AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0584820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584820 MtrunA17_Chr4g0019481 80.800 125 16 2 1 125 1 117 1.07e-59 179
Msa0584820 MtrunA17_Chr4g0019471 79.545 132 19 2 1 125 1 131 2.41e-59 179
Msa0584820 MtrunA17_Chr4g0019551 69.697 132 18 3 1 125 1 117 1.78e-45 143
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCACTCATCTGGTGTATA+AGG 0.223072 4_2:-4897972 None:intergenic
TCTGGTTGAGGCTGGTAATT+TGG 0.230425 4_2:-4897744 None:intergenic
GGTGGAGCTGGTGCATTTCT+TGG 0.287826 4_2:-4897867 None:intergenic
CTCGATTCTAATATATAATC+TGG 0.322005 4_2:-4897705 None:intergenic
AGGTCGAAAGCACGAACATT+AGG 0.411724 4_2:-4897939 None:intergenic
CTCACTCATCTGGTGTATAA+GGG 0.433158 4_2:-4897971 None:intergenic
GTGTATAAGGGAGATTATTA+AGG 0.444305 4_2:-4897959 None:intergenic
GGTTGAGGCTGGTAATTTGG+TGG 0.465939 4_2:-4897741 None:intergenic
GGTGCATTTCTTGGTGGAGC+CGG 0.469690 4_2:-4897858 None:intergenic
TGAGGCTGGTAATTTGGTGG+TGG 0.493466 4_2:-4897738 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.504409 4_2:-4897918 None:intergenic
AAGTCAAATGGCTGCACATG+TGG 0.521723 4_2:-4897906 None:intergenic
ACTGCTAAAGCTTGTGGAGA+TGG 0.545041 4_2:-4897660 None:intergenic
GGAGCTGGTGCATTTCTTGG+TGG 0.547442 4_2:-4897864 None:intergenic
AATGGCTGCACATGTGGAGG+TGG 0.555990 4_2:-4897900 None:intergenic
AAGCACGAACATTAGGAGGC+TGG 0.567243 4_2:-4897932 None:intergenic
ACATGCACTGCTAAAGCTTG+TGG 0.578207 4_2:-4897666 None:intergenic
TCGAAAGCACGAACATTAGG+AGG 0.607481 4_2:-4897936 None:intergenic
ACATCAACCACAAAATGCAC+CGG 0.623532 4_2:+4897839 Msa0584820:CDS
ATATTAGAATCGAGTAAACA+TGG 0.652245 4_2:+4897714 Msa0584820:CDS
TCAAATGGCTGCACATGTGG+AGG 0.671560 4_2:-4897903 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CTCGATTCTAATATATAATC+TGG - chr4_2:4897708-4897727 None:intergenic 25.0%
! ATATTAGAATCGAGTAAACA+TGG + chr4_2:4897714-4897733 Msa0584820:CDS 25.0%
GTGTATAAGGGAGATTATTA+AGG - chr4_2:4897962-4897981 None:intergenic 30.0%
!! GGTTGATGTTCAACATTTTG+TGG - chr4_2:4897786-4897805 None:intergenic 35.0%
! TGATGTTCAACATTTTGTGG+TGG - chr4_2:4897783-4897802 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG - chr4_2:4897786-4897805 None:intergenic 35.0%
!!! GATTGAGCATTTTCTGGTTG+AGG - chr4_2:4897759-4897778 None:intergenic 40.0%
! GGTTGAGATTGAGCATTTTC+TGG - chr4_2:4897765-4897784 None:intergenic 40.0%
ACATCAACCACAAAATGCAC+CGG + chr4_2:4897797-4897816 Msa0584820:CDS 40.0%
ACTGCTAAAGCTTGTGGAGA+TGG - chr4_2:4897663-4897682 None:intergenic 45.0%
ACATGCACTGCTAAAGCTTG+TGG - chr4_2:4897669-4897688 None:intergenic 45.0%
TCTGGTTGAGGCTGGTAATT+TGG - chr4_2:4897747-4897766 None:intergenic 45.0%
AAGTCAAATGGCTGCACATG+TGG - chr4_2:4897909-4897928 None:intergenic 45.0%
! TCGAAAGCACGAACATTAGG+AGG - chr4_2:4897939-4897958 None:intergenic 45.0%
! AGGTCGAAAGCACGAACATT+AGG - chr4_2:4897942-4897961 None:intergenic 45.0%
! TGAGGCTGGTAATTTGGTGG+TGG - chr4_2:4897741-4897760 None:intergenic 50.0%
GGTTGAGGCTGGTAATTTGG+TGG - chr4_2:4897744-4897763 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTGAGGC+TGG - chr4_2:4897755-4897774 None:intergenic 50.0%
! GGTGGAGCTAGTGCATTTTG+TGG - chr4_2:4897807-4897826 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG - chr4_2:4897891-4897910 None:intergenic 50.0%
TCAAATGGCTGCACATGTGG+AGG - chr4_2:4897906-4897925 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG - chr4_2:4897921-4897940 None:intergenic 50.0%
AAGCACGAACATTAGGAGGC+TGG - chr4_2:4897935-4897954 None:intergenic 50.0%
GGTGCATTTCTTGGTGGAGC+CGG - chr4_2:4897861-4897880 None:intergenic 55.0%
GGAGCTGGTGCATTTCTTGG+TGG - chr4_2:4897867-4897886 None:intergenic 55.0%
GGTGGAGCTGGTGCATTTCT+TGG - chr4_2:4897870-4897889 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG - chr4_2:4897882-4897901 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG - chr4_2:4897888-4897907 None:intergenic 55.0%
AATGGCTGCACATGTGGAGG+TGG - chr4_2:4897903-4897922 None:intergenic 55.0%
! GGTGGAGCCGGTGCATTTTG+TGG - chr4_2:4897849-4897868 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 4897615 4897992 4897615 ID=Msa0584820;Name=Msa0584820
chr4_2 mRNA 4897615 4897992 4897615 ID=Msa0584820-mRNA-1;Parent=Msa0584820;Name=Msa0584820-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|125
chr4_2 exon 4897615 4897992 4897615 ID=Msa0584820-mRNA-1:exon:1226;Parent=Msa0584820-mRNA-1
chr4_2 CDS 4897615 4897992 4897615 ID=Msa0584820-mRNA-1:cds;Parent=Msa0584820-mRNA-1
Gene Sequence

>Msa0584820

ATGTCAAAGCTAGAATTCTTATGCGATGAATGTGACACAAAGTTTCCATCTCCACAAGCTTTAGCAGTGCATGTTGTCGAAGAACATCATCCAGATTATATATTAGAATCGAGTAAACATGGTCCACCACCAAATTACCAGCCTCAACCAGAAAATGCTCAATCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACTAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCACCGGCTCCACCAAGAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAGCCATTTGACTTGAACCAGCCTCCTAATGTTCGTGCTTTCGACCTTAATAATCTCCCTTATACACCAGATGAGTGA
Protein sequence

>Msa0584820

MSKLEFLCDECDTKFPSPQALAVHVVEEHHPDYILESSKHGPPPNYQPQPENAQSQPQNVEHQPQNALAPPQNVEHQPQNAPAPPRNAPAPPQNAPPPHVQPFDLNQPPNVRAFDLNNLPYTPDE*