AutoCloner

Multiple sequence alignment - TraesCS3B01G148600

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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	TraesCS3B01G148600	chr3B	100.000	4270	0	0	1	4270	139835505	139831236	0.000000e+00	7886.0
1	TraesCS3B01G148600	chr3B	78.813	1095	144	42	2329	3401	139779147	139778119	0.000000e+00	656.0
2	TraesCS3B01G148600	chr3B	77.347	1161	172	60	1158	2268	139780391	139779272	1.700000e-168	603.0
3	TraesCS3B01G148600	chr3B	80.000	130	17	4	393	522	139781104	139780984	2.120000e-13	87.9
4	TraesCS3B01G148600	chr3B	100.000	31	0	0	319	349	139835159	139835129	1.660000e-04	58.4
5	TraesCS3B01G148600	chr3B	100.000	31	0	0	347	377	139835187	139835157	1.660000e-04	58.4
6	TraesCS3B01G148600	chr3A	88.145	4285	268	91	100	4270	106679809	106675651	0.000000e+00	4878.0
7	TraesCS3B01G148600	chr3A	93.995	766	41	2	3137	3897	106674680	106673915	0.000000e+00	1155.0
8	TraesCS3B01G148600	chr3A	78.403	1102	144	46	2329	3409	106661981	106660953	7.790000e-177	630.0
9	TraesCS3B01G148600	chr3A	89.933	447	36	7	3592	4035	106673478	106673038	6.200000e-158	568.0
10	TraesCS3B01G148600	chr3A	79.510	776	110	29	1067	1816	106663278	106662526	1.370000e-139	507.0
11	TraesCS3B01G148600	chr3A	91.327	196	17	0	2052	2247	106662290	106662095	7.040000e-68	268.0
12	TraesCS3B01G148600	chr3D	90.681	2468	127	44	863	3284	90381885	90379475	0.000000e+00	3188.0
13	TraesCS3B01G148600	chr3D	79.317	1112	149	44	2329	3409	90373826	90372765	0.000000e+00	704.0
14	TraesCS3B01G148600	chr3D	88.514	592	19	8	234	819	90382718	90382170	0.000000e+00	671.0
15	TraesCS3B01G148600	chr3D	84.626	696	52	20	3261	3953	90379471	90378828	3.600000e-180	641.0
16	TraesCS3B01G148600	chr3D	76.048	1169	174	68	1154	2268	90375064	90373948	1.060000e-140	510.0
17	TraesCS3B01G148600	chr3D	86.726	226	21	8	3	222	90391355	90391577	4.270000e-60	243.0
18	TraesCS3B01G148600	chr3D	85.455	55	8	0	393	447	90375773	90375719	1.660000e-04	58.4
19	TraesCS3B01G148600	chr7D	76.940	464	74	17	3822	4269	562645558	562645112	2.570000e-57	233.0
20	TraesCS3B01G148600	chr5A	90.854	164	15	0	2052	2215	311157734	311157571	2.000000e-53	220.0
21	TraesCS3B01G148600	chr4B	77.031	357	53	20	2339	2672	20366576	20366226	1.220000e-40	178.0
22	TraesCS3B01G148600	chr4B	73.301	412	88	15	2059	2455	20360638	20361042	9.630000e-27	132.0
23	TraesCS3B01G148600	chr4D	72.540	630	126	35	2059	2672	10834667	10835265	1.230000e-35	161.0
24	TraesCS3B01G148600	chr6D	83.636	165	23	4	3626	3786	143476621	143476457	7.400000e-33	152.0
25	TraesCS3B01G148600	chr6D	79.703	202	35	6	3627	3824	181729736	181729537	1.600000e-29	141.0
26	TraesCS3B01G148600	chr4A	82.286	175	31	0	2059	2233	592530375	592530549	7.400000e-33	152.0
27	TraesCS3B01G148600	chr4A	82.286	175	31	0	2059	2233	592816719	592816893	7.400000e-33	152.0
28	TraesCS3B01G148600	chr4A	82.286	175	31	0	2059	2233	593096932	593097106	7.400000e-33	152.0
29	TraesCS3B01G148600	chr6A	83.636	165	22	5	3626	3786	234170883	234170720	2.660000e-32	150.0
30	TraesCS3B01G148600	chr1B	83.030	165	24	4	3626	3786	449252302	449252138	3.440000e-31	147.0
31	TraesCS3B01G148600	chr2D	79.897	194	36	3	3628	3818	589535632	589535439	5.760000e-29	139.0
32	TraesCS3B01G148600	chr1D	79.208	202	37	5	3627	3824	481698014	481697814	7.450000e-28	135.0

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	TraesCS3B01G148600	chr3B	139831236	139835505	4269	True	2667.600000	7886	100.000000	1	4270	3	chr3B.!!$R2	4269
1	TraesCS3B01G148600	chr3B	139778119	139781104	2985	True	448.966667	656	78.720000	393	3401	3	chr3B.!!$R1	3008
2	TraesCS3B01G148600	chr3A	106673038	106679809	6771	True	2200.333333	4878	90.691000	100	4270	3	chr3A.!!$R2	4170
3	TraesCS3B01G148600	chr3A	106660953	106663278	2325	True	468.333333	630	83.080000	1067	3409	3	chr3A.!!$R1	2342
4	TraesCS3B01G148600	chr3D	90372765	90382718	9953	True	962.066667	3188	84.106833	234	3953	6	chr3D.!!$R1	3719

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
626	700	0.460987	GCAGCTGTGCGAGATAACCT	60.461	55.0	16.64	40.71	3.50	F
1948	2383	0.178068	ACACACGCAACACCTCTTCT	59.822	50.0	0.00	0.00	2.85	F
3204	3802	0.106268	TGCTCCACCAAAAGCCAAGA	60.106	50.0	0.00	37.73	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2324	2845	0.110238	GCACTCGTCCAACGTACGTA	60.110	55.000	23.12	2.73	43.14	3.57	R
3253	3851	0.322546	GGATCAACGGCCCAAGAACT	60.323	55.000	0.00	0.00	0.00	3.01	R
4152	4955	1.199097	CTTTGTCAATTTAGGCGCCGT	59.801	47.619	23.20	12.38	0.00	5.68	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability
23	24	6.024552	TGAATTTGAGGTTTGTAGCATTCC	57.975	37.500	3.01
24	25	5.047377	TGAATTTGAGGTTTGTAGCATTCCC	60.047	40.000	3.97
25	26	3.806949	TTGAGGTTTGTAGCATTCCCT	57.193	42.857	4.20
26	27	4.919774	TTGAGGTTTGTAGCATTCCCTA	57.080	40.909	3.53
27	28	4.919774	TGAGGTTTGTAGCATTCCCTAA	57.080	40.909	2.69
28	29	5.249780	TGAGGTTTGTAGCATTCCCTAAA	57.750	39.130	1.85
29	30	5.826643	TGAGGTTTGTAGCATTCCCTAAAT	58.173	37.500	1.40
30	31	5.885912	TGAGGTTTGTAGCATTCCCTAAATC	59.114	40.000	2.17
31	32	5.826643	AGGTTTGTAGCATTCCCTAAATCA	58.173	37.500	2.57
32	33	6.435164	AGGTTTGTAGCATTCCCTAAATCAT	58.565	36.000	2.45
33	34	6.547510	AGGTTTGTAGCATTCCCTAAATCATC	59.452	38.462	2.92
34	35	6.321181	GGTTTGTAGCATTCCCTAAATCATCA	59.679	38.462	3.07
35	36	7.147915	GGTTTGTAGCATTCCCTAAATCATCAA	60.148	37.037	2.57
36	37	6.942532	TGTAGCATTCCCTAAATCATCAAC	57.057	37.500	3.18
37	38	6.662755	TGTAGCATTCCCTAAATCATCAACT	58.337	36.000	3.16
38	39	7.118723	TGTAGCATTCCCTAAATCATCAACTT	58.881	34.615	2.66
39	40	6.461110	AGCATTCCCTAAATCATCAACTTG	57.539	37.500	3.16
40	41	6.189859	AGCATTCCCTAAATCATCAACTTGA	58.810	36.000	3.02
41	42	6.320672	AGCATTCCCTAAATCATCAACTTGAG	59.679	38.462	3.02
42	43	6.096001	GCATTCCCTAAATCATCAACTTGAGT	59.904	38.462	3.41
43	44	7.283127	GCATTCCCTAAATCATCAACTTGAGTA	59.717	37.037	2.59
44	45	9.347240	CATTCCCTAAATCATCAACTTGAGTAT	57.653	33.333	2.12
45	46	8.737168	TTCCCTAAATCATCAACTTGAGTATG	57.263	34.615	2.39
46	47	7.861629	TCCCTAAATCATCAACTTGAGTATGT	58.138	34.615	2.29
47	48	8.328758	TCCCTAAATCATCAACTTGAGTATGTT	58.671	33.333	2.71

Showing 1 to 25 of 164 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	End Stability
0	1	5.047377	GGGAATGCTACAAACCTCAAATTCA	60.047	40.000	0.00	0.00	2.57
1	2	5.185828	AGGGAATGCTACAAACCTCAAATTC	59.814	40.000	0.00	0.00	2.17
2	3	5.086621	AGGGAATGCTACAAACCTCAAATT	58.913	37.500	0.00	0.00	1.82
3	4	4.677182	AGGGAATGCTACAAACCTCAAAT	58.323	39.130	0.00	0.00	2.32
5	6	3.806949	AGGGAATGCTACAAACCTCAA	57.193	42.857	0.00	0.00	3.02
6	7	4.919774	TTAGGGAATGCTACAAACCTCA	57.080	40.909	0.00	0.00	3.86
7	8	5.885912	TGATTTAGGGAATGCTACAAACCTC	59.114	40.000	0.00	0.00	3.85
8	9	5.826643	TGATTTAGGGAATGCTACAAACCT	58.173	37.500	0.00	0.00	3.50
9	10	6.321181	TGATGATTTAGGGAATGCTACAAACC	59.679	38.462	0.00	0.00	3.27
10	11	7.333528	TGATGATTTAGGGAATGCTACAAAC	57.666	36.000	0.00	0.00	2.93
11	12	7.615365	AGTTGATGATTTAGGGAATGCTACAAA	59.385	33.333	0.00	0.00	2.83
12	13	7.118723	AGTTGATGATTTAGGGAATGCTACAA	58.881	34.615	0.00	0.00	2.41
13	14	6.662755	AGTTGATGATTTAGGGAATGCTACA	58.337	36.000	0.00	0.00	2.74
15	16	7.345691	TCAAGTTGATGATTTAGGGAATGCTA	58.654	34.615	0.08	0.00	3.49
16	17	6.189859	TCAAGTTGATGATTTAGGGAATGCT	58.810	36.000	0.08	0.00	3.79
17	18	6.096001	ACTCAAGTTGATGATTTAGGGAATGC	59.904	38.462	5.91	0.00	3.56
18	19	7.636150	ACTCAAGTTGATGATTTAGGGAATG	57.364	36.000	5.91	0.00	2.67
19	20	9.347240	CATACTCAAGTTGATGATTTAGGGAAT	57.653	33.333	5.91	0.00	3.01
20	21	8.328758	ACATACTCAAGTTGATGATTTAGGGAA	58.671	33.333	5.91	0.00	3.97
21	22	7.861629	ACATACTCAAGTTGATGATTTAGGGA	58.138	34.615	5.91	0.00	4.20
22	23	8.511604	AACATACTCAAGTTGATGATTTAGGG	57.488	34.615	5.91	0.00	3.53
23	24	9.994432	GAAACATACTCAAGTTGATGATTTAGG	57.006	33.333	5.91	0.00	2.69
26	27	9.903682	CAAGAAACATACTCAAGTTGATGATTT	57.096	29.630	5.91	5.82	2.17
27	28	9.071276	ACAAGAAACATACTCAAGTTGATGATT	57.929	29.630	5.91	3.23	2.57
28	29	8.627208	ACAAGAAACATACTCAAGTTGATGAT	57.373	30.769	5.91	0.00	2.45

Showing 1 to 25 of 179 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.