AutoCloner

Multiple sequence alignment - TraesCS2D01G197700

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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	TraesCS2D01G197700	chr2D	100.000	2433	0	0	1	2433	145366964	145364532	0.000000e+00	4494
1	TraesCS2D01G197700	chr2D	98.912	2298	18	2	1	2295	112882577	112884870	0.000000e+00	4098
2	TraesCS2D01G197700	chr1D	98.871	2302	17	3	1	2297	487823992	487821695	0.000000e+00	4098
3	TraesCS2D01G197700	chr1D	98.737	2296	27	2	1	2295	41900122	41897828	0.000000e+00	4078
4	TraesCS2D01G197700	chr7D	98.783	2300	23	2	1	2295	132173674	132171375	0.000000e+00	4087
5	TraesCS2D01G197700	chr7D	98.782	2298	21	3	1	2295	52805970	52808263	0.000000e+00	4082
6	TraesCS2D01G197700	chr7D	98.656	2306	19	5	1	2298	625483507	625481206	0.000000e+00	4076
7	TraesCS2D01G197700	chr3D	98.825	2298	20	2	1	2295	526059529	526057236	0.000000e+00	4087
8	TraesCS2D01G197700	chr3D	98.780	2296	18	4	1	2295	613577827	613575541	0.000000e+00	4076
9	TraesCS2D01G197700	chr3D	98.696	2301	20	4	1	2295	520060992	520063288	0.000000e+00	4074
10	TraesCS2D01G197700	chr2B	91.667	108	6	1	2326	2430	202931483	202931376	1.950000e-31	147

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	TraesCS2D01G197700	chr2D	145364532	145366964	2432	True	4494	4494	100.000	1	2433	1	chr2D.!!$R1	2432
1	TraesCS2D01G197700	chr2D	112882577	112884870	2293	False	4098	4098	98.912	1	2295	1	chr2D.!!$F1	2294
2	TraesCS2D01G197700	chr1D	487821695	487823992	2297	True	4098	4098	98.871	1	2297	1	chr1D.!!$R2	2296
3	TraesCS2D01G197700	chr1D	41897828	41900122	2294	True	4078	4078	98.737	1	2295	1	chr1D.!!$R1	2294
4	TraesCS2D01G197700	chr7D	132171375	132173674	2299	True	4087	4087	98.783	1	2295	1	chr7D.!!$R1	2294
5	TraesCS2D01G197700	chr7D	52805970	52808263	2293	False	4082	4082	98.782	1	2295	1	chr7D.!!$F1	2294
6	TraesCS2D01G197700	chr7D	625481206	625483507	2301	True	4076	4076	98.656	1	2298	1	chr7D.!!$R2	2297
7	TraesCS2D01G197700	chr3D	526057236	526059529	2293	True	4087	4087	98.825	1	2295	1	chr3D.!!$R1	2294
8	TraesCS2D01G197700	chr3D	613575541	613577827	2286	True	4076	4076	98.780	1	2295	1	chr3D.!!$R2	2294
9	TraesCS2D01G197700	chr3D	520060992	520063288	2296	False	4074	4074	98.696	1	2295	1	chr3D.!!$F1	2294

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
656	659	5.046376	GGATGGGTTTTGAAGACCATGAAAT	60.046	40.0	7.23	0.0	43.4	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2325	2334	0.034477	CCCGGCAACTGTAATCCCTT	60.034	55.0	0.0	0.0	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
656	659	5.046376	GGATGGGTTTTGAAGACCATGAAAT	60.046	40.000	7.23	0.00	43.40	2.17
1149	1152	1.473257	CCATACGTGCCACTAGTGCAT	60.473	52.381	17.86	7.77	41.46	3.96
1297	1300	7.985476	ACTATGTTTTTCAACAGATAATCCCG	58.015	34.615	0.00	0.00	46.25	5.14
1656	1659	4.343239	TCGATGACTGTGAGGATGATGATT	59.657	41.667	0.00	0.00	0.00	2.57
2279	2288	0.702316	ATGAACCGGGGTAAAAGCCT	59.298	50.000	6.32	0.00	35.71	4.58
2298	2307	3.518303	GCCTCTTTTCCTACTAGTGGGAA	59.482	47.826	30.80	30.80	46.51	3.97
2306	2315	6.713731	TTCCTACTAGTGGGAAGGAATTTT	57.286	37.500	30.80	0.00	43.91	1.82
2307	2316	6.309389	TCCTACTAGTGGGAAGGAATTTTC	57.691	41.667	24.50	0.00	37.29	2.29
2308	2317	6.030082	TCCTACTAGTGGGAAGGAATTTTCT	58.970	40.000	24.50	0.00	37.29	2.52
2309	2318	6.504279	TCCTACTAGTGGGAAGGAATTTTCTT	59.496	38.462	24.50	0.00	37.29	2.52
2310	2319	7.018249	TCCTACTAGTGGGAAGGAATTTTCTTT	59.982	37.037	24.50	0.00	37.29	2.52
2311	2320	7.670140	CCTACTAGTGGGAAGGAATTTTCTTTT	59.330	37.037	20.19	0.00	32.26	2.27
2312	2321	7.914427	ACTAGTGGGAAGGAATTTTCTTTTT	57.086	32.000	0.00	0.00	0.00	1.94
2341	2350	6.136541	CTTTATGAAGGGATTACAGTTGCC	57.863	41.667	0.00	0.00	0.00	4.52
2342	2351	2.107950	TGAAGGGATTACAGTTGCCG	57.892	50.000	0.00	0.00	0.00	5.69
2343	2352	1.339631	TGAAGGGATTACAGTTGCCGG	60.340	52.381	0.00	0.00	0.00	6.13
2344	2353	0.034477	AAGGGATTACAGTTGCCGGG	60.034	55.000	2.18	0.00	0.00	5.73
2345	2354	2.119029	GGGATTACAGTTGCCGGGC	61.119	63.158	13.32	13.32	0.00	6.13
2346	2355	2.119029	GGATTACAGTTGCCGGGCC	61.119	63.158	17.97	1.16	0.00	5.80
2347	2356	2.437716	ATTACAGTTGCCGGGCCG	60.438	61.111	21.46	21.46	0.00	6.13
2348	2357	3.262448	ATTACAGTTGCCGGGCCGT	62.262	57.895	26.32	10.85	0.00	5.68
2349	2358	2.757980	ATTACAGTTGCCGGGCCGTT	62.758	55.000	26.32	1.51	0.00	4.44
2360	2369	4.324991	GGCCGTTGGACCCGAAGT	62.325	66.667	0.00	0.00	0.00	3.01
2361	2370	2.741211	GCCGTTGGACCCGAAGTC	60.741	66.667	0.00	0.00	45.51	3.01
2362	2371	3.057337	CCGTTGGACCCGAAGTCT	58.943	61.111	5.67	0.00	45.54	3.24
2363	2372	1.880819	GCCGTTGGACCCGAAGTCTA	61.881	60.000	5.67	0.00	45.54	2.59
2364	2373	0.604578	CCGTTGGACCCGAAGTCTAA	59.395	55.000	5.67	3.44	45.54	2.10
2367	2376	2.825861	TTGGACCCGAAGTCTAACAC	57.174	50.000	5.67	0.00	45.54	3.32
2368	2377	0.599558	TGGACCCGAAGTCTAACACG	59.400	55.000	5.67	0.00	45.54	4.49
2369	2378	0.108945	GGACCCGAAGTCTAACACGG	60.109	60.000	0.00	0.00	45.54	4.94
2370	2379	0.735287	GACCCGAAGTCTAACACGGC	60.735	60.000	0.00	0.00	42.69	5.68
2371	2380	1.290955	CCCGAAGTCTAACACGGCA	59.709	57.895	0.00	0.00	43.37	5.69
2372	2381	0.320073	CCCGAAGTCTAACACGGCAA	60.320	55.000	0.00	0.00	43.37	4.52
2373	2382	0.788391	CCGAAGTCTAACACGGCAAC	59.212	55.000	0.00	0.00	38.98	4.17
2374	2383	1.493772	CGAAGTCTAACACGGCAACA	58.506	50.000	0.00	0.00	0.00	3.33
2375	2384	1.191647	CGAAGTCTAACACGGCAACAC	59.808	52.381	0.00	0.00	0.00	3.32
2376	2385	1.529865	GAAGTCTAACACGGCAACACC	59.470	52.381	0.00	0.00	0.00	4.16
2392	2401	4.787286	CCGCATGGCCCGGTTACA	62.787	66.667	10.49	0.00	40.84	2.41
2393	2402	3.505184	CGCATGGCCCGGTTACAC	61.505	66.667	0.00	0.00	0.00	2.90
2394	2403	3.138128	GCATGGCCCGGTTACACC	61.138	66.667	0.00	0.00	34.05	4.16
2395	2404	2.439519	CATGGCCCGGTTACACCC	60.440	66.667	0.00	0.00	33.75	4.61
2396	2405	2.936584	ATGGCCCGGTTACACCCA	60.937	61.111	0.00	0.00	33.75	4.51
2397	2406	3.276642	ATGGCCCGGTTACACCCAC	62.277	63.158	0.00	0.00	33.75	4.61
2398	2407	4.728110	GGCCCGGTTACACCCACC	62.728	72.222	0.00	0.00	33.75	4.61
2399	2408	3.643554	GCCCGGTTACACCCACCT	61.644	66.667	0.00	0.00	33.75	4.00
2400	2409	2.666812	CCCGGTTACACCCACCTC	59.333	66.667	0.00	0.00	33.75	3.85
2401	2410	2.263540	CCGGTTACACCCACCTCG	59.736	66.667	0.00	0.00	33.75	4.63
2402	2411	2.263540	CGGTTACACCCACCTCGG	59.736	66.667	0.00	0.00	33.75	4.63
2403	2412	2.576832	CGGTTACACCCACCTCGGT	61.577	63.158	0.00	0.00	33.75	4.69
2404	2413	1.756665	GGTTACACCCACCTCGGTT	59.243	57.895	0.00	0.00	32.17	4.44
2405	2414	0.604511	GGTTACACCCACCTCGGTTG	60.605	60.000	0.00	0.00	32.17	3.77
2406	2415	0.604511	GTTACACCCACCTCGGTTGG	60.605	60.000	4.75	4.75	37.01	3.77
2407	2416	0.763604	TTACACCCACCTCGGTTGGA	60.764	55.000	12.73	0.00	35.22	3.53
2408	2417	1.474332	TACACCCACCTCGGTTGGAC	61.474	60.000	12.73	0.00	35.22	4.02
2409	2418	3.246880	ACCCACCTCGGTTGGACC	61.247	66.667	12.73	0.00	35.22	4.46
2410	2419	2.928396	CCCACCTCGGTTGGACCT	60.928	66.667	0.00	0.00	35.66	3.85
2411	2420	2.526046	CCCACCTCGGTTGGACCTT	61.526	63.158	0.00	0.00	35.66	3.50
2412	2421	1.003718	CCACCTCGGTTGGACCTTC	60.004	63.158	0.00	0.00	35.66	3.46
2413	2422	1.003718	CACCTCGGTTGGACCTTCC	60.004	63.158	0.00	0.00	35.66	3.46
2414	2423	1.460689	ACCTCGGTTGGACCTTCCA	60.461	57.895	0.00	0.00	46.61	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
354	357	4.212004	CGTCCGAGTACGACATTTCCTATA	59.788	45.833	0.00	0.00	45.68	1.31
782	785	5.126061	GTGACAAGCATACCCTCATCAAAAT	59.874	40.000	0.00	0.00	0.00	1.82
1149	1152	5.772825	AGTAGTTACCGTAGTTCAACACA	57.227	39.130	0.00	0.00	0.00	3.72
1297	1300	4.464008	TCAAATGAGGCATACAATCCTCC	58.536	43.478	5.90	0.00	46.39	4.30
1307	1310	6.208797	CCATTCTGATACATCAAATGAGGCAT	59.791	38.462	18.46	0.00	37.41	4.40
1949	1952	5.064558	GTGTCCTCTCTTATATCTCCGTGA	58.935	45.833	0.00	0.00	0.00	4.35
2279	2288	5.019657	TCCTTCCCACTAGTAGGAAAAGA	57.980	43.478	21.12	17.54	41.54	2.52
2318	2327	5.220854	CGGCAACTGTAATCCCTTCATAAAG	60.221	44.000	0.00	0.00	0.00	1.85
2319	2328	4.638421	CGGCAACTGTAATCCCTTCATAAA	59.362	41.667	0.00	0.00	0.00	1.40
2320	2329	4.196193	CGGCAACTGTAATCCCTTCATAA	58.804	43.478	0.00	0.00	0.00	1.90
2321	2330	3.433031	CCGGCAACTGTAATCCCTTCATA	60.433	47.826	0.00	0.00	0.00	2.15
2322	2331	2.643551	CGGCAACTGTAATCCCTTCAT	58.356	47.619	0.00	0.00	0.00	2.57
2323	2332	1.339631	CCGGCAACTGTAATCCCTTCA	60.340	52.381	0.00	0.00	0.00	3.02
2324	2333	1.379527	CCGGCAACTGTAATCCCTTC	58.620	55.000	0.00	0.00	0.00	3.46
2325	2334	0.034477	CCCGGCAACTGTAATCCCTT	60.034	55.000	0.00	0.00	0.00	3.95
2326	2335	1.607612	CCCGGCAACTGTAATCCCT	59.392	57.895	0.00	0.00	0.00	4.20
2327	2336	2.119029	GCCCGGCAACTGTAATCCC	61.119	63.158	3.91	0.00	0.00	3.85
2328	2337	2.119029	GGCCCGGCAACTGTAATCC	61.119	63.158	12.58	0.00	0.00	3.01
2329	2338	2.469516	CGGCCCGGCAACTGTAATC	61.470	63.158	12.58	0.00	0.00	1.75
2330	2339	2.437716	CGGCCCGGCAACTGTAAT	60.438	61.111	12.58	0.00	0.00	1.89
2331	2340	3.479127	AACGGCCCGGCAACTGTAA	62.479	57.895	12.58	0.00	0.00	2.41
2332	2341	3.943691	AACGGCCCGGCAACTGTA	61.944	61.111	12.58	0.00	0.00	2.74
2343	2352	4.324991	ACTTCGGGTCCAACGGCC	62.325	66.667	0.00	0.00	0.00	6.13
2344	2353	1.880819	TAGACTTCGGGTCCAACGGC	61.881	60.000	5.97	0.00	45.54	5.68
2345	2354	0.604578	TTAGACTTCGGGTCCAACGG	59.395	55.000	5.97	0.00	45.54	4.44
2346	2355	1.000060	TGTTAGACTTCGGGTCCAACG	60.000	52.381	12.59	0.00	45.15	4.10
2347	2356	2.410939	GTGTTAGACTTCGGGTCCAAC	58.589	52.381	11.32	11.32	45.54	3.77
2348	2357	1.000060	CGTGTTAGACTTCGGGTCCAA	60.000	52.381	5.97	0.00	45.54	3.53
2349	2358	0.599558	CGTGTTAGACTTCGGGTCCA	59.400	55.000	5.97	0.00	45.54	4.02
2350	2359	0.108945	CCGTGTTAGACTTCGGGTCC	60.109	60.000	5.97	0.00	45.54	4.46
2351	2360	0.735287	GCCGTGTTAGACTTCGGGTC	60.735	60.000	13.50	2.08	44.80	4.46
2352	2361	1.291272	GCCGTGTTAGACTTCGGGT	59.709	57.895	13.50	0.00	42.71	5.28
2353	2362	0.320073	TTGCCGTGTTAGACTTCGGG	60.320	55.000	13.50	0.00	42.71	5.14
2354	2363	0.788391	GTTGCCGTGTTAGACTTCGG	59.212	55.000	0.00	0.00	44.86	4.30
2355	2364	1.191647	GTGTTGCCGTGTTAGACTTCG	59.808	52.381	0.00	0.00	0.00	3.79
2356	2365	1.529865	GGTGTTGCCGTGTTAGACTTC	59.470	52.381	0.00	0.00	0.00	3.01
2357	2366	1.589803	GGTGTTGCCGTGTTAGACTT	58.410	50.000	0.00	0.00	0.00	3.01
2358	2367	3.300711	GGTGTTGCCGTGTTAGACT	57.699	52.632	0.00	0.00	0.00	3.24
2373	2382	4.787286	TAACCGGGCCATGCGGTG	62.787	66.667	22.97	0.45	36.03	4.94
2374	2383	4.789123	GTAACCGGGCCATGCGGT	62.789	66.667	17.69	17.69	37.66	5.68
2375	2384	4.787286	TGTAACCGGGCCATGCGG	62.787	66.667	16.37	16.37	0.00	5.69
2376	2385	3.505184	GTGTAACCGGGCCATGCG	61.505	66.667	6.32	0.00	0.00	4.73
2392	2401	3.246880	GGTCCAACCGAGGTGGGT	61.247	66.667	14.99	0.00	44.64	4.51
2393	2402	2.465055	GAAGGTCCAACCGAGGTGGG	62.465	65.000	9.47	9.47	44.90	4.61
2394	2403	1.003718	GAAGGTCCAACCGAGGTGG	60.004	63.158	0.00	1.83	44.90	4.61
2395	2404	1.003718	GGAAGGTCCAACCGAGGTG	60.004	63.158	0.00	0.00	44.90	4.00
2396	2405	1.460689	TGGAAGGTCCAACCGAGGT	60.461	57.895	0.00	0.00	45.00	3.85
2397	2406	3.478780	TGGAAGGTCCAACCGAGG	58.521	61.111	0.00	0.00	45.00	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.