AutoCloner

Multiple sequence alignment - TraesCS2B01G452000

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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	TraesCS2B01G452000	chr2B	100.000	2519	0	0	1	2519	646062903	646060385	0.000000e+00	4652
1	TraesCS2B01G452000	chr2B	86.785	1922	233	13	614	2519	45662963	45661047	0.000000e+00	2122
2	TraesCS2B01G452000	chr1B	88.692	2538	253	23	9	2519	661118728	661116198	0.000000e+00	3066
3	TraesCS2B01G452000	chr1B	87.037	2538	279	30	8	2519	426078592	426076079	0.000000e+00	2819
4	TraesCS2B01G452000	chr1B	84.697	379	45	12	8	379	661064690	661064318	1.420000e-97	366
5	TraesCS2B01G452000	chr1A	85.782	2539	324	25	4	2516	368400977	368403504	0.000000e+00	2654
6	TraesCS2B01G452000	chr6B	85.118	2540	340	28	8	2519	699068340	699065811	0.000000e+00	2562
7	TraesCS2B01G452000	chr2D	84.146	2542	330	48	8	2516	50105908	50108409	0.000000e+00	2394
8	TraesCS2B01G452000	chr4D	84.171	2508	335	45	43	2516	389196245	389198724	0.000000e+00	2375
9	TraesCS2B01G452000	chr7B	81.901	2536	411	34	8	2516	74362230	74364744	0.000000e+00	2097
10	TraesCS2B01G452000	chr5B	81.854	2535	418	29	8	2519	271054477	271051962	0.000000e+00	2095
11	TraesCS2B01G452000	chr3A	84.717	2048	276	26	162	2195	642203995	642206019	0.000000e+00	2013

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	TraesCS2B01G452000	chr2B	646060385	646062903	2518	True	4652	4652	100.000	1	2519	1	chr2B.!!$R2	2518
1	TraesCS2B01G452000	chr2B	45661047	45662963	1916	True	2122	2122	86.785	614	2519	1	chr2B.!!$R1	1905
2	TraesCS2B01G452000	chr1B	661116198	661118728	2530	True	3066	3066	88.692	9	2519	1	chr1B.!!$R3	2510
3	TraesCS2B01G452000	chr1B	426076079	426078592	2513	True	2819	2819	87.037	8	2519	1	chr1B.!!$R1	2511
4	TraesCS2B01G452000	chr1A	368400977	368403504	2527	False	2654	2654	85.782	4	2516	1	chr1A.!!$F1	2512
5	TraesCS2B01G452000	chr6B	699065811	699068340	2529	True	2562	2562	85.118	8	2519	1	chr6B.!!$R1	2511
6	TraesCS2B01G452000	chr2D	50105908	50108409	2501	False	2394	2394	84.146	8	2516	1	chr2D.!!$F1	2508
7	TraesCS2B01G452000	chr4D	389196245	389198724	2479	False	2375	2375	84.171	43	2516	1	chr4D.!!$F1	2473
8	TraesCS2B01G452000	chr7B	74362230	74364744	2514	False	2097	2097	81.901	8	2516	1	chr7B.!!$F1	2508
9	TraesCS2B01G452000	chr5B	271051962	271054477	2515	True	2095	2095	81.854	8	2519	1	chr5B.!!$R1	2511
10	TraesCS2B01G452000	chr3A	642203995	642206019	2024	False	2013	2013	84.717	162	2195	1	chr3A.!!$F1	2033

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
842	900	0.179127	CGAGAGCTCTTCGCCAATGA	60.179	55.0	19.36	0.0	40.39	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1964	2024	0.740149	TGCCACTTCAGTGCTTTGTG	59.26	50.0	1.01	0.0	44.34	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
32	33	2.303890	AGTGCAGAGGTGATGTCATCAA	59.696	45.455	17.11	0.00	41.69	2.57
37	38	3.106054	AGAGGTGATGTCATCAAGCTCT	58.894	45.455	25.28	25.28	41.69	4.09
60	61	4.127040	AGCTGGCAGACGCGAGAG	62.127	66.667	20.86	2.00	46.14	3.20
107	108	3.684788	CGGGAAGATTTGAACGAGTCAAT	59.315	43.478	7.04	0.00	45.71	2.57
110	111	5.393962	GGAAGATTTGAACGAGTCAATTGG	58.606	41.667	5.42	0.00	45.71	3.16
115	117	3.201353	TGAACGAGTCAATTGGGTTGA	57.799	42.857	5.42	0.00	44.36	3.18
128	131	1.448497	GGTTGAGTTGGTGGGTCGA	59.552	57.895	0.00	0.00	0.00	4.20
253	280	2.703536	TGAGCCTCTCGTCTATCTCTCT	59.296	50.000	0.00	0.00	32.35	3.10
321	368	3.197790	CCATGGTTGCGCTCTCCG	61.198	66.667	9.73	0.00	40.75	4.63
370	417	1.444917	CGATCAGGTCCGATCCACGA	61.445	60.000	14.29	0.00	45.77	4.35
452	507	1.468736	CCCGTCTCGTACCTAGCAAAC	60.469	57.143	0.00	0.00	0.00	2.93
453	508	1.471684	CCGTCTCGTACCTAGCAAACT	59.528	52.381	0.00	0.00	0.00	2.66
555	611	1.289380	GACGACGACCTTCAAGCCT	59.711	57.895	0.00	0.00	0.00	4.58
566	622	0.618458	TTCAAGCCTAACCCGCAGAT	59.382	50.000	0.00	0.00	0.00	2.90
576	634	1.522355	CCCGCAGATGCTTCATCGT	60.522	57.895	2.95	0.00	44.67	3.73
661	719	1.228124	CAAGTGGGAAGCGGTGGAA	60.228	57.895	0.00	0.00	0.00	3.53
710	768	1.349973	GCGAAGATTTCCGAGCAGC	59.650	57.895	0.00	0.00	0.00	5.25
712	770	0.460987	CGAAGATTTCCGAGCAGCCT	60.461	55.000	0.00	0.00	0.00	4.58
713	771	1.202417	CGAAGATTTCCGAGCAGCCTA	60.202	52.381	0.00	0.00	0.00	3.93
842	900	0.179127	CGAGAGCTCTTCGCCAATGA	60.179	55.000	19.36	0.00	40.39	2.57
854	912	0.737219	GCCAATGACATCAGAGGTGC	59.263	55.000	0.00	0.00	0.00	5.01
855	913	1.681166	GCCAATGACATCAGAGGTGCT	60.681	52.381	0.00	0.00	0.00	4.40
1009	1068	5.361857	CAGTGGATGCCTAAGATGGATTTTT	59.638	40.000	0.00	0.00	0.00	1.94
1152	1211	1.740025	GCTCACTGGTACCAAGCATTC	59.260	52.381	25.60	7.79	33.21	2.67
1167	1226	2.168106	AGCATTCAAACAAACAGGTGCA	59.832	40.909	0.00	0.00	34.01	4.57
1224	1283	6.631971	TTGCAAGAGTTTGATGTGAATGTA	57.368	33.333	0.00	0.00	36.36	2.29
1294	1354	3.568007	TGTGGAGGAATACAAGCAACAAC	59.432	43.478	0.00	0.00	0.00	3.32
1300	1360	6.092807	GGAGGAATACAAGCAACAACTCTTAG	59.907	42.308	0.00	0.00	0.00	2.18
1303	1363	7.173390	AGGAATACAAGCAACAACTCTTAGAAC	59.827	37.037	0.00	0.00	0.00	3.01
1313	1373	6.420913	ACAACTCTTAGAACTGGTGTACAT	57.579	37.500	0.00	0.00	0.00	2.29
1360	1420	6.701145	TCAGTGATACATTCCTAGTCACTC	57.299	41.667	6.88	0.00	45.48	3.51
1516	1576	5.951747	AGTTTTACCAAGACACCATATGCAT	59.048	36.000	3.79	3.79	0.00	3.96
1520	1580	5.573380	ACCAAGACACCATATGCATAGAT	57.427	39.130	12.79	0.00	0.00	1.98
1527	1587	8.427902	AGACACCATATGCATAGATAGAGAAA	57.572	34.615	12.79	0.00	0.00	2.52
1539	1599	7.493367	CATAGATAGAGAAAAAGTCGGGTCTT	58.507	38.462	0.00	0.00	0.00	3.01
1546	1606	2.922740	AAAGTCGGGTCTTGCTACAA	57.077	45.000	0.00	0.00	0.00	2.41
1585	1645	2.579873	AGCAATGCAAGGAATATCGCT	58.420	42.857	8.35	0.00	0.00	4.93
1617	1677	5.163290	TGGACTGTGTTATAAGTGTGGTGAA	60.163	40.000	0.00	0.00	0.00	3.18
1620	1680	7.040686	GGACTGTGTTATAAGTGTGGTGAAAAT	60.041	37.037	0.00	0.00	0.00	1.82
1810	1870	5.119125	GCTGCTCATCCAAAAACAATACAAC	59.881	40.000	0.00	0.00	0.00	3.32
1870	1930	2.280389	ACTCAGGCAGCACACACG	60.280	61.111	0.00	0.00	0.00	4.49
1989	2049	1.160137	GCACTGAAGTGGCACCTAAG	58.840	55.000	15.27	6.53	45.72	2.18
2196	2256	5.564848	GCCTGTCAAACAAGAGGAAATTACC	60.565	44.000	0.00	0.00	31.31	2.85
2302	2374	2.485479	CCTGCCACTGAAGTACAACAGT	60.485	50.000	15.76	15.76	46.32	3.55
2308	2380	4.798387	CCACTGAAGTACAACAGTTTTTGC	59.202	41.667	17.93	0.00	43.52	3.68
2364	2436	0.179048	TGCCTCCACACAGAGTGTTG	60.179	55.000	0.00	0.00	45.08	3.33
2426	2498	1.879575	TGCAGGCCCTACAGATACTT	58.120	50.000	0.00	0.00	0.00	2.24
2482	2555	5.298276	GTGAAAGAAATGTTGGACAGTGGTA	59.702	40.000	0.00	0.00	0.00	3.25
2516	2589	4.412075	GAGCCCTTTTGCTGCTCT	57.588	55.556	0.00	0.00	46.19	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.224305	ACCTCTGCACTTACAACCTGAC	60.224	50.000	0.00	0.00	0.00	3.51
1	2	2.047061	ACCTCTGCACTTACAACCTGA	58.953	47.619	0.00	0.00	0.00	3.86
2	3	2.146342	CACCTCTGCACTTACAACCTG	58.854	52.381	0.00	0.00	0.00	4.00
3	4	2.047061	TCACCTCTGCACTTACAACCT	58.953	47.619	0.00	0.00	0.00	3.50
5	6	3.403038	ACATCACCTCTGCACTTACAAC	58.597	45.455	0.00	0.00	0.00	3.32
6	7	3.070878	TGACATCACCTCTGCACTTACAA	59.929	43.478	0.00	0.00	0.00	2.41
37	38	4.383861	CGTCTGCCAGCTCTGCCA	62.384	66.667	2.46	0.00	0.00	4.92
107	108	0.106419	GACCCACCAACTCAACCCAA	60.106	55.000	0.00	0.00	0.00	4.12
110	111	0.602905	CTCGACCCACCAACTCAACC	60.603	60.000	0.00	0.00	0.00	3.77
115	117	1.343465	CTACAACTCGACCCACCAACT	59.657	52.381	0.00	0.00	0.00	3.16
119	121	1.079336	GCCTACAACTCGACCCACC	60.079	63.158	0.00	0.00	0.00	4.61
152	155	2.813726	CCCACACACCGACCCTCAA	61.814	63.158	0.00	0.00	0.00	3.02
253	280	0.944999	AGGATAAGAGCAGGGGAGGA	59.055	55.000	0.00	0.00	0.00	3.71
286	317	0.393132	GGCGAGGAGAAGGGGAAAAG	60.393	60.000	0.00	0.00	0.00	2.27
321	368	1.423921	AGGTAGCTAGAGAGAGGAGCC	59.576	57.143	0.00	0.00	36.87	4.70
370	417	3.621558	TCTGATACCAGACTGTCACGAT	58.378	45.455	10.88	0.00	44.01	3.73
490	545	1.482593	CCTCAGGTCAGGAATTACGCT	59.517	52.381	0.00	0.00	35.20	5.07
566	622	1.613317	ATCCCGTCCACGATGAAGCA	61.613	55.000	0.00	0.00	43.02	3.91
710	768	1.064825	ACCTGGTCCAACCTTGTAGG	58.935	55.000	0.00	0.00	39.58	3.18
712	770	2.105821	CTGAACCTGGTCCAACCTTGTA	59.894	50.000	0.00	0.00	39.58	2.41
713	771	0.923358	TGAACCTGGTCCAACCTTGT	59.077	50.000	0.00	0.00	39.58	3.16
842	900	0.545171	CCATCCAGCACCTCTGATGT	59.455	55.000	0.00	0.00	45.72	3.06
854	912	0.901580	GCCCCCAATATGCCATCCAG	60.902	60.000	0.00	0.00	0.00	3.86
855	913	1.155859	GCCCCCAATATGCCATCCA	59.844	57.895	0.00	0.00	0.00	3.41
900	958	2.173758	TACCTGAATTGGACGCGGCA	62.174	55.000	17.00	0.00	0.00	5.69
1009	1068	4.080919	CACATCAGACCCATCAAACCTAGA	60.081	45.833	0.00	0.00	0.00	2.43
1152	1211	1.280066	GCAGTGCACCTGTTTGTTTG	58.720	50.000	14.63	2.66	43.55	2.93
1167	1226	0.185901	ATTGGTCCCAAGTGTGCAGT	59.814	50.000	4.87	0.00	39.47	4.40
1224	1283	6.051717	CAGGTCCTTCATCTTTTGTCGATAT	58.948	40.000	0.00	0.00	0.00	1.63
1294	1354	7.392494	TGACTATGTACACCAGTTCTAAGAG	57.608	40.000	12.04	0.00	0.00	2.85
1303	1363	9.684448	CTCATATAACTTGACTATGTACACCAG	57.316	37.037	0.00	0.68	0.00	4.00
1313	1373	9.143155	TGATTGTAGGCTCATATAACTTGACTA	57.857	33.333	0.00	0.00	0.00	2.59
1360	1420	2.816087	CCTTGAGCCCCATGATAAATCG	59.184	50.000	0.00	0.00	0.00	3.34
1516	1576	6.627508	GCAAGACCCGACTTTTTCTCTATCTA	60.628	42.308	0.00	0.00	0.00	1.98
1520	1580	3.323979	AGCAAGACCCGACTTTTTCTCTA	59.676	43.478	0.00	0.00	0.00	2.43
1527	1587	2.550208	CCTTGTAGCAAGACCCGACTTT	60.550	50.000	10.12	0.00	0.00	2.66
1539	1599	3.517296	TTCCACAAATCCCTTGTAGCA	57.483	42.857	0.00	0.00	46.91	3.49
1546	1606	2.250924	CTTGGCTTTCCACAAATCCCT	58.749	47.619	0.00	0.00	43.33	4.20
1570	1630	1.134431	TGCTCAGCGATATTCCTTGCA	60.134	47.619	0.00	0.00	0.00	4.08
1571	1631	1.586422	TGCTCAGCGATATTCCTTGC	58.414	50.000	0.00	0.00	0.00	4.01
1585	1645	6.149308	CACTTATAACACAGTCCATTTGCTCA	59.851	38.462	0.00	0.00	0.00	4.26
1617	1677	3.776417	ACATATGGCCAGGAGCAAAATTT	59.224	39.130	13.05	0.00	46.50	1.82
1620	1680	2.101783	CACATATGGCCAGGAGCAAAA	58.898	47.619	13.05	0.00	46.50	2.44
1810	1870	2.300152	TGTTTCCCACTAGTGCTCTCAG	59.700	50.000	17.86	2.49	0.00	3.35
1870	1930	1.782028	AAAGCCTGGTCGACAAACGC	61.782	55.000	18.91	10.65	42.26	4.84
1964	2024	0.740149	TGCCACTTCAGTGCTTTGTG	59.260	50.000	1.01	0.00	44.34	3.33
1989	2049	1.463674	CCTGCATCCACCAAGTTACC	58.536	55.000	0.00	0.00	0.00	2.85
2196	2256	1.878522	CTGATCGGCGGAAACCTCG	60.879	63.158	7.21	0.00	0.00	4.63
2205	2265	2.510012	TTCAGCAGCTGATCGGCG	60.510	61.111	25.94	15.92	40.39	6.46
2302	2374	5.146010	ACTTCCTTGTTTCTGTGCAAAAA	57.854	34.783	0.00	0.00	0.00	1.94
2308	2380	7.930217	TCTTGAAATACTTCCTTGTTTCTGTG	58.070	34.615	0.00	0.00	33.06	3.66
2364	2436	6.646267	TGGTAGTAAGTTGATATTGTGGTCC	58.354	40.000	0.00	0.00	0.00	4.46
2482	2555	2.105477	GGCTCATACTGGGTGTGATCAT	59.895	50.000	0.00	0.00	33.55	2.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.