AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908490


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 72 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 6_2:-9650055 Msa0908490:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_2:+9650168 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:-9650253 Msa0908490:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:+9650116 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_2:-9649911 Msa0908490:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_2:-9649943 Msa0908490:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:-9650216 Msa0908490:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_2:-9649910 Msa0908490:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:+9650243 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_2:-9649870 Msa0908490:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:+9650234 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:-9650300 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_2:+9649871 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_2:+9649954 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_2:-9649865 Msa0908490:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_2:-9649942 Msa0908490:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_2:-9650054 Msa0908490:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:+9650292 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_2:+9649859 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_2:+9650060 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_2:+9649877 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_2:+9649798 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.480800 6_2:+9649804 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:-9650106 Msa0908490:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_2:+9650059 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_2:+9650169 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_2:+9649853 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_2:+9649930 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:+9650244 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_2:-9649833 Msa0908490:CDS
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_2:+9649854 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_2:-9649869 Msa0908490:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:+9650091 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_2:+9649992 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:+9650206 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_2:+9649857 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_2:+9649910 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_2:+9650018 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_2:+9649858 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:+9650123 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_2:+9649931 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:+9650293 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:+9650124 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_2:-9649939 Msa0908490:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_2:-9649909 Msa0908490:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_2:-9649992 Msa0908490:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_2:-9650090 Msa0908490:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:+9650264 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_2:-9650016 Msa0908490:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_2:+9649926 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_2:+9649797 None:intergenic
ATGCAAGTCGAACGGGAAGT+GGG 0.601698 6_2:+9649805 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_2:+9650019 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_2:+9649901 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_2:+9650182 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_2:+9649929 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:+9650161 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_2:+9650031 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:+9650261 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:+9650109 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_2:+9649959 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:+9650217 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:-9650139 Msa0908490:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_2:+9649913 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_2:-9650032 Msa0908490:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_2:+9650170 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_2:+9650001 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:+9650106 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_2:+9649975 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_2:+9649978 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:-9650223 Msa0908490:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_2:+9650061 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr6_2:9649927-9649946 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr6_2:9649852-9649871 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr6_2:9649926-9649945 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr6_2:9649928-9649947 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr6_2:9649935-9649954 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr6_2:9649954-9649973 Msa0908490:CDS 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr6_2:9649853-9649872 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr6_2:9649914-9649933 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr6_2:9649931-9649950 Msa0908490:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr6_2:9649952-9649971 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr6_2:9650019-9650038 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr6_2:9650118-9650137 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr6_2:9650121-9650140 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr6_2:9650137-9650156 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr6_2:9649835-9649854 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr6_2:9649840-9649859 Msa0908490:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr6_2:9649862-9649881 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr6_2:9649870-9649889 Msa0908490:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr6_2:9650020-9650039 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr6_2:9650077-9650096 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr6_2:9650077-9650096 Msa0908490:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr6_2:9650142-9650161 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr6_2:9650182-9650201 Msa0908490:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr6_2:9650195-9650214 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr6_2:9650219-9650238 None:intergenic 50.0%
!! GAAGTGGGTTTTTCCAGTGG+CGG + chr6_2:9650276-9650295 None:intergenic 50.0%
ATGCAAGTCGAACGGGAAGT+GGG + chr6_2:9650291-9650310 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr6_2:9649972-9649991 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr6_2:9649973-9649992 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr6_2:9649972-9649991 Msa0908490:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr6_2:9649980-9649999 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr6_2:9650050-9650069 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr6_2:9650078-9650097 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr6_2:9650095-9650114 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr6_2:9650183-9650202 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr6_2:9650183-9650202 Msa0908490:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr6_2:9650184-9650203 Msa0908490:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr6_2:9650224-9650243 Msa0908490:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr6_2:9650237-9650256 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr6_2:9650238-9650257 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr6_2:9650242-9650261 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr6_2:9650243-9650262 None:intergenic 55.0%
!! TGGGTTTTTCCAGTGGCGGA+CGG + chr6_2:9650272-9650291 None:intergenic 55.0%
!! CGGGAAGTGGGTTTTTCCAG+TGG + chr6_2:9650279-9650298 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr6_2:9650292-9650311 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr6_2:9649832-9649851 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr6_2:9649890-9649909 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr6_2:9650005-9650024 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr6_2:9650003-9650022 Msa0908490:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr6_2:9650049-9650068 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr6_2:9650061-9650080 Msa0908490:intron 60.0%
GCCACACTGGGACTGAGACA+AGG + chr6_2:9650065-9650084 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr6_2:9650104-9650123 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr6_2:9650101-9650120 Msa0908490:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr6_2:9650166-9650185 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr6_2:9650167-9650186 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr6_2:9650170-9650189 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr6_2:9650186-9650205 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr6_2:9650225-9650244 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr6_2:9650223-9650242 Msa0908490:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr6_2:9650239-9650258 None:intergenic 60.0%
!!! GGGTTTTTCCAGTGGCGGAC+GGG + chr6_2:9650271-9650290 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr6_2:9649879-9649898 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr6_2:9649877-9649896 Msa0908490:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr6_2:9650035-9650054 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr6_2:9650036-9650055 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr6_2:9650037-9650056 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr6_2:9650038-9650057 Msa0908490:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr6_2:9650039-9650058 Msa0908490:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr6_2:9650046-9650065 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr6_2:9650150-9650169 Msa0908490:intron 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr6_2:9650151-9650170 Msa0908490:intron 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr6_2:9650165-9650184 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr6_2:9650228-9650247 Msa0908490:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr6_2:9650260-9650279 Msa0908490:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr6_2:9649987-9650006 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr6_2:9649990-9650009 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr6_2:9649987-9650006 Msa0908490:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr6_2:9650031-9650050 Msa0908490:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr6_2:9650154-9650173 Msa0908490:intron 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9649802 9650313 9649802 ID=Msa0908490;Name=Msa0908490
chr6_2 mRNA 9649802 9650313 9649802 ID=Msa0908490-mRNA-1;Parent=Msa0908490;Name=Msa0908490-mRNA-1;_AED=0.21;_eAED=0.29;_QI=0|0|0|1|0.5|0.33|3|0|165
chr6_2 exon 9650176 9650313 9650176 ID=Msa0908490-mRNA-1:exon:2340;Parent=Msa0908490-mRNA-1
chr6_2 exon 9650067 9650162 9650067 ID=Msa0908490-mRNA-1:exon:2339;Parent=Msa0908490-mRNA-1
chr6_2 exon 9649802 9650062 9649802 ID=Msa0908490-mRNA-1:exon:2338;Parent=Msa0908490-mRNA-1
chr6_2 CDS 9650176 9650313 9650176 ID=Msa0908490-mRNA-1:cds;Parent=Msa0908490-mRNA-1
chr6_2 CDS 9650067 9650162 9650067 ID=Msa0908490-mRNA-1:cds;Parent=Msa0908490-mRNA-1
chr6_2 CDS 9649802 9650062 9649802 ID=Msa0908490-mRNA-1:cds;Parent=Msa0908490-mRNA-1
Gene Sequence

>Msa0908490

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAAAACCCACTTCCCGTTCGACTTGCATGTG

Protein sequence

>Msa0908490

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGKTHFPFDLHV