AutoCloner

Multiple sequence alignment - TraesCS6D01G221500

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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	TraesCS6D01G221500	chr6D	100.000	2552	0	0	1	2552	312544891	312542340	0.000000e+00	4713.0
1	TraesCS6D01G221500	chr6D	92.509	1989	107	15	592	2552	12108135	12106161	0.000000e+00	2809.0
2	TraesCS6D01G221500	chr6D	96.422	587	21	0	3	589	39289107	39289693	0.000000e+00	968.0
3	TraesCS6D01G221500	chr6D	95.925	589	24	0	1	589	149632872	149633460	0.000000e+00	955.0
4	TraesCS6D01G221500	chr6D	95.918	588	24	0	2	589	131895126	131894539	0.000000e+00	953.0
5	TraesCS6D01G221500	chr1A	94.124	1974	106	8	584	2552	556201756	556203724	0.000000e+00	2994.0
6	TraesCS6D01G221500	chr5D	93.180	1994	91	21	589	2552	44511942	44513920	0.000000e+00	2887.0
7	TraesCS6D01G221500	chr5D	93.333	270	9	2	2292	2552	275161468	275161199	8.560000e-105	390.0
8	TraesCS6D01G221500	chr5D	91.705	217	14	4	2339	2552	514512594	514512379	5.340000e-77	298.0
9	TraesCS6D01G221500	chr4D	92.814	1990	103	12	589	2552	78732770	78730795	0.000000e+00	2846.0
10	TraesCS6D01G221500	chr4D	96.435	589	21	0	1	589	442120919	442121507	0.000000e+00	972.0
11	TraesCS6D01G221500	chr4D	96.259	588	22	0	2	589	324361799	324361212	0.000000e+00	965.0
12	TraesCS6D01G221500	chrUn	93.186	1952	84	22	633	2552	43407879	43409813	0.000000e+00	2822.0
13	TraesCS6D01G221500	chrUn	92.474	1993	111	13	590	2552	20573301	20575284	0.000000e+00	2813.0
14	TraesCS6D01G221500	chr7D	92.024	2006	109	22	590	2552	372082798	372084795	0.000000e+00	2771.0
15	TraesCS6D01G221500	chr7D	96.095	589	22	1	1	589	551005481	551006068	0.000000e+00	959.0
16	TraesCS6D01G221500	chr7A	91.250	2000	120	20	590	2552	12744485	12742504	0.000000e+00	2673.0
17	TraesCS6D01G221500	chr5A	90.959	1991	125	19	589	2552	702815061	702813099	0.000000e+00	2628.0
18	TraesCS6D01G221500	chr5A	92.248	387	27	2	2169	2552	553436302	553435916	1.730000e-151	545.0
19	TraesCS6D01G221500	chr3A	89.679	1996	132	38	590	2552	706125756	706123802	0.000000e+00	2477.0
20	TraesCS6D01G221500	chr3A	91.045	268	14	3	2294	2552	102545482	102545216	1.120000e-93	353.0
21	TraesCS6D01G221500	chr1D	96.265	589	22	0	1	589	96886015	96885427	0.000000e+00	966.0
22	TraesCS6D01G221500	chr2D	96.075	586	23	0	1	586	474776202	474776787	0.000000e+00	955.0
23	TraesCS6D01G221500	chr2D	95.925	589	23	1	1	589	474480613	474480026	0.000000e+00	953.0
24	TraesCS6D01G221500	chr2D	93.834	519	20	3	2041	2549	218366133	218366649	0.000000e+00	771.0
25	TraesCS6D01G221500	chr2D	92.193	269	13	1	2292	2552	547241036	547240768	8.620000e-100	374.0
26	TraesCS6D01G221500	chr2B	91.852	270	13	2	2292	2552	774567004	774567273	4.010000e-98	368.0
27	TraesCS6D01G221500	chr2B	93.846	65	4	0	588	652	182163777	182163841	5.810000e-17	99.0
28	TraesCS6D01G221500	chr3B	94.737	38	1	1	596	633	702849778	702849814	9.860000e-05	58.4

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	TraesCS6D01G221500	chr6D	312542340	312544891	2551	True	4713	4713	100.000	1	2552	1	chr6D.!!$R3	2551
1	TraesCS6D01G221500	chr6D	12106161	12108135	1974	True	2809	2809	92.509	592	2552	1	chr6D.!!$R1	1960
2	TraesCS6D01G221500	chr6D	39289107	39289693	586	False	968	968	96.422	3	589	1	chr6D.!!$F1	586
3	TraesCS6D01G221500	chr6D	149632872	149633460	588	False	955	955	95.925	1	589	1	chr6D.!!$F2	588
4	TraesCS6D01G221500	chr6D	131894539	131895126	587	True	953	953	95.918	2	589	1	chr6D.!!$R2	587
5	TraesCS6D01G221500	chr1A	556201756	556203724	1968	False	2994	2994	94.124	584	2552	1	chr1A.!!$F1	1968
6	TraesCS6D01G221500	chr5D	44511942	44513920	1978	False	2887	2887	93.180	589	2552	1	chr5D.!!$F1	1963
7	TraesCS6D01G221500	chr4D	78730795	78732770	1975	True	2846	2846	92.814	589	2552	1	chr4D.!!$R1	1963
8	TraesCS6D01G221500	chr4D	442120919	442121507	588	False	972	972	96.435	1	589	1	chr4D.!!$F1	588
9	TraesCS6D01G221500	chr4D	324361212	324361799	587	True	965	965	96.259	2	589	1	chr4D.!!$R2	587
10	TraesCS6D01G221500	chrUn	43407879	43409813	1934	False	2822	2822	93.186	633	2552	1	chrUn.!!$F2	1919
11	TraesCS6D01G221500	chrUn	20573301	20575284	1983	False	2813	2813	92.474	590	2552	1	chrUn.!!$F1	1962
12	TraesCS6D01G221500	chr7D	372082798	372084795	1997	False	2771	2771	92.024	590	2552	1	chr7D.!!$F1	1962
13	TraesCS6D01G221500	chr7D	551005481	551006068	587	False	959	959	96.095	1	589	1	chr7D.!!$F2	588
14	TraesCS6D01G221500	chr7A	12742504	12744485	1981	True	2673	2673	91.250	590	2552	1	chr7A.!!$R1	1962
15	TraesCS6D01G221500	chr5A	702813099	702815061	1962	True	2628	2628	90.959	589	2552	1	chr5A.!!$R2	1963
16	TraesCS6D01G221500	chr3A	706123802	706125756	1954	True	2477	2477	89.679	590	2552	1	chr3A.!!$R2	1962
17	TraesCS6D01G221500	chr1D	96885427	96886015	588	True	966	966	96.265	1	589	1	chr1D.!!$R1	588
18	TraesCS6D01G221500	chr2D	474776202	474776787	585	False	955	955	96.075	1	586	1	chr2D.!!$F2	585
19	TraesCS6D01G221500	chr2D	474480026	474480613	587	True	953	953	95.925	1	589	1	chr2D.!!$R1	588
20	TraesCS6D01G221500	chr2D	218366133	218366649	516	False	771	771	93.834	2041	2549	1	chr2D.!!$F1	508

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
634	635	1.160137	GGTGTCCATGTGCTCAGTTC	58.840	55.000	0.0	0.0	0.0	3.01	F
989	1035	1.898154	CGTTGAGATCCCCTTCGGT	59.102	57.895	0.0	0.0	0.0	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1503	1550	2.083774	ACAACCAGTGCGATTACCATG	58.916	47.619	0.0	0.0	0.0	3.66	R
1795	1851	2.092968	CAGTTGGCCCATTAGTCTAGCA	60.093	50.000	0.0	0.0	0.0	3.49	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
23	24	4.093952	CCGCAAGCAGCCGAACAG	62.094	66.667	0.00	0.00	41.38	3.16
54	55	6.127619	TGAGATCTCAGTTGTGTCAACGATAT	60.128	38.462	21.67	6.20	34.14	1.63
58	59	7.095695	TCTCAGTTGTGTCAACGATATATGA	57.904	36.000	6.92	4.21	0.00	2.15
105	106	1.817099	GCGCATGGAAGTCCTCTGG	60.817	63.158	0.30	0.00	36.82	3.86
177	178	5.235516	CCTTTCCGCTTTAAGTTGAGACTA	58.764	41.667	0.00	0.00	34.21	2.59
185	186	6.292919	CGCTTTAAGTTGAGACTAAAGCAGTT	60.293	38.462	19.90	0.00	43.39	3.16
389	390	2.466846	AGACACGTAACAGGTTTCACG	58.533	47.619	6.06	6.06	40.15	4.35
544	545	8.340002	TGATGCCTATCCAACTCTATACTAGAT	58.660	37.037	0.00	0.00	31.43	1.98
569	570	3.481453	AGTTTGAAGGCTTGAGAAGGAC	58.519	45.455	3.46	0.00	0.00	3.85
634	635	1.160137	GGTGTCCATGTGCTCAGTTC	58.840	55.000	0.00	0.00	0.00	3.01
758	760	3.533079	TACAGGTGGGACCAGGCGA	62.533	63.158	0.00	0.00	41.95	5.54
903	908	3.749064	GACAGAGAGCACGGCGGA	61.749	66.667	13.24	0.00	0.00	5.54
934	980	3.885901	CGAGAGAGAGAGAGAGAGAGAGA	59.114	52.174	0.00	0.00	0.00	3.10
936	982	3.640967	AGAGAGAGAGAGAGAGAGAGAGC	59.359	52.174	0.00	0.00	0.00	4.09
937	983	3.378512	AGAGAGAGAGAGAGAGAGAGCA	58.621	50.000	0.00	0.00	0.00	4.26
947	993	2.364842	AGAGAGCAGCGGTGGGAT	60.365	61.111	17.54	0.00	0.00	3.85
989	1035	1.898154	CGTTGAGATCCCCTTCGGT	59.102	57.895	0.00	0.00	0.00	4.69
1115	1161	2.187958	TGATCGGAGGGTTTCTCACAT	58.812	47.619	0.00	0.00	44.19	3.21
1294	1341	5.258841	TGGCAAAGACTCTGATGAATGAAT	58.741	37.500	0.00	0.00	0.00	2.57
1503	1550	4.529109	TTACTTTTGGGCATTTGTAGGC	57.471	40.909	0.00	0.00	0.00	3.93
1634	1681	9.442047	TTGGTCAAAGTTGTTTAAATGTTGAAT	57.558	25.926	0.00	0.00	0.00	2.57
1795	1851	4.208632	GCGTAGAGCCAAGTGCAT	57.791	55.556	0.00	0.00	44.83	3.96
1865	1923	5.465935	TCTCTTGCGTGTTTTTCTGTTTTT	58.534	33.333	0.00	0.00	0.00	1.94
2072	2132	0.332972	TGCCTCAGCTCTGGTAGAGA	59.667	55.000	9.89	0.00	45.07	3.10
2077	2137	4.283212	GCCTCAGCTCTGGTAGAGATTTAT	59.717	45.833	9.89	0.00	45.07	1.40
2195	2265	3.368190	CTGCAGCTGGGGACTCGAG	62.368	68.421	17.12	11.84	0.00	4.04
2392	2470	0.319083	ATGTTTGCACTGCCACATGG	59.681	50.000	12.92	0.00	32.56	3.66
2504	2680	1.479323	TCTCACCCCCTACGATTTTCG	59.521	52.381	0.00	0.00	46.93	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	3.196463	CACAACTGAGATCTCATCAGCC	58.804	50.000	25.30	0.00	46.64	4.85
34	35	7.095695	TCATATATCGTTGACACAACTGAGA	57.904	36.000	11.79	8.76	0.00	3.27
54	55	4.964897	CCATACAGCTAGGGATGGATCATA	59.035	45.833	9.32	0.00	41.23	2.15
58	59	1.912043	GCCATACAGCTAGGGATGGAT	59.088	52.381	17.62	0.00	41.23	3.41
95	96	3.683802	CAAAGAAGATGCCAGAGGACTT	58.316	45.455	0.00	0.00	0.00	3.01
105	106	5.056894	AGTCAAAGATGCAAAGAAGATGC	57.943	39.130	0.00	0.00	44.08	3.91
177	178	3.005155	GCCTCAATCAGTTCAACTGCTTT	59.995	43.478	13.15	6.23	45.54	3.51
185	186	0.321346	TCGCTGCCTCAATCAGTTCA	59.679	50.000	0.00	0.00	34.21	3.18
276	277	2.612285	TGAGGACAGTGAGATGACCT	57.388	50.000	0.00	0.00	46.04	3.85
491	492	4.065088	CTCCACTGCTGTTTACTTTGCTA	58.935	43.478	0.00	0.00	0.00	3.49
544	545	4.339247	CCTTCTCAAGCCTTCAAACTTTGA	59.661	41.667	0.00	0.00	38.04	2.69
601	602	1.620822	GACACCACTGAGGGCAAAAT	58.379	50.000	0.00	0.00	43.89	1.82
634	635	0.179089	CGATTCACCTCTGAGGGCAG	60.179	60.000	26.56	15.96	40.58	4.85
645	646	2.918131	GCAAAACTGAGCACGATTCACC	60.918	50.000	0.00	0.00	0.00	4.02
758	760	3.378512	TGATTGTCTAGGGCATCTCTGT	58.621	45.455	0.00	0.00	0.00	3.41
903	908	1.747367	CTCTCTCTCGCCGTGGTCT	60.747	63.158	0.00	0.00	0.00	3.85
936	982	2.590007	GCTAGCATCCCACCGCTG	60.590	66.667	10.63	0.00	39.30	5.18
937	983	2.765807	AGCTAGCATCCCACCGCT	60.766	61.111	18.83	0.00	42.34	5.52
947	993	2.607442	TGCCCTCCACAGCTAGCA	60.607	61.111	18.83	0.00	0.00	3.49
989	1035	0.537188	GGAAGACATGGAGCTCGGAA	59.463	55.000	7.83	0.00	0.00	4.30
1061	1107	0.663568	CCACGGACAGACGAAGACAC	60.664	60.000	0.00	0.00	37.61	3.67
1115	1161	1.747355	GACGATTCTGGTTCCTCGGTA	59.253	52.381	0.00	0.00	35.52	4.02
1275	1322	6.829229	TGCAATTCATTCATCAGAGTCTTT	57.171	33.333	0.00	0.00	0.00	2.52
1294	1341	4.082408	CCATTCTTCATGCTCTTCTTGCAA	60.082	41.667	0.00	0.00	44.01	4.08
1459	1506	6.655078	ATTGCAAATGGGTATTGGTATCTC	57.345	37.500	1.71	0.00	0.00	2.75
1461	1508	7.951591	AGTAATTGCAAATGGGTATTGGTATC	58.048	34.615	1.71	0.00	0.00	2.24
1503	1550	2.083774	ACAACCAGTGCGATTACCATG	58.916	47.619	0.00	0.00	0.00	3.66
1634	1681	8.519799	AATGTTGGTCACTTCTTCTCTTTTTA	57.480	30.769	0.00	0.00	0.00	1.52
1795	1851	2.092968	CAGTTGGCCCATTAGTCTAGCA	60.093	50.000	0.00	0.00	0.00	3.49
1901	1959	6.695278	TCAATTAGCTTCCACAAAAAGTTTCG	59.305	34.615	0.00	0.00	0.00	3.46
2072	2132	8.986991	TCATTAATTTTGGCACCAGGTATAAAT	58.013	29.630	0.00	0.00	0.00	1.40
2077	2137	5.540337	TGTTCATTAATTTTGGCACCAGGTA	59.460	36.000	0.00	0.00	0.00	3.08
2177	2247	3.368190	CTCGAGTCCCCAGCTGCAG	62.368	68.421	10.11	10.11	0.00	4.41
2392	2470	3.243401	CCAAGTGCCACTCTAACCAAAAC	60.243	47.826	0.00	0.00	0.00	2.43
2504	2680	5.237779	TCGAGAACTTGTGGTTTCCATTAAC	59.762	40.000	0.00	0.00	38.41	2.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.