.00	4.26
440	512	0.601558	ATGCTGGCTTCTGTTTGCTG	59.398	50.000	0.00	0.00	0.00	4.41
442	514	0.599558	TCATGCTGGCTTCTGTTTGC	59.400	50.000	0.00	0.00	0.00	3.68
443	515	3.587797	ATTCATGCTGGCTTCTGTTTG	57.412	42.857	0.00	0.00	0.00	2.93
444	516	6.516194	GCATATATTCATGCTGGCTTCTGTTT	60.516	38.462	3.61	0.00	46.35	2.83
458	530	5.463286	CAACCAACGCATGCATATATTCAT	58.537	37.500	19.57	0.00	0.00	2.57
459	531	4.792380	GCAACCAACGCATGCATATATTCA	60.792	41.667	19.57	0.00	39.81	2.57
496	592	0.848305	CGCCGCGTGTTACCTTATAC	59.152	55.000	4.92	0.00	0.00	1.47
553	651	3.587797	TTCGACTTAATTCGGAGTGCT	57.412	42.857	14.32	0.00	39.58	4.40
554	652	4.859629	AATTCGACTTAATTCGGAGTGC	57.140	40.909	14.32	0.00	39.58	4.40
555	653	8.126871	TCAATAATTCGACTTAATTCGGAGTG	57.873	34.615	14.32	7.93	39.58	3.51
579	4365	1.916181	TCAATCAACCTCTCCCCCTTC	59.084	52.381	0.00	0.00	0.00	3.46
671	4482	2.343758	GGCCTCGAGTGAGCAACA	59.656	61.111	12.31	0.00	41.13	3.33
776	4614	4.452733	CAAGGAGGTCCGTCCCGC	62.453	72.222	2.52	0.00	42.08	6.13
817	4671	2.687418	GATGGATGGATGGGCAGCGT	62.687	60.000	0.00	0.00	0.00	5.07
981	4901	2.507769	GCTTGGCGATGCAAAGGC	60.508	61.111	7.94	10.68	39.76	4.35
982	4902	1.952102	ATGGCTTGGCGATGCAAAGG	61.952	55.000	7.94	0.00	39.76	3.11
983	4903	0.804544	CATGGCTTGGCGATGCAAAG	60.805	55.000	8.78	1.49	42.08	2.77
984	4904	1.215912	CATGGCTTGGCGATGCAAA	59.784	52.632	8.78	0.00	37.87	3.68
985	4905	2.712944	CCATGGCTTGGCGATGCAA	61.713	57.895	6.47	0.00	42.05	4.08
986	4906	3.142162	CCATGGCTTGGCGATGCA	61.142	61.111	6.47	0.00	42.05	3.96
994	4914	3.443045	GTCCACGGCCATGGCTTG	61.443	66.667	34.70	28.75	39.85	4.01
995	4915	4.740822	GGTCCACGGCCATGGCTT	62.741	66.667	34.70	20.19	39.85	4.35
1137	5111	2.125512	GGCGGCGTGAAGATGTCT	60.126	61.111	9.37	0.00	0.00	3.41
1283	5287	4.813526	CGAGCACCGACGAGGACG	62.814	72.222	8.56	0.00	45.00	4.79
1284	5288	4.477975	CCGAGCACCGACGAGGAC	62.478	72.222	8.56	1.13	45.00	3.85
1379	5394	1.581602	CAAACGCGGCGATTAATTTGG	59.418	47.619	30.94	5.19	0.00	3.28
1406	5440	4.842574	ACAACAAACAAAGGCCAGAAAAT	58.157	34.783	5.01	0.00	0.00	1.82
1413	5447	2.861335	CCGTTAACAACAAACAAAGGCC	59.139	45.455	6.39	0.00	0.00	5.19
1416	5460	4.324936	CACCACCGTTAACAACAAACAAAG	59.675	41.667	6.39	0.00	0.00	2.77
1505	5578	1.005512	CCACGGTGGACACGATCAA	60.006	57.895	22.77	0.00	40.96	2.57
2197	7731	0.465460	TGGTCGCAGCCCAAATATCC	60.465	55.000	0.00	0.00	0.00	2.59
2203	7737	4.659172	CCCTTGGTCGCAGCCCAA	62.659	66.667	3.37	3.37	0.00	4.12
2225	7760	2.579787	CTCACCTAAGTCGCCGCG	60.580	66.667	6.39	6.39	0.00	6.46
2257	7803	5.344743	AATGTCTCCACGTGTCTGATTAT	57.655	39.130	15.65	5.88	0.00	1.28
2340	7939	1.468914	GCTCGCCCTCTTTACCTTTTG	59.531	52.381	0.00	0.00	0.00	2.44
2376	7975	2.423373	CCCATCCACCCATTTCTCGAAT	60.423	50.000	0.00	0.00	0.00	3.34
2400	8003	3.192422	CCAATTTCTAAATCGCACCACCA	59.808	43.478	0.00	0.00	0.00	4.17
2403	8006	3.192422	CCACCAATTTCTAAATCGCACCA	59.808	43.478	0.00	0.00	0.00	4.17
2406	8009	5.394005	CCAATCCACCAATTTCTAAATCGCA	60.394	40.000	0.00	0.00	0.00	5.10
2410	8013	6.897413	AGTAGCCAATCCACCAATTTCTAAAT	59.103	34.615	0.00	0.00	0.00	1.40
2413	8016	5.192927	CAGTAGCCAATCCACCAATTTCTA	58.807	41.667	0.00	0.00	0.00	2.10
2434	8037	6.065374	TGTCTAGATCTCTAAACCCTAGCAG	58.935	44.000	0.00	0.00	0.00	4.24
2437	8040	7.013846	CCAGTTGTCTAGATCTCTAAACCCTAG	59.986	44.444	0.00	0.00	0.00	3.02
2468	8072	1.048724	CGGGCTCTATCTTCACCCCA	61.049	60.000	0.00	0.00	37.25	4.96
2520	8130	5.324697	CAGCCGAGCAAACTTTCTATAAAC	58.675	41.667	0.00	0.00	0.00	2.01
2561	8171	6.013085	CCGTATAGTCGTTTGTGTGAATTTG	58.987	40.000	0.00	0.00	0.00	2.32
2612	8223	2.545537	AACGGACACCTTCTTTCTCC	57.454	50.000	0.00	0.00	0.00	3.71
2686	8523	7.204604	TGAATATGGTTCGTATCTCGCTTTTA	58.795	34.615	0.00	0.00	39.67	1.52
2692	8529	5.122512	ACCTGAATATGGTTCGTATCTCG	57.877	43.478	0.00	0.00	41.41	4.04
2699	8536	7.280205	ACTTAGCTTAAACCTGAATATGGTTCG	59.720	37.037	0.00	0.00	45.99	3.95
2773	8610	3.638316	TCGCCGCAAACCCCCTTA	61.638	61.111	0.00	0.00	0.00	2.69
2851	8705	5.886960	AGTTGTAGATGTCATTTCCTTGC	57.113	39.130	0.00	0.00	0.00	4.01
2879	8733	0.546598	CCCTAATGTTTCGCCCCTCT	59.453	55.000	0.00	0.00	0.00	3.69
2891	8745	5.251764	CCATCTATCCTTCTTGCCCTAATG	58.748	45.833	0.00	0.00	0.00	1.90
2956	8810	7.660617	GGTTAGATCCCTAAACCATAAACTAGC	59.339	40.741	10.44	0.00	36.75	3.42
2965	8819	3.120108	CCCTGGTTAGATCCCTAAACCA	58.880	50.000	15.04	15.04	40.91	3.67
2973	8827	0.106894	CCGCTTCCCTGGTTAGATCC	59.893	60.000	0.00	0.00	0.00	3.36
2982	8836	2.045926	CTTCACCCCGCTTCCCTG	60.046	66.667	0.00	0.00	0.00	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.