AutoCloner

Multiple sequence alignment - TraesCS4B01G166900

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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	TraesCS4B01G166900	chr4B	100.000	2499	0	0	1	2499	362748359	362745861	0	4615
1	TraesCS4B01G166900	chr5B	93.490	2504	134	14	1	2499	234165590	234168069	0	3694
2	TraesCS4B01G166900	chr5B	92.022	2507	175	20	1	2499	78448718	78446229	0	3498
3	TraesCS4B01G166900	chr3B	92.900	2507	157	16	1	2499	276871492	276868999	0	3624
4	TraesCS4B01G166900	chr3B	91.573	2504	192	15	1	2499	467936878	467939367	0	3437
5	TraesCS4B01G166900	chr3B	87.896	1578	139	27	944	2499	705854030	705855577	0	1808
6	TraesCS4B01G166900	chr6B	92.381	2507	168	20	1	2499	290886898	290889389	0	3550
7	TraesCS4B01G166900	chr6B	91.653	2504	186	17	1	2499	437833401	437835886	0	3445
8	TraesCS4B01G166900	chr1B	92.185	2508	177	13	1	2499	218454246	218451749	0	3528
9	TraesCS4B01G166900	chr1B	91.166	2513	197	20	1	2499	569691285	569688784	0	3387
10	TraesCS4B01G166900	chr7B	90.419	2505	179	33	1	2499	134469874	134472323	0	3240

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	TraesCS4B01G166900	chr4B	362745861	362748359	2498	True	4615	4615	100.000	1	2499	1	chr4B.!!$R1	2498
1	TraesCS4B01G166900	chr5B	234165590	234168069	2479	False	3694	3694	93.490	1	2499	1	chr5B.!!$F1	2498
2	TraesCS4B01G166900	chr5B	78446229	78448718	2489	True	3498	3498	92.022	1	2499	1	chr5B.!!$R1	2498
3	TraesCS4B01G166900	chr3B	276868999	276871492	2493	True	3624	3624	92.900	1	2499	1	chr3B.!!$R1	2498
4	TraesCS4B01G166900	chr3B	467936878	467939367	2489	False	3437	3437	91.573	1	2499	1	chr3B.!!$F1	2498
5	TraesCS4B01G166900	chr3B	705854030	705855577	1547	False	1808	1808	87.896	944	2499	1	chr3B.!!$F2	1555
6	TraesCS4B01G166900	chr6B	290886898	290889389	2491	False	3550	3550	92.381	1	2499	1	chr6B.!!$F1	2498
7	TraesCS4B01G166900	chr6B	437833401	437835886	2485	False	3445	3445	91.653	1	2499	1	chr6B.!!$F2	2498
8	TraesCS4B01G166900	chr1B	218451749	218454246	2497	True	3528	3528	92.185	1	2499	1	chr1B.!!$R1	2498
9	TraesCS4B01G166900	chr1B	569688784	569691285	2501	True	3387	3387	91.166	1	2499	1	chr1B.!!$R2	2498
10	TraesCS4B01G166900	chr7B	134469874	134472323	2449	False	3240	3240	90.419	1	2499	1	chr7B.!!$F1	2498

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
191	193	0.599204	AAGCGTAACGTCCACACCAG	60.599	55.0	0.0	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1566	1597	0.235665	GCACCACGTGATCACTTGTG	59.764	55.0	25.46	24.53	35.23	3.33	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
115	116	1.661341	GAGCAGAACCAGCTGTATGG	58.339	55.000	13.81	0.00	43.58	2.74
139	140	1.469308	TGTCAAGCGTTTTGGAAACGT	59.531	42.857	22.06	10.16	44.69	3.99
191	193	0.599204	AAGCGTAACGTCCACACCAG	60.599	55.000	0.00	0.00	0.00	4.00
262	269	7.119553	CCAGCCATGCTTTGTTTATGTTTTATT	59.880	33.333	0.00	0.00	36.40	1.40
383	392	0.904865	TCGACCTGGGTGATCTTGCT	60.905	55.000	0.00	0.00	0.00	3.91
402	411	0.681733	TGAGTCTGTGAGGCCACTTC	59.318	55.000	5.01	0.00	43.55	3.01
404	413	0.827925	AGTCTGTGAGGCCACTTCGA	60.828	55.000	5.01	0.00	43.55	3.71
428	437	5.940192	AAATGTCGAAGAATGTAGTTGCA	57.060	34.783	0.00	0.00	39.69	4.08
500	509	3.674410	CGATCATGCAGTACAGTGTGACT	60.674	47.826	5.88	2.92	0.00	3.41
539	549	6.785076	TGGTGACTTCAACCATAAAATCCTA	58.215	36.000	0.00	0.00	31.06	2.94
660	673	7.390440	TGTTTTGTTAGTAGCTATGCTTCACAT	59.610	33.333	0.00	0.00	40.44	3.21
661	674	7.921786	TTTGTTAGTAGCTATGCTTCACATT	57.078	32.000	0.00	0.00	40.44	2.71
766	784	7.117523	TGCAAATTATGTGGCAACTTGAATTAC	59.882	33.333	0.00	0.00	32.54	1.89
822	841	7.014711	TGGCAACTTCTTTTAATTACACATGGA	59.985	33.333	0.00	0.00	37.61	3.41
1015	1039	0.620556	TCCCATGTTCCAGGAGCTTC	59.379	55.000	4.73	0.00	0.00	3.86
1016	1040	0.622665	CCCATGTTCCAGGAGCTTCT	59.377	55.000	4.73	0.00	0.00	2.85
1115	1139	3.325870	TCGATTCAATGCGTTCAGAAGT	58.674	40.909	0.00	0.00	0.00	3.01
1155	1179	6.525578	ACACATGCTGAATTCTTCATCAAT	57.474	33.333	7.05	0.00	39.02	2.57
1175	1199	6.778821	TCAATAACCTCAAAGAGACATGGAA	58.221	36.000	0.00	0.00	0.00	3.53
1221	1245	6.126968	GGGTCCAGATCAATCATTTTCCAATT	60.127	38.462	0.00	0.00	0.00	2.32
1329	1356	5.316167	TCTCCTGTGCATCAAAGTTTATGT	58.684	37.500	0.00	0.00	0.00	2.29
1467	1495	1.503542	CAATGGTCGTTGAGCTGCC	59.496	57.895	0.00	0.00	0.00	4.85
1490	1520	5.478679	CCCAAAATACACATGGAACTGGTTA	59.521	40.000	0.00	0.00	36.27	2.85
1516	1546	3.138304	CTGAAGATTTCAACACGTGGGA	58.862	45.455	21.57	14.17	39.58	4.37
1521	1551	1.822506	TTTCAACACGTGGGACAACA	58.177	45.000	21.57	0.00	44.16	3.33
1528	1558	4.848685	GTGGGACAACACACGAGT	57.151	55.556	0.00	0.00	44.16	4.18
1529	1559	3.972107	GTGGGACAACACACGAGTA	57.028	52.632	0.00	0.00	44.16	2.59
1548	1578	5.009110	CGAGTATTCATAGAGGAAGCTGTCA	59.991	44.000	0.00	0.00	0.00	3.58
1601	1632	2.509336	GCTCCATACACGCACGCT	60.509	61.111	0.00	0.00	0.00	5.07
1836	1873	0.975887	GGTTGGTAGTACCGGTTGGA	59.024	55.000	15.04	0.00	42.58	3.53
1976	2026	4.516321	GGCAACTGCATGATATGTGACATA	59.484	41.667	7.86	7.86	44.36	2.29
1981	2031	5.469084	ACTGCATGATATGTGACATAGCAAG	59.531	40.000	24.81	21.42	33.78	4.01
2035	2085	7.976135	TTATTTAACATGGCAAATGCAGTTT	57.024	28.000	7.80	0.00	44.36	2.66
2066	2116	6.264292	ACATGGCAACTATAGTTTTGTGTCAA	59.736	34.615	15.60	0.00	35.83	3.18
2097	2148	4.188937	AGATACCATTCCACATGGCAAT	57.811	40.909	0.00	0.00	42.82	3.56
2126	2178	6.641169	TTTGATTACACATGGCAACTGTAA	57.359	33.333	17.67	17.67	38.57	2.41
2143	2196	5.375417	CTGTAAGTGATTCACATGGCAAA	57.625	39.130	18.57	0.00	36.74	3.68
2146	2199	7.643569	TGTAAGTGATTCACATGGCAAATAT	57.356	32.000	18.57	0.00	36.74	1.28
2149	2202	6.971726	AGTGATTCACATGGCAAATATGAT	57.028	33.333	18.57	0.00	36.74	2.45
2150	2203	7.356089	AGTGATTCACATGGCAAATATGATT	57.644	32.000	18.57	0.00	36.74	2.57
2151	2204	7.788026	AGTGATTCACATGGCAAATATGATTT	58.212	30.769	18.57	0.00	36.74	2.17
2152	2205	8.262227	AGTGATTCACATGGCAAATATGATTTT	58.738	29.630	18.57	0.00	36.74	1.82
2206	2263	7.679400	GCCATTTTTCAATAGATCGACATGTCA	60.679	37.037	24.93	12.75	0.00	3.58
2207	2264	8.183536	CCATTTTTCAATAGATCGACATGTCAA	58.816	33.333	24.93	7.97	0.00	3.18
2468	2530	0.030638	CTTTTATGGATTGCCCGCCG	59.969	55.000	0.00	0.00	37.93	6.46
2492	2554	7.068955	CGCTTTCTTTGTTTTCTTGTGTTTTT	58.931	30.769	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	0.698238	CCTCACAAATCCAGGGGTGA	59.302	55.000	0.00	0.00	37.89	4.02
115	116	4.145756	CGTTTCCAAAACGCTTGACAATAC	59.854	41.667	11.45	0.00	36.82	1.89
139	140	0.321671	GTGCTTGCTACTGGACCTCA	59.678	55.000	0.00	0.00	0.00	3.86
191	193	4.336280	AGAAAAGCAAGTGAGGGGTTATC	58.664	43.478	0.00	0.00	0.00	1.75
383	392	0.681733	GAAGTGGCCTCACAGACTCA	59.318	55.000	3.32	0.00	45.91	3.41
402	411	6.031417	GCAACTACATTCTTCGACATTTTTCG	59.969	38.462	0.00	0.00	40.53	3.46
404	413	6.734137	TGCAACTACATTCTTCGACATTTTT	58.266	32.000	0.00	0.00	0.00	1.94
500	509	4.352009	AGTCACCATCCCATATTTTGCAA	58.648	39.130	0.00	0.00	0.00	4.08
539	549	2.328319	TGCTGGGCAAAATTCTTCCTT	58.672	42.857	0.00	0.00	34.76	3.36
766	784	9.874205	ATGTATGAACAAAGTTTCCCAATATTG	57.126	29.630	8.58	8.58	39.58	1.90
922	942	9.681692	CATCAAAAAGAACAATGATGTAGTTGA	57.318	29.630	6.47	0.00	42.53	3.18
1115	1139	6.154534	AGCATGTGTAGTAAGGTCTGTATCAA	59.845	38.462	0.00	0.00	0.00	2.57
1155	1179	4.562757	CGGTTCCATGTCTCTTTGAGGTTA	60.563	45.833	0.00	0.00	0.00	2.85
1175	1199	4.315803	CCTTGAGTTTTCATAGTGACGGT	58.684	43.478	0.00	0.00	32.27	4.83
1221	1245	1.643880	TCGTAGTCGCGACATACTCA	58.356	50.000	37.85	21.32	35.83	3.41
1351	1378	9.088987	TGCCTATAAAAGAAAAAGAATCAGGTT	57.911	29.630	0.00	0.00	0.00	3.50
1467	1495	5.467035	AACCAGTTCCATGTGTATTTTGG	57.533	39.130	0.00	0.00	0.00	3.28
1490	1520	5.277974	CCACGTGTTGAAATCTTCAGTCATT	60.278	40.000	15.65	0.00	41.38	2.57
1516	1546	5.417894	TCCTCTATGAATACTCGTGTGTTGT	59.582	40.000	4.27	0.00	0.00	3.32
1521	1551	4.890581	AGCTTCCTCTATGAATACTCGTGT	59.109	41.667	0.00	0.00	0.00	4.49
1566	1597	0.235665	GCACCACGTGATCACTTGTG	59.764	55.000	25.46	24.53	35.23	3.33
1656	1689	8.830580	GCAGTCATAACATAGAACACATACATT	58.169	33.333	0.00	0.00	0.00	2.71
1661	1694	6.094048	GGTTGCAGTCATAACATAGAACACAT	59.906	38.462	0.00	0.00	0.00	3.21
1667	1700	5.428253	GAAGGGTTGCAGTCATAACATAGA	58.572	41.667	0.00	0.00	0.00	1.98
1772	1809	8.681486	TGAAACATAAACATAGCTGCTATCAT	57.319	30.769	18.87	8.03	0.00	2.45
1836	1873	5.889853	AGGCATCATAGACACATTCAAACAT	59.110	36.000	0.00	0.00	0.00	2.71
1976	2026	6.207417	GCCATGTTATATGTTATCCACTTGCT	59.793	38.462	0.00	0.00	0.00	3.91
1981	2031	7.647715	GTGTTTGCCATGTTATATGTTATCCAC	59.352	37.037	0.00	0.00	0.00	4.02
2066	2116	6.957631	TGTGGAATGGTATCTAGTTGACATT	58.042	36.000	0.00	0.00	0.00	2.71
2097	2148	4.891260	TGCCATGTGTAATCAAAATGCAA	58.109	34.783	0.00	0.00	0.00	4.08
2126	2178	6.971726	ATCATATTTGCCATGTGAATCACT	57.028	33.333	14.97	0.00	35.11	3.41
2162	2219	7.726033	AAATGGCAACTGGGTACATTATAAA	57.274	32.000	0.00	0.00	32.03	1.40
2227	2287	5.174035	CGCATATTTTTCGTTTTCACACCAA	59.826	36.000	0.00	0.00	0.00	3.67
2468	2530	8.282592	AGAAAAACACAAGAAAACAAAGAAAGC	58.717	29.630	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.