AutoCloner

Multiple sequence alignment - TraesCS5B01G104400

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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	TraesCS5B01G104400	chr5B	100.000	3491	0	0	1	3491	139264943	139261453	0.000000e+00	6447
1	TraesCS5B01G104400	chr7B	93.534	3418	210	10	79	3491	560848553	560845142	0.000000e+00	5077
2	TraesCS5B01G104400	chr1B	92.378	3503	240	14	1	3491	409880864	409884351	0.000000e+00	4964
3	TraesCS5B01G104400	chr1B	92.362	3260	230	16	242	3491	497611700	497614950	0.000000e+00	4623
4	TraesCS5B01G104400	chr2D	92.388	3429	232	23	81	3491	376028662	376025245	0.000000e+00	4859
5	TraesCS5B01G104400	chr2D	92.010	388	14	2	1	387	172099462	172099091	2.390000e-146	529
6	TraesCS5B01G104400	chr3D	92.367	3354	221	23	79	3409	364943189	364939848	0.000000e+00	4743
7	TraesCS5B01G104400	chr3D	93.089	3198	202	14	308	3491	110958404	110961596	0.000000e+00	4663
8	TraesCS5B01G104400	chr4D	91.562	3425	272	12	79	3491	148264741	148268160	0.000000e+00	4708
9	TraesCS5B01G104400	chr7D	91.468	3434	258	27	79	3491	341105477	341108896	0.000000e+00	4686
10	TraesCS5B01G104400	chr7A	91.105	3429	277	19	80	3491	469517486	469520903	0.000000e+00	4617
11	TraesCS5B01G104400	chr7A	84.163	3435	393	77	1	3389	333028675	333025346	0.000000e+00	3190

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	TraesCS5B01G104400	chr5B	139261453	139264943	3490	True	6447	6447	100.000	1	3491	1	chr5B.!!$R1	3490
1	TraesCS5B01G104400	chr7B	560845142	560848553	3411	True	5077	5077	93.534	79	3491	1	chr7B.!!$R1	3412
2	TraesCS5B01G104400	chr1B	409880864	409884351	3487	False	4964	4964	92.378	1	3491	1	chr1B.!!$F1	3490
3	TraesCS5B01G104400	chr1B	497611700	497614950	3250	False	4623	4623	92.362	242	3491	1	chr1B.!!$F2	3249
4	TraesCS5B01G104400	chr2D	376025245	376028662	3417	True	4859	4859	92.388	81	3491	1	chr2D.!!$R2	3410
5	TraesCS5B01G104400	chr3D	364939848	364943189	3341	True	4743	4743	92.367	79	3409	1	chr3D.!!$R1	3330
6	TraesCS5B01G104400	chr3D	110958404	110961596	3192	False	4663	4663	93.089	308	3491	1	chr3D.!!$F1	3183
7	TraesCS5B01G104400	chr4D	148264741	148268160	3419	False	4708	4708	91.562	79	3491	1	chr4D.!!$F1	3412
8	TraesCS5B01G104400	chr7D	341105477	341108896	3419	False	4686	4686	91.468	79	3491	1	chr7D.!!$F1	3412
9	TraesCS5B01G104400	chr7A	469517486	469520903	3417	False	4617	4617	91.105	80	3491	1	chr7A.!!$F1	3411
10	TraesCS5B01G104400	chr7A	333025346	333028675	3329	True	3190	3190	84.163	1	3389	1	chr7A.!!$R1	3388

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
944	978	0.184451	ATTGCCGCTTCCATCTCCAT	59.816	50.000	0.00	0.0	0.0	3.41	F
1177	1212	1.902508	CCAGTGAACTAGAGAAGGCCA	59.097	52.381	5.01	0.0	0.0	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2450	2517	0.759812	GTAGTAGGGGTCAGCCTCCC	60.760	65.0	0.0	0.4	43.90	4.30	R
2829	2929	0.815734	TGAGCGTCCAAGGCTACTAC	59.184	55.0	0.0	0.0	39.71	2.73	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
196	198	9.362539	CTGCTAAAATGCAAGAAGTTCAAATAT	57.637	29.630	5.50	0.00	42.83	1.28
292	305	6.770785	TCGTAAATAATCTCAATCCCCCAAAG	59.229	38.462	0.00	0.00	0.00	2.77
341	355	6.995686	TGACATCAGTACTAAAAAGCAGGAAA	59.004	34.615	0.00	0.00	0.00	3.13
444	461	8.502161	CACTAAACCATAAGTGCACTAAAAAC	57.498	34.615	22.01	0.00	36.96	2.43
445	462	8.349983	CACTAAACCATAAGTGCACTAAAAACT	58.650	33.333	22.01	5.66	36.96	2.66
547	570	3.807553	AGGGCACTGAAAAATGTTTTGG	58.192	40.909	0.00	0.00	0.00	3.28
571	594	7.140048	GGGATCAACTAGTGTATAAGACTTCG	58.860	42.308	0.00	0.00	0.00	3.79
679	705	2.619849	CCTGAGACATGCAAGTGGGATT	60.620	50.000	0.00	0.00	0.00	3.01
691	717	3.760580	AGTGGGATTAGCAGCTGATAC	57.239	47.619	20.43	4.86	0.00	2.24
704	730	3.300853	CAGCTGATACGTACAACTTGACG	59.699	47.826	8.42	10.37	44.57	4.35
718	744	5.163540	ACAACTTGACGAGACTACTCAGTTT	60.164	40.000	0.00	0.00	42.72	2.66
871	899	2.184322	CCACACATCCCCGTCGAG	59.816	66.667	0.00	0.00	0.00	4.04
907	936	2.092538	CCCATTGTCTTCCATCTCTGCT	60.093	50.000	0.00	0.00	0.00	4.24
944	978	0.184451	ATTGCCGCTTCCATCTCCAT	59.816	50.000	0.00	0.00	0.00	3.41
961	995	2.361757	TCCATTGCAGACAAACCACAAG	59.638	45.455	0.00	0.00	39.77	3.16
1092	1127	4.117661	GTCTCCGGCGAGAAGCGT	62.118	66.667	9.30	0.00	46.74	5.07
1170	1205	4.001652	TCGTCTACACCAGTGAACTAGAG	58.998	47.826	4.48	0.00	0.00	2.43
1177	1212	1.902508	CCAGTGAACTAGAGAAGGCCA	59.097	52.381	5.01	0.00	0.00	5.36
1325	1360	2.299297	AGGAACTCTTCTTGGTGTACCG	59.701	50.000	0.00	0.00	39.43	4.02
1335	1370	2.813474	GTGTACCGCATCGCAGCA	60.813	61.111	0.00	0.00	0.00	4.41
1369	1405	7.736881	TGGTAACCCATACTACTGTTCATTA	57.263	36.000	0.00	0.00	35.17	1.90
1372	1408	9.623000	GGTAACCCATACTACTGTTCATTAATT	57.377	33.333	0.00	0.00	34.74	1.40
1763	1823	7.010771	AGATGTATCAAGCACTGGTATAGGTA	58.989	38.462	0.00	0.00	0.00	3.08
1963	2028	8.100164	TGAACTACATTCATCCATGACTTGTAA	58.900	33.333	0.00	0.00	42.62	2.41
2001	2066	9.784531	CTACCTCATGGATTATCACTTGTAAAT	57.215	33.333	0.00	0.00	37.04	1.40
2027	2093	7.387948	TCAAAAAGAGGGAGAACTAAATCTTCG	59.612	37.037	0.00	0.00	0.00	3.79
2062	2128	5.983333	AATCTTCAATATGTGTCTCCCCT	57.017	39.130	0.00	0.00	0.00	4.79
2180	2246	2.076863	GTCTGGTTTGGAGATCAACCG	58.923	52.381	7.87	4.13	34.67	4.44
2248	2315	3.335579	ACCAAATTCTACGACTCCTTGC	58.664	45.455	0.00	0.00	0.00	4.01
2274	2341	2.515523	GCAGCCAGCGTCATCCAT	60.516	61.111	0.00	0.00	0.00	3.41
2319	2386	3.772025	AGAACATCGACAAGGAGGAAGAT	59.228	43.478	0.00	0.00	0.00	2.40
2413	2480	8.667076	CATGTACAAGTCATGGAAGATAATCA	57.333	34.615	0.00	0.00	38.97	2.57
2450	2517	4.399303	AGGTTGGGATATTTCAAAAGAGCG	59.601	41.667	0.00	0.00	0.00	5.03
2559	2630	8.567948	TGTCCTTAATCTTGTTGTTTCAGATTC	58.432	33.333	0.00	0.00	32.37	2.52
2611	2707	5.874810	GCTTCCTTATGTTATGTGTGTCAGA	59.125	40.000	0.00	0.00	0.00	3.27
2664	2760	7.377766	AGTACATCATTTGCTTATGTCGTTT	57.622	32.000	0.00	0.00	35.54	3.60
2829	2929	7.078228	GCAAACTAACTAAGGACAACATCAAG	58.922	38.462	0.00	0.00	0.00	3.02
2856	2956	1.269831	CCTTGGACGCTCAGTATAGCC	60.270	57.143	0.00	0.00	39.43	3.93
2944	3047	2.568623	AAGTTTCAGCCGAGGACAAT	57.431	45.000	0.00	0.00	0.00	2.71
3017	3120	4.141869	ACTGCAACAGGAAAAGCAAAGAAT	60.142	37.500	0.00	0.00	36.44	2.40
3082	3188	5.546621	AGTACTGGTACACTTGAACACAT	57.453	39.130	12.54	0.00	38.48	3.21
3120	3230	8.862085	TCTACAAAAATAAAAAGGAACGGGAAT	58.138	29.630	0.00	0.00	0.00	3.01
3163	3273	7.715265	AACACAGTGACACACTAAGAATAAG	57.285	36.000	7.81	0.00	43.43	1.73
3346	3460	0.111061	ACAGAAGCATCAGCCCACAA	59.889	50.000	0.00	0.00	43.56	3.33
3352	3466	0.454600	GCATCAGCCCACAATGACTG	59.545	55.000	0.00	0.00	33.58	3.51
3374	3488	6.182507	TGGTGAGGTACTAGTTTCAAACAT	57.817	37.500	0.00	0.00	41.55	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
150	152	6.963796	AGCAGTTGAACTTGTCAGATTTTAG	58.036	36.000	0.00	0.00	37.61	1.85
341	355	1.344953	TGGTGTGAGTGGCCTGACTT	61.345	55.000	3.32	0.00	0.00	3.01
547	570	7.140048	CCGAAGTCTTATACACTAGTTGATCC	58.860	42.308	0.00	0.00	0.00	3.36
679	705	4.157105	TCAAGTTGTACGTATCAGCTGCTA	59.843	41.667	9.47	0.00	0.00	3.49
691	717	4.084171	TGAGTAGTCTCGTCAAGTTGTACG	60.084	45.833	16.68	16.68	43.09	3.67
704	730	8.541312	GTTTTTACTGTCAAACTGAGTAGTCTC	58.459	37.037	0.00	0.00	40.79	3.36
718	744	4.642885	CCAAGTCAAGGGTTTTTACTGTCA	59.357	41.667	0.00	0.00	0.00	3.58
782	810	1.898574	CTTCCTTGTGGCAACCGCT	60.899	57.895	0.00	0.00	38.60	5.52
871	899	1.111277	ATGGGTTATTTTCCAGCGCC	58.889	50.000	2.29	0.00	36.38	6.53
907	936	3.164268	CAATGGTGGTTCTGGGAATGAA	58.836	45.455	0.00	0.00	0.00	2.57
944	978	1.473258	AGCTTGTGGTTTGTCTGCAA	58.527	45.000	0.00	0.00	0.00	4.08
961	995	1.223211	GGGCTTGGGAGAGAGAAGC	59.777	63.158	0.00	0.00	41.18	3.86
1017	1051	1.647545	CGCCATGATGACGCTTGGTT	61.648	55.000	0.00	0.00	35.96	3.67
1078	1112	4.116328	CTCACGCTTCTCGCCGGA	62.116	66.667	5.05	0.00	43.23	5.14
1092	1127	2.960384	TGTGAGGGTTTTCGTCTACTCA	59.040	45.455	0.00	0.00	33.05	3.41
1140	1175	1.678627	CTGGTGTAGACGATCTCCAGG	59.321	57.143	10.66	0.00	39.89	4.45
1170	1205	2.208431	CTCATCATCTCGTTGGCCTTC	58.792	52.381	3.32	0.00	0.00	3.46
1177	1212	0.829333	AGCCTGCTCATCATCTCGTT	59.171	50.000	0.00	0.00	0.00	3.85
1254	1289	3.107601	CTGGGGAGGTTCATCTTCACTA	58.892	50.000	0.00	0.00	0.00	2.74
1257	1292	2.342406	TCTGGGGAGGTTCATCTTCA	57.658	50.000	0.00	0.00	0.00	3.02
1313	1348	1.447140	GCGATGCGGTACACCAAGA	60.447	57.895	0.00	0.00	35.14	3.02
1325	1360	3.678717	CTTGTGGCTGCTGCGATGC	62.679	63.158	9.65	0.00	40.82	3.91
1653	1695	3.930848	GACCTATACCACTTCACCAAACG	59.069	47.826	0.00	0.00	0.00	3.60
1802	1863	6.835174	ACCAGAGTCAATGATATATGTGCTT	58.165	36.000	0.00	0.00	0.00	3.91
2001	2066	7.387948	CGAAGATTTAGTTCTCCCTCTTTTTGA	59.612	37.037	0.00	0.00	0.00	2.69
2009	2075	7.450903	TCTTTTTCGAAGATTTAGTTCTCCCT	58.549	34.615	0.00	0.00	35.04	4.20
2010	2076	7.668525	TCTTTTTCGAAGATTTAGTTCTCCC	57.331	36.000	0.00	0.00	35.04	4.30
2180	2246	3.382855	TGCATGTTGATGAAGTTGTTGC	58.617	40.909	0.00	0.00	0.00	4.17
2228	2295	2.678336	GGCAAGGAGTCGTAGAATTTGG	59.322	50.000	0.00	0.00	39.69	3.28
2248	2315	3.818787	GCTGGCTGCAACATCGGG	61.819	66.667	11.80	0.00	42.31	5.14
2274	2341	5.178096	TCTTCATGCCTTTGTAGAATGGA	57.822	39.130	8.57	0.00	0.00	3.41
2413	2480	1.946768	CCAACCTGTCACGATGTTGTT	59.053	47.619	0.00	0.00	37.08	2.83
2450	2517	0.759812	GTAGTAGGGGTCAGCCTCCC	60.760	65.000	0.00	0.40	43.90	4.30
2528	2595	6.463995	AACAACAAGATTAAGGACAAGCAA	57.536	33.333	0.00	0.00	0.00	3.91
2559	2630	4.209703	TCAACCTAACGAAAGCAAACTACG	59.790	41.667	0.00	0.00	33.83	3.51
2611	2707	5.594317	AGACATAGGCAAACTTGTTCAAACT	59.406	36.000	0.00	0.00	0.00	2.66
2664	2760	3.492102	AGGAAGCTAGCAAACTTGTCA	57.508	42.857	18.83	0.00	0.00	3.58
2798	2897	4.141574	TGTCCTTAGTTAGTTTGCCACAGT	60.142	41.667	0.00	0.00	0.00	3.55
2799	2898	4.385825	TGTCCTTAGTTAGTTTGCCACAG	58.614	43.478	0.00	0.00	0.00	3.66
2800	2899	4.425180	TGTCCTTAGTTAGTTTGCCACA	57.575	40.909	0.00	0.00	0.00	4.17
2807	2906	8.648693	ACTACTTGATGTTGTCCTTAGTTAGTT	58.351	33.333	0.00	0.00	28.98	2.24
2829	2929	0.815734	TGAGCGTCCAAGGCTACTAC	59.184	55.000	0.00	0.00	39.71	2.73
2856	2956	7.654923	TGTGATAGTACTACCGTACATGTCTAG	59.345	40.741	0.00	0.00	46.68	2.43
2905	3007	9.932699	GAAACTTAGTCTTTTTAGTGTTCTTCC	57.067	33.333	0.00	0.00	0.00	3.46
3017	3120	6.827251	AGTGACTAGGAAATACGTACTGATGA	59.173	38.462	0.00	0.00	0.00	2.92
3120	3230	3.007506	TGTTAGGGAATGCGAACTGAAGA	59.992	43.478	0.00	0.00	0.00	2.87
3346	3460	5.084519	TGAAACTAGTACCTCACCAGTCAT	58.915	41.667	0.00	0.00	0.00	3.06
3352	3466	7.658575	TGTTATGTTTGAAACTAGTACCTCACC	59.341	37.037	9.69	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.