AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0667010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0667010 MtrunA17_Chr4g0005501 95.413 218 7 1 1 218 1 215 1.84e-151 419
Msa0667010 MtrunA17_Chr7g0243271 65.775 187 56 3 36 215 1 186 8.40e-77 229
Msa0667010 MtrunA17_Chr5g0437611 62.941 170 58 3 42 209 39 205 2.15e-70 213
Msa0667010 MtrunA17_Chr3g0114121 61.988 171 60 4 47 216 64 230 3.12e-69 211
Msa0667010 MtrunA17_Chr1g0158871 45.902 183 94 2 31 213 5 182 5.49e-55 174
Msa0667010 MtrunA17_Chr5g0411391 53.659 164 72 2 49 208 44 207 6.75e-55 174
Msa0667010 MtrunA17_Chr8g0347191 48.171 164 84 1 49 212 73 235 9.30e-54 172
Msa0667010 MtrunA17_Chr1g0151661 52.500 160 72 3 49 206 39 196 4.07e-53 169
Msa0667010 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
Msa0667010 AT2G38310.1 67.052 173 53 2 47 218 37 206 4.58e-73 221
Msa0667010 AT5G05440.1 64.815 162 53 2 45 205 41 199 2.24e-70 214
Msa0667010 AT2G40330.1 59.064 171 65 3 45 211 44 213 3.49e-66 203
Msa0667010 AT5G53160.2 48.485 165 84 1 49 213 19 182 3.46e-56 177
Msa0667010 AT1G01360.1 47.531 162 84 1 52 213 24 184 1.42e-55 175
Msa0667010 AT4G01026.1 49.068 161 81 1 53 213 27 186 1.11e-53 171
Msa0667010 AT2G26040.1 49.398 166 82 1 43 206 16 181 1.63e-53 170
Msa0667010 AT4G27920.1 46.667 165 88 0 49 213 14 178 5.29e-52 166
Msa0667010 AT4G17870.1 48.810 168 85 1 45 211 13 180 7.88e-52 166
Msa0667010 AT1G73000.1 46.199 171 82 4 43 203 31 201 3.48e-44 147
Msa0667010 AT5G46790.2 49.412 170 80 3 45 209 40 208 1.09e-43 146
Msa0667010 AT5G46790.1 49.412 170 80 3 45 209 40 208 1.09e-43 146
Msa0667010 AT5G45860.1 52.055 146 69 1 64 209 12 156 4.50e-42 140
Msa0667010 AT5G45870.1 50.676 148 71 1 64 211 12 157 1.01e-41 139
Msa0667010 AT4G18620.1 45.963 161 80 2 58 211 4 164 2.23e-34 120
Msa0667010 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_4:+7240940 None:intergenic
CGTTCGGTGCTGCGTGCAGC+AGG 0.323719 4_4:+7240592 None:intergenic
GGACGACCGCCGAGCATAAT+TGG 0.334740 4_4:+7240767 None:intergenic
TGATAGTGGGCTATAGTATT+AGG 0.336898 4_4:+7240811 None:intergenic
CAGCAGGGAGGCCAGATATA+AGG 0.373259 4_4:+7240608 None:intergenic
TTAGGAATGGTGTTGGTGAC+AGG 0.377606 4_4:+7240829 None:intergenic
TGATGGAGGCGGTTGTCTCT+TGG 0.388404 4_4:+7240746 None:intergenic
TCCACAGAGGGTGACTGTTC+CGG 0.392902 4_4:-7240469 Msa0667010:CDS
AGGGAGGTCAACCTTATATC+TGG 0.399072 4_4:-7240619 Msa0667010:CDS
GTCATCAGTTTCAGTGTTGT+TGG 0.412398 4_4:-7240541 Msa0667010:CDS
CACTGACCAAACGGCGGTGA+TGG 0.428126 4_4:+7240729 None:intergenic
ATATTGAGTGTGTGTGATAG+TGG 0.451535 4_4:+7240797 None:intergenic
GAAGACTTTGGTGGATTTGG+AGG 0.457214 4_4:+7240943 None:intergenic
CCGCCTCCATCACCGCCGTT+TGG 0.479222 4_4:-7240735 Msa0667010:CDS
ATCGAGGATCTCAAGGCGTT+CGG 0.483659 4_4:+7240576 None:intergenic
CGTTGGTGGCGACGGTGATG+TGG 0.489155 4_4:-7240650 Msa0667010:CDS
GCGGCGAACCACTGACCAAA+CGG 0.490188 4_4:+7240720 None:intergenic
CTATGTGGTGGATATTCCTT+CGG 0.490303 4_4:-7240428 Msa0667010:CDS
GAGGTCGTGGTGGTTGGTGA+TGG 0.514354 4_4:+7240882 None:intergenic
GCCGTGGAGGTCGTGGTGGT+TGG 0.515521 4_4:+7240876 None:intergenic
AGTCTTCACTTCTCCTCCAC+AGG 0.523366 4_4:-7240927 Msa0667010:CDS
TGTTTGTTGATACAATTGTT+CGG 0.525160 4_4:-7240381 Msa0667010:CDS
CATCACCGCCGTTTGGTCAG+TGG 0.527329 4_4:-7240728 Msa0667010:CDS
TATAGTATTAGGAATGGTGT+TGG 0.528924 4_4:+7240822 None:intergenic
AGGAGAAGTGAAGACTTTGG+TGG 0.533916 4_4:+7240934 None:intergenic
ACGGTGATGTGGGCACACTC+AGG 0.539446 4_4:-7240639 Msa0667010:CDS
CCAAACGGCGGTGATGGAGG+CGG 0.539681 4_4:+7240735 None:intergenic
CAACACTGAAACTGATGACA+TGG 0.539899 4_4:+7240545 None:intergenic
ATCAGTTTCAGTGTTGTTGG+TGG 0.541299 4_4:-7240538 Msa0667010:CDS
TGTAACCTCGTTGGTGGCGA+CGG 0.546094 4_4:-7240658 Msa0667010:CDS
ATCAAGAGTTGTAACCTCGT+TGG 0.547255 4_4:-7240667 Msa0667010:CDS
GTTGGTGATGGTCGTAGTGG+TGG 0.548645 4_4:+7240894 None:intergenic
CGGTGATGTGGGCACACTCA+GGG 0.556265 4_4:-7240638 Msa0667010:CDS
GTTCGGTGCTGCGTGCAGCA+GGG 0.556567 4_4:+7240593 None:intergenic
CTGTTTGTGCAAGTGACTGA+AGG 0.564175 4_4:+7240353 None:intergenic
GATCCTCATCGAGGATCTCA+AGG 0.566346 4_4:+7240569 None:intergenic
TAGGAATGGTGTTGGTGACA+GGG 0.566710 4_4:+7240830 None:intergenic
AAGAGTTGTAACCTCGTTGG+TGG 0.571438 4_4:-7240664 Msa0667010:CDS
AGGCTTGTGGTTTGTCGAAG+CGG 0.573243 4_4:+7240701 None:intergenic
GGAACAGTCACCCTCTGTGG+AGG 0.574183 4_4:+7240471 None:intergenic
TGGTGACAGGGTTGATGAAG+AGG 0.574991 4_4:+7240842 None:intergenic
TGGTGGTGTGGTTGATCCTG+TGG 0.579437 4_4:+7240911 None:intergenic
TCCTTCGGAAAATACTAAAG+AGG 0.584494 4_4:-7240413 Msa0667010:CDS
ATCATCCGACCAATTATGCT+CGG 0.584649 4_4:-7240776 Msa0667010:CDS
TGACCAAACGGCGGTGATGG+AGG 0.585643 4_4:+7240732 None:intergenic
ACACTTCATCCCTCCACAGA+GGG 0.594198 4_4:-7240481 Msa0667010:CDS
GGTGACAGGGTTGATGAAGA+GGG 0.596139 4_4:+7240843 None:intergenic
GCCGGAACAGTCACCCTCTG+TGG 0.599614 4_4:+7240468 None:intergenic
GGACTCAACTATCACCGTGC+CGG 0.603129 4_4:+7240450 None:intergenic
GAACAGTCACCCTCTGTGGA+GGG 0.606405 4_4:+7240472 None:intergenic
GACCGCCGAGCATAATTGGT+CGG 0.608055 4_4:+7240771 None:intergenic
GTGGGCTATAGTATTAGGAA+TGG 0.608376 4_4:+7240816 None:intergenic
GTTGGTGGCGACGGTGATGT+GGG 0.610157 4_4:-7240649 Msa0667010:CDS
CGAAGGAATATCCACCACAT+AGG 0.619850 4_4:+7240429 None:intergenic
TGGAGGAGAAGTGAAGACTT+TGG 0.627794 4_4:+7240931 None:intergenic
ACCAACCACCACGACCTCCA+CGG 0.628316 4_4:-7240877 Msa0667010:CDS
AGAGGGTGACTGTTCCGGCA+CGG 0.639448 4_4:-7240464 Msa0667010:CDS
GGAGGGATGAAGTGTAGTAA+CGG 0.646842 4_4:+7240489 None:intergenic
TGATGGTCGTAGTGGTGGTG+TGG 0.646910 4_4:+7240899 None:intergenic
GTGGTTGGTGATGGTCGTAG+TGG 0.657655 4_4:+7240891 None:intergenic
CGGTGCTGCGTGCAGCAGGG+AGG 0.659975 4_4:+7240596 None:intergenic
TATTGAGTGTGTGTGATAGT+GGG 0.661022 4_4:+7240798 None:intergenic
TGGTGTGGTTGATCCTGTGG+AGG 0.662950 4_4:+7240914 None:intergenic
GATGAAGTGTAGTAACGGAA+CGG 0.672049 4_4:+7240494 None:intergenic
ACGCCTTGAGATCCTCGATG+AGG 0.696994 4_4:-7240572 Msa0667010:CDS
TTTCGCCGTGGAGGTCGTGG+TGG 0.698954 4_4:+7240872 None:intergenic
ATCCGACCAATTATGCTCGG+CGG 0.704061 4_4:-7240773 Msa0667010:CDS
GATAGTTGAGTCCTATGTGG+TGG 0.708119 4_4:-7240440 Msa0667010:CDS
GGTGATAGTTGAGTCCTATG+TGG 0.715010 4_4:-7240443 Msa0667010:CDS
TGATGTGGGCACACTCAGGG+AGG 0.725955 4_4:-7240635 Msa0667010:CDS
CATCACCGTCGCCACCAACG+AGG 0.726271 4_4:+7240653 None:intergenic
TACACTTCATCCCTCCACAG+AGG 0.732326 4_4:-7240482 Msa0667010:CDS
TGACATGGCGATCCTCATCG+AGG 0.742190 4_4:+7240560 None:intergenic
GCGAACCACTGACCAAACGG+CGG 0.744614 4_4:+7240723 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCTTGATGAAATTTTTGT+AGG + chr4_4:7240580-7240599 None:intergenic 25.0%
!! TGTTTGTTGATACAATTGTT+CGG - chr4_4:7240877-7240896 Msa0667010:CDS 25.0%
TATAGTATTAGGAATGGTGT+TGG + chr4_4:7240439-7240458 None:intergenic 30.0%
! ATGAAATTTTTGTAGGCTTG+TGG + chr4_4:7240573-7240592 None:intergenic 30.0%
!! TGATAGTGGGCTATAGTATT+AGG + chr4_4:7240450-7240469 None:intergenic 35.0%
TATTGAGTGTGTGTGATAGT+GGG + chr4_4:7240463-7240482 None:intergenic 35.0%
ATATTGAGTGTGTGTGATAG+TGG + chr4_4:7240464-7240483 None:intergenic 35.0%
TCCTTCGGAAAATACTAAAG+AGG - chr4_4:7240845-7240864 Msa0667010:CDS 35.0%
! TCCTCTTTAGTATTTTCCGA+AGG + chr4_4:7240849-7240868 None:intergenic 35.0%
!! AGTGAAGACTTTGGTGGATT+TGG + chr4_4:7240321-7240340 None:intergenic 40.0%
! GTGGGCTATAGTATTAGGAA+TGG + chr4_4:7240445-7240464 None:intergenic 40.0%
ATCATCCGACCAATTATGCT+CGG - chr4_4:7240482-7240501 Msa0667010:CDS 40.0%
ATCAAGAGTTGTAACCTCGT+TGG - chr4_4:7240591-7240610 Msa0667010:CDS 40.0%
CAACACTGAAACTGATGACA+TGG + chr4_4:7240716-7240735 None:intergenic 40.0%
GTCATCAGTTTCAGTGTTGT+TGG - chr4_4:7240717-7240736 Msa0667010:CDS 40.0%
! ATCAGTTTCAGTGTTGTTGG+TGG - chr4_4:7240720-7240739 Msa0667010:CDS 40.0%
! GATGAAGTGTAGTAACGGAA+CGG + chr4_4:7240767-7240786 None:intergenic 40.0%
!! CTATGTGGTGGATATTCCTT+CGG - chr4_4:7240830-7240849 Msa0667010:CDS 40.0%
!! GAAGACTTTGGTGGATTTGG+AGG + chr4_4:7240318-7240337 None:intergenic 45.0%
AGGAGAAGTGAAGACTTTGG+TGG + chr4_4:7240327-7240346 None:intergenic 45.0%
TGGAGGAGAAGTGAAGACTT+TGG + chr4_4:7240330-7240349 None:intergenic 45.0%
!! TAGGAATGGTGTTGGTGACA+GGG + chr4_4:7240431-7240450 None:intergenic 45.0%
!! TTAGGAATGGTGTTGGTGAC+AGG + chr4_4:7240432-7240451 None:intergenic 45.0%
AAGAGTTGTAACCTCGTTGG+TGG - chr4_4:7240594-7240613 Msa0667010:CDS 45.0%
AGGGAGGTCAACCTTATATC+TGG - chr4_4:7240639-7240658 Msa0667010:CDS 45.0%
GGAGGGATGAAGTGTAGTAA+CGG + chr4_4:7240772-7240791 None:intergenic 45.0%
GGTGATAGTTGAGTCCTATG+TGG - chr4_4:7240815-7240834 Msa0667010:CDS 45.0%
GATAGTTGAGTCCTATGTGG+TGG - chr4_4:7240818-7240837 Msa0667010:CDS 45.0%
CGAAGGAATATCCACCACAT+AGG + chr4_4:7240832-7240851 None:intergenic 45.0%
CTGTTTGTGCAAGTGACTGA+AGG + chr4_4:7240908-7240927 None:intergenic 45.0%
AGTCTTCACTTCTCCTCCAC+AGG - chr4_4:7240331-7240350 Msa0667010:CDS 50.0%
!! GGTGACAGGGTTGATGAAGA+GGG + chr4_4:7240418-7240437 None:intergenic 50.0%
!! TGGTGACAGGGTTGATGAAG+AGG + chr4_4:7240419-7240438 None:intergenic 50.0%
ATCCGACCAATTATGCTCGG+CGG - chr4_4:7240485-7240504 Msa0667010:CDS 50.0%
! AGGCTTGTGGTTTGTCGAAG+CGG + chr4_4:7240560-7240579 None:intergenic 50.0%
! ATCGAGGATCTCAAGGCGTT+CGG + chr4_4:7240685-7240704 None:intergenic 50.0%
GATCCTCATCGAGGATCTCA+AGG + chr4_4:7240692-7240711 None:intergenic 50.0%
TACACTTCATCCCTCCACAG+AGG - chr4_4:7240776-7240795 Msa0667010:CDS 50.0%
ACACTTCATCCCTCCACAGA+GGG - chr4_4:7240777-7240796 Msa0667010:CDS 50.0%
TGGTGTGGTTGATCCTGTGG+AGG + chr4_4:7240347-7240366 None:intergenic 55.0%
! TGGTGGTGTGGTTGATCCTG+TGG + chr4_4:7240350-7240369 None:intergenic 55.0%
! TGATGGTCGTAGTGGTGGTG+TGG + chr4_4:7240362-7240381 None:intergenic 55.0%
!! GTTGGTGATGGTCGTAGTGG+TGG + chr4_4:7240367-7240386 None:intergenic 55.0%
!! GTGGTTGGTGATGGTCGTAG+TGG + chr4_4:7240370-7240389 None:intergenic 55.0%
!!! AGAGGGTGTTGTTTTCGCCG+TGG + chr4_4:7240401-7240420 None:intergenic 55.0%
GACCGCCGAGCATAATTGGT+CGG + chr4_4:7240490-7240509 None:intergenic 55.0%
TGATGGAGGCGGTTGTCTCT+TGG + chr4_4:7240515-7240534 None:intergenic 55.0%
!! TGTAACCTCGTTGGTGGCGA+CGG - chr4_4:7240600-7240619 Msa0667010:CDS 55.0%
CAGCAGGGAGGCCAGATATA+AGG + chr4_4:7240653-7240672 None:intergenic 55.0%
ACGCCTTGAGATCCTCGATG+AGG - chr4_4:7240686-7240705 Msa0667010:CDS 55.0%
TGACATGGCGATCCTCATCG+AGG + chr4_4:7240701-7240720 None:intergenic 55.0%
GAACAGTCACCCTCTGTGGA+GGG + chr4_4:7240789-7240808 None:intergenic 55.0%
TCCACAGAGGGTGACTGTTC+CGG - chr4_4:7240789-7240808 Msa0667010:CDS 55.0%
GGACTCAACTATCACCGTGC+CGG + chr4_4:7240811-7240830 None:intergenic 55.0%
!! GAGGTCGTGGTGGTTGGTGA+TGG + chr4_4:7240379-7240398 None:intergenic 60.0%
ACCAACCACCACGACCTCCA+CGG - chr4_4:7240381-7240400 Msa0667010:CDS 60.0%
! TGTTTTCGCCGTGGAGGTCG+TGG + chr4_4:7240392-7240411 None:intergenic 60.0%
!!! GGGTGTTGTTTTCGCCGTGG+AGG + chr4_4:7240398-7240417 None:intergenic 60.0%
GGACGACCGCCGAGCATAAT+TGG + chr4_4:7240494-7240513 None:intergenic 60.0%
! TGACCAAACGGCGGTGATGG+AGG + chr4_4:7240529-7240548 None:intergenic 60.0%
CACTGACCAAACGGCGGTGA+TGG + chr4_4:7240532-7240551 None:intergenic 60.0%
CATCACCGCCGTTTGGTCAG+TGG - chr4_4:7240530-7240549 Msa0667010:CDS 60.0%
GCGAACCACTGACCAAACGG+CGG + chr4_4:7240538-7240557 None:intergenic 60.0%
GCGGCGAACCACTGACCAAA+CGG + chr4_4:7240541-7240560 None:intergenic 60.0%
!! GTTGGTGGCGACGGTGATGT+GGG - chr4_4:7240609-7240628 Msa0667010:CDS 60.0%
ACGGTGATGTGGGCACACTC+AGG - chr4_4:7240619-7240638 Msa0667010:CDS 60.0%
CGGTGATGTGGGCACACTCA+GGG - chr4_4:7240620-7240639 Msa0667010:CDS 60.0%
TGATGTGGGCACACTCAGGG+AGG - chr4_4:7240623-7240642 Msa0667010:CDS 60.0%
GGAACAGTCACCCTCTGTGG+AGG + chr4_4:7240790-7240809 None:intergenic 60.0%
AGAGGGTGACTGTTCCGGCA+CGG - chr4_4:7240794-7240813 Msa0667010:CDS 60.0%
TTTCGCCGTGGAGGTCGTGG+TGG + chr4_4:7240389-7240408 None:intergenic 65.0%
!! CCAAACGGCGGTGATGGAGG+CGG + chr4_4:7240526-7240545 None:intergenic 65.0%
CATCACCGTCGCCACCAACG+AGG + chr4_4:7240608-7240627 None:intergenic 65.0%
!! CGTTGGTGGCGACGGTGATG+TGG - chr4_4:7240608-7240627 Msa0667010:CDS 65.0%
!! GTTCGGTGCTGCGTGCAGCA+GGG + chr4_4:7240668-7240687 None:intergenic 65.0%
GCCGGAACAGTCACCCTCTG+TGG + chr4_4:7240793-7240812 None:intergenic 65.0%
GCCGTGGAGGTCGTGGTGGT+TGG + chr4_4:7240385-7240404 None:intergenic 70.0%
CCGCCTCCATCACCGCCGTT+TGG - chr4_4:7240523-7240542 Msa0667010:CDS 70.0%
!! CGTTCGGTGCTGCGTGCAGC+AGG + chr4_4:7240669-7240688 None:intergenic 70.0%
!! CGGTGCTGCGTGCAGCAGGG+AGG + chr4_4:7240665-7240684 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 7240312 7240968 7240312 ID=Msa0667010;Name=Msa0667010
chr4_4 mRNA 7240312 7240968 7240312 ID=Msa0667010-mRNA-1;Parent=Msa0667010;Name=Msa0667010-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|218
chr4_4 exon 7240312 7240968 7240312 ID=Msa0667010-mRNA-1:exon:2357;Parent=Msa0667010-mRNA-1
chr4_4 CDS 7240312 7240968 7240312 ID=Msa0667010-mRNA-1:cds;Parent=Msa0667010-mRNA-1
Gene Sequence

>Msa0667010

ATGCCTCCAAATCCACCAAAGTCTTCACTTCTCCTCCACAGGATCAACCACACCACCACTACGACCATCACCAACCACCACGACCTCCACGGCGAAAACAACACCCTCTTCATCAACCCTGTCACCAACACCATTCCTAATACTATAGCCCACTATCACACACACTCAATATCATCCGACCAATTATGCTCGGCGGTCGTCCAAGAGACAACCGCCTCCATCACCGCCGTTTGGTCAGTGGTTCGCCGCTTCGACAAACCACAAGCCTACAAAAATTTCATCAAGAGTTGTAACCTCGTTGGTGGCGACGGTGATGTGGGCACACTCAGGGAGGTCAACCTTATATCTGGCCTCCCTGCTGCACGCAGCACCGAACGCCTTGAGATCCTCGATGAGGATCGCCATGTCATCAGTTTCAGTGTTGTTGGTGGTGATCACAAGCTTGCTAACTACCGTTCCGTTACTACACTTCATCCCTCCACAGAGGGTGACTGTTCCGGCACGGTGATAGTTGAGTCCTATGTGGTGGATATTCCTTCGGAAAATACTAAAGAGGACACACATGTGTTTGTTGATACAATTGTTCGGTGTAACCTTCAGTCACTTGCACAAACAGCAGAGAACATTACACAGCAAAACAACAAGAGTTGTTCCTGA
Protein sequence

>Msa0667010

MPPNPPKSSLLLHRINHTTTTTITNHHDLHGENNTLFINPVTNTIPNTIAHYHTHSISSDQLCSAVVQETTASITAVWSVVRRFDKPQAYKNFIKSCNLVGGDGDVGTLREVNLISGLPAARSTERLEILDEDRHVISFSVVGGDHKLANYRSVTTLHPSTEGDCSGTVIVESYVVDIPSENTKEDTHVFVDTIVRCNLQSLAQTAENITQQNNKSCS*