AutoCloner

Multiple sequence alignment - TraesCS2D01G254200

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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	TraesCS2D01G254200	chr2D	100.000	3612	0	0	2416	6027	306484746	306488357	0.000000e+00	6671.0
1	TraesCS2D01G254200	chr2D	100.000	1827	0	0	1	1827	306482331	306484157	0.000000e+00	3374.0
2	TraesCS2D01G254200	chr2B	95.536	3629	113	11	2433	6027	374679845	374683458	0.000000e+00	5758.0
3	TraesCS2D01G254200	chr2B	95.095	1366	43	14	454	1812	374677144	374678492	0.000000e+00	2130.0
4	TraesCS2D01G254200	chr2B	93.148	467	18	7	1	461	374676452	374676910	0.000000e+00	673.0
5	TraesCS2D01G254200	chr2B	86.047	86	11	1	5939	6024	559911887	559911971	2.310000e-14	91.6
6	TraesCS2D01G254200	chr2A	97.414	2977	41	6	2529	5502	385976485	385979428	0.000000e+00	5038.0
7	TraesCS2D01G254200	chr2A	95.106	1083	34	11	736	1812	385974673	385975742	0.000000e+00	1688.0
8	TraesCS2D01G254200	chr2A	94.523	493	25	2	5536	6027	385979429	385979920	0.000000e+00	760.0
9	TraesCS2D01G254200	chr2A	93.333	495	22	6	241	730	385970114	385970602	0.000000e+00	721.0
10	TraesCS2D01G254200	chr2A	88.889	90	10	0	5335	5424	524333404	524333493	1.780000e-20	111.0
11	TraesCS2D01G254200	chr7A	92.437	119	2	3	610	728	677696247	677696358	4.830000e-36	163.0
12	TraesCS2D01G254200	chr7A	82.635	167	22	6	252	413	129268417	129268253	2.260000e-29	141.0
13	TraesCS2D01G254200	chr7A	83.200	125	20	1	5543	5667	122679586	122679463	4.940000e-21	113.0
14	TraesCS2D01G254200	chr7A	81.818	132	21	3	5542	5671	638849146	638849016	2.300000e-19	108.0
15	TraesCS2D01G254200	chr7D	90.833	120	9	2	610	728	108349391	108349509	6.250000e-35	159.0
16	TraesCS2D01G254200	chr6D	91.667	120	3	4	609	728	428908500	428908388	6.250000e-35	159.0
17	TraesCS2D01G254200	chr6D	89.773	88	9	0	5335	5422	90111817	90111904	4.940000e-21	113.0
18	TraesCS2D01G254200	chr6A	91.597	119	3	4	610	728	609593112	609593001	2.250000e-34	158.0
19	TraesCS2D01G254200	chr1A	90.909	121	4	3	610	730	39438838	39438951	8.090000e-34	156.0
20	TraesCS2D01G254200	chr1A	81.667	120	18	3	5553	5671	146960014	146960130	4.970000e-16	97.1
21	TraesCS2D01G254200	chr6B	89.231	130	5	5	610	739	192059947	192060067	2.910000e-33	154.0
22	TraesCS2D01G254200	chr5B	89.431	123	6	4	606	728	478307171	478307286	1.350000e-31	148.0
23	TraesCS2D01G254200	chr5B	88.372	86	9	1	5335	5419	499083066	499082981	1.070000e-17	102.0
24	TraesCS2D01G254200	chr5D	78.774	212	25	13	214	414	227452417	227452215	2.280000e-24	124.0
25	TraesCS2D01G254200	chr5D	87.356	87	11	0	5334	5420	442203726	442203812	3.840000e-17	100.0
26	TraesCS2D01G254200	chr1D	90.698	86	8	0	5335	5420	279101376	279101461	1.370000e-21	115.0
27	TraesCS2D01G254200	chr3A	87.500	88	11	0	5332	5419	491189423	491189510	1.070000e-17	102.0
28	TraesCS2D01G254200	chr1B	88.372	86	9	1	5335	5420	378835729	378835813	1.070000e-17	102.0
29	TraesCS2D01G254200	chr3B	81.250	112	12	7	5554	5662	474845257	474845152	1.390000e-11	82.4

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	TraesCS2D01G254200	chr2D	306482331	306488357	6026	False	5022.500000	6671	100.000	1	6027	2	chr2D.!!$F1	6026
1	TraesCS2D01G254200	chr2B	374676452	374683458	7006	False	2853.666667	5758	94.593	1	6027	3	chr2B.!!$F2	6026
2	TraesCS2D01G254200	chr2A	385974673	385979920	5247	False	2495.333333	5038	95.681	736	6027	3	chr2A.!!$F3	5291

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
46	47	0.472044	ACGGCCCCATTTTGCTTTTT	59.528	45.000	0.0	0.0	0.00	1.94	F
219	223	0.734889	CGTATCGTCCGGTGGTAGTT	59.265	55.000	0.0	0.0	0.00	2.24	F
1776	2033	1.609580	GCAAGTACCCGTGGAATGTGA	60.610	52.381	0.0	0.0	0.00	3.58	F
2516	3952	2.680312	TGACCATGTAGAGCAAGCTC	57.320	50.000	14.0	14.0	43.03	4.09	F
2962	4410	1.002257	ACATGATTGGCCGTGCTCA	60.002	52.632	0.0	0.0	0.00	4.26	F
3623	5072	4.454728	TTTTGCATGAATCCCTTGCTAC	57.545	40.909	0.0	0.0	43.84	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1776	2033	5.688807	AGCTATGCACCAAATAGTTCTGAT	58.311	37.500	31.43	2.90	R
2428	2782	7.581213	TGAAGCAACTTTTTCCTCTTTCATA	57.419	32.000	0.00	2.15	R
2962	4410	4.081142	CCAAGGTTTTTCCAGTTCCAGTTT	60.081	41.667	39.02	2.66	R
4183	5632	5.366477	TCTTGTGCTGTTCATATCCATAGGA	59.634	40.000	35.55	2.94	R
4760	6209	1.104630	GAAGGTCGTCGAGAATCCCT	58.895	55.000	0.00	4.20	R
5798	7275	3.449377	TCGGCAAGATGTATTGTACCTCA	59.551	43.478	32.56	3.86	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
46	47	0.472044	ACGGCCCCATTTTGCTTTTT	59.528	45.000	0.00	0.00	0.00	1.94
48	49	1.813477	CGGCCCCATTTTGCTTTTTGT	60.813	47.619	0.00	0.00	0.00	2.83
57	58	3.889520	TTTGCTTTTTGTACGGGGTTT	57.110	38.095	0.00	0.00	0.00	3.27
62	63	3.304861	GCTTTTTGTACGGGGTTTCGAAT	60.305	43.478	0.00	0.00	0.00	3.34
63	64	4.793678	GCTTTTTGTACGGGGTTTCGAATT	60.794	41.667	0.00	0.00	0.00	2.17
64	65	4.486574	TTTTGTACGGGGTTTCGAATTC	57.513	40.909	0.00	0.00	0.00	2.17
65	66	2.097680	TGTACGGGGTTTCGAATTCC	57.902	50.000	0.00	4.99	0.00	3.01
66	67	1.624813	TGTACGGGGTTTCGAATTCCT	59.375	47.619	15.99	3.25	0.00	3.36
74	75	4.323257	GGGGTTTCGAATTCCTAGAGACAA	60.323	45.833	15.99	0.00	0.00	3.18
75	76	5.429130	GGGTTTCGAATTCCTAGAGACAAT	58.571	41.667	15.99	0.00	0.00	2.71
160	161	2.292016	TGCCACACCAACATTTTCTACG	59.708	45.455	0.00	0.00	0.00	3.51
170	171	9.061610	CACCAACATTTTCTACGTGATTATTTC	57.938	33.333	0.00	0.00	0.00	2.17
206	210	8.528917	TTAATCTGGGAAAATACATCGTATCG	57.471	34.615	0.00	0.00	0.00	2.92
219	223	0.734889	CGTATCGTCCGGTGGTAGTT	59.265	55.000	0.00	0.00	0.00	2.24
250	257	9.362151	TCATGTCTCATATACTATGTGGTACAA	57.638	33.333	0.00	0.00	44.16	2.41
524	772	5.180868	ACATACTAGCCGTAGATACTTTCCG	59.819	44.000	0.00	0.00	0.00	4.30
546	794	3.306703	GGTTTGACAACATGCAACACAAG	59.693	43.478	0.00	0.00	34.15	3.16
549	797	4.446994	TGACAACATGCAACACAAGAAA	57.553	36.364	0.00	0.00	0.00	2.52
563	811	7.096477	GCAACACAAGAAACTCATGAATGTAAC	60.096	37.037	0.00	0.00	0.00	2.50
571	819	8.306761	AGAAACTCATGAATGTAACATTTTCCC	58.693	33.333	0.00	0.00	29.63	3.97
614	866	3.703921	AGGGAGACTCAAGTTCTACTCC	58.296	50.000	4.53	0.00	41.90	3.85
630	882	5.961897	TCTACTCCCTCCGTTCCTAAATAT	58.038	41.667	0.00	0.00	0.00	1.28
721	973	4.631377	TGTAGATTCACTCATTTTGCTCCG	59.369	41.667	0.00	0.00	0.00	4.63
1116	1370	3.687321	CTGTCCCCAGCCATGTCGG	62.687	68.421	0.00	0.00	38.11	4.79
1688	1945	5.418524	TGGTCTATTGATTCCAACCATGTTG	59.581	40.000	0.00	0.00	34.72	3.33
1776	2033	1.609580	GCAAGTACCCGTGGAATGTGA	60.610	52.381	0.00	0.00	0.00	3.58
2464	3900	8.565896	AAAAAGTTGCTTCAAAGAAGGAAAAT	57.434	26.923	13.93	5.11	29.52	1.82
2465	3901	9.665719	AAAAAGTTGCTTCAAAGAAGGAAAATA	57.334	25.926	13.93	0.00	29.52	1.40
2466	3902	9.665719	AAAAGTTGCTTCAAAGAAGGAAAATAA	57.334	25.926	13.93	0.00	29.52	1.40
2477	3913	9.639601	CAAAGAAGGAAAATAAAACTCCATACC	57.360	33.333	0.00	0.00	0.00	2.73
2478	3914	7.625828	AGAAGGAAAATAAAACTCCATACCG	57.374	36.000	0.00	0.00	0.00	4.02
2516	3952	2.680312	TGACCATGTAGAGCAAGCTC	57.320	50.000	14.00	14.00	43.03	4.09
2690	4138	9.474920	TTCCTGTGAACAAATGAACAATAAATC	57.525	29.630	0.00	0.00	0.00	2.17
2816	4264	5.583457	GGCAAGATGCTATTTTCTGCAAATT	59.417	36.000	2.00	0.00	44.28	1.82
2819	4267	7.360607	GCAAGATGCTATTTTCTGCAAATTTGT	60.361	33.333	19.03	0.53	42.74	2.83
2962	4410	1.002257	ACATGATTGGCCGTGCTCA	60.002	52.632	0.00	0.00	0.00	4.26
3623	5072	4.454728	TTTTGCATGAATCCCTTGCTAC	57.545	40.909	0.00	0.00	43.84	3.58
4173	5622	4.576463	CCAATGTTGATCTAGTAAGTGGCC	59.424	45.833	0.00	0.00	0.00	5.36
4183	5632	7.510685	TGATCTAGTAAGTGGCCTGAGATATTT	59.489	37.037	3.32	0.00	0.00	1.40
4492	5941	8.564574	GGTTTCATGTTAGTACTGATGTGAAAA	58.435	33.333	21.23	10.00	36.47	2.29
4999	6448	2.364970	TGGTTTTGGCACCTCTGATTTG	59.635	45.455	0.00	0.00	37.75	2.32
5126	6577	5.070446	AGTTCACCAATCTCTGTGTAGTTCA	59.930	40.000	0.00	0.00	34.14	3.18
5317	6768	2.753029	GTCAGGCTCAGGCAGGTT	59.247	61.111	0.00	0.00	40.87	3.50
5321	6772	0.676151	CAGGCTCAGGCAGGTTTCTC	60.676	60.000	0.00	0.00	40.87	2.87
5322	6773	0.839853	AGGCTCAGGCAGGTTTCTCT	60.840	55.000	0.00	0.00	40.87	3.10
5363	6814	6.157211	CCTCCGTATCAAAATATAAGACGCT	58.843	40.000	0.00	0.00	0.00	5.07
5364	6815	6.645415	CCTCCGTATCAAAATATAAGACGCTT	59.355	38.462	0.00	0.00	0.00	4.68
5566	7019	6.057321	ACTCCCTCGGTTCACAAATATAAA	57.943	37.500	0.00	0.00	0.00	1.40
5637	7114	7.138736	CCGTGTTTGTTCACTTATTTCAATCT	58.861	34.615	0.00	0.00	36.33	2.40
5776	7253	8.250143	AGTTTGATCCAGTTTACAAGGAAAAT	57.750	30.769	0.00	0.00	34.62	1.82
5798	7275	7.856145	AATCTGATCGAAAATCTTAAGTGCT	57.144	32.000	1.63	0.00	0.00	4.40
5821	7298	4.051922	GAGGTACAATACATCTTGCCGAG	58.948	47.826	0.00	0.00	36.61	4.63
5857	7334	0.463654	ACACAGAACACCACGTGCAT	60.464	50.000	10.91	0.00	36.98	3.96
5920	7397	4.010349	GAGTTGAATTTAGGTGGGTGGAG	58.990	47.826	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	3.388345	TGGGGCCGTAAAATTTGAAAC	57.612	42.857	0.00	0.00	0.00	2.78
18	19	4.319177	CAAAATGGGGCCGTAAAATTTGA	58.681	39.130	0.00	0.00	0.00	2.69
46	47	1.624813	AGGAATTCGAAACCCCGTACA	59.375	47.619	17.27	0.00	0.00	2.90
48	49	3.364549	TCTAGGAATTCGAAACCCCGTA	58.635	45.455	17.27	6.59	0.00	4.02
57	58	8.239038	AGATAACATTGTCTCTAGGAATTCGA	57.761	34.615	0.00	0.00	0.00	3.71
74	75	7.446931	AGACTACGACATCATGAGAGATAACAT	59.553	37.037	0.09	0.00	0.00	2.71
75	76	6.768381	AGACTACGACATCATGAGAGATAACA	59.232	38.462	0.09	0.00	0.00	2.41
88	89	8.462143	TGTTGAATAAAGAAGACTACGACATC	57.538	34.615	0.00	0.00	0.00	3.06
188	189	3.671928	CGGACGATACGATGTATTTTCCC	59.328	47.826	0.00	0.00	0.00	3.97
190	191	4.147653	CACCGGACGATACGATGTATTTTC	59.852	45.833	9.46	0.00	0.00	2.29
191	192	4.046462	CACCGGACGATACGATGTATTTT	58.954	43.478	9.46	0.00	0.00	1.82
193	194	2.030540	CCACCGGACGATACGATGTATT	60.031	50.000	9.46	0.00	0.00	1.89
195	196	0.946528	CCACCGGACGATACGATGTA	59.053	55.000	9.46	0.00	0.00	2.29
197	198	0.946528	TACCACCGGACGATACGATG	59.053	55.000	9.46	0.00	0.00	3.84
198	199	1.233019	CTACCACCGGACGATACGAT	58.767	55.000	9.46	0.00	0.00	3.73
199	200	0.107703	ACTACCACCGGACGATACGA	60.108	55.000	9.46	0.00	0.00	3.43
201	202	2.287248	GCTAACTACCACCGGACGATAC	60.287	54.545	9.46	0.00	0.00	2.24
206	210	0.459078	GAGGCTAACTACCACCGGAC	59.541	60.000	9.46	0.00	0.00	4.79
219	223	7.340487	CCACATAGTATATGAGACATGAGGCTA	59.660	40.741	0.00	0.00	0.00	3.93
428	435	4.423625	ACTCCCTTCGATCCAAATAAGG	57.576	45.455	0.00	0.00	38.58	2.69
510	758	4.487948	TGTCAAACCGGAAAGTATCTACG	58.512	43.478	9.46	0.00	0.00	3.51
524	772	2.886081	TGTGTTGCATGTTGTCAAACC	58.114	42.857	0.00	0.00	35.25	3.27
546	794	8.306761	AGGGAAAATGTTACATTCATGAGTTTC	58.693	33.333	11.24	8.99	0.00	2.78
549	797	7.781324	AAGGGAAAATGTTACATTCATGAGT	57.219	32.000	11.24	0.00	0.00	3.41
599	851	2.225066	ACGGAGGGAGTAGAACTTGAGT	60.225	50.000	0.00	0.00	0.00	3.41
614	866	8.959705	AAAAGACTTATATTTAGGAACGGAGG	57.040	34.615	0.00	0.00	0.00	4.30
699	951	4.631813	ACGGAGCAAAATGAGTGAATCTAC	59.368	41.667	0.00	0.00	0.00	2.59
705	957	3.937814	ACATACGGAGCAAAATGAGTGA	58.062	40.909	0.00	0.00	0.00	3.41
894	1147	1.932511	ACGACGACGGTATCTTCTCTC	59.067	52.381	12.58	0.00	44.46	3.20
1417	1673	8.754230	ATCATGACTCGTATCTACAATGATTG	57.246	34.615	3.16	3.16	0.00	2.67
1688	1945	6.868864	TGTGAAGCTACATGTCTAAGAGAAAC	59.131	38.462	0.00	0.00	0.00	2.78
1776	2033	5.688807	AGCTATGCACCAAATAGTTCTGAT	58.311	37.500	0.00	0.00	31.43	2.90
2426	2780	9.295825	TGAAGCAACTTTTTCCTCTTTCATATA	57.704	29.630	0.00	0.00	0.00	0.86
2427	2781	8.181904	TGAAGCAACTTTTTCCTCTTTCATAT	57.818	30.769	0.00	0.00	0.00	1.78
2428	2782	7.581213	TGAAGCAACTTTTTCCTCTTTCATA	57.419	32.000	0.00	0.00	0.00	2.15
2429	2783	6.469782	TGAAGCAACTTTTTCCTCTTTCAT	57.530	33.333	0.00	0.00	0.00	2.57
2464	3900	7.980662	TCGTATCAAATTCGGTATGGAGTTTTA	59.019	33.333	0.00	0.00	0.00	1.52
2465	3901	6.819649	TCGTATCAAATTCGGTATGGAGTTTT	59.180	34.615	0.00	0.00	0.00	2.43
2466	3902	6.257193	GTCGTATCAAATTCGGTATGGAGTTT	59.743	38.462	0.00	0.00	0.00	2.66
2477	3913	8.515473	TGGTCATATTAGTCGTATCAAATTCG	57.485	34.615	0.00	0.00	0.00	3.34
2488	3924	6.013842	TGCTCTACATGGTCATATTAGTCG	57.986	41.667	0.00	0.00	0.00	4.18
2516	3952	1.438651	TACAGCAAGGCAAACTAGCG	58.561	50.000	0.00	0.00	34.64	4.26
2690	4138	8.980610	GTCAATATGTCATGAGAGATCTTTCAG	58.019	37.037	19.57	12.35	0.00	3.02
2962	4410	4.081142	CCAAGGTTTTTCCAGTTCCAGTTT	60.081	41.667	0.00	0.00	39.02	2.66
4183	5632	5.366477	TCTTGTGCTGTTCATATCCATAGGA	59.634	40.000	0.00	0.00	35.55	2.94
4391	5840	8.087982	ACAGTTCTACTTTGTTCATATGTGTG	57.912	34.615	1.90	0.00	0.00	3.82
4497	5946	6.646240	GCAAAAAGAAATCAGCCAATGAGTTA	59.354	34.615	0.00	0.00	45.77	2.24
4760	6209	1.104630	GAAGGTCGTCGAGAATCCCT	58.895	55.000	0.00	0.00	0.00	4.20
4999	6448	4.437587	ATGCTGCCTGGTCTGCCC	62.438	66.667	14.01	0.00	0.00	5.36
5126	6577	7.595819	TCTCAAACAACCCAAGATACAAAAT	57.404	32.000	0.00	0.00	0.00	1.82
5317	6768	7.125356	GGAGGGAGTATAAACCAACTTAGAGAA	59.875	40.741	0.00	0.00	0.00	2.87
5321	6772	5.128335	ACGGAGGGAGTATAAACCAACTTAG	59.872	44.000	0.00	0.00	0.00	2.18
5322	6773	5.025453	ACGGAGGGAGTATAAACCAACTTA	58.975	41.667	0.00	0.00	0.00	2.24
5566	7019	9.739276	TCCAATCAAGATAAGTGTTAGAACATT	57.261	29.630	0.00	0.00	41.59	2.71
5600	7077	6.579666	GTGAACAAACACGGTAAAACATATCC	59.420	38.462	0.00	0.00	0.00	2.59
5776	7253	6.398095	TCAGCACTTAAGATTTTCGATCAGA	58.602	36.000	10.09	0.00	0.00	3.27
5798	7275	3.449377	TCGGCAAGATGTATTGTACCTCA	59.551	43.478	0.00	0.00	32.56	3.86
5821	7298	8.612619	TGTTCTGTGTTTTCTATCTTCTTGTTC	58.387	33.333	0.00	0.00	0.00	3.18
5857	7334	6.914259	TGATCTTTGTGTTGTGTTGTAACAA	58.086	32.000	0.00	0.00	41.21	2.83
5976	7454	8.526147	AGAGATGCTACATTTGCTGTAATTTTT	58.474	29.630	0.00	0.00	39.82	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.