AutoCloner

Multiple sequence alignment - TraesCS3B01G312800

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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	TraesCS3B01G312800	chr3B	100.000	2627	0	0	1	2627	502647964	502645338	0.000000e+00	4852.0
1	TraesCS3B01G312800	chr3B	95.222	293	14	0	134	426	201510452	201510744	5.120000e-127	464.0
2	TraesCS3B01G312800	chr3B	89.041	73	5	2	1807	1879	764449007	764449076	1.300000e-13	87.9
3	TraesCS3B01G312800	chr3B	94.000	50	1	2	1	48	153536365	153536316	1.010000e-09	75.0
4	TraesCS3B01G312800	chr3D	91.737	2009	89	25	1	1945	386441619	386439624	0.000000e+00	2719.0
5	TraesCS3B01G312800	chr3D	89.739	575	35	9	1957	2530	386439640	386439089	0.000000e+00	713.0
6	TraesCS3B01G312800	chr3D	95.563	293	13	0	134	426	21901413	21901705	1.100000e-128	470.0
7	TraesCS3B01G312800	chr3D	95.918	49	1	1	1	48	102647113	102647065	7.800000e-11	78.7
8	TraesCS3B01G312800	chr3D	100.000	31	0	0	1760	1790	429086060	429086090	1.020000e-04	58.4
9	TraesCS3B01G312800	chr3A	86.320	1155	76	36	1389	2509	508169192	508168086	0.000000e+00	1182.0
10	TraesCS3B01G312800	chr3A	89.859	779	55	14	672	1433	508174609	508173838	0.000000e+00	979.0
11	TraesCS3B01G312800	chr3A	86.919	581	63	8	98	675	508175508	508174938	7.930000e-180	640.0
12	TraesCS3B01G312800	chr3A	86.145	498	35	13	1474	1945	508173845	508173356	8.390000e-140	507.0
13	TraesCS3B01G312800	chr3A	90.278	144	10	2	2035	2174	508171671	508171528	4.460000e-43	185.0
14	TraesCS3B01G312800	chr3A	91.406	128	9	2	2500	2627	508167902	508167777	9.660000e-40	174.0
15	TraesCS3B01G312800	chr3A	81.000	100	9	2	1806	1898	739325109	739325013	1.300000e-08	71.3
16	TraesCS3B01G312800	chr3A	97.059	34	1	0	1397	1430	508169214	508169181	1.020000e-04	58.4
17	TraesCS3B01G312800	chr5D	95.563	293	13	0	134	426	449151830	449151538	1.100000e-128	470.0
18	TraesCS3B01G312800	chr5D	95.222	293	14	0	134	426	240135029	240135321	5.120000e-127	464.0
19	TraesCS3B01G312800	chr5D	82.692	104	5	9	1806	1900	163638804	163638705	2.170000e-11	80.5
20	TraesCS3B01G312800	chr5D	95.652	46	2	0	1	46	11310732	11310687	1.010000e-09	75.0
21	TraesCS3B01G312800	chr1D	95.563	293	13	0	134	426	254495334	254495626	1.100000e-128	470.0
22	TraesCS3B01G312800	chr1D	95.222	293	14	0	134	426	483917279	483916987	5.120000e-127	464.0
23	TraesCS3B01G312800	chr1D	96.875	32	1	0	1759	1790	401925654	401925685	1.000000e-03	54.7
24	TraesCS3B01G312800	chr1D	96.875	32	1	0	1759	1790	402010870	402010901	1.000000e-03	54.7
25	TraesCS3B01G312800	chr2B	95.222	293	14	0	134	426	474898274	474897982	5.120000e-127	464.0
26	TraesCS3B01G312800	chr2B	82.292	96	10	6	1806	1898	140239250	140239341	2.800000e-10	76.8
27	TraesCS3B01G312800	chr4A	86.508	378	41	3	423	800	91338439	91338072	8.750000e-110	407.0
28	TraesCS3B01G312800	chr4A	86.250	80	9	2	1806	1883	622126056	622126135	4.660000e-13	86.1
29	TraesCS3B01G312800	chr1B	85.942	377	46	4	425	800	299437486	299437856	1.890000e-106	396.0
30	TraesCS3B01G312800	chr1B	86.905	84	6	4	1797	1878	643174939	643174859	3.600000e-14	89.8
31	TraesCS3B01G312800	chr1B	88.000	75	6	2	1806	1880	16764385	16764456	4.660000e-13	86.1
32	TraesCS3B01G312800	chr7A	77.820	266	50	6	1154	1416	424534831	424535090	3.500000e-34	156.0
33	TraesCS3B01G312800	chr7B	77.528	267	49	8	1154	1416	372008285	372008544	1.630000e-32	150.0
34	TraesCS3B01G312800	chr7B	76.233	223	47	6	580	800	412092324	412092542	2.140000e-21	113.0
35	TraesCS3B01G312800	chr7D	75.940	266	54	7	1154	1416	376941261	376941519	7.630000e-26	128.0
36	TraesCS3B01G312800	chr7D	87.952	83	10	0	9	91	178277263	178277345	5.980000e-17	99.0
37	TraesCS3B01G312800	chr5B	84.127	126	17	2	1154	1279	6869542	6869664	4.590000e-23	119.0
38	TraesCS3B01G312800	chr5B	87.356	87	6	4	1813	1898	522919975	522919893	7.740000e-16	95.3
39	TraesCS3B01G312800	chr5B	86.486	74	10	0	1806	1879	566672206	566672133	6.030000e-12	82.4
40	TraesCS3B01G312800	chrUn	89.041	73	5	2	1807	1879	232156214	232156283	1.300000e-13	87.9
41	TraesCS3B01G312800	chrUn	89.041	73	5	2	1807	1879	237975253	237975322	1.300000e-13	87.9
42	TraesCS3B01G312800	chrUn	96.875	32	1	0	1759	1790	105627942	105627973	1.000000e-03	54.7
43	TraesCS3B01G312800	chr5A	84.211	95	6	4	1790	1878	26532058	26532149	1.680000e-12	84.2
44	TraesCS3B01G312800	chr4B	82.178	101	5	4	1812	1902	673102031	673101934	1.010000e-09	75.0
45	TraesCS3B01G312800	chr6B	92.683	41	3	0	1750	1790	619862920	619862880	2.820000e-05	60.2
46	TraesCS3B01G312800	chr6B	96.970	33	0	1	1758	1790	620978749	620978780	1.000000e-03	54.7
47	TraesCS3B01G312800	chr6D	100.000	30	0	0	1761	1790	266954692	266954721	3.650000e-04	56.5

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	TraesCS3B01G312800	chr3B	502645338	502647964	2626	True	4852.0	4852	100.000000	1	2627	1	chr3B.!!$R2	2626
1	TraesCS3B01G312800	chr3D	386439089	386441619	2530	True	1716.0	2719	90.738000	1	2530	2	chr3D.!!$R2	2529
2	TraesCS3B01G312800	chr3A	508167777	508175508	7731	True	532.2	1182	89.712286	98	2627	7	chr3A.!!$R2	2529

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
453	455	0.03601	ATGGAGTCAAGGAGGTTGCG	60.036	55.0	0.0	0.0	35.94	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1717	6781	0.540365	ACACCAGGGCAAACTCCATG	60.54	55.0	0.0	0.0	37.63	3.66	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
52	54	2.032071	GGGTGTGCGCCTTGTACT	59.968	61.111	4.18	0.00	33.83	2.73
57	59	1.459592	GTGTGCGCCTTGTACTGTTAG	59.540	52.381	4.18	0.00	33.83	2.34
70	72	1.753073	ACTGTTAGCGCTATAACGGGT	59.247	47.619	27.30	19.78	43.43	5.28
126	128	1.535028	CAGCCGTATGCAGAAACACAA	59.465	47.619	0.00	0.00	44.83	3.33
145	147	0.250727	AACGGTCAGTGGGTTCCATG	60.251	55.000	0.00	0.00	35.28	3.66
168	170	7.292713	TGGTTTCTATGGTTCCCTTTTAAAC	57.707	36.000	0.00	0.00	0.00	2.01
221	223	7.153985	CCTTTCTTTCATCAAAAGGTATTGCA	58.846	34.615	5.20	0.00	43.88	4.08
269	271	7.897575	GGCTCTACCAATTCATTATAGAGTG	57.102	40.000	15.23	0.00	37.24	3.51
355	357	2.176889	GTAGCTGACCCTGTTAGTCCA	58.823	52.381	0.00	0.00	33.09	4.02
383	385	8.052748	TCTTTTAAGATAAAGGAGCATAAGCCA	58.947	33.333	0.00	0.00	37.31	4.75
453	455	0.036010	ATGGAGTCAAGGAGGTTGCG	60.036	55.000	0.00	0.00	35.94	4.85
454	456	1.118965	TGGAGTCAAGGAGGTTGCGA	61.119	55.000	0.00	0.00	35.94	5.10
543	545	0.319555	TTGCCTCCGACTCGAAACAG	60.320	55.000	0.00	0.00	0.00	3.16
569	571	2.859165	AGCGACATTGAGAAGGGAAA	57.141	45.000	0.00	0.00	0.00	3.13
575	577	4.515191	CGACATTGAGAAGGGAAAGAACAA	59.485	41.667	0.00	0.00	0.00	2.83
609	611	4.701651	CACATTATCAAGGAGGTCAAGCAA	59.298	41.667	0.00	0.00	0.00	3.91
710	1044	1.492176	GAATTCTCTGGATGAGGGGCA	59.508	52.381	0.00	0.00	42.86	5.36
726	1064	2.612721	GGGGCATCATGTTTGGTTTCAC	60.613	50.000	0.00	0.00	0.00	3.18
731	1069	0.316841	CATGTTTGGTTTCACCCCCG	59.683	55.000	0.00	0.00	37.50	5.73
792	1130	6.544650	TCAACAAAGTTTAGCCATTACCCTA	58.455	36.000	0.00	0.00	0.00	3.53
793	1131	6.657541	TCAACAAAGTTTAGCCATTACCCTAG	59.342	38.462	0.00	0.00	0.00	3.02
952	1326	2.510768	ACGGCGGATTTCTGATCTAC	57.489	50.000	13.24	0.00	0.00	2.59
1637	6701	3.385755	GGCGACTATTAGGTTAAGGGTGA	59.614	47.826	0.00	0.00	0.00	4.02
1650	6714	0.700564	AGGGTGACAATGCCATCTGT	59.299	50.000	0.00	0.00	0.00	3.41
1704	6768	5.599732	AGTGTTACATTTTGCTTTGCATCA	58.400	33.333	0.00	0.00	38.76	3.07
1717	6781	0.798159	TGCATCACAAGCATGTCGAC	59.202	50.000	9.11	9.11	37.82	4.20
1809	6902	9.413048	GTTCTTTATGGACTACATACTGATAGC	57.587	37.037	0.00	0.00	41.61	2.97
1824	6917	8.877779	CATACTGATAGCCATATTTTAGAGTGC	58.122	37.037	0.00	0.00	0.00	4.40
1826	6919	7.282585	ACTGATAGCCATATTTTAGAGTGCAA	58.717	34.615	0.00	0.00	0.00	4.08
1849	6942	8.624701	CAAATTCACTCATTTTGCTAGTATGG	57.375	34.615	0.00	0.00	0.00	2.74
1856	6949	7.712639	CACTCATTTTGCTAGTATGGATGTAGT	59.287	37.037	0.00	0.00	0.00	2.73
1912	7013	2.668625	GGAGTACAAGGGGTAGAGAGG	58.331	57.143	0.00	0.00	31.13	3.69
1918	7019	3.768878	ACAAGGGGTAGAGAGGATATCG	58.231	50.000	0.00	0.00	0.00	2.92
1940	7041	5.048364	TCGGGTGAAACGAATTGAAAATCAT	60.048	36.000	0.00	0.00	38.12	2.45
1941	7042	5.060816	CGGGTGAAACGAATTGAAAATCATG	59.939	40.000	0.00	0.00	38.12	3.07
1942	7043	5.925969	GGGTGAAACGAATTGAAAATCATGT	59.074	36.000	0.00	0.00	38.12	3.21
1943	7044	6.423604	GGGTGAAACGAATTGAAAATCATGTT	59.576	34.615	0.00	0.00	38.12	2.71
1944	7045	7.042119	GGGTGAAACGAATTGAAAATCATGTTT	60.042	33.333	0.00	0.00	38.12	2.83
1945	7046	8.973378	GGTGAAACGAATTGAAAATCATGTTTA	58.027	29.630	0.00	0.00	38.12	2.01
2029	7132	8.635765	AGTGTAACATAATCCACAAGTTTCAT	57.364	30.769	0.00	0.00	41.43	2.57
2149	7254	5.146010	TGGTTGCCAAATTTATGTCCTTC	57.854	39.130	0.00	0.00	0.00	3.46
2169	7274	6.730507	TCCTTCATCATAGCTCCCATAATACA	59.269	38.462	0.00	0.00	0.00	2.29
2427	7548	1.446792	CGAGTCCATCAAGCGCACT	60.447	57.895	11.47	1.04	0.00	4.40
2441	7563	1.685820	GCACTCAAGGGTAAGGCCT	59.314	57.895	0.00	0.00	37.43	5.19
2443	7565	0.035056	CACTCAAGGGTAAGGCCTGG	60.035	60.000	5.69	0.00	37.43	4.45
2446	7568	0.770557	TCAAGGGTAAGGCCTGGTGT	60.771	55.000	5.69	0.00	37.43	4.16
2519	7834	1.916273	AGCCACCACCGTCACCATA	60.916	57.895	0.00	0.00	0.00	2.74
2532	7847	3.512680	GTCACCATAAGACTCGACCAAG	58.487	50.000	0.00	0.00	33.29	3.61
2548	7863	0.820891	CAAGAAGTGCAGCCACCACT	60.821	55.000	0.00	0.00	44.92	4.00
2617	7932	4.864334	CACCGCCCTGGCATCCTC	62.864	72.222	9.17	0.00	43.94	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.759205	GGCCCAGCCCATTTCCGT	62.759	66.667	0.00	0.00	44.06	4.69
46	48	4.353737	CCGTTATAGCGCTAACAGTACAA	58.646	43.478	22.98	0.00	32.27	2.41
52	54	1.803625	GCACCCGTTATAGCGCTAACA	60.804	52.381	22.98	9.72	32.27	2.41
57	59	1.137513	CTAAGCACCCGTTATAGCGC	58.862	55.000	0.00	0.00	0.00	5.92
70	72	0.459585	CCTAAACGGCGCTCTAAGCA	60.460	55.000	6.90	0.00	42.58	3.91
126	128	0.250727	CATGGAACCCACTGACCGTT	60.251	55.000	0.00	0.00	35.80	4.44
168	170	1.760613	TGTATAAAGAGGGCCTCACCG	59.239	52.381	33.86	0.00	40.62	4.94
343	345	9.681062	TTATCTTAAAAGAATGGACTAACAGGG	57.319	33.333	0.00	0.00	38.77	4.45
430	432	1.280457	ACCTCCTTGACTCCATGGAC	58.720	55.000	11.44	2.34	40.46	4.02
453	455	0.038709	AGGCGATCGCTTCTAGCATC	60.039	55.000	36.25	18.19	42.58	3.91
454	456	0.319383	CAGGCGATCGCTTCTAGCAT	60.319	55.000	36.25	11.91	42.58	3.79
493	495	6.625532	ATTTTGAAGTAGCAAATCCCCAAT	57.374	33.333	0.00	0.00	37.57	3.16
523	525	0.320374	TGTTTCGAGTCGGAGGCAAT	59.680	50.000	13.54	0.00	0.00	3.56
543	545	3.557595	CCTTCTCAATGTCGCTTATCACC	59.442	47.826	0.00	0.00	0.00	4.02
569	571	8.713971	TGATAATGTGTCCATAGGTATTGTTCT	58.286	33.333	0.00	0.00	0.00	3.01
575	577	7.038017	CCTCCTTGATAATGTGTCCATAGGTAT	60.038	40.741	0.00	0.00	0.00	2.73
609	611	5.142061	TGCAATTCAAGTTTGATGCTCAT	57.858	34.783	16.80	0.00	41.43	2.90
624	626	6.017325	GCCTTCGAAAATGAATTTGCAATTC	58.983	36.000	0.00	7.27	0.00	2.17
772	1110	7.696992	TTTCTAGGGTAATGGCTAAACTTTG	57.303	36.000	0.00	0.00	0.00	2.77
864	1211	6.971726	TCTTTAGGGGAGTTTTTCTTTTCC	57.028	37.500	0.00	0.00	0.00	3.13
952	1326	6.638873	CGAACTGCTGTTTGGTATAGATAGAG	59.361	42.308	14.34	0.00	36.39	2.43
1637	6701	6.655078	AGAAAACTAAACAGATGGCATTGT	57.345	33.333	0.00	5.48	0.00	2.71
1671	6735	8.630054	AGCAAAATGTAACACTATTCACCTAA	57.370	30.769	0.00	0.00	0.00	2.69
1672	6736	8.630054	AAGCAAAATGTAACACTATTCACCTA	57.370	30.769	0.00	0.00	0.00	3.08
1673	6737	7.524717	AAGCAAAATGTAACACTATTCACCT	57.475	32.000	0.00	0.00	0.00	4.00
1689	6753	3.468770	TGCTTGTGATGCAAAGCAAAAT	58.531	36.364	18.70	0.00	43.62	1.82
1717	6781	0.540365	ACACCAGGGCAAACTCCATG	60.540	55.000	0.00	0.00	37.63	3.66
1791	6872	8.435931	AAATATGGCTATCAGTATGTAGTCCA	57.564	34.615	0.00	0.00	37.40	4.02
1803	6896	8.696043	ATTTGCACTCTAAAATATGGCTATCA	57.304	30.769	0.00	0.00	0.00	2.15
1824	6917	8.461222	TCCATACTAGCAAAATGAGTGAATTTG	58.539	33.333	0.00	0.00	37.17	2.32
1826	6919	8.627403	CATCCATACTAGCAAAATGAGTGAATT	58.373	33.333	0.00	0.00	0.00	2.17
1877	6970	4.098894	TGTACTCCCTCCGTTCCTAAATT	58.901	43.478	0.00	0.00	0.00	1.82
1912	7013	5.728351	TTCAATTCGTTTCACCCGATATC	57.272	39.130	0.00	0.00	33.81	1.63
1918	7019	5.925969	ACATGATTTTCAATTCGTTTCACCC	59.074	36.000	0.00	0.00	0.00	4.61
2016	7119	7.495901	TCTTGCATTTTTATGAAACTTGTGGA	58.504	30.769	0.00	0.00	0.00	4.02
2081	7184	8.579006	TGAGTTATTGAAAGTGATGCTGATTTT	58.421	29.630	0.00	0.00	0.00	1.82
2149	7254	5.104610	AGGCTGTATTATGGGAGCTATGATG	60.105	44.000	0.00	0.00	0.00	3.07
2169	7274	2.720915	GCCTGAAAAATGAGAGAGGCT	58.279	47.619	0.00	0.00	42.33	4.58
2267	7375	7.646922	CGTGTTACTTTCTATATAAAGCGAGGT	59.353	37.037	9.81	0.00	39.59	3.85
2339	7459	3.307242	GCGGTGCAATTTTTGTTGTACAA	59.693	39.130	3.59	3.59	43.63	2.41
2340	7460	2.860735	GCGGTGCAATTTTTGTTGTACA	59.139	40.909	9.42	0.00	43.63	2.90
2372	7492	3.752665	TGCGTTGTTAAGGGGATTTGTA	58.247	40.909	0.00	0.00	0.00	2.41
2427	7548	0.770557	ACACCAGGCCTTACCCTTGA	60.771	55.000	0.00	0.00	40.58	3.02
2441	7563	0.837691	AGTGATCCTGGCTCACACCA	60.838	55.000	27.06	0.00	44.37	4.17
2443	7565	2.622436	GTAAGTGATCCTGGCTCACAC	58.378	52.381	27.06	16.38	44.37	3.82
2446	7568	0.824109	CGGTAAGTGATCCTGGCTCA	59.176	55.000	0.00	0.00	0.00	4.26
2519	7834	1.412710	TGCACTTCTTGGTCGAGTCTT	59.587	47.619	0.00	0.00	0.00	3.01
2532	7847	3.348236	CAGTGGTGGCTGCACTTC	58.652	61.111	0.50	0.00	0.00	3.01
2548	7863	2.265739	GCGAGTCTCATGGTGGCA	59.734	61.111	0.00	0.00	0.00	4.92
2603	7918	4.899239	GTCGAGGATGCCAGGGCG	62.899	72.222	5.74	0.00	45.51	6.13
2604	7919	4.554036	GGTCGAGGATGCCAGGGC	62.554	72.222	2.62	2.62	42.35	5.19
2605	7920	2.196997	TTTGGTCGAGGATGCCAGGG	62.197	60.000	0.00	0.00	33.41	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.