AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0931230


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0931230 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0931230 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0931230 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0931230 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa0931230 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa0931230 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa0931230 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
Msa0931230 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:-80387947 Msa0931230:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 6_2:-80388513 Msa0931230:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 6_2:-80388512 Msa0931230:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 6_2:+80388073 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 6_2:-80388309 Msa0931230:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 6_2:+80388143 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 6_2:-80387946 Msa0931230:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 6_2:-80388473 Msa0931230:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 6_2:+80388422 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 6_2:+80388066 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 6_2:-80387886 Msa0931230:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 6_2:+80388194 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 6_2:-80388472 Msa0931230:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 6_2:+80388195 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 6_2:+80388035 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 6_2:+80388297 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 6_2:-80388330 Msa0931230:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 6_2:+80387940 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 6_2:+80387946 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 6_2:+80388402 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 6_2:-80388521 Msa0931230:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 6_2:-80387875 Msa0931230:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 6_2:+80388358 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 6_2:+80388084 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 6_2:-80388537 Msa0931230:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 6_2:+80388036 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 6_2:-80388342 Msa0931230:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 6_2:+80388088 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 6_2:-80388231 Msa0931230:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 6_2:+80387885 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 6_2:+80388078 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 6_2:-80388402 Msa0931230:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 6_2:+80388390 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 6_2:-80388150 Msa0931230:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 6_2:-80388511 Msa0931230:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 6_2:+80387958 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 6_2:-80387871 Msa0931230:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 6_2:-80388322 Msa0931230:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 6_2:-80388323 Msa0931230:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 6_2:-80387931 Msa0931230:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 6_2:+80388383 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 6_2:+80388306 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 6_2:-80388151 Msa0931230:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 6_2:+80388458 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 6_2:+80388216 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr6_2:80388168-80388187 Msa0931230:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr6_2:80388212-80388231 Msa0931230:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr6_2:80388251-80388270 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr6_2:80388252-80388271 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr6_2:80388380-80388399 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr6_2:80387931-80387950 Msa0931230:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr6_2:80388063-80388082 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr6_2:80388149-80388168 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr6_2:80388209-80388228 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr6_2:80388323-80388342 Msa0931230:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr6_2:80387922-80387941 Msa0931230:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr6_2:80387930-80387949 Msa0931230:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr6_2:80387932-80387951 Msa0931230:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr6_2:80387971-80387990 Msa0931230:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr6_2:80388173-80388192 Msa0931230:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr6_2:80388174-80388193 Msa0931230:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr6_2:80388308-80388327 Msa0931230:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr6_2:80388313-80388332 Msa0931230:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr6_2:80388368-80388387 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr6_2:80388373-80388392 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr6_2:80388410-80388429 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr6_2:80388411-80388430 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr6_2:80388413-80388432 Msa0931230:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr6_2:80388506-80388525 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr6_2:80388512-80388531 Msa0931230:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr6_2:80388572-80388591 Msa0931230:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr6_2:80387970-80387989 Msa0931230:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr6_2:80388024-80388043 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr6_2:80388113-80388132 Msa0931230:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr6_2:80388175-80388194 Msa0931230:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr6_2:80388303-80388322 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr6_2:80388488-80388507 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr6_2:80388496-80388515 Msa0931230:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr6_2:80388497-80388516 Msa0931230:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr6_2:80388547-80388566 Msa0931230:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr6_2:80388568-80388587 Msa0931230:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr6_2:80387906-80387925 Msa0931230:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr6_2:80387988-80388007 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr6_2:80388292-80388311 Msa0931230:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr6_2:80388293-80388312 Msa0931230:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr6_2:80388358-80388377 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr6_2:80388362-80388381 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr6_2:80388500-80388519 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr6_2:80388056-80388075 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr6_2:80388088-80388107 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr6_2:80388100-80388119 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr6_2:80388101-80388120 Msa0931230:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr6_2:80388120-80388139 Msa0931230:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr6_2:80388121-80388140 Msa0931230:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr6_2:80388140-80388159 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr6_2:80388557-80388576 Msa0931230:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr6_2:80388561-80388580 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr6_2:80388044-80388063 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr6_2:80388041-80388060 Msa0931230:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr6_2:80388230-80388249 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr6_2:80388134-80388153 Msa0931230:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr6_2:80388189-80388208 Msa0931230:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 80387861 80388604 80387861 ID=Msa0931230;Name=Msa0931230
chr6_2 mRNA 80387861 80388604 80387861 ID=Msa0931230-mRNA-1;Parent=Msa0931230;Name=Msa0931230-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
chr6_2 exon 80387861 80388604 80387861 ID=Msa0931230-mRNA-1:exon:14107;Parent=Msa0931230-mRNA-1
chr6_2 CDS 80387861 80388604 80387861 ID=Msa0931230-mRNA-1:cds;Parent=Msa0931230-mRNA-1
Gene Sequence

>Msa0931230

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa0931230

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*