AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene001558


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001558.t1 MTR_2g019190 60.000 95 27 3 17 102 41 133 1.62e-31 108
MS.gene001558.t1 MTR_8g107300 57.292 96 25 4 10 101 33 116 8.55e-28 98.6
MS.gene001558.t1 MTR_8g107300 59.770 87 22 3 19 101 4 81 4.22e-27 95.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001558.t1 AT1G30135 46.988 83 41 2 23 102 46 128 1.57e-15 67.4

Find 19 sgRNAs with CRISPR-Local

Find 113 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATCCGATTCTTCCTCTTT+TGG 0.250942 4.1:+16118956 None:intergenic
GACTGATGCCACTGAGATTC+AGG 0.303605 4.1:-16121019 MS.gene001558:intron
TCTTCTCATTTATCTTAAGA+TGG 0.423225 4.1:+16118917 None:intergenic
TTCTCCAAAAGAGGAAGAAT+CGG 0.429979 4.1:-16118960 MS.gene001558:CDS
TCATTTATCTTAAGATGGTA+AGG 0.430837 4.1:+16118922 None:intergenic
GAAATGGTGAGGACACCAAC+TGG 0.450322 4.1:-16119069 MS.gene001558:CDS
AAGATCATAAGCAGCAGTAC+AGG 0.470194 4.1:-16121077 MS.gene001558:CDS
TGCAGAGGTTTCTCCAAAAG+AGG 0.484466 4.1:-16118969 MS.gene001558:CDS
TGCTGCTTATGATCTTCTTG+TGG 0.500195 4.1:+16121084 None:intergenic
CCGTTGACCATTGTCTATGA+TGG 0.521959 4.1:-16121054 MS.gene001558:CDS
CATTTATCTTAAGATGGTAA+GGG 0.531668 4.1:+16118923 None:intergenic
TGCATGGAAAGAGAAGTACT+AGG 0.548727 4.1:+16119000 None:intergenic
TGCAAGCATTAAAATGGACC+TGG 0.550717 4.1:+16119098 None:intergenic
GCATGGAAAGAGAAGTACTA+GGG 0.573020 4.1:+16119001 None:intergenic
ATTTATCTTAAGATGGTAAG+GGG 0.589050 4.1:+16118924 None:intergenic
AATCTTGCCATCATAGACAA+TGG 0.643141 4.1:+16121047 None:intergenic
CCATCATAGACAATGGTCAA+CGG 0.652322 4.1:+16121054 None:intergenic
GGCTCTGATGATGATCCAGT+TGG 0.655026 4.1:+16119054 None:intergenic
TGAACACACCTGAATCTCAG+TGG 0.730872 4.1:+16121011 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAATTTTAATATATTA+AGG + chr4.1:16120735-16120754 None:intergenic 0.0%
!!! TTTTTTTATTTTTTAAAATA+TGG - chr4.1:16119634-16119653 MS.gene001558:intron 0.0%
!! ATAATAGTTTGAATTAAAAT+TGG - chr4.1:16120863-16120882 MS.gene001558:intron 10.0%
!!! TAAGTAAAAAAACAATTTTT+AGG + chr4.1:16119458-16119477 None:intergenic 10.0%
!! CATTGAATAAATAATGTATA+TGG - chr4.1:16119394-16119413 MS.gene001558:intron 15.0%
!! GAAAAAAAAATCAAAAAACA+TGG + chr4.1:16120679-16120698 None:intergenic 15.0%
!!! ATATACGTTTTTTATTTTTC+TGG + chr4.1:16119505-16119524 None:intergenic 15.0%
!!! CTATTTATTAATTTTTTCTG+CGG - chr4.1:16120227-16120246 MS.gene001558:intron 15.0%
!!! TATGCAATTTTTGTTTTTTT+AGG + chr4.1:16119211-16119230 None:intergenic 15.0%
!!! TTTTTACTTATAAATGTGAA+CGG - chr4.1:16119468-16119487 MS.gene001558:intron 15.0%
!! AGCTACAAATTTAGTAATAA+AGG - chr4.1:16120444-16120463 MS.gene001558:intron 20.0%
!! ATTAAAAGAGAGAAGATAAA+TGG + chr4.1:16119791-16119810 None:intergenic 20.0%
!! CAATGATATTAGTACTTAAT+AGG + chr4.1:16120276-16120295 None:intergenic 20.0%
!! CATAGAATAATTAATGTATC+TGG + chr4.1:16119433-16119452 None:intergenic 20.0%
!! GATATAAATAAATCAGTAAG+CGG - chr4.1:16120531-16120550 MS.gene001558:intron 20.0%
!! GCTACAAATTTAGTAATAAA+GGG - chr4.1:16120445-16120464 MS.gene001558:intron 20.0%
!! TAAAATTGGAATTAAGTAGT+GGG - chr4.1:16120877-16120896 MS.gene001558:intron 20.0%
!! TATAAATGCAAACTACAAAT+TGG - chr4.1:16120477-16120496 MS.gene001558:intron 20.0%
!! TTAAAATTGGAATTAAGTAG+TGG - chr4.1:16120876-16120895 MS.gene001558:intron 20.0%
!!! AATTTGCTTATAAATGTGAA+CGG + chr4.1:16119148-16119167 None:intergenic 20.0%
!!! ATTTGTAGTTTGCATTTATA+AGG + chr4.1:16120477-16120496 None:intergenic 20.0%
!!! TAAGCAAAACACAATTTTTA+AGG - chr4.1:16119369-16119388 MS.gene001558:intron 20.0%
!!! TCAAACTATTATTGATGATA+AGG + chr4.1:16120855-16120874 None:intergenic 20.0%
!!! TCTTTTCATCATATAATCTT+TGG + chr4.1:16120411-16120430 None:intergenic 20.0%
!!! TTTTTTTGCAAGCATTAAAA+TGG + chr4.1:16120940-16120959 None:intergenic 20.0%
! AAAATTGGAATTAAGTAGTG+GGG - chr4.1:16120878-16120897 MS.gene001558:intron 25.0%
! AAATTGCATATAAATGTGAC+CGG - chr4.1:16119221-16119240 MS.gene001558:intron 25.0%
! AATGCTTGCAAAAAAAGAAA+TGG - chr4.1:16120944-16120963 MS.gene001558:intron 25.0%
! ATGCATTATTGTACATGATA+TGG + chr4.1:16119329-16119348 None:intergenic 25.0%
! ATGTGAATTGTATATATTGC+AGG - chr4.1:16120908-16120927 MS.gene001558:intron 25.0%
! ATTTATCTTAAGATGGTAAG+GGG + chr4.1:16121108-16121127 None:intergenic 25.0%
! CATTTATCTTAAGATGGTAA+GGG + chr4.1:16121109-16121128 None:intergenic 25.0%
! CTATACAAGTTAAAAACTGA+TGG + chr4.1:16121008-16121027 None:intergenic 25.0%
! TCATTTATCTTAAGATGGTA+AGG + chr4.1:16121110-16121129 None:intergenic 25.0%
! TCTTCTCATTTATCTTAAGA+TGG + chr4.1:16121115-16121134 None:intergenic 25.0%
! TGTGTACAATTTATTACGTA+TGG + chr4.1:16120158-16120177 None:intergenic 25.0%
! TTTATATCTTTCGTTTGTCT+TGG + chr4.1:16120519-16120538 None:intergenic 25.0%
!! ACAACATAACACTTCATTTT+TGG + chr4.1:16120346-16120365 None:intergenic 25.0%
!! ATTTGTTGACCTCAAAATTT+GGG - chr4.1:16120618-16120637 MS.gene001558:intron 25.0%
!! TATTAATTCTGGTGCTAAAT+AGG + chr4.1:16120048-16120067 None:intergenic 25.0%
!! TTTTCAAAAAATGCATATGC+AGG - chr4.1:16119549-16119568 MS.gene001558:intron 25.0%
AATAGCATCATCATCTAGTT+AGG - chr4.1:16120755-16120774 MS.gene001558:intron 30.0%
ACAAGAATTAAAGAGAGAGA+GGG + chr4.1:16120132-16120151 None:intergenic 30.0%
AGAGATTCAGAAATTACTCA+AGG - chr4.1:16119858-16119877 MS.gene001558:intron 30.0%
TCTCTCTCTTTAATTCTTGT+GGG - chr4.1:16120132-16120151 MS.gene001558:intron 30.0%
TTGAATGAAAGTTTGGTTGA+GGG + chr4.1:16119754-16119773 None:intergenic 30.0%
TTGCAAAAAAAGAAATGGTG+AGG - chr4.1:16120949-16120968 MS.gene001558:intron 30.0%
! AAGCATTTTCTTTCCACAAT+GGG + chr4.1:16120077-16120096 None:intergenic 30.0%
! AATAGTTAGAGCATTCACAA+TGG - chr4.1:16120011-16120030 MS.gene001558:intron 30.0%
! ATGAAGTGTTATGTTGTAGA+TGG - chr4.1:16120349-16120368 MS.gene001558:intron 30.0%
! CATTTGTTGACCTCAAAATT+TGG - chr4.1:16120617-16120636 MS.gene001558:intron 30.0%
! CGGATTACTCAAAAAACTTT+TGG + chr4.1:16119683-16119702 None:intergenic 30.0%
! GTTTTGCTTATAAATGTGAC+CGG + chr4.1:16119359-16119378 None:intergenic 30.0%
! TAAGGTGAGTTGAAAAAGAA+TGG + chr4.1:16120717-16120736 None:intergenic 30.0%
! TTAAAAACTGATGGTGAAGA+TGG + chr4.1:16120999-16121018 None:intergenic 30.0%
!!! CAAATTTTGAGGTCAACAAA+TGG + chr4.1:16120619-16120638 None:intergenic 30.0%
!!! GTTTTTTGAGTAATCCGTTT+TGG - chr4.1:16119686-16119705 MS.gene001558:intron 30.0%
!!! TTCATTTTTGGTGCTTAAGT+GGG + chr4.1:16120334-16120353 None:intergenic 30.0%
AATCTTGCCATCATAGACAA+TGG + chr4.1:16118985-16119004 None:intergenic 35.0%
AATTGTATATATTGCAGGCC+AGG - chr4.1:16120913-16120932 MS.gene001558:intron 35.0%
AGTTTAAAAACTACTCCCTC+CGG + chr4.1:16119243-16119262 None:intergenic 35.0%
CACAAGAATTAAAGAGAGAG+AGG + chr4.1:16120133-16120152 None:intergenic 35.0%
CATTGTGGAAAGAAAATGCT+TGG - chr4.1:16120076-16120095 MS.gene001558:intron 35.0%
CTCTAAATCAACTACCTACA+AGG + chr4.1:16119725-16119744 None:intergenic 35.0%
CTCTCTCTCTTTAATTCTTG+TGG - chr4.1:16120131-16120150 MS.gene001558:intron 35.0%
CTTGAATGAAAGTTTGGTTG+AGG + chr4.1:16119755-16119774 None:intergenic 35.0%
GAAAGAAGAAGAAGAAGAAG+AGG - chr4.1:16118915-16118934 MS.gene001558:CDS 35.0%
TCTCTTGAGTGATCACAATA+TGG + chr4.1:16120830-16120849 None:intergenic 35.0%
TGAGAGCTTGAATGAAAGTT+TGG + chr4.1:16119761-16119780 None:intergenic 35.0%
TTCTCCAAAAGAGGAAGAAT+CGG - chr4.1:16121069-16121088 MS.gene001558:CDS 35.0%
! AGCATTTTCTTTCCACAATG+GGG + chr4.1:16120076-16120095 None:intergenic 35.0%
! ATAGTTGTGCCCAAATTTTG+AGG + chr4.1:16120630-16120649 None:intergenic 35.0%
! CAAGCATTTTCTTTCCACAA+TGG + chr4.1:16120078-16120097 None:intergenic 35.0%
! CTTGTAGGTAGTTGATTTAG+AGG - chr4.1:16119723-16119742 MS.gene001558:intron 35.0%
!!! CTTCATTTTTGGTGCTTAAG+TGG + chr4.1:16120335-16120354 None:intergenic 35.0%
!!! TTAATTTTTTCTGCGGTGCT+AGG - chr4.1:16120234-16120253 MS.gene001558:intron 35.0%
AAGATCATAAGCAGCAGTAC+AGG - chr4.1:16118952-16118971 MS.gene001558:CDS 40.0%
ACAAATGGATGCAGTGCATT+TGG + chr4.1:16120604-16120623 None:intergenic 40.0%
ACAATAATGCATACTCCCTC+CGG - chr4.1:16119337-16119356 MS.gene001558:intron 40.0%
AGCATCATCATCTAGTTAGG+AGG - chr4.1:16120758-16120777 MS.gene001558:intron 40.0%
ATTAATAAGCACCCCCATTG+TGG - chr4.1:16120061-16120080 MS.gene001558:intron 40.0%
CCAACTTCACTTCATTCACA+AGG + chr4.1:16120573-16120592 None:intergenic 40.0%
CCATCATAGACAATGGTCAA+CGG + chr4.1:16118978-16118997 None:intergenic 40.0%
CCTTGTGAATGAAGTGAAGT+TGG - chr4.1:16120570-16120589 MS.gene001558:intron 40.0%
GAGAACAGATCTCTCCAAAA+CGG + chr4.1:16119703-16119722 None:intergenic 40.0%
TCAAGGAGAGTTTGATCAAG+AGG - chr4.1:16119875-16119894 MS.gene001558:intron 40.0%
TGCAAGCATTAAAATGGACC+TGG + chr4.1:16120934-16120953 None:intergenic 40.0%
TGCATATAAATGTGACCGGA+GGG - chr4.1:16119225-16119244 MS.gene001558:intron 40.0%
TGCTTATAAATGTGACCGGA+GGG + chr4.1:16119355-16119374 None:intergenic 40.0%
TTGCATATAAATGTGACCGG+AGG - chr4.1:16119224-16119243 MS.gene001558:intron 40.0%
TTGCTTATAAATGTGACCGG+AGG + chr4.1:16119356-16119375 None:intergenic 40.0%
! AGTTAGAGCATTCACAATGG+TGG - chr4.1:16120014-16120033 MS.gene001558:intron 40.0%
! GAATCCGATTCTTCCTCTTT+TGG + chr4.1:16121076-16121095 None:intergenic 40.0%
! GCATTTTCTTTCCACAATGG+GGG + chr4.1:16120075-16120094 None:intergenic 40.0%
! GTTAGAGCATTCACAATGGT+GGG - chr4.1:16120015-16120034 MS.gene001558:intron 40.0%
! TGCTGCTTATGATCTTCTTG+TGG + chr4.1:16118948-16118967 None:intergenic 40.0%
! TTGGTGCTTACAGAGAAATG+TGG - chr4.1:16120095-16120114 MS.gene001558:intron 40.0%
!! ATGGGGGTGCTTATTAATTC+TGG + chr4.1:16120059-16120078 None:intergenic 40.0%
!! GCATGGAAAGAGAAGTACTA+GGG + chr4.1:16121031-16121050 None:intergenic 40.0%
!! TGCATGGAAAGAGAAGTACT+AGG + chr4.1:16121032-16121051 None:intergenic 40.0%
!!! AACTTTTGGTGACGTTCAAG+AGG + chr4.1:16119669-16119688 None:intergenic 40.0%
CCATGCAAAAATCGTTGCAG+AGG - chr4.1:16121045-16121064 MS.gene001558:CDS 45.0%
CCGTTGACCATTGTCTATGA+TGG - chr4.1:16118975-16118994 MS.gene001558:CDS 45.0%
GAGAGATCTGTTCTCCTTGT+AGG - chr4.1:16119708-16119727 MS.gene001558:intron 45.0%
TGAACACACCTGAATCTCAG+TGG + chr4.1:16119021-16119040 None:intergenic 45.0%
TGCAGAGGTTTCTCCAAAAG+AGG - chr4.1:16121060-16121079 MS.gene001558:CDS 45.0%
TGCAGGTCTTACTACACATG+TGG - chr4.1:16119566-16119585 MS.gene001558:intron 45.0%
! CCTCTGCAACGATTTTTGCA+TGG + chr4.1:16121048-16121067 None:intergenic 45.0%
!!! TTTTTTCTGCGGTGCTAGGT+TGG - chr4.1:16120238-16120257 MS.gene001558:intron 45.0%
GAAATGGTGAGGACACCAAC+TGG - chr4.1:16120960-16120979 MS.gene001558:intron 50.0%
GACTGATGCCACTGAGATTC+AGG - chr4.1:16119010-16119029 MS.gene001558:CDS 50.0%
! CGGTGCTAGGTTGGAGAAAT+TGG - chr4.1:16120247-16120266 MS.gene001558:intron 50.0%
! GGCTCTGATGATGATCCAGT+TGG + chr4.1:16120978-16120997 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 16118912 16121139 16118912 ID=MS.gene001558
chr4.1 mRNA 16118912 16121139 16118912 ID=MS.gene001558.t1;Parent=MS.gene001558
chr4.1 exon 16121020 16121139 16121020 ID=MS.gene001558.t1.exon1;Parent=MS.gene001558.t1
chr4.1 CDS 16121020 16121139 16121020 ID=cds.MS.gene001558.t1;Parent=MS.gene001558.t1
chr4.1 exon 16118912 16119121 16118912 ID=MS.gene001558.t1.exon2;Parent=MS.gene001558.t1
chr4.1 CDS 16118912 16119121 16118912 ID=cds.MS.gene001558.t1;Parent=MS.gene001558.t1
Gene Sequence

>MS.gene001558

AATGAAAGAAGAAGAAGAAGAAGAGGTGAGAGTCCACAAGAAGATCATAAGCAGCAGTACAGGCCGTTGACCATTGTCTATGATGGCAAGATTTCTGTGACTGATGCCACTGAGATTCAGGTGTGTTCATGATTGTTCAATTTTCTGATTTTGAAAATAAAATAACTGAGATCTCTTCTTTTTTGTTTTTACTTTAATAATGTATTGTATTATTTGCTAATCTTATACTCACTCCGTTCACATTTATAAGCAAATTTTACTTTTTCAGATTCTAGATACATTACTTATTTAATGAACCTAAAAAAACAAAAATTGCATATAAATGTGACCGGAGGGAGTAGTTTTTAAACTACTATATATCTCTACAAATTATCTATGTGAACATGAAAAAAAGAATAACTAATGATTAATAAACCATATCATGTACAATAATGCATACTCCCTCCGGTCACATTTATAAGCAAAACACAATTTTTAAGGTTCATTGAATAAATAATGTATATGGTGTATAAATGTGACCAGATACATTAATTATTCTATGAACCTAAAAATTGTTTTTTTACTTATAAATGTGAACGGAGAGAAGTACACCAGAAAAATAAAAAACGTATATAGCTAGCTTTGTATTTATTTTCTCTTTTCAAAAAATGCATATGCAGGTCTTACTACACATGTGGTTAAGAATTCATACTTAGATTTTCATCTCTCAAAATATGTTTTTATTTTTTTATTTTTTAAAATATGGTTGTTTAATCCTCTTGAACGTCACCAAAAGTTTTTTGAGTAATCCGTTTTGGAGAGATCTGTTCTCCTTGTAGGTAGTTGATTTAGAGGTGATTCCCTCAACCAAACTTTCATTCAAGCTCTCATTCATCTCCATTTATCTTCTCTCTTTTAATTAAGAGAGAAATAAAGAGATTGATTTTATAAAGAAAGAAAGAAATAAAGAGATTCAGAAATTACTCAAGGAGAGTTTGATCAAGAGGATCAACTATTGTTGACTCTTTTATCATCATGAAACAAATTTTTTATGAAGCATGCATTTAGATTTTCTATACAATTAAAGAGATTAATTATATATAACTAAAATTTTAAATTAAATAGTTAGAGCATTCACAATGGTGGGTTCTTCACCTATTTAGCACCAGAATTAATAAGCACCCCCATTGTGGAAAGAAAATGCTTGGTGCTTACAGAGAAATGTGGCTCTATAATCACCCTCTCTCTCTTTAATTCTTGTGGGCCATACGTAATAAATTGTACACAAAACAATAAACTTTGTTGAAATACAATGACATTGAGTTATTAATATGATCTATTTATTAATTTTTTCTGCGGTGCTAGGTTGGAGAAATTGGATGCCTATTAAGTACTAATATCATTGAAAATTAAAAAAATAGATGATGTGTACATGCATGACCCACTTAAGCACCAAAAATGAAGTGTTATGTTGTAGATGGTCATGTAAAGTTAATTTTTACTACTAATAATCAAGACCAAAGATTATATGATGAAAAGACAAGTGAGAGAAAAGCTACAAATTTAGTAATAAAGGGAAAATTCCTTATAAATGCAAACTACAAATTGGTGATAGTTAAGCAAGACCAAGACAAACGAAAGATATAAATAAATCAGTAAGCGGTCTACATCTGAACTGTCCTTGTGAATGAAGTGAAGTTGGCTAAATTTCCAAATGCACTGCATCCATTTGTTGACCTCAAAATTTGGGCACAACTATATATATACACACATTTCTATATATATCCATGTTTTTTGATTTTTTTTTCTTTCTTTCTCAAGAGCCATTCTTTTTCAACTCACCTTAATATATTAAAATTAAAATAATAGCATCATCATCTAGTTAGGAGGCACGTAGCTAGACACTATTTTATTATAGCTCTTCAATTTTCACGTGCCATATTGTGATCACTCAAGAGATTCCTTATCATCAATAATAGTTTGAATTAAAATTGGAATTAAGTAGTGGGGTAATATAATGTGAATTGTATATATTGCAGGCCAGGTCCATTTTAATGCTTGCAAAAAAAGAAATGGTGAGGACACCAACTGGATCATCATCAGAGCCATCTTCACCATCAGTTTTTAACTTGTATAGCCCTAGTACTTCTCTTTCCATGCAAAAATCGTTGCAGAGGTTTCTCCAAAAGAGGAAGAATCGGATTCAAGAAGCATCCCCTTACCATCTTAAGATAAATGAGAAGAATTAA

Protein sequence

>MS.gene001558.t1

NERRRRRRGESPQEDHKQQYRPLTIVYDGKISVTDATEIQARSILMLAKKEMVRTPTGSSSEPSSPSVFNLYSPSTSLSMQKSLQRFLQKRKNRIQEASPYHLKINEKN