AutoCloner

Multiple sequence alignment - TraesCS3A01G475700

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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	TraesCS3A01G475700	chr3A	100.000	2390	0	0	1	2390	707127199	707124810	0.000000e+00	4414.0
1	TraesCS3A01G475700	chr3A	100.000	83	0	0	1	83	574287993	574288075	1.140000e-33	154.0
2	TraesCS3A01G475700	chr3A	97.619	42	0	1	481	521	489193178	489193137	1.190000e-08	71.3
3	TraesCS3A01G475700	chr3A	95.455	44	0	2	484	525	580599743	580599700	4.260000e-08	69.4
4	TraesCS3A01G475700	chr3B	96.738	1870	57	2	521	2390	762309326	762307461	0.000000e+00	3112.0
5	TraesCS3A01G475700	chr3B	85.246	305	33	10	101	398	762309647	762309348	1.070000e-78	303.0
6	TraesCS3A01G475700	chr3B	100.000	43	0	0	450	492	762309364	762309322	1.970000e-11	80.5
7	TraesCS3A01G475700	chr3B	100.000	40	0	0	482	521	435816885	435816924	9.160000e-10	75.0
8	TraesCS3A01G475700	chr3B	97.619	42	0	1	481	521	478078448	478078407	1.190000e-08	71.3
9	TraesCS3A01G475700	chr3D	97.236	1773	37	4	620	2390	573121775	573120013	0.000000e+00	2992.0
10	TraesCS3A01G475700	chr3D	91.837	98	5	2	522	618	573122221	573122126	1.490000e-27	134.0
11	TraesCS3A01G475700	chr3D	100.000	35	0	0	450	484	573122253	573122219	5.510000e-07	65.8
12	TraesCS3A01G475700	chr3D	87.719	57	4	3	466	520	27936547	27936602	1.980000e-06	63.9
13	TraesCS3A01G475700	chr1D	94.147	1777	86	12	620	2390	423056987	423058751	0.000000e+00	2689.0
14	TraesCS3A01G475700	chr1B	93.528	1777	94	14	620	2389	572308822	572310584	0.000000e+00	2625.0
15	TraesCS3A01G475700	chr1A	94.156	1677	76	11	718	2390	518986666	518988324	0.000000e+00	2534.0
16	TraesCS3A01G475700	chr1A	100.000	82	0	0	1	82	373317663	373317582	4.110000e-33	152.0
17	TraesCS3A01G475700	chr1A	96.226	53	1	1	398	449	554284183	554284235	4.230000e-13	86.1
18	TraesCS3A01G475700	chr1A	96.226	53	1	1	398	449	554289510	554289458	4.230000e-13	86.1
19	TraesCS3A01G475700	chr1A	97.297	37	1	0	484	520	131963584	131963620	1.980000e-06	63.9
20	TraesCS3A01G475700	chr7D	93.000	600	34	4	1797	2389	139368876	139369474	0.000000e+00	869.0
21	TraesCS3A01G475700	chr7D	95.604	91	3	1	1	90	581296273	581296363	6.890000e-31	145.0
22	TraesCS3A01G475700	chr7D	98.077	52	0	1	399	449	183786052	183786001	3.270000e-14	89.8
23	TraesCS3A01G475700	chr4A	89.867	602	52	4	1797	2389	220627174	220627775	0.000000e+00	765.0
24	TraesCS3A01G475700	chr6A	93.210	162	10	1	1797	1957	395654132	395653971	1.100000e-58	237.0
25	TraesCS3A01G475700	chr6A	100.000	82	0	0	1	82	287115369	287115450	4.110000e-33	152.0
26	TraesCS3A01G475700	chr2A	91.975	162	12	1	1797	1957	315573836	315573675	2.390000e-55	226.0
27	TraesCS3A01G475700	chr2A	93.333	45	3	0	476	520	23630478	23630434	1.530000e-07	67.6
28	TraesCS3A01G475700	chr2A	93.333	45	3	0	477	521	703708998	703709042	1.530000e-07	67.6
29	TraesCS3A01G475700	chr6B	97.727	88	2	0	1	88	459601643	459601730	4.110000e-33	152.0
30	TraesCS3A01G475700	chr6B	96.296	54	1	1	397	449	585808079	585808026	1.180000e-13	87.9
31	TraesCS3A01G475700	chr6B	94.340	53	1	2	399	450	70569397	70569448	1.970000e-11	80.5
32	TraesCS3A01G475700	chr6B	95.455	44	1	1	477	520	551951965	551951923	4.260000e-08	69.4
33	TraesCS3A01G475700	chr6D	97.674	86	2	0	1	86	91845423	91845508	5.320000e-32	148.0
34	TraesCS3A01G475700	chr7A	96.591	88	3	0	1	88	301100504	301100417	1.910000e-31	147.0
35	TraesCS3A01G475700	chr2B	94.737	95	4	1	1	95	227115837	227115930	1.910000e-31	147.0
36	TraesCS3A01G475700	chr5D	95.455	88	4	0	1	88	37920312	37920399	8.910000e-30	141.0
37	TraesCS3A01G475700	chr5D	92.063	63	2	2	388	449	225256384	225256324	4.230000e-13	86.1
38	TraesCS3A01G475700	chr4D	96.226	53	1	1	398	449	401088681	401088629	4.230000e-13	86.1
39	TraesCS3A01G475700	chr4D	96.154	52	1	1	399	449	12449216	12449267	1.520000e-12	84.2
40	TraesCS3A01G475700	chr2D	96.154	52	1	1	399	449	512770203	512770254	1.520000e-12	84.2

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	TraesCS3A01G475700	chr3A	707124810	707127199	2389	True	4414.000000	4414	100.000000	1	2390	1	chr3A.!!$R3	2389
1	TraesCS3A01G475700	chr3B	762307461	762309647	2186	True	1165.166667	3112	93.994667	101	2390	3	chr3B.!!$R2	2289
2	TraesCS3A01G475700	chr3D	573120013	573122253	2240	True	1063.933333	2992	96.357667	450	2390	3	chr3D.!!$R1	1940
3	TraesCS3A01G475700	chr1D	423056987	423058751	1764	False	2689.000000	2689	94.147000	620	2390	1	chr1D.!!$F1	1770
4	TraesCS3A01G475700	chr1B	572308822	572310584	1762	False	2625.000000	2625	93.528000	620	2389	1	chr1B.!!$F1	1769
5	TraesCS3A01G475700	chr1A	518986666	518988324	1658	False	2534.000000	2534	94.156000	718	2390	1	chr1A.!!$F2	1672
6	TraesCS3A01G475700	chr7D	139368876	139369474	598	False	869.000000	869	93.000000	1797	2389	1	chr7D.!!$F1	592
7	TraesCS3A01G475700	chr4A	220627174	220627775	601	False	765.000000	765	89.867000	1797	2389	1	chr4A.!!$F1	592

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
429	434	0.039165	GGCACAGTGGTAAAAGCTGC	60.039	55.0	1.84	0.0	33.87	5.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2317	2686	2.954753	GAGGTCAACAAGTGGCGCG	61.955	63.158	0.0	0.0	29.99	6.86	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	Hairpin	End Stability
24	25	6.091437	CCCTCCGTAAACTAATATAAGAGCG	58.909	44.000	0.00	0.00	5.03
25	26	6.294397	CCCTCCGTAAACTAATATAAGAGCGT	60.294	42.308	0.00	0.00	5.07
26	27	7.144000	CCTCCGTAAACTAATATAAGAGCGTT	58.856	38.462	0.00	0.00	4.84
27	28	7.650903	CCTCCGTAAACTAATATAAGAGCGTTT	59.349	37.037	0.00	0.00	3.60
28	29	9.669353	CTCCGTAAACTAATATAAGAGCGTTTA	57.331	33.333	0.00	0.00	2.01
29	30	9.669353	TCCGTAAACTAATATAAGAGCGTTTAG	57.331	33.333	0.00	30.36	1.85
30	31	9.669353	CCGTAAACTAATATAAGAGCGTTTAGA	57.331	33.333	0.00	30.36	2.10
77	78	9.710818	ACACTCTTATATTAGTTTACAGAGGGA	57.289	33.333	2.59	34.50	4.20
79	80	9.939424	ACTCTTATATTAGTTTACAGAGGGAGT	57.061	33.333	0.00	32.21	3.85
85	86	9.939424	ATATTAGTTTACAGAGGGAGTAGAAGT	57.061	33.333	0.00	0.00	3.01
86	87	8.667592	ATTAGTTTACAGAGGGAGTAGAAGTT	57.332	34.615	0.00	0.00	2.66
87	88	9.765295	ATTAGTTTACAGAGGGAGTAGAAGTTA	57.235	33.333	0.00	0.00	2.24
88	89	7.706100	AGTTTACAGAGGGAGTAGAAGTTAG	57.294	40.000	0.00	0.00	2.34
89	90	7.240167	AGTTTACAGAGGGAGTAGAAGTTAGT	58.760	38.462	0.00	0.00	2.24
90	91	7.177041	AGTTTACAGAGGGAGTAGAAGTTAGTG	59.823	40.741	0.00	0.00	2.74
91	92	4.345854	ACAGAGGGAGTAGAAGTTAGTGG	58.654	47.826	0.00	0.00	4.00
92	93	4.044317	ACAGAGGGAGTAGAAGTTAGTGGA	59.956	45.833	0.00	0.00	4.02
93	94	5.017490	CAGAGGGAGTAGAAGTTAGTGGAA	58.983	45.833	0.00	0.00	3.53
94	95	5.126384	CAGAGGGAGTAGAAGTTAGTGGAAG	59.874	48.000	0.00	0.00	3.46
95	96	3.770388	AGGGAGTAGAAGTTAGTGGAAGC	59.230	47.826	0.00	0.00	3.86
96	97	3.429135	GGGAGTAGAAGTTAGTGGAAGCG	60.429	52.174	0.00	0.00	4.68
97	98	3.180613	GAGTAGAAGTTAGTGGAAGCGC	58.819	50.000	0.00	0.00	5.92
98	99	1.918609	GTAGAAGTTAGTGGAAGCGCG	59.081	52.381	0.00	0.00	6.86
99	100	0.389948	AGAAGTTAGTGGAAGCGCGG	60.390	55.000	8.83	0.00	6.46
126	127	2.952310	GTTCATTAGGAATGGGAGGCAC	59.048	50.000	0.00	39.38	5.01

Showing 1 to 25 of 142 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
0	1	6.091437	CGCTCTTATATTAGTTTACGGAGGG	58.909	44.000	0.00	4.30
1	2	6.675987	ACGCTCTTATATTAGTTTACGGAGG	58.324	40.000	0.00	4.30
2	3	8.571461	AAACGCTCTTATATTAGTTTACGGAG	57.429	34.615	31.14	4.63
3	4	9.669353	CTAAACGCTCTTATATTAGTTTACGGA	57.331	33.333	34.29	4.69
4	5	9.669353	TCTAAACGCTCTTATATTAGTTTACGG	57.331	33.333	34.29	4.02
51	52	9.710818	TCCCTCTGTAAACTAATATAAGAGTGT	57.289	33.333	0.00	3.55
53	54	9.939424	ACTCCCTCTGTAAACTAATATAAGAGT	57.061	33.333	0.00	3.24
59	60	9.939424	ACTTCTACTCCCTCTGTAAACTAATAT	57.061	33.333	0.00	1.28
60	61	9.765295	AACTTCTACTCCCTCTGTAAACTAATA	57.235	33.333	0.00	0.98
61	62	8.667592	AACTTCTACTCCCTCTGTAAACTAAT	57.332	34.615	0.00	1.73
62	63	9.240734	CTAACTTCTACTCCCTCTGTAAACTAA	57.759	37.037	0.00	2.24
63	64	8.389366	ACTAACTTCTACTCCCTCTGTAAACTA	58.611	37.037	0.00	2.24
64	65	7.177041	CACTAACTTCTACTCCCTCTGTAAACT	59.823	40.741	0.00	2.66
65	66	7.314393	CACTAACTTCTACTCCCTCTGTAAAC	58.686	42.308	0.00	2.01
66	67	6.436532	CCACTAACTTCTACTCCCTCTGTAAA	59.563	42.308	0.00	2.01
67	68	5.950549	CCACTAACTTCTACTCCCTCTGTAA	59.049	44.000	0.00	2.41
68	69	5.252397	TCCACTAACTTCTACTCCCTCTGTA	59.748	44.000	0.00	2.74
69	70	4.044317	TCCACTAACTTCTACTCCCTCTGT	59.956	45.833	0.00	3.41
70	71	4.601084	TCCACTAACTTCTACTCCCTCTG	58.399	47.826	0.00	3.35
71	72	4.949966	TCCACTAACTTCTACTCCCTCT	57.050	45.455	0.00	3.69
72	73	4.142116	GCTTCCACTAACTTCTACTCCCTC	60.142	50.000	0.00	4.30
73	74	3.770388	GCTTCCACTAACTTCTACTCCCT	59.230	47.826	0.00	4.20
74	75	3.429135	CGCTTCCACTAACTTCTACTCCC	60.429	52.174	0.00	4.30
75	76	3.771798	CGCTTCCACTAACTTCTACTCC	58.228	50.000	0.00	3.85
76	77	3.180613	GCGCTTCCACTAACTTCTACTC	58.819	50.000	0.00	2.59

Showing 1 to 25 of 164 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.