AutoCloner

Multiple sequence alignment - TraesCS4A01G106000

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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	TraesCS4A01G106000	chr4A	100.000	2234	0	0	1	2234	120143309	120141076	0.000000e+00	4126
1	TraesCS4A01G106000	chr4D	94.053	2270	77	21	1	2234	345428734	345430981	0.000000e+00	3391
2	TraesCS4A01G106000	chr4B	94.826	1836	71	14	81	1901	427068580	427070406	0.000000e+00	2843
3	TraesCS4A01G106000	chr4B	95.882	340	13	1	1896	2234	427070491	427070830	1.170000e-152	549
4	TraesCS4A01G106000	chr7B	91.339	635	46	7	655	1281	486675355	486675988	0.000000e+00	859
5	TraesCS4A01G106000	chr2B	91.574	629	44	7	655	1275	51990482	51991109	0.000000e+00	859
6	TraesCS4A01G106000	chr1A	91.574	629	42	8	655	1275	453783256	453782631	0.000000e+00	857
7	TraesCS4A01G106000	chr5B	91.388	627	48	5	655	1275	237113741	237114367	0.000000e+00	854
8	TraesCS4A01G106000	chr5A	91.097	629	47	7	655	1275	603009450	603010077	0.000000e+00	843
9	TraesCS4A01G106000	chr3B	90.709	635	41	8	658	1275	188240159	188239526	0.000000e+00	830
10	TraesCS4A01G106000	chr1B	88.571	630	43	8	655	1275	216530918	216531527	0.000000e+00	737
11	TraesCS4A01G106000	chr7D	87.302	630	45	13	655	1275	70124957	70124354	0.000000e+00	688

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	TraesCS4A01G106000	chr4A	120141076	120143309	2233	True	4126	4126	100.000	1	2234	1	chr4A.!!$R1	2233
1	TraesCS4A01G106000	chr4D	345428734	345430981	2247	False	3391	3391	94.053	1	2234	1	chr4D.!!$F1	2233
2	TraesCS4A01G106000	chr4B	427068580	427070830	2250	False	1696	2843	95.354	81	2234	2	chr4B.!!$F1	2153
3	TraesCS4A01G106000	chr7B	486675355	486675988	633	False	859	859	91.339	655	1281	1	chr7B.!!$F1	626
4	TraesCS4A01G106000	chr2B	51990482	51991109	627	False	859	859	91.574	655	1275	1	chr2B.!!$F1	620
5	TraesCS4A01G106000	chr1A	453782631	453783256	625	True	857	857	91.574	655	1275	1	chr1A.!!$R1	620
6	TraesCS4A01G106000	chr5B	237113741	237114367	626	False	854	854	91.388	655	1275	1	chr5B.!!$F1	620
7	TraesCS4A01G106000	chr5A	603009450	603010077	627	False	843	843	91.097	655	1275	1	chr5A.!!$F1	620
8	TraesCS4A01G106000	chr3B	188239526	188240159	633	True	830	830	90.709	658	1275	1	chr3B.!!$R1	617
9	TraesCS4A01G106000	chr1B	216530918	216531527	609	False	737	737	88.571	655	1275	1	chr1B.!!$F1	620
10	TraesCS4A01G106000	chr7D	70124354	70124957	603	True	688	688	87.302	655	1275	1	chr7D.!!$R1	620

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
529	531	0.250295	CGTGCTTCTCTTGGGTTCCA	60.25	55.0	0.0	0.0	0.0	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1351	1389	1.349688	ACTGGAAATTGTAGGTCGGCA	59.65	47.619	0.0	0.0	0.0	5.69	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
45	46	7.548196	TCTACACAAAACCAAACTGTAGAAG	57.452	36.000	3.84	0.00	40.07	2.85
53	54	3.391296	ACCAAACTGTAGAAGCTCTGGAA	59.609	43.478	0.00	0.00	0.00	3.53
58	59	7.174946	CCAAACTGTAGAAGCTCTGGAAATTTA	59.825	37.037	0.00	0.00	0.00	1.40
62	63	8.734386	ACTGTAGAAGCTCTGGAAATTTAATTG	58.266	33.333	0.00	0.00	0.00	2.32
64	65	8.730680	TGTAGAAGCTCTGGAAATTTAATTGAC	58.269	33.333	0.00	0.00	0.00	3.18
72	73	7.885297	TCTGGAAATTTAATTGACTGTCTTGG	58.115	34.615	9.51	0.00	0.00	3.61
79	80	1.909700	TTGACTGTCTTGGGGAATGC	58.090	50.000	9.51	0.00	0.00	3.56
86	87	4.706962	ACTGTCTTGGGGAATGCTAATTTC	59.293	41.667	0.00	0.00	0.00	2.17
87	88	4.934356	TGTCTTGGGGAATGCTAATTTCT	58.066	39.130	0.00	0.00	0.00	2.52
144	145	1.682257	GAGAGCAAGACCTTGGCCT	59.318	57.895	3.32	1.47	40.74	5.19
145	146	0.392327	GAGAGCAAGACCTTGGCCTC	60.392	60.000	3.32	9.66	40.74	4.70
211	213	2.238521	TGGAAATGCCTTTGTCTGACC	58.761	47.619	5.17	0.00	37.63	4.02
245	247	1.947456	TGGATACAGATCTGACGACCG	59.053	52.381	29.27	0.65	46.17	4.79
255	257	1.270550	TCTGACGACCGGGTCTTAAAC	59.729	52.381	23.86	11.11	37.81	2.01
275	277	2.428890	ACGACAAGATGAGATGGTCCTC	59.571	50.000	0.00	0.00	0.00	3.71
529	531	0.250295	CGTGCTTCTCTTGGGTTCCA	60.250	55.000	0.00	0.00	0.00	3.53
547	549	6.465035	GGGTTCCATCAGATTACTAGATGCTT	60.465	42.308	0.00	0.00	38.21	3.91
602	611	5.109903	CACTACAAGCTACCCATCACTAAC	58.890	45.833	0.00	0.00	0.00	2.34
667	683	4.773149	ACCTGAAGTTACTAGGAAGTGAGG	59.227	45.833	15.29	15.29	36.36	3.86
687	707	7.065085	AGTGAGGACTATGAAAAATTCACATCG	59.935	37.037	4.40	0.00	43.48	3.84
784	808	9.699410	ATAAAAGAGGATCCAATTGATGTACAA	57.301	29.630	15.82	0.00	38.37	2.41
998	1034	7.928307	ATGTATAGATTAGCAATGCCGAAAT	57.072	32.000	0.00	0.00	0.00	2.17
1008	1044	6.822667	AGCAATGCCGAAATGATGATAATA	57.177	33.333	0.00	0.00	0.00	0.98
1026	1062	4.515028	AATAGCCCCTACCAAGGTAAAC	57.485	45.455	0.00	0.00	41.89	2.01
1238	1276	5.984725	TGAGTCACCTGAAAAGTAAGACAA	58.015	37.500	0.00	0.00	0.00	3.18
1290	1328	5.802064	TCATCGTATACAAAATTCGGCAAC	58.198	37.500	3.32	0.00	0.00	4.17
1322	1360	1.135228	GTTTTCACCGGCAAACAGTGT	60.135	47.619	16.02	0.00	33.75	3.55
1374	1412	4.196971	GCCGACCTACAATTTCCAGTTAT	58.803	43.478	0.00	0.00	0.00	1.89
1413	1451	8.445493	CGCATATCAAATTCATATGTAGCTCAA	58.555	33.333	14.48	0.00	36.81	3.02
1433	1471	6.294955	GCTCAAGAAAATCCTCCAATCAAGTT	60.295	38.462	0.00	0.00	0.00	2.66
1539	1577	9.031360	GTTACGAAATATAACATGCTCTGAGAA	57.969	33.333	9.28	0.00	33.52	2.87
1555	1593	4.882427	TCTGAGAACGACTGAATACTAGGG	59.118	45.833	0.00	0.00	0.00	3.53
1629	1667	9.129532	AGGAATCACATATCCTTTTCTTTCATC	57.870	33.333	0.00	0.00	43.59	2.92
1630	1668	9.129532	GGAATCACATATCCTTTTCTTTCATCT	57.870	33.333	0.00	0.00	32.75	2.90
1647	1685	7.508636	TCTTTCATCTCTCTGCTGGATAATAGT	59.491	37.037	0.00	0.00	0.00	2.12
1648	1686	6.587206	TCATCTCTCTGCTGGATAATAGTG	57.413	41.667	0.00	0.00	0.00	2.74
1658	1696	4.443457	GCTGGATAATAGTGCTGGAGTTCA	60.443	45.833	0.00	0.00	0.00	3.18
1731	1793	4.439153	GGTGTACTGGATGTTTCGTCGATA	60.439	45.833	0.00	0.00	0.00	2.92
1732	1794	5.279384	GTGTACTGGATGTTTCGTCGATAT	58.721	41.667	0.00	0.00	0.00	1.63
1733	1795	5.747197	GTGTACTGGATGTTTCGTCGATATT	59.253	40.000	0.00	0.00	0.00	1.28
1930	2083	7.708998	TGAAACCTTTTACATACTGTTTCACC	58.291	34.615	10.54	0.00	43.68	4.02
2011	2167	9.802039	AGGTTACTGTTCCACTTCAAAATAATA	57.198	29.630	4.93	0.00	0.00	0.98
2137	2293	5.410355	ACTATGCGTAACAGGACCTTTTA	57.590	39.130	0.00	0.00	0.00	1.52
2146	2302	7.624974	GCGTAACAGGACCTTTTAAATCTAACC	60.625	40.741	1.57	0.00	0.00	2.85
2148	2304	6.208840	ACAGGACCTTTTAAATCTAACCCA	57.791	37.500	0.00	0.00	0.00	4.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	8.734386	CAATTAAATTTCCAGAGCTTCTACAGT	58.266	33.333	0.00	0.00	0.00	3.55
37	38	8.950210	TCAATTAAATTTCCAGAGCTTCTACAG	58.050	33.333	0.00	0.00	0.00	2.74
45	46	7.150783	AGACAGTCAATTAAATTTCCAGAGC	57.849	36.000	2.66	0.00	0.00	4.09
53	54	7.614494	CATTCCCCAAGACAGTCAATTAAATT	58.386	34.615	2.66	0.00	0.00	1.82
58	59	2.827921	GCATTCCCCAAGACAGTCAATT	59.172	45.455	2.66	0.00	0.00	2.32
62	63	3.350219	TTAGCATTCCCCAAGACAGTC	57.650	47.619	0.00	0.00	0.00	3.51
64	65	4.952335	AGAAATTAGCATTCCCCAAGACAG	59.048	41.667	0.00	0.00	0.00	3.51
72	73	5.904362	AACACTGAGAAATTAGCATTCCC	57.096	39.130	0.00	0.00	0.00	3.97
86	87	7.166638	CGATGCTAGTCTACAATTAACACTGAG	59.833	40.741	0.00	0.00	0.00	3.35
87	88	6.972901	CGATGCTAGTCTACAATTAACACTGA	59.027	38.462	0.00	0.00	0.00	3.41
144	145	7.939039	ACTTCTCATCCTTTAAACATTGAGTGA	59.061	33.333	12.66	6.14	33.88	3.41
145	146	8.103948	ACTTCTCATCCTTTAAACATTGAGTG	57.896	34.615	12.66	10.47	33.88	3.51
240	242	0.039256	TGTCGTTTAAGACCCGGTCG	60.039	55.000	12.04	0.00	40.26	4.79
245	247	4.817517	TCTCATCTTGTCGTTTAAGACCC	58.182	43.478	0.00	0.00	40.26	4.46
255	257	2.428530	TGAGGACCATCTCATCTTGTCG	59.571	50.000	0.00	0.00	38.70	4.35
295	297	5.066246	AGTTAGACTCTTAGACGGAATTCGG	59.934	44.000	11.17	11.17	44.45	4.30
297	299	7.983307	TGTAGTTAGACTCTTAGACGGAATTC	58.017	38.462	0.00	0.00	0.00	2.17
335	337	2.507484	TGGAGGCATCAAAACAGAGTG	58.493	47.619	0.00	0.00	0.00	3.51
391	393	9.700831	AGCAATTCAACTTACCTTATTTCCTAT	57.299	29.630	0.00	0.00	0.00	2.57
392	394	9.528489	AAGCAATTCAACTTACCTTATTTCCTA	57.472	29.630	0.00	0.00	0.00	2.94
529	531	6.351711	TGTGCAAAGCATCTAGTAATCTGAT	58.648	36.000	0.00	0.00	41.91	2.90
547	549	0.953727	GAGCAAGTGGACATGTGCAA	59.046	50.000	22.48	3.45	39.50	4.08
614	630	4.271049	GTGTGACCAACGGATCATCTAATG	59.729	45.833	0.00	0.00	0.00	1.90
667	683	6.677781	TCCCGATGTGAATTTTTCATAGTC	57.322	37.500	0.00	0.00	42.47	2.59
760	784	7.671398	ACTTGTACATCAATTGGATCCTCTTTT	59.329	33.333	14.23	0.00	35.35	2.27
784	808	7.069826	TCCTTCATTTTGGTGATTTTCTTCACT	59.930	33.333	4.75	0.00	44.39	3.41
998	1034	4.536090	CCTTGGTAGGGGCTATTATCATCA	59.464	45.833	0.00	0.00	37.94	3.07
1008	1044	0.997363	GGTTTACCTTGGTAGGGGCT	59.003	55.000	0.00	0.00	46.58	5.19
1026	1062	0.754957	TGTTGTGGACAAGCCCAAGG	60.755	55.000	0.00	0.00	38.06	3.61
1217	1254	6.650120	TCTTTGTCTTACTTTTCAGGTGACT	58.350	36.000	0.00	0.00	46.44	3.41
1238	1276	5.916318	TGTTTGCAGGTTGAATCATTTCTT	58.084	33.333	0.00	0.00	32.78	2.52
1290	1328	3.316283	CGGTGAAAACATCCACATTTGG	58.684	45.455	0.00	0.00	45.56	3.28
1351	1389	1.349688	ACTGGAAATTGTAGGTCGGCA	59.650	47.619	0.00	0.00	0.00	5.69
1355	1393	7.865706	ATGACATAACTGGAAATTGTAGGTC	57.134	36.000	0.00	0.00	0.00	3.85
1374	1412	7.910441	ATTTGATATGCGATGATGTATGACA	57.090	32.000	0.00	0.00	0.00	3.58
1413	1451	6.983906	AACAACTTGATTGGAGGATTTTCT	57.016	33.333	0.00	0.00	43.20	2.52
1539	1577	5.692928	AGTATGACCCTAGTATTCAGTCGT	58.307	41.667	0.00	0.00	0.00	4.34
1629	1667	4.558178	CAGCACTATTATCCAGCAGAGAG	58.442	47.826	0.00	0.00	0.00	3.20
1630	1668	3.323115	CCAGCACTATTATCCAGCAGAGA	59.677	47.826	0.00	0.00	0.00	3.10
1647	1685	2.356125	GCTCCCTTATTGAACTCCAGCA	60.356	50.000	0.00	0.00	0.00	4.41
1648	1686	2.092699	AGCTCCCTTATTGAACTCCAGC	60.093	50.000	0.00	0.00	0.00	4.85
1709	1771	2.937591	TCGACGAAACATCCAGTACAC	58.062	47.619	0.00	0.00	0.00	2.90
2011	2167	2.109834	TGGACCACCACTTCCATTCAAT	59.890	45.455	0.00	0.00	41.77	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.