AutoCloner

Multiple sequence alignment - TraesCS6B01G368300

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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	TraesCS6B01G368300	chr6B	100.000	2979	0	0	1	2979	642723111	642726089	0.000000e+00	5502.0
1	TraesCS6B01G368300	chr6B	99.485	582	3	0	1	582	85721267	85721848	0.000000e+00	1059.0
2	TraesCS6B01G368300	chr6B	99.144	584	5	0	1	584	89070897	89070314	0.000000e+00	1051.0
3	TraesCS6B01G368300	chr6B	98.969	582	6	0	1	582	174118268	174117687	0.000000e+00	1042.0
4	TraesCS6B01G368300	chr6B	82.863	496	46	17	709	1204	642466491	642466947	2.760000e-110	409.0
5	TraesCS6B01G368300	chr6B	96.154	130	5	0	2601	2730	214087270	214087141	2.330000e-51	213.0
6	TraesCS6B01G368300	chr6D	92.090	2086	79	26	583	2603	426983443	426985507	0.000000e+00	2859.0
7	TraesCS6B01G368300	chr6D	89.091	275	8	10	2726	2979	426985505	426985778	3.700000e-84	322.0
8	TraesCS6B01G368300	chr6D	95.192	104	3	2	2726	2828	426985803	426985905	2.380000e-36	163.0
9	TraesCS6B01G368300	chr6A	92.949	1475	50	19	583	2010	571682548	571684015	0.000000e+00	2098.0
10	TraesCS6B01G368300	chr6A	90.182	275	26	1	2048	2321	571684012	571684286	1.020000e-94	357.0
11	TraesCS6B01G368300	chr6A	92.308	195	8	6	2412	2600	571684290	571684483	1.360000e-68	270.0
12	TraesCS6B01G368300	chr6A	96.117	103	2	2	2727	2828	571684485	571684586	1.840000e-37	167.0
13	TraesCS6B01G368300	chr2B	99.313	582	4	0	1	582	31451531	31452112	0.000000e+00	1053.0
14	TraesCS6B01G368300	chr1B	99.141	582	5	0	1	582	15907124	15906543	0.000000e+00	1048.0
15	TraesCS6B01G368300	chr5A	98.625	582	8	0	1	582	55268097	55267516	0.000000e+00	1031.0
16	TraesCS6B01G368300	chr2D	98.625	582	8	0	1	582	91078335	91077754	0.000000e+00	1031.0
17	TraesCS6B01G368300	chr2D	87.701	187	23	0	1412	1598	544171159	544170973	5.000000e-53	219.0
18	TraesCS6B01G368300	chr2A	98.625	582	8	0	1	582	541204224	541203643	0.000000e+00	1031.0
19	TraesCS6B01G368300	chr2A	87.701	187	23	0	1412	1598	686777763	686777577	5.000000e-53	219.0
20	TraesCS6B01G368300	chr2A	87.421	159	20	0	1423	1581	686797568	686797726	1.820000e-42	183.0
21	TraesCS6B01G368300	chr2A	90.625	64	5	1	2909	2972	679995447	679995509	1.900000e-12	84.2
22	TraesCS6B01G368300	chr4A	98.456	583	9	0	1	583	724360341	724359759	0.000000e+00	1027.0
23	TraesCS6B01G368300	chrUn	96.183	131	5	0	2600	2730	17025258	17025388	6.470000e-52	215.0
24	TraesCS6B01G368300	chrUn	96.183	131	5	0	2600	2730	17027491	17027621	6.470000e-52	215.0
25	TraesCS6B01G368300	chrUn	96.183	131	5	0	2600	2730	292131188	292131058	6.470000e-52	215.0
26	TraesCS6B01G368300	chrUn	96.183	131	5	0	2600	2730	302852258	302852128	6.470000e-52	215.0
27	TraesCS6B01G368300	chrUn	96.183	131	5	0	2600	2730	302859297	302859427	6.470000e-52	215.0
28	TraesCS6B01G368300	chr1D	96.183	131	5	0	2600	2730	97537546	97537676	6.470000e-52	215.0
29	TraesCS6B01G368300	chr3B	95.489	133	6	0	2596	2728	139036922	139037054	2.330000e-51	213.0
30	TraesCS6B01G368300	chr3A	94.161	137	8	0	2592	2728	52198991	52198855	3.010000e-50	209.0
31	TraesCS6B01G368300	chr7A	87.578	161	20	0	1425	1585	620412453	620412293	1.410000e-43	187.0
32	TraesCS6B01G368300	chr7D	86.957	161	21	0	1425	1585	538895311	538895151	6.560000e-42	182.0
33	TraesCS6B01G368300	chr7D	81.481	162	30	0	1608	1769	538895028	538894867	1.860000e-27	134.0
34	TraesCS6B01G368300	chr7B	86.957	161	21	0	1425	1585	581395684	581395524	6.560000e-42	182.0
35	TraesCS6B01G368300	chr7B	86.503	163	20	2	1424	1585	581894034	581893873	8.490000e-41	178.0
36	TraesCS6B01G368300	chr7B	81.481	162	30	0	1608	1769	581395396	581395235	1.860000e-27	134.0

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	TraesCS6B01G368300	chr6B	642723111	642726089	2978	False	5502.000000	5502	100.000000	1	2979	1	chr6B.!!$F3	2978
1	TraesCS6B01G368300	chr6B	85721267	85721848	581	False	1059.000000	1059	99.485000	1	582	1	chr6B.!!$F1	581
2	TraesCS6B01G368300	chr6B	89070314	89070897	583	True	1051.000000	1051	99.144000	1	584	1	chr6B.!!$R1	583
3	TraesCS6B01G368300	chr6B	174117687	174118268	581	True	1042.000000	1042	98.969000	1	582	1	chr6B.!!$R2	581
4	TraesCS6B01G368300	chr6D	426983443	426985905	2462	False	1114.666667	2859	92.124333	583	2979	3	chr6D.!!$F1	2396
5	TraesCS6B01G368300	chr6A	571682548	571684586	2038	False	723.000000	2098	92.889000	583	2828	4	chr6A.!!$F1	2245
6	TraesCS6B01G368300	chr2B	31451531	31452112	581	False	1053.000000	1053	99.313000	1	582	1	chr2B.!!$F1	581
7	TraesCS6B01G368300	chr1B	15906543	15907124	581	True	1048.000000	1048	99.141000	1	582	1	chr1B.!!$R1	581
8	TraesCS6B01G368300	chr5A	55267516	55268097	581	True	1031.000000	1031	98.625000	1	582	1	chr5A.!!$R1	581
9	TraesCS6B01G368300	chr2D	91077754	91078335	581	True	1031.000000	1031	98.625000	1	582	1	chr2D.!!$R1	581
10	TraesCS6B01G368300	chr2A	541203643	541204224	581	True	1031.000000	1031	98.625000	1	582	1	chr2A.!!$R1	581
11	TraesCS6B01G368300	chr4A	724359759	724360341	582	True	1027.000000	1027	98.456000	1	583	1	chr4A.!!$R1	582
12	TraesCS6B01G368300	chrUn	17025258	17027621	2363	False	215.000000	215	96.183000	2600	2730	2	chrUn.!!$F2	130

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
872	890	1.494716	AATCGACCCCTTCCCCGTTT	61.495	55.0	0.0	0.0	0.0	3.6	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2212	2271	0.621082	AACCAGCTTAAGAGGGAGCC	59.379	55.0	16.96	0.0	39.71	4.7	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
741	759	2.542595	CGAGGCCGTGTTATTATCCAAC	59.457	50.000	0.00	0.00	0.00	3.77
872	890	1.494716	AATCGACCCCTTCCCCGTTT	61.495	55.000	0.00	0.00	0.00	3.60
873	891	1.907222	ATCGACCCCTTCCCCGTTTC	61.907	60.000	0.00	0.00	0.00	2.78
874	892	2.886134	CGACCCCTTCCCCGTTTCA	61.886	63.158	0.00	0.00	0.00	2.69
948	966	2.040278	AGGGCACAGGAGGAGGAG	59.960	66.667	0.00	0.00	0.00	3.69
949	967	3.086600	GGGCACAGGAGGAGGAGG	61.087	72.222	0.00	0.00	0.00	4.30
950	968	2.039624	GGCACAGGAGGAGGAGGA	59.960	66.667	0.00	0.00	0.00	3.71
951	969	2.063378	GGCACAGGAGGAGGAGGAG	61.063	68.421	0.00	0.00	0.00	3.69
972	990	2.619332	GGAAGAAGAAGGAAGGAAGGGC	60.619	54.545	0.00	0.00	0.00	5.19
1041	1059	5.415701	GTCTTCTTCTTGTTGGCATTCCATA	59.584	40.000	0.00	0.00	43.05	2.74
1050	1068	1.843206	TGGCATTCCATAGTGCTGGTA	59.157	47.619	0.00	0.00	41.04	3.25
1060	1078	0.401738	AGTGCTGGTAGCCATGTTGT	59.598	50.000	0.00	0.00	41.51	3.32
1066	1084	0.243636	GGTAGCCATGTTGTTGGTGC	59.756	55.000	0.00	0.00	39.11	5.01
1547	1595	3.319198	GCCTCTGGTTCGACCCCA	61.319	66.667	0.00	0.00	37.50	4.96
1612	1660	3.075005	ACGATCCTGGTGGACGGG	61.075	66.667	0.00	0.00	46.51	5.28
1861	1909	3.279116	TCGACGTGGTTCGACCGT	61.279	61.111	0.00	0.00	43.01	4.83
1975	2023	1.875963	CAAGGAATGCACCGTGGAC	59.124	57.895	0.00	0.00	36.17	4.02
1995	2043	7.147976	GTGGACTAGTTGCATGATTTTTCTTT	58.852	34.615	0.00	0.00	0.00	2.52
2007	2055	9.423061	GCATGATTTTTCTTTGTAGGTTTATGT	57.577	29.630	0.00	0.00	0.00	2.29
2013	2061	7.979444	TTTCTTTGTAGGTTTATGTCTCTGG	57.021	36.000	0.00	0.00	0.00	3.86
2014	2062	5.488341	TCTTTGTAGGTTTATGTCTCTGGC	58.512	41.667	0.00	0.00	0.00	4.85
2015	2063	5.248477	TCTTTGTAGGTTTATGTCTCTGGCT	59.752	40.000	0.00	0.00	0.00	4.75
2016	2064	6.439375	TCTTTGTAGGTTTATGTCTCTGGCTA	59.561	38.462	0.00	0.00	0.00	3.93
2029	2083	6.806751	TGTCTCTGGCTATGTACATTACTTC	58.193	40.000	14.77	1.06	0.00	3.01
2030	2084	6.607600	TGTCTCTGGCTATGTACATTACTTCT	59.392	38.462	14.77	0.00	0.00	2.85
2032	2086	7.650104	GTCTCTGGCTATGTACATTACTTCTTC	59.350	40.741	14.77	0.00	0.00	2.87
2034	2088	8.079211	TCTGGCTATGTACATTACTTCTTCTT	57.921	34.615	14.77	0.00	0.00	2.52
2151	2210	8.784043	AGAAATACATAAGAGTCGCAAAAGTTT	58.216	29.630	0.00	0.00	0.00	2.66
2153	2212	5.108385	ACATAAGAGTCGCAAAAGTTTGG	57.892	39.130	5.95	0.00	38.57	3.28
2212	2271	4.153475	ACCCAGACGATCAACAATTTAACG	59.847	41.667	0.00	0.00	0.00	3.18
2214	2273	4.088648	CAGACGATCAACAATTTAACGGC	58.911	43.478	0.00	0.00	0.00	5.68
2263	2322	9.034544	GTAAAAATAAATGAATGATCCTGGTGC	57.965	33.333	0.00	0.00	0.00	5.01
2272	2331	5.892686	TGAATGATCCTGGTGCAAATATGAA	59.107	36.000	0.00	0.00	0.00	2.57
2274	2333	5.777850	TGATCCTGGTGCAAATATGAATG	57.222	39.130	0.00	0.00	0.00	2.67
2289	2348	3.358707	TGAATGCTGCTTGTTGTGAAG	57.641	42.857	0.00	0.00	0.00	3.02
2387	2446	0.245539	TGACCCGCGGTAAGAGAAAG	59.754	55.000	26.12	7.62	35.25	2.62
2390	2449	2.165301	CCGCGGTAAGAGAAAGCCG	61.165	63.158	19.50	0.00	46.17	5.52
2391	2450	2.165301	CGCGGTAAGAGAAAGCCGG	61.165	63.158	0.00	0.00	43.90	6.13
2392	2451	1.217244	GCGGTAAGAGAAAGCCGGA	59.783	57.895	5.05	0.00	43.90	5.14
2393	2452	0.179081	GCGGTAAGAGAAAGCCGGAT	60.179	55.000	5.05	0.00	43.90	4.18
2394	2453	1.742750	GCGGTAAGAGAAAGCCGGATT	60.743	52.381	5.05	0.00	43.90	3.01
2395	2454	2.629051	CGGTAAGAGAAAGCCGGATTT	58.371	47.619	19.36	19.36	40.45	2.17
2396	2455	3.007635	CGGTAAGAGAAAGCCGGATTTT	58.992	45.455	20.30	11.62	40.45	1.82
2397	2456	3.063588	CGGTAAGAGAAAGCCGGATTTTC	59.936	47.826	20.30	19.40	40.45	2.29
2398	2457	3.063588	GGTAAGAGAAAGCCGGATTTTCG	59.936	47.826	20.30	0.00	39.07	3.46
2407	2466	8.617290	AGAAAGCCGGATTTTCGTATATTAAT	57.383	30.769	20.30	0.00	39.07	1.40
2559	2630	4.422984	AGGGTACTTCTACCTAACTGCAA	58.577	43.478	0.00	0.00	42.22	4.08
2560	2631	4.222366	AGGGTACTTCTACCTAACTGCAAC	59.778	45.833	0.00	0.00	42.22	4.17
2702	2774	8.792633	ACGTCTCTTTTTATCCATTTTGATGAA	58.207	29.630	0.00	0.00	0.00	2.57
2770	4439	3.078837	AGCAAATACCGTTCGGACAAAT	58.921	40.909	18.28	3.32	0.00	2.32
2824	4493	4.099266	ACTGCAACTAATGGCAAAACTCAA	59.901	37.500	0.00	0.00	39.93	3.02
2829	4498	6.311200	GCAACTAATGGCAAAACTCAAATAGG	59.689	38.462	0.00	0.00	0.00	2.57
2852	4523	4.934356	AGAAACAAATGGATCAGCCCTAA	58.066	39.130	0.00	0.00	34.97	2.69
2894	4858	9.713740	GATCACAGCTCAAGATTAAATACAAAG	57.286	33.333	0.00	0.00	0.00	2.77
2958	4941	1.739466	TGGCATCAGAAATGCGAAGAC	59.261	47.619	4.11	0.00	45.41	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
705	706	0.962489	CCTCGTGCATAGTAGGGGAG	59.038	60.000	0.00	0.00	0.00	4.30
706	707	1.113517	GCCTCGTGCATAGTAGGGGA	61.114	60.000	0.00	0.00	40.77	4.81
707	708	1.367840	GCCTCGTGCATAGTAGGGG	59.632	63.158	0.00	0.00	40.77	4.79
708	709	1.367840	GGCCTCGTGCATAGTAGGG	59.632	63.158	0.00	0.00	43.89	3.53
709	710	1.007271	CGGCCTCGTGCATAGTAGG	60.007	63.158	0.00	0.00	43.89	3.18
710	711	4.635925	CGGCCTCGTGCATAGTAG	57.364	61.111	0.00	0.00	43.89	2.57
741	759	2.385013	GCCTTATTTGGGGCTTGTTG	57.615	50.000	0.00	0.00	44.48	3.33
872	890	4.220163	CGGAAGATGGAGAGATGATGATGA	59.780	45.833	0.00	0.00	0.00	2.92
873	891	4.496360	CGGAAGATGGAGAGATGATGATG	58.504	47.826	0.00	0.00	0.00	3.07
874	892	3.055963	GCGGAAGATGGAGAGATGATGAT	60.056	47.826	0.00	0.00	0.00	2.45
948	966	3.054728	CCTTCCTTCCTTCTTCTTCCTCC	60.055	52.174	0.00	0.00	0.00	4.30
949	967	3.054728	CCCTTCCTTCCTTCTTCTTCCTC	60.055	52.174	0.00	0.00	0.00	3.71
950	968	2.916269	CCCTTCCTTCCTTCTTCTTCCT	59.084	50.000	0.00	0.00	0.00	3.36
951	969	2.619332	GCCCTTCCTTCCTTCTTCTTCC	60.619	54.545	0.00	0.00	0.00	3.46
972	990	4.441415	GGCTAACTAATTGACACGATCTCG	59.559	45.833	0.00	0.00	46.33	4.04
1041	1059	0.401738	ACAACATGGCTACCAGCACT	59.598	50.000	0.00	0.00	44.75	4.40
1050	1068	1.466025	CCAGCACCAACAACATGGCT	61.466	55.000	0.00	0.00	44.75	4.75
1060	1078	0.697658	TGATCCATGACCAGCACCAA	59.302	50.000	0.00	0.00	0.00	3.67
1066	1084	1.544982	GGCCATCTGATCCATGACCAG	60.545	57.143	0.00	0.00	0.00	4.00
1171	1189	4.863925	GAGGCAGAGCGCGAGGAC	62.864	72.222	12.10	0.00	43.84	3.85
1547	1595	4.309950	GGTGTGGAAGTCGGCGGT	62.310	66.667	7.21	0.00	0.00	5.68
1729	1777	3.470567	CAGTCCGTCTTGACGCGC	61.471	66.667	16.59	0.00	40.26	6.86
1975	2023	8.299570	ACCTACAAAGAAAAATCATGCAACTAG	58.700	33.333	0.00	0.00	0.00	2.57
1995	2043	5.661312	ACATAGCCAGAGACATAAACCTACA	59.339	40.000	0.00	0.00	0.00	2.74
2007	2055	7.561722	AGAAGAAGTAATGTACATAGCCAGAGA	59.438	37.037	9.21	0.00	0.00	3.10
2038	2092	5.544176	AGTTCTCAATCTAGACCAGAACCAA	59.456	40.000	24.01	5.31	42.63	3.67
2039	2093	5.087323	AGTTCTCAATCTAGACCAGAACCA	58.913	41.667	24.01	1.90	42.63	3.67
2040	2094	5.669164	AGTTCTCAATCTAGACCAGAACC	57.331	43.478	24.01	13.77	42.63	3.62
2041	2095	6.096282	AGCTAGTTCTCAATCTAGACCAGAAC	59.904	42.308	21.97	21.97	42.18	3.01
2042	2096	6.096141	CAGCTAGTTCTCAATCTAGACCAGAA	59.904	42.308	0.00	0.00	36.67	3.02
2138	2196	2.024414	AGAAGCCAAACTTTTGCGACT	58.976	42.857	0.00	0.00	39.29	4.18
2151	2210	1.202915	TCAAGACCAATGCAGAAGCCA	60.203	47.619	0.00	0.00	41.13	4.75
2153	2212	2.555757	ACTTCAAGACCAATGCAGAAGC	59.444	45.455	7.71	0.00	36.77	3.86
2161	2220	4.202357	TGCTGTCACTACTTCAAGACCAAT	60.202	41.667	0.00	0.00	0.00	3.16
2212	2271	0.621082	AACCAGCTTAAGAGGGAGCC	59.379	55.000	16.96	0.00	39.71	4.70
2214	2273	1.743996	GCAACCAGCTTAAGAGGGAG	58.256	55.000	16.96	10.40	41.15	4.30
2239	2298	7.622713	TGCACCAGGATCATTCATTTATTTTT	58.377	30.769	0.00	0.00	0.00	1.94
2244	2303	6.795144	ATTTGCACCAGGATCATTCATTTA	57.205	33.333	0.00	0.00	0.00	1.40
2263	2322	5.865013	TCACAACAAGCAGCATTCATATTTG	59.135	36.000	0.00	0.00	0.00	2.32
2272	2331	2.295349	CCTTCTTCACAACAAGCAGCAT	59.705	45.455	0.00	0.00	0.00	3.79
2274	2333	1.678101	ACCTTCTTCACAACAAGCAGC	59.322	47.619	0.00	0.00	0.00	5.25
2330	2389	8.048534	TCTGTGATTCAGAGAAAATCCAATTC	57.951	34.615	10.85	0.00	46.77	2.17
2387	2446	7.591006	TGAGATTAATATACGAAAATCCGGC	57.409	36.000	0.00	0.00	0.00	6.13
2559	2630	2.328319	TGGAAGTTTAGTGGTACCGGT	58.672	47.619	13.98	13.98	0.00	5.28
2560	2631	3.405823	TTGGAAGTTTAGTGGTACCGG	57.594	47.619	7.57	0.00	0.00	5.28
2593	2665	2.889045	CGGACGGAGGGAGTATCAAATA	59.111	50.000	0.00	0.00	36.25	1.40
2702	2774	1.208776	CCCTCCGTCCGGAAATACTTT	59.791	52.381	5.23	0.00	44.66	2.66
2824	4493	5.595952	GGCTGATCCATTTGTTTCTCCTATT	59.404	40.000	0.00	0.00	34.01	1.73
2829	4498	3.359950	AGGGCTGATCCATTTGTTTCTC	58.640	45.455	0.00	0.00	36.21	2.87
2852	4523	1.344438	TGATCGAGTGGACTGCAGTTT	59.656	47.619	22.65	7.32	0.00	2.66
2909	4876	8.331931	ACCTATTTTATCCTCATGGTACTCAA	57.668	34.615	0.00	0.00	34.23	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.