AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030209

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030209.t1 MTR_4g124360 98.851 87 0 1 1 87 1 86 9.19e-58 174
MS.gene030209.t1 MTR_4g124360 98.851 87 0 1 1 87 39 124 1.02e-57 175
MS.gene030209.t1 MTR_2g044910 54.348 92 25 3 4 87 12 94 5.01e-23 86.7
MS.gene030209.t1 MTR_2g044910 54.945 91 24 3 5 87 56 137 5.58e-23 86.7
MS.gene030209.t1 MTR_2g044910 54.945 91 24 3 5 87 56 137 9.94e-23 87.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGAGAAGAGTTCCATTTGC+AGG 0.345657 8.2:+9224930 MS.gene030209:CDS
CTTCTTCATTTCAGAAGACT+TGG 0.412093 8.2:-9224804 None:intergenic
TGGAGAAGAAGGGGTGGTAC+TGG 0.425231 8.2:-9224855 None:intergenic
GAGTTTCCTTGTGGAGAAGA+AGG 0.454205 8.2:-9224866 None:intergenic
TGATGGAATTCCTGCAGAAA+AGG 0.473301 8.2:+9224668 MS.gene030209:CDS
AGCACCTTGCATCCTGCAAA+TGG 0.473425 8.2:-9224942 None:intergenic
ATGGAACTCTTCTCAGCAGC+AGG 0.483824 8.2:-9224923 None:intergenic
ACTGGAAAAGAGTGAATTGA+AGG 0.506999 8.2:-9224837 None:intergenic
ATGGCAAACTGAGTTGTACC+AGG 0.519158 8.2:-9224618 None:intergenic
AGTTTCCTTGTGGAGAAGAA+GGG 0.523527 8.2:-9224865 None:intergenic
CATTTCAGAAGACTTGGCAT+TGG 0.534645 8.2:-9224798 None:intergenic
CAGCAGGAAAACCAACTGAT+GGG 0.556381 8.2:-9224907 None:intergenic
GCAGCAGGAAAACCAACTGA+TGG 0.557635 8.2:-9224908 None:intergenic
GGTGCATGAGATAATGATGA+TGG 0.567231 8.2:+9224769 MS.gene030209:intron
GGAAGCATGTGTGTATATGA+TGG 0.578130 8.2:+9224651 MS.gene030209:CDS
GGACTAAATGCAATGACCCC+TGG 0.578930 8.2:+9224600 None:intergenic
CATGCTTCCATTGTAGAGGA+TGG 0.585189 8.2:-9224637 None:intergenic
TCTTCTGAAATGAAGAAGAG+TGG 0.591559 8.2:+9224809 MS.gene030209:CDS
CAGTTTGCCATCCTCTACAA+TGG 0.597338 8.2:+9224630 MS.gene030209:CDS
CACACATGCTTCCATTGTAG+AGG 0.599209 8.2:-9224641 None:intergenic
GTTTCCTTGTGGAGAAGAAG+GGG 0.603228 8.2:-9224864 None:intergenic
AGCAGGAAAACCAACTGATG+GGG 0.615564 8.2:-9224906 None:intergenic
GCAGGAAAACCAACTGATGG+GGG 0.646756 8.2:-9224905 None:intergenic
AAATTGTCAGAGTTTCCTTG+TGG 0.648404 8.2:-9224875 None:intergenic
CTGGAAAAGAGTGAATTGAA+GGG 0.649560 8.2:-9224836 None:intergenic
TCCTTGTGGAGAAGAAGGGG+TGG 0.661903 8.2:-9224861 None:intergenic
TGGCAAACTGAGTTGTACCA+GGG 0.668253 8.2:-9224617 None:intergenic
ACCACCCCTTCTTCTCCACA+AGG 0.677252 8.2:+9224860 MS.gene030209:CDS
GGCAAACTGAGTTGTACCAG+GGG 0.692504 8.2:-9224616 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCTTTGCTTGTTAACAATTT+AGG + chr8.2:9224748-9224767 MS.gene030209:intron 25.0%
AAAGTAAACTAGTGAAGTGC+TGG - chr8.2:9224722-9224741 None:intergenic 35.0%
AAATTGTCAGAGTTTCCTTG+TGG - chr8.2:9224878-9224897 None:intergenic 35.0%
ACTGGAAAAGAGTGAATTGA+AGG - chr8.2:9224840-9224859 None:intergenic 35.0%
CTGGAAAAGAGTGAATTGAA+GGG - chr8.2:9224839-9224858 None:intergenic 35.0%
CTTCTTCATTTCAGAAGACT+TGG - chr8.2:9224807-9224826 None:intergenic 35.0%
!! TCTTCTGAAATGAAGAAGAG+TGG + chr8.2:9224809-9224828 MS.gene030209:CDS 35.0%
AGTTTCCTTGTGGAGAAGAA+GGG - chr8.2:9224868-9224887 None:intergenic 40.0%
CATTTCAGAAGACTTGGCAT+TGG - chr8.2:9224801-9224820 None:intergenic 40.0%
GGTGCATGAGATAATGATGA+TGG + chr8.2:9224769-9224788 MS.gene030209:intron 40.0%
TGATGGAATTCCTGCAGAAA+AGG + chr8.2:9224668-9224687 MS.gene030209:CDS 40.0%
! GGAAGCATGTGTGTATATGA+TGG + chr8.2:9224651-9224670 MS.gene030209:CDS 40.0%
! GTAGTGTTTACCTTTTCTGC+AGG - chr8.2:9224681-9224700 None:intergenic 40.0%
AGCAGGAAAACCAACTGATG+GGG - chr8.2:9224909-9224928 None:intergenic 45.0%
ATGGCAAACTGAGTTGTACC+AGG - chr8.2:9224621-9224640 None:intergenic 45.0%
CACACATGCTTCCATTGTAG+AGG - chr8.2:9224644-9224663 None:intergenic 45.0%
CAGCAGGAAAACCAACTGAT+GGG - chr8.2:9224910-9224929 None:intergenic 45.0%
CAGTTTGCCATCCTCTACAA+TGG + chr8.2:9224630-9224649 MS.gene030209:CDS 45.0%
CATGCTTCCATTGTAGAGGA+TGG - chr8.2:9224640-9224659 None:intergenic 45.0%
CTGAGAAGAGTTCCATTTGC+AGG + chr8.2:9224930-9224949 MS.gene030209:CDS 45.0%
GAGTTTCCTTGTGGAGAAGA+AGG - chr8.2:9224869-9224888 None:intergenic 45.0%
GTTTCCTTGTGGAGAAGAAG+GGG - chr8.2:9224867-9224886 None:intergenic 45.0%
TGGCAAACTGAGTTGTACCA+GGG - chr8.2:9224620-9224639 None:intergenic 45.0%
AAACCAACTGATGGGGGAGA+AGG - chr8.2:9224902-9224921 None:intergenic 50.0%
ATGGAACTCTTCTCAGCAGC+AGG - chr8.2:9224926-9224945 None:intergenic 50.0%
GCAGCAGGAAAACCAACTGA+TGG - chr8.2:9224911-9224930 None:intergenic 50.0%
GCAGGAAAACCAACTGATGG+GGG - chr8.2:9224908-9224927 None:intergenic 50.0%
GGCAAACTGAGTTGTACCAG+GGG - chr8.2:9224619-9224638 None:intergenic 50.0%
ACCACCCCTTCTTCTCCACA+AGG + chr8.2:9224860-9224879 MS.gene030209:CDS 55.0%
TCCTTGTGGAGAAGAAGGGG+TGG - chr8.2:9224864-9224883 None:intergenic 55.0%
TGGAGAAGAAGGGGTGGTAC+TGG - chr8.2:9224858-9224877 None:intergenic 55.0%
TTGCCTTCTCCCCCATCAGT+TGG + chr8.2:9224896-9224915 MS.gene030209:CDS 55.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 9224612 9224954 9224612 ID=MS.gene030209
chr8.2 mRNA 9224612 9224954 9224612 ID=MS.gene030209.t1;Parent=MS.gene030209
chr8.2 exon 9224612 9224689 9224612 ID=MS.gene030209.t1.exon1;Parent=MS.gene030209.t1
chr8.2 CDS 9224612 9224689 9224612 ID=cds.MS.gene030209.t1;Parent=MS.gene030209.t1
chr8.2 exon 9224770 9224954 9224770 ID=MS.gene030209.t1.exon2;Parent=MS.gene030209.t1
chr8.2 CDS 9224770 9224954 9224770 ID=cds.MS.gene030209.t1;Parent=MS.gene030209.t1
Gene Sequence

>MS.gene030209

ATGACCCCTGGTACAACTCAGTTTGCCATCCTCTACAATGGAAGCATGTGTGTATATGATGGAATTCCTGCAGAAAAGGTAAACACTACTTGTTGAAAGATGATATTCCAGCACTTCACTAGTTTACTTTATTAATTCTTTGCTTGTTAACAATTTAGGTGCATGAGATAATGATGATGGCTTCTGCCAATGCCAAGTCTTCTGAAATGAAGAAGAGTGGAATTCCCTTCAATTCACTCTTTTCCAGTACCACCCCTTCTTCTCCACAAGGAAACTCTGACAATTTGCCTTCTCCCCCATCAGTTGGTTTTCCTGCTGCTGAGAAGAGTTCCATTTGCAGGAT
Protein sequence

>MS.gene030209.t1

MTPGTTQFAILYNGSMCVYDGIPAEKVHEIMMMASANAKSSEMKKSGIPFNSLFSSTTPSSPQGNSDNLPSPPSVGFPAAEKSSICR