AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65310.t1 MTR_5g023880 76.111 180 24 3 1 169 1 172 4.11e-91 263
MS.gene65310.t1 MTR_5g023900 56.398 211 30 5 1 169 1 191 3.72e-68 205
MS.gene65310.t1 MTR_5g023870 56.579 152 29 4 1 152 1 115 1.10e-47 151
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 56 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTCAGAGTTCTTTAAGTA+TGG 0.229519 5.2:+14812791 MS.gene65310:CDS
TGTTTGCATCTATGACAATA+TGG 0.236317 5.2:-14812966 None:intergenic
TTCTCGGAAGGGTTAGGTTT+AGG 0.237072 5.2:-14812690 None:intergenic
TCTCGGAAGGGTTAGGTTTA+GGG 0.267292 5.2:-14812689 None:intergenic
GAGTTCAGAGCACGTGAAAA+TGG 0.284945 5.2:+14812855 MS.gene65310:CDS
ATACATCATTCTTCTTCATT+AGG 0.286612 5.2:-14813608 None:intergenic
TTGAGGGGACTTGTTGTTGG+TGG 0.289994 5.2:-14812721 None:intergenic
GTCTTGAGGGGACTTGTTGT+TGG 0.343036 5.2:-14812724 None:intergenic
AGTTGGGTTGGTTTCTTTGA+GGG 0.364234 5.2:-14812766 None:intergenic
GTTGAATTCTCGGAAGGGTT+AGG 0.378551 5.2:-14812696 None:intergenic
TAGTTGGGTTGGTTTCTTTG+AGG 0.387471 5.2:-14812767 None:intergenic
CTCTTCCTCCTCTTCATAGC+TGG 0.393408 5.2:-14812915 None:intergenic
TGAGGGGACTTGTTGTTGGT+GGG 0.402381 5.2:-14812720 None:intergenic
AAAGAACTCTGAAGGGTAGT+TGG 0.407097 5.2:-14812783 None:intergenic
AGGGGACTTGTTGTTGGTGG+GGG 0.408399 5.2:-14812718 None:intergenic
ACCTCAACCTGATCGATATG+AGG 0.421429 5.2:+14813112 MS.gene65310:CDS
GTTTGCATCTATGACAATAT+GGG 0.427069 5.2:-14812965 None:intergenic
AAGAACTCTGAAGGGTAGTT+GGG 0.428150 5.2:-14812782 None:intergenic
CATCAGAGGGAGGGTCTTGA+GGG 0.445658 5.2:-14812737 None:intergenic
CATCATTCTTCTTCATTAGG+AGG 0.456004 5.2:-14813605 None:intergenic
GCAAACATGTGTTTCCCACT+TGG 0.463748 5.2:+14812982 MS.gene65310:CDS
CCCTCATATCGATCAGGTTG+AGG 0.479409 5.2:-14813113 None:intergenic
GAAAACCGCTCTCGAAGTCT+TGG 0.485360 5.2:+14812830 MS.gene65310:CDS
AGTTCAGAGCACGTGAAAAT+GGG 0.494582 5.2:+14812856 MS.gene65310:CDS
AACCGCTCTCGAAGTCTTGG+TGG 0.499745 5.2:+14812833 MS.gene65310:CDS
TCATCAGAGGGAGGGTCTTG+AGG 0.508193 5.2:-14812738 None:intergenic
AAGCTAGCCAATGGAGATAG+AGG 0.512291 5.2:+14813563 MS.gene65310:intron
ACTCTGAAGGGTAGTTGGGT+TGG 0.513668 5.2:-14812778 None:intergenic
AGCACGTGAAAATGGGAAGC+TGG 0.516757 5.2:+14812863 MS.gene65310:CDS
GTCGAATCCTCTATCTCCAT+TGG 0.531072 5.2:-14813570 None:intergenic
AAGCTGGCAGCTGATGGAGA+TGG 0.543820 5.2:+14812879 MS.gene65310:CDS
GAGGGGACTTGTTGTTGGTG+GGG 0.544991 5.2:-14812719 None:intergenic
AATGGGAAGCTGGCAGCTGA+TGG 0.545369 5.2:+14812873 MS.gene65310:CDS
CCATACTTAAAGAACTCTGA+AGG 0.547193 5.2:-14812791 None:intergenic
CAAACATGTGTTTCCCACTT+GGG 0.553679 5.2:+14812983 MS.gene65310:CDS
TTTGAGGGATTCATCATCAG+AGG 0.561409 5.2:-14812751 None:intergenic
GATGGAGATGGAGGAAGTGC+TGG 0.565328 5.2:+14812891 MS.gene65310:CDS
TCGATCAGGTTGAGGTGGGA+TGG 0.568415 5.2:-14813105 None:intergenic
AGGTGGGATGGCTGTTGATG+TGG 0.572719 5.2:-14813093 None:intergenic
TCATATCGATCAGGTTGAGG+TGG 0.575699 5.2:-14813110 None:intergenic
TTGAGGGATTCATCATCAGA+GGG 0.579951 5.2:-14812750 None:intergenic
TCAGAGTTCTTTAAGTATGG+AGG 0.585929 5.2:+14812794 MS.gene65310:CDS
CTGGCAGCTGATGGAGATGG+AGG 0.586875 5.2:+14812882 MS.gene65310:CDS
CTGGTCCAGCTATGAAGAGG+AGG 0.594437 5.2:+14812910 MS.gene65310:CDS
CATATCGATCAGGTTGAGGT+GGG 0.619595 5.2:-14813109 None:intergenic
CCTCAACCTGATCGATATGA+GGG 0.620285 5.2:+14813113 MS.gene65310:CDS
CTCCACCAAGACTTCGAGAG+CGG 0.620960 5.2:-14812835 None:intergenic
CATACTTAAAGAACTCTGAA+GGG 0.620976 5.2:-14812790 None:intergenic
GTGCTGGTCCAGCTATGAAG+AGG 0.622703 5.2:+14812907 MS.gene65310:CDS
AGGGATTCATCATCAGAGGG+AGG 0.627786 5.2:-14812747 None:intergenic
TTTGCATCTATGACAATATG+GGG 0.633329 5.2:-14812964 None:intergenic
GGGATGGCTGTTGATGTGGA+CGG 0.637609 5.2:-14813089 None:intergenic
CTTCATCACAGCAGCCCAAG+TGG 0.638291 5.2:-14812997 None:intergenic
GGGATTCATCATCAGAGGGA+GGG 0.650027 5.2:-14812746 None:intergenic
ATCAGAGGGAGGGTCTTGAG+GGG 0.650850 5.2:-14812736 None:intergenic
TTCATCACAGCAGCCCAAGT+GGG 0.660567 5.2:-14812996 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATCAAATAATTGAATCT+TGG - chr5.2:14813256-14813275 None:intergenic 20.0%
!!! AATGTTTTTCTTTTGTTACT+AGG + chr5.2:14813531-14813550 MS.gene65310:intron 20.0%
!!! ACAATAAATAGTTTTGAGTT+AGG - chr5.2:14813158-14813177 None:intergenic 20.0%
!!! TTTCTCACACTATAATTTTT+AGG + chr5.2:14813186-14813205 MS.gene65310:intron 20.0%
! CATATATATGTTTGTGTGTA+TGG - chr5.2:14813352-14813371 None:intergenic 25.0%
! TTATGAGATCTAATTCATGT+AGG + chr5.2:14813395-14813414 MS.gene65310:intron 25.0%
!!! GTTTTATTGGCTATATATCA+TGG + chr5.2:14813230-14813249 MS.gene65310:intron 25.0%
!!! TAGTTTTGAGTTAGGAAATT+AGG - chr5.2:14813150-14813169 None:intergenic 25.0%
!!! TATTTTTGTTGTCATCCTAA+TGG + chr5.2:14813035-14813054 MS.gene65310:CDS 25.0%
CATACTTAAAGAACTCTGAA+GGG - chr5.2:14812793-14812812 None:intergenic 30.0%
GTTTGCATCTATGACAATAT+GGG - chr5.2:14812968-14812987 None:intergenic 30.0%
TATATAGCCAATAAAACCCT+AGG - chr5.2:14813227-14813246 None:intergenic 30.0%
TGTTTGCATCTATGACAATA+TGG - chr5.2:14812969-14812988 None:intergenic 30.0%
TTTGCATCTATGACAATATG+GGG - chr5.2:14812967-14812986 None:intergenic 30.0%
CCATACTTAAAGAACTCTGA+AGG - chr5.2:14812794-14812813 None:intergenic 35.0%
CCTTCAGAGTTCTTTAAGTA+TGG + chr5.2:14812791-14812810 MS.gene65310:CDS 35.0%
TCAGAGTTCTTTAAGTATGG+AGG + chr5.2:14812794-14812813 MS.gene65310:CDS 35.0%
AGTGAATAAAAACCAGGAGG+TGG - chr5.2:14813068-14813087 None:intergenic 40.0%
AGTTCAGAGCACGTGAAAAT+GGG + chr5.2:14812856-14812875 MS.gene65310:CDS 40.0%
CAAACATGTGTTTCCCACTT+GGG + chr5.2:14812983-14813002 MS.gene65310:CDS 40.0%
CCAATAAAACCCTAGGTCAT+TGG - chr5.2:14813220-14813239 None:intergenic 40.0%
GACGGAAGTGAATAAAAACC+AGG - chr5.2:14813074-14813093 None:intergenic 40.0%
GGAAGTGAATAAAAACCAGG+AGG - chr5.2:14813071-14813090 None:intergenic 40.0%
TTGAGGGATTCATCATCAGA+GGG - chr5.2:14812753-14812772 None:intergenic 40.0%
TTTGAGGGATTCATCATCAG+AGG - chr5.2:14812754-14812773 None:intergenic 40.0%
! AAAGAACTCTGAAGGGTAGT+TGG - chr5.2:14812786-14812805 None:intergenic 40.0%
! AAGAACTCTGAAGGGTAGTT+GGG - chr5.2:14812785-14812804 None:intergenic 40.0%
! GTTTTACCCTCATATCGATC+AGG - chr5.2:14813122-14813141 None:intergenic 40.0%
! TGATGATGAAAGCTAGCCAA+TGG + chr5.2:14813554-14813573 MS.gene65310:intron 40.0%
!! AGTTGGGTTGGTTTCTTTGA+GGG - chr5.2:14812769-14812788 None:intergenic 40.0%
!! CCAATGACCTAGGGTTTTAT+TGG + chr5.2:14813217-14813236 MS.gene65310:intron 40.0%
!! TAGTTGGGTTGGTTTCTTTG+AGG - chr5.2:14812770-14812789 None:intergenic 40.0%
AAGCTAGCCAATGGAGATAG+AGG + chr5.2:14813563-14813582 MS.gene65310:intron 45.0%
ACCTCAACCTGATCGATATG+AGG + chr5.2:14813112-14813131 MS.gene65310:CDS 45.0%
CCTCAACCTGATCGATATGA+GGG + chr5.2:14813113-14813132 MS.gene65310:CDS 45.0%
GAGTTCAGAGCACGTGAAAA+TGG + chr5.2:14812855-14812874 MS.gene65310:CDS 45.0%
GCAAACATGTGTTTCCCACT+TGG + chr5.2:14812982-14813001 MS.gene65310:CDS 45.0%
GGAGGTGGTGAAAAACCATT+AGG - chr5.2:14813053-14813072 None:intergenic 45.0%
GTCAACACTCCAATGACCTA+GGG + chr5.2:14813208-14813227 MS.gene65310:intron 45.0%
GTCGAATCCTCTATCTCCAT+TGG - chr5.2:14813573-14813592 None:intergenic 45.0%
GTTGAATTCTCGGAAGGGTT+AGG - chr5.2:14812699-14812718 None:intergenic 45.0%
TCTCGGAAGGGTTAGGTTTA+GGG - chr5.2:14812692-14812711 None:intergenic 45.0%
TTCTCGGAAGGGTTAGGTTT+AGG - chr5.2:14812693-14812712 None:intergenic 45.0%
! AATGGTTTTTCACCACCTCC+TGG + chr5.2:14813053-14813072 MS.gene65310:CDS 45.0%
!! CATATCGATCAGGTTGAGGT+GGG - chr5.2:14813112-14813131 None:intergenic 45.0%
!! TCATATCGATCAGGTTGAGG+TGG - chr5.2:14813113-14813132 None:intergenic 45.0%
!!! ATTTTTTTTTTATAACTTAT+TGG + chr5.2:14813436-14813455 MS.gene65310:intron 5.0%
AGCACGTGAAAATGGGAAGC+TGG + chr5.2:14812863-14812882 MS.gene65310:CDS 50.0%
AGGGATTCATCATCAGAGGG+AGG - chr5.2:14812750-14812769 None:intergenic 50.0%
CTCTTCCTCCTCTTCATAGC+TGG - chr5.2:14812918-14812937 None:intergenic 50.0%
GAAAACCGCTCTCGAAGTCT+TGG + chr5.2:14812830-14812849 MS.gene65310:CDS 50.0%
GGGATTCATCATCAGAGGGA+GGG - chr5.2:14812749-14812768 None:intergenic 50.0%
GGTCAACACTCCAATGACCT+AGG + chr5.2:14813207-14813226 MS.gene65310:intron 50.0%
TGGGGGTTGAATTCTCGGAA+GGG - chr5.2:14812704-14812723 None:intergenic 50.0%
TTCATCACAGCAGCCCAAGT+GGG - chr5.2:14812999-14813018 None:intergenic 50.0%
! ACTCTGAAGGGTAGTTGGGT+TGG - chr5.2:14812781-14812800 None:intergenic 50.0%
! AGACTTCGAGAGCGGTTTTC+AGG - chr5.2:14812830-14812849 None:intergenic 50.0%
! CCCTCATATCGATCAGGTTG+AGG - chr5.2:14813116-14813135 None:intergenic 50.0%
! GTTGGTGGGGGTTGAATTCT+CGG - chr5.2:14812709-14812728 None:intergenic 50.0%
!! GTCTTGAGGGGACTTGTTGT+TGG - chr5.2:14812727-14812746 None:intergenic 50.0%
!! TGAGGGGACTTGTTGTTGGT+GGG - chr5.2:14812723-14812742 None:intergenic 50.0%
!! TTGAGGGGACTTGTTGTTGG+TGG - chr5.2:14812724-14812743 None:intergenic 50.0%
AACCGCTCTCGAAGTCTTGG+TGG + chr5.2:14812833-14812852 MS.gene65310:CDS 55.0%
AAGCTGGCAGCTGATGGAGA+TGG + chr5.2:14812879-14812898 MS.gene65310:CDS 55.0%
AATGGGAAGCTGGCAGCTGA+TGG + chr5.2:14812873-14812892 MS.gene65310:CDS 55.0%
AGGTGGGATGGCTGTTGATG+TGG - chr5.2:14813096-14813115 None:intergenic 55.0%
ATCAGAGGGAGGGTCTTGAG+GGG - chr5.2:14812739-14812758 None:intergenic 55.0%
CATCAGAGGGAGGGTCTTGA+GGG - chr5.2:14812740-14812759 None:intergenic 55.0%
CTCCACCAAGACTTCGAGAG+CGG - chr5.2:14812838-14812857 None:intergenic 55.0%
CTGGTCCAGCTATGAAGAGG+AGG + chr5.2:14812910-14812929 MS.gene65310:CDS 55.0%
CTTCATCACAGCAGCCCAAG+TGG - chr5.2:14813000-14813019 None:intergenic 55.0%
GGGATGGCTGTTGATGTGGA+CGG - chr5.2:14813092-14813111 None:intergenic 55.0%
GTGGGGGTTGAATTCTCGGA+AGG - chr5.2:14812705-14812724 None:intergenic 55.0%
TCATCAGAGGGAGGGTCTTG+AGG - chr5.2:14812741-14812760 None:intergenic 55.0%
! GATGGAGATGGAGGAAGTGC+TGG + chr5.2:14812891-14812910 MS.gene65310:CDS 55.0%
! GTGCTGGTCCAGCTATGAAG+AGG + chr5.2:14812907-14812926 MS.gene65310:CDS 55.0%
!! AGGGGACTTGTTGTTGGTGG+GGG - chr5.2:14812721-14812740 None:intergenic 55.0%
!! GAGGGGACTTGTTGTTGGTG+GGG - chr5.2:14812722-14812741 None:intergenic 55.0%
!! TCGATCAGGTTGAGGTGGGA+TGG - chr5.2:14813108-14813127 None:intergenic 55.0%
CTGGCAGCTGATGGAGATGG+AGG + chr5.2:14812882-14812901 MS.gene65310:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 14812681 14813625 14812681 ID=MS.gene65310
chr5.2 mRNA 14812681 14813625 14812681 ID=MS.gene65310.t1;Parent=MS.gene65310
chr5.2 exon 14812681 14813134 14812681 ID=MS.gene65310.t1.exon1;Parent=MS.gene65310.t1
chr5.2 CDS 14812681 14813134 14812681 ID=cds.MS.gene65310.t1;Parent=MS.gene65310.t1
chr5.2 exon 14813570 14813625 14813570 ID=MS.gene65310.t1.exon2;Parent=MS.gene65310.t1
chr5.2 CDS 14813570 14813625 14813570 ID=cds.MS.gene65310.t1;Parent=MS.gene65310.t1
Gene Sequence

>MS.gene65310

ATGCAGAACCCTAAACCTAACCCTTCCGAGAATTCAACCCCCACCAACAACAAGTCCCCTCAAGACCCTCCCTCTGATGATGAATCCCTCAAAGAAACCAACCCAACTACCCTTCAGAGTTCTTTAAGTATGGAGGAAGATGATGTCCTGAAAACCGCTCTCGAAGTCTTGGTGGAGTTCAGAGCACGTGAAAATGGGAAGCTGGCAGCTGATGGAGATGGAGGAAGTGCTGGTCCAGCTATGAAGAGGAGGAAGAGTAATATTTGTGAAGTGAATGATGTATCCCCATATTGTCATAGATGCAAACATGTGTTTCCCACTTGGGCTGCTGTGATGAAGCATTTGCAAGAACACTATTTTTGTTGTCATCCTAATGGTTTTTCACCACCTCCTGGTTTTTATTCACTTCCGTCCACATCAACAGCCATCCCACCTCAACCTGATCGATATGAGGGTAAAACTTAAACCTAATTTCCTAACTCAAAACTATTTATTGTCATGTTTTTTTCTCACACTATAATTTTTAGGTCAACACTCCAATGACCTAGGGTTTTATTGGCTATATATCATGGCCAAGATTCAATTATTTGATGTTATGTCATTTTTTTCTTCATTTAATTATTTTGATTTCAAAGTACTTGTGTATAGAACATTCATAAAATACTGCACCATACACACAAACATATATATGTTCAATTTGAGTGTTGCTTAATTTTATGAGATCTAATTCATGTAGGCATCTAAATATATCTTTAATTTTTTTTTTATAACTTATTGGTTTTTAATTTAACAATATTTTTTTTCTTCAAACTAATGATTTTACAATGAAGCAATTATAATTATAATTTTGAATGTTTTTCTTTTGTTACTAGGTGATGATGAAAGCTAGCCAATGGAGATAGAGGATTCGACTTGAACGAGTTGCCTCCTAATGAAGAAGAATGA
Protein sequence

>MS.gene65310.t1

MQNPKPNPSENSTPTNNKSPQDPPSDDESLKETNPTTLQSSLSMEEDDVLKTALEVLVEFRARENGKLAADGDGGSAGPAMKRRKSNICEVNDVSPYCHRCKHVFPTWAAVMKHLQEHYFCCHPNGFSPPPGFYSLPSTSTAIPPQPDRYEANGDRGFDLNELPPNEEE