AutoCloner

Multiple sequence alignment - TraesCS2D01G053700

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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	TraesCS2D01G053700	chr2D	100.000	2369	0	0	1	2369	21087520	21089888	0.000000e+00	4375
1	TraesCS2D01G053700	chr2D	97.015	201	5	1	2170	2369	565692204	565692004	1.050000e-88	337
2	TraesCS2D01G053700	chr2D	95.283	212	10	0	2158	2369	586269510	586269721	1.050000e-88	337
3	TraesCS2D01G053700	chr2D	96.552	203	6	1	2167	2369	23187226	23187427	3.770000e-88	335
4	TraesCS2D01G053700	chr2D	82.967	182	22	6	138	316	136380338	136380513	3.150000e-34	156
5	TraesCS2D01G053700	chrUn	89.822	1572	103	19	626	2167	154084153	154082609	0.000000e+00	1964
6	TraesCS2D01G053700	chrUn	89.655	1566	105	18	626	2161	210798653	210800191	0.000000e+00	1941
7	TraesCS2D01G053700	chrUn	89.504	1572	108	17	626	2167	154097317	154095773	0.000000e+00	1936
8	TraesCS2D01G053700	chrUn	89.440	1572	109	18	626	2167	146913953	146912409	0.000000e+00	1930
9	TraesCS2D01G053700	chrUn	89.150	1576	110	21	626	2167	146898981	146897433	0.000000e+00	1906
10	TraesCS2D01G053700	chrUn	87.977	1572	107	18	626	2167	147072497	147070978	0.000000e+00	1781
11	TraesCS2D01G053700	chrUn	91.731	1040	63	5	1128	2167	427197590	427196574	0.000000e+00	1423
12	TraesCS2D01G053700	chrUn	87.636	275	21	7	626	892	426721309	426721578	8.220000e-80	307
13	TraesCS2D01G053700	chrUn	86.777	121	12	3	22	140	146899630	146899512	5.310000e-27	132
14	TraesCS2D01G053700	chrUn	86.777	121	12	3	22	140	146914601	146914483	5.310000e-27	132
15	TraesCS2D01G053700	chrUn	86.777	121	12	3	22	140	147073147	147073029	5.310000e-27	132
16	TraesCS2D01G053700	chrUn	86.777	121	12	3	22	140	154097965	154097847	5.310000e-27	132
17	TraesCS2D01G053700	chrUn	85.827	127	14	3	16	140	210797999	210798123	5.310000e-27	132
18	TraesCS2D01G053700	chrUn	85.827	127	14	3	16	140	356698538	356698662	5.310000e-27	132
19	TraesCS2D01G053700	chrUn	85.827	127	14	3	16	140	376173853	376173977	5.310000e-27	132
20	TraesCS2D01G053700	chrUn	85.827	127	14	3	16	140	413422548	413422672	5.310000e-27	132
21	TraesCS2D01G053700	chrUn	85.827	127	14	3	16	140	465978193	465978317	5.310000e-27	132
22	TraesCS2D01G053700	chr2A	89.758	1572	104	18	626	2167	22939601	22938057	0.000000e+00	1958
23	TraesCS2D01G053700	chr2A	89.726	1567	102	21	626	2161	22618965	22620503	0.000000e+00	1947
24	TraesCS2D01G053700	chr2A	89.719	1566	104	19	626	2161	22651347	22652885	0.000000e+00	1947
25	TraesCS2D01G053700	chr2A	89.567	1572	106	19	626	2167	22802512	22800969	0.000000e+00	1941
26	TraesCS2D01G053700	chr2A	86.369	873	65	16	626	1468	23190284	23191132	0.000000e+00	904
27	TraesCS2D01G053700	chr2A	86.775	741	62	16	626	1335	22664790	22665525	0.000000e+00	793
28	TraesCS2D01G053700	chr2A	80.978	184	24	8	136	315	207465042	207465218	4.110000e-28	135
29	TraesCS2D01G053700	chr2B	85.563	1704	168	40	502	2161	34453445	34455114	0.000000e+00	1712
30	TraesCS2D01G053700	chr1D	98.477	197	2	1	2174	2369	461394960	461394764	1.740000e-91	346
31	TraesCS2D01G053700	chr3D	97.044	203	6	0	2167	2369	9085848	9086050	2.250000e-90	342
32	TraesCS2D01G053700	chr3D	96.602	206	5	1	2164	2369	549135356	549135559	8.110000e-90	340
33	TraesCS2D01G053700	chr3D	97.044	203	5	1	2167	2369	560316638	560316437	8.110000e-90	340
34	TraesCS2D01G053700	chr3D	82.292	192	25	6	136	324	604800476	604800291	8.770000e-35	158
35	TraesCS2D01G053700	chr7D	97.030	202	5	1	2168	2369	563056068	563055868	2.920000e-89	339
36	TraesCS2D01G053700	chr7D	82.873	181	22	6	138	315	71982549	71982375	1.130000e-33	154
37	TraesCS2D01G053700	chr5D	96.569	204	6	1	2167	2369	488039497	488039294	1.050000e-88	337
38	TraesCS2D01G053700	chr5B	83.684	190	25	5	132	320	48871503	48871687	8.700000e-40	174
39	TraesCS2D01G053700	chr7A	84.971	173	20	5	144	315	60050968	60050801	1.130000e-38	171
40	TraesCS2D01G053700	chr7B	84.393	173	22	3	144	316	129311197	129311030	5.240000e-37	165
41	TraesCS2D01G053700	chr4D	82.873	181	22	6	138	315	507858194	507858368	1.130000e-33	154
42	TraesCS2D01G053700	chr4A	83.140	172	24	4	144	315	625795682	625795516	4.080000e-33	152

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	TraesCS2D01G053700	chr2D	21087520	21089888	2368	False	4375.0	4375	100.0000	1	2369	1	chr2D.!!$F1	2368
1	TraesCS2D01G053700	chrUn	154082609	154084153	1544	True	1964.0	1964	89.8220	626	2167	1	chrUn.!!$R1	1541
2	TraesCS2D01G053700	chrUn	427196574	427197590	1016	True	1423.0	1423	91.7310	1128	2167	1	chrUn.!!$R2	1039
3	TraesCS2D01G053700	chrUn	210797999	210800191	2192	False	1036.5	1941	87.7410	16	2161	2	chrUn.!!$F6	2145
4	TraesCS2D01G053700	chrUn	154095773	154097965	2192	True	1034.0	1936	88.1405	22	2167	2	chrUn.!!$R6	2145
5	TraesCS2D01G053700	chrUn	146912409	146914601	2192	True	1031.0	1930	88.1085	22	2167	2	chrUn.!!$R4	2145
6	TraesCS2D01G053700	chrUn	146897433	146899630	2197	True	1019.0	1906	87.9635	22	2167	2	chrUn.!!$R3	2145
7	TraesCS2D01G053700	chrUn	147070978	147073147	2169	True	956.5	1781	87.3770	22	2167	2	chrUn.!!$R5	2145
8	TraesCS2D01G053700	chr2A	22938057	22939601	1544	True	1958.0	1958	89.7580	626	2167	1	chr2A.!!$R2	1541
9	TraesCS2D01G053700	chr2A	22618965	22620503	1538	False	1947.0	1947	89.7260	626	2161	1	chr2A.!!$F1	1535
10	TraesCS2D01G053700	chr2A	22651347	22652885	1538	False	1947.0	1947	89.7190	626	2161	1	chr2A.!!$F2	1535
11	TraesCS2D01G053700	chr2A	22800969	22802512	1543	True	1941.0	1941	89.5670	626	2167	1	chr2A.!!$R1	1541
12	TraesCS2D01G053700	chr2A	23190284	23191132	848	False	904.0	904	86.3690	626	1468	1	chr2A.!!$F4	842
13	TraesCS2D01G053700	chr2A	22664790	22665525	735	False	793.0	793	86.7750	626	1335	1	chr2A.!!$F3	709
14	TraesCS2D01G053700	chr2B	34453445	34455114	1669	False	1712.0	1712	85.5630	502	2161	1	chr2B.!!$F1	1659

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
217	218	0.032267	GGTGCCGCTAGATGGTACTC	59.968	60.0	17.75	8.25	41.31	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2184	2475	0.038343	TTACGAACCGGCGCTAAAGT	60.038	50.0	7.64	3.16	33.86	2.66	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
36	37	6.735694	GCATGTCCATTTAATTAACCGAGCAT	60.736	38.462	0.00	0.00	0.00	3.79
38	39	8.514594	CATGTCCATTTAATTAACCGAGCATAT	58.485	33.333	0.00	0.00	0.00	1.78
52	53	6.946340	ACCGAGCATATTGTGGATTATATGA	58.054	36.000	0.00	0.00	37.04	2.15
54	55	6.018425	CCGAGCATATTGTGGATTATATGAGC	60.018	42.308	0.00	0.00	37.04	4.26
89	90	3.055385	GGTGATACCAGCAGACCTTACAA	60.055	47.826	0.00	0.00	40.34	2.41
96	97	4.184629	CCAGCAGACCTTACAATGTAGAC	58.815	47.826	0.00	0.00	0.00	2.59
99	100	5.521735	CAGCAGACCTTACAATGTAGACATC	59.478	44.000	0.00	0.00	35.10	3.06
104	105	8.251026	CAGACCTTACAATGTAGACATCAAGTA	58.749	37.037	0.00	0.00	35.10	2.24
108	109	9.823647	CCTTACAATGTAGACATCAAGTATTCT	57.176	33.333	0.00	0.00	35.10	2.40
134	135	8.990163	AGGTTAAAGGAAAATCAGAAGTAACA	57.010	30.769	0.00	0.00	0.00	2.41
135	136	8.847196	AGGTTAAAGGAAAATCAGAAGTAACAC	58.153	33.333	0.00	0.00	0.00	3.32
136	137	8.847196	GGTTAAAGGAAAATCAGAAGTAACACT	58.153	33.333	0.00	0.00	0.00	3.55
139	140	7.981102	AAGGAAAATCAGAAGTAACACTACC	57.019	36.000	0.00	0.00	0.00	3.18
140	141	7.074653	AGGAAAATCAGAAGTAACACTACCA	57.925	36.000	0.00	0.00	0.00	3.25
141	142	7.514721	AGGAAAATCAGAAGTAACACTACCAA	58.485	34.615	0.00	0.00	0.00	3.67
142	143	8.164070	AGGAAAATCAGAAGTAACACTACCAAT	58.836	33.333	0.00	0.00	0.00	3.16
143	144	8.237267	GGAAAATCAGAAGTAACACTACCAATG	58.763	37.037	0.00	0.00	0.00	2.82
144	145	8.691661	AAAATCAGAAGTAACACTACCAATGT	57.308	30.769	0.00	0.00	0.00	2.71
145	146	8.691661	AAATCAGAAGTAACACTACCAATGTT	57.308	30.769	0.00	0.00	42.78	2.71
146	147	8.691661	AATCAGAAGTAACACTACCAATGTTT	57.308	30.769	0.00	0.00	40.68	2.83
147	148	8.691661	ATCAGAAGTAACACTACCAATGTTTT	57.308	30.769	0.00	0.00	40.68	2.43
148	149	9.787435	ATCAGAAGTAACACTACCAATGTTTTA	57.213	29.630	0.00	0.00	40.68	1.52
149	150	9.616156	TCAGAAGTAACACTACCAATGTTTTAA	57.384	29.630	0.00	0.00	40.68	1.52
155	156	9.563898	GTAACACTACCAATGTTTTAAATAGCC	57.436	33.333	0.00	0.00	40.68	3.93
156	157	6.848451	ACACTACCAATGTTTTAAATAGCCG	58.152	36.000	0.00	0.00	0.00	5.52

Showing 1 to 25 of 364 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.887996	TTAAATGGACATGCAAAACTTGATC	57.112	32.000	0.00	0.00	0.00	2.92
1	2	8.851541	AATTAAATGGACATGCAAAACTTGAT	57.148	26.923	0.00	0.00	0.00	2.57
2	3	9.770097	TTAATTAAATGGACATGCAAAACTTGA	57.230	25.926	0.00	0.00	0.00	3.02
3	4	9.810231	GTTAATTAAATGGACATGCAAAACTTG	57.190	29.630	0.00	0.00	0.00	3.16
4	5	8.998377	GGTTAATTAAATGGACATGCAAAACTT	58.002	29.630	0.00	0.00	0.00	2.66
5	6	7.330700	CGGTTAATTAAATGGACATGCAAAACT	59.669	33.333	0.00	0.00	0.00	2.66
6	7	7.329717	TCGGTTAATTAAATGGACATGCAAAAC	59.670	33.333	0.00	0.00	0.00	2.43
7	8	7.378966	TCGGTTAATTAAATGGACATGCAAAA	58.621	30.769	0.00	0.00	0.00	2.44
8	9	6.925211	TCGGTTAATTAAATGGACATGCAAA	58.075	32.000	0.00	0.00	0.00	3.68
9	10	6.516739	TCGGTTAATTAAATGGACATGCAA	57.483	33.333	0.00	0.00	0.00	4.08
10	11	5.449862	GCTCGGTTAATTAAATGGACATGCA	60.450	40.000	0.00	0.00	0.00	3.96
11	12	4.976116	GCTCGGTTAATTAAATGGACATGC	59.024	41.667	0.00	0.00	0.00	4.06
12	13	6.130298	TGCTCGGTTAATTAAATGGACATG	57.870	37.500	0.00	0.00	0.00	3.21
13	14	6.959639	ATGCTCGGTTAATTAAATGGACAT	57.040	33.333	0.00	0.00	0.00	3.06
14	15	8.349245	CAATATGCTCGGTTAATTAAATGGACA	58.651	33.333	0.00	0.00	0.00	4.02
19	20	8.458573	TCCACAATATGCTCGGTTAATTAAAT	57.541	30.769	0.00	0.00	0.00	1.40
20	21	7.867305	TCCACAATATGCTCGGTTAATTAAA	57.133	32.000	0.00	0.00	0.00	1.52
38	39	9.905713	AAAAGAAGTAGCTCATATAATCCACAA	57.094	29.630	0.00	0.00	0.00	3.33
52	53	7.195374	TGGTATCACCATAAAAGAAGTAGCT	57.805	36.000	0.00	0.00	44.79	3.32
117	118	7.739498	TTGGTAGTGTTACTTCTGATTTTCC	57.261	36.000	0.00	0.00	0.00	3.13
118	119	8.784043	ACATTGGTAGTGTTACTTCTGATTTTC	58.216	33.333	0.00	0.00	0.00	2.29
121	122	8.691661	AAACATTGGTAGTGTTACTTCTGATT	57.308	30.769	0.00	0.00	38.76	2.57
122	123	8.691661	AAAACATTGGTAGTGTTACTTCTGAT	57.308	30.769	0.00	0.00	38.76	2.90
131	132	7.309920	CGGCTATTTAAAACATTGGTAGTGTT	58.690	34.615	0.00	0.00	41.28	3.32
132	133	6.127842	CCGGCTATTTAAAACATTGGTAGTGT	60.128	38.462	0.00	0.00	0.00	3.55

Showing 1 to 25 of 403 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.