AutoCloner

Multiple sequence alignment - TraesCS3A01G061200

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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	TraesCS3A01G061200	chr3A	100.000	3567	0	0	1	3567	36494178	36490612	0.000000e+00	6588.0
1	TraesCS3A01G061200	chr3D	97.116	2947	53	10	631	3567	26456283	26453359	0.000000e+00	4942.0
2	TraesCS3A01G061200	chr3D	88.193	559	30	7	4	528	26457817	26457261	5.020000e-178	634.0
3	TraesCS3A01G061200	chr3D	95.833	72	3	0	563	634	26457135	26457064	2.250000e-22	117.0
4	TraesCS3A01G061200	chr3B	96.742	2916	92	3	654	3567	44284886	44281972	0.000000e+00	4855.0
5	TraesCS3A01G061200	chr3B	93.143	525	25	6	119	634	44285898	44285376	0.000000e+00	760.0
6	TraesCS3A01G061200	chr3B	83.258	442	36	18	4	414	44485497	44485063	4.350000e-99	372.0
7	TraesCS3A01G061200	chr3B	77.889	597	78	28	1	564	810114311	810114886	4.440000e-84	322.0
8	TraesCS3A01G061200	chr3B	92.373	118	9	0	4	121	44286058	44285941	6.120000e-38	169.0
9	TraesCS3A01G061200	chr3B	97.917	48	1	0	8	55	44409684	44409637	2.280000e-12	84.2
10	TraesCS3A01G061200	chr3B	97.917	48	1	0	8	55	44677574	44677527	2.280000e-12	84.2
11	TraesCS3A01G061200	chr5A	77.759	589	80	29	7	564	31441476	31440908	7.430000e-82	315.0
12	TraesCS3A01G061200	chr5A	78.733	221	37	8	150	366	547797104	547796890	4.800000e-29	139.0
13	TraesCS3A01G061200	chr1D	78.636	220	37	7	151	366	57965113	57964900	1.730000e-28	137.0

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	TraesCS3A01G061200	chr3A	36490612	36494178	3566	True	6588.000000	6588	100.000	1	3567	1	chr3A.!!$R1	3566
1	TraesCS3A01G061200	chr3D	26453359	26457817	4458	True	1897.666667	4942	93.714	4	3567	3	chr3D.!!$R1	3563
2	TraesCS3A01G061200	chr3B	44281972	44286058	4086	True	1928.000000	4855	94.086	4	3567	3	chr3B.!!$R4	3563
3	TraesCS3A01G061200	chr3B	810114311	810114886	575	False	322.000000	322	77.889	1	564	1	chr3B.!!$F1	563
4	TraesCS3A01G061200	chr5A	31440908	31441476	568	True	315.000000	315	77.759	7	564	1	chr5A.!!$R1	557

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
239	290	0.752054	CCAAGGAACAAAGCCTGCAA	59.248	50.0	0.0	0.0	35.5	4.08	F
1305	2310	0.322816	GAATGGGAGGAGCAGCAACA	60.323	55.0	0.0	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2059	3064	1.452145	GGCGTTCCTTGTTGCTCCAA	61.452	55.0	0.00	0.0	0.0	3.53	R
2576	3581	1.221466	ATGCCGTGTCACTGTGTTCG	61.221	55.0	7.79	10.5	0.0	3.95	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	9.747898	AATGTTTATCATGGTTTTAGTGGTAGA	57.252	29.630	0.00	0.00	36.81	2.59
90	91	7.254692	GGTTTTAGTGGTAGAGTGACTGTTTTC	60.255	40.741	0.00	0.00	0.00	2.29
133	179	4.054671	CTCTAGCAAGATTCTTAAGGCGG	58.945	47.826	1.85	0.00	0.00	6.13
141	187	5.353394	AGATTCTTAAGGCGGATGTTGTA	57.647	39.130	1.85	0.00	0.00	2.41
143	189	5.760253	AGATTCTTAAGGCGGATGTTGTATG	59.240	40.000	1.85	0.00	0.00	2.39
145	191	5.092554	TCTTAAGGCGGATGTTGTATGAA	57.907	39.130	1.85	0.00	0.00	2.57
146	192	5.116180	TCTTAAGGCGGATGTTGTATGAAG	58.884	41.667	1.85	0.00	0.00	3.02
147	193	3.350219	AAGGCGGATGTTGTATGAAGT	57.650	42.857	0.00	0.00	0.00	3.01
148	194	2.906354	AGGCGGATGTTGTATGAAGTC	58.094	47.619	0.00	0.00	0.00	3.01
239	290	0.752054	CCAAGGAACAAAGCCTGCAA	59.248	50.000	0.00	0.00	35.50	4.08
274	325	8.558973	TGGTTTATTTAAATCCTTGCCAAATG	57.441	30.769	3.39	0.00	0.00	2.32
370	431	4.153475	GCGTGCTTTGACAATTCTACCTAA	59.847	41.667	0.00	0.00	0.00	2.69
373	434	7.254795	GCGTGCTTTGACAATTCTACCTAATAT	60.255	37.037	0.00	0.00	0.00	1.28
430	492	2.620115	CAGGGATGACATATGCAACCAC	59.380	50.000	20.06	13.13	30.52	4.16
437	499	1.027357	CATATGCAACCACTGGGAGC	58.973	55.000	0.00	3.60	38.58	4.70
462	524	2.171659	TGCTTAGTGTGTGGTCCTCAAA	59.828	45.455	0.00	0.00	0.00	2.69
555	622	5.813080	ACCGAGATATGGTTTTAAACTGC	57.187	39.130	7.79	0.00	35.82	4.40
796	1797	2.521733	AATAGCACGGCAAAACGCGG	62.522	55.000	12.47	0.00	45.98	6.46
979	1980	2.178912	TTTCAGTTTCCGGATTCGCT	57.821	45.000	4.15	0.00	34.56	4.93
1163	2164	2.039974	CACGGTGCTGCATGGCTTA	61.040	57.895	5.27	0.00	0.00	3.09
1236	2241	2.416202	GCTGAAAATGGAAAATTGCCCG	59.584	45.455	0.00	0.00	0.00	6.13
1300	2305	2.953284	ATGATGAATGGGAGGAGCAG	57.047	50.000	0.00	0.00	0.00	4.24
1305	2310	0.322816	GAATGGGAGGAGCAGCAACA	60.323	55.000	0.00	0.00	0.00	3.33
1348	2353	1.184970	TGAGCTCATCACCACGGACA	61.185	55.000	13.74	0.00	31.12	4.02
1708	2713	8.243426	TCATGTATGCTAAGTTCAAATGAAACC	58.757	33.333	0.00	0.00	35.58	3.27
1772	2777	7.230510	ACACCAATTCTTTATAGTTCAGTTGCA	59.769	33.333	0.00	0.00	0.00	4.08
1791	2796	6.141685	AGTTGCAACGAAACACGATAAATTTC	59.858	34.615	23.21	0.00	45.77	2.17
2059	3064	4.368315	GGCCAGAAATCGAAAACAAAGTT	58.632	39.130	0.00	0.00	0.00	2.66
2272	3277	0.445436	CAGATGACGAAGCACTTGCC	59.555	55.000	0.00	0.00	43.38	4.52
2311	3316	2.235155	TGCCCTAAATCTGTTAGACGCA	59.765	45.455	0.00	0.00	0.00	5.24
2612	3617	4.222886	CGGCATCAGTAGAGAGTTATTCG	58.777	47.826	0.00	0.00	0.00	3.34
2651	3656	0.541998	TGGAGGCGAAGACCAAGAGA	60.542	55.000	0.00	0.00	31.70	3.10
2725	3731	6.036626	GTGTGTTGTAAAATGAAACCAAAGGG	59.963	38.462	0.00	0.00	41.29	3.95
2815	3822	3.191078	ACCTCAGCACTATGATTCTGC	57.809	47.619	0.00	0.00	0.00	4.26
2826	3833	3.657398	ATGATTCTGCCACAGATTCCA	57.343	42.857	13.86	6.74	40.39	3.53
2880	3887	9.478019	CAACTCTACAGTTAATTTATGCGAAAG	57.522	33.333	0.00	0.00	41.24	2.62
2917	3932	6.933514	TGCCTATCACACTGAATATGGATA	57.066	37.500	0.00	0.00	0.00	2.59
2918	3933	6.701340	TGCCTATCACACTGAATATGGATAC	58.299	40.000	0.00	0.00	0.00	2.24
3166	4181	0.947244	CAAGCACAGAAAGTTCGCCT	59.053	50.000	0.00	0.00	0.00	5.52
3186	4201	2.926200	CTGTGTAATCTCTGCCACTTCG	59.074	50.000	0.00	0.00	0.00	3.79
3281	4296	5.401674	GCACTTCAATTCAAGCTTCTGAAAG	59.598	40.000	4.99	1.41	38.75	2.62
3560	4580	8.840321	GGAAGCTAATAAATGCAACAGATAAGA	58.160	33.333	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	3.129462	GGCAGCTAATCAAAGAGGGAAAC	59.871	47.826	0.00	0.00	0.00	2.78
20	21	2.036098	TTGGGCACATGGAGGCAG	59.964	61.111	14.32	0.00	0.00	4.85
133	179	5.808042	ACATGCTGACTTCATACAACATC	57.192	39.130	0.00	0.00	0.00	3.06
141	187	5.423015	ACGATAGAAACATGCTGACTTCAT	58.577	37.500	0.00	0.00	41.38	2.57
143	189	5.786401	AACGATAGAAACATGCTGACTTC	57.214	39.130	0.00	0.00	41.38	3.01
145	191	9.547753	AATTATAACGATAGAAACATGCTGACT	57.452	29.630	0.00	0.00	41.38	3.41
182	233	4.094442	GCGCCATATAACTAAGGCCATTAC	59.906	45.833	5.01	0.00	44.18	1.89
327	379	2.224018	GCTGAATCACCCTAGCAGAGAG	60.224	54.545	0.00	0.00	36.24	3.20
383	444	9.245481	GTACTGCCCACTAGATTTCTATAGTAT	57.755	37.037	0.00	0.00	31.10	2.12
389	450	4.649674	CCTGTACTGCCCACTAGATTTCTA	59.350	45.833	0.00	0.00	0.00	2.10
437	499	1.419374	GACCACACACTAAGCAGACG	58.581	55.000	0.00	0.00	0.00	4.18
555	622	4.647964	GCACAGGTACAATCAACATAACG	58.352	43.478	0.00	0.00	0.00	3.18
734	1735	5.126779	GTCAAGAGACCTCCAAAAACTCTT	58.873	41.667	0.00	0.00	44.99	2.85
796	1797	2.990830	GATTTCGGGAGGGTAGCGGC	62.991	65.000	0.00	0.00	0.00	6.53
979	1980	3.286353	TGTCTGTGTGCAGGAAATGAAA	58.714	40.909	0.00	0.00	42.78	2.69
1005	2006	5.072741	CCCTTCTTCAATTTTCTGAGTCCA	58.927	41.667	0.00	0.00	0.00	4.02
1163	2164	5.482878	AGGAGAGAATGGCAAAACATTGATT	59.517	36.000	0.00	0.00	40.92	2.57
1236	2241	2.708051	GGTCACCCAAGGTTAAGCTAC	58.292	52.381	7.76	1.04	31.02	3.58
1300	2305	4.976116	GGTGAAGGCGAATAATATTGTTGC	59.024	41.667	1.75	6.52	0.00	4.17
1305	2310	4.274950	CCAACGGTGAAGGCGAATAATATT	59.725	41.667	0.00	0.00	0.00	1.28
1708	2713	3.639094	CTGGAGATAGTTAGACAGGTGGG	59.361	52.174	0.00	0.00	0.00	4.61
1772	2777	8.173130	GGACATAGAAATTTATCGTGTTTCGTT	58.827	33.333	5.56	0.00	40.80	3.85
1791	2796	3.603532	ACTGCAGTTCACATGGACATAG	58.396	45.455	15.25	0.00	0.00	2.23
2059	3064	1.452145	GGCGTTCCTTGTTGCTCCAA	61.452	55.000	0.00	0.00	0.00	3.53
2272	3277	1.929836	GCAGCCTCAGTGATAACTTCG	59.070	52.381	0.00	0.00	0.00	3.79
2311	3316	3.760684	GCCTTTCAACATTCTCAGTCCAT	59.239	43.478	0.00	0.00	0.00	3.41
2501	3506	6.048732	TCTGCATGTCATAAGTTTCCAGTA	57.951	37.500	0.00	0.00	0.00	2.74
2576	3581	1.221466	ATGCCGTGTCACTGTGTTCG	61.221	55.000	7.79	10.50	0.00	3.95
2612	3617	6.406400	CCTCCAGCATCTATATACTGTAAGGC	60.406	46.154	0.00	0.00	39.30	4.35
2651	3656	4.230745	ACAAAGTATTACTCGGGGCATT	57.769	40.909	0.00	0.00	0.00	3.56
2725	3731	4.466827	TCCTGTACAAAGGAAAGAAACCC	58.533	43.478	1.43	0.00	43.57	4.11
2815	3822	6.375174	TCAGTTATTGTCAATGGAATCTGTGG	59.625	38.462	8.39	0.00	0.00	4.17
2851	3858	7.010183	TCGCATAAATTAACTGTAGAGTTGAGC	59.990	37.037	15.18	5.74	42.66	4.26
2888	3895	7.864379	CCATATTCAGTGTGATAGGCATTTTTC	59.136	37.037	0.00	0.00	0.00	2.29
2917	3932	8.806429	TGTGTTTCTTGTCATAATATGGATGT	57.194	30.769	0.00	0.00	0.00	3.06
3091	4106	4.081309	CCCGTAGTTCCTGATGTTCCTTTA	60.081	45.833	0.00	0.00	0.00	1.85
3166	4181	2.560981	TCGAAGTGGCAGAGATTACACA	59.439	45.455	0.00	0.00	36.35	3.72
3186	4201	5.178252	AGTGACATGCATGACGCTATTAATC	59.822	40.000	33.48	18.09	40.43	1.75
3281	4296	5.570234	TTGTTTTCTTTGTGTGTAGTCCC	57.430	39.130	0.00	0.00	0.00	4.46
3331	4346	3.687698	TGCAAGCTTACTACCGAATTTCC	59.312	43.478	0.00	0.00	0.00	3.13
3339	4359	5.873179	TTACACATTGCAAGCTTACTACC	57.127	39.130	4.94	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.