AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84933

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84933.t1 MTR_1g053530 56.279 215 76 6 52 262 36 236 1.11e-65 207
MS.gene84933.t1 MTR_1g046810 32.424 330 128 13 30 315 37 315 3.07e-28 111
MS.gene84933.t1 MTR_1g052185 30.137 292 152 13 31 313 30 278 1.01e-20 90.5
MS.gene84933.t1 MTR_4g073310 26.159 302 132 8 14 314 16 227 5.31e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 65 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGAAAGTTGTTGCCTCTA+TGG 0.288255 1.3:+37583333 None:intergenic
ACTCTCATCACAAAACAAAA+AGG 0.340650 1.3:-37583448 MS.gene84933:CDS
TCATCTTCACCAGGGTTGTT+TGG 0.341135 1.3:+37582672 None:intergenic
TCATCTTCACCAGGGTTGTT+TGG 0.341135 1.3:+37582711 None:intergenic
TGAGGAACCAACTCATGAAT+TGG 0.350528 1.3:-37582640 MS.gene84933:CDS
ATAATTCCAGCTCCGTTTCA+TGG 0.360348 1.3:+37583085 None:intergenic
GTTCTCTTCATTATCATCAT+TGG 0.362989 1.3:+37582770 None:intergenic
TCTTCGAAGTCGAACCATAT+TGG 0.367921 1.3:+37583186 None:intergenic
ATGAAATCGCACAGCCAATA+TGG 0.368027 1.3:-37583200 MS.gene84933:CDS
ATCATTGGAAGCAGATTGAT+TGG 0.381296 1.3:+37582785 None:intergenic
GAGGAACCAACTCATGAATT+GGG 0.382420 1.3:-37582639 MS.gene84933:CDS
AAATACTTTCTCAAATCAAT+TGG 0.400225 1.3:+37583128 None:intergenic
TGATTCCCAACAAGGTTGTT+AGG 0.405927 1.3:+37583005 None:intergenic
CGATCACCTAACAACCTTGT+TGG 0.409603 1.3:-37583011 MS.gene84933:CDS
TGCAGAAATGTGGGTGGGAA+TGG 0.425504 1.3:-37582957 MS.gene84933:CDS
AGAAGAACAAGTTGGTGGTT+AGG 0.425663 1.3:-37582851 MS.gene84933:CDS
TGCCTCTATGGAATGCTTTG+TGG 0.438332 1.3:+37583345 None:intergenic
GATCACCTAACAACCTTGTT+GGG 0.442776 1.3:-37583010 MS.gene84933:CDS
TCATCTGTCAATGCACTGAA+TGG 0.463276 1.3:-37583227 MS.gene84933:CDS
TGTGACAGAGAATTCTCAAC+TGG 0.474765 1.3:-37583383 MS.gene84933:CDS
TACTTTCTCAAATCAATTGG+TGG 0.486384 1.3:+37583131 None:intergenic
TCTGCTTCATCATCTTCACC+AGG 0.486883 1.3:+37582702 None:intergenic
GCAGAAATGTGGGTGGGAAT+GGG 0.488317 1.3:-37582956 MS.gene84933:CDS
TTTGCTTCATCATCTTCACC+AGG 0.497903 1.3:+37582663 None:intergenic
TTCATGGTCACATACCTCAT+TGG 0.503644 1.3:+37583101 None:intergenic
TTTAACCCCAATTCATGAGT+TGG 0.505846 1.3:+37582633 None:intergenic
CAATTGGTGGAAATTGATCC+AGG 0.509751 1.3:+37583144 None:intergenic
GGAATCACCGTGTCACGAAA+AGG 0.512728 1.3:-37582989 MS.gene84933:CDS
TTCTCAACTGGTAATGCTCT+CGG 0.517217 1.3:-37583371 MS.gene84933:CDS
GATCAAACTTTGCAGAAATG+TGG 0.524856 1.3:-37582967 MS.gene84933:CDS
ATATGGTTCGACTTCGAAGA+AGG 0.528018 1.3:-37583183 MS.gene84933:CDS
CAACAAGGTTGTTAGGTGAT+CGG 0.537111 1.3:+37583012 None:intergenic
ATGTGACCATGAAACGGAGC+TGG 0.548343 1.3:-37583091 MS.gene84933:CDS
ATCAAACTTTGCAGAAATGT+GGG 0.554714 1.3:-37582966 MS.gene84933:CDS
AAAAGGAGTGTTGTTGATCA+TGG 0.555395 1.3:-37583431 MS.gene84933:CDS
ATGGTCACATACCTCATTGG+TGG 0.556780 1.3:+37583104 None:intergenic
GGGTAGTAAGATTTATGACC+TGG 0.563188 1.3:-37583162 MS.gene84933:CDS
TGAGGTATGTGACCATGAAA+CGG 0.563267 1.3:-37583097 MS.gene84933:CDS
GAAGATCAGAGAGCAAGGTA+TGG 0.572806 1.3:-37582928 MS.gene84933:CDS
TTATGTTGCAGAAACAATGT+TGG 0.573586 1.3:-37583045 MS.gene84933:CDS
TCATCTGCATCATCATCCAC+TGG 0.575486 1.3:+37582579 None:intergenic
AATCAATGAGAAGAACAAGT+TGG 0.575910 1.3:-37582859 MS.gene84933:CDS
AACTTTGCAGAAATGTGGGT+GGG 0.585412 1.3:-37582962 MS.gene84933:CDS
GCAACGAACACATGAATGGT+TGG 0.590907 1.3:+37583262 None:intergenic
TGAAGATGATGAAGCAAATG+AGG 0.593094 1.3:-37582658 MS.gene84933:CDS
CAATGAGAAGAACAAGTTGG+TGG 0.593608 1.3:-37582856 MS.gene84933:CDS
CGATTTGAATGAGCTGCCAG+TGG 0.597243 1.3:-37582595 MS.gene84933:CDS
GATCAGAGAGCAAGGTATGG+TGG 0.597334 1.3:-37582925 MS.gene84933:CDS
AAGATGAAGATCAGAGAGCA+AGG 0.598147 1.3:-37582933 MS.gene84933:CDS
TATGGTTCGACTTCGAAGAA+GGG 0.600043 1.3:-37583182 MS.gene84933:CDS
TTGCTTCATCATCTTCACCA+GGG 0.604583 1.3:+37582664 None:intergenic
CTGCTTCATCATCTTCACCA+GGG 0.614062 1.3:+37582703 None:intergenic
TGACACGGTGATTCCCAACA+AGG 0.616814 1.3:+37582997 None:intergenic
AAACTTTGCAGAAATGTGGG+TGG 0.628923 1.3:-37582963 MS.gene84933:CDS
AGGAACCAACTCATGAATTG+GGG 0.629510 1.3:-37582638 MS.gene84933:CDS
TGAAGACGATGAAGCAGATG+AGG 0.631563 1.3:-37582736 MS.gene84933:CDS
GTTAGGTTAAAGATTCCGAA+TGG 0.637974 1.3:-37582834 MS.gene84933:CDS
GAAAGTATTTGCCACCAATG+AGG 0.638748 1.3:-37583115 MS.gene84933:CDS
GGCCACAAAGCATTCCATAG+AGG 0.645608 1.3:-37583347 MS.gene84933:CDS
TGCTGCAACGAACACATGAA+TGG 0.655011 1.3:+37583258 None:intergenic
TGAAGATGATGAAGCAGATG+AGG 0.659995 1.3:-37582697 MS.gene84933:CDS
AATGAAGAGAACAACAACAC+TGG 0.663304 1.3:-37582759 MS.gene84933:CDS
GATGAGGAACCAAACAACCC+TGG 0.684317 1.3:-37582681 MS.gene84933:CDS
GATGAGGAACCAAACAACCC+TGG 0.684317 1.3:-37582720 MS.gene84933:CDS
TCAACTGGTAATGCTCTCGG+CGG 0.775161 1.3:-37583368 MS.gene84933:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACTTTCTCAAATCAAT+TGG + chr1.3:37582938-37582957 None:intergenic 20.0%
AACAAAGAAAAACATGCTGA+TGG - chr1.3:37582764-37582783 MS.gene84933:CDS 30.0%
AATCAATGAGAAGAACAAGT+TGG - chr1.3:37583204-37583223 MS.gene84933:CDS 30.0%
ACTCTCATCACAAAACAAAA+AGG - chr1.3:37582615-37582634 MS.gene84933:CDS 30.0%
ATCAAACTTTGCAGAAATGT+GGG - chr1.3:37583097-37583116 MS.gene84933:CDS 30.0%
GTTCTCTTCATTATCATCAT+TGG + chr1.3:37583296-37583315 None:intergenic 30.0%
TACTTTCTCAAATCAATTGG+TGG + chr1.3:37582935-37582954 None:intergenic 30.0%
TTATGTTGCAGAAACAATGT+TGG - chr1.3:37583018-37583037 MS.gene84933:CDS 30.0%
! CTTGTGATTTTTGAATGACA+AGG + chr1.3:37583255-37583274 None:intergenic 30.0%
AAAGAAAGTTGTTGCCTCTA+TGG + chr1.3:37582733-37582752 None:intergenic 35.0%
AATGAAGAGAACAACAACAC+TGG - chr1.3:37583304-37583323 MS.gene84933:CDS 35.0%
ATCATTGGAAGCAGATTGAT+TGG + chr1.3:37583281-37583300 None:intergenic 35.0%
GATCAAACTTTGCAGAAATG+TGG - chr1.3:37583096-37583115 MS.gene84933:CDS 35.0%
GTTAGGTTAAAGATTCCGAA+TGG - chr1.3:37583229-37583248 MS.gene84933:CDS 35.0%
TGAAGATGATGAAGCAAATG+AGG - chr1.3:37583405-37583424 MS.gene84933:CDS 35.0%
TTTAACCCCAATTCATGAGT+TGG + chr1.3:37583433-37583452 None:intergenic 35.0%
! AGAGGCAACAACTTTCTTTT+AGG - chr1.3:37582734-37582753 MS.gene84933:CDS 35.0%
! TTTTGAATGACAAGGCCATT+CGG + chr1.3:37583247-37583266 None:intergenic 35.0%
!! AAAAGGAGTGTTGTTGATCA+TGG - chr1.3:37582632-37582651 MS.gene84933:CDS 35.0%
AAACTTTGCAGAAATGTGGG+TGG - chr1.3:37583100-37583119 MS.gene84933:CDS 40.0%
AACTTTGCAGAAATGTGGGT+GGG - chr1.3:37583101-37583120 MS.gene84933:CDS 40.0%
AAGATGAAGATCAGAGAGCA+AGG - chr1.3:37583130-37583149 MS.gene84933:CDS 40.0%
AGGAACCAACTCATGAATTG+GGG - chr1.3:37583425-37583444 MS.gene84933:CDS 40.0%
ATAATTCCAGCTCCGTTTCA+TGG + chr1.3:37582981-37583000 None:intergenic 40.0%
ATATGGTTCGACTTCGAAGA+AGG - chr1.3:37582880-37582899 MS.gene84933:CDS 40.0%
ATGAAATCGCACAGCCAATA+TGG - chr1.3:37582863-37582882 MS.gene84933:CDS 40.0%
CAACAAGGTTGTTAGGTGAT+CGG + chr1.3:37583054-37583073 None:intergenic 40.0%
CAATTGGTGGAAATTGATCC+AGG + chr1.3:37582922-37582941 None:intergenic 40.0%
GAGGAACCAACTCATGAATT+GGG - chr1.3:37583424-37583443 MS.gene84933:CDS 40.0%
GATCACCTAACAACCTTGTT+GGG - chr1.3:37583053-37583072 MS.gene84933:CDS 40.0%
GGGTAGTAAGATTTATGACC+TGG - chr1.3:37582901-37582920 MS.gene84933:CDS 40.0%
TATGGTTCGACTTCGAAGAA+GGG - chr1.3:37582881-37582900 MS.gene84933:CDS 40.0%
TCATCTGTCAATGCACTGAA+TGG - chr1.3:37582836-37582855 MS.gene84933:CDS 40.0%
TCTTCGAAGTCGAACCATAT+TGG + chr1.3:37582880-37582899 None:intergenic 40.0%
TGAAGATGATGAAGCAGATG+AGG - chr1.3:37583366-37583385 MS.gene84933:CDS 40.0%
TGAGGAACCAACTCATGAAT+TGG - chr1.3:37583423-37583442 MS.gene84933:CDS 40.0%
TGAGGTATGTGACCATGAAA+CGG - chr1.3:37582966-37582985 MS.gene84933:CDS 40.0%
TGATTCCCAACAAGGTTGTT+AGG + chr1.3:37583061-37583080 None:intergenic 40.0%
TGTGACAGAGAATTCTCAAC+TGG - chr1.3:37582680-37582699 MS.gene84933:CDS 40.0%
TTCATGGTCACATACCTCAT+TGG + chr1.3:37582965-37582984 None:intergenic 40.0%
TTGCTTCATCATCTTCACCA+GGG + chr1.3:37583402-37583421 None:intergenic 40.0%
TTTGCTTCATCATCTTCACC+AGG + chr1.3:37583403-37583422 None:intergenic 40.0%
! CAATGAGAAGAACAAGTTGG+TGG - chr1.3:37583207-37583226 MS.gene84933:CDS 40.0%
! GTTTGATCCTTTTCGTGACA+CGG + chr1.3:37583084-37583103 None:intergenic 40.0%
! TTCTCAACTGGTAATGCTCT+CGG - chr1.3:37582692-37582711 MS.gene84933:CDS 40.0%
!! AGAAGAACAAGTTGGTGGTT+AGG - chr1.3:37583212-37583231 MS.gene84933:CDS 40.0%
!! GAAAGTATTTGCCACCAATG+AGG - chr1.3:37582948-37582967 MS.gene84933:CDS 40.0%
ATGGTCACATACCTCATTGG+TGG + chr1.3:37582962-37582981 None:intergenic 45.0%
CGATCACCTAACAACCTTGT+TGG - chr1.3:37583052-37583071 MS.gene84933:CDS 45.0%
CTGCTTCATCATCTTCACCA+GGG + chr1.3:37583363-37583382 None:intergenic 45.0%
GAAGATCAGAGAGCAAGGTA+TGG - chr1.3:37583135-37583154 MS.gene84933:CDS 45.0%
GCAACGAACACATGAATGGT+TGG + chr1.3:37582804-37582823 None:intergenic 45.0%
TCATCTGCATCATCATCCAC+TGG + chr1.3:37583487-37583506 None:intergenic 45.0%
TCATCTTCACCAGGGTTGTT+TGG + chr1.3:37583355-37583374 None:intergenic 45.0%
TCTGCTTCATCATCTTCACC+AGG + chr1.3:37583364-37583383 None:intergenic 45.0%
TGAAGACGATGAAGCAGATG+AGG - chr1.3:37583327-37583346 MS.gene84933:CDS 45.0%
TGCCTCTATGGAATGCTTTG+TGG + chr1.3:37582721-37582740 None:intergenic 45.0%
TGCTGCAACGAACACATGAA+TGG + chr1.3:37582808-37582827 None:intergenic 45.0%
ATGTGACCATGAAACGGAGC+TGG - chr1.3:37582972-37582991 MS.gene84933:CDS 50.0%
CGATTTGAATGAGCTGCCAG+TGG - chr1.3:37583468-37583487 MS.gene84933:CDS 50.0%
GATCAGAGAGCAAGGTATGG+TGG - chr1.3:37583138-37583157 MS.gene84933:CDS 50.0%
GATGAGGAACCAAACAACCC+TGG - chr1.3:37583343-37583362 MS.gene84933:CDS 50.0%
GCAGAAATGTGGGTGGGAAT+GGG - chr1.3:37583107-37583126 MS.gene84933:CDS 50.0%
GGAATCACCGTGTCACGAAA+AGG - chr1.3:37583074-37583093 MS.gene84933:CDS 50.0%
TGACACGGTGATTCCCAACA+AGG + chr1.3:37583069-37583088 None:intergenic 50.0%
TGCAGAAATGTGGGTGGGAA+TGG - chr1.3:37583106-37583125 MS.gene84933:CDS 50.0%
! GGCCACAAAGCATTCCATAG+AGG - chr1.3:37582716-37582735 MS.gene84933:CDS 50.0%
! TCAACTGGTAATGCTCTCGG+CGG - chr1.3:37582695-37582714 MS.gene84933:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 37582566 37583519 37582566 ID=MS.gene84933
chr1.3 mRNA 37582566 37583519 37582566 ID=MS.gene84933.t1;Parent=MS.gene84933
chr1.3 exon 37582566 37583519 37582566 ID=MS.gene84933.t1.exon1;Parent=MS.gene84933.t1
chr1.3 CDS 37582566 37583519 37582566 ID=cds.MS.gene84933.t1;Parent=MS.gene84933.t1
Gene Sequence

>MS.gene84933

ATGAAGCATTTTTTTTCTTCTGCTTCTTCTTCTTCTTCTTCTTCATCTCACTCTCATCACAAAACAAAAAGGAGTGTTGTTGATCATGGTGCAAAACTTCACAAATGTGATTTGTGTGACAGAGAATTCTCAACTGGTAATGCTCTCGGCGGCCACAAAGCATTCCATAGAGGCAACAACTTTCTTTTAGGAAAAATCAACAAAGAAAAACATGCTGATGGTATTAAGATCGAAACCAACCATTCATGTGTTCGTTGCAGCAAGACTTTTTCATCTGTCAATGCACTGAATGGACACATGAAATCGCACAGCCAATATGGTTCGACTTCGAAGAAGGGTAGTAAGATTTATGACCTGGATCAATTTCCACCAATTGATTTGAGAAAGTATTTGCCACCAATGAGGTATGTGACCATGAAACGGAGCTGGAATTATGTTATTAATGTTGAAGCTTATGTTGCAGAAACAATGTTGGATCTGTCACACCGATCACCTAACAACCTTGTTGGGAATCACCGTGTCACGAAAAGGATCAAACTTTGCAGAAATGTGGGTGGGAATGGGAAGATGAAGATCAGAGAGCAAGGTATGGTGGTAAAACATTGTGTTGATGAAACAATTGTGAGAGAGACTGATCAAATCAATGAGAAGAACAAGTTGGTGGTTAGGTTAAAGATTCCGAATGGCCTTGTCATTCAAAAATCACAAGCTTCCAATCAATCTGCTTCCAATGATGATAATGAAGAGAACAACAACACTGGTGAAGACGATGAAGCAGATGAGGAACCAAACAACCCTGGTGAAGATGATGAAGCAGATGAGGAACCAAACAACCCTGGTGAAGATGATGAAGCAAATGAGGAACCAACTCATGAATTGGGGTTAAATGTTGTTCGAGATTTCGATTTGAATGAGCTGCCAGTGGATGATGATGCAGATGAAACCGCCCATTAG
Protein sequence

>MS.gene84933.t1

MKHFFSSASSSSSSSSHSHHKTKRSVVDHGAKLHKCDLCDREFSTGNALGGHKAFHRGNNFLLGKINKEKHADGIKIETNHSCVRCSKTFSSVNALNGHMKSHSQYGSTSKKGSKIYDLDQFPPIDLRKYLPPMRYVTMKRSWNYVINVEAYVAETMLDLSHRSPNNLVGNHRVTKRIKLCRNVGGNGKMKIREQGMVVKHCVDETIVRETDQINEKNKLVVRLKIPNGLVIQKSQASNQSASNDDNEENNNTGEDDEADEEPNNPGEDDEADEEPNNPGEDDEANEEPTHELGLNVVRDFDLNELPVDDDADETAH