AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380017136.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017136.01.T01 MTR_3g101630 65.278 72 14 2 15 75 151 222 1.79e-21 84.3
MsG0380017136.01.T01 MTR_3g101630 94.737 38 2 0 15 52 151 188 6.48e-20 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017136.01.T01 AT4G33350 53.247 77 28 2 7 75 161 237 8.08e-18 75.1
MsG0380017136.01.T01 AT4G33350 49.275 69 17 1 7 75 161 211 4.07e-14 64.7

Find 14 sgRNAs with CRISPR-Local

Find 109 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTACAGTCAGAACTTT+TGG 0.296051 3:+92479046 MsG0380017136.01.T01:intron
TCCATCAAAACCTTCCTTGC+TGG 0.381167 3:-92478662 None:intergenic
TTGCCCTGTATATTTCTCTA+AGG 0.385806 3:+92479094 MsG0380017136.01.T01:CDS
GTTCAATTATGAAATTAAAC+AGG 0.401667 3:+92480271 MsG0380017136.01.T01:CDS
CAAACCTTAGAGAAATATAC+AGG 0.430319 3:-92479098 None:intergenic
CTCAGAGCCGCCAGCAAGGA+AGG 0.460599 3:+92478652 MsG0380017136.01.T01:CDS
AATTAGTTCTGTGACTGAAC+AGG 0.462495 3:+92478564 MsG0380017136.01.T01:CDS
ATGCATGATAGTTGCGGCGT+GGG 0.520131 3:+92478541 MsG0380017136.01.T01:CDS
AATTATGAAATTAAACAGGT+TGG 0.538818 3:+92480275 MsG0380017136.01.T01:CDS
CGTAATATGCATGATAGTTG+CGG 0.559529 3:+92478535 None:intergenic
TCAGCTCAGAGCCGCCAGCA+AGG 0.614025 3:+92478648 MsG0380017136.01.T01:intron
ATCAAAACCTTCCTTGCTGG+CGG 0.637557 3:-92478659 None:intergenic
TATGCATGATAGTTGCGGCG+TGG 0.662631 3:+92478540 None:intergenic
AAACCTTAGAGAAATATACA+GGG 0.722468 3:-92479097 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTCTAAATTAAAAATAG+AGG - Chr3:92479190-92479209 None:intergenic 10.0%
!! ATTTCTAAATTAAAAATAGA+GGG - Chr3:92479189-92479208 None:intergenic 10.0%
!!! TTTATGTTTCTTTAATTTTA+TGG + Chr3:92479932-92479951 MsG0380017136.01.T01:intron 10.0%
!! TATAATTTATCATCATTTGA+AGG + Chr3:92480232-92480251 MsG0380017136.01.T01:intron 15.0%
!!! ATATTTTTAATTACGCAATT+TGG + Chr3:92479220-92479239 MsG0380017136.01.T01:intron 15.0%
!! AAATGTGATTATTAGTCAAT+AGG - Chr3:92479028-92479047 None:intergenic 20.0%
!! AATTATGAAATTAAACAGGT+TGG + Chr3:92480275-92480294 MsG0380017136.01.T01:CDS 20.0%
!! ATCTTCATTGTTAAACATTT+AGG + Chr3:92479541-92479560 MsG0380017136.01.T01:intron 20.0%
!! GTTCAATTATGAAATTAAAC+AGG + Chr3:92480271-92480290 MsG0380017136.01.T01:CDS 20.0%
!! TCATCATCATAGTTAAAAAT+TGG - Chr3:92479266-92479285 None:intergenic 20.0%
!! TCTTCATTGTTAAACATTTA+GGG + Chr3:92479542-92479561 MsG0380017136.01.T01:intron 20.0%
!! TTAAAAACCATCAAACTATT+TGG + Chr3:92478932-92478951 MsG0380017136.01.T01:intron 20.0%
!!! AAAATGTTTTCGAATAAACA+GGG + Chr3:92480082-92480101 MsG0380017136.01.T01:intron 20.0%
!!! ATAAAAACACATTTTTGGAT+GGG + Chr3:92479955-92479974 MsG0380017136.01.T01:intron 20.0%
!!! TATGGATAAAAACACATTTT+TGG + Chr3:92479950-92479969 MsG0380017136.01.T01:intron 20.0%
! AAACCTTAGAGAAATATACA+GGG - Chr3:92479100-92479119 None:intergenic 25.0%
! ACAATTGAAATCAGAACATA+AGG - Chr3:92480142-92480161 None:intergenic 25.0%
! ATTAACCCTAAATCTTAGTT+AGG + Chr3:92479646-92479665 MsG0380017136.01.T01:intron 25.0%
! ATTCTATACCATTATTTGCT+TGG - Chr3:92479789-92479808 None:intergenic 25.0%
! GAAGATGTACTGAAAAAAAT+GGG + Chr3:92480305-92480324 MsG0380017136.01.T01:CDS 25.0%
! TAACATATAAATTCCAAGAC+TGG + Chr3:92478901-92478920 MsG0380017136.01.T01:intron 25.0%
! TATATCAGTAGCTATAAGTT+TGG + Chr3:92478811-92478830 MsG0380017136.01.T01:intron 25.0%
! TGCGTAATTAAAAATATCGA+GGG - Chr3:92479217-92479236 None:intergenic 25.0%
! TGTGTAATACAAAAAACACT+CGG + Chr3:92479464-92479483 MsG0380017136.01.T01:intron 25.0%
! TTGCGTAATTAAAAATATCG+AGG - Chr3:92479218-92479237 None:intergenic 25.0%
!! ATATGATAGTTTTCGTTTGT+TGG + Chr3:92479693-92479712 MsG0380017136.01.T01:intron 25.0%
!! GAAAATGTTTTCGAATAAAC+AGG + Chr3:92480081-92480100 MsG0380017136.01.T01:intron 25.0%
!!! GATAAAAACACATTTTTGGA+TGG + Chr3:92479954-92479973 MsG0380017136.01.T01:intron 25.0%
!!! TAATTGTTTTAGTGCTAAAC+TGG + Chr3:92479901-92479920 MsG0380017136.01.T01:intron 25.0%
!!! TTCAAATTGTTATTTTCGCA+TGG - Chr3:92479987-92480006 None:intergenic 25.0%
!!! TTTTAACTATGATGATGATG+TGG + Chr3:92479268-92479287 MsG0380017136.01.T01:intron 25.0%
AACAACTACACCAACTTAAT+GGG + Chr3:92479407-92479426 MsG0380017136.01.T01:intron 30.0%
AACTTTGTGATCTTTCTTCA+TGG + Chr3:92480038-92480057 MsG0380017136.01.T01:intron 30.0%
ACAGGGAAAATTTATGTTTG+TGG + Chr3:92480099-92480118 MsG0380017136.01.T01:intron 30.0%
ACATGCCTAACTAAGATTTA+GGG - Chr3:92479654-92479673 None:intergenic 30.0%
AGAAAACATACCTGAAAAAC+AGG - Chr3:92478691-92478710 None:intergenic 30.0%
ATATGTTACATACCATGCAT+TGG - Chr3:92478889-92478908 None:intergenic 30.0%
ATGAACTATAGTCTCATACA+AGG - Chr3:92480012-92480031 None:intergenic 30.0%
ATGGAAAATGTTAGGAGAAA+GGG + Chr3:92480057-92480076 MsG0380017136.01.T01:intron 30.0%
ATTTATATCAGACTCCAGAT+GGG - Chr3:92478964-92478983 None:intergenic 30.0%
CAAACCTTAGAGAAATATAC+AGG - Chr3:92479101-92479120 None:intergenic 30.0%
CGAAGATGTACTGAAAAAAA+TGG + Chr3:92480304-92480323 MsG0380017136.01.T01:CDS 30.0%
CTTTCTTCATGGAAAATGTT+AGG + Chr3:92480049-92480068 MsG0380017136.01.T01:intron 30.0%
GTTTAACAATGAAGATGATG+CGG - Chr3:92479537-92479556 None:intergenic 30.0%
TAACAACTACACCAACTTAA+TGG + Chr3:92479406-92479425 MsG0380017136.01.T01:intron 30.0%
TACATGCCTAACTAAGATTT+AGG - Chr3:92479655-92479674 None:intergenic 30.0%
TATTGAACAGGAACTATCTA+AGG + Chr3:92479733-92479752 MsG0380017136.01.T01:intron 30.0%
TATTTATATCAGACTCCAGA+TGG - Chr3:92478965-92478984 None:intergenic 30.0%
TGCATATTGACCATAATAGA+GGG - Chr3:92479159-92479178 None:intergenic 30.0%
TTGCATATTGACCATAATAG+AGG - Chr3:92479160-92479179 None:intergenic 30.0%
! AGTTCTTTAGAGGACTAATT+GGG + Chr3:92478727-92478746 MsG0380017136.01.T01:intron 30.0%
! CTTCAGCATAATTGTTTTCA+AGG - Chr3:92479878-92479897 None:intergenic 30.0%
! TCAGGTATGTTTTCTTACTT+TGG + Chr3:92478696-92478715 MsG0380017136.01.T01:intron 30.0%
! TTTAGGGTTAATTGCACTTA+TGG - Chr3:92479638-92479657 None:intergenic 30.0%
!! GTTTTCGTTTGTTGGTTAAA+TGG + Chr3:92479701-92479720 MsG0380017136.01.T01:intron 30.0%
ATTATTTGCTTGGAAACTCC+AGG - Chr3:92479779-92479798 None:intergenic 35.0%
ATTGAATACGTGAAACGACA+TGG + Chr3:92479307-92479326 MsG0380017136.01.T01:intron 35.0%
ATTGCAGTTAAAGAGACCAA+TGG - Chr3:92479130-92479149 None:intergenic 35.0%
ATTGGCTGCAGTTAATTACT+TGG - Chr3:92478871-92478890 None:intergenic 35.0%
CATGGAAAATGTTAGGAGAA+AGG + Chr3:92480056-92480075 MsG0380017136.01.T01:intron 35.0%
GCAGATACCAAATAGTTTGA+TGG - Chr3:92478942-92478961 None:intergenic 35.0%
GTAATACAAAAAACACTCGG+TGG + Chr3:92479467-92479486 MsG0380017136.01.T01:intron 35.0%
TGGAGTTTCCAAGCAAATAA+TGG + Chr3:92479778-92479797 MsG0380017136.01.T01:intron 35.0%
TTAGGGACAACTTGACTAAT+GGG + Chr3:92479559-92479578 MsG0380017136.01.T01:intron 35.0%
TTGAACATGTGAAGCTAAGA+CGG - Chr3:92479493-92479512 None:intergenic 35.0%
TTGCAGTTAAAGAGACCAAT+GGG - Chr3:92479129-92479148 None:intergenic 35.0%
TTGCCCTGTATATTTCTCTA+AGG + Chr3:92479094-92479113 MsG0380017136.01.T01:CDS 35.0%
TTTAGGGACAACTTGACTAA+TGG + Chr3:92479558-92479577 MsG0380017136.01.T01:intron 35.0%
! CAATTAGTCCTCTAAAGAAC+TGG - Chr3:92478728-92478747 None:intergenic 35.0%
! CAGTTCTTTAGAGGACTAAT+TGG + Chr3:92478726-92478745 MsG0380017136.01.T01:intron 35.0%
! GTTCTTTAGAGGACTAATTG+GGG + Chr3:92478728-92478747 MsG0380017136.01.T01:intron 35.0%
! TAACTATGATGATGATGTGG+CGG + Chr3:92479271-92479290 MsG0380017136.01.T01:intron 35.0%
! TTGCTTACAGTCAGAACTTT+TGG + Chr3:92479046-92479065 MsG0380017136.01.T01:intron 35.0%
!! AATTAGTTCTGTGACTGAAC+AGG + Chr3:92478564-92478583 MsG0380017136.01.T01:CDS 35.0%
!! CATCCATACTTGCTATATTC+CGG - Chr3:92479436-92479455 None:intergenic 35.0%
AATTAACTGCAGCCAATGCA+TGG + Chr3:92478874-92478893 MsG0380017136.01.T01:intron 40.0%
ATTGGATGACAACTTGACAG+AGG - Chr3:92479248-92479267 None:intergenic 40.0%
CAATTCTGGTCCCTCTATTA+TGG + Chr3:92479146-92479165 MsG0380017136.01.T01:intron 40.0%
CTAAGGTTTGTCTAACCCAT+TGG + Chr3:92479111-92479130 MsG0380017136.01.T01:intron 40.0%
CTACCGGAATATAGCAAGTA+TGG + Chr3:92479430-92479449 MsG0380017136.01.T01:intron 40.0%
GACTAATTGGGGAATGTTGA+GGG + Chr3:92478739-92478758 MsG0380017136.01.T01:intron 40.0%
GGTCTCTTTAACTGCAATTC+TGG + Chr3:92479132-92479151 MsG0380017136.01.T01:intron 40.0%
TAGATGACCAAAGTGCAGAT+TGG + Chr3:92479599-92479618 MsG0380017136.01.T01:intron 40.0%
TAGTTAGGCATGTAGCTTGA+TGG + Chr3:92479661-92479680 MsG0380017136.01.T01:intron 40.0%
TGGACAGGAAGATATTGAAC+AGG + Chr3:92479721-92479740 MsG0380017136.01.T01:intron 40.0%
TTTAAGCTGTTTGCCAGTCT+TGG - Chr3:92478917-92478936 None:intergenic 40.0%
! AGGAACTATCTAAGGTTTCC+AGG + Chr3:92479741-92479760 MsG0380017136.01.T01:intron 40.0%
! CGTTTGTTGGTTAAATGGAC+AGG + Chr3:92479706-92479725 MsG0380017136.01.T01:intron 40.0%
! GGAACTATCTAAGGTTTCCA+GGG + Chr3:92479742-92479761 MsG0380017136.01.T01:intron 40.0%
!! ATGGCTATAGAGTGCTGATA+TGG + Chr3:92479326-92479345 MsG0380017136.01.T01:intron 40.0%
!! TGATGGAGTTCCTGTTTTTC+AGG + Chr3:92478678-92478697 MsG0380017136.01.T01:CDS 40.0%
ATCAAAACCTTCCTTGCTGG+CGG - Chr3:92478662-92478681 None:intergenic 45.0%
ATTCCGGTAGCCCATTAAGT+TGG - Chr3:92479420-92479439 None:intergenic 45.0%
CTATTTGGTATCTGCCCATC+TGG + Chr3:92478947-92478966 MsG0380017136.01.T01:intron 45.0%
CTTACTGCCAATCTGCACTT+TGG - Chr3:92479609-92479628 None:intergenic 45.0%
GGACTAATTGGGGAATGTTG+AGG + Chr3:92478738-92478757 MsG0380017136.01.T01:intron 45.0%
TCCATCAAAACCTTCCTTGC+TGG - Chr3:92478665-92478684 None:intergenic 45.0%
! TCCAGGACTTTTAGATACCC+TGG - Chr3:92479762-92479781 None:intergenic 45.0%
! TCCAGGGTATCTAAAAGTCC+TGG + Chr3:92479758-92479777 MsG0380017136.01.T01:intron 45.0%
!! ACACCAACTTAATGGGCTAC+CGG + Chr3:92479414-92479433 MsG0380017136.01.T01:intron 45.0%
ATGCATGATAGTTGCGGCGT+GGG + Chr3:92478541-92478560 MsG0380017136.01.T01:CDS 50.0%
ATTGGGGAATGTTGAGGGTG+TGG + Chr3:92478744-92478763 MsG0380017136.01.T01:intron 50.0%
GGCAGTCTCCAGTTCTTTAG+AGG + Chr3:92478717-92478736 MsG0380017136.01.T01:intron 50.0%
GTGCAGATTGGCAGTAAGAG+AGG + Chr3:92479611-92479630 MsG0380017136.01.T01:intron 50.0%
! TTGGGGAATGTTGAGGGTGT+GGG + Chr3:92478745-92478764 MsG0380017136.01.T01:intron 50.0%
!! GCCAGCAAGGAAGGTTTTGA+TGG + Chr3:92478661-92478680 MsG0380017136.01.T01:CDS 50.0%
! GGAATGTTGAGGGTGTGGGC+AGG + Chr3:92478749-92478768 MsG0380017136.01.T01:intron 60.0%
CTCAGAGCCGCCAGCAAGGA+AGG + Chr3:92478652-92478671 MsG0380017136.01.T01:CDS 65.0%
TCAGCTCAGAGCCGCCAGCA+AGG + Chr3:92478648-92478667 MsG0380017136.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 92478541 92480334 92478541 ID=MsG0380017136.01;Name=MsG0380017136.01
Chr3 mRNA 92478541 92480334 92478541 ID=MsG0380017136.01.T01;Parent=MsG0380017136.01;Name=MsG0380017136.01.T01;_AED=0.48;_eAED=0.64;_QI=0|0.33|0.5|1|0|0|4|0|77
Chr3 exon 92478541 92478585 92478541 ID=MsG0380017136.01.T01:exon:12578;Parent=MsG0380017136.01.T01
Chr3 exon 92478652 92478699 92478652 ID=MsG0380017136.01.T01:exon:12579;Parent=MsG0380017136.01.T01
Chr3 exon 92479056 92479115 92479056 ID=MsG0380017136.01.T01:exon:12580;Parent=MsG0380017136.01.T01
Chr3 exon 92480254 92480334 92480254 ID=MsG0380017136.01.T01:exon:12581;Parent=MsG0380017136.01.T01
Chr3 CDS 92478541 92478585 92478541 ID=MsG0380017136.01.T01:cds;Parent=MsG0380017136.01.T01
Chr3 CDS 92478652 92478699 92478652 ID=MsG0380017136.01.T01:cds;Parent=MsG0380017136.01.T01
Chr3 CDS 92479056 92479115 92479056 ID=MsG0380017136.01.T01:cds;Parent=MsG0380017136.01.T01
Chr3 CDS 92480254 92480334 92480254 ID=MsG0380017136.01.T01:cds;Parent=MsG0380017136.01.T01
Gene Sequence

>MsG0380017136.01.T01

ATGCATGATAGTTGCGGCGTGGGAATTAGTTCTGTGACTGAACAGCTCAGAGCCGCCAGCAAGGAAGGTTTTGATGGAGTTCCTGTTTTTCAGTCAGAACTTTTGGTTGTGAAGAAGAAGAATAAACGTTATTGCCCTGTATATTTCTCTAAGGTTAATTCTTATTTATTGTTCAATTATGAAATTAAACAGGTTGGTAGCTTCGAAGATGTACTGAAAAAAATGGGAGAGTAA

Protein sequence

>MsG0380017136.01.T01

MHDSCGVGISSVTEQLRAASKEGFDGVPVFQSELLVVKKKNKRYCPVYFSKVNSYLLFNYEIKQVGSFEDVLKKMGE*