AutoCloner

Multiple sequence alignment - TraesCS3B01G369300

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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	TraesCS3B01G369300	chr3B	100.000	7832	0	0	1	7832	581342244	581334413	0.000000e+00	14464
1	TraesCS3B01G369300	chr3B	100.000	113	0	0	1451	1563	581344418	581344530	7.960000e-50	209
2	TraesCS3B01G369300	chr4D	96.893	7305	171	20	182	7472	349007112	349014374	0.000000e+00	12181
3	TraesCS3B01G369300	chr4D	93.301	209	11	3	7498	7704	302343251	302343044	9.870000e-79	305
4	TraesCS3B01G369300	chr4D	95.699	186	8	0	1	186	349004869	349005054	4.590000e-77	300
5	TraesCS3B01G369300	chr4A	97.019	3959	99	11	3518	7466	115915522	115911573	0.000000e+00	6639
6	TraesCS3B01G369300	chr4A	95.785	1281	38	6	1117	2396	115918121	115916856	0.000000e+00	2052
7	TraesCS3B01G369300	chr4A	96.844	1109	30	5	2394	3500	115916615	115915510	0.000000e+00	1849
8	TraesCS3B01G369300	chr4A	96.186	1075	37	2	1	1074	115919604	115918533	0.000000e+00	1755
9	TraesCS3B01G369300	chr6A	95.816	3705	129	16	2164	5853	466340674	466336981	0.000000e+00	5960
10	TraesCS3B01G369300	chr6A	95.118	2745	99	5	1	2715	466330971	466328232	0.000000e+00	4294
11	TraesCS3B01G369300	chr6A	96.654	2570	65	8	4932	7498	466325242	466322691	0.000000e+00	4250
12	TraesCS3B01G369300	chr6A	95.317	1922	90	0	1	1922	466345379	466343458	0.000000e+00	3051
13	TraesCS3B01G369300	chr6A	95.021	1928	90	3	1	1922	466363405	466361478	0.000000e+00	3024
14	TraesCS3B01G369300	chr6A	93.757	1922	94	13	1	1922	466350192	466348297	0.000000e+00	2861
15	TraesCS3B01G369300	chr6A	92.564	1950	92	26	1	1922	466358584	466356660	0.000000e+00	2748
16	TraesCS3B01G369300	chr6A	96.602	1295	30	7	2748	4033	466328233	466326944	0.000000e+00	2135
17	TraesCS3B01G369300	chr6A	98.182	880	14	2	4043	4922	466326516	466325639	0.000000e+00	1535
18	TraesCS3B01G369300	chr6A	94.656	131	5	1	7704	7832	108072995	108072865	1.330000e-47	202
19	TraesCS3B01G369300	chr4B	96.741	3160	94	6	1	3155	429091943	429095098	0.000000e+00	5256
20	TraesCS3B01G369300	chr4B	96.778	3073	66	8	4597	7649	429095100	429098159	0.000000e+00	5096
21	TraesCS3B01G369300	chr4B	94.660	206	8	3	7501	7704	593592924	593592720	4.560000e-82	316
22	TraesCS3B01G369300	chr4B	95.161	124	6	0	7704	7827	565485100	565485223	6.200000e-46	196
23	TraesCS3B01G369300	chr4B	93.893	131	6	1	7704	7832	593592771	593592641	6.200000e-46	196
24	TraesCS3B01G369300	chr7D	94.203	207	10	2	7500	7704	293961616	293961822	1.640000e-81	315
25	TraesCS3B01G369300	chr7D	94.203	207	10	2	7500	7704	294114630	294114424	1.640000e-81	315
26	TraesCS3B01G369300	chr5B	94.175	206	9	3	7501	7704	278205665	278205461	2.120000e-80	311
27	TraesCS3B01G369300	chr5B	94.175	206	9	3	7501	7704	387152413	387152209	2.120000e-80	311
28	TraesCS3B01G369300	chr5B	93.750	208	10	3	7499	7704	418314664	418314870	7.630000e-80	309
29	TraesCS3B01G369300	chr2B	94.175	206	9	3	7501	7704	725997559	725997763	2.120000e-80	311
30	TraesCS3B01G369300	chr2B	94.656	131	5	1	7704	7832	590332658	590332528	1.330000e-47	202
31	TraesCS3B01G369300	chr6B	93.893	131	6	1	7704	7832	500564279	500564149	6.200000e-46	196
32	TraesCS3B01G369300	chr1D	93.893	131	6	1	7704	7832	88372444	88372314	6.200000e-46	196
33	TraesCS3B01G369300	chr1B	93.893	131	6	1	7704	7832	373130192	373130062	6.200000e-46	196
34	TraesCS3B01G369300	chr1B	93.893	131	6	1	7704	7832	475477027	475476897	6.200000e-46	196
35	TraesCS3B01G369300	chr1B	93.893	131	6	2	7704	7832	574352974	574353104	6.200000e-46	196

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	TraesCS3B01G369300	chr3B	581334413	581342244	7831	True	14464.000000	14464	100.000000	1	7832	1	chr3B.!!$R1	7831
1	TraesCS3B01G369300	chr4D	349004869	349014374	9505	False	6240.500000	12181	96.296000	1	7472	2	chr4D.!!$F1	7471
2	TraesCS3B01G369300	chr4A	115911573	115919604	8031	True	3073.750000	6639	96.458500	1	7466	4	chr4A.!!$R1	7465
3	TraesCS3B01G369300	chr6A	466336981	466350192	13211	True	3957.333333	5960	94.963333	1	5853	3	chr6A.!!$R3	5852
4	TraesCS3B01G369300	chr6A	466322691	466330971	8280	True	3053.500000	4294	96.639000	1	7498	4	chr6A.!!$R2	7497
5	TraesCS3B01G369300	chr6A	466356660	466363405	6745	True	2886.000000	3024	93.792500	1	1922	2	chr6A.!!$R4	1921
6	TraesCS3B01G369300	chr4B	429091943	429098159	6216	False	5176.000000	5256	96.759500	1	7649	2	chr4B.!!$F2	7648

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	Hairpin	End Stability	Orientation
782	7661	1.022982	TTGAGCATGCAGGAGAAGCG	61.023	55.000	21.98	33.85	4.68	F
1997	14075	0.734889	CGATGATGCCCAAACCTGTC	59.265	55.000	0.00	0.00	3.51	F
2971	17876	1.029681	TATCTCTTTAGCTGCGCCGA	58.970	50.000	4.18	0.00	5.54	F
3018	17923	4.215109	ACAGTTTTACATCAAGGCCAAGT	58.785	39.130	5.01	0.00	3.16	F
4427	19798	6.412362	AGGGTGATAATGATAGTGTCTGAC	57.588	41.667	0.00	0.00	3.51	F
5127	20891	0.673985	GGCCCAACTGTTTGAGGAAC	59.326	55.000	0.00	38.78	3.62	F
5678	21442	2.433868	TGCACAGGTAGAAACGACTC	57.566	50.000	0.00	0.00	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2543	17411	1.276622	AAATGAGCTACCAGGACCGT	58.723	50.000	0.00	4.83	R
3194	18099	2.554462	TCGATCAGTAGCTGGATGTAGC	59.446	50.000	44.01	3.58	R
4427	19798	4.022416	GGAGTGTATCTATCTGCTGTGGAG	60.022	50.000	0.00	3.86	R
4972	20732	7.121463	GGATCTAAAGAGAAGTGAGACTGTACA	59.879	40.741	34.61	2.90	R
5645	21409	0.325933	TGTGCATGAGTTCCTCCCAG	59.674	55.000	0.00	4.45	R
5953	21717	1.008538	CAAAGCTCAACACCGCACC	60.009	57.895	0.00	5.01	R
7446	23224	1.581934	CAAGAAACAGACACCAGCGA	58.418	50.000	0.00	4.93	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
32	33	2.501723	ACTGATACTGGGAGCGATGTTT	59.498	45.455	0.00	0.00	0.00	2.83
77	79	8.652290	ACCTGTATTTTTGGCAATTTACCTTTA	58.348	29.630	0.00	0.00	0.00	1.85
104	106	7.505585	TGTTCTTATCACCAGAAATCCTTTTGT	59.494	33.333	0.00	0.00	31.98	2.83
109	111	4.037923	TCACCAGAAATCCTTTTGTCAAGC	59.962	41.667	0.00	0.00	0.00	4.01
121	123	5.403897	TTTTGTCAAGCTGAAAGTACTCG	57.596	39.130	0.00	0.00	35.30	4.18
235	7114	5.914898	AACTTGCAAGTTTTACTCCACTT	57.085	34.783	33.85	12.06	46.52	3.16
523	7402	6.484977	GGTTGAAGATGAATTCTATCAGGTCC	59.515	42.308	7.05	6.38	33.05	4.46
559	7438	3.284617	ACCACATAATTCCCCTTAACGC	58.715	45.455	0.00	0.00	0.00	4.84
607	7486	1.104630	GTTCTCCCTACAGGTCCGAG	58.895	60.000	0.00	0.00	36.75	4.63
624	7503	2.226437	CCGAGCAGTTGCATGTAAAACT	59.774	45.455	6.90	1.40	45.16	2.66
782	7661	1.022982	TTGAGCATGCAGGAGAAGCG	61.023	55.000	21.98	0.00	33.85	4.68
834	7713	7.932120	AATGTATCTCGTGTAAGTTAGATGC	57.068	36.000	0.00	0.00	33.33	3.91
865	7744	9.908152	ATTGGTTCTTTATTTGTAGTTAACTGC	57.092	29.630	18.56	17.20	0.00	4.40
986	7865	5.500234	CAAAATCCTAGGGTCAGTGAATCA	58.500	41.667	9.46	0.00	0.00	2.57
1036	7915	3.264193	ACTTGATGGTCTCATTGCAGGTA	59.736	43.478	0.00	0.00	32.72	3.08
1301	8549	5.542779	ACTCTTTTCTTCTATGTTGCGACT	58.457	37.500	5.50	0.00	0.00	4.18
1597	8849	7.721842	TGTACCCATGTTCTTATTTTCTGTCAA	59.278	33.333	0.00	0.00	0.00	3.18
1609	8861	9.869844	CTTATTTTCTGTCAATCGTATGGAATC	57.130	33.333	0.00	0.00	0.00	2.52
1629	8881	8.860780	GGAATCTGAGAATATTCCAAGCTATT	57.139	34.615	11.92	6.70	46.95	1.73
1692	8945	7.223971	CAGGCTGCTAAGTAATTTGTAACGATA	59.776	37.037	0.00	0.00	0.00	2.92
1790	13840	9.219603	CAGTTTGATTTAGGACAACTGAATCTA	57.780	33.333	11.46	3.63	46.69	1.98
1997	14075	0.734889	CGATGATGCCCAAACCTGTC	59.265	55.000	0.00	0.00	0.00	3.51
2008	14086	3.636300	CCCAAACCTGTCACAAAAGATGA	59.364	43.478	0.00	0.00	0.00	2.92
2075	14153	5.523059	AGTTCGGACTTTTGGGTGAACCA	62.523	47.826	1.16	0.00	39.57	3.67
2234	16854	9.793259	AGACCGGAAAATGTATAATGTCATTAT	57.207	29.630	19.48	19.48	38.83	1.28

Showing 1 to 25 of 149 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	64	9.249053	TGATAAGAACATAAAGGTAAATTGCCA	57.751	29.630	2.39	0.00	0.00	4.92
77	79	8.526147	CAAAAGGATTTCTGGTGATAAGAACAT	58.474	33.333	0.00	0.00	37.28	2.71
104	106	2.866460	GCCACGAGTACTTTCAGCTTGA	60.866	50.000	0.00	0.00	0.00	3.02
109	111	3.745975	TCATTTGCCACGAGTACTTTCAG	59.254	43.478	0.00	0.00	0.00	3.02
121	123	6.985188	TCAGTAGTAAATCTCATTTGCCAC	57.015	37.500	0.00	0.00	35.77	5.01
235	7114	7.165485	ACAAAGCAGTTATCATTACAGTGGTA	58.835	34.615	0.00	0.00	0.00	3.25
313	7192	7.149569	TGAATGCTTCAATTCTTACTTCTGG	57.850	36.000	0.00	0.00	37.44	3.86
523	7402	8.833231	AATTATGTGGTATAAGAGAATGACCG	57.167	34.615	0.00	0.00	32.55	4.79
559	7438	4.577834	ACAATAAACAAAAGACACGGGG	57.422	40.909	0.00	0.00	0.00	5.73
607	7486	3.568538	CCAGAGTTTTACATGCAACTGC	58.431	45.455	9.62	0.00	42.50	4.40
624	7503	0.607489	GCTTTGCAAGAGCTCCCAGA	60.607	55.000	19.77	0.00	42.74	3.86
782	7661	6.558771	TGATAATTAGTACCATGTGCATGC	57.441	37.500	11.82	11.82	37.49	4.06
966	7845	3.135530	GCTGATTCACTGACCCTAGGATT	59.864	47.826	11.48	0.00	0.00	3.01
986	7865	9.696917	CAGATTTAAACATTTGAAGTTTAGGCT	57.303	29.630	0.00	0.00	41.06	4.58
1036	7915	4.166144	ACATACCTCCGGATTTTTCTCCAT	59.834	41.667	3.57	0.00	34.78	3.41
1145	8393	6.003950	AGGCTTTGTGTTACATTGACTACAT	58.996	36.000	0.00	0.00	0.00	2.29
1465	8714	5.276536	GCAGCAATTCTGAAAGTGAAAACAC	60.277	40.000	8.22	0.00	45.72	3.32
1609	8861	9.566432	AAGGTTAATAGCTTGGAATATTCTCAG	57.434	33.333	14.95	11.58	40.43	3.35
1692	8945	3.053917	ACAGTTGGGGTTGTGTAGACTTT	60.054	43.478	0.00	0.00	0.00	2.66
1701	8954	4.724279	AGAAATCTACAGTTGGGGTTGT	57.276	40.909	0.00	0.00	0.00	3.32
1997	14075	5.939883	TCAACAGGAGGTATCATCTTTTGTG	59.060	40.000	0.00	0.00	0.00	3.33
2008	14086	5.602978	CCAGGTATACTTCAACAGGAGGTAT	59.397	44.000	2.25	4.80	46.78	2.73
2234	16854	8.935844	CAAGTGTTAGATATCAGCAAACAACTA	58.064	33.333	5.32	0.00	32.32	2.24
2346	16967	6.078456	TGGGAATACATTCTCAAATGAGGT	57.922	37.500	10.37	3.77	43.82	3.85
2382	17003	8.175716	GTGGTTTTAGTCTTACATTGATAGCAC	58.824	37.037	0.00	0.00	0.00	4.40

Showing 1 to 25 of 118 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.