AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180002282.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAGATTGCTCGTAGAGTA+TGG 0.285487 1:+36201833 None:intergenic
GTGCAGTATTGTGAAGAAAA+TGG 0.290748 1:+36202978 MsG0180002282.01.T01:three_prime_UTR
GGAACATCAGATTAAAGCTT+TGG 0.317172 1:+36201855 MsG0180002282.01.T01:CDS
CTCTCCTTTCTGATGATCAT+TGG 0.320413 1:+36202802 MsG0180002282.01.T01:CDS
GTTATGGTGATGGTTTCATA+TGG 0.337418 1:+36203001 MsG0180002282.01.T01:three_prime_UTR
ATCAGATTGCTCGTAGAGTA+TGG 0.358368 1:+36201913 MsG0180002282.01.T01:CDS
AAGACGAATTGCGTTACATT+TGG 0.364857 1:+36202881 MsG0180002282.01.T01:three_prime_UTR
TTGTTTCTGTACTTATGAAT+TGG 0.402013 1:+36203086 MsG0180002282.01.T01:three_prime_UTR
AATGTCCCTTTCCTTGTCCT+TGG 0.407599 1:+36202827 MsG0180002282.01.T01:CDS
TCTCCTTTCTGATGATCATT+GGG 0.419966 1:+36202803 MsG0180002282.01.T01:CDS
TTATGAATTGGAAGTGTTGT+TGG 0.428792 1:+36203098 MsG0180002282.01.T01:three_prime_UTR
TCGTCTTCTGAGGCAGCATA+TGG 0.429799 1:-36202865 None:intergenic
GAACATCAGATTAAAGCTTT+GGG 0.450191 1:+36201856 MsG0180002282.01.T01:CDS
TTATGGTGATGGTTTCATAT+GGG 0.455567 1:+36203002 MsG0180002282.01.T01:three_prime_UTR
GACTTGAGCAACTTCACCAC+TGG 0.494395 1:+36202903 MsG0180002282.01.T01:three_prime_UTR
GGTAGATGCAGTGGTCTACT+TGG 0.495776 1:+36202728 MsG0180002282.01.T01:intron
TAGAGTTCTTTAGTAAGAGA+TGG 0.498869 1:+36203041 MsG0180002282.01.T01:three_prime_UTR
TGCAGTATTGTGAAGAAAAT+GGG 0.501905 1:+36202979 MsG0180002282.01.T01:three_prime_UTR
GTTCTTTAGTAAGAGATGGT+TGG 0.502006 1:+36203045 MsG0180002282.01.T01:three_prime_UTR
CATGGTCGGACATTTAAGTC+TGG 0.507963 1:-36202944 None:intergenic
TGTTTCCAAGGACAAGGAAA+GGG 0.516162 1:-36202832 None:intergenic
CTTCACCACTGGCAAGGGTA+AGG 0.533342 1:+36202914 MsG0180002282.01.T01:three_prime_UTR
TTGTTTCCAAGGACAAGGAA+AGG 0.540898 1:-36202833 None:intergenic
AAGAAAATGGGTTATGGTGA+TGG 0.542914 1:+36202991 MsG0180002282.01.T01:three_prime_UTR
GAGCAACTTCACCACTGGCA+AGG 0.544899 1:+36202908 MsG0180002282.01.T01:three_prime_UTR
ACCAAAATTAACTGAACTGT+AGG 0.558898 1:-36203185 None:intergenic
AGCAACTTCACCACTGGCAA+GGG 0.561923 1:+36202909 MsG0180002282.01.T01:three_prime_UTR
ATTGTGAAGAAAATGGGTTA+TGG 0.564263 1:+36202985 MsG0180002282.01.T01:three_prime_UTR
ATGGAAAGATTACTATGCCC+AGG 0.572618 1:+36201932 MsG0180002282.01.T01:CDS
TTTCCCAATGATCATCAGAA+AGG 0.574156 1:-36202806 None:intergenic
CTTGGTTAATGCTTATGACA+AGG 0.580833 1:+36202746 MsG0180002282.01.T01:CDS
TTTATTTCTATAAAATGACT+GGG 0.586086 1:+36203160 MsG0180002282.01.T01:three_prime_UTR
TCAGATTGCTCGTAGAGTAT+GGG 0.589961 1:+36201834 None:intergenic
CACATGAATACCTCCATGGT+CGG 0.599633 1:-36202958 None:intergenic
GTAACGCAATTCGTCTTCTG+AGG 0.630635 1:-36202875 None:intergenic
AATTACCTTACCCTTGCCAG+TGG 0.652580 1:-36202919 None:intergenic
TGCAATGCAGGTAGATGCAG+TGG 0.654691 1:+36202719 MsG0180002282.01.T01:intron
ACTGCACATGAATACCTCCA+TGG 0.667236 1:-36202962 None:intergenic
CAGACTTAAATGTCCGACCA+TGG 0.668721 1:+36202945 MsG0180002282.01.T01:three_prime_UTR
ACTTAAATGTCCGACCATGG+AGG 0.721595 1:+36202948 MsG0180002282.01.T01:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATCTTAATCATGAAAATT+TGG + Chr1:36202012-36202031 MsG0180002282.01.T01:intron 15.0%
!!! TAAGTTGTAAATTGATTTAA+CGG - Chr1:36202452-36202471 None:intergenic 15.0%
!!! TTTATTTCTATAAAATGACT+GGG + Chr1:36203160-36203179 MsG0180002282.01.T01:three_prime_UTR 15.0%
!!! TTTTATTTCTATAAAATGAC+TGG + Chr1:36203159-36203178 MsG0180002282.01.T01:three_prime_UTR 15.0%
!!! AAGTTTAAAGCTTTTGATTT+GGG + Chr1:36201885-36201904 MsG0180002282.01.T01:CDS 20.0%
!!! ATGCCTTAAATACTTTTTTA+TGG + Chr1:36201968-36201987 MsG0180002282.01.T01:CDS 20.0%
!!! TAGCCATAAAAAAGTATTTA+AGG - Chr1:36201974-36201993 None:intergenic 20.0%
! AAGATTTGATGAGTCAAAAA+AGG + Chr1:36202770-36202789 MsG0180002282.01.T01:CDS 25.0%
! ATACAATGGATAGAATAGAA+GGG - Chr1:36202397-36202416 None:intergenic 25.0%
! ATTATATTATGTCTTGGACT+TGG + Chr1:36202055-36202074 MsG0180002282.01.T01:intron 25.0%
! GATTAAGATATTCTTTCACT+TGG - Chr1:36202003-36202022 None:intergenic 25.0%
! TATACAATGGATAGAATAGA+AGG - Chr1:36202398-36202417 None:intergenic 25.0%
! TCCAAGACATAATATAATCA+GGG - Chr1:36202053-36202072 None:intergenic 25.0%
! TCTCAGTTAAATATTGAACA+GGG - Chr1:36202524-36202543 None:intergenic 25.0%
! TTATATGCTACTGTATACAA+TGG - Chr1:36202411-36202430 None:intergenic 25.0%
! TTCTCAGTTAAATATTGAAC+AGG - Chr1:36202525-36202544 None:intergenic 25.0%
!! CTATATTTGAAATCACTAAC+TGG - Chr1:36202135-36202154 None:intergenic 25.0%
!!! AGTTTAAAGCTTTTGATTTG+GGG + Chr1:36201886-36201905 MsG0180002282.01.T01:CDS 25.0%
!!! CAAGTTTAAAGCTTTTGATT+TGG + Chr1:36201884-36201903 MsG0180002282.01.T01:CDS 25.0%
!!! TTGTTTCTGTACTTATGAAT+TGG + Chr1:36203086-36203105 MsG0180002282.01.T01:three_prime_UTR 25.0%
ACTATGATTGTGTTTCCATT+AGG - Chr1:36202233-36202252 None:intergenic 30.0%
AGACATAATATAATCAGGGA+AGG - Chr1:36202049-36202068 None:intergenic 30.0%
AGATTCTAAGCCAATATCTT+AGG - Chr1:36202163-36202182 None:intergenic 30.0%
AGTACCTTATAAGACATTTC+TGG + Chr1:36202593-36202612 MsG0180002282.01.T01:intron 30.0%
CTAAAAGCAATAGAGTGAAA+AGG - Chr1:36202575-36202594 None:intergenic 30.0%
GAACATCAGATTAAAGCTTT+GGG + Chr1:36201856-36201875 MsG0180002282.01.T01:CDS 30.0%
GTCCAAGACATAATATAATC+AGG - Chr1:36202054-36202073 None:intergenic 30.0%
TAACTGAGAAACAAACTTGA+TGG + Chr1:36202489-36202508 MsG0180002282.01.T01:intron 30.0%
TAGAGTTCTTTAGTAAGAGA+TGG + Chr1:36203041-36203060 MsG0180002282.01.T01:three_prime_UTR 30.0%
TATAGAACTGCCTAAGATAT+TGG + Chr1:36202150-36202169 MsG0180002282.01.T01:intron 30.0%
TCCCTGATTATATTATGTCT+TGG + Chr1:36202049-36202068 MsG0180002282.01.T01:intron 30.0%
TGCAGTATTGTGAAGAAAAT+GGG + Chr1:36202979-36202998 MsG0180002282.01.T01:three_prime_UTR 30.0%
TTCTTATGTTCAGTACCTAA+TGG + Chr1:36202215-36202234 MsG0180002282.01.T01:intron 30.0%
! GTTGTAAATTGATTTAACGG+CGG - Chr1:36202449-36202468 None:intergenic 30.0%
!! ATTGTGAAGAAAATGGGTTA+TGG + Chr1:36202985-36203004 MsG0180002282.01.T01:three_prime_UTR 30.0%
!! GGAATATCATTTTGTTTCCA+AGG - Chr1:36202847-36202866 None:intergenic 30.0%
!! TTATGAATTGGAAGTGTTGT+TGG + Chr1:36203098-36203117 MsG0180002282.01.T01:three_prime_UTR 30.0%
!! TTATGGTGATGGTTTCATAT+GGG + Chr1:36203002-36203021 MsG0180002282.01.T01:three_prime_UTR 30.0%
!!! GTTTAAAGCTTTTGATTTGG+GGG + Chr1:36201887-36201906 MsG0180002282.01.T01:CDS 30.0%
!!! TTTAAAGCTTTTGATTTGGG+GGG + Chr1:36201888-36201907 MsG0180002282.01.T01:CDS 30.0%
AAGACGAATTGCGTTACATT+TGG + Chr1:36202881-36202900 MsG0180002282.01.T01:three_prime_UTR 35.0%
AGAGCCAGAAATGTCTTATA+AGG - Chr1:36202600-36202619 None:intergenic 35.0%
ATGAAAATTTGGATGCCACT+AGG + Chr1:36202023-36202042 MsG0180002282.01.T01:intron 35.0%
CTTGGTTAATGCTTATGACA+AGG + Chr1:36202746-36202765 MsG0180002282.01.T01:CDS 35.0%
GGAACATCAGATTAAAGCTT+TGG + Chr1:36201855-36201874 MsG0180002282.01.T01:CDS 35.0%
GTGCAGTATTGTGAAGAAAA+TGG + Chr1:36202978-36202997 MsG0180002282.01.T01:three_prime_UTR 35.0%
GTTCTTTAGTAAGAGATGGT+TGG + Chr1:36203045-36203064 MsG0180002282.01.T01:three_prime_UTR 35.0%
TCTCCTTTCTGATGATCATT+GGG + Chr1:36202803-36202822 MsG0180002282.01.T01:CDS 35.0%
TGATGAGTCAAAAAAGGAGT+TGG + Chr1:36202776-36202795 MsG0180002282.01.T01:CDS 35.0%
TTTCCCAATGATCATCAGAA+AGG - Chr1:36202809-36202828 None:intergenic 35.0%
!! AAGAAAATGGGTTATGGTGA+TGG + Chr1:36202991-36203010 MsG0180002282.01.T01:three_prime_UTR 35.0%
!! GTTATGGTGATGGTTTCATA+TGG + Chr1:36203001-36203020 MsG0180002282.01.T01:three_prime_UTR 35.0%
!! TCATTTTGTTTCCAAGGACA+AGG - Chr1:36202841-36202860 None:intergenic 35.0%
AACCGAGAAACATTACGTGT+TGG + Chr1:36202657-36202676 MsG0180002282.01.T01:intron 40.0%
ATCAGATTGCTCGTAGAGTA+TGG + Chr1:36201913-36201932 MsG0180002282.01.T01:CDS 40.0%
ATGGAAAGATTACTATGCCC+AGG + Chr1:36201932-36201951 MsG0180002282.01.T01:CDS 40.0%
CACCAACACGTAATGTTTCT+CGG - Chr1:36202662-36202681 None:intergenic 40.0%
CTCTCCTTTCTGATGATCAT+TGG + Chr1:36202802-36202821 MsG0180002282.01.T01:CDS 40.0%
GCATAGAAAAAGAGAGACCT+GGG - Chr1:36201952-36201971 None:intergenic 40.0%
TCAGATTGCTCGTAGAGTAT+GGG + Chr1:36201914-36201933 MsG0180002282.01.T01:CDS 40.0%
TGTTTCCAAGGACAAGGAAA+GGG - Chr1:36202835-36202854 None:intergenic 40.0%
TTGTTTCCAAGGACAAGGAA+AGG - Chr1:36202836-36202855 None:intergenic 40.0%
! GAGAAACAAACTTGATGGTC+TGG + Chr1:36202494-36202513 MsG0180002282.01.T01:intron 40.0%
!! TCATGAGTTTGTTGCAATGC+AGG + Chr1:36202707-36202726 MsG0180002282.01.T01:intron 40.0%
!! TTTTGTTTGTGTCGCTAGAC+AGG + Chr1:36202093-36202112 MsG0180002282.01.T01:intron 40.0%
AATGTCCCTTTCCTTGTCCT+TGG + Chr1:36202827-36202846 MsG0180002282.01.T01:CDS 45.0%
AATTACCTTACCCTTGCCAG+TGG - Chr1:36202922-36202941 None:intergenic 45.0%
ACTGCACATGAATACCTCCA+TGG - Chr1:36202965-36202984 None:intergenic 45.0%
ACTTAAATGTCCGACCATGG+AGG + Chr1:36202948-36202967 MsG0180002282.01.T01:three_prime_UTR 45.0%
CACATGAATACCTCCATGGT+CGG - Chr1:36202961-36202980 None:intergenic 45.0%
CAGACTTAAATGTCCGACCA+TGG + Chr1:36202945-36202964 MsG0180002282.01.T01:three_prime_UTR 45.0%
CATGGTCGGACATTTAAGTC+TGG - Chr1:36202947-36202966 None:intergenic 45.0%
GGCATAGAAAAAGAGAGACC+TGG - Chr1:36201953-36201972 None:intergenic 45.0%
GTAACGCAATTCGTCTTCTG+AGG - Chr1:36202878-36202897 None:intergenic 45.0%
TATAATCAGGGAAGGCCTAG+TGG - Chr1:36202041-36202060 None:intergenic 45.0%
AGCAACTTCACCACTGGCAA+GGG + Chr1:36202909-36202928 MsG0180002282.01.T01:three_prime_UTR 50.0%
GACTTGAGCAACTTCACCAC+TGG + Chr1:36202903-36202922 MsG0180002282.01.T01:three_prime_UTR 50.0%
GGTAGATGCAGTGGTCTACT+TGG + Chr1:36202728-36202747 MsG0180002282.01.T01:intron 50.0%
TGCAATGCAGGTAGATGCAG+TGG + Chr1:36202719-36202738 MsG0180002282.01.T01:intron 50.0%
!! TCGTCTTCTGAGGCAGCATA+TGG - Chr1:36202868-36202887 None:intergenic 50.0%
CTTCACCACTGGCAAGGGTA+AGG + Chr1:36202914-36202933 MsG0180002282.01.T01:three_prime_UTR 55.0%
GAGCAACTTCACCACTGGCA+AGG + Chr1:36202908-36202927 MsG0180002282.01.T01:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
Chr1 gene 36201838 36203196 36201838 ID=MsG0180002282.01;Name=MsG0180002282.01
Chr1 mRNA 36201838 36203196 36201838 ID=MsG0180002282.01.T01;Parent=MsG0180002282.01;Name=MsG0180002282.01.T01;_AED=0.11;_eAED=0.28;_QI=0|0|0.5|1|0|0|2|336|95
Chr1 exon 36201838 36201993 36201838 ID=MsG0180002282.01.T01:exon:1144;Parent=MsG0180002282.01.T01
Chr1 exon 36202729 36203196 36202729 ID=MsG0180002282.01.T01:exon:1145;Parent=MsG0180002282.01.T01
Chr1 CDS 36201838 36201993 36201838 ID=MsG0180002282.01.T01:cds;Parent=MsG0180002282.01.T01
Chr1 CDS 36202729 36202860 36202729 ID=MsG0180002282.01.T01:cds;Parent=MsG0180002282.01.T01
Chr1 three_prime_UTR 36202861 36203196 36202861 ID=MsG0180002282.01.T01:three_prime_utr;Parent=MsG0180002282.01.T01
Gene Sequence

>MsG0180002282.01.T01

ATTGCTCGTAGAGTATGGGAACATCAGATTAAAGCTTTGGGAAGATCAAGTTTAAAGCTTTTGATTTGGGGGGTCATCAGATTGCTCGTAGAGTATGGAAAGATTACTATGCCCAGGTCTCTCTTTTTCTATGCCTTAAATACTTTTTTATGGCTAGTAGATGCAGTGGTCTACTTGGTTAATGCTTATGACAAGGAAAGATTTGATGAGTCAAAAAAGGAGTTGGATGCTCTCCTTTCTGATGATCATTGGGAAATGTCCCTTTCCTTGTCCTTGGAAACAAAATGA

Protein sequence

>MsG0180002282.01.T01

IARRVWEHQIKALGRSSLKLLIWGVIRLLVEYGKITMPRSLFFYALNTFLWLVDAVVYLVNAYDKERFDESKKELDALLSDDHWEMSLSLSLETK*