AutoCloner

Multiple sequence alignment - TraesCS6D01G195900

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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	TraesCS6D01G195900	chr6D	100.000	4631	0	0	1	4631	271310006	271305376	0.000000e+00	8552.0
1	TraesCS6D01G195900	chr6D	92.962	611	43	0	1	611	361970575	361969965	0.000000e+00	891.0
2	TraesCS6D01G195900	chr6D	97.561	205	5	0	4073	4277	271305731	271305527	7.370000e-93	351.0
3	TraesCS6D01G195900	chr6D	97.561	205	5	0	4276	4480	271305934	271305730	7.370000e-93	351.0
4	TraesCS6D01G195900	chr6D	89.109	101	7	3	2464	2564	108505703	108505607	6.290000e-24	122.0
5	TraesCS6D01G195900	chr6A	92.600	3054	156	37	831	3838	384681171	384684200	0.000000e+00	4324.0
6	TraesCS6D01G195900	chr6A	89.899	198	16	3	612	808	384680985	384681179	7.690000e-63	252.0
7	TraesCS6D01G195900	chr6A	85.065	154	21	2	4475	4627	540263166	540263014	6.200000e-34	156.0
8	TraesCS6D01G195900	chr7B	94.014	1587	84	7	2251	3835	438013956	438012379	0.000000e+00	2394.0
9	TraesCS6D01G195900	chr7B	92.875	1614	84	19	655	2249	438002233	438003834	0.000000e+00	2314.0
10	TraesCS6D01G195900	chr7B	92.270	1617	90	21	652	2249	437998801	437997201	0.000000e+00	2261.0
11	TraesCS6D01G195900	chr7B	95.686	1298	41	6	867	2151	438015691	438014396	0.000000e+00	2073.0
12	TraesCS6D01G195900	chr7B	93.740	1214	69	5	2624	3835	437927097	437928305	0.000000e+00	1814.0
13	TraesCS6D01G195900	chr7B	97.035	371	11	0	2251	2621	438003866	438004236	3.930000e-175	625.0
14	TraesCS6D01G195900	chr7B	97.024	336	10	0	2251	2586	437997169	437996834	2.420000e-157	566.0
15	TraesCS6D01G195900	chr7B	88.106	227	17	7	652	876	438016842	438016624	1.280000e-65	261.0
16	TraesCS6D01G195900	chr7B	96.000	100	2	2	2151	2249	438014086	438013988	1.330000e-35	161.0
17	TraesCS6D01G195900	chr6B	93.486	1351	53	19	918	2249	432494655	432493321	0.000000e+00	1975.0
18	TraesCS6D01G195900	chr6B	94.475	1267	63	5	2564	3828	432492770	432491509	0.000000e+00	1945.0
19	TraesCS6D01G195900	chr6B	96.942	327	10	0	2251	2577	432493289	432492963	2.440000e-152	549.0
20	TraesCS6D01G195900	chr6B	86.833	281	28	7	652	930	432496386	432496113	5.820000e-79	305.0
21	TraesCS6D01G195900	chr6B	100.000	28	0	0	2559	2586	432492796	432492769	8.000000e-03	52.8
22	TraesCS6D01G195900	chr7D	93.954	612	37	0	1	612	311451752	311452363	0.000000e+00	926.0
23	TraesCS6D01G195900	chr7D	93.301	612	41	0	1	612	354622005	354621394	0.000000e+00	904.0
24	TraesCS6D01G195900	chr4D	93.791	612	38	0	1	612	104106809	104106198	0.000000e+00	920.0
25	TraesCS6D01G195900	chr2D	93.312	613	39	2	1	612	334249588	334248977	0.000000e+00	904.0
26	TraesCS6D01G195900	chr2D	92.799	611	44	0	1	611	344829619	344830229	0.000000e+00	885.0
27	TraesCS6D01G195900	chr2D	81.339	911	137	15	2729	3630	439435863	439434977	0.000000e+00	710.0
28	TraesCS6D01G195900	chr3D	93.137	612	42	0	1	612	406194678	406195289	0.000000e+00	898.0
29	TraesCS6D01G195900	chr3D	92.962	611	43	0	2	612	283862244	283861634	0.000000e+00	891.0
30	TraesCS6D01G195900	chr5D	93.257	608	41	0	1	608	191566975	191567582	0.000000e+00	896.0
31	TraesCS6D01G195900	chr5D	86.325	117	14	2	4476	4591	350589487	350589372	4.860000e-25	126.0
32	TraesCS6D01G195900	chr2B	83.186	904	148	4	2729	3630	517377348	517376447	0.000000e+00	824.0
33	TraesCS6D01G195900	chr2A	88.450	329	38	0	2729	3057	549684907	549685235	9.340000e-107	398.0
34	TraesCS6D01G195900	chr2A	88.710	124	14	0	4469	4592	761629960	761630083	8.030000e-33	152.0
35	TraesCS6D01G195900	chr7A	85.535	159	22	1	4469	4627	74879919	74880076	1.030000e-36	165.0
36	TraesCS6D01G195900	chr7A	90.000	100	10	0	4474	4573	209440741	209440642	3.760000e-26	130.0
37	TraesCS6D01G195900	chr1B	80.682	176	24	5	4460	4631	665272765	665272934	1.350000e-25	128.0
38	TraesCS6D01G195900	chrUn	89.109	101	7	3	2464	2564	45085046	45085142	6.290000e-24	122.0
39	TraesCS6D01G195900	chrUn	89.109	101	7	3	2464	2564	182460805	182460709	6.290000e-24	122.0
40	TraesCS6D01G195900	chr4B	89.109	101	7	3	2464	2564	209181543	209181447	6.290000e-24	122.0
41	TraesCS6D01G195900	chr1A	86.607	112	13	2	4474	4584	147169032	147168922	6.290000e-24	122.0
42	TraesCS6D01G195900	chr5B	86.420	81	9	2	4476	4555	175526941	175527020	2.300000e-13	87.9
43	TraesCS6D01G195900	chr5A	100.000	31	0	0	4337	4367	22636632	22636602	1.800000e-04	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	TraesCS6D01G195900	chr6D	271305376	271310006	4630	True	8552.00	8552	100.0000	1	4631	1	chr6D.!!$R2	4630
1	TraesCS6D01G195900	chr6D	361969965	361970575	610	True	891.00	891	92.9620	1	611	1	chr6D.!!$R3	610
2	TraesCS6D01G195900	chr6A	384680985	384684200	3215	False	2288.00	4324	91.2495	612	3838	2	chr6A.!!$F1	3226
3	TraesCS6D01G195900	chr7B	437927097	437928305	1208	False	1814.00	1814	93.7400	2624	3835	1	chr7B.!!$F1	1211
4	TraesCS6D01G195900	chr7B	438002233	438004236	2003	False	1469.50	2314	94.9550	655	2621	2	chr7B.!!$F2	1966
5	TraesCS6D01G195900	chr7B	437996834	437998801	1967	True	1413.50	2261	94.6470	652	2586	2	chr7B.!!$R1	1934
6	TraesCS6D01G195900	chr7B	438012379	438016842	4463	True	1222.25	2394	93.4515	652	3835	4	chr7B.!!$R2	3183
7	TraesCS6D01G195900	chr6B	432491509	432496386	4877	True	965.36	1975	94.3472	652	3828	5	chr6B.!!$R1	3176
8	TraesCS6D01G195900	chr7D	311451752	311452363	611	False	926.00	926	93.9540	1	612	1	chr7D.!!$F1	611
9	TraesCS6D01G195900	chr7D	354621394	354622005	611	True	904.00	904	93.3010	1	612	1	chr7D.!!$R1	611
10	TraesCS6D01G195900	chr4D	104106198	104106809	611	True	920.00	920	93.7910	1	612	1	chr4D.!!$R1	611
11	TraesCS6D01G195900	chr2D	334248977	334249588	611	True	904.00	904	93.3120	1	612	1	chr2D.!!$R1	611
12	TraesCS6D01G195900	chr2D	344829619	344830229	610	False	885.00	885	92.7990	1	611	1	chr2D.!!$F1	610
13	TraesCS6D01G195900	chr2D	439434977	439435863	886	True	710.00	710	81.3390	2729	3630	1	chr2D.!!$R2	901
14	TraesCS6D01G195900	chr3D	406194678	406195289	611	False	898.00	898	93.1370	1	612	1	chr3D.!!$F1	611
15	TraesCS6D01G195900	chr3D	283861634	283862244	610	True	891.00	891	92.9620	2	612	1	chr3D.!!$R1	610
16	TraesCS6D01G195900	chr5D	191566975	191567582	607	False	896.00	896	93.2570	1	608	1	chr5D.!!$F1	607
17	TraesCS6D01G195900	chr2B	517376447	517377348	901	True	824.00	824	83.1860	2729	3630	1	chr2B.!!$R1	901

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
816	818	0.172578	TGACAACGCTAGTCCGATGG	59.827	55.000	5.34	0.00	35.64	3.51	F
955	3369	0.250513	CTTCCCGTTCCAAGGAGAGG	59.749	60.000	5.32	5.32	32.57	3.69	F
2260	5032	1.371183	CCGAACTGTCCCTGCTTCA	59.629	57.895	0.00	0.00	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2249	4991	2.435059	GTCGGCTGAAGCAGGGAC	60.435	66.667	0.00	4.86	44.36	4.46	R
2727	5705	5.068987	AGCAATAGCAACCAAGTCTGAAAAA	59.931	36.000	0.00	0.00	45.49	1.94	R
4032	7041	0.032267	CCTAAGCTAGTACTGCCGGC	59.968	60.000	22.73	22.73	0.00	6.13	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
28	29	0.376152	CAAGCACATGAGATCACCGC	59.624	55.000	0.00	0.00	0.00	5.68
40	41	0.460284	ATCACCGCCATCACTCGTTC	60.460	55.000	0.00	0.00	0.00	3.95
196	197	1.002134	AATGGACCTCAACGCCTGG	60.002	57.895	0.00	0.00	0.00	4.45
216	217	2.094417	GGCGAAGAAATTCAAGAGACCG	59.906	50.000	0.00	0.00	0.00	4.79
221	222	5.177696	CGAAGAAATTCAAGAGACCGTTCTT	59.822	40.000	0.00	0.00	37.90	2.52
267	268	3.626930	TGGGTTATGTACTTTGATGGGC	58.373	45.455	0.00	0.00	0.00	5.36
335	336	1.115467	CCGGAGAGCACCTCAAGTAT	58.885	55.000	0.00	0.00	43.76	2.12
381	382	3.564225	GGAGAAATCAACGAACAACACCT	59.436	43.478	0.00	0.00	0.00	4.00
436	437	1.528824	CGGCAGACCTTGGGATCAT	59.471	57.895	0.00	0.00	0.00	2.45
482	483	2.479837	CAACTCGTGGTGAAGCAAGTA	58.520	47.619	0.00	0.00	0.00	2.24
485	486	3.740115	ACTCGTGGTGAAGCAAGTAAAT	58.260	40.909	0.00	0.00	0.00	1.40
511	512	2.685017	TCAGAGCCCGCTGATGGT	60.685	61.111	0.00	0.00	39.84	3.55
620	621	1.853319	CGACCTGTCGTTCACTTGC	59.147	57.895	11.37	0.00	46.99	4.01
621	622	0.874175	CGACCTGTCGTTCACTTGCA	60.874	55.000	11.37	0.00	46.99	4.08
622	623	0.582005	GACCTGTCGTTCACTTGCAC	59.418	55.000	0.00	0.00	0.00	4.57
628	629	2.869801	TGTCGTTCACTTGCACTAAAGG	59.130	45.455	0.00	0.00	0.00	3.11
638	639	5.049828	ACTTGCACTAAAGGTTTTCATTGC	58.950	37.500	0.00	0.00	0.00	3.56
699	701	9.198837	GAGGGACTAAATTAAAATTGCGAAAAA	57.801	29.630	0.00	0.00	41.55	1.94
760	762	9.508567	GAAGAAGCAACCACTCATAATATTTTC	57.491	33.333	0.00	0.00	0.00	2.29
763	765	7.338800	AGCAACCACTCATAATATTTTCCTG	57.661	36.000	0.00	0.00	0.00	3.86
809	811	2.902705	TTGTCCTTGACAACGCTAGT	57.097	45.000	5.59	0.00	45.88	2.57
810	812	2.433868	TGTCCTTGACAACGCTAGTC	57.566	50.000	0.00	0.00	39.78	2.59
811	813	1.000506	TGTCCTTGACAACGCTAGTCC	59.999	52.381	0.00	0.00	39.78	3.85
812	814	0.242825	TCCTTGACAACGCTAGTCCG	59.757	55.000	0.00	0.00	35.15	4.79
814	816	1.135083	CCTTGACAACGCTAGTCCGAT	60.135	52.381	0.00	0.00	35.15	4.18

Showing 1 to 25 of 676 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
196	197	2.737252	ACGGTCTCTTGAATTTCTTCGC	59.263	45.455	0.00	0.00	33.86	4.70
267	268	2.873288	GCCTTGCAGCGAGAAAGG	59.127	61.111	11.73	13.12	42.86	3.11
335	336	3.513515	GGGGAAAATGCATTTGGACTACA	59.486	43.478	24.74	0.00	0.00	2.74
381	382	2.134287	GCAGCCCCTCATACTCCGA	61.134	63.158	0.00	0.00	0.00	4.55
436	437	0.174845	CCCACGGACGATCAGCTTTA	59.825	55.000	0.00	0.00	0.00	1.85
482	483	4.042187	AGCGGGCTCTGATAATCCTTATTT	59.958	41.667	0.00	0.00	0.00	1.40
485	486	2.300152	CAGCGGGCTCTGATAATCCTTA	59.700	50.000	0.00	0.00	36.19	2.69
511	512	8.972127	ACTTTCTCACTTCATCTACATAAGCTA	58.028	33.333	0.00	0.00	0.00	3.32
612	613	5.906113	TGAAAACCTTTAGTGCAAGTGAA	57.094	34.783	0.00	0.00	0.00	3.18
613	614	6.272318	CAATGAAAACCTTTAGTGCAAGTGA	58.728	36.000	0.00	0.00	0.00	3.41
614	615	5.050837	GCAATGAAAACCTTTAGTGCAAGTG	60.051	40.000	0.00	0.00	40.62	3.16
615	616	5.049828	GCAATGAAAACCTTTAGTGCAAGT	58.950	37.500	0.00	0.00	40.62	3.16
616	617	5.049167	TGCAATGAAAACCTTTAGTGCAAG	58.951	37.500	2.83	0.00	45.45	4.01
617	618	5.016051	TGCAATGAAAACCTTTAGTGCAA	57.984	34.783	2.83	0.00	45.45	4.08
618	619	4.662468	TGCAATGAAAACCTTTAGTGCA	57.338	36.364	1.36	1.36	45.99	4.57
619	620	6.813152	ACATATGCAATGAAAACCTTTAGTGC	59.187	34.615	13.53	0.00	41.12	4.40
620	621	8.649841	CAACATATGCAATGAAAACCTTTAGTG	58.350	33.333	13.53	0.00	0.00	2.74
621	622	8.761575	CAACATATGCAATGAAAACCTTTAGT	57.238	30.769	13.53	0.00	0.00	2.24
670	671	6.540914	TCGCAATTTTAATTTAGTCCCTCGAT	59.459	34.615	0.00	0.00	0.00	3.59
760	762	2.478134	CTCGTTGCTTCTTCTTCACAGG	59.522	50.000	0.00	0.00	0.00	4.00
763	765	3.424170	GCATCTCGTTGCTTCTTCTTCAC	60.424	47.826	1.47	0.00	39.57	3.18
808	810	4.624452	GTACTGTTTAGTTGTCCATCGGAC	59.376	45.833	6.20	6.20	44.04	4.79
809	811	4.281435	TGTACTGTTTAGTTGTCCATCGGA	59.719	41.667	0.00	0.00	38.36	4.55
810	812	4.562082	TGTACTGTTTAGTTGTCCATCGG	58.438	43.478	0.00	0.00	38.36	4.18
811	813	4.091509	GCTGTACTGTTTAGTTGTCCATCG	59.908	45.833	1.46	0.00	38.36	3.84

Showing 1 to 25 of 645 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.