AutoCloner

Multiple sequence alignment - TraesCS5B01G269700

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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	TraesCS5B01G269700	chr5B	100.000	2255	0	0	1	2255	455626972	455629226	0	4165
1	TraesCS5B01G269700	chr1D	97.857	1680	34	2	577	2255	141314376	141312698	0	2902
2	TraesCS5B01G269700	chr2B	97.798	1680	35	2	577	2255	799246731	799248409	0	2896
3	TraesCS5B01G269700	chr7B	97.739	1681	36	1	577	2255	644466202	644467882	0	2892
4	TraesCS5B01G269700	chr7B	97.909	526	10	1	1	525	644460630	644460105	0	909
5	TraesCS5B01G269700	chrUn	97.679	1680	38	1	577	2255	225927012	225928691	0	2885
6	TraesCS5B01G269700	chrUn	98.286	525	9	0	1	525	395660661	395660137	0	920
7	TraesCS5B01G269700	chrUn	98.289	526	8	1	1	525	454076046	454075521	0	920
8	TraesCS5B01G269700	chrUn	97.909	526	10	1	1	525	384428970	384428445	0	909
9	TraesCS5B01G269700	chrUn	97.714	525	12	0	1	525	189404269	189403745	0	904
10	TraesCS5B01G269700	chr7A	97.619	1680	39	1	577	2255	60149528	60147849	0	2880
11	TraesCS5B01G269700	chr3A	97.619	1680	39	1	577	2255	633110013	633111692	0	2880
12	TraesCS5B01G269700	chr6B	97.381	1680	43	1	577	2255	306997231	306995552	0	2857
13	TraesCS5B01G269700	chr6B	97.917	528	10	1	1	527	307002793	307003320	0	913
14	TraesCS5B01G269700	chr1B	97.378	1678	43	1	579	2255	672477922	672479599	0	2854
15	TraesCS5B01G269700	chr1B	97.323	1681	42	3	577	2255	638701907	638700228	0	2852
16	TraesCS5B01G269700	chr1B	98.289	526	8	1	1	525	668811976	668812501	0	920
17	TraesCS5B01G269700	chr7D	97.909	526	10	1	1	525	382061865	382061340	0	909
18	TraesCS5B01G269700	chr6D	97.905	525	11	0	1	525	458909965	458909441	0	909

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	TraesCS5B01G269700	chr5B	455626972	455629226	2254	False	4165	4165	100.000	1	2255	1	chr5B.!!$F1	2254
1	TraesCS5B01G269700	chr1D	141312698	141314376	1678	True	2902	2902	97.857	577	2255	1	chr1D.!!$R1	1678
2	TraesCS5B01G269700	chr2B	799246731	799248409	1678	False	2896	2896	97.798	577	2255	1	chr2B.!!$F1	1678
3	TraesCS5B01G269700	chr7B	644466202	644467882	1680	False	2892	2892	97.739	577	2255	1	chr7B.!!$F1	1678
4	TraesCS5B01G269700	chr7B	644460105	644460630	525	True	909	909	97.909	1	525	1	chr7B.!!$R1	524
5	TraesCS5B01G269700	chrUn	225927012	225928691	1679	False	2885	2885	97.679	577	2255	1	chrUn.!!$F1	1678
6	TraesCS5B01G269700	chrUn	395660137	395660661	524	True	920	920	98.286	1	525	1	chrUn.!!$R3	524
7	TraesCS5B01G269700	chrUn	454075521	454076046	525	True	920	920	98.289	1	525	1	chrUn.!!$R4	524
8	TraesCS5B01G269700	chrUn	384428445	384428970	525	True	909	909	97.909	1	525	1	chrUn.!!$R2	524
9	TraesCS5B01G269700	chrUn	189403745	189404269	524	True	904	904	97.714	1	525	1	chrUn.!!$R1	524
10	TraesCS5B01G269700	chr7A	60147849	60149528	1679	True	2880	2880	97.619	577	2255	1	chr7A.!!$R1	1678
11	TraesCS5B01G269700	chr3A	633110013	633111692	1679	False	2880	2880	97.619	577	2255	1	chr3A.!!$F1	1678
12	TraesCS5B01G269700	chr6B	306995552	306997231	1679	True	2857	2857	97.381	577	2255	1	chr6B.!!$R1	1678
13	TraesCS5B01G269700	chr6B	307002793	307003320	527	False	913	913	97.917	1	527	1	chr6B.!!$F1	526
14	TraesCS5B01G269700	chr1B	672477922	672479599	1677	False	2854	2854	97.378	579	2255	1	chr1B.!!$F2	1676
15	TraesCS5B01G269700	chr1B	638700228	638701907	1679	True	2852	2852	97.323	577	2255	1	chr1B.!!$R1	1678
16	TraesCS5B01G269700	chr1B	668811976	668812501	525	False	920	920	98.289	1	525	1	chr1B.!!$F1	524
17	TraesCS5B01G269700	chr7D	382061340	382061865	525	True	909	909	97.909	1	525	1	chr7D.!!$R1	524
18	TraesCS5B01G269700	chr6D	458909441	458909965	524	True	909	909	97.905	1	525	1	chr6D.!!$R1	524

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
570	573	0.108585	AGTCCCGCAAGCTTTCTGAA	59.891	50.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1827	1833	0.03563	CAGTGAAGGAAGGGAGCCTG	60.036	60.0	0.0	0.0	35.5	4.85	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
88	89	3.102204	TCAGCTGAATCTGATCAGTGGA	58.898	45.455	21.92	4.02	46.85	4.02
225	226	4.853007	CAGTCTGGGATCCTTTCTTGATT	58.147	43.478	12.58	0.00	0.00	2.57
287	290	0.541863	ATACAGCCAAGACTTCCGGG	59.458	55.000	0.00	0.00	0.00	5.73
324	327	5.300411	TCTCCCTTTTCTACGAAGGTTTT	57.700	39.130	0.00	0.00	41.70	2.43
503	506	5.324409	AGAGAGTGAGAGAAAGAGTGTGAT	58.676	41.667	0.00	0.00	0.00	3.06
509	512	6.491745	AGTGAGAGAAAGAGTGTGATACTTGA	59.508	38.462	0.00	0.00	40.53	3.02
518	521	1.550524	TGTGATACTTGAGCCGCTCTT	59.449	47.619	20.87	8.22	0.00	2.85
527	530	2.503331	TGAGCCGCTCTTCATTTCAAA	58.497	42.857	20.87	0.00	0.00	2.69
528	531	2.485426	TGAGCCGCTCTTCATTTCAAAG	59.515	45.455	20.87	0.00	0.00	2.77
529	532	1.815003	AGCCGCTCTTCATTTCAAAGG	59.185	47.619	0.00	0.00	0.00	3.11
530	533	1.541588	GCCGCTCTTCATTTCAAAGGT	59.458	47.619	0.00	0.00	0.00	3.50
531	534	2.029918	GCCGCTCTTCATTTCAAAGGTT	60.030	45.455	0.00	0.00	0.00	3.50
532	535	3.568538	CCGCTCTTCATTTCAAAGGTTG	58.431	45.455	0.00	0.00	0.00	3.77
533	536	3.004734	CCGCTCTTCATTTCAAAGGTTGT	59.995	43.478	0.00	0.00	0.00	3.32
534	537	3.976942	CGCTCTTCATTTCAAAGGTTGTG	59.023	43.478	0.00	0.00	0.00	3.33
535	538	3.737774	GCTCTTCATTTCAAAGGTTGTGC	59.262	43.478	0.00	0.00	0.00	4.57
536	539	3.963665	TCTTCATTTCAAAGGTTGTGCG	58.036	40.909	0.00	0.00	0.00	5.34
537	540	2.791383	TCATTTCAAAGGTTGTGCGG	57.209	45.000	0.00	0.00	0.00	5.69
538	541	1.339610	TCATTTCAAAGGTTGTGCGGG	59.660	47.619	0.00	0.00	0.00	6.13
539	542	1.339610	CATTTCAAAGGTTGTGCGGGA	59.660	47.619	0.00	0.00	0.00	5.14
540	543	1.028905	TTTCAAAGGTTGTGCGGGAG	58.971	50.000	0.00	0.00	0.00	4.30
555	558	2.156098	CGGGAGCTGATCTAGTAGTCC	58.844	57.143	0.00	0.00	0.00	3.85
556	559	2.521126	GGGAGCTGATCTAGTAGTCCC	58.479	57.143	5.72	5.72	36.51	4.46
557	560	2.156098	GGAGCTGATCTAGTAGTCCCG	58.844	57.143	0.00	0.00	0.00	5.14
558	561	1.538075	GAGCTGATCTAGTAGTCCCGC	59.462	57.143	0.00	0.00	0.00	6.13
559	562	1.133761	AGCTGATCTAGTAGTCCCGCA	60.134	52.381	0.00	0.00	0.00	5.69
560	563	1.681793	GCTGATCTAGTAGTCCCGCAA	59.318	52.381	0.00	0.00	0.00	4.85
561	564	2.287909	GCTGATCTAGTAGTCCCGCAAG	60.288	54.545	0.00	0.00	0.00	4.01
562	565	1.681793	TGATCTAGTAGTCCCGCAAGC	59.318	52.381	0.00	0.00	0.00	4.01
563	566	1.957877	GATCTAGTAGTCCCGCAAGCT	59.042	52.381	0.00	0.00	0.00	3.74
564	567	1.848652	TCTAGTAGTCCCGCAAGCTT	58.151	50.000	0.00	0.00	0.00	3.74
565	568	2.176889	TCTAGTAGTCCCGCAAGCTTT	58.823	47.619	0.00	0.00	0.00	3.51
566	569	2.165845	TCTAGTAGTCCCGCAAGCTTTC	59.834	50.000	0.00	0.00	0.00	2.62
567	570	0.977395	AGTAGTCCCGCAAGCTTTCT	59.023	50.000	0.00	0.00	0.00	2.52
568	571	1.079503	GTAGTCCCGCAAGCTTTCTG	58.920	55.000	0.00	0.00	0.00	3.02
569	572	0.973632	TAGTCCCGCAAGCTTTCTGA	59.026	50.000	0.00	0.00	0.00	3.27
570	573	0.108585	AGTCCCGCAAGCTTTCTGAA	59.891	50.000	0.00	0.00	0.00	3.02
571	574	0.951558	GTCCCGCAAGCTTTCTGAAA	59.048	50.000	0.00	2.44	0.00	2.69
572	575	1.068954	GTCCCGCAAGCTTTCTGAAAG	60.069	52.381	22.62	22.62	41.46	2.62
573	576	0.954452	CCCGCAAGCTTTCTGAAAGT	59.046	50.000	26.02	13.52	40.64	2.66
574	577	1.338020	CCCGCAAGCTTTCTGAAAGTT	59.662	47.619	26.02	19.96	40.64	2.66
575	578	2.552315	CCCGCAAGCTTTCTGAAAGTTA	59.448	45.455	26.02	0.00	40.64	2.24
633	636	8.566260	GCTCTAAATACAGATTCAAAGCATCAT	58.434	33.333	0.00	0.00	0.00	2.45
838	841	1.541588	GCCAAAGGCTTTCTCATTCGT	59.458	47.619	10.08	0.00	46.69	3.85
1005	1010	3.202906	GCTGGTTATCGAGTTTATGGCA	58.797	45.455	0.00	0.00	0.00	4.92
1160	1165	5.329399	TGGCCTATCTTCTTTAAAAAGCCA	58.671	37.500	3.32	0.00	43.97	4.75
1209	1214	5.715070	TGCGTTCCTTTTTCTTTGAAAAGA	58.285	33.333	10.70	1.31	45.20	2.52
1400	1406	8.682936	AAATCATTAAAGATATGCTCGACCTT	57.317	30.769	0.00	0.00	0.00	3.50
1622	1628	2.315720	AGCAAAGGGAGGCTGAAAAT	57.684	45.000	0.00	0.00	39.30	1.82
1625	1631	2.528564	CAAAGGGAGGCTGAAAATCCA	58.471	47.619	0.00	0.00	34.62	3.41
1636	1642	4.640201	GGCTGAAAATCCATAGTGCTAACA	59.360	41.667	0.00	0.00	0.00	2.41
1668	1674	8.352942	CCTGTAGTTTTGAAGCTAAAAAGACAT	58.647	33.333	15.53	5.47	31.53	3.06
1732	1738	3.738281	GCGCTACTCTTCCTTTATGAGCA	60.738	47.826	0.00	0.00	33.62	4.26
1750	1756	4.583907	TGAGCAAGACTCTATCCAGATCTG	59.416	45.833	16.24	16.24	46.41	2.90
1753	1759	4.522405	GCAAGACTCTATCCAGATCTGCTA	59.478	45.833	17.76	7.80	0.00	3.49
1859	1865	3.648067	TCCTTCACTGAACTGATTCACCT	59.352	43.478	0.00	0.00	40.01	4.00
1949	1955	2.598787	CCCCGCCTCCACTTGGTTA	61.599	63.158	0.00	0.00	36.34	2.85
1995	2001	6.239396	GGACTACTTCCTTAAAGAGCCTTTT	58.761	40.000	5.65	0.00	41.95	2.27
2176	2183	4.141665	TGGTACCCGAATCCATTTACGATT	60.142	41.667	10.07	0.00	32.62	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	89	2.481441	TGGTGGATTAGGCAGAGACAT	58.519	47.619	0.00	0.00	0.00	3.06
225	226	2.677836	GCTGCGTATTCAGATCCAAACA	59.322	45.455	0.00	0.00	36.19	2.83
503	506	3.262420	GAAATGAAGAGCGGCTCAAGTA	58.738	45.455	29.88	14.38	32.06	2.24
509	512	1.815003	CCTTTGAAATGAAGAGCGGCT	59.185	47.619	0.00	0.00	0.00	5.52
518	521	1.339610	CCCGCACAACCTTTGAAATGA	59.660	47.619	0.00	0.00	0.00	2.57
527	530	2.527951	GATCAGCTCCCGCACAACCT	62.528	60.000	0.00	0.00	39.10	3.50
528	531	2.045926	ATCAGCTCCCGCACAACC	60.046	61.111	0.00	0.00	39.10	3.77
529	532	0.175760	TAGATCAGCTCCCGCACAAC	59.824	55.000	0.00	0.00	39.10	3.32
530	533	0.461548	CTAGATCAGCTCCCGCACAA	59.538	55.000	0.00	0.00	39.10	3.33
531	534	0.684479	ACTAGATCAGCTCCCGCACA	60.684	55.000	0.00	0.00	39.10	4.57
532	535	1.268352	CTACTAGATCAGCTCCCGCAC	59.732	57.143	0.00	0.00	39.10	5.34
533	536	1.133761	ACTACTAGATCAGCTCCCGCA	60.134	52.381	0.00	0.00	39.10	5.69
534	537	1.538075	GACTACTAGATCAGCTCCCGC	59.462	57.143	0.00	0.00	0.00	6.13
535	538	2.156098	GGACTACTAGATCAGCTCCCG	58.844	57.143	0.00	0.00	0.00	5.14
536	539	2.521126	GGGACTACTAGATCAGCTCCC	58.479	57.143	0.00	6.28	0.00	4.30
537	540	2.156098	CGGGACTACTAGATCAGCTCC	58.844	57.143	0.00	1.33	0.00	4.70
538	541	1.538075	GCGGGACTACTAGATCAGCTC	59.462	57.143	0.00	0.00	0.00	4.09
539	542	1.133761	TGCGGGACTACTAGATCAGCT	60.134	52.381	0.00	0.00	0.00	4.24
540	543	1.319541	TGCGGGACTACTAGATCAGC	58.680	55.000	0.00	2.06	0.00	4.26
541	544	2.287909	GCTTGCGGGACTACTAGATCAG	60.288	54.545	0.00	0.00	0.00	2.90
542	545	1.681793	GCTTGCGGGACTACTAGATCA	59.318	52.381	0.00	0.00	0.00	2.92
543	546	1.957877	AGCTTGCGGGACTACTAGATC	59.042	52.381	0.00	0.00	0.00	2.75
544	547	2.074729	AGCTTGCGGGACTACTAGAT	57.925	50.000	0.00	0.00	0.00	1.98
545	548	1.848652	AAGCTTGCGGGACTACTAGA	58.151	50.000	0.00	0.00	0.00	2.43
546	549	2.166664	AGAAAGCTTGCGGGACTACTAG	59.833	50.000	0.00	0.00	0.00	2.57
547	550	2.094182	CAGAAAGCTTGCGGGACTACTA	60.094	50.000	0.00	0.00	0.00	1.82
548	551	0.977395	AGAAAGCTTGCGGGACTACT	59.023	50.000	0.00	0.00	0.00	2.57
549	552	1.079503	CAGAAAGCTTGCGGGACTAC	58.920	55.000	0.00	0.00	0.00	2.73
550	553	0.973632	TCAGAAAGCTTGCGGGACTA	59.026	50.000	0.00	0.00	0.00	2.59
551	554	0.108585	TTCAGAAAGCTTGCGGGACT	59.891	50.000	0.00	0.00	0.00	3.85
552	555	0.951558	TTTCAGAAAGCTTGCGGGAC	59.048	50.000	0.00	0.00	0.00	4.46
553	556	1.238439	CTTTCAGAAAGCTTGCGGGA	58.762	50.000	10.03	0.00	0.00	5.14
554	557	0.954452	ACTTTCAGAAAGCTTGCGGG	59.046	50.000	21.00	0.00	42.27	6.13
555	558	2.781945	AACTTTCAGAAAGCTTGCGG	57.218	45.000	21.00	0.00	42.27	5.69
556	559	5.034554	TCATAACTTTCAGAAAGCTTGCG	57.965	39.130	21.00	7.91	42.27	4.85
557	560	7.880059	ATTTCATAACTTTCAGAAAGCTTGC	57.120	32.000	21.00	0.00	42.27	4.01
565	568	9.886132	GGGACTACTAATTTCATAACTTTCAGA	57.114	33.333	0.00	0.00	0.00	3.27
566	569	8.818057	CGGGACTACTAATTTCATAACTTTCAG	58.182	37.037	0.00	0.00	0.00	3.02
567	570	7.767198	CCGGGACTACTAATTTCATAACTTTCA	59.233	37.037	0.00	0.00	0.00	2.69
568	571	7.767659	ACCGGGACTACTAATTTCATAACTTTC	59.232	37.037	6.32	0.00	0.00	2.62
569	572	7.627311	ACCGGGACTACTAATTTCATAACTTT	58.373	34.615	6.32	0.00	0.00	2.66
570	573	7.191593	ACCGGGACTACTAATTTCATAACTT	57.808	36.000	6.32	0.00	0.00	2.66
571	574	6.803366	ACCGGGACTACTAATTTCATAACT	57.197	37.500	6.32	0.00	0.00	2.24
572	575	7.720442	ACTACCGGGACTACTAATTTCATAAC	58.280	38.462	6.32	0.00	0.00	1.89
573	576	7.902920	ACTACCGGGACTACTAATTTCATAA	57.097	36.000	6.32	0.00	0.00	1.90
574	577	7.201938	CCAACTACCGGGACTACTAATTTCATA	60.202	40.741	6.32	0.00	0.00	2.15
575	578	6.407752	CCAACTACCGGGACTACTAATTTCAT	60.408	42.308	6.32	0.00	0.00	2.57
659	662	8.669243	GCTTTCTACTTAAATTGCTATGACTGT	58.331	33.333	0.00	0.00	0.00	3.55
1005	1010	1.228306	TTTTTGGATGGTCGGCGGT	60.228	52.632	7.21	0.00	0.00	5.68
1160	1165	8.887036	AAAGTTTTGCGAAATCCTTATCTTTT	57.113	26.923	1.61	0.00	0.00	2.27
1209	1214	3.495276	CGGCCCAAAAATGGTAAGGTTTT	60.495	43.478	0.00	0.00	0.00	2.43
1213	1218	0.108377	GCGGCCCAAAAATGGTAAGG	60.108	55.000	0.00	0.00	0.00	2.69
1400	1406	5.924356	ACGATGATACCATGGACATAAACA	58.076	37.500	21.47	8.65	33.43	2.83
1622	1628	1.404986	GGCGTGTGTTAGCACTATGGA	60.405	52.381	11.22	0.00	45.44	3.41
1625	1631	0.902531	AGGGCGTGTGTTAGCACTAT	59.097	50.000	11.22	0.00	46.53	2.12
1636	1642	2.218603	CTTCAAAACTACAGGGCGTGT	58.781	47.619	17.69	17.69	43.86	4.49
1703	1709	1.064296	GAAGAGTAGCGCGCTAGCA	59.936	57.895	39.08	20.25	45.49	3.49
1732	1738	7.240897	AGATTAGCAGATCTGGATAGAGTCTT	58.759	38.462	23.89	0.00	36.14	3.01
1750	1756	3.301706	CTCGCGGAGTTCTTAGATTAGC	58.698	50.000	6.13	0.00	0.00	3.09
1753	1759	1.534175	CGCTCGCGGAGTTCTTAGATT	60.534	52.381	6.13	0.00	35.56	2.40
1827	1833	0.035630	CAGTGAAGGAAGGGAGCCTG	60.036	60.000	0.00	0.00	35.50	4.85
1941	1947	1.373812	GGCCCGACACTAACCAAGT	59.626	57.895	0.00	0.00	39.81	3.16
1949	1955	4.680537	ACTCTCGGGCCCGACACT	62.681	66.667	42.66	23.65	44.01	3.55
1953	1959	3.147595	CATCACTCTCGGGCCCGA	61.148	66.667	42.62	42.62	46.87	5.14
2176	2183	1.067846	CGATGTGTCTGGAAACTCGGA	60.068	52.381	5.49	0.00	0.00	4.55
2234	2241	3.059352	CCCACTCTTCTTTGATCCGTT	57.941	47.619	0.00	0.00	0.00	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.