AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49846

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 75 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATTCCAAATGGCATATTT+TGG 0.165050 4.2:+85313779 None:intergenic
CTTTCTCAAAACAAGTTAAT+TGG 0.165768 4.2:-85314102 MS.gene49846:CDS
GTGTCATACAACAACCTTTC+TGG 0.196091 4.2:-85313295 MS.gene49846:CDS
ATAAATCAAGGATCTCTATT+TGG 0.211548 4.2:+85313386 None:intergenic
AATTGTTCCATCCTAATAAA+AGG 0.283466 4.2:+85313899 None:intergenic
TTTAACTGACACAACTGATT+TGG 0.290154 4.2:+85313862 None:intergenic
GAGATCCAGTTGTGAACTTT+GGG 0.327643 4.2:+85314073 None:intergenic
GTCAACTTGGTTAGTTCATT+AGG 0.329348 4.2:+85313337 None:intergenic
GATCTCTATTTGGGTAAGAT+TGG 0.343167 4.2:+85313396 None:intergenic
CATTGAGCTTGTTCCTTGAT+AGG 0.343909 4.2:+85313821 None:intergenic
TGCTTCCAAAATATGCCATT+TGG 0.351607 4.2:-85313784 MS.gene49846:CDS
TTTGCCCATTGGTTCTCAAT+TGG 0.368200 4.2:-85313647 MS.gene49846:CDS
AGAGATCCAGTTGTGAACTT+TGG 0.388908 4.2:+85314072 None:intergenic
TAAATCAAGGATCTCTATTT+GGG 0.389355 4.2:+85313387 None:intergenic
ATCTTACATAACAATACTAT+TGG 0.391789 4.2:-85313083 MS.gene49846:CDS
CCATTTGGAATGAGACAATA+TGG 0.409879 4.2:-85313769 MS.gene49846:CDS
TTATCATGCAATAAACTAAC+AGG 0.411910 4.2:-85313511 MS.gene49846:CDS
AGTTCACAACTGGATCTCTA+AGG 0.423329 4.2:-85314068 MS.gene49846:CDS
CTGTCAAGTGATTATGTGAT+AGG 0.431935 4.2:+85313440 None:intergenic
AACTACAACTTCTAGATTTG+AGG 0.432468 4.2:-85313981 MS.gene49846:CDS
CACATTGAAGATTTCTAAAG+AGG 0.433565 4.2:+85313315 None:intergenic
TTGAAGAAATAATTCACATC+TGG 0.441019 4.2:+85313676 None:intergenic
TCAATCCCAAAGTTCACAAC+TGG 0.446733 4.2:-85314078 MS.gene49846:CDS
TTTCAGGTAAAATTCCCAAC+TGG 0.453913 4.2:-85313948 MS.gene49846:CDS
TTCAATGCTAGTTTGCCCAT+TGG 0.455334 4.2:-85313658 MS.gene49846:CDS
AGAGGTAATCCTGGTCTTTG+TGG 0.458550 4.2:-85313223 MS.gene49846:CDS
ACTACAACTTCTAGATTTGA+GGG 0.458773 4.2:-85313980 MS.gene49846:CDS
TTATCATACAATAACTTAAG+TGG 0.461003 4.2:-85313367 MS.gene49846:CDS
GGTACCATCCCTTCTCAACT+TGG 0.462250 4.2:-85313490 MS.gene49846:CDS
ATCCAATGACAATGGAGAAA+AGG 0.468182 4.2:-85313149 MS.gene49846:CDS
CACGTTCACACTTTCGATTG+AGG 0.477839 4.2:+85313194 None:intergenic
AGTTATTGTATGATAAATCA+AGG 0.481490 4.2:+85313374 None:intergenic
TTGCAACAGAATAATCTCTC+TGG 0.482301 4.2:-85314036 MS.gene49846:CDS
CCTAGACATCATGAGTGGAT+TGG 0.489647 4.2:-85313536 MS.gene49846:CDS
CGAGAGCTTGTCCATCCAGT+TGG 0.492826 4.2:+85313933 None:intergenic
ATGCACGTTGGCGTATGGCC+TGG 0.494295 4.2:-85313036 MS.gene49846:CDS
GACAGCTACAGAGGTAATCC+TGG 0.501158 4.2:-85313232 MS.gene49846:CDS
TACTAGGTGGTGTTCCAGAA+AGG 0.501275 4.2:+85313281 None:intergenic
CCAATCCACTCATGATGTCT+AGG 0.501611 4.2:+85313536 None:intergenic
TTGACATAATGGACCTATCA+AGG 0.503159 4.2:-85313834 MS.gene49846:CDS
TTGTCATTGGATTGTGATGA+AGG 0.504883 4.2:+85313160 None:intergenic
GGACAAGCTCTCGGAGTTGA+GGG 0.505119 4.2:-85313923 MS.gene49846:CDS
CCATATTGTCTCATTCCAAA+TGG 0.506465 4.2:+85313769 None:intergenic
AATTTGCTCTGTGAAATGTA+AGG 0.507904 4.2:+85313702 None:intergenic
CATGTCCAGTCTTCAAATGT+TGG 0.508908 4.2:-85314127 None:intergenic
CTATCACATAATCACTTGAC+AGG 0.516612 4.2:-85313439 MS.gene49846:CDS
GAGAGCTTGTCCATCCAGTT+GGG 0.517856 4.2:+85313934 None:intergenic
GATTTCTAAAGAGGTCAACT+TGG 0.519346 4.2:+85313324 None:intergenic
TGGACAAGCTCTCGGAGTTG+AGG 0.531042 4.2:-85313924 MS.gene49846:CDS
GTTGCAAACTGTCTTGTACT+AGG 0.532444 4.2:+85313265 None:intergenic
AGGTAAAATTCCCAACTGGA+TGG 0.536265 4.2:-85313944 MS.gene49846:CDS
TGCATGTCTCCAAGTTGAGA+AGG 0.536846 4.2:+85313481 None:intergenic
ATAAACCAATTGAGAACCAA+TGG 0.539227 4.2:+85313642 None:intergenic
CAACTGGATGGACAAGCTCT+CGG 0.544378 4.2:-85313932 MS.gene49846:CDS
GATGCACAACACTGTGATGA+AGG 0.553242 4.2:+85313060 None:intergenic
GTCTCCAAGTTGAGAAGGGA+TGG 0.553889 4.2:+85313486 None:intergenic
CATCAATGCACGTTGGCGTA+TGG 0.556225 4.2:-85313041 MS.gene49846:CDS
TAAACCAATTGAGAACCAAT+GGG 0.560026 4.2:+85313643 None:intergenic
GCATGTCTCCAAGTTGAGAA+GGG 0.561733 4.2:+85313482 None:intergenic
ATTTGCTCTGTGAAATGTAA+GGG 0.565793 4.2:+85313703 None:intergenic
TCAAATTCTTGATCTTCACT+CGG 0.567620 4.2:+85313607 None:intergenic
ATCTAGAAGTTGTAGTTGTG+AGG 0.574068 4.2:+85313987 None:intergenic
TGGAGAAAAGGAAACTGTTG+TGG 0.599113 4.2:-85313137 MS.gene49846:CDS
GGTGATGAAGATTATGAAGA+CGG 0.603031 4.2:-85313748 MS.gene49846:CDS
GAGGCTTCAGAGAGTTCAGA+TGG 0.606005 4.2:+85314006 None:intergenic
CTTACTTATGTAATAAAACC+AGG 0.618779 4.2:+85313018 None:intergenic
AGGAGTGGTCCACAAAGACC+AGG 0.619552 4.2:+85313214 None:intergenic
TCATCACAATCCAATGACAA+TGG 0.625600 4.2:-85313157 MS.gene49846:CDS
TCACACTTTCGATTGAGGAG+TGG 0.634892 4.2:+85313199 None:intergenic
TCTGTAGCTGTCCTCAACGA+AGG 0.654884 4.2:+85313243 None:intergenic
TTCGTTGAGGACAGCTACAG+AGG 0.657968 4.2:-85313241 MS.gene49846:CDS
GATATCCTAGACATCATGAG+TGG 0.659596 4.2:-85313541 MS.gene49846:CDS
ACAGTTTGCAACCTTCGTTG+AGG 0.677988 4.2:-85313254 MS.gene49846:CDS
GCAAACTGTCTTGTACTAGG+TGG 0.698750 4.2:+85313268 None:intergenic
TGTTGTGCATCAATGCACGT+TGG 0.774033 4.2:-85313048 MS.gene49846:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTTATTGTATGATAAATCA+AGG + chr4.2:85313770-85313789 None:intergenic 20.0%
!! ATCTTACATAACAATACTAT+TGG - chr4.2:85314058-85314077 MS.gene49846:CDS 20.0%
!! GTTAAAAAAGATTGACATAA+TGG - chr4.2:85313296-85313315 MS.gene49846:CDS 20.0%
!! TTATCATACAATAACTTAAG+TGG - chr4.2:85313774-85313793 MS.gene49846:CDS 20.0%
! AATTGTTCCATCCTAATAAA+AGG + chr4.2:85313245-85313264 None:intergenic 25.0%
! ATAAATCAAGGATCTCTATT+TGG + chr4.2:85313758-85313777 None:intergenic 25.0%
! CTTTCTCAAAACAAGTTAAT+TGG - chr4.2:85313039-85313058 MS.gene49846:CDS 25.0%
! TAAATCAAGGATCTCTATTT+GGG + chr4.2:85313757-85313776 None:intergenic 25.0%
! TTATCATGCAATAAACTAAC+AGG - chr4.2:85313630-85313649 MS.gene49846:CDS 25.0%
! TTGAAGAAATAATTCACATC+TGG + chr4.2:85313468-85313487 None:intergenic 25.0%
!! CACAATGAATACTTTTACAA+AGG - chr4.2:85313576-85313595 MS.gene49846:CDS 25.0%
!! TGGACATGATAACATTTTAT+TGG - chr4.2:85314024-85314043 MS.gene49846:CDS 25.0%
AACTACAACTTCTAGATTTG+AGG - chr4.2:85313160-85313179 MS.gene49846:CDS 30.0%
ACTACAACTTCTAGATTTGA+GGG - chr4.2:85313161-85313180 MS.gene49846:CDS 30.0%
ATAAACCAATTGAGAACCAA+TGG + chr4.2:85313502-85313521 None:intergenic 30.0%
ATTTGCTCTGTGAAATGTAA+GGG + chr4.2:85313441-85313460 None:intergenic 30.0%
GTAAGATTGGAAAAAGTGAT+TGG + chr4.2:85313735-85313754 None:intergenic 30.0%
TAAACCAATTGAGAACCAAT+GGG + chr4.2:85313501-85313520 None:intergenic 30.0%
TCAAATTCTTGATCTTCACT+CGG + chr4.2:85313537-85313556 None:intergenic 30.0%
TTGGAAAAAGTGATTGGAAT+AGG + chr4.2:85313729-85313748 None:intergenic 30.0%
TTTAACTGACACAACTGATT+TGG + chr4.2:85313282-85313301 None:intergenic 30.0%
! AATTTGCTCTGTGAAATGTA+AGG + chr4.2:85313442-85313461 None:intergenic 30.0%
! CACATTGAAGATTTCTAAAG+AGG + chr4.2:85313829-85313848 None:intergenic 30.0%
! TCATTCCAAATGGCATATTT+TGG + chr4.2:85313365-85313384 None:intergenic 30.0%
! TTAGGATGGAACAATTTTGA+AGG - chr4.2:85313249-85313268 MS.gene49846:CDS 30.0%
ATCCAATGACAATGGAGAAA+AGG - chr4.2:85313992-85314011 MS.gene49846:CDS 35.0%
ATCTAGAAGTTGTAGTTGTG+AGG + chr4.2:85313157-85313176 None:intergenic 35.0%
CCATATTGTCTCATTCCAAA+TGG + chr4.2:85313375-85313394 None:intergenic 35.0%
CTATCACATAATCACTTGAC+AGG - chr4.2:85313702-85313721 MS.gene49846:CDS 35.0%
CTGTCAAGTGATTATGTGAT+AGG + chr4.2:85313704-85313723 None:intergenic 35.0%
GATCTCTATTTGGGTAAGAT+TGG + chr4.2:85313748-85313767 None:intergenic 35.0%
GGTGATGAAGATTATGAAGA+CGG - chr4.2:85313393-85313412 MS.gene49846:CDS 35.0%
TCATCACAATCCAATGACAA+TGG - chr4.2:85313984-85314003 MS.gene49846:CDS 35.0%
TGCTTCCAAAATATGCCATT+TGG - chr4.2:85313357-85313376 MS.gene49846:CDS 35.0%
TTGCAACAGAATAATCTCTC+TGG - chr4.2:85313105-85313124 MS.gene49846:CDS 35.0%
TTGTCATTGGATTGTGATGA+AGG + chr4.2:85313984-85314003 None:intergenic 35.0%
! CCATTTGGAATGAGACAATA+TGG - chr4.2:85313372-85313391 MS.gene49846:CDS 35.0%
! GATTTCTAAAGAGGTCAACT+TGG + chr4.2:85313820-85313839 None:intergenic 35.0%
! GTCAACTTGGTTAGTTCATT+AGG + chr4.2:85313807-85313826 None:intergenic 35.0%
! TTCCTTTTCTCCATTGTCAT+TGG + chr4.2:85313997-85314016 None:intergenic 35.0%
! TTGAGGGAGAACAAATTTTC+AGG - chr4.2:85313177-85313196 MS.gene49846:CDS 35.0%
! TTTCAGGTAAAATTCCCAAC+TGG - chr4.2:85313193-85313212 MS.gene49846:CDS 35.0%
!! TTGACATAATGGACCTATCA+AGG - chr4.2:85313307-85313326 MS.gene49846:CDS 35.0%
AGAGATCCAGTTGTGAACTT+TGG + chr4.2:85313072-85313091 None:intergenic 40.0%
AGGTAAAATTCCCAACTGGA+TGG - chr4.2:85313197-85313216 MS.gene49846:CDS 40.0%
AGTTCACAACTGGATCTCTA+AGG - chr4.2:85313073-85313092 MS.gene49846:CDS 40.0%
GAGATCCAGTTGTGAACTTT+GGG + chr4.2:85313071-85313090 None:intergenic 40.0%
GATATCCTAGACATCATGAG+TGG - chr4.2:85313600-85313619 MS.gene49846:CDS 40.0%
GTGTCATACAACAACCTTTC+TGG - chr4.2:85313846-85313865 MS.gene49846:CDS 40.0%
GTTGCAAACTGTCTTGTACT+AGG + chr4.2:85313879-85313898 None:intergenic 40.0%
TCAATCCCAAAGTTCACAAC+TGG - chr4.2:85313063-85313082 MS.gene49846:CDS 40.0%
TGGAGAAAAGGAAACTGTTG+TGG - chr4.2:85314004-85314023 MS.gene49846:CDS 40.0%
! CATTGAGCTTGTTCCTTGAT+AGG + chr4.2:85313323-85313342 None:intergenic 40.0%
! GAGTTGAGGGTCCTTTTATT+AGG - chr4.2:85313231-85313250 MS.gene49846:CDS 40.0%
! TGAGGGTCCTTTTATTAGGA+TGG - chr4.2:85313235-85313254 MS.gene49846:CDS 40.0%
! TTCAATGCTAGTTTGCCCAT+TGG - chr4.2:85313483-85313502 MS.gene49846:CDS 40.0%
!! GGCATATTTTGGAAGCAAGA+TGG + chr4.2:85313354-85313373 None:intergenic 40.0%
!! TTTGCCCATTGGTTCTCAAT+TGG - chr4.2:85313494-85313513 MS.gene49846:CDS 40.0%
ACAGTTTGCAACCTTCGTTG+AGG - chr4.2:85313887-85313906 MS.gene49846:CDS 45.0%
CACGTTCACACTTTCGATTG+AGG + chr4.2:85313950-85313969 None:intergenic 45.0%
CCAATCCACTCATGATGTCT+AGG + chr4.2:85313608-85313627 None:intergenic 45.0%
CCTAGACATCATGAGTGGAT+TGG - chr4.2:85313605-85313624 MS.gene49846:CDS 45.0%
GATGCACAACACTGTGATGA+AGG + chr4.2:85314084-85314103 None:intergenic 45.0%
GCAAACTGTCTTGTACTAGG+TGG + chr4.2:85313876-85313895 None:intergenic 45.0%
TACTAGGTGGTGTTCCAGAA+AGG + chr4.2:85313863-85313882 None:intergenic 45.0%
TCACACTTTCGATTGAGGAG+TGG + chr4.2:85313945-85313964 None:intergenic 45.0%
TGTTGTGCATCAATGCACGT+TGG - chr4.2:85314093-85314112 MS.gene49846:CDS 45.0%
! AGAGGTAATCCTGGTCTTTG+TGG - chr4.2:85313918-85313937 MS.gene49846:CDS 45.0%
! GCATGTCTCCAAGTTGAGAA+GGG + chr4.2:85313662-85313681 None:intergenic 45.0%
! TGCATGTCTCCAAGTTGAGA+AGG + chr4.2:85313663-85313682 None:intergenic 45.0%
CAACTGGATGGACAAGCTCT+CGG - chr4.2:85313209-85313228 MS.gene49846:CDS 50.0%
CATCAATGCACGTTGGCGTA+TGG - chr4.2:85314100-85314119 MS.gene49846:CDS 50.0%
GACAGCTACAGAGGTAATCC+TGG - chr4.2:85313909-85313928 MS.gene49846:CDS 50.0%
GAGAGCTTGTCCATCCAGTT+GGG + chr4.2:85313210-85313229 None:intergenic 50.0%
GAGGCTTCAGAGAGTTCAGA+TGG + chr4.2:85313138-85313157 None:intergenic 50.0%
GGTACCATCCCTTCTCAACT+TGG - chr4.2:85313651-85313670 MS.gene49846:CDS 50.0%
TCTGTAGCTGTCCTCAACGA+AGG + chr4.2:85313901-85313920 None:intergenic 50.0%
TTCGTTGAGGACAGCTACAG+AGG - chr4.2:85313900-85313919 MS.gene49846:CDS 50.0%
! GTCTCCAAGTTGAGAAGGGA+TGG + chr4.2:85313658-85313677 None:intergenic 50.0%
AGGAGTGGTCCACAAAGACC+AGG + chr4.2:85313930-85313949 None:intergenic 55.0%
CGAGAGCTTGTCCATCCAGT+TGG + chr4.2:85313211-85313230 None:intergenic 55.0%
GGACAAGCTCTCGGAGTTGA+GGG - chr4.2:85313218-85313237 MS.gene49846:CDS 55.0%
TGGACAAGCTCTCGGAGTTG+AGG - chr4.2:85313217-85313236 MS.gene49846:CDS 55.0%
ATGCACGTTGGCGTATGGCC+TGG - chr4.2:85314105-85314124 MS.gene49846:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 85313023 85314140 85313023 ID=MS.gene49846
chr4.2 mRNA 85313023 85314140 85313023 ID=MS.gene49846.t1;Parent=MS.gene49846
chr4.2 exon 85313023 85314140 85313023 ID=MS.gene49846.t1.exon1;Parent=MS.gene49846.t1
chr4.2 CDS 85313023 85314140 85313023 ID=cds.MS.gene49846.t1;Parent=MS.gene49846.t1
Gene Sequence

>MS.gene49846

TCTTCAAATGTTGGATCTTTCTCAAAACAAGTTAATTGGATCAATCCCAAAGTTCACAACTGGATCTCTAAGGTTATTGTATTTGCAACAGAATAATCTCTCTGGATCTATACCATCTGAACTCTCTGAAGCCTCACAACTACAACTTCTAGATTTGAGGGAGAACAAATTTTCAGGTAAAATTCCCAACTGGATGGACAAGCTCTCGGAGTTGAGGGTCCTTTTATTAGGATGGAACAATTTTGAAGGAGAAATTCCAAATCAGTTGTGTCAGTTAAAAAAGATTGACATAATGGACCTATCAAGGAACAAGCTCAATGCTTCAATACCATCTTGCTTCCAAAATATGCCATTTGGAATGAGACAATATGGTGATGAAGATTATGAAGACGGTTCTATTTTTGAATTCTCAATTCCCTTACATTTCACAGAGCAAATTATTCCAGATGTGAATTATTTCTTCAATGCTAGTTTGCCCATTGGTTCTCAATTGGTTTATGATGAAAGTTCACCGAGTGAAGATCAAGAATTTGAAGTGCAGTTCAGAACAAAGCACAATGAATACTTTTACAAAGGTGATATCCTAGACATCATGAGTGGATTGGATTTATCATGCAATAAACTAACAGGTACCATCCCTTCTCAACTTGGAGACATGCAAAAAGTTCAAGTCTTGAACCTATCACATAATCACTTGACAGGTCCTATTCCAATCACTTTTTCCAATCTTACCCAAATAGAGATCCTTGATTTATCATACAATAACTTAAGTGGTAAGATACCTAATGAACTAACCAAGTTGACCTCTTTAGAAATCTTCAATGTGTCATACAACAACCTTTCTGGAACACCACCTAGTACAAGACAGTTTGCAACCTTCGTTGAGGACAGCTACAGAGGTAATCCTGGTCTTTGTGGACCACTCCTCAATCGAAAGTGTGAACGTGTCGAGTCTTCACCTTCATCACAATCCAATGACAATGGAGAAAAGGAAACTGTTGTGGACATGATAACATTTTATTGGAGTTTCACAGCATCTTACATAACAATACTATTGGCCTTCATCACAGTGTTGTGCATCAATGCACGTTGGCGTATGGCCTGGTTTTATTACATAA
Protein sequence

>MS.gene49846.t1

SSNVGSFSKQVNWINPKVHNWISKVIVFATEUSLWIYTIUTLUSLTTTTSRFEGEQIFRUNSQLDGQALGVEGPFIRMEQFURRNSKSVVSVKKDUHNGPIKEQAQCFNTILLPKYAIWNETIWUURLURRFYFUILNSLTFHRANYSRCELFLQCUFAHWFSIGLUUKFTEURSRIUSAVQNKAQUILLQRUYPRHHEWIGFIMQUTNRYHPFSTWRHAKSSSLEPITUSLDRSYSNHFFQSYPNRDPUFIIQULKWUDTUUTNQVDLFRNLQCVIQQPFWNTTUYKTVCNLRUGQLQRUSWSLWTTPQSKVUTCRVFTFITIQUQWRKGNCCGHDNILLEFHSILHNNTIGLHHSVVHQCTLAYGLVLLH