AutoCloner

Multiple sequence alignment - TraesCS5B01G116200

Loading Multiple Alignment...

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	TraesCS5B01G116200	chr5B	100.000	2918	0	0	1	2918	198029932	198027015	0.000000e+00	5389.0
1	TraesCS5B01G116200	chr5D	96.872	2110	60	3	1	2107	192951515	192949409	0.000000e+00	3526.0
2	TraesCS5B01G116200	chr5D	96.557	639	19	2	2283	2918	432896658	432896020	0.000000e+00	1055.0
3	TraesCS5B01G116200	chr5D	97.143	70	1	1	2105	2174	192947964	192947896	1.840000e-22	117.0
4	TraesCS5B01G116200	chr5D	97.959	49	1	0	2238	2286	432925126	432925078	5.180000e-13	86.1
5	TraesCS5B01G116200	chr5D	95.833	48	1	1	950	996	192950613	192950566	3.120000e-10	76.8
6	TraesCS5B01G116200	chr5A	96.569	1982	66	2	1	1981	250561336	250563316	0.000000e+00	3282.0
7	TraesCS5B01G116200	chr5A	96.581	117	3	1	2105	2221	250566894	250567009	2.970000e-45	193.0
8	TraesCS5B01G116200	chr5A	91.473	129	4	4	1979	2107	250566582	250566703	1.390000e-38	171.0
9	TraesCS5B01G116200	chr3D	97.744	399	9	0	2221	2619	63348621	63348223	0.000000e+00	688.0
10	TraesCS5B01G116200	chr3D	93.913	345	12	3	2578	2918	63348225	63347886	2.010000e-141	512.0
11	TraesCS5B01G116200	chr6D	83.368	475	46	20	2231	2686	463512206	463512666	2.710000e-110	409.0
12	TraesCS5B01G116200	chr4A	82.794	494	50	18	2222	2696	137183278	137183755	2.710000e-110	409.0
13	TraesCS5B01G116200	chr4A	82.688	491	50	18	2225	2696	479393412	479393886	1.260000e-108	403.0
14	TraesCS5B01G116200	chr4A	82.186	494	53	18	2222	2696	616208814	616208337	2.730000e-105	392.0
15	TraesCS5B01G116200	chrUn	85.152	330	36	8	2598	2918	332530633	332530308	2.800000e-85	326.0
16	TraesCS5B01G116200	chr7A	85.152	330	36	8	2598	2918	734475170	734475495	2.800000e-85	326.0
17	TraesCS5B01G116200	chr7A	87.031	293	20	8	2222	2501	734474851	734475138	6.070000e-82	315.0

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	TraesCS5B01G116200	chr5B	198027015	198029932	2917	True	5389.000000	5389	100.000000	1	2918	1	chr5B.!!$R1	2917
1	TraesCS5B01G116200	chr5D	192947896	192951515	3619	True	1239.933333	3526	96.616000	1	2174	3	chr5D.!!$R3	2173
2	TraesCS5B01G116200	chr5D	432896020	432896658	638	True	1055.000000	1055	96.557000	2283	2918	1	chr5D.!!$R1	635
3	TraesCS5B01G116200	chr5A	250561336	250567009	5673	False	1215.333333	3282	94.874333	1	2221	3	chr5A.!!$F1	2220
4	TraesCS5B01G116200	chr3D	63347886	63348621	735	True	600.000000	688	95.828500	2221	2918	2	chr3D.!!$R1	697
5	TraesCS5B01G116200	chr7A	734474851	734475495	644	False	320.500000	326	86.091500	2222	2918	2	chr7A.!!$F1	696

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
938	942	0.25589	TGGTGGGAAGCTATTGCCTC	59.744	55.0	0.0	0.0	46.62	4.7	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2611	7384	0.107459	GACCTGGTGATCTTGCCTCC	60.107	60.0	2.82	0.0	0.0	4.3	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
49	50	7.205515	ACTCTGTCCAAGATAATTGAGGATT	57.794	36.000	0.00	0.00	33.29	3.01
79	80	4.250464	CCTTACATTCTAGACGCACCAAA	58.750	43.478	0.00	0.00	0.00	3.28
255	256	7.786046	TTTACCTTCTGTTCAGATAGGTGTA	57.214	36.000	26.96	19.13	39.46	2.90
268	269	6.209589	TCAGATAGGTGTAAGGCATGAGTATC	59.790	42.308	0.00	0.00	0.00	2.24
770	774	2.428530	CAGCTGTACTGCCACTCATCTA	59.571	50.000	19.81	0.00	40.19	1.98
797	801	3.199946	TGAAGGGTTCTATTAGGTGGCTG	59.800	47.826	0.00	0.00	0.00	4.85
816	820	2.805099	CTGGTCTTGTCTCTTGCTTGAC	59.195	50.000	0.00	0.00	0.00	3.18
867	871	2.401967	GCCAGCTGCTTTGATCGAT	58.598	52.632	8.66	0.00	36.87	3.59
930	934	1.639635	CCATAGCCTGGTGGGAAGCT	61.640	60.000	0.00	0.00	40.49	3.74
938	942	0.255890	TGGTGGGAAGCTATTGCCTC	59.744	55.000	0.00	0.00	46.62	4.70
1068	1072	2.583441	CCGGTCTGTCAAGGAGGCA	61.583	63.158	0.00	0.00	0.00	4.75
1209	1213	2.487372	CTCAAAAGAGAAGCTTGAGGGC	59.513	50.000	2.10	0.00	41.47	5.19
1239	1243	1.280133	CTCATCAAGGGAAGCCACTCA	59.720	52.381	0.00	0.00	0.00	3.41
1340	1344	2.240921	TGTCTAATGCCCAGCCAATGTA	59.759	45.455	0.00	0.00	0.00	2.29
1382	1386	2.107750	CCAGGCATCATCGTCGCT	59.892	61.111	0.00	0.00	0.00	4.93
1448	1452	4.825634	GGAAGCCAATCTCATGATCATGAA	59.174	41.667	32.38	24.18	46.10	2.57
1590	1594	1.069823	CTCTCGAGGCTGGCATACATT	59.930	52.381	13.56	0.00	0.00	2.71
1875	1879	1.827969	AGGATGAACGACAAGGAGAGG	59.172	52.381	0.00	0.00	0.00	3.69
1926	1930	0.535335	GGCTGTCTTGATCGGTGGTA	59.465	55.000	0.00	0.00	0.00	3.25
2026	5297	8.974060	TTTCTCAGGTTCTGTGTTTAACTATT	57.026	30.769	0.00	0.00	32.61	1.73
2082	5353	5.600908	ATGATCAAATGTTTGCAGTTTGC	57.399	34.783	0.00	0.00	45.29	3.68
2153	6874	7.764331	TCGATCCCATATATTTCATGCAATTG	58.236	34.615	0.00	0.00	0.00	2.32
2174	6895	5.677319	TGACCATGCTACTATTATAGGGC	57.323	43.478	4.15	8.06	0.00	5.19
2191	6912	0.107459	GGCATCCTCAAGTGACTCCC	60.107	60.000	0.00	0.00	0.00	4.30
2323	7044	3.752222	ACAAGTGTACGAGAGAGTACCAG	59.248	47.826	5.04	0.00	44.59	4.00
2380	7101	8.745590	GGGGTAAAAATGTAATCTAGAAGCAAA	58.254	33.333	0.00	0.00	0.00	3.68
2487	7221	6.463049	CCATAATTCTTCACTGGGATAGACGT	60.463	42.308	0.00	0.00	0.00	4.34
2611	7384	1.301293	GAAGCAAGAGGACCAGGGG	59.699	63.158	0.00	0.00	0.00	4.79
2663	7436	0.320858	TCATGCGGGCGTTGTCTAAA	60.321	50.000	0.00	0.00	0.00	1.85
2696	7473	0.541392	TATGTGCGGTTGATCTGGCT	59.459	50.000	0.00	0.00	0.00	4.75
2725	7502	1.633432	TCAACATGAAAGGACGGGGAT	59.367	47.619	0.00	0.00	0.00	3.85
2786	7563	1.264020	GTGATGAACGAGTTGCTTGCA	59.736	47.619	0.00	0.00	0.00	4.08
2787	7564	1.946081	TGATGAACGAGTTGCTTGCAA	59.054	42.857	3.70	3.70	0.00	4.08
2788	7565	2.553602	TGATGAACGAGTTGCTTGCAAT	59.446	40.909	11.32	1.23	0.00	3.56
2789	7566	2.686558	TGAACGAGTTGCTTGCAATC	57.313	45.000	11.32	0.00	0.00	2.67
2790	7567	1.069973	TGAACGAGTTGCTTGCAATCG	60.070	47.619	24.02	24.02	39.22	3.34
2884	7674	4.534500	TCCAGAATTTGTAGCCAAGGTCTA	59.466	41.667	0.00	0.00	29.36	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	4.401519	CGTCTAGAATGTAAGGTCCTTGGA	59.598	45.833	14.84	0.53	0.00	3.53
79	80	4.272489	TCGCATCAGGGAAAAAGAATCAT	58.728	39.130	0.00	0.00	33.30	2.45
255	256	4.343526	CACTCAGGTAGATACTCATGCCTT	59.656	45.833	0.00	0.00	0.00	4.35
770	774	6.409349	GCCACCTAATAGAACCCTTCAAGTAT	60.409	42.308	0.00	0.00	0.00	2.12
797	801	1.795286	CGTCAAGCAAGAGACAAGACC	59.205	52.381	0.00	0.00	34.48	3.85
867	871	1.281419	TGAGGGGTTTATGAAGGCGA	58.719	50.000	0.00	0.00	0.00	5.54
930	934	1.820519	CAGCAGCTTTTGGAGGCAATA	59.179	47.619	0.00	0.00	0.00	1.90
955	959	4.392940	CTTCCCACCAGGCTATAGAAATG	58.607	47.826	3.21	0.00	34.51	2.32
1021	1025	2.734591	GGTGTCGACCTCTGCACA	59.265	61.111	14.12	0.00	39.47	4.57
1101	1105	1.597854	CGGCCTGAACTGTGCTTCA	60.598	57.895	0.00	0.00	0.00	3.02
1209	1213	2.568956	TCCCTTGATGAGGTCAGAACTG	59.431	50.000	0.00	0.00	44.71	3.16
1239	1243	0.525761	CGATGGCGTTTGGATTGGTT	59.474	50.000	0.00	0.00	0.00	3.67
1340	1344	2.214920	GGAGACAACGGGACCAGGT	61.215	63.158	0.00	0.00	0.00	4.00
1875	1879	3.510360	TGTAGAGCTCCTTCAGGTACAAC	59.490	47.826	10.93	0.00	36.34	3.32
1926	1930	4.708421	AGCACAAGTTTAATCAGCATGGAT	59.292	37.500	0.00	0.00	36.16	3.41
2026	5297	7.310072	TCCTTTCATTCACGCGATTAATAAA	57.690	32.000	15.93	5.69	0.00	1.40
2037	5308	3.118038	TCCCCCTAATCCTTTCATTCACG	60.118	47.826	0.00	0.00	0.00	4.35
2047	5318	5.136737	ACATTTGATCATTCCCCCTAATCCT	59.863	40.000	0.00	0.00	0.00	3.24
2107	5378	4.527564	GATTAACCTCACGTGCATAATGC	58.472	43.478	11.67	0.00	45.29	3.56
2153	6874	5.677319	TGCCCTATAATAGTAGCATGGTC	57.323	43.478	0.00	0.00	30.95	4.02
2174	6895	1.406614	GCAGGGAGTCACTTGAGGATG	60.407	57.143	0.00	0.00	0.00	3.51
2191	6912	2.555227	ACCCATGGTAACTGAAAGGCAG	60.555	50.000	11.73	0.00	41.89	4.85
2464	7198	6.515200	CGACGTCTATCCCAGTGAAGAATTAT	60.515	42.308	14.70	0.00	0.00	1.28
2611	7384	0.107459	GACCTGGTGATCTTGCCTCC	60.107	60.000	2.82	0.00	0.00	4.30
2633	7406	2.418777	CGCATGATGGAGCTCCGA	59.581	61.111	27.43	16.85	39.43	4.55
2663	7436	3.381045	CGCACATATGAACGTCCAGTAT	58.619	45.455	10.38	0.00	0.00	2.12
2696	7473	5.411361	CGTCCTTTCATGTTGAACCTTATCA	59.589	40.000	0.00	0.00	35.89	2.15
2725	7502	2.505407	TGCCTCTATAAAAGCAGCCAGA	59.495	45.455	0.00	0.00	0.00	3.86
2786	7563	6.494666	TTGTTATGGTAAGAGGGATCGATT	57.505	37.500	0.00	0.00	0.00	3.34
2787	7564	6.270000	TCATTGTTATGGTAAGAGGGATCGAT	59.730	38.462	0.00	0.00	32.40	3.59
2788	7565	5.600898	TCATTGTTATGGTAAGAGGGATCGA	59.399	40.000	0.00	0.00	32.40	3.59
2789	7566	5.853936	TCATTGTTATGGTAAGAGGGATCG	58.146	41.667	0.00	0.00	32.40	3.69
2790	7567	9.965902	AATATCATTGTTATGGTAAGAGGGATC	57.034	33.333	0.00	0.00	31.35	3.36
2827	7617	2.499197	TCGCTCATTTACACAGGCAAA	58.501	42.857	0.00	0.00	0.00	3.68
2884	7674	6.946340	TGCACGGGATGTATATCAATCTAAT	58.054	36.000	1.63	0.00	34.90	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.