AutoCloner

Multiple sequence alignment - TraesCS6D01G276700

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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	TraesCS6D01G276700	chr6D	100.000	3334	0	0	1	3334	385634284	385637617	0.000000e+00	6157.0
1	TraesCS6D01G276700	chr6D	76.559	401	58	15	1988	2359	385467215	385466822	1.580000e-43	187.0
2	TraesCS6D01G276700	chr6D	86.555	119	14	2	1877	1994	385467426	385467309	2.700000e-26	130.0
3	TraesCS6D01G276700	chr6A	90.454	2179	120	41	459	2596	530088383	530090514	0.000000e+00	2791.0
4	TraesCS6D01G276700	chr6A	86.693	511	50	15	2639	3146	530090518	530091013	4.860000e-153	551.0
5	TraesCS6D01G276700	chr6A	86.552	290	31	4	1	282	71709306	71709595	2.500000e-81	313.0
6	TraesCS6D01G276700	chr6A	75.806	620	93	30	918	1522	529609391	529608814	9.170000e-66	261.0
7	TraesCS6D01G276700	chr6A	88.268	179	17	4	281	458	71709626	71709801	9.370000e-51	211.0
8	TraesCS6D01G276700	chr6A	76.633	398	64	14	1988	2359	529605948	529605554	3.390000e-45	193.0
9	TraesCS6D01G276700	chr6A	89.623	106	9	2	1887	1991	529606151	529606047	2.090000e-27	134.0
10	TraesCS6D01G276700	chr6B	90.167	1200	49	32	459	1618	575924845	575926015	0.000000e+00	1498.0
11	TraesCS6D01G276700	chr6B	91.692	999	64	12	1643	2637	575926190	575927173	0.000000e+00	1367.0
12	TraesCS6D01G276700	chr6B	87.291	299	23	9	2934	3230	575936141	575936426	8.920000e-86	327.0
13	TraesCS6D01G276700	chr6B	77.215	632	84	34	918	1522	575379896	575379298	6.940000e-82	315.0
14	TraesCS6D01G276700	chr6B	86.598	291	29	6	1	282	715322719	715322430	2.500000e-81	313.0
15	TraesCS6D01G276700	chr6B	82.595	316	38	9	2634	2945	575935533	575935835	2.550000e-66	263.0
16	TraesCS6D01G276700	chr6B	77.591	357	54	11	1988	2323	575378390	575378039	3.390000e-45	193.0
17	TraesCS6D01G276700	chr6B	88.350	103	10	2	1890	1991	575378591	575378490	4.520000e-24	122.0
18	TraesCS6D01G276700	chr3D	95.464	463	13	4	1	462	118415371	118415826	0.000000e+00	732.0
19	TraesCS6D01G276700	chr5B	81.489	497	49	17	1	458	10131556	10132048	5.250000e-98	368.0
20	TraesCS6D01G276700	chr5B	80.730	493	55	19	3	458	160145835	160145346	6.850000e-92	348.0
21	TraesCS6D01G276700	chr5D	82.578	419	51	16	2833	3247	195652549	195652949	1.900000e-92	350.0
22	TraesCS6D01G276700	chr5D	89.205	176	17	1	282	457	37642460	37642633	5.600000e-53	219.0
23	TraesCS6D01G276700	chr1D	82.160	426	51	17	2831	3247	240611441	240611032	3.190000e-90	342.0
24	TraesCS6D01G276700	chr1D	79.419	413	57	19	2832	3239	175763664	175763275	1.970000e-67	267.0
25	TraesCS6D01G276700	chr1D	79.391	427	51	25	65	458	342188684	342189106	1.970000e-67	267.0
26	TraesCS6D01G276700	chr7D	83.113	379	42	15	2837	3207	288465460	288465096	3.210000e-85	326.0
27	TraesCS6D01G276700	chr7D	80.095	422	56	24	2832	3247	266385311	266384912	4.210000e-74	289.0
28	TraesCS6D01G276700	chr5A	81.384	419	57	15	2833	3247	232836199	232836600	4.150000e-84	322.0
29	TraesCS6D01G276700	chr1A	87.857	280	25	4	1	272	63856316	63856594	1.490000e-83	320.0
30	TraesCS6D01G276700	chrUn	85.467	289	31	7	1	282	43088052	43088336	1.170000e-74	291.0
31	TraesCS6D01G276700	chrUn	85.467	289	31	7	1	282	262834908	262835192	1.170000e-74	291.0
32	TraesCS6D01G276700	chrUn	85.467	289	31	7	1	282	306193772	306193488	1.170000e-74	291.0
33	TraesCS6D01G276700	chr2A	85.467	289	30	8	1	282	160041791	160042074	1.170000e-74	291.0
34	TraesCS6D01G276700	chr2A	79.419	413	66	18	2833	3241	307688595	307688992	1.180000e-69	274.0
35	TraesCS6D01G276700	chr2A	87.222	180	14	6	281	452	160042105	160042283	2.620000e-46	196.0
36	TraesCS6D01G276700	chr4B	86.264	182	17	4	281	461	571834418	571834592	1.220000e-44	191.0
37	TraesCS6D01G276700	chr1B	85.629	167	20	2	292	458	145572222	145572060	4.420000e-39	172.0
38	TraesCS6D01G276700	chr4A	97.297	37	1	0	3	39	614364279	614364315	2.780000e-06	63.9

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	TraesCS6D01G276700	chr6D	385634284	385637617	3333	False	6157.0	6157	100.0000	1	3334	1	chr6D.!!$F1	3333
1	TraesCS6D01G276700	chr6A	530088383	530091013	2630	False	1671.0	2791	88.5735	459	3146	2	chr6A.!!$F2	2687
2	TraesCS6D01G276700	chr6B	575924845	575927173	2328	False	1432.5	1498	90.9295	459	2637	2	chr6B.!!$F1	2178
3	TraesCS6D01G276700	chr6B	575935533	575936426	893	False	295.0	327	84.9430	2634	3230	2	chr6B.!!$F2	596
4	TraesCS6D01G276700	chr6B	575378039	575379896	1857	True	210.0	315	81.0520	918	2323	3	chr6B.!!$R2	1405

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
305	306	0.032130	GTCAGCAGTCCTGTGTTCGA	59.968	55.0	0.0	0.0	42.38	3.71	F
430	431	0.038343	GCGAAAGGGCAGCATTTTGA	60.038	50.0	11.9	0.0	0.00	2.69	F
437	438	0.039256	GGCAGCATTTTGACGCAGAA	60.039	50.0	0.0	0.0	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2079	2826	0.111253	CCTCCTTCCTGTTGGCAGTT	59.889	55.000	0.00	0.0	41.02	3.16	R
2165	2912	0.317603	CGGAGTTAGCCGTCGGTATG	60.318	60.000	13.94	0.0	46.07	2.39	R
2401	3191	1.728971	GGACAACTCATGCTCAACGAG	59.271	52.381	0.00	0.0	0.00	4.18	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
63	64	7.506296	AAAACTGTTCTTGCTTTAGAAAACG	57.494	32.000	0.00	0.00	36.01	3.60
64	65	5.169836	ACTGTTCTTGCTTTAGAAAACGG	57.830	39.130	0.00	0.00	36.01	4.44
65	66	4.638865	ACTGTTCTTGCTTTAGAAAACGGT	59.361	37.500	0.00	0.00	36.01	4.83
66	67	5.124936	ACTGTTCTTGCTTTAGAAAACGGTT	59.875	36.000	0.00	0.00	36.01	4.44
67	68	5.575019	TGTTCTTGCTTTAGAAAACGGTTC	58.425	37.500	0.00	0.00	36.01	3.62
68	69	5.124138	TGTTCTTGCTTTAGAAAACGGTTCA	59.876	36.000	0.00	0.00	36.01	3.18
69	70	5.164606	TCTTGCTTTAGAAAACGGTTCAC	57.835	39.130	0.00	0.00	0.00	3.18
70	71	4.636648	TCTTGCTTTAGAAAACGGTTCACA	59.363	37.500	0.00	0.00	0.00	3.58
71	72	4.966965	TGCTTTAGAAAACGGTTCACAA	57.033	36.364	0.00	0.00	0.00	3.33
72	73	5.312120	TGCTTTAGAAAACGGTTCACAAA	57.688	34.783	0.00	0.00	0.00	2.83
73	74	5.897050	TGCTTTAGAAAACGGTTCACAAAT	58.103	33.333	0.00	0.00	0.00	2.32
74	75	6.334202	TGCTTTAGAAAACGGTTCACAAATT	58.666	32.000	0.00	0.00	0.00	1.82
75	76	6.474102	TGCTTTAGAAAACGGTTCACAAATTC	59.526	34.615	0.00	0.00	0.00	2.17
76	77	6.695713	GCTTTAGAAAACGGTTCACAAATTCT	59.304	34.615	7.98	7.98	0.00	2.40
77	78	7.305993	GCTTTAGAAAACGGTTCACAAATTCTG	60.306	37.037	11.54	0.35	0.00	3.02
78	79	5.828299	AGAAAACGGTTCACAAATTCTGA	57.172	34.783	0.00	0.00	0.00	3.27
79	80	6.202516	AGAAAACGGTTCACAAATTCTGAA	57.797	33.333	0.00	0.00	0.00	3.02
80	81	6.626302	AGAAAACGGTTCACAAATTCTGAAA	58.374	32.000	0.00	0.00	29.44	2.69
81	82	7.093992	AGAAAACGGTTCACAAATTCTGAAAA	58.906	30.769	0.00	0.00	29.44	2.29
82	83	7.763985	AGAAAACGGTTCACAAATTCTGAAAAT	59.236	29.630	0.00	0.00	29.44	1.82
83	84	6.826893	AACGGTTCACAAATTCTGAAAATG	57.173	33.333	0.00	0.00	29.44	2.32
84	85	5.901552	ACGGTTCACAAATTCTGAAAATGT	58.098	33.333	0.00	0.00	29.44	2.71
85	86	6.337356	ACGGTTCACAAATTCTGAAAATGTT	58.663	32.000	8.24	0.00	29.44	2.71
86	87	6.475402	ACGGTTCACAAATTCTGAAAATGTTC	59.525	34.615	8.24	0.00	29.44	3.18
87	88	6.475076	CGGTTCACAAATTCTGAAAATGTTCA	59.525	34.615	0.00	0.00	41.57	3.18

Showing 1 to 25 of 327 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	7.062956	CCGTTTTCTAAAGCAAGAACAGTTTTT	59.937	33.333	0.00	0.00	35.25	1.94
39	40	6.530181	CCGTTTTCTAAAGCAAGAACAGTTTT	59.470	34.615	0.00	0.00	35.25	2.43
40	41	6.033966	CCGTTTTCTAAAGCAAGAACAGTTT	58.966	36.000	0.00	0.00	35.25	2.66
41	42	5.124936	ACCGTTTTCTAAAGCAAGAACAGTT	59.875	36.000	0.00	0.00	35.25	3.16
42	43	4.638865	ACCGTTTTCTAAAGCAAGAACAGT	59.361	37.500	0.00	0.00	35.25	3.55
43	44	5.169836	ACCGTTTTCTAAAGCAAGAACAG	57.830	39.130	0.00	0.00	35.25	3.16
44	45	5.124138	TGAACCGTTTTCTAAAGCAAGAACA	59.876	36.000	0.00	0.00	35.25	3.18
45	46	5.454554	GTGAACCGTTTTCTAAAGCAAGAAC	59.545	40.000	0.00	0.00	35.25	3.01
46	47	5.124138	TGTGAACCGTTTTCTAAAGCAAGAA	59.876	36.000	0.00	0.00	33.69	2.52
47	48	4.636648	TGTGAACCGTTTTCTAAAGCAAGA	59.363	37.500	0.00	0.00	0.00	3.02
48	49	4.915704	TGTGAACCGTTTTCTAAAGCAAG	58.084	39.130	0.00	0.00	0.00	4.01
49	50	4.966965	TGTGAACCGTTTTCTAAAGCAA	57.033	36.364	0.00	0.00	0.00	3.91
50	51	4.966965	TTGTGAACCGTTTTCTAAAGCA	57.033	36.364	0.00	0.00	0.00	3.91
51	52	6.695713	AGAATTTGTGAACCGTTTTCTAAAGC	59.304	34.615	0.00	0.00	0.00	3.51
52	53	7.913297	TCAGAATTTGTGAACCGTTTTCTAAAG	59.087	33.333	0.00	0.00	0.00	1.85
53	54	7.763356	TCAGAATTTGTGAACCGTTTTCTAAA	58.237	30.769	0.00	0.00	0.00	1.85
54	55	7.323049	TCAGAATTTGTGAACCGTTTTCTAA	57.677	32.000	0.00	0.00	0.00	2.10
55	56	6.928979	TCAGAATTTGTGAACCGTTTTCTA	57.071	33.333	0.00	0.00	0.00	2.10
56	57	5.828299	TCAGAATTTGTGAACCGTTTTCT	57.172	34.783	0.00	0.00	0.00	2.52
57	58	6.879188	TTTCAGAATTTGTGAACCGTTTTC	57.121	33.333	8.37	0.00	33.63	2.29
58	59	7.333174	ACATTTTCAGAATTTGTGAACCGTTTT	59.667	29.630	8.37	0.00	33.63	2.43
59	60	6.816140	ACATTTTCAGAATTTGTGAACCGTTT	59.184	30.769	8.37	0.00	33.63	3.60
60	61	6.337356	ACATTTTCAGAATTTGTGAACCGTT	58.663	32.000	8.37	0.00	33.63	4.44
61	62	5.901552	ACATTTTCAGAATTTGTGAACCGT	58.098	33.333	8.37	4.14	33.63	4.83
62	63	6.475076	TGAACATTTTCAGAATTTGTGAACCG	59.525	34.615	8.37	3.60	36.79	4.44

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.