AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0523140


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0523140 MtrunA17_Chr3g0142671 79.412 34 7 0 1 34 1 34 1.21e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 47 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTCTACCTATGACGCATTA+TGG 0.192228 3_4:-76478587 None:intergenic
GATTAGCTTGATTACTTAAA+AGG 0.201487 3_4:-76477648 None:intergenic
GCATGAGTTGGTGGTAATTA+AGG 0.235955 3_4:-76478537 None:intergenic
ACAAACGATTCAACATAAAT+TGG 0.238695 3_4:-76478672 None:intergenic
TAGTCACGTTCTTCAATTTC+CGG 0.261076 3_4:+76478748 Msa0523140:three_prime_UTR
CATAGCAGGGACACATTTCT+TGG 0.264407 3_4:-76478453 None:intergenic
TCTCCATCTTGTTCATGCTT+TGG 0.293177 3_4:+76477752 Msa0523140:CDS
GAAACAATACTTAAAGAAAA+AGG 0.298823 3_4:-76478650 None:intergenic
GGTGGTTTGGTTGGCATAGC+AGG 0.303830 3_4:-76478467 None:intergenic
GGCACTTGCGTCTGCCTCCA+TGG 0.330551 3_4:-76478489 None:intergenic
TGCGTGCCACCAGGAACTTC+TGG 0.331803 3_4:+76478427 Msa0523140:CDS
CACGGCCGCGCCTCTGCCAC+AGG 0.395156 3_4:+76478374 Msa0523140:CDS
TCTTGGTTACCAGAAGTTCC+TGG 0.400394 3_4:-76478436 None:intergenic
TTCTACCTATGACGCATTAT+GGG 0.409657 3_4:-76478586 None:intergenic
GTCTGCCTCCATGGGTGGTT+TGG 0.427775 3_4:-76478480 None:intergenic
GCCTCCATGGGTGGTTTGGT+TGG 0.435015 3_4:-76478476 None:intergenic
AATTTATGTTGAATCGTTTG+TGG 0.447176 3_4:+76478674 Msa0523140:three_prime_UTR
TTCCACATGCCCTGTGGCAG+AGG 0.454808 3_4:-76478384 None:intergenic
TTAAAGAGAGCCATTGCTAA+TGG 0.455287 3_4:-76477693 None:intergenic
GGCGCGGCCGTGATGATAAA+CGG 0.465640 3_4:-76478363 None:intergenic
CGCCTCTGCCACAGGGCATG+TGG 0.480960 3_4:+76478382 Msa0523140:CDS
TGCTACCCATAATGCGTCAT+AGG 0.485417 3_4:+76478581 Msa0523140:three_prime_UTR
GCACTTGCGTCTGCCTCCAT+GGG 0.498020 3_4:-76478488 None:intergenic
CTTGCGTCTGCCTCCATGGG+TGG 0.501890 3_4:-76478485 None:intergenic
GCTATAGCAATTTAGAAAAG+AGG 0.503051 3_4:-76477671 None:intergenic
TGATGATTCAACTCAATTCA+AGG 0.508747 3_4:-76478511 None:intergenic
CGGTGCAACTGCGTGCCACC+AGG 0.530335 3_4:+76478418 Msa0523140:CDS
AGCATGAACAAGATGGAGAA+TGG 0.540714 3_4:-76477748 None:intergenic
CTATAGCAATTTAGAAAAGA+GGG 0.541742 3_4:-76477670 None:intergenic
GTGGTTTGGTTGGCATAGCA+GGG 0.546195 3_4:-76478466 None:intergenic
TGTTCATGCTTTGGACCAGC+CGG 0.555470 3_4:+76477761 Msa0523140:CDS
GCAATGGAGCATGTGCTGCT+AGG 0.562822 3_4:+76478338 Msa0523140:CDS
AGTTGCATTGCATGAGTTGG+TGG 0.565582 3_4:-76478546 None:intergenic
ATATAAATTTCAGATTGCAA+TGG 0.566444 3_4:+76478322 Msa0523140:intron
GATGATTCAACTCAATTCAA+GGG 0.567646 3_4:-76478510 None:intergenic
GGTCCAAAGCATGAACAAGA+TGG 0.576917 3_4:-76477755 None:intergenic
ATAAGTTGCATTGCATGAGT+TGG 0.582143 3_4:-76478549 None:intergenic
CATGCCCTGTGGCAGAGGCG+CGG 0.598879 3_4:-76478379 None:intergenic
CATGTGGAACTTGCTGCAGT+CGG 0.613537 3_4:+76478398 Msa0523140:CDS
ACGGCCGCGCCTCTGCCACA+GGG 0.616011 3_4:+76478375 Msa0523140:CDS
CTAGGTGCCGTTTATCATCA+CGG 0.637583 3_4:+76478356 Msa0523140:CDS
TATGCCAACCAAACCACCCA+TGG 0.640986 3_4:+76478472 Msa0523140:CDS
ATTGCTATAGCCATTAGCAA+TGG 0.652040 3_4:+76477683 Msa0523140:exon
TGGTTACCAGAAGTTCCTGG+TGG 0.663688 3_4:-76478433 None:intergenic
GCCAACCAAACCACCCATGG+AGG 0.699460 3_4:+76478475 Msa0523140:CDS
AGCAAGTTCCACATGCCCTG+TGG 0.700479 3_4:-76478390 None:intergenic
TCACAATTCAGAGTATACAC+CGG 0.713855 3_4:-76478767 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAATTATTTGCTTAAAG+TGG + chr3_4:76477978-76477997 Msa0523140:intron 15.0%
!! TGGAAAAAATATAAAAAAAC+TGG + chr3_4:76477998-76478017 Msa0523140:intron 15.0%
!! AAAATATATGAACTAAACTA+AGG + chr3_4:76478044-76478063 Msa0523140:intron 15.0%
!!! TTTTAATTATTTGCTTAAAG+TGG + chr3_4:76477978-76477997 Msa0523140:intron 15.0%
!! TGGAAAAAATATAAAAAAAC+TGG + chr3_4:76477998-76478017 Msa0523140:intron 15.0%
!! AAAATATATGAACTAAACTA+AGG + chr3_4:76478044-76478063 Msa0523140:intron 15.0%
!!! TATTTTATAAAGAAAACGCT+TGG - chr3_4:76477836-76477855 None:intergenic 20.0%
!! GGATAAAAGATTAGTAAAAA+AGG + chr3_4:76478162-76478181 Msa0523140:intron 20.0%
!! ATATAAATTTCAGATTGCAA+TGG + chr3_4:76478322-76478341 Msa0523140:intron 20.0%
!! GAAACAATACTTAAAGAAAA+AGG - chr3_4:76478653-76478672 None:intergenic 20.0%
!!! TATTTTATAAAGAAAACGCT+TGG - chr3_4:76477836-76477855 None:intergenic 20.0%
!! GGATAAAAGATTAGTAAAAA+AGG + chr3_4:76478162-76478181 Msa0523140:intron 20.0%
!! ATATAAATTTCAGATTGCAA+TGG + chr3_4:76478322-76478341 Msa0523140:intron 20.0%
!! GAAACAATACTTAAAGAAAA+AGG - chr3_4:76478653-76478672 None:intergenic 20.0%
!!! GATTAGCTTGATTACTTAAA+AGG - chr3_4:76477651-76477670 None:intergenic 25.0%
! CTATAGCAATTTAGAAAAGA+GGG - chr3_4:76477673-76477692 None:intergenic 25.0%
!! TTAATTACATGTGTTTTCGT+AGG + chr3_4:76477872-76477891 Msa0523140:intron 25.0%
! TTAACGAATATGTATGCTAA+TGG + chr3_4:76478140-76478159 Msa0523140:intron 25.0%
! TAACGAATATGTATGCTAAT+GGG + chr3_4:76478141-76478160 Msa0523140:intron 25.0%
! ACAAACGATTCAACATAAAT+TGG - chr3_4:76478675-76478694 None:intergenic 25.0%
! AATTTATGTTGAATCGTTTG+TGG + chr3_4:76478674-76478693 Msa0523140:three_prime_UTR 25.0%
!!! GATTAGCTTGATTACTTAAA+AGG - chr3_4:76477651-76477670 None:intergenic 25.0%
! CTATAGCAATTTAGAAAAGA+GGG - chr3_4:76477673-76477692 None:intergenic 25.0%
!! TTAATTACATGTGTTTTCGT+AGG + chr3_4:76477872-76477891 Msa0523140:intron 25.0%
! TTAACGAATATGTATGCTAA+TGG + chr3_4:76478140-76478159 Msa0523140:intron 25.0%
! TAACGAATATGTATGCTAAT+GGG + chr3_4:76478141-76478160 Msa0523140:intron 25.0%
! ACAAACGATTCAACATAAAT+TGG - chr3_4:76478675-76478694 None:intergenic 25.0%
! AATTTATGTTGAATCGTTTG+TGG + chr3_4:76478674-76478693 Msa0523140:three_prime_UTR 25.0%
GCTATAGCAATTTAGAAAAG+AGG - chr3_4:76477674-76477693 None:intergenic 30.0%
!! CAACAATAGCTTTGAATTAC+CGG - chr3_4:76477783-76477802 None:intergenic 30.0%
! CTACTTCACACACATATTTT+TGG - chr3_4:76478290-76478309 None:intergenic 30.0%
GATGATTCAACTCAATTCAA+GGG - chr3_4:76478513-76478532 None:intergenic 30.0%
TGATGATTCAACTCAATTCA+AGG - chr3_4:76478514-76478533 None:intergenic 30.0%
GAATAAAAAGTCTATGTGTG+TGG + chr3_4:76478606-76478625 Msa0523140:three_prime_UTR 30.0%
GCTATAGCAATTTAGAAAAG+AGG - chr3_4:76477674-76477693 None:intergenic 30.0%
!! CAACAATAGCTTTGAATTAC+CGG - chr3_4:76477783-76477802 None:intergenic 30.0%
! CTACTTCACACACATATTTT+TGG - chr3_4:76478290-76478309 None:intergenic 30.0%
GATGATTCAACTCAATTCAA+GGG - chr3_4:76478513-76478532 None:intergenic 30.0%
TGATGATTCAACTCAATTCA+AGG - chr3_4:76478514-76478533 None:intergenic 30.0%
GAATAAAAAGTCTATGTGTG+TGG + chr3_4:76478606-76478625 Msa0523140:three_prime_UTR 30.0%
ATTGCTATAGCCATTAGCAA+TGG + chr3_4:76477683-76477702 Msa0523140:exon 35.0%
TTAAAGAGAGCCATTGCTAA+TGG - chr3_4:76477696-76477715 None:intergenic 35.0%
ATAAGTTGCATTGCATGAGT+TGG - chr3_4:76478552-76478571 None:intergenic 35.0%
TTCTACCTATGACGCATTAT+GGG - chr3_4:76478589-76478608 None:intergenic 35.0%
ATTCTACCTATGACGCATTA+TGG - chr3_4:76478590-76478609 None:intergenic 35.0%
TAGTCACGTTCTTCAATTTC+CGG + chr3_4:76478748-76478767 Msa0523140:three_prime_UTR 35.0%
TCACAATTCAGAGTATACAC+CGG - chr3_4:76478770-76478789 None:intergenic 35.0%
ATTGCTATAGCCATTAGCAA+TGG + chr3_4:76477683-76477702 Msa0523140:exon 35.0%
TTAAAGAGAGCCATTGCTAA+TGG - chr3_4:76477696-76477715 None:intergenic 35.0%
ATAAGTTGCATTGCATGAGT+TGG - chr3_4:76478552-76478571 None:intergenic 35.0%
TTCTACCTATGACGCATTAT+GGG - chr3_4:76478589-76478608 None:intergenic 35.0%
ATTCTACCTATGACGCATTA+TGG - chr3_4:76478590-76478609 None:intergenic 35.0%
TAGTCACGTTCTTCAATTTC+CGG + chr3_4:76478748-76478767 Msa0523140:three_prime_UTR 35.0%
TCACAATTCAGAGTATACAC+CGG - chr3_4:76478770-76478789 None:intergenic 35.0%
AGCATGAACAAGATGGAGAA+TGG - chr3_4:76477751-76477770 None:intergenic 40.0%
TCTCCATCTTGTTCATGCTT+TGG + chr3_4:76477752-76477771 Msa0523140:CDS 40.0%
!! AATAGCTTTGAATTACCGGC+TGG - chr3_4:76477779-76477798 None:intergenic 40.0%
TAAAGAAAACGCTTGGAGCT+TGG - chr3_4:76477829-76477848 None:intergenic 40.0%
! GTTTCTTTTCAGCAGCAGAT+AGG + chr3_4:76477921-76477940 Msa0523140:intron 40.0%
!! GCATGAGTTGGTGGTAATTA+AGG - chr3_4:76478540-76478559 None:intergenic 40.0%
AGCATGAACAAGATGGAGAA+TGG - chr3_4:76477751-76477770 None:intergenic 40.0%
TCTCCATCTTGTTCATGCTT+TGG + chr3_4:76477752-76477771 Msa0523140:CDS 40.0%
!! AATAGCTTTGAATTACCGGC+TGG - chr3_4:76477779-76477798 None:intergenic 40.0%
TAAAGAAAACGCTTGGAGCT+TGG - chr3_4:76477829-76477848 None:intergenic 40.0%
! GTTTCTTTTCAGCAGCAGAT+AGG + chr3_4:76477921-76477940 Msa0523140:intron 40.0%
!! GCATGAGTTGGTGGTAATTA+AGG - chr3_4:76478540-76478559 None:intergenic 40.0%
GGTCCAAAGCATGAACAAGA+TGG - chr3_4:76477758-76477777 None:intergenic 45.0%
TGAGTTTCTGCGTGTACATG+CGG - chr3_4:76477900-76477919 None:intergenic 45.0%
TTCCATCAACTGCTTCTGTC+TGG + chr3_4:76477955-76477974 Msa0523140:intron 45.0%
AACCAGACAGAAGCAGTTGA+TGG - chr3_4:76477960-76477979 None:intergenic 45.0%
!! CTAGGTGCCGTTTATCATCA+CGG + chr3_4:76478356-76478375 Msa0523140:CDS 45.0%
TCTTGGTTACCAGAAGTTCC+TGG - chr3_4:76478439-76478458 None:intergenic 45.0%
CATAGCAGGGACACATTTCT+TGG - chr3_4:76478456-76478475 None:intergenic 45.0%
! AGTTGCATTGCATGAGTTGG+TGG - chr3_4:76478549-76478568 None:intergenic 45.0%
TGCTACCCATAATGCGTCAT+AGG + chr3_4:76478581-76478600 Msa0523140:three_prime_UTR 45.0%
GGTCCAAAGCATGAACAAGA+TGG - chr3_4:76477758-76477777 None:intergenic 45.0%
TGAGTTTCTGCGTGTACATG+CGG - chr3_4:76477900-76477919 None:intergenic 45.0%
TTCCATCAACTGCTTCTGTC+TGG + chr3_4:76477955-76477974 Msa0523140:intron 45.0%
AACCAGACAGAAGCAGTTGA+TGG - chr3_4:76477960-76477979 None:intergenic 45.0%
!! CTAGGTGCCGTTTATCATCA+CGG + chr3_4:76478356-76478375 Msa0523140:CDS 45.0%
TCTTGGTTACCAGAAGTTCC+TGG - chr3_4:76478439-76478458 None:intergenic 45.0%
CATAGCAGGGACACATTTCT+TGG - chr3_4:76478456-76478475 None:intergenic 45.0%
! AGTTGCATTGCATGAGTTGG+TGG - chr3_4:76478549-76478568 None:intergenic 45.0%
TGCTACCCATAATGCGTCAT+AGG + chr3_4:76478581-76478600 Msa0523140:three_prime_UTR 45.0%
!! GTAATTAAATTAAATTAAAT+TGG - chr3_4:76477860-76477879 None:intergenic 5.0%
!! GTAATTAAATTAAATTAAAT+TGG - chr3_4:76477860-76477879 None:intergenic 5.0%
! TGTTCATGCTTTGGACCAGC+CGG + chr3_4:76477761-76477780 Msa0523140:CDS 50.0%
!! CATGTGGAACTTGCTGCAGT+CGG + chr3_4:76478398-76478417 Msa0523140:CDS 50.0%
TGGTTACCAGAAGTTCCTGG+TGG - chr3_4:76478436-76478455 None:intergenic 50.0%
!! GTGGTTTGGTTGGCATAGCA+GGG - chr3_4:76478469-76478488 None:intergenic 50.0%
TATGCCAACCAAACCACCCA+TGG + chr3_4:76478472-76478491 Msa0523140:CDS 50.0%
! TGTTCATGCTTTGGACCAGC+CGG + chr3_4:76477761-76477780 Msa0523140:CDS 50.0%
!! CATGTGGAACTTGCTGCAGT+CGG + chr3_4:76478398-76478417 Msa0523140:CDS 50.0%
TGGTTACCAGAAGTTCCTGG+TGG - chr3_4:76478436-76478455 None:intergenic 50.0%
!! GTGGTTTGGTTGGCATAGCA+GGG - chr3_4:76478469-76478488 None:intergenic 50.0%
TATGCCAACCAAACCACCCA+TGG + chr3_4:76478472-76478491 Msa0523140:CDS 50.0%
! GCAATGGAGCATGTGCTGCT+AGG + chr3_4:76478338-76478357 Msa0523140:CDS 55.0%
AGCAAGTTCCACATGCCCTG+TGG - chr3_4:76478393-76478412 None:intergenic 55.0%
!! GGTGGTTTGGTTGGCATAGC+AGG - chr3_4:76478470-76478489 None:intergenic 55.0%
! GCAATGGAGCATGTGCTGCT+AGG + chr3_4:76478338-76478357 Msa0523140:CDS 55.0%
AGCAAGTTCCACATGCCCTG+TGG - chr3_4:76478393-76478412 None:intergenic 55.0%
!! GGTGGTTTGGTTGGCATAGC+AGG - chr3_4:76478470-76478489 None:intergenic 55.0%
GGCGCGGCCGTGATGATAAA+CGG - chr3_4:76478366-76478385 None:intergenic 60.0%
TTCCACATGCCCTGTGGCAG+AGG - chr3_4:76478387-76478406 None:intergenic 60.0%
TGCGTGCCACCAGGAACTTC+TGG + chr3_4:76478427-76478446 Msa0523140:CDS 60.0%
GCCAACCAAACCACCCATGG+AGG + chr3_4:76478475-76478494 Msa0523140:CDS 60.0%
!! GCCTCCATGGGTGGTTTGGT+TGG - chr3_4:76478479-76478498 None:intergenic 60.0%
GTCTGCCTCCATGGGTGGTT+TGG - chr3_4:76478483-76478502 None:intergenic 60.0%
GCACTTGCGTCTGCCTCCAT+GGG - chr3_4:76478491-76478510 None:intergenic 60.0%
GGCGCGGCCGTGATGATAAA+CGG - chr3_4:76478366-76478385 None:intergenic 60.0%
TTCCACATGCCCTGTGGCAG+AGG - chr3_4:76478387-76478406 None:intergenic 60.0%
TGCGTGCCACCAGGAACTTC+TGG + chr3_4:76478427-76478446 Msa0523140:CDS 60.0%
GCCAACCAAACCACCCATGG+AGG + chr3_4:76478475-76478494 Msa0523140:CDS 60.0%
!! GCCTCCATGGGTGGTTTGGT+TGG - chr3_4:76478479-76478498 None:intergenic 60.0%
GTCTGCCTCCATGGGTGGTT+TGG - chr3_4:76478483-76478502 None:intergenic 60.0%
GCACTTGCGTCTGCCTCCAT+GGG - chr3_4:76478491-76478510 None:intergenic 60.0%
CTTGCGTCTGCCTCCATGGG+TGG - chr3_4:76478488-76478507 None:intergenic 65.0%
GGCACTTGCGTCTGCCTCCA+TGG - chr3_4:76478492-76478511 None:intergenic 65.0%
CTTGCGTCTGCCTCCATGGG+TGG - chr3_4:76478488-76478507 None:intergenic 65.0%
GGCACTTGCGTCTGCCTCCA+TGG - chr3_4:76478492-76478511 None:intergenic 65.0%
CATGCCCTGTGGCAGAGGCG+CGG - chr3_4:76478382-76478401 None:intergenic 70.0%
CGCCTCTGCCACAGGGCATG+TGG + chr3_4:76478382-76478401 Msa0523140:CDS 70.0%
CGGTGCAACTGCGTGCCACC+AGG + chr3_4:76478418-76478437 Msa0523140:CDS 70.0%
CATGCCCTGTGGCAGAGGCG+CGG - chr3_4:76478382-76478401 None:intergenic 70.0%
CGCCTCTGCCACAGGGCATG+TGG + chr3_4:76478382-76478401 Msa0523140:CDS 70.0%
CGGTGCAACTGCGTGCCACC+AGG + chr3_4:76478418-76478437 Msa0523140:CDS 70.0%
ACGGCCGCGCCTCTGCCACA+GGG + chr3_4:76478375-76478394 Msa0523140:CDS 75.0%
ACGGCCGCGCCTCTGCCACA+GGG + chr3_4:76478375-76478394 Msa0523140:CDS 75.0%
! CACGGCCGCGCCTCTGCCAC+AGG + chr3_4:76478374-76478393 Msa0523140:CDS 80.0%
! CACGGCCGCGCCTCTGCCAC+AGG + chr3_4:76478374-76478393 Msa0523140:CDS 80.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 76477640 76478812 76477640 ID=Msa0523140;Name=Msa0523140
chr3_4 mRNA 76477640 76478812 76477640 ID=Msa0523140-mRNA-1;Parent=Msa0523140;Name=Msa0523140-mRNA-1;_AED=0.22;_eAED=0.22;_QI=62|0.5|0.66|1|0.5|0.66|3|286|93
chr3_4 exon 76477640 76477782 76477640 ID=Msa0523140-mRNA-1:exon:22154;Parent=Msa0523140-mRNA-1
chr3_4 exon 76477894 76477902 76477894 ID=Msa0523140-mRNA-1:exon:22155;Parent=Msa0523140-mRNA-1
chr3_4 exon 76478335 76478812 76478335 ID=Msa0523140-mRNA-1:exon:22156;Parent=Msa0523140-mRNA-1
chr3_4 five_prime_UTR 76477640 76477701 76477640 ID=Msa0523140-mRNA-1:five_prime_utr;Parent=Msa0523140-mRNA-1
chr3_4 CDS 76477702 76477782 76477702 ID=Msa0523140-mRNA-1:cds;Parent=Msa0523140-mRNA-1
chr3_4 CDS 76477894 76477902 76477894 ID=Msa0523140-mRNA-1:cds;Parent=Msa0523140-mRNA-1
chr3_4 CDS 76478335 76478526 76478335 ID=Msa0523140-mRNA-1:cds;Parent=Msa0523140-mRNA-1
chr3_4 three_prime_UTR 76478527 76478812 76478527 ID=Msa0523140-mRNA-1:three_prime_utr;Parent=Msa0523140-mRNA-1
Gene Sequence

>Msa0523140

ATGGCTCTCTTTAAGCTTTTAGTTACATCTCTTCTTGTAACTTTTGCCATTCTCCATCTTGTTCATGCTTTGGACCAGCCGGAACCGCATATTGCAATGGAGCATGTGCTGCTAGGTGCCGTTTATCATCACGGCCGCGCCTCTGCCACAGGGCATGTGGAACTTGCTGCAGTCGGTGCAACTGCGTGCCACCAGGAACTTCTGGTAACCAAGAAATGTGTCCCTGCTATGCCAACCAAACCACCCATGGAGGCAGACGCAAGTGCCCTTGAATTGAGTTGA

Protein sequence

>Msa0523140

MALFKLLVTSLLVTFAILHLVHALDQPEPHIAMEHVLLGAVYHHGRASATGHVELAAVGATACHQELLVTKKCVPAMPTKPPMEADASALELS*