AutoCloner

Multiple sequence alignment - TraesCS7B01G497900

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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	TraesCS7B01G497900	chr7B	100.000	2660	0	0	1	2660	748607587	748610246	0.000000e+00	4913.0
1	TraesCS7B01G497900	chr7B	89.555	517	53	1	1194	1710	746744325	746744840	0.000000e+00	654.0
2	TraesCS7B01G497900	chr7B	82.425	569	82	8	350	917	748381547	748382098	5.150000e-132	481.0
3	TraesCS7B01G497900	chr7B	90.937	331	30	0	1138	1468	749292483	749292813	1.880000e-121	446.0
4	TraesCS7B01G497900	chr7B	73.096	1379	315	38	376	1731	744904335	744902990	8.740000e-120	440.0
5	TraesCS7B01G497900	chr7B	73.110	1376	314	37	376	1728	745065201	745066543	8.740000e-120	440.0
6	TraesCS7B01G497900	chr7B	88.421	285	26	7	2197	2478	202752435	202752715	1.180000e-88	337.0
7	TraesCS7B01G497900	chr7B	85.507	276	24	6	1844	2113	746758176	746758441	9.380000e-70	274.0
8	TraesCS7B01G497900	chr7B	77.209	215	42	6	869	1081	745217988	745217779	4.650000e-23	119.0
9	TraesCS7B01G497900	chr7B	87.500	64	7	1	1606	1669	744990938	744990876	3.670000e-09	73.1
10	TraesCS7B01G497900	chr7B	100.000	28	0	0	500	527	745277027	745277000	5.000000e-03	52.8
11	TraesCS7B01G497900	chr7A	97.257	2661	69	4	1	2660	734890790	734888133	0.000000e+00	4506.0
12	TraesCS7B01G497900	chr7A	72.587	1233	280	40	517	1726	734664038	734662841	4.210000e-93	351.0
13	TraesCS7B01G497900	chr7D	86.620	1420	153	10	565	1984	632775945	632774563	0.000000e+00	1535.0
14	TraesCS7B01G497900	chr7D	84.354	1061	92	26	1068	2114	632444533	632445533	0.000000e+00	972.0
15	TraesCS7B01G497900	chr7D	90.459	283	22	5	2198	2478	497790108	497789829	4.180000e-98	368.0
16	TraesCS7B01G497900	chr3B	90.141	284	22	5	2199	2478	733631365	733631646	5.410000e-97	364.0
17	TraesCS7B01G497900	chr3B	89.716	282	24	5	2200	2478	17636132	17635853	3.260000e-94	355.0
18	TraesCS7B01G497900	chr3B	86.159	289	33	6	2197	2481	571449246	571448961	3.330000e-79	305.0
19	TraesCS7B01G497900	chr5A	86.851	289	29	8	2196	2478	595886958	595886673	5.530000e-82	315.0
20	TraesCS7B01G497900	chrUn	86.760	287	25	10	2198	2478	313238244	313238523	9.250000e-80	307.0
21	TraesCS7B01G497900	chr6B	86.713	286	26	8	2198	2478	633356265	633355987	9.250000e-80	307.0
22	TraesCS7B01G497900	chr4D	69.910	1223	300	45	513	1713	39356954	39358130	9.860000e-35	158.0
23	TraesCS7B01G497900	chr4A	71.229	716	169	25	957	1661	560971051	560971740	2.130000e-31	147.0

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	TraesCS7B01G497900	chr7B	748607587	748610246	2659	False	4913	4913	100.000	1	2660	1	chr7B.!!$F6	2659
1	TraesCS7B01G497900	chr7B	746744325	746744840	515	False	654	654	89.555	1194	1710	1	chr7B.!!$F3	516
2	TraesCS7B01G497900	chr7B	748381547	748382098	551	False	481	481	82.425	350	917	1	chr7B.!!$F5	567
3	TraesCS7B01G497900	chr7B	744902990	744904335	1345	True	440	440	73.096	376	1731	1	chr7B.!!$R1	1355
4	TraesCS7B01G497900	chr7B	745065201	745066543	1342	False	440	440	73.110	376	1728	1	chr7B.!!$F2	1352
5	TraesCS7B01G497900	chr7A	734888133	734890790	2657	True	4506	4506	97.257	1	2660	1	chr7A.!!$R2	2659
6	TraesCS7B01G497900	chr7A	734662841	734664038	1197	True	351	351	72.587	517	1726	1	chr7A.!!$R1	1209
7	TraesCS7B01G497900	chr7D	632774563	632775945	1382	True	1535	1535	86.620	565	1984	1	chr7D.!!$R2	1419
8	TraesCS7B01G497900	chr7D	632444533	632445533	1000	False	972	972	84.354	1068	2114	1	chr7D.!!$F1	1046

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
237	238	0.031857	TTCCTTGTTTGCATGTGCCG	59.968	50.0	2.07	0.0	41.18	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1927	1955	0.768622	ACACAAGGACCCAAATCCGA	59.231	50.0	0.0	0.0	44.22	4.55	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
64	65	7.954666	TCAGACATAATATGGATGATCCGTA	57.045	36.000	15.31	15.31	41.85	4.02
75	76	2.330440	TGATCCGTAGTTGCATGCAT	57.670	45.000	23.37	10.46	0.00	3.96
95	96	6.151648	ATGCATGCATTGTTAACTGAGTAGTT	59.848	34.615	27.46	0.00	40.86	2.24
143	144	0.855349	CATGCATCTTACTCGACCGC	59.145	55.000	0.00	0.00	0.00	5.68
168	169	9.134734	GCTAAATTGATTAAACAAACCGAATCA	57.865	29.630	2.00	0.00	36.71	2.57
208	209	4.207955	AGGGAAACTCAAACTCAAACTCC	58.792	43.478	0.00	0.00	0.00	3.85
237	238	0.031857	TTCCTTGTTTGCATGTGCCG	59.968	50.000	2.07	0.00	41.18	5.69
272	273	1.221840	CTGATGTGGGTTCCCGAGG	59.778	63.158	3.27	0.00	0.00	4.63
289	290	2.579201	GCCGGTTAGAGCTGCTGA	59.421	61.111	7.01	0.00	0.00	4.26
332	333	8.948853	ACAAATTCTGTGTGTCAATATTAACG	57.051	30.769	0.00	0.00	36.69	3.18
705	713	0.485543	TGACTCTGGTCCACCCACTA	59.514	55.000	0.00	0.00	41.47	2.74
823	831	2.892425	GCGGCCTTGTCATCCTCG	60.892	66.667	0.00	0.00	0.00	4.63
843	851	3.196901	TCGGCCACTTACATGTCAATACT	59.803	43.478	0.00	0.00	0.00	2.12
921	932	4.731313	AACCACCTTCCTCTCAAAATCT	57.269	40.909	0.00	0.00	0.00	2.40
925	936	3.009473	CACCTTCCTCTCAAAATCTCCCA	59.991	47.826	0.00	0.00	0.00	4.37
1070	1081	4.282957	CACTGCCACATCATCCTCTAGTAT	59.717	45.833	0.00	0.00	0.00	2.12
1165	1176	1.002659	CAATCCTCCACGGTGGTGTTA	59.997	52.381	25.53	14.05	42.80	2.41
1168	1179	0.611200	CCTCCACGGTGGTGTTATCA	59.389	55.000	25.53	4.73	42.80	2.15
1493	1504	8.486210	TGATGTACTAGTTGAGCTTAATGGATT	58.514	33.333	0.00	0.00	0.00	3.01
1598	1609	1.834896	TCGGCAAAAGTATGGCTCCTA	59.165	47.619	0.00	0.00	43.23	2.94
1604	1615	2.868964	AAGTATGGCTCCTACTCCCA	57.131	50.000	0.00	0.00	0.00	4.37
1696	1707	6.408891	GCCAAGTAGGTAGGGTATGTTACAAT	60.409	42.308	0.00	0.00	40.61	2.71
1927	1955	6.108687	TCGATCATACAATCAAGAAAGCTGT	58.891	36.000	0.00	0.00	0.00	4.40
2003	2031	5.189928	TGTCGCCTTGGTGATTATACAATT	58.810	37.500	6.18	0.00	0.00	2.32
2007	2035	7.855904	GTCGCCTTGGTGATTATACAATTTTAG	59.144	37.037	6.18	0.00	0.00	1.85
2008	2036	7.012894	TCGCCTTGGTGATTATACAATTTTAGG	59.987	37.037	0.00	0.00	0.00	2.69
2158	2188	6.014840	AGCATCAATGAATGAGTTGAGGTTTT	60.015	34.615	0.00	0.00	42.53	2.43
2170	2200	5.388654	AGTTGAGGTTTTGGATGAAGATGT	58.611	37.500	0.00	0.00	0.00	3.06
2179	2209	7.556275	GGTTTTGGATGAAGATGTAATGGTAGA	59.444	37.037	0.00	0.00	0.00	2.59
2234	2264	2.615912	GCCTGAGTTGGTGAATAGCATC	59.384	50.000	0.00	0.00	33.73	3.91
2277	2307	3.150731	CACTTTCGTCCGTTTATTTCGC	58.849	45.455	0.00	0.00	0.00	4.70
2281	2311	0.372334	CGTCCGTTTATTTCGCTGGG	59.628	55.000	0.00	0.00	0.00	4.45
2325	2355	0.110373	CACCAGTTTAGTTTCGCGCC	60.110	55.000	0.00	0.00	0.00	6.53
2340	2370	1.560860	GCGCCACTCTCTCACACAAC	61.561	60.000	0.00	0.00	0.00	3.32
2341	2371	0.249447	CGCCACTCTCTCACACAACA	60.249	55.000	0.00	0.00	0.00	3.33
2342	2372	1.806247	CGCCACTCTCTCACACAACAA	60.806	52.381	0.00	0.00	0.00	2.83
2375	2405	4.456911	TGAACAGATCAGAACTTTCCATGC	59.543	41.667	0.00	0.00	33.04	4.06
2500	2530	2.809601	CGGAGGAGTTTGCGGTCG	60.810	66.667	0.00	0.00	0.00	4.79
2566	2596	0.251916	CACCTCACGCAATTCCCCTA	59.748	55.000	0.00	0.00	0.00	3.53
2607	2637	2.761195	GGGCCGAAATCAACGCCTC	61.761	63.158	0.00	0.00	0.00	4.70
2612	2642	0.736325	CGAAATCAACGCCTCGGTCT	60.736	55.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	3.504520	GCCTTGACCGGTAAGAAAAATCA	59.495	43.478	7.34	0.00	0.00	2.57
75	76	5.240623	CCCAAACTACTCAGTTAACAATGCA	59.759	40.000	8.61	0.00	44.41	3.96
81	82	6.990939	AGAACTTCCCAAACTACTCAGTTAAC	59.009	38.462	0.00	0.00	44.41	2.01
95	96	1.820519	GCATGCATGAGAACTTCCCAA	59.179	47.619	30.64	0.00	0.00	4.12
174	175	4.611367	TGAGTTTCCCTTGGTAACCAAAA	58.389	39.130	0.00	0.00	43.44	2.44
189	190	6.196079	AGTTGGAGTTTGAGTTTGAGTTTC	57.804	37.500	0.00	0.00	0.00	2.78
208	209	3.923461	TGCAAACAAGGAAAAACGAGTTG	59.077	39.130	0.00	0.00	0.00	3.16
237	238	2.959071	GCACGATCGAGCTGGCTC	60.959	66.667	27.01	12.09	39.55	4.70
272	273	1.811679	GTCAGCAGCTCTAACCGGC	60.812	63.158	0.00	0.00	0.00	6.13
276	277	2.301577	AATCCGTCAGCAGCTCTAAC	57.698	50.000	0.00	0.00	0.00	2.34
277	278	2.735444	CGAAATCCGTCAGCAGCTCTAA	60.735	50.000	0.00	0.00	0.00	2.10
332	333	1.671379	GTCTCCGGCTGGAAACCAC	60.671	63.158	16.91	6.31	45.87	4.16
392	393	0.555769	TTTGAGTTGGAGGCCTTGGT	59.444	50.000	6.77	0.00	0.00	3.67
487	489	3.667217	CTGGGAGGGGCAATGGTGG	62.667	68.421	0.00	0.00	0.00	4.61
823	831	3.555956	CGAGTATTGACATGTAAGTGGCC	59.444	47.826	0.00	0.00	0.00	5.36
843	851	2.159156	ACAGTGCTTGTACTTGTGTCGA	60.159	45.455	0.00	0.00	38.56	4.20
921	932	5.316167	GTGATGCTAATATGGACATTGGGA	58.684	41.667	0.00	0.00	0.00	4.37
925	936	5.072741	GGTGGTGATGCTAATATGGACATT	58.927	41.667	0.00	0.00	0.00	2.71
1095	1106	0.830444	ACAAGGAGTCACGGTGCCTA	60.830	55.000	2.51	0.00	0.00	3.93
1165	1176	1.264749	TGGTCCGCTAGCCAGTTGAT	61.265	55.000	9.66	0.00	0.00	2.57
1168	1179	1.221840	CATGGTCCGCTAGCCAGTT	59.778	57.895	9.66	0.00	38.27	3.16
1189	1200	6.115446	TCACATCATAGGTGAGGATTTGTTC	58.885	40.000	0.00	0.00	40.16	3.18
1493	1504	1.000506	CGTCTCCGTTCCTCTTTCCAA	59.999	52.381	0.00	0.00	0.00	3.53
1598	1609	4.137543	GTCAATCTCAAACAACTGGGAGT	58.862	43.478	0.00	0.00	0.00	3.85
1604	1615	3.953612	TGGCAAGTCAATCTCAAACAACT	59.046	39.130	0.00	0.00	0.00	3.16
1696	1707	5.943416	CACTGGATCAAGGTGGTAAATACAA	59.057	40.000	1.23	0.00	0.00	2.41
1801	1820	1.686110	GAGGTGGATCGGGTGGACT	60.686	63.158	0.00	0.00	0.00	3.85
1927	1955	0.768622	ACACAAGGACCCAAATCCGA	59.231	50.000	0.00	0.00	44.22	4.55
2003	2031	3.895656	CGACTGTAGATCCATCCCCTAAA	59.104	47.826	0.00	0.00	0.00	1.85
2007	2035	0.969894	CCGACTGTAGATCCATCCCC	59.030	60.000	0.00	0.00	0.00	4.81
2008	2036	1.889829	CTCCGACTGTAGATCCATCCC	59.110	57.143	0.00	0.00	0.00	3.85
2158	2188	5.596772	TCGTCTACCATTACATCTTCATCCA	59.403	40.000	0.00	0.00	0.00	3.41
2170	2200	6.045072	ACTTGTTCCAATCGTCTACCATTA	57.955	37.500	0.00	0.00	0.00	1.90
2179	2209	9.530633	GTAGAGATATAAACTTGTTCCAATCGT	57.469	33.333	0.00	0.00	0.00	3.73
2203	2233	1.833630	CCAACTCAGGCATCAGGAGTA	59.166	52.381	0.00	0.00	40.80	2.59
2234	2264	3.119280	GGTGGGATGAAAATAAACCGTGG	60.119	47.826	0.00	0.00	0.00	4.94
2375	2405	6.037172	AGACATTACTAAATAACTTGCGCCAG	59.963	38.462	4.18	5.76	0.00	4.85
2500	2530	1.129251	CAACGACATGCTCACCATCAC	59.871	52.381	0.00	0.00	29.71	3.06
2566	2596	4.790765	TCTGTCAGTTCTTGTCATCGAT	57.209	40.909	0.00	0.00	0.00	3.59
2607	2637	0.461870	TGATGATTTGGGCGAGACCG	60.462	55.000	0.00	0.00	40.62	4.79
2612	2642	0.617935	TCAGGTGATGATTTGGGCGA	59.382	50.000	0.00	0.00	31.12	5.54

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.