AutoCloner

Multiple sequence alignment - TraesCS3A01G410400

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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	TraesCS3A01G410400	chr3A	100.000	2999	0	0	1	2999	654517493	654520491	0.000000e+00	5539
1	TraesCS3A01G410400	chr3A	95.766	2740	106	8	261	2999	654498908	654501638	0.000000e+00	4409
2	TraesCS3A01G410400	chr3A	87.500	2016	235	17	950	2954	654584720	654582711	0.000000e+00	2311
3	TraesCS3A01G410400	chr3A	90.437	481	40	6	2237	2714	654559975	654560452	1.960000e-176	628
4	TraesCS3A01G410400	chr3A	84.524	420	60	3	494	908	654585148	654584729	7.740000e-111	411
5	TraesCS3A01G410400	chr3D	95.670	3002	118	12	1	2999	519596211	519599203	0.000000e+00	4813
6	TraesCS3A01G410400	chr3D	86.056	2467	290	36	499	2953	519644709	519642285	0.000000e+00	2601
7	TraesCS3A01G410400	chr3D	88.846	771	73	13	2233	2999	519620583	519621344	0.000000e+00	935
8	TraesCS3A01G410400	chr3D	88.753	489	49	6	5	491	582629045	582628561	7.160000e-166	593
9	TraesCS3A01G410400	chr3B	92.565	2865	188	15	151	2999	684137573	684134718	0.000000e+00	4087
10	TraesCS3A01G410400	chrUn	91.377	2528	186	26	494	2999	101062265	101064782	0.000000e+00	3432
11	TraesCS3A01G410400	chrUn	88.211	492	48	9	5	493	314598869	314598385	2.000000e-161	579
12	TraesCS3A01G410400	chr6A	91.192	2543	178	30	497	2999	35564038	35561502	0.000000e+00	3413
13	TraesCS3A01G410400	chr5A	88.641	493	46	9	2	491	613393727	613394212	2.570000e-165	592
14	TraesCS3A01G410400	chr6B	88.438	493	50	7	2	491	68733601	68734089	3.330000e-164	588
15	TraesCS3A01G410400	chr2B	88.548	489	51	5	6	492	733462331	733461846	3.330000e-164	588
16	TraesCS3A01G410400	chr7A	88.344	489	50	7	5	491	162762857	162762374	5.570000e-162	580
17	TraesCS3A01G410400	chr7A	72.755	1960	436	76	1043	2951	703549663	703551575	3.350000e-159	571
18	TraesCS3A01G410400	chr4A	88.081	495	49	9	2	493	652781857	652782344	2.000000e-161	579
19	TraesCS3A01G410400	chr7B	73.400	1594	365	44	1383	2944	702196545	702194979	9.460000e-150	540

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	TraesCS3A01G410400	chr3A	654517493	654520491	2998	False	5539	5539	100.000	1	2999	1	chr3A.!!$F2	2998
1	TraesCS3A01G410400	chr3A	654498908	654501638	2730	False	4409	4409	95.766	261	2999	1	chr3A.!!$F1	2738
2	TraesCS3A01G410400	chr3A	654582711	654585148	2437	True	1361	2311	86.012	494	2954	2	chr3A.!!$R1	2460
3	TraesCS3A01G410400	chr3D	519596211	519599203	2992	False	4813	4813	95.670	1	2999	1	chr3D.!!$F1	2998
4	TraesCS3A01G410400	chr3D	519642285	519644709	2424	True	2601	2601	86.056	499	2953	1	chr3D.!!$R1	2454
5	TraesCS3A01G410400	chr3D	519620583	519621344	761	False	935	935	88.846	2233	2999	1	chr3D.!!$F2	766
6	TraesCS3A01G410400	chr3B	684134718	684137573	2855	True	4087	4087	92.565	151	2999	1	chr3B.!!$R1	2848
7	TraesCS3A01G410400	chrUn	101062265	101064782	2517	False	3432	3432	91.377	494	2999	1	chrUn.!!$F1	2505
8	TraesCS3A01G410400	chr6A	35561502	35564038	2536	True	3413	3413	91.192	497	2999	1	chr6A.!!$R1	2502
9	TraesCS3A01G410400	chr7A	703549663	703551575	1912	False	571	571	72.755	1043	2951	1	chr7A.!!$F1	1908
10	TraesCS3A01G410400	chr7B	702194979	702196545	1566	True	540	540	73.400	1383	2944	1	chr7B.!!$R1	1561

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
23	24	0.115349	AGTCTGGGAGTAGCAGTGGT	59.885	55.0	0.0	0.0	0.00	4.16	F
1136	1188	0.671472	CGCACAAGCATCCTCTCACA	60.671	55.0	0.0	0.0	42.27	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1173	1225	0.038526	ACACGACCTCGCGAAAGATT	60.039	50.000	11.33	0.0	44.43	2.40	R
2275	2340	1.578215	AGGAGATAGCTTGGGACCTCT	59.422	52.381	0.00	0.0	0.00	3.69	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
23	24	0.115349	AGTCTGGGAGTAGCAGTGGT	59.885	55.000	0.00	0.00	0.00	4.16
62	63	6.879458	GTCAAGTCTAATGTACATGGAGGTTT	59.121	38.462	9.63	5.81	0.00	3.27
70	71	1.167851	ACATGGAGGTTTGACGCATG	58.832	50.000	0.00	0.00	0.00	4.06
127	128	5.891551	AGGTGGAGTTTGTTAGAATTGTGTT	59.108	36.000	0.00	0.00	0.00	3.32
170	171	2.310779	TACAGTTGGACTCTGAGCCT	57.689	50.000	15.75	0.00	36.81	4.58
506	509	6.899393	TTCTAACAATGCTTGATTGAAGGT	57.101	33.333	2.51	0.00	43.87	3.50
578	582	6.070021	TGAGAAGATTCTGGATAAGGCAAAGA	60.070	38.462	0.00	0.00	37.73	2.52
799	811	5.741011	ACTTTCCTCAAGTAAACTGACACA	58.259	37.500	0.00	0.00	44.56	3.72
817	829	3.380004	ACACAACCACACACCACTAAATG	59.620	43.478	0.00	0.00	0.00	2.32
841	853	2.763215	GCCACCCACCCTCATGAA	59.237	61.111	0.00	0.00	0.00	2.57
859	871	2.118076	CCCACCAAGCACCACCAT	59.882	61.111	0.00	0.00	0.00	3.55
936	986	6.532988	GTGTCCTCACCTCTAGTTTATTCT	57.467	41.667	0.00	0.00	38.51	2.40
943	993	6.023603	TCACCTCTAGTTTATTCTGTCCCTT	58.976	40.000	0.00	0.00	0.00	3.95
951	1001	1.562672	ATTCTGTCCCTTCACCCCCG	61.563	60.000	0.00	0.00	0.00	5.73
1112	1164	1.915141	CTCCCCTGCATCAAAGTTGT	58.085	50.000	0.00	0.00	0.00	3.32
1136	1188	0.671472	CGCACAAGCATCCTCTCACA	60.671	55.000	0.00	0.00	42.27	3.58
1155	1207	2.665000	CGATGGTGTGGCCTCTGT	59.335	61.111	3.32	0.00	38.35	3.41
1173	1225	0.465460	GTGCCCATCTCCGCCAAATA	60.465	55.000	0.00	0.00	0.00	1.40
1353	1408	2.187073	GGAGTTCGTCGCCTCCTTA	58.813	57.895	18.30	0.00	43.29	2.69
1354	1409	0.529378	GGAGTTCGTCGCCTCCTTAA	59.471	55.000	18.30	0.00	43.29	1.85
1375	1430	4.526438	ACCTCAAGCTTTGGCCTATTAT	57.474	40.909	3.32	0.00	39.73	1.28
1376	1431	4.464947	ACCTCAAGCTTTGGCCTATTATC	58.535	43.478	3.32	0.00	39.73	1.75
1381	1436	3.056080	AGCTTTGGCCTATTATCCAGGA	58.944	45.455	3.32	0.00	39.73	3.86
1492	1550	0.872021	CCCTATGCTCGAGACGTTGC	60.872	60.000	18.75	0.00	0.00	4.17
1888	1950	2.024177	AGTGTAGTAAGTCCCCTCTCCC	60.024	54.545	0.00	0.00	0.00	4.30
1986	2050	2.026262	GTCACTTTTCCCCTATGAGCCA	60.026	50.000	0.00	0.00	0.00	4.75
1996	2060	2.762327	CCCTATGAGCCAAACTTTGCAT	59.238	45.455	0.00	0.00	0.00	3.96
2033	2097	4.333926	GCATATGGTTGTTGACTTCTCTCC	59.666	45.833	4.56	0.00	0.00	3.71
2054	2118	6.319048	TCCTTTGGAGCTAGATCTCAAAAT	57.681	37.500	18.70	0.00	35.94	1.82
2227	2292	6.002082	AGCTTACATTTACTTTTCGGTCCTT	58.998	36.000	0.00	0.00	0.00	3.36
2722	2798	6.743575	ATTCTAAATGCTATAATCCCACGC	57.256	37.500	0.00	0.00	0.00	5.34
2894	2980	6.772360	TTGCATATGTATTCTGCTTTCCAA	57.228	33.333	4.29	0.00	36.84	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	0.534412	CCACTGCTACTCCCAGACTG	59.466	60.000	0.00	0.00	34.47	3.51
37	38	5.978814	ACCTCCATGTACATTAGACTTGAC	58.021	41.667	5.37	0.00	0.00	3.18
70	71	2.158696	CTCCACCTCCTTGGATTCATCC	60.159	54.545	0.00	0.00	44.97	3.51
143	144	6.350612	GCTCAGAGTCCAACTGTAATCTAACT	60.351	42.308	0.00	0.00	36.81	2.24
149	150	3.177228	AGGCTCAGAGTCCAACTGTAAT	58.823	45.455	11.98	0.00	36.81	1.89
170	171	8.177456	ACTCCATATCCTATCTACACACCATAA	58.823	37.037	0.00	0.00	0.00	1.90
280	281	2.809601	CCCGCGTGTCTGTGCTAC	60.810	66.667	4.92	0.00	0.00	3.58
506	509	7.695480	TGCAAAGTGGTAATAAATAGCTTGA	57.305	32.000	0.00	0.00	33.08	3.02
578	582	4.288105	CCTTAATACATGCCTCTCTCCCAT	59.712	45.833	0.00	0.00	0.00	4.00
617	621	2.489985	CCCCTTGTTGTATGTGGTCCAA	60.490	50.000	0.00	0.00	0.00	3.53
787	799	3.181504	GGTGTGTGGTTGTGTCAGTTTAC	60.182	47.826	0.00	0.00	0.00	2.01
799	811	3.219281	GGACATTTAGTGGTGTGTGGTT	58.781	45.455	0.00	0.00	0.00	3.67
841	853	2.310930	AATGGTGGTGCTTGGTGGGT	62.311	55.000	0.00	0.00	0.00	4.51
859	871	4.440829	GAGGAATGGGGGCGGCAA	62.441	66.667	12.47	0.00	0.00	4.52
951	1001	0.829990	CTCCAAAGAGAGAGAGGGGC	59.170	60.000	0.00	0.00	43.39	5.80
954	1004	1.494960	CCCCTCCAAAGAGAGAGAGG	58.505	60.000	0.00	0.00	43.39	3.69
955	1005	1.494960	CCCCCTCCAAAGAGAGAGAG	58.505	60.000	0.00	0.00	43.39	3.20
956	1006	3.719939	CCCCCTCCAAAGAGAGAGA	57.280	57.895	0.00	0.00	43.39	3.10
1136	1188	3.005539	AGAGGCCACACCATCGCT	61.006	61.111	5.01	0.00	43.14	4.93
1155	1207	0.257328	TTATTTGGCGGAGATGGGCA	59.743	50.000	0.00	0.00	38.28	5.36
1173	1225	0.038526	ACACGACCTCGCGAAAGATT	60.039	50.000	11.33	0.00	44.43	2.40
1198	1250	1.519455	GGAGTGCTGGTTCGATCGG	60.519	63.158	16.41	0.00	0.00	4.18
1311	1366	1.664649	CTCAAGTTCCGCAGCGACA	60.665	57.895	18.75	0.00	0.00	4.35
1353	1408	2.907458	ATAGGCCAAAGCTTGAGGTT	57.093	45.000	16.91	9.97	39.73	3.50
1354	1409	2.907458	AATAGGCCAAAGCTTGAGGT	57.093	45.000	16.91	3.99	39.73	3.85
1375	1430	4.801521	AATCAATGATGATGGTCCTGGA	57.198	40.909	0.00	0.00	45.60	3.86
1376	1431	4.500887	GCAAATCAATGATGATGGTCCTGG	60.501	45.833	0.00	0.00	45.60	4.45
1381	1436	4.682320	GCAAGGCAAATCAATGATGATGGT	60.682	41.667	0.00	0.00	45.60	3.55
1492	1550	1.033746	CCATTGCAGTGCAGTAGGGG	61.034	60.000	18.81	9.40	40.61	4.79
1613	1671	4.127171	TGAGTTTACAACAAGCTCCTGTC	58.873	43.478	0.00	0.00	0.00	3.51
1986	2050	6.765512	GCTTCTCTATCTCCTATGCAAAGTTT	59.234	38.462	0.00	0.00	0.00	2.66
1996	2060	7.013220	ACAACCATATGCTTCTCTATCTCCTA	58.987	38.462	0.00	0.00	0.00	2.94
2033	2097	8.991026	CATCTATTTTGAGATCTAGCTCCAAAG	58.009	37.037	0.00	0.00	34.36	2.77
2054	2118	4.458989	GTGCTCCAAAAACATGTCCATCTA	59.541	41.667	0.00	0.00	0.00	1.98
2227	2292	6.489603	TCTATTGGGCATTCTTCTTTTACCA	58.510	36.000	0.00	0.00	0.00	3.25
2275	2340	1.578215	AGGAGATAGCTTGGGACCTCT	59.422	52.381	0.00	0.00	0.00	3.69
2808	2891	7.446106	AAAAGGGAAACAAAGGTAAGGAAAT	57.554	32.000	0.00	0.00	0.00	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.