AutoCloner

Multiple sequence alignment - TraesCS2B01G434300

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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	TraesCS2B01G434300	chr2B	100.000	2828	0	0	1	2828	624356768	624353941	0.000000e+00	5223
1	TraesCS2B01G434300	chr2D	92.321	1719	73	24	142	1830	527294933	527293244	0.000000e+00	2388
2	TraesCS2B01G434300	chr2D	94.199	362	15	3	2472	2828	527292647	527292287	5.330000e-152	547
3	TraesCS2B01G434300	chr2D	90.808	359	17	7	1923	2267	527293210	527292854	1.530000e-127	466
4	TraesCS2B01G434300	chr2A	92.000	1325	76	18	585	1889	672293169	672291855	0.000000e+00	1832
5	TraesCS2B01G434300	chr2A	88.473	347	25	11	142	484	672293579	672293244	3.390000e-109	405
6	TraesCS2B01G434300	chr2A	86.761	355	26	12	1931	2267	672291850	672291499	2.660000e-100	375
7	TraesCS2B01G434300	chr2A	83.123	397	29	15	2470	2828	672291278	672290882	7.550000e-86	327
8	TraesCS2B01G434300	chr6D	89.575	259	27	0	1285	1543	326540360	326540618	2.100000e-86	329
9	TraesCS2B01G434300	chr6D	85.714	266	35	2	1285	1550	326760711	326760973	7.720000e-71	278
10	TraesCS2B01G434300	chr6B	89.575	259	27	0	1285	1543	495806711	495806453	2.100000e-86	329
11	TraesCS2B01G434300	chr6B	86.090	266	34	2	1285	1550	495543773	495543511	1.660000e-72	283
12	TraesCS2B01G434300	chr6A	89.575	259	27	0	1285	1543	465231917	465232175	2.100000e-86	329
13	TraesCS2B01G434300	chr6A	88.211	246	29	0	1285	1530	465389787	465390032	7.660000e-76	294
14	TraesCS2B01G434300	chr1A	85.606	264	33	4	1283	1542	388849402	388849664	3.590000e-69	272

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	TraesCS2B01G434300	chr2B	624353941	624356768	2827	True	5223.000000	5223	100.000000	1	2828	1	chr2B.!!$R1	2827
1	TraesCS2B01G434300	chr2D	527292287	527294933	2646	True	1133.666667	2388	92.442667	142	2828	3	chr2D.!!$R1	2686
2	TraesCS2B01G434300	chr2A	672290882	672293579	2697	True	734.750000	1832	87.589250	142	2828	4	chr2A.!!$R1	2686

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
95	96	0.034767	TAGTCTCCCGTCGATGGTGT	60.035	55.0	22.05	4.57	0.0	4.16	F
96	97	0.034767	AGTCTCCCGTCGATGGTGTA	60.035	55.0	22.05	6.67	0.0	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1098	1168	0.252239	TCTTGGGGAGCTCTAGCACA	60.252	55.000	14.64	0.83	45.16	4.57	R
2061	2138	1.225704	CCAGGGAAGTCCATCCTGC	59.774	63.158	0.00	0.00	44.87	4.85	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
26	27	9.909644	ATATTAACAGGAATACATAGTCGTCAC	57.090	33.333	0.00	0.00	0.00	3.67
27	28	4.650754	ACAGGAATACATAGTCGTCACC	57.349	45.455	0.00	0.00	0.00	4.02
28	29	3.066342	ACAGGAATACATAGTCGTCACCG	59.934	47.826	0.00	0.00	0.00	4.94
29	30	2.621998	AGGAATACATAGTCGTCACCGG	59.378	50.000	0.00	0.00	33.95	5.28
30	31	2.360165	GGAATACATAGTCGTCACCGGT	59.640	50.000	0.00	0.00	33.95	5.28
31	32	3.565482	GGAATACATAGTCGTCACCGGTA	59.435	47.826	6.87	0.00	33.95	4.02
32	33	4.036734	GGAATACATAGTCGTCACCGGTAA	59.963	45.833	6.87	0.00	33.95	2.85
33	34	5.278660	GGAATACATAGTCGTCACCGGTAAT	60.279	44.000	6.87	0.00	33.95	1.89
34	35	5.779529	ATACATAGTCGTCACCGGTAATT	57.220	39.130	6.87	0.00	33.95	1.40
35	36	4.460948	ACATAGTCGTCACCGGTAATTT	57.539	40.909	6.87	0.00	33.95	1.82
36	37	4.824289	ACATAGTCGTCACCGGTAATTTT	58.176	39.130	6.87	0.00	33.95	1.82
37	38	4.628333	ACATAGTCGTCACCGGTAATTTTG	59.372	41.667	6.87	0.40	33.95	2.44
38	39	2.419667	AGTCGTCACCGGTAATTTTGG	58.580	47.619	6.87	0.00	33.95	3.28
39	40	2.145536	GTCGTCACCGGTAATTTTGGT	58.854	47.619	6.87	0.00	36.10	3.67
40	41	2.549329	GTCGTCACCGGTAATTTTGGTT	59.451	45.455	6.87	0.00	32.48	3.67
41	42	3.745458	GTCGTCACCGGTAATTTTGGTTA	59.255	43.478	6.87	0.00	32.48	2.85
42	43	3.745458	TCGTCACCGGTAATTTTGGTTAC	59.255	43.478	6.87	0.00	32.48	2.50
43	44	3.497640	CGTCACCGGTAATTTTGGTTACA	59.502	43.478	6.87	0.00	36.51	2.41
44	45	4.154556	CGTCACCGGTAATTTTGGTTACAT	59.845	41.667	6.87	0.00	36.51	2.29
45	46	5.633927	GTCACCGGTAATTTTGGTTACATC	58.366	41.667	6.87	0.00	36.51	3.06
46	47	5.413523	GTCACCGGTAATTTTGGTTACATCT	59.586	40.000	6.87	0.00	36.51	2.90
47	48	6.594937	GTCACCGGTAATTTTGGTTACATCTA	59.405	38.462	6.87	0.00	36.51	1.98
48	49	7.119553	GTCACCGGTAATTTTGGTTACATCTAA	59.880	37.037	6.87	0.00	36.51	2.10
49	50	7.119553	TCACCGGTAATTTTGGTTACATCTAAC	59.880	37.037	6.87	0.00	36.51	2.34
50	51	6.092533	ACCGGTAATTTTGGTTACATCTAACG	59.907	38.462	4.49	0.00	36.51	3.18

Showing 1 to 25 of 230 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.909644	GTGACGACTATGTATTCCTGTTAATAT	57.090	33.333	0.00	0.00	0.00	1.28
1	2	8.355169	GGTGACGACTATGTATTCCTGTTAATA	58.645	37.037	0.00	0.00	0.00	0.98
2	3	7.208080	GGTGACGACTATGTATTCCTGTTAAT	58.792	38.462	0.00	0.00	0.00	1.40
3	4	6.567050	GGTGACGACTATGTATTCCTGTTAA	58.433	40.000	0.00	0.00	0.00	2.01
4	5	6.140303	GGTGACGACTATGTATTCCTGTTA	57.860	41.667	0.00	0.00	0.00	2.41
5	6	5.007385	GGTGACGACTATGTATTCCTGTT	57.993	43.478	0.00	0.00	0.00	3.16
6	7	4.650754	GGTGACGACTATGTATTCCTGT	57.349	45.455	0.00	0.00	0.00	4.00
22	23	5.413523	AGATGTAACCAAAATTACCGGTGAC	59.586	40.000	19.93	0.00	35.05	3.67
23	24	5.562635	AGATGTAACCAAAATTACCGGTGA	58.437	37.500	19.93	10.28	34.67	4.02
24	25	5.890424	AGATGTAACCAAAATTACCGGTG	57.110	39.130	19.93	0.00	34.67	4.94
25	26	6.092533	CGTTAGATGTAACCAAAATTACCGGT	59.907	38.462	13.98	13.98	35.96	5.28
26	27	6.457257	CCGTTAGATGTAACCAAAATTACCGG	60.457	42.308	0.00	0.00	35.96	5.28
27	28	6.457257	CCCGTTAGATGTAACCAAAATTACCG	60.457	42.308	7.14	0.00	35.96	4.02
28	29	6.678655	GCCCGTTAGATGTAACCAAAATTACC	60.679	42.308	7.14	0.00	35.96	2.85
29	30	6.127952	TGCCCGTTAGATGTAACCAAAATTAC	60.128	38.462	7.14	0.00	35.96	1.89
30	31	5.944599	TGCCCGTTAGATGTAACCAAAATTA	59.055	36.000	7.14	0.00	35.96	1.40
31	32	4.767928	TGCCCGTTAGATGTAACCAAAATT	59.232	37.500	7.14	0.00	35.96	1.82
32	33	4.337145	TGCCCGTTAGATGTAACCAAAAT	58.663	39.130	7.14	0.00	35.96	1.82
33	34	3.752665	TGCCCGTTAGATGTAACCAAAA	58.247	40.909	7.14	0.00	35.96	2.44
34	35	3.420300	TGCCCGTTAGATGTAACCAAA	57.580	42.857	7.14	0.00	35.96	3.28
35	36	3.420300	TTGCCCGTTAGATGTAACCAA	57.580	42.857	7.14	3.58	35.96	3.67
36	37	3.420300	TTTGCCCGTTAGATGTAACCA	57.580	42.857	7.14	0.00	35.96	3.67
37	38	4.976224	ATTTTGCCCGTTAGATGTAACC	57.024	40.909	7.14	0.00	35.96	2.85
38	39	7.080353	ACTTATTTTGCCCGTTAGATGTAAC	57.920	36.000	2.68	2.68	36.00	2.50
39	40	7.362229	CCAACTTATTTTGCCCGTTAGATGTAA	60.362	37.037	0.00	0.00	0.00	2.41

Showing 1 to 25 of 224 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.