AutoCloner

Multiple sequence alignment - TraesCS3B01G333500

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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	TraesCS3B01G333500	chr3B	100.000	2399	0	0	1	2399	540193285	540190887	0.000000e+00	4431
1	TraesCS3B01G333500	chr3B	90.769	130	10	2	2020	2148	201557413	201557285	3.170000e-39	172
2	TraesCS3B01G333500	chr3A	91.642	1675	90	12	768	2399	536774262	536775929	0.000000e+00	2272
3	TraesCS3B01G333500	chr3A	93.023	559	36	2	1	557	76341025	76340468	0.000000e+00	813
4	TraesCS3B01G333500	chr3D	89.791	1146	67	25	562	1690	414164797	414163685	0.000000e+00	1423
5	TraesCS3B01G333500	chr3D	92.006	688	42	5	1718	2399	414163537	414162857	0.000000e+00	953
6	TraesCS3B01G333500	chr5B	93.739	559	32	2	1	557	697695732	697696289	0.000000e+00	835
7	TraesCS3B01G333500	chr5B	92.559	551	38	2	1	549	404075917	404076466	0.000000e+00	787
8	TraesCS3B01G333500	chr4A	93.393	560	33	3	1	557	705574943	705575501	0.000000e+00	826
9	TraesCS3B01G333500	chr4A	92.777	443	26	5	1	441	664957031	664957469	9.350000e-179	636
10	TraesCS3B01G333500	chr2A	92.349	562	32	4	1	557	503628798	503629353	0.000000e+00	789
11	TraesCS3B01G333500	chr2A	92.899	507	32	3	54	557	121160701	121161206	0.000000e+00	734
12	TraesCS3B01G333500	chr1A	93.194	191	11	1	1	189	526625896	526626086	1.820000e-71	279
13	TraesCS3B01G333500	chr1A	90.722	97	5	4	2150	2243	94578688	94578593	2.500000e-25	126
14	TraesCS3B01G333500	chr5D	91.473	129	11	0	2020	2148	432422061	432421933	6.810000e-41	178
15	TraesCS3B01G333500	chr1D	91.473	129	10	1	2020	2148	254420129	254420256	2.450000e-40	176
16	TraesCS3B01G333500	chr1D	94.118	85	3	2	2152	2235	212447783	212447866	6.960000e-26	128
17	TraesCS3B01G333500	chrUn	90.698	129	12	0	2020	2148	390488509	390488381	3.170000e-39	172
18	TraesCS3B01G333500	chrUn	91.579	95	4	4	2152	2243	171006071	171005978	6.960000e-26	128
19	TraesCS3B01G333500	chr7D	90.698	129	12	0	2020	2148	231529351	231529479	3.170000e-39	172
20	TraesCS3B01G333500	chr7D	90.698	129	12	0	2020	2148	231529877	231530005	3.170000e-39	172
21	TraesCS3B01G333500	chr7D	91.579	95	4	4	2152	2243	382087589	382087496	6.960000e-26	128
22	TraesCS3B01G333500	chr7D	94.118	85	3	2	2152	2235	626713405	626713488	6.960000e-26	128
23	TraesCS3B01G333500	chr2D	90.698	129	12	0	2020	2148	33937214	33937342	3.170000e-39	172
24	TraesCS3B01G333500	chr4D	91.579	95	4	4	2152	2243	123399309	123399216	6.960000e-26	128
25	TraesCS3B01G333500	chr4D	91.579	95	4	4	2152	2243	134960799	134960706	6.960000e-26	128

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	TraesCS3B01G333500	chr3B	540190887	540193285	2398	True	4431	4431	100.0000	1	2399	1	chr3B.!!$R2	2398
1	TraesCS3B01G333500	chr3A	536774262	536775929	1667	False	2272	2272	91.6420	768	2399	1	chr3A.!!$F1	1631
2	TraesCS3B01G333500	chr3A	76340468	76341025	557	True	813	813	93.0230	1	557	1	chr3A.!!$R1	556
3	TraesCS3B01G333500	chr3D	414162857	414164797	1940	True	1188	1423	90.8985	562	2399	2	chr3D.!!$R1	1837
4	TraesCS3B01G333500	chr5B	697695732	697696289	557	False	835	835	93.7390	1	557	1	chr5B.!!$F2	556
5	TraesCS3B01G333500	chr5B	404075917	404076466	549	False	787	787	92.5590	1	549	1	chr5B.!!$F1	548
6	TraesCS3B01G333500	chr4A	705574943	705575501	558	False	826	826	93.3930	1	557	1	chr4A.!!$F2	556
7	TraesCS3B01G333500	chr2A	503628798	503629353	555	False	789	789	92.3490	1	557	1	chr2A.!!$F2	556
8	TraesCS3B01G333500	chr2A	121160701	121161206	505	False	734	734	92.8990	54	557	1	chr2A.!!$F1	503

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
180	183	0.106669	GGTAATCAACCTCCAGCCCC	60.107	60.000	0.0	0.0	45.75	5.80	F
1053	1070	1.938577	CTGATCCAGACATTCCGCAAG	59.061	52.381	0.0	0.0	32.44	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1359	1376	0.165295	CGACTTCGCTGTACTCGACA	59.835	55.0	9.66	3.02	35.51	4.35	R
2068	2245	0.253160	AGCCCATACCCAGAACTCCA	60.253	55.0	0.00	0.00	0.00	3.86	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
55	56	1.289231	AGTGCCTCTCTACCATGGAGA	59.711	52.381	21.47	15.41	38.07	3.71
132	135	6.938596	TCATGATCATGAATACTTGCCCTTAG	59.061	38.462	31.46	3.91	44.14	2.18
136	139	6.266131	TCATGAATACTTGCCCTTAGGAAT	57.734	37.500	0.00	0.00	33.47	3.01
180	183	0.106669	GGTAATCAACCTCCAGCCCC	60.107	60.000	0.00	0.00	45.75	5.80
302	309	3.008485	AGCTTCCTTCGGTTTTCATCTCT	59.992	43.478	0.00	0.00	0.00	3.10
380	387	5.010012	ACAACCTGAAACAACTCATGGAATC	59.990	40.000	0.00	0.00	0.00	2.52
413	420	2.095567	CCTGACAAACCGCTTTGATCAG	60.096	50.000	18.71	18.71	39.43	2.90
497	504	6.892658	ACTAGTGGCAATGTGTTCAAATTA	57.107	33.333	0.00	0.00	0.00	1.40
500	507	8.367156	ACTAGTGGCAATGTGTTCAAATTAAAT	58.633	29.630	0.00	0.00	0.00	1.40
507	514	8.531530	GCAATGTGTTCAAATTAAATATCGGAC	58.468	33.333	0.00	0.00	0.00	4.79
512	519	6.314152	TGTTCAAATTAAATATCGGACGAGCA	59.686	34.615	0.00	0.00	0.00	4.26
523	530	1.971167	GACGAGCAACCAATGGCCA	60.971	57.895	8.56	8.56	0.00	5.36
557	565	7.227512	CCCCAAATACTTATCAACTAGAGCTTG	59.772	40.741	0.00	0.00	0.00	4.01
558	566	7.987458	CCCAAATACTTATCAACTAGAGCTTGA	59.013	37.037	0.00	0.00	32.24	3.02
559	567	9.383519	CCAAATACTTATCAACTAGAGCTTGAA	57.616	33.333	0.00	0.00	31.48	2.69
566	574	9.593134	CTTATCAACTAGAGCTTGAACTTATGT	57.407	33.333	0.00	0.00	31.48	2.29
570	578	7.931407	TCAACTAGAGCTTGAACTTATGTTTGA	59.069	33.333	0.00	0.00	36.39	2.69
594	602	6.937436	ACTTGAAATTTTACACGTCTTCCT	57.063	33.333	0.00	0.00	0.00	3.36
601	609	4.966965	TTTACACGTCTTCCTGCAAAAA	57.033	36.364	0.00	0.00	0.00	1.94
602	610	4.545823	TTACACGTCTTCCTGCAAAAAG	57.454	40.909	2.07	2.07	0.00	2.27
606	614	4.082463	ACACGTCTTCCTGCAAAAAGAAAA	60.082	37.500	11.00	0.00	33.53	2.29
695	708	3.671008	AAACTAAATTTGGTTCCCCGC	57.329	42.857	18.78	0.00	30.15	6.13
739	755	9.948964	CATAGTTCTATTGATCCATTCACCATA	57.051	33.333	0.00	0.00	32.84	2.74
741	757	8.682936	AGTTCTATTGATCCATTCACCATAAC	57.317	34.615	0.00	0.00	32.84	1.89
742	758	8.497745	AGTTCTATTGATCCATTCACCATAACT	58.502	33.333	0.00	0.00	32.84	2.24
743	759	9.125026	GTTCTATTGATCCATTCACCATAACTT	57.875	33.333	0.00	0.00	32.84	2.66
744	760	9.699410	TTCTATTGATCCATTCACCATAACTTT	57.301	29.630	0.00	0.00	32.84	2.66
745	761	9.123902	TCTATTGATCCATTCACCATAACTTTG	57.876	33.333	0.00	0.00	32.84	2.77
746	762	6.528537	TTGATCCATTCACCATAACTTTGG	57.471	37.500	0.00	0.00	42.82	3.28
761	777	9.868277	CCATAACTTTGGTTTGCATTATTCTAA	57.132	29.630	0.00	0.00	36.92	2.10
794	810	5.499139	TGGTTTGCATCGATAATTTCTCC	57.501	39.130	0.00	0.00	0.00	3.71
795	811	5.192927	TGGTTTGCATCGATAATTTCTCCT	58.807	37.500	0.00	0.00	0.00	3.69
796	812	5.652014	TGGTTTGCATCGATAATTTCTCCTT	59.348	36.000	0.00	0.00	0.00	3.36
797	813	6.183360	TGGTTTGCATCGATAATTTCTCCTTC	60.183	38.462	0.00	0.00	0.00	3.46
838	854	2.926242	TTCGGCCTTCTTCCCGGT	60.926	61.111	0.00	0.00	44.45	5.28
874	890	2.328989	CCACGTTGTGCAGTGCAG	59.671	61.111	20.42	9.47	40.08	4.41
901	917	3.009143	AGCTAAATCCAGGTTTCTTCGGT	59.991	43.478	0.00	0.00	0.00	4.69
1053	1070	1.938577	CTGATCCAGACATTCCGCAAG	59.061	52.381	0.00	0.00	32.44	4.01
1180	1197	4.787280	AGGACTCCCTCAGGGCCG	62.787	72.222	4.08	0.17	43.94	6.13
1287	1304	3.854669	CTCCTCCGCAAGCCCGAT	61.855	66.667	0.00	0.00	0.00	4.18
1338	1355	4.426313	CCCGCCAAGGACTTCCCC	62.426	72.222	0.00	0.00	45.00	4.81
1359	1376	1.207329	GTCCCCTACGTCAATTCTGCT	59.793	52.381	0.00	0.00	0.00	4.24
1458	1481	0.908910	TAGGGTTCCGTGTCATGCAT	59.091	50.000	0.00	0.00	0.00	3.96
1480	1503	6.927381	GCATGCCTAATTGCAATCTTTATCTT	59.073	34.615	13.38	0.00	45.84	2.40
1499	1522	6.791887	ATCTTAATCAGTGTGTGTCTGTTG	57.208	37.500	0.00	0.00	34.86	3.33
1575	1600	3.199727	ACCCAACCTTGCTTTGTGAAATT	59.800	39.130	0.00	0.00	0.00	1.82
1580	1605	6.930722	CCAACCTTGCTTTGTGAAATTAGATT	59.069	34.615	0.00	0.00	0.00	2.40
1582	1607	8.490355	CAACCTTGCTTTGTGAAATTAGATTTC	58.510	33.333	6.48	6.48	46.75	2.17
1597	1622	6.899393	TTAGATTTCCTGTCTTGTTGCAAT	57.101	33.333	0.59	0.00	0.00	3.56
1600	1625	4.998671	TTTCCTGTCTTGTTGCAATTCA	57.001	36.364	0.59	0.00	0.00	2.57
1681	1708	1.700955	AGAGGGAAATGCATCATGCC	58.299	50.000	7.30	13.20	44.23	4.40
1728	1775	5.645067	TCATTGTGAATTGCTAAGTCTCTGG	59.355	40.000	0.00	0.00	0.00	3.86
1773	1950	7.062322	AGATATATTGGTTGGCTTGAACATCA	58.938	34.615	0.00	0.00	0.00	3.07
1775	1952	8.938801	ATATATTGGTTGGCTTGAACATCATA	57.061	30.769	0.00	0.00	0.00	2.15
1839	2016	4.528206	ACAAATCCTGTTTTCCATTCCCTC	59.472	41.667	0.00	0.00	32.99	4.30
1865	2042	1.920574	CTACTGACGCCACAAGAATCG	59.079	52.381	0.00	0.00	0.00	3.34
1866	2043	0.670546	ACTGACGCCACAAGAATCGG	60.671	55.000	0.00	0.00	0.00	4.18
1931	2108	1.983224	CCTGAGGGTTCATGTCGGT	59.017	57.895	0.00	0.00	31.68	4.69
1959	2136	3.454375	TCGAACCACTCACAACTTCTTC	58.546	45.455	0.00	0.00	0.00	2.87
2063	2240	2.029020	GCAGGTGGTTCCATTTCTTTCC	60.029	50.000	0.00	0.00	39.02	3.13
2068	2245	4.528206	GGTGGTTCCATTTCTTTCCTGATT	59.472	41.667	0.00	0.00	35.97	2.57
2171	2348	1.597027	CCCACAAGGTGACACCGAC	60.597	63.158	18.93	0.00	44.90	4.79
2194	2371	2.058125	TACCTCCTTTTGTGCGCCCA	62.058	55.000	4.18	0.00	0.00	5.36
2198	2375	1.080569	CCTTTTGTGCGCCCATCAC	60.081	57.895	4.18	0.00	35.14	3.06
2199	2376	1.080569	CTTTTGTGCGCCCATCACC	60.081	57.895	4.18	0.00	33.71	4.02
2200	2377	1.526575	CTTTTGTGCGCCCATCACCT	61.527	55.000	4.18	0.00	33.71	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	5.069516	GTCATCACATATTTGGAGGGCAATT	59.930	40.000	0.00	0.00	0.00	2.32
132	135	4.201822	GGAATCGTTGTGTGCTAGAATTCC	60.202	45.833	0.65	0.00	0.00	3.01
136	139	2.333926	CGGAATCGTTGTGTGCTAGAA	58.666	47.619	0.00	0.00	0.00	2.10
180	183	1.199789	TCAGGCTATGCTTGCAAAACG	59.800	47.619	0.00	0.00	35.58	3.60
221	224	0.337428	AGATGGAGGCATGGGCTTTT	59.663	50.000	0.00	0.00	38.98	2.27
302	309	1.120530	GGCTCGATTCTTCTGGGGTA	58.879	55.000	0.00	0.00	0.00	3.69
355	362	4.277476	TCCATGAGTTGTTTCAGGTTGTT	58.723	39.130	0.00	0.00	0.00	2.83
380	387	1.619654	TTGTCAGGCAATTCCCACAG	58.380	50.000	0.00	0.00	31.72	3.66
413	420	0.310854	CACCGCAACAAGGGAAGTTC	59.689	55.000	0.00	0.00	0.00	3.01
497	504	2.684001	TGGTTGCTCGTCCGATATTT	57.316	45.000	0.00	0.00	0.00	1.40
500	507	1.472552	CCATTGGTTGCTCGTCCGATA	60.473	52.381	0.00	0.00	0.00	2.92
507	514	0.458889	CAATGGCCATTGGTTGCTCG	60.459	55.000	39.89	19.56	43.25	5.03
523	530	2.252535	AAGTATTTGGGGCTGCCAAT	57.747	45.000	22.05	13.94	0.00	3.16
543	551	8.725148	CAAACATAAGTTCAAGCTCTAGTTGAT	58.275	33.333	0.00	0.00	36.84	2.57
566	574	8.973835	AAGACGTGTAAAATTTCAAGTTCAAA	57.026	26.923	0.00	0.00	0.00	2.69
570	578	7.193595	CAGGAAGACGTGTAAAATTTCAAGTT	58.806	34.615	0.00	0.00	0.00	2.66
713	729	8.859236	ATGGTGAATGGATCAATAGAACTATG	57.141	34.615	0.00	0.00	40.50	2.23
721	737	8.236585	CCAAAGTTATGGTGAATGGATCAATA	57.763	34.615	0.00	0.00	40.50	1.90
764	780	7.961325	ATTATCGATGCAAACCAAAGTTTTT	57.039	28.000	8.54	0.00	43.82	1.94
765	781	7.961325	AATTATCGATGCAAACCAAAGTTTT	57.039	28.000	8.54	0.00	43.82	2.43
785	801	5.074515	AGTGGTGGAAAGGAAGGAGAAATTA	59.925	40.000	0.00	0.00	0.00	1.40
794	810	0.954452	GCACAGTGGTGGAAAGGAAG	59.046	55.000	1.84	0.00	45.38	3.46
795	811	0.550914	AGCACAGTGGTGGAAAGGAA	59.449	50.000	3.92	0.00	45.38	3.36
796	812	0.108585	GAGCACAGTGGTGGAAAGGA	59.891	55.000	10.75	0.00	45.38	3.36
797	813	0.109342	AGAGCACAGTGGTGGAAAGG	59.891	55.000	10.75	0.00	45.38	3.11
838	854	1.323271	GCCTGATCTGGACCGTCTGA	61.323	60.000	21.91	0.00	0.00	3.27
874	890	4.464947	AGAAACCTGGATTTAGCTATGGC	58.535	43.478	0.00	0.00	39.06	4.40
1053	1070	0.875059	CCCACGGCTTCTTGAAGAAC	59.125	55.000	13.87	1.66	29.89	3.01
1172	1189	4.731853	TGGGGATGACGGCCCTGA	62.732	66.667	0.00	0.00	45.30	3.86
1180	1197	2.732619	GGTCGGAGGTGGGGATGAC	61.733	68.421	0.00	0.00	0.00	3.06
1287	1304	2.413351	GCCATGTAGCGCTCGAGA	59.587	61.111	16.34	0.00	0.00	4.04
1359	1376	0.165295	CGACTTCGCTGTACTCGACA	59.835	55.000	9.66	3.02	35.51	4.35
1480	1503	6.751514	AAAACAACAGACACACACTGATTA	57.248	33.333	0.00	0.00	38.55	1.75
1499	1522	8.129211	CCCCGAATCTACATTTGATTCTAAAAC	58.871	37.037	12.60	0.00	44.36	2.43
1540	1565	7.354312	AGCAAGGTTGGGTTATCAACTATATT	58.646	34.615	7.51	0.00	44.52	1.28
1575	1600	6.489700	TGAATTGCAACAAGACAGGAAATCTA	59.510	34.615	0.00	0.00	0.00	1.98
1580	1605	4.583907	TCATGAATTGCAACAAGACAGGAA	59.416	37.500	0.00	0.00	0.00	3.36
1582	1607	4.508461	TCATGAATTGCAACAAGACAGG	57.492	40.909	0.00	0.01	0.00	4.00
1623	1650	4.542697	AGTTGGGTTACAGTTGAACCAAT	58.457	39.130	8.83	0.00	46.98	3.16
1634	1661	3.866703	TGGTGATGAAGTTGGGTTACA	57.133	42.857	0.00	0.00	0.00	2.41
1681	1708	8.812147	TGATATACTTAACCTTGACTTATGCG	57.188	34.615	0.00	0.00	0.00	4.73
1713	1760	6.547510	ACTTGAAAAACCAGAGACTTAGCAAT	59.452	34.615	0.00	0.00	0.00	3.56
1722	1769	9.567776	TTTGATATACACTTGAAAAACCAGAGA	57.432	29.630	0.00	0.00	0.00	3.10
1724	1771	9.567776	TCTTTGATATACACTTGAAAAACCAGA	57.432	29.630	0.00	0.00	0.00	3.86
1839	2016	1.153745	GTGGCGTCAGTAGGCTCAG	60.154	63.158	0.00	0.00	36.72	3.35
1865	2042	1.682087	GGTAGGATGGTGCTGGAAACC	60.682	57.143	0.00	0.00	38.26	3.27
1866	2043	1.682087	GGGTAGGATGGTGCTGGAAAC	60.682	57.143	0.00	0.00	0.00	2.78
1918	2095	2.413310	ATGGTTACCGACATGAACCC	57.587	50.000	0.00	0.00	41.69	4.11
1931	2108	3.755112	TGTGAGTGGTTCGAATGGTTA	57.245	42.857	0.00	0.00	0.00	2.85
1959	2136	6.198650	TGCTTTGATTAGATGTTGTCATGG	57.801	37.500	0.00	0.00	34.06	3.66
2035	2212	4.584638	AATGGAACCACCTGCAGTATAA	57.415	40.909	13.81	0.00	39.86	0.98
2047	2224	4.527816	CCAATCAGGAAAGAAATGGAACCA	59.472	41.667	0.00	0.00	41.22	3.67
2063	2240	3.434167	CCCATACCCAGAACTCCAATCAG	60.434	52.174	0.00	0.00	0.00	2.90
2068	2245	0.253160	AGCCCATACCCAGAACTCCA	60.253	55.000	0.00	0.00	0.00	3.86
2156	2333	1.963464	AACCGTCGGTGTCACCTTGT	61.963	55.000	19.67	8.34	35.34	3.16
2171	2348	0.515564	CGCACAAAAGGAGGTAACCG	59.484	55.000	0.00	0.00	34.73	4.44
2266	2448	4.100189	CCTAAAATGTGATCTCGAGGACCT	59.900	45.833	13.56	0.00	0.00	3.85
2280	2462	3.181489	CGTCTCTACTCGGCCTAAAATGT	60.181	47.826	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.