AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0983620


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_4:+26755131 Msa0983620:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_4:-26755018 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_4:+26754933 Msa0983620:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_4:-26755070 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_4:+26755275 Msa0983620:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_4:+26755243 Msa0983620:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_4:+26754970 Msa0983620:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_4:+26755276 Msa0983620:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_4:-26754943 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_4:+26755316 Msa0983620:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_4:-26754952 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_4:+26754886 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_4:-26755315 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_4:-26755232 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_4:+26755321 Msa0983620:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_4:+26755244 Msa0983620:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_4:+26755132 Msa0983620:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_4:-26754894 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_4:-26755327 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_4:-26755126 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_4:-26755309 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_4:-26755387 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_4:+26755080 Msa0983620:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_4:-26755127 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_4:-26755017 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_4:-26755333 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_4:-26755256 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_4:-26755361 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_4:-26754942 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_4:-26755381 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_4:+26755353 Msa0983620:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_4:-26755362 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_4:-26755332 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_4:+26755317 Msa0983620:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_4:-26755095 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_4:-26755194 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_4:-26754980 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_4:-26755329 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_4:-26755276 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_4:-26755168 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_4:-26755328 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_4:-26755063 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_4:-26755255 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_4:-26754893 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_4:-26755062 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_4:+26755247 Msa0983620:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_4:+26755277 Msa0983620:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_4:+26755194 Msa0983620:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_4:+26755096 Msa0983620:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_4:-26754922 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_4:+26755170 Msa0983620:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_4:-26755260 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_4:-26755388 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_4:-26755418 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_4:-26755167 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_4:-26755285 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_4:-26755004 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_4:-26755369 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_4:-26755257 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_4:-26755366 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_4:-26755025 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_4:-26755155 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_4:-26754925 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_4:-26755077 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_4:-26755227 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_4:-26754969 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_4:-26755415 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_4:+26755047 Msa0983620:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_4:-26755273 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_4:+26755154 Msa0983620:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_4:-26755016 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_4:-26755185 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_4:-26755080 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_4:-26755211 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_4:-26755208 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_4:+26754963 Msa0983620:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_4:-26755125 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr6_4:26755020-26755039 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr6_4:26754945-26754964 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr6_4:26755019-26755038 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr6_4:26755021-26755040 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr6_4:26755028-26755047 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr6_4:26755047-26755066 Msa0983620:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr6_4:26755390-26755409 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr6_4:26755391-26755410 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr6_4:26754946-26754965 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr6_4:26755007-26755026 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr6_4:26755024-26755043 Msa0983620:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr6_4:26755045-26755064 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr6_4:26755112-26755131 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr6_4:26755211-26755230 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr6_4:26755214-26755233 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr6_4:26755230-26755249 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr6_4:26754928-26754947 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr6_4:26754933-26754952 Msa0983620:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr6_4:26754955-26754974 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr6_4:26754963-26754982 Msa0983620:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr6_4:26755113-26755132 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr6_4:26755170-26755189 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr6_4:26755170-26755189 Msa0983620:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr6_4:26755235-26755254 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr6_4:26755275-26755294 Msa0983620:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr6_4:26755288-26755307 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr6_4:26755312-26755331 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr6_4:26755065-26755084 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr6_4:26755066-26755085 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr6_4:26755065-26755084 Msa0983620:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr6_4:26755073-26755092 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr6_4:26755143-26755162 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr6_4:26755171-26755190 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr6_4:26755188-26755207 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr6_4:26755276-26755295 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr6_4:26755276-26755295 Msa0983620:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr6_4:26755277-26755296 Msa0983620:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr6_4:26755317-26755336 Msa0983620:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr6_4:26755330-26755349 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr6_4:26755331-26755350 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr6_4:26755335-26755354 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr6_4:26755336-26755355 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr6_4:26755369-26755388 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr6_4:26755372-26755391 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr6_4:26755384-26755403 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr6_4:26754925-26754944 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr6_4:26754983-26755002 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr6_4:26755098-26755117 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr6_4:26755096-26755115 Msa0983620:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr6_4:26755142-26755161 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr6_4:26755154-26755173 Msa0983620:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr6_4:26755158-26755177 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr6_4:26755197-26755216 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr6_4:26755194-26755213 Msa0983620:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr6_4:26755259-26755278 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr6_4:26755260-26755279 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr6_4:26755263-26755282 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr6_4:26755279-26755298 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr6_4:26755318-26755337 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr6_4:26755316-26755335 Msa0983620:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr6_4:26755332-26755351 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr6_4:26755364-26755383 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr6_4:26755365-26755384 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr6_4:26754972-26754991 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr6_4:26754970-26754989 Msa0983620:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr6_4:26755128-26755147 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr6_4:26755129-26755148 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr6_4:26755130-26755149 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr6_4:26755131-26755150 Msa0983620:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr6_4:26755132-26755151 Msa0983620:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr6_4:26755139-26755158 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr6_4:26755243-26755262 Msa0983620:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr6_4:26755244-26755263 Msa0983620:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr6_4:26755258-26755277 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr6_4:26755321-26755340 Msa0983620:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr6_4:26755353-26755372 Msa0983620:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr6_4:26755080-26755099 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr6_4:26755083-26755102 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr6_4:26755080-26755099 Msa0983620:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr6_4:26755124-26755143 Msa0983620:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr6_4:26755247-26755266 Msa0983620:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 26754895 26755430 26754895 ID=Msa0983620;Name=Msa0983620
chr6_4 mRNA 26754895 26755430 26754895 ID=Msa0983620-mRNA-1;Parent=Msa0983620;Name=Msa0983620-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr6_4 exon 26754895 26755032 26754895 ID=Msa0983620-mRNA-1:exon:7571;Parent=Msa0983620-mRNA-1
chr6_4 exon 26755046 26755141 26755046 ID=Msa0983620-mRNA-1:exon:7572;Parent=Msa0983620-mRNA-1
chr6_4 exon 26755146 26755430 26755146 ID=Msa0983620-mRNA-1:exon:7573;Parent=Msa0983620-mRNA-1
chr6_4 CDS 26754895 26755032 26754895 ID=Msa0983620-mRNA-1:cds;Parent=Msa0983620-mRNA-1
chr6_4 CDS 26755046 26755141 26755046 ID=Msa0983620-mRNA-1:cds;Parent=Msa0983620-mRNA-1
chr6_4 CDS 26755146 26755430 26755146 ID=Msa0983620-mRNA-1:cds;Parent=Msa0983620-mRNA-1
Gene Sequence

>Msa0983620

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0983620

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS