AutoCloner

Multiple sequence alignment - TraesCS2D01G247100

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	TraesCS2D01G247100	chr2D	100.000	1891	0	0	407	2297	291639871	291637981	0.000000e+00	3493
1	TraesCS2D01G247100	chr2D	96.730	1896	57	4	407	2297	644701933	644703828	0.000000e+00	3153
2	TraesCS2D01G247100	chr2D	100.000	161	0	0	1	161	291640277	291640117	4.800000e-77	298
3	TraesCS2D01G247100	chr2D	95.652	161	7	0	1	161	635069302	635069142	2.260000e-65	259
4	TraesCS2D01G247100	chr2D	95.652	161	7	0	1	161	644701759	644701919	2.260000e-65	259
5	TraesCS2D01G247100	chr5B	96.835	1896	55	4	407	2297	130613570	130615465	0.000000e+00	3164
6	TraesCS2D01G247100	chr5B	96.572	1896	60	4	407	2297	130608546	130610441	0.000000e+00	3136
7	TraesCS2D01G247100	chr5B	96.519	1896	61	4	407	2297	130570086	130568191	0.000000e+00	3131
8	TraesCS2D01G247100	chr5B	95.652	161	7	0	1	161	130608376	130608536	2.260000e-65	259
9	TraesCS2D01G247100	chr5B	95.652	161	7	0	1	161	130613400	130613560	2.260000e-65	259
10	TraesCS2D01G247100	chrUn	96.783	1896	56	4	407	2297	261514395	261512500	0.000000e+00	3158
11	TraesCS2D01G247100	chrUn	96.730	1896	57	4	407	2297	45099461	45101356	0.000000e+00	3153
12	TraesCS2D01G247100	chrUn	95.652	161	7	0	1	161	45099291	45099451	2.260000e-65	259
13	TraesCS2D01G247100	chrUn	95.652	161	7	0	1	161	261514567	261514407	2.260000e-65	259
14	TraesCS2D01G247100	chr7D	96.624	1896	59	4	407	2297	626648934	626650829	0.000000e+00	3142
15	TraesCS2D01G247100	chr7D	95.652	161	7	0	1	161	626648708	626648868	2.260000e-65	259
16	TraesCS2D01G247100	chr3A	96.466	1896	62	4	407	2297	66031644	66029749	0.000000e+00	3125
17	TraesCS2D01G247100	chr7B	96.414	1896	63	4	407	2297	743035031	743033136	0.000000e+00	3120
18	TraesCS2D01G247100	chr7B	95.652	161	7	0	1	161	743035202	743035042	2.260000e-65	259
19	TraesCS2D01G247100	chr1D	95.652	161	7	0	1	161	493802951	493803111	2.260000e-65	259

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	TraesCS2D01G247100	chr2D	291637981	291640277	2296	True	1895.5	3493	100.00000	1	2297	2	chr2D.!!$R2	2296
1	TraesCS2D01G247100	chr2D	644701759	644703828	2069	False	1706.0	3153	96.19100	1	2297	2	chr2D.!!$F1	2296
2	TraesCS2D01G247100	chr5B	130568191	130570086	1895	True	3131.0	3131	96.51900	407	2297	1	chr5B.!!$R1	1890
3	TraesCS2D01G247100	chr5B	130608376	130615465	7089	False	1704.5	3164	96.17775	1	2297	4	chr5B.!!$F1	2296
4	TraesCS2D01G247100	chrUn	261512500	261514567	2067	True	1708.5	3158	96.21750	1	2297	2	chrUn.!!$R1	2296
5	TraesCS2D01G247100	chrUn	45099291	45101356	2065	False	1706.0	3153	96.19100	1	2297	2	chrUn.!!$F1	2296
6	TraesCS2D01G247100	chr7D	626648708	626650829	2121	False	1700.5	3142	96.13800	1	2297	2	chr7D.!!$F1	2296
7	TraesCS2D01G247100	chr3A	66029749	66031644	1895	True	3125.0	3125	96.46600	407	2297	1	chr3A.!!$R1	1890
8	TraesCS2D01G247100	chr7B	743033136	743035202	2066	True	1689.5	3120	96.03300	1	2297	2	chr7B.!!$R1	2296

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
140	141	0.543749	GCTGCAACCTAGGGATCACT	59.456	55.0	14.81	1.44	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1532	6326	0.526211	CCCCTTTTTCGTTGCCTAGC	59.474	55.0	0.0	0.0	0.0	3.42	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
27	28	3.717707	ACGCTATTATGAATGTGCGACT	58.282	40.909	20.13	4.59	43.02	4.18
86	87	0.737219	CGTCGGTCGGTCCTAGAAAT	59.263	55.000	0.00	0.00	35.71	2.17
89	90	1.108776	CGGTCGGTCCTAGAAATGGA	58.891	55.000	0.00	0.00	0.00	3.41
92	93	2.108970	GTCGGTCCTAGAAATGGAGGT	58.891	52.381	0.00	0.00	33.78	3.85
140	141	0.543749	GCTGCAACCTAGGGATCACT	59.456	55.000	14.81	1.44	0.00	3.41
565	5356	0.691332	GACGGGAGGAAAGAAAGGGT	59.309	55.000	0.00	0.00	0.00	4.34
566	5357	0.691332	ACGGGAGGAAAGAAAGGGTC	59.309	55.000	0.00	0.00	0.00	4.46
567	5358	0.690762	CGGGAGGAAAGAAAGGGTCA	59.309	55.000	0.00	0.00	0.00	4.02
717	5508	2.119029	GGCGCCCATTCCTAACCAC	61.119	63.158	18.11	0.00	0.00	4.16
730	5521	4.969484	TCCTAACCACTTCTGAAAAGGTC	58.031	43.478	12.21	0.00	0.00	3.85
731	5522	4.410883	TCCTAACCACTTCTGAAAAGGTCA	59.589	41.667	12.21	0.10	34.17	4.02
769	5561	1.933021	ACCACTTAGTGATCGGTCCA	58.067	50.000	14.66	0.00	35.23	4.02
872	5665	7.664552	TTCCTTCGGTATCTAATAACCTTGA	57.335	36.000	0.00	0.00	33.34	3.02
1009	5803	5.106475	GCTGGTACCATTTCGATGTGTTTTA	60.106	40.000	16.75	0.00	0.00	1.52
1010	5804	6.404293	GCTGGTACCATTTCGATGTGTTTTAT	60.404	38.462	16.75	0.00	0.00	1.40
1166	5960	3.443329	TGGTTTTATGTGATCGCAGCATT	59.557	39.130	15.24	0.02	0.00	3.56
1256	6050	3.058501	GGAATATTATTGTTCGGGTGCGG	60.059	47.826	0.00	0.00	0.00	5.69
1338	6132	6.412214	ACGTAGTTGTAATTCTAGGGCAATT	58.588	36.000	0.00	0.00	37.78	2.32
1356	6150	4.590222	GCAATTGATCCACTTTCCCCATAT	59.410	41.667	10.34	0.00	0.00	1.78
1365	6159	3.722101	CACTTTCCCCATATCCCTAAGGT	59.278	47.826	0.00	0.00	0.00	3.50
1386	6180	1.015109	GTGTCTCGATCTCCTACGCA	58.985	55.000	0.00	0.00	0.00	5.24
1408	6202	5.565045	GCACGAAAGATAAGATACGGGAGAT	60.565	44.000	0.00	0.00	0.00	2.75
1431	6225	2.372172	GGGTCCTATGGTATGGGTCTTG	59.628	54.545	0.00	0.00	31.94	3.02
1554	6348	2.207229	GGCAACGAAAAAGGGGCCT	61.207	57.895	0.84	0.00	38.37	5.19
1804	6598	4.043037	GTCATAGGAACTTAGACCACCG	57.957	50.000	0.00	0.00	41.75	4.94
1810	6604	1.799258	AACTTAGACCACCGACGCGT	61.799	55.000	13.85	13.85	0.00	6.01
1830	6624	4.374843	GTTGGTAAACGAAAACCACCTT	57.625	40.909	6.95	0.00	45.31	3.50
1844	6638	1.191535	CACCTTGACCGGATCTACCA	58.808	55.000	9.46	0.00	38.90	3.25
1911	6705	1.128200	ACCAGCTTTCCCCCAAAAAC	58.872	50.000	0.00	0.00	0.00	2.43
1945	6739	2.484264	GCTTACTGCTCACGGAAACATT	59.516	45.455	0.00	0.00	38.95	2.71
1946	6740	3.058224	GCTTACTGCTCACGGAAACATTT	60.058	43.478	0.00	0.00	38.95	2.32
1955	6749	5.353123	GCTCACGGAAACATTTGACCTTATA	59.647	40.000	0.00	0.00	0.00	0.98
1968	6762	4.338012	TGACCTTATAGTCAAGTCGTCCA	58.662	43.478	0.00	0.00	43.65	4.02
1974	6768	6.713903	CCTTATAGTCAAGTCGTCCACCTATA	59.286	42.308	0.00	0.00	0.00	1.31
2014	6808	6.449387	CGTTTTTCGATCGCATAAAAAGTCAC	60.449	38.462	19.99	11.85	42.86	3.67
2103	6897	1.909302	CCATAGATGGGGCGTCCTATT	59.091	52.381	6.29	0.00	44.31	1.73
2105	6899	2.391926	TAGATGGGGCGTCCTATTCA	57.608	50.000	6.29	0.00	34.12	2.57
2142	6936	4.270834	AGCCTCTGTCGAGTAGTGAAATA	58.729	43.478	0.00	0.00	35.43	1.40
2192	6986	2.872245	CACACAAGTCGGTGATTCAAGT	59.128	45.455	0.00	0.00	41.32	3.16
2205	6999	0.756294	TTCAAGTCAAGAGTGCGGGA	59.244	50.000	0.00	0.00	0.00	5.14
2259	7055	0.468226	ACTGCTGGAACGAAAGACCA	59.532	50.000	0.00	0.00	38.67	4.02
2277	7073	6.777213	AGACCAGATGAGTATTTTCGTACT	57.223	37.500	0.00	0.00	37.61	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	66	4.233635	CTAGGACCGACCGACGCG	62.234	72.222	3.53	3.53	44.74	6.01
86	87	0.179015	CTCCTCGCTAGCTACCTCCA	60.179	60.000	13.93	0.00	0.00	3.86
89	90	2.950975	GTTAACTCCTCGCTAGCTACCT	59.049	50.000	13.93	0.00	0.00	3.08
92	93	2.611292	GTCGTTAACTCCTCGCTAGCTA	59.389	50.000	13.93	0.00	0.00	3.32
565	5356	4.937620	GCCCTTTCGCATTATCATCTATGA	59.062	41.667	0.00	0.00	41.70	2.15
566	5357	4.201753	CGCCCTTTCGCATTATCATCTATG	60.202	45.833	0.00	0.00	0.00	2.23
567	5358	3.935203	CGCCCTTTCGCATTATCATCTAT	59.065	43.478	0.00	0.00	0.00	1.98
685	5476	3.479203	CGCCACTATCCCAGCCCA	61.479	66.667	0.00	0.00	0.00	5.36
717	5508	4.070716	AGCATGAGTGACCTTTTCAGAAG	58.929	43.478	0.00	0.00	33.71	2.85
730	5521	3.430929	GGTTAGTACCTCCAGCATGAGTG	60.431	52.174	0.00	0.00	41.53	3.51
731	5522	2.766828	GGTTAGTACCTCCAGCATGAGT	59.233	50.000	0.00	0.00	41.53	3.41
769	5561	2.230508	TCTTCGGATTGCGTGAACTAGT	59.769	45.455	0.00	0.00	0.00	2.57
1146	5940	7.504922	TTTTAATGCTGCGATCACATAAAAC	57.495	32.000	0.00	0.00	0.00	2.43
1166	5960	9.801873	CAGTGGAAAATTCAGACTTTCTTTTTA	57.198	29.630	4.78	0.00	33.06	1.52
1191	5985	3.761218	TCAAATATTTTGAGCCGGCTTCA	59.239	39.130	33.34	25.57	0.00	3.02
1256	6050	2.806608	TTGATCGGTAGTATTCCGGC	57.193	50.000	0.00	0.00	46.82	6.13
1338	6132	2.716424	GGGATATGGGGAAAGTGGATCA	59.284	50.000	0.00	0.00	0.00	2.92
1356	6150	2.297698	TCGAGACACAACCTTAGGGA	57.702	50.000	2.32	0.00	36.25	4.20
1365	6159	1.400846	GCGTAGGAGATCGAGACACAA	59.599	52.381	0.00	0.00	0.00	3.33
1386	6180	5.047943	CCATCTCCCGTATCTTATCTTTCGT	60.048	44.000	0.00	0.00	0.00	3.85
1408	6202	0.651124	ACCCATACCATAGGACCCCA	59.349	55.000	0.00	0.00	0.00	4.96
1468	6262	2.432444	CCCCAATCTTCACTTTACGCA	58.568	47.619	0.00	0.00	0.00	5.24
1532	6326	0.526211	CCCCTTTTTCGTTGCCTAGC	59.474	55.000	0.00	0.00	0.00	3.42
1554	6348	5.408356	GTCGCTCCTTTAGTTGAAGTATCA	58.592	41.667	0.00	0.00	0.00	2.15
1598	6392	0.539986	AGAACGTGTGACACTGGGTT	59.460	50.000	14.42	10.40	31.34	4.11
1766	6560	1.536662	ACCGAGTCTTTCTGGCCCT	60.537	57.895	0.00	0.00	0.00	5.19
1810	6604	4.015084	TCAAGGTGGTTTTCGTTTACCAA	58.985	39.130	6.81	0.00	45.45	3.67
1830	6624	1.548081	TCGTTTGGTAGATCCGGTCA	58.452	50.000	0.00	0.00	39.52	4.02
1844	6638	2.671963	GGGCGGCCTTCTTCGTTT	60.672	61.111	22.87	0.00	0.00	3.60
1863	6657	5.365403	TTTGGCGTGTTAATTCTTTCGAT	57.635	34.783	0.00	0.00	0.00	3.59
1946	6740	4.157289	GTGGACGACTTGACTATAAGGTCA	59.843	45.833	0.00	0.00	43.41	4.02
1955	6749	5.657302	AGAAATATAGGTGGACGACTTGACT	59.343	40.000	0.00	0.00	0.00	3.41
1968	6762	9.838339	AAAACGAATGAGATCAGAAATATAGGT	57.162	29.630	0.00	0.00	0.00	3.08
1995	6789	3.503891	TCGTGACTTTTTATGCGATCGA	58.496	40.909	21.57	4.34	0.00	3.59
2103	6897	2.781757	AGGCTCCTCATTCATCCATTGA	59.218	45.455	0.00	0.00	0.00	2.57
2105	6899	3.054576	AGAGGCTCCTCATTCATCCATT	58.945	45.455	17.40	0.00	44.99	3.16
2142	6936	7.362660	GGTTTAACCGAAAAGCAGAATCCTATT	60.363	37.037	0.00	0.00	36.94	1.73
2171	6965	2.872245	ACTTGAATCACCGACTTGTGTG	59.128	45.455	0.00	0.00	37.51	3.82
2183	6977	2.416747	CCGCACTCTTGACTTGAATCA	58.583	47.619	0.00	0.00	0.00	2.57
2192	6986	1.344065	TAAGGTTCCCGCACTCTTGA	58.656	50.000	0.00	0.00	0.00	3.02
2205	6999	2.271944	AGCTTTGACCGCTTAAGGTT	57.728	45.000	4.29	0.00	46.09	3.50
2259	7055	7.341256	TGGAAGGTAGTACGAAAATACTCATCT	59.659	37.037	0.00	0.00	36.74	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.