AutoCloner

Multiple sequence alignment - TraesCS3B01G134400

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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	TraesCS3B01G134400	chr3B	100.000	2914	0	0	1	2914	116391274	116388361	0.000000e+00	5382.0
1	TraesCS3B01G134400	chr3B	94.267	2913	154	6	3	2914	116438737	116435837	0.000000e+00	4442.0
2	TraesCS3B01G134400	chr3B	83.853	353	50	6	709	1057	113930098	113930447	2.160000e-86	329.0
3	TraesCS3B01G134400	chr3B	74.684	316	61	13	713	1026	182203230	182203528	3.940000e-24	122.0
4	TraesCS3B01G134400	chr3D	94.444	2916	142	7	1	2914	71117057	71114160	0.000000e+00	4470.0
5	TraesCS3B01G134400	chr3D	83.573	347	49	7	715	1057	68072258	68071916	4.690000e-83	318.0
6	TraesCS3B01G134400	chr3D	73.354	319	60	18	713	1026	127903768	127904066	8.600000e-16	95.3
7	TraesCS3B01G134400	chr3A	94.437	2175	118	3	1	2172	82745282	82743108	0.000000e+00	3343.0
8	TraesCS3B01G134400	chr3A	93.304	672	45	0	2243	2914	82743111	82742440	0.000000e+00	992.0
9	TraesCS3B01G134400	chr3A	83.569	353	50	7	709	1057	80102515	80102863	1.010000e-84	324.0
10	TraesCS3B01G134400	chr3A	73.968	315	63	14	714	1026	79875912	79875615	3.070000e-20	110.0
11	TraesCS3B01G134400	chr4D	79.656	349	63	6	362	702	391471484	391471832	8.070000e-61	244.0
12	TraesCS3B01G134400	chr1D	79.880	333	64	3	378	708	41587932	41588263	1.040000e-59	241.0
13	TraesCS3B01G134400	chr1D	82.386	176	20	8	175	340	468869293	468869467	3.030000e-30	143.0
14	TraesCS3B01G134400	chr5D	76.180	466	81	14	175	638	249528310	249528747	4.890000e-53	219.0
15	TraesCS3B01G134400	chr2D	74.398	457	75	19	139	555	49347542	49347996	1.080000e-34	158.0
16	TraesCS3B01G134400	chr2D	100.000	30	0	0	2661	2690	485591202	485591231	4.060000e-04	56.5
17	TraesCS3B01G134400	chr2D	100.000	30	0	0	2661	2690	485634405	485634434	4.060000e-04	56.5
18	TraesCS3B01G134400	chr1B	77.619	210	31	4	136	329	121732762	121732971	2.370000e-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	TraesCS3B01G134400	chr3B	116388361	116391274	2913	True	5382.0	5382	100.0000	1	2914	1	chr3B.!!$R1	2913
1	TraesCS3B01G134400	chr3B	116435837	116438737	2900	True	4442.0	4442	94.2670	3	2914	1	chr3B.!!$R2	2911
2	TraesCS3B01G134400	chr3D	71114160	71117057	2897	True	4470.0	4470	94.4440	1	2914	1	chr3D.!!$R2	2913
3	TraesCS3B01G134400	chr3A	82742440	82745282	2842	True	2167.5	3343	93.8705	1	2914	2	chr3A.!!$R2	2913

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	End Stability	Orientation
528	530	0.812014	ACGACAATGCCAACACGACA	60.812	50.0	4.35	F
646	648	1.338107	TGAGACCGACCAACATGACT	58.662	50.0	3.41	F
1702	1705	0.400594	GTTGTGCCTACCCCTCTTGT	59.599	55.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1702	1705	1.198094	TGAGGAGGTGGCGAATGGAA	61.198	55.000	0.00	0.00	3.53	R
1715	1718	1.980784	CTCTGGGGCCATGTGAGGAG	61.981	65.000	4.39	0.00	3.69	R
2546	2550	2.104967	CATGAGGGCCATGTTGTCAAT	58.895	47.619	6.18	45.83	2.57	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
31	32	8.571336	GGTAATGATTTTTCATCCAAGATCGAT	58.429	33.333	0.00	0.00	0.00	3.59
117	118	5.354234	ACCAACTTTTATGTAGAAGATGGCG	59.646	40.000	15.18	0.00	44.85	5.69
333	334	4.623863	AGGCATGGTTTAAATGGAATCCT	58.376	39.130	0.00	0.00	0.00	3.24
433	435	5.350640	GTGCGCATCTTACCTAAATATACCC	59.649	44.000	15.91	0.00	0.00	3.69
462	464	7.094377	ACAATTTTGTTGTTCATATAGGCGAGT	60.094	33.333	0.00	0.00	38.47	4.18
468	470	5.079689	TGTTCATATAGGCGAGTGTTTGA	57.920	39.130	0.00	0.00	0.00	2.69
479	481	4.379082	GGCGAGTGTTTGACGGAAATTATT	60.379	41.667	0.00	0.00	0.00	1.40
523	525	1.609580	GGTCCTACGACAATGCCAACA	60.610	52.381	0.00	0.00	41.13	3.33
528	530	0.812014	ACGACAATGCCAACACGACA	60.812	50.000	0.00	0.00	0.00	4.35
646	648	1.338107	TGAGACCGACCAACATGACT	58.662	50.000	0.00	0.00	0.00	3.41
656	658	2.173519	CCAACATGACTCATTGGCCTT	58.826	47.619	3.32	0.00	36.72	4.35
952	954	8.467598	ACGAACACTATCATACCATATACATCC	58.532	37.037	0.00	0.00	0.00	3.51
1026	1028	5.365314	GGATCCTAATGGCTCCTATCCTAAG	59.635	48.000	3.84	0.00	43.48	2.18
1039	1041	7.523709	GCTCCTATCCTAAGAAAGTCAGATCTG	60.524	44.444	17.07	17.07	0.00	2.90
1040	1042	7.587258	TCCTATCCTAAGAAAGTCAGATCTGA	58.413	38.462	21.67	21.67	37.24	3.27
1056	1058	3.726557	TCTGATGAAAGTGAGGCCAAT	57.273	42.857	5.01	0.00	0.00	3.16
1209	1211	5.300034	ACATGTAGTTACCATGCCATCAATG	59.700	40.000	0.00	0.00	0.00	2.82
1259	1261	6.544928	AACCAGTGTATCACTATCATCACA	57.455	37.500	2.03	0.00	43.43	3.58
1298	1300	6.239008	CCTGATGCAAAGTTTACTCCTTCAAA	60.239	38.462	0.00	0.00	0.00	2.69
1353	1355	5.509498	CATAGGGAAATCTTTGAGAACCCA	58.491	41.667	15.33	6.79	38.05	4.51
1355	1357	2.488153	GGGAAATCTTTGAGAACCCACG	59.512	50.000	0.00	0.00	36.70	4.94
1381	1383	6.825721	AGAAATATTCTCGCACCAAGATTTCT	59.174	34.615	12.15	12.15	42.01	2.52
1470	1472	6.830912	TCCATCAATTACATCCTTACTCCAG	58.169	40.000	0.00	0.00	0.00	3.86
1626	1629	4.383850	TTTTGTCACCACTGACCAATTG	57.616	40.909	0.00	0.00	45.68	2.32
1673	1676	4.534401	GGGACGCTAACCCATGAC	57.466	61.111	0.00	0.00	46.05	3.06
1702	1705	0.400594	GTTGTGCCTACCCCTCTTGT	59.599	55.000	0.00	0.00	0.00	3.16
1715	1718	0.804989	CTCTTGTTCCATTCGCCACC	59.195	55.000	0.00	0.00	0.00	4.61
1753	1756	4.952957	CAGAGAAGACAAGACTCCTATGGA	59.047	45.833	0.00	0.00	0.00	3.41
1940	1943	3.091545	GAGTGCCAAAATGGATGAAGGA	58.908	45.455	0.00	0.00	40.96	3.36
1956	1959	6.240118	GGATGAAGGAAGATGTTCTATCCCAT	60.240	42.308	2.24	0.58	32.72	4.00
2110	2114	7.348080	TCCTTATGTAACTACCAGACTCATG	57.652	40.000	0.00	0.00	0.00	3.07
2197	2201	7.104290	ACAAAGAACCATTAGAGCTAGGTAAC	58.896	38.462	0.00	0.00	33.15	2.50
2240	2244	4.202441	ACGCTTGCATTCTTTATGGAGAT	58.798	39.130	0.00	0.00	35.86	2.75
2367	2371	3.691049	TTGGTTTTCTTGTCTTGCTCG	57.309	42.857	0.00	0.00	0.00	5.03
2387	2391	4.326826	TCGTTTCTCTGGCAATTCAAGAT	58.673	39.130	0.00	0.00	0.00	2.40
2781	2785	0.182299	CTCCTCCAGCCAATTCCCTC	59.818	60.000	0.00	0.00	0.00	4.30
2866	2870	5.073428	AGAGATATCCTTGCGTGTAGATCA	58.927	41.667	0.00	0.00	0.00	2.92
2876	2880	3.745975	TGCGTGTAGATCAAACTTTGAGG	59.254	43.478	9.97	0.00	43.98	3.86
2880	2884	5.643777	CGTGTAGATCAAACTTTGAGGGATT	59.356	40.000	9.97	0.00	43.98	3.01
2899	2903	1.072266	TGACTGGTAGGCCCATTTGT	58.928	50.000	0.00	0.00	44.15	2.83
2906	2910	2.583143	GTAGGCCCATTTGTATGACCC	58.417	52.381	0.00	0.00	33.37	4.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	6.125029	AGTCCATCGATCTTGGATGAAAAAT	58.875	36.000	15.05	0.00	44.75	1.82
71	72	6.094881	TGGTATTTATTCCTCTGGAAAAAGCG	59.905	38.462	2.98	0.00	45.41	4.68
73	74	9.025041	AGTTGGTATTTATTCCTCTGGAAAAAG	57.975	33.333	2.98	0.00	45.41	2.27
149	150	2.457323	AAGGCCAGGTTCGGGTCAA	61.457	57.895	5.01	0.00	30.51	3.18
266	267	6.547880	TCCACAAGGCAATGTAAAGTAAGAAA	59.452	34.615	0.00	0.00	33.74	2.52
272	273	3.561143	TGTCCACAAGGCAATGTAAAGT	58.439	40.909	0.00	0.00	33.74	2.66
433	435	7.218773	CGCCTATATGAACAACAAAATTGTCTG	59.781	37.037	0.00	3.69	41.31	3.51
462	464	9.226606	AGTCTATCAAATAATTTCCGTCAAACA	57.773	29.630	0.00	0.00	0.00	2.83
468	470	5.815740	ACGCAGTCTATCAAATAATTTCCGT	59.184	36.000	0.00	0.00	29.74	4.69
523	525	0.605083	TCAGCTGCAATCTCTGTCGT	59.395	50.000	9.47	0.00	0.00	4.34
528	530	2.500504	TCTCACATCAGCTGCAATCTCT	59.499	45.455	9.47	0.00	0.00	3.10
646	648	5.555966	GACCCAAAAATTTAAGGCCAATGA	58.444	37.500	5.01	0.00	0.00	2.57
656	658	3.637229	TCACTTGCCGACCCAAAAATTTA	59.363	39.130	0.00	0.00	0.00	1.40
952	954	5.693769	TCAGGAAAGGTATGGAAAGTAGG	57.306	43.478	0.00	0.00	0.00	3.18
1026	1028	6.313411	CCTCACTTTCATCAGATCTGACTTTC	59.687	42.308	27.37	0.00	43.11	2.62
1039	1041	6.238869	GGAGAAATATTGGCCTCACTTTCATC	60.239	42.308	3.32	7.90	0.00	2.92
1040	1042	5.595952	GGAGAAATATTGGCCTCACTTTCAT	59.404	40.000	3.32	0.00	0.00	2.57
1091	1093	2.093553	TCACTCAACATCGGCATGATCA	60.094	45.455	0.00	0.00	34.13	2.92
1316	1318	1.284785	CCCTATGGTTGGGCTGAGAAA	59.715	52.381	0.00	0.00	37.99	2.52
1381	1383	9.841295	AAAGTAGTTCCTAATAGTGTTTGACAA	57.159	29.630	0.00	0.00	0.00	3.18
1618	1621	4.638865	GTGGACCCTGTATAACAATTGGTC	59.361	45.833	10.83	3.93	39.06	4.02
1626	1629	7.994334	TGGTATATTTTGTGGACCCTGTATAAC	59.006	37.037	0.00	0.00	0.00	1.89
1669	1672	2.936498	GGCACAACATAAGTAGCGTCAT	59.064	45.455	0.00	0.00	0.00	3.06
1673	1676	2.864343	GGTAGGCACAACATAAGTAGCG	59.136	50.000	0.00	0.00	0.00	4.26
1702	1705	1.198094	TGAGGAGGTGGCGAATGGAA	61.198	55.000	0.00	0.00	0.00	3.53
1715	1718	1.980784	CTCTGGGGCCATGTGAGGAG	61.981	65.000	4.39	0.00	0.00	3.69
1753	1756	9.066892	CACTATTAGTAATGCCATTTGGTACAT	57.933	33.333	5.61	0.00	39.30	2.29
1785	1788	9.411801	CTTACGTGAACTCATAGTATTATGCAT	57.588	33.333	3.79	3.79	37.23	3.96
2100	2104	4.639334	CAGATAACCATCCATGAGTCTGG	58.361	47.826	0.00	0.00	37.66	3.86
2110	2114	6.874134	ACGATTAACATAGCAGATAACCATCC	59.126	38.462	0.00	0.00	0.00	3.51
2153	2157	8.001881	TCTTTGTTCAAAAGCATGGTTACTTA	57.998	30.769	11.15	0.00	0.00	2.24
2173	2177	7.331791	AGTTACCTAGCTCTAATGGTTCTTTG	58.668	38.462	0.00	0.00	34.33	2.77
2174	2178	7.497773	AGTTACCTAGCTCTAATGGTTCTTT	57.502	36.000	0.00	0.00	34.33	2.52
2197	2201	4.240096	GTCATTTGCCAATCCTTGTCAAG	58.760	43.478	5.53	5.53	0.00	3.02
2219	2223	4.825546	ATCTCCATAAAGAATGCAAGCG	57.174	40.909	0.00	0.00	33.92	4.68
2264	2268	8.691661	AAAACATAGCCATGGTATAGGTAAAG	57.308	34.615	14.67	0.04	36.39	1.85
2294	2298	2.288666	GAGCCACAAGAGAACACAACA	58.711	47.619	0.00	0.00	0.00	3.33
2304	2308	3.318839	CCAATTTTCACTGAGCCACAAGA	59.681	43.478	0.00	0.00	0.00	3.02
2367	2371	4.741342	CCATCTTGAATTGCCAGAGAAAC	58.259	43.478	0.00	0.00	0.00	2.78
2470	2474	8.894409	TGAACAAGCAATCAATAGTTTTATCG	57.106	30.769	0.00	0.00	0.00	2.92
2546	2550	2.104967	CATGAGGGCCATGTTGTCAAT	58.895	47.619	6.18	0.00	45.83	2.57
2632	2636	2.388735	TCTCTCGGGTGTTCTATGCAT	58.611	47.619	3.79	3.79	0.00	3.96
2781	2785	3.181487	GGGATTCCATGATTGGTTGTTCG	60.181	47.826	4.80	0.00	44.06	3.95
2866	2870	4.184649	ACCAGTCAATCCCTCAAAGTTT	57.815	40.909	0.00	0.00	0.00	2.66
2876	2880	2.307153	TGGGCCTACCAGTCAATCC	58.693	57.895	4.53	0.00	46.80	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.