AutoCloner

Multiple sequence alignment - TraesCS2A01G265500

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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	TraesCS2A01G265500	chr2A	100.000	2276	0	0	1	2276	421571603	421569328	0.000000e+00	4204
1	TraesCS2A01G265500	chr2A	94.125	2281	115	12	1	2276	421918658	421916392	0.000000e+00	3452
2	TraesCS2A01G265500	chr2A	89.054	740	79	2	566	1303	769613541	769614280	0.000000e+00	917
3	TraesCS2A01G265500	chr2D	94.054	740	42	2	565	1304	639641307	639640570	0.000000e+00	1122
4	TraesCS2A01G265500	chr2D	89.879	741	73	2	565	1304	116762433	116763172	0.000000e+00	952
5	TraesCS2A01G265500	chr2D	91.166	566	42	6	3	563	349754501	349755063	0.000000e+00	761
6	TraesCS2A01G265500	chr2D	90.799	576	39	11	1	566	462506720	462507291	0.000000e+00	758
7	TraesCS2A01G265500	chr2D	82.738	168	27	2	1839	2004	314164488	314164655	5.070000e-32	148
8	TraesCS2A01G265500	chr4A	91.734	738	61	0	565	1302	11108989	11109726	0.000000e+00	1026
9	TraesCS2A01G265500	chr4A	90.877	570	40	7	1	565	179965863	179965301	0.000000e+00	754
10	TraesCS2A01G265500	chr3D	89.276	746	74	4	565	1304	595113013	595113758	0.000000e+00	929
11	TraesCS2A01G265500	chr5A	89.233	743	78	2	565	1306	79273725	79274466	0.000000e+00	928
12	TraesCS2A01G265500	chr5A	90.829	567	44	5	1	563	466043222	466043784	0.000000e+00	752
13	TraesCS2A01G265500	chr6A	89.069	741	79	2	565	1303	510872775	510873515	0.000000e+00	918
14	TraesCS2A01G265500	chr3B	85.499	862	102	18	456	1304	82432411	82433262	0.000000e+00	878
15	TraesCS2A01G265500	chr1A	90.576	573	46	5	1	568	258441210	258441779	0.000000e+00	752
16	TraesCS2A01G265500	chr5D	90.718	571	38	10	1	563	103938818	103939381	0.000000e+00	747
17	TraesCS2A01G265500	chr3A	90.068	584	43	12	1	577	435078187	435077612	0.000000e+00	743
18	TraesCS2A01G265500	chr1B	90.543	571	40	11	1	563	268749797	268749233	0.000000e+00	743
19	TraesCS2A01G265500	chr2B	81.595	163	26	3	1839	1999	381921146	381921306	5.100000e-27	132

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	TraesCS2A01G265500	chr2A	421569328	421571603	2275	True	4204	4204	100.000	1	2276	1	chr2A.!!$R1	2275
1	TraesCS2A01G265500	chr2A	421916392	421918658	2266	True	3452	3452	94.125	1	2276	1	chr2A.!!$R2	2275
2	TraesCS2A01G265500	chr2A	769613541	769614280	739	False	917	917	89.054	566	1303	1	chr2A.!!$F1	737
3	TraesCS2A01G265500	chr2D	639640570	639641307	737	True	1122	1122	94.054	565	1304	1	chr2D.!!$R1	739
4	TraesCS2A01G265500	chr2D	116762433	116763172	739	False	952	952	89.879	565	1304	1	chr2D.!!$F1	739
5	TraesCS2A01G265500	chr2D	349754501	349755063	562	False	761	761	91.166	3	563	1	chr2D.!!$F3	560
6	TraesCS2A01G265500	chr2D	462506720	462507291	571	False	758	758	90.799	1	566	1	chr2D.!!$F4	565
7	TraesCS2A01G265500	chr4A	11108989	11109726	737	False	1026	1026	91.734	565	1302	1	chr4A.!!$F1	737
8	TraesCS2A01G265500	chr4A	179965301	179965863	562	True	754	754	90.877	1	565	1	chr4A.!!$R1	564
9	TraesCS2A01G265500	chr3D	595113013	595113758	745	False	929	929	89.276	565	1304	1	chr3D.!!$F1	739
10	TraesCS2A01G265500	chr5A	79273725	79274466	741	False	928	928	89.233	565	1306	1	chr5A.!!$F1	741
11	TraesCS2A01G265500	chr5A	466043222	466043784	562	False	752	752	90.829	1	563	1	chr5A.!!$F2	562
12	TraesCS2A01G265500	chr6A	510872775	510873515	740	False	918	918	89.069	565	1303	1	chr6A.!!$F1	738
13	TraesCS2A01G265500	chr3B	82432411	82433262	851	False	878	878	85.499	456	1304	1	chr3B.!!$F1	848
14	TraesCS2A01G265500	chr1A	258441210	258441779	569	False	752	752	90.576	1	568	1	chr1A.!!$F1	567
15	TraesCS2A01G265500	chr5D	103938818	103939381	563	False	747	747	90.718	1	563	1	chr5D.!!$F1	562
16	TraesCS2A01G265500	chr3A	435077612	435078187	575	True	743	743	90.068	1	577	1	chr3A.!!$R1	576
17	TraesCS2A01G265500	chr1B	268749233	268749797	564	True	743	743	90.543	1	563	1	chr1B.!!$R1	562

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
988	1016	1.002134	GCAAAGCTCAGGGGCTACA	60.002	57.895	0.0	0.0	42.24	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2046	2075	0.664761	CAATTAGGGATGCCACTGCG	59.335	55.0	5.86	0.0	41.78	5.18	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
69	74	1.414685	GGGGGCAACTAGGACTAGGAT	60.415	57.143	10.81	0.00	37.49	3.24
236	252	3.003068	CCTTCGGTCATATCGTCGTAGTT	59.997	47.826	0.00	0.00	0.00	2.24
350	369	2.583593	GGGACGTCATCGAGCTGC	60.584	66.667	18.91	0.00	40.62	5.25
370	389	1.285950	CGTGTGCTGAACTCGGAGA	59.714	57.895	12.86	0.00	41.05	3.71
470	489	3.610040	TTCAGTCTACGAGGGTACGTA	57.390	47.619	0.00	0.00	44.72	3.57
668	692	8.786826	ATATGGACTTCTCGAAACAATACAAA	57.213	30.769	0.00	0.00	0.00	2.83
768	792	1.266718	GAACATGCTCGTTTGCTTCCA	59.733	47.619	0.00	0.00	0.00	3.53
862	886	1.761780	AAGAGGAGGGGTGGGAGGAA	61.762	60.000	0.00	0.00	0.00	3.36
988	1016	1.002134	GCAAAGCTCAGGGGCTACA	60.002	57.895	0.00	0.00	42.24	2.74
1024	1052	0.904865	ATCCGACTGCTTGGAGGTCA	60.905	55.000	0.00	0.00	37.76	4.02
1041	1069	5.129485	GGAGGTCATTAATCTCTGGAACTCA	59.871	44.000	15.73	0.00	42.63	3.41
1092	1120	6.629515	CGCCTATCCTATCCGAAATATTGGAA	60.630	42.308	0.00	0.00	42.60	3.53
1246	1274	5.312895	TCATTGTAACTAGCCTTCTTGCAA	58.687	37.500	0.00	0.00	0.00	4.08
1363	1392	2.268076	GCCTGGCACGACATGGTTT	61.268	57.895	15.17	0.00	0.00	3.27
1433	1462	5.608676	GGCACAACCTCTTTCTAGTAAAC	57.391	43.478	0.00	0.00	34.51	2.01
1456	1485	1.593933	GTTGGCTCGACACACGTTTAA	59.406	47.619	0.00	0.00	43.13	1.52
1494	1523	8.915654	GTGCTTTTCGATCTAATTGATTGTTTT	58.084	29.630	0.00	0.00	37.72	2.43
1533	1562	4.134187	CGGTGCATCGTGTCGTGC	62.134	66.667	12.24	8.73	41.61	5.34
1535	1564	2.738521	GTGCATCGTGTCGTGCCT	60.739	61.111	0.00	0.00	40.56	4.75
1536	1565	2.738139	TGCATCGTGTCGTGCCTG	60.738	61.111	11.54	0.00	40.56	4.85
1554	1583	2.423185	CCTGCATGTCGAATTGGCTTTA	59.577	45.455	0.00	0.00	0.00	1.85
1566	1595	3.278157	GCTTTACAGCCCAGGCAC	58.722	61.111	12.03	0.00	44.88	5.01
1608	1637	2.682856	CCGGCACAACTAGTTTATGCAT	59.317	45.455	29.53	3.79	35.11	3.96
1614	1643	5.315982	CACAACTAGTTTATGCATGTGACG	58.684	41.667	10.16	0.00	39.10	4.35
1683	1712	2.426738	TGGCCAAGTTTGTCTTCAACAG	59.573	45.455	0.61	0.00	39.58	3.16
1687	1716	3.489738	CCAAGTTTGTCTTCAACAGGCTG	60.490	47.826	14.16	14.16	39.58	4.85
1690	1719	0.823356	TTGTCTTCAACAGGCTGCCC	60.823	55.000	16.57	0.00	39.58	5.36
1691	1720	1.228245	GTCTTCAACAGGCTGCCCA	60.228	57.895	16.57	0.00	0.00	5.36
1700	1729	0.105408	CAGGCTGCCCATAAATTGGC	59.895	55.000	16.57	0.00	44.97	4.52
1777	1806	4.616953	CCACCCAACAACATGTCTAAAAC	58.383	43.478	0.00	0.00	0.00	2.43
1778	1807	4.098654	CCACCCAACAACATGTCTAAAACA	59.901	41.667	0.00	0.00	43.51	2.83
1780	1809	5.920273	CACCCAACAACATGTCTAAAACATC	59.080	40.000	0.00	0.00	45.78	3.06
1786	1815	6.237901	ACAACATGTCTAAAACATCAGCCTA	58.762	36.000	0.00	0.00	45.78	3.93
2039	2068	0.318441	CTTCCAGCGACAGAAGGACA	59.682	55.000	0.00	0.00	36.63	4.02
2046	2075	0.456312	CGACAGAAGGACACGTAGGC	60.456	60.000	0.00	0.00	0.00	3.93
2051	2080	2.488087	GAAGGACACGTAGGCGCAGT	62.488	60.000	10.83	0.00	42.83	4.40
2075	2104	1.887707	CCCTAATTGGCCGCTCGAC	60.888	63.158	0.00	0.00	0.00	4.20
2076	2105	1.144057	CCTAATTGGCCGCTCGACT	59.856	57.895	0.00	0.00	0.00	4.18
2083	2112	3.760035	GCCGCTCGACTTCCTCCA	61.760	66.667	0.00	0.00	0.00	3.86
2084	2113	2.182030	CCGCTCGACTTCCTCCAC	59.818	66.667	0.00	0.00	0.00	4.02
2086	2115	2.182030	GCTCGACTTCCTCCACCG	59.818	66.667	0.00	0.00	0.00	4.94
2109	2138	0.731514	CGTGCATGACTACGGACGTT	60.732	55.000	0.00	0.00	41.36	3.99
2115	2144	0.251121	TGACTACGGACGTTACCCCA	60.251	55.000	1.57	0.00	0.00	4.96
2122	2151	0.392060	GGACGTTACCCCAATTCGCT	60.392	55.000	0.00	0.00	0.00	4.93
2144	2174	2.753966	CCCTCGTCTTGCCATTGCG	61.754	63.158	0.00	0.00	41.78	4.85
2145	2175	2.034879	CCTCGTCTTGCCATTGCGT	61.035	57.895	0.00	0.00	41.78	5.24
2179	2209	1.846648	GCACATAGCGAATCGTCCG	59.153	57.895	4.07	0.00	0.00	4.79
2181	2211	0.846401	CACATAGCGAATCGTCCGTG	59.154	55.000	4.07	3.59	0.00	4.94
2212	2242	0.396811	AAGTTGGTCACTAAGGCGCT	59.603	50.000	7.64	0.00	32.94	5.92
2230	2260	2.280797	GCCGTCAGCTTGTGGACA	60.281	61.111	3.18	0.00	38.99	4.02
2238	2268	2.074576	CAGCTTGTGGACATCTCTGTG	58.925	52.381	0.00	0.00	35.14	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	74	1.309006	GGGGAGGAACCGACTAGGA	59.691	63.158	0.00	0.00	45.00	2.94
350	369	1.278172	CTCCGAGTTCAGCACACGTG	61.278	60.000	15.48	15.48	37.75	4.49
470	489	0.040499	GAGAGGGGGAGAGTGTGTCT	59.960	60.000	0.00	0.00	38.71	3.41
602	626	0.173481	CTTGGCTCGATCCGACTCAA	59.827	55.000	0.03	0.00	0.00	3.02
768	792	1.852157	TGGCCTCCAACCATGACCT	60.852	57.895	3.32	0.00	30.29	3.85
862	886	1.379977	TGGAGAGGGAACGAGCGAT	60.380	57.895	0.00	0.00	0.00	4.58
962	986	2.419667	CCCTGAGCTTTGCAAAAATGG	58.580	47.619	13.84	10.55	0.00	3.16
988	1016	3.056107	TCGGATTCCATCACGACTTTCTT	60.056	43.478	3.09	0.00	30.73	2.52
1041	1069	4.160439	ACAACTGTCCTATCATCATGACGT	59.840	41.667	0.00	0.00	0.00	4.34
1092	1120	9.543783	CAAAAAGACCTAAAACTAGTAGAGTGT	57.456	33.333	3.59	0.00	38.87	3.55
1246	1274	2.191128	AACGAAGCCTCTGCAGAATT	57.809	45.000	18.85	12.64	41.13	2.17
1363	1392	3.689414	ACGACATGGCCGTGTAGA	58.311	55.556	35.94	2.58	38.97	2.59
1433	1462	3.041940	GTGTGTCGAGCCAACCCG	61.042	66.667	0.00	0.00	0.00	5.28
1466	1495	6.092122	ACAATCAATTAGATCGAAAAGCACGA	59.908	34.615	0.00	0.00	43.65	4.35
1494	1523	3.704545	AATCAATCCAAATAGCCCCCA	57.295	42.857	0.00	0.00	0.00	4.96
1533	1562	0.813184	AAGCCAATTCGACATGCAGG	59.187	50.000	0.00	0.00	0.00	4.85
1535	1564	2.816672	TGTAAAGCCAATTCGACATGCA	59.183	40.909	0.00	0.00	0.00	3.96
1536	1565	3.429085	CTGTAAAGCCAATTCGACATGC	58.571	45.455	0.00	0.00	0.00	4.06
1566	1595	3.414700	GCGACACACTTCGGGCTG	61.415	66.667	0.00	0.00	39.50	4.85
1597	1626	3.527533	GGTCCGTCACATGCATAAACTA	58.472	45.455	0.00	0.00	0.00	2.24
1600	1629	1.066787	TCGGTCCGTCACATGCATAAA	60.067	47.619	11.88	0.00	0.00	1.40
1608	1637	2.261361	CATGCTCGGTCCGTCACA	59.739	61.111	11.88	8.54	0.00	3.58
1614	1643	1.026182	TTGTCATGCATGCTCGGTCC	61.026	55.000	22.25	2.64	0.00	4.46
1690	1719	4.272504	ACGAACGGATAGTGCCAATTTATG	59.727	41.667	0.00	0.00	0.00	1.90
1691	1720	4.272504	CACGAACGGATAGTGCCAATTTAT	59.727	41.667	0.00	0.00	0.00	1.40
1700	1729	2.267426	TGCATTCACGAACGGATAGTG	58.733	47.619	0.00	0.00	37.24	2.74
1707	1736	1.358877	TCAGGATGCATTCACGAACG	58.641	50.000	7.96	0.00	34.76	3.95
1708	1737	2.032550	CCATCAGGATGCATTCACGAAC	59.967	50.000	7.96	0.00	37.49	3.95
1777	1806	6.688637	TTTCATCTGAAATGTAGGCTGATG	57.311	37.500	0.00	0.00	38.94	3.07
1778	1807	7.558807	TCATTTTCATCTGAAATGTAGGCTGAT	59.441	33.333	6.21	0.00	42.83	2.90
1780	1809	7.092137	TCATTTTCATCTGAAATGTAGGCTG	57.908	36.000	6.21	0.00	42.83	4.85
1822	1851	5.040715	TGAAATTCGTTCGATTTGCATGA	57.959	34.783	0.00	0.00	39.30	3.07
1948	1977	5.018240	GCGTACGAGGTTATCATACGATAC	58.982	45.833	21.65	0.00	40.76	2.24
1949	1978	4.690280	TGCGTACGAGGTTATCATACGATA	59.310	41.667	21.65	0.00	40.76	2.92
1950	1979	3.499537	TGCGTACGAGGTTATCATACGAT	59.500	43.478	21.65	0.00	40.76	3.73
1951	1980	2.871633	TGCGTACGAGGTTATCATACGA	59.128	45.455	21.65	0.00	40.76	3.43
1952	1981	3.257745	TGCGTACGAGGTTATCATACG	57.742	47.619	21.65	0.00	41.13	3.06
1954	1983	3.822167	TCCATGCGTACGAGGTTATCATA	59.178	43.478	21.65	0.00	0.00	2.15
1965	1994	1.226974	CAGGGAGTCCATGCGTACG	60.227	63.158	11.52	11.84	34.83	3.67
2039	2068	4.082523	ATGCCACTGCGCCTACGT	62.083	61.111	4.18	0.00	42.83	3.57
2046	2075	0.664761	CAATTAGGGATGCCACTGCG	59.335	55.000	5.86	0.00	41.78	5.18
2051	2080	1.152777	CGGCCAATTAGGGATGCCA	60.153	57.895	5.86	0.00	42.27	4.92
2075	2104	4.052229	ACGCGACGGTGGAGGAAG	62.052	66.667	15.93	0.00	0.00	3.46
2076	2105	4.351938	CACGCGACGGTGGAGGAA	62.352	66.667	15.93	0.00	34.27	3.36
2083	2112	2.985117	TAGTCATGCACGCGACGGT	61.985	57.895	15.93	0.00	37.23	4.83
2084	2113	2.202557	TAGTCATGCACGCGACGG	60.203	61.111	15.93	2.40	37.23	4.79
2086	2115	2.505498	CCGTAGTCATGCACGCGAC	61.505	63.158	15.93	4.74	36.85	5.19
2109	2138	1.379309	GGGCAAGCGAATTGGGGTA	60.379	57.895	3.40	0.00	39.47	3.69
2115	2144	1.745489	GACGAGGGGCAAGCGAATT	60.745	57.895	0.00	0.00	0.00	2.17
2122	2151	2.424842	AATGGCAAGACGAGGGGCAA	62.425	55.000	0.00	0.00	40.62	4.52
2159	2189	1.548973	GGACGATTCGCTATGTGCCG	61.549	60.000	5.86	0.00	38.78	5.69
2164	2194	1.548973	GGCACGGACGATTCGCTATG	61.549	60.000	5.86	1.17	0.00	2.23
2165	2195	1.299926	GGCACGGACGATTCGCTAT	60.300	57.895	5.86	0.00	0.00	2.97
2179	2209	1.334960	CCAACTTGTCACGATTGGCAC	60.335	52.381	0.00	0.00	36.96	5.01
2181	2211	0.951558	ACCAACTTGTCACGATTGGC	59.048	50.000	4.77	0.00	44.60	4.52
2212	2242	2.280797	GTCCACAAGCTGACGGCA	60.281	61.111	9.39	0.00	44.79	5.69
2219	2249	1.973515	TCACAGAGATGTCCACAAGCT	59.026	47.619	0.00	0.00	0.00	3.74
2230	2260	7.043300	ACCTATCTAGGATCATCACAGAGAT	57.957	40.000	10.25	0.00	46.63	2.75
2238	2268	4.953579	GTGGAGGACCTATCTAGGATCATC	59.046	50.000	10.25	9.99	46.63	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.