AutoCloner

Multiple sequence alignment - TraesCS4D01G090800

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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	TraesCS4D01G090800	chr4D	100.000	4206	0	0	1	4206	65933334	65937539	0.000000e+00	7768.0
1	TraesCS4D01G090800	chr4D	79.825	228	39	7	110	334	405747264	405747487	4.350000e-35	159.0
2	TraesCS4D01G090800	chr4A	95.886	3865	108	15	367	4206	529632601	529628763	0.000000e+00	6209.0
3	TraesCS4D01G090800	chr4A	94.334	353	17	3	1	352	529632934	529632584	4.780000e-149	538.0
4	TraesCS4D01G090800	chr4B	96.382	1824	44	8	2385	4206	96637887	96639690	0.000000e+00	2983.0
5	TraesCS4D01G090800	chr4B	93.362	1416	63	17	389	1782	96635964	96637370	0.000000e+00	2065.0
6	TraesCS4D01G090800	chr4B	93.450	458	18	11	1935	2383	96637394	96637848	0.000000e+00	669.0
7	TraesCS4D01G090800	chr3D	78.205	312	50	12	44	341	412076856	412076549	2.580000e-42	183.0
8	TraesCS4D01G090800	chr3D	79.221	231	43	5	110	337	607008336	607008108	5.630000e-34	156.0
9	TraesCS4D01G090800	chr6D	80.870	230	37	6	115	339	455095369	455095142	1.550000e-39	174.0
10	TraesCS4D01G090800	chr6D	98.077	52	1	0	1847	1898	90111206	90111257	1.610000e-14	91.6
11	TraesCS4D01G090800	chr5D	79.151	259	39	10	46	291	292155819	292155563	9.360000e-37	165.0
12	TraesCS4D01G090800	chr5D	77.600	250	43	11	95	339	32158876	32159117	5.670000e-29	139.0
13	TraesCS4D01G090800	chr7B	78.367	245	42	9	110	349	21662624	21662862	9.420000e-32	148.0
14	TraesCS4D01G090800	chr2D	79.018	224	38	8	121	341	1664474	1664257	1.220000e-30	145.0
15	TraesCS4D01G090800	chr7D	98.039	51	1	0	1851	1901	514658866	514658916	5.790000e-14	89.8
16	TraesCS4D01G090800	chr5A	98.039	51	1	0	1847	1897	40722004	40721954	5.790000e-14	89.8
17	TraesCS4D01G090800	chr6A	98.000	50	1	0	1851	1900	222554945	222554896	2.080000e-13	87.9
18	TraesCS4D01G090800	chr6A	94.545	55	2	1	1850	1903	445247834	445247780	2.690000e-12	84.2
19	TraesCS4D01G090800	chr3A	93.333	60	2	2	1851	1909	557420843	557420785	2.080000e-13	87.9
20	TraesCS4D01G090800	chr6B	97.959	49	1	0	1851	1899	42775673	42775625	7.490000e-13	86.1
21	TraesCS4D01G090800	chr1D	83.750	80	10	2	1818	1897	10647464	10647388	5.830000e-09	73.1

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	TraesCS4D01G090800	chr4D	65933334	65937539	4205	False	7768.000000	7768	100.000	1	4206	1	chr4D.!!$F1	4205
1	TraesCS4D01G090800	chr4A	529628763	529632934	4171	True	3373.500000	6209	95.110	1	4206	2	chr4A.!!$R1	4205
2	TraesCS4D01G090800	chr4B	96635964	96639690	3726	False	1905.666667	2983	94.398	389	4206	3	chr4B.!!$F1	3817

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
356	358	0.108186	TCGCGATGTTGAGATTGCCT	60.108	50.000	3.71	29.86	4.75	F
357	359	0.302890	CGCGATGTTGAGATTGCCTC	59.697	55.000	0.00	42.30	4.70	F
478	480	0.826715	TTTGAGGGAGATCTGCCGAG	59.173	55.000	25.71	46.59	4.63	F
2219	2274	1.193874	CGCTTACTTGTGGAAACCGAC	59.806	52.381	0.00	0.00	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1932	1985	1.127701	CGTGGGTTGTTTGATTTGCG	58.872	50.000	0.00	4.85	R
1960	2013	4.335416	TGGAGATTGTGATCCTTTGGAAC	58.665	43.478	34.34	3.62	R
2447	2549	3.410631	TGCAGGAGTTGTATTTTCGGA	57.589	42.857	0.00	4.55	R
4174	4277	0.036010	AGTGATCTTTGCCTGGTCCG	60.036	55.000	0.00	4.79	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
108	109	0.578683	CCTCTATGAATGCACGCACG	59.421	55.000	0.00	0.00	0.00	5.34
127	128	2.239400	CGACCCATATGAGCACCTCTA	58.761	52.381	3.65	0.00	0.00	2.43
129	130	3.305676	CGACCCATATGAGCACCTCTAAG	60.306	52.174	3.65	0.00	0.00	2.18
138	139	3.508012	TGAGCACCTCTAAGAGACTGAAC	59.492	47.826	0.00	0.00	0.00	3.18
141	142	3.367910	GCACCTCTAAGAGACTGAACCAG	60.368	52.174	0.00	0.00	37.52	4.00
160	161	4.196971	CCAGCACATCATCTTGAGATTGA	58.803	43.478	0.90	0.00	31.21	2.57
161	162	4.035324	CCAGCACATCATCTTGAGATTGAC	59.965	45.833	0.90	0.00	31.21	3.18
270	272	0.599558	TACGAGCGCCAGTGTAAGTT	59.400	50.000	14.57	0.00	0.00	2.66
278	280	3.367703	GCGCCAGTGTAAGTTTAGGTCTA	60.368	47.826	0.00	0.00	0.00	2.59
287	289	6.807720	GTGTAAGTTTAGGTCTAGAACTCTGC	59.192	42.308	15.16	5.46	32.79	4.26
313	315	3.685550	GCTGTGGGCATACTATTGTCCTT	60.686	47.826	0.00	0.00	42.12	3.36
321	323	6.465894	GGGCATACTATTGTCCTTCTAACCAT	60.466	42.308	0.00	0.00	38.40	3.55
339	341	2.742053	CCATCCACCACAAGTTAGTTCG	59.258	50.000	0.00	0.00	0.00	3.95
341	343	0.511221	CCACCACAAGTTAGTTCGCG	59.489	55.000	0.00	0.00	0.00	5.87
352	354	4.495422	AGTTAGTTCGCGATGTTGAGATT	58.505	39.130	10.88	0.00	0.00	2.40
353	355	4.327357	AGTTAGTTCGCGATGTTGAGATTG	59.673	41.667	10.88	0.00	0.00	2.67
354	356	1.394917	AGTTCGCGATGTTGAGATTGC	59.605	47.619	10.88	0.00	0.00	3.56
355	357	0.726827	TTCGCGATGTTGAGATTGCC	59.273	50.000	10.88	0.00	29.86	4.52
356	358	0.108186	TCGCGATGTTGAGATTGCCT	60.108	50.000	3.71	0.00	29.86	4.75
357	359	0.302890	CGCGATGTTGAGATTGCCTC	59.697	55.000	0.00	0.00	42.30	4.70
383	385	4.749245	AAAAAGTTCGCGATGTTGAGAT	57.251	36.364	10.88	0.00	0.00	2.75
384	386	5.856126	AAAAAGTTCGCGATGTTGAGATA	57.144	34.783	10.88	0.00	0.00	1.98
478	480	0.826715	TTTGAGGGAGATCTGCCGAG	59.173	55.000	25.71	0.00	46.59	4.63
562	565	5.772393	ACCAAACAACTCATATCCCTGTA	57.228	39.130	0.00	0.00	0.00	2.74
671	674	5.715070	TCGTTTTCAAGTTTCAACCATGTT	58.285	33.333	0.00	0.00	0.00	2.71
683	686	2.450609	ACCATGTTAGGACGTGTCAC	57.549	50.000	0.00	0.00	40.47	3.67
690	693	2.806244	GTTAGGACGTGTCACTGCAATT	59.194	45.455	0.00	0.00	0.00	2.32
711	714	7.540745	GCAATTCTGCGACTTTTTAAATCCTTA	59.459	33.333	0.00	0.00	39.20	2.69
718	721	8.353684	TGCGACTTTTTAAATCCTTACAATCAA	58.646	29.630	0.00	0.00	0.00	2.57
766	769	9.835389	ATTTACTAGCAAAATATGTTACCCGTA	57.165	29.630	2.60	0.00	0.00	4.02
953	956	2.726351	CCTCTTCCTCCTCCGGTGC	61.726	68.421	0.00	0.00	0.00	5.01
962	965	4.363990	CTCCGGTGCGTGCTCTGT	62.364	66.667	0.00	0.00	0.00	3.41
963	966	3.865929	CTCCGGTGCGTGCTCTGTT	62.866	63.158	0.00	0.00	0.00	3.16
990	993	3.693382	CTGCGCGGTCCACACGATA	62.693	63.158	8.83	0.00	0.00	2.92
991	994	2.954868	GCGCGGTCCACACGATAG	60.955	66.667	8.83	0.00	46.19	2.08
992	995	2.278596	CGCGGTCCACACGATAGG	60.279	66.667	0.00	0.00	43.77	2.57
993	996	2.767445	CGCGGTCCACACGATAGGA	61.767	63.158	0.00	0.00	43.77	2.94
1891	1943	4.486090	CGACAACTAATATGGATCGGAGG	58.514	47.826	0.00	0.00	0.00	4.30
1894	1946	4.528596	ACAACTAATATGGATCGGAGGGAG	59.471	45.833	0.00	0.00	0.00	4.30
1904	1956	3.522553	GATCGGAGGGAGTACAAACAAG	58.477	50.000	0.00	0.00	0.00	3.16
1960	2013	3.566322	TCAAACAACCCACGTAGGAAATG	59.434	43.478	7.14	5.42	41.22	2.32
2213	2267	3.181452	ACCCTTTACGCTTACTTGTGGAA	60.181	43.478	0.00	0.00	0.00	3.53
2217	2272	1.223187	ACGCTTACTTGTGGAAACCG	58.777	50.000	0.00	0.00	0.00	4.44
2219	2274	1.193874	CGCTTACTTGTGGAAACCGAC	59.806	52.381	0.00	0.00	0.00	4.79
2426	2526	2.781174	TCCCCATTCAACTACATACCCC	59.219	50.000	0.00	0.00	0.00	4.95
2610	2712	4.980573	TCTTGTATGTTTAGCAGGTGGTT	58.019	39.130	0.00	0.00	0.00	3.67
2883	2985	4.156739	GCTACATGGCAAGTTCTTTAGCTT	59.843	41.667	0.00	0.00	0.00	3.74
3247	3349	1.302752	TGCTCTGTGTGGGATGTGC	60.303	57.895	0.00	0.00	0.00	4.57
3372	3474	5.562298	ACCACATACACTACTGGAAACTT	57.438	39.130	0.00	0.00	0.00	2.66
3493	3595	7.574592	GCCATTAGCATGCAAATAAACCAAAAA	60.575	33.333	21.98	0.00	42.97	1.94
3596	3698	6.211184	ACCATATGCAGTCAATGGAAAAGAAA	59.789	34.615	20.75	0.00	42.36	2.52
3762	3865	8.931385	AATGTTTCTTTCATTGGCATACATAC	57.069	30.769	0.00	0.00	34.74	2.39
3794	3897	3.940303	CGGCTTAATGCTGTTACATGAC	58.060	45.455	0.00	0.00	42.87	3.06
3845	3948	4.378616	CCGCTTCACAAGAATTAAACAACG	59.621	41.667	0.00	0.00	32.31	4.10
3905	4008	8.531146	ACTAAGTACCAATATTTGCATTTTGCT	58.469	29.630	0.75	0.00	45.31	3.91
4174	4277	1.026182	TCACATCCAAGGTGATGCGC	61.026	55.000	0.00	0.00	44.84	6.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	2.882927	TGTGTATGTATGAGCGTCCC	57.117	50.000	0.00	0.00	0.00	4.46
108	109	3.898123	TCTTAGAGGTGCTCATATGGGTC	59.102	47.826	4.11	0.00	32.06	4.46
127	128	2.369860	TGATGTGCTGGTTCAGTCTCTT	59.630	45.455	0.00	0.00	33.43	2.85
129	130	2.462456	TGATGTGCTGGTTCAGTCTC	57.538	50.000	0.00	0.00	33.43	3.36
138	139	4.035324	GTCAATCTCAAGATGATGTGCTGG	59.965	45.833	0.00	0.00	34.49	4.85
141	142	3.867493	TCGTCAATCTCAAGATGATGTGC	59.133	43.478	0.00	0.00	34.49	4.57
160	161	1.947642	GGCGTTGTGTCGACTTCGT	60.948	57.895	17.92	0.00	40.80	3.85
161	162	2.844146	GGCGTTGTGTCGACTTCG	59.156	61.111	17.92	15.56	41.45	3.79
191	192	0.539986	TAGTGCGAGGGGATGTTTCC	59.460	55.000	0.00	0.00	41.77	3.13
215	216	2.620251	TCAGTCCTTCCGGCAATATG	57.380	50.000	0.00	0.00	0.00	1.78
217	218	3.644966	ATTTCAGTCCTTCCGGCAATA	57.355	42.857	0.00	0.00	0.00	1.90
270	272	3.366396	CCCAGCAGAGTTCTAGACCTAA	58.634	50.000	0.00	0.00	0.00	2.69
278	280	1.374190	CACAGCCCAGCAGAGTTCT	59.626	57.895	0.00	0.00	0.00	3.01
287	289	0.767375	ATAGTATGCCCACAGCCCAG	59.233	55.000	0.00	0.00	42.71	4.45
313	315	4.595781	ACTAACTTGTGGTGGATGGTTAGA	59.404	41.667	14.74	0.00	38.66	2.10
321	323	1.870580	CGCGAACTAACTTGTGGTGGA	60.871	52.381	0.00	0.00	0.00	4.02
362	364	4.749245	ATCTCAACATCGCGAACTTTTT	57.251	36.364	15.24	0.00	0.00	1.94
363	365	5.856126	TTATCTCAACATCGCGAACTTTT	57.144	34.783	15.24	0.34	0.00	2.27
364	366	5.351465	ACATTATCTCAACATCGCGAACTTT	59.649	36.000	15.24	3.28	0.00	2.66
365	367	4.870426	ACATTATCTCAACATCGCGAACTT	59.130	37.500	15.24	4.03	0.00	2.66
366	368	4.433615	ACATTATCTCAACATCGCGAACT	58.566	39.130	15.24	0.00	0.00	3.01
367	369	4.778842	ACATTATCTCAACATCGCGAAC	57.221	40.909	15.24	0.00	0.00	3.95
368	370	5.808030	TGTAACATTATCTCAACATCGCGAA	59.192	36.000	15.24	0.00	0.00	4.70
369	371	5.344884	TGTAACATTATCTCAACATCGCGA	58.655	37.500	13.09	13.09	0.00	5.87
370	372	5.635549	TGTAACATTATCTCAACATCGCG	57.364	39.130	0.00	0.00	0.00	5.87
371	373	6.847792	CACATGTAACATTATCTCAACATCGC	59.152	38.462	0.00	0.00	0.00	4.58
372	374	7.909267	ACACATGTAACATTATCTCAACATCG	58.091	34.615	0.00	0.00	0.00	3.84
375	377	9.936759	TTCTACACATGTAACATTATCTCAACA	57.063	29.630	0.00	0.00	0.00	3.33
478	480	1.680338	CCGATTCACCATTTCCCTCC	58.320	55.000	0.00	0.00	0.00	4.30
671	674	2.299013	AGAATTGCAGTGACACGTCCTA	59.701	45.455	0.00	0.00	0.00	2.94
690	693	7.499321	TTGTAAGGATTTAAAAAGTCGCAGA	57.501	32.000	0.00	0.00	0.00	4.26
700	703	7.093509	GGCCCTCTTTGATTGTAAGGATTTAAA	60.094	37.037	0.00	0.00	0.00	1.52
702	705	5.891551	GGCCCTCTTTGATTGTAAGGATTTA	59.108	40.000	0.00	0.00	0.00	1.40
706	709	2.025321	GGGCCCTCTTTGATTGTAAGGA	60.025	50.000	17.04	0.00	0.00	3.36
707	710	2.024941	AGGGCCCTCTTTGATTGTAAGG	60.025	50.000	22.28	0.00	0.00	2.69
711	714	1.075601	TGAGGGCCCTCTTTGATTGT	58.924	50.000	43.90	13.27	43.12	2.71
718	721	0.922626	GAAGGAATGAGGGCCCTCTT	59.077	55.000	43.90	37.20	43.12	2.85
724	727	4.273318	AGTAAATGTGAAGGAATGAGGGC	58.727	43.478	0.00	0.00	0.00	5.19
766	769	0.324943	AGCCGGTGCAATTACAGAGT	59.675	50.000	1.90	0.00	41.13	3.24
953	956	3.291585	CAGCAAGTTTTAACAGAGCACG	58.708	45.455	0.00	0.00	0.00	5.34
992	995	3.826466	CTGTCGGAAGCCATTTTTCTTC	58.174	45.455	0.00	0.00	38.30	2.87
993	996	2.029918	GCTGTCGGAAGCCATTTTTCTT	60.030	45.455	0.00	0.00	37.20	2.52
1480	1486	7.010923	GCAGGAAAAACACATTCACACATAAAA	59.989	33.333	0.00	0.00	0.00	1.52
1615	1621	7.519032	TTCATGAGGGGTACTTTTGTTAAAG	57.481	36.000	0.00	0.00	45.08	1.85
1914	1967	2.498167	GCGATTGCAGTCCATAGGATT	58.502	47.619	3.33	0.00	42.15	3.01
1932	1985	1.127701	CGTGGGTTGTTTGATTTGCG	58.872	50.000	0.00	0.00	0.00	4.85
1960	2013	4.335416	TGGAGATTGTGATCCTTTGGAAC	58.665	43.478	0.00	0.00	34.34	3.62
2447	2549	3.410631	TGCAGGAGTTGTATTTTCGGA	57.589	42.857	0.00	0.00	0.00	4.55
2600	2702	4.085876	GCATGTGAACCACCTGCT	57.914	55.556	16.36	0.00	46.83	4.24
2610	2712	2.106338	TCCTGGTTTTCTGAGCATGTGA	59.894	45.455	0.00	0.00	0.00	3.58
2921	3023	6.486253	AACACTATAAGTTCACAGTGCATG	57.514	37.500	9.98	0.00	41.67	4.06
3302	3404	4.732672	ACCCGAGACACTTTATTACTCC	57.267	45.455	0.00	0.00	0.00	3.85
3303	3405	5.107824	GGAACCCGAGACACTTTATTACTC	58.892	45.833	0.00	0.00	0.00	2.59
3304	3406	4.529377	TGGAACCCGAGACACTTTATTACT	59.471	41.667	0.00	0.00	0.00	2.24
3305	3407	4.824289	TGGAACCCGAGACACTTTATTAC	58.176	43.478	0.00	0.00	0.00	1.89
3372	3474	2.872245	GTTGCTACTCTGTTTGTCAGCA	59.128	45.455	0.00	0.00	43.32	4.41
3395	3497	3.003394	TCACCTGCCTCATATGGTTTG	57.997	47.619	2.13	0.00	0.00	2.93
3493	3595	7.329226	GCACATAGCAATGTAACATTCTTGTTT	59.671	33.333	0.00	0.00	44.70	2.83
3596	3698	5.933187	TTGTTGCACAGTATATCGTTTGT	57.067	34.783	0.00	0.00	0.00	2.83
3762	3865	7.225027	AACAGCATTAAGCCGTTTGAAGAAAG	61.225	38.462	0.00	0.00	40.89	2.62
3845	3948	7.172019	AGTCCATTTGTTCATCATTTTTGCTTC	59.828	33.333	0.00	0.00	0.00	3.86
3925	4028	2.617276	CCTGTTGCTCCAGACATGATGT	60.617	50.000	0.00	0.00	34.23	3.06
4174	4277	0.036010	AGTGATCTTTGCCTGGTCCG	60.036	55.000	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.