AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908460


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 77 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 6_2:-9609069 Msa0908460:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_2:+9609182 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:-9609267 Msa0908460:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:+9609130 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_2:-9608925 Msa0908460:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_2:-9608957 Msa0908460:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:-9609230 Msa0908460:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_2:-9608924 Msa0908460:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:+9609257 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_2:-9608884 Msa0908460:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:+9609248 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:-9609314 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_2:+9608885 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_2:+9608968 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_2:-9608879 Msa0908460:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_2:-9608956 Msa0908460:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_2:-9609068 Msa0908460:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:+9609306 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_2:+9608873 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_2:+9609074 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_2:+9608891 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_2:+9608813 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:-9609120 Msa0908460:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_2:+9609073 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_2:+9609183 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_2:+9608867 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_2:+9608944 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_2:+9608839 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:+9609258 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_2:+9608819 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_2:-9608847 Msa0908460:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_2:+9608838 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_2:+9608868 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_2:-9608883 Msa0908460:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:+9609105 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_2:+9609006 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:+9609220 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_2:+9608871 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_2:+9608924 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_2:+9609032 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_2:+9608872 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:+9609137 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_2:+9608945 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:+9609307 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:+9609138 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_2:-9608953 Msa0908460:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_2:-9608923 Msa0908460:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_2:-9609006 Msa0908460:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_2:-9609104 Msa0908460:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:+9609278 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_2:-9609030 Msa0908460:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_2:+9608940 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_2:+9608812 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_2:+9608782 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_2:+9609033 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_2:+9608915 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_2:+9609196 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_2:+9608831 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_2:+9608943 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_2:+9608834 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:+9609175 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_2:+9609045 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:+9609275 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:+9609123 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_2:+9608973 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:+9609231 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_2:+9608785 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:-9609153 Msa0908460:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_2:+9608927 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_2:-9609046 Msa0908460:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_2:+9609184 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_2:+9609015 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:+9609120 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_2:+9608989 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_2:+9608992 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:-9609237 Msa0908460:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_2:+9609075 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr6_2:9608917-9608936 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr6_2:9608842-9608861 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr6_2:9608916-9608935 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr6_2:9608918-9608937 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr6_2:9608925-9608944 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr6_2:9608944-9608963 Msa0908460:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr6_2:9609287-9609306 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr6_2:9609288-9609307 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr6_2:9608843-9608862 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr6_2:9608904-9608923 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr6_2:9608921-9608940 Msa0908460:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr6_2:9608942-9608961 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr6_2:9609009-9609028 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr6_2:9609108-9609127 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr6_2:9609111-9609130 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr6_2:9609127-9609146 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr6_2:9608825-9608844 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr6_2:9608830-9608849 Msa0908460:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr6_2:9608852-9608871 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr6_2:9608860-9608879 Msa0908460:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr6_2:9609010-9609029 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr6_2:9609067-9609086 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr6_2:9609067-9609086 Msa0908460:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr6_2:9609132-9609151 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr6_2:9609172-9609191 Msa0908460:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr6_2:9609185-9609204 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr6_2:9609209-9609228 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr6_2:9608962-9608981 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr6_2:9608963-9608982 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr6_2:9608962-9608981 Msa0908460:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr6_2:9608970-9608989 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr6_2:9609040-9609059 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr6_2:9609068-9609087 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr6_2:9609085-9609104 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr6_2:9609173-9609192 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr6_2:9609173-9609192 Msa0908460:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr6_2:9609174-9609193 Msa0908460:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr6_2:9609214-9609233 Msa0908460:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr6_2:9609227-9609246 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr6_2:9609228-9609247 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr6_2:9609232-9609251 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr6_2:9609233-9609252 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr6_2:9609266-9609285 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr6_2:9609269-9609288 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr6_2:9609281-9609300 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr6_2:9608822-9608841 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr6_2:9608880-9608899 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr6_2:9608995-9609014 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr6_2:9608993-9609012 Msa0908460:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr6_2:9609039-9609058 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr6_2:9609051-9609070 Msa0908460:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr6_2:9609055-9609074 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr6_2:9609094-9609113 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr6_2:9609091-9609110 Msa0908460:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr6_2:9609156-9609175 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr6_2:9609157-9609176 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr6_2:9609160-9609179 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr6_2:9609176-9609195 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr6_2:9609215-9609234 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr6_2:9609213-9609232 Msa0908460:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr6_2:9609229-9609248 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr6_2:9609261-9609280 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr6_2:9609262-9609281 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr6_2:9608869-9608888 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr6_2:9608867-9608886 Msa0908460:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr6_2:9609025-9609044 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr6_2:9609026-9609045 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr6_2:9609027-9609046 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr6_2:9609028-9609047 Msa0908460:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr6_2:9609029-9609048 Msa0908460:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr6_2:9609036-9609055 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr6_2:9609140-9609159 Msa0908460:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr6_2:9609141-9609160 Msa0908460:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr6_2:9609155-9609174 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr6_2:9609218-9609237 Msa0908460:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr6_2:9609250-9609269 Msa0908460:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr6_2:9608977-9608996 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr6_2:9608980-9608999 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr6_2:9608977-9608996 Msa0908460:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr6_2:9609021-9609040 Msa0908460:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr6_2:9609144-9609163 Msa0908460:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9608792 9609327 9608792 ID=Msa0908460;Name=Msa0908460
chr6_2 mRNA 9608792 9609327 9608792 ID=Msa0908460-mRNA-1;Parent=Msa0908460;Name=Msa0908460-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0.5|0|3|0|173
chr6_2 exon 9609190 9609327 9609190 ID=Msa0908460-mRNA-1:exon:2344;Parent=Msa0908460-mRNA-1
chr6_2 exon 9609081 9609176 9609081 ID=Msa0908460-mRNA-1:exon:2343;Parent=Msa0908460-mRNA-1
chr6_2 exon 9608792 9609076 9608792 ID=Msa0908460-mRNA-1:exon:2342;Parent=Msa0908460-mRNA-1
chr6_2 CDS 9609190 9609327 9609190 ID=Msa0908460-mRNA-1:cds;Parent=Msa0908460-mRNA-1
chr6_2 CDS 9609081 9609176 9609081 ID=Msa0908460-mRNA-1:cds;Parent=Msa0908460-mRNA-1
chr6_2 CDS 9608792 9609076 9608792 ID=Msa0908460-mRNA-1:cds;Parent=Msa0908460-mRNA-1
Gene Sequence

>Msa0908460

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0908460

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS