AutoCloner

Multiple sequence alignment - TraesCS3B01G210600

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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	TraesCS3B01G210600	chr3B	100.000	3434	0	0	1	3434	246996083	246992650	0.000000e+00	6342
1	TraesCS3B01G210600	chr3B	93.824	3449	196	10	1	3434	402661548	402664994	0.000000e+00	5173
2	TraesCS3B01G210600	chr5D	95.360	3448	140	11	1	3434	378825558	378822117	0.000000e+00	5463
3	TraesCS3B01G210600	chr5B	94.104	3443	190	7	1	3434	453090183	453086745	0.000000e+00	5221
4	TraesCS3B01G210600	chr6B	93.894	3439	197	7	1	3434	628277332	628273902	0.000000e+00	5175
5	TraesCS3B01G210600	chr6B	93.864	3439	198	7	1	3434	628323957	628320527	0.000000e+00	5169
6	TraesCS3B01G210600	chr2B	93.881	3448	186	13	1	3434	352032744	352036180	0.000000e+00	5175
7	TraesCS3B01G210600	chr2B	93.665	3441	207	8	1	3434	315008033	315011469	0.000000e+00	5136
8	TraesCS3B01G210600	chr7B	93.692	3440	196	15	1	3434	665789672	665793096	0.000000e+00	5131
9	TraesCS3B01G210600	chr1B	93.275	3450	205	16	1	3434	555911108	555907670	0.000000e+00	5060
10	TraesCS3B01G210600	chr3A	89.811	265	24	3	3171	3433	521370819	521371082	1.530000e-88	337

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	TraesCS3B01G210600	chr3B	246992650	246996083	3433	True	6342	6342	100.000	1	3434	1	chr3B.!!$R1	3433
1	TraesCS3B01G210600	chr3B	402661548	402664994	3446	False	5173	5173	93.824	1	3434	1	chr3B.!!$F1	3433
2	TraesCS3B01G210600	chr5D	378822117	378825558	3441	True	5463	5463	95.360	1	3434	1	chr5D.!!$R1	3433
3	TraesCS3B01G210600	chr5B	453086745	453090183	3438	True	5221	5221	94.104	1	3434	1	chr5B.!!$R1	3433
4	TraesCS3B01G210600	chr6B	628273902	628277332	3430	True	5175	5175	93.894	1	3434	1	chr6B.!!$R1	3433
5	TraesCS3B01G210600	chr6B	628320527	628323957	3430	True	5169	5169	93.864	1	3434	1	chr6B.!!$R2	3433
6	TraesCS3B01G210600	chr2B	352032744	352036180	3436	False	5175	5175	93.881	1	3434	1	chr2B.!!$F2	3433
7	TraesCS3B01G210600	chr2B	315008033	315011469	3436	False	5136	5136	93.665	1	3434	1	chr2B.!!$F1	3433
8	TraesCS3B01G210600	chr7B	665789672	665793096	3424	False	5131	5131	93.692	1	3434	1	chr7B.!!$F1	3433
9	TraesCS3B01G210600	chr1B	555907670	555911108	3438	True	5060	5060	93.275	1	3434	1	chr1B.!!$R1	3433

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
930	941	0.105760	TCCCACAAACCACCATTGCT	60.106	50.0	0.00	0.0	0.00	3.91	F
1317	1328	0.818296	AGTTATGCGTCGAGGAGCTT	59.182	50.0	9.75	5.3	0.00	3.74	F
2071	2085	1.003262	CACATTTGCCGGTTTCAGCG	61.003	55.0	1.90	0.0	39.06	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2294	2308	0.107361	TCCTGCGTACTCGATGAGGA	60.107	55.0	0.0	0.0	39.71	3.71	R
2325	2339	0.394938	ACCATGACTTGTACGTGGCA	59.605	50.0	0.0	0.0	45.22	4.92	R
3398	3458	0.380733	TATACACGGCGCTCACTCTG	59.619	55.0	6.9	0.0	0.00	3.35	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
224	226	8.255905	AGTCGTTAGTACAAAGGCATAGTAAAT	58.744	33.333	0.00	0.00	0.00	1.40
225	227	9.520204	GTCGTTAGTACAAAGGCATAGTAAATA	57.480	33.333	0.00	0.00	0.00	1.40
316	324	6.069440	TCCCAATTCAGAAAGACCATCAGTAT	60.069	38.462	0.00	0.00	0.00	2.12
530	538	2.120312	TCACCAGTCCAAGTACCACAA	58.880	47.619	0.00	0.00	0.00	3.33
570	578	0.541998	TCATCACCGACCCTGACACT	60.542	55.000	0.00	0.00	0.00	3.55
619	627	7.096884	AGTACAGCTTGACTATACGAATCAA	57.903	36.000	0.00	0.00	33.25	2.57
848	856	4.636435	CCACGCCCCCGACAAACT	62.636	66.667	0.00	0.00	38.29	2.66
871	879	1.211567	TCCCACAAATCCCCGTCCAT	61.212	55.000	0.00	0.00	0.00	3.41
877	885	0.916086	AAATCCCCGTCCATGCACTA	59.084	50.000	0.00	0.00	0.00	2.74
884	892	2.351350	CCCGTCCATGCACTACAAAAAC	60.351	50.000	0.00	0.00	0.00	2.43
930	941	0.105760	TCCCACAAACCACCATTGCT	60.106	50.000	0.00	0.00	0.00	3.91
1009	1020	2.514824	GGAAGGCGATGGTGGAGC	60.515	66.667	0.00	0.00	0.00	4.70
1071	1082	1.687494	GCAGCAACCTCGTCGACATC	61.687	60.000	17.16	0.00	0.00	3.06
1182	1193	3.495001	GCATACTAGAAAAGGCCGATGAC	59.505	47.826	0.00	0.00	0.00	3.06
1212	1223	1.682257	GCTCTGGAGGAAGCTTGGT	59.318	57.895	2.10	0.00	0.00	3.67
1269	1280	1.792949	GTGCACTACACCAACGAAGAG	59.207	52.381	10.32	0.00	44.02	2.85
1296	1307	1.340399	CCCAGATGGCAGCAGTCCTA	61.340	60.000	5.19	0.00	0.00	2.94
1302	1313	1.639722	TGGCAGCAGTCCTACAGTTA	58.360	50.000	0.00	0.00	0.00	2.24
1317	1328	0.818296	AGTTATGCGTCGAGGAGCTT	59.182	50.000	9.75	5.30	0.00	3.74
1340	1351	2.054458	TGGTGTACCACATCGCAGT	58.946	52.632	0.00	0.00	42.01	4.40
1425	1436	9.046296	AGTATCGTATCCTGAAAATTTCATCAC	57.954	33.333	9.02	4.43	39.30	3.06
1547	1559	6.604171	TGATGCACTGGATTACTATTTGGAT	58.396	36.000	0.00	0.00	0.00	3.41
1607	1619	7.085116	ACTAGTGTAGTTTCTCAAGTTGATCG	58.915	38.462	5.91	0.00	34.86	3.69
1679	1691	9.429359	ACTTGATGTAGTGAAGTATTTTCTGAG	57.571	33.333	0.00	0.00	32.17	3.35
1785	1798	9.563748	AAGTAAACTAAACTAGTACCAATGCAA	57.436	29.630	0.00	0.00	38.26	4.08
1803	1816	7.598118	CCAATGCAAAACATACAACATTGACTA	59.402	33.333	13.49	0.00	44.38	2.59
2071	2085	1.003262	CACATTTGCCGGTTTCAGCG	61.003	55.000	1.90	0.00	39.06	5.18
2103	2117	4.775236	ACAAAGAGAAGCTGAAGTTGTCT	58.225	39.130	0.00	0.00	0.00	3.41
2279	2293	2.636403	ACTACAAACTGTGGGGGACTAC	59.364	50.000	0.00	0.00	43.12	2.73
2294	2308	2.687200	TACCCCGCTGCCAGACAT	60.687	61.111	0.00	0.00	0.00	3.06
2375	2389	2.168521	ACTACATCACAGATGGTTCGGG	59.831	50.000	11.29	0.00	0.00	5.14
2412	2426	2.299521	GAGGCTGACCACTACTACGAT	58.700	52.381	0.00	0.00	39.06	3.73
2473	2487	2.500229	CCTGCCTTCGTTTTACTTCCA	58.500	47.619	0.00	0.00	0.00	3.53
2501	2515	5.175673	GTGCTTGCCTTTTATCTTGTTGTTC	59.824	40.000	0.00	0.00	0.00	3.18
2713	2727	6.919115	GGCTGCTCTAAAGTACTAGTTATGAC	59.081	42.308	0.00	0.00	0.00	3.06
2802	2816	3.814842	TGAGAACAATCAGCACAATTCGT	59.185	39.130	0.00	0.00	0.00	3.85
2897	2911	9.667107	TGTAGCTGCTAGAAAATTAACAAGTAT	57.333	29.630	10.13	0.00	0.00	2.12
3007	3022	9.178427	GATCGGACAGTACATAATTACTACAAC	57.822	37.037	0.00	0.00	30.76	3.32
3046	3061	1.938577	TCAGTCCGTAAGCGCTACTAG	59.061	52.381	12.05	5.44	33.53	2.57
3115	3131	4.103153	TCTGAAAATGACACCAGAAGACCT	59.897	41.667	0.00	0.00	33.26	3.85
3231	3248	9.841295	AACAAAAAGTATCAGTCCAAGTTACTA	57.159	29.630	0.00	0.00	0.00	1.82
3307	3355	4.767255	CAGTCGCAGGCCCTGACC	62.767	72.222	16.85	0.27	32.44	4.02
3317	3365	0.250640	GGCCCTGACCATGCTAGATG	60.251	60.000	0.00	0.00	0.00	2.90
3349	3397	1.300233	CCGTGAGCGAATCCCTAGC	60.300	63.158	0.00	0.00	41.33	3.42
3370	3418	4.988598	CCGCACAACGCAGGACCT	62.989	66.667	0.00	0.00	42.60	3.85
3398	3458	1.003233	GGCCCACAGGTCAAGAGAC	60.003	63.158	0.00	0.00	44.21	3.36
3403	3463	1.967066	CCACAGGTCAAGAGACAGAGT	59.033	52.381	0.00	0.00	46.80	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
112	113	0.386476	TGGTCGACAGTAGCGTTTGT	59.614	50.000	18.91	0.00	0.00	2.83
224	226	0.656785	GCGTTCACGGGTGTGTTTTA	59.343	50.000	0.81	0.00	46.49	1.52
225	227	1.430228	GCGTTCACGGGTGTGTTTT	59.570	52.632	0.81	0.00	46.49	2.43
619	627	3.016031	TGATGGCATTTTACTGTCGCAT	58.984	40.909	0.00	0.00	0.00	4.73
763	771	2.455565	AACTGCTCAGTGGGTGGCT	61.456	57.895	2.97	0.00	41.58	4.75
844	852	1.632589	GGATTTGTGGGAGGCAGTTT	58.367	50.000	0.00	0.00	0.00	2.66
848	856	2.770130	GGGGATTTGTGGGAGGCA	59.230	61.111	0.00	0.00	0.00	4.75
871	879	3.571590	AGAATGGGGTTTTTGTAGTGCA	58.428	40.909	0.00	0.00	0.00	4.57
877	885	3.922375	TGGAAGAGAATGGGGTTTTTGT	58.078	40.909	0.00	0.00	0.00	2.83
884	892	2.371510	GGAGAGATGGAAGAGAATGGGG	59.628	54.545	0.00	0.00	0.00	4.96
930	941	2.028112	GTGTGTAGTGGAGATGGAAGCA	60.028	50.000	0.00	0.00	0.00	3.91
1009	1020	3.039202	GATGCTTGGCGGACGGTTG	62.039	63.158	0.00	0.00	0.00	3.77
1166	1177	1.546923	TCACGTCATCGGCCTTTTCTA	59.453	47.619	0.00	0.00	41.85	2.10
1212	1223	1.134367	CTACGATTCGGACTCTTGCCA	59.866	52.381	11.29	0.00	0.00	4.92
1269	1280	2.308722	TGCCATCTGGGGAGGTTCC	61.309	63.158	0.00	0.00	37.04	3.62
1296	1307	0.179134	GCTCCTCGACGCATAACTGT	60.179	55.000	0.00	0.00	0.00	3.55
1302	1313	2.103042	GCAAAGCTCCTCGACGCAT	61.103	57.895	0.00	0.00	0.00	4.73
1364	1375	1.341976	ACCATACAGGGCAAATGGGTC	60.342	52.381	5.63	0.00	43.73	4.46
1367	1378	4.895297	AGATAAACCATACAGGGCAAATGG	59.105	41.667	0.00	0.00	44.76	3.16
1403	1414	6.878923	AGTGTGATGAAATTTTCAGGATACGA	59.121	34.615	16.34	3.43	43.98	3.43
1404	1415	7.076842	AGTGTGATGAAATTTTCAGGATACG	57.923	36.000	16.34	0.00	43.98	3.06
1425	1436	6.231211	AGTACATCTAGTTGGGAAACAAGTG	58.769	40.000	5.80	0.00	42.57	3.16
1607	1619	8.991026	ACATCGAGTACATAGACTACACTATTC	58.009	37.037	0.00	0.00	31.68	1.75
1644	1656	6.201044	ACTTCACTACATCAAGTTCAGAAACG	59.799	38.462	0.00	0.00	40.48	3.60
1868	1882	9.739276	ATGGATGAATGTACTTCAAAAACTAGA	57.261	29.630	0.00	0.00	46.62	2.43
1917	1931	3.877559	ACAAGCGATGAATCCATGAAGA	58.122	40.909	0.00	0.00	32.09	2.87
2071	2085	5.065218	TCAGCTTCTCTTTGTCACTTTCAAC	59.935	40.000	0.00	0.00	0.00	3.18
2079	2093	4.517285	ACAACTTCAGCTTCTCTTTGTCA	58.483	39.130	0.00	0.00	0.00	3.58
2208	2222	3.525609	TGCCTTTGTAGAATGGGTGGATA	59.474	43.478	6.66	0.00	0.00	2.59
2279	2293	4.864334	GGATGTCTGGCAGCGGGG	62.864	72.222	10.34	0.00	33.59	5.73
2294	2308	0.107361	TCCTGCGTACTCGATGAGGA	60.107	55.000	0.00	0.00	39.71	3.71
2325	2339	0.394938	ACCATGACTTGTACGTGGCA	59.605	50.000	0.00	0.00	45.22	4.92
2375	2389	1.423395	CTCCCGCTCTTTCGCATATC	58.577	55.000	0.00	0.00	0.00	1.63
2473	2487	4.342092	ACAAGATAAAAGGCAAGCACAAGT	59.658	37.500	0.00	0.00	0.00	3.16
2501	2515	8.082242	CCCAACAAGAGAAAACTACTAATTTGG	58.918	37.037	0.00	0.00	0.00	3.28
2516	2530	2.241176	ACTGGTTCAACCCAACAAGAGA	59.759	45.455	3.42	0.00	37.50	3.10
2668	2682	3.380142	CCACAACGTTCCATTCAAAAGG	58.620	45.455	0.00	0.00	0.00	3.11
2713	2727	2.941891	ACGTTGTGTGATTAGTTGCG	57.058	45.000	0.00	0.00	0.00	4.85
2802	2816	6.105333	ACTTTTGAAGCATTGTTAAGCAACA	58.895	32.000	0.00	0.00	42.93	3.33
2897	2911	9.862371	TGCTTCTTAACTTTTTCATGTTTGTAA	57.138	25.926	0.00	0.00	0.00	2.41
2907	2921	6.142958	GTGTGCTGATGCTTCTTAACTTTTTC	59.857	38.462	0.88	0.00	40.48	2.29
3007	3022	6.638468	GGACTGATGCTTCTTTGTACTTTTTG	59.362	38.462	0.88	0.00	0.00	2.44
3046	3061	5.419542	TGAGTTGTACTGATAGTGCATTCC	58.580	41.667	0.74	0.00	40.42	3.01
3179	3196	4.098416	GTTCTTGTCAGTTTTGTGTGAGC	58.902	43.478	0.00	0.00	0.00	4.26
3231	3248	7.015292	TGTTTGAATCTAGTACTTGACTCCAGT	59.985	37.037	12.15	0.00	39.81	4.00
3281	3329	2.743718	CTGCGACTGACCTTGGGT	59.256	61.111	0.00	0.00	39.44	4.51
3317	3365	2.048127	ACGGGCTCGAGTTCAAGC	60.048	61.111	15.95	0.00	40.11	4.01
3398	3458	0.380733	TATACACGGCGCTCACTCTG	59.619	55.000	6.90	0.00	0.00	3.35
3403	3463	1.587876	CGCTTATACACGGCGCTCA	60.588	57.895	6.90	0.00	42.28	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.