AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0569600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0569600 MtrunA17_Chr3g0143601 86.275 51 7 0 7 57 32 82 9.40e-27 92.0
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 132 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTTAGGGTGATATGATTT+TGG 0.179424 4_1:+71523040 Msa0569600:intron
TTGATCTTTCCCTTCCATTC+AGG 0.208013 4_1:-71523086 None:intergenic
ATAATTACCACACCTATCAT+TGG 0.386552 4_1:-71521970 None:intergenic
TTAGTAGTTGGAAGATGTCT+TGG 0.451398 4_1:+71521913 None:intergenic
GGGCAATGAGCATCTTGAAA+TGG 0.468221 4_1:+71522919 Msa0569600:CDS
GCATCTTGAAATGGTTATGA+TGG 0.484463 4_1:+71522928 Msa0569600:CDS
TTGGTCTAAAACATAGAAAG+AGG 0.534252 4_1:+71521932 Msa0569600:five_prime_UTR
AATGGTTATGATGGATTCGA+AGG 0.551631 4_1:+71522937 Msa0569600:CDS
GTGGTGATCACACACCTGAA+TGG 0.559813 4_1:+71523072 Msa0569600:CDS
TGATCACACACCTGAATGGA+AGG 0.561482 4_1:+71523076 Msa0569600:CDS
GACTTGAAGTATCCAATGAT+AGG 0.570031 4_1:+71521958 Msa0569600:exon
GAATGGAAGGGAAAGATCAA+AGG 0.591870 4_1:+71523089 Msa0569600:CDS
GTATTCTTGATATAGTGTTG+GGG 0.619055 4_1:+71522899 Msa0569600:intron
ATGACGTGTATCATCAACAA+TGG 0.659985 4_1:+71523116 Msa0569600:CDS
GAAGTATCCAATGATAGGTG+TGG 0.661110 4_1:+71521963 Msa0569600:exon
GATCACACACCTGAATGGAA+GGG 0.672624 4_1:+71523077 Msa0569600:CDS
ATTCAGGTGTGTGATCACCA+CGG 0.733008 4_1:-71523070 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTACTTTTGAATTAAAAT+AGG + chr4_1:71522381-71522400 Msa0569600:intron 10.0%
!!! TTTTACTTTTGAATTAAAAT+AGG + chr4_1:71522381-71522400 Msa0569600:intron 10.0%
!! TTTCAAAGATTGAAAAAATA+TGG - chr4_1:71522025-71522044 None:intergenic 15.0%
!!! TATTTTTTCAATCTTTGAAA+TGG + chr4_1:71522025-71522044 Msa0569600:intron 15.0%
!! TTTCAAAGATTGAAAAAATA+TGG - chr4_1:71522025-71522044 None:intergenic 15.0%
!!! TATTTTTTCAATCTTTGAAA+TGG + chr4_1:71522025-71522044 Msa0569600:intron 15.0%
!! GTGTGGTAATTATAAAATTA+TGG + chr4_1:71521980-71521999 Msa0569600:intron 20.0%
!! TAATTATAAAATTATGGACC+AGG + chr4_1:71521986-71522005 Msa0569600:intron 20.0%
!! AAGAAGATTTAACATTCTTA+TGG + chr4_1:71522597-71522616 Msa0569600:intron 20.0%
!! ACAGATTCTAACTAAAAAAA+TGG - chr4_1:71522690-71522709 None:intergenic 20.0%
!!! TCAACTCTTTTTTTCAATTT+AGG + chr4_1:71523025-71523044 Msa0569600:intron 20.0%
!!! CAACTCTTTTTTTCAATTTA+GGG + chr4_1:71523026-71523045 Msa0569600:intron 20.0%
!! GTGTGGTAATTATAAAATTA+TGG + chr4_1:71521980-71521999 Msa0569600:intron 20.0%
!! TAATTATAAAATTATGGACC+AGG + chr4_1:71521986-71522005 Msa0569600:intron 20.0%
!! AAGAAGATTTAACATTCTTA+TGG + chr4_1:71522597-71522616 Msa0569600:intron 20.0%
!! ACAGATTCTAACTAAAAAAA+TGG - chr4_1:71522690-71522709 None:intergenic 20.0%
!!! TCAACTCTTTTTTTCAATTT+AGG + chr4_1:71523025-71523044 Msa0569600:intron 20.0%
!!! CAACTCTTTTTTTCAATTTA+GGG + chr4_1:71523026-71523045 Msa0569600:intron 20.0%
! ACTATCCTGTTAGTAAAAAT+TGG + chr4_1:71522066-71522085 Msa0569600:intron 25.0%
!!! AACTTTAAAACATCTACCAT+AGG + chr4_1:71522252-71522271 Msa0569600:intron 25.0%
! ATATGTAAGGATATGATTCA+TGG + chr4_1:71522438-71522457 Msa0569600:intron 25.0%
! ACATATTCAAACTGGAAAAA+TGG - chr4_1:71522567-71522586 None:intergenic 25.0%
! AAAAATGTCAATGACTCTTA+AGG + chr4_1:71522855-71522874 Msa0569600:intron 25.0%
!!! AATTTAGGGTGATATGATTT+TGG + chr4_1:71523040-71523059 Msa0569600:intron 25.0%
! ACTATCCTGTTAGTAAAAAT+TGG + chr4_1:71522066-71522085 Msa0569600:intron 25.0%
!!! AACTTTAAAACATCTACCAT+AGG + chr4_1:71522252-71522271 Msa0569600:intron 25.0%
! ATATGTAAGGATATGATTCA+TGG + chr4_1:71522438-71522457 Msa0569600:intron 25.0%
! ACATATTCAAACTGGAAAAA+TGG - chr4_1:71522567-71522586 None:intergenic 25.0%
! AAAAATGTCAATGACTCTTA+AGG + chr4_1:71522855-71522874 Msa0569600:intron 25.0%
!!! AATTTAGGGTGATATGATTT+TGG + chr4_1:71523040-71523059 Msa0569600:intron 25.0%
! TTGGTCTAAAACATAGAAAG+AGG + chr4_1:71521932-71521951 Msa0569600:five_prime_UTR 30.0%
ATAATTACCACACCTATCAT+TGG - chr4_1:71521973-71521992 None:intergenic 30.0%
TATGGAAGATAAAAGTTACC+TGG - chr4_1:71522007-71522026 None:intergenic 30.0%
ATATCTCTTGACTCTTAGAT+AGG + chr4_1:71522127-71522146 Msa0569600:intron 30.0%
AATCATATCCTTACATATGC+CGG - chr4_1:71522436-71522455 None:intergenic 30.0%
! ATTTCAAAGAATACGCCTTT+TGG - chr4_1:71522521-71522540 None:intergenic 30.0%
ATGCATGTACATATTCAAAC+TGG - chr4_1:71522575-71522594 None:intergenic 30.0%
TTGTGCAGCAAACTTATTTA+TGG + chr4_1:71522755-71522774 Msa0569600:intron 30.0%
!!! ACATTTTTTGAACTCTGACT+TGG + chr4_1:71522782-71522801 Msa0569600:intron 30.0%
TCGTATTCTTGATATAGTGT+TGG + chr4_1:71522897-71522916 Msa0569600:intron 30.0%
CGTATTCTTGATATAGTGTT+GGG + chr4_1:71522898-71522917 Msa0569600:intron 30.0%
GTATTCTTGATATAGTGTTG+GGG + chr4_1:71522899-71522918 Msa0569600:intron 30.0%
! TTGGTCTAAAACATAGAAAG+AGG + chr4_1:71521932-71521951 Msa0569600:five_prime_UTR 30.0%
ATAATTACCACACCTATCAT+TGG - chr4_1:71521973-71521992 None:intergenic 30.0%
TATGGAAGATAAAAGTTACC+TGG - chr4_1:71522007-71522026 None:intergenic 30.0%
ATATCTCTTGACTCTTAGAT+AGG + chr4_1:71522127-71522146 Msa0569600:intron 30.0%
AATCATATCCTTACATATGC+CGG - chr4_1:71522436-71522455 None:intergenic 30.0%
! ATTTCAAAGAATACGCCTTT+TGG - chr4_1:71522521-71522540 None:intergenic 30.0%
ATGCATGTACATATTCAAAC+TGG - chr4_1:71522575-71522594 None:intergenic 30.0%
TTGTGCAGCAAACTTATTTA+TGG + chr4_1:71522755-71522774 Msa0569600:intron 30.0%
!!! ACATTTTTTGAACTCTGACT+TGG + chr4_1:71522782-71522801 Msa0569600:intron 30.0%
TCGTATTCTTGATATAGTGT+TGG + chr4_1:71522897-71522916 Msa0569600:intron 30.0%
CGTATTCTTGATATAGTGTT+GGG + chr4_1:71522898-71522917 Msa0569600:intron 30.0%
GTATTCTTGATATAGTGTTG+GGG + chr4_1:71522899-71522918 Msa0569600:intron 30.0%
! GACTTGAAGTATCCAATGAT+AGG + chr4_1:71521958-71521977 Msa0569600:exon 35.0%
! AGGGACCAATTTTTACTAAC+AGG - chr4_1:71522074-71522093 None:intergenic 35.0%
TCAAATACTTGCAAGCTTGA+GGG - chr4_1:71522093-71522112 None:intergenic 35.0%
TTCAAATACTTGCAAGCTTG+AGG - chr4_1:71522094-71522113 None:intergenic 35.0%
AATGTAGCTTCTTCAACACT+TGG - chr4_1:71522180-71522199 None:intergenic 35.0%
AAAACTCATGCTTCATCCTA+TGG - chr4_1:71522271-71522290 None:intergenic 35.0%
! TGAAATCCAACGTTTTCTTG+CGG + chr4_1:71522535-71522554 Msa0569600:intron 35.0%
AATCTGTACATGTGTGAACA+AGG + chr4_1:71522703-71522722 Msa0569600:intron 35.0%
TATCACACAGAAAGATGTCA+CGG + chr4_1:71522817-71522836 Msa0569600:intron 35.0%
CAATGACTCTTAAGGAAACA+TGG + chr4_1:71522863-71522882 Msa0569600:intron 35.0%
GCATCTTGAAATGGTTATGA+TGG + chr4_1:71522928-71522947 Msa0569600:CDS 35.0%
!! AATGGTTATGATGGATTCGA+AGG + chr4_1:71522937-71522956 Msa0569600:CDS 35.0%
ATGACGTGTATCATCAACAA+TGG + chr4_1:71523116-71523135 Msa0569600:CDS 35.0%
! GACTTGAAGTATCCAATGAT+AGG + chr4_1:71521958-71521977 Msa0569600:exon 35.0%
! AGGGACCAATTTTTACTAAC+AGG - chr4_1:71522074-71522093 None:intergenic 35.0%
TCAAATACTTGCAAGCTTGA+GGG - chr4_1:71522093-71522112 None:intergenic 35.0%
TTCAAATACTTGCAAGCTTG+AGG - chr4_1:71522094-71522113 None:intergenic 35.0%
AATGTAGCTTCTTCAACACT+TGG - chr4_1:71522180-71522199 None:intergenic 35.0%
AAAACTCATGCTTCATCCTA+TGG - chr4_1:71522271-71522290 None:intergenic 35.0%
! TGAAATCCAACGTTTTCTTG+CGG + chr4_1:71522535-71522554 Msa0569600:intron 35.0%
AATCTGTACATGTGTGAACA+AGG + chr4_1:71522703-71522722 Msa0569600:intron 35.0%
TATCACACAGAAAGATGTCA+CGG + chr4_1:71522817-71522836 Msa0569600:intron 35.0%
CAATGACTCTTAAGGAAACA+TGG + chr4_1:71522863-71522882 Msa0569600:intron 35.0%
GCATCTTGAAATGGTTATGA+TGG + chr4_1:71522928-71522947 Msa0569600:CDS 35.0%
!! AATGGTTATGATGGATTCGA+AGG + chr4_1:71522937-71522956 Msa0569600:CDS 35.0%
ATGACGTGTATCATCAACAA+TGG + chr4_1:71523116-71523135 Msa0569600:CDS 35.0%
! GAAGTATCCAATGATAGGTG+TGG + chr4_1:71521963-71521982 Msa0569600:exon 40.0%
CGGAGCATACTTATACATCT+GGG - chr4_1:71522416-71522435 None:intergenic 40.0%
CCAGATGTATAAGTATGCTC+CGG + chr4_1:71522414-71522433 Msa0569600:intron 40.0%
ATGATTCATGGATGTTCCGA+TGG + chr4_1:71522450-71522469 Msa0569600:intron 40.0%
! GAAATCCAACGTTTTCTTGC+GGG + chr4_1:71522536-71522555 Msa0569600:intron 40.0%
!!! ATGATTTTGGCTTTGATCCG+TGG + chr4_1:71523053-71523072 Msa0569600:CDS 40.0%
TTGATCTTTCCCTTCCATTC+AGG - chr4_1:71523089-71523108 None:intergenic 40.0%
GAATGGAAGGGAAAGATCAA+AGG + chr4_1:71523089-71523108 Msa0569600:CDS 40.0%
! GAAGTATCCAATGATAGGTG+TGG + chr4_1:71521963-71521982 Msa0569600:exon 40.0%
CGGAGCATACTTATACATCT+GGG - chr4_1:71522416-71522435 None:intergenic 40.0%
CCAGATGTATAAGTATGCTC+CGG + chr4_1:71522414-71522433 Msa0569600:intron 40.0%
ATGATTCATGGATGTTCCGA+TGG + chr4_1:71522450-71522469 Msa0569600:intron 40.0%
! GAAATCCAACGTTTTCTTGC+GGG + chr4_1:71522536-71522555 Msa0569600:intron 40.0%
!!! ATGATTTTGGCTTTGATCCG+TGG + chr4_1:71523053-71523072 Msa0569600:CDS 40.0%
TTGATCTTTCCCTTCCATTC+AGG - chr4_1:71523089-71523108 None:intergenic 40.0%
GAATGGAAGGGAAAGATCAA+AGG + chr4_1:71523089-71523108 Msa0569600:CDS 40.0%
CCGGAGCATACTTATACATC+TGG - chr4_1:71522417-71522436 None:intergenic 45.0%
AGTATGCTCCGGCATATGTA+AGG + chr4_1:71522425-71522444 Msa0569600:intron 45.0%
! ATTATGTCTGGGATCAGTCC+CGG - chr4_1:71522484-71522503 None:intergenic 45.0%
GGACTGATCCCAGACATAAT+GGG + chr4_1:71522484-71522503 Msa0569600:intron 45.0%
GGGCAATGAGCATCTTGAAA+TGG + chr4_1:71522919-71522938 Msa0569600:CDS 45.0%
ATTCAGGTGTGTGATCACCA+CGG - chr4_1:71523073-71523092 None:intergenic 45.0%
TGATCACACACCTGAATGGA+AGG + chr4_1:71523076-71523095 Msa0569600:CDS 45.0%
GATCACACACCTGAATGGAA+GGG + chr4_1:71523077-71523096 Msa0569600:CDS 45.0%
CCGGAGCATACTTATACATC+TGG - chr4_1:71522417-71522436 None:intergenic 45.0%
AGTATGCTCCGGCATATGTA+AGG + chr4_1:71522425-71522444 Msa0569600:intron 45.0%
! ATTATGTCTGGGATCAGTCC+CGG - chr4_1:71522484-71522503 None:intergenic 45.0%
GGACTGATCCCAGACATAAT+GGG + chr4_1:71522484-71522503 Msa0569600:intron 45.0%
GGGCAATGAGCATCTTGAAA+TGG + chr4_1:71522919-71522938 Msa0569600:CDS 45.0%
ATTCAGGTGTGTGATCACCA+CGG - chr4_1:71523073-71523092 None:intergenic 45.0%
TGATCACACACCTGAATGGA+AGG + chr4_1:71523076-71523095 Msa0569600:CDS 45.0%
GATCACACACCTGAATGGAA+GGG + chr4_1:71523077-71523096 Msa0569600:CDS 45.0%
TGTTCCGATGGTAGCAGAAC+CGG + chr4_1:71522462-71522481 Msa0569600:intron 50.0%
GGGACTGATCCCAGACATAA+TGG + chr4_1:71522483-71522502 Msa0569600:intron 50.0%
!! GATCCCAGACATAATGGGCT+TGG + chr4_1:71522489-71522508 Msa0569600:intron 50.0%
CAGCCAAGCCCATTATGTCT+GGG - chr4_1:71522495-71522514 None:intergenic 50.0%
ACAGCCAAGCCCATTATGTC+TGG - chr4_1:71522496-71522515 None:intergenic 50.0%
ACAGACCCGCAAGAAAACGT+TGG - chr4_1:71522544-71522563 None:intergenic 50.0%
GTGGTGATCACACACCTGAA+TGG + chr4_1:71523072-71523091 Msa0569600:CDS 50.0%
TGTTCCGATGGTAGCAGAAC+CGG + chr4_1:71522462-71522481 Msa0569600:intron 50.0%
GGGACTGATCCCAGACATAA+TGG + chr4_1:71522483-71522502 Msa0569600:intron 50.0%
!! GATCCCAGACATAATGGGCT+TGG + chr4_1:71522489-71522508 Msa0569600:intron 50.0%
CAGCCAAGCCCATTATGTCT+GGG - chr4_1:71522495-71522514 None:intergenic 50.0%
ACAGCCAAGCCCATTATGTC+TGG - chr4_1:71522496-71522515 None:intergenic 50.0%
ACAGACCCGCAAGAAAACGT+TGG - chr4_1:71522544-71522563 None:intergenic 50.0%
GTGGTGATCACACACCTGAA+TGG + chr4_1:71523072-71523091 Msa0569600:CDS 50.0%
GTTCCGATGGTAGCAGAACC+GGG + chr4_1:71522463-71522482 Msa0569600:intron 55.0%
AGTCCCGGTTCTGCTACCAT+CGG - chr4_1:71522469-71522488 None:intergenic 55.0%
TGGGCTTGGCTGTAGCCAAA+AGG + chr4_1:71522503-71522522 Msa0569600:intron 55.0%
GTTCCGATGGTAGCAGAACC+GGG + chr4_1:71522463-71522482 Msa0569600:intron 55.0%
AGTCCCGGTTCTGCTACCAT+CGG - chr4_1:71522469-71522488 None:intergenic 55.0%
TGGGCTTGGCTGTAGCCAAA+AGG + chr4_1:71522503-71522522 Msa0569600:intron 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 71521920 71523160 71521920 ID=Msa0569600;Name=Msa0569600
chr4_1 mRNA 71521920 71523160 71521920 ID=Msa0569600-mRNA-1;Parent=Msa0569600;Name=Msa0569600-mRNA-1;_AED=0.39;_eAED=0.39;_QI=53|0|0|0.66|0.5|0.33|3|0|57
chr4_1 exon 71521920 71521984 71521920 ID=Msa0569600-mRNA-1:exon:24321;Parent=Msa0569600-mRNA-1
chr4_1 exon 71522914 71522958 71522914 ID=Msa0569600-mRNA-1:exon:24322;Parent=Msa0569600-mRNA-1
chr4_1 exon 71523047 71523160 71523047 ID=Msa0569600-mRNA-1:exon:24323;Parent=Msa0569600-mRNA-1
chr4_1 five_prime_UTR 71521920 71521972 71521920 ID=Msa0569600-mRNA-1:five_prime_utr;Parent=Msa0569600-mRNA-1
chr4_1 CDS 71521973 71521984 71521973 ID=Msa0569600-mRNA-1:cds;Parent=Msa0569600-mRNA-1
chr4_1 CDS 71522914 71522958 71522914 ID=Msa0569600-mRNA-1:cds;Parent=Msa0569600-mRNA-1
chr4_1 CDS 71523047 71523160 71523047 ID=Msa0569600-mRNA-1:cds;Parent=Msa0569600-mRNA-1
Gene Sequence

>Msa0569600

ATGATAGGTGTGTGTTGGGGCAATGAGCATCTTGAAATGGTTATGATGGATTCGAAGGGTGATATGATTTTGGCTTTGATCCGTGGTGATCACACACCTGAATGGAAGGGAAAGATCAAAGGAGATATGACGTGTATCATCAACAATGGTGTTGTGTATGACAATGATTTT

Protein sequence

>Msa0569600

MIGVCWGNEHLEMVMMDSKGDMILALIRGDHTPEWKGKIKGDMTCIINNGVVYDNDF