AutoCloner

Multiple sequence alignment - TraesCS3A01G063800

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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	TraesCS3A01G063800	chr3A	100.000	2537	0	0	1	2537	38047218	38044682	0.000000e+00	4686
1	TraesCS3A01G063800	chr3A	90.683	2050	151	12	1	2014	38022072	38020027	0.000000e+00	2691
2	TraesCS3A01G063800	chr3A	87.924	1681	152	23	552	2201	38253303	38251643	0.000000e+00	1932
3	TraesCS3A01G063800	chr3A	89.201	1352	128	9	476	1815	38035802	38034457	0.000000e+00	1672
4	TraesCS3A01G063800	chr3A	85.816	1262	157	15	499	1744	10245080	10246335	0.000000e+00	1319
5	TraesCS3A01G063800	chr3A	85.747	884	95	14	1339	2201	38236382	38235509	0.000000e+00	905
6	TraesCS3A01G063800	chr3A	89.571	652	60	6	1890	2536	38031519	38030871	0.000000e+00	821
7	TraesCS3A01G063800	chr3A	88.956	498	49	5	2041	2536	38020031	38019538	6.000000e-171	610
8	TraesCS3A01G063800	chr3A	90.112	445	41	2	2093	2536	38027181	38026739	2.190000e-160	575
9	TraesCS3A01G063800	chr3A	79.114	316	54	7	1	310	10531813	10531504	9.200000e-50	207
10	TraesCS3A01G063800	chr3B	89.459	2533	214	16	1	2491	46281671	46284192	0.000000e+00	3149
11	TraesCS3A01G063800	chr3B	88.682	1661	140	19	569	2201	47453981	47452341	0.000000e+00	1982
12	TraesCS3A01G063800	chr3B	82.609	161	26	2	149	308	47454404	47454245	9.460000e-30	141
13	TraesCS3A01G063800	chr3D	91.221	1834	140	7	1	1815	27651861	27653692	0.000000e+00	2475
14	TraesCS3A01G063800	chr3D	90.099	1919	165	12	1	1902	28130527	28128617	0.000000e+00	2468
15	TraesCS3A01G063800	chr3D	88.490	2033	159	25	518	2512	27656723	27658718	0.000000e+00	2388
16	TraesCS3A01G063800	chr3D	90.006	1781	149	11	1	1766	28135348	28133582	0.000000e+00	2276
17	TraesCS3A01G063800	chr3D	87.767	1684	149	22	552	2201	28494915	28493255	0.000000e+00	1916
18	TraesCS3A01G063800	chr3D	85.886	1247	147	21	516	1744	4950858	4949623	0.000000e+00	1301
19	TraesCS3A01G063800	chr3D	86.283	1130	95	19	1249	2339	27870005	27871113	0.000000e+00	1173
20	TraesCS3A01G063800	chr3D	79.598	696	98	26	1867	2536	28133572	28132895	2.300000e-125	459
21	TraesCS3A01G063800	chr3D	82.609	161	26	2	149	308	28495321	28495162	9.460000e-30	141
22	TraesCS3A01G063800	chr2B	76.052	309	66	6	5	309	634172005	634172309	1.220000e-33	154

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	TraesCS3A01G063800	chr3A	38044682	38047218	2536	True	4686.000000	4686	100.000000	1	2537	1	chr3A.!!$R2	2536
1	TraesCS3A01G063800	chr3A	38251643	38253303	1660	True	1932.000000	1932	87.924000	552	2201	1	chr3A.!!$R4	1649
2	TraesCS3A01G063800	chr3A	38019538	38022072	2534	True	1650.500000	2691	89.819500	1	2536	2	chr3A.!!$R5	2535
3	TraesCS3A01G063800	chr3A	10245080	10246335	1255	False	1319.000000	1319	85.816000	499	1744	1	chr3A.!!$F1	1245
4	TraesCS3A01G063800	chr3A	38026739	38035802	9063	True	1022.666667	1672	89.628000	476	2536	3	chr3A.!!$R6	2060
5	TraesCS3A01G063800	chr3A	38235509	38236382	873	True	905.000000	905	85.747000	1339	2201	1	chr3A.!!$R3	862
6	TraesCS3A01G063800	chr3B	46281671	46284192	2521	False	3149.000000	3149	89.459000	1	2491	1	chr3B.!!$F1	2490
7	TraesCS3A01G063800	chr3B	47452341	47454404	2063	True	1061.500000	1982	85.645500	149	2201	2	chr3B.!!$R1	2052
8	TraesCS3A01G063800	chr3D	27651861	27658718	6857	False	2431.500000	2475	89.855500	1	2512	2	chr3D.!!$F2	2511
9	TraesCS3A01G063800	chr3D	28128617	28135348	6731	True	1734.333333	2468	86.567667	1	2536	3	chr3D.!!$R2	2535
10	TraesCS3A01G063800	chr3D	4949623	4950858	1235	True	1301.000000	1301	85.886000	516	1744	1	chr3D.!!$R1	1228
11	TraesCS3A01G063800	chr3D	27870005	27871113	1108	False	1173.000000	1173	86.283000	1249	2339	1	chr3D.!!$F1	1090
12	TraesCS3A01G063800	chr3D	28493255	28495321	2066	True	1028.500000	1916	85.188000	149	2201	2	chr3D.!!$R3	2052

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
814	5202	0.256177	GCTCGGGGAAGGAGGATTTT	59.744	55.0	0.0	0.0	32.1	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1654	6053	1.200948	GCTGAAGTGCTCACATTTCCC	59.799	52.381	2.63	0.0	40.73	3.97	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
90	91	2.697761	GCTCGCCTGTACGGTCAGA	61.698	63.158	10.01	0.00	37.61	3.27
165	166	6.312426	GTGTTGATGATTTCTTCGACATCTCT	59.688	38.462	15.60	0.00	42.58	3.10
283	284	2.249413	ATCGCAGTGCCCAAGAGAGG	62.249	60.000	10.11	0.00	0.00	3.69
312	313	0.909623	CGGGAGGGTGTAACAATCCT	59.090	55.000	3.23	3.23	41.31	3.24
324	355	7.336396	GGTGTAACAATCCTTGTATTAGGAGT	58.664	38.462	0.00	0.00	43.20	3.85
421	461	4.097892	ACGATTTTTCCACTTTCACTTGCT	59.902	37.500	0.00	0.00	0.00	3.91
460	500	1.203364	AGGTCATCTTCTGTCCCCTGT	60.203	52.381	0.00	0.00	33.95	4.00
462	502	2.838202	GGTCATCTTCTGTCCCCTGTTA	59.162	50.000	0.00	0.00	0.00	2.41
470	510	5.309543	TCTTCTGTCCCCTGTTAAATCAAGA	59.690	40.000	0.00	0.00	0.00	3.02
501	541	2.747855	GCTGAAAGTCCCCTGCCG	60.748	66.667	0.00	0.00	35.30	5.69
567	607	0.682209	CAGCTATTGGGCCAGCAAGT	60.682	55.000	17.35	1.52	40.36	3.16
637	5019	1.812571	CTGTAGGCGGCTTCATTTTGT	59.187	47.619	19.76	0.00	0.00	2.83
646	5028	3.305267	CGGCTTCATTTTGTTCACCATCA	60.305	43.478	0.00	0.00	0.00	3.07
677	5059	9.330063	CCTCAGCATCTTCTTTATATGTAAACA	57.670	33.333	0.00	0.00	0.00	2.83
701	5083	1.779569	ACACAACGACGGAATGAGAC	58.220	50.000	0.00	0.00	0.00	3.36
725	5113	2.707554	AGAAGAGGAAGAGTTTGGGGT	58.292	47.619	0.00	0.00	0.00	4.95
814	5202	0.256177	GCTCGGGGAAGGAGGATTTT	59.744	55.000	0.00	0.00	32.10	1.82
876	5264	5.009110	TGCAGTAAAATGTTTGGATCGAACA	59.991	36.000	13.54	13.54	41.27	3.18
877	5265	5.918011	GCAGTAAAATGTTTGGATCGAACAA	59.082	36.000	14.72	2.19	40.54	2.83
909	5297	2.154462	AGTGAATTTTCGGCAGAGGTG	58.846	47.619	0.00	0.00	0.00	4.00
975	5363	4.090761	TGGTTTCTGTGCAGAGAAATCT	57.909	40.909	35.65	0.00	41.72	2.40
985	5373	3.070734	TGCAGAGAAATCTCATAGGCTCC	59.929	47.826	12.65	0.00	45.21	4.70
1032	5420	5.146010	GATCCTTGGACAGATGGATCTAC	57.854	47.826	12.11	0.00	46.78	2.59
1058	5446	1.567649	ACATGACAATGATGCCCCTCT	59.432	47.619	0.00	0.00	37.24	3.69
1096	5484	4.550831	CGCGGTGCAAGATTATAACTCAAG	60.551	45.833	0.00	0.00	0.00	3.02
1110	5498	1.834263	ACTCAAGTAGCTAAGGGCCTG	59.166	52.381	6.92	0.00	43.05	4.85
1115	5503	1.834263	AGTAGCTAAGGGCCTGTCTTG	59.166	52.381	6.92	0.00	43.05	3.02
1116	5504	0.541863	TAGCTAAGGGCCTGTCTTGC	59.458	55.000	6.92	4.12	43.05	4.01
1125	5513	0.884704	GCCTGTCTTGCCTTCACGAA	60.885	55.000	0.00	0.00	0.00	3.85
1457	5845	3.764237	AAACAGTGATCGGTTGGTAGT	57.236	42.857	0.00	0.00	32.81	2.73
1522	5910	6.204882	GCAAGATGTGATTCAGATGATGATGA	59.795	38.462	0.29	0.00	37.89	2.92
1582	5981	6.012858	TGTCTCAGGTGGTAAAAGTATTGGAT	60.013	38.462	0.00	0.00	0.00	3.41
1621	6020	6.578023	AGACCTCAACATAGAGCATAACTTC	58.422	40.000	0.00	0.00	34.26	3.01
1653	6052	3.834231	ACTCCAGCAAATTTTGGTAGCAT	59.166	39.130	13.07	0.00	39.79	3.79
1654	6053	4.178540	CTCCAGCAAATTTTGGTAGCATG	58.821	43.478	13.07	1.77	39.79	4.06
1667	6066	2.368439	GTAGCATGGGAAATGTGAGCA	58.632	47.619	0.00	0.00	0.00	4.26
1744	6146	6.151144	ACAATTCTGACAAGGTAGGCAATTAC	59.849	38.462	0.00	0.00	0.00	1.89
1746	6148	5.235850	TCTGACAAGGTAGGCAATTACAA	57.764	39.130	0.00	0.00	0.00	2.41
1793	6198	9.612066	ATGTAAAACAAAATTCATGGTCTGTTT	57.388	25.926	0.00	0.19	38.32	2.83
1836	6249	6.428159	ACAACTCTTGAGTTATGCTAACTTGG	59.572	38.462	14.65	2.58	0.00	3.61
1915	9273	2.972713	TCTTTTGAGCTCCACCTGTAGT	59.027	45.455	12.15	0.00	0.00	2.73
2018	9397	1.568504	AGTAAATGGGCAGTCCGAGA	58.431	50.000	0.00	0.00	38.76	4.04
2019	9398	1.906574	AGTAAATGGGCAGTCCGAGAA	59.093	47.619	0.00	0.00	38.76	2.87
2100	9485	2.796593	GCAGCATGTTCACTTGGTTTTC	59.203	45.455	0.00	0.00	39.31	2.29
2176	9571	7.280356	ACCTATTGTAAGCCGTTATGAGAAAT	58.720	34.615	0.00	0.00	0.00	2.17
2227	13754	2.500229	TGCTCTTTCTTAAACACCCCG	58.500	47.619	0.00	0.00	0.00	5.73
2229	13756	2.551504	GCTCTTTCTTAAACACCCCGGA	60.552	50.000	0.73	0.00	0.00	5.14
2230	13757	3.872630	GCTCTTTCTTAAACACCCCGGAT	60.873	47.826	0.73	0.00	0.00	4.18
2252	13779	9.498307	CGGATATAACCAAAAAGTGTTGATAAC	57.502	33.333	0.00	0.00	0.00	1.89
2295	13827	4.478206	TCCATTGACTGTGAGAGGATTC	57.522	45.455	0.00	0.00	0.00	2.52
2297	13829	5.272402	TCCATTGACTGTGAGAGGATTCTA	58.728	41.667	0.00	0.00	32.53	2.10
2354	13886	4.761739	CCTTGCAAAAATGTGAGTAGGAGA	59.238	41.667	0.00	0.00	0.00	3.71
2367	13899	5.067283	GTGAGTAGGAGAAGGAACTCAGATC	59.933	48.000	4.37	0.00	46.54	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
90	91	1.736645	CGTGTTTGGCGATCGACCT	60.737	57.895	20.39	0.00	0.00	3.85
245	246	1.330234	TGTGATGTTGGCTGCACAAT	58.670	45.000	0.50	0.00	38.21	2.71
283	284	3.787001	CCCTCCCGGAGCCTTCAC	61.787	72.222	9.17	0.00	0.00	3.18
312	313	3.267483	GCTTTCCGCACTCCTAATACAA	58.733	45.455	0.00	0.00	38.92	2.41
421	461	2.338015	GGTAGTCTGTGCCCGTCGA	61.338	63.158	0.00	0.00	0.00	4.20
460	500	9.905713	AGCTGTAGGTGATATTTCTTGATTTAA	57.094	29.630	0.00	0.00	0.00	1.52
462	502	8.049117	TCAGCTGTAGGTGATATTTCTTGATTT	58.951	33.333	14.67	0.00	46.24	2.17
513	553	1.192428	GGGTCGGAGGTGTTACATCT	58.808	55.000	0.00	0.00	0.00	2.90
567	607	4.191544	CAGAGGCAGATTTCGGTTTCATA	58.808	43.478	0.00	0.00	0.00	2.15
595	635	4.938226	AGGAGCTAGAATTGCAACAACTAC	59.062	41.667	0.00	0.00	0.00	2.73
637	5019	2.040145	TGCTGAGGAACATGATGGTGAA	59.960	45.455	0.00	0.00	0.00	3.18
646	5028	8.216423	ACATATAAAGAAGATGCTGAGGAACAT	58.784	33.333	0.00	0.00	0.00	2.71
677	5059	3.199677	TCATTCCGTCGTTGTGTTCTTT	58.800	40.909	0.00	0.00	0.00	2.52
701	5083	3.330267	CCAAACTCTTCCTCTTCTTCCG	58.670	50.000	0.00	0.00	0.00	4.30
725	5113	3.411446	CTCATTGGTGTTCCTTGTAGCA	58.589	45.455	0.00	0.00	34.23	3.49
814	5202	3.374042	TTGTCCCTTGAAAACAGACCA	57.626	42.857	0.00	0.00	0.00	4.02
876	5264	5.357742	AAAATTCACTTTTGCCCTGACTT	57.642	34.783	0.00	0.00	35.71	3.01
877	5265	4.499696	CGAAAATTCACTTTTGCCCTGACT	60.500	41.667	0.00	0.00	37.18	3.41
909	5297	1.067425	TGAATGCTGCCAATTGTCTGC	60.067	47.619	10.94	10.94	0.00	4.26
975	5363	5.276694	ACTCATATACCAGGAGCCTATGA	57.723	43.478	0.00	0.00	38.68	2.15
985	5373	4.890158	TGGGCATGTACTCATATACCAG	57.110	45.455	0.00	0.00	31.51	4.00
1058	5446	1.083489	CCGCGTGCTCCAATCTAAAA	58.917	50.000	4.92	0.00	0.00	1.52
1096	5484	1.744114	GCAAGACAGGCCCTTAGCTAC	60.744	57.143	0.00	0.00	43.05	3.58
1110	5498	1.795286	CACTCTTCGTGAAGGCAAGAC	59.205	52.381	9.58	0.00	46.81	3.01
1115	5503	0.880278	TGTGCACTCTTCGTGAAGGC	60.880	55.000	19.41	6.16	46.81	4.35
1116	5504	1.581934	TTGTGCACTCTTCGTGAAGG	58.418	50.000	19.41	3.70	46.81	3.46
1125	5513	4.098349	TGAGCAATTCTTTTTGTGCACTCT	59.902	37.500	19.41	0.00	39.50	3.24
1457	5845	6.416455	GTCGTTGCTGTTATTGTCAATCAAAA	59.584	34.615	0.07	0.00	39.62	2.44
1506	5894	5.048713	TGCAAGCATCATCATCATCTGAATC	60.049	40.000	0.00	0.00	37.44	2.52
1562	5961	5.125417	CACCATCCAATACTTTTACCACCTG	59.875	44.000	0.00	0.00	0.00	4.00
1582	5981	0.613260	GGTCTACAGTCATGGCACCA	59.387	55.000	0.00	0.00	0.00	4.17
1621	6020	3.684103	TTTGCTGGAGTTGTTACAACG	57.316	42.857	20.52	9.11	0.00	4.10
1653	6052	2.507484	CTGAAGTGCTCACATTTCCCA	58.493	47.619	2.63	0.00	40.73	4.37
1654	6053	1.200948	GCTGAAGTGCTCACATTTCCC	59.799	52.381	2.63	0.00	40.73	3.97
1667	6066	1.893786	CTAGAGGTGGCGCTGAAGT	59.106	57.895	7.64	0.00	0.00	3.01
1833	6246	9.066892	GGTTTGCAATACTGAGATATTATCCAA	57.933	33.333	0.00	0.00	0.00	3.53
1915	9273	4.334552	TGATAGCTCAAACCAGATTTGCA	58.665	39.130	0.00	0.00	46.32	4.08
2100	9485	8.184192	GGAAATCAAACTGTACCTAATGTCATG	58.816	37.037	0.00	0.00	0.00	3.07
2141	9534	5.246307	GGCTTACAATAGGTTTGAGTCACT	58.754	41.667	0.00	0.00	0.00	3.41
2145	9538	4.281898	ACGGCTTACAATAGGTTTGAGT	57.718	40.909	0.00	0.00	0.00	3.41
2203	13730	5.508994	CGGGGTGTTTAAGAAAGAGCAAAAT	60.509	40.000	1.51	0.00	34.24	1.82
2252	13779	6.261603	TGGAAGCAAGCATAACATCTCATAAG	59.738	38.462	0.00	0.00	0.00	1.73
2254	13781	5.683681	TGGAAGCAAGCATAACATCTCATA	58.316	37.500	0.00	0.00	0.00	2.15
2267	13795	1.881973	TCACAGTCAATGGAAGCAAGC	59.118	47.619	0.00	0.00	0.00	4.01
2331	13863	4.761739	TCTCCTACTCACATTTTTGCAAGG	59.238	41.667	0.00	0.00	0.00	3.61
2354	13886	6.410540	AGCTAAATTTCGATCTGAGTTCCTT	58.589	36.000	0.00	0.00	0.00	3.36
2367	13899	6.695292	ATGAACTTTGCAAGCTAAATTTCG	57.305	33.333	0.00	0.00	32.56	3.46
2449	13985	6.943146	TCCATGTTGCACTGTTACCTTAATTA	59.057	34.615	0.00	0.00	0.00	1.40
2459	13995	2.485426	CGAAGATCCATGTTGCACTGTT	59.515	45.455	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.