AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0854000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0854000 MtrunA17_Chr5g0431211 96.000 225 9 0 1 225 1 225 1.31e-129 364
Msa0854000 MtrunA17_Chr3g0105921 75.000 180 41 2 3 178 4 183 1.28e-84 250
Msa0854000 MtrunA17_Chr4g0051251 63.830 188 52 2 33 204 42 229 6.44e-82 244
Msa0854000 MtrunA17_Chr1g0167411 80.000 125 25 0 37 161 65 189 5.13e-79 236
Msa0854000 MtrunA17_Chr1g0187671 78.014 141 31 0 27 167 43 183 7.71e-76 227
Msa0854000 MtrunA17_Chr2g0283861 67.550 151 48 1 20 170 19 168 1.51e-73 221
Msa0854000 MtrunA17_Chr2g0315791 73.333 135 36 0 36 170 32 166 2.07e-72 218
Msa0854000 MtrunA17_Chr7g0261381 79.104 134 28 0 34 167 61 194 3.22e-72 219
Msa0854000 MtrunA17_Chr1g0183761 80.153 131 26 0 37 167 45 175 3.08e-71 216
Msa0854000 MtrunA17_Chr2g0325831 72.441 127 35 0 34 160 20 146 4.45e-71 214
Msa0854000 MtrunA17_Chr4g0041141 68.462 130 41 0 31 160 23 152 1.88e-70 213
Msa0854000 MtrunA17_Chr7g0274631 67.568 148 42 4 36 180 26 170 4.09e-70 212
Msa0854000 MtrunA17_Chr1g0190231 73.427 143 38 0 37 179 40 182 6.40e-69 209
Msa0854000 MtrunA17_Chr8g0379061 72.800 125 34 0 36 160 84 208 2.45e-58 184
Msa0854000 MtrunA17_Chr1g0211641 71.111 45 13 0 31 75 65 109 4.45e-21 84.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0854000 AT1G07090.1 67.021 188 52 2 1 186 1 180 1.86e-89 262
Msa0854000 AT5G58500.1 68.715 179 42 3 35 212 17 182 3.15e-84 248
Msa0854000 AT2G31160.1 73.885 157 40 1 13 168 29 185 5.18e-74 224
Msa0854000 AT2G42610.1 72.794 136 37 0 34 169 22 157 6.99e-72 217
Msa0854000 AT2G42610.2 72.794 136 37 0 34 169 22 157 6.99e-72 217
Msa0854000 AT5G28490.1 71.053 152 39 1 15 166 8 154 1.77e-70 214
Msa0854000 AT3G23290.2 81.746 126 23 0 36 161 47 172 3.88e-70 213
Msa0854000 AT3G04510.1 76.154 130 31 0 37 166 33 162 6.60e-68 207
Msa0854000 AT1G78815.1 71.200 125 36 0 36 160 39 163 1.64e-67 206
Msa0854000 AT4G18610.1 67.460 126 40 1 36 160 36 161 1.48e-63 196
Msa0854000 AT1G16910.1 66.165 133 45 0 33 165 19 151 7.53e-63 193

Find 69 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCAAGTATCTTGATCAATT+TGG 0.199090 5_4:+46193220 Msa0854000:CDS
ACGCTCTCATCGGACGTCTT+AGG 0.202990 5_4:+46193341 Msa0854000:CDS
CTGCACAGTGCTAGGGTTAA+TGG 0.269012 5_4:-46193175 None:intergenic
CGGCTTGGTGTTGGTGTTGC+TGG 0.280001 5_4:-46193088 None:intergenic
GGGCTGTTAGGATTTATCTA+AGG 0.292690 5_4:+46193416 Msa0854000:CDS
CGTTTGGAACTCGGGCTGTT+AGG 0.341199 5_4:+46193404 Msa0854000:CDS
CTTCCCCACGCTTGTTTAAG+AGG 0.348758 5_4:-46193313 None:intergenic
GTGATAGGTTGTCCGTATTT+CGG 0.349075 5_4:+46193259 Msa0854000:CDS
CGCTCTCATCGGACGTCTTA+GGG 0.360799 5_4:+46193342 Msa0854000:CDS
GATTTATCTAAGGGAAGTTA+AGG 0.378556 5_4:+46193426 Msa0854000:CDS
GTTGGTGTTGCTGGTGATGA+AGG 0.383238 5_4:-46193079 None:intergenic
CGAGGAAAACGGAGGGAAAC+CGG 0.399464 5_4:+46193372 Msa0854000:CDS
TGTGACGGTGGTAGTATTAT+TGG 0.411712 5_4:-46193623 None:intergenic
GATGGTAACACCGAGAGAAT+TGG 0.417561 5_4:+46193580 Msa0854000:CDS
GAGTAATCCGTTTGGAACTC+GGG 0.435870 5_4:+46193396 Msa0854000:CDS
ACGTCTTAGGGCTGCTTTCG+AGG 0.442268 5_4:+46193354 Msa0854000:CDS
GCGCAAGGAGAAGGTGGGTT+AGG 0.457008 5_4:-46193286 None:intergenic
TGTGGTTACGTAGATATTGT+TGG 0.476151 5_4:-46193147 None:intergenic
GGTGACGGTGGTGGTATTGA+TGG 0.478331 5_4:+46193562 Msa0854000:CDS
GTGCTCCACTGCACAGTGCT+AGG 0.492585 5_4:-46193183 None:intergenic
AAAACTAAGGTGCATGTGAT+AGG 0.496763 5_4:+46193244 Msa0854000:CDS
AGTCACAAAAGCGACGAGAC+TGG 0.499984 5_4:+46193116 Msa0854000:CDS
TCGGCAATGGAAGCTGCATC+TGG 0.503318 5_4:+46192995 None:intergenic
ACCTATTGTTAGTGTTAGTA+CGG 0.504598 5_4:+46193645 Msa0854000:CDS
AGAGTAATCCGTTTGGAACT+CGG 0.507915 5_4:+46193395 Msa0854000:CDS
AGGGCTGCTTTCGAGGAAAA+CGG 0.508000 5_4:+46193361 Msa0854000:CDS
GGCTGTTAGGATTTATCTAA+GGG 0.509601 5_4:+46193417 Msa0854000:CDS
GCCGTACTAACACTAACAAT+AGG 0.510181 5_4:-46193646 None:intergenic
GGGTTAGGTTGTCCGAAATA+CGG 0.513501 5_4:-46193271 None:intergenic
GTTGCTGGTGATGAAGGTTG+TGG 0.519042 5_4:-46193073 None:intergenic
AAACCGGAGAGTAATCCGTT+TGG 0.519738 5_4:+46193388 Msa0854000:CDS
AGAGGACAAGCGCAAGGAGA+AGG 0.525742 5_4:-46193295 None:intergenic
GGTTGTGGTTGTGCTGCCTC+CGG 0.526300 5_4:-46193058 None:intergenic
TGCTCCACTGCACAGTGCTA+GGG 0.532151 5_4:-46193182 None:intergenic
GGACAAGCGCAAGGAGAAGG+TGG 0.534211 5_4:-46193292 None:intergenic
TTTGATGGTATTGACGGTGG+TGG 0.538750 5_4:-46193028 None:intergenic
GATGGTATTGACGGTGGTGG+TGG 0.541936 5_4:-46193025 None:intergenic
CTAGGGTTAATGGTGGTTTG+TGG 0.548564 5_4:-46193165 None:intergenic
CTTGTCCTCTTAAACAAGCG+TGG 0.557238 5_4:+46193308 Msa0854000:CDS
GCGGTGAATAGTAGTGGACT+TGG 0.557889 5_4:+46193541 Msa0854000:CDS
TTGTCCTCTTAAACAAGCGT+GGG 0.559800 5_4:+46193309 Msa0854000:CDS
AACACCAGCTCCAATTCTCT+CGG 0.568073 5_4:-46193590 None:intergenic
GGAAGTCTTGACGCTCTCAT+CGG 0.568235 5_4:+46193331 Msa0854000:CDS
GACGGTGGTAGTATTATTGG+TGG 0.568631 5_4:-46193620 None:intergenic
GTTCCAAACGGATTACTCTC+CGG 0.573710 5_4:-46193391 None:intergenic
AGTGGACTTGGTGACGGTGG+TGG 0.574244 5_4:+46193553 Msa0854000:CDS
TATCTAAGGGAAGTTAAGGA+TGG 0.596771 5_4:+46193430 Msa0854000:CDS
TGTGGTTGTGCTGCCTCCGG+TGG 0.598177 5_4:-46193055 None:intergenic
ATTGCAGCAGCGGTGACAGT+GGG 0.601286 5_4:-46193502 None:intergenic
GATGGTCAAGCTAAAGCTAG+AGG 0.604205 5_4:+46193448 Msa0854000:CDS
AACACTAACAATAGGTGTGA+CGG 0.607101 5_4:-46193638 None:intergenic
GCAATGGAAGCTGCATCTGG+TGG 0.607187 5_4:+46192998 None:intergenic
TATTGCAGCAGCGGTGACAG+TGG 0.608654 5_4:-46193503 None:intergenic
CTAACAGCCCGAGTTCCAAA+CGG 0.612600 5_4:-46193403 None:intergenic
GACAAGCGCAAGGAGAAGGT+GGG 0.614541 5_4:-46193291 None:intergenic
ACAGCAGCGGTGAATAGTAG+TGG 0.615069 5_4:+46193535 Msa0854000:CDS
TGTTTAAGAGGACAAGCGCA+AGG 0.622250 5_4:-46193301 None:intergenic
GAGAGAATTGGAGCTGGTGT+TGG 0.623654 5_4:+46193592 Msa0854000:CDS
AGTTGATATTATTGCAGCAG+CGG 0.629514 5_4:-46193512 None:intergenic
CACAGTGCTAGGGTTAATGG+TGG 0.634530 5_4:-46193172 None:intergenic
AATAGTAGTGGACTTGGTGA+CGG 0.643866 5_4:+46193547 Msa0854000:CDS
AACACCGAGAGAATTGGAGC+TGG 0.649987 5_4:+46193586 Msa0854000:CDS
CTGCTTTCGAGGAAAACGGA+GGG 0.652276 5_4:+46193365 Msa0854000:CDS
TTAACCCTAGCACTGTGCAG+TGG 0.666567 5_4:+46193178 Msa0854000:CDS
AATAATATCAACTACAGCAG+CGG 0.669859 5_4:+46193522 Msa0854000:CDS
GCTGCTTTCGAGGAAAACGG+AGG 0.681689 5_4:+46193364 Msa0854000:CDS
AGTAGTGGACTTGGTGACGG+TGG 0.690950 5_4:+46193550 Msa0854000:CDS
TGTCCTCTTAAACAAGCGTG+GGG 0.710607 5_4:+46193310 Msa0854000:CDS
ACTAACAATAGGTGTGACGG+TGG 0.726512 5_4:-46193635 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGATCAATTTGGAAAAACTA+AGG + chr5_4:46193231-46193250 Msa0854000:CDS 25.0%
! TTCCTTATGAGAAAAAGAAA+CGG + chr5_4:46193473-46193492 Msa0854000:CDS 25.0%
CTCAAGTATCTTGATCAATT+TGG + chr5_4:46193220-46193239 Msa0854000:CDS 30.0%
GATTTATCTAAGGGAAGTTA+AGG + chr5_4:46193426-46193445 Msa0854000:CDS 30.0%
! TTCCGTTTCTTTTTCTCATA+AGG - chr5_4:46193478-46193497 None:intergenic 30.0%
AATAATATCAACTACAGCAG+CGG + chr5_4:46193522-46193541 Msa0854000:CDS 30.0%
ACCTATTGTTAGTGTTAGTA+CGG + chr5_4:46193645-46193664 Msa0854000:CDS 30.0%
!! GGTGTTTTTGATGGTATTGA+CGG - chr5_4:46193037-46193056 None:intergenic 35.0%
AATACCATCAAAAACACCAC+CGG + chr5_4:46193039-46193058 Msa0854000:CDS 35.0%
TGTGGTTACGTAGATATTGT+TGG - chr5_4:46193150-46193169 None:intergenic 35.0%
AAAACTAAGGTGCATGTGAT+AGG + chr5_4:46193244-46193263 Msa0854000:CDS 35.0%
GGCTGTTAGGATTTATCTAA+GGG + chr5_4:46193417-46193436 Msa0854000:CDS 35.0%
TATCTAAGGGAAGTTAAGGA+TGG + chr5_4:46193430-46193449 Msa0854000:CDS 35.0%
ATGAGAAAAAGAAACGGAAG+AGG + chr5_4:46193479-46193498 Msa0854000:CDS 35.0%
! AGTTGATATTATTGCAGCAG+CGG - chr5_4:46193515-46193534 None:intergenic 35.0%
AACACTAACAATAGGTGTGA+CGG - chr5_4:46193641-46193660 None:intergenic 35.0%
!!! GTTTTTGATGGTATTGACGG+TGG - chr5_4:46193034-46193053 None:intergenic 40.0%
GTGATAGGTTGTCCGTATTT+CGG + chr5_4:46193259-46193278 Msa0854000:CDS 40.0%
TTGTCCTCTTAAACAAGCGT+GGG + chr5_4:46193309-46193328 Msa0854000:CDS 40.0%
! AGAGTAATCCGTTTGGAACT+CGG + chr5_4:46193395-46193414 Msa0854000:CDS 40.0%
GGGCTGTTAGGATTTATCTA+AGG + chr5_4:46193416-46193435 Msa0854000:CDS 40.0%
!! AATAGTAGTGGACTTGGTGA+CGG + chr5_4:46193547-46193566 Msa0854000:CDS 40.0%
TGTGACGGTGGTAGTATTAT+TGG - chr5_4:46193626-46193645 None:intergenic 40.0%
GCCGTACTAACACTAACAAT+AGG - chr5_4:46193649-46193668 None:intergenic 40.0%
!! TTTGATGGTATTGACGGTGG+TGG - chr5_4:46193031-46193050 None:intergenic 45.0%
! TTTTGTGACTCATAGCGGCT+TGG - chr5_4:46193106-46193125 None:intergenic 45.0%
!!! GTCGCTTTTGTGACTCATAG+CGG - chr5_4:46193111-46193130 None:intergenic 45.0%
CTAGGGTTAATGGTGGTTTG+TGG - chr5_4:46193168-46193187 None:intergenic 45.0%
! GGGTTAGGTTGTCCGAAATA+CGG - chr5_4:46193274-46193293 None:intergenic 45.0%
TGTTTAAGAGGACAAGCGCA+AGG - chr5_4:46193304-46193323 None:intergenic 45.0%
CTTGTCCTCTTAAACAAGCG+TGG + chr5_4:46193308-46193327 Msa0854000:CDS 45.0%
TGTCCTCTTAAACAAGCGTG+GGG + chr5_4:46193310-46193329 Msa0854000:CDS 45.0%
AAACCGGAGAGTAATCCGTT+TGG + chr5_4:46193388-46193407 Msa0854000:CDS 45.0%
!! GTTCCAAACGGATTACTCTC+CGG - chr5_4:46193394-46193413 None:intergenic 45.0%
! GAGTAATCCGTTTGGAACTC+GGG + chr5_4:46193396-46193415 Msa0854000:CDS 45.0%
GATGGTCAAGCTAAAGCTAG+AGG + chr5_4:46193448-46193467 Msa0854000:CDS 45.0%
GATGGTAACACCGAGAGAAT+TGG + chr5_4:46193580-46193599 Msa0854000:CDS 45.0%
AACACCAGCTCCAATTCTCT+CGG - chr5_4:46193593-46193612 None:intergenic 45.0%
GACGGTGGTAGTATTATTGG+TGG - chr5_4:46193623-46193642 None:intergenic 45.0%
ACTAACAATAGGTGTGACGG+TGG - chr5_4:46193638-46193657 None:intergenic 45.0%
ACCATCAAAAACACCACCGG+AGG + chr5_4:46193042-46193061 Msa0854000:CDS 50.0%
! GTTGCTGGTGATGAAGGTTG+TGG - chr5_4:46193076-46193095 None:intergenic 50.0%
!! GTTGGTGTTGCTGGTGATGA+AGG - chr5_4:46193082-46193101 None:intergenic 50.0%
AGTCACAAAAGCGACGAGAC+TGG + chr5_4:46193116-46193135 Msa0854000:CDS 50.0%
CACAGTGCTAGGGTTAATGG+TGG - chr5_4:46193175-46193194 None:intergenic 50.0%
CTGCACAGTGCTAGGGTTAA+TGG - chr5_4:46193178-46193197 None:intergenic 50.0%
TTAACCCTAGCACTGTGCAG+TGG + chr5_4:46193178-46193197 Msa0854000:CDS 50.0%
CTTCCCCACGCTTGTTTAAG+AGG - chr5_4:46193316-46193335 None:intergenic 50.0%
GGAAGTCTTGACGCTCTCAT+CGG + chr5_4:46193331-46193350 Msa0854000:CDS 50.0%
! AGGGCTGCTTTCGAGGAAAA+CGG + chr5_4:46193361-46193380 Msa0854000:CDS 50.0%
CTGCTTTCGAGGAAAACGGA+GGG + chr5_4:46193365-46193384 Msa0854000:CDS 50.0%
CTAACAGCCCGAGTTCCAAA+CGG - chr5_4:46193406-46193425 None:intergenic 50.0%
ACAGCAGCGGTGAATAGTAG+TGG + chr5_4:46193535-46193554 Msa0854000:CDS 50.0%
!! GCGGTGAATAGTAGTGGACT+TGG + chr5_4:46193541-46193560 Msa0854000:CDS 50.0%
AACACCGAGAGAATTGGAGC+TGG + chr5_4:46193586-46193605 Msa0854000:CDS 50.0%
GAGAGAATTGGAGCTGGTGT+TGG + chr5_4:46193592-46193611 Msa0854000:CDS 50.0%
!! GATGGTATTGACGGTGGTGG+TGG - chr5_4:46193028-46193047 None:intergenic 55.0%
!! GCCTCCGGTGGTGTTTTTGA+TGG - chr5_4:46193046-46193065 None:intergenic 55.0%
!! GACTCATAGCGGCTTGGTGT+TGG - chr5_4:46193100-46193119 None:intergenic 55.0%
TGCTCCACTGCACAGTGCTA+GGG - chr5_4:46193185-46193204 None:intergenic 55.0%
GACAAGCGCAAGGAGAAGGT+GGG - chr5_4:46193294-46193313 None:intergenic 55.0%
AGAGGACAAGCGCAAGGAGA+AGG - chr5_4:46193298-46193317 None:intergenic 55.0%
ACGCTCTCATCGGACGTCTT+AGG + chr5_4:46193341-46193360 Msa0854000:CDS 55.0%
CGCTCTCATCGGACGTCTTA+GGG + chr5_4:46193342-46193361 Msa0854000:CDS 55.0%
! ACGTCTTAGGGCTGCTTTCG+AGG + chr5_4:46193354-46193373 Msa0854000:CDS 55.0%
! GCTGCTTTCGAGGAAAACGG+AGG + chr5_4:46193364-46193383 Msa0854000:CDS 55.0%
CGAGGAAAACGGAGGGAAAC+CGG + chr5_4:46193372-46193391 Msa0854000:CDS 55.0%
! CGTTTGGAACTCGGGCTGTT+AGG + chr5_4:46193404-46193423 Msa0854000:CDS 55.0%
ATTGCAGCAGCGGTGACAGT+GGG - chr5_4:46193505-46193524 None:intergenic 55.0%
TATTGCAGCAGCGGTGACAG+TGG - chr5_4:46193506-46193525 None:intergenic 55.0%
!! AGTAGTGGACTTGGTGACGG+TGG + chr5_4:46193550-46193569 Msa0854000:CDS 55.0%
! GGTGACGGTGGTGGTATTGA+TGG + chr5_4:46193562-46193581 Msa0854000:CDS 55.0%
GGTTGTGGTTGTGCTGCCTC+CGG - chr5_4:46193061-46193080 None:intergenic 60.0%
!! CGGCTTGGTGTTGGTGTTGC+TGG - chr5_4:46193091-46193110 None:intergenic 60.0%
GTGCTCCACTGCACAGTGCT+AGG - chr5_4:46193186-46193205 None:intergenic 60.0%
! GCGCAAGGAGAAGGTGGGTT+AGG - chr5_4:46193289-46193308 None:intergenic 60.0%
GGACAAGCGCAAGGAGAAGG+TGG - chr5_4:46193295-46193314 None:intergenic 60.0%
!! AGTGGACTTGGTGACGGTGG+TGG + chr5_4:46193553-46193572 Msa0854000:CDS 60.0%
TGTGGTTGTGCTGCCTCCGG+TGG - chr5_4:46193058-46193077 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 46193001 46193678 46193001 ID=Msa0854000;Name=Msa0854000
chr5_4 mRNA 46193001 46193678 46193001 ID=Msa0854000-mRNA-1;Parent=Msa0854000;Name=Msa0854000-mRNA-1;_AED=0.20;_eAED=0.20;_QI=0|-1|0|1|-1|1|1|0|225
chr5_4 exon 46193001 46193678 46193001 ID=Msa0854000-mRNA-1:exon:14641;Parent=Msa0854000-mRNA-1
chr5_4 CDS 46193001 46193678 46193001 ID=Msa0854000-mRNA-1:cds;Parent=Msa0854000-mRNA-1
Gene Sequence

>Msa0854000

ATGGAAGCTGCATCTGGTGGAGAACCACCACCACCGTCAATACCATCAAAAACACCACCGGAGGCAGCACAACCACAACCTTCATCACCAGCAACACCAACACCAAGCCGCTATGAGTCACAAAAGCGACGAGACTGGAACACGTTCCAACAATATCTACGTAACCACAAACCACCATTAACCCTAGCACTGTGCAGTGGAGCACATGTGATCGAGTTTCTCAAGTATCTTGATCAATTTGGAAAAACTAAGGTGCATGTGATAGGTTGTCCGTATTTCGGACAACCTAACCCACCTTCTCCTTGCGCTTGTCCTCTTAAACAAGCGTGGGGAAGTCTTGACGCTCTCATCGGACGTCTTAGGGCTGCTTTCGAGGAAAACGGAGGGAAACCGGAGAGTAATCCGTTTGGAACTCGGGCTGTTAGGATTTATCTAAGGGAAGTTAAGGATGGTCAAGCTAAAGCTAGAGGAGTTCCTTATGAGAAAAAGAAACGGAAGAGGCCCACTGTCACCGCTGCTGCAATAATATCAACTACAGCAGCGGTGAATAGTAGTGGACTTGGTGACGGTGGTGGTATTGATGGTAACACCGAGAGAATTGGAGCTGGTGTTGGTGTTACCACCAATAATACTACCACCGTCACACCTATTGTTAGTGTTAGTACGGCTATAGTATAG
Protein sequence

>Msa0854000

MEAASGGEPPPPSIPSKTPPEAAQPQPSSPATPTPSRYESQKRRDWNTFQQYLRNHKPPLTLALCSGAHVIEFLKYLDQFGKTKVHVIGCPYFGQPNPPSPCACPLKQAWGSLDALIGRLRAAFEENGGKPESNPFGTRAVRIYLREVKDGQAKARGVPYEKKKRKRPTVTAAAIISTTAAVNSSGLGDGGGIDGNTERIGAGVGVTTNNTTTVTPIVSVSTAIV*