AutoCloner

Multiple sequence alignment - TraesCS1B01G201800

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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	TraesCS1B01G201800	chr1B	100.000	1536	0	0	789	2324	361462357	361460822	0.000000e+00	2837.0
1	TraesCS1B01G201800	chr1B	100.000	511	0	0	1	511	361463145	361462635	0.000000e+00	944.0
2	TraesCS1B01G201800	chr1D	90.413	1502	71	30	789	2229	252301518	252303007	0.000000e+00	1908.0
3	TraesCS1B01G201800	chr1D	86.755	453	25	17	76	511	252301041	252301475	2.700000e-129	472.0
4	TraesCS1B01G201800	chr1D	96.296	81	1	1	1	79	252300936	252301016	5.210000e-27	132.0
5	TraesCS1B01G201800	chr1D	93.258	89	6	0	2236	2324	252303115	252303203	5.210000e-27	132.0
6	TraesCS1B01G201800	chr1A	90.052	1337	53	32	789	2076	323205286	323203981	0.000000e+00	1659.0
7	TraesCS1B01G201800	chr1A	90.712	646	38	9	1460	2090	323203064	323202426	0.000000e+00	841.0
8	TraesCS1B01G201800	chr1A	84.894	470	24	18	76	511	323205789	323205333	4.590000e-117	431.0
9	TraesCS1B01G201800	chr1A	87.766	188	14	4	2141	2324	323202427	323202245	6.510000e-51	211.0
10	TraesCS1B01G201800	chr1A	92.632	95	2	2	2230	2324	323203692	323203603	5.210000e-27	132.0
11	TraesCS1B01G201800	chr1A	77.157	197	39	4	2127	2322	91478960	91479151	2.440000e-20	110.0
12	TraesCS1B01G201800	chr2B	84.545	110	14	3	2129	2237	463853800	463853907	3.160000e-19	106.0
13	TraesCS1B01G201800	chr2B	91.111	45	2	2	2210	2254	795983242	795983284	2.490000e-05	60.2
14	TraesCS1B01G201800	chr6A	76.596	188	35	6	2127	2307	459682074	459682259	6.840000e-16	95.3
15	TraesCS1B01G201800	chr7B	80.488	123	21	3	2132	2253	711478689	711478569	8.840000e-15	91.6
16	TraesCS1B01G201800	chr5A	81.739	115	15	5	2126	2237	41982447	41982558	8.840000e-15	91.6
17	TraesCS1B01G201800	chr5D	80.488	123	16	7	2132	2252	426972769	426972653	1.140000e-13	87.9
18	TraesCS1B01G201800	chr7A	94.444	36	0	2	187	220	115260836	115260801	1.000000e-03	54.7

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	TraesCS1B01G201800	chr1B	361460822	361463145	2323	True	1890.5	2837	100.0000	1	2324	2	chr1B.!!$R1	2323
1	TraesCS1B01G201800	chr1D	252300936	252303203	2267	False	661.0	1908	91.6805	1	2324	4	chr1D.!!$F1	2323
2	TraesCS1B01G201800	chr1A	323202245	323205789	3544	True	654.8	1659	89.2112	76	2324	5	chr1A.!!$R1	2248

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
254	304	0.034337	TCTCCCCAAAGAAACGACCG	59.966	55.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1350	1433	1.73172	AGAAACAGCAAGAGATCCGC	58.268	50.0	0.0	0.0	0.0	5.54	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
213	263	0.832135	GACCTGACCTGACCTGACCA	60.832	60.000	0.00	0.00	0.00	4.02
214	264	1.122019	ACCTGACCTGACCTGACCAC	61.122	60.000	0.00	0.00	0.00	4.16
215	265	1.674057	CTGACCTGACCTGACCACC	59.326	63.158	0.00	0.00	0.00	4.61
216	266	0.833834	CTGACCTGACCTGACCACCT	60.834	60.000	0.00	0.00	0.00	4.00
221	271	1.074850	TGACCTGACCACCTCACCA	60.075	57.895	0.00	0.00	0.00	4.17
227	277	2.038762	ACCACCTCACCACCCCTT	60.039	61.111	0.00	0.00	0.00	3.95
251	301	2.051692	TCCTTCTCCCCAAAGAAACGA	58.948	47.619	0.00	0.00	34.95	3.85
252	302	2.152016	CCTTCTCCCCAAAGAAACGAC	58.848	52.381	0.00	0.00	34.95	4.34
253	303	2.152016	CTTCTCCCCAAAGAAACGACC	58.848	52.381	0.00	0.00	34.95	4.79
254	304	0.034337	TCTCCCCAAAGAAACGACCG	59.966	55.000	0.00	0.00	0.00	4.79
255	305	1.574702	CTCCCCAAAGAAACGACCGC	61.575	60.000	0.00	0.00	0.00	5.68
256	306	2.622962	CCCCAAAGAAACGACCGCC	61.623	63.158	0.00	0.00	0.00	6.13
257	307	2.622962	CCCAAAGAAACGACCGCCC	61.623	63.158	0.00	0.00	0.00	6.13
258	308	2.622962	CCAAAGAAACGACCGCCCC	61.623	63.158	0.00	0.00	0.00	5.80
259	309	2.667199	AAAGAAACGACCGCCCCG	60.667	61.111	0.00	0.00	0.00	5.73
480	553	1.752198	CCAACAACGACCTCCTCCA	59.248	57.895	0.00	0.00	0.00	3.86
483	559	1.056660	AACAACGACCTCCTCCACAT	58.943	50.000	0.00	0.00	0.00	3.21
868	944	1.143970	CCTAACCCCAAACCCCTCCA	61.144	60.000	0.00	0.00	0.00	3.86
869	945	1.007607	CTAACCCCAAACCCCTCCAT	58.992	55.000	0.00	0.00	0.00	3.41
872	948	2.689813	CCCAAACCCCTCCATCCC	59.310	66.667	0.00	0.00	0.00	3.85
885	961	2.200092	ATCCCCCTCTCGAGCTCC	59.800	66.667	7.81	0.00	0.00	4.70
990	1070	3.362797	CAGCAGCAGCACCACCAG	61.363	66.667	3.17	0.00	45.49	4.00
999	1079	3.402681	CACCACCAGAGGGCGGAT	61.403	66.667	0.00	0.00	38.80	4.18
1435	1522	3.869473	TTGTTTCGCCCTCCGGTCG	62.869	63.158	0.00	1.34	37.59	4.79
1521	1632	3.865745	AGGACGAATTCGATGTTGATGAC	59.134	43.478	33.05	10.34	43.02	3.06
1524	1635	3.303495	ACGAATTCGATGTTGATGACGAC	59.697	43.478	33.05	0.00	43.02	4.34
1638	1768	8.692710	TCTCCGCAGAAAAAGTAGAAGAATATA	58.307	33.333	0.00	0.00	0.00	0.86
1655	1785	8.718102	AAGAATATATTGTTGCTTGTCTACGT	57.282	30.769	7.03	0.00	0.00	3.57
1658	1788	8.487313	AATATATTGTTGCTTGTCTACGTGAA	57.513	30.769	0.00	0.00	0.00	3.18
1660	1790	3.936902	TGTTGCTTGTCTACGTGAAAC	57.063	42.857	0.00	0.00	0.00	2.78
1664	1794	3.990092	TGCTTGTCTACGTGAAACATCT	58.010	40.909	0.00	0.00	35.74	2.90
1673	1814	3.834610	ACGTGAAACATCTTACTCCTCG	58.165	45.455	0.00	0.00	35.74	4.63
1674	1815	3.179830	CGTGAAACATCTTACTCCTCGG	58.820	50.000	0.00	0.00	35.74	4.63
1678	1819	5.125097	GTGAAACATCTTACTCCTCGGTCTA	59.875	44.000	0.00	0.00	36.32	2.59
1802	1949	1.064803	GACGGCACAATTCACAACACA	59.935	47.619	0.00	0.00	0.00	3.72
1912	2059	4.758773	ATATTCCGGGGTTCGTTCTTAA	57.241	40.909	0.00	0.00	37.11	1.85
2018	2168	3.142174	CCTCGGAAGGATGATTAAAGGC	58.858	50.000	0.00	0.00	46.67	4.35
2027	2177	7.201741	GGAAGGATGATTAAAGGCTTCACTAAC	60.202	40.741	0.00	0.00	0.00	2.34
2094	2244	6.759497	ATATTGCAAAGAGTACCAAAGACC	57.241	37.500	1.71	0.00	0.00	3.85
2119	2273	7.239763	CCCCCTCTATCTTTCTATCTTCTTC	57.760	44.000	0.00	0.00	0.00	2.87
2136	2489	8.634475	ATCTTCTTCCTTTGTTTTTCTTTTCG	57.366	30.769	0.00	0.00	0.00	3.46
2138	2491	8.466798	TCTTCTTCCTTTGTTTTTCTTTTCGAT	58.533	29.630	0.00	0.00	0.00	3.59
2144	3783	8.688151	TCCTTTGTTTTTCTTTTCGATAAAGGA	58.312	29.630	15.40	0.00	44.78	3.36
2182	3821	8.474006	TCTCAAAATGAAGCATCAAATGAATG	57.526	30.769	0.00	0.00	39.49	2.67
2195	3836	7.849026	GCATCAAATGAATGCAAACATATTGAC	59.151	33.333	20.85	13.56	40.72	3.18
2204	3845	4.400884	TGCAAACATATTGACCATACACCC	59.599	41.667	0.00	0.00	0.00	4.61
2208	3851	1.205055	TATTGACCATACACCCGGCA	58.795	50.000	0.00	0.00	0.00	5.69
2212	3855	0.532862	GACCATACACCCGGCATCTG	60.533	60.000	0.00	0.00	0.00	2.90
2249	3997	5.851177	GCACACAATCAACACTAATACACAC	59.149	40.000	0.00	0.00	0.00	3.82
2250	3998	6.512578	GCACACAATCAACACTAATACACACA	60.513	38.462	0.00	0.00	0.00	3.72
2251	3999	6.850823	CACACAATCAACACTAATACACACAC	59.149	38.462	0.00	0.00	0.00	3.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.535962	CTGCGAGGAGGAGGAGGC	61.536	72.222	0.00	0.00	34.34	4.70
189	239	2.217038	GGTCAGGTCAGGTCAGGCA	61.217	63.158	0.00	0.00	0.00	4.75
213	263	1.072930	AAGGAAGGGGTGGTGAGGT	60.073	57.895	0.00	0.00	0.00	3.85
214	264	1.685820	GAAGGAAGGGGTGGTGAGG	59.314	63.158	0.00	0.00	0.00	3.86
215	265	0.842467	AGGAAGGAAGGGGTGGTGAG	60.842	60.000	0.00	0.00	0.00	3.51
216	266	0.402861	AAGGAAGGAAGGGGTGGTGA	60.403	55.000	0.00	0.00	0.00	4.02
221	271	0.550393	GGGAGAAGGAAGGAAGGGGT	60.550	60.000	0.00	0.00	0.00	4.95
227	277	2.433444	TCTTTGGGGAGAAGGAAGGA	57.567	50.000	0.00	0.00	0.00	3.36
397	453	1.418908	TTATAGCAGCCCAGGAGCCC	61.419	60.000	0.00	0.00	0.00	5.19
398	454	0.474184	TTTATAGCAGCCCAGGAGCC	59.526	55.000	0.00	0.00	0.00	4.70
399	455	2.225467	CTTTTATAGCAGCCCAGGAGC	58.775	52.381	0.00	0.00	0.00	4.70
401	457	1.133792	GCCTTTTATAGCAGCCCAGGA	60.134	52.381	0.00	0.00	0.00	3.86
444	513	1.222113	GCGAGGAAGAAAGAGGGGG	59.778	63.158	0.00	0.00	0.00	5.40
451	520	0.941542	CGTTGTTGGCGAGGAAGAAA	59.058	50.000	0.00	0.00	0.00	2.52
868	944	2.200092	GGAGCTCGAGAGGGGGAT	59.800	66.667	18.75	0.00	0.00	3.85
869	945	4.507916	CGGAGCTCGAGAGGGGGA	62.508	72.222	18.75	0.00	42.43	4.81
885	961	3.967335	GAGGGAGATCGGACGGCG	61.967	72.222	4.80	4.80	0.00	6.46
990	1070	2.032681	GCCACCATATCCGCCCTC	59.967	66.667	0.00	0.00	0.00	4.30
999	1079	4.122149	CCCTTGGGCGCCACCATA	62.122	66.667	30.85	5.55	40.91	2.74
1285	1365	1.951130	CGAAGCGCGGCAGATGTAT	60.951	57.895	8.83	0.00	36.03	2.29
1287	1367	4.742201	ACGAAGCGCGGCAGATGT	62.742	61.111	8.83	0.00	46.49	3.06
1350	1433	1.731720	AGAAACAGCAAGAGATCCGC	58.268	50.000	0.00	0.00	0.00	5.54
1351	1434	3.499918	ACAAAGAAACAGCAAGAGATCCG	59.500	43.478	0.00	0.00	0.00	4.18
1435	1522	2.462889	CATGCATAACAAACCCATCGC	58.537	47.619	0.00	0.00	0.00	4.58
1510	1618	7.902917	TCATAATTTTTCGTCGTCATCAACATC	59.097	33.333	0.00	0.00	0.00	3.06
1521	1632	6.542852	ACACTTGGATCATAATTTTTCGTCG	58.457	36.000	0.00	0.00	0.00	5.12
1638	1768	4.334203	TGTTTCACGTAGACAAGCAACAAT	59.666	37.500	0.00	0.00	0.00	2.71
1655	1785	4.087182	AGACCGAGGAGTAAGATGTTTCA	58.913	43.478	0.00	0.00	0.00	2.69
1658	1788	5.892119	TCAATAGACCGAGGAGTAAGATGTT	59.108	40.000	0.00	0.00	0.00	2.71
1660	1790	5.561145	CGTCAATAGACCGAGGAGTAAGATG	60.561	48.000	0.00	0.00	41.87	2.90
1664	1794	2.947652	CCGTCAATAGACCGAGGAGTAA	59.052	50.000	0.00	0.00	41.87	2.24
1673	1814	4.685924	TCGTTATTTCCCGTCAATAGACC	58.314	43.478	0.00	0.00	41.87	3.85
1674	1815	6.651755	TTTCGTTATTTCCCGTCAATAGAC	57.348	37.500	0.00	0.00	41.46	2.59
1678	1819	5.575218	GCAAATTTCGTTATTTCCCGTCAAT	59.425	36.000	0.00	0.00	0.00	2.57
1802	1949	6.061441	TCCACCTCGTATGCATATCAATTTT	58.939	36.000	10.16	0.00	0.00	1.82
2117	2271	9.308318	CCTTTATCGAAAAGAAAAACAAAGGAA	57.692	29.630	16.62	0.00	41.17	3.36
2118	2272	8.688151	TCCTTTATCGAAAAGAAAAACAAAGGA	58.312	29.630	16.62	7.66	43.69	3.36
2119	2273	8.865590	TCCTTTATCGAAAAGAAAAACAAAGG	57.134	30.769	16.62	0.00	40.42	3.11
2157	3796	7.064134	GCATTCATTTGATGCTTCATTTTGAGA	59.936	33.333	2.75	0.00	38.22	3.27
2182	3821	4.497340	CGGGTGTATGGTCAATATGTTTGC	60.497	45.833	0.00	0.00	0.00	3.68
2195	3836	1.893808	GCAGATGCCGGGTGTATGG	60.894	63.158	2.18	0.00	34.31	2.74
2204	3845	4.658713	CATCTTAGTTATGCAGATGCCG	57.341	45.455	1.72	0.00	38.03	5.69
2285	4033	2.682856	TCGCTTGGGCATAACTTTGATC	59.317	45.455	0.00	0.00	38.60	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.