AutoCloner

Multiple sequence alignment - TraesCS6B01G246200

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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	TraesCS6B01G246200	chr6B	100.000	4772	0	0	1	4772	438917401	438912630	0.000000e+00	8813.0
1	TraesCS6B01G246200	chr6A	93.994	4695	153	41	64	4689	398637533	398642167	0.000000e+00	6988.0
2	TraesCS6B01G246200	chr6A	93.333	60	4	0	4713	4772	398974442	398974501	6.580000e-14	89.8
3	TraesCS6B01G246200	chr6D	94.190	2599	77	21	25	2583	277023781	277021217	0.000000e+00	3895.0
4	TraesCS6B01G246200	chr6D	94.991	2196	84	9	2586	4772	277021131	277018953	0.000000e+00	3422.0
5	TraesCS6B01G246200	chr3B	81.921	177	24	8	2212	2385	413032621	413032450	4.980000e-30	143.0
6	TraesCS6B01G246200	chr5B	76.639	244	33	13	2161	2389	281627779	281627545	3.900000e-21	113.0
7	TraesCS6B01G246200	chr5B	86.667	75	6	4	3124	3195	11043577	11043504	3.960000e-11	80.5
8	TraesCS6B01G246200	chr7D	86.000	100	12	2	2212	2310	598431028	598431126	6.530000e-19	106.0

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	TraesCS6B01G246200	chr6B	438912630	438917401	4771	True	8813.0	8813	100.0000	1	4772	1	chr6B.!!$R1	4771
1	TraesCS6B01G246200	chr6A	398637533	398642167	4634	False	6988.0	6988	93.9940	64	4689	1	chr6A.!!$F1	4625
2	TraesCS6B01G246200	chr6D	277018953	277023781	4828	True	3658.5	3895	94.5905	25	4772	2	chr6D.!!$R1	4747

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
547	572	0.104120	CCATCCATCTGGTTCGCGTA	59.896	55.000	5.77	0.00	36.34	4.42	F
725	751	1.202200	TGCCTTTTCGAAACAACGTGG	60.202	47.619	10.79	7.35	34.70	4.94	F
1123	1172	1.531149	CTGTTGTAAGCGTGTTCCTGG	59.469	52.381	0.00	0.00	0.00	4.45	F
2450	2513	0.250727	TACACCCCTTGCAGCACTTC	60.251	55.000	0.00	0.00	0.00	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2344	2407	0.610509	TAAGGCGCCCATGCTTTTCA	60.611	50.000	26.15	35.6	2.69	R
2434	2497	1.529244	GTGAAGTGCTGCAAGGGGT	60.529	57.895	2.77	0.0	4.95	R
3078	3226	4.329545	GGCTGCCGGTTCACTCCA	62.330	66.667	1.35	0.0	3.86	R
4033	4183	0.029300	CAAACCCGCACAGTTCACAG	59.971	55.000	0.00	0.0	3.66	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
32	33	2.210711	CCCCAGGGCTCTATCCGTC	61.211	68.421	0.00	0.00	0.00	4.79
247	250	1.264288	GAACACGGACAAGCCAAGAAG	59.736	52.381	0.00	0.00	35.94	2.85
315	318	2.752238	CCTCTCGCGTCCTGACCT	60.752	66.667	5.77	0.00	0.00	3.85
442	467	6.129179	CCATAGGGTTTTGATTGAGGTATGT	58.871	40.000	0.00	0.00	0.00	2.29
516	541	2.270850	GGGCGCACCACCATCTAA	59.729	61.111	10.83	0.00	39.85	2.10
546	571	1.153369	CCATCCATCTGGTTCGCGT	60.153	57.895	5.77	0.00	36.34	6.01
547	572	0.104120	CCATCCATCTGGTTCGCGTA	59.896	55.000	5.77	0.00	36.34	4.42
548	573	1.270305	CCATCCATCTGGTTCGCGTAT	60.270	52.381	5.77	0.00	36.34	3.06
658	683	2.093625	TCTGAACACGCGTTGCATATTC	59.906	45.455	10.22	7.55	34.75	1.75
725	751	1.202200	TGCCTTTTCGAAACAACGTGG	60.202	47.619	10.79	7.35	34.70	4.94
756	793	5.009631	TGTAAGCTGCAATTTCTACACCAT	58.990	37.500	1.02	0.00	0.00	3.55
842	879	5.525199	ACAATGTGGTCCGATGTTAAAAAC	58.475	37.500	0.00	0.00	0.00	2.43
888	926	5.283060	AGTTTCTTTACAGCACAATAGCG	57.717	39.130	0.00	0.00	40.15	4.26
1101	1139	8.122952	CGAAACTAATTCATGGTATGGAAGTTC	58.877	37.037	0.00	0.00	37.96	3.01
1123	1172	1.531149	CTGTTGTAAGCGTGTTCCTGG	59.469	52.381	0.00	0.00	0.00	4.45
1139	1188	2.401699	CTGGTGTGCAGGCAAGAGGA	62.402	60.000	0.00	0.00	0.00	3.71
1530	1579	4.601019	CGGACCTTTTCAATATGTGCATC	58.399	43.478	0.00	0.00	0.00	3.91
2075	2124	9.267084	TCCTTTTACCACAAAAGAAATATTTGC	57.733	29.630	5.17	0.00	40.58	3.68
2208	2259	4.760683	CGCACACATTTCAAAAATCAACC	58.239	39.130	0.00	0.00	0.00	3.77
2284	2347	9.695526	TCATATTCAAAAGAACTTTCAATGGTG	57.304	29.630	0.21	6.56	31.45	4.17
2449	2512	0.405585	ATACACCCCTTGCAGCACTT	59.594	50.000	0.00	0.00	0.00	3.16
2450	2513	0.250727	TACACCCCTTGCAGCACTTC	60.251	55.000	0.00	0.00	0.00	3.01
2683	2829	9.665264	GTCCTGTTTCAGTTTATTTACTTTGAG	57.335	33.333	0.00	0.00	0.00	3.02
2733	2880	7.010697	TGCATACTCGTATTAAACAATGGTG	57.989	36.000	0.00	0.00	0.00	4.17
2898	3046	8.666129	TTCTTCTCCTCTACTTATTCTTTGGA	57.334	34.615	0.00	0.00	0.00	3.53

Showing 1 to 25 of 57 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	1.623834	GGATAGAGCCCTGGGGATAGG	60.624	61.905	16.03	0.00	37.50	2.57
10	11	1.872773	GGATAGAGCCCTGGGGATAG	58.127	60.000	16.03	0.00	37.50	2.08
11	12	0.041238	CGGATAGAGCCCTGGGGATA	59.959	60.000	16.03	0.00	37.50	2.59
12	13	1.229336	CGGATAGAGCCCTGGGGAT	60.229	63.158	16.03	2.12	37.50	3.85
13	14	2.201490	CGGATAGAGCCCTGGGGA	59.799	66.667	16.03	0.00	37.50	4.81
14	15	2.122813	ACGGATAGAGCCCTGGGG	60.123	66.667	16.03	4.75	38.57	4.96
15	16	1.152440	AGACGGATAGAGCCCTGGG	60.152	63.158	8.86	8.86	0.00	4.45
16	17	1.519751	CGAGACGGATAGAGCCCTGG	61.520	65.000	0.00	0.00	0.00	4.45
17	18	1.953017	CGAGACGGATAGAGCCCTG	59.047	63.158	0.00	0.00	0.00	4.45
18	19	4.484987	CGAGACGGATAGAGCCCT	57.515	61.111	0.00	0.00	0.00	5.19
39	40	1.864082	GTTTTCATTTGTTGTGGCCCG	59.136	47.619	0.00	0.00	0.00	6.13
137	140	2.670148	CGGTGGGAAGGAAGAGGGG	61.670	68.421	0.00	0.00	0.00	4.79
247	250	0.670854	GAGACGCTGGGGAGTTGTTC	60.671	60.000	0.00	0.00	0.00	3.18
315	318	5.222171	GGAGGTAGGAGAGATTTAGAGCCTA	60.222	48.000	0.00	0.00	0.00	3.93
516	541	1.355718	ATGGATGGACAGGGCGGATT	61.356	55.000	0.00	0.00	0.00	3.01
546	571	6.628398	GCCCGAGAAGAAGAAGAAGAAGAATA	60.628	42.308	0.00	0.00	0.00	1.75
547	572	5.729510	CCCGAGAAGAAGAAGAAGAAGAAT	58.270	41.667	0.00	0.00	0.00	2.40
548	573	4.561734	GCCCGAGAAGAAGAAGAAGAAGAA	60.562	45.833	0.00	0.00	0.00	2.52
725	751	4.691860	AATTGCAGCTTACACATCAGAC	57.308	40.909	0.00	0.00	0.00	3.51
888	926	3.608474	GCAATACACAACGAGTTCCCAAC	60.608	47.826	0.00	0.00	0.00	3.77
947	985	4.398044	TCGAAAGCCTGGATGGAATTAAAC	59.602	41.667	0.00	0.00	38.35	2.01
953	991	0.253044	CCTCGAAAGCCTGGATGGAA	59.747	55.000	0.00	0.00	38.35	3.53
1101	1139	0.872388	GGAACACGCTTACAACAGGG	59.128	55.000	0.00	0.00	0.00	4.45
1123	1172	1.072159	AGTCCTCTTGCCTGCACAC	59.928	57.895	0.00	0.00	0.00	3.82
1139	1188	2.434884	CGCGTTCAGCCCATCAGT	60.435	61.111	0.00	0.00	44.76	3.41

Showing 1 to 25 of 67 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.