AutoCloner

Multiple sequence alignment - TraesCS3B01G086600

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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	TraesCS3B01G086600	chr3B	100.000	4523	0	0	1	4523	54793306	54797828	0.000000e+00	8353.0
1	TraesCS3B01G086600	chr3B	91.105	2226	184	8	2307	4523	54786056	54788276	0.000000e+00	3001.0
2	TraesCS3B01G086600	chr3B	86.934	1768	204	15	457	2213	54784286	54786037	0.000000e+00	1960.0
3	TraesCS3B01G086600	chr3B	84.681	470	43	11	1	450	54783636	54784096	4.150000e-120	442.0
4	TraesCS3B01G086600	chr3A	95.837	3603	136	9	1	3599	44638511	44642103	0.000000e+00	5810.0
5	TraesCS3B01G086600	chr3A	87.528	3985	406	30	566	4523	44709401	44713321	0.000000e+00	4521.0
6	TraesCS3B01G086600	chr3A	81.165	738	99	25	3613	4333	44642081	44642795	1.420000e-154	556.0
7	TraesCS3B01G086600	chr3A	79.345	397	54	19	1	378	44708850	44709237	2.090000e-63	254.0
8	TraesCS3B01G086600	chr3D	87.627	3944	427	28	605	4523	32299191	32303098	0.000000e+00	4523.0
9	TraesCS3B01G086600	chr3D	85.318	3140	402	31	481	3599	32278386	32281487	0.000000e+00	3190.0
10	TraesCS3B01G086600	chr3D	81.380	913	120	26	3613	4513	32281465	32282339	0.000000e+00	699.0
11	TraesCS3B01G086600	chr3D	80.253	395	57	16	1	378	32277742	32278132	1.240000e-70	278.0
12	TraesCS3B01G086600	chr5D	80.988	2977	468	47	625	3577	104257915	104255013	0.000000e+00	2272.0
13	TraesCS3B01G086600	chr5D	86.437	1305	155	9	975	2268	425838914	425840207	0.000000e+00	1410.0
14	TraesCS3B01G086600	chr4D	80.538	2975	492	55	597	3550	1994950	1997858	0.000000e+00	2206.0
15	TraesCS3B01G086600	chr5B	86.705	1384	155	13	901	2268	515184011	515185381	0.000000e+00	1509.0
16	TraesCS3B01G086600	chr5B	81.101	1508	227	28	2177	3678	14705918	14707373	0.000000e+00	1153.0
17	TraesCS3B01G086600	chr5B	82.583	1355	182	31	2230	3577	113676933	113675626	0.000000e+00	1146.0
18	TraesCS3B01G086600	chr5B	97.059	34	0	1	765	797	515183906	515183939	6.320000e-04	56.5
19	TraesCS3B01G086600	chr5A	85.560	1385	169	17	901	2268	540051895	540053265	0.000000e+00	1421.0
20	TraesCS3B01G086600	chrUn	78.604	1762	303	51	724	2444	47549307	47547579	0.000000e+00	1098.0
21	TraesCS3B01G086600	chr4B	82.907	1211	174	20	2478	3681	2336122	2334938	0.000000e+00	1059.0

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	TraesCS3B01G086600	chr3B	54793306	54797828	4522	False	8353.00	8353	100.000000	1	4523	1	chr3B.!!$F1	4522
1	TraesCS3B01G086600	chr3B	54783636	54788276	4640	False	1801.00	3001	87.573333	1	4523	3	chr3B.!!$F2	4522
2	TraesCS3B01G086600	chr3A	44638511	44642795	4284	False	3183.00	5810	88.501000	1	4333	2	chr3A.!!$F1	4332
3	TraesCS3B01G086600	chr3A	44708850	44713321	4471	False	2387.50	4521	83.436500	1	4523	2	chr3A.!!$F2	4522
4	TraesCS3B01G086600	chr3D	32299191	32303098	3907	False	4523.00	4523	87.627000	605	4523	1	chr3D.!!$F1	3918
5	TraesCS3B01G086600	chr3D	32277742	32282339	4597	False	1389.00	3190	82.317000	1	4513	3	chr3D.!!$F2	4512
6	TraesCS3B01G086600	chr5D	104255013	104257915	2902	True	2272.00	2272	80.988000	625	3577	1	chr5D.!!$R1	2952
7	TraesCS3B01G086600	chr5D	425838914	425840207	1293	False	1410.00	1410	86.437000	975	2268	1	chr5D.!!$F1	1293
8	TraesCS3B01G086600	chr4D	1994950	1997858	2908	False	2206.00	2206	80.538000	597	3550	1	chr4D.!!$F1	2953
9	TraesCS3B01G086600	chr5B	14705918	14707373	1455	False	1153.00	1153	81.101000	2177	3678	1	chr5B.!!$F1	1501
10	TraesCS3B01G086600	chr5B	113675626	113676933	1307	True	1146.00	1146	82.583000	2230	3577	1	chr5B.!!$R1	1347
11	TraesCS3B01G086600	chr5B	515183906	515185381	1475	False	782.75	1509	91.882000	765	2268	2	chr5B.!!$F2	1503
12	TraesCS3B01G086600	chr5A	540051895	540053265	1370	False	1421.00	1421	85.560000	901	2268	1	chr5A.!!$F1	1367
13	TraesCS3B01G086600	chrUn	47547579	47549307	1728	True	1098.00	1098	78.604000	724	2444	1	chrUn.!!$R1	1720
14	TraesCS3B01G086600	chr4B	2334938	2336122	1184	True	1059.00	1059	82.907000	2478	3681	1	chr4B.!!$R1	1203

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	Hairpin	End Stability	Orientation
818	1088	0.031857	CGATTGCAGGTTTTGTGGCA	59.968	50.000	0.00	4.92	F
1527	1855	0.675083	CCTTTGCACCATCAGCACAA	59.325	50.000	42.54	3.33	F
2035	2378	1.013596	CAACAACCAGACAACGCAGA	58.986	50.000	0.00	4.26	F
2082	2425	1.202382	GGAGGAATCGGTAGACCAACG	60.202	57.143	35.14	4.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1917	2260	0.400213	AGAAACCTGCATCAACCGGA	59.600	50.000	9.46	0.0	0.00	5.14	R
2550	2914	1.143183	GAAACCGCCTCTGCCGATA	59.857	57.895	0.00	0.0	0.00	2.92	R
2994	3358	1.321474	CAGTGCTCATGTGGGTGTTT	58.679	50.000	0.00	0.0	0.00	2.83	R
4054	4465	0.250038	ATCTGGCGACGCATAGCAAT	60.250	50.000	23.09	6.9	34.54	3.56	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
47	52	3.562176	GCATCCCCCTTCTCTTCTTTTCA	60.562	47.826	0.00	0.00	0.00	2.69
148	165	1.063183	CCCCAAATTTTGCCAAGGGA	58.937	50.000	13.17	0.00	38.60	4.20
335	355	1.331214	AGGCAAGTTGTCCACCAATG	58.669	50.000	15.71	0.00	35.02	2.82
441	472	5.121454	TGGTGTGAATTTTTCAAGCACAAAC	59.879	36.000	0.00	0.00	42.15	2.93
619	886	6.630444	ATTATTGAGCAGGCTTTGTCTATG	57.370	37.500	0.00	0.00	0.00	2.23
818	1088	0.031857	CGATTGCAGGTTTTGTGGCA	59.968	50.000	0.00	0.00	0.00	4.92
1045	1349	1.446907	CCTCACATTCCTCACACTGC	58.553	55.000	0.00	0.00	0.00	4.40
1120	1433	4.807643	GCCTTATCCTCCTAAATTGCGGAT	60.808	45.833	0.00	0.00	38.07	4.18
1527	1855	0.675083	CCTTTGCACCATCAGCACAA	59.325	50.000	0.00	0.00	42.54	3.33
1608	1936	5.079689	TCGCAACACCTGACATAAGATTA	57.920	39.130	0.00	0.00	0.00	1.75
1917	2260	8.472007	TGAACTACAACCTTACATGGATTTTT	57.528	30.769	0.00	0.00	0.00	1.94
2001	2344	2.338809	ACCAAGGTGAATCAGAGGTCA	58.661	47.619	0.00	0.00	0.00	4.02
2029	2372	5.863965	TCATCTACATCAACAACCAGACAA	58.136	37.500	0.00	0.00	0.00	3.18
2035	2378	1.013596	CAACAACCAGACAACGCAGA	58.986	50.000	0.00	0.00	0.00	4.26
2082	2425	1.202382	GGAGGAATCGGTAGACCAACG	60.202	57.143	0.00	0.00	35.14	4.10
2116	2459	8.798859	ATATGTTATCATGGCTATTGGTTCTC	57.201	34.615	0.00	0.00	35.70	2.87
2175	2518	7.416154	TCTTTCAAGTAAACCACAGTATTCG	57.584	36.000	0.00	0.00	0.00	3.34
2184	2527	3.620488	ACCACAGTATTCGGATGCAATT	58.380	40.909	0.00	0.00	0.00	2.32
2282	2628	4.439289	GCAAAAGCCTGATGTGAATCCTAC	60.439	45.833	0.00	0.00	0.00	3.18
2294	2640	8.170730	TGATGTGAATCCTACTAGGCTATCTAA	58.829	37.037	0.00	0.00	34.61	2.10
2394	2758	4.157656	GCCCTTTTCAGCATGTGTGTTATA	59.842	41.667	0.00	0.00	37.40	0.98
2550	2914	7.014615	ACCAAAGACTTTGATGAAGCACTTATT	59.985	33.333	26.14	0.00	43.26	1.40
3201	3565	1.328986	GCGCTATCTTGCTGGAAGAAC	59.671	52.381	15.62	7.62	44.11	3.01
3312	3676	4.214332	TGTGTAGCTGATCGTAGCATAGAG	59.786	45.833	7.70	0.00	46.07	2.43
3371	3735	4.719106	ACTCCAGCTGCAGCAGGC	62.719	66.667	37.70	16.14	45.96	4.85
3525	3904	2.159254	GCATGCAGAAGGCCGATAAAAA	60.159	45.455	14.21	0.00	43.89	1.94
3709	4101	4.878971	TCTCGGTCACTGACATTTCAAAAA	59.121	37.500	11.34	0.00	33.68	1.94
3710	4102	5.530915	TCTCGGTCACTGACATTTCAAAAAT	59.469	36.000	11.34	0.00	33.68	1.82
3711	4103	6.708502	TCTCGGTCACTGACATTTCAAAAATA	59.291	34.615	11.34	0.00	33.68	1.40
3712	4104	7.390440	TCTCGGTCACTGACATTTCAAAAATAT	59.610	33.333	11.34	0.00	33.68	1.28
3754	4156	7.721402	TGTTATTTTGCTACAAGGTTGTTCAT	58.279	30.769	0.00	0.00	42.35	2.57
3774	4176	3.627395	TTGCCTCGGTTATCTTGATGT	57.373	42.857	0.00	0.00	0.00	3.06
3835	4237	6.676632	TCAAGGATAAAGGAGGGATCTACAAA	59.323	38.462	0.00	0.00	0.00	2.83
3836	4238	6.755542	AGGATAAAGGAGGGATCTACAAAG	57.244	41.667	0.00	0.00	0.00	2.77
3849	4251	6.043938	GGGATCTACAAAGGACATATTACCCA	59.956	42.308	0.00	0.00	0.00	4.51
3918	4329	8.106462	TCAACAGTGTAATCAATCTAATTGGGA	58.894	33.333	0.00	0.00	40.61	4.37
3935	4346	1.095807	GGATTACGAAGGTGCCCAGC	61.096	60.000	0.00	0.00	0.00	4.85
3945	4356	1.148273	GTGCCCAGCGGATATCCAA	59.852	57.895	21.70	0.00	35.14	3.53
4121	4532	7.770366	TTACAGAGTGAAAGGTAGACATACA	57.230	36.000	0.00	0.00	33.21	2.29
4246	4661	8.006298	TCGCCCATTCATTTTACATAATCTTT	57.994	30.769	0.00	0.00	0.00	2.52
4299	4714	2.352342	TGCACTCGCATATTCATGTGTG	59.648	45.455	0.00	0.00	45.36	3.82
4408	4835	5.177696	GGAGCTAGTACAGTTTTTCAGTGTG	59.822	44.000	0.00	0.00	39.59	3.82
4467	4898	9.350357	CAGATATTGATTGTTTTGGAGTTTCTG	57.650	33.333	0.00	0.00	0.00	3.02
4494	4926	4.459337	GGTCAAGAGTTGTTATTCCTTGGG	59.541	45.833	0.00	0.00	36.01	4.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	52	6.127026	ACCGAATCAACTAGATAAAGGAGCTT	60.127	38.462	0.00	0.00	35.39	3.74
335	355	7.615582	TGATGATTCCACATCTACAAAAGAC	57.384	36.000	0.00	0.00	44.61	3.01
390	417	0.767375	ACACATGGAGCAACAGTCCT	59.233	50.000	0.00	0.00	34.86	3.85
530	795	4.256920	AGTGCGAGAATTTAGCTCAACAT	58.743	39.130	0.00	0.00	32.67	2.71
531	796	3.664107	AGTGCGAGAATTTAGCTCAACA	58.336	40.909	0.00	0.00	32.67	3.33
619	886	4.278669	TGAGAACAGTACCAGAAGACAGAC	59.721	45.833	0.00	0.00	0.00	3.51
818	1088	0.037232	GAAGTTGGCGCACCTAGAGT	60.037	55.000	10.83	0.00	36.63	3.24
828	1102	4.083537	TGCTATTGTTTAGTGAAGTTGGCG	60.084	41.667	0.00	0.00	0.00	5.69
832	1106	6.092259	GGATCGTGCTATTGTTTAGTGAAGTT	59.908	38.462	0.00	0.00	0.00	2.66
833	1107	5.581085	GGATCGTGCTATTGTTTAGTGAAGT	59.419	40.000	0.00	0.00	0.00	3.01
1045	1349	2.159184	TGGCAATCGACAAGAGAGCTAG	60.159	50.000	0.00	0.00	34.32	3.42
1225	1550	2.531942	GGGGGTGAGTGAAGGGGT	60.532	66.667	0.00	0.00	0.00	4.95
1527	1855	5.357878	CACAAATGCATAAGACCCATACTGT	59.642	40.000	0.00	0.00	0.00	3.55
1608	1936	2.497675	AGATGTGTTATCACCGCTGACT	59.502	45.455	1.53	0.00	43.26	3.41
1702	2030	3.692406	GCCCGAGTCACCTTCCGT	61.692	66.667	0.00	0.00	0.00	4.69
1748	2079	3.117888	CCCAGAGCCACCAAGTATGTATT	60.118	47.826	0.00	0.00	0.00	1.89
1917	2260	0.400213	AGAAACCTGCATCAACCGGA	59.600	50.000	9.46	0.00	0.00	5.14
2001	2344	7.335422	GTCTGGTTGTTGATGTAGATGAAGAAT	59.665	37.037	0.00	0.00	0.00	2.40
2029	2372	1.470098	GACATCCATTTGCTTCTGCGT	59.530	47.619	0.00	0.00	43.34	5.24
2035	2378	2.684881	GGACGATGACATCCATTTGCTT	59.315	45.455	9.87	0.00	35.17	3.91
2082	2425	7.969536	AGCCATGATAACATATTCAGTGTAC	57.030	36.000	0.00	0.00	35.09	2.90
2175	2518	3.003068	CGAGACCATTCAGAATTGCATCC	59.997	47.826	0.00	0.00	0.00	3.51
2184	2527	2.516227	AGACCTCGAGACCATTCAGA	57.484	50.000	15.71	0.00	0.00	3.27
2246	2592	0.875059	CTTTTGCGGAAGTGGAGGAC	59.125	55.000	0.00	0.00	0.00	3.85
2282	2628	8.964476	TTTTCTTTCACCATTAGATAGCCTAG	57.036	34.615	0.00	0.00	0.00	3.02
2294	2640	5.857268	CACCTTTGGATTTTCTTTCACCAT	58.143	37.500	0.00	0.00	0.00	3.55
2394	2758	2.358267	CGCTACCTTCTTCCGTCTGTAT	59.642	50.000	0.00	0.00	0.00	2.29
2550	2914	1.143183	GAAACCGCCTCTGCCGATA	59.857	57.895	0.00	0.00	0.00	2.92
2855	3219	1.985159	TGTGGAGGTAATGCAGTCCTT	59.015	47.619	8.22	0.00	0.00	3.36
2994	3358	1.321474	CAGTGCTCATGTGGGTGTTT	58.679	50.000	0.00	0.00	0.00	2.83
3201	3565	3.594603	ACAATCTCCTCAAGTACACCG	57.405	47.619	0.00	0.00	0.00	4.94
3265	3629	5.869753	TTCTCTGCTATCTCTGCAAAAAC	57.130	39.130	0.00	0.00	40.13	2.43
3312	3676	3.835810	ATCACCCATTGATGGCCTC	57.164	52.632	3.32	0.00	43.87	4.70
3709	4101	5.142806	ACAAAATAGCAACCTGGGGATAT	57.857	39.130	0.00	0.00	0.00	1.63
3710	4102	4.601406	ACAAAATAGCAACCTGGGGATA	57.399	40.909	0.00	0.00	0.00	2.59
3711	4103	3.473113	ACAAAATAGCAACCTGGGGAT	57.527	42.857	0.00	0.00	0.00	3.85
3712	4104	2.990740	ACAAAATAGCAACCTGGGGA	57.009	45.000	0.00	0.00	0.00	4.81
3754	4156	3.627395	ACATCAAGATAACCGAGGCAA	57.373	42.857	0.00	0.00	0.00	4.52
3835	4237	8.474831	GTGCTTAAAATTTGGGTAATATGTCCT	58.525	33.333	0.00	0.00	0.00	3.85
3836	4238	8.474831	AGTGCTTAAAATTTGGGTAATATGTCC	58.525	33.333	0.00	0.00	0.00	4.02
3849	4251	5.712446	GGAGAAGGGAGAGTGCTTAAAATTT	59.288	40.000	0.00	0.00	0.00	1.82
3935	4346	1.699634	AGGGGTGACATTGGATATCCG	59.300	52.381	17.04	5.47	39.43	4.18
3945	4356	3.184628	TGAGAATCAGAAGGGGTGACAT	58.815	45.455	0.00	0.00	42.56	3.06
4042	4453	3.405831	GCATAGCAATGATGAGGCTACA	58.594	45.455	0.00	0.00	42.36	2.74
4054	4465	0.250038	ATCTGGCGACGCATAGCAAT	60.250	50.000	23.09	6.90	34.54	3.56
4055	4466	0.387565	TATCTGGCGACGCATAGCAA	59.612	50.000	23.09	7.60	34.54	3.91
4390	4815	3.616219	TGGCACACTGAAAAACTGTACT	58.384	40.909	0.00	0.00	0.00	2.73
4408	4835	2.551032	AGTACGGTTAAAAAGTGCTGGC	59.449	45.455	0.00	0.00	30.00	4.85
4467	4898	6.635030	AGGAATAACAACTCTTGACCAAAC	57.365	37.500	0.00	0.00	0.00	2.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.