AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0397480

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0397480 MtrunA17_Chr3g0085011 75.510 98 17 1 1 91 1 98 3.78e-47 145
Msa0397480 MtrunA17_Chr3g0084961 75.824 91 12 2 1 91 1 81 1.39e-41 130
Msa0397480 MtrunA17_Chr3g0084991 88.060 67 8 0 25 91 28 94 2.78e-39 125
Msa0397480 MtrunA17_Chr3g0084931 65.217 69 24 0 23 91 13 81 4.98e-24 86.7
Msa0397480 MtrunA17_Chr5g0442291 47.619 63 33 0 29 91 8 70 3.34e-14 61.6
Msa0397480 MtrunA17_Chr1g0184411 44.444 63 35 0 29 91 8 70 7.20e-12 55.5
Msa0397480 MtrunA17_Chr5g0419531 41.270 63 37 0 29 91 7 69 2.21e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATTGTTCAAATGAGATT+TGG 0.239176 3_2:+16895284 Msa0397480:three_prime_UTR
TTAGAATAAACAAGGGGATT+TGG 0.263245 3_2:+16895356 Msa0397480:three_prime_UTR
TAGAATAAACAAGGGGATTT+GGG 0.271314 3_2:+16895357 Msa0397480:three_prime_UTR
TCAGACCAACTTCTTCTTGT+AGG 0.296174 3_2:-16895075 None:intergenic
CAACATACAATCGAACTCTT+TGG 0.322647 3_2:-16895209 None:intergenic
TCACTTGGCAAGGGTTCATT+TGG 0.330216 3_2:-16894608 None:intergenic
ATATTGTTCAAATGAGATTT+GGG 0.371910 3_2:+16895285 Msa0397480:three_prime_UTR
TTGATGAATCAACCAATTGT+TGG 0.386467 3_2:-16895258 None:intergenic
AGAAGCAGAGAGGAAAATAA+AGG 0.396970 3_2:+16895119 Msa0397480:CDS
GTATGTTGATGAATCTAATA+AGG 0.406117 3_2:+16895224 Msa0397480:CDS
AACATACAATCGAACTCTTT+GGG 0.421595 3_2:-16895208 None:intergenic
GTCACCAGGGCTCCAACAAT+TGG 0.468531 3_2:+16895246 Msa0397480:CDS
GGTTCATTTGGCTGCTCCTG+AGG 0.488032 3_2:-16894596 None:intergenic
AAAATAAAGGAAGAGATGCC+TGG 0.497171 3_2:+16895132 Msa0397480:CDS
GAAATTCGAGTGGTGCCTCC+TGG 0.516148 3_2:+16895159 Msa0397480:CDS
TCATTTGGCTGCTCCTGAGG+AGG 0.525124 3_2:-16894593 None:intergenic
ACCACTCGAATTTCAACTCC+AGG 0.541025 3_2:-16895150 None:intergenic
ACAAGGAACAAATCCTCCTC+AGG 0.544834 3_2:+16894580 Msa0397480:CDS
TCAACCAATTGTTGGAGCCC+TGG 0.547441 3_2:-16895250 None:intergenic
ACATTAGAACTCACTTGGCA+AGG 0.548421 3_2:-16894618 None:intergenic
ATAATCCTACAAGAAGAAGT+TGG 0.549258 3_2:+16895070 Msa0397480:CDS
TAGTTTGGTATTCATGGCAG+AGG 0.551246 3_2:+16894547 None:intergenic
ATGAATCTAATAAGGTCACC+AGG 0.557287 3_2:+16895232 Msa0397480:CDS
CATTAGAACTCACTTGGCAA+GGG 0.564463 3_2:-16894617 None:intergenic
AGAAGTTGGTCTGAGCTAGT+TGG 0.565121 3_2:+16895084 Msa0397480:CDS
TCAGCAGTAACAAAATAGCC+AGG 0.584623 3_2:-16895177 None:intergenic
TGTAATTTGAAGAATAAACA+AGG 0.595208 3_2:+16895393 Msa0397480:three_prime_UTR
AGATTTGGGTATAATGCTAG+AGG 0.635650 3_2:+16895299 Msa0397480:three_prime_UTR
GTAATTTGAAGAATAAACAA+GGG 0.646457 3_2:+16895394 Msa0397480:three_prime_UTR
TGAATCTAATAAGGTCACCA+GGG 0.698547 3_2:+16895233 Msa0397480:CDS
GCCTGGAGTTGAAATTCGAG+TGG 0.708630 3_2:+16895149 Msa0397480:CDS
TCACTGCAGAAGAAGCAGAG+AGG 0.716587 3_2:+16895109 Msa0397480:CDS
GCAGTAACAAAATAGCCAGG+AGG 0.750368 3_2:-16895174 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGATATTGAATATATATTT+TGG + chr3_2:16894988-16895007 Msa0397480:intron 10.0%
!!! TTTTTAATTAGAATAAACAA+GGG + chr3_2:16895349-16895368 Msa0397480:three_prime_UTR 10.0%
!!! ATGATATTGAATATATATTT+TGG + chr3_2:16894988-16895007 Msa0397480:intron 10.0%
!!! TTTTTAATTAGAATAAACAA+GGG + chr3_2:16895349-16895368 Msa0397480:three_prime_UTR 10.0%
!! CTAAATCTTATTGAATAATT+TGG - chr3_2:16894672-16894691 None:intergenic 15.0%
!! AAAGAAATATTATGTTACTA+TGG - chr3_2:16894926-16894945 None:intergenic 15.0%
!!! GTTTTTAATTAGAATAAACA+AGG + chr3_2:16895348-16895367 Msa0397480:three_prime_UTR 15.0%
!!! TTTTAATTAGAATAAACAAG+GGG + chr3_2:16895350-16895369 Msa0397480:three_prime_UTR 15.0%
!! CTAAATCTTATTGAATAATT+TGG - chr3_2:16894672-16894691 None:intergenic 15.0%
!! AAAGAAATATTATGTTACTA+TGG - chr3_2:16894926-16894945 None:intergenic 15.0%
!!! GTTTTTAATTAGAATAAACA+AGG + chr3_2:16895348-16895367 Msa0397480:three_prime_UTR 15.0%
!!! TTTTAATTAGAATAAACAAG+GGG + chr3_2:16895350-16895369 Msa0397480:three_prime_UTR 15.0%
!! AATATTGTTCAAATGAGATT+TGG + chr3_2:16895284-16895303 Msa0397480:three_prime_UTR 20.0%
!! ATATTGTTCAAATGAGATTT+GGG + chr3_2:16895285-16895304 Msa0397480:three_prime_UTR 20.0%
!! TGTAATTTGAAGAATAAACA+AGG + chr3_2:16895393-16895412 Msa0397480:three_prime_UTR 20.0%
!! GTAATTTGAAGAATAAACAA+GGG + chr3_2:16895394-16895413 Msa0397480:three_prime_UTR 20.0%
!! AATATTGTTCAAATGAGATT+TGG + chr3_2:16895284-16895303 Msa0397480:three_prime_UTR 20.0%
!! ATATTGTTCAAATGAGATTT+GGG + chr3_2:16895285-16895304 Msa0397480:three_prime_UTR 20.0%
!! TGTAATTTGAAGAATAAACA+AGG + chr3_2:16895393-16895412 Msa0397480:three_prime_UTR 20.0%
!! GTAATTTGAAGAATAAACAA+GGG + chr3_2:16895394-16895413 Msa0397480:three_prime_UTR 20.0%
! TAAAAATTCACGTGAATAAG+TGG + chr3_2:16894752-16894771 Msa0397480:intron 25.0%
! AAAAATTCACGTGAATAAGT+GGG + chr3_2:16894753-16894772 Msa0397480:intron 25.0%
!!! TCTAACTTTTATTTGACACA+CGG + chr3_2:16894896-16894915 Msa0397480:intron 25.0%
!! GTATGTTGATGAATCTAATA+AGG + chr3_2:16895224-16895243 Msa0397480:CDS 25.0%
! TAAAAATTCACGTGAATAAG+TGG + chr3_2:16894752-16894771 Msa0397480:intron 25.0%
! AAAAATTCACGTGAATAAGT+GGG + chr3_2:16894753-16894772 Msa0397480:intron 25.0%
!!! TCTAACTTTTATTTGACACA+CGG + chr3_2:16894896-16894915 Msa0397480:intron 25.0%
!! GTATGTTGATGAATCTAATA+AGG + chr3_2:16895224-16895243 Msa0397480:CDS 25.0%
ATAATCCTACAAGAAGAAGT+TGG + chr3_2:16895070-16895089 Msa0397480:CDS 30.0%
AACATACAATCGAACTCTTT+GGG - chr3_2:16895211-16895230 None:intergenic 30.0%
TTGATGAATCAACCAATTGT+TGG - chr3_2:16895261-16895280 None:intergenic 30.0%
TTAGAATAAACAAGGGGATT+TGG + chr3_2:16895356-16895375 Msa0397480:three_prime_UTR 30.0%
TAGAATAAACAAGGGGATTT+GGG + chr3_2:16895357-16895376 Msa0397480:three_prime_UTR 30.0%
ATAATCCTACAAGAAGAAGT+TGG + chr3_2:16895070-16895089 Msa0397480:CDS 30.0%
AACATACAATCGAACTCTTT+GGG - chr3_2:16895211-16895230 None:intergenic 30.0%
TTGATGAATCAACCAATTGT+TGG - chr3_2:16895261-16895280 None:intergenic 30.0%
TTAGAATAAACAAGGGGATT+TGG + chr3_2:16895356-16895375 Msa0397480:three_prime_UTR 30.0%
TAGAATAAACAAGGGGATTT+GGG + chr3_2:16895357-16895376 Msa0397480:three_prime_UTR 30.0%
GAGAAACATTAGAACTCACT+TGG - chr3_2:16894626-16894645 None:intergenic 35.0%
!! CAAACACAAGACTGTCATTT+TGG - chr3_2:16894705-16894724 None:intergenic 35.0%
ACAACTCATTGCATGATCTA+GGG - chr3_2:16894794-16894813 None:intergenic 35.0%
TACAACTCATTGCATGATCT+AGG - chr3_2:16894795-16894814 None:intergenic 35.0%
GTCACTGTGTTATGATAAGT+TGG - chr3_2:16894950-16894969 None:intergenic 35.0%
AGAAGCAGAGAGGAAAATAA+AGG + chr3_2:16895119-16895138 Msa0397480:CDS 35.0%
AAAATAAAGGAAGAGATGCC+TGG + chr3_2:16895132-16895151 Msa0397480:CDS 35.0%
CAACATACAATCGAACTCTT+TGG - chr3_2:16895212-16895231 None:intergenic 35.0%
ATGAATCTAATAAGGTCACC+AGG + chr3_2:16895232-16895251 Msa0397480:CDS 35.0%
TGAATCTAATAAGGTCACCA+GGG + chr3_2:16895233-16895252 Msa0397480:CDS 35.0%
AGATTTGGGTATAATGCTAG+AGG + chr3_2:16895299-16895318 Msa0397480:three_prime_UTR 35.0%
!!! GGGTTTTGTTGTGACATTTT+CGG + chr3_2:16895414-16895433 Msa0397480:three_prime_UTR 35.0%
!!! GGTTTTGTTGTGACATTTTC+GGG + chr3_2:16895415-16895434 Msa0397480:three_prime_UTR 35.0%
GAGAAACATTAGAACTCACT+TGG - chr3_2:16894626-16894645 None:intergenic 35.0%
!! CAAACACAAGACTGTCATTT+TGG - chr3_2:16894705-16894724 None:intergenic 35.0%
ACAACTCATTGCATGATCTA+GGG - chr3_2:16894794-16894813 None:intergenic 35.0%
TACAACTCATTGCATGATCT+AGG - chr3_2:16894795-16894814 None:intergenic 35.0%
GTCACTGTGTTATGATAAGT+TGG - chr3_2:16894950-16894969 None:intergenic 35.0%
AGAAGCAGAGAGGAAAATAA+AGG + chr3_2:16895119-16895138 Msa0397480:CDS 35.0%
AAAATAAAGGAAGAGATGCC+TGG + chr3_2:16895132-16895151 Msa0397480:CDS 35.0%
CAACATACAATCGAACTCTT+TGG - chr3_2:16895212-16895231 None:intergenic 35.0%
ATGAATCTAATAAGGTCACC+AGG + chr3_2:16895232-16895251 Msa0397480:CDS 35.0%
TGAATCTAATAAGGTCACCA+GGG + chr3_2:16895233-16895252 Msa0397480:CDS 35.0%
AGATTTGGGTATAATGCTAG+AGG + chr3_2:16895299-16895318 Msa0397480:three_prime_UTR 35.0%
!!! GGGTTTTGTTGTGACATTTT+CGG + chr3_2:16895414-16895433 Msa0397480:three_prime_UTR 35.0%
!!! GGTTTTGTTGTGACATTTTC+GGG + chr3_2:16895415-16895434 Msa0397480:three_prime_UTR 35.0%
CATTAGAACTCACTTGGCAA+GGG - chr3_2:16894620-16894639 None:intergenic 40.0%
ACATTAGAACTCACTTGGCA+AGG - chr3_2:16894621-16894640 None:intergenic 40.0%
TCAGACCAACTTCTTCTTGT+AGG - chr3_2:16895078-16895097 None:intergenic 40.0%
TCAGCAGTAACAAAATAGCC+AGG - chr3_2:16895180-16895199 None:intergenic 40.0%
CATTAGAACTCACTTGGCAA+GGG - chr3_2:16894620-16894639 None:intergenic 40.0%
ACATTAGAACTCACTTGGCA+AGG - chr3_2:16894621-16894640 None:intergenic 40.0%
TCAGACCAACTTCTTCTTGT+AGG - chr3_2:16895078-16895097 None:intergenic 40.0%
TCAGCAGTAACAAAATAGCC+AGG - chr3_2:16895180-16895199 None:intergenic 40.0%
GCAGAGGAAAAACAAGGACA+AGG + chr3_2:16894563-16894582 Msa0397480:CDS 45.0%
ACAAGGAACAAATCCTCCTC+AGG + chr3_2:16894580-16894599 Msa0397480:CDS 45.0%
TCACTTGGCAAGGGTTCATT+TGG - chr3_2:16894611-16894630 None:intergenic 45.0%
! AGAAGTTGGTCTGAGCTAGT+TGG + chr3_2:16895084-16895103 Msa0397480:CDS 45.0%
ACCACTCGAATTTCAACTCC+AGG - chr3_2:16895153-16895172 None:intergenic 45.0%
GCAGTAACAAAATAGCCAGG+AGG - chr3_2:16895177-16895196 None:intergenic 45.0%
GCAGAGGAAAAACAAGGACA+AGG + chr3_2:16894563-16894582 Msa0397480:CDS 45.0%
ACAAGGAACAAATCCTCCTC+AGG + chr3_2:16894580-16894599 Msa0397480:CDS 45.0%
TCACTTGGCAAGGGTTCATT+TGG - chr3_2:16894611-16894630 None:intergenic 45.0%
! AGAAGTTGGTCTGAGCTAGT+TGG + chr3_2:16895084-16895103 Msa0397480:CDS 45.0%
ACCACTCGAATTTCAACTCC+AGG - chr3_2:16895153-16895172 None:intergenic 45.0%
GCAGTAACAAAATAGCCAGG+AGG - chr3_2:16895177-16895196 None:intergenic 45.0%
!! AAAATTAAATAATTTATTTC+AGG + chr3_2:16895042-16895061 Msa0397480:intron 5.0%
!! AAATTAAATAATTTATTTCA+GGG + chr3_2:16895043-16895062 Msa0397480:intron 5.0%
!! AAAATTAAATAATTTATTTC+AGG + chr3_2:16895042-16895061 Msa0397480:intron 5.0%
!! AAATTAAATAATTTATTTCA+GGG + chr3_2:16895043-16895062 Msa0397480:intron 5.0%
TCACTGCAGAAGAAGCAGAG+AGG + chr3_2:16895109-16895128 Msa0397480:CDS 50.0%
GCCTGGAGTTGAAATTCGAG+TGG + chr3_2:16895149-16895168 Msa0397480:CDS 50.0%
TCAACCAATTGTTGGAGCCC+TGG - chr3_2:16895253-16895272 None:intergenic 50.0%
TCACTGCAGAAGAAGCAGAG+AGG + chr3_2:16895109-16895128 Msa0397480:CDS 50.0%
GCCTGGAGTTGAAATTCGAG+TGG + chr3_2:16895149-16895168 Msa0397480:CDS 50.0%
TCAACCAATTGTTGGAGCCC+TGG - chr3_2:16895253-16895272 None:intergenic 50.0%
TCATTTGGCTGCTCCTGAGG+AGG - chr3_2:16894596-16894615 None:intergenic 55.0%
GGTTCATTTGGCTGCTCCTG+AGG - chr3_2:16894599-16894618 None:intergenic 55.0%
GAAATTCGAGTGGTGCCTCC+TGG + chr3_2:16895159-16895178 Msa0397480:CDS 55.0%
GTCACCAGGGCTCCAACAAT+TGG + chr3_2:16895246-16895265 Msa0397480:CDS 55.0%
TCATTTGGCTGCTCCTGAGG+AGG - chr3_2:16894596-16894615 None:intergenic 55.0%
GGTTCATTTGGCTGCTCCTG+AGG - chr3_2:16894599-16894618 None:intergenic 55.0%
GAAATTCGAGTGGTGCCTCC+TGG + chr3_2:16895159-16895178 Msa0397480:CDS 55.0%
GTCACCAGGGCTCCAACAAT+TGG + chr3_2:16895246-16895265 Msa0397480:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 16894560 16895442 16894560 ID=Msa0397480;Name=Msa0397480
chr3_2 mRNA 16894560 16895442 16894560 ID=Msa0397480-mRNA-1;Parent=Msa0397480;Name=Msa0397480-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|1|0.5|1|1|1|2|170|91
chr3_2 exon 16894560 16894626 16894560 ID=Msa0397480-mRNA-1:exon:3839;Parent=Msa0397480-mRNA-1
chr3_2 exon 16895064 16895442 16895064 ID=Msa0397480-mRNA-1:exon:3840;Parent=Msa0397480-mRNA-1
chr3_2 CDS 16894560 16894626 16894560 ID=Msa0397480-mRNA-1:cds;Parent=Msa0397480-mRNA-1
chr3_2 CDS 16895064 16895272 16895064 ID=Msa0397480-mRNA-1:cds;Parent=Msa0397480-mRNA-1
chr3_2 three_prime_UTR 16895273 16895442 16895273 ID=Msa0397480-mRNA-1:three_prime_utr;Parent=Msa0397480-mRNA-1
Gene Sequence

>Msa0397480

ATGGCAGAGGAAAAACAAGGACAAGGAACAAATCCTCCTCAGGAGCAGCCAAATGAACCCTTGCCAAGGACAAATAATCCTACAAGAAGAAGTTGGTCTGAGCTAGTTGGTGTCACTGCAGAAGAAGCAGAGAGGAAAATAAAGGAAGAGATGCCTGGAGTTGAAATTCGAGTGGTGCCTCCTGGCTATTTTGTTACTGCTGATTATAAGACCCAAAGAGTTCGATTGTATGTTGATGAATCTAATAAGGTCACCAGGGCTCCAACAATTGGTTGA
Protein sequence

>Msa0397480

MAEEKQGQGTNPPQEQPNEPLPRTNNPTRRSWSELVGVTAEEAERKIKEEMPGVEIRVVPPGYFVTADYKTQRVRLYVDESNKVTRAPTIG*