AutoCloner

Multiple sequence alignment - TraesCS2B01G212900

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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	TraesCS2B01G212900	chr2B	100.000	2663	0	0	1	2663	197506961	197509623	0.000000e+00	4918.0
1	TraesCS2B01G212900	chr2B	85.437	1339	146	27	653	1974	197379422	197380728	0.000000e+00	1347.0
2	TraesCS2B01G212900	chr2B	84.641	599	74	9	1	590	197378662	197379251	4.940000e-162	580.0
3	TraesCS2B01G212900	chr2B	84.474	599	75	9	1	590	197353147	197353736	2.300000e-160	575.0
4	TraesCS2B01G212900	chr2D	93.533	2706	95	25	1	2663	138906706	138909374	0.000000e+00	3954.0
5	TraesCS2B01G212900	chr2D	87.266	1335	130	20	653	1974	138888392	138889699	0.000000e+00	1487.0
6	TraesCS2B01G212900	chr2D	86.767	597	66	4	1	590	138887630	138888220	0.000000e+00	652.0
7	TraesCS2B01G212900	chr2A	93.670	1722	69	8	654	2337	162070394	162068675	0.000000e+00	2540.0
8	TraesCS2B01G212900	chr2A	85.522	1340	145	25	653	1974	162214488	162213180	0.000000e+00	1354.0
9	TraesCS2B01G212900	chr2A	85.667	600	72	5	1	593	162215248	162214656	1.050000e-173	619.0
10	TraesCS2B01G212900	chr2A	92.837	349	11	5	2322	2663	162068661	162068320	6.620000e-136	494.0
11	TraesCS2B01G212900	chr2A	92.258	155	12	0	439	593	162070720	162070566	1.240000e-53	220.0
12	TraesCS2B01G212900	chr4D	74.806	258	37	19	1258	1492	52215437	52215689	1.020000e-14	91.6
13	TraesCS2B01G212900	chr1B	90.625	64	6	0	2196	2259	142121497	142121560	4.720000e-13	86.1
14	TraesCS2B01G212900	chr4A	80.000	115	13	8	1383	1492	544397565	544397674	2.840000e-10	76.8
15	TraesCS2B01G212900	chr6B	100.000	28	0	0	2196	2223	10051543	10051570	5.000000e-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	TraesCS2B01G212900	chr2B	197506961	197509623	2662	False	4918.000000	4918	100.000000	1	2663	1	chr2B.!!$F2	2662
1	TraesCS2B01G212900	chr2B	197378662	197380728	2066	False	963.500000	1347	85.039000	1	1974	2	chr2B.!!$F3	1973
2	TraesCS2B01G212900	chr2B	197353147	197353736	589	False	575.000000	575	84.474000	1	590	1	chr2B.!!$F1	589
3	TraesCS2B01G212900	chr2D	138906706	138909374	2668	False	3954.000000	3954	93.533000	1	2663	1	chr2D.!!$F1	2662
4	TraesCS2B01G212900	chr2D	138887630	138889699	2069	False	1069.500000	1487	87.016500	1	1974	2	chr2D.!!$F2	1973
5	TraesCS2B01G212900	chr2A	162068320	162070720	2400	True	1084.666667	2540	92.921667	439	2663	3	chr2A.!!$R1	2224
6	TraesCS2B01G212900	chr2A	162213180	162215248	2068	True	986.500000	1354	85.594500	1	1974	2	chr2A.!!$R2	1973

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
381	390	0.454452	GGTTAAGCAAGCGCCTTTCG	60.454	55.0	2.29	0.0	39.83	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2348	2576	0.039437	TGCGACGAGACTTCTGTTCC	60.039	55.0	0.0	0.0	0.0	3.62	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
124	131	5.927115	CACTTATCCGCCCTAACTTATCTTC	59.073	44.000	0.00	0.00	0.00	2.87
293	301	5.697633	AGGAAAATGCAACAATGTAGCAAAG	59.302	36.000	0.00	0.00	42.15	2.77
297	305	7.816945	AAATGCAACAATGTAGCAAAGATAC	57.183	32.000	0.00	0.00	42.15	2.24
341	349	4.987408	TTAACCGGATGTCTCGTGATTA	57.013	40.909	9.46	0.00	0.00	1.75
380	389	0.596082	TGGTTAAGCAAGCGCCTTTC	59.404	50.000	2.29	0.00	39.83	2.62
381	390	0.454452	GGTTAAGCAAGCGCCTTTCG	60.454	55.000	2.29	0.00	39.83	3.46
436	446	5.052481	GGCCTGAATTAAATGGAAAGATGC	58.948	41.667	0.00	0.00	0.00	3.91
513	523	2.139917	TGCACGCATATTATCCCGAAC	58.860	47.619	0.00	0.00	0.00	3.95
540	550	1.344953	TGGCGGGCCTAGATGTTGAT	61.345	55.000	11.55	0.00	36.94	2.57
543	553	1.475034	GCGGGCCTAGATGTTGATCAA	60.475	52.381	3.38	3.38	0.00	2.57
545	555	2.614057	CGGGCCTAGATGTTGATCAAAC	59.386	50.000	10.35	5.46	39.41	2.93
979	1117	4.308458	TCCGGTCAACCCTGCGTG	62.308	66.667	0.00	0.00	0.00	5.34
1006	1144	4.147449	CTCCGCCAGCCATGTCGA	62.147	66.667	0.00	0.00	0.00	4.20
1710	1858	3.616821	GCGGGATTTAGGTTTTTGATTGC	59.383	43.478	0.00	0.00	0.00	3.56
1712	1860	5.393678	GCGGGATTTAGGTTTTTGATTGCTA	60.394	40.000	0.00	0.00	0.00	3.49
1811	1964	2.546778	CGGTGTTGATATGGTAAGCGT	58.453	47.619	0.00	0.00	0.00	5.07
1813	1966	4.114073	CGGTGTTGATATGGTAAGCGTTA	58.886	43.478	0.00	0.00	0.00	3.18
1883	2036	5.417580	TGCTTACCTGTCCATATTTTTGACC	59.582	40.000	0.00	0.00	0.00	4.02
2006	2160	9.037737	CCTTTTCCAACTTCGTATCGAAATATA	57.962	33.333	6.10	0.00	45.23	0.86
2009	2163	9.976511	TTTCCAACTTCGTATCGAAATATATCT	57.023	29.630	6.10	0.00	45.23	1.98
2010	2164	9.976511	TTCCAACTTCGTATCGAAATATATCTT	57.023	29.630	6.10	0.00	45.23	2.40
2030	2184	7.907214	ATCTTAGTATGAAAGTGAAACGCTT	57.093	32.000	0.00	0.00	45.86	4.68
2031	2185	8.997621	ATCTTAGTATGAAAGTGAAACGCTTA	57.002	30.769	0.00	0.00	45.86	3.09
2074	2244	5.062809	CAGCTAGATCACGGAAAAAGAACTC	59.937	44.000	0.00	0.00	0.00	3.01
2078	2248	4.627467	AGATCACGGAAAAAGAACTCATCG	59.373	41.667	0.00	0.00	0.00	3.84
2084	2254	4.554723	CGGAAAAAGAACTCATCGTTGCTT	60.555	41.667	0.00	0.00	35.56	3.91
2235	2430	6.936279	TCTCAAACATAGGAAGGTTACAGAG	58.064	40.000	0.00	0.00	30.58	3.35
2237	2432	5.045869	TCAAACATAGGAAGGTTACAGAGGG	60.046	44.000	0.00	0.00	0.00	4.30
2460	2693	8.281212	AGCCATAGTTAGTTTCCATTAAGTTG	57.719	34.615	0.00	0.00	0.00	3.16
2588	2833	3.282831	AGCTTGTTGTTGAATAACGCC	57.717	42.857	0.49	0.00	39.71	5.68
2589	2834	2.884639	AGCTTGTTGTTGAATAACGCCT	59.115	40.909	0.49	0.00	39.71	5.52
2590	2835	3.058224	AGCTTGTTGTTGAATAACGCCTC	60.058	43.478	0.49	0.00	39.71	4.70
2591	2836	3.304391	GCTTGTTGTTGAATAACGCCTCA	60.304	43.478	0.49	0.00	39.71	3.86
2592	2837	4.466828	CTTGTTGTTGAATAACGCCTCAG	58.533	43.478	0.49	0.00	39.71	3.35
2593	2838	3.472652	TGTTGTTGAATAACGCCTCAGT	58.527	40.909	0.49	0.00	39.71	3.41
2645	2890	0.886563	CGACCTACGACCAGGACTTT	59.113	55.000	9.02	0.00	45.77	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
124	131	4.161333	GGATCACAAAAGTCAAAGCATCG	58.839	43.478	0.00	0.00	0.00	3.84
261	269	7.215789	ACATTGTTGCATTTTCCTTCACATTA	58.784	30.769	0.00	0.00	0.00	1.90
293	301	5.217393	CCTGCATGCAATATGTGTTGTATC	58.783	41.667	22.88	0.00	33.06	2.24
297	305	2.166870	ACCCTGCATGCAATATGTGTTG	59.833	45.455	22.88	6.32	0.00	3.33
341	349	9.661563	TTAACCATCGTATTTTACTCAAGTCAT	57.338	29.630	0.00	0.00	0.00	3.06
357	365	1.644786	GGCGCTTGCTTAACCATCGT	61.645	55.000	7.64	0.00	39.13	3.73
380	389	1.794222	CCGGCTGAAGCTTAAACCG	59.206	57.895	17.44	17.44	41.70	4.44
381	390	0.960861	AGCCGGCTGAAGCTTAAACC	60.961	55.000	32.33	0.00	41.70	3.27
436	446	4.934001	AGATTATAGATTCATGCACGCCTG	59.066	41.667	0.00	0.00	0.00	4.85
527	537	6.493116	CATCTTGTTTGATCAACATCTAGGC	58.507	40.000	7.89	0.00	45.17	3.93
547	557	4.851843	TGTGAATGAGAAGATTGGCATCT	58.148	39.130	0.00	0.00	42.05	2.90
804	931	1.180456	TCCTCCAGTGGTTACGCGAA	61.180	55.000	15.93	0.00	0.00	4.70
937	1075	0.252742	AGGGAGGTGGACAAGTAGGG	60.253	60.000	0.00	0.00	0.00	3.53
1228	1366	4.697756	CGCTCCCACGCCCTTCAA	62.698	66.667	0.00	0.00	0.00	2.69
1739	1888	6.442952	TGAACCAACCAAATAACAATCGAAG	58.557	36.000	0.00	0.00	0.00	3.79
1883	2036	0.393267	TTCTTTATCCAACGGCCGGG	60.393	55.000	31.76	22.26	0.00	5.73
2006	2160	7.907214	AAGCGTTTCACTTTCATACTAAGAT	57.093	32.000	0.00	0.00	0.00	2.40
2008	2162	9.872757	TTTTAAGCGTTTCACTTTCATACTAAG	57.127	29.630	0.00	0.00	0.00	2.18
2009	2163	9.872757	CTTTTAAGCGTTTCACTTTCATACTAA	57.127	29.630	0.00	0.00	0.00	2.24
2010	2164	9.263538	TCTTTTAAGCGTTTCACTTTCATACTA	57.736	29.630	0.00	0.00	0.00	1.82
2011	2165	8.149973	TCTTTTAAGCGTTTCACTTTCATACT	57.850	30.769	0.00	0.00	0.00	2.12
2014	2168	8.696410	TTTTCTTTTAAGCGTTTCACTTTCAT	57.304	26.923	0.00	0.00	0.00	2.57
2015	2169	8.696410	ATTTTCTTTTAAGCGTTTCACTTTCA	57.304	26.923	0.00	0.00	0.00	2.69
2018	2172	9.797556	AGTAATTTTCTTTTAAGCGTTTCACTT	57.202	25.926	0.00	0.00	0.00	3.16
2019	2173	9.233232	CAGTAATTTTCTTTTAAGCGTTTCACT	57.767	29.630	0.00	0.00	0.00	3.41
2020	2174	7.996551	GCAGTAATTTTCTTTTAAGCGTTTCAC	59.003	33.333	0.00	0.00	0.00	3.18
2021	2175	7.918562	AGCAGTAATTTTCTTTTAAGCGTTTCA	59.081	29.630	0.00	0.00	0.00	2.69
2022	2176	8.282124	AGCAGTAATTTTCTTTTAAGCGTTTC	57.718	30.769	0.00	0.00	0.00	2.78
2023	2177	8.642908	AAGCAGTAATTTTCTTTTAAGCGTTT	57.357	26.923	0.00	0.00	0.00	3.60
2024	2178	9.177304	GTAAGCAGTAATTTTCTTTTAAGCGTT	57.823	29.630	0.00	0.00	0.00	4.84
2025	2179	8.347035	TGTAAGCAGTAATTTTCTTTTAAGCGT	58.653	29.630	0.00	0.00	0.00	5.07
2026	2180	8.722342	TGTAAGCAGTAATTTTCTTTTAAGCG	57.278	30.769	0.00	0.00	0.00	4.68
2084	2254	5.620654	GCTGATGAAATAGTGAAAAGCAGCA	60.621	40.000	0.00	0.00	43.12	4.41
2235	2430	3.206957	GGTTGATTACGGCCGCCC	61.207	66.667	28.58	12.48	0.00	6.13
2344	2572	2.740452	GACGAGACTTCTGTTCCGTTT	58.260	47.619	0.00	0.00	35.72	3.60
2348	2576	0.039437	TGCGACGAGACTTCTGTTCC	60.039	55.000	0.00	0.00	0.00	3.62
2373	2601	6.464895	TGACTTTTGCTCTGTTTTTGTTTG	57.535	33.333	0.00	0.00	0.00	2.93
2377	2605	6.473455	CCTAGTTGACTTTTGCTCTGTTTTTG	59.527	38.462	0.00	0.00	0.00	2.44
2460	2693	4.392940	CCTCCCATGTGGAATTAGTCATC	58.607	47.826	0.00	0.00	44.57	2.92
2588	2833	1.804601	TGCATTGCACTGAGACTGAG	58.195	50.000	7.38	0.00	31.71	3.35
2589	2834	2.484742	ATGCATTGCACTGAGACTGA	57.515	45.000	14.66	0.00	43.04	3.41
2590	2835	4.895224	ATTATGCATTGCACTGAGACTG	57.105	40.909	14.66	0.00	43.04	3.51
2591	2836	6.555812	CATATTATGCATTGCACTGAGACT	57.444	37.500	14.66	0.00	43.04	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.