AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG008086

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG008086 MtrunA17_Chr2g0299621 96.422 587 18 2 1 587 1 584 0.0 1155
MsaG008086 MtrunA17_Chr2g0291741 44.906 530 264 10 48 559 45 564 5.52e-143 426
MsaG008086 MtrunA17_Chr5g0442661 38.938 565 314 11 17 564 21 571 1.29e-122 374
MsaG008086 MtrunA17_Chr1g0171771 31.183 372 212 9 68 403 24 387 2.91e-38 147
MsaG008086 MtrunA17_Chr7g0256321 30.914 372 214 7 68 403 24 388 2.67e-37 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG008086 AT1G64280.1 52.448 572 238 10 7 559 7 563 0.0 554
MsaG008086 AT4G26120.1 52.052 536 233 8 48 570 48 572 3.81e-174 507
MsaG008086 AT4G26120.2 52.052 536 233 8 48 570 49 573 4.02e-174 507
MsaG008086 AT5G45110.1 42.561 531 272 12 48 557 41 559 4.23e-121 370
MsaG008086 AT4G19660.1 42.026 533 269 12 48 556 35 551 1.32e-120 369
MsaG008086 AT4G19660.2 40.179 560 268 13 48 556 35 578 1.43e-115 356
MsaG008086 AT5G45110.2 41.770 486 250 12 48 515 41 511 9.35e-107 331
MsaG008086 AT3G57130.1 31.892 370 209 8 68 403 26 386 4.84e-40 152
MsaG008086 AT2G41370.1 30.423 378 212 9 68 403 25 393 4.05e-36 142

Find 100 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTGAATTTACTCCGAATT+TGG 0.080716 2:-27939685 MsaT008086.1:CDS
TGCGAGGAGTAGTTTCTTTA+AGG 0.142531 2:-27941206 MsaT008086.1:CDS
GCGCTTCACTTGTCGATCTT+CGG 0.290085 2:+27939194 None:intergenic
TGAATTGCTTGCTCTTTATC+AGG 0.291540 2:-27940939 MsaT008086.1:intron
ACTAGACATTCTTGACAAAA+TGG 0.299539 2:-27940636 MsaT008086.1:CDS
TATATTACTTGTTTCACTAT+AGG 0.308533 2:+27940476 None:intergenic
ATGTTTGTCTAGAAGATTTA+CGG 0.318420 2:+27940418 None:intergenic
ATCTAAAGCTCTATGTATTC+TGG 0.325893 2:+27940391 None:intergenic
CGCTTCACTTGTCGATCTTC+GGG 0.329375 2:+27939195 None:intergenic
CATGTTGGTGGTTCTTTCTA+TGG 0.332557 2:-27940603 MsaT008086.1:CDS
GCTACAAGAAGTTCTTAATA+AGG 0.338445 2:-27939157 MsaT008086.1:CDS
ACTACTGAGCTTCTTGATCT+TGG 0.343475 2:-27940263 MsaT008086.1:CDS
TCGATTGTGTATCGAGATAT+TGG 0.362910 2:-27940021 MsaT008086.1:CDS
TCTGAATTTACTCCGAATTT+GGG 0.369283 2:-27939684 MsaT008086.1:CDS
TCATCTTGAGCAGTGGAGTT+GGG 0.376033 2:-27939309 MsaT008086.1:intron
AATTCAGATGTGCCATCAAT+TGG 0.381830 2:+27939699 None:intergenic
CAGATGATGTAGAGTTAGTA+AGG 0.385561 2:-27940367 MsaT008086.1:CDS
AAAGAGGAGTTTGATAAATC+TGG 0.386748 2:-27939120 MsaT008086.1:CDS
GTTGCTAAGGATTATGATGT+TGG 0.387471 2:-27941139 MsaT008086.1:CDS
GAAGCAGTAGTAGTTGAAAT+TGG 0.392942 2:+27941382 None:intergenic
ATTGTTTACACTTTGGTTGT+TGG 0.395598 2:-27941018 MsaT008086.1:CDS
TCATCCTCATCCACGTCAAT+AGG 0.401640 2:-27939087 MsaT008086.1:CDS
CTCTGGCAACCACCCAAATT+CGG 0.404385 2:+27939672 None:intergenic
ATATACAAACGCAAACAATT+AGG 0.413643 2:-27940458 MsaT008086.1:CDS
GACAATCTAGCTTCGATACT+AGG 0.416933 2:-27941316 MsaT008086.1:CDS
TAAAAGAGGAGCATCTAATT+CGG 0.429046 2:-27939614 MsaT008086.1:CDS
GGAAACTTCTCGACCATCTC+TGG 0.429174 2:+27941249 None:intergenic
TCTCTTTCTCTTGCTAAGGC+AGG 0.429539 2:-27939960 MsaT008086.1:CDS
CTTTCTATGGCAAACATTTG+TGG 0.439277 2:-27940590 MsaT008086.1:CDS
CTCTTTCTCTTGCTAAGGCA+GGG 0.442710 2:-27939959 MsaT008086.1:CDS
GTCATCTTGAGCAGTGGAGT+TGG 0.451507 2:-27939310 MsaT008086.1:intron
ATCATACTATTATTAGCCCT+TGG 0.460763 2:+27939060 None:intergenic
GGCATCTCTTTCTCTTGCTA+AGG 0.467473 2:-27939964 MsaT008086.1:CDS
CCTATCGCAGCTTGCATGCA+TGG 0.468067 2:-27939229 MsaT008086.1:CDS
ATGGATATCAATCCAATTGA+TGG 0.475189 2:-27939711 MsaT008086.1:CDS
TTGCTAAGGATTATGATGTT+GGG 0.476464 2:-27941138 MsaT008086.1:CDS
ACGGTTCTTCCCTCGTTGCT+CGG 0.483600 2:-27939283 MsaT008086.1:CDS
TGAAGCATGAAATCAACAAC+AGG 0.485589 2:+27940995 None:intergenic
TCGATACTAGGTGATGATGC+AGG 0.489869 2:-27941304 MsaT008086.1:CDS
GTCGAGAAGTTTCCGTGCAC+CGG 0.497677 2:-27941240 MsaT008086.1:CDS
TGGTTGCCAGAGGACAACTA+TGG 0.504234 2:-27939661 MsaT008086.1:CDS
ATCACAACCTTTGCTTCCAT+CGG 0.509584 2:+27939732 None:intergenic
GAGCAGTGGAGTTGGGGAAA+CGG 0.514130 2:-27939302 MsaT008086.1:intron
TCTTTCTCTTGCTAAGGCAG+GGG 0.519191 2:-27939958 MsaT008086.1:CDS
ATTGTATCTTTGTTAACGAA+GGG 0.521494 2:-27940161 MsaT008086.1:CDS
TATTGTATCTTTGTTAACGA+AGG 0.522257 2:-27940162 MsaT008086.1:CDS
ATTGGAGCAAGCTGAGAGAA+GGG 0.524671 2:-27940003 MsaT008086.1:CDS
GATGATGATTGTTTACACTT+TGG 0.524715 2:-27941025 MsaT008086.1:CDS
TCAAGTCCATAGTTGTCCTC+TGG 0.532702 2:+27939655 None:intergenic
GGAAGTGTTGAACAAGATCA+TGG 0.534097 2:-27939262 MsaT008086.1:CDS
GTAATGATGTACTTGAGAAG+TGG 0.540852 2:-27941475 MsaT008086.1:CDS
TATTGGAGCAAGCTGAGAGA+AGG 0.543360 2:-27940004 MsaT008086.1:CDS
TATTATAAATCTACTGAGGA+AGG 0.543578 2:-27940062 MsaT008086.1:CDS
ATGAAGGCGTTGTCTAGAGC+AGG 0.543907 2:-27939591 MsaT008086.1:intron
CATTCCTATTGACGTGGATG+AGG 0.544059 2:+27939083 None:intergenic
CATCTTGAGCAGTGGAGTTG+GGG 0.545384 2:-27939308 MsaT008086.1:intron
ACTTGTTTCACTATAGGTTG+AGG 0.548262 2:+27940482 None:intergenic
GGCACCATTTAAAATAAAAG+AGG 0.551112 2:-27939628 MsaT008086.1:CDS
CCTTCTGAACTCACTTTCGA+TGG 0.555532 2:-27940131 MsaT008086.1:CDS
AGAAACGACGCTGCAACTGA+AGG 0.556254 2:-27941164 MsaT008086.1:CDS
GGAGCATCTAATTCGGATGA+AGG 0.559886 2:-27939607 MsaT008086.1:CDS
TGCAAGCTGCGATAGGTCAT+CGG 0.560452 2:+27939236 None:intergenic
CTATCGCAGCTTGCATGCAT+GGG 0.560772 2:-27939228 MsaT008086.1:CDS
GCAACTGAAGGAAGTTGCTA+AGG 0.566717 2:-27941152 MsaT008086.1:CDS
CCATGCATGCAAGCTGCGAT+AGG 0.568643 2:+27939229 None:intergenic
AGAGATGCCTCACCATGTAA+AGG 0.569360 2:+27939978 None:intergenic
GAGAGAAGGGAGCCTTTACA+TGG 0.569857 2:-27939990 MsaT008086.1:CDS
GCAAAGATCATCGCCAGAGA+TGG 0.571087 2:-27941262 MsaT008086.1:CDS
CCATCGAAAGTGAGTTCAGA+AGG 0.573318 2:+27940131 None:intergenic
CGATACTAGGTGATGATGCA+GGG 0.575438 2:-27941303 MsaT008086.1:CDS
TAAAGATGTTTGTGTTTGTG+TGG 0.576566 2:-27941047 MsaT008086.1:CDS
TTTGTTTCCGATGGAAGCAA+AGG 0.576921 2:-27939739 MsaT008086.1:CDS
AAGCAATTCAGAAATTTGAA+AGG 0.578420 2:+27940952 None:intergenic
GACAACTATGGACTTGAATG+AGG 0.586182 2:-27939649 MsaT008086.1:CDS
TCTTAATAAGGTCTTTCATG+AGG 0.586342 2:-27939145 MsaT008086.1:CDS
CGAATTTGGGTGGTTGCCAG+AGG 0.588649 2:-27939671 MsaT008086.1:CDS
GAATTTACTCCGAATTTGGG+TGG 0.588904 2:-27939681 MsaT008086.1:CDS
GATGGAAGCAAAGGTTGTGA+TGG 0.592814 2:-27939730 MsaT008086.1:CDS
TTTGTATAGTGAGAGAGTTG+AGG 0.592855 2:-27941086 MsaT008086.1:CDS
CCTTGGCATTCCTATTGACG+TGG 0.593232 2:+27939077 None:intergenic
AGACAAAATGCACCGGTGCA+CGG 0.596290 2:+27941228 None:intergenic
CCACGTCAATAGGAATGCCA+AGG 0.605123 2:-27939077 MsaT008086.1:CDS
ACAGCATAACTCACTAGCAC+TGG 0.609316 2:+27941414 None:intergenic
TCCTCGCAGACAAAATGCAC+CGG 0.610061 2:+27941221 None:intergenic
AAAGCGTAGTACGAAAGCTG+TGG 0.616351 2:-27940087 MsaT008086.1:CDS
AAGGGAGCCTTTACATGGTG+AGG 0.619314 2:-27939985 MsaT008086.1:CDS
GGTCTTTCATGAGGACAAAG+AGG 0.622648 2:-27939136 MsaT008086.1:CDS
GGCAATAGATGACATGTTGG+TGG 0.623200 2:-27940615 MsaT008086.1:CDS
TCTGGCGATGATCTTTGCGT+CGG 0.631296 2:+27941267 None:intergenic
AAGATCAAGAAGCTCAGTAG+TGG 0.633228 2:+27940265 None:intergenic
AGTGAAGCGCAGACGATACG+CGG 0.639553 2:-27939181 MsaT008086.1:CDS
AATGGCAATAGATGACATGT+TGG 0.639924 2:-27940618 MsaT008086.1:CDS
AAGCTAGATTGTCTGAGAGA+CGG 0.643516 2:+27941326 None:intergenic
TTGTCTGAGAGACGGTTCAG+AGG 0.648376 2:+27941334 None:intergenic
CACGTCAATAGGAATGCCAA+GGG 0.650742 2:-27939076 MsaT008086.1:CDS
AGGACACACTACTCTAGATG+AGG 0.655016 2:-27940330 MsaT008086.1:CDS
TCAACACTTCCGAGCAACGA+GGG 0.684586 2:+27939274 None:intergenic
TTCAACACTTCCGAGCAACG+AGG 0.701823 2:+27939273 None:intergenic
GGATTATTATAAATCTACTG+AGG 0.714422 2:-27940066 MsaT008086.1:CDS
TTGTTGTACCTAGAAAACCG+AGG 0.809311 2:-27939918 MsaT008086.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 27939044 27941494 27939044 ID=MsaG008086
Chr2 mRNA 27939044 27941494 27939044 ID=MsaT008086.1;Parent=MsaG008086
Chr2 exon 27939044 27939318 27939044 ID=MsaT008086.1.exon4;Parent=MsaT008086.1
Chr2 CDS 27939044 27939318 27939044 ID=cds.MsaT008086.1;Parent=MsaT008086.1
Chr2 exon 27939592 27939777 27939592 ID=MsaT008086.1.exon3;Parent=MsaT008086.1
Chr2 CDS 27939592 27939777 27939592 ID=cds.MsaT008086.1;Parent=MsaT008086.1
Chr2 exon 27939919 27940666 27939919 ID=MsaT008086.1.exon2;Parent=MsaT008086.1
Chr2 CDS 27939919 27940666 27939919 ID=cds.MsaT008086.1;Parent=MsaT008086.1
Chr2 exon 27940940 27941494 27940940 ID=MsaT008086.1.exon1;Parent=MsaT008086.1
Chr2 CDS 27940940 27941494 27940940 ID=cds.MsaT008086.1;Parent=MsaT008086.1
Gene Sequence

>MsaT008086.1

ATGATGTACTTGAGAAGTGGATTCTCTGAATATTCAAACGAAATCAGCAACAACACTGCCAGTGCTAGTGAGTTATGCTGTACAACAGCACCAATTTCAACTACTACTGCTTCACAAGATATCATCACAATCACACAACCTCTGAACCGTCTCTCAGACAATCTAGCTTCGATACTAGGTGATGATGCAGGGTTTGACTTCTTTTCCGACGCAAAGATCATCGCCAGAGATGGTCGAGAAGTTTCCGTGCACCGGTGCATTTTGTCTGCGAGGAGTAGTTTCTTTAAGGATGTTTTTAAGGGAAAGAAAGAAACGACGCTGCAACTGAAGGAAGTTGCTAAGGATTATGATGTTGGGTTTGAAGCGCTTAACGTTGTTCTGCGTTATTTGTATAGTGAGAGAGTTGAGGATCATCATTTGTCTGCTAAAGATGTTTGTGTTTGTGTGGATGATGATTGTTTACACTTTGGTTGTTGGCCTGTTGTTGATTTCATGCTTCAACTTCTCTATGCTTCATTCACCTTTCAAATTTCTGAATTGCTTGCTCTTTATCAGGATCATCTACTAGACATTCTTGACAAAATGGCAATAGATGACATGTTGGTGGTTCTTTCTATGGCAAACATTTGTGGTAAAACATGTGATAAACTACTAACAAGATGTACAGAGATAATAGTTGAATCTAATGTTGATATAACCACTCTTGAAAAATCACTGCCTCAACCTATAGTGAAACAAGTAATATACAAACGCAAACAATTAGGCTTAGACATGTATGAAACCGTAAATCTTCTAGACAAACATGTCACCAGAATACATAGAGCTTTAGATTCAGATGATGTAGAGTTAGTAAGGTTGCTTTTGAAAGAAGGACACACTACTCTAGATGAGGCTCATGCACTTCACTATGCTGTTGCTTATTGTGATGTCAAAACCACTACTGAGCTTCTTGATCTTGGACTTGCCGATGTAAATCATAAAAATCTTAGGGGCTATAGCGTGCTACATGTTGCTGCGAAGAGAAAAGAGCCGAAAATTATTGTATCTTTGTTAACGAAGGGCGCTCAACCTTCTGAACTCACTTTCGATGGCAGAAAAGCTCTTCAAATTTCAAAGCGTAGTACGAAAGCTGTGGATTATTATAAATCTACTGAGGAAGGAAAAGTTTCTTCGAATGATCGATTGTGTATCGAGATATTGGAGCAAGCTGAGAGAAGGGAGCCTTTACATGGTGAGGCATCTCTTTCTCTTGCTAAGGCAGGGGATGATTTACGTATGAAATTGTTGTACCTAGAAAACCGAGTTGGACTAGCAAAACTTTTGTTTCCGATGGAAGCAAAGGTTGTGATGGATATCAATCCAATTGATGGCACATCTGAATTTACTCCGAATTTGGGTGGTTGCCAGAGGACAACTATGGACTTGAATGAGGCACCATTTAAAATAAAAGAGGAGCATCTAATTCGGATGAAGGCGTTGTCTAGAGCAGTGGAGTTGGGGAAACGGTTCTTCCCTCGTTGCTCGGAAGTGTTGAACAAGATCATGGATGCCGATGACCTATCGCAGCTTGCATGCATGGGTCATGACAGTCCCGAAGATCGACAAGTGAAGCGCAGACGATACGCGGAGCTACAAGAAGTTCTTAATAAGGTCTTTCATGAGGACAAAGAGGAGTTTGATAAATCTGGCATGTCTTCATCATCCTCATCCACGTCAATAGGAATGCCAAGGGCTAATAATAGTATGATAGCAATGAATCATTGA
Protein sequence

>MsaT008086.1

MMYLRSGFSEYSNEISNNTASASELCCTTAPISTTTASQDIITITQPLNRLSDNLASILGDDAGFDFFSDAKIIARDGREVSVHRCILSARSSFFKDVFKGKKETTLQLKEVAKDYDVGFEALNVVLRYLYSERVEDHHLSAKDVCVCVDDDCLHFGCWPVVDFMLQLLYASFTFQISELLALYQDHLLDILDKMAIDDMLVVLSMANICGKTCDKLLTRCTEIIVESNVDITTLEKSLPQPIVKQVIYKRKQLGLDMYETVNLLDKHVTRIHRALDSDDVELVRLLLKEGHTTLDEAHALHYAVAYCDVKTTTELLDLGLADVNHKNLRGYSVLHVAAKRKEPKIIVSLLTKGAQPSELTFDGRKALQISKRSTKAVDYYKSTEEGKVSSNDRLCIEILEQAERREPLHGEASLSLAKAGDDLRMKLLYLENRVGLAKLLFPMEAKVVMDINPIDGTSEFTPNLGGCQRTTMDLNEAPFKIKEEHLIRMKALSRAVELGKRFFPRCSEVLNKIMDADDLSQLACMGHDSPEDRQVKRRRYAELQEVLNKVFHEDKEEFDKSGMSSSSSSTSIGMPRANNSMIAMNH*