AutoCloner

Multiple sequence alignment - TraesCS5B01G234700

Loading Multiple Alignment...

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	TraesCS5B01G234700	chr5B	100.000	6195	0	0	1	6195	412691306	412685112	0.000000e+00	11441
1	TraesCS5B01G234700	chr5B	97.059	68	2	0	522	589	516891224	516891291	1.410000e-21	115
2	TraesCS5B01G234700	chr5D	92.101	4165	172	68	579	4671	351482237	351478158	0.000000e+00	5723
3	TraesCS5B01G234700	chr5D	93.037	1393	63	6	4825	6193	351478159	351476777	0.000000e+00	2004
4	TraesCS5B01G234700	chr5D	91.351	185	6	4	4651	4826	274577993	274578176	1.730000e-60	244
5	TraesCS5B01G234700	chr5D	90.155	193	7	6	4654	4837	92111532	92111721	2.230000e-59	241
6	TraesCS5B01G234700	chr5D	88.811	143	7	5	2	136	351482372	351482231	3.840000e-37	167
7	TraesCS5B01G234700	chr5A	95.607	2208	78	11	2477	4671	451887804	451885603	0.000000e+00	3522
8	TraesCS5B01G234700	chr5A	90.472	1249	59	20	581	1790	451890158	451888931	0.000000e+00	1592
9	TraesCS5B01G234700	chr5A	91.438	946	30	6	4860	5794	451885563	451884658	0.000000e+00	1251
10	TraesCS5B01G234700	chr5A	85.596	722	62	19	1776	2477	451888913	451888214	0.000000e+00	719
11	TraesCS5B01G234700	chr5A	97.458	236	5	1	128	362	523834460	523834225	9.670000e-108	401
12	TraesCS5B01G234700	chr5A	92.537	268	17	1	5928	6195	451884054	451883790	1.260000e-101	381
13	TraesCS5B01G234700	chr5A	93.491	169	11	0	360	528	168438160	168437992	1.030000e-62	252
14	TraesCS5B01G234700	chr5A	89.404	151	13	1	5785	5935	451884276	451884129	2.950000e-43	187
15	TraesCS5B01G234700	chr5A	98.913	92	1	0	36	127	451890262	451890171	1.380000e-36	165
16	TraesCS5B01G234700	chr5A	100.000	62	0	0	522	583	96364610	96364549	1.410000e-21	115
17	TraesCS5B01G234700	chr5A	100.000	62	0	0	522	583	268724935	268724996	1.410000e-21	115
18	TraesCS5B01G234700	chr5A	100.000	62	0	0	522	583	464778082	464778021	1.410000e-21	115
19	TraesCS5B01G234700	chr7B	98.291	234	4	0	129	362	60066664	60066431	1.610000e-110	411
20	TraesCS5B01G234700	chr7B	97.009	234	7	0	129	362	519786939	519787172	1.620000e-105	394
21	TraesCS5B01G234700	chr7B	95.181	249	10	2	115	362	638416372	638416619	5.820000e-105	392
22	TraesCS5B01G234700	chr3B	97.872	235	5	0	128	362	697132805	697133039	2.080000e-109	407
23	TraesCS5B01G234700	chr3B	97.845	232	5	0	131	362	133388040	133387809	9.670000e-108	401
24	TraesCS5B01G234700	chr3A	97.845	232	5	0	131	362	20559482	20559251	9.670000e-108	401
25	TraesCS5B01G234700	chr3A	95.122	164	8	0	361	524	141960388	141960225	6.160000e-65	259
26	TraesCS5B01G234700	chr3A	94.220	173	2	2	4665	4829	744920942	744921114	2.220000e-64	257
27	TraesCS5B01G234700	chr3A	93.064	173	11	1	357	528	683431888	683432060	1.030000e-62	252
28	TraesCS5B01G234700	chr3A	92.571	175	11	2	361	535	710866859	710866687	3.710000e-62	250
29	TraesCS5B01G234700	chr3A	94.286	70	3	1	522	591	559703261	559703329	8.490000e-19	106
30	TraesCS5B01G234700	chrUn	97.414	232	6	0	131	362	50779631	50779862	4.500000e-106	396
31	TraesCS5B01G234700	chr1A	95.816	239	10	0	124	362	513746417	513746179	2.710000e-103	387
32	TraesCS5B01G234700	chr1A	93.491	169	11	0	360	528	582765076	582764908	1.030000e-62	252
33	TraesCS5B01G234700	chr1A	92.529	174	13	0	354	527	322177365	322177192	3.710000e-62	250
34	TraesCS5B01G234700	chr3D	87.119	295	32	6	131	421	471264642	471264350	4.630000e-86	329
35	TraesCS5B01G234700	chr3D	90.206	194	8	5	4642	4826	355892544	355892353	6.200000e-60	243
36	TraesCS5B01G234700	chr7A	92.222	180	12	2	361	540	17333454	17333631	2.870000e-63	254
37	TraesCS5B01G234700	chr7A	100.000	61	0	0	523	583	277526618	277526558	5.080000e-21	113
38	TraesCS5B01G234700	chr4B	95.062	162	6	1	4667	4826	19746353	19746514	2.870000e-63	254
39	TraesCS5B01G234700	chr4B	94.012	167	10	0	361	527	658178325	658178159	2.870000e-63	254
40	TraesCS5B01G234700	chr2B	94.012	167	10	0	361	527	710833392	710833226	2.870000e-63	254
41	TraesCS5B01G234700	chr6D	92.222	180	6	3	4658	4829	106701152	106700973	1.330000e-61	248
42	TraesCS5B01G234700	chr6D	96.970	66	2	0	522	587	4411813	4411748	1.830000e-20	111
43	TraesCS5B01G234700	chr4A	92.697	178	3	4	4658	4826	362068087	362067911	1.330000e-61	248
44	TraesCS5B01G234700	chr4A	100.000	62	0	0	522	583	4316406	4316345	1.410000e-21	115
45	TraesCS5B01G234700	chr2A	93.529	170	5	3	4667	4830	310407933	310408102	1.330000e-61	248
46	TraesCS5B01G234700	chr4D	91.803	183	5	4	4663	4836	75782046	75782227	4.800000e-61	246
47	TraesCS5B01G234700	chr6A	100.000	62	0	0	522	583	77056663	77056724	1.410000e-21	115

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	TraesCS5B01G234700	chr5B	412685112	412691306	6194	True	11441.000000	11441	100.000000	1	6195	1	chr5B.!!$R1	6194
1	TraesCS5B01G234700	chr5D	351476777	351482372	5595	True	2631.333333	5723	91.316333	2	6193	3	chr5D.!!$R1	6191
2	TraesCS5B01G234700	chr5A	451883790	451890262	6472	True	1116.714286	3522	91.995286	36	6195	7	chr5A.!!$R5	6159

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
231	240	0.103390	GAGAGAGAAGGTAAGCGGGC	59.897	60.0	0.00	0.00	0.00	6.13	F
242	251	0.108804	TAAGCGGGCTCTTCGTGAAG	60.109	55.0	3.17	3.17	39.71	3.02	F
251	260	0.244994	TCTTCGTGAAGAGCCAGCTC	59.755	55.0	11.78	11.78	42.06	4.09	F
373	382	0.248565	GGGTTGTACTCCCTCCGTTC	59.751	60.0	16.01	0.00	41.58	3.95	F
542	551	0.330604	AGATGACATGGCACTGGCTT	59.669	50.0	1.45	0.00	40.87	4.35	F
840	865	0.336737	GAGGTGGAGAGAGGGAGGAA	59.663	60.0	0.00	0.00	0.00	3.36	F
2535	3090	0.680921	AAGTGCTGTATTGGCGCCAT	60.681	50.0	33.25	22.08	40.59	4.40	F
2735	3290	0.389757	GCTCCCAGTCCCTCGTATTC	59.610	60.0	0.00	0.00	0.00	1.75	F
2957	3524	0.674895	ATCTTGGCTCACTTGGCGAC	60.675	55.0	0.00	0.00	35.06	5.19	F
4163	4732	0.897621	CCCCTTGTTTTCCATGCTCC	59.102	55.0	0.00	0.00	0.00	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1477	1524	0.038744	AATTGTCCCAGAGCACCAGG	59.961	55.000	0.00	0.00	4.45	R
2114	2256	0.828022	ACACCCGAGAACACTTCACA	59.172	50.000	0.00	0.00	3.58	R
2226	2368	6.051179	AGAATGTGTTCCTCCCTAAACTAC	57.949	41.667	0.00	34.81	2.73	R
2262	2404	3.753272	TCTGAGCAAAGAACAATAGCCAC	59.247	43.478	0.00	0.00	5.01	R
2535	3090	1.100510	GATCATGGAAAGCAGCAGCA	58.899	50.000	3.17	45.49	4.41	R
2704	3259	0.817634	CTGGGAGCGTGTTTGGTTCA	60.818	55.000	0.00	0.00	3.18	R
4160	4729	1.066358	GGAAAGGGGTTACAGTCGGAG	60.066	57.143	0.00	0.00	4.63	R
4361	4930	3.190535	GGACTGCGTTTGGTACATGATTT	59.809	43.478	0.00	39.30	2.17	R
4761	5338	0.608130	AGTGACTGCATACGGAGCAA	59.392	50.000	0.00	42.17	3.91	R
5684	6275	0.521291	TCAACAACATAGCCAAGCGC	59.479	50.000	0.00	37.98	5.92	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	Hairpin	End Stability
23	24	1.754803	ACAAGTGACCTGTGACGAAGA	59.245	47.619	0.00	0.00	2.87
24	25	2.365617	ACAAGTGACCTGTGACGAAGAT	59.634	45.455	0.00	0.00	2.40
27	28	2.029828	AGTGACCTGTGACGAAGATGAC	60.030	50.000	0.00	0.00	3.06
134	143	2.170434	GCAGCCAGAGCGTTAGAGC	61.170	63.158	0.00	46.67	4.09
135	144	1.216444	CAGCCAGAGCGTTAGAGCA	59.784	57.895	0.00	46.67	4.26
137	146	0.108424	AGCCAGAGCGTTAGAGCAAG	60.108	55.000	0.00	46.67	4.01
138	147	0.390472	GCCAGAGCGTTAGAGCAAGT	60.390	55.000	0.00	40.15	3.16
139	148	1.135083	GCCAGAGCGTTAGAGCAAGTA	60.135	52.381	0.00	40.15	2.24
140	149	2.482142	GCCAGAGCGTTAGAGCAAGTAT	60.482	50.000	0.00	40.15	2.12
141	150	3.243434	GCCAGAGCGTTAGAGCAAGTATA	60.243	47.826	0.00	40.15	1.47
142	151	4.736759	GCCAGAGCGTTAGAGCAAGTATAA	60.737	45.833	0.00	40.15	0.98
143	152	5.533482	CCAGAGCGTTAGAGCAAGTATAAT	58.467	41.667	0.00	40.15	1.28
144	153	6.678878	CCAGAGCGTTAGAGCAAGTATAATA	58.321	40.000	0.00	40.15	0.98
145	154	6.804295	CCAGAGCGTTAGAGCAAGTATAATAG	59.196	42.308	0.00	40.15	1.73
146	155	7.308649	CCAGAGCGTTAGAGCAAGTATAATAGA	60.309	40.741	0.00	40.15	1.98
147	156	7.748683	CAGAGCGTTAGAGCAAGTATAATAGAG	59.251	40.741	0.00	40.15	2.43
148	157	7.662258	AGAGCGTTAGAGCAAGTATAATAGAGA	59.338	37.037	0.00	40.15	3.10
149	158	8.343168	AGCGTTAGAGCAAGTATAATAGAGAT	57.657	34.615	0.00	40.15	2.75
150	159	8.240682	AGCGTTAGAGCAAGTATAATAGAGATG	58.759	37.037	0.00	40.15	2.90
151	160	8.237949	GCGTTAGAGCAAGTATAATAGAGATGA	58.762	37.037	0.00	37.05	2.92
152	161	9.767684	CGTTAGAGCAAGTATAATAGAGATGAG	57.232	37.037	0.00	0.00	2.90
155	164	8.932434	AGAGCAAGTATAATAGAGATGAGTCA	57.068	34.615	0.00	0.00	3.41
156	165	9.013229	AGAGCAAGTATAATAGAGATGAGTCAG	57.987	37.037	0.00	0.00	3.51
157	166	7.601856	AGCAAGTATAATAGAGATGAGTCAGC	58.398	38.462	0.00	0.00	4.26
158	167	7.232330	AGCAAGTATAATAGAGATGAGTCAGCA	59.768	37.037	11.60	0.00	4.41

Showing 1 to 25 of 457 entries

Previous1 2 3 4 5…19Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
0	1	1.067060	TCGTCACAGGTCACTTGTCAG	59.933	52.381	0.00	3.51
5	6	2.628178	TCATCTTCGTCACAGGTCACTT	59.372	45.455	0.00	3.16
23	24	3.441572	CCATTTCTTTTGCCTCTCGTCAT	59.558	43.478	0.00	3.06
24	25	2.813754	CCATTTCTTTTGCCTCTCGTCA	59.186	45.455	0.00	4.35
27	28	1.541147	TGCCATTTCTTTTGCCTCTCG	59.459	47.619	0.00	4.04
130	139	8.932434	TGACTCATCTCTATTATACTTGCTCT	57.068	34.615	0.00	4.09
131	140	7.754924	GCTGACTCATCTCTATTATACTTGCTC	59.245	40.741	0.00	4.26
132	141	7.232330	TGCTGACTCATCTCTATTATACTTGCT	59.768	37.037	0.00	3.91
134	143	8.791675	TCTGCTGACTCATCTCTATTATACTTG	58.208	37.037	0.00	3.16
135	144	8.932434	TCTGCTGACTCATCTCTATTATACTT	57.068	34.615	0.00	2.24
142	151	9.697990	TCATATAATCTGCTGACTCATCTCTAT	57.302	33.333	0.00	1.98
143	152	9.525826	TTCATATAATCTGCTGACTCATCTCTA	57.474	33.333	0.00	2.43
144	153	8.419922	TTCATATAATCTGCTGACTCATCTCT	57.580	34.615	0.00	3.10
145	154	9.656040	ATTTCATATAATCTGCTGACTCATCTC	57.344	33.333	0.00	2.75
181	190	9.349713	TCTCTTTCCTTCAACTAAGCAAAAATA	57.650	29.630	33.49	1.40
182	191	8.237811	TCTCTTTCCTTCAACTAAGCAAAAAT	57.762	30.769	33.49	1.82
183	192	7.639113	TCTCTTTCCTTCAACTAAGCAAAAA	57.361	32.000	33.49	1.94
184	193	7.556275	TCTTCTCTTTCCTTCAACTAAGCAAAA	59.444	33.333	33.49	2.44
185	194	7.054124	TCTTCTCTTTCCTTCAACTAAGCAAA	58.946	34.615	33.49	3.68
186	195	6.591935	TCTTCTCTTTCCTTCAACTAAGCAA	58.408	36.000	33.49	3.91
187	196	6.174720	TCTTCTCTTTCCTTCAACTAAGCA	57.825	37.500	33.49	3.91
188	197	5.641636	CCTCTTCTCTTTCCTTCAACTAAGC	59.358	44.000	33.49	3.09
189	198	6.998802	TCCTCTTCTCTTTCCTTCAACTAAG	58.001	40.000	34.73	2.18
190	199	6.782988	TCTCCTCTTCTCTTTCCTTCAACTAA	59.217	38.462	0.00	2.24
191	200	6.315714	TCTCCTCTTCTCTTTCCTTCAACTA	58.684	40.000	0.00	2.24

Showing 1 to 25 of 429 entries

Previous1 2 3 4 5…18Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.