AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66944

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66944.t1 MTR_3g070120 31.646 158 94 4 28 174 146 300 4.28e-13 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGATGTTTGCTTCTTTA+AGG 0.138534 6.1:-11966553 None:intergenic
CTTAGATTTCAAATCCAATT+TGG 0.142363 6.1:+11966629 MS.gene66944:CDS
TTTACCTTTCTCACAAGATT+TGG 0.226819 6.1:+11966838 MS.gene66944:CDS
GAAGAGGGTTTCTCTTGTTT+TGG 0.245975 6.1:-11966528 None:intergenic
GGAGCGTGCACGGTTAATTA+AGG 0.290096 6.1:+11966947 MS.gene66944:CDS
TCAAGAGCCGGAATTGGATT+TGG 0.301896 6.1:+11966926 MS.gene66944:CDS
TTACCTTTCTCACAAGATTT+GGG 0.302378 6.1:+11966839 MS.gene66944:CDS
TTTGGGGACAAGAGTTGATT+GGG 0.351467 6.1:+11966856 MS.gene66944:CDS
GGCAGCTTAGAAAGAGGATA+TGG 0.353135 6.1:+11966727 MS.gene66944:CDS
TTAGATTTCAAATCCAATTT+GGG 0.355655 6.1:+11966630 MS.gene66944:CDS
GAAAGTTCAAGAGCCGGAAT+TGG 0.391991 6.1:+11966920 MS.gene66944:CDS
ATTTGGGGACAAGAGTTGAT+TGG 0.406484 6.1:+11966855 MS.gene66944:CDS
ACAAGAGTTGATTGGGGAAT+CGG 0.415419 6.1:+11966863 MS.gene66944:CDS
GCACGCTCCAAATCCAATTC+CGG 0.440433 6.1:-11966933 None:intergenic
GTCCCCAAATCTTGTGAGAA+AGG 0.458776 6.1:-11966842 None:intergenic
TCAAGATCATTATAGAATCT+AGG 0.460182 6.1:-11966804 None:intergenic
CTAAGAAGCCATTGAGAATG+AGG 0.476463 6.1:-11966611 None:intergenic
ATCCTCTTTCTAAGCTGCCC+TGG 0.495595 6.1:-11966723 None:intergenic
ATATGAGAACATGAAGAAAG+AGG 0.508111 6.1:+11966764 MS.gene66944:CDS
CTTTCTAAGCTGCCCTGGTG+TGG 0.513545 6.1:-11966718 None:intergenic
GTCATTTCTAAGTTATTGCA+AGG 0.515777 6.1:+11966981 MS.gene66944:CDS
ATTCTATAATGATCTTGAGC+AGG 0.520209 6.1:+11966809 MS.gene66944:CDS
GACGAAATCCTCATTCTCAA+TGG 0.536241 6.1:+11966603 MS.gene66944:CDS
GGATAGAGTTGGATGAAATG+TGG 0.536445 6.1:+11966889 MS.gene66944:CDS
AATTGGATTTGGAGCGTGCA+CGG 0.556576 6.1:+11966937 MS.gene66944:CDS
GGAATTGAAAGTTCAAGAGC+CGG 0.565005 6.1:+11966914 MS.gene66944:CDS
CTTACTGTGAAAACCACACC+AGG 0.566823 6.1:+11966705 MS.gene66944:CDS
TGCTTCTTTAAGGAAGAAGA+GGG 0.572401 6.1:-11966543 None:intergenic
CACCAGGGCAGCTTAGAAAG+AGG 0.573849 6.1:+11966721 MS.gene66944:CDS
TACCTTTCTCACAAGATTTG+GGG 0.576919 6.1:+11966840 MS.gene66944:CDS
TTGGGGACAAGAGTTGATTG+GGG 0.578511 6.1:+11966857 MS.gene66944:CDS
TTGCTTCTTTAAGGAAGAAG+AGG 0.590446 6.1:-11966544 None:intergenic
AGAGTTGGATGAAATGTGGA+AGG 0.591400 6.1:+11966893 MS.gene66944:CDS
GGAATCGGATCGGATAGAGT+TGG 0.604264 6.1:+11966878 MS.gene66944:CDS
GATTTCGTCATCGAAAGTGA+AGG 0.605806 6.1:-11966589 None:intergenic
AGTTGATTGGGGAATCGGAT+CGG 0.606498 6.1:+11966868 MS.gene66944:CDS
AGATCATTATAGAATCTAGG+AGG 0.675424 6.1:-11966801 None:intergenic
TTACTGTGAAAACCACACCA+GGG 0.799910 6.1:+11966706 MS.gene66944:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGATTTCAAATCCAATTT+GGG + chr6.1:11966630-11966649 MS.gene66944:CDS 20.0%
! CTTAGATTTCAAATCCAATT+TGG + chr6.1:11966629-11966648 MS.gene66944:CDS 25.0%
! TCAAGATCATTATAGAATCT+AGG - chr6.1:11966807-11966826 None:intergenic 25.0%
!!! TTTCTCTTGTTTTGGATTTT+GGG - chr6.1:11966523-11966542 None:intergenic 25.0%
AGATCATTATAGAATCTAGG+AGG - chr6.1:11966804-11966823 None:intergenic 30.0%
ATATGAGAACATGAAGAAAG+AGG + chr6.1:11966764-11966783 MS.gene66944:CDS 30.0%
ATTCTATAATGATCTTGAGC+AGG + chr6.1:11966809-11966828 MS.gene66944:CDS 30.0%
GTCATTTCTAAGTTATTGCA+AGG + chr6.1:11966981-11967000 MS.gene66944:CDS 30.0%
GTTTGATGTTTGCTTCTTTA+AGG - chr6.1:11966556-11966575 None:intergenic 30.0%
TTACCTTTCTCACAAGATTT+GGG + chr6.1:11966839-11966858 MS.gene66944:CDS 30.0%
TTTACCTTTCTCACAAGATT+TGG + chr6.1:11966838-11966857 MS.gene66944:CDS 30.0%
! AGAATCTAGGAGGAAATTTT+TGG - chr6.1:11966794-11966813 None:intergenic 30.0%
!!! GTTTCTCTTGTTTTGGATTT+TGG - chr6.1:11966524-11966543 None:intergenic 30.0%
TACCTTTCTCACAAGATTTG+GGG + chr6.1:11966840-11966859 MS.gene66944:CDS 35.0%
! TGCTTCTTTAAGGAAGAAGA+GGG - chr6.1:11966546-11966565 None:intergenic 35.0%
! TTGCTTCTTTAAGGAAGAAG+AGG - chr6.1:11966547-11966566 None:intergenic 35.0%
!! CATTGCATTTTGACCCAAAT+TGG - chr6.1:11966646-11966665 None:intergenic 35.0%
AGAGTTGGATGAAATGTGGA+AGG + chr6.1:11966893-11966912 MS.gene66944:CDS 40.0%
CTAAGAAGCCATTGAGAATG+AGG - chr6.1:11966614-11966633 None:intergenic 40.0%
GACGAAATCCTCATTCTCAA+TGG + chr6.1:11966603-11966622 MS.gene66944:CDS 40.0%
GATTTCGTCATCGAAAGTGA+AGG - chr6.1:11966592-11966611 None:intergenic 40.0%
GGAATTGAAAGTTCAAGAGC+CGG + chr6.1:11966914-11966933 MS.gene66944:CDS 40.0%
GGATAGAGTTGGATGAAATG+TGG + chr6.1:11966889-11966908 MS.gene66944:CDS 40.0%
TTACTGTGAAAACCACACCA+GGG + chr6.1:11966706-11966725 MS.gene66944:CDS 40.0%
! ACAAGAGTTGATTGGGGAAT+CGG + chr6.1:11966863-11966882 MS.gene66944:CDS 40.0%
! ATTTGGGGACAAGAGTTGAT+TGG + chr6.1:11966855-11966874 MS.gene66944:CDS 40.0%
! TTTGGGGACAAGAGTTGATT+GGG + chr6.1:11966856-11966875 MS.gene66944:CDS 40.0%
!! GAAGAGGGTTTCTCTTGTTT+TGG - chr6.1:11966531-11966550 None:intergenic 40.0%
AGTTGATTGGGGAATCGGAT+CGG + chr6.1:11966868-11966887 MS.gene66944:CDS 45.0%
CTTACTGTGAAAACCACACC+AGG + chr6.1:11966705-11966724 MS.gene66944:CDS 45.0%
GAAAGTTCAAGAGCCGGAAT+TGG + chr6.1:11966920-11966939 MS.gene66944:CDS 45.0%
GGCAGCTTAGAAAGAGGATA+TGG + chr6.1:11966727-11966746 MS.gene66944:CDS 45.0%
GTCCCCAAATCTTGTGAGAA+AGG - chr6.1:11966845-11966864 None:intergenic 45.0%
TCAAGAGCCGGAATTGGATT+TGG + chr6.1:11966926-11966945 MS.gene66944:CDS 45.0%
! AATTGGATTTGGAGCGTGCA+CGG + chr6.1:11966937-11966956 MS.gene66944:CDS 45.0%
! TTGGGGACAAGAGTTGATTG+GGG + chr6.1:11966857-11966876 MS.gene66944:CDS 45.0%
ATCCTCTTTCTAAGCTGCCC+TGG - chr6.1:11966726-11966745 None:intergenic 50.0%
GCACGCTCCAAATCCAATTC+CGG - chr6.1:11966936-11966955 None:intergenic 50.0%
GGAATCGGATCGGATAGAGT+TGG + chr6.1:11966878-11966897 MS.gene66944:CDS 50.0%
GGAGCGTGCACGGTTAATTA+AGG + chr6.1:11966947-11966966 MS.gene66944:CDS 50.0%
CACCAGGGCAGCTTAGAAAG+AGG + chr6.1:11966721-11966740 MS.gene66944:CDS 55.0%
CTTTCTAAGCTGCCCTGGTG+TGG - chr6.1:11966721-11966740 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 11966489 11967019 11966489 ID=MS.gene66944
chr6.1 mRNA 11966489 11967019 11966489 ID=MS.gene66944.t1;Parent=MS.gene66944
chr6.1 exon 11966489 11967019 11966489 ID=MS.gene66944.t1.exon1;Parent=MS.gene66944.t1
chr6.1 CDS 11966489 11967019 11966489 ID=cds.MS.gene66944.t1;Parent=MS.gene66944.t1
Gene Sequence

>MS.gene66944

ATGGCAAAGAAATCAAGTTGTTCTTCTTCATCCCAAAATCCAAAACAAGAGAAACCCTCTTCTTCCTTAAAGAAGCAAACATCAAACTCACGTAAGAAAACCTTCACTTTCGATGACGAAATCCTCATTCTCAATGGCTTCTTAGATTTCAAATCCAATTTGGGTCAAAATGCAATGACAGATTACACACTTTTTTATAACTCTGTGAAAGATTTGCTTACTGTGAAAACCACACCAGGGCAGCTTAGAAAGAGGATATGGAAGTTAAAACAAAAATATGAGAACATGAAGAAAGAGGAAAACCAAAAATTTCCTCCTAGATTCTATAATGATCTTGAGCAGGAAATAATTTACCTTTCTCACAAGATTTGGGGACAAGAGTTGATTGGGGAATCGGATCGGATAGAGTTGGATGAAATGTGGAAGGAATTGAAAGTTCAAGAGCCGGAATTGGATTTGGAGCGTGCACGGTTAATTAAGGACTCGATTGACGTCATTTCTAAGTTATTGCAAGGATCATCTTCGTCTTAG
Protein sequence

>MS.gene66944.t1

MAKKSSCSSSSQNPKQEKPSSSLKKQTSNSRKKTFTFDDEILILNGFLDFKSNLGQNAMTDYTLFYNSVKDLLTVKTTPGQLRKRIWKLKQKYENMKKEENQKFPPRFYNDLEQEIIYLSHKIWGQELIGESDRIELDEMWKELKVQEPELDLERARLIKDSIDVISKLLQGSSSS