AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG025073

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025073 MtrunA17_Chr5g0397361 91.270 252 20 2 1 251 1 251 1.23e-161 447
MsaG025073 MtrunA17_Chr8g0387241 49.505 202 69 5 65 240 97 291 3.82e-54 177
MsaG025073 MtrunA17_Chr2g0311591 54.545 88 37 1 148 232 143 230 1.87e-22 93.2
MsaG025073 MtrunA17_Chr2g0327621 41.739 115 45 2 129 221 90 204 1.04e-19 85.1
MsaG025073 MtrunA17_Chr1g0168401 47.917 96 41 2 141 236 292 378 1.09e-19 87.4
MsaG025073 MtrunA17_Chr1g0186171 51.948 77 37 0 139 215 283 359 5.44e-19 85.5
MsaG025073 MtrunA17_Chr1g0147111 48.276 87 38 2 138 220 194 277 5.44e-17 78.6
MsaG025073 MtrunA17_Chr4g0030421 53.125 64 30 0 158 221 21 84 6.51e-16 72.4
MsaG025073 MtrunA17_Chr3g0126721 35.075 134 71 3 104 222 148 280 2.63e-15 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025073 AT5G41380.1 48.370 184 73 6 58 221 83 264 2.57e-40 141
MsaG025073 AT1G63820.1 49.342 152 54 5 117 248 117 265 2.51e-35 128
MsaG025073 AT3G12890.1 51.546 97 44 2 154 250 121 214 1.17e-21 90.9
MsaG025073 AT1G04500.4 33.484 221 107 8 34 234 146 346 4.72e-20 88.6
MsaG025073 AT1G04500.1 33.484 221 107 8 34 234 146 346 4.72e-20 88.6
MsaG025073 AT1G04500.3 33.484 221 107 8 34 234 137 337 4.81e-20 88.6
MsaG025073 AT2G33350.2 66.667 57 19 0 163 219 301 357 4.99e-18 82.8
MsaG025073 AT2G33350.1 66.667 57 19 0 163 219 302 358 5.91e-18 82.8
MsaG025073 AT2G33350.4 66.667 57 19 0 163 219 290 346 6.13e-18 82.8
MsaG025073 AT2G33350.5 66.667 57 19 0 163 219 310 366 6.36e-18 82.8
MsaG025073 AT4G27900.1 48.315 89 37 3 138 222 178 261 3.92e-16 76.3
MsaG025073 AT4G27900.2 48.315 89 37 3 138 222 178 261 3.92e-16 76.3
MsaG025073 AT5G53420.1 44.318 88 47 2 129 216 177 262 2.39e-15 73.9
MsaG025073 AT5G53420.2 44.318 88 47 2 129 216 98 183 2.94e-15 72.0
MsaG025073 AT5G53420.5 44.318 88 47 2 129 216 98 183 2.94e-15 72.0
MsaG025073 AT5G53420.4 44.318 88 47 2 129 216 98 183 2.94e-15 72.0
MsaG025073 AT5G59990.1 43.103 116 56 3 136 243 119 232 4.39e-14 70.1

Find 53 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTCATGCCATTGGAAATT+TGG 0.108434 5:-3666142 None:intergenic
TGTTTGGGCTTGAATGTTTA+TGG 0.196449 5:-3665829 None:intergenic
ATTCATGCCATTGGAAATTT+GGG 0.264246 5:-3666141 None:intergenic
ATCATCATGAAGACGAGTTC+TGG 0.270661 5:+3667017 MsaT025073.1:CDS
CAAAGTAGGGCGTTACAATT+TGG 0.279002 5:+3666495 MsaT025073.1:CDS
GGATCATAAGAGACTTTGTT+TGG 0.295719 5:-3665845 None:intergenic
AGCTCCTCTGCATTAACTTT+TGG 0.308354 5:-3666048 None:intergenic
GGAAATTTCTCTACTTTGGA+TGG 0.338370 5:+3665974 MsaT025073.1:CDS
GAACTTCCTCCGGCTTCTCT+TGG 0.364020 5:-3666551 None:intergenic
GCTTGGAAATTTCTCTACTT+TGG 0.370290 5:+3665970 MsaT025073.1:CDS
GAAGTTCAACAAGATTATTA+AGG 0.398859 5:+3666567 MsaT025073.1:CDS
GTGCAGTGCAGGAGATTTGC+AGG 0.405645 5:+3666210 MsaT025073.1:CDS
GATTGTCGGCTAGTGTCTTT+CGG 0.419573 5:-3666913 None:intergenic
TAAGCTTCAGAAGGAAAATC+AGG 0.424848 5:-3666097 None:intergenic
ATTTAGGTTGATTTCATTGA+AGG 0.428619 5:+3667156 MsaT025073.1:intron
TAATCTTGTTGAACTTCCTC+CGG 0.431668 5:-3666561 None:intergenic
GGGAGTCCATCTGTGTGTTA+TGG 0.434607 5:-3666120 None:intergenic
GAAAACTGAGGAATGTCAAA+TGG 0.438264 5:+3666006 MsaT025073.1:CDS
GCACGCCCTTCTTATTTGTC+CGG 0.440631 5:-3666191 None:intergenic
TGTTGTTGTGATCTTAATAG+AGG 0.449547 5:-3667194 None:intergenic
GATCATAAGAGACTTTGTTT+GGG 0.452048 5:-3665844 None:intergenic
TCTTCTCCAACCAGTGAGCT+TGG 0.454671 5:+3665953 MsaT025073.1:CDS
ACGTATGCGTGTTCGATTGT+CGG 0.459741 5:-3666927 None:intergenic
GAAATTTCTCTACTTTGGAT+GGG 0.461348 5:+3665975 MsaT025073.1:CDS
ATAAGAAGGGCGTGCAGTGC+AGG 0.462306 5:+3666199 MsaT025073.1:CDS
GATGAAGTAAACTTCAAAGT+AGG 0.477302 5:+3666481 MsaT025073.1:CDS
TCATCATGAAGACGAGTTCT+GGG 0.484075 5:+3667018 MsaT025073.1:CDS
GATCAGAACATGGCAACACC+TGG 0.484597 5:+3666448 MsaT025073.1:intron
CTGTTTCAATGTAATTGAAA+GGG 0.489672 5:-3665874 None:intergenic
ACTGTTTCAATGTAATTGAA+AGG 0.489675 5:-3665875 None:intergenic
TTTAGGTTGATTTCATTGAA+GGG 0.494868 5:+3667157 MsaT025073.1:intron
GGGAGCTCAATTCATGCCAT+TGG 0.496254 5:-3666150 None:intergenic
GGCAACACCTGGGTCTCAAA+CGG 0.500495 5:+3666459 MsaT025073.1:CDS
GATATAGAGCCAAGAGAAGC+CGG 0.504164 5:+3666542 MsaT025073.1:CDS
ACTTCATCCGTTTGAGACCC+AGG 0.512208 5:-3666466 None:intergenic
TCTTCACCGGACAAATAAGA+AGG 0.514231 5:+3666185 MsaT025073.1:CDS
AGAGAAATTTCCAAGCTCAC+TGG 0.521246 5:-3665963 None:intergenic
TTACATTGAAACAGTTCAAG+AGG 0.525691 5:+3665883 MsaT025073.1:CDS
CCCGAAAATAGTTTCTTCAC+CGG 0.538362 5:+3666172 MsaT025073.1:CDS
ATGAAGTAAACTTCAAAGTA+GGG 0.543162 5:+3666482 MsaT025073.1:CDS
AAAACTGAGGAATGTCAAAT+GGG 0.562447 5:+3666007 MsaT025073.1:CDS
AAATTTCCAAGCTCACTGGT+TGG 0.575257 5:-3665959 None:intergenic
ATGTAATTGAAAGGGTAATG+AGG 0.586254 5:-3665866 None:intergenic
AGCTTACCATAACACACAGA+TGG 0.590460 5:+3666114 MsaT025073.1:CDS
TTCATGCCATTGGAAATTTG+GGG 0.622889 5:-3666140 None:intergenic
CTTCACCGGACAAATAAGAA+GGG 0.624611 5:+3666186 MsaT025073.1:CDS
TGGACTCCCCAAATTTCCAA+TGG 0.637971 5:+3666134 MsaT025073.1:CDS
GTGTTATGGTAAGCTTCAGA+AGG 0.638279 5:-3666106 None:intergenic
ATCAGAACATGGCAACACCT+GGG 0.639682 5:+3666449 MsaT025073.1:intron
GACAATCGAACACGCATACG+TGG 0.645981 5:+3666929 MsaT025073.1:CDS
TGGGTCTCGTTTGAAAACTG+AGG 0.669045 5:+3665994 MsaT025073.1:CDS
ACTACCAAAAGTTAATGCAG+AGG 0.669632 5:+3666044 MsaT025073.1:CDS
ATAGAGCCAAGAGAAGCCGG+AGG 0.708071 5:+3666545 MsaT025073.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 3665788 3667203 3665788 ID=MsaG025073
Chr5 mRNA 3665788 3667203 3665788 ID=MsaT025073.1;Parent=MsaG025073
Chr5 exon 3665788 3666231 3665788 ID=MsaT025073.1.exon1;Parent=MsaT025073.1
Chr5 CDS 3665788 3666231 3665788 ID=cds.MsaT025073.1;Parent=MsaT025073.1
Chr5 exon 3666454 3666588 3666454 ID=MsaT025073.1.exon2;Parent=MsaT025073.1
Chr5 CDS 3666454 3666588 3666454 ID=cds.MsaT025073.1;Parent=MsaT025073.1
Chr5 exon 3666905 3667039 3666905 ID=MsaT025073.1.exon3;Parent=MsaT025073.1
Chr5 CDS 3666905 3667039 3666905 ID=cds.MsaT025073.1;Parent=MsaT025073.1
Chr5 exon 3667162 3667203 3667162 ID=MsaT025073.1.exon4;Parent=MsaT025073.1
Chr5 CDS 3667162 3667203 3667162 ID=cds.MsaT025073.1;Parent=MsaT025073.1
Gene Sequence

>MsaT025073.1

ATGTCTTCTGATAGTGATATCTATACTATTGATATTTCTTTCCATAAACATTCAAGCCCAAACAAAGTCTCTTATGATCCTCATTACCCTTTCAATTACATTGAAACAGTTCAAGAGGATTTGAACAATTCTCTTGACTCATTTTCCTCTTCCTTCTTTTCTTTTTCTTCTCCAACCAGTGAGCTTGGAAATTTCTCTACTTTGGATGGGTCTCGTTTGAAAACTGAGGAATGTCAAATGGGTGTAGATTACTCCTACTACCAAAAGTTAATGCAGAGGAGCTATAATTGTAACAATTTTCATGAGAAACCTGATTTTCCTTCTGAAGCTTACCATAACACACAGATGGACTCCCCAAATTTCCAATGGCATGAATTGAGCTCCCCCGAAAATAGTTTCTTCACCGGACAAATAAGAAGGGCGTGCAGTGCAGGAGATTTGCAGAACATGGCAACACCTGGGTCTCAAACGGATGAAGTAAACTTCAAAGTAGGGCGTTACAATTTGGAAGAACGAAAAGAAAAAATCTCTAGATATAGAGCCAAGAGAAGCCGGAGGAAGTTCAACAAGATTATTAAGTATGCATGCCGAAAGACACTAGCCGACAATCGAACACGCATACGTGGCAGATTCGCAAGTAACGACAAAACCAACGAGATTCCAAAACCTGTGTGTTCAAAAACAGAAAAATATCATCATGAAGACGAGTTCTGGGTTGATTTCATTGAAGGGTTAAATGACGAGCTCCTCTATTAA
Protein sequence

>MsaT025073.1

MSSDSDIYTIDISFHKHSSPNKVSYDPHYPFNYIETVQEDLNNSLDSFSSSFFSFSSPTSELGNFSTLDGSRLKTEECQMGVDYSYYQKLMQRSYNCNNFHEKPDFPSEAYHNTQMDSPNFQWHELSSPENSFFTGQIRRACSAGDLQNMATPGSQTDEVNFKVGRYNLEERKEKISRYRAKRSRRKFNKIIKYACRKTLADNRTRIRGRFASNDKTNEIPKPVCSKTEKYHHEDEFWVDFIEGLNDELLY*