AutoCloner

Multiple sequence alignment - TraesCS1D01G246900

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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	TraesCS1D01G246900	chr1D	100.000	2156	0	0	1	2156	339365377	339363222	0.000000e+00	3982
1	TraesCS1D01G246900	chr1D	81.000	300	51	6	64	360	80965751	80966047	1.290000e-57	233
2	TraesCS1D01G246900	chr1A	93.574	1665	91	9	497	2156	439302316	439300663	0.000000e+00	2468
3	TraesCS1D01G246900	chr1A	86.974	499	61	3	1	496	439302962	439302465	1.870000e-155	558
4	TraesCS1D01G246900	chr1B	94.579	1605	69	8	554	2156	454381945	454380357	0.000000e+00	2466
5	TraesCS1D01G246900	chr1B	85.176	425	59	4	1	423	454382630	454382208	1.180000e-117	433
6	TraesCS1D01G246900	chr1B	82.069	290	47	5	65	351	580531374	580531661	2.140000e-60	243
7	TraesCS1D01G246900	chr5D	80.902	377	38	16	762	1127	445387802	445387449	1.270000e-67	267
8	TraesCS1D01G246900	chr5D	85.075	134	18	2	365	496	370551116	370551249	3.730000e-28	135
9	TraesCS1D01G246900	chr5D	84.672	137	19	1	362	496	516815109	516815245	3.730000e-28	135
10	TraesCS1D01G246900	chr5B	79.744	390	48	13	762	1142	542991930	542991563	9.880000e-64	254
11	TraesCS1D01G246900	chr5B	79.885	348	65	5	1	346	375796204	375795860	1.280000e-62	250
12	TraesCS1D01G246900	chr5B	78.056	360	65	12	6	360	527487577	527487227	4.660000e-52	215
13	TraesCS1D01G246900	chr5B	88.321	137	14	2	362	496	344946343	344946207	1.710000e-36	163
14	TraesCS1D01G246900	chr5B	85.821	134	17	1	365	496	433895059	433894926	8.020000e-30	141
15	TraesCS1D01G246900	chr5A	78.540	452	49	22	712	1142	563062892	563062468	9.880000e-64	254
16	TraesCS1D01G246900	chr2A	82.545	275	46	2	73	346	2742042	2741769	7.690000e-60	241
17	TraesCS1D01G246900	chr2B	82.847	274	40	7	76	346	222623704	222623435	2.770000e-59	239
18	TraesCS1D01G246900	chr7A	82.182	275	47	2	73	346	142950679	142950406	3.580000e-58	235
19	TraesCS1D01G246900	chr4D	79.757	247	37	10	1027	1264	484110037	484110279	1.320000e-37	167
20	TraesCS1D01G246900	chr3D	84.932	146	21	1	348	492	94515616	94515471	1.720000e-31	147
21	TraesCS1D01G246900	chr3D	83.803	142	17	5	359	496	589674624	589674763	1.740000e-26	130
22	TraesCS1D01G246900	chr2D	84.828	145	20	2	354	496	565521457	565521313	6.200000e-31	145
23	TraesCS1D01G246900	chr6B	85.507	138	17	2	361	496	350035187	350035051	8.020000e-30	141

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	TraesCS1D01G246900	chr1D	339363222	339365377	2155	True	3982.0	3982	100.0000	1	2156	1	chr1D.!!$R1	2155
1	TraesCS1D01G246900	chr1A	439300663	439302962	2299	True	1513.0	2468	90.2740	1	2156	2	chr1A.!!$R1	2155
2	TraesCS1D01G246900	chr1B	454380357	454382630	2273	True	1449.5	2466	89.8775	1	2156	2	chr1B.!!$R1	2155

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
128	130	0.17691	TTCATCGGCGATGGTTGCTA	59.823	50.0	39.82	22.95	40.15	3.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1662	1830	0.105246	TGGCCCAAATTTGTGGAGGT	60.105	50.0	22.53	0.0	41.65	3.85	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	4.022589	TCTCGTGAGATTCGGTTAGTGTTT	60.023	41.667	0.00	0.00	40.84	2.83
37	38	4.210537	CGTGAGATTCGGTTAGTGTTTGTT	59.789	41.667	0.00	0.00	0.00	2.83
42	43	7.090953	AGATTCGGTTAGTGTTTGTTTTCAA	57.909	32.000	0.00	0.00	38.10	2.69
45	46	6.438259	TCGGTTAGTGTTTGTTTTCAATGA	57.562	33.333	0.00	0.00	39.70	2.57
48	49	7.976734	TCGGTTAGTGTTTGTTTTCAATGAATT	59.023	29.630	0.00	0.00	39.70	2.17
98	100	6.660521	TGTTTACATGCTTGATCCTTCTGATT	59.339	34.615	6.60	0.00	32.41	2.57
125	127	0.933097	CTCTTCATCGGCGATGGTTG	59.067	55.000	39.82	29.95	40.15	3.77
128	130	0.176910	TTCATCGGCGATGGTTGCTA	59.823	50.000	39.82	22.95	40.15	3.49
162	164	5.939764	TGGTTCTATGTGATCTTAGCACT	57.060	39.130	0.00	0.00	37.18	4.40
164	166	6.806751	TGGTTCTATGTGATCTTAGCACTAC	58.193	40.000	0.00	0.00	37.18	2.73
173	175	5.396947	GTGATCTTAGCACTACGATTTCTCG	59.603	44.000	0.00	0.00	40.58	4.04
207	209	0.868406	CAAGGTTTGTCCGACTCTGC	59.132	55.000	0.00	0.00	41.99	4.26
263	265	2.390938	TCGTTTCAGTGCTTGTAGTCG	58.609	47.619	0.00	0.00	0.00	4.18
299	301	6.149807	GTCCACGGACCTGATTGTAATTTTTA	59.850	38.462	4.78	0.00	39.08	1.52
304	306	8.392612	ACGGACCTGATTGTAATTTTTATTACG	58.607	33.333	0.00	0.00	39.27	3.18
328	330	7.121759	ACGTCTAGTACTCTTTGTATTGCCTTA	59.878	37.037	0.00	0.00	33.23	2.69
371	376	4.385358	AGATTTTTCGTGCAAACCAACT	57.615	36.364	0.00	0.00	0.00	3.16
396	401	5.251932	TGTGGTTGGATGGTTAGAAGGATAA	59.748	40.000	0.00	0.00	0.00	1.75
413	418	4.851639	GATAATGGTATCCTCAGCCCAT	57.148	45.455	0.00	0.00	39.34	4.00
443	448	1.537202	AGTTCTGGTGCTCGCATTTTC	59.463	47.619	0.00	0.00	0.00	2.29
446	451	1.277842	TCTGGTGCTCGCATTTTCCTA	59.722	47.619	0.00	0.00	0.00	2.94
447	452	2.092968	TCTGGTGCTCGCATTTTCCTAT	60.093	45.455	0.00	0.00	0.00	2.57
456	461	8.076178	GTGCTCGCATTTTCCTATATGTATTTT	58.924	33.333	0.00	0.00	0.00	1.82
475	480	9.832445	TGTATTTTAGGATTTCTGGAGATACAC	57.168	33.333	0.00	0.00	0.00	2.90
476	481	9.832445	GTATTTTAGGATTTCTGGAGATACACA	57.168	33.333	0.00	0.00	0.00	3.72
626	791	1.847328	TCTATGAGGTCCGAAGCACA	58.153	50.000	0.00	0.00	0.00	4.57
738	903	3.054655	GGATAGGTCCACCAAAGCAAGTA	60.055	47.826	0.00	0.00	44.42	2.24
810	975	0.322816	CCTGCCCTGTTGCATGTACT	60.323	55.000	0.00	0.00	41.16	2.73
841	1006	1.072806	ACTGCAGCATCTGAACTGGAA	59.927	47.619	15.27	0.00	33.60	3.53
882	1047	2.997485	TATCAGCATCGACAGATCCG	57.003	50.000	0.00	0.00	34.23	4.18
892	1057	1.067142	CGACAGATCCGTCCTTCCAAA	60.067	52.381	3.47	0.00	31.91	3.28
905	1070	5.297527	CGTCCTTCCAAATGATTCATCATGA	59.702	40.000	0.00	0.00	46.22	3.07
965	1130	4.645535	AGTCATTCAGAAAGCTTACTGCA	58.354	39.130	0.00	0.00	45.94	4.41
996	1161	7.918033	CCATAGCCTTCATATACAGAACTATCG	59.082	40.741	0.00	0.00	0.00	2.92
1207	1372	9.967346	TGTGTCTAGAACTGATAATATGTAAGC	57.033	33.333	0.00	0.00	0.00	3.09
1208	1373	9.967346	GTGTCTAGAACTGATAATATGTAAGCA	57.033	33.333	0.00	0.00	0.00	3.91
1211	1376	9.645059	TCTAGAACTGATAATATGTAAGCATGC	57.355	33.333	10.51	10.51	36.58	4.06
1212	1377	7.678947	AGAACTGATAATATGTAAGCATGCC	57.321	36.000	15.66	0.00	36.58	4.40
1213	1378	7.226441	AGAACTGATAATATGTAAGCATGCCA	58.774	34.615	15.66	5.74	36.58	4.92
1214	1379	6.808008	ACTGATAATATGTAAGCATGCCAC	57.192	37.500	15.66	13.53	36.58	5.01
1221	1386	2.324541	TGTAAGCATGCCACCCTTTTT	58.675	42.857	15.66	1.58	0.00	1.94
1445	1612	7.044798	AGGAGATCGTTTCTTAAGGATTTCTG	58.955	38.462	1.85	0.00	38.65	3.02
1483	1650	7.603784	ACTTTGGATTTTTGGTAGATCAATTGC	59.396	33.333	0.00	0.00	0.00	3.56
1491	1658	5.188327	TGGTAGATCAATTGCTCTACGAG	57.812	43.478	29.44	0.00	41.92	4.18
1569	1737	1.068474	CTTTTAGACCGCCAGTGTCG	58.932	55.000	0.00	0.00	37.80	4.35
1577	1745	2.430921	GCCAGTGTCGTGACCTCG	60.431	66.667	0.00	0.00	0.00	4.63
1859	2029	4.138290	GGGAGCCTTAGATTTTAGGAAGC	58.862	47.826	0.00	0.00	33.13	3.86
1868	2038	5.265350	AGATTTTAGGAAGCGGAGAGTAC	57.735	43.478	0.00	0.00	0.00	2.73
1873	2043	2.657143	AGGAAGCGGAGAGTACCTAAG	58.343	52.381	0.00	0.00	0.00	2.18
1884	2054	5.894964	GGAGAGTACCTAAGGAATCAAGTCT	59.105	44.000	0.00	0.00	0.00	3.24
1890	2060	4.202461	ACCTAAGGAATCAAGTCTGCACAA	60.202	41.667	0.00	0.00	0.00	3.33
1927	2097	7.949690	ACATAAGGGGTTTAGGTAAATTGAC	57.050	36.000	0.00	0.00	34.71	3.18
1988	2158	3.936453	GGACACTAAAGTCACACACAACA	59.064	43.478	0.00	0.00	40.29	3.33
2038	2208	9.765795	ACTATAGCCTTGATACTTCAAACATAC	57.234	33.333	0.00	0.00	41.22	2.39
2094	2264	6.474140	TCAGAAACACCTAGTACAACTTGA	57.526	37.500	0.00	0.00	0.00	3.02
2115	2285	6.617782	TGAATGCAAAAGAAAATATCCCCA	57.382	33.333	0.00	0.00	0.00	4.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	6.316640	TGAAAACAAACACTAACCGAATCTCA	59.683	34.615	0.00	0.00	0.00	3.27
37	38	9.598517	GGCTGGATATAAACAAATTCATTGAAA	57.401	29.630	2.68	0.00	41.85	2.69
42	43	8.310122	ACAAGGCTGGATATAAACAAATTCAT	57.690	30.769	0.00	0.00	0.00	2.57
45	46	8.592809	TGAAACAAGGCTGGATATAAACAAATT	58.407	29.630	0.00	0.00	0.00	1.82
48	49	6.719370	ACTGAAACAAGGCTGGATATAAACAA	59.281	34.615	0.00	0.00	0.00	2.83
62	63	5.186996	AGCATGTAAACACTGAAACAAGG	57.813	39.130	0.00	0.00	0.00	3.61
98	100	2.425668	TCGCCGATGAAGAGATGTGTAA	59.574	45.455	0.00	0.00	0.00	2.41
125	127	0.602905	AACCAACGCACCAGAGTAGC	60.603	55.000	0.00	0.00	0.00	3.58
128	130	1.045407	TAGAACCAACGCACCAGAGT	58.955	50.000	0.00	0.00	0.00	3.24
162	164	7.543947	TGTAGTAGACAATCGAGAAATCGTA	57.456	36.000	0.00	0.00	34.15	3.43
173	175	7.307811	GGACAAACCTTGTTGTAGTAGACAATC	60.308	40.741	0.00	0.00	45.52	2.67
207	209	3.083349	TCATCGCCCCTCCCACAG	61.083	66.667	0.00	0.00	0.00	3.66
263	265	0.314935	TCCGTGGACAACCTAACGAC	59.685	55.000	0.00	0.00	37.65	4.34
299	301	7.919621	GGCAATACAAAGAGTACTAGACGTAAT	59.080	37.037	0.00	0.00	35.05	1.89
304	306	8.468399	ACTAAGGCAATACAAAGAGTACTAGAC	58.532	37.037	0.00	0.00	35.05	2.59
352	354	4.092675	CACAAGTTGGTTTGCACGAAAAAT	59.907	37.500	7.96	0.00	0.00	1.82
358	363	2.956469	CCACAAGTTGGTTTGCACG	58.044	52.632	7.96	0.00	41.10	5.34
371	376	3.396276	TCCTTCTAACCATCCAACCACAA	59.604	43.478	0.00	0.00	0.00	3.33
396	401	1.983691	CTGATGGGCTGAGGATACCAT	59.016	52.381	0.00	0.00	45.87	3.55
413	418	1.476833	GCACCAGAACTTGAACCCTGA	60.477	52.381	0.00	0.00	0.00	3.86
456	461	7.345653	ACTGAATGTGTATCTCCAGAAATCCTA	59.654	37.037	0.00	0.00	0.00	2.94
467	472	5.592282	TCTCCTCTCACTGAATGTGTATCTC	59.408	44.000	0.00	0.00	46.27	2.75
475	480	7.912056	TTTTAACATCTCCTCTCACTGAATG	57.088	36.000	0.00	0.00	0.00	2.67
525	690	7.392673	CCCCACATCTATATGGAAAGAGAAATG	59.607	40.741	0.00	0.00	38.34	2.32
626	791	2.024941	CAGTCCAAATAAGAAGGGCCCT	60.025	50.000	22.28	22.28	0.00	5.19
738	903	4.017126	CTGATGCATATCATGAATGGGCT	58.983	43.478	0.00	0.00	42.19	5.19
795	960	2.159043	AGATCGAGTACATGCAACAGGG	60.159	50.000	0.00	0.00	0.00	4.45
810	975	1.463674	TGCTGCAGTGTAGAGATCGA	58.536	50.000	16.64	0.00	0.00	3.59
882	1047	6.320672	AGTCATGATGAATCATTTGGAAGGAC	59.679	38.462	0.00	6.37	44.70	3.85
996	1161	1.519455	CTTCGTCTCCGCCATGTCC	60.519	63.158	0.00	0.00	0.00	4.02
1207	1372	2.524306	TCCAGTAAAAAGGGTGGCATG	58.476	47.619	0.00	0.00	0.00	4.06
1208	1373	2.990740	TCCAGTAAAAAGGGTGGCAT	57.009	45.000	0.00	0.00	0.00	4.40
1209	1374	2.990740	ATCCAGTAAAAAGGGTGGCA	57.009	45.000	0.00	0.00	0.00	4.92
1210	1375	5.531287	CAGTATATCCAGTAAAAAGGGTGGC	59.469	44.000	0.00	0.00	0.00	5.01
1211	1376	6.895782	TCAGTATATCCAGTAAAAAGGGTGG	58.104	40.000	0.00	0.00	0.00	4.61
1212	1377	7.792032	TCTCAGTATATCCAGTAAAAAGGGTG	58.208	38.462	0.00	0.00	0.00	4.61
1213	1378	7.844779	TCTCTCAGTATATCCAGTAAAAAGGGT	59.155	37.037	0.00	0.00	0.00	4.34
1214	1379	8.251383	TCTCTCAGTATATCCAGTAAAAAGGG	57.749	38.462	0.00	0.00	0.00	3.95
1529	1696	6.481954	AAGATCAAAAGGTCGTAATCACAC	57.518	37.500	0.00	0.00	0.00	3.82
1569	1737	8.193438	ACCTATACTTATTTGTTACGAGGTCAC	58.807	37.037	0.00	0.00	0.00	3.67
1662	1830	0.105246	TGGCCCAAATTTGTGGAGGT	60.105	50.000	22.53	0.00	41.65	3.85
1859	2029	4.645588	ACTTGATTCCTTAGGTACTCTCCG	59.354	45.833	0.00	0.00	41.75	4.63
1868	2038	3.942829	TGTGCAGACTTGATTCCTTAGG	58.057	45.455	0.00	0.00	0.00	2.69
1873	2043	2.508526	ACCTTGTGCAGACTTGATTCC	58.491	47.619	0.00	0.00	0.00	3.01
1884	2054	4.769345	TGTATGATCCATACCTTGTGCA	57.231	40.909	12.81	0.00	44.11	4.57
1890	2060	5.676125	ACCCCTTATGTATGATCCATACCT	58.324	41.667	12.81	7.20	44.11	3.08
1927	2097	4.989044	ACTGTTTTAAAGTCAACCGTTGG	58.011	39.130	11.35	0.00	0.00	3.77
1965	2135	2.816689	TGTGTGTGACTTTAGTGTCCG	58.183	47.619	0.00	0.00	36.21	4.79
1988	2158	6.349243	TCATGCACTGGATTCAATCTTTTT	57.651	33.333	0.00	0.00	0.00	1.94
2068	2238	7.990886	TCAAGTTGTACTAGGTGTTTCTGAAAT	59.009	33.333	6.06	0.00	0.00	2.17
2094	2264	6.371595	TGTGGGGATATTTTCTTTTGCATT	57.628	33.333	0.00	0.00	0.00	3.56
2123	2293	1.390565	AGCGTGCGTCTAGGTTCTAT	58.609	50.000	0.00	0.00	0.00	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.