AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0995930


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0995930 MtrunA17_Chr6g0480541 97.273 110 3 0 1 110 1100 1209 6.91e-72 231
Msa0995930 MtrunA17_Chr6g0480291 91.765 85 6 1 26 110 1 84 2.39e-51 156
Msa0995930 MtrunA17_Chr5g0437131 55.556 108 48 0 1 108 605 712 3.33e-38 135
Msa0995930 MtrunA17_Chr6g0480471 97.917 48 1 0 1 48 25 72 6.52e-30 102
Msa0995930 MtrunA17_Chr6g0480191 97.619 42 1 0 69 110 1 42 5.11e-25 89.0
Msa0995930 MtrunA17_Chr6g0480331 90.244 41 4 0 48 88 2 42 1.43e-21 80.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0995930 AT1G73450.1 82.727 110 19 0 1 110 1043 1152 2.09e-62 205
Msa0995930 AT1G73460.2 82.727 110 19 0 1 110 1060 1169 2.79e-62 204
Msa0995930 AT1G73460.1 82.727 110 19 0 1 110 1060 1169 2.79e-62 204
Msa0995930 AT3G17750.1 85.455 110 16 0 1 110 1029 1138 2.93e-61 201
Msa0995930 AT4G03175.1 52.174 92 44 0 11 102 2 93 2.23e-33 112
Msa0995930 AT2G40120.1 50.000 102 51 0 1 102 463 564 1.77e-31 116

Find 36 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCAAAGAAGACATCTTTA+AGG 0.177345 6_4:+73413934 Msa0995930:CDS
ACATTACTAGCTAGGGTAAT+TGG 0.184368 6_4:+73413284 Msa0995930:CDS
TGCCTTAAAGATGTCTTCTT+TGG 0.239781 6_4:-73413936 None:intergenic
GATGCAGAAGGTCGCTTCTT+CGG 0.294316 6_4:-73414020 None:intergenic
AAGATGTCTTCTTTGGAATC+AGG 0.325420 6_4:-73413929 None:intergenic
ATGCAGAAGGTCGCTTCTTC+GGG 0.331076 6_4:-73414019 None:intergenic
ATGTTGTCGGGGAATCGTTT+TGG 0.373434 6_4:-73413265 None:intergenic
GCTAGCATACTTTGACCAAT+TGG 0.379617 6_4:-73413317 None:intergenic
CATTACTAGCTAGGGTAATT+GGG 0.412390 6_4:+73413285 Msa0995930:CDS
CCCTAGCTAGTAATGTTGTC+GGG 0.431529 6_4:-73413277 None:intergenic
AGAATACTTCAAGATGATAT+CGG 0.460893 6_4:-73414083 None:intergenic
TTGATATGCAGGAAATCAAC+AGG 0.465829 6_4:+73413898 Msa0995930:intron
CAAGATGATATCGGTTCGTA+AGG 0.480516 6_4:-73414074 None:intergenic
ACCCTAGCTAGTAATGTTGT+CGG 0.481543 6_4:-73413278 None:intergenic
ATTGGGATCATCGGTCCAAT+TGG 0.485357 6_4:+73413302 Msa0995930:CDS
TATGCTTTATGAGAGGAATC+AGG 0.494533 6_4:+73413379 Msa0995930:CDS
GGTCAAAGTATGCTAGCAAA+AGG 0.496032 6_4:+73413323 Msa0995930:CDS
CAACAAAGTCAATGAAGCCT+TGG 0.499867 6_4:-73413977 None:intergenic
CTGAAGCTCTAAAGCACCCC+TGG 0.508338 6_4:+73414042 Msa0995930:CDS
CCCCGACAACATTACTAGCT+AGG 0.522478 6_4:+73413276 Msa0995930:CDS
TTCGTAAGGGTATGATAACC+AGG 0.523874 6_4:-73414060 None:intergenic
CCCGACAACATTACTAGCTA+GGG 0.537010 6_4:+73413277 Msa0995930:CDS
TTTAAGGCATAGATTACCGA+TGG 0.553714 6_4:+73413950 Msa0995930:CDS
CTTTGTTGCTCATTTGCTCG+AGG 0.575791 6_4:+73413992 Msa0995930:CDS
AAGTATGCTAGCAAAAGGAC+GGG 0.589744 6_4:+73413328 Msa0995930:CDS
AAAGTATGCTAGCAAAAGGA+CGG 0.592834 6_4:+73413327 Msa0995930:CDS
GCTAGGGTAATTGGGATCAT+CGG 0.603278 6_4:+73413293 Msa0995930:CDS
TTAAGGCATAGATTACCGAT+GGG 0.609487 6_4:+73413951 Msa0995930:CDS
AAAATCATATGCTTTATGAG+AGG 0.623112 6_4:+73413372 Msa0995930:CDS
TTTAGAGCTTCAGATGCAGA+AGG 0.638379 6_4:-73414032 None:intergenic
CCTAGCTAGTAATGTTGTCG+GGG 0.653018 6_4:-73413276 None:intergenic
AAGATGATATCGGTTCGTAA+GGG 0.655236 6_4:-73414073 None:intergenic
TCGTAAGGGTATGATAACCA+GGG 0.667962 6_4:-73414059 None:intergenic
CGTAAGGGTATGATAACCAG+GGG 0.686121 6_4:-73414058 None:intergenic
AAGGCATAGATTACCGATGG+GGG 0.690111 6_4:+73413953 Msa0995930:CDS
TAAGGCATAGATTACCGATG+GGG 0.718545 6_4:+73413952 Msa0995930:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATAGAAAATAACATATAT+AGG - chr6_4:73413621-73413640 None:intergenic 10.0%
!! TTATAGAAAATAACATATAT+AGG - chr6_4:73413621-73413640 None:intergenic 10.0%
!!! AGTCAATTTTAGAAATTTTA+GGG - chr6_4:73413519-73413538 None:intergenic 15.0%
!!! TAGTCAATTTTAGAAATTTT+AGG - chr6_4:73413520-73413539 None:intergenic 15.0%
!!! AGTCAATTTTAGAAATTTTA+GGG - chr6_4:73413519-73413538 None:intergenic 15.0%
!!! TAGTCAATTTTAGAAATTTT+AGG - chr6_4:73413520-73413539 None:intergenic 15.0%
!! TTAAATTGTTTATCCAAACA+TGG - chr6_4:73413563-73413582 None:intergenic 20.0%
!! CATTGTATGTTTAATTATCA+TGG + chr6_4:73413848-73413867 Msa0995930:intron 20.0%
!! TTAAATTGTTTATCCAAACA+TGG - chr6_4:73413563-73413582 None:intergenic 20.0%
!! CATTGTATGTTTAATTATCA+TGG + chr6_4:73413848-73413867 Msa0995930:intron 20.0%
!! CTCATAAAGCATATGATTTT+TGG - chr6_4:73413372-73413391 None:intergenic 25.0%
! AAAATCATATGCTTTATGAG+AGG + chr6_4:73413372-73413391 Msa0995930:CDS 25.0%
! AGACTATTTGAGAGAATTTA+TGG - chr6_4:73413763-73413782 None:intergenic 25.0%
! ATGTTTAATATGAGCATGTT+TGG - chr6_4:73413827-73413846 None:intergenic 25.0%
!! CTCATAAAGCATATGATTTT+TGG - chr6_4:73413372-73413391 None:intergenic 25.0%
! AAAATCATATGCTTTATGAG+AGG + chr6_4:73413372-73413391 Msa0995930:CDS 25.0%
! AGACTATTTGAGAGAATTTA+TGG - chr6_4:73413763-73413782 None:intergenic 25.0%
! ATGTTTAATATGAGCATGTT+TGG - chr6_4:73413827-73413846 None:intergenic 25.0%
AATATGAGCATGTTTGGATT+GGG - chr6_4:73413821-73413840 None:intergenic 30.0%
TAATATGAGCATGTTTGGAT+TGG - chr6_4:73413822-73413841 None:intergenic 30.0%
TTCCAAAGAAGACATCTTTA+AGG + chr6_4:73413934-73413953 Msa0995930:CDS 30.0%
AATATGAGCATGTTTGGATT+GGG - chr6_4:73413821-73413840 None:intergenic 30.0%
TAATATGAGCATGTTTGGAT+TGG - chr6_4:73413822-73413841 None:intergenic 30.0%
TTCCAAAGAAGACATCTTTA+AGG + chr6_4:73413934-73413953 Msa0995930:CDS 30.0%
ACATTACTAGCTAGGGTAAT+TGG + chr6_4:73413284-73413303 Msa0995930:CDS 35.0%
CATTACTAGCTAGGGTAATT+GGG + chr6_4:73413285-73413304 Msa0995930:CDS 35.0%
AAAGTATGCTAGCAAAAGGA+CGG + chr6_4:73413327-73413346 Msa0995930:CDS 35.0%
TATGCTTTATGAGAGGAATC+AGG + chr6_4:73413379-73413398 Msa0995930:CDS 35.0%
TTGCAATCCTAGAGAGTTTA+CGG + chr6_4:73413695-73413714 Msa0995930:intron 35.0%
GTAATTTCCGTAAACTCTCT+AGG - chr6_4:73413705-73413724 None:intergenic 35.0%
CATGGAAAAATTATTCAGCG+AGG + chr6_4:73413866-73413885 Msa0995930:intron 35.0%
! GGTATTGTGTATTGATATGC+AGG + chr6_4:73413887-73413906 Msa0995930:intron 35.0%
TTGATATGCAGGAAATCAAC+AGG + chr6_4:73413898-73413917 Msa0995930:intron 35.0%
!! AAGATGTCTTCTTTGGAATC+AGG - chr6_4:73413932-73413951 None:intergenic 35.0%
TGCCTTAAAGATGTCTTCTT+TGG - chr6_4:73413939-73413958 None:intergenic 35.0%
! TTTAAGGCATAGATTACCGA+TGG + chr6_4:73413950-73413969 Msa0995930:CDS 35.0%
TTAAGGCATAGATTACCGAT+GGG + chr6_4:73413951-73413970 Msa0995930:CDS 35.0%
!! AAGATGATATCGGTTCGTAA+GGG - chr6_4:73414076-73414095 None:intergenic 35.0%
ACATTACTAGCTAGGGTAAT+TGG + chr6_4:73413284-73413303 Msa0995930:CDS 35.0%
CATTACTAGCTAGGGTAATT+GGG + chr6_4:73413285-73413304 Msa0995930:CDS 35.0%
AAAGTATGCTAGCAAAAGGA+CGG + chr6_4:73413327-73413346 Msa0995930:CDS 35.0%
TATGCTTTATGAGAGGAATC+AGG + chr6_4:73413379-73413398 Msa0995930:CDS 35.0%
TTGCAATCCTAGAGAGTTTA+CGG + chr6_4:73413695-73413714 Msa0995930:intron 35.0%
GTAATTTCCGTAAACTCTCT+AGG - chr6_4:73413705-73413724 None:intergenic 35.0%
CATGGAAAAATTATTCAGCG+AGG + chr6_4:73413866-73413885 Msa0995930:intron 35.0%
! GGTATTGTGTATTGATATGC+AGG + chr6_4:73413887-73413906 Msa0995930:intron 35.0%
TTGATATGCAGGAAATCAAC+AGG + chr6_4:73413898-73413917 Msa0995930:intron 35.0%
!! AAGATGTCTTCTTTGGAATC+AGG - chr6_4:73413932-73413951 None:intergenic 35.0%
TGCCTTAAAGATGTCTTCTT+TGG - chr6_4:73413939-73413958 None:intergenic 35.0%
! TTTAAGGCATAGATTACCGA+TGG + chr6_4:73413950-73413969 Msa0995930:CDS 35.0%
TTAAGGCATAGATTACCGAT+GGG + chr6_4:73413951-73413970 Msa0995930:CDS 35.0%
!! AAGATGATATCGGTTCGTAA+GGG - chr6_4:73414076-73414095 None:intergenic 35.0%
ACCCTAGCTAGTAATGTTGT+CGG - chr6_4:73413281-73413300 None:intergenic 40.0%
GCTAGCATACTTTGACCAAT+TGG - chr6_4:73413320-73413339 None:intergenic 40.0%
GGTCAAAGTATGCTAGCAAA+AGG + chr6_4:73413323-73413342 Msa0995930:CDS 40.0%
AAGTATGCTAGCAAAAGGAC+GGG + chr6_4:73413328-73413347 Msa0995930:CDS 40.0%
TCGCTTGTATTTGCCATGTT+TGG + chr6_4:73413547-73413566 Msa0995930:intron 40.0%
! AAATAGTCTCACAAGTGCTG+CGG + chr6_4:73413774-73413793 Msa0995930:intron 40.0%
TAAGGCATAGATTACCGATG+GGG + chr6_4:73413952-73413971 Msa0995930:CDS 40.0%
CAACAAAGTCAATGAAGCCT+TGG - chr6_4:73413980-73413999 None:intergenic 40.0%
! TTTAGAGCTTCAGATGCAGA+AGG - chr6_4:73414035-73414054 None:intergenic 40.0%
! TCGTAAGGGTATGATAACCA+GGG - chr6_4:73414062-73414081 None:intergenic 40.0%
! TTCGTAAGGGTATGATAACC+AGG - chr6_4:73414063-73414082 None:intergenic 40.0%
!! CAAGATGATATCGGTTCGTA+AGG - chr6_4:73414077-73414096 None:intergenic 40.0%
ACCCTAGCTAGTAATGTTGT+CGG - chr6_4:73413281-73413300 None:intergenic 40.0%
GCTAGCATACTTTGACCAAT+TGG - chr6_4:73413320-73413339 None:intergenic 40.0%
GGTCAAAGTATGCTAGCAAA+AGG + chr6_4:73413323-73413342 Msa0995930:CDS 40.0%
AAGTATGCTAGCAAAAGGAC+GGG + chr6_4:73413328-73413347 Msa0995930:CDS 40.0%
TCGCTTGTATTTGCCATGTT+TGG + chr6_4:73413547-73413566 Msa0995930:intron 40.0%
! AAATAGTCTCACAAGTGCTG+CGG + chr6_4:73413774-73413793 Msa0995930:intron 40.0%
TAAGGCATAGATTACCGATG+GGG + chr6_4:73413952-73413971 Msa0995930:CDS 40.0%
CAACAAAGTCAATGAAGCCT+TGG - chr6_4:73413980-73413999 None:intergenic 40.0%
! TTTAGAGCTTCAGATGCAGA+AGG - chr6_4:73414035-73414054 None:intergenic 40.0%
! TCGTAAGGGTATGATAACCA+GGG - chr6_4:73414062-73414081 None:intergenic 40.0%
! TTCGTAAGGGTATGATAACC+AGG - chr6_4:73414063-73414082 None:intergenic 40.0%
!! CAAGATGATATCGGTTCGTA+AGG - chr6_4:73414077-73414096 None:intergenic 40.0%
! ATGTTGTCGGGGAATCGTTT+TGG - chr6_4:73413268-73413287 None:intergenic 45.0%
CCTAGCTAGTAATGTTGTCG+GGG - chr6_4:73413279-73413298 None:intergenic 45.0%
CCCTAGCTAGTAATGTTGTC+GGG - chr6_4:73413280-73413299 None:intergenic 45.0%
CCCGACAACATTACTAGCTA+GGG + chr6_4:73413277-73413296 Msa0995930:CDS 45.0%
GCTAGGGTAATTGGGATCAT+CGG + chr6_4:73413293-73413312 Msa0995930:CDS 45.0%
ATTGGGATCATCGGTCCAAT+TGG + chr6_4:73413302-73413321 Msa0995930:CDS 45.0%
! AATAGTCTCACAAGTGCTGC+GGG + chr6_4:73413775-73413794 Msa0995930:intron 45.0%
AAGGCATAGATTACCGATGG+GGG + chr6_4:73413953-73413972 Msa0995930:CDS 45.0%
CTTTGTTGCTCATTTGCTCG+AGG + chr6_4:73413992-73414011 Msa0995930:CDS 45.0%
! CGTAAGGGTATGATAACCAG+GGG - chr6_4:73414061-73414080 None:intergenic 45.0%
! ATGTTGTCGGGGAATCGTTT+TGG - chr6_4:73413268-73413287 None:intergenic 45.0%
CCTAGCTAGTAATGTTGTCG+GGG - chr6_4:73413279-73413298 None:intergenic 45.0%
CCCTAGCTAGTAATGTTGTC+GGG - chr6_4:73413280-73413299 None:intergenic 45.0%
CCCGACAACATTACTAGCTA+GGG + chr6_4:73413277-73413296 Msa0995930:CDS 45.0%
GCTAGGGTAATTGGGATCAT+CGG + chr6_4:73413293-73413312 Msa0995930:CDS 45.0%
ATTGGGATCATCGGTCCAAT+TGG + chr6_4:73413302-73413321 Msa0995930:CDS 45.0%
! AATAGTCTCACAAGTGCTGC+GGG + chr6_4:73413775-73413794 Msa0995930:intron 45.0%
AAGGCATAGATTACCGATGG+GGG + chr6_4:73413953-73413972 Msa0995930:CDS 45.0%
CTTTGTTGCTCATTTGCTCG+AGG + chr6_4:73413992-73414011 Msa0995930:CDS 45.0%
! CGTAAGGGTATGATAACCAG+GGG - chr6_4:73414061-73414080 None:intergenic 45.0%
CCCCGACAACATTACTAGCT+AGG + chr6_4:73413276-73413295 Msa0995930:CDS 50.0%
ATGCAGAAGGTCGCTTCTTC+GGG - chr6_4:73414022-73414041 None:intergenic 50.0%
GATGCAGAAGGTCGCTTCTT+CGG - chr6_4:73414023-73414042 None:intergenic 50.0%
CCCCGACAACATTACTAGCT+AGG + chr6_4:73413276-73413295 Msa0995930:CDS 50.0%
ATGCAGAAGGTCGCTTCTTC+GGG - chr6_4:73414022-73414041 None:intergenic 50.0%
GATGCAGAAGGTCGCTTCTT+CGG - chr6_4:73414023-73414042 None:intergenic 50.0%
AGATTACCGATGGGGGACCA+AGG + chr6_4:73413960-73413979 Msa0995930:CDS 55.0%
ATGAAGCCTTGGTCCCCCAT+CGG - chr6_4:73413969-73413988 None:intergenic 55.0%
!! CTGAAGCTCTAAAGCACCCC+TGG + chr6_4:73414042-73414061 Msa0995930:CDS 55.0%
AGATTACCGATGGGGGACCA+AGG + chr6_4:73413960-73413979 Msa0995930:CDS 55.0%
ATGAAGCCTTGGTCCCCCAT+CGG - chr6_4:73413969-73413988 None:intergenic 55.0%
!! CTGAAGCTCTAAAGCACCCC+TGG + chr6_4:73414042-73414061 Msa0995930:CDS 55.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 73413257 73414097 73413257 ID=Msa0995930;Name=Msa0995930
chr6_4 mRNA 73413257 73414097 73413257 ID=Msa0995930-mRNA-1;Parent=Msa0995930;Name=Msa0995930-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|1|0|1|1|1|2|0|110
chr6_4 exon 73413257 73413400 73413257 ID=Msa0995930-mRNA-1:exon:13625;Parent=Msa0995930-mRNA-1
chr6_4 exon 73413909 73414097 73413909 ID=Msa0995930-mRNA-1:exon:13626;Parent=Msa0995930-mRNA-1
chr6_4 CDS 73413257 73413400 73413257 ID=Msa0995930-mRNA-1:cds;Parent=Msa0995930-mRNA-1
chr6_4 CDS 73413909 73414097 73413909 ID=Msa0995930-mRNA-1:cds;Parent=Msa0995930-mRNA-1
Gene Sequence

>Msa0995930

GTCTTATTCCAAAACGATTCCCCGACAACATTACTAGCTAGGGTAATTGGGATCATCGGTCCAATTGGTCAAAGTATGCTAGCAAAAGGACGGGATACTTATAAGTACTTCACCAAAAATCATATGCTTTATGAGAGGAATCAGGAAATCAACAGGTTAGAATACCTGATTCCAAAGAAGACATCTTTAAGGCATAGATTACCGATGGGGGACCAAGGCTTCATTGACTTTGTTGCTCATTTGCTCGAGGTTAACCCGAAGAAGCGACCTTCTGCATCTGAAGCTCTAAAGCACCCCTGGTTATCATACCCTTACGAACCGATATCATCTTGA

Protein sequence

>Msa0995930

VLFQNDSPTTLLARVIGIIGPIGQSMLAKGRDTYKYFTKNHMLYERNQEINRLEYLIPKKTSLRHRLPMGDQGFIDFVAHLLEVNPKKRPSASEALKHPWLSYPYEPISS*