AutoCloner

Multiple sequence alignment - TraesCS2B01G305200

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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	TraesCS2B01G305200	chr2B	100.000	2732	0	0	1	2732	435159349	435156618	0.000000e+00	5046.0
1	TraesCS2B01G305200	chr2A	96.557	1975	53	4	760	2732	495960164	495958203	0.000000e+00	3256.0
2	TraesCS2B01G305200	chr2A	85.175	371	25	9	241	582	495961226	495960857	1.200000e-93	353.0
3	TraesCS2B01G305200	chr2A	93.878	147	9	0	2	148	495961495	495961349	3.540000e-54	222.0
4	TraesCS2B01G305200	chr2A	96.970	99	3	0	656	754	495960597	495960499	1.680000e-37	167.0
5	TraesCS2B01G305200	chr2A	96.774	93	3	0	656	748	495960702	495960610	3.640000e-34	156.0
6	TraesCS2B01G305200	chr2D	95.611	1572	46	10	260	1813	366501032	366499466	0.000000e+00	2499.0
7	TraesCS2B01G305200	chr2D	98.050	923	18	0	1810	2732	366499386	366498464	0.000000e+00	1605.0
8	TraesCS2B01G305200	chr2D	95.270	148	7	0	1	148	366501290	366501143	4.550000e-58	235.0
9	TraesCS2B01G305200	chr2D	91.228	57	4	1	185	241	366501137	366501082	2.920000e-10	76.8
10	TraesCS2B01G305200	chr2D	97.500	40	1	0	150	189	116643915	116643954	4.880000e-08	69.4
11	TraesCS2B01G305200	chr5B	85.086	523	78	0	2074	2596	481143271	481142749	4.000000e-148	534.0
12	TraesCS2B01G305200	chr5D	84.895	523	79	0	2074	2596	402203920	402203398	1.860000e-146	529.0
13	TraesCS2B01G305200	chr5A	84.130	523	83	0	2074	2596	507967960	507967438	8.730000e-140	507.0
14	TraesCS2B01G305200	chr3A	77.692	520	114	2	2073	2591	683251724	683252242	1.580000e-82	316.0
15	TraesCS2B01G305200	chr4B	97.561	41	1	0	149	189	464528086	464528126	1.360000e-08	71.3
16	TraesCS2B01G305200	chr7A	97.500	40	1	0	149	188	435835225	435835264	4.880000e-08	69.4
17	TraesCS2B01G305200	chr6B	93.023	43	3	0	586	628	654847683	654847641	2.270000e-06	63.9

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	TraesCS2B01G305200	chr2B	435156618	435159349	2731	True	5046.00	5046	100.00000	1	2732	1	chr2B.!!$R1	2731
1	TraesCS2B01G305200	chr2A	495958203	495961495	3292	True	830.80	3256	93.87080	2	2732	5	chr2A.!!$R1	2730
2	TraesCS2B01G305200	chr2D	366498464	366501290	2826	True	1103.95	2499	95.03975	1	2732	4	chr2D.!!$R1	2731
3	TraesCS2B01G305200	chr5B	481142749	481143271	522	True	534.00	534	85.08600	2074	2596	1	chr5B.!!$R1	522
4	TraesCS2B01G305200	chr5D	402203398	402203920	522	True	529.00	529	84.89500	2074	2596	1	chr5D.!!$R1	522
5	TraesCS2B01G305200	chr5A	507967438	507967960	522	True	507.00	507	84.13000	2074	2596	1	chr5A.!!$R1	522
6	TraesCS2B01G305200	chr3A	683251724	683252242	518	False	316.00	316	77.69200	2073	2591	1	chr3A.!!$F1	518

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
468	557	0.749649	CGAGCAGGAGAGTATTGGCT	59.25	55.0	0.0	0.0	0.00	4.75	F
1296	1905	0.390340	ATGCTGCACTCAGTGGTACG	60.39	55.0	7.0	0.0	42.29	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1316	1925	1.303888	CTCACCTTGGCACCTGCAT	60.304	57.895	0.0	0.0	44.36	3.96	R
2580	3272	1.140252	GGTGGTGTTGTACAGAGGTGT	59.860	52.381	0.0	0.0	41.06	4.16	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
46	47	6.715264	ACGGTAGAAGAAATGGTTGAGAAATT	59.285	34.615	0.00	0.00	0.00	1.82
128	129	5.277779	CGCAACCCGTATCATGATGTATTTT	60.278	40.000	18.72	3.47	0.00	1.82
142	143	9.874205	CATGATGTATTTTATGTTCCCACTTTT	57.126	29.630	0.00	0.00	0.00	2.27
148	149	9.931210	GTATTTTATGTTCCCACTTTTCGATAG	57.069	33.333	0.00	0.00	0.00	2.08
165	166	5.771469	TCGATAGAACTAAAACCACAACGA	58.229	37.500	0.00	0.00	46.15	3.85
166	167	5.860182	TCGATAGAACTAAAACCACAACGAG	59.140	40.000	0.00	0.00	46.15	4.18
167	168	5.632347	CGATAGAACTAAAACCACAACGAGT	59.368	40.000	0.00	0.00	39.76	4.18
168	169	6.803320	CGATAGAACTAAAACCACAACGAGTA	59.197	38.462	0.00	0.00	39.76	2.59
169	170	7.326789	CGATAGAACTAAAACCACAACGAGTAA	59.673	37.037	0.00	0.00	39.76	2.24
170	171	8.891671	ATAGAACTAAAACCACAACGAGTAAA	57.108	30.769	0.00	0.00	0.00	2.01
171	172	7.797038	AGAACTAAAACCACAACGAGTAAAT	57.203	32.000	0.00	0.00	0.00	1.40
172	173	7.858583	AGAACTAAAACCACAACGAGTAAATC	58.141	34.615	0.00	0.00	0.00	2.17
186	187	4.492611	GAGTAAATCGAAACGAAGGGAGT	58.507	43.478	0.00	0.00	39.99	3.85
187	188	5.644644	GAGTAAATCGAAACGAAGGGAGTA	58.355	41.667	0.00	0.00	39.99	2.59
188	189	5.405797	AGTAAATCGAAACGAAGGGAGTAC	58.594	41.667	0.00	0.00	39.99	2.73
415	478	8.049117	AGGATCTGATTTTATTTGTCAGTGCTA	58.951	33.333	0.00	0.00	40.13	3.49
426	489	4.267357	TGTCAGTGCTAACAAACGAAAC	57.733	40.909	0.00	0.00	0.00	2.78
429	492	3.936453	TCAGTGCTAACAAACGAAACACT	59.064	39.130	0.00	0.00	37.37	3.55
430	493	4.393680	TCAGTGCTAACAAACGAAACACTT	59.606	37.500	0.00	0.00	34.84	3.16
431	494	5.581479	TCAGTGCTAACAAACGAAACACTTA	59.419	36.000	0.00	0.00	34.84	2.24
433	496	7.438757	TCAGTGCTAACAAACGAAACACTTATA	59.561	33.333	0.00	0.00	34.84	0.98
434	497	7.529519	CAGTGCTAACAAACGAAACACTTATAC	59.470	37.037	0.00	0.00	34.84	1.47
435	498	6.513991	GTGCTAACAAACGAAACACTTATACG	59.486	38.462	0.00	0.00	0.00	3.06
436	499	6.200665	TGCTAACAAACGAAACACTTATACGT	59.799	34.615	0.00	0.00	38.81	3.57
438	501	8.375465	GCTAACAAACGAAACACTTATACGTAT	58.625	33.333	13.54	13.54	36.20	3.06
439	502	9.877096	CTAACAAACGAAACACTTATACGTATC	57.123	33.333	12.24	0.00	36.20	2.24
440	503	8.524870	AACAAACGAAACACTTATACGTATCT	57.475	30.769	12.24	0.00	36.20	1.98
441	504	7.946043	ACAAACGAAACACTTATACGTATCTG	58.054	34.615	12.24	8.62	36.20	2.90
442	505	7.809331	ACAAACGAAACACTTATACGTATCTGA	59.191	33.333	12.24	0.00	36.20	3.27
443	506	8.804743	CAAACGAAACACTTATACGTATCTGAT	58.195	33.333	12.24	0.00	36.20	2.90
468	557	0.749649	CGAGCAGGAGAGTATTGGCT	59.250	55.000	0.00	0.00	0.00	4.75
551	640	8.618677	CATGATACCTTTAGTACTGTAGAACGA	58.381	37.037	5.39	0.00	32.46	3.85
590	716	5.770162	ACTTAGCCTCATGTAAAACAGCTTT	59.230	36.000	0.00	0.00	30.20	3.51
611	737	8.564574	AGCTTTCAAAAACGTCTTATATTGTGA	58.435	29.630	0.00	0.00	0.00	3.58
620	746	3.640029	GTCTTATATTGTGAGACGGGGGA	59.360	47.826	0.00	0.00	34.29	4.81
686	964	2.162681	CACCACCCTAGAAGCCTTTTG	58.837	52.381	0.00	0.00	0.00	2.44
756	1363	5.010617	AGGGTAACAATGAAACGCTTCAAAT	59.989	36.000	5.19	0.00	41.51	2.32
826	1434	2.230508	GGAAACCCGAGTCAAATTTCCC	59.769	50.000	14.14	2.37	41.59	3.97
839	1447	2.150014	ATTTCCCCCTCCGTTGGGTG	62.150	60.000	8.83	0.00	45.70	4.61
1293	1902	0.604780	GACATGCTGCACTCAGTGGT	60.605	55.000	7.00	0.00	42.29	4.16
1294	1903	0.686789	ACATGCTGCACTCAGTGGTA	59.313	50.000	7.00	0.00	42.29	3.25
1295	1904	1.081892	CATGCTGCACTCAGTGGTAC	58.918	55.000	7.00	0.00	42.29	3.34
1296	1905	0.390340	ATGCTGCACTCAGTGGTACG	60.390	55.000	7.00	0.00	42.29	3.67
1316	1925	7.660617	TGGTACGTACTTAATTTGTTGATGGAA	59.339	33.333	24.07	0.00	0.00	3.53
1377	1986	1.074752	CTGAGAAAGTTGAGCGCTCC	58.925	55.000	33.23	19.49	0.00	4.70
1492	2101	1.237285	CCTCCCAAACTGCAACGAGG	61.237	60.000	0.00	0.00	0.00	4.63
1499	2108	1.166531	AACTGCAACGAGGTTCAGGC	61.167	55.000	0.00	0.00	30.74	4.85
1596	2205	0.324943	GCTACCTCAAGGACAAGCCA	59.675	55.000	2.30	0.00	40.02	4.75
2002	2694	5.445939	GGCACTGTGTTTCTATTACATCACG	60.446	44.000	9.86	0.00	0.00	4.35
2034	2726	6.128138	AGTATGAACTATTTCTATGGGGCC	57.872	41.667	0.00	0.00	32.84	5.80
2063	2755	3.370953	GCAAAGAGGATGGGAAGCTCTTA	60.371	47.826	0.00	0.00	33.81	2.10
2255	2947	3.118920	CCTGCTTCATTGATGGATTTGCA	60.119	43.478	2.16	0.00	0.00	4.08
2604	3296	2.548067	CCTCTGTACAACACCACCACTC	60.548	54.545	0.00	0.00	0.00	3.51
2669	3361	7.950512	TCAGATTGGTCAAATTTTAGAAGCAA	58.049	30.769	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	2.076100	CGGTGCAAACAGAGCAAGATA	58.924	47.619	0.00	0.00	44.64	1.98
128	129	6.942976	AGTTCTATCGAAAAGTGGGAACATA	58.057	36.000	0.00	0.00	46.14	2.29
142	143	5.771469	TCGTTGTGGTTTTAGTTCTATCGA	58.229	37.500	0.00	0.00	0.00	3.59
148	149	6.788930	CGATTTACTCGTTGTGGTTTTAGTTC	59.211	38.462	0.00	0.00	42.56	3.01
149	150	6.652245	CGATTTACTCGTTGTGGTTTTAGTT	58.348	36.000	0.00	0.00	42.56	2.24
150	151	6.219302	CGATTTACTCGTTGTGGTTTTAGT	57.781	37.500	0.00	0.00	42.56	2.24
164	165	4.492611	ACTCCCTTCGTTTCGATTTACTC	58.507	43.478	0.00	0.00	35.23	2.59
165	166	4.532314	ACTCCCTTCGTTTCGATTTACT	57.468	40.909	0.00	0.00	35.23	2.24
166	167	5.405797	AGTACTCCCTTCGTTTCGATTTAC	58.594	41.667	0.00	0.00	35.23	2.01
167	168	5.649782	AGTACTCCCTTCGTTTCGATTTA	57.350	39.130	0.00	0.00	35.23	1.40
168	169	4.532314	AGTACTCCCTTCGTTTCGATTT	57.468	40.909	0.00	0.00	35.23	2.17
169	170	4.532314	AAGTACTCCCTTCGTTTCGATT	57.468	40.909	0.00	0.00	35.23	3.34
170	171	4.532314	AAAGTACTCCCTTCGTTTCGAT	57.468	40.909	0.00	0.00	35.23	3.59
171	172	4.326504	AAAAGTACTCCCTTCGTTTCGA	57.673	40.909	0.00	0.00	0.00	3.71
200	201	0.599204	CGTAAGCCCACTGTTGACGT	60.599	55.000	0.00	0.00	0.00	4.34
415	478	8.430063	CAGATACGTATAAGTGTTTCGTTTGTT	58.570	33.333	8.34	0.00	36.24	2.83
426	489	9.639636	CTCGCTATAATCAGATACGTATAAGTG	57.360	37.037	8.34	6.86	0.00	3.16
429	492	8.205131	TGCTCGCTATAATCAGATACGTATAA	57.795	34.615	8.34	0.00	0.00	0.98
430	493	7.041984	CCTGCTCGCTATAATCAGATACGTATA	60.042	40.741	8.34	0.00	0.00	1.47
431	494	6.238511	CCTGCTCGCTATAATCAGATACGTAT	60.239	42.308	8.05	8.05	0.00	3.06
433	496	4.142578	CCTGCTCGCTATAATCAGATACGT	60.143	45.833	0.00	0.00	0.00	3.57
434	497	4.095036	TCCTGCTCGCTATAATCAGATACG	59.905	45.833	0.00	0.00	0.00	3.06
435	498	5.355630	TCTCCTGCTCGCTATAATCAGATAC	59.644	44.000	0.00	0.00	0.00	2.24
436	499	5.501156	TCTCCTGCTCGCTATAATCAGATA	58.499	41.667	0.00	0.00	0.00	1.98
438	501	3.755905	CTCTCCTGCTCGCTATAATCAGA	59.244	47.826	0.00	0.00	0.00	3.27
439	502	3.505680	ACTCTCCTGCTCGCTATAATCAG	59.494	47.826	0.00	0.00	0.00	2.90
440	503	3.491342	ACTCTCCTGCTCGCTATAATCA	58.509	45.455	0.00	0.00	0.00	2.57
441	504	5.828299	ATACTCTCCTGCTCGCTATAATC	57.172	43.478	0.00	0.00	0.00	1.75
442	505	5.105554	CCAATACTCTCCTGCTCGCTATAAT	60.106	44.000	0.00	0.00	0.00	1.28
443	506	4.218635	CCAATACTCTCCTGCTCGCTATAA	59.781	45.833	0.00	0.00	0.00	0.98
445	508	2.560542	CCAATACTCTCCTGCTCGCTAT	59.439	50.000	0.00	0.00	0.00	2.97
468	557	2.176045	TCGGCAGTGGAACAGAAGATA	58.824	47.619	0.00	0.00	41.80	1.98
551	640	6.886459	TGAGGCTAAGTGAGAATAAGCAAATT	59.114	34.615	0.00	0.00	0.00	1.82
611	737	2.176247	ATGACATACTTCCCCCGTCT	57.824	50.000	0.00	0.00	0.00	4.18
620	746	7.031372	TCGCGTAAAAGTCTAATGACATACTT	58.969	34.615	5.77	0.00	45.20	2.24
756	1363	3.066208	AGGCAATATCCCTCCTCTTCA	57.934	47.619	0.00	0.00	0.00	3.02
797	1405	1.897802	GACTCGGGTTTCCTTGAGGTA	59.102	52.381	0.00	0.00	32.92	3.08
1008	1617	0.753262	CCTCTACCTCCGGTGAATGG	59.247	60.000	4.76	2.08	36.19	3.16
1293	1902	8.178964	GCATTCCATCAACAAATTAAGTACGTA	58.821	33.333	0.00	0.00	0.00	3.57
1294	1903	7.027161	GCATTCCATCAACAAATTAAGTACGT	58.973	34.615	0.00	0.00	0.00	3.57
1295	1904	7.026562	TGCATTCCATCAACAAATTAAGTACG	58.973	34.615	0.00	0.00	0.00	3.67
1296	1905	7.489113	CCTGCATTCCATCAACAAATTAAGTAC	59.511	37.037	0.00	0.00	0.00	2.73
1316	1925	1.303888	CTCACCTTGGCACCTGCAT	60.304	57.895	0.00	0.00	44.36	3.96
1400	2009	2.084546	GCTCGATTTTGTAAGTGCCCT	58.915	47.619	0.00	0.00	0.00	5.19
1401	2010	2.084546	AGCTCGATTTTGTAAGTGCCC	58.915	47.619	0.00	0.00	0.00	5.36
1492	2101	1.599576	GGTCCCTGAGAGCCTGAAC	59.400	63.158	0.00	0.00	36.99	3.18
1604	2213	2.416107	TTTGAGCAGGTCAGGGCAGG	62.416	60.000	1.86	0.00	36.21	4.85
1937	2629	3.819564	AGGCGTTATCTAACATGAGCA	57.180	42.857	0.00	0.00	35.99	4.26
2034	2726	2.173356	TCCCATCCTCTTTGCCACATAG	59.827	50.000	0.00	0.00	0.00	2.23
2063	2755	1.725803	AACCGTGGTAGGGAAGAGTT	58.274	50.000	0.00	0.00	35.02	3.01
2129	2821	1.838077	GAGGGTGTATACTTGCCACCT	59.162	52.381	4.17	2.85	46.30	4.00
2580	3272	1.140252	GGTGGTGTTGTACAGAGGTGT	59.860	52.381	0.00	0.00	41.06	4.16
2604	3296	9.191995	GTTTGGTTCCATTTATTTACTCACTTG	57.808	33.333	0.00	0.00	0.00	3.16
2669	3361	5.456186	GGGTGGTTACTATGCAAGGTATCAT	60.456	44.000	0.00	0.00	0.00	2.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.