AutoCloner

Multiple sequence alignment - TraesCS4D01G241600

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	TraesCS4D01G241600	chr4D	100.000	4009	0	0	1	4009	403908311	403912319	0.000000e+00	7404.0
1	TraesCS4D01G241600	chr4A	94.561	4045	151	36	1	4009	61357749	61361760	0.000000e+00	6187.0
2	TraesCS4D01G241600	chr4B	94.993	3535	115	28	494	4009	500526635	500530126	0.000000e+00	5491.0
3	TraesCS4D01G241600	chr4B	96.040	101	4	0	1	101	460541930	460541830	8.910000e-37	165.0
4	TraesCS4D01G241600	chr5D	92.275	233	17	1	99	330	9384193	9384425	2.990000e-86	329.0
5	TraesCS4D01G241600	chr2B	84.459	296	32	4	100	394	371895863	371896145	3.050000e-71	279.0
6	TraesCS4D01G241600	chr6D	96.970	99	3	0	1	99	418669128	418669030	2.480000e-37	167.0
7	TraesCS4D01G241600	chr2A	95.238	105	5	0	1	105	587581422	587581318	2.480000e-37	167.0
8	TraesCS4D01G241600	chr2A	96.000	100	4	0	1	100	221821687	221821786	3.210000e-36	163.0
9	TraesCS4D01G241600	chr1A	96.078	102	4	0	1	102	244769785	244769886	2.480000e-37	167.0
10	TraesCS4D01G241600	chr1A	95.192	104	5	0	1	104	377651670	377651773	8.910000e-37	165.0
11	TraesCS4D01G241600	chr7D	96.000	100	4	0	1	100	349329183	349329084	3.210000e-36	163.0
12	TraesCS4D01G241600	chr7D	94.286	105	6	0	1	105	638171186	638171082	1.150000e-35	161.0
13	TraesCS4D01G241600	chr7D	91.892	74	5	1	99	171	559021967	559022040	7.090000e-18	102.0
14	TraesCS4D01G241600	chr7A	79.459	185	32	6	256	438	24853071	24852891	4.210000e-25	126.0
15	TraesCS4D01G241600	chr3D	95.385	65	2	1	99	162	170175387	170175323	7.090000e-18	102.0
16	TraesCS4D01G241600	chr3A	95.385	65	2	1	99	162	207774395	207774331	7.090000e-18	102.0
17	TraesCS4D01G241600	chr3A	72.517	302	60	19	145	438	275545205	275544919	4.300000e-10	76.8
18	TraesCS4D01G241600	chr3A	97.436	39	1	0	2700	2738	700296561	700296523	2.590000e-07	67.6

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	TraesCS4D01G241600	chr4D	403908311	403912319	4008	False	7404	7404	100.000	1	4009	1	chr4D.!!$F1	4008
1	TraesCS4D01G241600	chr4A	61357749	61361760	4011	False	6187	6187	94.561	1	4009	1	chr4A.!!$F1	4008
2	TraesCS4D01G241600	chr4B	500526635	500530126	3491	False	5491	5491	94.993	494	4009	1	chr4B.!!$F1	3515

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	Hairpin	End Stability	Orientation
499	505	0.594796	GCCGTGTCTTGGTTTTGCAG	60.595	55.000	0.00	4.41	F
516	522	1.474077	GCAGATTTGTGGTGACCCATC	59.526	52.381	44.35	3.51	F
2219	2242	0.030638	GCTCCTGCTTTTTCAACGCA	59.969	50.000	36.03	5.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2198	2221	2.712057	CGTTGAAAAAGCAGGAGCAT	57.288	45.000	45.49	3.79	R
2501	2524	2.270205	CGCAGAGCCAACATCCCT	59.730	61.111	0.00	4.20	R
3044	3079	1.152138	AAACCCAACGAACTCCCCC	59.848	57.895	0.00	5.40	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
29	30	4.093408	TGCAGAGATGCGAACAAACTAATC	59.907	41.667	0.00	0.00	37.69	1.75
32	33	6.246449	CAGAGATGCGAACAAACTAATCTTG	58.754	40.000	0.00	0.00	0.00	3.02
75	76	6.653320	TGTCACTTTATGGTGAATGAAGGTAC	59.347	38.462	0.00	0.00	46.00	3.34
105	106	9.264719	CTTGGGGCATAAAATTTCTGAAATATC	57.735	33.333	15.45	2.91	0.00	1.63
112	113	9.612620	CATAAAATTTCTGAAATATCCCGCTAC	57.387	33.333	15.45	0.00	0.00	3.58
116	117	2.031420	TCTGAAATATCCCGCTACGACG	60.031	50.000	0.00	0.00	0.00	5.12
157	162	6.460261	GGGAGAGTTCAACAGGAAAAGAAAAG	60.460	42.308	0.00	0.00	37.23	2.27
161	166	6.856895	AGTTCAACAGGAAAAGAAAAGAGTG	58.143	36.000	0.00	0.00	37.23	3.51
173	178	1.416243	AAAGAGTGTGTCGTGGGGTA	58.584	50.000	0.00	0.00	0.00	3.69
191	196	4.322424	GGGGTATGATTTTTGTGTTGGGAC	60.322	45.833	0.00	0.00	0.00	4.46
192	197	4.526650	GGGTATGATTTTTGTGTTGGGACT	59.473	41.667	0.00	0.00	0.00	3.85
199	204	1.092921	TTGTGTTGGGACTGCGTGTC	61.093	55.000	1.55	1.55	44.63	3.67
215	220	2.603110	CGTGTCAAAGATACATGACGGG	59.397	50.000	0.00	0.00	46.99	5.28
231	236	1.549170	ACGGGTAGTCTGGACAATCAC	59.451	52.381	3.51	0.00	0.00	3.06
236	241	4.636206	GGGTAGTCTGGACAATCACATTTC	59.364	45.833	3.51	0.00	0.00	2.17
239	244	6.431234	GGTAGTCTGGACAATCACATTTCTTT	59.569	38.462	3.51	0.00	0.00	2.52
249	254	9.499585	GACAATCACATTTCTTTCTCACATATG	57.500	33.333	0.00	0.00	0.00	1.78
266	271	6.774170	TCACATATGGATTGGATTTGAGGAAG	59.226	38.462	7.80	0.00	0.00	3.46
320	325	0.609131	CCACTGGAAGCCCGTTTGAT	60.609	55.000	0.00	0.00	37.60	2.57
386	391	8.950210	TCAAGTTTGAAGATGACCTTAATCATC	58.050	33.333	10.00	10.00	42.38	2.92
417	422	9.653287	TGATCTATTTAAATATCTTGTAGCCCG	57.347	33.333	8.34	0.00	0.00	6.13
443	448	4.856487	GCAACGCACAAGCATTCTTTATAA	59.144	37.500	0.00	0.00	42.27	0.98
444	449	5.344665	GCAACGCACAAGCATTCTTTATAAA	59.655	36.000	0.00	0.00	42.27	1.40
492	498	3.192633	GGATTAAAATGCCGTGTCTTGGT	59.807	43.478	0.00	0.00	0.00	3.67
499	505	0.594796	GCCGTGTCTTGGTTTTGCAG	60.595	55.000	0.00	0.00	0.00	4.41
516	522	1.474077	GCAGATTTGTGGTGACCCATC	59.526	52.381	0.00	0.00	44.35	3.51
536	542	2.125350	GCTCCCTCTGCTCGGTTG	60.125	66.667	0.00	0.00	0.00	3.77
552	558	1.732259	GGTTGTGTGCTATCTCAACGG	59.268	52.381	12.10	0.00	40.46	4.44
707	721	3.327404	TGTTTCCCGGGGAGGAGC	61.327	66.667	23.50	5.23	45.00	4.70
871	888	6.925610	TTGATTGATTCCTTCTAACCGATG	57.074	37.500	0.00	0.00	0.00	3.84
914	931	2.743928	GCTCTGTGTCCAAGGCGG	60.744	66.667	0.00	0.00	0.00	6.13
2219	2242	0.030638	GCTCCTGCTTTTTCAACGCA	59.969	50.000	0.00	0.00	36.03	5.24
2360	2383	2.202610	CTGATCGACTGCGCCGAA	60.203	61.111	11.13	0.00	39.62	4.30
2468	2491	0.909610	ACTTGGAGGCGATGGAGGAA	60.910	55.000	0.00	0.00	0.00	3.36
2636	2659	0.905357	AGGTGAAGGACAAGATCGGG	59.095	55.000	0.00	0.00	0.00	5.14
2711	2734	2.688666	AAGGAGCTCGGGATGCCA	60.689	61.111	7.83	0.00	0.00	4.92
2989	3024	4.431131	CAAGCCGGGGCCAGATGT	62.431	66.667	4.39	0.00	43.17	3.06
2999	3034	1.315257	GGCCAGATGTCATTGCCGTT	61.315	55.000	0.00	0.00	31.55	4.44
3002	3037	1.621107	CAGATGTCATTGCCGTTTGC	58.379	50.000	0.00	0.00	41.77	3.68
3044	3079	3.363970	GCAAACACACTACTGACATTCCG	60.364	47.826	0.00	0.00	0.00	4.30
3051	3091	0.042131	TACTGACATTCCGGGGGAGT	59.958	55.000	0.00	0.00	31.21	3.85
3324	3364	7.572353	GCTCGTTGAGGAAATTACAATGTTACA	60.572	37.037	0.00	0.00	33.81	2.41
3934	3984	2.032636	GGACGGAAACTAAAACACACGG	60.033	50.000	0.00	0.00	0.00	4.94
3935	3985	2.609002	GACGGAAACTAAAACACACGGT	59.391	45.455	0.00	0.00	0.00	4.83
3936	3986	3.791245	ACGGAAACTAAAACACACGGTA	58.209	40.909	0.00	0.00	0.00	4.02
3937	3987	3.803778	ACGGAAACTAAAACACACGGTAG	59.196	43.478	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	8.895845	CAATTCAAGACAAGATTAGTTTGTTCG	58.104	33.333	0.00	0.00	38.78	3.95
29	30	4.823989	ACAGTTCTCCCAATTCAAGACAAG	59.176	41.667	0.00	0.00	0.00	3.16
32	33	4.214332	GTGACAGTTCTCCCAATTCAAGAC	59.786	45.833	0.00	0.00	0.00	3.01
75	76	5.185635	TCAGAAATTTTATGCCCCAAGACAG	59.814	40.000	0.00	0.00	0.00	3.51
112	113	2.334838	CCTCCTACTTGTTTTCCGTCG	58.665	52.381	0.00	0.00	0.00	5.12
116	117	2.910977	TCTCCCCTCCTACTTGTTTTCC	59.089	50.000	0.00	0.00	0.00	3.13
122	123	2.821437	TGAACTCTCCCCTCCTACTTG	58.179	52.381	0.00	0.00	0.00	3.16
157	162	0.892755	TCATACCCCACGACACACTC	59.107	55.000	0.00	0.00	0.00	3.51
161	166	3.504520	ACAAAAATCATACCCCACGACAC	59.495	43.478	0.00	0.00	0.00	3.67
173	178	3.552684	CGCAGTCCCAACACAAAAATCAT	60.553	43.478	0.00	0.00	0.00	2.45
191	196	3.241773	CGTCATGTATCTTTGACACGCAG	60.242	47.826	4.20	0.00	41.85	5.18
192	197	2.666022	CGTCATGTATCTTTGACACGCA	59.334	45.455	4.20	0.00	41.85	5.24
199	204	5.043903	CAGACTACCCGTCATGTATCTTTG	58.956	45.833	0.00	0.00	45.32	2.77
200	205	4.099573	CCAGACTACCCGTCATGTATCTTT	59.900	45.833	0.00	0.00	45.32	2.52
215	220	7.389053	AGAAAGAAATGTGATTGTCCAGACTAC	59.611	37.037	0.00	0.00	0.00	2.73
228	233	8.680001	CAATCCATATGTGAGAAAGAAATGTGA	58.320	33.333	1.24	0.00	0.00	3.58
231	236	8.229253	TCCAATCCATATGTGAGAAAGAAATG	57.771	34.615	1.24	0.00	0.00	2.32
236	241	8.229253	TCAAATCCAATCCATATGTGAGAAAG	57.771	34.615	1.24	0.00	0.00	2.62
239	244	6.101588	TCCTCAAATCCAATCCATATGTGAGA	59.898	38.462	13.04	0.31	33.41	3.27
249	254	2.615912	CGAGCTTCCTCAAATCCAATCC	59.384	50.000	0.00	0.00	38.00	3.01
266	271	0.878961	ACCGTTTGGACAGTTCGAGC	60.879	55.000	0.00	0.00	39.21	5.03
295	300	2.035783	GGCTTCCAGTGGGTTCCC	59.964	66.667	9.92	0.12	34.93	3.97
305	310	1.562008	TGGATATCAAACGGGCTTCCA	59.438	47.619	4.83	0.00	0.00	3.53
395	400	8.870879	GCTACGGGCTACAAGATATTTAAATAG	58.129	37.037	13.15	2.97	38.06	1.73
407	412	2.369870	CGTTGCTACGGGCTACAAG	58.630	57.895	13.04	0.26	44.60	3.16
417	422	3.773117	AATGCTTGTGCGTTGCTAC	57.227	47.368	0.00	0.00	45.65	3.58
473	478	4.657436	AAACCAAGACACGGCATTTTAA	57.343	36.364	0.00	0.00	0.00	1.52
479	485	1.315981	TGCAAAACCAAGACACGGCA	61.316	50.000	0.00	0.00	0.00	5.69
480	486	0.594796	CTGCAAAACCAAGACACGGC	60.595	55.000	0.00	0.00	0.00	5.68
492	498	2.102252	GGGTCACCACAAATCTGCAAAA	59.898	45.455	0.00	0.00	36.50	2.44
516	522	3.847602	CCGAGCAGAGGGAGCAGG	61.848	72.222	0.00	0.00	0.00	4.85
536	542	1.269166	CGTCCGTTGAGATAGCACAC	58.731	55.000	0.00	0.00	0.00	3.82
552	558	0.319641	GAGGTGAACTGGTGGACGTC	60.320	60.000	7.13	7.13	0.00	4.34
679	693	1.198759	CGGGAAACAGGAGGGAGGAA	61.199	60.000	0.00	0.00	0.00	3.36
707	721	5.747197	GTGCTTTTTATCTCTTCATGCATGG	59.253	40.000	25.97	11.53	0.00	3.66
871	888	2.739609	GCCGGTTACATGTACAGGTACC	60.740	54.545	19.29	19.82	35.26	3.34
914	931	0.835941	ATGACCTCACCAGATGGAGC	59.164	55.000	5.72	0.00	38.94	4.70
1382	1405	3.027292	CCGTAGAGCGAGGAGAGC	58.973	66.667	0.00	0.00	44.77	4.09
2198	2221	2.712057	CGTTGAAAAAGCAGGAGCAT	57.288	45.000	0.00	0.00	45.49	3.79
2501	2524	2.270205	CGCAGAGCCAACATCCCT	59.730	61.111	0.00	0.00	0.00	4.20
2636	2659	1.080995	CGTACTCCTGCAGCAGCTTC	61.081	60.000	17.81	4.34	42.74	3.86
3002	3037	0.108804	ATGTAACCGGTGCTCACGAG	60.109	55.000	8.52	0.00	0.00	4.18
3044	3079	1.152138	AAACCCAACGAACTCCCCC	59.848	57.895	0.00	0.00	0.00	5.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.