AutoCloner

Multiple sequence alignment - TraesCS2D01G380100

Loading Multiple Alignment...

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	TraesCS2D01G380100	chr2D	100.000	3356	0	0	1	3356	484791606	484788251	0.000000e+00	6198
1	TraesCS2D01G380100	chr6D	96.895	2158	64	2	190	2346	26643969	26641814	0.000000e+00	3611
2	TraesCS2D01G380100	chr6D	94.359	975	18	3	2382	3356	26637947	26637010	0.000000e+00	1461
3	TraesCS2D01G380100	chr6D	94.340	106	6	0	3	108	26644390	26644285	2.680000e-36	163
4	TraesCS2D01G380100	chr5B	87.005	2247	246	26	115	2346	74332638	74330423	0.000000e+00	2490
5	TraesCS2D01G380100	chr7A	84.918	2261	301	32	115	2347	142144437	142146685	0.000000e+00	2250
6	TraesCS2D01G380100	chr7A	85.009	2228	296	30	144	2347	140726672	140728885	0.000000e+00	2230
7	TraesCS2D01G380100	chr7A	84.567	2242	305	33	133	2347	140997464	140999691	0.000000e+00	2185
8	TraesCS2D01G380100	chr7A	84.211	2242	315	30	132	2347	141274805	141277033	0.000000e+00	2143
9	TraesCS2D01G380100	chr7A	84.548	2181	298	31	132	2286	141861501	141863668	0.000000e+00	2124
10	TraesCS2D01G380100	chr7A	84.228	2086	287	33	132	2188	141580525	141582597	0.000000e+00	1991
11	TraesCS2D01G380100	chr7A	87.419	771	71	13	2593	3356	141597889	141598640	0.000000e+00	863
12	TraesCS2D01G380100	chr7A	87.176	772	71	15	2593	3356	142151706	142152457	0.000000e+00	852
13	TraesCS2D01G380100	chr7A	86.770	771	75	14	2593	3356	141282054	141282804	0.000000e+00	833
14	TraesCS2D01G380100	chr7A	84.058	897	103	22	2463	3356	141004605	141005464	0.000000e+00	828
15	TraesCS2D01G380100	chr7A	86.518	764	77	13	2600	3356	141868728	141869472	0.000000e+00	817

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	TraesCS2D01G380100	chr2D	484788251	484791606	3355	True	6198	6198	100.000	1	3356	1	chr2D.!!$R1	3355
1	TraesCS2D01G380100	chr6D	26637010	26644390	7380	True	1745	3611	95.198	3	3356	3	chr6D.!!$R1	3353
2	TraesCS2D01G380100	chr5B	74330423	74332638	2215	True	2490	2490	87.005	115	2346	1	chr5B.!!$R1	2231
3	TraesCS2D01G380100	chr7A	142144437	142146685	2248	False	2250	2250	84.918	115	2347	1	chr7A.!!$F10	2232
4	TraesCS2D01G380100	chr7A	140726672	140728885	2213	False	2230	2230	85.009	144	2347	1	chr7A.!!$F1	2203
5	TraesCS2D01G380100	chr7A	140997464	140999691	2227	False	2185	2185	84.567	133	2347	1	chr7A.!!$F2	2214
6	TraesCS2D01G380100	chr7A	141274805	141277033	2228	False	2143	2143	84.211	132	2347	1	chr7A.!!$F4	2215
7	TraesCS2D01G380100	chr7A	141861501	141863668	2167	False	2124	2124	84.548	132	2286	1	chr7A.!!$F8	2154
8	TraesCS2D01G380100	chr7A	141580525	141582597	2072	False	1991	1991	84.228	132	2188	1	chr7A.!!$F6	2056
9	TraesCS2D01G380100	chr7A	141597889	141598640	751	False	863	863	87.419	2593	3356	1	chr7A.!!$F7	763
10	TraesCS2D01G380100	chr7A	142151706	142152457	751	False	852	852	87.176	2593	3356	1	chr7A.!!$F11	763
11	TraesCS2D01G380100	chr7A	141282054	141282804	750	False	833	833	86.770	2593	3356	1	chr7A.!!$F5	763
12	TraesCS2D01G380100	chr7A	141004605	141005464	859	False	828	828	84.058	2463	3356	1	chr7A.!!$F3	893
13	TraesCS2D01G380100	chr7A	141868728	141869472	744	False	817	817	86.518	2600	3356	1	chr7A.!!$F9	756

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
626	870	0.30289	GCGCCTTGAAGACATGATCG	59.697	55.0	0.0	0.0	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2624	6735	0.170561	CCAGAGCACTAGTTACGCGT	59.829	55.0	19.17	19.17	0.0	6.01	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
54	55	1.271488	ACGGAACAAAAAGGCCCGATA	60.271	47.619	0.00	0.00	42.49	2.92
55	56	1.400494	CGGAACAAAAAGGCCCGATAG	59.600	52.381	0.00	0.00	42.49	2.08
66	67	2.498885	AGGCCCGATAGAAAAAGTACGT	59.501	45.455	0.00	0.00	39.76	3.57
87	88	0.323816	TTTCTTGCACCACCACACCA	60.324	50.000	0.00	0.00	0.00	4.17
88	89	1.034838	TTCTTGCACCACCACACCAC	61.035	55.000	0.00	0.00	0.00	4.16
108	109	2.545106	ACCACACGAATAAACGTTGGTC	59.455	45.455	0.00	0.00	44.89	4.02
109	110	2.544686	CCACACGAATAAACGTTGGTCA	59.455	45.455	0.00	0.00	44.76	4.02
110	111	3.002451	CCACACGAATAAACGTTGGTCAA	59.998	43.478	0.00	0.00	44.76	3.18
111	112	4.208355	CACACGAATAAACGTTGGTCAAG	58.792	43.478	0.00	0.00	44.76	3.02
112	113	3.223157	CACGAATAAACGTTGGTCAAGC	58.777	45.455	0.00	0.00	44.76	4.01
113	114	2.224784	ACGAATAAACGTTGGTCAAGCC	59.775	45.455	0.00	0.00	44.14	4.35
125	126	1.312815	GTCAAGCCTGAACAGTGCTT	58.687	50.000	17.81	17.81	41.93	3.91
126	127	1.265365	GTCAAGCCTGAACAGTGCTTC	59.735	52.381	19.49	11.21	40.45	3.86
201	436	4.217550	GCAGAACAGTGGCTTTGGTTATTA	59.782	41.667	0.00	0.00	0.00	0.98
237	473	2.602676	CGGGGGTTGATGGGTGTCT	61.603	63.158	0.00	0.00	0.00	3.41
422	664	2.773993	ATAACGATTGGTGGGAACGT	57.226	45.000	0.00	0.00	38.81	3.99
623	867	1.741401	CCGCGCCTTGAAGACATGA	60.741	57.895	0.00	0.00	0.00	3.07
626	870	0.302890	GCGCCTTGAAGACATGATCG	59.697	55.000	0.00	0.00	0.00	3.69
852	1099	3.394836	GCTTCTGGAGGGAGCGGT	61.395	66.667	0.00	0.00	0.00	5.68
951	1199	2.939103	GCATACTGATGGAGCGTTCTTT	59.061	45.455	0.00	0.00	33.26	2.52
959	1207	2.912771	TGGAGCGTTCTTTGTTCTTGA	58.087	42.857	0.00	0.00	0.00	3.02
1272	1527	7.064371	GCGCTCAAGATAGATGATGATGTTTAT	59.936	37.037	0.00	0.00	0.00	1.40
1363	1618	3.643159	AAAGAAATGTTCCGCCTTCAC	57.357	42.857	0.00	0.00	0.00	3.18
1512	1767	1.045911	GGACCCAGGTTGGTTTTGCA	61.046	55.000	0.00	0.00	39.24	4.08
1755	2010	2.325583	TGTTTCCATCGTCCATAGGC	57.674	50.000	0.00	0.00	0.00	3.93
1832	2098	0.320771	AGGCATTGCGTTTCGACTCT	60.321	50.000	1.91	0.00	0.00	3.24
1976	2242	0.321671	ACGGTGTGATGAAGGTGAGG	59.678	55.000	0.00	0.00	0.00	3.86
2002	2268	3.630312	GGCCTCCATCGCAAGTTTAATTA	59.370	43.478	0.00	0.00	39.48	1.40
2084	2350	0.388907	CCAAAGCTTGCCATGGAACG	60.389	55.000	18.40	3.11	34.82	3.95
2217	2483	4.629200	GCCAAGGCTTTCATAGATAGATCG	59.371	45.833	3.29	0.00	38.26	3.69
2299	2565	2.471749	GCACTTAACGACGGAACAATCG	60.472	50.000	0.00	0.00	41.57	3.34
2470	6581	2.061509	ACACTGCCCTAAAACGGTTT	57.938	45.000	2.90	2.90	0.00	3.27
2582	6693	2.653234	AAGCTGGGATGATTAGGCTG	57.347	50.000	0.00	0.00	0.00	4.85
2624	6735	3.901570	ATTTAATATGGGAGGGCAGCA	57.098	42.857	0.00	0.00	0.00	4.41
2625	6736	2.656947	TTAATATGGGAGGGCAGCAC	57.343	50.000	0.00	0.00	0.00	4.40
2631	6742	4.752879	GGAGGGCAGCACGCGTAA	62.753	66.667	13.44	0.00	43.84	3.18
2632	6743	3.488090	GAGGGCAGCACGCGTAAC	61.488	66.667	13.44	7.51	43.84	2.50
2759	6875	1.839994	CTCCTAAGATGGAACCCTGCA	59.160	52.381	0.00	0.00	35.43	4.41
2770	6886	2.014010	AACCCTGCATGGTTGACAAT	57.986	45.000	23.67	0.24	46.76	2.71
2840	6956	0.800012	TCGCAAATCCTAAACGCACC	59.200	50.000	0.00	0.00	0.00	5.01
2847	6963	1.828979	TCCTAAACGCACCCAAATCC	58.171	50.000	0.00	0.00	0.00	3.01
2926	7043	0.328926	GGACAACCCAAATCCCGGTA	59.671	55.000	0.00	0.00	34.14	4.02
2948	7065	4.437682	TCCTTCCTGCGATTGGATTAAT	57.562	40.909	0.00	0.00	33.09	1.40
2949	7066	5.560722	TCCTTCCTGCGATTGGATTAATA	57.439	39.130	0.00	0.00	33.09	0.98
3059	7176	3.795688	TCTCCCATCTAATGCAATCCC	57.204	47.619	0.00	0.00	0.00	3.85
3061	7178	2.108776	CTCCCATCTAATGCAATCCCCA	59.891	50.000	0.00	0.00	0.00	4.96
3263	7380	3.634910	GGTTGGCAGGAAGAACTGTAAAA	59.365	43.478	0.00	0.00	40.59	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	2.897436	ACGTACTTTTTCTATCGGGCC	58.103	47.619	0.00	0.00	0.00	5.80
66	67	1.205893	GGTGTGGTGGTGCAAGAAAAA	59.794	47.619	0.00	0.00	0.00	1.94
87	88	2.545106	GACCAACGTTTATTCGTGTGGT	59.455	45.455	17.97	17.97	46.42	4.16
88	89	2.544686	TGACCAACGTTTATTCGTGTGG	59.455	45.455	0.00	0.00	43.38	4.17
108	109	0.236711	CGAAGCACTGTTCAGGCTTG	59.763	55.000	22.77	15.20	47.00	4.01
110	111	4.368391	CGAAGCACTGTTCAGGCT	57.632	55.556	4.82	7.23	40.14	4.58
237	473	1.063649	GCGAGTCGGACGAAGCATA	59.936	57.895	15.52	0.00	0.00	3.14
422	664	1.066908	CGCTCCTGCCAGTTTGAAAAA	59.933	47.619	0.00	0.00	35.36	1.94
512	754	0.242017	AGAATCCTTTGCAAGCACGC	59.758	50.000	0.00	0.00	0.00	5.34
887	1134	4.248859	CATTACATCGAGCAAGGGGATAG	58.751	47.826	0.00	0.00	0.00	2.08
982	1230	4.003648	GACATCTAACCTCCAACAACCAG	58.996	47.826	0.00	0.00	0.00	4.00
1363	1618	0.391661	ATCTGCGTTACCTGTGCTGG	60.392	55.000	0.00	0.00	0.00	4.85
1529	1784	4.618920	TTCTCCCTAGGACTGAAACAAC	57.381	45.455	11.48	0.00	0.00	3.32
1664	1919	4.785914	TCCCTTCCCTGTGTATTTCATGTA	59.214	41.667	0.00	0.00	0.00	2.29
1755	2010	7.190920	AGTCTGAACAAACGAAAATTAGAGG	57.809	36.000	0.00	0.00	0.00	3.69
1832	2098	0.313987	CAGCTGTACCAGTGTCGACA	59.686	55.000	15.76	15.76	33.43	4.35
1976	2242	1.817099	CTTGCGATGGAGGCCTGTC	60.817	63.158	12.00	4.42	0.00	3.51
2002	2268	2.866726	AAGGGCCGTGCGCAAAAAT	61.867	52.632	14.00	0.00	44.06	1.82
2084	2350	4.535526	TTTTGCTCCTAAGATTTTGGCC	57.464	40.909	0.00	0.00	0.00	5.36
2299	2565	1.987770	CATGTTTTCGTTCATGCAGGC	59.012	47.619	0.00	0.00	35.72	4.85
2347	2613	4.408821	CCTGCCCCGCTACAAGCA	62.409	66.667	0.00	0.00	42.58	3.91
2381	6492	3.496131	TTTTCTGATCCCGCGCGC	61.496	61.111	27.36	23.91	0.00	6.86
2382	6493	2.399611	GTTTTCTGATCCCGCGCG	59.600	61.111	25.67	25.67	0.00	6.86
2383	6494	1.376609	ATGGTTTTCTGATCCCGCGC	61.377	55.000	0.00	0.00	0.00	6.86
2384	6495	0.378257	CATGGTTTTCTGATCCCGCG	59.622	55.000	0.00	0.00	0.00	6.46
2385	6496	0.740737	CCATGGTTTTCTGATCCCGC	59.259	55.000	2.57	0.00	0.00	6.13
2386	6497	0.740737	GCCATGGTTTTCTGATCCCG	59.259	55.000	14.67	0.00	0.00	5.14
2387	6498	0.740737	CGCCATGGTTTTCTGATCCC	59.259	55.000	14.67	0.00	0.00	3.85
2582	6693	2.439156	AGAAGGGCCGAAGCATGC	60.439	61.111	10.51	10.51	42.56	4.06
2624	6735	0.170561	CCAGAGCACTAGTTACGCGT	59.829	55.000	19.17	19.17	0.00	6.01
2625	6736	0.525668	CCCAGAGCACTAGTTACGCG	60.526	60.000	3.53	3.53	0.00	6.01
2628	6739	0.179108	CGCCCCAGAGCACTAGTTAC	60.179	60.000	0.00	0.00	0.00	2.50
2629	6740	1.327690	CCGCCCCAGAGCACTAGTTA	61.328	60.000	0.00	0.00	0.00	2.24
2630	6741	2.660064	CCGCCCCAGAGCACTAGTT	61.660	63.158	0.00	0.00	0.00	2.24
2631	6742	3.077556	CCGCCCCAGAGCACTAGT	61.078	66.667	0.00	0.00	0.00	2.57
2632	6743	3.854669	CCCGCCCCAGAGCACTAG	61.855	72.222	0.00	0.00	0.00	2.57
2692	6808	3.057596	TCGTTGAAATGAAGGGCAACATC	60.058	43.478	0.00	0.00	40.32	3.06
2759	6875	4.766373	TGTACTGCAATCATTGTCAACCAT	59.234	37.500	0.00	0.00	0.00	3.55
2840	6956	1.068434	ACAGGTGCGTTTTGGATTTGG	59.932	47.619	0.00	0.00	0.00	3.28
2847	6963	3.426159	GGATATGTCACAGGTGCGTTTTG	60.426	47.826	0.00	0.00	0.00	2.44
2926	7043	4.437682	TTAATCCAATCGCAGGAAGGAT	57.562	40.909	0.00	0.00	40.71	3.24
3059	7176	1.068055	GCTCTTCAACAACTGGCATGG	60.068	52.381	0.00	0.00	0.00	3.66
3061	7178	2.283145	AGCTCTTCAACAACTGGCAT	57.717	45.000	0.00	0.00	0.00	4.40
3201	7318	3.111484	TGCCTGTACAACTGGGATATGA	58.889	45.455	3.14	0.00	37.64	2.15
3263	7380	6.321181	TGCTTACAACTCCATTTTCTTTGACT	59.679	34.615	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.