AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene26416

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene26416.t1 MTR_4g088035 85.841 226 20 3 1 221 50 268 5.95e-131 369
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 48 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTCTGACCCCAAATTTA+TGG 0.119750 4.3:-25130828 MS.gene26416:CDS
TTGGGCAAGACCCATAAATT+TGG 0.193828 4.3:+25130817 None:intergenic
CATCCTAAGTATTATTCTTT+TGG 0.211764 4.3:-25130458 MS.gene26416:CDS
TATTGAAAGAGAATGAATTT+TGG 0.212393 4.3:+25130798 None:intergenic
CAAAGTCTTGCAAGTAGTTC+TGG 0.228500 4.3:-25130572 MS.gene26416:CDS
TCCATACGGATATTCAAAAT+AGG 0.257950 4.3:+25130703 None:intergenic
TCCCTGCCTTTGTCTCTTGT+TGG 0.273999 4.3:-25130416 MS.gene26416:CDS
TGGGCAAGACCCATAAATTT+GGG 0.299976 4.3:+25130818 None:intergenic
TCTTCTGACCCCAAATTTAT+GGG 0.360429 4.3:-25130827 MS.gene26416:CDS
GTGATGCTAACAATGGAAAT+TGG 0.377075 4.3:-25130775 MS.gene26416:CDS
TATTATGACCAATCAACATA+TGG 0.380266 4.3:-25130504 MS.gene26416:CDS
TTATTGAACTGTGTTGTTGC+TGG 0.391668 4.3:-25130632 MS.gene26416:CDS
TTGTATTCCCATATGTTGAT+TGG 0.396164 4.3:+25130496 None:intergenic
CCATACGGATATTCAAAATA+GGG 0.399569 4.3:+25130704 None:intergenic
GCACCAAGTGGACCATTGAT+TGG 0.406811 4.3:+25130920 None:intergenic
GCATTGTTGTTAGCCACAAA+AGG 0.411788 4.3:+25130737 None:intergenic
CCGTATGGAGGAAATAGCTT+TGG 0.415315 4.3:-25130689 MS.gene26416:CDS
AAAGTCTTGCAAGTAGTTCT+GGG 0.449359 4.3:-25130571 MS.gene26416:CDS
ATAAATTTGGGGTCAGAAGA+TGG 0.471135 4.3:+25130830 None:intergenic
CATTGTTGTTAGCCACAAAA+GGG 0.471171 4.3:+25130738 None:intergenic
TTTGGTGTTGTCGTTGGAGT+AGG 0.480154 4.3:+25130858 None:intergenic
TTGTTGCTGGTGCTAATGTT+TGG 0.486568 4.3:-25130619 MS.gene26416:CDS
CACCAAGTGGACCATTGATT+GGG 0.487901 4.3:+25130921 None:intergenic
GGTCAGAAGATGGAACAGTT+TGG 0.523150 4.3:+25130840 None:intergenic
TGTCCAAAAGAATAATACTT+AGG 0.524172 4.3:+25130455 None:intergenic
TGCAAATAATTGTGTTGTGA+AGG 0.524425 4.3:+25130593 None:intergenic
GACCCAATCAATGGTCCACT+TGG 0.526304 4.3:-25130923 MS.gene26416:CDS
TTCCAACAAGAGACAAAGGC+AGG 0.528648 4.3:+25130414 None:intergenic
GAACAGTTTGGTGTTGTCGT+TGG 0.529232 4.3:+25130852 None:intergenic
ATTATGACCAATCAACATAT+GGG 0.537091 4.3:-25130503 MS.gene26416:CDS
TGGAAACAAGACCCAATCAA+TGG 0.537301 4.3:-25130932 MS.gene26416:CDS
CCAAAGCTATTTCCTCCATA+CGG 0.542651 4.3:+25130689 None:intergenic
CTCAGAAACCTTGATGAACA+AGG 0.552123 4.3:-25130998 MS.gene26416:CDS
TTCAATAGTGATGCTAACAA+TGG 0.552245 4.3:-25130782 MS.gene26416:CDS
GGAAATAGCTTTGGAAGTGT+AGG 0.563321 4.3:-25130680 MS.gene26416:CDS
TGTAGGTGCTTTGCAAAATG+AGG 0.574107 4.3:-25130663 MS.gene26416:CDS
TTGATTGGGAAGCAAAGATG+TGG 0.575226 4.3:-25130952 MS.gene26416:CDS
TTCCCAATCAAAAGACTCGA+TGG 0.576338 4.3:+25130964 None:intergenic
AATCAACATATGGGAATACA+AGG 0.587851 4.3:-25130494 MS.gene26416:CDS
TCAATTCCAACAAGAGACAA+AGG 0.608888 4.3:+25130410 None:intergenic
GGGCAAGACCCATAAATTTG+GGG 0.616540 4.3:+25130819 None:intergenic
CATATGGGAATACAAGGAGA+AGG 0.632124 4.3:-25130488 MS.gene26416:CDS
GCAGGGAAAAGAATGACTTA+CGG 0.636274 4.3:+25130432 None:intergenic
TCCAACAAGAGACAAAGGCA+GGG 0.647739 4.3:+25130415 None:intergenic
ATTGTTGTTAGCCACAAAAG+GGG 0.649584 4.3:+25130739 None:intergenic
TTCTGGGACTAACGTGACGG+TGG 0.658470 4.3:-25130555 MS.gene26416:CDS
GCTTCAGTGAATGCACCAAG+TGG 0.660474 4.3:+25130908 None:intergenic
TAGTTCTGGGACTAACGTGA+CGG 0.692517 4.3:-25130558 MS.gene26416:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGAAAGAGAATGAATTTT+GGG + chr4.3:25130563-25130582 None:intergenic 20.0%
!!! TATTGAAAGAGAATGAATTT+TGG + chr4.3:25130564-25130583 None:intergenic 20.0%
! ATTATGACCAATCAACATAT+GGG - chr4.3:25130856-25130875 MS.gene26416:CDS 25.0%
! TATTATGACCAATCAACATA+TGG - chr4.3:25130855-25130874 MS.gene26416:CDS 25.0%
! TGTCCAAAAGAATAATACTT+AGG + chr4.3:25130907-25130926 None:intergenic 25.0%
!! CATCCTAAGTATTATTCTTT+TGG - chr4.3:25130901-25130920 MS.gene26416:CDS 25.0%
AATCAACATATGGGAATACA+AGG - chr4.3:25130865-25130884 MS.gene26416:CDS 30.0%
CCATACGGATATTCAAAATA+GGG + chr4.3:25130658-25130677 None:intergenic 30.0%
GAAAAAGATGCCAAAGAAAA+TGG + chr4.3:25130985-25131004 None:intergenic 30.0%
TCCATACGGATATTCAAAAT+AGG + chr4.3:25130659-25130678 None:intergenic 30.0%
TGCAAATAATTGTGTTGTGA+AGG + chr4.3:25130769-25130788 None:intergenic 30.0%
TTCAATAGTGATGCTAACAA+TGG - chr4.3:25130577-25130596 MS.gene26416:CDS 30.0%
TTGTATTCCCATATGTTGAT+TGG + chr4.3:25130866-25130885 None:intergenic 30.0%
! TATTTGTGCACCATTTTCTT+TGG - chr4.3:25130972-25130991 MS.gene26416:CDS 30.0%
! TTTTTCTTCCTTGTTCATCA+AGG + chr4.3:25130372-25130391 None:intergenic 30.0%
!! TATTTTGAATATCCGTATGG+AGG - chr4.3:25130658-25130677 MS.gene26416:CDS 30.0%
AAAGTCTTGCAAGTAGTTCT+GGG - chr4.3:25130788-25130807 MS.gene26416:CDS 35.0%
ATCTTCTGACCCCAAATTTA+TGG - chr4.3:25130531-25130550 MS.gene26416:CDS 35.0%
GTGATGCTAACAATGGAAAT+TGG - chr4.3:25130584-25130603 MS.gene26416:CDS 35.0%
TCAATTCCAACAAGAGACAA+AGG + chr4.3:25130952-25130971 None:intergenic 35.0%
TCTTCTGACCCCAAATTTAT+GGG - chr4.3:25130532-25130551 MS.gene26416:CDS 35.0%
! ATAAATTTGGGGTCAGAAGA+TGG + chr4.3:25130532-25130551 None:intergenic 35.0%
! ATTGTTGTTAGCCACAAAAG+GGG + chr4.3:25130623-25130642 None:intergenic 35.0%
! CATTGTTGTTAGCCACAAAA+GGG + chr4.3:25130624-25130643 None:intergenic 35.0%
! TTATTGAACTGTGTTGTTGC+TGG - chr4.3:25130727-25130746 MS.gene26416:CDS 35.0%
!! CCCTATTTTGAATATCCGTA+TGG - chr4.3:25130655-25130674 MS.gene26416:CDS 35.0%
!!! TGGAAATTGGTCTTCTTTTG+AGG - chr4.3:25130597-25130616 MS.gene26416:CDS 35.0%
CAAAGTCTTGCAAGTAGTTC+TGG - chr4.3:25130787-25130806 MS.gene26416:CDS 40.0%
CATATGGGAATACAAGGAGA+AGG - chr4.3:25130871-25130890 MS.gene26416:CDS 40.0%
CTCAGAAACCTTGATGAACA+AGG - chr4.3:25130361-25130380 MS.gene26416:CDS 40.0%
GCAGGGAAAAGAATGACTTA+CGG + chr4.3:25130930-25130949 None:intergenic 40.0%
TGGAAACAAGACCCAATCAA+TGG - chr4.3:25130427-25130446 MS.gene26416:CDS 40.0%
TGGGCAAGACCCATAAATTT+GGG + chr4.3:25130544-25130563 None:intergenic 40.0%
TGTAGGTGCTTTGCAAAATG+AGG - chr4.3:25130696-25130715 MS.gene26416:CDS 40.0%
TTCCCAATCAAAAGACTCGA+TGG + chr4.3:25130398-25130417 None:intergenic 40.0%
TTGATTGGGAAGCAAAGATG+TGG - chr4.3:25130407-25130426 MS.gene26416:CDS 40.0%
TTGGGCAAGACCCATAAATT+TGG + chr4.3:25130545-25130564 None:intergenic 40.0%
! AAGCCATCGAGTCTTTTGAT+TGG - chr4.3:25130392-25130411 MS.gene26416:CDS 40.0%
! CCAAAGCTATTTCCTCCATA+CGG + chr4.3:25130673-25130692 None:intergenic 40.0%
! GCATTGTTGTTAGCCACAAA+AGG + chr4.3:25130625-25130644 None:intergenic 40.0%
! TTGTTGCTGGTGCTAATGTT+TGG - chr4.3:25130740-25130759 MS.gene26416:CDS 40.0%
!! AGCCATCGAGTCTTTTGATT+GGG - chr4.3:25130393-25130412 MS.gene26416:CDS 40.0%
!! GGAAATAGCTTTGGAAGTGT+AGG - chr4.3:25130679-25130698 MS.gene26416:CDS 40.0%
CCGTATGGAGGAAATAGCTT+TGG - chr4.3:25130670-25130689 MS.gene26416:CDS 45.0%
GGGCAAGACCCATAAATTTG+GGG + chr4.3:25130543-25130562 None:intergenic 45.0%
GGTCAGAAGATGGAACAGTT+TGG + chr4.3:25130522-25130541 None:intergenic 45.0%
TCCAACAAGAGACAAAGGCA+GGG + chr4.3:25130947-25130966 None:intergenic 45.0%
TTCCAACAAGAGACAAAGGC+AGG + chr4.3:25130948-25130967 None:intergenic 45.0%
! CACCAAGTGGACCATTGATT+GGG + chr4.3:25130441-25130460 None:intergenic 45.0%
!! GAACAGTTTGGTGTTGTCGT+TGG + chr4.3:25130510-25130529 None:intergenic 45.0%
!! TAGTTCTGGGACTAACGTGA+CGG - chr4.3:25130801-25130820 MS.gene26416:CDS 45.0%
!! TTTGGTGTTGTCGTTGGAGT+AGG + chr4.3:25130504-25130523 None:intergenic 45.0%
!!! TTCTTTTGAGGCCCCTTTTG+TGG - chr4.3:25130609-25130628 MS.gene26416:CDS 45.0%
GACCCAATCAATGGTCCACT+TGG - chr4.3:25130436-25130455 MS.gene26416:CDS 50.0%
GCACCAAGTGGACCATTGAT+TGG + chr4.3:25130442-25130461 None:intergenic 50.0%
GCTTCAGTGAATGCACCAAG+TGG + chr4.3:25130454-25130473 None:intergenic 50.0%
TCCCTGCCTTTGTCTCTTGT+TGG - chr4.3:25130943-25130962 MS.gene26416:CDS 50.0%
!! TTCTGGGACTAACGTGACGG+TGG - chr4.3:25130804-25130823 MS.gene26416:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 25130358 25131023 25130358 ID=MS.gene26416
chr4.3 mRNA 25130358 25131023 25130358 ID=MS.gene26416.t1;Parent=MS.gene26416
chr4.3 exon 25130358 25131023 25130358 ID=MS.gene26416.t1.exon1;Parent=MS.gene26416.t1
chr4.3 CDS 25130358 25131023 25130358 ID=cds.MS.gene26416.t1;Parent=MS.gene26416.t1
Gene Sequence

>MS.gene26416

ATGCTCAGAAACCTTGATGAACAAGGAAGAAAAAAAGCCATCGAGTCTTTTGATTGGGAAGCAAAGATGTGGAAACAAGACCCAATCAATGGTCCACTTGGTGCATTCACTGAAGCTCAGAATGAAATAGCACGACTACAAAACCTACTCCAACGACAACACCAAACTGTTCCATCTTCTGACCCCAAATTTATGGGTCTTGCCCAAAATTCATTCTCTTTCAATAGTGATGCTAACAATGGAAATTGGTCTTCTTTTGAGGCCCCTTTTGTGGCTAACAACAATGCTGTACACAATCCCTATTTTGAATATCCGTATGGAGGAAATAGCTTTGGAAGTGTAGGTGCTTTGCAAAATGAGGAAACAAGTTTATTGAACTGTGTTGTTGCTGGTGCTAATGTTTGGCAACCTTCACAACACAATTATTTGCAAAGTCTTGCAAGTAGTTCTGGGACTAACGTGACGGTGGATCAACGTTCTCAATATTATGATCATAATATTATGACCAATCAACATATGGGAATACAAGGAGAAGGTCAGCAGCATCCTAAGTATTATTCTTTTGGACACCGTAAGTCATTCTTTTCCCTGCCTTTGTCTCTTGTTGGAATTGATATTTGTGCACCATTTTCTTTGGCATCTTTTTCGTTGAAAATAAAGTGTTGA
Protein sequence

>MS.gene26416.t1

MLRNLDEQGRKKAIESFDWEAKMWKQDPINGPLGAFTEAQNEIARLQNLLQRQHQTVPSSDPKFMGLAQNSFSFNSDANNGNWSSFEAPFVANNNAVHNPYFEYPYGGNSFGSVGALQNEETSLLNCVVAGANVWQPSQHNYLQSLASSSGTNVTVDQRSQYYDHNIMTNQHMGIQGEGQQHPKYYSFGHRKSFFSLPLSLVGIDICAPFSLASFSLKIKC