AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0079360

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0079360 MtrunA17_Chr6g0473421 48.485 66 34 0 64 129 37 102 2.11e-18 75.9
Msa0079360 MtrunA17_Chr1g0172931 38.462 91 56 0 39 129 33 123 7.68e-18 74.7
Msa0079360 MtrunA17_Chr8g0389811 44.444 63 35 0 67 129 69 131 1.04e-14 67.4
Msa0079360 MtrunA17_Chr1g0203051 32.727 110 63 2 21 130 29 127 1.57e-14 68.9
Msa0079360 MtrunA17_Chr1g0171741 40.541 74 44 0 57 130 108 181 6.72e-13 63.5
Msa0079360 MtrunA17_Chr2g0331371 48.485 66 34 0 64 129 37 102 1.03e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATAAATATTTAATAGTTT+AGG 0.339187 1_2:+57197703 Msa0079360:five_prime_UTR
AACTGAAAATCCTGACATTC+TGG 0.342907 1_2:-57198583 None:intergenic
TCCGATTATGATAAAAGATA+TGG 0.367150 1_2:+57198458 Msa0079360:CDS
AAATTTGGTATTCAGAGAAA+TGG 0.369906 1_2:+57198176 Msa0079360:intron
ATTTGCAAACAAAGGTTTGC+TGG 0.371164 1_2:-57198647 None:intergenic
TTCAAATTCAGTTGAAGGCT+TGG 0.371929 1_2:+57198413 Msa0079360:CDS
TCTTGGTTTGCCAGAATGTC+AGG 0.393047 1_2:+57198573 Msa0079360:CDS
ATCTTCAACCGGGTATCAAC+TGG 0.407828 1_2:-57197865 None:intergenic
CAGAGAAATGGACGGACGTT+CGG 0.413413 1_2:+57198188 Msa0079360:intron
GGAAGTTCAAATTCAGTTGA+AGG 0.423460 1_2:+57198408 Msa0079360:CDS
TGTTCGTTATGATCTTCAAC+CGG 0.429920 1_2:-57197876 None:intergenic
CCGCATATAGTGGGTGAAAC+CGG 0.459104 1_2:+57197664 None:intergenic
GATAAATCATTTGCAAACAA+AGG 0.497307 1_2:-57198655 None:intergenic
AAATTCAGTTGAAGGCTTGG+AGG 0.512939 1_2:+57198416 Msa0079360:CDS
ACACCATTGCGCTCTAACAA+AGG 0.543044 1_2:-57198222 None:intergenic
TCGTAAGGGGCAAGTGGTGA+GGG 0.567327 1_2:+57198605 Msa0079360:CDS
AAAGGATCTGAGGTTGAAGA+AGG 0.567825 1_2:+57197837 Msa0079360:five_prime_UTR
TTCGTAAGGGGCAAGTGGTG+AGG 0.571006 1_2:+57198604 Msa0079360:CDS
TTCAGTTCGTAAGGGGCAAG+TGG 0.578338 1_2:+57198599 Msa0079360:CDS
TGATATAATGAAGATTGACC+TGG 0.579924 1_2:+57198482 Msa0079360:CDS
GTTCGTTATGATCTTCAACC+GGG 0.580394 1_2:-57197875 None:intergenic
CAAGTGGTGAGGGATCGAAA+TGG 0.589736 1_2:+57198615 Msa0079360:CDS
AGGCGAAACCAGTTGATACC+CGG 0.593446 1_2:+57197857 Msa0079360:five_prime_UTR
GAAGATCATAACGAACATCA+AGG 0.597977 1_2:+57197882 Msa0079360:five_prime_UTR
AAACCAAGAGTAAAACATGT+AGG 0.598768 1_2:-57198559 None:intergenic
ATACAAGTGCAAAGGATCTG+AGG 0.607043 1_2:+57197827 Msa0079360:five_prime_UTR
CTGAAAACATACAAGTGCAA+AGG 0.609745 1_2:+57197819 Msa0079360:five_prime_UTR
AGAAATGGACGGACGTTCGG+AGG 0.620957 1_2:+57198191 Msa0079360:exon
CCGGTTTCACCCACTATATG+CGG 0.648194 1_2:-57197664 None:intergenic
TTGGTATTCAGAGAAATGGA+CGG 0.649153 1_2:+57198180 Msa0079360:intron
CAAAGCAATGAAGATGTCAG+TGG 0.657097 1_2:+57198387 Msa0079360:CDS
AATCCTTTGTTAGAGCGCAA+TGG 0.668763 1_2:+57198219 Msa0079360:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAAAATGAAAAAAAAC+CGG - chr1_2:57197686-57197705 None:intergenic 10.0%
!! TTAAAAAAATGAAAAAAAAC+CGG - chr1_2:57197686-57197705 None:intergenic 10.0%
!!! ATTTGTTTGTTTAGTTTTTT+GGG - chr1_2:57197758-57197777 None:intergenic 15.0%
!!! AATTTGTTTGTTTAGTTTTT+TGG - chr1_2:57197759-57197778 None:intergenic 15.0%
!! ACAAACAAATTAAAAAAAAG+AGG + chr1_2:57197768-57197787 Msa0079360:five_prime_UTR 15.0%
!!! ATTTGTTTGTTTAGTTTTTT+GGG - chr1_2:57197758-57197777 None:intergenic 15.0%
!!! AATTTGTTTGTTTAGTTTTT+TGG - chr1_2:57197759-57197778 None:intergenic 15.0%
!! ACAAACAAATTAAAAAAAAG+AGG + chr1_2:57197768-57197787 Msa0079360:five_prime_UTR 15.0%
!! ACCTGATTCATTTAAAAATT+TGG + chr1_2:57198161-57198180 Msa0079360:intron 20.0%
!!! ACCAAATTTTTAAATGAATC+AGG - chr1_2:57198165-57198184 None:intergenic 20.0%
!!! TTTTAAATTAACTTAGCATG+TGG + chr1_2:57198297-57198316 Msa0079360:intron 20.0%
!!! CTAAAAGAAAATTTTCTTAC+AGG + chr1_2:57198320-57198339 Msa0079360:intron 20.0%
!!! ACCATATCTTTTATCATAAT+CGG - chr1_2:57198462-57198481 None:intergenic 20.0%
!! ACCTGATTCATTTAAAAATT+TGG + chr1_2:57198161-57198180 Msa0079360:intron 20.0%
!!! ACCAAATTTTTAAATGAATC+AGG - chr1_2:57198165-57198184 None:intergenic 20.0%
!!! TTTTAAATTAACTTAGCATG+TGG + chr1_2:57198297-57198316 Msa0079360:intron 20.0%
!!! CTAAAAGAAAATTTTCTTAC+AGG + chr1_2:57198320-57198339 Msa0079360:intron 20.0%
!!! ACCATATCTTTTATCATAAT+CGG - chr1_2:57198462-57198481 None:intergenic 20.0%
!!! ATCGATTGTTGTTTTGTTAA+GGG + chr1_2:57197957-57197976 Msa0079360:intron 25.0%
! TTAATAGTGATGAAATACGA+GGG - chr1_2:57198017-57198036 None:intergenic 25.0%
! TTTAATAGTGATGAAATACG+AGG - chr1_2:57198018-57198037 None:intergenic 25.0%
!! TAGAGACTTGTTTAGAAATT+AGG + chr1_2:57198072-57198091 Msa0079360:intron 25.0%
! AAATTTGGTATTCAGAGAAA+TGG + chr1_2:57198176-57198195 Msa0079360:intron 25.0%
! TCCGATTATGATAAAAGATA+TGG + chr1_2:57198458-57198477 Msa0079360:CDS 25.0%
!!! ATCGATTGTTGTTTTGTTAA+GGG + chr1_2:57197957-57197976 Msa0079360:intron 25.0%
! TTAATAGTGATGAAATACGA+GGG - chr1_2:57198017-57198036 None:intergenic 25.0%
! TTTAATAGTGATGAAATACG+AGG - chr1_2:57198018-57198037 None:intergenic 25.0%
!! TAGAGACTTGTTTAGAAATT+AGG + chr1_2:57198072-57198091 Msa0079360:intron 25.0%
! AAATTTGGTATTCAGAGAAA+TGG + chr1_2:57198176-57198195 Msa0079360:intron 25.0%
! TCCGATTATGATAAAAGATA+TGG + chr1_2:57198458-57198477 Msa0079360:CDS 25.0%
!!! GATCGATTGTTGTTTTGTTA+AGG + chr1_2:57197956-57197975 Msa0079360:intron 30.0%
!!! TCGATTGTTGTTTTGTTAAG+GGG + chr1_2:57197958-57197977 Msa0079360:intron 30.0%
AAACCTTTGAATGTTGAATG+AGG + chr1_2:57198036-57198055 Msa0079360:intron 30.0%
TTTATGTATCACACACACTT+TGG + chr1_2:57198116-57198135 Msa0079360:intron 30.0%
TTATGTATCACACACACTTT+GGG + chr1_2:57198117-57198136 Msa0079360:intron 30.0%
TGATATAATGAAGATTGACC+TGG + chr1_2:57198482-57198501 Msa0079360:CDS 30.0%
AAACCAAGAGTAAAACATGT+AGG - chr1_2:57198562-57198581 None:intergenic 30.0%
!!! GATCGATTGTTGTTTTGTTA+AGG + chr1_2:57197956-57197975 Msa0079360:intron 30.0%
!!! TCGATTGTTGTTTTGTTAAG+GGG + chr1_2:57197958-57197977 Msa0079360:intron 30.0%
AAACCTTTGAATGTTGAATG+AGG + chr1_2:57198036-57198055 Msa0079360:intron 30.0%
TTTATGTATCACACACACTT+TGG + chr1_2:57198116-57198135 Msa0079360:intron 30.0%
TTATGTATCACACACACTTT+GGG + chr1_2:57198117-57198136 Msa0079360:intron 30.0%
TGATATAATGAAGATTGACC+TGG + chr1_2:57198482-57198501 Msa0079360:CDS 30.0%
AAACCAAGAGTAAAACATGT+AGG - chr1_2:57198562-57198581 None:intergenic 30.0%
CTGAAAACATACAAGTGCAA+AGG + chr1_2:57197819-57197838 Msa0079360:five_prime_UTR 35.0%
TGTTCGTTATGATCTTCAAC+CGG - chr1_2:57197879-57197898 None:intergenic 35.0%
GAAGATCATAACGAACATCA+AGG + chr1_2:57197882-57197901 Msa0079360:five_prime_UTR 35.0%
AAGATGCACAACAACTAAAC+AGG - chr1_2:57197914-57197933 None:intergenic 35.0%
!!! ATTGTTGTTTTGTTAAGGGG+TGG + chr1_2:57197961-57197980 Msa0079360:intron 35.0%
CAACCTCATTCAACATTCAA+AGG - chr1_2:57198042-57198061 None:intergenic 35.0%
TTAGGCATGTTACTGTTGTT+TGG + chr1_2:57198090-57198109 Msa0079360:intron 35.0%
! TAGGCATGTTACTGTTGTTT+GGG + chr1_2:57198091-57198110 Msa0079360:intron 35.0%
TTGGTATTCAGAGAAATGGA+CGG + chr1_2:57198180-57198199 Msa0079360:intron 35.0%
!! CAGGATTTTGAAGATGAAAG+TGG + chr1_2:57198339-57198358 Msa0079360:intron 35.0%
!! GATTTTGAAGATGAAAGTGG+AGG + chr1_2:57198342-57198361 Msa0079360:CDS 35.0%
GGAAGTTCAAATTCAGTTGA+AGG + chr1_2:57198408-57198427 Msa0079360:CDS 35.0%
TTCAAATTCAGTTGAAGGCT+TGG + chr1_2:57198413-57198432 Msa0079360:CDS 35.0%
! TTGCCTACATGTTTTACTCT+TGG + chr1_2:57198556-57198575 Msa0079360:CDS 35.0%
AACTGAAAATCCTGACATTC+TGG - chr1_2:57198586-57198605 None:intergenic 35.0%
! TCAGGATTTTCAGTTCGTAA+GGG + chr1_2:57198591-57198610 Msa0079360:CDS 35.0%
ATTTGCAAACAAAGGTTTGC+TGG - chr1_2:57198650-57198669 None:intergenic 35.0%
CTGAAAACATACAAGTGCAA+AGG + chr1_2:57197819-57197838 Msa0079360:five_prime_UTR 35.0%
TGTTCGTTATGATCTTCAAC+CGG - chr1_2:57197879-57197898 None:intergenic 35.0%
GAAGATCATAACGAACATCA+AGG + chr1_2:57197882-57197901 Msa0079360:five_prime_UTR 35.0%
AAGATGCACAACAACTAAAC+AGG - chr1_2:57197914-57197933 None:intergenic 35.0%
!!! ATTGTTGTTTTGTTAAGGGG+TGG + chr1_2:57197961-57197980 Msa0079360:intron 35.0%
CAACCTCATTCAACATTCAA+AGG - chr1_2:57198042-57198061 None:intergenic 35.0%
TTAGGCATGTTACTGTTGTT+TGG + chr1_2:57198090-57198109 Msa0079360:intron 35.0%
! TAGGCATGTTACTGTTGTTT+GGG + chr1_2:57198091-57198110 Msa0079360:intron 35.0%
TTGGTATTCAGAGAAATGGA+CGG + chr1_2:57198180-57198199 Msa0079360:intron 35.0%
!! CAGGATTTTGAAGATGAAAG+TGG + chr1_2:57198339-57198358 Msa0079360:intron 35.0%
!! GATTTTGAAGATGAAAGTGG+AGG + chr1_2:57198342-57198361 Msa0079360:CDS 35.0%
GGAAGTTCAAATTCAGTTGA+AGG + chr1_2:57198408-57198427 Msa0079360:CDS 35.0%
TTCAAATTCAGTTGAAGGCT+TGG + chr1_2:57198413-57198432 Msa0079360:CDS 35.0%
! TTGCCTACATGTTTTACTCT+TGG + chr1_2:57198556-57198575 Msa0079360:CDS 35.0%
AACTGAAAATCCTGACATTC+TGG - chr1_2:57198586-57198605 None:intergenic 35.0%
! TCAGGATTTTCAGTTCGTAA+GGG + chr1_2:57198591-57198610 Msa0079360:CDS 35.0%
ATTTGCAAACAAAGGTTTGC+TGG - chr1_2:57198650-57198669 None:intergenic 35.0%
ATACAAGTGCAAAGGATCTG+AGG + chr1_2:57197827-57197846 Msa0079360:five_prime_UTR 40.0%
! AAAGGATCTGAGGTTGAAGA+AGG + chr1_2:57197837-57197856 Msa0079360:five_prime_UTR 40.0%
GTTCGTTATGATCTTCAACC+GGG - chr1_2:57197878-57197897 None:intergenic 40.0%
!! TTGTTTTGTTAAGGGGTGGA+GGG + chr1_2:57197965-57197984 Msa0079360:intron 40.0%
! AGGCATGTTACTGTTGTTTG+GGG + chr1_2:57198092-57198111 Msa0079360:intron 40.0%
AATCCTTTGTTAGAGCGCAA+TGG + chr1_2:57198219-57198238 Msa0079360:CDS 40.0%
CAAAGCAATGAAGATGTCAG+TGG + chr1_2:57198387-57198406 Msa0079360:CDS 40.0%
AAATTCAGTTGAAGGCTTGG+AGG + chr1_2:57198416-57198435 Msa0079360:CDS 40.0%
! TGACCTGGAAAACTTTTGTG+TGG + chr1_2:57198497-57198516 Msa0079360:CDS 40.0%
! AAACTTTTGTGTGGCTGATG+TGG + chr1_2:57198506-57198525 Msa0079360:CDS 40.0%
! GTCAGGATTTTCAGTTCGTA+AGG + chr1_2:57198590-57198609 Msa0079360:CDS 40.0%
! CAGGATTTTCAGTTCGTAAG+GGG + chr1_2:57198592-57198611 Msa0079360:CDS 40.0%
ATACAAGTGCAAAGGATCTG+AGG + chr1_2:57197827-57197846 Msa0079360:five_prime_UTR 40.0%
! AAAGGATCTGAGGTTGAAGA+AGG + chr1_2:57197837-57197856 Msa0079360:five_prime_UTR 40.0%
GTTCGTTATGATCTTCAACC+GGG - chr1_2:57197878-57197897 None:intergenic 40.0%
!! TTGTTTTGTTAAGGGGTGGA+GGG + chr1_2:57197965-57197984 Msa0079360:intron 40.0%
! AGGCATGTTACTGTTGTTTG+GGG + chr1_2:57198092-57198111 Msa0079360:intron 40.0%
AATCCTTTGTTAGAGCGCAA+TGG + chr1_2:57198219-57198238 Msa0079360:CDS 40.0%
CAAAGCAATGAAGATGTCAG+TGG + chr1_2:57198387-57198406 Msa0079360:CDS 40.0%
AAATTCAGTTGAAGGCTTGG+AGG + chr1_2:57198416-57198435 Msa0079360:CDS 40.0%
! TGACCTGGAAAACTTTTGTG+TGG + chr1_2:57198497-57198516 Msa0079360:CDS 40.0%
! AAACTTTTGTGTGGCTGATG+TGG + chr1_2:57198506-57198525 Msa0079360:CDS 40.0%
! GTCAGGATTTTCAGTTCGTA+AGG + chr1_2:57198590-57198609 Msa0079360:CDS 40.0%
! CAGGATTTTCAGTTCGTAAG+GGG + chr1_2:57198592-57198611 Msa0079360:CDS 40.0%
ATCTTCAACCGGGTATCAAC+TGG - chr1_2:57197868-57197887 None:intergenic 45.0%
!! GTTGTTTTGTTAAGGGGTGG+AGG + chr1_2:57197964-57197983 Msa0079360:intron 45.0%
ACACCATTGCGCTCTAACAA+AGG - chr1_2:57198225-57198244 None:intergenic 45.0%
! CAGCCACACAAAAGTTTTCC+AGG - chr1_2:57198503-57198522 None:intergenic 45.0%
!! TCTTGGTTTGCCAGAATGTC+AGG + chr1_2:57198573-57198592 Msa0079360:CDS 45.0%
ATCTTCAACCGGGTATCAAC+TGG - chr1_2:57197868-57197887 None:intergenic 45.0%
!! GTTGTTTTGTTAAGGGGTGG+AGG + chr1_2:57197964-57197983 Msa0079360:intron 45.0%
ACACCATTGCGCTCTAACAA+AGG - chr1_2:57198225-57198244 None:intergenic 45.0%
! CAGCCACACAAAAGTTTTCC+AGG - chr1_2:57198503-57198522 None:intergenic 45.0%
!! TCTTGGTTTGCCAGAATGTC+AGG + chr1_2:57198573-57198592 Msa0079360:CDS 45.0%
!! TAATAAATATTTAATAGTTT+AGG + chr1_2:57197703-57197722 Msa0079360:five_prime_UTR 5.0%
!! TAATAAATATTTAATAGTTT+AGG + chr1_2:57197703-57197722 Msa0079360:five_prime_UTR 5.0%
! AGGCGAAACCAGTTGATACC+CGG + chr1_2:57197857-57197876 Msa0079360:five_prime_UTR 50.0%
CAGAGAAATGGACGGACGTT+CGG + chr1_2:57198188-57198207 Msa0079360:intron 50.0%
TTCAGTTCGTAAGGGGCAAG+TGG + chr1_2:57198599-57198618 Msa0079360:CDS 50.0%
CAAGTGGTGAGGGATCGAAA+TGG + chr1_2:57198615-57198634 Msa0079360:CDS 50.0%
! AGGCGAAACCAGTTGATACC+CGG + chr1_2:57197857-57197876 Msa0079360:five_prime_UTR 50.0%
CAGAGAAATGGACGGACGTT+CGG + chr1_2:57198188-57198207 Msa0079360:intron 50.0%
TTCAGTTCGTAAGGGGCAAG+TGG + chr1_2:57198599-57198618 Msa0079360:CDS 50.0%
CAAGTGGTGAGGGATCGAAA+TGG + chr1_2:57198615-57198634 Msa0079360:CDS 50.0%
AGAAATGGACGGACGTTCGG+AGG + chr1_2:57198191-57198210 Msa0079360:exon 55.0%
TTCGTAAGGGGCAAGTGGTG+AGG + chr1_2:57198604-57198623 Msa0079360:CDS 55.0%
TCGTAAGGGGCAAGTGGTGA+GGG + chr1_2:57198605-57198624 Msa0079360:CDS 55.0%
AGAAATGGACGGACGTTCGG+AGG + chr1_2:57198191-57198210 Msa0079360:exon 55.0%
TTCGTAAGGGGCAAGTGGTG+AGG + chr1_2:57198604-57198623 Msa0079360:CDS 55.0%
TCGTAAGGGGCAAGTGGTGA+GGG + chr1_2:57198605-57198624 Msa0079360:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 57197666 57198671 57197666 ID=Msa0079360;Name=Msa0079360
chr1_2 mRNA 57197666 57198671 57197666 ID=Msa0079360-mRNA-1;Parent=Msa0079360;Name=Msa0079360-mRNA-1;_AED=0.07;_eAED=0.07;_QI=242|1|0.66|1|0.5|0.33|3|0|130
chr1_2 exon 57197666 57197903 57197666 ID=Msa0079360-mRNA-1:exon:18040;Parent=Msa0079360-mRNA-1
chr1_2 exon 57198191 57198257 57198191 ID=Msa0079360-mRNA-1:exon:18041;Parent=Msa0079360-mRNA-1
chr1_2 exon 57198342 57198671 57198342 ID=Msa0079360-mRNA-1:exon:18042;Parent=Msa0079360-mRNA-1
chr1_2 five_prime_UTR 57197666 57197903 57197666 ID=Msa0079360-mRNA-1:five_prime_utr;Parent=Msa0079360-mRNA-1
chr1_2 five_prime_UTR 57198191 57198194 57198191 ID=Msa0079360-mRNA-1:five_prime_utr;Parent=Msa0079360-mRNA-1
chr1_2 CDS 57198195 57198257 57198195 ID=Msa0079360-mRNA-1:cds;Parent=Msa0079360-mRNA-1
chr1_2 CDS 57198342 57198671 57198342 ID=Msa0079360-mRNA-1:cds;Parent=Msa0079360-mRNA-1
Gene Sequence

>Msa0079360

ATGGACGGACGTTCGGAGGCTGTGAATCCTTTGTTAGAGCGCAATGGTGTGAGAATTTCAAGAGATTTTGAAGATGAAAGTGGAGGTAATAACAACACAAATTGCGAACAAAGCAATGAAGATGTCAGTGGAAGTTCAAATTCAGTTGAAGGCTTGGAGGATGAAACTAATGAAGTCAATCCGATTATGATAAAAGATATGGTTGATATAATGAAGATTGACCTGGAAAACTTTTGTGTGGCTGATGTGGAAAGATATGAATTTGTTGCTTTAGATGTTGCCTACATGTTTTACTCTTGGTTTGCCAGAATGTCAGGATTTTCAGTTCGTAAGGGGCAAGTGGTGAGGGATCGAAATGGTGAAGTCGTCCAGCAAACCTTTGTTTGCAAATGA
Protein sequence

>Msa0079360

MDGRSEAVNPLLERNGVRISRDFEDESGGNNNTNCEQSNEDVSGSSNSVEGLEDETNEVNPIMIKDMVDIMKIDLENFCVADVERYEFVALDVAYMFYSWFARMSGFSVRKGQVVRDRNGEVVQQTFVCK*