AutoCloner

Multiple sequence alignment - TraesCS5D01G549500

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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	TraesCS5D01G549500	chr5D	100.000	5182	0	0	1	5182	556549106	556543925	0.000000e+00	9570.0
1	TraesCS5D01G549500	chr5D	87.500	272	25	5	3470	3737	556533737	556533471	6.520000e-79	305.0
2	TraesCS5D01G549500	chr5D	93.846	130	8	0	4272	4401	500133472	500133601	4.090000e-46	196.0
3	TraesCS5D01G549500	chr5D	100.000	28	0	0	2325	2352	346884114	346884141	9.000000e-03	52.8
4	TraesCS5D01G549500	chrUn	86.113	1325	123	23	2896	4195	244921260	244919972	0.000000e+00	1371.0
5	TraesCS5D01G549500	chrUn	86.113	1325	123	23	2896	4195	285317277	285315989	0.000000e+00	1371.0
6	TraesCS5D01G549500	chrUn	86.157	1322	122	24	2896	4192	295399241	295400526	0.000000e+00	1371.0
7	TraesCS5D01G549500	chrUn	86.157	1322	122	24	2896	4192	306003443	306004728	0.000000e+00	1371.0
8	TraesCS5D01G549500	chrUn	86.032	988	57	36	1345	2307	244922573	244921642	0.000000e+00	985.0
9	TraesCS5D01G549500	chrUn	86.032	988	57	36	1345	2307	285318590	285317659	0.000000e+00	985.0
10	TraesCS5D01G549500	chrUn	86.009	679	80	14	2354	3024	244921659	244920988	0.000000e+00	713.0
11	TraesCS5D01G549500	chrUn	86.009	679	80	14	2354	3024	285317676	285317005	0.000000e+00	713.0
12	TraesCS5D01G549500	chrUn	86.380	558	63	12	2471	3021	295398959	295399510	9.600000e-167	597.0
13	TraesCS5D01G549500	chrUn	86.462	554	63	11	2474	3021	306003165	306003712	9.600000e-167	597.0
14	TraesCS5D01G549500	chrUn	83.468	496	61	12	2848	3343	244921260	244920786	4.760000e-120	442.0
15	TraesCS5D01G549500	chrUn	83.468	496	61	12	2848	3343	285317277	285316803	4.760000e-120	442.0
16	TraesCS5D01G549500	chrUn	83.570	493	60	12	2845	3337	295399238	295399709	4.760000e-120	442.0
17	TraesCS5D01G549500	chrUn	83.570	493	60	12	2845	3337	306003440	306003911	4.760000e-120	442.0
18	TraesCS5D01G549500	chrUn	77.338	631	75	35	466	1053	244923401	244922796	1.400000e-80	311.0
19	TraesCS5D01G549500	chrUn	77.338	631	75	35	466	1053	285319418	285318813	1.400000e-80	311.0
20	TraesCS5D01G549500	chrUn	83.529	340	38	6	3	341	244923814	244923492	8.430000e-78	302.0
21	TraesCS5D01G549500	chrUn	84.541	207	26	4	136	341	285319710	285319509	3.160000e-47	200.0
22	TraesCS5D01G549500	chrUn	93.333	135	9	0	4274	4408	293609603	293609469	3.160000e-47	200.0
23	TraesCS5D01G549500	chrUn	94.574	129	7	0	4274	4402	314565200	314565328	3.160000e-47	200.0
24	TraesCS5D01G549500	chr5B	87.608	1041	92	24	2797	3815	710237812	710238837	0.000000e+00	1173.0
25	TraesCS5D01G549500	chr5B	88.426	985	58	18	1342	2299	710236470	710237425	0.000000e+00	1136.0
26	TraesCS5D01G549500	chr5B	84.359	991	124	16	2376	3344	710237423	710238404	0.000000e+00	942.0
27	TraesCS5D01G549500	chr5B	90.671	343	25	3	3934	4276	710238863	710239198	2.850000e-122	449.0
28	TraesCS5D01G549500	chr5B	87.871	371	35	4	1	363	710234507	710234875	1.330000e-115	427.0
29	TraesCS5D01G549500	chr5B	85.538	325	21	8	495	815	710235231	710235533	3.010000e-82	316.0
30	TraesCS5D01G549500	chr5B	95.276	127	6	0	4275	4401	50519943	50520069	8.800000e-48	202.0
31	TraesCS5D01G549500	chr5B	95.522	67	3	0	401	467	710235178	710235244	1.970000e-19	108.0
32	TraesCS5D01G549500	chr6B	91.418	536	42	3	4649	5180	599981097	599981632	0.000000e+00	732.0
33	TraesCS5D01G549500	chr6B	91.541	532	41	3	4655	5182	26217740	26218271	0.000000e+00	730.0
34	TraesCS5D01G549500	chr6B	92.537	134	10	0	4275	4408	69718560	69718427	5.300000e-45	193.0
35	TraesCS5D01G549500	chr7D	91.337	531	42	3	4654	5180	478798823	478799353	0.000000e+00	723.0
36	TraesCS5D01G549500	chr7D	90.890	483	33	6	1477	1956	600610752	600611226	5.660000e-179	638.0
37	TraesCS5D01G549500	chr7D	89.936	467	37	5	1487	1951	600557165	600557623	1.240000e-165	593.0
38	TraesCS5D01G549500	chr2B	91.321	530	43	2	4654	5180	452910177	452910706	0.000000e+00	721.0
39	TraesCS5D01G549500	chr1B	91.182	533	41	6	4653	5180	594704026	594703495	0.000000e+00	719.0
40	TraesCS5D01G549500	chr1B	90.625	544	46	4	4641	5180	643024939	643025481	0.000000e+00	717.0
41	TraesCS5D01G549500	chr1B	94.531	128	7	0	4274	4401	464481748	464481621	1.140000e-46	198.0
42	TraesCS5D01G549500	chr4A	91.304	529	41	4	4656	5180	728114294	728114821	0.000000e+00	717.0
43	TraesCS5D01G549500	chr3B	91.149	531	43	3	4654	5180	465345740	465345210	0.000000e+00	717.0
44	TraesCS5D01G549500	chr3B	100.000	31	0	0	3825	3855	263260945	263260975	2.020000e-04	58.4
45	TraesCS5D01G549500	chr3B	96.970	33	1	0	2323	2355	493117283	493117251	7.250000e-04	56.5
46	TraesCS5D01G549500	chr7B	90.706	538	44	5	4649	5182	657535554	657536089	0.000000e+00	712.0
47	TraesCS5D01G549500	chr7B	93.382	136	9	0	4272	4407	637617925	637618060	8.800000e-48	202.0
48	TraesCS5D01G549500	chr5A	87.844	617	53	17	1349	1956	296997574	296998177	0.000000e+00	704.0
49	TraesCS5D01G549500	chr5A	85.784	612	57	15	1349	1956	689246624	689246039	5.700000e-174	621.0
50	TraesCS5D01G549500	chr5A	93.182	44	3	0	3819	3862	679658592	679658635	1.200000e-06	65.8
51	TraesCS5D01G549500	chr3A	85.784	612	56	15	1349	1956	148181001	148181585	2.050000e-173	619.0
52	TraesCS5D01G549500	chr3A	84.967	612	61	14	1349	1956	148257607	148258191	4.470000e-165	592.0
53	TraesCS5D01G549500	chr2D	95.276	127	6	0	4275	4401	58672253	58672127	8.800000e-48	202.0
54	TraesCS5D01G549500	chr2D	94.531	128	7	0	4274	4401	78576479	78576606	1.140000e-46	198.0
55	TraesCS5D01G549500	chr2D	90.909	110	10	0	3820	3929	102942674	102942565	1.160000e-31	148.0
56	TraesCS5D01G549500	chr2D	93.478	46	3	0	2307	2352	506797936	506797981	9.310000e-08	69.4
57	TraesCS5D01G549500	chr1A	79.208	101	19	2	3825	3924	171453440	171453341	9.310000e-08	69.4

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	TraesCS5D01G549500	chr5D	556543925	556549106	5181	True	9570.000000	9570	100.000000	1	5182	1	chr5D.!!$R2	5181
1	TraesCS5D01G549500	chrUn	295398959	295400526	1567	False	803.333333	1371	85.369000	2471	4192	3	chrUn.!!$F2	1721
2	TraesCS5D01G549500	chrUn	306003165	306004728	1563	False	803.333333	1371	85.396333	2474	4192	3	chrUn.!!$F3	1718
3	TraesCS5D01G549500	chrUn	244919972	244923814	3842	True	687.333333	1371	83.748167	3	4195	6	chrUn.!!$R2	4192
4	TraesCS5D01G549500	chrUn	285315989	285319710	3721	True	670.333333	1371	83.916833	136	4195	6	chrUn.!!$R3	4059
5	TraesCS5D01G549500	chr5B	710234507	710239198	4691	False	650.142857	1173	88.570714	1	4276	7	chr5B.!!$F2	4275
6	TraesCS5D01G549500	chr6B	599981097	599981632	535	False	732.000000	732	91.418000	4649	5180	1	chr6B.!!$F2	531
7	TraesCS5D01G549500	chr6B	26217740	26218271	531	False	730.000000	730	91.541000	4655	5182	1	chr6B.!!$F1	527
8	TraesCS5D01G549500	chr7D	478798823	478799353	530	False	723.000000	723	91.337000	4654	5180	1	chr7D.!!$F1	526
9	TraesCS5D01G549500	chr2B	452910177	452910706	529	False	721.000000	721	91.321000	4654	5180	1	chr2B.!!$F1	526
10	TraesCS5D01G549500	chr1B	594703495	594704026	531	True	719.000000	719	91.182000	4653	5180	1	chr1B.!!$R2	527
11	TraesCS5D01G549500	chr1B	643024939	643025481	542	False	717.000000	717	90.625000	4641	5180	1	chr1B.!!$F1	539
12	TraesCS5D01G549500	chr4A	728114294	728114821	527	False	717.000000	717	91.304000	4656	5180	1	chr4A.!!$F1	524
13	TraesCS5D01G549500	chr3B	465345210	465345740	530	True	717.000000	717	91.149000	4654	5180	1	chr3B.!!$R1	526
14	TraesCS5D01G549500	chr7B	657535554	657536089	535	False	712.000000	712	90.706000	4649	5182	1	chr7B.!!$F2	533
15	TraesCS5D01G549500	chr5A	296997574	296998177	603	False	704.000000	704	87.844000	1349	1956	1	chr5A.!!$F1	607
16	TraesCS5D01G549500	chr5A	689246039	689246624	585	True	621.000000	621	85.784000	1349	1956	1	chr5A.!!$R1	607
17	TraesCS5D01G549500	chr3A	148181001	148181585	584	False	619.000000	619	85.784000	1349	1956	1	chr3A.!!$F1	607
18	TraesCS5D01G549500	chr3A	148257607	148258191	584	False	592.000000	592	84.967000	1349	1956	1	chr3A.!!$F2	607

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
510	796	0.109342	CCTACTCATGGCATGGGTCC	59.891	60.0	34.75	40.83	4.46	F
1295	2357	0.033601	TTGAGCCCAACCAACTGTGT	60.034	50.0	0.00	0.00	3.72	F
1337	2399	0.034756	TGTATCAATCATCCCGCCGG	59.965	55.0	0.00	0.00	6.13	F
2833	4023	0.038618	GTTCATCCCACCCGCAAAAC	60.039	55.0	0.00	0.00	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1318	2380	0.034756	CCGGCGGGATGATTGATACA	59.965	55.0	20.56	34.06	2.29	R
2864	4054	0.038890	TGGTTTTGCCGATGGGATGA	59.961	50.0	0.00	41.21	2.92	R
2874	4064	0.251787	AGATGGGTCCTGGTTTTGCC	60.252	55.0	0.00	37.90	4.52	R
4467	5740	0.033642	GGCATAGAGTCGCCCCTTAC	59.966	60.0	0.00	42.82	2.34	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
45	46	2.973420	GCGCTAATAAGTGACGCCT	58.027	52.632	0.00	0.00	43.58	5.52
63	65	4.081087	ACGCCTCTCAATGTAGGTTTGTAT	60.081	41.667	6.34	0.00	35.16	2.29
122	130	4.212716	ACTCCGCTGGTACTGTATCATTA	58.787	43.478	0.47	0.00	0.00	1.90
182	190	9.823098	CTAAGATGTCTGAGAAGTTCAAATTTG	57.177	33.333	12.15	12.15	34.81	2.32
239	247	1.270550	CAAGAGCTGGCAACCGATTTT	59.729	47.619	0.00	0.00	0.00	1.82
250	258	3.060339	GCAACCGATTTTTGCTTTCTGTG	60.060	43.478	0.00	0.00	44.96	3.66
256	264	5.063312	CCGATTTTTGCTTTCTGTGTTGTTT	59.937	36.000	0.00	0.00	0.00	2.83
343	352	1.470098	CTTGGCTGAAAATGGAGTCCG	59.530	52.381	4.30	0.00	0.00	4.79
348	357	0.953471	TGAAAATGGAGTCCGTGCCG	60.953	55.000	4.15	0.00	0.00	5.69
371	380	6.183360	CCGATGTTCCTAAAGAGATCTTCTGA	60.183	42.308	0.00	0.00	35.91	3.27
373	382	8.572185	CGATGTTCCTAAAGAGATCTTCTGATA	58.428	37.037	0.00	0.00	35.91	2.15
391	400	9.270640	CTTCTGATATATATTAATGGGCTCTGC	57.729	37.037	0.00	0.00	0.00	4.26
459	733	4.137116	TGGTCGGATTTCTGAACTATGG	57.863	45.455	6.04	0.00	39.65	2.74
477	763	1.349688	TGGACGTGTCTATTTTGCCCT	59.650	47.619	0.00	0.00	0.00	5.19
479	765	1.130561	GACGTGTCTATTTTGCCCTGC	59.869	52.381	0.00	0.00	0.00	4.85
495	781	4.468689	GCCTGCCCACGACCCTAC	62.469	72.222	0.00	0.00	0.00	3.18
502	788	1.144057	CCACGACCCTACTCATGGC	59.856	63.158	0.00	0.00	0.00	4.40
503	789	1.613317	CCACGACCCTACTCATGGCA	61.613	60.000	0.00	0.00	0.00	4.92
504	790	0.465705	CACGACCCTACTCATGGCAT	59.534	55.000	0.00	0.00	0.00	4.40
505	791	0.465705	ACGACCCTACTCATGGCATG	59.534	55.000	21.42	21.42	0.00	4.06
506	792	0.250038	CGACCCTACTCATGGCATGG	60.250	60.000	26.15	18.66	0.00	3.66
510	796	0.109342	CCTACTCATGGCATGGGTCC	59.891	60.000	34.75	0.00	40.83	4.46
529	815	5.070001	GGTCCATATTCGGATCCATTTTCA	58.930	41.667	13.41	0.00	37.41	2.69
540	826	3.613494	TCCATTTTCAATACCCGTCGA	57.387	42.857	0.00	0.00	0.00	4.20
553	839	1.214367	CCGTCGATTAACCATTCCCG	58.786	55.000	0.00	0.00	0.00	5.14

Showing 1 to 25 of 636 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
19	20	1.724623	CACTTATTAGCGCACACACGT	59.275	47.619	11.47	34.88	4.49
20	21	1.989864	TCACTTATTAGCGCACACACG	59.010	47.619	11.47	0.00	4.49
153	161	9.646427	ATTTGAACTTCTCAGACATCTTAGTAC	57.354	33.333	0.00	34.81	2.73
182	190	4.991472	ACTCCCTCGAAATAAAGTACGTC	58.009	43.478	0.00	0.00	4.34
232	240	4.111916	ACAACACAGAAAGCAAAAATCGG	58.888	39.130	0.00	0.00	4.18
269	277	9.158233	CGACCTTCACTATTGGAATTTACTTAA	57.842	33.333	0.00	0.00	1.85
273	281	5.353123	TGCGACCTTCACTATTGGAATTTAC	59.647	40.000	0.00	0.00	2.01
323	331	1.470098	CGGACTCCATTTTCAGCCAAG	59.530	52.381	0.00	0.00	3.61
343	352	3.247006	TCTCTTTAGGAACATCGGCAC	57.753	47.619	0.00	0.00	5.01
387	396	8.347004	TCAGAAACAAATGTAAATATGGCAGA	57.653	30.769	0.00	0.00	4.26
397	406	9.190858	GTGCACATAATTCAGAAACAAATGTAA	57.809	29.630	13.17	0.00	2.41
399	408	6.646240	GGTGCACATAATTCAGAAACAAATGT	59.354	34.615	20.43	0.00	2.71
445	719	5.407407	AGACACGTCCATAGTTCAGAAAT	57.593	39.130	0.00	0.00	2.17
459	733	1.130561	GCAGGGCAAAATAGACACGTC	59.869	52.381	0.00	0.00	4.34
479	765	2.683933	AGTAGGGTCGTGGGCAGG	60.684	66.667	0.00	0.00	4.85
488	774	0.109342	CCCATGCCATGAGTAGGGTC	59.891	60.000	6.18	28.68	4.46
495	781	2.893215	ATATGGACCCATGCCATGAG	57.107	50.000	6.18	45.39	2.90
502	788	2.991250	GGATCCGAATATGGACCCATG	58.009	52.381	11.61	41.99	3.66
505	791	3.721087	AATGGATCCGAATATGGACCC	57.279	47.619	7.39	42.85	4.46
506	792	5.070001	TGAAAATGGATCCGAATATGGACC	58.930	41.667	7.39	41.85	4.46
510	796	7.538575	GGGTATTGAAAATGGATCCGAATATG	58.461	38.462	7.39	0.00	1.78
529	815	4.383173	GGAATGGTTAATCGACGGGTATT	58.617	43.478	0.00	0.00	1.89
540	826	1.134310	GGGTCGACGGGAATGGTTAAT	60.134	52.381	9.92	0.00	1.40
625	911	8.333984	CCTTAATTACTTCTCCCCCTCTAAAAA	58.666	37.037	0.00	0.00	1.94
629	915	6.114151	ACCTTAATTACTTCTCCCCCTCTA	57.886	41.667	0.00	0.00	2.43

Showing 1 to 25 of 589 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.