AutoCloner

Multiple sequence alignment - TraesCS3D01G196300

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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	TraesCS3D01G196300	chr3D	100.000	2429	0	0	1	2429	194685861	194688289	0.000000e+00	4486.0
1	TraesCS3D01G196300	chr3D	85.921	831	110	7	1601	2427	133397103	133397930	0.000000e+00	880.0
2	TraesCS3D01G196300	chr1B	95.539	1614	58	3	1	1600	374333032	374334645	0.000000e+00	2569.0
3	TraesCS3D01G196300	chr1B	93.618	1614	88	4	1	1600	53736410	53738022	0.000000e+00	2396.0
4	TraesCS3D01G196300	chr6A	95.480	1615	57	7	1	1600	457605731	457604118	0.000000e+00	2564.0
5	TraesCS3D01G196300	chr6A	95.291	1614	62	3	1	1600	457588328	457586715	0.000000e+00	2547.0
6	TraesCS3D01G196300	chr3B	95.353	1614	61	3	1	1600	725371013	725372626	0.000000e+00	2553.0
7	TraesCS3D01G196300	chr5A	94.985	1615	65	8	1	1600	704587044	704585431	0.000000e+00	2519.0
8	TraesCS3D01G196300	chr2D	94.489	1615	73	4	1	1600	532132744	532134357	0.000000e+00	2475.0
9	TraesCS3D01G196300	chr2D	93.699	1587	86	6	34	1607	122038162	122036577	0.000000e+00	2364.0
10	TraesCS3D01G196300	chr2D	91.379	58	5	0	1544	1601	43254368	43254425	2.000000e-11	80.5
11	TraesCS3D01G196300	chrUn	95.238	1533	56	5	83	1600	62695869	62694339	0.000000e+00	2410.0
12	TraesCS3D01G196300	chr6B	95.306	1257	45	3	357	1600	437148581	437147326	0.000000e+00	1982.0
13	TraesCS3D01G196300	chr4D	88.448	831	91	5	1601	2429	239154962	239155789	0.000000e+00	998.0
14	TraesCS3D01G196300	chr4D	88.115	833	93	6	1601	2429	263063811	263064641	0.000000e+00	985.0
15	TraesCS3D01G196300	chr4D	87.966	831	94	6	1601	2429	168804418	168803592	0.000000e+00	976.0
16	TraesCS3D01G196300	chr4D	87.650	834	92	9	1601	2429	210689803	210690630	0.000000e+00	959.0
17	TraesCS3D01G196300	chr6D	87.426	843	85	10	1601	2429	325046894	325046059	0.000000e+00	950.0
18	TraesCS3D01G196300	chr6D	85.900	844	103	9	1601	2429	224854841	224853999	0.000000e+00	885.0
19	TraesCS3D01G196300	chr1D	86.691	834	102	8	1601	2429	190958852	190959681	0.000000e+00	917.0
20	TraesCS3D01G196300	chr5D	86.240	843	94	14	1601	2429	196516875	196517709	0.000000e+00	894.0
21	TraesCS3D01G196300	chr7A	91.065	291	13	5	1322	1600	680600125	680600414	4.900000e-102	381.0
22	TraesCS3D01G196300	chr1A	96.552	58	2	0	1543	1600	45850212	45850155	1.990000e-16	97.1

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	TraesCS3D01G196300	chr3D	194685861	194688289	2428	False	4486	4486	100.000	1	2429	1	chr3D.!!$F2	2428
1	TraesCS3D01G196300	chr3D	133397103	133397930	827	False	880	880	85.921	1601	2427	1	chr3D.!!$F1	826
2	TraesCS3D01G196300	chr1B	374333032	374334645	1613	False	2569	2569	95.539	1	1600	1	chr1B.!!$F2	1599
3	TraesCS3D01G196300	chr1B	53736410	53738022	1612	False	2396	2396	93.618	1	1600	1	chr1B.!!$F1	1599
4	TraesCS3D01G196300	chr6A	457604118	457605731	1613	True	2564	2564	95.480	1	1600	1	chr6A.!!$R2	1599
5	TraesCS3D01G196300	chr6A	457586715	457588328	1613	True	2547	2547	95.291	1	1600	1	chr6A.!!$R1	1599
6	TraesCS3D01G196300	chr3B	725371013	725372626	1613	False	2553	2553	95.353	1	1600	1	chr3B.!!$F1	1599
7	TraesCS3D01G196300	chr5A	704585431	704587044	1613	True	2519	2519	94.985	1	1600	1	chr5A.!!$R1	1599
8	TraesCS3D01G196300	chr2D	532132744	532134357	1613	False	2475	2475	94.489	1	1600	1	chr2D.!!$F2	1599
9	TraesCS3D01G196300	chr2D	122036577	122038162	1585	True	2364	2364	93.699	34	1607	1	chr2D.!!$R1	1573
10	TraesCS3D01G196300	chrUn	62694339	62695869	1530	True	2410	2410	95.238	83	1600	1	chrUn.!!$R1	1517
11	TraesCS3D01G196300	chr6B	437147326	437148581	1255	True	1982	1982	95.306	357	1600	1	chr6B.!!$R1	1243
12	TraesCS3D01G196300	chr4D	239154962	239155789	827	False	998	998	88.448	1601	2429	1	chr4D.!!$F2	828
13	TraesCS3D01G196300	chr4D	263063811	263064641	830	False	985	985	88.115	1601	2429	1	chr4D.!!$F3	828
14	TraesCS3D01G196300	chr4D	168803592	168804418	826	True	976	976	87.966	1601	2429	1	chr4D.!!$R1	828
15	TraesCS3D01G196300	chr4D	210689803	210690630	827	False	959	959	87.650	1601	2429	1	chr4D.!!$F1	828
16	TraesCS3D01G196300	chr6D	325046059	325046894	835	True	950	950	87.426	1601	2429	1	chr6D.!!$R2	828
17	TraesCS3D01G196300	chr6D	224853999	224854841	842	True	885	885	85.900	1601	2429	1	chr6D.!!$R1	828
18	TraesCS3D01G196300	chr1D	190958852	190959681	829	False	917	917	86.691	1601	2429	1	chr1D.!!$F1	828
19	TraesCS3D01G196300	chr5D	196516875	196517709	834	False	894	894	86.240	1601	2429	1	chr5D.!!$F1	828

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
796	804	1.118965	TCCAGAGTTCCGCACCAAGA	61.119	55.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1772	1807	0.111253	CCTCCCCTCTTTGTGTTGCT	59.889	55.0	0.0	0.0	0.0	3.91	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
30	31	8.364142	GGTATGTAGATACATCTTCTGCTTCTT	58.636	37.037	11.75	0.00	45.11	2.52
136	137	7.993183	GGAGTTGAATAATCTTACCCTTGATGA	59.007	37.037	0.00	0.00	0.00	2.92
202	204	7.519032	TGAAAGGAAACAATAAAGGGTACAG	57.481	36.000	0.00	0.00	0.00	2.74
285	288	1.970640	TCTGGCACTATGCGATATGGT	59.029	47.619	0.00	0.00	46.21	3.55
428	433	4.462834	AGTCATTGTCATCTACTCGTTGGA	59.537	41.667	0.00	0.00	0.00	3.53
437	442	4.966965	TCTACTCGTTGGAAGAGTCATC	57.033	45.455	1.87	0.00	44.87	2.92
455	460	4.629200	GTCATCTTGAGAGTGTTAAGGCTG	59.371	45.833	0.00	0.00	0.00	4.85
473	478	2.163412	GCTGTACGGATTCAAATGCCAA	59.837	45.455	5.68	0.00	0.00	4.52
486	491	5.090139	TCAAATGCCAAAAATAAGGGAGGA	58.910	37.500	0.00	0.00	0.00	3.71
488	493	5.619132	AATGCCAAAAATAAGGGAGGATG	57.381	39.130	0.00	0.00	0.00	3.51
551	556	2.829720	AGTGAAGCACAATCATTGGCAT	59.170	40.909	11.87	1.93	36.74	4.40
561	567	6.019318	GCACAATCATTGGCATAAATGAACTC	60.019	38.462	1.58	0.13	46.66	3.01
711	717	7.135467	GTCTGCTTTCCTTTTTCAAGAAGTAG	58.865	38.462	0.00	0.00	32.36	2.57
732	739	5.764487	AGAGAGAAACTGGCTTTTCAAAG	57.236	39.130	12.65	0.00	37.86	2.77
796	804	1.118965	TCCAGAGTTCCGCACCAAGA	61.119	55.000	0.00	0.00	0.00	3.02
922	930	5.460419	GTGGTCGATCAAGCTATAGTTTCAG	59.540	44.000	0.00	0.00	0.00	3.02
950	958	5.440610	CAGGAGGTTTGAGCAATATTAGGT	58.559	41.667	0.00	0.00	0.00	3.08
1022	1030	5.983333	ATGGATGATAAGAGTTTCCTGGT	57.017	39.130	0.00	0.00	0.00	4.00
1084	1092	4.910195	ACACAAAGACATTGATGGAGCTA	58.090	39.130	0.00	0.00	41.85	3.32
1220	1228	7.281999	TGCATACAGGATTTCGTTAATCATTCA	59.718	33.333	12.64	0.56	43.72	2.57
1244	1252	0.814457	ACTGTTGCAACTGCGGAAAA	59.186	45.000	29.69	8.80	45.83	2.29
1402	1410	7.655490	AGATTTCATTTCAAGGAACACAAGAG	58.345	34.615	0.00	0.00	0.00	2.85
1570	1592	2.547855	GCCCCATTTTTCTTTTCGCACT	60.548	45.455	0.00	0.00	0.00	4.40
1623	1645	0.742505	CAGATACCCGTACTTCGCCA	59.257	55.000	0.00	0.00	38.35	5.69
1643	1666	2.240667	CAGAAGGATGGGACCACTCAAT	59.759	50.000	0.00	0.00	0.00	2.57
1674	1697	2.431057	ACAAAGACAACGTCCTCACTCT	59.569	45.455	0.00	0.00	32.18	3.24
1694	1717	0.952984	GCTTCTTGTTCAGCTCCGCT	60.953	55.000	0.00	0.00	40.77	5.52
1772	1807	0.968405	GTTTCTTCCCCATTGCTGCA	59.032	50.000	0.00	0.00	0.00	4.41
1822	1862	2.261671	GCGACGGAAGGAGAAGCA	59.738	61.111	0.00	0.00	0.00	3.91
1842	1882	3.070018	CAAGATGAGGAACTGTCGCTTT	58.930	45.455	0.00	0.00	41.55	3.51
1851	1891	1.283793	CTGTCGCTTTGCTTGTGGG	59.716	57.895	0.00	0.00	0.00	4.61
1872	1915	1.607612	GGAAAAGATGGGAGCGGGA	59.392	57.895	0.00	0.00	0.00	5.14
1961	2004	1.654105	CGCGACGCTTCAGAAAGTTAT	59.346	47.619	19.02	0.00	34.79	1.89
2014	2057	0.717224	CACAACGCGCGGTAATTACT	59.283	50.000	35.22	7.19	0.00	2.24
2035	2078	3.081061	TCGAAAGTGGACATTGGATTGG	58.919	45.455	0.00	0.00	0.00	3.16
2305	2351	3.071312	AGGAGCAAGATATCAGCAAGAGG	59.929	47.826	18.60	0.00	0.00	3.69
2379	2425	2.299326	AGCAAGCAACCAAGATTCCT	57.701	45.000	0.00	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	7.530010	CCTAAGAAAGATTCTTCGATGCAAAA	58.470	34.615	8.51	0.00	46.62	2.44
127	128	3.054875	TCTCACATTGTCCTCATCAAGGG	60.055	47.826	0.00	0.00	46.23	3.95
136	137	1.905215	CCTGTCCTCTCACATTGTCCT	59.095	52.381	0.00	0.00	0.00	3.85
285	288	2.248280	TGCTTTACGGCAAGACTTCA	57.752	45.000	0.26	0.00	39.43	3.02
306	309	7.041030	TGCGTTGTATAATTCCAAAGAAGTTCA	60.041	33.333	5.50	0.00	34.86	3.18
307	310	7.302524	TGCGTTGTATAATTCCAAAGAAGTTC	58.697	34.615	0.00	0.00	34.86	3.01
428	433	6.696411	CCTTAACACTCTCAAGATGACTCTT	58.304	40.000	0.00	0.00	42.59	2.85
437	442	3.921021	CGTACAGCCTTAACACTCTCAAG	59.079	47.826	0.00	0.00	0.00	3.02
455	460	7.010091	CCTTATTTTTGGCATTTGAATCCGTAC	59.990	37.037	0.00	0.00	0.00	3.67
473	478	8.047310	CACTTGTAGTACATCCTCCCTTATTTT	58.953	37.037	3.28	0.00	0.00	1.82
486	491	4.997395	CAGTTTCAGCCACTTGTAGTACAT	59.003	41.667	3.28	0.00	0.00	2.29
488	493	4.628074	TCAGTTTCAGCCACTTGTAGTAC	58.372	43.478	0.00	0.00	0.00	2.73
551	556	6.642707	ATTCAAAACCACCGAGTTCATTTA	57.357	33.333	0.00	0.00	0.00	1.40
561	567	6.037098	TGACACTAAAAATTCAAAACCACCG	58.963	36.000	0.00	0.00	0.00	4.94
642	648	8.352201	GCAATATCAATAAGCATGTCCTTTGTA	58.648	33.333	0.00	0.00	0.00	2.41
643	649	7.147863	TGCAATATCAATAAGCATGTCCTTTGT	60.148	33.333	0.00	0.00	0.00	2.83
711	717	4.794329	GCCTTTGAAAAGCCAGTTTCTCTC	60.794	45.833	6.66	0.00	38.17	3.20
854	862	5.426689	AAATGACTCCTCTGCAGATTGTA	57.573	39.130	18.63	2.47	0.00	2.41
994	1002	8.591940	CAGGAAACTCTTATCATCCATAGATCA	58.408	37.037	0.00	0.00	40.21	2.92
1022	1030	5.335897	GCATCCTCAAGATTAACACAAGCAA	60.336	40.000	0.00	0.00	30.59	3.91
1131	1139	1.202927	AGAATATCAACGGGGCCCATG	60.203	52.381	26.86	20.68	0.00	3.66
1208	1216	7.020602	TGCAACAGTTACATGAATGATTAACG	58.979	34.615	0.00	0.00	0.00	3.18
1214	1222	5.761003	CAGTTGCAACAGTTACATGAATGA	58.239	37.500	30.11	0.00	0.00	2.57
1220	1228	1.266718	CCGCAGTTGCAACAGTTACAT	59.733	47.619	30.11	5.87	42.21	2.29
1244	1252	6.168270	ACAACTTGAGTTTAGAGAAGCTCT	57.832	37.500	2.22	2.22	41.96	4.09
1402	1410	7.554118	TCATTCTCTATTGAAAAGTGTCATCCC	59.446	37.037	0.00	0.00	0.00	3.85
1513	1522	5.173774	ACGCAAGCATAATCACCTAATTG	57.826	39.130	0.00	0.00	45.62	2.32
1570	1592	3.738481	CAGGAATTCGGGGGCCCA	61.738	66.667	26.86	3.62	35.37	5.36
1623	1645	2.044793	TTGAGTGGTCCCATCCTTCT	57.955	50.000	0.00	0.00	0.00	2.85
1643	1666	2.096174	CGTTGTCTTTGTTCCGTCCAAA	59.904	45.455	0.00	0.00	0.00	3.28
1674	1697	2.918571	CGGAGCTGAACAAGAAGCA	58.081	52.632	0.00	0.00	42.06	3.91
1694	1717	1.613255	GCCGAGGGGAACAAAAGATCA	60.613	52.381	0.00	0.00	34.06	2.92
1729	1752	1.335697	GAAGAAGTCGACGACCGTGC	61.336	60.000	23.76	10.98	39.75	5.34
1772	1807	0.111253	CCTCCCCTCTTTGTGTTGCT	59.889	55.000	0.00	0.00	0.00	3.91
1781	1816	2.237392	CTCAACGAATTCCTCCCCTCTT	59.763	50.000	0.00	0.00	0.00	2.85
1822	1862	3.070018	CAAAGCGACAGTTCCTCATCTT	58.930	45.455	0.00	0.00	0.00	2.40
1851	1891	1.453928	CGCTCCCATCTTTTCCCCC	60.454	63.158	0.00	0.00	0.00	5.40
1854	1894	0.748367	GTCCCGCTCCCATCTTTTCC	60.748	60.000	0.00	0.00	0.00	3.13
1855	1895	1.090052	CGTCCCGCTCCCATCTTTTC	61.090	60.000	0.00	0.00	0.00	2.29
1856	1896	1.078426	CGTCCCGCTCCCATCTTTT	60.078	57.895	0.00	0.00	0.00	2.27
1857	1897	1.961180	CTCGTCCCGCTCCCATCTTT	61.961	60.000	0.00	0.00	0.00	2.52
1872	1915	3.624861	GGCATGATTCATTTGTCTCTCGT	59.375	43.478	0.00	0.00	0.00	4.18
1882	1925	0.179048	TCGGAGCGGCATGATTCATT	60.179	50.000	1.45	0.00	0.00	2.57
1961	2004	3.468770	TGTTGCAGCTAAGGTAAAACGA	58.531	40.909	1.17	0.00	0.00	3.85
1974	2017	2.280797	TCGTGGGACTGTTGCAGC	60.281	61.111	0.00	0.00	34.37	5.25
2014	2057	3.081061	CCAATCCAATGTCCACTTTCGA	58.919	45.455	0.00	0.00	0.00	3.71
2035	2078	1.135689	CGGTTTGCCACAATGACTAGC	60.136	52.381	0.00	0.00	34.09	3.42
2154	2197	1.697432	TCTGCCCCTGTATATTTCCCG	59.303	52.381	0.00	0.00	0.00	5.14
2198	2242	0.396974	TGGCTTGTCCTTGGCTTGTT	60.397	50.000	0.00	0.00	35.26	2.83
2357	2403	2.353109	GGAATCTTGGTTGCTTGCTTCC	60.353	50.000	0.00	0.00	0.00	3.46
2398	2445	2.128507	GTGGTTCAACCCCCGCAAA	61.129	57.895	3.42	0.00	37.50	3.68
2400	2447	4.589675	GGTGGTTCAACCCCCGCA	62.590	66.667	3.42	0.00	37.50	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.