AutoCloner

Multiple sequence alignment - TraesCS6B01G044300

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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	TraesCS6B01G044300	chr6B	100.000	3524	0	0	1	3524	26627926	26624403	0.000000e+00	6508.0
1	TraesCS6B01G044300	chr6B	88.816	1681	171	12	854	2525	26634940	26633268	0.000000e+00	2047.0
2	TraesCS6B01G044300	chr6B	84.513	2021	267	26	597	2605	26646017	26644031	0.000000e+00	1956.0
3	TraesCS6B01G044300	chr6B	89.770	1525	156	0	1001	2525	26597775	26596251	0.000000e+00	1953.0
4	TraesCS6B01G044300	chr6B	75.519	241	43	13	559	788	26635286	26635051	1.730000e-18	104.0
5	TraesCS6B01G044300	chr6B	97.368	38	1	0	737	774	26618682	26618645	8.170000e-07	65.8
6	TraesCS6B01G044300	chr6D	93.799	3564	152	19	1	3522	14657600	14654064	0.000000e+00	5293.0
7	TraesCS6B01G044300	chr6D	85.336	2039	242	29	597	2605	14681181	14679170	0.000000e+00	2056.0
8	TraesCS6B01G044300	chr6D	89.430	1580	155	5	951	2525	14664582	14663010	0.000000e+00	1982.0
9	TraesCS6B01G044300	chr6D	89.836	1525	155	0	1001	2525	14625983	14624459	0.000000e+00	1958.0
10	TraesCS6B01G044300	chr6D	88.175	1649	179	10	1001	2641	14632985	14631345	0.000000e+00	1951.0
11	TraesCS6B01G044300	chr6D	94.872	39	0	2	743	781	14633254	14633218	3.800000e-05	60.2
12	TraesCS6B01G044300	chr6A	91.251	3086	217	21	1	3058	15746609	15749669	0.000000e+00	4154.0
13	TraesCS6B01G044300	chr6A	84.375	480	32	20	3057	3521	15750071	15750522	6.990000e-117	431.0
14	TraesCS6B01G044300	chr6A	84.076	157	14	7	125	275	15726847	15726998	1.320000e-29	141.0
15	TraesCS6B01G044300	chr6A	79.894	189	27	5	597	783	15734076	15734255	1.030000e-25	128.0
16	TraesCS6B01G044300	chr6A	100.000	34	0	0	741	774	15756381	15756414	2.940000e-06	63.9

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	TraesCS6B01G044300	chr6B	26624403	26627926	3523	True	6508.0	6508	100.0000	1	3524	1	chr6B.!!$R3	3523
1	TraesCS6B01G044300	chr6B	26644031	26646017	1986	True	1956.0	1956	84.5130	597	2605	1	chr6B.!!$R4	2008
2	TraesCS6B01G044300	chr6B	26596251	26597775	1524	True	1953.0	1953	89.7700	1001	2525	1	chr6B.!!$R1	1524
3	TraesCS6B01G044300	chr6B	26633268	26635286	2018	True	1075.5	2047	82.1675	559	2525	2	chr6B.!!$R5	1966
4	TraesCS6B01G044300	chr6D	14654064	14657600	3536	True	5293.0	5293	93.7990	1	3522	1	chr6D.!!$R2	3521
5	TraesCS6B01G044300	chr6D	14679170	14681181	2011	True	2056.0	2056	85.3360	597	2605	1	chr6D.!!$R4	2008
6	TraesCS6B01G044300	chr6D	14663010	14664582	1572	True	1982.0	1982	89.4300	951	2525	1	chr6D.!!$R3	1574
7	TraesCS6B01G044300	chr6D	14624459	14625983	1524	True	1958.0	1958	89.8360	1001	2525	1	chr6D.!!$R1	1524
8	TraesCS6B01G044300	chr6D	14631345	14633254	1909	True	1005.6	1951	91.5235	743	2641	2	chr6D.!!$R5	1898
9	TraesCS6B01G044300	chr6A	15746609	15750522	3913	False	2292.5	4154	87.8130	1	3521	2	chr6A.!!$F4	3520

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
964	1144	0.037303	CAAGCCTCCAAGGAGCAAGA	59.963	55.0	10.68	0.0	37.67	3.02	F
1218	1415	0.249911	GTGACAACCTCAACCTCGCT	60.250	55.0	0.00	0.0	0.00	4.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2226	2430	0.248907	CGGTGGAGTATTGCGACGAT	60.249	55.0	0.0	0.0	0.0	3.73	R
2993	3205	0.037697	CGTGGCAGTAGCTAACACCA	60.038	55.0	0.0	0.0	41.7	4.17	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
68	69	0.245539	CCAAGAGGCAGGCAACAATG	59.754	55.000	0.00	0.00	41.41	2.82
70	71	1.201647	CAAGAGGCAGGCAACAATGAG	59.798	52.381	0.00	0.00	41.41	2.90
71	72	0.964358	AGAGGCAGGCAACAATGAGC	60.964	55.000	0.00	0.00	41.41	4.26
195	196	2.231235	TGCAAAGTCAGAGCATCGACTA	59.769	45.455	2.80	0.00	44.10	2.59
196	197	3.118992	TGCAAAGTCAGAGCATCGACTAT	60.119	43.478	2.80	0.00	44.10	2.12
326	353	1.347378	TGCACCTGCTTCATCAGTACA	59.653	47.619	0.00	0.00	42.66	2.90
347	374	1.060937	CGTACGTACGTAGGCGCTT	59.939	57.895	33.95	0.52	44.13	4.68
349	376	0.375106	GTACGTACGTAGGCGCTTCT	59.625	55.000	27.48	0.00	42.83	2.85
356	383	1.411493	CGTAGGCGCTTCTCCGTTTC	61.411	60.000	7.64	0.00	0.00	2.78
358	385	1.537814	TAGGCGCTTCTCCGTTTCCA	61.538	55.000	7.64	0.00	0.00	3.53
359	386	1.745489	GGCGCTTCTCCGTTTCCAT	60.745	57.895	7.64	0.00	0.00	3.41
367	394	4.093556	GCTTCTCCGTTTCCATACTTTGAG	59.906	45.833	0.00	0.00	0.00	3.02
393	420	1.450312	GGCCGACATGGGTTCTCTG	60.450	63.158	0.00	0.00	38.63	3.35
453	480	2.183478	TCACACGGATTGTTGCATCT	57.817	45.000	0.00	0.00	35.67	2.90
454	481	2.076100	TCACACGGATTGTTGCATCTC	58.924	47.619	0.00	0.00	35.67	2.75
459	486	0.743097	GGATTGTTGCATCTCCAGGC	59.257	55.000	0.00	0.00	0.00	4.85
600	639	4.068282	CACGTGCTGAGCTGTGCG	62.068	66.667	15.22	11.97	31.69	5.34
605	644	0.798776	GTGCTGAGCTGTGCGTATTT	59.201	50.000	5.83	0.00	0.00	1.40
730	780	6.711645	ACCGCTGTTTAAACCTTTACTAATCA	59.288	34.615	15.59	0.00	0.00	2.57
784	835	8.977505	GCAATAATACATTCTTCTCTCTGTCTC	58.022	37.037	0.00	0.00	0.00	3.36
793	844	5.730550	TCTTCTCTCTGTCTCTCTGTCTAC	58.269	45.833	0.00	0.00	0.00	2.59
811	867	1.286248	ACCTTACCCTTCGGCTGATT	58.714	50.000	0.00	0.00	0.00	2.57
897	1076	0.175302	CAAAGCACCAAACCACAGCA	59.825	50.000	0.00	0.00	0.00	4.41
964	1144	0.037303	CAAGCCTCCAAGGAGCAAGA	59.963	55.000	10.68	0.00	37.67	3.02
978	1158	3.558958	GGAGCAAGAAGAGAAGAAGCCTT	60.559	47.826	0.00	0.00	34.81	4.35
1089	1286	1.140312	ACAAGGCCAAGTCCTTCAGA	58.860	50.000	5.01	0.00	44.24	3.27
1173	1370	1.801913	CTTCGTCTCCACCTTCGCG	60.802	63.158	0.00	0.00	0.00	5.87
1218	1415	0.249911	GTGACAACCTCAACCTCGCT	60.250	55.000	0.00	0.00	0.00	4.93
1713	1917	0.820871	CGAGTCTCCAGAAGAAGGGG	59.179	60.000	0.00	0.00	35.21	4.79
1731	1935	0.541764	GGGACATGGCCAAGGACAAA	60.542	55.000	22.13	0.00	36.35	2.83
1755	1959	1.971695	GAAGGTCCTTTGGGGTGCG	60.972	63.158	5.36	0.00	36.25	5.34
1941	2145	1.816863	CGCGTCCTATGGGTGGCTAT	61.817	60.000	0.00	0.00	32.63	2.97
2205	2409	2.045708	CAATGTTGGCGCAGGGCTA	61.046	57.895	10.83	0.00	42.94	3.93
2226	2430	4.695217	AACGCAACTTCTTTTCTTCACA	57.305	36.364	0.00	0.00	0.00	3.58
2316	2520	2.360475	GCTCTGGTGCACTTCCCC	60.360	66.667	17.98	0.00	0.00	4.81
2343	2547	1.604378	CTCCATGTTCTTCCCGGCT	59.396	57.895	0.00	0.00	0.00	5.52
2419	2623	3.074857	AGGGCAAGGGTCTCCATATTA	57.925	47.619	0.00	0.00	34.83	0.98
2537	2741	6.261381	CAGCACGTATAAGGCCCTTATTTTTA	59.739	38.462	20.70	0.40	37.72	1.52
2562	2767	8.918202	ATGTCACCTAAGAATTTTACTGTTCA	57.082	30.769	0.00	0.00	0.00	3.18
2631	2841	8.234546	GCGTAATAAGTTGTATGGGGATTTATG	58.765	37.037	0.00	0.00	0.00	1.90
2742	2954	3.556775	ACATGCACAGTTTTGATGTTTGC	59.443	39.130	0.00	0.00	0.00	3.68
2847	3059	9.480053	AGCCAATGTGCATTTCAAAATATATAC	57.520	29.630	0.00	0.00	0.00	1.47
2848	3060	9.480053	GCCAATGTGCATTTCAAAATATATACT	57.520	29.630	0.00	0.00	0.00	2.12
2991	3203	0.742990	TGAATTGGTCGATGCGTCCC	60.743	55.000	0.00	0.00	34.44	4.46
2993	3205	0.107214	AATTGGTCGATGCGTCCCAT	60.107	50.000	4.92	0.00	34.44	4.00
2994	3206	0.815213	ATTGGTCGATGCGTCCCATG	60.815	55.000	4.92	0.00	34.44	3.66
2995	3207	2.588877	GGTCGATGCGTCCCATGG	60.589	66.667	4.14	4.14	33.29	3.66
2996	3208	2.186903	GTCGATGCGTCCCATGGT	59.813	61.111	11.73	0.00	33.29	3.55
2997	3209	2.173669	GTCGATGCGTCCCATGGTG	61.174	63.158	11.73	2.15	33.29	4.17
3046	3259	3.546002	GCTGATCCTAGCTACAGTACG	57.454	52.381	9.95	0.00	40.52	3.67
3074	3690	3.181429	CCATTAGCATAAGTGGGACCCAT	60.181	47.826	18.51	3.78	35.28	4.00
3138	3757	6.295249	TCTTACGATAATTCATCCCAATGCA	58.705	36.000	0.00	0.00	32.58	3.96
3176	3795	9.303116	ACACTGTTTGGATATGGTTTTACATAA	57.697	29.630	0.00	0.00	36.94	1.90
3292	3911	3.960102	AGCAAGGTTGGTCTTTTGAATCA	59.040	39.130	0.00	0.00	32.71	2.57
3321	3940	8.469309	GGATTGAATCCTATGAGATTTTTCCA	57.531	34.615	16.79	0.00	46.19	3.53
3357	3976	9.683069	CTGTAATACATTTCATAGGCATTTTCC	57.317	33.333	0.00	0.00	0.00	3.13
3371	3990	6.252995	AGGCATTTTCCTTTAACATCCACTA	58.747	36.000	0.00	0.00	30.82	2.74
3428	4059	4.437239	TGATGCAAACAAACGAACCATTT	58.563	34.783	0.00	0.00	0.00	2.32
3438	4069	7.784633	ACAAACGAACCATTTCATTCAAATT	57.215	28.000	0.00	0.00	31.79	1.82
3486	4118	1.681538	TTCTGTGCCTGCGGTTTTTA	58.318	45.000	0.00	0.00	0.00	1.52
3490	4122	1.335496	TGTGCCTGCGGTTTTTAGAAC	59.665	47.619	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	0.720027	GTACGCCTTTTCTTCCGCTC	59.280	55.000	0.00	0.00	0.00	5.03
70	71	1.418755	CGTACGCCTTTTCTTCCGC	59.581	57.895	0.52	0.00	0.00	5.54
71	72	1.418755	GCGTACGCCTTTTCTTCCG	59.581	57.895	29.51	0.00	34.56	4.30
195	196	2.472695	AGGACGTGTACATTGCACAT	57.527	45.000	0.00	0.00	36.71	3.21
196	197	2.248280	AAGGACGTGTACATTGCACA	57.752	45.000	0.00	0.00	36.71	4.57
347	374	4.884668	ACTCAAAGTATGGAAACGGAGA	57.115	40.909	0.00	0.00	0.00	3.71
349	376	3.500680	GCAACTCAAAGTATGGAAACGGA	59.499	43.478	0.00	0.00	0.00	4.69
367	394	2.562912	CATGTCGGCCAGTGCAAC	59.437	61.111	2.24	0.00	40.13	4.17
393	420	2.538512	GAAGCTTCGGGTTCCCTCCC	62.539	65.000	11.40	0.00	44.06	4.30
459	486	4.096984	ACAGTTTGAGCTTCAGGTTTCTTG	59.903	41.667	0.00	0.00	0.00	3.02
600	639	4.279420	GGGCCAAGGATCAGATCAAAATAC	59.721	45.833	12.66	0.00	0.00	1.89
605	644	1.297968	TGGGCCAAGGATCAGATCAA	58.702	50.000	2.13	0.00	0.00	2.57
678	721	2.780714	ACGGAGTCGAGAGAGAAAGAA	58.219	47.619	0.00	0.00	43.49	2.52
730	780	1.547372	GGAATCATGGCTGCAACTTGT	59.453	47.619	0.50	0.00	0.00	3.16
811	867	3.118261	GGGATCAACATGCACCTCTCTTA	60.118	47.826	0.00	0.00	0.00	2.10
944	1123	0.964358	CTTGCTCCTTGGAGGCTTGG	60.964	60.000	17.33	0.00	34.61	3.61
964	1144	1.620819	TCGAGCAAGGCTTCTTCTCTT	59.379	47.619	14.72	0.00	39.88	2.85
1089	1286	0.321996	GGTTGGCGAAGGAGAAGAGT	59.678	55.000	0.00	0.00	0.00	3.24
1218	1415	1.071699	GCATTCCCTATGTCGGCCTTA	59.928	52.381	0.00	0.00	36.57	2.69
1713	1917	1.560505	ATTTGTCCTTGGCCATGTCC	58.439	50.000	6.09	1.79	0.00	4.02
1731	1935	1.282157	CCCCAAAGGACCTTCGAGAAT	59.718	52.381	7.34	0.00	38.24	2.40
1755	1959	0.611714	ATGTCCGGTAGTTGGTGACC	59.388	55.000	0.00	0.00	0.00	4.02
1941	2145	2.366469	GGCACCAAGGTCAGAGAGA	58.634	57.895	0.00	0.00	0.00	3.10
2106	2310	0.595588	CGCCAAATACAGCACCACAA	59.404	50.000	0.00	0.00	0.00	3.33
2205	2409	4.695217	TGTGAAGAAAAGAAGTTGCGTT	57.305	36.364	0.00	0.00	0.00	4.84
2226	2430	0.248907	CGGTGGAGTATTGCGACGAT	60.249	55.000	0.00	0.00	0.00	3.73
2343	2547	2.906182	CTTCCGTGGCATCAGCGCTA	62.906	60.000	10.99	0.00	43.41	4.26
2419	2623	0.465460	TCTGCGAACTTTTGGCCTGT	60.465	50.000	3.32	0.00	33.01	4.00
2537	2741	8.918202	TGAACAGTAAAATTCTTAGGTGACAT	57.082	30.769	0.00	0.00	0.00	3.06
2557	2761	8.136800	ACGGTTTGTATATATACGTGATGAACA	58.863	33.333	16.29	0.00	36.06	3.18
2742	2954	2.386661	AGGAAGGTGTATGAAGCACG	57.613	50.000	0.00	0.00	37.70	5.34
2970	3182	1.466950	GGACGCATCGACCAATTCAAA	59.533	47.619	3.12	0.00	40.91	2.69
2991	3203	2.009774	GTGGCAGTAGCTAACACCATG	58.990	52.381	11.76	0.00	38.44	3.66
2993	3205	0.037697	CGTGGCAGTAGCTAACACCA	60.038	55.000	0.00	0.00	41.70	4.17
2994	3206	1.359459	GCGTGGCAGTAGCTAACACC	61.359	60.000	0.00	0.00	41.70	4.16
2995	3207	1.359459	GGCGTGGCAGTAGCTAACAC	61.359	60.000	0.00	2.15	41.70	3.32
2996	3208	1.079405	GGCGTGGCAGTAGCTAACA	60.079	57.895	0.00	0.00	41.70	2.41
2997	3209	1.079405	TGGCGTGGCAGTAGCTAAC	60.079	57.895	0.00	0.00	41.70	2.34
3046	3259	6.206829	GGTCCCACTTATGCTAATGGTTATTC	59.793	42.308	0.00	0.00	0.00	1.75
3074	3690	0.104777	ATCCTCCAGCCTCTGCCATA	60.105	55.000	0.00	0.00	38.69	2.74
3182	3801	9.289782	GCACTTATAGAATTCCATTCCTACAAT	57.710	33.333	0.65	0.00	40.13	2.71
3197	3816	4.556697	TGATCAGGGAGGCACTTATAGAA	58.443	43.478	0.00	0.00	41.55	2.10
3206	3825	0.627451	ATGCTTTGATCAGGGAGGCA	59.373	50.000	5.29	5.29	0.00	4.75
3212	3831	4.635765	TCCTACGAAAATGCTTTGATCAGG	59.364	41.667	0.00	0.00	0.00	3.86
3428	4059	6.935208	TGCAATGTCATTTCCAATTTGAATGA	59.065	30.769	8.62	8.62	37.43	2.57
3473	4105	3.749609	TTAGAGTTCTAAAAACCGCAGGC	59.250	43.478	0.00	0.00	43.25	4.85
3486	4118	8.435931	AGGGCCATTTTAATTTTTAGAGTTCT	57.564	30.769	6.18	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.