AutoCloner

Multiple sequence alignment - TraesCS5D01G055400

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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	TraesCS5D01G055400	chr5D	100.000	6376	0	0	1	6376	52053582	52059957	0.000000e+00	11775.0
1	TraesCS5D01G055400	chr5D	92.941	170	11	1	4541	4710	6162092	6162260	4.940000e-61	246.0
2	TraesCS5D01G055400	chr5D	92.262	168	12	1	4541	4708	6260085	6260251	2.970000e-58	237.0
3	TraesCS5D01G055400	chr5D	91.765	170	13	1	4541	4710	503306690	503306522	1.070000e-57	235.0
4	TraesCS5D01G055400	chr5D	91.765	170	13	1	4541	4710	512405731	512405563	1.070000e-57	235.0
5	TraesCS5D01G055400	chr5A	94.567	4804	146	42	57	4793	41301858	41306613	0.000000e+00	7319.0
6	TraesCS5D01G055400	chr5A	93.485	1581	56	19	4824	6376	41306614	41308175	0.000000e+00	2305.0
7	TraesCS5D01G055400	chr5B	93.931	2768	109	22	525	3255	55179032	55181777	0.000000e+00	4126.0
8	TraesCS5D01G055400	chr5B	94.415	2650	99	22	3745	6373	55182994	55185615	0.000000e+00	4028.0
9	TraesCS5D01G055400	chr5B	96.620	503	17	0	3241	3743	55182330	55182832	0.000000e+00	835.0
10	TraesCS5D01G055400	chr5B	91.133	406	11	9	114	508	55178242	55178633	1.570000e-145	527.0
11	TraesCS5D01G055400	chr7D	92.353	170	12	1	4541	4710	231596079	231596247	2.300000e-59	241.0
12	TraesCS5D01G055400	chr1D	92.727	165	11	1	4546	4710	254449830	254449667	2.970000e-58	237.0
13	TraesCS5D01G055400	chr7B	91.176	170	14	1	4541	4710	137679680	137679512	4.970000e-56	230.0
14	TraesCS5D01G055400	chr7B	89.130	46	4	1	18	63	272121575	272121619	8.930000e-04	56.5
15	TraesCS5D01G055400	chr6B	92.308	65	5	0	963	1027	145900601	145900665	6.810000e-15	93.5
16	TraesCS5D01G055400	chr4B	91.111	45	4	0	18	62	128034497	128034541	1.920000e-05	62.1
17	TraesCS5D01G055400	chr6D	96.774	31	1	0	20	50	471908909	471908939	1.200000e-02	52.8

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	TraesCS5D01G055400	chr5D	52053582	52059957	6375	False	11775	11775	100.00000	1	6376	1	chr5D.!!$F3	6375
1	TraesCS5D01G055400	chr5A	41301858	41308175	6317	False	4812	7319	94.02600	57	6376	2	chr5A.!!$F1	6319
2	TraesCS5D01G055400	chr5B	55178242	55185615	7373	False	2379	4126	94.02475	114	6373	4	chr5B.!!$F1	6259

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	Hairpin	End Stability	Orientation
526	559	0.033208	AGTGGAGCCAGAGAGAGAGG	60.033	60.0	0.00	0.00	3.69	F
532	941	0.550914	GCCAGAGAGAGAGGGAGAGA	59.449	60.0	0.00	0.00	3.10	F
1900	2385	0.037326	CGCACTGTTTCAGGGAGCTA	60.037	55.0	3.02	36.97	3.32	F
2032	2517	0.307760	CGTTGCTGGAGGTTGTTCAC	59.692	55.0	0.00	0.00	3.18	F
3553	4605	1.133809	TGGTGCCAGGTTAGAAGCCT	61.134	55.0	0.00	36.66	4.58	F
4397	5609	0.178950	TGCCAGGTGAGTCTGTCTCT	60.179	55.0	3.71	43.13	3.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1624	2080	0.267960	AAGGTCAGATATCCCCCGGT	59.732	55.000	0.00	0.00	0.00	5.28	R
2013	2498	0.307760	GTGAACAACCTCCAGCAACG	59.692	55.000	0.00	0.00	0.00	4.10	R
3423	4475	1.270907	AACTCTACCCCACTCTGCAG	58.729	55.000	7.63	7.63	0.00	4.41	R
3579	4631	1.676529	GCTGGAGCGATACACTCACTA	59.323	52.381	0.00	0.00	35.79	2.74	R
4806	6018	1.649664	CCATGAGCAAAGGAGTCGAG	58.350	55.000	0.00	0.00	0.00	4.04	R
6327	7579	0.036732	TGACACATCCTTCCACTGGC	59.963	55.000	0.00	0.00	0.00	4.85	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
21	22	3.958704	CATGCTCTCTCACCGTACTAAG	58.041	50.000	0.00	0.00	0.00	2.18
22	23	1.743958	TGCTCTCTCACCGTACTAAGC	59.256	52.381	0.00	0.00	0.00	3.09
23	24	2.018515	GCTCTCTCACCGTACTAAGCT	58.981	52.381	0.00	0.00	0.00	3.74
24	25	2.424246	GCTCTCTCACCGTACTAAGCTT	59.576	50.000	3.48	3.48	0.00	3.74
25	26	3.732471	GCTCTCTCACCGTACTAAGCTTG	60.732	52.174	9.86	1.57	0.00	4.01
26	27	3.418995	TCTCTCACCGTACTAAGCTTGT	58.581	45.455	9.86	7.95	0.00	3.16
27	28	4.582869	TCTCTCACCGTACTAAGCTTGTA	58.417	43.478	9.86	6.92	0.00	2.41
28	29	4.394300	TCTCTCACCGTACTAAGCTTGTAC	59.606	45.833	20.29	20.29	37.50	2.90
29	30	4.330250	TCTCACCGTACTAAGCTTGTACT	58.670	43.478	24.11	12.56	38.39	2.73
30	31	4.394300	TCTCACCGTACTAAGCTTGTACTC	59.606	45.833	24.11	10.00	38.39	2.59
31	32	3.441572	TCACCGTACTAAGCTTGTACTCC	59.558	47.826	24.11	9.53	38.39	3.85
32	33	2.757314	ACCGTACTAAGCTTGTACTCCC	59.243	50.000	24.11	9.29	38.39	4.30
33	34	3.022406	CCGTACTAAGCTTGTACTCCCT	58.978	50.000	24.11	0.00	38.39	4.20
34	35	3.066481	CCGTACTAAGCTTGTACTCCCTC	59.934	52.174	24.11	8.58	38.39	4.30
35	36	3.946558	CGTACTAAGCTTGTACTCCCTCT	59.053	47.826	24.11	0.00	38.39	3.69
36	37	5.121811	CGTACTAAGCTTGTACTCCCTCTA	58.878	45.833	24.11	0.00	38.39	2.43
37	38	5.764192	CGTACTAAGCTTGTACTCCCTCTAT	59.236	44.000	24.11	0.00	38.39	1.98
38	39	6.933521	CGTACTAAGCTTGTACTCCCTCTATA	59.066	42.308	24.11	0.00	38.39	1.31
39	40	7.443575	CGTACTAAGCTTGTACTCCCTCTATAA	59.556	40.741	24.11	0.00	38.39	0.98
40	41	9.129532	GTACTAAGCTTGTACTCCCTCTATAAA	57.870	37.037	21.76	0.00	37.76	1.40
41	42	8.009622	ACTAAGCTTGTACTCCCTCTATAAAC	57.990	38.462	9.86	0.00	0.00	2.01
42	43	7.840210	ACTAAGCTTGTACTCCCTCTATAAACT	59.160	37.037	9.86	0.00	0.00	2.66
43	44	9.352191	CTAAGCTTGTACTCCCTCTATAAACTA	57.648	37.037	9.86	0.00	0.00	2.24
44	45	8.605325	AAGCTTGTACTCCCTCTATAAACTAA	57.395	34.615	0.00	0.00	0.00	2.24
45	46	8.785184	AGCTTGTACTCCCTCTATAAACTAAT	57.215	34.615	0.00	0.00	0.00	1.73

Showing 1 to 25 of 144 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.793801	GCTTAGTACGGTGAGAGAGCATG	60.794	52.174	0.00	0.00	0.00	4.06
1	2	2.359531	GCTTAGTACGGTGAGAGAGCAT	59.640	50.000	0.00	0.00	0.00	3.79
2	3	1.743958	GCTTAGTACGGTGAGAGAGCA	59.256	52.381	0.00	0.00	0.00	4.26
4	5	3.440872	ACAAGCTTAGTACGGTGAGAGAG	59.559	47.826	0.00	0.00	0.00	3.20
8	9	4.438472	GGAGTACAAGCTTAGTACGGTGAG	60.438	50.000	22.29	3.47	44.92	3.51
9	10	3.441572	GGAGTACAAGCTTAGTACGGTGA	59.558	47.826	22.29	0.61	44.92	4.02
10	11	3.428589	GGGAGTACAAGCTTAGTACGGTG	60.429	52.174	22.29	5.24	44.92	4.94
12	13	3.022406	AGGGAGTACAAGCTTAGTACGG	58.978	50.000	22.29	5.83	44.92	4.02
13	14	3.946558	AGAGGGAGTACAAGCTTAGTACG	59.053	47.826	22.29	6.42	44.92	3.67
14	15	8.688747	TTATAGAGGGAGTACAAGCTTAGTAC	57.311	38.462	21.63	21.63	41.59	2.73
15	16	9.129532	GTTTATAGAGGGAGTACAAGCTTAGTA	57.870	37.037	0.00	1.51	0.00	1.82
16	17	7.840210	AGTTTATAGAGGGAGTACAAGCTTAGT	59.160	37.037	0.00	2.56	0.00	2.24
17	18	8.240267	AGTTTATAGAGGGAGTACAAGCTTAG	57.760	38.462	0.00	0.00	0.00	2.18
18	19	9.705103	TTAGTTTATAGAGGGAGTACAAGCTTA	57.295	33.333	0.00	0.00	0.00	3.09
19	20	8.605325	TTAGTTTATAGAGGGAGTACAAGCTT	57.395	34.615	0.00	0.00	0.00	3.74
20	21	8.785184	ATTAGTTTATAGAGGGAGTACAAGCT	57.215	34.615	0.00	0.00	0.00	3.74
142	144	9.498176	GTGGGTGTAGTACTAATTATTAATGGG	57.502	37.037	3.61	0.00	0.00	4.00
164	169	3.450096	TCTGAGAAGATGATGACTGTGGG	59.550	47.826	0.00	0.00	0.00	4.61
239	253	2.024846	TGGGTGGTTAGAGAGAGAGAGG	60.025	54.545	0.00	0.00	0.00	3.69
248	268	1.546961	ACGAGAGTGGGTGGTTAGAG	58.453	55.000	0.00	0.00	46.97	2.43
249	269	3.759865	ACGAGAGTGGGTGGTTAGA	57.240	52.632	0.00	0.00	46.97	2.10
265	285	1.079127	GTGGGGGTGATGACTGACG	60.079	63.158	0.00	0.00	0.00	4.35
332	359	1.850345	GGGAGGAGAGAGAGGAAGAGA	59.150	57.143	0.00	0.00	0.00	3.10
333	360	1.568597	TGGGAGGAGAGAGAGGAAGAG	59.431	57.143	0.00	0.00	0.00	2.85
334	361	1.687492	TGGGAGGAGAGAGAGGAAGA	58.313	55.000	0.00	0.00	0.00	2.87

Showing 1 to 25 of 136 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.