AutoCloner

Multiple sequence alignment - TraesCS4B01G281200

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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	TraesCS4B01G281200	chr4B	100.000	2630	0	0	1	2630	564224788	564222159	0.000000e+00	4857
1	TraesCS4B01G281200	chr4D	93.720	1035	44	11	774	1791	451057429	451056399	0.000000e+00	1531
2	TraesCS4B01G281200	chr4A	94.850	932	35	8	871	1791	15890521	15891450	0.000000e+00	1443
3	TraesCS4B01G281200	chr4A	86.975	476	40	11	2157	2628	682767700	682767243	1.400000e-142	516
4	TraesCS4B01G281200	chr1B	96.114	772	27	3	1	772	225785478	225784710	0.000000e+00	1256
5	TraesCS4B01G281200	chr3B	95.850	771	31	1	1	771	16114456	16113687	0.000000e+00	1245
6	TraesCS4B01G281200	chr3B	95.460	771	34	1	1	771	798499130	798499899	0.000000e+00	1229
7	TraesCS4B01G281200	chr6B	95.844	770	31	1	1	770	205091129	205090361	0.000000e+00	1243
8	TraesCS4B01G281200	chr6B	86.863	373	44	5	2259	2628	127127491	127127861	1.880000e-111	412
9	TraesCS4B01G281200	chr1A	95.725	772	31	2	1	772	23177342	23176573	0.000000e+00	1242
10	TraesCS4B01G281200	chr7B	95.720	771	31	2	1	771	74089794	74090562	0.000000e+00	1240
11	TraesCS4B01G281200	chr7B	95.466	772	33	2	1	772	121162210	121162979	0.000000e+00	1230
12	TraesCS4B01G281200	chr7B	95.466	772	33	2	1	771	638789184	638789954	0.000000e+00	1230
13	TraesCS4B01G281200	chr7B	95.337	772	34	2	1	772	121110848	121111617	0.000000e+00	1225
14	TraesCS4B01G281200	chr7B	86.514	393	47	5	2237	2628	166994647	166995034	6.730000e-116	427
15	TraesCS4B01G281200	chr7B	84.733	393	56	4	2239	2628	66877928	66878319	8.830000e-105	390
16	TraesCS4B01G281200	chr6D	86.802	394	50	2	2237	2628	265994571	265994178	3.110000e-119	438
17	TraesCS4B01G281200	chr6D	85.859	396	52	4	2237	2628	127763670	127763275	4.050000e-113	418
18	TraesCS4B01G281200	chr3D	84.557	395	57	4	2237	2628	65762667	65762274	3.170000e-104	388
19	TraesCS4B01G281200	chr2B	84.896	384	53	3	2247	2628	158041538	158041158	1.480000e-102	383
20	TraesCS4B01G281200	chr6A	83.838	396	59	4	2237	2628	16133217	16132823	3.200000e-99	372

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	TraesCS4B01G281200	chr4B	564222159	564224788	2629	True	4857	4857	100.000	1	2630	1	chr4B.!!$R1	2629
1	TraesCS4B01G281200	chr4D	451056399	451057429	1030	True	1531	1531	93.720	774	1791	1	chr4D.!!$R1	1017
2	TraesCS4B01G281200	chr4A	15890521	15891450	929	False	1443	1443	94.850	871	1791	1	chr4A.!!$F1	920
3	TraesCS4B01G281200	chr1B	225784710	225785478	768	True	1256	1256	96.114	1	772	1	chr1B.!!$R1	771
4	TraesCS4B01G281200	chr3B	16113687	16114456	769	True	1245	1245	95.850	1	771	1	chr3B.!!$R1	770
5	TraesCS4B01G281200	chr3B	798499130	798499899	769	False	1229	1229	95.460	1	771	1	chr3B.!!$F1	770
6	TraesCS4B01G281200	chr6B	205090361	205091129	768	True	1243	1243	95.844	1	770	1	chr6B.!!$R1	769
7	TraesCS4B01G281200	chr1A	23176573	23177342	769	True	1242	1242	95.725	1	772	1	chr1A.!!$R1	771
8	TraesCS4B01G281200	chr7B	74089794	74090562	768	False	1240	1240	95.720	1	771	1	chr7B.!!$F2	770
9	TraesCS4B01G281200	chr7B	121162210	121162979	769	False	1230	1230	95.466	1	772	1	chr7B.!!$F4	771
10	TraesCS4B01G281200	chr7B	638789184	638789954	770	False	1230	1230	95.466	1	771	1	chr7B.!!$F6	770
11	TraesCS4B01G281200	chr7B	121110848	121111617	769	False	1225	1225	95.337	1	772	1	chr7B.!!$F3	771

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
633	636	0.032952	GCACGTGTGTAAGAGGGACA	59.967	55.0	18.38	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2243	2267	0.034059	CATCGGCATAGGTCACCCTC	59.966	60.0	0.0	0.0	41.45	4.3	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
180	182	6.707440	TGGCAACTCTTTCTTTTTACATGA	57.293	33.333	0.00	0.00	37.61	3.07
409	412	1.059098	TGACCTGAGATGGCAACTGT	58.941	50.000	0.51	0.00	37.61	3.55
453	456	1.149401	TTGTCCGACATGGCAACCA	59.851	52.632	1.09	0.00	38.19	3.67
461	464	2.746904	CGACATGGCAACCATAGTTCAA	59.253	45.455	0.00	0.00	43.15	2.69
633	636	0.032952	GCACGTGTGTAAGAGGGACA	59.967	55.000	18.38	0.00	0.00	4.02
772	776	1.125633	GGCAGTTATCGGGACCCTAA	58.874	55.000	9.41	0.00	0.00	2.69
773	777	1.070289	GGCAGTTATCGGGACCCTAAG	59.930	57.143	9.41	0.00	0.00	2.18
774	778	1.070289	GCAGTTATCGGGACCCTAAGG	59.930	57.143	9.41	0.00	40.04	2.69
1080	1088	2.366916	CACTTCTATCTTCCGCCTCCAT	59.633	50.000	0.00	0.00	0.00	3.41
1263	1271	2.333014	GACCAAGAAGCTGAAGACGAG	58.667	52.381	0.00	0.00	0.00	4.18
1446	1460	1.069935	GAGCTTCATCCCCTACGGC	59.930	63.158	0.00	0.00	0.00	5.68
1663	1681	4.389992	GGTGGTAACTCGGTTAAGCTTAAC	59.610	45.833	32.35	32.35	39.09	2.01
1700	1720	5.049405	ACAATTTCTTCTTCTTGCTGTACGG	60.049	40.000	0.00	0.00	0.00	4.02
1739	1763	2.303208	TTCTTGTGCGCGTGTGTGTG	62.303	55.000	8.43	0.00	0.00	3.82
1760	1784	6.529463	GTGAAACAATGAGATTTTGTTGGG	57.471	37.500	2.86	0.00	44.32	4.12
1771	1795	3.451141	TTTTGTTGGGCAATCACTCAC	57.549	42.857	0.00	0.00	36.89	3.51
1778	1802	2.308570	TGGGCAATCACTCACCAGTAAT	59.691	45.455	0.00	0.00	0.00	1.89
1781	1805	3.561725	GGCAATCACTCACCAGTAATAGC	59.438	47.826	0.00	0.00	0.00	2.97
1791	1815	0.941463	CAGTAATAGCCGGAGCAGCG	60.941	60.000	5.05	0.00	43.56	5.18
1792	1816	1.067582	GTAATAGCCGGAGCAGCGT	59.932	57.895	5.05	0.00	43.56	5.07
1793	1817	1.067416	TAATAGCCGGAGCAGCGTG	59.933	57.895	5.05	0.00	43.56	5.34
1794	1818	2.363711	TAATAGCCGGAGCAGCGTGG	62.364	60.000	5.05	0.00	43.56	4.94
1800	1824	4.626081	GGAGCAGCGTGGTGTGGT	62.626	66.667	0.64	0.00	0.00	4.16
1801	1825	3.349006	GAGCAGCGTGGTGTGGTG	61.349	66.667	0.64	0.00	37.86	4.17
1802	1826	4.175337	AGCAGCGTGGTGTGGTGT	62.175	61.111	0.64	0.00	37.18	4.16

Showing 1 to 25 of 647 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
6	7	0.597118	GCAAAACGCATGGCAACTGA	60.597	50.000	0.00	41.79	3.41
32	33	2.028112	TCACACTAGGGCAGTTGTCATC	60.028	50.000	0.00	34.26	2.92
36	37	2.783135	CAATCACACTAGGGCAGTTGT	58.217	47.619	0.00	34.26	3.32
127	129	4.379174	CACGCTAGGGCAGTTTGT	57.621	55.556	6.73	38.60	2.83
180	182	2.210116	CAAGCACGTTAGGACAGTTGT	58.790	47.619	0.00	0.00	3.32
376	379	4.103153	TCTCAGGTCAAACTTCCAGATTGT	59.897	41.667	0.00	31.03	2.71
409	412	2.038952	AGTTGCCATGTCTGCTCAACTA	59.961	45.455	4.36	40.10	2.24
453	456	3.436704	CAGTTGCCATGTCGTTGAACTAT	59.563	43.478	0.00	0.00	2.12
461	464	0.819259	AAGTGCAGTTGCCATGTCGT	60.819	50.000	5.84	41.18	4.34
619	622	1.552486	CCTCCCTGTCCCTCTTACACA	60.552	57.143	0.00	0.00	3.72
902	910	2.136878	CGGCCTAGAGCACCCAGAT	61.137	63.158	0.00	46.50	2.90
941	949	3.435566	GACATCTTATCTCGAACACGCA	58.564	45.455	0.00	0.00	5.24
942	950	2.789893	GGACATCTTATCTCGAACACGC	59.210	50.000	0.00	0.00	5.34
949	957	3.068732	TGGCAAGAGGACATCTTATCTCG	59.931	47.826	1.37	46.91	4.04
1152	1160	1.078143	GATGACTTTGGGCTCCGCT	60.078	57.895	0.00	0.00	5.52
1188	1196	2.100631	GCGCCGCTTGCTCTTCTTA	61.101	57.895	0.00	38.05	2.10
1253	1261	1.388547	CTCCTCCTCCTCGTCTTCAG	58.611	60.000	0.00	0.00	3.02
1263	1271	0.178935	CCTCCTCATCCTCCTCCTCC	60.179	65.000	0.00	0.00	4.30
1446	1460	1.402984	CCGAAGAAGACGAAGGACAGG	60.403	57.143	0.00	0.00	4.00
1565	1579	2.203788	ACTCCCAGAAGACGGGCA	60.204	61.111	0.00	44.11	5.36
1631	1648	0.977395	GAGTTACCACCACAGAGCCT	59.023	55.000	0.00	0.00	4.58
1632	1649	0.389948	CGAGTTACCACCACAGAGCC	60.390	60.000	0.00	0.00	4.70
1633	1650	0.389948	CCGAGTTACCACCACAGAGC	60.390	60.000	0.00	0.00	4.09
1634	1651	0.966920	ACCGAGTTACCACCACAGAG	59.033	55.000	0.00	0.00	3.35
1635	1652	1.416243	AACCGAGTTACCACCACAGA	58.584	50.000	0.00	0.00	3.41

Showing 1 to 25 of 627 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.