AutoCloner

Multiple sequence alignment - TraesCS2A01G145000

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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	TraesCS2A01G145000	chr2A	100.000	3137	0	0	1	3137	90046974	90043838	0.000000e+00	5794.0
1	TraesCS2A01G145000	chr2A	82.762	1050	136	24	1312	2339	90030032	90029006	0.000000e+00	894.0
2	TraesCS2A01G145000	chr2A	75.072	698	139	27	1438	2122	95158453	95159128	3.060000e-75	292.0
3	TraesCS2A01G145000	chr2A	80.593	371	38	18	754	1094	90030741	90030375	4.010000e-64	255.0
4	TraesCS2A01G145000	chr2D	90.890	2382	166	22	14	2353	90310853	90308481	0.000000e+00	3149.0
5	TraesCS2A01G145000	chr2D	74.608	701	137	31	1438	2122	96680149	96680824	1.430000e-68	270.0
6	TraesCS2A01G145000	chr2D	92.727	55	3	1	1208	1262	96679884	96679937	9.330000e-11	78.7
7	TraesCS2A01G145000	chr2D	92.727	55	3	1	1208	1262	96749671	96749724	9.330000e-11	78.7
8	TraesCS2A01G145000	chr2B	91.211	1536	89	25	861	2353	142945861	142944329	0.000000e+00	2047.0
9	TraesCS2A01G145000	chr2B	86.817	311	28	5	462	760	142946174	142945865	5.010000e-88	335.0
10	TraesCS2A01G145000	chr2B	74.312	763	150	33	1356	2101	147830407	147831140	6.620000e-72	281.0
11	TraesCS2A01G145000	chr2B	74.312	763	150	33	1356	2101	147870160	147870893	6.620000e-72	281.0
12	TraesCS2A01G145000	chr2B	74.140	785	155	35	1356	2122	148037152	148037906	6.620000e-72	281.0
13	TraesCS2A01G145000	chr4A	95.564	789	22	3	2351	3137	632705426	632704649	0.000000e+00	1251.0
14	TraesCS2A01G145000	chr5D	92.443	794	50	7	2351	3137	462894636	462893846	0.000000e+00	1125.0
15	TraesCS2A01G145000	chr5D	91.593	797	50	11	2351	3137	378899753	378900542	0.000000e+00	1085.0
16	TraesCS2A01G145000	chr3D	92.211	796	47	11	2351	3137	608913526	608914315	0.000000e+00	1112.0
17	TraesCS2A01G145000	chr3D	91.511	801	52	10	2347	3137	365121519	365120725	0.000000e+00	1088.0
18	TraesCS2A01G145000	chr3D	90.363	799	58	9	2351	3137	582925158	582924367	0.000000e+00	1031.0
19	TraesCS2A01G145000	chr3D	90.363	799	55	10	2351	3137	582912729	582911941	0.000000e+00	1029.0
20	TraesCS2A01G145000	chr4D	91.489	799	50	13	2351	3137	487348485	487349277	0.000000e+00	1083.0
21	TraesCS2A01G145000	chr1D	91.080	796	47	16	2351	3137	460877578	460876798	0.000000e+00	1055.0
22	TraesCS2A01G145000	chr6D	79.389	393	61	16	1581	1969	410054899	410054523	3.100000e-65	259.0
23	TraesCS2A01G145000	chr6D	87.736	212	20	5	1582	1791	409882866	409883073	3.130000e-60	243.0
24	TraesCS2A01G145000	chr6D	77.340	203	35	7	1354	1555	409872560	409872752	3.310000e-20	110.0
25	TraesCS2A01G145000	chr6D	91.228	57	4	1	1206	1262	409882469	409882524	3.350000e-10	76.8
26	TraesCS2A01G145000	chr6A	79.135	393	60	16	1582	1969	555323823	555324198	5.190000e-63	252.0
27	TraesCS2A01G145000	chr7A	80.070	286	46	7	129	411	178299661	178299384	5.310000e-48	202.0
28	TraesCS2A01G145000	chr7A	76.786	112	20	3	1438	1549	54818186	54818291	1.220000e-04	58.4
29	TraesCS2A01G145000	chr3A	75.059	421	56	26	27	408	151651148	151650738	1.950000e-32	150.0
30	TraesCS2A01G145000	chr1A	73.746	339	73	12	1438	1771	497585179	497584852	5.500000e-23	119.0
31	TraesCS2A01G145000	chr1A	72.406	424	96	17	1354	1771	497580219	497579811	7.110000e-22	115.0
32	TraesCS2A01G145000	chr5A	76.113	247	37	13	133	368	447530967	447530732	3.310000e-20	110.0
33	TraesCS2A01G145000	chr7B	74.913	287	40	18	129	411	141868047	141867789	5.540000e-18	102.0
34	TraesCS2A01G145000	chr4B	76.617	201	30	9	133	322	660088085	660088279	9.260000e-16	95.3
35	TraesCS2A01G145000	chr3B	87.500	64	5	3	27	88	773799753	773799815	1.560000e-08	71.3
36	TraesCS2A01G145000	chr7D	88.889	45	5	0	1438	1482	52000059	52000103	4.370000e-04	56.5

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	TraesCS2A01G145000	chr2A	90043838	90046974	3136	True	5794.0	5794	100.0000	1	3137	1	chr2A.!!$R1	3136
1	TraesCS2A01G145000	chr2A	90029006	90030741	1735	True	574.5	894	81.6775	754	2339	2	chr2A.!!$R2	1585
2	TraesCS2A01G145000	chr2A	95158453	95159128	675	False	292.0	292	75.0720	1438	2122	1	chr2A.!!$F1	684
3	TraesCS2A01G145000	chr2D	90308481	90310853	2372	True	3149.0	3149	90.8900	14	2353	1	chr2D.!!$R1	2339
4	TraesCS2A01G145000	chr2B	142944329	142946174	1845	True	1191.0	2047	89.0140	462	2353	2	chr2B.!!$R1	1891
5	TraesCS2A01G145000	chr2B	147830407	147831140	733	False	281.0	281	74.3120	1356	2101	1	chr2B.!!$F1	745
6	TraesCS2A01G145000	chr2B	147870160	147870893	733	False	281.0	281	74.3120	1356	2101	1	chr2B.!!$F2	745
7	TraesCS2A01G145000	chr2B	148037152	148037906	754	False	281.0	281	74.1400	1356	2122	1	chr2B.!!$F3	766
8	TraesCS2A01G145000	chr4A	632704649	632705426	777	True	1251.0	1251	95.5640	2351	3137	1	chr4A.!!$R1	786
9	TraesCS2A01G145000	chr5D	462893846	462894636	790	True	1125.0	1125	92.4430	2351	3137	1	chr5D.!!$R1	786
10	TraesCS2A01G145000	chr5D	378899753	378900542	789	False	1085.0	1085	91.5930	2351	3137	1	chr5D.!!$F1	786
11	TraesCS2A01G145000	chr3D	608913526	608914315	789	False	1112.0	1112	92.2110	2351	3137	1	chr3D.!!$F1	786
12	TraesCS2A01G145000	chr3D	365120725	365121519	794	True	1088.0	1088	91.5110	2347	3137	1	chr3D.!!$R1	790
13	TraesCS2A01G145000	chr3D	582924367	582925158	791	True	1031.0	1031	90.3630	2351	3137	1	chr3D.!!$R3	786
14	TraesCS2A01G145000	chr3D	582911941	582912729	788	True	1029.0	1029	90.3630	2351	3137	1	chr3D.!!$R2	786
15	TraesCS2A01G145000	chr4D	487348485	487349277	792	False	1083.0	1083	91.4890	2351	3137	1	chr4D.!!$F1	786
16	TraesCS2A01G145000	chr1D	460876798	460877578	780	True	1055.0	1055	91.0800	2351	3137	1	chr1D.!!$R1	786

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
794	843	0.256752	TGAGATTGTGCTCCCCATGG	59.743	55.0	4.14	4.14	33.95	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2551	2792	0.173481	TCCTGTCTCGAATCTTGGCG	59.827	55.0	0.0	0.0	0.0	5.69	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
23	24	6.453926	GTACCAACTCCCTTAGAAGTAGAG	57.546	45.833	5.46	5.46	33.26	2.43
34	35	8.228206	TCCCTTAGAAGTAGAGACATATGTGAT	58.772	37.037	14.43	0.91	0.00	3.06
91	93	8.153479	TGTGGTATTATGATAGTTGTGATTGC	57.847	34.615	0.00	0.00	0.00	3.56
96	98	9.831737	GTATTATGATAGTTGTGATTGCCATTC	57.168	33.333	0.00	0.00	0.00	2.67
113	115	7.328404	TGCCATTCAATAGTAGGGATAATGA	57.672	36.000	0.00	0.00	0.00	2.57
173	175	8.742554	ATTTTGTTTTGGAATGTTATCGAGAC	57.257	30.769	0.00	0.00	0.00	3.36
178	180	8.356657	TGTTTTGGAATGTTATCGAGACAAATT	58.643	29.630	8.28	0.50	0.00	1.82
268	270	6.317789	ACGTGATTGAATTGAATCAACACT	57.682	33.333	19.93	2.70	42.58	3.55
269	271	7.433708	ACGTGATTGAATTGAATCAACACTA	57.566	32.000	19.93	0.00	42.58	2.74
271	273	7.173218	ACGTGATTGAATTGAATCAACACTAGT	59.827	33.333	19.93	11.25	42.58	2.57
291	293	4.165779	AGTCAAAACAAGCACGAAACAAG	58.834	39.130	0.00	0.00	0.00	3.16
292	294	4.083003	AGTCAAAACAAGCACGAAACAAGA	60.083	37.500	0.00	0.00	0.00	3.02
296	298	4.474226	AACAAGCACGAAACAAGATCTC	57.526	40.909	0.00	0.00	0.00	2.75
308	310	6.095440	CGAAACAAGATCTCCCCATTTAATGT	59.905	38.462	4.15	0.00	0.00	2.71
315	317	6.552350	AGATCTCCCCATTTAATGTGATTTGG	59.448	38.462	4.15	0.00	0.00	3.28
357	370	7.895429	AGAAAATAAACCAATGAGAAGGGATGA	59.105	33.333	0.00	0.00	0.00	2.92
371	384	1.070445	GATGATGGGAGGTGAGGCG	59.930	63.158	0.00	0.00	0.00	5.52
372	385	2.388890	GATGATGGGAGGTGAGGCGG	62.389	65.000	0.00	0.00	0.00	6.13
373	386	2.764128	GATGGGAGGTGAGGCGGA	60.764	66.667	0.00	0.00	0.00	5.54
374	387	2.765807	ATGGGAGGTGAGGCGGAG	60.766	66.667	0.00	0.00	0.00	4.63
378	391	1.677552	GGAGGTGAGGCGGAGAAAA	59.322	57.895	0.00	0.00	0.00	2.29
380	393	1.157585	GAGGTGAGGCGGAGAAAAAC	58.842	55.000	0.00	0.00	0.00	2.43
382	395	0.875059	GGTGAGGCGGAGAAAAACAG	59.125	55.000	0.00	0.00	0.00	3.16
384	397	1.531578	GTGAGGCGGAGAAAAACAGAC	59.468	52.381	0.00	0.00	0.00	3.51
386	399	1.531578	GAGGCGGAGAAAAACAGACAC	59.468	52.381	0.00	0.00	0.00	3.67
394	407	6.640907	GCGGAGAAAAACAGACACAAATAAAT	59.359	34.615	0.00	0.00	0.00	1.40
397	410	8.073768	GGAGAAAAACAGACACAAATAAATCGA	58.926	33.333	0.00	0.00	0.00	3.59
411	424	8.153550	ACAAATAAATCGATGAGGAGAAGCTAT	58.846	33.333	0.00	0.00	0.00	2.97
412	425	8.441608	CAAATAAATCGATGAGGAGAAGCTATG	58.558	37.037	0.00	0.00	0.00	2.23
486	499	4.825199	AGCCCTTTAGGAGTAGAGAGAT	57.175	45.455	0.00	0.00	38.24	2.75
539	556	3.514309	AGTCCTACTATTGCTTCGTTGGT	59.486	43.478	0.00	0.00	0.00	3.67
546	563	0.745128	TTGCTTCGTTGGTGAACCGT	60.745	50.000	0.00	0.00	39.43	4.83
623	656	1.863267	CCGCTGGATCTCAGATTCAC	58.137	55.000	13.48	0.00	46.18	3.18
625	658	2.625314	CCGCTGGATCTCAGATTCACTA	59.375	50.000	13.48	0.00	46.18	2.74
630	663	3.640498	TGGATCTCAGATTCACTAGGCAG	59.360	47.826	0.00	0.00	0.00	4.85
641	674	3.538591	TCACTAGGCAGCATTTGATCAG	58.461	45.455	0.00	0.00	0.00	2.90
648	681	2.731341	GCAGCATTTGATCAGTGTGAGC	60.731	50.000	10.66	8.83	32.56	4.26
675	708	3.378427	CAGAAAATCCTTCGAACATCCCC	59.622	47.826	0.00	0.00	0.00	4.81
676	709	3.010138	AGAAAATCCTTCGAACATCCCCA	59.990	43.478	0.00	0.00	0.00	4.96
678	711	3.449746	AATCCTTCGAACATCCCCAAA	57.550	42.857	0.00	0.00	0.00	3.28
723	772	4.993584	GCTGGTCATTGGTCACAGATATAG	59.006	45.833	0.00	0.00	0.00	1.31
725	774	5.215845	TGGTCATTGGTCACAGATATAGGA	58.784	41.667	0.00	0.00	0.00	2.94
726	775	5.846164	TGGTCATTGGTCACAGATATAGGAT	59.154	40.000	0.00	0.00	0.00	3.24
760	809	1.815003	GAGCACCTAAGCTGCAATGTT	59.185	47.619	1.02	0.00	46.75	2.71
788	837	1.028868	GGGCTGTGAGATTGTGCTCC	61.029	60.000	0.00	0.00	33.95	4.70
794	843	0.256752	TGAGATTGTGCTCCCCATGG	59.743	55.000	4.14	4.14	33.95	3.66
835	884	1.266718	CACACACATGCAACCTACCAC	59.733	52.381	0.00	0.00	0.00	4.16
954	1009	2.444766	ACCCATCTCTGATCAATTCCCC	59.555	50.000	0.00	0.00	0.00	4.81
974	1029	1.101049	CCTCCACTCTCTCGAGCTCC	61.101	65.000	7.81	0.00	41.09	4.70
1132	1252	1.461559	GCTCACCTACGGTCACTACT	58.538	55.000	0.00	0.00	31.02	2.57
1141	1261	0.170561	CGGTCACTACTCCAAGGTCG	59.829	60.000	0.00	0.00	0.00	4.79
1209	1329	4.353437	GAGGTGAACCGCGACCGT	62.353	66.667	8.23	0.00	42.08	4.83
1296	1416	1.320555	GAGTTACATACGCTGCACACG	59.679	52.381	0.00	2.94	0.00	4.49
1306	1428	1.136872	GCTGCACACGTCGATCTCTC	61.137	60.000	0.00	0.00	0.00	3.20
1371	1586	2.671070	CAGGGTTGCGATGGGTCT	59.329	61.111	0.00	0.00	0.00	3.85
1596	1811	1.342555	TGTACTTCGAAATGCCGTCG	58.657	50.000	0.00	0.00	39.88	5.12
1682	1897	0.596083	GACATCACGATGCTCGAGGG	60.596	60.000	15.58	0.00	43.74	4.30
1692	1907	3.011760	GCTCGAGGGTTTGTTCGCG	62.012	63.158	15.58	0.00	36.79	5.87
1803	2018	1.303282	GCCCAACCCTTCTTCGGAT	59.697	57.895	0.00	0.00	0.00	4.18
1825	2040	1.138859	CCATGGCCATGAACTCTACGA	59.861	52.381	41.32	0.00	41.20	3.43
1934	2149	8.380644	CAACCAATACTACAAGAACGTGATTAG	58.619	37.037	0.00	0.00	0.00	1.73
2029	2244	1.133009	AGTTCTCTGTGGACTGGGAGT	60.133	52.381	0.00	0.00	0.00	3.85
2170	2400	2.538449	CGACCAGAGTTGTGTGTGTTAC	59.462	50.000	0.00	0.00	0.00	2.50
2224	2454	9.810545	TTAATTATTATTTGGCACTAAGGTTGC	57.189	29.630	0.00	0.00	0.00	4.17
2434	2672	8.450578	TTCATAATAAAGGACATGATGGTCAC	57.549	34.615	0.00	0.00	39.59	3.67
2633	2874	2.513753	CCACTTAACATGGTTGCAGGA	58.486	47.619	0.00	0.00	32.08	3.86
2923	3182	6.459670	ACTTGGTGAACGTTTTCCTAAATT	57.540	33.333	18.62	3.46	0.00	1.82
3083	3359	7.201145	TGAATTTGTTTTGCCAAAATTGATGG	58.799	30.769	5.81	6.23	37.81	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.095300	GTCTCTACTTCTAAGGGAGTTGGTAC	59.905	46.154	11.78	0.00	34.20	3.34
1	2	6.186234	GTCTCTACTTCTAAGGGAGTTGGTA	58.814	44.000	11.78	0.00	34.20	3.25
2	3	5.018149	GTCTCTACTTCTAAGGGAGTTGGT	58.982	45.833	11.78	0.00	34.20	3.67
3	4	5.017490	TGTCTCTACTTCTAAGGGAGTTGG	58.983	45.833	11.78	0.00	34.20	3.77
4	5	6.783708	ATGTCTCTACTTCTAAGGGAGTTG	57.216	41.667	11.78	0.00	34.20	3.16
5	6	8.062536	ACATATGTCTCTACTTCTAAGGGAGTT	58.937	37.037	1.41	5.08	34.20	3.01
6	7	7.504238	CACATATGTCTCTACTTCTAAGGGAGT	59.496	40.741	5.07	0.00	34.20	3.85
7	8	7.721842	TCACATATGTCTCTACTTCTAAGGGAG	59.278	40.741	5.07	7.97	34.00	4.30
8	9	7.583625	TCACATATGTCTCTACTTCTAAGGGA	58.416	38.462	5.07	0.00	0.00	4.20
9	10	7.825331	TCACATATGTCTCTACTTCTAAGGG	57.175	40.000	5.07	0.00	0.00	3.95
16	17	9.823647	CTTACCAAATCACATATGTCTCTACTT	57.176	33.333	5.07	0.00	0.00	2.24
69	71	7.744087	TGGCAATCACAACTATCATAATACC	57.256	36.000	0.00	0.00	0.00	2.73
76	78	6.778834	ATTGAATGGCAATCACAACTATCA	57.221	33.333	4.38	0.00	43.64	2.15
80	82	6.319658	CCTACTATTGAATGGCAATCACAACT	59.680	38.462	4.38	0.00	43.64	3.16
198	200	9.933723	CATCATATATGTGAGATCACCTTTGTA	57.066	33.333	12.42	0.00	45.88	2.41
199	201	8.435187	ACATCATATATGTGAGATCACCTTTGT	58.565	33.333	12.42	1.78	45.88	2.83
200	202	8.843885	ACATCATATATGTGAGATCACCTTTG	57.156	34.615	12.42	1.21	45.88	2.77
222	224	9.436957	ACGTAACTAAGAAATCAGAATTCACAT	57.563	29.630	8.44	0.00	0.00	3.21
225	227	9.653287	ATCACGTAACTAAGAAATCAGAATTCA	57.347	29.630	8.44	0.00	0.00	2.57
242	244	7.803189	AGTGTTGATTCAATTCAATCACGTAAC	59.197	33.333	4.01	1.34	41.52	2.50
245	247	6.317789	AGTGTTGATTCAATTCAATCACGT	57.682	33.333	4.01	0.00	41.52	4.49
246	248	7.521529	ACTAGTGTTGATTCAATTCAATCACG	58.478	34.615	4.01	0.00	41.52	4.35
258	260	6.414987	GTGCTTGTTTTGACTAGTGTTGATTC	59.585	38.462	0.00	0.00	0.00	2.52
264	266	3.527533	TCGTGCTTGTTTTGACTAGTGT	58.472	40.909	0.00	0.00	0.00	3.55
268	270	4.948608	TGTTTCGTGCTTGTTTTGACTA	57.051	36.364	0.00	0.00	0.00	2.59
269	271	3.840890	TGTTTCGTGCTTGTTTTGACT	57.159	38.095	0.00	0.00	0.00	3.41
271	273	4.427096	TCTTGTTTCGTGCTTGTTTTGA	57.573	36.364	0.00	0.00	0.00	2.69
291	293	6.324770	ACCAAATCACATTAAATGGGGAGATC	59.675	38.462	0.00	0.00	33.47	2.75
292	294	6.204555	ACCAAATCACATTAAATGGGGAGAT	58.795	36.000	0.00	0.00	33.47	2.75
296	298	7.757941	AAAAACCAAATCACATTAAATGGGG	57.242	32.000	0.00	0.00	33.47	4.96
321	323	9.527157	TCATTGGTTTATTTTCTCACTCCAATA	57.473	29.630	0.00	0.00	40.81	1.90
324	326	7.230747	TCTCATTGGTTTATTTTCTCACTCCA	58.769	34.615	0.00	0.00	0.00	3.86
329	331	7.237982	TCCCTTCTCATTGGTTTATTTTCTCA	58.762	34.615	0.00	0.00	0.00	3.27
357	370	2.765807	CTCCGCCTCACCTCCCAT	60.766	66.667	0.00	0.00	0.00	4.00
371	384	8.073768	TCGATTTATTTGTGTCTGTTTTTCTCC	58.926	33.333	0.00	0.00	0.00	3.71
372	385	9.612620	ATCGATTTATTTGTGTCTGTTTTTCTC	57.387	29.630	0.00	0.00	0.00	2.87
373	386	9.398170	CATCGATTTATTTGTGTCTGTTTTTCT	57.602	29.630	0.00	0.00	0.00	2.52
374	387	9.393249	TCATCGATTTATTTGTGTCTGTTTTTC	57.607	29.630	0.00	0.00	0.00	2.29
378	391	6.878923	TCCTCATCGATTTATTTGTGTCTGTT	59.121	34.615	0.00	0.00	0.00	3.16
380	393	6.758416	TCTCCTCATCGATTTATTTGTGTCTG	59.242	38.462	0.00	0.00	0.00	3.51
382	395	7.539712	TTCTCCTCATCGATTTATTTGTGTC	57.460	36.000	0.00	0.00	0.00	3.67
384	397	6.259608	AGCTTCTCCTCATCGATTTATTTGTG	59.740	38.462	0.00	0.00	0.00	3.33
386	399	6.857777	AGCTTCTCCTCATCGATTTATTTG	57.142	37.500	0.00	0.00	0.00	2.32
394	407	4.586421	ACATTCATAGCTTCTCCTCATCGA	59.414	41.667	0.00	0.00	0.00	3.59
397	410	5.821470	CACAACATTCATAGCTTCTCCTCAT	59.179	40.000	0.00	0.00	0.00	2.90
449	462	3.511477	AGGGCTTCTTCTCACAAGTAGA	58.489	45.455	0.00	0.00	0.00	2.59
505	521	9.594936	AGCAATAGTAGGACTATTACAAGATCT	57.405	33.333	10.70	0.00	46.48	2.75
518	534	3.617263	CACCAACGAAGCAATAGTAGGAC	59.383	47.826	0.00	0.00	0.00	3.85
532	549	0.460722	TTCTCACGGTTCACCAACGA	59.539	50.000	0.00	0.00	35.14	3.85
539	556	3.678806	GCACCTGATATTCTCACGGTTCA	60.679	47.826	0.00	0.00	34.87	3.18
546	563	1.688735	CCGGAGCACCTGATATTCTCA	59.311	52.381	0.00	0.00	0.00	3.27
577	610	2.664185	CATCGGAGCATGGGAGCG	60.664	66.667	0.00	0.00	40.15	5.03
623	656	3.064958	CACACTGATCAAATGCTGCCTAG	59.935	47.826	0.00	0.00	0.00	3.02
625	658	1.816835	CACACTGATCAAATGCTGCCT	59.183	47.619	0.00	0.00	0.00	4.75
630	663	3.844577	AAGCTCACACTGATCAAATGC	57.155	42.857	0.00	0.00	0.00	3.56
641	674	3.005155	AGGATTTTCTGCAAAGCTCACAC	59.995	43.478	0.00	0.00	30.95	3.82
648	681	4.858935	TGTTCGAAGGATTTTCTGCAAAG	58.141	39.130	0.00	0.00	0.00	2.77
675	708	2.278854	CCGGGCCAAAGCATTATTTTG	58.721	47.619	4.39	0.00	42.56	2.44
676	709	1.905894	ACCGGGCCAAAGCATTATTTT	59.094	42.857	6.32	0.00	42.56	1.82
678	711	2.445682	TACCGGGCCAAAGCATTATT	57.554	45.000	6.32	0.00	42.56	1.40
723	772	0.598680	CTCCGATGCGACCTCAATCC	60.599	60.000	0.00	0.00	0.00	3.01
725	774	1.227380	GCTCCGATGCGACCTCAAT	60.227	57.895	0.00	0.00	0.00	2.57
726	775	2.184322	GCTCCGATGCGACCTCAA	59.816	61.111	0.00	0.00	0.00	3.02
788	837	1.005805	TCAACCAGGAACATCCATGGG	59.994	52.381	13.02	0.00	39.61	4.00
794	843	2.485814	GCTCAAGTCAACCAGGAACATC	59.514	50.000	0.00	0.00	0.00	3.06
835	884	5.847670	TTTGTTTTTGTTTCTTGAACCGG	57.152	34.783	0.00	0.00	37.45	5.28
974	1029	4.845387	TGCTAGCTCTCGAAACTAATACG	58.155	43.478	17.23	0.00	0.00	3.06
1080	1157	3.193782	AGGAGGAAGAAACCCATAGCTT	58.806	45.455	0.00	0.00	0.00	3.74
1132	1252	2.832129	AGCAAGTATTCTCGACCTTGGA	59.168	45.455	0.00	0.00	35.86	3.53
1296	1416	0.782981	CATGCATGCGAGAGATCGAC	59.217	55.000	14.93	0.00	34.64	4.20
1306	1428	1.080298	AAATGGCAAACATGCATGCG	58.920	45.000	26.53	15.83	43.47	4.73
1626	1841	2.683933	TTGGGGAGGGTCTCGCTC	60.684	66.667	10.90	5.46	42.06	5.03
1750	1965	1.536943	AAGGACGAGCAGTGGGAGAC	61.537	60.000	0.00	0.00	0.00	3.36
1803	2018	1.490490	GTAGAGTTCATGGCCATGGGA	59.510	52.381	38.81	27.02	39.24	4.37
1825	2040	1.331214	CTTGTCACCAAGTTGGCCAT	58.669	50.000	22.25	0.00	42.67	4.40
1846	2061	3.117171	GTCGCCTCTGCTGCACTG	61.117	66.667	0.00	0.00	34.43	3.66
1934	2149	2.553079	TTTCAACAACACTTCGTGGC	57.447	45.000	0.00	0.00	37.94	5.01
2029	2244	2.442413	CATGGCTTCCCCGAACTTTAA	58.558	47.619	0.00	0.00	35.87	1.52
2211	2441	1.730612	GAGTTACGCAACCTTAGTGCC	59.269	52.381	0.00	0.00	35.05	5.01
2305	2542	4.220602	GTGCCTCTAAACCAAAACCATGAT	59.779	41.667	0.00	0.00	0.00	2.45
2306	2543	3.572255	GTGCCTCTAAACCAAAACCATGA	59.428	43.478	0.00	0.00	0.00	3.07
2312	2549	3.135994	GACGAGTGCCTCTAAACCAAAA	58.864	45.455	0.00	0.00	0.00	2.44
2317	2554	2.726832	AGTGACGAGTGCCTCTAAAC	57.273	50.000	0.00	0.00	0.00	2.01
2512	2752	5.721000	TGCAATTTAAAGAGATGGTTGGGAT	59.279	36.000	0.00	0.00	0.00	3.85
2551	2792	0.173481	TCCTGTCTCGAATCTTGGCG	59.827	55.000	0.00	0.00	0.00	5.69
2666	2907	7.073208	AGAAGTAAAGAAGAAATTTGGGGGAA	58.927	34.615	0.00	0.00	0.00	3.97
2861	3119	7.492669	TCGCAAATTTTGTTAAAAGTCCATTCA	59.507	29.630	10.65	0.00	33.22	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.