AutoCloner

Multiple sequence alignment - TraesCS5D01G085100

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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	TraesCS5D01G085100	chr5D	100.000	4029	0	0	1	4029	89378998	89383026	0.000000e+00	7441
1	TraesCS5D01G085100	chr5A	95.414	4056	136	30	1	4027	83275472	83279506	0.000000e+00	6414
2	TraesCS5D01G085100	chr5B	91.579	4097	208	80	3	4029	94679370	94675341	0.000000e+00	5528
3	TraesCS5D01G085100	chr4B	85.814	571	73	4	2419	2985	74681886	74681320	2.070000e-167	599
4	TraesCS5D01G085100	chr4B	83.844	359	54	4	1938	2294	74682362	74682006	4.990000e-89	339
5	TraesCS5D01G085100	chr4B	78.060	433	70	20	999	1423	74683171	74682756	2.400000e-62	250
6	TraesCS5D01G085100	chr4A	84.122	592	86	4	2398	2985	546211420	546212007	2.100000e-157	566
7	TraesCS5D01G085100	chr4A	83.708	356	54	4	1938	2291	546210960	546211313	2.320000e-87	333
8	TraesCS5D01G085100	chr4A	79.499	439	65	19	993	1423	546210160	546210581	5.090000e-74	289
9	TraesCS5D01G085100	chr4D	83.959	586	86	4	2404	2985	50770642	50770061	4.550000e-154	555
10	TraesCS5D01G085100	chr4D	85.237	359	49	4	1938	2294	50771110	50770754	2.290000e-97	366
11	TraesCS5D01G085100	chr4D	79.582	431	67	14	999	1423	50771914	50771499	5.090000e-74	289

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	TraesCS5D01G085100	chr5D	89378998	89383026	4028	False	7441.000000	7441	100.000000	1	4029	1	chr5D.!!$F1	4028
1	TraesCS5D01G085100	chr5A	83275472	83279506	4034	False	6414.000000	6414	95.414000	1	4027	1	chr5A.!!$F1	4026
2	TraesCS5D01G085100	chr5B	94675341	94679370	4029	True	5528.000000	5528	91.579000	3	4029	1	chr5B.!!$R1	4026
3	TraesCS5D01G085100	chr4B	74681320	74683171	1851	True	396.000000	599	82.572667	999	2985	3	chr4B.!!$R1	1986
4	TraesCS5D01G085100	chr4A	546210160	546212007	1847	False	396.000000	566	82.443000	993	2985	3	chr4A.!!$F1	1992
5	TraesCS5D01G085100	chr4D	50770061	50771914	1853	True	403.333333	555	82.926000	999	2985	3	chr4D.!!$R1	1986

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	Hairpin	End Stability	Orientation
797	905	0.745128	AGTCCAGTCCTAGTCGCTCG	60.745	60.000	0.00	5.03	F
888	996	1.600485	CGTTTATATTCGCACCCCACC	59.400	52.381	0.00	4.61	F
2071	2471	0.523519	CTACTGAGTGCGAGACAGCA	59.476	55.000	45.96	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2012	2412	0.106708	ATGGCATACGAGTTGCGGAT	59.893	50.0	0.00	0.00	46.80	4.18	R
2350	2750	1.157870	ACTCCGTTTTCGTGCACTGG	61.158	55.0	16.19	6.99	42.35	4.00	R
3462	3877	1.111277	AAACCAAAGCACACTGGACC	58.889	50.0	0.00	0.00	36.49	4.46	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
85	91	8.598916	TCTTTCCTTGTTTTTCCTTTTAGGTTT	58.401	29.630	0.00	0.00	36.53	3.27
126	133	7.067372	AGCATAAGAATTGTTGCTGTTGCTATA	59.933	33.333	1.25	0.00	43.96	1.31
130	137	7.024340	AGAATTGTTGCTGTTGCTATATGAG	57.976	36.000	0.00	0.00	40.48	2.90
184	191	9.745018	ATCACTTTCTATGAATGAAAAGGAAGA	57.255	29.630	0.00	0.00	33.70	2.87
215	222	5.354234	GGTAATCTGTGTGTCCTTTGTATGG	59.646	44.000	0.00	0.00	0.00	2.74
420	435	6.481134	GGTTATTACGGCTTTAAGTTGCTAC	58.519	40.000	0.00	0.00	0.00	3.58
436	451	2.664568	TGCTACGAAAACGTATGCAGAC	59.335	45.455	0.08	0.08	30.92	3.51
449	464	1.246649	TGCAGACAAACATGCGGAAT	58.753	45.000	0.00	0.00	45.54	3.01
490	505	3.797256	CACGCTAATGGTCTAGCTTACAC	59.203	47.826	0.00	0.00	41.86	2.90
530	545	9.604626	TTAAACAAAGCAACAACATTTCAAAAG	57.395	25.926	0.00	0.00	0.00	2.27
661	769	6.833933	ACAGTACAAAGAAAATCCCTGAAGTT	59.166	34.615	0.00	0.00	0.00	2.66
663	771	8.197439	CAGTACAAAGAAAATCCCTGAAGTTTT	58.803	33.333	0.00	0.00	0.00	2.43
664	772	9.416284	AGTACAAAGAAAATCCCTGAAGTTTTA	57.584	29.630	0.00	0.00	0.00	1.52
667	775	8.758829	ACAAAGAAAATCCCTGAAGTTTTACTT	58.241	29.630	0.00	0.00	41.95	2.24
797	905	0.745128	AGTCCAGTCCTAGTCGCTCG	60.745	60.000	0.00	0.00	0.00	5.03
888	996	1.600485	CGTTTATATTCGCACCCCACC	59.400	52.381	0.00	0.00	0.00	4.61
894	1002	4.642488	TCGCACCCCACCCCACTA	62.642	66.667	0.00	0.00	0.00	2.74
949	1057	2.394563	GCCTGAGGCTTTGTCTCGC	61.395	63.158	17.96	0.00	46.69	5.03
1731	2124	6.039717	TCAGCAAGGGTTCATATTATTTGCTC	59.960	38.462	5.90	0.00	45.48	4.26
2012	2412	0.901124	GCAGAAGCTCCTCTCCTCAA	59.099	55.000	0.00	0.00	37.91	3.02
2071	2471	0.523519	CTACTGAGTGCGAGACAGCA	59.476	55.000	0.00	0.00	45.96	4.41
2257	2657	1.607178	TGCACATTCTGCCAAGGGG	60.607	57.895	0.00	0.00	46.51	4.79
2339	2739	3.113260	AGGTGGTCTTTTCTCAGTTCG	57.887	47.619	0.00	0.00	0.00	3.95
2350	2750	4.485024	TTCTCAGTTCGTCTACACACTC	57.515	45.455	0.00	0.00	0.00	3.51
2611	3025	2.233922	TCTTGTCCACCTCGAAGATTCC	59.766	50.000	0.00	0.00	33.89	3.01
3096	3510	9.527157	TCATTTTGATGAATGTAGGGTAGAAAA	57.473	29.630	0.00	0.00	38.04	2.29
3178	3592	2.072298	GTCAAGCAGTCACATGGTCTC	58.928	52.381	0.00	0.00	0.00	3.36
3272	3686	7.793948	AATGGTGTAGTAGGTAGTCTTTCTT	57.206	36.000	0.00	0.00	0.00	2.52
3333	3748	2.239654	GTGTTCTCCTCCATCCATCCAA	59.760	50.000	0.00	0.00	0.00	3.53
3374	3789	2.328099	GGTGGTGCTGCTCTTTCCG	61.328	63.158	0.00	0.00	0.00	4.30
3446	3861	1.424493	GGCAGCCGAGAGTGATTTCG	61.424	60.000	0.00	0.00	36.62	3.46
3462	3877	4.501559	TGATTTCGTCGTTCCTAATTAGCG	59.498	41.667	6.99	5.87	0.00	4.26
3721	4146	1.656594	GTGTTTTTCCGTTTGTGCACC	59.343	47.619	15.69	0.00	0.00	5.01
3757	4186	7.182761	CACTTTTACTATACATGCTGAAGTGC	58.817	38.462	0.00	0.00	36.29	4.40
3764	4193	0.520404	CATGCTGAAGTGCTGGTGAC	59.480	55.000	0.00	0.00	0.00	3.67
3909	4339	1.597797	ATTGGTGCCCATGTGCTTCG	61.598	55.000	0.86	0.00	31.53	3.79
3989	4420	5.618640	GCTTTGCCTCTTGTGTTATCTCTTG	60.619	44.000	0.00	0.00	0.00	3.02
3994	4425	5.391416	GCCTCTTGTGTTATCTCTTGCTTTC	60.391	44.000	0.00	0.00	0.00	2.62
3996	4427	6.091986	CCTCTTGTGTTATCTCTTGCTTTCTC	59.908	42.308	0.00	0.00	0.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
95	101	5.125900	ACAGCAACAATTCTTATGCTATGCA	59.874	36.000	0.00	0.00	46.75	3.96
126	133	6.018469	TGGATTCACATTTCCTTTTCCTCAT	58.982	36.000	0.00	0.00	32.95	2.90
130	137	9.101655	CAATATTGGATTCACATTTCCTTTTCC	57.898	33.333	7.62	0.00	32.95	3.13
184	191	3.511934	GGACACACAGATTACCTCTCACT	59.488	47.826	0.00	0.00	29.16	3.41
215	222	1.264288	GTGTGTACAAAGAGCCAGTGC	59.736	52.381	0.00	0.00	37.95	4.40
387	402	2.842208	CCGTAATAACCGGTCGTACA	57.158	50.000	8.04	0.00	40.59	2.90
420	435	7.100627	GCATGTTTGTCTGCATACGTTTTCG	62.101	44.000	0.00	0.00	42.47	3.46
436	451	4.433186	TGGAGTTTATTCCGCATGTTTG	57.567	40.909	0.00	0.00	40.27	2.93
449	464	4.260866	GCGTGCTTTACAAGTTGGAGTTTA	60.261	41.667	7.96	0.00	0.00	2.01
473	488	5.588240	CATGTCGTGTAAGCTAGACCATTA	58.412	41.667	0.00	0.00	33.04	1.90
490	505	6.128876	TGCTTTGTTTAATTGAATGCATGTCG	60.129	34.615	0.00	0.00	0.00	4.35
552	571	3.253188	TCTGTAATGGTGTTTGCAAGAGC	59.747	43.478	0.00	0.85	42.57	4.09
709	817	0.033405	TGAGCTTACCCTCCGCTACT	60.033	55.000	0.00	0.00	33.47	2.57
710	818	0.102663	GTGAGCTTACCCTCCGCTAC	59.897	60.000	0.00	0.00	33.47	3.58
711	819	1.041447	GGTGAGCTTACCCTCCGCTA	61.041	60.000	16.76	0.00	34.56	4.26
797	905	2.657237	CCGAGTGTGTGACCTCCC	59.343	66.667	0.00	0.00	0.00	4.30
865	973	2.937799	TGGGGTGCGAATATAAACGAAC	59.062	45.455	0.00	5.56	37.34	3.95
888	996	2.498078	GACAAAGAGAGGGAGTAGTGGG	59.502	54.545	0.00	0.00	0.00	4.61
894	1002	0.832135	TGGCGACAAAGAGAGGGAGT	60.832	55.000	0.00	0.00	37.44	3.85
949	1057	4.421479	AGACCACGAGCGCCTTCG	62.421	66.667	16.44	16.44	45.70	3.79
1315	1435	2.586245	CCCGAGCAGCATCCTCAA	59.414	61.111	0.00	0.00	0.00	3.02
1428	1548	0.612744	AAGCAGAGAGAAGGGAGCAC	59.387	55.000	0.00	0.00	0.00	4.40
1606	1998	5.737757	GGAAAACGTCAAAGAACAGTTTCTC	59.262	40.000	0.00	0.00	41.56	2.87
1607	1999	5.392703	GGGAAAACGTCAAAGAACAGTTTCT	60.393	40.000	0.00	0.00	44.53	2.52
1608	2000	4.796830	GGGAAAACGTCAAAGAACAGTTTC	59.203	41.667	0.00	0.00	34.42	2.78
1609	2001	4.461431	AGGGAAAACGTCAAAGAACAGTTT	59.539	37.500	0.00	0.00	36.70	2.66
1610	2002	4.014406	AGGGAAAACGTCAAAGAACAGTT	58.986	39.130	0.00	0.00	0.00	3.16
1611	2003	3.377172	CAGGGAAAACGTCAAAGAACAGT	59.623	43.478	0.00	0.00	0.00	3.55
1612	2004	3.625764	TCAGGGAAAACGTCAAAGAACAG	59.374	43.478	0.00	0.00	0.00	3.16
1613	2005	3.611970	TCAGGGAAAACGTCAAAGAACA	58.388	40.909	0.00	0.00	0.00	3.18
1614	2006	4.625972	TTCAGGGAAAACGTCAAAGAAC	57.374	40.909	0.00	0.00	0.00	3.01
2012	2412	0.106708	ATGGCATACGAGTTGCGGAT	59.893	50.000	0.00	0.00	46.80	4.18
2071	2471	2.915659	TTCCTCACGACACGGCCT	60.916	61.111	0.00	0.00	0.00	5.19
2350	2750	1.157870	ACTCCGTTTTCGTGCACTGG	61.158	55.000	16.19	6.99	42.35	4.00
2611	3025	2.611518	GACTGAATTCGAGTGAGGTGG	58.388	52.381	13.14	0.00	0.00	4.61
2764	3178	1.604308	CTTGGTGTGGCTCATGGCA	60.604	57.895	8.20	0.00	46.87	4.92
3096	3510	4.570719	CCAAATCCTCCTTTAGCCCTTCTT	60.571	45.833	0.00	0.00	0.00	2.52
3160	3574	1.446907	GGAGACCATGTGACTGCTTG	58.553	55.000	0.00	0.00	0.00	4.01
3178	3592	1.981495	GGTCAGGGATATGGAAGAGGG	59.019	57.143	0.00	0.00	0.00	4.30
3374	3789	7.332182	GCCTCTGATAATTAGTATTGCTACCAC	59.668	40.741	0.00	0.00	0.00	4.16
3446	3861	2.159198	TGGACCGCTAATTAGGAACGAC	60.159	50.000	14.28	6.98	0.00	4.34
3462	3877	1.111277	AAACCAAAGCACACTGGACC	58.889	50.000	0.00	0.00	36.49	4.46
3596	4015	1.978580	GTGTGAAGGAGAAAGGGAGGA	59.021	52.381	0.00	0.00	0.00	3.71
3597	4016	1.699634	TGTGTGAAGGAGAAAGGGAGG	59.300	52.381	0.00	0.00	0.00	4.30
3721	4146	3.238788	AGTAAAAGTGGGGTTGAAGGG	57.761	47.619	0.00	0.00	0.00	3.95
3757	4186	5.048504	ACATCACAAAGCTAAATGTCACCAG	60.049	40.000	0.00	0.00	0.00	4.00
3764	4193	4.177165	TGGCACATCACAAAGCTAAATG	57.823	40.909	0.00	0.00	0.00	2.32
3909	4339	3.810310	ATACAGTACAGAAGCTGAGGC	57.190	47.619	0.82	0.00	36.62	4.70
3959	4390	4.773323	ACACAAGAGGCAAAGCTAATTC	57.227	40.909	0.00	0.00	0.00	2.17
3989	4420	3.034635	TCTATGGAGTGGAGGAGAAAGC	58.965	50.000	0.00	0.00	0.00	3.51
3994	4425	2.607499	AGCATCTATGGAGTGGAGGAG	58.393	52.381	0.00	0.00	0.00	3.69
3996	4427	2.702478	TGAAGCATCTATGGAGTGGAGG	59.298	50.000	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.