AutoCloner

Multiple sequence alignment - TraesCS6D01G388600

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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	TraesCS6D01G388600	chr6D	100.000	2414	0	0	1	2414	464756821	464759234	0.000000e+00	4458
1	TraesCS6D01G388600	chr6D	94.679	1278	50	3	561	1820	357453539	357452262	0.000000e+00	1967
2	TraesCS6D01G388600	chr6D	94.733	1272	54	3	561	1820	273131113	273132383	0.000000e+00	1965
3	TraesCS6D01G388600	chr1D	94.120	2279	93	9	1	2265	449355515	449357766	0.000000e+00	3428
4	TraesCS6D01G388600	chr1D	93.449	1847	87	12	1	1820	194854493	194852654	0.000000e+00	2710
5	TraesCS6D01G388600	chr1D	94.357	443	25	0	1821	2263	194852603	194852161	0.000000e+00	680
6	TraesCS6D01G388600	chr2D	94.175	2266	99	9	13	2264	517399807	517397561	0.000000e+00	3422
7	TraesCS6D01G388600	chr2D	92.822	1839	87	18	3	1820	400571484	400569670	0.000000e+00	2623
8	TraesCS6D01G388600	chr2D	94.082	1487	69	8	1	1470	600490003	600488519	0.000000e+00	2241
9	TraesCS6D01G388600	chr2D	90.904	1660	119	23	3	1654	409562441	409560806	0.000000e+00	2200
10	TraesCS6D01G388600	chr2D	95.290	1274	46	4	561	1820	260387532	260386259	0.000000e+00	2008
11	TraesCS6D01G388600	chr2D	94.831	445	23	0	1821	2265	422704377	422704821	0.000000e+00	695
12	TraesCS6D01G388600	chr6B	92.807	1835	107	12	3	1820	144742053	144743879	0.000000e+00	2634
13	TraesCS6D01G388600	chr6B	89.246	1711	139	31	3	1694	436047340	436049024	0.000000e+00	2098
14	TraesCS6D01G388600	chr3D	91.351	1665	109	23	1	1654	356669812	356671452	0.000000e+00	2244
15	TraesCS6D01G388600	chr3D	94.890	1272	53	3	561	1820	397849936	397851207	0.000000e+00	1978
16	TraesCS6D01G388600	chr3D	94.753	1277	47	4	561	1820	541034352	541033079	0.000000e+00	1969
17	TraesCS6D01G388600	chr3D	92.600	473	33	2	1805	2276	349442923	349442452	0.000000e+00	678
18	TraesCS6D01G388600	chr5D	90.409	1710	122	29	1	1691	434733250	434734936	0.000000e+00	2211
19	TraesCS6D01G388600	chr5D	94.271	803	37	4	1475	2269	101945670	101946471	0.000000e+00	1219
20	TraesCS6D01G388600	chr5D	93.626	455	28	1	1812	2265	405358531	405358985	0.000000e+00	678
21	TraesCS6D01G388600	chr5D	91.915	470	30	7	1805	2268	192524331	192523864	0.000000e+00	651
22	TraesCS6D01G388600	chr4D	91.019	1659	115	25	2	1654	14237809	14239439	0.000000e+00	2207
23	TraesCS6D01G388600	chr4D	90.674	1662	118	31	3	1654	63531839	63533473	0.000000e+00	2176
24	TraesCS6D01G388600	chr4D	94.749	1276	48	6	561	1820	65498831	65497559	0.000000e+00	1967
25	TraesCS6D01G388600	chr4D	94.101	712	34	1	1554	2265	359752933	359753636	0.000000e+00	1075
26	TraesCS6D01G388600	chr4D	95.023	442	22	0	1821	2262	65497508	65497067	0.000000e+00	695
27	TraesCS6D01G388600	chr1A	91.416	466	38	2	1805	2269	100547471	100547935	2.620000e-179	638
28	TraesCS6D01G388600	chr7D	90.889	461	36	5	1805	2262	215219486	215219943	4.410000e-172	614
29	TraesCS6D01G388600	chr5A	90.043	462	40	4	1805	2265	596228445	596228901	5.750000e-166	593

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	TraesCS6D01G388600	chr6D	464756821	464759234	2413	False	4458	4458	100.000	1	2414	1	chr6D.!!$F2	2413
1	TraesCS6D01G388600	chr6D	357452262	357453539	1277	True	1967	1967	94.679	561	1820	1	chr6D.!!$R1	1259
2	TraesCS6D01G388600	chr6D	273131113	273132383	1270	False	1965	1965	94.733	561	1820	1	chr6D.!!$F1	1259
3	TraesCS6D01G388600	chr1D	449355515	449357766	2251	False	3428	3428	94.120	1	2265	1	chr1D.!!$F1	2264
4	TraesCS6D01G388600	chr1D	194852161	194854493	2332	True	1695	2710	93.903	1	2263	2	chr1D.!!$R1	2262
5	TraesCS6D01G388600	chr2D	517397561	517399807	2246	True	3422	3422	94.175	13	2264	1	chr2D.!!$R4	2251
6	TraesCS6D01G388600	chr2D	400569670	400571484	1814	True	2623	2623	92.822	3	1820	1	chr2D.!!$R2	1817
7	TraesCS6D01G388600	chr2D	600488519	600490003	1484	True	2241	2241	94.082	1	1470	1	chr2D.!!$R5	1469
8	TraesCS6D01G388600	chr2D	409560806	409562441	1635	True	2200	2200	90.904	3	1654	1	chr2D.!!$R3	1651
9	TraesCS6D01G388600	chr2D	260386259	260387532	1273	True	2008	2008	95.290	561	1820	1	chr2D.!!$R1	1259
10	TraesCS6D01G388600	chr6B	144742053	144743879	1826	False	2634	2634	92.807	3	1820	1	chr6B.!!$F1	1817
11	TraesCS6D01G388600	chr6B	436047340	436049024	1684	False	2098	2098	89.246	3	1694	1	chr6B.!!$F2	1691
12	TraesCS6D01G388600	chr3D	356669812	356671452	1640	False	2244	2244	91.351	1	1654	1	chr3D.!!$F1	1653
13	TraesCS6D01G388600	chr3D	397849936	397851207	1271	False	1978	1978	94.890	561	1820	1	chr3D.!!$F2	1259
14	TraesCS6D01G388600	chr3D	541033079	541034352	1273	True	1969	1969	94.753	561	1820	1	chr3D.!!$R2	1259
15	TraesCS6D01G388600	chr5D	434733250	434734936	1686	False	2211	2211	90.409	1	1691	1	chr5D.!!$F3	1690
16	TraesCS6D01G388600	chr5D	101945670	101946471	801	False	1219	1219	94.271	1475	2269	1	chr5D.!!$F1	794
17	TraesCS6D01G388600	chr4D	14237809	14239439	1630	False	2207	2207	91.019	2	1654	1	chr4D.!!$F1	1652
18	TraesCS6D01G388600	chr4D	63531839	63533473	1634	False	2176	2176	90.674	3	1654	1	chr4D.!!$F2	1651
19	TraesCS6D01G388600	chr4D	65497067	65498831	1764	True	1331	1967	94.886	561	2262	2	chr4D.!!$R1	1701
20	TraesCS6D01G388600	chr4D	359752933	359753636	703	False	1075	1075	94.101	1554	2265	1	chr4D.!!$F3	711

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
449	461	0.036164	CCCACCACTGATTCCGTGAA	59.964	55.0	9.52	0.0	34.35	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2121	2238	0.673644	CGTCGGGTCCTTGCTTTGAT	60.674	55.0	0.0	0.0	0.0	2.57	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
188	197	1.143073	AGTGAAAGCCTTCGAAACCCT	59.857	47.619	0.00	0.00	33.94	4.34
449	461	0.036164	CCCACCACTGATTCCGTGAA	59.964	55.000	9.52	0.00	34.35	3.18
631	659	6.841443	TTTGCATCGTTTGAAATCAATTGT	57.159	29.167	5.13	0.00	35.55	2.71
759	790	3.998672	ACGGATTCCCACGCGTGT	61.999	61.111	34.81	18.94	0.00	4.49
836	867	1.374560	CCGATGTTGCGATGGGTTTA	58.625	50.000	0.00	0.00	0.00	2.01
893	935	1.162698	CGGCTAGCACTACGGCTATA	58.837	55.000	18.24	0.00	44.78	1.31
1292	1336	2.419739	GCCGGGTGTTTTGGTGTGT	61.420	57.895	2.18	0.00	0.00	3.72
1333	1377	1.304254	CACCCACAACATGTTCACGA	58.696	50.000	8.48	0.00	0.00	4.35
1387	1431	1.214589	CACACTCTTCCGTACCCCG	59.785	63.158	0.00	0.00	0.00	5.73
1442	1490	0.560688	GGAGGAGGAGAGAGGTGGAT	59.439	60.000	0.00	0.00	0.00	3.41
1533	1593	5.061853	CCCATTGAACTATGTGAGAGATGG	58.938	45.833	0.00	0.00	0.00	3.51
1546	1606	3.266772	TGAGAGATGGTATGGGCTTGTTT	59.733	43.478	0.00	0.00	0.00	2.83
1695	1762	4.822026	AGAGTGCTCGCTTTGTTAGTAAT	58.178	39.130	0.00	0.00	34.09	1.89
1843	1960	3.753294	AAATCGAGGAGACAAGTGTGT	57.247	42.857	0.00	0.00	42.10	3.72
1929	2046	0.740868	CTCGGTCAATGCATCGTGGT	60.741	55.000	0.00	0.00	0.00	4.16
2007	2124	1.152902	GGGTGCATGCATAGCAGGA	60.153	57.895	25.64	0.00	43.36	3.86
2130	2247	4.149922	CGTCAGAGTTAACGATCAAAGCAA	59.850	41.667	0.00	0.00	41.29	3.91
2131	2248	5.612865	GTCAGAGTTAACGATCAAAGCAAG	58.387	41.667	0.00	0.00	0.00	4.01
2141	2258	1.301401	CAAAGCAAGGACCCGACGA	60.301	57.895	0.00	0.00	0.00	4.20
2194	2318	0.252239	GGCAAGGGAGTGGGGAAAAT	60.252	55.000	0.00	0.00	0.00	1.82
2226	2350	1.987807	AAGAGCGTGGGGATGGATGG	61.988	60.000	0.00	0.00	0.00	3.51
2248	2372	0.417841	AGAGCTAAGGAACCAGGGGA	59.582	55.000	0.00	0.00	0.00	4.81
2265	2389	5.264395	CAGGGGAACAGATGTAAAAATCCT	58.736	41.667	1.76	0.00	0.00	3.24
2267	2391	6.889722	CAGGGGAACAGATGTAAAAATCCTTA	59.110	38.462	1.76	0.00	0.00	2.69
2270	2394	8.758829	GGGGAACAGATGTAAAAATCCTTAAAT	58.241	33.333	1.76	0.00	0.00	1.40
2298	2422	9.772973	ATATAGCAATAAATCGAACCAAGTACA	57.227	29.630	0.00	0.00	0.00	2.90
2299	2423	6.422776	AGCAATAAATCGAACCAAGTACAG	57.577	37.500	0.00	0.00	0.00	2.74
2300	2424	6.170506	AGCAATAAATCGAACCAAGTACAGA	58.829	36.000	0.00	0.00	0.00	3.41
2301	2425	6.653320	AGCAATAAATCGAACCAAGTACAGAA	59.347	34.615	0.00	0.00	0.00	3.02
2302	2426	7.174253	AGCAATAAATCGAACCAAGTACAGAAA	59.826	33.333	0.00	0.00	0.00	2.52
2303	2427	7.806014	GCAATAAATCGAACCAAGTACAGAAAA	59.194	33.333	0.00	0.00	0.00	2.29
2304	2428	9.840427	CAATAAATCGAACCAAGTACAGAAAAT	57.160	29.630	0.00	0.00	0.00	1.82
2307	2431	8.617290	AAATCGAACCAAGTACAGAAAATAGT	57.383	30.769	0.00	0.00	0.00	2.12
2308	2432	8.617290	AATCGAACCAAGTACAGAAAATAGTT	57.383	30.769	0.00	0.00	0.00	2.24
2309	2433	8.617290	ATCGAACCAAGTACAGAAAATAGTTT	57.383	30.769	0.00	0.00	0.00	2.66
2310	2434	8.441312	TCGAACCAAGTACAGAAAATAGTTTT	57.559	30.769	0.00	0.00	35.12	2.43
2311	2435	8.339714	TCGAACCAAGTACAGAAAATAGTTTTG	58.660	33.333	0.00	0.00	31.94	2.44
2312	2436	8.126700	CGAACCAAGTACAGAAAATAGTTTTGT	58.873	33.333	0.00	8.00	31.94	2.83
2315	2439	9.623000	ACCAAGTACAGAAAATAGTTTTGTACT	57.377	29.630	22.99	22.99	43.67	2.73
2363	2487	8.715191	ACATGTTACAAAAATTGTTGTCATGT	57.285	26.923	27.43	27.43	42.22	3.21
2364	2488	9.809096	ACATGTTACAAAAATTGTTGTCATGTA	57.191	25.926	29.65	10.56	44.92	2.29
2371	2495	8.991026	ACAAAAATTGTTGTCATGTAATCATGG	58.009	29.630	8.26	0.00	44.87	3.66
2380	2504	4.577834	CATGTAATCATGGATGCAGCAA	57.422	40.909	3.51	0.00	45.30	3.91
2381	2505	4.939271	CATGTAATCATGGATGCAGCAAA	58.061	39.130	3.51	0.00	45.30	3.68
2382	2506	5.353111	CATGTAATCATGGATGCAGCAAAA	58.647	37.500	3.51	0.00	45.30	2.44
2383	2507	5.402997	TGTAATCATGGATGCAGCAAAAA	57.597	34.783	3.51	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	12	5.585390	GAGGTCAAATGAGCACCATTAATG	58.415	41.667	14.36	8.58	44.28	1.90
171	180	1.605753	ACAGGGTTTCGAAGGCTTTC	58.394	50.000	0.00	0.00	0.00	2.62
188	197	1.398692	GGGTTTTGAGCTGGTCAACA	58.601	50.000	20.72	12.66	45.23	3.33
285	294	0.341258	AGAAGGCCAGATCTGAGGGA	59.659	55.000	24.62	0.00	0.00	4.20
321	330	1.524002	GAGCCTGCACATAGCCAGA	59.476	57.895	0.00	0.00	44.83	3.86
631	659	5.895636	ATTGGTCATTTTCTACGCAATGA	57.104	34.783	0.00	0.00	37.12	2.57
815	846	3.585990	CCCATCGCAACATCGGGC	61.586	66.667	0.00	0.00	0.00	6.13
828	859	5.597594	TGAAGTAACCCGTTTTTAAACCCAT	59.402	36.000	0.10	0.00	35.51	4.00
836	867	6.037726	GTCAAATGTGAAGTAACCCGTTTTT	58.962	36.000	0.00	0.00	34.87	1.94
1333	1377	2.714250	TGGGGAAGATGTTGGTGTACTT	59.286	45.455	0.00	0.00	0.00	2.24
1442	1490	1.669999	GAACCCTAGACGCCGCCTTA	61.670	60.000	0.00	0.00	0.00	2.69
1677	1744	3.682858	GGTGATTACTAACAAAGCGAGCA	59.317	43.478	0.00	0.00	0.00	4.26
1695	1762	1.078214	GGCTGCATGCACTAGGTGA	60.078	57.895	18.46	0.00	45.15	4.02
1806	1873	5.180271	TCGATTTAGAACCCGTTTTGCTAT	58.820	37.500	0.00	0.00	0.00	2.97
1843	1960	0.891373	CGCTGGTTCCTCTCTTCTCA	59.109	55.000	0.00	0.00	0.00	3.27
2031	2148	1.161843	CCGTCCCTTGCATTAAACGT	58.838	50.000	10.12	0.00	0.00	3.99
2121	2238	0.673644	CGTCGGGTCCTTGCTTTGAT	60.674	55.000	0.00	0.00	0.00	2.57
2174	2291	1.368268	TTTTCCCCACTCCCTTGCCT	61.368	55.000	0.00	0.00	0.00	4.75
2194	2318	3.003275	CCACGCTCTTAACTTTTGCTCAA	59.997	43.478	0.00	0.00	0.00	3.02
2226	2350	1.763545	CCCTGGTTCCTTAGCTCTACC	59.236	57.143	0.00	0.00	0.00	3.18
2272	2396	9.772973	TGTACTTGGTTCGATTTATTGCTATAT	57.227	29.630	0.00	0.00	0.00	0.86
2273	2397	9.256477	CTGTACTTGGTTCGATTTATTGCTATA	57.744	33.333	0.00	0.00	0.00	1.31
2274	2398	7.985184	TCTGTACTTGGTTCGATTTATTGCTAT	59.015	33.333	0.00	0.00	0.00	2.97
2275	2399	7.324935	TCTGTACTTGGTTCGATTTATTGCTA	58.675	34.615	0.00	0.00	0.00	3.49
2276	2400	6.170506	TCTGTACTTGGTTCGATTTATTGCT	58.829	36.000	0.00	0.00	0.00	3.91
2277	2401	6.417191	TCTGTACTTGGTTCGATTTATTGC	57.583	37.500	0.00	0.00	0.00	3.56
2278	2402	9.840427	ATTTTCTGTACTTGGTTCGATTTATTG	57.160	29.630	0.00	0.00	0.00	1.90
2281	2405	9.715121	ACTATTTTCTGTACTTGGTTCGATTTA	57.285	29.630	0.00	0.00	0.00	1.40
2282	2406	8.617290	ACTATTTTCTGTACTTGGTTCGATTT	57.383	30.769	0.00	0.00	0.00	2.17
2283	2407	8.617290	AACTATTTTCTGTACTTGGTTCGATT	57.383	30.769	0.00	0.00	0.00	3.34
2284	2408	8.617290	AAACTATTTTCTGTACTTGGTTCGAT	57.383	30.769	0.00	0.00	0.00	3.59
2285	2409	8.339714	CAAAACTATTTTCTGTACTTGGTTCGA	58.660	33.333	0.00	0.00	0.00	3.71
2286	2410	8.126700	ACAAAACTATTTTCTGTACTTGGTTCG	58.873	33.333	0.00	0.00	0.00	3.95
2289	2413	9.623000	AGTACAAAACTATTTTCTGTACTTGGT	57.377	29.630	17.62	6.39	41.10	3.67
2337	2461	9.809096	ACATGACAACAATTTTTGTAACATGTA	57.191	25.926	26.94	7.39	46.50	2.29
2338	2462	8.715191	ACATGACAACAATTTTTGTAACATGT	57.285	26.923	24.75	24.75	45.32	3.21
2360	2484	5.601583	TTTTGCTGCATCCATGATTACAT	57.398	34.783	1.84	0.00	37.19	2.29
2361	2485	5.402997	TTTTTGCTGCATCCATGATTACA	57.597	34.783	1.84	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.