AutoCloner

Multiple sequence alignment - TraesCS2D01G192500

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	TraesCS2D01G192500	chr2D	100.000	2934	0	0	1	2934	136522348	136519415	0.000000e+00	5419.0
1	TraesCS2D01G192500	chr2D	81.840	837	92	33	1135	1943	136754486	136755290	0.000000e+00	649.0
2	TraesCS2D01G192500	chr2D	85.671	328	26	9	2523	2849	136755972	136756279	2.820000e-85	326.0
3	TraesCS2D01G192500	chr2D	93.496	123	6	2	2521	2642	136477258	136477137	6.460000e-42	182.0
4	TraesCS2D01G192500	chr2D	83.740	123	7	5	754	868	136526494	136526377	1.440000e-18	104.0
5	TraesCS2D01G192500	chr2D	83.505	97	2	4	795	888	136608477	136608392	8.720000e-11	78.7
6	TraesCS2D01G192500	chr2B	85.483	1233	107	38	1047	2235	195005961	195004757	0.000000e+00	1219.0
7	TraesCS2D01G192500	chr2B	77.759	1169	145	60	1135	2240	195456054	195457170	1.930000e-171	612.0
8	TraesCS2D01G192500	chr2B	78.802	835	99	38	1171	1977	194995877	194995093	9.450000e-135	490.0
9	TraesCS2D01G192500	chr2B	85.549	346	39	7	2536	2877	194944173	194943835	4.650000e-93	351.0
10	TraesCS2D01G192500	chr2B	81.776	428	58	10	1382	1808	194950643	194950235	1.010000e-89	340.0
11	TraesCS2D01G192500	chr2B	84.795	342	30	12	2595	2924	773987644	773987313	1.010000e-84	324.0
12	TraesCS2D01G192500	chr2B	87.444	223	12	11	749	961	195168743	195168527	2.920000e-60	243.0
13	TraesCS2D01G192500	chr2B	82.381	210	28	6	2312	2519	194944556	194944354	1.080000e-39	174.0
14	TraesCS2D01G192500	chr2B	87.755	147	16	2	2536	2681	194992590	194992445	1.400000e-38	171.0
15	TraesCS2D01G192500	chr2B	80.702	228	31	9	2297	2519	195457184	195457403	6.510000e-37	165.0
16	TraesCS2D01G192500	chr2B	81.977	172	19	6	709	876	195060211	195060048	5.100000e-28	135.0
17	TraesCS2D01G192500	chr2B	78.926	242	17	9	756	995	195006329	195006120	1.830000e-27	134.0
18	TraesCS2D01G192500	chr2B	93.939	66	4	0	1188	1253	194952865	194952800	1.860000e-17	100.0
19	TraesCS2D01G192500	chr2B	97.959	49	1	0	272	320	195007659	195007611	5.210000e-13	86.1
20	TraesCS2D01G192500	chr2B	92.000	50	1	1	995	1041	195006100	195006051	1.890000e-07	67.6
21	TraesCS2D01G192500	chr2A	88.154	1013	77	16	1502	2485	165004144	165005142	0.000000e+00	1166.0
22	TraesCS2D01G192500	chr2A	93.402	682	32	10	747	1418	165003437	165004115	0.000000e+00	998.0
23	TraesCS2D01G192500	chr2A	78.038	1111	130	69	1171	2228	165009184	165010233	1.950000e-166	595.0
24	TraesCS2D01G192500	chr2A	76.877	1172	151	56	1135	2240	164768218	164767101	1.190000e-153	553.0
25	TraesCS2D01G192500	chr2A	88.278	418	39	6	2521	2932	164766194	164765781	2.630000e-135	492.0
26	TraesCS2D01G192500	chr2A	86.154	260	23	7	2533	2789	165010669	165010918	4.820000e-68	268.0
27	TraesCS2D01G192500	chr2A	81.395	344	36	15	365	691	164998755	164999087	3.750000e-64	255.0
28	TraesCS2D01G192500	chr2A	85.000	260	28	6	2533	2789	165017652	165017903	1.350000e-63	254.0
29	TraesCS2D01G192500	chr2A	83.737	289	21	12	410	686	164876814	164877088	1.750000e-62	250.0
30	TraesCS2D01G192500	chr2A	81.553	309	29	12	2627	2932	165230266	165230549	2.270000e-56	230.0
31	TraesCS2D01G192500	chr2A	82.353	255	35	7	2268	2519	165010236	165010483	2.290000e-51	213.0
32	TraesCS2D01G192500	chr2A	86.432	199	19	6	83	275	673059326	673059522	8.240000e-51	211.0
33	TraesCS2D01G192500	chr2A	86.387	191	22	3	89	276	9137631	9137820	3.830000e-49	206.0
34	TraesCS2D01G192500	chr2A	83.556	225	23	9	272	485	165000656	165000877	6.410000e-47	198.0
35	TraesCS2D01G192500	chr2A	91.045	134	12	0	2799	2932	165011271	165011404	6.460000e-42	182.0
36	TraesCS2D01G192500	chr2A	87.013	154	16	3	121	274	9137912	9138061	1.400000e-38	171.0
37	TraesCS2D01G192500	chr2A	86.923	130	12	4	2518	2642	165114696	165114825	1.100000e-29	141.0
38	TraesCS2D01G192500	chr2A	93.548	93	6	0	1	93	165000568	165000660	3.940000e-29	139.0
39	TraesCS2D01G192500	chr2A	85.882	85	7	4	879	961	164980863	164980944	5.210000e-13	86.1
40	TraesCS2D01G192500	chr2A	100.000	38	0	0	1443	1480	165004107	165004144	1.460000e-08	71.3
41	TraesCS2D01G192500	chr2A	95.238	42	2	0	648	689	165003100	165003141	1.890000e-07	67.6
42	TraesCS2D01G192500	chr3B	87.640	267	18	7	2595	2850	131506374	131506112	2.210000e-76	296.0
43	TraesCS2D01G192500	chr3B	85.714	91	10	3	2837	2924	131506093	131506003	3.110000e-15	93.5
44	TraesCS2D01G192500	chr3D	83.486	327	21	14	2523	2849	131228437	131228730	1.040000e-69	274.0
45	TraesCS2D01G192500	chr3D	79.245	159	20	8	2075	2229	131227924	131228073	6.690000e-17	99.0
46	TraesCS2D01G192500	chr3D	85.333	75	5	2	1863	1937	131227626	131227694	4.060000e-09	73.1
47	TraesCS2D01G192500	chr6B	89.840	187	17	1	89	275	440533735	440533919	3.780000e-59	239.0
48	TraesCS2D01G192500	chr6B	82.609	184	29	3	91	272	678342601	678342783	3.030000e-35	159.0
49	TraesCS2D01G192500	chr7D	87.831	189	19	3	88	276	322360437	322360621	4.920000e-53	219.0
50	TraesCS2D01G192500	chr7D	85.106	188	21	3	89	275	37274287	37274468	4.990000e-43	185.0
51	TraesCS2D01G192500	chr7D	79.861	144	18	6	2089	2229	216469321	216469456	8.660000e-16	95.3
52	TraesCS2D01G192500	chr7D	75.814	215	16	18	1863	2067	216469087	216469275	3.140000e-10	76.8
53	TraesCS2D01G192500	chr6D	87.113	194	21	3	89	279	37664541	37664349	1.770000e-52	217.0
54	TraesCS2D01G192500	chr4B	83.333	186	22	7	99	278	429609599	429609417	2.340000e-36	163.0
55	TraesCS2D01G192500	chr4D	74.257	404	33	29	1863	2229	111556218	111556587	1.440000e-18	104.0
56	TraesCS2D01G192500	chr7A	80.556	144	17	6	2089	2229	697134009	697134144	1.860000e-17	100.0
57	TraesCS2D01G192500	chr6A	80.556	144	17	6	2089	2229	4623836	4623971	1.860000e-17	100.0

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	TraesCS2D01G192500	chr2D	136519415	136522348	2933	True	5419.000000	5419	100.000000	1	2934	1	chr2D.!!$R2	2933
1	TraesCS2D01G192500	chr2D	136754486	136756279	1793	False	487.500000	649	83.755500	1135	2849	2	chr2D.!!$F1	1714
2	TraesCS2D01G192500	chr2B	195456054	195457403	1349	False	388.500000	612	79.230500	1135	2519	2	chr2B.!!$F1	1384
3	TraesCS2D01G192500	chr2B	195004757	195007659	2902	True	376.675000	1219	88.592000	272	2235	4	chr2B.!!$R7	1963
4	TraesCS2D01G192500	chr2B	194992445	194995877	3432	True	330.500000	490	83.278500	1171	2681	2	chr2B.!!$R6	1510
5	TraesCS2D01G192500	chr2B	194943835	194944556	721	True	262.500000	351	83.965000	2312	2877	2	chr2B.!!$R4	565
6	TraesCS2D01G192500	chr2B	194950235	194952865	2630	True	220.000000	340	87.857500	1188	1808	2	chr2B.!!$R5	620
7	TraesCS2D01G192500	chr2A	164765781	164768218	2437	True	522.500000	553	82.577500	1135	2932	2	chr2A.!!$R1	1797
8	TraesCS2D01G192500	chr2A	164998755	165005142	6387	False	413.557143	1166	90.756143	1	2485	7	chr2A.!!$F8	2484
9	TraesCS2D01G192500	chr2A	165009184	165011404	2220	False	314.500000	595	84.397500	1171	2932	4	chr2A.!!$F9	1761

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
580	2756	0.031314	CTCTGTCTATGCGCCATCGT	59.969	55.0	4.18	0.0	38.14	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2093	8954	1.003118	TGTCCCCCGAATGAAGTCAAG	59.997	52.381	0.0	0.0	0.0	3.02	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	End Stability
77	1891	1.198178	GGAGATGCGCCGTTTTGTTTA	59.802	47.619	4.18	0.00	2.01
86	1900	5.032220	GCGCCGTTTTGTTTAATTAGCTAT	58.968	37.500	0.00	0.00	2.97
87	1901	6.183360	TGCGCCGTTTTGTTTAATTAGCTATA	60.183	34.615	4.18	0.00	1.31
106	1920	7.680730	AGCTATATTAGACCTTGTACAATGGG	58.319	38.462	20.95	16.79	4.00
107	1921	7.512746	AGCTATATTAGACCTTGTACAATGGGA	59.487	37.037	18.16	6.31	4.37
108	1922	7.819900	GCTATATTAGACCTTGTACAATGGGAG	59.180	40.741	18.16	3.01	4.30
109	1923	7.931015	ATATTAGACCTTGTACAATGGGAGA	57.069	36.000	18.16	7.25	3.71
110	1924	6.831664	ATTAGACCTTGTACAATGGGAGAT	57.168	37.500	18.16	7.75	2.75
111	1925	4.494091	AGACCTTGTACAATGGGAGATG	57.506	45.455	18.16	1.25	2.90
112	1926	2.945668	GACCTTGTACAATGGGAGATGC	59.054	50.000	18.16	2.00	3.91
113	1927	2.578021	ACCTTGTACAATGGGAGATGCT	59.422	45.455	18.16	0.00	3.79
114	1928	3.010584	ACCTTGTACAATGGGAGATGCTT	59.989	43.478	18.16	0.00	3.91
115	1929	4.227300	ACCTTGTACAATGGGAGATGCTTA	59.773	41.667	18.16	0.00	3.09
116	1930	4.818546	CCTTGTACAATGGGAGATGCTTAG	59.181	45.833	9.13	0.00	2.18
117	1931	5.396772	CCTTGTACAATGGGAGATGCTTAGA	60.397	44.000	9.13	0.00	2.10
118	1932	5.282055	TGTACAATGGGAGATGCTTAGAG	57.718	43.478	0.00	0.00	2.43
119	1933	3.853355	ACAATGGGAGATGCTTAGAGG	57.147	47.619	0.00	0.00	3.69
120	1934	3.387962	ACAATGGGAGATGCTTAGAGGA	58.612	45.455	0.00	0.00	3.71
121	1935	3.390639	ACAATGGGAGATGCTTAGAGGAG	59.609	47.826	0.00	0.00	3.69
122	1936	2.094100	TGGGAGATGCTTAGAGGAGG	57.906	55.000	0.00	0.00	4.30
123	1937	1.292242	TGGGAGATGCTTAGAGGAGGT	59.708	52.381	0.00	0.00	3.85
124	1938	1.691434	GGGAGATGCTTAGAGGAGGTG	59.309	57.143	0.00	0.00	4.00
125	1939	1.069978	GGAGATGCTTAGAGGAGGTGC	59.930	57.143	0.00	0.00	5.01
126	1940	2.038659	GAGATGCTTAGAGGAGGTGCT	58.961	52.381	0.00	0.00	4.40
127	1941	2.433970	GAGATGCTTAGAGGAGGTGCTT	59.566	50.000	0.00	0.00	3.91

Showing 1 to 25 of 267 entries

Previous1 2 3 4 5…11Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	End Stability
4	5	2.593468	TAAGCGCCATCCTCCACAGC	62.593	60.000	2.29	0.00	4.40
34	1848	0.250640	ATGATCCATCTTCGGCAGGC	60.251	55.000	0.00	0.00	4.85
86	1900	7.689313	GCATCTCCCATTGTACAAGGTCTAATA	60.689	40.741	18.13	0.54	0.98
87	1901	6.595682	CATCTCCCATTGTACAAGGTCTAAT	58.404	40.000	18.13	4.91	1.73
93	1907	3.287867	AGCATCTCCCATTGTACAAGG	57.712	47.619	14.65	13.92	3.61
94	1908	5.674525	TCTAAGCATCTCCCATTGTACAAG	58.325	41.667	14.65	6.30	3.16
95	1909	5.396772	CCTCTAAGCATCTCCCATTGTACAA	60.397	44.000	11.41	11.41	2.41
96	1910	4.101585	CCTCTAAGCATCTCCCATTGTACA	59.898	45.833	0.00	0.00	2.90
97	1911	4.345257	TCCTCTAAGCATCTCCCATTGTAC	59.655	45.833	0.00	0.00	2.90
98	1912	4.556697	TCCTCTAAGCATCTCCCATTGTA	58.443	43.478	0.00	0.00	2.41
99	1913	3.387962	TCCTCTAAGCATCTCCCATTGT	58.612	45.455	0.00	0.00	2.71
100	1914	3.244491	CCTCCTCTAAGCATCTCCCATTG	60.244	52.174	0.00	0.00	2.82
101	1915	2.978278	CCTCCTCTAAGCATCTCCCATT	59.022	50.000	0.00	0.00	3.16
102	1916	2.090267	ACCTCCTCTAAGCATCTCCCAT	60.090	50.000	0.00	0.00	4.00
103	1917	1.292242	ACCTCCTCTAAGCATCTCCCA	59.708	52.381	0.00	0.00	4.37
104	1918	1.691434	CACCTCCTCTAAGCATCTCCC	59.309	57.143	0.00	0.00	4.30
105	1919	1.069978	GCACCTCCTCTAAGCATCTCC	59.930	57.143	0.00	0.00	3.71
106	1920	2.038659	AGCACCTCCTCTAAGCATCTC	58.961	52.381	0.00	0.00	2.75
107	1921	2.173126	AGCACCTCCTCTAAGCATCT	57.827	50.000	0.00	0.00	2.90
108	1922	2.998316	AAGCACCTCCTCTAAGCATC	57.002	50.000	0.00	0.00	3.91
109	1923	4.471386	TCTTTAAGCACCTCCTCTAAGCAT	59.529	41.667	0.00	0.00	3.79
110	1924	3.838317	TCTTTAAGCACCTCCTCTAAGCA	59.162	43.478	0.00	0.00	3.91
111	1925	4.473477	TCTTTAAGCACCTCCTCTAAGC	57.527	45.455	0.00	0.00	3.09
112	1926	9.449719	TTTATTTCTTTAAGCACCTCCTCTAAG	57.550	33.333	0.00	0.00	2.18
113	1927	9.227777	GTTTATTTCTTTAAGCACCTCCTCTAA	57.772	33.333	0.00	0.00	2.10

Showing 1 to 25 of 278 entries

Previous1 2 3 4 5…12Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.