AutoCloner

Multiple sequence alignment - TraesCS2A01G582800

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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	TraesCS2A01G582800	chr2A	100.000	2494	0	0	1	2494	775063923	775066416	0.000000e+00	4606
1	TraesCS2A01G582800	chr2A	96.364	550	19	1	1	549	213111706	213111157	0.000000e+00	904
2	TraesCS2A01G582800	chr2A	96.007	551	20	2	1	549	27136646	27137196	0.000000e+00	894
3	TraesCS2A01G582800	chr2D	95.957	1410	43	5	1096	2494	649781509	649780103	0.000000e+00	2276
4	TraesCS2A01G582800	chr2D	95.643	459	14	2	671	1128	649781966	649781513	0.000000e+00	732
5	TraesCS2A01G582800	chr2D	98.198	111	2	0	561	671	649782111	649782001	7.040000e-46	195
6	TraesCS2A01G582800	chr2B	92.286	1076	45	16	993	2043	785821506	785820444	0.000000e+00	1493
7	TraesCS2A01G582800	chr2B	96.175	549	19	2	3	549	93633842	93634390	0.000000e+00	896
8	TraesCS2A01G582800	chr2B	95.993	549	22	0	1	549	23320177	23319629	0.000000e+00	893
9	TraesCS2A01G582800	chr2B	92.358	458	30	2	676	1128	785821885	785821428	0.000000e+00	647
10	TraesCS2A01G582800	chr2B	95.880	267	6	4	2035	2299	785797101	785796838	6.370000e-116	427
11	TraesCS2A01G582800	chr2B	96.273	161	5	1	2335	2494	785796849	785796689	1.900000e-66	263
12	TraesCS2A01G582800	chr2B	95.699	93	4	0	561	653	785822028	785821936	1.550000e-32	150
13	TraesCS2A01G582800	chr6A	96.364	550	18	2	1	549	158467260	158466712	0.000000e+00	904
14	TraesCS2A01G582800	chr6A	96.000	550	21	1	1	549	525961307	525960758	0.000000e+00	893
15	TraesCS2A01G582800	chrUn	95.993	549	22	0	1	549	64108967	64109515	0.000000e+00	893
16	TraesCS2A01G582800	chr5A	96.000	550	21	1	1	549	107455364	107454815	0.000000e+00	893
17	TraesCS2A01G582800	chr5A	96.000	550	21	1	1	549	708586959	708586410	0.000000e+00	893

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	TraesCS2A01G582800	chr2A	775063923	775066416	2493	False	4606.000000	4606	100.000000	1	2494	1	chr2A.!!$F2	2493
1	TraesCS2A01G582800	chr2A	213111157	213111706	549	True	904.000000	904	96.364000	1	549	1	chr2A.!!$R1	548
2	TraesCS2A01G582800	chr2A	27136646	27137196	550	False	894.000000	894	96.007000	1	549	1	chr2A.!!$F1	548
3	TraesCS2A01G582800	chr2D	649780103	649782111	2008	True	1067.666667	2276	96.599333	561	2494	3	chr2D.!!$R1	1933
4	TraesCS2A01G582800	chr2B	93633842	93634390	548	False	896.000000	896	96.175000	3	549	1	chr2B.!!$F1	546
5	TraesCS2A01G582800	chr2B	23319629	23320177	548	True	893.000000	893	95.993000	1	549	1	chr2B.!!$R1	548
6	TraesCS2A01G582800	chr2B	785820444	785822028	1584	True	763.333333	1493	93.447667	561	2043	3	chr2B.!!$R3	1482
7	TraesCS2A01G582800	chr6A	158466712	158467260	548	True	904.000000	904	96.364000	1	549	1	chr6A.!!$R1	548
8	TraesCS2A01G582800	chr6A	525960758	525961307	549	True	893.000000	893	96.000000	1	549	1	chr6A.!!$R2	548
9	TraesCS2A01G582800	chrUn	64108967	64109515	548	False	893.000000	893	95.993000	1	549	1	chrUn.!!$F1	548
10	TraesCS2A01G582800	chr5A	107454815	107455364	549	True	893.000000	893	96.000000	1	549	1	chr5A.!!$R1	548
11	TraesCS2A01G582800	chr5A	708586410	708586959	549	True	893.000000	893	96.000000	1	549	1	chr5A.!!$R2	548

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
549	553	1.373812	CGGGGTCGTCCTCCTTTTT	59.626	57.895	0.0	0.0	35.33	1.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2323	2457	0.179004	TCATGGCCACGTGAAAAGGT	60.179	50.0	19.3	0.0	39.59	3.5	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
110	111	4.056125	CGCAGTGGAGACTCGGCA	62.056	66.667	0.00	0.00	43.72	5.69
206	207	1.667151	GCCAAGGTTGATGCAGCAA	59.333	52.632	14.49	14.49	0.00	3.91
379	381	5.547465	CTGTGTGGTCTGTTTGGTATTAGA	58.453	41.667	0.00	0.00	0.00	2.10
514	517	6.648879	ATTAATAAAGTGGCCGTATGCATT	57.351	33.333	3.54	0.00	43.89	3.56
549	553	1.373812	CGGGGTCGTCCTCCTTTTT	59.626	57.895	0.00	0.00	35.33	1.94
618	622	7.502120	AGAATCTCCAACAAAATCCGATATG	57.498	36.000	0.00	0.00	0.00	1.78
760	807	3.399181	CAGGAAGCCACGCCCCTA	61.399	66.667	0.00	0.00	32.38	3.53
960	1011	3.458163	GGGACTCGCCGGTGATCA	61.458	66.667	19.93	0.00	37.63	2.92
1010	1062	1.154225	CGCGACCAATGGCAGAAAC	60.154	57.895	0.00	0.00	0.00	2.78
1103	1155	0.106268	TCACAACCAATGGCACCACT	60.106	50.000	0.00	0.00	0.00	4.00
1121	1251	0.388907	CTGCAACCAATGGCGGAAAG	60.389	55.000	0.00	0.00	38.70	2.62
1385	1516	2.048690	GGCTCCTGATCGGATCGC	60.049	66.667	12.99	9.72	42.12	4.58
1487	1618	2.509336	GCCGTCTGGGTGATCGTG	60.509	66.667	0.00	0.00	38.44	4.35
1499	1630	5.198207	TGGGTGATCGTGAAGTAGAGATTA	58.802	41.667	0.00	0.00	0.00	1.75
1505	1636	2.728922	GTGAAGTAGAGATTACGCCCG	58.271	52.381	0.00	0.00	0.00	6.13
1514	1645	0.094046	GATTACGCCCGTGAACGTTG	59.906	55.000	5.00	0.00	43.35	4.10
1590	1721	2.545946	GACTTCACAGAGGCAAGAACAC	59.454	50.000	0.00	0.00	0.00	3.32
1631	1762	0.258484	ATGATGCCGTTGGAATGGGA	59.742	50.000	0.00	0.00	39.86	4.37
1632	1763	0.394216	TGATGCCGTTGGAATGGGAG	60.394	55.000	0.00	0.00	38.88	4.30
1687	1818	4.461198	ACGTCTCTTTTTCACCTTCCATT	58.539	39.130	0.00	0.00	0.00	3.16
1759	1892	6.088173	CAGGTTGTGTTGTCATTGACATATG	58.912	40.000	19.63	0.00	42.40	1.78
1961	2094	1.136961	TGTTACCCACTGCCATCCCA	61.137	55.000	0.00	0.00	0.00	4.37
1971	2104	1.901159	CTGCCATCCCACAATTTTCCA	59.099	47.619	0.00	0.00	0.00	3.53
2037	2170	9.001542	CATTTTATTGAACCACATTTGTTCCAT	57.998	29.630	0.00	0.00	41.08	3.41
2041	2174	4.474394	TGAACCACATTTGTTCCATGGTA	58.526	39.130	12.58	0.00	42.90	3.25
2067	2200	9.592196	AAAATATTATTGAGGTGAGGTGCATAT	57.408	29.630	0.00	0.00	0.00	1.78
2266	2400	9.791801	AAACCATAAGCAAACAAGGAAATAAAT	57.208	25.926	0.00	0.00	0.00	1.40
2323	2457	2.367648	ACACCACACCCTCCCACA	60.368	61.111	0.00	0.00	0.00	4.17
2325	2459	3.175710	ACCACACCCTCCCACACC	61.176	66.667	0.00	0.00	0.00	4.16
2333	2467	0.889186	CCCTCCCACACCTTTTCACG	60.889	60.000	0.00	0.00	0.00	4.35
2409	2551	0.109412	GAATGCAGCTCGCTTTGCTT	60.109	50.000	11.90	0.00	43.06	3.91
2453	2595	3.064207	GTCTGAATCCTAACACGCACAA	58.936	45.455	0.00	0.00	0.00	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
110	111	0.397675	TCCATCTCCGCTCATCAGGT	60.398	55.000	0.00	0.00	0.00	4.00
206	207	5.752472	CACGAATTCATCTTCAGAGCTGTAT	59.248	40.000	6.22	0.00	0.00	2.29
379	381	2.032681	GGCGCTGAAAGTCTGGGT	59.967	61.111	7.64	0.00	35.30	4.51
459	461	7.068348	ACACAAGACCGTACAGAGTCATATAAT	59.932	37.037	9.57	0.00	35.38	1.28
462	464	4.705507	ACACAAGACCGTACAGAGTCATAT	59.294	41.667	9.57	0.00	35.38	1.78
514	517	2.993008	GGCCTCTGCATCTGGACA	59.007	61.111	0.00	0.00	40.13	4.02
550	554	7.325660	TCTTTGCATGCATGGTTTTTAAAAA	57.674	28.000	27.34	9.31	0.00	1.94
551	555	6.932356	TCTTTGCATGCATGGTTTTTAAAA	57.068	29.167	27.34	7.58	0.00	1.52
552	556	6.765036	TCTTCTTTGCATGCATGGTTTTTAAA	59.235	30.769	27.34	8.36	0.00	1.52
553	557	6.286758	TCTTCTTTGCATGCATGGTTTTTAA	58.713	32.000	27.34	9.13	0.00	1.52
554	558	5.851720	TCTTCTTTGCATGCATGGTTTTTA	58.148	33.333	27.34	0.00	0.00	1.52
555	559	4.706035	TCTTCTTTGCATGCATGGTTTTT	58.294	34.783	27.34	0.00	0.00	1.94
556	560	4.339872	TCTTCTTTGCATGCATGGTTTT	57.660	36.364	27.34	0.00	0.00	2.43
557	561	4.546829	ATCTTCTTTGCATGCATGGTTT	57.453	36.364	27.34	0.62	0.00	3.27
558	562	5.664294	TTATCTTCTTTGCATGCATGGTT	57.336	34.783	27.34	5.76	0.00	3.67
559	563	5.361571	TGATTATCTTCTTTGCATGCATGGT	59.638	36.000	27.34	8.49	0.00	3.55
745	792	0.400594	ATATTAGGGGCGTGGCTTCC	59.599	55.000	0.00	0.00	0.00	3.46
760	807	8.560124	ACTTTGAGATGGAGAAGGACTATATT	57.440	34.615	0.00	0.00	0.00	1.28
960	1011	2.505982	CGGCGAGTGATGGGGATT	59.494	61.111	0.00	0.00	0.00	3.01
1010	1062	3.264897	GTGGTGCTATCGCTGCGG	61.265	66.667	23.03	7.34	36.97	5.69
1084	1136	0.106268	AGTGGTGCCATTGGTTGTGA	60.106	50.000	4.26	0.00	0.00	3.58
1103	1155	1.664873	CTTTCCGCCATTGGTTGCA	59.335	52.632	4.26	0.00	0.00	4.08
1385	1516	1.952296	AGCAGAAACACCAGCAAGAAG	59.048	47.619	0.00	0.00	0.00	2.85
1487	1618	2.357009	TCACGGGCGTAATCTCTACTTC	59.643	50.000	0.00	0.00	0.00	3.01
1505	1636	0.661020	CCTGTTGTCCCAACGTTCAC	59.339	55.000	0.00	0.00	0.00	3.18
1514	1645	3.701664	AGAATCAAATCCCTGTTGTCCC	58.298	45.455	0.00	0.00	0.00	4.46
1631	1762	2.572104	AGGCGACAAATCCTTTAGTCCT	59.428	45.455	0.00	0.00	0.00	3.85
1632	1763	2.937149	GAGGCGACAAATCCTTTAGTCC	59.063	50.000	0.00	0.00	31.71	3.85
1666	1797	5.438761	AAATGGAAGGTGAAAAAGAGACG	57.561	39.130	0.00	0.00	0.00	4.18
1687	1818	8.637986	ACAATAACTAATTCTCAGCACCAAAAA	58.362	29.630	0.00	0.00	0.00	1.94
1759	1892	0.968405	TCTGGAATTTTGCAGCCACC	59.032	50.000	6.92	0.00	45.01	4.61
1891	2024	1.462283	CAAGTGACTTCATCGGCACTG	59.538	52.381	0.00	0.00	40.43	3.66
1961	2094	4.202111	CGAGAGTTTGGGTTGGAAAATTGT	60.202	41.667	0.00	0.00	0.00	2.71
2037	2170	7.284489	GCACCTCACCTCAATAATATTTTACCA	59.716	37.037	0.00	0.00	0.00	3.25
2041	2174	7.902920	ATGCACCTCACCTCAATAATATTTT	57.097	32.000	0.00	0.00	0.00	1.82
2067	2200	8.307483	TGTGGTTTGAATTTCTTTGTTGAACTA	58.693	29.630	0.00	0.00	0.00	2.24
2150	2284	9.489084	GTGGTGCTTGTGATTGAACTATATATA	57.511	33.333	0.00	0.00	0.00	0.86
2266	2400	4.748102	CCGAAGAGTGCACAAGTTTACTTA	59.252	41.667	21.04	0.00	34.28	2.24
2307	2441	2.113139	GTGTGGGAGGGTGTGGTG	59.887	66.667	0.00	0.00	0.00	4.17
2323	2457	0.179004	TCATGGCCACGTGAAAAGGT	60.179	50.000	19.30	0.00	39.59	3.50
2325	2459	0.950836	TGTCATGGCCACGTGAAAAG	59.049	50.000	19.30	0.29	43.81	2.27
2333	2467	1.448540	CGGAGAGTGTCATGGCCAC	60.449	63.158	8.16	0.00	0.00	5.01
2409	2551	2.730382	TGATCACTCGGCCAGTTAGTA	58.270	47.619	2.24	0.00	30.26	1.82
2453	2595	4.730613	GCATGTTTCGTCTTGAACACTGTT	60.731	41.667	0.00	0.00	35.97	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.