AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0591250


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 44 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 4_2:+15586334 Msa0591260:intron
CGCTTTACGCCCAATCATTC+CGG 0.287091 4_2:+15586136 Msa0591260:CDS
ACCTGTCCAGGGTTGAGCCC+TGG 0.327938 4_2:+15586079 None:intergenic
CCTGTCCAGGGTTGAGCCCT+GGG 0.363036 4_2:+15586080 None:intergenic
CAAGCGTTATCCGGAATGAT+TGG 0.365557 4_2:-15586146 Msa0591250:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 4_2:-15586155 Msa0591250:CDS
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 4_2:+15586089 None:intergenic
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 4_2:+15586335 Msa0591260:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 4_2:-15586097 Msa0591250:CDS
TCTCATGGAGAGTTTGATCC+TGG 0.473913 4_2:-15586638 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 4_2:-15586329 Msa0591250:CDS
TTTACACATGCAAGTCGAAC+GGG 0.480570 4_2:-15586590 Msa0591250:CDS
CCACGCGGCATTGCTCCGTC+AGG 0.484232 4_2:+15586283 Msa0591260:intron
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 4_2:-15586330 Msa0591250:CDS
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 4_2:-15586564 Msa0591250:intron
CCCAGGGCTCAACCCTGGAC+AGG 0.508220 4_2:-15586080 Msa0591250:CDS
AAGCGTTATCCGGAATGATT+GGG 0.511219 4_2:-15586145 Msa0591250:CDS
CATGCAAGTCGAACGGGAAG+TGG 0.511388 4_2:-15586584 Msa0591250:CDS
GCCAGCGTTCATCCTGAGCC+AGG 0.514091 4_2:+15586620 None:intergenic
GGAGAGTTTGATCCTGGCTC+AGG 0.515428 4_2:-15586632 Msa0591250:CDS
GTTACTCACCCGTCCGCCAC+TGG 0.515654 4_2:+15586556 Msa0591260:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 4_2:-15586565 Msa0591250:CDS
AGACAAGGCCCAGACTCCTA+CGG 0.532637 4_2:-15586343 Msa0591250:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 4_2:-15586298 Msa0591250:CDS
GACAAGGCCCAGACTCCTAC+GGG 0.538124 4_2:-15586342 Msa0591250:CDS
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 4_2:-15586183 Msa0591250:intron
CAAATCCCAGGGCTCAACCC+TGG 0.557720 4_2:-15586085 Msa0591250:CDS
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 4_2:-15586096 Msa0591250:CDS
AGGGCTCAACCCTGGACAGG+TGG 0.567008 4_2:-15586077 Msa0591250:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 4_2:+15586299 Msa0591260:intron
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 4_2:-15586125 Msa0591250:CDS
CTTTACACATGCAAGTCGAA+CGG 0.597034 4_2:-15586591 Msa0591250:CDS
TCCTGGCTCAGGATGAACGC+TGG 0.603603 4_2:-15586621 Msa0591250:CDS
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 4_2:-15586572 Msa0591250:CDS
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 4_2:-15586569 Msa0591250:CDS
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 4_2:-15586128 Msa0591250:CDS
GACGGAGCAATGCCGCGTGG+AGG 0.640730 4_2:-15586280 Msa0591250:intron
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 4_2:-15586172 Msa0591250:CDS
TGGCTCAGGATGAACGCTGG+CGG 0.650788 4_2:-15586618 Msa0591250:CDS
TCCCCACTGCTGCCTCCCGT+AGG 0.661092 4_2:+15586327 Msa0591260:intron
AAGGCCCAGACTCCTACGGG+AGG 0.671976 4_2:-15586339 Msa0591250:CDS
CCTGACGGAGCAATGCCGCG+TGG 0.711882 4_2:-15586283 Msa0591250:CDS
TTGCATCCTCTGTCTTACCG+CGG 0.760348 4_2:+15586166 Msa0591260:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 4_2:-15586328 Msa0591250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAAAGAATTTCATGACCCGT+AGG + chr4_2:15586451-15586470 Msa0591260:CDS 35.0%
AAGAAACAATGACGGTATCT+GGG - chr4_2:15586478-15586497 Msa0591250:intron 35.0%
CTTTACACATGCAAGTCGAA+CGG - chr4_2:15586107-15586126 Msa0591250:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr4_2:15586108-15586127 Msa0591250:CDS 40.0%
! GGGTCATGAAATTCTTTTCC+TGG - chr4_2:15586453-15586472 Msa0591250:intron 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr4_2:15586470-15586489 Msa0591250:intron 40.0%
GAAGAAACAATGACGGTATC+TGG - chr4_2:15586477-15586496 Msa0591250:intron 40.0%
AGAAACAATGACGGTATCTG+GGG - chr4_2:15586479-15586498 Msa0591250:intron 40.0%
AAGCGTTATCCGGAATGATT+GGG - chr4_2:15586553-15586572 Msa0591250:intron 40.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr4_2:15586268-15586287 Msa0591250:intron 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr4_2:15586284-15586303 Msa0591250:CDS 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr4_2:15586287-15586306 Msa0591250:CDS 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr4_2:15586386-15586405 Msa0591250:intron 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr4_2:15586474-15586493 Msa0591260:CDS 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr4_2:15586491-15586510 Msa0591250:intron 45.0%
CAAGCGTTATCCGGAATGAT+TGG - chr4_2:15586552-15586571 Msa0591250:intron 45.0%
! TAGTTTTCACCACCTGTCCA+GGG + chr4_2:15586633-15586652 None:intergenic 45.0%
AGGGGAACAACAGCTGGAAA+CGG - chr4_2:15586186-15586205 Msa0591250:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr4_2:15586210-15586229 Msa0591250:intron 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr4_2:15586223-15586242 Msa0591260:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr4_2:15586263-15586282 Msa0591250:intron 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr4_2:15586328-15586347 Msa0591260:intron 50.0%
AGAGGATGATCAGCCACACT+GGG - chr4_2:15586328-15586347 Msa0591250:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr4_2:15586385-15586404 Msa0591250:intron 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr4_2:15586535-15586554 Msa0591260:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr4_2:15586543-15586562 Msa0591250:intron 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr4_2:15586565-15586584 Msa0591260:CDS 50.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr4_2:15586570-15586589 Msa0591250:CDS 50.0%
TAAGTTCGCCGTCAAATCCC+AGG - chr4_2:15586601-15586620 Msa0591250:CDS 50.0%
AAGTTCGCCGTCAAATCCCA+GGG - chr4_2:15586602-15586621 Msa0591250:CDS 50.0%
! GTAGTTTTCACCACCTGTCC+AGG + chr4_2:15586634-15586653 None:intergenic 50.0%
GGAGAGTTTGATCCTGGCTC+AGG - chr4_2:15586066-15586085 Msa0591250:CDS 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr4_2:15586114-15586133 Msa0591250:CDS 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr4_2:15586126-15586145 Msa0591250:CDS 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr4_2:15586129-15586148 Msa0591250:CDS 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr4_2:15586162-15586181 Msa0591250:CDS 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr4_2:15586163-15586182 Msa0591250:CDS 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr4_2:15586167-15586186 Msa0591250:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr4_2:15586168-15586187 Msa0591250:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr4_2:15586181-15586200 Msa0591260:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr4_2:15586221-15586240 Msa0591260:CDS 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr4_2:15586222-15586241 Msa0591260:CDS 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr4_2:15586222-15586241 Msa0591250:intron 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr4_2:15586310-15586329 Msa0591250:CDS 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr4_2:15586327-15586346 Msa0591250:CDS 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr4_2:15586355-15586374 Msa0591250:intron 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr4_2:15586425-15586444 Msa0591250:intron 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr4_2:15586433-15586452 Msa0591260:CDS 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr4_2:15586432-15586451 Msa0591250:intron 55.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr4_2:15586433-15586452 Msa0591250:intron 55.0%
GGTTGAGCCCTGGGATTTGA+CGG + chr4_2:15586612-15586631 Msa0591260:CDS 55.0%
TCCTGGCTCAGGATGAACGC+TGG - chr4_2:15586077-15586096 Msa0591250:CDS 60.0%
TGGCTCAGGATGAACGCTGG+CGG - chr4_2:15586080-15586099 Msa0591250:CDS 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr4_2:15586133-15586152 Msa0591250:CDS 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr4_2:15586134-15586153 Msa0591250:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr4_2:15586166-15586185 Msa0591250:CDS 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr4_2:15586182-15586201 Msa0591260:CDS 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr4_2:15586180-15586199 Msa0591250:intron 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr4_2:15586219-15586238 Msa0591250:intron 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr4_2:15586235-15586254 Msa0591250:intron 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr4_2:15586238-15586257 Msa0591250:intron 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr4_2:15586239-15586258 Msa0591250:intron 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr4_2:15586304-15586323 Msa0591260:intron 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr4_2:15586301-15586320 Msa0591250:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr4_2:15586340-15586359 Msa0591250:CDS 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr4_2:15586344-15586363 Msa0591260:intron 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr4_2:15586356-15586375 Msa0591250:intron 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr4_2:15586402-15586421 Msa0591260:CDS 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr4_2:15586400-15586419 Msa0591250:intron 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr4_2:15586515-15586534 Msa0591250:intron 60.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr4_2:15586573-15586592 Msa0591250:CDS 60.0%
CAAATCCCAGGGCTCAACCC+TGG - chr4_2:15586613-15586632 Msa0591250:CDS 60.0%
GCCAGCGTTCATCCTGAGCC+AGG + chr4_2:15586081-15586100 None:intergenic 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr4_2:15586145-15586164 Msa0591260:CDS 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr4_2:15586177-15586196 Msa0591260:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr4_2:15586240-15586259 Msa0591250:intron 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr4_2:15586254-15586273 Msa0591260:intron 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr4_2:15586255-15586274 Msa0591260:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr4_2:15586359-15586378 Msa0591250:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr4_2:15586366-15586385 Msa0591260:intron 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr4_2:15586367-15586386 Msa0591260:intron 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr4_2:15586368-15586387 Msa0591250:intron 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr4_2:15586369-15586388 Msa0591250:intron 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr4_2:15586370-15586389 Msa0591250:intron 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr4_2:15586528-15586547 Msa0591260:CDS 65.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr4_2:15586526-15586545 Msa0591250:intron 65.0%
CCTGTCCAGGGTTGAGCCCT+GGG + chr4_2:15586621-15586640 None:intergenic 65.0%
ACCTGTCCAGGGTTGAGCCC+TGG + chr4_2:15586622-15586641 None:intergenic 65.0%
AGGGCTCAACCCTGGACAGG+TGG - chr4_2:15586621-15586640 Msa0591250:CDS 65.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr4_2:15586374-15586393 Msa0591260:CDS 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr4_2:15586418-15586437 Msa0591260:CDS 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr4_2:15586415-15586434 Msa0591250:intron 70.0%
GACGGAGCAATGCCGCGTGG+AGG - chr4_2:15586418-15586437 Msa0591250:intron 70.0%
CCCAGGGCTCAACCCTGGAC+AGG - chr4_2:15586618-15586637 Msa0591250:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr4_2:15586251-15586270 Msa0591260:intron 75.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 15586064 15586656 15586064 ID=Msa0591250;Name=Msa0591250
chr4_2 mRNA 15586064 15586656 15586064 ID=Msa0591250-mRNA-1;Parent=Msa0591250;Name=Msa0591250-mRNA-1;_AED=0.88;_eAED=1.00;_QI=0|0|0|0.33|1|1|3|0|100
chr4_2 exon 15586565 15586656 15586565 ID=Msa0591250-mRNA-1:exon:4524;Parent=Msa0591250-mRNA-1
chr4_2 exon 15586281 15586363 15586281 ID=Msa0591250-mRNA-1:exon:4523;Parent=Msa0591250-mRNA-1
chr4_2 exon 15586064 15586191 15586064 ID=Msa0591250-mRNA-1:exon:4522;Parent=Msa0591250-mRNA-1
chr4_2 CDS 15586565 15586656 15586565 ID=Msa0591250-mRNA-1:cds;Parent=Msa0591250-mRNA-1
chr4_2 CDS 15586281 15586363 15586281 ID=Msa0591250-mRNA-1:cds;Parent=Msa0591250-mRNA-1
chr4_2 CDS 15586064 15586191 15586064 ID=Msa0591250-mRNA-1:cds;Parent=Msa0591250-mRNA-1
Gene Sequence

>Msa0591250

ATGGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTTACACATGCAAGTCGAACGGGAAGTGGTGTTTCCAGTGGCGGACGGACAAGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTTCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGTGGTGAAAACTACTAA

Protein sequence

>Msa0591250

MESLILAQDERWRHALHMQVEREVVFPVADGQGPDSYGRQQWGIFRNGRKPDGAMPRGAAAVRQRMQALSGMIGRKASVGGFLSSPSNPRAQPWTGGENY*