AutoCloner

Multiple sequence alignment - TraesCS5B01G083200

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	TraesCS5B01G083200	chr5B	100.000	3438	0	0	1	3438	104504796	104501359	0	6349
1	TraesCS5B01G083200	chr5B	94.870	3450	153	16	1	3438	197387107	197390544	0	5369
2	TraesCS5B01G083200	chr1B	95.622	3449	130	10	1	3438	256706754	256710192	0	5513
3	TraesCS5B01G083200	chr1B	94.910	3458	143	19	1	3438	164401135	164397691	0	5380
4	TraesCS5B01G083200	chr4B	95.395	3453	133	14	1	3438	310225949	310222508	0	5472
5	TraesCS5B01G083200	chr4B	95.019	3453	144	18	1	3438	407695548	407692109	0	5398
6	TraesCS5B01G083200	chr4B	94.958	3451	150	17	1	3438	224372269	224375708	0	5387
7	TraesCS5B01G083200	chr2B	95.226	3435	138	18	17	3438	506424421	506421000	0	5411
8	TraesCS5B01G083200	chr2B	94.878	3456	146	22	1	3438	300243649	300240207	0	5373
9	TraesCS5B01G083200	chr7B	95.019	3453	143	18	1	3438	381026456	381023018	0	5397

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	TraesCS5B01G083200	chr5B	104501359	104504796	3437	True	6349	6349	100.000	1	3438	1	chr5B.!!$R1	3437
1	TraesCS5B01G083200	chr5B	197387107	197390544	3437	False	5369	5369	94.870	1	3438	1	chr5B.!!$F1	3437
2	TraesCS5B01G083200	chr1B	256706754	256710192	3438	False	5513	5513	95.622	1	3438	1	chr1B.!!$F1	3437
3	TraesCS5B01G083200	chr1B	164397691	164401135	3444	True	5380	5380	94.910	1	3438	1	chr1B.!!$R1	3437
4	TraesCS5B01G083200	chr4B	310222508	310225949	3441	True	5472	5472	95.395	1	3438	1	chr4B.!!$R1	3437
5	TraesCS5B01G083200	chr4B	407692109	407695548	3439	True	5398	5398	95.019	1	3438	1	chr4B.!!$R2	3437
6	TraesCS5B01G083200	chr4B	224372269	224375708	3439	False	5387	5387	94.958	1	3438	1	chr4B.!!$F1	3437
7	TraesCS5B01G083200	chr2B	506421000	506424421	3421	True	5411	5411	95.226	17	3438	1	chr2B.!!$R2	3421
8	TraesCS5B01G083200	chr2B	300240207	300243649	3442	True	5373	5373	94.878	1	3438	1	chr2B.!!$R1	3437
9	TraesCS5B01G083200	chr7B	381023018	381026456	3438	True	5397	5397	95.019	1	3438	1	chr7B.!!$R1	3437

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
797	810	0.685785	TGCCACAAGGGACTGCAAAA	60.686	50.000	0.0	0.0	40.86	2.44	F
1150	1165	1.067565	GCAACGAGACACTGGAGATCA	60.068	52.381	0.0	0.0	0.00	2.92	F
1283	1298	1.542375	AACCTCCCCAGATGGCAGT	60.542	57.895	0.0	0.0	0.00	4.40	F
1734	1754	2.024414	GACTTGGTGAAGCACTGGTTT	58.976	47.619	0.0	0.0	34.40	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2020	2047	1.134310	TCATGATGCAGCATCTCGGTT	60.134	47.619	31.02	11.83	41.06	4.44	R
2198	2225	1.852157	AATGGGTGGATGACGCTGGT	61.852	55.000	0.00	0.00	38.35	4.00	R
2277	2304	2.031163	GGTTGTCTGGCAGCTCGT	59.969	61.111	10.34	0.00	0.00	4.18	R
3268	3300	3.148279	CGCTAGTCGAGGGGGCTT	61.148	66.667	0.98	0.00	41.67	4.35	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
226	231	7.819900	ACAAAAGGCATAGTAAAACAAACACAA	59.180	29.630	0.00	0.00	0.00	3.33
227	232	8.660373	CAAAAGGCATAGTAAAACAAACACAAA	58.340	29.630	0.00	0.00	0.00	2.83
228	233	7.764695	AAGGCATAGTAAAACAAACACAAAC	57.235	32.000	0.00	0.00	0.00	2.93
229	234	6.868622	AGGCATAGTAAAACAAACACAAACA	58.131	32.000	0.00	0.00	0.00	2.83
242	247	1.735018	CACAAACACCAGTGAACGACA	59.265	47.619	4.48	0.00	37.97	4.35
312	320	4.289410	TCCCAATTCAGAAAGACCATCAGA	59.711	41.667	0.00	0.00	0.00	3.27
517	529	4.698201	TTACACTTCAATCACCAGTCCA	57.302	40.909	0.00	0.00	0.00	4.02
588	600	1.559219	TGCAAGTGGGATAAGCAGCTA	59.441	47.619	0.00	0.00	0.00	3.32
596	608	7.560796	AGTGGGATAAGCAGCTAATAAGTAT	57.439	36.000	0.00	0.00	0.00	2.12
638	650	2.230992	TGCCACAGTAAAATGCCATCAC	59.769	45.455	0.00	0.00	0.00	3.06
650	662	2.032528	CATCACCACCACCGCAGT	59.967	61.111	0.00	0.00	0.00	4.40
695	707	5.877012	CAGGTCATAAGTACAGCTTGACAAT	59.123	40.000	13.02	0.66	36.93	2.71
797	810	0.685785	TGCCACAAGGGACTGCAAAA	60.686	50.000	0.00	0.00	40.86	2.44
838	852	2.741092	CACTACACACACGCCCCT	59.259	61.111	0.00	0.00	0.00	4.79
970	985	5.102313	CACACAAACCAAAAACTTCTCTCC	58.898	41.667	0.00	0.00	0.00	3.71
1116	1131	2.818751	ACACAACAACCCTCAAAGGA	57.181	45.000	0.00	0.00	37.67	3.36
1140	1155	1.300931	GCTCCACAGCAACGAGACA	60.301	57.895	0.00	0.00	46.06	3.41
1150	1165	1.067565	GCAACGAGACACTGGAGATCA	60.068	52.381	0.00	0.00	0.00	2.92
1283	1298	1.542375	AACCTCCCCAGATGGCAGT	60.542	57.895	0.00	0.00	0.00	4.40
1493	1511	5.163814	GCACTACTGCATTTTCTCAAGTAGG	60.164	44.000	11.60	3.77	43.62	3.18
1528	1546	7.701539	ATGTATTTTTGAACCTGATGCACTA	57.298	32.000	0.00	0.00	0.00	2.74
1734	1754	2.024414	GACTTGGTGAAGCACTGGTTT	58.976	47.619	0.00	0.00	34.40	3.27
1736	1756	3.626930	ACTTGGTGAAGCACTGGTTTTA	58.373	40.909	0.00	0.00	34.40	1.52
1738	1758	4.649218	ACTTGGTGAAGCACTGGTTTTATT	59.351	37.500	0.00	0.00	34.40	1.40
1767	1787	8.161699	TCCCATTTCAACAAAAGTAGACTAAC	57.838	34.615	0.00	0.00	0.00	2.34
2198	2225	3.141398	GACTCCTTGACTGATGTTGCAA	58.859	45.455	0.00	0.00	0.00	4.08
2239	2266	6.899393	TTCTACAAAGGCATGAAGAACAAT	57.101	33.333	0.00	0.00	0.00	2.71
2319	2346	1.941294	CGAGTACGCAGGAGTAGATGT	59.059	52.381	0.00	0.00	0.00	3.06
2431	2458	0.260523	GCCCCTATTGCCCCTTTACA	59.739	55.000	0.00	0.00	0.00	2.41
2473	2500	0.869730	GCCTTCGTTTTACTTCCGCA	59.130	50.000	0.00	0.00	0.00	5.69
2532	2559	2.435372	TGCTCTTGTTGGGTTGAACT	57.565	45.000	0.00	0.00	0.00	3.01
2857	2884	6.775594	ATGCACTATCAGTACAACTCAGTA	57.224	37.500	0.00	0.00	0.00	2.74
2907	2934	3.068732	TGACACCAGAAGACACTTGAGAG	59.931	47.826	0.00	0.00	0.00	3.20
2999	3026	8.561738	AACTGACAAGAACTAGAACAAAAAGA	57.438	30.769	0.00	0.00	0.00	2.52
3235	3267	5.871396	AAGTGTTCAGAGGAGTTTGACTA	57.129	39.130	0.00	0.00	0.00	2.59
3268	3300	3.857052	CTGCACTTATAAACAGGTCCGA	58.143	45.455	0.00	0.00	0.00	4.55
3312	3344	1.080093	CTAAACCCAGAGCGCACGA	60.080	57.895	11.47	0.00	0.00	4.35
3313	3345	0.460284	CTAAACCCAGAGCGCACGAT	60.460	55.000	11.47	0.00	0.00	3.73
3344	3382	2.427740	GCGCGGACGAGCTATCTC	60.428	66.667	8.83	0.00	43.93	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	7.887996	TTCAAATTTATTTGTGACTGCATCC	57.112	32.000	13.28	0.00	45.49	3.51
226	231	2.102070	TTGTGTCGTTCACTGGTGTT	57.898	45.000	12.67	0.00	46.27	3.32
227	232	2.102070	TTTGTGTCGTTCACTGGTGT	57.898	45.000	12.67	0.00	46.27	4.16
228	233	3.479505	TTTTTGTGTCGTTCACTGGTG	57.520	42.857	12.67	0.00	46.27	4.17
352	360	4.848357	AGATTTTCACCAGTACAGGATGG	58.152	43.478	11.86	4.21	43.62	3.51
452	464	6.436218	AGTGAGACTATGTGTGTGGTAATGTA	59.564	38.462	0.00	0.00	0.00	2.29
454	466	5.578336	CAGTGAGACTATGTGTGTGGTAATG	59.422	44.000	0.00	0.00	0.00	1.90
517	529	7.722285	GGTCTGAACTCCTCTACTATCATACTT	59.278	40.741	0.00	0.00	0.00	2.24
596	608	4.556104	GCACCGATTCGTATAGTCAAGCTA	60.556	45.833	5.20	0.00	0.00	3.32
638	650	4.602259	ACGTCACTGCGGTGGTGG	62.602	66.667	25.15	16.15	43.17	4.61
650	662	0.950836	CAAATCCCACTTGCACGTCA	59.049	50.000	0.00	0.00	0.00	4.35
695	707	8.259411	TGGTTTTTACTGTTGAACTGACTAGTA	58.741	33.333	9.24	0.00	35.69	1.82
838	852	3.235481	TGGGAGGCGGTTCGTTCA	61.235	61.111	0.00	0.00	0.00	3.18
894	909	0.816373	GGAACGAGGGAGAGGTGTAC	59.184	60.000	0.00	0.00	0.00	2.90
970	985	3.365265	GCGACTGTGGGCTTTGGG	61.365	66.667	0.00	0.00	0.00	4.12
1092	1107	4.582656	CCTTTGAGGGTTGTTGTGTATTCA	59.417	41.667	0.00	0.00	0.00	2.57
1095	1110	4.141251	ACTCCTTTGAGGGTTGTTGTGTAT	60.141	41.667	0.00	0.00	43.29	2.29
1116	1131	0.882042	CGTTGCTGTGGAGCTCAACT	60.882	55.000	21.84	0.00	46.39	3.16
1129	1144	1.203523	GATCTCCAGTGTCTCGTTGCT	59.796	52.381	0.00	0.00	0.00	3.91
1140	1155	1.485480	CTGGTGCAGATGATCTCCAGT	59.515	52.381	16.51	0.00	38.48	4.00
1150	1165	1.219124	CTGGTACGCTGGTGCAGAT	59.781	57.895	0.00	0.00	39.64	2.90
1283	1298	0.319555	GACGCACAACTGCAGGACTA	60.320	55.000	19.93	0.00	44.50	2.59
1439	1457	6.655848	ACTTTTCACAAACCACACTAGTACAA	59.344	34.615	0.00	0.00	0.00	2.41
1528	1546	8.527810	TCCGCAAAATTTTCCAAATAGTAATCT	58.472	29.630	0.00	0.00	0.00	2.40
1547	1565	7.214467	ACTTCAGAATTTAATCTTCCGCAAA	57.786	32.000	0.00	0.00	0.00	3.68
1738	1758	9.362151	AGTCTACTTTTGTTGAAATGGGATAAA	57.638	29.630	0.00	0.00	36.08	1.40
1767	1787	5.670485	TGTATGTTCTGCATTGGTACTAGG	58.330	41.667	0.00	0.00	38.94	3.02
2020	2047	1.134310	TCATGATGCAGCATCTCGGTT	60.134	47.619	31.02	11.83	41.06	4.44
2078	2105	4.336713	GGACAACTTCAGCTTCTCTTTGTT	59.663	41.667	0.00	0.00	0.00	2.83
2165	2192	4.828387	AGTCAAGGAGTCGTACTCTTTTCT	59.172	41.667	12.62	9.78	41.00	2.52
2198	2225	1.852157	AATGGGTGGATGACGCTGGT	61.852	55.000	0.00	0.00	38.35	4.00
2239	2266	3.508402	TGTAGTCTTCCTGCGTGTTGATA	59.492	43.478	0.00	0.00	0.00	2.15
2277	2304	2.031163	GGTTGTCTGGCAGCTCGT	59.969	61.111	10.34	0.00	0.00	4.18
2431	2458	4.283978	CAGGCTCTGATGTATCTTCATCCT	59.716	45.833	4.59	0.00	42.24	3.24
2473	2500	5.221501	ACAACAAGATAAAAGGCAAGCACAT	60.222	36.000	0.00	0.00	0.00	3.21
2532	2559	6.801575	TGACAAGCACGACATAATCATACTA	58.198	36.000	0.00	0.00	0.00	1.82
2656	2683	8.302438	CCATTCAGAAGCTACTTTTCAATTTCT	58.698	33.333	0.00	0.00	0.00	2.52
2657	2684	8.299570	TCCATTCAGAAGCTACTTTTCAATTTC	58.700	33.333	0.00	0.00	0.00	2.17
2857	2884	5.593679	AGAACTATGGTACTTGCGTGTAT	57.406	39.130	0.00	0.00	0.00	2.29
2880	2907	5.652014	TCAAGTGTCTTCTGGTGTCATTTTT	59.348	36.000	0.00	0.00	0.00	1.94
2999	3026	3.650942	TCCACCAGTAACTTGGACTGATT	59.349	43.478	4.38	0.00	46.01	2.57
3061	3092	4.660938	GCCTGACCTTGGGCGGTT	62.661	66.667	0.09	0.00	38.91	4.44
3268	3300	3.148279	CGCTAGTCGAGGGGGCTT	61.148	66.667	0.98	0.00	41.67	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.