AutoCloner

Multiple sequence alignment - TraesCS2D01G392300

Loading Multiple Alignment...

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	TraesCS2D01G392300	chr2D	100.000	2198	0	0	1	2198	499752559	499750362	0.000000e+00	4060.0
1	TraesCS2D01G392300	chr2D	84.861	469	47	14	1	456	481652290	481652747	3.330000e-123	451.0
2	TraesCS2D01G392300	chr2D	88.380	284	16	10	2	269	186311898	186312180	2.100000e-85	326.0
3	TraesCS2D01G392300	chr2D	100.000	41	0	0	2158	2198	499744858	499744818	2.340000e-10	76.8
4	TraesCS2D01G392300	chr2A	90.965	1306	84	18	470	1759	644308813	644307526	0.000000e+00	1727.0
5	TraesCS2D01G392300	chr2A	84.322	472	48	11	1	456	198742104	198742565	2.590000e-119	438.0
6	TraesCS2D01G392300	chr2A	81.971	477	61	16	1	455	775590217	775589744	4.430000e-102	381.0
7	TraesCS2D01G392300	chr2B	89.655	1305	70	16	468	1767	587255670	587254426	0.000000e+00	1602.0
8	TraesCS2D01G392300	chr2B	89.258	391	27	4	1765	2155	587253860	587253485	1.970000e-130	475.0
9	TraesCS2D01G392300	chr2B	82.030	473	67	13	1	456	730644469	730644940	9.520000e-104	387.0
10	TraesCS2D01G392300	chr4D	88.172	465	36	10	1	456	289348729	289349183	8.930000e-149	536.0
11	TraesCS2D01G392300	chr4D	84.314	357	33	15	121	456	461778025	461778379	5.850000e-86	327.0
12	TraesCS2D01G392300	chr3D	85.062	482	45	12	1	456	555187882	555188362	1.190000e-127	466.0
13	TraesCS2D01G392300	chr3A	84.244	476	51	14	3	456	230986903	230987376	2.000000e-120	442.0
14	TraesCS2D01G392300	chr6D	83.932	473	52	19	1	453	291390546	291391014	4.340000e-117	431.0
15	TraesCS2D01G392300	chr5B	82.390	477	60	13	3	456	638767375	638767850	5.690000e-106	394.0
16	TraesCS2D01G392300	chr5B	77.944	467	78	15	1	456	598133734	598133282	3.600000e-68	268.0
17	TraesCS2D01G392300	chr6A	83.726	424	43	16	51	456	557143126	557142711	5.730000e-101	377.0
18	TraesCS2D01G392300	chr4B	85.399	363	50	2	1759	2121	456604256	456603897	7.410000e-100	374.0
19	TraesCS2D01G392300	chr7D	80.962	478	65	20	1	456	84419248	84419721	2.680000e-94	355.0
20	TraesCS2D01G392300	chr1D	82.637	311	34	18	169	463	463924938	463924632	7.790000e-65	257.0
21	TraesCS2D01G392300	chr5A	97.561	41	1	0	2158	2198	350807480	350807520	1.090000e-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	TraesCS2D01G392300	chr2D	499750362	499752559	2197	True	4060.0	4060	100.0000	1	2198	1	chr2D.!!$R2	2197
1	TraesCS2D01G392300	chr2A	644307526	644308813	1287	True	1727.0	1727	90.9650	470	1759	1	chr2A.!!$R1	1289
2	TraesCS2D01G392300	chr2B	587253485	587255670	2185	True	1038.5	1602	89.4565	468	2155	2	chr2B.!!$R1	1687

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
225	226	0.035458	GCATAGCTGGGGCGTAATCT	59.965	55.0	0.0	0.0	44.37	2.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1584	1609	0.035317	CCAGCCACAACAGTCTAGCA	59.965	55.0	0.0	0.0	0.0	3.49	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
25	26	3.518998	CGAGGAGGACGGCGTCAT	61.519	66.667	37.13	33.17	33.68	3.06
26	27	2.413765	GAGGAGGACGGCGTCATC	59.586	66.667	37.74	37.74	41.78	2.92
27	28	3.471244	GAGGAGGACGGCGTCATCG	62.471	68.421	37.53	0.70	43.16	3.84
28	29	3.823330	GGAGGACGGCGTCATCGT	61.823	66.667	37.53	22.08	43.16	3.73
33	34	4.175489	ACGGCGTCATCGTCCTCG	62.175	66.667	6.77	0.00	38.56	4.63
48	49	2.745100	TCGACACCGACGAGGAGG	60.745	66.667	8.56	0.00	45.00	4.30
49	50	3.812019	CGACACCGACGAGGAGGG	61.812	72.222	8.56	1.29	45.00	4.30
50	51	4.131088	GACACCGACGAGGAGGGC	62.131	72.222	8.56	0.00	45.00	5.19
89	90	4.101790	CCACCACGCATCGGCAAC	62.102	66.667	0.00	0.00	41.24	4.17
90	91	4.101790	CACCACGCATCGGCAACC	62.102	66.667	0.00	0.00	41.24	3.77
93	94	3.803082	CACGCATCGGCAACCCTG	61.803	66.667	0.00	0.00	41.24	4.45
108	109	3.390521	CTGGCGAGGGGTGCAGTA	61.391	66.667	0.00	0.00	0.00	2.74
109	110	3.376935	CTGGCGAGGGGTGCAGTAG	62.377	68.421	0.00	0.00	0.00	2.57
110	111	4.162690	GGCGAGGGGTGCAGTAGG	62.163	72.222	0.00	0.00	0.00	3.18
111	112	4.162690	GCGAGGGGTGCAGTAGGG	62.163	72.222	0.00	0.00	0.00	3.53
112	113	2.363795	CGAGGGGTGCAGTAGGGA	60.364	66.667	0.00	0.00	0.00	4.20
113	114	2.722201	CGAGGGGTGCAGTAGGGAC	61.722	68.421	0.00	0.00	37.06	4.46
114	115	2.683933	AGGGGTGCAGTAGGGACG	60.684	66.667	0.00	0.00	39.01	4.79
115	116	3.782443	GGGGTGCAGTAGGGACGG	61.782	72.222	0.00	0.00	39.01	4.79
116	117	3.001406	GGGTGCAGTAGGGACGGT	61.001	66.667	0.00	0.00	39.01	4.83
117	118	2.264794	GGTGCAGTAGGGACGGTG	59.735	66.667	0.00	0.00	39.01	4.94
118	119	2.264794	GTGCAGTAGGGACGGTGG	59.735	66.667	0.00	0.00	0.00	4.61
119	120	3.702048	TGCAGTAGGGACGGTGGC	61.702	66.667	0.00	0.00	0.00	5.01
120	121	4.814294	GCAGTAGGGACGGTGGCG	62.814	72.222	0.00	0.00	0.00	5.69
121	122	4.143333	CAGTAGGGACGGTGGCGG	62.143	72.222	0.00	0.00	0.00	6.13

Showing 1 to 25 of 346 entries

Previous1 2 3 4 5…14Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	3.471244	GATGACGCCGTCCTCCTCG	62.471	68.421	15.60	0.00	0.00	4.63
10	11	3.518998	CGATGACGCCGTCCTCCT	61.519	66.667	15.60	0.00	0.00	3.69
11	12	3.823330	ACGATGACGCCGTCCTCC	61.823	66.667	15.60	2.76	43.96	4.30
16	17	4.175489	CGAGGACGATGACGCCGT	62.175	66.667	0.00	0.00	43.96	5.68
17	18	3.872728	TCGAGGACGATGACGCCG	61.873	66.667	0.00	0.00	43.81	6.46
31	32	2.745100	CCTCCTCGTCGGTGTCGA	60.745	66.667	0.00	0.00	43.86	4.20
32	33	3.812019	CCCTCCTCGTCGGTGTCG	61.812	72.222	0.00	0.00	37.82	4.35
33	34	4.131088	GCCCTCCTCGTCGGTGTC	62.131	72.222	0.00	0.00	0.00	3.67
72	73	4.101790	GTTGCCGATGCGTGGTGG	62.102	66.667	0.00	0.00	41.78	4.61
73	74	4.101790	GGTTGCCGATGCGTGGTG	62.102	66.667	0.00	0.00	41.78	4.17
76	77	3.803082	CAGGGTTGCCGATGCGTG	61.803	66.667	0.00	0.00	41.78	5.34
80	81	4.776322	TCGCCAGGGTTGCCGATG	62.776	66.667	0.00	0.00	0.00	3.84
81	82	4.473520	CTCGCCAGGGTTGCCGAT	62.474	66.667	0.00	0.00	0.00	4.18
91	92	3.376935	CTACTGCACCCCTCGCCAG	62.377	68.421	0.00	0.00	0.00	4.85
92	93	3.390521	CTACTGCACCCCTCGCCA	61.391	66.667	0.00	0.00	0.00	5.69
93	94	4.162690	CCTACTGCACCCCTCGCC	62.163	72.222	0.00	0.00	0.00	5.54
94	95	4.162690	CCCTACTGCACCCCTCGC	62.163	72.222	0.00	0.00	0.00	5.03
95	96	2.363795	TCCCTACTGCACCCCTCG	60.364	66.667	0.00	0.00	0.00	4.63
96	97	2.722201	CGTCCCTACTGCACCCCTC	61.722	68.421	0.00	0.00	0.00	4.30
97	98	2.683933	CGTCCCTACTGCACCCCT	60.684	66.667	0.00	0.00	0.00	4.79
98	99	3.782443	CCGTCCCTACTGCACCCC	61.782	72.222	0.00	0.00	0.00	4.95
99	100	3.001406	ACCGTCCCTACTGCACCC	61.001	66.667	0.00	0.00	0.00	4.61
100	101	2.264794	CACCGTCCCTACTGCACC	59.735	66.667	0.00	0.00	0.00	5.01
101	102	2.264794	CCACCGTCCCTACTGCAC	59.735	66.667	0.00	0.00	0.00	4.57
102	103	3.702048	GCCACCGTCCCTACTGCA	61.702	66.667	0.00	0.00	0.00	4.41

Showing 1 to 25 of 344 entries

Previous1 2 3 4 5…14Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.