AutoCloner

Multiple sequence alignment - TraesCS3D01G102900

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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	TraesCS3D01G102900	chr3D	100.000	2840	0	0	1	2840	55349348	55352187	0.000000e+00	5245.0
1	TraesCS3D01G102900	chr3D	89.879	988	60	10	869	1850	55536868	55535915	0.000000e+00	1234.0
2	TraesCS3D01G102900	chr3D	84.560	1114	105	37	606	1686	55780997	55779918	0.000000e+00	1042.0
3	TraesCS3D01G102900	chr3D	93.433	533	32	1	1	533	55558042	55557513	0.000000e+00	787.0
4	TraesCS3D01G102900	chr3D	86.357	645	72	8	5	648	56281696	56282325	0.000000e+00	689.0
5	TraesCS3D01G102900	chr3D	85.930	661	75	10	2	657	56349705	56350352	0.000000e+00	689.0
6	TraesCS3D01G102900	chr3D	82.105	855	81	39	1732	2572	55779926	55779130	0.000000e+00	665.0
7	TraesCS3D01G102900	chr3D	93.871	310	15	2	742	1047	55943824	55943515	5.540000e-127	464.0
8	TraesCS3D01G102900	chr3D	86.339	183	21	4	1047	1227	56349038	56349218	2.230000e-46	196.0
9	TraesCS3D01G102900	chr3D	91.304	92	8	0	2748	2839	55534207	55534116	2.970000e-25	126.0
10	TraesCS3D01G102900	chr3D	93.902	82	4	1	2328	2409	55943425	55943345	3.840000e-24	122.0
11	TraesCS3D01G102900	chr3D	78.500	200	30	8	815	1012	56414372	56414560	4.970000e-23	119.0
12	TraesCS3D01G102900	chr3D	95.775	71	1	1	650	718	55557468	55557398	2.310000e-21	113.0
13	TraesCS3D01G102900	chr3D	100.000	30	0	0	746	775	56350433	56350462	3.950000e-04	56.5
14	TraesCS3D01G102900	chr3A	85.651	2265	188	63	1	2208	65766297	65764113	0.000000e+00	2255.0
15	TraesCS3D01G102900	chr3A	85.507	2063	174	57	1	2017	65700162	65702145	0.000000e+00	2037.0
16	TraesCS3D01G102900	chr3A	92.707	617	37	6	2230	2840	65702677	65703291	0.000000e+00	883.0
17	TraesCS3D01G102900	chr3A	82.729	689	93	14	1043	1718	65869036	65869711	8.760000e-165	590.0
18	TraesCS3D01G102900	chr3A	90.196	255	23	2	2587	2840	65763653	65763400	5.860000e-87	331.0
19	TraesCS3D01G102900	chr3A	91.772	158	13	0	2032	2189	65702232	65702389	1.320000e-53	220.0
20	TraesCS3D01G102900	chr3B	87.393	1047	93	16	5	1038	85339839	85340859	0.000000e+00	1166.0
21	TraesCS3D01G102900	chr3B	87.808	894	88	13	701	1580	85239628	85240514	0.000000e+00	1027.0
22	TraesCS3D01G102900	chr3B	89.189	740	63	9	1035	1772	85349855	85350579	0.000000e+00	907.0
23	TraesCS3D01G102900	chr3B	88.615	650	60	5	1	649	85237194	85237830	0.000000e+00	778.0
24	TraesCS3D01G102900	chr3B	80.853	1008	146	30	2	983	87717927	87718913	0.000000e+00	749.0
25	TraesCS3D01G102900	chr3B	89.713	593	46	10	2233	2816	85354383	85354969	0.000000e+00	743.0
26	TraesCS3D01G102900	chr3B	85.175	742	72	20	1587	2323	85241140	85241848	0.000000e+00	726.0
27	TraesCS3D01G102900	chr3B	86.190	601	80	2	2	602	88201951	88202548	0.000000e+00	647.0
28	TraesCS3D01G102900	chr3B	82.655	565	81	10	1040	1590	88971275	88971836	4.250000e-133	484.0
29	TraesCS3D01G102900	chr3B	92.157	255	20	0	1953	2207	85352912	85353166	7.480000e-96	361.0
30	TraesCS3D01G102900	chr3B	88.672	256	25	3	2587	2840	85242734	85242987	2.750000e-80	309.0
31	TraesCS3D01G102900	chr3B	87.083	240	11	11	1765	2003	85350744	85350964	1.310000e-63	254.0
32	TraesCS3D01G102900	chr3B	77.937	349	45	21	1764	2099	88977148	88977477	3.740000e-44	189.0
33	TraesCS3D01G102900	chr3B	93.976	83	5	0	2304	2386	85241860	85241942	2.970000e-25	126.0
34	TraesCS3D01G102900	chr3B	73.779	389	63	28	638	1012	88202639	88203002	1.790000e-22	117.0
35	TraesCS3D01G102900	chr3B	79.612	103	13	5	2171	2271	85352815	85352911	1.830000e-07	67.6

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	TraesCS3D01G102900	chr3D	55349348	55352187	2839	False	5245.000000	5245	100.000000	1	2840	1	chr3D.!!$F1	2839
1	TraesCS3D01G102900	chr3D	55779130	55780997	1867	True	853.500000	1042	83.332500	606	2572	2	chr3D.!!$R3	1966
2	TraesCS3D01G102900	chr3D	56281696	56282325	629	False	689.000000	689	86.357000	5	648	1	chr3D.!!$F2	643
3	TraesCS3D01G102900	chr3D	55534116	55536868	2752	True	680.000000	1234	90.591500	869	2839	2	chr3D.!!$R1	1970
4	TraesCS3D01G102900	chr3D	55557398	55558042	644	True	450.000000	787	94.604000	1	718	2	chr3D.!!$R2	717
5	TraesCS3D01G102900	chr3D	56349038	56350462	1424	False	313.833333	689	90.756333	2	1227	3	chr3D.!!$F4	1225
6	TraesCS3D01G102900	chr3A	65763400	65766297	2897	True	1293.000000	2255	87.923500	1	2840	2	chr3A.!!$R1	2839
7	TraesCS3D01G102900	chr3A	65700162	65703291	3129	False	1046.666667	2037	89.995333	1	2840	3	chr3A.!!$F2	2839
8	TraesCS3D01G102900	chr3A	65869036	65869711	675	False	590.000000	590	82.729000	1043	1718	1	chr3A.!!$F1	675
9	TraesCS3D01G102900	chr3B	85339839	85340859	1020	False	1166.000000	1166	87.393000	5	1038	1	chr3B.!!$F1	1033
10	TraesCS3D01G102900	chr3B	87717927	87718913	986	False	749.000000	749	80.853000	2	983	1	chr3B.!!$F2	981
11	TraesCS3D01G102900	chr3B	85237194	85242987	5793	False	593.200000	1027	88.849200	1	2840	5	chr3B.!!$F5	2839
12	TraesCS3D01G102900	chr3B	88971275	88971836	561	False	484.000000	484	82.655000	1040	1590	1	chr3B.!!$F3	550
13	TraesCS3D01G102900	chr3B	85349855	85354969	5114	False	466.520000	907	87.550800	1035	2816	5	chr3B.!!$F6	1781
14	TraesCS3D01G102900	chr3B	88201951	88203002	1051	False	382.000000	647	79.984500	2	1012	2	chr3B.!!$F7	1010

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
604	1274	0.962356	GCCATGTTCCACCACTGAGG	60.962	60.0	0.0	0.0	45.67	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2446	9680	0.594796	GCACTTGGGTTGTTTGCTCG	60.595	55.0	0.0	0.0	0.0	5.03	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
27	694	0.986527	TCAGCCTTGCAGAAGGATCA	59.013	50.000	8.71	0.00	45.26	2.92
107	774	2.731348	GCCAGATCGTCGATCGCC	60.731	66.667	25.34	15.54	43.17	5.54
293	960	1.380302	GAGTTGCCACCTGTCCCAT	59.620	57.895	0.00	0.00	0.00	4.00
599	1269	3.747976	GCCGCCATGTTCCACCAC	61.748	66.667	0.00	0.00	0.00	4.16
600	1270	2.034066	CCGCCATGTTCCACCACT	59.966	61.111	0.00	0.00	0.00	4.00
601	1271	2.334946	CCGCCATGTTCCACCACTG	61.335	63.158	0.00	0.00	0.00	3.66
602	1272	1.302431	CGCCATGTTCCACCACTGA	60.302	57.895	0.00	0.00	0.00	3.41
603	1273	1.300971	CGCCATGTTCCACCACTGAG	61.301	60.000	0.00	0.00	0.00	3.35
604	1274	0.962356	GCCATGTTCCACCACTGAGG	60.962	60.000	0.00	0.00	45.67	3.86
905	3466	4.142609	TCTGATCAACTGAATACCTGGC	57.857	45.455	0.00	0.00	0.00	4.85
954	3516	3.004629	GTGAAGATGTTGTGTCATGGCAA	59.995	43.478	0.00	0.00	0.00	4.52
955	3517	3.004629	TGAAGATGTTGTGTCATGGCAAC	59.995	43.478	0.00	11.16	43.60	4.17
985	3547	1.757306	CAAGCTGGGACCTGTCAGT	59.243	57.895	0.00	0.00	33.81	3.41
1041	3627	1.993301	GGGGAGGGGAGAAAGAAAGAA	59.007	52.381	0.00	0.00	0.00	2.52
1048	3634	6.267492	AGGGGAGAAAGAAAGAAAGAAAGA	57.733	37.500	0.00	0.00	0.00	2.52
1876	5317	0.101579	TGATGCCGTAGCGATTCGAA	59.898	50.000	10.88	0.00	44.31	3.71
1877	5318	0.503117	GATGCCGTAGCGATTCGAAC	59.497	55.000	10.88	6.11	44.31	3.95
1878	5319	0.102481	ATGCCGTAGCGATTCGAACT	59.898	50.000	10.88	0.65	44.31	3.01
1931	5373	6.208599	TCCCAGAATTACTTGTTGGTGATTTC	59.791	38.462	0.00	0.00	0.00	2.17
1983	7420	7.854337	AGTACCATGCATGATGTATGATGATA	58.146	34.615	28.31	8.34	42.03	2.15
2026	7549	5.759273	AGGTACGTGCTTAATGTGTTTGTTA	59.241	36.000	3.01	0.00	0.00	2.41
2208	7739	5.245531	TCCACAAGCAACTCCAATACTTAG	58.754	41.667	0.00	0.00	0.00	2.18
2209	7740	4.142600	CCACAAGCAACTCCAATACTTAGC	60.143	45.833	0.00	0.00	0.00	3.09
2210	7741	4.697352	CACAAGCAACTCCAATACTTAGCT	59.303	41.667	0.00	0.00	0.00	3.32
2211	7742	5.874810	CACAAGCAACTCCAATACTTAGCTA	59.125	40.000	0.00	0.00	0.00	3.32
2212	7743	6.371548	CACAAGCAACTCCAATACTTAGCTAA	59.628	38.462	5.94	5.94	0.00	3.09
2213	7744	7.066284	CACAAGCAACTCCAATACTTAGCTAAT	59.934	37.037	6.64	0.41	0.00	1.73
2214	7745	7.281100	ACAAGCAACTCCAATACTTAGCTAATC	59.719	37.037	6.64	0.00	0.00	1.75
2215	7746	7.130681	AGCAACTCCAATACTTAGCTAATCT	57.869	36.000	6.64	0.00	0.00	2.40
2216	7747	7.569240	AGCAACTCCAATACTTAGCTAATCTT	58.431	34.615	6.64	0.00	0.00	2.40
2217	7748	7.497249	AGCAACTCCAATACTTAGCTAATCTTG	59.503	37.037	6.64	10.44	0.00	3.02
2386	9156	4.361451	AAGGTGCAAAAGAATATGAGCG	57.639	40.909	0.00	0.00	0.00	5.03
2446	9680	3.426159	CCAATCACGTGCAATTCCAGTAC	60.426	47.826	11.67	0.00	0.00	2.73
2596	10832	3.633986	GCCTAGGCTTTAGAATGTGCAAT	59.366	43.478	27.17	0.00	38.26	3.56
2604	10840	5.624281	GCTTTAGAATGTGCAATTAGCCCAA	60.624	40.000	0.00	0.00	44.83	4.12
2669	10905	0.602638	GACGTGTTGCATGGTCCTCA	60.603	55.000	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	681	0.035152	ACGCCATGATCCTTCTGCAA	60.035	50.000	0.00	0.00	0.00	4.08
27	694	4.547905	CGAGTACGCCGACGCCAT	62.548	66.667	5.00	0.00	45.53	4.40
84	751	4.129737	CGACGATCTGGCCGTGGT	62.130	66.667	0.00	0.00	40.67	4.16
202	869	2.125310	CCAAGTCGCACGGCCATA	60.125	61.111	2.24	0.00	0.00	2.74
517	1187	1.204704	CGATAGCGGAGGCCATCAATA	59.795	52.381	5.01	0.00	37.16	1.90
518	1188	0.036952	CGATAGCGGAGGCCATCAAT	60.037	55.000	5.01	0.00	37.16	2.57
519	1189	1.367471	CGATAGCGGAGGCCATCAA	59.633	57.895	5.01	0.00	37.16	2.57
596	1266	4.767255	GCGGAGTGGCCTCAGTGG	62.767	72.222	3.32	0.00	39.64	4.00
633	1303	4.851214	AGGGAGGGAGAGAGGCGC	62.851	72.222	0.00	0.00	0.00	6.53
634	1304	2.520741	GAGGGAGGGAGAGAGGCG	60.521	72.222	0.00	0.00	0.00	5.52
635	1305	1.152546	GAGAGGGAGGGAGAGAGGC	60.153	68.421	0.00	0.00	0.00	4.70
640	1369	0.628522	CACAGAGAGAGGGAGGGAGA	59.371	60.000	0.00	0.00	0.00	3.71
648	1377	0.600557	AACAGCGTCACAGAGAGAGG	59.399	55.000	0.00	0.00	0.00	3.69
877	3438	6.155221	AGGTATTCAGTTGATCAGAAGCTACA	59.845	38.462	0.00	0.00	0.00	2.74
889	3450	0.623723	GGGGCCAGGTATTCAGTTGA	59.376	55.000	4.39	0.00	0.00	3.18
891	3452	0.331616	GTGGGGCCAGGTATTCAGTT	59.668	55.000	4.39	0.00	0.00	3.16
954	3516	1.610624	CCAGCTTGGTCAACATACCGT	60.611	52.381	0.00	0.00	42.91	4.83
955	3517	1.086696	CCAGCTTGGTCAACATACCG	58.913	55.000	0.00	0.00	42.91	4.02
1041	3627	7.614494	CCATTTCTCTCTCTCTCTTCTTTCTT	58.386	38.462	0.00	0.00	0.00	2.52
1048	3634	2.159114	GCGCCATTTCTCTCTCTCTCTT	60.159	50.000	0.00	0.00	0.00	2.85
1153	3739	4.829518	CAGATCGTCACGCGCGGA	62.830	66.667	35.22	24.51	41.07	5.54
1796	5234	3.006967	AGTGCTAACAACAGAACCGAGAT	59.993	43.478	0.00	0.00	0.00	2.75
1876	5317	4.940463	TCGACAAACAGCAAAGTAGTAGT	58.060	39.130	0.00	0.00	0.00	2.73
1877	5318	5.864474	AGATCGACAAACAGCAAAGTAGTAG	59.136	40.000	0.00	0.00	0.00	2.57
1878	5319	5.633601	CAGATCGACAAACAGCAAAGTAGTA	59.366	40.000	0.00	0.00	0.00	1.82
1957	5399	7.243604	TCATCATACATCATGCATGGTACTA	57.756	36.000	25.97	12.24	36.72	1.82
1958	5400	6.117975	TCATCATACATCATGCATGGTACT	57.882	37.500	25.97	10.40	36.72	2.73
1959	5401	6.997239	ATCATCATACATCATGCATGGTAC	57.003	37.500	25.97	0.00	36.72	3.34
1960	5402	6.757947	CGTATCATCATACATCATGCATGGTA	59.242	38.462	25.97	20.04	36.72	3.25
1961	5403	5.583457	CGTATCATCATACATCATGCATGGT	59.417	40.000	25.97	17.67	36.72	3.55
1962	5404	5.583457	ACGTATCATCATACATCATGCATGG	59.417	40.000	25.97	13.66	36.72	3.66
1963	5405	6.507456	CGACGTATCATCATACATCATGCATG	60.507	42.308	21.07	21.07	35.44	4.06
1964	5406	5.517770	CGACGTATCATCATACATCATGCAT	59.482	40.000	0.00	0.00	35.44	3.96
1965	5407	4.858692	CGACGTATCATCATACATCATGCA	59.141	41.667	0.00	0.00	35.44	3.96
1966	5408	5.095490	TCGACGTATCATCATACATCATGC	58.905	41.667	0.00	0.00	35.44	4.06
1983	7420	2.000215	TACGCAGGCATGATCGACGT	62.000	55.000	0.62	4.18	36.17	4.34
2012	7458	7.598869	TGTTGCAAGTTGTAACAAACACATTAA	59.401	29.630	29.77	8.99	46.94	1.40
2017	7463	7.275719	TGTCTGTTGCAAGTTGTAACAAACAC	61.276	38.462	30.22	26.08	43.04	3.32
2026	7549	3.631686	TGCTAATGTCTGTTGCAAGTTGT	59.368	39.130	0.00	0.00	0.00	3.32
2155	7684	4.070009	CAAGCCTTAAGTCTTTACCGGTT	58.930	43.478	15.04	0.00	0.00	4.44
2208	7739	9.434559	GTGGTATATTTTTCGTTCAAGATTAGC	57.565	33.333	0.00	0.00	0.00	3.09
2213	7744	9.672086	CTTTTGTGGTATATTTTTCGTTCAAGA	57.328	29.630	0.00	0.00	0.00	3.02
2214	7745	9.458374	ACTTTTGTGGTATATTTTTCGTTCAAG	57.542	29.630	0.00	0.00	0.00	3.02
2386	9156	5.470368	GGTTCAGAAATGAAGCCTAAAACC	58.530	41.667	8.59	0.00	39.56	3.27
2446	9680	0.594796	GCACTTGGGTTGTTTGCTCG	60.595	55.000	0.00	0.00	0.00	5.03
2521	9762	8.190784	AGAAATGGTAGTACATTATTTTGCTGC	58.809	33.333	2.06	0.00	40.01	5.25
2596	10832	2.441410	TCGAAATGTGCATTGGGCTAA	58.559	42.857	0.00	0.00	45.15	3.09
2604	10840	8.034215	TCCAATTTTAGATTTCGAAATGTGCAT	58.966	29.630	27.27	13.63	0.00	3.96
2732	10969	7.479352	TGATTCTCATGGCTTTTTAAATGGA	57.521	32.000	0.00	0.00	0.00	3.41
2816	11055	1.725641	TGACTGCCATAGCTTTGACG	58.274	50.000	5.65	0.00	40.80	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.