AutoCloner

Multiple sequence alignment - TraesCS6D01G021500

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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	TraesCS6D01G021500	chr6D	100.000	5558	0	0	1	5558	8545893	8540336	0.000000e+00	10264.0
1	TraesCS6D01G021500	chr6D	97.809	2738	51	7	2575	5309	8809377	8812108	0.000000e+00	4715.0
2	TraesCS6D01G021500	chr6D	86.866	3746	302	86	543	4200	34081027	34084670	0.000000e+00	4017.0
3	TraesCS6D01G021500	chr6D	94.601	2130	70	11	543	2637	8807260	8809379	0.000000e+00	3254.0
4	TraesCS6D01G021500	chr6D	96.893	1191	34	1	1202	2389	8561403	8560213	0.000000e+00	1991.0
5	TraesCS6D01G021500	chr6D	94.474	1122	39	3	81	1201	8562846	8561747	0.000000e+00	1707.0
6	TraesCS6D01G021500	chr6D	95.455	594	24	2	3138	3730	8560053	8559462	0.000000e+00	944.0
7	TraesCS6D01G021500	chr6D	94.847	524	26	1	3728	4250	8559338	8558815	0.000000e+00	817.0
8	TraesCS6D01G021500	chr6D	97.778	225	2	1	5337	5558	8812173	8812397	8.730000e-103	385.0
9	TraesCS6D01G021500	chr6D	92.800	250	13	3	4278	4527	8558744	8558500	1.900000e-94	357.0
10	TraesCS6D01G021500	chr6D	93.909	197	10	2	4526	4722	34084972	34085166	4.210000e-76	296.0
11	TraesCS6D01G021500	chr6D	95.238	168	5	2	2931	3098	8560216	8560052	4.270000e-66	263.0
12	TraesCS6D01G021500	chr6D	91.379	116	10	0	4883	4998	8557316	8557201	5.760000e-35	159.0
13	TraesCS6D01G021500	chr6D	87.143	140	18	0	411	550	469779298	469779159	5.760000e-35	159.0
14	TraesCS6D01G021500	chr6D	87.143	140	18	0	411	550	469786952	469786813	5.760000e-35	159.0
15	TraesCS6D01G021500	chr6D	95.789	95	4	0	1	95	8563275	8563181	2.680000e-33	154.0
16	TraesCS6D01G021500	chr6D	90.265	113	10	1	301	412	8807150	8807262	4.490000e-31	147.0
17	TraesCS6D01G021500	chr6D	83.077	130	15	3	4404	4527	34084816	34084944	1.640000e-20	111.0
18	TraesCS6D01G021500	chr6B	93.834	4022	186	27	543	4527	16440040	16444036	0.000000e+00	5997.0
19	TraesCS6D01G021500	chr6B	94.451	3658	162	20	543	4180	15210684	15207048	0.000000e+00	5592.0
20	TraesCS6D01G021500	chr6B	93.237	414	25	3	1	412	16439630	16440042	1.710000e-169	606.0
21	TraesCS6D01G021500	chr6B	92.512	414	28	3	1	412	15211094	15210682	1.720000e-164	590.0
22	TraesCS6D01G021500	chr6B	88.309	479	35	11	4526	5003	16444064	16444522	6.290000e-154	555.0
23	TraesCS6D01G021500	chr6A	91.459	3243	192	42	543	3730	9481935	9485147	0.000000e+00	4375.0
24	TraesCS6D01G021500	chr6A	91.657	827	41	14	3728	4527	9485271	9486096	0.000000e+00	1120.0
25	TraesCS6D01G021500	chr6A	93.462	413	26	1	1	412	9481525	9481937	3.680000e-171	612.0
26	TraesCS6D01G021500	chr6A	91.667	300	20	5	5013	5309	9480840	9481137	1.440000e-110	411.0
27	TraesCS6D01G021500	chr6A	100.000	28	0	0	4999	5026	9480645	9480672	1.000000e-02	52.8
28	TraesCS6D01G021500	chr5B	85.432	3240	307	73	543	3718	556786546	556783408	0.000000e+00	3216.0
29	TraesCS6D01G021500	chr5B	85.282	496	42	15	3728	4194	556783276	556782783	3.010000e-132	483.0
30	TraesCS6D01G021500	chr5B	83.673	441	47	9	4526	4955	17672999	17673425	5.220000e-105	392.0
31	TraesCS6D01G021500	chr5B	84.740	308	25	9	4526	4833	556782259	556781974	7.040000e-74	289.0
32	TraesCS6D01G021500	chr5B	89.024	82	8	1	4445	4526	556782368	556782288	3.540000e-17	100.0
33	TraesCS6D01G021500	chr4A	73.732	1439	256	77	796	2181	737063916	737062547	8.490000e-123	451.0
34	TraesCS6D01G021500	chr4A	85.841	113	15	1	3972	4083	737067112	737067000	9.780000e-23	119.0
35	TraesCS6D01G021500	chr5D	88.814	295	27	2	3890	4179	42078790	42079083	1.900000e-94	357.0
36	TraesCS6D01G021500	chr5D	87.200	125	15	1	420	543	170399624	170399748	2.090000e-29	141.0
37	TraesCS6D01G021500	chr2A	90.426	94	8	1	412	505	497015011	497015103	7.560000e-24	122.0
38	TraesCS6D01G021500	chr7A	83.453	139	14	6	5106	5240	604392155	604392022	2.720000e-23	121.0
39	TraesCS6D01G021500	chr2B	84.906	106	14	2	5101	5205	63295276	63295172	7.610000e-19	106.0
40	TraesCS6D01G021500	chr2B	90.476	42	3	1	5144	5184	323090214	323090173	3.000000e-03	54.7
41	TraesCS6D01G021500	chr5A	87.654	81	10	0	463	543	648945642	648945562	1.650000e-15	95.3
42	TraesCS6D01G021500	chr2D	83.019	106	16	2	5101	5205	36792738	36792634	1.650000e-15	95.3

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	TraesCS6D01G021500	chr6D	8540336	8545893	5557	True	10264.000000	10264	100.000000	1	5558	1	chr6D.!!$R1	5557
1	TraesCS6D01G021500	chr6D	8807150	8812397	5247	False	2125.250000	4715	95.113250	301	5558	4	chr6D.!!$F1	5257
2	TraesCS6D01G021500	chr6D	34081027	34085166	4139	False	1474.666667	4017	87.950667	543	4722	3	chr6D.!!$F2	4179
3	TraesCS6D01G021500	chr6D	8557201	8563275	6074	True	799.000000	1991	94.609375	1	4998	8	chr6D.!!$R4	4997
4	TraesCS6D01G021500	chr6B	15207048	15211094	4046	True	3091.000000	5592	93.481500	1	4180	2	chr6B.!!$R1	4179
5	TraesCS6D01G021500	chr6B	16439630	16444522	4892	False	2386.000000	5997	91.793333	1	5003	3	chr6B.!!$F1	5002
6	TraesCS6D01G021500	chr6A	9480645	9486096	5451	False	1314.160000	4375	93.649000	1	5309	5	chr6A.!!$F1	5308
7	TraesCS6D01G021500	chr5B	556781974	556786546	4572	True	1022.000000	3216	86.119500	543	4833	4	chr5B.!!$R1	4290
8	TraesCS6D01G021500	chr4A	737062547	737067112	4565	True	285.000000	451	79.786500	796	4083	2	chr4A.!!$R1	3287

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
315	1546	0.469917	AGATGACCCCGATGCGAAAT	59.530	50.000	0.00	0.00	0.0	2.17	F
942	3392	1.133976	CATCCATTCACTCCCTGTCCC	60.134	57.143	0.00	0.00	0.0	4.46	F
1566	4404	0.528033	TGTTTCGGTTCTTCGCGTGA	60.528	50.000	5.77	2.87	0.0	4.35	F
1846	4695	0.951525	CGTTCCGTACACATTGGCCA	60.952	55.000	0.00	0.00	0.0	5.36	F
2515	5454	0.817229	TGTTCCGCACACATCAAGCA	60.817	50.000	0.00	0.00	0.0	3.91	F
3643	6663	3.288092	ACGAAAAGCTGGGTTCTCTTTT	58.712	40.909	0.00	0.00	41.2	2.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1215	4031	1.078143	GATGAAGTCTGGGGCGCTT	60.078	57.895	7.64	0.0	0.00	4.68	R
1969	4830	1.606903	TACAACGGCCAATCGGTTTT	58.393	45.000	2.24	0.0	36.27	2.43	R
2515	5454	3.070159	TGTGAAGTGCTACTCTTTGAGCT	59.930	43.478	0.00	0.0	39.54	4.09	R
3643	6663	1.965990	ATTGCCGTCAATGCTGCAA	59.034	47.368	6.36	8.3	46.51	4.08	R
4066	7245	3.441101	AGTAGTACCTGAAGCATGTGGA	58.559	45.455	0.00	0.0	0.00	4.02	R
5156	9368	1.215647	GCTACTCAGTGACCCACCG	59.784	63.158	0.00	0.0	34.49	4.94	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
315	1546	0.469917	AGATGACCCCGATGCGAAAT	59.530	50.000	0.00	0.00	0.00	2.17
450	1682	2.264166	GCTCTGCAACTCCGCTCT	59.736	61.111	0.00	0.00	0.00	4.09
482	1714	3.751175	CGGCATGTAGTTGTAATATGGGG	59.249	47.826	0.00	0.00	0.00	4.96
596	1828	1.497991	TTGTTGAGTACTGCTGTCGC	58.502	50.000	0.00	0.00	0.00	5.19
730	1965	6.721208	TCTGCAAATAAAAGTTCTCCAAGGAT	59.279	34.615	0.00	0.00	0.00	3.24
902	3307	5.541258	TCCAACTCCCCTATATATACGGT	57.459	43.478	6.93	0.00	0.00	4.83
942	3392	1.133976	CATCCATTCACTCCCTGTCCC	60.134	57.143	0.00	0.00	0.00	4.46
1024	3474	1.303317	GCCCCGATGTTGAACCAGT	60.303	57.895	0.00	0.00	0.00	4.00
1215	4031	0.911045	TGCAGATGCTCCAGGAAGGA	60.911	55.000	6.35	0.00	45.91	3.36
1349	4165	1.073125	ACCCATGTTGTGTGATCCGAA	59.927	47.619	0.00	0.00	0.00	4.30
1432	4248	1.705186	ACAAGCCCTGTGTGGACTATT	59.295	47.619	0.00	0.00	36.69	1.73
1566	4404	0.528033	TGTTTCGGTTCTTCGCGTGA	60.528	50.000	5.77	2.87	0.00	4.35
1845	4694	1.641123	CCGTTCCGTACACATTGGCC	61.641	60.000	0.00	0.00	0.00	5.36
1846	4695	0.951525	CGTTCCGTACACATTGGCCA	60.952	55.000	0.00	0.00	0.00	5.36
1847	4696	1.240256	GTTCCGTACACATTGGCCAA	58.760	50.000	23.00	23.00	0.00	4.52
1969	4830	8.022550	TCGTACTGTTTGTGATTTAGATACGAA	58.977	33.333	0.00	0.00	38.10	3.85
2011	4872	6.782298	ATTGTTCTATGATCTGCATTCGAG	57.218	37.500	0.00	0.00	38.44	4.04
2075	4977	5.871834	ACAAACAGTTAGGCCATTGTACTA	58.128	37.500	5.01	0.00	29.89	1.82
2221	5126	2.899900	ACCAGACAGCTCAATGAGTACA	59.100	45.455	12.29	0.00	31.39	2.90
2368	5292	6.858478	GCACTTCACATCTCCTTTTTAAAGTC	59.142	38.462	1.91	0.00	34.20	3.01
2399	5324	9.945904	CTCCTATAGTTAATTTGGGAGGATTAC	57.054	37.037	0.00	0.00	36.28	1.89
2515	5454	0.817229	TGTTCCGCACACATCAAGCA	60.817	50.000	0.00	0.00	0.00	3.91
2731	5730	9.338622	ACTAGTTGATAGTTTTGCAAGTTTAGT	57.661	29.630	0.00	0.00	42.30	2.24
2838	5842	4.609691	AGTTAAGTCCGTGTGTGTTTTG	57.390	40.909	0.00	0.00	0.00	2.44
2866	5870	9.561069	GTCTATACATGTGGTTCTTATGGAATT	57.439	33.333	9.11	0.00	36.24	2.17
3354	6364	6.813649	TGTTACTCAAATCTCATACTGACTGC	59.186	38.462	0.00	0.00	0.00	4.40
3534	6548	4.626172	GGTTAGGAATATAACTGCGCTAGC	59.374	45.833	9.73	4.06	36.19	3.42
3643	6663	3.288092	ACGAAAAGCTGGGTTCTCTTTT	58.712	40.909	0.00	0.00	41.20	2.27
3644	6664	3.699538	ACGAAAAGCTGGGTTCTCTTTTT	59.300	39.130	0.00	0.00	39.34	1.94
3645	6665	4.044426	CGAAAAGCTGGGTTCTCTTTTTG	58.956	43.478	0.00	0.00	39.34	2.44
3883	7035	4.870636	AGGCAAATTGTAATGGGATGAGA	58.129	39.130	0.00	0.00	0.00	3.27
4066	7245	2.559231	TGATGTGTGCAGCATGTTCAAT	59.441	40.909	0.00	0.00	35.94	2.57
4118	7298	8.713737	AAAACTCGTCTTAAACTCTTTGTAGT	57.286	30.769	0.00	0.00	0.00	2.73
4237	7546	8.959548	TGTTAATGAGATGAATGCAGTATTTGT	58.040	29.630	0.00	0.00	0.00	2.83
4543	7936	1.676967	CCAGCAGGTCCAAGCCTTC	60.677	63.158	2.96	0.00	36.58	3.46
4703	8096	1.801178	GCGGCAAGCTAATCATCTACC	59.199	52.381	0.00	0.00	44.04	3.18
4761	8155	6.729690	TTTGGAATTCTCAGTGGTCAAATT	57.270	33.333	5.23	0.00	0.00	1.82
4783	8178	7.713764	ATTAAAAATTCAGCTGTGGTTGTTC	57.286	32.000	14.67	0.00	0.00	3.18
4821	8216	5.885912	TGGTTAATCTGGTGCCTTATTTCTC	59.114	40.000	0.00	0.00	0.00	2.87
5027	9238	3.493877	TGTGCACATTATGTTTTGCTTGC	59.506	39.130	17.42	0.00	35.91	4.01
5032	9243	4.691685	CACATTATGTTTTGCTTGCATGGT	59.308	37.500	0.00	0.00	0.00	3.55
5080	9291	1.280710	TCGTTTAGGCATGGATGTGGT	59.719	47.619	0.00	0.00	0.00	4.16
5090	9301	0.107643	TGGATGTGGTTCGCAACTCA	59.892	50.000	0.00	0.00	0.00	3.41
5156	9368	4.965200	AAGTGGCTGATTATCCCTACTC	57.035	45.455	1.07	0.00	0.00	2.59
5174	9386	1.215647	CGGTGGGTCACTGAGTAGC	59.784	63.158	0.88	0.00	42.79	3.58
5175	9387	1.251527	CGGTGGGTCACTGAGTAGCT	61.252	60.000	0.88	0.00	42.79	3.32
5176	9388	0.977395	GGTGGGTCACTGAGTAGCTT	59.023	55.000	0.00	0.00	34.40	3.74
5249	9461	0.392998	CCAGCCGACCAACAGCTAAT	60.393	55.000	0.00	0.00	34.38	1.73
5304	9517	5.576774	TGTTAGCATACAAGATGACAACGAG	59.423	40.000	0.00	0.00	0.00	4.18
5306	9519	4.820897	AGCATACAAGATGACAACGAGAA	58.179	39.130	0.00	0.00	0.00	2.87
5308	9521	5.877012	AGCATACAAGATGACAACGAGAATT	59.123	36.000	0.00	0.00	0.00	2.17
5310	9523	6.684555	GCATACAAGATGACAACGAGAATTTC	59.315	38.462	0.00	0.00	0.00	2.17
5312	9525	9.087424	CATACAAGATGACAACGAGAATTTCTA	57.913	33.333	0.00	0.00	0.00	2.10
5313	9526	7.962964	ACAAGATGACAACGAGAATTTCTAA	57.037	32.000	0.00	0.00	0.00	2.10
5315	9528	8.660373	ACAAGATGACAACGAGAATTTCTAATC	58.340	33.333	0.00	0.00	0.00	1.75
5316	9529	8.877779	CAAGATGACAACGAGAATTTCTAATCT	58.122	33.333	0.00	0.00	0.00	2.40
5317	9530	8.417780	AGATGACAACGAGAATTTCTAATCTG	57.582	34.615	0.00	0.00	0.00	2.90
5318	9531	8.253810	AGATGACAACGAGAATTTCTAATCTGA	58.746	33.333	0.00	0.00	0.00	3.27
5319	9532	7.818493	TGACAACGAGAATTTCTAATCTGAG	57.182	36.000	0.00	0.00	0.00	3.35
5320	9533	6.311445	TGACAACGAGAATTTCTAATCTGAGC	59.689	38.462	0.00	0.00	0.00	4.26
5321	9534	5.582665	ACAACGAGAATTTCTAATCTGAGCC	59.417	40.000	0.00	0.00	0.00	4.70
5322	9535	4.698575	ACGAGAATTTCTAATCTGAGCCC	58.301	43.478	0.00	0.00	0.00	5.19
5324	9537	5.598830	ACGAGAATTTCTAATCTGAGCCCTA	59.401	40.000	0.00	0.00	0.00	3.53
5325	9538	6.268847	ACGAGAATTTCTAATCTGAGCCCTAT	59.731	38.462	0.00	0.00	0.00	2.57
5326	9539	6.811170	CGAGAATTTCTAATCTGAGCCCTATC	59.189	42.308	0.00	0.00	0.00	2.08
5329	9542	7.958583	AGAATTTCTAATCTGAGCCCTATCCTA	59.041	37.037	0.00	0.00	0.00	2.94
5330	9543	8.511748	AATTTCTAATCTGAGCCCTATCCTAA	57.488	34.615	0.00	0.00	0.00	2.69
5331	9544	8.692682	ATTTCTAATCTGAGCCCTATCCTAAT	57.307	34.615	0.00	0.00	0.00	1.73
5332	9545	7.726033	TTCTAATCTGAGCCCTATCCTAATC	57.274	40.000	0.00	0.00	0.00	1.75
5333	9546	7.050493	TCTAATCTGAGCCCTATCCTAATCT	57.950	40.000	0.00	0.00	0.00	2.40
5334	9547	6.894654	TCTAATCTGAGCCCTATCCTAATCTG	59.105	42.308	0.00	0.00	0.00	2.90
5335	9548	4.749048	TCTGAGCCCTATCCTAATCTGA	57.251	45.455	0.00	0.00	0.00	3.27
5432	9681	1.136305	TCGTGATTAGGCCTTTCTCGG	59.864	52.381	26.25	15.32	0.00	4.63

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
315	1546	1.555075	ACCGAATAGCAGAGCTTTGGA	59.445	47.619	6.36	0.00	40.44	3.53
461	1693	4.980573	TCCCCATATTACAACTACATGCC	58.019	43.478	0.00	0.00	0.00	4.40
482	1714	3.198489	GCGCCAGGTTAGCAGCTC	61.198	66.667	0.00	0.00	0.00	4.09
644	1876	3.262420	CCATCTGTTTACAGCTAAGCGT	58.738	45.455	5.00	0.00	43.46	5.07
730	1965	7.338703	ACTTGATTCGACTGGTTAGACATAGTA	59.661	37.037	0.00	0.00	0.00	1.82
902	3307	2.225934	TGGAGATTGGGGTTGGTAGGTA	60.226	50.000	0.00	0.00	0.00	3.08
942	3392	3.013219	GGAAGAAAGCTAAGCAAGGAGG	58.987	50.000	0.00	0.00	0.00	4.30
1024	3474	0.693622	TTGGCCACGAGGGTATTGAA	59.306	50.000	3.88	0.00	39.65	2.69
1029	3479	1.298340	CATGTTGGCCACGAGGGTA	59.702	57.895	3.88	0.00	39.65	3.69
1079	3530	8.694540	CACCTCAATAAATTCCACATAATTGGA	58.305	33.333	0.00	0.00	44.39	3.53
1146	3618	3.694566	CCTAGCCCACCAAATAAAGACAC	59.305	47.826	0.00	0.00	0.00	3.67
1215	4031	1.078143	GATGAAGTCTGGGGCGCTT	60.078	57.895	7.64	0.00	0.00	4.68
1349	4165	5.562298	AACCAACCACTCTACACTAATGT	57.438	39.130	0.00	0.00	43.30	2.71
1419	4235	5.147330	TCACCTTGTAATAGTCCACACAG	57.853	43.478	0.00	0.00	0.00	3.66
1432	4248	1.944024	CACAAAACGGCTCACCTTGTA	59.056	47.619	0.00	0.00	31.86	2.41
1566	4404	4.760204	ACAGCGAGCTAAACACCTAATTTT	59.240	37.500	0.00	0.00	0.00	1.82
1600	4438	3.480470	CCAAGATGATTGGACGCCTTAT	58.520	45.455	0.12	0.00	42.06	1.73
1845	4694	5.551233	TGGGAAGATCTACTTGTTGAGTTG	58.449	41.667	0.00	0.00	39.86	3.16
1846	4695	5.825593	TGGGAAGATCTACTTGTTGAGTT	57.174	39.130	0.00	0.00	39.86	3.01
1847	4696	6.380079	AATGGGAAGATCTACTTGTTGAGT	57.620	37.500	0.00	0.00	42.55	3.41
1969	4830	1.606903	TACAACGGCCAATCGGTTTT	58.393	45.000	2.24	0.00	36.27	2.43
2075	4977	3.807553	TGTCGGATGCATATCACACAAT	58.192	40.909	0.00	0.00	34.90	2.71
2221	5126	1.764134	TCGGTTGGACCACTTTACACT	59.236	47.619	0.00	0.00	38.47	3.55
2368	5292	4.324267	CCAAATTAACTATAGGAGGCCCG	58.676	47.826	0.00	0.00	37.58	6.13
2515	5454	3.070159	TGTGAAGTGCTACTCTTTGAGCT	59.930	43.478	0.00	0.00	39.54	4.09
2579	5518	5.324697	GGAATGTTGTGACGATAAAAGAGC	58.675	41.667	0.00	0.00	0.00	4.09
2798	5797	3.085952	CTTGATTAGGCAAGGGGACAA	57.914	47.619	0.00	0.00	41.15	3.18
2838	5842	6.042781	TCCATAAGAACCACATGTATAGACCC	59.957	42.308	0.00	0.00	0.00	4.46
2878	5882	4.345859	AAAGTGGTAACGACTCATTGGA	57.654	40.909	0.00	0.00	42.51	3.53
3005	6009	5.927281	AGCAATTTATTTCACCAGAGCAT	57.073	34.783	0.00	0.00	0.00	3.79
3006	6010	5.726980	AAGCAATTTATTTCACCAGAGCA	57.273	34.783	0.00	0.00	0.00	4.26
3073	6080	6.987386	AGCACTATTATCATCTGTACCTGAC	58.013	40.000	0.00	0.00	0.00	3.51
3086	6093	8.918961	AAGCGAATAGATGTAGCACTATTATC	57.081	34.615	0.00	0.00	38.76	1.75
3643	6663	1.965990	ATTGCCGTCAATGCTGCAA	59.034	47.368	6.36	8.30	46.51	4.08
3644	6664	3.684113	ATTGCCGTCAATGCTGCA	58.316	50.000	4.13	4.13	41.12	4.41
4066	7245	3.441101	AGTAGTACCTGAAGCATGTGGA	58.559	45.455	0.00	0.00	0.00	4.02
4118	7298	8.322828	TGGCATTCCAGTTTTACTACTGTAATA	58.677	33.333	0.00	0.00	43.17	0.98
4237	7546	8.123639	ACTCTAGACAACTCATTTTAGCACTA	57.876	34.615	0.00	0.00	0.00	2.74
4490	7854	4.021981	ACCCATTAAGAAAAGCTTGCACTC	60.022	41.667	0.00	0.00	37.42	3.51
4543	7936	4.800993	CGCTCAAGTCTACAGTTTAGGATG	59.199	45.833	0.00	0.00	0.00	3.51
4578	7971	4.019792	TGTACCATCAGAAACATGCAGT	57.980	40.909	0.00	0.00	0.00	4.40
4703	8096	7.841277	CGAACAATAACAAAGACATCGATACTG	59.159	37.037	0.00	0.00	0.00	2.74
4761	8155	6.127479	ACAGAACAACCACAGCTGAATTTTTA	60.127	34.615	23.35	0.00	0.00	1.52
4783	8178	6.039717	CCAGATTAACCACCAATAATCCACAG	59.960	42.308	0.00	0.00	38.65	3.66
4821	8216	2.390938	TCTACGAGCAACAAACTGACG	58.609	47.619	0.00	0.00	0.00	4.35
5027	9238	5.200368	AGTTCAAAAGCCTACAAACCATG	57.800	39.130	0.00	0.00	0.00	3.66
5032	9243	5.763204	CAGGAGTAGTTCAAAAGCCTACAAA	59.237	40.000	0.00	0.00	34.78	2.83
5080	9291	5.693104	ACGAAATAAAGTACTGAGTTGCGAA	59.307	36.000	16.97	0.00	0.00	4.70
5156	9368	1.215647	GCTACTCAGTGACCCACCG	59.784	63.158	0.00	0.00	34.49	4.94
5174	9386	4.988540	TCGGCCGATAAATCAGTTGATAAG	59.011	41.667	27.28	0.00	33.73	1.73
5175	9387	4.951254	TCGGCCGATAAATCAGTTGATAA	58.049	39.130	27.28	0.00	33.73	1.75
5176	9388	4.594123	TCGGCCGATAAATCAGTTGATA	57.406	40.909	27.28	0.00	33.73	2.15
5304	9517	7.014988	AGGATAGGGCTCAGATTAGAAATTC	57.985	40.000	0.00	0.00	0.00	2.17
5306	9519	8.692682	ATTAGGATAGGGCTCAGATTAGAAAT	57.307	34.615	0.00	0.00	0.00	2.17
5308	9521	7.398618	CAGATTAGGATAGGGCTCAGATTAGAA	59.601	40.741	0.00	0.00	0.00	2.10
5310	9523	6.894654	TCAGATTAGGATAGGGCTCAGATTAG	59.105	42.308	0.00	0.00	0.00	1.73
5312	9525	5.659503	TCAGATTAGGATAGGGCTCAGATT	58.340	41.667	0.00	0.00	0.00	2.40
5313	9526	5.282436	TCAGATTAGGATAGGGCTCAGAT	57.718	43.478	0.00	0.00	0.00	2.90
5315	9528	4.382901	GCATCAGATTAGGATAGGGCTCAG	60.383	50.000	0.00	0.00	0.00	3.35
5316	9529	3.517100	GCATCAGATTAGGATAGGGCTCA	59.483	47.826	0.00	0.00	0.00	4.26
5317	9530	3.774216	AGCATCAGATTAGGATAGGGCTC	59.226	47.826	0.00	0.00	0.00	4.70
5318	9531	3.518705	CAGCATCAGATTAGGATAGGGCT	59.481	47.826	0.00	0.00	0.00	5.19
5319	9532	3.262915	ACAGCATCAGATTAGGATAGGGC	59.737	47.826	0.00	0.00	0.00	5.19
5320	9533	6.805016	ATACAGCATCAGATTAGGATAGGG	57.195	41.667	0.00	0.00	0.00	3.53
5321	9534	9.512588	AAAAATACAGCATCAGATTAGGATAGG	57.487	33.333	0.00	0.00	0.00	2.57
5324	9537	9.512588	CCTAAAAATACAGCATCAGATTAGGAT	57.487	33.333	0.00	0.00	39.32	3.24
5325	9538	8.713971	TCCTAAAAATACAGCATCAGATTAGGA	58.286	33.333	6.39	6.39	41.98	2.94
5326	9539	8.908786	TCCTAAAAATACAGCATCAGATTAGG	57.091	34.615	0.00	0.00	38.67	2.69
5432	9681	6.426025	AGGTGGAAATAAACAACTCTAACGAC	59.574	38.462	0.00	0.00	25.25	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.