AutoCloner

Multiple sequence alignment - TraesCS1D01G216900

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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	TraesCS1D01G216900	chr1D	100.000	2864	0	0	1	2864	302690061	302692924	0.000000e+00	5289.0
1	TraesCS1D01G216900	chr1D	92.727	55	4	0	1034	1088	11789267	11789321	2.370000e-11	80.5
2	TraesCS1D01G216900	chr1B	90.724	2609	127	53	12	2554	409598012	409600571	0.000000e+00	3371.0
3	TraesCS1D01G216900	chr1B	93.980	299	6	5	2575	2864	409600556	409600851	2.620000e-120	442.0
4	TraesCS1D01G216900	chr1B	91.571	261	19	2	1502	1762	668439509	668439252	9.760000e-95	357.0
5	TraesCS1D01G216900	chr1A	89.987	2277	78	49	646	2864	377207635	377209819	0.000000e+00	2804.0
6	TraesCS1D01G216900	chr1A	96.960	329	9	1	8	335	377207006	377207334	4.170000e-153	551.0
7	TraesCS1D01G216900	chr1A	85.816	282	27	9	377	652	377207338	377207612	1.300000e-73	287.0
8	TraesCS1D01G216900	chr1A	87.037	108	8	2	1034	1141	22682953	22682852	1.800000e-22	117.0
9	TraesCS1D01G216900	chr1A	100.000	30	0	0	509	538	377207543	377207572	3.990000e-04	56.5
10	TraesCS1D01G216900	chr5B	87.569	362	41	2	1466	1827	419524808	419525165	1.590000e-112	416.0
11	TraesCS1D01G216900	chr5B	90.189	265	23	2	1498	1762	458926805	458927066	2.730000e-90	342.0
12	TraesCS1D01G216900	chr4B	91.698	265	18	3	1498	1762	7048819	7049079	5.830000e-97	364.0
13	TraesCS1D01G216900	chr2B	91.698	265	19	2	1498	1762	699046148	699046409	5.830000e-97	364.0
14	TraesCS1D01G216900	chr7B	90.566	265	22	2	1498	1762	104245479	104245740	5.870000e-92	348.0
15	TraesCS1D01G216900	chr7B	90.805	261	21	2	1502	1762	656421777	656422034	2.110000e-91	346.0
16	TraesCS1D01G216900	chr3D	92.116	241	10	7	842	1081	68387145	68386913	5.910000e-87	331.0
17	TraesCS1D01G216900	chr2D	83.333	108	12	3	1039	1146	114648229	114648330	8.450000e-16	95.3
18	TraesCS1D01G216900	chr5A	88.889	72	8	0	1034	1105	502394919	502394990	3.930000e-14	89.8

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	TraesCS1D01G216900	chr1D	302690061	302692924	2863	False	5289.000	5289	100.00000	1	2864	1	chr1D.!!$F2	2863
1	TraesCS1D01G216900	chr1B	409598012	409600851	2839	False	1906.500	3371	92.35200	12	2864	2	chr1B.!!$F1	2852
2	TraesCS1D01G216900	chr1A	377207006	377209819	2813	False	924.625	2804	93.19075	8	2864	4	chr1A.!!$F1	2856

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
394	415	0.109913	GGGTCAAAGGGTCCGTTTCT	59.89	55.0	6.58	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2317	2425	0.179059	TCTTCTTGCTCGTGGTGCAA	60.179	50.0	5.19	5.19	46.48	4.08	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
147	148	0.620700	GGAGTCCACATACCCCCACT	60.621	60.000	3.60	0.00	0.00	4.00
276	293	2.739913	CCGTTATTTTGAGAACTGGCGA	59.260	45.455	0.00	0.00	0.00	5.54
349	369	1.527736	CGACCGTTTTTCGTGAATGGA	59.472	47.619	11.47	0.00	36.79	3.41
352	372	2.287368	ACCGTTTTTCGTGAATGGAAGC	60.287	45.455	11.47	0.00	36.79	3.86
353	373	2.315901	CGTTTTTCGTGAATGGAAGCC	58.684	47.619	0.00	0.00	34.52	4.35
354	374	2.672714	GTTTTTCGTGAATGGAAGCCC	58.327	47.619	0.00	0.00	0.00	5.19
355	375	1.253100	TTTTCGTGAATGGAAGCCCC	58.747	50.000	0.00	0.00	0.00	5.80
394	415	0.109913	GGGTCAAAGGGTCCGTTTCT	59.890	55.000	6.58	0.00	0.00	2.52
399	420	2.685897	TCAAAGGGTCCGTTTCTGTTTG	59.314	45.455	6.58	0.00	0.00	2.93
407	428	1.002900	CCGTTTCTGTTTGTCACGCAT	60.003	47.619	0.00	0.00	0.00	4.73
411	432	3.773860	TTCTGTTTGTCACGCATGTTT	57.226	38.095	0.00	0.00	0.00	2.83
546	573	4.083802	CGATCTAGACACGAGATACATGCA	60.084	45.833	13.63	0.00	33.71	3.96
571	599	6.520792	AGTGTAGACGTGTACAAAATGTTC	57.479	37.500	25.18	12.19	34.69	3.18
587	615	8.194769	ACAAAATGTTCTTAACGGTCATTTTCT	58.805	29.630	6.78	0.00	42.67	2.52
601	629	4.007659	TCATTTTCTTTAGAGAACGGGCC	58.992	43.478	0.00	0.00	41.46	5.80
612	640	4.031611	AGAGAACGGGCCTATTTCTAAGT	58.968	43.478	0.84	0.00	29.54	2.24
813	884	1.308326	CGTCCTCCCTCTCCCTCTT	59.692	63.158	0.00	0.00	0.00	2.85
1491	1573	2.279517	CTGTCGGCCATAGTCCGC	60.280	66.667	2.24	0.00	46.05	5.54
1970	2052	1.865788	GACCTTTTGCTGATGCGCCA	61.866	55.000	4.18	0.00	43.34	5.69
2066	2148	1.471829	TTGAACGGGAGCAGAGCAGA	61.472	55.000	0.00	0.00	0.00	4.26
2067	2149	1.293498	GAACGGGAGCAGAGCAGAA	59.707	57.895	0.00	0.00	0.00	3.02
2072	2154	2.099431	GGAGCAGAGCAGAACAGCG	61.099	63.158	0.00	0.00	40.15	5.18
2073	2155	2.738695	GAGCAGAGCAGAACAGCGC	61.739	63.158	0.00	0.00	40.15	5.92
2320	2428	1.353076	GGCATTGTTTAGCTGCTTGC	58.647	50.000	7.79	10.47	43.29	4.01
2321	2429	1.337074	GGCATTGTTTAGCTGCTTGCA	60.337	47.619	19.68	9.49	45.94	4.08
2323	2431	2.331194	CATTGTTTAGCTGCTTGCACC	58.669	47.619	7.79	0.00	45.94	5.01
2465	2580	1.943340	GGGCAGTGATTAGCTTAGCAC	59.057	52.381	12.94	12.94	0.00	4.40
2466	2581	2.420687	GGGCAGTGATTAGCTTAGCACT	60.421	50.000	17.27	17.27	41.90	4.40
2467	2582	2.869192	GGCAGTGATTAGCTTAGCACTC	59.131	50.000	19.85	14.20	39.40	3.51
2468	2583	2.869192	GCAGTGATTAGCTTAGCACTCC	59.131	50.000	19.85	8.51	39.40	3.85
2469	2584	3.431486	GCAGTGATTAGCTTAGCACTCCT	60.431	47.826	19.85	0.00	39.40	3.69
2470	2585	4.367450	CAGTGATTAGCTTAGCACTCCTC	58.633	47.826	19.85	0.00	39.40	3.71
2524	2639	2.027100	TCGAGTGAGAGAAGCTGGACTA	60.027	50.000	0.00	0.00	0.00	2.59
2525	2640	2.948979	CGAGTGAGAGAAGCTGGACTAT	59.051	50.000	0.00	0.00	0.00	2.12
2526	2641	4.130857	CGAGTGAGAGAAGCTGGACTATA	58.869	47.826	0.00	0.00	0.00	1.31
2527	2642	4.024387	CGAGTGAGAGAAGCTGGACTATAC	60.024	50.000	0.00	0.00	0.00	1.47
2528	2643	5.124036	AGTGAGAGAAGCTGGACTATACT	57.876	43.478	0.00	0.00	0.00	2.12
2656	2787	6.443995	TCACATCACCATTAGGATGATGAT	57.556	37.500	22.21	2.43	45.59	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.675641	GCGGCAAACCAGAGGTCAT	60.676	57.895	0.00	0.00	33.12	3.06
1	2	2.281484	GCGGCAAACCAGAGGTCA	60.281	61.111	0.00	0.00	33.12	4.02
2	3	2.180159	TAGGCGGCAAACCAGAGGTC	62.180	60.000	13.08	0.00	33.12	3.85
3	4	2.221299	TAGGCGGCAAACCAGAGGT	61.221	57.895	13.08	0.00	37.65	3.85
4	5	1.745489	GTAGGCGGCAAACCAGAGG	60.745	63.158	13.08	0.00	34.57	3.69
5	6	0.605319	TTGTAGGCGGCAAACCAGAG	60.605	55.000	13.08	0.00	34.57	3.35
6	7	0.179015	TTTGTAGGCGGCAAACCAGA	60.179	50.000	13.08	0.00	34.57	3.86
276	293	2.671399	AAAGGGGAGGGGGTGGACTT	62.671	60.000	0.00	0.00	0.00	3.01
432	458	5.343249	GTGCTCAATAAATTGCGGATCTTT	58.657	37.500	0.00	0.00	37.68	2.52
546	573	6.913873	ACATTTTGTACACGTCTACACTTT	57.086	33.333	2.92	0.00	0.00	2.66
571	599	7.950496	CGTTCTCTAAAGAAAATGACCGTTAAG	59.050	37.037	0.00	0.00	43.04	1.85
587	615	6.155737	ACTTAGAAATAGGCCCGTTCTCTAAA	59.844	38.462	14.64	5.64	33.70	1.85
612	640	5.722021	TGCAAGTGAAGTGAGTATAGTGA	57.278	39.130	0.00	0.00	0.00	3.41
813	884	4.742201	GGTTGGCTCGCTCGCTCA	62.742	66.667	0.00	0.00	0.00	4.26
985	1061	3.237741	CATCGGCCCTCTCCTCCC	61.238	72.222	0.00	0.00	0.00	4.30
1272	1354	1.142965	GAAGAAGAGGAGCTCGGGC	59.857	63.158	7.83	0.00	35.36	6.13
1982	2064	4.500116	GTCGTCTCTCAGCGGGCC	62.500	72.222	0.00	0.00	0.00	5.80
1985	2067	2.031044	CTCTCGTCGTCTCTCAGCGG	62.031	65.000	0.00	0.00	0.00	5.52
2066	2148	1.375853	TTGACACAAGCTGCGCTGTT	61.376	50.000	16.05	7.02	39.62	3.16
2067	2149	1.168407	ATTGACACAAGCTGCGCTGT	61.168	50.000	16.05	6.79	39.62	4.40
2072	2154	2.721797	CGTCGTAATTGACACAAGCTGC	60.722	50.000	0.00	0.00	38.84	5.25
2073	2155	2.729360	TCGTCGTAATTGACACAAGCTG	59.271	45.455	0.00	0.00	38.84	4.24
2083	2170	2.174764	CAGGTCGTCTCGTCGTAATTG	58.825	52.381	0.00	0.00	0.00	2.32
2240	2329	0.673437	ATGGAAAAACACAGGCACGG	59.327	50.000	0.00	0.00	0.00	4.94
2317	2425	0.179059	TCTTCTTGCTCGTGGTGCAA	60.179	50.000	5.19	5.19	46.48	4.08
2320	2428	2.154854	TCTTCTTCTTGCTCGTGGTG	57.845	50.000	0.00	0.00	0.00	4.17
2321	2429	2.760374	CTTCTTCTTCTTGCTCGTGGT	58.240	47.619	0.00	0.00	0.00	4.16
2323	2431	2.411904	AGCTTCTTCTTCTTGCTCGTG	58.588	47.619	0.00	0.00	0.00	4.35
2400	2511	9.350951	GTACAAGGCTTTATCCACCTTTTATAT	57.649	33.333	0.00	0.00	41.90	0.86
2402	2513	7.339466	CAGTACAAGGCTTTATCCACCTTTTAT	59.661	37.037	0.00	0.00	41.90	1.40
2465	2580	1.383803	CCCAAGGGAGGAGGAGGAG	60.384	68.421	0.00	0.00	37.50	3.69
2466	2581	1.460839	TTCCCAAGGGAGGAGGAGGA	61.461	60.000	8.06	0.00	46.06	3.71
2467	2582	1.082954	TTCCCAAGGGAGGAGGAGG	59.917	63.158	8.06	0.00	46.06	4.30
2468	2583	0.252927	AGTTCCCAAGGGAGGAGGAG	60.253	60.000	8.06	0.00	46.06	3.69
2469	2584	0.547712	CAGTTCCCAAGGGAGGAGGA	60.548	60.000	8.06	0.00	46.06	3.71
2470	2585	0.547712	TCAGTTCCCAAGGGAGGAGG	60.548	60.000	8.06	0.41	46.06	4.30
2524	2639	1.289231	TCTCACCCTCTCCAGCAGTAT	59.711	52.381	0.00	0.00	0.00	2.12
2525	2640	0.704664	TCTCACCCTCTCCAGCAGTA	59.295	55.000	0.00	0.00	0.00	2.74
2526	2641	0.042431	ATCTCACCCTCTCCAGCAGT	59.958	55.000	0.00	0.00	0.00	4.40
2527	2642	0.464870	CATCTCACCCTCTCCAGCAG	59.535	60.000	0.00	0.00	0.00	4.24
2528	2643	0.041684	TCATCTCACCCTCTCCAGCA	59.958	55.000	0.00	0.00	0.00	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.