AutoCloner

Multiple sequence alignment - TraesCS1D01G308000

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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	TraesCS1D01G308000	chr1D	100.000	2453	0	0	1	2453	404138340	404135888	0.000000e+00	4530.0
1	TraesCS1D01G308000	chr1D	88.283	495	53	4	1861	2352	431820038	431820530	2.720000e-164	588.0
2	TraesCS1D01G308000	chr1D	96.552	58	2	0	2337	2394	431820553	431820610	2.010000e-16	97.1
3	TraesCS1D01G308000	chr1A	92.000	1075	44	19	791	1825	499784116	499783044	0.000000e+00	1471.0
4	TraesCS1D01G308000	chr1A	83.192	589	27	29	1	556	499785072	499784523	7.940000e-130	473.0
5	TraesCS1D01G308000	chr1A	100.000	54	0	0	2337	2390	539735885	539735832	1.550000e-17	100.0
6	TraesCS1D01G308000	chr1A	93.939	66	1	2	556	621	499784432	499784370	2.010000e-16	97.1
7	TraesCS1D01G308000	chr1B	91.895	1024	40	21	792	1791	543496866	543495862	0.000000e+00	1391.0
8	TraesCS1D01G308000	chr1B	87.823	542	44	8	1826	2352	37567003	37567537	1.250000e-172	616.0
9	TraesCS1D01G308000	chr1B	94.624	279	5	4	1	277	543497815	543497545	8.110000e-115	424.0
10	TraesCS1D01G308000	chr1B	78.715	249	22	9	313	558	543497543	543497323	1.180000e-28	137.0
11	TraesCS1D01G308000	chr1B	95.385	65	3	0	557	621	543497183	543497119	1.200000e-18	104.0
12	TraesCS1D01G308000	chr6B	88.302	530	54	4	1826	2352	122792958	122793482	1.600000e-176	628.0
13	TraesCS1D01G308000	chr3B	87.454	542	48	7	1826	2352	757924530	757923994	7.500000e-170	606.0
14	TraesCS1D01G308000	chr3B	87.242	533	59	6	1826	2352	530993782	530993253	1.260000e-167	599.0
15	TraesCS1D01G308000	chr3B	87.085	542	51	6	1826	2352	606574024	606573487	1.620000e-166	595.0
16	TraesCS1D01G308000	chr3B	94.667	75	4	0	1	75	578401725	578401799	1.540000e-22	117.0
17	TraesCS1D01G308000	chr5D	87.361	538	52	10	1830	2352	538101133	538100597	9.700000e-169	603.0
18	TraesCS1D01G308000	chr5D	96.610	59	1	1	2337	2395	411744308	411744365	2.010000e-16	97.1
19	TraesCS1D01G308000	chr2A	86.492	533	63	7	1826	2352	14943147	14943676	5.880000e-161	577.0
20	TraesCS1D01G308000	chr2A	98.246	57	1	0	2337	2393	16636435	16636379	1.550000e-17	100.0
21	TraesCS1D01G308000	chr2A	98.214	56	1	0	2337	2392	52256429	52256484	5.580000e-17	99.0
22	TraesCS1D01G308000	chr3D	86.817	531	50	10	1826	2352	422748787	422749301	2.120000e-160	575.0
23	TraesCS1D01G308000	chr3D	93.333	75	5	0	1	75	441147698	441147772	7.170000e-21	111.0
24	TraesCS1D01G308000	chr3A	87.437	398	39	7	1826	2217	630797438	630797046	4.810000e-122	448.0
25	TraesCS1D01G308000	chr3A	93.333	75	5	0	1	75	581274320	581274394	7.170000e-21	111.0
26	TraesCS1D01G308000	chr2D	88.327	257	27	3	1826	2080	627961949	627961694	3.060000e-79	305.0
27	TraesCS1D01G308000	chr2D	90.541	74	7	0	1	74	49877645	49877718	5.580000e-17	99.0
28	TraesCS1D01G308000	chr4D	93.151	73	5	0	1	73	312800396	312800324	9.280000e-20	108.0
29	TraesCS1D01G308000	chr4D	98.182	55	1	0	2337	2391	95516721	95516775	2.010000e-16	97.1
30	TraesCS1D01G308000	chr4A	93.151	73	5	0	1	73	163819038	163819110	9.280000e-20	108.0
31	TraesCS1D01G308000	chr4B	91.781	73	6	0	1	73	390281039	390281111	4.320000e-18	102.0
32	TraesCS1D01G308000	chrUn	96.667	60	1	1	2337	2396	55739489	55739431	5.580000e-17	99.0
33	TraesCS1D01G308000	chr6D	96.491	57	2	0	2337	2393	136701688	136701744	7.220000e-16	95.3
34	TraesCS1D01G308000	chr6A	93.548	62	3	1	2337	2398	386895024	386894964	9.340000e-15	91.6

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	TraesCS1D01G308000	chr1D	404135888	404138340	2452	True	4530.000000	4530	100.000000	1	2453	1	chr1D.!!$R1	2452
1	TraesCS1D01G308000	chr1D	431820038	431820610	572	False	342.550000	588	92.417500	1861	2394	2	chr1D.!!$F1	533
2	TraesCS1D01G308000	chr1A	499783044	499785072	2028	True	680.366667	1471	89.710333	1	1825	3	chr1A.!!$R2	1824
3	TraesCS1D01G308000	chr1B	37567003	37567537	534	False	616.000000	616	87.823000	1826	2352	1	chr1B.!!$F1	526
4	TraesCS1D01G308000	chr1B	543495862	543497815	1953	True	514.000000	1391	90.154750	1	1791	4	chr1B.!!$R1	1790
5	TraesCS1D01G308000	chr6B	122792958	122793482	524	False	628.000000	628	88.302000	1826	2352	1	chr6B.!!$F1	526
6	TraesCS1D01G308000	chr3B	757923994	757924530	536	True	606.000000	606	87.454000	1826	2352	1	chr3B.!!$R3	526
7	TraesCS1D01G308000	chr3B	530993253	530993782	529	True	599.000000	599	87.242000	1826	2352	1	chr3B.!!$R1	526
8	TraesCS1D01G308000	chr3B	606573487	606574024	537	True	595.000000	595	87.085000	1826	2352	1	chr3B.!!$R2	526
9	TraesCS1D01G308000	chr5D	538100597	538101133	536	True	603.000000	603	87.361000	1830	2352	1	chr5D.!!$R1	522
10	TraesCS1D01G308000	chr2A	14943147	14943676	529	False	577.000000	577	86.492000	1826	2352	1	chr2A.!!$F1	526
11	TraesCS1D01G308000	chr3D	422748787	422749301	514	False	575.000000	575	86.817000	1826	2352	1	chr3D.!!$F1	526

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
436	468	0.033781	TTGGCATGCTTGGTTTCTGC	59.966	50.0	18.92	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2167	2570	0.118144	AGGAGGAGGAGGAGCTTGTT	59.882	55.0	0.0	0.0	0.0	2.83	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
111	117	2.017049	CCCTCCCACGAAATAAGCTTG	58.983	52.381	9.86	0.00	0.00	4.01
160	166	0.035317	ATGCCAGACAGACTCGCAAA	59.965	50.000	0.00	0.00	44.83	3.68
179	185	5.443170	CGCAAAGTTGTATTTTGTGCTATGC	60.443	40.000	0.00	0.00	38.64	3.14
180	186	5.443170	GCAAAGTTGTATTTTGTGCTATGCG	60.443	40.000	0.46	0.00	37.73	4.73
181	187	3.758300	AGTTGTATTTTGTGCTATGCGC	58.242	40.909	0.00	0.00	39.75	6.09
182	188	2.842208	TGTATTTTGTGCTATGCGCC	57.158	45.000	4.18	0.00	38.39	6.53
183	189	2.364632	TGTATTTTGTGCTATGCGCCT	58.635	42.857	4.18	0.00	38.39	5.52
184	190	2.097304	TGTATTTTGTGCTATGCGCCTG	59.903	45.455	4.18	0.00	38.39	4.85
185	191	1.176527	ATTTTGTGCTATGCGCCTGT	58.823	45.000	4.18	0.00	38.39	4.00
299	315	1.885887	TGGTTGTGGCACTTATCTTGC	59.114	47.619	19.83	0.18	39.41	4.01
348	364	1.720781	AGGGGCTTTGTGCAAATCTT	58.279	45.000	0.00	0.00	45.15	2.40
354	371	3.248363	GGCTTTGTGCAAATCTTGGTTTC	59.752	43.478	0.00	0.00	45.15	2.78
363	380	0.323725	ATCTTGGTTTCGCCCTGCAT	60.324	50.000	0.00	0.00	36.04	3.96
367	384	1.621992	TGGTTTCGCCCTGCATTTTA	58.378	45.000	0.00	0.00	36.04	1.52
368	385	1.964223	TGGTTTCGCCCTGCATTTTAA	59.036	42.857	0.00	0.00	36.04	1.52
369	386	2.365617	TGGTTTCGCCCTGCATTTTAAA	59.634	40.909	0.00	0.00	36.04	1.52
389	406	5.590530	AAATGTCTGCTTGGTTTGTGTTA	57.409	34.783	0.00	0.00	0.00	2.41
413	445	4.578928	GCCGGAAGTACATTGTATGGATTT	59.421	41.667	5.05	0.00	33.60	2.17
431	463	3.488778	TTTCATTTGGCATGCTTGGTT	57.511	38.095	18.92	0.00	0.00	3.67
432	464	3.488778	TTCATTTGGCATGCTTGGTTT	57.511	38.095	18.92	0.00	0.00	3.27
433	465	3.042871	TCATTTGGCATGCTTGGTTTC	57.957	42.857	18.92	0.00	0.00	2.78
436	468	0.033781	TTGGCATGCTTGGTTTCTGC	59.966	50.000	18.92	0.00	0.00	4.26
438	470	1.580942	GCATGCTTGGTTTCTGCGA	59.419	52.632	11.37	0.00	0.00	5.10
439	471	0.039256	GCATGCTTGGTTTCTGCGAA	60.039	50.000	11.37	0.00	0.00	4.70
440	472	1.689959	CATGCTTGGTTTCTGCGAAC	58.310	50.000	0.00	0.00	0.00	3.95
441	473	1.267806	CATGCTTGGTTTCTGCGAACT	59.732	47.619	0.00	0.00	0.00	3.01
442	474	1.388547	TGCTTGGTTTCTGCGAACTT	58.611	45.000	0.00	0.00	0.00	2.66
443	475	1.748493	TGCTTGGTTTCTGCGAACTTT	59.252	42.857	0.00	0.00	0.00	2.66
444	476	2.119457	GCTTGGTTTCTGCGAACTTTG	58.881	47.619	0.00	0.00	0.00	2.77
445	477	2.479560	GCTTGGTTTCTGCGAACTTTGT	60.480	45.455	0.00	0.00	0.00	2.83
446	478	3.242936	GCTTGGTTTCTGCGAACTTTGTA	60.243	43.478	0.00	0.00	0.00	2.41
447	479	3.955771	TGGTTTCTGCGAACTTTGTAC	57.044	42.857	0.00	0.00	0.00	2.90
482	517	0.174389	GATCTCTGAACTGCGCTGGA	59.826	55.000	18.98	5.25	0.00	3.86
521	556	1.662122	AGTTGTTGGACGACGAAACAC	59.338	47.619	0.00	4.99	37.57	3.32
575	771	5.118510	GCATTGTATTTGCAACTTGTACCAC	59.881	40.000	0.00	0.00	39.90	4.16
589	785	8.896744	CAACTTGTACCACATCTTATGATTGAT	58.103	33.333	0.00	0.00	0.00	2.57
645	883	4.038282	TGCTATGATGATCAATTGTTGGGC	59.962	41.667	5.13	0.00	0.00	5.36
677	919	3.123804	CGCCAGCTCGTTGAACTATTAT	58.876	45.455	0.00	0.00	0.00	1.28
678	920	3.555956	CGCCAGCTCGTTGAACTATTATT	59.444	43.478	0.00	0.00	0.00	1.40
679	921	4.318121	CGCCAGCTCGTTGAACTATTATTC	60.318	45.833	0.00	0.00	0.00	1.75
701	943	5.020132	TCTTTTTCCCTTTTCAACCTGTCA	58.980	37.500	0.00	0.00	0.00	3.58
709	951	5.126384	CCCTTTTCAACCTGTCAGTTGTTTA	59.874	40.000	12.12	0.00	45.90	2.01
732	974	4.158394	ACATCAAAGCATAAGCCGTTGATT	59.842	37.500	13.76	6.39	46.00	2.57
850	1168	8.481314	AGTTGTCATTGCTTATGATCTCTCTTA	58.519	33.333	5.57	0.00	44.75	2.10
960	1279	5.252863	TCAATCAGTCCATTTCTTTCCCCTA	59.747	40.000	0.00	0.00	0.00	3.53
973	1292	0.343372	TCCCCTATCCCTTCAGCAGT	59.657	55.000	0.00	0.00	0.00	4.40
993	1312	2.418368	TCAGCTCTCTCTGGTCTCTC	57.582	55.000	0.00	0.00	34.91	3.20
1484	1814	1.796982	CGCTGATCCATCGATCGATCC	60.797	57.143	27.20	16.22	46.89	3.36
1514	1844	0.600255	GGACTGGTGGACTGTTGTCG	60.600	60.000	0.00	0.00	43.79	4.35
1523	1856	0.319641	GACTGTTGTCGGGTGAGGAC	60.320	60.000	0.00	0.00	33.15	3.85
1546	1879	4.255833	TGGTGCCATGTTTCTTGATTTC	57.744	40.909	0.00	0.00	0.00	2.17
1547	1880	3.006752	TGGTGCCATGTTTCTTGATTTCC	59.993	43.478	0.00	0.00	0.00	3.13
1560	1893	5.982356	TCTTGATTTCCTGATGTACTCCTG	58.018	41.667	0.00	0.00	0.00	3.86
1583	1917	5.163530	TGCTGGTTTGCTGTAATATTGGATG	60.164	40.000	0.00	0.00	0.00	3.51
1584	1918	5.067674	GCTGGTTTGCTGTAATATTGGATGA	59.932	40.000	0.00	0.00	0.00	2.92
1585	1919	6.698008	TGGTTTGCTGTAATATTGGATGAG	57.302	37.500	0.00	0.00	0.00	2.90
1586	1920	6.422333	TGGTTTGCTGTAATATTGGATGAGA	58.578	36.000	0.00	0.00	0.00	3.27
1682	2044	3.682377	ACGACGATTTTGCACATGTATCA	59.318	39.130	0.00	0.00	0.00	2.15
1784	2146	4.337060	GCACCCCGCCGTTTCAAC	62.337	66.667	0.00	0.00	32.94	3.18
1793	2155	2.414138	CCGCCGTTTCAACTTACTTAGG	59.586	50.000	0.00	0.00	0.00	2.69
1903	2301	1.080974	GATACGCCCCCGATACGTG	60.081	63.158	0.00	0.00	40.78	4.49
2015	2413	0.621571	TAAGAGCCCACTCAGCCCAT	60.622	55.000	0.00	0.00	46.09	4.00
2030	2428	1.899142	GCCCATTTAAGAGGCAACCAA	59.101	47.619	7.41	0.00	46.34	3.67
2032	2430	3.165071	CCCATTTAAGAGGCAACCAACT	58.835	45.455	0.00	0.00	37.17	3.16
2038	2436	0.693049	AGAGGCAACCAACTACCCTG	59.307	55.000	0.00	0.00	37.17	4.45
2044	2442	2.046314	CCAACTACCCTGGTGCCG	60.046	66.667	0.00	0.00	0.00	5.69
2045	2443	2.747686	CAACTACCCTGGTGCCGT	59.252	61.111	0.00	0.00	0.00	5.68
2053	2451	4.415150	CTGGTGCCGTGATGCCCT	62.415	66.667	0.00	0.00	0.00	5.19
2055	2453	4.101448	GGTGCCGTGATGCCCTCT	62.101	66.667	0.00	0.00	0.00	3.69
2081	2481	0.395312	TCCCTCACAACGTCTTTCCC	59.605	55.000	0.00	0.00	0.00	3.97
2084	2484	0.396811	CTCACAACGTCTTTCCCCCT	59.603	55.000	0.00	0.00	0.00	4.79
2141	2541	2.608988	CTGCTCACCCAGGTCCCT	60.609	66.667	0.00	0.00	0.00	4.20
2189	2592	0.641601	AAGCTCCTCCTCCTCCTCAT	59.358	55.000	0.00	0.00	0.00	2.90
2221	2628	0.392863	TCACGCAGCAGCCATGTATT	60.393	50.000	0.00	0.00	37.52	1.89
2256	2663	1.035932	CATTTCTCCTGCCCAGCCAG	61.036	60.000	0.00	0.00	0.00	4.85
2291	2698	7.395190	TCTTCTTTCTTCTCTGATCTCTGAG	57.605	40.000	0.00	0.00	41.50	3.35
2295	2702	6.896860	TCTTTCTTCTCTGATCTCTGAGGATT	59.103	38.462	4.59	0.00	40.82	3.01
2303	2710	9.211410	TCTCTGATCTCTGAGGATTTCTTATTT	57.789	33.333	4.59	0.00	40.82	1.40
2317	2724	8.628280	GGATTTCTTATTTTCATCTTCTCCAGG	58.372	37.037	0.00	0.00	0.00	4.45
2326	2733	2.276732	TCTTCTCCAGGTTGCTTTGG	57.723	50.000	0.00	0.00	35.74	3.28
2390	2835	0.937304	CCGTATCGGTGCATTCAAGG	59.063	55.000	0.00	0.00	42.73	3.61
2394	2839	2.779755	ATCGGTGCATTCAAGGTGTA	57.220	45.000	0.00	0.00	0.00	2.90
2395	2840	2.779755	TCGGTGCATTCAAGGTGTAT	57.220	45.000	0.00	0.00	0.00	2.29
2396	2841	3.066291	TCGGTGCATTCAAGGTGTATT	57.934	42.857	0.00	0.00	0.00	1.89
2397	2842	4.209307	TCGGTGCATTCAAGGTGTATTA	57.791	40.909	0.00	0.00	0.00	0.98
2398	2843	3.936453	TCGGTGCATTCAAGGTGTATTAC	59.064	43.478	0.00	0.00	0.00	1.89
2399	2844	3.938963	CGGTGCATTCAAGGTGTATTACT	59.061	43.478	0.00	0.00	0.00	2.24
2400	2845	5.105269	TCGGTGCATTCAAGGTGTATTACTA	60.105	40.000	0.00	0.00	0.00	1.82
2401	2846	5.758296	CGGTGCATTCAAGGTGTATTACTAT	59.242	40.000	0.00	0.00	0.00	2.12
2402	2847	6.073765	CGGTGCATTCAAGGTGTATTACTATC	60.074	42.308	0.00	0.00	0.00	2.08
2403	2848	6.073765	GGTGCATTCAAGGTGTATTACTATCG	60.074	42.308	0.00	0.00	0.00	2.92
2404	2849	6.479001	GTGCATTCAAGGTGTATTACTATCGT	59.521	38.462	0.00	0.00	0.00	3.73
2405	2850	7.011109	GTGCATTCAAGGTGTATTACTATCGTT	59.989	37.037	0.00	0.00	0.00	3.85
2406	2851	7.011016	TGCATTCAAGGTGTATTACTATCGTTG	59.989	37.037	0.00	4.94	0.00	4.10
2407	2852	7.011109	GCATTCAAGGTGTATTACTATCGTTGT	59.989	37.037	13.40	0.00	0.00	3.32
2408	2853	9.524106	CATTCAAGGTGTATTACTATCGTTGTA	57.476	33.333	13.40	8.71	0.00	2.41
2410	2855	9.577110	TTCAAGGTGTATTACTATCGTTGTAAG	57.423	33.333	13.40	0.00	34.03	2.34
2411	2856	8.742777	TCAAGGTGTATTACTATCGTTGTAAGT	58.257	33.333	13.40	0.00	34.03	2.24
2412	2857	9.362539	CAAGGTGTATTACTATCGTTGTAAGTT	57.637	33.333	0.00	0.00	34.03	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
111	117	5.047802	TCCAATCCACTTGAGAGCAAATTTC	60.048	40.000	0.00	0.00	36.97	2.17
299	315	4.386867	TGATAAGACGAAGCCTAACAGG	57.613	45.455	0.00	0.00	38.80	4.00
300	316	4.747108	CCATGATAAGACGAAGCCTAACAG	59.253	45.833	0.00	0.00	0.00	3.16
301	317	4.404394	TCCATGATAAGACGAAGCCTAACA	59.596	41.667	0.00	0.00	0.00	2.41
302	318	4.945246	TCCATGATAAGACGAAGCCTAAC	58.055	43.478	0.00	0.00	0.00	2.34
303	319	5.607939	TTCCATGATAAGACGAAGCCTAA	57.392	39.130	0.00	0.00	0.00	2.69
304	320	5.808366	ATTCCATGATAAGACGAAGCCTA	57.192	39.130	0.00	0.00	0.00	3.93
305	321	4.696479	ATTCCATGATAAGACGAAGCCT	57.304	40.909	0.00	0.00	0.00	4.58
306	322	5.757850	AAATTCCATGATAAGACGAAGCC	57.242	39.130	0.00	0.00	0.00	4.35
307	323	6.073003	CCCTAAATTCCATGATAAGACGAAGC	60.073	42.308	0.00	0.00	0.00	3.86
308	324	6.428159	CCCCTAAATTCCATGATAAGACGAAG	59.572	42.308	0.00	0.00	0.00	3.79
348	364	1.621992	TAAAATGCAGGGCGAAACCA	58.378	45.000	0.00	0.00	42.05	3.67
354	371	3.181397	CAGACATTTAAAATGCAGGGCG	58.819	45.455	0.00	0.00	0.00	6.13
363	380	6.402222	ACACAAACCAAGCAGACATTTAAAA	58.598	32.000	0.00	0.00	0.00	1.52
367	384	4.470334	AACACAAACCAAGCAGACATTT	57.530	36.364	0.00	0.00	0.00	2.32
368	385	4.499696	GCTAACACAAACCAAGCAGACATT	60.500	41.667	0.00	0.00	33.38	2.71
369	386	3.004734	GCTAACACAAACCAAGCAGACAT	59.995	43.478	0.00	0.00	33.38	3.06
389	406	2.769663	TCCATACAATGTACTTCCGGCT	59.230	45.455	0.00	0.00	0.00	5.52
413	445	2.633967	AGAAACCAAGCATGCCAAATGA	59.366	40.909	15.66	0.00	0.00	2.57
431	463	4.260051	CGAAGTTGTACAAAGTTCGCAGAA	60.260	41.667	27.86	0.00	45.90	3.02
432	464	3.244345	CGAAGTTGTACAAAGTTCGCAGA	59.756	43.478	27.86	0.00	34.47	4.26
433	465	3.531982	CGAAGTTGTACAAAGTTCGCAG	58.468	45.455	27.86	12.73	34.47	5.18
436	468	3.302870	CCACCGAAGTTGTACAAAGTTCG	60.303	47.826	29.98	29.98	38.09	3.95
438	470	3.613030	ACCACCGAAGTTGTACAAAGTT	58.387	40.909	10.51	7.02	0.00	2.66
439	471	3.271055	ACCACCGAAGTTGTACAAAGT	57.729	42.857	10.51	0.39	0.00	2.66
440	472	4.210537	CACTACCACCGAAGTTGTACAAAG	59.789	45.833	10.51	2.52	0.00	2.77
441	473	4.121317	CACTACCACCGAAGTTGTACAAA	58.879	43.478	10.51	0.00	0.00	2.83
442	474	3.384146	TCACTACCACCGAAGTTGTACAA	59.616	43.478	3.59	3.59	0.00	2.41
443	475	2.957680	TCACTACCACCGAAGTTGTACA	59.042	45.455	0.00	0.00	0.00	2.90
444	476	3.648339	TCACTACCACCGAAGTTGTAC	57.352	47.619	0.00	0.00	0.00	2.90
445	477	4.084287	AGATCACTACCACCGAAGTTGTA	58.916	43.478	0.00	0.00	0.00	2.41
446	478	2.897969	AGATCACTACCACCGAAGTTGT	59.102	45.455	0.00	0.00	0.00	3.32
447	479	3.193691	AGAGATCACTACCACCGAAGTTG	59.806	47.826	0.00	0.00	0.00	3.16
482	517	1.812571	CTGTACCAAGGCGAATTTGCT	59.187	47.619	17.19	0.00	34.52	3.91
521	556	1.487482	TTCGCTGTCGACTTGAGTTG	58.513	50.000	17.92	3.62	45.43	3.16
575	771	9.177304	CATTTGGTTTCGATCAATCATAAGATG	57.823	33.333	0.00	0.00	33.90	2.90
645	883	4.424566	GCTGGCGCCAACCATGTG	62.425	66.667	32.09	17.97	39.54	3.21
677	919	5.482175	TGACAGGTTGAAAAGGGAAAAAGAA	59.518	36.000	0.00	0.00	0.00	2.52
678	920	5.020132	TGACAGGTTGAAAAGGGAAAAAGA	58.980	37.500	0.00	0.00	0.00	2.52
679	921	5.105351	ACTGACAGGTTGAAAAGGGAAAAAG	60.105	40.000	7.51	0.00	0.00	2.27
701	943	6.389906	GGCTTATGCTTTGATGTAAACAACT	58.610	36.000	0.13	0.00	39.59	3.16
709	951	3.081061	TCAACGGCTTATGCTTTGATGT	58.919	40.909	11.55	0.00	36.76	3.06
757	1019	6.058833	TGCCGATTTTAGCATCTTTATGGTA	58.941	36.000	0.00	0.00	41.96	3.25
766	1028	3.623060	TGAACTCTGCCGATTTTAGCATC	59.377	43.478	0.00	0.00	38.56	3.91
771	1033	3.120338	CGCTTTGAACTCTGCCGATTTTA	60.120	43.478	0.00	0.00	0.00	1.52
777	1039	0.798776	AATCGCTTTGAACTCTGCCG	59.201	50.000	0.00	0.00	0.00	5.69
892	1210	1.136336	GTTCGTCACGATGAAGCAACC	60.136	52.381	0.00	0.00	37.04	3.77
960	1279	0.990374	AGCTGAACTGCTGAAGGGAT	59.010	50.000	5.47	0.00	42.33	3.85
973	1292	2.620367	GGAGAGACCAGAGAGAGCTGAA	60.620	54.545	0.00	0.00	38.14	3.02
1484	1814	4.227134	CCAGTCCCCAGATCGGCG	62.227	72.222	0.00	0.00	0.00	6.46
1514	1844	2.044946	GGCACCATGTCCTCACCC	60.045	66.667	0.00	0.00	0.00	4.61
1546	1879	1.198713	ACCAGCAGGAGTACATCAGG	58.801	55.000	0.35	0.00	38.69	3.86
1547	1880	3.005554	CAAACCAGCAGGAGTACATCAG	58.994	50.000	0.35	0.00	38.69	2.90
1560	1893	4.981806	TCCAATATTACAGCAAACCAGC	57.018	40.909	0.00	0.00	0.00	4.85
1583	1917	1.500108	CCAGAGCATTCGCATCTCTC	58.500	55.000	0.00	0.00	42.27	3.20
1584	1918	0.532417	GCCAGAGCATTCGCATCTCT	60.532	55.000	0.00	0.00	42.27	3.10
1585	1919	0.532417	AGCCAGAGCATTCGCATCTC	60.532	55.000	0.00	0.00	43.56	2.75
1586	1920	0.814410	CAGCCAGAGCATTCGCATCT	60.814	55.000	0.00	0.00	43.56	2.90
1682	2044	4.972591	GCGCTGGCAATGTCTTTT	57.027	50.000	0.00	0.00	39.62	2.27
1818	2181	3.786516	TCCGTGCATTCGAGTAATACA	57.213	42.857	0.00	0.00	0.00	2.29
1819	2182	5.458891	AGTATCCGTGCATTCGAGTAATAC	58.541	41.667	0.00	2.16	0.00	1.89
1903	2301	6.732896	TTTATTCTCAGATACTCCAGGGAC	57.267	41.667	0.00	0.00	0.00	4.46
2015	2413	3.396611	AGGGTAGTTGGTTGCCTCTTAAA	59.603	43.478	0.00	0.00	0.00	1.52
2030	2428	1.612442	ATCACGGCACCAGGGTAGT	60.612	57.895	0.00	0.00	0.00	2.73
2032	2430	2.986290	CATCACGGCACCAGGGTA	59.014	61.111	0.00	0.00	0.00	3.69
2038	2436	2.044806	ATAGAGGGCATCACGGCACC	62.045	60.000	0.58	0.00	43.60	5.01
2044	2442	2.224646	GGGAAAGGATAGAGGGCATCAC	60.225	54.545	0.58	0.00	0.00	3.06
2045	2443	2.057922	GGGAAAGGATAGAGGGCATCA	58.942	52.381	0.58	0.00	0.00	3.07
2053	2451	3.170717	ACGTTGTGAGGGAAAGGATAGA	58.829	45.455	0.00	0.00	0.00	1.98
2055	2453	3.170717	AGACGTTGTGAGGGAAAGGATA	58.829	45.455	0.00	0.00	0.00	2.59
2081	2481	2.358737	GTGTGAGCACGGGAAGGG	60.359	66.667	0.00	0.00	35.75	3.95
2084	2484	2.425592	CTGGTGTGAGCACGGGAA	59.574	61.111	0.00	0.00	46.13	3.97
2165	2568	1.270907	GAGGAGGAGGAGCTTGTTGA	58.729	55.000	0.00	0.00	0.00	3.18
2167	2570	0.118144	AGGAGGAGGAGGAGCTTGTT	59.882	55.000	0.00	0.00	0.00	2.83
2189	2592	2.927580	GCGTGAGAGGGGACGTTGA	61.928	63.158	0.00	0.00	37.89	3.18
2221	2628	6.498651	AGGAGAAATGGAGAAGAGAAGTGTAA	59.501	38.462	0.00	0.00	0.00	2.41
2256	2663	4.162131	AGAAGAAAGAAGAGGAGATGAGCC	59.838	45.833	0.00	0.00	0.00	4.70
2291	2698	8.628280	CCTGGAGAAGATGAAAATAAGAAATCC	58.372	37.037	0.00	0.00	0.00	3.01
2295	2702	7.094205	GCAACCTGGAGAAGATGAAAATAAGAA	60.094	37.037	0.00	0.00	0.00	2.52
2303	2710	3.795688	AAGCAACCTGGAGAAGATGAA	57.204	42.857	0.00	0.00	0.00	2.57
2317	2724	2.095919	CGTTGTAGCTACCCAAAGCAAC	60.096	50.000	21.01	14.58	45.30	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.