AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0438320

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0438320 MtrunA17_Chr1g0152901 86.301 146 13 1 1 146 1 139 4.57e-86 248
Msa0438320 MtrunA17_Chr3g0134391 60.909 110 41 2 11 119 13 121 2.19e-39 130
Msa0438320 MtrunA17_Chr1g0185561 35.417 96 60 1 24 117 6 101 2.29e-15 72.0
Msa0438320 MtrunA17_Chr1g0205881 32.941 85 55 1 35 117 20 104 1.16e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0438320 AT1G47200.1 49.624 133 55 3 1 131 28 150 1.28e-36 124
Msa0438320 AT5G43070.1 51.969 127 55 3 18 139 27 152 2.51e-35 120
Msa0438320 AT5G27940.1 43.878 98 51 2 33 130 51 144 2.57e-21 84.3
Msa0438320 AT3G63130.1 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0438320 AT3G63130.2 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0438320 AT5G19320.1 34.118 85 54 1 35 117 16 100 1.00e-11 61.6
Msa0438320 AT5G19320.2 34.118 85 54 1 35 117 16 100 1.00e-11 61.6

Find 57 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGTTCGGGTTTGGCTTCC+GGG 0.228499 3_3:+2646027 None:intergenic
TCTTGTTCGGGTTTGGCTTC+CGG 0.236651 3_3:+2646026 None:intergenic
GAGTAGTTTCCGGTGAAATT+TGG 0.305396 3_3:+2645957 None:intergenic
GGAGGAGTCTTGTTCGGGTT+TGG 0.340745 3_3:+2646019 None:intergenic
AGCGAGGGAGGAGTCTTGTT+CGG 0.384493 3_3:+2646013 None:intergenic
GCGAGGGAGGAGTCTTGTTC+GGG 0.389014 3_3:+2646014 None:intergenic
GCGTTGTGCGGGAGGCCATA+TGG 0.389468 3_3:+2645935 None:intergenic
GCTATCGTTGCCCGTGGAAG+TGG 0.401756 3_3:+2645767 None:intergenic
CTCGATCTGGCTAGCGGCGG+CGG 0.404744 3_3:+2645818 None:intergenic
AGGCCATATGGAGTAGTTTC+CGG 0.410196 3_3:+2645947 None:intergenic
GAGACGAGATTTAGCTTTAA+CGG 0.420770 3_3:+2645692 None:intergenic
AGAAAGCTTCGTCCTCGATC+TGG 0.425698 3_3:+2645805 None:intergenic
GGACATTGTGCCGTAGCGTT+TGG 0.463221 3_3:+2645854 None:intergenic
GGAGCCTCCGTAGAGGGAGG+TGG 0.466455 3_3:+2645990 None:intergenic
CAATCAAGATTCAAAACAGC+GGG 0.470125 3_3:+2645618 None:intergenic
CCTCGCTCCACCTCCCTCTA+CGG 0.475624 3_3:-2645997 Msa0438320:CDS
TGGAAAGTGTTTCGATCAAA+CGG 0.476905 3_3:+2645892 None:intergenic
GGGGAATCAGCGGCAGAGGA+AGG 0.480076 3_3:+2645639 None:intergenic
TCACCGGAAACTACTCCATA+TGG 0.480969 3_3:-2645950 Msa0438320:CDS
GCGTCGCGAGTGCGTTGTGC+GGG 0.482089 3_3:+2645924 None:intergenic
AGAGGGAGGTGGAGCGAGGG+AGG 0.486555 3_3:+2646001 None:intergenic
CGCCGATGCTTCCACTTCCA+CGG 0.489244 3_3:-2645778 Msa0438320:CDS
CGTAGAGGGAGGTGGAGCGA+GGG 0.494922 3_3:+2645998 None:intergenic
TTCGGGTTTGGCTTCCGGGT+CGG 0.497869 3_3:+2646031 None:intergenic
GGCAGAGGAAGGAGCTCCGA+CGG 0.510995 3_3:+2645650 None:intergenic
TTTGGTGAGGACTGAGGGAG+TGG 0.512643 3_3:+2645872 None:intergenic
TGCGGTGGAGCCTCCGTAGA+GGG 0.519645 3_3:+2645984 None:intergenic
GTGAAATTTGGTTGTTGCGG+TGG 0.524980 3_3:+2645969 None:intergenic
TCGCGAGTGCGTTGTGCGGG+AGG 0.530415 3_3:+2645927 None:intergenic
GCCGATGCTTCCACTTCCAC+GGG 0.537590 3_3:-2645777 Msa0438320:CDS
TAGCGTTTGGTGAGGACTGA+GGG 0.560021 3_3:+2645867 None:intergenic
CCGTAGAGGGAGGTGGAGCG+AGG 0.564877 3_3:+2645997 None:intergenic
AAATCTCGTCTCGCTGATGA+CGG 0.565498 3_3:-2645681 Msa0438320:CDS
GCCCGTGGAAGTGGAAGCAT+CGG 0.569170 3_3:+2645776 None:intergenic
CGCTCCACCTCCCTCTACGG+AGG 0.572005 3_3:-2645994 Msa0438320:CDS
GGCGTCGCGAGTGCGTTGTG+CGG 0.572105 3_3:+2645923 None:intergenic
CCGCAACAACCAAATTTCAC+CGG 0.575174 3_3:-2645966 Msa0438320:CDS
CGATAGCGTTACGATTCTTG+AGG 0.579942 3_3:-2645751 Msa0438320:CDS
GATTCTTGAGGTTTACTCGA+AGG 0.581915 3_3:-2645739 Msa0438320:CDS
CCGGTGAAATTTGGTTGTTG+CGG 0.585855 3_3:+2645966 None:intergenic
CGCCGCCGCTAGCCAGATCG+AGG 0.588312 3_3:-2645817 Msa0438320:CDS
GGAAGTGGAAGCATCGGCGA+CGG 0.598077 3_3:+2645782 None:intergenic
GTAGCGTTTGGTGAGGACTG+AGG 0.608047 3_3:+2645866 None:intergenic
AGAGGAAGGAGCTCCGACGG+AGG 0.609670 3_3:+2645653 None:intergenic
GATGACGGTAACGCCTCCGT+CGG 0.613328 3_3:-2645666 Msa0438320:CDS
TTGCGGTGGAGCCTCCGTAG+AGG 0.615033 3_3:+2645983 None:intergenic
TTGTGCCGTAGCGTTTGGTG+AGG 0.632497 3_3:+2645859 None:intergenic
GGCGGCGGAAGCTTCGTCAG+CGG 0.636492 3_3:+2645833 None:intergenic
ATTCCTCACAATGTCCGACC+CGG 0.637935 3_3:-2646045 None:intergenic
GGTGGAGCCTCCGTAGAGGG+AGG 0.638102 3_3:+2645987 None:intergenic
TCAGTCCTCACCAAACGCTA+CGG 0.644599 3_3:-2645864 Msa0438320:CDS
CGTAACGCTATCGTTGCCCG+TGG 0.647560 3_3:+2645761 None:intergenic
TTCGTCCTCGATCTGGCTAG+CGG 0.649591 3_3:+2645812 None:intergenic
ATCAAGATTCAAAACAGCGG+GGG 0.654507 3_3:+2645620 None:intergenic
GTCCTCGATCTGGCTAGCGG+CGG 0.689668 3_3:+2645815 None:intergenic
TCAATCAAGATTCAAAACAG+CGG 0.702532 3_3:+2645617 None:intergenic
AATCAAGATTCAAAACAGCG+GGG 0.726201 3_3:+2645619 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCAATCAAGATTCAAAACAG+CGG + chr3_3:2646038-2646057 None:intergenic 30.0%
! TTCGATCAAACGGTTTTTGA+CGG + chr3_3:2645753-2645772 None:intergenic 35.0%
!! TGGAAAGTGTTTCGATCAAA+CGG + chr3_3:2645763-2645782 None:intergenic 35.0%
!! GAGACGAGATTTAGCTTTAA+CGG + chr3_3:2645963-2645982 None:intergenic 35.0%
AATCAAGATTCAAAACAGCG+GGG + chr3_3:2646036-2646055 None:intergenic 35.0%
CAATCAAGATTCAAAACAGC+GGG + chr3_3:2646037-2646056 None:intergenic 35.0%
GAGTAGTTTCCGGTGAAATT+TGG + chr3_3:2645698-2645717 None:intergenic 40.0%
GATTCTTGAGGTTTACTCGA+AGG - chr3_3:2645913-2645932 Msa0438320:CDS 40.0%
ATCAAGATTCAAAACAGCGG+GGG + chr3_3:2646035-2646054 None:intergenic 40.0%
GTGAAATTTGGTTGTTGCGG+TGG + chr3_3:2645686-2645705 None:intergenic 45.0%
CCGGTGAAATTTGGTTGTTG+CGG + chr3_3:2645689-2645708 None:intergenic 45.0%
CCGCAACAACCAAATTTCAC+CGG - chr3_3:2645686-2645705 Msa0438320:CDS 45.0%
TCACCGGAAACTACTCCATA+TGG - chr3_3:2645702-2645721 Msa0438320:CDS 45.0%
AGGCCATATGGAGTAGTTTC+CGG + chr3_3:2645708-2645727 None:intergenic 45.0%
CGATAGCGTTACGATTCTTG+AGG - chr3_3:2645901-2645920 Msa0438320:CDS 45.0%
AAATCTCGTCTCGCTGATGA+CGG - chr3_3:2645971-2645990 Msa0438320:CDS 45.0%
! TCTTGTTCGGGTTTGGCTTC+CGG + chr3_3:2645629-2645648 None:intergenic 50.0%
! TAGCGTTTGGTGAGGACTGA+GGG + chr3_3:2645788-2645807 None:intergenic 50.0%
TCAGTCCTCACCAAACGCTA+CGG - chr3_3:2645788-2645807 Msa0438320:CDS 50.0%
AGAAAGCTTCGTCCTCGATC+TGG + chr3_3:2645850-2645869 None:intergenic 50.0%
! CTTGTTCGGGTTTGGCTTCC+GGG + chr3_3:2645628-2645647 None:intergenic 55.0%
!! GGAGGAGTCTTGTTCGGGTT+TGG + chr3_3:2645636-2645655 None:intergenic 55.0%
!! AGCGAGGGAGGAGTCTTGTT+CGG + chr3_3:2645642-2645661 None:intergenic 55.0%
TTTGGTGAGGACTGAGGGAG+TGG + chr3_3:2645783-2645802 None:intergenic 55.0%
! GTAGCGTTTGGTGAGGACTG+AGG + chr3_3:2645789-2645808 None:intergenic 55.0%
! TTGTGCCGTAGCGTTTGGTG+AGG + chr3_3:2645796-2645815 None:intergenic 55.0%
GGACATTGTGCCGTAGCGTT+TGG + chr3_3:2645801-2645820 None:intergenic 55.0%
TTCGTCCTCGATCTGGCTAG+CGG + chr3_3:2645843-2645862 None:intergenic 55.0%
CAAAACAGCGGGGGAATCAG+CGG + chr3_3:2646026-2646045 None:intergenic 55.0%
! TTCGGGTTTGGCTTCCGGGT+CGG + chr3_3:2645624-2645643 None:intergenic 60.0%
!! GCGAGGGAGGAGTCTTGTTC+GGG + chr3_3:2645641-2645660 None:intergenic 60.0%
!! GGAAGTGGAAGCATCGGCGA+CGG + chr3_3:2645873-2645892 None:intergenic 60.0%
CGCCGATGCTTCCACTTCCA+CGG - chr3_3:2645874-2645893 Msa0438320:CDS 60.0%
GCCGATGCTTCCACTTCCAC+GGG - chr3_3:2645875-2645894 Msa0438320:CDS 60.0%
! GCCCGTGGAAGTGGAAGCAT+CGG + chr3_3:2645879-2645898 None:intergenic 60.0%
GCTATCGTTGCCCGTGGAAG+TGG + chr3_3:2645888-2645907 None:intergenic 60.0%
CGTAACGCTATCGTTGCCCG+TGG + chr3_3:2645894-2645913 None:intergenic 60.0%
! GATGACGGTAACGCCTCCGT+CGG - chr3_3:2645986-2646005 Msa0438320:CDS 60.0%
CGTAGAGGGAGGTGGAGCGA+GGG + chr3_3:2645657-2645676 None:intergenic 65.0%
CCTCGCTCCACCTCCCTCTA+CGG - chr3_3:2645655-2645674 Msa0438320:CDS 65.0%
TGCGGTGGAGCCTCCGTAGA+GGG + chr3_3:2645671-2645690 None:intergenic 65.0%
TTGCGGTGGAGCCTCCGTAG+AGG + chr3_3:2645672-2645691 None:intergenic 65.0%
GCGTTGTGCGGGAGGCCATA+TGG + chr3_3:2645720-2645739 None:intergenic 65.0%
GTCCTCGATCTGGCTAGCGG+CGG + chr3_3:2645840-2645859 None:intergenic 65.0%
AGAGGAAGGAGCTCCGACGG+AGG + chr3_3:2646002-2646021 None:intergenic 65.0%
GGCAGAGGAAGGAGCTCCGA+CGG + chr3_3:2646005-2646024 None:intergenic 65.0%
GGGGAATCAGCGGCAGAGGA+AGG + chr3_3:2646016-2646035 None:intergenic 65.0%
AGAGGGAGGTGGAGCGAGGG+AGG + chr3_3:2645654-2645673 None:intergenic 70.0%
CCGTAGAGGGAGGTGGAGCG+AGG + chr3_3:2645658-2645677 None:intergenic 70.0%
CGCTCCACCTCCCTCTACGG+AGG - chr3_3:2645658-2645677 Msa0438320:CDS 70.0%
GGAGCCTCCGTAGAGGGAGG+TGG + chr3_3:2645665-2645684 None:intergenic 70.0%
GGTGGAGCCTCCGTAGAGGG+AGG + chr3_3:2645668-2645687 None:intergenic 70.0%
TCGCGAGTGCGTTGTGCGGG+AGG + chr3_3:2645728-2645747 None:intergenic 70.0%
GCGTCGCGAGTGCGTTGTGC+GGG + chr3_3:2645731-2645750 None:intergenic 70.0%
GGCGTCGCGAGTGCGTTGTG+CGG + chr3_3:2645732-2645751 None:intergenic 70.0%
GGCGGCGGAAGCTTCGTCAG+CGG + chr3_3:2645822-2645841 None:intergenic 70.0%
CTCGATCTGGCTAGCGGCGG+CGG + chr3_3:2645837-2645856 None:intergenic 70.0%
AGCGGGGGAATCAGCGGCAG+AGG + chr3_3:2646020-2646039 None:intergenic 70.0%
CGCCGCCGCTAGCCAGATCG+AGG - chr3_3:2645835-2645854 Msa0438320:CDS 75.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 2645617 2646057 2645617 ID=Msa0438320;Name=Msa0438320
chr3_3 mRNA 2645617 2646057 2645617 ID=Msa0438320-mRNA-1;Parent=Msa0438320;Name=Msa0438320-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|146
chr3_3 exon 2645617 2646057 2645617 ID=Msa0438320-mRNA-1:exon:606;Parent=Msa0438320-mRNA-1
chr3_3 CDS 2645617 2646057 2645617 ID=Msa0438320-mRNA-1:cds;Parent=Msa0438320-mRNA-1
Gene Sequence

>Msa0438320

ATGTCCGACCCGGAAGCCAAACCCGAACAAGACTCCTCCCTCGCTCCACCTCCCTCTACGGAGGCTCCACCGCAACAACCAAATTTCACCGGAAACTACTCCATATGGCCTCCCGCACAACGCACTCGCGACGCCGTCAAAAACCGTTTGATCGAAACACTTTCCACTCCCTCAGTCCTCACCAAACGCTACGGCACAATGTCCGCTGACGAAGCTTCCGCCGCCGCTAGCCAGATCGAGGACGAAGCTTTCTCCGTCGCCGATGCTTCCACTTCCACGGGCAACGATAGCGTTACGATTCTTGAGGTTTACTCGAAGGAGATCAGTAAGCGCATGATCGAAACCGTTAAAGCTAAATCTCGTCTCGCTGATGACGGTAACGCCTCCGTCGGAGCTCCTTCCTCTGCCGCTGATTCCCCCGCTGTTTTGAATCTTGATTGA
Protein sequence

>Msa0438320

MSDPEAKPEQDSSLAPPPSTEAPPQQPNFTGNYSIWPPAQRTRDAVKNRLIETLSTPSVLTKRYGTMSADEASAAASQIEDEAFSVADASTSTGNDSVTILEVYSKEISKRMIETVKAKSRLADDGNASVGAPSSAADSPAVLNLD*