AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0618070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0618070 MtrunA17_Chr8g0379441 94.118 170 10 0 1 170 1 170 1.29e-100 286
Msa0618070 MtrunA17_Chr8g0379451 71.951 82 23 0 89 170 1 82 6.70e-36 120
Msa0618070 MtrunA17_Chr5g0437991 35.669 157 86 7 1 154 25 169 3.04e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0618070 AT1G29270.1 38.365 159 88 4 1 156 1 152 5.58e-26 97.4
Msa0618070 AT1G29270.2 41.085 129 67 3 30 156 7 128 7.12e-24 91.3
Msa0618070 AT2G40435.1 35.669 157 86 8 1 152 1 147 1.08e-12 62.8

Find 39 sgRNAs with CRISPR-Local

Find 115 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCAAAAGCCTCTAAAAT+TGG 0.235711 4_2:-68861955 None:intergenic
TAGAAAAGTACTCTTGTTAA+TGG 0.243551 4_2:-68861626 None:intergenic
GCAAGAGTTTCATGTGAAAA+TGG 0.245398 4_2:+68862000 Msa0618070:CDS
ATGTTAAGATAGAGAAAATA+AGG 0.252575 4_2:+68861878 Msa0618070:CDS
GACATGTTTGGATGTTTATA+CGG 0.283042 4_2:+68862375 Msa0618070:three_prime_UTR
AGTGAAACCAAACATAAATT+AGG 0.299754 4_2:-68862330 None:intergenic
ACTCTCTTCTTGCGGCTATC+AGG 0.318826 4_2:-68861702 None:intergenic
TTCTCATCCTAATTTATGTT+TGG 0.329997 4_2:+68862323 Msa0618070:three_prime_UTR
GAAGCACTTCTAAAAGCTAT+TGG 0.338458 4_2:+68862084 Msa0618070:CDS
GACATTATTCAATAAGCTAA+TGG 0.375889 4_2:-68861725 None:intergenic
AAACTAAATAAATTTACCTT+TGG 0.379235 4_2:+68862400 Msa0618070:three_prime_UTR
AATATTAGAGATGGCTTGTA+AGG 0.412524 4_2:+68861342 Msa0618070:exon
GGATTAGAAGCTACAAATCA+TGG 0.413552 4_2:-68862423 None:intergenic
TGTTAAGATAGAGAAAATAA+GGG 0.418872 4_2:+68861879 Msa0618070:CDS
CTTGTTAATGGAATTTCTGT+TGG 0.425108 4_2:-68861614 None:intergenic
TGGCTTGTAAGGTGCAGAAA+AGG 0.441174 4_2:+68861353 Msa0618070:CDS
TCACTTAAGATGTAATCAAT+TGG 0.452566 4_2:+68862348 Msa0618070:three_prime_UTR
CATTATTGTTGGAGTTGGTA+AGG 0.458218 4_2:-68861411 None:intergenic
TGGAAAGCAGAGTGGTGAAA+AGG 0.477572 4_2:+68862104 Msa0618070:CDS
GTAAAGGTCACATGTGAGAA+AGG 0.513294 4_2:+68861916 Msa0618070:CDS
GGAAAGCAGAGTGGTGAAAA+GGG 0.519153 4_2:+68862105 Msa0618070:CDS
GAGGATGAAAATCTTGATGT+TGG 0.539252 4_2:+68862051 Msa0618070:CDS
TTCTATGGAAGCTATTATTG+TGG 0.540454 4_2:+68862026 Msa0618070:CDS
GGAAGCTATTATTGTGGCTG+AGG 0.546345 4_2:+68862032 Msa0618070:CDS
GGCTTGTAAGGTGCAGAAAA+GGG 0.547566 4_2:+68861354 Msa0618070:CDS
TATGTAATAGTATTGTTGAA+TGG 0.555192 4_2:+68862249 Msa0618070:three_prime_UTR
AAAGCAGTAAATATTAGAGA+TGG 0.580276 4_2:+68861333 Msa0618070:exon
TGAGAAAGGAGGTGACAAGT+TGG 0.586233 4_2:+68861930 Msa0618070:CDS
GAATAATGTCTATGATAACA+AGG 0.596304 4_2:+68861738 Msa0618070:CDS
CAACATTCACAAATCACAAG+AGG 0.597444 4_2:+68861304 None:intergenic
GTTAAGATAGAGAAAATAAG+GGG 0.609952 4_2:+68861880 Msa0618070:CDS
AAGCTACAAATCATGGCCAA+AGG 0.621786 4_2:-68862416 None:intergenic
AGTATTGTTGAATGGTGACA+TGG 0.624222 4_2:+68862257 Msa0618070:three_prime_UTR
GCTAATGGACTCTCTTCTTG+CGG 0.625040 4_2:-68861710 None:intergenic
AAGATAGAGAAAATAAGGGG+AGG 0.627338 4_2:+68861883 Msa0618070:CDS
AGAGATGTGTGTGAATGTTG+AGG 0.643020 4_2:+68861975 Msa0618070:CDS
AAAGCTATTGGAAAGCAGAG+TGG 0.675693 4_2:+68862096 Msa0618070:CDS
AAGGTCACATGTGAGAAAGG+AGG 0.686761 4_2:+68861919 Msa0618070:CDS
GTATTGTTGAATGGTGACAT+GGG 0.693521 4_2:+68862258 Msa0618070:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTTTTTTTTATTATAAC+AGG + chr4_2:68861855-68861874 Msa0618070:intron 10.0%
!!! ATGTTTTTTTTTATTATAAC+AGG + chr4_2:68861855-68861874 Msa0618070:intron 10.0%
!!! TGTTAATTTTACATTATTGT+TGG - chr4_2:68861425-68861444 None:intergenic 15.0%
!! GAATGTAAAAAAAGAAAAAA+AGG - chr4_2:68861454-68861473 None:intergenic 15.0%
!! AAACTAAATAAATTTACCTT+TGG + chr4_2:68862400-68862419 Msa0618070:three_prime_UTR 15.0%
!!! TGTTAATTTTACATTATTGT+TGG - chr4_2:68861425-68861444 None:intergenic 15.0%
!! GAATGTAAAAAAAGAAAAAA+AGG - chr4_2:68861454-68861473 None:intergenic 15.0%
!! AAACTAAATAAATTTACCTT+TGG + chr4_2:68862400-68862419 Msa0618070:three_prime_UTR 15.0%
!! TCAGTGGAAAAAAATAATAA+TGG - chr4_2:68861485-68861504 None:intergenic 20.0%
!! TAATATTTATATATAGGCCT+TGG - chr4_2:68861813-68861832 None:intergenic 20.0%
!!! AAAAACATGTTATTTTTGCT+TGG - chr4_2:68861843-68861862 None:intergenic 20.0%
!! ATGTTAAGATAGAGAAAATA+AGG + chr4_2:68861878-68861897 Msa0618070:CDS 20.0%
!! TGTTAAGATAGAGAAAATAA+GGG + chr4_2:68861879-68861898 Msa0618070:CDS 20.0%
!!! AAATATGTAAAAACTTGTTG+AGG - chr4_2:68862208-68862227 None:intergenic 20.0%
!! TATGTAATAGTATTGTTGAA+TGG + chr4_2:68862249-68862268 Msa0618070:three_prime_UTR 20.0%
!!! TAAATATTGTTTTGAAAGCT+TGG + chr4_2:68862286-68862305 Msa0618070:three_prime_UTR 20.0%
!! TCAGTGGAAAAAAATAATAA+TGG - chr4_2:68861485-68861504 None:intergenic 20.0%
!! TAATATTTATATATAGGCCT+TGG - chr4_2:68861813-68861832 None:intergenic 20.0%
!!! AAAAACATGTTATTTTTGCT+TGG - chr4_2:68861843-68861862 None:intergenic 20.0%
!! ATGTTAAGATAGAGAAAATA+AGG + chr4_2:68861878-68861897 Msa0618070:CDS 20.0%
!! TGTTAAGATAGAGAAAATAA+GGG + chr4_2:68861879-68861898 Msa0618070:CDS 20.0%
!!! AAATATGTAAAAACTTGTTG+AGG - chr4_2:68862208-68862227 None:intergenic 20.0%
!! TATGTAATAGTATTGTTGAA+TGG + chr4_2:68862249-68862268 Msa0618070:three_prime_UTR 20.0%
!!! TAAATATTGTTTTGAAAGCT+TGG + chr4_2:68862286-68862305 Msa0618070:three_prime_UTR 20.0%
! AAAGCAGTAAATATTAGAGA+TGG + chr4_2:68861333-68861352 Msa0618070:exon 25.0%
!! TTTTACATTATTGTTGGAGT+TGG - chr4_2:68861419-68861438 None:intergenic 25.0%
! GATTAAATTTGTGAAATCAG+TGG - chr4_2:68861501-68861520 None:intergenic 25.0%
!!! TTGTTACTTGTTTGTTTTGA+AGG + chr4_2:68861591-68861610 Msa0618070:intron 25.0%
!!! TAGAAAAGTACTCTTGTTAA+TGG - chr4_2:68861629-68861648 None:intergenic 25.0%
! GACATTATTCAATAAGCTAA+TGG - chr4_2:68861728-68861747 None:intergenic 25.0%
! GAATAATGTCTATGATAACA+AGG + chr4_2:68861738-68861757 Msa0618070:CDS 25.0%
! TATAGAAAAACACAAAACCA+AGG + chr4_2:68861793-68861812 Msa0618070:intron 25.0%
! GTTAAGATAGAGAAAATAAG+GGG + chr4_2:68861880-68861899 Msa0618070:CDS 25.0%
!!! ATGTGAAAATGGATTTTCTA+TGG + chr4_2:68862011-68862030 Msa0618070:CDS 25.0%
! TTCTCATCCTAATTTATGTT+TGG + chr4_2:68862323-68862342 Msa0618070:three_prime_UTR 25.0%
! AGTGAAACCAAACATAAATT+AGG - chr4_2:68862333-68862352 None:intergenic 25.0%
! TCACTTAAGATGTAATCAAT+TGG + chr4_2:68862348-68862367 Msa0618070:three_prime_UTR 25.0%
!! TGAGTGTAAAAATCACATTT+TGG - chr4_2:68862447-68862466 None:intergenic 25.0%
! AAAGCAGTAAATATTAGAGA+TGG + chr4_2:68861333-68861352 Msa0618070:exon 25.0%
!! TTTTACATTATTGTTGGAGT+TGG - chr4_2:68861419-68861438 None:intergenic 25.0%
! GATTAAATTTGTGAAATCAG+TGG - chr4_2:68861501-68861520 None:intergenic 25.0%
!!! TTGTTACTTGTTTGTTTTGA+AGG + chr4_2:68861591-68861610 Msa0618070:intron 25.0%
!!! TAGAAAAGTACTCTTGTTAA+TGG - chr4_2:68861629-68861648 None:intergenic 25.0%
! GACATTATTCAATAAGCTAA+TGG - chr4_2:68861728-68861747 None:intergenic 25.0%
! GAATAATGTCTATGATAACA+AGG + chr4_2:68861738-68861757 Msa0618070:CDS 25.0%
! TATAGAAAAACACAAAACCA+AGG + chr4_2:68861793-68861812 Msa0618070:intron 25.0%
! GTTAAGATAGAGAAAATAAG+GGG + chr4_2:68861880-68861899 Msa0618070:CDS 25.0%
!!! ATGTGAAAATGGATTTTCTA+TGG + chr4_2:68862011-68862030 Msa0618070:CDS 25.0%
! TTCTCATCCTAATTTATGTT+TGG + chr4_2:68862323-68862342 Msa0618070:three_prime_UTR 25.0%
! AGTGAAACCAAACATAAATT+AGG - chr4_2:68862333-68862352 None:intergenic 25.0%
! TCACTTAAGATGTAATCAAT+TGG + chr4_2:68862348-68862367 Msa0618070:three_prime_UTR 25.0%
!! TGAGTGTAAAAATCACATTT+TGG - chr4_2:68862447-68862466 None:intergenic 25.0%
! AATATTAGAGATGGCTTGTA+AGG + chr4_2:68861342-68861361 Msa0618070:exon 30.0%
CTTGTTAATGGAATTTCTGT+TGG - chr4_2:68861617-68861636 None:intergenic 30.0%
!! TCTTCAAAAGCCTCTAAAAT+TGG - chr4_2:68861958-68861977 None:intergenic 30.0%
TTCTATGGAAGCTATTATTG+TGG + chr4_2:68862026-68862045 Msa0618070:CDS 30.0%
!!! TCAATTGGTTTTGACATGTT+TGG + chr4_2:68862363-68862382 Msa0618070:three_prime_UTR 30.0%
GACATGTTTGGATGTTTATA+CGG + chr4_2:68862375-68862394 Msa0618070:three_prime_UTR 30.0%
TATTATCCTCTTGTGATTTG+TGG - chr4_2:68861313-68861332 None:intergenic 30.0%
! AATATTAGAGATGGCTTGTA+AGG + chr4_2:68861342-68861361 Msa0618070:exon 30.0%
CTTGTTAATGGAATTTCTGT+TGG - chr4_2:68861617-68861636 None:intergenic 30.0%
!! TCTTCAAAAGCCTCTAAAAT+TGG - chr4_2:68861958-68861977 None:intergenic 30.0%
TTCTATGGAAGCTATTATTG+TGG + chr4_2:68862026-68862045 Msa0618070:CDS 30.0%
!!! TCAATTGGTTTTGACATGTT+TGG + chr4_2:68862363-68862382 Msa0618070:three_prime_UTR 30.0%
GACATGTTTGGATGTTTATA+CGG + chr4_2:68862375-68862394 Msa0618070:three_prime_UTR 30.0%
!! CATTATTGTTGGAGTTGGTA+AGG - chr4_2:68861414-68861433 None:intergenic 35.0%
AAGATAGAGAAAATAAGGGG+AGG + chr4_2:68861883-68861902 Msa0618070:CDS 35.0%
! AATAAGGGGAGGAACTTTTA+TGG + chr4_2:68861894-68861913 Msa0618070:CDS 35.0%
!!! CAAGTTGGTTCCAATTTTAG+AGG + chr4_2:68861945-68861964 Msa0618070:CDS 35.0%
GCAAGAGTTTCATGTGAAAA+TGG + chr4_2:68862000-68862019 Msa0618070:CDS 35.0%
GAGGATGAAAATCTTGATGT+TGG + chr4_2:68862051-68862070 Msa0618070:CDS 35.0%
! GAAGCACTTCTAAAAGCTAT+TGG + chr4_2:68862084-68862103 Msa0618070:CDS 35.0%
AGTATTGTTGAATGGTGACA+TGG + chr4_2:68862257-68862276 Msa0618070:three_prime_UTR 35.0%
GTATTGTTGAATGGTGACAT+GGG + chr4_2:68862258-68862277 Msa0618070:three_prime_UTR 35.0%
GGATTAGAAGCTACAAATCA+TGG - chr4_2:68862426-68862445 None:intergenic 35.0%
!! CATTATTGTTGGAGTTGGTA+AGG - chr4_2:68861414-68861433 None:intergenic 35.0%
AAGATAGAGAAAATAAGGGG+AGG + chr4_2:68861883-68861902 Msa0618070:CDS 35.0%
! AATAAGGGGAGGAACTTTTA+TGG + chr4_2:68861894-68861913 Msa0618070:CDS 35.0%
!!! CAAGTTGGTTCCAATTTTAG+AGG + chr4_2:68861945-68861964 Msa0618070:CDS 35.0%
GCAAGAGTTTCATGTGAAAA+TGG + chr4_2:68862000-68862019 Msa0618070:CDS 35.0%
GAGGATGAAAATCTTGATGT+TGG + chr4_2:68862051-68862070 Msa0618070:CDS 35.0%
! GAAGCACTTCTAAAAGCTAT+TGG + chr4_2:68862084-68862103 Msa0618070:CDS 35.0%
AGTATTGTTGAATGGTGACA+TGG + chr4_2:68862257-68862276 Msa0618070:three_prime_UTR 35.0%
GTATTGTTGAATGGTGACAT+GGG + chr4_2:68862258-68862277 Msa0618070:three_prime_UTR 35.0%
GGATTAGAAGCTACAAATCA+TGG - chr4_2:68862426-68862445 None:intergenic 35.0%
! GGGAGGAACTTTTATGGTAA+AGG + chr4_2:68861900-68861919 Msa0618070:CDS 40.0%
GTAAAGGTCACATGTGAGAA+AGG + chr4_2:68861916-68861935 Msa0618070:CDS 40.0%
AGAGATGTGTGTGAATGTTG+AGG + chr4_2:68861975-68861994 Msa0618070:CDS 40.0%
AAAGCTATTGGAAAGCAGAG+TGG + chr4_2:68862096-68862115 Msa0618070:CDS 40.0%
AAGCTACAAATCATGGCCAA+AGG - chr4_2:68862419-68862438 None:intergenic 40.0%
! GGGAGGAACTTTTATGGTAA+AGG + chr4_2:68861900-68861919 Msa0618070:CDS 40.0%
GTAAAGGTCACATGTGAGAA+AGG + chr4_2:68861916-68861935 Msa0618070:CDS 40.0%
AGAGATGTGTGTGAATGTTG+AGG + chr4_2:68861975-68861994 Msa0618070:CDS 40.0%
AAAGCTATTGGAAAGCAGAG+TGG + chr4_2:68862096-68862115 Msa0618070:CDS 40.0%
AAGCTACAAATCATGGCCAA+AGG - chr4_2:68862419-68862438 None:intergenic 40.0%
! TGGCTTGTAAGGTGCAGAAA+AGG + chr4_2:68861353-68861372 Msa0618070:CDS 45.0%
GGCTTGTAAGGTGCAGAAAA+GGG + chr4_2:68861354-68861373 Msa0618070:CDS 45.0%
!! GCTAATGGACTCTCTTCTTG+CGG - chr4_2:68861713-68861732 None:intergenic 45.0%
AAGGTCACATGTGAGAAAGG+AGG + chr4_2:68861919-68861938 Msa0618070:CDS 45.0%
TGAGAAAGGAGGTGACAAGT+TGG + chr4_2:68861930-68861949 Msa0618070:CDS 45.0%
GGAAGCTATTATTGTGGCTG+AGG + chr4_2:68862032-68862051 Msa0618070:CDS 45.0%
TGGAAAGCAGAGTGGTGAAA+AGG + chr4_2:68862104-68862123 Msa0618070:CDS 45.0%
GGAAAGCAGAGTGGTGAAAA+GGG + chr4_2:68862105-68862124 Msa0618070:CDS 45.0%
! TGGCTTGTAAGGTGCAGAAA+AGG + chr4_2:68861353-68861372 Msa0618070:CDS 45.0%
GGCTTGTAAGGTGCAGAAAA+GGG + chr4_2:68861354-68861373 Msa0618070:CDS 45.0%
!! GCTAATGGACTCTCTTCTTG+CGG - chr4_2:68861713-68861732 None:intergenic 45.0%
AAGGTCACATGTGAGAAAGG+AGG + chr4_2:68861919-68861938 Msa0618070:CDS 45.0%
TGAGAAAGGAGGTGACAAGT+TGG + chr4_2:68861930-68861949 Msa0618070:CDS 45.0%
GGAAGCTATTATTGTGGCTG+AGG + chr4_2:68862032-68862051 Msa0618070:CDS 45.0%
TGGAAAGCAGAGTGGTGAAA+AGG + chr4_2:68862104-68862123 Msa0618070:CDS 45.0%
GGAAAGCAGAGTGGTGAAAA+GGG + chr4_2:68862105-68862124 Msa0618070:CDS 45.0%
!!! TTTTAGTAATATTTATATAT+AGG - chr4_2:68861819-68861838 None:intergenic 5.0%
!!! TTTTAGTAATATTTATATAT+AGG - chr4_2:68861819-68861838 None:intergenic 5.0%
ACTCTCTTCTTGCGGCTATC+AGG - chr4_2:68861705-68861724 None:intergenic 50.0%
ACTCTCTTCTTGCGGCTATC+AGG - chr4_2:68861705-68861724 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 68861311 68862480 68861311 ID=Msa0618070;Name=Msa0618070
chr4_2 mRNA 68861311 68862480 68861311 ID=Msa0618070-mRNA-1;Parent=Msa0618070;Name=Msa0618070-mRNA-1;_AED=0.13;_eAED=0.13;_QI=41|1|1|1|1|1|3|319|170
chr4_2 exon 68861311 68861432 68861311 ID=Msa0618070-mRNA-1:exon:19814;Parent=Msa0618070-mRNA-1
chr4_2 exon 68861613 68861759 68861613 ID=Msa0618070-mRNA-1:exon:19815;Parent=Msa0618070-mRNA-1
chr4_2 exon 68861877 68862480 68861877 ID=Msa0618070-mRNA-1:exon:19816;Parent=Msa0618070-mRNA-1
chr4_2 five_prime_UTR 68861311 68861351 68861311 ID=Msa0618070-mRNA-1:five_prime_utr;Parent=Msa0618070-mRNA-1
chr4_2 CDS 68861352 68861432 68861352 ID=Msa0618070-mRNA-1:cds;Parent=Msa0618070-mRNA-1
chr4_2 CDS 68861613 68861759 68861613 ID=Msa0618070-mRNA-1:cds;Parent=Msa0618070-mRNA-1
chr4_2 CDS 68861877 68862161 68861877 ID=Msa0618070-mRNA-1:cds;Parent=Msa0618070-mRNA-1
chr4_2 three_prime_UTR 68862162 68862480 68862162 ID=Msa0618070-mRNA-1:three_prime_utr;Parent=Msa0618070-mRNA-1
Gene Sequence

>Msa0618070

ATGGCTTGTAAGGTGCAGAAAAGGGTATCACTTCGCAGAAGACTTCACATTCTGCGAGTCCTTACCAACTCCAACAATAATGCCAACAGAAATTCCATTAACAAGAGTACTTTTCTACACATTCATAAGCTAAAGCTTGCACTAGAAACTCTCAAAAGAGAGTATGAAAACCTGATAGCCGCAAGAAGAGAGTCCATTAGCTTATTGAATAATGTCTATGATAACAAGGATGTTAAGATAGAGAAAATAAGGGGAGGAACTTTTATGGTAAAGGTCACATGTGAGAAAGGAGGTGACAAGTTGGTTCCAATTTTAGAGGCTTTTGAAGAGATGTGTGTGAATGTTGAGGAAGCAAGAGTTTCATGTGAAAATGGATTTTCTATGGAAGCTATTATTGTGGCTGAGGATGAAAATCTTGATGTTGGAGATGTTAATGAAGCACTTCTAAAAGCTATTGGAAAGCAGAGTGGTGAAAAGGGTTCAAAAGAGCTTGACAACTGTAGTAATTTGTGA
Protein sequence

>Msa0618070

MACKVQKRVSLRRRLHILRVLTNSNNNANRNSINKSTFLHIHKLKLALETLKREYENLIAARRESISLLNNVYDNKDVKIEKIRGGTFMVKVTCEKGGDKLVPILEAFEEMCVNVEEARVSCENGFSMEAIIVAEDENLDVGDVNEALLKAIGKQSGEKGSKELDNCSNL*