AutoCloner

Multiple sequence alignment - TraesCS6D01G229400

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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	TraesCS6D01G229400	chr6D	100.000	3570	0	0	624	4193	321776898	321773329	0.000000e+00	6593.0
1	TraesCS6D01G229400	chr6D	100.000	381	0	0	1	381	321777521	321777141	0.000000e+00	704.0
2	TraesCS6D01G229400	chr6D	85.034	147	13	8	4040	4180	56853571	56853428	1.570000e-29	141.0
3	TraesCS6D01G229400	chr6D	85.294	136	14	3	4040	4171	309592477	309592610	7.310000e-28	135.0
4	TraesCS6D01G229400	chr6B	95.806	3624	66	21	624	4193	501770595	501774186	0.000000e+00	5771.0
5	TraesCS6D01G229400	chr6B	89.062	192	13	3	1	186	501770192	501770381	9.070000e-57	231.0
6	TraesCS6D01G229400	chr6B	88.108	185	20	2	3780	3963	487136363	487136180	7.060000e-53	219.0
7	TraesCS6D01G229400	chr6B	88.050	159	7	5	228	381	501770392	501770543	1.200000e-40	178.0
8	TraesCS6D01G229400	chr6B	86.131	137	11	6	4040	4171	477230324	477230457	1.570000e-29	141.0
9	TraesCS6D01G229400	chr6A	95.618	3286	84	22	649	3898	459077453	459074192	0.000000e+00	5216.0
10	TraesCS6D01G229400	chr6A	90.769	260	13	6	1	249	459082033	459081774	1.870000e-88	337.0
11	TraesCS6D01G229400	chr6A	95.652	115	5	0	267	381	459077997	459077883	7.160000e-43	185.0
12	TraesCS6D01G229400	chr6A	90.083	121	10	2	4075	4193	459074155	459074035	5.610000e-34	156.0
13	TraesCS6D01G229400	chr4B	90.286	175	16	1	3789	3963	471307836	471308009	1.170000e-55	228.0
14	TraesCS6D01G229400	chr7A	89.655	174	17	1	3790	3963	230300984	230301156	1.960000e-53	220.0
15	TraesCS6D01G229400	chr5D	89.205	176	17	2	3788	3963	201311966	201312139	7.060000e-53	219.0
16	TraesCS6D01G229400	chr5D	91.667	96	8	0	3962	4057	34800688	34800593	2.630000e-27	134.0
17	TraesCS6D01G229400	chr5D	91.667	96	8	0	3960	4055	128577586	128577681	2.630000e-27	134.0
18	TraesCS6D01G229400	chr4A	89.205	176	16	2	3788	3963	176860123	176859951	2.540000e-52	217.0
19	TraesCS6D01G229400	chr4A	87.368	190	20	4	3775	3963	166729942	166730128	9.130000e-52	215.0
20	TraesCS6D01G229400	chr3B	89.143	175	18	1	3789	3963	254193186	254193013	2.540000e-52	217.0
21	TraesCS6D01G229400	chr3B	95.876	97	4	0	3954	4050	824388922	824389018	1.560000e-34	158.0
22	TraesCS6D01G229400	chr1B	87.943	141	10	5	4040	4175	555630389	555630527	4.340000e-35	159.0
23	TraesCS6D01G229400	chr3A	86.765	136	15	1	4043	4175	102531052	102531187	9.390000e-32	148.0
24	TraesCS6D01G229400	chrUn	97.647	85	2	0	3962	4046	37028911	37028995	3.380000e-31	147.0
25	TraesCS6D01G229400	chr5B	97.647	85	2	0	3962	4046	655891243	655891159	3.380000e-31	147.0
26	TraesCS6D01G229400	chr5B	91.667	96	8	0	3960	4055	140965928	140966023	2.630000e-27	134.0
27	TraesCS6D01G229400	chr5A	85.315	143	16	2	4039	4177	616351690	616351831	4.370000e-30	143.0
28	TraesCS6D01G229400	chr5A	90.816	98	7	2	3960	4056	679658528	679658432	3.400000e-26	130.0
29	TraesCS6D01G229400	chr1D	84.615	143	18	2	4040	4178	461273178	461273320	5.650000e-29	139.0
30	TraesCS6D01G229400	chr1D	87.736	106	13	0	3953	4058	209139268	209139373	1.580000e-24	124.0
31	TraesCS6D01G229400	chr2D	91.579	95	8	0	3959	4053	643235821	643235915	9.460000e-27	132.0
32	TraesCS6D01G229400	chr1A	95.556	45	1	1	2091	2135	569372540	569372497	2.090000e-08	71.3
33	TraesCS6D01G229400	chr3D	100.000	28	0	0	1751	1778	6340602	6340575	8.000000e-03	52.8

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	TraesCS6D01G229400	chr6D	321773329	321777521	4192	True	3648.5	6593	100.000000	1	4193	2	chr6D.!!$R2	4192
1	TraesCS6D01G229400	chr6B	501770192	501774186	3994	False	2060.0	5771	90.972667	1	4193	3	chr6B.!!$F2	4192
2	TraesCS6D01G229400	chr6A	459074035	459082033	7998	True	1473.5	5216	93.030500	1	4193	4	chr6A.!!$R1	4192

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
217	228	0.461961	ATTGACGACTAGCCTCAGCC	59.538	55.000	0.00	41.25	4.85	F
1011	5015	0.540830	CTAGGTAGATGAGGGCGGCT	60.541	60.000	9.56	0.00	5.52	F
2368	6378	1.227943	GCCGCTTCCTGCATCCATA	60.228	57.895	0.00	43.06	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1058	5062	1.144936	CACAGATCCTTCCCTCCGC	59.855	63.158	0.00	0.00	0.00	5.54	R
2413	6423	0.814410	CGATGAGCAAGCTCCTGCAT	60.814	55.000	18.54	6.64	45.18	3.96	R
3804	7823	2.293122	CCAACGTTTTCAGAATCCTGCA	59.707	45.455	0.00	0.00	40.20	4.41	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
60	65	2.027469	TCTCAGTCTACGGCAGTACTGA	60.027	50.000	27.08	17.86	35.15	3.41
81	92	2.297880	ACACTGTAGCATTACGACACCA	59.702	45.455	0.00	0.00	32.21	4.17
156	167	0.535102	AACAGCCGTCAAAGTCCCAG	60.535	55.000	0.00	0.00	0.00	4.45
210	221	0.855349	CCGCATGATTGACGACTAGC	59.145	55.000	0.00	0.00	0.00	3.42
217	228	0.461961	ATTGACGACTAGCCTCAGCC	59.538	55.000	0.00	0.00	41.25	4.85
218	229	0.612174	TTGACGACTAGCCTCAGCCT	60.612	55.000	0.00	0.00	41.25	4.58
219	230	1.032657	TGACGACTAGCCTCAGCCTC	61.033	60.000	0.00	0.00	41.25	4.70
220	231	1.000771	ACGACTAGCCTCAGCCTCA	60.001	57.895	0.00	0.00	41.25	3.86
238	256	2.804167	GCTCAGCTCAGCTCGCTA	59.196	61.111	0.67	0.00	36.40	4.26
259	277	8.689061	TCGCTACAATAATTTTGGTCTCTACTA	58.311	33.333	0.00	0.00	0.00	1.82
261	279	9.819267	GCTACAATAATTTTGGTCTCTACTACT	57.181	33.333	0.00	0.00	0.00	2.57
265	4042	9.110502	CAATAATTTTGGTCTCTACTACTTCCC	57.889	37.037	0.00	0.00	0.00	3.97
271	4048	3.625313	GGTCTCTACTACTTCCCACGTAC	59.375	52.174	0.00	0.00	0.00	3.67
272	4049	4.256920	GTCTCTACTACTTCCCACGTACA	58.743	47.826	0.00	0.00	0.00	2.90
689	4634	2.634940	GCATCCAGGGAAGATAGCAGTA	59.365	50.000	0.00	0.00	0.00	2.74
690	4635	3.306641	GCATCCAGGGAAGATAGCAGTAG	60.307	52.174	0.00	0.00	0.00	2.57
1011	5015	0.540830	CTAGGTAGATGAGGGCGGCT	60.541	60.000	9.56	0.00	0.00	5.52
1308	5318	2.517166	GAGCTTCCGCCCATTCCC	60.517	66.667	0.00	0.00	36.60	3.97
1498	5508	2.202756	GCGGCTTCGGATTCTCGT	60.203	61.111	0.00	0.00	0.00	4.18
1761	5771	2.417719	CTCTTCAACCAGTACCAGCAC	58.582	52.381	0.00	0.00	0.00	4.40
1766	5776	1.705002	AACCAGTACCAGCACCAGCA	61.705	55.000	0.00	0.00	45.49	4.41
1767	5777	1.672356	CCAGTACCAGCACCAGCAC	60.672	63.158	0.00	0.00	45.49	4.40
1768	5778	1.672356	CAGTACCAGCACCAGCACC	60.672	63.158	0.00	0.00	45.49	5.01
1769	5779	2.146724	AGTACCAGCACCAGCACCA	61.147	57.895	0.00	0.00	45.49	4.17
1770	5780	1.672356	GTACCAGCACCAGCACCAG	60.672	63.158	0.00	0.00	45.49	4.00

Showing 1 to 25 of 39 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	1.926511	CTGACGATGGGCAGGCAAAC	61.927	60.000	1.90	0.00	0.00	2.93
60	65	2.297880	TGGTGTCGTAATGCTACAGTGT	59.702	45.455	0.00	0.00	0.00	3.55
235	253	9.819267	AGTAGTAGAGACCAAAATTATTGTAGC	57.181	33.333	0.00	0.00	0.00	3.58
238	256	9.668497	GGAAGTAGTAGAGACCAAAATTATTGT	57.332	33.333	0.00	0.00	0.00	2.71
259	277	2.895404	ACTGTATGTGTACGTGGGAAGT	59.105	45.455	0.00	0.00	33.36	3.01
261	279	2.231964	GGACTGTATGTGTACGTGGGAA	59.768	50.000	0.00	0.00	33.36	3.97
262	280	1.820519	GGACTGTATGTGTACGTGGGA	59.179	52.381	0.00	0.00	33.36	4.37
265	4042	2.984471	GTGTGGACTGTATGTGTACGTG	59.016	50.000	0.00	0.00	33.36	4.49
271	4048	4.891627	TTGTTTGTGTGGACTGTATGTG	57.108	40.909	0.00	0.00	0.00	3.21
272	4049	7.575414	TTATTTGTTTGTGTGGACTGTATGT	57.425	32.000	0.00	0.00	0.00	2.29
689	4634	2.022035	TCTCTCCCCTCTCTCTCTCTCT	60.022	54.545	0.00	0.00	0.00	3.10
690	4635	2.104963	GTCTCTCCCCTCTCTCTCTCTC	59.895	59.091	0.00	0.00	0.00	3.20
1055	5059	4.610714	GATCCTTCCCTCCGCCGC	62.611	72.222	0.00	0.00	0.00	6.53
1056	5060	2.840102	AGATCCTTCCCTCCGCCG	60.840	66.667	0.00	0.00	0.00	6.46
1057	5061	2.066999	ACAGATCCTTCCCTCCGCC	61.067	63.158	0.00	0.00	0.00	6.13
1058	5062	1.144936	CACAGATCCTTCCCTCCGC	59.855	63.158	0.00	0.00	0.00	5.54
1059	5063	1.144936	GCACAGATCCTTCCCTCCG	59.855	63.158	0.00	0.00	0.00	4.63
1060	5064	1.414550	GTAGCACAGATCCTTCCCTCC	59.585	57.143	0.00	0.00	0.00	4.30
1061	5065	2.102252	CAGTAGCACAGATCCTTCCCTC	59.898	54.545	0.00	0.00	0.00	4.30
1062	5066	2.114616	CAGTAGCACAGATCCTTCCCT	58.885	52.381	0.00	0.00	0.00	4.20
1503	5513	4.516195	GAGAAGCCGAGCGGGTCC	62.516	72.222	14.44	0.81	46.38	4.46
1707	5717	3.157949	CCGAGGAGAGGGGGCTTC	61.158	72.222	0.00	0.00	0.00	3.86
1938	5948	2.377810	TGAGCCATGTAGCAGGGGG	61.378	63.158	1.98	0.00	35.67	5.40
2368	6378	4.836825	ACACCAAGATCGAAGTCAATGAT	58.163	39.130	0.00	0.00	0.00	2.45
2413	6423	0.814410	CGATGAGCAAGCTCCTGCAT	60.814	55.000	18.54	6.64	45.18	3.96

Showing 1 to 25 of 40 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.