AutoCloner

Multiple sequence alignment - TraesCS2A01G436700

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	TraesCS2A01G436700	chr2A	100.000	4274	0	0	1	4274	688623665	688619392	0.000000e+00	7893.0
1	TraesCS2A01G436700	chr2A	100.000	31	0	0	2716	2746	688620526	688620496	1.660000e-04	58.4
2	TraesCS2A01G436700	chr2A	100.000	31	0	0	3140	3170	688620950	688620920	1.660000e-04	58.4
3	TraesCS2A01G436700	chr2B	89.550	1933	121	38	2	1880	651358728	651360633	0.000000e+00	2375.0
4	TraesCS2A01G436700	chr2B	90.555	847	55	17	1971	2802	651360755	651361591	0.000000e+00	1098.0
5	TraesCS2A01G436700	chr2B	93.020	702	31	12	2928	3614	651361788	651362486	0.000000e+00	1009.0
6	TraesCS2A01G436700	chr2B	88.226	637	42	12	3662	4269	651362574	651363206	0.000000e+00	730.0
7	TraesCS2A01G436700	chr2B	97.436	39	1	0	3137	3175	651361499	651361537	2.760000e-07	67.6
8	TraesCS2A01G436700	chr2D	93.290	1550	81	12	1971	3502	544883275	544884819	0.000000e+00	2265.0
9	TraesCS2A01G436700	chr2D	91.945	807	50	11	2	803	544880522	544881318	0.000000e+00	1116.0
10	TraesCS2A01G436700	chr2D	95.865	653	25	2	3620	4272	544885000	544885650	0.000000e+00	1055.0
11	TraesCS2A01G436700	chr2D	93.893	524	22	5	926	1442	544882005	544882525	0.000000e+00	782.0
12	TraesCS2A01G436700	chr2D	88.827	179	19	1	1507	1685	544882686	544882863	7.200000e-53	219.0
13	TraesCS2A01G436700	chr2D	94.872	39	2	0	3137	3175	544884025	544884063	1.280000e-05	62.1
14	TraesCS2A01G436700	chrUn	92.857	42	3	0	3621	3662	216303000	216303041	1.280000e-05	62.1
15	TraesCS2A01G436700	chr5A	86.207	58	6	2	3605	3662	585092658	585092713	1.280000e-05	62.1
16	TraesCS2A01G436700	chr4D	92.857	42	3	0	3621	3662	131330633	131330674	1.280000e-05	62.1
17	TraesCS2A01G436700	chr7A	92.500	40	3	0	3620	3659	121396066	121396105	1.660000e-04	58.4

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	TraesCS2A01G436700	chr2A	688619392	688623665	4273	True	2669.933333	7893	100.000000	1	4274	3	chr2A.!!$R1	4273
1	TraesCS2A01G436700	chr2B	651358728	651363206	4478	False	1055.920000	2375	91.757400	2	4269	5	chr2B.!!$F1	4267
2	TraesCS2A01G436700	chr2D	544880522	544885650	5128	False	916.516667	2265	93.115333	2	4272	6	chr2D.!!$F1	4270

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
136	137	0.033894	GCCCTGGGGTAATTTCCGAA	60.034	55.0	16.03	0.00	37.65	4.30	F
1445	2045	0.730834	CGTGAACTGGAGTCTCAGCG	60.731	60.0	1.47	1.93	38.26	5.18	F
1661	2366	0.173708	CCTTCCCTCTGTGACTACGC	59.826	60.0	0.00	0.00	0.00	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1642	2347	0.173708	GCGTAGTCACAGAGGGAAGG	59.826	60.0	0.00	3.46	R
2314	3192	0.512952	GCTACAGTTGCCACGTTCAG	59.487	55.0	0.00	3.02	R
3509	4503	0.179113	CCGGGTGGCAAATTACATGC	60.179	55.0	43.08	4.06	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
75	76	1.026718	CGATGGGGAGTCACCAAAGC	61.027	60.000	20.41	10.13	42.17	3.51
108	109	4.008453	CCTCCCTATGGCATGGGT	57.992	61.111	25.85	0.00	43.74	4.51
132	133	1.685180	GGAGTGCCCTGGGGTAATTTC	60.685	57.143	16.03	0.00	37.65	2.17
134	135	1.035385	GTGCCCTGGGGTAATTTCCG	61.035	60.000	16.03	0.00	37.65	4.30
135	136	1.208844	TGCCCTGGGGTAATTTCCGA	61.209	55.000	16.03	0.00	37.65	4.55
136	137	0.033894	GCCCTGGGGTAATTTCCGAA	60.034	55.000	16.03	0.00	37.65	4.30
138	139	1.683938	CCCTGGGGTAATTTCCGAACC	60.684	57.143	4.27	0.00	0.00	3.62
147	148	3.842732	AATTTCCGAACCCTTTTAGCG	57.157	42.857	0.00	0.00	0.00	4.26
150	151	0.906775	TCCGAACCCTTTTAGCGGAT	59.093	50.000	0.00	0.00	45.18	4.18
152	153	1.669265	CCGAACCCTTTTAGCGGATTC	59.331	52.381	0.00	0.00	44.43	2.52
165	166	1.726853	CGGATTCGAGAAGCACCTTT	58.273	50.000	3.47	0.00	39.00	3.11
183	184	8.360390	AGCACCTTTTCTTTTGGTATTCTTAAG	58.640	33.333	0.00	0.00	32.13	1.85
184	185	8.141909	GCACCTTTTCTTTTGGTATTCTTAAGT	58.858	33.333	1.63	0.00	32.13	2.24
211	212	1.490490	TCCTAATTTGCGCAGGAGGAT	59.510	47.619	21.01	6.92	33.48	3.24
286	287	9.631452	GAAAAGATTATGGGAGCATATTTTAGC	57.369	33.333	0.00	0.00	0.00	3.09
373	374	3.065371	CGATGGTTCTGGCTATTGGTTTC	59.935	47.826	0.00	0.00	0.00	2.78
442	443	3.259374	TCCCTGATTGTCAAGACAGTCTC	59.741	47.826	21.23	12.38	45.00	3.36
529	530	1.448985	TTTCGAGCCTTTGGAATCCG	58.551	50.000	0.00	0.00	0.00	4.18
539	540	1.541310	TTGGAATCCGGACTCAGCGT	61.541	55.000	15.87	0.00	0.00	5.07
540	541	1.519455	GGAATCCGGACTCAGCGTG	60.519	63.158	15.87	0.00	0.00	5.34
541	542	1.215647	GAATCCGGACTCAGCGTGT	59.784	57.895	6.12	0.00	0.00	4.49
673	678	4.042271	TGGGAGTTTTTCCTTGATACCC	57.958	45.455	0.00	0.00	45.98	3.69
687	692	3.334691	TGATACCCGCAGAAACTGAAAG	58.665	45.455	2.81	0.00	42.29	2.62
699	704	5.300286	CAGAAACTGAAAGGTTTCCAGTGAT	59.700	40.000	14.00	0.00	45.56	3.06
715	720	4.404640	CAGTGATATTCATGGGCTCCAAT	58.595	43.478	0.00	0.00	36.95	3.16

Showing 1 to 25 of 140 entries

Previous1 2 3 4 5 6Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.824904	ATCTCGGTTGAAGAAATTGATGG	57.175	39.130	0.00	0.00	0.00	3.51
132	133	1.669265	GAATCCGCTAAAAGGGTTCGG	59.331	52.381	0.00	0.00	38.88	4.30
134	135	2.608090	CTCGAATCCGCTAAAAGGGTTC	59.392	50.000	0.00	0.00	43.58	3.62
135	136	2.235402	TCTCGAATCCGCTAAAAGGGTT	59.765	45.455	0.00	0.00	34.21	4.11
136	137	1.829222	TCTCGAATCCGCTAAAAGGGT	59.171	47.619	0.00	0.00	35.37	4.34
138	139	2.285488	GCTTCTCGAATCCGCTAAAAGG	59.715	50.000	0.00	0.00	35.37	3.11
147	148	3.339141	AGAAAAGGTGCTTCTCGAATCC	58.661	45.455	0.00	0.00	0.00	3.01
150	151	4.202010	CCAAAAGAAAAGGTGCTTCTCGAA	60.202	41.667	0.00	0.00	31.85	3.71
152	153	3.066760	ACCAAAAGAAAAGGTGCTTCTCG	59.933	43.478	0.00	0.00	31.85	4.04
183	184	4.403453	CTGCGCAAATTAGGACAACTTAC	58.597	43.478	13.05	0.00	0.00	2.34
184	185	3.438781	CCTGCGCAAATTAGGACAACTTA	59.561	43.478	13.05	0.00	33.33	2.24
211	212	1.017177	GTAAACGGATGCACGCCTGA	61.017	55.000	5.94	0.00	37.37	3.86
286	287	1.519455	GCATTCCTCCGAGTCCACG	60.519	63.158	0.00	0.00	0.00	4.94
373	374	5.662211	CAACATTGCAGGAAAGAAAAAGG	57.338	39.130	0.00	0.00	0.00	3.11
521	522	1.982395	ACGCTGAGTCCGGATTCCA	60.982	57.895	22.80	12.81	0.00	3.53
529	530	1.813786	ACTCTAAGACACGCTGAGTCC	59.186	52.381	0.00	0.00	36.68	3.85
539	540	7.179966	TCTGGGATAGTTGTAACTCTAAGACA	58.820	38.462	0.00	0.00	40.37	3.41
540	541	7.642082	TCTGGGATAGTTGTAACTCTAAGAC	57.358	40.000	0.00	0.00	40.37	3.01
541	542	8.840200	AATCTGGGATAGTTGTAACTCTAAGA	57.160	34.615	0.00	0.52	40.37	2.10
580	585	4.960938	ACAGTGAGAGCAATGAACAGTTA	58.039	39.130	0.00	0.00	42.40	2.24
687	692	3.319122	GCCCATGAATATCACTGGAAACC	59.681	47.826	0.00	0.00	31.23	3.27
699	704	3.969466	TTGGATTGGAGCCCATGAATA	57.031	42.857	0.00	0.00	31.53	1.75
715	720	3.551846	GGGAATTTCGGCTCTATTTGGA	58.448	45.455	0.00	0.00	0.00	3.53
717	722	3.555966	AGGGGAATTTCGGCTCTATTTG	58.444	45.455	0.00	0.00	0.00	2.32
718	723	3.953542	AGGGGAATTTCGGCTCTATTT	57.046	42.857	0.00	0.00	0.00	1.40

Showing 1 to 25 of 141 entries

Previous1 2 3 4 5 6Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.