AutoCloner

Multiple sequence alignment - TraesCS5B01G327400

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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	TraesCS5B01G327400	chr5B	100.000	6612	0	0	1	6612	511311884	511305273	0.000000e+00	12211
1	TraesCS5B01G327400	chr5A	85.635	1448	145	31	4302	5733	536985146	536983746	0.000000e+00	1463
2	TraesCS5B01G327400	chr5A	83.095	1331	155	32	1434	2735	536987959	536986670	0.000000e+00	1147
3	TraesCS5B01G327400	chr5A	84.489	851	97	18	3000	3822	536986672	536985829	0.000000e+00	808
4	TraesCS5B01G327400	chr5A	89.429	473	44	3	3818	4290	536985798	536985332	5.710000e-165	592
5	TraesCS5B01G327400	chr5A	89.623	318	25	3	804	1121	537106370	537106061	1.340000e-106	398
6	TraesCS5B01G327400	chr5A	79.783	460	32	22	321	779	536989963	536989564	1.820000e-70	278
7	TraesCS5B01G327400	chr5A	86.885	244	23	3	76	318	536990415	536990180	1.410000e-66	265
8	TraesCS5B01G327400	chr5D	84.668	1461	158	33	4302	5736	423503129	423501709	0.000000e+00	1397
9	TraesCS5B01G327400	chr5D	84.199	1329	153	27	1434	2735	423505943	423504645	0.000000e+00	1238
10	TraesCS5B01G327400	chr5D	84.390	852	97	14	3000	3822	423504647	423503803	0.000000e+00	804
11	TraesCS5B01G327400	chr5D	88.358	481	48	4	3820	4298	423503770	423503296	7.440000e-159	571
12	TraesCS5B01G327400	chr5D	81.569	510	42	23	287	776	423507679	423507202	2.250000e-99	374
13	TraesCS5B01G327400	chr5D	85.714	266	36	2	2735	2999	19002592	19002328	5.050000e-71	279
14	TraesCS5B01G327400	chr5D	91.241	137	10	2	108	242	423507813	423507677	1.130000e-42	185
15	TraesCS5B01G327400	chrUn	85.502	269	37	2	2732	2999	67497328	67497595	5.050000e-71	279
16	TraesCS5B01G327400	chrUn	85.714	266	36	2	2735	2999	199878502	199878238	5.050000e-71	279
17	TraesCS5B01G327400	chrUn	85.714	266	36	2	2735	2999	237315377	237315113	5.050000e-71	279
18	TraesCS5B01G327400	chrUn	85.714	266	36	2	2735	2999	245698512	245698248	5.050000e-71	279
19	TraesCS5B01G327400	chrUn	85.714	266	36	2	2735	2999	245701090	245700826	5.050000e-71	279
20	TraesCS5B01G327400	chrUn	85.502	269	37	2	2732	2999	274336029	274336296	5.050000e-71	279
21	TraesCS5B01G327400	chr7D	85.714	266	36	2	2735	2999	73832420	73832156	5.050000e-71	279
22	TraesCS5B01G327400	chr7D	85.502	269	38	1	2732	3000	73842196	73842463	5.050000e-71	279
23	TraesCS5B01G327400	chr4D	75.517	580	123	15	1976	2546	94375357	94375926	3.930000e-67	267
24	TraesCS5B01G327400	chr4D	86.897	145	19	0	1554	1698	94374647	94374791	5.310000e-36	163
25	TraesCS5B01G327400	chr4B	85.517	145	21	0	1554	1698	133589751	133589895	1.150000e-32	152
26	TraesCS5B01G327400	chr4A	81.295	139	16	5	1647	1780	574784945	574785078	3.260000e-18	104

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	TraesCS5B01G327400	chr5B	511305273	511311884	6611	True	12211.000000	12211	100.0000	1	6612	1	chr5B.!!$R1	6611
1	TraesCS5B01G327400	chr5A	536983746	536990415	6669	True	758.833333	1463	84.8860	76	5733	6	chr5A.!!$R2	5657
2	TraesCS5B01G327400	chr5D	423501709	423507813	6104	True	761.500000	1397	85.7375	108	5736	6	chr5D.!!$R2	5628
3	TraesCS5B01G327400	chrUn	245698248	245701090	2842	True	279.000000	279	85.7140	2735	2999	2	chrUn.!!$R3	264
4	TraesCS5B01G327400	chr4D	94374647	94375926	1279	False	215.000000	267	81.2070	1554	2546	2	chr4D.!!$F1	992

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	Hairpin	End Stability	Orientation
674	931	0.250295	TTGACTTGACCTGGCTTCCG	60.250	55.0	0.00	0.00	4.30	F
918	1207	0.250901	AAACCACTGATTGAGCGGCT	60.251	50.0	0.00	0.00	5.52	F
1027	1812	0.445436	GATGAACAAGCTGCGACAGG	59.555	55.0	8.57	31.21	4.00	F
2826	4564	0.390735	ATTTCTGGGTCCGTGTACGC	60.391	55.0	0.00	38.18	4.42	F
3228	6899	0.398318	GGGAGCTGTGGAGAACTGTT	59.602	55.0	0.00	0.00	3.16	F
3863	7596	0.403655	TTGCAGGTGCTACCCATTCA	59.596	50.0	3.18	39.75	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2616	4221	0.039618	TCTCCCTTGGCCCATTTGTC	59.960	55.0	0.00	0.00	0.00	3.18	R
2678	4283	0.386113	GCCGAGTCTCCACAGGATAC	59.614	60.0	0.00	0.00	0.00	2.24	R
2944	4742	0.249573	CAAACGTACACGGACCCTGT	60.250	55.0	6.72	1.59	44.95	4.00	R
4681	8593	0.458669	TTTCCTGCGGATAGTCGGAC	59.541	55.0	0.00	0.00	0.00	4.79	R
4952	8867	0.259938	GAACCATCCCTCCCAATGCT	59.740	55.0	0.00	0.00	0.00	3.79	R
5857	9802	0.172352	CGTGTTGTGCCTTGGTTGTT	59.828	50.0	0.00	0.00	0.00	2.83	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	7.865706	TTTTAGCACAACTCTCTTCTTCTTT	57.134	32.000	0.00	0.00	0.00	2.52
59	60	6.851222	TTAGCACAACTCTCTTCTTCTTTG	57.149	37.500	0.00	0.00	0.00	2.77
61	62	3.563390	GCACAACTCTCTTCTTCTTTGCT	59.437	43.478	0.00	0.00	0.00	3.91
62	63	4.036144	GCACAACTCTCTTCTTCTTTGCTT	59.964	41.667	0.00	0.00	0.00	3.91
63	64	5.237344	GCACAACTCTCTTCTTCTTTGCTTA	59.763	40.000	0.00	0.00	0.00	3.09
64	65	6.238484	GCACAACTCTCTTCTTCTTTGCTTAA	60.238	38.462	0.00	0.00	0.00	1.85
65	66	7.128976	CACAACTCTCTTCTTCTTTGCTTAAC	58.871	38.462	0.00	0.00	0.00	2.01
67	68	7.500559	ACAACTCTCTTCTTCTTTGCTTAACAT	59.499	33.333	0.00	0.00	0.00	2.71
69	70	9.561069	AACTCTCTTCTTCTTTGCTTAACATAA	57.439	29.630	0.00	0.00	0.00	1.90
70	71	9.213799	ACTCTCTTCTTCTTTGCTTAACATAAG	57.786	33.333	0.00	0.00	0.00	1.73
71	72	9.429359	CTCTCTTCTTCTTTGCTTAACATAAGA	57.571	33.333	1.42	0.00	0.00	2.10
72	73	9.429359	TCTCTTCTTCTTTGCTTAACATAAGAG	57.571	33.333	0.00	0.00	38.24	2.85
73	74	9.429359	CTCTTCTTCTTTGCTTAACATAAGAGA	57.571	33.333	0.00	0.00	38.86	3.10
74	75	9.209175	TCTTCTTCTTTGCTTAACATAAGAGAC	57.791	33.333	1.42	0.00	31.52	3.36
90	91	1.520787	GACCATCAAGTACCGGGCG	60.521	63.158	6.32	0.00	0.00	6.13
103	104	2.281970	GGGCGACCGGGAAAAGTT	60.282	61.111	6.32	0.00	43.64	2.66
104	105	1.900016	GGGCGACCGGGAAAAGTTT	60.900	57.895	6.32	0.00	43.64	2.66
189	190	8.039603	TGTGTGGAAAAAGCATAGTTATGTAG	57.960	34.615	1.49	0.00	36.11	2.74
207	208	8.658609	GTTATGTAGGTTTAGCGTGTCAAATAA	58.341	33.333	0.00	0.00	0.00	1.40
209	210	7.298507	TGTAGGTTTAGCGTGTCAAATAATC	57.701	36.000	0.00	0.00	0.00	1.75
215	217	9.434559	GGTTTAGCGTGTCAAATAATCTATTTC	57.565	33.333	0.00	0.00	36.29	2.17
274	277	9.525007	GCACATGTGTTTATATAATTAGTACGC	57.475	33.333	26.01	1.80	0.00	4.42
277	280	9.721933	CATGTGTTTATATAATTAGTACGCACG	57.278	33.333	10.97	2.41	0.00	5.34
292	295	1.917955	CGCACGTACACTCCATTGTAG	59.082	52.381	0.00	0.00	32.53	2.74
293	296	2.670229	CGCACGTACACTCCATTGTAGT	60.670	50.000	0.00	0.00	32.53	2.73

Showing 1 to 25 of 1,020 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	7.865706	AAGAAGAAGAGAGTTGTGCTAAAAA	57.134	32.000	0.00	0.00	0.00	1.94
34	35	7.679638	GCAAAGAAGAAGAGAGTTGTGCTAAAA	60.680	37.037	0.00	0.00	0.00	1.52
35	36	6.238484	GCAAAGAAGAAGAGAGTTGTGCTAAA	60.238	38.462	0.00	0.00	0.00	1.85
36	37	5.237344	GCAAAGAAGAAGAGAGTTGTGCTAA	59.763	40.000	0.00	0.00	0.00	3.09
37	38	4.752101	GCAAAGAAGAAGAGAGTTGTGCTA	59.248	41.667	0.00	0.00	0.00	3.49
38	39	3.563390	GCAAAGAAGAAGAGAGTTGTGCT	59.437	43.478	0.00	0.00	0.00	4.40
39	40	3.563390	AGCAAAGAAGAAGAGAGTTGTGC	59.437	43.478	0.00	0.00	0.00	4.57
41	42	6.823689	TGTTAAGCAAAGAAGAAGAGAGTTGT	59.176	34.615	0.00	0.00	0.00	3.32
42	43	7.251704	TGTTAAGCAAAGAAGAAGAGAGTTG	57.748	36.000	0.00	0.00	0.00	3.16
43	44	9.561069	TTATGTTAAGCAAAGAAGAAGAGAGTT	57.439	29.630	0.00	0.00	0.00	3.01
44	45	9.213799	CTTATGTTAAGCAAAGAAGAAGAGAGT	57.786	33.333	0.00	0.00	0.00	3.24
46	47	9.429359	CTCTTATGTTAAGCAAAGAAGAAGAGA	57.571	33.333	13.12	0.00	37.03	3.10
47	48	9.429359	TCTCTTATGTTAAGCAAAGAAGAAGAG	57.571	33.333	12.64	12.64	36.65	2.85
49	50	8.447053	GGTCTCTTATGTTAAGCAAAGAAGAAG	58.553	37.037	0.00	0.00	29.75	2.85
53	54	7.882791	TGATGGTCTCTTATGTTAAGCAAAGAA	59.117	33.333	0.00	0.00	0.00	2.52
54	55	7.394016	TGATGGTCTCTTATGTTAAGCAAAGA	58.606	34.615	0.00	0.00	0.00	2.52
56	57	7.665559	ACTTGATGGTCTCTTATGTTAAGCAAA	59.334	33.333	0.00	0.00	0.00	3.68
58	59	6.711277	ACTTGATGGTCTCTTATGTTAAGCA	58.289	36.000	0.00	0.00	0.00	3.91
59	60	7.224949	GGTACTTGATGGTCTCTTATGTTAAGC	59.775	40.741	0.00	0.00	0.00	3.09
61	62	7.262772	CGGTACTTGATGGTCTCTTATGTTAA	58.737	38.462	0.00	0.00	0.00	2.01
62	63	6.183360	CCGGTACTTGATGGTCTCTTATGTTA	60.183	42.308	0.00	0.00	0.00	2.41
63	64	5.395324	CCGGTACTTGATGGTCTCTTATGTT	60.395	44.000	0.00	0.00	0.00	2.71
64	65	4.099573	CCGGTACTTGATGGTCTCTTATGT	59.900	45.833	0.00	0.00	0.00	2.29
65	66	4.501571	CCCGGTACTTGATGGTCTCTTATG	60.502	50.000	0.00	0.00	0.00	1.90
67	68	3.028850	CCCGGTACTTGATGGTCTCTTA	58.971	50.000	0.00	0.00	0.00	2.10

Showing 1 to 25 of 1,119 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.