AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0189990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0189990 MtrunA17_Chr5g0426511 51.351 148 43 7 1 123 1 144 1.07e-23 89.0
Msa0189990 MtrunA17_Chr2g0279541 62.097 124 14 5 1 123 1 92 1.13e-22 84.7
Msa0189990 MtrunA17_Chr4g0049911 46.789 109 40 3 1 100 1 100 1.21e-15 67.8
Msa0189990 MtrunA17_Chr4g0049921 52.885 104 41 3 1 100 1 100 4.06e-15 66.6
Msa0189990 MtrunA17_Chr4g0049951 45.872 109 41 3 1 100 1 100 6.49e-15 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0189990 AT5G09520.1 36.290 124 65 6 2 112 5 127 1.27e-11 58.2

Find 40 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGAAGTGTTGGTGTAGT+TGG 0.341757 2_1:+5429093 None:intergenic
ATAGATGGCTGAGTAGGTTT+TGG 0.351476 2_1:+5428982 None:intergenic
GGGATTGTAGTAGGAATGTT+TGG 0.366842 2_1:+5428904 None:intergenic
TTTGGCAATGCTGGGATTGT+AGG 0.373136 2_1:+5429000 None:intergenic
GGGAATGTTGGCATAGTGAT+TGG 0.393983 2_1:+5428883 None:intergenic
TGAGGCAATGTTGGAATTGT+TGG 0.400561 2_1:+5429042 None:intergenic
TGTGGAATAGTTGGAATTGT+AGG 0.403230 2_1:+5428946 None:intergenic
TGAAGGTGGTGGAGAAAAGA+AGG 0.426869 2_1:+5428861 None:intergenic
AATGTTGGCAATGTTGGTTT+TGG 0.454379 2_1:+5429075 None:intergenic
GGGATAGTACTAGGAATAGA+TGG 0.460146 2_1:+5428967 None:intergenic
TGCTAAAATGAAGGAACTAT+AGG 0.465331 2_1:+5429188 None:intergenic
TGCTATTTCCTTCTCAAACA+TGG 0.466175 2_1:-5429157 Msa0189990:CDS
AAGAAGATTGCGAGCTGCTA+GGG 0.477055 2_1:+5429128 None:intergenic
GGTGGCAATGTTGGCAATGT+TGG 0.477572 2_1:+5429069 None:intergenic
ACATTTCCTTGAGGCAATGT+TGG 0.483996 2_1:+5429033 None:intergenic
GGAATGTTGGCATAGTGATT+GGG 0.491312 2_1:+5428884 None:intergenic
ATAGTGATTGGGATTGTAGT+AGG 0.509782 2_1:+5428895 None:intergenic
GGAGAAAAGAAGGGGAATGT+TGG 0.509998 2_1:+5428871 None:intergenic
AATGAAAATTGCTAAAATGA+AGG 0.510394 2_1:+5429179 None:intergenic
AGAGTGAACTGTGGAATAGT+TGG 0.512404 2_1:+5428937 None:intergenic
GAAGGTGGTGGAGAAAAGAA+GGG 0.525536 2_1:+5428862 None:intergenic
GAAGAAGATTGCGAGCTGCT+AGG 0.529340 2_1:+5429127 None:intergenic
GTGGAATAGTTGGAATTGTA+GGG 0.531662 2_1:+5428947 None:intergenic
GTTGGAATTGTTGGCAAAGG+TGG 0.537047 2_1:+5429051 None:intergenic
CTAGGAATAGATGGCTGAGT+AGG 0.540861 2_1:+5428976 None:intergenic
GTAGTAGGAATGTTTGGAAG+TGG 0.541956 2_1:+5428910 None:intergenic
GTTGGCAAAGGTGGCAATGT+TGG 0.545513 2_1:+5429060 None:intergenic
GGAATTGTAGGGATAGTACT+AGG 0.546673 2_1:+5428958 None:intergenic
GCTGGGATTGTAGGCAAAGG+TGG 0.549782 2_1:+5429009 None:intergenic
GTAGGAATGTTTGGAAGTGG+TGG 0.557881 2_1:+5428913 None:intergenic
GAAGGAACTATAGGAGGCCA+TGG 0.565486 2_1:+5429197 None:intergenic
TAAAATGAAGGAACTATAGG+AGG 0.579978 2_1:+5429191 None:intergenic
GGTAATGTCCATGTTTGAGA+AGG 0.594515 2_1:+5429149 None:intergenic
TTGACACGAACTTCAAGGAG+TGG 0.601056 2_1:+5428834 None:intergenic
ACAATTCCAACATTGCCTCA+AGG 0.633830 2_1:-5429039 Msa0189990:CDS
AAGGTGGTGGAGAAAAGAAG+GGG 0.639486 2_1:+5428863 None:intergenic
AATGTTGGAATTGTTGGCAA+AGG 0.641702 2_1:+5429048 None:intergenic
AGTGGTGGAAGAGTGAACTG+TGG 0.689745 2_1:+5428928 None:intergenic
AAAGGTGGAACATTTCCTTG+AGG 0.706888 2_1:+5429024 None:intergenic
AATGCTGGGATTGTAGGCAA+AGG 0.711188 2_1:+5429006 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGAAAATTGCTAAAATGA+AGG + chr2_1:5428865-5428884 None:intergenic 20.0%
TAAAATGAAGGAACTATAGG+AGG + chr2_1:5428853-5428872 None:intergenic 30.0%
TGCTAAAATGAAGGAACTAT+AGG + chr2_1:5428856-5428875 None:intergenic 30.0%
!! TGCTATTTCCTTCTCAAACA+TGG - chr2_1:5428884-5428903 Msa0189990:CDS 35.0%
!!! AATGTTGGTTTTGGAAGTGT+TGG + chr2_1:5428960-5428979 None:intergenic 35.0%
!!! AATGTTGGCAATGTTGGTTT+TGG + chr2_1:5428969-5428988 None:intergenic 35.0%
AATGTTGGAATTGTTGGCAA+AGG + chr2_1:5428996-5429015 None:intergenic 35.0%
GTGGAATAGTTGGAATTGTA+GGG + chr2_1:5429097-5429116 None:intergenic 35.0%
TGTGGAATAGTTGGAATTGT+AGG + chr2_1:5429098-5429117 None:intergenic 35.0%
ATAGTGATTGGGATTGTAGT+AGG + chr2_1:5429149-5429168 None:intergenic 35.0%
GGTAATGTCCATGTTTGAGA+AGG + chr2_1:5428895-5428914 None:intergenic 40.0%
!! TTTGGAAGTGTTGGTGTAGT+TGG + chr2_1:5428951-5428970 None:intergenic 40.0%
TGAGGCAATGTTGGAATTGT+TGG + chr2_1:5429002-5429021 None:intergenic 40.0%
ACAATTCCAACATTGCCTCA+AGG - chr2_1:5429002-5429021 Msa0189990:CDS 40.0%
ACATTTCCTTGAGGCAATGT+TGG + chr2_1:5429011-5429030 None:intergenic 40.0%
AAAGGTGGAACATTTCCTTG+AGG + chr2_1:5429020-5429039 None:intergenic 40.0%
! ATAGATGGCTGAGTAGGTTT+TGG + chr2_1:5429062-5429081 None:intergenic 40.0%
GGGATAGTACTAGGAATAGA+TGG + chr2_1:5429077-5429096 None:intergenic 40.0%
GGAATTGTAGGGATAGTACT+AGG + chr2_1:5429086-5429105 None:intergenic 40.0%
AGAGTGAACTGTGGAATAGT+TGG + chr2_1:5429107-5429126 None:intergenic 40.0%
GTAGTAGGAATGTTTGGAAG+TGG + chr2_1:5429134-5429153 None:intergenic 40.0%
GGGATTGTAGTAGGAATGTT+TGG + chr2_1:5429140-5429159 None:intergenic 40.0%
GGAATGTTGGCATAGTGATT+GGG + chr2_1:5429160-5429179 None:intergenic 40.0%
AAGAAGATTGCGAGCTGCTA+GGG + chr2_1:5428916-5428935 None:intergenic 45.0%
GTTGGAATTGTTGGCAAAGG+TGG + chr2_1:5428993-5429012 None:intergenic 45.0%
AATGCTGGGATTGTAGGCAA+AGG + chr2_1:5429038-5429057 None:intergenic 45.0%
TTTGGCAATGCTGGGATTGT+AGG + chr2_1:5429044-5429063 None:intergenic 45.0%
!! GAGTAGGTTTTGGCAATGCT+GGG + chr2_1:5429052-5429071 None:intergenic 45.0%
!! TGAGTAGGTTTTGGCAATGC+TGG + chr2_1:5429053-5429072 None:intergenic 45.0%
CTAGGAATAGATGGCTGAGT+AGG + chr2_1:5429068-5429087 None:intergenic 45.0%
GTAGGAATGTTTGGAAGTGG+TGG + chr2_1:5429131-5429150 None:intergenic 45.0%
GGGAATGTTGGCATAGTGAT+TGG + chr2_1:5429161-5429180 None:intergenic 45.0%
GGAGAAAAGAAGGGGAATGT+TGG + chr2_1:5429173-5429192 None:intergenic 45.0%
!! AAGGTGGTGGAGAAAAGAAG+GGG + chr2_1:5429181-5429200 None:intergenic 45.0%
!! GAAGGTGGTGGAGAAAAGAA+GGG + chr2_1:5429182-5429201 None:intergenic 45.0%
!! TGAAGGTGGTGGAGAAAAGA+AGG + chr2_1:5429183-5429202 None:intergenic 45.0%
!! CAAGGAGTGGTTTTTGAAGG+TGG + chr2_1:5429197-5429216 None:intergenic 45.0%
GAAGAAGATTGCGAGCTGCT+AGG + chr2_1:5428917-5428936 None:intergenic 50.0%
GGTGGCAATGTTGGCAATGT+TGG + chr2_1:5428975-5428994 None:intergenic 50.0%
GTTGGCAAAGGTGGCAATGT+TGG + chr2_1:5428984-5429003 None:intergenic 50.0%
! AGTGGTGGAAGAGTGAACTG+TGG + chr2_1:5429116-5429135 None:intergenic 50.0%
!! GGAGTGGTTTTTGAAGGTGG+TGG + chr2_1:5429194-5429213 None:intergenic 50.0%
GCTGGGATTGTAGGCAAAGG+TGG + chr2_1:5429035-5429054 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 5428846 5429217 5428846 ID=Msa0189990;Name=Msa0189990
chr2_1 mRNA 5428846 5429217 5428846 ID=Msa0189990-mRNA-1;Parent=Msa0189990;Name=Msa0189990-mRNA-1;_AED=0.00;_eAED=0.10;_QI=0|-1|0|1|-1|1|1|0|123
chr2_1 exon 5428846 5429217 5428846 ID=Msa0189990-mRNA-1:exon:2448;Parent=Msa0189990-mRNA-1
chr2_1 CDS 5428846 5429217 5428846 ID=Msa0189990-mRNA-1:cds;Parent=Msa0189990-mRNA-1
Gene Sequence

>Msa0189990

ATGGCCTCCTATAGTTCCTTCATTTTAGCAATTTTCATTGCTATTTCCTTCTCAAACATGGACATTACCCTAGCAGCTCGCAATCTTCTTCAGACAACAAATCCAACTACACCAACACTTCCAAAACCAACATTGCCAACATTGCCACCTTTGCCAACAATTCCAACATTGCCTCAAGGAAATGTTCCACCTTTGCCTACAATCCCAGCATTGCCAAAACCTACTCAGCCATCTATTCCTAGTACTATCCCTACAATTCCAACTATTCCACAGTTCACTCTTCCACCACTTCCAAACATTCCTACTACAATCCCAATCACTATGCCAACATTCCCCTTCTTTTCTCCACCACCTTCAAAAACCACTCCTTGA
Protein sequence

>Msa0189990

MASYSSFILAIFIAISFSNMDITLAARNLLQTTNPTTPTLPKPTLPTLPPLPTIPTLPQGNVPPLPTIPALPKPTQPSIPSTIPTIPTIPQFTLPPLPNIPTTIPITMPTFPFFSPPPSKTTP*