AutoCloner

Multiple sequence alignment - TraesCS2B01G487700

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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	TraesCS2B01G487700	chr2B	100.000	4523	0	0	1	4523	683751480	683756002	0.000000e+00	8353
1	TraesCS2B01G487700	chr2B	74.369	515	89	29	2127	2630	97375521	97375039	3.590000e-41	180
2	TraesCS2B01G487700	chr2D	97.614	3521	72	6	1	3512	571876937	571880454	0.000000e+00	6026
3	TraesCS2B01G487700	chr2D	96.838	1012	30	2	3513	4523	571880487	571881497	0.000000e+00	1690
4	TraesCS2B01G487700	chr2A	97.165	3281	76	10	245	3512	710354804	710358080	0.000000e+00	5528
5	TraesCS2B01G487700	chr2A	96.640	1012	32	2	3513	4523	710358113	710359123	0.000000e+00	1679
6	TraesCS2B01G487700	chr2A	91.829	257	21	0	1	257	710354528	710354784	4.300000e-95	359
7	TraesCS2B01G487700	chr5D	74.671	987	216	21	1048	2020	553967491	553966525	1.510000e-109	407
8	TraesCS2B01G487700	chr5D	74.518	985	221	20	1048	2020	554345655	554346621	7.050000e-108	401
9	TraesCS2B01G487700	chr7A	74.145	994	229	21	1040	2019	726737474	726738453	1.970000e-103	387
10	TraesCS2B01G487700	chr7A	74.186	891	207	19	1136	2016	5527023	5527900	2.590000e-92	350
11	TraesCS2B01G487700	chr7A	79.551	401	77	4	2109	2505	6236391	6236790	9.580000e-72	281
12	TraesCS2B01G487700	chr7A	79.052	401	79	4	2109	2505	5527915	5528314	2.070000e-68	270
13	TraesCS2B01G487700	chr7A	77.000	400	83	7	2112	2505	726710855	726710459	2.120000e-53	220
14	TraesCS2B01G487700	chr7D	74.299	891	210	15	1136	2018	631060306	631059427	4.300000e-95	359
15	TraesCS2B01G487700	chr7D	74.157	890	209	17	1136	2016	5009554	5010431	2.590000e-92	350
16	TraesCS2B01G487700	chr7D	74.553	727	160	18	1136	1851	638648195	638647483	1.230000e-75	294
17	TraesCS2B01G487700	chr7D	78.554	401	81	4	2109	2505	5010446	5010845	4.490000e-65	259
18	TraesCS2B01G487700	chr7D	72.321	896	221	22	1137	2020	631231691	631232571	5.810000e-64	255
19	TraesCS2B01G487700	chr4A	74.907	805	184	14	1136	1933	738046155	738046948	7.200000e-93	351
20	TraesCS2B01G487700	chrUn	74.845	807	182	16	1136	1933	294521822	294522616	3.350000e-91	346
21	TraesCS2B01G487700	chrUn	73.855	895	211	18	1136	2020	248487392	248488273	7.250000e-88	335
22	TraesCS2B01G487700	chrUn	73.009	904	215	23	1136	2027	88657835	88656949	1.590000e-74	291
23	TraesCS2B01G487700	chrUn	77.363	402	82	7	2110	2505	248488303	248488701	3.520000e-56	230
24	TraesCS2B01G487700	chrUn	75.931	403	86	10	2110	2505	88656924	88656526	3.570000e-46	196

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	TraesCS2B01G487700	chr2B	683751480	683756002	4522	False	8353.0	8353	100.000000	1	4523	1	chr2B.!!$F1	4522
1	TraesCS2B01G487700	chr2D	571876937	571881497	4560	False	3858.0	6026	97.226000	1	4523	2	chr2D.!!$F1	4522
2	TraesCS2B01G487700	chr2A	710354528	710359123	4595	False	2522.0	5528	95.211333	1	4523	3	chr2A.!!$F1	4522
3	TraesCS2B01G487700	chr5D	553966525	553967491	966	True	407.0	407	74.671000	1048	2020	1	chr5D.!!$R1	972
4	TraesCS2B01G487700	chr5D	554345655	554346621	966	False	401.0	401	74.518000	1048	2020	1	chr5D.!!$F1	972
5	TraesCS2B01G487700	chr7A	726737474	726738453	979	False	387.0	387	74.145000	1040	2019	1	chr7A.!!$F2	979
6	TraesCS2B01G487700	chr7A	5527023	5528314	1291	False	310.0	350	76.619000	1136	2505	2	chr7A.!!$F3	1369
7	TraesCS2B01G487700	chr7D	631059427	631060306	879	True	359.0	359	74.299000	1136	2018	1	chr7D.!!$R1	882
8	TraesCS2B01G487700	chr7D	5009554	5010845	1291	False	304.5	350	76.355500	1136	2505	2	chr7D.!!$F2	1369
9	TraesCS2B01G487700	chr7D	638647483	638648195	712	True	294.0	294	74.553000	1136	1851	1	chr7D.!!$R2	715
10	TraesCS2B01G487700	chr7D	631231691	631232571	880	False	255.0	255	72.321000	1137	2020	1	chr7D.!!$F1	883
11	TraesCS2B01G487700	chr4A	738046155	738046948	793	False	351.0	351	74.907000	1136	1933	1	chr4A.!!$F1	797
12	TraesCS2B01G487700	chrUn	294521822	294522616	794	False	346.0	346	74.845000	1136	1933	1	chrUn.!!$F1	797
13	TraesCS2B01G487700	chrUn	248487392	248488701	1309	False	282.5	335	75.609000	1136	2505	2	chrUn.!!$F2	1369
14	TraesCS2B01G487700	chrUn	88656526	88657835	1309	True	243.5	291	74.470000	1136	2505	2	chrUn.!!$R1	1369

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
169	170	1.546029	TGACAGAGGGACGTCAATCTG	59.454	52.381	31.67	31.67	43.81	2.90	F
1923	1976	1.545582	CGCATTTGGATTTCACAGGGT	59.454	47.619	0.00	0.00	0.00	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2104	2157	0.521242	GCATAGCAAGTTTGTCCGCG	60.521	55.000	0.0	0.00	0.0	6.46	R
3863	3951	1.132643	GCCTGATGAAGAAGCTTGCAG	59.867	52.381	2.1	1.59	0.0	4.41	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
140	141	9.477484	TTTAAACACTGTCAAAAAGCAGTTAAA	57.523	25.926	0.00	0.00	43.27	1.52
169	170	1.546029	TGACAGAGGGACGTCAATCTG	59.454	52.381	31.67	31.67	43.81	2.90
189	190	3.476552	TGGAACAACCATGTCAAGAGTC	58.523	45.455	0.00	0.00	44.64	3.36
204	205	4.654262	TCAAGAGTCAGGGTTGTAAGAACT	59.346	41.667	0.00	0.00	0.00	3.01
317	351	3.302415	GCGCACCTGTTTTCATTTTCAAC	60.302	43.478	0.30	0.00	0.00	3.18
482	518	4.812626	TGCATGTATACATTGTGCTCTGAG	59.187	41.667	23.49	0.00	33.61	3.35
489	525	4.833478	ACATTGTGCTCTGAGAGGTAAT	57.167	40.909	12.01	0.48	0.00	1.89
503	539	5.659971	TGAGAGGTAATAGGTAACCTTGGAC	59.340	44.000	0.00	0.00	46.22	4.02
524	560	5.523552	GGACAATTTTATGCTAAATGTGGCC	59.476	40.000	0.00	0.00	32.14	5.36
581	623	3.947868	ACCATGAAGATTGGAGAGTGTG	58.052	45.455	0.00	0.00	37.69	3.82
685	731	3.079578	AGCATGATGTTTGTCTGGACAG	58.920	45.455	0.00	0.00	42.94	3.51
957	1003	9.832445	TTCAATAGGATACAGGAAATAACTCAC	57.168	33.333	0.00	0.00	41.41	3.51
1541	1594	4.850386	ACAAAGGATAGGTACCCTTGAACT	59.150	41.667	8.74	0.00	41.61	3.01
1923	1976	1.545582	CGCATTTGGATTTCACAGGGT	59.454	47.619	0.00	0.00	0.00	4.34
2026	2079	3.114668	TGCAGCAAGTTGAATGCAAAT	57.885	38.095	25.22	0.00	45.09	2.32
2028	2081	3.989167	TGCAGCAAGTTGAATGCAAATAC	59.011	39.130	25.22	4.84	45.09	1.89
2068	2121	8.272545	TCGAGATGAAATTTTTGTCATGAGAT	57.727	30.769	0.00	0.00	34.61	2.75
2104	2157	6.205658	AGTTGTAAGAGAAGAGCCATTTCAAC	59.794	38.462	0.00	0.00	0.00	3.18
2107	2160	0.798776	AGAAGAGCCATTTCAACGCG	59.201	50.000	3.53	3.53	0.00	6.01
2117	2170	2.181426	TTTCAACGCGGACAAACTTG	57.819	45.000	12.47	3.78	0.00	3.16
2587	2643	7.437748	AGTATTAGACACTGGCTCATACATTC	58.562	38.462	15.69	0.00	29.22	2.67
2760	2816	7.170965	AGATAACACAACTTCAGTCCATGAAT	58.829	34.615	0.00	0.00	46.71	2.57
2937	2993	1.542915	CTTGAACCACATCCAGGCTTG	59.457	52.381	0.00	0.00	0.00	4.01
3018	3074	6.257630	GCAATTTTTCAGTTACCTCTTTGCAA	59.742	34.615	0.00	0.00	36.61	4.08
3021	3077	5.906113	TTTCAGTTACCTCTTTGCAAACA	57.094	34.783	8.05	0.00	0.00	2.83
3128	3184	5.870978	ACATGCAGAAAATAATGGAAGCAAC	59.129	36.000	0.00	0.00	34.15	4.17
3195	3251	3.149196	GGAGAAATGTTCCTGCAGTTCA	58.851	45.455	13.81	8.94	43.37	3.18
3196	3252	3.569701	GGAGAAATGTTCCTGCAGTTCAA	59.430	43.478	13.81	0.00	43.37	2.69
3305	3361	7.945033	TTAAATTCGAAAGCAAGCAGAAATT	57.055	28.000	0.00	0.00	0.00	1.82
3355	3411	6.769134	TTATCTACGATTGTCCTCACTTGA	57.231	37.500	0.00	0.00	0.00	3.02
3386	3442	1.355720	CCCTCTTCCACCTTCAACCAT	59.644	52.381	0.00	0.00	0.00	3.55
3399	3455	7.031372	CACCTTCAACCATATGTTCTGAATTG	58.969	38.462	1.24	4.66	34.00	2.32
3456	3512	3.973973	AGGGATCATCCGGAGAAACATTA	59.026	43.478	11.34	0.00	37.43	1.90
3473	3529	5.890424	ACATTAAAAATCGACGGTCCAAT	57.110	34.783	1.91	0.00	0.00	3.16
3627	3715	6.825610	TGGAAATAAGCAATTGTGGAAAACT	58.174	32.000	7.40	0.00	0.00	2.66
3635	3723	6.044682	AGCAATTGTGGAAAACTTTTCTCTG	58.955	36.000	12.88	4.67	0.00	3.35
3765	3853	1.812235	TCTTTGATGCTGCGACATGT	58.188	45.000	0.00	0.00	0.00	3.21
3786	3874	3.998341	GTGACGGCTCTAATGGTGTTAAA	59.002	43.478	0.00	0.00	0.00	1.52
3863	3951	6.314896	CAGTCAGTCAAATCTTATCTCAACCC	59.685	42.308	0.00	0.00	0.00	4.11
4086	4174	1.675116	GCTGCTCTCATCTTCAGTGCA	60.675	52.381	0.00	0.00	37.89	4.57
4108	4196	5.511716	GCATATTGATGGAAATGATGGCCAA	60.512	40.000	10.96	0.00	34.95	4.52
4151	4239	3.054875	CCCTCAATCACTTGGACATCTCA	60.055	47.826	0.00	0.00	32.95	3.27
4152	4240	4.384978	CCCTCAATCACTTGGACATCTCAT	60.385	45.833	0.00	0.00	32.95	2.90
4161	4249	1.620323	TGGACATCTCATGATAGCCGG	59.380	52.381	0.00	0.00	31.56	6.13
4213	4301	1.839994	CCAAGGAATCTCACCTGCCTA	59.160	52.381	0.00	0.00	37.85	3.93
4297	4385	3.181493	GCACTGGAGGAGTTGCATATTTG	60.181	47.826	0.00	0.00	29.75	2.32
4315	4403	2.797278	GGGGATGTCCATCGCTCGT	61.797	63.158	19.67	0.00	46.29	4.18
4423	4511	1.620819	AGGTTATGAGCTATGCCCTCG	59.379	52.381	0.00	0.00	31.98	4.63
4471	4559	0.036765	TGTGTCCTTACCACGCCATC	60.037	55.000	0.00	0.00	35.56	3.51
4472	4560	0.249398	GTGTCCTTACCACGCCATCT	59.751	55.000	0.00	0.00	0.00	2.90
4473	4561	0.249120	TGTCCTTACCACGCCATCTG	59.751	55.000	0.00	0.00	0.00	2.90
4474	4562	1.090052	GTCCTTACCACGCCATCTGC	61.090	60.000	0.00	0.00	0.00	4.26
4475	4563	1.078497	CCTTACCACGCCATCTGCA	60.078	57.895	0.00	0.00	41.33	4.41
4477	4565	1.382522	CTTACCACGCCATCTGCAAT	58.617	50.000	0.00	0.00	41.33	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
140	141	0.904865	TCCCTCTGTCACTTCCGCAT	60.905	55.000	0.00	0.00	0.00	4.73
149	150	1.546029	CAGATTGACGTCCCTCTGTCA	59.454	52.381	25.22	1.48	42.98	3.58
169	170	3.476552	TGACTCTTGACATGGTTGTTCC	58.523	45.455	0.00	0.00	35.79	3.62
189	190	3.866449	GCTCTGGAGTTCTTACAACCCTG	60.866	52.174	0.00	0.00	0.00	4.45
204	205	1.372683	GCTGGTCAGTTGCTCTGGA	59.627	57.895	8.98	0.00	43.76	3.86
455	491	6.416750	CAGAGCACAATGTATACATGCAAATG	59.583	38.462	24.55	18.19	36.56	2.32
482	518	5.945144	TGTCCAAGGTTACCTATTACCTC	57.055	43.478	3.55	0.00	43.88	3.85
489	525	7.179269	AGCATAAAATTGTCCAAGGTTACCTA	58.821	34.615	3.55	0.00	31.13	3.08
503	539	8.836268	ATATGGCCACATTTAGCATAAAATTG	57.164	30.769	8.16	0.00	38.53	2.32
581	623	3.485947	TTTTGTGCACTCTGAACACAC	57.514	42.857	19.41	2.93	43.57	3.82
821	867	1.401409	CCAATTACAACAGGTGCAGCG	60.401	52.381	10.78	8.17	0.00	5.18
862	908	2.442413	CAACTCCTCGTCTCTTCTCCT	58.558	52.381	0.00	0.00	0.00	3.69
957	1003	4.956700	TCCTCTAGGATGTCTTGTAACTGG	59.043	45.833	0.00	0.00	39.78	4.00
1377	1430	2.169832	TGAGCAGAAACCTTTCCGAG	57.830	50.000	0.00	0.00	37.92	4.63
1541	1594	2.582052	CCAAAGCACCTAAGTTGACCA	58.418	47.619	0.00	0.00	0.00	4.02
2026	2079	1.469703	TCGAAAACGGATGCTCTCGTA	59.530	47.619	0.00	0.00	38.78	3.43
2028	2081	0.917259	CTCGAAAACGGATGCTCTCG	59.083	55.000	0.00	0.00	0.00	4.04
2068	2121	8.063200	TCTTCTCTTACAACTCGATTATGGAA	57.937	34.615	0.00	0.00	0.00	3.53
2104	2157	0.521242	GCATAGCAAGTTTGTCCGCG	60.521	55.000	0.00	0.00	0.00	6.46
2107	2160	4.396166	ACACATAGCATAGCAAGTTTGTCC	59.604	41.667	0.00	0.00	0.00	4.02
2117	2170	1.972872	AAGGCCACACATAGCATAGC	58.027	50.000	5.01	0.00	0.00	2.97
2188	2241	6.949578	CAAAATTTCGTTGCACCATAGATT	57.050	33.333	0.00	0.00	0.00	2.40
2443	2499	6.202954	CACACGAAGGAACTAAAATCAGAAGT	59.797	38.462	0.00	0.00	38.49	3.01
2760	2816	1.694150	ACACCTAGTTGCAGAAGCTCA	59.306	47.619	0.00	0.00	42.74	4.26
2937	2993	2.227388	CCCAAATATCCGCAGATGCTTC	59.773	50.000	2.95	0.00	39.32	3.86
3018	3074	5.485353	TCCACAATCCTCTAGATGAAGTGTT	59.515	40.000	21.34	5.13	34.56	3.32
3021	3077	5.523588	TCTCCACAATCCTCTAGATGAAGT	58.476	41.667	1.57	1.91	34.56	3.01
3128	3184	1.740025	GCTCCTCCAATGAAGGAAACG	59.260	52.381	0.00	0.00	37.20	3.60
3195	3251	9.838339	CTTAAACTAGAGTTCATATCCCACATT	57.162	33.333	0.00	0.00	37.25	2.71
3196	3252	9.213777	TCTTAAACTAGAGTTCATATCCCACAT	57.786	33.333	0.00	0.00	37.25	3.21
3355	3411	3.421844	GTGGAAGAGGGTGCATTACTTT	58.578	45.455	0.00	0.00	0.00	2.66
3399	3455	6.414987	GCAGTGTTGAAACTCTGTTGATAAAC	59.585	38.462	20.38	0.00	46.63	2.01
3485	3541	4.017591	TCCACATCTCATAAAACCACCCAT	60.018	41.667	0.00	0.00	0.00	4.00
3627	3715	8.687242	CACACTCTGGTATATCTACAGAGAAAA	58.313	37.037	25.68	1.14	37.01	2.29
3635	3723	3.895656	TGGGCACACTCTGGTATATCTAC	59.104	47.826	0.00	0.00	0.00	2.59
3765	3853	3.965379	TTAACACCATTAGAGCCGTCA	57.035	42.857	0.00	0.00	0.00	4.35
3805	3893	9.838339	CCCTCTTCTATTGATAACTGTGTTATT	57.162	33.333	4.72	0.00	0.00	1.40
3863	3951	1.132643	GCCTGATGAAGAAGCTTGCAG	59.867	52.381	2.10	1.59	0.00	4.41
4081	4169	5.279306	GCCATCATTTCCATCAATATGCACT	60.279	40.000	0.00	0.00	0.00	4.40
4086	4174	5.842328	ACTTGGCCATCATTTCCATCAATAT	59.158	36.000	6.09	0.00	0.00	1.28
4108	4196	3.008485	GGAGGAGACAACTTCCATTCACT	59.992	47.826	0.00	0.00	36.30	3.41
4151	4239	3.367498	GCTCGAGAATAACCGGCTATCAT	60.367	47.826	18.75	0.00	0.00	2.45
4152	4240	2.030185	GCTCGAGAATAACCGGCTATCA	60.030	50.000	18.75	0.00	0.00	2.15
4161	4249	2.979299	GCAGCATTGCTCGAGAATAAC	58.021	47.619	18.75	8.67	46.95	1.89
4234	4322	7.173390	GCTGTAGAGACTCCAAACTTTTATTGT	59.827	37.037	0.00	0.00	0.00	2.71
4297	4385	2.029666	CGAGCGATGGACATCCCC	59.970	66.667	6.71	0.00	34.40	4.81
4315	4403	1.304962	TGGAAGCCCTCTAGTGCGA	60.305	57.895	0.00	0.00	0.00	5.10
4423	4511	3.319122	ACTGGTCACAAGCTTTTCCAATC	59.681	43.478	0.00	0.00	0.00	2.67
4471	4559	1.022735	GGGATGTGAGCTGATTGCAG	58.977	55.000	0.00	0.00	45.94	4.41
4472	4560	0.622136	AGGGATGTGAGCTGATTGCA	59.378	50.000	0.00	0.00	45.94	4.08
4473	4561	2.216898	GTAGGGATGTGAGCTGATTGC	58.783	52.381	0.00	0.00	43.29	3.56
4474	4562	3.548745	TGTAGGGATGTGAGCTGATTG	57.451	47.619	0.00	0.00	0.00	2.67
4475	4563	3.679917	CGTTGTAGGGATGTGAGCTGATT	60.680	47.826	0.00	0.00	0.00	2.57
4477	4565	1.204704	CGTTGTAGGGATGTGAGCTGA	59.795	52.381	0.00	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.