AutoCloner

Multiple sequence alignment - TraesCS3A01G059800

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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	TraesCS3A01G059800	chr3A	100.000	2259	0	0	1	2259	36229190	36226932	0.000000e+00	4172.0
1	TraesCS3A01G059800	chr3A	84.779	565	39	25	253	779	36191930	36191375	7.150000e-145	523.0
2	TraesCS3A01G059800	chr3A	82.507	383	43	14	963	1323	36191171	36190791	4.680000e-82	315.0
3	TraesCS3A01G059800	chr3D	87.021	809	44	28	1	779	26261046	26261823	0.000000e+00	856.0
4	TraesCS3A01G059800	chr3D	79.342	760	74	39	253	965	26211149	26210426	7.350000e-125	457.0
5	TraesCS3A01G059800	chr3D	83.298	473	51	12	1407	1855	26213859	26213391	5.810000e-111	411.0
6	TraesCS3A01G059800	chr3D	81.621	506	48	20	1326	1793	26209880	26209382	5.890000e-101	377.0
7	TraesCS3A01G059800	chr3D	83.951	405	30	14	1038	1412	26210306	26209907	2.760000e-94	355.0
8	TraesCS3A01G059800	chr3D	82.232	439	39	13	963	1365	26262031	26262466	2.150000e-90	342.0
9	TraesCS3A01G059800	chr3D	92.670	191	13	1	1851	2041	26213212	26213023	7.950000e-70	274.0
10	TraesCS3A01G059800	chr3D	82.320	181	18	8	796	965	26261811	26261988	6.500000e-31	145.0
11	TraesCS3A01G059800	chr3D	80.576	139	25	1	1872	2008	164398428	164398566	3.070000e-19	106.0
12	TraesCS3A01G059800	chr3B	94.409	465	16	7	4	459	43736577	43736114	0.000000e+00	706.0
13	TraesCS3A01G059800	chr3B	92.157	153	12	0	627	779	43735803	43735651	1.360000e-52	217.0
14	TraesCS3A01G059800	chr3B	78.028	355	62	6	963	1303	43735444	43735092	2.270000e-50	209.0
15	TraesCS3A01G059800	chr3B	89.571	163	11	6	1880	2041	658461453	658461296	3.800000e-48	202.0
16	TraesCS3A01G059800	chr3B	82.353	204	27	5	1610	1804	43734539	43734336	3.860000e-38	169.0
17	TraesCS3A01G059800	chr3B	82.778	180	18	8	796	965	43735663	43735487	5.030000e-32	148.0
18	TraesCS3A01G059800	chr4A	95.890	219	9	0	2037	2255	640236064	640235846	2.760000e-94	355.0
19	TraesCS3A01G059800	chr5A	94.977	219	11	0	2037	2255	483329625	483329843	5.970000e-91	344.0
20	TraesCS3A01G059800	chr5A	93.722	223	14	0	2037	2259	673705760	673705538	3.600000e-88	335.0
21	TraesCS3A01G059800	chr5A	87.912	91	11	0	1918	2008	631309972	631309882	8.530000e-20	108.0
22	TraesCS3A01G059800	chr7A	94.570	221	12	0	2035	2255	129261359	129261579	2.150000e-90	342.0
23	TraesCS3A01G059800	chr7A	94.521	219	12	0	2037	2255	401405379	401405161	2.780000e-89	339.0
24	TraesCS3A01G059800	chr7A	93.722	223	14	0	2037	2259	492343060	492342838	3.600000e-88	335.0
25	TraesCS3A01G059800	chr7A	87.500	80	10	0	1929	2008	592200578	592200499	2.390000e-15	93.5
26	TraesCS3A01G059800	chr6A	94.170	223	13	0	2033	2255	459511747	459511969	7.730000e-90	340.0
27	TraesCS3A01G059800	chr6A	94.170	223	13	0	2037	2259	606612049	606611827	7.730000e-90	340.0
28	TraesCS3A01G059800	chr6A	87.879	66	8	0	1943	2008	94264219	94264284	6.690000e-11	78.7
29	TraesCS3A01G059800	chr2A	94.521	219	12	0	2037	2255	27936341	27936559	2.780000e-89	339.0
30	TraesCS3A01G059800	chr6B	88.535	157	12	6	1884	2037	719234437	719234590	3.830000e-43	185.0
31	TraesCS3A01G059800	chrUn	86.624	157	13	6	1884	2037	62885216	62885367	1.390000e-37	167.0
32	TraesCS3A01G059800	chr2D	87.324	71	9	0	1943	2013	38479906	38479836	5.170000e-12	82.4

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	TraesCS3A01G059800	chr3A	36226932	36229190	2258	True	4172.000000	4172	100.000000	1	2259	1	chr3A.!!$R1	2258
1	TraesCS3A01G059800	chr3A	36190791	36191930	1139	True	419.000000	523	83.643000	253	1323	2	chr3A.!!$R2	1070
2	TraesCS3A01G059800	chr3D	26261046	26262466	1420	False	447.666667	856	83.857667	1	1365	3	chr3D.!!$F2	1364
3	TraesCS3A01G059800	chr3D	26209382	26213859	4477	True	374.800000	457	84.176400	253	2041	5	chr3D.!!$R1	1788
4	TraesCS3A01G059800	chr3B	43734336	43736577	2241	True	289.800000	706	85.945000	4	1804	5	chr3B.!!$R2	1800

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
937	3598	0.652592	CTAATCCAGTTCGCAAGCCG	59.347	55.0	0.0	0.0	38.61	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1838	4948	0.104934	GGCCCCAGAGGAGATTAGGA	60.105	60.0	0.0	0.0	38.24	2.94	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
32	33	2.645838	TGAAGAAGTTTGAGCAGGCT	57.354	45.000	0.00	0.00	0.00	4.58
170	185	1.678970	GCAATATCATCCCCCGCCC	60.679	63.158	0.00	0.00	0.00	6.13
187	202	1.079543	CCACTCTGTGCGGAGGAAG	60.080	63.158	12.12	2.66	37.63	3.46
312	2775	6.318648	TGTGTTATTATTAAGCAAGGCCAGAG	59.681	38.462	5.01	0.00	0.00	3.35
352	2815	6.085979	CGAGAACTTTACTACACTGTTGTACG	59.914	42.308	3.31	1.78	37.15	3.67
420	2885	3.320626	CTGATTGTCATGTGTCGTGTCT	58.679	45.455	0.00	0.00	0.00	3.41
515	3130	9.391006	GTCTACCAGACATAGGATTAGAGATAG	57.609	40.741	1.46	0.00	44.45	2.08
516	3131	9.118367	TCTACCAGACATAGGATTAGAGATAGT	57.882	37.037	0.00	0.00	0.00	2.12
573	3197	7.814587	GTCCTAATTTGAAGCTTTGCTAACAAT	59.185	33.333	0.00	0.00	38.25	2.71
574	3198	8.367156	TCCTAATTTGAAGCTTTGCTAACAATT	58.633	29.630	0.00	1.31	38.25	2.32
576	3200	5.655893	TTTGAAGCTTTGCTAACAATTGC	57.344	34.783	5.05	0.00	38.25	3.56
578	3202	3.243367	TGAAGCTTTGCTAACAATTGCGT	60.243	39.130	5.05	0.00	38.25	5.24
582	3206	6.189677	AGCTTTGCTAACAATTGCGTATAA	57.810	33.333	5.05	0.00	39.26	0.98
590	3215	6.687105	GCTAACAATTGCGTATAAGAAACAGG	59.313	38.462	5.05	0.00	0.00	4.00
591	3216	6.811253	AACAATTGCGTATAAGAAACAGGA	57.189	33.333	5.05	0.00	0.00	3.86
601	3226	6.537301	CGTATAAGAAACAGGAAGGCATAACA	59.463	38.462	0.00	0.00	0.00	2.41
647	3287	3.930229	GGTCCTTTGTTTTCAAACCACAC	59.070	43.478	0.00	0.00	43.72	3.82
662	3306	8.958119	TCAAACCACACCTCTGTATTATATTC	57.042	34.615	0.00	0.00	0.00	1.75
713	3357	6.070824	ACCAGAACCAACAGATTTGTTCTTTT	60.071	34.615	0.00	0.00	44.40	2.27
766	3414	5.738619	TTCCATACCTGTCGCATACATAT	57.261	39.130	0.00	0.00	37.50	1.78
767	3415	5.072040	TCCATACCTGTCGCATACATATG	57.928	43.478	0.00	0.00	37.50	1.78
768	3416	4.770010	TCCATACCTGTCGCATACATATGA	59.230	41.667	10.38	0.00	34.82	2.15
769	3417	5.245075	TCCATACCTGTCGCATACATATGAA	59.755	40.000	10.38	0.00	34.82	2.57
770	3418	5.931724	CCATACCTGTCGCATACATATGAAA	59.068	40.000	10.38	0.00	34.82	2.69
771	3419	6.595326	CCATACCTGTCGCATACATATGAAAT	59.405	38.462	10.38	0.00	34.82	2.17

Showing 1 to 25 of 374 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	0.605319	CGTAGTTGCCCTTGGAAGCA	60.605	55.000	0.00	0.00	37.18	3.91
170	185	0.668706	CACTTCCTCCGCACAGAGTG	60.669	60.000	0.00	0.00	36.51	3.51
187	202	1.132588	GCTCTCTTCGTGTGACACAC	58.867	55.000	25.76	25.76	45.26	3.82
312	2775	9.291664	GTAAAGTTCTCGCATATATATCTGTCC	57.708	37.037	0.00	0.00	0.00	4.02
352	2815	6.751514	TGACACCCAATAATGTAACACATC	57.248	37.500	0.00	0.00	37.97	3.06
420	2885	5.070001	CACCCATCCAAGTAACAAGAAAGA	58.930	41.667	0.00	0.00	0.00	2.52
532	3151	9.878667	TCAAATTAGGACATCAACTTATCGTTA	57.121	29.630	0.00	0.00	33.63	3.18
535	3154	7.852945	GCTTCAAATTAGGACATCAACTTATCG	59.147	37.037	0.00	0.00	0.00	2.92
540	3159	7.373493	CAAAGCTTCAAATTAGGACATCAACT	58.627	34.615	0.00	0.00	0.00	3.16
573	3197	3.687698	GCCTTCCTGTTTCTTATACGCAA	59.312	43.478	0.00	0.00	0.00	4.85
574	3198	3.267483	GCCTTCCTGTTTCTTATACGCA	58.733	45.455	0.00	0.00	0.00	5.24
576	3200	6.537301	TGTTATGCCTTCCTGTTTCTTATACG	59.463	38.462	0.00	0.00	0.00	3.06
578	3202	8.736244	GTTTGTTATGCCTTCCTGTTTCTTATA	58.264	33.333	0.00	0.00	0.00	0.98
582	3206	4.280929	GGTTTGTTATGCCTTCCTGTTTCT	59.719	41.667	0.00	0.00	0.00	2.52
590	3215	4.953579	TCTAATGGGGTTTGTTATGCCTTC	59.046	41.667	0.00	0.00	0.00	3.46
591	3216	4.941713	TCTAATGGGGTTTGTTATGCCTT	58.058	39.130	0.00	0.00	0.00	4.35
601	3226	7.006509	CCTCATGACATAATCTAATGGGGTTT	58.993	38.462	0.00	0.00	0.00	3.27
662	3306	6.486657	TCAAGGAAGACCAATACAAAGAACAG	59.513	38.462	0.00	0.00	38.94	3.16
786	3434	7.254863	GGACAAGATGCAATTTCATGTGTTTTT	60.255	33.333	1.66	0.00	0.00	1.94
787	3435	6.203338	GGACAAGATGCAATTTCATGTGTTTT	59.797	34.615	1.66	0.00	0.00	2.43
788	3436	5.697633	GGACAAGATGCAATTTCATGTGTTT	59.302	36.000	1.66	0.00	0.00	2.83
789	3437	5.011329	AGGACAAGATGCAATTTCATGTGTT	59.989	36.000	1.66	0.00	0.00	3.32
790	3438	4.525487	AGGACAAGATGCAATTTCATGTGT	59.475	37.500	1.66	0.00	0.00	3.72
791	3439	5.068234	AGGACAAGATGCAATTTCATGTG	57.932	39.130	1.66	0.00	0.00	3.21
792	3440	5.014858	AGAGGACAAGATGCAATTTCATGT	58.985	37.500	0.00	0.00	0.00	3.21

Showing 1 to 25 of 330 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.