AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0648740

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 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCCTATCGTTGGATA+TGG 0.258835 4_3:-55228598 Msa0648740:CDS
CACAGTGCATGTACAAAATC+AGG 0.330296 4_3:-55229023 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 4_3:+55228447 None:intergenic
AGGAATTTGCCAAAAGTATC+AGG 0.344083 4_3:+55228467 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 4_3:-55228476 Msa0648740:CDS
AAGTTTACGGAATAAGTTTA+CGG 0.358796 4_3:+55228947 None:intergenic
CGATCATTCTACGAGTTTAG+TGG 0.373999 4_3:-55228753 Msa0648740:five_prime_UTR
CTGCCGCACTCATGAATGAT+AGG 0.376746 4_3:+55228641 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 4_3:+55228712 None:intergenic
ACCTTTGAAGTTCCTATCGT+TGG 0.439777 4_3:-55228604 Msa0648740:CDS
CGAACATCACATTTGGTATG+TGG 0.461685 4_3:+55228363 None:intergenic
TCTTCGACATCCTAGAAGTT+AGG 0.464212 4_3:+55228918 None:intergenic
CACATACCAAATGTGATGTT+CGG 0.472080 4_3:-55228362 Msa0648740:CDS
CCAAATGTGATGTTCGGAAA+AGG 0.475440 4_3:-55228356 Msa0648740:CDS
GTCATGTGTTTATCAACGCT+TGG 0.483566 4_3:+55228238 None:intergenic
TTCTATTTAAATAAGATGAA+CGG 0.500399 4_3:-55228973 Msa0648740:five_prime_UTR
ACAGGAATTATATTGTCATA+AGG 0.502590 4_3:+55228407 None:intergenic
ATTATTGCTTTCCAGTACCT+TGG 0.503165 4_3:-55228723 Msa0648740:five_prime_UTR
TGAATATTTCTACGAGCTAC+CGG 0.507354 4_3:-55228874 Msa0648740:five_prime_UTR
AAATATTCAGCAACGAAGAA+TGG 0.515537 4_3:+55228888 None:intergenic
TTGTGCTGCCAATGGTAATG+AGG 0.528690 4_3:-55228321 Msa0648740:CDS
GACCGTTGTTGACAGATGGT+TGG 0.541630 4_3:-55228785 Msa0648740:five_prime_UTR
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 4_3:-55228720 Msa0648740:five_prime_UTR
TCTAGCAAGTGTCATTGCTC+CGG 0.553561 4_3:+55228855 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 4_3:+55228389 None:intergenic
GTCTCCGCCCTCATTACCAT+TGG 0.590161 4_3:+55228313 None:intergenic
TTTCAAGTACAAGTGCGTCA+TGG 0.590751 4_3:-55228282 Msa0648740:CDS
CACGATTACGTCATGTTGTG+CGG 0.590860 4_3:-55228431 Msa0648740:CDS
TGTCGACCGTTGTTGACAGA+TGG 0.592680 4_3:-55228789 Msa0648740:five_prime_UTR
TGTGCTGCCAATGGTAATGA+GGG 0.601107 4_3:-55228320 Msa0648740:CDS
GACACTTGCTAGATTGTGAT+GGG 0.605898 4_3:-55228845 Msa0648740:five_prime_UTR
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 4_3:-55228352 Msa0648740:CDS
TCCAACGATAGGAACTTCAA+AGG 0.611311 4_3:+55228603 None:intergenic
TGACACTTGCTAGATTGTGA+TGG 0.613078 4_3:-55228846 Msa0648740:five_prime_UTR
CACCCTATCATTCATGAGTG+CGG 0.617271 4_3:-55228644 Msa0648740:exon
ATCGATCCATATCCAACGAT+AGG 0.618850 4_3:+55228592 None:intergenic
TGCCGCACTCATGAATGATA+GGG 0.652145 4_3:+55228642 None:intergenic
TGGATCGATGAAATCACCGA+AGG 0.671115 4_3:-55228578 Msa0648740:intron
CGCACTCATGAATGATAGGG+TGG 0.678351 4_3:+55228645 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 4_3:+55228706 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.687205 4_3:+55228783 None:intergenic
GCTGCCAATGGTAATGAGGG+CGG 0.755038 4_3:-55228317 Msa0648740:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTATTTAAATAAGATGAA+CGG - chr4_3:55228296-55228315 Msa0648740:CDS 15.0%
!!! TGTCATTAACATTTTTTTTT+AGG - chr4_3:55228774-55228793 Msa0648740:five_prime_UTR 15.0%
!! TTCTATTTAAATAAGATGAA+CGG - chr4_3:55228296-55228315 Msa0648740:CDS 15.0%
!!! TGTCATTAACATTTTTTTTT+AGG - chr4_3:55228774-55228793 Msa0648740:five_prime_UTR 15.0%
!! AAAAAACAATAAACAACCTT+CGG + chr4_3:55228710-55228729 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+CGG + chr4_3:55228710-55228729 None:intergenic 20.0%
! AAGTTTACGGAATAAGTTTA+CGG + chr4_3:55228325-55228344 None:intergenic 25.0%
! ACAGGAATTATATTGTCATA+AGG + chr4_3:55228865-55228884 None:intergenic 25.0%
! AAGTTTACGGAATAAGTTTA+CGG + chr4_3:55228325-55228344 None:intergenic 25.0%
! ACAGGAATTATATTGTCATA+AGG + chr4_3:55228865-55228884 None:intergenic 25.0%
AGTTAGGCAGAAAAAGTTTA+CGG + chr4_3:55228338-55228357 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG + chr4_3:55228384-55228403 None:intergenic 30.0%
AGTTAGGCAGAAAAAGTTTA+CGG + chr4_3:55228338-55228357 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG + chr4_3:55228384-55228403 None:intergenic 30.0%
!! ACTTTTTCTGCCTAACTTCT+AGG - chr4_3:55228341-55228360 Msa0648740:CDS 35.0%
! TGAATATTTCTACGAGCTAC+CGG - chr4_3:55228395-55228414 Msa0648740:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr4_3:55228546-55228565 Msa0648740:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr4_3:55228566-55228585 None:intergenic 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr4_3:55228793-55228812 Msa0648740:five_prime_UTR 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr4_3:55228805-55228824 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG + chr4_3:55228825-55228844 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr4_3:55228883-55228902 None:intergenic 35.0%
CACATACCAAATGTGATGTT+CGG - chr4_3:55228907-55228926 Msa0648740:five_prime_UTR 35.0%
!! ACTTTTTCTGCCTAACTTCT+AGG - chr4_3:55228341-55228360 Msa0648740:CDS 35.0%
! TGAATATTTCTACGAGCTAC+CGG - chr4_3:55228395-55228414 Msa0648740:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr4_3:55228546-55228565 Msa0648740:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr4_3:55228566-55228585 None:intergenic 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr4_3:55228793-55228812 Msa0648740:five_prime_UTR 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr4_3:55228805-55228824 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG + chr4_3:55228825-55228844 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr4_3:55228883-55228902 None:intergenic 35.0%
CACATACCAAATGTGATGTT+CGG - chr4_3:55228907-55228926 Msa0648740:five_prime_UTR 35.0%
TCTTCGACATCCTAGAAGTT+AGG + chr4_3:55228354-55228373 None:intergenic 40.0%
! TGACACTTGCTAGATTGTGA+TGG - chr4_3:55228423-55228442 Msa0648740:CDS 40.0%
! GACACTTGCTAGATTGTGAT+GGG - chr4_3:55228424-55228443 Msa0648740:CDS 40.0%
CGATCATTCTACGAGTTTAG+TGG - chr4_3:55228516-55228535 Msa0648740:intron 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG - chr4_3:55228665-55228684 Msa0648740:five_prime_UTR 40.0%
TCCAACGATAGGAACTTCAA+AGG + chr4_3:55228669-55228688 None:intergenic 40.0%
GAAGTTCCTATCGTTGGATA+TGG - chr4_3:55228671-55228690 Msa0648740:five_prime_UTR 40.0%
ATCGATCCATATCCAACGAT+AGG + chr4_3:55228680-55228699 None:intergenic 40.0%
CGAACATCACATTTGGTATG+TGG + chr4_3:55228909-55228928 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr4_3:55228916-55228935 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr4_3:55228913-55228932 Msa0648740:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr4_3:55228917-55228936 Msa0648740:five_prime_UTR 40.0%
! TTTCAAGTACAAGTGCGTCA+TGG - chr4_3:55228987-55229006 Msa0648740:five_prime_UTR 40.0%
TCTTCGACATCCTAGAAGTT+AGG + chr4_3:55228354-55228373 None:intergenic 40.0%
! TGACACTTGCTAGATTGTGA+TGG - chr4_3:55228423-55228442 Msa0648740:CDS 40.0%
! GACACTTGCTAGATTGTGAT+GGG - chr4_3:55228424-55228443 Msa0648740:CDS 40.0%
CGATCATTCTACGAGTTTAG+TGG - chr4_3:55228516-55228535 Msa0648740:intron 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG - chr4_3:55228665-55228684 Msa0648740:five_prime_UTR 40.0%
TCCAACGATAGGAACTTCAA+AGG + chr4_3:55228669-55228688 None:intergenic 40.0%
GAAGTTCCTATCGTTGGATA+TGG - chr4_3:55228671-55228690 Msa0648740:five_prime_UTR 40.0%
ATCGATCCATATCCAACGAT+AGG + chr4_3:55228680-55228699 None:intergenic 40.0%
CGAACATCACATTTGGTATG+TGG + chr4_3:55228909-55228928 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr4_3:55228916-55228935 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr4_3:55228913-55228932 Msa0648740:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr4_3:55228917-55228936 Msa0648740:five_prime_UTR 40.0%
! TTTCAAGTACAAGTGCGTCA+TGG - chr4_3:55228987-55229006 Msa0648740:five_prime_UTR 40.0%
! TCTAGCAAGTGTCATTGCTC+CGG + chr4_3:55228417-55228436 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr4_3:55228489-55228508 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr4_3:55228549-55228568 Msa0648740:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr4_3:55228560-55228579 None:intergenic 45.0%
CACCCTATCATTCATGAGTG+CGG - chr4_3:55228625-55228644 Msa0648740:CDS 45.0%
TGCCGCACTCATGAATGATA+GGG + chr4_3:55228630-55228649 None:intergenic 45.0%
TGGATCGATGAAATCACCGA+AGG - chr4_3:55228691-55228710 Msa0648740:five_prime_UTR 45.0%
CACGATTACGTCATGTTGTG+CGG - chr4_3:55228838-55228857 Msa0648740:five_prime_UTR 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr4_3:55228940-55228959 Msa0648740:five_prime_UTR 45.0%
! TTGTGCTGCCAATGGTAATG+AGG - chr4_3:55228948-55228967 Msa0648740:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTAATGA+GGG - chr4_3:55228949-55228968 Msa0648740:five_prime_UTR 45.0%
! TCTAGCAAGTGTCATTGCTC+CGG + chr4_3:55228417-55228436 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr4_3:55228489-55228508 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr4_3:55228549-55228568 Msa0648740:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr4_3:55228560-55228579 None:intergenic 45.0%
CACCCTATCATTCATGAGTG+CGG - chr4_3:55228625-55228644 Msa0648740:CDS 45.0%
TGCCGCACTCATGAATGATA+GGG + chr4_3:55228630-55228649 None:intergenic 45.0%
TGGATCGATGAAATCACCGA+AGG - chr4_3:55228691-55228710 Msa0648740:five_prime_UTR 45.0%
CACGATTACGTCATGTTGTG+CGG - chr4_3:55228838-55228857 Msa0648740:five_prime_UTR 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr4_3:55228940-55228959 Msa0648740:five_prime_UTR 45.0%
! TTGTGCTGCCAATGGTAATG+AGG - chr4_3:55228948-55228967 Msa0648740:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTAATGA+GGG - chr4_3:55228949-55228968 Msa0648740:five_prime_UTR 45.0%
TGTCGACCGTTGTTGACAGA+TGG - chr4_3:55228480-55228499 Msa0648740:intron 50.0%
GACCGTTGTTGACAGATGGT+TGG - chr4_3:55228484-55228503 Msa0648740:intron 50.0%
CGCACTCATGAATGATAGGG+TGG + chr4_3:55228627-55228646 None:intergenic 50.0%
CTGCCGCACTCATGAATGAT+AGG + chr4_3:55228631-55228650 None:intergenic 50.0%
TGTCGACCGTTGTTGACAGA+TGG - chr4_3:55228480-55228499 Msa0648740:intron 50.0%
GACCGTTGTTGACAGATGGT+TGG - chr4_3:55228484-55228503 Msa0648740:intron 50.0%
CGCACTCATGAATGATAGGG+TGG + chr4_3:55228627-55228646 None:intergenic 50.0%
CTGCCGCACTCATGAATGAT+AGG + chr4_3:55228631-55228650 None:intergenic 50.0%
! GCTGCCAATGGTAATGAGGG+CGG - chr4_3:55228952-55228971 Msa0648740:five_prime_UTR 55.0%
GTCTCCGCCCTCATTACCAT+TGG + chr4_3:55228959-55228978 None:intergenic 55.0%
! GCTGCCAATGGTAATGAGGG+CGG - chr4_3:55228952-55228971 Msa0648740:five_prime_UTR 55.0%
GTCTCCGCCCTCATTACCAT+TGG + chr4_3:55228959-55228978 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 55228250 55229041 55228250 ID=Msa0648740;Name=Msa0648740
chr4_3 mRNA 55228250 55229041 55228250 ID=Msa0648740-mRNA-1;Parent=Msa0648740;Name=Msa0648740-mRNA-1;_AED=0.04;_eAED=0.04;_QI=388|1|0.5|1|1|1|2|0|106
chr4_3 exon 55228250 55228495 55228250 ID=Msa0648740-mRNA-1:exon:14084;Parent=Msa0648740-mRNA-1
chr4_3 exon 55228579 55229041 55228579 ID=Msa0648740-mRNA-1:exon:14083;Parent=Msa0648740-mRNA-1
chr4_3 five_prime_UTR 55228654 55229041 55228654 ID=Msa0648740-mRNA-1:five_prime_utr;Parent=Msa0648740-mRNA-1
chr4_3 CDS 55228579 55228653 55228579 ID=Msa0648740-mRNA-1:cds;Parent=Msa0648740-mRNA-1
chr4_3 CDS 55228250 55228495 55228250 ID=Msa0648740-mRNA-1:cds;Parent=Msa0648740-mRNA-1
Gene Sequence

>Msa0648740

ATGAGTGCGGCAGCATCATGTTATTGTACCTTTGAAGTTCCTATCGTTGGATATGGATCGATGAAATCACCGAAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATAATTCCTGTGAGACTCAAATATACAGACGACCACATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTAATGAGGGCGGAGACGTGTTGATTTTCAAGTACAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0648740

MSAAASCYCTFEVPIVGYGSMKSPKELPDTFGKFLRVKHHDYVMLCGPYDNIIPVRLKYTDDHIPNVMFGKGWTSFCAANGNEGGDVLIFKYKCVMDKKYVIVSKR*