AutoCloner

Multiple sequence alignment - TraesCS1B01G297200

Loading Multiple Alignment...

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	TraesCS1B01G297200	chr1B	100.000	2312	0	0	1	2312	516972658	516970347	0.000000e+00	4270.0
1	TraesCS1B01G297200	chr1B	97.659	598	13	1	3	599	128023868	128023271	0.000000e+00	1026.0
2	TraesCS1B01G297200	chr1B	88.256	562	50	15	762	1313	607316998	607316443	0.000000e+00	658.0
3	TraesCS1B01G297200	chr1B	87.826	575	51	12	789	1357	608042961	608042400	0.000000e+00	656.0
4	TraesCS1B01G297200	chr1B	87.722	562	53	15	762	1313	607137865	607137310	1.940000e-180	641.0
5	TraesCS1B01G297200	chr1B	88.246	536	52	9	786	1314	527288096	527288627	4.190000e-177	630.0
6	TraesCS1B01G297200	chr1B	91.525	59	2	3	2256	2312	1193099	1193042	6.850000e-11	78.7
7	TraesCS1B01G297200	chr1D	91.383	1648	76	29	672	2287	384847399	384845786	0.000000e+00	2196.0
8	TraesCS1B01G297200	chr1D	88.174	575	45	15	789	1357	445367016	445366459	0.000000e+00	664.0
9	TraesCS1B01G297200	chr1D	87.054	533	53	14	762	1284	394491947	394491421	2.560000e-164	588.0
10	TraesCS1B01G297200	chr1A	90.836	873	45	12	665	1521	485013237	485012384	0.000000e+00	1136.0
11	TraesCS1B01G297200	chr1A	87.002	577	51	14	789	1359	541343621	541344179	1.510000e-176	628.0
12	TraesCS1B01G297200	chr3B	97.333	600	15	1	2	600	171120677	171120078	0.000000e+00	1018.0
13	TraesCS1B01G297200	chr3B	96.700	606	18	2	3	607	22549857	22550461	0.000000e+00	1007.0
14	TraesCS1B01G297200	chr3A	97.176	602	16	1	1	601	522043981	522043380	0.000000e+00	1016.0
15	TraesCS1B01G297200	chr6B	96.870	607	17	2	3	607	664618999	664619605	0.000000e+00	1014.0
16	TraesCS1B01G297200	chr2B	97.324	598	14	2	4	600	438875779	438875183	0.000000e+00	1014.0
17	TraesCS1B01G297200	chr2B	97.167	600	15	2	3	601	683096645	683096047	0.000000e+00	1013.0
18	TraesCS1B01G297200	chr5A	97.005	601	17	1	1	600	482426903	482426303	0.000000e+00	1009.0
19	TraesCS1B01G297200	chr4B	96.854	604	16	3	3	605	53068828	53068227	0.000000e+00	1007.0
20	TraesCS1B01G297200	chr4B	91.525	59	2	3	2256	2312	105628378	105628435	6.850000e-11	78.7
21	TraesCS1B01G297200	chr4B	91.525	59	2	3	2256	2312	530491181	530491124	6.850000e-11	78.7
22	TraesCS1B01G297200	chr7B	95.918	49	2	0	2264	2312	711721481	711721529	1.900000e-11	80.5
23	TraesCS1B01G297200	chr4D	95.918	49	2	0	2264	2312	98448063	98448015	1.900000e-11	80.5
24	TraesCS1B01G297200	chr7A	91.525	59	2	3	2256	2312	17936447	17936390	6.850000e-11	78.7
25	TraesCS1B01G297200	chr5B	97.826	46	0	1	2268	2312	632062558	632062603	6.850000e-11	78.7
26	TraesCS1B01G297200	chr5B	95.833	48	2	0	2265	2312	704079119	704079166	6.850000e-11	78.7
27	TraesCS1B01G297200	chr5B	88.136	59	7	0	2251	2309	194191137	194191079	1.150000e-08	71.3

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	TraesCS1B01G297200	chr1B	516970347	516972658	2311	True	4270	4270	100.000	1	2312	1	chr1B.!!$R3	2311
1	TraesCS1B01G297200	chr1B	128023271	128023868	597	True	1026	1026	97.659	3	599	1	chr1B.!!$R2	596
2	TraesCS1B01G297200	chr1B	607316443	607316998	555	True	658	658	88.256	762	1313	1	chr1B.!!$R5	551
3	TraesCS1B01G297200	chr1B	608042400	608042961	561	True	656	656	87.826	789	1357	1	chr1B.!!$R6	568
4	TraesCS1B01G297200	chr1B	607137310	607137865	555	True	641	641	87.722	762	1313	1	chr1B.!!$R4	551
5	TraesCS1B01G297200	chr1B	527288096	527288627	531	False	630	630	88.246	786	1314	1	chr1B.!!$F1	528
6	TraesCS1B01G297200	chr1D	384845786	384847399	1613	True	2196	2196	91.383	672	2287	1	chr1D.!!$R1	1615
7	TraesCS1B01G297200	chr1D	445366459	445367016	557	True	664	664	88.174	789	1357	1	chr1D.!!$R3	568
8	TraesCS1B01G297200	chr1D	394491421	394491947	526	True	588	588	87.054	762	1284	1	chr1D.!!$R2	522
9	TraesCS1B01G297200	chr1A	485012384	485013237	853	True	1136	1136	90.836	665	1521	1	chr1A.!!$R1	856
10	TraesCS1B01G297200	chr1A	541343621	541344179	558	False	628	628	87.002	789	1359	1	chr1A.!!$F1	570
11	TraesCS1B01G297200	chr3B	171120078	171120677	599	True	1018	1018	97.333	2	600	1	chr3B.!!$R1	598
12	TraesCS1B01G297200	chr3B	22549857	22550461	604	False	1007	1007	96.700	3	607	1	chr3B.!!$F1	604
13	TraesCS1B01G297200	chr3A	522043380	522043981	601	True	1016	1016	97.176	1	601	1	chr3A.!!$R1	600
14	TraesCS1B01G297200	chr6B	664618999	664619605	606	False	1014	1014	96.870	3	607	1	chr6B.!!$F1	604
15	TraesCS1B01G297200	chr2B	438875183	438875779	596	True	1014	1014	97.324	4	600	1	chr2B.!!$R1	596
16	TraesCS1B01G297200	chr2B	683096047	683096645	598	True	1013	1013	97.167	3	601	1	chr2B.!!$R2	598
17	TraesCS1B01G297200	chr5A	482426303	482426903	600	True	1009	1009	97.005	1	600	1	chr5A.!!$R1	599
18	TraesCS1B01G297200	chr4B	53068227	53068828	601	True	1007	1007	96.854	3	605	1	chr4B.!!$R1	602

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
725	729	1.102978	GCCCAACAGCCGAAATATGT	58.897	50.0	0.0	0.0	0.0	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1798	1840	0.03831	ACTTCCCTAAAGCACCAGGC	59.962	55.0	0.0	0.0	45.3	4.85	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	3.657956	TTTTTGCCAGAAGTTGCCG	57.342	47.368	0.00	0.00	0.00	5.69
28	29	1.813753	GCCAGAAGTTGCCGCGATA	60.814	57.895	8.23	0.00	0.00	2.92
149	150	6.980593	TCCAGTACTTTGACCATGAAAATTG	58.019	36.000	0.00	0.00	0.00	2.32
235	236	8.635765	TCATGGCAAGTCTAGTTTCTTAATTT	57.364	30.769	0.00	0.00	0.00	1.82
647	649	9.509855	TTTTTAGCAACAACATAACAGTACTTG	57.490	29.630	0.00	0.00	0.00	3.16
648	650	8.439993	TTTAGCAACAACATAACAGTACTTGA	57.560	30.769	0.00	0.00	0.00	3.02
649	651	8.615878	TTAGCAACAACATAACAGTACTTGAT	57.384	30.769	0.00	0.00	0.00	2.57
650	652	7.510549	AGCAACAACATAACAGTACTTGATT	57.489	32.000	0.00	0.00	0.00	2.57
651	653	8.615878	AGCAACAACATAACAGTACTTGATTA	57.384	30.769	0.00	0.00	0.00	1.75
652	654	8.721478	AGCAACAACATAACAGTACTTGATTAG	58.279	33.333	0.00	0.00	0.00	1.73
653	655	8.504005	GCAACAACATAACAGTACTTGATTAGT	58.496	33.333	0.00	0.00	41.04	2.24
679	681	8.511604	TTTTTGAGGTAATTTGCAAAATGGAA	57.488	26.923	17.19	0.53	39.21	3.53
722	726	1.747367	CCGCCCAACAGCCGAAATA	60.747	57.895	0.00	0.00	0.00	1.40
725	729	1.102978	GCCCAACAGCCGAAATATGT	58.897	50.000	0.00	0.00	0.00	2.29
756	760	3.310774	CCTGATCTGACGAAATTTGCGAT	59.689	43.478	3.21	1.95	0.00	4.58
757	761	4.507756	CCTGATCTGACGAAATTTGCGATA	59.492	41.667	3.21	0.00	0.00	2.92
762	766	2.417239	TGACGAAATTTGCGATACACCC	59.583	45.455	3.21	0.00	0.00	4.61
889	903	2.760385	CTCCTCCGGTCCTCCCAC	60.760	72.222	0.00	0.00	0.00	4.61
890	904	4.393778	TCCTCCGGTCCTCCCACC	62.394	72.222	0.00	0.00	0.00	4.61
922	936	2.384828	CTTTAAAATCCCCTTCCCCCG	58.615	52.381	0.00	0.00	0.00	5.73
959	975	3.402681	CCATCACCACCGCTCCCT	61.403	66.667	0.00	0.00	0.00	4.20
1005	1038	0.749649	GAGGATCGTCAGCCATGTCT	59.250	55.000	10.50	0.00	0.00	3.41
1221	1254	2.503375	GACGCCGTCACCTACACG	60.503	66.667	13.23	0.00	36.99	4.49
1335	1376	1.153549	GCCAGATGGTCGTCAGTCC	60.154	63.158	0.00	0.00	37.57	3.85
1439	1481	3.507622	CCTTGTTTCCCATTTCCTCTGTC	59.492	47.826	0.00	0.00	0.00	3.51
1450	1492	3.685139	TTCCTCTGTCTGTTTAGCTGG	57.315	47.619	0.00	0.00	0.00	4.85
1463	1505	8.844244	GTCTGTTTAGCTGGATCATGAAATTAT	58.156	33.333	0.00	0.00	0.00	1.28
1464	1506	8.843262	TCTGTTTAGCTGGATCATGAAATTATG	58.157	33.333	0.00	0.00	0.00	1.90
1465	1507	8.523915	TGTTTAGCTGGATCATGAAATTATGT	57.476	30.769	0.00	0.00	0.00	2.29
1466	1508	9.625747	TGTTTAGCTGGATCATGAAATTATGTA	57.374	29.630	0.00	0.00	0.00	2.29
1467	1509	9.884465	GTTTAGCTGGATCATGAAATTATGTAC	57.116	33.333	0.00	0.00	0.00	2.90
1508	1550	2.143925	CCAGAGTTCGAACTGAAACCC	58.856	52.381	34.23	18.52	39.88	4.11
1521	1563	1.644786	GAAACCCGCATCCCTTGTCG	61.645	60.000	0.00	0.00	0.00	4.35
1528	1570	2.276201	CGCATCCCTTGTCGTGAATTA	58.724	47.619	0.00	0.00	0.00	1.40
1542	1584	4.082841	TCGTGAATTATGTGCAAATGCTGT	60.083	37.500	0.00	0.00	42.66	4.40
1548	1590	0.388659	TGTGCAAATGCTGTGTTCCC	59.611	50.000	6.97	0.00	42.66	3.97
1549	1591	0.319813	GTGCAAATGCTGTGTTCCCC	60.320	55.000	6.97	0.00	42.66	4.81
1550	1592	0.469705	TGCAAATGCTGTGTTCCCCT	60.470	50.000	6.97	0.00	42.66	4.79
1551	1593	0.244721	GCAAATGCTGTGTTCCCCTC	59.755	55.000	0.00	0.00	38.21	4.30
1552	1594	1.915141	CAAATGCTGTGTTCCCCTCT	58.085	50.000	0.00	0.00	0.00	3.69
1556	1598	2.024176	TGCTGTGTTCCCCTCTTCTA	57.976	50.000	0.00	0.00	0.00	2.10
1557	1599	2.551270	TGCTGTGTTCCCCTCTTCTAT	58.449	47.619	0.00	0.00	0.00	1.98
1561	1603	4.396478	GCTGTGTTCCCCTCTTCTATTTTC	59.604	45.833	0.00	0.00	0.00	2.29
1577	1619	7.548196	TCTATTTTCTTGTGAAAGTTCGTGT	57.452	32.000	0.00	0.00	42.34	4.49
1585	1627	4.438148	TGTGAAAGTTCGTGTGAGATTGA	58.562	39.130	0.00	0.00	0.00	2.57
1623	1665	4.691685	GCATTTCAGATGAACAAATTGGCA	59.308	37.500	0.00	0.00	33.13	4.92
1634	1676	2.004017	CAAATTGGCAGCGCAAATCAT	58.996	42.857	11.47	0.00	29.96	2.45
1648	1690	5.107491	GCGCAAATCATGATATCGTTCAGTA	60.107	40.000	9.04	0.00	0.00	2.74
1649	1691	6.292129	CGCAAATCATGATATCGTTCAGTAC	58.708	40.000	9.04	0.00	0.00	2.73
1656	1698	7.496747	TCATGATATCGTTCAGTACAATCCAA	58.503	34.615	0.00	0.00	0.00	3.53
1657	1699	8.150296	TCATGATATCGTTCAGTACAATCCAAT	58.850	33.333	0.00	0.00	0.00	3.16
1662	1704	5.109210	TCGTTCAGTACAATCCAATAGCAG	58.891	41.667	0.00	0.00	0.00	4.24
1674	1716	2.621998	CCAATAGCAGCATTTCCTCTGG	59.378	50.000	0.00	0.00	0.00	3.86
1704	1746	1.000955	CAGCACTCTGTTCCGTAACCT	59.999	52.381	0.00	0.00	35.61	3.50
1719	1761	5.597182	TCCGTAACCTGCTTATCAGTAGAAT	59.403	40.000	0.00	0.00	41.25	2.40
1725	1767	5.843421	ACCTGCTTATCAGTAGAATGATCCT	59.157	40.000	0.00	0.00	40.40	3.24
1769	1811	6.237901	ACAATGCTTATTAGGAGTGACACAA	58.762	36.000	7.67	0.00	39.77	3.33
1770	1812	6.886459	ACAATGCTTATTAGGAGTGACACAAT	59.114	34.615	7.67	1.38	39.77	2.71
1771	1813	6.932356	ATGCTTATTAGGAGTGACACAATG	57.068	37.500	8.59	0.00	0.00	2.82
1802	1844	2.046023	TGGGAACATGAGCGCCTG	60.046	61.111	2.29	1.55	33.40	4.85
1814	1858	2.668632	CGCCTGGTGCTTTAGGGA	59.331	61.111	0.00	0.00	38.05	4.20
1820	1864	3.135895	GCCTGGTGCTTTAGGGAAGTATA	59.864	47.826	0.00	0.00	37.69	1.47
1900	1944	4.340617	ACATTTCAGATAAAAAGGGGCGA	58.659	39.130	0.00	0.00	0.00	5.54
1905	1949	3.699038	TCAGATAAAAAGGGGCGAATTGG	59.301	43.478	0.00	0.00	0.00	3.16
1999	2043	2.816087	CTCAAGGGTCCTGTGAATTGTG	59.184	50.000	0.00	0.00	0.00	3.33
2001	2045	2.276732	AGGGTCCTGTGAATTGTGTG	57.723	50.000	0.00	0.00	0.00	3.82
2084	2128	7.121020	TGAGAGCACATAATACAGATTGCAAAA	59.879	33.333	1.71	0.00	0.00	2.44
2148	2192	2.249139	ACGTAAGGAAGTCTGCTCCTT	58.751	47.619	10.15	10.15	44.98	3.36
2149	2193	2.633481	ACGTAAGGAAGTCTGCTCCTTT	59.367	45.455	10.48	0.00	43.04	3.11
2162	2206	3.343617	TGCTCCTTTTACTGGCATGTAC	58.656	45.455	0.00	0.00	0.00	2.90
2173	2217	3.005554	CTGGCATGTACAACTTCAGGAG	58.994	50.000	0.00	0.00	0.00	3.69
2223	2281	1.334869	GTGGTGCAAACAGTCTGAAGG	59.665	52.381	6.91	0.00	0.00	3.46
2239	2297	6.784969	AGTCTGAAGGTAGGATACAAGCATAT	59.215	38.462	0.00	0.00	45.43	1.78
2243	2301	3.055819	AGGTAGGATACAAGCATATGCCG	60.056	47.826	23.96	17.47	45.43	5.69
2287	2345	5.299949	TGTTAAAAACTACTCCCTCCGTTC	58.700	41.667	0.00	0.00	0.00	3.95
2288	2346	3.413846	AAAAACTACTCCCTCCGTTCC	57.586	47.619	0.00	0.00	0.00	3.62
2289	2347	0.893447	AAACTACTCCCTCCGTTCCG	59.107	55.000	0.00	0.00	0.00	4.30
2290	2348	0.038744	AACTACTCCCTCCGTTCCGA	59.961	55.000	0.00	0.00	0.00	4.55
2291	2349	0.258194	ACTACTCCCTCCGTTCCGAT	59.742	55.000	0.00	0.00	0.00	4.18
2292	2350	1.341778	ACTACTCCCTCCGTTCCGATT	60.342	52.381	0.00	0.00	0.00	3.34
2293	2351	1.755380	CTACTCCCTCCGTTCCGATTT	59.245	52.381	0.00	0.00	0.00	2.17
2294	2352	1.856629	ACTCCCTCCGTTCCGATTTA	58.143	50.000	0.00	0.00	0.00	1.40
2295	2353	1.479730	ACTCCCTCCGTTCCGATTTAC	59.520	52.381	0.00	0.00	0.00	2.01
2296	2354	1.755380	CTCCCTCCGTTCCGATTTACT	59.245	52.381	0.00	0.00	0.00	2.24
2297	2355	1.753073	TCCCTCCGTTCCGATTTACTC	59.247	52.381	0.00	0.00	0.00	2.59
2299	2357	1.133790	CCTCCGTTCCGATTTACTCGT	59.866	52.381	0.00	0.00	46.18	4.18
2300	2358	2.448219	CTCCGTTCCGATTTACTCGTC	58.552	52.381	0.00	0.00	46.18	4.20
2301	2359	1.186030	CCGTTCCGATTTACTCGTCG	58.814	55.000	0.00	0.00	46.18	5.12
2302	2360	1.466360	CCGTTCCGATTTACTCGTCGT	60.466	52.381	0.00	0.00	46.18	4.34
2303	2361	1.576246	CGTTCCGATTTACTCGTCGTG	59.424	52.381	0.00	0.00	46.18	4.35
2304	2362	1.916000	GTTCCGATTTACTCGTCGTGG	59.084	52.381	0.00	0.00	46.18	4.94
2305	2363	1.167851	TCCGATTTACTCGTCGTGGT	58.832	50.000	0.00	0.00	46.18	4.16
2306	2364	1.541147	TCCGATTTACTCGTCGTGGTT	59.459	47.619	0.00	0.00	46.18	3.67
2307	2365	2.030007	TCCGATTTACTCGTCGTGGTTT	60.030	45.455	0.00	0.00	46.18	3.27
2308	2366	2.733026	CCGATTTACTCGTCGTGGTTTT	59.267	45.455	0.00	0.00	46.18	2.43
2309	2367	3.919804	CCGATTTACTCGTCGTGGTTTTA	59.080	43.478	0.00	0.00	46.18	1.52
2310	2368	4.030977	CCGATTTACTCGTCGTGGTTTTAG	59.969	45.833	0.00	0.00	46.18	1.85
2311	2369	4.618489	CGATTTACTCGTCGTGGTTTTAGT	59.382	41.667	0.00	0.00	42.56	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	3.354397	GCAACTGCAGTGTAAATATCGC	58.646	45.455	22.49	8.24	41.59	4.58
28	29	3.696051	CCTATGGCAACTGCAGTGTAAAT	59.304	43.478	22.49	14.43	44.36	1.40
621	623	9.509855	CAAGTACTGTTATGTTGTTGCTAAAAA	57.490	29.630	0.00	0.00	0.00	1.94
622	624	8.894731	TCAAGTACTGTTATGTTGTTGCTAAAA	58.105	29.630	0.00	0.00	0.00	1.52
623	625	8.439993	TCAAGTACTGTTATGTTGTTGCTAAA	57.560	30.769	0.00	0.00	0.00	1.85
624	626	8.615878	ATCAAGTACTGTTATGTTGTTGCTAA	57.384	30.769	0.00	0.00	0.00	3.09
625	627	8.615878	AATCAAGTACTGTTATGTTGTTGCTA	57.384	30.769	0.00	0.00	0.00	3.49
626	628	7.510549	AATCAAGTACTGTTATGTTGTTGCT	57.489	32.000	0.00	0.00	0.00	3.91
627	629	8.504005	ACTAATCAAGTACTGTTATGTTGTTGC	58.496	33.333	0.00	0.00	36.36	4.17
654	656	8.511604	TTCCATTTTGCAAATTACCTCAAAAA	57.488	26.923	13.65	0.00	40.40	1.94
655	657	8.511604	TTTCCATTTTGCAAATTACCTCAAAA	57.488	26.923	13.65	3.84	40.99	2.44
656	658	8.511604	TTTTCCATTTTGCAAATTACCTCAAA	57.488	26.923	13.65	4.37	0.00	2.69
657	659	8.511604	TTTTTCCATTTTGCAAATTACCTCAA	57.488	26.923	13.65	0.00	0.00	3.02
679	681	1.518302	GTGGGGGTTGTGCGTTTTT	59.482	52.632	0.00	0.00	0.00	1.94
717	719	1.532868	CAGGCGCCAGCTACATATTTC	59.467	52.381	31.54	0.00	44.37	2.17
722	726	1.070445	GATCAGGCGCCAGCTACAT	59.930	57.895	31.54	10.13	44.37	2.29
725	729	1.758122	TCAGATCAGGCGCCAGCTA	60.758	57.895	31.54	11.12	44.37	3.32
756	760	3.315949	GGTGAGTGGCGGGGTGTA	61.316	66.667	0.00	0.00	0.00	2.90
762	766	4.873129	CCGATCGGTGAGTGGCGG	62.873	72.222	26.35	0.00	0.00	6.13
879	893	2.365768	GAGAGGGGTGGGAGGACC	60.366	72.222	0.00	0.00	40.81	4.46
880	894	2.760385	CGAGAGGGGTGGGAGGAC	60.760	72.222	0.00	0.00	0.00	3.85
889	903	0.909623	TTTAAAGGAGGCGAGAGGGG	59.090	55.000	0.00	0.00	0.00	4.79
890	904	2.781681	TTTTAAAGGAGGCGAGAGGG	57.218	50.000	0.00	0.00	0.00	4.30
922	936	1.400242	GGTGCTGTGATTTGCGAGAAC	60.400	52.381	0.00	0.00	0.00	3.01
959	975	2.125552	CTGCGCGAGTGGGATTGA	60.126	61.111	12.10	0.00	0.00	2.57
1065	1098	0.389817	CCTGGATGTTGTCGCGAAGA	60.390	55.000	12.06	0.00	0.00	2.87
1068	1101	2.264480	CCCTGGATGTTGTCGCGA	59.736	61.111	3.71	3.71	0.00	5.87
1203	1236	2.646719	GTGTAGGTGACGGCGTCA	59.353	61.111	36.29	36.29	40.50	4.35
1358	1399	1.005394	AACGGGCGGACTAACACAG	60.005	57.895	0.00	0.00	0.00	3.66
1439	1481	8.627403	ACATAATTTCATGATCCAGCTAAACAG	58.373	33.333	0.00	0.00	0.00	3.16
1463	1505	7.686438	ATGCAAACATCTTCATTACAGTACA	57.314	32.000	0.00	0.00	0.00	2.90
1508	1550	1.086696	AATTCACGACAAGGGATGCG	58.913	50.000	0.00	0.00	35.57	4.73
1521	1563	4.925054	ACACAGCATTTGCACATAATTCAC	59.075	37.500	5.20	0.00	45.16	3.18
1528	1570	1.001181	GGGAACACAGCATTTGCACAT	59.999	47.619	5.20	0.00	45.16	3.21
1542	1584	6.003950	CACAAGAAAATAGAAGAGGGGAACA	58.996	40.000	0.00	0.00	0.00	3.18
1548	1590	8.012241	CGAACTTTCACAAGAAAATAGAAGAGG	58.988	37.037	0.00	0.00	42.78	3.69
1549	1591	8.552034	ACGAACTTTCACAAGAAAATAGAAGAG	58.448	33.333	0.00	0.00	42.78	2.85
1550	1592	8.335356	CACGAACTTTCACAAGAAAATAGAAGA	58.665	33.333	0.00	0.00	42.78	2.87
1551	1593	8.122952	ACACGAACTTTCACAAGAAAATAGAAG	58.877	33.333	0.00	0.00	42.78	2.85
1552	1594	7.908082	CACACGAACTTTCACAAGAAAATAGAA	59.092	33.333	0.00	0.00	42.78	2.10
1556	1598	6.093495	TCTCACACGAACTTTCACAAGAAAAT	59.907	34.615	0.00	0.00	42.78	1.82
1557	1599	5.410132	TCTCACACGAACTTTCACAAGAAAA	59.590	36.000	0.00	0.00	42.78	2.29
1561	1603	5.006649	TCAATCTCACACGAACTTTCACAAG	59.993	40.000	0.00	0.00	35.92	3.16
1591	1633	5.011139	GTTCATCTGAAATGCGACACATCG	61.011	45.833	0.00	0.00	42.63	3.84
1594	1636	3.137533	TGTTCATCTGAAATGCGACACA	58.862	40.909	0.00	0.00	35.58	3.72
1595	1637	3.811722	TGTTCATCTGAAATGCGACAC	57.188	42.857	0.00	0.00	35.58	3.67
1623	1665	3.809279	TGAACGATATCATGATTTGCGCT	59.191	39.130	14.65	6.81	0.00	5.92
1634	1676	7.598869	GCTATTGGATTGTACTGAACGATATCA	59.401	37.037	3.12	0.00	31.87	2.15
1648	1690	4.284178	AGGAAATGCTGCTATTGGATTGT	58.716	39.130	0.00	0.00	0.00	2.71
1649	1691	4.583489	AGAGGAAATGCTGCTATTGGATTG	59.417	41.667	0.00	0.00	0.00	2.67
1656	1698	4.450305	AATCCAGAGGAAATGCTGCTAT	57.550	40.909	0.00	0.00	34.34	2.97
1657	1699	3.939740	AATCCAGAGGAAATGCTGCTA	57.060	42.857	0.00	0.00	34.34	3.49
1662	1704	5.663456	TGCAAATAAATCCAGAGGAAATGC	58.337	37.500	0.00	0.00	34.34	3.56
1674	1716	5.098211	GGAACAGAGTGCTGCAAATAAATC	58.902	41.667	2.77	0.00	46.26	2.17
1748	1790	6.540189	GTCATTGTGTCACTCCTAATAAGCAT	59.460	38.462	4.27	0.00	0.00	3.79
1755	1797	5.622233	CGAGATGTCATTGTGTCACTCCTAA	60.622	44.000	4.27	0.00	0.00	2.69
1756	1798	4.142381	CGAGATGTCATTGTGTCACTCCTA	60.142	45.833	4.27	0.00	0.00	2.94
1757	1799	3.367806	CGAGATGTCATTGTGTCACTCCT	60.368	47.826	4.27	0.00	0.00	3.69
1769	1811	4.141642	TGTTCCCATGATTCGAGATGTCAT	60.142	41.667	0.00	0.00	33.08	3.06
1770	1812	3.197549	TGTTCCCATGATTCGAGATGTCA	59.802	43.478	0.00	0.00	0.00	3.58
1771	1813	3.797039	TGTTCCCATGATTCGAGATGTC	58.203	45.455	0.00	0.00	0.00	3.06
1798	1840	0.038310	ACTTCCCTAAAGCACCAGGC	59.962	55.000	0.00	0.00	45.30	4.85
1802	1844	4.691326	AGCTATACTTCCCTAAAGCACC	57.309	45.455	0.00	0.00	38.67	5.01
1811	1855	8.368962	ACTATTGGATCTAAGCTATACTTCCC	57.631	38.462	0.00	0.00	39.97	3.97
1820	1864	7.785506	ACCTACTGTTACTATTGGATCTAAGCT	59.214	37.037	0.00	0.00	0.00	3.74
1900	1944	5.552870	ATCATAAGTAGGTCGCTCCAATT	57.447	39.130	0.00	0.00	39.02	2.32
1905	1949	5.348986	TCACAAATCATAAGTAGGTCGCTC	58.651	41.667	0.00	0.00	0.00	5.03
1960	2004	5.220739	CCTTGAGCCAAAAGATCAGTAATCG	60.221	44.000	0.00	0.00	43.01	3.34
1999	2043	1.615392	AGCTGTTCTGGAAATTGGCAC	59.385	47.619	0.00	0.00	0.00	5.01
2001	2045	1.888512	TGAGCTGTTCTGGAAATTGGC	59.111	47.619	0.00	0.00	0.00	4.52
2063	2107	7.990541	TGATTTTGCAATCTGTATTATGTGC	57.009	32.000	0.00	0.00	39.81	4.57
2084	2128	4.478206	ACTGTTCTGACGGAATGATGAT	57.522	40.909	0.00	0.00	36.24	2.45
2148	2192	4.759693	CCTGAAGTTGTACATGCCAGTAAA	59.240	41.667	0.00	0.00	0.00	2.01
2149	2193	4.041075	TCCTGAAGTTGTACATGCCAGTAA	59.959	41.667	0.00	0.00	0.00	2.24
2162	2206	2.029838	AATAGGCGCTCCTGAAGTTG	57.970	50.000	7.64	0.00	44.08	3.16
2173	2217	1.787155	CAGTCGTGTCATAATAGGCGC	59.213	52.381	0.00	0.00	0.00	6.53
2223	2281	4.188247	TCGGCATATGCTTGTATCCTAC	57.812	45.455	26.12	5.51	41.70	3.18
2239	2297	3.690139	TCTTTTTGTTGTGTACTTCGGCA	59.310	39.130	0.00	0.00	0.00	5.69
2243	2301	6.190954	ACAGGTCTTTTTGTTGTGTACTTC	57.809	37.500	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.