AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1069760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1069760 MtrunA17_Chr7g0251841 89.326 178 13 2 1 178 1 172 4.89e-71 212
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1069760 AT1G12830.1 68.750 80 22 1 91 170 116 192 8.86e-17 75.1

Find 57 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCGTGGTTGTTGGTTT+CGG 0.192971 7_2:-65551559 None:intergenic
CGTCGATGAGGTTGGATTCT+TGG 0.206975 7_2:-65551674 None:intergenic
TCTTCGTGGTTGTTGGTTTC+GGG 0.218487 7_2:-65551558 None:intergenic
CAGACTGGAGTGCACATTTC+TGG 0.227098 7_2:+65552041 Msa1069760:CDS
GATTCTGACGGCAATGTTTC+GGG 0.258012 7_2:+65551933 Msa1069760:CDS
TCCACTTGCGGAGGTTGATT+TGG 0.320599 7_2:+65551980 Msa1069760:CDS
TGATTCTGACGGCAATGTTT+CGG 0.357245 7_2:+65551932 Msa1069760:CDS
TTCTTGATCGGGTTTGCGTT+TGG 0.373289 7_2:-65551595 None:intergenic
GGATTCTTGGTCTACGGTGG+TGG 0.378862 7_2:-65551661 None:intergenic
AGGGATTATGCGCGATGATA+AGG 0.420684 7_2:+65551839 Msa1069760:CDS
GTGATGGGTTTCTTCTTGAT+CGG 0.423416 7_2:-65551607 None:intergenic
TTCGGGTTCGTTGTTGGGAA+CGG 0.430062 7_2:-65551733 None:intergenic
GTGGTGGGAGTAGTTATCTT+GGG 0.430123 7_2:-65551645 None:intergenic
TGTGGGTTCTTCGTGGTTGT+TGG 0.430236 7_2:-65551565 None:intergenic
TGATGGGTTTCTTCTTGATC+GGG 0.431013 7_2:-65551606 None:intergenic
TTTCCTTTCCTGTCCACCAC+AGG 0.432598 7_2:-65551816 None:intergenic
TTGCGTTTGGTGGGGAATGT+GGG 0.446781 7_2:-65551582 None:intergenic
TGATCGGGTTTGCGTTTGGT+GGG 0.446814 7_2:-65551591 None:intergenic
TTTGCGTTTGGTGGGGAATG+TGG 0.460274 7_2:-65551583 None:intergenic
GGGATTATGCGCGATGATAA+GGG 0.461736 7_2:+65551840 Msa1069760:CDS
ATTGACGGTGGTGGGAAGTT+CGG 0.464983 7_2:-65551697 None:intergenic
ACATTCTTCCGTCTAGGACT+CGG 0.465560 7_2:+65552006 Msa1069760:CDS
TTCGTTGTTGGGAACGGCGT+CGG 0.465767 7_2:-65551727 None:intergenic
GGTGGTGGGAGTAGTTATCT+TGG 0.470330 7_2:-65551646 None:intergenic
TTGATCGGGTTTGCGTTTGG+TGG 0.477903 7_2:-65551592 None:intergenic
ATGAAGAGCCTGTGGTGGAC+AGG 0.489672 7_2:+65551808 Msa1069760:CDS
TGCGCGATGATAAGGGAAAA+GGG 0.491143 7_2:+65551847 Msa1069760:CDS
TGGGGAATGTGGGTTCTTCG+TGG 0.491435 7_2:-65551572 None:intergenic
ATGCGCGATGATAAGGGAAA+AGG 0.491640 7_2:+65551846 Msa1069760:CDS
GAGGTTGGATTCTTGGTCTA+CGG 0.496324 7_2:-65551667 None:intergenic
GATTCTTGGTCTACGGTGGT+GGG 0.496695 7_2:-65551660 None:intergenic
CGGCGGCGAACTGCTCAGAC+TGG 0.498986 7_2:+65552026 Msa1069760:CDS
GTGGTGGACAGGAAAGGAAA+AGG 0.506647 7_2:+65551819 Msa1069760:CDS
AGTAGAATCTAATCAGCATT+CGG 0.511857 7_2:-65552071 None:intergenic
GGAAGAAGAATTGACGGTGG+TGG 0.527818 7_2:-65551706 None:intergenic
AAGTTCGGCGTCGATGAGGT+TGG 0.528090 7_2:-65551682 None:intergenic
TGGATAACATTCTTCCGTCT+AGG 0.534730 7_2:+65552000 Msa1069760:CDS
GATCGGGTTTGCGTTTGGTG+GGG 0.540763 7_2:-65551590 None:intergenic
TGGTGGGAGTAGTTATCTTG+GGG 0.541044 7_2:-65551644 None:intergenic
GAAGAAGAATTGACGGTGGT+GGG 0.545012 7_2:-65551705 None:intergenic
TCCAAATCAACCTCCGCAAG+TGG 0.550043 7_2:-65551981 None:intergenic
GGCGTCGGAAGAAGAATTGA+CGG 0.559067 7_2:-65551712 None:intergenic
GTCCACCACAGGCTCTTCAT+CGG 0.559628 7_2:-65551805 None:intergenic
TGGTGGACAGGAAAGGAAAA+GGG 0.564198 7_2:+65551820 Msa1069760:CDS
AATGATTGAAGAAGAAGATG+AGG 0.573565 7_2:+65551872 Msa1069760:CDS
GAGCCTGTGGTGGACAGGAA+AGG 0.591770 7_2:+65551813 Msa1069760:CDS
TTCTGATGATCCACTTGCGG+AGG 0.598405 7_2:+65551971 Msa1069760:CDS
TTCCGATGAAGAGCCTGTGG+TGG 0.608098 7_2:+65551803 Msa1069760:CDS
TGGGAAGTTCGGCGTCGATG+AGG 0.608955 7_2:-65551686 None:intergenic
GGTGGGAGTAGTTATCTTGG+GGG 0.650526 7_2:-65551643 None:intergenic
CGATGATGAAGACGACGACG+AGG 0.653015 7_2:+65551773 Msa1069760:CDS
GTTGGATTCTTGGTCTACGG+TGG 0.656018 7_2:-65551664 None:intergenic
ACTGGAGTGCACATTTCTGG+TGG 0.678942 7_2:+65552044 Msa1069760:CDS
GATAGCGATGATGATTCTGA+CGG 0.698753 7_2:+65551921 Msa1069760:CDS
GAATTCCGATGAAGAGCCTG+TGG 0.723860 7_2:+65551800 Msa1069760:CDS
TTCTTCCGTCTAGGACTCGG+CGG 0.732545 7_2:+65552009 Msa1069760:CDS
GTCGGAAGAAGAATTGACGG+TGG 0.750092 7_2:-65551709 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATGATTGAAGAAGAAGATG+AGG + chr7_2:65551872-65551891 Msa1069760:CDS 30.0%
! TTTTTCTGATGATCCACTTG+CGG + chr7_2:65551968-65551987 Msa1069760:CDS 35.0%
!! TTCTTCGTGGTTGTTGGTTT+CGG - chr7_2:65551562-65551581 None:intergenic 40.0%
!! TGATGGGTTTCTTCTTGATC+GGG - chr7_2:65551609-65551628 None:intergenic 40.0%
!! GTGATGGGTTTCTTCTTGAT+CGG - chr7_2:65551610-65551629 None:intergenic 40.0%
!!! GGTTTTGTTAGGAAGGTGAT+GGG - chr7_2:65551625-65551644 None:intergenic 40.0%
!!! GTTATCTTGGGGGTTTTGTT+AGG - chr7_2:65551636-65551655 None:intergenic 40.0%
!!! TTGTTTTCGGGTTCGTTGTT+GGG - chr7_2:65551741-65551760 None:intergenic 40.0%
!!! TCATCGTCAGTGTTGTTTTC+GGG - chr7_2:65551753-65551772 None:intergenic 40.0%
!!! GTCATCGTCAGTGTTGTTTT+CGG - chr7_2:65551754-65551773 None:intergenic 40.0%
GATAGCGATGATGATTCTGA+CGG + chr7_2:65551921-65551940 Msa1069760:CDS 40.0%
TGATTCTGACGGCAATGTTT+CGG + chr7_2:65551932-65551951 Msa1069760:CDS 40.0%
TGGATAACATTCTTCCGTCT+AGG + chr7_2:65552000-65552019 Msa1069760:CDS 40.0%
!! TCTTCGTGGTTGTTGGTTTC+GGG - chr7_2:65551561-65551580 None:intergenic 45.0%
TTCTTGATCGGGTTTGCGTT+TGG - chr7_2:65551598-65551617 None:intergenic 45.0%
!!! GGGTTTTGTTAGGAAGGTGA+TGG - chr7_2:65551626-65551645 None:intergenic 45.0%
!!! TCTTGGGGGTTTTGTTAGGA+AGG - chr7_2:65551632-65551651 None:intergenic 45.0%
TGGTGGGAGTAGTTATCTTG+GGG - chr7_2:65551647-65551666 None:intergenic 45.0%
! GTGGTGGGAGTAGTTATCTT+GGG - chr7_2:65551648-65551667 None:intergenic 45.0%
GAGGTTGGATTCTTGGTCTA+CGG - chr7_2:65551670-65551689 None:intergenic 45.0%
GAAGAAGAATTGACGGTGGT+GGG - chr7_2:65551708-65551727 None:intergenic 45.0%
!!! GTTGTTTTCGGGTTCGTTGT+TGG - chr7_2:65551742-65551761 None:intergenic 45.0%
! TGGTGGACAGGAAAGGAAAA+GGG + chr7_2:65551820-65551839 Msa1069760:CDS 45.0%
AGGGATTATGCGCGATGATA+AGG + chr7_2:65551839-65551858 Msa1069760:CDS 45.0%
GGGATTATGCGCGATGATAA+GGG + chr7_2:65551840-65551859 Msa1069760:CDS 45.0%
ATGCGCGATGATAAGGGAAA+AGG + chr7_2:65551846-65551865 Msa1069760:CDS 45.0%
TGCGCGATGATAAGGGAAAA+GGG + chr7_2:65551847-65551866 Msa1069760:CDS 45.0%
GATTCTGACGGCAATGTTTC+GGG + chr7_2:65551933-65551952 Msa1069760:CDS 45.0%
! ACATTCTTCCGTCTAGGACT+CGG + chr7_2:65552006-65552025 Msa1069760:CDS 45.0%
TGTGGGTTCTTCGTGGTTGT+TGG - chr7_2:65551568-65551587 None:intergenic 50.0%
! TTGCGTTTGGTGGGGAATGT+GGG - chr7_2:65551585-65551604 None:intergenic 50.0%
! TTTGCGTTTGGTGGGGAATG+TGG - chr7_2:65551586-65551605 None:intergenic 50.0%
TGATCGGGTTTGCGTTTGGT+GGG - chr7_2:65551594-65551613 None:intergenic 50.0%
TTGATCGGGTTTGCGTTTGG+TGG - chr7_2:65551595-65551614 None:intergenic 50.0%
GGTGGGAGTAGTTATCTTGG+GGG - chr7_2:65551646-65551665 None:intergenic 50.0%
!! GGTGGTGGGAGTAGTTATCT+TGG - chr7_2:65551649-65551668 None:intergenic 50.0%
GATTCTTGGTCTACGGTGGT+GGG - chr7_2:65551663-65551682 None:intergenic 50.0%
GTTGGATTCTTGGTCTACGG+TGG - chr7_2:65551667-65551686 None:intergenic 50.0%
CGTCGATGAGGTTGGATTCT+TGG - chr7_2:65551677-65551696 None:intergenic 50.0%
!! ATTGACGGTGGTGGGAAGTT+CGG - chr7_2:65551700-65551719 None:intergenic 50.0%
GGAAGAAGAATTGACGGTGG+TGG - chr7_2:65551709-65551728 None:intergenic 50.0%
GTCGGAAGAAGAATTGACGG+TGG - chr7_2:65551712-65551731 None:intergenic 50.0%
! GGCGTCGGAAGAAGAATTGA+CGG - chr7_2:65551715-65551734 None:intergenic 50.0%
! TTCGGGTTCGTTGTTGGGAA+CGG - chr7_2:65551736-65551755 None:intergenic 50.0%
GAATTCCGATGAAGAGCCTG+TGG + chr7_2:65551800-65551819 Msa1069760:CDS 50.0%
TTTCCTTTCCTGTCCACCAC+AGG - chr7_2:65551819-65551838 None:intergenic 50.0%
!! GTGGTGGACAGGAAAGGAAA+AGG + chr7_2:65551819-65551838 Msa1069760:CDS 50.0%
TTCTGATGATCCACTTGCGG+AGG + chr7_2:65551971-65551990 Msa1069760:CDS 50.0%
! TCCACTTGCGGAGGTTGATT+TGG + chr7_2:65551980-65551999 Msa1069760:CDS 50.0%
TCCAAATCAACCTCCGCAAG+TGG - chr7_2:65551984-65552003 None:intergenic 50.0%
CAGACTGGAGTGCACATTTC+TGG + chr7_2:65552041-65552060 Msa1069760:CDS 50.0%
! ACTGGAGTGCACATTTCTGG+TGG + chr7_2:65552044-65552063 Msa1069760:CDS 50.0%
TGGGGAATGTGGGTTCTTCG+TGG - chr7_2:65551575-65551594 None:intergenic 55.0%
! GATCGGGTTTGCGTTTGGTG+GGG - chr7_2:65551593-65551612 None:intergenic 55.0%
GGATTCTTGGTCTACGGTGG+TGG - chr7_2:65551664-65551683 None:intergenic 55.0%
!! AAGTTCGGCGTCGATGAGGT+TGG - chr7_2:65551685-65551704 None:intergenic 55.0%
TTCGTTGTTGGGAACGGCGT+CGG - chr7_2:65551730-65551749 None:intergenic 55.0%
CGATGATGAAGACGACGACG+AGG + chr7_2:65551773-65551792 Msa1069760:CDS 55.0%
TTCCGATGAAGAGCCTGTGG+TGG + chr7_2:65551803-65551822 Msa1069760:CDS 55.0%
GTCCACCACAGGCTCTTCAT+CGG - chr7_2:65551808-65551827 None:intergenic 55.0%
!! ATGAAGAGCCTGTGGTGGAC+AGG + chr7_2:65551808-65551827 Msa1069760:CDS 55.0%
! TTCTTCCGTCTAGGACTCGG+CGG + chr7_2:65552009-65552028 Msa1069760:CDS 55.0%
!! TGGGAAGTTCGGCGTCGATG+AGG - chr7_2:65551689-65551708 None:intergenic 60.0%
!! GAGCCTGTGGTGGACAGGAA+AGG + chr7_2:65551813-65551832 Msa1069760:CDS 60.0%
GTTCGCCGCCGAGTCCTAGA+CGG - chr7_2:65552017-65552036 None:intergenic 65.0%
CGGCGGCGAACTGCTCAGAC+TGG + chr7_2:65552026-65552045 Msa1069760:CDS 70.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 65551549 65552085 65551549 ID=Msa1069760;Name=Msa1069760
chr7_2 mRNA 65551549 65552085 65551549 ID=Msa1069760-mRNA-1;Parent=Msa1069760;Name=Msa1069760-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|178
chr7_2 exon 65551549 65552085 65551549 ID=Msa1069760-mRNA-1:exon:13799;Parent=Msa1069760-mRNA-1
chr7_2 CDS 65551549 65552085 65551549 ID=Msa1069760-mRNA-1:cds;Parent=Msa1069760-mRNA-1
Gene Sequence

>Msa1069760

ATGGCTGAACCCGAAACCAACAACCACGAAGAACCCACATTCCCCACCAAACGCAAACCCGATCAAGAAGAAACCCATCACCTTCCTAACAAAACCCCCAAGATAACTACTCCCACCACCGTAGACCAAGAATCCAACCTCATCGACGCCGAACTTCCCACCACCGTCAATTCTTCTTCCGACGCCGTTCCCAACAACGAACCCGAAAACAACACTGACGATGACGATGATGAAGACGACGACGAGGATGAGAATTCCGATGAAGAGCCTGTGGTGGACAGGAAAGGAAAAGGGATTATGCGCGATGATAAGGGAAAAGGGAAAATGATTGAAGAAGAAGATGAGGATGATGATGACAGTCACGATAGTGATGATAGCGATGATGATTCTGACGGCAATGTTTCGGGTAGTGACAGTGATTTTTCTGATGATCCACTTGCGGAGGTTGATTTGGATAACATTCTTCCGTCTAGGACTCGGCGGCGAACTGCTCAGACTGGAGTGCACATTTCTGGTGGCACGCCGAATGCTGATTAG
Protein sequence

>Msa1069760

MAEPETNNHEEPTFPTKRKPDQEETHHLPNKTPKITTPTTVDQESNLIDAELPTTVNSSSDAVPNNEPENNTDDDDDEDDDEDENSDEEPVVDRKGKGIMRDDKGKGKMIEEEDEDDDDSHDSDDSDDDSDGNVSGSDSDFSDDPLAEVDLDNILPSRTRRRTAQTGVHISGGTPNAD*