AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0509970


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0509970 MtrunA17_Chr3g0115121 98.795 166 2 0 1 166 1 166 1.36e-119 334
Msa0509970 MtrunA17_Chr4g0041831 47.727 132 69 0 21 152 6 137 2.83e-35 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0509970 AT5G14320.1 70.513 156 41 2 1 153 1 154 1.48e-76 226
Msa0509970 AT5G14320.2 62.069 116 39 2 1 113 1 114 3.02e-44 142
Msa0509970 AT1G77750.1 48.387 124 64 0 42 165 27 150 1.72e-37 126

Find 47 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGTCCTGCAGTTATTCT+TGG 0.227656 3_4:+58647655 None:intergenic
AATTCAATTCTCTTGTTGTT+TGG 0.264258 3_4:+58648025 None:intergenic
CAGAGGAATAAGGCATATTC+AGG 0.285946 3_4:-58647702 Msa0509970:CDS
AATTGTGTTACCTTTGACTT+TGG 0.293488 3_4:+58648154 None:intergenic
ATCAAGTAACTAAATTAAAA+AGG 0.325206 3_4:+58647580 None:intergenic
GGTAAGAAGGTTACTGTTGC+TGG 0.360552 3_4:-58647629 Msa0509970:CDS
GACTTTGGAGTGTTGAGAAC+TGG 0.363379 3_4:+58648169 None:intergenic
TTCAGTGTTACAGAGGAATA+AGG 0.379843 3_4:-58647712 Msa0509970:CDS
AAGAAGAGCTTATTAGTCTC+AGG 0.387619 3_4:-58647907 Msa0509970:CDS
ATACATGACTGAAGGAGATT+TGG 0.390225 3_4:-58647870 Msa0509970:intron
GGAGAAGTGACCATGGCCTT+TGG 0.397280 3_4:+58648207 None:intergenic
GGGAGATAATGATAAGGATA+TGG 0.401243 3_4:-58648317 Msa0509970:five_prime_UTR
GATTCTAACTGATATCAGTA+TGG 0.462554 3_4:-58647957 Msa0509970:CDS
TTGCAGTACATTCATGGAGT+TGG 0.465952 3_4:-58647998 Msa0509970:CDS
TTGAGCTGACAAATGCTAAG+AGG 0.469959 3_4:+58647399 None:intergenic
TTAATGCACTTAATATAAAG+AGG 0.487114 3_4:-58647745 Msa0509970:CDS
AACTGGGAAAGAAACTCGAT+TGG 0.508056 3_4:+58648186 None:intergenic
GAATAACTGCAGGACATTGA+AGG 0.525777 3_4:-58647651 Msa0509970:CDS
CAGGACATTGAAGGGTAAGA+AGG 0.533951 3_4:-58647642 Msa0509970:CDS
ATTGTGTGCGTTCGTGTTGG+TGG 0.534997 3_4:-58648058 Msa0509970:CDS
AAGGAGAAAACACCAACTCT+CGG 0.539577 3_4:-58648338 None:intergenic
AGGAGAAAACACCAACTCTC+GGG 0.541747 3_4:-58648337 None:intergenic
ATATTATGTGAACTACTGCT+TGG 0.543434 3_4:-58647454 Msa0509970:three_prime_UTR
AATAACTGCAGGACATTGAA+GGG 0.550619 3_4:-58647650 Msa0509970:CDS
ATTGAGAGTGAAGGTGCCAC+AGG 0.552065 3_4:+58648235 None:intergenic
ACTTTGGAGTGTTGAGAACT+GGG 0.555353 3_4:+58648170 None:intergenic
TATCATTATCTCCCGAGAGT+TGG 0.556639 3_4:+58648326 None:intergenic
TAATGATAAGGATATGGCTA+TGG 0.563231 3_4:-58648311 Msa0509970:five_prime_UTR
AACATTGTGTGCGTTCGTGT+TGG 0.564683 3_4:-58648061 Msa0509970:CDS
TGATTGAATTGTAGGTTCAG+AGG 0.566135 3_4:-58648087 Msa0509970:intron
TCAATCATCTCCAAAGGCCA+TGG 0.572793 3_4:-58648217 Msa0509970:CDS
GTGCGTTCGTGTTGGTGGTG+TGG 0.576835 3_4:-58648053 Msa0509970:CDS
TTGGTACGCTGTCCTCTACA+AGG 0.578588 3_4:+58647674 None:intergenic
ACTCTCGGGAGATAATGATA+AGG 0.580530 3_4:-58648323 Msa0509970:five_prime_UTR
AGAGGAATAAGGCATATTCA+GGG 0.580912 3_4:-58647701 Msa0509970:CDS
TCTCAACACTCCAAAGTCAA+AGG 0.589008 3_4:-58648164 Msa0509970:intron
GTTAACAAATACATGACTGA+AGG 0.596392 3_4:-58647878 Msa0509970:CDS
TATGGAGAATAAAGTTACAA+AGG 0.597785 3_4:-58647939 Msa0509970:CDS
AAAGAAATTCAGTGTTACAG+AGG 0.605461 3_4:-58647719 Msa0509970:CDS
TCACTCTCAATCATCTCCAA+AGG 0.619107 3_4:-58648223 Msa0509970:CDS
ATTCAGGGACTTCCTTGTAG+AGG 0.621863 3_4:-58647686 Msa0509970:CDS
AGTACATTCATGGAGTTGGA+AGG 0.622828 3_4:-58647994 Msa0509970:CDS
AGCGTACCAAGAATAACTGC+AGG 0.623820 3_4:-58647661 Msa0509970:CDS
AGAAGAGCTTATTAGTCTCA+GGG 0.625713 3_4:-58647906 Msa0509970:CDS
CTCGATTGGAGAAGTGACCA+TGG 0.660409 3_4:+58648200 None:intergenic
TTGGAGATGATTGAGAGTGA+AGG 0.661623 3_4:+58648226 None:intergenic
ACAAACACTCTCAATGCCTG+TGG 0.676701 3_4:-58648251 Msa0509970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_4:58647933-58647952 Msa0509970:CDS 15.0%
!! ATCAAGTAACTAAATTAAAA+AGG + chr3_4:58648154-58648173 None:intergenic 15.0%
!!! ATTGAGAAAAAAAAATGTTT+TGG - chr3_4:58648181-58648200 Msa0509970:CDS 15.0%
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_4:58647933-58647952 Msa0509970:CDS 15.0%
!! ATCAAGTAACTAAATTAAAA+AGG + chr3_4:58648154-58648173 None:intergenic 15.0%
!!! ATTGAGAAAAAAAAATGTTT+TGG - chr3_4:58648181-58648200 Msa0509970:CDS 15.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_4:58647986-58648005 Msa0509970:CDS 20.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_4:58647986-58648005 Msa0509970:CDS 20.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_4:58647709-58647728 None:intergenic 25.0%
! TATGGAGAATAAAGTTACAA+AGG - chr3_4:58647792-58647811 Msa0509970:intron 25.0%
!!! TGCGATTGTTTTTGTTAAAT+TGG - chr3_4:58648208-58648227 Msa0509970:CDS 25.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_4:58647709-58647728 None:intergenic 25.0%
! TATGGAGAATAAAGTTACAA+AGG - chr3_4:58647792-58647811 Msa0509970:intron 25.0%
!!! TGCGATTGTTTTTGTTAAAT+TGG - chr3_4:58648208-58648227 Msa0509970:CDS 25.0%
TAATGATAAGGATATGGCTA+TGG - chr3_4:58647420-58647439 Msa0509970:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_4:58647580-58647599 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_4:58647580-58647599 Msa0509970:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_4:58647581-58647600 Msa0509970:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_4:58647628-58647647 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_4:58647635-58647654 None:intergenic 30.0%
TCTGATTCTGATTGAATTGT+AGG - chr3_4:58647636-58647655 Msa0509970:CDS 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_4:58647774-58647793 Msa0509970:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_4:58647853-58647872 Msa0509970:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_4:58647962-58647981 Msa0509970:CDS 30.0%
AAAGAAATTCAGTGTTACAG+AGG - chr3_4:58648012-58648031 Msa0509970:CDS 30.0%
ATATTATGTGAACTACTGCT+TGG - chr3_4:58648277-58648296 Msa0509970:exon 30.0%
TAATGATAAGGATATGGCTA+TGG - chr3_4:58647420-58647439 Msa0509970:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_4:58647580-58647599 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_4:58647580-58647599 Msa0509970:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_4:58647581-58647600 Msa0509970:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_4:58647628-58647647 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_4:58647635-58647654 None:intergenic 30.0%
TCTGATTCTGATTGAATTGT+AGG - chr3_4:58647636-58647655 Msa0509970:CDS 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_4:58647774-58647793 Msa0509970:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_4:58647853-58647872 Msa0509970:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_4:58647962-58647981 Msa0509970:CDS 30.0%
AAAGAAATTCAGTGTTACAG+AGG - chr3_4:58648012-58648031 Msa0509970:CDS 30.0%
ATATTATGTGAACTACTGCT+TGG - chr3_4:58648277-58648296 Msa0509970:exon 30.0%
GGGAGATAATGATAAGGATA+TGG - chr3_4:58647414-58647433 Msa0509970:three_prime_UTR 35.0%
TCGCTGTTGAACAGAAAAAA+TGG - chr3_4:58647456-58647475 Msa0509970:three_prime_UTR 35.0%
TGATTGAATTGTAGGTTCAG+AGG - chr3_4:58647644-58647663 Msa0509970:CDS 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_4:58647727-58647746 Msa0509970:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_4:58647824-58647843 Msa0509970:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_4:58647825-58647844 Msa0509970:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_4:58647861-58647880 Msa0509970:intron 35.0%
TTCAGTGTTACAGAGGAATA+AGG - chr3_4:58648019-58648038 Msa0509970:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_4:58648030-58648049 Msa0509970:CDS 35.0%
AATAACTGCAGGACATTGAA+GGG - chr3_4:58648081-58648100 Msa0509970:intron 35.0%
GGGAGATAATGATAAGGATA+TGG - chr3_4:58647414-58647433 Msa0509970:three_prime_UTR 35.0%
TCGCTGTTGAACAGAAAAAA+TGG - chr3_4:58647456-58647475 Msa0509970:three_prime_UTR 35.0%
TGATTGAATTGTAGGTTCAG+AGG - chr3_4:58647644-58647663 Msa0509970:CDS 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_4:58647727-58647746 Msa0509970:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_4:58647824-58647843 Msa0509970:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_4:58647825-58647844 Msa0509970:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_4:58647861-58647880 Msa0509970:intron 35.0%
TTCAGTGTTACAGAGGAATA+AGG - chr3_4:58648019-58648038 Msa0509970:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_4:58648030-58648049 Msa0509970:CDS 35.0%
AATAACTGCAGGACATTGAA+GGG - chr3_4:58648081-58648100 Msa0509970:intron 35.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_4:58647408-58647427 Msa0509970:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_4:58647508-58647527 None:intergenic 40.0%
TCACTCTCAATCATCTCCAA+AGG - chr3_4:58647508-58647527 Msa0509970:three_prime_UTR 40.0%
AACTGGGAAAGAAACTCGAT+TGG + chr3_4:58647548-58647567 None:intergenic 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_4:58647564-58647583 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_4:58647567-58647586 Msa0509970:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_4:58647733-58647752 Msa0509970:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_4:58647737-58647756 Msa0509970:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_4:58648029-58648048 Msa0509970:CDS 40.0%
CAATGTCCTGCAGTTATTCT+TGG + chr3_4:58648079-58648098 None:intergenic 40.0%
GAATAACTGCAGGACATTGA+AGG - chr3_4:58648080-58648099 Msa0509970:intron 40.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_4:58647408-58647427 Msa0509970:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_4:58647508-58647527 None:intergenic 40.0%
TCACTCTCAATCATCTCCAA+AGG - chr3_4:58647508-58647527 Msa0509970:three_prime_UTR 40.0%
AACTGGGAAAGAAACTCGAT+TGG + chr3_4:58647548-58647567 None:intergenic 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_4:58647564-58647583 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_4:58647567-58647586 Msa0509970:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_4:58647733-58647752 Msa0509970:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_4:58647737-58647756 Msa0509970:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_4:58648029-58648048 Msa0509970:CDS 40.0%
CAATGTCCTGCAGTTATTCT+TGG + chr3_4:58648079-58648098 None:intergenic 40.0%
GAATAACTGCAGGACATTGA+AGG - chr3_4:58648080-58648099 Msa0509970:intron 40.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_4:58647480-58647499 Msa0509970:three_prime_UTR 45.0%
TCAATCATCTCCAAAGGCCA+TGG - chr3_4:58647514-58647533 Msa0509970:three_prime_UTR 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_4:58647565-58647584 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_4:58647670-58647689 Msa0509970:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_4:58648045-58648064 Msa0509970:CDS 45.0%
AGCGTACCAAGAATAACTGC+AGG - chr3_4:58648070-58648089 Msa0509970:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_4:58648089-58648108 Msa0509970:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_4:58648102-58648121 Msa0509970:intron 45.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_4:58647480-58647499 Msa0509970:three_prime_UTR 45.0%
TCAATCATCTCCAAAGGCCA+TGG - chr3_4:58647514-58647533 Msa0509970:three_prime_UTR 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_4:58647565-58647584 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_4:58647670-58647689 Msa0509970:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_4:58648045-58648064 Msa0509970:CDS 45.0%
AGCGTACCAAGAATAACTGC+AGG - chr3_4:58648070-58648089 Msa0509970:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_4:58648089-58648108 Msa0509970:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_4:58648102-58648121 Msa0509970:intron 45.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_4:58647499-58647518 None:intergenic 50.0%
CTCGATTGGAGAAGTGACCA+TGG + chr3_4:58647534-58647553 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_4:58647673-58647692 Msa0509970:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_4:58648060-58648079 None:intergenic 50.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_4:58647499-58647518 None:intergenic 50.0%
CTCGATTGGAGAAGTGACCA+TGG + chr3_4:58647534-58647553 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_4:58647673-58647692 Msa0509970:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_4:58648060-58648079 None:intergenic 50.0%
GGAGAAGTGACCATGGCCTT+TGG + chr3_4:58647527-58647546 None:intergenic 55.0%
GGAGAAGTGACCATGGCCTT+TGG + chr3_4:58647527-58647546 None:intergenic 55.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_4:58647678-58647697 Msa0509970:CDS 60.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_4:58647678-58647697 Msa0509970:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 58647407 58648346 58647407 ID=Msa0509970;Name=Msa0509970
chr3_4 mRNA 58647407 58648346 58647407 ID=Msa0509970-mRNA-1;Parent=Msa0509970;Name=Msa0509970-mRNA-1;_AED=0.09;_eAED=0.09;_QI=68|1|1|1|1|1|3|206|166
chr3_4 exon 58647407 58647774 58647407 ID=Msa0509970-mRNA-1:exon:13655;Parent=Msa0509970-mRNA-1
chr3_4 exon 58647871 58648095 58647871 ID=Msa0509970-mRNA-1:exon:13654;Parent=Msa0509970-mRNA-1
chr3_4 exon 58648165 58648346 58648165 ID=Msa0509970-mRNA-1:exon:13653;Parent=Msa0509970-mRNA-1
chr3_4 five_prime_UTR 58648279 58648346 58648279 ID=Msa0509970-mRNA-1:five_prime_utr;Parent=Msa0509970-mRNA-1
chr3_4 CDS 58648165 58648278 58648165 ID=Msa0509970-mRNA-1:cds;Parent=Msa0509970-mRNA-1
chr3_4 CDS 58647871 58648095 58647871 ID=Msa0509970-mRNA-1:cds;Parent=Msa0509970-mRNA-1
chr3_4 CDS 58647613 58647774 58647613 ID=Msa0509970-mRNA-1:cds;Parent=Msa0509970-mRNA-1
chr3_4 three_prime_UTR 58647407 58647612 58647407 ID=Msa0509970-mRNA-1:three_prime_utr;Parent=Msa0509970-mRNA-1
Gene Sequence

>Msa0509970

ATGGTACAAACACTCTCAATGCCTGTGGCACCTTCACTCTCAATCATCTCCAAAGGCCATGGTCACTTCTCCAATCGAGTTTCTTTCCCAGTTCTCAACACTCCAAAGTCAAAGGTTCAGAGGCTAAACATTGTGTGCGTTCGTGTTGGTGGTGTGGAAATTCCAAACAACAAGAGAATTGAATTTTCGTTGCAGTACATTCATGGAGTTGGAAGGAACAGAGCTAGACAGATTCTAACTGATATCAGTATGGAGAATAAAGTTACAAAGGAATTGAGTGAAGAAGAGCTTATTAGTCTCAGGGATGAAGTTAACAAATACATGACTGAAGGAGATTTGAGAAGGTTTAATGCACTTAATATAAAGAGGTTGAAAGAAATTCAGTGTTACAGAGGAATAAGGCATATTCAGGGACTTCCTTGTAGAGGACAGCGTACCAAGAATAACTGCAGGACATTGAAGGGTAAGAAGGTTACTGTTGCTGGAAAGAAGAAAAAGTAA

Protein sequence

>Msa0509970

MVQTLSMPVAPSLSIISKGHGHFSNRVSFPVLNTPKSKVQRLNIVCVRVGGVEIPNNKRIEFSLQYIHGVGRNRARQILTDISMENKVTKELSEEELISLRDEVNKYMTEGDLRRFNALNIKRLKEIQCYRGIRHIQGLPCRGQRTKNNCRTLKGKKVTVAGKKKK*