AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG002896

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002896 MtrunA17_Chr1g0179191 96.332 518 10 3 1 516 1 511 0.0 1031
MsaG002896 MtrunA17_Chr7g0265831 51.471 544 147 18 14 515 6 474 2.20e-152 444
MsaG002896 MtrunA17_Chr1g0198171 39.750 400 172 14 25 379 10 385 1.15e-77 252
MsaG002896 MtrunA17_Chr6g0463941 38.567 293 133 5 129 375 46 337 5.80e-41 156
MsaG002896 MtrunA17_Chr6g0463941 47.312 93 47 2 132 223 460 551 5.26e-20 93.6
MsaG002896 MtrunA17_Chr1g0201911 32.542 295 162 4 136 402 55 340 2.12e-35 139
MsaG002896 MtrunA17_Chr1g0201911 40.458 131 71 4 125 254 361 485 3.10e-22 100
MsaG002896 MtrunA17_Chr1g0201941 65.263 95 30 2 130 222 49 142 1.13e-32 132
MsaG002896 MtrunA17_Chr1g0201941 46.000 100 51 3 127 225 446 543 2.16e-20 94.7
MsaG002896 MtrunA17_Chr1g0201941 39.535 86 52 0 290 375 272 357 2.04e-13 72.8
MsaG002896 MtrunA17_Chr1g0190851 29.046 241 145 8 137 371 104 324 1.44e-14 76.3
MsaG002896 MtrunA17_Chr1g0190851 37.607 117 58 4 136 238 418 533 1.99e-12 69.7
MsaG002896 MtrunA17_Chr7g0273941 36.220 127 70 3 109 225 354 479 1.57e-14 75.9
MsaG002896 MtrunA17_Chr2g0290511 38.053 113 65 3 131 239 257 368 3.81e-14 74.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002896 AT5G03680.1 57.929 309 100 9 136 420 119 421 4.35e-101 316
MsaG002896 AT3G10000.1 44.170 446 198 13 103 513 49 478 6.41e-100 310
MsaG002896 AT3G10000.2 42.152 446 197 14 103 513 49 468 1.19e-89 283
MsaG002896 AT1G76890.2 33.654 312 135 7 129 375 34 338 1.96e-39 151
MsaG002896 AT1G76890.2 45.098 102 54 2 133 233 394 494 3.39e-19 91.3
MsaG002896 AT1G76880.1 63.918 97 32 2 136 232 61 154 1.60e-31 129
MsaG002896 AT1G76880.1 44.538 119 55 4 117 225 380 497 8.35e-19 90.1
MsaG002896 AT1G33240.3 64.368 87 30 1 136 222 62 147 1.20e-29 123
MsaG002896 AT1G33240.3 43.820 89 48 2 136 223 435 522 1.70e-16 82.8
MsaG002896 AT1G33240.1 64.368 87 30 1 136 222 62 147 1.76e-29 123
MsaG002896 AT1G33240.1 43.820 89 48 2 136 223 435 522 1.72e-16 83.2
MsaG002896 AT1G33240.2 43.820 89 48 2 136 223 396 483 1.95e-16 82.8
MsaG002896 AT1G33240.2 72.340 47 13 0 176 222 62 108 2.86e-15 79.3
MsaG002896 AT5G28300.1 39.604 101 49 4 136 225 459 558 1.30e-12 70.9
MsaG002896 AT5G47660.1 42.857 91 44 4 136 223 303 388 1.75e-11 66.6

Find 118 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATTAGCTTCTTTAAATTT+AGG 0.106926 1:-48923484 None:intergenic
GGAAATTTGTGGGAGAATTT+TGG 0.154763 1:+48925636 MsaT002896.1:CDS
ATTATTGTTGTTGACAAAAT+TGG 0.173365 1:-48924845 None:intergenic
CTCTCATCAGTTAATGGTTT+TGG 0.213143 1:-48925680 None:intergenic
TCCTGAGACCACAGGTTATA+TGG 0.215513 1:+48923387 MsaT002896.1:CDS
ATGGAAGCTTTGAAGAATTT+AGG 0.224314 1:+48925243 MsaT002896.1:CDS
AGCAAGGGATGCTGCTTTAA+TGG 0.232544 1:+48925224 MsaT002896.1:CDS
CGTCAACTTGAAGCTTTATA+TGG 0.241815 1:+48924790 MsaT002896.1:CDS
CATGATCATAAGGGTGTAAA+TGG 0.261143 1:+48925297 MsaT002896.1:CDS
GATTAGCTTCTTTAAATTTA+GGG 0.283381 1:-48923483 None:intergenic
GGCATGATGGTAAGCATTAC+AGG 0.285238 1:+48924761 MsaT002896.1:CDS
TTGTTGACAAAATTGGTTTC+TGG 0.294784 1:-48924838 None:intergenic
TATGATCATTGTGAGGGTTT+TGG 0.304071 1:-48924894 None:intergenic
AGGAGGTAGAGAAATGATTA+AGG 0.310468 1:+48925263 MsaT002896.1:CDS
GTTCTGATAATTGTACTCTA+AGG 0.329879 1:+48925388 MsaT002896.1:CDS
TCTCATACTGTTGTTGTTGT+TGG 0.335695 1:-48923243 None:intergenic
AAGGGTGTAAATGGAATAAC+TGG 0.343913 1:+48925306 MsaT002896.1:CDS
TTTGGCTATTACTTGTTTGT+TGG 0.348056 1:-48924876 None:intergenic
GTTGTTGTTATTGTTGTTGA+AGG 0.351204 1:-48923334 None:intergenic
TACTCTAAGGGATGATTCTA+AGG 0.354428 1:+48925401 MsaT002896.1:CDS
CCGTTGGTATAGATGGGAAA+TGG 0.375826 1:-48923132 None:intergenic
TATTACTTGTTTGTTGGAAA+TGG 0.383105 1:-48924870 None:intergenic
GTAGCCGCCGTTGGTATAGA+TGG 0.385326 1:-48923139 None:intergenic
TGGTTTCTGGTAGAGAAGTT+TGG 0.387708 1:-48924825 None:intergenic
TTTAAAGAAGCTAATCAAAA+AGG 0.402136 1:+48923490 MsaT002896.1:CDS
AGAGTAGTGGAAGAAGAAGT+TGG 0.406533 1:+48925001 MsaT002896.1:CDS
TCACCTTCTGATTCTAATGT+TGG 0.411980 1:+48925564 MsaT002896.1:CDS
TTAACAAAGCTGTCAGATTC+CGG 0.414479 1:-48923183 None:intergenic
AGAGTAAGAGTTTCTTGTCT+TGG 0.432446 1:-48923436 None:intergenic
TGAAGAAGCTCATGATCATA+AGG 0.433018 1:+48925287 MsaT002896.1:CDS
CCCATATAACCTGTGGTCTC+AGG 0.433556 1:-48923388 None:intergenic
TTGAGTTAGTAGTGAGACTA+AGG 0.450800 1:-48924918 None:intergenic
ATTCAAAATCAAAATGAAGA+TGG 0.456037 1:+48925336 MsaT002896.1:CDS
TTTGGAGTAATGAGAGAGCA+TGG 0.461952 1:+48925196 MsaT002896.1:CDS
CAGTATGAGATGATGATGTT+AGG 0.464776 1:+48923256 MsaT002896.1:CDS
CATATTGTTGTTGCTGCTGT+TGG 0.466902 1:-48923075 None:intergenic
ATCTATACCAACGGCGGCTA+CGG 0.468673 1:+48923141 MsaT002896.1:CDS
GTTGTTGCTGCTGTTGGTGA+TGG 0.468711 1:-48923069 None:intergenic
AAGACAAAAGAAGGTAAAGC+AGG 0.472275 1:+48924736 MsaT002896.1:CDS
ATGATTCTAAGGAAGGAAAC+AGG 0.472723 1:+48925412 MsaT002896.1:CDS
ATTGTTGTTGAAGGTGGTGG+TGG 0.473372 1:-48923325 None:intergenic
GTTATTGTTGTTGAAGGTGG+TGG 0.474694 1:-48923328 None:intergenic
GGAGGAAACAAGAGGCCAAA+AGG 0.485530 1:+48925154 MsaT002896.1:CDS
AGCTGTCAGATTCCGGTGAC+CGG 0.495878 1:-48923176 None:intergenic
GTTGTTATTGTTGTTGAAGG+TGG 0.496177 1:-48923331 None:intergenic
GATACGTCGTCGTCTGATGA+TGG 0.498562 1:+48924955 MsaT002896.1:CDS
CGTTGGTATAGATGGGAAAT+GGG 0.500347 1:-48923131 None:intergenic
CTTTCCTTTCATGATTAGTG+AGG 0.500450 1:+48925611 MsaT002896.1:CDS
CCTGAGACCACAGGTTATAT+GGG 0.501183 1:+48923388 MsaT002896.1:CDS
GATCTAAGACAGCTAGTGAA+TGG 0.501254 1:+48923097 MsaT002896.1:CDS
GACACTTGAGGACAAGGAAA+AGG 0.501629 1:+48925107 MsaT002896.1:CDS
GGAAGGAAACAGGAAGAGAA+AGG 0.505443 1:+48925422 MsaT002896.1:CDS
GGGCGTTAAGAGAAGAAGAG+TGG 0.505945 1:+48925133 MsaT002896.1:CDS
AACTCATCCGTAGCCGCCGT+TGG 0.510020 1:-48923148 None:intergenic
TTCAAAATCAAAATGAAGAT+GGG 0.510698 1:+48925337 MsaT002896.1:CDS
GGTGATGACCATGATTGTTA+TGG 0.519317 1:-48923036 None:intergenic
CAATGTTCTATGTACAATCA+AGG 0.520932 1:+48925471 MsaT002896.1:CDS
GCTGCTGTTGGTGATGGTGA+TGG 0.523244 1:-48923063 None:intergenic
CTAAGGGATGATTCTAAGGA+AGG 0.524712 1:+48925405 MsaT002896.1:CDS
CTAGAGACTTCATCCCATAA+AGG 0.525783 1:-48923514 None:intergenic
TTGTCTTGGCCATCTTCCAG+TGG 0.530040 1:-48923422 None:intergenic
TAGTGAGGGTGGAAATTTGT+GGG 0.530887 1:+48925626 MsaT002896.1:CDS
GTTGGTGATGGTGATGGTGA+GGG 0.532276 1:-48923057 None:intergenic
TTTCCTTTCATGATTAGTGA+GGG 0.536493 1:+48925612 MsaT002896.1:CDS
AAACTACAAAGGAATGATCA+TGG 0.537652 1:+48925537 MsaT002896.1:CDS
TATTACAAGAAGACAAAAGA+AGG 0.546022 1:+48924727 MsaT002896.1:CDS
AAGGGAAAGAAGAAGAGTAG+TGG 0.550255 1:+48924988 MsaT002896.1:CDS
CTTTATGGGATGAAGTCTCT+AGG 0.552690 1:+48923515 MsaT002896.1:CDS
GATGACCACCATAACAATCA+TGG 0.553172 1:+48923028 MsaT002896.1:CDS
GAGATGCATCCACTGGAAGA+TGG 0.561119 1:+48923413 MsaT002896.1:CDS
AATGTTGGAAATGTAGCTAA+TGG 0.561430 1:+48925579 MsaT002896.1:CDS
TTCTGATAATTGTACTCTAA+GGG 0.561784 1:+48925389 MsaT002896.1:CDS
GAGGAAACAAGAGGCCAAAA+GGG 0.564460 1:+48925155 MsaT002896.1:CDS
GAAGCTTTGAAGAATTTAGG+AGG 0.565385 1:+48925246 MsaT002896.1:CDS
ATGGGTGGAGATGCATCCAC+TGG 0.565514 1:+48923406 MsaT002896.1:CDS
GGTAAAGCAGGAAGGCATGA+TGG 0.566904 1:+48924748 MsaT002896.1:CDS
TAGTGGAAGAAGAAGTTGGA+AGG 0.571374 1:+48925005 MsaT002896.1:CDS
CCACCCTCACTAATCATGAA+AGG 0.571997 1:-48925615 None:intergenic
CCTTTCATGATTAGTGAGGG+TGG 0.572090 1:+48925615 MsaT002896.1:CDS
CTGAAGAACATGGATATCAA+AGG 0.576035 1:+48924662 MsaT002896.1:CDS
TCTATGTACAATCAAGGAAG+TGG 0.576269 1:+48925477 MsaT002896.1:CDS
GAGAGCATGGATTGAAGCAA+GGG 0.577276 1:+48925209 MsaT002896.1:CDS
GTTTCAACTCCTGAGACCAC+AGG 0.581549 1:+48923379 MsaT002896.1:CDS
GAAGAAGCTCATGATCATAA+GGG 0.582156 1:+48925288 MsaT002896.1:CDS
TTTCCAACATTAGAATCAGA+AGG 0.583715 1:-48925567 None:intergenic
AGAGAGCATGGATTGAAGCA+AGG 0.583741 1:+48925208 MsaT002896.1:CDS
TGTGAAGACACTTGAGGACA+AGG 0.590043 1:+48925101 MsaT002896.1:CDS
GAGATGATGATGTTAGGTCG+TGG 0.590941 1:+48923262 MsaT002896.1:CDS
GAACATGGATATCAAAGGAG+TGG 0.592797 1:+48924667 MsaT002896.1:CDS
GAAACAAGAGGCCAAAAGGG+TGG 0.597918 1:+48925158 MsaT002896.1:CDS
TAAGGCTATGATCATTGTGA+GGG 0.598377 1:-48924900 None:intergenic
TAGCCGCCGTTGGTATAGAT+GGG 0.598844 1:-48923138 None:intergenic
TGTTGGTGATGGTGATGGTG+AGG 0.604876 1:-48923058 None:intergenic
CAAAAGAAGGTAAAGCAGGA+AGG 0.606280 1:+48924740 MsaT002896.1:CDS
CCATTTCCCATCTATACCAA+CGG 0.613398 1:+48923132 MsaT002896.1:CDS
AGGATAATGTCTGAAGAACA+TGG 0.616822 1:+48924652 MsaT002896.1:intron
CTAAGGCTATGATCATTGTG+AGG 0.617388 1:-48924901 None:intergenic
AACACTAGCACTAGCAGTGG+TGG 0.618195 1:-48923359 None:intergenic
TGATGTTAATGATCAAAGAG+AGG 0.618449 1:+48925506 MsaT002896.1:CDS
TGATGATGGCAATGATGTGA+AGG 0.618528 1:+48924969 MsaT002896.1:CDS
GATGACCATGATTGTTATGG+TGG 0.618743 1:-48923033 None:intergenic
CGTTAAGAGAAGAAGAGTGG+AGG 0.619013 1:+48925136 MsaT002896.1:CDS
GACAGCTAGTGAATGGAACA+AGG 0.626911 1:+48923104 MsaT002896.1:CDS
ATCTTGAATAGTACTGTGAG+AGG 0.628009 1:+48925366 MsaT002896.1:CDS
AGAAGAGTGGAGGAAACAAG+AGG 0.631900 1:+48925146 MsaT002896.1:CDS
TGAGGACAAGGAAAAGGAGA+GGG 0.634562 1:+48925113 MsaT002896.1:CDS
AGGAGATTGTGAAACTACAA+AGG 0.636318 1:+48925526 MsaT002896.1:CDS
GAAGCTTGTGGAGAAGCAAG+AGG 0.641062 1:+48925062 MsaT002896.1:CDS
GAGACCACAGGTTATATGGG+TGG 0.648008 1:+48923391 MsaT002896.1:CDS
TGCACAAATGAAGAAGCTTG+TGG 0.649032 1:+48925050 MsaT002896.1:CDS
TTGTGGAGAAGCAAGAGGAG+TGG 0.656273 1:+48925067 MsaT002896.1:CDS
ATCTCCACCCATATAACCTG+TGG 0.658151 1:-48923395 None:intergenic
TGAAACACTAGCACTAGCAG+TGG 0.671025 1:-48923362 None:intergenic
TTGAGGACAAGGAAAAGGAG+AGG 0.672502 1:+48925112 MsaT002896.1:CDS
GATGATGGCAATGATGTGAA+GGG 0.683964 1:+48924970 MsaT002896.1:CDS
TTAGTGAGGGTGGAAATTTG+TGG 0.685166 1:+48925625 MsaT002896.1:CDS
TAAGCTTGTGAAGACACTTG+AGG 0.695179 1:+48925095 MsaT002896.1:CDS
TTTCCCATCTATACCAACGG+CGG 0.762867 1:+48923135 MsaT002896.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 48923025 48925692 48923025 ID=MsaG002896
Chr1 mRNA 48923025 48925692 48923025 ID=MsaT002896.1;Parent=MsaG002896
Chr1 exon 48923025 48923536 48923025 ID=MsaT002896.1.exon1;Parent=MsaT002896.1
Chr1 CDS 48923025 48923536 48923025 ID=cds.MsaT002896.1;Parent=MsaT002896.1
Chr1 exon 48924654 48925692 48924654 ID=MsaT002896.1.exon2;Parent=MsaT002896.1
Chr1 CDS 48924654 48925692 48924654 ID=cds.MsaT002896.1;Parent=MsaT002896.1
Gene Sequence

>MsaT002896.1

ATGGATGACCACCATAACAATCATGGTCATCACCCTCACCATCACCATCACCAACAGCAGCAACAACAATATGATCTAAGACAGCTAGTGAATGGAACAAGGTCAACCCATTTCCCATCTATACCAACGGCGGCTACGGATGAGTTTTTCTCCGGTCACCGGAATCTGACAGCTTTGTTAACTACTACTACTCATCCTAATCCACAGACACATCAAAACCAACAACAACAACAGTATGAGATGATGATGTTAGGTCGTGGAGTAGTTCTTGAAGATTTCAATAGTATCACTACTCATGTACCACCACCACCTTCAACAACAATAACAACAACAACCACCACTGCTAGTGCTAGTGTTTCAACTCCTGAGACCACAGGTTATATGGGTGGAGATGCATCCACTGGAAGATGGCCAAGACAAGAAACTCTTACTCTTCTTGAAATCAGATCTCGTCTTGACCCTAAATTTAAAGAAGCTAATCAAAAAGGTCCTTTATGGGATGAAGTCTCTAGGATAATGTCTGAAGAACATGGATATCAAAGGAGTGGAAAAAAGTGCAGAGAAAAATTTGAGAATCTGTACAAATATTACAAGAAGACAAAAGAAGGTAAAGCAGGAAGGCATGATGGTAAGCATTACAGGTTTTTTCGTCAACTTGAAGCTTTATATGGTGAAAACAGTAACCAAACTTCTCTACCAGAAACCAATTTTGTCAACAACAATAATTTCCATTTCCAACAAACAAGTAATAGCCAAAACCCTCACAATGATCATAGCCTTAGTCTCACTACTAACTCAACTGACTTTGAAATCGATACGTCGTCGTCTGATGATGGCAATGATGTGAAGGGAAAGAAGAAGAGTAGTGGAAGAAGAAGTTGGAAGGTGAAGATAAAAGACTTCATTGATGCACAAATGAAGAAGCTTGTGGAGAAGCAAGAGGAGTGGTTGAGTAAGCTTGTGAAGACACTTGAGGACAAGGAAAAGGAGAGGGCGTTAAGAGAAGAAGAGTGGAGGAAACAAGAGGCCAAAAGGGTGGAAAAAGAACAAAAGTTTTGGAGTAATGAGAGAGCATGGATTGAAGCAAGGGATGCTGCTTTAATGGAAGCTTTGAAGAATTTAGGAGGTAGAGAAATGATTAAGGTTGAAGAAGCTCATGATCATAAGGGTGTAAATGGAATAACTGGAGCAGAGATTCAAAATCAAAATGAAGATGGGAGTGAAATCTTGAATAGTACTGTGAGAGGTTCTGATAATTGTACTCTAAGGGATGATTCTAAGGAAGGAAACAGGAAGAGAAAGGAGAGTTTTTACTTCAACAATAATGAACAATGTTCTATGTACAATCAAGGAAGTGGTTATTGTGATGTTAATGATCAAAGAGAGGAGATTGTGAAACTACAAAGGAATGATCATGGTTCTTCACCTTCTGATTCTAATGTTGGAAATGTAGCTAATGGTGATACTTGCTTTCCTTTCATGATTAGTGAGGGTGGAAATTTGTGGGAGAATTTTGGCTTGAAGATCAATAAAGTAAACCAAAACCATTAA
Protein sequence

>MsaT002896.1

MDDHHNNHGHHPHHHHHQQQQQQYDLRQLVNGTRSTHFPSIPTAATDEFFSGHRNLTALLTTTTHPNPQTHQNQQQQQYEMMMLGRGVVLEDFNSITTHVPPPPSTTITTTTTTASASVSTPETTGYMGGDASTGRWPRQETLTLLEIRSRLDPKFKEANQKGPLWDEVSRIMSEEHGYQRSGKKCREKFENLYKYYKKTKEGKAGRHDGKHYRFFRQLEALYGENSNQTSLPETNFVNNNNFHFQQTSNSQNPHNDHSLSLTTNSTDFEIDTSSSDDGNDVKGKKKSSGRRSWKVKIKDFIDAQMKKLVEKQEEWLSKLVKTLEDKEKERALREEEWRKQEAKRVEKEQKFWSNERAWIEARDAALMEALKNLGGREMIKVEEAHDHKGVNGITGAEIQNQNEDGSEILNSTVRGSDNCTLRDDSKEGNRKRKESFYFNNNEQCSMYNQGSGYCDVNDQREEIVKLQRNDHGSSPSDSNVGNVANGDTCFPFMISEGGNLWENFGLKINKVNQNH*