AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0619250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0619250 MtrunA17_Chr8g0383161 86.486 148 12 2 1 148 1 140 8.38e-87 249
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0619250 AT5G64820.1 36.765 136 72 4 15 141 13 143 1.51e-17 74.7
Msa0619250 AT1G16850.1 34.884 129 73 2 12 135 13 135 1.47e-14 67.0

Find 34 sgRNAs with CRISPR-Local

Find 127 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGCTTTCACCACCAAATT+TGG 0.164001 4_2:-70362786 Msa0619250:CDS
TGTATGAAACAATTTATTTA+TGG 0.164572 4_2:-70362028 Msa0619250:three_prime_UTR
CTACAAACTTACTCCAAATT+TGG 0.167313 4_2:+70362773 None:intergenic
CAAAATTGTGATGCTGTTAT+TGG 0.228818 4_2:-70362073 Msa0619250:three_prime_UTR
TTCCAAGTATTGGCCTAAAT+TGG 0.235754 4_2:+70361969 None:intergenic
AACGGTGTCAGTTAGTAATT+TGG 0.243488 4_2:+70362877 None:intergenic
GAGAATCTTTGGCCACATTT+TGG 0.261276 4_2:+70362918 None:intergenic
GAAACGTATGCTAAGGTATA+TGG 0.379291 4_2:+70363089 None:intergenic
CAGGGGTTACATGCTGGAAT+TGG 0.395685 4_2:+70362957 None:intergenic
AAATCAGCAGCTGAATTTGT+TGG 0.419411 4_2:-70362210 Msa0619250:CDS
TACCAATTTAGGCCAATACT+TGG 0.442164 4_2:-70361971 Msa0619250:three_prime_UTR
TGGCCACCTTCATCAGCAGC+AGG 0.453286 4_2:+70362938 None:intergenic
ATTAAAATGACCCCAAAAGA+AGG 0.454890 4_2:+70362096 None:intergenic
CAGCAGCAGGGGTTACATGC+TGG 0.456273 4_2:+70362951 None:intergenic
AAAATCCCATGAAAGCTCTT+GGG 0.505602 4_2:-70362843 Msa0619250:CDS
AAAAGCAAAGAATCAGTTGA+AGG 0.507499 4_2:-70362240 Msa0619250:CDS
GTAACCCCTGCTGCTGATGA+AGG 0.514461 4_2:-70362944 Msa0619250:CDS
CAAACTTACTCCAAATTTGG+TGG 0.516547 4_2:+70362776 None:intergenic
GGCCACCTTCATCAGCAGCA+GGG 0.529923 4_2:+70362939 None:intergenic
AGACACTACAGATTCTGATA+AGG 0.542472 4_2:-70362154 Msa0619250:CDS
GCCACCTTCATCAGCAGCAG+GGG 0.559916 4_2:+70362940 None:intergenic
TTTCTCCCAAGAGCTTTCAT+GGG 0.569638 4_2:+70362838 None:intergenic
AAAGCTGCATCTGAAGATCA+TGG 0.570711 4_2:+70362801 None:intergenic
GATATGAGAAACGTATGCTA+AGG 0.583457 4_2:+70363082 None:intergenic
AATTGTGATGCTGTTATTGG+AGG 0.583515 4_2:-70362070 Msa0619250:three_prime_UTR
CGTATGCTAAGGTATATGGC+TGG 0.593588 4_2:+70363093 None:intergenic
AACTAGAAGCGTCATTCACA+TGG 0.599531 4_2:+70361874 None:intergenic
GATGCTGTTATTGGAGGAGA+TGG 0.605362 4_2:-70362064 Msa0619250:three_prime_UTR
TGTCAGTTAGTAATTTGGAA+AGG 0.607458 4_2:+70362882 None:intergenic
AATCCATAAGACAAAAGAGA+AGG 0.608547 4_2:-70362181 Msa0619250:CDS
GTTAGTAATTTGGAAAGGCG+TGG 0.619952 4_2:+70362887 None:intergenic
AGGGGAAAAGGAGAACATGA+AGG 0.650023 4_2:-70362294 Msa0619250:CDS
ACCCCTGCTGCTGATGAAGG+TGG 0.657057 4_2:-70362941 Msa0619250:CDS
TGATGAAGGTGGCCAAAATG+TGG 0.672717 4_2:-70362930 Msa0619250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCATATATATACATTAAAT+TGG + chr4_2:70362596-70362615 None:intergenic 10.0%
!! ATATATATGAATATTAATGT+AGG - chr4_2:70362605-70362624 Msa0619250:intron 10.0%
!! TTCATATATATACATTAAAT+TGG + chr4_2:70362596-70362615 None:intergenic 10.0%
!! ATATATATGAATATTAATGT+AGG - chr4_2:70362605-70362624 Msa0619250:intron 10.0%
!! AATTAAAAACTAATTGTTCA+AGG + chr4_2:70361903-70361922 None:intergenic 15.0%
!! AAAATAGTTTAATGTTGATA+TGG - chr4_2:70362320-70362339 Msa0619250:intron 15.0%
!! TGTAAATTCATAAAAATGAT+TGG + chr4_2:70362395-70362414 None:intergenic 15.0%
!!! ATATATATATGATTTGTTGA+CGG - chr4_2:70362510-70362529 Msa0619250:intron 15.0%
!!! AAATATTTTTTTCCTTCTTT+TGG - chr4_2:70362846-70362865 Msa0619250:CDS 15.0%
!!! AATATTTTTTTCCTTCTTTT+GGG - chr4_2:70362847-70362866 Msa0619250:CDS 15.0%
!! TGTATGAAACAATTTATTTA+TGG - chr4_2:70362926-70362945 Msa0619250:CDS 15.0%
!! AATTAAAAACTAATTGTTCA+AGG + chr4_2:70361903-70361922 None:intergenic 15.0%
!! AAAATAGTTTAATGTTGATA+TGG - chr4_2:70362320-70362339 Msa0619250:intron 15.0%
!! TGTAAATTCATAAAAATGAT+TGG + chr4_2:70362395-70362414 None:intergenic 15.0%
!!! ATATATATATGATTTGTTGA+CGG - chr4_2:70362510-70362529 Msa0619250:intron 15.0%
!!! AAATATTTTTTTCCTTCTTT+TGG - chr4_2:70362846-70362865 Msa0619250:CDS 15.0%
!!! AATATTTTTTTCCTTCTTTT+GGG - chr4_2:70362847-70362866 Msa0619250:CDS 15.0%
!! TGTATGAAACAATTTATTTA+TGG - chr4_2:70362926-70362945 Msa0619250:CDS 15.0%
!!! CAAAAGTCTATTTCATTTTT+AGG - chr4_2:70362209-70362228 Msa0619250:CDS 20.0%
!! CAATACAATCTTGAAATTAT+AGG - chr4_2:70362242-70362261 Msa0619250:CDS 20.0%
!!! TTATGACTGAATATTTTTCA+AGG + chr4_2:70362444-70362463 None:intergenic 20.0%
!! ATATGAATATTAATGTAGGT+AGG - chr4_2:70362609-70362628 Msa0619250:intron 20.0%
!!! ATATTTTTTTCCTTCTTTTG+GGG - chr4_2:70362848-70362867 Msa0619250:CDS 20.0%
!!! TTCATACATTTTACCAATTT+AGG - chr4_2:70362972-70362991 Msa0619250:CDS 20.0%
!!! GAATTGCTATTATGTATTTT+TGG + chr4_2:70363054-70363073 None:intergenic 20.0%
!!! CAAAAGTCTATTTCATTTTT+AGG - chr4_2:70362209-70362228 Msa0619250:CDS 20.0%
!! CAATACAATCTTGAAATTAT+AGG - chr4_2:70362242-70362261 Msa0619250:CDS 20.0%
!!! TTATGACTGAATATTTTTCA+AGG + chr4_2:70362444-70362463 None:intergenic 20.0%
!! ATATGAATATTAATGTAGGT+AGG - chr4_2:70362609-70362628 Msa0619250:intron 20.0%
!!! ATATTTTTTTCCTTCTTTTG+GGG - chr4_2:70362848-70362867 Msa0619250:CDS 20.0%
!!! TTCATACATTTTACCAATTT+AGG - chr4_2:70362972-70362991 Msa0619250:CDS 20.0%
!!! GAATTGCTATTATGTATTTT+TGG + chr4_2:70363054-70363073 None:intergenic 20.0%
!!! GTTTTTAATTAGCATTAGCA+TGG - chr4_2:70361913-70361932 Msa0619250:three_prime_UTR 25.0%
! AAAAAGAAGAAAAAGTAGGA+TGG + chr4_2:70361960-70361979 None:intergenic 25.0%
! TGCTAAAAAGAAGAAAAAGT+AGG + chr4_2:70361964-70361983 None:intergenic 25.0%
!!! TGTATCTATTTTTCAGTTTC+AGG - chr4_2:70362640-70362659 Msa0619250:intron 25.0%
!!! GTATCTATTTTTCAGTTTCA+GGG - chr4_2:70362641-70362660 Msa0619250:intron 25.0%
!!! TATCTATTTTTCAGTTTCAG+GGG - chr4_2:70362642-70362661 Msa0619250:intron 25.0%
!! TTTTCAAATCTTCCAAGTAT+TGG + chr4_2:70362998-70363017 None:intergenic 25.0%
!!! GTTTTTAATTAGCATTAGCA+TGG - chr4_2:70361913-70361932 Msa0619250:three_prime_UTR 25.0%
! AAAAAGAAGAAAAAGTAGGA+TGG + chr4_2:70361960-70361979 None:intergenic 25.0%
! TGCTAAAAAGAAGAAAAAGT+AGG + chr4_2:70361964-70361983 None:intergenic 25.0%
!!! TGTATCTATTTTTCAGTTTC+AGG - chr4_2:70362640-70362659 Msa0619250:intron 25.0%
!!! GTATCTATTTTTCAGTTTCA+GGG - chr4_2:70362641-70362660 Msa0619250:intron 25.0%
!!! TATCTATTTTTCAGTTTCAG+GGG - chr4_2:70362642-70362661 Msa0619250:intron 25.0%
!! TTTTCAAATCTTCCAAGTAT+TGG + chr4_2:70362998-70363017 None:intergenic 25.0%
TGTCAGTTAGTAATTTGGAA+AGG + chr4_2:70362075-70362094 None:intergenic 30.0%
!!! GGATTTTTTAAGCAGAGAAA+CGG + chr4_2:70362098-70362117 None:intergenic 30.0%
CTACAAACTTACTCCAAATT+TGG + chr4_2:70362184-70362203 None:intergenic 30.0%
TATATGTCTGACTTTAGACA+TGG + chr4_2:70362495-70362514 None:intergenic 30.0%
AAAAGCAAAGAATCAGTTGA+AGG - chr4_2:70362714-70362733 Msa0619250:intron 30.0%
AATCCATAAGACAAAAGAGA+AGG - chr4_2:70362773-70362792 Msa0619250:intron 30.0%
ATTAAAATGACCCCAAAAGA+AGG + chr4_2:70362861-70362880 None:intergenic 30.0%
CAAAATTGTGATGCTGTTAT+TGG - chr4_2:70362881-70362900 Msa0619250:CDS 30.0%
TGTCAGTTAGTAATTTGGAA+AGG + chr4_2:70362075-70362094 None:intergenic 30.0%
!!! GGATTTTTTAAGCAGAGAAA+CGG + chr4_2:70362098-70362117 None:intergenic 30.0%
CTACAAACTTACTCCAAATT+TGG + chr4_2:70362184-70362203 None:intergenic 30.0%
TATATGTCTGACTTTAGACA+TGG + chr4_2:70362495-70362514 None:intergenic 30.0%
AAAAGCAAAGAATCAGTTGA+AGG - chr4_2:70362714-70362733 Msa0619250:intron 30.0%
AATCCATAAGACAAAAGAGA+AGG - chr4_2:70362773-70362792 Msa0619250:intron 30.0%
ATTAAAATGACCCCAAAAGA+AGG + chr4_2:70362861-70362880 None:intergenic 30.0%
CAAAATTGTGATGCTGTTAT+TGG - chr4_2:70362881-70362900 Msa0619250:CDS 30.0%
GAAACGTATGCTAAGGTATA+TGG + chr4_2:70361868-70361887 None:intergenic 35.0%
GATATGAGAAACGTATGCTA+AGG + chr4_2:70361875-70361894 None:intergenic 35.0%
!! TGGTTTTTCTGGAGAATCTT+TGG + chr4_2:70362050-70362069 None:intergenic 35.0%
! AACGGTGTCAGTTAGTAATT+TGG + chr4_2:70362080-70362099 None:intergenic 35.0%
AAAAATCCCATGAAAGCTCT+TGG - chr4_2:70362110-70362129 Msa0619250:three_prime_UTR 35.0%
AAAATCCCATGAAAGCTCTT+GGG - chr4_2:70362111-70362130 Msa0619250:three_prime_UTR 35.0%
CAAACTTACTCCAAATTTGG+TGG + chr4_2:70362181-70362200 None:intergenic 35.0%
!! TTTTTCAGTTTCAGGGGAAA+AGG - chr4_2:70362648-70362667 Msa0619250:intron 35.0%
AAATCAGCAGCTGAATTTGT+TGG - chr4_2:70362744-70362763 Msa0619250:intron 35.0%
! TCACCTTCTCTTTTGTCTTA+TGG + chr4_2:70362779-70362798 None:intergenic 35.0%
AGACACTACAGATTCTGATA+AGG - chr4_2:70362800-70362819 Msa0619250:CDS 35.0%
AATTGTGATGCTGTTATTGG+AGG - chr4_2:70362884-70362903 Msa0619250:CDS 35.0%
TACCAATTTAGGCCAATACT+TGG - chr4_2:70362983-70363002 Msa0619250:CDS 35.0%
!! TTCCAAGTATTGGCCTAAAT+TGG + chr4_2:70362988-70363007 None:intergenic 35.0%
GAAACGTATGCTAAGGTATA+TGG + chr4_2:70361868-70361887 None:intergenic 35.0%
GATATGAGAAACGTATGCTA+AGG + chr4_2:70361875-70361894 None:intergenic 35.0%
!! TGGTTTTTCTGGAGAATCTT+TGG + chr4_2:70362050-70362069 None:intergenic 35.0%
! AACGGTGTCAGTTAGTAATT+TGG + chr4_2:70362080-70362099 None:intergenic 35.0%
AAAAATCCCATGAAAGCTCT+TGG - chr4_2:70362110-70362129 Msa0619250:three_prime_UTR 35.0%
AAAATCCCATGAAAGCTCTT+GGG - chr4_2:70362111-70362130 Msa0619250:three_prime_UTR 35.0%
CAAACTTACTCCAAATTTGG+TGG + chr4_2:70362181-70362200 None:intergenic 35.0%
!! TTTTTCAGTTTCAGGGGAAA+AGG - chr4_2:70362648-70362667 Msa0619250:intron 35.0%
AAATCAGCAGCTGAATTTGT+TGG - chr4_2:70362744-70362763 Msa0619250:intron 35.0%
! TCACCTTCTCTTTTGTCTTA+TGG + chr4_2:70362779-70362798 None:intergenic 35.0%
AGACACTACAGATTCTGATA+AGG - chr4_2:70362800-70362819 Msa0619250:CDS 35.0%
AATTGTGATGCTGTTATTGG+AGG - chr4_2:70362884-70362903 Msa0619250:CDS 35.0%
TACCAATTTAGGCCAATACT+TGG - chr4_2:70362983-70363002 Msa0619250:CDS 35.0%
!! TTCCAAGTATTGGCCTAAAT+TGG + chr4_2:70362988-70363007 None:intergenic 35.0%
! GAGAATCTTTGGCCACATTT+TGG + chr4_2:70362039-70362058 None:intergenic 40.0%
GTTAGTAATTTGGAAAGGCG+TGG + chr4_2:70362070-70362089 None:intergenic 40.0%
TTTCTCCCAAGAGCTTTCAT+GGG + chr4_2:70362119-70362138 None:intergenic 40.0%
! TTTTCTCCCAAGAGCTTTCA+TGG + chr4_2:70362120-70362139 None:intergenic 40.0%
AAAGCTGCATCTGAAGATCA+TGG + chr4_2:70362156-70362175 None:intergenic 40.0%
!! AACTAGAAGCGTCATTCACA+TGG + chr4_2:70363083-70363102 None:intergenic 40.0%
! GAGAATCTTTGGCCACATTT+TGG + chr4_2:70362039-70362058 None:intergenic 40.0%
GTTAGTAATTTGGAAAGGCG+TGG + chr4_2:70362070-70362089 None:intergenic 40.0%
TTTCTCCCAAGAGCTTTCAT+GGG + chr4_2:70362119-70362138 None:intergenic 40.0%
! TTTTCTCCCAAGAGCTTTCA+TGG + chr4_2:70362120-70362139 None:intergenic 40.0%
AAAGCTGCATCTGAAGATCA+TGG + chr4_2:70362156-70362175 None:intergenic 40.0%
!! AACTAGAAGCGTCATTCACA+TGG + chr4_2:70363083-70363102 None:intergenic 40.0%
TGATGAAGGTGGCCAAAATG+TGG - chr4_2:70362024-70362043 Msa0619250:three_prime_UTR 45.0%
!! TTGGAAAGGCGTGGTTTTTC+TGG + chr4_2:70362061-70362080 None:intergenic 45.0%
GCAGCTTTCACCACCAAATT+TGG - chr4_2:70362168-70362187 Msa0619250:CDS 45.0%
AGGGGAAAAGGAGAACATGA+AGG - chr4_2:70362660-70362679 Msa0619250:intron 45.0%
GATGCTGTTATTGGAGGAGA+TGG - chr4_2:70362890-70362909 Msa0619250:CDS 45.0%
CGTATGCTAAGGTATATGGC+TGG + chr4_2:70361864-70361883 None:intergenic 45.0%
TGATGAAGGTGGCCAAAATG+TGG - chr4_2:70362024-70362043 Msa0619250:three_prime_UTR 45.0%
!! TTGGAAAGGCGTGGTTTTTC+TGG + chr4_2:70362061-70362080 None:intergenic 45.0%
GCAGCTTTCACCACCAAATT+TGG - chr4_2:70362168-70362187 Msa0619250:CDS 45.0%
AGGGGAAAAGGAGAACATGA+AGG - chr4_2:70362660-70362679 Msa0619250:intron 45.0%
GATGCTGTTATTGGAGGAGA+TGG - chr4_2:70362890-70362909 Msa0619250:CDS 45.0%
CAGGGGTTACATGCTGGAAT+TGG + chr4_2:70362000-70362019 None:intergenic 50.0%
CAGGGGTTACATGCTGGAAT+TGG + chr4_2:70362000-70362019 None:intergenic 50.0%
GTAACCCCTGCTGCTGATGA+AGG - chr4_2:70362010-70362029 Msa0619250:three_prime_UTR 55.0%
GTAACCCCTGCTGCTGATGA+AGG - chr4_2:70362010-70362029 Msa0619250:three_prime_UTR 55.0%
CAGCAGCAGGGGTTACATGC+TGG + chr4_2:70362006-70362025 None:intergenic 60.0%
ACCCCTGCTGCTGATGAAGG+TGG - chr4_2:70362013-70362032 Msa0619250:three_prime_UTR 60.0%
GCCACCTTCATCAGCAGCAG+GGG + chr4_2:70362017-70362036 None:intergenic 60.0%
GGCCACCTTCATCAGCAGCA+GGG + chr4_2:70362018-70362037 None:intergenic 60.0%
TGGCCACCTTCATCAGCAGC+AGG + chr4_2:70362019-70362038 None:intergenic 60.0%
CAGCAGCAGGGGTTACATGC+TGG + chr4_2:70362006-70362025 None:intergenic 60.0%
ACCCCTGCTGCTGATGAAGG+TGG - chr4_2:70362013-70362032 Msa0619250:three_prime_UTR 60.0%
GCCACCTTCATCAGCAGCAG+GGG + chr4_2:70362017-70362036 None:intergenic 60.0%
GGCCACCTTCATCAGCAGCA+GGG + chr4_2:70362018-70362037 None:intergenic 60.0%
TGGCCACCTTCATCAGCAGC+AGG + chr4_2:70362019-70362038 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 70361862 70363114 70361862 ID=Msa0619250;Name=Msa0619250
chr4_2 mRNA 70361862 70363114 70361862 ID=Msa0619250-mRNA-1;Parent=Msa0619250;Name=Msa0619250-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|1|1|2|272|148
chr4_2 exon 70361862 70362320 70361862 ID=Msa0619250-mRNA-1:exon:20474;Parent=Msa0619250-mRNA-1
chr4_2 exon 70362785 70363114 70362785 ID=Msa0619250-mRNA-1:exon:20473;Parent=Msa0619250-mRNA-1
chr4_2 five_prime_UTR 70363045 70363114 70363045 ID=Msa0619250-mRNA-1:five_prime_utr;Parent=Msa0619250-mRNA-1
chr4_2 CDS 70362785 70363044 70362785 ID=Msa0619250-mRNA-1:cds;Parent=Msa0619250-mRNA-1
chr4_2 CDS 70362134 70362320 70362134 ID=Msa0619250-mRNA-1:cds;Parent=Msa0619250-mRNA-1
chr4_2 three_prime_UTR 70361862 70362133 70361862 ID=Msa0619250-mRNA-1:three_prime_utr;Parent=Msa0619250-mRNA-1
Gene Sequence

>Msa0619250

ATGGAAAATAAATTGATTAGCAGAACCATCCTACTTTTTCTTCTTTTTAGCATCTTGATCATTCTCCAATTCCAGCATGTAACCCCTGCTGCTGATGAAGGTGGCCAAAATGTGGCCAAAGATTCTCCAGAAAAACCACGCCTTTCCAAATTACTAACTGACACCGTTTCTCTGCTTAAAAAATCCCATGAAAGCTCTTGGGAGAAAATCAAAACTGTCATCCATGATCTTCAGATGCAGCTTTCACCACCAAATTTGGATTTCAGGGGAAAAGGAGAACATGAAGGAGTGAAAGAAGCAGTTGAGAAGAGTTTTGACAAAAGCAAAGAATCAGTTGAAGGAACTGCTAAATCAGCAGCTGAATTTGTTGGAGAAACAATCCATAAGACAAAAGAGAAGGTGAAAGACACTACAGATTCTGATAAGGATTCTAAAGCAGAACTTTGA
Protein sequence

>Msa0619250

MENKLISRTILLFLLFSILIILQFQHVTPAADEGGQNVAKDSPEKPRLSKLLTDTVSLLKKSHESSWEKIKTVIHDLQMQLSPPNLDFRGKGEHEGVKEAVEKSFDKSKESVEGTAKSAAEFVGETIHKTKEKVKDTTDSDKDSKAEL*