AutoCloner

Multiple sequence alignment - TraesCS3D01G507200

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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	TraesCS3D01G507200	chr3D	100.000	2643	0	0	1	2643	593766695	593764053	0.000000e+00	4881
1	TraesCS3D01G507200	chr3D	91.762	2088	127	20	5	2063	449746278	449748349	0.000000e+00	2861
2	TraesCS3D01G507200	chr3D	89.291	2073	152	22	1	2064	113913664	113911653	0.000000e+00	2534
3	TraesCS3D01G507200	chr7B	91.551	2083	138	18	1	2065	150841767	150843829	0.000000e+00	2837
4	TraesCS3D01G507200	chr5A	90.661	2088	166	11	1	2064	78332389	78334471	0.000000e+00	2748
5	TraesCS3D01G507200	chr1D	90.570	2089	157	19	1	2059	482488817	482486739	0.000000e+00	2730
6	TraesCS3D01G507200	chr2D	90.177	2087	155	22	1	2064	591013629	591015688	0.000000e+00	2673
7	TraesCS3D01G507200	chr5D	89.937	2077	181	16	1	2065	416789599	416791659	0.000000e+00	2652
8	TraesCS3D01G507200	chr5D	90.496	1210	85	9	876	2065	369344087	369345286	0.000000e+00	1570
9	TraesCS3D01G507200	chr1B	89.788	2076	178	18	1	2064	623939078	623937025	0.000000e+00	2628
10	TraesCS3D01G507200	chr7A	89.675	2092	150	30	1	2065	140769316	140767264	0.000000e+00	2606
11	TraesCS3D01G507200	chr7A	89.579	2092	157	29	1	2065	141058758	141056701	0.000000e+00	2599
12	TraesCS3D01G507200	chr4D	88.639	2086	164	27	1	2064	116524875	116522841	0.000000e+00	2471
13	TraesCS3D01G507200	chr3A	85.857	601	35	15	2074	2643	724745691	724745110	6.300000e-166	593
14	TraesCS3D01G507200	chrUn	93.438	320	19	1	2326	2643	41885671	41885990	8.560000e-130	473
15	TraesCS3D01G507200	chrUn	88.353	249	20	6	2084	2329	41885398	41885640	9.250000e-75	291

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	TraesCS3D01G507200	chr3D	593764053	593766695	2642	True	4881	4881	100.0000	1	2643	1	chr3D.!!$R2	2642
1	TraesCS3D01G507200	chr3D	449746278	449748349	2071	False	2861	2861	91.7620	5	2063	1	chr3D.!!$F1	2058
2	TraesCS3D01G507200	chr3D	113911653	113913664	2011	True	2534	2534	89.2910	1	2064	1	chr3D.!!$R1	2063
3	TraesCS3D01G507200	chr7B	150841767	150843829	2062	False	2837	2837	91.5510	1	2065	1	chr7B.!!$F1	2064
4	TraesCS3D01G507200	chr5A	78332389	78334471	2082	False	2748	2748	90.6610	1	2064	1	chr5A.!!$F1	2063
5	TraesCS3D01G507200	chr1D	482486739	482488817	2078	True	2730	2730	90.5700	1	2059	1	chr1D.!!$R1	2058
6	TraesCS3D01G507200	chr2D	591013629	591015688	2059	False	2673	2673	90.1770	1	2064	1	chr2D.!!$F1	2063
7	TraesCS3D01G507200	chr5D	416789599	416791659	2060	False	2652	2652	89.9370	1	2065	1	chr5D.!!$F2	2064
8	TraesCS3D01G507200	chr5D	369344087	369345286	1199	False	1570	1570	90.4960	876	2065	1	chr5D.!!$F1	1189
9	TraesCS3D01G507200	chr1B	623937025	623939078	2053	True	2628	2628	89.7880	1	2064	1	chr1B.!!$R1	2063
10	TraesCS3D01G507200	chr7A	140767264	140769316	2052	True	2606	2606	89.6750	1	2065	1	chr7A.!!$R1	2064
11	TraesCS3D01G507200	chr7A	141056701	141058758	2057	True	2599	2599	89.5790	1	2065	1	chr7A.!!$R2	2064
12	TraesCS3D01G507200	chr4D	116522841	116524875	2034	True	2471	2471	88.6390	1	2064	1	chr4D.!!$R1	2063
13	TraesCS3D01G507200	chr3A	724745110	724745691	581	True	593	593	85.8570	2074	2643	1	chr3A.!!$R1	569
14	TraesCS3D01G507200	chrUn	41885398	41885990	592	False	382	473	90.8955	2084	2643	2	chrUn.!!$F1	559

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
782	848	0.036732	ATGGAGCCAAAGTTCGAGCA	59.963	50.0	1.01	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2266	2398	0.871024	AGGGGAAATTTTGGTGGGGA	59.129	50.0	0.0	0.0	0.0	4.81	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
38	39	1.924731	TCGGAGGAGAGCAAGAAGAA	58.075	50.000	0.00	0.00	0.00	2.52
39	40	2.461695	TCGGAGGAGAGCAAGAAGAAT	58.538	47.619	0.00	0.00	0.00	2.40
54	55	4.227197	AGAAGAATACCGGACTCCATCAT	58.773	43.478	9.46	0.00	0.00	2.45
110	113	3.026630	CGGTAAGCACTTCTCTGTTCA	57.973	47.619	0.00	0.00	0.00	3.18
122	125	3.774066	TCTCTGTTCATCATGCACTACG	58.226	45.455	0.00	0.00	0.00	3.51
260	288	6.582636	ACTAGTTCATGCAAGATCGGAATAA	58.417	36.000	0.00	0.00	0.00	1.40
301	356	0.924226	AAGGGGGATTGGGGGTACAG	60.924	60.000	0.00	0.00	0.00	2.74
441	505	3.197614	TCGAGGTCGATCTGCCAC	58.802	61.111	0.91	0.00	44.22	5.01
489	553	3.134127	GGCATCTGCACCGGTTCC	61.134	66.667	2.97	0.00	44.36	3.62
490	554	2.045926	GCATCTGCACCGGTTCCT	60.046	61.111	2.97	0.00	41.59	3.36
491	555	2.109126	GCATCTGCACCGGTTCCTC	61.109	63.158	2.97	0.00	41.59	3.71
492	556	1.450312	CATCTGCACCGGTTCCTCC	60.450	63.158	2.97	0.00	0.00	4.30
501	565	1.308326	CGGTTCCTCCTCCTCCTCT	59.692	63.158	0.00	0.00	0.00	3.69
523	587	3.083997	GCTCCCCACCGATGACCT	61.084	66.667	0.00	0.00	0.00	3.85
559	623	1.863662	CGTCTCCCAGTACACTGCGT	61.864	60.000	3.75	0.00	42.47	5.24
677	743	3.545481	GTCGACTGCCATCGCACG	61.545	66.667	8.70	0.00	41.12	5.34
781	847	0.449388	CATGGAGCCAAAGTTCGAGC	59.551	55.000	0.00	0.00	0.00	5.03
782	848	0.036732	ATGGAGCCAAAGTTCGAGCA	59.963	50.000	1.01	0.00	0.00	4.26
852	918	1.617839	AGGAAGAAGGCCCTCCAGG	60.618	63.158	0.00	0.00	39.47	4.45
884	950	0.970427	GGAATGGGTTGGCGTTGGAT	60.970	55.000	0.00	0.00	0.00	3.41
890	956	0.608035	GGTTGGCGTTGGATCTGGAA	60.608	55.000	0.00	0.00	0.00	3.53
1000	1069	2.206536	GGGCGATGGAGAGGAGGAG	61.207	68.421	0.00	0.00	0.00	3.69
1001	1070	1.152652	GGCGATGGAGAGGAGGAGA	60.153	63.158	0.00	0.00	0.00	3.71
1027	1096	4.277174	AGTGACAATCATGCCGTTTTAACA	59.723	37.500	0.00	0.00	0.00	2.41
1089	1158	3.489355	ACTCCATGAATTGTGTGCAGAA	58.511	40.909	0.00	0.00	0.00	3.02
1174	1244	1.194218	TCATCCAATGCCTGACGAGA	58.806	50.000	0.00	0.00	0.00	4.04
1212	1282	1.511768	CGAGGAAGACCCGAAGACC	59.488	63.158	0.00	0.00	40.87	3.85
1291	1367	1.043116	CGGCCACTACCATCAGGAGA	61.043	60.000	2.24	0.00	38.69	3.71
1297	1373	2.437281	CACTACCATCAGGAGAATGGCT	59.563	50.000	2.10	0.00	38.99	4.75
1305	1381	2.842496	TCAGGAGAATGGCTCAACTCAT	59.158	45.455	0.00	0.00	45.81	2.90
1308	1384	5.045651	TCAGGAGAATGGCTCAACTCATTTA	60.046	40.000	0.00	0.00	45.81	1.40
1360	1437	3.988151	ATCCCCATGCCCCTGGACA	62.988	63.158	0.00	0.00	38.69	4.02
1457	1534	0.674895	AAGCTGATGAACGACAGGGC	60.675	55.000	0.00	0.00	35.05	5.19
1637	1714	0.321298	TTCGCCAACAAGGACTAGGC	60.321	55.000	0.00	0.00	41.22	3.93
1641	1718	1.550130	CCAACAAGGACTAGGCCCGA	61.550	60.000	12.37	0.00	41.22	5.14
1711	1795	7.436430	TGTTTATGGTTTATGCGTTGAACTA	57.564	32.000	0.00	0.67	0.00	2.24
1720	1816	7.376072	GGTTTATGCGTTGAACTATTATGAAGC	59.624	37.037	0.00	0.00	0.00	3.86
1784	1892	4.190001	CTCTGCTCTGCTTATGATGTGTT	58.810	43.478	0.00	0.00	0.00	3.32
1805	1914	2.037381	TGTACATGGTTGTGCCGAAGTA	59.963	45.455	0.00	0.00	41.21	2.24
1836	1945	2.079925	CTCACCAACTAGCCAAAGAGC	58.920	52.381	0.00	0.00	0.00	4.09
1880	1990	2.328319	ACAACCAATCACCATGCCTTT	58.672	42.857	0.00	0.00	0.00	3.11
1900	2010	4.475763	TTGGTTTGTGTACTAACATGCG	57.524	40.909	10.54	0.00	38.08	4.73
1931	2041	1.149174	CCAGGCAGTGTGGTTCAGT	59.851	57.895	0.00	0.00	0.00	3.41
1936	2062	1.003118	GGCAGTGTGGTTCAGTCCATA	59.997	52.381	0.00	0.00	39.81	2.74
1957	2084	3.834799	GCAAGAGGGCATGCAGGC	61.835	66.667	21.36	16.47	42.12	4.85
2025	2155	3.450457	AGAGTGAGTTGAGAAGGCTATGG	59.550	47.826	0.00	0.00	0.00	2.74
2046	2176	5.208890	TGGAATGCACCTACTGTAGACTAT	58.791	41.667	16.22	2.88	0.00	2.12
2065	2195	3.532155	GCAACCAAACACGCCCCA	61.532	61.111	0.00	0.00	0.00	4.96
2066	2196	3.082579	GCAACCAAACACGCCCCAA	62.083	57.895	0.00	0.00	0.00	4.12
2067	2197	1.517832	CAACCAAACACGCCCCAAA	59.482	52.632	0.00	0.00	0.00	3.28
2068	2198	0.808060	CAACCAAACACGCCCCAAAC	60.808	55.000	0.00	0.00	0.00	2.93
2069	2199	2.026879	CCAAACACGCCCCAAACG	59.973	61.111	0.00	0.00	0.00	3.60
2070	2200	2.776913	CCAAACACGCCCCAAACGT	61.777	57.895	0.00	0.00	46.42	3.99
2098	2228	0.537653	GGTGGGAAGGTAGCTGACTC	59.462	60.000	0.00	0.00	0.00	3.36
2100	2230	1.066787	GTGGGAAGGTAGCTGACTCAC	60.067	57.143	13.81	13.81	0.00	3.51
2101	2231	1.203187	TGGGAAGGTAGCTGACTCACT	60.203	52.381	0.00	0.00	0.00	3.41
2102	2232	1.205893	GGGAAGGTAGCTGACTCACTG	59.794	57.143	0.00	0.00	0.00	3.66
2104	2234	2.563179	GGAAGGTAGCTGACTCACTGAA	59.437	50.000	0.00	0.00	0.00	3.02
2105	2235	3.367910	GGAAGGTAGCTGACTCACTGAAG	60.368	52.174	0.00	0.00	0.00	3.02
2106	2236	3.162147	AGGTAGCTGACTCACTGAAGA	57.838	47.619	0.00	0.00	0.00	2.87
2107	2237	2.823154	AGGTAGCTGACTCACTGAAGAC	59.177	50.000	0.00	0.00	0.00	3.01
2108	2238	2.414824	GGTAGCTGACTCACTGAAGACG	60.415	54.545	0.00	0.00	0.00	4.18
2109	2239	1.323412	AGCTGACTCACTGAAGACGT	58.677	50.000	0.00	0.00	0.00	4.34
2110	2240	1.000827	AGCTGACTCACTGAAGACGTG	60.001	52.381	0.00	0.00	0.00	4.49
2111	2241	1.932604	GCTGACTCACTGAAGACGTGG	60.933	57.143	0.00	0.00	33.31	4.94
2266	2398	1.270518	CGCTCCTCCCATGAATCGAAT	60.271	52.381	0.00	0.00	0.00	3.34
2296	2428	2.058593	ATTTCCCCTTTCTGATCCGC	57.941	50.000	0.00	0.00	0.00	5.54
2342	2508	1.376037	GGCTGTTCCCTCGACCTTG	60.376	63.158	0.00	0.00	0.00	3.61
2385	2551	1.863662	CTCACGGCGCTATATCGGGT	61.864	60.000	6.90	0.00	0.00	5.28
2525	2691	1.153489	CAGGGTCTGCATGGTCTCG	60.153	63.158	0.00	0.00	0.00	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	1.257743	CCGATGATGGAGTCCGGTAT	58.742	55.000	4.30	0.00	35.83	2.73
39	40	1.461091	GCCGATGATGGAGTCCGGTA	61.461	60.000	4.30	0.00	41.95	4.02
54	55	1.437573	GTGATGATCCACTCGCCGA	59.562	57.895	0.00	0.00	34.38	5.54
110	113	1.060553	CGCGAAAACGTAGTGCATGAT	59.939	47.619	0.00	0.00	45.00	2.45
122	125	1.063412	GCCGGATCAAACGCGAAAAC	61.063	55.000	15.93	0.00	0.00	2.43
260	288	6.183360	CCTTCTACTTCATCTGCATCTACCTT	60.183	42.308	0.00	0.00	0.00	3.50
301	356	2.836944	GGTTAGCCGGTGTCTGTTC	58.163	57.895	1.90	0.00	0.00	3.18
441	505	1.302033	GGAGCCAGGCCATCATACG	60.302	63.158	8.22	0.00	0.00	3.06
501	565	0.619255	TCATCGGTGGGGAGCCTAAA	60.619	55.000	0.00	0.00	0.00	1.85
559	623	1.813859	CTCCTAATGACCGCCGTGA	59.186	57.895	0.00	0.00	0.00	4.35
771	837	1.583054	GAGGTGTGTGCTCGAACTTT	58.417	50.000	0.00	0.00	0.00	2.66
852	918	1.413118	CCATTCCCTTGGGGTATTGC	58.587	55.000	5.78	0.00	44.74	3.56
869	935	1.303236	CAGATCCAACGCCAACCCA	60.303	57.895	0.00	0.00	0.00	4.51
884	950	1.759445	GCCATGAGCTCTAGTTCCAGA	59.241	52.381	16.19	0.00	38.99	3.86
890	956	0.678395	CCATCGCCATGAGCTCTAGT	59.322	55.000	16.19	0.00	40.39	2.57
1000	1069	2.350522	ACGGCATGATTGTCACTCTTC	58.649	47.619	0.00	0.00	0.00	2.87
1001	1070	2.479566	ACGGCATGATTGTCACTCTT	57.520	45.000	0.00	0.00	0.00	2.85
1027	1096	4.951715	TCATGGCTTATTGAAGAGCATGTT	59.048	37.500	5.83	0.00	40.63	2.71
1089	1158	1.411977	CCATCTCATTGCTCTCCTCGT	59.588	52.381	0.00	0.00	0.00	4.18
1212	1282	3.691342	TCGTCGCCAACCTCAGGG	61.691	66.667	0.00	0.00	38.88	4.45
1291	1367	5.394883	CCTTGCATAAATGAGTTGAGCCATT	60.395	40.000	0.00	0.00	34.75	3.16
1297	1373	5.357878	GGATGACCTTGCATAAATGAGTTGA	59.642	40.000	0.00	0.00	0.00	3.18
1566	1643	0.460109	CCTCAATGCCATCGTCGTCA	60.460	55.000	0.00	0.00	0.00	4.35
1625	1702	1.686110	CCTCGGGCCTAGTCCTTGT	60.686	63.158	0.84	0.00	0.00	3.16
1711	1795	3.543680	AGCAGTACCACGCTTCATAAT	57.456	42.857	0.00	0.00	33.81	1.28
1720	1816	6.346919	GCATATTTCAGATAAGCAGTACCACG	60.347	42.308	0.00	0.00	0.00	4.94
1784	1892	1.202710	ACTTCGGCACAACCATGTACA	60.203	47.619	0.00	0.00	37.82	2.90
1836	1945	1.864711	CAACGTCTGGTGTGTGGTAAG	59.135	52.381	0.00	0.00	0.00	2.34
1880	1990	3.248841	CACGCATGTTAGTACACAAACCA	59.751	43.478	0.00	0.00	37.03	3.67
1888	1998	1.801771	TGGTTGCACGCATGTTAGTAC	59.198	47.619	0.00	0.00	0.00	2.73
1889	1999	2.171341	TGGTTGCACGCATGTTAGTA	57.829	45.000	0.00	0.00	0.00	1.82
1900	2010	1.227234	GCCTGGTGTTTGGTTGCAC	60.227	57.895	0.00	0.00	35.07	4.57
1931	2041	0.913934	TGCCCTCTTGCCTGTATGGA	60.914	55.000	0.00	0.00	38.35	3.41
1936	2062	2.362120	GCATGCCCTCTTGCCTGT	60.362	61.111	6.36	0.00	37.39	4.00
1957	2084	2.801679	GCACCATCATGTTGTTTGGTTG	59.198	45.455	3.19	2.96	40.44	3.77
1999	2129	1.345741	CCTTCTCAACTCACTCTGGCA	59.654	52.381	0.00	0.00	0.00	4.92
2006	2136	3.895232	TCCATAGCCTTCTCAACTCAC	57.105	47.619	0.00	0.00	0.00	3.51
2025	2155	5.533482	CCATAGTCTACAGTAGGTGCATTC	58.467	45.833	7.79	0.00	0.00	2.67
2100	2230	2.802787	AAGACTGACCACGTCTTCAG	57.197	50.000	17.64	17.64	45.81	3.02
2104	2234	1.693627	AGTGAAGACTGACCACGTCT	58.306	50.000	0.00	0.00	43.20	4.18
2257	2389	2.889170	TTTGGTGGGGATTCGATTCA	57.111	45.000	9.36	0.00	0.00	2.57
2266	2398	0.871024	AGGGGAAATTTTGGTGGGGA	59.129	50.000	0.00	0.00	0.00	4.81
2385	2551	2.570302	GTCTAAACAACCTGGGGAGCTA	59.430	50.000	0.00	0.00	0.00	3.32
2397	2563	2.358984	GGCCGCCGGTCTAAACAA	60.359	61.111	4.45	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.