AutoCloner

Multiple sequence alignment - TraesCS3B01G451400

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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	TraesCS3B01G451400	chr3B	100.000	3536	0	0	1	3536	691924939	691921404	0.000000e+00	6530.0
1	TraesCS3B01G451400	chr3B	95.153	392	13	1	770	1161	691752360	691751975	6.490000e-172	614.0
2	TraesCS3B01G451400	chr3B	84.202	595	46	17	1158	1752	691751891	691751345	5.200000e-148	534.0
3	TraesCS3B01G451400	chr3B	91.509	318	17	4	2482	2795	691750441	691750130	2.520000e-116	429.0
4	TraesCS3B01G451400	chr3B	82.411	506	35	23	1604	2097	691751346	691750883	3.310000e-105	392.0
5	TraesCS3B01G451400	chr3B	87.919	149	6	4	1604	1752	691751391	691751255	7.850000e-37	165.0
6	TraesCS3B01G451400	chr3B	93.000	100	4	1	1604	1703	691923285	691923189	3.680000e-30	143.0
7	TraesCS3B01G451400	chr3B	93.000	100	4	1	1655	1751	691923336	691923237	3.680000e-30	143.0
8	TraesCS3B01G451400	chr3B	85.235	149	7	6	1604	1752	691751433	691751300	4.760000e-29	139.0
9	TraesCS3B01G451400	chr3B	87.324	71	3	2	1604	1674	691751301	691751237	3.790000e-10	76.8
10	TraesCS3B01G451400	chr3B	100.000	35	0	0	1617	1651	691751168	691751134	8.190000e-07	65.8
11	TraesCS3B01G451400	chr3A	91.195	1590	63	19	1216	2795	658984605	658983083	0.000000e+00	2089.0
12	TraesCS3B01G451400	chr3A	85.892	964	79	29	1158	2097	658906754	658905824	0.000000e+00	974.0
13	TraesCS3B01G451400	chr3A	83.358	673	89	16	3	660	658986388	658985724	5.050000e-168	601.0
14	TraesCS3B01G451400	chr3A	89.770	391	17	12	771	1161	658907205	658906838	2.470000e-131	479.0
15	TraesCS3B01G451400	chr3A	90.785	293	18	6	437	725	658907470	658907183	1.990000e-102	383.0
16	TraesCS3B01G451400	chr3A	84.848	396	22	19	770	1158	658985054	658984690	7.210000e-97	364.0
17	TraesCS3B01G451400	chr3A	89.494	257	20	4	2482	2734	658905376	658905123	5.700000e-83	318.0
18	TraesCS3B01G451400	chr3A	84.804	204	23	3	1	202	658935215	658935018	7.740000e-47	198.0
19	TraesCS3B01G451400	chr3A	82.692	156	20	2	48	202	658930317	658930168	7.960000e-27	132.0
20	TraesCS3B01G451400	chr3A	76.761	284	29	16	1828	2097	658906009	658905749	1.330000e-24	124.0
21	TraesCS3B01G451400	chr3A	100.000	33	0	0	732	764	658907299	658907267	1.060000e-05	62.1
22	TraesCS3B01G451400	chr3D	90.022	912	49	18	1158	2066	524647840	524646968	0.000000e+00	1142.0
23	TraesCS3B01G451400	chr3D	83.642	972	56	38	1866	2795	524647258	524646348	0.000000e+00	819.0
24	TraesCS3B01G451400	chr3D	83.986	843	96	25	1604	2419	524310444	524309614	0.000000e+00	773.0
25	TraesCS3B01G451400	chr3D	84.533	750	84	15	1	725	524649029	524648287	0.000000e+00	713.0
26	TraesCS3B01G451400	chr3D	80.619	1001	112	48	1158	2129	524310962	524310015	0.000000e+00	699.0
27	TraesCS3B01G451400	chr3D	90.585	393	20	8	771	1160	524648309	524647931	4.070000e-139	505.0
28	TraesCS3B01G451400	chr3D	89.594	394	24	11	771	1161	524311428	524311049	5.310000e-133	484.0
29	TraesCS3B01G451400	chr3D	91.589	321	21	4	2479	2795	524309461	524309143	4.190000e-119	438.0
30	TraesCS3B01G451400	chr3D	92.614	176	7	4	507	679	524311674	524311502	7.580000e-62	248.0
31	TraesCS3B01G451400	chr3D	87.943	141	15	2	369	509	524312027	524311889	7.850000e-37	165.0
32	TraesCS3B01G451400	chr3D	90.909	110	10	0	616	725	524311515	524311406	7.910000e-32	148.0
33	TraesCS3B01G451400	chr3D	100.000	33	0	0	732	764	524311572	524311540	1.060000e-05	62.1

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	TraesCS3B01G451400	chr3B	691921404	691924939	3535	True	2272.000000	6530	95.333333	1	3536	3	chr3B.!!$R2	3535
1	TraesCS3B01G451400	chr3B	691750130	691752360	2230	True	301.950000	614	89.219125	770	2795	8	chr3B.!!$R1	2025
2	TraesCS3B01G451400	chr3A	658983083	658986388	3305	True	1018.000000	2089	86.467000	3	2795	3	chr3A.!!$R4	2792
3	TraesCS3B01G451400	chr3A	658905123	658907470	2347	True	390.016667	974	88.783667	437	2734	6	chr3A.!!$R3	2297
4	TraesCS3B01G451400	chr3D	524646348	524649029	2681	True	794.750000	1142	87.195500	1	2795	4	chr3D.!!$R2	2794
5	TraesCS3B01G451400	chr3D	524309143	524312027	2884	True	377.137500	773	89.656750	369	2795	8	chr3D.!!$R1	2426

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
708	1628	0.038343	CAGGCACCGAAATTGGGTTG	60.038	55.0	0.0	0.0	34.97	3.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2557	3976	0.736636	TGTATCACGCTGGTAGTCGG	59.263	55.0	0.0	0.0	0.0	4.79	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	Self end TH	Hairpin	End Stability
22	23	2.616842	TCCTTTTGAAAGAACGACTGGC	59.383	45.455	5.09	0.00	38.28	4.85
35	36	2.285083	CGACTGGCCGGATTTTCAATA	58.715	47.619	21.41	0.00	0.00	1.90
45	49	5.560183	GCCGGATTTTCAATACAAGATACCG	60.560	44.000	5.05	0.00	36.09	4.02
65	69	3.557475	CCGGTTGGTGGATAAGTTGTGTA	60.557	47.826	0.00	0.00	0.00	2.90
70	74	5.748670	TGGTGGATAAGTTGTGTAAGCTA	57.251	39.130	0.00	0.00	0.00	3.32
131	135	4.345257	GTCCCTTAGTGGCTATTGAGATGA	59.655	45.833	0.00	0.00	0.00	2.92
161	165	0.771755	AGACCAGGGTTGAACCTTCC	59.228	55.000	14.87	0.00	39.34	3.46
169	174	1.272313	GGTTGAACCTTCCCTAACCCC	60.272	57.143	7.20	0.00	35.82	4.95
171	176	0.178897	TGAACCTTCCCTAACCCCGA	60.179	55.000	0.00	0.00	0.00	5.14
217	222	2.667470	CTATCTTCGGTGGGAGGAGAA	58.333	52.381	0.00	0.00	33.86	2.87
219	224	0.903454	TCTTCGGTGGGAGGAGAACC	60.903	60.000	0.00	0.00	0.00	3.62
262	267	0.893727	AACCGCTGGGAAATGGTCAC	60.894	55.000	0.00	0.00	36.97	3.67
265	270	0.321564	CGCTGGGAAATGGTCACTCA	60.322	55.000	0.00	0.00	0.00	3.41
274	279	4.825085	GGAAATGGTCACTCAGGTTACAAA	59.175	41.667	0.00	0.00	0.00	2.83
276	281	6.183360	GGAAATGGTCACTCAGGTTACAAAAA	60.183	38.462	0.00	0.00	0.00	1.94
277	282	6.976934	AATGGTCACTCAGGTTACAAAAAT	57.023	33.333	0.00	0.00	0.00	1.82
320	330	3.630312	TGAGGCATCATGATCATGTGTTG	59.370	43.478	30.01	24.96	39.72	3.33
337	347	7.490725	TCATGTGTTGTTTTCGATTGTTTCAAT	59.509	29.630	0.00	0.00	0.00	2.57
407	427	5.773575	ACTATGTGGTAGTAGAATGATGCG	58.226	41.667	0.00	0.00	41.84	4.73
426	447	2.034685	GCGTACATCTATCAGTGCAGGA	59.965	50.000	0.00	0.00	0.00	3.86
433	454	0.252696	TATCAGTGCAGGACCTGGGT	60.253	55.000	23.09	5.08	31.21	4.51
495	518	4.142578	TGTGACACGTTAGCACAAATTGTT	60.143	37.500	11.22	0.00	39.36	2.83
541	780	1.819632	GTAAGCATCCCACCAGGCG	60.820	63.158	0.00	0.00	34.51	5.52
580	820	4.333649	CCATCAAATATGGCTCGCGAATAT	59.666	41.667	11.33	8.16	31.75	1.28
691	1611	2.757868	TGGAAATTTACATTCCCGCCAG	59.242	45.455	0.00	0.00	44.72	4.85

Showing 1 to 25 of 621 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	1.094785	ATTGAAAATCCGGCCAGTCG	58.905	50.000	2.24	0.00	0.00	4.18
22	23	5.049680	CCGGTATCTTGTATTGAAAATCCGG	60.050	44.000	0.00	0.00	44.87	5.14
35	36	1.354101	TCCACCAACCGGTATCTTGT	58.646	50.000	8.00	0.00	46.94	3.16
45	49	4.082949	GCTTACACAACTTATCCACCAACC	60.083	45.833	0.00	0.00	0.00	3.77
65	69	8.418597	AGGCATGATTCATCAATAATTAGCTT	57.581	30.769	0.00	0.00	40.69	3.74
70	74	6.210784	CCCAGAGGCATGATTCATCAATAATT	59.789	38.462	0.00	0.00	40.69	1.40
114	118	5.532557	CATTCGTCATCTCAATAGCCACTA	58.467	41.667	0.00	0.00	0.00	2.74
115	119	4.375272	CATTCGTCATCTCAATAGCCACT	58.625	43.478	0.00	0.00	0.00	4.00
119	123	4.053983	TCTGCATTCGTCATCTCAATAGC	58.946	43.478	0.00	0.00	0.00	2.97
122	126	4.569966	GTCTTCTGCATTCGTCATCTCAAT	59.430	41.667	0.00	0.00	0.00	2.57
131	135	0.036010	CCCTGGTCTTCTGCATTCGT	60.036	55.000	0.00	0.00	0.00	3.85
161	165	2.687935	CCAATTGATTGTCGGGGTTAGG	59.312	50.000	7.12	0.00	36.06	2.69
169	174	4.142622	ACACACATAGCCAATTGATTGTCG	60.143	41.667	7.12	1.84	36.06	4.35
171	176	4.082081	CCACACACATAGCCAATTGATTGT	60.082	41.667	7.12	2.10	36.06	2.71
217	222	3.704231	GAGTCCATGCATGCCCGGT	62.704	63.158	21.69	3.14	0.00	5.28
219	224	2.903855	GGAGTCCATGCATGCCCG	60.904	66.667	21.69	8.13	0.00	6.13
221	226	1.826921	CCTGGAGTCCATGCATGCC	60.827	63.158	21.69	16.61	30.82	4.40
254	259	6.976934	ATTTTTGTAACCTGAGTGACCATT	57.023	33.333	0.00	0.00	0.00	3.16
277	282	9.109393	GCCTCATGTGTCACTAATCTAATTAAA	57.891	33.333	4.27	0.00	0.00	1.52
346	356	7.264294	AGAGAGGACAAGATCAATTAAACCT	57.736	36.000	0.00	0.00	0.00	3.50
403	423	3.553715	CCTGCACTGATAGATGTACGCAT	60.554	47.826	0.00	0.00	38.18	4.73
407	427	3.639094	AGGTCCTGCACTGATAGATGTAC	59.361	47.826	0.00	0.00	0.00	2.90
418	439	0.178990	GAAAACCCAGGTCCTGCACT	60.179	55.000	13.99	0.00	0.00	4.40
419	440	0.178990	AGAAAACCCAGGTCCTGCAC	60.179	55.000	13.99	0.95	0.00	4.57
433	454	7.771826	TCTTTCTTTCGAAAAGAGGGTAGAAAA	59.228	33.333	12.41	4.44	38.58	2.29

Showing 1 to 25 of 619 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.