AutoCloner

Multiple sequence alignment - TraesCS1A01G286600

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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	TraesCS1A01G286600	chr1A	100.000	2501	0	0	1	2501	483605652	483608152	0.000000e+00	4619
1	TraesCS1A01G286600	chr1A	94.093	948	43	6	1563	2501	540629425	540630368	0.000000e+00	1428
2	TraesCS1A01G286600	chr1D	92.472	1169	62	11	992	2144	383656356	383657514	0.000000e+00	1648
3	TraesCS1A01G286600	chr1D	96.409	362	12	1	2140	2501	383682451	383682811	1.660000e-166	595
4	TraesCS1A01G286600	chr1D	83.815	173	10	4	840	994	383656009	383656181	5.570000e-32	148
5	TraesCS1A01G286600	chr1D	90.625	96	9	0	1348	1443	383719041	383718946	7.260000e-26	128
6	TraesCS1A01G286600	chr1B	95.759	896	28	4	1616	2501	514189599	514190494	0.000000e+00	1435
7	TraesCS1A01G286600	chr1B	86.277	736	59	17	841	1550	514161247	514161966	0.000000e+00	761
8	TraesCS1A01G286600	chr1B	93.617	188	12	0	1247	1434	514361851	514361664	5.270000e-72	281
9	TraesCS1A01G286600	chr6D	85.958	819	41	8	1	747	449142459	449141643	0.000000e+00	808
10	TraesCS1A01G286600	chr6D	95.652	69	3	0	773	841	449141581	449141513	7.310000e-21	111
11	TraesCS1A01G286600	chr2B	82.657	813	71	24	1	747	766522785	766521977	0.000000e+00	656
12	TraesCS1A01G286600	chr5B	81.304	813	78	22	3	744	428421249	428422058	2.140000e-165	592

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	TraesCS1A01G286600	chr1A	483605652	483608152	2500	False	4619.0	4619	100.0000	1	2501	1	chr1A.!!$F1	2500
1	TraesCS1A01G286600	chr1A	540629425	540630368	943	False	1428.0	1428	94.0930	1563	2501	1	chr1A.!!$F2	938
2	TraesCS1A01G286600	chr1D	383656009	383657514	1505	False	898.0	1648	88.1435	840	2144	2	chr1D.!!$F2	1304
3	TraesCS1A01G286600	chr1B	514189599	514190494	895	False	1435.0	1435	95.7590	1616	2501	1	chr1B.!!$F2	885
4	TraesCS1A01G286600	chr1B	514161247	514161966	719	False	761.0	761	86.2770	841	1550	1	chr1B.!!$F1	709
5	TraesCS1A01G286600	chr6D	449141513	449142459	946	True	459.5	808	90.8050	1	841	2	chr6D.!!$R1	840
6	TraesCS1A01G286600	chr2B	766521977	766522785	808	True	656.0	656	82.6570	1	747	1	chr2B.!!$R1	746
7	TraesCS1A01G286600	chr5B	428421249	428422058	809	False	592.0	592	81.3040	3	744	1	chr5B.!!$F1	741

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
401	458	0.179012	GAAACCCTTGGTCCGGTTCA	60.179	55.0	0.0	0.0	41.58	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1525	1855	0.184692	TGCCTGTTGTCCATGTCCAA	59.815	50.0	0.0	0.0	0.0	3.53	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
202	235	4.717629	TCTTGTGGGCGCGTCTCG	62.718	66.667	11.94	0.00	42.12	4.04
213	246	2.811317	CGTCTCGCCTTCCTGTGC	60.811	66.667	0.00	0.00	0.00	4.57
252	285	0.388649	GTTGTCATGTCCGCGTCTCT	60.389	55.000	4.92	0.00	0.00	3.10
273	307	1.268899	GACTCCGACGACTTCTTTGGA	59.731	52.381	0.00	0.00	0.00	3.53
286	343	1.133513	TCTTTGGAAAAGCCCTGCTCA	60.134	47.619	0.00	0.00	38.25	4.26
401	458	0.179012	GAAACCCTTGGTCCGGTTCA	60.179	55.000	0.00	0.00	41.58	3.18
429	486	2.583319	CAGCGACGGCGTCATGAT	60.583	61.111	35.62	19.23	46.35	2.45
441	498	1.935873	CGTCATGATGTCGCATCCTTT	59.064	47.619	6.77	1.26	0.00	3.11
456	513	1.021202	CCTTTGTGAAGGCGTTGTCA	58.979	50.000	0.00	0.00	45.59	3.58
505	578	1.900016	TGCTTGGTCTGGCTGCTTG	60.900	57.895	0.00	0.00	0.00	4.01
556	629	2.154462	CGAAATCACTGGCACTTCCTT	58.846	47.619	0.00	0.00	35.26	3.36
577	650	3.854669	CGCTTCCTCCTCCGGCAT	61.855	66.667	0.00	0.00	0.00	4.40
628	701	0.397957	TCTAGGCGCATAAGGTGGGA	60.398	55.000	10.83	0.00	43.02	4.37
632	705	0.396811	GGCGCATAAGGTGGGAGTAT	59.603	55.000	10.83	0.00	43.02	2.12
714	788	1.063972	CGGTTTGTGTGCCTGTGTG	59.936	57.895	0.00	0.00	0.00	3.82
727	801	0.236711	CTGTGTGCTTCTCTTTGCCG	59.763	55.000	0.00	0.00	0.00	5.69
744	818	1.429463	CCGTCTGTGGCTAGTGTTTC	58.571	55.000	0.00	0.00	0.00	2.78
771	881	3.619038	GGATGTGTAGCTTGTTAGTGCTC	59.381	47.826	0.00	0.00	40.35	4.26
782	892	3.653344	TGTTAGTGCTCTGCTGTAACTG	58.347	45.455	0.00	0.00	32.61	3.16
790	900	3.583806	CTCTGCTGTAACTGTTCTCCTG	58.416	50.000	0.00	0.00	0.00	3.86
791	901	2.072298	CTGCTGTAACTGTTCTCCTGC	58.928	52.381	0.00	3.38	0.00	4.85
908	1018	1.341383	ACTTTGCAGAATAGCCCCTGG	60.341	52.381	0.00	0.00	0.00	4.45
917	1027	4.584743	CAGAATAGCCCCTGGGTTTATTTC	59.415	45.833	12.71	8.06	37.65	2.17
919	1029	4.618378	ATAGCCCCTGGGTTTATTTCAA	57.382	40.909	12.71	0.00	37.65	2.69
920	1030	3.268034	AGCCCCTGGGTTTATTTCAAA	57.732	42.857	12.71	0.00	37.65	2.69
921	1031	3.802132	AGCCCCTGGGTTTATTTCAAAT	58.198	40.909	12.71	0.00	37.65	2.32
926	1036	7.070696	AGCCCCTGGGTTTATTTCAAATAATAC	59.929	37.037	12.71	5.38	37.65	1.89
989	1120	1.557269	ATCTTCCACTGCTCCCGCTT	61.557	55.000	0.00	0.00	36.97	4.68
1079	1390	3.844090	GCTGGACGAGAGGGAGCC	61.844	72.222	0.00	0.00	0.00	4.70
1119	1430	1.339438	ACCATCGCTGAGCTGTTGAAT	60.339	47.619	1.78	0.00	0.00	2.57
1154	1465	4.193334	CACCGCCGAGCTCGATGA	62.193	66.667	36.59	0.00	43.02	2.92
1157	1468	2.026734	CGCCGAGCTCGATGATGT	59.973	61.111	36.59	0.00	43.02	3.06
1188	1505	2.675423	TGCGACGGCTACAGGACT	60.675	61.111	0.00	0.00	40.82	3.85
1211	1528	1.670949	ATCGTCATGCTCGAGCCACT	61.671	55.000	33.23	16.06	40.57	4.00
1230	1547	1.767681	CTAGAAGGAGGCCAAGATGCT	59.232	52.381	5.01	0.00	0.00	3.79
1276	1593	2.586792	GCTCCTTCCTGCCATCGT	59.413	61.111	0.00	0.00	0.00	3.73
1424	1741	0.719465	GACAACAACATCTACCGCGG	59.281	55.000	26.86	26.86	0.00	6.46
1500	1830	3.218974	GGAGTCCCCCGATAACTGA	57.781	57.895	0.00	0.00	0.00	3.41
1540	1870	1.327303	GCCTTTGGACATGGACAACA	58.673	50.000	0.00	0.00	0.00	3.33
1709	2041	3.496130	ACTCTCTTGCAAAACGATCACTG	59.504	43.478	0.00	0.00	0.00	3.66
1794	2127	6.859112	AGAATATGACTACACCACTCAAGT	57.141	37.500	0.00	0.00	0.00	3.16
1946	2285	9.757227	AAAGAATTGAACAAATTTCCGACAATA	57.243	25.926	0.00	0.00	38.64	1.90
2224	2566	9.692325	AAAATAGAGCAAGGTGAGATCTTAAAT	57.308	29.630	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
231	264	0.037326	AGACGCGGACATGACAACAT	60.037	50.000	12.47	0.00	37.19	2.71
232	265	0.666274	GAGACGCGGACATGACAACA	60.666	55.000	12.47	0.00	0.00	3.33
252	285	1.000607	CCAAAGAAGTCGTCGGAGTCA	60.001	52.381	0.00	0.00	0.00	3.41
273	307	1.813728	GCAAGCTGAGCAGGGCTTTT	61.814	55.000	7.39	0.00	45.03	2.27
294	351	1.079197	TGTCGCCACTACCAGCATG	60.079	57.895	0.00	0.00	0.00	4.06
330	387	2.083774	CATGGTAGCGCCTTCAAGAAA	58.916	47.619	2.29	0.00	38.35	2.52
441	498	1.840630	CGCATGACAACGCCTTCACA	61.841	55.000	0.00	0.00	0.00	3.58
456	513	1.067974	CATCACAATCCAATGCCGCAT	59.932	47.619	0.00	0.00	0.00	4.73
505	578	0.106519	ATGATAGCCCACACCTTGGC	60.107	55.000	0.00	0.00	45.37	4.52
512	585	2.203195	GCGCCATGATAGCCCACA	60.203	61.111	0.00	0.00	0.00	4.17
556	629	3.452786	CGGAGGAGGAAGCGCTCA	61.453	66.667	12.06	0.00	0.00	4.26
577	650	2.871795	TAGGATGCAGGACTCGGCCA	62.872	60.000	2.24	0.00	33.09	5.36
628	701	5.241506	CCAACACAGACCAAATCAACATACT	59.758	40.000	0.00	0.00	0.00	2.12
632	705	2.692557	CCCAACACAGACCAAATCAACA	59.307	45.455	0.00	0.00	0.00	3.33
676	749	0.506932	CGTCACGACCAACACATGAC	59.493	55.000	0.00	0.00	37.02	3.06
714	788	0.514691	CACAGACGGCAAAGAGAAGC	59.485	55.000	0.00	0.00	0.00	3.86
727	801	1.270147	ACCGAAACACTAGCCACAGAC	60.270	52.381	0.00	0.00	0.00	3.51
744	818	1.808411	ACAAGCTACACATCCAACCG	58.192	50.000	0.00	0.00	0.00	4.44
771	881	2.072298	GCAGGAGAACAGTTACAGCAG	58.928	52.381	0.00	0.00	0.00	4.24
782	892	4.142609	TCATTGATAGGTGCAGGAGAAC	57.857	45.455	0.00	0.00	0.00	3.01
790	900	5.049474	TGCGTATCATTTCATTGATAGGTGC	60.049	40.000	12.85	9.54	42.39	5.01
791	901	6.544038	TGCGTATCATTTCATTGATAGGTG	57.456	37.500	12.85	2.03	42.39	4.00
885	995	2.041620	AGGGGCTATTCTGCAAAGTTCA	59.958	45.455	0.00	0.00	34.04	3.18
917	1027	9.614792	AACAGAGGGCTAAAGTAGTATTATTTG	57.385	33.333	0.00	0.00	0.00	2.32
926	1036	7.923414	AATGTTAAACAGAGGGCTAAAGTAG	57.077	36.000	0.00	0.00	0.00	2.57
1107	1418	2.679934	CGCCGCATTCAACAGCTCA	61.680	57.895	0.00	0.00	0.00	4.26
1150	1461	1.953138	CGGCTGGCTCGACATCATC	60.953	63.158	0.00	0.00	0.00	2.92
1151	1462	2.107750	CGGCTGGCTCGACATCAT	59.892	61.111	0.00	0.00	0.00	2.45
1152	1463	3.068064	TCGGCTGGCTCGACATCA	61.068	61.111	0.00	0.00	0.00	3.07
1188	1505	1.536072	GGCTCGAGCATGACGATGTAA	60.536	52.381	36.27	0.00	44.36	2.41
1211	1528	1.487976	CAGCATCTTGGCCTCCTTCTA	59.512	52.381	3.32	0.00	0.00	2.10
1230	1547	1.746470	CTCTGGCAGCATCAACATCA	58.254	50.000	10.34	0.00	0.00	3.07
1356	1673	0.411452	AGACCTCCTTGAGCTCCTCA	59.589	55.000	12.15	0.00	38.87	3.86
1424	1741	3.188786	GCGTCGGTGTCATCTGCC	61.189	66.667	0.00	0.00	0.00	4.85
1451	1780	1.802337	CGACAGGTCCAGGAACGACA	61.802	60.000	0.00	0.00	31.55	4.35
1459	1788	3.198068	CAATATGGTTCGACAGGTCCAG	58.802	50.000	0.00	0.00	33.33	3.86
1500	1830	2.363276	TATCCGCCGACACCAGGT	60.363	61.111	0.00	0.00	0.00	4.00
1525	1855	0.184692	TGCCTGTTGTCCATGTCCAA	59.815	50.000	0.00	0.00	0.00	3.53
1555	1885	6.746364	GCGGTCATTTCCTTCTAGTATATACG	59.254	42.308	7.23	0.00	0.00	3.06
1682	2014	1.869767	CGTTTTGCAAGAGAGTGAGCT	59.130	47.619	0.00	0.00	0.00	4.09
1794	2127	1.191535	CGGGGTCCTGTGTTCTATCA	58.808	55.000	0.00	0.00	0.00	2.15
2079	2418	8.598202	TTATACCAACTATTACTGACTGTGGA	57.402	34.615	0.00	0.00	0.00	4.02
2197	2539	6.998968	AAGATCTCACCTTGCTCTATTTTG	57.001	37.500	0.00	0.00	0.00	2.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.