AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0517720

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 42 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGTCTCTAACAGAGTAAT+TGG 0.209705 3_4:+69434308 Msa0517720:three_prime_UTR
AAGACTTTCCCCAGGGTTAT+TGG 0.227823 3_4:+69434145 Msa0517720:three_prime_UTR
CTGAATAAGAAACAAGTAAT+TGG 0.255290 3_4:-69434176 None:intergenic
TTGTGAAGATTACAATTTAC+TGG 0.272799 3_4:+69434341 Msa0517720:three_prime_UTR
AATGATGCAGTGCTCTGGTC+TGG 0.288648 3_4:+69433810 Msa0517720:five_prime_UTR
GTTCGTTCTAGTTGGATATT+CGG 0.303262 3_4:+69434386 Msa0517720:three_prime_UTR
TTCGTTCTAGTTGGATATTC+GGG 0.320406 3_4:+69434387 Msa0517720:three_prime_UTR
GTGAAATATACAAAATTTGA+TGG 0.349683 3_4:+69434210 Msa0517720:three_prime_UTR
GACCAGAGCACTGCATCATT+TGG 0.369423 3_4:-69433807 None:intergenic
ATGATGCAGTGCTCTGGTCT+GGG 0.389872 3_4:+69433811 Msa0517720:five_prime_UTR
AATGAAATTACGCATCAGTT+TGG 0.395899 3_4:+69434432 Msa0517720:three_prime_UTR
TACTTGTTTCTTATTCAGAT+AGG 0.399264 3_4:+69434181 Msa0517720:three_prime_UTR
ATGTCTCTAACAGAGTAATT+GGG 0.408223 3_4:+69434309 Msa0517720:three_prime_UTR
TTCTTATTCAGATAGGGATT+AGG 0.432512 3_4:+69434188 Msa0517720:three_prime_UTR
TTCCAAATGATGCAGTGCTC+TGG 0.443660 3_4:+69433805 Msa0517720:five_prime_UTR
CTGTGATTGTTCGTTCTAGT+TGG 0.444785 3_4:+69434378 Msa0517720:three_prime_UTR
CAGCACCACTCAACAACAAA+TGG 0.479475 3_4:-69434242 None:intergenic
TTAGTGGTTAATTGTTATGT+TGG 0.492565 3_4:-69433699 None:intergenic
ACTTGTTTCTTATTCAGATA+GGG 0.493076 3_4:+69434182 Msa0517720:three_prime_UTR
CTCTTAGTAAGACTTTCCCC+AGG 0.506029 3_4:+69434137 Msa0517720:three_prime_UTR
CATTTGGAAAATGTAAGCAT+TGG 0.510036 3_4:-69433791 None:intergenic
TTGGAAATGATGCGTCTTGT+GGG 0.515428 3_4:+69434279 Msa0517720:three_prime_UTR
CATCCTCTAGTATCTCATGC+AGG 0.523981 3_4:-69434095 None:intergenic
AAAATGTAAGCATTGGATGA+AGG 0.548595 3_4:-69433784 None:intergenic
GAGCGTGATCCAATAACCCT+GGG 0.562797 3_4:-69434154 None:intergenic
TTTGGAAATGATGCGTCTTG+TGG 0.570637 3_4:+69434278 Msa0517720:three_prime_UTR
TGAAATATACAAAATTTGAT+GGG 0.571498 3_4:+69434211 Msa0517720:three_prime_UTR
TGATGCAGTGCTCTGGTCTG+GGG 0.575620 3_4:+69433812 Msa0517720:five_prime_UTR
ATATTCGGGTATGCATATGC+TGG 0.577435 3_4:+69434401 Msa0517720:three_prime_UTR
GGAGCGTGATCCAATAACCC+TGG 0.583757 3_4:-69434155 None:intergenic
TTAAACCATTTGTTGTTGAG+TGG 0.588013 3_4:+69434237 Msa0517720:three_prime_UTR
ATCCTCTAGTATCTCATGCA+GGG 0.588051 3_4:-69434094 None:intergenic
TTTGTCAAGTGCAGTAGGAG+AGG 0.599753 3_4:-69433750 None:intergenic
AGTATCTCATGCAGGGAATG+TGG 0.603443 3_4:-69434087 None:intergenic
TGTCTCTAACAGAGTAATTG+GGG 0.610546 3_4:+69434310 Msa0517720:three_prime_UTR
TCTTAGTAAGACTTTCCCCA+GGG 0.611564 3_4:+69434138 Msa0517720:three_prime_UTR
AAACACAAGCCTCAGAGAGT+CGG 0.626180 3_4:+69433845 Msa0517720:five_prime_UTR
TCTCATGCAGGGAATGTGGT+CGG 0.637938 3_4:-69434083 None:intergenic
CAAGCCTCAGAGAGTCGGCA+AGG 0.642822 3_4:+69433850 Msa0517720:five_prime_UTR
TATACCTTGCCGACTCTCTG+AGG 0.656943 3_4:-69433854 None:intergenic
TTCCCTGCATGAGATACTAG+AGG 0.664860 3_4:+69434092 Msa0517720:CDS
AGCGTGATCCAATAACCCTG+GGG 0.773624 3_4:-69434153 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATATTTTTATTTTTTTGAA+TGG - chr3_4:69433731-69433750 None:intergenic 10.0%
!!! GATATTTTTATTTTTTTGAA+TGG - chr3_4:69433731-69433750 None:intergenic 10.0%
!! TGAAATATACAAAATTTGAT+GGG + chr3_4:69434211-69434230 Msa0517720:three_prime_UTR 15.0%
!! TGAAATATACAAAATTTGAT+GGG + chr3_4:69434211-69434230 Msa0517720:three_prime_UTR 15.0%
!!! TACGCAATTATCTTTATTTT+CGG + chr3_4:69433888-69433907 Msa0517720:intron 20.0%
!! GTGAAATATACAAAATTTGA+TGG + chr3_4:69434210-69434229 Msa0517720:three_prime_UTR 20.0%
!!! TACGCAATTATCTTTATTTT+CGG + chr3_4:69433888-69433907 Msa0517720:intron 20.0%
!! GTGAAATATACAAAATTTGA+TGG + chr3_4:69434210-69434229 Msa0517720:three_prime_UTR 20.0%
! TTAGTGGTTAATTGTTATGT+TGG - chr3_4:69433702-69433721 None:intergenic 25.0%
! CTGAATAAGAAACAAGTAAT+TGG - chr3_4:69434179-69434198 None:intergenic 25.0%
!! TACTTGTTTCTTATTCAGAT+AGG + chr3_4:69434181-69434200 Msa0517720:three_prime_UTR 25.0%
!! ACTTGTTTCTTATTCAGATA+GGG + chr3_4:69434182-69434201 Msa0517720:three_prime_UTR 25.0%
! TTGTGAAGATTACAATTTAC+TGG + chr3_4:69434341-69434360 Msa0517720:three_prime_UTR 25.0%
! TTAGTGGTTAATTGTTATGT+TGG - chr3_4:69433702-69433721 None:intergenic 25.0%
! CTGAATAAGAAACAAGTAAT+TGG - chr3_4:69434179-69434198 None:intergenic 25.0%
!! TACTTGTTTCTTATTCAGAT+AGG + chr3_4:69434181-69434200 Msa0517720:three_prime_UTR 25.0%
!! ACTTGTTTCTTATTCAGATA+GGG + chr3_4:69434182-69434201 Msa0517720:three_prime_UTR 25.0%
! TTGTGAAGATTACAATTTAC+TGG + chr3_4:69434341-69434360 Msa0517720:three_prime_UTR 25.0%
! TTTTGAATGGCAAATGTTAG+TGG - chr3_4:69433718-69433737 None:intergenic 30.0%
AAAAATTTGTCAAGTGCAGT+AGG - chr3_4:69433758-69433777 None:intergenic 30.0%
!! AAAATGTAAGCATTGGATGA+AGG - chr3_4:69433787-69433806 None:intergenic 30.0%
CATTTGGAAAATGTAAGCAT+TGG - chr3_4:69433794-69433813 None:intergenic 30.0%
CATGTTCCTGAAACATAATA+AGG - chr3_4:69433998-69434017 None:intergenic 30.0%
TTCTTATTCAGATAGGGATT+AGG + chr3_4:69434188-69434207 Msa0517720:three_prime_UTR 30.0%
!! TTAAACCATTTGTTGTTGAG+TGG + chr3_4:69434237-69434256 Msa0517720:three_prime_UTR 30.0%
!!! TGCTGTTTTTCTGTTAGTTT+TGG + chr3_4:69434260-69434279 Msa0517720:three_prime_UTR 30.0%
ATGTCTCTAACAGAGTAATT+GGG + chr3_4:69434309-69434328 Msa0517720:three_prime_UTR 30.0%
AATGAAATTACGCATCAGTT+TGG + chr3_4:69434432-69434451 Msa0517720:three_prime_UTR 30.0%
! TTTTGAATGGCAAATGTTAG+TGG - chr3_4:69433718-69433737 None:intergenic 30.0%
AAAAATTTGTCAAGTGCAGT+AGG - chr3_4:69433758-69433777 None:intergenic 30.0%
!! AAAATGTAAGCATTGGATGA+AGG - chr3_4:69433787-69433806 None:intergenic 30.0%
CATTTGGAAAATGTAAGCAT+TGG - chr3_4:69433794-69433813 None:intergenic 30.0%
CATGTTCCTGAAACATAATA+AGG - chr3_4:69433998-69434017 None:intergenic 30.0%
TTCTTATTCAGATAGGGATT+AGG + chr3_4:69434188-69434207 Msa0517720:three_prime_UTR 30.0%
!! TTAAACCATTTGTTGTTGAG+TGG + chr3_4:69434237-69434256 Msa0517720:three_prime_UTR 30.0%
!!! TGCTGTTTTTCTGTTAGTTT+TGG + chr3_4:69434260-69434279 Msa0517720:three_prime_UTR 30.0%
ATGTCTCTAACAGAGTAATT+GGG + chr3_4:69434309-69434328 Msa0517720:three_prime_UTR 30.0%
AATGAAATTACGCATCAGTT+TGG + chr3_4:69434432-69434451 Msa0517720:three_prime_UTR 30.0%
GTGAAGATGCATGTTATAAG+TGG + chr3_4:69433968-69433987 Msa0517720:intron 35.0%
! GGAATGCCTTATTATGTTTC+AGG + chr3_4:69433989-69434008 Msa0517720:intron 35.0%
CATGTCTCTAACAGAGTAAT+TGG + chr3_4:69434308-69434327 Msa0517720:three_prime_UTR 35.0%
TGTCTCTAACAGAGTAATTG+GGG + chr3_4:69434310-69434329 Msa0517720:three_prime_UTR 35.0%
! GTTCGTTCTAGTTGGATATT+CGG + chr3_4:69434386-69434405 Msa0517720:three_prime_UTR 35.0%
! TTCGTTCTAGTTGGATATTC+GGG + chr3_4:69434387-69434406 Msa0517720:three_prime_UTR 35.0%
GTGAAGATGCATGTTATAAG+TGG + chr3_4:69433968-69433987 Msa0517720:intron 35.0%
! GGAATGCCTTATTATGTTTC+AGG + chr3_4:69433989-69434008 Msa0517720:intron 35.0%
CATGTCTCTAACAGAGTAAT+TGG + chr3_4:69434308-69434327 Msa0517720:three_prime_UTR 35.0%
TGTCTCTAACAGAGTAATTG+GGG + chr3_4:69434310-69434329 Msa0517720:three_prime_UTR 35.0%
! GTTCGTTCTAGTTGGATATT+CGG + chr3_4:69434386-69434405 Msa0517720:three_prime_UTR 35.0%
! TTCGTTCTAGTTGGATATTC+GGG + chr3_4:69434387-69434406 Msa0517720:three_prime_UTR 35.0%
ATCCTCTAGTATCTCATGCA+GGG - chr3_4:69434097-69434116 None:intergenic 40.0%
TCTTAGTAAGACTTTCCCCA+GGG + chr3_4:69434138-69434157 Msa0517720:three_prime_UTR 40.0%
TTTGGAAATGATGCGTCTTG+TGG + chr3_4:69434278-69434297 Msa0517720:three_prime_UTR 40.0%
TTGGAAATGATGCGTCTTGT+GGG + chr3_4:69434279-69434298 Msa0517720:three_prime_UTR 40.0%
CTGTGATTGTTCGTTCTAGT+TGG + chr3_4:69434378-69434397 Msa0517720:three_prime_UTR 40.0%
ATATTCGGGTATGCATATGC+TGG + chr3_4:69434401-69434420 Msa0517720:three_prime_UTR 40.0%
ATCCTCTAGTATCTCATGCA+GGG - chr3_4:69434097-69434116 None:intergenic 40.0%
TCTTAGTAAGACTTTCCCCA+GGG + chr3_4:69434138-69434157 Msa0517720:three_prime_UTR 40.0%
TTTGGAAATGATGCGTCTTG+TGG + chr3_4:69434278-69434297 Msa0517720:three_prime_UTR 40.0%
TTGGAAATGATGCGTCTTGT+GGG + chr3_4:69434279-69434298 Msa0517720:three_prime_UTR 40.0%
CTGTGATTGTTCGTTCTAGT+TGG + chr3_4:69434378-69434397 Msa0517720:three_prime_UTR 40.0%
ATATTCGGGTATGCATATGC+TGG + chr3_4:69434401-69434420 Msa0517720:three_prime_UTR 40.0%
TTTGTCAAGTGCAGTAGGAG+AGG - chr3_4:69433753-69433772 None:intergenic 45.0%
TTCCAAATGATGCAGTGCTC+TGG + chr3_4:69433805-69433824 Msa0517720:five_prime_UTR 45.0%
AAACACAAGCCTCAGAGAGT+CGG + chr3_4:69433845-69433864 Msa0517720:five_prime_UTR 45.0%
AGTATCTCATGCAGGGAATG+TGG - chr3_4:69434090-69434109 None:intergenic 45.0%
TTCCCTGCATGAGATACTAG+AGG + chr3_4:69434092-69434111 Msa0517720:CDS 45.0%
CATCCTCTAGTATCTCATGC+AGG - chr3_4:69434098-69434117 None:intergenic 45.0%
CTCTTAGTAAGACTTTCCCC+AGG + chr3_4:69434137-69434156 Msa0517720:three_prime_UTR 45.0%
AAGACTTTCCCCAGGGTTAT+TGG + chr3_4:69434145-69434164 Msa0517720:three_prime_UTR 45.0%
CAGCACCACTCAACAACAAA+TGG - chr3_4:69434245-69434264 None:intergenic 45.0%
TTTGTCAAGTGCAGTAGGAG+AGG - chr3_4:69433753-69433772 None:intergenic 45.0%
TTCCAAATGATGCAGTGCTC+TGG + chr3_4:69433805-69433824 Msa0517720:five_prime_UTR 45.0%
AAACACAAGCCTCAGAGAGT+CGG + chr3_4:69433845-69433864 Msa0517720:five_prime_UTR 45.0%
AGTATCTCATGCAGGGAATG+TGG - chr3_4:69434090-69434109 None:intergenic 45.0%
TTCCCTGCATGAGATACTAG+AGG + chr3_4:69434092-69434111 Msa0517720:CDS 45.0%
CATCCTCTAGTATCTCATGC+AGG - chr3_4:69434098-69434117 None:intergenic 45.0%
CTCTTAGTAAGACTTTCCCC+AGG + chr3_4:69434137-69434156 Msa0517720:three_prime_UTR 45.0%
AAGACTTTCCCCAGGGTTAT+TGG + chr3_4:69434145-69434164 Msa0517720:three_prime_UTR 45.0%
CAGCACCACTCAACAACAAA+TGG - chr3_4:69434245-69434264 None:intergenic 45.0%
!! GACCAGAGCACTGCATCATT+TGG - chr3_4:69433810-69433829 None:intergenic 50.0%
AATGATGCAGTGCTCTGGTC+TGG + chr3_4:69433810-69433829 Msa0517720:five_prime_UTR 50.0%
ATGATGCAGTGCTCTGGTCT+GGG + chr3_4:69433811-69433830 Msa0517720:five_prime_UTR 50.0%
!! TATACCTTGCCGACTCTCTG+AGG - chr3_4:69433857-69433876 None:intergenic 50.0%
!! CAGGGAATGTGGTCGGTTTT+TGG - chr3_4:69434079-69434098 None:intergenic 50.0%
TCTCATGCAGGGAATGTGGT+CGG - chr3_4:69434086-69434105 None:intergenic 50.0%
AGCGTGATCCAATAACCCTG+GGG - chr3_4:69434156-69434175 None:intergenic 50.0%
GAGCGTGATCCAATAACCCT+GGG - chr3_4:69434157-69434176 None:intergenic 50.0%
!! GACCAGAGCACTGCATCATT+TGG - chr3_4:69433810-69433829 None:intergenic 50.0%
AATGATGCAGTGCTCTGGTC+TGG + chr3_4:69433810-69433829 Msa0517720:five_prime_UTR 50.0%
ATGATGCAGTGCTCTGGTCT+GGG + chr3_4:69433811-69433830 Msa0517720:five_prime_UTR 50.0%
!! TATACCTTGCCGACTCTCTG+AGG - chr3_4:69433857-69433876 None:intergenic 50.0%
!! CAGGGAATGTGGTCGGTTTT+TGG - chr3_4:69434079-69434098 None:intergenic 50.0%
TCTCATGCAGGGAATGTGGT+CGG - chr3_4:69434086-69434105 None:intergenic 50.0%
AGCGTGATCCAATAACCCTG+GGG - chr3_4:69434156-69434175 None:intergenic 50.0%
GAGCGTGATCCAATAACCCT+GGG - chr3_4:69434157-69434176 None:intergenic 50.0%
TGATGCAGTGCTCTGGTCTG+GGG + chr3_4:69433812-69433831 Msa0517720:five_prime_UTR 55.0%
GGAGCGTGATCCAATAACCC+TGG - chr3_4:69434158-69434177 None:intergenic 55.0%
TGATGCAGTGCTCTGGTCTG+GGG + chr3_4:69433812-69433831 Msa0517720:five_prime_UTR 55.0%
GGAGCGTGATCCAATAACCC+TGG - chr3_4:69434158-69434177 None:intergenic 55.0%
CAAGCCTCAGAGAGTCGGCA+AGG + chr3_4:69433850-69433869 Msa0517720:five_prime_UTR 60.0%
CAAGCCTCAGAGAGTCGGCA+AGG + chr3_4:69433850-69433869 Msa0517720:five_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 69433694 69434459 69433694 ID=Msa0517720;Name=Msa0517720
chr3_4 mRNA 69433694 69434459 69433694 ID=Msa0517720-mRNA-1;Parent=Msa0517720;Name=Msa0517720-mRNA-1;_AED=0.00;_eAED=0.00;_QI=182|1|1|1|0|0|2|337|35
chr3_4 exon 69433694 69433871 69433694 ID=Msa0517720-mRNA-1:exon:18478;Parent=Msa0517720-mRNA-1
chr3_4 exon 69434011 69434459 69434011 ID=Msa0517720-mRNA-1:exon:18479;Parent=Msa0517720-mRNA-1
chr3_4 five_prime_UTR 69433694 69433871 69433694 ID=Msa0517720-mRNA-1:five_prime_utr;Parent=Msa0517720-mRNA-1
chr3_4 five_prime_UTR 69434011 69434014 69434011 ID=Msa0517720-mRNA-1:five_prime_utr;Parent=Msa0517720-mRNA-1
chr3_4 CDS 69434015 69434122 69434015 ID=Msa0517720-mRNA-1:cds;Parent=Msa0517720-mRNA-1
chr3_4 three_prime_UTR 69434123 69434459 69434123 ID=Msa0517720-mRNA-1:three_prime_utr;Parent=Msa0517720-mRNA-1
Gene Sequence

>Msa0517720

ATGAACTTGAAGACGAAGACGTTGTTCAGATCATCAAGAAAGTATGAACTCAGTCAAACTTCCAAAAACCGACCACATTCCCTGCATGAGATACTAGAGGATGTCTGA
Protein sequence

>Msa0517720

MNLKTKTLFRSSRKYELSQTSKNRPHSLHEILEDV*