AutoCloner

Multiple sequence alignment - TraesCS7A01G477000

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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	TraesCS7A01G477000	chr7A	100.000	2906	0	0	1	2906	670890692	670887787	0.000000e+00	5367
1	TraesCS7A01G477000	chr7A	97.297	1073	29	0	837	1909	626956485	626957557	0.000000e+00	1821
2	TraesCS7A01G477000	chr7A	93.103	841	48	7	1	836	609375604	609374769	0.000000e+00	1223
3	TraesCS7A01G477000	chr7A	87.035	779	82	10	1959	2730	626928313	626929079	0.000000e+00	861
4	TraesCS7A01G477000	chr7A	78.401	838	139	24	1931	2764	670917888	670917089	9.290000e-140	507
5	TraesCS7A01G477000	chr7A	94.681	188	7	2	2715	2902	626937993	626938177	3.660000e-74	289
6	TraesCS7A01G477000	chr7B	97.390	1073	28	0	837	1909	643127880	643126808	0.000000e+00	1827
7	TraesCS7A01G477000	chr7B	89.349	845	57	10	1912	2749	643122477	643121659	0.000000e+00	1031
8	TraesCS7A01G477000	chr7B	78.640	838	145	21	1931	2764	643501272	643502079	2.570000e-145	525
9	TraesCS7A01G477000	chr7B	96.386	166	3	3	2741	2906	643119409	643119247	1.330000e-68	270
10	TraesCS7A01G477000	chr7B	88.235	119	11	1	2766	2884	643199836	643199721	3.900000e-29	139
11	TraesCS7A01G477000	chr7B	89.623	106	8	1	2766	2871	643200207	643200105	6.530000e-27	132
12	TraesCS7A01G477000	chr5A	97.024	840	18	4	1	836	601210720	601209884	0.000000e+00	1406
13	TraesCS7A01G477000	chr4A	95.169	828	30	7	1	823	616833782	616834604	0.000000e+00	1299
14	TraesCS7A01G477000	chr7D	90.261	996	76	7	1912	2906	579050503	579049528	0.000000e+00	1282
15	TraesCS7A01G477000	chr7D	79.556	856	136	26	1915	2764	579093017	579092195	2.510000e-160	575
16	TraesCS7A01G477000	chr7D	90.566	106	7	1	2766	2871	579092162	579092060	1.400000e-28	137
17	TraesCS7A01G477000	chr3A	94.174	841	42	4	1	837	80513566	80514403	0.000000e+00	1275
18	TraesCS7A01G477000	chr6D	93.750	832	36	10	1	823	41249479	41250303	0.000000e+00	1234
19	TraesCS7A01G477000	chr6D	93.136	845	43	8	1	836	126418466	126417628	0.000000e+00	1225
20	TraesCS7A01G477000	chr6D	92.663	845	44	12	1	836	46867823	46868658	0.000000e+00	1201
21	TraesCS7A01G477000	chr6D	82.994	1082	158	20	839	1907	395370786	395369718	0.000000e+00	955
22	TraesCS7A01G477000	chr1D	93.630	832	38	9	1	823	491937792	491938617	0.000000e+00	1229
23	TraesCS7A01G477000	chr3D	93.269	832	39	11	1	823	11407976	11408799	0.000000e+00	1210
24	TraesCS7A01G477000	chr3D	77.613	1014	205	20	880	1882	26019260	26018258	1.930000e-166	595
25	TraesCS7A01G477000	chr3D	77.483	1017	205	23	878	1882	26073759	26074763	3.230000e-164	588
26	TraesCS7A01G477000	chr2A	83.426	1080	157	18	839	1907	19125382	19126450	0.000000e+00	983
27	TraesCS7A01G477000	chr2D	83.427	1068	161	12	839	1897	17830744	17831804	0.000000e+00	977
28	TraesCS7A01G477000	chr2D	83.005	1065	162	15	839	1892	17955356	17956412	0.000000e+00	946
29	TraesCS7A01G477000	chr3B	76.862	1007	217	16	880	1878	74177094	74178092	3.270000e-154	555

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	TraesCS7A01G477000	chr7A	670887787	670890692	2905	True	5367.0	5367	100.0000	1	2906	1	chr7A.!!$R2	2905
1	TraesCS7A01G477000	chr7A	626956485	626957557	1072	False	1821.0	1821	97.2970	837	1909	1	chr7A.!!$F3	1072
2	TraesCS7A01G477000	chr7A	609374769	609375604	835	True	1223.0	1223	93.1030	1	836	1	chr7A.!!$R1	835
3	TraesCS7A01G477000	chr7A	626928313	626929079	766	False	861.0	861	87.0350	1959	2730	1	chr7A.!!$F1	771
4	TraesCS7A01G477000	chr7A	670917089	670917888	799	True	507.0	507	78.4010	1931	2764	1	chr7A.!!$R3	833
5	TraesCS7A01G477000	chr7B	643126808	643127880	1072	True	1827.0	1827	97.3900	837	1909	1	chr7B.!!$R1	1072
6	TraesCS7A01G477000	chr7B	643119247	643122477	3230	True	650.5	1031	92.8675	1912	2906	2	chr7B.!!$R2	994
7	TraesCS7A01G477000	chr7B	643501272	643502079	807	False	525.0	525	78.6400	1931	2764	1	chr7B.!!$F1	833
8	TraesCS7A01G477000	chr5A	601209884	601210720	836	True	1406.0	1406	97.0240	1	836	1	chr5A.!!$R1	835
9	TraesCS7A01G477000	chr4A	616833782	616834604	822	False	1299.0	1299	95.1690	1	823	1	chr4A.!!$F1	822
10	TraesCS7A01G477000	chr7D	579049528	579050503	975	True	1282.0	1282	90.2610	1912	2906	1	chr7D.!!$R1	994
11	TraesCS7A01G477000	chr7D	579092060	579093017	957	True	356.0	575	85.0610	1915	2871	2	chr7D.!!$R2	956
12	TraesCS7A01G477000	chr3A	80513566	80514403	837	False	1275.0	1275	94.1740	1	837	1	chr3A.!!$F1	836
13	TraesCS7A01G477000	chr6D	41249479	41250303	824	False	1234.0	1234	93.7500	1	823	1	chr6D.!!$F1	822
14	TraesCS7A01G477000	chr6D	126417628	126418466	838	True	1225.0	1225	93.1360	1	836	1	chr6D.!!$R1	835
15	TraesCS7A01G477000	chr6D	46867823	46868658	835	False	1201.0	1201	92.6630	1	836	1	chr6D.!!$F2	835
16	TraesCS7A01G477000	chr6D	395369718	395370786	1068	True	955.0	955	82.9940	839	1907	1	chr6D.!!$R2	1068
17	TraesCS7A01G477000	chr1D	491937792	491938617	825	False	1229.0	1229	93.6300	1	823	1	chr1D.!!$F1	822
18	TraesCS7A01G477000	chr3D	11407976	11408799	823	False	1210.0	1210	93.2690	1	823	1	chr3D.!!$F1	822
19	TraesCS7A01G477000	chr3D	26018258	26019260	1002	True	595.0	595	77.6130	880	1882	1	chr3D.!!$R1	1002
20	TraesCS7A01G477000	chr3D	26073759	26074763	1004	False	588.0	588	77.4830	878	1882	1	chr3D.!!$F2	1004
21	TraesCS7A01G477000	chr2A	19125382	19126450	1068	False	983.0	983	83.4260	839	1907	1	chr2A.!!$F1	1068
22	TraesCS7A01G477000	chr2D	17830744	17831804	1060	False	977.0	977	83.4270	839	1897	1	chr2D.!!$F1	1058
23	TraesCS7A01G477000	chr2D	17955356	17956412	1056	False	946.0	946	83.0050	839	1892	1	chr2D.!!$F2	1053
24	TraesCS7A01G477000	chr3B	74177094	74178092	998	False	555.0	555	76.8620	880	1878	1	chr3B.!!$F1	998

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
253	258	1.745489	GCCCAGTGTGTTCGGATCC	60.745	63.158	0.00	0.00	0.0	3.36	F
1056	1067	1.552337	GCTCTCCCTTCAGTGATCACA	59.448	52.381	27.02	5.13	0.0	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1087	1098	0.112218	TACTTGTGGGCAGCACCATT	59.888	50.0	5.96	0.00	43.59	3.16	R
2379	2411	0.252197	TGATCTCTGTCGGACTCGGA	59.748	55.0	9.88	5.04	36.95	4.55	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
25	26	1.915141	CTGAGGGACAGGCAAAATGT	58.085	50.000	0.00	0.00	42.39	2.71
27	28	1.962807	TGAGGGACAGGCAAAATGTTG	59.037	47.619	0.00	0.00	37.83	3.33
251	256	2.047274	CGCCCAGTGTGTTCGGAT	60.047	61.111	0.00	0.00	0.00	4.18
252	257	2.100631	CGCCCAGTGTGTTCGGATC	61.101	63.158	0.00	0.00	0.00	3.36
253	258	1.745489	GCCCAGTGTGTTCGGATCC	60.745	63.158	0.00	0.00	0.00	3.36
331	337	5.018374	AGGGCCCAAGGTTAAAGAATTTA	57.982	39.130	27.56	0.00	40.09	1.40
489	495	4.903149	TCAAGGGGGAGAATGTTAGGATA	58.097	43.478	0.00	0.00	0.00	2.59
602	608	6.040955	CCTGTCACCTGCACTATATAAAGAGA	59.959	42.308	0.00	0.00	0.00	3.10
654	660	4.467084	CAGCGCCGTACACCCCAT	62.467	66.667	2.29	0.00	0.00	4.00
682	689	3.842206	CCCTACCGATCTAGGGTTAGTT	58.158	50.000	15.95	0.00	45.94	2.24
794	805	8.120084	CCACAAGGAAAGGTAATACCTATCACC	61.120	44.444	13.03	12.81	42.87	4.02
862	873	4.223032	TCCTCTACACTTCCAAATCCACTC	59.777	45.833	0.00	0.00	0.00	3.51
1056	1067	1.552337	GCTCTCCCTTCAGTGATCACA	59.448	52.381	27.02	5.13	0.00	3.58
1087	1098	2.092753	GTGAGGCCCATCTTTGATGAGA	60.093	50.000	0.00	0.00	0.00	3.27
1097	1108	2.751259	TCTTTGATGAGAATGGTGCTGC	59.249	45.455	0.00	0.00	0.00	5.25
1149	1160	4.814234	GGAATGCACGATGGTTATAACTCA	59.186	41.667	15.05	11.46	0.00	3.41
1408	1422	3.092301	GCTTTTGATCTTAGTGGGCCTT	58.908	45.455	4.53	0.00	0.00	4.35
1504	1518	1.952296	GGGGTGATCTGCTGCTTATTG	59.048	52.381	0.00	0.00	0.00	1.90
1767	1781	4.576463	ACGGGATTGAAGAATAATCACTGC	59.424	41.667	0.00	0.00	36.13	4.40
1909	1923	5.542779	CATCAGTAGGGGTAGCTTGAATAC	58.457	45.833	0.00	0.00	0.00	1.89
1910	1924	4.880164	TCAGTAGGGGTAGCTTGAATACT	58.120	43.478	0.00	0.00	0.00	2.12
2030	2044	2.225017	GGGTTTGGTCTTTGGATCCTCA	60.225	50.000	14.23	0.00	0.00	3.86
2032	2046	3.255888	GGTTTGGTCTTTGGATCCTCAAC	59.744	47.826	14.23	5.99	0.00	3.18
2037	2051	2.489722	GTCTTTGGATCCTCAACAAGCC	59.510	50.000	14.23	0.00	0.00	4.35
2042	2056	1.556911	GGATCCTCAACAAGCCTCAGA	59.443	52.381	3.84	0.00	0.00	3.27
2047	2061	2.600731	CTCAACAAGCCTCAGACTACG	58.399	52.381	0.00	0.00	0.00	3.51
2050	2064	1.853963	ACAAGCCTCAGACTACGGAT	58.146	50.000	0.00	0.00	0.00	4.18
2059	2073	1.410517	CAGACTACGGATGGCAGACAT	59.589	52.381	0.00	0.00	44.18	3.06
2063	2077	1.000955	CTACGGATGGCAGACATACCC	59.999	57.143	0.00	0.00	40.72	3.69
2134	2161	9.231297	CCTCTCTTGGTCAATTTACTGAAATAA	57.769	33.333	0.00	0.00	34.01	1.40
2249	2281	7.112452	TGCACAAGAGTTAGAGAAGCATATA	57.888	36.000	0.00	0.00	0.00	0.86
2337	2369	6.433716	TGTGTTGCATCTTCTTGGATTGAATA	59.566	34.615	0.00	0.00	0.00	1.75
2378	2410	2.541055	GACTTAAGGTCGTCCGAGAC	57.459	55.000	7.53	0.00	40.25	3.36
2379	2411	2.083002	GACTTAAGGTCGTCCGAGACT	58.917	52.381	7.53	0.00	40.76	3.24
2380	2412	2.083002	ACTTAAGGTCGTCCGAGACTC	58.917	52.381	7.53	0.00	40.76	3.36
2381	2413	1.401199	CTTAAGGTCGTCCGAGACTCC	59.599	57.143	0.00	6.40	40.76	3.85
2382	2414	0.742281	TAAGGTCGTCCGAGACTCCG	60.742	60.000	0.00	0.00	40.76	4.63
2716	2756	3.155998	CGAAAATGTGCGACATCTTCAC	58.844	45.455	12.62	0.00	35.78	3.18
2720	2760	1.080093	GTGCGACATCTTCACGGGA	60.080	57.895	0.00	0.00	0.00	5.14
2782	5111	8.264347	TGGTAAGTGAGATGCAACAAGAATATA	58.736	33.333	0.00	0.00	0.00	0.86
2783	5112	8.768955	GGTAAGTGAGATGCAACAAGAATATAG	58.231	37.037	0.00	0.00	0.00	1.31
2784	5113	9.319143	GTAAGTGAGATGCAACAAGAATATAGT	57.681	33.333	0.00	0.00	0.00	2.12
2865	5194	7.941919	TGTGCCGTTTATATGCCAATTATAAA	58.058	30.769	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	0.907704	ACTCCGGGTACAGGCATCAA	60.908	55.000	0.00	0.00	45.49	2.57
27	28	0.462047	CAACTCCGGGTACAGGCATC	60.462	60.000	0.00	0.00	45.49	3.91
251	256	0.671796	ATGTCGACTGTGTGTTCGGA	59.328	50.000	17.92	0.00	0.00	4.55
252	257	0.784178	CATGTCGACTGTGTGTTCGG	59.216	55.000	17.92	0.00	0.00	4.30
253	258	0.784178	CCATGTCGACTGTGTGTTCG	59.216	55.000	17.92	0.00	0.00	3.95
331	337	5.820947	ACAACGTACCTCTCTGTTTTGAAAT	59.179	36.000	0.00	0.00	0.00	2.17
654	660	4.587976	CCTAGATCGGTAGGGGATTAGA	57.412	50.000	0.00	0.00	36.63	2.10
682	689	2.068915	TGCTTCCCATCAGCACTGA	58.931	52.632	2.25	2.25	42.49	3.41
862	873	2.447887	GGCATGCGACACTCTCACG	61.448	63.158	12.44	0.00	0.00	4.35
1056	1067	1.000396	GGGCCTCACCTGCTCAATT	60.000	57.895	0.84	0.00	39.10	2.32
1087	1098	0.112218	TACTTGTGGGCAGCACCATT	59.888	50.000	5.96	0.00	43.59	3.16
1097	1108	4.194640	CCATGAGAGTTCATACTTGTGGG	58.805	47.826	0.00	0.00	42.12	4.61
1149	1160	4.401022	TGTCAAGAGCAAAGATTGATGGT	58.599	39.130	0.00	0.00	35.56	3.55
1408	1422	6.878923	CCCATAATTATCTTCATACTGGCGAA	59.121	38.462	0.00	0.00	0.00	4.70
1504	1518	5.324832	TCATAATCCCCAAAGATTCTCCC	57.675	43.478	0.00	0.00	37.62	4.30
1595	1609	4.717279	TCCTTAAGTTTACTTGCCACCT	57.283	40.909	5.41	0.00	37.40	4.00
1695	1709	5.171339	AGTAGACATGATTTGCCTTGAGT	57.829	39.130	0.00	0.00	0.00	3.41
1767	1781	2.586258	AATCGAGAACTCCCATGTCG	57.414	50.000	0.00	0.00	35.16	4.35
2030	2044	1.629043	TCCGTAGTCTGAGGCTTGTT	58.371	50.000	0.00	0.00	0.00	2.83
2032	2046	1.202463	CCATCCGTAGTCTGAGGCTTG	60.202	57.143	0.00	0.00	0.00	4.01
2037	2051	1.066303	GTCTGCCATCCGTAGTCTGAG	59.934	57.143	0.00	0.00	0.00	3.35
2042	2056	1.687123	GGTATGTCTGCCATCCGTAGT	59.313	52.381	0.00	0.00	34.86	2.73
2047	2061	1.071471	CCGGGTATGTCTGCCATCC	59.929	63.158	0.00	0.00	34.86	3.51
2050	2064	1.195442	TTGTCCGGGTATGTCTGCCA	61.195	55.000	0.00	0.00	0.00	4.92
2059	2073	1.919816	GAAGGGGGTTGTCCGGGTA	60.920	63.158	0.00	0.00	36.01	3.69
2063	2077	4.016706	AGCGAAGGGGGTTGTCCG	62.017	66.667	0.00	0.00	36.01	4.79
2249	2281	5.437060	TCCAAAGCAAAGAAGTCAGTAACT	58.563	37.500	0.00	0.00	41.10	2.24
2337	2369	7.588169	AGTCTCCTTATAACACTACAGATCCT	58.412	38.462	0.00	0.00	0.00	3.24
2355	2387	1.004044	TCGGACGACCTTAAGTCTCCT	59.996	52.381	1.72	0.00	43.91	3.69
2375	2407	0.391927	CTCTGTCGGACTCGGAGTCT	60.392	60.000	30.92	2.91	44.46	3.24
2376	2408	0.391395	TCTCTGTCGGACTCGGAGTC	60.391	60.000	26.28	26.28	44.32	3.36
2377	2409	0.253610	ATCTCTGTCGGACTCGGAGT	59.746	55.000	11.09	11.09	38.84	3.85
2378	2410	0.941542	GATCTCTGTCGGACTCGGAG	59.058	60.000	9.88	13.12	39.03	4.63
2379	2411	0.252197	TGATCTCTGTCGGACTCGGA	59.748	55.000	9.88	5.04	36.95	4.55
2380	2412	1.001924	CATGATCTCTGTCGGACTCGG	60.002	57.143	9.88	0.34	36.95	4.63
2381	2413	1.001924	CCATGATCTCTGTCGGACTCG	60.002	57.143	9.88	0.88	37.82	4.18
2382	2414	1.339610	CCCATGATCTCTGTCGGACTC	59.660	57.143	9.88	0.00	0.00	3.36
2578	2618	1.802136	GCTCGTGATCCTCTGCTTCAG	60.802	57.143	0.00	0.00	0.00	3.02
2702	2742	0.460284	ATCCCGTGAAGATGTCGCAC	60.460	55.000	0.00	0.00	36.47	5.34
2720	2760	8.650143	AAACATTACATTTCACAGAAGGGTAT	57.350	30.769	0.00	0.00	0.00	2.73
2788	5117	6.931838	ACATGAAAATCAATGACAGCTTGAT	58.068	32.000	0.00	0.00	43.42	2.57
2865	5194	7.973402	TGGATATATACATGTACAGCCAAACT	58.027	34.615	7.96	0.00	0.00	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.