AutoCloner

Multiple sequence alignment - TraesCS1B01G060500

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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	TraesCS1B01G060500	chr1B	100.000	4212	0	0	1	4212	44001239	44005450	0.000000e+00	7779
1	TraesCS1B01G060500	chr1B	97.608	4222	88	5	1	4212	43985082	43989300	0.000000e+00	7225
2	TraesCS1B01G060500	chr1B	84.740	865	109	21	3362	4212	392152757	392153612	0.000000e+00	845
3	TraesCS1B01G060500	chr1B	85.616	730	100	5	3485	4212	608458647	608457921	0.000000e+00	761
4	TraesCS1B01G060500	chr5D	87.302	882	103	8	3337	4212	48055104	48055982	0.000000e+00	1000
5	TraesCS1B01G060500	chr5D	90.000	240	22	2	3337	3575	48060226	48060464	4.090000e-80	309
6	TraesCS1B01G060500	chr5B	84.722	864	113	17	3362	4212	547067795	547068652	0.000000e+00	846
7	TraesCS1B01G060500	chr5B	85.464	743	97	10	3474	4212	640094640	640093905	0.000000e+00	763
8	TraesCS1B01G060500	chr5B	85.675	726	94	9	3494	4212	289143493	289142771	0.000000e+00	756
9	TraesCS1B01G060500	chr2B	84.009	863	121	15	3362	4212	768790825	768789968	0.000000e+00	813
10	TraesCS1B01G060500	chr2B	86.420	729	94	5	3485	4212	33930298	33929574	0.000000e+00	793

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	TraesCS1B01G060500	chr1B	44001239	44005450	4211	False	7779	7779	100.000	1	4212	1	chr1B.!!$F2	4211
1	TraesCS1B01G060500	chr1B	43985082	43989300	4218	False	7225	7225	97.608	1	4212	1	chr1B.!!$F1	4211
2	TraesCS1B01G060500	chr1B	392152757	392153612	855	False	845	845	84.740	3362	4212	1	chr1B.!!$F3	850
3	TraesCS1B01G060500	chr1B	608457921	608458647	726	True	761	761	85.616	3485	4212	1	chr1B.!!$R1	727
4	TraesCS1B01G060500	chr5D	48055104	48055982	878	False	1000	1000	87.302	3337	4212	1	chr5D.!!$F1	875
5	TraesCS1B01G060500	chr5B	547067795	547068652	857	False	846	846	84.722	3362	4212	1	chr5B.!!$F1	850
6	TraesCS1B01G060500	chr5B	640093905	640094640	735	True	763	763	85.464	3474	4212	1	chr5B.!!$R2	738
7	TraesCS1B01G060500	chr5B	289142771	289143493	722	True	756	756	85.675	3494	4212	1	chr5B.!!$R1	718
8	TraesCS1B01G060500	chr2B	768789968	768790825	857	True	813	813	84.009	3362	4212	1	chr2B.!!$R2	850
9	TraesCS1B01G060500	chr2B	33929574	33930298	724	True	793	793	86.420	3485	4212	1	chr2B.!!$R1	727

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
311	314	0.886563	AACAGGAACCTCGACTACGG	59.113	55.000	40.21	4.02	F
1758	1768	1.555075	GCAGGTGGTGGATCTCTTACA	59.445	52.381	0.00	2.41	F
2882	2892	1.000843	GGGGAGTTTCCAACAATGCAC	59.999	52.381	38.64	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2233	2243	0.034186	TGGTGATGGACTTGGGCATC	60.034	55.0	3.91	R
2965	2975	0.179020	CCCTGCCTGTTTCACTGACA	60.179	55.0	3.58	R
4028	4059	0.811281	GATTGGTTCCCTTTCTGCGG	59.189	55.0	5.69	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
72	73	4.789012	ATTTCCTTTCGCATGAATGTGT	57.211	36.364	0.00	0.00	39.25	3.72
91	92	5.718146	TGTGTGGTGCCAAATTATGTTATG	58.282	37.500	0.00	0.00	0.00	1.90
191	194	4.476628	AATGAAATTGGGGTGAATGCTC	57.523	40.909	0.00	0.00	33.44	4.26
198	201	1.177401	GGGGTGAATGCTCCTCAAAC	58.823	55.000	0.00	0.00	0.00	2.93
311	314	0.886563	AACAGGAACCTCGACTACGG	59.113	55.000	0.00	0.00	40.21	4.02
450	453	8.816640	TTTGTTTGCAGAAGATAGAAAATTCC	57.183	30.769	0.00	0.00	0.00	3.01
451	454	7.523293	TGTTTGCAGAAGATAGAAAATTCCA	57.477	32.000	0.00	0.00	0.00	3.53
470	480	4.575885	TCCAGGTTCAGCAATACAGTAAC	58.424	43.478	0.00	0.00	0.00	2.50
480	490	3.560453	GCAATACAGTAACCCCAGGTTCA	60.560	47.826	1.46	0.00	43.05	3.18
533	543	8.028938	GTCAAATCTTTGTGCTATTACAATGGT	58.971	33.333	2.82	0.00	40.00	3.55
537	547	9.632638	AATCTTTGTGCTATTACAATGGTCTAT	57.367	29.630	0.00	0.00	40.00	1.98
555	565	7.284074	TGGTCTATCGGATTTTATTTAGGCAA	58.716	34.615	0.00	0.00	0.00	4.52
645	655	7.742089	GGCGAACATAGAAAATATCGAATGAAG	59.258	37.037	0.00	0.00	33.23	3.02
672	682	1.832883	ACAAATGCTGCGATACCCAA	58.167	45.000	0.00	0.00	0.00	4.12
788	798	5.705609	TCCTCAATTCAAGTTAAGGTTGC	57.294	39.130	0.00	0.00	0.00	4.17
898	908	6.381420	TGGAAAACCACCATTACTTTCTGAAA	59.619	34.615	2.44	2.44	32.03	2.69
957	967	6.947733	ACATCTATGGTGTCAAATTCCAAGAA	59.052	34.615	0.00	0.00	34.80	2.52
1219	1229	7.539034	AAAGCTACTCTTTCTTTCTCTCTCT	57.461	36.000	0.00	0.00	40.89	3.10
1220	1230	6.759497	AGCTACTCTTTCTTTCTCTCTCTC	57.241	41.667	0.00	0.00	0.00	3.20
1746	1756	1.915489	TCATGGTATCAAGCAGGTGGT	59.085	47.619	0.00	0.00	36.35	4.16
1758	1768	1.555075	GCAGGTGGTGGATCTCTTACA	59.445	52.381	0.00	0.00	0.00	2.41
2077	2087	1.734388	GCAACCAAGTCCCACACCAC	61.734	60.000	0.00	0.00	0.00	4.16
2233	2243	7.703298	TCTCAAAATCTTGCAGAACAAATTG	57.297	32.000	0.00	0.00	37.96	2.32
2569	2579	1.560505	TCTGTCAGCTAGCACCATGA	58.439	50.000	18.83	8.98	0.00	3.07
2698	2708	5.977129	TGTTTTTCTTTTCCTTTCGAGATGC	59.023	36.000	0.00	0.00	0.00	3.91
2710	2720	5.008415	CCTTTCGAGATGCTGCATTTCTTAT	59.992	40.000	24.88	0.59	0.00	1.73
2734	2744	3.027974	ACGTGTTAGAAGAGCCTGTTC	57.972	47.619	0.00	0.00	0.00	3.18
2882	2892	1.000843	GGGGAGTTTCCAACAATGCAC	59.999	52.381	0.00	0.00	38.64	4.57
2941	2951	1.550524	TCGCCTTTCAGTGATGCTAGT	59.449	47.619	0.00	0.00	0.00	2.57
2965	2975	2.200081	AGCTATGTGGGACATTCACCT	58.800	47.619	0.00	0.00	44.52	4.00
3113	3123	0.910088	ACCACTCAGGGTAGAAGGCC	60.910	60.000	0.00	0.00	43.89	5.19
3335	3345	1.842381	GCCCTCCTGCCAGTACTTGT	61.842	60.000	0.00	0.00	0.00	3.16
3364	3374	2.885135	TCCTGTACGTGGTCCTTAGA	57.115	50.000	0.00	0.00	0.00	2.10
3471	3491	9.144298	TCTCTACCTTTCTTTCTTCTCAAGTTA	57.856	33.333	0.00	0.00	0.00	2.24
3595	3618	3.454858	TGGTAATCAGAGCCTCCTCTTT	58.545	45.455	0.00	0.00	46.16	2.52
3639	3666	1.409251	TTTGTGCCAGCCATGCCTTT	61.409	50.000	0.00	0.00	0.00	3.11
3808	3836	1.202510	CGCCTTCTCATCTCCAAGGAG	60.203	57.143	9.90	9.90	39.36	3.69
3980	4011	1.620413	GCTTGCAGGCATGTTTTCGC	61.620	55.000	16.98	0.00	0.00	4.70
4003	4034	0.320771	AGTCTTTGAGCCGCGTCAAT	60.321	50.000	12.26	0.00	36.34	2.57
4028	4059	2.362736	TCTGCACTGCCTTGATCAATC	58.637	47.619	8.96	4.83	0.00	2.67
4191	4223	3.532155	GTCTCCGCCCTCGATGCT	61.532	66.667	5.65	0.00	38.10	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	7.281999	AGCAGAAGAAATAAGTTCCAATAGAGC	59.718	37.037	0.00	0.00	36.86	4.09
72	73	5.019470	TGACCATAACATAATTTGGCACCA	58.981	37.500	0.00	0.00	32.26	4.17
91	92	3.875727	CAGATCAATCACACCATCTGACC	59.124	47.826	2.19	0.00	43.39	4.02
256	259	7.697691	AGAAACTAAATATGCACTTGATTCCG	58.302	34.615	0.00	0.00	0.00	4.30
293	296	0.037303	TCCGTAGTCGAGGTTCCTGT	59.963	55.000	0.00	0.00	39.71	4.00
354	357	4.082625	TGTGATGGCTAGCTGTTCAAAATG	60.083	41.667	15.72	0.00	0.00	2.32
407	410	9.083080	GCAAACAAAAGTCTTACAAACATAGTT	57.917	29.630	0.00	0.00	0.00	2.24
422	425	9.822185	AATTTTCTATCTTCTGCAAACAAAAGT	57.178	25.926	0.00	0.00	0.00	2.66
450	453	3.689649	GGGTTACTGTATTGCTGAACCTG	59.310	47.826	6.40	0.00	37.18	4.00
451	454	3.308188	GGGGTTACTGTATTGCTGAACCT	60.308	47.826	6.40	0.00	37.18	3.50
645	655	2.998772	TCGCAGCATTTGTTCTCAAAC	58.001	42.857	0.00	0.00	44.69	2.93
672	682	5.069119	TGCCATTATGTCTTGTCTCGAGTAT	59.931	40.000	13.13	0.32	0.00	2.12
788	798	2.240493	AAACTCACCGTGAAGGACAG	57.760	50.000	2.19	0.00	45.00	3.51
1219	1229	7.807198	TGCTTAGACTATTAAGGAGAGAGAGA	58.193	38.462	0.00	0.00	32.47	3.10
1220	1230	7.308589	GCTGCTTAGACTATTAAGGAGAGAGAG	60.309	44.444	15.52	0.00	46.17	3.20
1746	1756	4.910195	ACTGTGCAAATGTAAGAGATCCA	58.090	39.130	0.00	0.00	0.00	3.41
1758	1768	3.950397	TCCGGATTCTTACTGTGCAAAT	58.050	40.909	0.00	0.00	0.00	2.32
2077	2087	5.473504	AGGATGCAAGTGTAAACCTACTTTG	59.526	40.000	0.00	0.00	35.08	2.77
2233	2243	0.034186	TGGTGATGGACTTGGGCATC	60.034	55.000	0.00	0.00	0.00	3.91
2698	2708	9.820229	TTCTAACACGTTAAATAAGAAATGCAG	57.180	29.630	0.00	0.00	0.00	4.41
2710	2720	4.952460	ACAGGCTCTTCTAACACGTTAAA	58.048	39.130	0.00	0.00	0.00	1.52
2734	2744	9.565213	GAAGAAATAAGATGGTGTTCAAATCAG	57.435	33.333	0.00	0.00	0.00	2.90
2882	2892	1.982612	TCGCAGACAGTCGAATCAAG	58.017	50.000	0.00	0.00	0.00	3.02
2941	2951	5.606749	AGGTGAATGTCCCACATAGCTTATA	59.393	40.000	0.00	0.00	37.97	0.98
2965	2975	0.179020	CCCTGCCTGTTTCACTGACA	60.179	55.000	0.00	0.00	0.00	3.58
3113	3123	2.054232	TGTCCCTCGTAGCTTCTAGG	57.946	55.000	4.12	4.12	0.00	3.02
3291	3301	1.066787	GTGTTGTCCTCCAGTCTAGCC	60.067	57.143	0.00	0.00	0.00	3.93
3297	3307	1.878102	GCAATCGTGTTGTCCTCCAGT	60.878	52.381	5.48	0.00	0.00	4.00
3364	3374	5.515106	AGTAATCTTCTCTAGGCTGTCACT	58.485	41.667	0.00	0.00	0.00	3.41
3471	3491	2.932614	GCGCACACAGTTGAGAGATTAT	59.067	45.455	0.30	0.00	0.00	1.28
3639	3666	4.565652	GGTTTGATTGGAAGGCACTAGAGA	60.566	45.833	0.00	0.00	38.49	3.10
3941	3969	2.593725	CATCCAGAGGGCATGCGG	60.594	66.667	12.44	6.93	0.00	5.69
3980	4011	3.793144	GCGGCTCAAAGACTGCGG	61.793	66.667	0.00	0.00	0.00	5.69
4003	4034	2.857186	TCAAGGCAGTGCAGATGTTA	57.143	45.000	18.61	0.00	0.00	2.41
4028	4059	0.811281	GATTGGTTCCCTTTCTGCGG	59.189	55.000	0.00	0.00	0.00	5.69
4191	4223	2.106938	GAGACCGGCATGATGCGA	59.893	61.111	11.75	0.00	46.21	5.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.