AutoCloner

Multiple sequence alignment - TraesCS5D01G356300

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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	TraesCS5D01G356300	chr5D	100.000	2438	0	0	1	2438	437529130	437526693	0.000000e+00	4503
1	TraesCS5D01G356300	chr5D	85.859	1874	237	17	564	2417	421110041	421111906	0.000000e+00	1967
2	TraesCS5D01G356300	chr5D	88.506	87	8	2	8	93	24575276	24575191	1.190000e-18	104
3	TraesCS5D01G356300	chr5B	91.176	1870	147	7	564	2420	339553033	339554897	0.000000e+00	2523
4	TraesCS5D01G356300	chr5B	98.039	561	10	1	1	561	531612276	531611717	0.000000e+00	974
5	TraesCS5D01G356300	chr5B	90.722	485	33	6	1	481	100037953	100037477	9.510000e-179	636
6	TraesCS5D01G356300	chr3D	86.293	1875	226	22	564	2420	7522491	7524352	0.000000e+00	2010
7	TraesCS5D01G356300	chr7D	86.261	1856	235	15	569	2413	395184714	395186560	0.000000e+00	1997
8	TraesCS5D01G356300	chr1B	85.461	1864	244	21	571	2420	116133000	116131150	0.000000e+00	1916
9	TraesCS5D01G356300	chr1B	84.673	1866	252	23	569	2420	146958851	146960696	0.000000e+00	1831
10	TraesCS5D01G356300	chr3B	84.735	1867	255	21	564	2417	9644597	9646446	0.000000e+00	1842
11	TraesCS5D01G356300	chr4D	84.562	1859	263	19	569	2420	69407908	69406067	0.000000e+00	1821
12	TraesCS5D01G356300	chr3A	84.030	1866	272	17	569	2420	673433207	673431354	0.000000e+00	1772
13	TraesCS5D01G356300	chr6B	97.464	552	14	0	1	552	607123522	607122971	0.000000e+00	942
14	TraesCS5D01G356300	chr6B	92.647	68	5	0	8	75	711757706	711757773	5.550000e-17	99
15	TraesCS5D01G356300	chr5A	88.036	560	38	8	1	559	396224110	396223579	9.510000e-179	636
16	TraesCS5D01G356300	chr6A	89.024	82	9	0	8	89	125261820	125261901	4.290000e-18	102
17	TraesCS5D01G356300	chr6A	89.024	82	9	0	8	89	611903590	611903671	4.290000e-18	102

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	TraesCS5D01G356300	chr5D	437526693	437529130	2437	True	4503	4503	100.000	1	2438	1	chr5D.!!$R2	2437
1	TraesCS5D01G356300	chr5D	421110041	421111906	1865	False	1967	1967	85.859	564	2417	1	chr5D.!!$F1	1853
2	TraesCS5D01G356300	chr5B	339553033	339554897	1864	False	2523	2523	91.176	564	2420	1	chr5B.!!$F1	1856
3	TraesCS5D01G356300	chr5B	531611717	531612276	559	True	974	974	98.039	1	561	1	chr5B.!!$R2	560
4	TraesCS5D01G356300	chr3D	7522491	7524352	1861	False	2010	2010	86.293	564	2420	1	chr3D.!!$F1	1856
5	TraesCS5D01G356300	chr7D	395184714	395186560	1846	False	1997	1997	86.261	569	2413	1	chr7D.!!$F1	1844
6	TraesCS5D01G356300	chr1B	116131150	116133000	1850	True	1916	1916	85.461	571	2420	1	chr1B.!!$R1	1849
7	TraesCS5D01G356300	chr1B	146958851	146960696	1845	False	1831	1831	84.673	569	2420	1	chr1B.!!$F1	1851
8	TraesCS5D01G356300	chr3B	9644597	9646446	1849	False	1842	1842	84.735	564	2417	1	chr3B.!!$F1	1853
9	TraesCS5D01G356300	chr4D	69406067	69407908	1841	True	1821	1821	84.562	569	2420	1	chr4D.!!$R1	1851
10	TraesCS5D01G356300	chr3A	673431354	673433207	1853	True	1772	1772	84.030	569	2420	1	chr3A.!!$R1	1851
11	TraesCS5D01G356300	chr6B	607122971	607123522	551	True	942	942	97.464	1	552	1	chr6B.!!$R1	551
12	TraesCS5D01G356300	chr5A	396223579	396224110	531	True	636	636	88.036	1	559	1	chr5A.!!$R1	558

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
868	876	0.384309	CCATTAGTGACTCGCGGCTA	59.616	55.0	6.13	0.0	0.0	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2048	2065	0.106335	CGGCGGAGAGGAGTCTACTA	59.894	60.0	0.0	0.0	30.17	1.82	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
60	61	1.363744	CAGCGGTGAATCTGAAGGAC	58.636	55.000	9.50	0.00	32.26	3.85
526	527	1.006832	GCGCATCAGTTGATACGGTT	58.993	50.000	14.54	0.00	40.60	4.44
561	562	4.122776	GAGGCTGAACTATACATGTGGTG	58.877	47.826	9.11	0.32	0.00	4.17
562	563	3.519510	AGGCTGAACTATACATGTGGTGT	59.480	43.478	9.11	0.99	44.95	4.16
631	633	4.840545	GGGTCTCCCTCCTCCAAT	57.159	61.111	0.00	0.00	41.34	3.16
632	634	3.970426	GGGTCTCCCTCCTCCAATA	57.030	57.895	0.00	0.00	41.34	1.90
633	635	2.424684	GGGTCTCCCTCCTCCAATAT	57.575	55.000	0.00	0.00	41.34	1.28
643	645	5.901853	TCCCTCCTCCAATATATATGCTGAG	59.098	44.000	0.00	3.29	0.00	3.35
765	770	2.499289	AGAGCGAAGTGATGATCCTTGT	59.501	45.455	1.72	0.00	0.00	3.16
868	876	0.384309	CCATTAGTGACTCGCGGCTA	59.616	55.000	6.13	0.00	0.00	3.93
909	917	1.058748	CAGTAACGCGGATGCAACG	59.941	57.895	12.47	9.51	42.97	4.10
981	990	2.497675	TCTCATTAACTCCTCGCTTGCT	59.502	45.455	0.00	0.00	0.00	3.91
984	993	3.447586	TCATTAACTCCTCGCTTGCTAGT	59.552	43.478	0.00	0.00	0.00	2.57
1074	1085	1.763770	CAGGTTCTTCTGGGCAGGT	59.236	57.895	0.00	0.00	0.00	4.00
1123	1134	2.180017	GCTGGCCTGACATTTGCG	59.820	61.111	14.77	0.00	0.00	4.85
1160	1171	2.838202	GTGGTCTTGGGATCTTGTCCTA	59.162	50.000	0.00	0.00	46.91	2.94
1258	1273	5.592688	ACCATTGTCCGGAATAAATACCTTG	59.407	40.000	5.23	0.00	0.00	3.61
1293	1308	4.742201	TTCTGTCAGCGCTCCGGC	62.742	66.667	7.13	0.00	0.00	6.13
1312	1327	1.821061	CGTCTCCCAGTTCTGGCAGT	61.821	60.000	15.27	0.00	0.00	4.40
1341	1356	3.003113	GCTTCTCCCCGTGCTACGT	62.003	63.158	0.00	0.00	40.58	3.57
1486	1501	2.750637	TCTGTCGAGTCGGCCCTC	60.751	66.667	15.66	0.00	0.00	4.30
1560	1576	1.901085	CTTGGGACTCCCTTCTCCG	59.099	63.158	15.64	0.00	45.70	4.63
1593	1609	2.827190	CCCGATGGACGTCGAGGA	60.827	66.667	12.85	0.00	44.06	3.71
1595	1611	2.404186	CCGATGGACGTCGAGGACA	61.404	63.158	12.85	10.57	44.06	4.02
1597	1613	1.226323	GATGGACGTCGAGGACACG	60.226	63.158	12.85	1.56	43.13	4.49
1609	1625	0.891373	AGGACACGTCTGACTCCATG	59.109	55.000	14.69	6.91	0.00	3.66
1644	1660	2.739996	CCTCTGGCCGCTTCTCCAT	61.740	63.158	0.00	0.00	0.00	3.41
1645	1661	1.523258	CTCTGGCCGCTTCTCCATG	60.523	63.158	0.00	0.00	0.00	3.66
1837	1853	1.896183	CATGTGTGGCACGGTGGAA	60.896	57.895	13.77	0.00	37.14	3.53
1915	1932	2.697761	CGAGACGGTCGGTGGACAT	61.698	63.158	1.89	0.00	45.58	3.06
2026	2043	0.465460	TTGCTTGGACGCTTTGGACT	60.465	50.000	0.00	0.00	0.00	3.85
2027	2044	1.165907	TGCTTGGACGCTTTGGACTG	61.166	55.000	0.00	0.00	0.00	3.51
2035	2052	0.028770	CGCTTTGGACTGTTCGCAAA	59.971	50.000	0.00	0.00	0.00	3.68
2036	2053	1.334960	CGCTTTGGACTGTTCGCAAAT	60.335	47.619	0.00	0.00	0.00	2.32
2048	2065	5.183140	ACTGTTCGCAAATAGCTGGTTATTT	59.817	36.000	0.00	0.00	42.61	1.40
2051	2068	6.373216	TGTTCGCAAATAGCTGGTTATTTAGT	59.627	34.615	0.00	0.00	42.61	2.24
2173	2190	2.187493	CCTCCTCGCCGATCTTCGA	61.187	63.158	0.00	6.12	43.74	3.71
2338	2363	5.880332	ACTTCTTTGTGCTTTGTGAGACTTA	59.120	36.000	0.00	0.00	0.00	2.24
2339	2364	5.991328	TCTTTGTGCTTTGTGAGACTTAG	57.009	39.130	0.00	0.00	0.00	2.18
2341	2366	5.294306	TCTTTGTGCTTTGTGAGACTTAGTG	59.706	40.000	0.00	0.00	0.00	2.74
2357	2397	6.495872	AGACTTAGTGTGTGTATGGAACCTTA	59.504	38.462	0.00	0.00	0.00	2.69
2383	2423	1.758514	TTTGGCTTGGGCGGTTTGA	60.759	52.632	0.00	0.00	39.81	2.69
2420	2462	2.400399	GGCAAAAGCCTTTTTCGGTAC	58.600	47.619	0.00	0.00	34.34	3.34
2421	2463	2.400399	GCAAAAGCCTTTTTCGGTACC	58.600	47.619	0.16	0.16	34.34	3.34
2422	2464	2.035449	GCAAAAGCCTTTTTCGGTACCT	59.965	45.455	10.90	0.00	34.34	3.08
2423	2465	3.253921	GCAAAAGCCTTTTTCGGTACCTA	59.746	43.478	10.90	0.00	34.34	3.08
2424	2466	4.082408	GCAAAAGCCTTTTTCGGTACCTAT	60.082	41.667	10.90	0.00	34.34	2.57
2425	2467	5.124297	GCAAAAGCCTTTTTCGGTACCTATA	59.876	40.000	10.90	0.00	34.34	1.31
2426	2468	6.549061	CAAAAGCCTTTTTCGGTACCTATAC	58.451	40.000	10.90	0.00	34.34	1.47
2427	2469	5.425196	AAGCCTTTTTCGGTACCTATACA	57.575	39.130	10.90	0.00	32.40	2.29
2428	2470	5.625568	AGCCTTTTTCGGTACCTATACAT	57.374	39.130	10.90	0.00	32.40	2.29
2429	2471	5.365619	AGCCTTTTTCGGTACCTATACATG	58.634	41.667	10.90	0.00	32.40	3.21
2430	2472	5.104652	AGCCTTTTTCGGTACCTATACATGT	60.105	40.000	10.90	2.69	32.40	3.21
2431	2473	5.007332	GCCTTTTTCGGTACCTATACATGTG	59.993	44.000	9.11	0.00	32.40	3.21
2432	2474	5.526111	CCTTTTTCGGTACCTATACATGTGG	59.474	44.000	9.11	3.60	32.40	4.17
2433	2475	5.680594	TTTTCGGTACCTATACATGTGGT	57.319	39.130	9.11	10.14	37.83	4.16
2434	2476	4.924305	TTCGGTACCTATACATGTGGTC	57.076	45.455	9.11	2.24	35.48	4.02
2435	2477	3.900971	TCGGTACCTATACATGTGGTCA	58.099	45.455	9.11	0.00	35.48	4.02
2436	2478	3.887110	TCGGTACCTATACATGTGGTCAG	59.113	47.826	9.11	3.15	35.48	3.51
2437	2479	3.552273	CGGTACCTATACATGTGGTCAGC	60.552	52.174	9.11	5.73	35.48	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
60	61	4.556898	GCCAGTCTATCATACAGGTACACG	60.557	50.000	0.00	0.00	0.00	4.49
526	527	3.891805	TCAGCCTCCAGATCTCATAGA	57.108	47.619	0.00	0.00	0.00	1.98
673	675	2.885135	TCAGGTTGGCAATGTCAGAT	57.115	45.000	1.92	0.00	0.00	2.90
765	770	1.612442	GCCTCCTCAGGTGGGTACA	60.612	63.158	13.96	0.00	42.74	2.90
868	876	2.251642	GCGAAGGTCAGCAACGGTT	61.252	57.895	0.00	0.00	0.00	4.44
937	946	1.301401	CCCGAGTTGCCTTCGACAA	60.301	57.895	3.54	0.00	40.36	3.18
981	990	4.935578	TCATGAGAAACCAGAGGAGACTA	58.064	43.478	0.00	0.00	44.43	2.59
984	993	2.499289	GCTCATGAGAAACCAGAGGAGA	59.501	50.000	27.04	0.00	0.00	3.71
1074	1085	4.962362	TGATACTTCTGCTTATCACCCTCA	59.038	41.667	0.00	0.00	31.17	3.86
1160	1171	2.876955	CAATGTTCATGCGCCGGT	59.123	55.556	4.18	0.00	0.00	5.28
1312	1327	1.330655	GGGAGAAGCTGGATCACGGA	61.331	60.000	0.00	0.00	0.00	4.69
1341	1356	1.206132	ACCGAGATTGACGTGCCAATA	59.794	47.619	0.00	0.00	36.93	1.90
1353	1368	3.760580	GATCCAGATCCAACCGAGATT	57.239	47.619	0.00	0.00	31.76	2.40
1486	1501	1.398390	GCAAGACGCCCTAAGTCAATG	59.602	52.381	0.00	0.00	40.84	2.82
1560	1576	2.506472	GGAGAAGGGCGATGTCCC	59.494	66.667	0.00	0.00	46.93	4.46
1644	1660	2.742348	TGGCCGAGTATAAGGACTTCA	58.258	47.619	0.00	0.00	36.23	3.02
1645	1661	3.612004	CGATGGCCGAGTATAAGGACTTC	60.612	52.174	0.00	1.23	41.76	3.01
1778	1794	1.065199	TCCATTGCGCTTGAGGATCTT	60.065	47.619	9.73	0.00	34.92	2.40
1781	1797	0.749454	GGTCCATTGCGCTTGAGGAT	60.749	55.000	9.73	0.00	0.00	3.24
2035	2052	8.228905	AGAGGAGTCTACTAAATAACCAGCTAT	58.771	37.037	0.00	0.00	0.00	2.97
2036	2053	7.584532	AGAGGAGTCTACTAAATAACCAGCTA	58.415	38.462	0.00	0.00	0.00	3.32
2048	2065	0.106335	CGGCGGAGAGGAGTCTACTA	59.894	60.000	0.00	0.00	30.17	1.82
2051	2068	1.451567	CACGGCGGAGAGGAGTCTA	60.452	63.158	13.24	0.00	30.97	2.59
2077	2094	2.687935	ACCACACAGTTTGAAAATCGCT	59.312	40.909	0.00	0.00	0.00	4.93
2173	2190	1.039233	CCAAGCGGAAGGCCATTGAT	61.039	55.000	5.01	0.00	45.17	2.57
2338	2363	5.013704	TCCAATAAGGTTCCATACACACACT	59.986	40.000	0.00	0.00	39.02	3.55
2339	2364	5.250200	TCCAATAAGGTTCCATACACACAC	58.750	41.667	0.00	0.00	39.02	3.82
2341	2366	5.885912	ACATCCAATAAGGTTCCATACACAC	59.114	40.000	0.00	0.00	39.02	3.82
2357	2397	0.614812	GCCCAAGCCAAACATCCAAT	59.385	50.000	0.00	0.00	0.00	3.16
2383	2423	7.320399	GCTTTTGCCCCGCTTTATATATAAAT	58.680	34.615	16.41	0.00	40.15	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.