AutoCloner

Multiple sequence alignment - TraesCS4B01G319700

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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	TraesCS4B01G319700	chr4B	100.000	3170	0	0	1	3170	610436485	610433316	0.000000e+00	5854.0
1	TraesCS4B01G319700	chr4B	75.598	209	40	11	1617	1820	531094081	531094283	3.370000e-15	93.5
2	TraesCS4B01G319700	chr4D	89.449	2360	119	53	559	2891	481448896	481446640	0.000000e+00	2859.0
3	TraesCS4B01G319700	chr4D	89.236	576	23	13	1	551	481449498	481448937	0.000000e+00	684.0
4	TraesCS4B01G319700	chr4D	91.071	280	25	0	2891	3170	481440496	481440217	2.310000e-101	379.0
5	TraesCS4B01G319700	chr5A	87.466	1827	127	56	259	2033	661220799	661222575	0.000000e+00	2012.0
6	TraesCS4B01G319700	chr5A	90.395	531	40	3	2647	3169	661223280	661223807	0.000000e+00	688.0
7	TraesCS4B01G319700	chr5A	89.474	456	25	14	2192	2642	661222805	661223242	3.570000e-154	555.0
8	TraesCS4B01G319700	chr5A	91.000	100	6	1	2101	2197	661222603	661222702	7.130000e-27	132.0
9	TraesCS4B01G319700	chr5A	98.246	57	1	0	1	57	661220613	661220669	2.010000e-17	100.0
10	TraesCS4B01G319700	chr4A	75.641	234	43	14	1617	1843	34294923	34295149	1.560000e-18	104.0

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	TraesCS4B01G319700	chr4B	610433316	610436485	3169	True	5854.0	5854	100.0000	1	3170	1	chr4B.!!$R1	3169
1	TraesCS4B01G319700	chr4D	481446640	481449498	2858	True	1771.5	2859	89.3425	1	2891	2	chr4D.!!$R2	2890
2	TraesCS4B01G319700	chr5A	661220613	661223807	3194	False	697.4	2012	91.3162	1	3169	5	chr5A.!!$F1	3168

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
620	695	0.320421	TTGCTTGCGTGGACTAGGAC	60.32	55.0	0.0	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2293	2520	0.977627	ACTCGGCCTCATGATGGTCA	60.978	55.0	13.82	3.55	0.0	4.02	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)

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	73	4.819761	TCAGCTCATCACGGCCGC	62.820	66.667	28.58	6.76	0.00	6.53
92	99	3.261981	ACCTAACCAACCGATGCTTAG	57.738	47.619	0.00	0.00	30.19	2.18
100	107	5.797051	ACCAACCGATGCTTAGTTAACTAA	58.203	37.500	23.31	23.31	36.99	2.24
101	108	6.412214	ACCAACCGATGCTTAGTTAACTAAT	58.588	36.000	24.61	12.93	37.75	1.73
102	109	7.558604	ACCAACCGATGCTTAGTTAACTAATA	58.441	34.615	24.61	17.85	37.75	0.98
217	232	5.294306	GTCGAGCAAATGAGGTATGATGAAA	59.706	40.000	0.00	0.00	0.00	2.69
330	352	1.034838	AGCAAACAAAGTGGCGTCCA	61.035	50.000	0.00	0.00	0.00	4.02
333	355	1.021968	AAACAAAGTGGCGTCCAGTC	58.978	50.000	6.67	0.00	35.94	3.51
342	364	2.425592	CGTCCAGTCCCAGCACAA	59.574	61.111	0.00	0.00	0.00	3.33
343	365	1.669115	CGTCCAGTCCCAGCACAAG	60.669	63.158	0.00	0.00	0.00	3.16
347	369	1.526686	CAGTCCCAGCACAAGCACA	60.527	57.895	0.00	0.00	45.49	4.57
370	392	2.417933	CGTTTCTTCCAAGGCATCTCAG	59.582	50.000	0.00	0.00	0.00	3.35
377	399	2.367894	TCCAAGGCATCTCAGCTCATAG	59.632	50.000	0.00	0.00	34.17	2.23
378	400	2.104451	CCAAGGCATCTCAGCTCATAGT	59.896	50.000	0.00	0.00	34.17	2.12
379	401	3.323115	CCAAGGCATCTCAGCTCATAGTA	59.677	47.826	0.00	0.00	34.17	1.82
380	402	4.558178	CAAGGCATCTCAGCTCATAGTAG	58.442	47.826	0.00	0.00	34.17	2.57
381	403	3.843422	AGGCATCTCAGCTCATAGTAGT	58.157	45.455	0.00	0.00	34.17	2.73
382	404	4.991776	AGGCATCTCAGCTCATAGTAGTA	58.008	43.478	0.00	0.00	34.17	1.82
383	405	5.009631	AGGCATCTCAGCTCATAGTAGTAG	58.990	45.833	0.00	0.00	34.17	2.57
384	406	4.764823	GGCATCTCAGCTCATAGTAGTAGT	59.235	45.833	0.00	0.00	34.17	2.73
385	407	5.941058	GGCATCTCAGCTCATAGTAGTAGTA	59.059	44.000	0.00	0.00	34.17	1.82
445	476	8.737168	TCTGATCCACAAATCAAATAGGTTAG	57.263	34.615	0.00	0.00	35.32	2.34
446	477	8.328758	TCTGATCCACAAATCAAATAGGTTAGT	58.671	33.333	0.00	0.00	35.32	2.24
447	478	9.613428	CTGATCCACAAATCAAATAGGTTAGTA	57.387	33.333	0.00	0.00	35.32	1.82
448	479	9.391006	TGATCCACAAATCAAATAGGTTAGTAC	57.609	33.333	0.00	0.00	32.80	2.73

Showing 1 to 25 of 111 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	73	3.427503	GCATCGGTTGGTTAGGTTTCATG	60.428	47.826	0.00	0.00	0.00	3.07
67	74	2.752903	GCATCGGTTGGTTAGGTTTCAT	59.247	45.455	0.00	0.00	0.00	2.57
191	206	4.406648	TCATACCTCATTTGCTCGACAT	57.593	40.909	0.00	0.00	0.00	3.06
217	232	2.159448	CGTCTCTCTCTCGTTGCTTCAT	60.159	50.000	0.00	0.00	0.00	2.57
330	352	1.228063	CTGTGCTTGTGCTGGGACT	60.228	57.895	0.00	0.00	40.48	3.85
333	355	4.034258	CGCTGTGCTTGTGCTGGG	62.034	66.667	0.00	0.00	40.48	4.45
342	364	0.947244	CTTGGAAGAAACGCTGTGCT	59.053	50.000	0.00	0.00	0.00	4.40
343	365	0.040067	CCTTGGAAGAAACGCTGTGC	60.040	55.000	0.00	0.00	0.00	4.57
347	369	1.168714	GATGCCTTGGAAGAAACGCT	58.831	50.000	0.00	0.00	0.00	5.07
377	399	9.856803	GTCGCTACAAACTAATACTACTACTAC	57.143	37.037	0.00	0.00	0.00	2.73
378	400	9.599866	TGTCGCTACAAACTAATACTACTACTA	57.400	33.333	0.00	0.00	30.91	1.82
379	401	8.498054	TGTCGCTACAAACTAATACTACTACT	57.502	34.615	0.00	0.00	30.91	2.57
380	402	8.394121	ACTGTCGCTACAAACTAATACTACTAC	58.606	37.037	0.00	0.00	34.49	2.73
381	403	8.498054	ACTGTCGCTACAAACTAATACTACTA	57.502	34.615	0.00	0.00	34.49	1.82
382	404	7.388460	ACTGTCGCTACAAACTAATACTACT	57.612	36.000	0.00	0.00	34.49	2.57
383	405	7.854916	CCTACTGTCGCTACAAACTAATACTAC	59.145	40.741	0.00	0.00	34.49	2.73
384	406	7.770433	TCCTACTGTCGCTACAAACTAATACTA	59.230	37.037	0.00	0.00	34.49	1.82
385	407	6.600822	TCCTACTGTCGCTACAAACTAATACT	59.399	38.462	0.00	0.00	34.49	2.12
445	476	6.992715	GGATGGGCCTGATTATACATATGTAC	59.007	42.308	17.69	6.04	32.72	2.90
446	477	6.101150	GGGATGGGCCTGATTATACATATGTA	59.899	42.308	17.65	17.65	36.66	2.29
447	478	5.103940	GGGATGGGCCTGATTATACATATGT	60.104	44.000	13.93	13.93	36.66	2.29
448	479	5.103982	TGGGATGGGCCTGATTATACATATG	60.104	44.000	4.53	0.00	36.66	1.78
449	480	5.045831	TGGGATGGGCCTGATTATACATAT	58.954	41.667	4.53	0.00	36.66	1.78
450	481	4.443658	TGGGATGGGCCTGATTATACATA	58.556	43.478	4.53	0.00	36.66	2.29
451	482	3.268146	TGGGATGGGCCTGATTATACAT	58.732	45.455	4.53	0.00	36.66	2.29

Showing 1 to 25 of 136 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.