AutoCloner

Multiple sequence alignment - TraesCS5A01G126000

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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	TraesCS5A01G126000	chr5A	100.000	2477	0	0	1	2477	277717772	277720248	0.000000e+00	4575.0
1	TraesCS5A01G126000	chr5A	81.522	92	10	2	329	413	326060088	326059997	4.420000e-08	69.4
2	TraesCS5A01G126000	chr5D	93.128	2343	84	33	172	2476	213469947	213472250	0.000000e+00	3363.0
3	TraesCS5A01G126000	chr5D	97.248	109	2	1	1	108	213467501	213467609	1.510000e-42	183.0
4	TraesCS5A01G126000	chr5D	100.000	28	0	0	479	506	8051253	8051226	4.000000e-03	52.8
5	TraesCS5A01G126000	chr5B	95.662	1729	51	8	591	2305	227831068	227832786	0.000000e+00	2756.0
6	TraesCS5A01G126000	chr5B	85.095	577	38	19	2	565	227808265	227808806	1.680000e-151	545.0
7	TraesCS5A01G126000	chr5B	98.286	175	3	0	2303	2477	227832868	227833042	8.600000e-80	307.0
8	TraesCS5A01G126000	chr5B	94.286	35	1	1	478	511	653860955	653860921	4.000000e-03	52.8
9	TraesCS5A01G126000	chr3D	84.043	94	10	2	351	443	91033312	91033223	4.390000e-13	86.1
10	TraesCS5A01G126000	chr2A	83.562	73	12	0	2320	2392	764097378	764097306	4.420000e-08	69.4
11	TraesCS5A01G126000	chr2D	82.667	75	9	3	2320	2392	638156237	638156309	2.060000e-06	63.9
12	TraesCS5A01G126000	chr7A	100.000	29	0	0	478	506	717778308	717778280	1.000000e-03	54.7
13	TraesCS5A01G126000	chr4B	100.000	29	0	0	478	506	149715897	149715925	1.000000e-03	54.7
14	TraesCS5A01G126000	chr7B	96.875	32	0	1	480	511	46902646	46902676	4.000000e-03	52.8
15	TraesCS5A01G126000	chr4D	100.000	28	0	0	343	370	115065506	115065533	4.000000e-03	52.8
16	TraesCS5A01G126000	chr4D	100.000	28	0	0	478	505	414605214	414605241	4.000000e-03	52.8
17	TraesCS5A01G126000	chr1D	100.000	28	0	0	478	505	5423658	5423685	4.000000e-03	52.8
18	TraesCS5A01G126000	chr1D	100.000	28	0	0	480	507	10718930	10718957	4.000000e-03	52.8

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	TraesCS5A01G126000	chr5A	277717772	277720248	2476	False	4575.0	4575	100.000	1	2477	1	chr5A.!!$F1	2476
1	TraesCS5A01G126000	chr5D	213467501	213472250	4749	False	1773.0	3363	95.188	1	2476	2	chr5D.!!$F1	2475
2	TraesCS5A01G126000	chr5B	227831068	227833042	1974	False	1531.5	2756	96.974	591	2477	2	chr5B.!!$F2	1886
3	TraesCS5A01G126000	chr5B	227808265	227808806	541	False	545.0	545	85.095	2	565	1	chr5B.!!$F1	563

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
509	2818	0.320697	GGGACGGAGGGAATATTCGG	59.679	60.0	9.32	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2140	4480	0.035317	TGCGTGTTCAGCAGAGGAAT	59.965	50.0	0.0	0.0	40.01	3.01	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
208	2491	1.949015	CTAGCAGCGAACGTGCAGTG	61.949	60.000	17.85	0.00	43.82	3.66
223	2506	4.232221	GTGCAGTGATGAAAACCTGAATG	58.768	43.478	0.00	0.00	0.00	2.67
226	2509	5.048782	TGCAGTGATGAAAACCTGAATGTAC	60.049	40.000	0.00	0.00	0.00	2.90
235	2518	7.947282	TGAAAACCTGAATGTACCCTTAAAAG	58.053	34.615	0.00	0.00	0.00	2.27
236	2519	5.977489	AACCTGAATGTACCCTTAAAAGC	57.023	39.130	0.00	0.00	0.00	3.51
343	2626	8.628280	GTTATAACTACTACTTCCTCCGTTCAT	58.372	37.037	8.41	0.00	0.00	2.57
473	2779	2.044630	ACCTTAGTTAGCACTCCCTCCT	59.955	50.000	0.00	0.00	34.06	3.69
499	2808	5.918608	CCATCTTATATTATGGGACGGAGG	58.081	45.833	6.11	0.00	39.23	4.30
500	2809	5.163301	CCATCTTATATTATGGGACGGAGGG	60.163	48.000	6.11	0.00	39.23	4.30
501	2810	5.279562	TCTTATATTATGGGACGGAGGGA	57.720	43.478	0.00	0.00	0.00	4.20
502	2811	5.657446	TCTTATATTATGGGACGGAGGGAA	58.343	41.667	0.00	0.00	0.00	3.97
504	2813	7.424172	TCTTATATTATGGGACGGAGGGAATA	58.576	38.462	0.00	0.00	0.00	1.75
506	2815	8.632731	TTATATTATGGGACGGAGGGAATATT	57.367	34.615	0.00	0.00	0.00	1.28
507	2816	4.903045	TTATGGGACGGAGGGAATATTC	57.097	45.455	6.93	6.93	0.00	1.75
508	2817	1.045407	TGGGACGGAGGGAATATTCG	58.955	55.000	9.32	0.88	0.00	3.34
509	2818	0.320697	GGGACGGAGGGAATATTCGG	59.679	60.000	9.32	0.00	0.00	4.30
512	2821	1.962100	GACGGAGGGAATATTCGGAGT	59.038	52.381	9.32	5.15	0.00	3.85
513	2822	3.152341	GACGGAGGGAATATTCGGAGTA	58.848	50.000	9.32	0.00	0.00	2.59
514	2823	3.762823	GACGGAGGGAATATTCGGAGTAT	59.237	47.826	9.32	0.00	0.00	2.12
553	2868	7.931015	TCTACCATAAGACACAGGGAATATT	57.069	36.000	0.00	0.00	0.00	1.28
567	2882	8.636213	CACAGGGAATATTTAATTTCTGATGCT	58.364	33.333	0.00	0.00	0.00	3.79
746	3064	2.592993	GGCCCAGGCACTACTCACA	61.593	63.158	11.50	0.00	44.11	3.58
747	3065	1.374947	GCCCAGGCACTACTCACAA	59.625	57.895	3.12	0.00	41.49	3.33
770	3088	7.673926	ACAACTCCCTCCAAACAAATTGTATAT	59.326	33.333	0.00	0.00	37.32	0.86
776	3098	9.717942	CCCTCCAAACAAATTGTATATTTTGAA	57.282	29.630	12.12	0.00	37.32	2.69
879	3203	3.054361	GTGAATTTGCTTCCCCCTCTCTA	60.054	47.826	0.00	0.00	32.49	2.43
880	3204	3.054361	TGAATTTGCTTCCCCCTCTCTAC	60.054	47.826	0.00	0.00	32.49	2.59
881	3205	1.286248	TTTGCTTCCCCCTCTCTACC	58.714	55.000	0.00	0.00	0.00	3.18
1484	3814	3.382832	CCGGCCGTGACTTCTCCT	61.383	66.667	26.12	0.00	0.00	3.69
1533	3865	2.224523	TGCACCTCCGTGAATTCTCTTT	60.225	45.455	7.05	0.00	43.14	2.52
1586	3918	8.443160	TGCGATTAGATTCTTTTGTAGAGTTTG	58.557	33.333	0.00	0.00	33.51	2.93
1783	4122	9.710900	AGGAAAACAATTGAAGTAAATTGATCC	57.289	29.630	13.59	15.93	46.13	3.36
2028	4368	1.455773	GGGGCTTAGGGTTGATGGC	60.456	63.158	0.00	0.00	0.00	4.40
2056	4396	0.937304	GAACTTCAGCGACAACTGCA	59.063	50.000	0.00	0.00	37.59	4.41
2089	4429	1.012841	CAAAGAGAGATTCCTGCGGC	58.987	55.000	0.00	0.00	0.00	6.53
2140	4480	3.269906	AGGGACTCCAGCTAGACTTCTTA	59.730	47.826	0.00	0.00	34.83	2.10
2289	4629	6.183361	ACAGGCAGGATGTTCAGGATATTTAT	60.183	38.462	0.00	0.00	39.31	1.40
2362	4786	2.289547	CTGGTTTCACGTTTGTGGTAGG	59.710	50.000	0.00	0.00	46.42	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
136	2271	1.268133	ACGCGTTGCAACACGTAATTT	60.268	42.857	36.24	17.20	44.69	1.82
138	2273	1.125384	CTACGCGTTGCAACACGTAAT	59.875	47.619	37.27	23.65	45.55	1.89
153	2288	9.582431	TTTGTATAGATAGATAATTGCCTACGC	57.418	33.333	0.00	0.00	0.00	4.42
208	2491	7.696992	TTAAGGGTACATTCAGGTTTTCATC	57.303	36.000	0.00	0.00	0.00	2.92
223	2506	4.224594	ACCACTAGAGGCTTTTAAGGGTAC	59.775	45.833	6.07	0.00	0.00	3.34
226	2509	3.679083	CGACCACTAGAGGCTTTTAAGGG	60.679	52.174	6.07	0.00	0.00	3.95
235	2518	4.299978	GAACATATTCGACCACTAGAGGC	58.700	47.826	6.07	0.00	0.00	4.70
236	2519	4.585162	AGGAACATATTCGACCACTAGAGG	59.415	45.833	4.44	4.44	35.48	3.69
312	2595	9.866798	CGGAGGAAGTAGTAGTTATAACTTTTT	57.133	33.333	22.66	11.36	40.37	1.94
313	2596	9.029368	ACGGAGGAAGTAGTAGTTATAACTTTT	57.971	33.333	22.66	13.59	40.37	2.27
314	2597	8.586879	ACGGAGGAAGTAGTAGTTATAACTTT	57.413	34.615	22.66	10.89	40.37	2.66
315	2598	8.586879	AACGGAGGAAGTAGTAGTTATAACTT	57.413	34.615	22.66	9.06	40.37	2.66
316	2599	7.831193	TGAACGGAGGAAGTAGTAGTTATAACT	59.169	37.037	21.35	21.35	42.91	2.24
317	2600	7.989826	TGAACGGAGGAAGTAGTAGTTATAAC	58.010	38.462	7.57	7.57	0.00	1.89
318	2601	8.757982	ATGAACGGAGGAAGTAGTAGTTATAA	57.242	34.615	0.00	0.00	0.00	0.98
319	2602	9.851686	TTATGAACGGAGGAAGTAGTAGTTATA	57.148	33.333	0.00	0.00	0.00	0.98
320	2603	8.757982	TTATGAACGGAGGAAGTAGTAGTTAT	57.242	34.615	0.00	0.00	0.00	1.89
321	2604	8.757982	ATTATGAACGGAGGAAGTAGTAGTTA	57.242	34.615	0.00	0.00	0.00	2.24
322	2605	7.657023	ATTATGAACGGAGGAAGTAGTAGTT	57.343	36.000	0.00	0.00	0.00	2.24
323	2606	8.757982	TTATTATGAACGGAGGAAGTAGTAGT	57.242	34.615	0.00	0.00	0.00	2.73
324	2607	9.064706	TCTTATTATGAACGGAGGAAGTAGTAG	57.935	37.037	0.00	0.00	0.00	2.57
325	2608	8.985315	TCTTATTATGAACGGAGGAAGTAGTA	57.015	34.615	0.00	0.00	0.00	1.82
326	2609	7.893124	TCTTATTATGAACGGAGGAAGTAGT	57.107	36.000	0.00	0.00	0.00	2.73
442	2747	7.255486	GGAGTGCTAACTAAGGTGTTTTGATTT	60.255	37.037	0.00	0.00	36.52	2.17
443	2748	6.206829	GGAGTGCTAACTAAGGTGTTTTGATT	59.793	38.462	0.00	0.00	36.52	2.57
444	2749	5.705905	GGAGTGCTAACTAAGGTGTTTTGAT	59.294	40.000	0.00	0.00	36.52	2.57
445	2750	5.061179	GGAGTGCTAACTAAGGTGTTTTGA	58.939	41.667	0.00	0.00	36.52	2.69
446	2751	4.215613	GGGAGTGCTAACTAAGGTGTTTTG	59.784	45.833	0.00	0.00	36.52	2.44
453	2759	2.753247	AGGAGGGAGTGCTAACTAAGG	58.247	52.381	0.00	0.00	36.52	2.69
494	2803	4.803098	AATACTCCGAATATTCCCTCCG	57.197	45.455	9.87	0.00	0.00	4.63
542	2857	8.773033	AGCATCAGAAATTAAATATTCCCTGT	57.227	30.769	0.00	0.00	0.00	4.00
573	2888	5.410439	CGTTTTAGCTGCTTTTTAGGGACTA	59.590	40.000	7.79	0.00	41.75	2.59
735	3053	1.066787	GGAGGGAGTTGTGAGTAGTGC	60.067	57.143	0.00	0.00	0.00	4.40
746	3064	8.664669	AATATACAATTTGTTTGGAGGGAGTT	57.335	30.769	7.45	0.00	39.80	3.01
747	3065	8.664669	AAATATACAATTTGTTTGGAGGGAGT	57.335	30.769	7.45	0.00	39.80	3.85
770	3088	8.994170	CACAAAAAGGTTTTAAGGACTTCAAAA	58.006	29.630	0.00	0.00	0.00	2.44
776	3098	5.449999	CGAGCACAAAAAGGTTTTAAGGACT	60.450	40.000	0.00	0.00	0.00	3.85
864	3188	1.003051	GGGTAGAGAGGGGGAAGCA	59.997	63.158	0.00	0.00	0.00	3.91
885	3209	3.312890	AGAGAGGAGAGAGAGAGAGAGG	58.687	54.545	0.00	0.00	0.00	3.69
940	3264	7.227314	TGGTGGATTGATAAGAATCGAATCAAG	59.773	37.037	13.29	0.00	41.50	3.02
1484	3814	4.758251	CATGGAGGTGCGCCGTCA	62.758	66.667	11.42	13.59	40.50	4.35
1586	3918	0.108851	CAACCCAAACATAAGCCGGC	60.109	55.000	21.89	21.89	0.00	6.13
1764	4103	8.755696	TTTTCCGGATCAATTTACTTCAATTG	57.244	30.769	4.15	0.00	43.04	2.32
1809	4149	3.058914	GCATGTTGTAGACTTGTGGTGAC	60.059	47.826	0.00	0.00	36.18	3.67
2028	4368	4.139420	CTGAAGTTCTGCGCGCGG	62.139	66.667	33.66	33.66	0.00	6.46
2056	4396	2.373169	TCTCTTTGACAACCCTGATGCT	59.627	45.455	0.00	0.00	0.00	3.79
2140	4480	0.035317	TGCGTGTTCAGCAGAGGAAT	59.965	50.000	0.00	0.00	40.01	3.01
2322	4746	4.801330	CAGGGGTAAAAACTGGAATTCC	57.199	45.455	18.17	18.17	0.00	3.01
2362	4786	7.611770	AGAATTTCTGCTAAATGGGGTAAAAC	58.388	34.615	0.00	0.00	0.00	2.43
2441	4865	3.181471	GGCATATACACAGTCAGCAGAGT	60.181	47.826	0.00	0.00	0.00	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.