AutoCloner

Multiple sequence alignment - TraesCS2B01G626200

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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	TraesCS2B01G626200	chr2B	100.000	2640	0	0	1	2640	798600946	798603585	0.000000e+00	4876
1	TraesCS2B01G626200	chr2B	91.527	2691	153	32	1	2640	45595961	45598627	0.000000e+00	3637
2	TraesCS2B01G626200	chr2B	95.854	2002	59	8	651	2640	154584885	154582896	0.000000e+00	3216
3	TraesCS2B01G626200	chr2B	94.336	1589	69	6	651	2224	717652702	717654284	0.000000e+00	2416
4	TraesCS2B01G626200	chr2B	92.905	1635	73	15	660	2279	153865762	153867368	0.000000e+00	2337
5	TraesCS2B01G626200	chr2B	90.191	1254	79	30	608	1825	579908715	579909960	0.000000e+00	1594
6	TraesCS2B01G626200	chr2B	92.265	724	44	7	1917	2640	364336139	364335428	0.000000e+00	1016
7	TraesCS2B01G626200	chr2B	91.941	546	29	10	2096	2640	770083417	770082886	0.000000e+00	750
8	TraesCS2B01G626200	chr2B	90.816	490	36	3	1742	2223	138733566	138734054	0.000000e+00	647
9	TraesCS2B01G626200	chr2B	87.705	488	48	9	1738	2224	563915374	563914898	2.300000e-155	558
10	TraesCS2B01G626200	chr2B	95.469	309	12	2	1917	2224	364336021	364335714	2.360000e-135	492
11	TraesCS2B01G626200	chr2B	89.920	377	30	4	1738	2106	42195162	42195538	1.840000e-131	479
12	TraesCS2B01G626200	chr2B	90.000	210	13	2	1744	1945	29752781	29752572	5.600000e-67	265
13	TraesCS2B01G626200	chr7B	96.742	2640	60	3	1	2640	707572956	707570343	0.000000e+00	4375
14	TraesCS2B01G626200	chr7B	94.661	2004	77	7	647	2640	707617239	707619222	0.000000e+00	3081
15	TraesCS2B01G626200	chr7B	93.052	1756	114	3	1	1750	34282311	34280558	0.000000e+00	2560
16	TraesCS2B01G626200	chr7B	93.600	625	23	5	2028	2640	577213230	577213849	0.000000e+00	917
17	TraesCS2B01G626200	chr3B	93.037	2183	105	17	1	2142	112909775	112911951	0.000000e+00	3145
18	TraesCS2B01G626200	chr3B	98.122	1704	26	2	1	1704	179362664	179360967	0.000000e+00	2964
19	TraesCS2B01G626200	chr3B	94.838	833	36	4	1	833	16124532	16123707	0.000000e+00	1293
20	TraesCS2B01G626200	chr3B	93.062	836	52	3	1	836	16203548	16202719	0.000000e+00	1218
21	TraesCS2B01G626200	chr3B	94.868	604	15	4	2049	2640	179360966	179360367	0.000000e+00	929
22	TraesCS2B01G626200	chr3A	96.868	1756	49	1	1	1750	44774229	44772474	0.000000e+00	2933
23	TraesCS2B01G626200	chr2A	93.394	1756	108	2	1	1750	372742759	372744512	0.000000e+00	2593
24	TraesCS2B01G626200	chr2A	92.613	731	38	10	1911	2640	728935618	728936333	0.000000e+00	1037
25	TraesCS2B01G626200	chr5D	91.840	1875	117	16	1	1847	387840686	387838820	0.000000e+00	2582
26	TraesCS2B01G626200	chr5A	92.339	731	42	9	1911	2640	300956869	300957586	0.000000e+00	1027
27	TraesCS2B01G626200	chr1B	92.105	646	39	7	1995	2640	302770445	302769812	0.000000e+00	900

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	TraesCS2B01G626200	chr2B	798600946	798603585	2639	False	4876.0	4876	100.000	1	2640	1	chr2B.!!$F7	2639
1	TraesCS2B01G626200	chr2B	45595961	45598627	2666	False	3637.0	3637	91.527	1	2640	1	chr2B.!!$F2	2639
2	TraesCS2B01G626200	chr2B	154582896	154584885	1989	True	3216.0	3216	95.854	651	2640	1	chr2B.!!$R2	1989
3	TraesCS2B01G626200	chr2B	717652702	717654284	1582	False	2416.0	2416	94.336	651	2224	1	chr2B.!!$F6	1573
4	TraesCS2B01G626200	chr2B	153865762	153867368	1606	False	2337.0	2337	92.905	660	2279	1	chr2B.!!$F4	1619
5	TraesCS2B01G626200	chr2B	579908715	579909960	1245	False	1594.0	1594	90.191	608	1825	1	chr2B.!!$F5	1217
6	TraesCS2B01G626200	chr2B	364335428	364336139	711	True	754.0	1016	93.867	1917	2640	2	chr2B.!!$R5	723
7	TraesCS2B01G626200	chr2B	770082886	770083417	531	True	750.0	750	91.941	2096	2640	1	chr2B.!!$R4	544
8	TraesCS2B01G626200	chr7B	707570343	707572956	2613	True	4375.0	4375	96.742	1	2640	1	chr7B.!!$R2	2639
9	TraesCS2B01G626200	chr7B	707617239	707619222	1983	False	3081.0	3081	94.661	647	2640	1	chr7B.!!$F2	1993
10	TraesCS2B01G626200	chr7B	34280558	34282311	1753	True	2560.0	2560	93.052	1	1750	1	chr7B.!!$R1	1749
11	TraesCS2B01G626200	chr7B	577213230	577213849	619	False	917.0	917	93.600	2028	2640	1	chr7B.!!$F1	612
12	TraesCS2B01G626200	chr3B	112909775	112911951	2176	False	3145.0	3145	93.037	1	2142	1	chr3B.!!$F1	2141
13	TraesCS2B01G626200	chr3B	179360367	179362664	2297	True	1946.5	2964	96.495	1	2640	2	chr3B.!!$R3	2639
14	TraesCS2B01G626200	chr3B	16123707	16124532	825	True	1293.0	1293	94.838	1	833	1	chr3B.!!$R1	832
15	TraesCS2B01G626200	chr3B	16202719	16203548	829	True	1218.0	1218	93.062	1	836	1	chr3B.!!$R2	835
16	TraesCS2B01G626200	chr3A	44772474	44774229	1755	True	2933.0	2933	96.868	1	1750	1	chr3A.!!$R1	1749
17	TraesCS2B01G626200	chr2A	372742759	372744512	1753	False	2593.0	2593	93.394	1	1750	1	chr2A.!!$F1	1749
18	TraesCS2B01G626200	chr2A	728935618	728936333	715	False	1037.0	1037	92.613	1911	2640	1	chr2A.!!$F2	729
19	TraesCS2B01G626200	chr5D	387838820	387840686	1866	True	2582.0	2582	91.840	1	1847	1	chr5D.!!$R1	1846
20	TraesCS2B01G626200	chr5A	300956869	300957586	717	False	1027.0	1027	92.339	1911	2640	1	chr5A.!!$F1	729
21	TraesCS2B01G626200	chr1B	302769812	302770445	633	True	900.0	900	92.105	1995	2640	1	chr1B.!!$R1	645

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
28	29	0.106708	AGCAAGCAAGTCTTCACGGA	59.893	50.0	0.0	0.0	31.27	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1987	2158	1.44854	GCGTCTGGGTGTCCATCAG	60.449	63.158	0.0	0.0	43.11	2.9	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
28	29	0.106708	AGCAAGCAAGTCTTCACGGA	59.893	50.000	0.00	0.00	31.27	4.69
29	30	0.514691	GCAAGCAAGTCTTCACGGAG	59.485	55.000	0.00	0.00	31.27	4.63
45	46	8.258007	TCTTCACGGAGACAAGTTATCATATTT	58.742	33.333	0.00	0.00	0.00	1.40
293	294	3.116096	AGCTACTAGGTTGACATGGGA	57.884	47.619	0.00	0.00	0.00	4.37
382	383	0.908198	CCCTCTTCTGAAGGTGGAGG	59.092	60.000	22.66	18.44	42.10	4.30
650	651	0.389166	GGAAGCACGAGTGTCAGAGG	60.389	60.000	5.07	0.00	0.00	3.69
1075	1193	2.113243	GAAGACGTGGTTGGAGGCCT	62.113	60.000	3.86	3.86	0.00	5.19
1723	1842	7.048512	ACTTATTATTAGAGACCTTGTGTGGC	58.951	38.462	0.00	0.00	0.00	5.01
1976	2147	3.314331	AGGTGACCAGACAGGCCG	61.314	66.667	3.63	0.00	43.14	6.13
1977	2148	3.626924	GGTGACCAGACAGGCCGT	61.627	66.667	0.00	0.00	43.14	5.68
1978	2149	2.048127	GTGACCAGACAGGCCGTC	60.048	66.667	16.80	16.80	45.77	4.79
1987	2158	2.357517	CAGGCCGTCTGGTGTGTC	60.358	66.667	0.00	0.00	39.76	3.67
1988	2159	2.524394	AGGCCGTCTGGTGTGTCT	60.524	61.111	0.00	0.00	37.67	3.41
1989	2160	2.357517	GGCCGTCTGGTGTGTCTG	60.358	66.667	0.00	0.00	37.67	3.51
1990	2161	2.734591	GCCGTCTGGTGTGTCTGA	59.265	61.111	0.00	0.00	37.67	3.27
1991	2162	1.293498	GCCGTCTGGTGTGTCTGAT	59.707	57.895	0.00	0.00	37.67	2.90
1992	2163	1.016130	GCCGTCTGGTGTGTCTGATG	61.016	60.000	0.00	0.00	37.67	3.07
1993	2164	0.390340	CCGTCTGGTGTGTCTGATGG	60.390	60.000	0.00	0.00	36.12	3.51
1994	2165	0.603065	CGTCTGGTGTGTCTGATGGA	59.397	55.000	0.00	0.00	0.00	3.41
1995	2166	1.670087	CGTCTGGTGTGTCTGATGGAC	60.670	57.143	0.00	0.00	44.70	4.02
2008	2179	3.164977	TGGACACCCAGACGCCAA	61.165	61.111	0.00	0.00	37.58	4.52
2009	2180	2.358737	GGACACCCAGACGCCAAG	60.359	66.667	0.00	0.00	0.00	3.61
2010	2181	2.358737	GACACCCAGACGCCAAGG	60.359	66.667	0.00	0.00	0.00	3.61
2011	2182	3.168528	ACACCCAGACGCCAAGGT	61.169	61.111	0.00	0.00	0.00	3.50
2012	2183	2.669569	CACCCAGACGCCAAGGTG	60.670	66.667	0.00	0.00	43.50	4.00
2013	2184	4.643387	ACCCAGACGCCAAGGTGC	62.643	66.667	0.00	0.00	0.00	5.01
2022	2193	4.988598	CCAAGGTGCGTGGCGTCT	62.989	66.667	0.00	0.00	0.00	4.18
2023	2194	3.716006	CAAGGTGCGTGGCGTCTG	61.716	66.667	0.00	0.00	0.00	3.51
2035	2206	4.394712	CGTCTGCCTCCCACACCC	62.395	72.222	0.00	0.00	0.00	4.61
2036	2207	3.249189	GTCTGCCTCCCACACCCA	61.249	66.667	0.00	0.00	0.00	4.51
2037	2208	2.930019	TCTGCCTCCCACACCCAG	60.930	66.667	0.00	0.00	0.00	4.45
2038	2209	2.930019	CTGCCTCCCACACCCAGA	60.930	66.667	0.00	0.00	0.00	3.86
2039	2210	3.249189	TGCCTCCCACACCCAGAC	61.249	66.667	0.00	0.00	0.00	3.51
2040	2211	4.394712	GCCTCCCACACCCAGACG	62.395	72.222	0.00	0.00	0.00	4.18
2041	2212	4.394712	CCTCCCACACCCAGACGC	62.395	72.222	0.00	0.00	0.00	5.19
2042	2213	4.394712	CTCCCACACCCAGACGCC	62.395	72.222	0.00	0.00	0.00	5.68
2044	2215	4.704833	CCCACACCCAGACGCCAG	62.705	72.222	0.00	0.00	0.00	4.85
2045	2216	4.704833	CCACACCCAGACGCCAGG	62.705	72.222	0.00	0.00	0.00	4.45
2046	2217	3.625897	CACACCCAGACGCCAGGA	61.626	66.667	0.00	0.00	0.00	3.86
2047	2218	2.847234	ACACCCAGACGCCAGGAA	60.847	61.111	0.00	0.00	0.00	3.36
2048	2219	2.358737	CACCCAGACGCCAGGAAC	60.359	66.667	0.00	0.00	0.00	3.62
2049	2220	3.637273	ACCCAGACGCCAGGAACC	61.637	66.667	0.00	0.00	0.00	3.62
2050	2221	4.410400	CCCAGACGCCAGGAACCC	62.410	72.222	0.00	0.00	0.00	4.11
2063	2234	3.553095	GAACCCTGGCGTCTGGCTT	62.553	63.158	7.54	0.00	42.94	4.35
2064	2235	3.850098	AACCCTGGCGTCTGGCTTG	62.850	63.158	7.54	0.00	42.94	4.01
2073	2244	1.208614	GTCTGGCTTGCTTTGCTCG	59.791	57.895	0.00	0.00	0.00	5.03
2074	2245	2.126580	CTGGCTTGCTTTGCTCGC	60.127	61.111	0.00	0.00	0.00	5.03
2091	2262	2.734723	CGCAGGTGACCAGACACG	60.735	66.667	3.63	0.00	41.12	4.49
2092	2263	3.044305	GCAGGTGACCAGACACGC	61.044	66.667	3.63	0.00	41.12	5.34
2093	2264	2.357517	CAGGTGACCAGACACGCC	60.358	66.667	3.63	0.00	41.12	5.68
2130	2301	2.669569	CACCCAGACGCCAAGGTG	60.670	66.667	0.00	0.00	43.50	4.00
2234	2490	3.406361	GTGTGTCGCGCAGGTGAG	61.406	66.667	8.75	0.00	32.31	3.51
2248	2549	1.300931	GTGAGCAGACGTGAGCCAA	60.301	57.895	0.00	0.00	0.00	4.52
2384	2967	3.319198	GACGCCAAGGTCCCTGGA	61.319	66.667	11.05	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	65	3.449737	CCACCTGGCTCATCAATTTGATT	59.550	43.478	9.19	0.00	34.28	2.57
293	294	3.532641	AGAAAGGGTGAAATCTTGGCT	57.467	42.857	0.00	0.00	0.00	4.75
382	383	1.826096	AGTTCTCCTTCTACCCTTCGC	59.174	52.381	0.00	0.00	0.00	4.70
650	651	1.471684	CTCTACGACCACCACTACCAC	59.528	57.143	0.00	0.00	0.00	4.16
1075	1193	3.045634	TCTCCTTCTCCTTGTCCAAACA	58.954	45.455	0.00	0.00	0.00	2.83
1723	1842	6.758416	TCTCGAATGACAGAAATAGTTCATGG	59.242	38.462	5.62	0.00	36.09	3.66
1976	2147	2.086054	GTCCATCAGACACACCAGAC	57.914	55.000	0.00	0.00	45.55	3.51
1985	2156	3.842869	GTCTGGGTGTCCATCAGAC	57.157	57.895	13.81	13.81	46.66	3.51
1986	2157	1.888436	GCGTCTGGGTGTCCATCAGA	61.888	60.000	0.00	0.00	43.11	3.27
1987	2158	1.448540	GCGTCTGGGTGTCCATCAG	60.449	63.158	0.00	0.00	43.11	2.90
1988	2159	2.662596	GCGTCTGGGTGTCCATCA	59.337	61.111	0.00	0.00	43.11	3.07
1989	2160	2.125106	GGCGTCTGGGTGTCCATC	60.125	66.667	0.00	0.00	43.11	3.51
1990	2161	2.469465	CTTGGCGTCTGGGTGTCCAT	62.469	60.000	0.00	0.00	43.11	3.41
1991	2162	3.164977	TTGGCGTCTGGGTGTCCA	61.165	61.111	0.00	0.00	41.58	4.02
1992	2163	2.358737	CTTGGCGTCTGGGTGTCC	60.359	66.667	0.00	0.00	0.00	4.02
1993	2164	2.358737	CCTTGGCGTCTGGGTGTC	60.359	66.667	0.00	0.00	0.00	3.67
1994	2165	3.168528	ACCTTGGCGTCTGGGTGT	61.169	61.111	3.86	0.00	0.00	4.16
1995	2166	2.669569	CACCTTGGCGTCTGGGTG	60.670	66.667	15.11	15.11	42.29	4.61
1996	2167	4.643387	GCACCTTGGCGTCTGGGT	62.643	66.667	4.80	1.98	0.00	4.51
2005	2176	4.988598	AGACGCCACGCACCTTGG	62.989	66.667	0.00	0.00	37.17	3.61
2006	2177	3.716006	CAGACGCCACGCACCTTG	61.716	66.667	0.00	0.00	0.00	3.61
2018	2189	4.394712	GGGTGTGGGAGGCAGACG	62.395	72.222	0.00	0.00	0.00	4.18
2019	2190	3.249189	TGGGTGTGGGAGGCAGAC	61.249	66.667	0.00	0.00	0.00	3.51
2020	2191	2.930019	CTGGGTGTGGGAGGCAGA	60.930	66.667	0.00	0.00	0.00	4.26
2021	2192	2.930019	TCTGGGTGTGGGAGGCAG	60.930	66.667	0.00	0.00	0.00	4.85
2022	2193	3.249189	GTCTGGGTGTGGGAGGCA	61.249	66.667	0.00	0.00	0.00	4.75
2023	2194	4.394712	CGTCTGGGTGTGGGAGGC	62.395	72.222	0.00	0.00	0.00	4.70
2024	2195	4.394712	GCGTCTGGGTGTGGGAGG	62.395	72.222	0.00	0.00	0.00	4.30
2025	2196	4.394712	GGCGTCTGGGTGTGGGAG	62.395	72.222	0.00	0.00	0.00	4.30
2027	2198	4.704833	CTGGCGTCTGGGTGTGGG	62.705	72.222	0.00	0.00	0.00	4.61
2028	2199	4.704833	CCTGGCGTCTGGGTGTGG	62.705	72.222	4.79	0.00	0.00	4.17
2029	2200	3.177194	TTCCTGGCGTCTGGGTGTG	62.177	63.158	13.43	0.00	33.38	3.82
2030	2201	2.847234	TTCCTGGCGTCTGGGTGT	60.847	61.111	13.43	0.00	33.38	4.16
2031	2202	2.358737	GTTCCTGGCGTCTGGGTG	60.359	66.667	13.43	0.00	33.38	4.61
2032	2203	3.637273	GGTTCCTGGCGTCTGGGT	61.637	66.667	13.43	0.00	33.38	4.51
2033	2204	4.410400	GGGTTCCTGGCGTCTGGG	62.410	72.222	13.43	3.07	33.38	4.45
2034	2205	3.322466	AGGGTTCCTGGCGTCTGG	61.322	66.667	6.60	6.60	29.57	3.86
2043	2214	3.322466	CCAGACGCCAGGGTTCCT	61.322	66.667	0.00	0.00	0.00	3.36
2045	2216	3.553095	AAGCCAGACGCCAGGGTTC	62.553	63.158	0.00	0.00	41.44	3.62
2046	2217	3.570212	AAGCCAGACGCCAGGGTT	61.570	61.111	0.00	0.00	40.54	4.11
2047	2218	4.335647	CAAGCCAGACGCCAGGGT	62.336	66.667	0.00	0.00	38.78	4.34
2049	2220	4.711949	AGCAAGCCAGACGCCAGG	62.712	66.667	0.00	0.00	38.78	4.45
2050	2221	2.263741	AAAGCAAGCCAGACGCCAG	61.264	57.895	0.00	0.00	38.78	4.85
2073	2244	3.044305	GTGTCTGGTCACCTGCGC	61.044	66.667	0.00	0.00	32.81	6.09
2074	2245	2.734723	CGTGTCTGGTCACCTGCG	60.735	66.667	0.00	0.00	35.18	5.18
2079	2250	2.733593	GACGGCGTGTCTGGTCAC	60.734	66.667	21.19	0.00	44.58	3.67
2091	2262	1.016130	CATCAGACACACCAGACGGC	61.016	60.000	0.00	0.00	34.57	5.68
2092	2263	0.390340	CCATCAGACACACCAGACGG	60.390	60.000	0.00	0.00	38.77	4.79
2093	2264	0.603065	TCCATCAGACACACCAGACG	59.397	55.000	0.00	0.00	0.00	4.18
2234	2490	2.551270	CGTTTGGCTCACGTCTGC	59.449	61.111	1.05	1.05	32.80	4.26
2240	2496	2.130073	GACCTTGGCGTTTGGCTCAC	62.130	60.000	0.00	0.00	42.94	3.51
2241	2497	1.896660	GACCTTGGCGTTTGGCTCA	60.897	57.895	0.00	0.00	42.94	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.