AutoCloner

Multiple sequence alignment - TraesCS6B01G243500

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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	TraesCS6B01G243500	chr6B	100.000	4086	0	0	1	4086	433273909	433269824	0.000000e+00	7546.0
1	TraesCS6B01G243500	chr6B	84.009	444	65	6	3647	4086	700209283	700209724	4.880000e-114	422.0
2	TraesCS6B01G243500	chr6D	95.229	3647	96	32	1	3602	272110684	272107071	0.000000e+00	5699.0
3	TraesCS6B01G243500	chr6A	94.989	2355	87	11	587	2923	388211473	388209132	0.000000e+00	3666.0
4	TraesCS6B01G243500	chr6A	92.253	697	27	13	2926	3600	388208873	388208182	0.000000e+00	963.0
5	TraesCS6B01G243500	chr6A	96.915	551	17	0	1	551	388212001	388211451	0.000000e+00	924.0
6	TraesCS6B01G243500	chr6A	82.524	309	54	0	3778	4086	607919185	607918877	5.200000e-69	272.0
7	TraesCS6B01G243500	chr6A	100.000	31	0	0	3382	3412	91906104	91906134	1.590000e-04	58.4
8	TraesCS6B01G243500	chr7B	97.969	1723	24	4	1	1717	438422420	438420703	0.000000e+00	2977.0
9	TraesCS6B01G243500	chr7B	97.548	1142	13	3	1709	2839	438399763	438398626	0.000000e+00	1940.0
10	TraesCS6B01G243500	chr7B	93.095	1260	44	9	2831	4086	438396804	438395584	0.000000e+00	1805.0
11	TraesCS6B01G243500	chr1A	86.907	443	50	5	3650	4086	549483920	549483480	1.320000e-134	490.0
12	TraesCS6B01G243500	chr2D	84.615	390	43	11	3710	4086	131086255	131085870	4.990000e-99	372.0
13	TraesCS6B01G243500	chr2D	82.759	319	49	3	3769	4086	31501406	31501093	3.110000e-71	279.0
14	TraesCS6B01G243500	chr2D	90.217	92	9	0	1942	2033	537459936	537459845	1.990000e-23	121.0
15	TraesCS6B01G243500	chr7D	81.573	445	77	3	3647	4086	199623405	199622961	3.000000e-96	363.0
16	TraesCS6B01G243500	chr7D	81.264	443	78	4	3647	4086	548335687	548335247	1.810000e-93	353.0
17	TraesCS6B01G243500	chr5D	81.088	386	69	3	3704	4086	245684030	245683646	5.130000e-79	305.0
18	TraesCS6B01G243500	chr2A	78.371	356	54	19	2391	2736	679993204	679992862	4.140000e-50	209.0
19	TraesCS6B01G243500	chr2A	83.471	121	18	2	1915	2033	679993950	679993830	1.200000e-20	111.0
20	TraesCS6B01G243500	chr2B	89.130	92	10	0	1942	2033	640104664	640104573	9.280000e-22	115.0

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	TraesCS6B01G243500	chr6B	433269824	433273909	4085	True	7546.0	7546	100.0000	1	4086	1	chr6B.!!$R1	4085
1	TraesCS6B01G243500	chr6D	272107071	272110684	3613	True	5699.0	5699	95.2290	1	3602	1	chr6D.!!$R1	3601
2	TraesCS6B01G243500	chr6A	388208182	388212001	3819	True	1851.0	3666	94.7190	1	3600	3	chr6A.!!$R2	3599
3	TraesCS6B01G243500	chr7B	438420703	438422420	1717	True	2977.0	2977	97.9690	1	1717	1	chr7B.!!$R1	1716
4	TraesCS6B01G243500	chr7B	438395584	438399763	4179	True	1872.5	1940	95.3215	1709	4086	2	chr7B.!!$R2	2377

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
493	494	0.321564	TTGTTCAGAGCCATGGGTCG	60.322	55.000	32.46	26.69	46.10	4.79	F
559	560	2.302445	TGGCACCAATGAAATGGAAAGG	59.698	45.455	0.00	0.00	43.54	3.11	F
1707	1725	7.814264	ACAGAATTCAAGTCAAATTCAGAGT	57.186	32.000	8.44	4.35	42.81	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1507	1516	0.664166	CCGTGGAAGCAATTGCACAC	60.664	55.000	30.89	29.31	42.40	3.82	R
1707	1725	2.093288	CAGGAGCATCTGCAGGAGTAAA	60.093	50.000	15.13	0.00	45.16	2.01	R
3437	5601	1.140252	CCAACTATTCGTACCAGGGGG	59.860	57.143	0.00	0.00	41.29	5.40	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
462	463	2.264794	CCGCGCCTAAGTGGTTCT	59.735	61.111	0.00	0.00	37.04	3.01
493	494	0.321564	TTGTTCAGAGCCATGGGTCG	60.322	55.000	32.46	26.69	46.10	4.79
559	560	2.302445	TGGCACCAATGAAATGGAAAGG	59.698	45.455	0.00	0.00	43.54	3.11
1707	1725	7.814264	ACAGAATTCAAGTCAAATTCAGAGT	57.186	32.000	8.44	4.35	42.81	3.24
1907	1929	4.371786	TCTCTGTTGCTGTCTACTTTGTG	58.628	43.478	0.00	0.00	0.00	3.33
1990	2012	5.584551	AAGTTTGATCCAACCTTCTACCT	57.415	39.130	6.07	0.00	0.00	3.08
2747	2790	8.535690	AAGTTAAGATGCTCTGTTACTGTTAC	57.464	34.615	0.00	0.00	0.00	2.50
2827	2883	5.058490	AGTTTGTACTGTTTAAAGGCGCTA	58.942	37.500	7.64	0.00	31.99	4.26
2980	5122	6.097696	AGGTAAAATTTTGTTACAGCAGTGGT	59.902	34.615	13.76	0.00	33.86	4.16
3437	5601	2.010497	GGAGGCTCGACCAAGATTTTC	58.990	52.381	8.69	0.00	43.14	2.29
3441	5605	1.751437	CTCGACCAAGATTTTCCCCC	58.249	55.000	0.00	0.00	0.00	5.40
3517	5681	2.611971	GGAGATCACGTGTTGCAAGGTA	60.612	50.000	16.51	0.00	0.00	3.08
3520	5684	1.577468	TCACGTGTTGCAAGGTACAG	58.423	50.000	16.51	0.00	0.00	2.74
3525	5689	2.547218	CGTGTTGCAAGGTACAGGTAGT	60.547	50.000	0.00	0.00	0.00	2.73
3578	5742	3.181440	TGGCTTCTGACCACAAAGATCTT	60.181	43.478	0.88	0.88	30.29	2.40
3597	5761	5.916661	TCTTGCCTTACTCGAAGTAGATT	57.083	39.130	0.00	0.00	31.47	2.40
3602	5766	6.640518	TGCCTTACTCGAAGTAGATTTTCAT	58.359	36.000	0.00	0.00	31.47	2.57
3603	5767	6.535150	TGCCTTACTCGAAGTAGATTTTCATG	59.465	38.462	0.00	0.00	31.47	3.07
3604	5768	6.757010	GCCTTACTCGAAGTAGATTTTCATGA	59.243	38.462	0.00	0.00	31.47	3.07
3605	5769	7.277981	GCCTTACTCGAAGTAGATTTTCATGAA	59.722	37.037	3.38	3.38	31.47	2.57
3606	5770	8.812329	CCTTACTCGAAGTAGATTTTCATGAAG	58.188	37.037	8.41	0.00	31.47	3.02
3607	5771	9.360093	CTTACTCGAAGTAGATTTTCATGAAGT	57.640	33.333	8.41	1.61	31.47	3.01
3609	5773	8.918961	ACTCGAAGTAGATTTTCATGAAGTAG	57.081	34.615	8.41	0.00	0.00	2.57
3610	5774	8.740906	ACTCGAAGTAGATTTTCATGAAGTAGA	58.259	33.333	8.41	0.00	0.00	2.59
3611	5775	9.743057	CTCGAAGTAGATTTTCATGAAGTAGAT	57.257	33.333	8.41	2.24	0.00	1.98
3612	5776	9.737427	TCGAAGTAGATTTTCATGAAGTAGATC	57.263	33.333	8.41	10.63	0.00	2.75
3613	5777	9.743057	CGAAGTAGATTTTCATGAAGTAGATCT	57.257	33.333	20.01	20.01	0.00	2.75
3622	5786	3.388552	TGAAGTAGATCTCCAGGCTCA	57.611	47.619	0.00	0.00	0.00	4.26
3662	5826	2.184322	CTATGTGCCGCCTCACGT	59.816	61.111	3.62	3.62	41.42	4.49
3664	5828	3.657448	TATGTGCCGCCTCACGTGG	62.657	63.158	17.00	6.38	45.80	4.94
3691	5855	4.271816	CGGCATCGACCTCCGGAG	62.272	72.222	25.36	25.36	39.52	4.63
3749	5916	1.267383	GCCGAATAAGAAGAAACGCCG	60.267	52.381	0.00	0.00	0.00	6.46
3751	5918	1.659098	CGAATAAGAAGAAACGCCGCT	59.341	47.619	0.00	0.00	0.00	5.52
3756	5923	0.531974	AGAAGAAACGCCGCTGTCAA	60.532	50.000	0.00	0.00	0.00	3.18
3854	6021	1.883021	GTCCCCCGTGCTTCAATTG	59.117	57.895	0.00	0.00	0.00	2.32
3863	6030	2.275380	GCTTCAATTGCGGGGTGGT	61.275	57.895	0.00	0.00	0.00	4.16
3882	6049	1.067295	TGGGCCACTCTCAAGTCAAT	58.933	50.000	0.00	0.00	31.71	2.57
3885	6052	2.508526	GGCCACTCTCAAGTCAATTGT	58.491	47.619	5.13	0.00	40.05	2.71
3956	6123	2.588034	GTGCCCGAATAGACCGGC	60.588	66.667	0.00	0.00	45.24	6.13
3962	6129	1.168407	CCGAATAGACCGGCGACCTA	61.168	60.000	9.30	9.64	40.54	3.08
3975	6142	2.335752	GCGACCTATGAGCTCATGATG	58.664	52.381	34.48	24.27	37.15	3.07
4015	6182	1.296715	CTGGGGTTCTTCCACCTCG	59.703	63.158	0.00	0.00	40.76	4.63
4068	6235	0.604073	TCCAAGCGATTGTCACGGTA	59.396	50.000	13.05	0.00	40.47	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
462	463	4.505039	GGCTCTGAACAAGTAAAGGGAAGA	60.505	45.833	0.00	0.00	0.00	2.87
493	494	1.032014	TGAAACTGAAGGGTTGCAGC	58.968	50.000	0.00	0.00	35.57	5.25
1507	1516	0.664166	CCGTGGAAGCAATTGCACAC	60.664	55.000	30.89	29.31	42.40	3.82
1625	1640	2.436115	GTACCTTGCGGTGCCTCC	60.436	66.667	0.00	0.00	45.18	4.30
1707	1725	2.093288	CAGGAGCATCTGCAGGAGTAAA	60.093	50.000	15.13	0.00	45.16	2.01
1713	1731	2.192443	CCCAGGAGCATCTGCAGG	59.808	66.667	15.13	0.00	45.16	4.85
2044	2066	6.433093	ACCCAAAAGATTTACTAAACGAGCAT	59.567	34.615	0.00	0.00	0.00	3.79
2980	5122	6.762187	TGGTCGTGAGTAAACTTGACAAAATA	59.238	34.615	10.97	0.00	0.00	1.40
3437	5601	1.140252	CCAACTATTCGTACCAGGGGG	59.860	57.143	0.00	0.00	41.29	5.40
3441	5605	2.572191	TCGCCAACTATTCGTACCAG	57.428	50.000	0.00	0.00	0.00	4.00
3517	5681	3.307059	GCTTCTTCATGGACACTACCTGT	60.307	47.826	0.00	0.00	34.96	4.00
3520	5684	3.334583	TGCTTCTTCATGGACACTACC	57.665	47.619	0.00	0.00	0.00	3.18
3525	5689	2.229792	GTGGTTGCTTCTTCATGGACA	58.770	47.619	0.00	0.00	0.00	4.02
3578	5742	6.032956	TGAAAATCTACTTCGAGTAAGGCA	57.967	37.500	0.00	0.00	39.73	4.75
3597	5761	4.718774	AGCCTGGAGATCTACTTCATGAAA	59.281	41.667	9.88	0.00	33.12	2.69
3602	5766	3.388552	TGAGCCTGGAGATCTACTTCA	57.611	47.619	6.49	2.55	32.52	3.02
3603	5767	4.830046	TGTATGAGCCTGGAGATCTACTTC	59.170	45.833	6.49	0.00	0.00	3.01
3604	5768	4.809193	TGTATGAGCCTGGAGATCTACTT	58.191	43.478	6.49	0.00	0.00	2.24
3605	5769	4.461450	TGTATGAGCCTGGAGATCTACT	57.539	45.455	6.49	0.00	0.00	2.57
3606	5770	5.069781	AGTTTGTATGAGCCTGGAGATCTAC	59.930	44.000	0.00	0.00	0.00	2.59
3607	5771	5.211973	AGTTTGTATGAGCCTGGAGATCTA	58.788	41.667	0.00	0.00	0.00	1.98
3608	5772	4.036518	AGTTTGTATGAGCCTGGAGATCT	58.963	43.478	0.00	0.00	0.00	2.75
3609	5773	4.414337	AGTTTGTATGAGCCTGGAGATC	57.586	45.455	0.00	0.00	0.00	2.75
3610	5774	4.472833	AGAAGTTTGTATGAGCCTGGAGAT	59.527	41.667	0.00	0.00	0.00	2.75
3611	5775	3.840666	AGAAGTTTGTATGAGCCTGGAGA	59.159	43.478	0.00	0.00	0.00	3.71
3612	5776	4.213564	AGAAGTTTGTATGAGCCTGGAG	57.786	45.455	0.00	0.00	0.00	3.86
3613	5777	4.326826	CAAGAAGTTTGTATGAGCCTGGA	58.673	43.478	0.00	0.00	0.00	3.86
3622	5786	9.911788	ATAGTGAATGATCCAAGAAGTTTGTAT	57.088	29.630	0.00	0.00	0.00	2.29
3726	5890	1.669265	CGTTTCTTCTTATTCGGCCCC	59.331	52.381	0.00	0.00	0.00	5.80
3729	5893	1.267383	CGGCGTTTCTTCTTATTCGGC	60.267	52.381	0.00	0.00	39.68	5.54
3863	6030	1.067295	ATTGACTTGAGAGTGGCCCA	58.933	50.000	0.00	0.00	35.88	5.36
3868	6035	5.504665	GGTTGACACAATTGACTTGAGAGTG	60.505	44.000	13.59	0.00	38.29	3.51
3882	6049	0.546122	AGCACTGAGGGTTGACACAA	59.454	50.000	0.00	0.00	0.00	3.33
3885	6052	1.227943	GCAGCACTGAGGGTTGACA	60.228	57.895	1.66	0.00	0.00	3.58
3945	6112	1.884579	TCATAGGTCGCCGGTCTATTC	59.115	52.381	1.90	0.00	0.00	1.75
3946	6113	1.887198	CTCATAGGTCGCCGGTCTATT	59.113	52.381	1.90	0.00	0.00	1.73
3956	6123	3.657015	ACATCATGAGCTCATAGGTCG	57.343	47.619	28.27	15.86	45.17	4.79
3975	6142	0.597637	CCTCGATGCCGTGGTCATAC	60.598	60.000	0.00	0.00	42.61	2.39
3996	6163	1.481056	CGAGGTGGAAGAACCCCAGT	61.481	60.000	0.00	0.00	41.54	4.00
4064	6231	1.746517	GCCACCCTATCCACTACCG	59.253	63.158	0.00	0.00	0.00	4.02
4068	6235	4.401657	GAGGCCACCCTATCCACT	57.598	61.111	5.01	0.00	43.12	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.