AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0924880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0924880 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0924880 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0924880 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0924880 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa0924880 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa0924880 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa0924880 MtrunA17_Chr6g0460191 74.468 94 24 0 154 247 8 101 1.73e-28 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0924880 ATCG00150.1 91.165 249 20 1 1 247 1 249 1.75e-151 422

Find 45 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTATACCTGTTATGTTTC+TGG 0.052609 6_2:-67466073 Msa0924880:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 6_2:-67466639 Msa0924880:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 6_2:-67466638 Msa0924880:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 6_2:+67466199 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 6_2:-67466435 Msa0924880:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 6_2:+67466269 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 6_2:-67466072 Msa0924880:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 6_2:-67466599 Msa0924880:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 6_2:+67466548 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 6_2:+67466192 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 6_2:-67466012 Msa0924880:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 6_2:+67466320 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 6_2:-67466598 Msa0924880:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 6_2:+67466321 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 6_2:+67466161 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 6_2:+67466423 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 6_2:-67466456 Msa0924880:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 6_2:+67466066 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 6_2:+67466072 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 6_2:+67466528 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 6_2:-67466647 Msa0924880:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 6_2:-67466001 Msa0924880:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 6_2:+67466484 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 6_2:+67466210 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 6_2:-67466663 Msa0924880:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 6_2:+67466162 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 6_2:-67466468 Msa0924880:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 6_2:+67466214 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 6_2:-67466357 Msa0924880:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 6_2:+67466011 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 6_2:+67466204 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 6_2:-67466528 Msa0924880:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 6_2:+67466516 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 6_2:-67466276 Msa0924880:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 6_2:-67466637 Msa0924880:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 6_2:+67466084 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 6_2:-67465997 Msa0924880:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 6_2:-67466448 Msa0924880:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 6_2:-67466449 Msa0924880:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 6_2:-67466057 Msa0924880:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 6_2:+67466509 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 6_2:+67466432 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 6_2:-67466277 Msa0924880:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 6_2:+67466584 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 6_2:+67466342 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr6_2:67466294-67466313 Msa0924880:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr6_2:67466338-67466357 Msa0924880:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr6_2:67466377-67466396 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr6_2:67466378-67466397 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr6_2:67466506-67466525 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr6_2:67466057-67466076 Msa0924880:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr6_2:67466189-67466208 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr6_2:67466275-67466294 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr6_2:67466335-67466354 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr6_2:67466449-67466468 Msa0924880:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr6_2:67466048-67466067 Msa0924880:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr6_2:67466056-67466075 Msa0924880:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr6_2:67466058-67466077 Msa0924880:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr6_2:67466097-67466116 Msa0924880:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr6_2:67466299-67466318 Msa0924880:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr6_2:67466300-67466319 Msa0924880:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr6_2:67466434-67466453 Msa0924880:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr6_2:67466439-67466458 Msa0924880:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr6_2:67466494-67466513 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr6_2:67466499-67466518 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr6_2:67466536-67466555 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr6_2:67466537-67466556 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr6_2:67466539-67466558 Msa0924880:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr6_2:67466632-67466651 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr6_2:67466638-67466657 Msa0924880:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr6_2:67466698-67466717 Msa0924880:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr6_2:67466096-67466115 Msa0924880:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr6_2:67466150-67466169 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr6_2:67466239-67466258 Msa0924880:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr6_2:67466301-67466320 Msa0924880:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr6_2:67466429-67466448 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr6_2:67466614-67466633 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr6_2:67466622-67466641 Msa0924880:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr6_2:67466623-67466642 Msa0924880:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr6_2:67466673-67466692 Msa0924880:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr6_2:67466694-67466713 Msa0924880:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr6_2:67466032-67466051 Msa0924880:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr6_2:67466114-67466133 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr6_2:67466418-67466437 Msa0924880:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr6_2:67466419-67466438 Msa0924880:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr6_2:67466484-67466503 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr6_2:67466488-67466507 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr6_2:67466626-67466645 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr6_2:67466182-67466201 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr6_2:67466214-67466233 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr6_2:67466226-67466245 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr6_2:67466227-67466246 Msa0924880:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr6_2:67466246-67466265 Msa0924880:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr6_2:67466247-67466266 Msa0924880:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr6_2:67466266-67466285 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr6_2:67466683-67466702 Msa0924880:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr6_2:67466687-67466706 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr6_2:67466170-67466189 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr6_2:67466167-67466186 Msa0924880:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr6_2:67466356-67466375 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr6_2:67466260-67466279 Msa0924880:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr6_2:67466315-67466334 Msa0924880:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 67465987 67466730 67465987 ID=Msa0924880;Name=Msa0924880
chr6_2 mRNA 67465987 67466730 67465987 ID=Msa0924880-mRNA-1;Parent=Msa0924880;Name=Msa0924880-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|247
chr6_2 exon 67465987 67466730 67465987 ID=Msa0924880-mRNA-1:exon:10658;Parent=Msa0924880-mRNA-1
chr6_2 CDS 67465987 67466730 67465987 ID=Msa0924880-mRNA-1:cds;Parent=Msa0924880-mRNA-1
Gene Sequence

>Msa0924880

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa0924880

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*