AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1299070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTGGCGTCTCATTTCTAT+TGG 0.299749 8_3:+60060739 Msa1299070:CDS
TTCAGATGGTTGTTTGATAT+CGG 0.319233 8_3:+60061834 Msa1299070:intron
CAACTCTGGTTTCATATTGA+TGG 0.346474 8_3:-60060817 None:intergenic
TACCGATATGAGTTTGCCTT+TGG 0.356761 8_3:-60060882 None:intergenic
ACCGATATGAGTTTGCCTTT+GGG 0.423892 8_3:-60060881 None:intergenic
TCCCAAAGGCAAACTCATAT+CGG 0.440825 8_3:+60060880 Msa1299070:CDS
TATGGAAAGCAGTGCATCAC+TGG 0.453269 8_3:+60060722 None:intergenic
TTTGAAAGGCGAACCAACTC+TGG 0.457019 8_3:-60060831 None:intergenic
CGCCTTTCAAAGCGGACAAA+GGG 0.468681 8_3:+60060843 Msa1299070:CDS
TTGTTTGATATCGGTAAAGA+TGG 0.480615 8_3:+60061843 Msa1299070:CDS
CGTCTCATTTCTATTGGTCG+AGG 0.484592 8_3:+60060745 Msa1299070:CDS
GACCCTTTGTCCGCTTTGAA+AGG 0.514780 8_3:-60060845 None:intergenic
TCGCCTTTCAAAGCGGACAA+AGG 0.563719 8_3:+60060842 Msa1299070:CDS
CATCAATATGAAACCAGAGT+TGG 0.583017 8_3:+60060818 Msa1299070:CDS
TCTTACACACATACTCCCAA+AGG 0.672768 8_3:+60060866 Msa1299070:CDS
AGTTGGTTCGCCTTTCAAAG+CGG 0.685581 8_3:+60060835 Msa1299070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAGAAAATACATTTAT+GGG + chr8_3:60061527-60061546 Msa1299070:intron 10.0%
!! TAAAAAGAAAATACATTTAT+GGG + chr8_3:60061527-60061546 Msa1299070:intron 10.0%
!! AAAGAAAAAGAAAAACAATT+CGG - chr8_3:60061032-60061051 None:intergenic 15.0%
!!! TTATTTTCAGTTTTTCTTTT+CGG + chr8_3:60061076-60061095 Msa1299070:intron 15.0%
!!! ATCAGTTTTTTTTTTTTTTG+TGG + chr8_3:60061393-60061412 Msa1299070:intron 15.0%
!! GTAAAAAGAAAATACATTTA+TGG + chr8_3:60061526-60061545 Msa1299070:intron 15.0%
!! CAGCAAAAAAATTAAAAAAT+TGG - chr8_3:60061578-60061597 None:intergenic 15.0%
!!! TGAAAGTATTTTTTTTTTTG+AGG + chr8_3:60061609-60061628 Msa1299070:intron 15.0%
!!! GAAAGTATTTTTTTTTTTGA+GGG + chr8_3:60061610-60061629 Msa1299070:intron 15.0%
!! AGTTTATAAAATGATTCTAT+CGG - chr8_3:60061687-60061706 None:intergenic 15.0%
!! TTATAAACTTCTCATTAATT+TGG + chr8_3:60061698-60061717 Msa1299070:intron 15.0%
!!! TTTTTTGAATAATTTTCAGA+TGG + chr8_3:60061820-60061839 Msa1299070:intron 15.0%
!! AAAGAAAAAGAAAAACAATT+CGG - chr8_3:60061032-60061051 None:intergenic 15.0%
!!! TTATTTTCAGTTTTTCTTTT+CGG + chr8_3:60061076-60061095 Msa1299070:intron 15.0%
!!! ATCAGTTTTTTTTTTTTTTG+TGG + chr8_3:60061393-60061412 Msa1299070:intron 15.0%
!! GTAAAAAGAAAATACATTTA+TGG + chr8_3:60061526-60061545 Msa1299070:intron 15.0%
!! CAGCAAAAAAATTAAAAAAT+TGG - chr8_3:60061578-60061597 None:intergenic 15.0%
!!! TGAAAGTATTTTTTTTTTTG+AGG + chr8_3:60061609-60061628 Msa1299070:intron 15.0%
!!! GAAAGTATTTTTTTTTTTGA+GGG + chr8_3:60061610-60061629 Msa1299070:intron 15.0%
!! AGTTTATAAAATGATTCTAT+CGG - chr8_3:60061687-60061706 None:intergenic 15.0%
!! TTATAAACTTCTCATTAATT+TGG + chr8_3:60061698-60061717 Msa1299070:intron 15.0%
!!! TTTTTTGAATAATTTTCAGA+TGG + chr8_3:60061820-60061839 Msa1299070:intron 15.0%
!!! TGAATGAATATCACTTATTT+TGG + chr8_3:60061504-60061523 Msa1299070:intron 20.0%
!!! TTTTGATTTGCTTAATGAAA+AGG - chr8_3:60061767-60061786 None:intergenic 20.0%
!!! TGAATGAATATCACTTATTT+TGG + chr8_3:60061504-60061523 Msa1299070:intron 20.0%
!!! TTTTGATTTGCTTAATGAAA+AGG - chr8_3:60061767-60061786 None:intergenic 20.0%
!!! AGGATTTTTCAAATTACACT+AGG + chr8_3:60060765-60060784 Msa1299070:CDS 25.0%
!!! GGATTTTTCAAATTACACTA+GGG + chr8_3:60060766-60060785 Msa1299070:CDS 25.0%
!!! GATTTTTCAAATTACACTAG+GGG + chr8_3:60060767-60060786 Msa1299070:CDS 25.0%
!!! ATTTTTCAAATTACACTAGG+GGG + chr8_3:60060768-60060787 Msa1299070:CDS 25.0%
! ATCGGTATGAATTAGATTAA+TGG + chr8_3:60060898-60060917 Msa1299070:intron 25.0%
!!! CTTCTCTGATTATTGATTTA+TGG + chr8_3:60060980-60060999 Msa1299070:intron 25.0%
! AAAAAGAAAAACAATTCGGA+GGG - chr8_3:60061028-60061047 None:intergenic 25.0%
!!! TTTTATTTTCCGTTTTAGTG+CGG + chr8_3:60061164-60061183 Msa1299070:intron 25.0%
!! ATTTGAAACCATGAGTATTT+CGG + chr8_3:60061238-60061257 Msa1299070:intron 25.0%
!!! AGGATTTTTCAAATTACACT+AGG + chr8_3:60060765-60060784 Msa1299070:CDS 25.0%
!!! GGATTTTTCAAATTACACTA+GGG + chr8_3:60060766-60060785 Msa1299070:CDS 25.0%
!!! GATTTTTCAAATTACACTAG+GGG + chr8_3:60060767-60060786 Msa1299070:CDS 25.0%
!!! ATTTTTCAAATTACACTAGG+GGG + chr8_3:60060768-60060787 Msa1299070:CDS 25.0%
! ATCGGTATGAATTAGATTAA+TGG + chr8_3:60060898-60060917 Msa1299070:intron 25.0%
!!! CTTCTCTGATTATTGATTTA+TGG + chr8_3:60060980-60060999 Msa1299070:intron 25.0%
! AAAAAGAAAAACAATTCGGA+GGG - chr8_3:60061028-60061047 None:intergenic 25.0%
!!! TTTTATTTTCCGTTTTAGTG+CGG + chr8_3:60061164-60061183 Msa1299070:intron 25.0%
!! ATTTGAAACCATGAGTATTT+CGG + chr8_3:60061238-60061257 Msa1299070:intron 25.0%
TAGATTAATGGAACTATTGC+AGG + chr8_3:60060910-60060929 Msa1299070:intron 30.0%
GAAAAAGAAAAACAATTCGG+AGG - chr8_3:60061029-60061048 None:intergenic 30.0%
AAATAAACACCGCACTAAAA+CGG - chr8_3:60061176-60061195 None:intergenic 30.0%
!! TCGGATATTCAAGTTGAATT+TGG - chr8_3:60061668-60061687 None:intergenic 30.0%
TTCAGATGGTTGTTTGATAT+CGG + chr8_3:60061834-60061853 Msa1299070:intron 30.0%
TTGTTTGATATCGGTAAAGA+TGG + chr8_3:60061843-60061862 Msa1299070:CDS 30.0%
TAGATTAATGGAACTATTGC+AGG + chr8_3:60060910-60060929 Msa1299070:intron 30.0%
GAAAAAGAAAAACAATTCGG+AGG - chr8_3:60061029-60061048 None:intergenic 30.0%
AAATAAACACCGCACTAAAA+CGG - chr8_3:60061176-60061195 None:intergenic 30.0%
!! TCGGATATTCAAGTTGAATT+TGG - chr8_3:60061668-60061687 None:intergenic 30.0%
TTCAGATGGTTGTTTGATAT+CGG + chr8_3:60061834-60061853 Msa1299070:intron 30.0%
TTGTTTGATATCGGTAAAGA+TGG + chr8_3:60061843-60061862 Msa1299070:CDS 30.0%
! CAACTCTGGTTTCATATTGA+TGG - chr8_3:60060820-60060839 None:intergenic 35.0%
CATCAATATGAAACCAGAGT+TGG + chr8_3:60060818-60060837 Msa1299070:CDS 35.0%
!!! GTGCGGTGTTTATTTTATTC+AGG + chr8_3:60061181-60061200 Msa1299070:intron 35.0%
TGATAAAGACAATGCATGCA+AGG - chr8_3:60061441-60061460 None:intergenic 35.0%
! CAACTCTGGTTTCATATTGA+TGG - chr8_3:60060820-60060839 None:intergenic 35.0%
CATCAATATGAAACCAGAGT+TGG + chr8_3:60060818-60060837 Msa1299070:CDS 35.0%
!!! GTGCGGTGTTTATTTTATTC+AGG + chr8_3:60061181-60061200 Msa1299070:intron 35.0%
TGATAAAGACAATGCATGCA+AGG - chr8_3:60061441-60061460 None:intergenic 35.0%
AAATTACACTAGGGGGTCTT+AGG + chr8_3:60060775-60060794 Msa1299070:CDS 40.0%
TCTTACACACATACTCCCAA+AGG + chr8_3:60060866-60060885 Msa1299070:CDS 40.0%
TCCCAAAGGCAAACTCATAT+CGG + chr8_3:60060880-60060899 Msa1299070:CDS 40.0%
ACCGATATGAGTTTGCCTTT+GGG - chr8_3:60060884-60060903 None:intergenic 40.0%
TACCGATATGAGTTTGCCTT+TGG - chr8_3:60060885-60060904 None:intergenic 40.0%
TGAAACCATGAGTATTTCGG+TGG + chr8_3:60061241-60061260 Msa1299070:intron 40.0%
AAATTACACTAGGGGGTCTT+AGG + chr8_3:60060775-60060794 Msa1299070:CDS 40.0%
TCTTACACACATACTCCCAA+AGG + chr8_3:60060866-60060885 Msa1299070:CDS 40.0%
TCCCAAAGGCAAACTCATAT+CGG + chr8_3:60060880-60060899 Msa1299070:CDS 40.0%
ACCGATATGAGTTTGCCTTT+GGG - chr8_3:60060884-60060903 None:intergenic 40.0%
TACCGATATGAGTTTGCCTT+TGG - chr8_3:60060885-60060904 None:intergenic 40.0%
TGAAACCATGAGTATTTCGG+TGG + chr8_3:60061241-60061260 Msa1299070:intron 40.0%
CACTGGCGTCTCATTTCTAT+TGG + chr8_3:60060739-60060758 Msa1299070:CDS 45.0%
CGTCTCATTTCTATTGGTCG+AGG + chr8_3:60060745-60060764 Msa1299070:CDS 45.0%
TAGGGGGTCTTAGGACAATA+TGG + chr8_3:60060784-60060803 Msa1299070:CDS 45.0%
AGGGGGTCTTAGGACAATAT+GGG + chr8_3:60060785-60060804 Msa1299070:CDS 45.0%
TTTGAAAGGCGAACCAACTC+TGG - chr8_3:60060834-60060853 None:intergenic 45.0%
!! AGTTGGTTCGCCTTTCAAAG+CGG + chr8_3:60060835-60060854 Msa1299070:CDS 45.0%
TGGAACTCTCCTTGAATTGC+TGG + chr8_3:60060946-60060965 Msa1299070:intron 45.0%
TCCTTGAATTGCTGGAGCAA+TGG + chr8_3:60060954-60060973 Msa1299070:intron 45.0%
TCCATTGCTCCAGCAATTCA+AGG - chr8_3:60060958-60060977 None:intergenic 45.0%
TCAAGCCACCGAAATACTCA+TGG - chr8_3:60061249-60061268 None:intergenic 45.0%
TAGAGTATATGTCCCTCGTG+AGG - chr8_3:60061474-60061493 None:intergenic 45.0%
CACTGGCGTCTCATTTCTAT+TGG + chr8_3:60060739-60060758 Msa1299070:CDS 45.0%
CGTCTCATTTCTATTGGTCG+AGG + chr8_3:60060745-60060764 Msa1299070:CDS 45.0%
TAGGGGGTCTTAGGACAATA+TGG + chr8_3:60060784-60060803 Msa1299070:CDS 45.0%
AGGGGGTCTTAGGACAATAT+GGG + chr8_3:60060785-60060804 Msa1299070:CDS 45.0%
TTTGAAAGGCGAACCAACTC+TGG - chr8_3:60060834-60060853 None:intergenic 45.0%
!! AGTTGGTTCGCCTTTCAAAG+CGG + chr8_3:60060835-60060854 Msa1299070:CDS 45.0%
TGGAACTCTCCTTGAATTGC+TGG + chr8_3:60060946-60060965 Msa1299070:intron 45.0%
TCCTTGAATTGCTGGAGCAA+TGG + chr8_3:60060954-60060973 Msa1299070:intron 45.0%
TCCATTGCTCCAGCAATTCA+AGG - chr8_3:60060958-60060977 None:intergenic 45.0%
TCAAGCCACCGAAATACTCA+TGG - chr8_3:60061249-60061268 None:intergenic 45.0%
TAGAGTATATGTCCCTCGTG+AGG - chr8_3:60061474-60061493 None:intergenic 45.0%
TCGCCTTTCAAAGCGGACAA+AGG + chr8_3:60060842-60060861 Msa1299070:CDS 50.0%
CGCCTTTCAAAGCGGACAAA+GGG + chr8_3:60060843-60060862 Msa1299070:CDS 50.0%
! GACCCTTTGTCCGCTTTGAA+AGG - chr8_3:60060848-60060867 None:intergenic 50.0%
!! TTGCAGGAGTACCTGTACGA+TGG + chr8_3:60060926-60060945 Msa1299070:intron 50.0%
CAAGGAGAGTTCCATCGTAC+AGG - chr8_3:60060940-60060959 None:intergenic 50.0%
GACAATGCATGCAAGGTCTG+AGG - chr8_3:60061434-60061453 None:intergenic 50.0%
TCAACTGAGCTAACCTCACG+AGG + chr8_3:60061458-60061477 Msa1299070:intron 50.0%
CAACTGAGCTAACCTCACGA+GGG + chr8_3:60061459-60061478 Msa1299070:intron 50.0%
TCGCCTTTCAAAGCGGACAA+AGG + chr8_3:60060842-60060861 Msa1299070:CDS 50.0%
CGCCTTTCAAAGCGGACAAA+GGG + chr8_3:60060843-60060862 Msa1299070:CDS 50.0%
! GACCCTTTGTCCGCTTTGAA+AGG - chr8_3:60060848-60060867 None:intergenic 50.0%
!! TTGCAGGAGTACCTGTACGA+TGG + chr8_3:60060926-60060945 Msa1299070:intron 50.0%
CAAGGAGAGTTCCATCGTAC+AGG - chr8_3:60060940-60060959 None:intergenic 50.0%
GACAATGCATGCAAGGTCTG+AGG - chr8_3:60061434-60061453 None:intergenic 50.0%
TCAACTGAGCTAACCTCACG+AGG + chr8_3:60061458-60061477 Msa1299070:intron 50.0%
CAACTGAGCTAACCTCACGA+GGG + chr8_3:60061459-60061478 Msa1299070:intron 50.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 60060723 60061881 60060723 ID=Msa1299070;Name=Msa1299070
chr8_3 mRNA 60060723 60061881 60060723 ID=Msa1299070-mRNA-1;Parent=Msa1299070;Name=Msa1299070-mRNA-1;_AED=0.89;_eAED=1.00;_QI=0|0|0|0.5|1|1|2|0|73
chr8_3 exon 60060723 60060901 60060723 ID=Msa1299070-mRNA-1:exon:17456;Parent=Msa1299070-mRNA-1
chr8_3 exon 60061839 60061881 60061839 ID=Msa1299070-mRNA-1:exon:17457;Parent=Msa1299070-mRNA-1
chr8_3 CDS 60060723 60060901 60060723 ID=Msa1299070-mRNA-1:cds;Parent=Msa1299070-mRNA-1
chr8_3 CDS 60061839 60061881 60061839 ID=Msa1299070-mRNA-1:cds;Parent=Msa1299070-mRNA-1
Gene Sequence

>Msa1299070

ATGGAAAGCAGTGCATCACTGGCGTCTCATTTCTATTGGTCGAGGATTTTTCAAATTACACTAGGGGGTCTTAGGACAATATGGGCACAATGCGCCATCAATATGAAACCAGAGTTGGTTCGCCTTTCAAAGCGGACAAAGGGTCTTACACACATACTCCCAAAGGCAAACTCATATCGATGGTTGTTTGATATCGGTAAAGATGGAAGAAGAATAGTGTGA

Protein sequence

>Msa1299070

MESSASLASHFYWSRIFQITLGGLRTIWAQCAINMKPELVRLSKRTKGLTHILPKANSYRWLFDIGKDGRRIV*