AutoCloner

Multiple sequence alignment - TraesCS2A01G149200

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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	TraesCS2A01G149200	chr2A	100.000	5288	0	0	1	5288	95990811	95996098	0.000000e+00	9766
1	TraesCS2A01G149200	chr2B	95.710	5338	156	21	1	5288	148236498	148241812	0.000000e+00	8521
2	TraesCS2A01G149200	chr2D	97.728	4313	79	9	595	4892	97219730	97224038	0.000000e+00	7404
3	TraesCS2A01G149200	chr2D	93.761	577	21	4	2	566	97218991	97219564	0.000000e+00	852
4	TraesCS2A01G149200	chr2D	95.288	382	15	3	4910	5288	97224238	97224619	2.110000e-168	603
5	TraesCS2A01G149200	chr3A	93.711	4134	204	31	566	4665	165420533	165416422	0.000000e+00	6143
6	TraesCS2A01G149200	chr3A	84.861	502	39	15	93	566	165421081	165420589	6.200000e-129	472
7	TraesCS2A01G149200	chr3D	93.852	4099	197	32	568	4635	147817432	147821506	0.000000e+00	6122
8	TraesCS2A01G149200	chr3B	94.814	3818	160	22	566	4362	214564063	214560263	0.000000e+00	5919
9	TraesCS2A01G149200	chr1D	87.044	3396	425	11	914	4301	309078483	309081871	0.000000e+00	3819
10	TraesCS2A01G149200	chr1D	82.258	372	45	7	208	562	108107475	108107108	8.610000e-78	302
11	TraesCS2A01G149200	chr1B	87.107	3374	425	9	924	4292	418810313	418813681	0.000000e+00	3812
12	TraesCS2A01G149200	chr1B	81.383	376	46	8	208	562	158537242	158537614	8.670000e-73	285
13	TraesCS2A01G149200	chr1A	86.653	3394	439	12	914	4301	388838748	388842133	0.000000e+00	3746
14	TraesCS2A01G149200	chr1A	82.527	372	45	6	208	562	111129732	111129364	5.140000e-80	309
15	TraesCS2A01G149200	chr5B	82.317	3229	522	40	1079	4284	47579640	47576438	0.000000e+00	2754
16	TraesCS2A01G149200	chr4B	80.645	310	42	5	227	521	329806272	329805966	1.920000e-54	224

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	TraesCS2A01G149200	chr2A	95990811	95996098	5287	False	9766.0	9766	100.000000	1	5288	1	chr2A.!!$F1	5287
1	TraesCS2A01G149200	chr2B	148236498	148241812	5314	False	8521.0	8521	95.710000	1	5288	1	chr2B.!!$F1	5287
2	TraesCS2A01G149200	chr2D	97218991	97224619	5628	False	2953.0	7404	95.592333	2	5288	3	chr2D.!!$F1	5286
3	TraesCS2A01G149200	chr3A	165416422	165421081	4659	True	3307.5	6143	89.286000	93	4665	2	chr3A.!!$R1	4572
4	TraesCS2A01G149200	chr3D	147817432	147821506	4074	False	6122.0	6122	93.852000	568	4635	1	chr3D.!!$F1	4067
5	TraesCS2A01G149200	chr3B	214560263	214564063	3800	True	5919.0	5919	94.814000	566	4362	1	chr3B.!!$R1	3796
6	TraesCS2A01G149200	chr1D	309078483	309081871	3388	False	3819.0	3819	87.044000	914	4301	1	chr1D.!!$F1	3387
7	TraesCS2A01G149200	chr1B	418810313	418813681	3368	False	3812.0	3812	87.107000	924	4292	1	chr1B.!!$F2	3368
8	TraesCS2A01G149200	chr1A	388838748	388842133	3385	False	3746.0	3746	86.653000	914	4301	1	chr1A.!!$F1	3387
9	TraesCS2A01G149200	chr5B	47576438	47579640	3202	True	2754.0	2754	82.317000	1079	4284	1	chr5B.!!$R1	3205

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
25	26	0.467474	TACTCATCCCATCGCCGTCT	60.467	55.000	0.00	4.18	F
240	258	3.003378	GCTTCATAATCCGGCCTACAAAC	59.997	47.826	0.00	2.93	F
1524	1722	0.768221	TGAGGGGCTTTGGTCTGTCT	60.768	55.000	0.00	3.41	F
1854	2052	1.636003	GTGATCCCACCTTTTCCTCCT	59.364	52.381	37.33	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1353	1548	0.535780	CCTCTGCAGCAGGAAACACA	60.536	55.000	22.62	0.00	31.91	3.72	R
1854	2052	5.836024	TTCCTTCTAAGGCCTTCAACTTA	57.164	39.130	24.49	1.44	46.06	2.24	R
2376	2574	3.008330	CTCCTTGTCATTCTGGCTCTTG	58.992	50.000	0.00	0.00	0.00	3.02	R
4330	4537	7.222611	TGCAGTGAGAAAAAGACAAAAATAAGC	59.777	33.333	0.00	0.00	0.00	3.09	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
20	21	1.000283	CTCAGGTACTCATCCCATCGC	60.000	57.143	0.00	0.00	34.60	4.58
25	26	0.467474	TACTCATCCCATCGCCGTCT	60.467	55.000	0.00	0.00	0.00	4.18
115	116	3.746949	CTGGGGCAGGCAGATCGAC	62.747	68.421	0.00	0.00	0.00	4.20
137	143	7.012943	CGACGCTGATTCTTATGTTTTGTAAA	58.987	34.615	0.00	0.00	0.00	2.01
138	144	7.532546	CGACGCTGATTCTTATGTTTTGTAAAA	59.467	33.333	0.00	0.00	0.00	1.52
240	258	3.003378	GCTTCATAATCCGGCCTACAAAC	59.997	47.826	0.00	0.00	0.00	2.93
244	262	4.638421	TCATAATCCGGCCTACAAACTTTG	59.362	41.667	0.00	0.00	0.00	2.77
266	284	5.056480	TGTACACAGAAACAAGGTCATGAG	58.944	41.667	0.00	0.00	0.00	2.90
284	303	7.013846	GGTCATGAGTGCTATCTTTCTAGTACT	59.986	40.741	0.00	0.00	44.26	2.73
418	447	9.415544	GAAATGTTATCTGCAGAAAGTGAATTT	57.584	29.630	22.50	19.46	0.00	1.82
547	581	4.749245	ACTTTCATCCACGTGAATCAAC	57.251	40.909	19.30	0.00	37.88	3.18
618	791	4.668289	TCTTCTTTTTCTTGTGCCGTTTC	58.332	39.130	0.00	0.00	0.00	2.78
771	956	6.845302	TGATGTCTTGATGATGTTTGCTTAC	58.155	36.000	0.00	0.00	0.00	2.34
777	962	5.041951	TGATGATGTTTGCTTACGGTTTC	57.958	39.130	0.00	0.00	0.00	2.78
835	1022	5.716228	TGGCTTTCATATCCATGAGTTTGTT	59.284	36.000	0.00	0.00	42.11	2.83
840	1027	9.347240	CTTTCATATCCATGAGTTTGTTAGGAT	57.653	33.333	0.00	0.00	42.11	3.24
889	1077	7.743104	AGATTGCACTACTAAAATTCGTTCAG	58.257	34.615	0.00	0.00	0.00	3.02
903	1091	9.533253	AAAATTCGTTCAGAAAAATGTCTCATT	57.467	25.926	0.00	0.00	42.91	2.57
1353	1548	3.256704	TCAACAGTATGGAAACCCTCCT	58.743	45.455	0.00	0.00	45.64	3.69
1524	1722	0.768221	TGAGGGGCTTTGGTCTGTCT	60.768	55.000	0.00	0.00	0.00	3.41
1854	2052	1.636003	GTGATCCCACCTTTTCCTCCT	59.364	52.381	0.00	0.00	37.33	3.69
2230	2428	2.156917	CGCCAGATGATTACATGGCAT	58.843	47.619	14.76	0.00	42.22	4.40
2376	2574	4.775236	AGGTGTGCCTTGATCTTAAGATC	58.225	43.478	30.59	30.59	44.18	2.75
3249	3447	2.044650	GCCCTTGCTGATGCTGGA	60.045	61.111	0.00	0.00	40.48	3.86
3691	3889	3.012119	TTGCAGGCACCCCGGATA	61.012	61.111	0.73	0.00	35.76	2.59
4345	4553	8.465273	AGGTACTCAAGCTTATTTTTGTCTTT	57.535	30.769	0.00	0.00	29.36	2.52
4414	4623	3.369385	AGACTACAACTGACACGTTTCG	58.631	45.455	0.00	0.00	0.00	3.46
4437	4646	5.637810	CGTTCTGCACCTTTAGATTCTGTTA	59.362	40.000	0.00	0.00	0.00	2.41
4471	4694	7.333423	TGTGTATGAGGACATAGTTTTTAGCAC	59.667	37.037	0.00	0.00	39.29	4.40
4604	4828	3.620488	TGCCTTGTGATACCATTTCCTC	58.380	45.455	0.00	0.00	0.00	3.71
4740	4971	1.976474	GGCCGTTGGATTTGGAGCA	60.976	57.895	0.00	0.00	0.00	4.26
4755	4986	2.052414	GCATGAATCTCAGCGCGC	60.052	61.111	26.66	26.66	0.00	6.86
4779	5010	2.092646	TGGCTGTGTTTGTCAGGTTACT	60.093	45.455	0.00	0.00	33.98	2.24
4783	5014	1.607148	GTGTTTGTCAGGTTACTGGGC	59.393	52.381	0.00	0.00	44.99	5.36
5002	5417	3.986006	GCAGTCACCGTCGGTCCA	61.986	66.667	15.67	0.38	31.02	4.02
5017	5432	1.489230	GGTCCATTTATCCCTCCACGT	59.511	52.381	0.00	0.00	0.00	4.49
5020	5435	1.488812	CCATTTATCCCTCCACGTCCA	59.511	52.381	0.00	0.00	0.00	4.02
5052	5468	5.543714	TGTATGTGTTTCATTGTCTACGGT	58.456	37.500	0.00	0.00	37.91	4.83
5124	5542	1.440618	TGCACTTCCCCCTTGACTTA	58.559	50.000	0.00	0.00	0.00	2.24
5185	5603	0.981183	TTGCCCTAGATGGTTGACGT	59.019	50.000	0.00	0.00	0.00	4.34
5189	5607	1.831736	CCCTAGATGGTTGACGTCCTT	59.168	52.381	14.12	0.00	35.63	3.36
5258	5676	0.792640	CAGTTCATGTGTCCTGCGTC	59.207	55.000	0.00	0.00	0.00	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
115	116	9.559958	AGATTTTACAAAACATAAGAATCAGCG	57.440	29.630	0.00	0.00	0.00	5.18
137	143	2.237392	ACTAGAAGAAAGCCGCCAGATT	59.763	45.455	0.00	0.00	0.00	2.40
138	144	1.834263	ACTAGAAGAAAGCCGCCAGAT	59.166	47.619	0.00	0.00	0.00	2.90
240	258	5.811399	TGACCTTGTTTCTGTGTACAAAG	57.189	39.130	6.72	6.72	34.17	2.77
244	262	5.050091	CACTCATGACCTTGTTTCTGTGTAC	60.050	44.000	0.00	0.00	0.00	2.90
266	284	6.771749	TCCCTGTAGTACTAGAAAGATAGCAC	59.228	42.308	1.87	0.00	0.00	4.40
284	303	3.585732	AGTCCCTCGAAATTTTCCCTGTA	59.414	43.478	3.61	0.00	0.00	2.74
418	447	4.905429	TCTTGGACAATGCTTGCTAACTA	58.095	39.130	0.00	0.00	0.00	2.24
547	581	6.127196	AGGGAACTAAGTATCTTGAGCTCAAG	60.127	42.308	39.37	39.37	46.74	3.02
618	791	7.066887	TGTGTAGGTTGGTATATTTGATGCAAG	59.933	37.037	0.00	0.00	0.00	4.01
840	1027	9.884636	TCTCCTTGAATATCTCGTTTCAAAATA	57.115	29.630	0.00	0.00	40.31	1.40
841	1028	8.792830	TCTCCTTGAATATCTCGTTTCAAAAT	57.207	30.769	0.00	0.00	40.31	1.82
842	1029	8.792830	ATCTCCTTGAATATCTCGTTTCAAAA	57.207	30.769	0.00	0.00	40.31	2.44
988	1181	6.698008	ATTTGATGACATTTTCCTGCGATA	57.302	33.333	0.00	0.00	0.00	2.92
1353	1548	0.535780	CCTCTGCAGCAGGAAACACA	60.536	55.000	22.62	0.00	31.91	3.72
1854	2052	5.836024	TTCCTTCTAAGGCCTTCAACTTA	57.164	39.130	24.49	1.44	46.06	2.24
2230	2428	5.927689	CAGGCTTTGTGATTAAATCTTGCAA	59.072	36.000	0.00	0.00	0.00	4.08
2376	2574	3.008330	CTCCTTGTCATTCTGGCTCTTG	58.992	50.000	0.00	0.00	0.00	3.02
4330	4537	7.222611	TGCAGTGAGAAAAAGACAAAAATAAGC	59.777	33.333	0.00	0.00	0.00	3.09
4345	4553	7.665559	AGAAAACCACTAATATGCAGTGAGAAA	59.334	33.333	15.90	0.00	45.10	2.52
4414	4623	5.948992	AACAGAATCTAAAGGTGCAGAAC	57.051	39.130	0.00	0.00	0.00	3.01
4437	4646	9.959721	AACTATGTCCTCATACACAAAAACTAT	57.040	29.630	0.00	0.00	35.70	2.12
4471	4694	5.185454	TGCTTTACCTGACACCATTATGAG	58.815	41.667	0.00	0.00	0.00	2.90
4713	4944	2.741759	ATCCAACGGCCACAAAATTC	57.258	45.000	2.24	0.00	0.00	2.17
4755	4986	0.664761	CCTGACAAACACAGCCACAG	59.335	55.000	0.00	0.00	34.47	3.66
4779	5010	1.076632	AAACCCACAACGAAGCCCA	60.077	52.632	0.00	0.00	0.00	5.36
4783	5014	1.961793	TCCAGAAACCCACAACGAAG	58.038	50.000	0.00	0.00	0.00	3.79
4835	5066	2.358003	GCTCGCAGCAGACAACCT	60.358	61.111	0.00	0.00	41.89	3.50
4960	5374	1.439644	GCTAACTCTCTCAGGGCGG	59.560	63.158	0.00	0.00	0.00	6.13
4991	5406	0.466963	GGGATAAATGGACCGACGGT	59.533	55.000	21.93	21.93	39.44	4.83
5002	5417	1.489230	GGTGGACGTGGAGGGATAAAT	59.511	52.381	0.00	0.00	0.00	1.40
5017	5432	2.344592	ACACATACAGGGAAAGGTGGA	58.655	47.619	0.00	0.00	0.00	4.02
5020	5435	4.447138	TGAAACACATACAGGGAAAGGT	57.553	40.909	0.00	0.00	0.00	3.50
5124	5542	3.003763	GAGGGGACGCCTCCTTGT	61.004	66.667	24.65	0.00	36.68	3.16
5258	5676	9.734620	TCTCATGTAAAAACAAAGACAAATCAG	57.265	29.630	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.