AutoCloner

Multiple sequence alignment - TraesCS1A01G254300

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	TraesCS1A01G254300	chr1A	100.000	2276	0	0	1	2276	445913307	445915582	0.000000e+00	4204
1	TraesCS1A01G254300	chr3D	93.282	1295	86	1	1	1294	127221493	127220199	0.000000e+00	1908
2	TraesCS1A01G254300	chr4A	91.596	1297	106	2	1	1295	285950328	285949033	0.000000e+00	1788
3	TraesCS1A01G254300	chr4A	91.912	952	61	6	362	1311	2782215	2781278	0.000000e+00	1317
4	TraesCS1A01G254300	chr2B	89.895	1049	100	1	1	1043	548636147	548635099	0.000000e+00	1345
5	TraesCS1A01G254300	chr2B	91.005	856	77	0	1	856	65438410	65437555	0.000000e+00	1155
6	TraesCS1A01G254300	chr2B	89.953	846	85	0	1	846	442324195	442323350	0.000000e+00	1092
7	TraesCS1A01G254300	chrUn	88.557	769	86	2	1	768	335288478	335289245	0.000000e+00	931
8	TraesCS1A01G254300	chrUn	88.296	769	88	2	1	768	335285774	335286541	0.000000e+00	920
9	TraesCS1A01G254300	chr5B	88.296	769	88	2	1	768	688966156	688966923	0.000000e+00	920
10	TraesCS1A01G254300	chr5B	76.817	1087	234	18	232	1311	73390387	73389312	1.510000e-166	595
11	TraesCS1A01G254300	chr1B	87.011	793	50	26	1309	2055	464484472	464483687	0.000000e+00	845
12	TraesCS1A01G254300	chr1B	98.958	96	1	0	2181	2276	464483554	464483459	3.010000e-39	172
13	TraesCS1A01G254300	chr1D	76.802	1207	263	17	85	1282	375358698	375359896	0.000000e+00	662
14	TraesCS1A01G254300	chr1D	76.395	1165	269	6	121	1282	416785819	416786980	6.900000e-175	623
15	TraesCS1A01G254300	chr1D	97.531	324	8	0	1733	2056	345712570	345712893	2.550000e-154	555
16	TraesCS1A01G254300	chr1D	88.517	418	17	21	1309	1700	345711871	345712283	5.690000e-131	477
17	TraesCS1A01G254300	chr1D	94.043	235	5	2	2051	2276	345712919	345713153	4.650000e-92	348
18	TraesCS1A01G254300	chr6B	75.951	1314	298	17	4	1309	563088165	563086862	0.000000e+00	660
19	TraesCS1A01G254300	chr6B	89.568	278	29	0	1743	2020	223657721	223657444	1.000000e-93	353
20	TraesCS1A01G254300	chr6B	77.577	388	81	6	923	1309	75272749	75272367	1.760000e-56	230
21	TraesCS1A01G254300	chr4D	87.898	157	19	0	1137	1293	471213319	471213163	3.860000e-43	185

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	TraesCS1A01G254300	chr1A	445913307	445915582	2275	False	4204.0	4204	100.000000	1	2276	1	chr1A.!!$F1	2275
1	TraesCS1A01G254300	chr3D	127220199	127221493	1294	True	1908.0	1908	93.282000	1	1294	1	chr3D.!!$R1	1293
2	TraesCS1A01G254300	chr4A	285949033	285950328	1295	True	1788.0	1788	91.596000	1	1295	1	chr4A.!!$R2	1294
3	TraesCS1A01G254300	chr4A	2781278	2782215	937	True	1317.0	1317	91.912000	362	1311	1	chr4A.!!$R1	949
4	TraesCS1A01G254300	chr2B	548635099	548636147	1048	True	1345.0	1345	89.895000	1	1043	1	chr2B.!!$R3	1042
5	TraesCS1A01G254300	chr2B	65437555	65438410	855	True	1155.0	1155	91.005000	1	856	1	chr2B.!!$R1	855
6	TraesCS1A01G254300	chr2B	442323350	442324195	845	True	1092.0	1092	89.953000	1	846	1	chr2B.!!$R2	845
7	TraesCS1A01G254300	chrUn	335285774	335289245	3471	False	925.5	931	88.426500	1	768	2	chrUn.!!$F1	767
8	TraesCS1A01G254300	chr5B	688966156	688966923	767	False	920.0	920	88.296000	1	768	1	chr5B.!!$F1	767
9	TraesCS1A01G254300	chr5B	73389312	73390387	1075	True	595.0	595	76.817000	232	1311	1	chr5B.!!$R1	1079
10	TraesCS1A01G254300	chr1B	464483459	464484472	1013	True	508.5	845	92.984500	1309	2276	2	chr1B.!!$R1	967
11	TraesCS1A01G254300	chr1D	375358698	375359896	1198	False	662.0	662	76.802000	85	1282	1	chr1D.!!$F1	1197
12	TraesCS1A01G254300	chr1D	416785819	416786980	1161	False	623.0	623	76.395000	121	1282	1	chr1D.!!$F2	1161
13	TraesCS1A01G254300	chr1D	345711871	345713153	1282	False	460.0	555	93.363667	1309	2276	3	chr1D.!!$F3	967
14	TraesCS1A01G254300	chr6B	563086862	563088165	1303	True	660.0	660	75.951000	4	1309	1	chr6B.!!$R3	1305

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
372	3077	0.105408	GGTACGTGTGTTCTGGTGGT	59.895	55.0	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1683	4433	0.241481	AACTCTGTCTTCCTCGTCGC	59.759	55.0	0.0	0.0	0.0	5.19	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
99	2804	7.276658	TGATACTAATAATTGGACTTGGCGAA	58.723	34.615	0.00	0.00	0.00	4.70
306	3011	4.561938	CGGTTACCAATACCTCACAGACAA	60.562	45.833	1.13	0.00	33.35	3.18
372	3077	0.105408	GGTACGTGTGTTCTGGTGGT	59.895	55.000	0.00	0.00	0.00	4.16
462	3167	1.951602	GCAATGTCTGCCATGCTATGA	59.048	47.619	0.00	0.00	46.13	2.15
740	3445	1.628846	GAGGACCTGGCCTTGTTAGAA	59.371	52.381	3.32	0.00	38.73	2.10
930	3642	2.039746	TGTTGGAGTGACGGATCCATTT	59.960	45.455	13.41	0.00	44.87	2.32
1076	3788	2.489938	TCTGTGATGGCACCTTTACC	57.510	50.000	0.00	0.00	44.51	2.85
1113	3825	8.462016	GGAGAGCTTGCTTTATCTTTTGATTTA	58.538	33.333	0.00	0.00	40.19	1.40
1143	3855	2.899900	TCAATATGTATCCAGAGCGGCT	59.100	45.455	0.00	0.00	33.14	5.52
1199	3911	1.215382	CGCTGATGGTCACCGAGAA	59.785	57.895	0.00	0.00	27.45	2.87
1206	3918	0.323629	TGGTCACCGAGAATTGGACC	59.676	55.000	0.00	0.00	45.05	4.46
1225	3937	1.455248	CGACTCGAGACCTTCCTTCT	58.545	55.000	21.68	0.00	0.00	2.85
1252	3964	4.883585	TCACCAGTTTATTGGCTGATGATC	59.116	41.667	0.00	0.00	42.18	2.92
1253	3965	4.885907	CACCAGTTTATTGGCTGATGATCT	59.114	41.667	0.00	0.00	42.18	2.75
1257	3969	6.994496	CCAGTTTATTGGCTGATGATCTAAGA	59.006	38.462	0.00	0.00	34.87	2.10
1295	4007	1.986882	AAGCTCCCAGGTTTGAACAG	58.013	50.000	0.00	0.00	30.79	3.16
1296	4008	1.140312	AGCTCCCAGGTTTGAACAGA	58.860	50.000	0.00	0.00	0.00	3.41
1297	4009	1.202818	AGCTCCCAGGTTTGAACAGAC	60.203	52.381	0.00	0.00	0.00	3.51
1298	4010	1.476833	GCTCCCAGGTTTGAACAGACA	60.477	52.381	0.00	0.00	0.00	3.41
1301	4013	1.676006	CCCAGGTTTGAACAGACACAC	59.324	52.381	0.00	0.00	0.00	3.82
1359	4077	3.195661	CCGTCCAGATTAAAGTACAGCC	58.804	50.000	0.00	0.00	0.00	4.85
1363	4081	3.589735	TCCAGATTAAAGTACAGCCCCAA	59.410	43.478	0.00	0.00	0.00	4.12
1451	4169	1.301479	CGGCGAGCCTTATTACCCC	60.301	63.158	12.70	0.00	0.00	4.95
1493	4223	4.488136	CCGCCCTGGCTGCACATA	62.488	66.667	6.60	0.00	39.32	2.29
1494	4224	3.204827	CGCCCTGGCTGCACATAC	61.205	66.667	6.60	0.00	39.32	2.39
1495	4225	2.045045	GCCCTGGCTGCACATACA	60.045	61.111	0.50	0.00	38.26	2.29
1496	4226	1.454479	GCCCTGGCTGCACATACAT	60.454	57.895	0.50	0.00	38.26	2.29
1505	4236	0.389166	TGCACATACATCACGCACGA	60.389	50.000	0.00	0.00	0.00	4.35
1507	4238	1.908065	CACATACATCACGCACGAGA	58.092	50.000	0.00	0.00	0.00	4.04
1617	4365	2.441532	TCCCGTCCCGTGATCCTC	60.442	66.667	0.00	0.00	0.00	3.71
1644	4392	4.179599	GGCTAGCCTCCCTCCCCT	62.180	72.222	27.17	0.00	0.00	4.79
1660	4410	4.403734	CTCCCCTCTCCTAGATAACACTC	58.596	52.174	0.00	0.00	0.00	3.51
1694	4444	4.856607	GGCGAGGCGACGAGGAAG	62.857	72.222	0.00	0.00	35.09	3.46
1700	4450	1.137825	GGCGACGAGGAAGACAGAG	59.862	63.158	0.00	0.00	0.00	3.35
1701	4451	1.587933	GGCGACGAGGAAGACAGAGT	61.588	60.000	0.00	0.00	0.00	3.24
1702	4452	0.241481	GCGACGAGGAAGACAGAGTT	59.759	55.000	0.00	0.00	0.00	3.01
1706	4456	1.819903	ACGAGGAAGACAGAGTTAGGC	59.180	52.381	0.00	0.00	0.00	3.93
1707	4457	1.202200	CGAGGAAGACAGAGTTAGGCG	60.202	57.143	0.00	0.00	0.00	5.52
1710	4460	1.135333	GGAAGACAGAGTTAGGCGGAG	59.865	57.143	0.00	0.00	0.00	4.63
1711	4461	1.135333	GAAGACAGAGTTAGGCGGAGG	59.865	57.143	0.00	0.00	0.00	4.30
1712	4462	0.039911	AGACAGAGTTAGGCGGAGGT	59.960	55.000	0.00	0.00	0.00	3.85
1713	4463	0.896226	GACAGAGTTAGGCGGAGGTT	59.104	55.000	0.00	0.00	0.00	3.50
1714	4464	0.896226	ACAGAGTTAGGCGGAGGTTC	59.104	55.000	0.00	0.00	0.00	3.62
1716	4466	1.141234	GAGTTAGGCGGAGGTTCGG	59.859	63.158	0.00	0.00	0.00	4.30
1746	4750	0.524392	GAGCAGTGATGTCGGACGAG	60.524	60.000	3.34	0.00	0.00	4.18
2037	5041	1.801765	GCCGAGGACGACAAGGTAATC	60.802	57.143	0.00	0.00	42.66	1.75
2087	5131	2.174349	CGGCTTTCGCTGACAAGC	59.826	61.111	12.31	12.31	45.62	4.01
2167	5220	0.167470	CAGTGCTCCAGTGCGAATTG	59.833	55.000	0.00	0.00	35.36	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	2.283173	GTTGGGGCAAGGGTGGAG	60.283	66.667	0.00	0.00	0.00	3.86
81	2786	3.023832	CCCTTCGCCAAGTCCAATTATT	58.976	45.455	0.00	0.00	0.00	1.40
99	2804	1.404843	GTGTCTCGGATTAGCTCCCT	58.595	55.000	0.00	0.00	41.49	4.20
306	3011	2.839486	TTCTTCCACATCTGCTCGTT	57.161	45.000	0.00	0.00	0.00	3.85
462	3167	4.275810	AGTGCATGCATTAAGTCCTCATT	58.724	39.130	25.64	0.00	0.00	2.57
552	3257	1.486310	CCAGGTACTAGGATGCAAGCA	59.514	52.381	0.00	0.00	36.02	3.91
740	3445	2.042639	GCATGGGCCTGTGGGATT	60.043	61.111	4.53	0.00	33.58	3.01
930	3642	1.985159	AGTGCCAAGGTCTCACCAATA	59.015	47.619	0.00	0.00	41.95	1.90
1032	3744	5.461032	AACTATTGTGGCGATTTTTCCAA	57.539	34.783	0.00	0.00	33.57	3.53
1076	3788	3.195396	AGCAAGCTCTCCAACTTCTAGAG	59.805	47.826	0.00	0.00	39.81	2.43
1176	3888	1.965930	GGTGACCATCAGCGTGCAA	60.966	57.895	0.00	0.00	35.04	4.08
1199	3911	0.323542	AGGTCTCGAGTCGGTCCAAT	60.324	55.000	13.54	0.00	0.00	3.16
1206	3918	1.455248	AGAAGGAAGGTCTCGAGTCG	58.545	55.000	13.13	6.09	0.00	4.18
1225	3937	2.557924	CAGCCAATAAACTGGTGAGCAA	59.442	45.455	0.00	0.00	38.86	3.91
1253	3965	9.659830	GCTTTTATTCAACGAAAGAACTTCTTA	57.340	29.630	4.41	0.00	35.27	2.10
1257	3969	7.139392	GGAGCTTTTATTCAACGAAAGAACTT	58.861	34.615	0.00	0.00	33.35	2.66
1352	4070	1.750778	CATGGATTGTTGGGGCTGTAC	59.249	52.381	0.00	0.00	0.00	2.90
1359	4077	1.512230	CGGTGCATGGATTGTTGGG	59.488	57.895	0.00	0.00	0.00	4.12
1363	4081	3.133464	CGCCGGTGCATGGATTGT	61.133	61.111	11.80	0.00	37.32	2.71
1493	4223	1.154207	CTCGTCTCGTGCGTGATGT	60.154	57.895	13.22	0.00	0.00	3.06
1494	4224	0.859374	CTCTCGTCTCGTGCGTGATG	60.859	60.000	8.90	8.90	32.67	3.07
1495	4225	1.425825	CTCTCGTCTCGTGCGTGAT	59.574	57.895	0.00	0.00	32.67	3.06
1496	4226	2.861006	CTCTCGTCTCGTGCGTGA	59.139	61.111	0.00	0.00	0.00	4.35
1505	4236	2.820479	CCCTCGTCGCTCTCGTCT	60.820	66.667	0.00	0.00	36.96	4.18
1507	4238	2.820479	CTCCCTCGTCGCTCTCGT	60.820	66.667	0.00	0.00	36.96	4.18
1568	4316	2.920076	TTTCTGTGGTGGTGGTGGCC	62.920	60.000	0.00	0.00	0.00	5.36
1642	4390	3.892588	GTGGGAGTGTTATCTAGGAGAGG	59.107	52.174	0.00	0.00	0.00	3.69
1644	4392	3.271225	TGGTGGGAGTGTTATCTAGGAGA	59.729	47.826	0.00	0.00	0.00	3.71
1677	4427	4.856607	CTTCCTCGTCGCCTCGCC	62.857	72.222	0.00	0.00	0.00	5.54
1678	4428	3.812019	TCTTCCTCGTCGCCTCGC	61.812	66.667	0.00	0.00	0.00	5.03
1683	4433	0.241481	AACTCTGTCTTCCTCGTCGC	59.759	55.000	0.00	0.00	0.00	5.19
1684	4434	2.096174	CCTAACTCTGTCTTCCTCGTCG	59.904	54.545	0.00	0.00	0.00	5.12
1694	4444	0.896226	AACCTCCGCCTAACTCTGTC	59.104	55.000	0.00	0.00	0.00	3.51
1700	4450	2.510918	GCCGAACCTCCGCCTAAC	60.511	66.667	0.00	0.00	0.00	2.34
1701	4451	2.998480	TGCCGAACCTCCGCCTAA	60.998	61.111	0.00	0.00	0.00	2.69
1702	4452	3.458163	CTGCCGAACCTCCGCCTA	61.458	66.667	0.00	0.00	0.00	3.93
1711	4461	4.373116	TCCTCCGTGCTGCCGAAC	62.373	66.667	11.24	0.00	0.00	3.95
1712	4462	4.069232	CTCCTCCGTGCTGCCGAA	62.069	66.667	11.24	0.00	0.00	4.30
1716	4466	4.385405	ACTGCTCCTCCGTGCTGC	62.385	66.667	0.00	0.00	32.50	5.25
1717	4467	2.236223	ATCACTGCTCCTCCGTGCTG	62.236	60.000	0.00	0.00	34.65	4.41
1718	4468	1.986757	ATCACTGCTCCTCCGTGCT	60.987	57.895	0.00	0.00	0.00	4.40
1719	4469	1.812922	CATCACTGCTCCTCCGTGC	60.813	63.158	0.00	0.00	0.00	5.34
1731	4494	2.052690	CCCCTCGTCCGACATCACT	61.053	63.158	0.00	0.00	0.00	3.41
2037	5041	4.368808	CGCCGCGGACAAACTGTG	62.369	66.667	33.48	0.68	35.38	3.66
2087	5131	1.856539	ATGGCCTGGACCACTTGAGG	61.857	60.000	3.32	0.00	44.17	3.86
2088	5132	0.393537	GATGGCCTGGACCACTTGAG	60.394	60.000	3.32	0.00	44.17	3.02
2167	5220	8.749499	CAAAAGACAGAGAAACATCATTTTGTC	58.251	33.333	0.00	0.00	32.96	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.