AutoCloner

Multiple sequence alignment - TraesCS7D01G370000

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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	TraesCS7D01G370000	chr7D	100.000	3301	0	0	1	3301	478574724	478578024	0.000000e+00	6096.0
1	TraesCS7D01G370000	chr7D	82.246	552	91	5	1625	2174	478891975	478891429	1.390000e-128	470.0
2	TraesCS7D01G370000	chr7D	80.446	404	65	10	1712	2108	478328304	478328700	2.490000e-76	296.0
3	TraesCS7D01G370000	chr7D	75.600	500	108	12	1615	2107	478370860	478371352	5.510000e-58	235.0
4	TraesCS7D01G370000	chr7D	90.741	162	11	1	1643	1800	478781162	478781323	2.580000e-51	213.0
5	TraesCS7D01G370000	chr7D	86.316	190	26	0	1312	1501	478892233	478892044	1.200000e-49	207.0
6	TraesCS7D01G370000	chr7D	82.283	254	18	13	1473	1726	478758458	478758684	9.350000e-46	195.0
7	TraesCS7D01G370000	chr7D	83.088	136	23	0	1350	1485	478327941	478328076	1.240000e-24	124.0
8	TraesCS7D01G370000	chr7B	91.753	1831	85	29	941	2744	504456005	504457796	0.000000e+00	2484.0
9	TraesCS7D01G370000	chr7B	93.132	1558	75	15	849	2396	504439232	504440767	0.000000e+00	2255.0
10	TraesCS7D01G370000	chr7B	91.537	709	45	7	2589	3296	504440768	504441462	0.000000e+00	963.0
11	TraesCS7D01G370000	chr7B	91.103	562	37	8	1	553	504454850	504455407	0.000000e+00	749.0
12	TraesCS7D01G370000	chr7B	90.214	562	36	12	1	553	504438085	504438636	0.000000e+00	715.0
13	TraesCS7D01G370000	chr7B	91.721	459	20	7	2741	3198	504457935	504458376	3.620000e-174	621.0
14	TraesCS7D01G370000	chr7B	82.428	552	90	5	1625	2174	504493454	504492908	2.980000e-130	475.0
15	TraesCS7D01G370000	chr7B	90.514	253	19	2	554	806	504438687	504438934	2.460000e-86	329.0
16	TraesCS7D01G370000	chr7B	89.844	256	17	3	556	806	504455490	504455741	1.480000e-83	320.0
17	TraesCS7D01G370000	chr7B	77.218	496	101	12	1618	2107	503496774	503497263	2.510000e-71	279.0
18	TraesCS7D01G370000	chr7B	75.150	499	112	11	1615	2107	503506894	503507386	1.190000e-54	224.0
19	TraesCS7D01G370000	chr7B	83.929	224	36	0	989	1212	504495273	504495496	7.170000e-52	215.0
20	TraesCS7D01G370000	chr7B	78.899	218	37	9	1626	1838	503499274	503499487	4.440000e-29	139.0
21	TraesCS7D01G370000	chr7B	94.253	87	5	0	819	905	504455912	504455998	2.070000e-27	134.0
22	TraesCS7D01G370000	chr7B	82.432	148	26	0	1350	1497	643462619	643462766	2.670000e-26	130.0
23	TraesCS7D01G370000	chr7A	88.487	1520	82	42	848	2335	516515180	516513722	0.000000e+00	1751.0
24	TraesCS7D01G370000	chr7A	81.782	505	69	12	997	1501	516151817	516152298	5.130000e-108	401.0
25	TraesCS7D01G370000	chr7A	82.439	410	36	16	157	556	516795565	516795182	3.180000e-85	326.0
26	TraesCS7D01G370000	chr7A	90.805	174	10	3	589	762	516515552	516515385	9.220000e-56	228.0
27	TraesCS7D01G370000	chr7A	81.646	158	29	0	1350	1507	516997854	516997697	7.430000e-27	132.0
28	TraesCS7D01G370000	chr7A	81.757	148	27	0	1350	1497	670946874	670946727	1.240000e-24	124.0
29	TraesCS7D01G370000	chrUn	91.624	394	27	5	16	407	479838833	479839222	1.040000e-149	540.0
30	TraesCS7D01G370000	chrUn	95.385	65	3	0	1612	1676	97111654	97111590	1.620000e-18	104.0
31	TraesCS7D01G370000	chr2D	94.161	137	7	1	2416	2551	291992024	291991888	1.200000e-49	207.0
32	TraesCS7D01G370000	chr2A	93.431	137	8	1	2416	2551	342647530	342647394	5.590000e-48	202.0
33	TraesCS7D01G370000	chr1B	93.333	135	7	2	2417	2549	40182223	40182357	7.230000e-47	198.0
34	TraesCS7D01G370000	chr1B	91.971	137	9	2	2416	2550	436689020	436689156	1.210000e-44	191.0
35	TraesCS7D01G370000	chr3D	93.233	133	8	1	2416	2547	400274668	400274800	9.350000e-46	195.0
36	TraesCS7D01G370000	chr3D	92.593	135	9	1	2416	2549	482202447	482202313	3.360000e-45	193.0
37	TraesCS7D01G370000	chr6D	93.182	132	8	1	2416	2546	145462493	145462624	3.360000e-45	193.0
38	TraesCS7D01G370000	chr5A	93.182	132	8	1	2416	2546	320214375	320214244	3.360000e-45	193.0
39	TraesCS7D01G370000	chr4D	74.658	146	35	2	1064	1208	97605324	97605468	2.750000e-06	63.9
40	TraesCS7D01G370000	chr4D	75.000	128	30	2	1082	1208	97720717	97720843	1.280000e-04	58.4
41	TraesCS7D01G370000	chr4A	73.973	146	36	2	1064	1208	478302665	478302521	1.280000e-04	58.4
42	TraesCS7D01G370000	chr4A	73.973	146	36	2	1064	1208	478339968	478339824	1.280000e-04	58.4

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	TraesCS7D01G370000	chr7D	478574724	478578024	3300	False	6096.0	6096	100.00000	1	3301	1	chr7D.!!$F2	3300
1	TraesCS7D01G370000	chr7D	478891429	478892233	804	True	338.5	470	84.28100	1312	2174	2	chr7D.!!$R1	862
2	TraesCS7D01G370000	chr7D	478327941	478328700	759	False	210.0	296	81.76700	1350	2108	2	chr7D.!!$F5	758
3	TraesCS7D01G370000	chr7B	504438085	504441462	3377	False	1065.5	2255	91.34925	1	3296	4	chr7B.!!$F5	3295
4	TraesCS7D01G370000	chr7B	504454850	504458376	3526	False	861.6	2484	91.73480	1	3198	5	chr7B.!!$F6	3197
5	TraesCS7D01G370000	chr7B	504492908	504493454	546	True	475.0	475	82.42800	1625	2174	1	chr7B.!!$R1	549
6	TraesCS7D01G370000	chr7B	503496774	503499487	2713	False	209.0	279	78.05850	1618	2107	2	chr7B.!!$F4	489
7	TraesCS7D01G370000	chr7A	516513722	516515552	1830	True	989.5	1751	89.64600	589	2335	2	chr7A.!!$R4	1746

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
212	213	0.458716	TCGCGCAAATCGGTCATGTA	60.459	50.0	8.75	0.0	38.94	2.29	F
1213	1612	0.036952	CTGCTTCGTCCAGGTGATGT	60.037	55.0	0.00	0.0	0.00	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1609	2064	0.107654	GCCCGTGGAGCTACAGATTT	60.108	55.00	0.00	0.0	0.0	2.17	R
2956	4776	5.663795	ATTCATAAGACATGTGTGCGATC	57.336	39.13	1.15	0.0	0.0	3.69	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
38	39	4.893608	TGTTGTATCAAGCTACTGCAAGA	58.106	39.130	0.00	0.00	42.74	3.02
39	40	5.304778	TGTTGTATCAAGCTACTGCAAGAA	58.695	37.500	0.00	0.00	42.74	2.52
40	41	5.409520	TGTTGTATCAAGCTACTGCAAGAAG	59.590	40.000	0.00	0.00	42.74	2.85
45	46	4.248859	TCAAGCTACTGCAAGAAGATGTC	58.751	43.478	0.00	0.00	42.74	3.06
48	49	2.935201	GCTACTGCAAGAAGATGTCTGG	59.065	50.000	0.00	0.00	36.40	3.86
82	83	9.823098	GCAACTAAATGAATAGCTTATGATCTG	57.177	33.333	0.00	0.00	0.00	2.90
138	139	7.121315	AGTCTGTCCTAATACAAATTTGCCTTC	59.879	37.037	18.12	1.50	0.00	3.46
154	155	5.620738	TGCCTTCTGTTAGAGCAATCTAT	57.379	39.130	0.00	0.00	0.00	1.98
195	196	1.855978	TGTGTTAGTTGTTCGCACTCG	59.144	47.619	0.00	0.00	0.00	4.18
211	212	1.695893	CTCGCGCAAATCGGTCATGT	61.696	55.000	8.75	0.00	38.94	3.21
212	213	0.458716	TCGCGCAAATCGGTCATGTA	60.459	50.000	8.75	0.00	38.94	2.29
221	222	6.142817	GCAAATCGGTCATGTATATTGAACC	58.857	40.000	0.00	0.00	0.00	3.62
227	228	6.267699	TCGGTCATGTATATTGAACCTCTCAT	59.732	38.462	0.00	0.00	32.78	2.90
267	268	8.885494	TGGCATTTTATAGAAACATAAATGGC	57.115	30.769	19.24	19.24	36.45	4.40
391	393	7.057894	ACACCAAGGAAACTACATAGAAAACA	58.942	34.615	0.00	0.00	42.68	2.83
414	416	6.697019	ACAGTCATGAAATCTTTTTGAAACCG	59.303	34.615	0.00	0.00	0.00	4.44
416	418	6.918022	AGTCATGAAATCTTTTTGAAACCGAC	59.082	34.615	0.00	0.00	0.00	4.79
427	429	8.331742	TCTTTTTGAAACCGACATTAAATTTGC	58.668	29.630	0.00	0.00	0.00	3.68
549	555	6.049955	CCCATGGGAATATAACGTAGATGT	57.950	41.667	28.27	0.00	37.50	3.06
551	557	6.940298	CCCATGGGAATATAACGTAGATGTTT	59.060	38.462	28.27	0.00	37.50	2.83
552	558	8.098286	CCCATGGGAATATAACGTAGATGTTTA	58.902	37.037	28.27	0.00	37.50	2.01
564	653	5.694910	ACGTAGATGTTTACAACTTGGACTG	59.305	40.000	0.00	0.00	31.27	3.51
567	656	7.383029	CGTAGATGTTTACAACTTGGACTGTAA	59.617	37.037	0.00	0.00	36.48	2.41
572	661	8.967664	TGTTTACAACTTGGACTGTAACTTAT	57.032	30.769	0.00	0.00	37.66	1.73
573	662	9.398538	TGTTTACAACTTGGACTGTAACTTATT	57.601	29.630	0.00	0.00	37.66	1.40
586	675	7.231467	ACTGTAACTTATTCAGGACACCATTT	58.769	34.615	0.00	0.00	34.02	2.32
588	677	9.226606	CTGTAACTTATTCAGGACACCATTTAA	57.773	33.333	0.00	0.00	0.00	1.52
623	712	4.096382	GTGGCACCATATTTAGTGTGGAAG	59.904	45.833	6.29	0.00	41.35	3.46
707	798	9.178427	CATTTCTTTTCTCTCTCAAAACACATC	57.822	33.333	0.00	0.00	0.00	3.06
708	799	7.864108	TTCTTTTCTCTCTCAAAACACATCA	57.136	32.000	0.00	0.00	0.00	3.07
709	800	7.864108	TCTTTTCTCTCTCAAAACACATCAA	57.136	32.000	0.00	0.00	0.00	2.57
710	801	8.279970	TCTTTTCTCTCTCAAAACACATCAAA	57.720	30.769	0.00	0.00	0.00	2.69
769	863	3.818387	AGATACACCATATAACGCGTCG	58.182	45.455	14.44	0.00	0.00	5.12
807	901	8.049721	ACTCCATATAAGCTAAATATTGGAGCC	58.950	37.037	24.96	2.94	37.68	4.70
808	902	7.927788	TCCATATAAGCTAAATATTGGAGCCA	58.072	34.615	15.61	7.59	36.87	4.75
809	903	8.560039	TCCATATAAGCTAAATATTGGAGCCAT	58.440	33.333	15.61	12.53	36.87	4.40
810	904	9.851686	CCATATAAGCTAAATATTGGAGCCATA	57.148	33.333	15.61	13.77	36.87	2.74
817	911	9.678260	AGCTAAATATTGGAGCCATAAATAGAG	57.322	33.333	15.61	0.00	36.87	2.43
1092	1491	3.001414	CTCGACGACTTTCTACTCCAGA	58.999	50.000	0.00	0.00	0.00	3.86
1101	1500	0.468214	TCTACTCCAGATCCTGCCCG	60.468	60.000	0.00	0.00	0.00	6.13
1104	1503	1.760086	CTCCAGATCCTGCCCGAGT	60.760	63.158	0.00	0.00	0.00	4.18
1105	1504	0.468214	CTCCAGATCCTGCCCGAGTA	60.468	60.000	0.00	0.00	0.00	2.59
1137	1536	1.169661	TGTGGGCGGTGATGAAACAC	61.170	55.000	0.00	0.00	39.70	3.32
1213	1612	0.036952	CTGCTTCGTCCAGGTGATGT	60.037	55.000	0.00	0.00	0.00	3.06
1217	1616	1.546029	CTTCGTCCAGGTGATGTCTCA	59.454	52.381	0.00	0.00	0.00	3.27
1219	1618	1.478105	TCGTCCAGGTGATGTCTCATG	59.522	52.381	0.00	0.00	32.98	3.07
1222	1621	2.499289	GTCCAGGTGATGTCTCATGACT	59.501	50.000	0.00	0.00	43.29	3.41
1338	1740	0.524862	GTGACGGCTCGGTTCTTCTA	59.475	55.000	0.00	0.00	0.00	2.10
1348	1750	0.246635	GGTTCTTCTAGACGCTGGCA	59.753	55.000	0.00	0.00	0.00	4.92
1550	2002	2.034812	CCCGGAGTACTCTGCTCATTAC	59.965	54.545	24.04	3.35	34.69	1.89
1551	2003	2.688446	CCGGAGTACTCTGCTCATTACA	59.312	50.000	24.04	0.00	34.69	2.41
1605	2060	9.248291	CTTATTAATGTGTCTGCTTTGTTTGTT	57.752	29.630	0.00	0.00	0.00	2.83
1606	2061	7.698836	ATTAATGTGTCTGCTTTGTTTGTTC	57.301	32.000	0.00	0.00	0.00	3.18
1607	2062	4.989279	ATGTGTCTGCTTTGTTTGTTCT	57.011	36.364	0.00	0.00	0.00	3.01
1608	2063	4.095410	TGTGTCTGCTTTGTTTGTTCTG	57.905	40.909	0.00	0.00	0.00	3.02
1609	2064	3.755905	TGTGTCTGCTTTGTTTGTTCTGA	59.244	39.130	0.00	0.00	0.00	3.27
1610	2065	4.217334	TGTGTCTGCTTTGTTTGTTCTGAA	59.783	37.500	0.00	0.00	0.00	3.02
1611	2066	5.160641	GTGTCTGCTTTGTTTGTTCTGAAA	58.839	37.500	0.00	0.00	0.00	2.69
1612	2067	5.807011	GTGTCTGCTTTGTTTGTTCTGAAAT	59.193	36.000	0.00	0.00	0.00	2.17
1613	2068	6.020360	GTGTCTGCTTTGTTTGTTCTGAAATC	60.020	38.462	0.00	0.00	0.00	2.17
1614	2069	6.127647	TGTCTGCTTTGTTTGTTCTGAAATCT	60.128	34.615	0.00	0.00	0.00	2.40
1615	2070	6.197842	GTCTGCTTTGTTTGTTCTGAAATCTG	59.802	38.462	0.00	0.00	0.00	2.90
1616	2071	5.964758	TGCTTTGTTTGTTCTGAAATCTGT	58.035	33.333	0.00	0.00	0.00	3.41
1691	2146	4.021925	GCCAGTCCCTCGCCAACT	62.022	66.667	0.00	0.00	0.00	3.16
1852	2313	2.093306	TCTACGGCAACTCCAACATG	57.907	50.000	0.00	0.00	34.01	3.21
2245	3894	7.938140	AGCAAAACATAGTATACCATGTGTT	57.062	32.000	16.22	14.27	35.59	3.32
2386	4040	8.112822	TCTTTTAAGATGGTCCCAAATGATACA	58.887	33.333	0.00	0.00	0.00	2.29
2411	4065	5.765182	AGTCATCTGTTTTTGTTACTCCCTG	59.235	40.000	0.00	0.00	0.00	4.45
2414	4068	1.335496	TGTTTTTGTTACTCCCTGCGC	59.665	47.619	0.00	0.00	0.00	6.09
2418	4072	2.380084	TTGTTACTCCCTGCGCTTAG	57.620	50.000	9.73	0.00	0.00	2.18
2431	4104	5.106791	CCCTGCGCTTAGAGATTTCAATATG	60.107	44.000	9.73	0.00	0.00	1.78
2498	4171	6.678878	TCACTCATTTGCTCCGTATATAGTC	58.321	40.000	0.00	0.00	0.00	2.59
2543	4220	6.494146	AGACTTATATTTAGGAACGGAGGGAG	59.506	42.308	0.00	0.00	0.00	4.30
2964	4784	6.530120	ACACTTAAATATATGGGATCGCACA	58.470	36.000	15.49	3.33	0.00	4.57
3138	4961	5.865085	ACGAACCAACCATATATAGTGCAT	58.135	37.500	0.00	0.00	0.00	3.96
3249	5072	3.866910	CCAAATTTGCCCTTGATCAATCG	59.133	43.478	12.92	3.10	0.00	3.34
3258	5081	3.181462	CCCTTGATCAATCGATGACTGGA	60.181	47.826	8.96	0.00	41.93	3.86
3261	5084	4.743057	TGATCAATCGATGACTGGAGTT	57.257	40.909	0.00	0.00	41.93	3.01
3298	5121	2.690840	TCTTATGGGGTAAGAGGGAGC	58.309	52.381	0.00	0.00	42.94	4.70
3299	5122	2.022428	TCTTATGGGGTAAGAGGGAGCA	60.022	50.000	0.00	0.00	42.94	4.26
3300	5123	2.815357	TATGGGGTAAGAGGGAGCAT	57.185	50.000	0.00	0.00	0.00	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	5.939883	TCTTGCAGTAGCTTGATACAACAAT	59.060	36.000	0.00	0.00	42.74	2.71
38	39	4.019860	AGTTGCACTATCACCAGACATCTT	60.020	41.667	0.00	0.00	0.00	2.40
39	40	3.517100	AGTTGCACTATCACCAGACATCT	59.483	43.478	0.00	0.00	0.00	2.90
40	41	3.866651	AGTTGCACTATCACCAGACATC	58.133	45.455	0.00	0.00	0.00	3.06
45	46	6.741992	TTCATTTAGTTGCACTATCACCAG	57.258	37.500	0.00	0.00	29.64	4.00
48	49	8.147642	AGCTATTCATTTAGTTGCACTATCAC	57.852	34.615	0.00	0.00	29.64	3.06
105	106	7.776618	TTTGTATTAGGACAGACTTCTGAGA	57.223	36.000	13.27	0.00	46.59	3.27
110	111	7.121315	AGGCAAATTTGTATTAGGACAGACTTC	59.879	37.037	19.03	0.00	0.00	3.01
115	116	7.094205	ACAGAAGGCAAATTTGTATTAGGACAG	60.094	37.037	19.03	3.74	0.00	3.51
117	118	7.158099	ACAGAAGGCAAATTTGTATTAGGAC	57.842	36.000	19.03	0.27	0.00	3.85
123	124	6.434028	TGCTCTAACAGAAGGCAAATTTGTAT	59.566	34.615	19.03	5.82	0.00	2.29
126	127	5.125100	TGCTCTAACAGAAGGCAAATTTG	57.875	39.130	14.03	14.03	0.00	2.32
154	155	0.911769	ACTGCTACCAGGCATAAGCA	59.088	50.000	6.30	6.30	43.53	3.91
162	163	3.740115	ACTAACACAAACTGCTACCAGG	58.260	45.455	0.00	0.00	43.53	4.45
167	168	4.260456	GCGAACAACTAACACAAACTGCTA	60.260	41.667	0.00	0.00	0.00	3.49
168	169	3.486875	GCGAACAACTAACACAAACTGCT	60.487	43.478	0.00	0.00	0.00	4.24
195	196	4.084066	TCAATATACATGACCGATTTGCGC	60.084	41.667	0.00	0.00	39.11	6.09
202	203	5.596772	TGAGAGGTTCAATATACATGACCGA	59.403	40.000	0.00	0.00	31.34	4.69
203	204	5.842907	TGAGAGGTTCAATATACATGACCG	58.157	41.667	0.00	0.00	31.34	4.79
205	206	9.988815	ACTTATGAGAGGTTCAATATACATGAC	57.011	33.333	0.00	0.00	39.77	3.06
221	222	8.893219	TGCCAAATGATTAGTACTTATGAGAG	57.107	34.615	0.00	0.00	0.00	3.20
261	262	4.420522	AAAGGTTTCACATGTGCCATTT	57.579	36.364	21.38	16.41	0.00	2.32
267	268	8.454106	CCTAGATTCTAAAAGGTTTCACATGTG	58.546	37.037	20.18	20.18	0.00	3.21
391	393	6.918022	GTCGGTTTCAAAAAGATTTCATGACT	59.082	34.615	0.00	0.00	0.00	3.41
401	403	8.331742	GCAAATTTAATGTCGGTTTCAAAAAGA	58.668	29.630	0.00	0.00	0.00	2.52
424	426	8.691797	GGGTTTCAGACTAATTATATTTGGCAA	58.308	33.333	0.00	0.00	0.00	4.52
425	427	7.836685	TGGGTTTCAGACTAATTATATTTGGCA	59.163	33.333	0.00	0.00	0.00	4.92
440	442	4.825085	TGGTATTCAGTTTGGGTTTCAGAC	59.175	41.667	0.00	0.00	0.00	3.51
454	456	8.310382	TGGTCCAAAATGTTTAATGGTATTCAG	58.690	33.333	0.00	0.00	34.50	3.02
549	555	9.616156	TGAATAAGTTACAGTCCAAGTTGTAAA	57.384	29.630	1.45	0.00	40.35	2.01
551	557	7.876068	CCTGAATAAGTTACAGTCCAAGTTGTA	59.124	37.037	1.45	0.00	0.00	2.41
552	558	6.710744	CCTGAATAAGTTACAGTCCAAGTTGT	59.289	38.462	1.45	0.00	0.00	3.32
595	684	4.640201	ACACTAAATATGGTGCCACATCAC	59.360	41.667	0.00	0.00	41.40	3.06
653	742	3.259374	TCTTGGTTTTGGTGCAAAGAACA	59.741	39.130	0.00	0.00	34.72	3.18
839	1102	7.328737	CCCGGGAGTAGAAATTATATGGTAAG	58.671	42.308	18.48	0.00	0.00	2.34
907	1299	0.036306	GGGTGTTGTTGGATCGTCCT	59.964	55.000	5.77	0.00	37.46	3.85
1092	1491	0.188587	TCTCCATACTCGGGCAGGAT	59.811	55.000	0.00	0.00	0.00	3.24
1101	1500	2.607187	CACACGGTGTTCTCCATACTC	58.393	52.381	11.82	0.00	0.00	2.59
1104	1503	0.611200	CCCACACGGTGTTCTCCATA	59.389	55.000	11.82	0.00	0.00	2.74
1105	1504	1.374947	CCCACACGGTGTTCTCCAT	59.625	57.895	11.82	0.00	0.00	3.41
1213	1612	0.881796	AAGTGCGACGAGTCATGAGA	59.118	50.000	0.00	0.00	0.00	3.27
1217	1616	0.598562	AGTCAAGTGCGACGAGTCAT	59.401	50.000	0.00	0.00	40.98	3.06
1219	1618	2.546195	ATAGTCAAGTGCGACGAGTC	57.454	50.000	0.00	0.00	40.98	3.36
1222	1621	2.745821	ACTGTATAGTCAAGTGCGACGA	59.254	45.455	0.00	0.00	40.98	4.20
1261	1660	5.970023	GCGAACTGTGAGATACTACGTTATT	59.030	40.000	0.00	0.00	0.00	1.40
1262	1661	5.065602	TGCGAACTGTGAGATACTACGTTAT	59.934	40.000	0.00	0.00	0.00	1.89
1263	1662	4.392754	TGCGAACTGTGAGATACTACGTTA	59.607	41.667	0.00	0.00	0.00	3.18
1264	1663	3.189910	TGCGAACTGTGAGATACTACGTT	59.810	43.478	0.00	0.00	0.00	3.99
1265	1664	2.745821	TGCGAACTGTGAGATACTACGT	59.254	45.455	0.00	0.00	0.00	3.57
1266	1665	3.400505	TGCGAACTGTGAGATACTACG	57.599	47.619	0.00	0.00	0.00	3.51
1267	1666	4.921547	TCATGCGAACTGTGAGATACTAC	58.078	43.478	0.00	0.00	0.00	2.73
1605	2060	2.166459	CCGTGGAGCTACAGATTTCAGA	59.834	50.000	0.00	0.00	0.00	3.27
1606	2061	2.544685	CCGTGGAGCTACAGATTTCAG	58.455	52.381	0.00	0.00	0.00	3.02
1607	2062	1.207089	CCCGTGGAGCTACAGATTTCA	59.793	52.381	0.00	0.00	0.00	2.69
1608	2063	1.941325	CCCGTGGAGCTACAGATTTC	58.059	55.000	0.00	0.00	0.00	2.17
1609	2064	0.107654	GCCCGTGGAGCTACAGATTT	60.108	55.000	0.00	0.00	0.00	2.17
1610	2065	1.522569	GCCCGTGGAGCTACAGATT	59.477	57.895	0.00	0.00	0.00	2.40
1611	2066	2.435693	GGCCCGTGGAGCTACAGAT	61.436	63.158	0.00	0.00	0.00	2.90
1612	2067	3.075005	GGCCCGTGGAGCTACAGA	61.075	66.667	0.00	0.00	0.00	3.41
1613	2068	4.514577	CGGCCCGTGGAGCTACAG	62.515	72.222	0.00	0.00	0.00	2.74
1615	2070	4.509737	GTCGGCCCGTGGAGCTAC	62.510	72.222	1.63	0.00	0.00	3.58
1691	2146	2.707257	AGTTCACCGAGGGAAGGTTAAA	59.293	45.455	0.00	0.00	40.59	1.52
1807	2262	4.988598	CGGAAGGTGGTGCAGCGT	62.989	66.667	11.91	0.00	36.92	5.07
1906	2370	2.123468	AAGGGCGCCAGGTTGTTT	60.123	55.556	30.85	7.31	0.00	2.83
2262	3911	8.988934	TGTAAGATTACATCACTTCTTGTGTTC	58.011	33.333	1.30	0.00	41.49	3.18
2386	4040	6.263168	CAGGGAGTAACAAAAACAGATGACTT	59.737	38.462	0.00	0.00	0.00	3.01
2411	4065	7.183580	AGTTCATATTGAAATCTCTAAGCGC	57.816	36.000	0.00	0.00	38.22	5.92
2477	4150	6.025749	TGGACTATATACGGAGCAAATGAG	57.974	41.667	0.00	0.00	0.00	2.90
2938	4758	8.151596	TGTGCGATCCCATATATTTAAGTGTTA	58.848	33.333	0.00	0.00	0.00	2.41
2939	4759	6.995686	TGTGCGATCCCATATATTTAAGTGTT	59.004	34.615	0.00	0.00	0.00	3.32
2956	4776	5.663795	ATTCATAAGACATGTGTGCGATC	57.336	39.130	1.15	0.00	0.00	3.69
3212	5035	9.019656	GGGCAAATTTGGTGTACATATATATGA	57.980	33.333	26.05	9.59	37.15	2.15
3235	5058	2.547211	CAGTCATCGATTGATCAAGGGC	59.453	50.000	14.54	5.12	36.54	5.19
3249	5072	4.633565	GTGAGGAATTGAACTCCAGTCATC	59.366	45.833	0.00	0.00	35.20	2.92
3258	5081	6.441088	AAGAGGTAAGTGAGGAATTGAACT	57.559	37.500	0.00	0.00	0.00	3.01
3261	5084	6.126768	CCCATAAGAGGTAAGTGAGGAATTGA	60.127	42.308	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.