AutoCloner

Multiple sequence alignment - TraesCS7B01G143700

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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	TraesCS7B01G143700	chr7B	100.000	2690	0	0	1	2690	184483106	184485795	0.000000e+00	4968
1	TraesCS7B01G143700	chr7B	95.615	935	32	3	1	930	693860768	693861698	0.000000e+00	1491
2	TraesCS7B01G143700	chr7B	95.187	935	41	2	3	933	684817090	684818024	0.000000e+00	1474
3	TraesCS7B01G143700	chr7B	94.984	937	38	3	1	932	84207883	84208815	0.000000e+00	1461
4	TraesCS7B01G143700	chr7B	94.692	942	44	3	1	937	71344050	71344990	0.000000e+00	1458
5	TraesCS7B01G143700	chr7B	93.962	944	47	4	1	936	733489049	733488108	0.000000e+00	1419
6	TraesCS7B01G143700	chr7D	94.627	1768	54	17	938	2690	215333352	215331611	0.000000e+00	2700
7	TraesCS7B01G143700	chr7A	93.159	1798	55	27	930	2690	228852266	228850500	0.000000e+00	2577
8	TraesCS7B01G143700	chr2B	95.101	939	39	4	1	933	548392704	548391767	0.000000e+00	1472
9	TraesCS7B01G143700	chr2B	94.237	937	44	4	1	932	30137542	30136611	0.000000e+00	1423
10	TraesCS7B01G143700	chr2B	93.923	938	47	4	1	930	778457770	778456835	0.000000e+00	1408
11	TraesCS7B01G143700	chr4B	94.557	937	43	4	1	933	28496487	28495555	0.000000e+00	1441
12	TraesCS7B01G143700	chr1B	91.250	80	7	0	1477	1556	67502940	67502861	2.830000e-20	110

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	TraesCS7B01G143700	chr7B	184483106	184485795	2689	False	4968	4968	100.000	1	2690	1	chr7B.!!$F3	2689
1	TraesCS7B01G143700	chr7B	693860768	693861698	930	False	1491	1491	95.615	1	930	1	chr7B.!!$F5	929
2	TraesCS7B01G143700	chr7B	684817090	684818024	934	False	1474	1474	95.187	3	933	1	chr7B.!!$F4	930
3	TraesCS7B01G143700	chr7B	84207883	84208815	932	False	1461	1461	94.984	1	932	1	chr7B.!!$F2	931
4	TraesCS7B01G143700	chr7B	71344050	71344990	940	False	1458	1458	94.692	1	937	1	chr7B.!!$F1	936
5	TraesCS7B01G143700	chr7B	733488108	733489049	941	True	1419	1419	93.962	1	936	1	chr7B.!!$R1	935
6	TraesCS7B01G143700	chr7D	215331611	215333352	1741	True	2700	2700	94.627	938	2690	1	chr7D.!!$R1	1752
7	TraesCS7B01G143700	chr7A	228850500	228852266	1766	True	2577	2577	93.159	930	2690	1	chr7A.!!$R1	1760
8	TraesCS7B01G143700	chr2B	548391767	548392704	937	True	1472	1472	95.101	1	933	1	chr2B.!!$R2	932
9	TraesCS7B01G143700	chr2B	30136611	30137542	931	True	1423	1423	94.237	1	932	1	chr2B.!!$R1	931
10	TraesCS7B01G143700	chr2B	778456835	778457770	935	True	1408	1408	93.923	1	930	1	chr2B.!!$R3	929
11	TraesCS7B01G143700	chr4B	28495555	28496487	932	True	1441	1441	94.557	1	933	1	chr4B.!!$R1	932

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
871	882	0.171455	CTCAGAAGCCGAACTAGCGT	59.829	55.0	0.0	0.0	34.64	5.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2645	2702	0.809636	CATGACATCCAACGGCGCTA	60.81	55.0	6.9	0.0	0.0	4.26	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
352	353	2.734606	CCGTCGCTAATGAAGAACAACA	59.265	45.455	0.00	0.00	0.00	3.33
583	590	0.591741	GAACGACGCCTCTACATCGG	60.592	60.000	0.00	0.00	38.88	4.18
765	775	4.975242	CGATCGCCGGATTCGCGA	62.975	66.667	5.05	3.71	44.03	5.87
816	827	0.918983	AATTTCCCGCATCCTGGAGA	59.081	50.000	1.52	0.00	30.91	3.71
858	869	1.000486	AGCTAGGTCGCCCTCAGAA	60.000	57.895	0.00	0.00	41.45	3.02
871	882	0.171455	CTCAGAAGCCGAACTAGCGT	59.829	55.000	0.00	0.00	34.64	5.07
949	964	0.747255	TAGATCGCAGCAAGAGGGTC	59.253	55.000	0.00	0.00	0.00	4.46
1049	1066	4.559300	GCTCCAATTTGCAAAAGCTACTCA	60.559	41.667	21.03	0.00	0.00	3.41
1279	1306	4.697756	CGAAGGGCGGCAAGGTCA	62.698	66.667	12.47	0.00	36.03	4.02
1321	1348	0.386858	CGTGTCGTCGTCCTTGTCAT	60.387	55.000	0.00	0.00	0.00	3.06
1347	1374	3.753434	CAGCCGCTGTCCTCGTCT	61.753	66.667	12.54	0.00	0.00	4.18
1494	1521	1.829970	TGGCCTCGAGATGAGCGAT	60.830	57.895	15.71	0.00	43.82	4.58
1762	1789	4.345257	AGTGAAGGTATACATGGCTCGATT	59.655	41.667	5.01	0.00	0.00	3.34
1763	1790	5.538813	AGTGAAGGTATACATGGCTCGATTA	59.461	40.000	5.01	0.00	0.00	1.75
1792	1819	5.831702	ACGAACTATATCTTCTTGGACGT	57.168	39.130	0.00	0.00	0.00	4.34
1819	1846	6.580476	CAATAAACCGAATTGTTTGCAAGAC	58.420	36.000	0.00	2.08	38.79	3.01
1861	1894	2.323959	GTGTGTGTGTGTGTGTTTTGG	58.676	47.619	0.00	0.00	0.00	3.28
1863	1896	0.109551	TGTGTGTGTGTGTTTTGGCG	60.110	50.000	0.00	0.00	0.00	5.69
1992	2025	4.957296	ACATCCGTCCCTACAATGTAATC	58.043	43.478	0.00	0.00	32.64	1.75
1993	2026	3.720949	TCCGTCCCTACAATGTAATCG	57.279	47.619	0.00	0.00	0.00	3.34
2004	2037	1.048601	ATGTAATCGAGCCCGTGGAT	58.951	50.000	0.00	0.00	37.05	3.41
2005	2038	0.387929	TGTAATCGAGCCCGTGGATC	59.612	55.000	0.00	0.00	34.38	3.36
2015	2048	2.842462	CGTGGATCGGGATGGGGA	60.842	66.667	0.00	0.00	35.71	4.81
2028	2061	2.771762	GGGGATCCTGAGCTGGCT	60.772	66.667	12.58	0.00	0.00	4.75
2042	2075	4.395854	TGAGCTGGCTAAATGTACATGTTG	59.604	41.667	9.63	6.09	0.00	3.33
2078	2111	6.833839	TGCAAAAGCAAATCAATAAGCATTC	58.166	32.000	0.00	0.00	0.00	2.67
2109	2142	5.636965	CCTGAATCAAAGTACTCAGTCAGTG	59.363	44.000	18.25	10.67	36.43	3.66
2168	2204	6.091986	GTGAGATTCAGATCTGGTTCTTGTTC	59.908	42.308	22.42	12.35	42.66	3.18
2314	2352	0.526524	CGCGAACTGATCAGGGAGAC	60.527	60.000	26.08	10.65	0.00	3.36
2317	2355	1.202200	CGAACTGATCAGGGAGACGAC	60.202	57.143	26.08	7.45	0.00	4.34
2332	2370	4.389576	GACAGCAACTTGGCGCCG	62.390	66.667	23.90	11.34	39.27	6.46
2334	2372	3.434319	CAGCAACTTGGCGCCGAT	61.434	61.111	23.90	6.50	39.27	4.18
2338	2376	4.388499	AACTTGGCGCCGATCGGT	62.388	61.111	33.33	11.89	38.94	4.69
2384	2422	3.872771	GTCTATCTTCGTCTTCTCCTCGT	59.127	47.826	0.00	0.00	0.00	4.18
2389	2427	1.380524	TCGTCTTCTCCTCGTGATCC	58.619	55.000	0.00	0.00	0.00	3.36
2448	2502	0.324738	CTGAGGGAGGGTGAGCTACA	60.325	60.000	0.00	0.00	0.00	2.74
2462	2516	1.743958	AGCTACAACGCGATGTCTACT	59.256	47.619	25.82	17.42	34.75	2.57
2471	2525	1.471964	CGATGTCTACTCGCTGAAGC	58.528	55.000	0.00	0.00	37.78	3.86
2472	2526	1.846541	GATGTCTACTCGCTGAAGCC	58.153	55.000	0.00	0.00	37.91	4.35
2645	2702	2.281761	CTCAGCCCCAACGTGCTT	60.282	61.111	0.00	0.00	35.12	3.91
2682	2739	5.691305	TGTCATGCACAAATCTTAAAGCAAC	59.309	36.000	0.00	0.00	35.45	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
331	332	2.734606	TGTTGTTCTTCATTAGCGACGG	59.265	45.455	0.00	0.00	0.00	4.79
352	353	0.905357	AGCAGGTCGAGCTTAATGGT	59.095	50.000	15.83	7.45	39.87	3.55
765	775	0.391597	TTCCCGCTCTCAAAAGACGT	59.608	50.000	0.00	0.00	0.00	4.34
917	932	2.139118	GCGATCTAAGGGCATCTTCAC	58.861	52.381	0.00	0.00	36.93	3.18
920	935	1.542108	GCTGCGATCTAAGGGCATCTT	60.542	52.381	0.00	0.00	39.40	2.40
949	964	3.740115	ACTGCTAGTTACACCAAACTGG	58.260	45.455	0.00	0.00	45.02	4.00
986	1003	1.204704	TGTGCATAGAGAAGTGGACCG	59.795	52.381	0.00	0.00	36.05	4.79
1049	1066	1.482365	GGGTGGGTTGGGTCAATTCTT	60.482	52.381	0.00	0.00	0.00	2.52
1242	1269	4.778143	GCGCCCCCATTCGTCACT	62.778	66.667	0.00	0.00	0.00	3.41
1279	1306	4.778143	GCGCATCCCGGACAGGTT	62.778	66.667	0.73	0.00	38.74	3.50
1321	1348	4.399395	CAGCGGCTGGAGGCTCAA	62.399	66.667	22.11	3.56	37.41	3.02
1762	1789	8.304596	CCAAGAAGATATAGTTCGTAGCCATTA	58.695	37.037	0.00	0.00	0.00	1.90
1763	1790	7.015292	TCCAAGAAGATATAGTTCGTAGCCATT	59.985	37.037	0.00	0.00	0.00	3.16
1792	1819	3.743396	GCAAACAATTCGGTTTATTGCCA	59.257	39.130	0.00	0.00	38.86	4.92
1819	1846	2.332104	CCGTGCTATATGCTGCTAGTG	58.668	52.381	0.00	0.00	43.37	2.74
1863	1896	1.269778	TGGATCATCTGCGATCGTTCC	60.270	52.381	17.81	11.58	42.35	3.62
2008	2041	1.759881	CCAGCTCAGGATCCCCATC	59.240	63.158	8.55	0.00	33.88	3.51
2009	2042	2.459086	GCCAGCTCAGGATCCCCAT	61.459	63.158	8.55	0.00	33.88	4.00
2010	2043	2.256156	TAGCCAGCTCAGGATCCCCA	62.256	60.000	8.55	0.00	33.88	4.96
2011	2044	1.056700	TTAGCCAGCTCAGGATCCCC	61.057	60.000	8.55	0.00	0.00	4.81
2012	2045	0.839946	TTTAGCCAGCTCAGGATCCC	59.160	55.000	8.55	0.00	0.00	3.85
2013	2046	2.158696	ACATTTAGCCAGCTCAGGATCC	60.159	50.000	2.48	2.48	0.00	3.36
2014	2047	3.205784	ACATTTAGCCAGCTCAGGATC	57.794	47.619	0.00	0.00	0.00	3.36
2015	2048	3.455910	TGTACATTTAGCCAGCTCAGGAT	59.544	43.478	0.00	0.00	0.00	3.24
2018	2051	4.194640	ACATGTACATTTAGCCAGCTCAG	58.805	43.478	5.37	0.00	0.00	3.35
2042	2075	3.776043	GCTTTTGCAATGTGTTACAGC	57.224	42.857	0.00	0.00	46.58	4.40
2078	2111	4.911390	AGTACTTTGATTCAGGTTCCAGG	58.089	43.478	0.00	0.00	0.00	4.45
2109	2142	4.965119	AACAGAACACCAAGTTTGTCTC	57.035	40.909	0.00	0.00	41.51	3.36
2168	2204	1.002502	GAAAGGGACCCCGAACCAG	60.003	63.158	7.00	0.00	41.95	4.00
2240	2277	1.212229	GGAGGAGGACGACGACAAC	59.788	63.158	0.00	0.00	0.00	3.32
2241	2278	1.975407	GGGAGGAGGACGACGACAA	60.975	63.158	0.00	0.00	0.00	3.18
2242	2279	2.360852	GGGAGGAGGACGACGACA	60.361	66.667	0.00	0.00	0.00	4.35
2314	2352	4.389576	GGCGCCAAGTTGCTGTCG	62.390	66.667	24.80	0.00	0.00	4.35
2317	2355	3.386867	GATCGGCGCCAAGTTGCTG	62.387	63.158	28.98	7.38	38.85	4.41
2332	2370	4.530857	CCCGCACCTCCACCGATC	62.531	72.222	0.00	0.00	0.00	3.69
2334	2372	4.682334	TACCCGCACCTCCACCGA	62.682	66.667	0.00	0.00	0.00	4.69
2338	2376	3.000819	CACCTACCCGCACCTCCA	61.001	66.667	0.00	0.00	0.00	3.86
2384	2422	6.926515	TGGTCCTACCATACATACATGGATCA	60.927	42.308	9.06	0.00	44.79	2.92
2462	2516	2.048222	CCTTCACGGCTTCAGCGA	60.048	61.111	0.00	0.00	43.26	4.93
2465	2519	1.672356	CCCACCTTCACGGCTTCAG	60.672	63.158	0.00	0.00	35.61	3.02
2466	2520	2.429930	CCCACCTTCACGGCTTCA	59.570	61.111	0.00	0.00	35.61	3.02
2467	2521	3.056328	GCCCACCTTCACGGCTTC	61.056	66.667	0.00	0.00	39.70	3.86
2468	2522	3.884774	TGCCCACCTTCACGGCTT	61.885	61.111	0.00	0.00	43.42	4.35
2469	2523	4.643387	GTGCCCACCTTCACGGCT	62.643	66.667	0.00	0.00	43.42	5.52
2470	2524	4.947147	TGTGCCCACCTTCACGGC	62.947	66.667	0.00	0.00	43.32	5.68
2471	2525	2.034066	ATGTGCCCACCTTCACGG	59.966	61.111	0.00	0.00	36.06	4.94
2472	2526	2.981560	GCATGTGCCCACCTTCACG	61.982	63.158	0.00	0.00	36.06	4.35
2645	2702	0.809636	CATGACATCCAACGGCGCTA	60.810	55.000	6.90	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.