AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582920


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582920 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582920 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582920 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582920 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa0582920 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa0582920 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa0582920 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
Msa0582920 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 4_2:-1283963 Msa0582920:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 4_2:-1284529 Msa0582920:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 4_2:-1284528 Msa0582920:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 4_2:+1284089 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 4_2:-1284325 Msa0582920:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 4_2:+1284159 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 4_2:-1283962 Msa0582920:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 4_2:-1284489 Msa0582920:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 4_2:+1284438 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 4_2:+1284082 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 4_2:-1283902 Msa0582920:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 4_2:+1284210 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 4_2:-1284488 Msa0582920:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 4_2:+1284211 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 4_2:+1284051 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 4_2:+1284313 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 4_2:-1284346 Msa0582920:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 4_2:+1283956 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 4_2:+1283962 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 4_2:+1284418 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 4_2:-1284537 Msa0582920:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 4_2:-1283891 Msa0582920:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 4_2:+1284374 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 4_2:+1284100 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 4_2:-1284553 Msa0582920:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 4_2:+1284052 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 4_2:-1284358 Msa0582920:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 4_2:+1284104 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 4_2:-1284247 Msa0582920:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 4_2:+1283901 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 4_2:+1284094 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 4_2:-1284418 Msa0582920:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 4_2:+1284406 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 4_2:-1284166 Msa0582920:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 4_2:-1284527 Msa0582920:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 4_2:+1283974 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 4_2:-1283887 Msa0582920:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 4_2:-1284338 Msa0582920:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 4_2:-1284339 Msa0582920:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 4_2:-1283947 Msa0582920:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 4_2:+1284399 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 4_2:+1284322 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 4_2:-1284167 Msa0582920:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 4_2:+1284474 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 4_2:+1284232 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr4_2:1284184-1284203 Msa0582920:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr4_2:1284228-1284247 Msa0582920:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr4_2:1284267-1284286 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr4_2:1284268-1284287 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr4_2:1284396-1284415 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr4_2:1283947-1283966 Msa0582920:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr4_2:1284079-1284098 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr4_2:1284165-1284184 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr4_2:1284225-1284244 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr4_2:1284339-1284358 Msa0582920:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr4_2:1283938-1283957 Msa0582920:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr4_2:1283946-1283965 Msa0582920:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr4_2:1283948-1283967 Msa0582920:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr4_2:1283987-1284006 Msa0582920:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr4_2:1284189-1284208 Msa0582920:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr4_2:1284190-1284209 Msa0582920:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr4_2:1284324-1284343 Msa0582920:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr4_2:1284329-1284348 Msa0582920:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr4_2:1284384-1284403 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr4_2:1284389-1284408 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr4_2:1284426-1284445 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr4_2:1284427-1284446 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr4_2:1284429-1284448 Msa0582920:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr4_2:1284522-1284541 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr4_2:1284528-1284547 Msa0582920:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr4_2:1284588-1284607 Msa0582920:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr4_2:1283986-1284005 Msa0582920:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr4_2:1284040-1284059 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr4_2:1284129-1284148 Msa0582920:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr4_2:1284191-1284210 Msa0582920:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr4_2:1284319-1284338 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr4_2:1284504-1284523 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr4_2:1284512-1284531 Msa0582920:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr4_2:1284513-1284532 Msa0582920:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr4_2:1284563-1284582 Msa0582920:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr4_2:1284584-1284603 Msa0582920:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr4_2:1283922-1283941 Msa0582920:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr4_2:1284004-1284023 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr4_2:1284308-1284327 Msa0582920:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr4_2:1284309-1284328 Msa0582920:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr4_2:1284374-1284393 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr4_2:1284378-1284397 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr4_2:1284516-1284535 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr4_2:1284072-1284091 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr4_2:1284104-1284123 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr4_2:1284116-1284135 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr4_2:1284117-1284136 Msa0582920:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr4_2:1284136-1284155 Msa0582920:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr4_2:1284137-1284156 Msa0582920:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr4_2:1284156-1284175 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr4_2:1284573-1284592 Msa0582920:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr4_2:1284577-1284596 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr4_2:1284060-1284079 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr4_2:1284057-1284076 Msa0582920:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr4_2:1284246-1284265 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr4_2:1284150-1284169 Msa0582920:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr4_2:1284205-1284224 Msa0582920:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1283877 1284620 1283877 ID=Msa0582920;Name=Msa0582920
chr4_2 mRNA 1283877 1284620 1283877 ID=Msa0582920-mRNA-1;Parent=Msa0582920;Name=Msa0582920-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|247
chr4_2 exon 1283877 1284620 1283877 ID=Msa0582920-mRNA-1:exon:352;Parent=Msa0582920-mRNA-1
chr4_2 CDS 1283877 1284620 1283877 ID=Msa0582920-mRNA-1:cds;Parent=Msa0582920-mRNA-1
Gene Sequence

>Msa0582920

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa0582920

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*