AutoCloner

Multiple sequence alignment - TraesCS5B01G141300

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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	TraesCS5B01G141300	chr5B	100.000	3815	0	0	1	3815	266520141	266516327	0.000000e+00	7046.0
1	TraesCS5B01G141300	chr5B	81.679	131	16	7	163	286	15358649	15358778	6.740000e-18	102.0
2	TraesCS5B01G141300	chr5B	79.195	149	27	3	3	150	655020234	655020379	2.420000e-17	100.0
3	TraesCS5B01G141300	chr5D	95.118	3851	132	25	1	3815	238545562	238549392	0.000000e+00	6019.0
4	TraesCS5B01G141300	chr5A	95.191	3327	123	19	517	3815	316096835	316093518	0.000000e+00	5223.0
5	TraesCS5B01G141300	chr5A	83.281	317	41	9	1	311	316098943	316098633	8.070000e-72	281.0
6	TraesCS5B01G141300	chr5A	81.919	271	33	7	157	424	316098417	316098160	8.300000e-52	215.0
7	TraesCS5B01G141300	chr4D	86.405	1883	206	19	990	2826	107690748	107692626	0.000000e+00	2013.0
8	TraesCS5B01G141300	chr4D	87.037	54	5	2	150	203	223879105	223879054	4.120000e-05	60.2
9	TraesCS5B01G141300	chr4D	88.235	51	4	2	150	200	345432943	345432991	4.120000e-05	60.2
10	TraesCS5B01G141300	chr4B	86.595	1865	197	19	999	2817	168996642	168994785	0.000000e+00	2010.0
11	TraesCS5B01G141300	chr4A	86.516	1854	198	23	999	2817	468628966	468627130	0.000000e+00	1991.0
12	TraesCS5B01G141300	chr4A	76.761	142	27	6	65	204	162407615	162407478	1.470000e-09	75.0
13	TraesCS5B01G141300	chr3D	93.063	591	41	0	2188	2778	456924808	456925398	0.000000e+00	865.0
14	TraesCS5B01G141300	chr6B	92.586	553	41	0	2222	2774	642929626	642930178	0.000000e+00	795.0
15	TraesCS5B01G141300	chr2A	77.323	269	50	11	25	285	749854364	749854099	8.540000e-32	148.0
16	TraesCS5B01G141300	chr2B	76.639	244	44	13	50	285	312379910	312379672	5.180000e-24	122.0
17	TraesCS5B01G141300	chr2D	80.769	130	17	7	163	286	600323535	600323408	1.130000e-15	95.3
18	TraesCS5B01G141300	chr6A	88.889	54	4	2	150	203	601670233	601670284	8.850000e-07	65.8

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	TraesCS5B01G141300	chr5B	266516327	266520141	3814	True	7046.000000	7046	100.000	1	3815	1	chr5B.!!$R1	3814
1	TraesCS5B01G141300	chr5D	238545562	238549392	3830	False	6019.000000	6019	95.118	1	3815	1	chr5D.!!$F1	3814
2	TraesCS5B01G141300	chr5A	316093518	316098943	5425	True	1906.333333	5223	86.797	1	3815	3	chr5A.!!$R1	3814
3	TraesCS5B01G141300	chr4D	107690748	107692626	1878	False	2013.000000	2013	86.405	990	2826	1	chr4D.!!$F1	1836
4	TraesCS5B01G141300	chr4B	168994785	168996642	1857	True	2010.000000	2010	86.595	999	2817	1	chr4B.!!$R1	1818
5	TraesCS5B01G141300	chr4A	468627130	468628966	1836	True	1991.000000	1991	86.516	999	2817	1	chr4A.!!$R2	1818
6	TraesCS5B01G141300	chr3D	456924808	456925398	590	False	865.000000	865	93.063	2188	2778	1	chr3D.!!$F1	590
7	TraesCS5B01G141300	chr6B	642929626	642930178	552	False	795.000000	795	92.586	2222	2774	1	chr6B.!!$F1	552

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
743	2380	0.374758	CCGCGTGTCATCCAATGAAG	59.625	55.0	4.92	0.0	41.69	3.02	F
2433	4121	0.913451	AGGGAAGCTCAGCCATCACT	60.913	55.0	0.00	0.0	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2449	4137	0.038159	CGGAACTTCTTCGCACTCCT	60.038	55.000	0.0	0.0	0.00	3.69	R
3255	4958	4.703575	TGGCAACATAGAGTAGAGTAACGT	59.296	41.667	0.0	0.0	46.17	3.99	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
20	21	4.814294	CTACTGGACCACGCCCGC	62.814	72.222	0.00	0.00	0.00	6.13
41	42	4.561123	CGCCTCTCATCTTATCTCTGCAAT	60.561	45.833	0.00	0.00	0.00	3.56
43	44	6.101332	GCCTCTCATCTTATCTCTGCAATAG	58.899	44.000	0.00	0.00	0.00	1.73
63	64	2.554032	AGTGGTGTTGTTGCAGAATAGC	59.446	45.455	0.00	0.00	0.00	2.97
160	162	3.374988	TGCAGAAAATTAGATGCCGTGAG	59.625	43.478	6.31	0.00	37.89	3.51
205	207	5.825507	ACAAGAGTCTTGTTGCAGAAAATC	58.174	37.500	28.97	0.00	31.07	2.17
209	211	6.866480	AGAGTCTTGTTGCAGAAAATCAAAA	58.134	32.000	0.00	0.00	0.00	2.44
210	212	7.495055	AGAGTCTTGTTGCAGAAAATCAAAAT	58.505	30.769	0.00	0.00	0.00	1.82
213	215	9.768662	AGTCTTGTTGCAGAAAATCAAAATAAT	57.231	25.926	0.00	0.00	0.00	1.28
253	258	9.295825	TCTTGTTGCAGAAAATTATAAAGGAGA	57.704	29.630	0.00	0.00	0.00	3.71
272	277	6.643388	AGGAGAAAGTTTTGCAACAAAGATT	58.357	32.000	0.00	0.00	35.05	2.40
328	706	2.747446	GCAGCAAAAAGGAGGAACGATA	59.253	45.455	0.00	0.00	0.00	2.92
330	708	4.003648	CAGCAAAAAGGAGGAACGATACT	58.996	43.478	0.00	0.00	0.00	2.12
346	724	6.465439	ACGATACTGACAACTCCATCAATA	57.535	37.500	0.00	0.00	0.00	1.90
365	743	5.588648	TCAATAAATCAAACGGCTTCCTAGG	59.411	40.000	0.82	0.82	0.00	3.02
384	762	1.066430	GGCGGTGGATCTTACACAGAA	60.066	52.381	5.23	0.00	40.54	3.02
395	773	4.242475	TCTTACACAGAAACGTAGCATGG	58.758	43.478	0.00	0.00	0.00	3.66
551	2187	1.831106	TCACAATCATACGCTGGACCT	59.169	47.619	0.00	0.00	0.00	3.85
574	2210	3.863041	AGCCCATAAAAGTCTCTCGAAC	58.137	45.455	0.00	0.00	0.00	3.95
684	2321	0.879090	GAACAACCCACCGGAATGTC	59.121	55.000	9.46	0.00	33.50	3.06
685	2322	0.538746	AACAACCCACCGGAATGTCC	60.539	55.000	9.46	0.00	33.50	4.02
688	2325	1.848886	AACCCACCGGAATGTCCTCC	61.849	60.000	9.46	0.00	33.30	4.30
743	2380	0.374758	CCGCGTGTCATCCAATGAAG	59.625	55.000	4.92	0.00	41.69	3.02
782	2419	1.797441	CTCGACTCCAGTGACGAGG	59.203	63.158	15.59	0.00	44.09	4.63
927	2565	2.110578	CCCAATCCAAACTCCATTCCC	58.889	52.381	0.00	0.00	0.00	3.97
935	2573	3.201290	CAAACTCCATTCCCAGATCTCG	58.799	50.000	0.00	0.00	0.00	4.04
1359	3041	2.743718	CACCTCCACAACCTCGCT	59.256	61.111	0.00	0.00	0.00	4.93
1530	3215	1.747367	CGAGGACTCTGACGCCTCT	60.747	63.158	15.26	0.00	44.73	3.69
1572	3257	2.188207	GGGAGAAGGAAGAGGCGC	59.812	66.667	0.00	0.00	0.00	6.53
1878	3566	3.376078	GGGTCGGTGGTCACGCTA	61.376	66.667	0.00	0.00	0.00	4.26
2247	3935	1.737838	CTGCGGATGTTGTGTATGGT	58.262	50.000	0.00	0.00	0.00	3.55
2337	4025	2.356665	TTTGGGTTGCTTACTCTGCA	57.643	45.000	0.00	0.00	38.80	4.41
2433	4121	0.913451	AGGGAAGCTCAGCCATCACT	60.913	55.000	0.00	0.00	0.00	3.41
2449	4137	5.685861	GCCATCACTAAGAGTGGATTCATCA	60.686	44.000	6.77	0.00	45.94	3.07
2475	4163	0.669625	CGAAGAAGTTCCGGTGGGTC	60.670	60.000	0.00	0.00	33.83	4.46
2794	4482	6.486320	TGTTGCTGTCAGTTCTTTCATGATTA	59.514	34.615	0.00	0.00	0.00	1.75
2858	4549	5.451520	GCTGATGATTCTTTCATTCCCAAGG	60.452	44.000	0.00	0.00	45.29	3.61
2902	4593	7.184067	TCTCTCTAAATAAAGGAGGTTGACC	57.816	40.000	0.00	0.00	0.00	4.02
2979	4677	4.622740	GCAGCCTGACAAACATTGTAATTC	59.377	41.667	0.00	0.00	45.52	2.17
2986	4684	6.036470	TGACAAACATTGTAATTCGCAACAA	58.964	32.000	0.00	0.00	45.52	2.83
2990	4688	9.294257	ACAAACATTGTAATTCGCAACAACTGC	62.294	37.037	0.00	0.00	44.54	4.40
3001	4699	1.943116	AACAACTGCGTTGCTTGGCA	61.943	50.000	17.42	0.00	46.20	4.92
3029	4727	8.470805	TCATGTTTTTAGTGATAGAGGAGAGTC	58.529	37.037	0.00	0.00	0.00	3.36
3066	4764	3.140895	ACTGCCCCATTAGCAAAGGATAT	59.859	43.478	0.00	0.00	40.35	1.63
3079	4782	5.706369	AGCAAAGGATATCAGATTCAGATGC	59.294	40.000	4.83	3.60	0.00	3.91
3095	4798	2.019984	GATGCCAACCTGATTCTGACC	58.980	52.381	0.00	0.00	0.00	4.02
3101	4804	4.848357	CCAACCTGATTCTGACCTACAAT	58.152	43.478	0.00	0.00	0.00	2.71
3228	4931	7.956420	TCGTGTCTGTATCAATAAAGTTGTT	57.044	32.000	0.00	0.00	0.00	2.83
3249	4952	7.897575	TGTTTCAAGTTTTTAGTGTGCAAAT	57.102	28.000	0.00	0.00	0.00	2.32
3252	4955	9.683651	GTTTCAAGTTTTTAGTGTGCAAATAAC	57.316	29.630	0.00	0.00	0.00	1.89
3253	4956	9.646427	TTTCAAGTTTTTAGTGTGCAAATAACT	57.354	25.926	0.00	0.00	0.00	2.24
3254	4957	8.850454	TCAAGTTTTTAGTGTGCAAATAACTC	57.150	30.769	5.52	0.00	0.00	3.01
3255	4958	8.462811	TCAAGTTTTTAGTGTGCAAATAACTCA	58.537	29.630	5.52	0.00	0.00	3.41
3281	4985	6.199154	CGTTACTCTACTCTATGTTGCCATTG	59.801	42.308	0.00	0.00	32.29	2.82
3333	5037	9.899226	AAACAATTTTTAGCTTAGCTACTTGAG	57.101	29.630	14.08	5.49	41.12	3.02
3523	5229	6.675413	ACAAGTGTCATAGGGTACTTTACA	57.325	37.500	0.00	0.00	31.47	2.41
3552	5258	6.449635	TCTAACTTGCAATTTGTGTGACTT	57.550	33.333	11.94	0.00	0.00	3.01
3553	5259	7.561021	TCTAACTTGCAATTTGTGTGACTTA	57.439	32.000	11.94	0.00	0.00	2.24
3613	5319	7.971722	CAGTGATTTGATTAATTCATGTGCTCA	59.028	33.333	0.00	0.00	33.34	4.26
3661	5367	5.459762	GTGTGTTGTCAGAAAATCATGGTTG	59.540	40.000	0.00	0.00	0.00	3.77
3721	5429	2.426522	CCGAGATGTCAACACATGGTT	58.573	47.619	0.00	0.00	43.79	3.67
3786	5494	2.040544	CCGTGCACAGATCCAACCC	61.041	63.158	18.64	0.00	0.00	4.11
3804	5519	4.156455	ACCCATGCTAACATTCTGTAGG	57.844	45.455	0.00	0.00	32.87	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	7.092079	CACTATTGCAGAGATAAGATGAGAGG	58.908	42.308	4.81	0.00	0.00	3.69
41	42	3.751175	GCTATTCTGCAACAACACCACTA	59.249	43.478	0.00	0.00	0.00	2.74
43	44	2.665519	CGCTATTCTGCAACAACACCAC	60.666	50.000	0.00	0.00	0.00	4.16
63	64	3.759828	GGTCGTCGTTCGTTGCCG	61.760	66.667	0.00	0.00	40.80	5.69
136	137	4.398988	TCACGGCATCTAATTTTCTGCAAT	59.601	37.500	7.74	0.00	36.34	3.56
140	141	4.191544	TCCTCACGGCATCTAATTTTCTG	58.808	43.478	0.00	0.00	0.00	3.02
213	215	8.347004	TCTGCAACAAGATCCATGTTAAATTA	57.653	30.769	12.62	0.00	38.90	1.40
214	216	7.230849	TCTGCAACAAGATCCATGTTAAATT	57.769	32.000	12.62	0.00	38.90	1.82
218	223	6.647334	TTTTCTGCAACAAGATCCATGTTA	57.353	33.333	12.62	0.80	38.90	2.41
253	258	9.288124	GCAATAAAATCTTTGTTGCAAAACTTT	57.712	25.926	21.39	0.00	39.92	2.66
293	671	2.330440	TGCTGCAACAAGACTCTTGA	57.670	45.000	23.08	2.27	0.00	3.02
328	706	8.299570	GTTTGATTTATTGATGGAGTTGTCAGT	58.700	33.333	0.00	0.00	0.00	3.41
330	708	7.304735	CGTTTGATTTATTGATGGAGTTGTCA	58.695	34.615	0.00	0.00	0.00	3.58
346	724	2.092323	GCCTAGGAAGCCGTTTGATTT	58.908	47.619	14.75	0.00	0.00	2.17
365	743	2.380084	TTCTGTGTAAGATCCACCGC	57.620	50.000	0.00	0.00	33.93	5.68
369	747	4.021807	TGCTACGTTTCTGTGTAAGATCCA	60.022	41.667	0.00	0.00	33.93	3.41
384	762	0.037590	TCAAAGGGCCATGCTACGTT	59.962	50.000	6.18	0.00	0.00	3.99
395	773	0.735978	CGGCCGAATTTTCAAAGGGC	60.736	55.000	24.07	0.00	43.12	5.19
515	2151	0.038526	GTGAGACCGCATATACCCCG	60.039	60.000	0.00	0.00	0.00	5.73
551	2187	3.096852	TCGAGAGACTTTTATGGGCTCA	58.903	45.455	0.00	0.00	33.31	4.26
574	2210	2.583520	GGCTCAGGTCCAGCTCTG	59.416	66.667	1.50	0.00	37.05	3.35
605	2242	3.181464	GGGCTGGTTCTGACCTAGTAATC	60.181	52.174	0.00	0.00	46.66	1.75
608	2245	1.078159	TGGGCTGGTTCTGACCTAGTA	59.922	52.381	0.00	0.00	46.66	1.82
609	2246	0.178903	TGGGCTGGTTCTGACCTAGT	60.179	55.000	0.00	0.00	46.66	2.57
610	2247	0.539051	CTGGGCTGGTTCTGACCTAG	59.461	60.000	0.00	0.00	46.66	3.02
693	2330	3.978193	TGGGGCCCGCTTGTCATT	61.978	61.111	19.83	0.00	0.00	2.57
765	2402	2.333417	GCCTCGTCACTGGAGTCGA	61.333	63.158	0.00	0.00	0.00	4.20
767	2404	2.179517	CGCCTCGTCACTGGAGTC	59.820	66.667	0.00	0.00	0.00	3.36
768	2405	3.374402	CCGCCTCGTCACTGGAGT	61.374	66.667	0.00	0.00	0.00	3.85
927	2565	2.030007	GGAGAGGAATGCTCGAGATCTG	60.030	54.545	18.75	0.00	33.19	2.90
935	2573	0.467804	GTGGGAGGAGAGGAATGCTC	59.532	60.000	0.00	0.00	36.96	4.26
986	2629	1.673993	ACCATTGGCGCATCAACGA	60.674	52.632	10.83	0.00	34.06	3.85
1530	3215	1.511305	GGCGTCAGAATCGGAGTCA	59.489	57.895	8.28	0.00	0.00	3.41
1878	3566	2.357154	CCGGATCTTGGTTCCATCCTTT	60.357	50.000	0.00	0.00	34.89	3.11
2085	3773	4.416516	TCATGTACTGGAACCTCTTCTGA	58.583	43.478	0.00	0.00	0.00	3.27
2247	3935	2.294233	GGATTCAAGCAAAGCTGTGACA	59.706	45.455	8.49	0.00	39.62	3.58
2316	4004	2.360801	TGCAGAGTAAGCAACCCAAAAC	59.639	45.455	0.00	0.00	39.39	2.43
2328	4016	2.610433	CTCAGCGACAATGCAGAGTAA	58.390	47.619	0.00	0.00	41.84	2.24
2337	4025	0.806868	CCACATTGCTCAGCGACAAT	59.193	50.000	0.00	0.00	36.96	2.71
2433	4121	4.141846	GCACTCCTGATGAATCCACTCTTA	60.142	45.833	0.00	0.00	0.00	2.10
2449	4137	0.038159	CGGAACTTCTTCGCACTCCT	60.038	55.000	0.00	0.00	0.00	3.69
2475	4163	2.681848	GTCCACTGGATCATCAAGCTTG	59.318	50.000	20.81	20.81	32.73	4.01
2794	4482	4.457257	GCATCAAAGCTTCTCTGTTAACCT	59.543	41.667	0.00	0.00	0.00	3.50
2858	4549	1.227674	CAAGCCTCAGGTATCCCGC	60.228	63.158	0.00	0.00	35.12	6.13
2864	4555	1.006519	AGAGAGAGCAAGCCTCAGGTA	59.993	52.381	11.34	0.00	43.31	3.08
2877	4568	7.269316	GGTCAACCTCCTTTATTTAGAGAGAG	58.731	42.308	0.00	0.00	0.00	3.20
2902	4593	0.949397	CATGGCATGATCCTCAACCG	59.051	55.000	22.91	0.00	31.47	4.44
3001	4699	9.829507	CTCTCCTCTATCACTAAAAACATGATT	57.170	33.333	0.00	0.00	34.86	2.57
3029	4727	1.517242	GCAGTTGGAGAGTGGAACAG	58.483	55.000	0.00	0.00	41.80	3.16
3066	4764	2.573009	TCAGGTTGGCATCTGAATCTGA	59.427	45.455	15.63	6.77	37.11	3.27
3079	4782	3.981071	TGTAGGTCAGAATCAGGTTGG	57.019	47.619	0.00	0.00	0.00	3.77
3095	4798	3.350219	AGTGTACCTTGCCCATTGTAG	57.650	47.619	0.00	0.00	0.00	2.74
3187	4890	7.921214	ACAGACACGAATACAACATTATCCTAG	59.079	37.037	0.00	0.00	0.00	3.02
3228	4931	9.296400	GAGTTATTTGCACACTAAAAACTTGAA	57.704	29.630	0.00	0.00	0.00	2.69
3252	4955	5.966503	GCAACATAGAGTAGAGTAACGTGAG	59.033	44.000	0.00	0.00	0.00	3.51
3253	4956	5.163683	GGCAACATAGAGTAGAGTAACGTGA	60.164	44.000	0.00	0.00	0.00	4.35
3254	4957	5.035443	GGCAACATAGAGTAGAGTAACGTG	58.965	45.833	0.00	0.00	0.00	4.49
3255	4958	4.703575	TGGCAACATAGAGTAGAGTAACGT	59.296	41.667	0.00	0.00	46.17	3.99
3281	4985	7.425606	ACAAACATCAATTCTGTCAGGTAAAC	58.574	34.615	0.00	0.00	0.00	2.01
3352	5056	7.201767	GCTTGCTCTCATTGTAAGAATGGTATT	60.202	37.037	0.00	0.00	0.00	1.89
3479	5185	8.041323	ACTTGTTCTTTCAGAGTTCAGACTAAA	58.959	33.333	0.00	0.00	35.88	1.85
3523	5229	6.919662	CACACAAATTGCAAGTTAGATGTCTT	59.080	34.615	12.36	0.00	0.00	3.01
3600	5306	8.687292	ATCAACAGTATATGAGCACATGAATT	57.313	30.769	6.91	0.00	37.87	2.17
3638	5344	5.126869	ACAACCATGATTTTCTGACAACACA	59.873	36.000	0.00	0.00	0.00	3.72
3661	5367	8.035394	TCTATGAGTTTGTCTGGTTCAAGATAC	58.965	37.037	0.00	0.00	0.00	2.24
3721	5429	9.942850	TGATAGATGAAAGATTACTGACAAACA	57.057	29.630	0.00	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.