AutoCloner

Multiple sequence alignment - TraesCS2B01G335200

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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	TraesCS2B01G335200	chr2B	100.000	5994	0	0	1	5994	478891717	478897710	0.000000e+00	11069.0
1	TraesCS2B01G335200	chr2B	95.238	231	8	3	74	302	237318334	237318563	4.420000e-96	363.0
2	TraesCS2B01G335200	chr2D	92.208	3465	142	51	317	3722	404404264	404400869	0.000000e+00	4785.0
3	TraesCS2B01G335200	chr2D	89.846	1300	68	28	4485	5758	404399413	404398152	0.000000e+00	1611.0
4	TraesCS2B01G335200	chr2D	93.575	607	38	1	3871	4477	404400622	404400017	0.000000e+00	904.0
5	TraesCS2B01G335200	chr2D	87.383	214	13	8	5781	5994	404398100	404397901	3.610000e-57	233.0
6	TraesCS2B01G335200	chr2D	98.182	55	1	0	3746	3800	404400870	404400816	4.940000e-16	97.1
7	TraesCS2B01G335200	chr2A	91.069	3359	178	49	505	3800	542663737	542660438	0.000000e+00	4429.0
8	TraesCS2B01G335200	chr2A	90.949	1149	72	19	4480	5618	542659165	542658039	0.000000e+00	1517.0
9	TraesCS2B01G335200	chr2A	95.222	607	28	1	3871	4477	542660309	542659704	0.000000e+00	959.0
10	TraesCS2B01G335200	chr2A	82.081	173	10	2	308	479	542663946	542663794	1.750000e-25	128.0
11	TraesCS2B01G335200	chr7B	96.364	220	8	0	75	294	44809706	44809487	4.420000e-96	363.0
12	TraesCS2B01G335200	chr4A	95.495	222	10	0	75	296	675226330	675226109	7.390000e-94	355.0
13	TraesCS2B01G335200	chr4A	92.857	84	6	0	1	84	694884856	694884939	8.160000e-24	122.0
14	TraesCS2B01G335200	chr1B	95.111	225	11	0	75	299	283290447	283290223	7.390000e-94	355.0
15	TraesCS2B01G335200	chr1B	95.495	222	10	0	75	296	596317653	596317874	7.390000e-94	355.0
16	TraesCS2B01G335200	chr1B	93.991	233	13	1	75	307	615614813	615614582	9.560000e-93	351.0
17	TraesCS2B01G335200	chr1B	88.087	277	33	0	20	296	570480224	570479948	4.480000e-86	329.0
18	TraesCS2B01G335200	chr6B	94.397	232	10	3	75	306	279087202	279087430	2.660000e-93	353.0
19	TraesCS2B01G335200	chr5B	94.737	228	11	1	75	302	648994943	648995169	2.660000e-93	353.0
20	TraesCS2B01G335200	chr6A	94.253	87	4	1	1	87	57708353	57708268	1.360000e-26	132.0
21	TraesCS2B01G335200	chr6A	96.203	79	3	0	1	79	603303971	603303893	4.880000e-26	130.0
22	TraesCS2B01G335200	chr4D	95.181	83	4	0	4	86	4098711	4098629	1.360000e-26	132.0
23	TraesCS2B01G335200	chr3B	97.403	77	2	0	1	77	564250122	564250198	1.360000e-26	132.0
24	TraesCS2B01G335200	chr3B	97.403	77	2	0	1	77	786512737	786512813	1.360000e-26	132.0
25	TraesCS2B01G335200	chr3D	95.000	80	4	0	1	80	554686242	554686321	6.310000e-25	126.0
26	TraesCS2B01G335200	chr4B	85.577	104	15	0	6	109	551080521	551080624	6.350000e-20	110.0

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	TraesCS2B01G335200	chr2B	478891717	478897710	5993	False	11069.00	11069	100.00000	1	5994	1	chr2B.!!$F2	5993
1	TraesCS2B01G335200	chr2D	404397901	404404264	6363	True	1526.02	4785	92.23880	317	5994	5	chr2D.!!$R1	5677
2	TraesCS2B01G335200	chr2A	542658039	542663946	5907	True	1758.25	4429	89.83025	308	5618	4	chr2A.!!$R1	5310

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
174	175	0.029834	GCATTGGGAAGCGCTATGTG	59.970	55.0	12.05	5.56	33.74	3.21	F
293	294	0.043334	ACTCCCACTATGACCAGCCT	59.957	55.0	0.00	0.00	0.00	4.58	F
1295	1376	0.172127	GCGATCTGCTGTGACTCTGA	59.828	55.0	0.00	0.00	41.73	3.27	F
2412	2535	0.040157	CGAGTGTTCACCGTTCGGTA	60.040	55.0	16.51	0.00	36.64	4.02	F
3273	3413	0.899717	TTTGGGATGCCTTGACTGCC	60.900	55.0	4.35	0.00	0.00	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1316	1397	0.166814	GTCGAACATCTGCAACCAGC	59.833	55.0	0.00	0.00	45.96	4.85	R
1820	1933	1.645034	AAACGATGATCAGCCGACAG	58.355	50.0	22.04	4.55	0.00	3.51	R
2554	2678	0.993509	TCTAAGGGGGCCAATCTGGG	60.994	60.0	4.39	0.00	38.19	4.45	R
3312	3452	0.171679	CAATTTGATCCGCTGCAGCA	59.828	50.0	36.03	20.16	42.21	4.41	R
5188	6069	0.108945	AGAGGTAGCCGTTAACACGC	60.109	55.0	6.39	6.49	45.72	5.34	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	Self any TH	Hairpin	End Stability
45	46	9.788960	AAAACTTTGACTTAGAACAAAAGCTAG	57.211	29.630	0.00	35.95	3.42
46	47	8.732746	AACTTTGACTTAGAACAAAAGCTAGA	57.267	30.769	0.00	35.95	2.43
47	48	8.732746	ACTTTGACTTAGAACAAAAGCTAGAA	57.267	30.769	0.00	35.95	2.10
48	49	8.831550	ACTTTGACTTAGAACAAAAGCTAGAAG	58.168	33.333	0.00	35.95	2.85
49	50	8.732746	TTTGACTTAGAACAAAAGCTAGAAGT	57.267	30.769	0.00	33.90	3.01
50	51	9.826574	TTTGACTTAGAACAAAAGCTAGAAGTA	57.173	29.630	0.00	33.90	2.24
51	52	8.813643	TGACTTAGAACAAAAGCTAGAAGTAC	57.186	34.615	0.00	0.00	2.73
52	53	8.418662	TGACTTAGAACAAAAGCTAGAAGTACA	58.581	33.333	0.00	0.00	2.90
53	54	8.590719	ACTTAGAACAAAAGCTAGAAGTACAC	57.409	34.615	0.00	0.00	2.90
54	55	8.422566	ACTTAGAACAAAAGCTAGAAGTACACT	58.577	33.333	0.00	0.00	3.55
55	56	9.262358	CTTAGAACAAAAGCTAGAAGTACACTT	57.738	33.333	0.00	39.23	3.16
58	59	9.780186	AGAACAAAAGCTAGAAGTACACTTATT	57.220	29.630	0.00	36.11	1.40
60	61	8.240883	ACAAAAGCTAGAAGTACACTTATTCG	57.759	34.615	0.00	36.11	3.34
61	62	6.889019	AAAGCTAGAAGTACACTTATTCGC	57.111	37.500	0.00	36.11	4.70
62	63	4.599047	AGCTAGAAGTACACTTATTCGCG	58.401	43.478	0.00	36.11	5.87
63	64	3.729716	GCTAGAAGTACACTTATTCGCGG	59.270	47.826	6.13	36.11	6.46
64	65	4.497006	GCTAGAAGTACACTTATTCGCGGA	60.497	45.833	6.13	36.11	5.54
65	66	3.767278	AGAAGTACACTTATTCGCGGAC	58.233	45.455	6.13	36.11	4.79
66	67	3.192001	AGAAGTACACTTATTCGCGGACA	59.808	43.478	6.13	36.11	4.02
67	68	3.146618	AGTACACTTATTCGCGGACAG	57.853	47.619	6.13	0.00	3.51
68	69	2.751259	AGTACACTTATTCGCGGACAGA	59.249	45.455	6.13	0.00	3.41
69	70	2.279582	ACACTTATTCGCGGACAGAG	57.720	50.000	6.13	0.00	3.35
70	71	1.135083	ACACTTATTCGCGGACAGAGG	60.135	52.381	6.13	0.00	3.69
71	72	0.460311	ACTTATTCGCGGACAGAGGG	59.540	55.000	6.13	0.00	4.30
72	73	0.744874	CTTATTCGCGGACAGAGGGA	59.255	55.000	6.13	0.00	4.20

Showing 1 to 25 of 426 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	9.788960	CTAGCTTTTGTTCTAAGTCAAAGTTTT	57.211	29.630	0.00	0.00	35.47	2.43
20	21	9.174166	TCTAGCTTTTGTTCTAAGTCAAAGTTT	57.826	29.630	0.00	0.00	35.47	2.66
21	22	8.732746	TCTAGCTTTTGTTCTAAGTCAAAGTT	57.267	30.769	0.00	0.00	35.47	2.66
22	23	8.732746	TTCTAGCTTTTGTTCTAAGTCAAAGT	57.267	30.769	0.00	0.00	35.47	2.66
23	24	8.831550	ACTTCTAGCTTTTGTTCTAAGTCAAAG	58.168	33.333	0.00	0.00	35.47	2.77
24	25	8.732746	ACTTCTAGCTTTTGTTCTAAGTCAAA	57.267	30.769	0.00	0.00	32.75	2.69
25	26	9.257651	GTACTTCTAGCTTTTGTTCTAAGTCAA	57.742	33.333	0.00	0.00	0.00	3.18
26	27	8.418662	TGTACTTCTAGCTTTTGTTCTAAGTCA	58.581	33.333	0.00	0.00	0.00	3.41
27	28	8.701540	GTGTACTTCTAGCTTTTGTTCTAAGTC	58.298	37.037	0.00	0.00	0.00	3.01
28	29	8.422566	AGTGTACTTCTAGCTTTTGTTCTAAGT	58.577	33.333	0.00	0.00	0.00	2.24
29	30	8.819643	AGTGTACTTCTAGCTTTTGTTCTAAG	57.180	34.615	0.00	0.00	0.00	2.18
32	33	9.780186	AATAAGTGTACTTCTAGCTTTTGTTCT	57.220	29.630	0.00	0.00	37.40	3.01
34	35	8.709646	CGAATAAGTGTACTTCTAGCTTTTGTT	58.290	33.333	0.00	0.00	37.40	2.83
35	36	7.148623	GCGAATAAGTGTACTTCTAGCTTTTGT	60.149	37.037	0.00	0.00	37.40	2.83
36	37	7.174082	GCGAATAAGTGTACTTCTAGCTTTTG	58.826	38.462	0.00	0.00	37.40	2.44
37	38	6.034683	CGCGAATAAGTGTACTTCTAGCTTTT	59.965	38.462	0.00	0.00	37.40	2.27
38	39	5.515626	CGCGAATAAGTGTACTTCTAGCTTT	59.484	40.000	0.00	0.00	37.40	3.51
39	40	5.035443	CGCGAATAAGTGTACTTCTAGCTT	58.965	41.667	0.00	0.00	37.40	3.74
40	41	4.497674	CCGCGAATAAGTGTACTTCTAGCT	60.498	45.833	8.23	0.00	37.40	3.32
41	42	3.729716	CCGCGAATAAGTGTACTTCTAGC	59.270	47.826	8.23	3.15	37.40	3.42
42	43	4.968788	GTCCGCGAATAAGTGTACTTCTAG	59.031	45.833	8.23	0.00	37.40	2.43
43	44	4.395854	TGTCCGCGAATAAGTGTACTTCTA	59.604	41.667	8.23	0.00	37.40	2.10
44	45	3.192001	TGTCCGCGAATAAGTGTACTTCT	59.808	43.478	8.23	0.00	37.40	2.85
45	46	3.504863	TGTCCGCGAATAAGTGTACTTC	58.495	45.455	8.23	0.00	37.40	3.01
46	47	3.192001	TCTGTCCGCGAATAAGTGTACTT	59.808	43.478	8.23	2.51	39.85	2.24

Showing 1 to 25 of 414 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.