AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0700160


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 8 sgRNAs with CRISPR-Local

Find 146 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTTCAGGTTTCTTCTTAT+TGG 0.157724 4_4:+71050134 None:intergenic
TCAAAACTTCAAAATGTTTC+AGG 0.190026 4_4:+71050120 None:intergenic
TTATTGGAGCTTTGAAGATA+TGG 0.315067 4_4:+71050150 None:intergenic
ATCTTACTTCATCTTGTAGT+AGG 0.421868 4_4:+71050033 None:intergenic
ACAAGCAACAATTACTTCCA+CGG 0.542293 4_4:-71050209 Msa0700160:intron
ATTACTTCCACGGAACGAGC+TGG 0.555290 4_4:-71050199 Msa0700160:CDS
AGCTTTGAAGATATGGACGT+TGG 0.560270 4_4:+71050157 None:intergenic
TCAATATCCAGCTCGTTCCG+TGG 0.603928 4_4:+71050192 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAAATCAACAAAATAA+AGG + chr4_4:71050152-71050171 None:intergenic 10.0%
!! ATATAAAATCAACAAAATAA+AGG + chr4_4:71050152-71050171 None:intergenic 10.0%
!! CAAAATAAAGGAATTATAAA+TGG + chr4_4:71050140-71050159 None:intergenic 15.0%
!! TCAAAACATATTAAATTCTA+GGG + chr4_4:71050580-71050599 None:intergenic 15.0%
!! CAAAATAAAGGAATTATAAA+TGG + chr4_4:71050140-71050159 None:intergenic 15.0%
!! TCAAAACATATTAAATTCTA+GGG + chr4_4:71050580-71050599 None:intergenic 15.0%
!!! TTTTTTGGTAGTTATATCAA+TGG - chr4_4:71050041-71050060 Msa0700160:CDS 20.0%
!! AACTGATTAATTGTATAAAC+AGG + chr4_4:71050184-71050203 None:intergenic 20.0%
!! TGTTCCTTTAATATATTACA+GGG + chr4_4:71050207-71050226 None:intergenic 20.0%
!! ATGTTCCTTTAATATATTAC+AGG + chr4_4:71050208-71050227 None:intergenic 20.0%
!! ATTAGTTAGAGAAACAAATA+AGG - chr4_4:71050472-71050491 Msa0700160:intron 20.0%
!! TTAGTTAGAGAAACAAATAA+GGG - chr4_4:71050473-71050492 Msa0700160:intron 20.0%
!! GTCAAAACATATTAAATTCT+AGG + chr4_4:71050581-71050600 None:intergenic 20.0%
!! ATATAACATGATTATCATCT+AGG + chr4_4:71050853-71050872 None:intergenic 20.0%
!! ATGGAAATGTTATATTAGAA+TGG + chr4_4:71051013-71051032 None:intergenic 20.0%
!! ACATAAAAAATTCCCTAATA+CGG - chr4_4:71051037-71051056 Msa0700160:intron 20.0%
!!! TTTTTTGGTAGTTATATCAA+TGG - chr4_4:71050041-71050060 Msa0700160:CDS 20.0%
!! AACTGATTAATTGTATAAAC+AGG + chr4_4:71050184-71050203 None:intergenic 20.0%
!! TGTTCCTTTAATATATTACA+GGG + chr4_4:71050207-71050226 None:intergenic 20.0%
!! ATGTTCCTTTAATATATTAC+AGG + chr4_4:71050208-71050227 None:intergenic 20.0%
!! ATTAGTTAGAGAAACAAATA+AGG - chr4_4:71050472-71050491 Msa0700160:intron 20.0%
!! TTAGTTAGAGAAACAAATAA+GGG - chr4_4:71050473-71050492 Msa0700160:intron 20.0%
!! GTCAAAACATATTAAATTCT+AGG + chr4_4:71050581-71050600 None:intergenic 20.0%
!! ATATAACATGATTATCATCT+AGG + chr4_4:71050853-71050872 None:intergenic 20.0%
!! ATGGAAATGTTATATTAGAA+TGG + chr4_4:71051013-71051032 None:intergenic 20.0%
!! ACATAAAAAATTCCCTAATA+CGG - chr4_4:71051037-71051056 Msa0700160:intron 20.0%
! AGTTATATCAATGGTGTATT+TGG - chr4_4:71050050-71050069 Msa0700160:CDS 25.0%
! AAAAAAACGATGCGTTAATT+TGG - chr4_4:71050103-71050122 Msa0700160:CDS 25.0%
! AGTTCCCTGTAATATATTAA+AGG - chr4_4:71050200-71050219 Msa0700160:CDS 25.0%
! AAATCGACAAAAATTACACT+GGG + chr4_4:71050328-71050347 None:intergenic 25.0%
!!! AGTGTTCATTTTTAAACTAG+AGG - chr4_4:71050501-71050520 Msa0700160:intron 25.0%
!!! GTGTTCATTTTTAAACTAGA+GGG - chr4_4:71050502-71050521 Msa0700160:intron 25.0%
!!! TGTTCATTTTTAAACTAGAG+GGG - chr4_4:71050503-71050522 Msa0700160:intron 25.0%
!! CATTTTCAATGAATTGACAT+GGG - chr4_4:71050736-71050755 Msa0700160:intron 25.0%
! TGATCTGTCTCTTAATATTT+CGG + chr4_4:71050879-71050898 None:intergenic 25.0%
!!! TGTACTGATTTCTAAGTTTA+GGG + chr4_4:71050904-71050923 None:intergenic 25.0%
!!! TTGTACTGATTTCTAAGTTT+AGG + chr4_4:71050905-71050924 None:intergenic 25.0%
!! TATATTAGAATGGCATGTTT+TGG + chr4_4:71051003-71051022 None:intergenic 25.0%
! CTTGAATTATTACCGTATTA+GGG + chr4_4:71051052-71051071 None:intergenic 25.0%
! TCAAAACTTCAAAATGTTTC+AGG + chr4_4:71051169-71051188 None:intergenic 25.0%
! AGTTATATCAATGGTGTATT+TGG - chr4_4:71050050-71050069 Msa0700160:CDS 25.0%
! AAAAAAACGATGCGTTAATT+TGG - chr4_4:71050103-71050122 Msa0700160:CDS 25.0%
! AGTTCCCTGTAATATATTAA+AGG - chr4_4:71050200-71050219 Msa0700160:CDS 25.0%
! AAATCGACAAAAATTACACT+GGG + chr4_4:71050328-71050347 None:intergenic 25.0%
!!! AGTGTTCATTTTTAAACTAG+AGG - chr4_4:71050501-71050520 Msa0700160:intron 25.0%
!!! GTGTTCATTTTTAAACTAGA+GGG - chr4_4:71050502-71050521 Msa0700160:intron 25.0%
!!! TGTTCATTTTTAAACTAGAG+GGG - chr4_4:71050503-71050522 Msa0700160:intron 25.0%
!! CATTTTCAATGAATTGACAT+GGG - chr4_4:71050736-71050755 Msa0700160:intron 25.0%
! TGATCTGTCTCTTAATATTT+CGG + chr4_4:71050879-71050898 None:intergenic 25.0%
!!! TGTACTGATTTCTAAGTTTA+GGG + chr4_4:71050904-71050923 None:intergenic 25.0%
!!! TTGTACTGATTTCTAAGTTT+AGG + chr4_4:71050905-71050924 None:intergenic 25.0%
!! TATATTAGAATGGCATGTTT+TGG + chr4_4:71051003-71051022 None:intergenic 25.0%
! CTTGAATTATTACCGTATTA+GGG + chr4_4:71051052-71051071 None:intergenic 25.0%
! TCAAAACTTCAAAATGTTTC+AGG + chr4_4:71051169-71051188 None:intergenic 25.0%
!!! TCGTTTTTTTTTTTGTGCGT+TGG + chr4_4:71050093-71050112 None:intergenic 30.0%
AATCGACAAAAATTACACTG+GGG + chr4_4:71050327-71050346 None:intergenic 30.0%
CAAATCGACAAAAATTACAC+TGG + chr4_4:71050329-71050348 None:intergenic 30.0%
AGTTAACTTCTTTGCTACAA+TGG + chr4_4:71050416-71050435 None:intergenic 30.0%
!! GTTCATTTTTAAACTAGAGG+GGG - chr4_4:71050504-71050523 Msa0700160:intron 30.0%
!! TTCATTTTTAAACTAGAGGG+GGG - chr4_4:71050505-71050524 Msa0700160:intron 30.0%
ACTTAAACGCATTTCATAAG+AGG + chr4_4:71050626-71050645 None:intergenic 30.0%
CCATGTCAATTCATTGAAAA+TGG + chr4_4:71050738-71050757 None:intergenic 30.0%
! CCATTTTCAATGAATTGACA+TGG - chr4_4:71050735-71050754 Msa0700160:intron 30.0%
GATCTGTCTCTTAATATTTC+GGG + chr4_4:71050878-71050897 None:intergenic 30.0%
AAACAACTGTGTAGATTGTT+GGG + chr4_4:71050941-71050960 None:intergenic 30.0%
AAAACAACTGTGTAGATTGT+TGG + chr4_4:71050942-71050961 None:intergenic 30.0%
CCTTGAATTATTACCGTATT+AGG + chr4_4:71051053-71051072 None:intergenic 30.0%
CCTAATACGGTAATAATTCA+AGG - chr4_4:71051050-71051069 Msa0700160:intron 30.0%
!! TTATTGGAGCTTTGAAGATA+TGG + chr4_4:71051139-71051158 None:intergenic 30.0%
!! TGTTTCAGGTTTCTTCTTAT+TGG + chr4_4:71051155-71051174 None:intergenic 30.0%
ATCTTACTTCATCTTGTAGT+AGG + chr4_4:71051256-71051275 None:intergenic 30.0%
!!! TCGTTTTTTTTTTTGTGCGT+TGG + chr4_4:71050093-71050112 None:intergenic 30.0%
AATCGACAAAAATTACACTG+GGG + chr4_4:71050327-71050346 None:intergenic 30.0%
CAAATCGACAAAAATTACAC+TGG + chr4_4:71050329-71050348 None:intergenic 30.0%
AGTTAACTTCTTTGCTACAA+TGG + chr4_4:71050416-71050435 None:intergenic 30.0%
!! GTTCATTTTTAAACTAGAGG+GGG - chr4_4:71050504-71050523 Msa0700160:intron 30.0%
!! TTCATTTTTAAACTAGAGGG+GGG - chr4_4:71050505-71050524 Msa0700160:intron 30.0%
ACTTAAACGCATTTCATAAG+AGG + chr4_4:71050626-71050645 None:intergenic 30.0%
CCATGTCAATTCATTGAAAA+TGG + chr4_4:71050738-71050757 None:intergenic 30.0%
! CCATTTTCAATGAATTGACA+TGG - chr4_4:71050735-71050754 Msa0700160:intron 30.0%
GATCTGTCTCTTAATATTTC+GGG + chr4_4:71050878-71050897 None:intergenic 30.0%
AAACAACTGTGTAGATTGTT+GGG + chr4_4:71050941-71050960 None:intergenic 30.0%
AAAACAACTGTGTAGATTGT+TGG + chr4_4:71050942-71050961 None:intergenic 30.0%
CCTTGAATTATTACCGTATT+AGG + chr4_4:71051053-71051072 None:intergenic 30.0%
CCTAATACGGTAATAATTCA+AGG - chr4_4:71051050-71051069 Msa0700160:intron 30.0%
!! TTATTGGAGCTTTGAAGATA+TGG + chr4_4:71051139-71051158 None:intergenic 30.0%
!! TGTTTCAGGTTTCTTCTTAT+TGG + chr4_4:71051155-71051174 None:intergenic 30.0%
ATCTTACTTCATCTTGTAGT+AGG + chr4_4:71051256-71051275 None:intergenic 30.0%
ATCAATGGTGTATTTGGTAG+CGG - chr4_4:71050056-71050075 Msa0700160:CDS 35.0%
! GATACGTTGTTTGAGTTCTA+TGG - chr4_4:71050267-71050286 Msa0700160:intron 35.0%
!!! TTTTGTCGATTTGCAAGAGA+TGG - chr4_4:71050336-71050355 Msa0700160:intron 35.0%
!! TTTGTCGATTTGCAAGAGAT+GGG - chr4_4:71050337-71050356 Msa0700160:intron 35.0%
ACAGTGTTAACTTACAAGAG+AGG - chr4_4:71050444-71050463 Msa0700160:intron 35.0%
GTTAGAGAAACAAATAAGGG+AGG - chr4_4:71050476-71050495 Msa0700160:intron 35.0%
! TTTAAGTTTGCAGTTAGCTG+AGG - chr4_4:71050639-71050658 Msa0700160:intron 35.0%
!! ATTAGAATGGCATGTTTTGG+AGG + chr4_4:71051000-71051019 None:intergenic 35.0%
!!! GGGAATTTTTTATGTCGTGA+TGG + chr4_4:71051032-71051051 None:intergenic 35.0%
ACAAGCAACAATTACTTCCA+CGG - chr4_4:71051077-71051096 Msa0700160:intron 35.0%
! GACATTTTTGTTACACACAC+AGG - chr4_4:71051211-71051230 Msa0700160:intron 35.0%
ATCAATGGTGTATTTGGTAG+CGG - chr4_4:71050056-71050075 Msa0700160:CDS 35.0%
! GATACGTTGTTTGAGTTCTA+TGG - chr4_4:71050267-71050286 Msa0700160:intron 35.0%
!!! TTTTGTCGATTTGCAAGAGA+TGG - chr4_4:71050336-71050355 Msa0700160:intron 35.0%
!! TTTGTCGATTTGCAAGAGAT+GGG - chr4_4:71050337-71050356 Msa0700160:intron 35.0%
ACAGTGTTAACTTACAAGAG+AGG - chr4_4:71050444-71050463 Msa0700160:intron 35.0%
GTTAGAGAAACAAATAAGGG+AGG - chr4_4:71050476-71050495 Msa0700160:intron 35.0%
! TTTAAGTTTGCAGTTAGCTG+AGG - chr4_4:71050639-71050658 Msa0700160:intron 35.0%
!! ATTAGAATGGCATGTTTTGG+AGG + chr4_4:71051000-71051019 None:intergenic 35.0%
!!! GGGAATTTTTTATGTCGTGA+TGG + chr4_4:71051032-71051051 None:intergenic 35.0%
ACAAGCAACAATTACTTCCA+CGG - chr4_4:71051077-71051096 Msa0700160:intron 35.0%
! GACATTTTTGTTACACACAC+AGG - chr4_4:71051211-71051230 Msa0700160:intron 35.0%
!! TTGTCGATTTGCAAGAGATG+GGG - chr4_4:71050338-71050357 Msa0700160:intron 40.0%
GGATACCAATTTCACATGCA+AGG - chr4_4:71050359-71050378 Msa0700160:intron 40.0%
TGCATCCTTGCATGTGAAAT+TGG + chr4_4:71050367-71050386 None:intergenic 40.0%
TGTTGTCTAAGGAAGTCTCA+GGG - chr4_4:71050534-71050553 Msa0700160:intron 40.0%
TTTCATAAGAGGCAGGCAAA+GGG + chr4_4:71050615-71050634 None:intergenic 40.0%
ATTTCATAAGAGGCAGGCAA+AGG + chr4_4:71050616-71050635 None:intergenic 40.0%
AAACGCATTTCATAAGAGGC+AGG + chr4_4:71050622-71050641 None:intergenic 40.0%
! CACTGTTCTGAGCATGATTT+AGG + chr4_4:71050799-71050818 None:intergenic 40.0%
!! AGCTTTGAAGATATGGACGT+TGG + chr4_4:71051132-71051151 None:intergenic 40.0%
!! TTGTCGATTTGCAAGAGATG+GGG - chr4_4:71050338-71050357 Msa0700160:intron 40.0%
GGATACCAATTTCACATGCA+AGG - chr4_4:71050359-71050378 Msa0700160:intron 40.0%
TGCATCCTTGCATGTGAAAT+TGG + chr4_4:71050367-71050386 None:intergenic 40.0%
TGTTGTCTAAGGAAGTCTCA+GGG - chr4_4:71050534-71050553 Msa0700160:intron 40.0%
TTTCATAAGAGGCAGGCAAA+GGG + chr4_4:71050615-71050634 None:intergenic 40.0%
ATTTCATAAGAGGCAGGCAA+AGG + chr4_4:71050616-71050635 None:intergenic 40.0%
AAACGCATTTCATAAGAGGC+AGG + chr4_4:71050622-71050641 None:intergenic 40.0%
! CACTGTTCTGAGCATGATTT+AGG + chr4_4:71050799-71050818 None:intergenic 40.0%
!! AGCTTTGAAGATATGGACGT+TGG + chr4_4:71051132-71051151 None:intergenic 40.0%
GTGTTGTCTAAGGAAGTCTC+AGG - chr4_4:71050533-71050552 Msa0700160:intron 45.0%
GTTGTCTAAGGAAGTCTCAG+GGG - chr4_4:71050535-71050554 Msa0700160:intron 45.0%
TTGTCTAAGGAAGTCTCAGG+GGG - chr4_4:71050536-71050555 Msa0700160:intron 45.0%
TTCATAAGAGGCAGGCAAAG+GGG + chr4_4:71050614-71050633 None:intergenic 45.0%
GTGTTGTCTAAGGAAGTCTC+AGG - chr4_4:71050533-71050552 Msa0700160:intron 45.0%
GTTGTCTAAGGAAGTCTCAG+GGG - chr4_4:71050535-71050554 Msa0700160:intron 45.0%
TTGTCTAAGGAAGTCTCAGG+GGG - chr4_4:71050536-71050555 Msa0700160:intron 45.0%
TTCATAAGAGGCAGGCAAAG+GGG + chr4_4:71050614-71050633 None:intergenic 45.0%
! GGGGGTATGTGTGTTGTCTA+AGG - chr4_4:71050523-71050542 Msa0700160:intron 50.0%
TGTCTAAGGAAGTCTCAGGG+GGG - chr4_4:71050537-71050556 Msa0700160:intron 50.0%
ATTACTTCCACGGAACGAGC+TGG - chr4_4:71051087-71051106 Msa0700160:intron 50.0%
TCAATATCCAGCTCGTTCCG+TGG + chr4_4:71051097-71051116 None:intergenic 50.0%
! GGGGGTATGTGTGTTGTCTA+AGG - chr4_4:71050523-71050542 Msa0700160:intron 50.0%
TGTCTAAGGAAGTCTCAGGG+GGG - chr4_4:71050537-71050556 Msa0700160:intron 50.0%
ATTACTTCCACGGAACGAGC+TGG - chr4_4:71051087-71051106 Msa0700160:intron 50.0%
TCAATATCCAGCTCGTTCCG+TGG + chr4_4:71051097-71051116 None:intergenic 50.0%
CTAAGGAAGTCTCAGGGGGG+AGG - chr4_4:71050540-71050559 Msa0700160:intron 60.0%
CTAAGGAAGTCTCAGGGGGG+AGG - chr4_4:71050540-71050559 Msa0700160:intron 60.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 71050031 71051277 71050031 ID=Msa0700160;Name=Msa0700160
chr4_4 mRNA 71050031 71051277 71050031 ID=Msa0700160-mRNA-1;Parent=Msa0700160;Name=Msa0700160-mRNA-1;_AED=0.40;_eAED=0.42;_QI=0|0|0|1|0|0|2|0|66
chr4_4 exon 71051273 71051277 71051273 ID=Msa0700160-mRNA-1:exon:21572;Parent=Msa0700160-mRNA-1
chr4_4 exon 71050031 71050226 71050031 ID=Msa0700160-mRNA-1:exon:21571;Parent=Msa0700160-mRNA-1
chr4_4 CDS 71051273 71051277 71051273 ID=Msa0700160-mRNA-1:cds;Parent=Msa0700160-mRNA-1
chr4_4 CDS 71050031 71050226 71050031 ID=Msa0700160-mRNA-1:cds;Parent=Msa0700160-mRNA-1
Gene Sequence

>Msa0700160

ATGGTCAACAATTACTTCCACGGAACGAGCTGGATATTGAGTTGTGATAAGTCCAACGTCCATATCTTCAAAGCTCCAATAAGAAGAAACCTGAAACATTTTGAAGTTTTGAAATTAGAACACAACAAAAATGAGACATTTTTGTTACACACACAGGTCAATCAAGAAAAACTAAACCTACTACAAGATGAAGTAAGATAA

Protein sequence

>Msa0700160

MVNNYFHGTSWILSCDKSNVHIFKAPIRRNLKHFEVLKLEHNKNETFLLHTQVNQEKLNLLQDEVR*