AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380012065.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380012065.01.T01 MTR_3g013460 96.635 208 7 0 1 208 62 269 4.15e-139 390
MsG0380012065.01.T01 MTR_3g013460 96.635 208 7 0 1 208 1 208 2.77e-138 385
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380012065.01.T01 AT5G07020 62.209 172 51 3 1 170 62 221 1.23e-66 205

Find 42 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCTGCAGGAGAGCTTTC+AGG 0.242491 3:-10418579 None:intergenic
CTCAGCGGGCGCGATGCTCT+CGG 0.325266 3:-10418493 None:intergenic
TCAGCGGGCGCGATGCTCTC+GGG 0.434622 3:-10418492 None:intergenic
GCAGAAAGTGCTATAAGTTC+AGG 0.456072 3:+10418177 MsG0380012065.01.T01:CDS
GCTATAAGTTCAGGAACATC+TGG 0.456974 3:+10418186 MsG0380012065.01.T01:CDS
TTGGACAGGTTATGTTGAAA+AGG 0.463563 3:+10417319 MsG0380012065.01.T01:CDS
CAGAACACAGCAGCAATTGC+TGG 0.464297 3:+10418228 MsG0380012065.01.T01:CDS
CGTCGTAAGCAGGGTTGGAC+AGG 0.496434 3:+10417305 MsG0380012065.01.T01:CDS
GGCATCATCAATACTTCTAC+AGG 0.502782 3:+10418278 MsG0380012065.01.T01:CDS
ATACCCACCACGTCGTAAGC+AGG 0.512722 3:+10417295 MsG0380012065.01.T01:CDS
TTTCCAGCCAGCAGTTTATG+TGG 0.517990 3:+10418155 MsG0380012065.01.T01:intron
ACATCTGGTTCTTCTTCTGA+TGG 0.519250 3:+10418201 MsG0380012065.01.T01:CDS
GAGGAGAAGACAAAAGTAGT+AGG 0.520284 3:+10417269 MsG0380012065.01.T01:CDS
TATGTTGAAAAGGATACTGC+TGG 0.525880 3:+10417329 MsG0380012065.01.T01:CDS
TGGTAAGAACTCTCCACCTC+AGG 0.530436 3:+10418302 MsG0380012065.01.T01:CDS
GTAGGCACATCACTCTCTGT+TGG 0.543592 3:-10418441 None:intergenic
GTAGTAACTAAGTGATGGCC+CGG 0.545619 3:-10418343 None:intergenic
CACCACGTCGTAAGCAGGGT+TGG 0.545868 3:+10417300 MsG0380012065.01.T01:CDS
TGAACTTGAGAAACTTCTGC+AGG 0.547339 3:-10418591 None:intergenic
CTTTCTGCCACATAAACTGC+TGG 0.548485 3:-10418162 None:intergenic
TTGGAAAGGTGAGTATGGAA+TGG 0.566949 3:+10417240 None:intergenic
GATGATAGTTCTGTCTCAGC+GGG 0.567883 3:-10418507 None:intergenic
CAACCCTGCTTACGACGTGG+TGG 0.579503 3:-10417299 None:intergenic
AGAAGTTTCTCAAGTTCAAG+TGG 0.583738 3:+10418596 MsG0380012065.01.T01:CDS
GATGATAGTTCTGTCTGAGT+AGG 0.588370 3:-10418459 None:intergenic
AGATACAGTGTCCACACTTG+AGG 0.588380 3:-10418640 None:intergenic
TCATCAATACTTCTACAGGT+TGG 0.599103 3:+10418282 MsG0380012065.01.T01:CDS
TGGAACAGATATCGATGCAT+CGG 0.615005 3:-10418556 None:intergenic
AACCCTGCTTACGACGTGGT+GGG 0.615593 3:-10417298 None:intergenic
GACAAATATATATTCAGTCG+AGG 0.616952 3:+10417355 MsG0380012065.01.T01:CDS
TTGATGTAGTAACTAAGTGA+TGG 0.619070 3:-10418348 None:intergenic
GAGTATGGAATGGTTAGCTG+AGG 0.620372 3:+10417250 None:intergenic
TCTGCAGGAGAGCTTTCAGG+TGG 0.631281 3:-10418576 None:intergenic
GTCCAACCCTGCTTACGACG+TGG 0.637764 3:-10417302 None:intergenic
TACCCACCACGTCGTAAGCA+GGG 0.638589 3:+10417296 MsG0380012065.01.T01:CDS
TCTGTCTCAGTAGACACAGA+GGG 0.638624 3:-10418402 None:intergenic
TGCACTGATCTCAATTGCCG+CGG 0.650728 3:+10418257 MsG0380012065.01.T01:CDS
TAGAAGTATTGATGATGCCG+CGG 0.657463 3:-10418274 None:intergenic
TCAGACAGAGACCTCAAGTG+TGG 0.661605 3:+10418629 MsG0380012065.01.T01:CDS
AACACAGCAGCAATTGCTGG+TGG 0.671200 3:+10418231 MsG0380012065.01.T01:CDS
TGATGATAGTTCTGTCTCAG+CGG 0.697894 3:-10418508 None:intergenic
CTCTGTCTCAGTAGACACAG+AGG 0.722923 3:-10418403 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGAAATTTTTCTTTTATTA+AGG + Chr3:10417379-10417398 MsG0380012065.01.T01:intron 10.0%
! GTAATACAAAAATCACAGTT+TGG + Chr3:10417742-10417761 MsG0380012065.01.T01:intron 25.0%
! TTAAATAAGTCAATCCAAAC+AGG + Chr3:10418005-10418024 MsG0380012065.01.T01:intron 25.0%
!! CATATCAATTTTACAGTATC+TGG + Chr3:10417566-10417585 MsG0380012065.01.T01:intron 25.0%
ACATGCTCAACAAAATCAAA+AGG - Chr3:10417473-10417492 None:intergenic 30.0%
CATACACACATAAAGATCAA+AGG - Chr3:10417439-10417458 None:intergenic 30.0%
GACAAATATATATTCAGTCG+AGG + Chr3:10417355-10417374 MsG0380012065.01.T01:CDS 30.0%
TTGATGTAGTAACTAAGTGA+TGG - Chr3:10418351-10418370 None:intergenic 30.0%
TTTAAGGACCTAGATTCTTA+AGG - Chr3:10418089-10418108 None:intergenic 30.0%
! AATTTTACAGTATCTGGTTG+AGG + Chr3:10417572-10417591 MsG0380012065.01.T01:intron 30.0%
! ATTTTACAGTATCTGGTTGA+GGG + Chr3:10417573-10417592 MsG0380012065.01.T01:intron 30.0%
! TTATTTTCATAAGCTCTCCA+AGG - Chr3:10417912-10417931 None:intergenic 30.0%
AAACGATGCCTTAAGAATCT+AGG + Chr3:10418078-10418097 MsG0380012065.01.T01:intron 35.0%
AGAAGTTTCTCAAGTTCAAG+TGG + Chr3:10418596-10418615 MsG0380012065.01.T01:CDS 35.0%
AGTATAACCACTTGTGAAAC+TGG - Chr3:10417974-10417993 None:intergenic 35.0%
TATGTTGAAAAGGATACTGC+TGG + Chr3:10417329-10417348 MsG0380012065.01.T01:CDS 35.0%
TCATCAATACTTCTACAGGT+TGG + Chr3:10418282-10418301 MsG0380012065.01.T01:CDS 35.0%
TTGGACAGGTTATGTTGAAA+AGG + Chr3:10417319-10417338 MsG0380012065.01.T01:CDS 35.0%
! AAATTTTCCCCACATTCGAT+AGG - Chr3:10417645-10417664 None:intergenic 35.0%
! CTAGGTCCTTAAATTTTCTC+TGG + Chr3:10418096-10418115 MsG0380012065.01.T01:intron 35.0%
!!! GTTGTTTTTGTAAGCTCTCT+TGG + Chr3:10417885-10417904 MsG0380012065.01.T01:intron 35.0%
CGAACGCCAGAGAAAATTTA+AGG - Chr3:10418105-10418124 None:intergenic 40.0%
CTGATTCTCCTATCGAATGT+GGG + Chr3:10417634-10417653 MsG0380012065.01.T01:intron 40.0%
GAATGTGGGGAAAATTTGCA+TGG + Chr3:10417648-10417667 MsG0380012065.01.T01:intron 40.0%
GAGGAGAAGACAAAAGTAGT+AGG + Chr3:10417269-10417288 MsG0380012065.01.T01:CDS 40.0%
GCTATAAGTTCAGGAACATC+TGG + Chr3:10418186-10418205 MsG0380012065.01.T01:CDS 40.0%
GGCATCATCAATACTTCTAC+AGG + Chr3:10418278-10418297 MsG0380012065.01.T01:CDS 40.0%
GTCCAAAAAGTCGAATACTC+CGG + Chr3:10418324-10418343 MsG0380012065.01.T01:CDS 40.0%
TCCAAAAAGTCGAATACTCC+GGG + Chr3:10418325-10418344 MsG0380012065.01.T01:CDS 40.0%
TGAACTTGAGAAACTTCTGC+AGG - Chr3:10418594-10418613 None:intergenic 40.0%
TGATTCTCCTATCGAATGTG+GGG + Chr3:10417635-10417654 MsG0380012065.01.T01:intron 40.0%
TGGAACAGATATCGATGCAT+CGG - Chr3:10418559-10418578 None:intergenic 40.0%
! GATGATAGTTCTGTCTGAGT+AGG - Chr3:10418462-10418481 None:intergenic 40.0%
! TATTCGACTTTTTGGACCTG+AGG - Chr3:10418321-10418340 None:intergenic 40.0%
! TGATGATAGTTCTGTCTCAG+CGG - Chr3:10418511-10418530 None:intergenic 40.0%
!! ACATCTGGTTCTTCTTCTGA+TGG + Chr3:10418201-10418220 MsG0380012065.01.T01:CDS 40.0%
!! GCAGAAAGTGCTATAAGTTC+AGG + Chr3:10418177-10418196 MsG0380012065.01.T01:CDS 40.0%
!! TAGAAGTATTGATGATGCCG+CGG - Chr3:10418277-10418296 None:intergenic 40.0%
AGATACAGTGTCCACACTTG+AGG - Chr3:10418643-10418662 None:intergenic 45.0%
AGCATGACTTTGTGCCTGTT+TGG - Chr3:10418022-10418041 None:intergenic 45.0%
ATCTGGTTGAGGGAAAATGC+AGG + Chr3:10417583-10417602 MsG0380012065.01.T01:intron 45.0%
CCACATTCGATAGGAGAATC+AGG - Chr3:10417636-10417655 None:intergenic 45.0%
CCTGATTCTCCTATCGAATG+TGG + Chr3:10417633-10417652 MsG0380012065.01.T01:intron 45.0%
CTCTCAACCAGTTTCACAAG+TGG + Chr3:10417964-10417983 MsG0380012065.01.T01:intron 45.0%
CTTTCTGCCACATAAACTGC+TGG - Chr3:10418165-10418184 None:intergenic 45.0%
GGGGAAAATTTGCATGGTAG+AGG + Chr3:10417654-10417673 MsG0380012065.01.T01:intron 45.0%
GTAGTAACTAAGTGATGGCC+CGG - Chr3:10418346-10418365 None:intergenic 45.0%
TCTGGTTGAGGGAAAATGCA+GGG + Chr3:10417584-10417603 MsG0380012065.01.T01:intron 45.0%
TCTGTCTCAGTAGACACAGA+GGG - Chr3:10418405-10418424 None:intergenic 45.0%
TTGTAAGCTCTCTTGGTCCT+TGG + Chr3:10417892-10417911 MsG0380012065.01.T01:intron 45.0%
TTTCCAGCCAGCAGTTTATG+TGG + Chr3:10418155-10418174 MsG0380012065.01.T01:intron 45.0%
! CATAAACTGCTGGCTGGAAA+AGG - Chr3:10418155-10418174 None:intergenic 45.0%
! GATGATAGTTCTGTCTCAGC+GGG - Chr3:10418510-10418529 None:intergenic 45.0%
AACACAGCAGCAATTGCTGG+TGG + Chr3:10418231-10418250 MsG0380012065.01.T01:CDS 50.0%
ACTTCTGCAGGAGAGCTTTC+AGG - Chr3:10418582-10418601 None:intergenic 50.0%
CAGAACACAGCAGCAATTGC+TGG + Chr3:10418228-10418247 MsG0380012065.01.T01:CDS 50.0%
CTCTGTCTCAGTAGACACAG+AGG - Chr3:10418406-10418425 None:intergenic 50.0%
GTAGGCACATCACTCTCTGT+TGG - Chr3:10418444-10418463 None:intergenic 50.0%
GTTGAGGGAAAATGCAGGGA+GGG + Chr3:10417588-10417607 MsG0380012065.01.T01:intron 50.0%
TCAGACAGAGACCTCAAGTG+TGG + Chr3:10418629-10418648 MsG0380012065.01.T01:CDS 50.0%
TGGTAAGAACTCTCCACCTC+AGG + Chr3:10418302-10418321 MsG0380012065.01.T01:CDS 50.0%
TTGAGGGAAAATGCAGGGAG+GGG + Chr3:10417589-10417608 MsG0380012065.01.T01:intron 50.0%
! TCGACTTTTTGGACCTGAGG+TGG - Chr3:10418318-10418337 None:intergenic 50.0%
! TGCACTGATCTCAATTGCCG+CGG + Chr3:10418257-10418276 MsG0380012065.01.T01:CDS 50.0%
!! GCCCGGAGTATTCGACTTTT+TGG - Chr3:10418329-10418348 None:intergenic 50.0%
AAAATGCAGGGAGGGGACTC+AGG + Chr3:10417596-10417615 MsG0380012065.01.T01:intron 55.0%
AAATGCAGGGAGGGGACTCA+GGG + Chr3:10417597-10417616 MsG0380012065.01.T01:intron 55.0%
AACCCTGCTTACGACGTGGT+GGG - Chr3:10417301-10417320 None:intergenic 55.0%
ATACCCACCACGTCGTAAGC+AGG + Chr3:10417295-10417314 MsG0380012065.01.T01:CDS 55.0%
CTGCCACATAAACTGCTGGC+TGG - Chr3:10418161-10418180 None:intergenic 55.0%
GGTTGAGGGAAAATGCAGGG+AGG + Chr3:10417587-10417606 MsG0380012065.01.T01:intron 55.0%
TACCCACCACGTCGTAAGCA+GGG + Chr3:10417296-10417315 MsG0380012065.01.T01:CDS 55.0%
TCTGCAGGAGAGCTTTCAGG+TGG - Chr3:10418579-10418598 None:intergenic 55.0%
CAACCCTGCTTACGACGTGG+TGG - Chr3:10417302-10417321 None:intergenic 60.0%
CACCACGTCGTAAGCAGGGT+TGG + Chr3:10417300-10417319 MsG0380012065.01.T01:CDS 60.0%
CGTCGTAAGCAGGGTTGGAC+AGG + Chr3:10417305-10417324 MsG0380012065.01.T01:CDS 60.0%
GTCCAACCCTGCTTACGACG+TGG - Chr3:10417305-10417324 None:intergenic 60.0%
CTCAGCGGGCGCGATGCTCT+CGG - Chr3:10418496-10418515 None:intergenic 70.0%
TCAGCGGGCGCGATGCTCTC+GGG - Chr3:10418495-10418514 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr3 gene 10417254 10418665 10417254 ID=MsG0380012065.01;Name=MsG0380012065.01
Chr3 mRNA 10417254 10418665 10417254 ID=MsG0380012065.01.T01;Parent=MsG0380012065.01;Name=MsG0380012065.01.T01;_AED=0.50;_eAED=0.50;_QI=0|0|0|1|1|1|2|0|208
Chr3 exon 10417254 10417376 10417254 ID=MsG0380012065.01.T01:exon:20983;Parent=MsG0380012065.01.T01
Chr3 exon 10418162 10418665 10418162 ID=MsG0380012065.01.T01:exon:20984;Parent=MsG0380012065.01.T01
Chr3 CDS 10417254 10417376 10417254 ID=MsG0380012065.01.T01:cds;Parent=MsG0380012065.01.T01
Chr3 CDS 10418162 10418665 10418162 ID=MsG0380012065.01.T01:cds;Parent=MsG0380012065.01.T01
Gene Sequence

>MsG0380012065.01.T01

ATGGAATGGTTAGCTGAGGAGAAGACAAAAGTAGTAGGTACATACCCACCACGTCGTAAGCAGGGTTGGACAGGTTATGTTGAAAAGGATACTGCTGGACAGACAAATATATATTCAGTCGAGCCAGCAGTTTATGTGGCAGAAAGTGCTATAAGTTCAGGAACATCTGGTTCTTCTTCTGATGGAGCTCAGAACACAGCAGCAATTGCTGGTGGTCTTGCACTGATCTCAATTGCCGCGGCATCATCAATACTTCTACAGGTTGGTAAGAACTCTCCACCTCAGGTCCAAAAAGTCGAATACTCCGGGCCATCACTTAGTTACTACATCAACGAGTTCAAAACACAAGAAATTACTCAAGCGCCCTCTGTGTCTACTGAGACAGAGCTATCATTGTCTGTTCCAACAGAGAGTGATGTGCCTACTCAGACAGAACTATCATCATCTGTTCAACCCGAGAGCATCGCGCCCGCTGAGACAGAACTATCATCATCTATTCAAACTGAGAGTGTTGCGACCGATGCATCGATATCTGTTCCACCTGAAAGCTCTCCTGCAGAAGTTTCTCAAGTTCAAGTGGAATCTCAAATTCAGACAGAGACCTCAAGTGTGGACACTGTATCTTAA

Protein sequence

>MsG0380012065.01.T01

MEWLAEEKTKVVGTYPPRRKQGWTGYVEKDTAGQTNIYSVEPAVYVAESAISSGTSGSSSDGAQNTAAIAGGLALISIAAASSILLQVGKNSPPQVQKVEYSGPSLSYYINEFKTQEITQAPSVSTETELSLSVPTESDVPTQTELSSSVQPESIAPAETELSSSIQTESVATDASISVPPESSPAEVSQVQVESQIQTETSSVDTVS*