AutoCloner

Multiple sequence alignment - TraesCS3A01G107900

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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	TraesCS3A01G107900	chr3A	100.000	4985	0	0	1	4985	72700594	72695610	0.000000e+00	9206.0
1	TraesCS3A01G107900	chr3A	93.169	527	23	3	4472	4985	705923186	705923712	0.000000e+00	761.0
2	TraesCS3A01G107900	chr3B	92.909	3878	168	50	621	4442	103035998	103032172	0.000000e+00	5539.0
3	TraesCS3A01G107900	chr3B	77.174	460	93	12	38	491	12546199	12545746	1.780000e-64	257.0
4	TraesCS3A01G107900	chr3B	90.769	195	13	3	1939	2131	103034401	103034210	6.400000e-64	255.0
5	TraesCS3A01G107900	chr3B	84.158	202	21	5	4615	4805	582001895	582002096	8.520000e-43	185.0
6	TraesCS3A01G107900	chr3B	84.694	98	15	0	4490	4587	104419250	104419153	1.140000e-16	99.0
7	TraesCS3A01G107900	chr3D	93.349	3789	158	30	619	4379	63414524	63410802	0.000000e+00	5515.0
8	TraesCS3A01G107900	chr3D	88.718	195	16	4	1939	2131	63412948	63412758	3.000000e-57	233.0
9	TraesCS3A01G107900	chr3D	87.129	202	15	5	2224	2418	63413241	63413044	8.400000e-53	219.0
10	TraesCS3A01G107900	chr3D	94.340	53	0	1	4374	4426	63410785	63410736	1.490000e-10	78.7
11	TraesCS3A01G107900	chr1D	96.176	523	14	3	4469	4985	481038083	481038605	0.000000e+00	850.0
12	TraesCS3A01G107900	chr4B	84.896	384	35	9	4615	4978	559846840	559847220	2.840000e-97	366.0
13	TraesCS3A01G107900	chr4B	71.548	478	112	23	76	541	567171566	567171101	1.900000e-19	108.0
14	TraesCS3A01G107900	chr4B	92.857	42	2	1	4480	4520	378033120	378033079	5.390000e-05	60.2
15	TraesCS3A01G107900	chr6D	87.307	323	33	5	4663	4978	75896975	75896654	3.670000e-96	363.0
16	TraesCS3A01G107900	chr7B	84.302	344	51	3	38	380	565202356	565202015	2.880000e-87	333.0
17	TraesCS3A01G107900	chr7B	80.965	373	65	5	52	421	141825581	141825950	1.760000e-74	291.0
18	TraesCS3A01G107900	chr7D	79.093	397	73	7	39	433	175946177	175946565	1.060000e-66	265.0
19	TraesCS3A01G107900	chr7D	92.105	38	3	0	4449	4486	565530213	565530250	3.000000e-03	54.7
20	TraesCS3A01G107900	chr5B	85.470	234	33	1	48	281	655727944	655728176	4.990000e-60	243.0
21	TraesCS3A01G107900	chr5B	94.340	53	2	1	38	90	45019897	45019846	4.140000e-11	80.5
22	TraesCS3A01G107900	chr5B	95.455	44	2	0	2988	3031	429901633	429901676	2.490000e-08	71.3
23	TraesCS3A01G107900	chr2D	87.895	190	17	3	4615	4798	175291202	175291013	8.400000e-53	219.0
24	TraesCS3A01G107900	chr2B	86.224	196	16	5	4621	4805	44922142	44921947	8.460000e-48	202.0
25	TraesCS3A01G107900	chr6B	92.308	39	3	0	4448	4486	24729549	24729511	6.970000e-04	56.5
26	TraesCS3A01G107900	chr6B	92.105	38	3	0	4449	4486	625284496	625284533	3.000000e-03	54.7
27	TraesCS3A01G107900	chrUn	92.105	38	3	0	4449	4486	69458517	69458480	3.000000e-03	54.7
28	TraesCS3A01G107900	chrUn	92.105	38	3	0	4449	4486	274279078	274279115	3.000000e-03	54.7
29	TraesCS3A01G107900	chr5D	90.244	41	4	0	4446	4486	40890196	40890236	3.000000e-03	54.7
30	TraesCS3A01G107900	chr5A	100.000	28	0	0	4459	4486	362398385	362398412	9.000000e-03	52.8

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	TraesCS3A01G107900	chr3A	72695610	72700594	4984	True	9206.000	9206	100.000	1	4985	1	chr3A.!!$R1	4984
1	TraesCS3A01G107900	chr3A	705923186	705923712	526	False	761.000	761	93.169	4472	4985	1	chr3A.!!$F1	513
2	TraesCS3A01G107900	chr3B	103032172	103035998	3826	True	2897.000	5539	91.839	621	4442	2	chr3B.!!$R3	3821
3	TraesCS3A01G107900	chr3D	63410736	63414524	3788	True	1511.425	5515	90.884	619	4426	4	chr3D.!!$R1	3807
4	TraesCS3A01G107900	chr1D	481038083	481038605	522	False	850.000	850	96.176	4469	4985	1	chr1D.!!$F1	516

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	End Stability	Orientation
410	411	0.033796	CAGCTCAACCACCCCATCAT	60.034	55.0	2.45	F
414	415	0.035534	TCAACCACCCCATCATCGTG	60.036	55.0	4.35	F
547	548	0.035725	CCTTAACCCAACCGTCCTCC	60.036	60.0	4.30	F
561	562	0.183971	TCCTCCGGCTTTTTCCAACA	59.816	50.0	3.33	F
562	563	0.598065	CCTCCGGCTTTTTCCAACAG	59.402	55.0	3.16	F
934	935	0.611896	CCCAATTCCAAACTCCGCCT	60.612	55.0	5.52	F
935	936	0.811281	CCAATTCCAAACTCCGCCTC	59.189	55.0	4.70	F
1283	1285	0.842905	TGGGCTGCTGGTTAGGGTTA	60.843	55.0	2.85	F
3049	3067	0.736325	GAAGGACGATGTGTGGGACG	60.736	60.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1296	1298	0.521735	GACCATTTCAACGCCTGGAC	59.478	55.000	0.00	32.92	4.02	R
1588	1597	0.536724	TGAGAATGCTGCGAAGGCTA	59.463	50.000	0.00	40.82	3.93	R
2425	2442	1.066858	CGTAACTGATGCTCCACCTGT	60.067	52.381	0.00	0.00	4.00	R
2557	2574	1.625818	AGACGAGGGTGAAATGAAGCT	59.374	47.619	0.00	0.00	3.74	R
2597	2615	2.542205	GGTAAACACGGGTCTGCAAAAC	60.542	50.000	0.00	0.00	2.43	R
2898	2916	4.773323	ACAATTGAAGCAAAGTAGAGCC	57.227	40.909	13.59	0.00	4.70	R
2932	2950	6.791867	ATGTAAACACCAGAGAGCATACTA	57.208	37.500	0.00	0.00	1.82	R
3165	3183	1.197721	CTCCACTGGACAAATCGCAAC	59.802	52.381	0.00	0.00	4.17	R
4442	4520	0.751452	CCCCCGCCTCTAGTAAAGAC	59.249	60.000	0.00	0.00	3.01	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
17	18	3.398920	GTCATCCACATGGCGACG	58.601	61.111	0.00	0.00	34.44	5.12
18	19	2.511373	TCATCCACATGGCGACGC	60.511	61.111	12.43	12.43	34.44	5.19
19	20	2.512286	CATCCACATGGCGACGCT	60.512	61.111	20.77	0.00	34.44	5.07
20	21	2.108514	CATCCACATGGCGACGCTT	61.109	57.895	20.77	4.81	34.44	4.68
21	22	0.809636	CATCCACATGGCGACGCTTA	60.810	55.000	20.77	9.80	34.44	3.09
22	23	0.530650	ATCCACATGGCGACGCTTAG	60.531	55.000	20.77	11.68	34.44	2.18
23	24	1.153647	CCACATGGCGACGCTTAGA	60.154	57.895	20.77	1.75	0.00	2.10
24	25	1.421410	CCACATGGCGACGCTTAGAC	61.421	60.000	20.77	2.65	0.00	2.59
25	26	0.735978	CACATGGCGACGCTTAGACA	60.736	55.000	20.77	9.06	0.00	3.41
26	27	0.458543	ACATGGCGACGCTTAGACAG	60.459	55.000	20.77	5.70	0.00	3.51
27	28	1.141881	ATGGCGACGCTTAGACAGG	59.858	57.895	20.77	0.00	0.00	4.00
28	29	1.605058	ATGGCGACGCTTAGACAGGT	61.605	55.000	20.77	0.00	0.00	4.00
29	30	1.080025	GGCGACGCTTAGACAGGTT	60.080	57.895	20.77	0.00	0.00	3.50
30	31	0.171903	GGCGACGCTTAGACAGGTTA	59.828	55.000	20.77	0.00	0.00	2.85
31	32	1.202382	GGCGACGCTTAGACAGGTTAT	60.202	52.381	20.77	0.00	0.00	1.89
32	33	2.117910	GCGACGCTTAGACAGGTTATC	58.882	52.381	13.73	0.00	0.00	1.75
33	34	2.223525	GCGACGCTTAGACAGGTTATCT	60.224	50.000	13.73	0.00	0.00	1.98
34	35	3.619729	CGACGCTTAGACAGGTTATCTC	58.380	50.000	0.00	0.00	0.00	2.75
35	36	3.619729	GACGCTTAGACAGGTTATCTCG	58.380	50.000	0.00	0.00	0.00	4.04
36	37	3.276857	ACGCTTAGACAGGTTATCTCGA	58.723	45.455	0.00	0.00	0.00	4.04
37	38	3.312973	ACGCTTAGACAGGTTATCTCGAG	59.687	47.826	5.93	5.93	0.00	4.04
38	39	3.312973	CGCTTAGACAGGTTATCTCGAGT	59.687	47.826	13.13	2.46	0.00	4.18
39	40	4.201930	CGCTTAGACAGGTTATCTCGAGTT	60.202	45.833	13.13	6.80	0.00	3.01
40	41	5.652518	GCTTAGACAGGTTATCTCGAGTTT	58.347	41.667	13.13	4.09	0.00	2.66
41	42	6.100668	GCTTAGACAGGTTATCTCGAGTTTT	58.899	40.000	13.13	1.46	0.00	2.43

Showing 1 to 25 of 516 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	2.813179	GCGTCGCCATGTGGATGAC	61.813	63.158	5.75	8.72	38.18	3.06
1	2	2.511373	GCGTCGCCATGTGGATGA	60.511	61.111	5.75	0.00	37.39	2.92
2	3	0.809636	TAAGCGTCGCCATGTGGATG	60.810	55.000	14.86	0.00	37.39	3.51
3	4	0.530650	CTAAGCGTCGCCATGTGGAT	60.531	55.000	14.86	0.00	37.39	3.41
4	5	1.153647	CTAAGCGTCGCCATGTGGA	60.154	57.895	14.86	0.00	37.39	4.02
5	6	1.153647	TCTAAGCGTCGCCATGTGG	60.154	57.895	14.86	0.00	38.53	4.17
6	7	0.735978	TGTCTAAGCGTCGCCATGTG	60.736	55.000	14.86	0.24	0.00	3.21
7	8	0.458543	CTGTCTAAGCGTCGCCATGT	60.459	55.000	14.86	0.00	0.00	3.21
8	9	1.148157	CCTGTCTAAGCGTCGCCATG	61.148	60.000	14.86	4.06	0.00	3.66
9	10	1.141881	CCTGTCTAAGCGTCGCCAT	59.858	57.895	14.86	5.94	0.00	4.40
10	11	1.812686	AACCTGTCTAAGCGTCGCCA	61.813	55.000	14.86	3.08	0.00	5.69
11	12	0.171903	TAACCTGTCTAAGCGTCGCC	59.828	55.000	14.86	0.00	0.00	5.54
12	13	2.117910	GATAACCTGTCTAAGCGTCGC	58.882	52.381	9.80	9.80	0.00	5.19
13	14	3.619729	GAGATAACCTGTCTAAGCGTCG	58.380	50.000	0.00	0.00	0.00	5.12
14	15	3.311871	TCGAGATAACCTGTCTAAGCGTC	59.688	47.826	0.00	0.00	0.00	5.19
15	16	3.276857	TCGAGATAACCTGTCTAAGCGT	58.723	45.455	0.00	0.00	0.00	5.07
16	17	3.312973	ACTCGAGATAACCTGTCTAAGCG	59.687	47.826	21.68	0.00	0.00	4.68
17	18	4.904253	ACTCGAGATAACCTGTCTAAGC	57.096	45.455	21.68	0.00	0.00	3.09
40	41	6.616577	AGTGACAACTATTTCCCCCTAAAAA	58.383	36.000	0.00	0.00	33.79	1.94
41	42	6.208840	AGTGACAACTATTTCCCCCTAAAA	57.791	37.500	0.00	0.00	33.79	1.52
42	43	5.853572	AGTGACAACTATTTCCCCCTAAA	57.146	39.130	0.00	0.00	33.79	1.85
43	44	5.853572	AAGTGACAACTATTTCCCCCTAA	57.146	39.130	0.00	0.00	34.77	2.69
44	45	5.853572	AAAGTGACAACTATTTCCCCCTA	57.146	39.130	0.00	0.00	34.77	3.53
45	46	4.741928	AAAGTGACAACTATTTCCCCCT	57.258	40.909	0.00	0.00	34.77	4.79
46	47	6.661805	TGAATAAAGTGACAACTATTTCCCCC	59.338	38.462	0.00	0.00	34.77	5.40

Showing 1 to 25 of 519 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.