AutoCloner

Multiple sequence alignment - TraesCS2D01G168900

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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	TraesCS2D01G168900	chr2D	100.000	2609	0	0	1	2609	112864289	112866897	0.000000e+00	4819.0
1	TraesCS2D01G168900	chr2D	77.492	311	48	15	2137	2428	2507877	2508184	1.610000e-37	167.0
2	TraesCS2D01G168900	chr2A	91.517	2617	105	35	64	2609	114299641	114302211	0.000000e+00	3494.0
3	TraesCS2D01G168900	chr2B	95.408	1960	70	8	655	2609	163231144	163233088	0.000000e+00	3103.0
4	TraesCS2D01G168900	chr2B	89.624	665	18	9	22	650	163230058	163230707	0.000000e+00	798.0
5	TraesCS2D01G168900	chr5D	73.538	975	195	50	808	1746	456752250	456751303	1.950000e-81	313.0
6	TraesCS2D01G168900	chr5D	85.714	84	6	1	2486	2563	118221083	118221000	1.660000e-12	84.2
7	TraesCS2D01G168900	chr5B	72.970	973	204	48	808	1746	558687516	558686569	4.250000e-73	285.0
8	TraesCS2D01G168900	chr5B	73.171	410	79	20	2137	2530	160118471	160118865	4.560000e-23	119.0
9	TraesCS2D01G168900	chr5B	81.119	143	27	0	2286	2428	249715505	249715647	5.900000e-22	115.0
10	TraesCS2D01G168900	chr5A	72.951	976	199	51	808	1746	574785794	574784847	1.980000e-71	279.0
11	TraesCS2D01G168900	chr6D	74.948	479	93	19	2137	2609	457478153	457477696	7.370000e-46	195.0
12	TraesCS2D01G168900	chr4B	73.497	449	97	18	2124	2555	71337183	71337626	1.620000e-32	150.0
13	TraesCS2D01G168900	chr7D	78.894	199	37	5	2285	2481	65578934	65579129	2.110000e-26	130.0
14	TraesCS2D01G168900	chr4A	75.665	263	39	18	2137	2379	669402203	669402460	9.870000e-20	108.0

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	TraesCS2D01G168900	chr2D	112864289	112866897	2608	False	4819.0	4819	100.000	1	2609	1	chr2D.!!$F2	2608
1	TraesCS2D01G168900	chr2A	114299641	114302211	2570	False	3494.0	3494	91.517	64	2609	1	chr2A.!!$F1	2545
2	TraesCS2D01G168900	chr2B	163230058	163233088	3030	False	1950.5	3103	92.516	22	2609	2	chr2B.!!$F1	2587
3	TraesCS2D01G168900	chr5D	456751303	456752250	947	True	313.0	313	73.538	808	1746	1	chr5D.!!$R2	938
4	TraesCS2D01G168900	chr5B	558686569	558687516	947	True	285.0	285	72.970	808	1746	1	chr5B.!!$R1	938
5	TraesCS2D01G168900	chr5A	574784847	574785794	947	True	279.0	279	72.951	808	1746	1	chr5A.!!$R1	938

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
581	647	0.037326	TAGCTGTCGCACAAGGAAGG	60.037	55.0	0.0	0.0	39.1	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2279	2878	0.340558	TTAGGTGTGCTAGGGGCCTA	59.659	55.0	0.84	0.0	40.92	3.93	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
45	46	1.068610	TGGCTCGAAATTTGGAAAGCG	60.069	47.619	4.38	0.00	0.00	4.68
283	314	4.309933	GCTTTCTTTTCACCCAATCCTTG	58.690	43.478	0.00	0.00	0.00	3.61
307	338	4.160626	TCAGATTTGCATGGCATTGATTCA	59.839	37.500	0.00	0.00	38.76	2.57
335	366	5.123186	CCAACTGGAAACGCAAATACTATCA	59.877	40.000	0.00	0.00	37.39	2.15
336	367	5.796350	ACTGGAAACGCAAATACTATCAC	57.204	39.130	0.00	0.00	0.00	3.06
442	484	4.670896	CTTTCAAGCCAAGGAAAGGAAA	57.329	40.909	6.30	0.00	43.85	3.13
528	578	2.559440	CCACCACCACCAAAAACAATG	58.441	47.619	0.00	0.00	0.00	2.82
531	581	2.172293	ACCACCACCAAAAACAATGCAT	59.828	40.909	0.00	0.00	0.00	3.96
577	643	0.742281	ATGCTAGCTGTCGCACAAGG	60.742	55.000	17.23	0.00	39.21	3.61
581	647	0.037326	TAGCTGTCGCACAAGGAAGG	60.037	55.000	0.00	0.00	39.10	3.46
650	723	7.598493	GCACCCGCAAAATAATCAATAATGTAT	59.402	33.333	0.00	0.00	38.36	2.29
651	724	8.914654	CACCCGCAAAATAATCAATAATGTATG	58.085	33.333	0.00	0.00	0.00	2.39
652	725	8.855110	ACCCGCAAAATAATCAATAATGTATGA	58.145	29.630	0.00	0.00	0.00	2.15
759	1268	8.394667	TGTATATACGATGATTGAAATCTCGC	57.605	34.615	17.23	7.35	38.46	5.03
779	1288	1.067364	CCCCGTTTTACACCACCAAAC	59.933	52.381	0.00	0.00	0.00	2.93
787	1299	5.365403	TTTACACCACCAAACGAATGATC	57.635	39.130	0.00	0.00	0.00	2.92
1086	1670	4.101448	GCCATGGACTCCGGCAGT	62.101	66.667	18.40	0.47	45.52	4.40
2131	2729	0.178932	AGGTTTTCTGGCTTTCCCCC	60.179	55.000	0.00	0.00	0.00	5.40
2132	2730	0.471022	GGTTTTCTGGCTTTCCCCCA	60.471	55.000	0.00	0.00	0.00	4.96
2133	2731	1.644509	GTTTTCTGGCTTTCCCCCAT	58.355	50.000	0.00	0.00	0.00	4.00
2134	2732	1.977854	GTTTTCTGGCTTTCCCCCATT	59.022	47.619	0.00	0.00	0.00	3.16
2172	2771	2.037251	ACAGCTGAACAAGGTACACGAT	59.963	45.455	23.35	0.00	33.90	3.73
2188	2787	4.035684	ACACGATCGAACGATACAAGATG	58.964	43.478	24.34	9.09	34.60	2.90
2189	2788	4.035684	CACGATCGAACGATACAAGATGT	58.964	43.478	24.34	0.00	34.60	3.06
2217	2816	4.039366	GTGACCCTCTTATAAAGCCGATCT	59.961	45.833	0.00	0.00	0.00	2.75
2223	2822	5.455056	TCTTATAAAGCCGATCTGAGGAC	57.545	43.478	0.00	0.00	0.00	3.85
2279	2878	0.179468	ACAACACAACACTACGCCCT	59.821	50.000	0.00	0.00	0.00	5.19
2280	2879	1.413445	ACAACACAACACTACGCCCTA	59.587	47.619	0.00	0.00	0.00	3.53
2281	2880	2.066262	CAACACAACACTACGCCCTAG	58.934	52.381	0.00	0.00	0.00	3.02
2282	2881	0.606604	ACACAACACTACGCCCTAGG	59.393	55.000	0.06	0.06	0.00	3.02
2283	2882	0.739813	CACAACACTACGCCCTAGGC	60.740	60.000	2.05	0.00	46.75	3.93
2299	2898	0.549169	AGGCCCCTAGCACACCTAAA	60.549	55.000	0.00	0.00	46.50	1.85
2323	2922	1.810030	CGACAACGCCCTTAGGAGC	60.810	63.158	0.00	0.23	36.16	4.70
2330	2929	1.144276	GCCCTTAGGAGCGAGAACC	59.856	63.158	0.00	0.00	33.47	3.62
2332	2931	1.321074	CCCTTAGGAGCGAGAACCGT	61.321	60.000	0.00	0.00	36.37	4.83
2334	2933	0.526662	CTTAGGAGCGAGAACCGTGT	59.473	55.000	0.00	0.00	41.15	4.49
2379	2978	2.198406	CGACGAACAAAGGTCTTCACA	58.802	47.619	0.00	0.00	0.00	3.58
2394	2993	3.991051	ACACGGAGCCCTGTCACG	61.991	66.667	0.00	0.00	0.00	4.35
2479	3078	2.730672	CTGAGGCGCCGAGTTTTCG	61.731	63.158	23.20	4.79	46.29	3.46
2553	3152	4.829388	ATCCCCAGTTCCGGATCA	57.171	55.556	14.83	0.00	33.38	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.810720	GCCTGGGCCATGTTATGTATACAT	60.811	45.833	21.57	21.57	36.70	2.29
1	2	3.497763	GCCTGGGCCATGTTATGTATACA	60.498	47.826	6.72	8.27	34.56	2.29
2	3	3.081804	GCCTGGGCCATGTTATGTATAC	58.918	50.000	6.72	0.00	34.56	1.47
3	4	3.433306	GCCTGGGCCATGTTATGTATA	57.567	47.619	6.72	0.00	34.56	1.47
4	5	2.292828	GCCTGGGCCATGTTATGTAT	57.707	50.000	6.72	0.00	34.56	2.29
5	6	3.819245	GCCTGGGCCATGTTATGTA	57.181	52.632	6.72	0.00	34.56	2.29
6	7	4.684623	GCCTGGGCCATGTTATGT	57.315	55.556	6.72	0.00	34.56	2.29
19	20	0.171903	CAAATTTCGAGCCAGGCCTG	59.828	55.000	26.87	26.87	0.00	4.85
20	21	0.967380	CCAAATTTCGAGCCAGGCCT	60.967	55.000	8.22	0.00	0.00	5.19
45	46	0.518559	GCAAACGCAACGCTAGCTAC	60.519	55.000	13.93	0.00	0.00	3.58
50	51	1.395608	GGATAAGCAAACGCAACGCTA	59.604	47.619	0.00	0.00	34.11	4.26
51	52	0.168128	GGATAAGCAAACGCAACGCT	59.832	50.000	0.00	0.00	37.68	5.07
52	53	0.168128	AGGATAAGCAAACGCAACGC	59.832	50.000	0.00	0.00	0.00	4.84
53	54	1.196808	ACAGGATAAGCAAACGCAACG	59.803	47.619	0.00	0.00	0.00	4.10
54	55	2.989422	ACAGGATAAGCAAACGCAAC	57.011	45.000	0.00	0.00	0.00	4.17
55	56	4.314740	AAAACAGGATAAGCAAACGCAA	57.685	36.364	0.00	0.00	0.00	4.85
56	57	4.614993	GCTAAAACAGGATAAGCAAACGCA	60.615	41.667	0.00	0.00	33.38	5.24
57	58	3.851969	GCTAAAACAGGATAAGCAAACGC	59.148	43.478	0.00	0.00	33.38	4.84
58	59	4.851558	GTGCTAAAACAGGATAAGCAAACG	59.148	41.667	0.00	0.00	44.16	3.60
59	60	5.629435	GTGTGCTAAAACAGGATAAGCAAAC	59.371	40.000	0.59	0.59	44.16	2.93
225	252	7.728847	GGATTGGCCCAAATTGAATAAATAC	57.271	36.000	0.00	0.00	0.00	1.89
283	314	3.513680	TCAATGCCATGCAAATCTGAC	57.486	42.857	0.00	0.00	43.62	3.51
307	338	2.270352	TTGCGTTTCCAGTTGGAGAT	57.730	45.000	0.51	0.00	46.36	2.75
335	366	5.512749	GCATGGTCAAGGATGAGATGATAGT	60.513	44.000	0.00	0.00	35.88	2.12
336	367	4.936411	GCATGGTCAAGGATGAGATGATAG	59.064	45.833	0.00	0.00	35.88	2.08
442	484	2.639839	ACTGTAGAATGTGTGGCTTCCT	59.360	45.455	0.00	0.00	0.00	3.36
528	578	6.291377	TGGTGGAGAGATTATTACTTGATGC	58.709	40.000	0.00	0.00	0.00	3.91
531	581	7.252612	TGTTGGTGGAGAGATTATTACTTGA	57.747	36.000	0.00	0.00	0.00	3.02
577	643	5.551233	TGTCCGATGATTATTCCATCCTTC	58.449	41.667	0.00	0.00	37.67	3.46
581	647	3.686726	GGCTGTCCGATGATTATTCCATC	59.313	47.826	0.00	0.00	37.60	3.51
650	723	8.485392	TGGAATTTGTAGACATACATGATCTCA	58.515	33.333	0.00	0.00	41.49	3.27
651	724	8.893219	TGGAATTTGTAGACATACATGATCTC	57.107	34.615	0.00	0.00	41.49	2.75
652	725	9.857656	AATGGAATTTGTAGACATACATGATCT	57.142	29.630	0.00	0.00	41.49	2.75
758	1267	1.108132	TTGGTGGTGTAAAACGGGGC	61.108	55.000	0.00	0.00	0.00	5.80
759	1268	1.067364	GTTTGGTGGTGTAAAACGGGG	59.933	52.381	0.00	0.00	0.00	5.73
779	1288	3.379240	CAGCACTAGTGGAGATCATTCG	58.621	50.000	23.95	0.00	0.00	3.34
1086	1670	3.177884	AACCAGCTCCAGGGCACA	61.178	61.111	0.00	0.00	34.17	4.57
1521	2114	2.110213	AACTCCAACCGCTTCGCA	59.890	55.556	0.00	0.00	0.00	5.10
2148	2747	1.946768	TGTACCTTGTTCAGCTGTTGC	59.053	47.619	14.67	5.83	40.05	4.17
2156	2755	3.311106	GTTCGATCGTGTACCTTGTTCA	58.689	45.455	15.94	0.00	0.00	3.18
2172	2771	4.082408	ACCTCAACATCTTGTATCGTTCGA	60.082	41.667	0.00	0.00	0.00	3.71
2217	2816	1.153647	CGTATGCCGCTTGTCCTCA	60.154	57.895	0.00	0.00	0.00	3.86
2279	2878	0.340558	TTAGGTGTGCTAGGGGCCTA	59.659	55.000	0.84	0.00	40.92	3.93
2280	2879	0.549169	TTTAGGTGTGCTAGGGGCCT	60.549	55.000	0.84	0.00	40.92	5.19
2281	2880	0.393944	GTTTAGGTGTGCTAGGGGCC	60.394	60.000	0.00	0.00	40.92	5.80
2282	2881	0.618981	AGTTTAGGTGTGCTAGGGGC	59.381	55.000	0.00	0.00	42.22	5.80
2283	2882	1.209747	GGAGTTTAGGTGTGCTAGGGG	59.790	57.143	0.00	0.00	0.00	4.79
2299	2898	1.466025	TAAGGGCGTTGTCGTGGAGT	61.466	55.000	2.08	0.00	39.49	3.85
2323	2922	0.706729	GACGCTTTACACGGTTCTCG	59.293	55.000	0.00	0.00	45.88	4.04
2360	2959	2.034001	CGTGTGAAGACCTTTGTTCGTC	60.034	50.000	0.00	0.00	0.00	4.20
2379	2978	4.988716	TCCGTGACAGGGCTCCGT	62.989	66.667	9.40	0.00	0.00	4.69
2394	2993	0.465097	TCGTCGTGGGTATCCTCTCC	60.465	60.000	0.00	0.00	0.00	3.71
2462	3061	2.736995	CGAAAACTCGGCGCCTCA	60.737	61.111	26.68	10.09	0.00	3.86
2470	3069	1.131420	GCTGCTGAGCGAAAACTCG	59.869	57.895	0.00	0.00	39.68	4.18
2479	3078	2.113433	CATGGGTGAGCTGCTGAGC	61.113	63.158	7.01	8.67	46.64	4.26
2553	3152	1.746220	CCTTAGCACTAGTGACGCTCT	59.254	52.381	27.08	15.12	37.20	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.