AutoCloner

Multiple sequence alignment - TraesCS1B01G108500

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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	TraesCS1B01G108500	chr1B	100.000	6430	0	0	1	6430	120648590	120642161	0.000000e+00	11875.0
1	TraesCS1B01G108500	chr1B	96.175	183	4	2	6251	6430	662242361	662242543	4.870000e-76	296.0
2	TraesCS1B01G108500	chrUn	93.736	2682	146	7	2400	5068	778702	781374	0.000000e+00	4002.0
3	TraesCS1B01G108500	chrUn	93.736	2682	146	7	2400	5068	253484840	253487512	0.000000e+00	4002.0
4	TraesCS1B01G108500	chrUn	93.736	2682	146	7	2400	5068	264409051	264411723	0.000000e+00	4002.0
5	TraesCS1B01G108500	chrUn	95.309	1620	69	5	247	1860	253482717	253484335	0.000000e+00	2564.0
6	TraesCS1B01G108500	chrUn	95.326	1412	59	5	455	1860	776787	778197	0.000000e+00	2235.0
7	TraesCS1B01G108500	chrUn	95.326	1412	59	5	455	1860	264407136	264408546	0.000000e+00	2235.0
8	TraesCS1B01G108500	chrUn	89.980	499	30	5	5712	6206	781689	782171	1.520000e-175	627.0
9	TraesCS1B01G108500	chrUn	89.980	499	30	5	5712	6206	253487827	253488309	1.520000e-175	627.0
10	TraesCS1B01G108500	chrUn	89.980	499	30	5	5712	6206	264412038	264412520	1.520000e-175	627.0
11	TraesCS1B01G108500	chrUn	93.769	337	14	4	2017	2352	778195	778525	3.460000e-137	499.0
12	TraesCS1B01G108500	chrUn	93.769	337	14	4	2017	2352	253484333	253484663	3.460000e-137	499.0
13	TraesCS1B01G108500	chrUn	93.769	337	14	4	2017	2352	264408544	264408874	3.460000e-137	499.0
14	TraesCS1B01G108500	chrUn	93.519	216	13	1	5221	5435	781372	781587	2.890000e-83	320.0
15	TraesCS1B01G108500	chrUn	93.519	216	13	1	5221	5435	253487510	253487725	2.890000e-83	320.0
16	TraesCS1B01G108500	chrUn	93.519	216	13	1	5221	5435	264411721	264411936	2.890000e-83	320.0
17	TraesCS1B01G108500	chrUn	98.160	163	1	1	1859	2019	60492499	60492661	3.800000e-72	283.0
18	TraesCS1B01G108500	chrUn	98.160	163	1	1	1859	2019	318520652	318520490	3.800000e-72	283.0
19	TraesCS1B01G108500	chr1D	95.279	2224	91	7	2849	5068	76978589	76976376	0.000000e+00	3513.0
20	TraesCS1B01G108500	chr1D	93.698	1698	73	8	170	1860	76981191	76979521	0.000000e+00	2512.0
21	TraesCS1B01G108500	chr1D	92.544	845	46	10	2017	2854	76979523	76978689	0.000000e+00	1195.0
22	TraesCS1B01G108500	chr1D	94.144	444	21	3	5718	6158	76976055	76975614	0.000000e+00	671.0
23	TraesCS1B01G108500	chr1D	91.667	216	17	1	5221	5435	76976378	76976163	1.360000e-76	298.0
24	TraesCS1B01G108500	chr2A	97.753	178	3	1	6254	6430	376100169	376099992	8.100000e-79	305.0
25	TraesCS1B01G108500	chr2A	90.566	159	12	3	5068	5223	449270948	449271106	2.350000e-49	207.0
26	TraesCS1B01G108500	chr2A	95.238	42	2	0	6217	6258	746693002	746692961	4.160000e-07	67.6
27	TraesCS1B01G108500	chr3B	96.685	181	2	2	6250	6430	434649143	434649319	1.360000e-76	298.0
28	TraesCS1B01G108500	chr3B	93.048	187	7	4	1842	2026	54754898	54755080	1.060000e-67	268.0
29	TraesCS1B01G108500	chr3B	95.455	44	1	1	6216	6258	479679797	479679754	1.160000e-07	69.4
30	TraesCS1B01G108500	chr7A	99.383	162	1	0	6269	6430	111848520	111848359	1.750000e-75	294.0
31	TraesCS1B01G108500	chr7A	91.824	159	8	5	5069	5223	552975377	552975534	3.900000e-52	217.0
32	TraesCS1B01G108500	chr7B	98.204	167	2	1	6265	6430	639079054	639079220	2.270000e-74	291.0
33	TraesCS1B01G108500	chr7B	96.532	173	5	1	6259	6430	624794953	624795125	1.060000e-72	285.0
34	TraesCS1B01G108500	chr4B	98.773	163	2	0	6268	6430	240179854	240180016	2.270000e-74	291.0
35	TraesCS1B01G108500	chr4B	95.954	173	2	3	1850	2020	85935668	85935837	6.350000e-70	276.0
36	TraesCS1B01G108500	chr4B	94.886	176	7	1	1846	2019	82014083	82014258	2.280000e-69	274.0
37	TraesCS1B01G108500	chr1A	96.610	177	2	2	6254	6430	453788253	453788081	2.270000e-74	291.0
38	TraesCS1B01G108500	chr1A	95.376	173	6	1	1859	2029	492657471	492657299	2.280000e-69	274.0
39	TraesCS1B01G108500	chr1A	91.139	158	11	3	5069	5223	24135786	24135943	1.820000e-50	211.0
40	TraesCS1B01G108500	chr1A	87.500	176	18	4	5074	5246	153512713	153512539	3.930000e-47	200.0
41	TraesCS1B01G108500	chr1A	71.552	696	185	12	1027	1714	1698577	1697887	6.630000e-40	176.0
42	TraesCS1B01G108500	chr6D	98.160	163	1	1	1859	2019	81746930	81746768	3.800000e-72	283.0
43	TraesCS1B01G108500	chr6D	92.405	158	9	3	5069	5223	267532965	267532808	8.390000e-54	222.0
44	TraesCS1B01G108500	chr6B	94.565	184	7	3	6250	6430	24751090	24751273	1.360000e-71	281.0
45	TraesCS1B01G108500	chr2B	96.988	166	3	1	1857	2020	793708292	793708457	1.770000e-70	278.0
46	TraesCS1B01G108500	chr2B	94.382	178	8	1	1855	2030	717471610	717471787	8.210000e-69	272.0
47	TraesCS1B01G108500	chr6A	92.949	156	9	2	5069	5223	381088858	381088704	6.490000e-55	226.0
48	TraesCS1B01G108500	chr5D	92.053	151	10	2	5069	5218	152753958	152754107	1.820000e-50	211.0
49	TraesCS1B01G108500	chr5D	97.059	34	1	0	6222	6255	533555438	533555471	2.500000e-04	58.4
50	TraesCS1B01G108500	chr5B	90.683	161	8	5	5069	5223	373680197	373680038	2.350000e-49	207.0
51	TraesCS1B01G108500	chr2D	88.304	171	15	4	5069	5236	380416680	380416512	3.930000e-47	200.0
52	TraesCS1B01G108500	chr7D	97.500	40	1	0	6219	6258	148153772	148153733	1.160000e-07	69.4

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	TraesCS1B01G108500	chr1B	120642161	120648590	6429	True	11875.0	11875	100.0000	1	6430	1	chr1B.!!$R1	6429
1	TraesCS1B01G108500	chrUn	253482717	253488309	5592	False	1602.4	4002	93.2626	247	6206	5	chrUn.!!$F3	5959
2	TraesCS1B01G108500	chrUn	776787	782171	5384	False	1536.6	4002	93.2660	455	6206	5	chrUn.!!$F2	5751
3	TraesCS1B01G108500	chrUn	264407136	264412520	5384	False	1536.6	4002	93.2660	455	6206	5	chrUn.!!$F4	5751
4	TraesCS1B01G108500	chr1D	76975614	76981191	5577	True	1637.8	3513	93.4664	170	6158	5	chr1D.!!$R1	5988

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
166	167	1.001815	GTGACGTTGGATTTGTGGTGG	60.002	52.381	0.0	0.0	0.00	4.61	F
1345	1357	1.089481	GCCGAAACATCGCCATCAGA	61.089	55.000	0.0	0.0	0.00	3.27	F
1735	1747	0.489567	AGGAGTGGGGTTCTCAGACT	59.510	55.000	0.0	0.0	34.04	3.24	F
2322	2336	0.254178	CCAACTCCTGCTGCACCTAT	59.746	55.000	0.0	0.0	0.00	2.57	F
2323	2337	1.486310	CCAACTCCTGCTGCACCTATA	59.514	52.381	0.0	0.0	0.00	1.31	F
3981	4277	1.880027	GCAGTACTTGGAAACACTGGG	59.120	52.381	0.0	0.0	42.67	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1361	1373	0.179015	TGCACGGGCCTTGAGTTTAA	60.179	50.000	15.11	0.0	40.13	1.52	R
2276	2289	0.107508	ATGTGAATCTGTGCCCTCCG	60.108	55.000	0.00	0.0	0.00	4.63	R
3096	3389	0.966179	AAACGCAAGGGGTTCCATTC	59.034	50.000	0.00	0.0	46.39	2.67	R
4112	4408	1.204941	GTGGACACCAAGCGTCTCTAT	59.795	52.381	0.00	0.0	34.18	1.98	R
4184	4480	2.039084	CCAGCTGTACTTTCAACCTCCT	59.961	50.000	13.81	0.0	0.00	3.69	R
5572	5869	0.036952	AGCGCACTTGCAGATACACT	60.037	50.000	11.47	0.0	42.21	3.55	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	4.717299	CGACATATTTCGTTTGTAAGCACG	59.283	41.667	3.06	0.00	37.77	5.34
26	27	4.965062	ACATATTTCGTTTGTAAGCACGG	58.035	39.130	0.00	0.00	37.02	4.94
27	28	2.325509	ATTTCGTTTGTAAGCACGGC	57.674	45.000	0.00	0.00	37.02	5.68
28	29	1.015109	TTTCGTTTGTAAGCACGGCA	58.985	45.000	0.00	0.00	37.02	5.69
29	30	1.015109	TTCGTTTGTAAGCACGGCAA	58.985	45.000	0.00	0.00	37.02	4.52
30	31	1.231221	TCGTTTGTAAGCACGGCAAT	58.769	45.000	0.00	0.00	37.02	3.56
31	32	1.604755	TCGTTTGTAAGCACGGCAATT	59.395	42.857	0.00	0.00	37.02	2.32
32	33	2.033550	TCGTTTGTAAGCACGGCAATTT	59.966	40.909	0.00	0.00	37.02	1.82
33	34	2.792116	CGTTTGTAAGCACGGCAATTTT	59.208	40.909	0.00	0.00	32.58	1.82
34	35	3.121496	CGTTTGTAAGCACGGCAATTTTC	60.121	43.478	0.00	0.00	32.58	2.29
35	36	4.048504	GTTTGTAAGCACGGCAATTTTCT	58.951	39.130	0.00	0.00	0.00	2.52
36	37	5.216648	GTTTGTAAGCACGGCAATTTTCTA	58.783	37.500	0.00	0.00	0.00	2.10
37	38	5.440234	TTGTAAGCACGGCAATTTTCTAA	57.560	34.783	0.00	0.00	0.00	2.10
38	39	4.789784	TGTAAGCACGGCAATTTTCTAAC	58.210	39.130	0.00	0.00	0.00	2.34
39	40	4.276183	TGTAAGCACGGCAATTTTCTAACA	59.724	37.500	0.00	0.00	0.00	2.41
40	41	3.559238	AGCACGGCAATTTTCTAACAG	57.441	42.857	0.00	0.00	0.00	3.16
41	42	3.146066	AGCACGGCAATTTTCTAACAGA	58.854	40.909	0.00	0.00	0.00	3.41
42	43	3.568007	AGCACGGCAATTTTCTAACAGAA	59.432	39.130	0.00	0.00	31.28	3.02
43	44	4.037446	AGCACGGCAATTTTCTAACAGAAA	59.963	37.500	0.00	0.00	42.00	2.52
67	68	8.729805	AAAAATAAACTGAGATGGTTTTGCAA	57.270	26.923	0.00	0.00	37.88	4.08
68	69	8.907222	AAAATAAACTGAGATGGTTTTGCAAT	57.093	26.923	0.00	0.00	37.88	3.56
69	70	7.894376	AATAAACTGAGATGGTTTTGCAATG	57.106	32.000	0.00	0.00	37.88	2.82
70	71	3.308438	ACTGAGATGGTTTTGCAATGC	57.692	42.857	0.00	0.00	0.00	3.56
71	72	2.895404	ACTGAGATGGTTTTGCAATGCT	59.105	40.909	6.82	0.00	0.00	3.79
72	73	3.057033	ACTGAGATGGTTTTGCAATGCTC	60.057	43.478	6.82	2.22	0.00	4.26

Showing 1 to 25 of 663 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.717299	CGTGCTTACAAACGAAATATGTCG	59.283	41.667	13.85	13.85	46.54	4.35
3	4	5.019498	CCGTGCTTACAAACGAAATATGTC	58.981	41.667	0.00	0.00	42.32	3.06
4	5	4.670735	GCCGTGCTTACAAACGAAATATGT	60.671	41.667	0.00	0.00	42.32	2.29
5	6	3.783943	GCCGTGCTTACAAACGAAATATG	59.216	43.478	0.00	0.00	42.32	1.78
6	7	3.437395	TGCCGTGCTTACAAACGAAATAT	59.563	39.130	0.00	0.00	42.32	1.28
7	8	2.806818	TGCCGTGCTTACAAACGAAATA	59.193	40.909	0.00	0.00	42.32	1.40
8	9	1.604755	TGCCGTGCTTACAAACGAAAT	59.395	42.857	0.00	0.00	42.32	2.17
9	10	1.015109	TGCCGTGCTTACAAACGAAA	58.985	45.000	0.00	0.00	42.32	3.46
10	11	1.015109	TTGCCGTGCTTACAAACGAA	58.985	45.000	0.00	0.00	42.32	3.85
11	12	1.231221	ATTGCCGTGCTTACAAACGA	58.769	45.000	0.00	0.00	42.32	3.85
12	13	2.044888	AATTGCCGTGCTTACAAACG	57.955	45.000	0.00	0.00	39.48	3.60
13	14	4.048504	AGAAAATTGCCGTGCTTACAAAC	58.951	39.130	0.00	0.00	0.00	2.93
14	15	4.314740	AGAAAATTGCCGTGCTTACAAA	57.685	36.364	0.00	0.00	0.00	2.83
15	16	5.216648	GTTAGAAAATTGCCGTGCTTACAA	58.783	37.500	0.00	0.00	0.00	2.41
16	17	4.276183	TGTTAGAAAATTGCCGTGCTTACA	59.724	37.500	0.00	0.00	0.00	2.41
17	18	4.789784	TGTTAGAAAATTGCCGTGCTTAC	58.210	39.130	0.00	0.00	0.00	2.34
18	19	4.757657	TCTGTTAGAAAATTGCCGTGCTTA	59.242	37.500	0.00	0.00	0.00	3.09
19	20	3.568007	TCTGTTAGAAAATTGCCGTGCTT	59.432	39.130	0.00	0.00	0.00	3.91
20	21	3.146066	TCTGTTAGAAAATTGCCGTGCT	58.854	40.909	0.00	0.00	0.00	4.40
21	22	3.552604	TCTGTTAGAAAATTGCCGTGC	57.447	42.857	0.00	0.00	0.00	5.34
42	43	8.729805	TTGCAAAACCATCTCAGTTTATTTTT	57.270	26.923	0.00	0.00	36.44	1.94
43	44	8.776470	CATTGCAAAACCATCTCAGTTTATTTT	58.224	29.630	1.71	0.00	36.44	1.82
44	45	7.095102	GCATTGCAAAACCATCTCAGTTTATTT	60.095	33.333	1.71	0.00	36.44	1.40
45	46	6.369615	GCATTGCAAAACCATCTCAGTTTATT	59.630	34.615	1.71	0.00	36.44	1.40
46	47	5.870978	GCATTGCAAAACCATCTCAGTTTAT	59.129	36.000	1.71	0.00	36.44	1.40

Showing 1 to 25 of 723 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.