AutoCloner

Multiple sequence alignment - TraesCS1B01G167800

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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	TraesCS1B01G167800	chr1B	100.000	8679	0	0	1	8679	297091598	297100276	0.000000e+00	16028.0
1	TraesCS1B01G167800	chr1B	92.079	101	8	0	2337	2437	507106477	507106377	9.080000e-30	143.0
2	TraesCS1B01G167800	chr1B	91.089	101	9	0	2337	2437	507061150	507061050	4.230000e-28	137.0
3	TraesCS1B01G167800	chr1B	88.462	104	11	1	2345	2447	12433296	12433193	3.290000e-24	124.0
4	TraesCS1B01G167800	chr1B	89.796	98	8	1	2346	2441	396753981	396754078	3.290000e-24	124.0
5	TraesCS1B01G167800	chr1A	97.371	3271	54	16	2428	5674	257553246	257556508	0.000000e+00	5535.0
6	TraesCS1B01G167800	chr1A	94.189	2461	82	22	6006	8429	257556676	257559112	0.000000e+00	3696.0
7	TraesCS1B01G167800	chr1A	91.478	1631	70	17	749	2347	257551655	257553248	0.000000e+00	2178.0
8	TraesCS1B01G167800	chr1A	85.981	749	75	10	2	745	257550951	257551674	0.000000e+00	774.0
9	TraesCS1B01G167800	chr1A	93.627	204	11	2	8414	8615	257559164	257559367	3.940000e-78	303.0
10	TraesCS1B01G167800	chr1A	94.675	169	5	1	5729	5893	257556511	257556679	8.640000e-65	259.0
11	TraesCS1B01G167800	chr1A	92.405	79	6	0	6451	6529	107472095	107472017	7.120000e-21	113.0
12	TraesCS1B01G167800	chr1A	93.151	73	4	1	8607	8679	257564732	257564803	1.190000e-18	106.0
13	TraesCS1B01G167800	chr1D	95.366	2050	57	16	6006	8045	203290944	203292965	0.000000e+00	3225.0
14	TraesCS1B01G167800	chr1D	97.046	1794	35	11	2474	4252	203285639	203287429	0.000000e+00	3003.0
15	TraesCS1B01G167800	chr1D	97.890	1659	28	3	4239	5893	203289292	203290947	0.000000e+00	2863.0
16	TraesCS1B01G167800	chr1D	94.466	1536	42	17	784	2305	203284136	203285642	0.000000e+00	2326.0
17	TraesCS1B01G167800	chr1D	87.974	765	59	18	1	741	203283262	203284017	0.000000e+00	872.0
18	TraesCS1B01G167800	chr1D	92.164	268	19	2	8414	8679	203293369	203293636	2.290000e-100	377.0
19	TraesCS1B01G167800	chr1D	91.322	242	10	4	8196	8429	203293079	203293317	3.910000e-83	320.0
20	TraesCS1B01G167800	chr1D	95.238	105	5	0	8107	8211	203292961	203293065	5.390000e-37	167.0
21	TraesCS1B01G167800	chr1D	95.652	92	4	0	2345	2436	473933015	473932924	1.950000e-31	148.0
22	TraesCS1B01G167800	chr1D	90.291	103	8	2	2343	2444	96041028	96041129	5.470000e-27	134.0
23	TraesCS1B01G167800	chr1D	94.915	59	3	0	2502	2560	203285823	203285881	9.280000e-15	93.5
24	TraesCS1B01G167800	chr6D	75.323	620	113	32	5041	5631	47662474	47661866	2.400000e-65	261.0
25	TraesCS1B01G167800	chr6B	75.323	620	112	30	5041	5631	123843275	123843882	8.640000e-65	259.0
26	TraesCS1B01G167800	chr6B	92.500	80	5	1	6449	6528	672163647	672163725	7.120000e-21	113.0
27	TraesCS1B01G167800	chr6B	83.607	122	16	3	2345	2463	521118926	521119046	2.560000e-20	111.0
28	TraesCS1B01G167800	chr5B	93.333	135	8	1	5884	6017	619116603	619116737	1.910000e-46	198.0
29	TraesCS1B01G167800	chr5B	85.443	158	13	6	2176	2325	98663178	98663333	1.170000e-33	156.0
30	TraesCS1B01G167800	chr5B	83.571	140	20	2	2155	2292	317304047	317304185	2.540000e-25	128.0
31	TraesCS1B01G167800	chr5B	93.590	78	5	0	6452	6529	574956515	574956438	5.500000e-22	117.0
32	TraesCS1B01G167800	chr7A	96.610	118	4	0	5890	6007	105313853	105313736	6.870000e-46	196.0
33	TraesCS1B01G167800	chr7A	93.396	106	6	1	2187	2292	201987013	201987117	1.170000e-33	156.0
34	TraesCS1B01G167800	chr7A	96.667	90	3	0	2344	2433	32008556	32008467	5.430000e-32	150.0
35	TraesCS1B01G167800	chr2A	94.531	128	6	1	5889	6016	78845692	78845566	6.870000e-46	196.0
36	TraesCS1B01G167800	chr2A	94.681	94	5	0	2344	2437	111412090	111412183	7.020000e-31	147.0
37	TraesCS1B01G167800	chr2A	80.405	148	28	1	6113	6259	750108162	750108309	2.560000e-20	111.0
38	TraesCS1B01G167800	chr5A	95.122	123	6	0	5885	6007	649239373	649239251	2.470000e-45	195.0
39	TraesCS1B01G167800	chr5A	84.810	158	14	3	2176	2325	86662019	86662174	5.430000e-32	150.0
40	TraesCS1B01G167800	chr5A	83.803	142	20	2	2153	2292	368554875	368554735	1.970000e-26	132.0
41	TraesCS1B01G167800	chr5A	89.552	67	7	0	8032	8098	374902378	374902312	1.550000e-12	86.1
42	TraesCS1B01G167800	chr2B	95.833	120	5	0	5888	6007	643184739	643184620	2.470000e-45	195.0
43	TraesCS1B01G167800	chr2B	89.431	123	12	1	4591	4713	707609879	707610000	4.200000e-33	154.0
44	TraesCS1B01G167800	chr2B	90.566	53	5	0	2389	2441	504483468	504483416	4.350000e-08	71.3
45	TraesCS1B01G167800	chr2D	95.122	123	5	1	5891	6013	294973455	294973576	8.890000e-45	193.0
46	TraesCS1B01G167800	chr2D	91.453	117	9	1	2176	2292	122864263	122864148	9.020000e-35	159.0
47	TraesCS1B01G167800	chr2D	94.595	74	4	0	6449	6522	617437222	617437295	1.980000e-21	115.0
48	TraesCS1B01G167800	chr3D	94.309	123	7	0	5889	6011	94848841	94848719	1.150000e-43	189.0
49	TraesCS1B01G167800	chr3D	91.241	137	10	2	5872	6007	609106331	609106196	1.490000e-42	185.0
50	TraesCS1B01G167800	chr3D	91.729	133	10	1	5875	6007	107670947	107671078	5.350000e-42	183.0
51	TraesCS1B01G167800	chr3D	96.629	89	3	0	2345	2433	172830740	172830828	1.950000e-31	148.0
52	TraesCS1B01G167800	chr3D	93.878	98	5	1	2340	2437	604391405	604391501	7.020000e-31	147.0
53	TraesCS1B01G167800	chr3D	84.800	125	14	4	2164	2286	29167283	29167404	4.260000e-23	121.0
54	TraesCS1B01G167800	chr3D	91.860	86	4	3	6452	6534	422517724	422517809	5.500000e-22	117.0
55	TraesCS1B01G167800	chr7B	90.083	121	10	2	2173	2292	155471163	155471282	1.170000e-33	156.0
56	TraesCS1B01G167800	chr4B	94.681	94	4	1	2345	2437	117191185	117191092	2.530000e-30	145.0
57	TraesCS1B01G167800	chr4B	86.957	115	6	4	2183	2297	92547359	92547254	4.260000e-23	121.0
58	TraesCS1B01G167800	chr4B	85.088	114	15	2	2185	2298	232097930	232097819	1.980000e-21	115.0
59	TraesCS1B01G167800	chr7D	93.750	96	5	1	2337	2432	622185155	622185061	9.080000e-30	143.0
60	TraesCS1B01G167800	chr7D	88.660	97	11	0	2345	2441	69957061	69956965	1.530000e-22	119.0
61	TraesCS1B01G167800	chr4D	84.722	144	18	4	2183	2325	397160001	397159861	3.270000e-29	141.0
62	TraesCS1B01G167800	chr5D	83.221	149	20	4	2176	2324	265961978	265961835	1.970000e-26	132.0
63	TraesCS1B01G167800	chr6A	85.039	127	17	2	2166	2292	184388167	184388291	2.540000e-25	128.0
64	TraesCS1B01G167800	chr3A	84.000	125	15	4	2164	2286	38393163	38393284	1.980000e-21	115.0
65	TraesCS1B01G167800	chr3A	94.595	74	4	0	6449	6522	353624523	353624596	1.980000e-21	115.0
66	TraesCS1B01G167800	chr3A	94.521	73	4	0	6452	6524	127196456	127196384	7.120000e-21	113.0
67	TraesCS1B01G167800	chr3A	87.755	98	10	2	2344	2440	653512622	653512526	7.120000e-21	113.0
68	TraesCS1B01G167800	chr3A	86.598	97	12	1	2345	2441	600920364	600920459	1.190000e-18	106.0
69	TraesCS1B01G167800	chr3B	84.906	106	14	2	2337	2442	238571845	238571742	1.190000e-18	106.0

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	TraesCS1B01G167800	chr1B	297091598	297100276	8678	False	16028.000000	16028	100.000000	1	8679	1	chr1B.!!$F1	8678
1	TraesCS1B01G167800	chr1A	257550951	257559367	8416	False	2124.166667	5535	92.886833	2	8615	6	chr1A.!!$F2	8613
2	TraesCS1B01G167800	chr1D	203283262	203293636	10374	False	1471.833333	3225	94.042333	1	8679	9	chr1D.!!$F2	8678
3	TraesCS1B01G167800	chr6D	47661866	47662474	608	True	261.000000	261	75.323000	5041	5631	1	chr6D.!!$R1	590
4	TraesCS1B01G167800	chr6B	123843275	123843882	607	False	259.000000	259	75.323000	5041	5631	1	chr6B.!!$F1	590

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
645	671	0.107643	GGGTCCATGAAGCTCCTAGC	59.892	60.000	0.00	0.00	42.84	3.42	F
1576	1687	0.413037	TGTTGGGATGGGGCTCATTT	59.587	50.000	0.00	0.00	35.97	2.32	F
2882	3027	2.230266	CCAAATACAGAAAACACCCGGG	59.770	50.000	22.25	22.25	0.00	5.73	F
3120	3271	0.725784	CGTCGCGCTTCTTTTGCATT	60.726	50.000	5.56	0.00	0.00	3.56	F
3520	3674	1.660607	CACACATCGATTTGGTCCTCG	59.339	52.381	15.58	0.00	36.25	4.63	F
4741	6783	1.780503	AATGGTGCTGCCTAAATCCC	58.219	50.000	0.00	0.00	38.35	3.85	F
5920	7984	0.034896	GTCCGAGAAAGCTTGTCCCA	59.965	55.000	0.00	0.00	0.00	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1709	1840	0.826062	CCCTATTGCTTTGGCCTTGG	59.174	55.000	3.32	37.74	3.61	R
3000	3145	0.817634	CGGAGTGGCAAACTTGTGGA	60.818	55.000	0.00	40.07	4.02	R
4719	6761	3.256631	GGGATTTAGGCAGCACCATTATG	59.743	47.826	0.00	43.14	1.90	R
5002	7044	9.883142	ATGAAGTTCAAAATTGTACTCCAAAAA	57.117	25.926	10.14	37.75	1.94	R
5676	7736	4.758688	CCCATAATGCTTTTTCAGAACCC	58.241	43.478	0.00	0.00	4.11	R
5994	8058	0.033228	GATCATGCTCCCTCTGTCCG	59.967	60.000	0.00	0.00	4.79	R
8053	10148	0.183492	CCTAGGCATGCTTAAGGGCA	59.817	55.000	18.92	46.63	5.36	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	5.201910	TCGACTCAACAATTTAGTTTTGCG	58.798	37.500	0.00	0.00	0.00	4.85
45	46	1.336755	GTTTTGCGGATTGTGTGGACT	59.663	47.619	0.00	0.00	0.00	3.85
114	115	0.187117	TTTGGTGTGATCCAAGCCCA	59.813	50.000	0.00	0.00	46.27	5.36
123	124	2.309755	TGATCCAAGCCCAGATGTCTTT	59.690	45.455	0.00	0.00	0.00	2.52
221	222	1.337728	ACGTCGATGGCTGATGACAAA	60.338	47.619	9.90	0.00	33.27	2.83
248	249	1.571460	CCTGATTTATCGCGGCTGC	59.429	57.895	7.70	7.70	37.91	5.25
276	298	4.133796	GCCATGGCAGCGGGTTTC	62.134	66.667	32.08	0.00	41.49	2.78
277	299	2.676121	CCATGGCAGCGGGTTTCA	60.676	61.111	0.00	0.00	0.00	2.69
280	302	1.973281	ATGGCAGCGGGTTTCACTG	60.973	57.895	0.00	0.00	34.48	3.66
281	303	2.281484	GGCAGCGGGTTTCACTGA	60.281	61.111	0.00	0.00	33.10	3.41
284	306	1.237285	GCAGCGGGTTTCACTGACAT	61.237	55.000	0.00	0.00	33.10	3.06
285	307	0.518636	CAGCGGGTTTCACTGACATG	59.481	55.000	0.00	0.00	33.10	3.21
286	308	0.606401	AGCGGGTTTCACTGACATGG	60.606	55.000	0.00	0.00	0.00	3.66
287	309	1.875963	CGGGTTTCACTGACATGGC	59.124	57.895	0.00	0.00	0.00	4.40
289	311	1.327303	GGGTTTCACTGACATGGCAA	58.673	50.000	1.11	0.00	0.00	4.52
290	312	1.000274	GGGTTTCACTGACATGGCAAC	60.000	52.381	1.11	0.00	0.00	4.17
331	356	3.123050	ACAACGCTTTTGAATTTGGCTC	58.877	40.909	2.19	0.00	0.00	4.70
353	378	3.181483	CCCATAGCAACATTTTCCTCTGC	60.181	47.826	0.00	0.00	0.00	4.26
355	380	4.883585	CCATAGCAACATTTTCCTCTGCTA	59.116	41.667	4.70	4.70	46.46	3.49
360	385	3.550437	ACATTTTCCTCTGCTATCGCT	57.450	42.857	0.00	0.00	36.97	4.93
424	449	1.535028	AGCGACAACAATGCGAAATCA	59.465	42.857	0.00	0.00	0.00	2.57
431	456	5.295950	ACAACAATGCGAAATCAAAATGGA	58.704	33.333	0.00	0.00	0.00	3.41
437	463	1.469079	CGAAATCAAAATGGACGGCCC	60.469	52.381	3.83	0.00	0.00	5.80
443	469	1.135024	CAAAATGGACGGCCCTTCATG	60.135	52.381	3.83	0.14	35.38	3.07
467	493	1.468054	GGTGTTCATGATTGAAGCGGC	60.468	52.381	0.00	0.00	42.41	6.53

Showing 1 to 25 of 256 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	4.000988	ACGTAATCAAGTCCACACAATCC	58.999	43.478	0.00	0.00	0.00	3.01
45	46	8.624367	TCTTCTTTCCCAATTAACGTAATCAA	57.376	30.769	0.00	0.00	0.00	2.57
114	115	2.175202	AGACAGGAGCGAAAGACATCT	58.825	47.619	0.00	0.00	0.00	2.90
123	124	1.178276	GAGAAGGAAGACAGGAGCGA	58.822	55.000	0.00	0.00	0.00	4.93
179	180	1.141053	GGATCATCCAACCTAACCGCT	59.859	52.381	0.00	0.00	36.28	5.52
221	222	3.306364	CGCGATAAATCAGGGAGAGGATT	60.306	47.826	0.00	0.00	35.34	3.01
248	249	3.506096	CCATGGCAGCTGACGCAG	61.506	66.667	20.43	8.44	39.10	5.18
268	290	1.875963	CCATGTCAGTGAAACCCGC	59.124	57.895	0.00	0.00	37.80	6.13
270	292	1.000274	GTTGCCATGTCAGTGAAACCC	60.000	52.381	0.00	0.00	37.80	4.11
271	293	1.680735	TGTTGCCATGTCAGTGAAACC	59.319	47.619	0.00	0.00	37.80	3.27
272	294	2.358898	AGTGTTGCCATGTCAGTGAAAC	59.641	45.455	0.00	0.00	0.00	2.78
276	298	0.877071	GGAGTGTTGCCATGTCAGTG	59.123	55.000	0.00	0.00	0.00	3.66
277	299	0.473755	TGGAGTGTTGCCATGTCAGT	59.526	50.000	0.00	0.00	0.00	3.41
280	302	3.319755	CAAAATGGAGTGTTGCCATGTC	58.680	45.455	0.00	0.00	45.11	3.06
281	303	2.548493	GCAAAATGGAGTGTTGCCATGT	60.548	45.455	0.00	0.00	45.11	3.21
284	306	3.984838	GCAAAATGGAGTGTTGCCA	57.015	47.368	0.00	0.00	41.41	4.92
286	308	1.142474	GCAGCAAAATGGAGTGTTGC	58.858	50.000	0.00	0.00	46.35	4.17
287	309	1.068895	TGGCAGCAAAATGGAGTGTTG	59.931	47.619	0.00	0.00	0.00	3.33
289	311	1.274167	CATGGCAGCAAAATGGAGTGT	59.726	47.619	0.00	0.00	0.00	3.55
290	312	1.546923	TCATGGCAGCAAAATGGAGTG	59.453	47.619	0.00	0.00	0.00	3.51
291	313	1.547372	GTCATGGCAGCAAAATGGAGT	59.453	47.619	0.00	0.00	0.00	3.85
292	314	1.546923	TGTCATGGCAGCAAAATGGAG	59.453	47.619	0.00	0.00	0.00	3.86
331	356	3.181483	GCAGAGGAAAATGTTGCTATGGG	60.181	47.826	12.97	0.00	42.71	4.00
353	378	0.460284	AACTCCGGCACAAGCGATAG	60.460	55.000	0.00	0.00	43.41	2.08
355	380	0.460284	CTAACTCCGGCACAAGCGAT	60.460	55.000	0.00	0.00	43.41	4.58

Showing 1 to 25 of 287 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.