AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0425110

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0425110 MtrunA17_Chr3g0127111 93.671 79 4 1 1 78 1 79 1.36e-49 150
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGGTTTCTTTGAATGCTT+TGG 0.177524 3_2:+75450888 None:intergenic
TTCTTTGAATGCTTTGGGTT+GGG 0.313836 3_2:+75450894 None:intergenic
AAACCAAGAGGATGACTAAA+AGG 0.335491 3_2:+75451480 None:intergenic
CAGGTTTCTTTGAATGCTTT+GGG 0.352628 3_2:+75450889 None:intergenic
AGGTATTAATAAATAAAGTA+TGG 0.361284 3_2:-75450660 Msa0425110:three_prime_UTR
TGATTAGTAATTAGTTGTTA+AGG 0.392811 3_2:+75450849 None:intergenic
TTTCTTTGAATGCTTTGGGT+TGG 0.396872 3_2:+75450893 None:intergenic
TTGTAAAGAAAGTTATTAGT+AGG 0.421064 3_2:+75451312 None:intergenic
TACTAATAACTTTCTTTACA+AGG 0.464774 3_2:-75451310 Msa0425110:intron
TGAGTGTATTGTAACTTATG+AGG 0.474983 3_2:-75450680 Msa0425110:three_prime_UTR
GGTGTTTAACGACCCTTGCC+AGG 0.478184 3_2:+75450870 None:intergenic
TTCATTGCATATACTTGCCA+TGG 0.509554 3_2:-75451522 Msa0425110:exon
ATGAATATAAATGACTTGGC+AGG 0.510347 3_2:+75451587 None:intergenic
CCAAAGCATTCAAAGAAACC+TGG 0.549609 3_2:-75450888 Msa0425110:CDS
AATCGAGCTAGTTTCTTCAC+CGG 0.549992 3_2:-75450713 Msa0425110:three_prime_UTR
TAAAATGAATATAAATGACT+TGG 0.575545 3_2:+75451583 None:intergenic
ATACACTCAAGTAGTGGCTC+CGG 0.581091 3_2:+75450694 None:intergenic
GTGTTGGATTATGATGAAGC+AGG 0.583814 3_2:-75450918 Msa0425110:CDS
GCATTCAAAGAAACCTGGCA+AGG 0.596187 3_2:-75450883 Msa0425110:CDS
ATTTATTTACCTGAAGACAA+AGG 0.597528 3_2:+75451446 None:intergenic
CATTCAAAGAAACCTGGCAA+GGG 0.630511 3_2:-75450882 Msa0425110:CDS
GTTACAATACACTCAAGTAG+TGG 0.639021 3_2:+75450688 None:intergenic
GAAAATGAATGAAAACCAAG+AGG 0.671422 3_2:+75451468 None:intergenic
ATGGTGTAAAGATGAACTCG+AGG 0.686471 3_2:-75450962 Msa0425110:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTCATATAGTTTTAAA+TGG - chr3_2:75450964-75450983 Msa0425110:CDS 10.0%
!!! TTATTTGTAAACATTATTTT+GGG + chr3_2:75451139-75451158 None:intergenic 10.0%
!!! TTTATTTGTAAACATTATTT+TGG + chr3_2:75451140-75451159 None:intergenic 10.0%
!!! AGATTACAATTTTTTTTTAT+AGG + chr3_2:75451174-75451193 None:intergenic 10.0%
!!! TTTTTTCATATAGTTTTAAA+TGG - chr3_2:75450964-75450983 Msa0425110:CDS 10.0%
!!! TTATTTGTAAACATTATTTT+GGG + chr3_2:75451139-75451158 None:intergenic 10.0%
!!! TTTATTTGTAAACATTATTT+TGG + chr3_2:75451140-75451159 None:intergenic 10.0%
!!! AGATTACAATTTTTTTTTAT+AGG + chr3_2:75451174-75451193 None:intergenic 10.0%
!! TAAAATGAATATAAATGACT+TGG + chr3_2:75450659-75450678 None:intergenic 15.0%
!!! AATTTATTTTTTGCTCTTTT+AGG - chr3_2:75450873-75450892 Msa0425110:exon 15.0%
!! AGGTATTAATAAATAAAGTA+TGG - chr3_2:75451579-75451598 Msa0425110:five_prime_UTR 15.0%
!! TAAAATGAATATAAATGACT+TGG + chr3_2:75450659-75450678 None:intergenic 15.0%
!!! AATTTATTTTTTGCTCTTTT+AGG - chr3_2:75450873-75450892 Msa0425110:exon 15.0%
!! AGGTATTAATAAATAAAGTA+TGG - chr3_2:75451579-75451598 Msa0425110:five_prime_UTR 15.0%
!! AAATCTTTACTTGATATAAG+TGG - chr3_2:75450812-75450831 Msa0425110:three_prime_UTR 20.0%
!! TTGTAAAGAAAGTTATTAGT+AGG + chr3_2:75450930-75450949 None:intergenic 20.0%
!! TACTAATAACTTTCTTTACA+AGG - chr3_2:75450929-75450948 Msa0425110:CDS 20.0%
!! CTATATGAAAAAAGATAGTA+AGG + chr3_2:75450957-75450976 None:intergenic 20.0%
!! AAAATTAAGATGAATACAGA+TGG - chr3_2:75451048-75451067 Msa0425110:intron 20.0%
!!! ACATTATTTTGGGATTATAT+GGG + chr3_2:75451129-75451148 None:intergenic 20.0%
!!! AACATTATTTTGGGATTATA+TGG + chr3_2:75451130-75451149 None:intergenic 20.0%
!!! CAATTTAGTATTTGATGATT+AGG - chr3_2:75451209-75451228 Msa0425110:intron 20.0%
!!! TTTTTAACTAACAAGTACTT+TGG - chr3_2:75451241-75451260 Msa0425110:intron 20.0%
!! TGATTAGTAATTAGTTGTTA+AGG + chr3_2:75451393-75451412 None:intergenic 20.0%
!! AAATCTTTACTTGATATAAG+TGG - chr3_2:75450812-75450831 Msa0425110:three_prime_UTR 20.0%
!! TTGTAAAGAAAGTTATTAGT+AGG + chr3_2:75450930-75450949 None:intergenic 20.0%
!! TACTAATAACTTTCTTTACA+AGG - chr3_2:75450929-75450948 Msa0425110:CDS 20.0%
!! CTATATGAAAAAAGATAGTA+AGG + chr3_2:75450957-75450976 None:intergenic 20.0%
!! AAAATTAAGATGAATACAGA+TGG - chr3_2:75451048-75451067 Msa0425110:intron 20.0%
!!! ACATTATTTTGGGATTATAT+GGG + chr3_2:75451129-75451148 None:intergenic 20.0%
!!! AACATTATTTTGGGATTATA+TGG + chr3_2:75451130-75451149 None:intergenic 20.0%
!!! CAATTTAGTATTTGATGATT+AGG - chr3_2:75451209-75451228 Msa0425110:intron 20.0%
!!! TTTTTAACTAACAAGTACTT+TGG - chr3_2:75451241-75451260 Msa0425110:intron 20.0%
!! TGATTAGTAATTAGTTGTTA+AGG + chr3_2:75451393-75451412 None:intergenic 20.0%
! ATTTATTTACCTGAAGACAA+AGG + chr3_2:75450796-75450815 None:intergenic 25.0%
!! TATGTTCATCTTAAGTATTG+TGG + chr3_2:75451016-75451035 None:intergenic 25.0%
!! ACATGAACAAAACATTTTGA+GGG + chr3_2:75451474-75451493 None:intergenic 25.0%
!! TACATGAACAAAACATTTTG+AGG + chr3_2:75451475-75451494 None:intergenic 25.0%
!!! AAATGTTTTGTTCATGTAAG+AGG - chr3_2:75451477-75451496 Msa0425110:CDS 25.0%
! ATTTATTTACCTGAAGACAA+AGG + chr3_2:75450796-75450815 None:intergenic 25.0%
!! TATGTTCATCTTAAGTATTG+TGG + chr3_2:75451016-75451035 None:intergenic 25.0%
!! ACATGAACAAAACATTTTGA+GGG + chr3_2:75451474-75451493 None:intergenic 25.0%
!! TACATGAACAAAACATTTTG+AGG + chr3_2:75451475-75451494 None:intergenic 25.0%
!!! AAATGTTTTGTTCATGTAAG+AGG - chr3_2:75451477-75451496 Msa0425110:CDS 25.0%
! ATGAATATAAATGACTTGGC+AGG + chr3_2:75450655-75450674 None:intergenic 30.0%
!!! TTTTAGCTTCTCATAAAGAG+AGG - chr3_2:75450674-75450693 Msa0425110:three_prime_UTR 30.0%
GAAAATGAATGAAAACCAAG+AGG + chr3_2:75450774-75450793 None:intergenic 30.0%
! ATTCATTTTCCTTTGTCTTC+AGG - chr3_2:75450784-75450803 Msa0425110:three_prime_UTR 30.0%
! AGTACTTTGGTATTGAATGA+AGG - chr3_2:75451254-75451273 Msa0425110:intron 30.0%
! CATGAACAAAACATTTTGAG+GGG + chr3_2:75451473-75451492 None:intergenic 30.0%
TGAGTGTATTGTAACTTATG+AGG - chr3_2:75451559-75451578 Msa0425110:five_prime_UTR 30.0%
! ATGAATATAAATGACTTGGC+AGG + chr3_2:75450655-75450674 None:intergenic 30.0%
!!! TTTTAGCTTCTCATAAAGAG+AGG - chr3_2:75450674-75450693 Msa0425110:three_prime_UTR 30.0%
GAAAATGAATGAAAACCAAG+AGG + chr3_2:75450774-75450793 None:intergenic 30.0%
! ATTCATTTTCCTTTGTCTTC+AGG - chr3_2:75450784-75450803 Msa0425110:three_prime_UTR 30.0%
! AGTACTTTGGTATTGAATGA+AGG - chr3_2:75451254-75451273 Msa0425110:intron 30.0%
! CATGAACAAAACATTTTGAG+GGG + chr3_2:75451473-75451492 None:intergenic 30.0%
TGAGTGTATTGTAACTTATG+AGG - chr3_2:75451559-75451578 Msa0425110:five_prime_UTR 30.0%
TTCATTGCATATACTTGCCA+TGG - chr3_2:75450717-75450736 Msa0425110:three_prime_UTR 35.0%
!!! AGTTTTGACTTTGTGTTCCA+TGG + chr3_2:75450737-75450756 None:intergenic 35.0%
! TTTCCTTTTAGTCATCCTCT+TGG - chr3_2:75450756-75450775 Msa0425110:three_prime_UTR 35.0%
AAACCAAGAGGATGACTAAA+AGG + chr3_2:75450762-75450781 None:intergenic 35.0%
GGCAAATGCTAATATTTGCT+TGG - chr3_2:75451091-75451110 Msa0425110:intron 35.0%
! CTTTGGTATTGAATGAAGGA+TGG - chr3_2:75451258-75451277 Msa0425110:intron 35.0%
! ATTGTCTCATGCTTTTGTGT+TGG - chr3_2:75451305-75451324 Msa0425110:intron 35.0%
! TTCTTTGAATGCTTTGGGTT+GGG + chr3_2:75451348-75451367 None:intergenic 35.0%
! TTTCTTTGAATGCTTTGGGT+TGG + chr3_2:75451349-75451368 None:intergenic 35.0%
CAGGTTTCTTTGAATGCTTT+GGG + chr3_2:75451353-75451372 None:intergenic 35.0%
GTTACAATACACTCAAGTAG+TGG + chr3_2:75451554-75451573 None:intergenic 35.0%
TTCATTGCATATACTTGCCA+TGG - chr3_2:75450717-75450736 Msa0425110:three_prime_UTR 35.0%
!!! AGTTTTGACTTTGTGTTCCA+TGG + chr3_2:75450737-75450756 None:intergenic 35.0%
! TTTCCTTTTAGTCATCCTCT+TGG - chr3_2:75450756-75450775 Msa0425110:three_prime_UTR 35.0%
AAACCAAGAGGATGACTAAA+AGG + chr3_2:75450762-75450781 None:intergenic 35.0%
GGCAAATGCTAATATTTGCT+TGG - chr3_2:75451091-75451110 Msa0425110:intron 35.0%
! CTTTGGTATTGAATGAAGGA+TGG - chr3_2:75451258-75451277 Msa0425110:intron 35.0%
! ATTGTCTCATGCTTTTGTGT+TGG - chr3_2:75451305-75451324 Msa0425110:intron 35.0%
! TTCTTTGAATGCTTTGGGTT+GGG + chr3_2:75451348-75451367 None:intergenic 35.0%
! TTTCTTTGAATGCTTTGGGT+TGG + chr3_2:75451349-75451368 None:intergenic 35.0%
CAGGTTTCTTTGAATGCTTT+GGG + chr3_2:75451353-75451372 None:intergenic 35.0%
GTTACAATACACTCAAGTAG+TGG + chr3_2:75451554-75451573 None:intergenic 35.0%
!!! GCTCTTTTAGGATTGACTGA+AGG - chr3_2:75450885-75450904 Msa0425110:CDS 40.0%
GAGCTACTACATTCACATTG+AGG - chr3_2:75451070-75451089 Msa0425110:intron 40.0%
ATGGTGTAAAGATGAACTCG+AGG - chr3_2:75451277-75451296 Msa0425110:intron 40.0%
GTGTTGGATTATGATGAAGC+AGG - chr3_2:75451321-75451340 Msa0425110:CDS 40.0%
CCAGGTTTCTTTGAATGCTT+TGG + chr3_2:75451354-75451373 None:intergenic 40.0%
! CCAAAGCATTCAAAGAAACC+TGG - chr3_2:75451351-75451370 Msa0425110:intron 40.0%
CATTCAAAGAAACCTGGCAA+GGG - chr3_2:75451357-75451376 Msa0425110:intron 40.0%
! AATCGAGCTAGTTTCTTCAC+CGG - chr3_2:75451526-75451545 Msa0425110:five_prime_UTR 40.0%
!!! GCTCTTTTAGGATTGACTGA+AGG - chr3_2:75450885-75450904 Msa0425110:CDS 40.0%
GAGCTACTACATTCACATTG+AGG - chr3_2:75451070-75451089 Msa0425110:intron 40.0%
ATGGTGTAAAGATGAACTCG+AGG - chr3_2:75451277-75451296 Msa0425110:intron 40.0%
GTGTTGGATTATGATGAAGC+AGG - chr3_2:75451321-75451340 Msa0425110:CDS 40.0%
CCAGGTTTCTTTGAATGCTT+TGG + chr3_2:75451354-75451373 None:intergenic 40.0%
! CCAAAGCATTCAAAGAAACC+TGG - chr3_2:75451351-75451370 Msa0425110:intron 40.0%
CATTCAAAGAAACCTGGCAA+GGG - chr3_2:75451357-75451376 Msa0425110:intron 40.0%
! AATCGAGCTAGTTTCTTCAC+CGG - chr3_2:75451526-75451545 Msa0425110:five_prime_UTR 40.0%
GCATTCAAAGAAACCTGGCA+AGG - chr3_2:75451356-75451375 Msa0425110:intron 45.0%
ATACACTCAAGTAGTGGCTC+CGG + chr3_2:75451548-75451567 None:intergenic 45.0%
GCATTCAAAGAAACCTGGCA+AGG - chr3_2:75451356-75451375 Msa0425110:intron 45.0%
ATACACTCAAGTAGTGGCTC+CGG + chr3_2:75451548-75451567 None:intergenic 45.0%
GGTGTTTAACGACCCTTGCC+AGG + chr3_2:75451372-75451391 None:intergenic 55.0%
GGTGTTTAACGACCCTTGCC+AGG + chr3_2:75451372-75451391 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 75450647 75451614 75450647 ID=Msa0425110;Name=Msa0425110
chr3_2 mRNA 75450647 75451614 75450647 ID=Msa0425110-mRNA-1;Parent=Msa0425110;Name=Msa0425110-mRNA-1;_AED=0.01;_eAED=0.01;_QI=89|1|1|1|1|1|3|228|78
chr3_2 exon 75450647 75450985 75450647 ID=Msa0425110-mRNA-1:exon:19321;Parent=Msa0425110-mRNA-1
chr3_2 exon 75451311 75451366 75451311 ID=Msa0425110-mRNA-1:exon:19320;Parent=Msa0425110-mRNA-1
chr3_2 exon 75451456 75451614 75451456 ID=Msa0425110-mRNA-1:exon:19319;Parent=Msa0425110-mRNA-1
chr3_2 five_prime_UTR 75451526 75451614 75451526 ID=Msa0425110-mRNA-1:five_prime_utr;Parent=Msa0425110-mRNA-1
chr3_2 CDS 75451456 75451525 75451456 ID=Msa0425110-mRNA-1:cds;Parent=Msa0425110-mRNA-1
chr3_2 CDS 75451311 75451366 75451311 ID=Msa0425110-mRNA-1:cds;Parent=Msa0425110-mRNA-1
chr3_2 CDS 75450875 75450985 75450875 ID=Msa0425110-mRNA-1:cds;Parent=Msa0425110-mRNA-1
chr3_2 three_prime_UTR 75450647 75450874 75450647 ID=Msa0425110-mRNA-1:three_prime_utr;Parent=Msa0425110-mRNA-1
Gene Sequence

>Msa0425110

ATGGAACACAAAGTCAAAACTTTCCTTTTAGTCATCCTCTTGGTTTTCATTCATTTTCCTTTGTCTTCAGGATTGACTGAAGGATTCAGAGAAAATATGCATCCTACTAATAACTTTCTTTACAAGGATGGTGTAAAGATGAACTCGAGGAAGCTATTGTCTCATGCTTTTGTGTTGGATTATGATGAAGCAGGACCCAACCCAAAGCATTCAAAGAAACCTGGCAAGGGTCGTTAA
Protein sequence

>Msa0425110

MEHKVKTFLLVILLVFIHFPLSSGLTEGFRENMHPTNNFLYKDGVKMNSRKLLSHAFVLDYDEAGPNPKHSKKPGKGR*