AutoCloner

Multiple sequence alignment - TraesCS5D01G066900

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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	TraesCS5D01G066900	chr5D	100.000	5867	0	0	1	5867	62203825	62209691	0.000000e+00	10835.0
1	TraesCS5D01G066900	chr5D	77.452	989	153	42	3132	4082	62205954	62206910	1.450000e-145	527.0
2	TraesCS5D01G066900	chr5D	77.452	989	153	42	2130	3086	62206956	62207906	1.450000e-145	527.0
3	TraesCS5D01G066900	chr5D	82.109	531	50	22	214	702	62063447	62063974	4.230000e-111	412.0
4	TraesCS5D01G066900	chr5D	87.766	188	15	6	38	221	62063119	62063302	4.610000e-51	213.0
5	TraesCS5D01G066900	chr5D	79.630	108	16	6	5085	5189	62209013	62208909	8.160000e-09	73.1
6	TraesCS5D01G066900	chr5D	97.500	40	1	0	1	40	403646206	403646167	1.050000e-07	69.4
7	TraesCS5D01G066900	chr5D	97.500	40	1	0	1	40	411142714	411142675	1.050000e-07	69.4
8	TraesCS5D01G066900	chr5A	85.909	880	96	14	343	1207	52258270	52259136	0.000000e+00	913.0
9	TraesCS5D01G066900	chr5A	85.795	880	97	14	343	1207	52251213	52252079	0.000000e+00	907.0
10	TraesCS5D01G066900	chr5A	86.305	701	79	5	5165	5864	52260257	52260941	0.000000e+00	747.0
11	TraesCS5D01G066900	chr5A	86.020	701	81	5	5165	5864	52253201	52253885	0.000000e+00	736.0
12	TraesCS5D01G066900	chr5A	87.736	318	16	8	51	362	52244239	52244539	3.360000e-92	350.0
13	TraesCS5D01G066900	chr5A	100.000	37	0	0	1	37	53429365	53429401	1.050000e-07	69.4
14	TraesCS5D01G066900	chrUn	86.120	317	23	7	51	362	455110207	455109907	7.330000e-84	322.0
15	TraesCS5D01G066900	chrUn	85.893	319	22	7	51	362	449769142	449768840	9.490000e-83	318.0
16	TraesCS5D01G066900	chrUn	90.960	177	12	3	187	362	405785939	405786112	9.830000e-58	235.0
17	TraesCS5D01G066900	chrUn	90.960	177	12	3	187	362	431720579	431720752	9.830000e-58	235.0
18	TraesCS5D01G066900	chrUn	84.375	128	7	1	51	178	405785772	405785886	4.810000e-21	113.0
19	TraesCS5D01G066900	chr7D	100.000	41	0	0	1	41	26654038	26654078	6.300000e-10	76.8
20	TraesCS5D01G066900	chr7D	97.561	41	1	0	1	41	617195302	617195342	2.930000e-08	71.3
21	TraesCS5D01G066900	chr6D	97.674	43	1	0	1	43	43962456	43962414	2.270000e-09	75.0
22	TraesCS5D01G066900	chr6D	100.000	39	0	0	1	39	298954021	298954059	8.160000e-09	73.1
23	TraesCS5D01G066900	chr4D	97.619	42	1	0	2	43	489332836	489332877	8.160000e-09	73.1
24	TraesCS5D01G066900	chr4D	100.000	30	0	0	2979	3008	468272650	468272679	8.210000e-04	56.5
25	TraesCS5D01G066900	chr7B	100.000	38	0	0	1	38	683401471	683401434	2.930000e-08	71.3

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	TraesCS5D01G066900	chr5D	62203825	62209691	5866	False	3963.0	10835	84.9680	1	5867	3	chr5D.!!$F2	5866
1	TraesCS5D01G066900	chr5D	62063119	62063974	855	False	312.5	412	84.9375	38	702	2	chr5D.!!$F1	664
2	TraesCS5D01G066900	chr5A	52258270	52260941	2671	False	830.0	913	86.1070	343	5864	2	chr5A.!!$F4	5521
3	TraesCS5D01G066900	chr5A	52251213	52253885	2672	False	821.5	907	85.9075	343	5864	2	chr5A.!!$F3	5521

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
212	216	0.250038	CCCCCGTGCTAGTGATCATG	60.250	60.0	0.00	0.00	0.00	3.07	F
1325	1535	0.034477	AGGGTACGCTTGGAAATGGG	60.034	55.0	6.62	0.00	0.00	4.00	F
2193	2406	0.035458	GCTTACCACTGGAGCTGTGT	59.965	55.0	0.71	0.00	32.65	3.72	F
3173	3386	0.034059	CGTGGGTAGATGAGGATGCC	59.966	60.0	0.00	0.00	0.00	4.40	F
3450	3663	0.111061	ACAGTTGGCCAATCTGAGCA	59.889	50.0	34.89	9.75	33.93	4.26	F
4313	4526	0.108138	AGTAGCTGCTTGGCGGTTAG	60.108	55.0	7.79	0.00	37.24	2.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2174	2387	0.035458	ACACAGCTCCAGTGGTAAGC	59.965	55.0	13.75	13.75	41.21	3.09	R
3154	3367	0.034059	GGCATCCTCATCTACCCACG	59.966	60.0	0.00	0.00	0.00	4.94	R
3431	3644	0.111061	TGCTCAGATTGGCCAACTGT	59.889	50.0	30.39	16.35	33.93	3.55	R
4294	4507	0.108138	CTAACCGCCAAGCAGCTACT	60.108	55.0	0.00	0.00	0.00	2.57	R
4392	4605	0.178068	GATGGCCCTGCGAAGAGTAA	59.822	55.0	0.00	0.00	0.00	2.24	R
5722	5957	0.468585	TGCTCCCCATGGCAATCATC	60.469	55.0	6.09	0.00	35.40	2.92	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
33	34	9.953697	TGTATTATAATGCACCGTAAAATTTCC	57.046	29.630	11.69	0.00	0.00	3.13
34	35	9.401873	GTATTATAATGCACCGTAAAATTTCCC	57.598	33.333	8.28	0.00	0.00	3.97
35	36	5.923733	ATAATGCACCGTAAAATTTCCCA	57.076	34.783	0.00	0.00	0.00	4.37
36	37	4.608948	AATGCACCGTAAAATTTCCCAA	57.391	36.364	0.00	0.00	0.00	4.12
37	38	4.608948	ATGCACCGTAAAATTTCCCAAA	57.391	36.364	0.00	0.00	0.00	3.28
38	39	4.402056	TGCACCGTAAAATTTCCCAAAA	57.598	36.364	0.00	0.00	0.00	2.44
39	40	4.766375	TGCACCGTAAAATTTCCCAAAAA	58.234	34.783	0.00	0.00	0.00	1.94
124	125	2.905996	TACCTGGGCTGGGTGCTTG	61.906	63.158	11.09	0.00	42.39	4.01
154	155	2.949714	ACAAATGACAGAGCGAAACG	57.050	45.000	0.00	0.00	0.00	3.60
169	170	1.977412	GAAACGGTCGTTCGAGAAGAG	59.023	52.381	9.24	0.00	37.35	2.85
189	193	1.334689	GCTTTAACTGGGTGTTCACGC	60.335	52.381	12.03	12.03	39.89	5.34
210	214	3.628989	CCCCCGTGCTAGTGATCA	58.371	61.111	0.00	0.00	0.00	2.92
211	215	2.136791	CCCCCGTGCTAGTGATCAT	58.863	57.895	0.00	0.00	0.00	2.45
212	216	0.250038	CCCCCGTGCTAGTGATCATG	60.250	60.000	0.00	0.00	0.00	3.07
219	373	0.888285	GCTAGTGATCATGGCCTGCC	60.888	60.000	3.32	0.00	0.00	4.85
234	388	2.812178	GCCGTGCCGTCGTATGTT	60.812	61.111	0.00	0.00	0.00	2.71
235	389	3.077705	CCGTGCCGTCGTATGTTG	58.922	61.111	0.00	0.00	0.00	3.33
237	391	1.735198	CGTGCCGTCGTATGTTGGT	60.735	57.895	0.00	0.00	0.00	3.67
244	398	2.186891	CGTCGTATGTTGGTTATGCGA	58.813	47.619	0.00	0.00	39.66	5.10
247	401	3.441163	TCGTATGTTGGTTATGCGACTC	58.559	45.455	0.00	0.00	37.65	3.36
250	404	1.705256	TGTTGGTTATGCGACTCGAC	58.295	50.000	1.63	0.00	0.00	4.20
261	415	4.681978	ACTCGACCGCACAAGGGC	62.682	66.667	0.00	0.00	35.43	5.19
292	446	3.450457	ACAGTTGCATCCAAACTTTCCAA	59.550	39.130	0.00	0.00	31.68	3.53
294	448	3.706086	AGTTGCATCCAAACTTTCCAACT	59.294	39.130	0.00	0.00	37.27	3.16
295	449	3.731652	TGCATCCAAACTTTCCAACTG	57.268	42.857	0.00	0.00	0.00	3.16

Showing 1 to 25 of 1,687 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	9.738832	AAATTTTACGGTGCATTATAATACACC	57.261	29.630	27.91	27.91	45.41	4.16
7	8	9.953697	GGAAATTTTACGGTGCATTATAATACA	57.046	29.630	0.00	0.00	0.00	2.29
8	9	9.401873	GGGAAATTTTACGGTGCATTATAATAC	57.598	33.333	0.00	0.00	0.00	1.89
9	10	9.132923	TGGGAAATTTTACGGTGCATTATAATA	57.867	29.630	0.00	0.00	0.00	0.98
10	11	8.012957	TGGGAAATTTTACGGTGCATTATAAT	57.987	30.769	0.00	0.00	0.00	1.28
11	12	7.406031	TGGGAAATTTTACGGTGCATTATAA	57.594	32.000	0.00	0.00	0.00	0.98
12	13	7.406031	TTGGGAAATTTTACGGTGCATTATA	57.594	32.000	0.00	0.00	0.00	0.98
13	14	5.923733	TGGGAAATTTTACGGTGCATTAT	57.076	34.783	0.00	0.00	0.00	1.28
14	15	5.723672	TTGGGAAATTTTACGGTGCATTA	57.276	34.783	0.00	0.00	0.00	1.90
15	16	4.608948	TTGGGAAATTTTACGGTGCATT	57.391	36.364	0.00	0.00	0.00	3.56
16	17	4.608948	TTTGGGAAATTTTACGGTGCAT	57.391	36.364	0.00	0.00	0.00	3.96
17	18	4.402056	TTTTGGGAAATTTTACGGTGCA	57.598	36.364	0.00	0.00	0.00	4.57
41	42	0.031178	CGGAGCAGTGCAAGCTTTTT	59.969	50.000	19.20	0.00	43.58	1.94
42	43	0.819259	TCGGAGCAGTGCAAGCTTTT	60.819	50.000	19.20	0.00	43.58	2.27
46	47	2.758089	CCATCGGAGCAGTGCAAGC	61.758	63.158	19.20	5.98	0.00	4.01
54	55	3.785859	GGAGGTGCCATCGGAGCA	61.786	66.667	0.00	0.00	38.08	4.26
75	76	2.357517	AGCAACCTCGCCTCAACG	60.358	61.111	0.00	0.00	0.00	4.10
77	78	2.347490	GGAGCAACCTCGCCTCAA	59.653	61.111	0.00	0.00	39.06	3.02
80	81	4.379243	CACGGAGCAACCTCGCCT	62.379	66.667	0.00	0.00	39.06	5.52
124	125	3.501828	TCTGTCATTTGTACATGTGCACC	59.498	43.478	16.75	0.00	0.00	5.01
134	135	2.734606	CCGTTTCGCTCTGTCATTTGTA	59.265	45.455	0.00	0.00	0.00	2.41
137	138	1.798813	GACCGTTTCGCTCTGTCATTT	59.201	47.619	0.00	0.00	0.00	2.32
154	155	2.067414	AAAGCTCTTCTCGAACGACC	57.933	50.000	0.00	0.00	0.00	4.79
161	162	2.996621	CACCCAGTTAAAGCTCTTCTCG	59.003	50.000	0.00	0.00	0.00	4.04
169	170	1.334689	GCGTGAACACCCAGTTAAAGC	60.335	52.381	0.00	0.00	41.51	3.51

Showing 1 to 25 of 1,708 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.