AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0629220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0629220 MtrunA17_Chr4g0005501 95.413 218 7 1 1 218 1 215 8.89e-153 422
Msa0629220 MtrunA17_Chr7g0243271 65.775 187 56 3 36 215 1 186 8.40e-77 229
Msa0629220 MtrunA17_Chr5g0437611 62.941 170 58 3 42 209 39 205 2.67e-70 213
Msa0629220 MtrunA17_Chr3g0114121 61.988 171 60 4 47 216 64 230 4.00e-69 211
Msa0629220 MtrunA17_Chr5g0411391 53.659 164 72 2 49 208 44 207 5.43e-55 174
Msa0629220 MtrunA17_Chr1g0158871 48.485 165 84 1 49 213 19 182 7.69e-55 173
Msa0629220 MtrunA17_Chr8g0347191 48.171 164 84 1 49 212 73 235 8.81e-54 172
Msa0629220 MtrunA17_Chr1g0151661 52.500 160 72 3 49 206 39 196 3.24e-53 170
Msa0629220 MtrunA17_Chr3g0126471 43.956 182 97 2 32 213 8 184 1.08e-52 168
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0629220 AT2G38310.1 67.052 173 53 2 47 218 37 206 5.58e-73 220
Msa0629220 AT5G05440.1 64.815 162 53 2 45 205 41 199 3.00e-70 213
Msa0629220 AT2G40330.1 59.064 171 65 3 45 211 44 213 4.11e-66 203
Msa0629220 AT5G53160.2 48.485 165 84 1 49 213 19 182 4.44e-56 177
Msa0629220 AT1G01360.1 47.531 162 84 1 52 213 24 184 1.89e-55 175
Msa0629220 AT2G26040.1 49.398 166 82 1 43 206 16 181 1.44e-53 170
Msa0629220 AT4G01026.1 49.068 161 81 1 53 213 27 186 1.48e-53 171
Msa0629220 AT4G27920.1 46.667 165 88 0 49 213 14 178 7.02e-52 166
Msa0629220 AT4G17870.1 48.810 168 85 1 45 211 13 180 8.32e-52 166
Msa0629220 AT1G73000.1 46.199 171 82 4 43 203 31 201 3.72e-44 147
Msa0629220 AT5G46790.2 49.412 170 80 3 45 209 40 208 1.10e-43 146
Msa0629220 AT5G46790.1 49.412 170 80 3 45 209 40 208 1.10e-43 146
Msa0629220 AT5G45860.1 52.055 146 69 1 64 209 12 156 4.13e-42 140
Msa0629220 AT5G45870.1 50.676 148 71 1 64 211 12 157 1.07e-41 139
Msa0629220 AT4G18620.1 45.963 161 80 2 58 211 4 164 2.43e-34 120
Msa0629220 AT5G53160.1 50.495 101 49 1 49 149 19 118 6.77e-32 114

Find 72 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_3:+10096813 None:intergenic
CGTTCGGTGCTGCGTGCAGC+AGG 0.323719 4_3:+10096465 None:intergenic
GGACGACCGCCGAGCATAAT+TGG 0.334740 4_3:+10096640 None:intergenic
TGATAGTGGGCTATAGTATT+AGG 0.336898 4_3:+10096684 None:intergenic
CAGCAGGGAGGCCAGATATA+AGG 0.373259 4_3:+10096481 None:intergenic
TTAGGAATGGTGTTGGTGAC+AGG 0.377606 4_3:+10096702 None:intergenic
TGATGGAGGCGGTTGTCTCT+TGG 0.388404 4_3:+10096619 None:intergenic
TCCACAGAGGGTGACTGTTC+CGG 0.392902 4_3:-10096342 Msa0629220:CDS
AGGGAGGTCAACCTTATATC+TGG 0.399072 4_3:-10096492 Msa0629220:CDS
CACTGACCAAACGGCGGTGA+TGG 0.428126 4_3:+10096602 None:intergenic
ATATTGAGTGTGTGTGATAG+TGG 0.451535 4_3:+10096670 None:intergenic
GAAGACTTTGGTGGATTTGG+AGG 0.457214 4_3:+10096816 None:intergenic
CCGCCTCCATCACCGCCGTT+TGG 0.479222 4_3:-10096608 Msa0629220:CDS
ATCGAGGATCTCAAGGCGTT+CGG 0.483659 4_3:+10096449 None:intergenic
CGTTGGTGGCGACGGTGATG+TGG 0.489155 4_3:-10096523 Msa0629220:CDS
GCGGCGAACCACTGACCAAA+CGG 0.490188 4_3:+10096593 None:intergenic
CTATGTGGTGGATATTCCTT+CGG 0.490303 4_3:-10096301 Msa0629220:CDS
GAGGTCGTGGTGGTTGGTGA+TGG 0.511327 4_3:+10096755 None:intergenic
AGTCTTCACTTCTCCTCCAC+AGG 0.523366 4_3:-10096800 Msa0629220:CDS
TGTTTGTTGATACAATTGTT+CGG 0.525160 4_3:-10096254 Msa0629220:CDS
CATCACCGCCGTTTGGTCAG+TGG 0.527329 4_3:-10096601 Msa0629220:CDS
TATAGTATTAGGAATGGTGT+TGG 0.528924 4_3:+10096695 None:intergenic
GCAGTGGAGGTCGTGGTGGT+TGG 0.529799 4_3:+10096749 None:intergenic
AGGAGAAGTGAAGACTTTGG+TGG 0.533916 4_3:+10096807 None:intergenic
ACGGTGATGTGGGCACACTC+AGG 0.539446 4_3:-10096512 Msa0629220:CDS
CCAAACGGCGGTGATGGAGG+CGG 0.539681 4_3:+10096608 None:intergenic
TGTAACCTCGTTGGTGGCGA+CGG 0.546094 4_3:-10096531 Msa0629220:CDS
ATCAAGAGTTGTAACCTCGT+TGG 0.547255 4_3:-10096540 Msa0629220:CDS
GTTGGTGATGGTCGTAGTGG+TGG 0.548645 4_3:+10096767 None:intergenic
CGGTGATGTGGGCACACTCA+GGG 0.556265 4_3:-10096511 Msa0629220:CDS
GTTCGGTGCTGCGTGCAGCA+GGG 0.556567 4_3:+10096466 None:intergenic
CAACACTAAAACTGATGACA+TGG 0.557856 4_3:+10096418 None:intergenic
GATCCTCATCGAGGATCTCA+AGG 0.566346 4_3:+10096442 None:intergenic
TAGGAATGGTGTTGGTGACA+GGG 0.566710 4_3:+10096703 None:intergenic
AAGAGTTGTAACCTCGTTGG+TGG 0.571438 4_3:-10096537 Msa0629220:CDS
AGGCTTGTGGTTTGTCGAAG+CGG 0.573243 4_3:+10096574 None:intergenic
GGAACAGTCACCCTCTGTGG+AGG 0.574183 4_3:+10096344 None:intergenic
TGGTGGTGTGGTTGATCCTG+TGG 0.579437 4_3:+10096784 None:intergenic
TCCTTCGGAAAATACTAAAG+AGG 0.584494 4_3:-10096286 Msa0629220:CDS
ATCATCCGACCAATTATGCT+CGG 0.584649 4_3:-10096649 Msa0629220:CDS
TGACCAAACGGCGGTGATGG+AGG 0.585643 4_3:+10096605 None:intergenic
ACACTTCATCCCTCCACAGA+GGG 0.594198 4_3:-10096354 Msa0629220:CDS
CGGTTTGTGCAAGTGACTGA+AGG 0.594264 4_3:+10096226 None:intergenic
GCCGGAACAGTCACCCTCTG+TGG 0.599614 4_3:+10096341 None:intergenic
GGACTCAACTATCACCGTGC+CGG 0.603129 4_3:+10096323 None:intergenic
GAACAGTCACCCTCTGTGGA+GGG 0.606405 4_3:+10096345 None:intergenic
GACCGCCGAGCATAATTGGT+CGG 0.608055 4_3:+10096644 None:intergenic
GTGGGCTATAGTATTAGGAA+TGG 0.608376 4_3:+10096689 None:intergenic
GTTGGTGGCGACGGTGATGT+GGG 0.610157 4_3:-10096522 Msa0629220:CDS
CGAAGGAATATCCACCACAT+AGG 0.619850 4_3:+10096302 None:intergenic
TGGAGGAGAAGTGAAGACTT+TGG 0.627794 4_3:+10096804 None:intergenic
AGAGGGTGACTGTTCCGGCA+CGG 0.639448 4_3:-10096337 Msa0629220:CDS
GGAGGGATGAAGTGTAGTAA+CGG 0.646842 4_3:+10096362 None:intergenic
TGATGGTCGTAGTGGTGGTG+TGG 0.646910 4_3:+10096772 None:intergenic
GTGGTTGGTGATGGTCGTAG+TGG 0.657655 4_3:+10096764 None:intergenic
CGGTGCTGCGTGCAGCAGGG+AGG 0.659975 4_3:+10096469 None:intergenic
TATTGAGTGTGTGTGATAGT+GGG 0.661022 4_3:+10096671 None:intergenic
TGGTGACAGGGTTGACGAAG+AGG 0.662879 4_3:+10096715 None:intergenic
TGGTGTGGTTGATCCTGTGG+AGG 0.662950 4_3:+10096787 None:intergenic
GGTGACAGGGTTGACGAAGA+GGG 0.665804 4_3:+10096716 None:intergenic
GATGAAGTGTAGTAACGGAA+CGG 0.672049 4_3:+10096367 None:intergenic
TTTCGCAGTGGAGGTCGTGG+TGG 0.685087 4_3:+10096745 None:intergenic
ACGCCTTGAGATCCTCGATG+AGG 0.696994 4_3:-10096445 Msa0629220:CDS
ATCCGACCAATTATGCTCGG+CGG 0.704061 4_3:-10096646 Msa0629220:CDS
TTGCTGTGTAATGTTCTCTG+CGG 0.706407 4_3:+10096206 None:intergenic
GATAGTTGAGTCCTATGTGG+TGG 0.708119 4_3:-10096313 Msa0629220:CDS
GGTGATAGTTGAGTCCTATG+TGG 0.715010 4_3:-10096316 Msa0629220:CDS
TGATGTGGGCACACTCAGGG+AGG 0.725955 4_3:-10096508 Msa0629220:CDS
CATCACCGTCGCCACCAACG+AGG 0.726271 4_3:+10096526 None:intergenic
TACACTTCATCCCTCCACAG+AGG 0.732326 4_3:-10096355 Msa0629220:CDS
TGACATGGCGATCCTCATCG+AGG 0.742190 4_3:+10096433 None:intergenic
GCGAACCACTGACCAAACGG+CGG 0.744614 4_3:+10096596 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCTTGATGAAATTTTTGT+AGG + chr4_3:10096453-10096472 None:intergenic 25.0%
!! TGTTTGTTGATACAATTGTT+CGG - chr4_3:10096750-10096769 Msa0629220:CDS 25.0%
TATAGTATTAGGAATGGTGT+TGG + chr4_3:10096312-10096331 None:intergenic 30.0%
! ATGAAATTTTTGTAGGCTTG+TGG + chr4_3:10096446-10096465 None:intergenic 30.0%
!! TGATAGTGGGCTATAGTATT+AGG + chr4_3:10096323-10096342 None:intergenic 35.0%
TATTGAGTGTGTGTGATAGT+GGG + chr4_3:10096336-10096355 None:intergenic 35.0%
ATATTGAGTGTGTGTGATAG+TGG + chr4_3:10096337-10096356 None:intergenic 35.0%
CAACACTAAAACTGATGACA+TGG + chr4_3:10096589-10096608 None:intergenic 35.0%
!! GTCATCAGTTTTAGTGTTGT+TGG - chr4_3:10096590-10096609 Msa0629220:CDS 35.0%
!! ATCAGTTTTAGTGTTGTTGG+TGG - chr4_3:10096593-10096612 Msa0629220:CDS 35.0%
TCCTTCGGAAAATACTAAAG+AGG - chr4_3:10096718-10096737 Msa0629220:CDS 35.0%
! TCCTCTTTAGTATTTTCCGA+AGG + chr4_3:10096722-10096741 None:intergenic 35.0%
!! AGTGAAGACTTTGGTGGATT+TGG + chr4_3:10096194-10096213 None:intergenic 40.0%
! GTGGGCTATAGTATTAGGAA+TGG + chr4_3:10096318-10096337 None:intergenic 40.0%
ATCATCCGACCAATTATGCT+CGG - chr4_3:10096355-10096374 Msa0629220:CDS 40.0%
ATCAAGAGTTGTAACCTCGT+TGG - chr4_3:10096464-10096483 Msa0629220:CDS 40.0%
! GATGAAGTGTAGTAACGGAA+CGG + chr4_3:10096640-10096659 None:intergenic 40.0%
!! CTATGTGGTGGATATTCCTT+CGG - chr4_3:10096703-10096722 Msa0629220:CDS 40.0%
TTGCTGTGTAATGTTCTCTG+CGG + chr4_3:10096801-10096820 None:intergenic 40.0%
!! GAAGACTTTGGTGGATTTGG+AGG + chr4_3:10096191-10096210 None:intergenic 45.0%
AGGAGAAGTGAAGACTTTGG+TGG + chr4_3:10096200-10096219 None:intergenic 45.0%
TGGAGGAGAAGTGAAGACTT+TGG + chr4_3:10096203-10096222 None:intergenic 45.0%
!! TAGGAATGGTGTTGGTGACA+GGG + chr4_3:10096304-10096323 None:intergenic 45.0%
!! TTAGGAATGGTGTTGGTGAC+AGG + chr4_3:10096305-10096324 None:intergenic 45.0%
AAGAGTTGTAACCTCGTTGG+TGG - chr4_3:10096467-10096486 Msa0629220:CDS 45.0%
AGGGAGGTCAACCTTATATC+TGG - chr4_3:10096512-10096531 Msa0629220:CDS 45.0%
GGAGGGATGAAGTGTAGTAA+CGG + chr4_3:10096645-10096664 None:intergenic 45.0%
GGTGATAGTTGAGTCCTATG+TGG - chr4_3:10096688-10096707 Msa0629220:CDS 45.0%
GATAGTTGAGTCCTATGTGG+TGG - chr4_3:10096691-10096710 Msa0629220:CDS 45.0%
CGAAGGAATATCCACCACAT+AGG + chr4_3:10096705-10096724 None:intergenic 45.0%
AGTCTTCACTTCTCCTCCAC+AGG - chr4_3:10096204-10096223 Msa0629220:CDS 50.0%
!!! AGAGGGTGTTGTTTTCGCAG+TGG + chr4_3:10096274-10096293 None:intergenic 50.0%
ATCCGACCAATTATGCTCGG+CGG - chr4_3:10096358-10096377 Msa0629220:CDS 50.0%
! AGGCTTGTGGTTTGTCGAAG+CGG + chr4_3:10096433-10096452 None:intergenic 50.0%
! ATCGAGGATCTCAAGGCGTT+CGG + chr4_3:10096558-10096577 None:intergenic 50.0%
GATCCTCATCGAGGATCTCA+AGG + chr4_3:10096565-10096584 None:intergenic 50.0%
TACACTTCATCCCTCCACAG+AGG - chr4_3:10096649-10096668 Msa0629220:CDS 50.0%
ACACTTCATCCCTCCACAGA+GGG - chr4_3:10096650-10096669 Msa0629220:CDS 50.0%
CGGTTTGTGCAAGTGACTGA+AGG + chr4_3:10096781-10096800 None:intergenic 50.0%
TGGTGTGGTTGATCCTGTGG+AGG + chr4_3:10096220-10096239 None:intergenic 55.0%
! TGGTGGTGTGGTTGATCCTG+TGG + chr4_3:10096223-10096242 None:intergenic 55.0%
! TGATGGTCGTAGTGGTGGTG+TGG + chr4_3:10096235-10096254 None:intergenic 55.0%
!! GTTGGTGATGGTCGTAGTGG+TGG + chr4_3:10096240-10096259 None:intergenic 55.0%
!! GTGGTTGGTGATGGTCGTAG+TGG + chr4_3:10096243-10096262 None:intergenic 55.0%
! TGTTTTCGCAGTGGAGGTCG+TGG + chr4_3:10096265-10096284 None:intergenic 55.0%
!!! GGGTGTTGTTTTCGCAGTGG+AGG + chr4_3:10096271-10096290 None:intergenic 55.0%
GGTGACAGGGTTGACGAAGA+GGG + chr4_3:10096291-10096310 None:intergenic 55.0%
TGGTGACAGGGTTGACGAAG+AGG + chr4_3:10096292-10096311 None:intergenic 55.0%
GACCGCCGAGCATAATTGGT+CGG + chr4_3:10096363-10096382 None:intergenic 55.0%
TGATGGAGGCGGTTGTCTCT+TGG + chr4_3:10096388-10096407 None:intergenic 55.0%
!! TGTAACCTCGTTGGTGGCGA+CGG - chr4_3:10096473-10096492 Msa0629220:CDS 55.0%
CAGCAGGGAGGCCAGATATA+AGG + chr4_3:10096526-10096545 None:intergenic 55.0%
ACGCCTTGAGATCCTCGATG+AGG - chr4_3:10096559-10096578 Msa0629220:CDS 55.0%
TGACATGGCGATCCTCATCG+AGG + chr4_3:10096574-10096593 None:intergenic 55.0%
GAACAGTCACCCTCTGTGGA+GGG + chr4_3:10096662-10096681 None:intergenic 55.0%
TCCACAGAGGGTGACTGTTC+CGG - chr4_3:10096662-10096681 Msa0629220:CDS 55.0%
GGACTCAACTATCACCGTGC+CGG + chr4_3:10096684-10096703 None:intergenic 55.0%
!! GAGGTCGTGGTGGTTGGTGA+TGG + chr4_3:10096252-10096271 None:intergenic 60.0%
TTTCGCAGTGGAGGTCGTGG+TGG + chr4_3:10096262-10096281 None:intergenic 60.0%
GGACGACCGCCGAGCATAAT+TGG + chr4_3:10096367-10096386 None:intergenic 60.0%
! TGACCAAACGGCGGTGATGG+AGG + chr4_3:10096402-10096421 None:intergenic 60.0%
CACTGACCAAACGGCGGTGA+TGG + chr4_3:10096405-10096424 None:intergenic 60.0%
CATCACCGCCGTTTGGTCAG+TGG - chr4_3:10096403-10096422 Msa0629220:CDS 60.0%
GCGAACCACTGACCAAACGG+CGG + chr4_3:10096411-10096430 None:intergenic 60.0%
GCGGCGAACCACTGACCAAA+CGG + chr4_3:10096414-10096433 None:intergenic 60.0%
!! GTTGGTGGCGACGGTGATGT+GGG - chr4_3:10096482-10096501 Msa0629220:CDS 60.0%
ACGGTGATGTGGGCACACTC+AGG - chr4_3:10096492-10096511 Msa0629220:CDS 60.0%
CGGTGATGTGGGCACACTCA+GGG - chr4_3:10096493-10096512 Msa0629220:CDS 60.0%
TGATGTGGGCACACTCAGGG+AGG - chr4_3:10096496-10096515 Msa0629220:CDS 60.0%
GGAACAGTCACCCTCTGTGG+AGG + chr4_3:10096663-10096682 None:intergenic 60.0%
AGAGGGTGACTGTTCCGGCA+CGG - chr4_3:10096667-10096686 Msa0629220:CDS 60.0%
GCAGTGGAGGTCGTGGTGGT+TGG + chr4_3:10096258-10096277 None:intergenic 65.0%
!! CCAAACGGCGGTGATGGAGG+CGG + chr4_3:10096399-10096418 None:intergenic 65.0%
CATCACCGTCGCCACCAACG+AGG + chr4_3:10096481-10096500 None:intergenic 65.0%
!! CGTTGGTGGCGACGGTGATG+TGG - chr4_3:10096481-10096500 Msa0629220:CDS 65.0%
!! GTTCGGTGCTGCGTGCAGCA+GGG + chr4_3:10096541-10096560 None:intergenic 65.0%
GCCGGAACAGTCACCCTCTG+TGG + chr4_3:10096666-10096685 None:intergenic 65.0%
CCGCCTCCATCACCGCCGTT+TGG - chr4_3:10096396-10096415 Msa0629220:CDS 70.0%
!! CGTTCGGTGCTGCGTGCAGC+AGG + chr4_3:10096542-10096561 None:intergenic 70.0%
!! CGGTGCTGCGTGCAGCAGGG+AGG + chr4_3:10096538-10096557 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 10096185 10096841 10096185 ID=Msa0629220;Name=Msa0629220
chr4_3 mRNA 10096185 10096841 10096185 ID=Msa0629220-mRNA-1;Parent=Msa0629220;Name=Msa0629220-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|218
chr4_3 exon 10096185 10096841 10096185 ID=Msa0629220-mRNA-1:exon:3054;Parent=Msa0629220-mRNA-1
chr4_3 CDS 10096185 10096841 10096185 ID=Msa0629220-mRNA-1:cds;Parent=Msa0629220-mRNA-1
Gene Sequence

>Msa0629220

ATGCCTCCAAATCCACCAAAGTCTTCACTTCTCCTCCACAGGATCAACCACACCACCACTACGACCATCACCAACCACCACGACCTCCACTGCGAAAACAACACCCTCTTCGTCAACCCTGTCACCAACACCATTCCTAATACTATAGCCCACTATCACACACACTCAATATCATCCGACCAATTATGCTCGGCGGTCGTCCAAGAGACAACCGCCTCCATCACCGCCGTTTGGTCAGTGGTTCGCCGCTTCGACAAACCACAAGCCTACAAAAATTTCATCAAGAGTTGTAACCTCGTTGGTGGCGACGGTGATGTGGGCACACTCAGGGAGGTCAACCTTATATCTGGCCTCCCTGCTGCACGCAGCACCGAACGCCTTGAGATCCTCGATGAGGATCGCCATGTCATCAGTTTTAGTGTTGTTGGTGGTGATCACAAGCTTGCTAACTACCGTTCCGTTACTACACTTCATCCCTCCACAGAGGGTGACTGTTCCGGCACGGTGATAGTTGAGTCCTATGTGGTGGATATTCCTTCGGAAAATACTAAAGAGGACACACATGTGTTTGTTGATACAATTGTTCGGTGTAACCTTCAGTCACTTGCACAAACCGCAGAGAACATTACACAGCAAAACAACAAGAGTTGTTCCTGA
Protein sequence

>Msa0629220

MPPNPPKSSLLLHRINHTTTTTITNHHDLHCENNTLFVNPVTNTIPNTIAHYHTHSISSDQLCSAVVQETTASITAVWSVVRRFDKPQAYKNFIKSCNLVGGDGDVGTLREVNLISGLPAARSTERLEILDEDRHVISFSVVGGDHKLANYRSVTTLHPSTEGDCSGTVIVESYVVDIPSENTKEDTHVFVDTIVRCNLQSLAQTAENITQQNNKSCS*