AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0047040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0047040 MtrunA17_Chr7g0245951 97.895 95 2 0 1 95 1 95 1.29e-63 187
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0047040 AT3G60890.2 47.692 65 33 1 23 86 34 98 6.34e-13 59.7

Find 43 sgRNAs with CRISPR-Local

Find 119 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGATATAAGAAACTAAA+AGG 0.249578 1_1:+79588321 None:intergenic
CAAGCTATTAATTAAATTCA+TGG 0.344700 1_1:-79587408 Msa0047040:three_prime_UTR
GTGAAATATTGTTGGTGTAT+TGG 0.350232 1_1:-79587537 Msa0047040:three_prime_UTR
TGACATCCTAAGGGTATGTT+TGG 0.359081 1_1:-79587504 Msa0047040:three_prime_UTR
TGAGGTGAGGTGTAACAATT+AGG 0.362948 1_1:+79588268 None:intergenic
CAATATTATGTTCTATGTAA+TGG 0.366989 1_1:+79587559 None:intergenic
GTGATATAATAAAGATGAAT+AGG 0.370948 1_1:-79587599 Msa0047040:three_prime_UTR
GGTGTAACAATTAGGAAATA+AGG 0.376836 1_1:+79588276 None:intergenic
TTCAAATGTTTGACATCCTA+AGG 0.376934 1_1:-79587514 Msa0047040:three_prime_UTR
GAGAAACCTTATCTCTCAAA+AGG 0.386939 1_1:-79588192 Msa0047040:five_prime_UTR
TTTGTTGTGAAAGTTTCATT+TGG 0.391141 1_1:+79587802 None:intergenic
CATGAATTTAATTAATAGCT+TGG 0.405233 1_1:+79587409 None:intergenic
TTCTATGTAATGGTTACAAT+TGG 0.414110 1_1:+79587569 None:intergenic
CTTCTCATTCTGCTCTATGA+TGG 0.425083 1_1:+79587881 None:intergenic
ATAATATTGTGAAATATTGT+TGG 0.425924 1_1:-79587545 Msa0047040:three_prime_UTR
GTGTAACAATTAGGAAATAA+GGG 0.425973 1_1:+79588277 None:intergenic
CCTTCTCCAAACATACCCTT+AGG 0.436649 1_1:+79587498 None:intergenic
AAATAATAGCTAGTTATTGT+TGG 0.453707 1_1:+79587770 None:intergenic
GTGCCTACAGTTGTGTCTCT+TGG 0.458566 1_1:+79588115 None:intergenic
TCATTTGGAGCTGAGACATA+AGG 0.458680 1_1:+79587817 None:intergenic
TTAGGTTGAGCCACCTCAAA+AGG 0.471420 1_1:-79588091 Msa0047040:intron
GACACAACTGTAGGCACCTT+AGG 0.478643 1_1:-79588109 Msa0047040:CDS
ATTCTCTTTGTGAAGAAGCA+TGG 0.505800 1_1:+79587845 None:intergenic
TTTGATATAAGAAACTAAAA+GGG 0.512408 1_1:+79588322 None:intergenic
GACTCATGATTACAAAGGGC+AGG 0.516917 1_1:+79588439 None:intergenic
AAGCTATTAATTAAATTCAT+GGG 0.521024 1_1:-79587407 Msa0047040:three_prime_UTR
CCTAAGGGTATGTTTGGAGA+AGG 0.529938 1_1:-79587498 Msa0047040:three_prime_UTR
ATTGGTGATGCAGAAGGAAA+AGG 0.539434 1_1:-79587965 Msa0047040:intron
GTTTGATAGTTAGTGAGGTG+AGG 0.540735 1_1:+79588255 None:intergenic
TGATAGTTTGATAGTTAGTG+AGG 0.542097 1_1:+79588250 None:intergenic
TGTAACAATTAGGAAATAAG+GGG 0.546354 1_1:+79588278 None:intergenic
AGAAACCTTATCTCTCAAAA+GGG 0.550420 1_1:-79588191 Msa0047040:five_prime_UTR
TAAGGACTCATGATTACAAA+GGG 0.567020 1_1:+79588435 None:intergenic
CAGTTGTGTCTCTTGGAAAG+AGG 0.570084 1_1:+79588122 None:intergenic
TTTATGGTAATGATGGCGTA+AGG 0.575171 1_1:+79588417 None:intergenic
CTAAGGGTATGTTTGGAGAA+GGG 0.575665 1_1:-79587497 Msa0047040:three_prime_UTR
CAGAAGGAAAAGGATGATTG+AGG 0.594182 1_1:-79587955 Msa0047040:CDS
TCAAATGTTTGACATCCTAA+GGG 0.607895 1_1:-79587513 Msa0047040:three_prime_UTR
ACAAAGGGCAGGAATAGAAG+AGG 0.621775 1_1:+79588450 None:intergenic
GTAAGGACTCATGATTACAA+AGG 0.633201 1_1:+79588434 None:intergenic
GTAACAATTAGGAAATAAGG+GGG 0.644045 1_1:+79588279 None:intergenic
TTTCCAAGAGACACAACTGT+AGG 0.666230 1_1:-79588118 Msa0047040:CDS
TAACAATTAGGAAATAAGGG+GGG 0.750535 1_1:+79588280 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGATATAAGAAACTAAAA+GGG + chr1_1:79587508-79587527 None:intergenic 15.0%
!! ATTTGATATAAGAAACTAAA+AGG + chr1_1:79587509-79587528 None:intergenic 15.0%
!!! GAAAAATTTGAAATTGTATA+TGG - chr1_1:79587914-79587933 Msa0047040:CDS 15.0%
!! TTAAAAAACTAAAACAAACA+AGG + chr1_1:79588178-79588197 None:intergenic 15.0%
!! ATAATATTGTGAAATATTGT+TGG - chr1_1:79588282-79588301 Msa0047040:five_prime_UTR 15.0%
!! AAGCTATTAATTAAATTCAT+GGG - chr1_1:79588420-79588439 Msa0047040:five_prime_UTR 15.0%
!! TTTGATATAAGAAACTAAAA+GGG + chr1_1:79587508-79587527 None:intergenic 15.0%
!! ATTTGATATAAGAAACTAAA+AGG + chr1_1:79587509-79587528 None:intergenic 15.0%
!!! GAAAAATTTGAAATTGTATA+TGG - chr1_1:79587914-79587933 Msa0047040:CDS 15.0%
!! TTAAAAAACTAAAACAAACA+AGG + chr1_1:79588178-79588197 None:intergenic 15.0%
!! ATAATATTGTGAAATATTGT+TGG - chr1_1:79588282-79588301 Msa0047040:five_prime_UTR 15.0%
!! AAGCTATTAATTAAATTCAT+GGG - chr1_1:79588420-79588439 Msa0047040:five_prime_UTR 15.0%
!!! GATTAATTAACTTGTATGAT+TGG - chr1_1:79587844-79587863 Msa0047040:CDS 20.0%
!! AAATAATAGCTAGTTATTGT+TGG + chr1_1:79588060-79588079 None:intergenic 20.0%
!! GTGATATAATAAAGATGAAT+AGG - chr1_1:79588228-79588247 Msa0047040:five_prime_UTR 20.0%
!! CAATATTATGTTCTATGTAA+TGG + chr1_1:79588271-79588290 None:intergenic 20.0%
!! CATGAATTTAATTAATAGCT+TGG + chr1_1:79588421-79588440 None:intergenic 20.0%
!! CAAGCTATTAATTAAATTCA+TGG - chr1_1:79588419-79588438 Msa0047040:five_prime_UTR 20.0%
!!! GATTAATTAACTTGTATGAT+TGG - chr1_1:79587844-79587863 Msa0047040:CDS 20.0%
!! AAATAATAGCTAGTTATTGT+TGG + chr1_1:79588060-79588079 None:intergenic 20.0%
!! GTGATATAATAAAGATGAAT+AGG - chr1_1:79588228-79588247 Msa0047040:five_prime_UTR 20.0%
!! CAATATTATGTTCTATGTAA+TGG + chr1_1:79588271-79588290 None:intergenic 20.0%
!! CATGAATTTAATTAATAGCT+TGG + chr1_1:79588421-79588440 None:intergenic 20.0%
!! CAAGCTATTAATTAAATTCA+TGG - chr1_1:79588419-79588438 Msa0047040:five_prime_UTR 20.0%
! TGTAACAATTAGGAAATAAG+GGG + chr1_1:79587552-79587571 None:intergenic 25.0%
! GTGTAACAATTAGGAAATAA+GGG + chr1_1:79587553-79587572 None:intergenic 25.0%
!! TATTAGAAGAATACCTTTTG+AGG + chr1_1:79587752-79587771 None:intergenic 25.0%
!! TTTGTTGTGAAAGTTTCATT+TGG + chr1_1:79588028-79588047 None:intergenic 25.0%
! TTCTATGTAATGGTTACAAT+TGG + chr1_1:79588261-79588280 None:intergenic 25.0%
! GAATAGAGAAAAAAATGTCT+TGG - chr1_1:79588359-79588378 Msa0047040:five_prime_UTR 25.0%
! TGTAACAATTAGGAAATAAG+GGG + chr1_1:79587552-79587571 None:intergenic 25.0%
! GTGTAACAATTAGGAAATAA+GGG + chr1_1:79587553-79587572 None:intergenic 25.0%
!! TATTAGAAGAATACCTTTTG+AGG + chr1_1:79587752-79587771 None:intergenic 25.0%
!! TTTGTTGTGAAAGTTTCATT+TGG + chr1_1:79588028-79588047 None:intergenic 25.0%
! TTCTATGTAATGGTTACAAT+TGG + chr1_1:79588261-79588280 None:intergenic 25.0%
! GAATAGAGAAAAAAATGTCT+TGG - chr1_1:79588359-79588378 Msa0047040:five_prime_UTR 25.0%
TAAGGACTCATGATTACAAA+GGG + chr1_1:79587395-79587414 None:intergenic 30.0%
!! AGAGACTTTTATGGTAATGA+TGG + chr1_1:79587420-79587439 None:intergenic 30.0%
! AGATAAGAGAGAGACTTTTA+TGG + chr1_1:79587429-79587448 None:intergenic 30.0%
TAACAATTAGGAAATAAGGG+GGG + chr1_1:79587550-79587569 None:intergenic 30.0%
GTAACAATTAGGAAATAAGG+GGG + chr1_1:79587551-79587570 None:intergenic 30.0%
GGTGTAACAATTAGGAAATA+AGG + chr1_1:79587554-79587573 None:intergenic 30.0%
! TGATAGTTTGATAGTTAGTG+AGG + chr1_1:79587580-79587599 None:intergenic 30.0%
TCTTGCAACGAAAAAAATAG+GGG + chr1_1:79587617-79587636 None:intergenic 30.0%
CTCTTGCAACGAAAAAAATA+GGG + chr1_1:79587618-79587637 None:intergenic 30.0%
TCTCTTGCAACGAAAAAAAT+AGG + chr1_1:79587619-79587638 None:intergenic 30.0%
AGAAACCTTATCTCTCAAAA+GGG - chr1_1:79587636-79587655 Msa0047040:three_prime_UTR 30.0%
GTGAAATATTGTTGGTGTAT+TGG - chr1_1:79588290-79588309 Msa0047040:five_prime_UTR 30.0%
TTCAAATGTTTGACATCCTA+AGG - chr1_1:79588313-79588332 Msa0047040:five_prime_UTR 30.0%
TCAAATGTTTGACATCCTAA+GGG - chr1_1:79588314-79588333 Msa0047040:five_prime_UTR 30.0%
TAAGGACTCATGATTACAAA+GGG + chr1_1:79587395-79587414 None:intergenic 30.0%
!! AGAGACTTTTATGGTAATGA+TGG + chr1_1:79587420-79587439 None:intergenic 30.0%
! AGATAAGAGAGAGACTTTTA+TGG + chr1_1:79587429-79587448 None:intergenic 30.0%
TAACAATTAGGAAATAAGGG+GGG + chr1_1:79587550-79587569 None:intergenic 30.0%
GTAACAATTAGGAAATAAGG+GGG + chr1_1:79587551-79587570 None:intergenic 30.0%
GGTGTAACAATTAGGAAATA+AGG + chr1_1:79587554-79587573 None:intergenic 30.0%
! TGATAGTTTGATAGTTAGTG+AGG + chr1_1:79587580-79587599 None:intergenic 30.0%
TCTTGCAACGAAAAAAATAG+GGG + chr1_1:79587617-79587636 None:intergenic 30.0%
CTCTTGCAACGAAAAAAATA+GGG + chr1_1:79587618-79587637 None:intergenic 30.0%
TCTCTTGCAACGAAAAAAAT+AGG + chr1_1:79587619-79587638 None:intergenic 30.0%
AGAAACCTTATCTCTCAAAA+GGG - chr1_1:79587636-79587655 Msa0047040:three_prime_UTR 30.0%
GTGAAATATTGTTGGTGTAT+TGG - chr1_1:79588290-79588309 Msa0047040:five_prime_UTR 30.0%
TTCAAATGTTTGACATCCTA+AGG - chr1_1:79588313-79588332 Msa0047040:five_prime_UTR 30.0%
TCAAATGTTTGACATCCTAA+GGG - chr1_1:79588314-79588333 Msa0047040:five_prime_UTR 30.0%
GTAAGGACTCATGATTACAA+AGG + chr1_1:79587396-79587415 None:intergenic 35.0%
! TTTATGGTAATGATGGCGTA+AGG + chr1_1:79587413-79587432 None:intergenic 35.0%
! GAAATAAGGGGGGTATATAT+AGG + chr1_1:79587540-79587559 None:intergenic 35.0%
GAGAAACCTTATCTCTCAAA+AGG - chr1_1:79587635-79587654 Msa0047040:three_prime_UTR 35.0%
!! TGTTTCCCTTTTGAGAGATA+AGG + chr1_1:79587644-79587663 None:intergenic 35.0%
!! TAGAAGAATACCTTTTGAGG+TGG + chr1_1:79587749-79587768 None:intergenic 35.0%
ATTCTCTTTGTGAAGAAGCA+TGG + chr1_1:79587985-79588004 None:intergenic 35.0%
!! TGTCTTGGTTTTCTTCTCTT+AGG - chr1_1:79588374-79588393 Msa0047040:five_prime_UTR 35.0%
GTAAGGACTCATGATTACAA+AGG + chr1_1:79587396-79587415 None:intergenic 35.0%
! TTTATGGTAATGATGGCGTA+AGG + chr1_1:79587413-79587432 None:intergenic 35.0%
! GAAATAAGGGGGGTATATAT+AGG + chr1_1:79587540-79587559 None:intergenic 35.0%
GAGAAACCTTATCTCTCAAA+AGG - chr1_1:79587635-79587654 Msa0047040:three_prime_UTR 35.0%
!! TGTTTCCCTTTTGAGAGATA+AGG + chr1_1:79587644-79587663 None:intergenic 35.0%
!! TAGAAGAATACCTTTTGAGG+TGG + chr1_1:79587749-79587768 None:intergenic 35.0%
ATTCTCTTTGTGAAGAAGCA+TGG + chr1_1:79587985-79588004 None:intergenic 35.0%
!! TGTCTTGGTTTTCTTCTCTT+AGG - chr1_1:79588374-79588393 Msa0047040:five_prime_UTR 35.0%
TGAGGTGAGGTGTAACAATT+AGG + chr1_1:79587562-79587581 None:intergenic 40.0%
! GTTTGATAGTTAGTGAGGTG+AGG + chr1_1:79587575-79587594 None:intergenic 40.0%
TTTCCAAGAGACACAACTGT+AGG - chr1_1:79587709-79587728 Msa0047040:three_prime_UTR 40.0%
!! TGTATGATTGGTGATGCAGA+AGG - chr1_1:79587856-79587875 Msa0047040:CDS 40.0%
!! ATTGGTGATGCAGAAGGAAA+AGG - chr1_1:79587862-79587881 Msa0047040:CDS 40.0%
CAGAAGGAAAAGGATGATTG+AGG - chr1_1:79587872-79587891 Msa0047040:CDS 40.0%
CTTCTCATTCTGCTCTATGA+TGG + chr1_1:79587949-79587968 None:intergenic 40.0%
! TCATTTGGAGCTGAGACATA+AGG + chr1_1:79588013-79588032 None:intergenic 40.0%
! TGACATCCTAAGGGTATGTT+TGG - chr1_1:79588323-79588342 Msa0047040:five_prime_UTR 40.0%
! CTAAGGGTATGTTTGGAGAA+GGG - chr1_1:79588330-79588349 Msa0047040:five_prime_UTR 40.0%
TGAGGTGAGGTGTAACAATT+AGG + chr1_1:79587562-79587581 None:intergenic 40.0%
! GTTTGATAGTTAGTGAGGTG+AGG + chr1_1:79587575-79587594 None:intergenic 40.0%
TTTCCAAGAGACACAACTGT+AGG - chr1_1:79587709-79587728 Msa0047040:three_prime_UTR 40.0%
!! TGTATGATTGGTGATGCAGA+AGG - chr1_1:79587856-79587875 Msa0047040:CDS 40.0%
!! ATTGGTGATGCAGAAGGAAA+AGG - chr1_1:79587862-79587881 Msa0047040:CDS 40.0%
CAGAAGGAAAAGGATGATTG+AGG - chr1_1:79587872-79587891 Msa0047040:CDS 40.0%
CTTCTCATTCTGCTCTATGA+TGG + chr1_1:79587949-79587968 None:intergenic 40.0%
! TCATTTGGAGCTGAGACATA+AGG + chr1_1:79588013-79588032 None:intergenic 40.0%
! TGACATCCTAAGGGTATGTT+TGG - chr1_1:79588323-79588342 Msa0047040:five_prime_UTR 40.0%
! CTAAGGGTATGTTTGGAGAA+GGG - chr1_1:79588330-79588349 Msa0047040:five_prime_UTR 40.0%
GACTCATGATTACAAAGGGC+AGG + chr1_1:79587391-79587410 None:intergenic 45.0%
! AAGGGGGGTATATATAGGTG+AGG + chr1_1:79587535-79587554 None:intergenic 45.0%
CAGTTGTGTCTCTTGGAAAG+AGG + chr1_1:79587708-79587727 None:intergenic 45.0%
!!! TTTTGAGGTGGCTCAACCTA+AGG + chr1_1:79587737-79587756 None:intergenic 45.0%
!! TTAGGTTGAGCCACCTCAAA+AGG - chr1_1:79587736-79587755 Msa0047040:three_prime_UTR 45.0%
CCTTCTCCAAACATACCCTT+AGG + chr1_1:79588332-79588351 None:intergenic 45.0%
! CCTAAGGGTATGTTTGGAGA+AGG - chr1_1:79588329-79588348 Msa0047040:five_prime_UTR 45.0%
ACAAAGGGCAGGAATAGAAG+TGG + chr1_1:79587380-79587399 None:intergenic 45.0%
GACTCATGATTACAAAGGGC+AGG + chr1_1:79587391-79587410 None:intergenic 45.0%
! AAGGGGGGTATATATAGGTG+AGG + chr1_1:79587535-79587554 None:intergenic 45.0%
CAGTTGTGTCTCTTGGAAAG+AGG + chr1_1:79587708-79587727 None:intergenic 45.0%
!!! TTTTGAGGTGGCTCAACCTA+AGG + chr1_1:79587737-79587756 None:intergenic 45.0%
!! TTAGGTTGAGCCACCTCAAA+AGG - chr1_1:79587736-79587755 Msa0047040:three_prime_UTR 45.0%
CCTTCTCCAAACATACCCTT+AGG + chr1_1:79588332-79588351 None:intergenic 45.0%
! CCTAAGGGTATGTTTGGAGA+AGG - chr1_1:79588329-79588348 Msa0047040:five_prime_UTR 45.0%
GTGCCTACAGTTGTGTCTCT+TGG + chr1_1:79587715-79587734 None:intergenic 50.0%
GACACAACTGTAGGCACCTT+AGG - chr1_1:79587718-79587737 Msa0047040:three_prime_UTR 50.0%
GTGCCTACAGTTGTGTCTCT+TGG + chr1_1:79587715-79587734 None:intergenic 50.0%
GACACAACTGTAGGCACCTT+AGG - chr1_1:79587718-79587737 Msa0047040:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 79587380 79588469 79587380 ID=Msa0047040;Name=Msa0047040
chr1_1 mRNA 79587380 79588469 79587380 ID=Msa0047040-mRNA-1;Parent=Msa0047040;Name=Msa0047040-mRNA-1;_AED=0.05;_eAED=0.05;_QI=286|1|1|1|1|1|2|399|95
chr1_1 exon 79587380 79587974 79587380 ID=Msa0047040-mRNA-1:exon:27462;Parent=Msa0047040-mRNA-1
chr1_1 exon 79588092 79588469 79588092 ID=Msa0047040-mRNA-1:exon:27461;Parent=Msa0047040-mRNA-1
chr1_1 five_prime_UTR 79588184 79588469 79588184 ID=Msa0047040-mRNA-1:five_prime_utr;Parent=Msa0047040-mRNA-1
chr1_1 CDS 79588092 79588183 79588092 ID=Msa0047040-mRNA-1:cds;Parent=Msa0047040-mRNA-1
chr1_1 CDS 79587779 79587974 79587779 ID=Msa0047040-mRNA-1:cds;Parent=Msa0047040-mRNA-1
chr1_1 three_prime_UTR 79587380 79587778 79587380 ID=Msa0047040-mRNA-1:three_prime_utr;Parent=Msa0047040-mRNA-1
Gene Sequence

>Msa0047040

ATGTGTTGTTTCTCTTCACAACATGACACTCTTTATGCTCCTCTTTCCAAGAGACACAACTGTAGGCACCTTAGGTTGAGCCACCTCAAAAGAAGGAAAAGGATGATTGAGGTGAAAGCACAGATTAAGATGAAAAATTTGAAATTGTATATGGAGAATCAAACCATCATAGAGCAGAATGAGAAGTTGAGAAAACAAGCCATGCTTCTTCACAAAGAGAATCAAGACCTTATGTCTCAGCTCCAAATGAAACTTTCACAACAAAATATCAATACCAACAATAACTAG
Protein sequence

>Msa0047040

MCCFSSQHDTLYAPLSKRHNCRHLRLSHLKRRKRMIEVKAQIKMKNLKLYMENQTIIEQNEKLRKQAMLLHKENQDLMSQLQMKLSQQNINTNNN*