AutoCloner

Multiple sequence alignment - TraesCS7D01G420200

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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	TraesCS7D01G420200	chr7D	100.000	2684	0	0	1	2684	539826777	539824094	0.000000e+00	4957.0
1	TraesCS7D01G420200	chr7D	85.124	484	43	14	744	1213	539853164	539852696	4.050000e-128	468.0
2	TraesCS7D01G420200	chr7D	94.819	193	9	1	2181	2373	223859101	223858910	1.560000e-77	300.0
3	TraesCS7D01G420200	chr7D	87.135	171	13	4	1	162	565400987	565400817	4.560000e-43	185.0
4	TraesCS7D01G420200	chr7B	97.122	938	26	1	753	1690	582709792	582708856	0.000000e+00	1581.0
5	TraesCS7D01G420200	chr7B	92.625	339	18	3	875	1213	582739109	582738778	5.200000e-132	481.0
6	TraesCS7D01G420200	chr7B	83.007	306	37	8	1397	1687	582738675	582738370	2.050000e-66	263.0
7	TraesCS7D01G420200	chr7B	100.000	35	0	0	805	839	582739195	582739161	6.200000e-07	65.8
8	TraesCS7D01G420200	chr2D	92.639	557	37	4	1932	2487	599285136	599285689	0.000000e+00	798.0
9	TraesCS7D01G420200	chr2D	95.146	206	9	1	2480	2684	599285729	599285934	9.270000e-85	324.0
10	TraesCS7D01G420200	chr2D	94.301	193	10	1	2181	2373	574898687	574898878	7.270000e-76	294.0
11	TraesCS7D01G420200	chr7A	94.653	505	27	0	1184	1688	621044444	621043940	0.000000e+00	784.0
12	TraesCS7D01G420200	chr7A	89.913	575	47	5	169	738	157420846	157420278	0.000000e+00	730.0
13	TraesCS7D01G420200	chr7A	93.973	448	15	6	743	1190	621046673	621046238	0.000000e+00	667.0
14	TraesCS7D01G420200	chr7A	89.496	476	34	8	743	1213	621084292	621083828	2.980000e-164	588.0
15	TraesCS7D01G420200	chr7A	78.136	558	77	30	1397	1935	621083725	621083194	2.010000e-81	313.0
16	TraesCS7D01G420200	chr7A	85.526	152	19	3	1680	1831	621031157	621031009	3.580000e-34	156.0
17	TraesCS7D01G420200	chr4D	91.019	579	41	6	165	739	108255853	108256424	0.000000e+00	771.0
18	TraesCS7D01G420200	chr4D	84.187	683	45	30	1	653	336129387	336128738	2.960000e-169	604.0
19	TraesCS7D01G420200	chr4D	94.819	193	9	1	2181	2373	318290608	318290799	1.560000e-77	300.0
20	TraesCS7D01G420200	chr4D	92.667	150	10	1	2224	2373	234722159	234722307	5.820000e-52	215.0
21	TraesCS7D01G420200	chr1D	91.019	579	40	6	165	738	65560884	65561455	0.000000e+00	771.0
22	TraesCS7D01G420200	chr1D	93.970	199	10	2	2176	2373	122551473	122551670	1.560000e-77	300.0
23	TraesCS7D01G420200	chr1D	90.446	157	9	2	1	151	375977432	375977588	4.530000e-48	202.0
24	TraesCS7D01G420200	chr1D	96.429	112	4	0	1	112	456128193	456128304	4.560000e-43	185.0
25	TraesCS7D01G420200	chr4B	90.172	580	45	5	163	738	191715830	191715259	0.000000e+00	745.0
26	TraesCS7D01G420200	chr4B	89.573	585	47	6	165	742	404179527	404178950	0.000000e+00	730.0
27	TraesCS7D01G420200	chr4B	87.037	162	19	1	1	162	431585915	431586074	5.900000e-42	182.0
28	TraesCS7D01G420200	chr1B	90.155	579	47	4	165	739	134732966	134732394	0.000000e+00	745.0
29	TraesCS7D01G420200	chr1B	89.895	574	46	5	169	738	561872566	561873131	0.000000e+00	728.0
30	TraesCS7D01G420200	chr1A	89.673	581	49	6	163	738	584565615	584565041	0.000000e+00	730.0
31	TraesCS7D01G420200	chr1A	89.349	169	9	3	1	160	443680863	443681031	1.260000e-48	204.0
32	TraesCS7D01G420200	chr4A	89.619	578	48	6	165	738	626122956	626122387	0.000000e+00	725.0
33	TraesCS7D01G420200	chr6B	79.151	542	64	13	1926	2466	599300994	599301487	1.990000e-86	329.0
34	TraesCS7D01G420200	chr5A	93.689	206	12	1	2480	2684	689164522	689164727	9.330000e-80	307.0
35	TraesCS7D01G420200	chr5A	92.222	180	14	0	1932	2111	689161139	689161318	3.430000e-64	255.0
36	TraesCS7D01G420200	chr2B	87.435	191	22	2	2181	2370	236799450	236799639	4.500000e-53	219.0
37	TraesCS7D01G420200	chr5D	89.474	171	9	2	1	162	225241669	225241499	9.740000e-50	207.0
38	TraesCS7D01G420200	chr6D	88.304	171	11	3	1	162	312774419	312774249	2.110000e-46	196.0
39	TraesCS7D01G420200	chr6D	85.714	112	15	1	2245	2356	400444293	400444403	1.690000e-22	117.0
40	TraesCS7D01G420200	chr3B	87.421	159	14	2	1	153	347877903	347878061	7.640000e-41	178.0

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	TraesCS7D01G420200	chr7D	539824094	539826777	2683	True	4957.000000	4957	100.000000	1	2684	1	chr7D.!!$R2	2683
1	TraesCS7D01G420200	chr7B	582708856	582709792	936	True	1581.000000	1581	97.122000	753	1690	1	chr7B.!!$R1	937
2	TraesCS7D01G420200	chr7B	582738370	582739195	825	True	269.933333	481	91.877333	805	1687	3	chr7B.!!$R2	882
3	TraesCS7D01G420200	chr2D	599285136	599285934	798	False	561.000000	798	93.892500	1932	2684	2	chr2D.!!$F2	752
4	TraesCS7D01G420200	chr7A	157420278	157420846	568	True	730.000000	730	89.913000	169	738	1	chr7A.!!$R1	569
5	TraesCS7D01G420200	chr7A	621043940	621046673	2733	True	725.500000	784	94.313000	743	1688	2	chr7A.!!$R3	945
6	TraesCS7D01G420200	chr7A	621083194	621084292	1098	True	450.500000	588	83.816000	743	1935	2	chr7A.!!$R4	1192
7	TraesCS7D01G420200	chr4D	108255853	108256424	571	False	771.000000	771	91.019000	165	739	1	chr4D.!!$F1	574
8	TraesCS7D01G420200	chr4D	336128738	336129387	649	True	604.000000	604	84.187000	1	653	1	chr4D.!!$R1	652
9	TraesCS7D01G420200	chr1D	65560884	65561455	571	False	771.000000	771	91.019000	165	738	1	chr1D.!!$F1	573
10	TraesCS7D01G420200	chr4B	191715259	191715830	571	True	745.000000	745	90.172000	163	738	1	chr4B.!!$R1	575
11	TraesCS7D01G420200	chr4B	404178950	404179527	577	True	730.000000	730	89.573000	165	742	1	chr4B.!!$R2	577
12	TraesCS7D01G420200	chr1B	134732394	134732966	572	True	745.000000	745	90.155000	165	739	1	chr1B.!!$R1	574
13	TraesCS7D01G420200	chr1B	561872566	561873131	565	False	728.000000	728	89.895000	169	738	1	chr1B.!!$F1	569
14	TraesCS7D01G420200	chr1A	584565041	584565615	574	True	730.000000	730	89.673000	163	738	1	chr1A.!!$R1	575
15	TraesCS7D01G420200	chr4A	626122387	626122956	569	True	725.000000	725	89.619000	165	738	1	chr4A.!!$R1	573
16	TraesCS7D01G420200	chr5A	689161139	689164727	3588	False	281.000000	307	92.955500	1932	2684	2	chr5A.!!$F1	752

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
151	161	0.179153	TCTGCGCATCTCAAGACTCG	60.179	55.0	12.24	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2062	3962	0.535335	TTGCTACGGGTGGATCAGAC	59.465	55.0	0.0	0.0	0.0	3.51	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
51	52	2.280797	TGCGAGTTCTGGGTGCAC	60.281	61.111	8.80	8.80	0.00	4.57
133	143	2.572284	CCGGTGACCTCCTCGTTC	59.428	66.667	0.00	0.00	0.00	3.95
136	146	1.079750	GGTGACCTCCTCGTTCTGC	60.080	63.158	0.00	0.00	0.00	4.26
145	155	0.737367	CCTCGTTCTGCGCATCTCAA	60.737	55.000	12.24	0.00	41.07	3.02
150	160	1.658095	GTTCTGCGCATCTCAAGACTC	59.342	52.381	12.24	0.00	0.00	3.36
151	161	0.179153	TCTGCGCATCTCAAGACTCG	60.179	55.000	12.24	0.00	0.00	4.18
152	162	1.144565	CTGCGCATCTCAAGACTCGG	61.145	60.000	12.24	0.00	0.00	4.63
153	163	2.520904	GCGCATCTCAAGACTCGGC	61.521	63.158	0.30	0.00	0.00	5.54
154	164	1.140589	CGCATCTCAAGACTCGGCT	59.859	57.895	0.00	0.00	0.00	5.52
155	165	0.459237	CGCATCTCAAGACTCGGCTT	60.459	55.000	0.00	0.00	0.00	4.35
156	166	1.005340	GCATCTCAAGACTCGGCTTG	58.995	55.000	6.16	6.16	45.10	4.01
296	326	9.593134	TTGTGCTGTGAACTTGTTAATATTTTT	57.407	25.926	0.00	0.00	0.00	1.94
306	336	5.337578	TGTTAATATTTTTGCCAGGAGCC	57.662	39.130	0.00	0.00	42.71	4.70
329	363	3.313874	CGTGGAGCAGGGAAGGAT	58.686	61.111	0.00	0.00	0.00	3.24
351	386	7.522529	AGGATGATCCCCCTTCTTTTAATCTAT	59.477	37.037	8.08	0.00	37.19	1.98
354	389	7.290061	TGATCCCCCTTCTTTTAATCTATGTG	58.710	38.462	0.00	0.00	0.00	3.21
356	391	4.584743	CCCCCTTCTTTTAATCTATGTGGC	59.415	45.833	0.00	0.00	0.00	5.01
362	397	7.363268	CCTTCTTTTAATCTATGTGGCTTGCTT	60.363	37.037	0.00	0.00	0.00	3.91
374	409	2.102252	TGGCTTGCTTTCATTTCCGTTT	59.898	40.909	0.00	0.00	0.00	3.60
408	443	5.125100	TGATCTCATTTGGTTGCTTGTTC	57.875	39.130	0.00	0.00	0.00	3.18
456	491	2.908688	TCTGCTGTCAGTTGTGCTTA	57.091	45.000	0.93	0.00	41.10	3.09
477	512	0.883153	TGTTGTGCTGATCATGTGGC	59.117	50.000	0.00	0.00	0.00	5.01
498	533	1.818674	GGTAAGGCCACCACATTTGAG	59.181	52.381	5.01	0.00	38.55	3.02
584	619	3.566742	CCTAAGCACAAAAACGGTAACCT	59.433	43.478	0.00	0.00	0.00	3.50
679	717	4.223700	TGCATATGAAGAACCAGACTGACT	59.776	41.667	6.97	0.00	0.00	3.41
680	718	4.569966	GCATATGAAGAACCAGACTGACTG	59.430	45.833	6.97	0.00	45.36	3.51
723	761	0.524862	CGGGTACTGTAGCGAACTGT	59.475	55.000	10.55	9.14	42.33	3.55
739	777	1.520600	CTGTAACCAAACACGCCCCC	61.521	60.000	0.00	0.00	0.00	5.40
910	985	2.090524	CGTACGCCTTGGACGTTCC	61.091	63.158	0.52	0.00	41.93	3.62
991	1070	0.400594	TAGCCTCCGATCCGATCAGA	59.599	55.000	9.07	1.85	0.00	3.27
1194	3073	1.620822	ACTACCCGAACAAGTACCGT	58.379	50.000	0.00	0.00	0.00	4.83
1210	3089	1.414919	ACCGTAAGAAGGACTGCAACA	59.585	47.619	0.00	0.00	43.02	3.33
1350	3229	3.003173	TTCAGCCTGGTCCCTCGG	61.003	66.667	0.00	0.00	0.00	4.63
1400	3279	2.281276	GGCGAAGGTCCGGTTTGT	60.281	61.111	0.00	0.00	0.00	2.83
1431	3310	2.048503	GTGGTGACGTTCCCTCGG	60.049	66.667	7.98	0.00	34.94	4.63
1610	3493	1.985473	AAGGATGACTTGTGCAAGCA	58.015	45.000	11.43	10.58	41.99	3.91
1692	3587	9.807649	AAGTGTCTCGGTATATAAAATTACGTT	57.192	29.630	0.00	0.00	0.00	3.99
1711	3606	3.486841	CGTTTTACGGGGTCATACATACG	59.513	47.826	0.00	0.00	38.08	3.06
1712	3607	4.681744	GTTTTACGGGGTCATACATACGA	58.318	43.478	0.00	0.00	0.00	3.43
1713	3608	4.572985	TTTACGGGGTCATACATACGAG	57.427	45.455	0.00	0.00	0.00	4.18
1714	3609	2.062971	ACGGGGTCATACATACGAGT	57.937	50.000	0.00	0.00	0.00	4.18
1715	3610	3.213206	ACGGGGTCATACATACGAGTA	57.787	47.619	0.00	0.00	0.00	2.59
1716	3611	3.144506	ACGGGGTCATACATACGAGTAG	58.855	50.000	0.00	0.00	0.00	2.57
1728	3623	9.692749	CATACATACGAGTAGTATTCAAACCAT	57.307	33.333	0.00	0.00	43.12	3.55
1736	3631	7.699391	CGAGTAGTATTCAAACCATAGTTTCGA	59.301	37.037	0.00	0.00	44.47	3.71
1777	3672	9.967451	TGATGTTTTTGTCCCTATATAGTTCAA	57.033	29.630	8.92	7.85	0.00	2.69
1782	3677	6.553953	TTGTCCCTATATAGTTCAAGTGCA	57.446	37.500	8.92	0.00	0.00	4.57
1783	3678	5.914033	TGTCCCTATATAGTTCAAGTGCAC	58.086	41.667	9.40	9.40	0.00	4.57
1796	3691	5.418310	TCAAGTGCACTAGTTTAAACTGC	57.582	39.130	27.40	22.82	40.07	4.40
1799	3694	2.546789	GTGCACTAGTTTAAACTGCCGT	59.453	45.455	27.40	18.62	40.07	5.68
1800	3695	2.546368	TGCACTAGTTTAAACTGCCGTG	59.454	45.455	27.40	26.69	40.07	4.94
1801	3696	2.546789	GCACTAGTTTAAACTGCCGTGT	59.453	45.455	27.40	15.67	40.07	4.49
1802	3697	3.363673	GCACTAGTTTAAACTGCCGTGTC	60.364	47.826	27.40	20.18	40.07	3.67
1803	3698	3.054878	ACTAGTTTAAACTGCCGTGTCG	58.945	45.455	27.40	9.93	40.07	4.35
1804	3699	1.944032	AGTTTAAACTGCCGTGTCGT	58.056	45.000	19.94	0.00	37.98	4.34
1805	3700	1.595794	AGTTTAAACTGCCGTGTCGTG	59.404	47.619	19.94	0.00	37.98	4.35
1806	3701	1.593933	GTTTAAACTGCCGTGTCGTGA	59.406	47.619	11.18	0.00	0.00	4.35
1807	3702	1.937278	TTAAACTGCCGTGTCGTGAA	58.063	45.000	0.00	0.00	0.00	3.18
1808	3703	2.157834	TAAACTGCCGTGTCGTGAAT	57.842	45.000	0.00	0.00	0.00	2.57
1809	3704	1.305201	AAACTGCCGTGTCGTGAATT	58.695	45.000	0.00	0.00	0.00	2.17
1810	3705	2.157834	AACTGCCGTGTCGTGAATTA	57.842	45.000	0.00	0.00	0.00	1.40
1811	3706	2.380084	ACTGCCGTGTCGTGAATTAT	57.620	45.000	0.00	0.00	0.00	1.28
1812	3707	2.695359	ACTGCCGTGTCGTGAATTATT	58.305	42.857	0.00	0.00	0.00	1.40
1813	3708	3.071479	ACTGCCGTGTCGTGAATTATTT	58.929	40.909	0.00	0.00	0.00	1.40
1814	3709	4.247258	ACTGCCGTGTCGTGAATTATTTA	58.753	39.130	0.00	0.00	0.00	1.40
1815	3710	4.092383	ACTGCCGTGTCGTGAATTATTTAC	59.908	41.667	0.00	0.00	0.00	2.01
1816	3711	3.995048	TGCCGTGTCGTGAATTATTTACA	59.005	39.130	1.04	0.00	0.00	2.41
1817	3712	4.632251	TGCCGTGTCGTGAATTATTTACAT	59.368	37.500	1.04	0.00	0.00	2.29
1818	3713	5.811100	TGCCGTGTCGTGAATTATTTACATA	59.189	36.000	1.04	0.00	0.00	2.29
1823	3718	8.588789	CGTGTCGTGAATTATTTACATACTGAA	58.411	33.333	1.04	0.00	0.00	3.02
1857	3757	9.366216	TGTATTGATATATACGCCATGTTCTTC	57.634	33.333	0.00	0.00	34.42	2.87
1858	3758	9.587772	GTATTGATATATACGCCATGTTCTTCT	57.412	33.333	0.00	0.00	0.00	2.85
1875	3775	8.362464	TGTTCTTCTCTGGCTAACTAATCTAA	57.638	34.615	0.00	0.00	0.00	2.10
1876	3776	8.251721	TGTTCTTCTCTGGCTAACTAATCTAAC	58.748	37.037	0.00	0.00	0.00	2.34
1878	3778	8.001881	TCTTCTCTGGCTAACTAATCTAACTG	57.998	38.462	0.00	0.00	0.00	3.16
1884	3784	8.090831	TCTGGCTAACTAATCTAACTGCATATG	58.909	37.037	0.00	0.00	0.00	1.78
1887	3787	6.183360	GCTAACTAATCTAACTGCATATGCCG	60.183	42.308	24.54	20.45	41.18	5.69
1898	3798	2.187707	GCATATGCCGTTTCTTGCAAG	58.812	47.619	20.81	20.81	41.50	4.01
1899	3799	2.187707	CATATGCCGTTTCTTGCAAGC	58.812	47.619	21.99	10.33	41.50	4.01
1917	3817	8.909708	TTGCAAGCAATGTTATAGATTTGTAC	57.090	30.769	2.89	0.00	0.00	2.90
1918	3818	8.049655	TGCAAGCAATGTTATAGATTTGTACA	57.950	30.769	0.00	0.00	0.00	2.90
1987	3887	1.928653	CGTTTTCAGTCCGAACGCA	59.071	52.632	0.00	0.00	39.49	5.24
1989	3889	1.070175	CGTTTTCAGTCCGAACGCATT	60.070	47.619	0.00	0.00	39.49	3.56
1992	3892	4.148891	GTTTTCAGTCCGAACGCATTTAG	58.851	43.478	0.00	0.00	31.73	1.85
1993	3893	1.355971	TCAGTCCGAACGCATTTAGC	58.644	50.000	0.00	0.00	40.87	3.09
2080	3980	1.327690	GGTCTGATCCACCCGTAGCA	61.328	60.000	0.14	0.00	0.00	3.49
2104	4004	3.243234	ACGCCTCACTTTCTCTATCATCG	60.243	47.826	0.00	0.00	0.00	3.84
2120	6475	1.481056	ATCGGCCTTATCCCTTCCCG	61.481	60.000	0.00	0.00	37.21	5.14
2124	6479	1.342672	GCCTTATCCCTTCCCGTCCA	61.343	60.000	0.00	0.00	0.00	4.02
2128	6483	0.252789	TATCCCTTCCCGTCCAACCA	60.253	55.000	0.00	0.00	0.00	3.67
2131	6486	1.196104	CCCTTCCCGTCCAACCACTA	61.196	60.000	0.00	0.00	0.00	2.74
2142	6497	1.139853	CCAACCACTATGCTCTCTCCC	59.860	57.143	0.00	0.00	0.00	4.30
2252	6607	2.025727	GCCGCATTGCAGATCAGC	59.974	61.111	9.69	2.62	0.00	4.26
2332	7033	1.073397	ATCCCTCCACCATCTCCCC	60.073	63.158	0.00	0.00	0.00	4.81
2336	7037	4.414956	TCCACCATCTCCCCGCCT	62.415	66.667	0.00	0.00	0.00	5.52
2373	7074	3.864686	GCACGCATCGACGGCAAT	61.865	61.111	11.02	0.00	37.37	3.56
2565	7313	2.131294	GATCCAGCTCCGTATCGCGT	62.131	60.000	5.77	0.00	39.32	6.01
2606	7354	3.491619	CCTCGTCATAGACATTGGTGAGG	60.492	52.174	0.00	0.98	33.05	3.86
2618	7366	0.250295	TGGTGAGGTTTTCTGCTCGG	60.250	55.000	0.00	0.00	0.00	4.63
2623	7371	0.472471	AGGTTTTCTGCTCGGTTCCA	59.528	50.000	0.00	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	1.153329	ACCACTTGTTCGCCGACAA	60.153	52.632	0.00	0.00	37.87	3.18
38	39	2.426023	GGACGTGCACCCAGAACT	59.574	61.111	12.15	0.00	0.00	3.01
51	52	1.215647	CCCCTCGAAGTTCTGGACG	59.784	63.158	11.81	0.00	0.00	4.79
133	143	1.144565	CCGAGTCTTGAGATGCGCAG	61.145	60.000	18.32	0.00	0.00	5.18
136	146	0.459237	AAGCCGAGTCTTGAGATGCG	60.459	55.000	0.00	0.00	0.00	4.73
145	155	1.122019	ACCACCTTCAAGCCGAGTCT	61.122	55.000	0.00	0.00	0.00	3.24
150	160	1.068333	CAATGAACCACCTTCAAGCCG	60.068	52.381	0.00	0.00	42.37	5.52
151	161	1.337167	GCAATGAACCACCTTCAAGCC	60.337	52.381	0.00	0.00	42.37	4.35
152	162	1.340889	TGCAATGAACCACCTTCAAGC	59.659	47.619	0.00	0.00	42.37	4.01
153	163	2.608752	GCTGCAATGAACCACCTTCAAG	60.609	50.000	0.00	0.00	42.37	3.02
154	164	1.340889	GCTGCAATGAACCACCTTCAA	59.659	47.619	0.00	0.00	42.37	2.69
155	165	0.961019	GCTGCAATGAACCACCTTCA	59.039	50.000	0.00	0.00	43.28	3.02
156	166	0.961019	TGCTGCAATGAACCACCTTC	59.039	50.000	0.00	0.00	0.00	3.46
157	167	1.342174	CTTGCTGCAATGAACCACCTT	59.658	47.619	16.38	0.00	0.00	3.50
158	168	0.963962	CTTGCTGCAATGAACCACCT	59.036	50.000	16.38	0.00	0.00	4.00
159	169	0.668401	GCTTGCTGCAATGAACCACC	60.668	55.000	16.38	0.00	42.31	4.61
160	170	2.818350	GCTTGCTGCAATGAACCAC	58.182	52.632	16.38	0.00	42.31	4.16
188	214	4.348656	CATTGCATGCTCAATGTCACTAC	58.651	43.478	20.33	0.00	44.94	2.73
190	216	3.503827	CATTGCATGCTCAATGTCACT	57.496	42.857	20.33	0.00	44.94	3.41
329	363	7.290061	CACATAGATTAAAAGAAGGGGGATCA	58.710	38.462	0.00	0.00	0.00	2.92
339	374	7.176515	TGAAAGCAAGCCACATAGATTAAAAGA	59.823	33.333	0.00	0.00	0.00	2.52
342	377	6.832520	TGAAAGCAAGCCACATAGATTAAA	57.167	33.333	0.00	0.00	0.00	1.52
351	386	1.000385	CGGAAATGAAAGCAAGCCACA	60.000	47.619	0.00	0.00	0.00	4.17
354	389	2.438868	AACGGAAATGAAAGCAAGCC	57.561	45.000	0.00	0.00	0.00	4.35
356	391	4.084900	GCAAGAAACGGAAATGAAAGCAAG	60.085	41.667	0.00	0.00	0.00	4.01
362	397	5.004922	ACAAAGCAAGAAACGGAAATGAA	57.995	34.783	0.00	0.00	0.00	2.57
374	409	6.183360	ACCAAATGAGATCAAACAAAGCAAGA	60.183	34.615	0.00	0.00	0.00	3.02
408	443	1.862815	GCAAGCACTGACAGCAAACAG	60.863	52.381	1.25	0.00	39.65	3.16
456	491	2.156917	CCACATGATCAGCACAACAGT	58.843	47.619	0.00	0.00	0.00	3.55
477	512	0.525761	CAAATGTGGTGGCCTTACCG	59.474	55.000	3.32	0.00	43.87	4.02
498	533	3.120199	CGTTTGTGTTCTGATCATCCCAC	60.120	47.826	0.00	3.94	0.00	4.61
507	542	4.491234	ACAAACAACGTTTGTGTTCTGA	57.509	36.364	21.00	0.00	44.59	3.27
539	574	3.057736	GTGTGAGCAGATGCAAACTTCAT	60.058	43.478	7.68	0.00	45.16	2.57
584	619	0.326927	GCACTTACCCCCTGCTGTTA	59.673	55.000	0.00	0.00	0.00	2.41
679	717	2.506644	TGCATGTCCATCTCCATCTTCA	59.493	45.455	0.00	0.00	0.00	3.02
680	718	3.204306	TGCATGTCCATCTCCATCTTC	57.796	47.619	0.00	0.00	0.00	2.87
681	719	3.657398	TTGCATGTCCATCTCCATCTT	57.343	42.857	0.00	0.00	0.00	2.40
682	720	3.487372	CATTGCATGTCCATCTCCATCT	58.513	45.455	0.00	0.00	0.00	2.90
683	721	2.030185	GCATTGCATGTCCATCTCCATC	60.030	50.000	3.15	0.00	0.00	3.51
684	722	1.961394	GCATTGCATGTCCATCTCCAT	59.039	47.619	3.15	0.00	0.00	3.41
723	761	2.281622	CGGGGGCGTGTTTGGTTA	60.282	61.111	0.00	0.00	0.00	2.85
739	777	6.363626	CGTCCAGAATAAGATATCCTTTGTCG	59.636	42.308	0.00	0.00	36.34	4.35
910	985	0.320334	GGCGGTGGGTTTGGATTTTG	60.320	55.000	0.00	0.00	0.00	2.44
1068	1147	1.536073	CCTCCACCTTGAGCTCGTGA	61.536	60.000	18.44	3.39	0.00	4.35
1194	3073	1.270625	CCGGTGTTGCAGTCCTTCTTA	60.271	52.381	0.00	0.00	0.00	2.10
1210	3089	1.128188	GGGGCTGATATTCTCCCGGT	61.128	60.000	0.00	0.00	39.66	5.28
1331	3210	2.286523	CGAGGGACCAGGCTGAACT	61.287	63.158	17.94	7.98	0.00	3.01
1400	3279	2.897846	CCACGTGGCGTTCACCAA	60.898	61.111	24.02	0.00	42.70	3.67
1431	3310	0.593128	ACTCAACGCCATTGTGCTTC	59.407	50.000	0.00	0.00	39.54	3.86
1610	3493	1.301244	GCGCCCGTCAGATGATGAT	60.301	57.895	0.00	0.00	40.92	2.45
1692	3587	3.953612	ACTCGTATGTATGACCCCGTAAA	59.046	43.478	0.00	0.00	0.00	2.01
1694	3589	3.213206	ACTCGTATGTATGACCCCGTA	57.787	47.619	0.00	0.00	0.00	4.02
1695	3590	2.062971	ACTCGTATGTATGACCCCGT	57.937	50.000	0.00	0.00	0.00	5.28
1696	3591	3.144506	ACTACTCGTATGTATGACCCCG	58.855	50.000	0.00	0.00	0.00	5.73
1701	3596	8.905850	TGGTTTGAATACTACTCGTATGTATGA	58.094	33.333	0.00	0.00	38.78	2.15
1702	3597	9.692749	ATGGTTTGAATACTACTCGTATGTATG	57.307	33.333	0.00	0.00	38.78	2.39
1705	3600	8.910944	ACTATGGTTTGAATACTACTCGTATGT	58.089	33.333	0.00	0.00	38.78	2.29
1706	3601	9.745880	AACTATGGTTTGAATACTACTCGTATG	57.254	33.333	0.00	0.00	34.04	2.39
1708	3603	9.793252	GAAACTATGGTTTGAATACTACTCGTA	57.207	33.333	12.36	0.00	44.58	3.43
1709	3604	7.487189	CGAAACTATGGTTTGAATACTACTCGT	59.513	37.037	12.36	0.00	44.58	4.18
1710	3605	7.699391	TCGAAACTATGGTTTGAATACTACTCG	59.301	37.037	12.36	5.57	44.58	4.18
1711	3606	8.922058	TCGAAACTATGGTTTGAATACTACTC	57.078	34.615	12.36	0.00	44.58	2.59
1712	3607	9.886132	AATCGAAACTATGGTTTGAATACTACT	57.114	29.630	12.36	0.00	44.58	2.57
1739	3634	9.482627	GGGACAAAAACATCATTACAATTGTAA	57.517	29.630	28.30	28.30	43.71	2.41
1742	3637	9.874205	ATAGGGACAAAAACATCATTACAATTG	57.126	29.630	3.24	3.24	0.00	2.32
1751	3646	9.967451	TTGAACTATATAGGGACAAAAACATCA	57.033	29.630	14.25	0.00	0.00	3.07
1755	3650	8.182227	GCACTTGAACTATATAGGGACAAAAAC	58.818	37.037	14.25	5.70	0.00	2.43
1758	3653	6.821665	GTGCACTTGAACTATATAGGGACAAA	59.178	38.462	10.32	1.21	0.00	2.83
1759	3654	6.156256	AGTGCACTTGAACTATATAGGGACAA	59.844	38.462	15.25	13.87	30.45	3.18
1760	3655	5.661312	AGTGCACTTGAACTATATAGGGACA	59.339	40.000	15.25	7.92	30.45	4.02
1777	3672	2.806244	CGGCAGTTTAAACTAGTGCACT	59.194	45.455	25.12	25.12	42.42	4.40
1782	3677	3.054878	CGACACGGCAGTTTAAACTAGT	58.945	45.455	20.15	16.51	37.08	2.57
1783	3678	3.054878	ACGACACGGCAGTTTAAACTAG	58.945	45.455	20.15	15.93	37.08	2.57
1790	3685	1.305201	AATTCACGACACGGCAGTTT	58.695	45.000	0.00	0.00	0.00	2.66
1793	3688	3.740044	AAATAATTCACGACACGGCAG	57.260	42.857	0.00	0.00	0.00	4.85
1796	3691	7.221259	TCAGTATGTAAATAATTCACGACACGG	59.779	37.037	0.00	0.00	37.40	4.94
1840	3735	4.887748	CCAGAGAAGAACATGGCGTATAT	58.112	43.478	0.00	0.00	0.00	0.86
1842	3737	3.185246	CCAGAGAAGAACATGGCGTAT	57.815	47.619	0.00	0.00	0.00	3.06
1850	3750	6.859112	AGATTAGTTAGCCAGAGAAGAACA	57.141	37.500	0.00	0.00	0.00	3.18
1857	3757	5.907207	TGCAGTTAGATTAGTTAGCCAGAG	58.093	41.667	0.00	0.00	0.00	3.35
1858	3758	5.932619	TGCAGTTAGATTAGTTAGCCAGA	57.067	39.130	0.00	0.00	0.00	3.86
1863	3763	6.868864	ACGGCATATGCAGTTAGATTAGTTAG	59.131	38.462	28.07	3.71	46.84	2.34
1864	3764	6.755206	ACGGCATATGCAGTTAGATTAGTTA	58.245	36.000	28.07	0.00	46.84	2.24
1876	3776	1.132834	TGCAAGAAACGGCATATGCAG	59.867	47.619	28.07	25.92	44.36	4.41
1878	3778	2.187707	CTTGCAAGAAACGGCATATGC	58.812	47.619	22.31	19.79	40.17	3.14
1884	3784	0.785979	CATTGCTTGCAAGAAACGGC	59.214	50.000	30.39	14.66	0.00	5.68
1887	3787	8.693542	AATCTATAACATTGCTTGCAAGAAAC	57.306	30.769	30.39	12.88	0.00	2.78
1987	3887	8.106348	CGTAAAGAAAATCTAACGACGCTAAAT	58.894	33.333	0.00	0.00	37.87	1.40
1989	3889	6.801377	TCGTAAAGAAAATCTAACGACGCTAA	59.199	34.615	11.53	0.00	38.92	3.09
1992	3892	5.425941	TCGTAAAGAAAATCTAACGACGC	57.574	39.130	11.53	0.00	38.92	5.19
1993	3893	7.882644	AGATTCGTAAAGAAAATCTAACGACG	58.117	34.615	13.92	0.00	41.53	5.12
2062	3962	0.535335	TTGCTACGGGTGGATCAGAC	59.465	55.000	0.00	0.00	0.00	3.51
2080	3980	4.537135	TGATAGAGAAAGTGAGGCGTTT	57.463	40.909	0.00	0.00	0.00	3.60
2104	4004	1.450642	GACGGGAAGGGATAAGGCC	59.549	63.158	0.00	0.00	0.00	5.19
2120	6475	2.159028	GGAGAGAGCATAGTGGTTGGAC	60.159	54.545	0.00	0.00	0.00	4.02
2124	6479	2.114616	CAGGGAGAGAGCATAGTGGTT	58.885	52.381	0.00	0.00	0.00	3.67
2128	6483	1.743321	GCGCAGGGAGAGAGCATAGT	61.743	60.000	0.30	0.00	0.00	2.12
2131	6486	2.763292	AGCGCAGGGAGAGAGCAT	60.763	61.111	11.47	0.00	0.00	3.79
2314	7015	1.073397	GGGGAGATGGTGGAGGGAT	60.073	63.158	0.00	0.00	0.00	3.85
2332	7033	3.414700	GGCGTTGACTGTCAGGCG	61.415	66.667	23.12	23.12	31.22	5.52
2336	7037	2.338620	CGGAGGCGTTGACTGTCA	59.661	61.111	6.36	6.36	0.00	3.58
2358	7059	3.254654	CGATTGCCGTCGATGCGT	61.255	61.111	0.00	0.00	44.06	5.24
2405	7106	2.352805	CTCCTCCACACAAGGGCC	59.647	66.667	0.00	0.00	34.46	5.80
2606	7354	1.531578	GAGTGGAACCGAGCAGAAAAC	59.468	52.381	0.00	0.00	37.80	2.43
2618	7366	1.553704	AGACCGTTATGGGAGTGGAAC	59.446	52.381	0.00	0.00	44.64	3.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.