AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0228070


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 24 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGAAGAAAAGCTGAAATTT+TGG 0.216351 2_1:+79475742 Msa0228070:CDS
TCCTTCAATTCTACAGATTT+AGG 0.221306 2_1:-79474917 None:intergenic
CATTCTAAAACATCTGTTTC+CGG 0.297484 2_1:+79474675 Msa0228070:five_prime_UTR
ACAACACAAACAAGAGAAAA+TGG 0.315626 2_1:+79475792 Msa0228070:CDS
AAGCAGTGTTACTATTGTTA+TGG 0.340046 2_1:-79474583 None:intergenic
GAGGAACTTTCTGTGATTGA+TGG 0.376034 2_1:+79475668 Msa0228070:five_prime_UTR
TCTGTAGAATTGAAGGAAAT+TGG 0.387754 2_1:+79474923 Msa0228070:five_prime_UTR
CGAGATATAGTCAGACTTGT+TGG 0.426562 2_1:-79474734 None:intergenic
AGTCTGACTATATCTCGTTC+AGG 0.430003 2_1:+79474740 Msa0228070:five_prime_UTR
TCCTAAATCTGTAGAATTGA+AGG 0.458118 2_1:+79474916 Msa0228070:five_prime_UTR
TTCCGTGTAGTGTTCATGTA+AGG 0.489124 2_1:-79475645 None:intergenic
AGTGTTACTATTGTTATGGA+TGG 0.535489 2_1:-79474579 None:intergenic
GCAGATAAAATTAGGAACAG+TGG 0.540090 2_1:+79475587 Msa0228070:intron
GCATCATATATATGAAAAGC+AGG 0.552365 2_1:+79474889 Msa0228070:five_prime_UTR
ACATGAACACTACACGGAAG+AGG 0.568800 2_1:+79475649 Msa0228070:five_prime_UTR
TCTGTAAACAGTTAGGTGAA+AGG 0.571363 2_1:+79474644 Msa0228070:five_prime_UTR
TGTTACTGTGCTGTTAGTGC+AGG 0.580733 2_1:+79475709 Msa0228070:five_prime_UTR
GAACTTTCTGTGATTGATGG+AGG 0.597778 2_1:+79475671 Msa0228070:five_prime_UTR
CATATATATGAAAAGCAGGC+GGG 0.633112 2_1:+79474893 Msa0228070:five_prime_UTR
TTGAGACACTAAGCTCAGCA+AGG 0.634008 2_1:+79475899 Msa0228070:three_prime_UTR
GACCTTACATGAACACTACA+CGG 0.644746 2_1:+79475643 Msa0228070:five_prime_UTR
TCATATATATGAAAAGCAGG+CGG 0.651248 2_1:+79474892 Msa0228070:five_prime_UTR
TGAGACACTAAGCTCAGCAA+GGG 0.685905 2_1:+79475900 Msa0228070:three_prime_UTR
TATAGACGCAACTCAAAACG+TGG 0.698081 2_1:-79474947 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACCAATAATTCAATATTTTC+TGG + chr2_1:79475133-79475152 Msa0228070:intron 20.0%
!! ACCAGAAAATATTGAATTAT+TGG - chr2_1:79475137-79475156 None:intergenic 20.0%
!! GCAAGAAAATATAGAATTAT+TGG - chr2_1:79475193-79475212 None:intergenic 20.0%
!! TTCAAGAGAATATCTATTAT+TGG - chr2_1:79475232-79475251 None:intergenic 20.0%
!! AACTCAAACTAAAAAGTTAT+AGG - chr2_1:79475946-79475965 None:intergenic 20.0%
!!! ACCAATAATTCAATATTTTC+TGG + chr2_1:79475133-79475152 Msa0228070:intron 20.0%
!! ACCAGAAAATATTGAATTAT+TGG - chr2_1:79475137-79475156 None:intergenic 20.0%
!! GCAAGAAAATATAGAATTAT+TGG - chr2_1:79475193-79475212 None:intergenic 20.0%
!! TTCAAGAGAATATCTATTAT+TGG - chr2_1:79475232-79475251 None:intergenic 20.0%
!! AACTCAAACTAAAAAGTTAT+AGG - chr2_1:79475946-79475965 None:intergenic 20.0%
!!! AAACAGATGTTTTAGAATGT+TGG - chr2_1:79474674-79474693 None:intergenic 25.0%
!! AACCATTTTGTATCAACTTT+TGG + chr2_1:79475290-79475309 Msa0228070:intron 25.0%
!!! AACCAAAAGTTGATACAAAA+TGG - chr2_1:79475295-79475314 None:intergenic 25.0%
!! TTCAACTTTAGGAATAAGAT+TGG - chr2_1:79475546-79475565 None:intergenic 25.0%
!!! AGTTTTTGGTATTCAACTTT+AGG - chr2_1:79475557-79475576 None:intergenic 25.0%
!! AACCTTTTGCAGATAAAATT+AGG + chr2_1:79475579-79475598 Msa0228070:intron 25.0%
!! TTCCTAATTTTATCTGCAAA+AGG - chr2_1:79475584-79475603 None:intergenic 25.0%
!! TAGAAGAAAAGCTGAAATTT+TGG + chr2_1:79475742-79475761 Msa0228070:CDS 25.0%
!!! AAACAGATGTTTTAGAATGT+TGG - chr2_1:79474674-79474693 None:intergenic 25.0%
!! AACCATTTTGTATCAACTTT+TGG + chr2_1:79475290-79475309 Msa0228070:intron 25.0%
!!! AACCAAAAGTTGATACAAAA+TGG - chr2_1:79475295-79475314 None:intergenic 25.0%
!! TTCAACTTTAGGAATAAGAT+TGG - chr2_1:79475546-79475565 None:intergenic 25.0%
!!! AGTTTTTGGTATTCAACTTT+AGG - chr2_1:79475557-79475576 None:intergenic 25.0%
!! AACCTTTTGCAGATAAAATT+AGG + chr2_1:79475579-79475598 Msa0228070:intron 25.0%
!! TTCCTAATTTTATCTGCAAA+AGG - chr2_1:79475584-79475603 None:intergenic 25.0%
!! TAGAAGAAAAGCTGAAATTT+TGG + chr2_1:79475742-79475761 Msa0228070:CDS 25.0%
! AGTGTTACTATTGTTATGGA+TGG - chr2_1:79474582-79474601 None:intergenic 30.0%
! AAGCAGTGTTACTATTGTTA+TGG - chr2_1:79474586-79474605 None:intergenic 30.0%
! CTTTTTGTCTGTAAACAGTT+AGG + chr2_1:79474637-79474656 Msa0228070:five_prime_UTR 30.0%
!! CATTCTAAAACATCTGTTTC+CGG + chr2_1:79474675-79474694 Msa0228070:five_prime_UTR 30.0%
!! TCAGGTTAGTTTCATTTATC+CGG + chr2_1:79474758-79474777 Msa0228070:intron 30.0%
AAGTCAAATGCATAAAACAC+CGG - chr2_1:79474780-79474799 None:intergenic 30.0%
CTGTTAACTTTCTCTTGTTA+CGG + chr2_1:79474824-79474843 Msa0228070:intron 30.0%
GCATCATATATATGAAAAGC+AGG + chr2_1:79474889-79474908 Msa0228070:five_prime_UTR 30.0%
TCATATATATGAAAAGCAGG+CGG + chr2_1:79474892-79474911 Msa0228070:five_prime_UTR 30.0%
TCCTAAATCTGTAGAATTGA+AGG + chr2_1:79474916-79474935 Msa0228070:five_prime_UTR 30.0%
TCCTTCAATTCTACAGATTT+AGG - chr2_1:79474920-79474939 None:intergenic 30.0%
TCTGTAGAATTGAAGGAAAT+TGG + chr2_1:79474923-79474942 Msa0228070:five_prime_UTR 30.0%
TATAGCATATACGCAGTTTA+TGG + chr2_1:79475345-79475364 Msa0228070:intron 30.0%
!!! AATTTTTTTGAAATCGACGC+AGG + chr2_1:79475485-79475504 Msa0228070:intron 30.0%
!! GAAAAGCTGAAATTTTGGAA+TGG + chr2_1:79475747-79475766 Msa0228070:CDS 30.0%
ACAACACAAACAAGAGAAAA+TGG + chr2_1:79475792-79475811 Msa0228070:CDS 30.0%
! AGTGTTACTATTGTTATGGA+TGG - chr2_1:79474582-79474601 None:intergenic 30.0%
! AAGCAGTGTTACTATTGTTA+TGG - chr2_1:79474586-79474605 None:intergenic 30.0%
! CTTTTTGTCTGTAAACAGTT+AGG + chr2_1:79474637-79474656 Msa0228070:five_prime_UTR 30.0%
!! CATTCTAAAACATCTGTTTC+CGG + chr2_1:79474675-79474694 Msa0228070:five_prime_UTR 30.0%
!! TCAGGTTAGTTTCATTTATC+CGG + chr2_1:79474758-79474777 Msa0228070:intron 30.0%
AAGTCAAATGCATAAAACAC+CGG - chr2_1:79474780-79474799 None:intergenic 30.0%
CTGTTAACTTTCTCTTGTTA+CGG + chr2_1:79474824-79474843 Msa0228070:intron 30.0%
GCATCATATATATGAAAAGC+AGG + chr2_1:79474889-79474908 Msa0228070:five_prime_UTR 30.0%
TCATATATATGAAAAGCAGG+CGG + chr2_1:79474892-79474911 Msa0228070:five_prime_UTR 30.0%
TCCTAAATCTGTAGAATTGA+AGG + chr2_1:79474916-79474935 Msa0228070:five_prime_UTR 30.0%
TCCTTCAATTCTACAGATTT+AGG - chr2_1:79474920-79474939 None:intergenic 30.0%
TCTGTAGAATTGAAGGAAAT+TGG + chr2_1:79474923-79474942 Msa0228070:five_prime_UTR 30.0%
TATAGCATATACGCAGTTTA+TGG + chr2_1:79475345-79475364 Msa0228070:intron 30.0%
!!! AATTTTTTTGAAATCGACGC+AGG + chr2_1:79475485-79475504 Msa0228070:intron 30.0%
!! GAAAAGCTGAAATTTTGGAA+TGG + chr2_1:79475747-79475766 Msa0228070:CDS 30.0%
ACAACACAAACAAGAGAAAA+TGG + chr2_1:79475792-79475811 Msa0228070:CDS 30.0%
TCTGTAAACAGTTAGGTGAA+AGG + chr2_1:79474644-79474663 Msa0228070:five_prime_UTR 35.0%
!! ATACGTTTTGTGTCTGGTTT+TGG - chr2_1:79474703-79474722 None:intergenic 35.0%
! GTAACAATACGTTTTGTGTC+TGG - chr2_1:79474709-79474728 None:intergenic 35.0%
ATATTGTATCTGCTGCATAC+AGG + chr2_1:79474867-79474886 Msa0228070:intron 35.0%
CATATATATGAAAAGCAGGC+GGG + chr2_1:79474893-79474912 Msa0228070:five_prime_UTR 35.0%
!!! TTTTGAGTTGCGTCTATATC+AGG + chr2_1:79474952-79474971 Msa0228070:five_prime_UTR 35.0%
!! CTTTGTTGTTCGCAATTGTA+TGG + chr2_1:79475004-79475023 Msa0228070:intron 35.0%
TGAATATATTGTGCTGCAAC+TGG + chr2_1:79475086-79475105 Msa0228070:intron 35.0%
GAATATATTGTGCTGCAACT+GGG + chr2_1:79475087-79475106 Msa0228070:intron 35.0%
TATTTCTTGCGTCTCTAACT+TGG + chr2_1:79475258-79475277 Msa0228070:intron 35.0%
! CTGCAAAAGGTTTCAGTTTT+TGG - chr2_1:79475571-79475590 None:intergenic 35.0%
GCAGATAAAATTAGGAACAG+TGG + chr2_1:79475587-79475606 Msa0228070:intron 35.0%
TCTGTAAACAGTTAGGTGAA+AGG + chr2_1:79474644-79474663 Msa0228070:five_prime_UTR 35.0%
!! ATACGTTTTGTGTCTGGTTT+TGG - chr2_1:79474703-79474722 None:intergenic 35.0%
! GTAACAATACGTTTTGTGTC+TGG - chr2_1:79474709-79474728 None:intergenic 35.0%
ATATTGTATCTGCTGCATAC+AGG + chr2_1:79474867-79474886 Msa0228070:intron 35.0%
CATATATATGAAAAGCAGGC+GGG + chr2_1:79474893-79474912 Msa0228070:five_prime_UTR 35.0%
!!! TTTTGAGTTGCGTCTATATC+AGG + chr2_1:79474952-79474971 Msa0228070:five_prime_UTR 35.0%
!! CTTTGTTGTTCGCAATTGTA+TGG + chr2_1:79475004-79475023 Msa0228070:intron 35.0%
TGAATATATTGTGCTGCAAC+TGG + chr2_1:79475086-79475105 Msa0228070:intron 35.0%
GAATATATTGTGCTGCAACT+GGG + chr2_1:79475087-79475106 Msa0228070:intron 35.0%
TATTTCTTGCGTCTCTAACT+TGG + chr2_1:79475258-79475277 Msa0228070:intron 35.0%
! CTGCAAAAGGTTTCAGTTTT+TGG - chr2_1:79475571-79475590 None:intergenic 35.0%
GCAGATAAAATTAGGAACAG+TGG + chr2_1:79475587-79475606 Msa0228070:intron 35.0%
CGAGATATAGTCAGACTTGT+TGG - chr2_1:79474737-79474756 None:intergenic 40.0%
AGTCTGACTATATCTCGTTC+AGG + chr2_1:79474740-79474759 Msa0228070:five_prime_UTR 40.0%
TATAGACGCAACTCAAAACG+TGG - chr2_1:79474950-79474969 None:intergenic 40.0%
TGTTGTTCGCAATTGTATGG+AGG + chr2_1:79475007-79475026 Msa0228070:intron 40.0%
TTTCCCATCTGTTCTTGAGT+TGG + chr2_1:79475156-79475175 Msa0228070:intron 40.0%
AGACCAACTCAAGAACAGAT+GGG - chr2_1:79475162-79475181 None:intergenic 40.0%
GACCTTACATGAACACTACA+CGG + chr2_1:79475643-79475662 Msa0228070:five_prime_UTR 40.0%
TTCCGTGTAGTGTTCATGTA+AGG - chr2_1:79475648-79475667 None:intergenic 40.0%
GAGGAACTTTCTGTGATTGA+TGG + chr2_1:79475668-79475687 Msa0228070:five_prime_UTR 40.0%
GAACTTTCTGTGATTGATGG+AGG + chr2_1:79475671-79475690 Msa0228070:five_prime_UTR 40.0%
CGAGATATAGTCAGACTTGT+TGG - chr2_1:79474737-79474756 None:intergenic 40.0%
AGTCTGACTATATCTCGTTC+AGG + chr2_1:79474740-79474759 Msa0228070:five_prime_UTR 40.0%
TATAGACGCAACTCAAAACG+TGG - chr2_1:79474950-79474969 None:intergenic 40.0%
TGTTGTTCGCAATTGTATGG+AGG + chr2_1:79475007-79475026 Msa0228070:intron 40.0%
TTTCCCATCTGTTCTTGAGT+TGG + chr2_1:79475156-79475175 Msa0228070:intron 40.0%
AGACCAACTCAAGAACAGAT+GGG - chr2_1:79475162-79475181 None:intergenic 40.0%
GACCTTACATGAACACTACA+CGG + chr2_1:79475643-79475662 Msa0228070:five_prime_UTR 40.0%
TTCCGTGTAGTGTTCATGTA+AGG - chr2_1:79475648-79475667 None:intergenic 40.0%
GAGGAACTTTCTGTGATTGA+TGG + chr2_1:79475668-79475687 Msa0228070:five_prime_UTR 40.0%
GAACTTTCTGTGATTGATGG+AGG + chr2_1:79475671-79475690 Msa0228070:five_prime_UTR 40.0%
!!! TTTGTGTCTGGTTTTGGCAC+CGG - chr2_1:79474697-79474716 None:intergenic 45.0%
GAGACCAACTCAAGAACAGA+TGG - chr2_1:79475163-79475182 None:intergenic 45.0%
ACATGAACACTACACGGAAG+AGG + chr2_1:79475649-79475668 Msa0228070:five_prime_UTR 45.0%
! TGTTACTGTGCTGTTAGTGC+AGG + chr2_1:79475709-79475728 Msa0228070:five_prime_UTR 45.0%
TTGAGACACTAAGCTCAGCA+AGG + chr2_1:79475899-79475918 Msa0228070:three_prime_UTR 45.0%
TGAGACACTAAGCTCAGCAA+GGG + chr2_1:79475900-79475919 Msa0228070:three_prime_UTR 45.0%
!!! TTTGTGTCTGGTTTTGGCAC+CGG - chr2_1:79474697-79474716 None:intergenic 45.0%
GAGACCAACTCAAGAACAGA+TGG - chr2_1:79475163-79475182 None:intergenic 45.0%
ACATGAACACTACACGGAAG+AGG + chr2_1:79475649-79475668 Msa0228070:five_prime_UTR 45.0%
! TGTTACTGTGCTGTTAGTGC+AGG + chr2_1:79475709-79475728 Msa0228070:five_prime_UTR 45.0%
TTGAGACACTAAGCTCAGCA+AGG + chr2_1:79475899-79475918 Msa0228070:three_prime_UTR 45.0%
TGAGACACTAAGCTCAGCAA+GGG + chr2_1:79475900-79475919 Msa0228070:three_prime_UTR 45.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 79474559 79476033 79474559 ID=Msa0228070;Name=Msa0228070
chr2_1 mRNA 79474559 79476033 79474559 ID=Msa0228070-mRNA-1;Parent=Msa0228070;Name=Msa0228070-mRNA-1;_AED=0.00;_eAED=0.00;_QI=432|1|1|1|1|1|3|197|33
chr2_1 exon 79474559 79474761 79474559 ID=Msa0228070-mRNA-1:exon:24146;Parent=Msa0228070-mRNA-1
chr2_1 exon 79474889 79474973 79474889 ID=Msa0228070-mRNA-1:exon:24147;Parent=Msa0228070-mRNA-1
chr2_1 exon 79475591 79476033 79475591 ID=Msa0228070-mRNA-1:exon:24148;Parent=Msa0228070-mRNA-1
chr2_1 five_prime_UTR 79474559 79474761 79474559 ID=Msa0228070-mRNA-1:five_prime_utr;Parent=Msa0228070-mRNA-1
chr2_1 five_prime_UTR 79474889 79474973 79474889 ID=Msa0228070-mRNA-1:five_prime_utr;Parent=Msa0228070-mRNA-1
chr2_1 five_prime_UTR 79475591 79475734 79475591 ID=Msa0228070-mRNA-1:five_prime_utr;Parent=Msa0228070-mRNA-1
chr2_1 CDS 79475735 79475836 79475735 ID=Msa0228070-mRNA-1:cds;Parent=Msa0228070-mRNA-1
chr2_1 three_prime_UTR 79475837 79476033 79475837 ID=Msa0228070-mRNA-1:three_prime_utr;Parent=Msa0228070-mRNA-1
Gene Sequence

>Msa0228070

ATGCAGCTAGAAGAAAAGCTGAAATTTTGGAATGGTGATATTATTCAACAGTTTAGCACAACACAAACAAGAGAAAATGGAAATTGTGATGTGCTTGTATAA

Protein sequence

>Msa0228070

MQLEEKLKFWNGDIIQQFSTTQTRENGNCDVLV*