AutoCloner

Multiple sequence alignment - TraesCS6D01G297200

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	TraesCS6D01G297200	chr6D	100.000	2924	0	0	1	2924	408215873	408212950	0.000000e+00	5400
1	TraesCS6D01G297200	chr6D	80.623	1445	231	33	1038	2452	408184687	408183262	0.000000e+00	1072
2	TraesCS6D01G297200	chr6D	75.670	448	101	8	1139	1582	420560696	420560253	1.760000e-52	217
3	TraesCS6D01G297200	chr6D	75.056	445	103	7	1139	1579	59087679	59088119	1.780000e-47	200
4	TraesCS6D01G297200	chr6B	91.162	2727	171	31	1	2686	612859820	612857123	0.000000e+00	3637
5	TraesCS6D01G297200	chr6B	80.329	1459	249	29	1025	2452	612849441	612847990	0.000000e+00	1070
6	TraesCS6D01G297200	chr6B	76.577	444	98	6	1139	1579	612743769	612744209	3.770000e-59	239
7	TraesCS6D01G297200	chr6B	87.179	195	16	5	2723	2916	612857130	612856944	2.280000e-51	213
8	TraesCS6D01G297200	chr6A	91.510	2497	138	29	227	2674	554305121	554302650	0.000000e+00	3369
9	TraesCS6D01G297200	chr6A	80.123	1464	240	35	1019	2452	553927432	553925990	0.000000e+00	1044
10	TraesCS6D01G297200	chr6A	90.411	292	26	1	1	292	554305402	554305113	1.640000e-102	383
11	TraesCS6D01G297200	chr6A	75.893	448	100	8	1139	1582	563486208	563485765	3.790000e-54	222
12	TraesCS6D01G297200	chr6A	94.574	129	7	0	2662	2790	553943086	553942958	1.780000e-47	200
13	TraesCS6D01G297200	chr6A	91.667	108	6	1	2662	2766	554302600	554302493	2.350000e-31	147
14	TraesCS6D01G297200	chr2B	73.370	721	168	24	1128	1836	405263712	405263004	2.250000e-61	246
15	TraesCS6D01G297200	chr7A	86.260	131	18	0	2322	2452	26978240	26978370	3.040000e-30	143

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	TraesCS6D01G297200	chr6D	408212950	408215873	2923	True	5400.000000	5400	100.0000	1	2924	1	chr6D.!!$R2	2923
1	TraesCS6D01G297200	chr6D	408183262	408184687	1425	True	1072.000000	1072	80.6230	1038	2452	1	chr6D.!!$R1	1414
2	TraesCS6D01G297200	chr6B	612856944	612859820	2876	True	1925.000000	3637	89.1705	1	2916	2	chr6B.!!$R2	2915
3	TraesCS6D01G297200	chr6B	612847990	612849441	1451	True	1070.000000	1070	80.3290	1025	2452	1	chr6B.!!$R1	1427
4	TraesCS6D01G297200	chr6A	554302493	554305402	2909	True	1299.666667	3369	91.1960	1	2766	3	chr6A.!!$R4	2765
5	TraesCS6D01G297200	chr6A	553925990	553927432	1442	True	1044.000000	1044	80.1230	1019	2452	1	chr6A.!!$R1	1433
6	TraesCS6D01G297200	chr2B	405263004	405263712	708	True	246.000000	246	73.3700	1128	1836	1	chr2B.!!$R1	708

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
282	339	0.037877	ACTCATGGCTTTCTGCTGCT	59.962	50.0	0.0	0.0	42.39	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1944	2047	0.532573	ACTCACTACGTGCTCCATGG	59.467	55.0	4.97	4.97	32.98	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	Hairpin	End Stability
42	43	2.680913	CCGTTCTTTCAGCAGCCGG	61.681	63.158	0.00	6.13
178	180	9.981114	AGTTTTCAGACCACCAAAATAAATAAG	57.019	29.630	0.00	1.73
203	205	4.424061	TTTGCTGTTGTCATACTCATGC	57.576	40.909	31.73	4.06
241	243	6.665992	ATAAGCGACTATGTTCCCATCTTA	57.334	37.500	32.29	2.10
249	306	7.148738	CGACTATGTTCCCATCTTATTTGATCG	60.149	40.741	32.29	3.69
257	314	7.109501	TCCCATCTTATTTGATCGAACTTTGA	58.890	34.615	0.00	2.69
270	327	6.539649	TCGAACTTTGAAGTAAACTCATGG	57.460	37.500	38.57	3.66
281	338	0.886563	AACTCATGGCTTTCTGCTGC	59.113	50.000	42.39	5.25
282	339	0.037877	ACTCATGGCTTTCTGCTGCT	59.962	50.000	42.39	4.24
317	374	4.051922	CTCACAACCAACTCAGACAGTAC	58.948	47.826	32.30	2.73
319	376	2.223971	ACAACCAACTCAGACAGTACCG	60.224	50.000	32.30	4.02
504	561	5.334879	CCAAAATACTCGTTTCTTGACTGGG	60.335	44.000	0.00	4.45
607	664	3.440173	CCCATTGTACTGCGAAACTGAAT	59.560	43.478	0.00	2.57
608	665	4.082787	CCCATTGTACTGCGAAACTGAATT	60.083	41.667	0.00	2.17
686	743	5.008619	AGTCGTCTTCTCTATGTCTACGA	57.991	43.478	35.73	3.43
687	744	5.045215	AGTCGTCTTCTCTATGTCTACGAG	58.955	45.833	38.41	4.18
695	752	8.994170	TCTTCTCTATGTCTACGAGTATGAATG	58.006	37.037	0.00	2.67
696	753	7.674471	TCTCTATGTCTACGAGTATGAATGG	57.326	40.000	0.00	3.16
698	755	7.173390	TCTCTATGTCTACGAGTATGAATGGTG	59.827	40.741	0.00	4.17
701	758	5.647589	TGTCTACGAGTATGAATGGTGTTC	58.352	41.667	0.00	3.18
702	759	5.417894	TGTCTACGAGTATGAATGGTGTTCT	59.582	40.000	0.00	3.01
712	769	5.261209	TGAATGGTGTTCTTTTGTTCCTG	57.739	39.130	0.00	3.86
723	780	0.596600	TTGTTCCTGCGACACTCGAC	60.597	55.000	43.74	4.20
724	781	1.007734	GTTCCTGCGACACTCGACA	60.008	57.895	43.74	4.35
725	782	1.007734	TTCCTGCGACACTCGACAC	60.008	57.895	43.74	3.67

Showing 1 to 25 of 94 entries

Previous1 2 3 4Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	1.377333	CCTGGAAAGAACCCTCGGC	60.377	63.158	0.00	0.00	0.00	5.54
178	180	4.797471	TGAGTATGACAACAGCAAAATGC	58.203	39.130	0.00	0.00	45.46	3.56
191	193	7.970614	TCGACATATGAATAGCATGAGTATGAC	59.029	37.037	10.38	0.00	37.87	3.06
241	243	8.836413	TGAGTTTACTTCAAAGTTCGATCAAAT	58.164	29.630	0.00	0.00	40.37	2.32
249	306	6.319141	AGCCATGAGTTTACTTCAAAGTTC	57.681	37.500	0.00	0.00	40.37	3.01
257	314	4.773323	GCAGAAAGCCATGAGTTTACTT	57.227	40.909	0.00	0.00	37.23	2.24
270	327	3.065786	TGCAACATATAGCAGCAGAAAGC	59.934	43.478	0.00	0.00	46.19	3.51
281	338	3.313526	GGTTGTGAGCCTGCAACATATAG	59.686	47.826	14.09	0.00	44.70	1.31
282	339	3.278574	GGTTGTGAGCCTGCAACATATA	58.721	45.455	14.09	0.00	44.70	0.86
295	352	3.185246	ACTGTCTGAGTTGGTTGTGAG	57.815	47.619	0.00	0.00	0.00	3.51
317	374	1.899437	TTTGTAGCCTCAGCCTCCGG	61.899	60.000	0.00	0.00	41.25	5.14
319	376	0.324943	TGTTTGTAGCCTCAGCCTCC	59.675	55.000	0.00	0.00	41.25	4.30
397	454	2.140065	TCAGTTCAGCGAGTCAGTTG	57.860	50.000	0.00	0.00	0.00	3.16
607	664	4.555262	GAATTCCATTTTCTGGCGTGAAA	58.445	39.130	0.00	2.10	45.52	2.69
608	665	3.365868	CGAATTCCATTTTCTGGCGTGAA	60.366	43.478	0.00	0.00	45.52	3.18
653	710	0.528470	AAGACGACTACCAGCAGAGC	59.472	55.000	0.00	0.00	0.00	4.09
654	711	2.088423	AGAAGACGACTACCAGCAGAG	58.912	52.381	0.00	0.00	0.00	3.35
655	712	2.085320	GAGAAGACGACTACCAGCAGA	58.915	52.381	0.00	0.00	0.00	4.26
661	718	5.175491	CGTAGACATAGAGAAGACGACTACC	59.825	48.000	0.00	0.00	0.00	3.18
686	743	6.777580	AGGAACAAAAGAACACCATTCATACT	59.222	34.615	0.00	0.00	0.00	2.12
687	744	6.863126	CAGGAACAAAAGAACACCATTCATAC	59.137	38.462	0.00	0.00	0.00	2.39
695	752	1.673920	TCGCAGGAACAAAAGAACACC	59.326	47.619	0.00	0.00	0.00	4.16
696	753	2.096819	TGTCGCAGGAACAAAAGAACAC	59.903	45.455	0.00	0.00	0.00	3.32
698	755	2.354821	AGTGTCGCAGGAACAAAAGAAC	59.645	45.455	0.00	0.00	0.00	3.01
701	758	1.070577	CGAGTGTCGCAGGAACAAAAG	60.071	52.381	0.00	0.00	31.14	2.27

Showing 1 to 25 of 94 entries

Previous1 2 3 4Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.