AutoCloner

Multiple sequence alignment - TraesCS3B01G264700

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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	TraesCS3B01G264700	chr3B	100.000	3797	0	0	1	3797	423541466	423537670	0.000000e+00	7012.0
1	TraesCS3B01G264700	chr3B	98.608	862	12	0	1	862	197769164	197770025	0.000000e+00	1526.0
2	TraesCS3B01G264700	chr3B	97.912	862	18	0	1	862	828646252	828645391	0.000000e+00	1493.0
3	TraesCS3B01G264700	chr3B	96.984	862	24	2	1	861	170762609	170761749	0.000000e+00	1447.0
4	TraesCS3B01G264700	chr3D	96.908	2911	80	5	894	3797	326131744	326128837	0.000000e+00	4868.0
5	TraesCS3B01G264700	chr3A	96.819	2892	57	16	862	3731	438775895	438778773	0.000000e+00	4798.0
6	TraesCS3B01G264700	chr3A	96.970	99	3	0	3699	3797	438778775	438778873	2.350000e-37	167.0
7	TraesCS3B01G264700	chr3A	90.000	70	7	0	3533	3602	596167304	596167235	1.450000e-14	91.6
8	TraesCS3B01G264700	chr7A	98.394	872	12	2	1	870	12308491	12307620	0.000000e+00	1531.0
9	TraesCS3B01G264700	chr7A	96.181	864	30	3	2	863	214680016	214680878	0.000000e+00	1410.0
10	TraesCS3B01G264700	chr7B	98.262	863	14	1	1	862	729447340	729446478	0.000000e+00	1509.0
11	TraesCS3B01G264700	chr5A	97.914	863	18	0	1	863	32715910	32715048	0.000000e+00	1495.0
12	TraesCS3B01G264700	chr4A	97.572	865	20	1	1	864	382432349	382431485	0.000000e+00	1480.0
13	TraesCS3B01G264700	chr4A	97.106	864	24	1	1	864	550413393	550412531	0.000000e+00	1456.0

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	TraesCS3B01G264700	chr3B	423537670	423541466	3796	True	7012.0	7012	100.0000	1	3797	1	chr3B.!!$R2	3796
1	TraesCS3B01G264700	chr3B	197769164	197770025	861	False	1526.0	1526	98.6080	1	862	1	chr3B.!!$F1	861
2	TraesCS3B01G264700	chr3B	828645391	828646252	861	True	1493.0	1493	97.9120	1	862	1	chr3B.!!$R3	861
3	TraesCS3B01G264700	chr3B	170761749	170762609	860	True	1447.0	1447	96.9840	1	861	1	chr3B.!!$R1	860
4	TraesCS3B01G264700	chr3D	326128837	326131744	2907	True	4868.0	4868	96.9080	894	3797	1	chr3D.!!$R1	2903
5	TraesCS3B01G264700	chr3A	438775895	438778873	2978	False	2482.5	4798	96.8945	862	3797	2	chr3A.!!$F1	2935
6	TraesCS3B01G264700	chr7A	12307620	12308491	871	True	1531.0	1531	98.3940	1	870	1	chr7A.!!$R1	869
7	TraesCS3B01G264700	chr7A	214680016	214680878	862	False	1410.0	1410	96.1810	2	863	1	chr7A.!!$F1	861
8	TraesCS3B01G264700	chr7B	729446478	729447340	862	True	1509.0	1509	98.2620	1	862	1	chr7B.!!$R1	861
9	TraesCS3B01G264700	chr5A	32715048	32715910	862	True	1495.0	1495	97.9140	1	863	1	chr5A.!!$R1	862
10	TraesCS3B01G264700	chr4A	382431485	382432349	864	True	1480.0	1480	97.5720	1	864	1	chr4A.!!$R1	863
11	TraesCS3B01G264700	chr4A	550412531	550413393	862	True	1456.0	1456	97.1060	1	864	1	chr4A.!!$R2	863

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
765	771	0.612453	AGGAAGACGAGGACCTGGTC	60.612	60.000	24.89	24.89	39.05	4.02	F
831	837	1.153127	TGGACCAGCCGAAACGTTT	60.153	52.632	14.57	14.57	40.66	3.60	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2742	2764	0.668096	CAAACCGGTGGAATCGACGA	60.668	55.000	8.52	0.0	0.0	4.20	R
2942	2971	4.257267	TCCATCACCTCACTATTATGCG	57.743	45.455	0.00	0.0	0.0	4.73	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
87	89	1.096386	TACGGTTGCAGCAAAACGGT	61.096	50.000	27.40	20.75	41.91	4.83
765	771	0.612453	AGGAAGACGAGGACCTGGTC	60.612	60.000	24.89	24.89	39.05	4.02
831	837	1.153127	TGGACCAGCCGAAACGTTT	60.153	52.632	14.57	14.57	40.66	3.60
892	898	2.045926	GGCAATGCTGTCCCTCGT	60.046	61.111	4.82	0.00	0.00	4.18
922	928	3.138304	GAGTAACAATATCATGCCGGCA	58.862	45.455	34.80	34.80	0.00	5.69
992	1012	1.891060	GCGGCAGTCAAGTCGAACTG	61.891	60.000	10.06	10.06	39.34	3.16
1119	1141	2.123854	CAGCAGCTCCATGGCCAT	60.124	61.111	14.09	14.09	0.00	4.40
1239	1261	3.905678	CTCCGCGCCTTCCTCGAT	61.906	66.667	0.00	0.00	0.00	3.59
1847	1869	1.468520	CCTTGTGGATTGTGCTTACCG	59.531	52.381	0.00	0.00	34.57	4.02
2560	2582	5.568825	GCAGTAGTTAAGGATGTGGACAGAA	60.569	44.000	0.00	0.00	0.00	3.02
2742	2764	4.785376	AGAGTTGTGGTTCTCAGGGATAAT	59.215	41.667	0.00	0.00	33.63	1.28
2862	2891	4.383173	CTCACATGGATTCATCGATTGGA	58.617	43.478	0.00	0.00	0.00	3.53
2923	2952	4.871933	TGTGAACTCAGAAGCTGATACA	57.128	40.909	0.00	0.12	39.92	2.29
2977	3006	6.091076	AGGTGATGGATTCAATTTTAGGGA	57.909	37.500	0.00	0.00	35.70	4.20
2981	3010	4.916983	TGGATTCAATTTTAGGGATGCG	57.083	40.909	0.00	0.00	0.00	4.73
3069	3098	7.364144	CCACATAGTGCTGCTATATATTCAGGA	60.364	40.741	0.00	9.53	38.28	3.86
3263	3293	2.926200	CTCACAGAGCGATCGAACATTT	59.074	45.455	21.57	0.00	0.00	2.32
3269	3299	4.327357	CAGAGCGATCGAACATTTAGTTGT	59.673	41.667	21.57	0.00	41.51	3.32
3270	3300	4.327357	AGAGCGATCGAACATTTAGTTGTG	59.673	41.667	21.57	0.00	41.51	3.33
3281	3311	8.751335	CGAACATTTAGTTGTGCTTGTTTATTT	58.249	29.630	0.00	0.00	41.51	1.40
3585	3615	0.315251	TGCTCTTGTGAGACAGGTCG	59.685	55.000	0.00	0.00	42.73	4.79
3630	3660	6.071728	GGTCAACCTCAGTTCAATGATTTGAT	60.072	38.462	5.31	0.00	41.38	2.57
3716	3746	4.346709	TGGACTAGTTTGAGTGATCCAACA	59.653	41.667	0.00	0.00	0.00	3.33

Showing 1 to 23 of 23 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
87	89	2.104132	CCCGCGATGACGATGACA	59.896	61.111	8.23	0.00	42.66	3.58
259	263	2.993937	ACAACCGGTGACAGAAAAAGA	58.006	42.857	8.52	0.00	0.00	2.52
419	424	0.248702	TCCCGCTTGCGAACAAAAAC	60.249	50.000	16.99	0.00	34.74	2.43
819	825	3.656045	CGGCCAAACGTTTCGGCT	61.656	61.111	33.31	8.63	45.50	5.52
866	872	3.306641	GGGACAGCATTGCCATTGTTTAA	60.307	43.478	4.70	0.00	0.00	1.52
899	905	3.433615	GCCGGCATGATATTGTTACTCTC	59.566	47.826	24.80	0.00	0.00	3.20
910	916	2.558617	GCATGATGCCGGCATGATA	58.441	52.632	44.96	29.47	44.49	2.15
911	917	3.362262	GCATGATGCCGGCATGAT	58.638	55.556	44.96	38.44	44.49	2.45
922	928	3.484407	GAAAGGATAGTGCTGGCATGAT	58.516	45.455	0.00	0.00	0.00	2.45
937	943	2.342279	CTGCGTGGACGGAAAGGA	59.658	61.111	0.71	0.00	39.68	3.36
955	961	3.242936	GCCGCTTGAACTTTTTGTGTAGA	60.243	43.478	0.00	0.00	0.00	2.59
992	1012	2.032681	GCGGGGTCATATGGCTCC	59.967	66.667	16.88	16.88	36.79	4.70
1119	1141	2.257409	GATGGCCGCCCTTGAGAAGA	62.257	60.000	7.03	0.00	0.00	2.87
1215	1237	3.607370	GAAGGCGCGGAGGGAAAGT	62.607	63.158	8.83	0.00	46.37	2.66
1311	1333	3.314388	GAAGGCGTCAAAGGCTGCG	62.314	63.158	0.00	0.00	46.87	5.18
1491	1513	0.670546	ACATGTCAAGAACCGCCGAG	60.671	55.000	0.00	0.00	0.00	4.63
1632	1654	2.236382	CGAGCGGAAGATGCAGAGC	61.236	63.158	0.00	0.00	33.85	4.09
1847	1869	1.956802	GGTGCTGCACTAAACACCC	59.043	57.895	29.54	9.20	45.56	4.61
2533	2555	3.055385	TCCACATCCTTAACTACTGCACC	60.055	47.826	0.00	0.00	0.00	5.01
2742	2764	0.668096	CAAACCGGTGGAATCGACGA	60.668	55.000	8.52	0.00	0.00	4.20
2942	2971	4.257267	TCCATCACCTCACTATTATGCG	57.743	45.455	0.00	0.00	0.00	4.73
2977	3006	5.237048	ACTTATTGCAAAATTTCCACGCAT	58.763	33.333	1.71	0.00	31.67	4.73
2981	3010	6.223120	ACCAGACTTATTGCAAAATTTCCAC	58.777	36.000	1.71	0.00	0.00	4.02
3069	3098	1.632409	AGGCCACAGAGTCATGTTGAT	59.368	47.619	5.01	0.00	0.00	2.57
3269	3299	7.038659	CCCGGATAAAATGAAATAAACAAGCA	58.961	34.615	0.73	0.00	0.00	3.91

Showing 1 to 25 of 29 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.