AutoCloner

Multiple sequence alignment - TraesCS2D01G432200

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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	TraesCS2D01G432200	chr2D	100.000	2399	0	0	1	2399	544609580	544611978	0.000000e+00	4431.0
1	TraesCS2D01G432200	chr2B	87.960	1819	124	39	639	2399	650164300	650166081	0.000000e+00	2058.0
2	TraesCS2D01G432200	chr2B	96.719	640	13	8	1	634	543170611	543169974	0.000000e+00	1059.0
3	TraesCS2D01G432200	chr2A	90.167	1617	103	22	818	2399	686839154	686840749	0.000000e+00	2054.0
4	TraesCS2D01G432200	chr5D	97.653	639	8	7	1	633	450114509	450115146	0.000000e+00	1090.0
5	TraesCS2D01G432200	chr5D	97.344	640	9	8	1	633	89496400	89495762	0.000000e+00	1081.0
6	TraesCS2D01G432200	chr5D	97.188	640	11	7	1	634	562046775	562047413	0.000000e+00	1075.0
7	TraesCS2D01G432200	chr5D	96.130	646	16	9	1	638	447766219	447766863	0.000000e+00	1046.0
8	TraesCS2D01G432200	chr7D	96.594	646	13	9	1	638	558170616	558171260	0.000000e+00	1062.0
9	TraesCS2D01G432200	chr7D	96.557	639	12	10	1	632	614556928	614556293	0.000000e+00	1050.0
10	TraesCS2D01G432200	chr6D	96.285	646	14	9	1	639	99230002	99230644	0.000000e+00	1051.0
11	TraesCS2D01G432200	chr6D	77.465	426	63	21	1006	1418	363063888	363064293	8.630000e-55	224.0
12	TraesCS2D01G432200	chr6B	95.994	649	14	11	1	639	675225713	675225067	0.000000e+00	1044.0
13	TraesCS2D01G432200	chr6B	93.913	115	3	3	989	1099	545253413	545253527	1.140000e-38	171.0
14	TraesCS2D01G432200	chr4A	77.751	418	53	22	999	1408	5552539	5552154	1.120000e-53	220.0
15	TraesCS2D01G432200	chr4A	96.875	32	0	1	1258	1288	612083050	612083019	4.000000e-03	52.8
16	TraesCS2D01G432200	chr4B	76.794	418	60	21	999	1408	581068919	581069307	1.450000e-47	200.0
17	TraesCS2D01G432200	chr4D	76.214	412	50	25	999	1408	464660539	464660904	8.820000e-40	174.0
18	TraesCS2D01G432200	chr6A	96.117	103	4	0	996	1098	503769181	503769283	4.100000e-38	169.0
19	TraesCS2D01G432200	chr1A	96.970	33	0	1	1262	1294	587362037	587362006	1.000000e-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	TraesCS2D01G432200	chr2D	544609580	544611978	2398	False	4431	4431	100.000	1	2399	1	chr2D.!!$F1	2398
1	TraesCS2D01G432200	chr2B	650164300	650166081	1781	False	2058	2058	87.960	639	2399	1	chr2B.!!$F1	1760
2	TraesCS2D01G432200	chr2B	543169974	543170611	637	True	1059	1059	96.719	1	634	1	chr2B.!!$R1	633
3	TraesCS2D01G432200	chr2A	686839154	686840749	1595	False	2054	2054	90.167	818	2399	1	chr2A.!!$F1	1581
4	TraesCS2D01G432200	chr5D	450114509	450115146	637	False	1090	1090	97.653	1	633	1	chr5D.!!$F2	632
5	TraesCS2D01G432200	chr5D	89495762	89496400	638	True	1081	1081	97.344	1	633	1	chr5D.!!$R1	632
6	TraesCS2D01G432200	chr5D	562046775	562047413	638	False	1075	1075	97.188	1	634	1	chr5D.!!$F3	633
7	TraesCS2D01G432200	chr5D	447766219	447766863	644	False	1046	1046	96.130	1	638	1	chr5D.!!$F1	637
8	TraesCS2D01G432200	chr7D	558170616	558171260	644	False	1062	1062	96.594	1	638	1	chr7D.!!$F1	637
9	TraesCS2D01G432200	chr7D	614556293	614556928	635	True	1050	1050	96.557	1	632	1	chr7D.!!$R1	631
10	TraesCS2D01G432200	chr6D	99230002	99230644	642	False	1051	1051	96.285	1	639	1	chr6D.!!$F1	638
11	TraesCS2D01G432200	chr6B	675225067	675225713	646	True	1044	1044	95.994	1	639	1	chr6B.!!$R1	638

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
776	789	0.321475	AACTTGCTGCTGCCTCTCTC	60.321	55.0	13.47	0.0	38.71	3.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1815	1872	0.537653	TATCGGGCGGTTGTGATTGA	59.462	50.0	0.0	0.0	0.0	2.57	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
657	670	2.866762	GCAAGAAGATAGCCGTCGAAAT	59.133	45.455	0.00	0.00	0.00	2.17
659	672	4.112634	CAAGAAGATAGCCGTCGAAATCA	58.887	43.478	0.00	0.00	0.00	2.57
660	673	4.592485	AGAAGATAGCCGTCGAAATCAT	57.408	40.909	0.00	0.00	0.00	2.45
661	674	5.707242	AGAAGATAGCCGTCGAAATCATA	57.293	39.130	0.00	0.00	0.00	2.15
662	675	5.462405	AGAAGATAGCCGTCGAAATCATAC	58.538	41.667	0.00	0.00	0.00	2.39
663	676	5.241949	AGAAGATAGCCGTCGAAATCATACT	59.758	40.000	0.00	0.00	0.00	2.12
664	677	5.049398	AGATAGCCGTCGAAATCATACTC	57.951	43.478	0.00	0.00	0.00	2.59
667	680	1.767289	CCGTCGAAATCATACTCCCG	58.233	55.000	0.00	0.00	0.00	5.14
689	702	1.956170	CACGAGCGCTTGACCAACT	60.956	57.895	31.19	4.34	0.00	3.16
690	703	1.664965	ACGAGCGCTTGACCAACTC	60.665	57.895	31.19	4.41	0.00	3.01
698	711	1.814248	GCTTGACCAACTCTCCCGTTT	60.814	52.381	0.00	0.00	0.00	3.60
712	725	8.631480	ACTCTCCCGTTTTAAATTATTTGACT	57.369	30.769	0.00	0.00	0.00	3.41
713	726	9.074576	ACTCTCCCGTTTTAAATTATTTGACTT	57.925	29.630	0.00	0.00	0.00	3.01
755	768	1.525077	GCGGACCAGTCAAACACCA	60.525	57.895	0.00	0.00	0.00	4.17
763	776	2.529151	CAGTCAAACACCACAACTTGC	58.471	47.619	0.00	0.00	0.00	4.01
765	778	2.164219	AGTCAAACACCACAACTTGCTG	59.836	45.455	0.00	0.00	0.00	4.41
776	789	0.321475	AACTTGCTGCTGCCTCTCTC	60.321	55.000	13.47	0.00	38.71	3.20
778	791	2.181445	CTTGCTGCTGCCTCTCTCCA	62.181	60.000	13.47	0.00	38.71	3.86
786	799	0.619832	TGCCTCTCTCCATTCAGCCT	60.620	55.000	0.00	0.00	0.00	4.58
805	818	2.028020	CCTCTACCACCAACCTGAGAAC	60.028	54.545	0.00	0.00	0.00	3.01
807	820	3.248024	TCTACCACCAACCTGAGAACAT	58.752	45.455	0.00	0.00	0.00	2.71
847	860	4.199310	TCAGTCCCAGTCTTTGTTTTCTG	58.801	43.478	0.00	0.00	0.00	3.02
871	884	5.126699	TCCTATATAAACGCCCCCAAAAA	57.873	39.130	0.00	0.00	0.00	1.94
929	946	6.360370	TGTGACTAGAGCATACTCCTTTTT	57.640	37.500	0.00	0.00	44.65	1.94
936	953	1.401905	GCATACTCCTTTTTGGCGAGG	59.598	52.381	0.00	0.00	35.26	4.63
939	959	0.602905	ACTCCTTTTTGGCGAGGACG	60.603	55.000	0.00	0.00	37.15	4.79
958	978	2.288213	ACGAGTCGTCAGCAAATCAAGA	60.288	45.455	13.56	0.00	33.69	3.02
964	984	4.024893	GTCGTCAGCAAATCAAGAACAGAA	60.025	41.667	0.00	0.00	0.00	3.02
1003	1023	1.554617	TCCGTCAAGCAAGATCCATGA	59.445	47.619	0.00	0.00	0.00	3.07
1221	1241	3.361158	CGTTTCATGCCCGCCACA	61.361	61.111	0.00	0.00	0.00	4.17
1479	1503	3.636764	TGCTCTGTACTTCTGTCTGTTCA	59.363	43.478	0.00	0.00	0.00	3.18
1490	1514	5.236655	TCTGTCTGTTCAGTCTATTAGCG	57.763	43.478	0.00	0.00	36.85	4.26
1529	1559	8.465273	AATTGCAAATATAAGGAACTACTCCC	57.535	34.615	1.71	0.00	46.81	4.30
1535	1565	1.885163	AAGGAACTACTCCCGCCACG	61.885	60.000	0.00	0.00	46.81	4.94
1574	1610	1.461127	CGCTCCTGTCACAGCTTTTAC	59.539	52.381	0.00	0.00	33.09	2.01
1609	1651	4.061357	TCGGTTATTGTATGCGGATGAA	57.939	40.909	0.00	0.00	0.00	2.57
1633	1675	3.206150	GGTTGTATGCATCTCCGATGTT	58.794	45.455	0.19	0.00	0.00	2.71
1673	1715	8.735692	AAAGCTTCCATTCATGAAAAGAAAAA	57.264	26.923	18.38	5.96	0.00	1.94
1757	1812	1.438651	TTGAAAAGCGGTGATCCTCG	58.561	50.000	0.00	0.00	0.00	4.63
1842	1899	4.281435	TCACAACCGCCCGATAATAGAATA	59.719	41.667	0.00	0.00	0.00	1.75
1870	1936	5.694910	ACCAAACCGATTGATATATCACGTC	59.305	40.000	15.10	14.20	41.85	4.34
1897	1963	1.555075	TCTCCCAACATCCAGTAGCAC	59.445	52.381	0.00	0.00	0.00	4.40
1914	1980	5.768662	AGTAGCACTAGATAGCACGGATTTA	59.231	40.000	0.00	0.00	0.00	1.40
1970	2050	9.477484	AGAGTTGTTGTCTGTAGTAAAATGTAG	57.523	33.333	0.00	0.00	0.00	2.74
2064	2147	8.370493	TGCTGATCATAGATTAAAAGCTACAC	57.630	34.615	0.00	0.00	28.54	2.90
2165	2248	4.150897	ACACCACTTCTTACTTCTTGCA	57.849	40.909	0.00	0.00	0.00	4.08
2210	2293	7.676004	TGAGTACAACACCATGATCTAGAAAA	58.324	34.615	0.00	0.00	0.00	2.29
2212	2295	5.862924	ACAACACCATGATCTAGAAAACG	57.137	39.130	0.00	0.00	0.00	3.60
2213	2296	5.547465	ACAACACCATGATCTAGAAAACGA	58.453	37.500	0.00	0.00	0.00	3.85
2214	2297	5.995282	ACAACACCATGATCTAGAAAACGAA	59.005	36.000	0.00	0.00	0.00	3.85
2215	2298	6.147821	ACAACACCATGATCTAGAAAACGAAG	59.852	38.462	0.00	0.00	0.00	3.79
2224	2307	8.239038	TGATCTAGAAAACGAAGGTATGATCT	57.761	34.615	0.00	0.00	0.00	2.75
2261	2344	3.069443	GGGAGTTTTGTCTTCCAAATGCA	59.931	43.478	0.00	0.00	42.45	3.96
2268	2351	7.653311	AGTTTTGTCTTCCAAATGCAGTTATTC	59.347	33.333	0.00	0.00	42.45	1.75
2270	2353	5.076182	TGTCTTCCAAATGCAGTTATTCCA	58.924	37.500	0.00	0.00	0.00	3.53
2277	2360	2.128771	TGCAGTTATTCCAGAAGGCC	57.871	50.000	0.00	0.00	33.74	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
657	670	4.201679	CGTGCGCCGGGAGTATGA	62.202	66.667	4.18	0.00	0.00	2.15
659	672	3.900892	CTCGTGCGCCGGGAGTAT	61.901	66.667	12.06	0.00	40.44	2.12
686	699	9.074576	AGTCAAATAATTTAAAACGGGAGAGTT	57.925	29.630	0.00	0.00	35.59	3.01
689	702	9.292195	AGAAGTCAAATAATTTAAAACGGGAGA	57.708	29.630	0.00	0.00	0.00	3.71
690	703	9.341899	CAGAAGTCAAATAATTTAAAACGGGAG	57.658	33.333	0.00	0.00	0.00	4.30
698	711	8.934023	AGTGGGACAGAAGTCAAATAATTTAA	57.066	30.769	0.00	0.00	46.80	1.52
712	725	1.367471	CACTGCGAGTGGGACAGAA	59.633	57.895	8.03	0.00	42.35	3.02
713	726	3.051210	CACTGCGAGTGGGACAGA	58.949	61.111	8.03	0.00	42.35	3.41
755	768	0.888285	GAGAGGCAGCAGCAAGTTGT	60.888	55.000	2.65	0.00	44.61	3.32
763	776	0.540454	TGAATGGAGAGAGGCAGCAG	59.460	55.000	0.00	0.00	0.00	4.24
765	778	0.814812	GCTGAATGGAGAGAGGCAGC	60.815	60.000	0.00	0.00	41.38	5.25
776	789	0.911769	TGGTGGTAGAGGCTGAATGG	59.088	55.000	0.00	0.00	0.00	3.16
778	791	1.282157	GGTTGGTGGTAGAGGCTGAAT	59.718	52.381	0.00	0.00	0.00	2.57
786	799	2.684943	TGTTCTCAGGTTGGTGGTAGA	58.315	47.619	0.00	0.00	0.00	2.59
805	818	4.603131	TGAGATTTTGGAGGGGAGAAATG	58.397	43.478	0.00	0.00	0.00	2.32
807	820	3.657727	ACTGAGATTTTGGAGGGGAGAAA	59.342	43.478	0.00	0.00	0.00	2.52
847	860	1.626825	TGGGGGCGTTTATATAGGAGC	59.373	52.381	0.00	0.00	0.00	4.70
871	884	1.461075	CTATCCTGGGCTCCTGGCT	60.461	63.158	10.95	5.76	41.59	4.75
939	959	3.494626	TGTTCTTGATTTGCTGACGACTC	59.505	43.478	0.00	0.00	0.00	3.36
958	978	2.030490	TACGTGCGGGTGGTTCTGTT	62.030	55.000	0.00	0.00	0.00	3.16
964	984	4.651008	CACGTACGTGCGGGTGGT	62.651	66.667	32.93	5.60	39.39	4.16
1003	1023	0.467290	ACCTTGACGCCATTGTTGGT	60.467	50.000	0.00	0.00	45.57	3.67
1170	1190	2.569134	GCAGCGTTCCTCGTCTCT	59.431	61.111	0.00	0.00	42.13	3.10
1205	1225	2.568090	CTGTGGCGGGCATGAAAC	59.432	61.111	7.75	0.00	0.00	2.78
1409	1432	4.986622	ACGTCGTAACCAGGAGTATTTAC	58.013	43.478	0.00	0.00	0.00	2.01
1410	1433	4.201812	CGACGTCGTAACCAGGAGTATTTA	60.202	45.833	29.08	0.00	34.11	1.40
1472	1496	3.380637	GGGACGCTAATAGACTGAACAGA	59.619	47.826	8.87	0.00	0.00	3.41
1479	1503	4.451900	CCAAATTGGGACGCTAATAGACT	58.548	43.478	3.60	0.00	32.67	3.24
1529	1559	1.861202	GCAAATGAATCATCCGTGGCG	60.861	52.381	0.00	0.00	0.00	5.69
1535	1565	2.220133	GCGCAATGCAAATGAATCATCC	59.780	45.455	5.91	0.00	45.45	3.51
1574	1610	0.863144	AACCGAACACGTCCAAATCG	59.137	50.000	0.00	0.00	0.00	3.34
1609	1651	3.558931	TCGGAGATGCATACAACCAAT	57.441	42.857	0.00	0.00	0.00	3.16
1673	1715	2.097466	CACCAGAAGTTGCAAAACGTCT	59.903	45.455	0.00	0.14	41.09	4.18
1746	1801	4.227134	CAGGGCCGAGGATCACCG	62.227	72.222	0.00	0.00	41.83	4.94
1748	1803	3.112205	ATGCAGGGCCGAGGATCAC	62.112	63.158	0.00	0.00	33.17	3.06
1757	1812	1.514087	CACACAATGATGCAGGGCC	59.486	57.895	0.00	0.00	0.00	5.80
1815	1872	0.537653	TATCGGGCGGTTGTGATTGA	59.462	50.000	0.00	0.00	0.00	2.57
1842	1899	7.095229	CGTGATATATCAATCGGTTTGGTTGAT	60.095	37.037	16.97	8.30	43.06	2.57
1870	1936	3.133003	ACTGGATGTTGGGAGACGATAAG	59.867	47.826	0.00	0.00	0.00	1.73
1897	1963	4.235360	CGGGTTAAATCCGTGCTATCTAG	58.765	47.826	9.58	0.00	42.33	2.43
1914	1980	4.246712	TGGAGACTATCTTCTACGGGTT	57.753	45.455	0.00	0.00	0.00	4.11
1929	2009	7.931275	ACAACAACTCTAATTCTTTTGGAGAC	58.069	34.615	5.82	0.00	33.02	3.36
1986	2066	4.138290	TGGCTGAAGTTCGTCCAAATTTA	58.862	39.130	12.01	0.00	0.00	1.40
2064	2147	1.157870	ACTCACTTGCCGGTTGTTCG	61.158	55.000	1.90	0.00	0.00	3.95
2261	2344	1.209747	GACCGGCCTTCTGGAATAACT	59.790	52.381	0.00	0.00	41.45	2.24
2268	2351	2.359975	GTTGGACCGGCCTTCTGG	60.360	66.667	14.76	0.00	44.58	3.86
2270	2353	2.726822	GAACGTTGGACCGGCCTTCT	62.727	60.000	5.00	0.00	37.63	2.85
2277	2360	4.647964	CAATTTAGATGAACGTTGGACCG	58.352	43.478	5.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.