AutoCloner

Multiple sequence alignment - TraesCS3D01G027500

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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	TraesCS3D01G027500	chr3D	100.000	2732	0	0	1	2732	9317383	9320114	0.000000e+00	5046.0
1	TraesCS3D01G027500	chrUn	87.917	2516	142	69	1	2416	35763750	35766203	0.000000e+00	2813.0
2	TraesCS3D01G027500	chrUn	87.917	2516	142	69	1	2416	309685282	309682829	0.000000e+00	2813.0
3	TraesCS3D01G027500	chrUn	88.170	1978	112	39	1	1906	35126615	35124688	0.000000e+00	2244.0
4	TraesCS3D01G027500	chrUn	92.949	156	11	0	2144	2299	35118712	35118557	7.610000e-56	228.0
5	TraesCS3D01G027500	chrUn	90.173	173	15	2	2314	2484	333583061	333582889	9.840000e-55	224.0
6	TraesCS3D01G027500	chr3A	87.954	2067	117	48	748	2732	11808551	11806535	0.000000e+00	2316.0
7	TraesCS3D01G027500	chr3A	88.103	1513	103	30	1128	2573	11800861	11799359	0.000000e+00	1725.0
8	TraesCS3D01G027500	chr3A	93.256	771	34	5	1	755	11809550	11808782	0.000000e+00	1120.0
9	TraesCS3D01G027500	chr5B	88.170	1978	112	39	1	1906	670523859	670525786	0.000000e+00	2244.0
10	TraesCS3D01G027500	chr5B	84.456	193	20	5	2303	2486	51627531	51627340	6.010000e-42	182.0
11	TraesCS3D01G027500	chr1D	79.181	293	31	15	2303	2574	456131576	456131293	2.800000e-40	176.0
12	TraesCS3D01G027500	chr1D	94.828	58	2	1	639	696	421525897	421525841	3.750000e-14	89.8
13	TraesCS3D01G027500	chr4B	76.871	294	39	14	2302	2574	421705819	421705534	3.670000e-29	139.0
14	TraesCS3D01G027500	chr2B	84.956	113	13	4	2302	2413	772186381	772186272	8.000000e-21	111.0
15	TraesCS3D01G027500	chr6A	88.312	77	3	5	637	712	615776078	615776007	1.350000e-13	87.9
16	TraesCS3D01G027500	chr2A	94.643	56	3	0	639	694	734740494	734740439	1.350000e-13	87.9
17	TraesCS3D01G027500	chr2A	90.385	52	3	2	633	683	73555994	73556044	1.760000e-07	67.6
18	TraesCS3D01G027500	chr4D	96.154	52	1	1	632	682	484740212	484740161	1.740000e-12	84.2
19	TraesCS3D01G027500	chr1B	90.909	44	4	0	90	133	677039097	677039140	2.940000e-05	60.2

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	TraesCS3D01G027500	chr3D	9317383	9320114	2731	False	5046	5046	100.000	1	2732	1	chr3D.!!$F1	2731
1	TraesCS3D01G027500	chrUn	35763750	35766203	2453	False	2813	2813	87.917	1	2416	1	chrUn.!!$F1	2415
2	TraesCS3D01G027500	chrUn	309682829	309685282	2453	True	2813	2813	87.917	1	2416	1	chrUn.!!$R3	2415
3	TraesCS3D01G027500	chrUn	35124688	35126615	1927	True	2244	2244	88.170	1	1906	1	chrUn.!!$R2	1905
4	TraesCS3D01G027500	chr3A	11799359	11800861	1502	True	1725	1725	88.103	1128	2573	1	chr3A.!!$R1	1445
5	TraesCS3D01G027500	chr3A	11806535	11809550	3015	True	1718	2316	90.605	1	2732	2	chr3A.!!$R2	2731
6	TraesCS3D01G027500	chr5B	670523859	670525786	1927	False	2244	2244	88.170	1	1906	1	chr5B.!!$F1	1905

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
390	391	1.341976	ACCCCTTGCCAAATATTCGCT	60.342	47.619	8.47	0.0	0.0	4.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2019	2430	0.17576	GTCTGCTATGGAGGCGACAA	59.824	55.0	0.0	0.0	35.28	3.18	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
188	189	3.998341	AGTAAATGCGACGCTAGGAAAAA	59.002	39.130	22.08	0.00	0.00	1.94
233	234	4.090761	AGAGTTGGCAAGAATCTTCACA	57.909	40.909	0.00	0.00	0.00	3.58
334	335	6.260936	GTGACTCTTTGATCCTCTTTTCACAA	59.739	38.462	0.00	0.00	31.89	3.33
352	353	3.425193	CACAACGCTAAGTTTCATTTGGC	59.575	43.478	0.00	0.00	42.02	4.52
390	391	1.341976	ACCCCTTGCCAAATATTCGCT	60.342	47.619	8.47	0.00	0.00	4.93
604	626	3.445096	CACCCCTTCAGATTTCCATTCAC	59.555	47.826	0.00	0.00	0.00	3.18
627	649	3.315470	GGAAACCAAACACCTCAGTTCTC	59.685	47.826	0.00	0.00	0.00	2.87
662	684	9.205513	ACTACTCCCTCCGTAAAGAAATATAAA	57.794	33.333	0.00	0.00	0.00	1.40
1142	1452	1.228124	TGCAGTGTTTAAGCCGCCT	60.228	52.632	0.00	0.00	0.00	5.52
1206	1516	2.443016	AGCTAGAGTCCGCCCTGG	60.443	66.667	0.00	0.00	40.09	4.45
1207	1517	4.228567	GCTAGAGTCCGCCCTGGC	62.229	72.222	0.00	0.00	37.80	4.85
1319	1646	9.965824	TCTGATTTTCTGTTTGAAATTAAGGTC	57.034	29.630	0.00	0.00	43.34	3.85
1400	1727	1.522092	CATGGCCGTGGCTAAGAGA	59.478	57.895	17.90	0.00	41.60	3.10
1406	1733	1.519455	CGTGGCTAAGAGAAGGGCG	60.519	63.158	0.00	0.00	0.00	6.13
1446	1773	3.424529	GGACGTCGACAAGTTCAAAGTAG	59.575	47.826	17.16	0.00	0.00	2.57
1451	1778	4.444720	GTCGACAAGTTCAAAGTAGGACAG	59.555	45.833	11.55	0.00	0.00	3.51
1519	1872	4.553323	TGTTTCTTTACAGAGCGAGTACC	58.447	43.478	0.00	0.00	0.00	3.34
1533	1886	3.305361	GCGAGTACCAACTAATTTCGGAC	59.695	47.826	0.00	0.00	35.56	4.79
1548	1901	2.455557	TCGGACCGGATAACCAAACTA	58.544	47.619	15.25	0.00	35.59	2.24
1783	2165	2.890945	TCTGTCGACTGATGGTCTTTCA	59.109	45.455	19.81	0.00	42.44	2.69
1845	2229	8.722480	TGTATGATTCATCTTGTCGAAAATCT	57.278	30.769	1.55	0.00	32.91	2.40
1849	2233	7.521529	TGATTCATCTTGTCGAAAATCTCAAC	58.478	34.615	0.00	0.00	32.91	3.18
1857	2241	3.188667	GTCGAAAATCTCAACCACTTCCC	59.811	47.826	0.00	0.00	0.00	3.97
1874	2282	0.038166	CCCTCTTAAACAGCCCTGCA	59.962	55.000	0.00	0.00	0.00	4.41
1928	2336	4.404394	ACATGACATATAGGGTGAACGACA	59.596	41.667	0.00	0.00	0.00	4.35
1942	2350	2.087501	ACGACAATTGCACGATGGTA	57.912	45.000	24.88	0.00	0.00	3.25
1980	2391	3.134442	AAACAGTTGTTTCCATGCATGGT	59.866	39.130	38.18	19.60	44.15	3.55
1989	2400	1.452110	CCATGCATGGTCGTCTTCAA	58.548	50.000	33.68	0.00	43.05	2.69
2019	2430	5.122554	TGTGGTTCAAAAATCGTATACGCAT	59.877	36.000	20.42	11.63	39.60	4.73
2040	2451	1.075970	TCGCCTCCATAGCAGACCT	60.076	57.895	0.00	0.00	0.00	3.85
2045	2456	2.634940	GCCTCCATAGCAGACCTGATAA	59.365	50.000	0.47	0.00	34.93	1.75
2046	2457	3.262915	GCCTCCATAGCAGACCTGATAAT	59.737	47.826	0.47	0.00	34.93	1.28
2095	2506	4.119136	GCACTTGCCAATACAAAGTGTTT	58.881	39.130	14.27	0.00	34.24	2.83
2096	2507	5.163509	TGCACTTGCCAATACAAAGTGTTTA	60.164	36.000	14.27	2.06	41.18	2.01
2097	2508	5.751028	GCACTTGCCAATACAAAGTGTTTAA	59.249	36.000	14.27	0.00	34.24	1.52
2098	2509	6.423604	GCACTTGCCAATACAAAGTGTTTAAT	59.576	34.615	14.27	0.00	34.24	1.40
2099	2510	7.596995	GCACTTGCCAATACAAAGTGTTTAATA	59.403	33.333	14.27	0.00	34.24	0.98
2100	2511	9.638239	CACTTGCCAATACAAAGTGTTTAATAT	57.362	29.630	6.61	0.00	30.64	1.28
2101	2512	9.638239	ACTTGCCAATACAAAGTGTTTAATATG	57.362	29.630	0.00	0.00	0.00	1.78
2243	2663	2.880268	CTGGCATTGAATCGCTCCATAA	59.120	45.455	0.00	0.00	0.00	1.90
2352	2801	3.329300	AGCGTTCTGGTGCTTTGAT	57.671	47.368	0.00	0.00	38.57	2.57
2367	2816	1.710996	TTGATGGTTGTGGGGGTCGT	61.711	55.000	0.00	0.00	0.00	4.34
2382	2831	4.308458	CGTTGAGGACCCCACGCA	62.308	66.667	0.00	0.00	0.00	5.24
2580	3050	9.777843	GTGAATACTTTTTAAATTTGCGAACAG	57.222	29.630	0.00	0.00	0.00	3.16
2592	3062	7.581011	AATTTGCGAACAGTATTTGAAATCC	57.419	32.000	0.00	0.00	0.00	3.01
2596	3066	5.414144	TGCGAACAGTATTTGAAATCCATGA	59.586	36.000	0.00	0.00	0.00	3.07
2696	3191	3.297202	GCGAAAAAGAAATAAACGAGCGG	59.703	43.478	0.00	0.00	0.00	5.52
2699	3194	4.680171	AAAAGAAATAAACGAGCGGGAG	57.320	40.909	0.00	0.00	0.00	4.30
2703	3198	0.177373	AATAAACGAGCGGGAGGACC	59.823	55.000	0.00	0.00	0.00	4.46
2720	3215	2.438075	CAGGGAGCCAAGCTGAGC	60.438	66.667	0.00	0.00	39.88	4.26
2727	3222	1.023513	AGCCAAGCTGAGCGAATGAC	61.024	55.000	0.00	0.00	37.57	3.06
2729	3224	1.699656	CCAAGCTGAGCGAATGACCG	61.700	60.000	0.00	0.00	0.00	4.79
2730	3225	1.016130	CAAGCTGAGCGAATGACCGT	61.016	55.000	0.00	0.00	0.00	4.83
2731	3226	1.016130	AAGCTGAGCGAATGACCGTG	61.016	55.000	0.00	0.00	0.00	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
188	189	3.117888	ACAGCCATGTATTTCGGGATTCT	60.118	43.478	0.00	0.00	38.09	2.40
291	292	9.981460	AAGAGTCACCTAAAGATTATTCCAAAT	57.019	29.630	0.00	0.00	0.00	2.32
334	335	3.412386	AGAGCCAAATGAAACTTAGCGT	58.588	40.909	0.00	0.00	0.00	5.07
352	353	2.194271	GGTCGGCATCGTAAAAGAGAG	58.806	52.381	0.00	0.00	37.69	3.20
390	391	4.530553	TGGCTAGATCAGTAACCAAAGTCA	59.469	41.667	0.00	0.00	0.00	3.41
509	512	7.625828	AAGGCGCTATACTTCAATAAACTTT	57.374	32.000	7.64	0.00	0.00	2.66
511	514	8.904099	AATAAGGCGCTATACTTCAATAAACT	57.096	30.769	7.64	0.00	0.00	2.66
565	586	3.819564	GGTGAAGCCCTTCTTTGTTTT	57.180	42.857	9.23	0.00	40.14	2.43
604	626	1.675552	ACTGAGGTGTTTGGTTTCCG	58.324	50.000	0.00	0.00	0.00	4.30
627	649	2.488710	CGGAGGGAGTAGTTAGTAGGGG	60.489	59.091	0.00	0.00	0.00	4.79
735	786	5.127194	CCTTGGTATTCTCACTACTACAGCA	59.873	44.000	0.00	0.00	0.00	4.41
834	1125	6.646240	AGTCACGGCGATTAAAGTAAAGTTAA	59.354	34.615	16.62	0.00	0.00	2.01
941	1232	9.099454	GCCAATATATAGATGGTTGTAGCTTAC	57.901	37.037	15.28	0.00	36.57	2.34
1076	1379	6.170506	GGGACAAATATATATTCCGTCTGCA	58.829	40.000	23.76	0.00	32.73	4.41
1079	1382	5.416947	GCGGGACAAATATATATTCCGTCT	58.583	41.667	23.60	3.83	34.06	4.18
1142	1452	1.957177	CTCCAGTAATAGCCTCTGCGA	59.043	52.381	0.00	0.00	44.33	5.10
1208	1518	2.399356	GGTTTGCGCTAGAGGGTGC	61.399	63.158	9.73	0.00	42.34	5.01
1209	1519	0.535335	TAGGTTTGCGCTAGAGGGTG	59.465	55.000	9.73	0.00	0.00	4.61
1210	1520	1.413077	GATAGGTTTGCGCTAGAGGGT	59.587	52.381	9.73	0.00	0.00	4.34
1211	1521	1.270358	GGATAGGTTTGCGCTAGAGGG	60.270	57.143	9.73	0.00	0.00	4.30
1212	1522	1.603172	CGGATAGGTTTGCGCTAGAGG	60.603	57.143	9.73	0.00	0.00	3.69
1213	1523	1.603172	CCGGATAGGTTTGCGCTAGAG	60.603	57.143	9.73	0.00	34.51	2.43
1214	1524	0.387929	CCGGATAGGTTTGCGCTAGA	59.612	55.000	9.73	0.00	34.51	2.43
1215	1525	2.900528	CCGGATAGGTTTGCGCTAG	58.099	57.895	9.73	0.00	34.51	3.42
1319	1646	2.743752	CGCCCAGAACATGAGCACG	61.744	63.158	0.00	0.00	0.00	5.34
1400	1727	1.529244	GCAGAATATGGCCGCCCTT	60.529	57.895	7.03	0.00	0.00	3.95
1494	1832	6.472808	GGTACTCGCTCTGTAAAGAAACATAG	59.527	42.308	0.00	0.00	0.00	2.23
1498	1836	4.553323	TGGTACTCGCTCTGTAAAGAAAC	58.447	43.478	0.00	0.00	0.00	2.78
1519	1872	4.271776	GGTTATCCGGTCCGAAATTAGTTG	59.728	45.833	14.39	0.00	0.00	3.16
1533	1886	3.882888	ACATGCATAGTTTGGTTATCCGG	59.117	43.478	0.00	0.00	36.30	5.14
1548	1901	4.687948	GCAGTGATCGAGTTATACATGCAT	59.312	41.667	0.00	0.00	0.00	3.96
1709	2073	7.452189	TCATTTATATGTTGGCCATGATGATGT	59.548	33.333	6.09	0.00	34.86	3.06
1787	2169	9.693739	AACTGTTGATTCACCAATAATATACCA	57.306	29.630	0.00	0.00	0.00	3.25
1834	2218	3.813166	GGAAGTGGTTGAGATTTTCGACA	59.187	43.478	0.00	0.00	41.32	4.35
1845	2229	4.714632	CTGTTTAAGAGGGAAGTGGTTGA	58.285	43.478	0.00	0.00	0.00	3.18
1849	2233	2.437413	GGCTGTTTAAGAGGGAAGTGG	58.563	52.381	0.00	0.00	0.00	4.00
1857	2241	0.807496	GCTGCAGGGCTGTTTAAGAG	59.193	55.000	17.12	0.00	0.00	2.85
1874	2282	0.328592	TCCTAGACCGACAGAGTGCT	59.671	55.000	0.00	0.00	0.00	4.40
1928	2336	3.809832	GCTAGATGTACCATCGTGCAATT	59.190	43.478	14.70	0.00	38.17	2.32
1942	2350	2.226330	TGTTTGCAAACCGCTAGATGT	58.774	42.857	33.33	0.00	43.06	3.06
1980	2391	3.417069	ACCACAATCCATTGAAGACGA	57.583	42.857	6.29	0.00	40.14	4.20
1983	2394	6.477053	TTTTGAACCACAATCCATTGAAGA	57.523	33.333	6.29	0.00	40.14	2.87
1989	2400	5.467035	ACGATTTTTGAACCACAATCCAT	57.533	34.783	0.00	0.00	38.36	3.41
2019	2430	0.175760	GTCTGCTATGGAGGCGACAA	59.824	55.000	0.00	0.00	35.28	3.18
2064	2475	1.401761	TTGGCAAGTGCACAACTCAT	58.598	45.000	21.04	0.00	44.36	2.90
2180	2600	9.145865	TGGACAACAAAACTTGAAATTAGAAAC	57.854	29.630	0.00	0.00	0.00	2.78
2243	2663	3.026707	AGTGGTTGCTTGGTTTACCTT	57.973	42.857	0.00	0.00	36.82	3.50
2311	2760	6.319911	GCTTCAATTCAAGGGAGCTTAGTATT	59.680	38.462	0.00	0.00	0.00	1.89
2352	2801	2.193517	CAACGACCCCCACAACCA	59.806	61.111	0.00	0.00	0.00	3.67
2367	2816	2.674563	CTTGTGCGTGGGGTCCTCAA	62.675	60.000	0.00	0.00	0.00	3.02
2382	2831	5.715434	AAAACTAAACACCACACACTTGT	57.285	34.783	0.00	0.00	35.84	3.16
2528	2983	9.232082	CAAACTTTAAATGATCGTGAACTGAAA	57.768	29.630	0.00	0.00	0.00	2.69
2531	2986	7.855409	TCACAAACTTTAAATGATCGTGAACTG	59.145	33.333	0.00	0.00	0.00	3.16
2533	2988	8.555166	TTCACAAACTTTAAATGATCGTGAAC	57.445	30.769	12.52	0.00	36.30	3.18
2651	3143	0.615331	CCCCACTGCTAGCTGAAAGA	59.385	55.000	26.29	0.00	34.07	2.52
2652	3144	1.028868	GCCCCACTGCTAGCTGAAAG	61.029	60.000	26.29	12.96	0.00	2.62
2654	3146	2.671070	GCCCCACTGCTAGCTGAA	59.329	61.111	26.29	0.43	0.00	3.02
2656	3148	3.729965	CTCGCCCCACTGCTAGCTG	62.730	68.421	19.01	19.01	0.00	4.24
2696	3191	2.610859	TTGGCTCCCTGGTCCTCC	60.611	66.667	0.00	0.00	0.00	4.30
2699	3194	3.334054	AGCTTGGCTCCCTGGTCC	61.334	66.667	0.00	0.00	30.62	4.46
2703	3198	2.438075	GCTCAGCTTGGCTCCCTG	60.438	66.667	0.00	0.00	36.40	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.