AutoCloner

Multiple sequence alignment - TraesCS2D01G340300

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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	TraesCS2D01G340300	chr2D	100.000	2711	0	0	1	2711	434687933	434690643	0.000000e+00	5007
1	TraesCS2D01G340300	chr2D	83.808	2001	271	35	738	2711	582717314	582715340	0.000000e+00	1851
2	TraesCS2D01G340300	chr3A	91.980	1970	152	6	738	2704	732765114	732767080	0.000000e+00	2758
3	TraesCS2D01G340300	chr3A	89.428	1977	202	5	738	2711	411255782	411257754	0.000000e+00	2486
4	TraesCS2D01G340300	chr7B	89.884	1977	193	7	737	2708	28704877	28702903	0.000000e+00	2536
5	TraesCS2D01G340300	chr1A	89.716	1974	196	6	743	2711	238693563	238695534	0.000000e+00	2514
6	TraesCS2D01G340300	chr2B	86.364	1980	251	13	738	2711	373501767	373503733	0.000000e+00	2143
7	TraesCS2D01G340300	chr2B	90.133	679	26	14	41	717	513295695	513296334	0.000000e+00	845
8	TraesCS2D01G340300	chr1B	85.297	1986	261	25	738	2711	47129610	47131576	0.000000e+00	2021
9	TraesCS2D01G340300	chr1B	80.147	1773	314	27	959	2711	180531340	180529586	0.000000e+00	1290
10	TraesCS2D01G340300	chr7A	90.424	1180	109	4	1028	2207	719874881	719876056	0.000000e+00	1550
11	TraesCS2D01G340300	chr5D	85.652	1150	147	13	738	1879	135526086	135527225	0.000000e+00	1194
12	TraesCS2D01G340300	chr3B	82.310	1385	212	23	1343	2711	670328269	670326902	0.000000e+00	1170
13	TraesCS2D01G340300	chr2A	93.194	720	22	4	1	716	552472016	552471320	0.000000e+00	1033
14	TraesCS2D01G340300	chr2A	81.925	509	84	7	77	579	552490219	552489713	8.970000e-115	424

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	TraesCS2D01G340300	chr2D	434687933	434690643	2710	False	5007	5007	100.000	1	2711	1	chr2D.!!$F1	2710
1	TraesCS2D01G340300	chr2D	582715340	582717314	1974	True	1851	1851	83.808	738	2711	1	chr2D.!!$R1	1973
2	TraesCS2D01G340300	chr3A	732765114	732767080	1966	False	2758	2758	91.980	738	2704	1	chr3A.!!$F2	1966
3	TraesCS2D01G340300	chr3A	411255782	411257754	1972	False	2486	2486	89.428	738	2711	1	chr3A.!!$F1	1973
4	TraesCS2D01G340300	chr7B	28702903	28704877	1974	True	2536	2536	89.884	737	2708	1	chr7B.!!$R1	1971
5	TraesCS2D01G340300	chr1A	238693563	238695534	1971	False	2514	2514	89.716	743	2711	1	chr1A.!!$F1	1968
6	TraesCS2D01G340300	chr2B	373501767	373503733	1966	False	2143	2143	86.364	738	2711	1	chr2B.!!$F1	1973
7	TraesCS2D01G340300	chr2B	513295695	513296334	639	False	845	845	90.133	41	717	1	chr2B.!!$F2	676
8	TraesCS2D01G340300	chr1B	47129610	47131576	1966	False	2021	2021	85.297	738	2711	1	chr1B.!!$F1	1973
9	TraesCS2D01G340300	chr1B	180529586	180531340	1754	True	1290	1290	80.147	959	2711	1	chr1B.!!$R1	1752
10	TraesCS2D01G340300	chr7A	719874881	719876056	1175	False	1550	1550	90.424	1028	2207	1	chr7A.!!$F1	1179
11	TraesCS2D01G340300	chr5D	135526086	135527225	1139	False	1194	1194	85.652	738	1879	1	chr5D.!!$F1	1141
12	TraesCS2D01G340300	chr3B	670326902	670328269	1367	True	1170	1170	82.310	1343	2711	1	chr3B.!!$R1	1368
13	TraesCS2D01G340300	chr2A	552471320	552472016	696	True	1033	1033	93.194	1	716	1	chr2A.!!$R1	715
14	TraesCS2D01G340300	chr2A	552489713	552490219	506	True	424	424	81.925	77	579	1	chr2A.!!$R2	502

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	652	0.031515	TAGGATCTCTGGGCCGGAAA	60.032	55.0	17.43	2.88	0.0	3.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2422	2503	0.541392	AGTATGATGGCGAAGGTGCA	59.459	50.0	0.0	0.0	36.28	4.57	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
168	172	2.332063	ATGAAGAACAGCATACCCCG	57.668	50.000	0.00	0.00	0.00	5.73
218	222	3.065567	GATGGCCGCCCGGAAAAA	61.066	61.111	11.48	0.00	37.50	1.94
542	557	2.167693	CCGCCATTGTTCTGTACCTCTA	59.832	50.000	0.00	0.00	0.00	2.43
565	580	3.616721	AGCTGCGTCGTGGGTTCT	61.617	61.111	0.00	0.00	0.00	3.01
590	605	1.544759	GCCGAAAAGTGGAAGGGAGAA	60.545	52.381	0.00	0.00	0.00	2.87
633	652	0.031515	TAGGATCTCTGGGCCGGAAA	60.032	55.000	17.43	2.88	0.00	3.13
668	687	0.535335	TATCAGAAGACCACCACGGC	59.465	55.000	0.00	0.00	39.03	5.68
717	736	4.191033	TGCAGCAAATGAAATCGGATTT	57.809	36.364	15.45	15.45	34.64	2.17
718	737	5.321959	TGCAGCAAATGAAATCGGATTTA	57.678	34.783	15.50	5.71	31.47	1.40
719	738	5.904941	TGCAGCAAATGAAATCGGATTTAT	58.095	33.333	15.50	7.53	31.47	1.40
720	739	6.339730	TGCAGCAAATGAAATCGGATTTATT	58.660	32.000	15.50	12.13	31.47	1.40
721	740	6.817641	TGCAGCAAATGAAATCGGATTTATTT	59.182	30.769	15.50	16.12	31.47	1.40
722	741	7.333921	TGCAGCAAATGAAATCGGATTTATTTT	59.666	29.630	15.50	14.16	31.47	1.82
723	742	8.177013	GCAGCAAATGAAATCGGATTTATTTTT	58.823	29.630	15.50	12.10	31.47	1.94
795	818	1.270147	GGCGCCTTGAGATATACCGTT	60.270	52.381	22.15	0.00	0.00	4.44
819	843	4.043200	GCCGGTGGTTTGAGCTGC	62.043	66.667	1.90	0.00	0.00	5.25
836	860	3.550431	CGCATCCAGGGATCGGGT	61.550	66.667	0.00	0.00	31.62	5.28
941	973	1.836166	CCTGTGTCTGATCCAGATGGT	59.164	52.381	0.00	0.00	42.73	3.55
1105	1137	2.771943	TGGATGATTCTAGCCCGAGTTT	59.228	45.455	0.00	0.00	0.00	2.66
1261	1293	3.315949	GTGTGACCCAGGGCGGTA	61.316	66.667	4.91	0.00	35.79	4.02
1330	1362	9.629649	ATGGATATACAAAACCCTCCTCTATTA	57.370	33.333	0.00	0.00	0.00	0.98
1356	1388	1.227089	CACCTTCGAGATCTGGGCG	60.227	63.158	0.00	0.00	0.00	6.13
1401	1434	4.021104	GCTTTTCATGGAAAGGTTAAGGCT	60.021	41.667	24.77	0.00	37.17	4.58
1405	1438	5.772393	TCATGGAAAGGTTAAGGCTCTTA	57.228	39.130	0.00	0.00	0.00	2.10
1455	1488	3.445096	CCGAGCCTTCATCCTTTGATTTT	59.555	43.478	0.00	0.00	33.34	1.82
1766	1818	1.230635	GCGGCATACAATCCAGCGAT	61.231	55.000	0.00	0.00	0.00	4.58
1770	1822	3.403038	GGCATACAATCCAGCGATAAGT	58.597	45.455	0.00	0.00	0.00	2.24
1791	1843	2.094700	TCGACAAGAGGTACATGCAGAC	60.095	50.000	0.00	0.00	0.00	3.51
1824	1894	0.179234	TGGACAACAACAGGAAGCGA	59.821	50.000	0.00	0.00	0.00	4.93
1845	1915	1.100510	CGTCCGATCAGGTGGTTAGA	58.899	55.000	0.00	0.00	41.99	2.10
1864	1940	2.308866	AGATCTCCAAACCCCAAATCGT	59.691	45.455	0.00	0.00	0.00	3.73
1901	1977	3.112709	GGTGACGAAGCCGAGTGC	61.113	66.667	0.00	0.00	39.50	4.40
1919	1995	2.202932	GAGCACGGTGCCGATCAT	60.203	61.111	28.14	9.79	46.52	2.45
1944	2021	2.039879	TCCTCCTAAGCAAGACCCAAAC	59.960	50.000	0.00	0.00	0.00	2.93
1946	2023	1.777878	TCCTAAGCAAGACCCAAACCA	59.222	47.619	0.00	0.00	0.00	3.67
2209	2290	5.560722	TGTCTAGTTGAAACCCAGATCAA	57.439	39.130	0.00	0.00	33.37	2.57
2480	2561	2.682594	CTGTCCACCCTCCATGATCTA	58.317	52.381	0.00	0.00	0.00	1.98
2579	2660	1.138661	CAGATCCAGGGCTTCAGAGAC	59.861	57.143	0.00	0.00	0.00	3.36
2597	2678	2.586635	GCGGTTGACGTGTGTGGA	60.587	61.111	0.00	0.00	46.52	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
218	222	4.807039	GCACCGTATGGCCGACGT	62.807	66.667	23.71	12.33	38.65	4.34
383	398	2.229784	GTCCAATTGGCTCTCAAAGGTG	59.770	50.000	20.33	0.00	39.05	4.00
565	580	0.250727	CTTCCACTTTTCGGCCTCCA	60.251	55.000	0.00	0.00	0.00	3.86
590	605	0.695803	CCCTAGCCCCTGAAGACCAT	60.696	60.000	0.00	0.00	0.00	3.55
633	652	3.776969	TCTGATAACTGAGCCCAATCACT	59.223	43.478	0.00	0.00	0.00	3.41
780	803	3.057456	CGGGAGGAACGGTATATCTCAAG	60.057	52.174	0.00	0.00	0.00	3.02
819	843	3.521529	GACCCGATCCCTGGATGCG	62.522	68.421	2.75	7.14	34.60	4.73
887	915	0.313987	CTCGAACCAGCAAAAACCCC	59.686	55.000	0.00	0.00	0.00	4.95
1105	1137	6.753913	AGAGCTGAAATCCTTGTCCATATA	57.246	37.500	0.00	0.00	0.00	0.86
1261	1293	0.482446	TTTCCCCTGAAGTGCCATGT	59.518	50.000	0.00	0.00	0.00	3.21
1330	1362	3.999663	CAGATCTCGAAGGTGAAAAGCTT	59.000	43.478	0.00	0.00	0.00	3.74
1401	1434	7.502226	ACAAACTCACCAATCTTTGATGTAAGA	59.498	33.333	0.00	0.00	38.43	2.10
1405	1438	6.096705	TCAACAAACTCACCAATCTTTGATGT	59.903	34.615	0.00	0.00	31.73	3.06
1455	1488	9.847224	ACTTTGACTCTATAAAAGTTTCCTTCA	57.153	29.630	0.00	0.00	40.34	3.02
1766	1818	3.508402	TGCATGTACCTCTTGTCGACTTA	59.492	43.478	17.92	3.92	0.00	2.24
1770	1822	2.094700	GTCTGCATGTACCTCTTGTCGA	60.095	50.000	0.00	0.00	0.00	4.20
1772	1824	2.094700	TCGTCTGCATGTACCTCTTGTC	60.095	50.000	0.00	0.00	0.00	3.18
1824	1894	1.681793	CTAACCACCTGATCGGACGAT	59.318	52.381	6.95	6.95	37.59	3.73
1845	1915	2.723273	GACGATTTGGGGTTTGGAGAT	58.277	47.619	0.00	0.00	0.00	2.75
1864	1940	3.636231	CACCAGTTCCAGCCCCGA	61.636	66.667	0.00	0.00	0.00	5.14
1901	1977	4.794439	TGATCGGCACCGTGCTCG	62.794	66.667	22.41	21.77	44.28	5.03
1919	1995	1.622725	GGTCTTGCTTAGGAGGAGGGA	60.623	57.143	0.00	0.00	0.00	4.20
1944	2021	1.281867	TGCCCCATGAGTTTAGACTGG	59.718	52.381	0.00	0.00	35.88	4.00
1946	2023	2.551270	TCTGCCCCATGAGTTTAGACT	58.449	47.619	0.00	0.00	39.32	3.24
2209	2290	1.867363	ATTCTCAGCTCTTACCCCGT	58.133	50.000	0.00	0.00	0.00	5.28
2210	2291	2.939103	CAAATTCTCAGCTCTTACCCCG	59.061	50.000	0.00	0.00	0.00	5.73
2249	2330	4.143473	GCATCAACAGCAAAAGAACAATCG	60.143	41.667	0.00	0.00	0.00	3.34
2422	2503	0.541392	AGTATGATGGCGAAGGTGCA	59.459	50.000	0.00	0.00	36.28	4.57
2480	2561	1.902556	GCCTATACACACCCACGGT	59.097	57.895	0.00	0.00	35.62	4.83
2523	2604	2.291540	ACCCAATCCCGTCATGTTCATT	60.292	45.455	0.00	0.00	0.00	2.57
2579	2660	3.995669	CCACACACGTCAACCGCG	61.996	66.667	0.00	0.00	41.42	6.46
2597	2678	7.125792	ACCTTTGTATCCGAGATCAAGTAAT	57.874	36.000	0.00	0.00	0.00	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.