AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0137300


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 24 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAAGAAGGTAGAGGAAAA+AGG 0.256301 1_3:-69700117 None:intergenic
TTACCTTCTGATCGTAATTC+CGG 0.336812 1_3:-69700304 None:intergenic
GGATGTGGAGAGGAAGATTA+TGG 0.350307 1_3:-69700184 None:intergenic
CTTAATCGAAGAAACTTTAC+CGG 0.373555 1_3:+69700249 Msa0137300:CDS
GGAATTCGTTTCCGCCGTTC+CGG 0.384074 1_3:+69700285 Msa0137300:CDS
AGAGTTCAGATAAATGATAT+TGG 0.384122 1_3:+69701152 Msa0137300:three_prime_UTR
GGAACGGCGGAAACGAATTC+CGG 0.413854 1_3:-69700283 None:intergenic
GGGTGAGAGAAACGTGAATG+AGG 0.501643 1_3:-69700080 None:intergenic
TGATCGGAAATGAAGAAAGA+AGG 0.529484 1_3:-69700130 None:intergenic
AATTCCGGTGTGGTGGTCGC+CGG 0.565738 1_3:-69700268 None:intergenic
AAAAGGGTTTGATGGAGGGA+GGG 0.591330 1_3:-69700100 None:intergenic
GAAATGAAGAAAGAAGGTAG+AGG 0.595482 1_3:-69700124 None:intergenic
GTGAGGCGGACGGAGTTGAT+CGG 0.596132 1_3:-69700146 None:intergenic
TGGAGAGGCAATCAAACAGA+AGG 0.604393 1_3:+69701172 Msa0137300:three_prime_UTR
TGTGGAGAGGAAGATTATGG+TGG 0.615849 1_3:-69700181 None:intergenic
GGAAACGAATTCCGGTGTGG+TGG 0.624336 1_3:-69700275 None:intergenic
TTCTGATCGTAATTCCGGAA+CGG 0.632504 1_3:-69700299 None:intergenic
GTTCCGGAATTACGATCAGA+AGG 0.644287 1_3:+69700301 Msa0137300:CDS
GTTCTTTCAAGAACAAATCG+AGG 0.644335 1_3:+69700431 Msa0137300:CDS
TTTACCGGCGACCACCACAC+CGG 0.651318 1_3:+69700264 Msa0137300:CDS
TCAGATAAATGATATTGGAG+AGG 0.654158 1_3:+69701157 Msa0137300:three_prime_UTR
TCGAGGAAGCAGATTAACCA+AGG 0.681630 1_3:+69700448 Msa0137300:exon
GGCGGAAACGAATTCCGGTG+TGG 0.690128 1_3:-69700278 None:intergenic
TGATCGTAATTCCGGAACGG+CGG 0.697591 1_3:-69700296 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACAATATAAATGATTTGA+GGG - chr1_3:69700579-69700598 None:intergenic 15.0%
!!! CATTTATATTGTTTGTTTTT+TGG + chr1_3:69700585-69700604 Msa0137300:intron 15.0%
!! ATTGAACAAAAACAATATAT+TGG - chr1_3:69700650-69700669 None:intergenic 15.0%
!! TTATCTTATTAGTAACTTAT+TGG + chr1_3:69700788-69700807 Msa0137300:intron 15.0%
!!! CATAGATCTTATTAATTTTA+TGG + chr1_3:69700820-69700839 Msa0137300:intron 15.0%
!! AAACAATATAAATGATTTGA+GGG - chr1_3:69700579-69700598 None:intergenic 15.0%
!!! CATTTATATTGTTTGTTTTT+TGG + chr1_3:69700585-69700604 Msa0137300:intron 15.0%
!! ATTGAACAAAAACAATATAT+TGG - chr1_3:69700650-69700669 None:intergenic 15.0%
!! TTATCTTATTAGTAACTTAT+TGG + chr1_3:69700788-69700807 Msa0137300:intron 15.0%
!!! CATAGATCTTATTAATTTTA+TGG + chr1_3:69700820-69700839 Msa0137300:intron 15.0%
!!! AAATTTGGATTAGATAAATC+TGG - chr1_3:69700353-69700372 None:intergenic 20.0%
!! CAAACAATATAAATGATTTG+AGG - chr1_3:69700580-69700599 None:intergenic 20.0%
!!! TTTTTGGAGAGTTTAAAATT+TGG + chr1_3:69700601-69700620 Msa0137300:intron 20.0%
!! CTTATAAAAAAATACAACTC+TGG + chr1_3:69700757-69700776 Msa0137300:intron 20.0%
!!! AAATTTGGATTAGATAAATC+TGG - chr1_3:69700353-69700372 None:intergenic 20.0%
!! CAAACAATATAAATGATTTG+AGG - chr1_3:69700580-69700599 None:intergenic 20.0%
!!! TTTTTGGAGAGTTTAAAATT+TGG + chr1_3:69700601-69700620 Msa0137300:intron 20.0%
!! CTTATAAAAAAATACAACTC+TGG + chr1_3:69700757-69700776 Msa0137300:intron 20.0%
! GATTAGATAAATCTGGATTA+GGG - chr1_3:69700346-69700365 None:intergenic 25.0%
! TTGAAATTCAAATATCACCT+TGG - chr1_3:69700468-69700487 None:intergenic 25.0%
! AAACAAATTTCATCCCAAAA+TGG - chr1_3:69700527-69700546 None:intergenic 25.0%
! GAACAAAAACAATATATTGG+AGG - chr1_3:69700647-69700666 None:intergenic 25.0%
! TCTTATGTTGTATAACTGTT+AGG - chr1_3:69700848-69700867 None:intergenic 25.0%
! AGAGTTCAGATAAATGATAT+TGG + chr1_3:69701152-69701171 Msa0137300:three_prime_UTR 25.0%
! GATTAGATAAATCTGGATTA+GGG - chr1_3:69700346-69700365 None:intergenic 25.0%
! TTGAAATTCAAATATCACCT+TGG - chr1_3:69700468-69700487 None:intergenic 25.0%
! AAACAAATTTCATCCCAAAA+TGG - chr1_3:69700527-69700546 None:intergenic 25.0%
! GAACAAAAACAATATATTGG+AGG - chr1_3:69700647-69700666 None:intergenic 25.0%
! TCTTATGTTGTATAACTGTT+AGG - chr1_3:69700848-69700867 None:intergenic 25.0%
! AGAGTTCAGATAAATGATAT+TGG + chr1_3:69701152-69701171 Msa0137300:three_prime_UTR 25.0%
!!! TGAATGAGTGAGTTTTAAAG+AGG - chr1_3:69700208-69700227 None:intergenic 30.0%
CTTAATCGAAGAAACTTTAC+CGG + chr1_3:69700249-69700268 Msa0137300:CDS 30.0%
GGATTAGATAAATCTGGATT+AGG - chr1_3:69700347-69700366 None:intergenic 30.0%
TGCGAAAAAGAAGAGAAATT+TGG - chr1_3:69700368-69700387 None:intergenic 30.0%
TTCGGATCTGAGAAAAAAAT+GGG - chr1_3:69700499-69700518 None:intergenic 30.0%
TTTCGGATCTGAGAAAAAAA+TGG - chr1_3:69700500-69700519 None:intergenic 30.0%
!! CTCTGATTTTGTTTGTTGAT+AGG + chr1_3:69701113-69701132 Msa0137300:intron 30.0%
TCAGATAAATGATATTGGAG+AGG + chr1_3:69701157-69701176 Msa0137300:three_prime_UTR 30.0%
!!! TGAATGAGTGAGTTTTAAAG+AGG - chr1_3:69700208-69700227 None:intergenic 30.0%
CTTAATCGAAGAAACTTTAC+CGG + chr1_3:69700249-69700268 Msa0137300:CDS 30.0%
GGATTAGATAAATCTGGATT+AGG - chr1_3:69700347-69700366 None:intergenic 30.0%
TGCGAAAAAGAAGAGAAATT+TGG - chr1_3:69700368-69700387 None:intergenic 30.0%
TTCGGATCTGAGAAAAAAAT+GGG - chr1_3:69700499-69700518 None:intergenic 30.0%
TTTCGGATCTGAGAAAAAAA+TGG - chr1_3:69700500-69700519 None:intergenic 30.0%
!! CTCTGATTTTGTTTGTTGAT+AGG + chr1_3:69701113-69701132 Msa0137300:intron 30.0%
TCAGATAAATGATATTGGAG+AGG + chr1_3:69701157-69701176 Msa0137300:three_prime_UTR 30.0%
GAAAGAAGGTAGAGGAAAAA+GGG - chr1_3:69700119-69700138 None:intergenic 35.0%
AGAAAGAAGGTAGAGGAAAA+AGG - chr1_3:69700120-69700139 None:intergenic 35.0%
GAAATGAAGAAAGAAGGTAG+AGG - chr1_3:69700127-69700146 None:intergenic 35.0%
TGATCGGAAATGAAGAAAGA+AGG - chr1_3:69700133-69700152 None:intergenic 35.0%
!!! GGTTTTATTTTTGTGTGAGG+CGG - chr1_3:69700163-69700182 None:intergenic 35.0%
!!! GGTGGTTTTATTTTTGTGTG+AGG - chr1_3:69700166-69700185 None:intergenic 35.0%
!!! AGTGAGTTTTAAAGAGGATG+TGG - chr1_3:69700202-69700221 None:intergenic 35.0%
TTACCTTCTGATCGTAATTC+CGG - chr1_3:69700307-69700326 None:intergenic 35.0%
!! AGTTCATTCATTTTTCGTGC+AGG + chr1_3:69700409-69700428 Msa0137300:intron 35.0%
GTTCTTTCAAGAACAAATCG+AGG + chr1_3:69700431-69700450 Msa0137300:CDS 35.0%
!! CTGAGAAAAAAATGGGTTAG+AGG - chr1_3:69700492-69700511 None:intergenic 35.0%
! AGATCCGAAAATAGCCATTT+TGG + chr1_3:69700510-69700529 Msa0137300:intron 35.0%
!! GATCCGAAAATAGCCATTTT+GGG + chr1_3:69700511-69700530 Msa0137300:intron 35.0%
!! CATCCCAAAATGGCTATTTT+CGG - chr1_3:69700517-69700536 None:intergenic 35.0%
!!! TTTTTTTCCCTCTCCAAATC+AGG + chr1_3:69700695-69700714 Msa0137300:intron 35.0%
AAATGTGTAAGAGCTTGAGT+TGG - chr1_3:69700886-69700905 None:intergenic 35.0%
! TACACATTTTGTACAGCATG+AGG + chr1_3:69700897-69700916 Msa0137300:intron 35.0%
GAAAGAAGGTAGAGGAAAAA+GGG - chr1_3:69700119-69700138 None:intergenic 35.0%
AGAAAGAAGGTAGAGGAAAA+AGG - chr1_3:69700120-69700139 None:intergenic 35.0%
GAAATGAAGAAAGAAGGTAG+AGG - chr1_3:69700127-69700146 None:intergenic 35.0%
TGATCGGAAATGAAGAAAGA+AGG - chr1_3:69700133-69700152 None:intergenic 35.0%
!!! GGTTTTATTTTTGTGTGAGG+CGG - chr1_3:69700163-69700182 None:intergenic 35.0%
!!! GGTGGTTTTATTTTTGTGTG+AGG - chr1_3:69700166-69700185 None:intergenic 35.0%
!!! AGTGAGTTTTAAAGAGGATG+TGG - chr1_3:69700202-69700221 None:intergenic 35.0%
TTACCTTCTGATCGTAATTC+CGG - chr1_3:69700307-69700326 None:intergenic 35.0%
!! AGTTCATTCATTTTTCGTGC+AGG + chr1_3:69700409-69700428 Msa0137300:intron 35.0%
GTTCTTTCAAGAACAAATCG+AGG + chr1_3:69700431-69700450 Msa0137300:CDS 35.0%
!! CTGAGAAAAAAATGGGTTAG+AGG - chr1_3:69700492-69700511 None:intergenic 35.0%
! AGATCCGAAAATAGCCATTT+TGG + chr1_3:69700510-69700529 Msa0137300:intron 35.0%
!! GATCCGAAAATAGCCATTTT+GGG + chr1_3:69700511-69700530 Msa0137300:intron 35.0%
!! CATCCCAAAATGGCTATTTT+CGG - chr1_3:69700517-69700536 None:intergenic 35.0%
!!! TTTTTTTCCCTCTCCAAATC+AGG + chr1_3:69700695-69700714 Msa0137300:intron 35.0%
AAATGTGTAAGAGCTTGAGT+TGG - chr1_3:69700886-69700905 None:intergenic 35.0%
! TACACATTTTGTACAGCATG+AGG + chr1_3:69700897-69700916 Msa0137300:intron 35.0%
AGGAAAAAGGGTTTGATGGA+GGG - chr1_3:69700107-69700126 None:intergenic 40.0%
GTAGAGGAAAAAGGGTTTGA+TGG - chr1_3:69700111-69700130 None:intergenic 40.0%
!!! TTATTTTTGTGTGAGGCGGA+CGG - chr1_3:69700159-69700178 None:intergenic 40.0%
!!! GTTTTAAAGAGGATGTGGAG+AGG - chr1_3:69700197-69700216 None:intergenic 40.0%
TTCTGATCGTAATTCCGGAA+CGG - chr1_3:69700302-69700321 None:intergenic 40.0%
TCATCATATGCTCACCTCAA+AGG - chr1_3:69700724-69700743 None:intergenic 40.0%
AGGAAAAAGGGTTTGATGGA+GGG - chr1_3:69700107-69700126 None:intergenic 40.0%
GTAGAGGAAAAAGGGTTTGA+TGG - chr1_3:69700111-69700130 None:intergenic 40.0%
!!! TTATTTTTGTGTGAGGCGGA+CGG - chr1_3:69700159-69700178 None:intergenic 40.0%
!!! GTTTTAAAGAGGATGTGGAG+AGG - chr1_3:69700197-69700216 None:intergenic 40.0%
TTCTGATCGTAATTCCGGAA+CGG - chr1_3:69700302-69700321 None:intergenic 40.0%
TCATCATATGCTCACCTCAA+AGG - chr1_3:69700724-69700743 None:intergenic 40.0%
AAAAGGGTTTGATGGAGGGA+GGG - chr1_3:69700103-69700122 None:intergenic 45.0%
AAAAAGGGTTTGATGGAGGG+AGG - chr1_3:69700104-69700123 None:intergenic 45.0%
GAGGAAAAAGGGTTTGATGG+AGG - chr1_3:69700108-69700127 None:intergenic 45.0%
TGTGGAGAGGAAGATTATGG+TGG - chr1_3:69700184-69700203 None:intergenic 45.0%
GGATGTGGAGAGGAAGATTA+TGG - chr1_3:69700187-69700206 None:intergenic 45.0%
GTTCCGGAATTACGATCAGA+AGG + chr1_3:69700301-69700320 Msa0137300:CDS 45.0%
TCGAGGAAGCAGATTAACCA+AGG + chr1_3:69700448-69700467 Msa0137300:exon 45.0%
! TTTTCCCTCTCCAAATCAGG+TGG + chr1_3:69700698-69700717 Msa0137300:intron 45.0%
TGGAGAGGCAATCAAACAGA+AGG + chr1_3:69701172-69701191 Msa0137300:three_prime_UTR 45.0%
AAAAGGGTTTGATGGAGGGA+GGG - chr1_3:69700103-69700122 None:intergenic 45.0%
AAAAAGGGTTTGATGGAGGG+AGG - chr1_3:69700104-69700123 None:intergenic 45.0%
GAGGAAAAAGGGTTTGATGG+AGG - chr1_3:69700108-69700127 None:intergenic 45.0%
TGTGGAGAGGAAGATTATGG+TGG - chr1_3:69700184-69700203 None:intergenic 45.0%
GGATGTGGAGAGGAAGATTA+TGG - chr1_3:69700187-69700206 None:intergenic 45.0%
GTTCCGGAATTACGATCAGA+AGG + chr1_3:69700301-69700320 Msa0137300:CDS 45.0%
TCGAGGAAGCAGATTAACCA+AGG + chr1_3:69700448-69700467 Msa0137300:exon 45.0%
! TTTTCCCTCTCCAAATCAGG+TGG + chr1_3:69700698-69700717 Msa0137300:intron 45.0%
TGGAGAGGCAATCAAACAGA+AGG + chr1_3:69701172-69701191 Msa0137300:three_prime_UTR 45.0%
GGGTGAGAGAAACGTGAATG+AGG - chr1_3:69700083-69700102 None:intergenic 50.0%
TGATCGTAATTCCGGAACGG+CGG - chr1_3:69700299-69700318 None:intergenic 50.0%
!! AAGGCCACCTGATTTGGAGA+GGG - chr1_3:69700705-69700724 None:intergenic 50.0%
!! AAAGGCCACCTGATTTGGAG+AGG - chr1_3:69700706-69700725 None:intergenic 50.0%
TCCAAATCAGGTGGCCTTTG+AGG + chr1_3:69700707-69700726 Msa0137300:intron 50.0%
ACCTCAAAGGCCACCTGATT+TGG - chr1_3:69700711-69700730 None:intergenic 50.0%
GGGTGAGAGAAACGTGAATG+AGG - chr1_3:69700083-69700102 None:intergenic 50.0%
TGATCGTAATTCCGGAACGG+CGG - chr1_3:69700299-69700318 None:intergenic 50.0%
!! AAGGCCACCTGATTTGGAGA+GGG - chr1_3:69700705-69700724 None:intergenic 50.0%
!! AAAGGCCACCTGATTTGGAG+AGG - chr1_3:69700706-69700725 None:intergenic 50.0%
TCCAAATCAGGTGGCCTTTG+AGG + chr1_3:69700707-69700726 Msa0137300:intron 50.0%
ACCTCAAAGGCCACCTGATT+TGG - chr1_3:69700711-69700730 None:intergenic 50.0%
GGAAACGAATTCCGGTGTGG+TGG - chr1_3:69700278-69700297 None:intergenic 55.0%
GGAACGGCGGAAACGAATTC+CGG - chr1_3:69700286-69700305 None:intergenic 55.0%
GGAATTCGTTTCCGCCGTTC+CGG + chr1_3:69700285-69700304 Msa0137300:CDS 55.0%
GGAAACGAATTCCGGTGTGG+TGG - chr1_3:69700278-69700297 None:intergenic 55.0%
GGAACGGCGGAAACGAATTC+CGG - chr1_3:69700286-69700305 None:intergenic 55.0%
GGAATTCGTTTCCGCCGTTC+CGG + chr1_3:69700285-69700304 Msa0137300:CDS 55.0%
! GTGAGGCGGACGGAGTTGAT+CGG - chr1_3:69700149-69700168 None:intergenic 60.0%
TTTACCGGCGACCACCACAC+CGG + chr1_3:69700264-69700283 Msa0137300:CDS 60.0%
AATTCCGGTGTGGTGGTCGC+CGG - chr1_3:69700271-69700290 None:intergenic 60.0%
GGCGGAAACGAATTCCGGTG+TGG - chr1_3:69700281-69700300 None:intergenic 60.0%
! GTGAGGCGGACGGAGTTGAT+CGG - chr1_3:69700149-69700168 None:intergenic 60.0%
TTTACCGGCGACCACCACAC+CGG + chr1_3:69700264-69700283 Msa0137300:CDS 60.0%
AATTCCGGTGTGGTGGTCGC+CGG - chr1_3:69700271-69700290 None:intergenic 60.0%
GGCGGAAACGAATTCCGGTG+TGG - chr1_3:69700281-69700300 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 69700036 69701199 69700036 ID=Msa0137300;Name=Msa0137300
chr1_3 mRNA 69700036 69701199 69700036 ID=Msa0137300-mRNA-1;Parent=Msa0137300;Name=Msa0137300-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0.5|0.33|1|1|1|3|70|106
chr1_3 exon 69700036 69700322 69700036 ID=Msa0137300-mRNA-1:exon:24108;Parent=Msa0137300-mRNA-1
chr1_3 exon 69700431 69700469 69700431 ID=Msa0137300-mRNA-1:exon:24109;Parent=Msa0137300-mRNA-1
chr1_3 exon 69701135 69701199 69701135 ID=Msa0137300-mRNA-1:exon:24110;Parent=Msa0137300-mRNA-1
chr1_3 CDS 69700036 69700322 69700036 ID=Msa0137300-mRNA-1:cds;Parent=Msa0137300-mRNA-1
chr1_3 CDS 69700431 69700464 69700431 ID=Msa0137300-mRNA-1:cds;Parent=Msa0137300-mRNA-1
chr1_3 three_prime_UTR 69700465 69700469 69700465 ID=Msa0137300-mRNA-1:three_prime_utr;Parent=Msa0137300-mRNA-1
chr1_3 three_prime_UTR 69701135 69701199 69701135 ID=Msa0137300-mRNA-1:three_prime_utr;Parent=Msa0137300-mRNA-1
Gene Sequence

>Msa0137300

ACTTTCTATCTCACACACAAACATAACATAACTCTCTCTTTCTTCCTCATTCACGTTTCTCTCACCCTCCCTCCATCAAACCCTTTTTCCTCTACCTTCTTTCTTCATTTCCGATCAACTCCGTCCGCCTCACACAAAAATAAAACCACCATAATCTTCCTCTCCACATCCTCTTTAAAACTCACTCATTCATTTATATATCTATCAACTTTACTTAATCGAAGAAACTTTACCGGCGACCACCACACCGGAATTCGTTTCCGCCGTTCCGGAATTACGATCAGAAGGTTCTTTCAAGAACAAATCGAGGAAGCAGATTAA

Protein sequence

>Msa0137300

TFYLTHKHNITLSFFLIHVSLTLPPSNPFSSTFFLHFRSTPSASHKNKTTIIFLSTSSLKLTHSFIYLSTLLNRRNFTGDHHTGIRFRRSGITIRRFFQEQIEEAD*