AutoCloner

Multiple sequence alignment - TraesCS5A01G266800

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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	TraesCS5A01G266800	chr5A	100.000	2342	0	0	1	2342	478320019	478317678	0.000000e+00	4325
1	TraesCS5A01G266800	chr5A	98.644	959	4	1	1384	2342	467739461	467740410	0.000000e+00	1690
2	TraesCS5A01G266800	chr1D	99.686	954	3	0	1389	2342	111007374	111006421	0.000000e+00	1746
3	TraesCS5A01G266800	chrUn	98.253	973	5	1	1382	2342	280026492	280025520	0.000000e+00	1692
4	TraesCS5A01G266800	chr1B	97.694	954	7	1	1389	2342	495304004	495303066	0.000000e+00	1626
5	TraesCS5A01G266800	chr5B	90.346	1243	60	24	184	1385	450839614	450838391	0.000000e+00	1576
6	TraesCS5A01G266800	chr5B	93.189	969	36	15	1384	2342	704502607	704503555	0.000000e+00	1397
7	TraesCS5A01G266800	chr5B	92.857	966	49	14	1382	2342	541167700	541168650	0.000000e+00	1384
8	TraesCS5A01G266800	chr5B	81.538	195	8	11	1	188	450839965	450839792	4.060000e-28	135
9	TraesCS5A01G266800	chr5D	92.161	995	46	12	417	1385	377531623	377530635	0.000000e+00	1376
10	TraesCS5A01G266800	chr5D	91.045	201	15	1	151	351	377531996	377531799	3.840000e-68	268
11	TraesCS5A01G266800	chr5D	92.553	94	6	1	1	94	377532105	377532013	1.460000e-27	134
12	TraesCS5A01G266800	chr5D	98.387	62	1	0	348	409	377531762	377531701	2.460000e-20	110
13	TraesCS5A01G266800	chr2A	92.078	972	38	10	1382	2342	391875547	391876490	0.000000e+00	1332
14	TraesCS5A01G266800	chr7B	88.591	149	17	0	1385	1533	697279097	697278949	5.140000e-42	182
15	TraesCS5A01G266800	chr7B	80.851	141	15	8	1740	1873	164495657	164495792	1.480000e-17	100
16	TraesCS5A01G266800	chr4A	90.441	136	12	1	1385	1520	33727167	33727301	6.650000e-41	178
17	TraesCS5A01G266800	chr3B	95.789	95	4	0	2119	2213	715051533	715051627	1.120000e-33	154
18	TraesCS5A01G266800	chr2B	95.789	95	4	0	2119	2213	369028013	369028107	1.120000e-33	154

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	TraesCS5A01G266800	chr5A	478317678	478320019	2341	True	4325.0	4325	100.0000	1	2342	1	chr5A.!!$R1	2341
1	TraesCS5A01G266800	chr5A	467739461	467740410	949	False	1690.0	1690	98.6440	1384	2342	1	chr5A.!!$F1	958
2	TraesCS5A01G266800	chr1D	111006421	111007374	953	True	1746.0	1746	99.6860	1389	2342	1	chr1D.!!$R1	953
3	TraesCS5A01G266800	chrUn	280025520	280026492	972	True	1692.0	1692	98.2530	1382	2342	1	chrUn.!!$R1	960
4	TraesCS5A01G266800	chr1B	495303066	495304004	938	True	1626.0	1626	97.6940	1389	2342	1	chr1B.!!$R1	953
5	TraesCS5A01G266800	chr5B	704502607	704503555	948	False	1397.0	1397	93.1890	1384	2342	1	chr5B.!!$F2	958
6	TraesCS5A01G266800	chr5B	541167700	541168650	950	False	1384.0	1384	92.8570	1382	2342	1	chr5B.!!$F1	960
7	TraesCS5A01G266800	chr5B	450838391	450839965	1574	True	855.5	1576	85.9420	1	1385	2	chr5B.!!$R1	1384
8	TraesCS5A01G266800	chr5D	377530635	377532105	1470	True	472.0	1376	93.5365	1	1385	4	chr5D.!!$R1	1384
9	TraesCS5A01G266800	chr2A	391875547	391876490	943	False	1332.0	1332	92.0780	1382	2342	1	chr2A.!!$F1	960

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
833	1147	0.598065	AAAGCACCATGGAAACGCTC	59.402	50.0	21.47	0.0	31.17	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1686	2040	3.224324	GCGAGGCGTATGGAGGGA	61.224	66.667	0.0	0.0	0.0	4.2	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
94	102	3.206150	TCATGCCGAGCTAAGGATTTTC	58.794	45.455	11.57	0.00	0.00	2.29
96	104	2.632377	TGCCGAGCTAAGGATTTTCAG	58.368	47.619	11.57	0.00	0.00	3.02
98	106	3.010420	GCCGAGCTAAGGATTTTCAGTT	58.990	45.455	11.57	0.00	0.00	3.16
100	108	4.082733	GCCGAGCTAAGGATTTTCAGTTTT	60.083	41.667	11.57	0.00	0.00	2.43
102	110	6.086871	CCGAGCTAAGGATTTTCAGTTTTTC	58.913	40.000	1.60	0.00	0.00	2.29
103	111	6.293955	CCGAGCTAAGGATTTTCAGTTTTTCA	60.294	38.462	1.60	0.00	0.00	2.69
104	112	7.308435	CGAGCTAAGGATTTTCAGTTTTTCAT	58.692	34.615	0.00	0.00	0.00	2.57
106	114	8.822652	AGCTAAGGATTTTCAGTTTTTCATTG	57.177	30.769	0.00	0.00	0.00	2.82
108	116	8.490355	GCTAAGGATTTTCAGTTTTTCATTGTG	58.510	33.333	0.00	0.00	0.00	3.33
109	117	9.533253	CTAAGGATTTTCAGTTTTTCATTGTGT	57.467	29.630	0.00	0.00	0.00	3.72
110	118	7.775397	AGGATTTTCAGTTTTTCATTGTGTG	57.225	32.000	0.00	0.00	0.00	3.82
119	127	6.645827	CAGTTTTTCATTGTGTGCATTATGGA	59.354	34.615	0.00	0.00	0.00	3.41
120	128	7.332430	CAGTTTTTCATTGTGTGCATTATGGAT	59.668	33.333	0.00	0.00	0.00	3.41
189	379	0.886563	GCTGCAAATGGAACTCAGCT	59.113	50.000	5.40	0.00	44.71	4.24
194	384	2.490903	GCAAATGGAACTCAGCTGATGT	59.509	45.455	18.63	14.38	0.00	3.06
196	386	4.156556	GCAAATGGAACTCAGCTGATGTAA	59.843	41.667	18.63	2.73	0.00	2.41
255	450	1.983119	TACCAGGCCCAGCTATGCAC	61.983	60.000	0.00	0.00	0.00	4.57
331	526	9.280174	GAATGTTCCGGTATTAATTCTCCAATA	57.720	33.333	0.00	0.00	0.00	1.90
346	541	9.997172	AATTCTCCAATATTTCTTTCCCTTACT	57.003	29.630	0.00	0.00	0.00	2.24
466	769	7.925483	CCTGCCAACTTATATATATCTCAGCTC	59.075	40.741	0.00	0.00	0.00	4.09
510	813	5.630680	CCGTTCTTAACAGCTACGAAAACTA	59.369	40.000	4.57	0.00	32.56	2.24
520	824	4.870991	AGCTACGAAAACTAGCAATCTTCC	59.129	41.667	4.99	0.00	39.36	3.46
586	890	2.224426	ACATTGCTCGGTTTAGTCCACA	60.224	45.455	0.00	0.00	0.00	4.17
623	932	3.326747	CCTGTGTACCAGAGCACTTTAC	58.673	50.000	11.58	0.00	44.49	2.01
693	1007	3.385193	AAAATTCCAGCTTTGGGAACG	57.615	42.857	6.17	0.00	46.53	3.95
707	1021	1.203758	GGGAACGGCCATTTGTTTAGG	59.796	52.381	2.24	0.00	38.95	2.69
715	1029	2.675032	GCCATTTGTTTAGGCTTGGAGC	60.675	50.000	3.36	0.00	44.92	4.70
736	1050	2.124151	ATCAACGGCTGGCCCATC	60.124	61.111	0.00	0.00	0.00	3.51
786	1100	3.782443	GTCGTCCTCCGGGCCAAT	61.782	66.667	4.39	0.00	37.11	3.16
833	1147	0.598065	AAAGCACCATGGAAACGCTC	59.402	50.000	21.47	0.00	31.17	5.03
834	1148	1.244019	AAGCACCATGGAAACGCTCC	61.244	55.000	21.47	0.00	45.64	4.70
906	1226	0.925466	CCGCCACGTCTATAAAACCG	59.075	55.000	0.00	0.00	0.00	4.44
955	1279	2.215196	CACACATCATCATCCATCGCA	58.785	47.619	0.00	0.00	0.00	5.10
1029	1371	1.060622	GTCGTACGAGAGGCTGTCG	59.939	63.158	29.57	29.57	43.25	4.35
1352	1694	4.848357	TCCCTCCAGTGATTCATTCTTTC	58.152	43.478	0.00	0.00	0.00	2.62
1353	1695	3.624861	CCCTCCAGTGATTCATTCTTTCG	59.375	47.826	0.00	0.00	0.00	3.46
1370	1713	1.206578	CGGCGTTTTTGTGATCGCT	59.793	52.632	7.94	0.00	46.37	4.93
1387	1730	2.536725	CTCTGTGCGTTGTGAGCAT	58.463	52.632	0.00	0.00	46.96	3.79
1686	2040	0.462581	TAGACGCGTACAGATCCGGT	60.463	55.000	13.97	0.00	0.00	5.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	102	6.645827	TCCATAATGCACACAATGAAAAACTG	59.354	34.615	0.00	0.00	0.00	3.16
96	104	7.118101	ACATCCATAATGCACACAATGAAAAAC	59.882	33.333	0.00	0.00	39.12	2.43
98	106	6.699366	ACATCCATAATGCACACAATGAAAA	58.301	32.000	0.00	0.00	39.12	2.29
100	108	5.918426	ACATCCATAATGCACACAATGAA	57.082	34.783	0.00	0.00	39.12	2.57
102	110	5.289917	CACAACATCCATAATGCACACAATG	59.710	40.000	0.00	0.00	39.12	2.82
103	111	5.412640	CACAACATCCATAATGCACACAAT	58.587	37.500	0.00	0.00	39.12	2.71
104	112	4.807443	CACAACATCCATAATGCACACAA	58.193	39.130	0.00	0.00	39.12	3.33
106	114	3.181397	GCACAACATCCATAATGCACAC	58.819	45.455	0.00	0.00	39.12	3.82
108	116	3.507103	TGCACAACATCCATAATGCAC	57.493	42.857	0.00	0.00	38.11	4.57
109	117	3.510753	ACTTGCACAACATCCATAATGCA	59.489	39.130	0.00	0.00	41.08	3.96
110	118	4.114058	ACTTGCACAACATCCATAATGC	57.886	40.909	0.00	0.00	39.12	3.56
137	145	1.074248	ACCACCCGCCACCTAAAAG	59.926	57.895	0.00	0.00	0.00	2.27
138	146	1.228306	CACCACCCGCCACCTAAAA	60.228	57.895	0.00	0.00	0.00	1.52
139	147	2.432563	CACCACCCGCCACCTAAA	59.567	61.111	0.00	0.00	0.00	1.85
140	148	2.850130	ACACCACCCGCCACCTAA	60.850	61.111	0.00	0.00	0.00	2.69
167	175	0.599558	TGAGTTCCATTTGCAGCTGC	59.400	50.000	31.89	31.89	42.50	5.25
169	177	0.886563	GCTGAGTTCCATTTGCAGCT	59.113	50.000	0.00	0.00	46.17	4.24
189	379	0.894835	TGACAGGCGAGCTTACATCA	59.105	50.000	0.00	0.00	0.00	3.07
194	384	0.679505	ACAACTGACAGGCGAGCTTA	59.320	50.000	7.51	0.00	0.00	3.09
196	386	1.005630	GACAACTGACAGGCGAGCT	60.006	57.895	7.51	0.00	0.00	4.09
255	450	3.802685	GGTTAACGACTTGCTAGCATAGG	59.197	47.826	20.13	14.02	39.70	2.57
331	526	7.985589	TGGTCTAGAAAGTAAGGGAAAGAAAT	58.014	34.615	0.00	0.00	0.00	2.17
336	531	4.595781	TGCTGGTCTAGAAAGTAAGGGAAA	59.404	41.667	0.00	0.00	0.00	3.13
337	532	4.164981	TGCTGGTCTAGAAAGTAAGGGAA	58.835	43.478	0.00	0.00	0.00	3.97
338	533	3.786553	TGCTGGTCTAGAAAGTAAGGGA	58.213	45.455	0.00	0.00	0.00	4.20
339	534	4.762289	ATGCTGGTCTAGAAAGTAAGGG	57.238	45.455	0.00	0.00	0.00	3.95
340	535	5.755861	GCTAATGCTGGTCTAGAAAGTAAGG	59.244	44.000	0.00	0.00	36.03	2.69
341	536	6.341316	TGCTAATGCTGGTCTAGAAAGTAAG	58.659	40.000	0.00	0.00	40.48	2.34
342	537	6.294361	TGCTAATGCTGGTCTAGAAAGTAA	57.706	37.500	0.00	0.00	40.48	2.24
344	539	4.826274	TGCTAATGCTGGTCTAGAAAGT	57.174	40.909	0.00	0.00	40.48	2.66
345	540	7.157347	TGATATGCTAATGCTGGTCTAGAAAG	58.843	38.462	0.00	0.00	40.48	2.62
346	541	7.066307	TGATATGCTAATGCTGGTCTAGAAA	57.934	36.000	0.00	0.00	40.48	2.52
353	585	2.374504	AGCCTGATATGCTAATGCTGGT	59.625	45.455	0.00	0.00	37.28	4.00
463	766	5.009110	GGGGAGCTTAGTTAATTGATTGAGC	59.991	44.000	2.03	2.03	0.00	4.26
466	769	4.881850	ACGGGGAGCTTAGTTAATTGATTG	59.118	41.667	0.00	0.00	0.00	2.67
470	773	4.514401	AGAACGGGGAGCTTAGTTAATTG	58.486	43.478	0.00	0.00	0.00	2.32
510	813	0.466124	GAGTAGCCGGGAAGATTGCT	59.534	55.000	2.18	0.00	37.84	3.91
520	824	2.289565	GAAATTTCCAGGAGTAGCCGG	58.710	52.381	6.95	0.00	43.43	6.13
586	890	1.143684	ACAGGCTGTTGGTCACATTCT	59.856	47.619	15.88	0.00	33.76	2.40
623	932	7.423314	GTGTACGTTTGTATAAATAAAGTGGCG	59.577	37.037	0.00	0.00	32.11	5.69
721	1035	3.136123	CAGATGGGCCAGCCGTTG	61.136	66.667	19.93	6.64	36.85	4.10
748	1062	2.730672	CCGTTTCTCCGCTCGCTTG	61.731	63.158	0.00	0.00	0.00	4.01
833	1147	2.048503	GGGTGTGTCGTTCGAGGG	60.049	66.667	0.00	0.00	0.00	4.30
834	1148	2.048503	GGGGTGTGTCGTTCGAGG	60.049	66.667	0.00	0.00	0.00	4.63
918	1238	2.141448	TGGTGGTGGCGTTGGACTA	61.141	57.895	0.00	0.00	0.00	2.59
1352	1694	3.735894	GCGATCACAAAAACGCCG	58.264	55.556	0.00	0.00	44.27	6.46
1370	1713	1.229975	CCATGCTCACAACGCACAGA	61.230	55.000	0.00	0.00	40.65	3.41
1686	2040	3.224324	GCGAGGCGTATGGAGGGA	61.224	66.667	0.00	0.00	0.00	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.