AutoCloner

Multiple sequence alignment - TraesCS2D01G363100

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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	TraesCS2D01G363100	chr2D	100.000	2394	0	0	1	2394	468952960	468950567	0.000000e+00	4421
1	TraesCS2D01G363100	chr2D	90.000	340	14	15	1482	1801	617219950	617220289	2.850000e-114	422
2	TraesCS2D01G363100	chr1D	96.262	1819	50	11	1	1803	77843251	77841435	0.000000e+00	2966
3	TraesCS2D01G363100	chr1D	91.389	360	17	4	1457	1802	474300635	474300994	4.630000e-132	481
4	TraesCS2D01G363100	chr7D	95.262	1815	68	13	1	1800	13888666	13886855	0.000000e+00	2859
5	TraesCS2D01G363100	chr7D	94.989	1816	76	10	1	1802	48270008	48268194	0.000000e+00	2835
6	TraesCS2D01G363100	chr6D	94.176	1803	85	11	1	1802	19503052	19501269	0.000000e+00	2730
7	TraesCS2D01G363100	chr7A	91.004	1823	142	14	1	1806	34345438	34343621	0.000000e+00	2438
8	TraesCS2D01G363100	chr2B	90.575	1825	145	21	1	1804	396930983	396929165	0.000000e+00	2392
9	TraesCS2D01G363100	chr2B	94.639	429	17	5	1970	2394	547430818	547430392	0.000000e+00	660
10	TraesCS2D01G363100	chr2B	99.383	162	0	1	1803	1963	547431152	547430991	2.330000e-75	292
11	TraesCS2D01G363100	chr3A	94.352	1558	79	5	1	1550	467894070	467895626	0.000000e+00	2381
12	TraesCS2D01G363100	chr5A	90.461	1824	146	20	1	1803	527780384	527778568	0.000000e+00	2379
13	TraesCS2D01G363100	chr6A	89.454	1830	161	23	1	1803	606067633	606069457	0.000000e+00	2281
14	TraesCS2D01G363100	chr5D	94.645	915	33	8	901	1801	515272270	515271358	0.000000e+00	1404
15	TraesCS2D01G363100	chr4B	89.265	1034	87	16	787	1801	481520310	481521338	0.000000e+00	1273
16	TraesCS2D01G363100	chrUn	88.382	482	37	12	1338	1803	228437625	228437147	1.610000e-156	562

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	TraesCS2D01G363100	chr2D	468950567	468952960	2393	True	4421	4421	100.000	1	2394	1	chr2D.!!$R1	2393
1	TraesCS2D01G363100	chr1D	77841435	77843251	1816	True	2966	2966	96.262	1	1803	1	chr1D.!!$R1	1802
2	TraesCS2D01G363100	chr7D	13886855	13888666	1811	True	2859	2859	95.262	1	1800	1	chr7D.!!$R1	1799
3	TraesCS2D01G363100	chr7D	48268194	48270008	1814	True	2835	2835	94.989	1	1802	1	chr7D.!!$R2	1801
4	TraesCS2D01G363100	chr6D	19501269	19503052	1783	True	2730	2730	94.176	1	1802	1	chr6D.!!$R1	1801
5	TraesCS2D01G363100	chr7A	34343621	34345438	1817	True	2438	2438	91.004	1	1806	1	chr7A.!!$R1	1805
6	TraesCS2D01G363100	chr2B	396929165	396930983	1818	True	2392	2392	90.575	1	1804	1	chr2B.!!$R1	1803
7	TraesCS2D01G363100	chr2B	547430392	547431152	760	True	476	660	97.011	1803	2394	2	chr2B.!!$R2	591
8	TraesCS2D01G363100	chr3A	467894070	467895626	1556	False	2381	2381	94.352	1	1550	1	chr3A.!!$F1	1549
9	TraesCS2D01G363100	chr5A	527778568	527780384	1816	True	2379	2379	90.461	1	1803	1	chr5A.!!$R1	1802
10	TraesCS2D01G363100	chr6A	606067633	606069457	1824	False	2281	2281	89.454	1	1803	1	chr6A.!!$F1	1802
11	TraesCS2D01G363100	chr5D	515271358	515272270	912	True	1404	1404	94.645	901	1801	1	chr5D.!!$R1	900
12	TraesCS2D01G363100	chr4B	481520310	481521338	1028	False	1273	1273	89.265	787	1801	1	chr4B.!!$F1	1014

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
456	468	1.205064	CAAAGCAAGTGACTCGCCG	59.795	57.895	0.0	0.0	0.0	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2224	2438	0.171455	TTGTTGCCCACGTGAACAAC	59.829	50.0	30.56	30.56	42.1	3.32	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
214	220	5.584551	AGTGGGACAAACCTAGAAGAAAT	57.415	39.130	0.00	0.00	44.16	2.17
271	282	2.060050	TATGGTTAAATGGGGCCGTG	57.940	50.000	0.00	0.00	0.00	4.94
277	288	2.756207	GTTAAATGGGGCCGTGTATGTT	59.244	45.455	0.00	0.00	0.00	2.71
324	335	5.358725	GGGTGTTAAAGACTTGAGGAAACAA	59.641	40.000	0.00	0.00	0.00	2.83
425	437	6.937436	ATACTTCAAGAAAACTTCGGTTGT	57.063	33.333	0.00	0.00	38.30	3.32
456	468	1.205064	CAAAGCAAGTGACTCGCCG	59.795	57.895	0.00	0.00	0.00	6.46
628	640	7.254227	TGTATTGACCAAAACTGTACTGTTC	57.746	36.000	17.22	6.59	0.00	3.18
666	678	9.029368	TGTCTTGATCAGATCTCTTCTTTTAGA	57.971	33.333	11.83	0.00	32.60	2.10
862	874	6.811634	TTAAATGGATCTGGGATGCAAAAT	57.188	33.333	5.88	0.00	0.00	1.82
1070	1082	1.542492	CTTGGAACTGATTGCTGCCT	58.458	50.000	0.00	0.00	0.00	4.75
1158	1170	2.549992	CCGTTGGCTTGGCTGCTATATA	60.550	50.000	0.00	0.00	0.00	0.86
1333	1346	4.712476	AGATGCTGAAAGAGAACACAACT	58.288	39.130	0.00	0.00	34.07	3.16
1383	1397	1.214589	CAACTAGGGACGGACGTGG	59.785	63.158	0.53	0.00	0.00	4.94
1398	1412	0.324943	CGTGGTGGGAACTGAGGAAT	59.675	55.000	0.00	0.00	0.00	3.01
1435	1449	3.686726	CCTGATCAGTAAGTTTCTGGTGC	59.313	47.826	21.11	1.29	34.15	5.01
1447	1465	0.036732	TCTGGTGCTTTGGCGAAGAT	59.963	50.000	18.76	0.00	42.25	2.40
1461	1479	0.249238	GAAGATGAGCCGTCGATGCT	60.249	55.000	11.67	11.67	43.03	3.79
1480	1499	1.816863	TTCCTGGAGTCTCGTGTGCC	61.817	60.000	0.00	0.00	0.00	5.01
1512	1536	2.650322	GTGGTGTTCTTTGGTCCTTGA	58.350	47.619	0.00	0.00	0.00	3.02
1518	1542	3.117701	TGTTCTTTGGTCCTTGATGTGGA	60.118	43.478	0.00	0.00	0.00	4.02
1613	1659	0.457337	GTAGGTGTTCGTAGTGCGGG	60.457	60.000	0.00	0.00	41.72	6.13
1702	1748	2.112297	GGTGTTGCCCCGAACTCA	59.888	61.111	0.00	0.00	0.00	3.41
1966	2014	2.309764	GATGGAACCATCGCACACGC	62.310	60.000	16.46	0.00	42.55	5.34
1968	2016	2.476051	GAACCATCGCACACGCTG	59.524	61.111	0.00	0.00	39.84	5.18
1977	2025	3.964718	CACACGCTGGTGCATGTA	58.035	55.556	0.00	0.00	44.21	2.29
1978	2026	1.789751	CACACGCTGGTGCATGTAG	59.210	57.895	0.00	0.00	44.21	2.74
1979	2027	0.670239	CACACGCTGGTGCATGTAGA	60.670	55.000	0.00	0.00	44.21	2.59
2114	2328	1.269673	CCGATCTCGTCTCGTCTAGGA	60.270	57.143	0.00	0.00	37.74	2.94
2164	2378	6.201044	CAGATCGTGGATACCTGTGTATTTTC	59.799	42.308	0.00	0.00	37.80	2.29
2175	2389	1.676006	GTGTATTTTCCCGCTCCATGG	59.324	52.381	4.97	4.97	0.00	3.66
2205	2419	2.443952	ATCGATCGGGAGCCACCA	60.444	61.111	16.41	0.00	41.20	4.17
2215	2429	3.077556	AGCCACCAGTCGCTAGGG	61.078	66.667	0.00	0.00	32.26	3.53
2216	2430	4.162690	GCCACCAGTCGCTAGGGG	62.163	72.222	6.99	0.00	0.00	4.79
2224	2438	1.810030	GTCGCTAGGGGCACTTTCG	60.810	63.158	6.51	0.00	41.91	3.46
2243	2457	0.171455	GTTGTTCACGTGGGCAACAA	59.829	50.000	31.55	27.63	40.40	2.83
2253	2467	2.359900	GTGGGCAACAAGAGATCGATT	58.640	47.619	0.00	0.00	39.74	3.34
2257	2471	2.632377	GCAACAAGAGATCGATTGGGA	58.368	47.619	14.80	0.00	0.00	4.37
2281	2497	1.959226	TTTCGTGAGCCAGCGGAAC	60.959	57.895	0.00	0.00	0.00	3.62
2326	2544	5.278758	CGGAGGGTTTTTGCTTGAAATTCTA	60.279	40.000	0.00	0.00	0.00	2.10
2341	2559	1.581923	TTCTAGAGCCCTCGTCCCCT	61.582	60.000	0.00	0.00	34.09	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
265	276	1.745232	TTGGATCAACATACACGGCC	58.255	50.000	0.00	0.00	0.00	6.13
271	282	6.398095	CCCCTTTCTTTTTGGATCAACATAC	58.602	40.000	0.00	0.00	0.00	2.39
277	288	3.628832	ACCCCCTTTCTTTTTGGATCA	57.371	42.857	0.00	0.00	0.00	2.92
408	420	3.857093	CCACAACAACCGAAGTTTTCTTG	59.143	43.478	0.00	0.00	40.61	3.02
444	456	2.356313	CAGCACGGCGAGTCACTT	60.356	61.111	16.62	0.00	0.00	3.16
456	468	4.276926	ACTTTCAGAAGTGATTTCCAGCAC	59.723	41.667	0.00	0.00	44.27	4.40
555	567	7.928873	TGTCTTTAAAAGGGATTCTACCATCT	58.071	34.615	0.00	0.00	0.00	2.90
657	669	9.035890	TCATGAGACATCCTACTTCTAAAAGAA	57.964	33.333	0.00	0.00	36.30	2.52
666	678	5.009510	CGTCATCTCATGAGACATCCTACTT	59.990	44.000	27.37	5.71	40.53	2.24
669	681	4.718961	TCGTCATCTCATGAGACATCCTA	58.281	43.478	27.37	9.19	40.53	2.94
722	734	5.232838	GGCAAATCACTTTGTTTCAGAGTTG	59.767	40.000	0.00	0.00	43.07	3.16
1158	1170	1.050421	GGCCAGCCAAATAGCCCAAT	61.050	55.000	3.12	0.00	39.60	3.16
1321	1334	3.661944	CAGCATCTGAGTTGTGTTCTCT	58.338	45.455	0.00	0.00	32.44	3.10
1333	1346	1.880894	GCAAAGCAGCAGCATCTGA	59.119	52.632	3.17	0.00	45.49	3.27
1383	1397	3.522553	CGTCTTATTCCTCAGTTCCCAC	58.477	50.000	0.00	0.00	0.00	4.61
1398	1412	2.678934	AGGGTCCGCAGCGTCTTA	60.679	61.111	15.05	0.00	0.00	2.10
1435	1449	1.021390	ACGGCTCATCTTCGCCAAAG	61.021	55.000	0.00	0.00	46.62	2.77
1447	1465	2.184322	GGAAGCATCGACGGCTCA	59.816	61.111	13.22	0.00	41.66	4.26
1461	1479	1.666011	GCACACGAGACTCCAGGAA	59.334	57.895	0.00	0.00	0.00	3.36
1480	1499	0.250727	AACACCACCCTGTTCATCCG	60.251	55.000	0.00	0.00	27.41	4.18
1512	1536	5.505181	AAGAACTACCAGAACATCCACAT	57.495	39.130	0.00	0.00	0.00	3.21
1518	1542	5.061721	ACCCAAAAGAACTACCAGAACAT	57.938	39.130	0.00	0.00	0.00	2.71
1702	1748	5.090845	AGGCTAGAGAGAAAGAGGAAAAGT	58.909	41.667	0.00	0.00	0.00	2.66
1963	2011	1.219124	CCTCTACATGCACCAGCGT	59.781	57.895	0.00	0.00	46.23	5.07
1964	2012	1.522355	CCCTCTACATGCACCAGCG	60.522	63.158	0.00	0.00	46.23	5.18
1966	2014	0.463295	CAGCCCTCTACATGCACCAG	60.463	60.000	0.00	0.00	0.00	4.00
1968	2016	1.153086	CCAGCCCTCTACATGCACC	60.153	63.158	0.00	0.00	0.00	5.01
1969	2017	0.462759	GTCCAGCCCTCTACATGCAC	60.463	60.000	0.00	0.00	0.00	4.57
1970	2018	1.907739	GTCCAGCCCTCTACATGCA	59.092	57.895	0.00	0.00	0.00	3.96
1971	2019	1.227380	CGTCCAGCCCTCTACATGC	60.227	63.158	0.00	0.00	0.00	4.06
1972	2020	1.227380	GCGTCCAGCCCTCTACATG	60.227	63.158	0.00	0.00	40.81	3.21
1973	2021	3.221222	GCGTCCAGCCCTCTACAT	58.779	61.111	0.00	0.00	40.81	2.29
2060	2274	0.545309	TCTCACCTCCACTCCCCTTG	60.545	60.000	0.00	0.00	0.00	3.61
2114	2328	1.524863	CGGCGATACGATCCTTCCCT	61.525	60.000	0.00	0.00	35.47	4.20
2138	2352	2.457598	ACACAGGTATCCACGATCTGT	58.542	47.619	0.00	0.00	38.99	3.41
2175	2389	1.202087	CGATCGATCTCATACGGAGGC	60.202	57.143	22.43	0.00	44.19	4.70
2224	2438	0.171455	TTGTTGCCCACGTGAACAAC	59.829	50.000	30.56	30.56	42.10	3.32
2243	2457	1.047002	CTGCCTCCCAATCGATCTCT	58.953	55.000	0.00	0.00	0.00	3.10
2253	2467	1.371183	CTCACGAAACTGCCTCCCA	59.629	57.895	0.00	0.00	0.00	4.37
2257	2471	1.302033	CTGGCTCACGAAACTGCCT	60.302	57.895	0.00	0.00	45.11	4.75
2281	2497	4.083217	CCGTTTCCGAGTATATCTCTCCTG	60.083	50.000	0.00	0.00	40.75	3.86
2326	2544	3.547787	AACAGGGGACGAGGGCTCT	62.548	63.158	0.00	0.00	0.00	4.09
2341	2559	2.909965	GGGTTTGGGCGAGCAACA	60.910	61.111	0.00	0.00	0.00	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.