AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1093730

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 22 sgRNAs with CRISPR-Local

Find 154 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGCTTCTATTGTTATTAG+AGG 0.299366 7_3:+14430320 Msa1093730:CDS
TTACTGCTAAAACCTACAAT+AGG 0.332692 7_3:+14430032 Msa1093730:five_prime_UTR
TTTGACCACCTCATTATGTT+TGG 0.350446 7_3:-14430195 None:intergenic
TTCAATCAATGCCCTATTGT+AGG 0.402484 7_3:-14430044 None:intergenic
GTGATATAATAATTCACTAT+AGG 0.415802 7_3:+14428908 Msa1093730:five_prime_UTR
AACATAATGAGGTGGTCAAA+TGG 0.445874 7_3:+14430198 Msa1093730:exon
TACTGCTAAAACCTACAATA+GGG 0.475152 7_3:+14430033 Msa1093730:five_prime_UTR
ATTAAAAGAAAACTCTCAAA+TGG 0.477296 7_3:-14430379 None:intergenic
CAAGCAACTCTAATGTTAGT+AGG 0.483607 7_3:+14428946 Msa1093730:five_prime_UTR
AGGAGTTTGATGCATCTGAT+TGG 0.484432 7_3:+14428969 Msa1093730:five_prime_UTR
GATGCGACTGTTGGGTTCTA+CGG 0.493590 7_3:+14430220 Msa1093730:CDS
CAGATTGCAAATTAAAATTG+TGG 0.499851 7_3:+14428878 Msa1093730:five_prime_UTR
GTCAAATGGATGCGACTGTT+GGG 0.507592 7_3:+14430212 Msa1093730:exon
CAAATTAGCAAGATGTTGTA+CGG 0.521048 7_3:+14430270 Msa1093730:CDS
TTTGTGTTGAGTCAGGGCAT+TGG 0.523836 7_3:+14429994 Msa1093730:intron
ATCTTGCTAATTTGAGTGGA+AGG 0.525106 7_3:-14430261 None:intergenic
AGATTGCAAATTAAAATTGT+GGG 0.527384 7_3:+14428879 Msa1093730:five_prime_UTR
GGTCAAATGGATGCGACTGT+TGG 0.547730 7_3:+14430211 Msa1093730:exon
CAACATCTTGCTAATTTGAG+TGG 0.558198 7_3:-14430265 None:intergenic
ATGGCAGGCCAAACATAATG+AGG 0.609708 7_3:+14430187 Msa1093730:intron
GCAACTCTAATGTTAGTAGG+AGG 0.644150 7_3:+14428949 Msa1093730:five_prime_UTR
GCAGGCCAAACATAATGAGG+TGG 0.676255 7_3:+14430190 Msa1093730:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATAACTGAATTATTGAA+AGG + chr7_3:14429023-14429042 Msa1093730:intron 15.0%
!! AAGCTAAATGAAATAAAAAT+GGG - chr7_3:14429253-14429272 None:intergenic 15.0%
!! AAAGCTAAATGAAATAAAAA+TGG - chr7_3:14429254-14429273 None:intergenic 15.0%
!!! AGGTTTTGAAAATTATATAA+TGG - chr7_3:14429284-14429303 None:intergenic 15.0%
!! AAATTTCAAATTTGGTTATT+GGG + chr7_3:14429429-14429448 Msa1093730:intron 15.0%
!!! AAGTTTTTTGATTAATTTCA+TGG + chr7_3:14429494-14429513 Msa1093730:intron 15.0%
!!! AGTTTTTTGATTAATTTCAT+GGG + chr7_3:14429495-14429514 Msa1093730:intron 15.0%
!!! ATAGATTAATTTTCCTAAAT+TGG + chr7_3:14429792-14429811 Msa1093730:intron 15.0%
!! TTATATTGCAAATAAAATTG+TGG + chr7_3:14429835-14429854 Msa1093730:intron 15.0%
!! TTTATAACTGAATTATTGAA+AGG + chr7_3:14429023-14429042 Msa1093730:intron 15.0%
!! AAGCTAAATGAAATAAAAAT+GGG - chr7_3:14429253-14429272 None:intergenic 15.0%
!! AAAGCTAAATGAAATAAAAA+TGG - chr7_3:14429254-14429273 None:intergenic 15.0%
!!! AGGTTTTGAAAATTATATAA+TGG - chr7_3:14429284-14429303 None:intergenic 15.0%
!! AAATTTCAAATTTGGTTATT+GGG + chr7_3:14429429-14429448 Msa1093730:intron 15.0%
!!! AAGTTTTTTGATTAATTTCA+TGG + chr7_3:14429494-14429513 Msa1093730:intron 15.0%
!!! AGTTTTTTGATTAATTTCAT+GGG + chr7_3:14429495-14429514 Msa1093730:intron 15.0%
!!! ATAGATTAATTTTCCTAAAT+TGG + chr7_3:14429792-14429811 Msa1093730:intron 15.0%
!! TTATATTGCAAATAAAATTG+TGG + chr7_3:14429835-14429854 Msa1093730:intron 15.0%
!! AGATTGCAAATTAAAATTGT+GGG + chr7_3:14428879-14428898 Msa1093730:five_prime_UTR 20.0%
!! GTGATATAATAATTCACTAT+AGG + chr7_3:14428908-14428927 Msa1093730:five_prime_UTR 20.0%
!! ACAAATCAATGTAAATTTGT+GGG - chr7_3:14429216-14429235 None:intergenic 20.0%
!! AACAAATCAATGTAAATTTG+TGG - chr7_3:14429217-14429236 None:intergenic 20.0%
!!! TATATAATTTTCAAAACCTG+AGG + chr7_3:14429285-14429304 Msa1093730:intron 20.0%
!!! AACCAAATTTGAAATTTCTT+TGG - chr7_3:14429426-14429445 None:intergenic 20.0%
!! GAAATTTCAAATTTGGTTAT+TGG + chr7_3:14429428-14429447 Msa1093730:intron 20.0%
!!! GTTTTTTGATTAATTTCATG+GGG + chr7_3:14429496-14429515 Msa1093730:intron 20.0%
!!! TTTTAGTCATTTATAGCTTT+TGG + chr7_3:14429611-14429630 Msa1093730:intron 20.0%
!! ATGAAATCATTTACAAAGAT+GGG - chr7_3:14429670-14429689 None:intergenic 20.0%
!! AAGCATAACAAATAAAAAGA+TGG - chr7_3:14429754-14429773 None:intergenic 20.0%
!! AAAACTTCTAATATTTAGTG+TGG + chr7_3:14429912-14429931 Msa1093730:intron 20.0%
!!! TCTACTGATTTTTTTAATTG+TGG + chr7_3:14430301-14430320 Msa1093730:CDS 20.0%
!! ATTAAAAGAAAACTCTCAAA+TGG - chr7_3:14430382-14430401 None:intergenic 20.0%
!! AGATTGCAAATTAAAATTGT+GGG + chr7_3:14428879-14428898 Msa1093730:five_prime_UTR 20.0%
!! GTGATATAATAATTCACTAT+AGG + chr7_3:14428908-14428927 Msa1093730:five_prime_UTR 20.0%
!! ACAAATCAATGTAAATTTGT+GGG - chr7_3:14429216-14429235 None:intergenic 20.0%
!! AACAAATCAATGTAAATTTG+TGG - chr7_3:14429217-14429236 None:intergenic 20.0%
!!! TATATAATTTTCAAAACCTG+AGG + chr7_3:14429285-14429304 Msa1093730:intron 20.0%
!!! AACCAAATTTGAAATTTCTT+TGG - chr7_3:14429426-14429445 None:intergenic 20.0%
!! GAAATTTCAAATTTGGTTAT+TGG + chr7_3:14429428-14429447 Msa1093730:intron 20.0%
!!! GTTTTTTGATTAATTTCATG+GGG + chr7_3:14429496-14429515 Msa1093730:intron 20.0%
!!! TTTTAGTCATTTATAGCTTT+TGG + chr7_3:14429611-14429630 Msa1093730:intron 20.0%
!! ATGAAATCATTTACAAAGAT+GGG - chr7_3:14429670-14429689 None:intergenic 20.0%
!! AAGCATAACAAATAAAAAGA+TGG - chr7_3:14429754-14429773 None:intergenic 20.0%
!! AAAACTTCTAATATTTAGTG+TGG + chr7_3:14429912-14429931 Msa1093730:intron 20.0%
!!! TCTACTGATTTTTTTAATTG+TGG + chr7_3:14430301-14430320 Msa1093730:CDS 20.0%
!! ATTAAAAGAAAACTCTCAAA+TGG - chr7_3:14430382-14430401 None:intergenic 20.0%
! CAGATTGCAAATTAAAATTG+TGG + chr7_3:14428878-14428897 Msa1093730:five_prime_UTR 25.0%
!! AATTCACTATAGGATTTTGT+TGG + chr7_3:14428918-14428937 Msa1093730:five_prime_UTR 25.0%
!! ATTCACTATAGGATTTTGTT+GGG + chr7_3:14428919-14428938 Msa1093730:five_prime_UTR 25.0%
! TATGACTCAATTCTTTCTAT+GGG + chr7_3:14428992-14429011 Msa1093730:intron 25.0%
! CAAATCAATGTAAATTTGTG+GGG - chr7_3:14429215-14429234 None:intergenic 25.0%
! GACCAAAGAAATTTCAAATT+TGG + chr7_3:14429421-14429440 Msa1093730:intron 25.0%
! CATGAAATCATTTACAAAGA+TGG - chr7_3:14429671-14429690 None:intergenic 25.0%
! TAAGTAATTGATGCCAATTT+AGG - chr7_3:14429808-14429827 None:intergenic 25.0%
! CAGATTGCAAATTAAAATTG+TGG + chr7_3:14428878-14428897 Msa1093730:five_prime_UTR 25.0%
!! AATTCACTATAGGATTTTGT+TGG + chr7_3:14428918-14428937 Msa1093730:five_prime_UTR 25.0%
!! ATTCACTATAGGATTTTGTT+GGG + chr7_3:14428919-14428938 Msa1093730:five_prime_UTR 25.0%
! TATGACTCAATTCTTTCTAT+GGG + chr7_3:14428992-14429011 Msa1093730:intron 25.0%
! CAAATCAATGTAAATTTGTG+GGG - chr7_3:14429215-14429234 None:intergenic 25.0%
! GACCAAAGAAATTTCAAATT+TGG + chr7_3:14429421-14429440 Msa1093730:intron 25.0%
! CATGAAATCATTTACAAAGA+TGG - chr7_3:14429671-14429690 None:intergenic 25.0%
! TAAGTAATTGATGCCAATTT+AGG - chr7_3:14429808-14429827 None:intergenic 25.0%
GTATGACTCAATTCTTTCTA+TGG + chr7_3:14428991-14429010 Msa1093730:intron 30.0%
AAAAATGGGAAATACATAGG+TGG - chr7_3:14429119-14429138 None:intergenic 30.0%
CTCAAAAATGGGAAATACAT+AGG - chr7_3:14429122-14429141 None:intergenic 30.0%
TTGCAAAGACACTCAAAAAT+GGG - chr7_3:14429133-14429152 None:intergenic 30.0%
AAAGAAGGATTCAGAAAGAA+AGG - chr7_3:14429173-14429192 None:intergenic 30.0%
TACTGTCAACAAACAAAAGA+AGG - chr7_3:14429188-14429207 None:intergenic 30.0%
TAACTGCTATTCAAGTCATT+TGG - chr7_3:14429312-14429331 None:intergenic 30.0%
AACGTTTGCATCATTTCAAT+GGG + chr7_3:14429452-14429471 Msa1093730:intron 30.0%
! ATGTATCAAGCTTTTATCCT+TGG + chr7_3:14429550-14429569 Msa1093730:intron 30.0%
! CATTTATAGCTTTTGGATAG+AGG + chr7_3:14429618-14429637 Msa1093730:intron 30.0%
AAATTGTGGTATGAACTTCT+TGG + chr7_3:14429849-14429868 Msa1093730:intron 30.0%
TGTGGTCTTCTATGTATAAA+AGG + chr7_3:14429930-14429949 Msa1093730:intron 30.0%
TTACTGCTAAAACCTACAAT+AGG + chr7_3:14430032-14430051 Msa1093730:five_prime_UTR 30.0%
TACTGCTAAAACCTACAATA+GGG + chr7_3:14430033-14430052 Msa1093730:five_prime_UTR 30.0%
AAATTCTTTCTGTTGTCTTC+TGG + chr7_3:14430128-14430147 Msa1093730:intron 30.0%
CAAATTAGCAAGATGTTGTA+CGG + chr7_3:14430270-14430289 Msa1093730:CDS 30.0%
GTATGACTCAATTCTTTCTA+TGG + chr7_3:14428991-14429010 Msa1093730:intron 30.0%
AAAAATGGGAAATACATAGG+TGG - chr7_3:14429119-14429138 None:intergenic 30.0%
CTCAAAAATGGGAAATACAT+AGG - chr7_3:14429122-14429141 None:intergenic 30.0%
TTGCAAAGACACTCAAAAAT+GGG - chr7_3:14429133-14429152 None:intergenic 30.0%
AAAGAAGGATTCAGAAAGAA+AGG - chr7_3:14429173-14429192 None:intergenic 30.0%
TACTGTCAACAAACAAAAGA+AGG - chr7_3:14429188-14429207 None:intergenic 30.0%
TAACTGCTATTCAAGTCATT+TGG - chr7_3:14429312-14429331 None:intergenic 30.0%
AACGTTTGCATCATTTCAAT+GGG + chr7_3:14429452-14429471 Msa1093730:intron 30.0%
! ATGTATCAAGCTTTTATCCT+TGG + chr7_3:14429550-14429569 Msa1093730:intron 30.0%
! CATTTATAGCTTTTGGATAG+AGG + chr7_3:14429618-14429637 Msa1093730:intron 30.0%
AAATTGTGGTATGAACTTCT+TGG + chr7_3:14429849-14429868 Msa1093730:intron 30.0%
TGTGGTCTTCTATGTATAAA+AGG + chr7_3:14429930-14429949 Msa1093730:intron 30.0%
TTACTGCTAAAACCTACAAT+AGG + chr7_3:14430032-14430051 Msa1093730:five_prime_UTR 30.0%
TACTGCTAAAACCTACAATA+GGG + chr7_3:14430033-14430052 Msa1093730:five_prime_UTR 30.0%
AAATTCTTTCTGTTGTCTTC+TGG + chr7_3:14430128-14430147 Msa1093730:intron 30.0%
CAAATTAGCAAGATGTTGTA+CGG + chr7_3:14430270-14430289 Msa1093730:CDS 30.0%
CAAGCAACTCTAATGTTAGT+AGG + chr7_3:14428946-14428965 Msa1093730:five_prime_UTR 35.0%
GTTGCAAAGACACTCAAAAA+TGG - chr7_3:14429134-14429153 None:intergenic 35.0%
GAACGTTTGCATCATTTCAA+TGG + chr7_3:14429451-14429470 Msa1093730:intron 35.0%
!! CAAAGTTTCTGGTGTATTTC+AGG + chr7_3:14429523-14429542 Msa1093730:intron 35.0%
CAATTACTCGTTTCAAACCA+AGG - chr7_3:14429570-14429589 None:intergenic 35.0%
TTCAATCAATGCCCTATTGT+AGG - chr7_3:14430047-14430066 None:intergenic 35.0%
TTGAGTTAATTGATCCCGTT+TGG + chr7_3:14430156-14430175 Msa1093730:intron 35.0%
TTTGACCACCTCATTATGTT+TGG - chr7_3:14430198-14430217 None:intergenic 35.0%
AACATAATGAGGTGGTCAAA+TGG + chr7_3:14430198-14430217 Msa1093730:exon 35.0%
ATCTTGCTAATTTGAGTGGA+AGG - chr7_3:14430264-14430283 None:intergenic 35.0%
CAACATCTTGCTAATTTGAG+TGG - chr7_3:14430268-14430287 None:intergenic 35.0%
! GTGGCTTCTATTGTTATTAG+AGG + chr7_3:14430320-14430339 Msa1093730:CDS 35.0%
CAAGCAACTCTAATGTTAGT+AGG + chr7_3:14428946-14428965 Msa1093730:five_prime_UTR 35.0%
GTTGCAAAGACACTCAAAAA+TGG - chr7_3:14429134-14429153 None:intergenic 35.0%
GAACGTTTGCATCATTTCAA+TGG + chr7_3:14429451-14429470 Msa1093730:intron 35.0%
!! CAAAGTTTCTGGTGTATTTC+AGG + chr7_3:14429523-14429542 Msa1093730:intron 35.0%
CAATTACTCGTTTCAAACCA+AGG - chr7_3:14429570-14429589 None:intergenic 35.0%
TTCAATCAATGCCCTATTGT+AGG - chr7_3:14430047-14430066 None:intergenic 35.0%
TTGAGTTAATTGATCCCGTT+TGG + chr7_3:14430156-14430175 Msa1093730:intron 35.0%
TTTGACCACCTCATTATGTT+TGG - chr7_3:14430198-14430217 None:intergenic 35.0%
AACATAATGAGGTGGTCAAA+TGG + chr7_3:14430198-14430217 Msa1093730:exon 35.0%
ATCTTGCTAATTTGAGTGGA+AGG - chr7_3:14430264-14430283 None:intergenic 35.0%
CAACATCTTGCTAATTTGAG+TGG - chr7_3:14430268-14430287 None:intergenic 35.0%
! GTGGCTTCTATTGTTATTAG+AGG + chr7_3:14430320-14430339 Msa1093730:CDS 35.0%
GCAACTCTAATGTTAGTAGG+AGG + chr7_3:14428949-14428968 Msa1093730:five_prime_UTR 40.0%
AGGAGTTTGATGCATCTGAT+TGG + chr7_3:14428969-14428988 Msa1093730:five_prime_UTR 40.0%
ATTCAAGTCATTTGGACCTC+AGG - chr7_3:14429304-14429323 None:intergenic 40.0%
CATGGGGTATACAAAGTTTC+TGG + chr7_3:14429512-14429531 Msa1093730:intron 40.0%
! TATGAGCTTTGTGTTGAGTC+AGG + chr7_3:14429987-14430006 Msa1093730:intron 40.0%
! ATGAGCTTTGTGTTGAGTCA+GGG + chr7_3:14429988-14430007 Msa1093730:intron 40.0%
ATCCCGTTTGGATATTGACA+TGG + chr7_3:14430168-14430187 Msa1093730:intron 40.0%
TGCCATGTCAATATCCAAAC+GGG - chr7_3:14430173-14430192 None:intergenic 40.0%
CTGCCATGTCAATATCCAAA+CGG - chr7_3:14430174-14430193 None:intergenic 40.0%
GCAACTCTAATGTTAGTAGG+AGG + chr7_3:14428949-14428968 Msa1093730:five_prime_UTR 40.0%
AGGAGTTTGATGCATCTGAT+TGG + chr7_3:14428969-14428988 Msa1093730:five_prime_UTR 40.0%
ATTCAAGTCATTTGGACCTC+AGG - chr7_3:14429304-14429323 None:intergenic 40.0%
CATGGGGTATACAAAGTTTC+TGG + chr7_3:14429512-14429531 Msa1093730:intron 40.0%
! TATGAGCTTTGTGTTGAGTC+AGG + chr7_3:14429987-14430006 Msa1093730:intron 40.0%
! ATGAGCTTTGTGTTGAGTCA+GGG + chr7_3:14429988-14430007 Msa1093730:intron 40.0%
ATCCCGTTTGGATATTGACA+TGG + chr7_3:14430168-14430187 Msa1093730:intron 40.0%
TGCCATGTCAATATCCAAAC+GGG - chr7_3:14430173-14430192 None:intergenic 40.0%
CTGCCATGTCAATATCCAAA+CGG - chr7_3:14430174-14430193 None:intergenic 40.0%
AATGGGTCGTTTGCATCTCA+AGG + chr7_3:14429469-14429488 Msa1093730:intron 45.0%
TTTGTGTTGAGTCAGGGCAT+TGG + chr7_3:14429994-14430013 Msa1093730:intron 45.0%
CGTTTGGATATTGACATGGC+AGG + chr7_3:14430172-14430191 Msa1093730:intron 45.0%
ATGGCAGGCCAAACATAATG+AGG + chr7_3:14430187-14430206 Msa1093730:intron 45.0%
GTCAAATGGATGCGACTGTT+GGG + chr7_3:14430212-14430231 Msa1093730:exon 45.0%
AATGGGTCGTTTGCATCTCA+AGG + chr7_3:14429469-14429488 Msa1093730:intron 45.0%
TTTGTGTTGAGTCAGGGCAT+TGG + chr7_3:14429994-14430013 Msa1093730:intron 45.0%
CGTTTGGATATTGACATGGC+AGG + chr7_3:14430172-14430191 Msa1093730:intron 45.0%
ATGGCAGGCCAAACATAATG+AGG + chr7_3:14430187-14430206 Msa1093730:intron 45.0%
GTCAAATGGATGCGACTGTT+GGG + chr7_3:14430212-14430231 Msa1093730:exon 45.0%
!! AATGATTTAAATTATAAATA+TGG + chr7_3:14429386-14429405 Msa1093730:intron 5.0%
!! AATGATTTAAATTATAAATA+TGG + chr7_3:14429386-14429405 Msa1093730:intron 5.0%
GCAGGCCAAACATAATGAGG+TGG + chr7_3:14430190-14430209 Msa1093730:intron 50.0%
GGTCAAATGGATGCGACTGT+TGG + chr7_3:14430211-14430230 Msa1093730:exon 50.0%
GATGCGACTGTTGGGTTCTA+CGG + chr7_3:14430220-14430239 Msa1093730:CDS 50.0%
GCAGGCCAAACATAATGAGG+TGG + chr7_3:14430190-14430209 Msa1093730:intron 50.0%
GGTCAAATGGATGCGACTGT+TGG + chr7_3:14430211-14430230 Msa1093730:exon 50.0%
GATGCGACTGTTGGGTTCTA+CGG + chr7_3:14430220-14430239 Msa1093730:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 14428878 14430432 14428878 ID=Msa1093730;Name=Msa1093730
chr7_3 mRNA 14428878 14430432 14428878 ID=Msa1093730-mRNA-1;Parent=Msa1093730;Name=Msa1093730-mRNA-1;_AED=0.00;_eAED=0.00;_QI=229|1|1|1|0|0.33|3|93|40
chr7_3 exon 14428878 14428990 14428878 ID=Msa1093730-mRNA-1:exon:3315;Parent=Msa1093730-mRNA-1
chr7_3 exon 14430009 14430101 14430009 ID=Msa1093730-mRNA-1:exon:3316;Parent=Msa1093730-mRNA-1
chr7_3 exon 14430194 14430432 14430194 ID=Msa1093730-mRNA-1:exon:3317;Parent=Msa1093730-mRNA-1
chr7_3 five_prime_UTR 14428878 14428990 14428878 ID=Msa1093730-mRNA-1:five_prime_utr;Parent=Msa1093730-mRNA-1
chr7_3 five_prime_UTR 14430009 14430101 14430009 ID=Msa1093730-mRNA-1:five_prime_utr;Parent=Msa1093730-mRNA-1
chr7_3 five_prime_UTR 14430194 14430216 14430194 ID=Msa1093730-mRNA-1:five_prime_utr;Parent=Msa1093730-mRNA-1
chr7_3 CDS 14430217 14430339 14430217 ID=Msa1093730-mRNA-1:cds;Parent=Msa1093730-mRNA-1
chr7_3 three_prime_UTR 14430340 14430432 14430340 ID=Msa1093730-mRNA-1:three_prime_utr;Parent=Msa1093730-mRNA-1
Gene Sequence

>Msa1093730

ATGGATGCGACTGTTGGGTTCTACGGAAAAACATTCTCACTCTTCCTTCCACTCAAATTAGCAAGATGTTGTACGGATTCATTTTCTACTGATTTTTTTAATTGTGGCTTCTATTGTTATTAG
Protein sequence

>Msa1093730

MDATVGFYGKTFSLFLPLKLARCCTDSFSTDFFNCGFYCY*