AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014330.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 115 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTGTATGTTAGAGAATA+TGG 0.234780 3:-53012742 MsG0380014330.01.T01:three_prime_UTR
TATTCGCCTTCACTTAATAT+AGG 0.333763 3:+53012785 None:intergenic
ATGTATTTCTTGTTGGATAA+TGG 0.346325 3:-53012645 MsG0380014330.01.T01:three_prime_UTR
GATGACATCATGGGCTCGTT+TGG 0.377074 3:+53014125 None:intergenic
CCCTCATTCATTTCAGATGT+TGG 0.390993 3:-53012577 MsG0380014330.01.T01:three_prime_UTR
AACTGTAACACGACATTATC+CGG 0.398657 3:+53012608 None:intergenic
AAATTCTCCAGCAACCAATC+TGG 0.400263 3:+53012716 None:intergenic
AATGGCATTTCTGTTGTTGC+CGG 0.437003 3:-53012627 MsG0380014330.01.T01:three_prime_UTR
GATATGTATGTATTTCTTGT+TGG 0.443075 3:-53012652 MsG0380014330.01.T01:three_prime_UTR
GATTCGATGAACATGTGTAT+AGG 0.444147 3:-53013049 MsG0380014330.01.T01:CDS
ATGGATCCCAGATTGGTTGC+TGG 0.458535 3:-53012723 MsG0380014330.01.T01:three_prime_UTR
AGAGAATATGGATCCCAGAT+TGG 0.463662 3:-53012730 MsG0380014330.01.T01:three_prime_UTR
TCGCAGTGATGACCAGAGTT+AGG 0.478298 3:+53013970 None:intergenic
TACAAAACACAATAAGAAGT+TGG 0.483041 3:+53014091 None:intergenic
TCACTGCGACAATATGCTGC+TGG 0.508303 3:-53013956 MsG0380014330.01.T01:CDS
TTGCAGATTTCACCTAACTC+TGG 0.518466 3:-53013982 MsG0380014330.01.T01:intron
AATTCTCCAGCAACCAATCT+GGG 0.519667 3:+53012717 None:intergenic
ACCAACATCTGAAATGAATG+AGG 0.534895 3:+53012576 None:intergenic
ATGAACATTTGATGACATCA+TGG 0.539623 3:+53014115 None:intergenic
TGAACATTTGATGACATCAT+GGG 0.582658 3:+53014116 None:intergenic
CATCAATTTACTGAACAAAG+TGG 0.599574 3:+53013230 None:intergenic
AACATTTCATCATATCCTCA+AGG 0.603199 3:-53013082 MsG0380014330.01.T01:CDS
CTTAATATAGGTACTATGAG+TGG 0.606850 3:+53012797 None:intergenic
GAATCGTATCAAACTCCTTG+AGG 0.616247 3:+53013067 None:intergenic
ATAGTACCTATATTAAGTGA+AGG 0.620786 3:-53012791 MsG0380014330.01.T01:CDS
TGTGTATAGGCTATGTCTAG+AGG 0.627082 3:-53013036 MsG0380014330.01.T01:CDS
CCAACATCTGAAATGAATGA+GGG 0.630965 3:+53012577 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTTTTCATTTTCTAA+GGG + Chr3:53012869-53012888 None:intergenic 10.0%
!!! TTTTTTTTTTTCATTTTCTA+AGG + Chr3:53012870-53012889 None:intergenic 10.0%
!! AAACTAAATTTCACTAATAT+TGG + Chr3:53013368-53013387 None:intergenic 15.0%
!! AACTAAATTTCACTAATATT+GGG + Chr3:53013367-53013386 None:intergenic 15.0%
!!! TTTTTTTTTCATTTTCTAAG+GGG + Chr3:53012868-53012887 None:intergenic 15.0%
!! AAGATATTAGAAATATGTCA+AGG + Chr3:53012685-53012704 None:intergenic 20.0%
!!! AGTCATTGATTATTTTCTAA+GGG - Chr3:53014016-53014035 MsG0380014330.01.T01:intron 20.0%
!!! ATAGTTTTTTTTTTCTTAGC+TGG - Chr3:53013213-53013232 MsG0380014330.01.T01:CDS 20.0%
!!! TAGTTTTTTTTTTCTTAGCT+GGG - Chr3:53013214-53013233 MsG0380014330.01.T01:CDS 20.0%
! AGTTAATGAGTTAAAAAACC+AGG + Chr3:53013248-53013267 None:intergenic 25.0%
! ATAGTACCTATATTAAGTGA+AGG - Chr3:53013902-53013921 MsG0380014330.01.T01:intron 25.0%
! ATCGTCAAACTATTTACAAT+TGG + Chr3:53013508-53013527 None:intergenic 25.0%
! ATGACAAACATGACATTATA+TGG + Chr3:53013815-53013834 None:intergenic 25.0%
! ATGTATTTCTTGTTGGATAA+TGG - Chr3:53014048-53014067 MsG0380014330.01.T01:intron 25.0%
! GATATGTATGTATTTCTTGT+TGG - Chr3:53014041-53014060 MsG0380014330.01.T01:intron 25.0%
! GATATTACATTCTAAATGTG+TGG - Chr3:53013525-53013544 MsG0380014330.01.T01:intron 25.0%
! GTTAATGAGTTAAAAAACCA+GGG + Chr3:53013247-53013266 None:intergenic 25.0%
! TACAAAACACAATAAGAAGT+TGG + Chr3:53012605-53012624 None:intergenic 25.0%
! TAGACCAAACTAAAAGAAAA+CGG + Chr3:53012775-53012794 None:intergenic 25.0%
! TGTCTCATTAAGTGTAAAAA+CGG - Chr3:53013682-53013701 MsG0380014330.01.T01:intron 25.0%
! TTCTTGTATGTTAGAGAATA+TGG - Chr3:53013951-53013970 MsG0380014330.01.T01:CDS 25.0%
!!! GAGTCATTGATTATTTTCTA+AGG - Chr3:53014015-53014034 MsG0380014330.01.T01:intron 25.0%
AACATTTCATCATATCCTCA+AGG - Chr3:53013611-53013630 MsG0380014330.01.T01:intron 30.0%
AATAAGTTGTATGCCATTCT+TGG - Chr3:53012903-53012922 MsG0380014330.01.T01:intron 30.0%
AGACCAAACTAAAAGAAAAC+GGG + Chr3:53012774-53012793 None:intergenic 30.0%
CATCAATTTACTGAACAAAG+TGG + Chr3:53013466-53013485 None:intergenic 30.0%
CTTAATATAGGTACTATGAG+TGG + Chr3:53013899-53013918 None:intergenic 30.0%
GTCTCATTAAGTGTAAAAAC+GGG - Chr3:53013683-53013702 MsG0380014330.01.T01:intron 30.0%
TATTCGCCTTCACTTAATAT+AGG + Chr3:53013911-53013930 None:intergenic 30.0%
TTGATATGACCTATGAAACA+CGG + Chr3:53013184-53013203 None:intergenic 30.0%
! ATGAACATTTGATGACATCA+TGG + Chr3:53012581-53012600 None:intergenic 30.0%
! GACATGATTTTGTGTGTTTT+TGG - Chr3:53013028-53013047 MsG0380014330.01.T01:CDS 30.0%
! GAGATTAACTGACATTTTGA+TGG - Chr3:53013744-53013763 MsG0380014330.01.T01:intron 30.0%
! GTTTGGTCTAAAGTCAATAA+AGG - Chr3:53012785-53012804 MsG0380014330.01.T01:CDS 30.0%
! TATAATCATAAGTGCTGTGT+TGG + Chr3:53013119-53013138 None:intergenic 30.0%
! TCAGCATGAAGTTATTTCAT+GGG + Chr3:53012937-53012956 None:intergenic 30.0%
! TGAACATTTGATGACATCAT+GGG + Chr3:53012580-53012599 None:intergenic 30.0%
!! ATGCTTTTTAGGGAATTGAT+TGG - Chr3:53013433-53013452 MsG0380014330.01.T01:intron 30.0%
!! CATTGATTATTTTCTAAGGG+TGG - Chr3:53014019-53014038 MsG0380014330.01.T01:intron 30.0%
!! TGCTTTTTAGGGAATTGATT+GGG - Chr3:53013434-53013453 MsG0380014330.01.T01:intron 30.0%
AACTGTAACACGACATTATC+CGG + Chr3:53014088-53014107 None:intergenic 35.0%
ACATGTGTTATAGAGCCTAT+TGG + Chr3:53012657-53012676 None:intergenic 35.0%
ACTTACATTTGTTTCCACGA+GGG + Chr3:53013322-53013341 None:intergenic 35.0%
CAAAATCATGTCTGAGTGTA+AGG + Chr3:53013020-53013039 None:intergenic 35.0%
CAAATAGAAATTGTGCACCT+TGG - Chr3:53012816-53012835 MsG0380014330.01.T01:CDS 35.0%
GATTCGATGAACATGTGTAT+AGG - Chr3:53013644-53013663 MsG0380014330.01.T01:intron 35.0%
GATTCTTTAGTGATGCCAAT+AGG - Chr3:53012639-53012658 MsG0380014330.01.T01:three_prime_UTR 35.0%
TAAGGGGTAAATTCCTTATC+CGG + Chr3:53012852-53012871 None:intergenic 35.0%
TATTACGTCTCTCCTAAGAA+GGG - Chr3:53013406-53013425 MsG0380014330.01.T01:intron 35.0%
TTCCAAATCATTATCCGTGT+CGG - Chr3:53013155-53013174 MsG0380014330.01.T01:intron 35.0%
TTGATGGAATTCTCAGACAA+AGG - Chr3:53013760-53013779 MsG0380014330.01.T01:intron 35.0%
! AAAAGCATAATGCCCTTCTT+AGG + Chr3:53013421-53013440 None:intergenic 35.0%
! ACCAACATCTGAAATGAATG+AGG + Chr3:53014120-53014139 None:intergenic 35.0%
! CCAACATCTGAAATGAATGA+GGG + Chr3:53014119-53014138 None:intergenic 35.0%
! GTCAGCATGAAGTTATTTCA+TGG + Chr3:53012938-53012957 None:intergenic 35.0%
!! AGTCCCGTTTTCTTTTAGTT+TGG - Chr3:53012768-53012787 MsG0380014330.01.T01:exon 35.0%
!! GCTTTTTAGGGAATTGATTG+GGG - Chr3:53013435-53013454 MsG0380014330.01.T01:intron 35.0%
!!! AGAAGGGCATTATGCTTTTT+AGG - Chr3:53013422-53013441 MsG0380014330.01.T01:intron 35.0%
!!! AGCTCAACTTTTTTGAGCTA+AGG + Chr3:53013279-53013298 None:intergenic 35.0%
!!! GAAGGGCATTATGCTTTTTA+GGG - Chr3:53013423-53013442 MsG0380014330.01.T01:intron 35.0%
!!! GCTCAACTTTTTTGAGCTAA+GGG + Chr3:53013278-53013297 None:intergenic 35.0%
!!! TATGTCCAGAGGCTTTTTTT+GGG - Chr3:53013706-53013725 MsG0380014330.01.T01:intron 35.0%
!!! TGTGTTTTTGGTCATAAGCA+CGG - Chr3:53013040-53013059 MsG0380014330.01.T01:CDS 35.0%
AAAAAGTTGAGCTACCCAAC+CGG - Chr3:53013286-53013305 MsG0380014330.01.T01:intron 40.0%
AAATTCTCCAGCAACCAATC+TGG + Chr3:53013980-53013999 None:intergenic 40.0%
AAGGGGTAAATTCCTTATCC+GGG + Chr3:53012851-53012870 None:intergenic 40.0%
AATGGCATTTCTGTTGTTGC+CGG - Chr3:53014066-53014085 MsG0380014330.01.T01:intron 40.0%
AATTCTCCAGCAACCAATCT+GGG + Chr3:53013979-53013998 None:intergenic 40.0%
AGAGAATATGGATCCCAGAT+TGG - Chr3:53013963-53013982 MsG0380014330.01.T01:CDS 40.0%
ATGGGCAAGAAATCCAAGAA+TGG + Chr3:53012919-53012938 None:intergenic 40.0%
CCCTCATTCATTTCAGATGT+TGG - Chr3:53014116-53014135 MsG0380014330.01.T01:CDS 40.0%
CCTGATACAAGAAAAGACCA+AGG + Chr3:53013846-53013865 None:intergenic 40.0%
CTATTACGTCTCTCCTAAGA+AGG - Chr3:53013405-53013424 MsG0380014330.01.T01:intron 40.0%
CTGAGTGTAAGGAACATCTA+TGG + Chr3:53013009-53013028 None:intergenic 40.0%
GAATCGTATCAAACTCCTTG+AGG + Chr3:53013629-53013648 None:intergenic 40.0%
GACTTACATTTGTTTCCACG+AGG + Chr3:53013323-53013342 None:intergenic 40.0%
GTAAGTCAAGCCTTCATAGA+TGG - Chr3:53013336-53013355 MsG0380014330.01.T01:intron 40.0%
TATCCGGGGAAAATAAACCA+AGG + Chr3:53012836-53012855 None:intergenic 40.0%
TGTGTATAGGCTATGTCTAG+AGG - Chr3:53013657-53013676 MsG0380014330.01.T01:intron 40.0%
TTGCAGATTTCACCTAACTC+TGG - Chr3:53012711-53012730 MsG0380014330.01.T01:three_prime_UTR 40.0%
! GGTCTTTTCTTGTATCAGGT+GGG - Chr3:53013847-53013866 MsG0380014330.01.T01:intron 40.0%
! TGGTCTTTTCTTGTATCAGG+TGG - Chr3:53013846-53013865 MsG0380014330.01.T01:intron 40.0%
!! CCTTGGTCTTTTCTTGTATC+AGG - Chr3:53013843-53013862 MsG0380014330.01.T01:intron 40.0%
!! TGGTTTATTTTCCCCGGATA+AGG - Chr3:53012836-53012855 MsG0380014330.01.T01:intron 40.0%
!!! ATGTCCAGAGGCTTTTTTTG+GGG - Chr3:53013707-53013726 MsG0380014330.01.T01:intron 40.0%
!!! GTATGTCCAGAGGCTTTTTT+TGG - Chr3:53013705-53013724 MsG0380014330.01.T01:intron 40.0%
ACTAGGACATACCTAATCCG+AGG + Chr3:53013071-53013090 None:intergenic 45.0%
AGACGTAATAGCAACGCTCA+AGG + Chr3:53013396-53013415 None:intergenic 45.0%
AGGGGTAAATTCCTTATCCG+GGG + Chr3:53012850-53012869 None:intergenic 45.0%
CACCGACACGGATAATGATT+TGG + Chr3:53013160-53013179 None:intergenic 45.0%
GATTAGGTATGTCCTAGTGG+CGG - Chr3:53013073-53013092 MsG0380014330.01.T01:CDS 45.0%
GTAAAAACGGGTATGTCCAG+AGG - Chr3:53013695-53013714 MsG0380014330.01.T01:intron 45.0%
GTTTGTCATTGTGCTCACCT+TGG - Chr3:53013826-53013845 MsG0380014330.01.T01:intron 45.0%
TTGGGCTCATCCATCTATGA+AGG + Chr3:53013349-53013368 None:intergenic 45.0%
! TCGGATTAGGTATGTCCTAG+TGG - Chr3:53013070-53013089 MsG0380014330.01.T01:CDS 45.0%
!! GCACCTTGGTTTATTTTCCC+CGG - Chr3:53012830-53012849 MsG0380014330.01.T01:CDS 45.0%
!!! TTTTTTTGGGGAGGAGGATG+TGG - Chr3:53013719-53013738 MsG0380014330.01.T01:intron 45.0%
AGGGCTGTTATGAACCGGTT+GGG + Chr3:53013303-53013322 None:intergenic 50.0%
ATGAAACACGGACACCGACA+CGG + Chr3:53013172-53013191 None:intergenic 50.0%
GATGACATCATGGGCTCGTT+TGG + Chr3:53012571-53012590 None:intergenic 50.0%
TCACTGCGACAATATGCTGC+TGG - Chr3:53012737-53012756 MsG0380014330.01.T01:three_prime_UTR 50.0%
TCATAAGCACGGACACTCCT+CGG - Chr3:53013051-53013070 MsG0380014330.01.T01:CDS 50.0%
TCCTCCCCAAAAAAAGCCTC+TGG + Chr3:53013714-53013733 None:intergenic 50.0%
TCGCAGTGATGACCAGAGTT+AGG + Chr3:53012726-53012745 None:intergenic 50.0%
! ATGGATCCCAGATTGGTTGC+TGG - Chr3:53013970-53013989 MsG0380014330.01.T01:CDS 50.0%
! TGTCGGTGTCCGTGTTTCAT+AGG - Chr3:53013172-53013191 MsG0380014330.01.T01:intron 50.0%
!!! AGAGGCTTTTTTTGGGGAGG+AGG - Chr3:53013713-53013732 MsG0380014330.01.T01:intron 50.0%
!!! TCCAGAGGCTTTTTTTGGGG+AGG - Chr3:53013710-53013729 MsG0380014330.01.T01:intron 50.0%
CCACGAGGGCTGTTATGAAC+CGG + Chr3:53013308-53013327 None:intergenic 55.0%
GAGGGCTGTTATGAACCGGT+TGG + Chr3:53013304-53013323 None:intergenic 55.0%
!! TTTTGGGGAGGAGGATGTGG+AGG - Chr3:53013722-53013741 MsG0380014330.01.T01:intron 55.0%
ATTGACGCGTGTCCGCCACT+AGG + Chr3:53013088-53013107 None:intergenic 60.0%
CCGGTTCATAACAGCCCTCG+TGG - Chr3:53013305-53013324 MsG0380014330.01.T01:intron 60.0%
CTTAGCTGGGAGCTGAACCC+TGG - Chr3:53013227-53013246 MsG0380014330.01.T01:CDS 60.0%
GCACGGACACTCCTCGGATT+AGG - Chr3:53013057-53013076 MsG0380014330.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 53012558 53014157 53012558 ID=MsG0380014330.01;Name=MsG0380014330.01
Chr3 mRNA 53012558 53014157 53012558 ID=MsG0380014330.01.T01;Parent=MsG0380014330.01;Name=MsG0380014330.01.T01;_AED=0.50;_eAED=0.72;_QI=0|0|0.4|1|0|0.2|5|226|127
Chr3 exon 53012558 53012850 53012558 ID=MsG0380014330.01.T01:exon:9855;Parent=MsG0380014330.01.T01
Chr3 exon 53013011 53013122 53013011 ID=MsG0380014330.01.T01:exon:9854;Parent=MsG0380014330.01.T01
Chr3 exon 53013205 53013271 53013205 ID=MsG0380014330.01.T01:exon:9853;Parent=MsG0380014330.01.T01
Chr3 exon 53013951 53013998 53013951 ID=MsG0380014330.01.T01:exon:9852;Parent=MsG0380014330.01.T01
Chr3 exon 53014068 53014157 53014068 ID=MsG0380014330.01.T01:exon:9851;Parent=MsG0380014330.01.T01
Chr3 CDS 53014068 53014157 53014068 ID=MsG0380014330.01.T01:cds;Parent=MsG0380014330.01.T01
Chr3 CDS 53013951 53013998 53013951 ID=MsG0380014330.01.T01:cds;Parent=MsG0380014330.01.T01
Chr3 CDS 53013205 53013271 53013205 ID=MsG0380014330.01.T01:cds;Parent=MsG0380014330.01.T01
Chr3 CDS 53013011 53013122 53013011 ID=MsG0380014330.01.T01:cds;Parent=MsG0380014330.01.T01
Chr3 CDS 53012784 53012850 53012784 ID=MsG0380014330.01.T01:cds;Parent=MsG0380014330.01.T01
Chr3 three_prime_UTR 53012558 53012783 53012558 ID=MsG0380014330.01.T01:three_prime_utr;Parent=MsG0380014330.01.T01
Gene Sequence

>MsG0380014330.01.T01

ATGTTACAAACCAAACGAGCCCATGATGTCATCAAATGTTCATTCCAACTTCTTATTGTGTTTTGTAAAGCTCAGCATTCAGATTCTTTAATTTCACCTAACTCTGGTCATCACTGCGACAATATGCTGCTGGATGATGGAATTGATTGGGGCATTGCCACTTTGTTCAGTAAATTGATGTTTGTATATAATAACATGTCCAATTTTTCTGTTAATCATTATGAACATTTCATCATATCCTCAAGGAGTTTGATACGATTCGATGAACATGTGTATAGGCTATGTCTAGAGGTTTGTCTCATTAAGTGTAAAAACGGGTGGGCGATTGTATATCTAGCACAAATGAAACCACTCATAGTACCTATATTAAGTGAAGGCGAATAA

Protein sequence

>MsG0380014330.01.T01

MLQTKRAHDVIKCSFQLLIVFCKAQHSDSLISPNSGHHCDNMLLDDGIDWGIATLFSKLMFVYNNMSNFSVNHYEHFIISSRSLIRFDEHVYRLCLEVCLIKCKNGWAIVYLAQMKPLIVPILSEGE*