AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG040252

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040252 MtrunA17_Chr7g0268031 95.969 521 18 2 1 518 1 521 0.0 1022
MsaG040252 MtrunA17_Chr3g0132281 39.071 366 210 8 87 442 13 375 2.74e-73 250
MsaG040252 MtrunA17_Chr3g0117261 27.682 289 146 11 208 442 18 297 2.80e-15 78.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040252 AT5G06550.1 73.753 461 114 5 60 518 47 502 0.0 700
MsaG040252 AT1G78280.1 39.402 368 210 8 84 442 5 368 1.64e-78 265
MsaG040252 AT5G63080.1 27.758 281 155 9 208 449 12 283 5.67e-18 87.0

Find 137 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGGATTTGTTTGGTGTTT+TGG 0.172983 7:-98386652 MsaT040252.1:CDS
TTCCAAGCTGAAGTTGAATT+TGG 0.188370 7:+98386558 None:intergenic
GATTATAGGTGGATTATTAT+TGG 0.189791 7:-98386615 MsaT040252.1:CDS
ATGAAGCTTAAGGACTATTT+TGG 0.203220 7:-98386783 MsaT040252.1:CDS
TCTACCTTTGTTGTTTCTAA+TGG 0.205554 7:-98387113 MsaT040252.1:CDS
GAATTGGGATAGAGATTATT+TGG 0.233632 7:-98386853 MsaT040252.1:CDS
GTTGATGGGTTTCAGTATAA+TGG 0.244611 7:-98387146 MsaT040252.1:CDS
TGGAAGGGTGTATTGATAAT+TGG 0.249263 7:-98386887 MsaT040252.1:CDS
TATGTATGAATTTCTTTAAA+AGG 0.261215 7:+98385029 None:intergenic
TGGTAATAGTTTAGGGGTTT+TGG 0.265190 7:-98387243 MsaT040252.1:CDS
TGTTAGGAAGAGAGGGATTT+CGG 0.288689 7:-98386958 MsaT040252.1:CDS
GAGCTTGTTCTTGATATTCT+AGG 0.289370 7:-98387275 MsaT040252.1:CDS
GGGTACCCTTTGTTTGATAT+CGG 0.290302 7:-98387092 MsaT040252.1:CDS
AGAAGGAAAGTTTCCTTTGC+TGG 0.297251 7:+98385094 None:intergenic
CTACCTTTGTTGTTTCTAAT+GGG 0.312871 7:-98387112 MsaT040252.1:CDS
ATTGGGATGCATTGAGGAAT+TGG 0.321571 7:-98386869 MsaT040252.1:CDS
TAATGGAAGAAATGGGGTTT+TGG 0.321890 7:+98387474 None:intergenic
GAAGAGAGGGATTTCGGTTG+AGG 0.331066 7:-98386952 MsaT040252.1:CDS
TCATATTCCAAACCCAATTT+CGG 0.340210 7:+98386693 None:intergenic
GCAAAGGAAACTTTCCTTCT+GGG 0.341277 7:-98385091 MsaT040252.1:CDS
TTTATGGTGCAACAAAGAAT+TGG 0.346410 7:-98386407 MsaT040252.1:CDS
GATAATATTGTTAGGAAGAG+AGG 0.347047 7:-98386966 MsaT040252.1:CDS
AACCATTCAATTATTGAAAC+AGG 0.349564 7:+98386438 None:intergenic
AGCAAAGGAAACTTTCCTTC+TGG 0.361388 7:-98385092 MsaT040252.1:CDS
TTGATGGGTTTCAGTATAAT+GGG 0.365569 7:-98387145 MsaT040252.1:CDS
AAAAGTTCCGAAATTGGGTT+TGG 0.367524 7:-98386700 MsaT040252.1:CDS
AACGCAAGCACACTGGTATC+TGG 0.370811 7:-98385222 MsaT040252.1:CDS
GCCCAGTGGTTGGTGGCATT+TGG 0.374870 7:-98386334 MsaT040252.1:CDS
TGGAGAGGGATAATATTGTT+AGG 0.381335 7:-98386974 MsaT040252.1:CDS
CACCCACGGTGTTCAGCCCT+TGG 0.382559 7:-98387372 MsaT040252.1:CDS
TTGGGATGCATTGAGGAATT+GGG 0.385650 7:-98386868 MsaT040252.1:CDS
TGATCAAGGGGTCGAAGAAA+TGG 0.385678 7:-98386530 MsaT040252.1:CDS
ACCAGTGTCTCTGGAGTTGA+TGG 0.391428 7:+98387325 None:intergenic
GAGAAATTTGTTAAGTGTCT+TGG 0.391444 7:-98385262 MsaT040252.1:CDS
GGAAGGGTGTATTGATAATT+GGG 0.393852 7:-98386886 MsaT040252.1:CDS
ATTATTGGACCAGCTGGGTC+TGG 0.396567 7:-98386600 MsaT040252.1:CDS
GAAATGAGAGACCTGATTAT+AGG 0.398403 7:-98386629 MsaT040252.1:CDS
GAACACCGTGGGTGTGTGAC+GGG 0.400221 7:+98387381 None:intergenic
TCACTAATCATGAACCCCTT+TGG 0.406513 7:-98387193 MsaT040252.1:CDS
GGTTAATAAGCCGGTGTTGT+TGG 0.408373 7:-98386907 MsaT040252.1:CDS
GGGTTTGGAATATGAAGTTC+CGG 0.409696 7:-98386685 MsaT040252.1:CDS
CTCCTGTTTCAATAATTGAA+TGG 0.415829 7:-98386440 MsaT040252.1:CDS
ATAATAATCCACCTATAATC+AGG 0.419067 7:+98386618 None:intergenic
GCTAACATAGTTCTGTGTTA+TGG 0.419792 7:+98386287 None:intergenic
ATTACCTAAACCAGTGTCTC+TGG 0.422088 7:+98387316 None:intergenic
GATGCTACCTCTGCACCATC+AGG 0.424520 7:+98386462 None:intergenic
GGCAATCTCTATTTCAATCC+AGG 0.425479 7:-98387350 MsaT040252.1:CDS
TTGATATCGGGAGTGGCGTT+CGG 0.426068 7:-98387079 MsaT040252.1:CDS
AGCTTGGAATGCTGTGATCA+AGG 0.428224 7:-98386544 MsaT040252.1:CDS
AGCTTGTTCTTGATATTCTA+GGG 0.429419 7:-98387274 MsaT040252.1:CDS
AACTCCAGAGACACTGGTTT+AGG 0.430834 7:-98387320 MsaT040252.1:CDS
TGGATTATTATTGGACCAGC+TGG 0.431844 7:-98386606 MsaT040252.1:CDS
GCTTTACATATGCACTCAAT+TGG 0.441061 7:+98386375 None:intergenic
GGTACCCTTTGTTTGATATC+GGG 0.441137 7:-98387091 MsaT040252.1:CDS
TGAACACCGTGGGTGTGTGA+CGG 0.450073 7:+98387380 None:intergenic
GATTTCGGTTGAGGAGTTTG+TGG 0.461360 7:-98386943 MsaT040252.1:CDS
ATCCAAATTCAACTTCAGCT+TGG 0.469977 7:-98386560 MsaT040252.1:CDS
CACACTGGTATCTGGAACAA+AGG 0.473108 7:-98385214 MsaT040252.1:CDS
GATACCAGTGTGCTTGCGTT+CGG 0.473719 7:+98385225 None:intergenic
GTGTCTTGGAGTTTCTTAAG+AGG 0.477250 7:-98385248 MsaT040252.1:CDS
AATAAGCCGGTGTTGTTGGA+AGG 0.481648 7:-98386903 MsaT040252.1:CDS
GCTTGGAATGCTGTGATCAA+GGG 0.490367 7:-98386543 MsaT040252.1:CDS
CACCAAATGCCACCAACCAC+TGG 0.491804 7:+98386332 None:intergenic
CCTTTGTTTGATATCGGGAG+TGG 0.492650 7:-98387086 MsaT040252.1:CDS
TTTGATGTCGAAACATTCTT+CGG 0.495045 7:+98387412 None:intergenic
TGAAAGGTGAATGGTTGGAG+AGG 0.498202 7:-98386989 MsaT040252.1:CDS
ACCCACGGTGTTCAGCCCTT+GGG 0.502505 7:-98387371 MsaT040252.1:CDS
GCCTGTGGAGATGAAGCTTA+AGG 0.506931 7:-98386793 MsaT040252.1:CDS
GATCAAGGGGTCGAAGAAAT+GGG 0.508230 7:-98386529 MsaT040252.1:CDS
CAGATCAAGTTAGAGAAGAA+AGG 0.508713 7:-98386755 MsaT040252.1:CDS
TCTCTGGAGTTGATGGAACC+TGG 0.509296 7:+98387332 None:intergenic
CCTTTGGAGGAATCTTGTGT+TGG 0.509661 7:-98387177 MsaT040252.1:CDS
CTAATCATGAACCCCTTTGG+AGG 0.514583 7:-98387190 MsaT040252.1:CDS
CAACACAAGATTCCTCCAAA+GGG 0.515604 7:+98387178 None:intergenic
GTCAGTTCATCAATTGCTCC+AGG 0.519066 7:+98385141 None:intergenic
ATTGAGTGCATATGTAAAGC+GGG 0.520028 7:-98386372 MsaT040252.1:CDS
TCCTTAAGCTTCATCTCCAC+AGG 0.521980 7:+98386792 None:intergenic
ATAATATTGTTAGGAAGAGA+GGG 0.523338 7:-98386965 MsaT040252.1:CDS
TTATCTTTGTGCCCAGTGGT+TGG 0.523418 7:-98386344 MsaT040252.1:CDS
TCTTTGTGCCCAGTGGTTGG+TGG 0.525495 7:-98386341 MsaT040252.1:CDS
ACCTCTGCACCATCAGGGCT+AGG 0.527425 7:+98386468 None:intergenic
GAACTTGAAAGCTCCCACTC+TGG 0.530094 7:+98385053 None:intergenic
TAAGTTTAAGAATGCTATTG+AGG 0.530123 7:-98385172 MsaT040252.1:CDS
TTATGGCAATTGATTCCTCC+AGG 0.530459 7:+98386304 None:intergenic
CACTCCCGATATCAAACAAA+GGG 0.531337 7:+98387087 None:intergenic
GTGGCATTTGGTGATCAACC+TGG 0.533188 7:-98386322 MsaT040252.1:CDS
TAACACAGAACTATGTTAGC+AGG 0.539722 7:-98386284 MsaT040252.1:intron
TGAAATGAAAGGTGAATGGT+TGG 0.544161 7:-98386994 MsaT040252.1:CDS
GGTGTTCATCCTAGCCCTGA+TGG 0.546334 7:-98386477 MsaT040252.1:CDS
CCTCCCGATGTTATTCCGCC+CGG 0.551681 7:-98386498 MsaT040252.1:CDS
TCCATCAACTCCAGAGACAC+TGG 0.557132 7:-98387326 MsaT040252.1:CDS
GGTTTCAGTATAATGGGTCA+TGG 0.560008 7:-98387139 MsaT040252.1:CDS
ACCAAATGCCACCAACCACT+GGG 0.564265 7:+98386333 None:intergenic
CTTCTTCAACGAGAGATGAG+TGG 0.567416 7:+98387444 None:intergenic
GATTATTTGGTTAAGTTGTG+TGG 0.571733 7:-98386840 MsaT040252.1:CDS
TTGATAATTGGGATGCATTG+AGG 0.572075 7:-98386875 MsaT040252.1:CDS
GAAAGGTGAATGGTTGGAGA+GGG 0.572473 7:-98386988 MsaT040252.1:CDS
ATAAGCCGGTGTTGTTGGAA+GGG 0.582277 7:-98386902 MsaT040252.1:CDS
CCAACACAAGATTCCTCCAA+AGG 0.589735 7:+98387177 None:intergenic
ATCTTGAAATGAAAGGTGAA+TGG 0.590130 7:-98386998 MsaT040252.1:CDS
ACACCGGGCGGAATAACATC+GGG 0.595142 7:+98386495 None:intergenic
ATCAGGGCTAGGATGAACAC+CGG 0.595347 7:+98386479 None:intergenic
AAGAACAAGCTCATCAGTGA+GGG 0.597323 7:+98387286 None:intergenic
GCCCAAGGGCTGAACACCGT+GGG 0.602240 7:+98387370 None:intergenic
ATGAGAGACCTGATTATAGG+TGG 0.603392 7:-98386626 MsaT040252.1:CDS
TCCTAGCCCTGATGGTGCAG+AGG 0.603932 7:-98386469 MsaT040252.1:CDS
GAGGTTATCTTTGTGCCCAG+TGG 0.605601 7:-98386348 MsaT040252.1:CDS
GGATTATTATTGGACCAGCT+GGG 0.609112 7:-98386605 MsaT040252.1:CDS
AACACCGGGCGGAATAACAT+CGG 0.610276 7:+98386494 None:intergenic
TTTAGATGGTAATAGTTTAG+GGG 0.614858 7:-98387249 MsaT040252.1:CDS
TGTGCTAATCTTGAAATGAA+AGG 0.615147 7:-98387005 MsaT040252.1:CDS
CTTGGAATGCTGTGATCAAG+GGG 0.619460 7:-98386542 MsaT040252.1:CDS
AAAGACGATCCAGACCCAGC+TGG 0.622160 7:+98386591 None:intergenic
TCTGCCCCGTCACACACCCA+CGG 0.625768 7:-98387386 MsaT040252.1:CDS
AACACCGTGGGTGTGTGACG+GGG 0.625830 7:+98387382 None:intergenic
TTTGGATCAAACAGATACAA+CGG 0.630505 7:+98386732 None:intergenic
TCTGTTGCAGACACCAGAGT+GGG 0.640693 7:-98385066 MsaT040252.1:CDS
CCACTCCCGATATCAAACAA+AGG 0.643905 7:+98387086 None:intergenic
ATGCTACCTCTGCACCATCA+GGG 0.644492 7:+98386463 None:intergenic
TTGAGTGCATATGTAAAGCG+GGG 0.644930 7:-98386371 MsaT040252.1:CDS
AATTGAGTGCATATGTAAAG+CGG 0.648535 7:-98386373 MsaT040252.1:CDS
GAGGCCGAACGCAAGCACAC+TGG 0.652835 7:-98385229 MsaT040252.1:CDS
GTCTGCAACAGAATCCCAGA+AGG 0.653217 7:+98385077 None:intergenic
CAAGAACAAGCTCATCAGTG+AGG 0.659400 7:+98387285 None:intergenic
TTGAAATAGAGATTGCCCAA+GGG 0.664210 7:+98387356 None:intergenic
AAATCCTCCCGAAAATACAC+CGG 0.666892 7:+98386666 None:intergenic
TCAGGGCTAGGATGAACACC+GGG 0.669209 7:+98386480 None:intergenic
ATACACCCTTCCAACAACAC+CGG 0.670300 7:+98386897 None:intergenic
CCGGGCGGAATAACATCGGG+AGG 0.670441 7:+98386498 None:intergenic
TGCCCAAGGGCTGAACACCG+TGG 0.670914 7:+98387369 None:intergenic
ATTGAAATAGAGATTGCCCA+AGG 0.684435 7:+98387355 None:intergenic
TTCTGTTGCAGACACCAGAG+TGG 0.688725 7:-98385067 MsaT040252.1:CDS
GTACCCATTAGAAACAACAA+AGG 0.698809 7:+98387109 None:intergenic
AACACAAGATTCCTCCAAAG+GGG 0.706242 7:+98387179 None:intergenic
TGAGTGCATATGTAAAGCGG+GGG 0.706771 7:-98386370 MsaT040252.1:CDS
GCATTTGGTGATCAACCTGG+AGG 0.725951 7:-98386319 MsaT040252.1:CDS
GGGCTAGGATGAACACCGGG+CGG 0.735361 7:+98386483 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 98385044 98387600 98385044 ID=MsaG040252
Chr7 mRNA 98385044 98387600 98385044 ID=MsaT040252.1;Parent=MsaG040252
Chr7 exon 98385044 98385284 98385044 ID=MsaT040252.1.exon2;Parent=MsaT040252.1
Chr7 CDS 98385044 98385284 98385044 ID=cds.MsaT040252.1;Parent=MsaT040252.1
Chr7 exon 98386285 98387600 98386285 ID=MsaT040252.1.exon1;Parent=MsaT040252.1
Chr7 CDS 98386285 98387600 98386285 ID=cds.MsaT040252.1;Parent=MsaT040252.1
Gene Sequence

>MsaT040252.1

ATGTTGAGTTTCAGAATGATGAACTTGTTGTCCCGTATCAAAACAAGAACAAAGAAGAAAATCACCAAAAAAAACCGAAACAAAAACCCTCACAAACTCAAAAACCAAAACCCCATTTCTTCCATTACTAAAAACCACTCATCTCTCGTTGAAGAAGAAGAAGACGCCGAAGAATGTTTCGACATCAAAAGCTCTGCCCCGTCACACACCCACGGTGTTCAGCCCTTGGGCAATCTCTATTTCAATCCAGGTTCCATCAACTCCAGAGACACTGGTTTAGGTAATCTTCATACCCTCACTGATGAGCTTGTTCTTGATATTCTAGGGTTTTTAGATGGTAATAGTTTAGGGGTTTTGGCTTGTGTGAGTAAATCGTTTTATGTTTTCACTAATCATGAACCCCTTTGGAGGAATCTTGTGTTGGAGAATTTTGTTGATGGGTTTCAGTATAATGGGTCATGGAAATCTACCTTTGTTGTTTCTAATGGGTACCCTTTGTTTGATATCGGGAGTGGCGTTCGGAGTTTTAAAGTTAGAGACTTTTATTCGGATTATCTTTTTCAGAGTTGGTTATGTGCTAATCTTGAAATGAAAGGTGAATGGTTGGAGAGGGATAATATTGTTAGGAAGAGAGGGATTTCGGTTGAGGAGTTTGTGGCGAATTTTGAGGAGGTTAATAAGCCGGTGTTGTTGGAAGGGTGTATTGATAATTGGGATGCATTGAGGAATTGGGATAGAGATTATTTGGTTAAGTTGTGTGGTGATGATGTTAAGTTTTCGGTTGGGCCTGTGGAGATGAAGCTTAAGGACTATTTTGGTTACTCAGATCAAGTTAGAGAAGAAAGGCCGTTGTATCTGTTTGATCCAAAATTTGCTGAAAAAGTTCCGAAATTGGGTTTGGAATATGAAGTTCCGGTGTATTTTCGGGAGGATTTGTTTGGTGTTTTGGGAAATGAGAGACCTGATTATAGGTGGATTATTATTGGACCAGCTGGGTCTGGATCGTCTTTTCACGTTGATCCAAATTCAACTTCAGCTTGGAATGCTGTGATCAAGGGGTCGAAGAAATGGGTATTGTTTCCTCCCGATGTTATTCCGCCCGGTGTTCATCCTAGCCCTGATGGTGCAGAGGTAGCATCTCCTGTTTCAATAATTGAATGGTTCATGAACTTTTATGGTGCAACAAAGAATTGGAAAAAGAAGCCAATTGAGTGCATATGTAAAGCGGGGGAGGTTATCTTTGTGCCCAGTGGTTGGTGGCATTTGGTGATCAACCTGGAGGAATCAATTGCCATAACACAGAACTATGTTAGCAGGAGAAATTTGTTAAGTGTCTTGGAGTTTCTTAAGAGGCCGAACGCAAGCACACTGGTATCTGGAACAAAGGATAGAGTAAATTTGCATGATAAGTTTAAGAATGCTATTGAGGCTTCTTTTCCTGGAGCAATTGATGAACTGACCCAAAAAGAAGAAGAGAAAAAGATCCAGCAAAGGAAACTTTCCTTCTGGGATTCTGTTGCAGACACCAGAGTGGGAGCTTTCAAGTTCTCCTTTTAA
Protein sequence

>MsaT040252.1

MLSFRMMNLLSRIKTRTKKKITKKNRNKNPHKLKNQNPISSITKNHSSLVEEEEDAEECFDIKSSAPSHTHGVQPLGNLYFNPGSINSRDTGLGNLHTLTDELVLDILGFLDGNSLGVLACVSKSFYVFTNHEPLWRNLVLENFVDGFQYNGSWKSTFVVSNGYPLFDIGSGVRSFKVRDFYSDYLFQSWLCANLEMKGEWLERDNIVRKRGISVEEFVANFEEVNKPVLLEGCIDNWDALRNWDRDYLVKLCGDDVKFSVGPVEMKLKDYFGYSDQVREERPLYLFDPKFAEKVPKLGLEYEVPVYFREDLFGVLGNERPDYRWIIIGPAGSGSSFHVDPNSTSAWNAVIKGSKKWVLFPPDVIPPGVHPSPDGAEVASPVSIIEWFMNFYGATKNWKKKPIECICKAGEVIFVPSGWWHLVINLEESIAITQNYVSRRNLLSVLEFLKRPNASTLVSGTKDRVNLHDKFKNAIEASFPGAIDELTQKEEEKKIQQRKLSFWDSVADTRVGAFKFSF*