AutoCloner

Multiple sequence alignment - TraesCS3A01G418500

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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	TraesCS3A01G418500	chr3A	100.000	3560	0	0	1	3560	660241420	660237861	0.000000e+00	6575
1	TraesCS3A01G418500	chr3B	95.720	2710	87	12	854	3560	694328235	694325552	0.000000e+00	4335
2	TraesCS3A01G418500	chr3B	80.214	374	52	14	2884	3250	140590259	140589901	9.800000e-66	261
3	TraesCS3A01G418500	chr3D	96.132	1784	56	8	850	2631	526052563	526050791	0.000000e+00	2900
4	TraesCS3A01G418500	chr3D	94.973	935	35	6	2630	3560	526050626	526049700	0.000000e+00	1456
5	TraesCS3A01G418500	chr7A	97.070	819	22	2	1	818	63338677	63337860	0.000000e+00	1378
6	TraesCS3A01G418500	chr2A	96.314	814	29	1	1	814	611010343	611009531	0.000000e+00	1336
7	TraesCS3A01G418500	chr1A	95.961	817	31	2	1	817	482680152	482680966	0.000000e+00	1325
8	TraesCS3A01G418500	chr4A	94.963	814	39	2	1	814	618655786	618656597	0.000000e+00	1275
9	TraesCS3A01G418500	chr2B	93.643	818	49	3	1	817	56936075	56935260	0.000000e+00	1219
10	TraesCS3A01G418500	chr1B	91.789	816	65	2	1	816	600927638	600928451	0.000000e+00	1134
11	TraesCS3A01G418500	chrUn	91.294	827	62	8	1	825	171833431	171832613	0.000000e+00	1120
12	TraesCS3A01G418500	chr7B	91.176	816	70	2	1	816	32349245	32348432	0.000000e+00	1107
13	TraesCS3A01G418500	chr5D	88.142	818	92	5	2	817	561909188	561910002	0.000000e+00	968
14	TraesCS3A01G418500	chr7D	81.333	375	44	18	2881	3250	162017339	162017692	7.520000e-72	281

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	TraesCS3A01G418500	chr3A	660237861	660241420	3559	True	6575	6575	100.0000	1	3560	1	chr3A.!!$R1	3559
1	TraesCS3A01G418500	chr3B	694325552	694328235	2683	True	4335	4335	95.7200	854	3560	1	chr3B.!!$R2	2706
2	TraesCS3A01G418500	chr3D	526049700	526052563	2863	True	2178	2900	95.5525	850	3560	2	chr3D.!!$R1	2710
3	TraesCS3A01G418500	chr7A	63337860	63338677	817	True	1378	1378	97.0700	1	818	1	chr7A.!!$R1	817
4	TraesCS3A01G418500	chr2A	611009531	611010343	812	True	1336	1336	96.3140	1	814	1	chr2A.!!$R1	813
5	TraesCS3A01G418500	chr1A	482680152	482680966	814	False	1325	1325	95.9610	1	817	1	chr1A.!!$F1	816
6	TraesCS3A01G418500	chr4A	618655786	618656597	811	False	1275	1275	94.9630	1	814	1	chr4A.!!$F1	813
7	TraesCS3A01G418500	chr2B	56935260	56936075	815	True	1219	1219	93.6430	1	817	1	chr2B.!!$R1	816
8	TraesCS3A01G418500	chr1B	600927638	600928451	813	False	1134	1134	91.7890	1	816	1	chr1B.!!$F1	815
9	TraesCS3A01G418500	chrUn	171832613	171833431	818	True	1120	1120	91.2940	1	825	1	chrUn.!!$R1	824
10	TraesCS3A01G418500	chr7B	32348432	32349245	813	True	1107	1107	91.1760	1	816	1	chr7B.!!$R1	815
11	TraesCS3A01G418500	chr5D	561909188	561910002	814	False	968	968	88.1420	2	817	1	chr5D.!!$F1	815

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
26	27	0.036952	CTCCCTCACAAGCGACACAT	60.037	55.0	0.00	3.21	F
831	835	0.249657	GGAACCACGCAAATGGCAAA	60.250	50.0	44.33	3.68	F
1470	1475	0.884514	TCAACTCTCTCCTCTGCACG	59.115	55.0	0.00	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1800	1805	1.153005	CTCAATCCCAGCAGCCTCC	60.153	63.158	0.00	0.00	4.30	R
2192	2197	2.102578	GCACCATTGCTTCCCAATAGT	58.897	47.619	0.00	46.17	2.12	R
2584	2589	4.202050	GCTTTTCAGCTCCTCAAAAGACAA	60.202	41.667	15.86	43.51	3.18	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
26	27	0.036952	CTCCCTCACAAGCGACACAT	60.037	55.000	0.00	0.00	0.00	3.21
42	43	0.259938	ACATCATTCTTCAGGGGCCC	59.740	55.000	17.12	17.12	0.00	5.80
127	128	3.428532	TGCGAAAAGTACCTCTCCTACT	58.571	45.455	0.00	0.00	0.00	2.57
128	129	3.442977	TGCGAAAAGTACCTCTCCTACTC	59.557	47.826	0.00	0.00	0.00	2.59
242	243	1.049402	TTGGGTCACACCATCGTACA	58.951	50.000	0.00	0.00	41.02	2.90
390	391	2.372890	CCAGATCCCAGGCTGCTCA	61.373	63.158	9.56	0.00	0.00	4.26
424	425	3.745723	CCAACTTTGGCTGTAGGGT	57.254	52.632	0.00	0.00	42.21	4.34
558	559	2.385803	TCATCCTTTCTACCTCCGACC	58.614	52.381	0.00	0.00	0.00	4.79
829	833	3.046870	GGAACCACGCAAATGGCA	58.953	55.556	0.00	0.00	44.33	4.92
830	834	1.365633	GGAACCACGCAAATGGCAA	59.634	52.632	0.00	0.00	44.33	4.52
831	835	0.249657	GGAACCACGCAAATGGCAAA	60.250	50.000	0.00	0.00	44.33	3.68
832	836	1.576356	GAACCACGCAAATGGCAAAA	58.424	45.000	0.00	0.00	44.33	2.44
833	837	1.936547	GAACCACGCAAATGGCAAAAA	59.063	42.857	0.00	0.00	44.33	1.94
863	867	6.866480	AGTGGTCCACATATTAATTTTGCTG	58.134	36.000	24.02	0.00	36.74	4.41
999	1004	2.338500	CGAACAGTTCCTTAGCTGACC	58.662	52.381	7.76	0.00	36.62	4.02
1216	1221	2.203181	GCCTGCTCCTCCTCATGC	60.203	66.667	0.00	0.00	0.00	4.06
1470	1475	0.884514	TCAACTCTCTCCTCTGCACG	59.115	55.000	0.00	0.00	0.00	5.34
1584	1589	0.949105	ACGTCAATGCCGGTGACTTC	60.949	55.000	18.39	0.00	42.68	3.01
1620	1625	3.427503	GGGTGTTTGATGAAATGCCTACG	60.428	47.826	1.88	0.00	0.00	3.51
1674	1679	1.448985	GATACTGCAAAAGCGGGTCA	58.551	50.000	1.03	0.00	0.00	4.02
1686	1691	3.512516	GGGTCAATGCAGAGCGCC	61.513	66.667	2.29	0.00	41.33	6.53
1737	1742	2.865119	ATCTTGTGACATGGACAGCA	57.135	45.000	0.00	0.00	0.00	4.41
1777	1782	4.176752	GTGGGCGGCCTAAGGAGG	62.177	72.222	29.87	0.00	46.93	4.30
1796	1801	2.576191	AGGCACTAGCATTGTTTAGGGA	59.424	45.455	0.00	0.00	44.61	4.20
1800	1805	4.142600	GCACTAGCATTGTTTAGGGAACTG	60.143	45.833	0.00	0.00	40.70	3.16
2192	2197	2.026262	GGCTTGTTGATAGAGGGTTGGA	60.026	50.000	0.00	0.00	0.00	3.53
2346	2351	1.751927	CCATCCAGGTGCTCTTGGC	60.752	63.158	11.81	0.00	40.13	4.52
2584	2589	2.204059	AGAGGGAGCAAGGCAGGT	60.204	61.111	0.00	0.00	0.00	4.00
2723	2897	3.543680	TGCTAGCAAGGTACCTTCATC	57.456	47.619	24.73	15.64	33.42	2.92
2737	2911	3.260740	CCTTCATCTCTTCACAGCTCAC	58.739	50.000	0.00	0.00	0.00	3.51
2854	3028	4.326826	TGCTATTGCAGTTTAAGCTCTGT	58.673	39.130	0.00	0.00	45.31	3.41
3032	3208	5.221621	CCCCTCTAGAATCCAGATTGTTCTC	60.222	48.000	0.00	0.00	34.33	2.87
3099	3275	7.763528	AGATGTTTCTAGAACACATCAGATGAC	59.236	37.037	33.29	20.57	46.30	3.06
3126	3302	2.378547	TGGGGTTCAGTTAGAAGGCAAT	59.621	45.455	0.00	0.00	36.78	3.56
3183	3359	2.794910	AGATGATAACGTTCGGATTGCG	59.205	45.455	2.82	0.00	0.00	4.85
3194	3370	1.751351	TCGGATTGCGATCTCTCAACT	59.249	47.619	13.72	0.00	32.66	3.16
3213	3389	5.985530	TCAACTGTTTGATAGAGCATATCCG	59.014	40.000	6.52	0.00	36.79	4.18
3236	3412	7.042321	TCCGACGGCTAATATTTGAAGTTATTG	60.042	37.037	9.66	0.00	0.00	1.90
3238	3414	7.792508	CGACGGCTAATATTTGAAGTTATTGAC	59.207	37.037	0.77	0.00	0.00	3.18
3326	3502	2.915349	AGCTTAGTGTCATGATGCCTG	58.085	47.619	0.00	0.00	0.00	4.85
3415	3592	3.798202	AGATCAGGAAGCAACCGTATTC	58.202	45.455	0.00	0.00	34.73	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	1.923395	ACGGGCCCCTGAAGAATGA	60.923	57.895	18.66	0.00	0.00	2.57
42	43	0.163788	GGTGAAGATCAACGTGCACG	59.836	55.000	35.99	35.99	46.33	5.34
242	243	1.562942	ACATGCTGTGATCATCACCCT	59.437	47.619	15.44	0.00	46.40	4.34
424	425	7.576287	CGGTAGCTAGGGTTCATATCGATAAAA	60.576	40.741	9.61	4.46	0.00	1.52
558	559	1.595466	GCTGATGCCTCTTCATCTGG	58.405	55.000	10.94	4.00	42.44	3.86
831	835	7.931578	TTAATATGTGGACCACTCGATTTTT	57.068	32.000	24.81	11.15	35.11	1.94
832	836	8.519799	AATTAATATGTGGACCACTCGATTTT	57.480	30.769	24.81	13.45	35.11	1.82
833	837	8.519799	AAATTAATATGTGGACCACTCGATTT	57.480	30.769	24.81	16.99	35.11	2.17
834	838	8.405531	CAAAATTAATATGTGGACCACTCGATT	58.594	33.333	24.81	20.49	35.11	3.34
835	839	7.468631	GCAAAATTAATATGTGGACCACTCGAT	60.469	37.037	24.81	12.95	35.11	3.59
836	840	6.183360	GCAAAATTAATATGTGGACCACTCGA	60.183	38.462	24.81	10.71	35.11	4.04
837	841	5.971202	GCAAAATTAATATGTGGACCACTCG	59.029	40.000	24.81	0.00	35.11	4.18
838	842	6.974622	CAGCAAAATTAATATGTGGACCACTC	59.025	38.462	24.81	0.19	35.11	3.51
839	843	6.127366	CCAGCAAAATTAATATGTGGACCACT	60.127	38.462	24.81	13.01	35.11	4.00
840	844	6.042143	CCAGCAAAATTAATATGTGGACCAC	58.958	40.000	18.28	18.28	34.56	4.16
841	845	5.128499	CCCAGCAAAATTAATATGTGGACCA	59.872	40.000	16.06	0.00	0.00	4.02
842	846	5.362430	TCCCAGCAAAATTAATATGTGGACC	59.638	40.000	16.06	0.00	0.00	4.46
843	847	6.273071	GTCCCAGCAAAATTAATATGTGGAC	58.727	40.000	16.06	15.76	0.00	4.02
844	848	5.067153	CGTCCCAGCAAAATTAATATGTGGA	59.933	40.000	16.06	11.16	0.00	4.02
845	849	5.067153	TCGTCCCAGCAAAATTAATATGTGG	59.933	40.000	0.00	2.97	0.00	4.17
846	850	6.130298	TCGTCCCAGCAAAATTAATATGTG	57.870	37.500	0.00	0.00	0.00	3.21
847	851	6.377146	AGTTCGTCCCAGCAAAATTAATATGT	59.623	34.615	0.00	0.00	0.00	2.29
848	852	6.692681	CAGTTCGTCCCAGCAAAATTAATATG	59.307	38.462	0.00	0.00	0.00	1.78
849	853	6.377146	ACAGTTCGTCCCAGCAAAATTAATAT	59.623	34.615	0.00	0.00	0.00	1.28
850	854	5.708230	ACAGTTCGTCCCAGCAAAATTAATA	59.292	36.000	0.00	0.00	0.00	0.98
851	855	4.522789	ACAGTTCGTCCCAGCAAAATTAAT	59.477	37.500	0.00	0.00	0.00	1.40
852	856	3.886505	ACAGTTCGTCCCAGCAAAATTAA	59.113	39.130	0.00	0.00	0.00	1.40
879	883	3.734293	GCTGAGTATGACGGTCCAGTAAC	60.734	52.174	5.55	0.00	0.00	2.50
956	961	2.965147	GCTGGGGGCATGTTAATATGTT	59.035	45.455	13.03	0.00	41.35	2.71
961	966	1.075301	GGGCTGGGGGCATGTTAAT	60.075	57.895	0.00	0.00	44.01	1.40
962	967	2.362565	GGGCTGGGGGCATGTTAA	59.637	61.111	0.00	0.00	44.01	2.01
1026	1031	4.500116	GAGAGGTGGTCGAGGCGC	62.500	72.222	0.00	0.00	0.00	6.53
1437	1442	2.427905	TTGAACGAGACGGCGTCG	60.428	61.111	31.59	24.60	44.86	5.12
1506	1511	1.452833	GGGCATGGAGGTGAAGAGC	60.453	63.158	0.00	0.00	0.00	4.09
1686	1691	2.018542	TTTTATCGAACAGCTCCCGG	57.981	50.000	0.00	0.00	0.00	5.73
1737	1742	7.256048	CCACATTGAGCATACCCATTTATCATT	60.256	37.037	0.00	0.00	0.00	2.57
1777	1782	4.010349	AGTTCCCTAAACAATGCTAGTGC	58.990	43.478	0.00	0.00	40.56	4.40
1782	1787	3.562176	CCTCCAGTTCCCTAAACAATGCT	60.562	47.826	0.00	0.00	40.56	3.79
1785	1790	2.649816	AGCCTCCAGTTCCCTAAACAAT	59.350	45.455	0.00	0.00	40.56	2.71
1796	1801	1.504275	AATCCCAGCAGCCTCCAGTT	61.504	55.000	0.00	0.00	0.00	3.16
1800	1805	1.153005	CTCAATCCCAGCAGCCTCC	60.153	63.158	0.00	0.00	0.00	4.30
2192	2197	2.102578	GCACCATTGCTTCCCAATAGT	58.897	47.619	0.00	0.00	46.17	2.12
2584	2589	4.202050	GCTTTTCAGCTCCTCAAAAGACAA	60.202	41.667	15.86	0.00	43.51	3.18
2723	2897	6.312426	CCAAGTATAAAGTGAGCTGTGAAGAG	59.688	42.308	0.00	0.00	0.00	2.85
2737	2911	6.180472	ACCATGGTGAGTTCCAAGTATAAAG	58.820	40.000	18.99	0.00	41.09	1.85
2782	2956	9.628500	ATTATGGAAAAGTAACTCTGAATACCC	57.372	33.333	0.00	0.00	0.00	3.69
2882	3058	4.532276	TGCAAAGCACGTACAATTTACTG	58.468	39.130	0.00	0.00	31.71	2.74
3099	3275	4.319177	CTTCTAACTGAACCCCAACTCTG	58.681	47.826	0.00	0.00	0.00	3.35
3126	3302	8.196771	AGTTTTCAACTCATAAGATTTTGCACA	58.803	29.630	0.00	0.00	37.02	4.57
3194	3370	4.546570	CGTCGGATATGCTCTATCAAACA	58.453	43.478	8.50	0.00	0.00	2.83
3213	3389	8.609176	TGTCAATAACTTCAAATATTAGCCGTC	58.391	33.333	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.