AutoCloner

Multiple sequence alignment - TraesCS7D01G167900

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	TraesCS7D01G167900	chr7D	100.000	9454	0	0	1	9454	118145353	118154806	0.000000e+00	17459.0
1	TraesCS7D01G167900	chr7D	92.052	692	42	10	2842	3525	118147812	118148498	0.000000e+00	961.0
2	TraesCS7D01G167900	chr7D	92.052	692	42	10	2460	3146	118148194	118148877	0.000000e+00	961.0
3	TraesCS7D01G167900	chr7D	99.392	329	2	0	1	329	118132549	118132877	1.760000e-166	597.0
4	TraesCS7D01G167900	chr7D	99.392	329	2	0	1	329	148101920	148101592	1.760000e-166	597.0
5	TraesCS7D01G167900	chr7D	99.392	329	2	0	1	329	505801874	505802202	1.760000e-166	597.0
6	TraesCS7D01G167900	chr7D	96.512	86	3	0	6252	6337	81910954	81911039	9.900000e-30	143.0
7	TraesCS7D01G167900	chr7D	93.478	92	6	0	6252	6343	28032480	28032389	4.600000e-28	137.0
8	TraesCS7D01G167900	chr7A	94.046	3443	134	20	2842	6253	122489574	122492976	0.000000e+00	5156.0
9	TraesCS7D01G167900	chr7A	95.084	2441	91	13	6334	8747	122492973	122495411	0.000000e+00	3816.0
10	TraesCS7D01G167900	chr7A	87.923	1714	105	40	464	2139	122487667	122489316	0.000000e+00	1925.0
11	TraesCS7D01G167900	chr7A	95.368	950	42	2	2199	3146	122489313	122490262	0.000000e+00	1509.0
12	TraesCS7D01G167900	chr7A	85.539	408	27	18	9042	9444	122497490	122497870	1.910000e-106	398.0
13	TraesCS7D01G167900	chr7A	83.495	309	38	7	2465	2768	122489962	122490262	9.350000e-70	276.0
14	TraesCS7D01G167900	chr7A	80.892	314	47	7	3220	3525	122489574	122489882	1.590000e-57	235.0
15	TraesCS7D01G167900	chr7A	95.918	98	4	0	8943	9040	122495412	122495509	9.830000e-35	159.0
16	TraesCS7D01G167900	chr7A	89.908	109	10	1	7199	7307	610942475	610942368	1.280000e-28	139.0
17	TraesCS7D01G167900	chr7A	81.301	123	12	7	7331	7452	610939087	610938975	1.310000e-13	89.8
18	TraesCS7D01G167900	chr7A	95.745	47	1	1	2160	2206	333024770	333024725	3.660000e-09	75.0
19	TraesCS7D01G167900	chr7B	94.969	2445	87	17	6334	8747	79305897	79308336	0.000000e+00	3801.0
20	TraesCS7D01G167900	chr7B	93.392	1816	76	15	2842	4648	79302288	79304068	0.000000e+00	2649.0
21	TraesCS7D01G167900	chr7B	95.152	1650	50	7	4632	6253	79304253	79305900	0.000000e+00	2577.0
22	TraesCS7D01G167900	chr7B	90.571	1262	46	34	898	2139	79300822	79302030	0.000000e+00	1604.0
23	TraesCS7D01G167900	chr7B	95.258	949	41	3	2199	3146	79302027	79302972	0.000000e+00	1500.0
24	TraesCS7D01G167900	chr7B	87.476	511	40	13	8943	9448	79308337	79308828	1.380000e-157	568.0
25	TraesCS7D01G167900	chr7B	82.803	314	41	7	3220	3525	79302288	79302596	1.560000e-67	268.0
26	TraesCS7D01G167900	chr7B	91.919	99	7	1	7209	7307	570175212	570175115	4.600000e-28	137.0
27	TraesCS7D01G167900	chr7B	100.000	28	0	0	2133	2160	580986907	580986880	1.700000e-02	52.8
28	TraesCS7D01G167900	chr6D	99.392	329	2	0	1	329	85539340	85539012	1.760000e-166	597.0
29	TraesCS7D01G167900	chr6D	99.088	329	3	0	1	329	85515659	85515331	8.180000e-165	592.0
30	TraesCS7D01G167900	chr6D	93.478	92	6	0	6252	6343	469536403	469536312	4.600000e-28	137.0
31	TraesCS7D01G167900	chr6D	97.727	44	1	0	2160	2203	69585682	69585639	1.020000e-09	76.8
32	TraesCS7D01G167900	chr3D	98.799	333	4	0	1	333	483961601	483961933	2.270000e-165	593.0
33	TraesCS7D01G167900	chr3D	97.391	345	8	1	1	344	551449965	551450309	3.800000e-163	586.0
34	TraesCS7D01G167900	chr1D	99.088	329	3	0	1	329	405610566	405610894	8.180000e-165	592.0
35	TraesCS7D01G167900	chr1D	99.088	329	3	0	1	329	432510506	432510834	8.180000e-165	592.0
36	TraesCS7D01G167900	chr1D	89.231	65	2	2	2138	2202	332955050	332955109	1.020000e-09	76.8
37	TraesCS7D01G167900	chr1D	97.727	44	1	0	2160	2203	474055634	474055677	1.020000e-09	76.8
38	TraesCS7D01G167900	chr2A	95.556	90	4	0	6248	6337	57855601	57855690	2.750000e-30	145.0
39	TraesCS7D01G167900	chr6B	93.478	92	6	0	6252	6343	715678943	715678852	4.600000e-28	137.0
40	TraesCS7D01G167900	chr6B	100.000	28	0	0	2133	2160	26619173	26619146	1.700000e-02	52.8
41	TraesCS7D01G167900	chr2B	92.632	95	7	0	6243	6337	362897630	362897724	4.600000e-28	137.0
42	TraesCS7D01G167900	chr5A	92.553	94	7	0	6247	6340	519884868	519884775	1.660000e-27	135.0
43	TraesCS7D01G167900	chr5A	93.407	91	5	1	6249	6338	659866874	659866964	5.960000e-27	134.0
44	TraesCS7D01G167900	chr5A	97.727	44	1	0	2160	2203	113799707	113799750	1.020000e-09	76.8
45	TraesCS7D01G167900	chr2D	92.632	95	6	1	6244	6337	420176102	420176008	1.660000e-27	135.0
46	TraesCS7D01G167900	chr4D	97.727	44	1	0	2160	2203	14663853	14663810	1.020000e-09	76.8
47	TraesCS7D01G167900	chr1B	97.727	44	1	0	2160	2203	667944042	667944085	1.020000e-09	76.8
48	TraesCS7D01G167900	chr1B	100.000	28	0	0	2133	2160	22112661	22112634	1.700000e-02	52.8
49	TraesCS7D01G167900	chr1A	97.727	44	1	0	2159	2202	64857392	64857435	1.020000e-09	76.8
50	TraesCS7D01G167900	chr6A	95.745	47	1	1	2160	2206	611909632	611909677	3.660000e-09	75.0
51	TraesCS7D01G167900	chr5D	96.875	32	1	0	2129	2160	425034976	425034945	5.000000e-03	54.7

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	TraesCS7D01G167900	chr7D	118145353	118154806	9453	False	17459.000000	17459	100.000000	1	9454	1	chr7D.!!$F3	9453
1	TraesCS7D01G167900	chr7D	118147812	118148877	1065	False	961.000000	961	92.052000	2460	3525	2	chr7D.!!$F5	1065
2	TraesCS7D01G167900	chr7A	122487667	122497870	10203	False	1684.250000	5156	89.783125	464	9444	8	chr7A.!!$F1	8980
3	TraesCS7D01G167900	chr7B	79300822	79308828	8006	False	1852.428571	3801	91.374429	898	9448	7	chr7B.!!$F1	8550

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	Hairpin	End Stability	Orientation
280	281	0.098200	GGCGACGTTTTATTGGCTCC	59.902	55.000	0.00	0.00	4.70	F
1002	1018	0.038310	TCTTCGCCTCTGACTCTGGA	59.962	55.000	0.00	0.00	3.86	F
2153	2198	0.038744	AAGTACTCCCTCCGTTCCGA	59.961	55.000	0.00	0.00	4.55	F
2154	2199	0.258194	AGTACTCCCTCCGTTCCGAT	59.742	55.000	0.00	0.00	4.18	F
3088	3512	0.326595	TCGTTTATTCTGCTGCCCCA	59.673	50.000	0.00	0.00	4.96	F
3214	3638	0.031994	ATGTCGGTTTGCACTTTGGC	59.968	50.000	0.00	0.00	4.52	F
3230	3654	0.105760	TGGCAAAATCCACACCCACT	60.106	50.000	0.00	0.00	4.00	F
3381	3805	0.733729	TGTAACTGTTTTTGGCGCGT	59.266	45.000	8.43	0.00	6.01	F
4511	4966	0.971386	CTGCCAGAAGGTTTGCCATT	59.029	50.000	0.00	37.19	3.16	F
4522	4977	2.556559	GGTTTGCCATTACCCTCCTTGA	60.557	50.000	0.00	34.09	3.02	F
6266	6970	1.431633	TCAAGTACTCCCTCTGTCCCA	59.568	52.381	0.00	0.00	4.37	F
8045	8758	0.104304	ACAACGCGGTTCTGAAGTCT	59.896	50.000	12.47	0.00	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2185	2230	0.032515	TGCTACTCCCTCCATTCCGA	60.033	55.000	0.00	0.00	4.55	R
2200	2245	0.109723	AGCCCAAAAGGTCGTTGCTA	59.890	50.000	0.00	38.26	3.49	R
3195	3619	0.031994	GCCAAAGTGCAAACCGACAT	59.968	50.000	0.00	0.00	3.06	R
3211	3635	0.105760	AGTGGGTGTGGATTTTGCCA	60.106	50.000	0.00	35.02	4.92	R
4576	5032	0.396435	CACACTAGGGCACAACTGGA	59.604	55.000	0.00	0.00	3.86	R
4582	5038	1.263356	GACCTACACACTAGGGCACA	58.737	55.000	0.00	42.38	4.57	R
4842	5505	4.321718	AGGACCGATGCTAATTCATGATG	58.678	43.478	0.00	0.00	3.07	R
5365	6029	5.003804	AGAAGCAACATTCGGTGAAAGTAT	58.996	37.500	0.00	34.27	2.12	R
5388	6052	0.618680	AGCAGGCATCAGGGACTACA	60.619	55.000	0.00	36.02	2.74	R
6321	7025	1.273381	TGATTTACTCCCTCCGTCCCA	60.273	52.381	0.00	0.00	4.37	R
8073	8786	0.475906	AACCTGGCTTTCAGCTCTGT	59.524	50.000	0.00	41.99	3.41	R
9189	11913	0.032515	TCTATGGACCTCGCCAGGAA	60.033	55.000	3.62	43.65	3.36	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	2.700329	GCATAGTTGGCCTCTGAGC	58.300	57.895	3.32	7.64	0.00	4.26
19	20	0.107508	GCATAGTTGGCCTCTGAGCA	60.108	55.000	3.32	0.00	0.00	4.26
20	21	1.476471	GCATAGTTGGCCTCTGAGCAT	60.476	52.381	3.32	0.00	0.00	3.79
21	22	2.224378	GCATAGTTGGCCTCTGAGCATA	60.224	50.000	3.32	0.00	0.00	3.14
22	23	3.661944	CATAGTTGGCCTCTGAGCATAG	58.338	50.000	3.32	0.00	0.00	2.23
23	24	1.871418	AGTTGGCCTCTGAGCATAGA	58.129	50.000	3.32	0.00	0.00	1.98
24	25	1.761784	AGTTGGCCTCTGAGCATAGAG	59.238	52.381	3.32	9.57	43.04	2.43
25	26	1.484240	GTTGGCCTCTGAGCATAGAGT	59.516	52.381	3.32	0.00	42.09	3.24
26	27	1.871418	TGGCCTCTGAGCATAGAGTT	58.129	50.000	3.32	0.00	42.09	3.01
27	28	1.483827	TGGCCTCTGAGCATAGAGTTG	59.516	52.381	3.32	3.78	42.09	3.16
28	29	1.580815	GCCTCTGAGCATAGAGTTGC	58.419	55.000	13.96	8.78	42.09	4.17
29	30	1.809651	GCCTCTGAGCATAGAGTTGCC	60.810	57.143	13.96	0.10	43.83	4.52
30	31	1.761784	CCTCTGAGCATAGAGTTGCCT	59.238	52.381	13.96	0.00	43.83	4.75
31	32	2.170187	CCTCTGAGCATAGAGTTGCCTT	59.830	50.000	13.96	0.00	43.83	4.35
32	33	3.456280	CTCTGAGCATAGAGTTGCCTTC	58.544	50.000	8.60	0.00	43.83	3.46
33	34	3.102972	TCTGAGCATAGAGTTGCCTTCT	58.897	45.455	0.00	0.00	43.83	2.85
34	35	3.517100	TCTGAGCATAGAGTTGCCTTCTT	59.483	43.478	0.00	0.00	43.83	2.52
35	36	4.711846	TCTGAGCATAGAGTTGCCTTCTTA	59.288	41.667	0.00	0.00	43.83	2.10
36	37	5.016051	TGAGCATAGAGTTGCCTTCTTAG	57.984	43.478	0.00	0.00	43.83	2.18
37	38	3.802866	AGCATAGAGTTGCCTTCTTAGC	58.197	45.455	0.00	0.00	43.83	3.09
38	39	3.198635	AGCATAGAGTTGCCTTCTTAGCA	59.801	43.478	0.00	0.00	43.83	3.49
39	40	4.133078	GCATAGAGTTGCCTTCTTAGCAT	58.867	43.478	0.00	0.00	40.59	3.79
40	41	5.070981	AGCATAGAGTTGCCTTCTTAGCATA	59.929	40.000	0.00	0.00	43.83	3.14
41	42	5.407995	GCATAGAGTTGCCTTCTTAGCATAG	59.592	44.000	0.00	0.00	40.59	2.23
42	43	3.802866	AGAGTTGCCTTCTTAGCATAGC	58.197	45.455	0.00	0.00	40.59	2.97

Showing 1 to 25 of 1,019 entries

Previous1 2 3 4 5…41Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.107508	TGCTCAGAGGCCAACTATGC	60.108	55.000	5.01	11.63	38.31	3.14
1	2	2.634815	ATGCTCAGAGGCCAACTATG	57.365	50.000	5.01	0.00	39.78	2.23
2	3	3.577848	CTCTATGCTCAGAGGCCAACTAT	59.422	47.826	5.01	0.00	38.74	2.12
3	4	2.961741	CTCTATGCTCAGAGGCCAACTA	59.038	50.000	5.01	0.00	38.74	2.24
4	5	1.761784	CTCTATGCTCAGAGGCCAACT	59.238	52.381	5.01	0.00	38.74	3.16
5	6	1.484240	ACTCTATGCTCAGAGGCCAAC	59.516	52.381	5.01	0.00	45.36	3.77
6	7	1.871418	ACTCTATGCTCAGAGGCCAA	58.129	50.000	5.01	0.00	45.36	4.52
7	8	1.483827	CAACTCTATGCTCAGAGGCCA	59.516	52.381	5.01	0.00	45.36	5.36
8	9	1.809651	GCAACTCTATGCTCAGAGGCC	60.810	57.143	16.37	0.00	45.36	5.19
9	10	1.580815	GCAACTCTATGCTCAGAGGC	58.419	55.000	16.37	9.27	45.36	4.70
10	11	2.237393	GGCAACTCTATGCTCAGAGG	57.763	55.000	16.37	4.38	45.36	3.69
24	25	3.009723	TGTGCTATGCTAAGAAGGCAAC	58.990	45.455	0.00	0.00	43.14	4.17
25	26	3.009723	GTGTGCTATGCTAAGAAGGCAA	58.990	45.455	0.00	0.00	43.14	4.52
26	27	2.027285	TGTGTGCTATGCTAAGAAGGCA	60.027	45.455	0.00	0.00	44.05	4.75
27	28	2.352960	GTGTGTGCTATGCTAAGAAGGC	59.647	50.000	0.00	0.00	0.00	4.35
28	29	3.372206	GTGTGTGTGCTATGCTAAGAAGG	59.628	47.826	0.00	0.00	0.00	3.46
29	30	3.372206	GGTGTGTGTGCTATGCTAAGAAG	59.628	47.826	0.00	0.00	0.00	2.85
30	31	3.244387	TGGTGTGTGTGCTATGCTAAGAA	60.244	43.478	0.00	0.00	0.00	2.52
31	32	2.301583	TGGTGTGTGTGCTATGCTAAGA	59.698	45.455	0.00	0.00	0.00	2.10
32	33	2.698803	TGGTGTGTGTGCTATGCTAAG	58.301	47.619	0.00	0.00	0.00	2.18
33	34	2.849294	TGGTGTGTGTGCTATGCTAA	57.151	45.000	0.00	0.00	0.00	3.09
34	35	3.704061	TCTATGGTGTGTGTGCTATGCTA	59.296	43.478	0.00	0.00	0.00	3.49
35	36	2.501316	TCTATGGTGTGTGTGCTATGCT	59.499	45.455	0.00	0.00	0.00	3.79
36	37	2.905075	TCTATGGTGTGTGTGCTATGC	58.095	47.619	0.00	0.00	0.00	3.14
37	38	6.015940	TCTCTATCTATGGTGTGTGTGCTATG	60.016	42.308	0.00	0.00	0.00	2.23

Showing 1 to 25 of 1,052 entries

Previous1 2 3 4 5…43Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.