AutoCloner

Multiple sequence alignment - TraesCS3B01G146600

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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	TraesCS3B01G146600	chr3B	100.000	6298	0	0	1	6298	136479236	136485533	0.000000	11631.0
1	TraesCS3B01G146600	chr3B	97.222	684	16	2	5615	6298	119088872	119088192	0.000000	1155.0
2	TraesCS3B01G146600	chr3B	91.566	581	25	13	5059	5617	130308065	130307487	0.000000	780.0
3	TraesCS3B01G146600	chr3D	96.618	5648	123	15	1	5617	86351801	86357411	0.000000	9310.0
4	TraesCS3B01G146600	chr3D	89.520	687	55	8	5615	6298	73763799	73763127	0.000000	854.0
5	TraesCS3B01G146600	chr3A	95.646	5673	153	23	1	5616	102680373	102686008	0.000000	9022.0
6	TraesCS3B01G146600	chr3A	90.087	686	56	5	5615	6298	86628995	86628320	0.000000	880.0
7	TraesCS3B01G146600	chr7D	86.441	59	6	2	351	407	79210410	79210468	0.000005	63.9
8	TraesCS3B01G146600	chr7D	86.441	59	6	2	351	407	79267523	79267581	0.000005	63.9
9	TraesCS3B01G146600	chr7D	86.441	59	6	2	351	407	79301695	79301753	0.000005	63.9
10	TraesCS3B01G146600	chr7D	100.000	28	0	0	397	424	40156486	40156513	0.011000	52.8
11	TraesCS3B01G146600	chr7B	86.667	60	3	3	367	425	237486572	237486517	0.000019	62.1
12	TraesCS3B01G146600	chr7B	96.875	32	1	0	393	424	86648758	86648789	0.003000	54.7
13	TraesCS3B01G146600	chr4A	80.723	83	11	4	327	404	55957283	55957365	0.000068	60.2
14	TraesCS3B01G146600	chr2B	82.609	69	10	2	353	420	492284773	492284706	0.000068	60.2
15	TraesCS3B01G146600	chr1D	86.792	53	7	0	342	394	338872371	338872423	0.000068	60.2
16	TraesCS3B01G146600	chr1D	100.000	29	0	0	394	422	433281513	433281485	0.003000	54.7
17	TraesCS3B01G146600	chr2A	100.000	28	0	0	397	424	653371953	653371926	0.011000	52.8
18	TraesCS3B01G146600	chr1B	100.000	28	0	0	395	422	585312951	585312924	0.011000	52.8
19	TraesCS3B01G146600	chr1B	100.000	28	0	0	397	424	618005941	618005914	0.011000	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	TraesCS3B01G146600	chr3B	136479236	136485533	6297	False	11631	11631	100.000	1	6298	1	chr3B.!!$F1	6297
1	TraesCS3B01G146600	chr3B	119088192	119088872	680	True	1155	1155	97.222	5615	6298	1	chr3B.!!$R1	683
2	TraesCS3B01G146600	chr3B	130307487	130308065	578	True	780	780	91.566	5059	5617	1	chr3B.!!$R2	558
3	TraesCS3B01G146600	chr3D	86351801	86357411	5610	False	9310	9310	96.618	1	5617	1	chr3D.!!$F1	5616
4	TraesCS3B01G146600	chr3D	73763127	73763799	672	True	854	854	89.520	5615	6298	1	chr3D.!!$R1	683
5	TraesCS3B01G146600	chr3A	102680373	102686008	5635	False	9022	9022	95.646	1	5616	1	chr3A.!!$F1	5615
6	TraesCS3B01G146600	chr3A	86628320	86628995	675	True	880	880	90.087	5615	6298	1	chr3A.!!$R1	683

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
771	807	3.054802	GTGAAGACCATCATGGAAGGACT	60.055	47.826	11.90	0.00	40.96	3.85	F
1314	1351	0.250727	CACGGGACACCAAGGTTGAT	60.251	55.000	0.00	0.00	36.13	2.57	F
1923	1960	2.293399	GGACAAGGAAAACAATGAGCGT	59.707	45.455	0.00	0.00	0.00	5.07	F
2449	2486	0.250234	CTCACCGAGAATGGAAGGCA	59.750	55.000	0.00	0.00	0.00	4.75	F
4425	4479	0.673333	CTGCAACGAGCCATGGTACA	60.673	55.000	14.67	0.82	44.39	2.90	F
4447	4501	0.818296	CTGGACTTACCTCCTGACCG	59.182	60.000	0.00	0.00	39.86	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1920	1957	0.391661	TGGCAGAATCCTTCTCACGC	60.392	55.000	0.0	38.11	5.34	R
2447	2484	1.135859	CAGACGTCAGAAGGCAAATGC	60.136	52.381	19.5	41.14	3.56	R
3725	3765	0.807496	GCAGTTCTTGGATGGCAGAC	59.193	55.000	0.0	0.00	3.51	R
4429	4483	0.113776	ACGGTCAGGAGGTAAGTCCA	59.886	55.000	0.0	39.34	4.02	R
5246	5304	0.676736	GCGGATACTCCTTCCCAGAG	59.323	60.000	0.0	33.30	3.35	R
5432	5509	1.018148	CACAACACGGCCTACAACAA	58.982	50.000	0.0	0.00	2.83	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
771	807	3.054802	GTGAAGACCATCATGGAAGGACT	60.055	47.826	11.90	0.00	40.96	3.85
837	873	4.740922	TGCAACCCGAAGCATCAT	57.259	50.000	0.00	0.00	35.51	2.45
1314	1351	0.250727	CACGGGACACCAAGGTTGAT	60.251	55.000	0.00	0.00	36.13	2.57
1409	1446	5.052481	TGAGACTGATGTGAAGACAAACAG	58.948	41.667	0.00	0.00	41.86	3.16
1755	1792	6.714356	AGGACAGGAGAAAGAAAGATGAAAAG	59.286	38.462	0.00	0.00	0.00	2.27
1920	1957	5.278660	CCAGAAGGACAAGGAAAACAATGAG	60.279	44.000	0.00	0.00	36.89	2.90
1923	1960	2.293399	GGACAAGGAAAACAATGAGCGT	59.707	45.455	0.00	0.00	0.00	5.07
2387	2424	9.730705	AATAGCATAATAGTGTGTATGAGCATT	57.269	29.630	0.00	0.00	30.61	3.56
2399	2436	4.746611	TGTATGAGCATTGCTATCACGAAG	59.253	41.667	11.96	0.00	39.88	3.79
2435	2472	3.569701	TGGAAATTTGCACTTCTCTCACC	59.430	43.478	8.47	0.00	0.00	4.02
2447	2484	2.103373	TCTCTCACCGAGAATGGAAGG	58.897	52.381	0.00	0.00	45.55	3.46
2449	2486	0.250234	CTCACCGAGAATGGAAGGCA	59.750	55.000	0.00	0.00	0.00	4.75
2475	2512	4.038282	TGCCTTCTGACGTCTGTTTACTAA	59.962	41.667	17.92	4.64	0.00	2.24
2599	2636	8.174733	AGCTGAATAAAATGGAGTAATGGATG	57.825	34.615	0.00	0.00	0.00	3.51
2602	2639	8.463930	TGAATAAAATGGAGTAATGGATGGTC	57.536	34.615	0.00	0.00	0.00	4.02
2603	2640	8.058235	TGAATAAAATGGAGTAATGGATGGTCA	58.942	33.333	0.00	0.00	0.00	4.02
2706	2744	8.143193	TCACATTGAGATTTTACTGCACATTTT	58.857	29.630	0.00	0.00	0.00	1.82
2769	2807	3.007831	TCAAAATCCCTTCACATTTGGGC	59.992	43.478	0.00	0.00	40.69	5.36
2961	3000	3.620488	TGGTCCATTATCACCAGCTTTC	58.380	45.455	0.00	0.00	37.78	2.62
2968	3007	6.039717	TCCATTATCACCAGCTTTCTATTTGC	59.960	38.462	0.00	0.00	0.00	3.68
3095	3134	4.493618	AGCTACCCCAGATGCTAGAAATA	58.506	43.478	0.00	0.00	33.64	1.40
3201	3240	5.189180	ACTGATTCCTTAGGTGATTTCTGC	58.811	41.667	0.00	0.00	0.00	4.26
3259	3299	5.170748	CCTGTGTTGCTGGATTATTTTTCC	58.829	41.667	0.00	0.00	38.33	3.13
3314	3354	7.972832	AATGATGAACATTTGAAAGTGCATT	57.027	28.000	0.00	0.00	45.60	3.56
3512	3552	7.432148	TCTTCCATTAGCTACTTTATCCACA	57.568	36.000	0.00	0.00	0.00	4.17

Showing 1 to 25 of 62 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	100	3.388024	TGATATACCAACTGACCTGCTCC	59.612	47.826	0.00	0.00	0.00	4.70
134	144	6.435591	CAGGCCAGAAGATAGTAGATATCACA	59.564	42.308	5.01	0.00	42.51	3.58
188	198	2.344093	TTCCTACTTCCCCAAGCTCT	57.656	50.000	0.00	0.00	32.09	4.09
629	665	4.933400	ACGTGTACCAATAACAATCCAGAC	59.067	41.667	0.00	0.00	0.00	3.51
848	884	5.600908	TGTTTTTAAAGCTAGGCAGTACG	57.399	39.130	0.00	0.00	0.00	3.67
1314	1351	2.282180	GCTTTTGCCTCCCGGTCA	60.282	61.111	0.00	0.00	40.15	4.02
1409	1446	2.090400	TTCAGTGTCATCTGCTCTGC	57.910	50.000	0.00	0.00	35.63	4.26
1755	1792	6.019479	CGTCTCTTGCACCAAAATCTCTATAC	60.019	42.308	0.00	0.00	0.00	1.47
1920	1957	0.391661	TGGCAGAATCCTTCTCACGC	60.392	55.000	0.00	0.00	38.11	5.34
1923	1960	3.307975	CCTTCTTGGCAGAATCCTTCTCA	60.308	47.826	0.00	0.00	38.42	3.27
1954	1991	4.202357	TGTGTTCTCCTTGTCAACTGCTAT	60.202	41.667	0.00	0.00	0.00	2.97
2387	2424	2.279741	GGAATGTGCTTCGTGATAGCA	58.720	47.619	0.00	0.00	45.78	3.49
2399	2436	5.391203	GCAAATTTCCAGAAATGGAATGTGC	60.391	40.000	10.35	14.53	46.18	4.57
2435	2472	2.199291	GCAAATGCCTTCCATTCTCG	57.801	50.000	0.00	0.00	43.22	4.04
2447	2484	1.135859	CAGACGTCAGAAGGCAAATGC	60.136	52.381	19.50	0.00	41.14	3.56
2449	2486	2.550830	ACAGACGTCAGAAGGCAAAT	57.449	45.000	19.50	0.00	0.00	2.32
2492	2529	7.325694	AGATTTTTCAATGGGCTTATCACTTG	58.674	34.615	0.00	0.00	0.00	3.16
2613	2650	2.550855	GCTGTTGATGACTCCAGTTCCA	60.551	50.000	0.00	0.00	0.00	3.53
2706	2744	6.833933	TCAGAGCACTAAATCCTACAGTATGA	59.166	38.462	0.00	0.00	39.69	2.15
2715	2753	3.776969	TGGATGTCAGAGCACTAAATCCT	59.223	43.478	15.26	0.00	33.48	3.24
2769	2807	6.584942	GCATGTGCACATATAAAATGGATCAG	59.415	38.462	30.92	14.67	41.59	2.90
2968	3007	6.867550	TGCACCGATGAGGATATTAAGATAG	58.132	40.000	0.00	0.00	45.00	2.08
3095	3134	5.388654	AGGACCATTTTGTTGATTCTCAGT	58.611	37.500	0.00	0.00	0.00	3.41
3229	3268	3.367743	AGCAACACAGGCATGGCG	61.368	61.111	14.30	11.27	0.00	5.69
3259	3299	8.459635	GTTTCCCTTATGCTACTTAAGGAAAAG	58.540	37.037	16.72	0.29	45.76	2.27

Showing 1 to 25 of 72 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.