AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0532210

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0532210 MtrunA17_Chr4g0005501 95.413 218 7 1 1 218 1 215 1.84e-151 419
Msa0532210 MtrunA17_Chr7g0243271 65.775 187 56 3 36 215 1 186 8.40e-77 229
Msa0532210 MtrunA17_Chr5g0437611 62.941 170 58 3 42 209 39 205 2.15e-70 213
Msa0532210 MtrunA17_Chr3g0114121 61.988 171 60 4 47 216 64 230 3.12e-69 211
Msa0532210 MtrunA17_Chr1g0158871 45.902 183 94 2 31 213 5 182 5.49e-55 174
Msa0532210 MtrunA17_Chr5g0411391 53.659 164 72 2 49 208 44 207 6.75e-55 174
Msa0532210 MtrunA17_Chr8g0347191 48.171 164 84 1 49 212 73 235 9.30e-54 172
Msa0532210 MtrunA17_Chr1g0151661 52.500 160 72 3 49 206 39 196 4.07e-53 169
Msa0532210 MtrunA17_Chr3g0126471 43.956 182 97 2 32 213 8 184 1.05e-52 168
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0532210 AT2G38310.1 67.052 173 53 2 47 218 37 206 4.58e-73 221
Msa0532210 AT5G05440.1 64.815 162 53 2 45 205 41 199 2.24e-70 214
Msa0532210 AT2G40330.1 59.064 171 65 3 45 211 44 213 3.49e-66 203
Msa0532210 AT5G53160.2 48.485 165 84 1 49 213 19 182 3.46e-56 177
Msa0532210 AT1G01360.1 47.531 162 84 1 52 213 24 184 1.42e-55 175
Msa0532210 AT4G01026.1 49.068 161 81 1 53 213 27 186 1.11e-53 171
Msa0532210 AT2G26040.1 49.398 166 82 1 43 206 16 181 1.63e-53 170
Msa0532210 AT4G27920.1 46.667 165 88 0 49 213 14 178 5.29e-52 166
Msa0532210 AT4G17870.1 48.810 168 85 1 45 211 13 180 7.88e-52 166
Msa0532210 AT1G73000.1 46.199 171 82 4 43 203 31 201 3.48e-44 147
Msa0532210 AT5G46790.2 49.412 170 80 3 45 209 40 208 1.09e-43 146
Msa0532210 AT5G46790.1 49.412 170 80 3 45 209 40 208 1.09e-43 146
Msa0532210 AT5G45860.1 52.055 146 69 1 64 209 12 156 4.50e-42 140
Msa0532210 AT5G45870.1 50.676 148 71 1 64 211 12 157 1.01e-41 139
Msa0532210 AT4G18620.1 45.963 161 80 2 58 211 4 164 2.23e-34 120
Msa0532210 AT5G53160.1 50.495 101 49 1 49 149 19 118 5.76e-32 114

Find 74 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGAAGACTTTGGTGGATT+TGG 0.227133 4_1:+6228727 None:intergenic
CGTTCGGTGCTGCGTGCAGC+AGG 0.323719 4_1:+6228379 None:intergenic
GGACGACCGCCGAGCATAAT+TGG 0.334740 4_1:+6228554 None:intergenic
TGATAGTGGGCTATAGTATT+AGG 0.336898 4_1:+6228598 None:intergenic
CAGCAGGGAGGCCAGATATA+AGG 0.373259 4_1:+6228395 None:intergenic
TTAGGAATGGTGTTGGTGAC+AGG 0.377606 4_1:+6228616 None:intergenic
TGATGGAGGCGGTTGTCTCT+TGG 0.388404 4_1:+6228533 None:intergenic
TCCACAGAGGGTGACTGTTC+CGG 0.392902 4_1:-6228256 Msa0532210:CDS
AGGGAGGTCAACCTTATATC+TGG 0.399072 4_1:-6228406 Msa0532210:CDS
GTCATCAGTTTCAGTGTTGT+TGG 0.412398 4_1:-6228328 Msa0532210:CDS
CACTGACCAAACGGCGGTGA+TGG 0.428126 4_1:+6228516 None:intergenic
ATATTGAGTGTGTGTGATAG+TGG 0.451535 4_1:+6228584 None:intergenic
GAAGACTTTGGTGGATTTGG+AGG 0.457214 4_1:+6228730 None:intergenic
CCGCCTCCATCACCGCCGTT+TGG 0.479222 4_1:-6228522 Msa0532210:CDS
ATCGAGGATCTCAAGGCGTT+CGG 0.483659 4_1:+6228363 None:intergenic
CGTTGGTGGCGACGGTGATG+TGG 0.489155 4_1:-6228437 Msa0532210:CDS
GCGGCGAACCACTGACCAAA+CGG 0.490188 4_1:+6228507 None:intergenic
CTATGTGGTGGATATTCCTT+CGG 0.490303 4_1:-6228215 Msa0532210:CDS
GAGGTCGTGGTGGTTGGTGA+TGG 0.514354 4_1:+6228669 None:intergenic
GCCGTGGAGGTCGTGGTGGT+TGG 0.515521 4_1:+6228663 None:intergenic
AGTCTTCACTTCTCCTCCAC+AGG 0.523366 4_1:-6228714 Msa0532210:CDS
TGTTTGTTGATACAATTGTT+CGG 0.525160 4_1:-6228168 Msa0532210:CDS
CATCACCGCCGTTTGGTCAG+TGG 0.527329 4_1:-6228515 Msa0532210:CDS
TATAGTATTAGGAATGGTGT+TGG 0.528924 4_1:+6228609 None:intergenic
AGGAGAAGTGAAGACTTTGG+TGG 0.533916 4_1:+6228721 None:intergenic
ACGGTGATGTGGGCACACTC+AGG 0.539446 4_1:-6228426 Msa0532210:CDS
CCAAACGGCGGTGATGGAGG+CGG 0.539681 4_1:+6228522 None:intergenic
CAACACTGAAACTGATGACA+TGG 0.539899 4_1:+6228332 None:intergenic
ATCAGTTTCAGTGTTGTTGG+TGG 0.541299 4_1:-6228325 Msa0532210:CDS
TGTAACCTCGTTGGTGGCGA+CGG 0.546094 4_1:-6228445 Msa0532210:CDS
ATCAAGAGTTGTAACCTCGT+TGG 0.547255 4_1:-6228454 Msa0532210:CDS
GTTGGTGATGGTCGTAGTGG+TGG 0.548645 4_1:+6228681 None:intergenic
CGGTGATGTGGGCACACTCA+GGG 0.556265 4_1:-6228425 Msa0532210:CDS
GTTCGGTGCTGCGTGCAGCA+GGG 0.556567 4_1:+6228380 None:intergenic
CTGTTTGTGCAAGTGACTGA+AGG 0.564175 4_1:+6228140 None:intergenic
GATCCTCATCGAGGATCTCA+AGG 0.566346 4_1:+6228356 None:intergenic
TAGGAATGGTGTTGGTGACA+GGG 0.566710 4_1:+6228617 None:intergenic
AAGAGTTGTAACCTCGTTGG+TGG 0.571438 4_1:-6228451 Msa0532210:CDS
AGGCTTGTGGTTTGTCGAAG+CGG 0.573243 4_1:+6228488 None:intergenic
GGAACAGTCACCCTCTGTGG+AGG 0.574183 4_1:+6228258 None:intergenic
TGGTGACAGGGTTGATGAAG+AGG 0.574991 4_1:+6228629 None:intergenic
TGGTGGTGTGGTTGATCCTG+TGG 0.579437 4_1:+6228698 None:intergenic
TCCTTCGGAAAATACTAAAG+AGG 0.584494 4_1:-6228200 Msa0532210:CDS
ATCATCCGACCAATTATGCT+CGG 0.584649 4_1:-6228563 Msa0532210:CDS
TGACCAAACGGCGGTGATGG+AGG 0.585643 4_1:+6228519 None:intergenic
ACACTTCATCCCTCCACAGA+GGG 0.594198 4_1:-6228268 Msa0532210:CDS
GGTGACAGGGTTGATGAAGA+GGG 0.596139 4_1:+6228630 None:intergenic
GCCGGAACAGTCACCCTCTG+TGG 0.599614 4_1:+6228255 None:intergenic
GGACTCAACTATCACCGTGC+CGG 0.603129 4_1:+6228237 None:intergenic
GAACAGTCACCCTCTGTGGA+GGG 0.606405 4_1:+6228259 None:intergenic
GACCGCCGAGCATAATTGGT+CGG 0.608055 4_1:+6228558 None:intergenic
GTGGGCTATAGTATTAGGAA+TGG 0.608376 4_1:+6228603 None:intergenic
GTTGGTGGCGACGGTGATGT+GGG 0.610157 4_1:-6228436 Msa0532210:CDS
CGAAGGAATATCCACCACAT+AGG 0.619850 4_1:+6228216 None:intergenic
TGGAGGAGAAGTGAAGACTT+TGG 0.627794 4_1:+6228718 None:intergenic
ACCAACCACCACGACCTCCA+CGG 0.628316 4_1:-6228664 Msa0532210:CDS
AGAGGGTGACTGTTCCGGCA+CGG 0.639448 4_1:-6228251 Msa0532210:CDS
GGAGGGATGAAGTGTAGTAA+CGG 0.646842 4_1:+6228276 None:intergenic
TGATGGTCGTAGTGGTGGTG+TGG 0.646910 4_1:+6228686 None:intergenic
GTGGTTGGTGATGGTCGTAG+TGG 0.657655 4_1:+6228678 None:intergenic
CGGTGCTGCGTGCAGCAGGG+AGG 0.659975 4_1:+6228383 None:intergenic
TATTGAGTGTGTGTGATAGT+GGG 0.661022 4_1:+6228585 None:intergenic
TGGTGTGGTTGATCCTGTGG+AGG 0.662950 4_1:+6228701 None:intergenic
GATGAAGTGTAGTAACGGAA+CGG 0.672049 4_1:+6228281 None:intergenic
ACGCCTTGAGATCCTCGATG+AGG 0.696994 4_1:-6228359 Msa0532210:CDS
TTTCGCCGTGGAGGTCGTGG+TGG 0.698954 4_1:+6228659 None:intergenic
ATCCGACCAATTATGCTCGG+CGG 0.704061 4_1:-6228560 Msa0532210:CDS
GATAGTTGAGTCCTATGTGG+TGG 0.708119 4_1:-6228227 Msa0532210:CDS
GGTGATAGTTGAGTCCTATG+TGG 0.715010 4_1:-6228230 Msa0532210:CDS
TGATGTGGGCACACTCAGGG+AGG 0.725955 4_1:-6228422 Msa0532210:CDS
CATCACCGTCGCCACCAACG+AGG 0.726271 4_1:+6228440 None:intergenic
TACACTTCATCCCTCCACAG+AGG 0.732326 4_1:-6228269 Msa0532210:CDS
TGACATGGCGATCCTCATCG+AGG 0.742190 4_1:+6228347 None:intergenic
GCGAACCACTGACCAAACGG+CGG 0.744614 4_1:+6228510 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCTTGATGAAATTTTTGT+AGG + chr4_1:6228367-6228386 None:intergenic 25.0%
!! TGTTTGTTGATACAATTGTT+CGG - chr4_1:6228664-6228683 Msa0532210:CDS 25.0%
TATAGTATTAGGAATGGTGT+TGG + chr4_1:6228226-6228245 None:intergenic 30.0%
! ATGAAATTTTTGTAGGCTTG+TGG + chr4_1:6228360-6228379 None:intergenic 30.0%
!! TGATAGTGGGCTATAGTATT+AGG + chr4_1:6228237-6228256 None:intergenic 35.0%
TATTGAGTGTGTGTGATAGT+GGG + chr4_1:6228250-6228269 None:intergenic 35.0%
ATATTGAGTGTGTGTGATAG+TGG + chr4_1:6228251-6228270 None:intergenic 35.0%
TCCTTCGGAAAATACTAAAG+AGG - chr4_1:6228632-6228651 Msa0532210:CDS 35.0%
! TCCTCTTTAGTATTTTCCGA+AGG + chr4_1:6228636-6228655 None:intergenic 35.0%
!! AGTGAAGACTTTGGTGGATT+TGG + chr4_1:6228108-6228127 None:intergenic 40.0%
! GTGGGCTATAGTATTAGGAA+TGG + chr4_1:6228232-6228251 None:intergenic 40.0%
ATCATCCGACCAATTATGCT+CGG - chr4_1:6228269-6228288 Msa0532210:CDS 40.0%
ATCAAGAGTTGTAACCTCGT+TGG - chr4_1:6228378-6228397 Msa0532210:CDS 40.0%
CAACACTGAAACTGATGACA+TGG + chr4_1:6228503-6228522 None:intergenic 40.0%
GTCATCAGTTTCAGTGTTGT+TGG - chr4_1:6228504-6228523 Msa0532210:CDS 40.0%
! ATCAGTTTCAGTGTTGTTGG+TGG - chr4_1:6228507-6228526 Msa0532210:CDS 40.0%
! GATGAAGTGTAGTAACGGAA+CGG + chr4_1:6228554-6228573 None:intergenic 40.0%
!! CTATGTGGTGGATATTCCTT+CGG - chr4_1:6228617-6228636 Msa0532210:CDS 40.0%
!! GAAGACTTTGGTGGATTTGG+AGG + chr4_1:6228105-6228124 None:intergenic 45.0%
AGGAGAAGTGAAGACTTTGG+TGG + chr4_1:6228114-6228133 None:intergenic 45.0%
TGGAGGAGAAGTGAAGACTT+TGG + chr4_1:6228117-6228136 None:intergenic 45.0%
!! TAGGAATGGTGTTGGTGACA+GGG + chr4_1:6228218-6228237 None:intergenic 45.0%
!! TTAGGAATGGTGTTGGTGAC+AGG + chr4_1:6228219-6228238 None:intergenic 45.0%
AAGAGTTGTAACCTCGTTGG+TGG - chr4_1:6228381-6228400 Msa0532210:CDS 45.0%
AGGGAGGTCAACCTTATATC+TGG - chr4_1:6228426-6228445 Msa0532210:CDS 45.0%
GGAGGGATGAAGTGTAGTAA+CGG + chr4_1:6228559-6228578 None:intergenic 45.0%
GGTGATAGTTGAGTCCTATG+TGG - chr4_1:6228602-6228621 Msa0532210:CDS 45.0%
GATAGTTGAGTCCTATGTGG+TGG - chr4_1:6228605-6228624 Msa0532210:CDS 45.0%
CGAAGGAATATCCACCACAT+AGG + chr4_1:6228619-6228638 None:intergenic 45.0%
CTGTTTGTGCAAGTGACTGA+AGG + chr4_1:6228695-6228714 None:intergenic 45.0%
AGTCTTCACTTCTCCTCCAC+AGG - chr4_1:6228118-6228137 Msa0532210:CDS 50.0%
!! GGTGACAGGGTTGATGAAGA+GGG + chr4_1:6228205-6228224 None:intergenic 50.0%
!! TGGTGACAGGGTTGATGAAG+AGG + chr4_1:6228206-6228225 None:intergenic 50.0%
ATCCGACCAATTATGCTCGG+CGG - chr4_1:6228272-6228291 Msa0532210:CDS 50.0%
! AGGCTTGTGGTTTGTCGAAG+CGG + chr4_1:6228347-6228366 None:intergenic 50.0%
! ATCGAGGATCTCAAGGCGTT+CGG + chr4_1:6228472-6228491 None:intergenic 50.0%
GATCCTCATCGAGGATCTCA+AGG + chr4_1:6228479-6228498 None:intergenic 50.0%
TACACTTCATCCCTCCACAG+AGG - chr4_1:6228563-6228582 Msa0532210:CDS 50.0%
ACACTTCATCCCTCCACAGA+GGG - chr4_1:6228564-6228583 Msa0532210:CDS 50.0%
TGGTGTGGTTGATCCTGTGG+AGG + chr4_1:6228134-6228153 None:intergenic 55.0%
! TGGTGGTGTGGTTGATCCTG+TGG + chr4_1:6228137-6228156 None:intergenic 55.0%
! TGATGGTCGTAGTGGTGGTG+TGG + chr4_1:6228149-6228168 None:intergenic 55.0%
!! GTTGGTGATGGTCGTAGTGG+TGG + chr4_1:6228154-6228173 None:intergenic 55.0%
!! GTGGTTGGTGATGGTCGTAG+TGG + chr4_1:6228157-6228176 None:intergenic 55.0%
!!! AGAGGGTGTTGTTTTCGCCG+TGG + chr4_1:6228188-6228207 None:intergenic 55.0%
GACCGCCGAGCATAATTGGT+CGG + chr4_1:6228277-6228296 None:intergenic 55.0%
TGATGGAGGCGGTTGTCTCT+TGG + chr4_1:6228302-6228321 None:intergenic 55.0%
!! TGTAACCTCGTTGGTGGCGA+CGG - chr4_1:6228387-6228406 Msa0532210:CDS 55.0%
CAGCAGGGAGGCCAGATATA+AGG + chr4_1:6228440-6228459 None:intergenic 55.0%
ACGCCTTGAGATCCTCGATG+AGG - chr4_1:6228473-6228492 Msa0532210:CDS 55.0%
TGACATGGCGATCCTCATCG+AGG + chr4_1:6228488-6228507 None:intergenic 55.0%
GAACAGTCACCCTCTGTGGA+GGG + chr4_1:6228576-6228595 None:intergenic 55.0%
TCCACAGAGGGTGACTGTTC+CGG - chr4_1:6228576-6228595 Msa0532210:CDS 55.0%
GGACTCAACTATCACCGTGC+CGG + chr4_1:6228598-6228617 None:intergenic 55.0%
!! GAGGTCGTGGTGGTTGGTGA+TGG + chr4_1:6228166-6228185 None:intergenic 60.0%
ACCAACCACCACGACCTCCA+CGG - chr4_1:6228168-6228187 Msa0532210:CDS 60.0%
! TGTTTTCGCCGTGGAGGTCG+TGG + chr4_1:6228179-6228198 None:intergenic 60.0%
!!! GGGTGTTGTTTTCGCCGTGG+AGG + chr4_1:6228185-6228204 None:intergenic 60.0%
GGACGACCGCCGAGCATAAT+TGG + chr4_1:6228281-6228300 None:intergenic 60.0%
! TGACCAAACGGCGGTGATGG+AGG + chr4_1:6228316-6228335 None:intergenic 60.0%
CACTGACCAAACGGCGGTGA+TGG + chr4_1:6228319-6228338 None:intergenic 60.0%
CATCACCGCCGTTTGGTCAG+TGG - chr4_1:6228317-6228336 Msa0532210:CDS 60.0%
GCGAACCACTGACCAAACGG+CGG + chr4_1:6228325-6228344 None:intergenic 60.0%
GCGGCGAACCACTGACCAAA+CGG + chr4_1:6228328-6228347 None:intergenic 60.0%
!! GTTGGTGGCGACGGTGATGT+GGG - chr4_1:6228396-6228415 Msa0532210:CDS 60.0%
ACGGTGATGTGGGCACACTC+AGG - chr4_1:6228406-6228425 Msa0532210:CDS 60.0%
CGGTGATGTGGGCACACTCA+GGG - chr4_1:6228407-6228426 Msa0532210:CDS 60.0%
TGATGTGGGCACACTCAGGG+AGG - chr4_1:6228410-6228429 Msa0532210:CDS 60.0%
GGAACAGTCACCCTCTGTGG+AGG + chr4_1:6228577-6228596 None:intergenic 60.0%
AGAGGGTGACTGTTCCGGCA+CGG - chr4_1:6228581-6228600 Msa0532210:CDS 60.0%
TTTCGCCGTGGAGGTCGTGG+TGG + chr4_1:6228176-6228195 None:intergenic 65.0%
!! CCAAACGGCGGTGATGGAGG+CGG + chr4_1:6228313-6228332 None:intergenic 65.0%
CATCACCGTCGCCACCAACG+AGG + chr4_1:6228395-6228414 None:intergenic 65.0%
!! CGTTGGTGGCGACGGTGATG+TGG - chr4_1:6228395-6228414 Msa0532210:CDS 65.0%
!! GTTCGGTGCTGCGTGCAGCA+GGG + chr4_1:6228455-6228474 None:intergenic 65.0%
GCCGGAACAGTCACCCTCTG+TGG + chr4_1:6228580-6228599 None:intergenic 65.0%
GCCGTGGAGGTCGTGGTGGT+TGG + chr4_1:6228172-6228191 None:intergenic 70.0%
CCGCCTCCATCACCGCCGTT+TGG - chr4_1:6228310-6228329 Msa0532210:CDS 70.0%
!! CGTTCGGTGCTGCGTGCAGC+AGG + chr4_1:6228456-6228475 None:intergenic 70.0%
!! CGGTGCTGCGTGCAGCAGGG+AGG + chr4_1:6228452-6228471 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 6228099 6228755 6228099 ID=Msa0532210;Name=Msa0532210
chr4_1 mRNA 6228099 6228755 6228099 ID=Msa0532210-mRNA-1;Parent=Msa0532210;Name=Msa0532210-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|218
chr4_1 exon 6228099 6228755 6228099 ID=Msa0532210-mRNA-1:exon:2231;Parent=Msa0532210-mRNA-1
chr4_1 CDS 6228099 6228755 6228099 ID=Msa0532210-mRNA-1:cds;Parent=Msa0532210-mRNA-1
Gene Sequence

>Msa0532210

ATGCCTCCAAATCCACCAAAGTCTTCACTTCTCCTCCACAGGATCAACCACACCACCACTACGACCATCACCAACCACCACGACCTCCACGGCGAAAACAACACCCTCTTCATCAACCCTGTCACCAACACCATTCCTAATACTATAGCCCACTATCACACACACTCAATATCATCCGACCAATTATGCTCGGCGGTCGTCCAAGAGACAACCGCCTCCATCACCGCCGTTTGGTCAGTGGTTCGCCGCTTCGACAAACCACAAGCCTACAAAAATTTCATCAAGAGTTGTAACCTCGTTGGTGGCGACGGTGATGTGGGCACACTCAGGGAGGTCAACCTTATATCTGGCCTCCCTGCTGCACGCAGCACCGAACGCCTTGAGATCCTCGATGAGGATCGCCATGTCATCAGTTTCAGTGTTGTTGGTGGTGATCACAAGCTTGCTAACTACCGTTCCGTTACTACACTTCATCCCTCCACAGAGGGTGACTGTTCCGGCACGGTGATAGTTGAGTCCTATGTGGTGGATATTCCTTCGGAAAATACTAAAGAGGACACACATGTGTTTGTTGATACAATTGTTCGGTGTAACCTTCAGTCACTTGCACAAACAGCAGAGAACATTACACAGCAAAACAACAAGAGTTGTTCCTGA
Protein sequence

>Msa0532210

MPPNPPKSSLLLHRINHTTTTTITNHHDLHGENNTLFINPVTNTIPNTIAHYHTHSISSDQLCSAVVQETTASITAVWSVVRRFDKPQAYKNFIKSCNLVGGDGDVGTLREVNLISGLPAARSTERLEILDEDRHVISFSVVGGDHKLANYRSVTTLHPSTEGDCSGTVIVESYVVDIPSENTKEDTHVFVDTIVRCNLQSLAQTAENITQQNNKSCS*