AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0989510

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0989510 MtrunA17_Chr8g0390681 91.304 138 5 2 1 131 575 712 7.58e-17 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 75 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGGGAATTATATTGAATA+GGG 0.325054 6_4:+46441938 None:intergenic
CCACCACCTGCCCCTGCATA+TGG 0.326891 6_4:-46441853 Msa0989510:CDS
CCATATGCAGGGGCAGGTGG+TGG 0.338357 6_4:+46441853 None:intergenic
GCAGGGGCAGGTGGTGGAGG+AGG 0.354812 6_4:+46441859 None:intergenic
GGGGCAGGTGGTGGAGGAGG+CGG 0.362354 6_4:+46441862 None:intergenic
GGCGGTAATGTTGGCGGCGG+CGG 0.387131 6_4:+46441880 None:intergenic
TCTCAATCTCCACCTTCTAT+AGG 0.388259 6_4:-46442105 Msa0989510:CDS
GAACTGTAAATGTAATGAAC+AGG 0.393633 6_4:+46441904 None:intergenic
TATGCAGGGGCAGGTGGTGG+AGG 0.403418 6_4:+46441856 None:intergenic
GGCAATGGCCCTCCATATGC+AGG 0.405224 6_4:+46441841 None:intergenic
GGTGGTGGAGGTGAAGCGTA+TGG 0.407180 6_4:+46441802 None:intergenic
CCTCCATATGCAGGGGCAGG+TGG 0.439400 6_4:+46441850 None:intergenic
GATGGTGGTCCGGGTGGGGA+TGG 0.443717 6_4:+46442042 None:intergenic
AGAAGATGGTGGTCCGGGTG+GGG 0.450249 6_4:+46442038 None:intergenic
GTGGAAGAAGATGGTGGTCC+GGG 0.451623 6_4:+46442033 None:intergenic
GGTGGGGAATTATATTGAAT+AGG 0.454165 6_4:+46441937 None:intergenic
GTGAATGAGGACCTGTCGGT+GGG 0.459013 6_4:+46442133 None:intergenic
GACGGAGGAGGTCCTATAGA+AGG 0.468232 6_4:+46442093 None:intergenic
TAATAGAAAGGAGGTGGTGG+AGG 0.468957 6_4:+46441790 None:intergenic
CCACCTGCCCCTGCATATGG+AGG 0.471132 6_4:-46441850 Msa0989510:CDS
TGTGGAAGAAGATGGTGGTC+CGG 0.475742 6_4:+46442032 None:intergenic
AGTGAATGAGACGGTGGCAT+TGG 0.479767 6_4:+46442165 None:intergenic
GGCCCTCCATATGCAGGGGC+AGG 0.480738 6_4:+46441847 None:intergenic
GTATATTGAACCGGTGGATG+TGG 0.486887 6_4:+46441985 None:intergenic
TATCAAAAGAATTAATAGAA+AGG 0.487917 6_4:+46441778 None:intergenic
GGTGGAGGAGGCGGTAATGT+TGG 0.495346 6_4:+46441871 None:intergenic
GGTGTTGGTGTGGAAGAAGA+TGG 0.496924 6_4:+46442024 None:intergenic
GGTGAATGAGGACCTGTCGG+TGG 0.501289 6_4:+46442132 None:intergenic
GAATGAGGACCTGTCGGTGG+GGG 0.504934 6_4:+46442135 None:intergenic
AATTAATAGAAAGGAGGTGG+TGG 0.514078 6_4:+46441787 None:intergenic
GTGGTGGAGGTGAAGCGTAT+GGG 0.521432 6_4:+46441803 None:intergenic
GAAGGATGTGATGGTGATGG+AGG 0.524666 6_4:+46441961 None:intergenic
AAGAAGATGGTGGTCCGGGT+GGG 0.525321 6_4:+46442037 None:intergenic
AAGAATTAATAGAAAGGAGG+TGG 0.526142 6_4:+46441784 None:intergenic
GGAGGAGGCGGTAATGTTGG+CGG 0.534442 6_4:+46441874 None:intergenic
GAAGAAGATGGTGGTCCGGG+TGG 0.547061 6_4:+46442036 None:intergenic
TGAATGAGGACCTGTCGGTG+GGG 0.551488 6_4:+46442134 None:intergenic
GAAGGTGGAGATTGAGATGG+TGG 0.551772 6_4:+46442111 None:intergenic
GGGGAAGGATGTGATGGTGA+TGG 0.551839 6_4:+46441958 None:intergenic
TGAATAGGGGAAGGATGTGA+TGG 0.572572 6_4:+46441952 None:intergenic
ACATGTTTCTCCACATCCAC+CGG 0.573015 6_4:-46441995 Msa0989510:CDS
GGGGATGGATGCTCTTCACA+AGG 0.578773 6_4:+46442057 None:intergenic
GGGCCATTGCCACCTATCGT+TGG 0.580573 6_4:-46441829 Msa0989510:CDS
GATGGAGGAGTATATTGAAC+CGG 0.583019 6_4:+46441976 None:intergenic
GAATTATATTGAATAGGGGA+AGG 0.586468 6_4:+46441943 None:intergenic
CACCTGCCCCTGCATATGGA+GGG 0.588689 6_4:-46441849 Msa0989510:CDS
GCAATGGCCCTCCATATGCA+GGG 0.589083 6_4:+46441842 None:intergenic
GATTGAGATGGTGGTGAATG+AGG 0.591055 6_4:+46442120 None:intergenic
CAAAAGAATTAATAGAAAGG+AGG 0.595418 6_4:+46441781 None:intergenic
GAAACATGTACTGGTGGTGT+TGG 0.599374 6_4:+46442009 None:intergenic
GGAGGCGGTAATGTTGGCGG+CGG 0.600162 6_4:+46441877 None:intergenic
GGTGGTGATAGTGACGGAGG+AGG 0.607777 6_4:+46442081 None:intergenic
GGATGCTCTTCACAAGGTGG+TGG 0.613075 6_4:+46442063 None:intergenic
GATGGATGCTCTTCACAAGG+TGG 0.617137 6_4:+46442060 None:intergenic
ATGTACTGGTGGTGTTGGTG+TGG 0.617442 6_4:+46442014 None:intergenic
GAAGAGCATCCATCCCCACC+CGG 0.621909 6_4:-46442051 Msa0989510:CDS
TGGGGAATTATATTGAATAG+GGG 0.623637 6_4:+46441939 None:intergenic
TATGGGAGACCAACGATAGG+TGG 0.625670 6_4:+46441820 None:intergenic
GGAGGAGGTCCTATAGAAGG+TGG 0.625828 6_4:+46442096 None:intergenic
AGACCAACGATAGGTGGCAA+TGG 0.626277 6_4:+46441826 None:intergenic
CAATGGCCCTCCATATGCAG+GGG 0.628756 6_4:+46441843 None:intergenic
AACTGTAAATGTAATGAACA+GGG 0.629027 6_4:+46441905 None:intergenic
GGATGTGGAGAAACATGTAC+TGG 0.630253 6_4:+46442000 None:intergenic
CAAGGTGGTGGTGATAGTGA+CGG 0.649338 6_4:+46442075 None:intergenic
ATAGAAGGTGGAGATTGAGA+TGG 0.661668 6_4:+46442108 None:intergenic
GGTGGTGAATGAGGACCTGT+CGG 0.663617 6_4:+46442129 None:intergenic
GGAGGAGTATATTGAACCGG+TGG 0.673177 6_4:+46441979 None:intergenic
GCGTATGGGAGACCAACGAT+AGG 0.680209 6_4:+46441817 None:intergenic
GTTGGTGTGGAAGAAGATGG+TGG 0.695491 6_4:+46442027 None:intergenic
GGATATAGTGAATGAGACGG+TGG 0.701084 6_4:+46442159 None:intergenic
GGTGGATATAGTGAATGAGA+CGG 0.705252 6_4:+46442156 None:intergenic
GGTGGTGGTGATAGTGACGG+AGG 0.710089 6_4:+46442078 None:intergenic
CTGTAAATGTAATGAACAGG+GGG 0.716333 6_4:+46441907 None:intergenic
TGTGGAGAAACATGTACTGG+TGG 0.735634 6_4:+46442003 None:intergenic
ACTGTAAATGTAATGAACAG+GGG 0.756387 6_4:+46441906 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AACTGTAAATGTAATGAACA+GGG + chr6_4:46442049-46442068 None:intergenic 25.0%
GAATTATATTGAATAGGGGA+AGG + chr6_4:46442011-46442030 None:intergenic 30.0%
TGGGGAATTATATTGAATAG+GGG + chr6_4:46442015-46442034 None:intergenic 30.0%
GTGGGGAATTATATTGAATA+GGG + chr6_4:46442016-46442035 None:intergenic 30.0%
ACTGTAAATGTAATGAACAG+GGG + chr6_4:46442048-46442067 None:intergenic 30.0%
GAACTGTAAATGTAATGAAC+AGG + chr6_4:46442050-46442069 None:intergenic 30.0%
GGTGGGGAATTATATTGAAT+AGG + chr6_4:46442017-46442036 None:intergenic 35.0%
CTGTAAATGTAATGAACAGG+GGG + chr6_4:46442047-46442066 None:intergenic 35.0%
GGTGGATATAGTGAATGAGA+CGG + chr6_4:46441798-46441817 None:intergenic 40.0%
ATAGAAGGTGGAGATTGAGA+TGG + chr6_4:46441846-46441865 None:intergenic 40.0%
TCTCAATCTCCACCTTCTAT+AGG - chr6_4:46441846-46441865 Msa0989510:CDS 40.0%
! GATGGAGGAGTATATTGAAC+CGG + chr6_4:46441978-46441997 None:intergenic 40.0%
TAAATGTAATGAACAGGGGG+TGG + chr6_4:46442044-46442063 None:intergenic 40.0%
GGATATAGTGAATGAGACGG+TGG + chr6_4:46441795-46441814 None:intergenic 45.0%
! GATTGAGATGGTGGTGAATG+AGG + chr6_4:46441834-46441853 None:intergenic 45.0%
! GAAACATGTACTGGTGGTGT+TGG + chr6_4:46441945-46441964 None:intergenic 45.0%
TGTGGAGAAACATGTACTGG+TGG + chr6_4:46441951-46441970 None:intergenic 45.0%
GGATGTGGAGAAACATGTAC+TGG + chr6_4:46441954-46441973 None:intergenic 45.0%
ACATGTTTCTCCACATCCAC+CGG - chr6_4:46441956-46441975 Msa0989510:CDS 45.0%
GTATATTGAACCGGTGGATG+TGG + chr6_4:46441969-46441988 None:intergenic 45.0%
TGAATAGGGGAAGGATGTGA+TGG + chr6_4:46442002-46442021 None:intergenic 45.0%
! TAATAGAAAGGAGGTGGTGG+AGG + chr6_4:46442164-46442183 None:intergenic 45.0%
GAAGGTGGAGATTGAGATGG+TGG + chr6_4:46441843-46441862 None:intergenic 50.0%
! CAAGGTGGTGGTGATAGTGA+CGG + chr6_4:46441879-46441898 None:intergenic 50.0%
GATGGATGCTCTTCACAAGG+TGG + chr6_4:46441894-46441913 None:intergenic 50.0%
! TGTGGAAGAAGATGGTGGTC+CGG + chr6_4:46441922-46441941 None:intergenic 50.0%
GTTGGTGTGGAAGAAGATGG+TGG + chr6_4:46441927-46441946 None:intergenic 50.0%
!! GGTGTTGGTGTGGAAGAAGA+TGG + chr6_4:46441930-46441949 None:intergenic 50.0%
!! ATGTACTGGTGGTGTTGGTG+TGG + chr6_4:46441940-46441959 None:intergenic 50.0%
! GGAGGAGTATATTGAACCGG+TGG + chr6_4:46441975-46441994 None:intergenic 50.0%
!! GAAGGATGTGATGGTGATGG+AGG + chr6_4:46441993-46442012 None:intergenic 50.0%
ATGTAATGAACAGGGGGTGG+TGG + chr6_4:46442041-46442060 None:intergenic 50.0%
AGACCAACGATAGGTGGCAA+TGG + chr6_4:46442128-46442147 None:intergenic 50.0%
TATGGGAGACCAACGATAGG+TGG + chr6_4:46442134-46442153 None:intergenic 50.0%
TGAATGAGGACCTGTCGGTG+GGG + chr6_4:46441820-46441839 None:intergenic 55.0%
GTGAATGAGGACCTGTCGGT+GGG + chr6_4:46441821-46441840 None:intergenic 55.0%
GGTGGTGAATGAGGACCTGT+CGG + chr6_4:46441825-46441844 None:intergenic 55.0%
GGAGGAGGTCCTATAGAAGG+TGG + chr6_4:46441858-46441877 None:intergenic 55.0%
GACGGAGGAGGTCCTATAGA+AGG + chr6_4:46441861-46441880 None:intergenic 55.0%
GGATGCTCTTCACAAGGTGG+TGG + chr6_4:46441891-46441910 None:intergenic 55.0%
GGGGATGGATGCTCTTCACA+AGG + chr6_4:46441897-46441916 None:intergenic 55.0%
! AAGAAGATGGTGGTCCGGGT+GGG + chr6_4:46441917-46441936 None:intergenic 55.0%
! GTGGAAGAAGATGGTGGTCC+GGG + chr6_4:46441921-46441940 None:intergenic 55.0%
! GGGGAAGGATGTGATGGTGA+TGG + chr6_4:46441996-46442015 None:intergenic 55.0%
! TAATGAACAGGGGGTGGTGG+TGG + chr6_4:46442038-46442057 None:intergenic 55.0%
CAATGGCCCTCCATATGCAG+GGG + chr6_4:46442111-46442130 None:intergenic 55.0%
GCAATGGCCCTCCATATGCA+GGG + chr6_4:46442112-46442131 None:intergenic 55.0%
GCGTATGGGAGACCAACGAT+AGG + chr6_4:46442137-46442156 None:intergenic 55.0%
! GTGGTGGAGGTGAAGCGTAT+GGG + chr6_4:46442151-46442170 None:intergenic 55.0%
CTATATCCACCCCCACCGAC+AGG - chr6_4:46441807-46441826 Msa0989510:CDS 60.0%
GAATGAGGACCTGTCGGTGG+GGG + chr6_4:46441819-46441838 None:intergenic 60.0%
GGTGAATGAGGACCTGTCGG+TGG + chr6_4:46441822-46441841 None:intergenic 60.0%
! GGTGGTGATAGTGACGGAGG+AGG + chr6_4:46441873-46441892 None:intergenic 60.0%
! GGTGGTGGTGATAGTGACGG+AGG + chr6_4:46441876-46441895 None:intergenic 60.0%
!! GAAGAGCATCCATCCCCACC+CGG - chr6_4:46441900-46441919 Msa0989510:CDS 60.0%
! AGAAGATGGTGGTCCGGGTG+GGG + chr6_4:46441916-46441935 None:intergenic 60.0%
! GAAGAAGATGGTGGTCCGGG+TGG + chr6_4:46441918-46441937 None:intergenic 60.0%
GGAGGAGGCGGTAATGTTGG+CGG + chr6_4:46442080-46442099 None:intergenic 60.0%
GGTGGAGGAGGCGGTAATGT+TGG + chr6_4:46442083-46442102 None:intergenic 60.0%
CACCTGCCCCTGCATATGGA+GGG - chr6_4:46442102-46442121 Msa0989510:CDS 60.0%
GGCAATGGCCCTCCATATGC+AGG + chr6_4:46442113-46442132 None:intergenic 60.0%
GGGCCATTGCCACCTATCGT+TGG - chr6_4:46442122-46442141 Msa0989510:CDS 60.0%
!! GGTGGTGGAGGTGAAGCGTA+TGG + chr6_4:46442152-46442171 None:intergenic 60.0%
!! AACAGGGGGTGGTGGTGGTG+GGG + chr6_4:46442033-46442052 None:intergenic 65.0%
!! GAACAGGGGGTGGTGGTGGT+GGG + chr6_4:46442034-46442053 None:intergenic 65.0%
!! TGAACAGGGGGTGGTGGTGG+TGG + chr6_4:46442035-46442054 None:intergenic 65.0%
GGAGGCGGTAATGTTGGCGG+CGG + chr6_4:46442077-46442096 None:intergenic 65.0%
! TATGCAGGGGCAGGTGGTGG+AGG + chr6_4:46442098-46442117 None:intergenic 65.0%
CCATATGCAGGGGCAGGTGG+TGG + chr6_4:46442101-46442120 None:intergenic 65.0%
CCACCACCTGCCCCTGCATA+TGG - chr6_4:46442098-46442117 Msa0989510:CDS 65.0%
CCTCCATATGCAGGGGCAGG+TGG + chr6_4:46442104-46442123 None:intergenic 65.0%
CCACCTGCCCCTGCATATGG+AGG - chr6_4:46442101-46442120 Msa0989510:CDS 65.0%
TGAGGACCTGTCGGTGGGGG+TGG + chr6_4:46441816-46441835 None:intergenic 70.0%
! GATGGTGGTCCGGGTGGGGA+TGG + chr6_4:46441912-46441931 None:intergenic 70.0%
GGCGGTAATGTTGGCGGCGG+CGG + chr6_4:46442074-46442093 None:intergenic 70.0%
GGCCCTCCATATGCAGGGGC+AGG + chr6_4:46442107-46442126 None:intergenic 70.0%
!! GGGGCAGGTGGTGGAGGAGG+CGG + chr6_4:46442092-46442111 None:intergenic 75.0%
!! GCAGGGGCAGGTGGTGGAGG+AGG + chr6_4:46442095-46442114 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 46441789 46442184 46441789 ID=Msa0989510;Name=Msa0989510
chr6_4 mRNA 46441789 46442184 46441789 ID=Msa0989510-mRNA-1;Parent=Msa0989510;Name=Msa0989510-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|131
chr6_4 exon 46441789 46442184 46441789 ID=Msa0989510-mRNA-1:exon:10486;Parent=Msa0989510-mRNA-1
chr6_4 CDS 46441789 46442184 46441789 ID=Msa0989510-mRNA-1:cds;Parent=Msa0989510-mRNA-1
Gene Sequence

>Msa0989510

ATGCCACCGTCTCATTCACTATATCCACCCCCACCGACAGGTCCTCATTCACCACCATCTCAATCTCCACCTTCTATAGGACCTCCTCCGTCACTATCACCACCACCTTGTGAAGAGCATCCATCCCCACCCGGACCACCATCTTCTTCCACACCAACACCACCAGTACATGTTTCTCCACATCCACCGGTTCAATATACTCCTCCATCACCATCACATCCTTCCCCTATTCAATATAATTCCCCACCACCACCACCCCCTGTTCATTACATTTACAGTTCACCGCCGCCGCCAACATTACCGCCTCCTCCACCACCTGCCCCTGCATATGGAGGGCCATTGCCACCTATCGTTGGTCTCCCATACGCTTCACCTCCACCACCTCCTTTCTATTAA
Protein sequence

>Msa0989510

MPPSHSLYPPPPTGPHSPPSQSPPSIGPPPSLSPPPCEEHPSPPGPPSSSTPTPPVHVSPHPPVQYTPPSPSHPSPIQYNSPPPPPPVHYIYSSPPPPTLPPPPPPAPAYGGPLPPIVGLPYASPPPPPFY*