AutoCloner

Multiple sequence alignment - TraesCS2A01G465700

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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	TraesCS2A01G465700	chr2A	100.000	3545	0	0	1	3545	710366038	710362494	0.000000e+00	6547
1	TraesCS2A01G465700	chr2A	78.431	357	47	10	435	771	61481461	61481115	4.640000e-49	206
2	TraesCS2A01G465700	chr2A	89.552	134	14	0	641	774	61486181	61486314	1.690000e-38	171
3	TraesCS2A01G465700	chr2D	91.244	2147	98	26	929	3024	571884703	571882596	0.000000e+00	2841
4	TraesCS2A01G465700	chr2D	92.208	154	9	1	801	951	571885453	571885300	7.710000e-52	215
5	TraesCS2A01G465700	chr2B	90.005	2041	114	33	800	2790	683760406	683758406	0.000000e+00	2556
6	TraesCS2A01G465700	chr2B	87.736	212	18	5	2817	3024	2736926	2737133	1.270000e-59	241
7	TraesCS2A01G465700	chr2B	88.177	203	22	2	2822	3024	788800574	788800374	1.270000e-59	241
8	TraesCS2A01G465700	chr7B	90.700	828	41	12	1	799	100173796	100172976	0.000000e+00	1070
9	TraesCS2A01G465700	chr6B	90.700	828	41	12	1	799	126724595	126725415	0.000000e+00	1070
10	TraesCS2A01G465700	chr6B	77.599	558	74	28	267	799	62172064	62172595	1.240000e-74	291
11	TraesCS2A01G465700	chr7A	90.591	829	42	13	1	800	696290894	696291715	0.000000e+00	1066
12	TraesCS2A01G465700	chr1A	90.168	834	45	14	1	805	506672965	506672140	0.000000e+00	1051
13	TraesCS2A01G465700	chr1A	95.677	532	15	5	3022	3545	493928074	493927543	0.000000e+00	848
14	TraesCS2A01G465700	chr1A	95.825	527	17	2	3024	3545	551667703	551668229	0.000000e+00	846
15	TraesCS2A01G465700	chr1A	95.292	531	19	3	3021	3545	105280350	105280880	0.000000e+00	837
16	TraesCS2A01G465700	chr1A	95.292	531	20	2	3020	3545	273088924	273088394	0.000000e+00	837
17	TraesCS2A01G465700	chrUn	88.862	826	54	21	1	799	24928641	24927827	0.000000e+00	981
18	TraesCS2A01G465700	chrUn	87.678	211	21	4	2816	3024	437152368	437152575	1.270000e-59	241
19	TraesCS2A01G465700	chrUn	80.866	277	49	4	2260	2534	393374632	393374358	7.710000e-52	215
20	TraesCS2A01G465700	chr5A	96.023	528	15	3	3024	3545	365446071	365446598	0.000000e+00	854
21	TraesCS2A01G465700	chr5A	95.472	530	18	4	3022	3545	631637884	631638413	0.000000e+00	841
22	TraesCS2A01G465700	chr5A	95.158	537	17	4	3018	3545	264074690	264075226	0.000000e+00	839
23	TraesCS2A01G465700	chr5A	95.140	535	19	5	3017	3545	503477853	503477320	0.000000e+00	837
24	TraesCS2A01G465700	chr5A	77.717	552	74	27	272	799	632259309	632258783	3.460000e-75	292
25	TraesCS2A01G465700	chr5A	83.966	237	21	12	1016	1245	505536179	505535953	9.970000e-51	211
26	TraesCS2A01G465700	chr5A	79.403	335	38	16	1405	1710	505535764	505535432	1.290000e-49	207
27	TraesCS2A01G465700	chr3A	95.669	531	19	2	3019	3545	649850661	649850131	0.000000e+00	850
28	TraesCS2A01G465700	chr3A	96.043	278	10	1	5	281	33640932	33640655	5.400000e-123	451
29	TraesCS2A01G465700	chr3A	87.678	211	21	4	2816	3024	737854288	737854495	1.270000e-59	241
30	TraesCS2A01G465700	chr5D	83.137	510	68	9	2053	2554	399959896	399959397	1.940000e-122	449
31	TraesCS2A01G465700	chr5D	84.802	329	13	3	464	761	484295023	484295345	2.680000e-76	296
32	TraesCS2A01G465700	chr5D	87.500	216	20	6	2813	3024	41447789	41448001	3.540000e-60	243
33	TraesCS2A01G465700	chr5D	80.120	332	38	14	1405	1710	399960594	399960265	4.610000e-54	222
34	TraesCS2A01G465700	chr5D	84.362	243	19	13	1009	1246	399961005	399960777	1.660000e-53	220
35	TraesCS2A01G465700	chr5D	87.273	110	14	0	1586	1695	563725264	563725373	3.720000e-25	126
36	TraesCS2A01G465700	chr5B	81.977	516	65	20	2058	2554	479839576	479839070	2.550000e-111	412
37	TraesCS2A01G465700	chr5B	77.917	557	74	27	267	799	648308602	648308071	5.750000e-78	302
38	TraesCS2A01G465700	chr5B	77.907	430	55	29	1009	1416	479840730	479840319	7.650000e-57	231
39	TraesCS2A01G465700	chr5B	81.973	294	32	14	1438	1710	479840249	479839956	2.750000e-56	230
40	TraesCS2A01G465700	chr5B	81.667	240	27	11	1010	1245	479858883	479858657	2.170000e-42	183
41	TraesCS2A01G465700	chr4B	77.957	558	74	27	267	800	642630217	642630749	1.600000e-78	303
42	TraesCS2A01G465700	chr4B	80.866	277	49	4	2260	2534	514747292	514747018	7.710000e-52	215
43	TraesCS2A01G465700	chr4B	79.402	301	47	11	2245	2534	517623360	517623656	7.760000e-47	198
44	TraesCS2A01G465700	chr3B	90.500	200	14	5	2821	3019	445238893	445239088	3.510000e-65	259
45	TraesCS2A01G465700	chr3D	89.950	199	12	6	2821	3019	346091810	346092000	2.110000e-62	250
46	TraesCS2A01G465700	chr4D	87.558	217	14	10	2816	3024	508347988	508348199	4.570000e-59	239
47	TraesCS2A01G465700	chr4D	81.588	277	47	4	2260	2534	418397667	418397393	3.560000e-55	226
48	TraesCS2A01G465700	chr4A	82.079	279	48	2	2260	2537	46424207	46424484	1.640000e-58	237
49	TraesCS2A01G465700	chr1D	88.182	110	9	4	1163	1269	494561804	494561696	1.030000e-25	128
50	TraesCS2A01G465700	chr1B	93.976	83	5	0	1163	1245	687803708	687803626	3.720000e-25	126

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	TraesCS2A01G465700	chr2A	710362494	710366038	3544	True	6547	6547	100.000000	1	3545	1	chr2A.!!$R2	3544
1	TraesCS2A01G465700	chr2D	571882596	571885453	2857	True	1528	2841	91.726000	801	3024	2	chr2D.!!$R1	2223
2	TraesCS2A01G465700	chr2B	683758406	683760406	2000	True	2556	2556	90.005000	800	2790	1	chr2B.!!$R1	1990
3	TraesCS2A01G465700	chr7B	100172976	100173796	820	True	1070	1070	90.700000	1	799	1	chr7B.!!$R1	798
4	TraesCS2A01G465700	chr6B	126724595	126725415	820	False	1070	1070	90.700000	1	799	1	chr6B.!!$F2	798
5	TraesCS2A01G465700	chr6B	62172064	62172595	531	False	291	291	77.599000	267	799	1	chr6B.!!$F1	532
6	TraesCS2A01G465700	chr7A	696290894	696291715	821	False	1066	1066	90.591000	1	800	1	chr7A.!!$F1	799
7	TraesCS2A01G465700	chr1A	506672140	506672965	825	True	1051	1051	90.168000	1	805	1	chr1A.!!$R3	804
8	TraesCS2A01G465700	chr1A	493927543	493928074	531	True	848	848	95.677000	3022	3545	1	chr1A.!!$R2	523
9	TraesCS2A01G465700	chr1A	551667703	551668229	526	False	846	846	95.825000	3024	3545	1	chr1A.!!$F2	521
10	TraesCS2A01G465700	chr1A	105280350	105280880	530	False	837	837	95.292000	3021	3545	1	chr1A.!!$F1	524
11	TraesCS2A01G465700	chr1A	273088394	273088924	530	True	837	837	95.292000	3020	3545	1	chr1A.!!$R1	525
12	TraesCS2A01G465700	chrUn	24927827	24928641	814	True	981	981	88.862000	1	799	1	chrUn.!!$R1	798
13	TraesCS2A01G465700	chr5A	365446071	365446598	527	False	854	854	96.023000	3024	3545	1	chr5A.!!$F2	521
14	TraesCS2A01G465700	chr5A	631637884	631638413	529	False	841	841	95.472000	3022	3545	1	chr5A.!!$F3	523
15	TraesCS2A01G465700	chr5A	264074690	264075226	536	False	839	839	95.158000	3018	3545	1	chr5A.!!$F1	527
16	TraesCS2A01G465700	chr5A	503477320	503477853	533	True	837	837	95.140000	3017	3545	1	chr5A.!!$R1	528
17	TraesCS2A01G465700	chr5A	632258783	632259309	526	True	292	292	77.717000	272	799	1	chr5A.!!$R2	527
18	TraesCS2A01G465700	chr5A	505535432	505536179	747	True	209	211	81.684500	1016	1710	2	chr5A.!!$R3	694
19	TraesCS2A01G465700	chr3A	649850131	649850661	530	True	850	850	95.669000	3019	3545	1	chr3A.!!$R2	526
20	TraesCS2A01G465700	chr5D	399959397	399961005	1608	True	297	449	82.539667	1009	2554	3	chr5D.!!$R1	1545
21	TraesCS2A01G465700	chr5B	648308071	648308602	531	True	302	302	77.917000	267	799	1	chr5B.!!$R2	532
22	TraesCS2A01G465700	chr5B	479839070	479840730	1660	True	291	412	80.619000	1009	2554	3	chr5B.!!$R3	1545
23	TraesCS2A01G465700	chr4B	642630217	642630749	532	False	303	303	77.957000	267	800	1	chr4B.!!$F2	533

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
628	664	0.040603	GGAGCCGGAATCGTACGTAG	60.041	60.0	16.05	3.48	33.95	3.51	F
631	667	0.040603	GCCGGAATCGTACGTAGGAG	60.041	60.0	21.16	9.88	33.95	3.69	F
1292	2001	0.040958	GCTGTTCTTGCTTGTCCACG	60.041	55.0	0.00	0.00	0.00	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1717	2547	0.809241	CCTTGGTCGAGATGCTGAGC	60.809	60.0	0.00	0.00	4.26	R
2197	3124	1.218875	AAAGTGCGCGTGTGATCGAA	61.219	50.0	8.43	0.00	3.71	R
2819	3795	0.184933	TGGGTGCAGCCACTACTTTT	59.815	50.0	33.13	41.75	2.27	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
114	117	8.379902	GCAATCCCAAAAATTTGATACTTTACG	58.620	33.333	7.44	0.00	40.55	3.18
135	138	4.819630	ACGACAGTTTTGCCTTTGAATAGA	59.180	37.500	0.00	0.00	0.00	1.98
181	184	6.014669	TGTTTGCAGGGAAAAACATATAGCTT	60.015	34.615	0.00	0.00	40.41	3.74
275	278	6.372937	CCTGGTAGAAATCTTTGTCTTCCTTC	59.627	42.308	0.00	0.00	33.65	3.46
281	284	1.691976	TCTTTGTCTTCCTTCGAGGCA	59.308	47.619	0.00	0.00	34.61	4.75
283	286	2.859165	TTGTCTTCCTTCGAGGCAAT	57.141	45.000	0.00	0.00	34.09	3.56
397	401	0.757561	TCCGGCCCGAACTGATCATA	60.758	55.000	3.71	0.00	0.00	2.15
454	459	2.030007	TCGAGATGTTTACCGTTCCGTT	60.030	45.455	0.00	0.00	0.00	4.44
500	505	0.252696	ACTGGCCACTAGTCCCATCA	60.253	55.000	0.00	0.00	0.00	3.07
540	549	2.910199	CTCGGCCATGAGAAATTCAGA	58.090	47.619	2.24	0.00	39.68	3.27
543	552	3.628942	TCGGCCATGAGAAATTCAGAATG	59.371	43.478	2.24	0.00	39.68	2.67
551	560	5.266788	TGAGAAATTCAGAATGGAATGGCT	58.733	37.500	0.00	0.00	37.55	4.75
628	664	0.040603	GGAGCCGGAATCGTACGTAG	60.041	60.000	16.05	3.48	33.95	3.51
629	665	0.040603	GAGCCGGAATCGTACGTAGG	60.041	60.000	16.05	8.97	33.95	3.18
630	666	0.464373	AGCCGGAATCGTACGTAGGA	60.464	55.000	19.26	19.26	33.95	2.94
631	667	0.040603	GCCGGAATCGTACGTAGGAG	60.041	60.000	21.16	9.88	33.95	3.69
632	668	1.303309	CCGGAATCGTACGTAGGAGT	58.697	55.000	21.16	19.21	33.95	3.85
633	669	2.483876	CCGGAATCGTACGTAGGAGTA	58.516	52.381	21.16	1.23	33.95	2.59
684	722	2.342279	CCGAGCCGAGAACCAACA	59.658	61.111	0.00	0.00	0.00	3.33
722	760	1.359117	GAATCGTCGGATGGCGAGA	59.641	57.895	0.00	0.00	40.56	4.04
779	817	2.534903	GGCGAGATTTACAGCCCGC	61.535	63.158	0.00	0.00	43.54	6.13
905	946	4.708177	AGCTCAGTACAAGTGTCATTGTT	58.292	39.130	0.00	0.00	40.47	2.83
913	954	5.741388	ACAAGTGTCATTGTTCTCTCAAC	57.259	39.130	0.00	0.00	40.47	3.18
918	959	8.344831	CAAGTGTCATTGTTCTCTCAACAAATA	58.655	33.333	4.13	0.00	42.57	1.40
926	967	9.696917	ATTGTTCTCTCAACAAATAAAATGGTC	57.303	29.630	4.13	0.00	42.57	4.02
933	974	9.295825	TCTCAACAAATAAAATGGTCTGTGTAT	57.704	29.630	0.00	0.00	0.00	2.29
1053	1742	3.145286	CTGTCTCTCACTCACTCACTCA	58.855	50.000	0.00	0.00	0.00	3.41
1165	1873	4.353437	ACGTCGCCACCGTCTTCC	62.353	66.667	0.00	0.00	31.97	3.46
1166	1874	4.052229	CGTCGCCACCGTCTTCCT	62.052	66.667	0.00	0.00	35.54	3.36
1167	1875	2.432628	GTCGCCACCGTCTTCCTG	60.433	66.667	0.00	0.00	35.54	3.86
1168	1876	3.691342	TCGCCACCGTCTTCCTGG	61.691	66.667	0.00	0.00	35.54	4.45
1169	1877	3.691342	CGCCACCGTCTTCCTGGA	61.691	66.667	0.00	0.00	0.00	3.86
1170	1878	2.266055	GCCACCGTCTTCCTGGAG	59.734	66.667	0.00	0.00	0.00	3.86
1171	1879	2.283529	GCCACCGTCTTCCTGGAGA	61.284	63.158	0.00	0.00	0.00	3.71
1172	1880	1.617947	GCCACCGTCTTCCTGGAGAT	61.618	60.000	0.00	0.00	0.00	2.75
1173	1881	0.176680	CCACCGTCTTCCTGGAGATG	59.823	60.000	0.00	2.80	33.40	2.90
1174	1882	1.186200	CACCGTCTTCCTGGAGATGA	58.814	55.000	13.57	5.00	35.17	2.92
1289	1998	1.597742	TGAGCTGTTCTTGCTTGTCC	58.402	50.000	0.00	0.00	41.30	4.02
1292	2001	0.040958	GCTGTTCTTGCTTGTCCACG	60.041	55.000	0.00	0.00	0.00	4.94
1352	2086	4.572795	GCCTCTAGAACAAATCTTGGCTAC	59.427	45.833	6.61	0.00	41.03	3.58
1533	2341	3.118775	TCAAGGTACTGTCCAATCCATCG	60.119	47.826	0.00	0.00	40.86	3.84
1535	2343	3.638860	AGGTACTGTCCAATCCATCGTA	58.361	45.455	0.00	0.00	37.18	3.43
1542	2350	6.884832	ACTGTCCAATCCATCGTAGAAATTA	58.115	36.000	0.00	0.00	43.58	1.40
1568	2383	4.886489	TGATCCATCGATTTTAACATGGCA	59.114	37.500	0.00	0.00	36.49	4.92
1569	2384	5.359292	TGATCCATCGATTTTAACATGGCAA	59.641	36.000	0.00	0.00	36.49	4.52
1704	2534	1.207791	CCTGGCACCTCCAAGTAGAT	58.792	55.000	0.00	0.00	46.01	1.98
1717	2547	0.743688	AGTAGATGCTCTGCCTCACG	59.256	55.000	0.00	0.00	28.67	4.35
1809	2645	0.464013	GCTGTGAGATGCTGGCTGAT	60.464	55.000	0.00	0.00	0.00	2.90
2034	2894	1.283793	CAGAGCTGGCAAAACACCG	59.716	57.895	0.00	0.00	0.00	4.94
2035	2895	1.898574	AGAGCTGGCAAAACACCGG	60.899	57.895	0.00	0.00	36.57	5.28
2104	3021	2.927580	ATCAACACCGTCGGCGTCT	61.928	57.895	12.28	0.00	36.15	4.18
2142	3068	0.171231	TCGTCGTCATGCTCAAGGAG	59.829	55.000	0.00	0.00	0.00	3.69
2196	3123	1.133407	GTGAGAGCGTCCCTTACTCTG	59.867	57.143	0.00	0.00	40.80	3.35
2197	3124	1.271982	TGAGAGCGTCCCTTACTCTGT	60.272	52.381	0.00	0.00	40.80	3.41
2231	3162	3.603857	CGCACTTTCGTCCTTGTAAGTTG	60.604	47.826	0.00	0.00	0.00	3.16
2233	3164	4.508861	GCACTTTCGTCCTTGTAAGTTGTA	59.491	41.667	0.00	0.00	0.00	2.41
2359	3304	0.391597	GTGGACGGTGAACCTGAAGA	59.608	55.000	0.00	0.00	0.00	2.87
2377	3322	0.110823	GAACGTCCACAATGTGCGTC	60.111	55.000	16.73	8.89	32.90	5.19
2526	3474	2.801631	GGAGGTGCGCAGGCTAGAT	61.802	63.158	12.22	0.00	40.82	1.98
2566	3514	2.264480	CCTCCGTCCGTTGCATCA	59.736	61.111	0.00	0.00	0.00	3.07
2587	3535	1.795286	GCATATAGCCGTCTCAAGCAC	59.205	52.381	0.00	0.00	37.23	4.40
2603	3551	4.047822	CAAGCACGGCTCTTATCTTAGAG	58.952	47.826	0.00	0.00	43.66	2.43
2612	3560	4.084641	GCTCTTATCTTAGAGTGCAATGCG	60.085	45.833	0.00	0.00	42.93	4.73
2635	3583	3.561143	TGCATTGTGGTACCCCAATATC	58.439	45.455	20.47	15.52	44.15	1.63
2668	3638	5.734855	TTCGCTTGGATATGCTAGTTTTC	57.265	39.130	7.44	0.00	0.00	2.29
2784	3760	9.463902	AGAATCTGAAAATGTGATCTCAATCTT	57.536	29.630	0.90	0.00	32.75	2.40
2803	3779	3.068732	TCTTTACATCTCGATCAGGCCTG	59.931	47.826	27.87	27.87	0.00	4.85
2812	3788	1.743996	GATCAGGCCTGTGTCTTTCC	58.256	55.000	31.58	9.62	0.00	3.13
2816	3792	1.610522	CAGGCCTGTGTCTTTCCTTTG	59.389	52.381	25.53	0.00	0.00	2.77
2819	3795	1.478654	GCCTGTGTCTTTCCTTTGGGA	60.479	52.381	0.00	0.00	40.36	4.37
2831	3807	2.445525	TCCTTTGGGAAAAGTAGTGGCT	59.554	45.455	0.00	0.00	38.93	4.75
2832	3808	2.558359	CCTTTGGGAAAAGTAGTGGCTG	59.442	50.000	0.00	0.00	33.58	4.85
2833	3809	1.616159	TTGGGAAAAGTAGTGGCTGC	58.384	50.000	0.00	0.00	0.00	5.25
2834	3810	0.476338	TGGGAAAAGTAGTGGCTGCA	59.524	50.000	0.50	0.00	0.00	4.41
2835	3811	0.881796	GGGAAAAGTAGTGGCTGCAC	59.118	55.000	0.50	0.00	0.00	4.57
2836	3812	0.881796	GGAAAAGTAGTGGCTGCACC	59.118	55.000	0.50	0.00	39.84	5.01
2837	3813	0.881796	GAAAAGTAGTGGCTGCACCC	59.118	55.000	0.50	0.00	37.83	4.61
2838	3814	0.184933	AAAAGTAGTGGCTGCACCCA	59.815	50.000	0.50	0.00	37.83	4.51
2844	3820	4.641645	TGGCTGCACCCACCTTCG	62.642	66.667	0.50	0.00	37.83	3.79
2883	3859	7.429920	CGGTGAACAGTAAATTCGAAAAAGAAA	59.570	33.333	0.00	0.00	33.43	2.52
3150	4138	1.889829	CACCGAAATTGGCCCACTTTA	59.110	47.619	0.00	0.00	0.00	1.85
3176	4164	2.685897	CCAATTTCGGCGAATAAAGGGA	59.314	45.455	24.33	6.79	0.00	4.20
3391	4379	0.400525	CCCCCTTGAGCCTCCATAGA	60.401	60.000	0.00	0.00	0.00	1.98
3498	4486	3.181469	GCCGGTAGATGGTGATCAACTTA	60.181	47.826	12.94	0.00	30.80	2.24
3504	4492	5.957771	AGATGGTGATCAACTTAGGCTAA	57.042	39.130	12.94	6.80	0.00	3.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	117	7.816640	TGTATCTATTCAAAGGCAAAACTGTC	58.183	34.615	0.00	0.00	0.00	3.51
157	160	5.965922	AGCTATATGTTTTTCCCTGCAAAC	58.034	37.500	0.00	0.00	34.09	2.93
181	184	4.219115	TCCCTGTTGCAAAGGTTTTCATA	58.781	39.130	19.68	0.00	32.45	2.15
275	278	1.667724	GAATCTGACACCATTGCCTCG	59.332	52.381	0.00	0.00	0.00	4.63
281	284	0.327924	TGGCGGAATCTGACACCATT	59.672	50.000	0.00	0.00	0.00	3.16
283	286	0.392863	CATGGCGGAATCTGACACCA	60.393	55.000	0.00	0.00	0.00	4.17
397	401	1.480312	CGTCCTCTCCATCTCCATCCT	60.480	57.143	0.00	0.00	0.00	3.24
500	505	1.402456	GCGACCAGAACACATCTACGT	60.402	52.381	0.00	0.00	36.32	3.57
540	549	0.337428	AGGGAAGCAGCCATTCCATT	59.663	50.000	13.94	1.08	46.77	3.16
543	552	1.755783	CCAGGGAAGCAGCCATTCC	60.756	63.158	5.05	5.05	44.65	3.01
551	560	2.044650	GATGCAGCCAGGGAAGCA	60.045	61.111	7.42	7.42	41.73	3.91
628	664	3.153919	TCCAAAACTTGCCATGTACTCC	58.846	45.455	0.00	0.00	0.00	3.85
629	665	3.366374	GCTCCAAAACTTGCCATGTACTC	60.366	47.826	0.00	0.00	0.00	2.59
630	666	2.558359	GCTCCAAAACTTGCCATGTACT	59.442	45.455	0.00	0.00	0.00	2.73
631	667	2.352715	GGCTCCAAAACTTGCCATGTAC	60.353	50.000	0.00	0.00	44.34	2.90
632	668	1.892474	GGCTCCAAAACTTGCCATGTA	59.108	47.619	0.00	0.00	44.34	2.29
633	669	0.681175	GGCTCCAAAACTTGCCATGT	59.319	50.000	0.00	0.00	44.34	3.21
684	722	0.322975	ACTGCTCAGATGCTCGGTTT	59.677	50.000	3.60	0.00	0.00	3.27
722	760	2.852495	GATGACGCCACGTGGTCCAT	62.852	60.000	33.92	29.67	41.37	3.41
763	801	1.752501	CGTGCGGGCTGTAAATCTCG	61.753	60.000	0.00	0.00	0.00	4.04
810	848	6.490040	TCTCTTTCCAGTTCCTATTTTGTTGG	59.510	38.462	0.00	0.00	0.00	3.77
825	863	3.692257	ACACCACATCTCTCTTTCCAG	57.308	47.619	0.00	0.00	0.00	3.86
905	946	7.502226	ACACAGACCATTTTATTTGTTGAGAGA	59.498	33.333	0.00	0.00	0.00	3.10
913	954	8.924691	CACCAAATACACAGACCATTTTATTTG	58.075	33.333	0.00	0.00	36.97	2.32
918	959	4.343526	TGCACCAAATACACAGACCATTTT	59.656	37.500	0.00	0.00	0.00	1.82
926	967	5.571784	ATTCAGATGCACCAAATACACAG	57.428	39.130	0.00	0.00	0.00	3.66
933	974	4.148079	TGGTTGTATTCAGATGCACCAAA	58.852	39.130	0.00	0.00	31.52	3.28
1024	1704	0.902516	AGTGAGAGACAGGGGAGTGC	60.903	60.000	0.00	0.00	0.00	4.40
1157	1865	0.103937	GCTCATCTCCAGGAAGACGG	59.896	60.000	0.00	0.00	0.00	4.79
1158	1866	0.103937	GGCTCATCTCCAGGAAGACG	59.896	60.000	0.00	0.00	0.00	4.18
1159	1867	1.412343	GAGGCTCATCTCCAGGAAGAC	59.588	57.143	10.25	0.00	0.00	3.01
1160	1868	1.786937	GAGGCTCATCTCCAGGAAGA	58.213	55.000	10.25	0.00	0.00	2.87
1161	1869	0.388659	CGAGGCTCATCTCCAGGAAG	59.611	60.000	15.95	0.00	0.00	3.46
1162	1870	1.045350	CCGAGGCTCATCTCCAGGAA	61.045	60.000	15.95	0.00	0.00	3.36
1163	1871	1.456518	CCGAGGCTCATCTCCAGGA	60.457	63.158	15.95	0.00	0.00	3.86
1164	1872	3.136750	CCGAGGCTCATCTCCAGG	58.863	66.667	15.95	1.39	0.00	4.45
1165	1873	2.420890	GCCGAGGCTCATCTCCAG	59.579	66.667	15.95	0.00	38.26	3.86
1166	1874	2.364186	TGCCGAGGCTCATCTCCA	60.364	61.111	15.95	0.56	42.51	3.86
1167	1875	2.107953	GTGCCGAGGCTCATCTCC	59.892	66.667	15.95	0.00	42.51	3.71
1168	1876	2.107953	GGTGCCGAGGCTCATCTC	59.892	66.667	15.95	5.98	42.51	2.75
1169	1877	3.474570	GGGTGCCGAGGCTCATCT	61.475	66.667	15.95	0.00	42.51	2.90
1200	1908	4.875713	GTGGATGCGGCGGGGAAT	62.876	66.667	9.78	0.00	0.00	3.01
1352	2086	4.488126	TTTGATTTGCAACCGAGAGAAG	57.512	40.909	0.00	0.00	35.91	2.85
1436	2229	1.765904	TCACTCTGCCTGGTACAAACA	59.234	47.619	0.00	0.00	38.70	2.83
1533	2341	7.897575	AATCGATGGATCAGCTAATTTCTAC	57.102	36.000	0.00	0.00	30.81	2.59
1535	2343	7.814264	AAAATCGATGGATCAGCTAATTTCT	57.186	32.000	0.00	0.00	30.81	2.52
1542	2350	5.240183	CCATGTTAAAATCGATGGATCAGCT	59.760	40.000	0.00	0.00	38.10	4.24
1568	2383	3.119245	GCAGCATTCAACATGGATCAGTT	60.119	43.478	0.00	0.00	0.00	3.16
1569	2384	2.426024	GCAGCATTCAACATGGATCAGT	59.574	45.455	0.00	0.00	0.00	3.41
1717	2547	0.809241	CCTTGGTCGAGATGCTGAGC	60.809	60.000	0.00	0.00	0.00	4.26
1809	2645	2.507886	TCCAACTTCAACCTTCACCTGA	59.492	45.455	0.00	0.00	0.00	3.86
1870	2712	3.813166	TCCGCTCCAACTTCAACTTTAAG	59.187	43.478	0.00	0.00	0.00	1.85
1917	2777	3.435186	GCCCCGTTGCTGCTTCTC	61.435	66.667	0.00	0.00	0.00	2.87
2034	2894	2.038837	GTTGGCCGCCTTAGTGACC	61.039	63.158	11.61	0.00	0.00	4.02
2035	2895	1.298859	CTGTTGGCCGCCTTAGTGAC	61.299	60.000	11.61	0.91	0.00	3.67
2196	3123	1.886861	AAGTGCGCGTGTGATCGAAC	61.887	55.000	8.43	0.00	34.57	3.95
2197	3124	1.218875	AAAGTGCGCGTGTGATCGAA	61.219	50.000	8.43	0.00	0.00	3.71
2359	3304	1.827315	CGACGCACATTGTGGACGTT	61.827	55.000	18.93	7.42	33.84	3.99
2566	3514	1.688735	TGCTTGAGACGGCTATATGCT	59.311	47.619	12.27	0.00	42.39	3.79
2569	3517	2.423926	CGTGCTTGAGACGGCTATAT	57.576	50.000	0.00	0.00	33.08	0.86
2570	3518	3.938653	CGTGCTTGAGACGGCTATA	57.061	52.632	0.00	0.00	33.08	1.31
2587	3535	3.717400	TGCACTCTAAGATAAGAGCCG	57.283	47.619	0.86	0.00	45.81	5.52
2626	3574	5.702865	CGAAACTGCATATTGATATTGGGG	58.297	41.667	0.00	0.00	0.00	4.96
2635	3583	3.763097	TCCAAGCGAAACTGCATATTG	57.237	42.857	0.00	0.00	37.31	1.90
2668	3638	9.160496	GCTAATTAGATAATGAGGAGGTTGATG	57.840	37.037	16.85	0.00	0.00	3.07
2705	3679	3.797256	ACACGAAGCTAGCACGATAATTC	59.203	43.478	30.35	17.36	0.00	2.17
2707	3681	3.116300	CACACGAAGCTAGCACGATAAT	58.884	45.455	30.35	13.02	0.00	1.28
2712	3686	0.663269	TGTCACACGAAGCTAGCACG	60.663	55.000	24.92	24.92	0.00	5.34
2784	3760	2.101415	CACAGGCCTGATCGAGATGTAA	59.899	50.000	39.19	0.00	0.00	2.41
2812	3788	2.029918	GCAGCCACTACTTTTCCCAAAG	60.030	50.000	0.00	0.00	44.57	2.77
2816	3792	0.881796	GTGCAGCCACTACTTTTCCC	59.118	55.000	0.00	0.00	38.93	3.97
2819	3795	0.184933	TGGGTGCAGCCACTACTTTT	59.815	50.000	33.13	0.00	41.75	2.27
2899	3877	8.900781	CATACTCACATCCTTCAAATTTCAGAT	58.099	33.333	0.00	0.00	0.00	2.90
2900	3878	8.102676	TCATACTCACATCCTTCAAATTTCAGA	58.897	33.333	0.00	0.00	0.00	3.27
3016	3994	1.952296	GCTGAAGATGCCCTAACATGG	59.048	52.381	0.00	0.00	0.00	3.66
3176	4164	1.279271	GCCTATTCTCGCCCATATGGT	59.721	52.381	20.46	2.54	36.04	3.55
3504	4492	2.119495	CATACTACAGGCAGGGTCCTT	58.881	52.381	0.00	0.00	33.25	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.