AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580030008.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580030008.01.T01 MTR_5g096560 77.941 68 6 1 4 71 144 202 4.58e-18 76.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 138 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCACTGCCTCCACTGCATT+AGG 0.286004 5:+105043857 None:intergenic
TCACTGCCTCCACTGCATTA+GGG 0.318334 5:+105043858 None:intergenic
TCTAGATGGTCTTCGTCTAC+TGG 0.339022 5:-105041806 MsG0580030008.01.T01:CDS
TCAGAGGGTTCATCAATGAT+AGG 0.382601 5:-105041853 MsG0580030008.01.T01:intron
CTTACCTGTTTGATCCGTCT+TGG 0.409978 5:+105041780 None:intergenic
CTAGATGGTCTTCGTCTACT+GGG 0.415666 5:-105041805 MsG0580030008.01.T01:CDS
AATCATATTCTCAATCTAGA+TGG 0.477303 5:-105041820 MsG0580030008.01.T01:CDS
TGCCTATCTTCTTACTCCGC+AGG 0.480267 5:-105043931 MsG0580030008.01.T01:CDS
AGTTAGCTACATACTGTCTC+TGG 0.482116 5:+105043825 None:intergenic
CACTGCCTCCACTGCATTAG+GGG 0.499282 5:+105043859 None:intergenic
GCCCTGCGGAGTAAGAAGAT+AGG 0.509839 5:+105043929 None:intergenic
GGGGCCAAGACGGATCAAAC+AGG 0.523547 5:-105041784 MsG0580030008.01.T01:intron
GCCTATCTTCTTACTCCGCA+GGG 0.569141 5:-105043930 MsG0580030008.01.T01:CDS
TAGATGGTCTTCGTCTACTG+GGG 0.595054 5:-105041804 MsG0580030008.01.T01:CDS
GAAATTCTCCCCTAATGCAG+TGG 0.612114 5:-105043867 MsG0580030008.01.T01:CDS
ATTCTCCCCTAATGCAGTGG+AGG 0.636527 5:-105043864 MsG0580030008.01.T01:CDS
AGATGGTCTTCGTCTACTGG+GGG 0.656483 5:-105041803 MsG0580030008.01.T01:CDS
CTACTGCTGTGAGTGCCCTG+CGG 0.725771 5:+105043915 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATTCAACATGATTATAA+GGG + Chr5:105042027-105042046 None:intergenic 15.0%
!! AGACAATAATACTATATAAA+CGG - Chr5:105042850-105042869 MsG0580030008.01.T01:intron 15.0%
!! TCTAGAAAATTATTAAGATT+TGG + Chr5:105042432-105042451 None:intergenic 15.0%
!! TGTTACATTATTTATTTACT+GGG + Chr5:105041825-105041844 None:intergenic 15.0%
!!! ACTAGATATATATCTAATTT+TGG - Chr5:105042878-105042897 MsG0580030008.01.T01:intron 15.0%
!!! ATCCAAAAATTTTAATAAGT+GGG - Chr5:105042268-105042287 MsG0580030008.01.T01:intron 15.0%
!!! ATTCTTATATTTGTTGAAAA+AGG + Chr5:105042645-105042664 None:intergenic 15.0%
!!! ATTTTAACTTATGTAGTATT+AGG - Chr5:105043908-105043927 MsG0580030008.01.T01:CDS 15.0%
!!! CTAGATATATATCTAATTTT+GGG - Chr5:105042879-105042898 MsG0580030008.01.T01:intron 15.0%
!!! TACAAATAATGCTTATTTTT+AGG + Chr5:105042694-105042713 None:intergenic 15.0%
!!! TGAATTTTAATACATTCTTT+GGG - Chr5:105043656-105043675 MsG0580030008.01.T01:intron 15.0%
!! AATTTAATTCTTGACTGATT+CGG - Chr5:105043534-105043553 MsG0580030008.01.T01:intron 20.0%
!! ATATTCAACATGATTATAAG+GGG + Chr5:105042026-105042045 None:intergenic 20.0%
!! CTGTTACATTATTTATTTAC+TGG + Chr5:105041826-105041845 None:intergenic 20.0%
!! GAATATTCAACATGATTATA+AGG + Chr5:105042028-105042047 None:intergenic 20.0%
!! GACAATAATACTATATAAAC+GGG - Chr5:105042851-105042870 MsG0580030008.01.T01:intron 20.0%
!! TAACTTCATATCAAAATTGT+TGG - Chr5:105041759-105041778 MsG0580030008.01.T01:intron 20.0%
!! TATGTAAACTTTCGAAAAAT+TGG + Chr5:105043439-105043458 None:intergenic 20.0%
!! TCATACTAATATGATCAAAT+TGG + Chr5:105043464-105043483 None:intergenic 20.0%
!! TTAAAAATACAATACACATG+TGG - Chr5:105042902-105042921 MsG0580030008.01.T01:intron 20.0%
!!! AAATATTGTTAGAGTTTGTT+AGG + Chr5:105041974-105041993 None:intergenic 20.0%
!!! ACCTTTATAAGATTTTTAAC+TGG - Chr5:105043205-105043224 MsG0580030008.01.T01:intron 20.0%
!!! CCTTTATAAGATTTTTAACT+GGG - Chr5:105043206-105043225 MsG0580030008.01.T01:intron 20.0%
!!! CTGAATTTTAATACATTCTT+TGG - Chr5:105043655-105043674 MsG0580030008.01.T01:intron 20.0%
!!! GATCCAAAAATTTTAATAAG+TGG - Chr5:105042267-105042286 MsG0580030008.01.T01:intron 20.0%
!!! TCCAAAAATTTTAATAAGTG+GGG - Chr5:105042269-105042288 MsG0580030008.01.T01:intron 20.0%
! AATCATATTCTCAATCTAGA+TGG - Chr5:105043746-105043765 MsG0580030008.01.T01:intron 25.0%
! ACAAACTCTAACAATATTTC+TGG - Chr5:105041975-105041994 MsG0580030008.01.T01:intron 25.0%
! AGAATAGGGAAAAAAAGAAA+TGG - Chr5:105043309-105043328 MsG0580030008.01.T01:intron 25.0%
! CCCAGTTAAAAATCTTATAA+AGG + Chr5:105043209-105043228 None:intergenic 25.0%
! GAATAGAACATGATAAAAAC+TGG + Chr5:105042171-105042190 None:intergenic 25.0%
!! ACCCCACTTATTAAAATTTT+TGG + Chr5:105042273-105042292 None:intergenic 25.0%
!! GTTCTAATAATGGTAATGTT+AGG + Chr5:105042127-105042146 None:intergenic 25.0%
!!! TAATACATTCTTTGGGATTA+TGG - Chr5:105043663-105043682 MsG0580030008.01.T01:intron 25.0%
!!! TTACCATTTTAACTTTGATG+CGG - Chr5:105043140-105043159 MsG0580030008.01.T01:intron 25.0%
AAAAGAAATAACAAACCCGT+GGG + Chr5:105042490-105042509 None:intergenic 30.0%
AAAATACAATACACATGTGG+AGG - Chr5:105042905-105042924 MsG0580030008.01.T01:intron 30.0%
AACATATTCATGACTACACA+GGG + Chr5:105043113-105043132 None:intergenic 30.0%
AACCTAAAAGATAAACTGAC+AGG + Chr5:105042575-105042594 None:intergenic 30.0%
ACGGAAAAAGAAAAGATAAC+CGG - Chr5:105041897-105041916 MsG0580030008.01.T01:intron 30.0%
AGAATAGTAGCTAGATAATC+AGG - Chr5:105043046-105043065 MsG0580030008.01.T01:intron 30.0%
AGCTAACTTAAAATCAGTTG+CGG - Chr5:105043013-105043032 MsG0580030008.01.T01:intron 30.0%
ATTGGAAAGCAAAAAGTAAG+AGG + Chr5:105043838-105043857 None:intergenic 30.0%
CTATCAGATACATTTGGAAA+TGG + Chr5:105041800-105041819 None:intergenic 30.0%
TCTGCAATAACAGATACAAA+TGG - Chr5:105042223-105042242 MsG0580030008.01.T01:intron 30.0%
TTATCTAGCTACTATTCTCA+TGG + Chr5:105043044-105043063 None:intergenic 30.0%
! AACCTGTCAGTTTATCTTTT+AGG - Chr5:105042570-105042589 MsG0580030008.01.T01:intron 30.0%
! AATAATGGTAATGTTAGGAG+CGG + Chr5:105042122-105042141 None:intergenic 30.0%
! GCAAGCAAAAGTTCTAATAA+TGG + Chr5:105042137-105042156 None:intergenic 30.0%
!! ATTTTATCCCTTGTTTCAGA+GGG - Chr5:105043698-105043717 MsG0580030008.01.T01:intron 30.0%
!! GATTTTAAGTCATCTTCATC+AGG + Chr5:105042975-105042994 None:intergenic 30.0%
!!! TTTTGTTTTATTTCAGCCCA+CGG - Chr5:105042471-105042490 MsG0580030008.01.T01:intron 30.0%
AAAGTAAGAGGATGAACAGA+AGG + Chr5:105043826-105043845 None:intergenic 35.0%
AACTAAAGACAGCAAAGTGT+TGG + Chr5:105043867-105043886 None:intergenic 35.0%
AAGTAAGAGGATGAACAGAA+GGG + Chr5:105043825-105043844 None:intergenic 35.0%
ATGTTTAGACAGTGGAGAAT+AGG - Chr5:105043294-105043313 MsG0580030008.01.T01:intron 35.0%
CAAAAGAAATAACAAACCCG+TGG + Chr5:105042491-105042510 None:intergenic 35.0%
CAACCGCATCAAAGTTAAAA+TGG + Chr5:105043146-105043165 None:intergenic 35.0%
CTAACTTAAAATCAGTTGCG+GGG - Chr5:105043015-105043034 MsG0580030008.01.T01:intron 35.0%
GAACATATTCATGACTACAC+AGG + Chr5:105043114-105043133 None:intergenic 35.0%
GATGTAACATGTTTAGACAG+TGG - Chr5:105043286-105043305 MsG0580030008.01.T01:intron 35.0%
GCTAACTTAAAATCAGTTGC+GGG - Chr5:105043014-105043033 MsG0580030008.01.T01:intron 35.0%
TCCTATTCAGCCCATTTATT+AGG - Chr5:105042084-105042103 MsG0580030008.01.T01:intron 35.0%
TCCTCTCTTTCACACAAAAA+CGG + Chr5:105043264-105043283 None:intergenic 35.0%
TGGACCTATGCCTAATAAAT+GGG + Chr5:105042097-105042116 None:intergenic 35.0%
TGGGTTCTATCAGATACATT+TGG + Chr5:105041806-105041825 None:intergenic 35.0%
TGTTTAGACAGTGGAGAATA+GGG - Chr5:105043295-105043314 MsG0580030008.01.T01:intron 35.0%
TTCAACATGATTATAAGGGG+TGG + Chr5:105042023-105042042 None:intergenic 35.0%
TTGGACCTATGCCTAATAAA+TGG + Chr5:105042098-105042117 None:intergenic 35.0%
! ATAATGGTAATGTTAGGAGC+GGG + Chr5:105042121-105042140 None:intergenic 35.0%
! TTCTTTTCAAACTGCAGAGA+AGG + Chr5:105043564-105043583 None:intergenic 35.0%
! TTTTTGTGTGAAAGAGAGGA+TGG - Chr5:105043264-105043283 MsG0580030008.01.T01:intron 35.0%
!! GATTTTATCCCTTGTTTCAG+AGG - Chr5:105043697-105043716 MsG0580030008.01.T01:intron 35.0%
!!! TTTGTTTTATTTCAGCCCAC+GGG - Chr5:105042472-105042491 MsG0580030008.01.T01:intron 35.0%
AGAACATTATGCAGCCTAAG+AGG - Chr5:105042521-105042540 MsG0580030008.01.T01:intron 40.0%
AGTTAGCTACATACTGTCTC+TGG + Chr5:105041744-105041763 None:intergenic 40.0%
ATATTCATGACTACACAGGG+TGG + Chr5:105043110-105043129 None:intergenic 40.0%
GTGCTCTTAGTACACTCATT+AGG - Chr5:105042781-105042800 MsG0580030008.01.T01:intron 40.0%
TAAGTCATCTTCATCAGGCA+CGG + Chr5:105042970-105042989 None:intergenic 40.0%
TCAGAGGGTTCATCAATGAT+AGG - Chr5:105043713-105043732 MsG0580030008.01.T01:intron 40.0%
TCAGCCCATTTATTAGGCAT+AGG - Chr5:105042090-105042109 MsG0580030008.01.T01:intron 40.0%
TCTCTTTCACACAAAAACGG+AGG + Chr5:105043261-105043280 None:intergenic 40.0%
TGAACTCAAGAGCTCTACAA+TGG - Chr5:105041869-105041888 MsG0580030008.01.T01:intron 40.0%
TGGCTGATATAGCAATCAGT+TGG + Chr5:105042050-105042069 None:intergenic 40.0%
TTGTTAGGAGAGTTTCTCTC+TGG + Chr5:105041959-105041978 None:intergenic 40.0%
! TCTGTGTGAAACAGAGTGTT+TGG - Chr5:105043506-105043525 MsG0580030008.01.T01:intron 40.0%
!! CCTATCAAAAAGTGCCTCTT+AGG + Chr5:105042538-105042557 None:intergenic 40.0%
!! GCCTAATAAATGGGCTGAAT+AGG + Chr5:105042088-105042107 None:intergenic 40.0%
!! TCCGTTTTTGTGTGAAAGAG+AGG - Chr5:105043260-105043279 MsG0580030008.01.T01:intron 40.0%
!! TGATGAACCCTCTGAAACAA+GGG + Chr5:105043708-105043727 None:intergenic 40.0%
!! TTGATGAACCCTCTGAAACA+AGG + Chr5:105043709-105043728 None:intergenic 40.0%
!!! CCTAAGAGGCACTTTTTGAT+AGG - Chr5:105042535-105042554 MsG0580030008.01.T01:intron 40.0%
AATACACATGTGGAGGCAAG+TGG - Chr5:105042912-105042931 MsG0580030008.01.T01:intron 45.0%
ACTCAAGAGCTCTACAATGG+TGG - Chr5:105041872-105041891 MsG0580030008.01.T01:intron 45.0%
ATAAGGGGTGGAAGTAAGAG+AGG + Chr5:105042011-105042030 None:intergenic 45.0%
ATACACATGTGGAGGCAAGT+GGG - Chr5:105042913-105042932 MsG0580030008.01.T01:intron 45.0%
CTAGATGGTCTTCGTCTACT+GGG - Chr5:105043761-105043780 MsG0580030008.01.T01:intron 45.0%
CTTACCTGTTTGATCCGTCT+TGG + Chr5:105043789-105043808 None:intergenic 45.0%
GAAATTCTCCCCTAATGCAG+TGG - Chr5:105041699-105041718 MsG0580030008.01.T01:intron 45.0%
GGTTAGGAGTTCTTGAACTC+CGG + Chr5:105041919-105041938 None:intergenic 45.0%
TAAGAGGATGAACAGAAGGG+CGG + Chr5:105043822-105043841 None:intergenic 45.0%
TAAGGGGTGGAAGTAAGAGA+GGG + Chr5:105042010-105042029 None:intergenic 45.0%
TAGATGGTCTTCGTCTACTG+GGG - Chr5:105043762-105043781 MsG0580030008.01.T01:intron 45.0%
TAGGAGAGTTTCTCTCTGGT+AGG + Chr5:105041955-105041974 None:intergenic 45.0%
TCTAGATGGTCTTCGTCTAC+TGG - Chr5:105043760-105043779 MsG0580030008.01.T01:intron 45.0%
TGTGACTGACTGACGCAATA+CGG + Chr5:105042621-105042640 None:intergenic 45.0%
! AGGAGCATATTGCTCTGGTT+AGG + Chr5:105041935-105041954 None:intergenic 45.0%
! GAGCTCTACAATGGTGGAAA+CGG - Chr5:105041878-105041897 MsG0580030008.01.T01:intron 45.0%
!! GCAAAGTGTTGGCAGTGTAT+TGG + Chr5:105043856-105043875 None:intergenic 45.0%
!! CTATAAAAATTATAAAAAAA+AGG + Chr5:105042809-105042828 None:intergenic 5.0%
AGATGGTCTTCGTCTACTGG+GGG - Chr5:105043763-105043782 MsG0580030008.01.T01:intron 50.0%
ATAGCGTAGTCAGATGCAGG+AGG - Chr5:105042370-105042389 MsG0580030008.01.T01:intron 50.0%
ATCACTGCCTCCACTGCATT+AGG + Chr5:105041712-105041731 None:intergenic 50.0%
ATCAGGCACGGATCTAGTGT+GGG + Chr5:105042958-105042977 None:intergenic 50.0%
ATTCTCCCCTAATGCAGTGG+AGG - Chr5:105041702-105041721 MsG0580030008.01.T01:intron 50.0%
CTATATCAGCCATCGCTCCA+CGG - Chr5:105042058-105042077 MsG0580030008.01.T01:intron 50.0%
GCCTATCTTCTTACTCCGCA+GGG - Chr5:105041636-105041655 MsG0580030008.01.T01:CDS 50.0%
TACACATGTGGAGGCAAGTG+GGG - Chr5:105042914-105042933 MsG0580030008.01.T01:intron 50.0%
TAGCGTAGTCAGATGCAGGA+GGG - Chr5:105042371-105042390 MsG0580030008.01.T01:intron 50.0%
TATATCAGCCATCGCTCCAC+GGG - Chr5:105042059-105042078 MsG0580030008.01.T01:intron 50.0%
TCACTGCCTCCACTGCATTA+GGG + Chr5:105041711-105041730 None:intergenic 50.0%
TGCCTATCTTCTTACTCCGC+AGG - Chr5:105041635-105041654 MsG0580030008.01.T01:CDS 50.0%
! CTGGTAGGAGCATATTGCTC+TGG + Chr5:105041940-105041959 None:intergenic 50.0%
! TGGTAATGTTAGGAGCGGGT+TGG + Chr5:105042117-105042136 None:intergenic 50.0%
ATAGGAAACCCGTGGAGCGA+TGG + Chr5:105042070-105042089 None:intergenic 55.0%
CACTGCCTCCACTGCATTAG+GGG + Chr5:105041710-105041729 None:intergenic 55.0%
CATCAGGCACGGATCTAGTG+TGG + Chr5:105042959-105042978 None:intergenic 55.0%
CGCATAGCGTAGTCAGATGC+AGG - Chr5:105042367-105042386 MsG0580030008.01.T01:intron 55.0%
GCCCTGCGGAGTAAGAAGAT+AGG + Chr5:105041640-105041659 None:intergenic 55.0%
GGATCTAGTGTGGGGGCAAT+GGG + Chr5:105042949-105042968 None:intergenic 55.0%
TCAGGCACGGATCTAGTGTG+GGG + Chr5:105042957-105042976 None:intergenic 55.0%
TGGGCTGAATAGGAAACCCG+TGG + Chr5:105042078-105042097 None:intergenic 55.0%
! CTGACGCAATACGGAAGCGT+AGG + Chr5:105042612-105042631 None:intergenic 55.0%
CAGGCACGGATCTAGTGTGG+GGG + Chr5:105042956-105042975 None:intergenic 60.0%
CGGATCTAGTGTGGGGGCAA+TGG + Chr5:105042950-105042969 None:intergenic 60.0%
CTACTGCTGTGAGTGCCCTG+CGG + Chr5:105041654-105041673 None:intergenic 60.0%
GGGGCCAAGACGGATCAAAC+AGG - Chr5:105043782-105043801 MsG0580030008.01.T01:intron 60.0%
TCGTCTACTGGGGGCCAAGA+CGG - Chr5:105043772-105043791 MsG0580030008.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr5 gene 105041634 105043954 105041634 ID=MsG0580030008.01;Name=MsG0580030008.01
Chr5 mRNA 105041634 105043954 105041634 ID=MsG0580030008.01.T01;Parent=MsG0580030008.01;Name=MsG0580030008.01.T01;_AED=0.50;_eAED=0.60;_QI=0|0|0.33|1|0.5|0.33|3|0|86
Chr5 exon 105043812 105043954 105043812 ID=MsG0580030008.01.T01:exon:21902;Parent=MsG0580030008.01.T01
Chr5 exon 105041785 105041871 105041785 ID=MsG0580030008.01.T01:exon:21901;Parent=MsG0580030008.01.T01
Chr5 exon 105041634 105041664 105041634 ID=MsG0580030008.01.T01:exon:21900;Parent=MsG0580030008.01.T01
Chr5 CDS 105043812 105043954 105043812 ID=MsG0580030008.01.T01:cds;Parent=MsG0580030008.01.T01
Chr5 CDS 105041785 105041871 105041785 ID=MsG0580030008.01.T01:cds;Parent=MsG0580030008.01.T01
Chr5 CDS 105041634 105041664 105041634 ID=MsG0580030008.01.T01:cds;Parent=MsG0580030008.01.T01
Gene Sequence

>MsG0580030008.01.T01

ATGCCTATCTTCTTACTCCGCAGGGCACTCACAGCAGTAGAGTTGAGAAAGAAATTGCTTAGCAAGAAATTCTCCCCTAATGCAGTGGAGGCAGTGATAAACAAGCTCCAGAGACAGTATGTAGCTAACTTCATATCAAAATTAGGGTTCATCAATGATAGGTTGTATGCTGAATCATATTCTCAATCTAGATGGTCTTCGTCTACTGGGGGCCAAGACGGATCAAACAGTATTAGGAGTGAAAGATGTAGTACATTGTGA
Protein sequence

>MsG0580030008.01.T01

MPIFLLRRALTAVELRKKLLSKKFSPNAVEAVINKLQRQYVANFISKLGFINDRLYAESYSQSRWSSSTGGQDGSNSIRSERCSTL*