AutoCloner

Multiple sequence alignment - TraesCS2B01G079100

Loading Multiple Alignment...

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	TraesCS2B01G079100	chr2B	100.000	2729	0	0	1	2729	44275682	44272954	0.000000e+00	5040.0
1	TraesCS2B01G079100	chr2B	98.620	1812	25	0	1	1812	44193002	44191191	0.000000e+00	3208.0
2	TraesCS2B01G079100	chr2B	93.478	552	32	2	1279	1826	44286342	44285791	0.000000e+00	817.0
3	TraesCS2B01G079100	chr2B	90.123	567	32	8	1279	1823	44311220	44310656	0.000000e+00	715.0
4	TraesCS2B01G079100	chr2B	89.851	404	21	8	829	1227	44311840	44311452	4.060000e-138	501.0
5	TraesCS2B01G079100	chr2B	82.276	457	57	16	782	1229	44287181	44286740	9.230000e-100	374.0
6	TraesCS2B01G079100	chr2D	94.768	1835	84	6	1	1827	27855227	27853397	0.000000e+00	2846.0
7	TraesCS2B01G079100	chr2D	94.022	552	29	2	1279	1826	27860348	27859797	0.000000e+00	833.0
8	TraesCS2B01G079100	chr2D	87.431	724	52	18	507	1227	27884673	27883986	0.000000e+00	797.0
9	TraesCS2B01G079100	chr2D	91.166	566	27	11	1279	1823	27883755	27883192	0.000000e+00	747.0
10	TraesCS2B01G079100	chr2D	82.314	458	58	14	782	1229	27861194	27860750	2.570000e-100	375.0
11	TraesCS2B01G079100	chr2D	78.659	164	24	6	60	222	59822072	59822225	6.220000e-17	99.0
12	TraesCS2B01G079100	chr2A	93.764	1828	104	7	1	1827	30022489	30020671	0.000000e+00	2736.0
13	TraesCS2B01G079100	chr2A	93.659	552	31	2	1279	1826	30048492	30047941	0.000000e+00	822.0
14	TraesCS2B01G079100	chr2A	84.302	860	105	14	1873	2729	55869334	55870166	0.000000e+00	813.0
15	TraesCS2B01G079100	chr2A	87.483	727	50	14	507	1227	30073225	30072534	0.000000e+00	800.0
16	TraesCS2B01G079100	chr2A	94.351	478	19	7	1279	1750	30072303	30071828	0.000000e+00	726.0
17	TraesCS2B01G079100	chr2A	82.353	459	58	14	782	1229	30049340	30048894	7.130000e-101	377.0
18	TraesCS2B01G079100	chr2A	82.373	295	47	3	1867	2157	461151994	461152287	4.510000e-63	252.0
19	TraesCS2B01G079100	chr3B	88.360	799	82	6	1871	2664	459250621	459249829	0.000000e+00	950.0
20	TraesCS2B01G079100	chr3B	81.148	122	23	0	67	188	732145227	732145106	6.220000e-17	99.0
21	TraesCS2B01G079100	chr7D	86.275	867	106	8	1865	2729	71120548	71119693	0.000000e+00	929.0
22	TraesCS2B01G079100	chr6D	85.848	855	102	15	1883	2729	433694026	433693183	0.000000e+00	891.0
23	TraesCS2B01G079100	chr6D	79.333	150	26	3	30	178	161915451	161915596	1.730000e-17	100.0
24	TraesCS2B01G079100	chr5A	86.161	831	96	12	1900	2729	16973355	16972543	0.000000e+00	880.0
25	TraesCS2B01G079100	chr5D	85.563	852	103	10	1879	2729	484157693	484158525	0.000000e+00	874.0
26	TraesCS2B01G079100	chr5D	85.580	742	92	7	1966	2706	424916971	424916244	0.000000e+00	763.0
27	TraesCS2B01G079100	chrUn	83.133	830	118	14	1865	2688	44241128	44240315	0.000000e+00	737.0
28	TraesCS2B01G079100	chrUn	82.109	844	112	18	1865	2685	44577776	44578603	0.000000e+00	686.0
29	TraesCS2B01G079100	chr4A	83.313	821	79	15	1862	2674	376722951	376723721	0.000000e+00	704.0
30	TraesCS2B01G079100	chr6B	86.032	630	79	4	2103	2729	459376974	459377597	0.000000e+00	667.0
31	TraesCS2B01G079100	chr3A	80.858	862	142	17	1867	2717	688984275	688985124	0.000000e+00	656.0
32	TraesCS2B01G079100	chr3A	100.000	28	0	0	195	222	739970636	739970609	5.000000e-03	52.8
33	TraesCS2B01G079100	chr5B	81.218	197	33	4	62	255	381383175	381382980	3.640000e-34	156.0
34	TraesCS2B01G079100	chr3D	77.157	197	31	7	60	255	482611606	482611789	4.810000e-18	102.0
35	TraesCS2B01G079100	chr4B	94.286	35	2	0	607	641	87679401	87679367	1.000000e-03	54.7

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	TraesCS2B01G079100	chr2B	44272954	44275682	2728	True	5040.0	5040	100.0000	1	2729	1	chr2B.!!$R2	2728
1	TraesCS2B01G079100	chr2B	44191191	44193002	1811	True	3208.0	3208	98.6200	1	1812	1	chr2B.!!$R1	1811
2	TraesCS2B01G079100	chr2B	44310656	44311840	1184	True	608.0	715	89.9870	829	1823	2	chr2B.!!$R4	994
3	TraesCS2B01G079100	chr2B	44285791	44287181	1390	True	595.5	817	87.8770	782	1826	2	chr2B.!!$R3	1044
4	TraesCS2B01G079100	chr2D	27853397	27855227	1830	True	2846.0	2846	94.7680	1	1827	1	chr2D.!!$R1	1826
5	TraesCS2B01G079100	chr2D	27883192	27884673	1481	True	772.0	797	89.2985	507	1823	2	chr2D.!!$R3	1316
6	TraesCS2B01G079100	chr2D	27859797	27861194	1397	True	604.0	833	88.1680	782	1826	2	chr2D.!!$R2	1044
7	TraesCS2B01G079100	chr2A	30020671	30022489	1818	True	2736.0	2736	93.7640	1	1827	1	chr2A.!!$R1	1826
8	TraesCS2B01G079100	chr2A	55869334	55870166	832	False	813.0	813	84.3020	1873	2729	1	chr2A.!!$F1	856
9	TraesCS2B01G079100	chr2A	30071828	30073225	1397	True	763.0	800	90.9170	507	1750	2	chr2A.!!$R3	1243
10	TraesCS2B01G079100	chr2A	30047941	30049340	1399	True	599.5	822	88.0060	782	1826	2	chr2A.!!$R2	1044
11	TraesCS2B01G079100	chr3B	459249829	459250621	792	True	950.0	950	88.3600	1871	2664	1	chr3B.!!$R1	793
12	TraesCS2B01G079100	chr7D	71119693	71120548	855	True	929.0	929	86.2750	1865	2729	1	chr7D.!!$R1	864
13	TraesCS2B01G079100	chr6D	433693183	433694026	843	True	891.0	891	85.8480	1883	2729	1	chr6D.!!$R1	846
14	TraesCS2B01G079100	chr5A	16972543	16973355	812	True	880.0	880	86.1610	1900	2729	1	chr5A.!!$R1	829
15	TraesCS2B01G079100	chr5D	484157693	484158525	832	False	874.0	874	85.5630	1879	2729	1	chr5D.!!$F1	850
16	TraesCS2B01G079100	chr5D	424916244	424916971	727	True	763.0	763	85.5800	1966	2706	1	chr5D.!!$R1	740
17	TraesCS2B01G079100	chrUn	44240315	44241128	813	True	737.0	737	83.1330	1865	2688	1	chrUn.!!$R1	823
18	TraesCS2B01G079100	chrUn	44577776	44578603	827	False	686.0	686	82.1090	1865	2685	1	chrUn.!!$F1	820
19	TraesCS2B01G079100	chr4A	376722951	376723721	770	False	704.0	704	83.3130	1862	2674	1	chr4A.!!$F1	812
20	TraesCS2B01G079100	chr6B	459376974	459377597	623	False	667.0	667	86.0320	2103	2729	1	chr6B.!!$F1	626
21	TraesCS2B01G079100	chr3A	688984275	688985124	849	False	656.0	656	80.8580	1867	2717	1	chr3A.!!$F1	850

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
120	121	1.627297	CCCCTAAGGACCAGTGCTCC	61.627	65.0	0.0	0.0	38.24	4.7	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1837	2253	0.331954	AGCCCCTCTCGACTTCAGTA	59.668	55.0	0.0	0.0	0.0	2.74	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
25	26	2.704572	GCACAGAGACAAGCCACTAAT	58.295	47.619	0.00	0.00	0.00	1.73
90	91	2.750166	TCGATGACAGTCAGGAAGTCTC	59.250	50.000	9.64	0.00	33.56	3.36
120	121	1.627297	CCCCTAAGGACCAGTGCTCC	61.627	65.000	0.00	0.00	38.24	4.70
158	159	3.629398	GCTGTTGAATCCCTGAATCGATT	59.371	43.478	11.20	11.20	0.00	3.34
257	258	3.217743	CTACGTCGGAGCTCCCCC	61.218	72.222	27.20	16.02	0.00	5.40
280	281	4.399618	CGACAGAGGAACTTGAAGAGGATA	59.600	45.833	0.00	0.00	41.55	2.59
362	364	7.611855	CCCATGAGGACTAAAATTCTACTTGTT	59.388	37.037	0.00	0.00	38.24	2.83
376	378	5.671493	TCTACTTGTTTATTAGCCAGAGCC	58.329	41.667	0.00	0.00	41.25	4.70
590	593	5.450376	ACAAAAGTAGACATTCGCATACG	57.550	39.130	0.00	0.00	42.01	3.06
1827	2243	6.174451	AGCATGCATATGTAAATTCTAGCG	57.826	37.500	21.98	0.00	36.65	4.26
1828	2244	5.934043	AGCATGCATATGTAAATTCTAGCGA	59.066	36.000	21.98	0.00	36.65	4.93
1829	2245	6.427853	AGCATGCATATGTAAATTCTAGCGAA	59.572	34.615	21.98	0.00	36.65	4.70
1830	2246	7.041167	AGCATGCATATGTAAATTCTAGCGAAA	60.041	33.333	21.98	0.00	36.65	3.46
1831	2247	7.591057	GCATGCATATGTAAATTCTAGCGAAAA	59.409	33.333	14.21	0.00	36.65	2.29
1832	2248	9.449550	CATGCATATGTAAATTCTAGCGAAAAA	57.550	29.630	0.00	0.00	31.91	1.94
1834	2250	9.663904	TGCATATGTAAATTCTAGCGAAAAATC	57.336	29.630	4.29	0.00	31.91	2.17
1835	2251	9.884465	GCATATGTAAATTCTAGCGAAAAATCT	57.116	29.630	4.29	0.00	31.91	2.40
1846	2262	9.517609	TTCTAGCGAAAAATCTATACTGAAGTC	57.482	33.333	0.00	0.00	0.00	3.01
1847	2263	6.814076	AGCGAAAAATCTATACTGAAGTCG	57.186	37.500	0.00	0.00	0.00	4.18
1848	2264	6.561614	AGCGAAAAATCTATACTGAAGTCGA	58.438	36.000	0.00	0.00	0.00	4.20
1849	2265	6.693545	AGCGAAAAATCTATACTGAAGTCGAG	59.306	38.462	0.00	0.00	0.00	4.04
1850	2266	6.691818	GCGAAAAATCTATACTGAAGTCGAGA	59.308	38.462	0.00	0.00	0.00	4.04
1851	2267	7.096803	GCGAAAAATCTATACTGAAGTCGAGAG	60.097	40.741	0.00	0.00	0.00	3.20
1852	2268	7.377397	CGAAAAATCTATACTGAAGTCGAGAGG	59.623	40.741	0.00	0.00	0.00	3.69
1853	2269	6.642707	AAATCTATACTGAAGTCGAGAGGG	57.357	41.667	0.00	0.00	0.00	4.30
1854	2270	4.088056	TCTATACTGAAGTCGAGAGGGG	57.912	50.000	0.00	0.00	0.00	4.79
1855	2271	1.404843	ATACTGAAGTCGAGAGGGGC	58.595	55.000	0.00	0.00	0.00	5.80
1856	2272	0.331954	TACTGAAGTCGAGAGGGGCT	59.668	55.000	0.00	0.00	0.00	5.19
1857	2273	0.968393	ACTGAAGTCGAGAGGGGCTC	60.968	60.000	0.00	0.00	40.38	4.70
1888	2306	1.075450	CTAACCCTACCCGCTCCCT	60.075	63.158	0.00	0.00	0.00	4.20
1891	2309	2.687566	CCCTACCCGCTCCCTTGT	60.688	66.667	0.00	0.00	0.00	3.16
1893	2311	2.125106	CTACCCGCTCCCTTGTGC	60.125	66.667	0.00	0.00	0.00	4.57
2007	2430	2.598394	AAAGCCTGTGTGCCGCAT	60.598	55.556	0.00	0.00	0.00	4.73
2014	2437	3.294493	GTGTGCCGCATTGGTGGT	61.294	61.111	0.00	0.00	46.76	4.16
2036	2478	3.650369	GCGTTTCTCCTCGCCAAA	58.350	55.556	0.00	0.00	45.54	3.28
2039	2481	0.790814	CGTTTCTCCTCGCCAAAGAC	59.209	55.000	0.00	0.00	0.00	3.01
2337	2791	3.971702	GCCTGAGGCTGGGTGGTT	61.972	66.667	17.96	0.00	46.69	3.67
2402	2859	1.021202	CAGAGTTGCCGGTGAAAACA	58.979	50.000	1.90	0.00	0.00	2.83
2409	2866	3.253955	CGGTGAAAACAGAGCCGG	58.746	61.111	0.00	0.00	38.86	6.13
2437	2894	3.899981	ATGGCGGCTTCTTGCGTCA	62.900	57.895	11.43	0.00	44.05	4.35
2474	2931	3.649073	CATCGTGGTGTAACTTCTGTCA	58.351	45.455	0.00	0.00	36.74	3.58
2480	2937	3.139077	GGTGTAACTTCTGTCAACCCAG	58.861	50.000	0.00	0.00	36.74	4.45
2501	2959	2.034066	TGCTGCTTCGGGGGAAAG	59.966	61.111	0.00	0.00	0.00	2.62
2510	2968	3.370633	GCTTCGGGGGAAAGACTAAGATT	60.371	47.826	0.00	0.00	0.00	2.40
2563	3025	1.672145	GGTGTCGTTACTCTCTTGGGC	60.672	57.143	0.00	0.00	0.00	5.36
2585	3047	3.648982	CGTTTGTGGAGCAGCGCA	61.649	61.111	11.47	0.00	0.00	6.09
2592	3054	2.188994	GGAGCAGCGCAGGAAGAT	59.811	61.111	11.47	0.00	0.00	2.40
2614	3076	4.783621	GCATGAGGTGGAGCGGCA	62.784	66.667	1.45	0.00	0.00	5.69
2634	3097	0.106708	AAGTCTTGCACGGAGCTTCA	59.893	50.000	0.00	0.00	45.94	3.02
2636	3099	1.669115	TCTTGCACGGAGCTTCAGC	60.669	57.895	0.00	0.00	45.94	4.26
2660	3123	0.330604	ATGTCAAGTCATGCCTGGCT	59.669	50.000	21.03	2.27	39.63	4.75
2717	3180	3.710326	TGCTACGCACGATAGATCTTT	57.290	42.857	0.00	0.00	41.38	2.52
2720	3183	3.422546	GCTACGCACGATAGATCTTTCAC	59.577	47.826	12.82	1.96	41.38	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	0.881118	CAACGGTGCATTAGTGGCTT	59.119	50.000	0.00	0.00	0.00	4.35
90	91	1.111116	CCTTAGGGGCATGTGCATGG	61.111	60.000	13.28	0.00	44.36	3.66
131	132	1.019673	CAGGGATTCAACAGCGATGG	58.980	55.000	5.32	0.00	0.00	3.51
158	159	6.361433	TGAGATTTGGTGTCAGGTTCTTTAA	58.639	36.000	0.00	0.00	0.00	1.52
257	258	2.558795	TCCTCTTCAAGTTCCTCTGTCG	59.441	50.000	0.00	0.00	0.00	4.35
280	281	1.141858	GAGCCAATCTTTCGGGATCCT	59.858	52.381	12.58	0.00	31.04	3.24
353	354	5.671493	GGCTCTGGCTAATAAACAAGTAGA	58.329	41.667	0.00	0.00	38.73	2.59
362	364	0.393077	GCCTCGGCTCTGGCTAATAA	59.607	55.000	0.00	0.00	45.26	1.40
376	378	2.190578	GGGATTCCTGGTGCCTCG	59.809	66.667	2.01	0.00	0.00	4.63
590	593	0.179029	AGGGGGTGTTATACATGCGC	60.179	55.000	0.00	0.00	0.00	6.09
1827	2243	7.650104	CCCTCTCGACTTCAGTATAGATTTTTC	59.350	40.741	0.00	0.00	0.00	2.29
1828	2244	7.418025	CCCCTCTCGACTTCAGTATAGATTTTT	60.418	40.741	0.00	0.00	0.00	1.94
1829	2245	6.041069	CCCCTCTCGACTTCAGTATAGATTTT	59.959	42.308	0.00	0.00	0.00	1.82
1830	2246	5.536916	CCCCTCTCGACTTCAGTATAGATTT	59.463	44.000	0.00	0.00	0.00	2.17
1831	2247	5.074115	CCCCTCTCGACTTCAGTATAGATT	58.926	45.833	0.00	0.00	0.00	2.40
1832	2248	4.658063	CCCCTCTCGACTTCAGTATAGAT	58.342	47.826	0.00	0.00	0.00	1.98
1833	2249	3.748027	GCCCCTCTCGACTTCAGTATAGA	60.748	52.174	0.00	0.00	0.00	1.98
1834	2250	2.554893	GCCCCTCTCGACTTCAGTATAG	59.445	54.545	0.00	0.00	0.00	1.31
1835	2251	2.175069	AGCCCCTCTCGACTTCAGTATA	59.825	50.000	0.00	0.00	0.00	1.47
1836	2252	1.063567	AGCCCCTCTCGACTTCAGTAT	60.064	52.381	0.00	0.00	0.00	2.12
1837	2253	0.331954	AGCCCCTCTCGACTTCAGTA	59.668	55.000	0.00	0.00	0.00	2.74
1838	2254	0.968393	GAGCCCCTCTCGACTTCAGT	60.968	60.000	0.00	0.00	31.20	3.41
1839	2255	1.813192	GAGCCCCTCTCGACTTCAG	59.187	63.158	0.00	0.00	31.20	3.02
1840	2256	4.019983	GAGCCCCTCTCGACTTCA	57.980	61.111	0.00	0.00	31.20	3.02
1869	2285	2.804912	GGGAGCGGGTAGGGTTAGC	61.805	68.421	0.00	0.00	0.00	3.09
2014	2437	4.735132	CGAGGAGAAACGCCGCCA	62.735	66.667	0.00	0.00	0.00	5.69
2036	2478	3.063084	GCCGTCCTGACCGAGTCT	61.063	66.667	5.77	0.00	33.15	3.24
2063	2505	1.683385	CTGCTGTAGATCCGACCATCA	59.317	52.381	0.00	0.00	0.00	3.07
2069	2511	0.817654	CACCACTGCTGTAGATCCGA	59.182	55.000	0.00	0.00	0.00	4.55
2183	2636	3.592898	ATACGACATCAGCAAGTGTGA	57.407	42.857	0.00	0.00	0.00	3.58
2360	2817	2.270205	CCAACTCGCAGCTGGGAT	59.730	61.111	30.94	16.69	36.39	3.85
2427	2884	4.574892	TCATCAAGGTAATGACGCAAGAA	58.425	39.130	0.00	0.00	43.62	2.52
2459	2916	3.139077	CTGGGTTGACAGAAGTTACACC	58.861	50.000	0.00	0.00	40.97	4.16
2501	2959	5.694006	CGATCTGGATGACCAAATCTTAGTC	59.306	44.000	0.00	0.00	46.32	2.59
2563	3025	1.133253	CTGCTCCACAAACGATGCG	59.867	57.895	0.00	0.00	0.00	4.73
2585	3047	2.971330	CACCTCATGCCTCTATCTTCCT	59.029	50.000	0.00	0.00	0.00	3.36
2592	3054	1.395045	CGCTCCACCTCATGCCTCTA	61.395	60.000	0.00	0.00	0.00	2.43
2614	3076	1.230324	GAAGCTCCGTGCAAGACTTT	58.770	50.000	0.00	0.00	45.94	2.66
2634	3097	1.741732	GCATGACTTGACATCTCCGCT	60.742	52.381	0.00	0.00	0.00	5.52
2636	3099	1.134580	AGGCATGACTTGACATCTCCG	60.135	52.381	0.00	0.00	34.87	4.63
2660	3123	2.198406	GACACAACGTAGCACTTGTCA	58.802	47.619	0.00	0.00	34.71	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.