AutoCloner

Multiple sequence alignment - TraesCS2A01G565300

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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	TraesCS2A01G565300	chr2A	100.000	2264	0	0	1	2264	764946102	764943839	0.000000e+00	4181
1	TraesCS2A01G565300	chr2A	86.022	279	33	6	1881	2156	764943947	764944222	6.120000e-76	294
2	TraesCS2A01G565300	chr2A	76.903	381	58	24	1894	2264	14627532	14627172	2.970000e-44	189
3	TraesCS2A01G565300	chr1D	90.524	2100	137	25	1	2051	446419284	446421370	0.000000e+00	2719
4	TraesCS2A01G565300	chr3D	90.321	2087	140	16	1	2035	310406070	310408146	0.000000e+00	2678
5	TraesCS2A01G565300	chr3D	90.144	2009	138	18	1	1957	446922400	446924400	0.000000e+00	2558
6	TraesCS2A01G565300	chrUn	89.631	2112	147	30	1	2051	10399149	10401249	0.000000e+00	2621
7	TraesCS2A01G565300	chr7D	89.484	2092	154	22	1	2035	131689370	131691452	0.000000e+00	2584
8	TraesCS2A01G565300	chr7D	90.657	974	72	9	1095	2052	610729345	610728375	0.000000e+00	1277
9	TraesCS2A01G565300	chr7D	84.156	385	53	6	1882	2264	610728430	610728052	1.280000e-97	366
10	TraesCS2A01G565300	chr6D	89.502	2048	152	21	1	1997	62141216	62143251	0.000000e+00	2532
11	TraesCS2A01G565300	chr6D	92.071	1009	50	11	938	1918	377213143	377214149	0.000000e+00	1393
12	TraesCS2A01G565300	chr6D	83.073	384	55	8	1883	2264	377214185	377214560	7.740000e-90	340
13	TraesCS2A01G565300	chr5D	91.754	1819	98	13	1	1771	348341219	348343033	0.000000e+00	2481
14	TraesCS2A01G565300	chr5D	95.287	976	43	2	1	974	520878575	520879549	0.000000e+00	1544
15	TraesCS2A01G565300	chr5D	93.857	993	38	9	940	1914	520879546	520880533	0.000000e+00	1474
16	TraesCS2A01G565300	chr5D	87.256	871	66	26	1222	2057	445782519	445781659	0.000000e+00	952
17	TraesCS2A01G565300	chr2B	88.480	2118	159	34	6	2048	430232481	430230374	0.000000e+00	2481
18	TraesCS2A01G565300	chr2B	89.403	2010	151	19	1	1955	215847145	215849147	0.000000e+00	2475
19	TraesCS2A01G565300	chr2B	79.070	387	60	17	1886	2264	465663066	465662693	1.740000e-61	246
20	TraesCS2A01G565300	chr4B	88.965	1894	137	24	1	1845	588824066	588825936	0.000000e+00	2274
21	TraesCS2A01G565300	chr4B	82.099	648	76	20	1435	2049	310257593	310258233	3.330000e-143	518
22	TraesCS2A01G565300	chr4D	89.423	1144	86	16	938	2049	470195700	470194560	0.000000e+00	1410
23	TraesCS2A01G565300	chr6B	88.174	1150	97	18	938	2054	181110627	181109484	0.000000e+00	1334
24	TraesCS2A01G565300	chr6B	88.253	1013	68	15	768	1736	702946742	702945737	0.000000e+00	1164
25	TraesCS2A01G565300	chr3B	88.283	1101	64	15	695	1747	548879768	548880851	0.000000e+00	1258
26	TraesCS2A01G565300	chr3B	77.922	385	64	18	1886	2264	809557706	809557337	1.050000e-53	220
27	TraesCS2A01G565300	chr3B	80.000	280	44	10	1988	2264	732876127	732875857	1.770000e-46	196
28	TraesCS2A01G565300	chr6A	81.818	385	60	7	1882	2264	23006672	23007048	4.690000e-82	315
29	TraesCS2A01G565300	chr1A	78.462	390	60	14	1888	2264	311770612	311770234	1.350000e-57	233

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	TraesCS2A01G565300	chr2A	764943839	764946102	2263	True	4181.0	4181	100.0000	1	2264	1	chr2A.!!$R2	2263
1	TraesCS2A01G565300	chr1D	446419284	446421370	2086	False	2719.0	2719	90.5240	1	2051	1	chr1D.!!$F1	2050
2	TraesCS2A01G565300	chr3D	310406070	310408146	2076	False	2678.0	2678	90.3210	1	2035	1	chr3D.!!$F1	2034
3	TraesCS2A01G565300	chr3D	446922400	446924400	2000	False	2558.0	2558	90.1440	1	1957	1	chr3D.!!$F2	1956
4	TraesCS2A01G565300	chrUn	10399149	10401249	2100	False	2621.0	2621	89.6310	1	2051	1	chrUn.!!$F1	2050
5	TraesCS2A01G565300	chr7D	131689370	131691452	2082	False	2584.0	2584	89.4840	1	2035	1	chr7D.!!$F1	2034
6	TraesCS2A01G565300	chr7D	610728052	610729345	1293	True	821.5	1277	87.4065	1095	2264	2	chr7D.!!$R1	1169
7	TraesCS2A01G565300	chr6D	62141216	62143251	2035	False	2532.0	2532	89.5020	1	1997	1	chr6D.!!$F1	1996
8	TraesCS2A01G565300	chr6D	377213143	377214560	1417	False	866.5	1393	87.5720	938	2264	2	chr6D.!!$F2	1326
9	TraesCS2A01G565300	chr5D	348341219	348343033	1814	False	2481.0	2481	91.7540	1	1771	1	chr5D.!!$F1	1770
10	TraesCS2A01G565300	chr5D	520878575	520880533	1958	False	1509.0	1544	94.5720	1	1914	2	chr5D.!!$F2	1913
11	TraesCS2A01G565300	chr5D	445781659	445782519	860	True	952.0	952	87.2560	1222	2057	1	chr5D.!!$R1	835
12	TraesCS2A01G565300	chr2B	430230374	430232481	2107	True	2481.0	2481	88.4800	6	2048	1	chr2B.!!$R1	2042
13	TraesCS2A01G565300	chr2B	215847145	215849147	2002	False	2475.0	2475	89.4030	1	1955	1	chr2B.!!$F1	1954
14	TraesCS2A01G565300	chr4B	588824066	588825936	1870	False	2274.0	2274	88.9650	1	1845	1	chr4B.!!$F2	1844
15	TraesCS2A01G565300	chr4B	310257593	310258233	640	False	518.0	518	82.0990	1435	2049	1	chr4B.!!$F1	614
16	TraesCS2A01G565300	chr4D	470194560	470195700	1140	True	1410.0	1410	89.4230	938	2049	1	chr4D.!!$R1	1111
17	TraesCS2A01G565300	chr6B	181109484	181110627	1143	True	1334.0	1334	88.1740	938	2054	1	chr6B.!!$R1	1116
18	TraesCS2A01G565300	chr6B	702945737	702946742	1005	True	1164.0	1164	88.2530	768	1736	1	chr6B.!!$R2	968
19	TraesCS2A01G565300	chr3B	548879768	548880851	1083	False	1258.0	1258	88.2830	695	1747	1	chr3B.!!$F1	1052

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
265	266	0.394488	TGCACCTCAAAACCCGTTGA	60.394	50.0	0.0	0.0	36.15	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1446	1542	0.038526	GACGACGCTCTTCCTCCAAA	60.039	55.0	0.0	0.0	0.0	3.28	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	7.278868	CGAGTACTTCCTAAAGCATTCTGAAAT	59.721	37.037	0.00	0.00	35.81	2.17
83	84	2.352503	CAAGTGGATTGGCGAAAAGG	57.647	50.000	0.00	0.00	35.08	3.11
240	241	4.946157	CAGATCTTATGGTGGAGTTGCTTT	59.054	41.667	0.00	0.00	0.00	3.51
265	266	0.394488	TGCACCTCAAAACCCGTTGA	60.394	50.000	0.00	0.00	36.15	3.18
303	304	3.511146	CCACACAAGTATCATTGGCCTTT	59.489	43.478	3.32	0.00	34.36	3.11
320	321	2.098117	CCTTTCTCGCATTTGATGACCC	59.902	50.000	0.00	0.00	0.00	4.46
327	328	1.066929	GCATTTGATGACCCCAACACC	60.067	52.381	0.00	0.00	0.00	4.16
328	329	2.246469	CATTTGATGACCCCAACACCA	58.754	47.619	0.00	0.00	0.00	4.17
485	486	1.105167	CATTGTGCCAGATCCCGCAT	61.105	55.000	7.51	0.00	37.33	4.73
512	513	1.696884	GGCCTATGAGGGGAAGAAGAG	59.303	57.143	0.00	0.00	35.37	2.85
561	562	3.223674	TGATCTAGCTGGATACACCGA	57.776	47.619	13.16	0.00	46.17	4.69
618	619	1.313772	CCGGACACCAACAATTGTGA	58.686	50.000	12.82	0.00	0.00	3.58
708	715	2.544267	GTCAAACACGTGAAGGAAGGAG	59.456	50.000	25.01	1.44	0.00	3.69
881	932	1.201424	GTCGGGTTGATAGGGGAAGT	58.799	55.000	0.00	0.00	0.00	3.01
917	968	2.159379	GCTCAATCCGGATGGTTGAAAC	60.159	50.000	19.95	10.03	35.94	2.78
1026	1122	0.175760	CATCCGGTTCCATGACGAGT	59.824	55.000	0.00	0.00	0.00	4.18
1146	1242	3.256631	GTGGAGATGTTTGCAAGGTGAAT	59.743	43.478	0.00	0.00	0.00	2.57
1173	1269	0.721718	CCGACCGAAAGAAGTCATGC	59.278	55.000	0.00	0.00	33.08	4.06
1237	1333	2.177394	TCATGCGCTTCCAACTAACA	57.823	45.000	9.73	0.00	0.00	2.41
1293	1389	8.655378	GTAACATGTTACTCTAAAATGTGTGC	57.345	34.615	32.21	8.31	43.88	4.57
1446	1542	6.850752	TTTGAAGAAAGGTTTCAAAGAGGT	57.149	33.333	8.57	0.00	44.90	3.85
1467	1564	1.153997	GGAGGAAGAGCGTCGTCAC	60.154	63.158	8.03	0.00	34.74	3.67
1478	1575	1.687628	CGTCGTCACAAAGAGAGGAC	58.312	55.000	0.00	0.00	43.64	3.85
1507	1604	1.680522	GCAATGCGAGGAGGAGAGGA	61.681	60.000	0.00	0.00	0.00	3.71
1772	1901	5.997129	TCTAGAGATGTTTGCAATGTGTCAA	59.003	36.000	0.00	0.00	0.00	3.18
1854	1994	5.745312	TGTGCTGAGAAGAAGGATAGAAA	57.255	39.130	0.00	0.00	0.00	2.52
1866	2008	4.429854	AGGATAGAAACAGAGGATTGCC	57.570	45.455	0.00	0.00	0.00	4.52
1879	2023	1.203287	GGATTGCCCTGTTTTCTGAGC	59.797	52.381	0.00	0.00	0.00	4.26
1898	2121	0.958876	CTTCAAACCCTACCGCCACC	60.959	60.000	0.00	0.00	0.00	4.61
1900	2123	4.710167	AAACCCTACCGCCACCGC	62.710	66.667	0.00	0.00	0.00	5.68
1918	2141	2.662596	CTCTGGCGGTAGGTTGCA	59.337	61.111	0.00	0.00	0.00	4.08
1919	2142	1.741770	CTCTGGCGGTAGGTTGCAC	60.742	63.158	0.00	0.00	0.00	4.57
1923	2146	2.048503	GCGGTAGGTTGCACGACT	60.049	61.111	0.00	0.00	0.00	4.18
1943	2166	1.204146	CTACTGCCAGGTACCATGGT	58.796	55.000	23.55	23.55	40.17	3.55
1979	2209	0.965439	TTGCTGGGATGGGAAAAACG	59.035	50.000	0.00	0.00	0.00	3.60
1985	2254	1.305930	GGATGGGAAAAACGAGCGCT	61.306	55.000	11.27	11.27	0.00	5.92
2002	2271	1.218316	CTCTGGCGGTAGGGTCAAC	59.782	63.158	0.00	0.00	0.00	3.18
2020	2289	0.398098	ACCCCTACCACCATAGACCG	60.398	60.000	0.00	0.00	0.00	4.79
2072	2459	2.223386	TGCTTGTTTTTACCGTCACAGC	60.223	45.455	0.00	0.00	0.00	4.40
2078	2465	3.684103	TTTTACCGTCACAGCAAGTTG	57.316	42.857	0.00	0.00	0.00	3.16
2080	2467	2.605837	TACCGTCACAGCAAGTTGAA	57.394	45.000	7.16	0.00	0.00	2.69
2155	2542	0.108963	CGGTGGTGGTAGGGTTTGAA	59.891	55.000	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	4.395519	CAATCCACTTGGCCGTGA	57.604	55.556	11.94	0.00	37.06	4.35
303	304	0.617935	TGGGGTCATCAAATGCGAGA	59.382	50.000	0.00	0.00	0.00	4.04
320	321	1.002468	CAAGTTTCTCGCTGGTGTTGG	60.002	52.381	0.00	0.00	0.00	3.77
327	328	0.669318	TACGGGCAAGTTTCTCGCTG	60.669	55.000	0.00	0.00	0.00	5.18
328	329	0.249398	ATACGGGCAAGTTTCTCGCT	59.751	50.000	0.00	0.00	0.00	4.93
369	370	2.222289	CGTTCTAATGTGAACTCGTGCG	60.222	50.000	8.73	0.00	42.82	5.34
391	392	2.604174	CGCCCACGTCAACCTTGTC	61.604	63.158	0.00	0.00	33.53	3.18
485	486	1.067762	CCCCTCATAGGCCCCATGAA	61.068	60.000	16.28	3.92	32.73	2.57
492	493	1.696884	CTCTTCTTCCCCTCATAGGCC	59.303	57.143	0.00	0.00	32.73	5.19
512	513	3.325135	TCACTCCTGAACCTCTTCTTTCC	59.675	47.826	0.00	0.00	0.00	3.13
561	562	5.304101	TGACCACTACCAAATTGCTTCATTT	59.696	36.000	0.00	0.00	0.00	2.32
618	619	2.948979	TGTCCTGTTTCGTTGCATTCTT	59.051	40.909	0.00	0.00	0.00	2.52
681	688	4.951254	TCCTTCACGTGTTTGACTATTGA	58.049	39.130	16.51	0.00	0.00	2.57
684	691	4.039973	TCCTTCCTTCACGTGTTTGACTAT	59.960	41.667	16.51	0.00	0.00	2.12
708	715	2.732619	CGACCCCCTCCAAGGCTAC	61.733	68.421	0.00	0.00	32.73	3.58
881	932	3.394674	TTGAGCAACACGTTGATAGGA	57.605	42.857	13.97	0.00	42.93	2.94
917	968	9.289303	GCAAATAAAGTAGTACCATTCACATTG	57.711	33.333	0.00	0.00	0.00	2.82
1026	1122	1.702401	TCTTGGTTAGCACATGGTGGA	59.298	47.619	0.00	0.00	33.64	4.02
1146	1242	0.824595	TCTTTCGGTCGGTGGACTCA	60.825	55.000	0.00	0.00	42.97	3.41
1173	1269	5.186198	ACAAAATATCTCCTTCCTTCCGTG	58.814	41.667	0.00	0.00	0.00	4.94
1237	1333	0.252558	ACCGGTGGAAGGTCATAGGT	60.253	55.000	6.12	0.00	37.44	3.08
1293	1389	6.083630	CACATAAAACGGATGTTAGTGTTGG	58.916	40.000	0.00	0.00	37.31	3.77
1425	1521	6.350949	CCAAACCTCTTTGAAACCTTTCTTCA	60.351	38.462	0.00	0.00	39.43	3.02
1446	1542	0.038526	GACGACGCTCTTCCTCCAAA	60.039	55.000	0.00	0.00	0.00	3.28
1467	1564	1.153745	CCGCTCCGTCCTCTCTTTG	60.154	63.158	0.00	0.00	0.00	2.77
1478	1575	4.228097	CGCATTGCTTCCGCTCCG	62.228	66.667	7.12	0.00	36.97	4.63
1751	1880	4.823442	TCTTGACACATTGCAAACATCTCT	59.177	37.500	1.71	0.00	0.00	3.10
1772	1901	3.126831	CGCTGACAAACTGAAGTTCTCT	58.873	45.455	4.17	0.00	37.25	3.10
1854	1994	2.108952	AGAAAACAGGGCAATCCTCTGT	59.891	45.455	0.00	0.00	46.12	3.41
1866	2008	3.243535	GGGTTTGAAGCTCAGAAAACAGG	60.244	47.826	12.63	0.00	34.85	4.00
1879	2023	0.958876	GGTGGCGGTAGGGTTTGAAG	60.959	60.000	0.00	0.00	0.00	3.02
1900	2123	2.125106	GCAACCTACCGCCAGAGG	60.125	66.667	0.00	0.00	38.92	3.69
1902	2125	2.345991	GTGCAACCTACCGCCAGA	59.654	61.111	0.00	0.00	0.00	3.86
1918	2141	1.461559	GTACCTGGCAGTAGAGTCGT	58.538	55.000	14.43	4.67	0.00	4.34
1919	2142	0.739561	GGTACCTGGCAGTAGAGTCG	59.260	60.000	14.43	0.00	0.00	4.18
1923	2146	1.273609	ACCATGGTACCTGGCAGTAGA	60.274	52.381	18.10	0.00	37.27	2.59
1966	2196	1.136774	GCGCTCGTTTTTCCCATCC	59.863	57.895	0.00	0.00	0.00	3.51
1985	2254	2.288025	GGTTGACCCTACCGCCAGA	61.288	63.158	0.00	0.00	0.00	3.86
2002	2271	0.398098	ACGGTCTATGGTGGTAGGGG	60.398	60.000	0.00	0.00	0.00	4.79
2020	2289	2.046604	GGTCAACCCTACCGCCAC	60.047	66.667	0.00	0.00	0.00	5.01
2108	2495	0.828677	GGTAGGTTGCACGACCCTAT	59.171	55.000	3.86	0.00	40.73	2.57
2116	2503	1.741770	CTCTGGCGGTAGGTTGCAC	60.742	63.158	0.00	0.00	0.00	4.57
2137	2524	1.612676	GTTCAAACCCTACCACCACC	58.387	55.000	0.00	0.00	0.00	4.61
2138	2525	1.612676	GGTTCAAACCCTACCACCAC	58.387	55.000	0.10	0.00	43.43	4.16
2155	2542	2.424684	AACAGAGGAGAGGAAAGGGT	57.575	50.000	0.00	0.00	0.00	4.34
2160	2547	1.073923	GGGCAAAACAGAGGAGAGGAA	59.926	52.381	0.00	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.