AutoCloner

Multiple sequence alignment - TraesCS7D01G068200

Loading Multiple Alignment...

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	TraesCS7D01G068200	chr7D	100.000	2585	0	0	1	2585	38712029	38709445	0.000000e+00	4774
1	TraesCS7D01G068200	chr7D	93.118	465	29	3	1	462	75958269	75958733	0.000000e+00	678
2	TraesCS7D01G068200	chr7D	80.645	465	74	10	1841	2292	23545110	23544649	1.900000e-91	346
3	TraesCS7D01G068200	chr7D	77.295	621	96	28	862	1452	38793405	38794010	8.920000e-85	324
4	TraesCS7D01G068200	chr7D	79.406	471	69	16	999	1452	38551496	38551037	8.990000e-80	307
5	TraesCS7D01G068200	chr7D	80.189	424	55	15	1044	1453	38704165	38703757	9.050000e-75	291
6	TraesCS7D01G068200	chr3D	94.725	455	21	3	1	454	374392738	374393190	0.000000e+00	704
7	TraesCS7D01G068200	chr3D	94.493	454	24	1	1	453	607326942	607327395	0.000000e+00	699
8	TraesCS7D01G068200	chr3D	93.900	459	25	3	1	457	115643356	115643813	0.000000e+00	689
9	TraesCS7D01G068200	chr3D	82.109	531	78	12	1732	2249	29528948	29528422	3.050000e-119	438
10	TraesCS7D01G068200	chr1D	94.130	460	23	4	1	457	203156124	203155666	0.000000e+00	697
11	TraesCS7D01G068200	chr1D	78.938	565	101	12	1726	2276	443301919	443302479	4.060000e-98	368
12	TraesCS7D01G068200	chr5D	94.298	456	23	3	1	453	272355987	272356442	0.000000e+00	695
13	TraesCS7D01G068200	chr5B	93.926	461	23	5	1	457	566041801	566042260	0.000000e+00	691
14	TraesCS7D01G068200	chr5B	79.020	653	113	14	1721	2355	530653384	530654030	2.380000e-115	425
15	TraesCS7D01G068200	chr5B	78.477	604	112	15	1722	2313	568941283	568940686	1.880000e-101	379
16	TraesCS7D01G068200	chr7B	93.723	462	24	5	1	458	378921702	378921242	0.000000e+00	688
17	TraesCS7D01G068200	chr7B	79.615	520	84	15	1772	2275	546383426	546383939	1.140000e-93	353
18	TraesCS7D01G068200	chr7B	80.503	318	55	6	1716	2030	651456269	651455956	1.200000e-58	237
19	TraesCS7D01G068200	chr6D	93.860	456	25	3	3	455	17972699	17972244	0.000000e+00	684
20	TraesCS7D01G068200	chr4A	80.061	988	137	30	468	1452	642955254	642954324	0.000000e+00	678
21	TraesCS7D01G068200	chr4A	76.911	654	112	22	1716	2355	688391074	688390446	4.120000e-88	335
22	TraesCS7D01G068200	chr4A	75.000	620	110	30	863	1452	642950107	642949503	7.150000e-61	244
23	TraesCS7D01G068200	chr4A	85.446	213	21	5	468	674	642376954	642377162	2.010000e-51	213
24	TraesCS7D01G068200	chr4A	94.872	78	4	0	1478	1555	642949441	642949364	3.490000e-24	122
25	TraesCS7D01G068200	chr4D	80.680	559	84	16	1721	2263	5918223	5918773	1.850000e-111	412
26	TraesCS7D01G068200	chr4D	78.168	655	107	22	1715	2352	20454244	20454879	4.040000e-103	385
27	TraesCS7D01G068200	chr3A	80.036	551	91	14	1740	2276	374970782	374970237	8.670000e-105	390
28	TraesCS7D01G068200	chr3A	79.626	481	82	13	1721	2195	748862048	748861578	5.330000e-87	331
29	TraesCS7D01G068200	chr5A	79.275	579	98	17	1737	2300	1328900	1329471	4.040000e-103	385
30	TraesCS7D01G068200	chr7A	75.496	857	132	53	633	1452	38688788	38689603	5.290000e-92	348
31	TraesCS7D01G068200	chr7A	75.496	857	132	53	633	1452	38717230	38718045	5.290000e-92	348
32	TraesCS7D01G068200	chr7A	78.465	469	82	11	1808	2261	634603300	634603764	3.250000e-74	289
33	TraesCS7D01G068200	chr1A	77.667	600	106	18	1772	2355	30253302	30252715	8.860000e-90	340
34	TraesCS7D01G068200	chr3B	79.957	469	79	6	1732	2187	816217463	816217929	5.330000e-87	331
35	TraesCS7D01G068200	chr3B	78.557	485	82	14	1890	2359	751513638	751513161	1.500000e-77	300
36	TraesCS7D01G068200	chr4B	78.316	475	82	15	1746	2206	16394232	16393765	1.170000e-73	287

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	TraesCS7D01G068200	chr7D	38709445	38712029	2584	True	4774	4774	100.000	1	2585	1	chr7D.!!$R4	2584
1	TraesCS7D01G068200	chr7D	38793405	38794010	605	False	324	324	77.295	862	1452	1	chr7D.!!$F1	590
2	TraesCS7D01G068200	chr3D	29528422	29528948	526	True	438	438	82.109	1732	2249	1	chr3D.!!$R1	517
3	TraesCS7D01G068200	chr1D	443301919	443302479	560	False	368	368	78.938	1726	2276	1	chr1D.!!$F1	550
4	TraesCS7D01G068200	chr5B	530653384	530654030	646	False	425	425	79.020	1721	2355	1	chr5B.!!$F1	634
5	TraesCS7D01G068200	chr5B	568940686	568941283	597	True	379	379	78.477	1722	2313	1	chr5B.!!$R1	591
6	TraesCS7D01G068200	chr7B	546383426	546383939	513	False	353	353	79.615	1772	2275	1	chr7B.!!$F1	503
7	TraesCS7D01G068200	chr4A	642954324	642955254	930	True	678	678	80.061	468	1452	1	chr4A.!!$R1	984
8	TraesCS7D01G068200	chr4A	688390446	688391074	628	True	335	335	76.911	1716	2355	1	chr4A.!!$R2	639
9	TraesCS7D01G068200	chr4D	5918223	5918773	550	False	412	412	80.680	1721	2263	1	chr4D.!!$F1	542
10	TraesCS7D01G068200	chr4D	20454244	20454879	635	False	385	385	78.168	1715	2352	1	chr4D.!!$F2	637
11	TraesCS7D01G068200	chr3A	374970237	374970782	545	True	390	390	80.036	1740	2276	1	chr3A.!!$R1	536
12	TraesCS7D01G068200	chr5A	1328900	1329471	571	False	385	385	79.275	1737	2300	1	chr5A.!!$F1	563
13	TraesCS7D01G068200	chr7A	38688788	38689603	815	False	348	348	75.496	633	1452	1	chr7A.!!$F1	819
14	TraesCS7D01G068200	chr7A	38717230	38718045	815	False	348	348	75.496	633	1452	1	chr7A.!!$F2	819
15	TraesCS7D01G068200	chr1A	30252715	30253302	587	True	340	340	77.667	1772	2355	1	chr1A.!!$R1	583

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
405	406	0.107508	AATGAGTGGTGATGGAGGCG	60.108	55.0	0.0	0.0	0.0	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2206	2286	0.0293	CTTGTTGTTCTGGCCGTGTG	59.971	55.0	0.0	0.0	0.0	3.82	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
23	24	5.864418	AGACTTGCCATGCATCATAAATT	57.136	34.783	0.00	0.00	38.76	1.82
24	25	6.964807	AGACTTGCCATGCATCATAAATTA	57.035	33.333	0.00	0.00	38.76	1.40
25	26	7.350744	AGACTTGCCATGCATCATAAATTAA	57.649	32.000	0.00	0.00	38.76	1.40
26	27	7.784037	AGACTTGCCATGCATCATAAATTAAA	58.216	30.769	0.00	0.00	38.76	1.52
27	28	8.259411	AGACTTGCCATGCATCATAAATTAAAA	58.741	29.630	0.00	0.00	38.76	1.52
28	29	8.967664	ACTTGCCATGCATCATAAATTAAAAT	57.032	26.923	0.00	0.00	38.76	1.82
29	30	9.398538	ACTTGCCATGCATCATAAATTAAAATT	57.601	25.926	0.00	0.00	38.76	1.82
30	31	9.658475	CTTGCCATGCATCATAAATTAAAATTG	57.342	29.630	0.00	0.00	38.76	2.32
31	32	7.640852	TGCCATGCATCATAAATTAAAATTGC	58.359	30.769	0.00	0.00	31.71	3.56
32	33	7.079475	GCCATGCATCATAAATTAAAATTGCC	58.921	34.615	0.00	0.00	0.00	4.52
33	34	7.255173	GCCATGCATCATAAATTAAAATTGCCA	60.255	33.333	0.00	0.00	0.00	4.92
34	35	8.788806	CCATGCATCATAAATTAAAATTGCCAT	58.211	29.630	0.00	0.00	0.00	4.40
46	47	9.835389	AATTAAAATTGCCATTATACATGCACT	57.165	25.926	0.00	0.00	32.63	4.40
47	48	9.835389	ATTAAAATTGCCATTATACATGCACTT	57.165	25.926	0.00	0.00	32.63	3.16
50	51	9.664332	AAAATTGCCATTATACATGCACTTAAA	57.336	25.926	0.00	0.00	32.63	1.52
51	52	9.664332	AAATTGCCATTATACATGCACTTAAAA	57.336	25.926	0.00	0.00	32.63	1.52
52	53	9.835389	AATTGCCATTATACATGCACTTAAAAT	57.165	25.926	0.00	0.00	32.63	1.82
53	54	9.835389	ATTGCCATTATACATGCACTTAAAATT	57.165	25.926	0.00	0.00	32.63	1.82
54	55	8.645730	TGCCATTATACATGCACTTAAAATTG	57.354	30.769	0.00	0.00	0.00	2.32
55	56	8.256605	TGCCATTATACATGCACTTAAAATTGT	58.743	29.630	0.00	0.00	0.00	2.71
56	57	8.755018	GCCATTATACATGCACTTAAAATTGTC	58.245	33.333	0.00	0.00	0.00	3.18
57	58	9.800433	CCATTATACATGCACTTAAAATTGTCA	57.200	29.630	0.00	0.00	0.00	3.58
60	61	9.800433	TTATACATGCACTTAAAATTGTCATGG	57.200	29.630	15.08	0.00	35.47	3.66
61	62	6.100404	ACATGCACTTAAAATTGTCATGGT	57.900	33.333	15.08	0.00	35.47	3.55
62	63	6.523840	ACATGCACTTAAAATTGTCATGGTT	58.476	32.000	15.08	0.00	35.47	3.67

Showing 1 to 25 of 749 entries

Previous1 2 3 4 5…30Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	5.864418	AATTTATGATGCATGGCAAGTCT	57.136	34.783	2.46	0.00	43.62	3.24
2	3	8.422973	TTTTAATTTATGATGCATGGCAAGTC	57.577	30.769	2.46	0.00	43.62	3.01
3	4	8.967664	ATTTTAATTTATGATGCATGGCAAGT	57.032	26.923	2.46	0.00	43.62	3.16
4	5	9.658475	CAATTTTAATTTATGATGCATGGCAAG	57.342	29.630	2.46	0.00	43.62	4.01
6	7	7.255173	GGCAATTTTAATTTATGATGCATGGCA	60.255	33.333	2.46	0.00	44.86	4.92
7	8	7.079475	GGCAATTTTAATTTATGATGCATGGC	58.921	34.615	2.46	0.00	0.00	4.40
8	9	8.155821	TGGCAATTTTAATTTATGATGCATGG	57.844	30.769	2.46	0.00	0.00	3.66
20	21	9.835389	AGTGCATGTATAATGGCAATTTTAATT	57.165	25.926	0.00	0.00	38.10	1.40
21	22	9.835389	AAGTGCATGTATAATGGCAATTTTAAT	57.165	25.926	0.00	0.00	41.10	1.40
24	25	9.664332	TTTAAGTGCATGTATAATGGCAATTTT	57.336	25.926	10.37	0.00	41.10	1.82
25	26	9.664332	TTTTAAGTGCATGTATAATGGCAATTT	57.336	25.926	10.37	5.12	41.10	1.82
26	27	9.835389	ATTTTAAGTGCATGTATAATGGCAATT	57.165	25.926	10.09	10.09	45.12	2.32
27	28	9.835389	AATTTTAAGTGCATGTATAATGGCAAT	57.165	25.926	0.00	0.00	38.10	3.56
28	29	9.096160	CAATTTTAAGTGCATGTATAATGGCAA	57.904	29.630	0.00	0.00	38.10	4.52
29	30	8.256605	ACAATTTTAAGTGCATGTATAATGGCA	58.743	29.630	0.00	0.00	0.00	4.92
30	31	8.647143	ACAATTTTAAGTGCATGTATAATGGC	57.353	30.769	0.00	0.00	0.00	4.40
31	32	9.800433	TGACAATTTTAAGTGCATGTATAATGG	57.200	29.630	0.00	0.00	0.00	3.16
34	35	9.800433	CCATGACAATTTTAAGTGCATGTATAA	57.200	29.630	17.38	0.00	37.10	0.98
35	36	8.965819	ACCATGACAATTTTAAGTGCATGTATA	58.034	29.630	17.38	0.00	37.10	1.47
36	37	7.839907	ACCATGACAATTTTAAGTGCATGTAT	58.160	30.769	17.38	9.05	37.10	2.29
37	38	7.225784	ACCATGACAATTTTAAGTGCATGTA	57.774	32.000	17.38	0.00	37.10	2.29
38	39	6.100404	ACCATGACAATTTTAAGTGCATGT	57.900	33.333	17.38	0.00	37.10	3.21
39	40	6.645827	TGAACCATGACAATTTTAAGTGCATG	59.354	34.615	14.49	14.49	37.78	4.06
40	41	6.757237	TGAACCATGACAATTTTAAGTGCAT	58.243	32.000	0.00	0.00	0.00	3.96
41	42	6.154203	TGAACCATGACAATTTTAAGTGCA	57.846	33.333	0.00	0.00	0.00	4.57

Showing 1 to 25 of 696 entries

Previous1 2 3 4 5…28Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.