AutoCloner

Multiple sequence alignment - TraesCS2D01G486900

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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	TraesCS2D01G486900	chr2D	100.000	2957	0	0	1	2957	586995229	586998185	0.000000e+00	5461.0
1	TraesCS2D01G486900	chr2D	90.566	265	16	4	544	805	37526874	37526616	2.820000e-90	342.0
2	TraesCS2D01G486900	chr2D	88.849	278	17	9	532	803	583317297	583317028	2.200000e-86	329.0
3	TraesCS2D01G486900	chr2D	80.135	297	48	9	2644	2932	476342351	476342644	8.300000e-51	211.0
4	TraesCS2D01G486900	chr2B	93.404	1319	64	14	814	2130	708801445	708802742	0.000000e+00	1932.0
5	TraesCS2D01G486900	chr2B	84.058	276	37	6	2662	2932	642950892	642951165	2.920000e-65	259.0
6	TraesCS2D01G486900	chr2A	93.101	1290	56	18	801	2089	721834540	721835797	0.000000e+00	1858.0
7	TraesCS2D01G486900	chr2A	86.895	992	117	11	979	1962	6419573	6420559	0.000000e+00	1099.0
8	TraesCS2D01G486900	chr2A	91.120	259	16	4	544	800	100915931	100916184	7.850000e-91	344.0
9	TraesCS2D01G486900	chr2A	81.787	291	39	12	2651	2932	525029040	525029325	6.370000e-57	231.0
10	TraesCS2D01G486900	chr2A	100.000	28	0	0	2588	2615	707738154	707738181	5.000000e-03	52.8
11	TraesCS2D01G486900	chr5A	89.137	313	31	3	2236	2547	640351833	640351523	1.290000e-103	387.0
12	TraesCS2D01G486900	chr5A	80.268	299	55	4	1336	1632	479462084	479461788	3.840000e-54	222.0
13	TraesCS2D01G486900	chr5A	100.000	29	0	0	2586	2614	576400994	576401022	1.000000e-03	54.7
14	TraesCS2D01G486900	chr7A	89.667	300	28	2	2239	2538	700123978	700123682	2.150000e-101	379.0
15	TraesCS2D01G486900	chr7A	80.593	371	62	7	1336	1701	189718517	189718882	8.070000e-71	278.0
16	TraesCS2D01G486900	chr5B	90.943	265	14	6	545	805	276947044	276947302	6.070000e-92	348.0
17	TraesCS2D01G486900	chr5B	80.537	298	56	2	1336	1632	454907632	454907336	8.250000e-56	228.0
18	TraesCS2D01G486900	chr6B	91.440	257	13	4	543	795	4953244	4952993	7.850000e-91	344.0
19	TraesCS2D01G486900	chr6B	91.440	257	13	4	543	795	4975626	4975375	7.850000e-91	344.0
20	TraesCS2D01G486900	chr6B	91.051	257	14	4	543	795	5033021	5032770	3.650000e-89	339.0
21	TraesCS2D01G486900	chr6B	83.280	311	41	9	2239	2546	646138181	646138483	2.900000e-70	276.0
22	TraesCS2D01G486900	chr6B	80.471	297	48	9	2644	2932	245724485	245724779	4.960000e-53	219.0
23	TraesCS2D01G486900	chr4D	91.154	260	14	5	545	800	3381091	3381345	7.850000e-91	344.0
24	TraesCS2D01G486900	chr4D	80.286	350	55	9	2589	2931	8884107	8884449	4.890000e-63	252.0
25	TraesCS2D01G486900	chr3D	90.494	263	16	6	545	803	571005087	571004830	3.650000e-89	339.0
26	TraesCS2D01G486900	chr3D	82.095	296	43	8	2645	2932	2635807	2636100	8.190000e-61	244.0
27	TraesCS2D01G486900	chr6D	86.458	288	31	7	2650	2931	242987915	242988200	2.860000e-80	309.0
28	TraesCS2D01G486900	chr7D	80.441	363	63	6	1343	1701	181975914	181975556	1.350000e-68	270.0
29	TraesCS2D01G486900	chr7D	94.595	37	2	0	2587	2623	371253757	371253793	1.140000e-04	58.4
30	TraesCS2D01G486900	chr7D	100.000	28	0	0	2587	2614	469884667	469884694	5.000000e-03	52.8
31	TraesCS2D01G486900	chr7B	80.000	375	66	7	1332	1701	150188125	150187755	4.860000e-68	268.0
32	TraesCS2D01G486900	chr7B	85.098	255	30	7	2684	2932	195249445	195249193	1.360000e-63	254.0
33	TraesCS2D01G486900	chr7B	93.333	150	8	2	2239	2387	709901834	709901686	1.380000e-53	220.0
34	TraesCS2D01G486900	chr5D	81.208	298	54	2	1336	1632	379234797	379234501	3.810000e-59	239.0
35	TraesCS2D01G486900	chr5D	81.787	291	42	10	2650	2932	485993359	485993072	1.770000e-57	233.0
36	TraesCS2D01G486900	chr5D	100.000	28	0	0	2587	2614	268571171	268571198	5.000000e-03	52.8
37	TraesCS2D01G486900	chr5D	82.759	58	10	0	2587	2644	520650634	520650577	5.000000e-03	52.8
38	TraesCS2D01G486900	chr1D	83.621	116	17	2	87	202	286541739	286541626	1.120000e-19	108.0
39	TraesCS2D01G486900	chr1D	100.000	28	0	0	2587	2614	383180900	383180927	5.000000e-03	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	TraesCS2D01G486900	chr2D	586995229	586998185	2956	False	5461	5461	100.000	1	2957	1	chr2D.!!$F2	2956
1	TraesCS2D01G486900	chr2B	708801445	708802742	1297	False	1932	1932	93.404	814	2130	1	chr2B.!!$F2	1316
2	TraesCS2D01G486900	chr2A	721834540	721835797	1257	False	1858	1858	93.101	801	2089	1	chr2A.!!$F5	1288
3	TraesCS2D01G486900	chr2A	6419573	6420559	986	False	1099	1099	86.895	979	1962	1	chr2A.!!$F1	983

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
229	230	0.037975	CTGCAGCCAATTCCCACAAC	60.038	55.0	0.0	0.0	0.0	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2203	2209	0.305922	GGTAATCTGTGCGCATCTGC	59.694	55.0	15.91	0.0	37.78	4.26	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
38	39	3.950087	GCACACATGCGATCTCATTAA	57.050	42.857	0.00	0.00	43.33	1.40
39	40	4.277257	GCACACATGCGATCTCATTAAA	57.723	40.909	0.00	0.00	43.33	1.52
40	41	4.852138	GCACACATGCGATCTCATTAAAT	58.148	39.130	0.00	0.00	43.33	1.40
41	42	4.673761	GCACACATGCGATCTCATTAAATG	59.326	41.667	0.00	0.00	43.33	2.32
42	43	5.731406	GCACACATGCGATCTCATTAAATGT	60.731	40.000	0.00	0.00	43.33	2.71
43	44	6.260377	CACACATGCGATCTCATTAAATGTT	58.740	36.000	0.00	0.00	0.00	2.71
44	45	6.412943	CACACATGCGATCTCATTAAATGTTC	59.587	38.462	0.00	0.00	0.00	3.18
45	46	6.093909	ACACATGCGATCTCATTAAATGTTCA	59.906	34.615	0.00	0.00	0.00	3.18
46	47	6.412943	CACATGCGATCTCATTAAATGTTCAC	59.587	38.462	0.00	0.00	0.00	3.18
47	48	5.484173	TGCGATCTCATTAAATGTTCACC	57.516	39.130	0.00	0.00	0.00	4.02
48	49	4.940654	TGCGATCTCATTAAATGTTCACCA	59.059	37.500	0.00	0.00	0.00	4.17
49	50	5.589855	TGCGATCTCATTAAATGTTCACCAT	59.410	36.000	0.00	0.00	34.36	3.55
50	51	6.765512	TGCGATCTCATTAAATGTTCACCATA	59.234	34.615	0.00	0.00	31.97	2.74
51	52	7.281999	TGCGATCTCATTAAATGTTCACCATAA	59.718	33.333	0.00	0.00	31.97	1.90
52	53	8.128582	GCGATCTCATTAAATGTTCACCATAAA	58.871	33.333	0.00	0.00	31.97	1.40
56	57	9.585099	TCTCATTAAATGTTCACCATAAAATGC	57.415	29.630	0.00	0.00	36.58	3.56
57	58	9.368674	CTCATTAAATGTTCACCATAAAATGCA	57.631	29.630	0.00	0.00	36.58	3.96
58	59	9.887629	TCATTAAATGTTCACCATAAAATGCAT	57.112	25.926	0.00	0.00	36.58	3.96
59	60	9.923786	CATTAAATGTTCACCATAAAATGCATG	57.076	29.630	0.00	0.00	33.04	4.06
60	61	9.887629	ATTAAATGTTCACCATAAAATGCATGA	57.112	25.926	0.00	0.00	31.97	3.07
61	62	9.716531	TTAAATGTTCACCATAAAATGCATGAA	57.283	25.926	0.00	0.00	33.91	2.57
62	63	8.618702	AAATGTTCACCATAAAATGCATGAAA	57.381	26.923	0.00	0.00	36.36	2.69
63	64	8.618702	AATGTTCACCATAAAATGCATGAAAA	57.381	26.923	0.00	0.00	36.36	2.29
64	65	8.618702	ATGTTCACCATAAAATGCATGAAAAA	57.381	26.923	0.00	0.00	36.36	1.94
213	214	9.056005	TCATACAACCAAATCTCATAATACTGC	57.944	33.333	0.00	0.00	0.00	4.40

Showing 1 to 25 of 706 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.687210	CATGTGTGCATGCTAAGATAATTTAAT	57.313	29.630	20.33	0.00	44.87	1.40
19	20	5.813717	ACATTTAATGAGATCGCATGTGTG	58.186	37.500	13.00	11.48	0.00	3.82
20	21	6.093909	TGAACATTTAATGAGATCGCATGTGT	59.906	34.615	13.00	12.04	0.00	3.72
21	22	6.412943	GTGAACATTTAATGAGATCGCATGTG	59.587	38.462	13.00	11.49	0.00	3.21
22	23	6.458751	GGTGAACATTTAATGAGATCGCATGT	60.459	38.462	13.00	4.81	0.00	3.21
23	24	5.911280	GGTGAACATTTAATGAGATCGCATG	59.089	40.000	13.00	4.15	0.00	4.06
24	25	5.589855	TGGTGAACATTTAATGAGATCGCAT	59.410	36.000	12.28	6.07	0.00	4.73
25	26	4.940654	TGGTGAACATTTAATGAGATCGCA	59.059	37.500	12.28	0.28	0.00	5.10
26	27	5.484173	TGGTGAACATTTAATGAGATCGC	57.516	39.130	12.28	12.00	0.00	4.58
30	31	9.585099	GCATTTTATGGTGAACATTTAATGAGA	57.415	29.630	12.28	0.00	39.25	3.27
31	32	9.368674	TGCATTTTATGGTGAACATTTAATGAG	57.631	29.630	12.28	0.00	39.25	2.90
32	33	9.887629	ATGCATTTTATGGTGAACATTTAATGA	57.112	25.926	12.28	6.62	39.25	2.57
33	34	9.923786	CATGCATTTTATGGTGAACATTTAATG	57.076	29.630	0.00	3.07	41.03	1.90
34	35	9.887629	TCATGCATTTTATGGTGAACATTTAAT	57.112	25.926	0.00	0.00	41.03	1.40
35	36	9.716531	TTCATGCATTTTATGGTGAACATTTAA	57.283	25.926	0.00	0.00	41.03	1.52
36	37	9.716531	TTTCATGCATTTTATGGTGAACATTTA	57.283	25.926	0.00	0.00	41.03	1.40
37	38	8.618702	TTTCATGCATTTTATGGTGAACATTT	57.381	26.923	0.00	0.00	41.03	2.32
38	39	8.618702	TTTTCATGCATTTTATGGTGAACATT	57.381	26.923	0.00	0.00	41.03	2.71
39	40	8.618702	TTTTTCATGCATTTTATGGTGAACAT	57.381	26.923	0.00	0.00	43.68	2.71
187	188	9.056005	GCAGTATTATGAGATTTGGTTGTATGA	57.944	33.333	0.00	0.00	0.00	2.15
188	189	8.839343	TGCAGTATTATGAGATTTGGTTGTATG	58.161	33.333	0.00	0.00	0.00	2.39
189	190	8.978874	TGCAGTATTATGAGATTTGGTTGTAT	57.021	30.769	0.00	0.00	0.00	2.29
190	191	7.012327	GCTGCAGTATTATGAGATTTGGTTGTA	59.988	37.037	16.64	0.00	0.00	2.41
191	192	6.183360	GCTGCAGTATTATGAGATTTGGTTGT	60.183	38.462	16.64	0.00	0.00	3.32
192	193	6.204359	GCTGCAGTATTATGAGATTTGGTTG	58.796	40.000	16.64	0.00	0.00	3.77

Showing 1 to 25 of 698 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.