AutoCloner

Multiple sequence alignment - TraesCS7D01G367600

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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	TraesCS7D01G367600	chr7D	100.000	2851	0	0	1	2851	475725135	475727985	0.000000e+00	5265.0
1	TraesCS7D01G367600	chr7D	90.476	63	6	0	2345	2407	6744967	6744905	1.820000e-12	84.2
2	TraesCS7D01G367600	chr7D	96.000	50	1	1	2358	2407	577847792	577847840	2.350000e-11	80.5
3	TraesCS7D01G367600	chr7B	93.942	2179	66	31	1	2153	499870735	499872873	0.000000e+00	3232.0
4	TraesCS7D01G367600	chr7B	90.000	50	4	1	2358	2407	641326192	641326240	2.370000e-06	63.9
5	TraesCS7D01G367600	chr7A	89.177	2199	121	57	1	2153	520336610	520334483	0.000000e+00	2634.0
6	TraesCS7D01G367600	chr7A	82.927	205	11	11	1959	2153	520315820	520315630	2.270000e-36	163.0
7	TraesCS7D01G367600	chr5B	79.045	377	47	20	2484	2838	22759692	22759326	2.210000e-56	230.0
8	TraesCS7D01G367600	chr5B	89.655	58	6	0	2350	2407	185218510	185218453	1.100000e-09	75.0
9	TraesCS7D01G367600	chr6A	91.379	58	5	0	2350	2407	107509477	107509420	2.350000e-11	80.5
10	TraesCS7D01G367600	chr2A	91.489	47	4	0	2355	2401	764701081	764701127	6.590000e-07	65.8
11	TraesCS7D01G367600	chr5D	86.667	60	4	3	2346	2403	449506580	449506523	2.370000e-06	63.9
12	TraesCS7D01G367600	chr5D	92.308	39	1	1	2365	2403	449506500	449506464	1.000000e-03	54.7
13	TraesCS7D01G367600	chr3B	100.000	32	0	0	2370	2401	736323880	736323849	3.070000e-05	60.2

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	TraesCS7D01G367600	chr7D	475725135	475727985	2850	False	5265	5265	100.000	1	2851	1	chr7D.!!$F1	2850
1	TraesCS7D01G367600	chr7B	499870735	499872873	2138	False	3232	3232	93.942	1	2153	1	chr7B.!!$F1	2152
2	TraesCS7D01G367600	chr7A	520334483	520336610	2127	True	2634	2634	89.177	1	2153	1	chr7A.!!$R2	2152

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
771	802	0.250038	GCTAAGAGATCGCCATGGCA	60.25	55.0	34.93	22.41	42.06	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2306	2382	0.029834	GCCTAGGTTGATGCGCAATG	59.97	55.0	17.11	0.0	39.03	2.82	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
91	93	6.019479	CAGTGATCAAATCGAACTAAGTAGGC	60.019	42.308	0.00	0.00	0.00	3.93
93	95	3.777478	TCAAATCGAACTAAGTAGGCCG	58.223	45.455	0.00	0.00	0.00	6.13
378	387	2.167662	AGGACCAAAACATTAAGGGCG	58.832	47.619	0.00	0.00	0.00	6.13
432	441	3.214328	AGCGCCGAATCCAATTTAATCT	58.786	40.909	2.29	0.00	0.00	2.40
526	536	1.045407	AGACTAACCTGCACCGAACA	58.955	50.000	0.00	0.00	0.00	3.18
591	602	5.163301	GGCAACTAGAGTATCAATCCCTCAA	60.163	44.000	0.00	0.00	37.82	3.02
592	603	6.349300	GCAACTAGAGTATCAATCCCTCAAA	58.651	40.000	0.00	0.00	37.82	2.69
769	800	0.683973	AGGCTAAGAGATCGCCATGG	59.316	55.000	7.63	7.63	46.14	3.66
770	801	0.952984	GGCTAAGAGATCGCCATGGC	60.953	60.000	27.67	27.67	43.25	4.40
771	802	0.250038	GCTAAGAGATCGCCATGGCA	60.250	55.000	34.93	22.41	42.06	4.92
813	852	3.067480	GCATTGATGGCGGGTGGTG	62.067	63.158	0.00	0.00	0.00	4.17
943	989	0.400594	AAGGCACCCACTCAAGTACC	59.599	55.000	0.00	0.00	0.00	3.34
948	994	1.691976	CACCCACTCAAGTACCACTGA	59.308	52.381	0.00	0.00	0.00	3.41
959	1005	0.392706	TACCACTGACACTGCCACAG	59.607	55.000	0.00	0.00	37.52	3.66
981	1027	4.525100	AGTCCTCTTTGTCTCTACCACTTC	59.475	45.833	0.00	0.00	0.00	3.01
998	1044	2.229302	ACTTCGAGGAGTTCTTCGGAAG	59.771	50.000	11.54	11.54	44.21	3.46
1166	1212	8.327941	ACCTTGTTGCATATATAATACTGCTG	57.672	34.615	7.39	0.00	35.66	4.41
1187	1233	2.420022	GCCACGTACTTTTGCTGATCAT	59.580	45.455	0.00	0.00	0.00	2.45
1197	1243	2.541120	GCTGATCATGAGGCACGCC	61.541	63.158	0.09	0.00	0.00	5.68
1412	1461	0.321298	TCCTGCGAGTAAGGCAAACC	60.321	55.000	0.00	0.00	40.39	3.27
1505	1568	5.330455	TCTAACTGTAACTCTGCATCTGG	57.670	43.478	0.00	0.00	0.00	3.86
1592	1655	3.767268	ATCCTGGGCTCCCTCGGA	61.767	66.667	15.47	15.47	39.41	4.55
1605	1668	2.203640	TCGGAGAGGTGTGCCACT	60.204	61.111	0.00	0.00	38.43	4.00
1852	1915	0.256752	TACGCCTGCCACTACTAGGA	59.743	55.000	0.00	0.00	33.33	2.94
1853	1916	1.038130	ACGCCTGCCACTACTAGGAG	61.038	60.000	0.00	0.00	37.41	3.69

Showing 1 to 25 of 335 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	93	4.154737	TGCAGTGAAAAGATTCATCTTCGG	59.845	41.667	2.47	0.00	46.67	4.30
93	95	7.485277	CAGATTGCAGTGAAAAGATTCATCTTC	59.515	37.037	2.47	0.00	46.67	2.87
126	128	6.867662	ATCAATTTCTCTCGTGTTTTCTGT	57.132	33.333	0.00	0.00	0.00	3.41
211	219	9.970395	GATGGATTGCATGATCTACAAAATTAA	57.030	29.630	0.00	0.00	0.00	1.40
221	229	8.577296	CAGAAATTAAGATGGATTGCATGATCT	58.423	33.333	0.00	0.00	0.00	2.75
378	387	0.947244	CCCGCTATTTCATGGAGTGC	59.053	55.000	0.00	0.00	0.00	4.40
432	441	2.109387	CGGGTGTCGTTCCAACCA	59.891	61.111	7.22	0.00	42.70	3.67
602	613	6.744112	ACTCAAGTATGATAGCTGCTAGTTC	58.256	40.000	15.41	9.19	34.37	3.01
769	800	0.179702	TCATCCATCCAGCTCAGTGC	59.820	55.000	0.00	0.00	43.29	4.40
770	801	2.286872	GTTCATCCATCCAGCTCAGTG	58.713	52.381	0.00	0.00	0.00	3.66
771	802	1.211457	GGTTCATCCATCCAGCTCAGT	59.789	52.381	0.00	0.00	35.97	3.41
813	852	1.732417	CGGGTCGAGGGTAGTTAGCC	61.732	65.000	0.00	0.00	44.02	3.93
913	953	0.467290	GGGTGCCTTTGGACACTGAA	60.467	55.000	9.63	0.00	36.99	3.02
943	989	0.882042	GGACTGTGGCAGTGTCAGTG	60.882	60.000	12.56	3.06	45.44	3.66
948	994	0.839946	AAAGAGGACTGTGGCAGTGT	59.160	50.000	6.50	0.00	45.44	3.55
959	1005	4.616373	CGAAGTGGTAGAGACAAAGAGGAC	60.616	50.000	0.00	0.00	0.00	3.85
981	1027	1.174783	TCCTTCCGAAGAACTCCTCG	58.825	55.000	9.87	0.00	0.00	4.63
1163	1209	0.385974	CAGCAAAAGTACGTGGCAGC	60.386	55.000	0.00	0.00	0.00	5.25
1166	1212	1.804151	TGATCAGCAAAAGTACGTGGC	59.196	47.619	0.00	0.00	0.00	5.01
1187	1233	2.183300	GATACACGGCGTGCCTCA	59.817	61.111	37.21	21.21	36.98	3.86
1197	1243	4.016113	TGTTGAGATCGACAGATACACG	57.984	45.455	0.00	0.00	37.19	4.49
1361	1410	4.612412	GGGTCGACGGTGTTGGCA	62.612	66.667	9.92	0.00	0.00	4.92
1412	1461	4.753233	AGCAGATTATTATCTAGCGGCAG	58.247	43.478	1.45	0.00	39.11	4.85
1474	1528	6.647067	GCAGAGTTACAGTTAGAACAGATTGT	59.353	38.462	0.00	0.00	0.00	2.71
1476	1530	6.759272	TGCAGAGTTACAGTTAGAACAGATT	58.241	36.000	0.00	0.00	0.00	2.40

Showing 1 to 25 of 322 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.