AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64866

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64866.t1 MTR_5g023900 73.934 211 25 3 1 201 1 191 5.60e-103 295
MS.gene64866.t1 MTR_5g023880 71.144 201 29 4 1 201 1 172 1.52e-92 268
MS.gene64866.t1 MTR_5g023870 55.975 159 30 4 1 159 1 119 1.10e-49 157
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 68 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTAGTTGGGTTGGTTTCTT+TGG 0.162115 5.3:-13775917 None:intergenic
TTCTCGGAAGGGTTAGGTTT+AGG 0.237072 5.3:-13775838 None:intergenic
AACCGCTCTCGAAGTCTTAA+TGG 0.238654 5.3:+13775981 MS.gene64866:CDS
CCTTCAAAGTTCTTTAAGTA+TGG 0.240152 5.3:+13775939 MS.gene64866:CDS
TGTTTGCATCTATAACAATT+TGG 0.250606 5.3:-13776123 None:intergenic
GTAGTTGGGTTGGTTTCTTT+GGG 0.266039 5.3:-13775916 None:intergenic
TCTCGGAAGGGTTAGGTTTA+GGG 0.267292 5.3:-13775837 None:intergenic
AATGGTTTGTCAGCAGCTTC+TGG 0.287143 5.3:+13776210 MS.gene64866:CDS
TTGAGGGGACTTGTTGTTGG+TGG 0.289994 5.3:-13775869 None:intergenic
TCTGATGAAGGCGAAGGTTT+AGG 0.328241 5.3:+13776794 MS.gene64866:CDS
ATACATCACTCTTCTTCATT+AGG 0.332064 5.3:-13776839 None:intergenic
GTCTTGAGGGGACTTGTTGT+TGG 0.343036 5.3:-13775872 None:intergenic
TAGTTGGGTTGGTTTCTTTG+GGG 0.344689 5.3:-13775915 None:intergenic
GTTGAATTCTCGGAAGGGTT+AGG 0.378551 5.3:-13775844 None:intergenic
AAAGAACTTTGAAGGGTAGT+TGG 0.393444 5.3:-13775931 None:intergenic
TGAGGGGACTTGTTGTTGGT+GGG 0.402381 5.3:-13775868 None:intergenic
AGGGGACTTGTTGTTGGTGG+GGG 0.408399 5.3:-13775866 None:intergenic
AGGTGGGGTGGTTGTTGATG+TGG 0.426505 5.3:-13776250 None:intergenic
AAGAACTTTGAAGGGTAGTT+GGG 0.431057 5.3:-13775930 None:intergenic
CACTTCCTCCTCTTCATAGC+TGG 0.432066 5.3:-13776063 None:intergenic
GAGTTCAGAGCTCGTGAGAA+TGG 0.435144 5.3:+13776003 MS.gene64866:CDS
ACCTCAACCTGATCAATATG+AGG 0.437745 5.3:+13776269 MS.gene64866:CDS
TAACAATTTGGATATATAGA+AGG 0.438362 5.3:-13776111 None:intergenic
CATCAGAGGGAGGGTCTTGA+GGG 0.445658 5.3:-13775885 None:intergenic
CCATACTTAAAGAACTTTGA+AGG 0.446994 5.3:-13775939 None:intergenic
CCCTCATATTGATCAGGTTG+AGG 0.453934 5.3:-13776270 None:intergenic
GAAGCTGCTGACAAACCATT+AGG 0.476282 5.3:-13776207 None:intergenic
GCAAACATGTGTTTCCCACT+TGG 0.483219 5.3:+13776139 MS.gene64866:CDS
ACTTTGAAGGGTAGTTGGGT+TGG 0.489348 5.3:-13775926 None:intergenic
GGTCCTCTATCTCCATTGGC+TGG 0.500299 5.3:-13776727 None:intergenic
CATATTGATCAGGTTGAGGT+GGG 0.500892 5.3:-13776266 None:intergenic
TCATCAGAGGGAGGGTCTTG+AGG 0.508193 5.3:-13775886 None:intergenic
AGTTCAGAGCTCGTGAGAAT+GGG 0.512950 5.3:+13776004 MS.gene64866:CDS
AGCTCGTGAGAATGGGAAGC+TGG 0.512973 5.3:+13776011 MS.gene64866:CDS
AGTTGGGTTGGTTTCTTTGG+GGG 0.515909 5.3:-13775914 None:intergenic
CATCACTCTTCTTCATTAGG+AGG 0.517441 5.3:-13776836 None:intergenic
GAGGGGTCCTCTATCTCCAT+TGG 0.519182 5.3:-13776731 None:intergenic
AAGCCAGCCAATGGAGATAG+AGG 0.520626 5.3:+13776724 MS.gene64866:CDS
GACTGCATTGATGAACCATA+TGG 0.524295 5.3:+13776161 MS.gene64866:CDS
TTGATCAGGTTGAGGTGGGG+TGG 0.536734 5.3:-13776262 None:intergenic
GAGGGGACTTGTTGTTGGTG+GGG 0.544991 5.3:-13775867 None:intergenic
AATGGGAAGCTGGCAGCTGA+TGG 0.545369 5.3:+13776021 MS.gene64866:CDS
TCAAAGTTCTTTAAGTATGG+AGG 0.546799 5.3:+13775942 MS.gene64866:CDS
CATACTTAAAGAACTTTGAA+GGG 0.549185 5.3:-13775938 None:intergenic
TCATATTGATCAGGTTGAGG+TGG 0.558741 5.3:-13776267 None:intergenic
GTGTAATATTCGTGAAGTGA+AGG 0.578344 5.3:+13776083 MS.gene64866:CDS
TGATGATGAAAGCCAGCCAA+TGG 0.578386 5.3:+13776715 MS.gene64866:CDS
CTGGCAGCTGATGGAGAAGG+TGG 0.580844 5.3:+13776030 MS.gene64866:CDS
GGGGTGGTTGTTGATGTGGA+AGG 0.586960 5.3:-13776246 None:intergenic
ATATTGATCAGGTTGAGGTG+GGG 0.595131 5.3:-13776265 None:intergenic
CTCCATTAAGACTTCGAGAG+CGG 0.599694 5.3:-13775983 None:intergenic
ATGGTCCAGCTATGAAGAGG+AGG 0.603822 5.3:+13776058 MS.gene64866:CDS
CTCGGATGCAACATCATCAG+AGG 0.604023 5.3:-13776750 None:intergenic
GGGGATTCATCATCAGAGGG+AGG 0.610326 5.3:-13775895 None:intergenic
TCGGATGCAACATCATCAGA+GGG 0.613962 5.3:-13776749 None:intergenic
GATGGAGAAGGTGGAAGTGA+TGG 0.614959 5.3:+13776039 MS.gene64866:CDS
ACTGCATCTGAGTCTGATGA+AGG 0.623088 5.3:+13776782 MS.gene64866:CDS
AATTTGGATATATAGAAGGA+TGG 0.631395 5.3:-13776107 None:intergenic
TCTGAGTCTGATGAAGGCGA+AGG 0.633192 5.3:+13776788 MS.gene64866:CDS
TTCATCAATGCAGTCCAAGT+GGG 0.634799 5.3:-13776153 None:intergenic
GTGATGGTCCAGCTATGAAG+AGG 0.637063 5.3:+13776055 MS.gene64866:CDS
AAGCTGGCAGCTGATGGAGA+AGG 0.643145 5.3:+13776027 MS.gene64866:CDS
GTTCATCAATGCAGTCCAAG+TGG 0.645025 5.3:-13776154 None:intergenic
AGATGCAGTATCATCAGACT+CGG 0.649465 5.3:-13776768 None:intergenic
CCTCAACCTGATCAATATGA+GGG 0.650750 5.3:+13776270 MS.gene64866:CDS
ATCAGAGGGAGGGTCTTGAG+GGG 0.650850 5.3:-13775884 None:intergenic
GGGATTCATCATCAGAGGGA+GGG 0.659890 5.3:-13775894 None:intergenic
CGGATGCAACATCATCAGAG+GGG 0.768604 5.3:-13776748 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTTGAATTAGAAAATT+AGG - chr5.3:13776307-13776326 None:intergenic 15.0%
!! TTATAATTATAATTGCTTCA+TGG - chr5.3:13776667-13776686 None:intergenic 15.0%
!! AACATTACATAATTGAATCT+TGG - chr5.3:13776415-13776434 None:intergenic 20.0%
!! TAACAATTTGGATATATAGA+AGG - chr5.3:13776114-13776133 None:intergenic 20.0%
!!! AATGTTTTTCTTTTGTTACT+AGG + chr5.3:13776692-13776711 MS.gene64866:intron 20.0%
!!! TTTTTCGCACTATAATTTTT+AGG + chr5.3:13776345-13776364 MS.gene64866:intron 20.0%
! AATTTGGATATATAGAAGGA+TGG - chr5.3:13776110-13776129 None:intergenic 25.0%
! CATACTTAAAGAACTTTGAA+GGG - chr5.3:13775941-13775960 None:intergenic 25.0%
! CATATATATGTTTGTGTGTA+TGG - chr5.3:13776516-13776535 None:intergenic 25.0%
! TGTTTGCATCTATAACAATT+TGG - chr5.3:13776126-13776145 None:intergenic 25.0%
! TTATGAGATCAAATTCATGT+AGG + chr5.3:13776559-13776578 MS.gene64866:intron 25.0%
AAAAATGGTGTTCTTCCATA+TGG - chr5.3:13776179-13776198 None:intergenic 30.0%
CATTAGGATCACAACAAAAA+TGG - chr5.3:13776194-13776213 None:intergenic 30.0%
CCATACTTAAAGAACTTTGA+AGG - chr5.3:13775942-13775961 None:intergenic 30.0%
CCTTCAAAGTTCTTTAAGTA+TGG + chr5.3:13775939-13775958 MS.gene64866:CDS 30.0%
TATATAGCCAATAAAACCCT+AGG - chr5.3:13776386-13776405 None:intergenic 30.0%
TCAAAGTTCTTTAAGTATGG+AGG + chr5.3:13775942-13775961 MS.gene64866:CDS 30.0%
!! CATTTTTGTTGTGATCCTAA+TGG + chr5.3:13776192-13776211 MS.gene64866:CDS 30.0%
GTGTAATATTCGTGAAGTGA+AGG + chr5.3:13776083-13776102 MS.gene64866:CDS 35.0%
! AAAGAACTTTGAAGGGTAGT+TGG - chr5.3:13775934-13775953 None:intergenic 35.0%
! AAGAACTTTGAAGGGTAGTT+GGG - chr5.3:13775933-13775952 None:intergenic 35.0%
! GTTTTACCCTCATATTGATC+AGG - chr5.3:13776279-13776298 None:intergenic 35.0%
ACCTCAACCTGATCAATATG+AGG + chr5.3:13776269-13776288 MS.gene64866:CDS 40.0%
AGATGCAGTATCATCAGACT+CGG - chr5.3:13776771-13776790 None:intergenic 40.0%
CCAATAAAACCCTAGGTCAT+TGG - chr5.3:13776379-13776398 None:intergenic 40.0%
CCTCAACCTGATCAATATGA+GGG + chr5.3:13776270-13776289 MS.gene64866:CDS 40.0%
TTCATCAATGCAGTCCAAGT+GGG - chr5.3:13776156-13776175 None:intergenic 40.0%
! GACTGCATTGATGAACCATA+TGG + chr5.3:13776161-13776180 MS.gene64866:CDS 40.0%
!! ATATTGATCAGGTTGAGGTG+GGG - chr5.3:13776268-13776287 None:intergenic 40.0%
!! CATATTGATCAGGTTGAGGT+GGG - chr5.3:13776269-13776288 None:intergenic 40.0%
!! CCAATGACCTAGGGTTTTAT+TGG + chr5.3:13776376-13776395 MS.gene64866:intron 40.0%
!! GTAGTTGGGTTGGTTTCTTT+GGG - chr5.3:13775919-13775938 None:intergenic 40.0%
!! TAGTTGGGTTGGTTTCTTTG+GGG - chr5.3:13775918-13775937 None:intergenic 40.0%
!! TCATATTGATCAGGTTGAGG+TGG - chr5.3:13776270-13776289 None:intergenic 40.0%
AACCGCTCTCGAAGTCTTAA+TGG + chr5.3:13775981-13776000 MS.gene64866:CDS 45.0%
ACTGCATCTGAGTCTGATGA+AGG + chr5.3:13776782-13776801 MS.gene64866:CDS 45.0%
AGTTCAGAGCTCGTGAGAAT+GGG + chr5.3:13776004-13776023 MS.gene64866:CDS 45.0%
CTCCATTAAGACTTCGAGAG+CGG - chr5.3:13775986-13776005 None:intergenic 45.0%
GAAGCTGCTGACAAACCATT+AGG - chr5.3:13776210-13776229 None:intergenic 45.0%
GCAAACATGTGTTTCCCACT+TGG + chr5.3:13776139-13776158 MS.gene64866:CDS 45.0%
GTCAACACTCCAATGACCTA+GGG + chr5.3:13776367-13776386 MS.gene64866:intron 45.0%
GTTCATCAATGCAGTCCAAG+TGG - chr5.3:13776157-13776176 None:intergenic 45.0%
GTTGAATTCTCGGAAGGGTT+AGG - chr5.3:13775847-13775866 None:intergenic 45.0%
TCGGATGCAACATCATCAGA+GGG - chr5.3:13776752-13776771 None:intergenic 45.0%
TCTCGGAAGGGTTAGGTTTA+GGG - chr5.3:13775840-13775859 None:intergenic 45.0%
TCTGATGAAGGCGAAGGTTT+AGG + chr5.3:13776794-13776813 MS.gene64866:CDS 45.0%
TTCTCGGAAGGGTTAGGTTT+AGG - chr5.3:13775841-13775860 None:intergenic 45.0%
TTGGGGGATTCATCATCAGA+GGG - chr5.3:13775901-13775920 None:intergenic 45.0%
TTTGGGGGATTCATCATCAG+AGG - chr5.3:13775902-13775921 None:intergenic 45.0%
! AATGGTTTGTCAGCAGCTTC+TGG + chr5.3:13776210-13776229 MS.gene64866:CDS 45.0%
! ACTTTGAAGGGTAGTTGGGT+TGG - chr5.3:13775929-13775948 None:intergenic 45.0%
! CCCTCATATTGATCAGGTTG+AGG - chr5.3:13776273-13776292 None:intergenic 45.0%
! TGATGATGAAAGCCAGCCAA+TGG + chr5.3:13776715-13776734 MS.gene64866:CDS 45.0%
!! AGTTGGGTTGGTTTCTTTGG+GGG - chr5.3:13775917-13775936 None:intergenic 45.0%
!! GGTAGTTGGGTTGGTTTCTT+TGG - chr5.3:13775920-13775939 None:intergenic 45.0%
!!! TAATTTTTTTTTTAACTAAT+CGG + chr5.3:13776597-13776616 MS.gene64866:intron 5.0%
AAGCCAGCCAATGGAGATAG+AGG + chr5.3:13776724-13776743 MS.gene64866:CDS 50.0%
ATGGTCCAGCTATGAAGAGG+AGG + chr5.3:13776058-13776077 MS.gene64866:CDS 50.0%
CACTTCCTCCTCTTCATAGC+TGG - chr5.3:13776066-13776085 None:intergenic 50.0%
CGGATGCAACATCATCAGAG+GGG - chr5.3:13776751-13776770 None:intergenic 50.0%
CTCGGATGCAACATCATCAG+AGG - chr5.3:13776753-13776772 None:intergenic 50.0%
GAGTTCAGAGCTCGTGAGAA+TGG + chr5.3:13776003-13776022 MS.gene64866:CDS 50.0%
GATGGAGAAGGTGGAAGTGA+TGG + chr5.3:13776039-13776058 MS.gene64866:CDS 50.0%
GGGATTCATCATCAGAGGGA+GGG - chr5.3:13775897-13775916 None:intergenic 50.0%
GGTCAACACTCCAATGACCT+AGG + chr5.3:13776366-13776385 MS.gene64866:intron 50.0%
GTGATGGTCCAGCTATGAAG+AGG + chr5.3:13776055-13776074 MS.gene64866:CDS 50.0%
TCTGAGTCTGATGAAGGCGA+AGG + chr5.3:13776788-13776807 MS.gene64866:CDS 50.0%
TGGGGGTTGAATTCTCGGAA+GGG - chr5.3:13775852-13775871 None:intergenic 50.0%
! AGACTTCGAGAGCGGTTTTC+AGG - chr5.3:13775978-13775997 None:intergenic 50.0%
! GTTGGTGGGGGTTGAATTCT+CGG - chr5.3:13775857-13775876 None:intergenic 50.0%
!! GTCTTGAGGGGACTTGTTGT+TGG - chr5.3:13775875-13775894 None:intergenic 50.0%
!! TGAGGGGACTTGTTGTTGGT+GGG - chr5.3:13775871-13775890 None:intergenic 50.0%
!! TTGAGGGGACTTGTTGTTGG+TGG - chr5.3:13775872-13775891 None:intergenic 50.0%
AAGCTGGCAGCTGATGGAGA+AGG + chr5.3:13776027-13776046 MS.gene64866:CDS 55.0%
AATGGGAAGCTGGCAGCTGA+TGG + chr5.3:13776021-13776040 MS.gene64866:CDS 55.0%
AGCTCGTGAGAATGGGAAGC+TGG + chr5.3:13776011-13776030 MS.gene64866:CDS 55.0%
AGGTGGGGTGGTTGTTGATG+TGG - chr5.3:13776253-13776272 None:intergenic 55.0%
ATCAGAGGGAGGGTCTTGAG+GGG - chr5.3:13775887-13775906 None:intergenic 55.0%
CATCAGAGGGAGGGTCTTGA+GGG - chr5.3:13775888-13775907 None:intergenic 55.0%
GAGGGGTCCTCTATCTCCAT+TGG - chr5.3:13776734-13776753 None:intergenic 55.0%
GGGGATTCATCATCAGAGGG+AGG - chr5.3:13775898-13775917 None:intergenic 55.0%
GGGGTGGTTGTTGATGTGGA+AGG - chr5.3:13776249-13776268 None:intergenic 55.0%
GGTCCTCTATCTCCATTGGC+TGG - chr5.3:13776730-13776749 None:intergenic 55.0%
GTGGGGGTTGAATTCTCGGA+AGG - chr5.3:13775853-13775872 None:intergenic 55.0%
TCATCAGAGGGAGGGTCTTG+AGG - chr5.3:13775889-13775908 None:intergenic 55.0%
!! AGGGGACTTGTTGTTGGTGG+GGG - chr5.3:13775869-13775888 None:intergenic 55.0%
!! GAGGGGACTTGTTGTTGGTG+GGG - chr5.3:13775870-13775889 None:intergenic 55.0%
!! TTGATCAGGTTGAGGTGGGG+TGG - chr5.3:13776265-13776284 None:intergenic 55.0%
CTGGCAGCTGATGGAGAAGG+TGG + chr5.3:13776030-13776049 MS.gene64866:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 13775829 13776856 13775829 ID=MS.gene64866
chr5.3 mRNA 13775829 13776856 13775829 ID=MS.gene64866.t1;Parent=MS.gene64866
chr5.3 exon 13775829 13776291 13775829 ID=MS.gene64866.t1.exon1;Parent=MS.gene64866.t1
chr5.3 CDS 13775829 13776291 13775829 ID=cds.MS.gene64866.t1;Parent=MS.gene64866.t1
chr5.3 exon 13776714 13776856 13776714 ID=MS.gene64866.t1.exon2;Parent=MS.gene64866.t1
chr5.3 CDS 13776714 13776856 13776714 ID=cds.MS.gene64866.t1;Parent=MS.gene64866.t1
Gene Sequence

>MS.gene64866

ATGCAGAACCCTAAACCTAACCCTTCCGAGAATTCAACCCCCACCAACAACAAGTCCCCTCAAGACCCTCCCTCTGATGATGAATCCCCCAAAGAAACCAACCCAACTACCCTTCAAAGTTCTTTAAGTATGGAGGAAGAAGATGTCCTGAAAACCGCTCTCGAAGTCTTAATGGAGTTCAGAGCTCGTGAGAATGGGAAGCTGGCAGCTGATGGAGAAGGTGGAAGTGATGGTCCAGCTATGAAGAGGAGGAAGTGTAATATTCGTGAAGTGAAGGACCATCCTTCTATATATCCAAATTGTTATAGATGCAAACATGTGTTTCCCACTTGGACTGCATTGATGAACCATATGGAAGAACACCATTTTTGTTGTGATCCTAATGGTTTGTCAGCAGCTTCTGGTTTTTCTGCACTTCCTTCCACATCAACAACCACCCCACCTCAACCTGATCAATATGAGGGTAAAACTAAAACCTAATTTTCTAATTCAAACTATTTATTGTCATGTTTTTTTTTTTTCGCACTATAATTTTTAGGTCAACACTCCAATGACCTAGGGTTTTATTGGCTATATATCATGTCCAAGATTCAATTATGTAATGTTATGTCATTTTTTTTTTTTTTACATTTAATTATTTTGATTTCAAAGCACTTGTGTATAGAACATTCATAAAAGATTGTACCATACACACAAACATATATATGTTCACTTTGAGTGTTGCTTAAGTTTATGAGATCAAATTCATGTAGGCATCTAGATATAACTTAATTTTTTTTTTAACTAATCGGTTTTTAATTTGACGATTTGCTTTTTCTTCAAACTAATGTTTTTACCATGAAGCAATTATAATTATAATTTTGAATGTTTTTCTTTTGTTACTAGGTGATGATGAAAGCCAGCCAATGGAGATAGAGGACCCCTCTGATGATGTTGCATCCGAGTCTGATGATACTGCATCTGAGTCTGATGAAGGCGAAGGTTTAGGATTCGACTTGAACGAGTTGCCTCCTAATGAAGAAGAGTGA
Protein sequence

>MS.gene64866.t1

MQNPKPNPSENSTPTNNKSPQDPPSDDESPKETNPTTLQSSLSMEEEDVLKTALEVLMEFRARENGKLAADGEGGSDGPAMKRRKCNIREVKDHPSIYPNCYRCKHVFPTWTALMNHMEEHHFCCDPNGLSAASGFSALPSTSTTTPPQPDQYEGDDESQPMEIEDPSDDVASESDDTASESDEGEGLGFDLNELPPNEEE