AutoCloner

Multiple sequence alignment - TraesCS6D01G022500

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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	TraesCS6D01G022500	chr6D	100.000	2570	0	0	1	2570	8744560	8741991	0.000000e+00	4747.0
1	TraesCS6D01G022500	chr6D	98.759	1612	18	2	729	2338	8733146	8731535	0.000000e+00	2865.0
2	TraesCS6D01G022500	chr6D	98.737	475	5	1	2050	2523	8725428	8724954	0.000000e+00	843.0
3	TraesCS6D01G022500	chr6D	89.457	313	27	5	2215	2523	8786722	8786412	8.620000e-105	390.0
4	TraesCS6D01G022500	chr6D	100.000	35	0	0	2536	2570	8724700	8724666	5.940000e-07	65.8
5	TraesCS6D01G022500	chr6D	100.000	35	0	0	2536	2570	8729777	8729743	5.940000e-07	65.8
6	TraesCS6D01G022500	chrUn	98.759	1612	18	2	729	2338	355457795	355456184	0.000000e+00	2865.0
7	TraesCS6D01G022500	chrUn	98.425	1524	23	1	1001	2523	357590841	357589318	0.000000e+00	2680.0
8	TraesCS6D01G022500	chrUn	98.223	1013	16	2	1328	2338	450891099	450892111	0.000000e+00	1770.0
9	TraesCS6D01G022500	chrUn	97.683	863	17	3	1663	2523	393621589	393620728	0.000000e+00	1480.0
10	TraesCS6D01G022500	chrUn	98.737	475	5	1	2050	2523	351902700	351902226	0.000000e+00	843.0
11	TraesCS6D01G022500	chrUn	98.242	455	8	0	1663	2117	454162112	454162566	0.000000e+00	797.0
12	TraesCS6D01G022500	chrUn	98.305	413	6	1	2112	2523	364471045	364470633	0.000000e+00	723.0
13	TraesCS6D01G022500	chrUn	98.068	414	8	0	1707	2120	475069452	475069039	0.000000e+00	721.0
14	TraesCS6D01G022500	chrUn	99.587	242	1	0	1	242	422659328	422659087	2.350000e-120	442.0
15	TraesCS6D01G022500	chrUn	88.705	363	38	1	6	368	396627943	396628302	8.440000e-120	440.0
16	TraesCS6D01G022500	chrUn	88.705	363	38	1	6	368	433112672	433112313	8.440000e-120	440.0
17	TraesCS6D01G022500	chrUn	91.189	227	12	6	523	746	433112184	433111963	4.160000e-78	302.0
18	TraesCS6D01G022500	chrUn	100.000	35	0	0	2536	2570	80051502	80051536	5.940000e-07	65.8
19	TraesCS6D01G022500	chrUn	100.000	35	0	0	2536	2570	230375080	230375114	5.940000e-07	65.8
20	TraesCS6D01G022500	chrUn	100.000	35	0	0	2536	2570	351414325	351414359	5.940000e-07	65.8
21	TraesCS6D01G022500	chrUn	100.000	35	0	0	2536	2570	351454951	351454985	5.940000e-07	65.8
22	TraesCS6D01G022500	chrUn	100.000	35	0	0	2536	2570	351901972	351901938	5.940000e-07	65.8
23	TraesCS6D01G022500	chrUn	100.000	35	0	0	2536	2570	357589064	357589030	5.940000e-07	65.8
24	TraesCS6D01G022500	chrUn	100.000	35	0	0	2536	2570	364470380	364470346	5.940000e-07	65.8
25	TraesCS6D01G022500	chr6A	92.388	2010	133	13	523	2523	9134022	9136020	0.000000e+00	2846.0
26	TraesCS6D01G022500	chr6A	83.861	2020	234	63	523	2511	9128018	9129976	0.000000e+00	1840.0
27	TraesCS6D01G022500	chr6A	83.812	2020	235	63	523	2511	9103990	9105948	0.000000e+00	1834.0
28	TraesCS6D01G022500	chr6A	83.713	2020	237	62	523	2511	9113003	9114961	0.000000e+00	1823.0
29	TraesCS6D01G022500	chr6A	92.413	1239	86	3	607	1842	9053913	9055146	0.000000e+00	1760.0
30	TraesCS6D01G022500	chr6A	87.430	533	50	7	6	523	9069193	9069723	4.730000e-167	597.0
31	TraesCS6D01G022500	chr6A	89.256	363	36	1	6	368	9109509	9109868	3.900000e-123	451.0
32	TraesCS6D01G022500	chr6A	89.256	363	36	1	6	368	9115518	9115877	3.900000e-123	451.0
33	TraesCS6D01G022500	chr6A	89.256	363	36	1	6	368	9130533	9130892	3.900000e-123	451.0
34	TraesCS6D01G022500	chr6A	89.256	363	36	1	6	368	9133534	9133893	3.900000e-123	451.0
35	TraesCS6D01G022500	chr6A	88.705	363	38	1	6	368	9103501	9103860	8.440000e-120	440.0
36	TraesCS6D01G022500	chr6A	88.705	363	38	1	6	368	9106505	9106864	8.440000e-120	440.0
37	TraesCS6D01G022500	chr6A	89.407	236	22	3	284	517	9142531	9142765	6.950000e-76	294.0
38	TraesCS6D01G022500	chr6A	89.091	165	13	4	353	517	9097669	9097828	1.560000e-47	200.0
39	TraesCS6D01G022500	chr6B	91.195	1272	96	10	529	1789	15885679	15884413	0.000000e+00	1714.0
40	TraesCS6D01G022500	chr6B	88.835	206	22	1	313	517	15886091	15885886	4.240000e-63	252.0

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	TraesCS6D01G022500	chr6D	8741991	8744560	2569	True	4747.0	4747	100.000000	1	2570	1	chr6D.!!$R1	2569
1	TraesCS6D01G022500	chr6D	8729743	8733146	3403	True	1465.4	2865	99.379500	729	2570	2	chr6D.!!$R4	1841
2	TraesCS6D01G022500	chr6D	8724666	8725428	762	True	454.4	843	99.368500	2050	2570	2	chr6D.!!$R3	520
3	TraesCS6D01G022500	chrUn	355456184	355457795	1611	True	2865.0	2865	98.759000	729	2338	1	chrUn.!!$R1	1609
4	TraesCS6D01G022500	chrUn	450891099	450892111	1012	False	1770.0	1770	98.223000	1328	2338	1	chrUn.!!$F6	1010
5	TraesCS6D01G022500	chrUn	393620728	393621589	861	True	1480.0	1480	97.683000	1663	2523	1	chrUn.!!$R2	860
6	TraesCS6D01G022500	chrUn	357589030	357590841	1811	True	1372.9	2680	99.212500	1001	2570	2	chrUn.!!$R6	1569
7	TraesCS6D01G022500	chrUn	351901938	351902700	762	True	454.4	843	99.368500	2050	2570	2	chrUn.!!$R5	520
8	TraesCS6D01G022500	chrUn	364470346	364471045	699	True	394.4	723	99.152500	2112	2570	2	chrUn.!!$R7	458
9	TraesCS6D01G022500	chrUn	433111963	433112672	709	True	371.0	440	89.947000	6	746	2	chrUn.!!$R8	740
10	TraesCS6D01G022500	chr6A	9053913	9055146	1233	False	1760.0	1760	92.413000	607	1842	1	chr6A.!!$F1	1235
11	TraesCS6D01G022500	chr6A	9128018	9136020	8002	False	1397.0	2846	88.690250	6	2523	4	chr6A.!!$F6	2517
12	TraesCS6D01G022500	chr6A	9103501	9115877	12376	False	906.5	1834	87.241167	6	2511	6	chr6A.!!$F5	2505
13	TraesCS6D01G022500	chr6A	9069193	9069723	530	False	597.0	597	87.430000	6	523	1	chr6A.!!$F2	517
14	TraesCS6D01G022500	chr6B	15884413	15886091	1678	True	983.0	1714	90.015000	313	1789	2	chr6B.!!$R1	1476

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
61	6065	0.173708	CAACGTACAGAGGAGAGGGC	59.826	60.0	0.0	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2156	14430	0.178938	TCCTGCTTTTGAATGGCCCA	60.179	50.0	0.0	0.0	0.0	5.36	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
60	6064	0.818296	CCAACGTACAGAGGAGAGGG	59.182	60.000	0.00	0.00	0.00	4.30
61	6065	0.173708	CAACGTACAGAGGAGAGGGC	59.826	60.000	0.00	0.00	0.00	5.19
64	6068	1.388065	CGTACAGAGGAGAGGGCCAG	61.388	65.000	6.18	0.00	0.00	4.85
66	6070	1.221909	TACAGAGGAGAGGGCCAGGA	61.222	60.000	6.18	0.00	0.00	3.86
113	6117	2.356313	CCGGATCGGGCGATTCAG	60.356	66.667	6.35	0.00	44.15	3.02
136	6147	2.856231	TGGGGCCTGAATAATAAGTGGT	59.144	45.455	0.84	0.00	0.00	4.16
137	6148	3.270960	TGGGGCCTGAATAATAAGTGGTT	59.729	43.478	0.84	0.00	0.00	3.67
154	6165	4.279169	AGTGGTTCTGTCAATGTCAAATGG	59.721	41.667	0.00	0.00	0.00	3.16
168	6179	1.051556	AAATGGTGGGGCACGGTTTT	61.052	50.000	0.00	0.00	34.83	2.43
177	6188	1.442017	GCACGGTTTTCATGTCCGC	60.442	57.895	16.28	3.63	46.92	5.54
272	9290	5.717119	TGTCTCACGTAACTTAATTCTCCC	58.283	41.667	0.00	0.00	0.00	4.30
374	9393	8.953990	CGTAACTATAGGTGCAAATAAAAATGC	58.046	33.333	6.69	0.00	42.86	3.56
416	9435	2.146342	CAATGAACTGCACCTCTCGTT	58.854	47.619	0.00	0.00	0.00	3.85
439	9458	6.994421	TGTAGCATTATCTATGTTCTCCCA	57.006	37.500	0.00	0.00	36.57	4.37
485	9506	4.452825	TCGTGGTACCATTTTCAAGAACA	58.547	39.130	19.72	0.00	0.00	3.18
488	9509	5.449314	CGTGGTACCATTTTCAAGAACACAA	60.449	40.000	19.72	0.00	0.00	3.33
492	9513	6.695713	GGTACCATTTTCAAGAACACAAGAAC	59.304	38.462	7.15	0.00	0.00	3.01
517	9538	0.237235	ATGCACGTACGTGGCTTTTG	59.763	50.000	40.17	20.39	45.49	2.44
684	9934	9.590451	AACCTGTTCTGCAATATTTTTATCATG	57.410	29.630	0.00	0.00	0.00	3.07
999	10258	3.914312	TGAGCACTGTTCAGTAGCTAAC	58.086	45.455	20.54	13.97	35.36	2.34
2156	14430	5.927281	ACAAAATGGAGCAGCTTAATCAT	57.073	34.783	0.00	0.00	0.00	2.45
2164	14438	1.690352	GCAGCTTAATCATGGGCCATT	59.310	47.619	18.46	6.14	0.00	3.16
2496	14788	5.374080	GGTGCATGATTACGAATAATGACG	58.626	41.667	0.00	0.00	32.30	4.35
2523	14815	3.608506	GGCATACGAGCGTTATCATACTG	59.391	47.826	0.00	0.00	34.64	2.74
2524	14816	4.473199	GCATACGAGCGTTATCATACTGA	58.527	43.478	0.00	0.00	0.00	3.41
2526	14818	5.573282	GCATACGAGCGTTATCATACTGAAT	59.427	40.000	0.00	0.00	0.00	2.57
2527	14819	6.237332	GCATACGAGCGTTATCATACTGAATC	60.237	42.308	0.00	0.00	0.00	2.52
2528	14820	5.440234	ACGAGCGTTATCATACTGAATCT	57.560	39.130	0.00	0.00	0.00	2.40
2531	14823	6.024664	CGAGCGTTATCATACTGAATCTAGG	58.975	44.000	0.00	0.00	0.00	3.02
2533	14825	7.151999	AGCGTTATCATACTGAATCTAGGAG	57.848	40.000	0.00	0.00	0.00	3.69
2534	14826	6.717540	AGCGTTATCATACTGAATCTAGGAGT	59.282	38.462	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	6044	0.173708	CCTCTCCTCTGTACGTTGGC	59.826	60.000	0.00	0.00	0.00	4.52
64	6068	3.025619	CGATTCCAGCCGCAATCC	58.974	61.111	0.00	0.00	0.00	3.01
113	6117	2.887152	CACTTATTATTCAGGCCCCAGC	59.113	50.000	0.00	0.00	38.76	4.85
136	6147	3.573538	CCCACCATTTGACATTGACAGAA	59.426	43.478	0.00	0.00	0.00	3.02
137	6148	3.156293	CCCACCATTTGACATTGACAGA	58.844	45.455	0.00	0.00	0.00	3.41
154	6165	1.288752	CATGAAAACCGTGCCCCAC	59.711	57.895	0.00	0.00	0.00	4.61
168	6179	0.804544	GTCGAATTCGGCGGACATGA	60.805	55.000	26.47	1.93	40.29	3.07
243	6254	9.175312	AGAATTAAGTTACGTGAGACATCTCTA	57.825	33.333	10.18	0.00	43.25	2.43
247	9265	6.476053	GGGAGAATTAAGTTACGTGAGACATC	59.524	42.308	0.00	0.00	0.00	3.06
250	9268	4.797349	CGGGAGAATTAAGTTACGTGAGAC	59.203	45.833	0.00	0.00	0.00	3.36
252	9270	4.990257	TCGGGAGAATTAAGTTACGTGAG	58.010	43.478	0.00	0.00	34.75	3.51
254	9272	5.589192	AGATCGGGAGAATTAAGTTACGTG	58.411	41.667	0.00	0.00	45.37	4.49
255	9273	5.848833	AGATCGGGAGAATTAAGTTACGT	57.151	39.130	0.00	0.00	45.37	3.57
256	9274	9.903682	TTATTAGATCGGGAGAATTAAGTTACG	57.096	33.333	0.00	0.00	45.37	3.18
267	9285	6.667848	TGCCTCATATTTATTAGATCGGGAGA	59.332	38.462	0.00	0.00	46.90	3.71
288	9306	1.745087	CTGCACCGATGTAAAATGCCT	59.255	47.619	0.00	0.00	35.37	4.75
374	9393	3.432933	GCTGGTGCAACACATATTTTTGG	59.567	43.478	0.00	0.00	39.98	3.28
399	9418	3.289128	CAACGAGAGGTGCAGTTCA	57.711	52.632	0.00	0.00	44.78	3.18
416	9435	6.994421	TGGGAGAACATAGATAATGCTACA	57.006	37.500	0.00	0.00	39.39	2.74
439	9458	9.893305	CGAGAAGGAAATAAAATGTACAACTTT	57.107	29.630	0.00	5.61	0.00	2.66
485	9506	2.288666	ACGTGCATGTCTTGTTCTTGT	58.711	42.857	5.51	0.00	0.00	3.16
488	9509	2.058798	CGTACGTGCATGTCTTGTTCT	58.941	47.619	16.44	0.00	0.00	3.01
492	9513	0.438445	CCACGTACGTGCATGTCTTG	59.562	55.000	36.76	20.01	44.16	3.02
555	9802	0.251354	CACCATCTGAGGGTCACTGG	59.749	60.000	11.66	0.00	36.19	4.00
624	9874	9.234384	CTGAATGAATTGATAGCAACATTCTTC	57.766	33.333	25.10	17.14	42.30	2.87
684	9934	3.100671	AGACAGAGACAGGATTACACCC	58.899	50.000	0.00	0.00	0.00	4.61
999	10258	1.654954	GAGCTCTTGCAGTGGCCATG	61.655	60.000	9.72	9.86	42.74	3.66
2156	14430	0.178938	TCCTGCTTTTGAATGGCCCA	60.179	50.000	0.00	0.00	0.00	5.36
2164	14438	3.690460	GGATTCTTCCTCCTGCTTTTGA	58.310	45.455	0.00	0.00	39.14	2.69
2496	14788	0.458889	TAACGCTCGTATGCCACCAC	60.459	55.000	0.00	0.00	0.00	4.16
2523	14815	7.599245	CGTGGAATGGTAATAACTCCTAGATTC	59.401	40.741	0.00	0.00	0.00	2.52
2524	14816	7.442656	CGTGGAATGGTAATAACTCCTAGATT	58.557	38.462	0.00	0.00	0.00	2.40
2526	14818	5.303589	CCGTGGAATGGTAATAACTCCTAGA	59.696	44.000	0.00	0.00	38.54	2.43
2527	14819	5.539048	CCGTGGAATGGTAATAACTCCTAG	58.461	45.833	0.00	0.00	38.54	3.02
2528	14820	5.540400	CCGTGGAATGGTAATAACTCCTA	57.460	43.478	0.00	0.00	38.54	2.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.