AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0446000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0446000 MtrunA17_Chr5g0414621 54.839 93 31 2 1 82 964 1056 3.76e-20 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTTATCTACCGCTTTC+TGG 0.130682 3_3:+21144452 None:intergenic
TAAAGTCCGTCTCTTCTTAT+TGG 0.259805 3_3:+21144564 None:intergenic
AATAAGAAGAGACGGACTTT+AGG 0.309181 3_3:-21144562 Msa0446000:CDS
GCCTCTGATGTATCAATTAC+TGG 0.325593 3_3:-21143909 Msa0446000:CDS
ATATATCACAAACTGGATTA+TGG 0.342337 3_3:-21143644 Msa0446000:three_prime_UTR
ATAAGAAGAGACGGACTTTA+GGG 0.349221 3_3:-21144561 Msa0446000:CDS
AAAGTCCGTCTCTTCTTATT+GGG 0.349596 3_3:+21144565 None:intergenic
ACATTGGCACCAATTGTGTT+TGG 0.370210 3_3:+21144416 None:intergenic
TCAACTTGAAGGTACCAAAA+AGG 0.380776 3_3:+21143670 None:intergenic
GCAGATGGCATTGGTCCTTT+CGG 0.389048 3_3:-21144502 Msa0446000:CDS
TGATATATTCATCAACTTGA+AGG 0.410944 3_3:+21143659 None:intergenic
TTGATGAATATATCACAAAC+TGG 0.454854 3_3:-21143651 Msa0446000:three_prime_UTR
ATAGCTTCTTCTGTCGTAGC+TGG 0.476241 3_3:+21144475 None:intergenic
ACTTCATTTGCAGATGGCAT+TGG 0.490463 3_3:-21144511 Msa0446000:CDS
CACACTAGTGAATCAACCTT+CGG 0.524715 3_3:+21144604 None:intergenic
GAATTGTTGATTCTTGAGAA+TGG 0.539961 3_3:-21143954 Msa0446000:CDS
CTAGTGTGGGAAGAGGCGTC+AGG 0.540128 3_3:-21144589 Msa0446000:CDS
ATGACAACATTGATATCCTC+AGG 0.546933 3_3:+21143771 None:intergenic
CGAAGGTTGATTCACTAGTG+TGG 0.569035 3_3:-21144603 Msa0446000:CDS
GAAGGTTGATTCACTAGTGT+GGG 0.572254 3_3:-21144602 Msa0446000:CDS
TGATTCACTAGTGTGGGAAG+AGG 0.584042 3_3:-21144596 Msa0446000:CDS
GGATCTACTTCATTTGCAGA+TGG 0.584996 3_3:-21144517 Msa0446000:CDS
GGCCGCAGCTTGGACATCAG+AGG 0.592487 3_3:-21144538 Msa0446000:CDS
GGATTCTTCAACTCATCCGA+AGG 0.609941 3_3:-21144620 Msa0446000:CDS
AGAAGAAGCTATCCAGAAAG+CGG 0.623148 3_3:-21144464 Msa0446000:CDS
AAGAAGAGACGGACTTTAGG+GGG 0.623398 3_3:-21144559 Msa0446000:CDS
ATGCAGCAAGCACAAATGCA+AGG 0.625738 3_3:-21144364 Msa0446000:intron
CAGGTCCCAATAAGAAGAGA+CGG 0.631523 3_3:-21144570 Msa0446000:CDS
ATGCAAGGTGGAGTATCTGA+TGG 0.634174 3_3:-21144349 Msa0446000:intron
GTCGTAGCTGGAATTCCGAA+AGG 0.636065 3_3:+21144487 None:intergenic
ACACATTATAAAGAGAGATG+TGG 0.638163 3_3:+21143746 None:intergenic
TCCAGTAATTGATACATCAG+AGG 0.646595 3_3:+21143908 None:intergenic
TTAATGTCTGTGTATACCTG+AGG 0.650120 3_3:-21143787 Msa0446000:three_prime_UTR
CTTGAGAATGGTCAAACACG+TGG 0.651926 3_3:-21143942 Msa0446000:CDS
ATCCTCTGATGTCCAAGCTG+CGG 0.665558 3_3:+21144536 None:intergenic
TAAGAAGAGACGGACTTTAG+GGG 0.671920 3_3:-21144560 Msa0446000:CDS
GAGAATGGTCAAACACGTGG+TGG 0.694374 3_3:-21143939 Msa0446000:CDS
CAGCAAGCACAAATGCAAGG+TGG 0.698152 3_3:-21144361 Msa0446000:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATCCAGTTTTTTTTTTT+TGG - chr3_3:21144413-21144432 Msa0446000:intron 15.0%
!!! TTAATCCAGTTTTTTTTTTT+TGG - chr3_3:21144413-21144432 Msa0446000:intron 15.0%
!! ATTCTATGTTATTCAAAAGT+AGG - chr3_3:21143945-21143964 Msa0446000:CDS 20.0%
!!! ATATTGATTATGCTGAATTA+TGG - chr3_3:21144098-21144117 Msa0446000:intron 20.0%
!!! TATCTCATGTTTTCATATAT+AGG - chr3_3:21144136-21144155 Msa0446000:intron 20.0%
!! TAAATAGAAAGATAATAACG+TGG - chr3_3:21144248-21144267 Msa0446000:intron 20.0%
!! TTGTACCAAAAAAAAAAAAC+TGG + chr3_3:21144421-21144440 None:intergenic 20.0%
!!! AATGTGTTGAGATAAATTTT+TGG - chr3_3:21144515-21144534 Msa0446000:CDS 20.0%
!!! TAAATTTTTGGTAGAGATAT+TGG - chr3_3:21144527-21144546 Msa0446000:CDS 20.0%
!! ATTCTATGTTATTCAAAAGT+AGG - chr3_3:21143945-21143964 Msa0446000:CDS 20.0%
!!! ATATTGATTATGCTGAATTA+TGG - chr3_3:21144098-21144117 Msa0446000:intron 20.0%
!!! TATCTCATGTTTTCATATAT+AGG - chr3_3:21144136-21144155 Msa0446000:intron 20.0%
!! TAAATAGAAAGATAATAACG+TGG - chr3_3:21144248-21144267 Msa0446000:intron 20.0%
!! TTGTACCAAAAAAAAAAAAC+TGG + chr3_3:21144421-21144440 None:intergenic 20.0%
!!! AATGTGTTGAGATAAATTTT+TGG - chr3_3:21144515-21144534 Msa0446000:CDS 20.0%
!!! TAAATTTTTGGTAGAGATAT+TGG - chr3_3:21144527-21144546 Msa0446000:CDS 20.0%
! TGATATATTCATCAACTTGA+AGG + chr3_3:21144589-21144608 None:intergenic 25.0%
! TTGATGAATATATCACAAAC+TGG - chr3_3:21144594-21144613 Msa0446000:CDS 25.0%
! ATATATCACAAACTGGATTA+TGG - chr3_3:21144601-21144620 Msa0446000:CDS 25.0%
! TGATATATTCATCAACTTGA+AGG + chr3_3:21144589-21144608 None:intergenic 25.0%
! TTGATGAATATATCACAAAC+TGG - chr3_3:21144594-21144613 Msa0446000:CDS 25.0%
! ATATATCACAAACTGGATTA+TGG - chr3_3:21144601-21144620 Msa0446000:CDS 25.0%
! TTCTTTTGTCCAAACACAAT+TGG - chr3_3:21143820-21143839 Msa0446000:three_prime_UTR 30.0%
TGTCAATATGTCATTATCCA+CGG + chr3_3:21143987-21144006 None:intergenic 30.0%
TCACACAACAAAAACTCATA+TGG + chr3_3:21144035-21144054 None:intergenic 30.0%
GAAAACATGAGATATACAAC+TGG + chr3_3:21144130-21144149 None:intergenic 30.0%
!! GAATTGTTGATTCTTGAGAA+TGG - chr3_3:21144291-21144310 Msa0446000:intron 30.0%
! AAGATTTTGTGGTGAAGATA+TGG - chr3_3:21144376-21144395 Msa0446000:intron 30.0%
! AGATTTTGTGGTGAAGATAT+GGG - chr3_3:21144377-21144396 Msa0446000:intron 30.0%
ACACATTATAAAGAGAGATG+TGG + chr3_3:21144502-21144521 None:intergenic 30.0%
! TCTATGTATTGCTACCTTTT+TGG - chr3_3:21144561-21144580 Msa0446000:CDS 30.0%
! TTCTTTTGTCCAAACACAAT+TGG - chr3_3:21143820-21143839 Msa0446000:three_prime_UTR 30.0%
TGTCAATATGTCATTATCCA+CGG + chr3_3:21143987-21144006 None:intergenic 30.0%
TCACACAACAAAAACTCATA+TGG + chr3_3:21144035-21144054 None:intergenic 30.0%
GAAAACATGAGATATACAAC+TGG + chr3_3:21144130-21144149 None:intergenic 30.0%
!! GAATTGTTGATTCTTGAGAA+TGG - chr3_3:21144291-21144310 Msa0446000:intron 30.0%
! AAGATTTTGTGGTGAAGATA+TGG - chr3_3:21144376-21144395 Msa0446000:intron 30.0%
! AGATTTTGTGGTGAAGATAT+GGG - chr3_3:21144377-21144396 Msa0446000:intron 30.0%
ACACATTATAAAGAGAGATG+TGG + chr3_3:21144502-21144521 None:intergenic 30.0%
! TCTATGTATTGCTACCTTTT+TGG - chr3_3:21144561-21144580 Msa0446000:CDS 30.0%
AAAGTCCGTCTCTTCTTATT+GGG + chr3_3:21143683-21143702 None:intergenic 35.0%
TAAAGTCCGTCTCTTCTTAT+TGG + chr3_3:21143684-21143703 None:intergenic 35.0%
! AATAAGAAGAGACGGACTTT+AGG - chr3_3:21143683-21143702 Msa0446000:three_prime_UTR 35.0%
! ATAAGAAGAGACGGACTTTA+GGG - chr3_3:21143684-21143703 Msa0446000:three_prime_UTR 35.0%
GAGCTAATCATAGATAGGAT+TGG + chr3_3:21143860-21143879 None:intergenic 35.0%
GCATAGAGCTAATCATAGAT+AGG + chr3_3:21143865-21143884 None:intergenic 35.0%
! TATCTGATGGTATTTGAGGT+AGG - chr3_3:21143909-21143928 Msa0446000:CDS 35.0%
TCCAGTAATTGATACATCAG+AGG + chr3_3:21144340-21144359 None:intergenic 35.0%
! AGCAACTAGCAAAGATTTTG+TGG - chr3_3:21144365-21144384 Msa0446000:intron 35.0%
TTAATGTCTGTGTATACCTG+AGG - chr3_3:21144458-21144477 Msa0446000:CDS 35.0%
ATGACAACATTGATATCCTC+AGG + chr3_3:21144477-21144496 None:intergenic 35.0%
!! TCAACTTGAAGGTACCAAAA+AGG + chr3_3:21144578-21144597 None:intergenic 35.0%
AAAGTCCGTCTCTTCTTATT+GGG + chr3_3:21143683-21143702 None:intergenic 35.0%
TAAAGTCCGTCTCTTCTTAT+TGG + chr3_3:21143684-21143703 None:intergenic 35.0%
! AATAAGAAGAGACGGACTTT+AGG - chr3_3:21143683-21143702 Msa0446000:three_prime_UTR 35.0%
! ATAAGAAGAGACGGACTTTA+GGG - chr3_3:21143684-21143703 Msa0446000:three_prime_UTR 35.0%
GAGCTAATCATAGATAGGAT+TGG + chr3_3:21143860-21143879 None:intergenic 35.0%
GCATAGAGCTAATCATAGAT+AGG + chr3_3:21143865-21143884 None:intergenic 35.0%
! TATCTGATGGTATTTGAGGT+AGG - chr3_3:21143909-21143928 Msa0446000:CDS 35.0%
TCCAGTAATTGATACATCAG+AGG + chr3_3:21144340-21144359 None:intergenic 35.0%
! AGCAACTAGCAAAGATTTTG+TGG - chr3_3:21144365-21144384 Msa0446000:intron 35.0%
TTAATGTCTGTGTATACCTG+AGG - chr3_3:21144458-21144477 Msa0446000:CDS 35.0%
ATGACAACATTGATATCCTC+AGG + chr3_3:21144477-21144496 None:intergenic 35.0%
!! TCAACTTGAAGGTACCAAAA+AGG + chr3_3:21144578-21144597 None:intergenic 35.0%
CACACTAGTGAATCAACCTT+CGG + chr3_3:21143644-21143663 None:intergenic 40.0%
! GAAGGTTGATTCACTAGTGT+GGG - chr3_3:21143643-21143662 Msa0446000:three_prime_UTR 40.0%
! TAAGAAGAGACGGACTTTAG+GGG - chr3_3:21143685-21143704 Msa0446000:three_prime_UTR 40.0%
GGATCTACTTCATTTGCAGA+TGG - chr3_3:21143728-21143747 Msa0446000:three_prime_UTR 40.0%
ACTTCATTTGCAGATGGCAT+TGG - chr3_3:21143734-21143753 Msa0446000:three_prime_UTR 40.0%
AGAAGAAGCTATCCAGAAAG+CGG - chr3_3:21143781-21143800 Msa0446000:three_prime_UTR 40.0%
TTGCTTTATCTACCGCTTTC+TGG + chr3_3:21143796-21143815 None:intergenic 40.0%
ACATTGGCACCAATTGTGTT+TGG + chr3_3:21143832-21143851 None:intergenic 40.0%
!! AACACAATTGGTGCCAATGT+TGG - chr3_3:21143832-21143851 Msa0446000:three_prime_UTR 40.0%
! GGAGTATCTGATGGTATTTG+AGG - chr3_3:21143905-21143924 Msa0446000:CDS 40.0%
! GGACATTTTATTGCAGTGCT+TGG - chr3_3:21144269-21144288 Msa0446000:intron 40.0%
GCCTCTGATGTATCAATTAC+TGG - chr3_3:21144336-21144355 Msa0446000:intron 40.0%
CACACTAGTGAATCAACCTT+CGG + chr3_3:21143644-21143663 None:intergenic 40.0%
! GAAGGTTGATTCACTAGTGT+GGG - chr3_3:21143643-21143662 Msa0446000:three_prime_UTR 40.0%
! TAAGAAGAGACGGACTTTAG+GGG - chr3_3:21143685-21143704 Msa0446000:three_prime_UTR 40.0%
GGATCTACTTCATTTGCAGA+TGG - chr3_3:21143728-21143747 Msa0446000:three_prime_UTR 40.0%
ACTTCATTTGCAGATGGCAT+TGG - chr3_3:21143734-21143753 Msa0446000:three_prime_UTR 40.0%
AGAAGAAGCTATCCAGAAAG+CGG - chr3_3:21143781-21143800 Msa0446000:three_prime_UTR 40.0%
TTGCTTTATCTACCGCTTTC+TGG + chr3_3:21143796-21143815 None:intergenic 40.0%
ACATTGGCACCAATTGTGTT+TGG + chr3_3:21143832-21143851 None:intergenic 40.0%
!! AACACAATTGGTGCCAATGT+TGG - chr3_3:21143832-21143851 Msa0446000:three_prime_UTR 40.0%
! GGAGTATCTGATGGTATTTG+AGG - chr3_3:21143905-21143924 Msa0446000:CDS 40.0%
! GGACATTTTATTGCAGTGCT+TGG - chr3_3:21144269-21144288 Msa0446000:intron 40.0%
GCCTCTGATGTATCAATTAC+TGG - chr3_3:21144336-21144355 Msa0446000:intron 40.0%
GGATTCTTCAACTCATCCGA+AGG - chr3_3:21143625-21143644 Msa0446000:three_prime_UTR 45.0%
! CGAAGGTTGATTCACTAGTG+TGG - chr3_3:21143642-21143661 Msa0446000:three_prime_UTR 45.0%
TGATTCACTAGTGTGGGAAG+AGG - chr3_3:21143649-21143668 Msa0446000:three_prime_UTR 45.0%
CAGGTCCCAATAAGAAGAGA+CGG - chr3_3:21143675-21143694 Msa0446000:three_prime_UTR 45.0%
! AAGAAGAGACGGACTTTAGG+GGG - chr3_3:21143686-21143705 Msa0446000:three_prime_UTR 45.0%
ATAGCTTCTTCTGTCGTAGC+TGG + chr3_3:21143773-21143792 None:intergenic 45.0%
!! GATAGGATTGGCTCCAACAT+TGG + chr3_3:21143848-21143867 None:intergenic 45.0%
ATGCAGCAAGCACAAATGCA+AGG - chr3_3:21143881-21143900 Msa0446000:CDS 45.0%
! ATGCAAGGTGGAGTATCTGA+TGG - chr3_3:21143896-21143915 Msa0446000:CDS 45.0%
ATCCACGGTTCACAACTCTA+GGG + chr3_3:21143972-21143991 None:intergenic 45.0%
TATCCACGGTTCACAACTCT+AGG + chr3_3:21143973-21143992 None:intergenic 45.0%
CTTGAGAATGGTCAAACACG+TGG - chr3_3:21144303-21144322 Msa0446000:intron 45.0%
GGATTCTTCAACTCATCCGA+AGG - chr3_3:21143625-21143644 Msa0446000:three_prime_UTR 45.0%
! CGAAGGTTGATTCACTAGTG+TGG - chr3_3:21143642-21143661 Msa0446000:three_prime_UTR 45.0%
TGATTCACTAGTGTGGGAAG+AGG - chr3_3:21143649-21143668 Msa0446000:three_prime_UTR 45.0%
CAGGTCCCAATAAGAAGAGA+CGG - chr3_3:21143675-21143694 Msa0446000:three_prime_UTR 45.0%
! AAGAAGAGACGGACTTTAGG+GGG - chr3_3:21143686-21143705 Msa0446000:three_prime_UTR 45.0%
ATAGCTTCTTCTGTCGTAGC+TGG + chr3_3:21143773-21143792 None:intergenic 45.0%
!! GATAGGATTGGCTCCAACAT+TGG + chr3_3:21143848-21143867 None:intergenic 45.0%
ATGCAGCAAGCACAAATGCA+AGG - chr3_3:21143881-21143900 Msa0446000:CDS 45.0%
! ATGCAAGGTGGAGTATCTGA+TGG - chr3_3:21143896-21143915 Msa0446000:CDS 45.0%
ATCCACGGTTCACAACTCTA+GGG + chr3_3:21143972-21143991 None:intergenic 45.0%
TATCCACGGTTCACAACTCT+AGG + chr3_3:21143973-21143992 None:intergenic 45.0%
CTTGAGAATGGTCAAACACG+TGG - chr3_3:21144303-21144322 Msa0446000:intron 45.0%
ATCCTCTGATGTCCAAGCTG+CGG + chr3_3:21143712-21143731 None:intergenic 50.0%
!! GCAGATGGCATTGGTCCTTT+CGG - chr3_3:21143743-21143762 Msa0446000:three_prime_UTR 50.0%
GTCGTAGCTGGAATTCCGAA+AGG + chr3_3:21143761-21143780 None:intergenic 50.0%
CAGCAAGCACAAATGCAAGG+TGG - chr3_3:21143884-21143903 Msa0446000:CDS 50.0%
GAGAATGGTCAAACACGTGG+TGG - chr3_3:21144306-21144325 Msa0446000:intron 50.0%
ATCCTCTGATGTCCAAGCTG+CGG + chr3_3:21143712-21143731 None:intergenic 50.0%
!! GCAGATGGCATTGGTCCTTT+CGG - chr3_3:21143743-21143762 Msa0446000:three_prime_UTR 50.0%
GTCGTAGCTGGAATTCCGAA+AGG + chr3_3:21143761-21143780 None:intergenic 50.0%
CAGCAAGCACAAATGCAAGG+TGG - chr3_3:21143884-21143903 Msa0446000:CDS 50.0%
GAGAATGGTCAAACACGTGG+TGG - chr3_3:21144306-21144325 Msa0446000:intron 50.0%
GTCCCTAGAGTTGTGAACCG+TGG - chr3_3:21143967-21143986 Msa0446000:intron 55.0%
GTCCCTAGAGTTGTGAACCG+TGG - chr3_3:21143967-21143986 Msa0446000:intron 55.0%
!! CTAGTGTGGGAAGAGGCGTC+AGG - chr3_3:21143656-21143675 Msa0446000:three_prime_UTR 60.0%
!! CTAGTGTGGGAAGAGGCGTC+AGG - chr3_3:21143656-21143675 Msa0446000:three_prime_UTR 60.0%
! GACTTTAGGGGGCCGCAGCT+TGG - chr3_3:21143697-21143716 Msa0446000:three_prime_UTR 65.0%
GGCCGCAGCTTGGACATCAG+AGG - chr3_3:21143707-21143726 Msa0446000:three_prime_UTR 65.0%
! GACTTTAGGGGGCCGCAGCT+TGG - chr3_3:21143697-21143716 Msa0446000:three_prime_UTR 65.0%
GGCCGCAGCTTGGACATCAG+AGG - chr3_3:21143707-21143726 Msa0446000:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 21143605 21144662 21143605 ID=Msa0446000;Name=Msa0446000
chr3_3 mRNA 21143605 21144662 21143605 ID=Msa0446000-mRNA-1;Parent=Msa0446000;Name=Msa0446000-mRNA-1;_AED=0.20;_eAED=0.25;_QI=0|0|0.33|1|0|0.33|3|258|131
chr3_3 exon 21143605 21143982 21143605 ID=Msa0446000-mRNA-1:exon:4439;Parent=Msa0446000-mRNA-1
chr3_3 exon 21144350 21144380 21144350 ID=Msa0446000-mRNA-1:exon:4438;Parent=Msa0446000-mRNA-1
chr3_3 exon 21144418 21144662 21144418 ID=Msa0446000-mRNA-1:exon:4437;Parent=Msa0446000-mRNA-1
chr3_3 CDS 21144418 21144662 21144418 ID=Msa0446000-mRNA-1:cds;Parent=Msa0446000-mRNA-1
chr3_3 CDS 21144350 21144380 21144350 ID=Msa0446000-mRNA-1:cds;Parent=Msa0446000-mRNA-1
chr3_3 CDS 21143863 21143982 21143863 ID=Msa0446000-mRNA-1:cds;Parent=Msa0446000-mRNA-1
chr3_3 three_prime_UTR 21143605 21143862 21143605 ID=Msa0446000-mRNA-1:three_prime_utr;Parent=Msa0446000-mRNA-1
Gene Sequence

>Msa0446000

ATGTTGGAAAAATATGGAGAGGATTCTTCAACTCATCCGAAGGTTGATTCACTAGTGTGGGAAGAGGCGTCAGGTCCCAATAAGAAGAGACGGACTTTAGGGGGCCGCAGCTTGGACATCAGAGGATCTACTTCATTTGCAGATGGCATTGGTCCTTTCGGAATTCCAGCTACGACAGAAGAAGCTATCCAGAAAGCGGTAGATAAAGCAATGACTTCTTTTGTCCAAACACAATTGGTGCCAATCAAGCACAAATGCAAGGTGGAGTATCTGATGTGCTTGGAATTGTTGATTCTTGAGAATGGTCAAACACGTGGTGGTAGACGTGCCTCTGATGTATCAATTACTGGACTAGCAGCAACTAGCAAAGATTTTGTGGTGAAGATATGGGAATGA
Protein sequence

>Msa0446000

MLEKYGEDSSTHPKVDSLVWEEASGPNKKRRTLGGRSLDIRGSTSFADGIGPFGIPATTEEAIQKAVDKAMTSFVQTQLVPIKHKCKVEYLMCLELLILENGQTRGGRRASDVSITGLAATSKDFVVKIWE*