AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63772

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 26 sgRNAs with CRISPR-Local

Find 113 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGATTTAGGTTTATTTCAT+TGG 0.286261 3.4:-11130767 MS.gene63772:intron
TCGATGGAGCTTGAGCTTAC+TGG 0.328079 3.4:-11130733 MS.gene63772:CDS
CGGCGAGGGTGGAGGATTGC+TGG 0.330889 3.4:-11132055 MS.gene63772:CDS
TCCGTTGCGGCTGATGAATC+TGG 0.361892 3.4:+11131878 None:intergenic
CGTCAACATTGAACATATTC+CGG 0.385663 3.4:+11131847 None:intergenic
AACTATTCAGAGTTGGTTCA+AGG 0.418221 3.4:-11130109 MS.gene63772:CDS
CGAGGTCGCAACAGTAGATT+CGG 0.464707 3.4:+11131808 None:intergenic
CAGTAGATTCGGTTGTTCTC+CGG 0.469266 3.4:+11131819 None:intergenic
TGCGCTAGCAGCGGCGAGGG+TGG 0.470828 3.4:-11132066 None:intergenic
GCATGCGCTAGCAGCGGCGA+GGG 0.496549 3.4:-11132069 None:intergenic
CATAATTTCGAGCGAAGTCG+TGG 0.516262 3.4:-11130076 MS.gene63772:CDS
GCTAGCAGCGGCGAGGGTGG+AGG 0.519133 3.4:-11132063 None:intergenic
GTTCAATGTTGACGAGAGAC+CGG 0.524464 3.4:-11131838 MS.gene63772:CDS
TGTGCTTAACTATTCAGAGT+TGG 0.553654 3.4:-11130116 MS.gene63772:CDS
ATTGGAGAAGATGCCATCGA+TGG 0.555013 3.4:-11130749 MS.gene63772:CDS
TCCGGTGGTTTCATCCGTTG+CGG 0.563463 3.4:+11131865 None:intergenic
CGACCTCGCTAACGTACCCT+AGG 0.564837 3.4:-11131793 MS.gene63772:intron
TCCAGATTCATCAGCCGCAA+CGG 0.566551 3.4:-11131879 MS.gene63772:CDS
TGCATGCGCTAGCAGCGGCG+AGG 0.570502 3.4:-11132070 None:intergenic
TGGAGGATTGCTGGAGACAA+TGG 0.576512 3.4:-11132046 MS.gene63772:CDS
CTTACTGGATATCAATATGT+TGG 0.596237 3.4:-11130718 MS.gene63772:intron
GTAAGCTCAAGCTCCATCGA+TGG 0.619771 3.4:+11130736 None:intergenic
GCCGCAACGGATGAAACCAC+CGG 0.626069 3.4:-11131866 MS.gene63772:CDS
TGGCACAACCGCAAAAGTGA+AGG 0.628005 3.4:-11132026 MS.gene63772:intron
AAACCTAGGGTACGTTAGCG+AGG 0.629611 3.4:+11131790 None:intergenic
CAACATTGAACATATTCCGG+TGG 0.660528 3.4:+11131850 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATTAAAAAAAATGATAAAA+TGG + chr3.4:11131479-11131498 None:intergenic 10.0%
!!! ATATCATTATCATAAATTTT+AGG - chr3.4:11131646-11131665 MS.gene63772:intron 10.0%
!!! TTATTTTTTTTACATGATTT+AGG - chr3.4:11130384-11130403 MS.gene63772:intron 10.0%
!! AATATATGTTATCATGATTT+AGG - chr3.4:11131299-11131318 MS.gene63772:intron 15.0%
!! AATCATGTAAAAAAAATAAG+AGG + chr3.4:11130383-11130402 None:intergenic 15.0%
!! CAACTAAATAGAAAATTATA+GGG - chr3.4:11131005-11131024 MS.gene63772:intron 15.0%
!! TATCAGAAATAAAATGATAA+TGG + chr3.4:11131208-11131227 None:intergenic 15.0%
!! TCAACTAAATAGAAAATTAT+AGG - chr3.4:11131004-11131023 MS.gene63772:intron 15.0%
!!! ATAATTTTCTATTTAGTTGA+AGG + chr3.4:11131004-11131023 None:intergenic 15.0%
!!! ATCATTTTATCATTTATGTT+AGG - chr3.4:11131536-11131555 MS.gene63772:intron 15.0%
!!! ATCATTTTTTTTAATCAGTT+TGG - chr3.4:11131483-11131502 MS.gene63772:intron 15.0%
!!! TAATTTTCTATTTAGTTGAA+GGG + chr3.4:11131003-11131022 None:intergenic 15.0%
!!! TATTCTATAAGCATATATTT+TGG + chr3.4:11131914-11131933 None:intergenic 15.0%
!!! TCAAATGCATTTTATTTTAA+AGG - chr3.4:11130584-11130603 MS.gene63772:intron 15.0%
!! TGAAAGAAAAAGATACAATT+GGG - chr3.4:11131607-11131626 MS.gene63772:intron 20.0%
!! TTAAATACTTAAAGAAGAAC+AGG + chr3.4:11131430-11131449 None:intergenic 20.0%
!! TTCAAAAAGGTTTGAAAAAT+CGG - chr3.4:11130667-11130686 MS.gene63772:intron 20.0%
!! TTGAAAGAAAAAGATACAAT+TGG - chr3.4:11131606-11131625 MS.gene63772:intron 20.0%
!! TTGATATATTGTTTCAAATG+TGG - chr3.4:11130482-11130501 MS.gene63772:intron 20.0%
!!! AATTTTCTATTTAGTTGAAG+GGG + chr3.4:11131002-11131021 None:intergenic 20.0%
!!! ACATATATCATCTTTTTATC+TGG - chr3.4:11130875-11130894 MS.gene63772:intron 20.0%
!!! ACATTTGAAACAATATATCA+AGG + chr3.4:11130483-11130502 None:intergenic 20.0%
!!! ATGATTTAGGTTTATTTCAT+TGG - chr3.4:11131312-11131331 MS.gene63772:intron 20.0%
!!! CTTAAAATCATTTAATTTCC+TGG + chr3.4:11131060-11131079 None:intergenic 20.0%
!!! TATGTTACCTTTTTATCTTT+TGG + chr3.4:11130860-11130879 None:intergenic 20.0%
!!! TCTTCTTCTATCTTTAATTT+TGG - chr3.4:11130450-11130469 MS.gene63772:intron 20.0%
!!! TGATTTTCCAAAAGATAAAA+AGG - chr3.4:11130850-11130869 MS.gene63772:intron 20.0%
!!! TTTATCTTTTGGAAAATCAA+TGG + chr3.4:11130849-11130868 None:intergenic 20.0%
! AGTATTTAATTCTGATCACT+TGG - chr3.4:11131441-11131460 MS.gene63772:intron 25.0%
! TTATGTTAAGCATATACTAC+TGG - chr3.4:11131168-11131187 MS.gene63772:intron 25.0%
!! ATTTAGGTGATTTTTGCATT+TGG - chr3.4:11130400-11130419 MS.gene63772:intron 25.0%
!!! CTTCTATCTTTAATTTTGGT+TGG - chr3.4:11130454-11130473 MS.gene63772:intron 25.0%
!!! TAGCAGAAGATTTTTCAAAA+AGG - chr3.4:11130654-11130673 MS.gene63772:intron 25.0%
AAACATGTGACAATTCAAGT+TGG + chr3.4:11131032-11131051 None:intergenic 30.0%
CTTACTGGATATCAATATGT+TGG - chr3.4:11131361-11131380 MS.gene63772:intron 30.0%
TATACAAACTCAATACATGC+CGG + chr3.4:11131391-11131410 None:intergenic 30.0%
TGTACTTCAACTTCATATAC+TGG + chr3.4:11131274-11131293 None:intergenic 30.0%
TGTTAACTTCAATTATCCCT+TGG + chr3.4:11131089-11131108 None:intergenic 30.0%
TTCGATTCAATACTCAGTTA+TGG - chr3.4:11130631-11130650 MS.gene63772:intron 30.0%
TTCTCTTGGGATTTAAATCA+CGG + chr3.4:11130544-11130563 None:intergenic 30.0%
TTGATACTCAATAAGAAGCA+TGG + chr3.4:11131848-11131867 None:intergenic 30.0%
TTGTCACATGTTTATAATCC+AGG - chr3.4:11131039-11131058 MS.gene63772:intron 30.0%
! AACATGTGACAATTCAAGTT+GGG + chr3.4:11131031-11131050 None:intergenic 30.0%
! CAATAAGAAGCATGGAATAA+AGG + chr3.4:11131840-11131859 None:intergenic 30.0%
! TCAGATCGTCATATTTTGTA+CGG - chr3.4:11130174-11130193 MS.gene63772:intron 30.0%
! TCATTTTGTCTCATTCTGTT+AGG - chr3.4:11131563-11131582 MS.gene63772:intron 30.0%
! TTCAACTTCATATACTGGTT+TGG + chr3.4:11131269-11131288 None:intergenic 30.0%
! TTGAAATGTGTTGTTCTCTT+GGG + chr3.4:11130557-11130576 None:intergenic 30.0%
! TTTGAAATGTGTTGTTCTCT+TGG + chr3.4:11130558-11130577 None:intergenic 30.0%
!! AACAATAACCTTCACTTTTG+CGG + chr3.4:11130064-11130083 None:intergenic 30.0%
!! TCAACTTCATATACTGGTTT+GGG + chr3.4:11131268-11131287 None:intergenic 30.0%
!! TTTTCTGCATAATTTAGAGC+TGG - chr3.4:11132029-11132048 MS.gene63772:CDS 30.0%
!!! AATGTATTTTTGAGTGAGAG+AGG + chr3.4:11130096-11130115 None:intergenic 30.0%
!!! TTTTGGAGTTATGCTAACTA+AGG + chr3.4:11131897-11131916 None:intergenic 30.0%
AACTTCAATTATCCCTTGGT+TGG + chr3.4:11131085-11131104 None:intergenic 35.0%
AATGATGCACGATTCATCTT+CGG + chr3.4:11130955-11130974 None:intergenic 35.0%
ACGATTCATCTTCGGTTAAA+AGG + chr3.4:11130947-11130966 None:intergenic 35.0%
ACTGGATATCAATATGTTGG+TGG - chr3.4:11131364-11131383 MS.gene63772:intron 35.0%
CGTCAACATTGAACATATTC+CGG + chr3.4:11130235-11130254 None:intergenic 35.0%
CTGGATATCAATATGTTGGT+GGG - chr3.4:11131365-11131384 MS.gene63772:intron 35.0%
TACAATTACTGAGCAAACAG+AGG + chr3.4:11130737-11130756 None:intergenic 35.0%
TGTGCTTAACTATTCAGAGT+TGG - chr3.4:11131963-11131982 MS.gene63772:intron 35.0%
! AACTATTCAGAGTTGGTTCA+AGG - chr3.4:11131970-11131989 MS.gene63772:intron 35.0%
! AGGTGATTTTTGCATTTGGT+TGG - chr3.4:11130404-11130423 MS.gene63772:intron 35.0%
! GGAATAGTTTGTGCAAGATA+TGG + chr3.4:11131246-11131265 None:intergenic 35.0%
! TAAGTGTTTTCTCACCAAGT+GGG - chr3.4:11130918-11130937 MS.gene63772:intron 35.0%
! TTAAGTGTTTTCTCACCAAG+TGG - chr3.4:11130917-11130936 MS.gene63772:intron 35.0%
!! ATGATTTTAAGTGCCAACCA+AGG - chr3.4:11131069-11131088 MS.gene63772:intron 35.0%
!! CAACTTCATATACTGGTTTG+GGG + chr3.4:11131267-11131286 None:intergenic 35.0%
!! TGATTTTAAGTGCCAACCAA+GGG - chr3.4:11131070-11131089 MS.gene63772:intron 35.0%
AGTTCGTGAGATTGATATCG+AGG - chr3.4:11131679-11131698 MS.gene63772:intron 40.0%
ATGAATCGTGCATCATTGCT+TGG - chr3.4:11130958-11130977 MS.gene63772:intron 40.0%
ATTACTGAGCAAACAGAGGA+AGG + chr3.4:11130733-11130752 None:intergenic 40.0%
CAACATTGAACATATTCCGG+TGG + chr3.4:11130232-11130251 None:intergenic 40.0%
CCTAGTATTCCTCAAACCTA+GGG + chr3.4:11130305-11130324 None:intergenic 40.0%
TCCTAGTATTCCTCAAACCT+AGG + chr3.4:11130306-11130325 None:intergenic 40.0%
TGTGATGTTGAACTTGATGC+TGG - chr3.4:11131139-11131158 MS.gene63772:intron 40.0%
! AAGTGTTTTCTCACCAAGTG+GGG - chr3.4:11130919-11130938 MS.gene63772:intron 40.0%
! ATATCAATATGTTGGTGGGC+CGG - chr3.4:11131369-11131388 MS.gene63772:intron 40.0%
! TCACCAACACGAGTTATTTC+AGG - chr3.4:11130778-11130797 MS.gene63772:intron 40.0%
!! CATTGCTTGGTCTTGAAGAA+TGG - chr3.4:11130971-11130990 MS.gene63772:intron 40.0%
!!! TCCGTTACTTTTTCTGTGCA+GGG - chr3.4:11130141-11130160 MS.gene63772:intron 40.0%
ATTGGAGAAGATGCCATCGA+TGG - chr3.4:11131330-11131349 MS.gene63772:intron 45.0%
CATAATTTCGAGCGAAGTCG+TGG - chr3.4:11132003-11132022 MS.gene63772:intron 45.0%
CCCTAGGTTTGAGGAATACT+AGG - chr3.4:11130302-11130321 MS.gene63772:intron 45.0%
CCTCCTGAAATAACTCGTGT+TGG + chr3.4:11130784-11130803 None:intergenic 45.0%
GCCCTGCACAGAAAAAGTAA+CGG + chr3.4:11130145-11130164 None:intergenic 45.0%
GTTCAATGTTGACGAGAGAC+CGG - chr3.4:11130241-11130260 MS.gene63772:intron 45.0%
TGTTGAACTTGATGCTGGCA+TGG - chr3.4:11131144-11131163 MS.gene63772:intron 45.0%
TTGAGTGAGAGAGGAGAGAA+AGG + chr3.4:11130087-11130106 None:intergenic 45.0%
! CAGTAGATTCGGTTGTTCTC+CGG + chr3.4:11130263-11130282 None:intergenic 45.0%
! CCAACACGAGTTATTTCAGG+AGG - chr3.4:11130781-11130800 MS.gene63772:intron 45.0%
!! CTTGGTCTTGAAGAATGGAG+AGG - chr3.4:11130976-11130995 MS.gene63772:intron 45.0%
!!! CTCCGTTACTTTTTCTGTGC+AGG - chr3.4:11130140-11130159 MS.gene63772:intron 45.0%
!!! TAGAGCTGGTTTTCGACATG+TGG - chr3.4:11132043-11132062 MS.gene63772:CDS 45.0%
AAACCTAGGGTACGTTAGCG+AGG + chr3.4:11130292-11130311 None:intergenic 50.0%
AATCGGCCTGAATGTCAACG+CGG - chr3.4:11130684-11130703 MS.gene63772:intron 50.0%
CGAGGTCGCAACAGTAGATT+CGG + chr3.4:11130274-11130293 None:intergenic 50.0%
GCTAACGTACCCTAGGTTTG+AGG - chr3.4:11130293-11130312 MS.gene63772:intron 50.0%
GTAAGCTCAAGCTCCATCGA+TGG + chr3.4:11131346-11131365 None:intergenic 50.0%
TCCAGATTCATCAGCCGCAA+CGG - chr3.4:11130200-11130219 MS.gene63772:intron 50.0%
TCGATGGAGCTTGAGCTTAC+TGG - chr3.4:11131346-11131365 MS.gene63772:intron 50.0%
TGGAGGATTGCTGGAGACAA+TGG - chr3.4:11130033-11130052 MS.gene63772:CDS 50.0%
TGGCACAACCGCAAAAGTGA+AGG - chr3.4:11130053-11130072 MS.gene63772:CDS 50.0%
! GACTAACCGCGTTGACATTC+AGG + chr3.4:11130693-11130712 None:intergenic 50.0%
! TTTTCTGTGCAGGGCAGTGA+GGG - chr3.4:11130150-11130169 MS.gene63772:intron 50.0%
! TTTTTCTGTGCAGGGCAGTG+AGG - chr3.4:11130149-11130168 MS.gene63772:intron 50.0%
CGGTTAAAAGGCTCCCCACT+TGG + chr3.4:11130935-11130954 None:intergenic 55.0%
TCCGGTGGTTTCATCCGTTG+CGG + chr3.4:11130217-11130236 None:intergenic 55.0%
TCCGTTGCGGCTGATGAATC+TGG + chr3.4:11130204-11130223 None:intergenic 55.0%
CGACCTCGCTAACGTACCCT+AGG - chr3.4:11130286-11130305 MS.gene63772:intron 60.0%
GCCGCAACGGATGAAACCAC+CGG - chr3.4:11130213-11130232 MS.gene63772:intron 60.0%
CGGCGAGGGTGGAGGATTGC+TGG - chr3.4:11130024-11130043 MS.gene63772:CDS 70.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 11130021 11132080 11130021 ID=MS.gene63772
chr3.4 mRNA 11130021 11132080 11130021 ID=MS.gene63772.t1;Parent=MS.gene63772
chr3.4 exon 11132027 11132080 11132027 ID=MS.gene63772.t1.exon1;Parent=MS.gene63772.t1
chr3.4 CDS 11132027 11132080 11132027 ID=cds.MS.gene63772.t1;Parent=MS.gene63772.t1
chr3.4 exon 11131794 11131939 11131794 ID=MS.gene63772.t1.exon2;Parent=MS.gene63772.t1
chr3.4 CDS 11131794 11131939 11131794 ID=cds.MS.gene63772.t1;Parent=MS.gene63772.t1
chr3.4 exon 11130719 11130780 11130719 ID=MS.gene63772.t1.exon3;Parent=MS.gene63772.t1
chr3.4 CDS 11130719 11130780 11130719 ID=cds.MS.gene63772.t1;Parent=MS.gene63772.t1
chr3.4 exon 11130021 11130142 11130021 ID=MS.gene63772.t1.exon4;Parent=MS.gene63772.t1
chr3.4 CDS 11130021 11130142 11130021 ID=cds.MS.gene63772.t1;Parent=MS.gene63772.t1
Gene Sequence

>MS.gene63772

CAGCGGCGAGGGTGGAGGATTGCTGGAGACAATGGCACAACCGCAAAAGTGAAGGTTATTGTTCCTTTCTCTCCTCTCTCACTCAAAAATACATTTGATGTTCTTTTTATTTTTAATTTCTCCGTTACTTTTTCTGTGCAGGGCAGTGAGGGATCAGATCGTCATATTTTGTACGGCTGTCCAGATTCATCAGCCGCAACGGATGAAACCACCGGAATATGTTCAATGTTGACGAGAGACCGGAGAACAACCGAATCTACTGTTGCGACCTCGCTAACGTACCCTAGGTTTGAGGAATACTAGGACAAAAATATCTATATTGATGTGTGTAGATCTGTTTTGCTTTCAATTGATTTTTACCTCTTATTTTTTTTACATGATTTAGGTGATTTTTGCATTTGGTTGGTTTTTCTTCAGATGACTTCTTATTCTTCTTCTATCTTTAATTTTGGTTGGTTTCCTTGATATATTGTTTCAAATGTGGCTGCTAAAGTGATTCATGAAACTTGAAAAACTAACACCGTGATTTAAATCCCAAGAGAACAACACATTTCAAATGTAACTCAAATGCATTTTATTTTAAAGGTTTTAATGTTCTTTTTTAGTTTGTTTCGATTCAATACTCAGTTATGGTAGCAGAAGATTTTTCAAAAAGGTTTGAAAAATCGGCCTGAATGTCAACGCGGTTAGTCTGCTTTTGTTGTTCTTTCCTTCCTCTGTTTGCTCAGTAATTGTATAATCAATACTAAGTGTTTACTCACCAACACGAGTTATTTCAGGAGGAGATTTTTGCATCGTCTTTTGTAGTTACTGCGTATTTAAAATCCATTGATTTTCCAAAAGATAAAAAGGTAACATATATCATCTTTTTATCTGGAGTATGATTGAAACAAATATTAAGTGTTTTCTCACCAAGTGGGGAGCCTTTTAACCGAAGATGAATCGTGCATCATTGCTTGGTCTTGAAGAATGGAGAGGCCCCTTCAACTAAATAGAAAATTATAGGGCCCAACTTGAATTGTCACATGTTTATAATCCAGGAAATTAAATGATTTTAAGTGCCAACCAAGGGATAATTGAAGTTAACAATATTTATTTGTAAATTCTCTTATAGTAATTGTGATGTTGAACTTGATGCTGGCATGGTTTATGTTAAGCATATACTACTGGAGAAATACTATAGACCATTATCATTTTATTTCTGATATGCTATTTTCGAGTGCCATATCTTGCACAAACTATTCCCCAAACCAGTATATGAAGTTGAAGTACAGTACTAATATATGTTATCATGATTTAGGTTTATTTCATTGGAGAAGATGCCATCGATGGAGCTTGAGCTTACTGGATATCAATATGTTGGTGGGCCGGCATGTATTGAGTTTGTATATGTAAAAGCTTTACTACCTGTTCTTCTTTAAGTATTTAATTCTGATCACTTGGTAATGTGCAATACCATTTTATCATTTTTTTTAATCAGTTTGGAAAGAAGTTTGAAACATTGCTCATTCTTTGATCATTTTATCATTTATGTTAGGTATTTCATTTTGTCTCATTCTGTTAGGCAAATTCAACATTGTGAAGTTTGAAAGAAAAAGATACAATTGGGTGATCAAAGAAGAATTATATCATTATCATAAATTTTAGGCTTTATGTGAAGTTCGTGAGATTGATATCGAGGTCTGCAAAATTTAATGTAAAGTTTCTAAATCTTTTCTCTTTAAACTTTATGTCAACTATTTCTAAATCTTTGCTCTTTAAACTTTCTGCTTTTCTACTACTTTGTTAGTTTTTTCATCTATTTCTTGCTTCATTTCCTTTATTCCATGCTTCTTATTGAGTATCAACTTATTTTTGTTAAATTATGCATTAGCCTTAGTTAGCATAACTCCAAAATATATGCTTATAGAATATTTGTTTCTTTATTTTCATATTCAGATGTTGTGCTTAACTATTCAGAGTTGGTTCAAGGTAATTTTCAGCATAATTTCGAGCGAAGTCGTGGCAATTTTCTGCATAATTTAGAGCTGGTTTTCGACATGTGGACTAATGTAATGTAG
Protein sequence

>MS.gene63772.t1

QRRGWRIAGDNGTTAKVKGSEGSDRHILYGCPDSSAATDETTGICSMLTRDRRTTESTVATSLTYPRFISLEKMPSMELELTGYQYVDVVLNYSELVQGNFQHNFERSRGNFLHNLELVFDMWTNVM