AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0527890

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0527890 MtrunA17_Chr4g0001981 89.262 149 7 3 1 145 382 525 2.29e-83 253
Msa0527890 MtrunA17_Chr4g0073561 39.161 143 69 4 1 139 368 496 2.91e-20 85.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGAGTAAAATGTTTGATT+TGG 0.223076 4_1:+561804 Msa0527890:CDS
AAGAGTAAAATGTTTGATTT+GGG 0.305973 4_1:+561805 Msa0527890:CDS
TTTCTGAAGAAGGCAGTATA+AGG 0.405521 4_1:-561683 None:intergenic
CAAGATGATGATGATGCTTC+TGG 0.418720 4_1:+561835 Msa0527890:CDS
CTATCAGAATCCTCGGACAT+AGG 0.423015 4_1:-561955 None:intergenic
GGTAGCCAGCAGCAAGGAAA+TGG 0.434094 4_1:+561856 Msa0527890:CDS
AGCTCTGTCATTAGTGAAGC+TGG 0.450625 4_1:-561569 None:intergenic
ACAGACCATTTCCTTGCTGC+TGG 0.483280 4_1:-561861 None:intergenic
CACTAATGACAGAGCTGTGT+TGG 0.483298 4_1:+561576 Msa0527890:CDS
ATTTGCTTCTGAATCTTCCA+AGG 0.519721 4_1:+561905 Msa0527890:CDS
TGTGGCAGAGAAGCAATCCT+TGG 0.523882 4_1:-561922 None:intergenic
TAATGACAGAGCTGTGTTGG+AGG 0.526990 4_1:+561579 Msa0527890:CDS
TTCTGTTCATCATCAGAGAC+AGG 0.536856 4_1:-561640 None:intergenic
CAGGAGGGTCTTTCTGAAGA+AGG 0.541302 4_1:-561693 None:intergenic
CTGTCTAGGAAAGAATCAGC+TGG 0.542082 4_1:+561880 Msa0527890:CDS
AACATGACTATCAGAATCCT+CGG 0.577952 4_1:-561962 None:intergenic
AGCAAGGAAATGGTCTGTCT+AGG 0.585074 4_1:+561866 Msa0527890:CDS
GACATAGGAAACAGAAAATG+TGG 0.600386 4_1:-561940 None:intergenic
GAAGATAGAAAAGTTGATGA+GGG 0.606665 4_1:+561766 Msa0527890:CDS
TGAAGATAGAAAAGTTGATG+AGG 0.612436 4_1:+561765 Msa0527890:CDS
TGTTCATCATCAGAGACAGG+TGG 0.655949 4_1:-561637 None:intergenic
GCTTCTGGTAGCCAGCAGCA+AGG 0.673116 4_1:+561850 Msa0527890:CDS
ATGAACAGAATGTCATGACA+AGG 0.678824 4_1:+561653 Msa0527890:CDS
TGAACAGAATGTCATGACAA+GGG 0.758366 4_1:+561654 Msa0527890:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAGAGTAAAATGTTTGATT+TGG + chr4_1:561804-561823 Msa0527890:CDS 20.0%
!!! AAGAGTAAAATGTTTGATTT+GGG + chr4_1:561805-561824 Msa0527890:CDS 20.0%
!!! ATTTTGAACCTGTTTTTCTT+CGG - chr4_1:561722-561741 None:intergenic 25.0%
!! TTTTGAACCTGTTTTTCTTC+GGG - chr4_1:561721-561740 None:intergenic 30.0%
GAAGAAAAACAGGTTCAAAA+TGG + chr4_1:561721-561740 Msa0527890:CDS 30.0%
!! TGAAGATAGAAAAGTTGATG+AGG + chr4_1:561765-561784 Msa0527890:CDS 30.0%
!! GAAGATAGAAAAGTTGATGA+GGG + chr4_1:561766-561785 Msa0527890:CDS 30.0%
! TTAGTGAAGCTGGAATTTTC+AGG - chr4_1:561562-561581 None:intergenic 35.0%
ATGAACAGAATGTCATGACA+AGG + chr4_1:561653-561672 Msa0527890:CDS 35.0%
TGAACAGAATGTCATGACAA+GGG + chr4_1:561654-561673 Msa0527890:CDS 35.0%
! TTTCTGAAGAAGGCAGTATA+AGG - chr4_1:561686-561705 None:intergenic 35.0%
ATTTGCTTCTGAATCTTCCA+AGG + chr4_1:561905-561924 Msa0527890:CDS 35.0%
GACATAGGAAACAGAAAATG+TGG - chr4_1:561943-561962 None:intergenic 35.0%
AACATGACTATCAGAATCCT+CGG - chr4_1:561965-561984 None:intergenic 35.0%
TTCTGTTCATCATCAGAGAC+AGG - chr4_1:561643-561662 None:intergenic 40.0%
! CAAGATGATGATGATGCTTC+TGG + chr4_1:561835-561854 Msa0527890:CDS 40.0%
! TTTTCTGTTTCCTATGTCCG+AGG + chr4_1:561945-561964 Msa0527890:CDS 40.0%
AGCTCTGTCATTAGTGAAGC+TGG - chr4_1:561572-561591 None:intergenic 45.0%
CACTAATGACAGAGCTGTGT+TGG + chr4_1:561576-561595 Msa0527890:CDS 45.0%
TAATGACAGAGCTGTGTTGG+AGG + chr4_1:561579-561598 Msa0527890:CDS 45.0%
TGTTCATCATCAGAGACAGG+TGG - chr4_1:561640-561659 None:intergenic 45.0%
AGCAAGGAAATGGTCTGTCT+AGG + chr4_1:561866-561885 Msa0527890:CDS 45.0%
CTGTCTAGGAAAGAATCAGC+TGG + chr4_1:561880-561899 Msa0527890:CDS 45.0%
CTATCAGAATCCTCGGACAT+AGG - chr4_1:561958-561977 None:intergenic 45.0%
! CAGGAGGGTCTTTCTGAAGA+AGG - chr4_1:561696-561715 None:intergenic 50.0%
! GTTTTTCTTCGGGTGCAGGA+GGG - chr4_1:561711-561730 None:intergenic 50.0%
! TGTTTTTCTTCGGGTGCAGG+AGG - chr4_1:561712-561731 None:intergenic 50.0%
TCCTGCACCCGAAGAAAAAC+AGG + chr4_1:561711-561730 Msa0527890:CDS 50.0%
!! ACCTGTTTTTCTTCGGGTGC+AGG - chr4_1:561715-561734 None:intergenic 50.0%
ACAGACCATTTCCTTGCTGC+TGG - chr4_1:561864-561883 None:intergenic 50.0%
TGTGGCAGAGAAGCAATCCT+TGG - chr4_1:561925-561944 None:intergenic 50.0%
GGTAGCCAGCAGCAAGGAAA+TGG + chr4_1:561856-561875 Msa0527890:CDS 55.0%
GCTTCTGGTAGCCAGCAGCA+AGG + chr4_1:561850-561869 Msa0527890:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 561553 561990 561553 ID=Msa0527890;Name=Msa0527890
chr4_1 mRNA 561553 561990 561553 ID=Msa0527890-mRNA-1;Parent=Msa0527890;Name=Msa0527890-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|145
chr4_1 exon 561553 561990 561553 ID=Msa0527890-mRNA-1:exon:84;Parent=Msa0527890-mRNA-1
chr4_1 CDS 561553 561990 561553 ID=Msa0527890-mRNA-1:cds;Parent=Msa0527890-mRNA-1
Gene Sequence

>Msa0527890

ATGGGACCTGAAAATTCCAGCTTCACTAATGACAGAGCTGTGTTGGAGGAATTCACACAATATCTGTTCAATGACTCTCAGTTTCCACCTGTCTCTGATGATGAACAGAATGTCATGACAAGGGTGAACTCCTTATACTGCCTTCTTCAGAAAGACCCTCCTGCACCCGAAGAAAAACAGGTTCAAAATGGTAACAATTTTTTCGATGCTGCTGAAGATAGAAAAGTTGATGAGGGCAATAGTGCTGAACATAAGAGTAAAATGTTTGATTTGGGAATTCAACAAGATGATGATGATGCTTCTGGTAGCCAGCAGCAAGGAAATGGTCTGTCTAGGAAAGAATCAGCTGGAGATTTGCTTCTGAATCTTCCAAGGATTGCTTCTCTGCCACATTTTCTGTTTCCTATGTCCGAGGATTCTGATAGTCATGTTAGATAG
Protein sequence

>Msa0527890

MGPENSSFTNDRAVLEEFTQYLFNDSQFPPVSDDEQNVMTRVNSLYCLLQKDPPAPEEKQVQNGNNFFDAAEDRKVDEGNSAEHKSKMFDLGIQQDDDDASGSQQQGNGLSRKESAGDLLLNLPRIASLPHFLFPMSEDSDSHVR*