AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0907890

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0907890 MtrunA17_Chr2g0279561 89.000 100 5 1 1 100 1 94 6.17e-39 125
Msa0907890 MtrunA17_Chr3g0087151 38.393 112 55 5 1 100 1 110 4.68e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGGCTTCAATCAATTTC+TGG 0.164366 6_2:-8752113 Msa0907890:CDS
TGAGGCAAAGTTGGTACATT+AGG 0.250872 6_2:+8751928 None:intergenic
GGCAATTGTGGCTGTGTTAA+TGG 0.262929 6_2:+8751982 None:intergenic
GTTGGTACATTAGGGATTAC+TGG 0.335295 6_2:+8751937 None:intergenic
CCTCAGATTCCTACTGTTCC+TGG 0.365627 6_2:-8751883 Msa0907890:CDS
GAGGCAAAGTTGGTACATTA+GGG 0.367979 6_2:+8751929 None:intergenic
ATTACTGGAACACCTAAGTT+TGG 0.371975 6_2:+8751952 None:intergenic
ACTTTAGGTACTTATGGTTT+AGG 0.379485 6_2:+8751820 None:intergenic
ACACCTAAGTTTGGAATTGT+TGG 0.404545 6_2:+8751961 None:intergenic
GGCAATGGCACTGGCAGATT+AGG 0.425870 6_2:+8752003 None:intergenic
TGAGGCACAGTTGGTATTTG+AGG 0.431733 6_2:+8751910 None:intergenic
TCATCAATGACAAGTATTGA+AGG 0.467180 6_2:-8752057 Msa0907890:CDS
TTGCCAACAATTCCAAACTT+AGG 0.468746 6_2:-8751964 Msa0907890:CDS
TTTGGAATTGTTGGCAATTG+TGG 0.474516 6_2:+8751970 None:intergenic
GCAGGAATCTGAGGAATTTG+TGG 0.499516 6_2:+8751856 None:intergenic
GTTGGTATTTGAGGCAAAGT+TGG 0.507961 6_2:+8751919 None:intergenic
GTAGGAATCTGAGGTATTTG+AGG 0.535890 6_2:+8751892 None:intergenic
TGTGTTAATGGCAATGGCAC+TGG 0.535953 6_2:+8751994 None:intergenic
TTAGGCACACTAGGCACAGC+AGG 0.538529 6_2:+8751838 None:intergenic
TGAGGAATTTGTGGCACACC+AGG 0.542628 6_2:+8751865 None:intergenic
TGAGGTATTTGAGGCACAGT+TGG 0.543443 6_2:+8751901 None:intergenic
GAAAATGTTATGAGTAGAAG+TGG 0.572387 6_2:+8752078 None:intergenic
ACTTATGGTTTAGGCACACT+AGG 0.582264 6_2:+8751829 None:intergenic
CTAGGCACAGCAGGAATCTG+AGG 0.592705 6_2:+8751847 None:intergenic
GGCACTGGCAGATTAGGTAG+TGG 0.603557 6_2:+8752009 None:intergenic
TGTGGCACACCAGGAACAGT+AGG 0.606684 6_2:+8751874 None:intergenic
CCAGGAACAGTAGGAATCTG+AGG 0.616707 6_2:+8751883 None:intergenic
TGTGGCTGTGTTAATGGCAA+TGG 0.622083 6_2:+8751988 None:intergenic
ACTGGCAGATTAGGTAGTGG+TGG 0.639353 6_2:+8752012 None:intergenic
GTAGTGGTGGCAACTCAACA+AGG 0.734703 6_2:+8752025 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GAAAATGTTATGAGTAGAAG+TGG + chr6_2:8751867-8751886 None:intergenic 30.0%
!! TCATCAATGACAAGTATTGA+AGG - chr6_2:8751885-8751904 Msa0907890:CDS 30.0%
! TTTGGAATTGTTGGCAATTG+TGG + chr6_2:8751975-8751994 None:intergenic 35.0%
TTGCCAACAATTCCAAACTT+AGG - chr6_2:8751978-8751997 Msa0907890:CDS 35.0%
! ACACCTAAGTTTGGAATTGT+TGG + chr6_2:8751984-8752003 None:intergenic 35.0%
ATTACTGGAACACCTAAGTT+TGG + chr6_2:8751993-8752012 None:intergenic 35.0%
GTTGGTACATTAGGGATTAC+TGG + chr6_2:8752008-8752027 None:intergenic 40.0%
!! GAGGCAAAGTTGGTACATTA+GGG + chr6_2:8752016-8752035 None:intergenic 40.0%
!! TGAGGCAAAGTTGGTACATT+AGG + chr6_2:8752017-8752036 None:intergenic 40.0%
! GTTGGTATTTGAGGCAAAGT+TGG + chr6_2:8752026-8752045 None:intergenic 40.0%
! GTAGGAATCTGAGGTATTTG+AGG + chr6_2:8752053-8752072 None:intergenic 40.0%
TGTGTTAATGGCAATGGCAC+TGG + chr6_2:8751951-8751970 None:intergenic 45.0%
TGTGGCTGTGTTAATGGCAA+TGG + chr6_2:8751957-8751976 None:intergenic 45.0%
GGCAATTGTGGCTGTGTTAA+TGG + chr6_2:8751963-8751982 None:intergenic 45.0%
! TGAGGCACAGTTGGTATTTG+AGG + chr6_2:8752035-8752054 None:intergenic 45.0%
! TGAGGTATTTGAGGCACAGT+TGG + chr6_2:8752044-8752063 None:intergenic 45.0%
GCAGGAATCTGAGGAATTTG+TGG + chr6_2:8752089-8752108 None:intergenic 45.0%
GTAGTGGTGGCAACTCAACA+AGG + chr6_2:8751920-8751939 None:intergenic 50.0%
! ACTGGCAGATTAGGTAGTGG+TGG + chr6_2:8751933-8751952 None:intergenic 50.0%
CCAGGAACAGTAGGAATCTG+AGG + chr6_2:8752062-8752081 None:intergenic 50.0%
CCTCAGATTCCTACTGTTCC+TGG - chr6_2:8752059-8752078 Msa0907890:CDS 50.0%
TGAGGAATTTGTGGCACACC+AGG + chr6_2:8752080-8752099 None:intergenic 50.0%
!! GGCACTGGCAGATTAGGTAG+TGG + chr6_2:8751936-8751955 None:intergenic 55.0%
!! GGCAATGGCACTGGCAGATT+AGG + chr6_2:8751942-8751961 None:intergenic 55.0%
TGTGGCACACCAGGAACAGT+AGG + chr6_2:8752071-8752090 None:intergenic 55.0%
CTAGGCACAGCAGGAATCTG+AGG + chr6_2:8752098-8752117 None:intergenic 55.0%
TTAGGCACACTAGGCACAGC+AGG + chr6_2:8752107-8752126 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 8751831 8752133 8751831 ID=Msa0907890;Name=Msa0907890
chr6_2 mRNA 8751831 8752133 8751831 ID=Msa0907890-mRNA-1;Parent=Msa0907890;Name=Msa0907890-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|100
chr6_2 exon 8751831 8752133 8751831 ID=Msa0907890-mRNA-1:exon:2106;Parent=Msa0907890-mRNA-1
chr6_2 CDS 8751831 8752133 8751831 ID=Msa0907890-mRNA-1:cds;Parent=Msa0907890-mRNA-1
Gene Sequence

>Msa0907890

ATGGCTTCAATCAATTTCTGGTCATTCATTTTACCACTTCTACTCATAACATTTTCATCAATGACAAGTATTGAAGGAGCACGTAACCTTGTTGAGTTGCCACCACTACCTAATCTGCCAGTGCCATTGCCATTAACACAGCCACAATTGCCAACAATTCCAAACTTAGGTGTTCCAGTAATCCCTAATGTACCAACTTTGCCTCAAATACCAACTGTGCCTCAAATACCTCAGATTCCTACTGTTCCTGGTGTGCCACAAATTCCTCAGATTCCTGCTGTGCCTAGTGTGCCTAAACCATAA
Protein sequence

>Msa0907890

MASINFWSFILPLLLITFSSMTSIEGARNLVELPPLPNLPVPLPLTQPQLPTIPNLGVPVIPNVPTLPQIPTVPQIPQIPTVPGVPQIPQIPAVPSVPKP*