AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1397860


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1397860 MtrunA17_Chr1g0186411 97.143 35 1 0 1 35 402 436 3.69e-16 70.1
Msa1397860 MtrunA17_Chr1g0168221 80.000 35 7 0 1 35 406 440 3.05e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 140 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTGGGCTGCTATATGCTT+TGG 0.295273 tig0022193:-80772 Msa1397860:three_prime_UTR
ATGGCTAAATTATTCGTATA+AGG 0.295433 tig0022193:-81642 Msa1397860:three_prime_UTR
AGTTAGTACCATCTTGGAAT+TGG 0.364864 tig0022193:+81566 None:intergenic
AAAAGATGTATGAAGATATC+AGG 0.367738 tig0022193:-80992 Msa1397860:three_prime_UTR
GAAGCATCGTTGAAGATATT+AGG 0.369125 tig0022193:-80870 Msa1397860:three_prime_UTR
GCCATGATGCCTCTTCTTCA+CGG 0.372818 tig0022193:+81922 None:intergenic
TTCCCAGCTGATTAGAGTTA+TGG 0.402928 tig0022193:-81661 Msa1397860:exon
TAGCCATAACTCTAATCAGC+TGG 0.446311 tig0022193:+81658 None:intergenic
TTGCAAATTGATGTCTAAGC+TGG 0.453642 tig0022193:+81110 None:intergenic
TGTCGATCACTTGAGTGCCT+TGG 0.466505 tig0022193:+81083 None:intergenic
CTCAAGTGATCGACAAGACC+AGG 0.485596 tig0022193:-81075 Msa1397860:three_prime_UTR
TTTCTACTAGTATACCCATC+AGG 0.511384 tig0022193:-81156 Msa1397860:intron
ACCATCTTGGAATTGGACTT+AGG 0.515604 tig0022193:+81573 None:intergenic
GGGTAGAGTTAGTACCATCT+TGG 0.533104 tig0022193:+81560 None:intergenic
CGAACTCATCCGTGAAGAAG+AGG 0.538432 tig0022193:-81931 Msa1397860:CDS
CAAAACGTGGAGTCAATGAG+AGG 0.543462 tig0022193:-81878 Msa1397860:CDS
GAAGCACAAACAAATATGCT+TGG 0.548830 tig0022193:+81521 None:intergenic
CGACAAGACCAGGGTTGTGA+AGG 0.552215 tig0022193:-81065 Msa1397860:three_prime_UTR
AAAACTAGTTTAAGAGGTGA+AGG 0.552582 tig0022193:+81611 None:intergenic
CGATCATAGACCTTCCTGAT+GGG 0.559470 tig0022193:+81142 None:intergenic
AGTCAATGAGAGGGAAAAGA+AGG 0.577856 tig0022193:-81868 Msa1397860:CDS
TCCGTGAAGAAGAGGCATCA+TGG 0.580342 tig0022193:-81923 Msa1397860:CDS
GGTCAGTCGATCAAGAACCT+TGG 0.587010 tig0022193:+80902 None:intergenic
TTGAAGATCCTTCACAACCC+TGG 0.590563 tig0022193:+81057 None:intergenic
GAGGCATCATGGCAAGCTGA+AGG 0.593174 tig0022193:-81912 Msa1397860:CDS
AGCCATAACTCTAATCAGCT+GGG 0.594139 tig0022193:+81659 None:intergenic
TCGATCATAGACCTTCCTGA+TGG 0.594164 tig0022193:+81141 None:intergenic
ACCTAAGTCCAATTCCAAGA+TGG 0.606889 tig0022193:-81574 Msa1397860:three_prime_UTR
CGAACAAGTACAAGGAGTCA+AGG 0.618584 tig0022193:+80696 None:intergenic
TGTACATGCAAGTTTAACCA+AGG 0.622831 tig0022193:-80919 Msa1397860:three_prime_UTR
GCACAACTTACACTCAGGAC+TGG 0.628922 tig0022193:+81493 None:intergenic
TCTTCAATCGCGAATAAGAG+TGG 0.632552 tig0022193:-81041 Msa1397860:three_prime_UTR
AAAACGTGGAGTCAATGAGA+GGG 0.644020 tig0022193:-81877 Msa1397860:CDS
TACTAGTATACCCATCAGGA+AGG 0.654261 tig0022193:-81152 Msa1397860:intron
CATCAATTTGCAAAAGACCA+AGG 0.673397 tig0022193:-81100 Msa1397860:three_prime_UTR
GGTGATCAGAAAACAAAACG+TGG 0.704649 tig0022193:-81891 Msa1397860:CDS
TCAAGTGATCGACAAGACCA+GGG 0.710990 tig0022193:-81074 Msa1397860:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCATAATAAAGAATTAAATT+TGG + tig0022193:81186-81205 None:intergenic 10.0%
!! TCATAATAAAGAATTAAATT+TGG + tig0022193:81186-81205 None:intergenic 10.0%
!! TAATTCTTTATTATGATGTA+AGG - tig0022193:81190-81209 Msa1397860:intron 15.0%
!!! ATTTTAAAAGTGAAGATTTA+TGG - tig0022193:81670-81689 Msa1397860:exon 15.0%
!!! ATATGTTCATAGTTTTTTTA+GGG + tig0022193:81910-81929 None:intergenic 15.0%
!!! TATATGTTCATAGTTTTTTT+AGG + tig0022193:81911-81930 None:intergenic 15.0%
!! AAAAAAACTATGAACATATA+TGG - tig0022193:81911-81930 Msa1397860:CDS 15.0%
!! AAAAAAGAAATTTGTAAGAT+GGG - tig0022193:81958-81977 Msa1397860:CDS 15.0%
!! TAATTCTTTATTATGATGTA+AGG - tig0022193:81190-81209 Msa1397860:intron 15.0%
!!! ATTTTAAAAGTGAAGATTTA+TGG - tig0022193:81670-81689 Msa1397860:exon 15.0%
!!! ATATGTTCATAGTTTTTTTA+GGG + tig0022193:81910-81929 None:intergenic 15.0%
!!! TATATGTTCATAGTTTTTTT+AGG + tig0022193:81911-81930 None:intergenic 15.0%
!! AAAAAAACTATGAACATATA+TGG - tig0022193:81911-81930 Msa1397860:CDS 15.0%
!! AACAAATTGAAAAACAAACA+TGG + tig0022193:81302-81321 None:intergenic 20.0%
!!! TAATGTTAATTTTGAACTAC+AGG - tig0022193:81836-81855 Msa1397860:intron 20.0%
!! GAAAAAAGAAATTTGTAAGA+TGG - tig0022193:81957-81976 Msa1397860:CDS 20.0%
!! AACAAATTGAAAAACAAACA+TGG + tig0022193:81302-81321 None:intergenic 20.0%
!!! TAATGTTAATTTTGAACTAC+AGG - tig0022193:81836-81855 Msa1397860:intron 20.0%
! AGATTGAAATTGCATCATTA+AGG - tig0022193:80810-80829 Msa1397860:three_prime_UTR 25.0%
! ATGGCTAAATTATTCGTATA+AGG - tig0022193:80989-81008 Msa1397860:three_prime_UTR 25.0%
! AAAAGATGTATGAAGATATC+AGG - tig0022193:81639-81658 Msa1397860:three_prime_UTR 25.0%
! AGATTGAAATTGCATCATTA+AGG - tig0022193:80810-80829 Msa1397860:three_prime_UTR 25.0%
! ATGGCTAAATTATTCGTATA+AGG - tig0022193:80989-81008 Msa1397860:three_prime_UTR 25.0%
! AAAAGATGTATGAAGATATC+AGG - tig0022193:81639-81658 Msa1397860:three_prime_UTR 25.0%
! AAAACTAGTTTAAGAGGTGA+AGG + tig0022193:81023-81042 None:intergenic 30.0%
!!! TCACCTCTTAAACTAGTTTT+TGG - tig0022193:81023-81042 Msa1397860:three_prime_UTR 30.0%
! ACTCCAAAAACTAGTTTAAG+AGG + tig0022193:81029-81048 None:intergenic 30.0%
!!! TAAACTAGTTTTTGGAGTTG+AGG - tig0022193:81031-81050 Msa1397860:three_prime_UTR 30.0%
!!! TCTACCCTAGTTTTGTTTTT+GGG - tig0022193:81087-81106 Msa1397860:three_prime_UTR 30.0%
!! ATTGCAATGCATTTTGAAGA+AGG - tig0022193:81241-81260 Msa1397860:intron 30.0%
CTCAAGAACAACAATTTCAA+TGG + tig0022193:81273-81292 None:intergenic 30.0%
ATTAGGCAAAAAAAGTGAAG+TGG - tig0022193:81778-81797 Msa1397860:intron 30.0%
! TAATTTTGAACTACAGGCTT+TGG - tig0022193:81842-81861 Msa1397860:intron 30.0%
! AATTTTGAACTACAGGCTTT+GGG - tig0022193:81843-81862 Msa1397860:intron 30.0%
!!! TCTTTTTTCGAACAAGTACA+AGG + tig0022193:81946-81965 None:intergenic 30.0%
! AAAACTAGTTTAAGAGGTGA+AGG + tig0022193:81023-81042 None:intergenic 30.0%
!!! TCACCTCTTAAACTAGTTTT+TGG - tig0022193:81023-81042 Msa1397860:three_prime_UTR 30.0%
! ACTCCAAAAACTAGTTTAAG+AGG + tig0022193:81029-81048 None:intergenic 30.0%
!!! TAAACTAGTTTTTGGAGTTG+AGG - tig0022193:81031-81050 Msa1397860:three_prime_UTR 30.0%
!!! TCTACCCTAGTTTTGTTTTT+GGG - tig0022193:81087-81106 Msa1397860:three_prime_UTR 30.0%
!! ATTGCAATGCATTTTGAAGA+AGG - tig0022193:81241-81260 Msa1397860:intron 30.0%
CTCAAGAACAACAATTTCAA+TGG + tig0022193:81273-81292 None:intergenic 30.0%
ATTAGGCAAAAAAAGTGAAG+TGG - tig0022193:81778-81797 Msa1397860:intron 30.0%
! TAATTTTGAACTACAGGCTT+TGG - tig0022193:81842-81861 Msa1397860:intron 30.0%
! AATTTTGAACTACAGGCTTT+GGG - tig0022193:81843-81862 Msa1397860:intron 30.0%
!!! TCTTTTTTCGAACAAGTACA+AGG + tig0022193:81946-81965 None:intergenic 30.0%
AAAGAAGGCAAAGAAAAAGC+AGG - tig0022193:80778-80797 Msa1397860:three_prime_UTR 35.0%
AGTTAGTACCATCTTGGAAT+TGG + tig0022193:81068-81087 None:intergenic 35.0%
!!! CTCTACCCTAGTTTTGTTTT+TGG - tig0022193:81086-81105 Msa1397860:three_prime_UTR 35.0%
TTGGCCCAAAAACAAAACTA+GGG + tig0022193:81094-81113 None:intergenic 35.0%
GAAGCACAAACAAATATGCT+TGG + tig0022193:81113-81132 None:intergenic 35.0%
! TGTGCTAAGATCTCTGTTTT+TGG - tig0022193:81156-81175 Msa1397860:intron 35.0%
!! GTGCTAAGATCTCTGTTTTT+GGG - tig0022193:81157-81176 Msa1397860:intron 35.0%
TTTCTACTAGTATACCCATC+AGG - tig0022193:81475-81494 Msa1397860:intron 35.0%
TTGCAAATTGATGTCTAAGC+TGG + tig0022193:81524-81543 None:intergenic 35.0%
CATCAATTTGCAAAAGACCA+AGG - tig0022193:81531-81550 Msa1397860:three_prime_UTR 35.0%
TGTACATGCAAGTTTAACCA+AGG - tig0022193:81712-81731 Msa1397860:intron 35.0%
CAACGATGCTTCGAAAAATT+TGG + tig0022193:81753-81772 None:intergenic 35.0%
!! GAAGCATCGTTGAAGATATT+AGG - tig0022193:81761-81780 Msa1397860:intron 35.0%
AAAGAAGGCAAAGAAAAAGC+AGG - tig0022193:80778-80797 Msa1397860:three_prime_UTR 35.0%
AGTTAGTACCATCTTGGAAT+TGG + tig0022193:81068-81087 None:intergenic 35.0%
!!! CTCTACCCTAGTTTTGTTTT+TGG - tig0022193:81086-81105 Msa1397860:three_prime_UTR 35.0%
TTGGCCCAAAAACAAAACTA+GGG + tig0022193:81094-81113 None:intergenic 35.0%
GAAGCACAAACAAATATGCT+TGG + tig0022193:81113-81132 None:intergenic 35.0%
! TGTGCTAAGATCTCTGTTTT+TGG - tig0022193:81156-81175 Msa1397860:intron 35.0%
!! GTGCTAAGATCTCTGTTTTT+GGG - tig0022193:81157-81176 Msa1397860:intron 35.0%
TTTCTACTAGTATACCCATC+AGG - tig0022193:81475-81494 Msa1397860:intron 35.0%
TTGCAAATTGATGTCTAAGC+TGG + tig0022193:81524-81543 None:intergenic 35.0%
CATCAATTTGCAAAAGACCA+AGG - tig0022193:81531-81550 Msa1397860:three_prime_UTR 35.0%
TGTACATGCAAGTTTAACCA+AGG - tig0022193:81712-81731 Msa1397860:intron 35.0%
CAACGATGCTTCGAAAAATT+TGG + tig0022193:81753-81772 None:intergenic 35.0%
!! GAAGCATCGTTGAAGATATT+AGG - tig0022193:81761-81780 Msa1397860:intron 35.0%
GGTGATCAGAAAACAAAACG+TGG - tig0022193:80740-80759 Msa1397860:three_prime_UTR 40.0%
AAAACGTGGAGTCAATGAGA+GGG - tig0022193:80754-80773 Msa1397860:three_prime_UTR 40.0%
AGTCAATGAGAGGGAAAAGA+AGG - tig0022193:80763-80782 Msa1397860:three_prime_UTR 40.0%
TTCCCAGCTGATTAGAGTTA+TGG - tig0022193:80970-80989 Msa1397860:three_prime_UTR 40.0%
AGCCATAACTCTAATCAGCT+GGG + tig0022193:80975-80994 None:intergenic 40.0%
TAGCCATAACTCTAATCAGC+TGG + tig0022193:80976-80995 None:intergenic 40.0%
ACCTAAGTCCAATTCCAAGA+TGG - tig0022193:81057-81076 Msa1397860:three_prime_UTR 40.0%
ACCATCTTGGAATTGGACTT+AGG + tig0022193:81061-81080 None:intergenic 40.0%
CTTGGCCCAAAAACAAAACT+AGG + tig0022193:81095-81114 None:intergenic 40.0%
TCTTAGCACAACTTACACTC+AGG + tig0022193:81146-81165 None:intergenic 40.0%
!! GCAATGCATTTTGAAGAAGG+TGG - tig0022193:81244-81263 Msa1397860:intron 40.0%
GATCGTGCTCAATTATGACA+CGG - tig0022193:81339-81358 Msa1397860:intron 40.0%
CGCATTGTCGTGCTATATAT+TGG - tig0022193:81412-81431 Msa1397860:intron 40.0%
TGTCGTGCTATATATTGGCA+CGG - tig0022193:81417-81436 Msa1397860:intron 40.0%
TACTAGTATACCCATCAGGA+AGG - tig0022193:81479-81498 Msa1397860:intron 40.0%
TCTTCAATCGCGAATAAGAG+TGG - tig0022193:81590-81609 Msa1397860:three_prime_UTR 40.0%
GGTGATCAGAAAACAAAACG+TGG - tig0022193:80740-80759 Msa1397860:three_prime_UTR 40.0%
AAAACGTGGAGTCAATGAGA+GGG - tig0022193:80754-80773 Msa1397860:three_prime_UTR 40.0%
AGTCAATGAGAGGGAAAAGA+AGG - tig0022193:80763-80782 Msa1397860:three_prime_UTR 40.0%
TTCCCAGCTGATTAGAGTTA+TGG - tig0022193:80970-80989 Msa1397860:three_prime_UTR 40.0%
AGCCATAACTCTAATCAGCT+GGG + tig0022193:80975-80994 None:intergenic 40.0%
TAGCCATAACTCTAATCAGC+TGG + tig0022193:80976-80995 None:intergenic 40.0%
ACCTAAGTCCAATTCCAAGA+TGG - tig0022193:81057-81076 Msa1397860:three_prime_UTR 40.0%
ACCATCTTGGAATTGGACTT+AGG + tig0022193:81061-81080 None:intergenic 40.0%
CTTGGCCCAAAAACAAAACT+AGG + tig0022193:81095-81114 None:intergenic 40.0%
TCTTAGCACAACTTACACTC+AGG + tig0022193:81146-81165 None:intergenic 40.0%
!! GCAATGCATTTTGAAGAAGG+TGG - tig0022193:81244-81263 Msa1397860:intron 40.0%
GATCGTGCTCAATTATGACA+CGG - tig0022193:81339-81358 Msa1397860:intron 40.0%
CGCATTGTCGTGCTATATAT+TGG - tig0022193:81412-81431 Msa1397860:intron 40.0%
TGTCGTGCTATATATTGGCA+CGG - tig0022193:81417-81436 Msa1397860:intron 40.0%
TACTAGTATACCCATCAGGA+AGG - tig0022193:81479-81498 Msa1397860:intron 40.0%
TCTTCAATCGCGAATAAGAG+TGG - tig0022193:81590-81609 Msa1397860:three_prime_UTR 40.0%
CAAAACGTGGAGTCAATGAG+AGG - tig0022193:80753-80772 Msa1397860:three_prime_UTR 45.0%
GGGTAGAGTTAGTACCATCT+TGG + tig0022193:81074-81093 None:intergenic 45.0%
CGATCATAGACCTTCCTGAT+GGG + tig0022193:81492-81511 None:intergenic 45.0%
TCGATCATAGACCTTCCTGA+TGG + tig0022193:81493-81512 None:intergenic 45.0%
TCAAGTGATCGACAAGACCA+GGG - tig0022193:81557-81576 Msa1397860:three_prime_UTR 45.0%
TTGAAGATCCTTCACAACCC+TGG + tig0022193:81577-81596 None:intergenic 45.0%
CTTTGGGCTGCTATATGCTT+TGG - tig0022193:81859-81878 Msa1397860:CDS 45.0%
CGAACAAGTACAAGGAGTCA+AGG + tig0022193:81938-81957 None:intergenic 45.0%
CAAAACGTGGAGTCAATGAG+AGG - tig0022193:80753-80772 Msa1397860:three_prime_UTR 45.0%
GGGTAGAGTTAGTACCATCT+TGG + tig0022193:81074-81093 None:intergenic 45.0%
CGATCATAGACCTTCCTGAT+GGG + tig0022193:81492-81511 None:intergenic 45.0%
TCGATCATAGACCTTCCTGA+TGG + tig0022193:81493-81512 None:intergenic 45.0%
TCAAGTGATCGACAAGACCA+GGG - tig0022193:81557-81576 Msa1397860:three_prime_UTR 45.0%
TTGAAGATCCTTCACAACCC+TGG + tig0022193:81577-81596 None:intergenic 45.0%
CTTTGGGCTGCTATATGCTT+TGG - tig0022193:81859-81878 Msa1397860:CDS 45.0%
CGAACAAGTACAAGGAGTCA+AGG + tig0022193:81938-81957 None:intergenic 45.0%
CGAACTCATCCGTGAAGAAG+AGG - tig0022193:80700-80719 Msa1397860:three_prime_UTR 50.0%
!! TCCGTGAAGAAGAGGCATCA+TGG - tig0022193:80708-80727 Msa1397860:three_prime_UTR 50.0%
GCCATGATGCCTCTTCTTCA+CGG + tig0022193:80712-80731 None:intergenic 50.0%
GCACAACTTACACTCAGGAC+TGG + tig0022193:81141-81160 None:intergenic 50.0%
TGTCGATCACTTGAGTGCCT+TGG + tig0022193:81551-81570 None:intergenic 50.0%
CTCAAGTGATCGACAAGACC+AGG - tig0022193:81556-81575 Msa1397860:three_prime_UTR 50.0%
GGTCAGTCGATCAAGAACCT+TGG + tig0022193:81732-81751 None:intergenic 50.0%
CGAACTCATCCGTGAAGAAG+AGG - tig0022193:80700-80719 Msa1397860:three_prime_UTR 50.0%
!! TCCGTGAAGAAGAGGCATCA+TGG - tig0022193:80708-80727 Msa1397860:three_prime_UTR 50.0%
GCCATGATGCCTCTTCTTCA+CGG + tig0022193:80712-80731 None:intergenic 50.0%
GCACAACTTACACTCAGGAC+TGG + tig0022193:81141-81160 None:intergenic 50.0%
TGTCGATCACTTGAGTGCCT+TGG + tig0022193:81551-81570 None:intergenic 50.0%
CTCAAGTGATCGACAAGACC+AGG - tig0022193:81556-81575 Msa1397860:three_prime_UTR 50.0%
GGTCAGTCGATCAAGAACCT+TGG + tig0022193:81732-81751 None:intergenic 50.0%
! GAGGCATCATGGCAAGCTGA+AGG - tig0022193:80719-80738 Msa1397860:three_prime_UTR 55.0%
ACGGTCGTGTTCGTTTGCAC+TGG - tig0022193:81358-81377 Msa1397860:intron 55.0%
CGACAAGACCAGGGTTGTGA+AGG - tig0022193:81566-81585 Msa1397860:three_prime_UTR 55.0%
! GAGGCATCATGGCAAGCTGA+AGG - tig0022193:80719-80738 Msa1397860:three_prime_UTR 55.0%
ACGGTCGTGTTCGTTTGCAC+TGG - tig0022193:81358-81377 Msa1397860:intron 55.0%
CGACAAGACCAGGGTTGTGA+AGG - tig0022193:81566-81585 Msa1397860:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
tig0022193 gene 80674 81979 80674 ID=Msa1397860;Name=Msa1397860
tig0022193 mRNA 80674 81979 80674 ID=Msa1397860-mRNA-1;Parent=Msa1397860;Name=Msa1397860-mRNA-1;_AED=0.09;_eAED=0.16;_QI=0|1|0.66|1|0.5|0.33|3|664|59
tig0022193 exon 80674 81168 80674 ID=Msa1397860-mRNA-1:exon:16327;Parent=Msa1397860-mRNA-1
tig0022193 exon 81504 81726 81504 ID=Msa1397860-mRNA-1:exon:16326;Parent=Msa1397860-mRNA-1
tig0022193 exon 81854 81979 81854 ID=Msa1397860-mRNA-1:exon:16325;Parent=Msa1397860-mRNA-1
tig0022193 CDS 81854 81979 81854 ID=Msa1397860-mRNA-1:cds;Parent=Msa1397860-mRNA-1
tig0022193 CDS 81673 81726 81673 ID=Msa1397860-mRNA-1:cds;Parent=Msa1397860-mRNA-1
tig0022193 three_prime_UTR 81504 81672 81504 ID=Msa1397860-mRNA-1:three_prime_utr;Parent=Msa1397860-mRNA-1
tig0022193 three_prime_UTR 80674 81168 80674 ID=Msa1397860-mRNA-1:three_prime_utr;Parent=Msa1397860-mRNA-1
Gene Sequence

>Msa1397860

GAAGCTGTTGCTCTAAAGAGACAAGACGAACTCATCCGTGAAGAAGAGGCATCATGGCAAGCTGAAGGTGATCAGAAAACAAAACGTGGAGTCAATGAGAGGGAAAAGAAGGCAAAGAAAAAGCAGACTGAAATGCAATTGTCTGACAATTATATGAGATCTGTCGAGATTCCCAGCTGA

Protein sequence

>Msa1397860

EAVALKRQDELIREEEASWQAEGDQKTKRGVNEREKKAKKKQTEMQLSDNYMRSVEIPS*