AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1365980


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 tig0018442:-53151 Msa1365980:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0018442:+53264 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0018442:-53349 Msa1365980:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0018442:+53212 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0018442:-53007 Msa1365980:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0018442:-53039 Msa1365980:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0018442:-53312 Msa1365980:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0018442:-53006 Msa1365980:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0018442:+53339 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0018442:-52966 Msa1365980:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0018442:+53330 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0018442:-53396 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0018442:+52967 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0018442:+53050 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0018442:-52961 Msa1365980:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0018442:-53038 Msa1365980:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0018442:-53150 Msa1365980:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0018442:+53388 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0018442:+52955 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0018442:+53156 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0018442:+52973 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0018442:+52895 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0018442:-53202 Msa1365980:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0018442:+53155 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0018442:+53265 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0018442:+52949 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0018442:+53026 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0018442:+52921 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0018442:+53340 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0018442:+52901 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0018442:-52929 Msa1365980:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0018442:+52920 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0018442:+52950 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0018442:-52965 Msa1365980:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0018442:+53187 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0018442:+53088 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0018442:+53302 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0018442:+52953 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0018442:+53006 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0018442:+53114 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0018442:+52954 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0018442:+53219 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0018442:+53027 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0018442:+53389 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0018442:+53220 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0018442:-53035 Msa1365980:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0018442:-53005 Msa1365980:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0018442:-53088 Msa1365980:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0018442:-53186 Msa1365980:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0018442:+53360 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0018442:-53112 Msa1365980:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0018442:+53022 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0018442:+52894 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0018442:+52864 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0018442:+53115 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0018442:+52997 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0018442:+53278 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0018442:+52913 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0018442:+53025 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0018442:+52916 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0018442:+53257 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0018442:+53127 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0018442:+53357 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0018442:+53205 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0018442:+53055 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0018442:+53313 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0018442:+52867 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0018442:-53235 Msa1365980:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0018442:+53009 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0018442:-53128 Msa1365980:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0018442:+53266 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0018442:+53097 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0018442:+53202 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0018442:+53071 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0018442:+53074 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0018442:-53319 Msa1365980:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0018442:+53157 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + tig0018442:52999-53018 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + tig0018442:52924-52943 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + tig0018442:52998-53017 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + tig0018442:53000-53019 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + tig0018442:53007-53026 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - tig0018442:53026-53045 Msa1365980:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + tig0018442:53369-53388 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + tig0018442:53370-53389 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + tig0018442:52925-52944 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + tig0018442:52986-53005 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - tig0018442:53003-53022 Msa1365980:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + tig0018442:53024-53043 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + tig0018442:53091-53110 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + tig0018442:53190-53209 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + tig0018442:53193-53212 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + tig0018442:53209-53228 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + tig0018442:52907-52926 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - tig0018442:52912-52931 Msa1365980:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + tig0018442:52934-52953 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - tig0018442:52942-52961 Msa1365980:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + tig0018442:53092-53111 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + tig0018442:53149-53168 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - tig0018442:53149-53168 Msa1365980:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + tig0018442:53214-53233 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - tig0018442:53254-53273 Msa1365980:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + tig0018442:53267-53286 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + tig0018442:53291-53310 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + tig0018442:53044-53063 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + tig0018442:53045-53064 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - tig0018442:53044-53063 Msa1365980:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + tig0018442:53052-53071 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + tig0018442:53122-53141 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + tig0018442:53150-53169 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + tig0018442:53167-53186 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + tig0018442:53255-53274 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - tig0018442:53255-53274 Msa1365980:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - tig0018442:53256-53275 Msa1365980:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - tig0018442:53296-53315 Msa1365980:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + tig0018442:53309-53328 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + tig0018442:53310-53329 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + tig0018442:53314-53333 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + tig0018442:53315-53334 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + tig0018442:53348-53367 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + tig0018442:53351-53370 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + tig0018442:53363-53382 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + tig0018442:52904-52923 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + tig0018442:52962-52981 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + tig0018442:53077-53096 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - tig0018442:53075-53094 Msa1365980:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + tig0018442:53121-53140 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - tig0018442:53133-53152 Msa1365980:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + tig0018442:53137-53156 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + tig0018442:53176-53195 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - tig0018442:53173-53192 Msa1365980:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + tig0018442:53238-53257 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + tig0018442:53239-53258 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + tig0018442:53242-53261 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + tig0018442:53258-53277 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + tig0018442:53297-53316 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - tig0018442:53295-53314 Msa1365980:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + tig0018442:53311-53330 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + tig0018442:53343-53362 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + tig0018442:53344-53363 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + tig0018442:52951-52970 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - tig0018442:52949-52968 Msa1365980:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + tig0018442:53107-53126 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + tig0018442:53108-53127 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + tig0018442:53109-53128 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - tig0018442:53110-53129 Msa1365980:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - tig0018442:53111-53130 Msa1365980:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + tig0018442:53118-53137 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - tig0018442:53222-53241 Msa1365980:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - tig0018442:53223-53242 Msa1365980:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + tig0018442:53237-53256 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - tig0018442:53300-53319 Msa1365980:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - tig0018442:53332-53351 Msa1365980:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + tig0018442:53059-53078 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + tig0018442:53062-53081 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - tig0018442:53059-53078 Msa1365980:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - tig0018442:53103-53122 Msa1365980:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - tig0018442:53226-53245 Msa1365980:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0018442 gene 52874 53409 52874 ID=Msa1365980;Name=Msa1365980
tig0018442 mRNA 52874 53409 52874 ID=Msa1365980-mRNA-1;Parent=Msa1365980;Name=Msa1365980-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0018442 exon 53272 53409 53272 ID=Msa1365980-mRNA-1:exon:14905;Parent=Msa1365980-mRNA-1
tig0018442 exon 53163 53258 53163 ID=Msa1365980-mRNA-1:exon:14904;Parent=Msa1365980-mRNA-1
tig0018442 exon 52874 53158 52874 ID=Msa1365980-mRNA-1:exon:14903;Parent=Msa1365980-mRNA-1
tig0018442 CDS 53272 53409 53272 ID=Msa1365980-mRNA-1:cds;Parent=Msa1365980-mRNA-1
tig0018442 CDS 53163 53258 53163 ID=Msa1365980-mRNA-1:cds;Parent=Msa1365980-mRNA-1
tig0018442 CDS 52874 53158 52874 ID=Msa1365980-mRNA-1:cds;Parent=Msa1365980-mRNA-1
Gene Sequence

>Msa1365980

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1365980

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS