AutoCloner

Multiple sequence alignment - TraesCS2B01G266800

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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	TraesCS2B01G266800	chr2B	100.000	2628	0	0	1	2628	359314834	359317461	0.000000e+00	4854.0
1	TraesCS2B01G266800	chr2B	98.780	2049	24	1	581	2628	373109196	373107148	0.000000e+00	3644.0
2	TraesCS2B01G266800	chr2B	95.667	300	9	3	2004	2301	548972281	548971984	1.830000e-131	479.0
3	TraesCS2B01G266800	chr2B	95.833	288	11	1	2012	2298	87539684	87539971	5.120000e-127	464.0
4	TraesCS2B01G266800	chr2B	100.000	45	0	0	974	1018	359315762	359315806	1.680000e-12	84.2
5	TraesCS2B01G266800	chr2B	100.000	45	0	0	929	973	359315807	359315851	1.680000e-12	84.2
6	TraesCS2B01G266800	chr2B	100.000	45	0	0	929	973	373108803	373108759	1.680000e-12	84.2
7	TraesCS2B01G266800	chr2B	85.714	70	10	0	581	650	454847682	454847613	1.010000e-09	75.0
8	TraesCS2B01G266800	chr5B	98.440	2051	30	2	579	2628	577239398	577237349	0.000000e+00	3609.0
9	TraesCS2B01G266800	chr5B	96.651	1045	27	4	974	2017	342182055	342183092	0.000000e+00	1729.0
10	TraesCS2B01G266800	chr5B	96.388	886	31	1	1132	2016	118953507	118952622	0.000000e+00	1458.0
11	TraesCS2B01G266800	chr5B	96.183	393	15	0	581	973	342181707	342182099	0.000000e+00	643.0
12	TraesCS2B01G266800	chr5B	97.376	343	9	0	2286	2628	118952628	118952286	3.770000e-163	584.0
13	TraesCS2B01G266800	chr5B	94.884	215	11	0	759	973	118953804	118953590	1.170000e-88	337.0
14	TraesCS2B01G266800	chr5B	97.396	192	5	0	581	772	118956168	118955977	7.010000e-86	327.0
15	TraesCS2B01G266800	chr5B	96.094	128	5	0	974	1101	118953634	118953507	2.650000e-50	209.0
16	TraesCS2B01G266800	chr5B	100.000	45	0	0	974	1018	577239048	577239004	1.680000e-12	84.2
17	TraesCS2B01G266800	chr4B	97.129	1045	28	1	974	2016	535340961	535342005	0.000000e+00	1762.0
18	TraesCS2B01G266800	chr4B	96.793	343	9	1	2286	2628	535341999	535342339	2.930000e-159	571.0
19	TraesCS2B01G266800	chr4B	93.130	393	11	4	581	973	535340629	535341005	1.770000e-156	562.0
20	TraesCS2B01G266800	chr6D	96.080	1046	36	3	974	2016	17967982	17969025	0.000000e+00	1700.0
21	TraesCS2B01G266800	chr6D	95.718	397	16	1	580	975	17967633	17968029	2.850000e-179	638.0
22	TraesCS2B01G266800	chr6D	98.834	343	4	0	2286	2628	17969019	17969361	1.730000e-171	612.0
23	TraesCS2B01G266800	chr6D	95.115	348	17	0	1669	2016	425080991	425081338	1.370000e-152	549.0
24	TraesCS2B01G266800	chr6D	92.978	356	12	2	2286	2628	425081332	425081687	8.390000e-140	507.0
25	TraesCS2B01G266800	chr7D	94.837	1046	33	9	974	2016	10632947	10631920	0.000000e+00	1613.0
26	TraesCS2B01G266800	chr7D	96.709	395	12	1	580	973	10633297	10632903	0.000000e+00	656.0
27	TraesCS2B01G266800	chr7D	97.668	343	4	1	2286	2628	10631926	10631588	1.050000e-163	586.0
28	TraesCS2B01G266800	chr7D	93.064	346	24	0	1669	2014	536649684	536650029	8.390000e-140	507.0
29	TraesCS2B01G266800	chr7D	90.857	350	20	1	2288	2625	536650027	536650376	2.380000e-125	459.0
30	TraesCS2B01G266800	chr7D	96.727	275	9	0	2016	2290	618584047	618583773	2.380000e-125	459.0
31	TraesCS2B01G266800	chr7D	89.744	351	21	2	2288	2626	31945469	31945816	4.020000e-118	435.0
32	TraesCS2B01G266800	chr7D	75.989	708	126	29	979	1670	457111957	457112636	2.520000e-85	326.0
33	TraesCS2B01G266800	chr2A	89.810	579	27	14	1	574	430954751	430955302	0.000000e+00	713.0
34	TraesCS2B01G266800	chr2A	87.755	294	34	2	2014	2307	470800230	470799939	2.500000e-90	342.0
35	TraesCS2B01G266800	chr2A	88.153	287	33	1	2014	2300	262727558	262727843	9.010000e-90	340.0
36	TraesCS2B01G266800	chr2D	92.913	381	13	4	1	371	308982597	308982221	2.300000e-150	542.0
37	TraesCS2B01G266800	chr2D	88.532	218	14	5	367	580	308977752	308977542	1.210000e-63	254.0
38	TraesCS2B01G266800	chr7B	94.529	329	18	0	580	908	700631196	700631524	2.330000e-140	508.0
39	TraesCS2B01G266800	chr1B	96.057	279	11	0	2016	2294	99080102	99080380	3.080000e-124	455.0
40	TraesCS2B01G266800	chr4D	95.406	283	13	0	2011	2293	499547993	499547711	3.990000e-123	451.0
41	TraesCS2B01G266800	chr3A	95.714	280	12	0	2016	2295	55378047	55378326	3.990000e-123	451.0
42	TraesCS2B01G266800	chr3A	91.156	294	23	3	2016	2309	658985353	658985063	1.900000e-106	396.0
43	TraesCS2B01G266800	chr3A	87.755	294	34	2	2014	2307	592844661	592844952	2.500000e-90	342.0
44	TraesCS2B01G266800	chr3A	87.075	294	36	2	2014	2307	412675453	412675744	5.420000e-87	331.0
45	TraesCS2B01G266800	chr5D	91.358	324	15	2	2288	2599	404855490	404855168	5.200000e-117	431.0
46	TraesCS2B01G266800	chr3D	93.929	280	17	0	2016	2295	50014251	50013972	8.700000e-115	424.0
47	TraesCS2B01G266800	chr5A	87.629	291	34	2	2017	2307	518255966	518255678	1.170000e-88	337.0
48	TraesCS2B01G266800	chr6B	97.222	36	0	1	1038	1073	86439805	86439771	2.820000e-05	60.2

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	TraesCS2B01G266800	chr2B	359314834	359317461	2627	False	1674.133333	4854	100.000000	1	2628	3	chr2B.!!$F2	2627
1	TraesCS2B01G266800	chr2B	373107148	373109196	2048	True	1864.100000	3644	99.390000	581	2628	2	chr2B.!!$R3	2047
2	TraesCS2B01G266800	chr5B	577237349	577239398	2049	True	1846.600000	3609	99.220000	579	2628	2	chr5B.!!$R2	2049
3	TraesCS2B01G266800	chr5B	342181707	342183092	1385	False	1186.000000	1729	96.417000	581	2017	2	chr5B.!!$F1	1436
4	TraesCS2B01G266800	chr5B	118952286	118956168	3882	True	583.000000	1458	96.427600	581	2628	5	chr5B.!!$R1	2047
5	TraesCS2B01G266800	chr4B	535340629	535342339	1710	False	965.000000	1762	95.684000	581	2628	3	chr4B.!!$F1	2047
6	TraesCS2B01G266800	chr6D	17967633	17969361	1728	False	983.333333	1700	96.877333	580	2628	3	chr6D.!!$F1	2048
7	TraesCS2B01G266800	chr6D	425080991	425081687	696	False	528.000000	549	94.046500	1669	2628	2	chr6D.!!$F2	959
8	TraesCS2B01G266800	chr7D	10631588	10633297	1709	True	951.666667	1613	96.404667	580	2628	3	chr7D.!!$R2	2048
9	TraesCS2B01G266800	chr7D	536649684	536650376	692	False	483.000000	507	91.960500	1669	2625	2	chr7D.!!$F3	956
10	TraesCS2B01G266800	chr7D	457111957	457112636	679	False	326.000000	326	75.989000	979	1670	1	chr7D.!!$F2	691
11	TraesCS2B01G266800	chr2A	430954751	430955302	551	False	713.000000	713	89.810000	1	574	1	chr2A.!!$F2	573

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
195	196	1.000612	GTCCGGGAAGAGGGAGAGT	59.999	63.158	0.0	0.0	31.73	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1748	3987	4.596212	TGGATGACATGGATGCTCTAGAAT	59.404	41.667	0.0	0.0	0.0	2.4	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
153	154	2.055042	CCTCGGGGAGTGGAGACAG	61.055	68.421	0.00	0.00	36.12	3.51
195	196	1.000612	GTCCGGGAAGAGGGAGAGT	59.999	63.158	0.00	0.00	31.73	3.24
253	254	1.296715	GGTGTCACCTAGTGGCTGG	59.703	63.158	15.22	0.00	39.12	4.85
254	255	1.481056	GGTGTCACCTAGTGGCTGGT	61.481	60.000	15.22	0.00	39.12	4.00
255	256	1.263356	GTGTCACCTAGTGGCTGGTA	58.737	55.000	0.59	0.00	39.12	3.25
296	297	7.447374	ACATGTGATTCGTTCTTGGATTTTA	57.553	32.000	0.00	0.00	0.00	1.52
327	328	7.643123	TCCTAGGCCTCTTTTCTTTTATTCAT	58.357	34.615	9.68	0.00	0.00	2.57
366	367	9.503399	ACACGAAAATAGAAAAATTAGAGGACT	57.497	29.630	0.00	0.00	0.00	3.85
423	424	4.107622	GCATTGAGTATTTGATGCCACAC	58.892	43.478	0.00	0.00	39.08	3.82
428	429	6.154203	TGAGTATTTGATGCCACACAAAAA	57.846	33.333	0.00	0.00	39.01	1.94
454	456	9.710818	AATAGAGTAATTATAATAGAGGCCGGA	57.289	33.333	5.05	0.00	0.00	5.14
455	457	7.648039	AGAGTAATTATAATAGAGGCCGGAG	57.352	40.000	5.05	0.00	0.00	4.63
456	458	7.183460	AGAGTAATTATAATAGAGGCCGGAGT	58.817	38.462	5.05	0.00	0.00	3.85
457	459	7.122948	AGAGTAATTATAATAGAGGCCGGAGTG	59.877	40.741	5.05	0.00	0.00	3.51
465	467	1.001760	AGGCCGGAGTGGAGTGTAT	59.998	57.895	5.05	0.00	42.00	2.29
479	481	4.716784	TGGAGTGTATGCTAGATTTCCTGT	59.283	41.667	0.00	0.00	0.00	4.00
490	492	7.280356	TGCTAGATTTCCTGTTAAAGATACCC	58.720	38.462	0.00	0.00	0.00	3.69
491	493	6.424207	GCTAGATTTCCTGTTAAAGATACCCG	59.576	42.308	0.00	0.00	0.00	5.28
492	494	5.123936	AGATTTCCTGTTAAAGATACCCGC	58.876	41.667	0.00	0.00	0.00	6.13
494	496	3.985019	TCCTGTTAAAGATACCCGCAA	57.015	42.857	0.00	0.00	0.00	4.85
495	497	3.869065	TCCTGTTAAAGATACCCGCAAG	58.131	45.455	0.00	0.00	0.00	4.01
526	530	7.458409	AGATTCACAAAGTTCAGCATACAAT	57.542	32.000	0.00	0.00	0.00	2.71
527	531	7.889469	AGATTCACAAAGTTCAGCATACAATT	58.111	30.769	0.00	0.00	0.00	2.32
528	532	8.362639	AGATTCACAAAGTTCAGCATACAATTT	58.637	29.630	0.00	0.00	0.00	1.82
567	571	9.013229	TGATTTTTCACATGCTTCTGTAATAGT	57.987	29.630	0.00	0.00	0.00	2.12
574	578	8.424133	TCACATGCTTCTGTAATAGTCATGTAT	58.576	33.333	4.88	0.00	38.97	2.29
575	579	9.049523	CACATGCTTCTGTAATAGTCATGTATT	57.950	33.333	4.88	0.00	38.97	1.89
576	580	9.265901	ACATGCTTCTGTAATAGTCATGTATTC	57.734	33.333	0.00	0.00	39.09	1.75
577	581	9.486497	CATGCTTCTGTAATAGTCATGTATTCT	57.514	33.333	0.00	0.00	31.60	2.40
670	674	3.555956	GCACAGCGTATTTACTGCTATGT	59.444	43.478	11.52	5.10	37.42	2.29
778	2968	1.140312	ATGTCGGAGTGGCCCATAAT	58.860	50.000	0.00	0.00	0.00	1.28
820	3010	1.686355	CTACTGAGATGGCGTCCTCT	58.314	55.000	2.37	0.00	0.00	3.69
1124	3361	3.446161	AGGTACACGTTTAGCAGCTGATA	59.554	43.478	20.43	14.08	0.00	2.15
1746	3985	2.505819	GCTGGAAATCTGGGACTTAGGA	59.494	50.000	0.00	0.00	0.00	2.94
1748	3987	4.348168	GCTGGAAATCTGGGACTTAGGATA	59.652	45.833	0.00	0.00	0.00	2.59
1893	4133	0.535335	GGCACCCATCTCGTACAGAA	59.465	55.000	0.00	0.00	33.62	3.02
2070	4586	1.604604	TGCACTTGGGACTAGCAAAC	58.395	50.000	0.00	0.00	31.42	2.93
2074	4590	2.095059	CACTTGGGACTAGCAAACATGC	60.095	50.000	0.00	0.00	0.00	4.06
2128	4644	7.289310	AGAGGGTTAGAGTAACATAGGTAGAC	58.711	42.308	0.00	0.00	40.39	2.59
2130	4646	7.593653	AGGGTTAGAGTAACATAGGTAGACAT	58.406	38.462	0.00	0.00	40.39	3.06
2232	4748	5.648526	ACTATGCACTATGGAGGTAGTATCG	59.351	44.000	0.00	0.00	33.29	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
153	154	0.610687	CACACTCCCCTCTTGACTCC	59.389	60.000	0.00	0.00	0.00	3.85
195	196	2.107705	GCACGAGCTACCTCTGCTA	58.892	57.895	0.00	0.00	41.30	3.49
296	297	4.043596	AGAAAAGAGGCCTAGGATGACAT	58.956	43.478	14.75	0.00	0.00	3.06
355	356	6.116126	GGCATGTCACTTTAGTCCTCTAATT	58.884	40.000	0.00	0.00	36.25	1.40
356	357	5.396884	GGGCATGTCACTTTAGTCCTCTAAT	60.397	44.000	0.00	0.00	36.25	1.73
357	358	4.081087	GGGCATGTCACTTTAGTCCTCTAA	60.081	45.833	0.00	0.00	34.76	2.10
358	359	3.451178	GGGCATGTCACTTTAGTCCTCTA	59.549	47.826	0.00	0.00	0.00	2.43
359	360	2.237392	GGGCATGTCACTTTAGTCCTCT	59.763	50.000	0.00	0.00	0.00	3.69
360	361	2.633488	GGGCATGTCACTTTAGTCCTC	58.367	52.381	0.00	0.00	0.00	3.71
361	362	1.066143	CGGGCATGTCACTTTAGTCCT	60.066	52.381	0.00	0.00	0.00	3.85
362	363	1.369625	CGGGCATGTCACTTTAGTCC	58.630	55.000	0.00	0.00	0.00	3.85
363	364	0.727398	GCGGGCATGTCACTTTAGTC	59.273	55.000	0.00	0.00	0.00	2.59
364	365	0.324943	AGCGGGCATGTCACTTTAGT	59.675	50.000	0.00	0.00	0.00	2.24
365	366	1.131126	CAAGCGGGCATGTCACTTTAG	59.869	52.381	0.00	0.00	0.00	1.85
366	367	1.164411	CAAGCGGGCATGTCACTTTA	58.836	50.000	0.00	0.00	0.00	1.85
367	368	0.537143	TCAAGCGGGCATGTCACTTT	60.537	50.000	0.00	0.00	0.00	2.66
368	369	0.537143	TTCAAGCGGGCATGTCACTT	60.537	50.000	0.00	0.00	0.00	3.16
369	370	0.322816	ATTCAAGCGGGCATGTCACT	60.323	50.000	0.00	0.00	0.00	3.41
370	371	0.527565	AATTCAAGCGGGCATGTCAC	59.472	50.000	0.00	0.00	0.00	3.67
371	372	1.255882	AAATTCAAGCGGGCATGTCA	58.744	45.000	0.00	0.00	0.00	3.58
372	373	2.368655	AAAATTCAAGCGGGCATGTC	57.631	45.000	0.00	0.00	0.00	3.06
373	374	2.825532	AGTAAAATTCAAGCGGGCATGT	59.174	40.909	0.00	0.00	0.00	3.21
374	375	3.119531	TCAGTAAAATTCAAGCGGGCATG	60.120	43.478	0.00	0.00	0.00	4.06
428	429	9.710818	TCCGGCCTCTATTATAATTACTCTATT	57.289	33.333	2.68	0.00	0.00	1.73
440	442	2.158295	ACTCCACTCCGGCCTCTATTAT	60.158	50.000	0.00	0.00	33.14	1.28
450	452	1.338337	CTAGCATACACTCCACTCCGG	59.662	57.143	0.00	0.00	0.00	5.14
452	454	4.946478	AATCTAGCATACACTCCACTCC	57.054	45.455	0.00	0.00	0.00	3.85
453	455	5.069781	AGGAAATCTAGCATACACTCCACTC	59.930	44.000	0.00	0.00	0.00	3.51
454	456	4.965532	AGGAAATCTAGCATACACTCCACT	59.034	41.667	0.00	0.00	0.00	4.00
455	457	5.053145	CAGGAAATCTAGCATACACTCCAC	58.947	45.833	0.00	0.00	0.00	4.02
456	458	4.716784	ACAGGAAATCTAGCATACACTCCA	59.283	41.667	0.00	0.00	0.00	3.86
457	459	5.283457	ACAGGAAATCTAGCATACACTCC	57.717	43.478	0.00	0.00	0.00	3.85
465	467	7.280356	GGGTATCTTTAACAGGAAATCTAGCA	58.720	38.462	0.00	0.00	0.00	3.49
490	492	3.641437	TGTGAATCTTTTTCCCTTGCG	57.359	42.857	0.00	0.00	0.00	4.85
491	493	5.359756	ACTTTGTGAATCTTTTTCCCTTGC	58.640	37.500	0.00	0.00	0.00	4.01
492	494	7.041107	TGAACTTTGTGAATCTTTTTCCCTTG	58.959	34.615	0.00	0.00	0.00	3.61
494	496	6.683861	GCTGAACTTTGTGAATCTTTTTCCCT	60.684	38.462	0.00	0.00	0.00	4.20
495	497	5.463392	GCTGAACTTTGTGAATCTTTTTCCC	59.537	40.000	0.00	0.00	0.00	3.97
496	498	6.042143	TGCTGAACTTTGTGAATCTTTTTCC	58.958	36.000	0.00	0.00	0.00	3.13
497	499	7.704789	ATGCTGAACTTTGTGAATCTTTTTC	57.295	32.000	0.00	0.00	0.00	2.29
501	503	6.882610	TGTATGCTGAACTTTGTGAATCTT	57.117	33.333	0.00	0.00	0.00	2.40
502	504	6.882610	TTGTATGCTGAACTTTGTGAATCT	57.117	33.333	0.00	0.00	0.00	2.40
503	505	8.524870	AAATTGTATGCTGAACTTTGTGAATC	57.475	30.769	0.00	0.00	0.00	2.52
528	532	8.610896	CATGTGAAAAATCAGTTTGGCTAAAAA	58.389	29.630	0.00	0.00	0.00	1.94
545	549	7.977789	TGACTATTACAGAAGCATGTGAAAA	57.022	32.000	0.00	0.00	34.56	2.29
546	550	7.607607	ACATGACTATTACAGAAGCATGTGAAA	59.392	33.333	0.00	0.00	40.27	2.69
549	553	6.915544	ACATGACTATTACAGAAGCATGTG	57.084	37.500	0.00	0.00	40.27	3.21
567	571	2.809446	CCGTTCTCGCAGAATACATGA	58.191	47.619	0.00	0.00	36.50	3.07
574	578	1.154093	CGTAGCCGTTCTCGCAGAA	60.154	57.895	0.00	0.00	34.09	3.02
575	579	2.483745	CGTAGCCGTTCTCGCAGA	59.516	61.111	0.00	0.00	35.54	4.26
576	580	2.579787	CCGTAGCCGTTCTCGCAG	60.580	66.667	0.00	0.00	35.54	5.18
577	581	3.367743	ACCGTAGCCGTTCTCGCA	61.368	61.111	0.00	0.00	35.54	5.10
670	674	2.055838	GTACTCGACGTCAATGCACAA	58.944	47.619	17.16	0.00	0.00	3.33
778	2968	3.115892	GTTGACGGCGGCATTCGA	61.116	61.111	19.81	0.00	42.43	3.71
820	3010	0.111639	GGCACCCAAGTACCCTTTCA	59.888	55.000	0.00	0.00	0.00	2.69
973	3209	1.005630	GCTCTGTAGGCGGCTATGG	60.006	63.158	22.63	16.73	0.00	2.74
1124	3361	8.567285	AATCTTTTTCGAGAAGGATACAACAT	57.433	30.769	12.76	0.00	41.41	2.71
1746	3985	6.442885	TGGATGACATGGATGCTCTAGAATAT	59.557	38.462	0.00	0.00	0.00	1.28
1748	3987	4.596212	TGGATGACATGGATGCTCTAGAAT	59.404	41.667	0.00	0.00	0.00	2.40
2128	4644	8.265165	AGCATAGCACTTAACATGATATGATG	57.735	34.615	18.12	0.06	45.20	3.07
2130	4646	8.588472	AGTAGCATAGCACTTAACATGATATGA	58.412	33.333	18.12	2.74	45.20	2.15
2144	4660	4.728882	GCATGACACAAAGTAGCATAGCAC	60.729	45.833	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.