AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582770


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582770 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582770 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582770 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa0582770 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa0582770 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa0582770 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa0582770 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
Msa0582770 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:-1194002 Msa0582770:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 4_2:-1194568 Msa0582770:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 4_2:-1194567 Msa0582770:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 4_2:+1194128 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 4_2:-1194364 Msa0582770:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 4_2:+1194198 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 4_2:-1194001 Msa0582770:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 4_2:-1194528 Msa0582770:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 4_2:+1194477 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 4_2:+1194121 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 4_2:-1193941 Msa0582770:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 4_2:+1194249 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 4_2:-1194527 Msa0582770:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 4_2:+1194250 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 4_2:+1194090 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 4_2:+1194352 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 4_2:-1194385 Msa0582770:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 4_2:+1193995 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 4_2:+1194001 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 4_2:+1194457 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 4_2:-1194576 Msa0582770:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 4_2:-1193930 Msa0582770:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 4_2:+1194413 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 4_2:+1194139 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 4_2:-1194592 Msa0582770:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 4_2:+1194091 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 4_2:-1194397 Msa0582770:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 4_2:+1194143 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 4_2:-1194286 Msa0582770:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 4_2:+1193940 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 4_2:+1194133 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 4_2:-1194457 Msa0582770:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 4_2:+1194445 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 4_2:-1194205 Msa0582770:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 4_2:-1194566 Msa0582770:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 4_2:+1194013 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 4_2:-1193926 Msa0582770:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 4_2:-1194377 Msa0582770:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 4_2:-1194378 Msa0582770:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 4_2:-1193986 Msa0582770:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 4_2:+1194438 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 4_2:+1194361 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 4_2:-1194206 Msa0582770:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 4_2:+1194513 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 4_2:+1194271 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr4_2:1194223-1194242 Msa0582770:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr4_2:1194267-1194286 Msa0582770:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr4_2:1194306-1194325 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr4_2:1194307-1194326 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr4_2:1194435-1194454 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr4_2:1193986-1194005 Msa0582770:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr4_2:1194118-1194137 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr4_2:1194204-1194223 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr4_2:1194264-1194283 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr4_2:1194378-1194397 Msa0582770:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr4_2:1193977-1193996 Msa0582770:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr4_2:1193985-1194004 Msa0582770:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr4_2:1193987-1194006 Msa0582770:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr4_2:1194026-1194045 Msa0582770:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr4_2:1194228-1194247 Msa0582770:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr4_2:1194229-1194248 Msa0582770:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr4_2:1194363-1194382 Msa0582770:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr4_2:1194368-1194387 Msa0582770:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr4_2:1194423-1194442 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr4_2:1194428-1194447 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr4_2:1194465-1194484 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr4_2:1194466-1194485 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr4_2:1194468-1194487 Msa0582770:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr4_2:1194561-1194580 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr4_2:1194567-1194586 Msa0582770:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr4_2:1194627-1194646 Msa0582770:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr4_2:1194025-1194044 Msa0582770:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr4_2:1194079-1194098 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr4_2:1194168-1194187 Msa0582770:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr4_2:1194230-1194249 Msa0582770:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr4_2:1194358-1194377 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr4_2:1194543-1194562 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr4_2:1194551-1194570 Msa0582770:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr4_2:1194552-1194571 Msa0582770:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr4_2:1194602-1194621 Msa0582770:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr4_2:1194623-1194642 Msa0582770:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr4_2:1193961-1193980 Msa0582770:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr4_2:1194043-1194062 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr4_2:1194347-1194366 Msa0582770:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr4_2:1194348-1194367 Msa0582770:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr4_2:1194413-1194432 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr4_2:1194417-1194436 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr4_2:1194555-1194574 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr4_2:1194111-1194130 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr4_2:1194143-1194162 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr4_2:1194155-1194174 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr4_2:1194156-1194175 Msa0582770:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr4_2:1194175-1194194 Msa0582770:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr4_2:1194176-1194195 Msa0582770:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr4_2:1194195-1194214 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr4_2:1194612-1194631 Msa0582770:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr4_2:1194616-1194635 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr4_2:1194099-1194118 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr4_2:1194096-1194115 Msa0582770:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr4_2:1194285-1194304 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr4_2:1194189-1194208 Msa0582770:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr4_2:1194244-1194263 Msa0582770:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1193916 1194659 1193916 ID=Msa0582770;Name=Msa0582770
chr4_2 mRNA 1193916 1194659 1193916 ID=Msa0582770-mRNA-1;Parent=Msa0582770;Name=Msa0582770-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
chr4_2 exon 1193916 1194659 1193916 ID=Msa0582770-mRNA-1:exon:289;Parent=Msa0582770-mRNA-1
chr4_2 CDS 1193916 1194659 1193916 ID=Msa0582770-mRNA-1:cds;Parent=Msa0582770-mRNA-1
Gene Sequence

>Msa0582770

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa0582770

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*