AutoCloner

Multiple sequence alignment - TraesCS4D01G014900

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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	TraesCS4D01G014900	chr4D	100.000	2312	0	0	1	2312	6665131	6662820	0.000000e+00	4270
1	TraesCS4D01G014900	chr4D	96.875	128	3	1	1161	1288	6673283	6673157	1.800000e-51	213
2	TraesCS4D01G014900	chr7A	85.025	1202	54	57	1181	2312	44268762	44269907	0.000000e+00	1107
3	TraesCS4D01G014900	chr4A	87.102	597	29	14	107	686	596742391	596742956	1.170000e-177	632
4	TraesCS4D01G014900	chr4A	82.456	798	31	49	766	1517	596742955	596743689	4.250000e-167	597
5	TraesCS4D01G014900	chr4A	84.632	475	28	22	844	1288	596737907	596738366	4.560000e-117	431
6	TraesCS4D01G014900	chr4A	86.701	391	25	11	1885	2261	596744052	596744429	2.140000e-110	409
7	TraesCS4D01G014900	chr4A	93.711	159	10	0	1149	1307	596725478	596725636	2.970000e-59	239
8	TraesCS4D01G014900	chr4A	88.000	100	12	0	1629	1728	596743814	596743913	4.040000e-23	119
9	TraesCS4D01G014900	chr4B	83.666	551	48	22	994	1526	11928571	11928045	4.470000e-132	481
10	TraesCS4D01G014900	chr4B	82.033	423	27	21	1858	2269	11927711	11927327	4.800000e-82	315

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	TraesCS4D01G014900	chr4D	6662820	6665131	2311	True	4270.00	4270	100.00000	1	2312	1	chr4D.!!$R1	2311
1	TraesCS4D01G014900	chr7A	44268762	44269907	1145	False	1107.00	1107	85.02500	1181	2312	1	chr7A.!!$F1	1131
2	TraesCS4D01G014900	chr4A	596742391	596744429	2038	False	439.25	632	86.06475	107	2261	4	chr4A.!!$F3	2154
3	TraesCS4D01G014900	chr4B	11927327	11928571	1244	True	398.00	481	82.84950	994	2269	2	chr4B.!!$R1	1275

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
998	1048	0.034059	CATAGCTTAGCCAGGTCGGG	59.966	60.0	0.0	0.0	34.13	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1955	2235	0.379669	CGGCCAAGATCATCAGTTGC	59.62	55.0	2.24	0.0	0.0	4.17	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
18	19	3.976339	GGATAGCTGTCTCATGCGT	57.024	52.632	10.54	0.00	0.00	5.24
20	21	3.584406	GGATAGCTGTCTCATGCGTAT	57.416	47.619	10.54	0.00	0.00	3.06
21	22	3.249091	GGATAGCTGTCTCATGCGTATG	58.751	50.000	10.54	7.22	35.57	2.39
22	23	3.305676	GGATAGCTGTCTCATGCGTATGT	60.306	47.826	13.39	0.00	35.73	2.29
23	24	1.931906	AGCTGTCTCATGCGTATGTG	58.068	50.000	13.39	11.08	35.73	3.21
24	25	1.205655	AGCTGTCTCATGCGTATGTGT	59.794	47.619	13.39	0.00	35.73	3.72
25	26	1.590238	GCTGTCTCATGCGTATGTGTC	59.410	52.381	13.39	9.26	35.73	3.67
26	27	2.196749	CTGTCTCATGCGTATGTGTCC	58.803	52.381	13.39	7.10	35.73	4.02
27	28	1.200483	GTCTCATGCGTATGTGTCCG	58.800	55.000	13.39	0.00	35.73	4.79
35	36	2.554806	CGTATGTGTCCGCAGACTAA	57.445	50.000	1.05	0.00	43.91	2.24
36	37	3.079960	CGTATGTGTCCGCAGACTAAT	57.920	47.619	1.05	0.00	43.91	1.73
37	38	3.043586	CGTATGTGTCCGCAGACTAATC	58.956	50.000	1.05	0.00	43.91	1.75
38	39	3.488553	CGTATGTGTCCGCAGACTAATCA	60.489	47.826	1.05	0.00	43.91	2.57
39	40	3.827008	ATGTGTCCGCAGACTAATCAT	57.173	42.857	1.05	0.00	43.91	2.45
40	41	2.892374	TGTGTCCGCAGACTAATCATG	58.108	47.619	1.05	0.00	43.91	3.07
41	42	2.233676	TGTGTCCGCAGACTAATCATGT	59.766	45.455	1.05	0.00	43.91	3.21
42	43	2.860735	GTGTCCGCAGACTAATCATGTC	59.139	50.000	1.05	0.00	43.91	3.06
43	44	2.159099	TGTCCGCAGACTAATCATGTCC	60.159	50.000	1.05	0.00	43.91	4.02
44	45	2.107366	TCCGCAGACTAATCATGTCCA	58.893	47.619	0.00	0.00	35.21	4.02
45	46	2.700371	TCCGCAGACTAATCATGTCCAT	59.300	45.455	0.00	0.00	35.21	3.41
46	47	2.804527	CCGCAGACTAATCATGTCCATG	59.195	50.000	0.71	0.71	40.09	3.66
47	48	2.804527	CGCAGACTAATCATGTCCATGG	59.195	50.000	4.97	4.97	39.24	3.66
48	49	3.493176	CGCAGACTAATCATGTCCATGGA	60.493	47.826	11.44	11.44	39.24	3.41
49	50	4.454678	GCAGACTAATCATGTCCATGGAA	58.545	43.478	18.20	7.57	39.24	3.53
50	51	5.068636	GCAGACTAATCATGTCCATGGAAT	58.931	41.667	18.20	9.70	39.24	3.01

Showing 1 to 25 of 204 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	3.672397	CACATACGCATGAGACAGCTATC	59.328	47.826	2.50	0.00	35.96	2.08
2	3	3.068732	ACACATACGCATGAGACAGCTAT	59.931	43.478	2.50	0.00	35.96	2.97
3	4	2.427095	ACACATACGCATGAGACAGCTA	59.573	45.455	2.50	0.00	35.96	3.32
4	5	1.205655	ACACATACGCATGAGACAGCT	59.794	47.619	2.50	0.00	35.96	4.24
5	6	1.590238	GACACATACGCATGAGACAGC	59.410	52.381	2.50	0.00	35.96	4.40
6	7	2.196749	GGACACATACGCATGAGACAG	58.803	52.381	2.50	0.00	35.96	3.51
7	8	1.469079	CGGACACATACGCATGAGACA	60.469	52.381	2.50	0.00	35.96	3.41
8	9	1.200483	CGGACACATACGCATGAGAC	58.800	55.000	2.50	0.00	35.96	3.36
9	10	3.641031	CGGACACATACGCATGAGA	57.359	52.632	2.50	0.00	35.96	3.27
16	17	2.554806	TTAGTCTGCGGACACATACG	57.445	50.000	27.02	0.00	44.36	3.06
17	18	4.041740	TGATTAGTCTGCGGACACATAC	57.958	45.455	27.02	14.00	44.36	2.39
18	19	4.099419	ACATGATTAGTCTGCGGACACATA	59.901	41.667	27.02	8.66	44.36	2.29
19	20	3.118629	ACATGATTAGTCTGCGGACACAT	60.119	43.478	27.02	20.58	44.36	3.21
20	21	2.233676	ACATGATTAGTCTGCGGACACA	59.766	45.455	27.02	19.43	44.36	3.72
21	22	2.860735	GACATGATTAGTCTGCGGACAC	59.139	50.000	27.02	14.95	44.36	3.67
22	23	2.159099	GGACATGATTAGTCTGCGGACA	60.159	50.000	27.02	8.35	44.36	4.02
23	24	2.159099	TGGACATGATTAGTCTGCGGAC	60.159	50.000	18.39	18.39	42.41	4.79
24	25	2.107366	TGGACATGATTAGTCTGCGGA	58.893	47.619	0.00	0.00	36.29	5.54
25	26	2.602257	TGGACATGATTAGTCTGCGG	57.398	50.000	0.00	0.00	36.29	5.69
26	27	2.804527	CCATGGACATGATTAGTCTGCG	59.195	50.000	5.56	0.00	41.20	5.18
27	28	4.077300	TCCATGGACATGATTAGTCTGC	57.923	45.455	11.44	0.00	41.20	4.26
28	29	6.293698	TCATTCCATGGACATGATTAGTCTG	58.706	40.000	24.15	5.20	41.20	3.51
29	30	6.505048	TCATTCCATGGACATGATTAGTCT	57.495	37.500	24.15	0.00	41.20	3.24
30	31	6.713903	ACATCATTCCATGGACATGATTAGTC	59.286	38.462	30.06	0.00	41.20	2.59
31	32	6.489022	CACATCATTCCATGGACATGATTAGT	59.511	38.462	30.06	25.54	41.20	2.24

Showing 1 to 25 of 229 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.