AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65312

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65312.t1 MTR_5g023900 74.408 211 24 3 1 201 1 191 5.48e-104 297
MS.gene65312.t1 MTR_5g023880 71.144 201 29 4 1 201 1 172 1.81e-92 268
MS.gene65312.t1 MTR_5g023870 55.975 159 30 4 1 159 1 119 2.06e-49 157
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 67 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTAGTTGGGTTGGTTTCTT+TGG 0.162115 5.2:-14832680 None:intergenic
TTCTCGGAAGGGTTAGGTTT+AGG 0.237072 5.2:-14832601 None:intergenic
AACCGCTCTCGAAGTCTTAA+TGG 0.238654 5.2:+14832744 MS.gene65312:CDS
CCTTCAAAGTTCTTTAAGTA+TGG 0.240152 5.2:+14832702 MS.gene65312:CDS
TGTTTGCATCTATAACAATT+TGG 0.250606 5.2:-14832886 None:intergenic
GTAGTTGGGTTGGTTTCTTT+GGG 0.266039 5.2:-14832679 None:intergenic
TCTCGGAAGGGTTAGGTTTA+GGG 0.267292 5.2:-14832600 None:intergenic
AATGGTTTGTCAGCAGCTTC+TGG 0.287143 5.2:+14832973 MS.gene65312:CDS
TTGAGGGGACTTGTTGTTGG+TGG 0.289994 5.2:-14832632 None:intergenic
TCTGATGAAGGCGAAGGTTT+AGG 0.328241 5.2:+14833551 MS.gene65312:CDS
ATACATCACTCTTCTTCATT+AGG 0.332064 5.2:-14833596 None:intergenic
GTCTTGAGGGGACTTGTTGT+TGG 0.343036 5.2:-14832635 None:intergenic
TAGTTGGGTTGGTTTCTTTG+GGG 0.344689 5.2:-14832678 None:intergenic
GTTGAATTCTCGGAAGGGTT+AGG 0.378551 5.2:-14832607 None:intergenic
CTCTTCCTCCTCTTCATAGC+TGG 0.393408 5.2:-14832826 None:intergenic
AAAGAACTTTGAAGGGTAGT+TGG 0.393444 5.2:-14832694 None:intergenic
TGAGGGGACTTGTTGTTGGT+GGG 0.402381 5.2:-14832631 None:intergenic
AGGGGACTTGTTGTTGGTGG+GGG 0.408399 5.2:-14832629 None:intergenic
AGGTGGGGTGGTTGTTGATG+TGG 0.426505 5.2:-14833013 None:intergenic
AAGAACTTTGAAGGGTAGTT+GGG 0.431057 5.2:-14832693 None:intergenic
GAGTTCAGAGCTCGTGAGAA+TGG 0.435144 5.2:+14832766 MS.gene65312:CDS
ACCTCAACCTGATCAATATG+AGG 0.437745 5.2:+14833032 MS.gene65312:CDS
TAACAATTTGGATATATAGA+AGG 0.438362 5.2:-14832874 None:intergenic
CATCAGAGGGAGGGTCTTGA+GGG 0.445658 5.2:-14832648 None:intergenic
CCATACTTAAAGAACTTTGA+AGG 0.446994 5.2:-14832702 None:intergenic
CCCTCATATTGATCAGGTTG+AGG 0.453934 5.2:-14833033 None:intergenic
GAAGCTGCTGACAAACCATT+AGG 0.476282 5.2:-14832970 None:intergenic
GCAAACATGTGTTTCCCACT+TGG 0.483219 5.2:+14832902 MS.gene65312:CDS
ACTTTGAAGGGTAGTTGGGT+TGG 0.489348 5.2:-14832689 None:intergenic
GGTCCTCTATCTCCATTGGC+TGG 0.500299 5.2:-14833484 None:intergenic
CATATTGATCAGGTTGAGGT+GGG 0.500892 5.2:-14833029 None:intergenic
TCATCAGAGGGAGGGTCTTG+AGG 0.508193 5.2:-14832649 None:intergenic
AGTTCAGAGCTCGTGAGAAT+GGG 0.512950 5.2:+14832767 MS.gene65312:CDS
AGCTCGTGAGAATGGGAAGC+TGG 0.512973 5.2:+14832774 MS.gene65312:CDS
AGTTGGGTTGGTTTCTTTGG+GGG 0.515909 5.2:-14832677 None:intergenic
CATCACTCTTCTTCATTAGG+AGG 0.517441 5.2:-14833593 None:intergenic
GAGGGGTCCTCTATCTCCAT+TGG 0.519182 5.2:-14833488 None:intergenic
AAGCCAGCCAATGGAGATAG+AGG 0.520626 5.2:+14833481 MS.gene65312:CDS
GACTGCATTGATGAACCATA+TGG 0.524295 5.2:+14832924 MS.gene65312:CDS
TTGATCAGGTTGAGGTGGGG+TGG 0.536734 5.2:-14833025 None:intergenic
GAGGGGACTTGTTGTTGGTG+GGG 0.544991 5.2:-14832630 None:intergenic
AATGGGAAGCTGGCAGCTGA+TGG 0.545369 5.2:+14832784 MS.gene65312:CDS
TCAAAGTTCTTTAAGTATGG+AGG 0.546799 5.2:+14832705 MS.gene65312:CDS
CATACTTAAAGAACTTTGAA+GGG 0.549185 5.2:-14832701 None:intergenic
TCATATTGATCAGGTTGAGG+TGG 0.558741 5.2:-14833030 None:intergenic
GATGGAGAAGGTCGAAGTGA+TGG 0.574972 5.2:+14832802 MS.gene65312:CDS
TGATGATGAAAGCCAGCCAA+TGG 0.578386 5.2:+14833472 MS.gene65312:CDS
GAGTAATATTCGTGAAGTGA+AGG 0.580783 5.2:+14832846 MS.gene65312:CDS
GGGGTGGTTGTTGATGTGGA+AGG 0.586960 5.2:-14833009 None:intergenic
ATATTGATCAGGTTGAGGTG+GGG 0.595131 5.2:-14833028 None:intergenic
CTCCATTAAGACTTCGAGAG+CGG 0.599694 5.2:-14832746 None:intergenic
ATGGTCCAGCTATGAAGAGG+AGG 0.603822 5.2:+14832821 MS.gene65312:CDS
CTCGGATGCAACATCATCAG+AGG 0.604023 5.2:-14833507 None:intergenic
GGGGATTCATCATCAGAGGG+AGG 0.610326 5.2:-14832658 None:intergenic
TCGGATGCAACATCATCAGA+GGG 0.613962 5.2:-14833506 None:intergenic
ACTGCATCTGAGTCTGATGA+AGG 0.623088 5.2:+14833539 MS.gene65312:CDS
AATTTGGATATATAGAAGGA+TGG 0.631395 5.2:-14832870 None:intergenic
TCTGAGTCTGATGAAGGCGA+AGG 0.633192 5.2:+14833545 MS.gene65312:CDS
AAGCTGGCAGCTGATGGAGA+AGG 0.633635 5.2:+14832790 MS.gene65312:CDS
TTCATCAATGCAGTCCAAGT+GGG 0.634799 5.2:-14832916 None:intergenic
GTGATGGTCCAGCTATGAAG+AGG 0.637063 5.2:+14832818 MS.gene65312:CDS
GTTCATCAATGCAGTCCAAG+TGG 0.645025 5.2:-14832917 None:intergenic
AGATGCAGTATCATCAGACT+CGG 0.649465 5.2:-14833525 None:intergenic
CCTCAACCTGATCAATATGA+GGG 0.650750 5.2:+14833033 MS.gene65312:CDS
ATCAGAGGGAGGGTCTTGAG+GGG 0.650850 5.2:-14832647 None:intergenic
GGGATTCATCATCAGAGGGA+GGG 0.659890 5.2:-14832657 None:intergenic
CGGATGCAACATCATCAGAG+GGG 0.768604 5.2:-14833505 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTTGAATTAGAAAATT+AGG - chr5.2:14833070-14833089 None:intergenic 15.0%
!! AACATTACATAATTGAATCT+TGG - chr5.2:14833172-14833191 None:intergenic 20.0%
!! TAACAATTTGGATATATAGA+AGG - chr5.2:14832877-14832896 None:intergenic 20.0%
!!! AATGTTTTTCTTTTGTTACT+AGG + chr5.2:14833449-14833468 MS.gene65312:intron 20.0%
!!! TTTTTCGCACTATAATTTTT+AGG + chr5.2:14833102-14833121 MS.gene65312:intron 20.0%
! AATTTGGATATATAGAAGGA+TGG - chr5.2:14832873-14832892 None:intergenic 25.0%
! CATACTTAAAGAACTTTGAA+GGG - chr5.2:14832704-14832723 None:intergenic 25.0%
! CATATATATGTTTGTGTGTA+TGG - chr5.2:14833272-14833291 None:intergenic 25.0%
! TGTTTGCATCTATAACAATT+TGG - chr5.2:14832889-14832908 None:intergenic 25.0%
! TTATGAGATCAAATTCATGT+AGG + chr5.2:14833315-14833334 MS.gene65312:intron 25.0%
AAAAATGGTGTTCTTCCATA+TGG - chr5.2:14832942-14832961 None:intergenic 30.0%
CATTAGGATCACAACAAAAA+TGG - chr5.2:14832957-14832976 None:intergenic 30.0%
CCATACTTAAAGAACTTTGA+AGG - chr5.2:14832705-14832724 None:intergenic 30.0%
CCTTCAAAGTTCTTTAAGTA+TGG + chr5.2:14832702-14832721 MS.gene65312:CDS 30.0%
TATATAGCCAATAAAACCCT+AGG - chr5.2:14833143-14833162 None:intergenic 30.0%
TCAAAGTTCTTTAAGTATGG+AGG + chr5.2:14832705-14832724 MS.gene65312:CDS 30.0%
!! CATTTTTGTTGTGATCCTAA+TGG + chr5.2:14832955-14832974 MS.gene65312:CDS 30.0%
GAGTAATATTCGTGAAGTGA+AGG + chr5.2:14832846-14832865 MS.gene65312:CDS 35.0%
! AAAGAACTTTGAAGGGTAGT+TGG - chr5.2:14832697-14832716 None:intergenic 35.0%
! AAGAACTTTGAAGGGTAGTT+GGG - chr5.2:14832696-14832715 None:intergenic 35.0%
! GTTTTACCCTCATATTGATC+AGG - chr5.2:14833042-14833061 None:intergenic 35.0%
ACCTCAACCTGATCAATATG+AGG + chr5.2:14833032-14833051 MS.gene65312:CDS 40.0%
AGATGCAGTATCATCAGACT+CGG - chr5.2:14833528-14833547 None:intergenic 40.0%
CCAATAAAACCCTAGGTCAT+TGG - chr5.2:14833136-14833155 None:intergenic 40.0%
CCTCAACCTGATCAATATGA+GGG + chr5.2:14833033-14833052 MS.gene65312:CDS 40.0%
TTCATCAATGCAGTCCAAGT+GGG - chr5.2:14832919-14832938 None:intergenic 40.0%
! GACTGCATTGATGAACCATA+TGG + chr5.2:14832924-14832943 MS.gene65312:CDS 40.0%
!! ATATTGATCAGGTTGAGGTG+GGG - chr5.2:14833031-14833050 None:intergenic 40.0%
!! CATATTGATCAGGTTGAGGT+GGG - chr5.2:14833032-14833051 None:intergenic 40.0%
!! CCAATGACCTAGGGTTTTAT+TGG + chr5.2:14833133-14833152 MS.gene65312:intron 40.0%
!! GTAGTTGGGTTGGTTTCTTT+GGG - chr5.2:14832682-14832701 None:intergenic 40.0%
!! TAGTTGGGTTGGTTTCTTTG+GGG - chr5.2:14832681-14832700 None:intergenic 40.0%
!! TCATATTGATCAGGTTGAGG+TGG - chr5.2:14833033-14833052 None:intergenic 40.0%
AACCGCTCTCGAAGTCTTAA+TGG + chr5.2:14832744-14832763 MS.gene65312:CDS 45.0%
ACTGCATCTGAGTCTGATGA+AGG + chr5.2:14833539-14833558 MS.gene65312:CDS 45.0%
AGTTCAGAGCTCGTGAGAAT+GGG + chr5.2:14832767-14832786 MS.gene65312:CDS 45.0%
CTCCATTAAGACTTCGAGAG+CGG - chr5.2:14832749-14832768 None:intergenic 45.0%
GAAGCTGCTGACAAACCATT+AGG - chr5.2:14832973-14832992 None:intergenic 45.0%
GCAAACATGTGTTTCCCACT+TGG + chr5.2:14832902-14832921 MS.gene65312:CDS 45.0%
GTCAACACTCCAATGACCTA+GGG + chr5.2:14833124-14833143 MS.gene65312:intron 45.0%
GTTCATCAATGCAGTCCAAG+TGG - chr5.2:14832920-14832939 None:intergenic 45.0%
GTTGAATTCTCGGAAGGGTT+AGG - chr5.2:14832610-14832629 None:intergenic 45.0%
TCGGATGCAACATCATCAGA+GGG - chr5.2:14833509-14833528 None:intergenic 45.0%
TCTCGGAAGGGTTAGGTTTA+GGG - chr5.2:14832603-14832622 None:intergenic 45.0%
TCTGATGAAGGCGAAGGTTT+AGG + chr5.2:14833551-14833570 MS.gene65312:CDS 45.0%
TTCTCGGAAGGGTTAGGTTT+AGG - chr5.2:14832604-14832623 None:intergenic 45.0%
TTGGGGGATTCATCATCAGA+GGG - chr5.2:14832664-14832683 None:intergenic 45.0%
TTTGGGGGATTCATCATCAG+AGG - chr5.2:14832665-14832684 None:intergenic 45.0%
! AATGGTTTGTCAGCAGCTTC+TGG + chr5.2:14832973-14832992 MS.gene65312:CDS 45.0%
! ACTTTGAAGGGTAGTTGGGT+TGG - chr5.2:14832692-14832711 None:intergenic 45.0%
! CCCTCATATTGATCAGGTTG+AGG - chr5.2:14833036-14833055 None:intergenic 45.0%
! TGATGATGAAAGCCAGCCAA+TGG + chr5.2:14833472-14833491 MS.gene65312:CDS 45.0%
!! AGTTGGGTTGGTTTCTTTGG+GGG - chr5.2:14832680-14832699 None:intergenic 45.0%
!! GGTAGTTGGGTTGGTTTCTT+TGG - chr5.2:14832683-14832702 None:intergenic 45.0%
!!! ATTTTTTTTTTTTAACTAAT+CGG + chr5.2:14833355-14833374 MS.gene65312:intron 5.0%
AAGCCAGCCAATGGAGATAG+AGG + chr5.2:14833481-14833500 MS.gene65312:CDS 50.0%
ATGGTCCAGCTATGAAGAGG+AGG + chr5.2:14832821-14832840 MS.gene65312:CDS 50.0%
CGGATGCAACATCATCAGAG+GGG - chr5.2:14833508-14833527 None:intergenic 50.0%
CTCGGATGCAACATCATCAG+AGG - chr5.2:14833510-14833529 None:intergenic 50.0%
CTCTTCCTCCTCTTCATAGC+TGG - chr5.2:14832829-14832848 None:intergenic 50.0%
GAGTTCAGAGCTCGTGAGAA+TGG + chr5.2:14832766-14832785 MS.gene65312:CDS 50.0%
GATGGAGAAGGTCGAAGTGA+TGG + chr5.2:14832802-14832821 MS.gene65312:CDS 50.0%
GGGATTCATCATCAGAGGGA+GGG - chr5.2:14832660-14832679 None:intergenic 50.0%
GGTCAACACTCCAATGACCT+AGG + chr5.2:14833123-14833142 MS.gene65312:intron 50.0%
GTGATGGTCCAGCTATGAAG+AGG + chr5.2:14832818-14832837 MS.gene65312:CDS 50.0%
TCTGAGTCTGATGAAGGCGA+AGG + chr5.2:14833545-14833564 MS.gene65312:CDS 50.0%
TGGGGGTTGAATTCTCGGAA+GGG - chr5.2:14832615-14832634 None:intergenic 50.0%
! AGACTTCGAGAGCGGTTTTC+AGG - chr5.2:14832741-14832760 None:intergenic 50.0%
! GTTGGTGGGGGTTGAATTCT+CGG - chr5.2:14832620-14832639 None:intergenic 50.0%
!! GTCTTGAGGGGACTTGTTGT+TGG - chr5.2:14832638-14832657 None:intergenic 50.0%
!! TGAGGGGACTTGTTGTTGGT+GGG - chr5.2:14832634-14832653 None:intergenic 50.0%
!! TTGAGGGGACTTGTTGTTGG+TGG - chr5.2:14832635-14832654 None:intergenic 50.0%
AAGCTGGCAGCTGATGGAGA+AGG + chr5.2:14832790-14832809 MS.gene65312:CDS 55.0%
AATGGGAAGCTGGCAGCTGA+TGG + chr5.2:14832784-14832803 MS.gene65312:CDS 55.0%
AGCTCGTGAGAATGGGAAGC+TGG + chr5.2:14832774-14832793 MS.gene65312:CDS 55.0%
AGGTGGGGTGGTTGTTGATG+TGG - chr5.2:14833016-14833035 None:intergenic 55.0%
ATCAGAGGGAGGGTCTTGAG+GGG - chr5.2:14832650-14832669 None:intergenic 55.0%
CATCAGAGGGAGGGTCTTGA+GGG - chr5.2:14832651-14832670 None:intergenic 55.0%
GAGGGGTCCTCTATCTCCAT+TGG - chr5.2:14833491-14833510 None:intergenic 55.0%
GGGGATTCATCATCAGAGGG+AGG - chr5.2:14832661-14832680 None:intergenic 55.0%
GGGGTGGTTGTTGATGTGGA+AGG - chr5.2:14833012-14833031 None:intergenic 55.0%
GGTCCTCTATCTCCATTGGC+TGG - chr5.2:14833487-14833506 None:intergenic 55.0%
GTGGGGGTTGAATTCTCGGA+AGG - chr5.2:14832616-14832635 None:intergenic 55.0%
TCATCAGAGGGAGGGTCTTG+AGG - chr5.2:14832652-14832671 None:intergenic 55.0%
!! AGGGGACTTGTTGTTGGTGG+GGG - chr5.2:14832632-14832651 None:intergenic 55.0%
!! GAGGGGACTTGTTGTTGGTG+GGG - chr5.2:14832633-14832652 None:intergenic 55.0%
!! TTGATCAGGTTGAGGTGGGG+TGG - chr5.2:14833028-14833047 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 14832592 14833613 14832592 ID=MS.gene65312
chr5.2 mRNA 14832592 14833613 14832592 ID=MS.gene65312.t1;Parent=MS.gene65312
chr5.2 exon 14832592 14833054 14832592 ID=MS.gene65312.t1.exon1;Parent=MS.gene65312.t1
chr5.2 CDS 14832592 14833054 14832592 ID=cds.MS.gene65312.t1;Parent=MS.gene65312.t1
chr5.2 exon 14833471 14833613 14833471 ID=MS.gene65312.t1.exon2;Parent=MS.gene65312.t1
chr5.2 CDS 14833471 14833613 14833471 ID=cds.MS.gene65312.t1;Parent=MS.gene65312.t1
Gene Sequence

>MS.gene65312

ATGCAGAACCCTAAACCTAACCCTTCCGAGAATTCAACCCCCACCAACAACAAGTCCCCTCAAGACCCTCCCTCTGATGATGAATCCCCCAAAGAAACCAACCCAACTACCCTTCAAAGTTCTTTAAGTATGGAGGAAGAAGATGTCCTGAAAACCGCTCTCGAAGTCTTAATGGAGTTCAGAGCTCGTGAGAATGGGAAGCTGGCAGCTGATGGAGAAGGTCGAAGTGATGGTCCAGCTATGAAGAGGAGGAAGAGTAATATTCGTGAAGTGAAGGACCATCCTTCTATATATCCAAATTGTTATAGATGCAAACATGTGTTTCCCACTTGGACTGCATTGATGAACCATATGGAAGAACACCATTTTTGTTGTGATCCTAATGGTTTGTCAGCAGCTTCTGGTTTTTCTGCACTTCCTTCCACATCAACAACCACCCCACCTCAACCTGATCAATATGAGGGTAAAACTAAAACCTAATTTTCTAATTCAAACTATTTATTGTCATTTTTTTTCGCACTATAATTTTTAGGTCAACACTCCAATGACCTAGGGTTTTATTGGCTATATATCATGTCCAAGATTCAATTATGTAATGTTATGTCATTTTTTTTTTTTTACATTTAATTATTTTGATTTCAAAGTACTTGTGTATAGAACATTCATAAAAGATTGTACCATACACACAAACATATATATGTTCACTTTGAGTGTTGCTTAAGTTTATGAGATCAAATTCATGTAGGCATCTAGATATATCTTAATTTTTTTTTTTTAACTAATCGGTTTTTAATTTGACGATTTGCTTTTTCTTCAAACTAATGTTTTACATTGAAGCAATTATAATTTTAATTTTGAATGTTTTTCTTTTGTTACTAGGTGATGATGAAAGCCAGCCAATGGAGATAGAGGACCCCTCTGATGATGTTGCATCCGAGTCTGATGATACTGCATCTGAGTCTGATGAAGGCGAAGGTTTAGGATTCGACTTGAACGAGTTGCCTCCTAATGAAGAAGAGTGA
Protein sequence

>MS.gene65312.t1

MQNPKPNPSENSTPTNNKSPQDPPSDDESPKETNPTTLQSSLSMEEEDVLKTALEVLMEFRARENGKLAADGEGRSDGPAMKRRKSNIREVKDHPSIYPNCYRCKHVFPTWTALMNHMEEHHFCCDPNGLSAASGFSALPSTSTTTPPQPDQYEGDDESQPMEIEDPSDDVASESDDTASESDEGEGLGFDLNELPPNEEE