AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0094670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0094670 MtrunA17_Chr2g0281101 95.714 140 6 0 1 140 1 140 1.26e-99 281
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0094670 AT4G21445.1 77.778 90 20 0 51 140 65 154 2.74e-49 155

Find 43 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAACTTCATCAACAGAAAA+AGG 0.207487 1_2:-78020673 Msa0094670:three_prime_UTR
TTATCTTCCTTTGTGCTATC+AGG 0.247231 1_2:+78021334 None:intergenic
TGTTTGAAGACATGATTTAT+AGG 0.337289 1_2:+78021413 None:intergenic
TTTAACTTAATGTGAGAGAT+TGG 0.338033 1_2:+78021513 None:intergenic
AATTGTACTTTCTCATGAAT+CGG 0.359210 1_2:-78020711 Msa0094670:three_prime_UTR
AAATTTGTAAAGAAATGATA+TGG 0.389251 1_2:+78020628 None:intergenic
TGTTCTTCAGTGGGATGATT+CGG 0.397395 1_2:-78020920 Msa0094670:CDS
TCCTAAAAGACAAGCTCAAA+AGG 0.401395 1_2:-78020963 Msa0094670:CDS
GCTGGTTTGGTTGAGATGTC+TGG 0.414517 1_2:-78021234 Msa0094670:CDS
GACACTGGAAGAAGCTGGTT+TGG 0.416136 1_2:-78021247 Msa0094670:CDS
GAAAATTGATCAGCAATAGA+AGG 0.425165 1_2:+78020801 None:intergenic
GTTTGAAGACATGATTTATA+GGG 0.432921 1_2:+78021414 None:intergenic
ATTGTACTTTCTCATGAATC+GGG 0.441787 1_2:-78020710 Msa0094670:three_prime_UTR
TGATTTGTAACAAGGTTTGA+AGG 0.448700 1_2:+78021375 None:intergenic
CCAGCATTGAGCTCCTCTAC+TGG 0.451355 1_2:+78021003 None:intergenic
CTTTGTGTGGAGGAGGGTGA+TGG 0.454412 1_2:+78021562 None:intergenic
CTCTTGTGTTATTCTAAACA+AGG 0.466068 1_2:+78020748 None:intergenic
CTGTTAGCTTTGTGTGGAGG+AGG 0.467927 1_2:+78021555 None:intergenic
CCTTATCTGTTAGCTTTGTG+TGG 0.479941 1_2:+78021549 None:intergenic
TGATTCTGCTGTTCTTCAGT+GGG 0.485721 1_2:-78020929 Msa0094670:CDS
CCAGTAGAGGAGCTCAATGC+TGG 0.486468 1_2:-78021003 Msa0094670:CDS
TTCAATTATAACTATGTAGT+GGG 0.505484 1_2:+78020847 None:intergenic
GATTTGTAACAAGGTTTGAA+GGG 0.518410 1_2:+78021376 None:intergenic
CAGAAGAGAAGAAGAGTGAG+AGG 0.523957 1_2:-78021281 Msa0094670:CDS
TGAGAGATTGGAATGGGTTG+AGG 0.528179 1_2:+78021525 None:intergenic
TTGATTCTGCTGTTCTTCAG+TGG 0.529384 1_2:-78020930 Msa0094670:CDS
CCACACAAAGCTAACAGATA+AGG 0.541206 1_2:-78021549 Msa0094670:five_prime_UTR
TTTGTGTGGAGGAGGGTGAT+GGG 0.541825 1_2:+78021563 None:intergenic
AAGAAATGATATGGAGAACA+TGG 0.543069 1_2:+78020637 None:intergenic
TATCTGTTAGCTTTGTGTGG+AGG 0.550231 1_2:+78021552 None:intergenic
ATTCAATTATAACTATGTAG+TGG 0.555175 1_2:+78020846 None:intergenic
CTTAATGTGAGAGATTGGAA+TGG 0.560459 1_2:+78021518 None:intergenic
TGTTAGCTTTGTGTGGAGGA+GGG 0.565168 1_2:+78021556 None:intergenic
CCTAAAAGACAAGCTCAAAA+GGG 0.568726 1_2:-78020962 Msa0094670:CDS
TTAATGTGAGAGATTGGAAT+GGG 0.577438 1_2:+78021519 None:intergenic
GAGAGATTGGAATGGGTTGA+GGG 0.578878 1_2:+78021526 None:intergenic
ACAAGAAGGGTGTCCAGTAG+AGG 0.582601 1_2:-78021016 Msa0094670:CDS
ATGCTGGAAAGGTATGTGAT+TGG 0.593475 1_2:-78020987 Msa0094670:CDS
AAGTGATATCAGAACAAGAA+GGG 0.598781 1_2:-78021029 Msa0094670:CDS
AGAGGAGCTCAATGCTGGAA+AGG 0.602474 1_2:-78020998 Msa0094670:CDS
AAAGTGATATCAGAACAAGA+AGG 0.604912 1_2:-78021030 Msa0094670:CDS
TGTGTCTATGATTTGTAACA+AGG 0.620077 1_2:+78021367 None:intergenic
AAACAAGCCTGATAGCACAA+AGG 0.711054 1_2:-78021341 Msa0094670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTACAACTTTATATTTTA+GGG - chr1_2:78021301-78021320 Msa0094670:CDS 10.0%
!!! AATTACAACTTTATATTTTA+GGG - chr1_2:78021301-78021320 Msa0094670:CDS 10.0%
!! AGAAGAAAAAGAATTAAAAT+TGG + chr1_2:78021237-78021256 None:intergenic 15.0%
!!! GAATTACAACTTTATATTTT+AGG - chr1_2:78021300-78021319 Msa0094670:CDS 15.0%
!!! ATTACAACTTTATATTTTAG+GGG - chr1_2:78021302-78021321 Msa0094670:CDS 15.0%
!! AAATTTGTAAAGAAATGATA+TGG + chr1_2:78021502-78021521 None:intergenic 15.0%
!! AGAAGAAAAAGAATTAAAAT+TGG + chr1_2:78021237-78021256 None:intergenic 15.0%
!!! GAATTACAACTTTATATTTT+AGG - chr1_2:78021300-78021319 Msa0094670:CDS 15.0%
!!! ATTACAACTTTATATTTTAG+GGG - chr1_2:78021302-78021321 Msa0094670:CDS 15.0%
!! AAATTTGTAAAGAAATGATA+TGG + chr1_2:78021502-78021521 None:intergenic 15.0%
!! CACAAACAATATGAAAATTT+AGG + chr1_2:78021049-78021068 None:intergenic 20.0%
!! TTCAATTATAACTATGTAGT+GGG + chr1_2:78021283-78021302 None:intergenic 20.0%
!! ATTCAATTATAACTATGTAG+TGG + chr1_2:78021284-78021303 None:intergenic 20.0%
!!! TTACAACTTTATATTTTAGG+GGG - chr1_2:78021303-78021322 Msa0094670:CDS 20.0%
!!! TTATTCTAAACAAGGATTTT+TGG + chr1_2:78021374-78021393 None:intergenic 20.0%
!! CACAAACAATATGAAAATTT+AGG + chr1_2:78021049-78021068 None:intergenic 20.0%
!! TTCAATTATAACTATGTAGT+GGG + chr1_2:78021283-78021302 None:intergenic 20.0%
!! ATTCAATTATAACTATGTAG+TGG + chr1_2:78021284-78021303 None:intergenic 20.0%
!!! TTACAACTTTATATTTTAGG+GGG - chr1_2:78021303-78021322 Msa0094670:CDS 20.0%
!!! TTATTCTAAACAAGGATTTT+TGG + chr1_2:78021374-78021393 None:intergenic 20.0%
!! TTTAACTTAATGTGAGAGAT+TGG + chr1_2:78020617-78020636 None:intergenic 25.0%
! CTAAAAAAAAGAAGATAGCA+AGG - chr1_2:78020637-78020656 Msa0094670:three_prime_UTR 25.0%
!! TATTTTCAATCTCTTTCTCT+GGG + chr1_2:78020673-78020692 None:intergenic 25.0%
!! TTATTTTCAATCTCTTTCTC+TGG + chr1_2:78020674-78020693 None:intergenic 25.0%
! GTTTGAAGACATGATTTATA+GGG + chr1_2:78020716-78020735 None:intergenic 25.0%
! TGTTTGAAGACATGATTTAT+AGG + chr1_2:78020717-78020736 None:intergenic 25.0%
!! GAAAATTTAGGACATATACT+AGG + chr1_2:78021037-78021056 None:intergenic 25.0%
! AATTGTACTTTCTCATGAAT+CGG - chr1_2:78021416-78021435 Msa0094670:CDS 25.0%
!! TTTAACTTAATGTGAGAGAT+TGG + chr1_2:78020617-78020636 None:intergenic 25.0%
! CTAAAAAAAAGAAGATAGCA+AGG - chr1_2:78020637-78020656 Msa0094670:three_prime_UTR 25.0%
!! TATTTTCAATCTCTTTCTCT+GGG + chr1_2:78020673-78020692 None:intergenic 25.0%
!! TTATTTTCAATCTCTTTCTC+TGG + chr1_2:78020674-78020693 None:intergenic 25.0%
! GTTTGAAGACATGATTTATA+GGG + chr1_2:78020716-78020735 None:intergenic 25.0%
! TGTTTGAAGACATGATTTAT+AGG + chr1_2:78020717-78020736 None:intergenic 25.0%
!! GAAAATTTAGGACATATACT+AGG + chr1_2:78021037-78021056 None:intergenic 25.0%
! AATTGTACTTTCTCATGAAT+CGG - chr1_2:78021416-78021435 Msa0094670:CDS 25.0%
TTAATGTGAGAGATTGGAAT+GGG + chr1_2:78020611-78020630 None:intergenic 30.0%
GATTTGTAACAAGGTTTGAA+GGG + chr1_2:78020754-78020773 None:intergenic 30.0%
! TGATTTGTAACAAGGTTTGA+AGG + chr1_2:78020755-78020774 None:intergenic 30.0%
! TGTGTCTATGATTTGTAACA+AGG + chr1_2:78020763-78020782 None:intergenic 30.0%
CAATGAAGAAACAAAATCCT+AGG + chr1_2:78020995-78021014 None:intergenic 30.0%
!! CTAGGATTTTGTTTCTTCAT+TGG - chr1_2:78020993-78021012 Msa0094670:CDS 30.0%
AAAGTGATATCAGAACAAGA+AGG - chr1_2:78021097-78021116 Msa0094670:intron 30.0%
AAGTGATATCAGAACAAGAA+GGG - chr1_2:78021098-78021117 Msa0094670:intron 30.0%
GAAAATTGATCAGCAATAGA+AGG + chr1_2:78021329-78021348 None:intergenic 30.0%
!!! TTCCTTTTTTGTGCAAAATG+TGG - chr1_2:78021346-78021365 Msa0094670:CDS 30.0%
! CTCTTGTGTTATTCTAAACA+AGG + chr1_2:78021382-78021401 None:intergenic 30.0%
ATTGTACTTTCTCATGAATC+GGG - chr1_2:78021417-78021436 Msa0094670:CDS 30.0%
TGAACTTCATCAACAGAAAA+AGG - chr1_2:78021454-78021473 Msa0094670:five_prime_UTR 30.0%
AAGAAATGATATGGAGAACA+TGG + chr1_2:78021493-78021512 None:intergenic 30.0%
TTAATGTGAGAGATTGGAAT+GGG + chr1_2:78020611-78020630 None:intergenic 30.0%
GATTTGTAACAAGGTTTGAA+GGG + chr1_2:78020754-78020773 None:intergenic 30.0%
! TGATTTGTAACAAGGTTTGA+AGG + chr1_2:78020755-78020774 None:intergenic 30.0%
! TGTGTCTATGATTTGTAACA+AGG + chr1_2:78020763-78020782 None:intergenic 30.0%
CAATGAAGAAACAAAATCCT+AGG + chr1_2:78020995-78021014 None:intergenic 30.0%
!! CTAGGATTTTGTTTCTTCAT+TGG - chr1_2:78020993-78021012 Msa0094670:CDS 30.0%
AAAGTGATATCAGAACAAGA+AGG - chr1_2:78021097-78021116 Msa0094670:intron 30.0%
AAGTGATATCAGAACAAGAA+GGG - chr1_2:78021098-78021117 Msa0094670:intron 30.0%
GAAAATTGATCAGCAATAGA+AGG + chr1_2:78021329-78021348 None:intergenic 30.0%
!!! TTCCTTTTTTGTGCAAAATG+TGG - chr1_2:78021346-78021365 Msa0094670:CDS 30.0%
! CTCTTGTGTTATTCTAAACA+AGG + chr1_2:78021382-78021401 None:intergenic 30.0%
ATTGTACTTTCTCATGAATC+GGG - chr1_2:78021417-78021436 Msa0094670:CDS 30.0%
TGAACTTCATCAACAGAAAA+AGG - chr1_2:78021454-78021473 Msa0094670:five_prime_UTR 30.0%
AAGAAATGATATGGAGAACA+TGG + chr1_2:78021493-78021512 None:intergenic 30.0%
CTTAATGTGAGAGATTGGAA+TGG + chr1_2:78020612-78020631 None:intergenic 35.0%
TTATCTTCCTTTGTGCTATC+AGG + chr1_2:78020796-78020815 None:intergenic 35.0%
TCCTAAAAGACAAGCTCAAA+AGG - chr1_2:78021164-78021183 Msa0094670:intron 35.0%
CCTAAAAGACAAGCTCAAAA+GGG - chr1_2:78021165-78021184 Msa0094670:intron 35.0%
! AGCCACATTTTGCACAAAAA+AGG + chr1_2:78021351-78021370 None:intergenic 35.0%
CTTAATGTGAGAGATTGGAA+TGG + chr1_2:78020612-78020631 None:intergenic 35.0%
TTATCTTCCTTTGTGCTATC+AGG + chr1_2:78020796-78020815 None:intergenic 35.0%
TCCTAAAAGACAAGCTCAAA+AGG - chr1_2:78021164-78021183 Msa0094670:intron 35.0%
CCTAAAAGACAAGCTCAAAA+GGG - chr1_2:78021165-78021184 Msa0094670:intron 35.0%
! AGCCACATTTTGCACAAAAA+AGG + chr1_2:78021351-78021370 None:intergenic 35.0%
!! TATCTGTTAGCTTTGTGTGG+AGG + chr1_2:78020578-78020597 None:intergenic 40.0%
!! CCTTATCTGTTAGCTTTGTG+TGG + chr1_2:78020581-78020600 None:intergenic 40.0%
CCACACAAAGCTAACAGATA+AGG - chr1_2:78020578-78020597 Msa0094670:three_prime_UTR 40.0%
AAACAAGCCTGATAGCACAA+AGG - chr1_2:78020786-78020805 Msa0094670:three_prime_UTR 40.0%
! GAGGAAAACGTTTTTGACAC+TGG - chr1_2:78020865-78020884 Msa0094670:three_prime_UTR 40.0%
! TTTTTGACACTGGAAGAAGC+TGG - chr1_2:78020875-78020894 Msa0094670:three_prime_UTR 40.0%
! GCGTTTTCTATGTCGTCTAA+CGG - chr1_2:78020931-78020950 Msa0094670:CDS 40.0%
CCTTAACTCTGTTGTCTTGT+CGG - chr1_2:78020960-78020979 Msa0094670:CDS 40.0%
! ATGCTGGAAAGGTATGTGAT+TGG - chr1_2:78021140-78021159 Msa0094670:intron 40.0%
! CCCTTTTGAGCTTGTCTTTT+AGG + chr1_2:78021168-78021187 None:intergenic 40.0%
TTGATTCTGCTGTTCTTCAG+TGG - chr1_2:78021197-78021216 Msa0094670:CDS 40.0%
TGATTCTGCTGTTCTTCAGT+GGG - chr1_2:78021198-78021217 Msa0094670:CDS 40.0%
TGTTCTTCAGTGGGATGATT+CGG - chr1_2:78021207-78021226 Msa0094670:CDS 40.0%
!! TATCTGTTAGCTTTGTGTGG+AGG + chr1_2:78020578-78020597 None:intergenic 40.0%
!! CCTTATCTGTTAGCTTTGTG+TGG + chr1_2:78020581-78020600 None:intergenic 40.0%
CCACACAAAGCTAACAGATA+AGG - chr1_2:78020578-78020597 Msa0094670:three_prime_UTR 40.0%
AAACAAGCCTGATAGCACAA+AGG - chr1_2:78020786-78020805 Msa0094670:three_prime_UTR 40.0%
! GAGGAAAACGTTTTTGACAC+TGG - chr1_2:78020865-78020884 Msa0094670:three_prime_UTR 40.0%
! TTTTTGACACTGGAAGAAGC+TGG - chr1_2:78020875-78020894 Msa0094670:three_prime_UTR 40.0%
! GCGTTTTCTATGTCGTCTAA+CGG - chr1_2:78020931-78020950 Msa0094670:CDS 40.0%
CCTTAACTCTGTTGTCTTGT+CGG - chr1_2:78020960-78020979 Msa0094670:CDS 40.0%
! ATGCTGGAAAGGTATGTGAT+TGG - chr1_2:78021140-78021159 Msa0094670:intron 40.0%
! CCCTTTTGAGCTTGTCTTTT+AGG + chr1_2:78021168-78021187 None:intergenic 40.0%
TTGATTCTGCTGTTCTTCAG+TGG - chr1_2:78021197-78021216 Msa0094670:CDS 40.0%
TGATTCTGCTGTTCTTCAGT+GGG - chr1_2:78021198-78021217 Msa0094670:CDS 40.0%
TGTTCTTCAGTGGGATGATT+CGG - chr1_2:78021207-78021226 Msa0094670:CDS 40.0%
!! TGTTAGCTTTGTGTGGAGGA+GGG + chr1_2:78020574-78020593 None:intergenic 45.0%
!! GAGAGATTGGAATGGGTTGA+GGG + chr1_2:78020604-78020623 None:intergenic 45.0%
!! TGAGAGATTGGAATGGGTTG+AGG + chr1_2:78020605-78020624 None:intergenic 45.0%
CAGAAGAGAAGAAGAGTGAG+AGG - chr1_2:78020846-78020865 Msa0094670:three_prime_UTR 45.0%
CCGACAAGACAACAGAGTTA+AGG + chr1_2:78020963-78020982 None:intergenic 45.0%
CTTGTCGGATGATATGTCCT+AGG - chr1_2:78020975-78020994 Msa0094670:CDS 45.0%
!! TGTTAGCTTTGTGTGGAGGA+GGG + chr1_2:78020574-78020593 None:intergenic 45.0%
!! GAGAGATTGGAATGGGTTGA+GGG + chr1_2:78020604-78020623 None:intergenic 45.0%
!! TGAGAGATTGGAATGGGTTG+AGG + chr1_2:78020605-78020624 None:intergenic 45.0%
CAGAAGAGAAGAAGAGTGAG+AGG - chr1_2:78020846-78020865 Msa0094670:three_prime_UTR 45.0%
CCGACAAGACAACAGAGTTA+AGG + chr1_2:78020963-78020982 None:intergenic 45.0%
CTTGTCGGATGATATGTCCT+AGG - chr1_2:78020975-78020994 Msa0094670:CDS 45.0%
TTTGTGTGGAGGAGGGTGAT+GGG + chr1_2:78020567-78020586 None:intergenic 50.0%
!! CTGTTAGCTTTGTGTGGAGG+AGG + chr1_2:78020575-78020594 None:intergenic 50.0%
GACACTGGAAGAAGCTGGTT+TGG - chr1_2:78020880-78020899 Msa0094670:three_prime_UTR 50.0%
!! GCTGGTTTGGTTGAGATGTC+TGG - chr1_2:78020893-78020912 Msa0094670:exon 50.0%
!! ACAAGAAGGGTGTCCAGTAG+AGG - chr1_2:78021111-78021130 Msa0094670:intron 50.0%
AGAGGAGCTCAATGCTGGAA+AGG - chr1_2:78021129-78021148 Msa0094670:intron 50.0%
TTTGTGTGGAGGAGGGTGAT+GGG + chr1_2:78020567-78020586 None:intergenic 50.0%
!! CTGTTAGCTTTGTGTGGAGG+AGG + chr1_2:78020575-78020594 None:intergenic 50.0%
GACACTGGAAGAAGCTGGTT+TGG - chr1_2:78020880-78020899 Msa0094670:three_prime_UTR 50.0%
!! GCTGGTTTGGTTGAGATGTC+TGG - chr1_2:78020893-78020912 Msa0094670:exon 50.0%
!! ACAAGAAGGGTGTCCAGTAG+AGG - chr1_2:78021111-78021130 Msa0094670:intron 50.0%
AGAGGAGCTCAATGCTGGAA+AGG - chr1_2:78021129-78021148 Msa0094670:intron 50.0%
CTTTGTGTGGAGGAGGGTGA+TGG + chr1_2:78020568-78020587 None:intergenic 55.0%
! CCAGCATTGAGCTCCTCTAC+TGG + chr1_2:78021127-78021146 None:intergenic 55.0%
CCAGTAGAGGAGCTCAATGC+TGG - chr1_2:78021124-78021143 Msa0094670:intron 55.0%
CTTTGTGTGGAGGAGGGTGA+TGG + chr1_2:78020568-78020587 None:intergenic 55.0%
! CCAGCATTGAGCTCCTCTAC+TGG + chr1_2:78021127-78021146 None:intergenic 55.0%
CCAGTAGAGGAGCTCAATGC+TGG - chr1_2:78021124-78021143 Msa0094670:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 78020564 78021585 78020564 ID=Msa0094670;Name=Msa0094670
chr1_2 mRNA 78020564 78021585 78020564 ID=Msa0094670-mRNA-1;Parent=Msa0094670;Name=Msa0094670-mRNA-1;_AED=0.06;_eAED=0.06;_QI=134|1|1|1|1|1|2|342|140
chr1_2 exon 78020564 78021073 78020564 ID=Msa0094670-mRNA-1:exon:27782;Parent=Msa0094670-mRNA-1
chr1_2 exon 78021197 78021585 78021197 ID=Msa0094670-mRNA-1:exon:27781;Parent=Msa0094670-mRNA-1
chr1_2 five_prime_UTR 78021452 78021585 78021452 ID=Msa0094670-mRNA-1:five_prime_utr;Parent=Msa0094670-mRNA-1
chr1_2 CDS 78021197 78021451 78021197 ID=Msa0094670-mRNA-1:cds;Parent=Msa0094670-mRNA-1
chr1_2 CDS 78020906 78021073 78020906 ID=Msa0094670-mRNA-1:cds;Parent=Msa0094670-mRNA-1
chr1_2 three_prime_UTR 78020564 78020905 78020564 ID=Msa0094670-mRNA-1:three_prime_utr;Parent=Msa0094670-mRNA-1
Gene Sequence

>Msa0094670

ATGATTTGTCTACAACCCTATAAATCATGTCTTCAAACAACATTTGTATTCAGCCCTTCAAACCTTGTTACAAATCATAGACACACACAAACAAGCCTGATAGCACAAAGGAAGATAAAAGTACATAGAAGAAATGTCAAATGCAATGCAGAAGAGAAGAAGAGTGAGAGGAAAACGTTTTTGACACTGGAAGAAGCTGGTTTGGTTGAGATGTCTGGATTGAGCACTCATGAGCGTTTTCTATGTCGTCTAACGATATCTTCACTGAATTTACTAAAAGTGATATCAGAACAAGAAGGGTGTCCAGTAGAGGAGCTCAATGCTGGAAAGGTATGTGATTGGTTCCTAAAAGACAAGCTCAAAAGGGAGCAGAACATTGATTCTGCTGTTCTTCAGTGGGATGATTCGGATTTCCAATTTTAA

Protein sequence

>Msa0094670

MICLQPYKSCLQTTFVFSPSNLVTNHRHTQTSLIAQRKIKVHRRNVKCNAEEKKSERKTFLTLEEAGLVEMSGLSTHERFLCRLTISSLNLLKVISEQEGCPVEELNAGKVCDWFLKDKLKREQNIDSAVLQWDDSDFQF*