AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59923

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 11 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGATTTCATATAGATTTA+AGG 0.126167 8.1:+76465362 MS.gene59923:CDS
CTATATGAAATCAAAGTTAT+AGG 0.321947 8.1:-76465354 None:intergenic
GAAACGGAAGAAGAATTTCT+TGG 0.371083 8.1:+76464997 MS.gene59923:CDS
TTTGACAGGTTTGAGTGTAT+TGG 0.406027 8.1:+76465155 MS.gene59923:intron
TTATACTTGAGAGTGAGGTT+TGG 0.466348 8.1:-76465212 None:intergenic
AAATATTATACTTGAGAGTG+AGG 0.501284 8.1:-76465217 None:intergenic
GGTTGAAGAATATGAAGAAA+CGG 0.528087 8.1:+76464981 MS.gene59923:CDS
ATTATGTTTGCAGTGGCTCA+CGG 0.548221 8.1:+76465949 MS.gene59923:intron
TTGTTTAAATTAGGACTCTG+AGG 0.602642 8.1:+76464960 None:intergenic
AGTTATAGGATATGAATGCA+CGG 0.631860 8.1:-76465340 None:intergenic
GTGAACAATATAACTCGCGA+TGG 0.655757 8.1:+76465971 MS.gene59923:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTCAAAACATAAAAAA+TGG - chr8.1:76465425-76465444 None:intergenic 10.0%
!! AAATTCAAAACATAAAAAAT+GGG - chr8.1:76465424-76465443 None:intergenic 10.0%
!! TCAAATCTTAAAATTTATAT+TGG + chr8.1:76465086-76465105 MS.gene59923:intron 10.0%
!!! AAAAAAATTTAAGTTTGAAA+TGG + chr8.1:76465814-76465833 MS.gene59923:intron 10.0%
!! AATTCAAAACATAAAAAATG+GGG - chr8.1:76465423-76465442 None:intergenic 15.0%
!! CTTAAAAAAAATCATACAAA+AGG - chr8.1:76465661-76465680 None:intergenic 15.0%
!!! TTTGATTTCATATAGATTTA+AGG + chr8.1:76465362-76465381 MS.gene59923:CDS 15.0%
!! CTATATGAAATCAAAGTTAT+AGG - chr8.1:76465357-76465376 None:intergenic 20.0%
!!! AATTTATATTGGTTGAAATG+AGG + chr8.1:76465097-76465116 MS.gene59923:intron 20.0%
!!! ATTTATATTGGTTGAAATGA+GGG + chr8.1:76465098-76465117 MS.gene59923:intron 20.0%
!!! TTTATTATTGTTTTCAACAG+TGG + chr8.1:76465443-76465462 MS.gene59923:intron 20.0%
! AAATATTATACTTGAGAGTG+AGG - chr8.1:76465220-76465239 None:intergenic 25.0%
! ACTGTATAACTTGAATTCAT+TGG + chr8.1:76465862-76465881 MS.gene59923:intron 25.0%
! ATTAGTATCCAACAATGATT+TGG + chr8.1:76465629-76465648 MS.gene59923:intron 25.0%
! GCACATAACTAATCTAATAT+AGG - chr8.1:76465696-76465715 None:intergenic 25.0%
! TCTAATATAGGTTCAAAAAG+TGG - chr8.1:76465684-76465703 None:intergenic 25.0%
!! GTTTGAAATGGAAAGAATAT+TGG + chr8.1:76465826-76465845 MS.gene59923:intron 25.0%
!! TTTTTCTATTATGTTTGCAG+TGG + chr8.1:76465942-76465961 MS.gene59923:intron 25.0%
!!! AGTGTCATTATTTTGAGATT+GGG + chr8.1:76465545-76465564 MS.gene59923:intron 25.0%
!!! TCATGATTTTGAAATTGACT+TGG + chr8.1:76465510-76465529 MS.gene59923:intron 25.0%
!!! TTTTGAAACTATTTGAGTTG+TGG + chr8.1:76465040-76465059 MS.gene59923:intron 25.0%
ACAACTAGATAGGATTAACT+TGG + chr8.1:76465471-76465490 MS.gene59923:intron 30.0%
AGTGGTAATAACAACTAGAT+AGG + chr8.1:76465461-76465480 MS.gene59923:intron 30.0%
AGTTATAGGATATGAATGCA+CGG - chr8.1:76465343-76465362 None:intergenic 30.0%
CTGAAAAACCAGAAGAAAAT+GGG - chr8.1:76465308-76465327 None:intergenic 30.0%
GGTTGAAGAATATGAAGAAA+CGG + chr8.1:76464981-76465000 MS.gene59923:CDS 30.0%
TGCACAAAATAGTGAATACA+TGG - chr8.1:76465250-76465269 None:intergenic 30.0%
TTCTTGGTATGATGCTATAT+GGG + chr8.1:76465013-76465032 MS.gene59923:intron 30.0%
TTTCTTGGTATGATGCTATA+TGG + chr8.1:76465012-76465031 MS.gene59923:intron 30.0%
! AATTATGTCCCATTTTCTTC+TGG + chr8.1:76465297-76465316 MS.gene59923:intron 30.0%
!!! GAGTGTCATTATTTTGAGAT+TGG + chr8.1:76465544-76465563 MS.gene59923:intron 30.0%
!!! GTGTCATTATTTTGAGATTG+GGG + chr8.1:76465546-76465565 MS.gene59923:intron 30.0%
ATTGACCATCTCAATTTGCA+TGG - chr8.1:76465905-76465924 None:intergenic 35.0%
CACATGGCACAATATAAGTA+AGG - chr8.1:76465393-76465412 None:intergenic 35.0%
CCTGAAAAACCAGAAGAAAA+TGG - chr8.1:76465309-76465328 None:intergenic 35.0%
CTCTCAACAATGCTTTCATT+CGG + chr8.1:76465715-76465734 MS.gene59923:intron 35.0%
GAAACGGAAGAAGAATTTCT+TGG + chr8.1:76464997-76465016 MS.gene59923:CDS 35.0%
TGGGACATAATTCAGTCAAA+TGG - chr8.1:76465289-76465308 None:intergenic 35.0%
TTATACTTGAGAGTGAGGTT+TGG - chr8.1:76465215-76465234 None:intergenic 35.0%
TTGACCATCTCAATTTGCAT+GGG - chr8.1:76465904-76465923 None:intergenic 35.0%
TTTGACAGGTTTGAGTGTAT+TGG + chr8.1:76465155-76465174 MS.gene59923:intron 35.0%
! ATTTTCGTTCAAACCACCAT+TGG - chr8.1:76465611-76465630 None:intergenic 35.0%
!! TCATTGGATGTGATTTTGAC+AGG + chr8.1:76465141-76465160 MS.gene59923:intron 35.0%
!!! CCATTTTCTTCTGGTTTTTC+AGG + chr8.1:76465306-76465325 MS.gene59923:intron 35.0%
ATGAGGGTAAAGCATAGCAT+AGG + chr8.1:76465114-76465133 MS.gene59923:intron 40.0%
ATTATGTTTGCAGTGGCTCA+CGG + chr8.1:76465949-76465968 MS.gene59923:intron 40.0%
GGAGAGTTCCAAATCATTGT+TGG - chr8.1:76465640-76465659 None:intergenic 40.0%
GTGAACAATATAACTCGCGA+TGG + chr8.1:76465971-76465990 MS.gene59923:CDS 40.0%
TAGACCCATGCAAATTGAGA+TGG + chr8.1:76465897-76465916 MS.gene59923:intron 40.0%
AAAATGGGGCGCAAATCACA+TGG - chr8.1:76465409-76465428 None:intergenic 45.0%
GCATAGCATAGGAGCTTCAT+TGG + chr8.1:76465125-76465144 MS.gene59923:intron 45.0%
GTAGCCATATTGCCAACCAA+TGG + chr8.1:76465592-76465611 MS.gene59923:intron 45.0%
TCGTTCAAACCACCATTGGT+TGG - chr8.1:76465607-76465626 None:intergenic 45.0%
! ACCACCATTGGTTGGCAATA+TGG - chr8.1:76465599-76465618 None:intergenic 45.0%
!!! ATTTTGAGATTGGGGCTGCT+TGG + chr8.1:76465554-76465573 MS.gene59923:intron 45.0%
GCCATATTGCCAACCAATGG+TGG + chr8.1:76465595-76465614 MS.gene59923:intron 50.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 76464973 76466006 76464973 ID=MS.gene59923
chr8.1 mRNA 76464973 76466006 76464973 ID=MS.gene59923.t1;Parent=MS.gene59923
chr8.1 exon 76464973 76465018 76464973 ID=MS.gene59923.t1.exon1;Parent=MS.gene59923.t1
chr8.1 CDS 76464973 76465018 76464973 ID=cds.MS.gene59923.t1;Parent=MS.gene59923.t1
chr8.1 exon 76465163 76465228 76465163 ID=MS.gene59923.t1.exon2;Parent=MS.gene59923.t1
chr8.1 CDS 76465163 76465228 76465163 ID=cds.MS.gene59923.t1;Parent=MS.gene59923.t1
chr8.1 exon 76465328 76465383 76465328 ID=MS.gene59923.t1.exon3;Parent=MS.gene59923.t1
chr8.1 CDS 76465328 76465383 76465328 ID=cds.MS.gene59923.t1;Parent=MS.gene59923.t1
chr8.1 exon 76465962 76466006 76465962 ID=MS.gene59923.t1.exon4;Parent=MS.gene59923.t1
chr8.1 CDS 76465962 76466006 76465962 ID=cds.MS.gene59923.t1;Parent=MS.gene59923.t1
Gene Sequence

>MS.gene59923

GACTCTGAGGTTGAAGAATATGAAGAAACGGAAGAAGAATTTCTTGGTATGATGCTATATGGGATGCTTTTGAAACTATTTGAGTTGTGGCTAAATTGCATATTTTTTTCTTCTCAAATCTTAAAATTTATATTGGTTGAAATGAGGGTAAAGCATAGCATAGGAGCTTCATTGGATGTGATTTTGACAGGTTTGAGTGTATTGGAGCAGCTGAATACATCAAGCATTTGTATCAAATTCCAAACCTCACTCTCAAGTATAATATTTTTATCTTCCATGTATTCACTATTTTGTGCATTCAAGTCATATCATGCCATTTGACTGAATTATGTCCCATTTTCTTCTGGTTTTTCAGGTTGTCGCTTATCCGTGCATTCATATCCTATAACTTTGATTTCATATAGATTTAAGGTGAGTCCTTACTTATATTGTGCCATGTGATTTGCGCCCCATTTTTTATGTTTTGAATTTTTATTATTGTTTTCAACAGTGGTAATAACAACTAGATAGGATTAACTTGGTGTTTAAGCATGAGTGTCATGATTTTGAAATTGACTTGGTGCTTGAGAATGAGTGTCATTATTTTGAGATTGGGGCTGCTTGGTGCTACTTTGCTTTTGTAGCCATATTGCCAACCAATGGTGGTTTGAACGAAAATTAGTATCCAACAATGATTTGGAACTCTCCTTTTGTATGATTTTTTTTAAGCCACTTTTTGAACCTATATTAGATTAGTTATGTGCTCTCAACAATGCTTTCATTCGGTTATCGATTAGTGTCTTATGCTTGCATGTATCTTTCTATCTCAAGAGATCATTTTAAATTTGAAGTTTGTCTCTAAAAAAAAATTTAAGTTTGAAATGGAAAGAATATTGGTTGAGAAACTATTACTGTATAACTTGAATTCATTGGTGAGTTTTTTAGTAGACCCATGCAAATTGAGATGGTCAATTAGTTGTTCATAATTTTTTTTTCTATTATGTTTGCAGTGGCTCACGGTGAACAATATAACTCGCGATGGTATACATTCTTGA
Protein sequence

>MS.gene59923.t1

DSEVEEYEETEEEFLGLSVLEQLNTSSICIKFQTSLSSCRLSVHSYPITLISYRFKWLTVNNITRDGIHS