AutoCloner

Multiple sequence alignment - TraesCS6A01G074500

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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	TraesCS6A01G074500	chr6A	100.000	2639	0	0	1	2639	42646563	42643925	0.000000e+00	4874
1	TraesCS6A01G074500	chr6A	96.457	988	32	2	41	1026	42581922	42580936	0.000000e+00	1628
2	TraesCS6A01G074500	chr6A	96.457	988	32	2	41	1026	42617572	42616586	0.000000e+00	1628
3	TraesCS6A01G074500	chr6A	96.247	986	34	2	41	1024	42330004	42329020	0.000000e+00	1613
4	TraesCS6A01G074500	chr6A	96.247	986	34	2	41	1024	42552653	42551669	0.000000e+00	1613
5	TraesCS6A01G074500	chr6A	96.053	988	36	2	41	1026	42362929	42361943	0.000000e+00	1605
6	TraesCS6A01G074500	chr6A	95.450	989	37	7	41	1024	42507907	42506922	0.000000e+00	1570
7	TraesCS6A01G074500	chr6A	96.150	961	37	0	1679	2639	42523601	42522641	0.000000e+00	1570
8	TraesCS6A01G074500	chr6A	95.859	966	34	5	62	1024	42530294	42529332	0.000000e+00	1557
9	TraesCS6A01G074500	chr6A	95.838	961	40	0	1679	2639	42323289	42322329	0.000000e+00	1554
10	TraesCS6A01G074500	chr6A	95.630	961	42	0	1679	2639	42545937	42544977	0.000000e+00	1543
11	TraesCS6A01G074500	chr6A	98.812	589	7	0	2051	2639	42576160	42575572	0.000000e+00	1050
12	TraesCS6A01G074500	chr6A	98.472	589	9	0	2051	2639	42357166	42356578	0.000000e+00	1038
13	TraesCS6A01G074500	chr6A	98.472	589	9	0	2051	2639	42611810	42611222	0.000000e+00	1038
14	TraesCS6A01G074500	chr6A	95.177	622	27	3	1	621	42293949	42293330	0.000000e+00	979
15	TraesCS6A01G074500	chr6A	95.404	544	25	0	1021	1564	42524156	42523613	0.000000e+00	867
16	TraesCS6A01G074500	chr6A	95.221	544	26	0	1021	1564	42323844	42323301	0.000000e+00	861
17	TraesCS6A01G074500	chr6A	95.037	544	27	0	1021	1564	42546493	42545950	0.000000e+00	856
18	TraesCS6A01G074500	chr2A	87.951	2050	212	11	622	2639	756213309	756211263	0.000000e+00	2385
19	TraesCS6A01G074500	chr4A	84.308	2052	284	18	622	2639	544592777	544594824	0.000000e+00	1971
20	TraesCS6A01G074500	chr7A	84.405	2052	254	37	620	2639	126916795	126914778	0.000000e+00	1956
21	TraesCS6A01G074500	chrUn	96.457	988	32	2	41	1026	331978552	331977566	0.000000e+00	1628
22	TraesCS6A01G074500	chr1D	78.916	166	35	0	1000	1165	78402595	78402430	2.150000e-21	113
23	TraesCS6A01G074500	chr2D	79.141	163	33	1	997	1159	534496543	534496704	7.720000e-21	111

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	TraesCS6A01G074500	chr6A	42643925	42646563	2638	True	4874.0	4874	100.0000	1	2639	1	chr6A.!!$R12	2638
1	TraesCS6A01G074500	chr6A	42580936	42581922	986	True	1628.0	1628	96.4570	41	1026	1	chr6A.!!$R9	985
2	TraesCS6A01G074500	chr6A	42616586	42617572	986	True	1628.0	1628	96.4570	41	1026	1	chr6A.!!$R11	985
3	TraesCS6A01G074500	chr6A	42329020	42330004	984	True	1613.0	1613	96.2470	41	1024	1	chr6A.!!$R2	983
4	TraesCS6A01G074500	chr6A	42551669	42552653	984	True	1613.0	1613	96.2470	41	1024	1	chr6A.!!$R7	983
5	TraesCS6A01G074500	chr6A	42361943	42362929	986	True	1605.0	1605	96.0530	41	1026	1	chr6A.!!$R4	985
6	TraesCS6A01G074500	chr6A	42506922	42507907	985	True	1570.0	1570	95.4500	41	1024	1	chr6A.!!$R5	983
7	TraesCS6A01G074500	chr6A	42529332	42530294	962	True	1557.0	1557	95.8590	62	1024	1	chr6A.!!$R6	962
8	TraesCS6A01G074500	chr6A	42522641	42524156	1515	True	1218.5	1570	95.7770	1021	2639	2	chr6A.!!$R14	1618
9	TraesCS6A01G074500	chr6A	42322329	42323844	1515	True	1207.5	1554	95.5295	1021	2639	2	chr6A.!!$R13	1618
10	TraesCS6A01G074500	chr6A	42544977	42546493	1516	True	1199.5	1543	95.3335	1021	2639	2	chr6A.!!$R15	1618
11	TraesCS6A01G074500	chr6A	42575572	42576160	588	True	1050.0	1050	98.8120	2051	2639	1	chr6A.!!$R8	588
12	TraesCS6A01G074500	chr6A	42356578	42357166	588	True	1038.0	1038	98.4720	2051	2639	1	chr6A.!!$R3	588
13	TraesCS6A01G074500	chr6A	42611222	42611810	588	True	1038.0	1038	98.4720	2051	2639	1	chr6A.!!$R10	588
14	TraesCS6A01G074500	chr6A	42293330	42293949	619	True	979.0	979	95.1770	1	621	1	chr6A.!!$R1	620
15	TraesCS6A01G074500	chr2A	756211263	756213309	2046	True	2385.0	2385	87.9510	622	2639	1	chr2A.!!$R1	2017
16	TraesCS6A01G074500	chr4A	544592777	544594824	2047	False	1971.0	1971	84.3080	622	2639	1	chr4A.!!$F1	2017
17	TraesCS6A01G074500	chr7A	126914778	126916795	2017	True	1956.0	1956	84.4050	620	2639	1	chr7A.!!$R1	2019
18	TraesCS6A01G074500	chrUn	331977566	331978552	986	True	1628.0	1628	96.4570	41	1026	1	chrUn.!!$R1	985

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
108	110	0.927029	AGGGGCAAGAATAAGGGGAC	59.073	55.0	0.0	0.0	0.00	4.46	F
1338	1346	0.111061	AGGACCAGATTGTTGCTGCA	59.889	50.0	0.0	0.0	32.06	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1341	1349	0.682209	GGTGCCATCCAGCTTGATGT	60.682	55.000	22.41	0.0	40.43	3.06	R
2448	2512	2.107750	CATCCCGCTGCTCATCGT	59.892	61.111	0.00	0.0	0.00	3.73	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
108	110	0.927029	AGGGGCAAGAATAAGGGGAC	59.073	55.000	0.00	0.00	0.00	4.46
159	163	4.564041	AGAATTTGTTTGTGTGTGTGCAA	58.436	34.783	0.00	0.00	0.00	4.08
189	193	9.180678	CTATTTAATTTGTCTGTGTGGTGTTTC	57.819	33.333	0.00	0.00	0.00	2.78
214	218	7.829211	TCCTCTTGGTTCGATAAATCTTGATTT	59.171	33.333	12.42	12.42	34.23	2.17
305	309	2.026822	CACAAGTAACAGAGGCCCTCAT	60.027	50.000	14.46	1.03	32.06	2.90
387	391	2.194889	TACCTCACGTGTGCGACCA	61.195	57.895	16.51	0.00	42.00	4.02
413	417	1.832883	CCAAATGACAATGGACCCGA	58.167	50.000	4.96	0.00	39.12	5.14
429	433	2.430367	GAGAGCACCCCAACGGTT	59.570	61.111	0.00	0.00	45.36	4.44
903	908	1.072266	AATGTCCACTAGCCCAACCA	58.928	50.000	0.00	0.00	0.00	3.67
960	968	1.156736	CCATTCCCGTCTTGACACAC	58.843	55.000	1.59	0.00	0.00	3.82
1118	1126	0.676782	GCTAGGACCGGCAACAATGT	60.677	55.000	0.00	0.00	0.00	2.71
1264	1272	7.411480	CGAGTATGCGTTTTATCTTTTGTCAGA	60.411	37.037	0.00	0.00	0.00	3.27
1267	1275	6.371809	TGCGTTTTATCTTTTGTCAGACTT	57.628	33.333	1.31	0.00	0.00	3.01
1284	1292	3.865745	AGACTTGTCAGTGTCGTTTCTTG	59.134	43.478	3.49	0.00	38.16	3.02
1285	1293	3.857052	ACTTGTCAGTGTCGTTTCTTGA	58.143	40.909	0.00	0.00	0.00	3.02
1295	1303	3.687212	TGTCGTTTCTTGAAGTTTCAGCA	59.313	39.130	0.00	0.00	38.61	4.41
1338	1346	0.111061	AGGACCAGATTGTTGCTGCA	59.889	50.000	0.00	0.00	32.06	4.41
1341	1349	1.337703	GACCAGATTGTTGCTGCACAA	59.662	47.619	16.07	16.07	40.92	3.33
1362	1370	2.578586	ATCAAGCTGGATGGCACCCC	62.579	60.000	1.69	0.00	34.17	4.95
1388	1396	2.360165	GGCATGGATTCACAGTTCATCC	59.640	50.000	0.00	1.78	37.57	3.51
1390	1398	3.698040	GCATGGATTCACAGTTCATCCTT	59.302	43.478	8.65	1.35	37.88	3.36
1574	1630	1.968017	CAGTTGCCGTGCTCATGGT	60.968	57.895	9.62	0.00	39.68	3.55
1600	1656	1.601903	TCAACATGTTGCTCACCGTTC	59.398	47.619	29.84	0.00	40.24	3.95
1634	1690	3.432252	GTCGTGCTTGCTATGTACTTTGT	59.568	43.478	0.00	0.00	0.00	2.83
1669	1725	0.376152	GTGTGGATGAATCGCAGCTG	59.624	55.000	10.11	10.11	32.29	4.24
1673	1729	1.647629	GATGAATCGCAGCTGCTGG	59.352	57.895	34.22	21.04	39.32	4.85
1687	1744	0.963225	TGCTGGTGCGTAGTAGTTCA	59.037	50.000	0.00	0.00	43.34	3.18
1688	1745	1.548719	TGCTGGTGCGTAGTAGTTCAT	59.451	47.619	0.00	0.00	43.34	2.57
1714	1771	8.871629	TTAGGTTGGATTAATTGTAAGCAAGA	57.128	30.769	10.18	0.00	38.10	3.02
1809	1868	6.639632	ATTAGCATTTTCTATGGAACGCAT	57.360	33.333	8.97	0.00	0.00	4.73
1873	1937	5.649782	ATACCAGTTTGAGCAATTCTTGG	57.350	39.130	0.00	0.00	0.00	3.61
1927	1991	9.256477	CCATAATAAAGACATTTACGCTAGACA	57.744	33.333	0.00	0.00	33.78	3.41
2448	2512	4.286291	TCATAGATCGGAGTCTGGTAGCTA	59.714	45.833	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
108	110	0.321653	ACAAGGCAAGGGAGCGTAAG	60.322	55.000	0.00	0.00	43.44	2.34
159	163	8.514594	CACCACACAGACAAATTAAATAGTCAT	58.485	33.333	0.00	0.00	33.56	3.06
189	193	7.559590	AATCAAGATTTATCGAACCAAGAGG	57.440	36.000	0.00	0.00	42.21	3.69
214	218	8.090788	AGCAGATAGTATTTCCCTCAGTTAAA	57.909	34.615	0.00	0.00	0.00	1.52
305	309	1.102154	CTGTTTCCACTGTTGTGCCA	58.898	50.000	0.00	0.00	42.54	4.92
312	316	3.762288	TCGTAGCTATCTGTTTCCACTGT	59.238	43.478	0.00	0.00	0.00	3.55
316	320	2.693591	CCCTCGTAGCTATCTGTTTCCA	59.306	50.000	0.00	0.00	0.00	3.53
387	391	0.602562	CATTGTCATTTGGCGGTGGT	59.397	50.000	0.00	0.00	0.00	4.16
429	433	1.537889	AAGGGTCCATGACGGGTGA	60.538	57.895	0.00	0.00	32.65	4.02
777	782	0.034756	CGTCCATCTGTCCCACAACA	59.965	55.000	0.00	0.00	0.00	3.33
782	787	3.399181	GCCCGTCCATCTGTCCCA	61.399	66.667	0.00	0.00	0.00	4.37
903	908	1.207791	GAGGTGGATGAGGTGGTGAT	58.792	55.000	0.00	0.00	0.00	3.06
942	950	1.800586	CAGTGTGTCAAGACGGGAATG	59.199	52.381	0.00	0.00	0.00	2.67
949	957	1.001268	TCGAGCTCAGTGTGTCAAGAC	60.001	52.381	15.40	0.00	0.00	3.01
960	968	1.078918	TGGGCAATGTCGAGCTCAG	60.079	57.895	15.40	6.88	36.06	3.35
1118	1126	5.418676	TGCACTTGTAGAAATGATGATCGA	58.581	37.500	0.00	0.00	0.00	3.59
1127	1135	2.991250	AGCGGATGCACTTGTAGAAAT	58.009	42.857	0.00	0.00	46.23	2.17
1264	1272	3.857052	TCAAGAAACGACACTGACAAGT	58.143	40.909	0.00	0.00	36.98	3.16
1267	1275	3.857052	ACTTCAAGAAACGACACTGACA	58.143	40.909	0.00	0.00	0.00	3.58
1284	1292	2.729156	GCAATAGGCGTGCTGAAACTTC	60.729	50.000	3.98	0.00	39.00	3.01
1285	1293	1.200020	GCAATAGGCGTGCTGAAACTT	59.800	47.619	3.98	0.00	39.00	2.66
1338	1346	1.180029	GCCATCCAGCTTGATGTTGT	58.820	50.000	22.41	0.00	40.43	3.32
1341	1349	0.682209	GGTGCCATCCAGCTTGATGT	60.682	55.000	22.41	0.00	40.43	3.06
1362	1370	1.721664	CTGTGAATCCATGCCCAGCG	61.722	60.000	0.00	0.00	0.00	5.18
1537	1593	1.893786	CGGCTAGTCCTTGTGCTCT	59.106	57.895	0.00	0.00	0.00	4.09
1574	1630	2.022934	TGAGCAACATGTTGACAGCAA	58.977	42.857	36.65	15.50	42.93	3.91
1587	1643	1.282930	GGACGAGAACGGTGAGCAAC	61.283	60.000	0.00	0.00	44.46	4.17
1669	1725	2.295253	ATGAACTACTACGCACCAGC	57.705	50.000	0.00	0.00	37.42	4.85
1673	1729	5.063060	CCAACCTAAATGAACTACTACGCAC	59.937	44.000	0.00	0.00	0.00	5.34
1688	1745	9.303116	TCTTGCTTACAATTAATCCAACCTAAA	57.697	29.630	0.00	0.00	34.61	1.85
1714	1771	1.934459	TAGCGGTAGAGGGAGCCACT	61.934	60.000	0.00	0.00	0.00	4.00
1752	1811	3.190535	CCACATTTCTCTTAAACGGGGTG	59.809	47.826	0.00	0.00	0.00	4.61
1873	1937	2.256117	AACTATAGAATGCGGTGGCC	57.744	50.000	6.78	0.00	38.85	5.36
1927	1991	1.064017	TGCCCCAACACAAGAGAACTT	60.064	47.619	0.00	0.00	36.73	2.66
1998	2062	4.231439	CAGTTGCCCCAATTAACGTTAAC	58.769	43.478	22.30	9.50	0.00	2.01
2010	2074	3.070302	GTCCAAAAATTACAGTTGCCCCA	59.930	43.478	0.00	0.00	0.00	4.96
2425	2489	3.073209	AGCTACCAGACTCCGATCTATGA	59.927	47.826	0.00	0.00	0.00	2.15
2448	2512	2.107750	CATCCCGCTGCTCATCGT	59.892	61.111	0.00	0.00	0.00	3.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.