AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0020080


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 65 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.231913 1_1:-34999719 Msa0020080:intron
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 1_1:+34999780 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 1_1:-34999575 Msa0020080:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 1_1:-34999607 Msa0020080:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.328484 1_1:-34999880 Msa0020080:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 1_1:-34999574 Msa0020080:CDS
AAGAAACAATGACGGTATCT+AGG 0.347373 1_1:+34999833 None:intergenic
CAAGCGTTATCCGGAATGAT+TGG 0.365557 1_1:+34999907 None:intergenic
TAAGTTTGCCGTCAAATCTC+AGG 0.372659 1_1:+34999956 None:intergenic
CAGAGGATGCAAGCGTTATC+CGG 0.442617 1_1:+34999898 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 1_1:+34999618 None:intergenic
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 1_1:-34999606 Msa0020080:CDS
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 1_1:+34999724 None:intergenic
CTTTACACATGCAAGTCAAA+CGG 0.483049 1_1:+34999462 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 1_1:-34999770 Msa0020080:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.490776 1_1:-34999718 Msa0020080:intron
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 1_1:+34999723 None:intergenic
TTTACACATGCAAGTCAAAC+GGG 0.492517 1_1:+34999463 None:intergenic
GGTTGAGCCCTGAGATTTGA+CGG 0.500607 1_1:-34999964 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 1_1:+34999594 None:intergenic
AACGCGTAAGAATCTGCCCT+TGG 0.504406 1_1:+34999517 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 1_1:+34999489 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 1_1:+34999908 None:intergenic
TAAGAATCTGCCCTTGGGAG+AGG 0.514923 1_1:+34999523 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 1_1:-34999497 Msa0020080:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 1_1:+34999488 None:intergenic
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 1_1:+34999755 None:intergenic
CATGCAAGTCAAACGGGAAG+TGG 0.538166 1_1:+34999469 None:intergenic
ACGCGTAAGAATCTGCCCTT+GGG 0.539522 1_1:+34999518 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 1_1:+34999656 None:intergenic
TCCTGGCTCAGGATGAATGC+TGG 0.542991 1_1:+34999432 None:intergenic
AGAAACAATGACGGTATCTA+GGG 0.551942 1_1:+34999834 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 1_1:+34999574 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 1_1:+34999787 None:intergenic
AAGTTTGCCGTCAAATCTCA+GGG 0.561879 1_1:+34999957 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 1_1:+34999595 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 1_1:+34999788 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 1_1:-34999603 Msa0020080:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 1_1:-34999573 Msa0020080:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 1_1:-34999656 Msa0020080:CDS
ATTGGGCGTAAAACGTCTGT+AGG 0.583693 1_1:+34999925 None:intergenic
AGTGTGGTTGATCATCCTCT+CGG 0.585594 1_1:-34999680 Msa0020080:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 1_1:-34999754 Msa0020080:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 1_1:+34999590 None:intergenic
TAACTCTATGCCAGCAGCCG+CGG 0.596735 1_1:+34999870 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 1_1:+34999565 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 1_1:+34999593 None:intergenic
AGAGGATGATCAACCACACT+AGG 0.626241 1_1:+34999683 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 1_1:+34999484 None:intergenic
GGGCGTAAAACGTCTGTAGG+TGG 0.627335 1_1:+34999928 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 1_1:+34999825 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 1_1:+34999773 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 1_1:+34999623 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.650015 1_1:+34999481 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 1_1:+34999881 None:intergenic
GACTTGTCTCAGTCCTAGTG+TGG 0.650592 1_1:-34999696 Msa0020080:CDS
AAAAGAAGTTCATGACCCGT+AGG 0.653857 1_1:-34999803 Msa0020080:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 1_1:+34999577 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 1_1:+34999665 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 1_1:+34999770 None:intergenic
TGGCTCAGGATGAATGCTGG+CGG 0.720074 1_1:+34999435 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 1_1:+34999639 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 1_1:+34999642 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 1_1:-34999887 Msa0020080:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 1_1:+34999725 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AGAAACAATGACGGTATCTA+GGG + chr1_1:34999566-34999585 None:intergenic 35.0%
AAGAAACAATGACGGTATCT+AGG + chr1_1:34999567-34999586 None:intergenic 35.0%
TTTACACATGCAAGTCAAAC+GGG + chr1_1:34999937-34999956 None:intergenic 35.0%
CTTTACACATGCAAGTCAAA+CGG + chr1_1:34999938-34999957 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr1_1:34999492-34999511 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr1_1:34999575-34999594 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr1_1:34999594-34999613 Msa0020080:CDS 40.0%
AGAGGAAAAACAGCTGGAAA+CGG + chr1_1:34999859-34999878 None:intergenic 40.0%
ATTGGGCGTAAAACGTCTGT+AGG + chr1_1:34999475-34999494 None:intergenic 45.0%
! CGTTTTACGCCCAATCATTC+CGG - chr1_1:34999480-34999499 Msa0020080:CDS 45.0%
CAAGCGTTATCCGGAATGAT+TGG + chr1_1:34999493-34999512 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr1_1:34999571-34999590 Msa0020080:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr1_1:34999592-34999611 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr1_1:34999659-34999678 None:intergenic 45.0%
AGAGGATGATCAACCACACT+AGG + chr1_1:34999717-34999736 None:intergenic 45.0%
AGTGTGGTTGATCATCCTCT+CGG - chr1_1:34999717-34999736 Msa0020080:intron 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr1_1:34999758-34999777 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr1_1:34999761-34999780 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr1_1:34999777-34999796 None:intergenic 45.0%
!!! AGCTGTTTTTCCTCTCCCAA+GGG - chr1_1:34999864-34999883 Msa0020080:CDS 45.0%
CAGAGGATGCAAGCGTTATC+CGG + chr1_1:34999502-34999521 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr1_1:34999510-34999529 Msa0020080:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr1_1:34999660-34999679 None:intergenic 50.0%
AGACAAGTCCCAGACTCCTA+CGG + chr1_1:34999690-34999709 None:intergenic 50.0%
GACTTGTCTCAGTCCTAGTG+TGG - chr1_1:34999701-34999720 Msa0020080:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr1_1:34999782-34999801 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr1_1:34999822-34999841 Msa0020080:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr1_1:34999835-34999854 None:intergenic 50.0%
CTTGGGAGAGGAAAAACAGC+TGG + chr1_1:34999865-34999884 None:intergenic 50.0%
!!! CAGCTGTTTTTCCTCTCCCA+AGG - chr1_1:34999863-34999882 Msa0020080:CDS 50.0%
TAAGAATCTGCCCTTGGGAG+AGG + chr1_1:34999877-34999896 None:intergenic 50.0%
ACGCGTAAGAATCTGCCCTT+GGG + chr1_1:34999882-34999901 None:intergenic 50.0%
AACGCGTAAGAATCTGCCCT+TGG + chr1_1:34999883-34999902 None:intergenic 50.0%
CATGCAAGTCAAACGGGAAG+TGG + chr1_1:34999931-34999950 None:intergenic 50.0%
GGGCGTAAAACGTCTGTAGG+TGG + chr1_1:34999472-34999491 None:intergenic 55.0%
TAACTCTATGCCAGCAGCCG+CGG + chr1_1:34999530-34999549 None:intergenic 55.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr1_1:34999612-34999631 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr1_1:34999613-34999632 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr1_1:34999612-34999631 Msa0020080:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr1_1:34999620-34999639 None:intergenic 55.0%
GACAAGTCCCAGACTCCTAC+GGG + chr1_1:34999689-34999708 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr1_1:34999735-34999754 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr1_1:34999823-34999842 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr1_1:34999823-34999842 Msa0020080:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr1_1:34999824-34999843 Msa0020080:intron 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr1_1:34999916-34999935 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr1_1:34999919-34999938 None:intergenic 55.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr1_1:34999645-34999664 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr1_1:34999643-34999662 Msa0020080:CDS 60.0%
AAGTCCCAGACTCCTACGGG+AGG + chr1_1:34999686-34999705 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr1_1:34999744-34999763 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr1_1:34999741-34999760 Msa0020080:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr1_1:34999806-34999825 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr1_1:34999807-34999826 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr1_1:34999810-34999829 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr1_1:34999826-34999845 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr1_1:34999911-34999930 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr1_1:34999912-34999931 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr1_1:34999519-34999538 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr1_1:34999517-34999536 Msa0020080:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr1_1:34999675-34999694 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr1_1:34999676-34999695 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr1_1:34999677-34999696 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr1_1:34999678-34999697 Msa0020080:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr1_1:34999679-34999698 Msa0020080:CDS 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr1_1:34999790-34999809 Msa0020080:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr1_1:34999791-34999810 Msa0020080:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr1_1:34999805-34999824 None:intergenic 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr1_1:34999900-34999919 Msa0020080:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr1_1:34999627-34999646 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr1_1:34999630-34999649 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr1_1:34999627-34999646 Msa0020080:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr1_1:34999671-34999690 Msa0020080:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr1_1:34999794-34999813 Msa0020080:CDS 75.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 34999442 34999977 34999442 ID=Msa0020080;Name=Msa0020080
chr1_1 mRNA 34999442 34999977 34999442 ID=Msa0020080-mRNA-1;Parent=Msa0020080;Name=Msa0020080-mRNA-1;_AED=0.15;_eAED=0.19;_QI=0|0|0|1|0|0|3|0|173
chr1_1 exon 34999840 34999977 34999840 ID=Msa0020080-mRNA-1:exon:11141;Parent=Msa0020080-mRNA-1
chr1_1 exon 34999731 34999826 34999731 ID=Msa0020080-mRNA-1:exon:11140;Parent=Msa0020080-mRNA-1
chr1_1 exon 34999442 34999726 34999442 ID=Msa0020080-mRNA-1:exon:11139;Parent=Msa0020080-mRNA-1
chr1_1 CDS 34999840 34999977 34999840 ID=Msa0020080-mRNA-1:cds;Parent=Msa0020080-mRNA-1
chr1_1 CDS 34999731 34999826 34999731 ID=Msa0020080-mRNA-1:cds;Parent=Msa0020080-mRNA-1
chr1_1 CDS 34999442 34999726 34999442 ID=Msa0020080-mRNA-1:cds;Parent=Msa0020080-mRNA-1
Gene Sequence

>Msa0020080

CTGAGATTTGACGGCAAACTTAAAAAGCCACCTACAGACGTTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCATAGAGTTAGCTGATGCTTATTCCCTAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGACTTGTCTCAGTCCTAGTGTGGTTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTTTTCCTCTCCCAAGGGCAGATTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTTGACTTGCATGTGTAAAGCATGCCGCCAGCATTCATCC

Protein sequence

>Msa0020080

LRFDGKLKKPPTDVLRPIIPDNACILCLTAAAGIELADAYSLDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGTCLSPSVVDHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCFSSPKGRFLRVTHPSATGNTTSRLTCMCKACRQHSS