AutoCloner

Multiple sequence alignment - TraesCS2D01G333300

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	TraesCS2D01G333300	chr2D	100.000	4469	0	0	1	4469	426941498	426945966	0.000000e+00	8253.0
1	TraesCS2D01G333300	chr2D	96.154	78	3	0	3528	3605	426944956	426945033	1.300000e-25	128.0
2	TraesCS2D01G333300	chr2D	96.154	78	3	0	3459	3536	426945025	426945102	1.300000e-25	128.0
3	TraesCS2D01G333300	chr2D	89.333	75	7	1	2555	2629	76629924	76629997	4.760000e-15	93.5
4	TraesCS2D01G333300	chr2D	97.222	36	1	0	3413	3448	424678722	424678687	1.340000e-05	62.1
5	TraesCS2D01G333300	chr2A	95.695	3554	112	16	2	3536	561557503	561553972	0.000000e+00	5677.0
6	TraesCS2D01G333300	chr2A	91.027	925	50	10	3558	4458	561554019	561553104	0.000000e+00	1218.0
7	TraesCS2D01G333300	chr2A	72.588	456	104	19	1202	1645	761305507	761305953	3.630000e-26	130.0
8	TraesCS2D01G333300	chr2A	85.417	96	9	3	4316	4408	561553615	561553522	1.320000e-15	95.3
9	TraesCS2D01G333300	chr2A	97.059	34	1	0	3415	3448	563919128	563919161	1.740000e-04	58.4
10	TraesCS2D01G333300	chr2B	95.403	3546	141	9	2	3536	503769774	503773308	0.000000e+00	5626.0
11	TraesCS2D01G333300	chr2B	95.052	384	16	3	4087	4469	503773883	503774264	6.400000e-168	601.0
12	TraesCS2D01G333300	chr2B	81.261	587	34	23	3528	4066	503773230	503773788	5.380000e-109	405.0
13	TraesCS2D01G333300	chr2B	76.812	483	72	22	2575	3032	499561478	499561011	7.470000e-58	235.0
14	TraesCS2D01G333300	chr2B	82.857	140	7	9	4234	4371	503773589	503773713	4.730000e-20	110.0
15	TraesCS2D01G333300	chr2B	88.372	86	10	0	3949	4034	503774111	503774196	2.200000e-18	104.0
16	TraesCS2D01G333300	chr2B	97.222	36	1	0	3413	3448	499560880	499560845	1.340000e-05	62.1
17	TraesCS2D01G333300	chr7B	91.166	883	39	20	2610	3483	738144216	738145068	0.000000e+00	1162.0
18	TraesCS2D01G333300	chr7B	87.614	985	56	21	1542	2509	738143249	738144184	0.000000e+00	1083.0
19	TraesCS2D01G333300	chr7B	75.110	1137	204	58	1348	2452	540248443	540249532	4.070000e-125	459.0
20	TraesCS2D01G333300	chr7B	79.375	320	53	11	2131	2442	663488293	663488607	3.500000e-51	213.0
21	TraesCS2D01G333300	chr7D	77.892	977	194	18	2498	3463	511326202	511327167	4.980000e-164	588.0
22	TraesCS2D01G333300	chr7D	74.978	1143	198	66	1348	2452	511325037	511326129	3.170000e-121	446.0
23	TraesCS2D01G333300	chr7A	75.263	1140	200	62	1348	2452	583871780	583872872	6.770000e-128	468.0

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	TraesCS2D01G333300	chr2D	426941498	426945966	4468	False	2836.333333	8253	97.436	1	4469	3	chr2D.!!$F2	4468
1	TraesCS2D01G333300	chr2A	561553104	561557503	4399	True	2330.100000	5677	90.713	2	4458	3	chr2A.!!$R1	4456
2	TraesCS2D01G333300	chr2B	503769774	503774264	4490	False	1369.200000	5626	88.589	2	4469	5	chr2B.!!$F1	4467
3	TraesCS2D01G333300	chr7B	738143249	738145068	1819	False	1122.500000	1162	89.390	1542	3483	2	chr7B.!!$F3	1941
4	TraesCS2D01G333300	chr7B	540248443	540249532	1089	False	459.000000	459	75.110	1348	2452	1	chr7B.!!$F1	1104
5	TraesCS2D01G333300	chr7D	511325037	511327167	2130	False	517.000000	588	76.435	1348	3463	2	chr7D.!!$F1	2115
6	TraesCS2D01G333300	chr7A	583871780	583872872	1092	False	468.000000	468	75.263	1348	2452	1	chr7A.!!$F1	1104

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
797	801	1.463444	GCGGTCACACAATCTTACCAC	59.537	52.381	0.00	0.0	0.0	4.16	F
2562	2652	2.031314	TACACCAACGCGCACCAT	59.969	55.556	5.73	0.0	0.0	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2650	2740	0.676782	GGCTTCCCGTACAAGCACAT	60.677	55.0	15.81	0.0	46.94	3.21	R
3637	3763	0.253044	GAGTGGCTTGCCAGGATGTA	59.747	55.0	15.31	0.0	0.00	2.29	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
40	41	5.261216	ACAAATGGATCGATAAACCAAGGT	58.739	37.500	8.26	4.87	37.24	3.50
41	42	5.357032	ACAAATGGATCGATAAACCAAGGTC	59.643	40.000	8.26	0.00	37.24	3.85
42	43	3.173668	TGGATCGATAAACCAAGGTCG	57.826	47.619	0.00	0.00	35.55	4.79
108	109	6.670695	AGAAACCAAGGAATAATTTGCAGT	57.329	33.333	0.00	0.00	0.00	4.40
115	116	7.029563	CCAAGGAATAATTTGCAGTAAGACAC	58.970	38.462	0.00	0.00	0.00	3.67
127	128	5.761234	TGCAGTAAGACACGGAGTAAATTTT	59.239	36.000	0.00	0.00	41.61	1.82
457	460	7.387122	TCTGCTGAGAAATCATCTACAATATGC	59.613	37.037	0.00	0.00	38.96	3.14
522	526	5.557891	AGAGAAGAAGAATCATTTTGCGG	57.442	39.130	0.00	0.00	0.00	5.69
587	591	3.782046	ACGCATTACAGTACAGATGTCC	58.218	45.455	0.00	0.00	32.02	4.02
630	634	5.888724	TGGAAACTTCACAATACAGTTGGAA	59.111	36.000	0.00	0.00	31.00	3.53
631	635	6.378564	TGGAAACTTCACAATACAGTTGGAAA	59.621	34.615	0.00	0.00	31.00	3.13
771	775	2.202932	CCTCCGCGTCCATGGAAG	60.203	66.667	21.96	21.96	32.89	3.46
792	796	2.325082	GGCGCGGTCACACAATCTT	61.325	57.895	8.83	0.00	0.00	2.40
797	801	1.463444	GCGGTCACACAATCTTACCAC	59.537	52.381	0.00	0.00	0.00	4.16
875	887	2.100584	AGCAGTACTAGCTGACTGATGC	59.899	50.000	22.40	13.93	44.88	3.91
897	909	2.221906	CTGCCACCTTTGCATGCCTC	62.222	60.000	16.68	0.00	38.22	4.70
2561	2651	2.968156	GTACACCAACGCGCACCA	60.968	61.111	5.73	0.00	0.00	4.17
2562	2652	2.031314	TACACCAACGCGCACCAT	59.969	55.556	5.73	0.00	0.00	3.55
2649	2739	2.569134	GTCTCTCTCGCCAGCGTT	59.431	61.111	12.32	0.00	40.74	4.84
2650	2740	1.801332	GTCTCTCTCGCCAGCGTTA	59.199	57.895	12.32	0.57	40.74	3.18
2700	2790	0.972983	AGATGCACTACGTCCAGCCT	60.973	55.000	0.00	0.00	34.56	4.58
3007	3133	2.685017	AGCTCATCCTGCCGACCA	60.685	61.111	0.00	0.00	0.00	4.02
3025	3151	3.903208	ATGTTCCTGTACATGGCCC	57.097	52.632	0.00	0.00	37.36	5.80
3463	3589	4.033776	CCAGGGCCGACACCATGT	62.034	66.667	0.00	0.00	39.89	3.21
3476	3602	3.000041	ACACCATGTTGTAGCATGTACG	59.000	45.455	0.00	0.00	43.33	3.67

Showing 1 to 25 of 121 entries

Previous1 2 3 4 5Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	6.419791	ACCTTGGTTTATCGATCCATTTGTA	58.580	36.000	0.00	0.00	0.00	2.41
40	41	0.739462	CCTTTGCACTATGTCGGCGA	60.739	55.000	4.99	4.99	0.00	5.54
41	42	0.739462	TCCTTTGCACTATGTCGGCG	60.739	55.000	0.00	0.00	0.00	6.46
42	43	1.599542	GATCCTTTGCACTATGTCGGC	59.400	52.381	0.00	0.00	0.00	5.54
108	109	9.415544	GAGAACTAAAATTTACTCCGTGTCTTA	57.584	33.333	0.00	0.00	0.00	2.10
115	116	7.445836	CACTTCGAGAACTAAAATTTACTCCG	58.554	38.462	0.00	0.00	0.00	4.63
127	128	3.439476	GTCCAGTAGCACTTCGAGAACTA	59.561	47.826	0.00	0.00	0.00	2.24
482	485	5.032100	TCTCTAACATCGCGTATAGAAGC	57.968	43.478	5.77	0.00	0.00	3.86
587	591	3.070446	TCCACAGTAGTGTAAACCAGGTG	59.930	47.826	2.08	0.00	44.39	4.00
630	634	1.605712	GCCTGCGTCTGTTACTCTGTT	60.606	52.381	0.00	0.00	0.00	3.16
631	635	0.038159	GCCTGCGTCTGTTACTCTGT	60.038	55.000	0.00	0.00	0.00	3.41
632	636	0.038251	TGCCTGCGTCTGTTACTCTG	60.038	55.000	0.00	0.00	0.00	3.35
633	637	0.244994	CTGCCTGCGTCTGTTACTCT	59.755	55.000	0.00	0.00	0.00	3.24
634	638	0.038159	ACTGCCTGCGTCTGTTACTC	60.038	55.000	0.00	0.00	0.00	2.59
635	639	0.393077	AACTGCCTGCGTCTGTTACT	59.607	50.000	0.00	0.00	0.00	2.24
636	640	1.194772	GAAACTGCCTGCGTCTGTTAC	59.805	52.381	0.00	0.00	0.00	2.50
637	641	1.508632	GAAACTGCCTGCGTCTGTTA	58.491	50.000	0.00	0.00	0.00	2.41
773	777	3.799755	GATTGTGTGACCGCGCCC	61.800	66.667	0.00	0.00	0.00	6.13
792	796	0.480690	AGCATTTGTGGTGGGTGGTA	59.519	50.000	0.00	0.00	0.00	3.25
797	801	1.001181	CCTTGAAGCATTTGTGGTGGG	59.999	52.381	0.00	0.00	0.00	4.61
875	887	1.080093	CATGCAAAGGTGGCAGCAG	60.080	57.895	20.04	9.30	45.68	4.24
1054	1066	1.526575	ATTGCGCCCTTGGACTTGTG	61.527	55.000	4.18	0.00	0.00	3.33
1178	1196	0.387202	ATCATAAGCACTCGCGAGCT	59.613	50.000	34.83	25.41	45.49	4.09
1280	1298	3.066814	GCACCTCGACGTAGGGGT	61.067	66.667	15.28	15.28	42.56	4.95
1335	1353	3.068691	TCCGGGCTCGACTTCCTG	61.069	66.667	8.08	0.00	39.00	3.86

Showing 1 to 25 of 117 entries

Previous1 2 3 4 5Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.