SNP's and Indel detected in Coconut kinase sequences

SNP_indel_type
5_flanking seq
3_flanking seq
SNP_cutter enzyme
Primer Sequences
GC %
Annealing temp
Product size
Product after SNP cutter
A indel, T-A, G-T, T-G, A-T, T-G, C-T, C indel, C-G, T-C, A-T, T-A, C-T, A-C, A indel, T-C
ATCATG
ATAATA
Dde1 Hpy1881
FOR
CAAGCTTCTTAGGCACATGG
50.00
58.53
266
76-404
REV
AGAAGAGGAGGTTGCTTGGT
50.00
57.89
T-T, T-C, T-A, T-A, C-T, A-T
ACCACC
CAATGA
FOR
CAAGCTTCTTAGGCACATGG
50.00
58.53
265
REV
GAAGAGGAGGTTGCTTGGTT
50.00
58.32
G indel, T-G, C-T, T-C, A-T, C-A, A-C, T-A, G-T, C-G, G-C, A-T, T-A, G-T, A-G, T-A, T indel
AATGAT
TAATGG
AccI Hpy1661I BsrDI Tsp5091 MseI AseI
FOR
CAAGCTTCTTAGGCACATGG
50.00
58.53
208
125,355
REV
GAAGAGGAGGTTGCTTGGTT
50.00
58.32
G indel, C-G, T-C, G-T, T-G, C-T, T-C, G-T, A-G, G-A, A-G, G-A, C-A, A-C, C-A, T-C,T indel
AATCAA
GTCAGT
Mn1I, DdeI, Hpy1881, BsIHKAI, Bsp12861, HpyCH4111
FOR
ACCACCTTCTGTGTGGGATA
52.38
60.82
211
194, 286
REV
AAGAAGAGGAGGTTGCTTGG
50.00
58.52
A indel, T-A, A-TC-A, A-C, T-A, C-C, A-C, G-A, C-G, A-C, A-G, T-A, G-T, T-G, C indel
AAATAT
TTCACAGA
FaiI
FOR
CAAGCTTTGTCTGAGGAGCA
50.00
59.31
170
246,234
REV
GTACGAGCAAGTCCAAAGTCG
50.00
59.07
A indel, C-A, T-CG-T, T-G, G-T, A-G, T-A, A-T, G-A, A-G, T-A, T-indelC-T, C-T
AATGCT
TTTGGACT
HypCH4III MseI
FOR
CAAGCTTTGTCTGAGGAGCA
50.00
59.31
177
314,116
REV
TGAGGTAGTACGAGCAAGTCCA
50.00
59.94
A-indel, G-T, A-G, C-A, A-C, G-A, A-G, G-A, T-G, A-T, T-A, G-T, T-G, G-T, T-G, G-T, T-G, A-T, A-indel
TGATTTC
CAAGATGG
N1AIII BspHI FatI
FOR
CAAGCTTTGTCTGAGGAGCA
50.00
59.31
230
373,107
REV
AAATCTGGTGCCCGATACCATCTCT
57.89
60.90
T-C, C-A, A-G, G-A, A-G
ATGGTA
TTGAAT
NIaIV
FOR
AAACCAAGCAACCTCCTCTTC
47.62
59.74
166
396,84
REV
GCTGCAGTATACTCTGAAGAATTCAA
38.46
60.32
G-indel, A-G, G-A, T-A, A-T, T-A, A-T, C-A, T-C, G-T, C-G, A-C, G-A, C-G, A-C, T-A, G-T, A-G, T-A, G-T, T-G, C-T, T-G, G-T
.
AccI Hpy166II
FOR
ACCACCTTCTGTGTGGGATAC
52.38
58.78
386
430, 50
REV
GAAAATGCAACCGACTGACC
50.00
60.50