AutoCloner

Multiple sequence alignment - TraesCS6B01G040100

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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	TraesCS6B01G040100	chr6B	100.000	1500	0	0	1	1500	24940662	24939163	0.000000e+00	2771.0
1	TraesCS6B01G040100	chr6B	100.000	208	0	0	2045	2252	24938618	24938411	3.510000e-103	385.0
2	TraesCS6B01G040100	chr5B	95.342	1331	60	2	1	1329	38468086	38469416	0.000000e+00	2113.0
3	TraesCS6B01G040100	chr1A	94.824	1333	63	6	1	1329	281369411	281368081	0.000000e+00	2074.0
4	TraesCS6B01G040100	chr3A	94.586	1330	64	8	1	1327	58873095	58871771	0.000000e+00	2050.0
5	TraesCS6B01G040100	chr2A	94.365	1331	66	7	1	1329	709825387	709826710	0.000000e+00	2034.0
6	TraesCS6B01G040100	chr2A	94.708	1266	63	4	1	1264	23927720	23926457	0.000000e+00	1964.0
7	TraesCS6B01G040100	chr3B	94.215	1331	75	2	1	1329	750919799	750921129	0.000000e+00	2030.0
8	TraesCS6B01G040100	chr3B	93.910	1330	77	4	1	1328	485696231	485694904	0.000000e+00	2004.0
9	TraesCS6B01G040100	chr3B	92.982	57	3	1	1280	1335	750904376	750904320	5.160000e-12	82.4
10	TraesCS6B01G040100	chr7A	94.016	1337	78	2	1	1335	26584730	26583394	0.000000e+00	2025.0
11	TraesCS6B01G040100	chr1D	93.544	1332	79	6	1	1329	468700190	468701517	0.000000e+00	1977.0
12	TraesCS6B01G040100	chr6D	97.778	180	4	0	2073	2252	13298608	13298429	6.040000e-81	311.0
13	TraesCS6B01G040100	chr6D	91.908	173	4	5	1331	1495	13299309	13299139	1.340000e-57	233.0
14	TraesCS6B01G040100	chrUn	89.000	200	22	0	2053	2252	71388937	71389136	4.800000e-62	248.0

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	TraesCS6B01G040100	chr6B	24938411	24940662	2251	True	1578	2771	100.000	1	2252	2	chr6B.!!$R1	2251
1	TraesCS6B01G040100	chr5B	38468086	38469416	1330	False	2113	2113	95.342	1	1329	1	chr5B.!!$F1	1328
2	TraesCS6B01G040100	chr1A	281368081	281369411	1330	True	2074	2074	94.824	1	1329	1	chr1A.!!$R1	1328
3	TraesCS6B01G040100	chr3A	58871771	58873095	1324	True	2050	2050	94.586	1	1327	1	chr3A.!!$R1	1326
4	TraesCS6B01G040100	chr2A	709825387	709826710	1323	False	2034	2034	94.365	1	1329	1	chr2A.!!$F1	1328
5	TraesCS6B01G040100	chr2A	23926457	23927720	1263	True	1964	1964	94.708	1	1264	1	chr2A.!!$R1	1263
6	TraesCS6B01G040100	chr3B	750919799	750921129	1330	False	2030	2030	94.215	1	1329	1	chr3B.!!$F1	1328
7	TraesCS6B01G040100	chr3B	485694904	485696231	1327	True	2004	2004	93.910	1	1328	1	chr3B.!!$R1	1327
8	TraesCS6B01G040100	chr7A	26583394	26584730	1336	True	2025	2025	94.016	1	1335	1	chr7A.!!$R1	1334
9	TraesCS6B01G040100	chr1D	468700190	468701517	1327	False	1977	1977	93.544	1	1329	1	chr1D.!!$F1	1328
10	TraesCS6B01G040100	chr6D	13298429	13299309	880	True	272	311	94.843	1331	2252	2	chr6D.!!$R1	921

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
201	202	1.187087	GGAAGTCCGGTGATCAGAGT	58.813	55.0	0.0	0.0	0.0	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2066	2092	0.03467	GCTGCTCTGGAACCTGGAAT	60.035	55.0	0.0	0.0	0.0	3.01	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
190	191	1.555075	TCTCCTTTGATGGGAAGTCCG	59.445	52.381	0.00	0.00	38.76	4.79
201	202	1.187087	GGAAGTCCGGTGATCAGAGT	58.813	55.000	0.00	0.00	0.00	3.24
253	254	5.220931	CCCAGCATAGAAGTGAAAAGTATGC	60.221	44.000	4.78	4.78	44.14	3.14
258	259	6.183360	GCATAGAAGTGAAAAGTATGCGTCTT	60.183	38.462	0.00	0.00	37.36	3.01
269	270	2.420043	GCGTCTTAGGGCGCCATA	59.580	61.111	30.85	24.85	46.93	2.74
347	349	3.180507	AGTGAGATGAAAGGGAGAAGCT	58.819	45.455	0.00	0.00	0.00	3.74
558	561	3.063670	TGTCATTTGCAAATATCCGCG	57.936	42.857	23.69	10.99	0.00	6.46
621	624	9.479549	ACATTAATTCTTCTTCCATACACCATT	57.520	29.630	0.00	0.00	0.00	3.16
806	809	7.404671	AATCCCTACATTATCACACCAAAAC	57.595	36.000	0.00	0.00	0.00	2.43
971	974	1.206610	GATCTGCAGCTCTTGAGTGGA	59.793	52.381	9.47	0.00	0.00	4.02
1174	1178	2.335011	CCGACGTGACAGTCAGCA	59.665	61.111	2.53	0.00	40.98	4.41
1175	1179	1.080501	CCGACGTGACAGTCAGCAT	60.081	57.895	2.53	0.00	40.98	3.79
1210	1214	0.457166	CGTTGACCGAGGCGTTATGA	60.457	55.000	0.00	0.00	39.56	2.15
1225	1230	4.672409	CGTTATGATATCTAGCATGGCGA	58.328	43.478	3.98	0.00	34.79	5.54
1329	1335	6.237808	CCAAAGGTCAGTTTTGTGATTTTTCG	60.238	38.462	0.00	0.00	34.51	3.46
1340	1346	2.034053	GTGATTTTTCGCACCAACTCCA	59.966	45.455	0.00	0.00	0.00	3.86
1342	1348	1.028905	TTTTTCGCACCAACTCCAGG	58.971	50.000	0.00	0.00	0.00	4.45
1343	1349	0.106918	TTTTCGCACCAACTCCAGGT	60.107	50.000	0.00	0.00	40.85	4.00
1344	1350	0.534203	TTTCGCACCAACTCCAGGTC	60.534	55.000	0.00	0.00	37.23	3.85
1345	1351	1.407656	TTCGCACCAACTCCAGGTCT	61.408	55.000	0.00	0.00	37.23	3.85
1346	1352	0.541063	TCGCACCAACTCCAGGTCTA	60.541	55.000	0.00	0.00	37.23	2.59
1378	1384	2.813908	CTCGTCTTTTCCGCCCCG	60.814	66.667	0.00	0.00	0.00	5.73
1431	1437	9.881773	AATAATGACATTATTACATCCAACCCT	57.118	29.630	25.29	3.71	42.09	4.34
1452	1458	0.776479	TTGGTCCAATGGTGGGGGTA	60.776	55.000	0.00	0.00	46.01	3.69
1489	1501	0.982704	ATCTCAGAAGCCACTGCAGT	59.017	50.000	15.25	15.25	41.13	4.40
2066	2092	3.924114	TTTTTCTCTGTGACCCACTGA	57.076	42.857	6.53	6.53	39.36	3.41
2067	2093	4.437682	TTTTTCTCTGTGACCCACTGAT	57.562	40.909	7.04	0.00	40.46	2.90
2068	2094	4.437682	TTTTCTCTGTGACCCACTGATT	57.562	40.909	7.04	0.00	40.46	2.57
2069	2095	3.685139	TTCTCTGTGACCCACTGATTC	57.315	47.619	7.04	0.00	40.46	2.52
2070	2096	1.902508	TCTCTGTGACCCACTGATTCC	59.097	52.381	7.04	0.00	40.46	3.01
2071	2097	1.625315	CTCTGTGACCCACTGATTCCA	59.375	52.381	7.04	0.00	40.46	3.53
2083	2109	1.280133	CTGATTCCAGGTTCCAGAGCA	59.720	52.381	0.00	0.00	36.77	4.26
2087	2113	2.659016	CAGGTTCCAGAGCAGCGA	59.341	61.111	0.00	0.00	0.00	4.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	1.267235	GCTGATGCAGACGATGAAACG	60.267	52.381	0.00	0.00	39.41	3.60
190	191	3.118629	TGCAGGATGTTACTCTGATCACC	60.119	47.826	0.00	0.00	39.31	4.02
201	202	4.065088	GACTGTCACTTTGCAGGATGTTA	58.935	43.478	2.24	0.00	39.31	2.41
253	254	1.006102	CCTATGGCGCCCTAAGACG	60.006	63.158	26.77	6.35	0.00	4.18
258	259	1.827394	GTTGACCTATGGCGCCCTA	59.173	57.895	26.77	18.34	0.00	3.53
558	561	7.218773	CACATGTATGTATGTTTTTGCACTAGC	59.781	37.037	0.00	0.00	39.17	3.42
806	809	7.461182	TCCTTTTGTTGAAATGTATAGTGGG	57.539	36.000	0.00	0.00	0.00	4.61
971	974	1.003573	AAATCGCCCCTCCCTCTCT	59.996	57.895	0.00	0.00	0.00	3.10
1066	1069	2.631062	CGCCATACCCCTTCACTACATA	59.369	50.000	0.00	0.00	0.00	2.29
1132	1135	4.738998	TTGGGCCCATGACGCCTG	62.739	66.667	29.23	0.00	46.24	4.85
1165	1169	2.504899	CGCGTCGATGCTGACTGT	60.505	61.111	26.02	0.00	36.71	3.55
1184	1188	3.041940	CTCGGTCAACGGTGCCAC	61.042	66.667	13.22	0.00	44.45	5.01
1189	1193	1.880819	ATAACGCCTCGGTCAACGGT	61.881	55.000	0.00	0.00	44.45	4.83
1210	1214	0.532573	CGGGTCGCCATGCTAGATAT	59.467	55.000	0.00	0.00	0.00	1.63
1329	1335	3.031736	TCTATAGACCTGGAGTTGGTGC	58.968	50.000	0.00	0.00	38.03	5.01
1340	1346	7.011382	ACGAGGGACATTAATTCTATAGACCT	58.989	38.462	0.67	2.18	0.00	3.85
1342	1348	8.113173	AGACGAGGGACATTAATTCTATAGAC	57.887	38.462	0.67	0.00	0.00	2.59
1343	1349	8.707796	AAGACGAGGGACATTAATTCTATAGA	57.292	34.615	0.00	0.00	0.00	1.98
1344	1350	9.765795	AAAAGACGAGGGACATTAATTCTATAG	57.234	33.333	0.00	0.00	0.00	1.31
1345	1351	9.760077	GAAAAGACGAGGGACATTAATTCTATA	57.240	33.333	0.00	0.00	0.00	1.31
1346	1352	7.715686	GGAAAAGACGAGGGACATTAATTCTAT	59.284	37.037	0.00	0.00	0.00	1.98
1452	1458	3.970640	GAGATATGTCAGGTCTTTCCCCT	59.029	47.826	0.00	0.00	36.75	4.79
2046	2072	3.924114	TCAGTGGGTCACAGAGAAAAA	57.076	42.857	0.78	0.00	36.74	1.94
2047	2073	4.389374	GAATCAGTGGGTCACAGAGAAAA	58.611	43.478	0.78	0.00	33.70	2.29
2048	2074	3.244561	GGAATCAGTGGGTCACAGAGAAA	60.245	47.826	0.78	0.00	33.70	2.52
2049	2075	2.303022	GGAATCAGTGGGTCACAGAGAA	59.697	50.000	0.78	0.00	33.70	2.87
2050	2076	1.902508	GGAATCAGTGGGTCACAGAGA	59.097	52.381	0.78	0.00	33.70	3.10
2051	2077	1.625315	TGGAATCAGTGGGTCACAGAG	59.375	52.381	0.78	0.00	33.70	3.35
2052	2078	1.625315	CTGGAATCAGTGGGTCACAGA	59.375	52.381	0.78	0.00	36.74	3.41
2053	2079	1.339438	CCTGGAATCAGTGGGTCACAG	60.339	57.143	0.78	0.00	39.31	3.66
2054	2080	0.692476	CCTGGAATCAGTGGGTCACA	59.308	55.000	0.78	0.00	39.31	3.58
2055	2081	0.693049	ACCTGGAATCAGTGGGTCAC	59.307	55.000	0.00	0.00	39.31	3.67
2056	2082	1.351017	GAACCTGGAATCAGTGGGTCA	59.649	52.381	0.00	0.00	39.31	4.02
2057	2083	1.340114	GGAACCTGGAATCAGTGGGTC	60.340	57.143	0.00	0.00	39.31	4.46
2058	2084	0.698818	GGAACCTGGAATCAGTGGGT	59.301	55.000	0.00	0.00	39.31	4.51
2059	2085	0.698238	TGGAACCTGGAATCAGTGGG	59.302	55.000	0.00	0.00	39.31	4.61
2060	2086	1.630369	TCTGGAACCTGGAATCAGTGG	59.370	52.381	0.00	0.00	39.31	4.00
2061	2087	2.938756	GCTCTGGAACCTGGAATCAGTG	60.939	54.545	0.00	6.66	39.31	3.66
2062	2088	1.280421	GCTCTGGAACCTGGAATCAGT	59.720	52.381	0.00	0.00	39.31	3.41
2063	2089	1.280133	TGCTCTGGAACCTGGAATCAG	59.720	52.381	0.00	4.72	40.59	2.90
2064	2090	1.280133	CTGCTCTGGAACCTGGAATCA	59.720	52.381	0.00	0.00	0.00	2.57
2065	2091	2.016096	GCTGCTCTGGAACCTGGAATC	61.016	57.143	0.00	0.00	0.00	2.52
2066	2092	0.034670	GCTGCTCTGGAACCTGGAAT	60.035	55.000	0.00	0.00	0.00	3.01
2067	2093	1.376466	GCTGCTCTGGAACCTGGAA	59.624	57.895	0.00	0.00	0.00	3.53
2068	2094	2.947532	CGCTGCTCTGGAACCTGGA	61.948	63.158	0.00	0.00	0.00	3.86
2069	2095	2.435586	CGCTGCTCTGGAACCTGG	60.436	66.667	0.00	0.00	0.00	4.45
2070	2096	0.603707	TTTCGCTGCTCTGGAACCTG	60.604	55.000	0.00	0.00	0.00	4.00
2071	2097	0.326264	ATTTCGCTGCTCTGGAACCT	59.674	50.000	0.00	0.00	0.00	3.50
2083	2109	1.678970	GGCTGTTCCCCATTTCGCT	60.679	57.895	0.00	0.00	0.00	4.93
2087	2113	2.679996	GGCGGCTGTTCCCCATTT	60.680	61.111	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.