AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0032070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0032070 MtrunA17_Chr6g0473421 48.485 66 34 0 64 129 37 102 2.11e-18 75.9
Msa0032070 MtrunA17_Chr1g0172931 38.462 91 56 0 39 129 33 123 7.68e-18 74.7
Msa0032070 MtrunA17_Chr8g0389811 44.444 63 35 0 67 129 69 131 1.04e-14 67.4
Msa0032070 MtrunA17_Chr1g0203051 32.727 110 63 2 21 130 29 127 1.57e-14 68.9
Msa0032070 MtrunA17_Chr1g0171741 40.541 74 44 0 57 130 108 181 6.72e-13 63.5
Msa0032070 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 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATAAATATTTAATAGTTT+AGG 0.339187 1_1:+58998936 Msa0032070:five_prime_UTR
AACTGAAAATCCTGACATTC+TGG 0.342907 1_1:-58999817 None:intergenic
TCCGATTATGATAAAAGATA+TGG 0.367150 1_1:+58999692 Msa0032070:CDS
AAATTTGGTATTCAGAGAAA+TGG 0.369906 1_1:+58999410 Msa0032070:intron
TTCAAATTCAGTTGAAGGCT+TGG 0.371929 1_1:+58999647 Msa0032070:CDS
CCGCATATAGTGGGCGAAAC+CGG 0.385305 1_1:+58998897 None:intergenic
TCTTGGTTTGCCAGAATGTC+AGG 0.393047 1_1:+58999807 Msa0032070:CDS
ATCTTCAACCGGGTATCAAC+TGG 0.407828 1_1:-58999098 None:intergenic
CAGAGAAATGGACGGACGTT+CGG 0.413413 1_1:+58999422 Msa0032070:intron
GGAAGTTCAAATTCAGTTGA+AGG 0.423460 1_1:+58999642 Msa0032070:CDS
TGTTCGTTATGATCTTCAAC+CGG 0.429920 1_1:-58999109 None:intergenic
ATTTGCAAACAAAGGTCTGC+TGG 0.495786 1_1:-58999881 None:intergenic
AAATTCAGTTGAAGGCTTGG+AGG 0.512939 1_1:+58999650 Msa0032070:CDS
GATAAATCATTTGCAAACAA+AGG 0.526325 1_1:-58999889 None:intergenic
ACACCATTGCGCTCTAACAA+AGG 0.543044 1_1:-58999456 None:intergenic
TCGTAAGGGGCAAGTGGTGA+GGG 0.567327 1_1:+58999839 Msa0032070:CDS
AAAGGATCTGAGGTTGAAGA+AGG 0.567825 1_1:+58999070 Msa0032070:five_prime_UTR
TTCGTAAGGGGCAAGTGGTG+AGG 0.571006 1_1:+58999838 Msa0032070:CDS
TTCAGTTCGTAAGGGGCAAG+TGG 0.578338 1_1:+58999833 Msa0032070:CDS
TGATATAATGAAGATTGACC+TGG 0.579924 1_1:+58999716 Msa0032070:CDS
GTTCGTTATGATCTTCAACC+GGG 0.580394 1_1:-58999108 None:intergenic
CCGGTTTCGCCCACTATATG+CGG 0.582601 1_1:-58998897 None:intergenic
CAAGTGGTGAGGGATCGAAA+TGG 0.589736 1_1:+58999849 Msa0032070:CDS
AGGCGAAACCAGTTGATACC+CGG 0.593446 1_1:+58999090 Msa0032070:five_prime_UTR
GAAGATCATAACGAACATCA+AGG 0.597977 1_1:+58999115 Msa0032070:five_prime_UTR
AAACCAAGAGTAAAACATGT+AGG 0.598768 1_1:-58999793 None:intergenic
ATACAAGTGCAAAGGATCTG+AGG 0.607043 1_1:+58999060 Msa0032070:five_prime_UTR
CTGAAAACATACAAGTGCAA+AGG 0.609745 1_1:+58999052 Msa0032070:five_prime_UTR
AGAAATGGACGGACGTTCGG+AGG 0.620957 1_1:+58999425 Msa0032070:exon
TTGGTATTCAGAGAAATGGA+CGG 0.649153 1_1:+58999414 Msa0032070:intron
CAAAGCAATGAAGATGTCAG+TGG 0.657097 1_1:+58999621 Msa0032070:CDS
AATCCTTTGTTAGAGCGCAA+TGG 0.668763 1_1:+58999453 Msa0032070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAAAATGAAAAAAAAC+CGG - chr1_1:58998919-58998938 None:intergenic 10.0%
!! TTAAAAAAATGAAAAAAAAC+CGG - chr1_1:58998919-58998938 None:intergenic 10.0%
!!! ATTTGTTTGTTTAGTTTTTT+GGG - chr1_1:58998991-58999010 None:intergenic 15.0%
!!! AATTTGTTTGTTTAGTTTTT+TGG - chr1_1:58998992-58999011 None:intergenic 15.0%
!! ACAAACAAATTAAAAAAAAG+AGG + chr1_1:58999001-58999020 Msa0032070:five_prime_UTR 15.0%
!!! ATTTGTTTGTTTAGTTTTTT+GGG - chr1_1:58998991-58999010 None:intergenic 15.0%
!!! AATTTGTTTGTTTAGTTTTT+TGG - chr1_1:58998992-58999011 None:intergenic 15.0%
!! ACAAACAAATTAAAAAAAAG+AGG + chr1_1:58999001-58999020 Msa0032070:five_prime_UTR 15.0%
!! ACCTGATTCATTTAAAAATT+TGG + chr1_1:58999395-58999414 Msa0032070:intron 20.0%
!!! ACCAAATTTTTAAATGAATC+AGG - chr1_1:58999399-58999418 None:intergenic 20.0%
!!! ATGTGAAATTTGAAATTGAA+TGG + chr1_1:58999506-58999525 Msa0032070:intron 20.0%
!!! TTTTAAATTAACTTAGCATG+TGG + chr1_1:58999531-58999550 Msa0032070:intron 20.0%
!!! CTAAAAGAAAATTTTCTTAC+AGG + chr1_1:58999554-58999573 Msa0032070:intron 20.0%
!!! ACCATATCTTTTATCATAAT+CGG - chr1_1:58999696-58999715 None:intergenic 20.0%
!! ACCTGATTCATTTAAAAATT+TGG + chr1_1:58999395-58999414 Msa0032070:intron 20.0%
!!! ACCAAATTTTTAAATGAATC+AGG - chr1_1:58999399-58999418 None:intergenic 20.0%
!!! ATGTGAAATTTGAAATTGAA+TGG + chr1_1:58999506-58999525 Msa0032070:intron 20.0%
!!! TTTTAAATTAACTTAGCATG+TGG + chr1_1:58999531-58999550 Msa0032070:intron 20.0%
!!! CTAAAAGAAAATTTTCTTAC+AGG + chr1_1:58999554-58999573 Msa0032070:intron 20.0%
!!! ACCATATCTTTTATCATAAT+CGG - chr1_1:58999696-58999715 None:intergenic 20.0%
!!! ATCGATTGTTGTTTTGTTAA+GGG + chr1_1:58999190-58999209 Msa0032070:intron 25.0%
!! TAGAGACTTGTTTAGAAATT+AGG + chr1_1:58999306-58999325 Msa0032070:intron 25.0%
! AAATTTGGTATTCAGAGAAA+TGG + chr1_1:58999410-58999429 Msa0032070:intron 25.0%
! TCCGATTATGATAAAAGATA+TGG + chr1_1:58999692-58999711 Msa0032070:CDS 25.0%
!!! ATCGATTGTTGTTTTGTTAA+GGG + chr1_1:58999190-58999209 Msa0032070:intron 25.0%
!! TAGAGACTTGTTTAGAAATT+AGG + chr1_1:58999306-58999325 Msa0032070:intron 25.0%
! AAATTTGGTATTCAGAGAAA+TGG + chr1_1:58999410-58999429 Msa0032070:intron 25.0%
! TCCGATTATGATAAAAGATA+TGG + chr1_1:58999692-58999711 Msa0032070:CDS 25.0%
!!! GATCGATTGTTGTTTTGTTA+AGG + chr1_1:58999189-58999208 Msa0032070:intron 30.0%
!!! TCGATTGTTGTTTTGTTAAG+GGG + chr1_1:58999191-58999210 Msa0032070:intron 30.0%
TTAGTAGTGATGAAATACGA+GGG - chr1_1:58999250-58999269 None:intergenic 30.0%
TTTAGTAGTGATGAAATACG+AGG - chr1_1:58999251-58999270 None:intergenic 30.0%
AAACCTTTGAATGTTGAATG+AGG + chr1_1:58999270-58999289 Msa0032070:intron 30.0%
TTAGGCATGTTACTATTGTT+TGG + chr1_1:58999324-58999343 Msa0032070:intron 30.0%
TAGGCATGTTACTATTGTTT+GGG + chr1_1:58999325-58999344 Msa0032070:intron 30.0%
TTTATGTATCACACACACTT+TGG + chr1_1:58999350-58999369 Msa0032070:intron 30.0%
TTATGTATCACACACACTTT+GGG + chr1_1:58999351-58999370 Msa0032070:intron 30.0%
TGATATAATGAAGATTGACC+TGG + chr1_1:58999716-58999735 Msa0032070:CDS 30.0%
AAACCAAGAGTAAAACATGT+AGG - chr1_1:58999796-58999815 None:intergenic 30.0%
!!! GATCGATTGTTGTTTTGTTA+AGG + chr1_1:58999189-58999208 Msa0032070:intron 30.0%
!!! TCGATTGTTGTTTTGTTAAG+GGG + chr1_1:58999191-58999210 Msa0032070:intron 30.0%
TTAGTAGTGATGAAATACGA+GGG - chr1_1:58999250-58999269 None:intergenic 30.0%
TTTAGTAGTGATGAAATACG+AGG - chr1_1:58999251-58999270 None:intergenic 30.0%
AAACCTTTGAATGTTGAATG+AGG + chr1_1:58999270-58999289 Msa0032070:intron 30.0%
TTAGGCATGTTACTATTGTT+TGG + chr1_1:58999324-58999343 Msa0032070:intron 30.0%
TAGGCATGTTACTATTGTTT+GGG + chr1_1:58999325-58999344 Msa0032070:intron 30.0%
TTTATGTATCACACACACTT+TGG + chr1_1:58999350-58999369 Msa0032070:intron 30.0%
TTATGTATCACACACACTTT+GGG + chr1_1:58999351-58999370 Msa0032070:intron 30.0%
TGATATAATGAAGATTGACC+TGG + chr1_1:58999716-58999735 Msa0032070:CDS 30.0%
AAACCAAGAGTAAAACATGT+AGG - chr1_1:58999796-58999815 None:intergenic 30.0%
CTGAAAACATACAAGTGCAA+AGG + chr1_1:58999052-58999071 Msa0032070:five_prime_UTR 35.0%
TGTTCGTTATGATCTTCAAC+CGG - chr1_1:58999112-58999131 None:intergenic 35.0%
GAAGATCATAACGAACATCA+AGG + chr1_1:58999115-58999134 Msa0032070:five_prime_UTR 35.0%
AAGATGCACAACAACTAAAC+AGG - chr1_1:58999147-58999166 None:intergenic 35.0%
!!! ATTGTTGTTTTGTTAAGGGG+TGG + chr1_1:58999194-58999213 Msa0032070:intron 35.0%
CAACCTCATTCAACATTCAA+AGG - chr1_1:58999276-58999295 None:intergenic 35.0%
AGGCATGTTACTATTGTTTG+GGG + chr1_1:58999326-58999345 Msa0032070:intron 35.0%
TTGGTATTCAGAGAAATGGA+CGG + chr1_1:58999414-58999433 Msa0032070:intron 35.0%
!! CAGGATTTTGAAGATGAAAG+TGG + chr1_1:58999573-58999592 Msa0032070:intron 35.0%
!! GATTTTGAAGATGAAAGTGG+AGG + chr1_1:58999576-58999595 Msa0032070:CDS 35.0%
GGAAGTTCAAATTCAGTTGA+AGG + chr1_1:58999642-58999661 Msa0032070:CDS 35.0%
TTCAAATTCAGTTGAAGGCT+TGG + chr1_1:58999647-58999666 Msa0032070:CDS 35.0%
! TTGCCTACATGTTTTACTCT+TGG + chr1_1:58999790-58999809 Msa0032070:CDS 35.0%
AACTGAAAATCCTGACATTC+TGG - chr1_1:58999820-58999839 None:intergenic 35.0%
! TCAGGATTTTCAGTTCGTAA+GGG + chr1_1:58999825-58999844 Msa0032070:CDS 35.0%
CTGAAAACATACAAGTGCAA+AGG + chr1_1:58999052-58999071 Msa0032070:five_prime_UTR 35.0%
TGTTCGTTATGATCTTCAAC+CGG - chr1_1:58999112-58999131 None:intergenic 35.0%
GAAGATCATAACGAACATCA+AGG + chr1_1:58999115-58999134 Msa0032070:five_prime_UTR 35.0%
AAGATGCACAACAACTAAAC+AGG - chr1_1:58999147-58999166 None:intergenic 35.0%
!!! ATTGTTGTTTTGTTAAGGGG+TGG + chr1_1:58999194-58999213 Msa0032070:intron 35.0%
CAACCTCATTCAACATTCAA+AGG - chr1_1:58999276-58999295 None:intergenic 35.0%
AGGCATGTTACTATTGTTTG+GGG + chr1_1:58999326-58999345 Msa0032070:intron 35.0%
TTGGTATTCAGAGAAATGGA+CGG + chr1_1:58999414-58999433 Msa0032070:intron 35.0%
!! CAGGATTTTGAAGATGAAAG+TGG + chr1_1:58999573-58999592 Msa0032070:intron 35.0%
!! GATTTTGAAGATGAAAGTGG+AGG + chr1_1:58999576-58999595 Msa0032070:CDS 35.0%
GGAAGTTCAAATTCAGTTGA+AGG + chr1_1:58999642-58999661 Msa0032070:CDS 35.0%
TTCAAATTCAGTTGAAGGCT+TGG + chr1_1:58999647-58999666 Msa0032070:CDS 35.0%
! TTGCCTACATGTTTTACTCT+TGG + chr1_1:58999790-58999809 Msa0032070:CDS 35.0%
AACTGAAAATCCTGACATTC+TGG - chr1_1:58999820-58999839 None:intergenic 35.0%
! TCAGGATTTTCAGTTCGTAA+GGG + chr1_1:58999825-58999844 Msa0032070:CDS 35.0%
ATACAAGTGCAAAGGATCTG+AGG + chr1_1:58999060-58999079 Msa0032070:five_prime_UTR 40.0%
! AAAGGATCTGAGGTTGAAGA+AGG + chr1_1:58999070-58999089 Msa0032070:five_prime_UTR 40.0%
GTTCGTTATGATCTTCAACC+GGG - chr1_1:58999111-58999130 None:intergenic 40.0%
!! TTGTTTTGTTAAGGGGTGGA+GGG + chr1_1:58999198-58999217 Msa0032070:intron 40.0%
AATCCTTTGTTAGAGCGCAA+TGG + chr1_1:58999453-58999472 Msa0032070:CDS 40.0%
CAAAGCAATGAAGATGTCAG+TGG + chr1_1:58999621-58999640 Msa0032070:CDS 40.0%
AAATTCAGTTGAAGGCTTGG+AGG + chr1_1:58999650-58999669 Msa0032070:CDS 40.0%
! TGACCTGGAAAACTTTTGTG+TGG + chr1_1:58999731-58999750 Msa0032070:CDS 40.0%
! AAACTTTTGTGTGGCTGATG+TGG + chr1_1:58999740-58999759 Msa0032070:CDS 40.0%
! GTCAGGATTTTCAGTTCGTA+AGG + chr1_1:58999824-58999843 Msa0032070:CDS 40.0%
! CAGGATTTTCAGTTCGTAAG+GGG + chr1_1:58999826-58999845 Msa0032070:CDS 40.0%
ATTTGCAAACAAAGGTCTGC+TGG - chr1_1:58999884-58999903 None:intergenic 40.0%
ATACAAGTGCAAAGGATCTG+AGG + chr1_1:58999060-58999079 Msa0032070:five_prime_UTR 40.0%
! AAAGGATCTGAGGTTGAAGA+AGG + chr1_1:58999070-58999089 Msa0032070:five_prime_UTR 40.0%
GTTCGTTATGATCTTCAACC+GGG - chr1_1:58999111-58999130 None:intergenic 40.0%
!! TTGTTTTGTTAAGGGGTGGA+GGG + chr1_1:58999198-58999217 Msa0032070:intron 40.0%
AATCCTTTGTTAGAGCGCAA+TGG + chr1_1:58999453-58999472 Msa0032070:CDS 40.0%
CAAAGCAATGAAGATGTCAG+TGG + chr1_1:58999621-58999640 Msa0032070:CDS 40.0%
AAATTCAGTTGAAGGCTTGG+AGG + chr1_1:58999650-58999669 Msa0032070:CDS 40.0%
! TGACCTGGAAAACTTTTGTG+TGG + chr1_1:58999731-58999750 Msa0032070:CDS 40.0%
! AAACTTTTGTGTGGCTGATG+TGG + chr1_1:58999740-58999759 Msa0032070:CDS 40.0%
! GTCAGGATTTTCAGTTCGTA+AGG + chr1_1:58999824-58999843 Msa0032070:CDS 40.0%
! CAGGATTTTCAGTTCGTAAG+GGG + chr1_1:58999826-58999845 Msa0032070:CDS 40.0%
ATTTGCAAACAAAGGTCTGC+TGG - chr1_1:58999884-58999903 None:intergenic 40.0%
ATCTTCAACCGGGTATCAAC+TGG - chr1_1:58999101-58999120 None:intergenic 45.0%
!! GTTGTTTTGTTAAGGGGTGG+AGG + chr1_1:58999197-58999216 Msa0032070:intron 45.0%
ACACCATTGCGCTCTAACAA+AGG - chr1_1:58999459-58999478 None:intergenic 45.0%
! CAGCCACACAAAAGTTTTCC+AGG - chr1_1:58999737-58999756 None:intergenic 45.0%
!! TCTTGGTTTGCCAGAATGTC+AGG + chr1_1:58999807-58999826 Msa0032070:CDS 45.0%
ATCTTCAACCGGGTATCAAC+TGG - chr1_1:58999101-58999120 None:intergenic 45.0%
!! GTTGTTTTGTTAAGGGGTGG+AGG + chr1_1:58999197-58999216 Msa0032070:intron 45.0%
ACACCATTGCGCTCTAACAA+AGG - chr1_1:58999459-58999478 None:intergenic 45.0%
! CAGCCACACAAAAGTTTTCC+AGG - chr1_1:58999737-58999756 None:intergenic 45.0%
!! TCTTGGTTTGCCAGAATGTC+AGG + chr1_1:58999807-58999826 Msa0032070:CDS 45.0%
!! TAATAAATATTTAATAGTTT+AGG + chr1_1:58998936-58998955 Msa0032070:five_prime_UTR 5.0%
!! TAATAAATATTTAATAGTTT+AGG + chr1_1:58998936-58998955 Msa0032070:five_prime_UTR 5.0%
! AGGCGAAACCAGTTGATACC+CGG + chr1_1:58999090-58999109 Msa0032070:five_prime_UTR 50.0%
CAGAGAAATGGACGGACGTT+CGG + chr1_1:58999422-58999441 Msa0032070:intron 50.0%
TTCAGTTCGTAAGGGGCAAG+TGG + chr1_1:58999833-58999852 Msa0032070:CDS 50.0%
CAAGTGGTGAGGGATCGAAA+TGG + chr1_1:58999849-58999868 Msa0032070:CDS 50.0%
! AGGCGAAACCAGTTGATACC+CGG + chr1_1:58999090-58999109 Msa0032070:five_prime_UTR 50.0%
CAGAGAAATGGACGGACGTT+CGG + chr1_1:58999422-58999441 Msa0032070:intron 50.0%
TTCAGTTCGTAAGGGGCAAG+TGG + chr1_1:58999833-58999852 Msa0032070:CDS 50.0%
CAAGTGGTGAGGGATCGAAA+TGG + chr1_1:58999849-58999868 Msa0032070:CDS 50.0%
AGAAATGGACGGACGTTCGG+AGG + chr1_1:58999425-58999444 Msa0032070:exon 55.0%
TTCGTAAGGGGCAAGTGGTG+AGG + chr1_1:58999838-58999857 Msa0032070:CDS 55.0%
TCGTAAGGGGCAAGTGGTGA+GGG + chr1_1:58999839-58999858 Msa0032070:CDS 55.0%
AGAAATGGACGGACGTTCGG+AGG + chr1_1:58999425-58999444 Msa0032070:exon 55.0%
TTCGTAAGGGGCAAGTGGTG+AGG + chr1_1:58999838-58999857 Msa0032070:CDS 55.0%
TCGTAAGGGGCAAGTGGTGA+GGG + chr1_1:58999839-58999858 Msa0032070:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 58998899 58999905 58998899 ID=Msa0032070;Name=Msa0032070
chr1_1 mRNA 58998899 58999905 58998899 ID=Msa0032070-mRNA-1;Parent=Msa0032070;Name=Msa0032070-mRNA-1;_AED=0.07;_eAED=0.07;_QI=242|1|0.66|1|0.5|0.33|3|0|130
chr1_1 exon 58998899 58999136 58998899 ID=Msa0032070-mRNA-1:exon:18113;Parent=Msa0032070-mRNA-1
chr1_1 exon 58999425 58999491 58999425 ID=Msa0032070-mRNA-1:exon:18114;Parent=Msa0032070-mRNA-1
chr1_1 exon 58999576 58999905 58999576 ID=Msa0032070-mRNA-1:exon:18115;Parent=Msa0032070-mRNA-1
chr1_1 five_prime_UTR 58998899 58999136 58998899 ID=Msa0032070-mRNA-1:five_prime_utr;Parent=Msa0032070-mRNA-1
chr1_1 five_prime_UTR 58999425 58999428 58999425 ID=Msa0032070-mRNA-1:five_prime_utr;Parent=Msa0032070-mRNA-1
chr1_1 CDS 58999429 58999491 58999429 ID=Msa0032070-mRNA-1:cds;Parent=Msa0032070-mRNA-1
chr1_1 CDS 58999576 58999905 58999576 ID=Msa0032070-mRNA-1:cds;Parent=Msa0032070-mRNA-1
Gene Sequence

>Msa0032070

ATGGACGGACGTTCGGAGGCTGTGAATCCTTTGTTAGAGCGCAATGGTGTGAGAATTTCAAGAGATTTTGAAGATGAAAGTGGAGGTAATAACAACACAAATTGCGAACAAAGCAATGAAGATGTCAGTGGAAGTTCAAATTCAGTTGAAGGCTTGGAGGATGAAACTAATGAAGTCAATCCGATTATGATAAAAGATATGGTTGATATAATGAAGATTGACCTGGAAAACTTTTGTGTGGCTGATGTGGAAAGATATGAATTTGTTGCTTTAGATGTTGCCTACATGTTTTACTCTTGGTTTGCCAGAATGTCAGGATTTTCAGTTCGTAAGGGGCAAGTGGTGAGGGATCGAAATGGTGAAGTCGTCCAGCAGACCTTTGTTTGCAAATGA
Protein sequence

>Msa0032070

MDGRSEAVNPLLERNGVRISRDFEDESGGNNNTNCEQSNEDVSGSSNSVEGLEDETNEVNPIMIKDMVDIMKIDLENFCVADVERYEFVALDVAYMFYSWFARMSGFSVRKGQVVRDRNGEVVQQTFVCK*