AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1077620

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 37 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGACCTCGCACATGGTTCT+TGG 0.317375 7_2:-76357131 None:intergenic
GAGAGTTCAAATAATTCCTT+TGG 0.322300 7_2:+76357063 Msa1077620:CDS
GATGTTTAGATTCTGCTGTT+AGG 0.334474 7_2:+76357303 Msa1077620:three_prime_UTR
TTGGAATCTGCTTGATAGTT+CGG 0.358960 7_2:+76356694 Msa1077620:CDS
AGCGATGATGACATTATTAT+CGG 0.395438 7_2:+76357161 Msa1077620:three_prime_UTR
TGGAATCTGCTTGATAGTTC+GGG 0.399994 7_2:+76356695 Msa1077620:CDS
TCTCCGGTTCCTTGGTGCTT+AGG 0.419679 7_2:-76356889 None:intergenic
GTTGAGAATGAATTTGAATC+TGG 0.429771 7_2:+76357215 Msa1077620:three_prime_UTR
TCTCACACCGTAACTTTCAA+TGG 0.460244 7_2:+76356722 Msa1077620:CDS
AGAGTTCAAATAATTCCTTT+GGG 0.460985 7_2:+76357064 Msa1077620:CDS
TAGCCTAAGCACCAAGGAAC+CGG 0.468616 7_2:+76356886 Msa1077620:CDS
CAAAGTGATCTCCGGTTCCT+TGG 0.470398 7_2:-76356897 None:intergenic
TTAATATGATGGGAGAGAGT+TGG 0.472140 7_2:+76356675 None:intergenic
CCATGCAGTTTGTCAAGCTC+AGG 0.475149 7_2:+76357365 Msa1077620:three_prime_UTR
TATGACATGATGGAAATTCA+TGG 0.485397 7_2:-76356865 None:intergenic
ATAACAGATGAGCAAGAGAA+AGG 0.496848 7_2:-76357416 None:intergenic
CAAGGAACCGGAGATCACTT+TGG 0.515759 7_2:+76356898 Msa1077620:CDS
TCGGAGCACTTCAACATGGC+TGG 0.532953 7_2:+76357180 Msa1077620:three_prime_UTR
ATAATCACCATTGAAAGTTA+CGG 0.543094 7_2:-76356729 None:intergenic
TAACAGATGAGCAAGAGAAA+GGG 0.546999 7_2:-76357415 None:intergenic
ACCCTCTCTTGTCAGAAGGA+TGG 0.560748 7_2:+76356756 Msa1077620:CDS
TCCATCCTTCTGACAAGAGA+GGG 0.571301 7_2:-76356757 None:intergenic
GTGCTTAGGCTATGACATGA+TGG 0.574096 7_2:-76356875 None:intergenic
AGTTCATCCAAAGTGATCTC+CGG 0.575284 7_2:-76356905 None:intergenic
ATGACATGATGGAAATTCAT+GGG 0.586620 7_2:-76356864 None:intergenic
ACTATGGGGAGAACATATGC+TGG 0.600265 7_2:+76356839 Msa1077620:CDS
GCACACCCTCTCTTGTCAGA+AGG 0.601769 7_2:+76356752 Msa1077620:CDS
TTCCATCCTTCTGACAAGAG+AGG 0.608372 7_2:-76356758 None:intergenic
ATGAAATCTGACCTCGCACA+TGG 0.617664 7_2:-76357138 None:intergenic
GGTCAAAGTCATATTCCCAA+AGG 0.632209 7_2:-76357079 None:intergenic
CCTGAGCTTGACAAACTGCA+TGG 0.642851 7_2:-76357365 None:intergenic
ATTATCGGAGCACTTCAACA+TGG 0.644172 7_2:+76357176 Msa1077620:three_prime_UTR
GTATACTCAACTAATTGATG+CGG 0.659126 7_2:-76356941 None:intergenic
GATAGTTGTAAAATTCTCTG+AGG 0.683331 7_2:-76356784 None:intergenic
TACTCCAAGAACCATGTGCG+AGG 0.691982 7_2:+76357127 Msa1077620:three_prime_UTR
ATGTCATAGCCTAAGCACCA+AGG 0.698619 7_2:+76356880 Msa1077620:CDS
TTTGACCACCTGATCCTCTG+CGG 0.711505 7_2:+76357095 Msa1077620:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATACATTGTTTATCATATTT+AGG + chr7_2:76357031-76357050 Msa1077620:intron 15.0%
!! ATACATTGTTTATCATATTT+AGG + chr7_2:76357031-76357050 Msa1077620:intron 15.0%
!!! ATAAACAAATCAGTGTTTTT+CGG + chr7_2:76356813-76356832 Msa1077620:CDS 20.0%
!! AATGAGAATTATTAGTAGTT+TGG - chr7_2:76356970-76356989 None:intergenic 20.0%
!!! ATAAGATTCAAGTTTTTTGA+TGG + chr7_2:76357245-76357264 Msa1077620:three_prime_UTR 20.0%
!!! TAAGATTCAAGTTTTTTGAT+GGG + chr7_2:76357246-76357265 Msa1077620:three_prime_UTR 20.0%
!!! AAACATCTATTTTGAAAACA+TGG - chr7_2:76357290-76357309 None:intergenic 20.0%
!!! ATAAACAAATCAGTGTTTTT+CGG + chr7_2:76356813-76356832 Msa1077620:CDS 20.0%
!! AATGAGAATTATTAGTAGTT+TGG - chr7_2:76356970-76356989 None:intergenic 20.0%
!!! ATAAGATTCAAGTTTTTTGA+TGG + chr7_2:76357245-76357264 Msa1077620:three_prime_UTR 20.0%
!!! TAAGATTCAAGTTTTTTGAT+GGG + chr7_2:76357246-76357265 Msa1077620:three_prime_UTR 20.0%
!!! AAACATCTATTTTGAAAACA+TGG - chr7_2:76357290-76357309 None:intergenic 20.0%
! ATAATCACCATTGAAAGTTA+CGG - chr7_2:76356732-76356751 None:intergenic 25.0%
!! AGAGAATTTTACAACTATCA+GGG + chr7_2:76356788-76356807 Msa1077620:CDS 25.0%
! TGATAAACAATGTATACTCA+TGG - chr7_2:76357026-76357045 None:intergenic 25.0%
! AGAGTTCAAATAATTCCTTT+GGG + chr7_2:76357064-76357083 Msa1077620:CDS 25.0%
!!! TTTTGAAAACATGGACATAA+TGG - chr7_2:76357281-76357300 None:intergenic 25.0%
! ATAATCACCATTGAAAGTTA+CGG - chr7_2:76356732-76356751 None:intergenic 25.0%
!! AGAGAATTTTACAACTATCA+GGG + chr7_2:76356788-76356807 Msa1077620:CDS 25.0%
! TGATAAACAATGTATACTCA+TGG - chr7_2:76357026-76357045 None:intergenic 25.0%
! AGAGTTCAAATAATTCCTTT+GGG + chr7_2:76357064-76357083 Msa1077620:CDS 25.0%
!!! TTTTGAAAACATGGACATAA+TGG - chr7_2:76357281-76357300 None:intergenic 25.0%
GATAGTTGTAAAATTCTCTG+AGG - chr7_2:76356787-76356806 None:intergenic 30.0%
! CAGAGAATTTTACAACTATC+AGG + chr7_2:76356787-76356806 Msa1077620:CDS 30.0%
!! AGTGTTTTTCGGTTAACTAT+GGG + chr7_2:76356824-76356843 Msa1077620:CDS 30.0%
! ATGACATGATGGAAATTCAT+GGG - chr7_2:76356867-76356886 None:intergenic 30.0%
! TATGACATGATGGAAATTCA+TGG - chr7_2:76356868-76356887 None:intergenic 30.0%
GTATACTCAACTAATTGATG+CGG - chr7_2:76356944-76356963 None:intergenic 30.0%
GAGAGTTCAAATAATTCCTT+TGG + chr7_2:76357063-76357082 Msa1077620:CDS 30.0%
AGCGATGATGACATTATTAT+CGG + chr7_2:76357161-76357180 Msa1077620:three_prime_UTR 30.0%
GTTGAGAATGAATTTGAATC+TGG + chr7_2:76357215-76357234 Msa1077620:three_prime_UTR 30.0%
GATAGTTGTAAAATTCTCTG+AGG - chr7_2:76356787-76356806 None:intergenic 30.0%
! CAGAGAATTTTACAACTATC+AGG + chr7_2:76356787-76356806 Msa1077620:CDS 30.0%
!! AGTGTTTTTCGGTTAACTAT+GGG + chr7_2:76356824-76356843 Msa1077620:CDS 30.0%
! ATGACATGATGGAAATTCAT+GGG - chr7_2:76356867-76356886 None:intergenic 30.0%
! TATGACATGATGGAAATTCA+TGG - chr7_2:76356868-76356887 None:intergenic 30.0%
GTATACTCAACTAATTGATG+CGG - chr7_2:76356944-76356963 None:intergenic 30.0%
GAGAGTTCAAATAATTCCTT+TGG + chr7_2:76357063-76357082 Msa1077620:CDS 30.0%
AGCGATGATGACATTATTAT+CGG + chr7_2:76357161-76357180 Msa1077620:three_prime_UTR 30.0%
GTTGAGAATGAATTTGAATC+TGG + chr7_2:76357215-76357234 Msa1077620:three_prime_UTR 30.0%
! TTGGAATCTGCTTGATAGTT+CGG + chr7_2:76356694-76356713 Msa1077620:CDS 35.0%
!! CAGTGTTTTTCGGTTAACTA+TGG + chr7_2:76356823-76356842 Msa1077620:CDS 35.0%
!! GTGTTTTTCGGTTAACTATG+GGG + chr7_2:76356825-76356844 Msa1077620:CDS 35.0%
GATGTTTAGATTCTGCTGTT+AGG + chr7_2:76357303-76357322 Msa1077620:three_prime_UTR 35.0%
TAACAGATGAGCAAGAGAAA+GGG - chr7_2:76357418-76357437 None:intergenic 35.0%
ATAACAGATGAGCAAGAGAA+AGG - chr7_2:76357419-76357438 None:intergenic 35.0%
! TTGGAATCTGCTTGATAGTT+CGG + chr7_2:76356694-76356713 Msa1077620:CDS 35.0%
!! CAGTGTTTTTCGGTTAACTA+TGG + chr7_2:76356823-76356842 Msa1077620:CDS 35.0%
!! GTGTTTTTCGGTTAACTATG+GGG + chr7_2:76356825-76356844 Msa1077620:CDS 35.0%
GATGTTTAGATTCTGCTGTT+AGG + chr7_2:76357303-76357322 Msa1077620:three_prime_UTR 35.0%
TAACAGATGAGCAAGAGAAA+GGG - chr7_2:76357418-76357437 None:intergenic 35.0%
ATAACAGATGAGCAAGAGAA+AGG - chr7_2:76357419-76357438 None:intergenic 35.0%
! TGGAATCTGCTTGATAGTTC+GGG + chr7_2:76356695-76356714 Msa1077620:CDS 40.0%
TCTCACACCGTAACTTTCAA+TGG + chr7_2:76356722-76356741 Msa1077620:CDS 40.0%
AGTTCATCCAAAGTGATCTC+CGG - chr7_2:76356908-76356927 None:intergenic 40.0%
GGTCAAAGTCATATTCCCAA+AGG - chr7_2:76357082-76357101 None:intergenic 40.0%
! GAGTATCAAATTTTCCGCAG+AGG - chr7_2:76357112-76357131 None:intergenic 40.0%
! ATTATCGGAGCACTTCAACA+TGG + chr7_2:76357176-76357195 Msa1077620:three_prime_UTR 40.0%
! TGGAATCTGCTTGATAGTTC+GGG + chr7_2:76356695-76356714 Msa1077620:CDS 40.0%
TCTCACACCGTAACTTTCAA+TGG + chr7_2:76356722-76356741 Msa1077620:CDS 40.0%
AGTTCATCCAAAGTGATCTC+CGG - chr7_2:76356908-76356927 None:intergenic 40.0%
GGTCAAAGTCATATTCCCAA+AGG - chr7_2:76357082-76357101 None:intergenic 40.0%
! GAGTATCAAATTTTCCGCAG+AGG - chr7_2:76357112-76357131 None:intergenic 40.0%
! ATTATCGGAGCACTTCAACA+TGG + chr7_2:76357176-76357195 Msa1077620:three_prime_UTR 40.0%
TCCATCCTTCTGACAAGAGA+GGG - chr7_2:76356760-76356779 None:intergenic 45.0%
TTCCATCCTTCTGACAAGAG+AGG - chr7_2:76356761-76356780 None:intergenic 45.0%
ACTATGGGGAGAACATATGC+TGG + chr7_2:76356839-76356858 Msa1077620:CDS 45.0%
GTGCTTAGGCTATGACATGA+TGG - chr7_2:76356878-76356897 None:intergenic 45.0%
ATGTCATAGCCTAAGCACCA+AGG + chr7_2:76356880-76356899 Msa1077620:CDS 45.0%
! CAAATTTTCCGCAGAGGATC+AGG - chr7_2:76357106-76357125 None:intergenic 45.0%
ATGAAATCTGACCTCGCACA+TGG - chr7_2:76357141-76357160 None:intergenic 45.0%
TCCATCCTTCTGACAAGAGA+GGG - chr7_2:76356760-76356779 None:intergenic 45.0%
TTCCATCCTTCTGACAAGAG+AGG - chr7_2:76356761-76356780 None:intergenic 45.0%
ACTATGGGGAGAACATATGC+TGG + chr7_2:76356839-76356858 Msa1077620:CDS 45.0%
GTGCTTAGGCTATGACATGA+TGG - chr7_2:76356878-76356897 None:intergenic 45.0%
ATGTCATAGCCTAAGCACCA+AGG + chr7_2:76356880-76356899 Msa1077620:CDS 45.0%
! CAAATTTTCCGCAGAGGATC+AGG - chr7_2:76357106-76357125 None:intergenic 45.0%
ATGAAATCTGACCTCGCACA+TGG - chr7_2:76357141-76357160 None:intergenic 45.0%
ACCCTCTCTTGTCAGAAGGA+TGG + chr7_2:76356756-76356775 Msa1077620:CDS 50.0%
TAGCCTAAGCACCAAGGAAC+CGG + chr7_2:76356886-76356905 Msa1077620:CDS 50.0%
CAAAGTGATCTCCGGTTCCT+TGG - chr7_2:76356900-76356919 None:intergenic 50.0%
CAAGGAACCGGAGATCACTT+TGG + chr7_2:76356898-76356917 Msa1077620:CDS 50.0%
TTTGACCACCTGATCCTCTG+CGG + chr7_2:76357095-76357114 Msa1077620:exon 50.0%
! ATTTTCCGCAGAGGATCAGG+TGG - chr7_2:76357103-76357122 None:intergenic 50.0%
TACTCCAAGAACCATGTGCG+AGG + chr7_2:76357127-76357146 Msa1077620:three_prime_UTR 50.0%
CCTGAGCTTGACAAACTGCA+TGG - chr7_2:76357368-76357387 None:intergenic 50.0%
CCATGCAGTTTGTCAAGCTC+AGG + chr7_2:76357365-76357384 Msa1077620:three_prime_UTR 50.0%
ACCCTCTCTTGTCAGAAGGA+TGG + chr7_2:76356756-76356775 Msa1077620:CDS 50.0%
TAGCCTAAGCACCAAGGAAC+CGG + chr7_2:76356886-76356905 Msa1077620:CDS 50.0%
CAAAGTGATCTCCGGTTCCT+TGG - chr7_2:76356900-76356919 None:intergenic 50.0%
CAAGGAACCGGAGATCACTT+TGG + chr7_2:76356898-76356917 Msa1077620:CDS 50.0%
TTTGACCACCTGATCCTCTG+CGG + chr7_2:76357095-76357114 Msa1077620:exon 50.0%
! ATTTTCCGCAGAGGATCAGG+TGG - chr7_2:76357103-76357122 None:intergenic 50.0%
TACTCCAAGAACCATGTGCG+AGG + chr7_2:76357127-76357146 Msa1077620:three_prime_UTR 50.0%
CCTGAGCTTGACAAACTGCA+TGG - chr7_2:76357368-76357387 None:intergenic 50.0%
CCATGCAGTTTGTCAAGCTC+AGG + chr7_2:76357365-76357384 Msa1077620:three_prime_UTR 50.0%
GCACACCCTCTCTTGTCAGA+AGG + chr7_2:76356752-76356771 Msa1077620:CDS 55.0%
!! TCTCCGGTTCCTTGGTGCTT+AGG - chr7_2:76356892-76356911 None:intergenic 55.0%
CTGACCTCGCACATGGTTCT+TGG - chr7_2:76357134-76357153 None:intergenic 55.0%
! TCGGAGCACTTCAACATGGC+TGG + chr7_2:76357180-76357199 Msa1077620:three_prime_UTR 55.0%
GCACACCCTCTCTTGTCAGA+AGG + chr7_2:76356752-76356771 Msa1077620:CDS 55.0%
!! TCTCCGGTTCCTTGGTGCTT+AGG - chr7_2:76356892-76356911 None:intergenic 55.0%
CTGACCTCGCACATGGTTCT+TGG - chr7_2:76357134-76357153 None:intergenic 55.0%
! TCGGAGCACTTCAACATGGC+TGG + chr7_2:76357180-76357199 Msa1077620:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 76356683 76357443 76356683 ID=Msa1077620;Name=Msa1077620
chr7_2 mRNA 76356683 76357443 76356683 ID=Msa1077620-mRNA-1;Parent=Msa1077620;Name=Msa1077620-mRNA-1;_AED=0.43;_eAED=0.52;_QI=0|0|0.5|1|1|1|2|336|109
chr7_2 exon 76356683 76356957 76356683 ID=Msa1077620-mRNA-1:exon:18395;Parent=Msa1077620-mRNA-1
chr7_2 exon 76357053 76357443 76357053 ID=Msa1077620-mRNA-1:exon:18396;Parent=Msa1077620-mRNA-1
chr7_2 CDS 76356683 76356957 76356683 ID=Msa1077620-mRNA-1:cds;Parent=Msa1077620-mRNA-1
chr7_2 CDS 76357053 76357107 76357053 ID=Msa1077620-mRNA-1:cds;Parent=Msa1077620-mRNA-1
chr7_2 three_prime_UTR 76357108 76357443 76357108 ID=Msa1077620-mRNA-1:three_prime_utr;Parent=Msa1077620-mRNA-1
Gene Sequence

>Msa1077620

ATGGGAGAGAGTTGGAATCTGCTTGATAGTTCGGGAAATTCTCACACCGTAACTTTCAATGGTGATTATGCACACCCTCTCTTGTCAGAAGGATGGAATAACCTCAGAGAATTTTACAACTATCAGGGTCATAAACAAATCAGTGTTTTTCGGTTAACTATGGGGAGAACATATGCTGGTTCCCATGAATTTCCATCATGTCATAGCCTAAGCACCAAGGAACCGGAGATCACTTTGGATGAACTTGATTTTGCTGAACCGCATCAATTAGTTGAGTGCTTAATCGAGAGTTCAAATAATTCCTTTGGGAATATGACTTTGACCACCTGA
Protein sequence

>Msa1077620

MGESWNLLDSSGNSHTVTFNGDYAHPLLSEGWNNLREFYNYQGHKQISVFRLTMGRTYAGSHEFPSCHSLSTKEPEITLDELDFAEPHQLVECLIESSNNSFGNMTLTT*