AutoCloner

Multiple sequence alignment - TraesCS6B01G306100

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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	TraesCS6B01G306100	chr6B	100.000	2990	0	0	1	2990	549192325	549195314	0.000000e+00	5522.0
1	TraesCS6B01G306100	chr6B	78.125	480	91	10	1285	1760	704890682	704891151	2.920000e-75	292.0
2	TraesCS6B01G306100	chr6D	96.464	1838	48	6	829	2661	364226778	364228603	0.000000e+00	3018.0
3	TraesCS6B01G306100	chr6D	92.485	825	20	11	6	818	364225927	364226721	0.000000e+00	1142.0
4	TraesCS6B01G306100	chr6D	78.528	489	92	9	1276	1760	462422977	462423456	2.890000e-80	309.0
5	TraesCS6B01G306100	chr6D	95.035	141	6	1	2657	2797	364229157	364229296	1.400000e-53	220.0
6	TraesCS6B01G306100	chr6D	93.137	102	6	1	2794	2895	364230487	364230587	6.680000e-32	148.0
7	TraesCS6B01G306100	chr6D	97.143	35	1	0	2891	2925	364230764	364230798	3.220000e-05	60.2
8	TraesCS6B01G306100	chr6A	94.677	1935	61	16	831	2747	505247900	505245990	0.000000e+00	2964.0
9	TraesCS6B01G306100	chr6A	88.307	821	38	26	6	818	505248733	505247963	0.000000e+00	931.0
10	TraesCS6B01G306100	chr6A	78.125	480	91	10	1285	1760	609176301	609176770	2.920000e-75	292.0
11	TraesCS6B01G306100	chr6A	86.364	264	17	12	2745	2990	505245161	505244899	1.370000e-68	270.0
12	TraesCS6B01G306100	chr7A	77.925	829	126	47	956	1763	195218283	195217491	5.840000e-127	464.0
13	TraesCS6B01G306100	chr7B	77.063	824	139	42	956	1763	333129215	333130004	2.130000e-116	429.0
14	TraesCS6B01G306100	chr1B	75.647	464	97	12	1285	1743	39069377	39068925	1.800000e-52	217.0
15	TraesCS6B01G306100	chr1D	75.378	463	98	12	1286	1743	22863630	22864081	3.020000e-50	209.0

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	TraesCS6B01G306100	chr6B	549192325	549195314	2989	False	5522.000000	5522	100.000000	1	2990	1	chr6B.!!$F1	2989
1	TraesCS6B01G306100	chr6D	364225927	364230798	4871	False	917.640000	3018	94.852800	6	2925	5	chr6D.!!$F2	2919
2	TraesCS6B01G306100	chr6A	505244899	505248733	3834	True	1388.333333	2964	89.782667	6	2990	3	chr6A.!!$R1	2984
3	TraesCS6B01G306100	chr7A	195217491	195218283	792	True	464.000000	464	77.925000	956	1763	1	chr7A.!!$R1	807
4	TraesCS6B01G306100	chr7B	333129215	333130004	789	False	429.000000	429	77.063000	956	1763	1	chr7B.!!$F1	807

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
577	597	0.386985	GGCTTCGACCGATCCGTATC	60.387	60.0	0.0	0.0	0.0	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2374	2499	1.690352	ACGAAAACGAAGAGGAAGGGA	59.31	47.619	0.0	0.0	0.0	4.2	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
450	470	2.127297	CCCCCTTCTTCCTCCCCA	59.873	66.667	0.00	0.00	0.00	4.96
451	471	2.003548	CCCCCTTCTTCCTCCCCAG	61.004	68.421	0.00	0.00	0.00	4.45
453	473	1.617839	CCCTTCTTCCTCCCCAGCT	60.618	63.158	0.00	0.00	0.00	4.24
454	474	1.631071	CCCTTCTTCCTCCCCAGCTC	61.631	65.000	0.00	0.00	0.00	4.09
455	475	1.519719	CTTCTTCCTCCCCAGCTCG	59.480	63.158	0.00	0.00	0.00	5.03
456	476	2.585791	CTTCTTCCTCCCCAGCTCGC	62.586	65.000	0.00	0.00	0.00	5.03
457	477	4.168291	CTTCCTCCCCAGCTCGCC	62.168	72.222	0.00	0.00	0.00	5.54
458	478	4.722535	TTCCTCCCCAGCTCGCCT	62.723	66.667	0.00	0.00	0.00	5.52
489	509	0.610509	TGCCTGCCTTTAATTCGCCA	60.611	50.000	0.00	0.00	0.00	5.69
575	595	1.442526	GAGGCTTCGACCGATCCGTA	61.443	60.000	0.00	0.00	33.69	4.02
577	597	0.386985	GGCTTCGACCGATCCGTATC	60.387	60.000	0.00	0.00	0.00	2.24
589	609	2.242572	CCGTATCGCTCTCGGACGA	61.243	63.158	12.16	0.00	46.05	4.20
721	747	2.642311	TGCTGGAGGTAAGGAACATGAA	59.358	45.455	0.00	0.00	0.00	2.57
934	1013	0.397941	CTGAAGCCAAGGAGGTGTGA	59.602	55.000	0.00	0.00	40.61	3.58
1467	1575	2.340078	GTCTGCGTGCTGAGTGGA	59.660	61.111	1.39	0.00	0.00	4.02
1674	1791	1.071471	CAGCGTGGTGGGAACTCTT	59.929	57.895	0.00	0.00	0.00	2.85
1767	1884	2.726351	GGAGGAAGAGGAGGTGGCG	61.726	68.421	0.00	0.00	0.00	5.69
1902	2019	0.666274	TGTCGCTCTACAACCTTGCG	60.666	55.000	0.00	0.00	46.71	4.85
2030	2153	3.728076	TCCACAGTTCTACACTCACAC	57.272	47.619	0.00	0.00	30.92	3.82
2212	2335	2.334023	ACAGGAGGGAGATCTATTGGC	58.666	52.381	0.00	0.00	0.00	4.52
2222	2345	4.431809	GAGATCTATTGGCGATCATGAGG	58.568	47.826	0.09	0.00	39.73	3.86
2245	2368	4.021016	GGGTATACTATGTTCAGGGAGCTG	60.021	50.000	2.25	0.00	0.00	4.24
2343	2468	8.912988	AGTGAGATCCAATGTTTTGTTTTTCTA	58.087	29.630	0.00	0.00	0.00	2.10
2769	4295	3.712733	TGGTGGTGGTAGTACTCAGTTTT	59.287	43.478	0.00	0.00	0.00	2.43
2788	4314	1.904287	TTTGTTGCATACGCTCCCTT	58.096	45.000	0.00	0.00	39.64	3.95
2803	5523	0.179936	CCCTTCTAGCTCAGGCCAAG	59.820	60.000	5.01	2.53	39.73	3.61
2837	5557	3.372206	CCTCTCTATTTGTTTCACCTGCG	59.628	47.826	0.00	0.00	0.00	5.18
2860	5580	1.129998	CAGTCTTCAATGGCTTCTGCG	59.870	52.381	0.00	0.00	40.82	5.18
2861	5581	1.002430	AGTCTTCAATGGCTTCTGCGA	59.998	47.619	0.00	0.00	40.82	5.10
2862	5582	1.129437	GTCTTCAATGGCTTCTGCGAC	59.871	52.381	0.00	0.00	40.82	5.19
2925	5833	6.160576	GGCCTTTCATTGCCTTCAATTATA	57.839	37.500	0.00	0.00	44.46	0.98
2926	5834	6.218746	GGCCTTTCATTGCCTTCAATTATAG	58.781	40.000	0.00	0.00	44.46	1.31
2927	5835	6.040842	GGCCTTTCATTGCCTTCAATTATAGA	59.959	38.462	0.00	0.00	44.46	1.98
2928	5836	6.920210	GCCTTTCATTGCCTTCAATTATAGAC	59.080	38.462	0.00	0.00	40.74	2.59
2930	5838	5.673337	TCATTGCCTTCAATTATAGACGC	57.327	39.130	0.00	0.00	40.74	5.19
2931	5839	5.122519	TCATTGCCTTCAATTATAGACGCA	58.877	37.500	0.00	0.00	40.74	5.24
2933	5841	5.888691	TTGCCTTCAATTATAGACGCAAA	57.111	34.783	0.00	0.00	31.39	3.68
2934	5842	5.484173	TGCCTTCAATTATAGACGCAAAG	57.516	39.130	0.00	0.00	0.00	2.77
2935	5843	4.201910	TGCCTTCAATTATAGACGCAAAGC	60.202	41.667	0.00	0.00	0.00	3.51
2936	5844	4.201910	GCCTTCAATTATAGACGCAAAGCA	60.202	41.667	0.00	0.00	0.00	3.91
2937	5845	5.506317	GCCTTCAATTATAGACGCAAAGCAT	60.506	40.000	0.00	0.00	0.00	3.79
2938	5846	6.293407	GCCTTCAATTATAGACGCAAAGCATA	60.293	38.462	0.00	0.00	0.00	3.14
2940	5848	7.171508	CCTTCAATTATAGACGCAAAGCATAGA	59.828	37.037	0.00	0.00	0.00	1.98
2941	5849	8.607441	TTCAATTATAGACGCAAAGCATAGAT	57.393	30.769	0.00	0.00	0.00	1.98
2942	5850	8.021955	TCAATTATAGACGCAAAGCATAGATG	57.978	34.615	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.007271	CGTTGTGACCGCAGAGTCT	60.007	57.895	0.00	0.00	37.66	3.24
1	2	2.022129	CCGTTGTGACCGCAGAGTC	61.022	63.158	0.00	0.00	37.28	3.36
2	3	2.029073	CCGTTGTGACCGCAGAGT	59.971	61.111	0.00	0.00	0.00	3.24
3	4	3.414700	GCCGTTGTGACCGCAGAG	61.415	66.667	0.00	0.00	31.48	3.35
4	5	3.529341	ATGCCGTTGTGACCGCAGA	62.529	57.895	0.00	0.00	41.92	4.26
33	34	2.010582	GCGCTAGCTAGCTCCAGTGT	62.011	60.000	36.02	0.00	46.85	3.55
89	94	4.789075	CCCGCGGACACGTACCAG	62.789	72.222	30.73	0.44	43.45	4.00
244	253	3.051392	GCAATCCCAAAGCGACGGG	62.051	63.158	0.00	1.20	44.60	5.28
245	254	2.485122	GCAATCCCAAAGCGACGG	59.515	61.111	0.00	0.00	0.00	4.79
467	487	0.101219	CGAATTAAAGGCAGGCAGGC	59.899	55.000	0.00	0.00	44.61	4.85
468	488	0.101219	GCGAATTAAAGGCAGGCAGG	59.899	55.000	0.00	0.00	0.00	4.85
469	489	0.101219	GGCGAATTAAAGGCAGGCAG	59.899	55.000	0.00	0.00	0.00	4.85
470	490	0.610509	TGGCGAATTAAAGGCAGGCA	60.611	50.000	0.00	0.00	38.02	4.75
489	509	4.467107	GCGAGGGAGGGAGGGAGT	62.467	72.222	0.00	0.00	0.00	3.85
721	747	0.038159	AGTAAAGCAAGCTCGCGAGT	60.038	50.000	34.46	19.89	36.85	4.18
922	1001	1.672356	CGCCCTTCACACCTCCTTG	60.672	63.158	0.00	0.00	0.00	3.61
1902	2019	4.055227	TTCCCCACATTCCCGCCC	62.055	66.667	0.00	0.00	0.00	6.13
2030	2153	2.935042	ACTTCTGTGATGTCTTCGTCG	58.065	47.619	0.00	0.00	32.69	5.12
2212	2335	6.152831	TGAACATAGTATACCCCTCATGATCG	59.847	42.308	0.00	0.00	0.00	3.69
2222	2345	4.021016	CAGCTCCCTGAACATAGTATACCC	60.021	50.000	0.00	0.00	41.77	3.69
2245	2368	5.066593	CCCTTGAATAATCAGCTTCCTACC	58.933	45.833	0.00	0.00	36.78	3.18
2343	2468	2.017049	AGAAAAACACTCGCTGTTGCT	58.983	42.857	0.00	0.00	42.70	3.91
2366	2491	4.788679	ACGAAGAGGAAGGGAAAAAGAAA	58.211	39.130	0.00	0.00	0.00	2.52
2367	2492	4.432980	ACGAAGAGGAAGGGAAAAAGAA	57.567	40.909	0.00	0.00	0.00	2.52
2368	2493	4.432980	AACGAAGAGGAAGGGAAAAAGA	57.567	40.909	0.00	0.00	0.00	2.52
2369	2494	5.515797	AAAACGAAGAGGAAGGGAAAAAG	57.484	39.130	0.00	0.00	0.00	2.27
2370	2495	4.035909	CGAAAACGAAGAGGAAGGGAAAAA	59.964	41.667	0.00	0.00	0.00	1.94
2371	2496	3.562557	CGAAAACGAAGAGGAAGGGAAAA	59.437	43.478	0.00	0.00	0.00	2.29
2372	2497	3.135994	CGAAAACGAAGAGGAAGGGAAA	58.864	45.455	0.00	0.00	0.00	3.13
2373	2498	2.103601	ACGAAAACGAAGAGGAAGGGAA	59.896	45.455	0.00	0.00	0.00	3.97
2374	2499	1.690352	ACGAAAACGAAGAGGAAGGGA	59.310	47.619	0.00	0.00	0.00	4.20
2769	4295	1.810151	GAAGGGAGCGTATGCAACAAA	59.190	47.619	10.11	0.00	46.23	2.83
2773	4299	1.202533	GCTAGAAGGGAGCGTATGCAA	60.203	52.381	10.11	0.00	46.23	4.08
2803	5523	2.445682	TAGAGAGGGACAGAAGGCTC	57.554	55.000	0.00	0.00	0.00	4.70
2837	5557	2.095364	CAGAAGCCATTGAAGACTGCAC	60.095	50.000	0.00	0.00	0.00	4.57
2925	5833	3.808466	TCTCATCTATGCTTTGCGTCT	57.192	42.857	0.00	0.00	0.00	4.18
2926	5834	3.247173	CCTTCTCATCTATGCTTTGCGTC	59.753	47.826	0.00	0.00	0.00	5.19
2927	5835	3.201290	CCTTCTCATCTATGCTTTGCGT	58.799	45.455	0.00	0.00	0.00	5.24
2928	5836	2.032204	GCCTTCTCATCTATGCTTTGCG	60.032	50.000	0.00	0.00	0.00	4.85
2930	5838	7.157347	TGTATAGCCTTCTCATCTATGCTTTG	58.843	38.462	0.00	0.00	0.00	2.77
2931	5839	7.308450	TGTATAGCCTTCTCATCTATGCTTT	57.692	36.000	0.00	0.00	0.00	3.51
2933	5841	7.201776	CGTATGTATAGCCTTCTCATCTATGCT	60.202	40.741	0.00	0.00	0.00	3.79
2934	5842	6.915300	CGTATGTATAGCCTTCTCATCTATGC	59.085	42.308	0.00	0.00	0.00	3.14
2935	5843	7.912773	CACGTATGTATAGCCTTCTCATCTATG	59.087	40.741	0.00	0.00	0.00	2.23
2936	5844	7.612244	ACACGTATGTATAGCCTTCTCATCTAT	59.388	37.037	0.00	0.00	37.26	1.98
2937	5845	6.940867	ACACGTATGTATAGCCTTCTCATCTA	59.059	38.462	0.00	0.00	37.26	1.98
2938	5846	5.770663	ACACGTATGTATAGCCTTCTCATCT	59.229	40.000	0.00	0.00	37.26	2.90
2940	5848	6.151312	CCTACACGTATGTATAGCCTTCTCAT	59.849	42.308	0.00	0.00	40.57	2.90
2941	5849	5.472478	CCTACACGTATGTATAGCCTTCTCA	59.528	44.000	0.00	0.00	40.57	3.27
2942	5850	5.472820	ACCTACACGTATGTATAGCCTTCTC	59.527	44.000	0.00	0.00	40.57	2.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.