AutoCloner

Multiple sequence alignment - TraesCS4B01G322200

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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	TraesCS4B01G322200	chr4B	100.000	2944	0	0	1	2944	612878807	612875864	0.000000e+00	5437.0
1	TraesCS4B01G322200	chr4B	96.135	802	26	4	1	799	103052032	103051233	0.000000e+00	1304.0
2	TraesCS4B01G322200	chr4B	95.718	794	30	3	1	792	462208168	462207377	0.000000e+00	1275.0
3	TraesCS4B01G322200	chr4D	90.203	1480	69	24	792	2232	483041878	483040436	0.000000e+00	1860.0
4	TraesCS4B01G322200	chr4D	87.560	209	17	3	2292	2499	483040435	483040235	1.760000e-57	233.0
5	TraesCS4B01G322200	chr4D	84.831	178	25	2	2762	2937	360115656	360115833	8.380000e-41	178.0
6	TraesCS4B01G322200	chr4D	82.741	197	28	5	2495	2686	112722005	112721810	1.400000e-38	171.0
7	TraesCS4B01G322200	chr5A	83.725	1745	108	78	795	2501	663190454	663188848	0.000000e+00	1487.0
8	TraesCS4B01G322200	chr5A	77.060	449	46	23	2001	2428	432469229	432468817	3.850000e-49	206.0
9	TraesCS4B01G322200	chr5A	77.273	176	33	6	2508	2677	676905463	676905637	2.420000e-16	97.1
10	TraesCS4B01G322200	chr5B	97.613	796	17	2	1	794	609606349	609607144	0.000000e+00	1363.0
11	TraesCS4B01G322200	chr5B	93.921	806	33	4	1	792	633968437	633967634	0.000000e+00	1203.0
12	TraesCS4B01G322200	chr1B	96.442	787	25	2	1	786	552309481	552310265	0.000000e+00	1295.0
13	TraesCS4B01G322200	chr1B	80.447	179	30	4	2766	2940	434831956	434832133	6.620000e-27	132.0
14	TraesCS4B01G322200	chr2B	96.315	787	25	3	1	786	44907777	44908560	0.000000e+00	1290.0
15	TraesCS4B01G322200	chr2B	97.302	556	13	1	1	556	151499532	151500085	0.000000e+00	942.0
16	TraesCS4B01G322200	chr6B	98.090	733	13	1	1	733	687048214	687048945	0.000000e+00	1275.0
17	TraesCS4B01G322200	chr6B	82.836	134	17	3	1397	1527	717596746	717596616	6.670000e-22	115.0
18	TraesCS4B01G322200	chr3B	95.426	787	33	2	1	786	504065887	504065103	0.000000e+00	1251.0
19	TraesCS4B01G322200	chr3B	95.806	453	15	3	336	786	589555806	589555356	0.000000e+00	728.0
20	TraesCS4B01G322200	chr3B	94.292	473	18	4	321	786	21409432	21408962	0.000000e+00	715.0
21	TraesCS4B01G322200	chr3B	85.635	181	14	7	2762	2940	400306775	400306945	2.330000e-41	180.0
22	TraesCS4B01G322200	chr3B	82.734	139	16	5	2536	2672	739325339	739325207	1.850000e-22	117.0
23	TraesCS4B01G322200	chr3B	92.453	53	4	0	2890	2942	734747914	734747966	3.150000e-10	76.8
24	TraesCS4B01G322200	chr7B	93.895	475	24	4	321	792	380701934	380701462	0.000000e+00	712.0
25	TraesCS4B01G322200	chr7B	80.000	135	25	2	1393	1526	734430594	734430727	6.710000e-17	99.0
26	TraesCS4B01G322200	chr7B	89.583	48	4	1	1872	1919	671704634	671704588	3.170000e-05	60.2
27	TraesCS4B01G322200	chr3D	85.792	183	14	7	2762	2942	319856801	319856629	1.800000e-42	183.0
28	TraesCS4B01G322200	chr3D	78.723	188	29	9	2494	2680	593235186	593235009	6.670000e-22	115.0
29	TraesCS4B01G322200	chr3D	89.583	48	4	1	1872	1919	55347654	55347700	3.170000e-05	60.2
30	TraesCS4B01G322200	chr3A	84.153	183	26	3	2761	2942	606265613	606265793	1.080000e-39	174.0
31	TraesCS4B01G322200	chr3A	83.060	183	22	7	2497	2673	550706639	550706818	1.090000e-34	158.0
32	TraesCS4B01G322200	chr1D	83.607	183	29	1	2759	2940	139141526	139141344	1.400000e-38	171.0
33	TraesCS4B01G322200	chr1D	83.803	142	23	0	2799	2940	322161476	322161617	5.120000e-28	135.0
34	TraesCS4B01G322200	chr1D	85.484	62	5	4	2762	2819	402364674	402364735	8.810000e-06	62.1
35	TraesCS4B01G322200	chr4A	81.421	183	28	5	2762	2940	723750000	723750180	8.500000e-31	145.0
36	TraesCS4B01G322200	chr4A	84.043	94	11	4	2587	2678	36099640	36099731	1.450000e-13	87.9
37	TraesCS4B01G322200	chr7D	81.818	165	20	5	2523	2678	64007143	64007306	2.380000e-26	130.0
38	TraesCS4B01G322200	chr7D	89.583	48	4	1	1872	1919	531593716	531593670	3.170000e-05	60.2
39	TraesCS4B01G322200	chr6D	82.166	157	23	4	2762	2915	81162912	81163066	2.380000e-26	130.0
40	TraesCS4B01G322200	chr6D	85.417	96	14	0	1431	1526	472568598	472568503	1.870000e-17	100.0
41	TraesCS4B01G322200	chr6A	83.582	134	16	3	1397	1527	617097557	617097687	1.430000e-23	121.0
42	TraesCS4B01G322200	chr2A	82.308	130	9	10	2552	2672	649483335	649483459	1.870000e-17	100.0
43	TraesCS4B01G322200	chr2A	100.000	28	0	0	1944	1971	43817952	43817925	5.000000e-03	52.8
44	TraesCS4B01G322200	chr2A	100.000	28	0	0	1944	1971	43842238	43842211	5.000000e-03	52.8
45	TraesCS4B01G322200	chr2A	100.000	28	0	0	1944	1971	43900217	43900190	5.000000e-03	52.8
46	TraesCS4B01G322200	chr1A	78.621	145	28	2	2531	2672	480574196	480574340	3.120000e-15	93.5
47	TraesCS4B01G322200	chr7A	89.583	48	4	1	1872	1919	682896616	682896662	3.170000e-05	60.2

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	TraesCS4B01G322200	chr4B	612875864	612878807	2943	True	5437.0	5437	100.0000	1	2944	1	chr4B.!!$R3	2943
1	TraesCS4B01G322200	chr4B	103051233	103052032	799	True	1304.0	1304	96.1350	1	799	1	chr4B.!!$R1	798
2	TraesCS4B01G322200	chr4B	462207377	462208168	791	True	1275.0	1275	95.7180	1	792	1	chr4B.!!$R2	791
3	TraesCS4B01G322200	chr4D	483040235	483041878	1643	True	1046.5	1860	88.8815	792	2499	2	chr4D.!!$R2	1707
4	TraesCS4B01G322200	chr5A	663188848	663190454	1606	True	1487.0	1487	83.7250	795	2501	1	chr5A.!!$R2	1706
5	TraesCS4B01G322200	chr5B	609606349	609607144	795	False	1363.0	1363	97.6130	1	794	1	chr5B.!!$F1	793
6	TraesCS4B01G322200	chr5B	633967634	633968437	803	True	1203.0	1203	93.9210	1	792	1	chr5B.!!$R1	791
7	TraesCS4B01G322200	chr1B	552309481	552310265	784	False	1295.0	1295	96.4420	1	786	1	chr1B.!!$F2	785
8	TraesCS4B01G322200	chr2B	44907777	44908560	783	False	1290.0	1290	96.3150	1	786	1	chr2B.!!$F1	785
9	TraesCS4B01G322200	chr2B	151499532	151500085	553	False	942.0	942	97.3020	1	556	1	chr2B.!!$F2	555
10	TraesCS4B01G322200	chr6B	687048214	687048945	731	False	1275.0	1275	98.0900	1	733	1	chr6B.!!$F1	732
11	TraesCS4B01G322200	chr3B	504065103	504065887	784	True	1251.0	1251	95.4260	1	786	1	chr3B.!!$R2	785

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
989	1016	1.379916	CTGCCATTCCACTCCACCA	59.62	57.895	0.0	0.0	0.0	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2883	2984	0.034186	TGGATTTGAGGCTCCGCATT	60.034	50.0	12.86	0.0	34.05	3.56	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	89	2.358957	GTGTGGCTGCTGATGATTGTA	58.641	47.619	0.00	0.00	0.00	2.41
95	96	5.651576	TGGCTGCTGATGATTGTAATGTTTA	59.348	36.000	0.00	0.00	0.00	2.01
762	779	5.414454	CGGGGTCAGATCTTGATTTTGTTTA	59.586	40.000	0.00	0.00	38.29	2.01
812	830	2.933666	CACGCTGCAGACACACAG	59.066	61.111	20.43	1.24	36.96	3.66
816	834	2.968697	CTGCAGACACACAGCGCA	60.969	61.111	8.42	0.00	33.65	6.09
928	949	4.022155	GCCATTACTAGTAGGAGTACTGCC	60.022	50.000	11.20	6.99	39.96	4.85
986	1013	2.046023	CGCTGCCATTCCACTCCA	60.046	61.111	0.00	0.00	0.00	3.86
989	1016	1.379916	CTGCCATTCCACTCCACCA	59.620	57.895	0.00	0.00	0.00	4.17
1021	1053	0.672401	GTGATCCGGCCAAGAACGAA	60.672	55.000	2.24	0.00	0.00	3.85
1022	1054	0.672401	TGATCCGGCCAAGAACGAAC	60.672	55.000	2.24	0.00	0.00	3.95
1023	1055	1.366854	GATCCGGCCAAGAACGAACC	61.367	60.000	2.24	0.00	0.00	3.62
1024	1056	3.419759	CCGGCCAAGAACGAACCG	61.420	66.667	2.24	0.00	43.44	4.44
1025	1057	3.419759	CGGCCAAGAACGAACCGG	61.420	66.667	2.24	0.00	40.18	5.28
1026	1058	3.733960	GGCCAAGAACGAACCGGC	61.734	66.667	0.00	0.00	42.21	6.13
1027	1059	3.733960	GCCAAGAACGAACCGGCC	61.734	66.667	0.00	0.00	36.73	6.13
1028	1060	3.053896	CCAAGAACGAACCGGCCC	61.054	66.667	0.00	0.00	0.00	5.80
1029	1061	3.053896	CAAGAACGAACCGGCCCC	61.054	66.667	0.00	0.00	0.00	5.80
1030	1062	4.692475	AAGAACGAACCGGCCCCG	62.692	66.667	0.00	5.10	39.44	5.73
1420	1455	1.676678	GCCATCTGCCTGTCGGAGTA	61.677	60.000	0.00	0.00	32.71	2.59
1675	1716	1.501741	CCCGTTTCTTGCCATGACG	59.498	57.895	0.00	0.00	0.00	4.35
1730	1781	3.897325	CATGGATGCATAATGTGTCTGC	58.103	45.455	0.00	0.00	36.45	4.26
1732	1783	1.265095	GGATGCATAATGTGTCTGCGG	59.735	52.381	0.00	0.00	38.75	5.69
1816	1868	1.999735	TGTTTTCATGGACTCGATCGC	59.000	47.619	11.09	0.00	0.00	4.58
1860	1912	5.964958	ATCCGTTGAATTTCAGTTGACAT	57.035	34.783	0.00	0.00	0.00	3.06
1906	1958	7.282224	AGCAATTTCAGTACAACACAAGACTTA	59.718	33.333	0.00	0.00	0.00	2.24

Showing 1 to 25 of 376 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	89	8.539544	AGCCAAAATAGGTAGCAATTAAACATT	58.460	29.630	0.00	0.00	0.00	2.71
95	96	4.705023	ACGAAGCCAAAATAGGTAGCAATT	59.295	37.500	0.00	0.00	0.00	2.32
762	779	7.294473	CAAATTTCGTGTTTTGACCTTTTTGT	58.706	30.769	0.00	0.00	35.34	2.83
840	858	1.073722	CTGGTGCACCATGGTCACT	59.926	57.895	37.66	7.02	46.46	3.41
841	859	2.629656	GCTGGTGCACCATGGTCAC	61.630	63.158	37.66	26.51	46.46	3.67
870	888	2.507992	CTTGAGAGCGACAGCCGG	60.508	66.667	0.00	0.00	46.67	6.13
893	911	4.741676	ACTAGTAATGGCACGCGTATTAAC	59.258	41.667	13.44	5.96	0.00	2.01
1031	1063	4.776647	GACGCCATTGGTTGCCGC	62.777	66.667	4.26	0.00	0.00	6.53
1032	1064	4.459331	CGACGCCATTGGTTGCCG	62.459	66.667	4.26	1.71	0.00	5.69
1033	1065	4.114997	CCGACGCCATTGGTTGCC	62.115	66.667	4.26	0.00	0.00	4.52
1034	1066	4.776647	GCCGACGCCATTGGTTGC	62.777	66.667	4.26	0.00	33.66	4.17
1035	1067	4.459331	CGCCGACGCCATTGGTTG	62.459	66.667	4.26	0.00	33.66	3.77
1261	1296	0.695347	CCTCTTCTTGAGCCCCTTGT	59.305	55.000	0.00	0.00	41.35	3.16
1420	1455	3.680920	ATCTCCTCCTTCCCCGCGT	62.681	63.158	4.92	0.00	0.00	6.01
1602	1640	2.764128	GGACGCCTCCTCCATGGA	60.764	66.667	15.27	15.27	43.86	3.41
1730	1781	3.934579	TCACATTCACTGATTCACATCCG	59.065	43.478	0.00	0.00	0.00	4.18
1732	1783	6.492007	AACTCACATTCACTGATTCACATC	57.508	37.500	0.00	0.00	0.00	3.06
1816	1868	3.577649	TCAGAGTGAAAGCCTACTTCG	57.422	47.619	0.00	0.00	34.05	3.79
1870	1922	9.243637	GTTGTACTGAAATTGCTGAAATGTTTA	57.756	29.630	0.00	0.00	0.00	2.01
1929	1981	2.612721	GGCCAAAGCGAATTCAACCAAT	60.613	45.455	6.22	0.00	41.24	3.16
1943	1995	1.147473	GGTTTGCATTTCGGCCAAAG	58.853	50.000	2.24	0.00	0.00	2.77
2037	2089	2.899256	AGGCATGCAAACCAACTGTAAT	59.101	40.909	21.36	0.00	0.00	1.89
2039	2091	1.612950	CAGGCATGCAAACCAACTGTA	59.387	47.619	21.36	0.00	0.00	2.74
2057	2109	7.625817	GCAAATTCATAGATATGCTAGGCACAG	60.626	40.741	0.00	0.00	43.04	3.66
2112	2176	9.559732	TCTGAACTTTCTTGATGATAACTTTGA	57.440	29.630	0.00	0.00	0.00	2.69

Showing 1 to 25 of 351 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.