AutoCloner

Multiple sequence alignment - TraesCS1B01G122000

Loading Multiple Alignment...

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	TraesCS1B01G122000	chr1B	100.000	6660	0	0	1	6660	145458756	145452097	0.000000e+00	12299.0
1	TraesCS1B01G122000	chr1B	84.571	175	23	2	318	492	322488002	322488172	3.190000e-38	171.0
2	TraesCS1B01G122000	chr1B	97.143	70	1	1	5968	6036	145452754	145452685	4.220000e-22	117.0
3	TraesCS1B01G122000	chr1B	97.143	70	1	1	6003	6072	145452789	145452721	4.220000e-22	117.0
4	TraesCS1B01G122000	chr1B	95.714	70	3	0	2122	2191	145456569	145456500	5.460000e-21	113.0
5	TraesCS1B01G122000	chr1B	95.714	70	3	0	2188	2257	145456635	145456566	5.460000e-21	113.0
6	TraesCS1B01G122000	chr1D	97.472	5498	102	18	544	6036	90650487	90645022	0.000000e+00	9348.0
7	TraesCS1B01G122000	chr1D	94.991	539	16	5	6003	6536	90645091	90644559	0.000000e+00	835.0
8	TraesCS1B01G122000	chr1D	93.097	536	36	1	1	536	90651180	90650646	0.000000e+00	784.0
9	TraesCS1B01G122000	chr1D	95.714	70	3	0	2188	2257	90648909	90648840	5.460000e-21	113.0
10	TraesCS1B01G122000	chr1D	94.286	70	4	0	2122	2191	90648843	90648774	2.540000e-19	108.0
11	TraesCS1B01G122000	chr1A	96.714	5478	134	10	570	6036	86649495	86644053	0.000000e+00	9077.0
12	TraesCS1B01G122000	chr1A	89.159	535	27	10	6003	6536	86644122	86643618	7.280000e-179	638.0
13	TraesCS1B01G122000	chr1A	90.448	335	30	2	1	333	86649823	86649489	2.200000e-119	440.0
14	TraesCS1B01G122000	chr1A	95.714	70	3	0	2188	2257	86647942	86647873	5.460000e-21	113.0
15	TraesCS1B01G122000	chr4D	84.118	170	23	3	323	492	442397276	442397441	1.920000e-35	161.0
16	TraesCS1B01G122000	chr2A	84.118	170	23	3	323	492	680277627	680277462	1.920000e-35	161.0
17	TraesCS1B01G122000	chr2A	83.636	165	21	5	323	487	267885449	267885291	4.160000e-32	150.0
18	TraesCS1B01G122000	chr2A	100.000	30	0	0	323	352	527378723	527378752	1.000000e-03	56.5
19	TraesCS1B01G122000	chr5B	84.431	167	21	3	323	488	83902775	83902613	6.910000e-35	159.0
20	TraesCS1B01G122000	chr2B	85.235	149	16	5	323	470	550876474	550876331	1.500000e-31	148.0
21	TraesCS1B01G122000	chr2D	83.766	154	20	3	327	480	14695273	14695125	2.500000e-29	141.0
22	TraesCS1B01G122000	chr7D	84.956	113	16	1	374	486	3095342	3095231	5.460000e-21	113.0

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	TraesCS1B01G122000	chr1B	145452097	145458756	6659	True	12299.0	12299	100.00000	1	6660	1	chr1B.!!$R1	6659
1	TraesCS1B01G122000	chr1D	90644559	90651180	6621	True	2237.6	9348	95.11200	1	6536	5	chr1D.!!$R1	6535
2	TraesCS1B01G122000	chr1A	86643618	86649823	6205	True	2567.0	9077	93.00875	1	6536	4	chr1A.!!$R1	6535

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
90	93	0.389817	CGACTTGAAGTGCCCGATGA	60.390	55.000	0.90	0.00	0.00	2.92	F
938	1098	1.152139	CCCTCCATCTCCTCCTCCC	60.152	68.421	0.00	0.00	0.00	4.30	F
2117	2277	1.165270	AGCAGGTTGTTGATAACGGC	58.835	50.000	0.00	0.00	34.05	5.68	F
2884	3048	1.264557	GCTGCAGCTGCTAATGATCAG	59.735	52.381	36.61	24.05	42.66	2.90	F
2941	3105	1.280421	GGTGAGGAGAATGAAGGTGCT	59.720	52.381	0.00	0.00	0.00	4.40	F
3920	4084	1.146263	GATACACCAGGCCTTCGGG	59.854	63.158	13.51	9.95	36.74	5.14	F
4948	5112	1.679944	GCAAGGCCTGTTCTAGATGCA	60.680	52.381	5.69	0.00	0.00	3.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1512	1672	1.654220	CACGTTGCCCACTTCCTTG	59.346	57.895	0.00	0.00	0.00	3.61	R
2896	3060	0.318120	TGTCTTCGTCATCAGCTGCA	59.682	50.000	9.47	0.00	0.00	4.41	R
3013	3177	0.178068	CACCCTCATTACCACTCCCG	59.822	60.000	0.00	0.00	0.00	5.14	R
3920	4084	0.819582	CCTTGGTCCATCACATTGGC	59.180	55.000	0.00	0.00	36.66	4.52	R
4339	4503	2.289882	TGAGTAGCACAAGAGCAGCATT	60.290	45.455	0.00	0.00	36.85	3.56	R
5290	5454	1.021390	CCACTAACGCCAGCCTCTTG	61.021	60.000	0.00	0.00	0.00	3.02	R
6025	6190	0.252558	TCTGGGTTGGTACTCCCTCC	60.253	60.000	17.33	4.96	41.88	4.30	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	1.603455	CCTGGGTGTGAATTGCGGT	60.603	57.895	0.00	0.00	0.00	5.68
90	93	0.389817	CGACTTGAAGTGCCCGATGA	60.390	55.000	0.90	0.00	0.00	2.92
140	143	8.847196	GGTTGTAGTCAGTTTTCCTTTAAGAAT	58.153	33.333	0.00	0.00	0.00	2.40
151	154	9.594478	GTTTTCCTTTAAGAATTTGAGTTTCCA	57.406	29.630	0.00	0.00	0.00	3.53
210	213	9.319143	TGTTTTTGTTATAAATTGGTCAACTGG	57.681	29.630	0.00	0.00	0.00	4.00
251	254	9.874215	CTACTATATCTCGTTGTTATCGTTGAA	57.126	33.333	0.00	0.00	0.00	2.69
262	265	4.637977	TGTTATCGTTGAATGGCTATTGCA	59.362	37.500	0.00	0.00	41.91	4.08
300	303	5.481122	TGTATAGTGTAGGTGTTTGCAGGTA	59.519	40.000	0.00	0.00	0.00	3.08
307	310	1.544246	GGTGTTTGCAGGTATTCCCAC	59.456	52.381	0.00	0.00	34.66	4.61
347	350	5.951747	AGCAATTTTAACATGCTCCCTCTTA	59.048	36.000	0.00	0.00	46.98	2.10
381	384	6.593382	CCCTCTTCACATGAGAAGTAAGAAAG	59.407	42.308	25.81	16.98	44.18	2.62
401	404	9.722184	AAGAAAGTAAGAGTTAATTAGACCCAC	57.278	33.333	0.00	0.00	0.00	4.61
536	539	4.702392	GCAGACGCCGAATAATCAAATAG	58.298	43.478	0.00	0.00	0.00	1.73
537	540	4.447724	GCAGACGCCGAATAATCAAATAGA	59.552	41.667	0.00	0.00	0.00	1.98
538	541	5.050363	GCAGACGCCGAATAATCAAATAGAA	60.050	40.000	0.00	0.00	0.00	2.10
539	542	6.347725	GCAGACGCCGAATAATCAAATAGAAT	60.348	38.462	0.00	0.00	0.00	2.40
541	544	8.708742	CAGACGCCGAATAATCAAATAGAATAA	58.291	33.333	0.00	0.00	0.00	1.40
542	545	8.926710	AGACGCCGAATAATCAAATAGAATAAG	58.073	33.333	0.00	0.00	0.00	1.73
703	860	8.159344	ACACAGAACAGAAAATAGAAAAGGAG	57.841	34.615	0.00	0.00	0.00	3.69
717	874	5.995446	AGAAAAGGAGTAAGGAGGCAATAG	58.005	41.667	0.00	0.00	0.00	1.73
861	1021	6.354883	CGAATTGAGCTATATATACTCGCGAC	59.645	42.308	3.71	0.00	32.98	5.19
938	1098	1.152139	CCCTCCATCTCCTCCTCCC	60.152	68.421	0.00	0.00	0.00	4.30
1072	1232	3.120105	CTGATGCGGACGAGGCTA	58.880	61.111	0.00	0.00	0.00	3.93
1640	1800	2.570181	CGAGAAGGCGGTTACGGT	59.430	61.111	0.00	0.00	41.36	4.83
1642	1802	2.047560	AGAAGGCGGTTACGGTGC	60.048	61.111	0.00	0.00	41.36	5.01

Showing 1 to 25 of 203 entries

Previous1 2 3 4 5…9Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	1.602323	GGACCGCAATTCACACCCA	60.602	57.895	0.00	0.00	0.00	4.51
98	101	0.617820	AACCTCGCCACCACCTAGAT	60.618	55.000	0.00	0.00	0.00	1.98
164	167	8.519799	AAAACAGGACCGAAAATCATACATAT	57.480	30.769	0.00	0.00	0.00	1.78
166	169	6.834168	AAAACAGGACCGAAAATCATACAT	57.166	33.333	0.00	0.00	0.00	2.29
179	182	8.145122	TGACCAATTTATAACAAAAACAGGACC	58.855	33.333	0.00	0.00	0.00	4.46
210	213	0.889306	AGTAGTCGTGGAAGGAGCAC	59.111	55.000	0.00	0.00	0.00	4.40
251	254	3.129988	GCTTTGAAGACTGCAATAGCCAT	59.870	43.478	14.65	0.00	41.13	4.40
262	265	5.539048	ACACTATACAACGCTTTGAAGACT	58.461	37.500	10.27	0.00	36.48	3.24
300	303	4.016479	TCCTAGACAGTAAGAGGTGGGAAT	60.016	45.833	0.00	0.00	0.00	3.01
307	310	5.606348	AATTGCTCCTAGACAGTAAGAGG	57.394	43.478	0.00	0.00	0.00	3.69
462	465	3.895232	TGACATGCTTCCTCTTACCTC	57.105	47.619	0.00	0.00	0.00	3.85
488	491	6.183360	CGAAGCTTGAAAAATTACTAGGGAGG	60.183	42.308	2.10	0.00	0.00	4.30
489	492	6.183360	CCGAAGCTTGAAAAATTACTAGGGAG	60.183	42.308	2.10	0.00	0.00	4.30
490	493	5.646360	CCGAAGCTTGAAAAATTACTAGGGA	59.354	40.000	2.10	0.00	0.00	4.20
536	539	4.620184	ACTACACGCGTTGACTTCTTATTC	59.380	41.667	10.22	0.00	0.00	1.75
537	540	4.553323	ACTACACGCGTTGACTTCTTATT	58.447	39.130	10.22	0.00	0.00	1.40
538	541	4.170292	ACTACACGCGTTGACTTCTTAT	57.830	40.909	10.22	0.00	0.00	1.73
539	542	3.631145	ACTACACGCGTTGACTTCTTA	57.369	42.857	10.22	0.00	0.00	2.10
541	544	2.503920	AACTACACGCGTTGACTTCT	57.496	45.000	10.22	0.00	0.00	2.85
542	545	2.283351	ACAAACTACACGCGTTGACTTC	59.717	45.455	10.22	0.00	0.00	3.01
549	703	6.897259	AATTATATCACAAACTACACGCGT	57.103	33.333	5.58	5.58	0.00	6.01
600	754	8.433421	AACGATAGAAAAGAAGAAGAACAACA	57.567	30.769	0.00	0.00	41.38	3.33
663	818	4.729227	TCTGTGTTTGGGGTTTTTCTTC	57.271	40.909	0.00	0.00	0.00	2.87
672	828	4.670896	ATTTTCTGTTCTGTGTTTGGGG	57.329	40.909	0.00	0.00	0.00	4.96
703	860	4.730903	GCGCTTTTTCTATTGCCTCCTTAC	60.731	45.833	0.00	0.00	0.00	2.34

Showing 1 to 25 of 181 entries

Previous1 2 3 4 5…8Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.