AutoCloner

Multiple sequence alignment - TraesCS3B01G049000

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	TraesCS3B01G049000	chr3B	100.000	2952	0	0	1	2952	24834841	24831890	0.000000e+00	5452.0
1	TraesCS3B01G049000	chr3D	94.653	2955	148	9	4	2952	17289079	17286129	0.000000e+00	4573.0
2	TraesCS3B01G049000	chr3D	94.888	2778	130	11	4	2773	17324218	17321445	0.000000e+00	4333.0
3	TraesCS3B01G049000	chr3D	95.376	930	39	3	2026	2952	17238611	17237683	0.000000e+00	1476.0
4	TraesCS3B01G049000	chr3D	92.263	517	36	4	4	518	17239558	17239044	0.000000e+00	730.0
5	TraesCS3B01G049000	chr3D	91.748	206	14	3	1	205	179343059	179343262	1.730000e-72	283.0
6	TraesCS3B01G049000	chr3D	91.089	202	15	2	5	205	326256257	326256456	1.350000e-68	270.0
7	TraesCS3B01G049000	chr3D	94.268	157	9	0	2796	2952	17321333	17321177	1.060000e-59	241.0
8	TraesCS3B01G049000	chr5D	90.554	2763	215	18	204	2952	35479358	35476628	0.000000e+00	3615.0
9	TraesCS3B01G049000	chr5D	87.500	160	16	2	584	740	241946282	241946440	6.500000e-42	182.0
10	TraesCS3B01G049000	chrUn	91.388	2067	166	10	204	2262	334202217	334200155	0.000000e+00	2820.0
11	TraesCS3B01G049000	chrUn	90.309	1940	177	7	1022	2951	324174626	324176564	0.000000e+00	2531.0
12	TraesCS3B01G049000	chrUn	91.463	820	65	5	204	1020	373420164	373419347	0.000000e+00	1122.0
13	TraesCS3B01G049000	chrUn	86.567	67	9	0	216	282	221267093	221267027	1.130000e-09	75.0
14	TraesCS3B01G049000	chr2B	92.118	203	14	2	1	203	557110178	557109978	4.820000e-73	285.0
15	TraesCS3B01G049000	chr2B	86.585	164	17	3	573	732	93696004	93696166	3.020000e-40	176.0
16	TraesCS3B01G049000	chr2B	87.143	70	9	0	213	282	517600075	517600144	2.440000e-11	80.5
17	TraesCS3B01G049000	chr1A	91.667	204	14	3	1	203	126032078	126031877	2.240000e-71	279.0
18	TraesCS3B01G049000	chr1D	91.133	203	17	1	1	203	189418256	189418457	1.040000e-69	274.0
19	TraesCS3B01G049000	chr3A	90.640	203	17	2	4	205	361211139	361210938	4.850000e-68	268.0
20	TraesCS3B01G049000	chr7B	88.608	158	14	2	587	740	715286769	715286926	3.880000e-44	189.0
21	TraesCS3B01G049000	chr7A	87.821	156	16	1	588	740	474509228	474509073	2.340000e-41	180.0
22	TraesCS3B01G049000	chr7D	85.143	175	22	2	579	749	141135355	141135529	3.020000e-40	176.0
23	TraesCS3B01G049000	chr2D	87.143	70	9	0	213	282	439567374	439567443	2.440000e-11	80.5

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	TraesCS3B01G049000	chr3B	24831890	24834841	2951	True	5452	5452	100.0000	1	2952	1	chr3B.!!$R1	2951
1	TraesCS3B01G049000	chr3D	17286129	17289079	2950	True	4573	4573	94.6530	4	2952	1	chr3D.!!$R1	2948
2	TraesCS3B01G049000	chr3D	17321177	17324218	3041	True	2287	4333	94.5780	4	2952	2	chr3D.!!$R3	2948
3	TraesCS3B01G049000	chr3D	17237683	17239558	1875	True	1103	1476	93.8195	4	2952	2	chr3D.!!$R2	2948
4	TraesCS3B01G049000	chr5D	35476628	35479358	2730	True	3615	3615	90.5540	204	2952	1	chr5D.!!$R1	2748
5	TraesCS3B01G049000	chrUn	334200155	334202217	2062	True	2820	2820	91.3880	204	2262	1	chrUn.!!$R2	2058
6	TraesCS3B01G049000	chrUn	324174626	324176564	1938	False	2531	2531	90.3090	1022	2951	1	chrUn.!!$F1	1929
7	TraesCS3B01G049000	chrUn	373419347	373420164	817	True	1122	1122	91.4630	204	1020	1	chrUn.!!$R3	816

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
56	57	4.564782	ATTGATCTGCTCTTCTGGAACA	57.435	40.909	0.0	0.0	0.0	3.18	F
1206	1219	0.398098	CCGGTAGTGATGGGGTAGGT	60.398	60.000	0.0	0.0	0.0	3.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1748	1766	0.107993	ATGCATCGGTGAGGACAGTG	60.108	55.000	0.0	0.0	0.0	3.66	R
2724	2745	1.062587	CTTGTAATTCCGCGCCTTCTG	59.937	52.381	0.0	0.0	0.0	3.02	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
46	47	5.049129	GCCCAGTAACATAATTGATCTGCTC	60.049	44.000	0.00	0.00	0.00	4.26
51	52	8.549548	CAGTAACATAATTGATCTGCTCTTCTG	58.450	37.037	0.00	0.00	0.00	3.02
56	57	4.564782	ATTGATCTGCTCTTCTGGAACA	57.435	40.909	0.00	0.00	0.00	3.18
70	71	7.765307	TCTTCTGGAACATGATAAATTCTTGC	58.235	34.615	0.00	0.00	38.20	4.01
76	77	9.504708	TGGAACATGATAAATTCTTGCATTTTT	57.495	25.926	0.00	0.00	33.80	1.94
106	107	9.903682	CAGATGATTGATATACAAATTTCCCAC	57.096	33.333	0.00	0.00	42.03	4.61
121	123	8.616942	CAAATTTCCCACGTTTTCCTAATTTTT	58.383	29.630	0.00	0.00	0.00	1.94
157	159	7.013178	GGACTAGTAGAAGTATGGTAGTTGTCC	59.987	44.444	3.59	0.00	35.94	4.02
170	172	5.247337	TGGTAGTTGTCCACATCATTACAGA	59.753	40.000	0.00	0.00	0.00	3.41
1054	1067	0.912487	TATCAACTTGGCCCCGTCCT	60.912	55.000	0.00	0.00	0.00	3.85
1055	1068	1.789576	ATCAACTTGGCCCCGTCCTT	61.790	55.000	0.00	0.00	0.00	3.36
1075	1088	2.507992	CGACCCTCAAGCTGCTCG	60.508	66.667	1.00	0.00	0.00	5.03
1135	1148	2.835156	GGAAAGGAGGCTGTAGACTTCT	59.165	50.000	0.00	0.00	42.10	2.85
1206	1219	0.398098	CCGGTAGTGATGGGGTAGGT	60.398	60.000	0.00	0.00	0.00	3.08
1309	1322	2.094675	CATGTAGGCCCTTGTTCCTTG	58.905	52.381	0.00	0.00	34.02	3.61
1344	1357	4.641645	CACCCAGCGGCACCTTCA	62.642	66.667	1.45	0.00	0.00	3.02
1479	1492	2.327325	ATGGGTCTATCATAGCCGGT	57.673	50.000	1.90	0.00	37.31	5.28
1566	1579	1.956170	CATATCCGCGGTGGTGCTC	60.956	63.158	27.15	0.00	39.52	4.26
1600	1613	1.850345	ACAGGGAACAAAAGGACCTCA	59.150	47.619	0.00	0.00	0.00	3.86
1648	1661	4.602340	GGTAACAAAGAGGTGAGACTCA	57.398	45.455	0.00	0.00	39.97	3.41
1659	1677	6.638610	AGAGGTGAGACTCACTGAATTATTG	58.361	40.000	29.70	0.00	46.19	1.90
1687	1705	9.846248	AGCACTTATGATTTGTTTCTTATGTTC	57.154	29.630	0.00	0.00	0.00	3.18
1748	1766	5.047802	TCTCAAGGCTTCAATGAATTCCAAC	60.048	40.000	14.07	0.00	0.00	3.77
1765	1783	0.320771	AACACTGTCCTCACCGATGC	60.321	55.000	0.00	0.00	0.00	3.91
1766	1784	1.293179	CACTGTCCTCACCGATGCA	59.707	57.895	0.00	0.00	0.00	3.96
1856	1874	6.655003	GTGAGAAGAAACAAGATAACATCCCA	59.345	38.462	0.00	0.00	0.00	4.37
1967	1985	3.124466	TCATTCTTGTATTTGCGTGACCG	59.876	43.478	0.00	0.00	37.07	4.79
1972	1990	2.756829	TGTATTTGCGTGACCGAAGAA	58.243	42.857	0.00	0.00	35.63	2.52
2093	2111	5.372066	AGATCTCTAGAGCCATTCCCATTTT	59.628	40.000	15.35	0.00	0.00	1.82
2181	2199	3.573110	AGTACAACTGTCAGACTACCACC	59.427	47.826	6.91	0.00	0.00	4.61
2195	2213	6.096987	CAGACTACCACCAGTACTATTGTCAT	59.903	42.308	0.00	0.00	0.00	3.06
2379	2400	6.071952	ACACAATAGGAAAGTGCCATTTACAG	60.072	38.462	0.00	0.00	36.76	2.74
2478	2499	6.040955	TGCCTGGTTATACAACAATCACAAAA	59.959	34.615	0.00	0.00	36.29	2.44
2536	2557	2.061028	GCCAAATTCCAAAGTGCTTCG	58.939	47.619	0.00	0.00	0.00	3.79
2602	2623	8.308931	AGATGATTCAAAGTTGCAATACACAAT	58.691	29.630	0.59	0.00	0.00	2.71
2609	2630	7.433719	TCAAAGTTGCAATACACAATGTGTTAC	59.566	33.333	24.78	11.75	45.08	2.50
2642	2663	9.605275	TGATAAAGAGTTGAGATGATACAAAGG	57.395	33.333	0.00	0.00	0.00	3.11
2644	2665	6.627087	AAGAGTTGAGATGATACAAAGGGA	57.373	37.500	0.00	0.00	0.00	4.20
2761	2783	9.774742	GAATTACAAGAAAGTGTTGGATCATAC	57.225	33.333	0.00	0.00	32.75	2.39
2842	2953	8.839343	CACTTTTGGACACATATAGAATATGCA	58.161	33.333	6.79	0.00	0.00	3.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	7.714377	AGAAGAGCAGATCAATTATGTTACTGG	59.286	37.037	0.00	0.00	0.00	4.00
46	47	7.541162	TGCAAGAATTTATCATGTTCCAGAAG	58.459	34.615	0.00	0.00	0.00	2.85
134	136	7.338703	TGTGGACAACTACCATACTTCTACTAG	59.661	40.741	0.00	0.00	39.69	2.57
138	140	6.666113	TGATGTGGACAACTACCATACTTCTA	59.334	38.462	0.00	0.00	39.69	2.10
140	142	5.730550	TGATGTGGACAACTACCATACTTC	58.269	41.667	0.00	0.00	39.69	3.01
192	194	8.524487	AGTACAAACAGTTGGTATTGAAAACAA	58.476	29.630	3.72	0.00	39.22	2.83
255	257	6.219417	TCAATCTGTTTGTTGTCCATGTTT	57.781	33.333	0.00	0.00	36.65	2.83
461	467	9.044150	AGGAAACAACACAAACAATTAATGATG	57.956	29.630	0.00	0.00	0.00	3.07
472	478	8.702438	CATGATAAATGAGGAAACAACACAAAC	58.298	33.333	0.00	0.00	0.00	2.93
732	738	7.414222	AATGCATGTTGATAGTTCTCCAATT	57.586	32.000	0.00	0.00	0.00	2.32
966	977	6.183360	GGTGCCCACGACCTCATATATATAAT	60.183	42.308	0.00	0.00	0.00	1.28
1054	1067	1.192146	AGCAGCTTGAGGGTCGGTAA	61.192	55.000	0.00	0.00	0.00	2.85
1055	1068	1.605058	GAGCAGCTTGAGGGTCGGTA	61.605	60.000	0.00	0.00	0.00	4.02
1075	1088	0.721718	CGATTGGCCTTCTTGTCGAC	59.278	55.000	9.11	9.11	0.00	4.20
1135	1148	1.410517	CATCGCTAGGAGGCTGAAGAA	59.589	52.381	0.00	0.00	0.00	2.52
1191	1204	1.874129	CCACACCTACCCCATCACTA	58.126	55.000	0.00	0.00	0.00	2.74
1206	1219	2.764010	ACTATCGTAGATGTTGGCCACA	59.236	45.455	3.88	7.85	45.12	4.17
1309	1322	1.463444	GTGTGTTGTGATAGGGCGTTC	59.537	52.381	0.00	0.00	0.00	3.95
1344	1357	1.647545	CGTGAACAGATGCCCGCATT	61.648	55.000	3.24	0.00	36.70	3.56
1419	1432	4.783621	TCTGCTGCCATGCCCGTC	62.784	66.667	0.00	0.00	0.00	4.79
1566	1579	3.071874	TCCCTGTTGAGCTTGGTTATG	57.928	47.619	0.00	0.00	0.00	1.90
1600	1613	1.476085	CACAGACTTCTCCTCGAGCAT	59.524	52.381	6.99	0.00	0.00	3.79
1659	1677	9.846248	ACATAAGAAACAAATCATAAGTGCTTC	57.154	29.630	0.00	0.00	0.00	3.86
1748	1766	0.107993	ATGCATCGGTGAGGACAGTG	60.108	55.000	0.00	0.00	0.00	3.66
1765	1783	8.771766	CATCAGTATTGTTGTCAGATAGGAATG	58.228	37.037	0.00	0.00	0.00	2.67
1766	1784	8.489489	ACATCAGTATTGTTGTCAGATAGGAAT	58.511	33.333	0.00	0.00	33.08	3.01
1796	1814	5.130477	ACGAGCCCTTTTATTCTTGGATAGA	59.870	40.000	0.00	0.00	0.00	1.98
2093	2111	8.028354	AGACGATTTGATGAATTTATGTTGCAA	58.972	29.630	0.00	0.00	0.00	4.08
2181	2199	4.499865	CCCGTCTGGATGACAATAGTACTG	60.500	50.000	5.39	0.00	45.60	2.74
2195	2213	1.352017	TGACAGTAGTACCCGTCTGGA	59.648	52.381	17.04	0.53	37.49	3.86
2310	2329	8.789825	TCAAAATTAAATGGGTTCCAATGATG	57.210	30.769	0.00	0.00	36.95	3.07
2357	2378	6.757897	TCTGTAAATGGCACTTTCCTATTG	57.242	37.500	0.00	0.00	0.00	1.90
2536	2557	9.092876	TCATGTAATTTGGAACTTTGTTTTGTC	57.907	29.630	0.00	0.00	0.00	3.18
2624	2645	5.762179	TGTCCCTTTGTATCATCTCAACT	57.238	39.130	0.00	0.00	0.00	3.16
2642	2663	7.762615	TGTGTACTAGCACTTTATGTATTGTCC	59.237	37.037	0.00	0.00	39.89	4.02
2644	2665	8.092068	TGTGTGTACTAGCACTTTATGTATTGT	58.908	33.333	13.75	0.00	39.89	2.71
2724	2745	1.062587	CTTGTAATTCCGCGCCTTCTG	59.937	52.381	0.00	0.00	0.00	3.02
2842	2953	8.860088	AGTAATTTGGAATTGTCTTGCTAACTT	58.140	29.630	0.00	0.00	0.00	2.66
2858	2969	8.629158	GCAATTCCATACACATAGTAATTTGGA	58.371	33.333	0.00	0.00	37.52	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.