AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0346900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0346900 MtrunA17_Chr5g0393501 28.485 165 115 1 3 164 77 241 3.74e-22 89.0
Msa0346900 MtrunA17_Chr4g0044671 29.333 150 98 3 5 150 62 207 9.54e-13 63.5
Msa0346900 MtrunA17_Chr4g0034781 29.252 147 96 3 8 150 59 201 3.85e-12 62.0
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
TGATACACTGTTTGACTTCT+AGG 0.109128 3_1:-7772862 Msa0346900:five_prime_UTR
GAAATTTCTATCGCTGGATA+TGG 0.221860 3_1:-7772532 Msa0346900:CDS
CCCATACCAATTGTGATGTT+TGG 0.340839 3_1:-7772272 Msa0346900:CDS
AGGAATTTGCCAAAAGTATC+AGG 0.344083 3_1:+7772377 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 3_1:-7772386 Msa0346900:CDS
AGTCGTGATGTTTCACTCTA+AGG 0.360647 3_1:+7772357 None:intergenic
CGATTATTCAACGAATTTAG+TGG 0.380966 3_1:-7772688 Msa0346900:CDS
TCCAAACATCACAATTGGTA+TGG 0.411232 3_1:+7772271 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 3_1:+7772647 None:intergenic
CCAAACATCACAATTGGTAT+GGG 0.452680 3_1:+7772272 None:intergenic
GAGCAATGGCACTTGCTAGA+TGG 0.455163 3_1:-7772786 Msa0346900:five_prime_UTR
CTGTTTGACTTCTAGGATGT+TGG 0.457667 3_1:-7772855 Msa0346900:five_prime_UTR
TTGTGCTGCCAATGGTATTG+AGG 0.463000 3_1:-7772231 Msa0346900:CDS
ACAGGAATGACGTAGTCATA+TGG 0.475988 3_1:+7772317 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 3_1:-7772720 Msa0346900:CDS
ACACGATGCTACCGCACTCA+TGG 0.499582 3_1:+7772567 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 3_1:-7772230 Msa0346900:CDS
ATTATTGCTTTCCAGTACCT+TGG 0.503165 3_1:-7772658 Msa0346900:CDS
TCAATATTTCTACGAGCTAC+CGG 0.507354 3_1:-7772808 Msa0346900:five_prime_UTR
CCAATTGTGATGTTTGGAAA+AGG 0.511741 3_1:-7772266 Msa0346900:CDS
AAATATTGAGCAACGAAGAA+TGG 0.513098 3_1:+7772822 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 3_1:-7772724 Msa0346900:CDS
TCTAGCAAGTGCCATTGCTC+CGG 0.534587 3_1:+7772789 None:intergenic
AAGGGAAAACAACTGCAAGC+TGG 0.535824 3_1:+7772889 None:intergenic
TTGTGATGTTTGGAAAAGGC+TGG 0.536068 3_1:-7772262 Msa0346900:CDS
TGGTAAGGTGGATAATCAGC+TGG 0.541144 3_1:+7772592 None:intergenic
TTTCAAGTGCAAGTGTGTCA+TGG 0.544420 3_1:-7772192 Msa0346900:CDS
ATGCTACCGCACTCATGGAA+TGG 0.547467 3_1:+7772572 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 3_1:-7772655 Msa0346900:CDS
TCTGTATATTTGAGTCTCAC+AGG 0.555272 3_1:+7772299 None:intergenic
GTCTCCGCCCTCAATACCAT+TGG 0.581950 3_1:+7772223 None:intergenic
ACCGCACTCATGGAATGGTA+AGG 0.593653 3_1:+7772577 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.603582 3_1:-7772780 Msa0346900:five_prime_UTR
TCTACGAGCTACCGGAGCAA+TGG 0.612965 3_1:-7772800 Msa0346900:five_prime_UTR
TGTTAAACAAATCAGTTAGT+CGG 0.616534 3_1:-7772741 Msa0346900:CDS
CAAACATCACAATTGGTATG+GGG 0.630299 3_1:+7772273 None:intergenic
GCACTCATGGAATGGTAAGG+TGG 0.647237 3_1:+7772580 None:intergenic
ACCTTACCATTCCATGAGTG+CGG 0.651296 3_1:-7772578 Msa0346900:CDS
CTCCAACCATCTGTCAACAA+CGG 0.679074 3_1:+7772718 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 3_1:+7772641 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 3_1:-7772512 Msa0346900:intron
GCTGCCAATGGTATTGAGGG+CGG 0.739556 3_1:-7772227 Msa0346900:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGAAAATTAAATTCTTTTT+TGG - chr3_1:7772172-7772191 Msa0346900:CDS 10.0%
!!! ATGAAAATTAAATTCTTTTT+TGG - chr3_1:7772172-7772191 Msa0346900:CDS 10.0%
!!! AAATTAAATTCTTTTTTGGT+TGG - chr3_1:7772176-7772195 Msa0346900:CDS 15.0%
!!! TTATACATGCTATTTTAATA+CGG - chr3_1:7772666-7772685 Msa0346900:CDS 15.0%
!!! AAATTAAATTCTTTTTTGGT+TGG - chr3_1:7772176-7772195 Msa0346900:CDS 15.0%
!!! TTATACATGCTATTTTAATA+CGG - chr3_1:7772666-7772685 Msa0346900:CDS 15.0%
! CAAACAGTGTATCAAAAAAA+GGG + chr3_1:7772247-7772266 None:intergenic 25.0%
! TCAAACAGTGTATCAAAAAA+AGG + chr3_1:7772248-7772267 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG - chr3_1:7772374-7772393 Msa0346900:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG + chr3_1:7772622-7772641 None:intergenic 25.0%
!! TTTTCATGCTATTCAATTAG+AGG - chr3_1:7772642-7772661 Msa0346900:CDS 25.0%
! AAAAATATGTTATCGTATCC+AGG - chr3_1:7772949-7772968 Msa0346900:five_prime_UTR 25.0%
! CAAACAGTGTATCAAAAAAA+GGG + chr3_1:7772247-7772266 None:intergenic 25.0%
! TCAAACAGTGTATCAAAAAA+AGG + chr3_1:7772248-7772267 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG - chr3_1:7772374-7772393 Msa0346900:CDS 25.0%
! AAAAAACAACAAACAACCTT+CGG + chr3_1:7772622-7772641 None:intergenic 25.0%
!! TTTTCATGCTATTCAATTAG+AGG - chr3_1:7772642-7772661 Msa0346900:CDS 25.0%
! AAAAATATGTTATCGTATCC+AGG - chr3_1:7772949-7772968 Msa0346900:five_prime_UTR 25.0%
AAATATTGAGCAACGAAGAA+TGG + chr3_1:7772296-7772315 None:intergenic 30.0%
CGATTATTCAACGAATTTAG+TGG - chr3_1:7772427-7772446 Msa0346900:intron 30.0%
!!! ACTTTTGAAATTTCTATCGC+TGG - chr3_1:7772577-7772596 Msa0346900:CDS 30.0%
AAATATTGAGCAACGAAGAA+TGG + chr3_1:7772296-7772315 None:intergenic 30.0%
CGATTATTCAACGAATTTAG+TGG - chr3_1:7772427-7772446 Msa0346900:intron 30.0%
!!! ACTTTTGAAATTTCTATCGC+TGG - chr3_1:7772577-7772596 Msa0346900:CDS 30.0%
! TGATACACTGTTTGACTTCT+AGG - chr3_1:7772253-7772272 Msa0346900:CDS 35.0%
! TCAATATTTCTACGAGCTAC+CGG - chr3_1:7772307-7772326 Msa0346900:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr3_1:7772457-7772476 Msa0346900:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr3_1:7772477-7772496 None:intergenic 35.0%
GAAATTTCTATCGCTGGATA+TGG - chr3_1:7772583-7772602 Msa0346900:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr3_1:7772729-7772748 Msa0346900:CDS 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr3_1:7772741-7772760 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr3_1:7772819-7772838 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG + chr3_1:7772845-7772864 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG + chr3_1:7772846-7772865 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG + chr3_1:7772847-7772866 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG + chr3_1:7772852-7772871 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG - chr3_1:7772849-7772868 Msa0346900:five_prime_UTR 35.0%
! TGATACACTGTTTGACTTCT+AGG - chr3_1:7772253-7772272 Msa0346900:CDS 35.0%
! TCAATATTTCTACGAGCTAC+CGG - chr3_1:7772307-7772326 Msa0346900:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr3_1:7772457-7772476 Msa0346900:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr3_1:7772477-7772496 None:intergenic 35.0%
GAAATTTCTATCGCTGGATA+TGG - chr3_1:7772583-7772602 Msa0346900:CDS 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr3_1:7772729-7772748 Msa0346900:CDS 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr3_1:7772741-7772760 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr3_1:7772819-7772838 None:intergenic 35.0%
CAAACATCACAATTGGTATG+GGG + chr3_1:7772845-7772864 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG + chr3_1:7772846-7772865 None:intergenic 35.0%
TCCAAACATCACAATTGGTA+TGG + chr3_1:7772847-7772866 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG + chr3_1:7772852-7772871 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG - chr3_1:7772849-7772868 Msa0346900:five_prime_UTR 35.0%
!! CTGTTTGACTTCTAGGATGT+TGG - chr3_1:7772260-7772279 Msa0346900:CDS 40.0%
AGTCGTGATGTTTCACTCTA+AGG + chr3_1:7772761-7772780 None:intergenic 40.0%
ACAGGAATGACGTAGTCATA+TGG + chr3_1:7772801-7772820 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG - chr3_1:7772843-7772862 Msa0346900:five_prime_UTR 40.0%
TTGTGATGTTTGGAAAAGGC+TGG - chr3_1:7772853-7772872 Msa0346900:five_prime_UTR 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG - chr3_1:7772923-7772942 Msa0346900:five_prime_UTR 40.0%
!! CTGTTTGACTTCTAGGATGT+TGG - chr3_1:7772260-7772279 Msa0346900:CDS 40.0%
AGTCGTGATGTTTCACTCTA+AGG + chr3_1:7772761-7772780 None:intergenic 40.0%
ACAGGAATGACGTAGTCATA+TGG + chr3_1:7772801-7772820 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG - chr3_1:7772843-7772862 Msa0346900:five_prime_UTR 40.0%
TTGTGATGTTTGGAAAAGGC+TGG - chr3_1:7772853-7772872 Msa0346900:five_prime_UTR 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG - chr3_1:7772923-7772942 Msa0346900:five_prime_UTR 40.0%
AAGGGAAAACAACTGCAAGC+TGG + chr3_1:7772229-7772248 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr3_1:7772400-7772419 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr3_1:7772460-7772479 Msa0346900:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr3_1:7772471-7772490 None:intergenic 45.0%
TGGTAAGGTGGATAATCAGC+TGG + chr3_1:7772526-7772545 None:intergenic 45.0%
ACCTTACCATTCCATGAGTG+CGG - chr3_1:7772537-7772556 Msa0346900:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr3_1:7772876-7772895 Msa0346900:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr3_1:7772884-7772903 Msa0346900:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr3_1:7772885-7772904 Msa0346900:five_prime_UTR 45.0%
AAGGGAAAACAACTGCAAGC+TGG + chr3_1:7772229-7772248 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG + chr3_1:7772400-7772419 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr3_1:7772460-7772479 Msa0346900:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr3_1:7772471-7772490 None:intergenic 45.0%
TGGTAAGGTGGATAATCAGC+TGG + chr3_1:7772526-7772545 None:intergenic 45.0%
ACCTTACCATTCCATGAGTG+CGG - chr3_1:7772537-7772556 Msa0346900:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr3_1:7772876-7772895 Msa0346900:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr3_1:7772884-7772903 Msa0346900:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr3_1:7772885-7772904 Msa0346900:five_prime_UTR 45.0%
!!! AATTTTTTTGTTTTTTTTTT+AGG - chr3_1:7772710-7772729 Msa0346900:CDS 5.0%
!!! AATTTTTTTGTTTTTTTTTT+AGG - chr3_1:7772710-7772729 Msa0346900:CDS 5.0%
! TCTAGCAAGTGCCATTGCTC+CGG + chr3_1:7772329-7772348 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG - chr3_1:7772329-7772348 Msa0346900:CDS 50.0%
! TGGCACTTGCTAGATGGTGA+TGG - chr3_1:7772335-7772354 Msa0346900:CDS 50.0%
GCACTCATGGAATGGTAAGG+TGG + chr3_1:7772538-7772557 None:intergenic 50.0%
ACCGCACTCATGGAATGGTA+AGG + chr3_1:7772541-7772560 None:intergenic 50.0%
ATGCTACCGCACTCATGGAA+TGG + chr3_1:7772546-7772565 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr3_1:7772603-7772622 Msa0346900:CDS 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG + chr3_1:7772329-7772348 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG - chr3_1:7772329-7772348 Msa0346900:CDS 50.0%
! TGGCACTTGCTAGATGGTGA+TGG - chr3_1:7772335-7772354 Msa0346900:CDS 50.0%
GCACTCATGGAATGGTAAGG+TGG + chr3_1:7772538-7772557 None:intergenic 50.0%
ACCGCACTCATGGAATGGTA+AGG + chr3_1:7772541-7772560 None:intergenic 50.0%
ATGCTACCGCACTCATGGAA+TGG + chr3_1:7772546-7772565 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG - chr3_1:7772603-7772622 Msa0346900:CDS 50.0%
TCTACGAGCTACCGGAGCAA+TGG - chr3_1:7772315-7772334 Msa0346900:CDS 55.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr3_1:7772391-7772410 Msa0346900:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr3_1:7772395-7772414 Msa0346900:intron 55.0%
ACACGATGCTACCGCACTCA+TGG + chr3_1:7772551-7772570 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr3_1:7772888-7772907 Msa0346900:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr3_1:7772895-7772914 None:intergenic 55.0%
TCTACGAGCTACCGGAGCAA+TGG - chr3_1:7772315-7772334 Msa0346900:CDS 55.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr3_1:7772391-7772410 Msa0346900:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr3_1:7772395-7772414 Msa0346900:intron 55.0%
ACACGATGCTACCGCACTCA+TGG + chr3_1:7772551-7772570 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr3_1:7772888-7772907 Msa0346900:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr3_1:7772895-7772914 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 7772160 7772977 7772160 ID=Msa0346900;Name=Msa0346900
chr3_1 mRNA 7772160 7772977 7772160 ID=Msa0346900-mRNA-1;Parent=Msa0346900;Name=Msa0346900-mRNA-1;_AED=0.05;_eAED=0.05;_QI=213|1|0.5|1|1|1|2|0|165
chr3_1 exon 7772160 7772405 7772160 ID=Msa0346900-mRNA-1:exon:2165;Parent=Msa0346900-mRNA-1
chr3_1 exon 7772513 7772977 7772513 ID=Msa0346900-mRNA-1:exon:2164;Parent=Msa0346900-mRNA-1
chr3_1 five_prime_UTR 7772765 7772977 7772765 ID=Msa0346900-mRNA-1:five_prime_utr;Parent=Msa0346900-mRNA-1
chr3_1 CDS 7772513 7772764 7772513 ID=Msa0346900-mRNA-1:cds;Parent=Msa0346900-mRNA-1
chr3_1 CDS 7772160 7772405 7772160 ID=Msa0346900-mRNA-1:cds;Parent=Msa0346900-mRNA-1
Gene Sequence

>Msa0346900

ATGTTAAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTACGATTATTCAACGAATTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCCAGCTGATTATCCACCTTACCATTCCATGAGTGCGGTAGCATCGTGTTATTGTACTTTTGAAATTTCTATCGCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGACTACGTCATGTTGTGCGCTCCATATGACTACGTCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAATTGTGATGTTTGGAAAAGGCTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTAATTTTCAAGTGCAAGTGTGTCATGGACAAAAAATATGTTATCGTATCCAGGCGTTGA
Protein sequence

>Msa0346900

MLNKSVSRPLLTDGWSALRLFNEFSGSKIIAFQYLGGSRFQIFVFAHNITPADYPPYHSMSAVASCYCTFEISIAGYGSTKSPKELPDTFGKFLRVKHHDYVMLCAPYDYVIPVRLKYTDDPIPIVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSRR*