AutoCloner

Multiple sequence alignment - TraesCS5B01G431700

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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	TraesCS5B01G431700	chr5B	100.000	3170	0	0	1	3170	606303760	606300591	0.000000e+00	5854
1	TraesCS5B01G431700	chr5B	78.857	1050	199	18	1106	2136	45394594	45393549	0.000000e+00	688
2	TraesCS5B01G431700	chr5B	79.720	286	55	2	2243	2525	45392655	45392370	1.490000e-48	204
3	TraesCS5B01G431700	chr5D	94.526	2777	98	30	416	3170	491529472	491526728	0.000000e+00	4237
4	TraesCS5B01G431700	chr5D	93.885	278	10	4	1	276	491529896	491529624	2.280000e-111	412
5	TraesCS5B01G431700	chr5D	80.000	285	54	2	2244	2525	45379803	45380087	1.150000e-49	207
6	TraesCS5B01G431700	chr5A	90.293	2967	142	60	286	3170	613702537	613699635	0.000000e+00	3749
7	TraesCS5B01G431700	chr5A	78.857	1050	196	21	1106	2136	36331896	36330854	0.000000e+00	686
8	TraesCS5B01G431700	chr5A	94.265	279	8	4	1	276	613702951	613702678	1.360000e-113	420
9	TraesCS5B01G431700	chr2B	92.732	798	45	3	1144	1941	298514427	298515211	0.000000e+00	1140
10	TraesCS5B01G431700	chr2B	91.685	457	38	0	1148	1604	105743366	105742910	4.460000e-178	634
11	TraesCS5B01G431700	chr4A	78.833	1063	204	14	1086	2136	597015752	597014699	0.000000e+00	697
12	TraesCS5B01G431700	chr4D	78.998	1038	193	18	1113	2136	6425451	6424425	0.000000e+00	686
13	TraesCS5B01G431700	chr4B	78.491	1060	213	11	1086	2136	11656176	11657229	0.000000e+00	680
14	TraesCS5B01G431700	chr3B	92.140	458	36	0	1147	1604	130115694	130115237	0.000000e+00	647
15	TraesCS5B01G431700	chr3D	76.875	960	177	35	1163	2095	593237118	593236177	4.720000e-138	501
16	TraesCS5B01G431700	chr6A	74.673	995	197	33	1163	2131	609158789	609157824	1.070000e-104	390
17	TraesCS5B01G431700	chr6B	74.400	1000	191	43	1163	2131	704851666	704852631	5.000000e-98	368
18	TraesCS5B01G431700	chr1A	76.142	197	43	4	1360	1554	539757340	539757146	2.010000e-17	100

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	TraesCS5B01G431700	chr5B	606300591	606303760	3169	True	5854.0	5854	100.0000	1	3170	1	chr5B.!!$R1	3169
1	TraesCS5B01G431700	chr5B	45392370	45394594	2224	True	446.0	688	79.2885	1106	2525	2	chr5B.!!$R2	1419
2	TraesCS5B01G431700	chr5D	491526728	491529896	3168	True	2324.5	4237	94.2055	1	3170	2	chr5D.!!$R1	3169
3	TraesCS5B01G431700	chr5A	613699635	613702951	3316	True	2084.5	3749	92.2790	1	3170	2	chr5A.!!$R2	3169
4	TraesCS5B01G431700	chr5A	36330854	36331896	1042	True	686.0	686	78.8570	1106	2136	1	chr5A.!!$R1	1030
5	TraesCS5B01G431700	chr2B	298514427	298515211	784	False	1140.0	1140	92.7320	1144	1941	1	chr2B.!!$F1	797
6	TraesCS5B01G431700	chr4A	597014699	597015752	1053	True	697.0	697	78.8330	1086	2136	1	chr4A.!!$R1	1050
7	TraesCS5B01G431700	chr4D	6424425	6425451	1026	True	686.0	686	78.9980	1113	2136	1	chr4D.!!$R1	1023
8	TraesCS5B01G431700	chr4B	11656176	11657229	1053	False	680.0	680	78.4910	1086	2136	1	chr4B.!!$F1	1050
9	TraesCS5B01G431700	chr3D	593236177	593237118	941	True	501.0	501	76.8750	1163	2095	1	chr3D.!!$R1	932
10	TraesCS5B01G431700	chr6A	609157824	609158789	965	True	390.0	390	74.6730	1163	2131	1	chr6A.!!$R1	968
11	TraesCS5B01G431700	chr6B	704851666	704852631	965	False	368.0	368	74.4000	1163	2131	1	chr6B.!!$F1	968

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
535	677	0.533491	TGCCTGCATTGGAAGCATTC	59.467	50.0	0.0	0.0	46.67	2.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2218	3236	1.539869	AGCCCCTCTTCCTCTTGCA	60.54	57.895	0.0	0.0	0.0	4.08	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
30	31	9.899661	AGGTGCACTTCTGTTTATTTACATATA	57.100	29.630	17.98	0.00	0.00	0.86
180	183	6.642131	GTGTGTTATGTGTTCAAATCAGCAAT	59.358	34.615	0.00	0.00	0.00	3.56
181	184	7.807433	GTGTGTTATGTGTTCAAATCAGCAATA	59.193	33.333	0.00	0.00	0.00	1.90
182	185	7.807433	TGTGTTATGTGTTCAAATCAGCAATAC	59.193	33.333	0.00	0.00	0.00	1.89
183	186	8.023128	GTGTTATGTGTTCAAATCAGCAATACT	58.977	33.333	0.00	0.00	0.00	2.12
216	221	7.782897	TTATACTATGAGTTGGAGAGGGATG	57.217	40.000	0.00	0.00	0.00	3.51
231	236	5.995446	AGAGGGATGTTGTAGAAAAGATCC	58.005	41.667	4.88	4.88	45.12	3.36
234	239	4.640647	GGGATGTTGTAGAAAAGATCCACC	59.359	45.833	13.25	0.00	46.77	4.61
235	240	5.253330	GGATGTTGTAGAAAAGATCCACCA	58.747	41.667	7.92	0.00	45.16	4.17
236	241	5.355350	GGATGTTGTAGAAAAGATCCACCAG	59.645	44.000	7.92	0.00	45.16	4.00
278	283	6.225703	CAGATCACTGTCAGAGAAAAACAG	57.774	41.667	6.91	0.00	44.68	3.16
280	285	6.145858	CAGATCACTGTCAGAGAAAAACAGAG	59.854	42.308	6.91	1.28	42.37	3.35
283	419	4.872691	CACTGTCAGAGAAAAACAGAGTGT	59.127	41.667	6.91	0.00	42.37	3.55
284	420	5.006165	CACTGTCAGAGAAAAACAGAGTGTC	59.994	44.000	6.91	0.00	42.37	3.67
291	427	7.011763	TCAGAGAAAAACAGAGTGTCTGATTTG	59.988	37.037	10.89	1.13	44.95	2.32
292	428	6.825721	AGAGAAAAACAGAGTGTCTGATTTGT	59.174	34.615	10.89	9.31	44.95	2.83
295	431	8.956426	AGAAAAACAGAGTGTCTGATTTGTTTA	58.044	29.630	10.89	0.00	44.95	2.01
303	439	8.836413	AGAGTGTCTGATTTGTTTATTTTTCGA	58.164	29.630	0.00	0.00	0.00	3.71
322	458	7.400599	TTTCGACAGATTACATAGTGGTACT	57.599	36.000	0.00	0.00	0.00	2.73
330	466	8.820933	CAGATTACATAGTGGTACTTGTTGATG	58.179	37.037	0.00	0.00	0.00	3.07
332	468	8.948631	ATTACATAGTGGTACTTGTTGATGAG	57.051	34.615	0.00	0.00	0.00	2.90
384	526	8.462143	AGTAAGTACAGTATTGATCAACAACG	57.538	34.615	11.07	10.58	41.52	4.10
389	531	4.690748	ACAGTATTGATCAACAACGGAGTG	59.309	41.667	21.65	14.48	45.00	3.51
401	543	5.871396	ACAACGGAGTGGTATAATCATCT	57.129	39.130	0.00	0.00	46.84	2.90
402	544	5.601662	ACAACGGAGTGGTATAATCATCTG	58.398	41.667	0.00	0.00	46.84	2.90
403	545	5.128827	ACAACGGAGTGGTATAATCATCTGT	59.871	40.000	0.00	0.00	46.84	3.41
404	546	6.322969	ACAACGGAGTGGTATAATCATCTGTA	59.677	38.462	0.00	0.00	46.84	2.74
405	547	6.576662	ACGGAGTGGTATAATCATCTGTAG	57.423	41.667	0.00	0.00	42.51	2.74
406	548	5.477291	ACGGAGTGGTATAATCATCTGTAGG	59.523	44.000	0.00	0.00	42.51	3.18
407	549	5.622460	CGGAGTGGTATAATCATCTGTAGGC	60.622	48.000	0.00	0.00	0.00	3.93
408	550	5.482175	GGAGTGGTATAATCATCTGTAGGCT	59.518	44.000	0.00	0.00	0.00	4.58
409	551	6.350612	GGAGTGGTATAATCATCTGTAGGCTC	60.351	46.154	0.00	0.00	0.00	4.70
410	552	6.318913	AGTGGTATAATCATCTGTAGGCTCT	58.681	40.000	0.00	0.00	0.00	4.09
411	553	6.210385	AGTGGTATAATCATCTGTAGGCTCTG	59.790	42.308	0.00	0.00	0.00	3.35
412	554	5.047021	TGGTATAATCATCTGTAGGCTCTGC	60.047	44.000	0.00	0.00	0.00	4.26
535	677	0.533491	TGCCTGCATTGGAAGCATTC	59.467	50.000	0.00	0.00	46.67	2.67
641	788	4.881273	TGCAGTACTATATTGCCAACCAAG	59.119	41.667	0.00	0.00	40.27	3.61
706	855	5.026121	TCTGGGACTCTGAATCAACTGTAT	58.974	41.667	0.00	0.00	0.00	2.29
707	856	6.194967	TCTGGGACTCTGAATCAACTGTATA	58.805	40.000	0.00	0.00	0.00	1.47
742	917	5.764686	TCAGCAAGTACAACACATCAAGATT	59.235	36.000	0.00	0.00	0.00	2.40
872	1055	5.426689	TGCCATCTGAACATATATCCTCC	57.573	43.478	0.00	0.00	0.00	4.30
907	1090	2.415090	CCAGTACAAAGACTCGTACCGG	60.415	54.545	0.00	0.00	39.03	5.28
991	1175	7.541783	TCAACTGATGAAAAACAAGTCTGTTTG	59.458	33.333	4.13	0.00	43.32	2.93
1195	1379	3.986006	TCGCACGCCTCGTCCTTT	61.986	61.111	0.00	0.00	38.32	3.11
1273	1457	4.537433	CCGTAGCAGCTGGAGCCC	62.537	72.222	17.12	0.00	43.38	5.19
1275	1459	2.914289	GTAGCAGCTGGAGCCCAT	59.086	61.111	17.12	0.00	43.38	4.00
2098	2309	0.736325	CGAAGGTGCCGTTGTAGGAG	60.736	60.000	0.00	0.00	0.00	3.69
2154	2365	2.543848	TGCGAACAGAACAGAACATCAC	59.456	45.455	0.00	0.00	0.00	3.06
2376	3397	0.683179	ACCATGACCTCGATGTCGGA	60.683	55.000	17.35	3.26	38.11	4.55
2592	3613	2.045438	ATTCACCGCCGCCATTGA	60.045	55.556	0.00	0.00	0.00	2.57
2593	3614	1.653094	GATTCACCGCCGCCATTGAA	61.653	55.000	0.00	0.00	32.71	2.69
2607	3628	0.990374	ATTGAACAGGCCTCTCTGCT	59.010	50.000	0.00	0.00	38.26	4.24
2619	3640	4.116328	TCTGCTCTCCGGCGAACG	62.116	66.667	9.30	0.00	43.80	3.95
2680	3701	0.332972	AATCCAGGAACAGGGGAAGC	59.667	55.000	0.00	0.00	34.89	3.86
2745	3771	1.472878	CGAGATTCAGTCGAACAGGGA	59.527	52.381	0.00	0.00	39.92	4.20
2848	3889	1.154225	GATTGCGCACGGAAACCAG	60.154	57.895	11.12	0.00	0.00	4.00
2866	3907	0.959553	AGACGCGGTTTCTTCTGAGA	59.040	50.000	12.47	0.00	0.00	3.27
2931	3972	1.427895	GGGGAGAAAGGGATAGGGGC	61.428	65.000	0.00	0.00	0.00	5.80
2932	3973	0.697854	GGGAGAAAGGGATAGGGGCA	60.698	60.000	0.00	0.00	0.00	5.36
2933	3974	0.767998	GGAGAAAGGGATAGGGGCAG	59.232	60.000	0.00	0.00	0.00	4.85
2934	3975	0.767998	GAGAAAGGGATAGGGGCAGG	59.232	60.000	0.00	0.00	0.00	4.85
2957	3998	2.614779	CGAGACTCACATGTGAATGCT	58.385	47.619	27.63	22.76	39.39	3.79
2977	4018	2.394604	GAAATTCCTTCCCGGAGCG	58.605	57.895	0.73	0.00	44.28	5.03
3004	4045	1.266989	GCAAGAAACGAAACAGAGGGG	59.733	52.381	0.00	0.00	0.00	4.79
3063	4115	1.623359	CGGCGAAGAAAGAGAGAGTG	58.377	55.000	0.00	0.00	0.00	3.51
3110	4168	0.820871	CGAGGTTGAGAGGGAAGGAG	59.179	60.000	0.00	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
181	184	8.677300	CCAACTCATAGTATAAAATGCACAAGT	58.323	33.333	0.00	0.00	0.00	3.16
182	185	8.892723	TCCAACTCATAGTATAAAATGCACAAG	58.107	33.333	0.00	0.00	0.00	3.16
183	186	8.800370	TCCAACTCATAGTATAAAATGCACAA	57.200	30.769	0.00	0.00	0.00	3.33
216	221	6.465084	ACTACTGGTGGATCTTTTCTACAAC	58.535	40.000	0.00	0.00	37.55	3.32
231	236	3.927142	GCAGCAAACTACTACTACTGGTG	59.073	47.826	0.00	0.00	35.84	4.17
234	239	4.556233	TGTGCAGCAAACTACTACTACTG	58.444	43.478	0.00	0.00	0.00	2.74
235	240	4.523173	TCTGTGCAGCAAACTACTACTACT	59.477	41.667	0.00	0.00	0.00	2.57
236	241	4.806330	TCTGTGCAGCAAACTACTACTAC	58.194	43.478	0.00	0.00	0.00	2.73
276	281	8.895845	CGAAAAATAAACAAATCAGACACTCTG	58.104	33.333	0.00	0.00	45.59	3.35
278	283	8.892905	GTCGAAAAATAAACAAATCAGACACTC	58.107	33.333	0.00	0.00	0.00	3.51
280	285	8.555166	TGTCGAAAAATAAACAAATCAGACAC	57.445	30.769	0.00	0.00	0.00	3.67
295	431	9.095065	GTACCACTATGTAATCTGTCGAAAAAT	57.905	33.333	0.00	0.00	0.00	1.82
297	433	7.833786	AGTACCACTATGTAATCTGTCGAAAA	58.166	34.615	0.00	0.00	0.00	2.29
302	438	8.033038	TCAACAAGTACCACTATGTAATCTGTC	58.967	37.037	0.00	0.00	0.00	3.51
303	439	7.903145	TCAACAAGTACCACTATGTAATCTGT	58.097	34.615	0.00	0.00	0.00	3.41
309	445	7.476540	ACTCATCAACAAGTACCACTATGTA	57.523	36.000	0.00	0.00	0.00	2.29
317	453	7.849804	ATCATTGTACTCATCAACAAGTACC	57.150	36.000	9.48	0.00	44.66	3.34
359	495	7.544566	CCGTTGTTGATCAATACTGTACTTACT	59.455	37.037	12.12	0.00	38.38	2.24
361	497	7.604549	TCCGTTGTTGATCAATACTGTACTTA	58.395	34.615	12.12	0.00	38.38	2.24
362	498	6.460781	TCCGTTGTTGATCAATACTGTACTT	58.539	36.000	12.12	0.00	38.38	2.24
363	499	6.032956	TCCGTTGTTGATCAATACTGTACT	57.967	37.500	12.12	0.00	38.38	2.73
364	500	5.867716	ACTCCGTTGTTGATCAATACTGTAC	59.132	40.000	12.12	3.20	38.38	2.90
365	501	5.867174	CACTCCGTTGTTGATCAATACTGTA	59.133	40.000	12.12	0.00	38.38	2.74
367	503	4.093408	CCACTCCGTTGTTGATCAATACTG	59.907	45.833	12.12	9.55	38.38	2.74
382	524	5.477291	CCTACAGATGATTATACCACTCCGT	59.523	44.000	0.00	0.00	0.00	4.69
384	526	5.482175	AGCCTACAGATGATTATACCACTCC	59.518	44.000	0.00	0.00	0.00	3.85
388	530	5.047021	GCAGAGCCTACAGATGATTATACCA	60.047	44.000	0.00	0.00	0.00	3.25
389	531	5.415221	GCAGAGCCTACAGATGATTATACC	58.585	45.833	0.00	0.00	0.00	2.73
413	555	6.702716	TTCAGTTTTTAACCACCTACCAAG	57.297	37.500	0.00	0.00	0.00	3.61
414	556	7.477945	TTTTCAGTTTTTAACCACCTACCAA	57.522	32.000	0.00	0.00	0.00	3.67
641	788	6.183360	TGGAGTATATACAAAGTGAGCAGGAC	60.183	42.308	15.18	0.00	0.00	3.85
773	956	4.428294	TCAGAATCCCAGATCCAATGAC	57.572	45.455	0.00	0.00	0.00	3.06
774	957	5.133153	TCATTCAGAATCCCAGATCCAATGA	59.867	40.000	0.00	0.00	0.00	2.57
872	1055	5.654603	TTGTACTGGAGGCATATATACCG	57.345	43.478	0.00	0.00	0.00	4.02
907	1090	7.028926	TCAGCAGTAGTTACTAGCAGTAATC	57.971	40.000	10.56	6.40	42.06	1.75
991	1175	5.107530	GCTCTTGATGTCGCATTAGAGAATC	60.108	44.000	22.12	11.04	32.79	2.52
1762	1967	2.354305	GTCGACGGCGTCAACACT	60.354	61.111	35.62	1.56	38.98	3.55
2136	2347	5.929697	TGATGTGATGTTCTGTTCTGTTC	57.070	39.130	0.00	0.00	0.00	3.18
2145	2356	8.072321	ACTACTTACTGATGATGTGATGTTCT	57.928	34.615	0.00	0.00	0.00	3.01
2146	2357	7.436673	GGACTACTTACTGATGATGTGATGTTC	59.563	40.741	0.00	0.00	0.00	3.18
2147	2358	7.093333	TGGACTACTTACTGATGATGTGATGTT	60.093	37.037	0.00	0.00	0.00	2.71
2148	2359	6.381133	TGGACTACTTACTGATGATGTGATGT	59.619	38.462	0.00	0.00	0.00	3.06
2149	2360	6.809869	TGGACTACTTACTGATGATGTGATG	58.190	40.000	0.00	0.00	0.00	3.07
2150	2361	7.288621	TCATGGACTACTTACTGATGATGTGAT	59.711	37.037	0.00	0.00	0.00	3.06
2151	2362	6.607198	TCATGGACTACTTACTGATGATGTGA	59.393	38.462	0.00	0.00	0.00	3.58
2152	2363	6.809869	TCATGGACTACTTACTGATGATGTG	58.190	40.000	0.00	0.00	0.00	3.21
2154	2365	7.495901	AGTTCATGGACTACTTACTGATGATG	58.504	38.462	4.30	0.00	0.00	3.07
2218	3236	1.539869	AGCCCCTCTTCCTCTTGCA	60.540	57.895	0.00	0.00	0.00	4.08
2592	3613	1.264045	GGAGAGCAGAGAGGCCTGTT	61.264	60.000	12.00	0.00	36.57	3.16
2593	3614	1.685421	GGAGAGCAGAGAGGCCTGT	60.685	63.158	12.00	5.74	36.57	4.00
2619	3640	3.449377	AGATCTTCTCCCTTCTTTCGTCC	59.551	47.826	0.00	0.00	0.00	4.79
2644	3665	1.366111	ATTCCCAAACCGTCGCATCG	61.366	55.000	0.00	0.00	0.00	3.84
2647	3668	1.673009	GGATTCCCAAACCGTCGCA	60.673	57.895	0.00	0.00	0.00	5.10
2680	3701	0.940126	CGGATCGGCAAATCTTGAGG	59.060	55.000	0.00	0.00	0.00	3.86
2848	3889	1.061485	GTCTCAGAAGAAACCGCGTC	58.939	55.000	4.92	0.00	31.93	5.19
2866	3907	2.708325	GGATCAGATAGGAAAGCCCAGT	59.292	50.000	0.00	0.00	37.41	4.00
2910	3951	1.128188	CCCTATCCCTTTCTCCCCCG	61.128	65.000	0.00	0.00	0.00	5.73
2931	3972	1.153489	CATGTGAGTCTCGCCCCTG	60.153	63.158	10.87	2.71	0.00	4.45
2932	3973	1.610673	ACATGTGAGTCTCGCCCCT	60.611	57.895	10.87	0.00	0.00	4.79
2933	3974	1.448540	CACATGTGAGTCTCGCCCC	60.449	63.158	21.64	0.00	0.00	5.80
2934	3975	0.037326	TTCACATGTGAGTCTCGCCC	60.037	55.000	26.48	0.00	41.13	6.13
2977	4018	5.099575	TCTGTTTCGTTTCTTGCCTTTTTC	58.900	37.500	0.00	0.00	0.00	2.29
3004	4045	0.529992	CCTCGACGCTTTCCATACCC	60.530	60.000	0.00	0.00	0.00	3.69
3110	4168	3.264845	TGCCCCCTTTCTGACCCC	61.265	66.667	0.00	0.00	0.00	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.