AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268570


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268570 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0268570 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0268570 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0268570 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa0268570 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa0268570 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa0268570 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
Msa0268570 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 2_2:-70308053 Msa0268570:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 2_2:-70308619 Msa0268570:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 2_2:-70308618 Msa0268570:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 2_2:+70308179 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 2_2:-70308415 Msa0268570:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 2_2:+70308249 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 2_2:-70308052 Msa0268570:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 2_2:-70308579 Msa0268570:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 2_2:+70308528 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 2_2:+70308172 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 2_2:-70307992 Msa0268570:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 2_2:+70308300 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 2_2:-70308578 Msa0268570:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 2_2:+70308301 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 2_2:+70308141 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 2_2:+70308403 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 2_2:-70308436 Msa0268570:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 2_2:+70308046 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 2_2:+70308052 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 2_2:+70308508 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 2_2:-70308627 Msa0268570:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 2_2:-70307981 Msa0268570:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 2_2:+70308464 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 2_2:+70308190 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 2_2:-70308643 Msa0268570:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 2_2:+70308142 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 2_2:-70308448 Msa0268570:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 2_2:+70308194 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 2_2:-70308337 Msa0268570:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 2_2:+70307991 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 2_2:+70308184 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 2_2:-70308508 Msa0268570:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 2_2:+70308496 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 2_2:-70308256 Msa0268570:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 2_2:-70308617 Msa0268570:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 2_2:+70308064 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 2_2:-70307977 Msa0268570:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 2_2:-70308428 Msa0268570:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 2_2:-70308429 Msa0268570:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 2_2:-70308037 Msa0268570:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 2_2:+70308489 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 2_2:+70308412 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 2_2:-70308257 Msa0268570:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 2_2:+70308564 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 2_2:+70308322 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr2_2:70308274-70308293 Msa0268570:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr2_2:70308318-70308337 Msa0268570:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr2_2:70308357-70308376 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr2_2:70308358-70308377 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr2_2:70308486-70308505 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr2_2:70308037-70308056 Msa0268570:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr2_2:70308169-70308188 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr2_2:70308255-70308274 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr2_2:70308315-70308334 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr2_2:70308429-70308448 Msa0268570:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr2_2:70308028-70308047 Msa0268570:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr2_2:70308036-70308055 Msa0268570:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr2_2:70308038-70308057 Msa0268570:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr2_2:70308077-70308096 Msa0268570:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr2_2:70308279-70308298 Msa0268570:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr2_2:70308280-70308299 Msa0268570:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr2_2:70308414-70308433 Msa0268570:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr2_2:70308419-70308438 Msa0268570:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr2_2:70308474-70308493 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr2_2:70308479-70308498 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr2_2:70308516-70308535 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr2_2:70308517-70308536 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr2_2:70308519-70308538 Msa0268570:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr2_2:70308612-70308631 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr2_2:70308618-70308637 Msa0268570:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr2_2:70308678-70308697 Msa0268570:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr2_2:70308076-70308095 Msa0268570:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr2_2:70308130-70308149 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr2_2:70308219-70308238 Msa0268570:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr2_2:70308281-70308300 Msa0268570:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr2_2:70308409-70308428 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr2_2:70308594-70308613 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr2_2:70308602-70308621 Msa0268570:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr2_2:70308603-70308622 Msa0268570:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr2_2:70308653-70308672 Msa0268570:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr2_2:70308674-70308693 Msa0268570:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr2_2:70308012-70308031 Msa0268570:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr2_2:70308094-70308113 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr2_2:70308398-70308417 Msa0268570:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr2_2:70308399-70308418 Msa0268570:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr2_2:70308464-70308483 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr2_2:70308468-70308487 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr2_2:70308606-70308625 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr2_2:70308162-70308181 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr2_2:70308194-70308213 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr2_2:70308206-70308225 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr2_2:70308207-70308226 Msa0268570:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr2_2:70308226-70308245 Msa0268570:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr2_2:70308227-70308246 Msa0268570:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr2_2:70308246-70308265 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr2_2:70308663-70308682 Msa0268570:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr2_2:70308667-70308686 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr2_2:70308150-70308169 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr2_2:70308147-70308166 Msa0268570:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr2_2:70308336-70308355 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr2_2:70308240-70308259 Msa0268570:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr2_2:70308295-70308314 Msa0268570:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70307967 70308710 70307967 ID=Msa0268570;Name=Msa0268570
chr2_2 mRNA 70307967 70308710 70307967 ID=Msa0268570-mRNA-1;Parent=Msa0268570;Name=Msa0268570-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
chr2_2 exon 70307967 70308710 70307967 ID=Msa0268570-mRNA-1:exon:22582;Parent=Msa0268570-mRNA-1
chr2_2 CDS 70307967 70308710 70307967 ID=Msa0268570-mRNA-1:cds;Parent=Msa0268570-mRNA-1
Gene Sequence

>Msa0268570

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa0268570

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*