AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0298720


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 17 sgRNAs with CRISPR-Local

Find 148 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATTTCCCACTTGATGATT+TGG 0.254005 2_3:+52927101 None:intergenic
CACTTGATGATTTGGTGATT+TGG 0.295699 2_3:+52927109 None:intergenic
CCTCAGGCTGCGTGCATAGA+AGG 0.357626 2_3:-52926206 Msa0298720:intron
GAAACTTACTTATCAAGCTC+AGG 0.383818 2_3:-52927729 Msa0298720:CDS
ATAAGTAAGTTTCAAACTCA+TGG 0.391180 2_3:+52927739 None:intergenic
ACCGTATGGGTTTGTGTGGT+TGG 0.413547 2_3:-52926163 Msa0298720:CDS
GCTTTACATGGGCTACCGTA+TGG 0.471604 2_3:-52926177 Msa0298720:CDS
CTTTACATGGGCTACCGTAT+GGG 0.531745 2_3:-52926176 Msa0298720:CDS
AGAAGGAGCAGAGCTTTACA+TGG 0.539130 2_3:-52926189 Msa0298720:CDS
ACAAAGTTGTTGAATTGAAG+AGG 0.541562 2_3:-52927137 Msa0298720:CDS
AAACTTACTTATCAAGCTCA+GGG 0.578266 2_3:-52927728 Msa0298720:CDS
CAAATCACCAAATCATCAAG+TGG 0.587707 2_3:-52927108 Msa0298720:CDS
TCCAACCACACAAACCCATA+CGG 0.615960 2_3:+52926162 None:intergenic
GGCTACCGTATGGGTTTGTG+TGG 0.617990 2_3:-52926167 Msa0298720:CDS
AAATCACCAAATCATCAAGT+GGG 0.643117 2_3:-52927107 Msa0298720:CDS
AAAGCAAGATGAGTCACATG+AGG 0.653902 2_3:-52927070 Msa0298720:intron
GAAGGAGCAGAGCTTTACAT+GGG 0.680127 2_3:-52926188 Msa0298720:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGAATAAACTTAATATA+TGG + chr2_3:52926243-52926262 None:intergenic 10.0%
!! ATGAATAAAATTTATCAAAA+TGG + chr2_3:52926268-52926287 None:intergenic 10.0%
!! AAATGAATAAACTTAATATA+TGG + chr2_3:52926243-52926262 None:intergenic 10.0%
!! ATGAATAAAATTTATCAAAA+TGG + chr2_3:52926268-52926287 None:intergenic 10.0%
!! TTGATGTTTATAATTGAAAT+TGG - chr2_3:52926658-52926677 Msa0298720:intron 15.0%
!!! TTTTTTTGTTTATTTATCCA+GGG + chr2_3:52927092-52927111 None:intergenic 15.0%
!!! ATTTTTTTGTTTATTTATCC+AGG + chr2_3:52927093-52927112 None:intergenic 15.0%
!! AAATCAATATTCTTATACAT+AGG - chr2_3:52927226-52927245 Msa0298720:intron 15.0%
!! AATCAATATTCTTATACATA+GGG - chr2_3:52927227-52927246 Msa0298720:intron 15.0%
!! AAAATCTTCAATAAAATACT+CGG - chr2_3:52927484-52927503 Msa0298720:intron 15.0%
!! ATTATGAATCATAAGTTTAT+TGG - chr2_3:52927553-52927572 Msa0298720:intron 15.0%
!! TTGATGTTTATAATTGAAAT+TGG - chr2_3:52926658-52926677 Msa0298720:intron 15.0%
!!! TTTTTTTGTTTATTTATCCA+GGG + chr2_3:52927092-52927111 None:intergenic 15.0%
!!! ATTTTTTTGTTTATTTATCC+AGG + chr2_3:52927093-52927112 None:intergenic 15.0%
!! AAATCAATATTCTTATACAT+AGG - chr2_3:52927226-52927245 Msa0298720:intron 15.0%
!! AATCAATATTCTTATACATA+GGG - chr2_3:52927227-52927246 Msa0298720:intron 15.0%
!! AAAATCTTCAATAAAATACT+CGG - chr2_3:52927484-52927503 Msa0298720:intron 15.0%
!! ATTATGAATCATAAGTTTAT+TGG - chr2_3:52927553-52927572 Msa0298720:intron 15.0%
!! TAGATTTAGTAATCTCAAAA+AGG + chr2_3:52926345-52926364 None:intergenic 20.0%
!! GAATAAGAACAACAAATATT+TGG + chr2_3:52926958-52926977 None:intergenic 20.0%
!! AATATTGAAAAGATGCAAAA+TGG - chr2_3:52927052-52927071 Msa0298720:intron 20.0%
!!! TAAGAATATTGATTTGTTTG+AGG + chr2_3:52927221-52927240 None:intergenic 20.0%
!! ATCAATATTCTTATACATAG+GGG - chr2_3:52927228-52927247 Msa0298720:intron 20.0%
!!! AATTTTATATTCCCTAAACA+TGG - chr2_3:52927276-52927295 Msa0298720:intron 20.0%
!!! ATTTTATATTCCCTAAACAT+GGG - chr2_3:52927277-52927296 Msa0298720:intron 20.0%
!!! GAGTATTTTATTGAAGATTT+TGG + chr2_3:52927485-52927504 None:intergenic 20.0%
!! TAGATTTAGTAATCTCAAAA+AGG + chr2_3:52926345-52926364 None:intergenic 20.0%
!! GAATAAGAACAACAAATATT+TGG + chr2_3:52926958-52926977 None:intergenic 20.0%
!! AATATTGAAAAGATGCAAAA+TGG - chr2_3:52927052-52927071 Msa0298720:intron 20.0%
!!! TAAGAATATTGATTTGTTTG+AGG + chr2_3:52927221-52927240 None:intergenic 20.0%
!! ATCAATATTCTTATACATAG+GGG - chr2_3:52927228-52927247 Msa0298720:intron 20.0%
!!! AATTTTATATTCCCTAAACA+TGG - chr2_3:52927276-52927295 Msa0298720:intron 20.0%
!!! ATTTTATATTCCCTAAACAT+GGG - chr2_3:52927277-52927296 Msa0298720:intron 20.0%
!!! GAGTATTTTATTGAAGATTT+TGG + chr2_3:52927485-52927504 None:intergenic 20.0%
! ATAGATATAGATATGGAATG+AGG + chr2_3:52926297-52926316 None:intergenic 25.0%
! CAGATCAATAGATATAGATA+TGG + chr2_3:52926304-52926323 None:intergenic 25.0%
! TGCATTTACTAAACCTAAAA+TGG - chr2_3:52926421-52926440 Msa0298720:intron 25.0%
!! TATGAAACACATACCATTTT+AGG + chr2_3:52926437-52926456 None:intergenic 25.0%
!!! GTTTTAGATCTTACAAGAAA+TGG - chr2_3:52926469-52926488 Msa0298720:intron 25.0%
!! GTTCTATTCACCTTTTATTA+CGG - chr2_3:52926692-52926711 Msa0298720:intron 25.0%
! AGTAACTTATCCGTAATAAA+AGG + chr2_3:52926705-52926724 None:intergenic 25.0%
! TTGATGTGTTCTTAAAAACA+CGG - chr2_3:52926860-52926879 Msa0298720:intron 25.0%
!!! ACTTGTTGTAACTATATTAC+TGG + chr2_3:52926893-52926912 None:intergenic 25.0%
! GCAAAATGGATATAAATTCA+TGG - chr2_3:52927066-52927085 Msa0298720:intron 25.0%
!! TAGGGGTTATAAGTATTTTA+TGG - chr2_3:52927245-52927264 Msa0298720:intron 25.0%
!! TTTTATATTCCCTAAACATG+GGG - chr2_3:52927278-52927297 Msa0298720:intron 25.0%
! ATAGATATAGATATGGAATG+AGG + chr2_3:52926297-52926316 None:intergenic 25.0%
! CAGATCAATAGATATAGATA+TGG + chr2_3:52926304-52926323 None:intergenic 25.0%
! TGCATTTACTAAACCTAAAA+TGG - chr2_3:52926421-52926440 Msa0298720:intron 25.0%
!! TATGAAACACATACCATTTT+AGG + chr2_3:52926437-52926456 None:intergenic 25.0%
!!! GTTTTAGATCTTACAAGAAA+TGG - chr2_3:52926469-52926488 Msa0298720:intron 25.0%
!! GTTCTATTCACCTTTTATTA+CGG - chr2_3:52926692-52926711 Msa0298720:intron 25.0%
! AGTAACTTATCCGTAATAAA+AGG + chr2_3:52926705-52926724 None:intergenic 25.0%
! TTGATGTGTTCTTAAAAACA+CGG - chr2_3:52926860-52926879 Msa0298720:intron 25.0%
!!! ACTTGTTGTAACTATATTAC+TGG + chr2_3:52926893-52926912 None:intergenic 25.0%
! GCAAAATGGATATAAATTCA+TGG - chr2_3:52927066-52927085 Msa0298720:intron 25.0%
!! TAGGGGTTATAAGTATTTTA+TGG - chr2_3:52927245-52927264 Msa0298720:intron 25.0%
!! TTTTATATTCCCTAAACATG+GGG - chr2_3:52927278-52927297 Msa0298720:intron 25.0%
AAACTTACTTATCAAGCTCA+GGG - chr2_3:52926163-52926182 Msa0298720:CDS 30.0%
TTAACACATACTAATTGTCG+AGG + chr2_3:52926379-52926398 None:intergenic 30.0%
GCAAAAAATCGCATCTTAAA+TGG - chr2_3:52926525-52926544 Msa0298720:intron 30.0%
TAACTCATAATCAAGTTCTG+AGG - chr2_3:52926567-52926586 Msa0298720:intron 30.0%
ACAAAGTTGTTGAATTGAAG+AGG - chr2_3:52926754-52926773 Msa0298720:intron 30.0%
AAATCACCAAATCATCAAGT+GGG - chr2_3:52926784-52926803 Msa0298720:intron 30.0%
! AAATTTCCCACTTGATGATT+TGG + chr2_3:52926793-52926812 None:intergenic 30.0%
! TCATCAAGTGGGAAATTTTA+TGG - chr2_3:52926795-52926814 Msa0298720:intron 30.0%
AAAAAATGTAAAACACCGCA+CGG - chr2_3:52927106-52927125 Msa0298720:CDS 30.0%
AGACTTACAAAATCTTTCTC+TGG - chr2_3:52927130-52927149 Msa0298720:CDS 30.0%
AGTGAAAGACTGAAAATACA+TGG + chr2_3:52927157-52927176 None:intergenic 30.0%
CTAGTAAAGACAACAAAAAG+AGG - chr2_3:52927411-52927430 Msa0298720:intron 30.0%
GACAAATCGTATTTATACTG+TGG + chr2_3:52927632-52927651 None:intergenic 30.0%
AAACTTACTTATCAAGCTCA+GGG - chr2_3:52926163-52926182 Msa0298720:CDS 30.0%
TTAACACATACTAATTGTCG+AGG + chr2_3:52926379-52926398 None:intergenic 30.0%
GCAAAAAATCGCATCTTAAA+TGG - chr2_3:52926525-52926544 Msa0298720:intron 30.0%
TAACTCATAATCAAGTTCTG+AGG - chr2_3:52926567-52926586 Msa0298720:intron 30.0%
ACAAAGTTGTTGAATTGAAG+AGG - chr2_3:52926754-52926773 Msa0298720:intron 30.0%
AAATCACCAAATCATCAAGT+GGG - chr2_3:52926784-52926803 Msa0298720:intron 30.0%
! AAATTTCCCACTTGATGATT+TGG + chr2_3:52926793-52926812 None:intergenic 30.0%
! TCATCAAGTGGGAAATTTTA+TGG - chr2_3:52926795-52926814 Msa0298720:intron 30.0%
AAAAAATGTAAAACACCGCA+CGG - chr2_3:52927106-52927125 Msa0298720:CDS 30.0%
AGACTTACAAAATCTTTCTC+TGG - chr2_3:52927130-52927149 Msa0298720:CDS 30.0%
AGTGAAAGACTGAAAATACA+TGG + chr2_3:52927157-52927176 None:intergenic 30.0%
CTAGTAAAGACAACAAAAAG+AGG - chr2_3:52927411-52927430 Msa0298720:intron 30.0%
GACAAATCGTATTTATACTG+TGG + chr2_3:52927632-52927651 None:intergenic 30.0%
GAAACTTACTTATCAAGCTC+AGG - chr2_3:52926162-52926181 Msa0298720:CDS 35.0%
AATGTGATCTGAGTTTCTCA+TGG - chr2_3:52926599-52926618 Msa0298720:intron 35.0%
TTGTGTTCTTATTACTCTGC+AGG - chr2_3:52926728-52926747 Msa0298720:intron 35.0%
!! CACTTGATGATTTGGTGATT+TGG + chr2_3:52926785-52926804 None:intergenic 35.0%
CAAATCACCAAATCATCAAG+TGG - chr2_3:52926783-52926802 Msa0298720:intron 35.0%
AAAAATGTAAAACACCGCAC+GGG - chr2_3:52927107-52927126 Msa0298720:CDS 35.0%
TACTTATAGCCCCATGTTTA+GGG + chr2_3:52927290-52927309 None:intergenic 35.0%
ATACTTATAGCCCCATGTTT+AGG + chr2_3:52927291-52927310 None:intergenic 35.0%
!!! GATTTTGGTTGTGATAGACT+TGG + chr2_3:52927470-52927489 None:intergenic 35.0%
GAAACTTACTTATCAAGCTC+AGG - chr2_3:52926162-52926181 Msa0298720:CDS 35.0%
AATGTGATCTGAGTTTCTCA+TGG - chr2_3:52926599-52926618 Msa0298720:intron 35.0%
TTGTGTTCTTATTACTCTGC+AGG - chr2_3:52926728-52926747 Msa0298720:intron 35.0%
!! CACTTGATGATTTGGTGATT+TGG + chr2_3:52926785-52926804 None:intergenic 35.0%
CAAATCACCAAATCATCAAG+TGG - chr2_3:52926783-52926802 Msa0298720:intron 35.0%
AAAAATGTAAAACACCGCAC+GGG - chr2_3:52927107-52927126 Msa0298720:CDS 35.0%
TACTTATAGCCCCATGTTTA+GGG + chr2_3:52927290-52927309 None:intergenic 35.0%
ATACTTATAGCCCCATGTTT+AGG + chr2_3:52927291-52927310 None:intergenic 35.0%
!!! GATTTTGGTTGTGATAGACT+TGG + chr2_3:52927470-52927489 None:intergenic 35.0%
AAAGCAAGATGAGTCACATG+AGG - chr2_3:52926821-52926840 Msa0298720:intron 40.0%
TGGATATAAATTCATGGCCC+TGG - chr2_3:52927072-52927091 Msa0298720:CDS 40.0%
CTCGTGGCGTTAACAAATTA+TGG + chr2_3:52927353-52927372 None:intergenic 40.0%
!! TATTGGTTTCTGCCTTGAGT+TGG - chr2_3:52927570-52927589 Msa0298720:intron 40.0%
! ATTGGTTTCTGCCTTGAGTT+GGG - chr2_3:52927571-52927590 Msa0298720:intron 40.0%
! TTTTATGCTACTGCTACCTC+AGG - chr2_3:52927669-52927688 Msa0298720:intron 40.0%
AAAGCAAGATGAGTCACATG+AGG - chr2_3:52926821-52926840 Msa0298720:intron 40.0%
TGGATATAAATTCATGGCCC+TGG - chr2_3:52927072-52927091 Msa0298720:CDS 40.0%
CTCGTGGCGTTAACAAATTA+TGG + chr2_3:52927353-52927372 None:intergenic 40.0%
!! TATTGGTTTCTGCCTTGAGT+TGG - chr2_3:52927570-52927589 Msa0298720:intron 40.0%
! ATTGGTTTCTGCCTTGAGTT+GGG - chr2_3:52927571-52927590 Msa0298720:intron 40.0%
! TTTTATGCTACTGCTACCTC+AGG - chr2_3:52927669-52927688 Msa0298720:intron 40.0%
! GATTTTGTAAGTCTCCCGTG+CGG + chr2_3:52927124-52927143 None:intergenic 45.0%
GGGCTAACAAAGATTTCTCG+TGG + chr2_3:52927369-52927388 None:intergenic 45.0%
CATTTCTGCAACCCAACTCA+AGG + chr2_3:52927585-52927604 None:intergenic 45.0%
AGAAGGAGCAGAGCTTTACA+TGG - chr2_3:52927702-52927721 Msa0298720:CDS 45.0%
GAAGGAGCAGAGCTTTACAT+GGG - chr2_3:52927703-52927722 Msa0298720:CDS 45.0%
! CTTTACATGGGCTACCGTAT+GGG - chr2_3:52927715-52927734 Msa0298720:CDS 45.0%
TCCAACCACACAAACCCATA+CGG + chr2_3:52927732-52927751 None:intergenic 45.0%
! GATTTTGTAAGTCTCCCGTG+CGG + chr2_3:52927124-52927143 None:intergenic 45.0%
GGGCTAACAAAGATTTCTCG+TGG + chr2_3:52927369-52927388 None:intergenic 45.0%
CATTTCTGCAACCCAACTCA+AGG + chr2_3:52927585-52927604 None:intergenic 45.0%
AGAAGGAGCAGAGCTTTACA+TGG - chr2_3:52927702-52927721 Msa0298720:CDS 45.0%
GAAGGAGCAGAGCTTTACAT+GGG - chr2_3:52927703-52927722 Msa0298720:CDS 45.0%
! CTTTACATGGGCTACCGTAT+GGG - chr2_3:52927715-52927734 Msa0298720:CDS 45.0%
TCCAACCACACAAACCCATA+CGG + chr2_3:52927732-52927751 None:intergenic 45.0%
! GCTTTACATGGGCTACCGTA+TGG - chr2_3:52927714-52927733 Msa0298720:CDS 50.0%
ACCGTATGGGTTTGTGTGGT+TGG - chr2_3:52927728-52927747 Msa0298720:CDS 50.0%
! GCTTTACATGGGCTACCGTA+TGG - chr2_3:52927714-52927733 Msa0298720:CDS 50.0%
ACCGTATGGGTTTGTGTGGT+TGG - chr2_3:52927728-52927747 Msa0298720:CDS 50.0%
TTGTTAGCCCGTGCGTTGCA+CGG - chr2_3:52927379-52927398 Msa0298720:intron 55.0%
ATTTCCACCCGTGCAACGCA+CGG + chr2_3:52927390-52927409 None:intergenic 55.0%
GGCTACCGTATGGGTTTGTG+TGG - chr2_3:52927724-52927743 Msa0298720:CDS 55.0%
TTGTTAGCCCGTGCGTTGCA+CGG - chr2_3:52927379-52927398 Msa0298720:intron 55.0%
ATTTCCACCCGTGCAACGCA+CGG + chr2_3:52927390-52927409 None:intergenic 55.0%
GGCTACCGTATGGGTTTGTG+TGG - chr2_3:52927724-52927743 Msa0298720:CDS 55.0%
TGTTAGCCCGTGCGTTGCAC+GGG - chr2_3:52927380-52927399 Msa0298720:intron 60.0%
TTTCCACCCGTGCAACGCAC+GGG + chr2_3:52927389-52927408 None:intergenic 60.0%
CCTTCTATGCACGCAGCCTG+AGG + chr2_3:52927688-52927707 None:intergenic 60.0%
CCTCAGGCTGCGTGCATAGA+AGG - chr2_3:52927685-52927704 Msa0298720:CDS 60.0%
TGTTAGCCCGTGCGTTGCAC+GGG - chr2_3:52927380-52927399 Msa0298720:intron 60.0%
TTTCCACCCGTGCAACGCAC+GGG + chr2_3:52927389-52927408 None:intergenic 60.0%
CCTTCTATGCACGCAGCCTG+AGG + chr2_3:52927688-52927707 None:intergenic 60.0%
CCTCAGGCTGCGTGCATAGA+AGG - chr2_3:52927685-52927704 Msa0298720:CDS 60.0%
TAGCCCGTGCGTTGCACGGG+TGG - chr2_3:52927383-52927402 Msa0298720:intron 70.0%
TAGCCCGTGCGTTGCACGGG+TGG - chr2_3:52927383-52927402 Msa0298720:intron 70.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 52926154 52927759 52926154 ID=Msa0298720;Name=Msa0298720
chr2_3 mRNA 52926154 52927759 52926154 ID=Msa0298720-mRNA-1;Parent=Msa0298720;Name=Msa0298720-mRNA-1;_AED=0.60;_eAED=0.60;_QI=0|0|0|0.33|1|1|3|0|79
chr2_3 exon 52927682 52927759 52927682 ID=Msa0298720-mRNA-1:exon:16965;Parent=Msa0298720-mRNA-1
chr2_3 exon 52927071 52927163 52927071 ID=Msa0298720-mRNA-1:exon:16964;Parent=Msa0298720-mRNA-1
chr2_3 exon 52926154 52926222 52926154 ID=Msa0298720-mRNA-1:exon:16963;Parent=Msa0298720-mRNA-1
chr2_3 CDS 52927682 52927759 52927682 ID=Msa0298720-mRNA-1:cds;Parent=Msa0298720-mRNA-1
chr2_3 CDS 52927071 52927163 52927071 ID=Msa0298720-mRNA-1:cds;Parent=Msa0298720-mRNA-1
chr2_3 CDS 52926154 52926222 52926154 ID=Msa0298720-mRNA-1:cds;Parent=Msa0298720-mRNA-1
Gene Sequence

>Msa0298720

ATGAGTTTGAAACTTACTTATCAAGCTCAGGGTACTACTAGCAACTGTGAAACAACTAAAGCTATACTCATTTTGAAAGTGCACAAAGTTGTTGAATTGAAGAGGACTTACCAAATCACCAAATCATCAAGTGGGAAATTTTATGGTTTAAAGCAAGATGAGTCACATGAGGCTGCGTGCATAGAAGGAGCAGAGCTTTACATGGGCTACCGTATGGGTTTGTGTGGTTGGAATACGTAA

Protein sequence

>Msa0298720

MSLKLTYQAQGTTSNCETTKAILILKVHKVVELKRTYQITKSSSGKFYGLKQDESHEAACIEGAELYMGYRMGLCGWNT*