AutoCloner

Multiple sequence alignment - TraesCS1D01G035600

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	TraesCS1D01G035600	chr1D	100.000	7931	0	0	1	7931	16409856	16401926	0.000000e+00	14646.0
1	TraesCS1D01G035600	chr1D	84.615	780	87	19	3586	4362	11620979	11621728	0.000000e+00	745.0
2	TraesCS1D01G035600	chr1D	82.362	686	81	25	5279	5948	11622490	11623151	1.930000e-155	560.0
3	TraesCS1D01G035600	chr1D	82.516	612	79	15	6086	6690	11623217	11623807	5.490000e-141	512.0
4	TraesCS1D01G035600	chr1D	93.333	285	19	0	4418	4702	11621740	11622024	9.520000e-114	422.0
5	TraesCS1D01G035600	chr1D	85.500	400	47	10	2473	2866	11619766	11620160	2.660000e-109	407.0
6	TraesCS1D01G035600	chr1D	82.196	337	41	16	3221	3550	11620656	11620980	1.010000e-68	272.0
7	TraesCS1D01G035600	chr1D	81.206	282	48	5	7492	7770	297543514	297543235	1.040000e-53	222.0
8	TraesCS1D01G035600	chr1D	81.988	161	27	2	7492	7652	41462351	41462509	1.390000e-27	135.0
9	TraesCS1D01G035600	chr1D	75.479	261	56	7	5614	5870	339111482	339111738	3.890000e-23	121.0
10	TraesCS1D01G035600	chr1D	95.349	43	2	0	4276	4318	16405481	16405439	1.430000e-07	69.4
11	TraesCS1D01G035600	chr1D	95.349	43	2	0	4376	4418	16405581	16405539	1.430000e-07	69.4
12	TraesCS1D01G035600	chr1A	92.852	1315	81	10	2447	3758	16915006	16916310	0.000000e+00	1895.0
13	TraesCS1D01G035600	chr1A	88.031	1554	110	42	799	2317	16913389	16914901	0.000000e+00	1770.0
14	TraesCS1D01G035600	chr1A	92.301	1143	59	14	5558	6695	16917930	16919048	0.000000e+00	1596.0
15	TraesCS1D01G035600	chr1A	86.733	1010	67	28	4413	5372	16916940	16917932	0.000000e+00	1061.0
16	TraesCS1D01G035600	chr1A	94.951	515	24	2	3849	4362	16916422	16916935	0.000000e+00	806.0
17	TraesCS1D01G035600	chr1A	84.744	780	87	19	3586	4362	13765424	13766174	0.000000e+00	752.0
18	TraesCS1D01G035600	chr1A	89.739	536	45	4	7317	7850	16920142	16919615	0.000000e+00	676.0
19	TraesCS1D01G035600	chr1A	89.883	514	41	8	6697	7199	16919100	16919613	0.000000e+00	651.0
20	TraesCS1D01G035600	chr1A	83.333	588	74	15	5371	5948	13766914	13767487	9.120000e-144	521.0
21	TraesCS1D01G035600	chr1A	88.131	396	26	7	425	801	16911072	16911465	1.210000e-122	451.0
22	TraesCS1D01G035600	chr1A	93.103	290	18	2	4413	4702	13766183	13766470	2.650000e-114	424.0
23	TraesCS1D01G035600	chr1A	85.037	401	51	8	2471	2866	13764214	13764610	4.460000e-107	399.0
24	TraesCS1D01G035600	chr1A	84.752	282	34	9	3271	3550	13765151	13765425	2.820000e-69	274.0
25	TraesCS1D01G035600	chr1A	74.183	306	73	6	5614	5916	438697783	438698085	1.080000e-23	122.0
26	TraesCS1D01G035600	chr1B	85.340	764	79	20	3597	4358	17383315	17384047	0.000000e+00	760.0
27	TraesCS1D01G035600	chr1B	81.304	690	88	23	5279	5951	17384963	17385628	9.120000e-144	521.0
28	TraesCS1D01G035600	chr1B	94.138	290	17	0	4413	4702	17384045	17384334	7.300000e-120	442.0
29	TraesCS1D01G035600	chr1B	83.641	434	64	5	7491	7919	588755509	588755078	1.240000e-107	401.0
30	TraesCS1D01G035600	chr1B	88.095	252	26	4	2471	2721	17381991	17382239	6.020000e-76	296.0
31	TraesCS1D01G035600	chr1B	84.397	282	35	9	3271	3550	17383030	17383304	1.310000e-67	268.0
32	TraesCS1D01G035600	chr1B	84.496	258	26	3	7491	7736	550635648	550635393	7.950000e-60	243.0
33	TraesCS1D01G035600	chr1B	94.702	151	8	0	7325	7475	30329390	30329240	1.330000e-57	235.0
34	TraesCS1D01G035600	chr1B	94.702	151	8	0	7325	7475	30374799	30374649	1.330000e-57	235.0
35	TraesCS1D01G035600	chr1B	82.775	209	28	5	6800	7002	550635647	550635441	6.320000e-41	180.0
36	TraesCS1D01G035600	chr1B	73.856	306	74	6	5614	5916	453878849	453879151	5.030000e-22	117.0
37	TraesCS1D01G035600	chr3D	83.761	351	53	4	3910	4258	238626519	238626867	5.930000e-86	329.0
38	TraesCS1D01G035600	chr3D	83.090	343	56	2	5576	5917	238628831	238629172	2.150000e-80	311.0
39	TraesCS1D01G035600	chr3B	83.761	351	53	4	3910	4258	349942757	349942409	5.930000e-86	329.0
40	TraesCS1D01G035600	chr3B	81.471	340	61	2	5579	5917	349936487	349936149	2.180000e-70	278.0
41	TraesCS1D01G035600	chr3B	84.783	138	20	1	7492	7629	572832829	572832693	3.860000e-28	137.0
42	TraesCS1D01G035600	chr6D	81.250	336	46	12	6799	7122	352367993	352367663	1.020000e-63	255.0
43	TraesCS1D01G035600	chr6D	85.926	135	13	5	7499	7630	12472722	12472853	1.070000e-28	139.0
44	TraesCS1D01G035600	chr2D	81.915	282	46	5	7492	7770	613437943	613437664	4.790000e-57	233.0
45	TraesCS1D01G035600	chr2D	79.787	282	46	10	6800	7074	609889998	609889721	2.260000e-45	195.0
46	TraesCS1D01G035600	chr7D	89.796	147	13	2	6800	6945	553601862	553601717	3.780000e-43	187.0
47	TraesCS1D01G035600	chr7D	84.932	146	22	0	6800	6945	55084581	55084436	1.780000e-31	148.0
48	TraesCS1D01G035600	chr4A	88.966	145	16	0	6792	6936	647100972	647101116	6.320000e-41	180.0
49	TraesCS1D01G035600	chrUn	77.313	335	52	11	6800	7122	400537380	400537058	8.180000e-40	176.0
50	TraesCS1D01G035600	chrUn	87.671	146	18	0	6800	6945	319461680	319461535	3.810000e-38	171.0
51	TraesCS1D01G035600	chr7B	87.681	138	16	1	6800	6936	537782012	537782149	8.240000e-35	159.0
52	TraesCS1D01G035600	chr2B	83.234	167	21	7	7491	7654	54443486	54443648	6.410000e-31	147.0
53	TraesCS1D01G035600	chr5D	82.308	130	18	5	330	459	451543517	451543393	3.030000e-19	108.0
54	TraesCS1D01G035600	chr6B	100.000	28	0	0	2950	2977	610810786	610810759	1.400000e-02	52.8

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	TraesCS1D01G035600	chr1D	16401926	16409856	7930	True	14646.000000	14646	100.000000	1	7931	1	chr1D.!!$R1	7930
1	TraesCS1D01G035600	chr1D	11619766	11623807	4041	False	486.333333	745	85.087000	2473	6690	6	chr1D.!!$F3	4217
2	TraesCS1D01G035600	chr1A	16911072	16919613	8541	False	1175.714286	1895	90.411714	425	7199	7	chr1A.!!$F3	6774
3	TraesCS1D01G035600	chr1A	16919615	16920142	527	True	676.000000	676	89.739000	7317	7850	1	chr1A.!!$R1	533
4	TraesCS1D01G035600	chr1A	13764214	13767487	3273	False	474.000000	752	86.193800	2471	5948	5	chr1A.!!$F2	3477
5	TraesCS1D01G035600	chr1B	17381991	17385628	3637	False	457.400000	760	86.654800	2471	5951	5	chr1B.!!$F2	3480
6	TraesCS1D01G035600	chr3D	238626519	238629172	2653	False	320.000000	329	83.425500	3910	5917	2	chr3D.!!$F1	2007

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
210	211	0.040204	CCAGCAGGTGGGGAAGAATT	59.960	55.000	11.19	0.0	43.63	2.17	F
845	2791	0.168788	CGTGACAATGACATGGTGGC	59.831	55.000	0.00	0.0	0.00	5.01	F
1613	3596	0.036105	ATGAGTTGATCCAGCACGCA	60.036	50.000	0.00	0.0	0.00	5.24	F
2273	4263	0.108615	ACTGCTTGCGCTACTAGGTG	60.109	55.000	9.73	0.0	36.97	4.00	F
3263	5516	1.063942	GTTTAGCCTGCCTACCCCAAT	60.064	52.381	0.00	0.0	0.00	3.16	F
3776	6039	0.475906	AGTATTCATCCAGGCAGGGC	59.524	55.000	0.00	0.0	38.24	5.19	F
4411	7259	0.738975	GGCGTTTCCATAGCCTTTCC	59.261	55.000	0.00	0.0	46.83	3.13	F
5557	9168	0.179111	TCGAATGGTGATCGCTGTCC	60.179	55.000	6.18	0.0	40.04	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1152	3120	0.034960	GAGCAGAAGGGGGAAGAACC	60.035	60.0	0.00	0.00	38.08	3.62	R
1658	3641	0.037326	GCTGCTGCAGTGTAGGTACA	60.037	55.0	28.50	0.67	39.41	2.90	R
2776	4867	1.608055	CCACAATTGTGCCAGTCTGA	58.392	50.0	29.42	0.00	44.34	3.27	R
3758	6021	0.538287	GGCCCTGCCTGGATGAATAC	60.538	60.0	0.00	0.00	46.69	1.89	R
4282	6621	0.313672	TGGAAACGCCATGAAACTGC	59.686	50.0	0.00	0.00	43.33	4.40	R
5467	9066	0.096454	GCGAAATAACAGGCACCGAC	59.904	55.0	0.00	0.00	0.00	4.79	R
5574	9190	0.108472	GGAATGCTGCAAAAGAGGCC	60.108	55.0	6.36	0.00	0.00	5.19	R
7046	10732	0.032217	AGAAGGGAGGCAGAGAGGAG	60.032	60.0	0.00	0.00	0.00	3.69	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
24	25	7.827819	ATTCGAGTTATTGTTTCGATTCTCA	57.172	32.000	0.00	0.00	42.21	3.27
25	26	6.871044	TCGAGTTATTGTTTCGATTCTCAG	57.129	37.500	0.00	0.00	38.32	3.35
26	27	5.288712	TCGAGTTATTGTTTCGATTCTCAGC	59.711	40.000	0.00	0.00	38.32	4.26
27	28	5.289675	CGAGTTATTGTTTCGATTCTCAGCT	59.710	40.000	0.00	0.00	36.49	4.24
28	29	6.414408	AGTTATTGTTTCGATTCTCAGCTG	57.586	37.500	7.63	7.63	0.00	4.24
29	30	3.754188	ATTGTTTCGATTCTCAGCTGC	57.246	42.857	9.47	0.00	0.00	5.25
30	31	1.442769	TGTTTCGATTCTCAGCTGCC	58.557	50.000	9.47	0.00	0.00	4.85
31	32	0.371645	GTTTCGATTCTCAGCTGCCG	59.628	55.000	9.47	7.34	0.00	5.69
32	33	0.740868	TTTCGATTCTCAGCTGCCGG	60.741	55.000	9.47	0.00	0.00	6.13
33	34	3.267860	CGATTCTCAGCTGCCGGC	61.268	66.667	22.73	22.73	42.19	6.13
34	35	2.899339	GATTCTCAGCTGCCGGCC	60.899	66.667	26.77	9.73	43.05	6.13
35	36	3.687321	GATTCTCAGCTGCCGGCCA	62.687	63.158	26.77	11.42	43.05	5.36
36	37	2.955022	GATTCTCAGCTGCCGGCCAT	62.955	60.000	26.77	6.65	43.05	4.40
37	38	1.699054	ATTCTCAGCTGCCGGCCATA	61.699	55.000	26.77	3.87	43.05	2.74
38	39	1.909459	TTCTCAGCTGCCGGCCATAA	61.909	55.000	26.77	3.41	43.05	1.90
39	40	1.451927	CTCAGCTGCCGGCCATAAA	60.452	57.895	26.77	2.93	43.05	1.40
40	41	1.442526	CTCAGCTGCCGGCCATAAAG	61.443	60.000	26.77	15.70	43.05	1.85
41	42	2.830370	AGCTGCCGGCCATAAAGC	60.830	61.111	26.77	25.21	43.05	3.51
70	71	7.596749	TTTAGAGTAGATACTTGCTTGTTGC	57.403	36.000	0.00	0.00	38.31	4.17
71	72	4.177026	AGAGTAGATACTTGCTTGTTGCG	58.823	43.478	0.00	0.00	39.79	4.85
72	73	3.926616	AGTAGATACTTGCTTGTTGCGT	58.073	40.909	0.00	0.00	46.63	5.24
73	74	5.068234	AGTAGATACTTGCTTGTTGCGTA	57.932	39.130	0.00	0.00	46.63	4.42
74	75	5.103000	AGTAGATACTTGCTTGTTGCGTAG	58.897	41.667	0.00	0.00	46.63	3.51
75	76	3.262420	AGATACTTGCTTGTTGCGTAGG	58.738	45.455	0.00	0.00	46.63	3.18
76	77	2.823924	TACTTGCTTGTTGCGTAGGA	57.176	45.000	0.00	0.00	46.63	2.94

Showing 1 to 25 of 945 entries

Previous1 2 3 4 5…38Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.464710	GCTGAGAATCGAAACAATAACTCGAAT	60.465	37.037	0.00	0.00	44.06	3.34
1	2	6.183360	GCTGAGAATCGAAACAATAACTCGAA	60.183	38.462	0.00	0.00	44.06	3.71
2	3	5.288712	GCTGAGAATCGAAACAATAACTCGA	59.711	40.000	0.00	0.00	44.87	4.04
4	5	6.473521	CAGCTGAGAATCGAAACAATAACTC	58.526	40.000	8.42	0.00	38.61	3.01
6	7	5.024555	GCAGCTGAGAATCGAAACAATAAC	58.975	41.667	20.43	0.00	38.61	1.89
8	9	3.623060	GGCAGCTGAGAATCGAAACAATA	59.377	43.478	20.43	0.00	38.61	1.90
9	10	2.421424	GGCAGCTGAGAATCGAAACAAT	59.579	45.455	20.43	0.00	38.61	2.71
10	11	1.806542	GGCAGCTGAGAATCGAAACAA	59.193	47.619	20.43	0.00	38.61	2.83
11	12	1.442769	GGCAGCTGAGAATCGAAACA	58.557	50.000	20.43	0.00	38.61	2.83
12	13	0.371645	CGGCAGCTGAGAATCGAAAC	59.628	55.000	20.43	0.00	38.61	2.78
13	14	0.740868	CCGGCAGCTGAGAATCGAAA	60.741	55.000	20.43	0.00	38.61	3.46
14	15	1.153568	CCGGCAGCTGAGAATCGAA	60.154	57.895	20.43	0.00	38.61	3.71
15	16	2.496341	CCGGCAGCTGAGAATCGA	59.504	61.111	20.43	0.00	38.61	3.59
16	17	3.267860	GCCGGCAGCTGAGAATCG	61.268	66.667	24.80	11.83	38.61	3.34
17	18	2.899339	GGCCGGCAGCTGAGAATC	60.899	66.667	30.85	1.84	43.05	2.52
18	19	1.699054	TATGGCCGGCAGCTGAGAAT	61.699	55.000	30.85	10.18	43.05	2.40
19	20	1.909459	TTATGGCCGGCAGCTGAGAA	61.909	55.000	30.85	8.88	43.05	2.87
20	21	1.909459	TTTATGGCCGGCAGCTGAGA	61.909	55.000	30.85	4.26	43.05	3.27
21	22	1.442526	CTTTATGGCCGGCAGCTGAG	61.443	60.000	30.85	15.98	43.05	3.35
22	23	1.451927	CTTTATGGCCGGCAGCTGA	60.452	57.895	30.85	9.90	43.05	4.26
23	24	3.113745	CTTTATGGCCGGCAGCTG	58.886	61.111	30.85	10.11	43.05	4.24
24	25	2.830370	GCTTTATGGCCGGCAGCT	60.830	61.111	30.85	14.46	43.05	4.24
25	26	3.904479	GGCTTTATGGCCGGCAGC	61.904	66.667	30.85	26.74	42.82	5.25
44	45	8.504005	GCAACAAGCAAGTATCTACTCTAAAAA	58.496	33.333	0.00	0.00	44.79	1.94
45	46	7.148639	CGCAACAAGCAAGTATCTACTCTAAAA	60.149	37.037	0.00	0.00	46.13	1.52

Showing 1 to 25 of 980 entries

Previous1 2 3 4 5…40Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.