AutoCloner

Multiple sequence alignment - TraesCS6B01G458800

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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	TraesCS6B01G458800	chr6B	100.000	2663	0	0	1	2663	713722235	713724897	0.000000e+00	4918.0
1	TraesCS6B01G458800	chr6B	96.076	1376	50	4	1288	2663	713149486	713150857	0.000000e+00	2239.0
2	TraesCS6B01G458800	chr6B	82.029	690	109	12	1	681	713148243	713148926	8.270000e-160	573.0
3	TraesCS6B01G458800	chr6B	77.669	712	130	20	1	688	713939724	713939018	8.880000e-110	407.0
4	TraesCS6B01G458800	chr6B	78.405	602	103	18	1	579	713453234	713452637	1.510000e-97	366.0
5	TraesCS6B01G458800	chr6B	87.823	271	30	3	1593	1862	713472818	713473086	5.530000e-82	315.0
6	TraesCS6B01G458800	chr6B	78.501	507	61	22	706	1186	713148996	713149480	3.350000e-74	289.0
7	TraesCS6B01G458800	chr6A	86.375	1211	136	8	1	1191	613951871	613953072	0.000000e+00	1295.0
8	TraesCS6B01G458800	chr6A	84.519	717	86	17	1132	1843	613953070	613953766	0.000000e+00	686.0
9	TraesCS6B01G458800	chr6A	82.849	688	110	8	1	681	613893895	613893209	6.300000e-171	610.0
10	TraesCS6B01G458800	chr6A	84.368	435	59	8	1248	1679	613892646	613892218	4.100000e-113	418.0
11	TraesCS6B01G458800	chr6A	81.699	153	22	3	1761	1907	613888987	613888835	3.600000e-24	122.0
12	TraesCS6B01G458800	chr6D	79.415	1982	280	65	1	1911	467785517	467783593	0.000000e+00	1282.0
13	TraesCS6B01G458800	chr6D	82.581	1108	149	17	706	1785	467799029	467797938	0.000000e+00	937.0
14	TraesCS6B01G458800	chr6D	81.208	1043	139	20	706	1706	467831866	467832893	0.000000e+00	787.0
15	TraesCS6B01G458800	chr6D	82.177	634	101	11	1	625	467831128	467831758	3.900000e-148	534.0
16	TraesCS6B01G458800	chr6D	81.504	665	88	22	1	638	467799797	467799141	5.080000e-142	514.0
17	TraesCS6B01G458800	chr6D	84.431	334	40	8	1908	2234	467833178	467833506	4.280000e-83	318.0
18	TraesCS6B01G458800	chr6D	92.262	168	12	1	1741	1908	467832894	467833060	1.230000e-58	237.0
19	TraesCS6B01G458800	chr6D	77.867	375	72	10	1288	1655	467812886	467812516	3.450000e-54	222.0
20	TraesCS6B01G458800	chr5A	77.237	1933	333	65	1	1868	482423416	482425306	0.000000e+00	1033.0
21	TraesCS6B01G458800	chr5A	79.151	1626	237	50	313	1882	482371122	482372701	0.000000e+00	1031.0
22	TraesCS6B01G458800	chr5A	76.682	1338	222	55	4	1279	482366914	482368223	0.000000e+00	660.0
23	TraesCS6B01G458800	chr5A	78.626	524	88	15	1	503	482398040	482397520	2.560000e-85	326.0
24	TraesCS6B01G458800	chr5A	92.405	79	6	0	2055	2133	350822986	350823064	2.170000e-21	113.0
25	TraesCS6B01G458800	chr7D	78.481	395	76	8	1256	1647	631281216	631281604	1.580000e-62	250.0
26	TraesCS6B01G458800	chr7D	78.095	210	40	6	977	1183	631069104	631069310	7.740000e-26	128.0
27	TraesCS6B01G458800	chr7D	75.393	191	39	8	989	1175	5012242	5012428	4.720000e-13	86.1
28	TraesCS6B01G458800	chr7D	92.683	41	2	1	740	780	5011928	5011967	1.030000e-04	58.4
29	TraesCS6B01G458800	chr7A	77.830	212	42	5	977	1186	726729263	726729055	2.780000e-25	126.0
30	TraesCS6B01G458800	chr7A	81.046	153	20	5	2275	2421	411920294	411920443	2.170000e-21	113.0
31	TraesCS6B01G458800	chr7A	91.250	80	6	1	2055	2133	411920203	411920282	1.010000e-19	108.0
32	TraesCS6B01G458800	chr7A	85.149	101	14	1	2055	2155	279933943	279933844	4.690000e-18	102.0
33	TraesCS6B01G458800	chr7A	75.393	191	39	8	989	1175	6168127	6168313	4.720000e-13	86.1
34	TraesCS6B01G458800	chr3D	82.051	156	21	4	2271	2421	287514473	287514626	2.780000e-25	126.0
35	TraesCS6B01G458800	chr4A	81.410	156	22	4	2271	2421	524261955	524261802	1.290000e-23	121.0
36	TraesCS6B01G458800	chr4A	92.500	80	5	1	2055	2133	524262042	524261963	2.170000e-21	113.0
37	TraesCS6B01G458800	chr5D	73.867	375	61	30	2058	2421	163242893	163242545	6.020000e-22	115.0
38	TraesCS6B01G458800	chr3A	79.167	120	25	0	1052	1171	691712561	691712442	1.700000e-12	84.2

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	TraesCS6B01G458800	chr6B	713722235	713724897	2662	False	4918.000000	4918	100.000000	1	2663	1	chr6B.!!$F2	2662
1	TraesCS6B01G458800	chr6B	713148243	713150857	2614	False	1033.666667	2239	85.535333	1	2663	3	chr6B.!!$F3	2662
2	TraesCS6B01G458800	chr6B	713939018	713939724	706	True	407.000000	407	77.669000	1	688	1	chr6B.!!$R2	687
3	TraesCS6B01G458800	chr6B	713452637	713453234	597	True	366.000000	366	78.405000	1	579	1	chr6B.!!$R1	578
4	TraesCS6B01G458800	chr6A	613951871	613953766	1895	False	990.500000	1295	85.447000	1	1843	2	chr6A.!!$F1	1842
5	TraesCS6B01G458800	chr6A	613888835	613893895	5060	True	383.333333	610	82.972000	1	1907	3	chr6A.!!$R1	1906
6	TraesCS6B01G458800	chr6D	467783593	467785517	1924	True	1282.000000	1282	79.415000	1	1911	1	chr6D.!!$R1	1910
7	TraesCS6B01G458800	chr6D	467797938	467799797	1859	True	725.500000	937	82.042500	1	1785	2	chr6D.!!$R3	1784
8	TraesCS6B01G458800	chr6D	467831128	467833506	2378	False	469.000000	787	85.019500	1	2234	4	chr6D.!!$F1	2233
9	TraesCS6B01G458800	chr5A	482423416	482425306	1890	False	1033.000000	1033	77.237000	1	1868	1	chr5A.!!$F2	1867
10	TraesCS6B01G458800	chr5A	482366914	482372701	5787	False	845.500000	1031	77.916500	4	1882	2	chr5A.!!$F3	1878
11	TraesCS6B01G458800	chr5A	482397520	482398040	520	True	326.000000	326	78.626000	1	503	1	chr5A.!!$R1	502

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
831	4896	0.034896	GTCTCCTCCGGCTTGAACAA	59.965	55.0	0.0	0.0	0.0	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1988	9440	0.389948	CACTGGAACGTACAGGAGGC	60.39	60.0	20.19	0.0	40.23	4.7	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
58	60	7.939039	TGAGGTGTTTGATCTATTTCAGAAAGT	59.061	33.333	1.28	0.00	36.67	2.66
78	80	7.934120	AGAAAGTTCATAGCTACAAAAGTGAGT	59.066	33.333	0.00	0.00	0.00	3.41
110	116	2.893489	GTTGCCCAATCTGAGGAAACTT	59.107	45.455	0.00	0.00	44.43	2.66
117	123	6.515696	GCCCAATCTGAGGAAACTTATTATGC	60.516	42.308	0.00	0.00	44.43	3.14
122	128	5.064707	TCTGAGGAAACTTATTATGCGCAAC	59.935	40.000	17.11	0.00	44.43	4.17
172	178	4.142093	CCTTCCACCTTCAGCCATATTTTG	60.142	45.833	0.00	0.00	0.00	2.44
198	210	9.750882	GTAAACTATCAATTAACGAGGTTTCAC	57.249	33.333	0.00	7.27	0.00	3.18
237	249	6.266330	GGAGGGATCTTCCATGGAAAAATTAG	59.734	42.308	26.87	14.84	38.64	1.73
240	252	6.836007	GGGATCTTCCATGGAAAAATTAGAGT	59.164	38.462	26.87	10.15	38.64	3.24
455	4380	1.276859	TGCCAGAGCAGACCCATGAT	61.277	55.000	0.00	0.00	46.52	2.45
476	4401	6.788243	TGATGACATGATAACTGCAAATGAC	58.212	36.000	0.00	0.00	0.00	3.06
486	4411	2.061773	CTGCAAATGACGACGTTCTCT	58.938	47.619	0.13	0.00	0.00	3.10
580	4505	2.747446	CACCGACCCTAAAGGAATTGTG	59.253	50.000	0.00	0.00	39.89	3.33
655	4580	4.165372	TGTTCAACCAAACCTTCTCCTAGT	59.835	41.667	0.00	0.00	0.00	2.57
667	4631	4.563786	CCTTCTCCTAGTTTTCGAGGCTTT	60.564	45.833	0.00	0.00	41.52	3.51
668	4632	5.337330	CCTTCTCCTAGTTTTCGAGGCTTTA	60.337	44.000	0.00	0.00	41.52	1.85
704	4734	0.740868	ATGGAGTCGTGCACATTCCG	60.741	55.000	18.64	1.94	0.00	4.30
705	4735	1.080093	GGAGTCGTGCACATTCCGA	60.080	57.895	18.64	4.78	0.00	4.55
706	4736	0.460284	GGAGTCGTGCACATTCCGAT	60.460	55.000	18.64	0.00	32.68	4.18
707	4737	1.359848	GAGTCGTGCACATTCCGATT	58.640	50.000	18.64	4.39	32.68	3.34
708	4738	1.324736	GAGTCGTGCACATTCCGATTC	59.675	52.381	18.64	10.30	32.68	2.52
709	4739	0.373716	GTCGTGCACATTCCGATTCC	59.626	55.000	18.64	0.00	32.68	3.01
786	4816	0.620556	TAGGGAAGGCTTTGCTGGAG	59.379	55.000	0.00	0.00	0.00	3.86
795	4833	1.612726	GCTTTGCTGGAGTCCTCACAT	60.613	52.381	11.33	0.00	0.00	3.21
800	4853	1.137872	GCTGGAGTCCTCACATGTAGG	59.862	57.143	11.33	6.53	35.26	3.18
821	4874	0.818296	AACGGAAGATGTCTCCTCCG	59.182	55.000	17.30	17.30	46.42	4.63
824	4877	1.045911	GGAAGATGTCTCCTCCGGCT	61.046	60.000	0.00	0.00	0.00	5.52
825	4878	0.827368	GAAGATGTCTCCTCCGGCTT	59.173	55.000	0.00	0.00	0.00	4.35
826	4879	0.539051	AAGATGTCTCCTCCGGCTTG	59.461	55.000	0.00	0.00	0.00	4.01
827	4880	0.324738	AGATGTCTCCTCCGGCTTGA	60.325	55.000	0.00	0.00	0.00	3.02
831	4896	0.034896	GTCTCCTCCGGCTTGAACAA	59.965	55.000	0.00	0.00	0.00	2.83
971	5048	7.065683	GGCATTGGACGATTTGGAAATTAAATT	59.934	33.333	0.00	0.00	0.00	1.82
1022	5099	1.745087	GCAATCGCTTGGAATCCTCAA	59.255	47.619	0.00	0.00	32.72	3.02
1094	5175	2.544359	CACGTCGCTGGAACGTTG	59.456	61.111	5.00	0.00	38.07	4.10
1119	5200	6.404734	GGGAAATTGATGATTGTAGTTCGCTT	60.405	38.462	0.00	0.00	0.00	4.68
1126	5207	4.123506	TGATTGTAGTTCGCTTGTCACAA	58.876	39.130	0.00	0.00	0.00	3.33
1159	5297	1.825474	GATCCCTCGTGAACCTCAAGA	59.175	52.381	0.00	0.00	33.97	3.02
1171	5309	8.289618	TCGTGAACCTCAAGAATTTGAAAATAG	58.710	33.333	0.00	0.00	42.48	1.73
1199	5337	0.631212	CCTGCCTTGGGTTCCCTTAT	59.369	55.000	9.43	0.00	0.00	1.73
1206	5344	4.871822	CCTTGGGTTCCCTTATCTCATTT	58.128	43.478	9.43	0.00	0.00	2.32
1209	5347	4.855340	TGGGTTCCCTTATCTCATTTGAC	58.145	43.478	9.43	0.00	0.00	3.18
1234	5372	6.112058	AGTTATGAGCCAACTGAGAGATTTC	58.888	40.000	0.00	0.00	34.96	2.17
1266	5404	4.164988	AGCTATGAGTTATTCCCTGCACTT	59.835	41.667	0.00	0.00	0.00	3.16
1286	5424	6.953167	CACTTGAAAGTCTCGAGATCGATGC	61.953	48.000	19.90	4.24	41.79	3.91
1319	5457	4.701651	CCTTAACATGTCATTCTGCAAGGA	59.298	41.667	0.00	0.00	33.11	3.36
1432	5570	0.803740	CCTGCAAGAGCTCTGCTTTC	59.196	55.000	27.19	13.70	39.88	2.62
1434	5572	1.465387	CTGCAAGAGCTCTGCTTTCAG	59.535	52.381	27.19	20.26	39.88	3.02
1567	5705	1.004560	CCTGCGCTGGAAGAACTGA	60.005	57.895	27.72	0.00	34.07	3.41
1646	5784	5.124457	GCAAGCTAGAGGTCAAAATTGATGA	59.876	40.000	0.00	0.00	39.73	2.92
1671	5809	2.604046	ATGTGGACTGATTACCGAGC	57.396	50.000	0.00	0.00	0.00	5.03
1679	5817	3.798202	ACTGATTACCGAGCATCTTTCC	58.202	45.455	0.00	0.00	0.00	3.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	66	7.549488	ACCATGACTTATACTCACTTTTGTAGC	59.451	37.037	0.00	0.00	0.00	3.58
69	71	6.151144	GGCAACCATGACTTATACTCACTTTT	59.849	38.462	0.00	0.00	0.00	2.27
110	116	3.535280	TGAGGACAGTTGCGCATAATA	57.465	42.857	12.75	0.00	0.00	0.98
117	123	0.671472	TGCAGATGAGGACAGTTGCG	60.671	55.000	0.00	0.00	40.05	4.85
122	128	3.519579	CTGTACTTGCAGATGAGGACAG	58.480	50.000	12.90	12.90	45.51	3.51
172	178	9.750882	GTGAAACCTCGTTAATTGATAGTTTAC	57.249	33.333	0.00	0.00	0.00	2.01
198	210	5.638133	AGATCCCTCCATTGTCATAATTGG	58.362	41.667	0.00	0.00	0.00	3.16
237	249	8.448615	ACACAAAAGTTTATATCCGCTAAACTC	58.551	33.333	8.10	0.00	44.56	3.01
240	252	8.325421	TCACACAAAAGTTTATATCCGCTAAA	57.675	30.769	0.00	0.00	0.00	1.85
273	303	5.943706	TGGAATGCCAAAATTTTGTCATG	57.056	34.783	23.77	12.78	42.49	3.07
455	4380	4.934602	TCGTCATTTGCAGTTATCATGTCA	59.065	37.500	0.00	0.00	0.00	3.58
486	4411	7.602753	TCAATATCAAGACTTTCAAGAGACGA	58.397	34.615	0.00	0.00	0.00	4.20
580	4505	4.393680	TCAACTGTGGGCAATCGTATAAAC	59.606	41.667	0.00	0.00	0.00	2.01
655	4580	4.199310	CCCTGATGATAAAGCCTCGAAAA	58.801	43.478	0.00	0.00	0.00	2.29
667	4631	4.428570	TCCATCTGCATACCCTGATGATA	58.571	43.478	11.74	0.00	41.14	2.15
668	4632	3.254089	TCCATCTGCATACCCTGATGAT	58.746	45.455	11.74	0.00	41.14	2.45
786	4816	1.134788	CCGTTCCCTACATGTGAGGAC	60.135	57.143	16.03	11.24	35.99	3.85
795	4833	2.758979	GAGACATCTTCCGTTCCCTACA	59.241	50.000	0.00	0.00	0.00	2.74
800	4853	1.137282	GGAGGAGACATCTTCCGTTCC	59.863	57.143	0.00	0.00	41.40	3.62
821	4874	3.119137	AGACCAAACAAGTTGTTCAAGCC	60.119	43.478	21.10	10.01	40.14	4.35
824	4877	5.913137	ATCAGACCAAACAAGTTGTTCAA	57.087	34.783	21.10	2.93	40.14	2.69
825	4878	5.913137	AATCAGACCAAACAAGTTGTTCA	57.087	34.783	21.10	1.32	40.14	3.18
826	4879	7.595130	GGAATAATCAGACCAAACAAGTTGTTC	59.405	37.037	21.10	9.31	40.14	3.18
827	4880	7.433680	GGAATAATCAGACCAAACAAGTTGTT	58.566	34.615	15.58	15.58	43.41	2.83
831	4896	5.640147	TGGGAATAATCAGACCAAACAAGT	58.360	37.500	0.00	0.00	0.00	3.16
906	4980	8.299570	AGTTGTAGATATTCCAAACTTTTGCTG	58.700	33.333	0.00	0.00	36.86	4.41
971	5048	2.456000	GCGACGAGCTGATTGGAAA	58.544	52.632	0.00	0.00	44.04	3.13
1094	5175	5.066505	AGCGAACTACAATCATCAATTTCCC	59.933	40.000	0.00	0.00	0.00	3.97
1119	5200	1.675714	CGCAAGCCCTCTATTGTGACA	60.676	52.381	0.00	0.00	38.83	3.58
1126	5207	2.062070	GGGATCGCAAGCCCTCTAT	58.938	57.895	4.64	0.00	41.31	1.98
1159	5297	6.405842	GCAGGGGAATCGACTATTTTCAAATT	60.406	38.462	0.00	0.00	0.00	1.82
1171	5309	1.452108	CCAAGGCAGGGGAATCGAC	60.452	63.158	0.00	0.00	0.00	4.20
1199	5337	5.164620	TGGCTCATAACTGTCAAATGAGA	57.835	39.130	21.98	7.82	46.22	3.27
1228	5366	7.372260	ACTCATAGCTATGACTTGGAAATCT	57.628	36.000	28.69	4.13	37.76	2.40
1231	5369	9.547753	GAATAACTCATAGCTATGACTTGGAAA	57.452	33.333	28.69	13.37	37.76	3.13
1234	5372	6.876257	GGGAATAACTCATAGCTATGACTTGG	59.124	42.308	28.69	21.51	37.76	3.61
1286	5424	3.009033	TGACATGTTAAGGGGAGACAAGG	59.991	47.826	0.00	0.00	0.00	3.61
1319	5457	2.203788	TTCGGAGGCAGGTGAGGT	60.204	61.111	0.00	0.00	0.00	3.85
1353	5491	2.625737	AGTCTCGTTGCATCCTTCATG	58.374	47.619	0.00	0.00	35.29	3.07
1354	5492	4.184629	GTTAGTCTCGTTGCATCCTTCAT	58.815	43.478	0.00	0.00	0.00	2.57
1356	5494	3.585862	TGTTAGTCTCGTTGCATCCTTC	58.414	45.455	0.00	0.00	0.00	3.46
1357	5495	3.258372	TCTGTTAGTCTCGTTGCATCCTT	59.742	43.478	0.00	0.00	0.00	3.36
1358	5496	2.826128	TCTGTTAGTCTCGTTGCATCCT	59.174	45.455	0.00	0.00	0.00	3.24
1432	5570	0.176680	ACGAGATGCCTACAAGCCTG	59.823	55.000	0.00	0.00	0.00	4.85
1434	5572	1.136305	TGTACGAGATGCCTACAAGCC	59.864	52.381	0.00	0.00	0.00	4.35
1473	5611	0.618968	TCTTGAGGGAAGGGAGGCTC	60.619	60.000	5.78	5.78	31.85	4.70
1552	5690	2.485814	AGATTTTCAGTTCTTCCAGCGC	59.514	45.455	0.00	0.00	0.00	5.92
1567	5705	4.009675	TCGGCACTGCAATAGAAGATTTT	58.990	39.130	2.82	0.00	0.00	1.82
1646	5784	3.637229	CGGTAATCAGTCCACATAGTCCT	59.363	47.826	0.00	0.00	0.00	3.85
1679	5817	8.660295	TGGGTATATGGTAGAAGTATACCTTG	57.340	38.462	16.18	0.00	44.91	3.61
1988	9440	0.389948	CACTGGAACGTACAGGAGGC	60.390	60.000	20.19	0.00	40.23	4.70
2088	9545	6.768029	AATACAACATCATTGCACAACAAC	57.232	33.333	0.00	0.00	42.27	3.32
2164	9621	1.628340	CTATCCACCCAGACAACACCA	59.372	52.381	0.00	0.00	0.00	4.17
2426	9883	4.836175	TCTTACACACCACAATACTCTGGA	59.164	41.667	0.00	0.00	0.00	3.86
2539	9996	1.584380	CCTCTGTTCTGCTTGCTGCC	61.584	60.000	0.00	0.00	42.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.