AutoCloner

Multiple sequence alignment - TraesCS5B01G190900

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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	TraesCS5B01G190900	chr5B	100.000	2786	0	0	1	2786	344629966	344632751	0	5145
1	TraesCS5B01G190900	chr5B	97.236	1664	25	4	2	1663	82189942	82188298	0	2798
2	TraesCS5B01G190900	chr5B	97.115	1525	40	3	2	1525	443102767	443101246	0	2569
3	TraesCS5B01G190900	chr5B	98.422	1014	16	0	1773	2786	82176590	82175577	0	1784
4	TraesCS5B01G190900	chr5B	98.323	1014	17	0	1773	2786	443096501	443095488	0	1779
5	TraesCS5B01G190900	chrUn	98.646	1772	21	2	2	1772	15876322	15874553	0	3136
6	TraesCS5B01G190900	chrUn	99.014	1014	10	0	1773	2786	15872626	15871613	0	1818
7	TraesCS5B01G190900	chr4B	98.031	1270	24	1	503	1772	74330788	74332056	0	2206
8	TraesCS5B01G190900	chr4B	97.480	1270	30	1	503	1772	635891517	635892784	0	2167
9	TraesCS5B01G190900	chr4B	97.239	1014	28	0	1773	2786	74335766	74336779	0	1718
10	TraesCS5B01G190900	chr7B	97.799	1272	24	3	503	1772	688939657	688940926	0	2191
11	TraesCS5B01G190900	chr2B	97.874	1270	19	5	503	1772	408281285	408280024	0	2189
12	TraesCS5B01G190900	chr2B	97.482	1271	27	4	503	1772	571306518	571305252	0	2165
13	TraesCS5B01G190900	chr2B	97.929	1014	20	1	1773	2786	200684575	200683563	0	1755
14	TraesCS5B01G190900	chr2B	97.649	808	15	3	2	809	200689183	200688380	0	1384
15	TraesCS5B01G190900	chr2B	94.504	746	33	4	2	739	548109215	548109960	0	1144
16	TraesCS5B01G190900	chr4A	97.874	1270	15	5	503	1772	667698472	667697215	0	2185
17	TraesCS5B01G190900	chr4A	99.014	1014	10	0	1773	2786	667695133	667694120	0	1818
18	TraesCS5B01G190900	chr3B	98.225	1014	18	0	1773	2786	485245986	485246999	0	1773
19	TraesCS5B01G190900	chr3B	97.535	1014	25	0	1773	2786	823971105	823970092	0	1735
20	TraesCS5B01G190900	chr3B	97.164	811	17	3	2	809	161305118	161304311	0	1365
21	TraesCS5B01G190900	chr3B	97.425	699	16	2	2	699	823973615	823972918	0	1190
22	TraesCS5B01G190900	chr1B	98.028	1014	20	0	1773	2786	324871960	324872973	0	1762
23	TraesCS5B01G190900	chr1B	97.564	698	17	0	2	699	324865208	324865905	0	1195
24	TraesCS5B01G190900	chr6B	96.084	715	25	3	2	714	708345804	708345091	0	1162

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	TraesCS5B01G190900	chr5B	344629966	344632751	2785	False	5145.0	5145	100.000	1	2786	1	chr5B.!!$F1	2785
1	TraesCS5B01G190900	chr5B	82188298	82189942	1644	True	2798.0	2798	97.236	2	1663	1	chr5B.!!$R2	1661
2	TraesCS5B01G190900	chr5B	443101246	443102767	1521	True	2569.0	2569	97.115	2	1525	1	chr5B.!!$R4	1523
3	TraesCS5B01G190900	chr5B	82175577	82176590	1013	True	1784.0	1784	98.422	1773	2786	1	chr5B.!!$R1	1013
4	TraesCS5B01G190900	chr5B	443095488	443096501	1013	True	1779.0	1779	98.323	1773	2786	1	chr5B.!!$R3	1013
5	TraesCS5B01G190900	chrUn	15871613	15876322	4709	True	2477.0	3136	98.830	2	2786	2	chrUn.!!$R1	2784
6	TraesCS5B01G190900	chr4B	635891517	635892784	1267	False	2167.0	2167	97.480	503	1772	1	chr4B.!!$F1	1269
7	TraesCS5B01G190900	chr4B	74330788	74336779	5991	False	1962.0	2206	97.635	503	2786	2	chr4B.!!$F2	2283
8	TraesCS5B01G190900	chr7B	688939657	688940926	1269	False	2191.0	2191	97.799	503	1772	1	chr7B.!!$F1	1269
9	TraesCS5B01G190900	chr2B	408280024	408281285	1261	True	2189.0	2189	97.874	503	1772	1	chr2B.!!$R1	1269
10	TraesCS5B01G190900	chr2B	571305252	571306518	1266	True	2165.0	2165	97.482	503	1772	1	chr2B.!!$R2	1269
11	TraesCS5B01G190900	chr2B	200683563	200689183	5620	True	1569.5	1755	97.789	2	2786	2	chr2B.!!$R3	2784
12	TraesCS5B01G190900	chr2B	548109215	548109960	745	False	1144.0	1144	94.504	2	739	1	chr2B.!!$F1	737
13	TraesCS5B01G190900	chr4A	667694120	667698472	4352	True	2001.5	2185	98.444	503	2786	2	chr4A.!!$R1	2283
14	TraesCS5B01G190900	chr3B	485245986	485246999	1013	False	1773.0	1773	98.225	1773	2786	1	chr3B.!!$F1	1013
15	TraesCS5B01G190900	chr3B	823970092	823973615	3523	True	1462.5	1735	97.480	2	2786	2	chr3B.!!$R2	2784
16	TraesCS5B01G190900	chr3B	161304311	161305118	807	True	1365.0	1365	97.164	2	809	1	chr3B.!!$R1	807
17	TraesCS5B01G190900	chr1B	324871960	324872973	1013	False	1762.0	1762	98.028	1773	2786	1	chr1B.!!$F2	1013
18	TraesCS5B01G190900	chr1B	324865208	324865905	697	False	1195.0	1195	97.564	2	699	1	chr1B.!!$F1	697
19	TraesCS5B01G190900	chr6B	708345091	708345804	713	True	1162.0	1162	96.084	2	714	1	chr6B.!!$R1	712

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
247	251	1.687563	CGGGAGTTTGGTGGAGTTTT	58.312	50.000	0.00	0.0	0.00	2.43	F
492	496	2.696707	TGCTCCGGTAATATTTCGGACT	59.303	45.455	21.23	0.0	46.48	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1355	1628	1.303317	GGATCGTTGCCACCTTGGT	60.303	57.895	0.00	0.00	40.46	3.67	R
2249	7029	2.190841	TCAGTGACGACGTCTGGCA	61.191	57.895	26.86	12.71	33.15	4.92	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
247	251	1.687563	CGGGAGTTTGGTGGAGTTTT	58.312	50.000	0.00	0.00	0.00	2.43
417	421	5.221541	TGGTGAGCATTTTATTTTCCCGTTT	60.222	36.000	0.00	0.00	0.00	3.60
418	422	5.699001	GGTGAGCATTTTATTTTCCCGTTTT	59.301	36.000	0.00	0.00	0.00	2.43
419	423	6.347321	GGTGAGCATTTTATTTTCCCGTTTTG	60.347	38.462	0.00	0.00	0.00	2.44
423	427	7.217906	AGCATTTTATTTTCCCGTTTTGGTTA	58.782	30.769	0.00	0.00	35.15	2.85
424	428	7.386573	AGCATTTTATTTTCCCGTTTTGGTTAG	59.613	33.333	0.00	0.00	35.15	2.34
425	429	7.514805	CATTTTATTTTCCCGTTTTGGTTAGC	58.485	34.615	0.00	0.00	35.15	3.09
426	430	5.786264	TTATTTTCCCGTTTTGGTTAGCA	57.214	34.783	0.00	0.00	35.15	3.49
430	434	4.674281	TTCCCGTTTTGGTTAGCATTTT	57.326	36.364	0.00	0.00	35.15	1.82
431	435	5.786264	TTCCCGTTTTGGTTAGCATTTTA	57.214	34.783	0.00	0.00	35.15	1.52
432	436	5.986501	TCCCGTTTTGGTTAGCATTTTAT	57.013	34.783	0.00	0.00	35.15	1.40
437	441	8.030106	CCCGTTTTGGTTAGCATTTTATTTAGA	58.970	33.333	0.00	0.00	35.15	2.10
438	442	9.581099	CCGTTTTGGTTAGCATTTTATTTAGAT	57.419	29.630	0.00	0.00	0.00	1.98
456	460	4.685169	AGATGTCAACTAATTGGTTGCG	57.315	40.909	25.17	7.59	44.19	4.85
460	464	5.752892	TGTCAACTAATTGGTTGCGTAAA	57.247	34.783	25.17	8.94	44.19	2.01
461	465	6.132791	TGTCAACTAATTGGTTGCGTAAAA	57.867	33.333	25.17	8.29	44.19	1.52
463	467	7.203910	TGTCAACTAATTGGTTGCGTAAAAAT	58.796	30.769	25.17	0.00	44.19	1.82
464	468	7.168302	TGTCAACTAATTGGTTGCGTAAAAATG	59.832	33.333	25.17	3.64	44.19	2.32
468	472	7.649973	ACTAATTGGTTGCGTAAAAATGTGTA	58.350	30.769	0.00	0.00	0.00	2.90
469	473	7.806014	ACTAATTGGTTGCGTAAAAATGTGTAG	59.194	33.333	0.00	0.00	0.00	2.74
470	474	5.502153	TTGGTTGCGTAAAAATGTGTAGT	57.498	34.783	0.00	0.00	0.00	2.73
471	475	5.502153	TGGTTGCGTAAAAATGTGTAGTT	57.498	34.783	0.00	0.00	0.00	2.24
472	476	5.274718	TGGTTGCGTAAAAATGTGTAGTTG	58.725	37.500	0.00	0.00	0.00	3.16
473	477	4.147479	GGTTGCGTAAAAATGTGTAGTTGC	59.853	41.667	0.00	0.00	0.00	4.17
474	478	4.822036	TGCGTAAAAATGTGTAGTTGCT	57.178	36.364	0.00	0.00	0.00	3.91
475	479	4.778904	TGCGTAAAAATGTGTAGTTGCTC	58.221	39.130	0.00	0.00	0.00	4.26
476	480	4.156182	GCGTAAAAATGTGTAGTTGCTCC	58.844	43.478	0.00	0.00	0.00	4.70
481	485	3.688694	AATGTGTAGTTGCTCCGGTAA	57.311	42.857	0.00	0.00	0.00	2.85
483	487	5.347620	AATGTGTAGTTGCTCCGGTAATA	57.652	39.130	0.00	0.00	0.00	0.98
484	488	5.546621	ATGTGTAGTTGCTCCGGTAATAT	57.453	39.130	0.00	0.00	0.00	1.28
485	489	5.347620	TGTGTAGTTGCTCCGGTAATATT	57.652	39.130	0.00	0.00	0.00	1.28
488	492	5.045215	TGTAGTTGCTCCGGTAATATTTCG	58.955	41.667	0.00	0.00	0.00	3.46
491	495	3.102052	TGCTCCGGTAATATTTCGGAC	57.898	47.619	21.23	18.36	46.48	4.79
492	496	2.696707	TGCTCCGGTAATATTTCGGACT	59.303	45.455	21.23	0.00	46.48	3.85
497	501	6.696148	GCTCCGGTAATATTTCGGACTATATG	59.304	42.308	21.23	14.55	46.48	1.78
498	502	7.415989	GCTCCGGTAATATTTCGGACTATATGA	60.416	40.741	21.23	6.21	46.48	2.15
499	503	8.352137	TCCGGTAATATTTCGGACTATATGAA	57.648	34.615	21.23	4.30	46.48	2.57
500	504	8.974238	TCCGGTAATATTTCGGACTATATGAAT	58.026	33.333	21.23	0.00	46.48	2.57
631	697	6.067263	TGTGTAAAAATGTGTAGTTGCTCC	57.933	37.500	0.00	0.00	0.00	4.70
641	707	5.113383	TGTGTAGTTGCTCCGGTAATATTG	58.887	41.667	0.00	0.00	0.00	1.90
642	708	4.025145	GTGTAGTTGCTCCGGTAATATTGC	60.025	45.833	0.00	0.00	0.00	3.56
1355	1628	0.036732	GGGGTCACTGCACATGAAGA	59.963	55.000	0.00	0.00	0.00	2.87
1511	1785	4.547671	CAGAATAGTCAGGTAGAAGGGGA	58.452	47.826	0.00	0.00	0.00	4.81

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
332	336	4.235939	ACAATAATTGCACGCAACTTCA	57.764	36.364	6.60	0.00	38.88	3.02
442	446	6.981559	ACACATTTTTACGCAACCAATTAGTT	59.018	30.769	0.00	0.00	0.00	2.24
444	448	7.806014	ACTACACATTTTTACGCAACCAATTAG	59.194	33.333	0.00	0.00	0.00	1.73
446	450	6.508777	ACTACACATTTTTACGCAACCAATT	58.491	32.000	0.00	0.00	0.00	2.32
448	452	5.502153	ACTACACATTTTTACGCAACCAA	57.498	34.783	0.00	0.00	0.00	3.67
449	453	5.274718	CAACTACACATTTTTACGCAACCA	58.725	37.500	0.00	0.00	0.00	3.67
450	454	4.147479	GCAACTACACATTTTTACGCAACC	59.853	41.667	0.00	0.00	0.00	3.77
453	457	4.319911	GGAGCAACTACACATTTTTACGCA	60.320	41.667	0.00	0.00	0.00	5.24
454	458	4.156182	GGAGCAACTACACATTTTTACGC	58.844	43.478	0.00	0.00	0.00	4.42
455	459	4.391358	CGGAGCAACTACACATTTTTACG	58.609	43.478	0.00	0.00	0.00	3.18
456	460	4.214758	ACCGGAGCAACTACACATTTTTAC	59.785	41.667	9.46	0.00	0.00	2.01
460	464	2.561478	ACCGGAGCAACTACACATTT	57.439	45.000	9.46	0.00	0.00	2.32
461	465	3.688694	TTACCGGAGCAACTACACATT	57.311	42.857	9.46	0.00	0.00	2.71
463	467	5.347620	AATATTACCGGAGCAACTACACA	57.652	39.130	9.46	0.00	0.00	3.72
464	468	5.051240	CGAAATATTACCGGAGCAACTACAC	60.051	44.000	9.46	0.00	0.00	2.90
468	472	3.133362	TCCGAAATATTACCGGAGCAACT	59.867	43.478	21.13	0.00	46.17	3.16
469	473	3.460103	TCCGAAATATTACCGGAGCAAC	58.540	45.455	21.13	0.00	46.17	4.17
470	474	3.823281	TCCGAAATATTACCGGAGCAA	57.177	42.857	21.13	0.00	46.17	3.91
497	501	9.990888	CGTTTACTACTCGAGCAAATAATATTC	57.009	33.333	13.61	0.00	0.00	1.75
498	502	9.525409	ACGTTTACTACTCGAGCAAATAATATT	57.475	29.630	13.61	0.00	0.00	1.28
501	505	8.915871	TTACGTTTACTACTCGAGCAAATAAT	57.084	30.769	13.61	0.00	0.00	1.28
502	506	8.741101	TTTACGTTTACTACTCGAGCAAATAA	57.259	30.769	13.61	3.70	0.00	1.40
504	508	7.823149	ATTTACGTTTACTACTCGAGCAAAT	57.177	32.000	13.61	0.00	0.00	2.32
505	509	8.915871	ATATTTACGTTTACTACTCGAGCAAA	57.084	30.769	13.61	5.22	0.00	3.68
602	668	9.458374	GCAACTACACATTTTTACACAACTAAT	57.542	29.630	0.00	0.00	0.00	1.73
609	675	5.144359	CGGAGCAACTACACATTTTTACAC	58.856	41.667	0.00	0.00	0.00	2.90
631	697	7.654568	TCCATATATAGTCCGCAATATTACCG	58.345	38.462	0.00	0.00	0.00	4.02
641	707	6.452494	AGTACACATCCATATATAGTCCGC	57.548	41.667	0.00	0.00	0.00	5.54
983	1253	3.452627	AGACATCTCGGCTCACCTATTTT	59.547	43.478	0.00	0.00	0.00	1.82
1355	1628	1.303317	GGATCGTTGCCACCTTGGT	60.303	57.895	0.00	0.00	40.46	3.67
1511	1785	5.350633	CATTGTATTCACCATCGGCATTTT	58.649	37.500	0.00	0.00	0.00	1.82
2249	7029	2.190841	TCAGTGACGACGTCTGGCA	61.191	57.895	26.86	12.71	33.15	4.92
2420	7200	6.163476	TGTTGTACGAGCATTCTGTTCTATT	58.837	36.000	0.00	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.