AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1199090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1199090 MtrunA17_Chr8g0368831 95.726 117 5 0 1 117 7 123 4.61e-76 221
Msa1199090 MtrunA17_Chr8g0368861 97.391 115 3 0 3 117 1 115 4.88e-76 220
Msa1199090 MtrunA17_Chr7g0240471 50.000 94 45 2 25 117 20 112 1.39e-23 87.8
Msa1199090 MtrunA17_Chr7g0240451 50.000 90 43 2 29 117 24 112 3.91e-22 84.0
Msa1199090 MtrunA17_Chr7g0240441 56.364 55 23 1 65 119 38 91 1.73e-14 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1199090 AT2G37870.1 71.296 108 28 1 10 117 6 110 1.76e-47 148
Msa1199090 AT5G05960.1 44.068 118 58 3 3 118 1 112 9.83e-26 93.6
Msa1199090 AT3G53980.2 44.444 90 49 1 29 118 22 110 2.94e-24 89.7
Msa1199090 AT3G53980.1 44.444 90 49 1 29 118 22 110 2.94e-24 89.7

Find 28 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCATCAAGTGTGTTAATTT+TGG 0.227059 8_1:+50954064 Msa1199090:CDS
TGCTAGTCTAAGTCCATGTT+TGG 0.283707 8_1:+50954136 Msa1199090:CDS
ATCTTAGCTTGTTTAGCAAT+AGG 0.376748 8_1:-50954263 None:intergenic
TTCCTAATGTTGCATCTCTT+AGG 0.378053 8_1:-50954311 None:intergenic
TGGGTGCTGTACGTAATGTT+AGG 0.392658 8_1:+50954156 Msa1199090:CDS
AACAATGGTGATGGAATTCA+AGG 0.431133 8_1:+50954004 None:intergenic
GAATGTGGAAGGACACCAAT+TGG 0.434211 8_1:+50954104 Msa1199090:CDS
AGAACAGAACAAAGACATCT+TGG 0.469439 8_1:-50954233 None:intergenic
CTTCCACATTTCTTTCCAGC+AGG 0.469545 8_1:-50954338 None:intergenic
CTAGCAGCTGCTGACCCAAT+TGG 0.471716 8_1:-50954119 None:intergenic
CCAACTCTAGCACAACAAAC+TGG 0.478057 8_1:-50954191 None:intergenic
TTCCTAAGAGATGCAACATT+AGG 0.493031 8_1:+50954309 Msa1199090:CDS
GGGTGCTGTACGTAATGTTA+GGG 0.506383 8_1:+50954157 Msa1199090:CDS
GCTAGTCTAAGTCCATGTTT+GGG 0.506563 8_1:+50954137 Msa1199090:CDS
CCAGTTTGTTGTGCTAGAGT+TGG 0.508251 8_1:+50954191 Msa1199090:CDS
CACATTTCTTTCCAGCAGGT+CGG 0.514268 8_1:-50954334 None:intergenic
AATGTGGAAGGACACCAATT+GGG 0.523864 8_1:+50954105 Msa1199090:CDS
CACAGTGGTGATGTTTCTGT+TGG 0.525534 8_1:+50954043 Msa1199090:CDS
AACATTAGGAACCGACCTGC+TGG 0.527493 8_1:+50954323 Msa1199090:CDS
AGTGAGGCAGCTGGAGAATG+TGG 0.550647 8_1:+50954089 Msa1199090:CDS
GGAACAGTGATAGCAATAGC+AGG 0.582273 8_1:-50954290 None:intergenic
GAAACATCACCACTGTGGCT+AGG 0.584675 8_1:-50954037 None:intergenic
TTACGTACAGCACCCAAACA+TGG 0.602239 8_1:-50954149 None:intergenic
CGACCTGCTGGAAAGAAATG+TGG 0.609362 8_1:+50954335 Msa1199090:CDS
AGGCAGCTGGAGAATGTGGA+AGG 0.611703 8_1:+50954093 Msa1199090:CDS
ACTCTAGCACAACAAACTGG+TGG 0.633479 8_1:-50954188 None:intergenic
CAACAGAAACATCACCACTG+TGG 0.756055 8_1:-50954042 None:intergenic
AAGAACTTTCCTAGCCACAG+TGG 0.766481 8_1:+50954028 Msa1199090:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTGTTAATTTTGGAAAGTG+AGG + chr8_1:50954073-50954092 Msa1199090:CDS 30.0%
!! ATCTTAGCTTGTTTAGCAAT+AGG - chr8_1:50954266-50954285 None:intergenic 30.0%
! GGCATCAAGTGTGTTAATTT+TGG + chr8_1:50954064-50954083 Msa1199090:CDS 35.0%
AGAACAGAACAAAGACATCT+TGG - chr8_1:50954236-50954255 None:intergenic 35.0%
TTCCTAAGAGATGCAACATT+AGG + chr8_1:50954309-50954328 Msa1199090:CDS 35.0%
TTCCTAATGTTGCATCTCTT+AGG - chr8_1:50954314-50954333 None:intergenic 35.0%
AATGTGGAAGGACACCAATT+GGG + chr8_1:50954105-50954124 Msa1199090:CDS 40.0%
! TGCTAGTCTAAGTCCATGTT+TGG + chr8_1:50954136-50954155 Msa1199090:CDS 40.0%
! GCTAGTCTAAGTCCATGTTT+GGG + chr8_1:50954137-50954156 Msa1199090:CDS 40.0%
AAGAACTTTCCTAGCCACAG+TGG + chr8_1:50954028-50954047 Msa1199090:CDS 45.0%
CAACAGAAACATCACCACTG+TGG - chr8_1:50954045-50954064 None:intergenic 45.0%
! CACAGTGGTGATGTTTCTGT+TGG + chr8_1:50954043-50954062 Msa1199090:CDS 45.0%
!! ATTTTGGAAAGTGAGGCAGC+TGG + chr8_1:50954080-50954099 Msa1199090:CDS 45.0%
GAATGTGGAAGGACACCAAT+TGG + chr8_1:50954104-50954123 Msa1199090:CDS 45.0%
TTACGTACAGCACCCAAACA+TGG - chr8_1:50954152-50954171 None:intergenic 45.0%
! TGGGTGCTGTACGTAATGTT+AGG + chr8_1:50954156-50954175 Msa1199090:CDS 45.0%
! GGGTGCTGTACGTAATGTTA+GGG + chr8_1:50954157-50954176 Msa1199090:CDS 45.0%
ACTCTAGCACAACAAACTGG+TGG - chr8_1:50954191-50954210 None:intergenic 45.0%
CCAACTCTAGCACAACAAAC+TGG - chr8_1:50954194-50954213 None:intergenic 45.0%
!! CCAGTTTGTTGTGCTAGAGT+TGG + chr8_1:50954191-50954210 Msa1199090:CDS 45.0%
GGAACAGTGATAGCAATAGC+AGG - chr8_1:50954293-50954312 None:intergenic 45.0%
CACATTTCTTTCCAGCAGGT+CGG - chr8_1:50954337-50954356 None:intergenic 45.0%
CTTCCACATTTCTTTCCAGC+AGG - chr8_1:50954341-50954360 None:intergenic 45.0%
GAAACATCACCACTGTGGCT+AGG - chr8_1:50954040-50954059 None:intergenic 50.0%
AACATTAGGAACCGACCTGC+TGG + chr8_1:50954323-50954342 Msa1199090:CDS 50.0%
CGACCTGCTGGAAAGAAATG+TGG + chr8_1:50954335-50954354 Msa1199090:CDS 50.0%
AGTGAGGCAGCTGGAGAATG+TGG + chr8_1:50954089-50954108 Msa1199090:CDS 55.0%
AGGCAGCTGGAGAATGTGGA+AGG + chr8_1:50954093-50954112 Msa1199090:CDS 55.0%
CTAGCAGCTGCTGACCCAAT+TGG - chr8_1:50954122-50954141 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 50954008 50954367 50954008 ID=Msa1199090;Name=Msa1199090
chr8_1 mRNA 50954008 50954367 50954008 ID=Msa1199090-mRNA-1;Parent=Msa1199090;Name=Msa1199090-mRNA-1;_AED=0.43;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|119
chr8_1 exon 50954008 50954367 50954008 ID=Msa1199090-mRNA-1:exon:16090;Parent=Msa1199090-mRNA-1
chr8_1 CDS 50954008 50954367 50954008 ID=Msa1199090-mRNA-1:cds;Parent=Msa1199090-mRNA-1
Gene Sequence

>Msa1199090

ATGGTGATGGAATTCAAGGTAAGAACTTTCCTAGCCACAGTGGTGATGTTTCTGTTGGCATCAAGTGTGTTAATTTTGGAAAGTGAGGCAGCTGGAGAATGTGGAAGGACACCAATTGGGTCAGCAGCTGCTAGTCTAAGTCCATGTTTGGGTGCTGTACGTAATGTTAGGGCAAAAGTTCCACCAGTTTGTTGTGCTAGAGTTGGTGCTTTGATTAGAACTTCTCCAAGATGTCTTTGTTCTGTTCTTTTGTCACCTATTGCTAAACAAGCTAAGATTAATCCTGCTATTGCTATCACTGTTCCTAAGAGATGCAACATTAGGAACCGACCTGCTGGAAAGAAATGTGGAAGTAAGTAA
Protein sequence

>Msa1199090

MVMEFKVRTFLATVVMFLLASSVLILESEAAGECGRTPIGSAAASLSPCLGAVRNVRAKVPPVCCARVGALIRTSPRCLCSVLLSPIAKQAKINPAIAITVPKRCNIRNRPAGKKCGSK*