AutoCloner

Multiple sequence alignment - TraesCS3A01G172400

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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	bitscore
0	TraesCS3A01G172400	chr3A	100.000	3219	0	0	1	3219	187252817	187249599	5945
1	TraesCS3A01G172400	chr3D	96.530	2738	41	8	1	2697	160703640	160700916	4481
2	TraesCS3A01G172400	chr3D	93.690	523	27	3	2695	3216	160700801	160700284	778
3	TraesCS3A01G172400	chr3B	89.609	2791	166	56	1	2697	237337342	237334582	3434
4	TraesCS3A01G172400	chr3B	91.028	535	32	8	2695	3219	237334453	237333925	708

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	TraesCS3A01G172400	chr3A	187249599	187252817	3218	True	5945.0	5945	100.0000	1	3219	1	chr3A.!!$R1	3218
1	TraesCS3A01G172400	chr3D	160700284	160703640	3356	True	2629.5	4481	95.1100	1	3216	2	chr3D.!!$R1	3215
2	TraesCS3A01G172400	chr3B	237333925	237337342	3417	True	2071.0	3434	90.3185	1	3219	2	chr3B.!!$R1	3218

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
603	677	1.072806	TCTGATGTGCATATGGCCCTC	59.927	52.381	0.0	0.0	43.89	4.30	F
615	689	2.031465	GCCCTCGTCGGAAACCAA	59.969	61.111	0.0	0.0	33.16	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1509	1640	1.593196	CGGTTCAGGAACAAAGCTCA	58.407	50.0	13.62	0.0	42.85	4.26	R
2479	2618	2.887152	GGGTCCAAATCCATGTGATAGC	59.113	50.0	0.00	0.0	31.83	2.97	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
348	386	1.530293	CGCAGCTTGCTTGGATAGATC	59.470	52.381	6.58	0.00	42.25	2.75
349	387	1.878734	GCAGCTTGCTTGGATAGATCC	59.121	52.381	1.24	1.24	43.01	3.36
350	388	3.694566	GCAGCTTGCTTGGATAGATCCG	61.695	54.545	4.12	0.00	44.43	4.18
351	389	5.912184	GCAGCTTGCTTGGATAGATCCGA	62.912	52.174	4.12	1.29	44.43	4.55
519	563	9.056005	GCATGACCTTGTTAATACATCTATCAA	57.944	33.333	0.00	0.00	33.44	2.57
551	625	9.952188	CGATATGATTGAGTTACTTCTACAGAA	57.048	33.333	0.00	0.00	0.00	3.02
603	677	1.072806	TCTGATGTGCATATGGCCCTC	59.927	52.381	0.00	0.00	43.89	4.30
615	689	2.031465	GCCCTCGTCGGAAACCAA	59.969	61.111	0.00	0.00	33.16	3.67
806	936	6.252995	TCCCTAAAAGTTTTATGTGGCTGAT	58.747	36.000	8.48	0.00	0.00	2.90
1049	1179	4.219507	TGTCAATGGAGAGACTCTGAAGAC	59.780	45.833	10.44	10.63	35.81	3.01
1654	1786	5.011329	CCAGGTGACTACTTGTGTTTACCTA	59.989	44.000	0.00	0.00	40.21	3.08
1717	1850	3.889520	ACCAAAACCGTAAAGCCAAAA	57.110	38.095	0.00	0.00	0.00	2.44
2240	2379	5.498393	AGAATTCAGCATCACACAGAAGAT	58.502	37.500	8.44	0.00	0.00	2.40
2369	2508	2.223112	GCGCACTTATCAGGACATGTTG	60.223	50.000	0.30	0.00	0.00	3.33
2479	2618	7.224557	AGCAAAGTAAACCAAAGCTTTATGTTG	59.775	33.333	20.67	12.43	30.98	3.33
2547	2686	1.138859	GATGGTGTGTGATGATCCCGA	59.861	52.381	0.00	0.00	0.00	5.14
2577	2716	7.068348	CACCTTGATGATTTCTGATGAATCCTT	59.932	37.037	0.88	0.00	31.56	3.36
2578	2717	7.284944	ACCTTGATGATTTCTGATGAATCCTTC	59.715	37.037	0.88	0.02	31.56	3.46
2579	2718	7.284716	CCTTGATGATTTCTGATGAATCCTTCA	59.715	37.037	0.88	0.00	45.01	3.02
2603	2742	9.290988	TCATAGAATCATAGTCCAGACTACTTC	57.709	37.037	9.63	12.09	45.61	3.01
2728	2999	1.160137	GTGGTGAATTCAAGCGAGCT	58.840	50.000	10.35	0.00	0.00	4.09
2769	3040	7.340232	TGGATTATCAGTTGAAATTTCCTCCAG	59.660	37.037	15.48	2.61	0.00	3.86
2823	3099	9.958180	TGATCTAATCAAGTGGTGATCTAAAAA	57.042	29.630	0.00	0.00	46.80	1.94
2877	3157	2.083774	CTTTCCCTGCAATTCGTAGCA	58.916	47.619	0.00	0.00	39.25	3.49
2968	3248	4.222114	CCAAGAAAATGAACTTGCGACTC	58.778	43.478	0.00	0.00	41.15	3.36

Showing 1 to 25 of 34 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
123	131	0.193574	ACTGGGAGGTTTGGGAGAGA	59.806	55.000	0.00	0.00	0.00	3.10
350	388	0.389948	AAACTGGATGCGACTCGGTC	60.390	55.000	0.00	0.00	0.00	4.79
351	389	0.892755	TAAACTGGATGCGACTCGGT	59.107	50.000	0.00	0.00	0.00	4.69
551	625	0.248661	CGTGGATCGATCTCGCACTT	60.249	55.000	23.96	0.00	42.86	3.16
554	628	0.816421	TACCGTGGATCGATCTCGCA	60.816	55.000	23.96	11.62	42.86	5.10
603	677	2.250188	GCATTTCATTGGTTTCCGACG	58.750	47.619	0.00	0.00	0.00	5.12
615	689	3.634504	TGTTCATAGCCCTGCATTTCAT	58.365	40.909	0.00	0.00	0.00	2.57
806	936	6.791867	AAGATGTAACCATGCTACAGAGTA	57.208	37.500	10.52	0.00	32.96	2.59
1049	1179	1.663702	ACTCGTCGCCCAAGAAACG	60.664	57.895	0.00	0.00	36.50	3.60
1509	1640	1.593196	CGGTTCAGGAACAAAGCTCA	58.407	50.000	13.62	0.00	42.85	4.26
1592	1724	8.420189	GCTCTCAAACAAAATTAGATTTGAACG	58.580	33.333	6.76	6.97	41.73	3.95
1654	1786	8.577296	GGGAAACAGCTTCTAAACTTAGAATTT	58.423	33.333	11.38	9.31	45.67	1.82
1663	1795	8.112016	AGAATAAAGGGAAACAGCTTCTAAAC	57.888	34.615	0.00	0.00	34.17	2.01
1717	1850	4.721776	TCCTGCCCAATAGATTAAGTCAGT	59.278	41.667	0.00	0.00	0.00	3.41
2057	2196	6.830838	AGATGTTGACTCAAGAAAAAGAAGGT	59.169	34.615	0.00	0.00	0.00	3.50
2187	2326	5.603596	ACAGGTAATTGTACTTGTCGTTCA	58.396	37.500	0.00	0.00	44.76	3.18
2191	2330	5.120208	CAGGAACAGGTAATTGTACTTGTCG	59.880	44.000	2.60	0.00	46.60	4.35
2240	2379	4.309099	GAGCATGCTTGATTTTCCAAACA	58.691	39.130	23.61	0.00	0.00	2.83
2369	2508	9.451002	TCATACAGCTACTACATAGATTAGGTC	57.549	37.037	0.00	0.00	31.83	3.85
2479	2618	2.887152	GGGTCCAAATCCATGTGATAGC	59.113	50.000	0.00	0.00	31.83	2.97
2547	2686	5.655090	TCATCAGAAATCATCAAGGTGCATT	59.345	36.000	0.00	0.00	0.00	3.56
2577	2716	9.290988	GAAGTAGTCTGGACTATGATTCTATGA	57.709	37.037	12.72	0.00	44.73	2.15
2578	2717	8.519526	GGAAGTAGTCTGGACTATGATTCTATG	58.480	40.741	12.72	0.00	44.73	2.23
2579	2718	8.228206	TGGAAGTAGTCTGGACTATGATTCTAT	58.772	37.037	12.72	0.00	44.73	1.98
2580	2719	7.583625	TGGAAGTAGTCTGGACTATGATTCTA	58.416	38.462	12.72	11.91	44.73	2.10

Showing 1 to 25 of 43 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.