AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268750


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268750 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0268750 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0268750 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0268750 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa0268750 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa0268750 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa0268750 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
Msa0268750 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:-70388163 Msa0268750:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 2_2:-70388729 Msa0268750:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 2_2:-70388728 Msa0268750:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 2_2:+70388289 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 2_2:-70388525 Msa0268750:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 2_2:+70388359 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 2_2:-70388162 Msa0268750:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 2_2:-70388689 Msa0268750:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 2_2:+70388638 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 2_2:+70388282 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 2_2:-70388102 Msa0268750:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 2_2:+70388410 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 2_2:-70388688 Msa0268750:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 2_2:+70388411 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 2_2:+70388251 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 2_2:+70388513 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 2_2:-70388546 Msa0268750:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 2_2:+70388156 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 2_2:+70388162 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 2_2:+70388618 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 2_2:-70388737 Msa0268750:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 2_2:-70388091 Msa0268750:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 2_2:+70388574 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 2_2:+70388300 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 2_2:-70388753 Msa0268750:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 2_2:+70388252 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 2_2:-70388558 Msa0268750:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 2_2:+70388304 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 2_2:-70388447 Msa0268750:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 2_2:+70388101 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 2_2:+70388294 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 2_2:-70388618 Msa0268750:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 2_2:+70388606 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 2_2:-70388366 Msa0268750:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 2_2:-70388727 Msa0268750:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 2_2:+70388174 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 2_2:-70388087 Msa0268750:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 2_2:-70388538 Msa0268750:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 2_2:-70388539 Msa0268750:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 2_2:-70388147 Msa0268750:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 2_2:+70388599 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 2_2:+70388522 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 2_2:-70388367 Msa0268750:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 2_2:+70388674 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 2_2:+70388432 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr2_2:70388384-70388403 Msa0268750:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr2_2:70388428-70388447 Msa0268750:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr2_2:70388467-70388486 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr2_2:70388468-70388487 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr2_2:70388596-70388615 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr2_2:70388147-70388166 Msa0268750:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr2_2:70388279-70388298 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr2_2:70388365-70388384 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr2_2:70388425-70388444 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr2_2:70388539-70388558 Msa0268750:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr2_2:70388138-70388157 Msa0268750:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr2_2:70388146-70388165 Msa0268750:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr2_2:70388148-70388167 Msa0268750:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr2_2:70388187-70388206 Msa0268750:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr2_2:70388389-70388408 Msa0268750:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr2_2:70388390-70388409 Msa0268750:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr2_2:70388524-70388543 Msa0268750:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr2_2:70388529-70388548 Msa0268750:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr2_2:70388584-70388603 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr2_2:70388589-70388608 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr2_2:70388626-70388645 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr2_2:70388627-70388646 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr2_2:70388629-70388648 Msa0268750:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr2_2:70388722-70388741 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr2_2:70388728-70388747 Msa0268750:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr2_2:70388788-70388807 Msa0268750:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr2_2:70388186-70388205 Msa0268750:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr2_2:70388240-70388259 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr2_2:70388329-70388348 Msa0268750:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr2_2:70388391-70388410 Msa0268750:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr2_2:70388519-70388538 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr2_2:70388704-70388723 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr2_2:70388712-70388731 Msa0268750:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr2_2:70388713-70388732 Msa0268750:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr2_2:70388763-70388782 Msa0268750:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr2_2:70388784-70388803 Msa0268750:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr2_2:70388122-70388141 Msa0268750:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr2_2:70388204-70388223 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr2_2:70388508-70388527 Msa0268750:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr2_2:70388509-70388528 Msa0268750:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr2_2:70388574-70388593 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr2_2:70388578-70388597 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr2_2:70388716-70388735 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr2_2:70388272-70388291 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr2_2:70388304-70388323 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr2_2:70388316-70388335 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr2_2:70388317-70388336 Msa0268750:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr2_2:70388336-70388355 Msa0268750:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr2_2:70388337-70388356 Msa0268750:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr2_2:70388356-70388375 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr2_2:70388773-70388792 Msa0268750:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr2_2:70388777-70388796 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr2_2:70388260-70388279 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr2_2:70388257-70388276 Msa0268750:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr2_2:70388446-70388465 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr2_2:70388350-70388369 Msa0268750:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr2_2:70388405-70388424 Msa0268750:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70388077 70388820 70388077 ID=Msa0268750;Name=Msa0268750
chr2_2 mRNA 70388077 70388820 70388077 ID=Msa0268750-mRNA-1;Parent=Msa0268750;Name=Msa0268750-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|247
chr2_2 exon 70388077 70388820 70388077 ID=Msa0268750-mRNA-1:exon:22645;Parent=Msa0268750-mRNA-1
chr2_2 CDS 70388077 70388820 70388077 ID=Msa0268750-mRNA-1:cds;Parent=Msa0268750-mRNA-1
Gene Sequence

>Msa0268750

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa0268750

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*