AutoCloner

Multiple sequence alignment - TraesCS3B01G155100

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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	TraesCS3B01G155100	chr3B	100.000	3345	0	0	1	3345	147609901	147606557	0.000000e+00	6178.0
1	TraesCS3B01G155100	chr3B	88.278	418	38	8	2934	3342	819548314	819548729	1.080000e-134	490.0
2	TraesCS3B01G155100	chr3B	87.972	424	35	9	2934	3342	154434623	154435045	1.400000e-133	486.0
3	TraesCS3B01G155100	chr3B	87.648	421	38	10	2934	3342	819547334	819547752	8.400000e-131	477.0
4	TraesCS3B01G155100	chr3D	92.984	1126	40	15	742	1866	96412131	96411044	0.000000e+00	1605.0
5	TraesCS3B01G155100	chr3D	94.615	520	23	2	1938	2457	96411025	96410511	0.000000e+00	800.0
6	TraesCS3B01G155100	chr3D	88.342	386	21	9	2568	2945	96410506	96410137	3.060000e-120	442.0
7	TraesCS3B01G155100	chr3A	91.451	1123	52	19	742	1863	114445643	114444564	0.000000e+00	1502.0
8	TraesCS3B01G155100	chr3A	93.175	674	35	4	1941	2608	114444532	114443864	0.000000e+00	979.0
9	TraesCS3B01G155100	chr3A	81.439	264	12	9	2683	2945	114442024	114441797	7.370000e-42	182.0
10	TraesCS3B01G155100	chr3A	88.732	71	6	1	2616	2684	114442436	114442366	5.950000e-13	86.1
11	TraesCS3B01G155100	chr6B	88.180	423	36	11	2934	3345	279204702	279204283	3.000000e-135	492.0
12	TraesCS3B01G155100	chr6B	87.470	423	37	10	2934	3345	68262334	68261917	1.090000e-129	473.0
13	TraesCS3B01G155100	chr6B	100.000	28	0	0	2700	2727	15789224	15789197	6.000000e-03	52.8
14	TraesCS3B01G155100	chr1B	87.381	420	37	11	2934	3342	639091472	639091886	5.050000e-128	468.0
15	TraesCS3B01G155100	chr1B	86.574	432	42	10	2925	3342	493859540	493859969	2.350000e-126	462.0
16	TraesCS3B01G155100	chr5B	87.561	410	36	10	2949	3345	228169514	228169107	8.460000e-126	460.0
17	TraesCS3B01G155100	chr5B	86.824	425	36	12	2934	3345	456390627	456390210	1.090000e-124	457.0

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	TraesCS3B01G155100	chr3B	147606557	147609901	3344	True	6178.000	6178	100.000000	1	3345	1	chr3B.!!$R1	3344
1	TraesCS3B01G155100	chr3B	819547334	819548729	1395	False	483.500	490	87.963000	2934	3342	2	chr3B.!!$F2	408
2	TraesCS3B01G155100	chr3D	96410137	96412131	1994	True	949.000	1605	91.980333	742	2945	3	chr3D.!!$R1	2203
3	TraesCS3B01G155100	chr3A	114441797	114445643	3846	True	687.275	1502	88.699250	742	2945	4	chr3A.!!$R1	2203

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	Hairpin	End Stability	Orientation
407	408	0.031994	GGCGTGCCACTTCACAATTT	59.968	50.0	5.89	36.8	1.82	F
686	687	0.032403	TACAAACAGGTGGACGGACG	59.968	55.0	0.00	0.0	4.79	F
688	689	0.032403	CAAACAGGTGGACGGACGTA	59.968	55.0	0.00	0.0	3.57	F
689	690	0.032540	AAACAGGTGGACGGACGTAC	59.967	55.0	0.00	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1924	1926	0.103572	ACCGTGTCAGTTACAACGCT	59.896	50.000	0.00	0.00	40.63	5.07	R
1925	1927	0.231279	CACCGTGTCAGTTACAACGC	59.769	55.000	0.00	0.00	40.63	4.84	R
2308	2319	0.932399	ATTATTCGTTACCGCGGTGC	59.068	50.000	40.02	28.95	0.00	5.01	R
2434	2445	1.134670	AGAATCGTAGGCAGCAAGTCC	60.135	52.381	0.00	0.00	0.00	3.85	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	Hairpin	End Stability
21	22	3.717294	GGACCAGCCCACGGACAT	61.717	66.667	0.00	3.06
22	23	2.351276	GACCAGCCCACGGACATT	59.649	61.111	0.00	2.71
23	24	1.303317	GACCAGCCCACGGACATTT	60.303	57.895	0.00	2.32
24	25	1.586154	GACCAGCCCACGGACATTTG	61.586	60.000	0.00	2.32
25	26	2.342650	CCAGCCCACGGACATTTGG	61.343	63.158	0.00	3.28
26	27	1.603455	CAGCCCACGGACATTTGGT	60.603	57.895	0.00	3.67
27	28	1.603455	AGCCCACGGACATTTGGTG	60.603	57.895	0.00	4.17
28	29	1.602323	GCCCACGGACATTTGGTGA	60.602	57.895	33.58	4.02
29	30	1.175983	GCCCACGGACATTTGGTGAA	61.176	55.000	33.58	3.18
30	31	1.544724	CCCACGGACATTTGGTGAAT	58.455	50.000	33.58	2.57
31	32	2.717390	CCCACGGACATTTGGTGAATA	58.283	47.619	33.58	1.75
32	33	2.682856	CCCACGGACATTTGGTGAATAG	59.317	50.000	33.58	1.73
33	34	3.343617	CCACGGACATTTGGTGAATAGT	58.656	45.455	33.58	2.12
34	35	3.126858	CCACGGACATTTGGTGAATAGTG	59.873	47.826	33.58	2.74
35	36	2.747446	ACGGACATTTGGTGAATAGTGC	59.253	45.455	0.00	4.40
36	37	3.009723	CGGACATTTGGTGAATAGTGCT	58.990	45.455	0.00	4.40
37	38	3.181507	CGGACATTTGGTGAATAGTGCTG	60.182	47.826	0.00	4.41
38	39	3.129287	GGACATTTGGTGAATAGTGCTGG	59.871	47.826	0.00	4.85
39	40	4.009675	GACATTTGGTGAATAGTGCTGGA	58.990	43.478	0.00	3.86
40	41	4.603131	ACATTTGGTGAATAGTGCTGGAT	58.397	39.130	0.00	3.41
41	42	4.400251	ACATTTGGTGAATAGTGCTGGATG	59.600	41.667	0.00	3.51
42	43	2.715749	TGGTGAATAGTGCTGGATGG	57.284	50.000	0.00	3.51
43	44	1.312815	GGTGAATAGTGCTGGATGGC	58.687	55.000	0.00	4.40
44	45	1.133976	GGTGAATAGTGCTGGATGGCT	60.134	52.381	0.00	4.75
45	46	2.104792	GGTGAATAGTGCTGGATGGCTA	59.895	50.000	0.00	3.93

Showing 1 to 25 of 617 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
4	5	2.764637	AAATGTCCGTGGGCTGGTCC	62.765	60.000	0.00	4.46
5	6	1.303317	AAATGTCCGTGGGCTGGTC	60.303	57.895	0.00	4.02
6	7	1.603455	CAAATGTCCGTGGGCTGGT	60.603	57.895	0.00	4.00
7	8	2.342650	CCAAATGTCCGTGGGCTGG	61.343	63.158	0.00	4.85
8	9	1.603455	ACCAAATGTCCGTGGGCTG	60.603	57.895	39.39	4.85
9	10	1.603455	CACCAAATGTCCGTGGGCT	60.603	57.895	39.39	5.19
10	11	1.175983	TTCACCAAATGTCCGTGGGC	61.176	55.000	39.39	5.36
11	12	1.544724	ATTCACCAAATGTCCGTGGG	58.455	50.000	39.39	4.61
12	13	3.126858	CACTATTCACCAAATGTCCGTGG	59.873	47.826	41.00	4.94
13	14	3.426159	GCACTATTCACCAAATGTCCGTG	60.426	47.826	0.00	4.94
14	15	2.747446	GCACTATTCACCAAATGTCCGT	59.253	45.455	0.00	4.69
15	16	3.009723	AGCACTATTCACCAAATGTCCG	58.990	45.455	0.00	4.79
16	17	3.129287	CCAGCACTATTCACCAAATGTCC	59.871	47.826	0.00	4.02
17	18	4.009675	TCCAGCACTATTCACCAAATGTC	58.990	43.478	0.00	3.06
18	19	4.032960	TCCAGCACTATTCACCAAATGT	57.967	40.909	0.00	2.71
19	20	4.202080	CCATCCAGCACTATTCACCAAATG	60.202	45.833	0.00	2.32
20	21	3.956199	CCATCCAGCACTATTCACCAAAT	59.044	43.478	0.00	2.32
21	22	3.355378	CCATCCAGCACTATTCACCAAA	58.645	45.455	0.00	3.28
22	23	2.945440	GCCATCCAGCACTATTCACCAA	60.945	50.000	0.00	3.67
23	24	1.408683	GCCATCCAGCACTATTCACCA	60.409	52.381	0.00	4.17
24	25	1.133976	AGCCATCCAGCACTATTCACC	60.134	52.381	34.23	4.02
25	26	2.338577	AGCCATCCAGCACTATTCAC	57.661	50.000	34.23	3.18
26	27	4.502105	TTTAGCCATCCAGCACTATTCA	57.498	40.909	34.23	2.57
27	28	4.320788	GCATTTAGCCATCCAGCACTATTC	60.321	45.833	37.23	1.75
28	29	3.571401	GCATTTAGCCATCCAGCACTATT	59.429	43.478	37.23	1.73

Showing 1 to 25 of 660 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.