AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0256900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0256900 MtrunA17_Chr5g0393501 29.091 165 114 1 3 164 77 241 1.68e-22 90.1
Msa0256900 MtrunA17_Chr4g0044671 30.000 150 97 3 5 150 62 207 4.00e-13 64.7
Msa0256900 MtrunA17_Chr4g0034781 29.932 147 95 3 8 150 59 201 1.79e-12 62.8
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 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATACACTGTTTCACTTCT+AGG 0.134619 2_2:-52350728 Msa0256900:five_prime_UTR
GAAATTCCTATCGCTGGATA+TGG 0.237538 2_2:-52350398 Msa0256900:CDS
CCCATACCAATTGTGATGTT+TGG 0.340839 2_2:-52350144 Msa0256900:CDS
AGGAATTTGCCAAAAGTATC+AGG 0.344083 2_2:+52350249 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 2_2:-52350258 Msa0256900:CDS
CGATTATTCAACGAATTTAG+TGG 0.373935 2_2:-52350554 Msa0256900:CDS
TCCAAACATCACAATTGGTA+TGG 0.411232 2_2:+52350143 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 2_2:+52350513 None:intergenic
CCAAACATCACAATTGGTAT+GGG 0.452680 2_2:+52350144 None:intergenic
CTGTTTCACTTCTAGGATGT+TGG 0.457667 2_2:-52350721 Msa0256900:five_prime_UTR
ACAGGAATGACGTAGTCATA+TGG 0.475988 2_2:+52350189 None:intergenic
GAGCAATGGCGCTTGCTACA+TGG 0.487319 2_2:-52350652 Msa0256900:five_prime_UTR
GGCCGTTGTTGACAGATGGT+TGG 0.487397 2_2:-52350586 Msa0256900:CDS
ACACGATGCTACCGCACTCA+TGG 0.499582 2_2:+52350433 None:intergenic
ATTATTGCTTTCCAGTACCT+TGG 0.503165 2_2:-52350524 Msa0256900:CDS
TGTAGCAAGCGCCATTGCTC+CGG 0.505715 2_2:+52350655 None:intergenic
TCAATATTTCTACGAGCTAC+CGG 0.507354 2_2:-52350674 Msa0256900:five_prime_UTR
CCAATTGTGATGTTTGGAAA+AGG 0.511741 2_2:-52350138 Msa0256900:CDS
AAATATTGAGCAACGAAGAA+TGG 0.513098 2_2:+52350688 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.517120 2_2:-52350103 Msa0256900:CDS
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 2_2:-52350590 Msa0256900:CDS
AAGGGAAAACAACTGCAAGC+TGG 0.535824 2_2:+52350755 None:intergenic
TTGTGATGTTTGGAAAAGGC+TGG 0.536068 2_2:-52350134 Msa0256900:CDS
TGGTAAGGTGGATAATCAGC+TGG 0.541144 2_2:+52350458 None:intergenic
TTTCAAGTGCAAGTGTGTCA+TGG 0.544420 2_2:-52350064 Msa0256900:CDS
ATGCTACCGCACTCATGGAA+TGG 0.547467 2_2:+52350438 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 2_2:-52350521 Msa0256900:CDS
TCTGTATATTTGAGTCTCAC+AGG 0.555272 2_2:+52350171 None:intergenic
CTTGAAAATTAACACGTCTC+CGG 0.575972 2_2:+52350080 None:intergenic
TCTACGAGCTACCGGAGCAA+TGG 0.577510 2_2:-52350666 Msa0256900:five_prime_UTR
GTCTCCGGCCTCAATACCAT+TGG 0.581950 2_2:+52350095 None:intergenic
TGGCGCTTGCTACATGGTGA+TGG 0.584756 2_2:-52350646 Msa0256900:five_prime_UTR
ACCGCACTCATGGAATGGTA+AGG 0.593653 2_2:+52350443 None:intergenic
TGTTAAACAAATCAGTTAGT+CGG 0.616534 2_2:-52350607 Msa0256900:CDS
GTCGATCCATATCCAGCGAT+AGG 0.621657 2_2:+52350392 None:intergenic
GCTGCCAATGGTATTGAGGC+CGG 0.624728 2_2:-52350099 Msa0256900:CDS
CAAACATCACAATTGGTATG+GGG 0.630299 2_2:+52350145 None:intergenic
GCACTCATGGAATGGTAAGG+TGG 0.647237 2_2:+52350446 None:intergenic
ACCTTACCATTCCATGAGTG+CGG 0.651296 2_2:-52350444 Msa0256900:CDS
CTCCAACCATCTGTCAACAA+CGG 0.679074 2_2:+52350584 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 2_2:+52350507 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 2_2:-52350378 Msa0256900:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGAAAATTAAATTCTTTTT+TGG - chr2_2:52350044-52350063 Msa0256900:CDS 10.0%
!!! TTATATATGCTATTTTAATA+TGG - chr2_2:52350535-52350554 Msa0256900:CDS 10.0%
!!! ATGAAAATTAAATTCTTTTT+TGG - chr2_2:52350044-52350063 Msa0256900:CDS 10.0%
!!! TTATATATGCTATTTTAATA+TGG - chr2_2:52350535-52350554 Msa0256900:CDS 10.0%
!!! AAATTAAATTCTTTTTTGGT+TGG - chr2_2:52350048-52350067 Msa0256900:CDS 15.0%
!!! TCTGAATTTTTTGTTTTTTT+AGG - chr2_2:52350576-52350595 Msa0256900:CDS 15.0%
!!! AAATTAAATTCTTTTTTGGT+TGG - chr2_2:52350048-52350067 Msa0256900:CDS 15.0%
!!! TCTGAATTTTTTGTTTTTTT+AGG - chr2_2:52350576-52350595 Msa0256900:CDS 15.0%
! GAAACAGTGTATCAAAAAAA+GGG + chr2_2:52350119-52350138 None:intergenic 25.0%
! TGAAACAGTGTATCAAAAAA+AGG + chr2_2:52350120-52350139 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG - chr2_2:52350246-52350265 Msa0256900:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG + chr2_2:52350494-52350513 None:intergenic 25.0%
!! TTTTCATGCTATTCAATTAG+AGG - chr2_2:52350511-52350530 Msa0256900:CDS 25.0%
! GAAACAGTGTATCAAAAAAA+GGG + chr2_2:52350119-52350138 None:intergenic 25.0%
! TGAAACAGTGTATCAAAAAA+AGG + chr2_2:52350120-52350139 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG - chr2_2:52350246-52350265 Msa0256900:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG + chr2_2:52350494-52350513 None:intergenic 25.0%
!! TTTTCATGCTATTCAATTAG+AGG - chr2_2:52350511-52350530 Msa0256900:CDS 25.0%
AAATATTGAGCAACGAAGAA+TGG + chr2_2:52350168-52350187 None:intergenic 30.0%
CGATTATTCAACGAATTTAG+TGG - chr2_2:52350299-52350318 Msa0256900:intron 30.0%
AAATATTGAGCAACGAAGAA+TGG + chr2_2:52350168-52350187 None:intergenic 30.0%
CGATTATTCAACGAATTTAG+TGG - chr2_2:52350299-52350318 Msa0256900:intron 30.0%
TGATACACTGTTTCACTTCT+AGG - chr2_2:52350125-52350144 Msa0256900:CDS 35.0%
! TCAATATTTCTACGAGCTAC+CGG - chr2_2:52350179-52350198 Msa0256900:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr2_2:52350329-52350348 Msa0256900:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr2_2:52350349-52350368 None:intergenic 35.0%
!!! ACTTTTGAAATTCCTATCGC+TGG - chr2_2:52350449-52350468 Msa0256900:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr2_2:52350595-52350614 Msa0256900:CDS 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr2_2:52350607-52350626 None:intergenic 35.0%
! AGTCGTGATGTTTTACTCTA+AGG + chr2_2:52350627-52350646 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr2_2:52350685-52350704 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG + chr2_2:52350711-52350730 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG + chr2_2:52350712-52350731 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG + chr2_2:52350713-52350732 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG + chr2_2:52350718-52350737 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG - chr2_2:52350715-52350734 Msa0256900:five_prime_UTR 35.0%
CTTGAAAATTAACACGTCTC+CGG + chr2_2:52350776-52350795 None:intergenic 35.0%
TGATACACTGTTTCACTTCT+AGG - chr2_2:52350125-52350144 Msa0256900:CDS 35.0%
! TCAATATTTCTACGAGCTAC+CGG - chr2_2:52350179-52350198 Msa0256900:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr2_2:52350329-52350348 Msa0256900:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr2_2:52350349-52350368 None:intergenic 35.0%
!!! ACTTTTGAAATTCCTATCGC+TGG - chr2_2:52350449-52350468 Msa0256900:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr2_2:52350595-52350614 Msa0256900:CDS 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr2_2:52350607-52350626 None:intergenic 35.0%
! AGTCGTGATGTTTTACTCTA+AGG + chr2_2:52350627-52350646 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr2_2:52350685-52350704 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG + chr2_2:52350711-52350730 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG + chr2_2:52350712-52350731 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG + chr2_2:52350713-52350732 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG + chr2_2:52350718-52350737 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG - chr2_2:52350715-52350734 Msa0256900:five_prime_UTR 35.0%
CTTGAAAATTAACACGTCTC+CGG + chr2_2:52350776-52350795 None:intergenic 35.0%
!! CTGTTTCACTTCTAGGATGT+TGG - chr2_2:52350132-52350151 Msa0256900:CDS 40.0%
GAAATTCCTATCGCTGGATA+TGG - chr2_2:52350455-52350474 Msa0256900:CDS 40.0%
ACAGGAATGACGTAGTCATA+TGG + chr2_2:52350667-52350686 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG - chr2_2:52350709-52350728 Msa0256900:five_prime_UTR 40.0%
TTGTGATGTTTGGAAAAGGC+TGG - chr2_2:52350719-52350738 Msa0256900:five_prime_UTR 40.0%
! ACAAGTTTTTGTGCTGCCAA+TGG - chr2_2:52350742-52350761 Msa0256900:five_prime_UTR 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG - chr2_2:52350789-52350808 Msa0256900:five_prime_UTR 40.0%
!! CTGTTTCACTTCTAGGATGT+TGG - chr2_2:52350132-52350151 Msa0256900:CDS 40.0%
GAAATTCCTATCGCTGGATA+TGG - chr2_2:52350455-52350474 Msa0256900:CDS 40.0%
ACAGGAATGACGTAGTCATA+TGG + chr2_2:52350667-52350686 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG - chr2_2:52350709-52350728 Msa0256900:five_prime_UTR 40.0%
TTGTGATGTTTGGAAAAGGC+TGG - chr2_2:52350719-52350738 Msa0256900:five_prime_UTR 40.0%
! ACAAGTTTTTGTGCTGCCAA+TGG - chr2_2:52350742-52350761 Msa0256900:five_prime_UTR 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG - chr2_2:52350789-52350808 Msa0256900:five_prime_UTR 40.0%
AAGGGAAAACAACTGCAAGC+TGG + chr2_2:52350101-52350120 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr2_2:52350272-52350291 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr2_2:52350332-52350351 Msa0256900:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr2_2:52350343-52350362 None:intergenic 45.0%
TGGTAAGGTGGATAATCAGC+TGG + chr2_2:52350398-52350417 None:intergenic 45.0%
ACCTTACCATTCCATGAGTG+CGG - chr2_2:52350409-52350428 Msa0256900:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr2_2:52350750-52350769 Msa0256900:five_prime_UTR 45.0%
AAGGGAAAACAACTGCAAGC+TGG + chr2_2:52350101-52350120 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr2_2:52350272-52350291 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr2_2:52350332-52350351 Msa0256900:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr2_2:52350343-52350362 None:intergenic 45.0%
TGGTAAGGTGGATAATCAGC+TGG + chr2_2:52350398-52350417 None:intergenic 45.0%
ACCTTACCATTCCATGAGTG+CGG - chr2_2:52350409-52350428 Msa0256900:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr2_2:52350750-52350769 Msa0256900:five_prime_UTR 45.0%
GCACTCATGGAATGGTAAGG+TGG + chr2_2:52350410-52350429 None:intergenic 50.0%
ACCGCACTCATGGAATGGTA+AGG + chr2_2:52350413-52350432 None:intergenic 50.0%
ATGCTACCGCACTCATGGAA+TGG + chr2_2:52350418-52350437 None:intergenic 50.0%
GTCGATCCATATCCAGCGAT+AGG + chr2_2:52350464-52350483 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr2_2:52350475-52350494 Msa0256900:CDS 50.0%
GCACTCATGGAATGGTAAGG+TGG + chr2_2:52350410-52350429 None:intergenic 50.0%
ACCGCACTCATGGAATGGTA+AGG + chr2_2:52350413-52350432 None:intergenic 50.0%
ATGCTACCGCACTCATGGAA+TGG + chr2_2:52350418-52350437 None:intergenic 50.0%
GTCGATCCATATCCAGCGAT+AGG + chr2_2:52350464-52350483 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr2_2:52350475-52350494 Msa0256900:CDS 50.0%
TCTACGAGCTACCGGAGCAA+TGG - chr2_2:52350187-52350206 Msa0256900:CDS 55.0%
TGTAGCAAGCGCCATTGCTC+CGG + chr2_2:52350201-52350220 None:intergenic 55.0%
! GAGCAATGGCGCTTGCTACA+TGG - chr2_2:52350201-52350220 Msa0256900:CDS 55.0%
! TGGCGCTTGCTACATGGTGA+TGG - chr2_2:52350207-52350226 Msa0256900:CDS 55.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr2_2:52350263-52350282 Msa0256900:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr2_2:52350267-52350286 Msa0256900:intron 55.0%
ACACGATGCTACCGCACTCA+TGG + chr2_2:52350423-52350442 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGC+CGG - chr2_2:52350754-52350773 Msa0256900:five_prime_UTR 55.0%
GTCTCCGGCCTCAATACCAT+TGG + chr2_2:52350761-52350780 None:intergenic 55.0%
TCTACGAGCTACCGGAGCAA+TGG - chr2_2:52350187-52350206 Msa0256900:CDS 55.0%
TGTAGCAAGCGCCATTGCTC+CGG + chr2_2:52350201-52350220 None:intergenic 55.0%
! GAGCAATGGCGCTTGCTACA+TGG - chr2_2:52350201-52350220 Msa0256900:CDS 55.0%
! TGGCGCTTGCTACATGGTGA+TGG - chr2_2:52350207-52350226 Msa0256900:CDS 55.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr2_2:52350263-52350282 Msa0256900:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr2_2:52350267-52350286 Msa0256900:intron 55.0%
ACACGATGCTACCGCACTCA+TGG + chr2_2:52350423-52350442 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGC+CGG - chr2_2:52350754-52350773 Msa0256900:five_prime_UTR 55.0%
GTCTCCGGCCTCAATACCAT+TGG + chr2_2:52350761-52350780 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 52350032 52350843 52350032 ID=Msa0256900;Name=Msa0256900
chr2_2 mRNA 52350032 52350843 52350032 ID=Msa0256900-mRNA-1;Parent=Msa0256900;Name=Msa0256900-mRNA-1;_AED=0.05;_eAED=0.05;_QI=213|1|0.5|1|1|1|2|0|165
chr2_2 exon 52350032 52350277 52350032 ID=Msa0256900-mRNA-1:exon:15745;Parent=Msa0256900-mRNA-1
chr2_2 exon 52350379 52350843 52350379 ID=Msa0256900-mRNA-1:exon:15744;Parent=Msa0256900-mRNA-1
chr2_2 five_prime_UTR 52350631 52350843 52350631 ID=Msa0256900-mRNA-1:five_prime_utr;Parent=Msa0256900-mRNA-1
chr2_2 CDS 52350379 52350630 52350379 ID=Msa0256900-mRNA-1:cds;Parent=Msa0256900-mRNA-1
chr2_2 CDS 52350032 52350277 52350032 ID=Msa0256900-mRNA-1:cds;Parent=Msa0256900-mRNA-1
Gene Sequence

>Msa0256900

ATGTTAAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTGCGATTATTCAACGAATTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCCAGCTGATTATCCACCTTACCATTCCATGAGTGCGGTAGCATCGTGTTATTGTACTTTTGAAATTCCTATCGCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTAAAACATCACGACTACGTCATGTTGTGCGCTCCATATGACTACGTCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAATTGTGATGTTTGGAAAAGGCTGGACAAGTTTTTGTGCTGCCAATGGTATTGAGGCCGGAGACGTGTTAATTTTCAAGTGCAAGTGTGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0256900

MLNKSVSRPLLTDGWSALRLFNEFSGSKIIAFQYLGGSRFQIFVFAHNITPADYPPYHSMSAVASCYCTFEIPIAGYGSTKSPKELPDTFGKFLRVKHHDYVMLCAPYDYVIPVRLKYTDDPIPIVMFGKGWTSFCAANGIEAGDVLIFKCKCVMDKKYVIVSKR*