AutoCloner

Multiple sequence alignment - TraesCS5B01G225800

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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	TraesCS5B01G225800	chr5B	100.000	2276	0	0	1	2276	402575377	402577652	0.000000e+00	4204.0
1	TraesCS5B01G225800	chr2B	96.846	1300	41	0	1	1300	382727893	382729192	0.000000e+00	2174.0
2	TraesCS5B01G225800	chr1B	96.157	1301	48	2	1	1300	343998119	343999418	0.000000e+00	2124.0
3	TraesCS5B01G225800	chr1B	83.990	1168	187	0	63	1230	28311083	28312250	0.000000e+00	1122.0
4	TraesCS5B01G225800	chr7B	95.853	1302	51	3	1	1301	686802820	686804119	0.000000e+00	2102.0
5	TraesCS5B01G225800	chr7B	80.583	103	16	4	1620	1722	18198500	18198402	2.420000e-10	76.8
6	TraesCS5B01G225800	chr3A	94.943	1305	66	0	1	1305	193916854	193915550	0.000000e+00	2045.0
7	TraesCS5B01G225800	chr3A	94.154	1300	74	1	1	1300	194072245	194070948	0.000000e+00	1978.0
8	TraesCS5B01G225800	chr3A	83.945	1308	202	6	2	1302	606270448	606269142	0.000000e+00	1245.0
9	TraesCS5B01G225800	chr4A	93.774	1301	80	1	1	1301	48931088	48932387	0.000000e+00	1953.0
10	TraesCS5B01G225800	chr3B	92.308	1300	95	3	2	1301	811417270	811415976	0.000000e+00	1842.0
11	TraesCS5B01G225800	chr5D	90.329	972	71	11	1323	2276	342610873	342611839	0.000000e+00	1253.0
12	TraesCS5B01G225800	chr5A	83.455	822	108	13	1475	2276	443587105	443587918	0.000000e+00	739.0
13	TraesCS5B01G225800	chr2D	82.051	117	13	6	1620	1732	121293420	121293532	2.410000e-15	93.5

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	TraesCS5B01G225800	chr5B	402575377	402577652	2275	False	4204	4204	100.000	1	2276	1	chr5B.!!$F1	2275
1	TraesCS5B01G225800	chr2B	382727893	382729192	1299	False	2174	2174	96.846	1	1300	1	chr2B.!!$F1	1299
2	TraesCS5B01G225800	chr1B	343998119	343999418	1299	False	2124	2124	96.157	1	1300	1	chr1B.!!$F2	1299
3	TraesCS5B01G225800	chr1B	28311083	28312250	1167	False	1122	1122	83.990	63	1230	1	chr1B.!!$F1	1167
4	TraesCS5B01G225800	chr7B	686802820	686804119	1299	False	2102	2102	95.853	1	1301	1	chr7B.!!$F1	1300
5	TraesCS5B01G225800	chr3A	193915550	193916854	1304	True	2045	2045	94.943	1	1305	1	chr3A.!!$R1	1304
6	TraesCS5B01G225800	chr3A	194070948	194072245	1297	True	1978	1978	94.154	1	1300	1	chr3A.!!$R2	1299
7	TraesCS5B01G225800	chr3A	606269142	606270448	1306	True	1245	1245	83.945	2	1302	1	chr3A.!!$R3	1300
8	TraesCS5B01G225800	chr4A	48931088	48932387	1299	False	1953	1953	93.774	1	1301	1	chr4A.!!$F1	1300
9	TraesCS5B01G225800	chr3B	811415976	811417270	1294	True	1842	1842	92.308	2	1301	1	chr3B.!!$R1	1299
10	TraesCS5B01G225800	chr5D	342610873	342611839	966	False	1253	1253	90.329	1323	2276	1	chr5D.!!$F1	953
11	TraesCS5B01G225800	chr5A	443587105	443587918	813	False	739	739	83.455	1475	2276	1	chr5A.!!$F1	801

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
558	559	0.394938	TCAAGTTGCCGGAGCTACAA	59.605	50.0	5.05	0.0	45.74	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1813	1843	0.107017	AATCGGATGGCCCAACTGAG	60.107	55.0	8.6	0.0	34.14	3.35	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
281	282	4.285775	GCAATTAGCTCTAGAGGAAGGGAT	59.714	45.833	21.23	0.00	41.15	3.85
345	346	5.638234	ACGACTATGGAAACTAAAAGTGCTC	59.362	40.000	0.00	0.00	0.00	4.26
558	559	0.394938	TCAAGTTGCCGGAGCTACAA	59.605	50.000	5.05	0.00	45.74	2.41
563	564	0.978151	TTGCCGGAGCTACAACCTTA	59.022	50.000	5.05	0.00	40.80	2.69
598	599	6.287589	AGGATATCCTTTATGATCCACGTC	57.712	41.667	19.18	0.00	46.09	4.34
728	730	4.803098	AGCGTATAAGAGAAACACTGGT	57.197	40.909	0.00	0.00	0.00	4.00
917	920	2.037144	GAGTAAGCCTTACCCCGATGA	58.963	52.381	10.94	0.00	36.81	2.92
1089	1094	4.201456	GCGCCGCTACTTTTAAAAATTGAC	60.201	41.667	0.00	0.00	0.00	3.18
1230	1241	4.489771	CCGCCCGGCTTCCTCATT	62.490	66.667	8.05	0.00	0.00	2.57
1233	1244	1.527370	GCCCGGCTTCCTCATTACT	59.473	57.895	0.71	0.00	0.00	2.24
1267	1278	0.665835	TCGTGTTGGTGCCATTGTTC	59.334	50.000	0.00	0.00	0.00	3.18
1417	1429	2.290641	CGTGGGCTGCCATTTCTATAAC	59.709	50.000	22.05	0.00	0.00	1.89
1450	1462	5.575606	AGGTTTGATCACGATACAACTAACG	59.424	40.000	0.00	0.00	0.00	3.18
1456	1468	4.722194	TCACGATACAACTAACGTACACC	58.278	43.478	0.00	0.00	37.22	4.16
1714	1742	1.172180	CGGTTGCATGTTGAGGGTGT	61.172	55.000	0.00	0.00	0.00	4.16
1735	1764	3.928375	GTGCCTTTTTCCATGTATGCAAG	59.072	43.478	0.00	0.00	0.00	4.01
1738	1767	5.655974	TGCCTTTTTCCATGTATGCAAGATA	59.344	36.000	0.00	0.00	0.00	1.98
1768	1797	4.642437	TGACATACTTGTAGAGAGCTCCTG	59.358	45.833	10.93	0.00	35.79	3.86
1773	1802	3.761752	ACTTGTAGAGAGCTCCTGTTCTC	59.238	47.826	10.93	0.00	46.57	2.87
1812	1842	2.510238	GCAGGCGCTCACGAGATT	60.510	61.111	7.64	0.00	43.93	2.40
1813	1843	2.520904	GCAGGCGCTCACGAGATTC	61.521	63.158	7.64	0.00	43.93	2.52
1826	1856	1.134280	CGAGATTCTCAGTTGGGCCAT	60.134	52.381	7.26	0.00	0.00	4.40
1875	1905	1.000827	CTCGATCGCTTGATAGGCACT	60.001	52.381	11.09	0.00	46.37	4.40
1886	1916	0.033796	ATAGGCACTGGCTTGCACAT	60.034	50.000	10.87	0.00	44.94	3.21
1950	1980	4.301637	ACCGTTGACCATTGAGTTTTTC	57.698	40.909	0.00	0.00	0.00	2.29
1951	1981	3.067601	ACCGTTGACCATTGAGTTTTTCC	59.932	43.478	0.00	0.00	0.00	3.13
1952	1982	3.552068	CCGTTGACCATTGAGTTTTTCCC	60.552	47.826	0.00	0.00	0.00	3.97
2071	2102	8.984891	ATTAAAATTGTTCATGAATTCGAGCA	57.015	26.923	12.12	0.47	0.00	4.26
2126	2157	6.385649	TCGCAAAAGTCTAAAAAGGTTCAT	57.614	33.333	0.00	0.00	0.00	2.57
2127	2158	6.205784	TCGCAAAAGTCTAAAAAGGTTCATG	58.794	36.000	0.00	0.00	0.00	3.07
2166	2197	4.403432	CCAGGAACATGGAATAGTTTGCAT	59.597	41.667	0.00	0.00	43.81	3.96
2253	2288	9.277783	TGAAAAGGTTCACAAATTCAAAAGAAA	57.722	25.926	0.00	0.00	38.88	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	0.318441	TCTGCCACTGTGTAGAGTGC	59.682	55.000	7.08	2.41	41.85	4.40
345	346	0.909623	AGAATACACGGACCTTGGGG	59.090	55.000	2.65	0.00	38.88	4.96
558	559	1.903860	TCCTTGCACCACGTATAAGGT	59.096	47.619	12.29	3.08	39.11	3.50
563	564	2.972713	AGGATATCCTTGCACCACGTAT	59.027	45.455	19.18	0.00	46.09	3.06
587	588	2.101582	GCCTCAGTAAGACGTGGATCAT	59.898	50.000	0.00	0.00	0.00	2.45
598	599	1.517832	CCCTGTCCGCCTCAGTAAG	59.482	63.158	0.00	0.00	0.00	2.34
728	730	7.344612	TCTGCTCCAATGGTAGTTCTAATAGAA	59.655	37.037	0.00	0.00	0.00	2.10
735	737	3.177228	AGTCTGCTCCAATGGTAGTTCT	58.823	45.455	0.00	0.00	0.00	3.01
917	920	6.229733	GCTTCTGCAATAAGAGGATCTGTAT	58.770	40.000	11.65	0.00	41.95	2.29
1081	1086	4.816925	GGATAAGGCTAGCTCGTCAATTTT	59.183	41.667	15.72	0.00	0.00	1.82
1089	1094	4.329462	AAGAAAGGATAAGGCTAGCTCG	57.671	45.455	15.72	0.00	0.00	5.03
1230	1241	1.266989	CGATCAGCCATCACGCTAGTA	59.733	52.381	0.00	0.00	36.82	1.82
1233	1244	0.249031	CACGATCAGCCATCACGCTA	60.249	55.000	0.00	0.00	36.82	4.26
1267	1278	6.719365	CGGGAAACTATGAGCTTTATTCAAG	58.281	40.000	0.00	0.00	35.29	3.02
1305	1317	0.448990	CCGGTTGCATGACACATGAG	59.551	55.000	14.65	0.00	0.00	2.90
1306	1318	0.250684	ACCGGTTGCATGACACATGA	60.251	50.000	0.00	0.00	0.00	3.07
1307	1319	0.597568	AACCGGTTGCATGACACATG	59.402	50.000	21.56	7.29	0.00	3.21
1308	1320	0.597568	CAACCGGTTGCATGACACAT	59.402	50.000	32.87	0.00	33.45	3.21
1309	1321	2.028936	CAACCGGTTGCATGACACA	58.971	52.632	32.87	0.00	33.45	3.72
1310	1322	4.942090	CAACCGGTTGCATGACAC	57.058	55.556	32.87	0.00	33.45	3.67
1318	1330	2.069273	CTACTCTTCAGCAACCGGTTG	58.931	52.381	37.53	37.53	43.14	3.77
1319	1331	1.968493	TCTACTCTTCAGCAACCGGTT	59.032	47.619	15.86	15.86	0.00	4.44
1320	1332	1.272769	GTCTACTCTTCAGCAACCGGT	59.727	52.381	0.00	0.00	0.00	5.28
1321	1333	1.272490	TGTCTACTCTTCAGCAACCGG	59.728	52.381	0.00	0.00	0.00	5.28
1393	1405	0.827507	AGAAATGGCAGCCCACGTTT	60.828	50.000	9.64	4.96	45.77	3.60
1417	1429	1.986378	GTGATCAAACCTCGTGTCTCG	59.014	52.381	0.00	0.00	41.41	4.04
1450	1462	4.004982	ACGATTTGTTGTATGGGGTGTAC	58.995	43.478	0.00	0.00	0.00	2.90
1456	1468	2.999331	AGGGACGATTTGTTGTATGGG	58.001	47.619	0.00	0.00	0.00	4.00
1714	1742	3.831333	TCTTGCATACATGGAAAAAGGCA	59.169	39.130	0.00	0.00	37.67	4.75
1738	1767	7.038659	GCTCTCTACAAGTATGTCAACTCAAT	58.961	38.462	0.00	0.00	41.05	2.57
1768	1797	0.393808	TTGGGCATTAGGCGGAGAAC	60.394	55.000	0.00	0.00	46.16	3.01
1773	1802	0.530431	GCAATTTGGGCATTAGGCGG	60.530	55.000	0.00	0.00	46.16	6.13
1812	1842	0.982852	ATCGGATGGCCCAACTGAGA	60.983	55.000	8.60	0.00	34.14	3.27
1813	1843	0.107017	AATCGGATGGCCCAACTGAG	60.107	55.000	8.60	0.00	34.14	3.35
1826	1856	1.415288	CGGACGCGCTTTAAATCGGA	61.415	55.000	5.73	0.00	0.00	4.55
1853	1883	1.340657	GCCTATCAAGCGATCGAGCG	61.341	60.000	20.40	20.40	43.00	5.03
1875	1905	0.955428	GAGGTCGAATGTGCAAGCCA	60.955	55.000	0.00	0.00	0.00	4.75
1886	1916	0.832135	AACCAGCAGGAGAGGTCGAA	60.832	55.000	0.35	0.00	38.69	3.71
1944	1974	8.902540	AATCCTATTGACTTTTTGGGAAAAAC	57.097	30.769	0.00	0.00	35.57	2.43
2060	2091	7.807907	GGACTTTTTCTAATTTGCTCGAATTCA	59.192	33.333	6.22	0.00	31.96	2.57
2142	2173	4.016444	GCAAACTATTCCATGTTCCTGGA	58.984	43.478	0.00	0.00	43.62	3.86
2143	2174	3.763360	TGCAAACTATTCCATGTTCCTGG	59.237	43.478	0.00	0.00	37.66	4.45
2146	2177	7.715657	TGAATATGCAAACTATTCCATGTTCC	58.284	34.615	13.44	0.00	35.96	3.62
2180	2212	8.586570	AATTCATGAACTTTTTCGTATTTGCA	57.413	26.923	11.07	0.00	34.04	4.08
2223	2257	9.712305	TTTTGAATTTGTGAACCTTTTCAACTA	57.288	25.926	0.00	0.00	43.52	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.