AutoCloner

Multiple sequence alignment - TraesCS3D01G526500

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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	TraesCS3D01G526500	chr3D	100.000	2453	0	0	1	2453	605225020	605222568	0.000000e+00	4530
1	TraesCS3D01G526500	chr3D	91.827	1823	115	20	544	2353	605131873	605133674	0.000000e+00	2510
2	TraesCS3D01G526500	chr3D	91.171	555	35	4	1	547	605120795	605121343	0.000000e+00	741
3	TraesCS3D01G526500	chr3B	91.252	2389	167	22	1	2365	813021366	813023736	0.000000e+00	3216
4	TraesCS3D01G526500	chr3B	91.518	2193	157	16	192	2365	813520565	813522747	0.000000e+00	2992
5	TraesCS3D01G526500	chr3B	89.404	1727	135	29	769	2453	813515514	813517234	0.000000e+00	2132
6	TraesCS3D01G526500	chr3B	90.409	636	46	7	1	627	813664771	813665400	0.000000e+00	822
7	TraesCS3D01G526500	chr3A	90.216	2504	180	36	1	2453	736816109	736818598	0.000000e+00	3206
8	TraesCS3D01G526500	chr3A	90.807	2219	174	18	1	2200	736267130	736269337	0.000000e+00	2940
9	TraesCS3D01G526500	chr3A	90.580	690	52	6	1	680	736730020	736730706	0.000000e+00	902
10	TraesCS3D01G526500	chr3A	89.816	599	48	6	1	591	736263118	736263711	0.000000e+00	756
11	TraesCS3D01G526500	chr3A	93.452	168	10	1	2198	2365	736287480	736287646	5.240000e-62	248
12	TraesCS3D01G526500	chrUn	91.713	1605	107	19	1	1588	361519949	361521544	0.000000e+00	2204
13	TraesCS3D01G526500	chrUn	91.708	1604	108	18	1	1588	361579715	361581309	0.000000e+00	2202
14	TraesCS3D01G526500	chrUn	89.486	1693	129	25	802	2453	363569358	363567674	0.000000e+00	2095
15	TraesCS3D01G526500	chr7A	93.559	1242	68	5	1	1231	519524700	519525940	0.000000e+00	1840
16	TraesCS3D01G526500	chr7A	90.233	1116	95	10	1249	2354	519525925	519527036	0.000000e+00	1445

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	TraesCS3D01G526500	chr3D	605222568	605225020	2452	True	4530.0	4530	100.0000	1	2453	1	chr3D.!!$R1	2452
1	TraesCS3D01G526500	chr3D	605131873	605133674	1801	False	2510.0	2510	91.8270	544	2353	1	chr3D.!!$F2	1809
2	TraesCS3D01G526500	chr3D	605120795	605121343	548	False	741.0	741	91.1710	1	547	1	chr3D.!!$F1	546
3	TraesCS3D01G526500	chr3B	813021366	813023736	2370	False	3216.0	3216	91.2520	1	2365	1	chr3B.!!$F1	2364
4	TraesCS3D01G526500	chr3B	813515514	813522747	7233	False	2562.0	2992	90.4610	192	2453	2	chr3B.!!$F3	2261
5	TraesCS3D01G526500	chr3B	813664771	813665400	629	False	822.0	822	90.4090	1	627	1	chr3B.!!$F2	626
6	TraesCS3D01G526500	chr3A	736816109	736818598	2489	False	3206.0	3206	90.2160	1	2453	1	chr3A.!!$F3	2452
7	TraesCS3D01G526500	chr3A	736263118	736269337	6219	False	1848.0	2940	90.3115	1	2200	2	chr3A.!!$F4	2199
8	TraesCS3D01G526500	chr3A	736730020	736730706	686	False	902.0	902	90.5800	1	680	1	chr3A.!!$F2	679
9	TraesCS3D01G526500	chrUn	361519949	361521544	1595	False	2204.0	2204	91.7130	1	1588	1	chrUn.!!$F1	1587
10	TraesCS3D01G526500	chrUn	361579715	361581309	1594	False	2202.0	2202	91.7080	1	1588	1	chrUn.!!$F2	1587
11	TraesCS3D01G526500	chrUn	363567674	363569358	1684	True	2095.0	2095	89.4860	802	2453	1	chrUn.!!$R1	1651
12	TraesCS3D01G526500	chr7A	519524700	519527036	2336	False	1642.5	1840	91.8960	1	2354	2	chr7A.!!$F1	2353

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
221	5081	2.042464	AGTGTCGGTGGCTGATCATAT	58.958	47.619	0.00	0.00	0.00	1.78	F
1267	6151	1.874231	CATGCAAGGATCTAGCTGCTG	59.126	52.381	13.43	2.51	35.78	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1306	6190	0.037046	CCAAACAAATCCCTGCAGGC	60.037	55.0	28.39	0.0	34.51	4.85	R
2430	7362	0.538287	GAGCCAGCCAACTCCTGTTT	60.538	55.0	0.00	0.0	33.52	2.83	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
148	4164	8.739972	ACTAATCTGAAACTTTCTCTCTCTCTC	58.260	37.037	3.22	0.00	0.00	3.20
149	4165	7.781324	AATCTGAAACTTTCTCTCTCTCTCT	57.219	36.000	3.22	0.00	0.00	3.10
221	5081	2.042464	AGTGTCGGTGGCTGATCATAT	58.958	47.619	0.00	0.00	0.00	1.78
224	5084	2.224281	TGTCGGTGGCTGATCATATTCC	60.224	50.000	0.00	0.00	0.00	3.01
287	5149	5.311265	TCAATGAATGATCTGCCTACCATC	58.689	41.667	0.00	0.00	31.50	3.51
346	5208	3.823304	GGCAGAATATCCAACCATCCTTC	59.177	47.826	0.00	0.00	0.00	3.46
366	5229	8.830915	TCCTTCAAGAATTCAGATAGACTACT	57.169	34.615	8.44	0.00	0.00	2.57
393	5256	2.158385	AGCTGGACCGATTCCTCTAGAT	60.158	50.000	0.00	0.00	46.10	1.98
407	5271	9.838339	GATTCCTCTAGATGGTCTTTGATTTTA	57.162	33.333	0.00	0.00	0.00	1.52
464	5342	5.560953	GCAAGTCTACAAAACTACAAGCCAG	60.561	44.000	0.00	0.00	0.00	4.85
486	5364	5.012893	AGAAACTGGGATGAAATGTTCCTC	58.987	41.667	0.00	0.00	32.34	3.71
526	5404	2.309755	TCCTTCAGTGCATGATTTCCCT	59.690	45.455	0.00	0.00	37.89	4.20
529	5407	2.715046	TCAGTGCATGATTTCCCTGTC	58.285	47.619	0.00	0.00	31.12	3.51
590	5468	6.336566	ACATCATTTGTGTAGAGAGCTAGTG	58.663	40.000	0.00	0.00	37.11	2.74
652	5530	5.586243	ACATCGTCCCATACAAGAGAAAATG	59.414	40.000	0.00	0.00	0.00	2.32
915	5796	5.392767	TGAGCGAGATGGGAGTAAATATC	57.607	43.478	0.00	0.00	0.00	1.63
1127	6008	7.344871	TCCTTTCTCCTATCAACTAAAGTAGGG	59.655	40.741	0.00	0.00	35.50	3.53
1216	6100	9.575783	GGTGTGTGTTTTTCTTTACAGATAAAA	57.424	29.630	0.00	0.00	33.36	1.52
1261	6145	6.309737	GCAAAGAAAAACATGCAAGGATCTAG	59.690	38.462	0.00	0.00	38.63	2.43
1267	6151	1.874231	CATGCAAGGATCTAGCTGCTG	59.126	52.381	13.43	2.51	35.78	4.41
1306	6190	2.529780	TTTGTCAAAATGCCAGCTGG	57.470	45.000	29.34	29.34	38.53	4.85
1333	6217	1.824852	GGGATTTGTTTGGAGCGGAAT	59.175	47.619	0.00	0.00	0.00	3.01
1337	6221	4.555262	GATTTGTTTGGAGCGGAATTCAA	58.445	39.130	7.93	0.00	0.00	2.69
1340	6224	2.955660	TGTTTGGAGCGGAATTCAAAGT	59.044	40.909	7.93	0.00	30.97	2.66
1341	6225	4.138290	TGTTTGGAGCGGAATTCAAAGTA	58.862	39.130	7.93	0.00	30.97	2.24
1352	6236	6.511767	GCGGAATTCAAAGTATCATGGTGTAG	60.512	42.308	7.93	0.00	0.00	2.74
1358	6242	3.887621	AGTATCATGGTGTAGCAACGT	57.112	42.857	0.00	0.00	0.00	3.99
1382	6266	5.012664	TCGTCCCATACTATTGGCATTGTAT	59.987	40.000	0.00	0.00	33.19	2.29
1402	6287	2.907634	TGTGCCGTGTCTGTTTTAGAA	58.092	42.857	0.00	0.00	37.12	2.10
1414	6299	5.915196	GTCTGTTTTAGAATTGCACTGAACC	59.085	40.000	0.00	0.00	37.12	3.62
1479	6364	7.876936	AAATCTTCTTGTGACATGCATCTAT	57.123	32.000	0.00	0.00	0.00	1.98
1484	6370	8.373220	TCTTCTTGTGACATGCATCTATGATAT	58.627	33.333	0.00	0.00	0.00	1.63
1515	6401	8.592809	TGATTGCCAAATTTAGGTGTTCTATTT	58.407	29.630	0.00	0.00	0.00	1.40
1548	6437	8.634475	TTCATGTGCGATATATTATCTGCTAC	57.366	34.615	0.00	8.42	0.00	3.58
1635	6532	1.684983	GCTAACTATACCGGCAGTCCA	59.315	52.381	0.00	0.00	0.00	4.02
1636	6533	2.288273	GCTAACTATACCGGCAGTCCAG	60.288	54.545	0.00	5.16	0.00	3.86
1731	6628	5.614923	ACTTGTAGGATCAGATATCGACG	57.385	43.478	0.00	0.00	0.00	5.12
1877	6778	5.447818	GGCGAATGGAAGAATAACTCAACAG	60.448	44.000	0.00	0.00	0.00	3.16
1882	6783	7.693969	ATGGAAGAATAACTCAACAGGAAAG	57.306	36.000	0.00	0.00	0.00	2.62
1920	6821	3.594603	TGCAAGGCAGACTAGTAAGAC	57.405	47.619	0.00	0.00	33.32	3.01
1953	6854	1.589196	GCCTACTAGCGGCGTTCAG	60.589	63.158	9.37	5.86	37.87	3.02
1956	6857	1.546834	CTACTAGCGGCGTTCAGAAC	58.453	55.000	9.37	2.85	0.00	3.01
1972	6873	6.348132	CGTTCAGAACATGTATTTAGTGGCAA	60.348	38.462	13.82	0.00	0.00	4.52
2010	6911	1.977854	AGTGTGATGGCAGTGGTAAGA	59.022	47.619	0.00	0.00	0.00	2.10
2094	6999	5.918011	CACGCAACACCACTAACAAATTATT	59.082	36.000	0.00	0.00	0.00	1.40
2096	7001	7.591795	CACGCAACACCACTAACAAATTATTAA	59.408	33.333	0.00	0.00	0.00	1.40
2124	7029	0.882042	CATGGACGGTAGATGCCAGC	60.882	60.000	0.00	0.00	33.26	4.85
2166	7071	1.645034	GCTGATGCTCGCTTTGTCTA	58.355	50.000	0.00	0.00	36.03	2.59
2167	7072	2.002586	GCTGATGCTCGCTTTGTCTAA	58.997	47.619	0.00	0.00	36.03	2.10
2171	7076	1.086696	TGCTCGCTTTGTCTAATGGC	58.913	50.000	0.00	0.00	0.00	4.40
2361	7293	1.264826	TCAAACTAAAAGGAACGCCGC	59.735	47.619	0.00	0.00	39.96	6.53
2366	7298	1.363145	TAAAAGGAACGCCGCGATGG	61.363	55.000	21.79	0.00	39.96	3.51
2397	7329	2.027377	CCTCATGGTCATAGATGGAGCC	60.027	54.545	0.00	0.00	31.96	4.70
2403	7335	5.074746	TGGTCATAGATGGAGCCTAAGTA	57.925	43.478	0.00	0.00	31.96	2.24
2405	7337	5.081032	GGTCATAGATGGAGCCTAAGTACT	58.919	45.833	0.00	0.00	0.00	2.73
2426	7358	1.676746	CACATTGGATGGAGGAGCAG	58.323	55.000	0.00	0.00	33.60	4.24
2430	7362	3.157252	GGATGGAGGAGCAGCCGA	61.157	66.667	0.00	0.00	43.43	5.54
2432	7364	1.221840	GATGGAGGAGCAGCCGAAA	59.778	57.895	0.00	0.00	43.43	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
221	5081	2.315176	CACCCCTTGTGTCAAATGGAA	58.685	47.619	0.00	0.00	40.26	3.53
224	5084	0.968405	CCCACCCCTTGTGTCAAATG	59.032	55.000	0.00	0.00	43.85	2.32
323	5185	2.108952	AGGATGGTTGGATATTCTGCCC	59.891	50.000	0.00	0.00	0.00	5.36
346	5208	7.978414	TCAAGCAGTAGTCTATCTGAATTCTTG	59.022	37.037	7.05	12.74	33.59	3.02
366	5229	0.391661	GAATCGGTCCAGCTCAAGCA	60.392	55.000	4.59	0.00	45.16	3.91
393	5256	8.417884	ACCGAAAGAAAATAAAATCAAAGACCA	58.582	29.630	0.00	0.00	0.00	4.02
464	5342	5.012893	AGAGGAACATTTCATCCCAGTTTC	58.987	41.667	0.00	0.00	41.13	2.78
480	5358	5.687828	CGGATAGTTATACGTGAGAGGAAC	58.312	45.833	0.00	0.00	35.36	3.62
526	5404	8.074613	AGGTATTAGTGTAGCATGTTTAGACA	57.925	34.615	0.00	0.00	40.71	3.41
529	5407	9.464714	CTGTAGGTATTAGTGTAGCATGTTTAG	57.535	37.037	0.00	0.00	0.00	1.85
590	5468	4.172505	TGTCAATTCTGCACACACAAAAC	58.827	39.130	0.00	0.00	0.00	2.43
652	5530	0.392193	CAGCTGACCATCACCTGTCC	60.392	60.000	8.42	0.00	28.16	4.02
1077	5958	7.129504	GGAAACATATATAGGGATGGGGAGATT	59.870	40.741	0.00	0.00	0.00	2.40
1216	6100	1.482593	CGGGTGAACTAGATCCTTGCT	59.517	52.381	0.00	0.00	0.00	3.91
1267	6151	3.488090	GCACTCACGGCCGTAAGC	61.488	66.667	33.70	26.44	42.60	3.09
1270	6154	2.974935	AAAACGCACTCACGGCCGTA	62.975	55.000	33.70	18.19	37.37	4.02
1271	6155	4.903010	AAACGCACTCACGGCCGT	62.903	61.111	28.70	28.70	37.37	5.68
1306	6190	0.037046	CCAAACAAATCCCTGCAGGC	60.037	55.000	28.39	0.00	34.51	4.85
1313	6197	1.253100	TTCCGCTCCAAACAAATCCC	58.747	50.000	0.00	0.00	0.00	3.85
1314	6198	3.056891	TGAATTCCGCTCCAAACAAATCC	60.057	43.478	2.27	0.00	0.00	3.01
1333	6217	5.121611	CGTTGCTACACCATGATACTTTGAA	59.878	40.000	0.00	0.00	0.00	2.69
1337	6221	4.181578	GACGTTGCTACACCATGATACTT	58.818	43.478	0.00	0.00	0.00	2.24
1340	6224	2.164827	ACGACGTTGCTACACCATGATA	59.835	45.455	1.65	0.00	0.00	2.15
1341	6225	1.067142	ACGACGTTGCTACACCATGAT	60.067	47.619	1.65	0.00	0.00	2.45
1352	6236	2.503920	ATAGTATGGGACGACGTTGC	57.496	50.000	0.13	0.00	0.00	4.17
1358	6242	3.135712	ACAATGCCAATAGTATGGGACGA	59.864	43.478	7.86	0.00	44.11	4.20
1382	6266	2.605837	TCTAAAACAGACACGGCACA	57.394	45.000	0.00	0.00	0.00	4.57
1402	6287	2.421073	CGACATGATGGTTCAGTGCAAT	59.579	45.455	0.00	0.00	34.73	3.56
1414	6299	6.807720	TCATTTGTCCATTTTTCGACATGATG	59.192	34.615	0.00	0.00	38.72	3.07
1522	6408	9.087424	GTAGCAGATAATATATCGCACATGAAA	57.913	33.333	0.00	0.00	0.00	2.69
1523	6409	8.470002	AGTAGCAGATAATATATCGCACATGAA	58.530	33.333	0.00	0.00	0.00	2.57
1548	6437	3.129287	ACGAGGCCATGCAAATCTAAAAG	59.871	43.478	5.01	0.00	0.00	2.27
1555	6444	1.477553	AATCACGAGGCCATGCAAAT	58.522	45.000	5.01	0.00	0.00	2.32
1593	6490	6.753180	AGCTCAGTTCATTCATGTCGTATAT	58.247	36.000	0.00	0.00	0.00	0.86
1635	6532	1.073199	CTGGGCCCGTCAGAAAACT	59.927	57.895	19.37	0.00	34.36	2.66
1636	6533	0.536460	TTCTGGGCCCGTCAGAAAAC	60.536	55.000	19.37	0.00	45.02	2.43
1645	6542	2.672996	CCTTGTGTTCTGGGCCCG	60.673	66.667	19.37	12.57	0.00	6.13
1685	6582	7.234988	AGTTTCTACCACTAAACATACTCACCT	59.765	37.037	0.00	0.00	37.92	4.00
1751	6648	2.408565	TCACCCCCTCTGGTTGATATC	58.591	52.381	0.00	0.00	36.12	1.63
1752	6649	2.587060	TCACCCCCTCTGGTTGATAT	57.413	50.000	0.00	0.00	36.12	1.63
1754	6651	1.285962	CATTCACCCCCTCTGGTTGAT	59.714	52.381	0.00	0.00	36.12	2.57
1755	6652	0.698238	CATTCACCCCCTCTGGTTGA	59.302	55.000	0.00	0.00	36.12	3.18
1756	6653	0.405585	ACATTCACCCCCTCTGGTTG	59.594	55.000	0.00	0.00	36.12	3.77
1757	6654	0.405585	CACATTCACCCCCTCTGGTT	59.594	55.000	0.00	0.00	36.12	3.67
1758	6655	0.475632	TCACATTCACCCCCTCTGGT	60.476	55.000	0.00	0.00	39.96	4.00
1759	6656	0.698238	TTCACATTCACCCCCTCTGG	59.302	55.000	0.00	0.00	0.00	3.86
1761	6658	2.649312	TCAATTCACATTCACCCCCTCT	59.351	45.455	0.00	0.00	0.00	3.69
1762	6659	3.085952	TCAATTCACATTCACCCCCTC	57.914	47.619	0.00	0.00	0.00	4.30
1838	6739	6.361433	TCCATTCGCCAATCTCCTTTTAATA	58.639	36.000	0.00	0.00	0.00	0.98
1849	6750	5.296780	TGAGTTATTCTTCCATTCGCCAATC	59.703	40.000	0.00	0.00	0.00	2.67
1877	6778	7.494625	TGCATGCTACTAAGTTGTATACTTTCC	59.505	37.037	20.33	0.00	44.73	3.13
1882	6783	6.292919	GCCTTGCATGCTACTAAGTTGTATAC	60.293	42.308	20.33	0.00	0.00	1.47
1903	6804	6.628398	GCACTTATGTCTTACTAGTCTGCCTT	60.628	42.308	0.00	0.00	0.00	4.35
1909	6810	8.812329	CATTTCTGCACTTATGTCTTACTAGTC	58.188	37.037	0.00	0.00	0.00	2.59
1953	6854	7.417612	CACCTATTGCCACTAAATACATGTTC	58.582	38.462	2.30	0.00	0.00	3.18
1956	6857	5.762045	GCACCTATTGCCACTAAATACATG	58.238	41.667	0.00	0.00	46.63	3.21
1972	6873	2.159819	CTAGCGGCATCGGCACCTAT	62.160	60.000	1.45	0.00	43.71	2.57
2010	6911	1.380246	TGGACGCCGGTAGTACCAT	60.380	57.895	19.41	1.25	38.47	3.55
2094	6999	1.834896	ACCGTCCATGGTGCAGTATTA	59.165	47.619	12.58	0.00	41.85	0.98
2096	7001	1.412710	CTACCGTCCATGGTGCAGTAT	59.587	52.381	12.58	0.00	43.68	2.12
2166	7071	3.737559	TTACTGACATTGGGAGCCATT	57.262	42.857	0.00	0.00	31.53	3.16
2167	7072	3.245229	TGTTTACTGACATTGGGAGCCAT	60.245	43.478	0.00	0.00	31.53	4.40
2171	7076	4.021102	AGGTGTTTACTGACATTGGGAG	57.979	45.455	0.00	0.00	0.00	4.30
2281	7186	4.621068	ATCTGTGTAAAATGTGGATGCG	57.379	40.909	0.00	0.00	0.00	4.73
2342	7247	1.681825	GCGGCGTTCCTTTTAGTTTG	58.318	50.000	9.37	0.00	0.00	2.93
2366	7298	1.639298	GACCATGAGGCTGTTGTCGC	61.639	60.000	0.00	0.00	39.06	5.19
2374	7306	2.905085	CTCCATCTATGACCATGAGGCT	59.095	50.000	0.00	0.00	39.06	4.58
2379	7311	4.285517	ACTTAGGCTCCATCTATGACCATG	59.714	45.833	0.00	0.00	0.00	3.66
2426	7358	1.600916	AGCCAACTCCTGTTTCGGC	60.601	57.895	0.00	0.00	39.90	5.54
2430	7362	0.538287	GAGCCAGCCAACTCCTGTTT	60.538	55.000	0.00	0.00	33.52	2.83
2432	7364	2.121992	CTGAGCCAGCCAACTCCTGT	62.122	60.000	0.00	0.00	31.65	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.