AutoCloner

Multiple sequence alignment - TraesCS3D01G508900

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	TraesCS3D01G508900	chr3D	100.000	2375	0	0	1	2375	594801584	594803958	0.000000e+00	4386.0
1	TraesCS3D01G508900	chr3A	93.531	1886	65	17	507	2369	725565414	725567265	0.000000e+00	2754.0
2	TraesCS3D01G508900	chr3A	93.425	1886	66	18	507	2369	725607745	725609595	0.000000e+00	2743.0
3	TraesCS3D01G508900	chr3A	96.299	1324	38	7	1054	2369	725524255	725525575	0.000000e+00	2163.0
4	TraesCS3D01G508900	chr3A	96.161	1016	31	5	1364	2375	725633940	725634951	0.000000e+00	1653.0
5	TraesCS3D01G508900	chr3A	86.461	938	91	23	901	1821	725470444	725471362	0.000000e+00	996.0
6	TraesCS3D01G508900	chr3A	91.651	527	26	7	507	1018	725523640	725524163	0.000000e+00	713.0
7	TraesCS3D01G508900	chr3A	87.327	505	43	10	14	507	725564684	725565178	2.060000e-155	558.0
8	TraesCS3D01G508900	chr3A	87.327	505	43	12	14	507	725607015	725607509	2.060000e-155	558.0
9	TraesCS3D01G508900	chr3A	86.733	505	46	10	14	507	725522910	725523404	2.080000e-150	542.0
10	TraesCS3D01G508900	chr3A	79.402	301	54	5	1113	1409	725553954	725554250	3.090000e-49	206.0
11	TraesCS3D01G508900	chr3A	79.402	301	54	5	1113	1409	725596503	725596799	3.090000e-49	206.0
12	TraesCS3D01G508900	chr3A	100.000	45	0	0	1473	1517	725495673	725495717	1.510000e-12	84.2
13	TraesCS3D01G508900	chr3B	94.559	1213	51	10	1164	2375	798286634	798287832	0.000000e+00	1860.0
14	TraesCS3D01G508900	chr3B	87.540	939	90	21	905	1821	798236417	798237350	0.000000e+00	1061.0
15	TraesCS3D01G508900	chr3B	88.152	422	23	8	489	888	798286050	798286466	5.940000e-131	477.0
16	TraesCS3D01G508900	chr3B	84.848	396	47	9	14	404	798282881	798283268	1.030000e-103	387.0
17	TraesCS3D01G508900	chr3B	82.328	232	38	1	1113	1344	798229956	798230184	5.180000e-47	198.0
18	TraesCS3D01G508900	chr3B	93.827	81	4	1	411	491	798283897	798283976	1.150000e-23	121.0
19	TraesCS3D01G508900	chr2D	83.885	453	59	10	1829	2280	112537950	112537511	1.020000e-113	420.0
20	TraesCS3D01G508900	chr7A	81.856	485	66	15	1813	2282	271628388	271628865	2.860000e-104	388.0
21	TraesCS3D01G508900	chr1B	82.183	449	60	17	1838	2273	458149877	458150318	3.730000e-98	368.0
22	TraesCS3D01G508900	chr5D	80.294	477	77	15	1815	2282	441939504	441939972	6.280000e-91	344.0

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	TraesCS3D01G508900	chr3D	594801584	594803958	2374	False	4386.000000	4386	100.0000	1	2375	1	chr3D.!!$F1	2374
1	TraesCS3D01G508900	chr3A	725564684	725567265	2581	False	1656.000000	2754	90.4290	14	2369	2	chr3A.!!$F7	2355
2	TraesCS3D01G508900	chr3A	725633940	725634951	1011	False	1653.000000	1653	96.1610	1364	2375	1	chr3A.!!$F5	1011
3	TraesCS3D01G508900	chr3A	725607015	725609595	2580	False	1650.500000	2743	90.3760	14	2369	2	chr3A.!!$F8	2355
4	TraesCS3D01G508900	chr3A	725522910	725525575	2665	False	1139.333333	2163	91.5610	14	2369	3	chr3A.!!$F6	2355
5	TraesCS3D01G508900	chr3A	725470444	725471362	918	False	996.000000	996	86.4610	901	1821	1	chr3A.!!$F1	920
6	TraesCS3D01G508900	chr3B	798236417	798237350	933	False	1061.000000	1061	87.5400	905	1821	1	chr3B.!!$F2	916
7	TraesCS3D01G508900	chr3B	798282881	798287832	4951	False	711.250000	1860	90.3465	14	2375	4	chr3B.!!$F3	2361

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
124	125	0.169451	GGTGTTAATTTGGTCGCCCG	59.831	55.0	0.0	0.0	0.0	6.13	F
823	3791	0.331954	AGGAGAGAGAGGCCGTTGTA	59.668	55.0	0.0	0.0	0.0	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1047	4125	1.206849	GCTAACTCTGCTCTTCAGCCT	59.793	52.381	0.0	0.0	46.26	4.58	R
2036	5136	1.409064	CCGTTCTACTATCTGCCAGCA	59.591	52.381	0.0	0.0	0.00	4.41	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
36	37	1.966451	GGTGTTGCCCCGACTTCAG	60.966	63.158	0.00	0.00	0.00	3.02
111	112	5.880887	TGTGTTGAAGTATTGTGTGGTGTTA	59.119	36.000	0.00	0.00	0.00	2.41
124	125	0.169451	GGTGTTAATTTGGTCGCCCG	59.831	55.000	0.00	0.00	0.00	6.13
128	129	0.523966	TTAATTTGGTCGCCCGCTTG	59.476	50.000	0.00	0.00	0.00	4.01
129	130	0.606944	TAATTTGGTCGCCCGCTTGT	60.607	50.000	0.00	0.00	0.00	3.16
130	131	2.141122	AATTTGGTCGCCCGCTTGTG	62.141	55.000	0.00	0.00	0.00	3.33
141	142	3.660111	GCTTGTGGTGGTCGTGGC	61.660	66.667	0.00	0.00	0.00	5.01
143	144	4.920112	TTGTGGTGGTCGTGGCCG	62.920	66.667	0.00	0.00	0.00	6.13
163	164	3.377439	CGTGTCTTGTGTGCAGTTAGTA	58.623	45.455	0.00	0.00	0.00	1.82
200	201	2.525877	GGGCCGGGTCCATAGCTA	60.526	66.667	14.16	0.00	0.00	3.32
207	208	1.367840	GGTCCATAGCTAGCCGTGG	59.632	63.158	23.48	23.48	0.00	4.94
255	256	6.407202	TGAGTTTCCCTCTATTGTTCTAAGC	58.593	40.000	0.00	0.00	41.11	3.09
262	263	5.168569	CCTCTATTGTTCTAAGCGTGACAA	58.831	41.667	0.00	0.00	0.00	3.18
265	277	7.060600	TCTATTGTTCTAAGCGTGACAATTG	57.939	36.000	3.24	3.24	0.00	2.32
268	280	6.606234	TTGTTCTAAGCGTGACAATTGTTA	57.394	33.333	13.36	5.62	0.00	2.41
273	285	7.290857	TCTAAGCGTGACAATTGTTATTCTC	57.709	36.000	13.36	0.00	0.00	2.87
275	287	3.370978	AGCGTGACAATTGTTATTCTCGG	59.629	43.478	13.36	0.00	0.00	4.63
372	384	5.782845	AGATATATTCCCAAGTCTCCTCCAC	59.217	44.000	0.00	0.00	0.00	4.02
533	3480	5.065218	CACAAAAATCCCATCTTCTACCGAG	59.935	44.000	0.00	0.00	0.00	4.63
535	3482	5.693769	AAAATCCCATCTTCTACCGAGAA	57.306	39.130	0.00	0.00	39.47	2.87
647	3594	6.640518	TCGCCATTATCCTATTCTATCAACC	58.359	40.000	0.00	0.00	0.00	3.77
699	3667	3.367498	GCACAGACCCTACTTACTGACAG	60.367	52.174	0.00	0.00	34.88	3.51
823	3791	0.331954	AGGAGAGAGAGGCCGTTGTA	59.668	55.000	0.00	0.00	0.00	2.41
875	3843	0.371645	GCTCAAGCTCGAATGGAACG	59.628	55.000	0.00	0.00	38.21	3.95
883	3851	6.929049	TCAAGCTCGAATGGAACGAAATATAT	59.071	34.615	0.00	0.00	39.23	0.86
884	3852	8.085909	TCAAGCTCGAATGGAACGAAATATATA	58.914	33.333	0.00	0.00	39.23	0.86
885	3853	7.813852	AGCTCGAATGGAACGAAATATATAC	57.186	36.000	0.00	0.00	39.23	1.47
1044	4122	3.793465	GCAAAGAGCAGCGAAGTTTTTCT	60.793	43.478	0.00	0.00	44.79	2.52
1045	4123	3.615849	AAGAGCAGCGAAGTTTTTCTG	57.384	42.857	0.00	0.00	0.00	3.02
1047	4125	3.728845	AGAGCAGCGAAGTTTTTCTGTA	58.271	40.909	0.00	0.00	0.00	2.74
1048	4126	3.743396	AGAGCAGCGAAGTTTTTCTGTAG	59.257	43.478	0.00	0.00	0.00	2.74
1171	4250	0.969894	CCAAGAACACGTCCTCCTCT	59.030	55.000	0.00	0.00	0.00	3.69
1183	4265	0.633921	CCTCCTCTTCCTCCTCCTCA	59.366	60.000	0.00	0.00	0.00	3.86
1197	4291	4.575885	TCCTCCTCATCGTTTGTTAAAGG	58.424	43.478	0.00	0.00	0.00	3.11
1405	4501	3.067742	TGTGTTCTCCTATTAGCCTACGC	59.932	47.826	0.00	0.00	0.00	4.42
1727	4825	7.678218	GCAAAAGCAAACAAAATGTTACATCCA	60.678	33.333	0.00	0.00	40.14	3.41
1781	4880	6.936900	ACATTATACTTGAAGAAGTGCACTGT	59.063	34.615	22.49	14.29	42.66	3.55
2047	5147	1.450134	CAACCGCTGCTGGCAGATA	60.450	57.895	24.40	5.11	46.30	1.98
2052	5152	0.670706	CGCTGCTGGCAGATAGTAGA	59.329	55.000	24.40	0.00	46.30	2.59
2087	5187	1.545582	ACCGATTTGGATGGCAAACTG	59.454	47.619	0.00	0.00	42.00	3.16
2258	5362	0.109723	TTTGATGTATAGGCCGGGGC	59.890	55.000	13.58	13.58	41.06	5.80

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	5.393027	GGCAACACCATCTTAATTTCGATGT	60.393	40.000	12.74	0.00	38.86	3.06
3	4	5.036737	GGCAACACCATCTTAATTTCGATG	58.963	41.667	8.79	8.79	38.86	3.84
5	6	3.442273	GGGCAACACCATCTTAATTTCGA	59.558	43.478	0.00	0.00	42.05	3.71
6	7	3.428862	GGGGCAACACCATCTTAATTTCG	60.429	47.826	0.00	0.00	42.05	3.46
7	8	3.428862	CGGGGCAACACCATCTTAATTTC	60.429	47.826	0.00	0.00	42.05	2.17
8	9	2.495669	CGGGGCAACACCATCTTAATTT	59.504	45.455	0.00	0.00	42.05	1.82
9	10	2.099405	CGGGGCAACACCATCTTAATT	58.901	47.619	0.00	0.00	42.05	1.40
10	11	1.283613	TCGGGGCAACACCATCTTAAT	59.716	47.619	0.00	0.00	42.05	1.40
11	12	0.693622	TCGGGGCAACACCATCTTAA	59.306	50.000	0.00	0.00	42.05	1.85
12	13	0.035820	GTCGGGGCAACACCATCTTA	60.036	55.000	0.00	0.00	42.05	2.10
15	16	1.303317	AAGTCGGGGCAACACCATC	60.303	57.895	0.00	0.00	42.05	3.51
22	23	4.344865	GGGCTGAAGTCGGGGCAA	62.345	66.667	0.00	0.00	0.00	4.52
36	37	2.514824	GAAGTGGCGAGATGGGGC	60.515	66.667	0.00	0.00	0.00	5.80
124	125	3.660111	GCCACGACCACCACAAGC	61.660	66.667	0.00	0.00	0.00	4.01
141	142	1.526887	CTAACTGCACACAAGACACGG	59.473	52.381	0.00	0.00	0.00	4.94
143	144	4.377431	GCATACTAACTGCACACAAGACAC	60.377	45.833	0.00	0.00	39.46	3.67
163	164	0.176680	GTGATCTCCCACGAGTGCAT	59.823	55.000	0.00	0.00	37.40	3.96
171	172	4.530857	CGGCCCGTGATCTCCCAC	62.531	72.222	0.00	0.00	0.00	4.61
187	188	2.201022	ACGGCTAGCTATGGACCCG	61.201	63.158	15.72	9.38	41.31	5.28
189	190	1.367840	CCACGGCTAGCTATGGACC	59.632	63.158	25.16	3.73	33.80	4.46
193	194	2.037251	ACCAATACCACGGCTAGCTATG	59.963	50.000	15.72	12.76	0.00	2.23
194	195	2.326428	ACCAATACCACGGCTAGCTAT	58.674	47.619	15.72	0.84	0.00	2.97
200	201	1.078708	CCGAACCAATACCACGGCT	60.079	57.895	0.00	0.00	37.32	5.52
207	208	3.047093	GTTGTTGTTGCCGAACCAATAC	58.953	45.455	0.00	0.00	0.00	1.89
255	256	3.124466	TGCCGAGAATAACAATTGTCACG	59.876	43.478	12.39	9.41	0.00	4.35
262	263	2.287915	GCACGATGCCGAGAATAACAAT	59.712	45.455	0.00	0.00	37.42	2.71
265	277	1.004927	GTGCACGATGCCGAGAATAAC	60.005	52.381	0.00	0.00	44.23	1.89
268	280	1.815421	GGTGCACGATGCCGAGAAT	60.815	57.895	11.45	0.00	44.23	2.40
275	287	3.188786	GTCGGAGGTGCACGATGC	61.189	66.667	11.45	6.44	45.29	3.91
284	296	4.052229	CGCTTGGTCGTCGGAGGT	62.052	66.667	0.00	0.00	0.00	3.85
311	323	5.690997	AAAAATCCTTCCGAACTGAGTTC	57.309	39.130	15.12	15.12	38.97	3.01
332	344	9.162764	GGAATATATCTAGCTCCGCAATAAAAA	57.837	33.333	0.00	0.00	0.00	1.94
357	369	1.879575	TATGGTGGAGGAGACTTGGG	58.120	55.000	0.00	0.00	44.43	4.12
359	371	6.425210	TCATAATATGGTGGAGGAGACTTG	57.575	41.667	0.00	0.00	44.43	3.16
372	384	8.066612	AGTTGTCCCAACTTTTCATAATATGG	57.933	34.615	3.85	0.00	0.00	2.74
427	1061	7.872113	AGGATAGTTTGAATCATTTGAGGAC	57.128	36.000	0.00	0.00	0.00	3.85
528	3475	6.238648	ACTTCCATTTGTTTCTATTCTCGGT	58.761	36.000	0.00	0.00	0.00	4.69
533	3480	9.827411	GTTACAGACTTCCATTTGTTTCTATTC	57.173	33.333	0.00	0.00	0.00	1.75
535	3482	7.942341	TGGTTACAGACTTCCATTTGTTTCTAT	59.058	33.333	0.00	0.00	0.00	1.98
647	3594	4.925646	GCTTGTTGAATTTTCCTTAGCCTG	59.074	41.667	0.00	0.00	0.00	4.85
784	3752	2.707529	TTCATCGGCAGTGACGCACA	62.708	55.000	15.27	0.00	36.74	4.57
1034	4112	5.334491	GCTCTTCAGCCTACAGAAAAACTTC	60.334	44.000	0.00	0.00	40.14	3.01
1044	4122	1.930251	ACTCTGCTCTTCAGCCTACA	58.070	50.000	0.00	0.00	46.26	2.74
1045	4123	3.736740	GCTAACTCTGCTCTTCAGCCTAC	60.737	52.174	0.00	0.00	46.26	3.18
1047	4125	1.206849	GCTAACTCTGCTCTTCAGCCT	59.793	52.381	0.00	0.00	46.26	4.58
1048	4126	1.206849	AGCTAACTCTGCTCTTCAGCC	59.793	52.381	0.00	0.00	46.26	4.85
1171	4250	2.257207	ACAAACGATGAGGAGGAGGAA	58.743	47.619	0.00	0.00	0.00	3.36
1183	4265	3.251487	CACCGGAACCTTTAACAAACGAT	59.749	43.478	9.46	0.00	0.00	3.73
1420	4516	2.812591	GACAATGGAGCTATGCATCCTG	59.187	50.000	0.19	0.00	36.30	3.86
1781	4880	3.188159	AGCAGAACTGTTCGGTTGTAA	57.812	42.857	19.22	0.00	34.02	2.41
2036	5136	1.409064	CCGTTCTACTATCTGCCAGCA	59.591	52.381	0.00	0.00	0.00	4.41
2042	5142	9.400638	GTTGAAGATAATCCGTTCTACTATCTG	57.599	37.037	0.00	0.00	31.33	2.90
2047	5147	5.359009	TCGGTTGAAGATAATCCGTTCTACT	59.641	40.000	0.00	0.00	41.58	2.57
2052	5152	5.065988	CCAAATCGGTTGAAGATAATCCGTT	59.934	40.000	0.00	0.00	39.87	4.44
2087	5187	9.209175	CAATGACTAAACACCTAGCCTATTATC	57.791	37.037	0.00	0.00	0.00	1.75
2307	5411	2.702592	ATCGTCGGCCATTCCTTTTA	57.297	45.000	2.24	0.00	0.00	1.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.