AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66907

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66907.t1 MTR_0019s0170 51.316 76 37 0 1 76 177 252 3.46e-22 89.4
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 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCATATACTAGCTATGTT+AGG 0.273702 2.3:+37056615 MS.gene66907:CDS
CCCAGGTAAAAGTAAGTCTT+TGG 0.288403 2.3:-37056786 None:intergenic
AAGTAAGTCTTTGGCAATTC+GGG 0.309359 2.3:-37056777 None:intergenic
GCTTGTTCGGCAGGGTCTTC+AGG 0.315875 2.3:-37056707 None:intergenic
CCTGGGAAACATTTCATTCC+CGG 0.348099 2.3:+37056803 MS.gene66907:CDS
AAAGTAAGTCTTTGGCAATT+CGG 0.353021 2.3:-37056778 None:intergenic
TTCATATACTAGCTATGTTA+GGG 0.381409 2.3:+37056616 MS.gene66907:CDS
TTCACCTAAGTAAGTGCTTA+TGG 0.381800 2.3:-37056666 None:intergenic
CTTCAGGTGGGTCAAGCTCA+AGG 0.406380 2.3:-37056691 None:intergenic
GAACAAGCACTTTGTGAGTA+TGG 0.412435 2.3:+37056722 MS.gene66907:CDS
TCACAAAGTGCTTGTTCGGC+AGG 0.438345 2.3:-37056716 None:intergenic
GGCAATTCGGGAAAAGCTAT+AGG 0.439073 2.3:-37056765 None:intergenic
ATACTCACAAAGTGCTTGTT+CGG 0.450276 2.3:-37056720 None:intergenic
TTCAGGTGGGTCAAGCTCAA+GGG 0.470360 2.3:-37056690 None:intergenic
AGTTCAAAGAGCTCAAGCAC+AGG 0.508319 2.3:+37057330 MS.gene66907:CDS
GGCATCTCGGTCAAATCGTA+CGG 0.511109 2.3:-37056645 None:intergenic
GCAGAGAGACCTTCATATGA+TGG 0.526429 2.3:+37057354 MS.gene66907:CDS
GTTCGGCAGGGTCTTCAGGT+GGG 0.529765 2.3:-37056703 None:intergenic
CCGGGAATGAAATGTTTCCC+AGG 0.533595 2.3:-37056803 None:intergenic
TGTTCGGCAGGGTCTTCAGG+TGG 0.535295 2.3:-37056704 None:intergenic
CACAAAGTGCTTGTTCGGCA+GGG 0.556045 2.3:-37056715 None:intergenic
TCAGGTGGGTCAAGCTCAAG+GGG 0.558431 2.3:-37056689 None:intergenic
CTGTTTGGTCCATCATATGA+AGG 0.567520 2.3:-37057363 None:intergenic
GATGCCATAAGCACTTACTT+AGG 0.572042 2.3:+37056662 MS.gene66907:CDS
GCATCTCGGTCAAATCGTAC+GGG 0.594715 2.3:-37056644 None:intergenic
AGTAAGTGCTTATGGCATCT+CGG 0.596492 2.3:-37056658 None:intergenic
TCATATACTAGCTATGTTAG+GGG 0.619131 2.3:+37056617 MS.gene66907:CDS
GCAAAGAGGACAAAACAGCT+AGG 0.621709 2.3:+37056834 MS.gene66907:CDS
TCCCGGAAAGAAAAGCAAAG+AGG 0.672041 2.3:+37056820 MS.gene66907:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGATTTTACATCTTTTC+AGG + chr2.3:37057279-37057298 MS.gene66907:intron 20.0%
! CAACATTATGTACCAAAAAT+TGG - chr2.3:37056895-37056914 None:intergenic 25.0%
! TTCATATACTAGCTATGTTA+GGG + chr2.3:37056616-37056635 MS.gene66907:CDS 25.0%
! TTTCATATACTAGCTATGTT+AGG + chr2.3:37056615-37056634 MS.gene66907:CDS 25.0%
!! TGGCATTATTTTCCAATTTT+TGG + chr2.3:37056880-37056899 MS.gene66907:intron 25.0%
AAAGTAAGTCTTTGGCAATT+CGG - chr2.3:37056781-37056800 None:intergenic 30.0%
AACAGAAAAGCTAAAAGGAA+CGG + chr2.3:37057129-37057148 MS.gene66907:intron 30.0%
TCATATACTAGCTATGTTAG+GGG + chr2.3:37056617-37056636 MS.gene66907:CDS 30.0%
!! TACATCTTTTCAGGCATATA+TGG + chr2.3:37057288-37057307 MS.gene66907:intron 30.0%
AAGTAAGTCTTTGGCAATTC+GGG - chr2.3:37056780-37056799 None:intergenic 35.0%
ACATTGAAATCCATGCACAA+AGG + chr2.3:37057164-37057183 MS.gene66907:intron 35.0%
ATAATGCGACATGCTTCATT+TGG - chr2.3:37057018-37057037 None:intergenic 35.0%
CCTAGAACAGAAAAGCTAAA+AGG + chr2.3:37057124-37057143 MS.gene66907:intron 35.0%
GTTTAAAGACTTGCAACTTG+AGG + chr2.3:37056856-37056875 MS.gene66907:intron 35.0%
TCGCATTATGTGGTTTCATA+GGG + chr2.3:37057029-37057048 MS.gene66907:intron 35.0%
TTCACCTAAGTAAGTGCTTA+TGG - chr2.3:37056669-37056688 None:intergenic 35.0%
! ATACTCACAAAGTGCTTGTT+CGG - chr2.3:37056723-37056742 None:intergenic 35.0%
!! CCAAAGACTTACTTTTACCT+GGG + chr2.3:37056786-37056805 MS.gene66907:CDS 35.0%
!!! CCTTTTAGCTTTTCTGTTCT+AGG - chr2.3:37057127-37057146 None:intergenic 35.0%
AATGCTCCAGAGTAAAGGAA+GGG - chr2.3:37056954-37056973 None:intergenic 40.0%
AGTAAGTGCTTATGGCATCT+CGG - chr2.3:37056661-37056680 None:intergenic 40.0%
ATAACCAAGCTATCCTTTCC+TGG + chr2.3:37057055-37057074 MS.gene66907:intron 40.0%
ATCCTTTCCTGGTCTACTTA+TGG + chr2.3:37057066-37057085 MS.gene66907:intron 40.0%
ATGAAGCATGTCGCATTATG+TGG + chr2.3:37057019-37057038 MS.gene66907:intron 40.0%
CCCAGGTAAAAGTAAGTCTT+TGG - chr2.3:37056789-37056808 None:intergenic 40.0%
GAACAAGCACTTTGTGAGTA+TGG + chr2.3:37056722-37056741 MS.gene66907:CDS 40.0%
GATGCCATAAGCACTTACTT+AGG + chr2.3:37056662-37056681 MS.gene66907:CDS 40.0%
GTCGCATTATGTGGTTTCAT+AGG + chr2.3:37057028-37057047 MS.gene66907:intron 40.0%
TCCTTTCCTGGTCTACTTAT+GGG + chr2.3:37057067-37057086 MS.gene66907:intron 40.0%
TTCACAATGCTCCAGAGTAA+AGG - chr2.3:37056959-37056978 None:intergenic 40.0%
!! GCCAAAGACTTACTTTTACC+TGG + chr2.3:37056785-37056804 MS.gene66907:CDS 40.0%
!! GTCCTCTTTGCTTTTCTTTC+CGG - chr2.3:37056825-37056844 None:intergenic 40.0%
!! TCCTCTTTGCTTTTCTTTCC+GGG - chr2.3:37056824-37056843 None:intergenic 40.0%
!! TTACTCTGGAGCATTGTGAA+AGG + chr2.3:37056959-37056978 MS.gene66907:intron 40.0%
AAAGACTTGCAACTTGAGGC+TGG + chr2.3:37056860-37056879 MS.gene66907:intron 45.0%
ACCCATAAGTAGACCAGGAA+AGG - chr2.3:37057071-37057090 None:intergenic 45.0%
AGTAGACCCATAAGTAGACC+AGG - chr2.3:37057076-37057095 None:intergenic 45.0%
AGTTCAAAGAGCTCAAGCAC+AGG + chr2.3:37057330-37057349 MS.gene66907:CDS 45.0%
ATCCATGCACAAAGGTTAGC+TGG + chr2.3:37057172-37057191 MS.gene66907:intron 45.0%
ATGGGTCTACTGAAAGACCA+AGG + chr2.3:37057085-37057104 MS.gene66907:intron 45.0%
CAATGCTCCAGAGTAAAGGA+AGG - chr2.3:37056955-37056974 None:intergenic 45.0%
CCTGGGAAACATTTCATTCC+CGG + chr2.3:37056803-37056822 MS.gene66907:CDS 45.0%
GCAAAGAGGACAAAACAGCT+AGG + chr2.3:37056834-37056853 MS.gene66907:CDS 45.0%
GGCAATTCGGGAAAAGCTAT+AGG - chr2.3:37056768-37056787 None:intergenic 45.0%
GTGGTGGTAACATGACTTCT+AGG - chr2.3:37056920-37056939 None:intergenic 45.0%
TAGACCAGGAAAGGATAGCT+TGG - chr2.3:37057062-37057081 None:intergenic 45.0%
TCCCGGAAAGAAAAGCAAAG+AGG + chr2.3:37056820-37056839 MS.gene66907:CDS 45.0%
! TCAAAAGAAGCATGCTGCTG+TGG - chr2.3:37057265-37057284 None:intergenic 45.0%
!! AGCTTTTCTGTTCTAGGCTC+AGG - chr2.3:37057121-37057140 None:intergenic 45.0%
AGTAAAGGAAGGGCAGCCAT+GGG - chr2.3:37056944-37056963 None:intergenic 50.0%
CCGGGAATGAAATGTTTCCC+AGG - chr2.3:37056806-37056825 None:intergenic 50.0%
GCATCTCGGTCAAATCGTAC+GGG - chr2.3:37056647-37056666 None:intergenic 50.0%
GCTCAGGTATGATGACTCCT+TGG - chr2.3:37057105-37057124 None:intergenic 50.0%
GGCATCTCGGTCAAATCGTA+CGG - chr2.3:37056648-37056667 None:intergenic 50.0%
GTACATCATGTGGCATCTGC+TGG - chr2.3:37057243-37057262 None:intergenic 50.0%
GTCCAGCTAACCTTTGTGCA+TGG - chr2.3:37057177-37057196 None:intergenic 50.0%
TCATGTTACCACCACTCCCA+TGG + chr2.3:37056925-37056944 MS.gene66907:intron 50.0%
TGCTGCTGTGGTACATCATG+TGG - chr2.3:37057253-37057272 None:intergenic 50.0%
TTCAGGTGGGTCAAGCTCAA+GGG - chr2.3:37056693-37056712 None:intergenic 50.0%
! CACAAAGTGCTTGTTCGGCA+GGG - chr2.3:37056718-37056737 None:intergenic 50.0%
! TCACAAAGTGCTTGTTCGGC+AGG - chr2.3:37056719-37056738 None:intergenic 50.0%
CTTCAGGTGGGTCAAGCTCA+AGG - chr2.3:37056694-37056713 None:intergenic 55.0%
GAGTAAAGGAAGGGCAGCCA+TGG - chr2.3:37056945-37056964 None:intergenic 55.0%
TCAGGTGGGTCAAGCTCAAG+GGG - chr2.3:37056692-37056711 None:intergenic 55.0%
TGGCATCTGCTGGTCATGCT+CGG - chr2.3:37057233-37057252 None:intergenic 55.0%
TGGCTCAGTCTCAGGCTCAT+GGG - chr2.3:37057206-37057225 None:intergenic 55.0%
TGGCTGCCCTTCCTTTACTC+TGG + chr2.3:37056945-37056964 MS.gene66907:intron 55.0%
CTGGCTCAGTCTCAGGCTCA+TGG - chr2.3:37057207-37057226 None:intergenic 60.0%
GCTTGTTCGGCAGGGTCTTC+AGG - chr2.3:37056710-37056729 None:intergenic 60.0%
GGCATCTGCTGGTCATGCTC+GGG - chr2.3:37057232-37057251 None:intergenic 60.0%
GGCTCAGTCTCAGGCTCATG+GGG - chr2.3:37057205-37057224 None:intergenic 60.0%
GTTCGGCAGGGTCTTCAGGT+GGG - chr2.3:37056706-37056725 None:intergenic 60.0%
TGTTCGGCAGGGTCTTCAGG+TGG - chr2.3:37056707-37056726 None:intergenic 60.0%
AAGGGCAGCCATGGGAGTGG+TGG - chr2.3:37056936-37056955 None:intergenic 65.0%
AGGAAGGGCAGCCATGGGAG+TGG - chr2.3:37056939-37056958 None:intergenic 65.0%
TGCTGGTCATGCTCGGGCTC+TGG - chr2.3:37057226-37057245 None:intergenic 65.0%
! TCGGGCTCTGGCTCAGTCTC+AGG - chr2.3:37057214-37057233 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 37056602 37057373 37056602 ID=MS.gene66907
chr2.3 mRNA 37056602 37057373 37056602 ID=MS.gene66907.t1;Parent=MS.gene66907
chr2.3 exon 37056602 37056855 37056602 ID=MS.gene66907.t1.exon1;Parent=MS.gene66907.t1
chr2.3 CDS 37056602 37056855 37056602 ID=cds.MS.gene66907.t1;Parent=MS.gene66907.t1
chr2.3 exon 37057301 37057373 37057301 ID=MS.gene66907.t1.exon2;Parent=MS.gene66907.t1
chr2.3 CDS 37057301 37057373 37057301 ID=cds.MS.gene66907.t1;Parent=MS.gene66907.t1
Gene Sequence

>MS.gene66907

ATGGATGCTAGGTTTTCATATACTAGCTATGTTAGGGGTGTTCCCGTACGATTTGACCGAGATGCCATAAGCACTTACTTAGGTGAACCCCTTGAGCTTGACCCACCTGAAGACCCTGCCGAACAAGCACTTTGTGAGTATGGTCAGATGTTAAAAGACTATACCTATAGCTTTTCCCGAATTGCCAAAGACTTACTTTTACCTGGGAAACATTTCATTCCCGGAAAGAAAAGCAAAGAGGACAAAACAGCTAGGTTTAAAGACTTGCAACTTGAGGCTGGCATTATTTTCCAATTTTTGGTACATAATGTTGTTCCTAGAAGTCATGTTACCACCACTCCCATGGCTGCCCTTCCTTTACTCTGGAGCATTGTGAAAGGAAAACAAGTCGACATAGCACGAGTAATTTCAGACCAAATGAAGCATGTCGCATTATGTGGTTTCATAGGGAAAATAACCAAGCTATCCTTTCCTGGTCTACTTATGGGTCTACTGAAAGACCAAGGAGTCATCATACCTGAGCCTAGAACAGAAAAGCTAAAAGGAACGGTTGATGATCGATACATTGAAATCCATGCACAAAGGTTAGCTGGACTTATACCCCATGAGCCTGAGACTGAGCCAGAGCCCGAGCATGACCAGCAGATGCCACATGATGTACCACAGCAGCATGCTTCTTTTGATTTTACATCTTTTCAGGCATATATGGCTCAGTATGAGCAGCGAGCAGTTCAAAGAGCTCAAGCACAGGAGCAGAGAGACCTTCATATGA
Protein sequence

>MS.gene66907.t1

MDARFSYTSYVRGVPVRFDRDAISTYLGEPLELDPPEDPAEQALCEYGQMLKDYTYSFSRIAKDLLLPGKHFIPGKKSKEDKTARHIWLSMSSEQFKELKHRSRETFI