AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0648170


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 8 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGAGACCAGGTTTCTGTT+AGG 0.396356 4_3:+54585485 Msa0648170:CDS
CTAGTCAGCAACAACTTGTC+AGG 0.473473 4_3:+54585530 Msa0648170:CDS
AGACAGACTAACAGAAGTCT+TGG 0.503643 4_3:-54585509 None:intergenic
ATTACTTTGAAAACACAGAA+AGG 0.514773 4_3:+54584806 Msa0648170:CDS
TAGAAGATATAGTTGAGACC+AGG 0.610471 4_3:+54585474 Msa0648170:CDS
GTCAGCAACAACTTGTCAGG+AGG 0.612718 4_3:+54585533 Msa0648170:CDS
TCTTGGTCCTAACAGAAACC+TGG 0.619787 4_3:-54585492 None:intergenic
TCAGCAACAACTTGTCAGGA+GGG 0.640123 4_3:+54585534 Msa0648170:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGATGAATAAATAATTAGAT+GGG - chr4_3:54585130-54585149 None:intergenic 15.0%
!! TTGATGAATAAATAATTAGA+TGG - chr4_3:54585131-54585150 None:intergenic 15.0%
!! TGTAAAACAATTTACAATAT+GGG - chr4_3:54585206-54585225 None:intergenic 15.0%
!! TTGTAAAACAATTTACAATA+TGG - chr4_3:54585207-54585226 None:intergenic 15.0%
!! TGATGAATAAATAATTAGAT+GGG - chr4_3:54585130-54585149 None:intergenic 15.0%
!! TTGATGAATAAATAATTAGA+TGG - chr4_3:54585131-54585150 None:intergenic 15.0%
!! TGTAAAACAATTTACAATAT+GGG - chr4_3:54585206-54585225 None:intergenic 15.0%
!! TTGTAAAACAATTTACAATA+TGG - chr4_3:54585207-54585226 None:intergenic 15.0%
!!! ACTATTTTCAACAATAAGTT+GGG + chr4_3:54585001-54585020 Msa0648170:intron 20.0%
!! ATAAATAATTAGATGGGTAT+GGG - chr4_3:54585124-54585143 None:intergenic 20.0%
!! AATAAATAATTAGATGGGTA+TGG - chr4_3:54585125-54585144 None:intergenic 20.0%
!!! TTTTATTCATCATTAGACAA+AGG + chr4_3:54585428-54585447 Msa0648170:intron 20.0%
!!! ACTATTTTCAACAATAAGTT+GGG + chr4_3:54585001-54585020 Msa0648170:intron 20.0%
!! ATAAATAATTAGATGGGTAT+GGG - chr4_3:54585124-54585143 None:intergenic 20.0%
!! AATAAATAATTAGATGGGTA+TGG - chr4_3:54585125-54585144 None:intergenic 20.0%
!!! TTTTATTCATCATTAGACAA+AGG + chr4_3:54585428-54585447 Msa0648170:intron 20.0%
!! ATTACTTTGAAAACACAGAA+AGG + chr4_3:54584806-54584825 Msa0648170:CDS 25.0%
!!! AATTAATCCTTGTTTTAGCT+GGG - chr4_3:54584908-54584927 None:intergenic 25.0%
!!! TAATTAATCCTTGTTTTAGC+TGG - chr4_3:54584909-54584928 None:intergenic 25.0%
! ATTAAACCATCTATAAAGAG+AGG + chr4_3:54584925-54584944 Msa0648170:intron 25.0%
! TTAAACCATCTATAAAGAGA+GGG + chr4_3:54584926-54584945 Msa0648170:intron 25.0%
!! GACTATTTTCAACAATAAGT+TGG + chr4_3:54585000-54585019 Msa0648170:intron 25.0%
!! ATTACTTTGAAAACACAGAA+AGG + chr4_3:54584806-54584825 Msa0648170:CDS 25.0%
!!! AATTAATCCTTGTTTTAGCT+GGG - chr4_3:54584908-54584927 None:intergenic 25.0%
!!! TAATTAATCCTTGTTTTAGC+TGG - chr4_3:54584909-54584928 None:intergenic 25.0%
! ATTAAACCATCTATAAAGAG+AGG + chr4_3:54584925-54584944 Msa0648170:intron 25.0%
! TTAAACCATCTATAAAGAGA+GGG + chr4_3:54584926-54584945 Msa0648170:intron 25.0%
!! GACTATTTTCAACAATAAGT+TGG + chr4_3:54585000-54585019 Msa0648170:intron 25.0%
! ATATAACATGCTCTCTTTTG+TGG + chr4_3:54584735-54584754 Msa0648170:intron 30.0%
TTGGATTATGTAGCTCATTA+GGG - chr4_3:54585101-54585120 None:intergenic 30.0%
GCATGGATGATTTAACAATA+AGG - chr4_3:54585270-54585289 None:intergenic 30.0%
! GTTTGCTGAAATGTTAAGAA+AGG + chr4_3:54585339-54585358 Msa0648170:intron 30.0%
TTAGAGACGTGAGATATTAT+TGG + chr4_3:54585365-54585384 Msa0648170:intron 30.0%
! ATATAACATGCTCTCTTTTG+TGG + chr4_3:54584735-54584754 Msa0648170:intron 30.0%
TTGGATTATGTAGCTCATTA+GGG - chr4_3:54585101-54585120 None:intergenic 30.0%
GCATGGATGATTTAACAATA+AGG - chr4_3:54585270-54585289 None:intergenic 30.0%
! GTTTGCTGAAATGTTAAGAA+AGG + chr4_3:54585339-54585358 Msa0648170:intron 30.0%
TTAGAGACGTGAGATATTAT+TGG + chr4_3:54585365-54585384 Msa0648170:intron 30.0%
! GTCTATGTTTTATGTGCCAT+AGG + chr4_3:54585057-54585076 Msa0648170:intron 35.0%
GTTGGATTATGTAGCTCATT+AGG - chr4_3:54585102-54585121 None:intergenic 35.0%
ATAATTAGATGGGTATGGGT+TGG - chr4_3:54585120-54585139 None:intergenic 35.0%
CGTGAGATATTATTGGACAA+AGG + chr4_3:54585372-54585391 Msa0648170:intron 35.0%
TAGAAGATATAGTTGAGACC+AGG + chr4_3:54585474-54585493 Msa0648170:CDS 35.0%
! GTCTATGTTTTATGTGCCAT+AGG + chr4_3:54585057-54585076 Msa0648170:intron 35.0%
GTTGGATTATGTAGCTCATT+AGG - chr4_3:54585102-54585121 None:intergenic 35.0%
ATAATTAGATGGGTATGGGT+TGG - chr4_3:54585120-54585139 None:intergenic 35.0%
CGTGAGATATTATTGGACAA+AGG + chr4_3:54585372-54585391 Msa0648170:intron 35.0%
TAGAAGATATAGTTGAGACC+AGG + chr4_3:54585474-54585493 Msa0648170:CDS 35.0%
!! TGCTAGTTAGCTTTATCTGC+AGG + chr4_3:54584670-54584689 Msa0648170:intron 40.0%
!! GCAAAAGTTCAAGTTGTGCA+TGG + chr4_3:54584841-54584860 Msa0648170:intron 40.0%
AACTCTCAGTAGTCAATGCA+TGG - chr4_3:54585287-54585306 None:intergenic 40.0%
TGACTACTGAGAGTTTGTCT+TGG + chr4_3:54585292-54585311 Msa0648170:intron 40.0%
AGAGTTTGTCTTGGCTATGA+GGG + chr4_3:54585301-54585320 Msa0648170:intron 40.0%
AGACAGACTAACAGAAGTCT+TGG - chr4_3:54585512-54585531 None:intergenic 40.0%
!! TGCTAGTTAGCTTTATCTGC+AGG + chr4_3:54584670-54584689 Msa0648170:intron 40.0%
!! GCAAAAGTTCAAGTTGTGCA+TGG + chr4_3:54584841-54584860 Msa0648170:intron 40.0%
AACTCTCAGTAGTCAATGCA+TGG - chr4_3:54585287-54585306 None:intergenic 40.0%
TGACTACTGAGAGTTTGTCT+TGG + chr4_3:54585292-54585311 Msa0648170:intron 40.0%
AGAGTTTGTCTTGGCTATGA+GGG + chr4_3:54585301-54585320 Msa0648170:intron 40.0%
AGACAGACTAACAGAAGTCT+TGG - chr4_3:54585512-54585531 None:intergenic 40.0%
!! AGCCTTTGAGGTCATATCCA+AGG + chr4_3:54584868-54584887 Msa0648170:intron 45.0%
TGCCTTGGATATGACCTCAA+AGG - chr4_3:54584873-54584892 None:intergenic 45.0%
! GGTCATATCCAAGGCATCAA+TGG + chr4_3:54584877-54584896 Msa0648170:intron 45.0%
GGAGATTCCCAGCTAAAACA+AGG + chr4_3:54584898-54584917 Msa0648170:intron 45.0%
CTTGGCCCTCTCTTTATAGA+TGG - chr4_3:54584934-54584953 None:intergenic 45.0%
AGCATATGGCTCAGAACCTA+TGG - chr4_3:54585076-54585095 None:intergenic 45.0%
AGCTCATTAGGGCAAGCATA+TGG - chr4_3:54585090-54585109 None:intergenic 45.0%
GAGAGTTTGTCTTGGCTATG+AGG + chr4_3:54585300-54585319 Msa0648170:intron 45.0%
TCTTGGCTATGAGGGTTTGA+AGG + chr4_3:54585309-54585328 Msa0648170:intron 45.0%
CTTGGCTATGAGGGTTTGAA+GGG + chr4_3:54585310-54585329 Msa0648170:intron 45.0%
TTGGCTATGAGGGTTTGAAG+GGG + chr4_3:54585311-54585330 Msa0648170:intron 45.0%
GTTGAGACCAGGTTTCTGTT+AGG + chr4_3:54585485-54585504 Msa0648170:CDS 45.0%
TCTTGGTCCTAACAGAAACC+TGG - chr4_3:54585495-54585514 None:intergenic 45.0%
CTAGTCAGCAACAACTTGTC+AGG + chr4_3:54585530-54585549 Msa0648170:CDS 45.0%
TCAGCAACAACTTGTCAGGA+GGG + chr4_3:54585534-54585553 Msa0648170:CDS 45.0%
!! AGCCTTTGAGGTCATATCCA+AGG + chr4_3:54584868-54584887 Msa0648170:intron 45.0%
TGCCTTGGATATGACCTCAA+AGG - chr4_3:54584873-54584892 None:intergenic 45.0%
! GGTCATATCCAAGGCATCAA+TGG + chr4_3:54584877-54584896 Msa0648170:intron 45.0%
GGAGATTCCCAGCTAAAACA+AGG + chr4_3:54584898-54584917 Msa0648170:intron 45.0%
CTTGGCCCTCTCTTTATAGA+TGG - chr4_3:54584934-54584953 None:intergenic 45.0%
AGCATATGGCTCAGAACCTA+TGG - chr4_3:54585076-54585095 None:intergenic 45.0%
AGCTCATTAGGGCAAGCATA+TGG - chr4_3:54585090-54585109 None:intergenic 45.0%
GAGAGTTTGTCTTGGCTATG+AGG + chr4_3:54585300-54585319 Msa0648170:intron 45.0%
TCTTGGCTATGAGGGTTTGA+AGG + chr4_3:54585309-54585328 Msa0648170:intron 45.0%
CTTGGCTATGAGGGTTTGAA+GGG + chr4_3:54585310-54585329 Msa0648170:intron 45.0%
TTGGCTATGAGGGTTTGAAG+GGG + chr4_3:54585311-54585330 Msa0648170:intron 45.0%
GTTGAGACCAGGTTTCTGTT+AGG + chr4_3:54585485-54585504 Msa0648170:CDS 45.0%
TCTTGGTCCTAACAGAAACC+TGG - chr4_3:54585495-54585514 None:intergenic 45.0%
CTAGTCAGCAACAACTTGTC+AGG + chr4_3:54585530-54585549 Msa0648170:CDS 45.0%
TCAGCAACAACTTGTCAGGA+GGG + chr4_3:54585534-54585553 Msa0648170:CDS 45.0%
!! TATAAATTAGAAAAAAATTT+AGG - chr4_3:54585029-54585048 None:intergenic 5.0%
!! TATAAATTAGAAAAAAATTT+AGG - chr4_3:54585029-54585048 None:intergenic 5.0%
GTGCATGGTAAGAGCCTTTG+AGG + chr4_3:54584856-54584875 Msa0648170:intron 50.0%
GGGAATCTCCATTGATGCCT+TGG - chr4_3:54584888-54584907 None:intergenic 50.0%
TATAAAGAGAGGGCCAAGCG+AGG + chr4_3:54584936-54584955 Msa0648170:intron 50.0%
GTCAGCAACAACTTGTCAGG+AGG + chr4_3:54585533-54585552 Msa0648170:CDS 50.0%
GTGCATGGTAAGAGCCTTTG+AGG + chr4_3:54584856-54584875 Msa0648170:intron 50.0%
GGGAATCTCCATTGATGCCT+TGG - chr4_3:54584888-54584907 None:intergenic 50.0%
TATAAAGAGAGGGCCAAGCG+AGG + chr4_3:54584936-54584955 Msa0648170:intron 50.0%
GTCAGCAACAACTTGTCAGG+AGG + chr4_3:54585533-54585552 Msa0648170:CDS 50.0%
CTCACACTGAAAGCCTCGCT+TGG - chr4_3:54584952-54584971 None:intergenic 55.0%
GCTATGAGGGTTTGAAGGGG+AGG + chr4_3:54585314-54585333 Msa0648170:intron 55.0%
ATGAGGGTTTGAAGGGGAGG+TGG + chr4_3:54585317-54585336 Msa0648170:intron 55.0%
CTCACACTGAAAGCCTCGCT+TGG - chr4_3:54584952-54584971 None:intergenic 55.0%
GCTATGAGGGTTTGAAGGGG+AGG + chr4_3:54585314-54585333 Msa0648170:intron 55.0%
ATGAGGGTTTGAAGGGGAGG+TGG + chr4_3:54585317-54585336 Msa0648170:intron 55.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 54584669 54585568 54584669 ID=Msa0648170;Name=Msa0648170
chr4_3 mRNA 54584669 54585568 54584669 ID=Msa0648170-mRNA-1;Parent=Msa0648170;Name=Msa0648170-mRNA-1;_AED=0.51;_eAED=0.51;_QI=0|0|0|0.66|1|1|3|0|62
chr4_3 exon 54584669 54584674 54584669 ID=Msa0648170-mRNA-1:exon:13855;Parent=Msa0648170-mRNA-1
chr4_3 exon 54584764 54584827 54584764 ID=Msa0648170-mRNA-1:exon:13856;Parent=Msa0648170-mRNA-1
chr4_3 exon 54585450 54585568 54585450 ID=Msa0648170-mRNA-1:exon:13857;Parent=Msa0648170-mRNA-1
chr4_3 CDS 54584669 54584674 54584669 ID=Msa0648170-mRNA-1:cds;Parent=Msa0648170-mRNA-1
chr4_3 CDS 54584764 54584827 54584764 ID=Msa0648170-mRNA-1:cds;Parent=Msa0648170-mRNA-1
chr4_3 CDS 54585450 54585568 54585450 ID=Msa0648170-mRNA-1:cds;Parent=Msa0648170-mRNA-1
Gene Sequence

>Msa0648170

ATGCTAAGCATAAATATTGCAGTTATGAGCTATACAAGAATATTAAGAATTACTTTGAAAACACAGAAAGGTAGATCTGTTGCAAAAATAGTTGTAGAAGATATAGTTGAGACCAGGTTTCTGTTAGGACCAAGACTTCTGTTAGTCTGTCTAGTCAGCAACAACTTGTCAGGAGGGATTAACGTATAG

Protein sequence

>Msa0648170

MLSINIAVMSYTRILRITLKTQKGRSVAKIVVEDIVETRFLLGPRLLLVCLVSNNLSGGINV*