AutoCloner

Multiple sequence alignment - TraesCS1B01G105900

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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	TraesCS1B01G105900	chr1B	100.000	2162	0	0	1	2162	117531530	117533691	0.000000e+00	3993
1	TraesCS1B01G105900	chr1B	87.698	1008	116	5	1162	2162	677703728	677704734	0.000000e+00	1168
2	TraesCS1B01G105900	chr1B	95.619	388	13	4	787	1171	633728884	633728498	8.480000e-174	619
3	TraesCS1B01G105900	chr6B	89.980	1008	91	6	1162	2162	103626534	103625530	0.000000e+00	1293
4	TraesCS1B01G105900	chr6B	93.663	789	47	3	1	787	391303384	391304171	0.000000e+00	1177
5	TraesCS1B01G105900	chr6B	93.974	780	44	2	9	787	580281293	580280516	0.000000e+00	1177
6	TraesCS1B01G105900	chr3B	94.246	782	43	2	7	787	825768897	825769677	0.000000e+00	1194
7	TraesCS1B01G105900	chr3B	93.974	780	46	1	9	787	416931074	416930295	0.000000e+00	1179
8	TraesCS1B01G105900	chr3B	93.870	783	47	1	9	790	563929250	563930032	0.000000e+00	1179
9	TraesCS1B01G105900	chr3B	93.854	781	44	4	9	787	572088818	572088040	0.000000e+00	1173
10	TraesCS1B01G105900	chr3B	87.413	1009	115	11	1159	2162	84592500	84591499	0.000000e+00	1149
11	TraesCS1B01G105900	chr3B	95.619	388	13	3	787	1171	201560794	201560408	8.480000e-174	619
12	TraesCS1B01G105900	chr4B	94.231	780	44	1	9	788	518865168	518865946	0.000000e+00	1190
13	TraesCS1B01G105900	chr4B	87.426	1010	117	5	1162	2162	338026219	338025211	0.000000e+00	1153
14	TraesCS1B01G105900	chr7B	93.774	787	47	2	1	785	350404249	350403463	0.000000e+00	1181
15	TraesCS1B01G105900	chr7B	87.810	1009	113	7	1162	2162	500978021	500977015	0.000000e+00	1173
16	TraesCS1B01G105900	chr7B	86.892	1007	122	10	1159	2162	250413257	250412258	0.000000e+00	1120
17	TraesCS1B01G105900	chr7B	96.124	387	13	2	787	1171	662738925	662739311	3.920000e-177	630
18	TraesCS1B01G105900	chr2B	93.878	784	44	4	9	790	573819150	573818369	0.000000e+00	1179
19	TraesCS1B01G105900	chr2B	87.747	1012	110	10	1162	2162	627833151	627832143	0.000000e+00	1170
20	TraesCS1B01G105900	chr2B	86.083	1006	132	7	1162	2162	111647158	111646156	0.000000e+00	1075
21	TraesCS1B01G105900	chr7D	86.441	1003	130	6	1162	2162	579585525	579586523	0.000000e+00	1094
22	TraesCS1B01G105900	chrUn	96.649	388	9	3	787	1171	327663324	327662938	1.810000e-180	641
23	TraesCS1B01G105900	chr3A	96.649	388	9	3	787	1171	672878452	672878066	1.810000e-180	641
24	TraesCS1B01G105900	chr2D	97.113	381	9	2	787	1166	33933796	33934175	1.810000e-180	641
25	TraesCS1B01G105900	chr2D	96.649	388	9	3	787	1171	272801678	272801292	1.810000e-180	641
26	TraesCS1B01G105900	chr2D	97.113	381	9	2	787	1166	630270273	630270652	1.810000e-180	641
27	TraesCS1B01G105900	chr2D	96.850	381	10	2	787	1166	630269208	630269587	8.420000e-179	636

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	TraesCS1B01G105900	chr1B	117531530	117533691	2161	False	3993.0	3993	100.0000	1	2162	1	chr1B.!!$F1	2161
1	TraesCS1B01G105900	chr1B	677703728	677704734	1006	False	1168.0	1168	87.6980	1162	2162	1	chr1B.!!$F2	1000
2	TraesCS1B01G105900	chr6B	103625530	103626534	1004	True	1293.0	1293	89.9800	1162	2162	1	chr6B.!!$R1	1000
3	TraesCS1B01G105900	chr6B	391303384	391304171	787	False	1177.0	1177	93.6630	1	787	1	chr6B.!!$F1	786
4	TraesCS1B01G105900	chr6B	580280516	580281293	777	True	1177.0	1177	93.9740	9	787	1	chr6B.!!$R2	778
5	TraesCS1B01G105900	chr3B	825768897	825769677	780	False	1194.0	1194	94.2460	7	787	1	chr3B.!!$F2	780
6	TraesCS1B01G105900	chr3B	416930295	416931074	779	True	1179.0	1179	93.9740	9	787	1	chr3B.!!$R3	778
7	TraesCS1B01G105900	chr3B	563929250	563930032	782	False	1179.0	1179	93.8700	9	790	1	chr3B.!!$F1	781
8	TraesCS1B01G105900	chr3B	572088040	572088818	778	True	1173.0	1173	93.8540	9	787	1	chr3B.!!$R4	778
9	TraesCS1B01G105900	chr3B	84591499	84592500	1001	True	1149.0	1149	87.4130	1159	2162	1	chr3B.!!$R1	1003
10	TraesCS1B01G105900	chr4B	518865168	518865946	778	False	1190.0	1190	94.2310	9	788	1	chr4B.!!$F1	779
11	TraesCS1B01G105900	chr4B	338025211	338026219	1008	True	1153.0	1153	87.4260	1162	2162	1	chr4B.!!$R1	1000
12	TraesCS1B01G105900	chr7B	350403463	350404249	786	True	1181.0	1181	93.7740	1	785	1	chr7B.!!$R2	784
13	TraesCS1B01G105900	chr7B	500977015	500978021	1006	True	1173.0	1173	87.8100	1162	2162	1	chr7B.!!$R3	1000
14	TraesCS1B01G105900	chr7B	250412258	250413257	999	True	1120.0	1120	86.8920	1159	2162	1	chr7B.!!$R1	1003
15	TraesCS1B01G105900	chr2B	573818369	573819150	781	True	1179.0	1179	93.8780	9	790	1	chr2B.!!$R2	781
16	TraesCS1B01G105900	chr2B	627832143	627833151	1008	True	1170.0	1170	87.7470	1162	2162	1	chr2B.!!$R3	1000
17	TraesCS1B01G105900	chr2B	111646156	111647158	1002	True	1075.0	1075	86.0830	1162	2162	1	chr2B.!!$R1	1000
18	TraesCS1B01G105900	chr7D	579585525	579586523	998	False	1094.0	1094	86.4410	1162	2162	1	chr7D.!!$F1	1000
19	TraesCS1B01G105900	chr2D	630269208	630270652	1444	False	638.5	641	96.9815	787	1166	2	chr2D.!!$F2	379

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
96	97	1.215382	CAAGTCTCCGCGGATGTCA	59.785	57.895	31.19	10.38	0.0	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2044	2592	0.535335	GTTGGTGTCCGGCTCTATCA	59.465	55.0	0.0	0.0	0.0	2.15	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
96	97	1.215382	CAAGTCTCCGCGGATGTCA	59.785	57.895	31.19	10.38	0.00	3.58
214	216	3.834610	CCGCCGAATACGAAGATCTATT	58.165	45.455	0.00	0.00	42.66	1.73
253	255	1.491670	CTGGATCGCATCGTTGTAGG	58.508	55.000	0.00	0.00	0.00	3.18
285	287	2.176364	AGCCATCAAGCCTTATGGTGAT	59.824	45.455	9.75	0.00	43.87	3.06
356	359	2.019272	ATCTCGGGTAGGGGGTCCT	61.019	63.158	0.00	0.00	46.96	3.85
548	552	9.658799	GAAGCTAGCCTATGATTATGATTGTTA	57.341	33.333	12.13	0.00	0.00	2.41
641	647	6.102897	ACAAGGAAGGGAATCTACATATCG	57.897	41.667	0.00	0.00	0.00	2.92
649	655	4.330074	GGGAATCTACATATCGGAATTGCG	59.670	45.833	13.75	13.75	0.00	4.85
651	657	5.289675	GGAATCTACATATCGGAATTGCGAG	59.710	44.000	25.95	15.57	0.00	5.03
729	736	9.334947	CAATCTTGTATCTTCATAGTCCAACAT	57.665	33.333	0.00	0.00	0.00	2.71
758	765	2.440539	AGCATATAGTCCGGCTTTCG	57.559	50.000	0.00	0.00	31.34	3.46
768	775	3.009714	GGCTTTCGGAGGACCCCT	61.010	66.667	0.00	0.00	36.03	4.79
816	823	3.041211	ACCGAGGATGAGAATGGATCAA	58.959	45.455	0.00	0.00	0.00	2.57
1046	1579	6.734137	TCATGAGTTATGGTCAACAAACAAC	58.266	36.000	0.00	0.00	37.39	3.32
1139	1672	8.575649	ACGATTCACTACCCTTATGAAAAATT	57.424	30.769	0.00	0.00	36.03	1.82
1159	1692	7.448748	AAATTAATTACACCAGAGCGTTTCT	57.551	32.000	0.01	0.00	36.25	2.52
1160	1693	8.556213	AAATTAATTACACCAGAGCGTTTCTA	57.444	30.769	0.01	0.00	33.83	2.10
1167	1700	1.825474	CCAGAGCGTTTCTAGAGGGAA	59.175	52.381	0.00	0.00	33.83	3.97
1240	1773	6.758886	GTCTGTTGGACTATGAAGATACAAGG	59.241	42.308	0.00	0.00	41.46	3.61
1350	1883	2.880443	ACCGACTCTGTGTAACCCTAA	58.120	47.619	0.00	0.00	34.36	2.69
1351	1884	2.560105	ACCGACTCTGTGTAACCCTAAC	59.440	50.000	0.00	0.00	34.36	2.34
1397	1933	2.168728	GAGGGTTTAGCCTGTAGGACAG	59.831	54.545	5.00	0.00	45.53	3.51
1404	1940	0.875059	GCCTGTAGGACAGCAACAAC	59.125	55.000	1.17	0.00	44.63	3.32
1416	1952	5.822519	GGACAGCAACAACCATAATCATAGA	59.177	40.000	0.00	0.00	0.00	1.98
1417	1953	6.318648	GGACAGCAACAACCATAATCATAGAA	59.681	38.462	0.00	0.00	0.00	2.10
1572	2109	1.210967	CCCGCCTCCTGTTACCATTAA	59.789	52.381	0.00	0.00	0.00	1.40
1584	2121	6.772716	CCTGTTACCATTAACCTTAGATGCAT	59.227	38.462	0.00	0.00	37.39	3.96
1616	2153	4.511246	TACCCGAGATCCGCCGGT	62.511	66.667	1.63	11.60	43.93	5.28
1626	2163	0.820074	ATCCGCCGGTTTTTGACACA	60.820	50.000	1.63	0.00	0.00	3.72
1722	2260	0.398522	ATGCGATCCAGGGTGAGGTA	60.399	55.000	0.00	0.00	0.00	3.08
1807	2345	5.153950	TCTAGAGCAGATCGATAGCTACA	57.846	43.478	20.87	12.56	39.02	2.74
1813	2351	2.894126	CAGATCGATAGCTACACCCCTT	59.106	50.000	0.00	0.00	0.00	3.95
1814	2352	3.057174	CAGATCGATAGCTACACCCCTTC	60.057	52.174	0.00	0.00	0.00	3.46
1819	2357	2.280308	TAGCTACACCCCTTCCCATT	57.720	50.000	0.00	0.00	0.00	3.16
1859	2397	4.158025	CCTGAACTACACTACCGACATCTT	59.842	45.833	0.00	0.00	0.00	2.40
1860	2398	5.336531	CCTGAACTACACTACCGACATCTTT	60.337	44.000	0.00	0.00	0.00	2.52
1875	2413	5.641209	CGACATCTTTGGAGACTTGATCTTT	59.359	40.000	0.00	0.00	38.00	2.52
1953	2501	1.826024	GGCGGTCAGGAGATCACAT	59.174	57.895	0.00	0.00	0.00	3.21
1978	2526	0.028110	GCTGCCTCGGCTTTAAATCG	59.972	55.000	9.65	5.16	42.51	3.34
1988	2536	2.291741	GGCTTTAAATCGGGAGCAGATG	59.708	50.000	0.00	0.00	36.87	2.90
2018	2566	1.616628	GGACAGGTGGATGGACCCT	60.617	63.158	0.00	0.00	36.56	4.34
2024	2572	2.531428	TGGATGGACCCTGCCACA	60.531	61.111	0.00	0.00	41.56	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.304525	GCATGACTTAGATCTGCCATTGC	60.305	47.826	5.18	4.21	38.26	3.56
96	97	1.002544	GGAAGCCTGAACTACACTGCT	59.997	52.381	0.00	0.00	34.37	4.24
253	255	2.098770	GCTTGATGGCTCCTTCAATCAC	59.901	50.000	14.95	6.98	38.70	3.06
300	302	3.742369	CCAACATTGGTGCTTTCATTGAC	59.258	43.478	2.22	0.00	43.43	3.18
356	359	0.679505	AGCCTTAGACGCACAGTTCA	59.320	50.000	0.00	0.00	0.00	3.18
506	509	3.839778	AGCTTCTAGGGTTAGCCTCTAG	58.160	50.000	6.12	12.16	37.17	2.43
586	590	2.326974	TAACCCTAGCCCCCTCCGA	61.327	63.158	0.00	0.00	0.00	4.55
641	647	2.048603	AGGCAAGCCTCGCAATTCC	61.049	57.895	8.02	0.00	44.43	3.01
729	736	3.368013	CGGACTATATGCTTATGCCGGAA	60.368	47.826	5.05	0.00	38.71	4.30
755	762	1.273953	TGGATTAAGGGGTCCTCCGAA	60.274	52.381	0.00	0.00	35.49	4.30
758	765	1.141185	CCTGGATTAAGGGGTCCTCC	58.859	60.000	0.00	0.00	35.49	4.30
768	775	3.048600	CCATGAGGGAGTCCTGGATTAA	58.951	50.000	9.58	0.00	45.05	1.40
854	861	4.854173	TGTTAATAAGAGATTGCCCAGCA	58.146	39.130	0.00	0.00	36.47	4.41
855	862	5.450550	GGTTGTTAATAAGAGATTGCCCAGC	60.451	44.000	0.00	0.00	0.00	4.85
991	1524	8.164070	AGTTACCATAGGGAACATATTCATTCC	58.836	37.037	13.30	0.00	43.23	3.01
1046	1579	3.119245	ACCTATGTACCTTGTAGCACGTG	60.119	47.826	12.28	12.28	0.00	4.49
1139	1672	6.405508	CCTCTAGAAACGCTCTGGTGTAATTA	60.406	42.308	0.00	0.00	34.33	1.40
1197	1730	3.928992	CAGACCGGCATAAGCATATAGTG	59.071	47.826	0.00	0.00	44.61	2.74
1216	1749	6.440647	ACCTTGTATCTTCATAGTCCAACAGA	59.559	38.462	0.00	0.00	0.00	3.41
1351	1884	4.286291	GGTTTATATAGACACCAGAGGGGG	59.714	50.000	5.83	0.00	46.04	5.40
1397	1933	8.103948	AGCTATTCTATGATTATGGTTGTTGC	57.896	34.615	0.00	0.00	0.00	4.17
1404	1940	8.986991	ACCCTAGAAGCTATTCTATGATTATGG	58.013	37.037	0.00	0.00	44.95	2.74
1416	1952	4.821940	AGAGGCTAACCCTAGAAGCTATT	58.178	43.478	0.00	0.00	46.60	1.73
1417	1953	4.479156	AGAGGCTAACCCTAGAAGCTAT	57.521	45.455	0.00	0.00	46.60	2.97
1572	2109	3.069729	GTCCCGAACTATGCATCTAAGGT	59.930	47.826	0.19	0.00	0.00	3.50
1616	2153	3.446873	AGCACCAATGTCTGTGTCAAAAA	59.553	39.130	0.00	0.00	34.94	1.94
1626	2163	4.401022	TCTCAATGAAAGCACCAATGTCT	58.599	39.130	0.00	0.00	0.00	3.41
1722	2260	3.519510	TGAAGATCTGTTCGGGGAGAAAT	59.480	43.478	0.00	0.00	41.10	2.17
1807	2345	1.596496	CTGACCTAATGGGAAGGGGT	58.404	55.000	0.00	0.00	38.54	4.95
1813	2351	2.638325	TCCAAACCTGACCTAATGGGA	58.362	47.619	0.00	0.00	38.76	4.37
1814	2352	3.356290	CTTCCAAACCTGACCTAATGGG	58.644	50.000	0.00	0.00	41.89	4.00
1819	2357	1.742308	AGGCTTCCAAACCTGACCTA	58.258	50.000	0.00	0.00	34.07	3.08
1859	2397	3.323691	TCCGTCAAAGATCAAGTCTCCAA	59.676	43.478	0.00	0.00	35.67	3.53
1860	2398	2.897326	TCCGTCAAAGATCAAGTCTCCA	59.103	45.455	0.00	0.00	35.67	3.86
1875	2413	0.617935	TCATGGGCTTGAATCCGTCA	59.382	50.000	0.00	0.00	0.00	4.35
1937	2485	1.537776	GCAGATGTGATCTCCTGACCG	60.538	57.143	0.00	0.00	37.58	4.79
1939	2487	2.823984	CTGCAGATGTGATCTCCTGAC	58.176	52.381	8.42	0.00	37.58	3.51
1988	2536	2.292267	CACCTGTCCTTGTATGGCATC	58.708	52.381	1.65	0.00	0.00	3.91
1996	2544	0.693049	GTCCATCCACCTGTCCTTGT	59.307	55.000	0.00	0.00	0.00	3.16
2024	2572	4.385405	GCTGAGTGTGCGGCCTCT	62.385	66.667	0.00	0.00	34.06	3.69
2044	2592	0.535335	GTTGGTGTCCGGCTCTATCA	59.465	55.000	0.00	0.00	0.00	2.15
2055	2603	2.158813	TCTTGGAAGTGAGGTTGGTGTC	60.159	50.000	0.00	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.