AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0132070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0132070 MtrunA17_Chr6g0473421 48.485 66 34 0 64 129 37 102 2.11e-18 75.9
Msa0132070 MtrunA17_Chr1g0172931 38.462 91 56 0 39 129 33 123 7.68e-18 74.7
Msa0132070 MtrunA17_Chr8g0389811 44.444 63 35 0 67 129 69 131 1.04e-14 67.4
Msa0132070 MtrunA17_Chr1g0203051 32.727 110 63 2 21 130 29 127 1.57e-14 68.9
Msa0132070 MtrunA17_Chr1g0171741 40.541 74 44 0 57 130 108 181 6.72e-13 63.5
Msa0132070 MtrunA17_Chr2g0331371 48.485 66 34 0 64 129 37 102 1.03e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATAAATATTTAATAGTTT+AGG 0.339187 1_3:+63042265 Msa0132070:five_prime_UTR
AACTGAAAATCCTGACATTC+TGG 0.342907 1_3:-63043144 None:intergenic
TCCGATTATGATAAAAGATA+TGG 0.367150 1_3:+63043019 Msa0132070:CDS
AAATTTGGTATTCAGAGAAA+TGG 0.369906 1_3:+63042737 Msa0132070:intron
TTCAAATTCAGTTGAAGGCT+TGG 0.371929 1_3:+63042974 Msa0132070:CDS
TCTTGGTTTGCCAGAATGTC+AGG 0.393047 1_3:+63043134 Msa0132070:CDS
ATCTTCAACCGGGTATCAAC+TGG 0.407828 1_3:-63042426 None:intergenic
CAGAGAAATGGACGGACGTT+CGG 0.413413 1_3:+63042749 Msa0132070:intron
GGAAGTTCAAATTCAGTTGA+AGG 0.423460 1_3:+63042969 Msa0132070:CDS
TGTTCGTTATGATCTTCAAC+CGG 0.429920 1_3:-63042437 None:intergenic
CCGCATATAGTGGGTGAAAC+CGG 0.459104 1_3:+63042227 None:intergenic
ATTTGCAAACAAAGGTCTGC+TGG 0.495786 1_3:-63043208 None:intergenic
AAATTCAGTTGAAGGCTTGG+AGG 0.512939 1_3:+63042977 Msa0132070:CDS
GATAAATCATTTGCAAACAA+AGG 0.526325 1_3:-63043216 None:intergenic
ACACCATTGCGCTCTAACAA+AGG 0.543044 1_3:-63042783 None:intergenic
TCGTAAGGGGCAAGTGGTGA+GGG 0.567327 1_3:+63043166 Msa0132070:CDS
TTCGTAAGGGGCAAGTGGTG+AGG 0.571006 1_3:+63043165 Msa0132070:CDS
TTCAGTTCGTAAGGGGCAAG+TGG 0.578338 1_3:+63043160 Msa0132070:CDS
TGATATAATGAAGATTGACC+TGG 0.579924 1_3:+63043043 Msa0132070:CDS
GTTCGTTATGATCTTCAACC+GGG 0.580394 1_3:-63042436 None:intergenic
CAAGTGGTGAGGGATCGAAA+TGG 0.589736 1_3:+63043176 Msa0132070:CDS
AGTCGAAACCAGTTGATACC+CGG 0.596773 1_3:+63042418 Msa0132070:five_prime_UTR
GAAGATCATAACGAACATCA+AGG 0.597977 1_3:+63042443 Msa0132070:five_prime_UTR
AAACCAAGAGTAAAACATGT+AGG 0.598768 1_3:-63043120 None:intergenic
ATACAAGTGCAAAGGATCTG+AGG 0.607043 1_3:+63042388 Msa0132070:five_prime_UTR
CTGAAAACATACAAGTGCAA+AGG 0.609745 1_3:+63042380 Msa0132070:five_prime_UTR
AGAAATGGACGGACGTTCGG+AGG 0.620957 1_3:+63042752 Msa0132070:exon
CCGGTTTCACCCACTATATG+CGG 0.648194 1_3:-63042227 None:intergenic
TTGGTATTCAGAGAAATGGA+CGG 0.649153 1_3:+63042741 Msa0132070:intron
CAAAGCAATGAAGATGTCAG+TGG 0.657097 1_3:+63042948 Msa0132070:CDS
AATCCTTTGTTAGAGCGCAA+TGG 0.668763 1_3:+63042780 Msa0132070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAAAAAATGAAAAAAAC+CGG - chr1_3:63042249-63042268 None:intergenic 10.0%
!! ATTAAAAAAATGAAAAAAAC+CGG - chr1_3:63042249-63042268 None:intergenic 10.0%
!!! ATTTGTTTGTTTAGTTTTTT+GGG - chr1_3:63042320-63042339 None:intergenic 15.0%
!!! AATTTGTTTGTTTAGTTTTT+TGG - chr1_3:63042321-63042340 None:intergenic 15.0%
!! AACAAACAAATTAAAAAAAG+AGG + chr1_3:63042329-63042348 Msa0132070:five_prime_UTR 15.0%
!!! ATTTGTTTGTTTAGTTTTTT+GGG - chr1_3:63042320-63042339 None:intergenic 15.0%
!!! AATTTGTTTGTTTAGTTTTT+TGG - chr1_3:63042321-63042340 None:intergenic 15.0%
!! AACAAACAAATTAAAAAAAG+AGG + chr1_3:63042329-63042348 Msa0132070:five_prime_UTR 15.0%
!! ACCTGATTCATTTAAAAATT+TGG + chr1_3:63042722-63042741 Msa0132070:intron 20.0%
!!! ACCAAATTTTTAAATGAATC+AGG - chr1_3:63042726-63042745 None:intergenic 20.0%
!!! ATGTGAAATTTGAAATTGAA+TGG + chr1_3:63042833-63042852 Msa0132070:intron 20.0%
!!! TTTTAAATTAACTTAGCATG+TGG + chr1_3:63042858-63042877 Msa0132070:intron 20.0%
!!! CTAAAAGAAAATTTTCTTAC+AGG + chr1_3:63042881-63042900 Msa0132070:intron 20.0%
!!! ACCATATCTTTTATCATAAT+CGG - chr1_3:63043023-63043042 None:intergenic 20.0%
!! ACCTGATTCATTTAAAAATT+TGG + chr1_3:63042722-63042741 Msa0132070:intron 20.0%
!!! ACCAAATTTTTAAATGAATC+AGG - chr1_3:63042726-63042745 None:intergenic 20.0%
!!! ATGTGAAATTTGAAATTGAA+TGG + chr1_3:63042833-63042852 Msa0132070:intron 20.0%
!!! TTTTAAATTAACTTAGCATG+TGG + chr1_3:63042858-63042877 Msa0132070:intron 20.0%
!!! CTAAAAGAAAATTTTCTTAC+AGG + chr1_3:63042881-63042900 Msa0132070:intron 20.0%
!!! ACCATATCTTTTATCATAAT+CGG - chr1_3:63043023-63043042 None:intergenic 20.0%
!!! ATCGATTGTTGTTTTGTTAA+GGG + chr1_3:63042518-63042537 Msa0132070:intron 25.0%
! TTAATAGTGATGAAATACGA+GGG - chr1_3:63042578-63042597 None:intergenic 25.0%
! TTTAATAGTGATGAAATACG+AGG - chr1_3:63042579-63042598 None:intergenic 25.0%
!! TAGAGACTTGTTTAGAAATT+AGG + chr1_3:63042633-63042652 Msa0132070:intron 25.0%
! AAATTTGGTATTCAGAGAAA+TGG + chr1_3:63042737-63042756 Msa0132070:intron 25.0%
! TCCGATTATGATAAAAGATA+TGG + chr1_3:63043019-63043038 Msa0132070:CDS 25.0%
!!! ATCGATTGTTGTTTTGTTAA+GGG + chr1_3:63042518-63042537 Msa0132070:intron 25.0%
! TTAATAGTGATGAAATACGA+GGG - chr1_3:63042578-63042597 None:intergenic 25.0%
! TTTAATAGTGATGAAATACG+AGG - chr1_3:63042579-63042598 None:intergenic 25.0%
!! TAGAGACTTGTTTAGAAATT+AGG + chr1_3:63042633-63042652 Msa0132070:intron 25.0%
! AAATTTGGTATTCAGAGAAA+TGG + chr1_3:63042737-63042756 Msa0132070:intron 25.0%
! TCCGATTATGATAAAAGATA+TGG + chr1_3:63043019-63043038 Msa0132070:CDS 25.0%
!!! GATCGATTGTTGTTTTGTTA+AGG + chr1_3:63042517-63042536 Msa0132070:intron 30.0%
!!! TCGATTGTTGTTTTGTTAAG+GGG + chr1_3:63042519-63042538 Msa0132070:intron 30.0%
AAACCTTTGAATGTTGAATG+AGG + chr1_3:63042597-63042616 Msa0132070:intron 30.0%
TTTATGTATCACACACACTT+TGG + chr1_3:63042677-63042696 Msa0132070:intron 30.0%
TTATGTATCACACACACTTT+GGG + chr1_3:63042678-63042697 Msa0132070:intron 30.0%
TGATATAATGAAGATTGACC+TGG + chr1_3:63043043-63043062 Msa0132070:CDS 30.0%
AAACCAAGAGTAAAACATGT+AGG - chr1_3:63043123-63043142 None:intergenic 30.0%
!!! GATCGATTGTTGTTTTGTTA+AGG + chr1_3:63042517-63042536 Msa0132070:intron 30.0%
!!! TCGATTGTTGTTTTGTTAAG+GGG + chr1_3:63042519-63042538 Msa0132070:intron 30.0%
AAACCTTTGAATGTTGAATG+AGG + chr1_3:63042597-63042616 Msa0132070:intron 30.0%
TTTATGTATCACACACACTT+TGG + chr1_3:63042677-63042696 Msa0132070:intron 30.0%
TTATGTATCACACACACTTT+GGG + chr1_3:63042678-63042697 Msa0132070:intron 30.0%
TGATATAATGAAGATTGACC+TGG + chr1_3:63043043-63043062 Msa0132070:CDS 30.0%
AAACCAAGAGTAAAACATGT+AGG - chr1_3:63043123-63043142 None:intergenic 30.0%
CTGAAAACATACAAGTGCAA+AGG + chr1_3:63042380-63042399 Msa0132070:five_prime_UTR 35.0%
TGTTCGTTATGATCTTCAAC+CGG - chr1_3:63042440-63042459 None:intergenic 35.0%
GAAGATCATAACGAACATCA+AGG + chr1_3:63042443-63042462 Msa0132070:five_prime_UTR 35.0%
AAGATGCACAACAACTAAAC+AGG - chr1_3:63042475-63042494 None:intergenic 35.0%
!!! ATTGTTGTTTTGTTAAGGGG+TGG + chr1_3:63042522-63042541 Msa0132070:intron 35.0%
CAACCTCATTCAACATTCAA+AGG - chr1_3:63042603-63042622 None:intergenic 35.0%
TTAGGCATGTTACTGTTGTT+TGG + chr1_3:63042651-63042670 Msa0132070:intron 35.0%
! TAGGCATGTTACTGTTGTTT+GGG + chr1_3:63042652-63042671 Msa0132070:intron 35.0%
TTGGTATTCAGAGAAATGGA+CGG + chr1_3:63042741-63042760 Msa0132070:intron 35.0%
!! CAGGATTTTGAAGATGAAAG+TGG + chr1_3:63042900-63042919 Msa0132070:intron 35.0%
!! GATTTTGAAGATGAAAGTGG+AGG + chr1_3:63042903-63042922 Msa0132070:CDS 35.0%
GGAAGTTCAAATTCAGTTGA+AGG + chr1_3:63042969-63042988 Msa0132070:CDS 35.0%
TTCAAATTCAGTTGAAGGCT+TGG + chr1_3:63042974-63042993 Msa0132070:CDS 35.0%
! TTGCCTACATGTTTTACTCT+TGG + chr1_3:63043117-63043136 Msa0132070:CDS 35.0%
AACTGAAAATCCTGACATTC+TGG - chr1_3:63043147-63043166 None:intergenic 35.0%
! TCAGGATTTTCAGTTCGTAA+GGG + chr1_3:63043152-63043171 Msa0132070:CDS 35.0%
CTGAAAACATACAAGTGCAA+AGG + chr1_3:63042380-63042399 Msa0132070:five_prime_UTR 35.0%
TGTTCGTTATGATCTTCAAC+CGG - chr1_3:63042440-63042459 None:intergenic 35.0%
GAAGATCATAACGAACATCA+AGG + chr1_3:63042443-63042462 Msa0132070:five_prime_UTR 35.0%
AAGATGCACAACAACTAAAC+AGG - chr1_3:63042475-63042494 None:intergenic 35.0%
!!! ATTGTTGTTTTGTTAAGGGG+TGG + chr1_3:63042522-63042541 Msa0132070:intron 35.0%
CAACCTCATTCAACATTCAA+AGG - chr1_3:63042603-63042622 None:intergenic 35.0%
TTAGGCATGTTACTGTTGTT+TGG + chr1_3:63042651-63042670 Msa0132070:intron 35.0%
! TAGGCATGTTACTGTTGTTT+GGG + chr1_3:63042652-63042671 Msa0132070:intron 35.0%
TTGGTATTCAGAGAAATGGA+CGG + chr1_3:63042741-63042760 Msa0132070:intron 35.0%
!! CAGGATTTTGAAGATGAAAG+TGG + chr1_3:63042900-63042919 Msa0132070:intron 35.0%
!! GATTTTGAAGATGAAAGTGG+AGG + chr1_3:63042903-63042922 Msa0132070:CDS 35.0%
GGAAGTTCAAATTCAGTTGA+AGG + chr1_3:63042969-63042988 Msa0132070:CDS 35.0%
TTCAAATTCAGTTGAAGGCT+TGG + chr1_3:63042974-63042993 Msa0132070:CDS 35.0%
! TTGCCTACATGTTTTACTCT+TGG + chr1_3:63043117-63043136 Msa0132070:CDS 35.0%
AACTGAAAATCCTGACATTC+TGG - chr1_3:63043147-63043166 None:intergenic 35.0%
! TCAGGATTTTCAGTTCGTAA+GGG + chr1_3:63043152-63043171 Msa0132070:CDS 35.0%
ATACAAGTGCAAAGGATCTG+AGG + chr1_3:63042388-63042407 Msa0132070:five_prime_UTR 40.0%
GTTCGTTATGATCTTCAACC+GGG - chr1_3:63042439-63042458 None:intergenic 40.0%
!! TTGTTTTGTTAAGGGGTGGA+GGG + chr1_3:63042526-63042545 Msa0132070:intron 40.0%
! AGGCATGTTACTGTTGTTTG+GGG + chr1_3:63042653-63042672 Msa0132070:intron 40.0%
AATCCTTTGTTAGAGCGCAA+TGG + chr1_3:63042780-63042799 Msa0132070:CDS 40.0%
CAAAGCAATGAAGATGTCAG+TGG + chr1_3:63042948-63042967 Msa0132070:CDS 40.0%
AAATTCAGTTGAAGGCTTGG+AGG + chr1_3:63042977-63042996 Msa0132070:CDS 40.0%
! TGACCTGGAAAACTTTTGTG+TGG + chr1_3:63043058-63043077 Msa0132070:CDS 40.0%
! AAACTTTTGTGTGGCTGATG+TGG + chr1_3:63043067-63043086 Msa0132070:CDS 40.0%
! GTCAGGATTTTCAGTTCGTA+AGG + chr1_3:63043151-63043170 Msa0132070:CDS 40.0%
! CAGGATTTTCAGTTCGTAAG+GGG + chr1_3:63043153-63043172 Msa0132070:CDS 40.0%
ATTTGCAAACAAAGGTCTGC+TGG - chr1_3:63043211-63043230 None:intergenic 40.0%
ATACAAGTGCAAAGGATCTG+AGG + chr1_3:63042388-63042407 Msa0132070:five_prime_UTR 40.0%
GTTCGTTATGATCTTCAACC+GGG - chr1_3:63042439-63042458 None:intergenic 40.0%
!! TTGTTTTGTTAAGGGGTGGA+GGG + chr1_3:63042526-63042545 Msa0132070:intron 40.0%
! AGGCATGTTACTGTTGTTTG+GGG + chr1_3:63042653-63042672 Msa0132070:intron 40.0%
AATCCTTTGTTAGAGCGCAA+TGG + chr1_3:63042780-63042799 Msa0132070:CDS 40.0%
CAAAGCAATGAAGATGTCAG+TGG + chr1_3:63042948-63042967 Msa0132070:CDS 40.0%
AAATTCAGTTGAAGGCTTGG+AGG + chr1_3:63042977-63042996 Msa0132070:CDS 40.0%
! TGACCTGGAAAACTTTTGTG+TGG + chr1_3:63043058-63043077 Msa0132070:CDS 40.0%
! AAACTTTTGTGTGGCTGATG+TGG + chr1_3:63043067-63043086 Msa0132070:CDS 40.0%
! GTCAGGATTTTCAGTTCGTA+AGG + chr1_3:63043151-63043170 Msa0132070:CDS 40.0%
! CAGGATTTTCAGTTCGTAAG+GGG + chr1_3:63043153-63043172 Msa0132070:CDS 40.0%
ATTTGCAAACAAAGGTCTGC+TGG - chr1_3:63043211-63043230 None:intergenic 40.0%
! AGTCGAAACCAGTTGATACC+CGG + chr1_3:63042418-63042437 Msa0132070:five_prime_UTR 45.0%
ATCTTCAACCGGGTATCAAC+TGG - chr1_3:63042429-63042448 None:intergenic 45.0%
!! GTTGTTTTGTTAAGGGGTGG+AGG + chr1_3:63042525-63042544 Msa0132070:intron 45.0%
ACACCATTGCGCTCTAACAA+AGG - chr1_3:63042786-63042805 None:intergenic 45.0%
! CAGCCACACAAAAGTTTTCC+AGG - chr1_3:63043064-63043083 None:intergenic 45.0%
!! TCTTGGTTTGCCAGAATGTC+AGG + chr1_3:63043134-63043153 Msa0132070:CDS 45.0%
! AGTCGAAACCAGTTGATACC+CGG + chr1_3:63042418-63042437 Msa0132070:five_prime_UTR 45.0%
ATCTTCAACCGGGTATCAAC+TGG - chr1_3:63042429-63042448 None:intergenic 45.0%
!! GTTGTTTTGTTAAGGGGTGG+AGG + chr1_3:63042525-63042544 Msa0132070:intron 45.0%
ACACCATTGCGCTCTAACAA+AGG - chr1_3:63042786-63042805 None:intergenic 45.0%
! CAGCCACACAAAAGTTTTCC+AGG - chr1_3:63043064-63043083 None:intergenic 45.0%
!! TCTTGGTTTGCCAGAATGTC+AGG + chr1_3:63043134-63043153 Msa0132070:CDS 45.0%
!! TAATAAATATTTAATAGTTT+AGG + chr1_3:63042265-63042284 Msa0132070:five_prime_UTR 5.0%
!! TAATAAATATTTAATAGTTT+AGG + chr1_3:63042265-63042284 Msa0132070:five_prime_UTR 5.0%
CAGAGAAATGGACGGACGTT+CGG + chr1_3:63042749-63042768 Msa0132070:intron 50.0%
TTCAGTTCGTAAGGGGCAAG+TGG + chr1_3:63043160-63043179 Msa0132070:CDS 50.0%
CAAGTGGTGAGGGATCGAAA+TGG + chr1_3:63043176-63043195 Msa0132070:CDS 50.0%
CAGAGAAATGGACGGACGTT+CGG + chr1_3:63042749-63042768 Msa0132070:intron 50.0%
TTCAGTTCGTAAGGGGCAAG+TGG + chr1_3:63043160-63043179 Msa0132070:CDS 50.0%
CAAGTGGTGAGGGATCGAAA+TGG + chr1_3:63043176-63043195 Msa0132070:CDS 50.0%
AGAAATGGACGGACGTTCGG+AGG + chr1_3:63042752-63042771 Msa0132070:exon 55.0%
TTCGTAAGGGGCAAGTGGTG+AGG + chr1_3:63043165-63043184 Msa0132070:CDS 55.0%
TCGTAAGGGGCAAGTGGTGA+GGG + chr1_3:63043166-63043185 Msa0132070:CDS 55.0%
AGAAATGGACGGACGTTCGG+AGG + chr1_3:63042752-63042771 Msa0132070:exon 55.0%
TTCGTAAGGGGCAAGTGGTG+AGG + chr1_3:63043165-63043184 Msa0132070:CDS 55.0%
TCGTAAGGGGCAAGTGGTGA+GGG + chr1_3:63043166-63043185 Msa0132070:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 63042229 63043232 63042229 ID=Msa0132070;Name=Msa0132070
chr1_3 mRNA 63042229 63043232 63042229 ID=Msa0132070-mRNA-1;Parent=Msa0132070;Name=Msa0132070-mRNA-1;_AED=0.07;_eAED=0.07;_QI=240|1|0.66|1|0.5|0.66|3|0|130
chr1_3 exon 63042229 63042464 63042229 ID=Msa0132070-mRNA-1:exon:21098;Parent=Msa0132070-mRNA-1
chr1_3 exon 63042752 63042818 63042752 ID=Msa0132070-mRNA-1:exon:21099;Parent=Msa0132070-mRNA-1
chr1_3 exon 63042903 63043232 63042903 ID=Msa0132070-mRNA-1:exon:21100;Parent=Msa0132070-mRNA-1
chr1_3 five_prime_UTR 63042229 63042464 63042229 ID=Msa0132070-mRNA-1:five_prime_utr;Parent=Msa0132070-mRNA-1
chr1_3 five_prime_UTR 63042752 63042755 63042752 ID=Msa0132070-mRNA-1:five_prime_utr;Parent=Msa0132070-mRNA-1
chr1_3 CDS 63042756 63042818 63042756 ID=Msa0132070-mRNA-1:cds;Parent=Msa0132070-mRNA-1
chr1_3 CDS 63042903 63043232 63042903 ID=Msa0132070-mRNA-1:cds;Parent=Msa0132070-mRNA-1
Gene Sequence

>Msa0132070

ATGGACGGACGTTCGGAGGCTGTGAATCCTTTGTTAGAGCGCAATGGTGTGAGAATTTCAAGAGATTTTGAAGATGAAAGTGGAGGTAATAACAACACAAATTGCGAACAAAGCAATGAAGATGTCAGTGGAAGTTCAAATTCAGTTGAAGGCTTGGAGGATGAAACTAATGAAGTCAATCCGATTATGATAAAAGATATGGTTGATATAATGAAGATTGACCTGGAAAACTTTTGTGTGGCTGATGTGGAAAGATATGAATTTGTTGCTTTAGATGTTGCCTACATGTTTTACTCTTGGTTTGCCAGAATGTCAGGATTTTCAGTTCGTAAGGGGCAAGTGGTGAGGGATCGAAATGGTGAAGTCGTCCAGCAGACCTTTGTTTGCAAATGA
Protein sequence

>Msa0132070

MDGRSEAVNPLLERNGVRISRDFEDESGGNNNTNCEQSNEDVSGSSNSVEGLEDETNEVNPIMIKDMVDIMKIDLENFCVADVERYEFVALDVAYMFYSWFARMSGFSVRKGQVVRDRNGEVVQQTFVCK*