AutoCloner

Multiple sequence alignment - TraesCS5A01G142600

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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	TraesCS5A01G142600	chr5A	100.000	3956	0	0	1	3956	316097402	316093447	0.000000e+00	7306
1	TraesCS5A01G142600	chr5D	97.171	3393	86	6	568	3956	238546077	238549463	0.000000e+00	5725
2	TraesCS5A01G142600	chr5D	91.667	516	31	8	1	512	543615130	543615637	0.000000e+00	704
3	TraesCS5A01G142600	chr5D	85.797	521	60	10	1	514	400416889	400417402	1.250000e-149	540
4	TraesCS5A01G142600	chr5B	95.291	3398	123	19	568	3956	266519625	266516256	0.000000e+00	5354
5	TraesCS5A01G142600	chr4B	86.863	1865	192	19	1051	2869	168996642	168994785	0.000000e+00	2037
6	TraesCS5A01G142600	chr4D	86.649	1880	201	20	1042	2875	107690748	107692623	0.000000e+00	2036
7	TraesCS5A01G142600	chr4A	86.839	1854	192	28	1051	2869	468628966	468627130	0.000000e+00	2025
8	TraesCS5A01G142600	chr3D	92.893	591	42	0	2240	2830	456924808	456925398	0.000000e+00	859
9	TraesCS5A01G142600	chr3D	92.692	520	31	5	1	517	460450314	460450829	0.000000e+00	743
10	TraesCS5A01G142600	chr3D	91.555	521	36	6	1	518	460451479	460451994	0.000000e+00	712
11	TraesCS5A01G142600	chr2A	94.646	523	22	3	1	518	754347560	754348081	0.000000e+00	806
12	TraesCS5A01G142600	chr2A	94.264	523	25	2	1	518	527377853	527378375	0.000000e+00	795
13	TraesCS5A01G142600	chr6B	93.078	549	38	0	2278	2826	642929630	642930178	0.000000e+00	804
14	TraesCS5A01G142600	chr7D	92.278	518	34	3	1	516	579330219	579329706	0.000000e+00	730
15	TraesCS5A01G142600	chr6D	85.385	520	61	7	1	513	316228821	316228310	3.500000e-145	525
16	TraesCS5A01G142600	chr3B	81.532	444	66	16	7	441	51921707	51921271	6.290000e-93	351

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	TraesCS5A01G142600	chr5A	316093447	316097402	3955	True	7306.0	7306	100.0000	1	3956	1	chr5A.!!$R1	3955
1	TraesCS5A01G142600	chr5D	238546077	238549463	3386	False	5725.0	5725	97.1710	568	3956	1	chr5D.!!$F1	3388
2	TraesCS5A01G142600	chr5D	543615130	543615637	507	False	704.0	704	91.6670	1	512	1	chr5D.!!$F3	511
3	TraesCS5A01G142600	chr5D	400416889	400417402	513	False	540.0	540	85.7970	1	514	1	chr5D.!!$F2	513
4	TraesCS5A01G142600	chr5B	266516256	266519625	3369	True	5354.0	5354	95.2910	568	3956	1	chr5B.!!$R1	3388
5	TraesCS5A01G142600	chr4B	168994785	168996642	1857	True	2037.0	2037	86.8630	1051	2869	1	chr4B.!!$R1	1818
6	TraesCS5A01G142600	chr4D	107690748	107692623	1875	False	2036.0	2036	86.6490	1042	2875	1	chr4D.!!$F1	1833
7	TraesCS5A01G142600	chr4A	468627130	468628966	1836	True	2025.0	2025	86.8390	1051	2869	1	chr4A.!!$R1	1818
8	TraesCS5A01G142600	chr3D	456924808	456925398	590	False	859.0	859	92.8930	2240	2830	1	chr3D.!!$F1	590
9	TraesCS5A01G142600	chr3D	460450314	460451994	1680	False	727.5	743	92.1235	1	518	2	chr3D.!!$F2	517
10	TraesCS5A01G142600	chr2A	754347560	754348081	521	False	806.0	806	94.6460	1	518	1	chr2A.!!$F2	517
11	TraesCS5A01G142600	chr2A	527377853	527378375	522	False	795.0	795	94.2640	1	518	1	chr2A.!!$F1	517
12	TraesCS5A01G142600	chr6B	642929630	642930178	548	False	804.0	804	93.0780	2278	2826	1	chr6B.!!$F1	548
13	TraesCS5A01G142600	chr7D	579329706	579330219	513	True	730.0	730	92.2780	1	516	1	chr7D.!!$R1	515
14	TraesCS5A01G142600	chr6D	316228310	316228821	511	True	525.0	525	85.3850	1	513	1	chr6D.!!$R1	512

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
690	1869	0.034616	CAGCCCAGCTATCTACCAGC	59.965	60.0	0.0	0.0	36.4	4.85	F
998	2179	0.692419	TCTCCAGCATTCCTCTCCCC	60.692	60.0	0.0	0.0	0.0	4.81	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2074	3301	0.884704	GCTTCTTCAGCCCGTTGTCA	60.885	55.0	0.0	0.00	43.65	3.58	R
2964	4383	0.388907	GACAACATGGCATGCACCAC	60.389	55.0	26.7	11.21	44.17	4.16	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
47	49	5.508200	AAGTGTTGTTTTCGCCAGAATTA	57.492	34.783	0.00	0.00	36.09	1.40
66	68	9.956797	CAGAATTATTTAATTTTGCCTTCAACG	57.043	29.630	1.94	0.00	36.13	4.10
376	388	2.126071	GTCTAGAGCGGCGCAACA	60.126	61.111	35.02	16.56	0.00	3.33
397	409	1.297689	GCTGATGGTGACTGGAGCA	59.702	57.895	0.00	0.00	0.00	4.26
432	444	2.125229	CTCGAGCAGCAGCCATGT	60.125	61.111	0.00	0.00	43.56	3.21
493	1669	3.791320	AGGATAAGAGGACAAGGACACA	58.209	45.455	0.00	0.00	0.00	3.72
518	1694	3.536917	CATAGGAGGCGGCGGACA	61.537	66.667	9.78	0.00	0.00	4.02
519	1695	2.762459	ATAGGAGGCGGCGGACAA	60.762	61.111	9.78	0.00	0.00	3.18
520	1696	2.140792	ATAGGAGGCGGCGGACAAT	61.141	57.895	9.78	0.00	0.00	2.71
521	1697	0.830444	ATAGGAGGCGGCGGACAATA	60.830	55.000	9.78	0.00	0.00	1.90
522	1698	1.461091	TAGGAGGCGGCGGACAATAG	61.461	60.000	9.78	0.00	0.00	1.73
523	1699	2.967615	GAGGCGGCGGACAATAGC	60.968	66.667	9.78	0.00	0.00	2.97
524	1700	3.733344	GAGGCGGCGGACAATAGCA	62.733	63.158	9.78	0.00	34.54	3.49
525	1701	2.591715	GGCGGCGGACAATAGCAT	60.592	61.111	9.78	0.00	34.54	3.79
526	1702	2.186826	GGCGGCGGACAATAGCATT	61.187	57.895	9.78	0.00	34.54	3.56
527	1703	1.724582	GGCGGCGGACAATAGCATTT	61.725	55.000	9.78	0.00	34.54	2.32
528	1704	0.100503	GCGGCGGACAATAGCATTTT	59.899	50.000	9.78	0.00	34.54	1.82
529	1705	1.859998	GCGGCGGACAATAGCATTTTC	60.860	52.381	9.78	0.00	34.54	2.29
530	1706	1.268539	CGGCGGACAATAGCATTTTCC	60.269	52.381	0.00	0.00	34.54	3.13
531	1707	2.024414	GGCGGACAATAGCATTTTCCT	58.976	47.619	10.39	0.00	34.54	3.36
532	1708	2.427095	GGCGGACAATAGCATTTTCCTT	59.573	45.455	10.39	0.00	34.54	3.36
533	1709	3.119137	GGCGGACAATAGCATTTTCCTTT	60.119	43.478	10.39	0.00	34.54	3.11
534	1710	4.494484	GCGGACAATAGCATTTTCCTTTT	58.506	39.130	10.39	0.00	0.00	2.27
535	1711	4.562789	GCGGACAATAGCATTTTCCTTTTC	59.437	41.667	10.39	0.00	0.00	2.29
536	1712	5.622233	GCGGACAATAGCATTTTCCTTTTCT	60.622	40.000	10.39	0.00	0.00	2.52
537	1713	6.389906	CGGACAATAGCATTTTCCTTTTCTT	58.610	36.000	10.39	0.00	0.00	2.52
538	1714	6.868339	CGGACAATAGCATTTTCCTTTTCTTT	59.132	34.615	10.39	0.00	0.00	2.52
539	1715	7.384932	CGGACAATAGCATTTTCCTTTTCTTTT	59.615	33.333	10.39	0.00	0.00	2.27
540	1716	9.056005	GGACAATAGCATTTTCCTTTTCTTTTT	57.944	29.630	6.75	0.00	0.00	1.94
597	1773	2.543031	GCGGTCTCACAATCATACGCTA	60.543	50.000	0.00	0.00	42.18	4.26
618	1794	0.107848	ACCCGAGCCCATAAAAGTCG	60.108	55.000	0.00	0.00	0.00	4.18
619	1795	0.177141	CCCGAGCCCATAAAAGTCGA	59.823	55.000	0.00	0.00	32.32	4.20
620	1796	1.406341	CCCGAGCCCATAAAAGTCGAA	60.406	52.381	0.00	0.00	32.32	3.71
622	1798	2.343101	CGAGCCCATAAAAGTCGAACA	58.657	47.619	0.00	0.00	32.32	3.18
623	1799	2.348666	CGAGCCCATAAAAGTCGAACAG	59.651	50.000	0.00	0.00	32.32	3.16
669	1848	1.576356	GCCTCGCAATTAGGTCAGAG	58.424	55.000	0.00	0.00	36.43	3.35
690	1869	0.034616	CAGCCCAGCTATCTACCAGC	59.965	60.000	0.00	0.00	36.40	4.85
712	1891	4.677378	GCAGTAGTGACTATTACGCATCAG	59.323	45.833	0.42	0.00	33.32	2.90
751	1931	2.026262	TGTTTCTCCCCTATGACAAGCC	60.026	50.000	0.00	0.00	0.00	4.35
784	1964	3.307108	TGGTCCCGCGTGTCATCA	61.307	61.111	4.92	0.00	0.00	3.07
925	2105	5.059833	CCCAAAACCAAAATTCCGAAATCA	58.940	37.500	0.00	0.00	0.00	2.57
973	2153	2.110578	CCCCCAATCCAAACTCCATTC	58.889	52.381	0.00	0.00	0.00	2.67
997	2178	1.347378	GATCTCCAGCATTCCTCTCCC	59.653	57.143	0.00	0.00	0.00	4.30
998	2179	0.692419	TCTCCAGCATTCCTCTCCCC	60.692	60.000	0.00	0.00	0.00	4.81
1000	2181	2.507944	CAGCATTCCTCTCCCCCG	59.492	66.667	0.00	0.00	0.00	5.73
1002	2183	4.570874	GCATTCCTCTCCCCCGCC	62.571	72.222	0.00	0.00	0.00	6.13
1156	2350	2.812619	CCTGATCCTCCCTTCCGCC	61.813	68.421	0.00	0.00	0.00	6.13
1247	2441	3.070987	ATCTACCCCGTCGCCTCCT	62.071	63.158	0.00	0.00	0.00	3.69
1288	2482	3.760035	GCCTCCTTCTCCGCGTCA	61.760	66.667	4.92	0.00	0.00	4.35
1552	2776	2.338984	GACGAGCACCTCCGTGTT	59.661	61.111	0.00	0.00	42.39	3.32
1597	2821	1.173444	CCTCCGACTCCGATTCCGAT	61.173	60.000	0.00	0.00	38.22	4.18
2074	3301	0.689623	CCAAGCTCAAGACCTGGAGT	59.310	55.000	0.00	0.00	33.66	3.85
2254	3481	2.294078	CCGGAGCTTCCTGAGGGTT	61.294	63.158	0.00	0.00	33.30	4.11
2396	3631	2.738147	GCATACTCTGCGTTGTCGT	58.262	52.632	0.00	0.00	41.97	4.34
2596	3831	5.163550	GGCACTTACCAAGTTCTGTTTCTTT	60.164	40.000	0.00	0.00	40.46	2.52
2876	4295	1.749634	AGAAGCTTTGATGCCATGCTC	59.250	47.619	0.00	0.00	33.48	4.26
2909	4328	6.040616	GCTGATGATTCTTTCATTCCCAAGAT	59.959	38.462	0.00	0.00	45.29	2.40
2964	4383	1.352352	AGGTTGACTGGTTGAGGATGG	59.648	52.381	0.00	0.00	0.00	3.51
3009	4428	8.310382	CCACCTGATATTTTCACCAAATTACAA	58.690	33.333	0.00	0.00	36.43	2.41
3028	4447	3.636300	ACAAATAGCAGCCTGACAAACAA	59.364	39.130	0.00	0.00	0.00	2.83
3035	4454	4.082571	AGCAGCCTGACAAACAATGTAATC	60.083	41.667	0.00	0.00	44.12	1.75
3128	4547	4.768968	CCCCATTAGCAAAGGATAATCCAG	59.231	45.833	0.00	0.00	39.61	3.86
3294	4714	9.944663	TTTCTGTATCAATAAAGTTGTGTCAAC	57.055	29.630	4.69	4.69	0.00	3.18
3510	4931	2.092753	CACAGGGCTATGGATGAACTGT	60.093	50.000	0.00	0.00	38.13	3.55
3585	5006	8.147244	AGAACAAGTGTCATAGGGTACTTTAT	57.853	34.615	0.00	0.00	31.47	1.40
3676	5098	3.409851	TTGATTCATTCATGTGCTCGC	57.590	42.857	0.00	0.00	33.34	5.03
3751	5173	7.119387	TCTTGAACCAGACAGACTCATAGATA	58.881	38.462	0.00	0.00	0.00	1.98
3863	5286	5.660417	AGATCCAACCGATGCTATCTATGAT	59.340	40.000	0.00	0.00	31.89	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
168	178	3.237746	TCATGTTGCAAAAATCCTCCCA	58.762	40.909	0.00	0.00	0.00	4.37
214	225	3.842428	CAGCAAACGACATCATCTTTTCG	59.158	43.478	0.00	0.00	37.50	3.46
376	388	0.617413	CTCCAGTCACCATCAGCCTT	59.383	55.000	0.00	0.00	0.00	4.35
432	444	4.492160	CTTACGCCCGCTCGCAGA	62.492	66.667	0.00	0.00	0.00	4.26
493	1669	0.469917	CCGCCTCCTATGTCCAACAT	59.530	55.000	0.00	0.00	42.35	2.71
562	1738	3.054287	TGAGACCGCATATACCCCAAAAA	60.054	43.478	0.00	0.00	0.00	1.94
563	1739	2.506231	TGAGACCGCATATACCCCAAAA	59.494	45.455	0.00	0.00	0.00	2.44
564	1740	2.120312	TGAGACCGCATATACCCCAAA	58.880	47.619	0.00	0.00	0.00	3.28
565	1741	1.414919	GTGAGACCGCATATACCCCAA	59.585	52.381	0.00	0.00	0.00	4.12
566	1742	1.045407	GTGAGACCGCATATACCCCA	58.955	55.000	0.00	0.00	0.00	4.96
597	1773	1.209747	GACTTTTATGGGCTCGGGTCT	59.790	52.381	0.00	0.00	0.00	3.85
618	1794	3.386078	TCAGGTCCAGCATCTATCTGTTC	59.614	47.826	0.00	0.00	0.00	3.18
619	1795	3.378512	TCAGGTCCAGCATCTATCTGTT	58.621	45.455	0.00	0.00	0.00	3.16
620	1796	2.964464	CTCAGGTCCAGCATCTATCTGT	59.036	50.000	0.00	0.00	0.00	3.41
622	1798	1.969923	GCTCAGGTCCAGCATCTATCT	59.030	52.381	0.00	0.00	36.82	1.98
623	1799	1.001860	GGCTCAGGTCCAGCATCTATC	59.998	57.143	3.76	0.00	38.77	2.08
657	1833	0.548510	GGGCTGGCTCTGACCTAATT	59.451	55.000	0.00	0.00	0.00	1.40
669	1848	1.373059	GGTAGATAGCTGGGCTGGC	59.627	63.158	0.00	0.00	40.10	4.85
690	1869	5.683302	CACTGATGCGTAATAGTCACTACTG	59.317	44.000	0.00	0.00	36.36	2.74
700	1879	3.936453	GGGTTGTTCACTGATGCGTAATA	59.064	43.478	0.00	0.00	0.00	0.98
712	1891	0.596082	CATTCCGGTGGGTTGTTCAC	59.404	55.000	0.00	0.00	33.83	3.18
784	1964	1.944234	GCCGCCCCGATGTTTCATTT	61.944	55.000	0.00	0.00	0.00	2.32
838	2018	2.230660	GGCTTTTGGGGATAGGAATCG	58.769	52.381	0.00	0.00	32.44	3.34
973	2153	1.072015	GAGGAATGCTGGAGATCTGGG	59.928	57.143	0.00	0.00	0.00	4.45
1000	2181	0.323451	ATTTTCGGTGGAGAAGGGGC	60.323	55.000	0.00	0.00	0.00	5.80
1002	2183	3.010420	GAGAATTTTCGGTGGAGAAGGG	58.990	50.000	0.00	0.00	0.00	3.95
1005	2186	3.671008	TCGAGAATTTTCGGTGGAGAA	57.329	42.857	17.26	0.00	40.83	2.87
1006	2187	3.447586	AGATCGAGAATTTTCGGTGGAGA	59.552	43.478	17.26	0.00	40.83	3.71
1301	2519	1.745141	GCCCCAGTTGATGAGTAGCAG	60.745	57.143	0.00	0.00	0.00	4.24
1552	2776	1.378250	GTCCTCGTCCTCCTCCGAA	60.378	63.158	0.00	0.00	31.92	4.30
1597	2821	4.465446	CTCCTCCCTCCCTCGGCA	62.465	72.222	0.00	0.00	0.00	5.69
1660	2887	1.302033	CTTGCCGAACAGCCTCACT	60.302	57.895	0.00	0.00	0.00	3.41
2074	3301	0.884704	GCTTCTTCAGCCCGTTGTCA	60.885	55.000	0.00	0.00	43.65	3.58
2185	3412	3.378112	GCAGGAACCGATCAAATTCATCA	59.622	43.478	0.00	0.00	0.00	3.07
2191	3418	1.281867	TCAGGCAGGAACCGATCAAAT	59.718	47.619	0.00	0.00	33.69	2.32
2254	3481	2.253610	ACCTTGGATCTGTAACCGTGA	58.746	47.619	0.00	0.00	0.00	4.35
2396	3631	2.089201	CAGCTGATCCACATTGCTCAA	58.911	47.619	8.42	0.00	0.00	3.02
2575	3810	7.110155	TCAGAAAGAAACAGAACTTGGTAAGT	58.890	34.615	0.00	0.00	45.46	2.24
2596	3831	2.169978	CTCCTTCAGTGCATCCATCAGA	59.830	50.000	0.00	0.00	0.00	3.27
2909	4328	1.360393	AACAGGCCTCAGGTTTCCCA	61.360	55.000	0.00	0.00	0.00	4.37
2924	4343	8.314751	TCAACCTCCTTTATTTAGAGAGAACAG	58.685	37.037	0.00	0.00	0.00	3.16
2964	4383	0.388907	GACAACATGGCATGCACCAC	60.389	55.000	26.70	11.21	44.17	4.16
3009	4428	3.828451	ACATTGTTTGTCAGGCTGCTATT	59.172	39.130	10.34	0.00	30.89	1.73
3028	4447	6.432607	CAACTCAGATGTTGCAGATTACAT	57.567	37.500	1.37	1.37	40.40	2.29
3128	4547	3.603532	TCAGGTTGACATCTGAATCTGC	58.396	45.455	6.56	0.00	37.11	4.26
3266	4686	9.114952	TGACACAACTTTATTGATACAGAAACA	57.885	29.630	0.00	0.00	0.00	2.83
3294	4714	5.537410	CGTGTTTGTTTGCACACTAAAAAG	58.463	37.500	4.37	0.00	41.07	2.27
3510	4931	5.070180	TCAGAACATTTGGGCAGAAAAATGA	59.930	36.000	13.43	2.68	43.41	2.57
3585	5006	6.262944	ACACAAATTGCAAGTTAGATGTCTCA	59.737	34.615	12.36	0.00	0.00	3.27
3676	5098	7.653713	ACGCTAAGGATTTCTATCAACAGTATG	59.346	37.037	0.00	0.00	35.56	2.39
3751	5173	2.768253	TCTCGGCACACTCATCAAAT	57.232	45.000	0.00	0.00	0.00	2.32
3838	5261	5.481824	TCATAGATAGCATCGGTTGGATCTT	59.518	40.000	0.00	0.00	31.28	2.40
3863	5286	6.935167	TGTCAAGCATAGAACTACAGAATGA	58.065	36.000	0.00	0.00	39.69	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.