AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480022954.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480022954.01.T01 MTR_8g080380 91.398 93 8 0 1 93 92 184 1.09e-60 183
MsG0480022954.01.T01 MTR_3g085510 77.419 93 21 0 1 93 1 93 3.63e-50 153
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480022954.01.T01 AT4G40042 77.215 79 18 0 1 79 1 79 3.56e-42 133
MsG0480022954.01.T01 AT2G22425 72.043 93 25 1 1 93 1 92 6.26e-42 132
MsG0480022954.01.T01 AT2G22425 72.043 93 25 1 1 93 1 92 6.26e-42 132

Find 35 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTTGCTGTGATTGCATT+TGG 0.297854 4:-78997308 MsG0480022954.01.T01:CDS
TTGCTTATGTTGGTACTTAG+TGG 0.361552 4:-78997066 MsG0480022954.01.T01:three_prime_UTR
GCCCCATTCACAGATGGTTC+TGG 0.371797 4:+78997131 None:intergenic
CATATGTGAGGATCATTGTT+TGG 0.377646 4:+78997261 None:intergenic
TTCACAGATGGTTCTGGCTT+AGG 0.396810 4:+78997137 None:intergenic
CTTTGCTTGATTAGATGGAT+TGG 0.415898 4:-78997376 MsG0480022954.01.T01:intron
ATGGTTGAAGAAGGGCCAAT+TGG 0.421141 4:+78997202 None:intergenic
AGCCAGAACCATCTGTGAAT+GGG 0.423930 4:-78997133 MsG0480022954.01.T01:CDS
CTCGGGTCCAACCACTTAAG+AGG 0.441788 4:+78997176 None:intergenic
TCAACCATCACCCTCTTAAG+TGG 0.455788 4:-78997187 MsG0480022954.01.T01:CDS
CATTAGTCACTATTCCCAAT+TGG 0.473943 4:-78997217 MsG0480022954.01.T01:CDS
CGAGAGAGAAACGGAGAAGA+AGG 0.482700 4:+78998098 None:intergenic
TTTGCTTGATTAGATGGATT+GGG 0.484747 4:-78997375 MsG0480022954.01.T01:intron
TGGTTGAAGAAGGGCCAATT+GGG 0.491266 4:+78997203 None:intergenic
AAGCCAGAACCATCTGTGAA+TGG 0.495835 4:-78997134 MsG0480022954.01.T01:CDS
TTCTCCGTTTCTCTCTCGAA+AGG 0.520672 4:-78998093 MsG0480022954.01.T01:intron
GCTGTGATTGCATTTGGAGC+TGG 0.523448 4:-78997302 MsG0480022954.01.T01:CDS
AAGAGGGTGATGGTTGAAGA+AGG 0.527062 4:+78997193 None:intergenic
TTTGTAGCCCCATTCACAGA+TGG 0.528383 4:+78997125 None:intergenic
ACAATGATCCTCACATATGC+TGG 0.532761 4:-78997257 MsG0480022954.01.T01:CDS
AGTACATCGTATTGTGGAGA+AGG 0.546779 4:+78996999 None:intergenic
CCATCACCCTCTTAAGTGGT+TGG 0.557168 4:-78997183 MsG0480022954.01.T01:CDS
ATTTGGAGCTGGATATCTCA+CGG 0.563264 4:-78997291 MsG0480022954.01.T01:CDS
GATACCTTTCGAGAGAGAAA+CGG 0.572798 4:+78998089 None:intergenic
GAGAGAAACGGAGAAGAAGG+TGG 0.586821 4:+78998101 None:intergenic
CTTGATTAGATGGATTGGGA+AGG 0.597000 4:-78997371 MsG0480022954.01.T01:intron
TCGGGTCCAACCACTTAAGA+GGG 0.612466 4:+78997177 None:intergenic
GCCAGAACCATCTGTGAATG+GGG 0.614435 4:-78997132 MsG0480022954.01.T01:CDS
AAGTTAAGTACATCGTATTG+TGG 0.615316 4:+78996993 None:intergenic
AGAGGGTGATGGTTGAAGAA+GGG 0.639069 4:+78997194 None:intergenic
CCAACCACTTAAGAGGGTGA+TGG 0.648150 4:+78997183 None:intergenic
GTGGTTGGACCCGAGCGAAG+CGG 0.659606 4:-78997168 MsG0480022954.01.T01:CDS
CAACACCACCAGCATATGTG+AGG 0.672885 4:+78997249 None:intergenic
ATGATCCTCACATATGCTGG+TGG 0.731619 4:-78997254 MsG0480022954.01.T01:CDS
ATTGGGAATAGTGACTAATG+TGG 0.776405 4:+78997220 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAAAATGTATAATGTTTT+TGG - Chr4:78997627-78997646 MsG0480022954.01.T01:intron 10.0%
!!! AAAACATTATACATTTTTTT+AGG + Chr4:78997627-78997646 None:intergenic 10.0%
!!! AAACATTATACATTTTTTTA+GGG + Chr4:78997626-78997645 None:intergenic 10.0%
!! AATATTAAGTATTAGATGTA+AGG - Chr4:78997410-78997429 MsG0480022954.01.T01:intron 15.0%
!! CATTTACTAACATAAAATTA+AGG + Chr4:78997389-78997408 None:intergenic 15.0%
!!! AAAATAAACCTACTTTTTAA+CGG + Chr4:78997974-78997993 None:intergenic 15.0%
!!! CTATATAATTGTTTTCTTTT+CGG - Chr4:78998107-78998126 MsG0480022954.01.T01:five_prime_UTR 15.0%
!! AAAGAAAACGAAAGTAAAAA+CGG + Chr4:78997022-78997041 None:intergenic 20.0%
!!! AGTTATAAGCATTTTAAAAC+TGG - Chr4:78997165-78997184 MsG0480022954.01.T01:CDS 20.0%
! GAAAAAATCCGTTAAAAAGT+AGG - Chr4:78997963-78997982 MsG0480022954.01.T01:intron 25.0%
!! GTGTATTGATAACATGTATT+TGG - Chr4:78997512-78997531 MsG0480022954.01.T01:intron 25.0%
AACGCTTAATCAATTGTGAA+AGG + Chr4:78997457-78997476 None:intergenic 30.0%
AAGTTAAGTACATCGTATTG+TGG + Chr4:78998075-78998094 None:intergenic 30.0%
ACGCTTAATCAATTGTGAAA+GGG + Chr4:78997456-78997475 None:intergenic 30.0%
AGGGAAAATGCAATGAAAAT+TGG + Chr4:78997046-78997065 None:intergenic 30.0%
ATAAGCTGTAAAACAGCTAA+TGG + Chr4:78997203-78997222 None:intergenic 30.0%
ATTAAGCTGTTTATCGATAC+AGG - Chr4:78997362-78997381 MsG0480022954.01.T01:CDS 30.0%
ATTGTCTTTGCTTGATTAGA+TGG - Chr4:78997684-78997703 MsG0480022954.01.T01:intron 30.0%
GCTTATAACTAGATCTATTG+TGG + Chr4:78997155-78997174 None:intergenic 30.0%
TTAAGCTGTTTATCGATACA+GGG - Chr4:78997363-78997382 MsG0480022954.01.T01:CDS 30.0%
TTCACAATTGATTAAGCGTT+TGG - Chr4:78997457-78997476 MsG0480022954.01.T01:intron 30.0%
! TTTGCTTGATTAGATGGATT+GGG - Chr4:78997690-78997709 MsG0480022954.01.T01:intron 30.0%
!! TGTATTTGGCTTTCAAAATG+TGG - Chr4:78997526-78997545 MsG0480022954.01.T01:intron 30.0%
!!! ATTTTTGCTGTTGCTTATGT+TGG - Chr4:78997989-78998008 MsG0480022954.01.T01:intron 30.0%
AATCAAATTGGCTACGAGTT+GGG + Chr4:78997563-78997582 None:intergenic 35.0%
ATTGGGAATAGTGACTAATG+TGG + Chr4:78997848-78997867 None:intergenic 35.0%
CATATGTGAGGATCATTGTT+TGG + Chr4:78997807-78997826 None:intergenic 35.0%
CATTAGTCACTATTCCCAAT+TGG - Chr4:78997848-78997867 MsG0480022954.01.T01:intron 35.0%
CGCTTAATCAATTGTGAAAG+GGG + Chr4:78997455-78997474 None:intergenic 35.0%
CTTTGCTTGATTAGATGGAT+TGG - Chr4:78997689-78997708 MsG0480022954.01.T01:intron 35.0%
TAACGAGCGTACAATCAAAT+TGG + Chr4:78997575-78997594 None:intergenic 35.0%
TTGCTTATGTTGGTACTTAG+TGG - Chr4:78997999-78998018 MsG0480022954.01.T01:intron 35.0%
! GTTGTGAAAGCACGTAAAAA+GGG + Chr4:78997065-78997084 None:intergenic 35.0%
! TGTTGTGAAAGCACGTAAAA+AGG + Chr4:78997066-78997085 None:intergenic 35.0%
! TTTTGGCATTCATTTCTGTG+TGG - Chr4:78997644-78997663 MsG0480022954.01.T01:intron 35.0%
ACAATGATCCTCACATATGC+TGG - Chr4:78997808-78997827 MsG0480022954.01.T01:intron 40.0%
AGTACATCGTATTGTGGAGA+AGG + Chr4:78998069-78998088 None:intergenic 40.0%
CAATCAAATTGGCTACGAGT+TGG + Chr4:78997564-78997583 None:intergenic 40.0%
CTTATTTCCACAAGCTCTCT+CGG - Chr4:78997218-78997237 MsG0480022954.01.T01:CDS 40.0%
GATACCTTTCGAGAGAGAAA+CGG + Chr4:78996979-78996998 None:intergenic 40.0%
! ATTTGGAGCTGGATATCTCA+CGG - Chr4:78997774-78997793 MsG0480022954.01.T01:intron 40.0%
!! CTTGATTAGATGGATTGGGA+AGG - Chr4:78997694-78997713 MsG0480022954.01.T01:intron 40.0%
!! GCATTTGCTGTGATTGCATT+TGG - Chr4:78997757-78997776 MsG0480022954.01.T01:intron 40.0%
AAACTATCCGAGAGAGCTTG+TGG + Chr4:78997228-78997247 None:intergenic 45.0%
AAGCCAGAACCATCTGTGAA+TGG - Chr4:78997931-78997950 MsG0480022954.01.T01:intron 45.0%
AGCCAGAACCATCTGTGAAT+GGG - Chr4:78997932-78997951 MsG0480022954.01.T01:intron 45.0%
ATGATCCTCACATATGCTGG+TGG - Chr4:78997811-78997830 MsG0480022954.01.T01:intron 45.0%
ATGGTTGAAGAAGGGCCAAT+TGG + Chr4:78997866-78997885 None:intergenic 45.0%
TCAACCATCACCCTCTTAAG+TGG - Chr4:78997878-78997897 MsG0480022954.01.T01:intron 45.0%
TGGTTGAAGAAGGGCCAATT+GGG + Chr4:78997865-78997884 None:intergenic 45.0%
TTCTCCGTTTCTCTCTCGAA+AGG - Chr4:78996972-78996991 MsG0480022954.01.T01:three_prime_UTR 45.0%
TTTGTAGCCCCATTCACAGA+TGG + Chr4:78997943-78997962 None:intergenic 45.0%
! AAGAGGGTGATGGTTGAAGA+AGG + Chr4:78997875-78997894 None:intergenic 45.0%
! AGAGGGTGATGGTTGAAGAA+GGG + Chr4:78997874-78997893 None:intergenic 45.0%
!! TTCACAGATGGTTCTGGCTT+AGG + Chr4:78997931-78997950 None:intergenic 45.0%
CAACACCACCAGCATATGTG+AGG + Chr4:78997819-78997838 None:intergenic 50.0%
CCAACCACTTAAGAGGGTGA+TGG + Chr4:78997885-78997904 None:intergenic 50.0%
CCATCACCCTCTTAAGTGGT+TGG - Chr4:78997882-78997901 MsG0480022954.01.T01:intron 50.0%
CGAGAGAGAAACGGAGAAGA+AGG + Chr4:78996970-78996989 None:intergenic 50.0%
GAGAGAAACGGAGAAGAAGG+TGG + Chr4:78996967-78996986 None:intergenic 50.0%
GCCAGAACCATCTGTGAATG+GGG - Chr4:78997933-78997952 MsG0480022954.01.T01:intron 50.0%
TCGGGTCCAACCACTTAAGA+GGG + Chr4:78997891-78997910 None:intergenic 50.0%
! GCTGTGATTGCATTTGGAGC+TGG - Chr4:78997763-78997782 MsG0480022954.01.T01:intron 50.0%
CTCGGGTCCAACCACTTAAG+AGG + Chr4:78997892-78997911 None:intergenic 55.0%
GCCCCATTCACAGATGGTTC+TGG + Chr4:78997937-78997956 None:intergenic 55.0%
! GATGCTTTTCCGCTTCGCTC+GGG + Chr4:78997909-78997928 None:intergenic 55.0%
! GGATGCTTTTCCGCTTCGCT+CGG + Chr4:78997910-78997929 None:intergenic 55.0%
GTGGTTGGACCCGAGCGAAG+CGG - Chr4:78997897-78997916 MsG0480022954.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr4 gene 78996959 78998128 78996959 ID=MsG0480022954.01;Name=MsG0480022954.01
Chr4 mRNA 78996959 78998128 78996959 ID=MsG0480022954.01.T01;Parent=MsG0480022954.01;Name=MsG0480022954.01.T01;_AED=0.34;_eAED=0.34;_QI=35|1|1|1|0|0.5|2|144|93
Chr4 exon 78996959 78997384 78996959 ID=MsG0480022954.01.T01:exon:23575;Parent=MsG0480022954.01.T01
Chr4 exon 78998094 78998128 78998094 ID=MsG0480022954.01.T01:exon:23574;Parent=MsG0480022954.01.T01
Chr4 five_prime_UTR 78998094 78998128 78998094 ID=MsG0480022954.01.T01:five_prime_utr;Parent=MsG0480022954.01.T01
Chr4 CDS 78997103 78997384 78997103 ID=MsG0480022954.01.T01:cds;Parent=MsG0480022954.01.T01
Chr4 three_prime_UTR 78996959 78997102 78996959 ID=MsG0480022954.01.T01:three_prime_utr;Parent=MsG0480022954.01.T01
Gene Sequence

>MsG0480022954.01.T01

ATGGATTGGGAAGGACAAAAGCTAGCAGAGCAGCTGATGCAGATAATGCTGCTTGCATTTGCTGTGATTGCATTTGGAGCTGGATATCTCACGGCTTCTTTCCAAACAATGATCCTCACATATGCTGGTGGTGTTGTTCTCACCACATTAGTCACTATTCCCAATTGGCCCTTCTTCAACCATCACCCTCTTAAGTGGTTGGACCCGAGCGAAGCGGAAAAGCATCCTAAGCCAGAACCATCTGTGAATGGGGCTACAAAGAAAAAATCCGTTAAAAAGTAG
Protein sequence

>MsG0480022954.01.T01

MDWEGQKLAEQLMQIMLLAFAVIAFGAGYLTASFQTMILTYAGGVVLTTLVTIPNWPFFNHHPLKWLDPSEAEKHPKPEPSVNGATKKKSVKK*