AutoCloner

Multiple sequence alignment - TraesCS7D01G361200

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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	TraesCS7D01G361200	chr7D	100.000	4302	0	0	1	4302	463896096	463891795	0.000000e+00	7945.0
1	TraesCS7D01G361200	chr7D	83.614	415	61	6	91	501	206847407	206846996	2.430000e-102	383.0
2	TraesCS7D01G361200	chr7D	74.865	923	159	48	2266	3165	463962441	463961569	6.840000e-93	351.0
3	TraesCS7D01G361200	chr7D	80.815	417	66	6	89	502	579966692	579967097	8.980000e-82	315.0
4	TraesCS7D01G361200	chr7D	79.675	246	48	2	4045	4289	355562409	355562653	4.420000e-40	176.0
5	TraesCS7D01G361200	chr7A	92.413	2346	110	30	1083	3385	536506921	536509241	0.000000e+00	3284.0
6	TraesCS7D01G361200	chr7A	90.935	706	27	19	3604	4302	536509372	536510047	0.000000e+00	915.0
7	TraesCS7D01G361200	chr7A	88.596	456	44	6	646	1094	536506287	536506741	8.130000e-152	547.0
8	TraesCS7D01G361200	chr7A	74.674	920	162	47	2268	3165	536124249	536125119	4.120000e-90	342.0
9	TraesCS7D01G361200	chr7A	80.488	246	46	2	4051	4295	377980890	377980646	2.040000e-43	187.0
10	TraesCS7D01G361200	chr7B	96.047	1366	36	7	827	2189	487800132	487801482	0.000000e+00	2207.0
11	TraesCS7D01G361200	chr7B	94.837	1317	52	7	2256	3562	487801573	487802883	0.000000e+00	2041.0
12	TraesCS7D01G361200	chr7B	96.453	733	24	1	3570	4302	487802998	487803728	0.000000e+00	1208.0
13	TraesCS7D01G361200	chr7B	94.673	657	34	1	180	836	487798024	487798679	0.000000e+00	1018.0
14	TraesCS7D01G361200	chr7B	74.295	922	162	50	2268	3165	487220991	487221861	1.930000e-83	320.0
15	TraesCS7D01G361200	chr7B	80.488	246	46	2	4045	4289	307363421	307363665	2.040000e-43	187.0
16	TraesCS7D01G361200	chr7B	82.243	107	14	5	652	757	164158912	164159014	2.130000e-13	87.9
17	TraesCS7D01G361200	chr7B	88.732	71	8	0	703	773	226444341	226444271	2.130000e-13	87.9
18	TraesCS7D01G361200	chr5D	86.321	424	46	8	89	501	404474546	404474968	6.560000e-123	451.0
19	TraesCS7D01G361200	chr2B	83.924	423	62	5	89	507	148249701	148250121	2.410000e-107	399.0
20	TraesCS7D01G361200	chr2B	94.915	59	3	0	3852	3910	30133312	30133370	4.580000e-15	93.5
21	TraesCS7D01G361200	chr2D	82.464	422	67	5	89	507	97231246	97231663	3.160000e-96	363.0
22	TraesCS7D01G361200	chr2D	84.857	350	49	2	89	436	71257021	71256674	2.460000e-92	350.0
23	TraesCS7D01G361200	chr2D	85.065	308	37	5	119	423	83826448	83826749	5.400000e-79	305.0
24	TraesCS7D01G361200	chr2D	85.200	250	36	1	256	505	491956535	491956287	5.520000e-64	255.0
25	TraesCS7D01G361200	chr2D	85.294	68	9	1	700	766	558161404	558161337	7.720000e-08	69.4
26	TraesCS7D01G361200	chr1B	81.146	419	68	5	89	505	645086117	645085708	4.150000e-85	326.0
27	TraesCS7D01G361200	chr3B	80.193	414	55	14	89	502	574721214	574721600	7.040000e-73	285.0
28	TraesCS7D01G361200	chr1D	82.462	325	51	3	176	494	11252968	11252644	3.280000e-71	279.0
29	TraesCS7D01G361200	chr5A	86.420	81	11	0	561	641	353156963	353157043	5.930000e-14	89.8
30	TraesCS7D01G361200	chr5A	80.882	68	11	2	664	730	92218781	92218847	8.000000e-03	52.8
31	TraesCS7D01G361200	chr3A	84.416	77	10	2	696	771	66909028	66908953	1.660000e-09	75.0
32	TraesCS7D01G361200	chr1A	80.000	105	18	2	659	762	577888623	577888725	1.660000e-09	75.0
33	TraesCS7D01G361200	chr4A	95.238	42	2	0	602	643	610038950	610038909	2.780000e-07	67.6
34	TraesCS7D01G361200	chr2A	82.667	75	13	0	700	774	168978009	168977935	2.780000e-07	67.6
35	TraesCS7D01G361200	chr4D	83.333	72	10	2	659	729	401634007	401634077	9.990000e-07	65.8
36	TraesCS7D01G361200	chr5B	82.857	70	11	1	700	768	572341190	572341121	1.290000e-05	62.1

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	TraesCS7D01G361200	chr7D	463891795	463896096	4301	True	7945.0	7945	100.0000	1	4302	1	chr7D.!!$R2	4301
1	TraesCS7D01G361200	chr7D	463961569	463962441	872	True	351.0	351	74.8650	2266	3165	1	chr7D.!!$R3	899
2	TraesCS7D01G361200	chr7A	536506287	536510047	3760	False	1582.0	3284	90.6480	646	4302	3	chr7A.!!$F2	3656
3	TraesCS7D01G361200	chr7A	536124249	536125119	870	False	342.0	342	74.6740	2268	3165	1	chr7A.!!$F1	897
4	TraesCS7D01G361200	chr7B	487798024	487803728	5704	False	1618.5	2207	95.5025	180	4302	4	chr7B.!!$F4	4122
5	TraesCS7D01G361200	chr7B	487220991	487221861	870	False	320.0	320	74.2950	2268	3165	1	chr7B.!!$F3	897

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
151	152	0.297525	CCGTACGCGTTGACATGATG	59.702	55.0	20.78	1.98	36.15	3.07	F
764	765	0.625849	AAGGTGCTCATAGGGGTTGG	59.374	55.0	0.00	0.00	0.00	3.77	F
2189	3865	0.035343	GCAGGTCCAAGGGGTAAGAC	60.035	60.0	0.00	0.00	34.93	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1629	3305	0.034896	TTCAGTTCAGTTCCTCGGGC	59.965	55.0	0.00	0.00	6.13	R
2237	3952	0.263172	ACAAAACCCCCACCATGTCA	59.737	50.0	0.00	0.00	3.58	R
3356	5101	0.103937	TGGAAGGCCTTTGTTTTGCG	59.896	50.0	21.54	34.31	4.85	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	Hairpin	End Stability
73	74	2.201210	GGGGGCATATTGGGGGTG	59.799	66.667	0.00	4.61
74	75	2.524148	GGGGCATATTGGGGGTGC	60.524	66.667	38.12	5.01
75	76	2.912025	GGGCATATTGGGGGTGCG	60.912	66.667	39.69	5.34
76	77	2.912025	GGCATATTGGGGGTGCGG	60.912	66.667	39.69	5.69
77	78	3.605664	GCATATTGGGGGTGCGGC	61.606	66.667	0.00	6.53
78	79	2.195683	CATATTGGGGGTGCGGCT	59.804	61.111	0.00	5.52
79	80	2.195567	CATATTGGGGGTGCGGCTG	61.196	63.158	0.00	4.85
80	81	2.382770	ATATTGGGGGTGCGGCTGA	61.383	57.895	0.00	4.26
81	82	1.932156	ATATTGGGGGTGCGGCTGAA	61.932	55.000	0.00	3.02
82	83	2.550699	TATTGGGGGTGCGGCTGAAG	62.551	60.000	0.00	3.02
84	85	4.115199	GGGGGTGCGGCTGAAGAT	62.115	66.667	0.00	2.40
85	86	2.825836	GGGGTGCGGCTGAAGATG	60.826	66.667	0.00	2.90
86	87	3.512516	GGGTGCGGCTGAAGATGC	61.513	66.667	0.00	3.91
87	88	2.437359	GGTGCGGCTGAAGATGCT	60.437	61.111	0.00	3.79
88	89	2.042831	GGTGCGGCTGAAGATGCTT	61.043	57.895	0.00	3.91
89	90	1.589716	GGTGCGGCTGAAGATGCTTT	61.590	55.000	0.00	3.51
90	91	0.455633	GTGCGGCTGAAGATGCTTTG	60.456	55.000	0.00	2.77
91	92	0.606130	TGCGGCTGAAGATGCTTTGA	60.606	50.000	0.00	2.69
92	93	0.523072	GCGGCTGAAGATGCTTTGAA	59.477	50.000	0.00	2.69
93	94	1.133790	GCGGCTGAAGATGCTTTGAAT	59.866	47.619	0.00	2.57
94	95	2.793933	GCGGCTGAAGATGCTTTGAATC	60.794	50.000	0.00	2.52
95	96	2.421073	CGGCTGAAGATGCTTTGAATCA	59.579	45.455	0.00	2.57
96	97	3.066342	CGGCTGAAGATGCTTTGAATCAT	59.934	43.478	0.00	2.45
97	98	4.439700	CGGCTGAAGATGCTTTGAATCATT	60.440	41.667	0.00	2.57
98	99	5.041940	GGCTGAAGATGCTTTGAATCATTC	58.958	41.667	0.00	2.67

Showing 1 to 25 of 209 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	57	2.201210	CACCCCCAATATGCCCCC	59.799	66.667	0.00	0.00	0.00	5.40
57	58	2.524148	GCACCCCCAATATGCCCC	60.524	66.667	0.00	0.00	33.06	5.80
58	59	2.912025	CGCACCCCCAATATGCCC	60.912	66.667	0.00	0.00	35.91	5.36
59	60	2.912025	CCGCACCCCCAATATGCC	60.912	66.667	0.00	0.00	35.91	4.40
60	61	3.605664	GCCGCACCCCCAATATGC	61.606	66.667	0.00	0.00	35.96	3.14
61	62	2.195567	CAGCCGCACCCCCAATATG	61.196	63.158	0.00	0.00	0.00	1.78
62	63	1.932156	TTCAGCCGCACCCCCAATAT	61.932	55.000	0.00	0.00	0.00	1.28
63	64	2.550699	CTTCAGCCGCACCCCCAATA	62.551	60.000	0.00	0.00	0.00	1.90
64	65	3.944250	CTTCAGCCGCACCCCCAAT	62.944	63.158	0.00	0.00	0.00	3.16
65	66	4.659172	CTTCAGCCGCACCCCCAA	62.659	66.667	0.00	0.00	0.00	4.12
67	68	4.115199	ATCTTCAGCCGCACCCCC	62.115	66.667	0.00	0.00	0.00	5.40
68	69	2.825836	CATCTTCAGCCGCACCCC	60.826	66.667	0.00	0.00	0.00	4.95
69	70	3.512516	GCATCTTCAGCCGCACCC	61.513	66.667	0.00	0.00	0.00	4.61
70	71	1.589716	AAAGCATCTTCAGCCGCACC	61.590	55.000	0.00	0.00	0.00	5.01
71	72	0.455633	CAAAGCATCTTCAGCCGCAC	60.456	55.000	0.00	0.00	0.00	5.34
72	73	0.606130	TCAAAGCATCTTCAGCCGCA	60.606	50.000	0.00	0.00	0.00	5.69
73	74	0.523072	TTCAAAGCATCTTCAGCCGC	59.477	50.000	0.00	0.00	0.00	6.53
74	75	2.421073	TGATTCAAAGCATCTTCAGCCG	59.579	45.455	0.00	0.00	0.00	5.52
75	76	4.650754	ATGATTCAAAGCATCTTCAGCC	57.349	40.909	0.00	0.00	26.60	4.85
76	77	5.647589	TGAATGATTCAAAGCATCTTCAGC	58.352	37.500	5.21	0.00	36.59	4.26
77	78	7.973944	TGAATGAATGATTCAAAGCATCTTCAG	59.026	33.333	12.36	0.00	46.19	3.02
78	79	7.832769	TGAATGAATGATTCAAAGCATCTTCA	58.167	30.769	12.36	12.01	46.19	3.02
89	90	6.676213	GCAACATCGAGTGAATGAATGATTCA	60.676	38.462	10.65	10.65	46.85	2.57
90	91	5.680229	GCAACATCGAGTGAATGAATGATTC	59.320	40.000	0.00	0.00	40.99	2.52
91	92	5.356190	AGCAACATCGAGTGAATGAATGATT	59.644	36.000	0.00	0.00	0.00	2.57

Showing 1 to 25 of 195 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.