AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280007412.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280007412.01.T01 MTR_2g024380 65.134 261 46 2 3 218 186 446 3.49e-112 329
MsG0280007412.01.T01 MTR_2g024350 72.727 176 42 1 49 218 28 203 8.24e-87 256
MsG0280007412.01.T01 MTR_7g104980 52.482 141 67 0 50 190 18 158 2.85e-44 147
MsG0280007412.01.T01 MTR_6g053200 35.514 214 117 5 12 218 313 512 5.24e-31 119
MsG0280007412.01.T01 MTR_8g067635 36.782 174 83 5 13 161 333 504 7.81e-23 96.3
MsG0280007412.01.T01 MTR_8g067650 35.028 177 87 6 2 152 312 486 5.80e-20 88.2
MsG0280007412.01.T01 MTR_4g052030 87.805 41 5 0 47 87 11 51 2.29e-19 78.6
MsG0280007412.01.T01 MTR_8g069935 51.429 70 33 1 49 118 351 419 5.31e-15 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 50 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCTTAAATGCTAGAAATT+TGG 0.075722 2:+15052021 MsG0280007412.01.T01:CDS
ACCCAAATTTCTAGCATTTA+AGG 0.127042 2:-15052023 None:intergenic
CTCTCTAATAGTTCTATTTC+TGG 0.157050 2:-15051968 None:intergenic
ATGAATCCAGTTTCAGAATA+AGG 0.224140 2:-15052123 None:intergenic
TCCTTAAATGCTAGAAATTT+GGG 0.273355 2:+15052022 MsG0280007412.01.T01:CDS
TATTCTGAAACTGGATTCAT+TGG 0.302973 2:+15052126 MsG0280007412.01.T01:CDS
ATAGTTCTATTTCTGGATAA+AGG 0.309444 2:-15051961 None:intergenic
CACCCGTAACATTGCTACTT+TGG 0.313841 2:-15052080 None:intergenic
AACCTCCCTTATTCTGAAAC+TGG 0.323380 2:+15052117 MsG0280007412.01.T01:CDS
CACTATGCGGATCAAGAAAA+AGG 0.357686 2:+15051113 MsG0280007412.01.T01:CDS
ACCCGTAACATTGCTACTTT+GGG 0.360041 2:-15052079 None:intergenic
TTACACTCTGCGGAAGAAAC+TGG 0.365125 2:+15051833 MsG0280007412.01.T01:CDS
AAATCCAGGTTCCCCTAGTA+TGG 0.366946 2:+15051874 MsG0280007412.01.T01:CDS
ATCTGCAACATCACCATACT+AGG 0.367397 2:-15051887 None:intergenic
ATCAATGCATGCAACATGTT+TGG 0.367904 2:-15051044 None:intergenic
TCAATGCATGCAACATGTTT+GGG 0.386538 2:-15051043 None:intergenic
TTTAATAAGAATGTTGTTGT+TGG 0.409716 2:+15051779 MsG0280007412.01.T01:CDS
CAGCGCAAGTCACTGGAGAC+TGG 0.413600 2:+15051809 MsG0280007412.01.T01:CDS
TTGATTGATCAGCGAGAACC+TGG 0.424637 2:-15051934 None:intergenic
ACAACATTCTTATTAAATGT+TGG 0.443200 2:-15051773 None:intergenic
TGAATCCAGTTTCAGAATAA+GGG 0.447038 2:-15052122 None:intergenic
AGCCCAAAGTAGCAATGTTA+CGG 0.449510 2:+15052077 MsG0280007412.01.T01:CDS
GCCCAAAGTAGCAATGTTAC+GGG 0.463271 2:+15052078 MsG0280007412.01.T01:CDS
TACATCCCAGCGCAAGTCAC+TGG 0.469837 2:+15051802 MsG0280007412.01.T01:CDS
ACCTGGGTATTGCTGCTCTC+CGG 0.486470 2:-15051917 None:intergenic
TTACCCTCTGTGGAAGAAGT+TGG 0.488537 2:+15051995 MsG0280007412.01.T01:CDS
CAGTCTCCAGTGACTTGCGC+TGG 0.491501 2:-15051808 None:intergenic
ATCACCATACTAGGGGAACC+TGG 0.508434 2:-15051878 None:intergenic
ACTTATATTGTAACATATGA+AGG 0.520110 2:+15051731 MsG0280007412.01.T01:CDS
GATGTTGCAGATCGATCATC+CGG 0.525110 2:+15051898 MsG0280007412.01.T01:CDS
CGCATAGTGCAACCGATGGA+TGG 0.529058 2:-15051099 None:intergenic
AGTCTCCAGTGACTTGCGCT+GGG 0.530524 2:-15051807 None:intergenic
TCTACAAACATCACAAATCC+AGG 0.538062 2:+15051860 MsG0280007412.01.T01:CDS
AGCGCAAGTCACTGGAGACT+GGG 0.541737 2:+15051810 MsG0280007412.01.T01:CDS
TATAATTTCCCAATGCACGC+TGG 0.543748 2:+15050977 None:intergenic
AGATTGTCCAGCAAGAAGAA+AGG 0.576880 2:+15051682 MsG0280007412.01.T01:CDS
TCTGCAACATCACCATACTA+GGG 0.581668 2:-15051886 None:intergenic
TCCGGAGAGCAGCAATACCC+AGG 0.606173 2:+15051916 MsG0280007412.01.T01:CDS
ATCCAGTTTCAGAATAAGGG+AGG 0.616537 2:-15052119 None:intergenic
GCTATTACAAATGTAGCACT+TGG 0.623098 2:+15051657 MsG0280007412.01.T01:CDS
GATCCGCATAGTGCAACCGA+TGG 0.649098 2:-15051103 None:intergenic
GATCCAACTTCTTCCACAGA+GGG 0.650056 2:-15051998 None:intergenic
CATCCATCGGTTGCACTATG+CGG 0.659476 2:+15051100 MsG0280007412.01.T01:CDS
AGAGAGTCACTTACCCTCTG+TGG 0.665669 2:+15051985 MsG0280007412.01.T01:CDS
TGATTGATCAGCGAGAACCT+GGG 0.667246 2:-15051933 None:intergenic
GTATGCACGTTCAAAATGAG+TGG 0.675266 2:-15051074 None:intergenic
ACGTGCATACAACCATCCAT+CGG 0.691580 2:+15051087 MsG0280007412.01.T01:CDS
CTGCAACATCACCATACTAG+GGG 0.719168 2:-15051885 None:intergenic
GGAGACTGGGTTACACTCTG+CGG 0.721711 2:+15051823 MsG0280007412.01.T01:CDS
TGATCCAACTTCTTCCACAG+AGG 0.749435 2:-15051999 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAAATTATTGTTTATAATG+TGG - Chr2:15051430-15051449 None:intergenic 15.0%
!!! AATTTTAAAACATCAAAAAC+TGG + Chr2:15051579-15051598 MsG0280007412.01.T01:intron 15.0%
!! ACAACATTCTTATTAAATGT+TGG - Chr2:15051776-15051795 None:intergenic 20.0%
!! ACTTATATTGTAACATATGA+AGG + Chr2:15051731-15051750 MsG0280007412.01.T01:CDS 20.0%
!! ATTTCTTTCAACATCATTTA+TGG - Chr2:15051617-15051636 None:intergenic 20.0%
!! TAGAAAACATAATAACCAAA+TGG + Chr2:15051260-15051279 MsG0280007412.01.T01:intron 20.0%
!! TTTAATAAGAATGTTGTTGT+TGG + Chr2:15051779-15051798 MsG0280007412.01.T01:CDS 20.0%
!!! TGTTTTCTATAAGAAAAGAA+AGG - Chr2:15051249-15051268 None:intergenic 20.0%
!!! TTTTGAATATTTGTAAACCT+CGG - Chr2:15051378-15051397 None:intergenic 20.0%
! AAATCAATAAATGATGTTGC+AGG + Chr2:15051633-15051652 MsG0280007412.01.T01:intron 25.0%
! ATCCTTAAATGCTAGAAATT+TGG + Chr2:15052021-15052040 MsG0280007412.01.T01:CDS 25.0%
! TCCTTAAATGCTAGAAATTT+GGG + Chr2:15052022-15052041 MsG0280007412.01.T01:CDS 25.0%
!!! ATAGTTCTATTTCTGGATAA+AGG - Chr2:15051964-15051983 None:intergenic 25.0%
ACATAATAACCAAATGGCAT+TGG + Chr2:15051266-15051285 MsG0280007412.01.T01:intron 30.0%
ATGAATCCAGTTTCAGAATA+AGG - Chr2:15052126-15052145 None:intergenic 30.0%
TGAATCCAGTTTCAGAATAA+GGG - Chr2:15052125-15052144 None:intergenic 30.0%
! CTCTCTAATAGTTCTATTTC+TGG - Chr2:15051971-15051990 None:intergenic 30.0%
! TACAATTATATGCACTGACA+AGG - Chr2:15051512-15051531 None:intergenic 30.0%
!! ACCCAAATTTCTAGCATTTA+AGG - Chr2:15052026-15052045 None:intergenic 30.0%
!! TATTCTGAAACTGGATTCAT+TGG + Chr2:15052126-15052145 MsG0280007412.01.T01:CDS 30.0%
ATATTTGTAAACCTCGGATG+TGG - Chr2:15051372-15051391 None:intergenic 35.0%
ATCAATGCATGCAACATGTT+TGG - Chr2:15051047-15051066 None:intergenic 35.0%
ATGGGCAAAAACCCATTAAA+GGG + Chr2:15051343-15051362 MsG0280007412.01.T01:intron 35.0%
GCTATTACAAATGTAGCACT+TGG + Chr2:15051657-15051676 MsG0280007412.01.T01:CDS 35.0%
TATGGGCAAAAACCCATTAA+AGG + Chr2:15051342-15051361 MsG0280007412.01.T01:intron 35.0%
TCAATGCATGCAACATGTTT+GGG - Chr2:15051046-15051065 None:intergenic 35.0%
TCTACAAACATCACAAATCC+AGG + Chr2:15051860-15051879 MsG0280007412.01.T01:CDS 35.0%
! CATCACTGTTTAAAACACGA+GGG - Chr2:15051475-15051494 None:intergenic 35.0%
! TTTTCAACCTTTCTTCTTGC+TGG - Chr2:15051692-15051711 None:intergenic 35.0%
AGATTGTCCAGCAAGAAGAA+AGG + Chr2:15051682-15051701 MsG0280007412.01.T01:CDS 40.0%
AGCCCAAAGTAGCAATGTTA+CGG + Chr2:15052077-15052096 MsG0280007412.01.T01:CDS 40.0%
ATCCAGTTTCAGAATAAGGG+AGG - Chr2:15052122-15052141 None:intergenic 40.0%
ATCTGCAACATCACCATACT+AGG - Chr2:15051890-15051909 None:intergenic 40.0%
CACTATGCGGATCAAGAAAA+AGG + Chr2:15051113-15051132 MsG0280007412.01.T01:CDS 40.0%
GTATGCACGTTCAAAATGAG+TGG - Chr2:15051077-15051096 None:intergenic 40.0%
TATAGCACACCAATGCCATT+TGG - Chr2:15051278-15051297 None:intergenic 40.0%
TCTGCAACATCACCATACTA+GGG - Chr2:15051889-15051908 None:intergenic 40.0%
! CCATCACTGTTTAAAACACG+AGG - Chr2:15051476-15051495 None:intergenic 40.0%
!! AACCTCCCTTATTCTGAAAC+TGG + Chr2:15052117-15052136 MsG0280007412.01.T01:CDS 40.0%
!! ACCCGTAACATTGCTACTTT+GGG - Chr2:15052082-15052101 None:intergenic 40.0%
!! CCTCGTGTTTTAAACAGTGA+TGG + Chr2:15051473-15051492 MsG0280007412.01.T01:intron 40.0%
AAATCCAGGTTCCCCTAGTA+TGG + Chr2:15051874-15051893 MsG0280007412.01.T01:CDS 45.0%
ACGTGCATACAACCATCCAT+CGG + Chr2:15051087-15051106 MsG0280007412.01.T01:CDS 45.0%
CTGCAACATCACCATACTAG+GGG - Chr2:15051888-15051907 None:intergenic 45.0%
GATCCAACTTCTTCCACAGA+GGG - Chr2:15052001-15052020 None:intergenic 45.0%
GATGTTGCAGATCGATCATC+CGG + Chr2:15051898-15051917 MsG0280007412.01.T01:CDS 45.0%
GCCCAAAGTAGCAATGTTAC+GGG + Chr2:15052078-15052097 MsG0280007412.01.T01:CDS 45.0%
GGATGTGGAGACCCTTTAAT+GGG - Chr2:15051357-15051376 None:intergenic 45.0%
TGATCCAACTTCTTCCACAG+AGG - Chr2:15052002-15052021 None:intergenic 45.0%
TGATTGATCAGCGAGAACCT+GGG - Chr2:15051936-15051955 None:intergenic 45.0%
TTACACTCTGCGGAAGAAAC+TGG + Chr2:15051833-15051852 MsG0280007412.01.T01:CDS 45.0%
TTACCCTCTGTGGAAGAAGT+TGG + Chr2:15051995-15052014 MsG0280007412.01.T01:CDS 45.0%
TTGATTGATCAGCGAGAACC+TGG - Chr2:15051937-15051956 None:intergenic 45.0%
! CACCCGTAACATTGCTACTT+TGG - Chr2:15052083-15052102 None:intergenic 45.0%
!! AGGGTGCGAGTGTTTGTTTT+AGG - Chr2:15051456-15051475 None:intergenic 45.0%
!! GGCATTGGTGTGCTATATGA+GGG + Chr2:15051281-15051300 MsG0280007412.01.T01:intron 45.0%
!! TGGCATTGGTGTGCTATATG+AGG + Chr2:15051280-15051299 MsG0280007412.01.T01:intron 45.0%
AGAGAGTCACTTACCCTCTG+TGG + Chr2:15051985-15052004 MsG0280007412.01.T01:CDS 50.0%
ATCACCATACTAGGGGAACC+TGG - Chr2:15051881-15051900 None:intergenic 50.0%
ATGAGCTTCCAAAAGACCCG+TGG + Chr2:15051307-15051326 MsG0280007412.01.T01:intron 50.0%
CATATTTCCTCCATGCCCAC+GGG - Chr2:15051326-15051345 None:intergenic 50.0%
CCATATTTCCTCCATGCCCA+CGG - Chr2:15051327-15051346 None:intergenic 50.0%
CGGATGTGGAGACCCTTTAA+TGG - Chr2:15051358-15051377 None:intergenic 50.0%
CGTGGGCATGGAGGAAATAT+GGG + Chr2:15051325-15051344 MsG0280007412.01.T01:intron 50.0%
TGAGCTTCCAAAAGACCCGT+GGG + Chr2:15051308-15051327 MsG0280007412.01.T01:intron 50.0%
TTAAAGGGTCTCCACATCCG+AGG + Chr2:15051358-15051377 MsG0280007412.01.T01:intron 50.0%
! CATCCATCGGTTGCACTATG+CGG + Chr2:15051100-15051119 MsG0280007412.01.T01:CDS 50.0%
AGCGCAAGTCACTGGAGACT+GGG + Chr2:15051810-15051829 MsG0280007412.01.T01:CDS 55.0%
CCGTGGGCATGGAGGAAATA+TGG + Chr2:15051324-15051343 MsG0280007412.01.T01:intron 55.0%
CGCATAGTGCAACCGATGGA+TGG - Chr2:15051102-15051121 None:intergenic 55.0%
GATCCGCATAGTGCAACCGA+TGG - Chr2:15051106-15051125 None:intergenic 55.0%
GGAGACTGGGTTACACTCTG+CGG + Chr2:15051823-15051842 MsG0280007412.01.T01:CDS 55.0%
TACATCCCAGCGCAAGTCAC+TGG + Chr2:15051802-15051821 MsG0280007412.01.T01:CDS 55.0%
TTCCAAAAGACCCGTGGGCA+TGG + Chr2:15051313-15051332 MsG0280007412.01.T01:intron 55.0%
! ACCTGGGTATTGCTGCTCTC+CGG - Chr2:15051920-15051939 None:intergenic 55.0%
! AGTCTCCAGTGACTTGCGCT+GGG - Chr2:15051810-15051829 None:intergenic 55.0%
CAAAAGACCCGTGGGCATGG+AGG + Chr2:15051316-15051335 MsG0280007412.01.T01:intron 60.0%
CAGCGCAAGTCACTGGAGAC+TGG + Chr2:15051809-15051828 MsG0280007412.01.T01:CDS 60.0%
TCCGGAGAGCAGCAATACCC+AGG + Chr2:15051916-15051935 MsG0280007412.01.T01:CDS 60.0%
! CAGTCTCCAGTGACTTGCGC+TGG - Chr2:15051811-15051830 None:intergenic 60.0%
! CTCCATGCCCACGGGTCTTT+TGG - Chr2:15051318-15051337 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 15050989 15052177 15050989 ID=MsG0280007412.01;Name=MsG0280007412.01
Chr2 mRNA 15050989 15052177 15050989 ID=MsG0280007412.01.T01;Parent=MsG0280007412.01;Name=MsG0280007412.01.T01;_AED=0.51;_eAED=0.53;_QI=0|0|0|0.5|1|1|2|0|222
Chr2 exon 15050989 15051134 15050989 ID=MsG0280007412.01.T01:exon:3217;Parent=MsG0280007412.01.T01
Chr2 exon 15051655 15052177 15051655 ID=MsG0280007412.01.T01:exon:3218;Parent=MsG0280007412.01.T01
Chr2 CDS 15050989 15051134 15050989 ID=MsG0280007412.01.T01:cds;Parent=MsG0280007412.01.T01
Chr2 CDS 15051655 15052177 15051655 ID=MsG0280007412.01.T01:cds;Parent=MsG0280007412.01.T01
Gene Sequence

>MsG0280007412.01.T01

ATGCACGCTGGACAAAAACAGATTCAACAAAACATCAACAATCAAGTGTCTGTTCCCAAACATGTTGCATGCATTGATATCACAACCACTCATTTTGAACGTGCATACAACCATCCATCGGTTGCACTATGCGGATCAAGAAAAAGGAGCTATTACAAATGTAGCACTTGGTCAGATTGTCCAGCAAGAAGAAAGGTTGAAAAATGCAAAACTCAAGAGAACACTTATATTGTAACATATGAAGGAGAGCACAATCATGCAAAGCCAACATTTAATAAGAATGTTGTTGTTGGTACATCCCAGCGCAAGTCACTGGAGACTGGGTTACACTCTGCGGAAGAAACTGGATCATCTACAAACATCACAAATCCAGGTTCCCCTAGTATGGTGATGTTGCAGATCGATCATCCGGAGAGCAGCAATACCCAGGTTCTCGCTGATCAATCAAAAATCCTTTATCCAGAAATAGAACTATTAGAGAGTCACTTACCCTCTGTGGAAGAAGTTGGATCATCCTTAAATGCTAGAAATTTGGGTTCACATAACAAAATGATTATGCAATTTGATGAGCCCAAAGTAGCAATGTTACGGGTGTTGTCGATGACTCAAACCTCCCTTATTCTGAAACTGGATTCATTGGAAGCTTTGATGATAATGATGACATTTTGA
Protein sequence

>MsG0280007412.01.T01

MHAGQKQIQQNINNQVSVPKHVACIDITTTHFERAYNHPSVALCGSRKRSYYKCSTWSDCPARRKVEKCKTQENTYIVTYEGEHNHAKPTFNKNVVVGTSQRKSLETGLHSAEETGSSTNITNPGSPSMVMLQIDHPESSNTQVLADQSKILYPEIELLESHLPSVEEVGSSLNARNLGSHNKMIMQFDEPKVAMLRVLSMTQTSLILKLDSLEALMIMMTF*