AutoCloner

Multiple sequence alignment - TraesCS5D01G544700

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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	TraesCS5D01G544700	chr5D	100.000	5339	0	0	2750	8088	554345109	554350447	0.000000e+00	9860
1	TraesCS5D01G544700	chr5D	86.767	4262	528	19	2935	7169	554142519	554146771	0.000000e+00	4713
2	TraesCS5D01G544700	chr5D	86.607	4271	526	11	2948	7199	553967839	553963596	0.000000e+00	4676
3	TraesCS5D01G544700	chr5D	100.000	2428	0	0	1	2428	554342360	554344787	0.000000e+00	4484
4	TraesCS5D01G544700	chr5D	80.508	354	42	13	1000	1335	554140920	554141264	6.270000e-61	246
5	TraesCS5D01G544700	chr4A	86.441	4425	516	25	2948	7310	614256666	614252264	0.000000e+00	4771
6	TraesCS5D01G544700	chr4A	87.500	168	17	4	7923	8088	604661766	604661931	2.980000e-44	191
7	TraesCS5D01G544700	chr5B	86.855	3507	421	16	3714	7193	696445507	696449000	0.000000e+00	3886
8	TraesCS5D01G544700	chr5B	85.911	1306	157	14	2955	4249	696437757	696439046	0.000000e+00	1367
9	TraesCS5D01G544700	chr5B	89.097	587	58	1	4252	4832	696444309	696444895	0.000000e+00	725
10	TraesCS5D01G544700	chr2D	73.856	1966	429	65	3140	5052	572067691	572069624	0.000000e+00	704
11	TraesCS5D01G544700	chrUn	72.744	1585	365	51	3083	4626	248487088	248488646	9.500000e-129	472
12	TraesCS5D01G544700	chr6D	72.989	1492	344	44	3295	4758	467787199	467785739	1.230000e-127	468
13	TraesCS5D01G544700	chr5A	73.031	1498	336	53	3295	4761	482355070	482356530	4.420000e-127	466
14	TraesCS5D01G544700	chr5A	72.721	1492	348	46	3295	4758	482369154	482370614	5.760000e-121	446
15	TraesCS5D01G544700	chr5A	89.820	167	14	3	7923	8088	546884312	546884148	2.290000e-50	211
16	TraesCS5D01G544700	chr5A	87.879	165	15	3	7925	8088	568049558	568049398	1.070000e-43	189
17	TraesCS5D01G544700	chr6B	74.476	1144	239	41	3298	4416	713067184	713066069	5.760000e-121	446
18	TraesCS5D01G544700	chr7D	71.761	1721	418	56	3083	4761	631231386	631233080	2.700000e-114	424
19	TraesCS5D01G544700	chr7D	89.222	167	16	2	7923	8088	117544236	117544071	2.960000e-49	207
20	TraesCS5D01G544700	chr2B	74.518	985	221	20	3296	4262	683752527	683753499	1.260000e-107	401
21	TraesCS5D01G544700	chr2B	73.114	1153	233	59	4265	5395	686812615	686813712	2.800000e-89	340
22	TraesCS5D01G544700	chr2A	74.595	988	215	24	3296	4262	710355616	710356588	1.260000e-107	401
23	TraesCS5D01G544700	chr7A	92.262	168	10	3	7923	8088	135898170	135898336	1.360000e-57	235
24	TraesCS5D01G544700	chr7A	88.757	169	16	2	7923	8088	56980244	56980076	3.830000e-48	204
25	TraesCS5D01G544700	chr7B	89.024	164	15	3	7923	8084	66884036	66883874	4.950000e-47	200
26	TraesCS5D01G544700	chr7B	87.879	165	18	2	7925	8088	711233387	711233550	8.280000e-45	193
27	TraesCS5D01G544700	chr1A	87.425	167	17	3	7923	8088	74276455	74276292	1.070000e-43	189

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	TraesCS5D01G544700	chr5D	554342360	554350447	8087	False	7172.0	9860	100.0000	1	8088	2	chr5D.!!$F2	8087
1	TraesCS5D01G544700	chr5D	553963596	553967839	4243	True	4676.0	4676	86.6070	2948	7199	1	chr5D.!!$R1	4251
2	TraesCS5D01G544700	chr5D	554140920	554146771	5851	False	2479.5	4713	83.6375	1000	7169	2	chr5D.!!$F1	6169
3	TraesCS5D01G544700	chr4A	614252264	614256666	4402	True	4771.0	4771	86.4410	2948	7310	1	chr4A.!!$R1	4362
4	TraesCS5D01G544700	chr5B	696444309	696449000	4691	False	2305.5	3886	87.9760	3714	7193	2	chr5B.!!$F2	3479
5	TraesCS5D01G544700	chr5B	696437757	696439046	1289	False	1367.0	1367	85.9110	2955	4249	1	chr5B.!!$F1	1294
6	TraesCS5D01G544700	chr2D	572067691	572069624	1933	False	704.0	704	73.8560	3140	5052	1	chr2D.!!$F1	1912
7	TraesCS5D01G544700	chrUn	248487088	248488646	1558	False	472.0	472	72.7440	3083	4626	1	chrUn.!!$F1	1543
8	TraesCS5D01G544700	chr6D	467785739	467787199	1460	True	468.0	468	72.9890	3295	4758	1	chr6D.!!$R1	1463
9	TraesCS5D01G544700	chr5A	482355070	482356530	1460	False	466.0	466	73.0310	3295	4761	1	chr5A.!!$F1	1466
10	TraesCS5D01G544700	chr5A	482369154	482370614	1460	False	446.0	446	72.7210	3295	4758	1	chr5A.!!$F2	1463
11	TraesCS5D01G544700	chr6B	713066069	713067184	1115	True	446.0	446	74.4760	3298	4416	1	chr6B.!!$R1	1118
12	TraesCS5D01G544700	chr7D	631231386	631233080	1694	False	424.0	424	71.7610	3083	4761	1	chr7D.!!$F1	1678
13	TraesCS5D01G544700	chr2B	683752527	683753499	972	False	401.0	401	74.5180	3296	4262	1	chr2B.!!$F1	966
14	TraesCS5D01G544700	chr2B	686812615	686813712	1097	False	340.0	340	73.1140	4265	5395	1	chr2B.!!$F2	1130
15	TraesCS5D01G544700	chr2A	710355616	710356588	972	False	401.0	401	74.5950	3296	4262	1	chr2A.!!$F1	966

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
188	189	0.035439	CGGCCACAAGGTATGTTCCT	60.035	55.000	2.24	0.00	41.46	3.36	F
1876	1929	0.029433	GATGAATTCGAAAGGCCCGC	59.971	55.000	0.00	0.00	0.00	6.13	F
2367	2420	0.030638	TTTCGCTGCTTTGCCTCAAC	59.969	50.000	0.00	0.00	0.00	3.18	F
2402	2455	0.039618	GGGGATTTGGTTGCTGAGGA	59.960	55.000	0.00	0.00	0.00	3.71	F
2897	3041	0.250858	TGGTGATGTCTTGGCCACAG	60.251	55.000	3.88	6.78	0.00	3.66	F
3117	3573	0.435008	GATGACGAGTCAACACACGC	59.565	55.000	10.15	0.00	43.58	5.34	F
3213	3669	1.637553	AGGCACATCAAGGGTTCTGAT	59.362	47.619	0.00	0.00	0.00	2.90	F
5148	5664	0.895559	CTTGAGGGCCTTCAACCACC	60.896	60.000	25.26	0.00	33.71	4.61	F
5224	5740	0.175760	GGCTTGCCGACAGTATCTCA	59.824	55.000	0.00	0.00	0.00	3.27	F
6540	7068	0.179100	CTACAGCTGCGTACCTGCAT	60.179	55.000	15.27	0.00	45.26	3.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1896	1949	0.034476	CAGTTGAGCTCTGAGCCACA	59.966	55.000	25.09	21.33	43.77	4.17	R
2880	2933	0.036732	TCCTGTGGCCAAGACATCAC	59.963	55.000	7.24	0.00	0.00	3.06	R
3882	4368	1.016627	TGCTATTCGCAGTCCAATGC	58.983	50.000	0.00	0.00	45.47	3.56	R
4195	4681	3.013219	GTCCATTCCTTTCTCCTCAAGC	58.987	50.000	0.00	0.00	0.00	4.01	R
4470	4980	1.391485	CGGCGAACATGTTCTTCTCAG	59.609	52.381	30.45	17.75	37.44	3.35	R
5061	5577	0.462581	TTCATCATCTGGCGAGGCAC	60.463	55.000	0.00	0.00	0.00	5.01	R
5191	5707	1.986882	CAAGCCAAGTTGGGAAGAGT	58.013	50.000	23.36	0.00	38.19	3.24	R
6803	7346	0.612229	TGAAGCCCTCTCTCTTGCTG	59.388	55.000	0.00	0.00	33.59	4.41	R
6896	7442	0.670546	TTCTTGAGCGAAGGAAGCCG	60.671	55.000	0.00	0.00	34.64	5.52	R
7595	8175	0.031043	CAACATGGCGGTGCATATGG	59.969	55.000	4.56	0.00	31.95	2.74	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	Hairpin	End Stability
17	18	2.885388	TCTCCCCAACCCCATCCT	59.115	61.111	0.00	0.00	3.24
18	19	1.619363	TCTCCCCAACCCCATCCTG	60.619	63.158	0.00	0.00	3.86
19	20	3.346734	TCCCCAACCCCATCCTGC	61.347	66.667	0.00	0.00	4.85
20	21	4.820744	CCCCAACCCCATCCTGCG	62.821	72.222	0.00	0.00	5.18
21	22	4.047125	CCCAACCCCATCCTGCGT	62.047	66.667	0.00	0.00	5.24
22	23	2.751436	CCAACCCCATCCTGCGTG	60.751	66.667	0.00	0.00	5.34
23	24	3.443045	CAACCCCATCCTGCGTGC	61.443	66.667	0.00	0.00	5.34
24	25	4.740822	AACCCCATCCTGCGTGCC	62.741	66.667	0.00	0.00	5.01
36	37	4.170062	CGTGCCTGCGCCAAGATG	62.170	66.667	4.18	0.00	2.90
37	38	3.058160	GTGCCTGCGCCAAGATGT	61.058	61.111	4.18	0.00	3.06
38	39	2.282391	TGCCTGCGCCAAGATGTT	60.282	55.556	4.18	0.00	2.71
42	43	0.449388	CCTGCGCCAAGATGTTCTTC	59.551	55.000	4.18	33.78	2.87
44	45	0.250684	TGCGCCAAGATGTTCTTCCA	60.251	50.000	4.18	33.78	3.53
45	46	0.449388	GCGCCAAGATGTTCTTCCAG	59.551	55.000	0.00	33.78	3.86
47	48	2.154462	CGCCAAGATGTTCTTCCAGTT	58.846	47.619	0.00	33.78	3.16
48	49	2.160417	CGCCAAGATGTTCTTCCAGTTC	59.840	50.000	0.00	33.78	3.01
49	50	3.149196	GCCAAGATGTTCTTCCAGTTCA	58.851	45.455	0.00	33.78	3.18
50	51	3.760684	GCCAAGATGTTCTTCCAGTTCAT	59.239	43.478	0.00	33.78	2.57
51	52	4.142513	GCCAAGATGTTCTTCCAGTTCATC	60.143	45.833	0.00	33.78	2.92
53	54	3.265791	AGATGTTCTTCCAGTTCATCGC	58.734	45.455	0.00	39.54	4.58
54	55	1.808411	TGTTCTTCCAGTTCATCGCC	58.192	50.000	0.00	0.00	5.54
55	56	0.721718	GTTCTTCCAGTTCATCGCCG	59.278	55.000	0.00	0.00	6.46
56	57	0.320374	TTCTTCCAGTTCATCGCCGT	59.680	50.000	0.00	0.00	5.68
57	58	0.108804	TCTTCCAGTTCATCGCCGTC	60.109	55.000	0.00	0.00	4.79
58	59	1.413767	CTTCCAGTTCATCGCCGTCG	61.414	60.000	0.00	0.00	5.12

Showing 1 to 25 of 1,748 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.619363	CAGGATGGGGTTGGGGAGA	60.619	63.158	0.00	0.00	0.00	3.71
1	2	3.010144	CAGGATGGGGTTGGGGAG	58.990	66.667	0.00	0.00	0.00	4.30
2	3	3.346734	GCAGGATGGGGTTGGGGA	61.347	66.667	0.00	0.00	35.86	4.81
3	4	4.820744	CGCAGGATGGGGTTGGGG	62.821	72.222	0.00	0.00	46.46	4.96
23	24	0.449388	GAAGAACATCTTGGCGCAGG	59.551	55.000	10.83	0.00	36.73	4.85
24	25	0.449388	GGAAGAACATCTTGGCGCAG	59.551	55.000	10.83	0.00	36.73	5.18
26	27	0.449388	CTGGAAGAACATCTTGGCGC	59.551	55.000	0.00	0.00	36.73	6.53
28	29	3.149196	TGAACTGGAAGAACATCTTGGC	58.851	45.455	0.00	0.00	36.73	4.52
29	30	4.093998	CGATGAACTGGAAGAACATCTTGG	59.906	45.833	0.00	0.00	42.59	3.61
30	31	4.436584	GCGATGAACTGGAAGAACATCTTG	60.437	45.833	0.00	0.00	42.59	3.02
31	32	3.686726	GCGATGAACTGGAAGAACATCTT	59.313	43.478	0.00	0.00	42.59	2.40
34	35	2.359900	GGCGATGAACTGGAAGAACAT	58.640	47.619	0.00	0.00	37.43	2.71
35	36	1.808411	GGCGATGAACTGGAAGAACA	58.192	50.000	0.00	0.00	37.43	3.18
36	37	0.721718	CGGCGATGAACTGGAAGAAC	59.278	55.000	0.00	0.00	37.43	3.01
37	38	0.320374	ACGGCGATGAACTGGAAGAA	59.680	50.000	16.62	0.00	37.43	2.52
38	39	0.108804	GACGGCGATGAACTGGAAGA	60.109	55.000	16.62	0.00	37.43	2.87
42	43	2.126071	ACGACGGCGATGAACTGG	60.126	61.111	22.49	0.00	41.64	4.00
44	45	2.181021	GGACGACGGCGATGAACT	59.819	61.111	22.49	0.00	41.64	3.01
45	46	2.158959	CAGGACGACGGCGATGAAC	61.159	63.158	22.49	1.54	41.64	3.18
47	48	3.822192	CCAGGACGACGGCGATGA	61.822	66.667	22.49	0.00	41.64	2.92
48	49	4.873129	CCCAGGACGACGGCGATG	62.873	72.222	22.49	13.39	41.64	3.84
54	55	3.461773	ATCCAGCCCAGGACGACG	61.462	66.667	0.00	0.00	41.30	5.12
55	56	2.187946	CATCCAGCCCAGGACGAC	59.812	66.667	0.00	0.00	41.30	4.34
56	57	3.083349	CCATCCAGCCCAGGACGA	61.083	66.667	0.00	0.00	41.30	4.20
57	58	4.864334	GCCATCCAGCCCAGGACG	62.864	72.222	0.00	0.00	41.30	4.79

Showing 1 to 25 of 1,699 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.