AutoCloner

Multiple sequence alignment - TraesCS3B01G534200

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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	TraesCS3B01G534200	chr3B	100.000	2471	0	0	1	2471	773896423	773898893	0.000000e+00	4564.0
1	TraesCS3B01G534200	chr3B	92.643	802	59	0	872	1673	773762532	773761731	0.000000e+00	1155.0
2	TraesCS3B01G534200	chr3B	87.304	827	47	17	1674	2471	773761623	773760826	0.000000e+00	893.0
3	TraesCS3B01G534200	chr3B	90.694	634	53	2	872	1500	773746169	773745537	0.000000e+00	839.0
4	TraesCS3B01G534200	chr3B	94.872	39	2	0	1710	1748	617265980	617266018	7.380000e-06	62.1
5	TraesCS3B01G534200	chr7A	99.426	871	5	0	1	871	51614889	51615759	0.000000e+00	1581.0
6	TraesCS3B01G534200	chr4B	99.426	871	5	0	1	871	612642843	612643713	0.000000e+00	1581.0
7	TraesCS3B01G534200	chr4B	99.199	874	7	0	1	874	47244800	47245673	0.000000e+00	1576.0
8	TraesCS3B01G534200	chr4B	90.678	118	11	0	871	988	430672648	430672765	9.150000e-35	158.0
9	TraesCS3B01G534200	chrUn	99.311	871	6	0	1	871	172137751	172136881	0.000000e+00	1576.0
10	TraesCS3B01G534200	chr4A	99.424	868	5	0	1	868	542582322	542583189	0.000000e+00	1576.0
11	TraesCS3B01G534200	chr4A	99.199	874	6	1	1	874	97312316	97313188	0.000000e+00	1574.0
12	TraesCS3B01G534200	chr4A	99.199	874	5	2	1	874	677710871	677711742	0.000000e+00	1574.0
13	TraesCS3B01G534200	chr4A	92.920	113	8	0	871	983	714667750	714667862	5.470000e-37	165.0
14	TraesCS3B01G534200	chr2B	99.088	877	7	1	1	876	151961719	151962595	0.000000e+00	1574.0
15	TraesCS3B01G534200	chr1B	99.087	876	8	0	1	876	12454059	12453184	0.000000e+00	1574.0
16	TraesCS3B01G534200	chr3D	92.804	806	57	1	872	1676	579583866	579584671	0.000000e+00	1166.0
17	TraesCS3B01G534200	chr3D	91.798	634	47	1	872	1500	579425675	579425042	0.000000e+00	878.0
18	TraesCS3B01G534200	chr3D	86.874	838	45	29	1671	2471	579584763	579585572	0.000000e+00	878.0
19	TraesCS3B01G534200	chr3D	90.909	352	32	0	2120	2471	579396258	579395907	8.000000e-130	473.0
20	TraesCS3B01G534200	chr3D	90.057	352	35	0	2120	2471	579423948	579423597	8.050000e-125	457.0
21	TraesCS3B01G534200	chr3D	84.375	288	20	7	1800	2087	579396523	579396261	2.440000e-65	259.0
22	TraesCS3B01G534200	chr3D	86.607	112	15	0	909	1020	579397669	579397558	9.280000e-25	124.0
23	TraesCS3B01G534200	chr3A	95.142	597	21	3	1883	2471	714643357	714643953	0.000000e+00	935.0
24	TraesCS3B01G534200	chr3A	91.461	609	52	0	892	1500	714594291	714593683	0.000000e+00	837.0
25	TraesCS3B01G534200	chr3A	92.857	574	41	0	925	1498	714603624	714603051	0.000000e+00	833.0
26	TraesCS3B01G534200	chr3A	90.424	637	52	1	873	1500	714625222	714625858	0.000000e+00	830.0
27	TraesCS3B01G534200	chr3A	89.489	352	37	0	2120	2471	714591755	714591404	1.740000e-121	446.0
28	TraesCS3B01G534200	chr3A	91.379	290	22	3	1800	2087	714592046	714591758	6.410000e-106	394.0
29	TraesCS3B01G534200	chr3A	92.279	272	19	1	1800	2071	714627505	714627774	3.850000e-103	385.0
30	TraesCS3B01G534200	chr3A	94.340	106	3	2	1783	1888	714643154	714643256	2.540000e-35	159.0
31	TraesCS3B01G534200	chr3A	92.982	57	4	0	1527	1583	714602967	714602911	1.570000e-12	84.2
32	TraesCS3B01G534200	chr1D	91.358	81	7	0	1669	1749	394864461	394864541	7.220000e-21	111.0
33	TraesCS3B01G534200	chr1D	95.000	40	2	0	1710	1749	110779051	110779090	2.050000e-06	63.9
34	TraesCS3B01G534200	chr7B	90.741	54	5	0	1689	1742	368148165	368148218	3.410000e-09	73.1
35	TraesCS3B01G534200	chr6A	86.957	69	4	1	1674	1742	610899097	610899034	3.410000e-09	73.1
36	TraesCS3B01G534200	chr1A	88.000	50	5	1	1710	1758	116708230	116708279	9.540000e-05	58.4

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	TraesCS3B01G534200	chr3B	773896423	773898893	2470	False	4564.000000	4564	100.000000	1	2471	1	chr3B.!!$F2	2470
1	TraesCS3B01G534200	chr3B	773760826	773762532	1706	True	1024.000000	1155	89.973500	872	2471	2	chr3B.!!$R2	1599
2	TraesCS3B01G534200	chr3B	773745537	773746169	632	True	839.000000	839	90.694000	872	1500	1	chr3B.!!$R1	628
3	TraesCS3B01G534200	chr7A	51614889	51615759	870	False	1581.000000	1581	99.426000	1	871	1	chr7A.!!$F1	870
4	TraesCS3B01G534200	chr4B	612642843	612643713	870	False	1581.000000	1581	99.426000	1	871	1	chr4B.!!$F3	870
5	TraesCS3B01G534200	chr4B	47244800	47245673	873	False	1576.000000	1576	99.199000	1	874	1	chr4B.!!$F1	873
6	TraesCS3B01G534200	chrUn	172136881	172137751	870	True	1576.000000	1576	99.311000	1	871	1	chrUn.!!$R1	870
7	TraesCS3B01G534200	chr4A	542582322	542583189	867	False	1576.000000	1576	99.424000	1	868	1	chr4A.!!$F2	867
8	TraesCS3B01G534200	chr4A	97312316	97313188	872	False	1574.000000	1574	99.199000	1	874	1	chr4A.!!$F1	873
9	TraesCS3B01G534200	chr4A	677710871	677711742	871	False	1574.000000	1574	99.199000	1	874	1	chr4A.!!$F3	873
10	TraesCS3B01G534200	chr2B	151961719	151962595	876	False	1574.000000	1574	99.088000	1	876	1	chr2B.!!$F1	875
11	TraesCS3B01G534200	chr1B	12453184	12454059	875	True	1574.000000	1574	99.087000	1	876	1	chr1B.!!$R1	875
12	TraesCS3B01G534200	chr3D	579583866	579585572	1706	False	1022.000000	1166	89.839000	872	2471	2	chr3D.!!$F1	1599
13	TraesCS3B01G534200	chr3D	579423597	579425675	2078	True	667.500000	878	90.927500	872	2471	2	chr3D.!!$R2	1599
14	TraesCS3B01G534200	chr3D	579395907	579397669	1762	True	285.333333	473	87.297000	909	2471	3	chr3D.!!$R1	1562
15	TraesCS3B01G534200	chr3A	714625222	714627774	2552	False	607.500000	830	91.351500	873	2071	2	chr3A.!!$F1	1198
16	TraesCS3B01G534200	chr3A	714591404	714594291	2887	True	559.000000	837	90.776333	892	2471	3	chr3A.!!$R1	1579
17	TraesCS3B01G534200	chr3A	714643154	714643953	799	False	547.000000	935	94.741000	1783	2471	2	chr3A.!!$F2	688
18	TraesCS3B01G534200	chr3A	714602911	714603624	713	True	458.600000	833	92.919500	925	1583	2	chr3A.!!$R2	658

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
970	973	6.226787	AGTTACATCTCCACTCTGAACTTTG	58.773	40.0	0.0	0.0	0.0	2.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2355	4253	1.525077	GTTGGCAACCCAGACGACA	60.525	57.895	19.57	0.0	43.37	4.35	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
940	943	9.986833	TTTCATCATGTATGATAAAAACGTGAG	57.013	29.630	7.01	0.00	45.23	3.51
969	972	6.426646	AGTTACATCTCCACTCTGAACTTT	57.573	37.500	0.00	0.00	0.00	2.66
970	973	6.226787	AGTTACATCTCCACTCTGAACTTTG	58.773	40.000	0.00	0.00	0.00	2.77
1017	1034	1.767681	AGCATGGACTCCCTTCATCTC	59.232	52.381	0.00	0.00	0.00	2.75
1064	1081	1.207089	CATTCTCACGCTAACTCCCCA	59.793	52.381	0.00	0.00	0.00	4.96
1090	1107	0.893727	ATCGCCGCCTTCCTTTGTTT	60.894	50.000	0.00	0.00	0.00	2.83
1092	1109	1.739667	GCCGCCTTCCTTTGTTTGT	59.260	52.632	0.00	0.00	0.00	2.83
1109	1126	0.107606	TGTTGTGGCCGTACAGTTGT	60.108	50.000	0.00	0.00	0.00	3.32
1176	1193	0.321996	AGTTTCTCCGCTTCCTGGTC	59.678	55.000	0.00	0.00	0.00	4.02
1190	1207	1.434622	CTGGTCGATGATGGCACTGC	61.435	60.000	0.00	0.00	0.00	4.40
1191	1208	1.153289	GGTCGATGATGGCACTGCT	60.153	57.895	0.00	0.00	0.00	4.24
1297	1314	3.880047	TGAAAATGTCGGAGGTCGTAT	57.120	42.857	0.00	0.00	40.32	3.06
1361	1378	2.102252	ACCGTGGTGCAATTCAAATTGT	59.898	40.909	14.97	0.00	45.77	2.71
1364	1381	3.555139	CGTGGTGCAATTCAAATTGTTGT	59.445	39.130	14.97	0.00	45.77	3.32
1386	1403	3.436577	AGAGACGTGGTTCTAGAGGAA	57.563	47.619	0.00	0.00	0.00	3.36
1478	1495	1.321474	CCTTCTGCTTGAGGTTTGCA	58.679	50.000	0.00	0.00	35.30	4.08
1513	1551	3.609853	TGCTCTGTGTTTCTTTCTGTGT	58.390	40.909	0.00	0.00	0.00	3.72
1678	1858	5.370679	GGTGAAGTAACCAAGGTTTAGTCA	58.629	41.667	10.13	8.16	40.22	3.41
1693	1971	4.704833	TCAGCCCTGGAGTTGCGC	62.705	66.667	0.00	0.00	0.00	6.09
1705	1983	2.297597	GGAGTTGCGCCTCATAGACTAT	59.702	50.000	14.42	0.00	32.91	2.12
1749	2027	2.014857	CCTTCGACTCGTAGTCCATGA	58.985	52.381	0.00	0.46	42.12	3.07
1769	2047	3.263425	TGAAAGTAATGAGTGGGTCCCTC	59.737	47.826	10.00	5.53	0.00	4.30
1770	2048	1.486211	AGTAATGAGTGGGTCCCTCG	58.514	55.000	10.00	0.00	0.00	4.63
1778	2056	0.395312	GTGGGTCCCTCGTTCTGAAA	59.605	55.000	10.00	0.00	0.00	2.69
1779	2057	1.003233	GTGGGTCCCTCGTTCTGAAAT	59.997	52.381	10.00	0.00	0.00	2.17
2028	3924	7.159322	TCAACTGCAAGGTTAGTTTTTGTAA	57.841	32.000	0.00	0.00	39.30	2.41
2195	4093	1.528129	CCCTTCAGTTCAGTGCTTCC	58.472	55.000	0.00	0.00	0.00	3.46
2345	4243	3.370978	GGCATATGGTTCAACGATATCCG	59.629	47.826	4.56	0.00	45.44	4.18
2355	4253	1.591594	CGATATCCGGTTGCGCACT	60.592	57.895	11.12	0.00	33.91	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
209	210	3.766691	CCCCACTACCCACGTCCG	61.767	72.222	0.00	0.00	0.00	4.79
935	938	3.003897	GGAGATGTAACTAGAGCCTCACG	59.996	52.174	0.00	0.00	0.00	4.35
940	943	4.037446	CAGAGTGGAGATGTAACTAGAGCC	59.963	50.000	0.00	0.00	0.00	4.70
969	972	2.445427	CATACAACCCATGAGGCAACA	58.555	47.619	0.00	0.00	40.58	3.33
970	973	1.134946	GCATACAACCCATGAGGCAAC	59.865	52.381	0.00	0.00	40.58	4.17
1017	1034	1.202568	CAGAAGCTTGACGTGCACG	59.797	57.895	35.99	35.99	46.33	5.34
1039	1056	1.816835	AGTTAGCGTGAGAATGTCGGA	59.183	47.619	0.00	0.00	0.00	4.55
1045	1062	1.568504	TGGGGAGTTAGCGTGAGAAT	58.431	50.000	0.00	0.00	0.00	2.40
1064	1081	0.814010	GGAAGGCGGCGATGTATGTT	60.814	55.000	12.98	0.00	0.00	2.71
1090	1107	0.107606	ACAACTGTACGGCCACAACA	60.108	50.000	2.24	2.22	0.00	3.33
1092	1109	1.301423	GAACAACTGTACGGCCACAA	58.699	50.000	2.24	0.00	0.00	3.33
1176	1193	0.098200	CACAAGCAGTGCCATCATCG	59.902	55.000	12.58	0.00	42.15	3.84
1361	1378	4.458295	CCTCTAGAACCACGTCTCTAACAA	59.542	45.833	0.00	0.00	0.00	2.83
1364	1381	4.564782	TCCTCTAGAACCACGTCTCTAA	57.435	45.455	0.00	0.00	0.00	2.10
1478	1495	4.411540	ACACAGAGCATAAGATCCTCCAAT	59.588	41.667	0.00	0.00	0.00	3.16
1513	1551	3.880490	ACGATGTTTGGCTCAACAGTAAA	59.120	39.130	8.47	0.00	0.00	2.01
1584	1656	3.788227	AGTTGCAACTGACCCTAATGA	57.212	42.857	30.66	0.00	37.98	2.57
1647	1720	1.493022	TGGTTACTTCACCCAAGTGCT	59.507	47.619	0.00	0.00	45.60	4.40
1665	1738	1.614317	CCAGGGCTGACTAAACCTTGG	60.614	57.143	0.00	0.00	43.38	3.61
1749	2027	2.236395	CGAGGGACCCACTCATTACTTT	59.764	50.000	14.60	0.00	34.66	2.66
1769	2047	6.771188	ACTTTCTCTGTACATTTCAGAACG	57.229	37.500	0.00	3.02	40.68	3.95
1770	2048	8.660373	CCATACTTTCTCTGTACATTTCAGAAC	58.340	37.037	0.00	0.00	40.68	3.01
1778	2056	7.616150	AGACTACACCATACTTTCTCTGTACAT	59.384	37.037	0.00	0.00	0.00	2.29
1779	2057	6.946583	AGACTACACCATACTTTCTCTGTACA	59.053	38.462	0.00	0.00	0.00	2.90
1997	3893	3.942130	AACCTTGCAGTTGAAATAGGC	57.058	42.857	0.00	0.00	0.00	3.93
2028	3924	9.225436	GAAGACAGAGGAAAATTTAGAGTGAAT	57.775	33.333	0.00	0.00	0.00	2.57
2118	4016	5.749462	AGAAAAGGCAGATGCATACTTACT	58.251	37.500	0.00	3.59	44.36	2.24
2124	4022	3.054139	AGTGGAGAAAAGGCAGATGCATA	60.054	43.478	0.00	0.00	44.36	3.14
2209	4107	2.985847	GCCAGGGACAAGCACACC	60.986	66.667	0.00	0.00	0.00	4.16
2345	4243	2.661866	AGACGACAGTGCGCAACC	60.662	61.111	14.00	0.00	33.86	3.77
2355	4253	1.525077	GTTGGCAACCCAGACGACA	60.525	57.895	19.57	0.00	43.37	4.35
2375	4273	2.671351	GCATCGGTGATCGGATTATCGT	60.671	50.000	14.02	1.08	39.77	3.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.