AutoCloner

Multiple sequence alignment - TraesCS7D01G378000

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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	TraesCS7D01G378000	chr7D	100.000	3113	0	0	1	3113	489163552	489160440	0.000000e+00	5749
1	TraesCS7D01G378000	chr7D	89.810	1786	122	27	639	2397	33807375	33809127	0.000000e+00	2235
2	TraesCS7D01G378000	chr7D	95.094	1325	38	12	1056	2372	425723994	425725299	0.000000e+00	2061
3	TraesCS7D01G378000	chr7D	98.871	620	7	0	391	1010	425723375	425723994	0.000000e+00	1107
4	TraesCS7D01G378000	chr3D	96.416	2037	33	11	391	2407	508191458	508189442	0.000000e+00	3321
5	TraesCS7D01G378000	chr4D	96.300	2027	32	8	391	2398	471493432	471495434	0.000000e+00	3288
6	TraesCS7D01G378000	chr6B	94.205	2019	80	10	396	2393	184169704	184171706	0.000000e+00	3046
7	TraesCS7D01G378000	chr2D	93.888	2045	58	22	396	2395	33330210	33328188	0.000000e+00	3022
8	TraesCS7D01G378000	chr1B	91.429	2030	125	10	396	2397	11630724	11632732	0.000000e+00	2739
9	TraesCS7D01G378000	chr6A	90.467	2014	141	23	400	2394	119336774	119334793	0.000000e+00	2608
10	TraesCS7D01G378000	chr6A	84.161	423	59	6	403	823	184710744	184711160	1.340000e-108	403
11	TraesCS7D01G378000	chr5B	93.273	1650	75	7	501	2131	429803177	429804809	0.000000e+00	2399
12	TraesCS7D01G378000	chr5D	94.834	1510	41	8	904	2394	376685282	376686773	0.000000e+00	2322
13	TraesCS7D01G378000	chr2B	94.370	1261	52	5	399	1656	503979091	503977847	0.000000e+00	1917
14	TraesCS7D01G378000	chr6D	95.507	1046	25	5	1373	2398	428443242	428444285	0.000000e+00	1652
15	TraesCS7D01G378000	chr7B	94.518	912	33	3	1499	2393	23262382	23263293	0.000000e+00	1391
16	TraesCS7D01G378000	chr7B	86.486	259	24	5	2857	3113	517922272	517922023	1.100000e-69	274
17	TraesCS7D01G378000	chr7B	80.060	331	32	19	2533	2863	517922612	517922316	6.760000e-52	215
18	TraesCS7D01G378000	chr7B	90.323	124	11	1	2884	3006	517851136	517851259	8.930000e-36	161
19	TraesCS7D01G378000	chr3B	94.267	907	36	3	1505	2395	144196921	144197827	0.000000e+00	1373
20	TraesCS7D01G378000	chr7A	82.523	555	65	17	2567	3113	556357717	556357187	2.830000e-125	459
21	TraesCS7D01G378000	chr7A	73.879	513	81	37	2536	3029	556481331	556480853	4.160000e-34	156

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	TraesCS7D01G378000	chr7D	489160440	489163552	3112	True	5749.0	5749	100.0000	1	3113	1	chr7D.!!$R1	3112
1	TraesCS7D01G378000	chr7D	33807375	33809127	1752	False	2235.0	2235	89.8100	639	2397	1	chr7D.!!$F1	1758
2	TraesCS7D01G378000	chr7D	425723375	425725299	1924	False	1584.0	2061	96.9825	391	2372	2	chr7D.!!$F2	1981
3	TraesCS7D01G378000	chr3D	508189442	508191458	2016	True	3321.0	3321	96.4160	391	2407	1	chr3D.!!$R1	2016
4	TraesCS7D01G378000	chr4D	471493432	471495434	2002	False	3288.0	3288	96.3000	391	2398	1	chr4D.!!$F1	2007
5	TraesCS7D01G378000	chr6B	184169704	184171706	2002	False	3046.0	3046	94.2050	396	2393	1	chr6B.!!$F1	1997
6	TraesCS7D01G378000	chr2D	33328188	33330210	2022	True	3022.0	3022	93.8880	396	2395	1	chr2D.!!$R1	1999
7	TraesCS7D01G378000	chr1B	11630724	11632732	2008	False	2739.0	2739	91.4290	396	2397	1	chr1B.!!$F1	2001
8	TraesCS7D01G378000	chr6A	119334793	119336774	1981	True	2608.0	2608	90.4670	400	2394	1	chr6A.!!$R1	1994
9	TraesCS7D01G378000	chr5B	429803177	429804809	1632	False	2399.0	2399	93.2730	501	2131	1	chr5B.!!$F1	1630
10	TraesCS7D01G378000	chr5D	376685282	376686773	1491	False	2322.0	2322	94.8340	904	2394	1	chr5D.!!$F1	1490
11	TraesCS7D01G378000	chr2B	503977847	503979091	1244	True	1917.0	1917	94.3700	399	1656	1	chr2B.!!$R1	1257
12	TraesCS7D01G378000	chr6D	428443242	428444285	1043	False	1652.0	1652	95.5070	1373	2398	1	chr6D.!!$F1	1025
13	TraesCS7D01G378000	chr7B	23262382	23263293	911	False	1391.0	1391	94.5180	1499	2393	1	chr7B.!!$F1	894
14	TraesCS7D01G378000	chr7B	517922023	517922612	589	True	244.5	274	83.2730	2533	3113	2	chr7B.!!$R1	580
15	TraesCS7D01G378000	chr3B	144196921	144197827	906	False	1373.0	1373	94.2670	1505	2395	1	chr3B.!!$F1	890
16	TraesCS7D01G378000	chr7A	556357187	556357717	530	True	459.0	459	82.5230	2567	3113	1	chr7A.!!$R1	546

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	End Stability	Orientation
215	216	0.033920	ATGTCGCAGTCTGAGCAACA	59.966	50.0	3.32	2.23	3.33	F
346	347	0.037790	AGTCAGCTTCTTCACCTCGC	60.038	55.0	0.00	0.00	5.03	F
1051	1080	0.038166	GTTGCCTCTGTCAATGGGGA	59.962	55.0	0.00	0.00	4.81	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1052	1081	0.736325	GTCGTCCCCATTGACAGTCG	60.736	60.000	34.88	4.18	R
1239	1278	1.955778	CAACCCTCATTTGTGTCTGCA	59.044	47.619	0.00	4.41	R
2722	2808	0.179062	ATCTGCCGCTTCCATCTGAC	60.179	55.000	0.00	3.51	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	Hairpin	End Stability
18	19	1.377856	GGGAAGAACAGGCCTCAGC	60.378	63.158	38.76	4.26
28	29	4.852962	GCCTCAGCCTCACTCATC	57.147	61.111	0.00	2.92
29	30	1.903294	GCCTCAGCCTCACTCATCA	59.097	57.895	0.00	3.07
30	31	0.179078	GCCTCAGCCTCACTCATCAG	60.179	60.000	0.00	2.90
31	32	0.464870	CCTCAGCCTCACTCATCAGG	59.535	60.000	0.00	3.86
32	33	1.193323	CTCAGCCTCACTCATCAGGT	58.807	55.000	31.65	4.00
33	34	1.136695	CTCAGCCTCACTCATCAGGTC	59.863	57.143	31.65	3.85
34	35	1.193323	CAGCCTCACTCATCAGGTCT	58.807	55.000	31.65	3.85
35	36	1.136695	CAGCCTCACTCATCAGGTCTC	59.863	57.143	31.65	3.36
36	37	1.006998	AGCCTCACTCATCAGGTCTCT	59.993	52.381	31.65	3.10
37	38	1.408702	GCCTCACTCATCAGGTCTCTC	59.591	57.143	31.65	3.20
38	39	2.031120	CCTCACTCATCAGGTCTCTCC	58.969	57.143	0.00	3.71
39	40	2.031120	CTCACTCATCAGGTCTCTCCC	58.969	57.143	36.75	4.30
40	41	1.643286	TCACTCATCAGGTCTCTCCCT	59.357	52.381	36.75	4.20
41	42	2.031120	CACTCATCAGGTCTCTCCCTC	58.969	57.143	36.75	4.30
42	43	1.929494	ACTCATCAGGTCTCTCCCTCT	59.071	52.381	36.75	3.69
43	44	2.091885	ACTCATCAGGTCTCTCCCTCTC	60.092	54.545	36.75	3.20
44	45	1.216678	TCATCAGGTCTCTCCCTCTCC	59.783	57.143	36.75	3.71
45	46	0.560688	ATCAGGTCTCTCCCTCTCCC	59.439	60.000	36.75	4.30
46	47	0.553862	TCAGGTCTCTCCCTCTCCCT	60.554	60.000	36.75	4.20
47	48	0.106217	CAGGTCTCTCCCTCTCCCTC	60.106	65.000	36.75	4.30
48	49	0.254107	AGGTCTCTCCCTCTCCCTCT	60.254	60.000	36.75	3.69
49	50	0.185175	GGTCTCTCCCTCTCCCTCTC	59.815	65.000	0.00	3.20
50	51	1.222567	GTCTCTCCCTCTCCCTCTCT	58.777	60.000	0.00	3.10
51	52	1.143073	GTCTCTCCCTCTCCCTCTCTC	59.857	61.905	0.00	3.20

Showing 1 to 25 of 416 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	1.377856	GCTGAGGCCTGTTCTTCCC	60.378	63.158	12.00	0.00	3.97
1	2	4.310288	GCTGAGGCCTGTTCTTCC	57.690	61.111	12.00	0.00	3.46
11	12	0.179078	CTGATGAGTGAGGCTGAGGC	60.179	60.000	0.00	37.82	4.70
12	13	0.464870	CCTGATGAGTGAGGCTGAGG	59.535	60.000	0.00	0.00	3.86
13	14	1.136695	GACCTGATGAGTGAGGCTGAG	59.863	57.143	0.00	30.90	3.35
14	15	1.189752	GACCTGATGAGTGAGGCTGA	58.810	55.000	0.00	30.90	4.26
15	16	1.136695	GAGACCTGATGAGTGAGGCTG	59.863	57.143	0.00	30.90	4.85
16	17	1.006998	AGAGACCTGATGAGTGAGGCT	59.993	52.381	0.00	30.90	4.58
17	18	1.408702	GAGAGACCTGATGAGTGAGGC	59.591	57.143	0.00	30.90	4.70
18	19	2.031120	GGAGAGACCTGATGAGTGAGG	58.969	57.143	0.00	34.49	3.86
19	20	2.031120	GGGAGAGACCTGATGAGTGAG	58.969	57.143	0.00	38.98	3.51
20	21	1.643286	AGGGAGAGACCTGATGAGTGA	59.357	52.381	0.00	40.04	3.41
21	22	2.031120	GAGGGAGAGACCTGATGAGTG	58.969	57.143	0.00	42.10	3.51
22	23	1.929494	AGAGGGAGAGACCTGATGAGT	59.071	52.381	0.00	42.10	3.41
23	24	2.586425	GAGAGGGAGAGACCTGATGAG	58.414	57.143	0.00	42.10	2.90
24	25	1.216678	GGAGAGGGAGAGACCTGATGA	59.783	57.143	0.00	42.10	2.92
25	26	1.703411	GGAGAGGGAGAGACCTGATG	58.297	60.000	0.00	42.10	3.07
26	27	0.560688	GGGAGAGGGAGAGACCTGAT	59.439	60.000	0.00	42.10	2.90
27	28	0.553862	AGGGAGAGGGAGAGACCTGA	60.554	60.000	0.00	42.10	3.86
28	29	0.106217	GAGGGAGAGGGAGAGACCTG	60.106	65.000	0.00	42.10	4.00
29	30	0.254107	AGAGGGAGAGGGAGAGACCT	60.254	60.000	0.00	45.57	3.85
30	31	0.185175	GAGAGGGAGAGGGAGAGACC	59.815	65.000	0.00	38.08	3.85
31	32	1.143073	GAGAGAGGGAGAGGGAGAGAC	59.857	61.905	0.00	0.00	3.36
32	33	1.010793	AGAGAGAGGGAGAGGGAGAGA	59.989	57.143	0.00	0.00	3.10
33	34	1.421646	GAGAGAGAGGGAGAGGGAGAG	59.578	61.905	0.00	0.00	3.20

Showing 1 to 25 of 402 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.