AutoCloner

Multiple sequence alignment - TraesCS1A01G253700

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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	TraesCS1A01G253700	chr1A	100.000	2357	0	0	1	2357	445526773	445529129	0.000000e+00	4353
1	TraesCS1A01G253700	chr4B	98.654	966	13	0	1392	2357	624639465	624640430	0.000000e+00	1712
2	TraesCS1A01G253700	chr4B	98.347	968	16	0	1390	2357	573082519	573083486	0.000000e+00	1700
3	TraesCS1A01G253700	chr5A	98.653	965	13	0	1393	2357	546347919	546348883	0.000000e+00	1711
4	TraesCS1A01G253700	chr4A	98.349	969	16	0	1389	2357	220048928	220049896	0.000000e+00	1701
5	TraesCS1A01G253700	chr4A	98.447	966	15	0	1392	2357	583943442	583942477	0.000000e+00	1701
6	TraesCS1A01G253700	chr7A	98.446	965	15	0	1393	2357	651794078	651795042	0.000000e+00	1700
7	TraesCS1A01G253700	chr3B	98.446	965	15	0	1393	2357	440125041	440124077	0.000000e+00	1700
8	TraesCS1A01G253700	chr2B	98.344	966	16	0	1392	2357	762811505	762810540	0.000000e+00	1696
9	TraesCS1A01G253700	chr1B	98.344	966	16	0	1392	2357	60540788	60539823	0.000000e+00	1696
10	TraesCS1A01G253700	chr1B	87.904	1422	103	25	1	1393	465366459	465365078	0.000000e+00	1609
11	TraesCS1A01G253700	chr1D	85.613	1265	100	37	164	1393	345413930	345415147	0.000000e+00	1253
12	TraesCS1A01G253700	chr6B	84.681	235	33	1	322	553	52574992	52575226	5.070000e-57	231

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	TraesCS1A01G253700	chr1A	445526773	445529129	2356	False	4353	4353	100.000	1	2357	1	chr1A.!!$F1	2356
1	TraesCS1A01G253700	chr4B	624639465	624640430	965	False	1712	1712	98.654	1392	2357	1	chr4B.!!$F2	965
2	TraesCS1A01G253700	chr4B	573082519	573083486	967	False	1700	1700	98.347	1390	2357	1	chr4B.!!$F1	967
3	TraesCS1A01G253700	chr5A	546347919	546348883	964	False	1711	1711	98.653	1393	2357	1	chr5A.!!$F1	964
4	TraesCS1A01G253700	chr4A	220048928	220049896	968	False	1701	1701	98.349	1389	2357	1	chr4A.!!$F1	968
5	TraesCS1A01G253700	chr4A	583942477	583943442	965	True	1701	1701	98.447	1392	2357	1	chr4A.!!$R1	965
6	TraesCS1A01G253700	chr7A	651794078	651795042	964	False	1700	1700	98.446	1393	2357	1	chr7A.!!$F1	964
7	TraesCS1A01G253700	chr3B	440124077	440125041	964	True	1700	1700	98.446	1393	2357	1	chr3B.!!$R1	964
8	TraesCS1A01G253700	chr2B	762810540	762811505	965	True	1696	1696	98.344	1392	2357	1	chr2B.!!$R1	965
9	TraesCS1A01G253700	chr1B	60539823	60540788	965	True	1696	1696	98.344	1392	2357	1	chr1B.!!$R1	965
10	TraesCS1A01G253700	chr1B	465365078	465366459	1381	True	1609	1609	87.904	1	1393	1	chr1B.!!$R2	1392
11	TraesCS1A01G253700	chr1D	345413930	345415147	1217	False	1253	1253	85.613	164	1393	1	chr1D.!!$F1	1229

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
391	432	0.306228	TGCATGTTGACCAACGAACG	59.694	50.0	8.18	0.0	43.94	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1377	1446	0.253044	TTACAGTCCATGGCCTGCTC	59.747	55.0	22.51	1.27	31.76	4.26	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
385	426	0.522626	CGCTCATGCATGTTGACCAA	59.477	50.000	25.43	4.22	39.64	3.67
391	432	0.306228	TGCATGTTGACCAACGAACG	59.694	50.000	8.18	0.00	43.94	3.95
408	449	0.393808	ACGGCTGTTGGTGTGTTCTT	60.394	50.000	0.00	0.00	0.00	2.52
430	471	0.744414	TTCGTGCATGCTAAGAGGGC	60.744	55.000	20.33	0.00	0.00	5.19
449	490	1.238439	CATTTGGGCTGAACTCGTGT	58.762	50.000	0.00	0.00	0.00	4.49
454	495	1.090052	GGGCTGAACTCGTGTATGCC	61.090	60.000	15.47	15.47	36.17	4.40
483	543	2.922950	CGTGCAGGCTGCCAAACAT	61.923	57.895	34.58	0.00	44.23	2.71
484	544	1.368579	GTGCAGGCTGCCAAACATT	59.631	52.632	34.58	0.00	44.23	2.71
492	552	4.996122	CAGGCTGCCAAACATTCAAAAATA	59.004	37.500	22.65	0.00	0.00	1.40
500	560	6.473455	GCCAAACATTCAAAAATAGATCGAGG	59.527	38.462	0.00	0.00	0.00	4.63
505	565	4.689612	TCAAAAATAGATCGAGGAGGGG	57.310	45.455	0.00	0.00	0.00	4.79
523	583	1.888512	GGGACTTTTGAGCTCATGCAA	59.111	47.619	19.04	6.20	42.74	4.08
531	591	1.005097	TGAGCTCATGCAACCTCCATT	59.995	47.619	13.74	0.00	42.74	3.16
534	594	2.029623	GCTCATGCAACCTCCATTCAT	58.970	47.619	0.00	0.00	39.41	2.57
536	596	3.118884	GCTCATGCAACCTCCATTCATTT	60.119	43.478	0.00	0.00	39.41	2.32
539	599	5.964758	TCATGCAACCTCCATTCATTTTAC	58.035	37.500	0.00	0.00	0.00	2.01
545	605	6.520272	CAACCTCCATTCATTTTACCAAACA	58.480	36.000	0.00	0.00	0.00	2.83
564	624	1.545582	CACACCCTAAAATGCACCCTG	59.454	52.381	0.00	0.00	0.00	4.45
566	626	1.818674	CACCCTAAAATGCACCCTGTC	59.181	52.381	0.00	0.00	0.00	3.51
603	665	2.787994	AGCTCCCATTGTGAAGTTCAG	58.212	47.619	5.62	0.00	0.00	3.02
604	666	2.107204	AGCTCCCATTGTGAAGTTCAGT	59.893	45.455	5.62	0.00	0.00	3.41
605	667	2.485814	GCTCCCATTGTGAAGTTCAGTC	59.514	50.000	5.62	0.00	0.00	3.51
606	668	3.743521	CTCCCATTGTGAAGTTCAGTCA	58.256	45.455	5.62	0.00	0.00	3.41
607	669	4.330250	CTCCCATTGTGAAGTTCAGTCAT	58.670	43.478	5.62	0.00	0.00	3.06
608	670	5.491070	CTCCCATTGTGAAGTTCAGTCATA	58.509	41.667	5.62	0.00	0.00	2.15
609	671	6.065976	TCCCATTGTGAAGTTCAGTCATAT	57.934	37.500	5.62	0.00	0.00	1.78
624	686	6.530120	TCAGTCATATATATGGGCAACGTTT	58.470	36.000	20.18	0.00	34.50	3.60
660	722	3.184683	CGCTGCTTCTCGCCACTC	61.185	66.667	0.00	0.00	38.05	3.51
671	733	2.932234	CGCCACTCTCAACGAGGGT	61.932	63.158	0.00	0.00	45.21	4.34
674	736	4.945645	ACTCTCAACGAGGGTGGA	57.054	55.556	0.00	0.00	42.39	4.02
759	821	1.374758	CACTCTCCGACCAGGCAAC	60.375	63.158	0.00	0.00	40.77	4.17
936	999	3.461061	TCATAGCGTAGTACGTAGCACT	58.539	45.455	22.81	13.49	44.73	4.40
1377	1446	2.610308	CGCGCGAGAAATCTGACG	59.390	61.111	28.94	0.00	0.00	4.35
1378	1447	1.867812	CGCGCGAGAAATCTGACGA	60.868	57.895	28.94	0.00	0.00	4.20
1387	1456	0.254178	AAATCTGACGAGCAGGCCAT	59.746	50.000	5.01	0.00	44.98	4.40
1405	1474	4.947388	GGCCATGGACTGTAAGACAATAAA	59.053	41.667	18.40	0.00	37.43	1.40
1416	1485	9.100197	ACTGTAAGACAATAAATTTTGGGGAAT	57.900	29.630	0.00	0.00	37.43	3.01
1582	1651	2.487265	CCTACAAGCCTCAAACTGTGGT	60.487	50.000	0.00	0.00	33.76	4.16
1774	1843	6.012858	TGTTATCACACCAAAGAATAGGAGGT	60.013	38.462	0.00	0.00	0.00	3.85
1831	1900	3.285484	CTGCACCCAAATAATCTCTGCT	58.715	45.455	0.00	0.00	0.00	4.24
1922	1991	3.706594	ACTCCAGGCGATCAAATTAGAGA	59.293	43.478	0.00	0.00	0.00	3.10
1966	2035	0.687427	TGGATCGCCTGTCATCTGGA	60.687	55.000	0.00	0.00	35.11	3.86
2032	2101	1.873591	GAAGTCGGCCGAATATGCATT	59.126	47.619	32.93	13.01	0.00	3.56
2148	2217	8.363390	CCTGTTAACAGCATAAGAGATATCTGA	58.637	37.037	27.05	0.00	42.47	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	9.617975	TTTTTCATGTTTCCAAAAATTGTTCAC	57.382	25.926	0.00	0.00	0.00	3.18
385	426	2.177580	CACACCAACAGCCGTTCGT	61.178	57.895	0.00	0.00	31.13	3.85
391	432	2.024414	AGAAAGAACACACCAACAGCC	58.976	47.619	0.00	0.00	0.00	4.85
400	441	2.286950	GCATGCACGAAGAAAGAACACA	60.287	45.455	14.21	0.00	0.00	3.72
408	449	2.621338	CCTCTTAGCATGCACGAAGAA	58.379	47.619	21.98	9.04	0.00	2.52
430	471	1.238439	ACACGAGTTCAGCCCAAATG	58.762	50.000	0.00	0.00	0.00	2.32
471	512	5.237048	TCTATTTTTGAATGTTTGGCAGCC	58.763	37.500	3.66	3.66	0.00	4.85
472	513	6.237648	CGATCTATTTTTGAATGTTTGGCAGC	60.238	38.462	0.00	0.00	0.00	5.25
475	535	6.473455	CCTCGATCTATTTTTGAATGTTTGGC	59.527	38.462	0.00	0.00	0.00	4.52
483	543	4.719773	TCCCCTCCTCGATCTATTTTTGAA	59.280	41.667	0.00	0.00	0.00	2.69
484	544	4.101119	GTCCCCTCCTCGATCTATTTTTGA	59.899	45.833	0.00	0.00	0.00	2.69
492	552	1.834263	CAAAAGTCCCCTCCTCGATCT	59.166	52.381	0.00	0.00	0.00	2.75
500	560	2.363683	CATGAGCTCAAAAGTCCCCTC	58.636	52.381	22.50	0.00	0.00	4.30
505	565	2.555757	AGGTTGCATGAGCTCAAAAGTC	59.444	45.455	22.50	11.27	42.74	3.01
523	583	5.600484	TGTGTTTGGTAAAATGAATGGAGGT	59.400	36.000	0.00	0.00	0.00	3.85
531	591	7.419711	TTTTAGGGTGTGTTTGGTAAAATGA	57.580	32.000	0.00	0.00	0.00	2.57
534	594	6.049790	GCATTTTAGGGTGTGTTTGGTAAAA	58.950	36.000	0.00	0.00	0.00	1.52
536	596	4.649674	TGCATTTTAGGGTGTGTTTGGTAA	59.350	37.500	0.00	0.00	0.00	2.85
539	599	3.389221	GTGCATTTTAGGGTGTGTTTGG	58.611	45.455	0.00	0.00	0.00	3.28
545	605	1.146982	ACAGGGTGCATTTTAGGGTGT	59.853	47.619	0.00	0.00	0.00	4.16
578	640	3.614092	ACTTCACAATGGGAGCTATGTG	58.386	45.455	8.82	8.82	43.42	3.21
603	665	6.183360	CGAGAAACGTTGCCCATATATATGAC	60.183	42.308	21.97	14.37	35.10	3.06
604	666	5.867174	CGAGAAACGTTGCCCATATATATGA	59.133	40.000	21.97	1.73	35.10	2.15
605	667	5.445939	GCGAGAAACGTTGCCCATATATATG	60.446	44.000	14.78	14.78	44.60	1.78
606	668	4.630069	GCGAGAAACGTTGCCCATATATAT	59.370	41.667	0.00	0.00	44.60	0.86
607	669	3.991773	GCGAGAAACGTTGCCCATATATA	59.008	43.478	0.00	0.00	44.60	0.86
608	670	2.806244	GCGAGAAACGTTGCCCATATAT	59.194	45.455	0.00	0.00	44.60	0.86
609	671	2.206750	GCGAGAAACGTTGCCCATATA	58.793	47.619	0.00	0.00	44.60	0.86
650	712	4.074647	TCGTTGAGAGTGGCGAGA	57.925	55.556	0.00	0.00	0.00	4.04
658	720	2.143925	GTTTTCCACCCTCGTTGAGAG	58.856	52.381	0.00	0.00	46.44	3.20
660	722	0.865769	CGTTTTCCACCCTCGTTGAG	59.134	55.000	0.00	0.00	0.00	3.02
671	733	1.959226	GAGCACCGCTCGTTTTCCA	60.959	57.895	0.00	0.00	45.85	3.53
770	832	1.094785	GGCTCGCTTTAAAGGCATGA	58.905	50.000	16.78	3.15	37.94	3.07
1373	1442	3.002583	TCCATGGCCTGCTCGTCA	61.003	61.111	6.96	0.00	0.00	4.35
1374	1443	2.512515	GTCCATGGCCTGCTCGTC	60.513	66.667	6.96	0.00	0.00	4.20
1377	1446	0.253044	TTACAGTCCATGGCCTGCTC	59.747	55.000	22.51	1.27	31.76	4.26
1378	1447	0.254178	CTTACAGTCCATGGCCTGCT	59.746	55.000	22.51	12.10	31.76	4.24
1387	1456	7.039363	CCCCAAAATTTATTGTCTTACAGTCCA	60.039	37.037	0.00	0.00	0.00	4.02
1405	1474	2.302733	GGTTGTGCTGATTCCCCAAAAT	59.697	45.455	0.00	0.00	0.00	1.82
1492	1561	6.930475	AGGGAGGGTGTTAGACTATGTATAA	58.070	40.000	0.00	0.00	0.00	0.98
1582	1651	3.765511	TCTTCACTAAGCCTTTACCGCTA	59.234	43.478	0.00	0.00	34.84	4.26
1774	1843	2.516227	TGGGTTTGTCTCAACCACAA	57.484	45.000	5.03	0.00	40.78	3.33
1922	1991	4.278310	GGGGGTTATGCAGTATTCTTTGT	58.722	43.478	0.00	0.00	0.00	2.83
1966	2035	0.921896	ATGCAGATTGGGCTGGTAGT	59.078	50.000	0.00	0.00	36.41	2.73
2032	2101	2.441375	TCAGTTCACCCTGACATTTGGA	59.559	45.455	0.00	0.00	36.57	3.53
2148	2217	3.939592	TCAGTACTTGACGATCACGAGAT	59.060	43.478	10.07	0.00	42.66	2.75
2256	2325	2.747022	CGACCACCACACCCATGA	59.253	61.111	0.00	0.00	0.00	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.