AutoCloner

Multiple sequence alignment - TraesCS2D01G421500

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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	TraesCS2D01G421500	chr2D	100.000	3458	0	0	1	3458	535095637	535099094	0.000000e+00	6386.0
1	TraesCS2D01G421500	chr2D	100.000	48	0	0	2731	2778	535098321	535098368	4.750000e-14	89.8
2	TraesCS2D01G421500	chr2D	100.000	48	0	0	2685	2732	535098367	535098414	4.750000e-14	89.8
3	TraesCS2D01G421500	chr2A	97.125	1287	32	5	1451	2732	678361220	678362506	0.000000e+00	2167.0
4	TraesCS2D01G421500	chr2A	89.013	1256	64	25	192	1444	678359987	678361171	0.000000e+00	1487.0
5	TraesCS2D01G421500	chr2A	90.909	385	13	5	2731	3093	678362459	678362843	6.660000e-137	497.0
6	TraesCS2D01G421500	chr2A	88.150	346	27	7	3114	3458	678363174	678363506	1.930000e-107	399.0
7	TraesCS2D01G421500	chr2B	95.257	1286	36	11	1451	2732	636462049	636463313	0.000000e+00	2013.0
8	TraesCS2D01G421500	chr2B	92.741	799	41	10	654	1446	636461215	636462002	0.000000e+00	1138.0
9	TraesCS2D01G421500	chr2B	96.186	472	13	4	2731	3199	636463267	636463736	0.000000e+00	767.0
10	TraesCS2D01G421500	chr2B	92.830	265	18	1	3194	3458	636467188	636467451	1.950000e-102	383.0
11	TraesCS2D01G421500	chr2B	100.000	28	0	0	3273	3300	231633284	231633257	6.000000e-03	52.8
12	TraesCS2D01G421500	chr3B	93.023	43	3	0	988	1030	642217911	642217869	2.880000e-06	63.9
13	TraesCS2D01G421500	chr6B	96.875	32	0	1	3269	3300	585997474	585997504	6.000000e-03	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	TraesCS2D01G421500	chr2D	535095637	535099094	3457	False	2188.533333	6386	100.00000	1	3458	3	chr2D.!!$F1	3457
1	TraesCS2D01G421500	chr2A	678359987	678363506	3519	False	1137.500000	2167	91.29925	192	3458	4	chr2A.!!$F1	3266
2	TraesCS2D01G421500	chr2B	636461215	636467451	6236	False	1075.250000	2013	94.25350	654	3458	4	chr2B.!!$F1	2804

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
821	822	0.038744	CTCCCATCCCACACAAGCTT	59.961	55.0	0.0	0.0	0.0	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2753	2806	2.039879	GGAGCAGAGTTTTCCTAACCCA	59.96	50.0	0.0	0.0	0.0	4.51	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
31	32	8.961294	AATCCATGTTTCTTTTGAATCAAACA	57.039	26.923	8.06	3.95	41.64	2.83
32	33	8.961294	ATCCATGTTTCTTTTGAATCAAACAA	57.039	26.923	8.06	1.81	40.97	2.83
33	34	8.783833	TCCATGTTTCTTTTGAATCAAACAAA	57.216	26.923	8.06	7.75	40.97	2.83
34	35	9.393512	TCCATGTTTCTTTTGAATCAAACAAAT	57.606	25.926	8.06	0.00	40.97	2.32
35	36	9.440784	CCATGTTTCTTTTGAATCAAACAAATG	57.559	29.630	8.06	6.86	40.97	2.32
45	46	9.474920	TTTGAATCAAACAAATGAATAGTGTCC	57.525	29.630	4.03	0.00	33.25	4.02
46	47	8.175925	TGAATCAAACAAATGAATAGTGTCCA	57.824	30.769	0.00	0.00	32.06	4.02
47	48	8.081633	TGAATCAAACAAATGAATAGTGTCCAC	58.918	33.333	0.00	0.00	32.06	4.02
48	49	6.951062	TCAAACAAATGAATAGTGTCCACA	57.049	33.333	0.00	0.00	0.00	4.17
49	50	6.969366	TCAAACAAATGAATAGTGTCCACAG	58.031	36.000	0.00	0.00	0.00	3.66
50	51	6.770303	TCAAACAAATGAATAGTGTCCACAGA	59.230	34.615	0.00	0.00	0.00	3.41
51	52	6.808008	AACAAATGAATAGTGTCCACAGAG	57.192	37.500	0.00	0.00	0.00	3.35
52	53	6.114187	ACAAATGAATAGTGTCCACAGAGA	57.886	37.500	0.00	0.00	0.00	3.10
53	54	6.533730	ACAAATGAATAGTGTCCACAGAGAA	58.466	36.000	0.00	0.00	0.00	2.87
54	55	6.998074	ACAAATGAATAGTGTCCACAGAGAAA	59.002	34.615	0.00	0.00	0.00	2.52
55	56	7.502226	ACAAATGAATAGTGTCCACAGAGAAAA	59.498	33.333	0.00	0.00	0.00	2.29
56	57	7.678947	AATGAATAGTGTCCACAGAGAAAAG	57.321	36.000	0.00	0.00	0.00	2.27
57	58	6.419484	TGAATAGTGTCCACAGAGAAAAGA	57.581	37.500	0.00	0.00	0.00	2.52
58	59	6.459066	TGAATAGTGTCCACAGAGAAAAGAG	58.541	40.000	0.00	0.00	0.00	2.85
59	60	3.118905	AGTGTCCACAGAGAAAAGAGC	57.881	47.619	0.00	0.00	0.00	4.09
60	61	2.147150	GTGTCCACAGAGAAAAGAGCC	58.853	52.381	0.00	0.00	0.00	4.70
61	62	1.768275	TGTCCACAGAGAAAAGAGCCA	59.232	47.619	0.00	0.00	0.00	4.75
62	63	2.147150	GTCCACAGAGAAAAGAGCCAC	58.853	52.381	0.00	0.00	0.00	5.01
63	64	2.050144	TCCACAGAGAAAAGAGCCACT	58.950	47.619	0.00	0.00	0.00	4.00
64	65	3.006967	GTCCACAGAGAAAAGAGCCACTA	59.993	47.826	0.00	0.00	0.00	2.74

Showing 1 to 25 of 221 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	9.393512	TGTTTGATTCAAAAGAAACATGGATTT	57.606	25.926	13.21	0.00	35.03	2.17
6	7	8.961294	TGTTTGATTCAAAAGAAACATGGATT	57.039	26.923	13.21	0.00	35.03	3.01
7	8	8.961294	TTGTTTGATTCAAAAGAAACATGGAT	57.039	26.923	13.21	0.00	37.94	3.41
8	9	8.783833	TTTGTTTGATTCAAAAGAAACATGGA	57.216	26.923	13.21	0.00	37.94	3.41
9	10	9.440784	CATTTGTTTGATTCAAAAGAAACATGG	57.559	29.630	13.21	4.35	37.94	3.66
19	20	9.474920	GGACACTATTCATTTGTTTGATTCAAA	57.525	29.630	7.74	7.74	38.77	2.69
20	21	8.637099	TGGACACTATTCATTTGTTTGATTCAA	58.363	29.630	0.00	0.00	0.00	2.69
21	22	8.081633	GTGGACACTATTCATTTGTTTGATTCA	58.918	33.333	0.00	0.00	0.00	2.57
22	23	8.081633	TGTGGACACTATTCATTTGTTTGATTC	58.918	33.333	3.91	0.00	0.00	2.52
23	24	7.950512	TGTGGACACTATTCATTTGTTTGATT	58.049	30.769	3.91	0.00	0.00	2.57
24	25	7.448161	TCTGTGGACACTATTCATTTGTTTGAT	59.552	33.333	3.91	0.00	0.00	2.57
25	26	6.770303	TCTGTGGACACTATTCATTTGTTTGA	59.230	34.615	3.91	0.00	0.00	2.69
26	27	6.969366	TCTGTGGACACTATTCATTTGTTTG	58.031	36.000	3.91	0.00	0.00	2.93
27	28	6.998074	TCTCTGTGGACACTATTCATTTGTTT	59.002	34.615	3.91	0.00	0.00	2.83
28	29	6.533730	TCTCTGTGGACACTATTCATTTGTT	58.466	36.000	3.91	0.00	0.00	2.83
29	30	6.114187	TCTCTGTGGACACTATTCATTTGT	57.886	37.500	3.91	0.00	0.00	2.83
30	31	7.439157	TTTCTCTGTGGACACTATTCATTTG	57.561	36.000	3.91	0.00	0.00	2.32
31	32	7.939039	TCTTTTCTCTGTGGACACTATTCATTT	59.061	33.333	3.91	0.00	0.00	2.32
32	33	7.453393	TCTTTTCTCTGTGGACACTATTCATT	58.547	34.615	3.91	0.00	0.00	2.57
33	34	7.009179	TCTTTTCTCTGTGGACACTATTCAT	57.991	36.000	3.91	0.00	0.00	2.57
34	35	6.419484	TCTTTTCTCTGTGGACACTATTCA	57.581	37.500	3.91	0.00	0.00	2.57
35	36	5.350091	GCTCTTTTCTCTGTGGACACTATTC	59.650	44.000	3.91	0.00	0.00	1.75
36	37	5.241662	GCTCTTTTCTCTGTGGACACTATT	58.758	41.667	3.91	0.00	0.00	1.73
37	38	4.323104	GGCTCTTTTCTCTGTGGACACTAT	60.323	45.833	3.91	0.00	0.00	2.12
38	39	3.006967	GGCTCTTTTCTCTGTGGACACTA	59.993	47.826	3.91	0.00	0.00	2.74

Showing 1 to 25 of 248 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.