AutoCloner

Multiple sequence alignment - TraesCS7D01G134100

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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	TraesCS7D01G134100	chr7D	100.000	5326	0	0	1	5326	85211210	85205885	0.000000e+00	9836
1	TraesCS7D01G134100	chr7D	82.007	817	117	17	2925	3725	84804898	84804096	0.000000e+00	667
2	TraesCS7D01G134100	chr7D	77.120	979	170	35	3093	4062	85291190	85290257	7.910000e-143	518
3	TraesCS7D01G134100	chr7D	83.871	403	35	15	4149	4544	84803415	84803036	1.820000e-94	357
4	TraesCS7D01G134100	chr7B	94.687	2748	105	18	1793	4519	34824405	34821678	0.000000e+00	4228
5	TraesCS7D01G134100	chr7B	97.078	1369	39	1	384	1752	34825770	34824403	0.000000e+00	2305
6	TraesCS7D01G134100	chr7B	79.106	1230	171	47	2925	4102	34517953	34516758	0.000000e+00	769
7	TraesCS7D01G134100	chr7B	88.658	529	47	8	1	521	34826127	34825604	2.710000e-177	632
8	TraesCS7D01G134100	chr7B	78.782	985	168	28	3100	4075	34893432	34892480	1.630000e-174	623
9	TraesCS7D01G134100	chr7B	77.721	983	176	31	3093	4062	34991663	34990711	3.600000e-156	562
10	TraesCS7D01G134100	chr7B	91.791	402	21	4	4931	5326	34712213	34711818	2.800000e-152	549
11	TraesCS7D01G134100	chr7B	77.143	980	182	29	3093	4062	34941135	34940188	1.020000e-146	531
12	TraesCS7D01G134100	chr7B	86.835	395	27	11	4149	4540	34516813	34516441	8.250000e-113	418
13	TraesCS7D01G134100	chr7B	84.901	404	28	14	4149	4544	34497779	34497401	1.400000e-100	377
14	TraesCS7D01G134100	chr7B	91.358	162	14	0	559	720	677889233	677889394	6.940000e-54	222
15	TraesCS7D01G134100	chr7B	86.243	189	14	7	4602	4780	34712478	34712292	1.510000e-45	195
16	TraesCS7D01G134100	chr7B	86.777	121	15	1	4290	4409	34990619	34990499	3.350000e-27	134
17	TraesCS7D01G134100	chr7A	91.400	1500	82	20	2725	4201	86229476	86228001	0.000000e+00	2012
18	TraesCS7D01G134100	chr7A	93.203	1280	80	4	721	2000	86231379	86230107	0.000000e+00	1875
19	TraesCS7D01G134100	chr7A	92.244	722	46	10	4042	4755	86228112	86227393	0.000000e+00	1014
20	TraesCS7D01G134100	chr7A	93.721	653	35	6	2051	2697	86230114	86229462	0.000000e+00	974
21	TraesCS7D01G134100	chr7A	92.857	532	23	4	4802	5326	86227398	86226875	0.000000e+00	758
22	TraesCS7D01G134100	chr7A	90.796	565	41	6	4	562	86231937	86231378	0.000000e+00	745
23	TraesCS7D01G134100	chr7A	78.852	993	166	31	3093	4075	86470592	86469634	9.730000e-177	630
24	TraesCS7D01G134100	chr7A	78.012	996	175	29	3093	4075	86427242	86426278	2.140000e-163	586
25	TraesCS7D01G134100	chr7A	82.586	379	30	14	4149	4526	85965154	85964811	8.670000e-78	302
26	TraesCS7D01G134100	chr7A	82.635	167	26	3	4233	4397	86426251	86426086	1.550000e-30	145
27	TraesCS7D01G134100	chr2D	92.308	169	12	1	557	724	611551049	611551217	6.890000e-59	239
28	TraesCS7D01G134100	chr4B	90.964	166	14	1	559	724	344463459	344463295	6.940000e-54	222
29	TraesCS7D01G134100	chr4B	89.017	173	16	2	555	727	665401415	665401246	1.500000e-50	211
30	TraesCS7D01G134100	chr1D	91.463	164	10	4	559	720	454203999	454203838	6.940000e-54	222
31	TraesCS7D01G134100	chr1B	90.854	164	15	0	557	720	623195846	623195683	2.500000e-53	220
32	TraesCS7D01G134100	chr4D	90.361	166	16	0	559	724	23422598	23422433	8.980000e-53	219
33	TraesCS7D01G134100	chr2B	90.000	170	15	2	553	720	331238760	331238591	8.980000e-53	219

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	TraesCS7D01G134100	chr7D	85205885	85211210	5325	True	9836.000000	9836	100.000000	1	5326	1	chr7D.!!$R1	5325
1	TraesCS7D01G134100	chr7D	85290257	85291190	933	True	518.000000	518	77.120000	3093	4062	1	chr7D.!!$R2	969
2	TraesCS7D01G134100	chr7D	84803036	84804898	1862	True	512.000000	667	82.939000	2925	4544	2	chr7D.!!$R3	1619
3	TraesCS7D01G134100	chr7B	34821678	34826127	4449	True	2388.333333	4228	93.474333	1	4519	3	chr7B.!!$R6	4518
4	TraesCS7D01G134100	chr7B	34892480	34893432	952	True	623.000000	623	78.782000	3100	4075	1	chr7B.!!$R2	975
5	TraesCS7D01G134100	chr7B	34516441	34517953	1512	True	593.500000	769	82.970500	2925	4540	2	chr7B.!!$R4	1615
6	TraesCS7D01G134100	chr7B	34940188	34941135	947	True	531.000000	531	77.143000	3093	4062	1	chr7B.!!$R3	969
7	TraesCS7D01G134100	chr7B	34711818	34712478	660	True	372.000000	549	89.017000	4602	5326	2	chr7B.!!$R5	724
8	TraesCS7D01G134100	chr7B	34990499	34991663	1164	True	348.000000	562	82.249000	3093	4409	2	chr7B.!!$R7	1316
9	TraesCS7D01G134100	chr7A	86226875	86231937	5062	True	1229.666667	2012	92.370167	4	5326	6	chr7A.!!$R3	5322
10	TraesCS7D01G134100	chr7A	86469634	86470592	958	True	630.000000	630	78.852000	3093	4075	1	chr7A.!!$R2	982
11	TraesCS7D01G134100	chr7A	86426086	86427242	1156	True	365.500000	586	80.323500	3093	4397	2	chr7A.!!$R4	1304

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	Hairpin	End Stability	Orientation
66	67	2.101249	CTGGTTTTGGTGTGTGCAAGAT	59.899	45.455	0.00	0.00	2.40	F
1114	1150	0.999712	GGTGAAATGGAAGGAGGGGA	59.000	55.000	0.00	0.00	4.81	F
1220	1256	0.822532	CCTACCTAGACGACGCCCAT	60.823	60.000	0.00	0.00	4.00	F
1229	1265	1.255667	ACGACGCCCATGAAGGTAGT	61.256	55.000	0.00	34.66	2.73	F
1761	1797	1.302033	AAGTTGACCAGAGGCAGCG	60.302	57.895	0.00	0.00	5.18	F
1777	1813	1.520342	GCGGTCCTGCTCATCTCAC	60.520	63.158	0.00	0.00	3.51	F
1790	1826	1.833630	CATCTCACCTGGCCTAACTCA	59.166	52.381	3.32	0.00	3.41	F
3648	3731	1.167851	CGCTTGTTGGTCATGATGGT	58.832	50.000	0.00	0.00	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1203	1239	0.107066	TCATGGGCGTCGTCTAGGTA	60.107	55.000	0.00	0.00	0.00	3.08	R
2038	2076	1.105457	ATCCCAACACGCCATGAATG	58.895	50.000	0.00	0.00	0.00	2.67	R
2047	2085	1.361668	CTGCGAGGAATCCCAACACG	61.362	60.000	0.00	0.00	33.88	4.49	R
2244	2285	2.502947	TGGATTGTGATGACCTGAGGAG	59.497	50.000	4.99	0.00	0.00	3.69	R
3560	3643	1.128692	GCAGATACACGCCAGACAAAC	59.871	52.381	0.00	0.00	0.00	2.93	R
3648	3731	2.342279	CCACCGCCGAAGAGACAA	59.658	61.111	0.00	0.00	0.00	3.18	R
3971	4436	4.937620	GGTTCTCACTTGCAATAGATGTGA	59.062	41.667	15.26	15.26	36.42	3.58	R
5086	5633	0.042731	TGGAGGAATCGGAAGGAGGT	59.957	55.000	0.00	0.00	0.00	3.85	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
66	67	2.101249	CTGGTTTTGGTGTGTGCAAGAT	59.899	45.455	0.00	0.00	0.00	2.40
75	76	3.557054	GGTGTGTGCAAGATCCACTTAGA	60.557	47.826	6.04	0.00	37.03	2.10
135	136	4.583907	TGCACAAATTCCAATGACTTCTCA	59.416	37.500	0.00	0.00	0.00	3.27
205	211	8.225603	AGGATGCACGATTACTATGAAAAATT	57.774	30.769	0.00	0.00	0.00	1.82
209	215	8.667987	TGCACGATTACTATGAAAAATTTGAC	57.332	30.769	0.00	0.00	0.00	3.18
383	389	6.575267	CCAAAGATGGCATAACAATCAATCA	58.425	36.000	0.00	0.00	40.58	2.57
384	390	7.042950	CCAAAGATGGCATAACAATCAATCAA	58.957	34.615	0.00	0.00	40.58	2.57
385	391	7.549842	CCAAAGATGGCATAACAATCAATCAAA	59.450	33.333	0.00	0.00	40.58	2.69
386	392	8.600625	CAAAGATGGCATAACAATCAATCAAAG	58.399	33.333	0.00	0.00	0.00	2.77
387	393	7.414222	AGATGGCATAACAATCAATCAAAGT	57.586	32.000	0.00	0.00	0.00	2.66
388	394	7.486647	AGATGGCATAACAATCAATCAAAGTC	58.513	34.615	0.00	0.00	0.00	3.01
389	395	5.964758	TGGCATAACAATCAATCAAAGTCC	58.035	37.500	0.00	0.00	0.00	3.85
390	396	5.479724	TGGCATAACAATCAATCAAAGTCCA	59.520	36.000	0.00	0.00	0.00	4.02
391	397	6.014755	TGGCATAACAATCAATCAAAGTCCAA	60.015	34.615	0.00	0.00	0.00	3.53
392	398	6.873076	GGCATAACAATCAATCAAAGTCCAAA	59.127	34.615	0.00	0.00	0.00	3.28
393	399	7.063780	GGCATAACAATCAATCAAAGTCCAAAG	59.936	37.037	0.00	0.00	0.00	2.77
394	400	7.814107	GCATAACAATCAATCAAAGTCCAAAGA	59.186	33.333	0.00	0.00	0.00	2.52
395	401	9.865321	CATAACAATCAATCAAAGTCCAAAGAT	57.135	29.630	0.00	0.00	0.00	2.40
396	402	9.865321	ATAACAATCAATCAAAGTCCAAAGATG	57.135	29.630	0.00	0.00	0.00	2.90
523	558	2.810439	TTGCCATCTTTGGGTTTTCG	57.190	45.000	0.00	0.00	43.84	3.46
584	619	6.041751	ACTCCCTCCGTTCCTAAATATAAGTG	59.958	42.308	0.00	0.00	0.00	3.16
623	658	7.014115	CACTACGAACTACATACGGATGTATC	58.986	42.308	20.64	14.85	45.42	2.24
663	698	7.576236	AGTGTTGATTCACTCATTTTACTTCG	58.424	34.615	0.00	0.00	44.07	3.79
851	887	3.462982	TCCACGATAATGTTTGATCCCG	58.537	45.455	0.00	0.00	0.00	5.14
932	968	4.959723	CCACAAAATGGTCAAAGGACAAT	58.040	39.130	0.00	0.00	46.17	2.71
1027	1063	6.670695	AAAAGCTCTGGGTTTGTTCATATT	57.329	33.333	0.00	0.00	41.52	1.28
1114	1150	0.999712	GGTGAAATGGAAGGAGGGGA	59.000	55.000	0.00	0.00	0.00	4.81
1150	1186	3.071837	TGAGGCGGTGTATGGCGA	61.072	61.111	0.00	0.00	36.92	5.54
1203	1239	2.053865	CAACCCATCATTGGCGCCT	61.054	57.895	29.70	4.80	42.15	5.52
1220	1256	0.822532	CCTACCTAGACGACGCCCAT	60.823	60.000	0.00	0.00	0.00	4.00
1229	1265	1.255667	ACGACGCCCATGAAGGTAGT	61.256	55.000	0.00	0.00	34.66	2.73
1265	1301	2.813474	CGCTCATCGTTTCCCGCA	60.813	61.111	0.00	0.00	36.19	5.69
1761	1797	1.302033	AAGTTGACCAGAGGCAGCG	60.302	57.895	0.00	0.00	0.00	5.18
1777	1813	1.520342	GCGGTCCTGCTCATCTCAC	60.520	63.158	0.00	0.00	0.00	3.51
1790	1826	1.833630	CATCTCACCTGGCCTAACTCA	59.166	52.381	3.32	0.00	0.00	3.41
1802	1838	3.344515	GCCTAACTCACACCTTTTAGGG	58.655	50.000	8.05	0.00	40.58	3.53
2038	2076	8.643752	CAATTGGTGGTTTATTTCGTTACAATC	58.356	33.333	0.00	0.00	0.00	2.67
2047	2085	8.531530	GTTTATTTCGTTACAATCATTCATGGC	58.468	33.333	0.00	0.00	0.00	4.40
2165	2203	4.635765	TCAGTGCTATAATCAGTTTGCCAC	59.364	41.667	0.00	0.00	0.00	5.01
3253	3318	5.646360	CCGTGGAACTGTTATTTATGAGGTT	59.354	40.000	0.00	0.00	31.75	3.50
3254	3319	6.150474	CCGTGGAACTGTTATTTATGAGGTTT	59.850	38.462	0.00	0.00	31.75	3.27
3255	3320	7.021196	CGTGGAACTGTTATTTATGAGGTTTG	58.979	38.462	0.00	0.00	31.75	2.93
3423	3505	5.237127	TGTTTCCTTTATCAGCATATCGCAG	59.763	40.000	0.00	0.00	46.13	5.18
3436	3518	4.036262	GCATATCGCAGGGAAAACATAACA	59.964	41.667	0.00	0.00	41.79	2.41
3560	3643	4.676196	GCAGGGCTATTTTGACATTGTCTG	60.676	45.833	17.26	4.96	33.15	3.51
3648	3731	1.167851	CGCTTGTTGGTCATGATGGT	58.832	50.000	0.00	0.00	0.00	3.55
3831	4275	4.911390	AGTTAAAGGCTATGTGTGCTTCT	58.089	39.130	0.00	0.00	0.00	2.85
4055	4525	0.606401	CGCAGGTGGTCATTGGAAGT	60.606	55.000	0.00	0.00	0.00	3.01
4062	4532	5.534654	CAGGTGGTCATTGGAAGTTTTCTAA	59.465	40.000	0.00	0.00	34.56	2.10
4084	4557	9.003658	TCTAACTGATGAAAAAGAGATCAAACC	57.996	33.333	0.00	0.00	0.00	3.27
4099	4572	2.063015	AAACCGGATGTGGCCAGTGA	62.063	55.000	9.46	0.00	0.00	3.41
4121	4594	3.655276	AGGTTTGCAGCTGATGAAAAG	57.345	42.857	20.43	0.00	37.09	2.27
4155	4679	0.464554	GGATGTGGCTAGTGGAAGGC	60.465	60.000	0.00	0.00	42.19	4.35
4172	4696	1.544691	AGGCTTGCAGCTGATGAAAAG	59.455	47.619	20.43	12.68	41.99	2.27
4235	4759	3.695606	GGACCGACTGCTGCTCCA	61.696	66.667	0.00	0.00	0.00	3.86
4312	4836	4.365514	TCAACACCAGCTTCCTATTTCA	57.634	40.909	0.00	0.00	0.00	2.69
4369	4894	6.699575	TCCTAGCTCCAAATGCTTATTTTC	57.300	37.500	0.00	0.00	41.46	2.29
4478	5005	7.136772	GTGGTCAAGTTATGTTTTTGTACCTC	58.863	38.462	0.00	0.00	0.00	3.85
4705	5246	4.737352	GCTTTGCAGGAACATCTTGTTTGA	60.737	41.667	0.00	0.00	41.28	2.69
4708	5249	5.336150	TGCAGGAACATCTTGTTTGAAAA	57.664	34.783	0.00	0.00	41.28	2.29
4740	5283	9.445786	AGTTTTATGTACAAAAACAGAATGACG	57.554	29.630	28.23	0.00	45.17	4.35
4774	5317	2.421751	TGGTCGTCCACCTTTCAAAA	57.578	45.000	0.00	0.00	46.98	2.44
4775	5318	2.724454	TGGTCGTCCACCTTTCAAAAA	58.276	42.857	0.00	0.00	46.98	1.94
4793	5336	3.957671	AAAAGAAAAGAACGGTCGTCC	57.042	42.857	0.00	0.00	0.00	4.79
4794	5337	2.607631	AAGAAAAGAACGGTCGTCCA	57.392	45.000	0.00	0.00	0.00	4.02
4795	5338	1.861971	AGAAAAGAACGGTCGTCCAC	58.138	50.000	0.00	0.00	0.00	4.02
4796	5339	0.863799	GAAAAGAACGGTCGTCCACC	59.136	55.000	0.00	0.00	42.69	4.61
4797	5340	0.466963	AAAAGAACGGTCGTCCACCT	59.533	50.000	0.00	0.00	44.21	4.00
4798	5341	0.466963	AAAGAACGGTCGTCCACCTT	59.533	50.000	0.00	0.00	44.21	3.50
4799	5342	0.466963	AAGAACGGTCGTCCACCTTT	59.533	50.000	0.00	0.00	44.21	3.11
4800	5343	2.525422	GAACGGTCGTCCACCTTTC	58.475	57.895	0.00	0.00	44.01	2.62
4801	5344	1.824658	AACGGTCGTCCACCTTTCA	59.175	52.632	0.00	0.00	44.21	2.69
4802	5345	0.178533	AACGGTCGTCCACCTTTCAA	59.821	50.000	0.00	0.00	44.21	2.69
4803	5346	0.178533	ACGGTCGTCCACCTTTCAAA	59.821	50.000	0.00	0.00	44.21	2.69
4804	5347	1.301423	CGGTCGTCCACCTTTCAAAA	58.699	50.000	0.00	0.00	44.21	2.44
4805	5348	1.671845	CGGTCGTCCACCTTTCAAAAA	59.328	47.619	0.00	0.00	44.21	1.94
4824	5367	4.483476	AAAAGAAAAGAATGGTCGTCCG	57.517	40.909	0.00	0.00	36.30	4.79
4876	5423	0.247736	TTCAAGGGAGAAGAGAGCGC	59.752	55.000	0.00	0.00	0.00	5.92
4880	5427	1.448717	GGGAGAAGAGAGCGCCAAC	60.449	63.158	2.29	0.00	0.00	3.77
4921	5468	4.500887	CCATGCCAAACCAATCTCATCATC	60.501	45.833	0.00	0.00	0.00	2.92
5141	5688	3.524606	CCCACGGATCCGCGTACT	61.525	66.667	33.62	11.56	44.19	2.73
5210	5757	1.078143	ATCTCCTTGGAAGCGGTGC	60.078	57.895	0.00	0.00	0.00	5.01
5211	5758	2.543067	ATCTCCTTGGAAGCGGTGCC	62.543	60.000	4.07	4.07	0.00	5.01
5212	5759	3.551496	CTCCTTGGAAGCGGTGCCA	62.551	63.158	11.24	11.24	0.00	4.92
5213	5760	3.058160	CCTTGGAAGCGGTGCCAG	61.058	66.667	15.33	9.10	35.23	4.85
5214	5761	2.281761	CTTGGAAGCGGTGCCAGT	60.282	61.111	15.33	0.00	35.23	4.00
5215	5762	2.594303	TTGGAAGCGGTGCCAGTG	60.594	61.111	15.33	0.00	35.23	3.66
5317	5870	1.453379	GGATCCTCCTCCGTCGTCA	60.453	63.158	3.84	0.00	32.53	4.35
5321	5874	0.748367	TCCTCCTCCGTCGTCATCTG	60.748	60.000	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
135	136	2.996621	GCATCGAAAACTGCTAGACTGT	59.003	45.455	1.49	0.00	35.49	3.55
209	215	7.614192	ACATTAGATGGTTTAGGTTTTACCTGG	59.386	37.037	8.61	0.00	41.26	4.45
243	249	0.391130	GTTACCATGCACTCGAGCCA	60.391	55.000	13.61	10.70	0.00	4.75
346	352	1.923356	TCTTTGGACTTTCATGGGCC	58.077	50.000	0.00	0.00	0.00	5.80
369	375	9.865321	ATCTTTGGACTTTGATTGATTGTTATG	57.135	29.630	0.00	0.00	0.00	1.90
370	376	9.865321	CATCTTTGGACTTTGATTGATTGTTAT	57.135	29.630	0.00	0.00	0.00	1.89
371	377	8.306038	CCATCTTTGGACTTTGATTGATTGTTA	58.694	33.333	0.00	0.00	46.92	2.41
372	378	7.156673	CCATCTTTGGACTTTGATTGATTGTT	58.843	34.615	0.00	0.00	46.92	2.83
373	379	6.694447	CCATCTTTGGACTTTGATTGATTGT	58.306	36.000	0.00	0.00	46.92	2.71
374	380	5.579511	GCCATCTTTGGACTTTGATTGATTG	59.420	40.000	0.00	0.00	46.92	2.67
375	381	5.246656	TGCCATCTTTGGACTTTGATTGATT	59.753	36.000	0.00	0.00	46.92	2.57
376	382	4.773674	TGCCATCTTTGGACTTTGATTGAT	59.226	37.500	0.00	0.00	46.92	2.57
377	383	4.151121	TGCCATCTTTGGACTTTGATTGA	58.849	39.130	0.00	0.00	46.92	2.57
378	384	4.524316	TGCCATCTTTGGACTTTGATTG	57.476	40.909	0.00	0.00	46.92	2.67
379	385	5.163478	GCTATGCCATCTTTGGACTTTGATT	60.163	40.000	0.00	0.00	46.92	2.57
380	386	4.340381	GCTATGCCATCTTTGGACTTTGAT	59.660	41.667	0.00	0.00	46.92	2.57
381	387	3.696051	GCTATGCCATCTTTGGACTTTGA	59.304	43.478	0.00	0.00	46.92	2.69
382	388	3.698040	AGCTATGCCATCTTTGGACTTTG	59.302	43.478	0.00	0.00	46.92	2.77
383	389	3.973425	AGCTATGCCATCTTTGGACTTT	58.027	40.909	0.00	0.00	46.92	2.66
384	390	3.659183	AGCTATGCCATCTTTGGACTT	57.341	42.857	0.00	0.00	46.92	3.01
385	391	4.989875	ATAGCTATGCCATCTTTGGACT	57.010	40.909	5.15	0.00	46.92	3.85
386	392	7.693969	ATTAATAGCTATGCCATCTTTGGAC	57.306	36.000	7.09	0.00	46.92	4.02
387	393	9.806448	TTTATTAATAGCTATGCCATCTTTGGA	57.194	29.630	7.09	0.00	46.92	3.53
458	493	6.223351	TGGATTTTCATTGATTGCTATGCA	57.777	33.333	0.00	0.00	36.47	3.96
584	619	6.388278	AGTTCGTAGTGGAATCTCTAACAAC	58.612	40.000	0.00	0.00	0.00	3.32
623	658	9.208022	TGAATCAACACTCTAAAACATGTCTAG	57.792	33.333	0.00	3.67	0.00	2.43
663	698	6.803642	AGAAATTCCACTACGGACTACATAC	58.196	40.000	0.00	0.00	46.36	2.39
693	728	5.859205	ACCTCCGTTCCTAAATATACGTT	57.141	39.130	0.00	0.00	32.45	3.99
932	968	7.936496	TGGAATTCACATGAGCTATTTACAA	57.064	32.000	7.93	0.00	0.00	2.41
1073	1109	3.331150	TCTCGACACAACAACAACAACT	58.669	40.909	0.00	0.00	0.00	3.16
1141	1177	4.855105	GCATGTCCTCGCCATACA	57.145	55.556	0.00	0.00	0.00	2.29
1150	1186	2.679716	GGCTCTTGGGCATGTCCT	59.320	61.111	19.09	0.00	40.53	3.85
1203	1239	0.107066	TCATGGGCGTCGTCTAGGTA	60.107	55.000	0.00	0.00	0.00	3.08
1220	1256	4.383118	GCAGAATAGGAAGCACTACCTTCA	60.383	45.833	0.00	0.00	42.31	3.02
1229	1265	0.744414	GCGGTGCAGAATAGGAAGCA	60.744	55.000	0.00	0.00	34.10	3.91
1340	1376	1.684734	ATCTGGGGCGTACTTCCGT	60.685	57.895	0.00	0.00	0.00	4.69
1350	1386	0.108774	GGCTTAGTACCATCTGGGGC	59.891	60.000	0.54	0.00	42.91	5.80
1761	1797	0.177604	CAGGTGAGATGAGCAGGACC	59.822	60.000	0.00	0.00	0.00	4.46
1769	1805	2.111384	GAGTTAGGCCAGGTGAGATGA	58.889	52.381	5.01	0.00	0.00	2.92
1772	1808	1.267121	GTGAGTTAGGCCAGGTGAGA	58.733	55.000	5.01	0.00	0.00	3.27
1777	1813	0.693049	AAGGTGTGAGTTAGGCCAGG	59.307	55.000	5.01	0.00	0.00	4.45
1790	1826	3.806949	TCTTGCATCCCTAAAAGGTGT	57.193	42.857	0.00	0.00	31.93	4.16
1817	1855	5.010820	ACACTAACTAGCGAGAAAGGTCTTT	59.989	40.000	0.00	0.00	32.80	2.52
1819	1857	4.080687	ACACTAACTAGCGAGAAAGGTCT	58.919	43.478	0.00	0.00	36.55	3.85
2038	2076	1.105457	ATCCCAACACGCCATGAATG	58.895	50.000	0.00	0.00	0.00	2.67
2047	2085	1.361668	CTGCGAGGAATCCCAACACG	61.362	60.000	0.00	0.00	33.88	4.49
2219	2260	4.385405	AGTCGCACCTGGCTCTGC	62.385	66.667	0.00	0.00	41.67	4.26
2244	2285	2.502947	TGGATTGTGATGACCTGAGGAG	59.497	50.000	4.99	0.00	0.00	3.69
2341	2383	6.549364	CCCTGATATCCAGTAGTATCCAGATC	59.451	46.154	0.00	0.00	41.33	2.75
2455	2498	6.767456	TCACATAACGTTAAGTAGGGGAAAA	58.233	36.000	15.15	0.00	0.00	2.29
3040	3105	9.083422	CAGAATAGATAACCTATGGAAGAGACA	57.917	37.037	0.00	0.00	38.08	3.41
3253	3318	6.264292	TCCAAGCTAAAACAATAGAGCAACAA	59.736	34.615	0.00	0.00	37.40	2.83
3254	3319	5.767665	TCCAAGCTAAAACAATAGAGCAACA	59.232	36.000	0.00	0.00	37.40	3.33
3255	3320	6.254281	TCCAAGCTAAAACAATAGAGCAAC	57.746	37.500	0.00	0.00	37.40	4.17
3423	3505	6.989759	AGAACCACAAAATGTTATGTTTTCCC	59.010	34.615	0.00	0.00	0.00	3.97
3436	3518	3.909732	TGGAAGACCAGAACCACAAAAT	58.090	40.909	0.00	0.00	41.77	1.82
3560	3643	1.128692	GCAGATACACGCCAGACAAAC	59.871	52.381	0.00	0.00	0.00	2.93
3648	3731	2.342279	CCACCGCCGAAGAGACAA	59.658	61.111	0.00	0.00	0.00	3.18
3971	4436	4.937620	GGTTCTCACTTGCAATAGATGTGA	59.062	41.667	15.26	15.26	36.42	3.58
4062	4532	5.182001	CCGGTTTGATCTCTTTTTCATCAGT	59.818	40.000	0.00	0.00	0.00	3.41
4084	4557	1.308069	CCTTTCACTGGCCACATCCG	61.308	60.000	0.00	0.00	0.00	4.18
4099	4572	4.374399	CTTTTCATCAGCTGCAAACCTTT	58.626	39.130	9.47	0.00	0.00	3.11
4121	4594	3.539604	CACATCCTGTTTGATCTCCTCC	58.460	50.000	0.00	0.00	0.00	4.30
4155	4679	2.163815	CCTCCTTTTCATCAGCTGCAAG	59.836	50.000	9.47	5.74	0.00	4.01
4172	4696	3.539604	CACATCCTGTTTCATCTCCTCC	58.460	50.000	0.00	0.00	0.00	4.30
4219	4743	0.674895	ATTTGGAGCAGCAGTCGGTC	60.675	55.000	0.00	0.00	0.00	4.79
4235	4759	4.164988	CCTGGACCACTAGAGGATTCATTT	59.835	45.833	13.71	0.00	0.00	2.32
4312	4836	3.369787	GGAATTTAAGCTGGCTGGCATTT	60.370	43.478	3.74	5.41	34.17	2.32
4369	4894	3.277142	AGCGTTTGGAAATAGTAGGGG	57.723	47.619	0.00	0.00	0.00	4.79
4478	5005	7.977490	ACTATAATATCACGAAGCATCATCG	57.023	36.000	0.00	0.00	45.47	3.84
4515	5048	3.747529	CAGATGTGCGCAATATGTCCATA	59.252	43.478	14.00	0.00	0.00	2.74
4520	5053	3.469739	TGATCAGATGTGCGCAATATGT	58.530	40.909	14.00	5.59	0.00	2.29
4740	5283	4.571176	GGACGACCATTCTTTCATAGGAAC	59.429	45.833	0.00	0.00	35.97	3.62
4772	5315	3.690628	TGGACGACCGTTCTTTTCTTTTT	59.309	39.130	2.33	0.00	39.42	1.94
4773	5316	3.064408	GTGGACGACCGTTCTTTTCTTTT	59.936	43.478	2.33	0.00	39.42	2.27
4774	5317	2.610833	GTGGACGACCGTTCTTTTCTTT	59.389	45.455	2.33	0.00	39.42	2.52
4775	5318	2.207590	GTGGACGACCGTTCTTTTCTT	58.792	47.619	2.33	0.00	39.42	2.52
4776	5319	1.539712	GGTGGACGACCGTTCTTTTCT	60.540	52.381	2.33	0.00	39.42	2.52
4777	5320	0.863799	GGTGGACGACCGTTCTTTTC	59.136	55.000	2.33	0.00	39.42	2.29
4778	5321	2.996444	GGTGGACGACCGTTCTTTT	58.004	52.632	2.33	0.00	39.42	2.27
4779	5322	4.764896	GGTGGACGACCGTTCTTT	57.235	55.556	2.33	0.00	39.42	2.52
4802	5345	4.261447	CCGGACGACCATTCTTTTCTTTTT	60.261	41.667	0.00	0.00	35.59	1.94
4803	5346	3.252458	CCGGACGACCATTCTTTTCTTTT	59.748	43.478	0.00	0.00	35.59	2.27
4804	5347	2.812011	CCGGACGACCATTCTTTTCTTT	59.188	45.455	0.00	0.00	35.59	2.52
4805	5348	2.423577	CCGGACGACCATTCTTTTCTT	58.576	47.619	0.00	0.00	35.59	2.52
4806	5349	1.338769	CCCGGACGACCATTCTTTTCT	60.339	52.381	0.73	0.00	35.59	2.52
4807	5350	1.084289	CCCGGACGACCATTCTTTTC	58.916	55.000	0.73	0.00	35.59	2.29
4824	5367	1.897560	CTTGTGGGTTCAGTCTTCCC	58.102	55.000	0.00	0.00	41.41	3.97
4876	5423	1.290203	CGATGAGTTGGATCGGTTGG	58.710	55.000	0.00	0.00	39.23	3.77
4880	5427	0.598680	GGAGCGATGAGTTGGATCGG	60.599	60.000	0.00	0.00	42.42	4.18
4921	5468	2.295253	ATACGGCCTGAGAGAAAACG	57.705	50.000	0.00	0.00	0.00	3.60
5084	5631	0.386113	GAGGAATCGGAAGGAGGTCG	59.614	60.000	0.00	0.00	0.00	4.79
5086	5633	0.042731	TGGAGGAATCGGAAGGAGGT	59.957	55.000	0.00	0.00	0.00	3.85
5134	5681	3.446570	AGGGGAACGGAGTACGCG	61.447	66.667	3.53	3.53	45.00	6.01
5138	5685	1.229082	ACAGCAGGGGAACGGAGTA	60.229	57.895	0.00	0.00	45.00	2.59
5141	5688	3.319198	GGACAGCAGGGGAACGGA	61.319	66.667	0.00	0.00	0.00	4.69
5184	5731	3.204526	GCTTCCAAGGAGATGATGACAG	58.795	50.000	0.00	0.00	0.00	3.51
5210	5757	4.928398	CTGGAGCTACAGCACTGG	57.072	61.111	14.40	0.00	45.16	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.