AutoCloner

Multiple sequence alignment - TraesCS5B01G025900

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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	TraesCS5B01G025900	chr5B	100.000	2804	0	0	1	2804	24420063	24417260	0.000000e+00	5179.0
1	TraesCS5B01G025900	chr5B	95.038	2217	71	11	1	2200	6677471	6675277	0.000000e+00	3448.0
2	TraesCS5B01G025900	chr5B	91.043	1630	117	9	552	2154	48301381	48303008	0.000000e+00	2174.0
3	TraesCS5B01G025900	chr5B	92.098	1506	91	13	718	2216	30865105	30866589	0.000000e+00	2097.0
4	TraesCS5B01G025900	chr5B	93.642	519	29	4	2290	2804	30866722	30867240	0.000000e+00	773.0
5	TraesCS5B01G025900	chr5B	88.029	543	36	11	11	552	30989818	30989304	1.430000e-172	616.0
6	TraesCS5B01G025900	chr5B	87.477	543	39	15	11	552	30915623	30915109	1.440000e-167	599.0
7	TraesCS5B01G025900	chr5B	93.243	74	3	1	2220	2293	30866627	30866698	1.060000e-19	108.0
8	TraesCS5B01G025900	chr5A	92.173	1597	88	21	840	2404	4018703	4017112	0.000000e+00	2222.0
9	TraesCS5B01G025900	chr5A	92.870	547	35	4	1	546	3966738	3967281	0.000000e+00	791.0
10	TraesCS5B01G025900	chr5A	84.199	443	41	14	2367	2804	4017111	4016693	1.210000e-108	403.0
11	TraesCS5B01G025900	chr5A	87.838	222	27	0	822	1043	4711301	4711080	7.700000e-66	261.0
12	TraesCS5B01G025900	chr5A	89.820	167	17	0	551	717	4020102	4019936	6.080000e-52	215.0
13	TraesCS5B01G025900	chr5A	88.462	78	9	0	827	904	4711578	4711501	8.270000e-16	95.3
14	TraesCS5B01G025900	chr5A	86.747	83	11	0	822	904	4711442	4711360	2.970000e-15	93.5
15	TraesCS5B01G025900	chr2D	82.796	93	14	2	160	251	35325362	35325453	6.440000e-12	82.4

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	TraesCS5B01G025900	chr5B	24417260	24420063	2803	True	5179.000000	5179	100.000000	1	2804	1	chr5B.!!$R2	2803
1	TraesCS5B01G025900	chr5B	6675277	6677471	2194	True	3448.000000	3448	95.038000	1	2200	1	chr5B.!!$R1	2199
2	TraesCS5B01G025900	chr5B	48301381	48303008	1627	False	2174.000000	2174	91.043000	552	2154	1	chr5B.!!$F1	1602
3	TraesCS5B01G025900	chr5B	30865105	30867240	2135	False	992.666667	2097	92.994333	718	2804	3	chr5B.!!$F2	2086
4	TraesCS5B01G025900	chr5B	30989304	30989818	514	True	616.000000	616	88.029000	11	552	1	chr5B.!!$R4	541
5	TraesCS5B01G025900	chr5B	30915109	30915623	514	True	599.000000	599	87.477000	11	552	1	chr5B.!!$R3	541
6	TraesCS5B01G025900	chr5A	4016693	4020102	3409	True	946.666667	2222	88.730667	551	2804	3	chr5A.!!$R1	2253
7	TraesCS5B01G025900	chr5A	3966738	3967281	543	False	791.000000	791	92.870000	1	546	1	chr5A.!!$F1	545

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
744	989	0.883833	CACAGCCAAATGGACTGGAC	59.116	55.0	20.41	0.0	40.9	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1915	3042	1.553706	CCAAAGCAAGGCAAGAGGAT	58.446	50.0	0.0	0.0	0.0	3.24	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
265	268	6.364701	ACACAAACATATGCACATATACCCT	58.635	36.000	1.58	0.00	33.01	4.34
586	590	8.856247	CATATCATTTTTGCATCAATGGATACG	58.144	33.333	15.07	4.96	42.51	3.06
613	617	8.814235	GTGAATGATTGGATCAATTTGATGAAC	58.186	33.333	16.41	7.35	43.50	3.18
623	627	8.684520	GGATCAATTTGATGAACAAGAAGAGAT	58.315	33.333	16.41	0.00	37.20	2.75
668	896	1.060713	CACTTCCGCTTGTGTAGACG	58.939	55.000	0.00	0.00	0.00	4.18
722	967	2.103771	TCAAGAGCTCACAGCCCATATC	59.896	50.000	17.77	0.00	43.77	1.63
742	987	0.896940	AGCACAGCCAAATGGACTGG	60.897	55.000	20.41	13.59	40.90	4.00
744	989	0.883833	CACAGCCAAATGGACTGGAC	59.116	55.000	20.41	0.00	40.90	4.02
767	1012	2.186532	TGGTAATGTTTGCCGCACTA	57.813	45.000	0.00	0.00	38.38	2.74
842	1969	5.530171	ACCTATCATGCTTATTTCTGCTGTG	59.470	40.000	0.00	0.00	0.00	3.66
886	2013	9.774742	AATGAATCTAGTGAAAAATAAGTTCGC	57.225	29.630	0.00	0.00	36.05	4.70
892	2019	4.819630	AGTGAAAAATAAGTTCGCAGGTCA	59.180	37.500	0.00	0.00	37.84	4.02
990	2117	9.179552	CGTTGATCACAAATTGACTATTTTTCA	57.820	29.630	0.00	0.00	36.92	2.69
1599	2726	3.662759	ACAACTGTTTCTTCAAGGGGA	57.337	42.857	0.00	0.00	0.00	4.81
1894	3021	6.662616	TCTATTAGTAACGCTCATTCCGTAC	58.337	40.000	0.00	0.00	38.06	3.67
2027	3159	5.407995	AGTGTAAGTCTCGTGAGTACAGTAC	59.592	44.000	13.19	2.05	31.24	2.73
2055	3187	0.806868	CGCAGGCATGTGTTCTTCAT	59.193	50.000	3.23	0.00	32.04	2.57
2061	3193	5.471116	GCAGGCATGTGTTCTTCATATATGA	59.529	40.000	11.49	11.49	34.44	2.15
2108	3241	7.064253	CCTCATCCATGCATTTTCTTTCTTTTC	59.936	37.037	0.00	0.00	0.00	2.29
2150	3285	8.715088	GTTTGGTAAGTGTACGATCTATGTTTT	58.285	33.333	0.00	0.00	0.00	2.43
2216	3355	7.716998	AGCTGTATATTAGTCCCATTTTCTGTG	59.283	37.037	0.00	0.00	0.00	3.66
2233	3406	1.074752	GTGCTGTGTTCAGAGCTAGC	58.925	55.000	19.58	6.62	43.76	3.42
2238	3411	1.694150	TGTGTTCAGAGCTAGCTTGGT	59.306	47.619	20.42	3.88	0.00	3.67
2239	3412	2.897326	TGTGTTCAGAGCTAGCTTGGTA	59.103	45.455	20.42	5.26	0.00	3.25
2280	3453	3.034721	TGTACAGCTAGTTTGGGTTCG	57.965	47.619	0.00	0.00	0.00	3.95
2281	3454	2.366266	TGTACAGCTAGTTTGGGTTCGT	59.634	45.455	0.00	0.00	0.00	3.85
2369	3570	0.673985	GGGGGCTGTGTTGTTTTCTC	59.326	55.000	0.00	0.00	0.00	2.87
2405	3642	4.199310	CCAAGAGTGTTTGGTTCAGAGAA	58.801	43.478	0.00	0.00	42.16	2.87
2450	3687	3.301899	GCTAGCGCAATTCGTAGAACTTC	60.302	47.826	11.47	0.00	41.07	3.01
2504	3741	3.991773	GTCATGCAGCAATTTGTGTGATT	59.008	39.130	0.00	0.00	0.00	2.57
2518	3755	9.797556	AATTTGTGTGATTATCATTCATCTGTG	57.202	29.630	0.00	0.00	0.00	3.66
2529	3766	7.789202	ATCATTCATCTGTGGTATAGCTAGT	57.211	36.000	0.00	0.00	0.00	2.57
2559	3796	3.508793	ACTGCTATGTTGCTTGCTTCATT	59.491	39.130	7.89	0.00	0.00	2.57
2566	3803	3.825585	TGTTGCTTGCTTCATTCATGGTA	59.174	39.130	0.00	0.00	0.00	3.25
2616	3855	5.779771	AGCTTTTTCCAATTATTGAGTGGGA	59.220	36.000	6.50	0.00	43.67	4.37
2630	3869	3.245839	TGAGTGGGATGTACAGGACCTAA	60.246	47.826	0.33	0.00	0.00	2.69
2645	3884	6.326843	ACAGGACCTAAATACCTTATCTGTCC	59.673	42.308	0.00	0.00	35.15	4.02
2750	3991	5.068329	TCACTGTTTTGTATGCATGGTTCAA	59.932	36.000	10.16	6.87	0.00	2.69
2772	4014	8.055279	TCAAAAGTTCAGATGGGATTTATGTC	57.945	34.615	0.00	0.00	0.00	3.06
2773	4015	7.122650	TCAAAAGTTCAGATGGGATTTATGTCC	59.877	37.037	0.00	0.00	37.56	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	8.986477	ATTTTGTACAGAAATACCATTGCTTC	57.014	30.769	2.58	0.00	0.00	3.86
584	588	5.418524	TCAAATTGATCCAATCATTCACCGT	59.581	36.000	0.00	0.00	39.39	4.83
586	590	7.494211	TCATCAAATTGATCCAATCATTCACC	58.506	34.615	5.36	0.00	39.39	4.02
613	617	7.789273	ACTATTCTGCATTCATCTCTTCTTG	57.211	36.000	0.00	0.00	0.00	3.02
623	627	5.584251	TGCGAACATAACTATTCTGCATTCA	59.416	36.000	0.00	0.00	33.00	2.57
668	896	6.554334	TCACTCTGGCATAAACAAACTTAC	57.446	37.500	0.00	0.00	0.00	2.34
680	908	4.202357	TGAGTTGTAGTTTCACTCTGGCAT	60.202	41.667	0.00	0.00	0.00	4.40
722	967	0.242825	CAGTCCATTTGGCTGTGCTG	59.757	55.000	10.87	0.00	35.81	4.41
744	989	2.411409	GTGCGGCAAACATTACCAAATG	59.589	45.455	3.23	0.00	46.66	2.32
749	994	1.131693	GGTAGTGCGGCAAACATTACC	59.868	52.381	3.23	8.46	41.37	2.85
761	1006	2.350522	AGAGCATCAAAAGGTAGTGCG	58.649	47.619	0.00	0.00	40.54	5.34
767	1012	7.147976	GTGAATGTTTAAGAGCATCAAAAGGT	58.852	34.615	0.00	0.00	37.82	3.50
842	1969	9.617975	AGATTCATTGTCGAAAATTCTCTTTTC	57.382	29.630	0.00	1.30	35.63	2.29
886	2013	1.741706	GTGGATGCAGTGATTGACCTG	59.258	52.381	0.00	0.00	0.00	4.00
892	2019	1.180029	GCAAGGTGGATGCAGTGATT	58.820	50.000	0.00	0.00	43.29	2.57
990	2117	4.471908	TCCGCCATCGTGCTGCAT	62.472	61.111	5.27	0.00	0.00	3.96
1599	2726	2.428171	CAAAGGATCGGGCATGTCAATT	59.572	45.455	0.00	0.00	0.00	2.32
1680	2807	2.014128	CCGTTTGAGTTGAACAGTGGT	58.986	47.619	0.00	0.00	0.00	4.16
1873	3000	4.201950	ACGTACGGAATGAGCGTTACTAAT	60.202	41.667	21.06	0.00	31.37	1.73
1915	3042	1.553706	CCAAAGCAAGGCAAGAGGAT	58.446	50.000	0.00	0.00	0.00	3.24
2027	3159	3.118454	ATGCCTGCGGTTTCGTCG	61.118	61.111	0.00	0.00	38.89	5.12
2055	3187	7.888021	GGGGAATGAACACCACATAATCATATA	59.112	37.037	0.00	0.00	32.85	0.86
2061	3193	3.642141	GGGGGAATGAACACCACATAAT	58.358	45.455	0.00	0.00	34.56	1.28
2108	3241	5.947228	ACCAAACACACAACATATCTGAG	57.053	39.130	0.00	0.00	0.00	3.35
2216	3355	1.731160	CAAGCTAGCTCTGAACACAGC	59.269	52.381	19.65	0.00	35.73	4.40
2280	3453	8.364142	AGACACTCTAATAGCAATCCTGATTAC	58.636	37.037	0.00	0.00	0.00	1.89
2281	3454	8.484214	AGACACTCTAATAGCAATCCTGATTA	57.516	34.615	0.00	0.00	0.00	1.75
2369	3570	3.438087	CACTCTTGGCTAACCTCACATTG	59.562	47.826	0.00	0.00	36.63	2.82
2405	3642	5.237344	GCAGCTACCTACATTTTCGATCATT	59.763	40.000	0.00	0.00	0.00	2.57
2450	3687	4.616953	ACCAAAAACGGCACAAGAATTAG	58.383	39.130	0.00	0.00	0.00	1.73
2504	3741	8.885693	ACTAGCTATACCACAGATGAATGATA	57.114	34.615	0.00	0.00	0.00	2.15
2518	3755	1.785430	GTGCGCGAAACTAGCTATACC	59.215	52.381	12.10	0.00	0.00	2.73
2559	3796	2.749076	GCAACTGCAGTGAATACCATGA	59.251	45.455	22.49	0.00	41.59	3.07
2616	3855	8.871125	CAGATAAGGTATTTAGGTCCTGTACAT	58.129	37.037	0.00	0.00	0.00	2.29
2645	3884	9.203421	TGATGTACCTACGCTGAAATTTATATG	57.797	33.333	0.00	0.00	0.00	1.78
2691	3930	8.487176	CCAAATAACAACAAAGCAATGAGTTAC	58.513	33.333	10.85	0.00	32.05	2.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.