AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1237660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1237660 MtrunA17_Chr8g0343071 97.802 182 4 0 1 182 1 182 4.88e-129 359
Msa1237660 MtrunA17_Chr2g0329891 75.141 177 44 0 6 182 12 188 4.24e-77 228
Msa1237660 MtrunA17_Chr1g0190881 55.135 185 80 3 1 182 1 185 4.25e-68 205
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1237660 AT1G72750.1 70.430 186 50 2 2 182 3 188 3.76e-81 239
Msa1237660 AT1G17530.1 66.667 183 57 2 2 182 7 187 1.10e-77 230
Msa1237660 AT1G17530.2 67.039 179 55 2 2 178 7 183 3.88e-76 226
Msa1237660 AT3G04800.1 54.802 177 79 1 7 182 12 188 1.43e-53 169

Find 74 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGGAGTTTGTAGAGGTTT+TGG 0.238988 8_2:+17171153 None:intergenic
GGAAACCGGGTTGGGATTAT+TGG 0.254619 8_2:-17170912 Msa1237660:CDS
CTGGACATTCGGGTCGGACT+TGG 0.267106 8_2:-17170935 Msa1237660:CDS
GTGAGATCGGCCGCGGTTGC+TGG 0.309664 8_2:-17170774 Msa1237660:CDS
TTTGAATGCGTCTGGACATT+CGG 0.314203 8_2:-17170946 Msa1237660:CDS
GCTGTTGGTGGGGTTGTTGT+TGG 0.333786 8_2:-17170750 Msa1237660:CDS
TTGAATGCGTCTGGACATTC+GGG 0.335254 8_2:-17170945 Msa1237660:CDS
CCAAACGTAAACGCCGTTCT+TGG 0.336189 8_2:-17171100 Msa1237660:CDS
TGGACATTCGGGTCGGACTT+GGG 0.337558 8_2:-17170934 Msa1237660:CDS
CTTACCCTCACACTTCAAAT+AGG 0.341231 8_2:+17170687 None:intergenic
AGCTGCTGTGGCTGCGAAGC+GGG 0.345994 8_2:-17170727 Msa1237660:CDS
TGGCGGCCGGGCTTGCGACT+GGG 0.352478 8_2:-17170821 Msa1237660:CDS
GAAACCGGGTTGGGATTATT+GGG 0.370521 8_2:-17170911 Msa1237660:CDS
GGACTTGGGGAAACCGGGTT+GGG 0.379487 8_2:-17170920 Msa1237660:CDS
CTTTGTATGGATTGTAGAAT+CGG 0.394913 8_2:+17171192 None:intergenic
CAAACGTAAACGCCGTTCTT+GGG 0.395053 8_2:-17171099 Msa1237660:CDS
ATTATTGGGTTGTTGTATGC+TGG 0.396327 8_2:-17170897 Msa1237660:CDS
CAACCGACACTGCGAAGCTT+CGG 0.409904 8_2:-17170980 Msa1237660:CDS
GCGGTTGCTGGTGCTGTTGG+TGG 0.411376 8_2:-17170762 Msa1237660:CDS
CGGTTGCTGGTGCTGTTGGT+GGG 0.413058 8_2:-17170761 Msa1237660:CDS
GGCGGTTCAATCGCCGGTGC+CGG 0.417557 8_2:-17171038 Msa1237660:CDS
CGCAGTGTCGGTTGATTCAA+AGG 0.434906 8_2:+17170989 None:intergenic
TCAATCGCCGGTGCCGGAGT+TGG 0.438544 8_2:-17171032 Msa1237660:CDS
CTGCGAAGCTTCGGGTGAAT+CGG 0.460276 8_2:-17170971 Msa1237660:CDS
TACCTCGGCGGTTCAATCGC+CGG 0.467905 8_2:-17171044 Msa1237660:CDS
AACCGCCCCAGTCGCAAGCC+CGG 0.473998 8_2:+17170815 None:intergenic
AGAGATACTCCGGTGAGGTT+GGG 0.474381 8_2:+17171135 None:intergenic
GGAAGTTCGAGGTCTTTGTA+TGG 0.477706 8_2:+17171179 None:intergenic
GCCGGAGTTGGACTTGTTGA+AGG 0.481478 8_2:-17171020 Msa1237660:CDS
CGGACTTGGGGAAACCGGGT+TGG 0.489803 8_2:-17170921 Msa1237660:CDS
AACCGACACTGCGAAGCTTC+GGG 0.494471 8_2:-17170979 Msa1237660:CDS
GGACATTCGGGTCGGACTTG+GGG 0.496747 8_2:-17170933 Msa1237660:CDS
GGATTGTAGAATCGGGTTTG+AGG 0.497254 8_2:+17171200 None:intergenic
CGGTTTATAGAGCGGCGAGA+GGG 0.499763 8_2:-17170797 Msa1237660:CDS
CTTGGAATAGTGTGGCGGCC+GGG 0.508945 8_2:-17170833 Msa1237660:CDS
TTTGTATGGATTGTAGAATC+GGG 0.513661 8_2:+17171193 None:intergenic
CACCCGAAGCTTCGCAGTGT+CGG 0.514005 8_2:+17170977 None:intergenic
TGAGGGATGTTGATGATGCT+TGG 0.516589 8_2:-17170851 Msa1237660:CDS
TGCTGTGGCTGCGAAGCGGG+TGG 0.517028 8_2:-17170724 Msa1237660:CDS
AACAAGTCCAACTCCGGCAC+CGG 0.520038 8_2:+17171025 None:intergenic
GCCGCGGTTGCTGGTGCTGT+TGG 0.522340 8_2:-17170765 Msa1237660:CDS
GGTTGTTGTTGGAGCTGCTG+TGG 0.524367 8_2:-17170739 Msa1237660:CDS
GGCCGGGCTTGCGACTGGGG+CGG 0.527216 8_2:-17170817 Msa1237660:CDS
TAAGATTCTCGCCCCAAGAA+CGG 0.528444 8_2:+17171087 None:intergenic
GCTTGGAATAGTGTGGCGGC+CGG 0.528571 8_2:-17170834 Msa1237660:CDS
GGCGGCCGGGCTTGCGACTG+GGG 0.534392 8_2:-17170820 Msa1237660:CDS
TACACCGGTTGCGGTTACCT+CGG 0.535719 8_2:-17171059 Msa1237660:CDS
GGTTGCTGGTGCTGTTGGTG+GGG 0.542315 8_2:-17170760 Msa1237660:CDS
GAGCTGCTGTGGCTGCGAAG+CGG 0.548860 8_2:-17170728 Msa1237660:CDS
AGCGGCGAGAGGGGTGAGAT+CGG 0.551230 8_2:-17170787 Msa1237660:CDS
GAGAGGGGTGAGATCGGCCG+CGG 0.562356 8_2:-17170781 Msa1237660:CDS
TTGTATGCTGGAATTGAGAG+TGG 0.564300 8_2:-17170885 Msa1237660:CDS
GTGAGGTTGGGAGTTTGTAG+AGG 0.573117 8_2:+17171147 None:intergenic
TCGGGTTTGAGGATCTTGAT+CGG 0.578030 8_2:+17171211 None:intergenic
ACCAACAGCACCAGCAACCG+CGG 0.578061 8_2:+17170764 None:intergenic
GAGTGGGATTGAGGCTGTGA+GGG 0.578683 8_2:-17170868 Msa1237660:CDS
ACCTTCAACAAGTCCAACTC+CGG 0.578709 8_2:+17171019 None:intergenic
AAACGTAAACGCCGTTCTTG+GGG 0.585932 8_2:-17171098 Msa1237660:CDS
CTACAAACTCCCAACCTCAC+CGG 0.586121 8_2:-17171144 Msa1237660:CDS
TGGAATTGAGAGTGGGATTG+AGG 0.602728 8_2:-17170877 Msa1237660:CDS
TGTATGCTGGAATTGAGAGT+GGG 0.606585 8_2:-17170884 Msa1237660:CDS
GGTTTATAGAGCGGCGAGAG+GGG 0.608946 8_2:-17170796 Msa1237660:CDS
GCGGTTTATAGAGCGGCGAG+AGG 0.611195 8_2:-17170798 Msa1237660:CDS
ACCGGTTGCGGTTACCTCGG+CGG 0.621308 8_2:-17171056 Msa1237660:CDS
GACTGGGGCGGTTTATAGAG+CGG 0.627870 8_2:-17170805 Msa1237660:CDS
TGTCGGTTGATTCAAAGGAT+CGG 0.630967 8_2:+17170994 None:intergenic
ATGCGTCTGGACATTCGGGT+CGG 0.644981 8_2:-17170941 Msa1237660:CDS
TCTTCGTCGAAGAGATACTC+CGG 0.653572 8_2:+17171125 None:intergenic
CACCGGCGATTGAACCGCCG+AGG 0.670132 8_2:+17171042 None:intergenic
AGAGTGGGATTGAGGCTGTG+AGG 0.684010 8_2:-17170869 Msa1237660:CDS
ACAACCCAATAATCCCAACC+CGG 0.687669 8_2:+17170907 None:intergenic
TGATGATGCTTGGAATAGTG+TGG 0.705715 8_2:-17170841 Msa1237660:CDS
TGATGCTTGGAATAGTGTGG+CGG 0.725712 8_2:-17170838 Msa1237660:CDS
GTCGAAGAGATACTCCGGTG+AGG 0.727648 8_2:+17171130 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTTGTATGGATTGTAGAATC+GGG + chr8_2:17170738-17170757 None:intergenic 30.0%
! CTTTGTATGGATTGTAGAAT+CGG + chr8_2:17170739-17170758 None:intergenic 30.0%
!!! GAGAATCTTACTTTTTACAC+CGG - chr8_2:17170854-17170873 Msa1237660:CDS 30.0%
!!! AGTTTGTAGAGGTTTTGGAT+TGG + chr8_2:17170773-17170792 None:intergenic 35.0%
! ATTATTGGGTTGTTGTATGC+TGG - chr8_2:17171031-17171050 Msa1237660:CDS 35.0%
! TTGGGAGTTTGTAGAGGTTT+TGG + chr8_2:17170778-17170797 None:intergenic 40.0%
!!! CTTACTTTTTACACCGGTTG+CGG - chr8_2:17170860-17170879 Msa1237660:CDS 40.0%
! TGTCGGTTGATTCAAAGGAT+CGG + chr8_2:17170937-17170956 None:intergenic 40.0%
! AATCGGATTTTGAATGCGTC+TGG - chr8_2:17170974-17170993 Msa1237660:CDS 40.0%
TTTGAATGCGTCTGGACATT+CGG - chr8_2:17170982-17171001 Msa1237660:CDS 40.0%
TTGTATGCTGGAATTGAGAG+TGG - chr8_2:17171043-17171062 Msa1237660:CDS 40.0%
TGTATGCTGGAATTGAGAGT+GGG - chr8_2:17171044-17171063 Msa1237660:CDS 40.0%
! TGATGATGCTTGGAATAGTG+TGG - chr8_2:17171087-17171106 Msa1237660:CDS 40.0%
TCGGGTTTGAGGATCTTGAT+CGG + chr8_2:17170720-17170739 None:intergenic 45.0%
GGATTGTAGAATCGGGTTTG+AGG + chr8_2:17170731-17170750 None:intergenic 45.0%
GGAAGTTCGAGGTCTTTGTA+TGG + chr8_2:17170752-17170771 None:intergenic 45.0%
!!! GGTTTTGGATTGGAAGTTCG+AGG + chr8_2:17170763-17170782 None:intergenic 45.0%
TCTTCGTCGAAGAGATACTC+CGG + chr8_2:17170806-17170825 None:intergenic 45.0%
CAAACGTAAACGCCGTTCTT+GGG - chr8_2:17170829-17170848 Msa1237660:CDS 45.0%
AAACGTAAACGCCGTTCTTG+GGG - chr8_2:17170830-17170849 Msa1237660:CDS 45.0%
TAAGATTCTCGCCCCAAGAA+CGG + chr8_2:17170844-17170863 None:intergenic 45.0%
ACCTTCAACAAGTCCAACTC+CGG + chr8_2:17170912-17170931 None:intergenic 45.0%
TTGAATGCGTCTGGACATTC+GGG - chr8_2:17170983-17171002 Msa1237660:CDS 45.0%
! GAAACCGGGTTGGGATTATT+GGG - chr8_2:17171017-17171036 Msa1237660:CDS 45.0%
ACAACCCAATAATCCCAACC+CGG + chr8_2:17171024-17171043 None:intergenic 45.0%
TGGAATTGAGAGTGGGATTG+AGG - chr8_2:17171051-17171070 Msa1237660:CDS 45.0%
!! TGAGGGATGTTGATGATGCT+TGG - chr8_2:17171077-17171096 Msa1237660:CDS 45.0%
TGATGCTTGGAATAGTGTGG+CGG - chr8_2:17171090-17171109 Msa1237660:CDS 45.0%
GTGAGGTTGGGAGTTTGTAG+AGG + chr8_2:17170784-17170803 None:intergenic 50.0%
CTACAAACTCCCAACCTCAC+CGG - chr8_2:17170784-17170803 Msa1237660:CDS 50.0%
AGAGATACTCCGGTGAGGTT+GGG + chr8_2:17170796-17170815 None:intergenic 50.0%
AAGAGATACTCCGGTGAGGT+TGG + chr8_2:17170797-17170816 None:intergenic 50.0%
CCAAGAACGGCGTTTACGTT+TGG + chr8_2:17170831-17170850 None:intergenic 50.0%
CCAAACGTAAACGCCGTTCT+TGG - chr8_2:17170828-17170847 Msa1237660:CDS 50.0%
!! CGCAGTGTCGGTTGATTCAA+AGG + chr8_2:17170942-17170961 None:intergenic 50.0%
! GGAAACCGGGTTGGGATTAT+TGG - chr8_2:17171016-17171035 Msa1237660:CDS 50.0%
GTCGAAGAGATACTCCGGTG+AGG + chr8_2:17170801-17170820 None:intergenic 55.0%
! TACACCGGTTGCGGTTACCT+CGG - chr8_2:17170869-17170888 Msa1237660:CDS 55.0%
AACAAGTCCAACTCCGGCAC+CGG + chr8_2:17170906-17170925 None:intergenic 55.0%
!! GCCGGAGTTGGACTTGTTGA+AGG - chr8_2:17170908-17170927 Msa1237660:CDS 55.0%
CAACCGACACTGCGAAGCTT+CGG - chr8_2:17170948-17170967 Msa1237660:CDS 55.0%
AACCGACACTGCGAAGCTTC+GGG - chr8_2:17170949-17170968 Msa1237660:CDS 55.0%
CTGCGAAGCTTCGGGTGAAT+CGG - chr8_2:17170957-17170976 Msa1237660:CDS 55.0%
ATGCGTCTGGACATTCGGGT+CGG - chr8_2:17170987-17171006 Msa1237660:CDS 55.0%
TGGACATTCGGGTCGGACTT+GGG - chr8_2:17170994-17171013 Msa1237660:CDS 55.0%
AGAGTGGGATTGAGGCTGTG+AGG - chr8_2:17171059-17171078 Msa1237660:CDS 55.0%
GAGTGGGATTGAGGCTGTGA+GGG - chr8_2:17171060-17171079 Msa1237660:CDS 55.0%
GACTGGGGCGGTTTATAGAG+CGG - chr8_2:17171123-17171142 Msa1237660:CDS 55.0%
CGGTTTATAGAGCGGCGAGA+GGG - chr8_2:17171131-17171150 Msa1237660:CDS 55.0%
GGTTTATAGAGCGGCGAGAG+GGG - chr8_2:17171132-17171151 Msa1237660:CDS 55.0%
! GCTGTTGGTGGGGTTGTTGT+TGG - chr8_2:17171178-17171197 Msa1237660:CDS 55.0%
! GGTTGTTGTTGGAGCTGCTG+TGG - chr8_2:17171189-17171208 Msa1237660:CDS 55.0%
TACCTCGGCGGTTCAATCGC+CGG - chr8_2:17170884-17170903 Msa1237660:CDS 60.0%
CACCCGAAGCTTCGCAGTGT+CGG + chr8_2:17170954-17170973 None:intergenic 60.0%
CTGGACATTCGGGTCGGACT+TGG - chr8_2:17170993-17171012 Msa1237660:CDS 60.0%
GGACATTCGGGTCGGACTTG+GGG - chr8_2:17170995-17171014 Msa1237660:CDS 60.0%
GGACTTGGGGAAACCGGGTT+GGG - chr8_2:17171008-17171027 Msa1237660:CDS 60.0%
GCTTGGAATAGTGTGGCGGC+CGG - chr8_2:17171094-17171113 Msa1237660:CDS 60.0%
CTTGGAATAGTGTGGCGGCC+GGG - chr8_2:17171095-17171114 Msa1237660:CDS 60.0%
GCGGTTTATAGAGCGGCGAG+AGG - chr8_2:17171130-17171149 Msa1237660:CDS 60.0%
ACCAACAGCACCAGCAACCG+CGG + chr8_2:17171167-17171186 None:intergenic 60.0%
!! CGGTTGCTGGTGCTGTTGGT+GGG - chr8_2:17171167-17171186 Msa1237660:CDS 60.0%
!! GGTTGCTGGTGCTGTTGGTG+GGG - chr8_2:17171168-17171187 Msa1237660:CDS 60.0%
ACCGGTTGCGGTTACCTCGG+CGG - chr8_2:17170872-17170891 Msa1237660:CDS 65.0%
ACCGCCGAGGTAACCGCAAC+CGG + chr8_2:17170876-17170895 None:intergenic 65.0%
! TCAATCGCCGGTGCCGGAGT+TGG - chr8_2:17170896-17170915 Msa1237660:CDS 65.0%
CGGGTCGGACTTGGGGAAAC+CGG - chr8_2:17171002-17171021 Msa1237660:CDS 65.0%
GGGTCGGACTTGGGGAAACC+GGG - chr8_2:17171003-17171022 Msa1237660:CDS 65.0%
CGGACTTGGGGAAACCGGGT+TGG - chr8_2:17171007-17171026 Msa1237660:CDS 65.0%
AGCGGCGAGAGGGGTGAGAT+CGG - chr8_2:17171141-17171160 Msa1237660:CDS 65.0%
!! GCGGTTGCTGGTGCTGTTGG+TGG - chr8_2:17171166-17171185 Msa1237660:CDS 65.0%
GAGCTGCTGTGGCTGCGAAG+CGG - chr8_2:17171200-17171219 Msa1237660:CDS 65.0%
AGCTGCTGTGGCTGCGAAGC+GGG - chr8_2:17171201-17171220 Msa1237660:CDS 65.0%
CACCGGCGATTGAACCGCCG+AGG + chr8_2:17170889-17170908 None:intergenic 70.0%
GGCGGTTCAATCGCCGGTGC+CGG - chr8_2:17170890-17170909 Msa1237660:CDS 70.0%
AACCGCCCCAGTCGCAAGCC+CGG + chr8_2:17171116-17171135 None:intergenic 70.0%
GAGAGGGGTGAGATCGGCCG+CGG - chr8_2:17171147-17171166 Msa1237660:CDS 70.0%
GTGAGATCGGCCGCGGTTGC+TGG - chr8_2:17171154-17171173 Msa1237660:CDS 70.0%
!! GCCGCGGTTGCTGGTGCTGT+TGG - chr8_2:17171163-17171182 Msa1237660:CDS 70.0%
TGCTGTGGCTGCGAAGCGGG+TGG - chr8_2:17171204-17171223 Msa1237660:CDS 70.0%
TGGCGGCCGGGCTTGCGACT+GGG - chr8_2:17171107-17171126 Msa1237660:CDS 75.0%
! GTGGCGGCCGGGCTTGCGAC+TGG - chr8_2:17171106-17171125 Msa1237660:CDS 80.0%
! GGCGGCCGGGCTTGCGACTG+GGG - chr8_2:17171108-17171127 Msa1237660:CDS 80.0%
! GGCCGGGCTTGCGACTGGGG+CGG - chr8_2:17171111-17171130 Msa1237660:CDS 80.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 17170701 17171249 17170701 ID=Msa1237660;Name=Msa1237660
chr8_2 mRNA 17170701 17171249 17170701 ID=Msa1237660-mRNA-1;Parent=Msa1237660;Name=Msa1237660-mRNA-1;_AED=0.25;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|182
chr8_2 exon 17170701 17171249 17170701 ID=Msa1237660-mRNA-1:exon:6477;Parent=Msa1237660-mRNA-1
chr8_2 CDS 17170701 17171249 17170701 ID=Msa1237660-mRNA-1:cds;Parent=Msa1237660-mRNA-1
Gene Sequence

>Msa1237660

ATGGCGAACAACGAATCCGATCAAGATCCTCAAACCCGATTCTACAATCCATACAAAGACCTCGAACTTCCAATCCAAAACCTCTACAAACTCCCAACCTCACCGGAGTATCTCTTCGACGAAGAAGCCAAACGTAAACGCCGTTCTTGGGGCGAGAATCTTACTTTTTACACCGGTTGCGGTTACCTCGGCGGTTCAATCGCCGGTGCCGGAGTTGGACTTGTTGAAGGTATCCGATCCTTTGAATCAACCGACACTGCGAAGCTTCGGGTGAATCGGATTTTGAATGCGTCTGGACATTCGGGTCGGACTTGGGGAAACCGGGTTGGGATTATTGGGTTGTTGTATGCTGGAATTGAGAGTGGGATTGAGGCTGTGAGGGATGTTGATGATGCTTGGAATAGTGTGGCGGCCGGGCTTGCGACTGGGGCGGTTTATAGAGCGGCGAGAGGGGTGAGATCGGCCGCGGTTGCTGGTGCTGTTGGTGGGGTTGTTGTTGGAGCTGCTGTGGCTGCGAAGCGGGTGGCGAAACGATATGTGCCTATTTGA
Protein sequence

>Msa1237660

MANNESDQDPQTRFYNPYKDLELPIQNLYKLPTSPEYLFDEEAKRKRRSWGENLTFYTGCGYLGGSIAGAGVGLVEGIRSFESTDTAKLRVNRILNASGHSGRTWGNRVGIIGLLYAGIESGIEAVRDVDDAWNSVAAGLATGAVYRAARGVRSAAVAGAVGGVVVGAAVAAKRVAKRYVPI*