AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180002454.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180002454.01.T02 MTR_1g050700 87.805 123 11 3 1 123 1 119 3.37e-62 189
MsG0180002454.01.T01 MTR_1g050700 83.051 118 12 2 1 111 3 119 3.24e-56 174
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180002454.01.T02 AT4G40045 34.959 123 72 4 3 124 1 116 1.92e-14 67.4
MsG0180002454.01.T01 AT4G40045 34.426 122 64 5 1 112 1 116 1.46e-11 59.7

Find 35 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCTTGCTCTTGGATTAAC+TGG 0.244904 1:-38593629 MsG0180002454.01.T01:CDS
TACTCCAATTCAAACCAAAA+AGG 0.278323 1:+38593678 None:intergenic
AGTAGCGATATGAGCATGTT+AGG 0.301511 1:-38593932 None:intergenic
ACAACAACAATAACAGTAAT+GGG 0.303617 1:-38593781 MsG0180002454.01.T01:CDS
CAGCCACCACCCTCTTCTTC+TGG 0.310803 1:-38593728 MsG0180002454.01.T01:intron
ATTACTGTTATTGTTGTTGT+TGG 0.325641 1:+38593784 None:intergenic
GGCAACTCTTGTTTATCTCT+TGG 0.339757 1:-38593574 MsG0180002454.01.T01:CDS
TCATGTTCATATATATCTAA+TGG 0.359226 1:-38593443 MsG0180002454.01.T01:CDS
TATCAGGATCTCGATCTAAA+AGG 0.368319 1:+38593654 None:intergenic
CCAAGAGCAAGGATATTATC+AGG 0.403482 1:+38593638 None:intergenic
TGATGATGAGAGTATGAAAT+TGG 0.419509 1:+38593904 None:intergenic
CCTGATAATATCCTTGCTCT+TGG 0.439533 1:-38593638 MsG0180002454.01.T01:CDS
TAGCTTTAACATAATATAAA+CGG 0.444429 1:+38593393 None:intergenic
AACAACAACAATAACAGTAA+TGG 0.472073 1:-38593782 MsG0180002454.01.T01:CDS
AGAATTGAAGGTGATGGAAA+TGG 0.474902 1:+38593838 None:intergenic
CAGCAATAAAAGAGTATTTG+AGG 0.478257 1:+38593535 None:intergenic
AGCAATAAAAGAGTATTTGA+GGG 0.510084 1:+38593536 None:intergenic
GCAGACAATGGAAGTGGGCG+TGG 0.515571 1:+38593809 None:intergenic
GTAGCGATATGAGCATGTTA+GGG 0.530080 1:-38593931 None:intergenic
TGTGGTTTGTATTGAAGAGA+AGG 0.538229 1:+38593872 None:intergenic
TTGTTCTTGTCCAGAAGAAG+AGG 0.549136 1:+38593718 None:intergenic
GATTAACTGGTATTCTCACA+TGG 0.554210 1:-38593616 MsG0180002454.01.T01:CDS
TTGGATGCAGACAATGGAAG+TGG 0.569995 1:+38593803 None:intergenic
GTGGTTTGTATTGAAGAGAA+GGG 0.591887 1:+38593873 None:intergenic
CAGTAATGGGGTAAAAGAAG+AGG 0.595417 1:-38593768 MsG0180002454.01.T01:CDS
TGTCCAGAAGAAGAGGGTGG+TGG 0.605698 1:+38593725 None:intergenic
TGTTCTTGTCCAGAAGAAGA+GGG 0.609557 1:+38593719 None:intergenic
TACCAGTTAATCCAAGAGCA+AGG 0.615971 1:+38593627 None:intergenic
GGGCAAGTGTTCAAGTTCTG+TGG 0.624018 1:-38593595 MsG0180002454.01.T01:CDS
TTGTTGTTGGATGCAGACAA+TGG 0.657108 1:+38593797 None:intergenic
ATTAACTGGTATTCTCACAT+GGG 0.657152 1:-38593615 MsG0180002454.01.T01:CDS
GAAATGGTAGAAAAGTGTTG+TGG 0.660859 1:+38593854 None:intergenic
CAACAACAATAACAGTAATG+GGG 0.675070 1:-38593780 MsG0180002454.01.T01:CDS
TCTTGTCCAGAAGAAGAGGG+TGG 0.700548 1:+38593722 None:intergenic
TGGATGCAGACAATGGAAGT+GGG 0.712085 1:+38593804 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGCTTTAACATAATATAAA+CGG + Chr1:38593903-38593922 None:intergenic 15.0%
!! TCATGTTCATATATATCTAA+TGG - Chr1:38593850-38593869 MsG0180002454.01.T01:CDS 20.0%
! AACAACAACAATAACAGTAA+TGG - Chr1:38593511-38593530 MsG0180002454.01.T01:CDS 25.0%
! ACAACAACAATAACAGTAAT+GGG - Chr1:38593512-38593531 MsG0180002454.01.T01:CDS 25.0%
!! ATTACTGTTATTGTTGTTGT+TGG + Chr1:38593512-38593531 None:intergenic 25.0%
!!! AGCAATAAAAGAGTATTTGA+GGG + Chr1:38593760-38593779 None:intergenic 25.0%
ACTCCAATTCAAACCAAAAA+GGG + Chr1:38593617-38593636 None:intergenic 30.0%
ATTAACTGGTATTCTCACAT+GGG - Chr1:38593678-38593697 MsG0180002454.01.T01:CDS 30.0%
CAACAACAATAACAGTAATG+GGG - Chr1:38593513-38593532 MsG0180002454.01.T01:CDS 30.0%
TACTCCAATTCAAACCAAAA+AGG + Chr1:38593618-38593637 None:intergenic 30.0%
! TGATGATGAGAGTATGAAAT+TGG + Chr1:38593392-38593411 None:intergenic 30.0%
!! CAGCAATAAAAGAGTATTTG+AGG + Chr1:38593761-38593780 None:intergenic 30.0%
CTCCAATTCAAACCAAAAAG+GGG + Chr1:38593616-38593635 None:intergenic 35.0%
GATTAACTGGTATTCTCACA+TGG - Chr1:38593677-38593696 MsG0180002454.01.T01:CDS 35.0%
TATCAGGATCTCGATCTAAA+AGG + Chr1:38593642-38593661 None:intergenic 35.0%
! CAAGAAAAACTACCCCTTTT+TGG - Chr1:38593601-38593620 MsG0180002454.01.T01:CDS 35.0%
! GTGGTTTGTATTGAAGAGAA+GGG + Chr1:38593423-38593442 None:intergenic 35.0%
! TGTGGTTTGTATTGAAGAGA+AGG + Chr1:38593424-38593443 None:intergenic 35.0%
!! AGAATTGAAGGTGATGGAAA+TGG + Chr1:38593458-38593477 None:intergenic 35.0%
!! GAAATGGTAGAAAAGTGTTG+TGG + Chr1:38593442-38593461 None:intergenic 35.0%
!! TTTTCGAGAATTGAAGGTGA+TGG + Chr1:38593464-38593483 None:intergenic 35.0%
!!! TACCCCTTTTTGGTTTGAAT+TGG - Chr1:38593611-38593630 MsG0180002454.01.T01:CDS 35.0%
ATCCTTGCTCTTGGATTAAC+TGG - Chr1:38593664-38593683 MsG0180002454.01.T01:CDS 40.0%
CCAAGAGCAAGGATATTATC+AGG + Chr1:38593658-38593677 None:intergenic 40.0%
CCTGATAATATCCTTGCTCT+TGG - Chr1:38593655-38593674 MsG0180002454.01.T01:CDS 40.0%
TACCAGTTAATCCAAGAGCA+AGG + Chr1:38593669-38593688 None:intergenic 40.0%
TGTTCTTGTCCAGAAGAAGA+GGG + Chr1:38593577-38593596 None:intergenic 40.0%
TTGTTCTTGTCCAGAAGAAG+AGG + Chr1:38593578-38593597 None:intergenic 40.0%
! CAGTAATGGGGTAAAAGAAG+AGG - Chr1:38593525-38593544 MsG0180002454.01.T01:CDS 40.0%
! GGCAACTCTTGTTTATCTCT+TGG - Chr1:38593719-38593738 MsG0180002454.01.T01:intron 40.0%
! TTGTTGTTGGATGCAGACAA+TGG + Chr1:38593499-38593518 None:intergenic 40.0%
TGGATGCAGACAATGGAAGT+GGG + Chr1:38593492-38593511 None:intergenic 45.0%
TTGGATGCAGACAATGGAAG+TGG + Chr1:38593493-38593512 None:intergenic 45.0%
!! GCGTGGTTTTCGAGAATTGA+AGG + Chr1:38593470-38593489 None:intergenic 45.0%
TCTTGTCCAGAAGAAGAGGG+TGG + Chr1:38593574-38593593 None:intergenic 50.0%
! GGGCAAGTGTTCAAGTTCTG+TGG - Chr1:38593698-38593717 MsG0180002454.01.T01:CDS 50.0%
TGTCCAGAAGAAGAGGGTGG+TGG + Chr1:38593571-38593590 None:intergenic 55.0%
CAGCCACCACCCTCTTCTTC+TGG - Chr1:38593565-38593584 MsG0180002454.01.T01:CDS 60.0%
GCAGACAATGGAAGTGGGCG+TGG + Chr1:38593487-38593506 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 38593370 38593945 38593370 ID=MsG0180002454.01;Name=MsG0180002454.01
Chr1 mRNA 38593370 38593939 38593370 ID=MsG0180002454.01.T01;Parent=MsG0180002454.01;Name=MsG0180002454.01.T01;_AED=0.47;_eAED=0.60;_QI=0|0|0|1|0|0|2|0|179
Chr1 exon 38593753 38593939 38593753 ID=MsG0180002454.01.T01:exon:12785;Parent=MsG0180002454.01.T01
Chr1 exon 38593370 38593722 38593370 ID=MsG0180002454.01.T01:exon:12786;Parent=MsG0180002454.01.T01
Chr1 CDS 38593753 38593939 38593753 ID=MsG0180002454.01.T01:cds;Parent=MsG0180002454.01.T01
Chr1 CDS 38593370 38593722 38593370 ID=MsG0180002454.01.T01:cds;Parent=MsG0180002454.01.T01
Chr1 mRNA 38593370 38593945 38593370 ID=MsG0180002454.01.T02;Parent=MsG0180002454.01;Name=MsG0180002454.01.T02;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|0|1|0|191
Chr1 exon 38593370 38593945 38593370 ID=MsG0180002454.01.T02:exon:12787;Parent=MsG0180002454.01.T02
Chr1 CDS 38593370 38593945 38593370 ID=MsG0180002454.01.T02:cds;Parent=MsG0180002454.01.T02
Gene Sequence

>MsG0180002454.01.T02

ATGAGCATGTTAGGGTTAACCAATTTCATACTCTCATCATCACTGTCAATCCCTTCTCTTCAATACAAACCACAACACTTTTCTACCATTTCCATCACCTTCAATTCTCGAAAACCACGCCCACTTCCATTGTCTGCATCCAACAACAACAATAACAGTAATGGGGTAAAAGAAGAGGACAAAAATTCACAACAACAGCCACCACCCTCTTCTTCTGGACAAGAACAAAAACAAGAAAAACTACCCCTTTTTGGTTTGAATTGGAGTAGCCTTTTAGATCGAGATCCTGATAATATCCTTGCTCTTGGATTAACTGGTATTCTCACATGGGCAAGTGTTCAAGTTCTGTGGCAACTCTTGTTTATCTCTTGGCTATTCTCGTTGCTGCCCTCAAATACTCTTTTATTGCTGCTCTTCTCATTTTCATTCTCATCGCTCTTCTCTAATTCATTACATTTTCTTGCTCACTTGTTTGTAATGTCATGTTCATATATATCTAATGGAAAGAAAATTCATTACATAATTATTTTCCGTTTATATTATGTTAAAGCTATTGTGCATAAGACCTCAAAATGA

>MsG0180002454.01.T01

ATGTTAGGGTTAACCAATTTCATACTCTCATCATCACTGTCAATCCCTTCTCTTCAATACAAACCACAACACTTTTCTACCATTTCCATCACCTTCAATTCTCGAAAACCACGCCCACTTCCATTGTCTGCATCCAACAACAACAATAACAGTAATGGGGTAAAAGAAGAGGACAAAAATTCACAACAACAAAAACAAGAAAAACTACCCCTTTTTGGTTTGAATTGGAGTAGCCTTTTAGATCGAGATCCTGATAATATCCTTGCTCTTGGATTAACTGGTATTCTCACATGGGCAAGTGTTCAAGTTCTGTGGCAACTCTTGTTTATCTCTTGGCTATTCTCGTTGCTGCCCTCAAATACTCTTTTATTGCTGCTCTTCTCATTTTCATTCTCATCGCTCTTCTCTAATTCATTACATTTTCTTGCTCACTTGTTTGTAATGTCATGTTCATATATATCTAATGGAAAGAAAATTCATTACATAATTATTTTCCGTTTATATTATGTTAAAGCTATTGTGCATAAGACCTCAAAATGA

Protein sequence

>MsG0180002454.01.T02

MSMLGLTNFILSSSLSIPSLQYKPQHFSTISITFNSRKPRPLPLSASNNNNNSNGVKEEDKNSQQQPPPSSSGQEQKQEKLPLFGLNWSSLLDRDPDNILALGLTGILTWASVQVLWQLLFISWLFSLLPSNTLLLLLFSFSFSSLFSNSLHFLAHLFVMSCSYISNGKKIHYIIIFRLYYVKAIVHKTSK*

>MsG0180002454.01.T01

MLGLTNFILSSSLSIPSLQYKPQHFSTISITFNSRKPRPLPLSASNNNNNSNGVKEEDKNSQQQKQEKLPLFGLNWSSLLDRDPDNILALGLTGILTWASVQVLWQLLFISWLFSLLPSNTLLLLLFSFSFSSLFSNSLHFLAHLFVMSCSYISNGKKIHYIIIFRLYYVKAIVHKTSK*