AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG012601

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012601 MtrunA17_Chr1g0203051 43.172 227 128 1 92 318 56 281 4.47e-55 197
MsaG012601 MtrunA17_Chr1g0203051 25.556 180 77 4 297 419 442 621 1.66e-11 67.0
MsaG012601 MtrunA17_Chr1g0171741 39.167 240 127 7 9 245 38 261 1.96e-42 153
MsaG012601 MtrunA17_Chr2g0308841 37.306 193 64 3 296 431 34 226 1.09e-36 137
MsaG012601 MtrunA17_Chr8g0389811 40.000 135 81 0 93 227 61 195 7.06e-31 119
MsaG012601 MtrunA17_Chr2g0287651 30.901 233 154 3 93 318 47 279 1.46e-30 127
MsaG012601 MtrunA17_Chr2g0331371 41.667 132 77 0 96 227 35 166 1.07e-24 102
MsaG012601 MtrunA17_Chr6g0473421 43.750 96 54 0 96 191 35 130 1.67e-22 94.4
MsaG012601 MtrunA17_Chr1g0202341 28.750 240 156 5 93 321 20 255 3.93e-20 94.7
MsaG012601 MtrunA17_Chr5g0448761 28.497 193 135 3 122 311 66 258 5.89e-18 87.8
MsaG012601 MtrunA17_Chr1g0198761 31.156 199 119 8 121 305 52 246 8.89e-17 84.0
MsaG012601 MtrunA17_Chr1g0172931 36.893 103 65 0 96 198 56 158 1.12e-16 77.8
MsaG012601 MtrunA17_Chr8g0340801 36.957 92 58 0 227 318 1 92 4.15e-16 74.3
MsaG012601 MtrunA17_Chr2g0294841 32.414 145 84 5 122 256 51 191 1.21e-14 77.4
MsaG012601 MtrunA17_Chr5g0431001 28.155 206 134 6 121 314 66 269 7.63e-14 74.3
MsaG012601 MtrunA17_Chr2g0290391 26.554 177 114 5 120 287 55 224 1.62e-13 73.6
MsaG012601 MtrunA17_Chr2g0276841 28.736 174 112 6 121 286 75 244 3.23e-13 72.8
MsaG012601 MtrunA17_Chr1g0203721 27.053 207 133 7 121 317 68 266 1.19e-12 70.9
MsaG012601 MtrunA17_Chr8g0363841 27.933 179 122 4 128 304 29 202 3.59e-11 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012601 AT5G28530.1 27.950 161 112 3 121 278 60 219 4.18e-16 82.4
MsaG012601 AT5G28530.4 27.950 161 112 3 121 278 60 219 4.26e-16 82.0
MsaG012601 AT5G28530.3 27.950 161 112 3 121 278 60 219 4.30e-16 82.4
MsaG012601 AT5G28530.2 27.950 161 112 3 121 278 60 219 4.30e-16 82.4
MsaG012601 AT5G28530.5 27.950 161 112 3 121 278 60 219 4.46e-16 82.0
MsaG012601 AT4G38180.1 27.805 205 142 5 108 309 67 268 4.28e-15 79.3
MsaG012601 AT1G10240.2 29.078 141 93 4 121 256 53 191 8.01e-13 72.0
MsaG012601 AT1G10240.1 29.078 141 93 4 121 256 53 191 8.01e-13 72.0

Find 114 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAATATGCACACGAAATT+TGG 0.121650 3:+28235838 None:intergenic
TGTGCAATCTAGAAGGTTTC+AGG 0.214603 3:-28235931 MsaT012601.1:CDS
ATGTTTCGAAGCTGCTATTT+AGG 0.224870 3:-28236069 MsaT012601.1:CDS
GAAAGTGATGAAGCTTTCTT+AGG 0.257531 3:-28236283 MsaT012601.1:CDS
TCGATGATGGTTCGCATTAC+TGG 0.258334 3:-28234397 MsaT012601.1:CDS
CCACACTTGGTTTCATGTTT+CGG 0.303172 3:+28235869 None:intergenic
TCGGTGACCCATTGCATTCC+TGG 0.316189 3:+28234136 None:intergenic
TAAGGTAGGATTTCTGAAAA+AGG 0.322031 3:-28235615 MsaT012601.1:CDS
TGTCTTAGAATGGAACCTAT+TGG 0.323771 3:-28234536 MsaT012601.1:CDS
ACATGCAGATGATGAGGATT+TGG 0.329267 3:-28236212 MsaT012601.1:CDS
CATTTGCGTAACTTTGATTC+CGG 0.344195 3:+28235673 None:intergenic
ACTGGAACATGTAAATTATC+TGG 0.359467 3:+28234218 None:intergenic
GCATTACTGGGATTCTCATT+TGG 0.360721 3:-28234384 MsaT012601.1:CDS
GGTTGCTAGGCATGCAAATC+TGG 0.375083 3:-28234363 MsaT012601.1:CDS
ACACCCTTTGCTTCTTGAAC+AGG 0.385272 3:+28234169 None:intergenic
GGGATTCTCATTTGGTTGCT+AGG 0.387530 3:-28234376 MsaT012601.1:CDS
TGCATGTTCTTGTCTTAGAA+TGG 0.389352 3:-28234546 MsaT012601.1:CDS
AAGATTCAAGTTACCAACTT+TGG 0.389423 3:-28235701 MsaT012601.1:CDS
CCAGACAATTCCCTTCAAAC+AGG 0.391320 3:-28234026 MsaT012601.1:CDS
GGTTTGCGACCTATCATATA+AGG 0.392932 3:-28234324 MsaT012601.1:CDS
TGTGGGATTTGCGGTGCATC+TGG 0.402584 3:-28234098 MsaT012601.1:CDS
ACATTTGTGTGCAATCTAGA+AGG 0.405952 3:-28235938 MsaT012601.1:CDS
TTTGCCAAGGAGTCAATTAG+AGG 0.406502 3:-28234425 MsaT012601.1:CDS
TGAGAAACATTGTGCATTGC+TGG 0.406720 3:-28235753 MsaT012601.1:CDS
CAAACATCAATGGATCTTTA+CGG 0.412190 3:+28235510 None:intergenic
CATCGACATCCTTATATGAT+AGG 0.424049 3:+28234315 None:intergenic
GGTAGGCTAAAGTCAAAGTA+TGG 0.424767 3:-28234254 MsaT012601.1:CDS
CGATGATGGTTCGCATTACT+GGG 0.424955 3:-28234396 MsaT012601.1:CDS
GATGCGGAAGGGGATGATTA+TGG 0.429464 3:-28236385 MsaT012601.1:CDS
AGTATGCTATCCACCTCAAC+TGG 0.435161 3:+28234200 None:intergenic
TAGAAGGTTTCAGGAGGGAC+AGG 0.441933 3:-28235922 MsaT012601.1:CDS
ATTAGAGGTAATTTCGATGA+TGG 0.442189 3:-28234410 MsaT012601.1:CDS
TGAGGCGTTTCATAGCCATA+TGG 0.443562 3:-28234903 MsaT012601.1:CDS
TGTTTCATATTTCCGCTTCA+AGG 0.445860 3:-28234822 MsaT012601.1:CDS
ATCAAAGTTACGCAAATGAT+TGG 0.447493 3:-28235668 MsaT012601.1:CDS
AAGGGTGTGGAGCTAGCGCC+AGG 0.459648 3:-28234154 MsaT012601.1:CDS
ATTACCTCTAATTGACTCCT+TGG 0.463779 3:+28234421 None:intergenic
GTTACCAACTTTGGCAATGC+CGG 0.467106 3:-28235692 MsaT012601.1:CDS
TGTCCTACACTTGATGTAGA+TGG 0.468333 3:-28234059 MsaT012601.1:CDS
AGCGTACTGACCCTGTTTGA+AGG 0.476847 3:+28234015 None:intergenic
CCTGTTTGAAGGGAATTGTC+TGG 0.485680 3:+28234026 None:intergenic
GGAAATATGAAACACACATA+TGG 0.489773 3:+28234831 None:intergenic
TGCCGCTGGCGGGTATGATA+AGG 0.500952 3:-28235633 MsaT012601.1:CDS
CGTTTGCAAATGCCGCTGGC+GGG 0.501798 3:-28235643 MsaT012601.1:CDS
ATTGAGAATTAAAATCAGCT+TGG 0.511014 3:+28234795 None:intergenic
GATTCCGGCATTGCCAAAGT+TGG 0.511513 3:+28235688 None:intergenic
AAATCTGGTGTATCTTAGTA+AGG 0.512374 3:-28234348 MsaT012601.1:CDS
GGTGCGTTTGCAAATGCCGC+TGG 0.512886 3:-28235647 MsaT012601.1:CDS
ACACAAACATGTGGGATTTG+CGG 0.513808 3:-28234107 MsaT012601.1:CDS
ATTGATGTTTGTTGCACATA+CGG 0.513952 3:-28235498 MsaT012601.1:CDS
TGCTCACAACGAATTCCAAT+AGG 0.514755 3:+28234521 None:intergenic
CGATTCAGCACTAAAGACTT+AGG 0.516281 3:+28234458 None:intergenic
AAGTCAAAGTATGGTGAAGA+AGG 0.516408 3:-28234245 MsaT012601.1:CDS
TTTGGCTTTACAACCACACT+TGG 0.533447 3:+28235856 None:intergenic
GAATATCTAACGGATGAACT+TGG 0.536705 3:-28234275 MsaT012601.1:CDS
GGAGATAGTGGTGACGATGA+AGG 0.538420 3:-28236328 MsaT012601.1:CDS
GCGTACTGACCCTGTTTGAA+GGG 0.538891 3:+28234016 None:intergenic
CTTCCTGTTCAAGAAGCAAA+GGG 0.539411 3:-28234172 MsaT012601.1:CDS
TTTACATGTTCCAGTTGAGG+TGG 0.540673 3:-28234210 MsaT012601.1:CDS
GTATGTGCAACAAACATCAA+TGG 0.540697 3:+28235500 None:intergenic
GAGAATGAAGCTGATGCGGA+AGG 0.541363 3:-28236397 MsaT012601.1:CDS
AGAAGGTTTCAGGAGGGACA+GGG 0.542204 3:-28235921 MsaT012601.1:CDS
TCTTCCTGTTCAAGAAGCAA+AGG 0.542587 3:-28234173 MsaT012601.1:CDS
TGATTATTTCGTTGATCGCA+AGG 0.543891 3:-28236242 MsaT012601.1:CDS
TAATTTACATGTTCCAGTTG+AGG 0.544755 3:-28234213 MsaT012601.1:CDS
CATGCAAATTCATCTTTCGA+TGG 0.545431 3:+28234563 None:intergenic
TTGATATAATTACTCAACGT+TGG 0.545692 3:-28235820 MsaT012601.1:CDS
TGTTGACGATATTGTCAAGA+TGG 0.549540 3:-28236116 MsaT012601.1:CDS
AGTGTATAAACAGACCCATA+TGG 0.552491 3:+28234888 None:intergenic
CGGTGTTACAGACTAATTTG+AGG 0.552900 3:-28234763 MsaT012601.1:CDS
CTAATTTGAGGTCGTTTGAG+AGG 0.553122 3:-28234751 MsaT012601.1:intron
GGTGACGGTGAAGGAGATAG+TGG 0.555627 3:-28236340 MsaT012601.1:CDS
GAGGCGTTTCATAGCCATAT+GGG 0.556657 3:-28234902 MsaT012601.1:CDS
TGTTGGTTTGCAAAGATGAA+CGG 0.565674 3:-28236019 MsaT012601.1:CDS
AGTCTTTAGTGCTGAATCGT+TGG 0.565841 3:-28234454 MsaT012601.1:CDS
GCACATACGGTTGGTGCAGA+TGG 0.566353 3:-28235485 MsaT012601.1:intron
CAGCTTGGACTTCCTTGAAG+CGG 0.570119 3:+28234810 None:intergenic
CATATCATGATTGTGATCAA+AGG 0.574576 3:+28235781 None:intergenic
AGCTAGCGCCAGGAATGCAA+TGG 0.576600 3:-28234144 MsaT012601.1:CDS
GAATGAAGCTGATGCGGAAG+GGG 0.582207 3:-28236395 MsaT012601.1:CDS
GCTGCTATTTAGGAGTCTTG+AGG 0.582337 3:-28236059 MsaT012601.1:CDS
AATTTCACATGCAGATGATG+AGG 0.582843 3:-28236218 MsaT012601.1:CDS
ATGTTTGTTGCACATACGGT+TGG 0.585388 3:-28235494 MsaT012601.1:CDS
GCTAGCGCCAGGAATGCAAT+GGG 0.585612 3:-28234143 MsaT012601.1:CDS
AGAATGAAGCTGATGCGGAA+GGG 0.586018 3:-28236396 MsaT012601.1:CDS
AAGGTTTCAGGAGGGACAGG+GGG 0.586631 3:-28235919 MsaT012601.1:CDS
TGTTCAAGAAGCAAAGGGTG+TGG 0.590795 3:-28234167 MsaT012601.1:CDS
GCGTTTGCAAATGCCGCTGG+CGG 0.592180 3:-28235644 MsaT012601.1:CDS
CACATGTTTGTGTTCTACGT+CGG 0.597562 3:+28234117 None:intergenic
GATGATGATGGTGACGGTGA+AGG 0.603427 3:-28236349 MsaT012601.1:CDS
TCGTTGGTCAATATTTGCCA+AGG 0.607507 3:-28234438 MsaT012601.1:CDS
GAAGGTTTCAGGAGGGACAG+GGG 0.607984 3:-28235920 MsaT012601.1:CDS
AAAATATCTAGAATATCTAA+CGG 0.609010 3:-28234285 MsaT012601.1:CDS
CAGACAATTCCCTTCAAACA+GGG 0.611490 3:-28234025 MsaT012601.1:CDS
GAAGGGGATGATTATGGTGA+CGG 0.613814 3:-28236379 MsaT012601.1:CDS
ACATGAGAATGAAGCTGATG+CGG 0.618775 3:-28236401 MsaT012601.1:CDS
CGACGTAGAACACAAACATG+TGG 0.621039 3:-28234116 MsaT012601.1:CDS
TCTGGTGTATCTTAGTAAGG+AGG 0.621844 3:-28234345 MsaT012601.1:CDS
TAATTCTCAATATGGGAGTG+CGG 0.626872 3:-28234783 MsaT012601.1:CDS
GACGGTGAAGCAGATGATGA+TGG 0.628757 3:-28236361 MsaT012601.1:CDS
GACGTAGAACACAAACATGT+GGG 0.632169 3:-28234115 MsaT012601.1:CDS
GCAGATGATGAGGATTTGGA+CGG 0.633477 3:-28236208 MsaT012601.1:CDS
TCACCATCTACATCAAGTGT+AGG 0.634744 3:+28234056 None:intergenic
TAGAACAACATCTCGTTGTG+AGG 0.642950 3:-28234921 MsaT012601.1:CDS
ATCTAACGGATGAACTTGGT+AGG 0.646613 3:-28234271 MsaT012601.1:CDS
CAGATCTTTAAGATACGTAA+CGG 0.651380 3:+28235535 None:intergenic
ACAGTAGAGGAACGCAAGCG+TGG 0.652435 3:-28235893 MsaT012601.1:CDS
TACCTTATCATACCCGCCAG+CGG 0.668297 3:+28235631 None:intergenic
GCAATCTAGAAGGTTTCAGG+AGG 0.669041 3:-28235928 MsaT012601.1:CDS
CAATCTAGAAGGTTTCAGGA+GGG 0.698915 3:-28235927 MsaT012601.1:CDS
GCTGGCGGGTATGATAAGGT+AGG 0.701917 3:-28235629 MsaT012601.1:CDS
GGACGGAAATTCTGACGATG+TGG 0.703394 3:-28236191 MsaT012601.1:CDS
GAAGCAGATGATGATGGTGA+CGG 0.705391 3:-28236355 MsaT012601.1:CDS
CCGAAACATGAAACCAAGTG+TGG 0.722967 3:-28235869 MsaT012601.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 28233998 28236437 28233998 ID=MsaG012601
Chr3 mRNA 28233998 28236437 28233998 ID=MsaT012601.1;Parent=MsaG012601
Chr3 exon 28233998 28234586 28233998 ID=MsaT012601.1.exon3;Parent=MsaT012601.1
Chr3 CDS 28233998 28234586 28233998 ID=cds.MsaT012601.1;Parent=MsaT012601.1
Chr3 exon 28234752 28234947 28234752 ID=MsaT012601.1.exon2;Parent=MsaT012601.1
Chr3 CDS 28234752 28234947 28234752 ID=cds.MsaT012601.1;Parent=MsaT012601.1
Chr3 exon 28235486 28236437 28235486 ID=MsaT012601.1.exon1;Parent=MsaT012601.1
Chr3 CDS 28235486 28236437 28235486 ID=cds.MsaT012601.1;Parent=MsaT012601.1
Gene Sequence

>MsaT012601.1

ATGGATGAGATTAGACATGAGAATGAAGCTGATGCGGAAGGGGATGATTATGGTGACGGTGAAGCAGATGATGATGGTGACGGTGAAGGAGATAGTGGTGACGATGAAGGTCAGTTATCAGCAGAAGAAAACGAAAGTGATGAAGCTTTCTTAGGTTCTGAATACGATGAAGTTGATTATTTCGTTGATCGCAAGGAAATTTCACATGCAGATGATGAGGATTTGGACGGAAATTCTGACGATGTGGATGAGTCAATATTTTCAGTTCGAAGTGAAGATGAATCAATTGTAATAGAGAGTGTTGACGATATTGTCAAGATGGATATGTATAATTTGCAAAATGAAGATGTTTCGAAGCTGCTATTTAGGAGTCTTGAGGTTGCCTACAATTTTTATTGTTGGTTTGCAAAGATGAACGGTTTTGCTGTGAGGAAAGGTCAAGTAATAAAAAATAAGAATGGAGATGTTCTTCAACAAACATTTGTGTGCAATCTAGAAGGTTTCAGGAGGGACAGGGGGTTAACAGTAGAGGAACGCAAGCGTGGTCCGAAACATGAAACCAAGTGTGGTTGTAAAGCCAAATTTCGTGTGCATATTGATATAATTACTCAACGTTGGTACATCACAATTTTCACCTTTGATCACAATCATGATATGTTGAGTGAGAAACATTGTGCATTGCTGGCTGCTCATATGAAGCTGACTAAGTCTGATAAGATTCAAGTTACCAACTTTGGCAATGCCGGAATCAAAGTTACGCAAATGATTGGTGCGTTTGCAAATGCCGCTGGCGGGTATGATAAGGTAGGATTTCTGAAAAAGGATTTACACAATCAAATTCTAAGACAAAGAAAAGTGATGTTTTCGGATGCTAAAGGTGCCGTTACGTATCTTAAAGATCTGCGCCGTAAAGATCCATTGATGTTTGTTGCACATACGGTTGGTGCAGATGGAATTAGAACAACATCTCGTTGTGAGGCGTTTCATAGCCATATGGGTCTGTTTATACACTCGAAGATGAATATGACAGATTTTGTTAAGCACTTCCATATGTGTGTTTCATATTTCCGCTTCAAGGAAGTCCAAGCTGATTTTAATTCTCAATATGGGAGTGCGGTGTTACAGACTAATTTGAGGTCGTTTGAGAGTCCATCGAAAGATGAATTTGCATGTTCTTGTCTTAGAATGGAACCTATTGGAATTCGTTGTGAGCATATCATCGATGTGCTAGTATATCTTGATTTTGATGAAATTCCTAAGTCTTTAGTGCTGAATCGTTGGTCAATATTTGCCAAGGAGTCAATTAGAGGTAATTTCGATGATGGTTCGCATTACTGGGATTCTCATTTGGTTGCTAGGCATGCAAATCTGGTGTATCTTAGTAAGGAGGTTTGCGACCTATCATATAAGGATGTCGATGATTATAAAAAATATCTAGAATATCTAACGGATGAACTTGGTAGGCTAAAGTCAAAGTATGGTGAAGAAGGTGAACCAGATAATTTACATGTTCCAGTTGAGGTGGATAGCATACTGAACTCTTCCTGTTCAAGAAGCAAAGGGTGTGGAGCTAGCGCCAGGAATGCAATGGGTCACCGACGTAGAACACAAACATGTGGGATTTGCGGTGCATCTGGACACAACAGTCGATCTTGTCCTACACTTGATGTAGATGGTGAATATGTTCCAGACAATTCCCTTCAAACAGGGTCAGTACGCTTAAGTGATGACGTTTAA
Protein sequence

>MsaT012601.1

MDEIRHENEADAEGDDYGDGEADDDGDGEGDSGDDEGQLSAEENESDEAFLGSEYDEVDYFVDRKEISHADDEDLDGNSDDVDESIFSVRSEDESIVIESVDDIVKMDMYNLQNEDVSKLLFRSLEVAYNFYCWFAKMNGFAVRKGQVIKNKNGDVLQQTFVCNLEGFRRDRGLTVEERKRGPKHETKCGCKAKFRVHIDIITQRWYITIFTFDHNHDMLSEKHCALLAAHMKLTKSDKIQVTNFGNAGIKVTQMIGAFANAAGGYDKVGFLKKDLHNQILRQRKVMFSDAKGAVTYLKDLRRKDPLMFVAHTVGADGIRTTSRCEAFHSHMGLFIHSKMNMTDFVKHFHMCVSYFRFKEVQADFNSQYGSAVLQTNLRSFESPSKDEFACSCLRMEPIGIRCEHIIDVLVYLDFDEIPKSLVLNRWSIFAKESIRGNFDDGSHYWDSHLVARHANLVYLSKEVCDLSYKDVDDYKKYLEYLTDELGRLKSKYGEEGEPDNLHVPVEVDSILNSSCSRSKGCGASARNAMGHRRRTQTCGICGASGHNSRSCPTLDVDGEYVPDNSLQTGSVRLSDDV*