AutoCloner

Multiple sequence alignment - TraesCS6B01G339800

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	TraesCS6B01G339800	chr6B	100.000	2318	0	0	1	2318	599121531	599123848	0.000000e+00	4281.0
1	TraesCS6B01G339800	chr6B	86.170	188	23	1	1355	1539	599122972	599123159	1.400000e-47	200.0
2	TraesCS6B01G339800	chr6B	82.805	221	33	4	2099	2317	508532723	508532506	2.350000e-45	193.0
3	TraesCS6B01G339800	chr6A	95.997	1349	32	6	203	1539	545883305	545884643	0.000000e+00	2172.0
4	TraesCS6B01G339800	chr6A	95.567	564	15	3	1446	2002	545884457	545885017	0.000000e+00	894.0
5	TraesCS6B01G339800	chr6A	90.282	319	19	6	2004	2318	545885325	545885635	7.710000e-110	407.0
6	TraesCS6B01G339800	chr6A	84.018	219	30	4	2104	2318	333858406	333858623	3.020000e-49	206.0
7	TraesCS6B01G339800	chr6A	91.156	147	8	3	72	218	545883143	545883284	6.540000e-46	195.0
8	TraesCS6B01G339800	chr6D	96.460	1243	35	2	341	1583	400088817	400090050	0.000000e+00	2043.0
9	TraesCS6B01G339800	chr6D	92.079	808	41	6	1383	2190	400089812	400090596	0.000000e+00	1116.0
10	TraesCS6B01G339800	chr6D	90.968	155	10	4	64	218	400088542	400088692	3.020000e-49	206.0
11	TraesCS6B01G339800	chr6D	84.324	185	26	1	1358	1539	400089867	400090051	6.580000e-41	178.0
12	TraesCS6B01G339800	chr3B	84.681	235	31	3	2088	2318	417488782	417489015	1.790000e-56	230.0
13	TraesCS6B01G339800	chr3B	93.182	44	3	0	805	848	807976563	807976520	5.350000e-07	65.8
14	TraesCS6B01G339800	chr7B	83.404	235	34	4	2088	2318	35636756	35636523	1.800000e-51	213.0
15	TraesCS6B01G339800	chr7D	82.906	234	34	4	2088	2317	104369155	104368924	3.020000e-49	206.0
16	TraesCS6B01G339800	chr4D	82.143	224	36	3	2099	2318	369096904	369096681	3.040000e-44	189.0
17	TraesCS6B01G339800	chr4D	97.143	35	1	0	38	72	178096320	178096354	2.490000e-05	60.2
18	TraesCS6B01G339800	chr1A	80.833	240	42	2	2083	2318	538801338	538801577	3.930000e-43	185.0
19	TraesCS6B01G339800	chr5D	81.818	231	29	11	2088	2312	509287536	509287759	5.090000e-42	182.0
20	TraesCS6B01G339800	chr2A	100.000	44	0	0	554	597	595832087	595832130	5.310000e-12	82.4
21	TraesCS6B01G339800	chr2A	100.000	44	0	0	554	597	595872773	595872816	5.310000e-12	82.4
22	TraesCS6B01G339800	chr3A	90.909	44	4	0	805	848	730116394	730116437	2.490000e-05	60.2

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	TraesCS6B01G339800	chr6B	599121531	599123848	2317	False	2240.50	4281	93.08500	1	2318	2	chr6B.!!$F1	2317
1	TraesCS6B01G339800	chr6A	545883143	545885635	2492	False	917.00	2172	93.25050	72	2318	4	chr6A.!!$F2	2246
2	TraesCS6B01G339800	chr6D	400088542	400090596	2054	False	885.75	2043	90.95775	64	2190	4	chr6D.!!$F1	2126

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
264	301	0.106149	GCCCCGATCGATAACCTTGT	59.894	55.0	18.66	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1855	1898	1.227089	CCATTCGCTCTCCTCCACG	60.227	63.158	0.0	0.0	0.0	4.94	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
21	22	4.899352	GCCCACCATGAAGATAGATAGT	57.101	45.455	0.00	0.00	0.00	2.12
23	24	6.360370	GCCCACCATGAAGATAGATAGTAA	57.640	41.667	0.00	0.00	0.00	2.24
24	25	6.166982	GCCCACCATGAAGATAGATAGTAAC	58.833	44.000	0.00	0.00	0.00	2.50
25	26	6.239600	GCCCACCATGAAGATAGATAGTAACA	60.240	42.308	0.00	0.00	0.00	2.41
26	27	7.527868	GCCCACCATGAAGATAGATAGTAACAT	60.528	40.741	0.00	0.00	0.00	2.71
27	28	7.821359	CCCACCATGAAGATAGATAGTAACATG	59.179	40.741	0.00	0.00	35.26	3.21
28	29	7.332926	CCACCATGAAGATAGATAGTAACATGC	59.667	40.741	0.00	0.00	34.51	4.06
29	30	7.874528	CACCATGAAGATAGATAGTAACATGCA	59.125	37.037	0.00	0.00	34.51	3.96
30	31	8.600668	ACCATGAAGATAGATAGTAACATGCAT	58.399	33.333	0.00	0.00	34.51	3.96
41	42	9.277783	AGATAGTAACATGCATAACAATCTTCC	57.722	33.333	0.00	0.00	0.00	3.46
42	43	6.699575	AGTAACATGCATAACAATCTTCCC	57.300	37.500	0.00	0.00	0.00	3.97
43	44	6.186957	AGTAACATGCATAACAATCTTCCCA	58.813	36.000	0.00	0.00	0.00	4.37
44	45	4.989279	ACATGCATAACAATCTTCCCAC	57.011	40.909	0.00	0.00	0.00	4.61
45	46	4.603131	ACATGCATAACAATCTTCCCACT	58.397	39.130	0.00	0.00	0.00	4.00
46	47	5.754782	ACATGCATAACAATCTTCCCACTA	58.245	37.500	0.00	0.00	0.00	2.74
47	48	6.367983	ACATGCATAACAATCTTCCCACTAT	58.632	36.000	0.00	0.00	0.00	2.12
48	49	6.263842	ACATGCATAACAATCTTCCCACTATG	59.736	38.462	0.00	0.00	0.00	2.23
49	50	6.000246	TGCATAACAATCTTCCCACTATGA	58.000	37.500	0.00	0.00	0.00	2.15
50	51	6.604171	TGCATAACAATCTTCCCACTATGAT	58.396	36.000	0.00	0.00	0.00	2.45
51	52	6.712095	TGCATAACAATCTTCCCACTATGATC	59.288	38.462	0.00	0.00	0.00	2.92
52	53	6.712095	GCATAACAATCTTCCCACTATGATCA	59.288	38.462	0.00	0.00	0.00	2.92
53	54	7.392673	GCATAACAATCTTCCCACTATGATCAT	59.607	37.037	13.81	13.81	0.00	2.45
54	55	9.948964	CATAACAATCTTCCCACTATGATCATA	57.051	33.333	14.64	14.64	0.00	2.15
79	80	8.524870	AGTAACATAAACTAGTAAACACGTGG	57.475	34.615	21.57	2.04	0.00	4.94
111	112	6.558488	AATGCTGATTTAATTAGGGGCAAA	57.442	33.333	0.00	0.00	32.28	3.68
123	124	9.920946	TTAATTAGGGGCAAAGATATATGATCC	57.079	33.333	0.00	0.00	0.00	3.36
134	135	9.228949	CAAAGATATATGATCCAAAGAAGAGGG	57.771	37.037	0.00	0.00	0.00	4.30
135	136	7.507797	AGATATATGATCCAAAGAAGAGGGG	57.492	40.000	0.00	0.00	0.00	4.79
141	142	5.079643	TGATCCAAAGAAGAGGGGAAAAAG	58.920	41.667	0.00	0.00	32.25	2.27
169	170	9.767684	GAATACAAATAACACATCAATGTCGAA	57.232	29.630	0.00	0.00	39.39	3.71
239	276	8.925700	CAAGAATTAATTAAACTTGCTTCACCC	58.074	33.333	22.93	0.00	32.05	4.61
264	301	0.106149	GCCCCGATCGATAACCTTGT	59.894	55.000	18.66	0.00	0.00	3.16
293	330	1.494721	GAAGATATCCCAAGGCCACCA	59.505	52.381	5.01	0.00	0.00	4.17
403	446	2.516589	CGCATCGATCACACGGTGG	61.517	63.158	13.48	1.73	43.42	4.61
405	448	0.179121	GCATCGATCACACGGTGGTA	60.179	55.000	13.48	0.00	43.42	3.25
812	855	2.360475	GAACTCCTGGCAGTGGGC	60.360	66.667	14.43	0.00	43.74	5.36
1672	1715	1.547755	AGGAGGAGGAGGGACAGGA	60.548	63.158	0.00	0.00	0.00	3.86
1837	1880	1.302832	GGTGGAGGAGTGTTGCAGG	60.303	63.158	0.00	0.00	0.00	4.85
1855	1898	3.140814	GGATGTTTGCCGGAGCCC	61.141	66.667	5.05	0.00	38.69	5.19
1962	2005	4.788690	CATGCACCATCTACTAGTACGAG	58.211	47.826	0.00	0.91	0.00	4.18
2043	2393	1.558741	CTGCGCTGTTTGCTTTCAAA	58.441	45.000	9.73	0.00	39.67	2.69
2044	2394	1.925847	CTGCGCTGTTTGCTTTCAAAA	59.074	42.857	9.73	0.00	43.12	2.44
2045	2395	2.341257	TGCGCTGTTTGCTTTCAAAAA	58.659	38.095	9.73	0.00	43.12	1.94
2091	2441	3.119990	TGCGCTGTTAGCCTGTTATTTTC	60.120	43.478	9.73	0.00	38.18	2.29
2095	2445	5.569059	CGCTGTTAGCCTGTTATTTTCTTTG	59.431	40.000	0.00	0.00	38.18	2.77
2096	2446	6.567701	CGCTGTTAGCCTGTTATTTTCTTTGA	60.568	38.462	0.00	0.00	38.18	2.69
2097	2447	7.315890	GCTGTTAGCCTGTTATTTTCTTTGAT	58.684	34.615	0.00	0.00	34.48	2.57
2102	2453	7.158099	AGCCTGTTATTTTCTTTGATACACC	57.842	36.000	0.00	0.00	0.00	4.16
2171	2522	9.753674	TTTGATCTAAGACCCAAGAAAATACAT	57.246	29.630	0.00	0.00	0.00	2.29
2234	2588	9.904198	TGAAAACATCTTCATGGTATCAATCTA	57.096	29.630	0.00	0.00	33.82	1.98
2248	2602	8.585018	TGGTATCAATCTATGCTCGAAGAAATA	58.415	33.333	0.00	0.00	34.09	1.40
2255	2609	6.507900	TCTATGCTCGAAGAAATACTCCAAG	58.492	40.000	0.00	0.00	34.09	3.61
2256	2610	3.861840	TGCTCGAAGAAATACTCCAAGG	58.138	45.455	0.00	0.00	34.09	3.61
2272	2626	2.302157	CCAAGGACTTCGGTAAAGAGGT	59.698	50.000	0.00	0.00	38.44	3.85
2283	2637	5.741011	TCGGTAAAGAGGTTGCAATTAGAT	58.259	37.500	0.59	0.00	0.00	1.98
2285	2639	7.332557	TCGGTAAAGAGGTTGCAATTAGATTA	58.667	34.615	0.59	0.00	0.00	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.899352	ACTATCTATCTTCATGGTGGGC	57.101	45.455	0.00	0.00	0.00	5.36
1	2	7.303182	TGTTACTATCTATCTTCATGGTGGG	57.697	40.000	0.00	0.00	0.00	4.61
3	4	7.874528	TGCATGTTACTATCTATCTTCATGGTG	59.125	37.037	0.00	0.00	34.13	4.17
4	5	7.966812	TGCATGTTACTATCTATCTTCATGGT	58.033	34.615	0.00	0.00	34.13	3.55
15	16	9.277783	GGAAGATTGTTATGCATGTTACTATCT	57.722	33.333	19.43	19.43	35.58	1.98
16	17	8.507249	GGGAAGATTGTTATGCATGTTACTATC	58.493	37.037	10.16	14.84	0.00	2.08
17	18	7.998383	TGGGAAGATTGTTATGCATGTTACTAT	59.002	33.333	10.16	7.20	0.00	2.12
18	19	7.282224	GTGGGAAGATTGTTATGCATGTTACTA	59.718	37.037	10.16	2.45	0.00	1.82
19	20	6.095440	GTGGGAAGATTGTTATGCATGTTACT	59.905	38.462	10.16	0.00	0.00	2.24
20	21	6.095440	AGTGGGAAGATTGTTATGCATGTTAC	59.905	38.462	10.16	5.50	0.00	2.50
21	22	6.186957	AGTGGGAAGATTGTTATGCATGTTA	58.813	36.000	10.16	0.00	0.00	2.41
22	23	5.018809	AGTGGGAAGATTGTTATGCATGTT	58.981	37.500	10.16	0.00	0.00	2.71
23	24	4.603131	AGTGGGAAGATTGTTATGCATGT	58.397	39.130	10.16	0.00	0.00	3.21
24	25	6.487668	TCATAGTGGGAAGATTGTTATGCATG	59.512	38.462	10.16	0.00	0.00	4.06
25	26	6.604171	TCATAGTGGGAAGATTGTTATGCAT	58.396	36.000	3.79	3.79	0.00	3.96
26	27	6.000246	TCATAGTGGGAAGATTGTTATGCA	58.000	37.500	0.00	0.00	0.00	3.96
27	28	6.712095	TGATCATAGTGGGAAGATTGTTATGC	59.288	38.462	0.00	0.00	0.00	3.14
28	29	8.859236	ATGATCATAGTGGGAAGATTGTTATG	57.141	34.615	6.36	0.00	0.00	1.90
53	54	9.624697	CCACGTGTTTACTAGTTTATGTTACTA	57.375	33.333	15.65	0.00	0.00	1.82
54	55	8.359642	TCCACGTGTTTACTAGTTTATGTTACT	58.640	33.333	15.65	0.00	0.00	2.24
55	56	8.519492	TCCACGTGTTTACTAGTTTATGTTAC	57.481	34.615	15.65	0.00	0.00	2.50
56	57	9.539825	TTTCCACGTGTTTACTAGTTTATGTTA	57.460	29.630	15.65	0.00	0.00	2.41
57	58	8.436046	TTTCCACGTGTTTACTAGTTTATGTT	57.564	30.769	15.65	0.00	0.00	2.71
58	59	8.436046	TTTTCCACGTGTTTACTAGTTTATGT	57.564	30.769	15.65	0.00	0.00	2.29
59	60	9.161684	GTTTTTCCACGTGTTTACTAGTTTATG	57.838	33.333	15.65	0.00	0.00	1.90
60	61	8.344831	GGTTTTTCCACGTGTTTACTAGTTTAT	58.655	33.333	15.65	0.00	35.97	1.40
61	62	7.335422	TGGTTTTTCCACGTGTTTACTAGTTTA	59.665	33.333	15.65	0.00	41.93	2.01
62	63	6.150809	TGGTTTTTCCACGTGTTTACTAGTTT	59.849	34.615	15.65	0.00	41.93	2.66
63	64	5.647225	TGGTTTTTCCACGTGTTTACTAGTT	59.353	36.000	15.65	0.00	41.93	2.24
64	65	5.184711	TGGTTTTTCCACGTGTTTACTAGT	58.815	37.500	15.65	0.00	41.93	2.57
65	66	5.738118	TGGTTTTTCCACGTGTTTACTAG	57.262	39.130	15.65	0.00	41.93	2.57
90	91	5.268387	TCTTTGCCCCTAATTAAATCAGCA	58.732	37.500	0.00	0.00	0.00	4.41
105	106	7.667219	TCTTCTTTGGATCATATATCTTTGCCC	59.333	37.037	0.00	0.00	0.00	5.36
111	112	7.259391	TCCCCTCTTCTTTGGATCATATATCT	58.741	38.462	0.00	0.00	0.00	1.98
123	124	5.852282	TTCACTTTTTCCCCTCTTCTTTG	57.148	39.130	0.00	0.00	0.00	2.77
141	142	8.998989	CGACATTGATGTGTTATTTGTATTCAC	58.001	33.333	0.57	0.00	41.95	3.18
254	291	1.800681	GGGTGCGCACAAGGTTATC	59.199	57.895	38.60	20.12	0.00	1.75
264	301	1.069090	GGATATCTTCGGGTGCGCA	59.931	57.895	5.66	5.66	0.00	6.09
293	330	1.163420	TGCGCGTTGAGTTTCCACAT	61.163	50.000	8.43	0.00	0.00	3.21
323	366	0.955428	ACGTGCTGCATCGACCATTT	60.955	50.000	23.94	5.03	0.00	2.32
403	446	1.140375	CCTACAACGACGGGCCTAC	59.860	63.158	0.84	0.00	0.00	3.18
405	448	4.078516	GCCTACAACGACGGGCCT	62.079	66.667	0.84	0.00	38.77	5.19
1837	1880	3.140814	GGCTCCGGCAAACATCCC	61.141	66.667	0.00	0.00	40.87	3.85
1855	1898	1.227089	CCATTCGCTCTCCTCCACG	60.227	63.158	0.00	0.00	0.00	4.94
1962	2005	2.126580	ACGGACACGCTACTTCGC	60.127	61.111	0.00	0.00	46.04	4.70
2071	2421	4.946784	AGAAAATAACAGGCTAACAGCG	57.053	40.909	0.00	0.00	43.62	5.18
2095	2445	8.773404	AGTGTGAATTAAGTTACAGGTGTATC	57.227	34.615	0.30	0.00	0.00	2.24
2096	2446	7.544566	CGAGTGTGAATTAAGTTACAGGTGTAT	59.455	37.037	0.30	0.00	0.00	2.29
2097	2447	6.864685	CGAGTGTGAATTAAGTTACAGGTGTA	59.135	38.462	0.30	0.00	0.00	2.90
2102	2453	9.741168	CAATTACGAGTGTGAATTAAGTTACAG	57.259	33.333	0.30	0.00	0.00	2.74
2111	2462	6.708949	ACCTGTAACAATTACGAGTGTGAATT	59.291	34.615	0.00	0.00	38.98	2.17
2198	2549	7.484007	CCATGAAGATGTTTTCAAGAGATTTCG	59.516	37.037	0.00	0.00	40.21	3.46
2234	2588	4.162320	TCCTTGGAGTATTTCTTCGAGCAT	59.838	41.667	0.00	0.00	32.90	3.79
2236	2590	3.866327	GTCCTTGGAGTATTTCTTCGAGC	59.134	47.826	0.00	0.00	32.90	5.03
2248	2602	3.236896	TCTTTACCGAAGTCCTTGGAGT	58.763	45.455	0.00	0.00	36.70	3.85
2255	2609	2.074576	GCAACCTCTTTACCGAAGTCC	58.925	52.381	0.00	0.00	36.70	3.85
2256	2610	2.762745	TGCAACCTCTTTACCGAAGTC	58.237	47.619	0.00	0.00	36.70	3.01
2272	2626	6.316140	ACATCGTTGCTCTAATCTAATTGCAA	59.684	34.615	0.00	0.00	37.96	4.08
2283	2637	3.987868	GAGTGACAACATCGTTGCTCTAA	59.012	43.478	6.77	0.00	0.00	2.10
2285	2639	2.036475	AGAGTGACAACATCGTTGCTCT	59.964	45.455	6.77	7.90	0.00	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.