AutoCloner

Multiple sequence alignment - TraesCS6D01G389300

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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	TraesCS6D01G389300	chr6D	100.000	2407	0	0	1	2407	464978715	464981121	0.000000e+00	4446.0
1	TraesCS6D01G389300	chr5A	91.357	1481	73	15	1	1439	114383417	114384884	0.000000e+00	1975.0
2	TraesCS6D01G389300	chrUn	90.231	1474	87	18	1	1434	76464072	76462616	0.000000e+00	1871.0
3	TraesCS6D01G389300	chr6B	90.801	1348	73	17	1	1310	708967836	708969170	0.000000e+00	1755.0
4	TraesCS6D01G389300	chr6B	93.526	726	36	8	1691	2407	708984125	708984848	0.000000e+00	1070.0
5	TraesCS6D01G389300	chr6B	91.667	528	40	3	915	1438	35529748	35530275	0.000000e+00	728.0
6	TraesCS6D01G389300	chr6B	74.084	1501	303	56	1	1441	716600025	716598551	2.720000e-149	538.0
7	TraesCS6D01G389300	chr6B	88.358	335	16	7	1353	1686	708969168	708969480	4.860000e-102	381.0
8	TraesCS6D01G389300	chr1B	87.843	1275	106	24	109	1357	108078793	108080044	0.000000e+00	1450.0
9	TraesCS6D01G389300	chr1B	75.450	888	162	26	1	851	47924885	47925753	4.860000e-102	381.0
10	TraesCS6D01G389300	chr1B	93.333	120	8	0	1	120	108075686	108075567	6.840000e-41	178.0
11	TraesCS6D01G389300	chr6A	85.675	719	74	16	1694	2405	611501191	611501887	0.000000e+00	730.0
12	TraesCS6D01G389300	chr6A	90.000	90	5	2	1469	1554	611499733	611499822	1.960000e-21	113.0
13	TraesCS6D01G389300	chr3D	74.015	1497	301	59	1	1439	519324562	519326028	1.640000e-146	529.0
14	TraesCS6D01G389300	chr3B	100.000	56	0	0	1377	1432	13443684	13443629	1.180000e-18	104.0
15	TraesCS6D01G389300	chr3B	80.645	124	22	2	346	468	13953479	13953357	7.080000e-16	95.3
16	TraesCS6D01G389300	chr7A	80.672	119	21	2	342	459	55434736	55434853	9.160000e-15	91.6
17	TraesCS6D01G389300	chr2A	83.824	68	5	4	2098	2164	79209869	79209931	2.580000e-05	60.2

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	TraesCS6D01G389300	chr6D	464978715	464981121	2406	False	4446.0	4446	100.0000	1	2407	1	chr6D.!!$F1	2406
1	TraesCS6D01G389300	chr5A	114383417	114384884	1467	False	1975.0	1975	91.3570	1	1439	1	chr5A.!!$F1	1438
2	TraesCS6D01G389300	chrUn	76462616	76464072	1456	True	1871.0	1871	90.2310	1	1434	1	chrUn.!!$R1	1433
3	TraesCS6D01G389300	chr6B	708984125	708984848	723	False	1070.0	1070	93.5260	1691	2407	1	chr6B.!!$F2	716
4	TraesCS6D01G389300	chr6B	708967836	708969480	1644	False	1068.0	1755	89.5795	1	1686	2	chr6B.!!$F3	1685
5	TraesCS6D01G389300	chr6B	35529748	35530275	527	False	728.0	728	91.6670	915	1438	1	chr6B.!!$F1	523
6	TraesCS6D01G389300	chr6B	716598551	716600025	1474	True	538.0	538	74.0840	1	1441	1	chr6B.!!$R1	1440
7	TraesCS6D01G389300	chr1B	108078793	108080044	1251	False	1450.0	1450	87.8430	109	1357	1	chr1B.!!$F2	1248
8	TraesCS6D01G389300	chr1B	47924885	47925753	868	False	381.0	381	75.4500	1	851	1	chr1B.!!$F1	850
9	TraesCS6D01G389300	chr6A	611499733	611501887	2154	False	421.5	730	87.8375	1469	2405	2	chr6A.!!$F1	936
10	TraesCS6D01G389300	chr3D	519324562	519326028	1466	False	529.0	529	74.0150	1	1439	1	chr3D.!!$F1	1438

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
658	701	0.169672	TACTAGAACGGTGCAGCGAC	59.83	55.0	41.29	31.12	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1669	3024	0.530744	CACAAGCACGCTCCCTACTA	59.469	55.0	0.0	0.0	0.0	1.82	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
218	220	4.695455	GCACTCACTTTATGCCTCTTTACA	59.305	41.667	0.00	0.00	33.06	2.41
224	226	5.580691	CACTTTATGCCTCTTTACATCGACA	59.419	40.000	0.00	0.00	0.00	4.35
321	344	0.320421	TTGGCCCTCGACGAGAAAAG	60.320	55.000	26.11	12.22	0.00	2.27
334	357	5.244785	ACGAGAAAAGTCGCACATCTATA	57.755	39.130	0.00	0.00	44.06	1.31
335	358	5.833082	ACGAGAAAAGTCGCACATCTATAT	58.167	37.500	0.00	0.00	44.06	0.86
336	359	6.967135	ACGAGAAAAGTCGCACATCTATATA	58.033	36.000	0.00	0.00	44.06	0.86
337	360	7.594714	ACGAGAAAAGTCGCACATCTATATAT	58.405	34.615	0.00	0.00	44.06	0.86
440	468	0.901114	TACTGGCTTGGCGAGTGGTA	60.901	55.000	15.37	2.15	46.30	3.25
522	550	1.703411	CCCTTTGTGTGGTGTGGAAT	58.297	50.000	0.00	0.00	0.00	3.01
550	578	3.188773	CGTACCACGTCTTCTGCAA	57.811	52.632	0.00	0.00	36.74	4.08
595	623	4.277552	CGCCATGGAGGAGTCCTA	57.722	61.111	18.40	0.00	44.30	2.94
643	686	2.038033	GGAGTGGTTGTTGCACCTACTA	59.962	50.000	0.00	0.00	37.75	1.82
658	701	0.169672	TACTAGAACGGTGCAGCGAC	59.830	55.000	41.29	31.12	0.00	5.19
735	785	8.902540	TGTACATAATGAGATTACCCACAATC	57.097	34.615	0.00	0.00	35.53	2.67
853	903	0.393537	GGGAAGATGGTGGTCAGCTG	60.394	60.000	7.63	7.63	41.91	4.24
876	926	1.801178	GTCAGGCGAAGAGGAAACAAG	59.199	52.381	0.00	0.00	0.00	3.16
1016	1069	6.238484	GCTGCTGGTATGATTCTTCGTAATTT	60.238	38.462	0.00	0.00	0.00	1.82
1018	1071	6.821160	TGCTGGTATGATTCTTCGTAATTTCA	59.179	34.615	0.00	0.00	0.00	2.69
1373	1429	2.224281	TGCCCCTGAACATATCTTAGCG	60.224	50.000	0.00	0.00	0.00	4.26
1459	1517	4.889995	AGAGAAAAGGACAAGGAAAACCAG	59.110	41.667	0.00	0.00	0.00	4.00
1546	1609	2.260481	GTAGCAGAGCGAACCTACAAC	58.740	52.381	0.00	0.00	32.48	3.32
1547	1610	0.388649	AGCAGAGCGAACCTACAACG	60.389	55.000	0.00	0.00	0.00	4.10
1548	1611	0.388134	GCAGAGCGAACCTACAACGA	60.388	55.000	0.00	0.00	0.00	3.85
1549	1612	1.618861	CAGAGCGAACCTACAACGAG	58.381	55.000	0.00	0.00	0.00	4.18
1550	1613	1.068472	CAGAGCGAACCTACAACGAGT	60.068	52.381	0.00	0.00	0.00	4.18
1551	1614	1.199558	AGAGCGAACCTACAACGAGTC	59.800	52.381	0.00	0.00	0.00	3.36
1552	1615	0.243095	AGCGAACCTACAACGAGTCC	59.757	55.000	0.00	0.00	0.00	3.85
1553	1616	0.243095	GCGAACCTACAACGAGTCCT	59.757	55.000	0.00	0.00	0.00	3.85
1554	1617	1.336609	GCGAACCTACAACGAGTCCTT	60.337	52.381	0.00	0.00	0.00	3.36
1555	1618	2.865276	GCGAACCTACAACGAGTCCTTT	60.865	50.000	0.00	0.00	0.00	3.11
1556	1619	3.387397	CGAACCTACAACGAGTCCTTTT	58.613	45.455	0.00	0.00	0.00	2.27
1557	1620	3.805971	CGAACCTACAACGAGTCCTTTTT	59.194	43.478	0.00	0.00	0.00	1.94
1665	3020	0.676466	TTGCTGGCTACAATGGGTCG	60.676	55.000	0.00	0.00	0.00	4.79
1669	3024	0.907704	TGGCTACAATGGGTCGACCT	60.908	55.000	32.52	16.13	41.11	3.85
1680	3035	1.165284	GGTCGACCTAGTAGGGAGCG	61.165	65.000	27.64	18.66	40.58	5.03
1686	3041	0.103208	CCTAGTAGGGAGCGTGCTTG	59.897	60.000	8.50	0.00	0.00	4.01
1687	3042	0.818296	CTAGTAGGGAGCGTGCTTGT	59.182	55.000	0.00	0.00	0.00	3.16
1688	3043	0.530744	TAGTAGGGAGCGTGCTTGTG	59.469	55.000	0.00	0.00	0.00	3.33
1689	3044	2.047274	TAGGGAGCGTGCTTGTGC	60.047	61.111	0.00	0.00	40.20	4.57
1928	3285	8.527567	TTGATTCAGTTTTCTGTTTCGTTTTT	57.472	26.923	0.00	0.00	46.98	1.94
2069	3429	5.181245	ACATTTCTGAAATACACAGGGAACG	59.819	40.000	14.78	2.03	36.22	3.95
2246	3606	7.359595	TCACTGATTTTTGTTAGTACACATGC	58.640	34.615	0.00	0.00	32.98	4.06
2249	3611	6.960468	TGATTTTTGTTAGTACACATGCGAA	58.040	32.000	0.00	0.00	32.98	4.70
2350	3712	2.089980	TGAAAACCCGACGAAAAACCA	58.910	42.857	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
218	220	6.763135	TCAGCTTTATCTTGCTTATTGTCGAT	59.237	34.615	0.00	0.00	37.44	3.59
224	226	4.582240	GGGCTCAGCTTTATCTTGCTTATT	59.418	41.667	0.00	0.00	37.44	1.40
377	400	1.006519	CACCCCCATAACATGTCCCAA	59.993	52.381	0.00	0.00	0.00	4.12
522	550	2.250646	CGTGGTACGTGTCCTCTCA	58.749	57.895	0.00	0.00	36.74	3.27
595	623	2.874701	CGTATTAGCTTTGGCATGCTCT	59.125	45.455	18.92	9.49	40.35	4.09
643	686	3.865929	CTGGTCGCTGCACCGTTCT	62.866	63.158	13.83	0.00	39.62	3.01
853	903	0.034896	TTTCCTCTTCGCCTGACCAC	59.965	55.000	0.00	0.00	0.00	4.16
876	926	2.229784	CAGCAAGGGAAATGTGGTCTTC	59.770	50.000	0.00	0.00	0.00	2.87
1016	1069	3.523157	TGCAAATATCACCTCTCCCTTGA	59.477	43.478	0.00	0.00	0.00	3.02
1018	1071	4.414846	AGATGCAAATATCACCTCTCCCTT	59.585	41.667	0.00	0.00	0.00	3.95
1373	1429	7.382759	GGAGCATTACAGTCTAGCTTACATAAC	59.617	40.741	0.00	0.00	35.36	1.89
1437	1495	4.499865	GCTGGTTTTCCTTGTCCTTTTCTC	60.500	45.833	0.00	0.00	41.38	2.87
1441	1499	1.681264	CGCTGGTTTTCCTTGTCCTTT	59.319	47.619	0.00	0.00	41.38	3.11
1442	1500	1.133915	TCGCTGGTTTTCCTTGTCCTT	60.134	47.619	0.00	0.00	41.38	3.36
1443	1501	0.472471	TCGCTGGTTTTCCTTGTCCT	59.528	50.000	0.00	0.00	41.38	3.85
1444	1502	1.314730	TTCGCTGGTTTTCCTTGTCC	58.685	50.000	0.00	0.00	41.38	4.02
1459	1517	8.466086	AATCTTTGGTTCTTTTGATTATTCGC	57.534	30.769	0.00	0.00	0.00	4.70
1555	1618	6.440328	ACTCGTTGTAGGTATACCCCTAAAAA	59.560	38.462	18.65	0.87	36.32	1.94
1556	1619	5.957774	ACTCGTTGTAGGTATACCCCTAAAA	59.042	40.000	18.65	4.12	38.79	1.52
1557	1620	5.518865	ACTCGTTGTAGGTATACCCCTAAA	58.481	41.667	18.65	5.64	38.79	1.85
1558	1621	5.129368	ACTCGTTGTAGGTATACCCCTAA	57.871	43.478	18.65	8.11	38.79	2.69
1559	1622	4.446311	GGACTCGTTGTAGGTATACCCCTA	60.446	50.000	18.65	2.42	35.97	3.53
1560	1623	3.560105	GACTCGTTGTAGGTATACCCCT	58.440	50.000	18.65	3.48	38.70	4.79
1561	1624	2.625314	GGACTCGTTGTAGGTATACCCC	59.375	54.545	18.65	10.04	36.42	4.95
1562	1625	3.560105	AGGACTCGTTGTAGGTATACCC	58.440	50.000	18.65	4.75	36.42	3.69
1563	1626	5.372373	AGTAGGACTCGTTGTAGGTATACC	58.628	45.833	14.54	14.54	0.00	2.73
1564	1627	6.934048	AAGTAGGACTCGTTGTAGGTATAC	57.066	41.667	0.00	0.00	0.00	1.47
1565	1628	9.632638	ATTAAAGTAGGACTCGTTGTAGGTATA	57.367	33.333	0.00	0.00	0.00	1.47
1566	1629	7.944729	TTAAAGTAGGACTCGTTGTAGGTAT	57.055	36.000	0.00	0.00	0.00	2.73
1613	1676	3.730761	CAGTGCAACGCCTCAGGC	61.731	66.667	5.22	5.22	45.86	4.85
1665	3020	0.752376	AGCACGCTCCCTACTAGGTC	60.752	60.000	1.25	0.00	31.93	3.85
1669	3024	0.530744	CACAAGCACGCTCCCTACTA	59.469	55.000	0.00	0.00	0.00	1.82
1680	3035	4.077188	GACGCTCCGCACAAGCAC	62.077	66.667	3.28	0.00	42.27	4.40
1686	3041	1.222115	AAACAGAAGACGCTCCGCAC	61.222	55.000	0.00	0.00	0.00	5.34
1687	3042	1.069090	AAACAGAAGACGCTCCGCA	59.931	52.632	0.00	0.00	0.00	5.69
1688	3043	0.944311	TCAAACAGAAGACGCTCCGC	60.944	55.000	0.00	0.00	0.00	5.54
1689	3044	0.784778	GTCAAACAGAAGACGCTCCG	59.215	55.000	0.00	0.00	0.00	4.63
2039	3398	6.016360	CCTGTGTATTTCAGAAATGTTCACCA	60.016	38.462	17.38	12.20	35.20	4.17
2053	3412	7.325097	CACATTAAAACGTTCCCTGTGTATTTC	59.675	37.037	17.87	0.00	0.00	2.17
2326	3688	4.023792	GGTTTTTCGTCGGGTTTTCACTAT	60.024	41.667	0.00	0.00	0.00	2.12
2363	3725	6.183360	CCATTCTACCCGTGAGCAATTTTAAT	60.183	38.462	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.