AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0780039223.01

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 65 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGGGGCCTTCTTTCTTTC+TGG 0.050172 7:+60114838 MsG0780039223.01.T01:CDS
CTCCACCATAATATGTAATT+TGG 0.141380 7:-60114635 None:intergenic
GTGTAACGCCGTCGACTTAT+TGG 0.204366 7:+60115261 MsG0780039223.01.T01:CDS
GACAATTCCTTCTCTTGATA+TGG 0.259836 7:+60114800 MsG0780039223.01.T01:CDS
CATCCCCAAATTACATATTA+TGG 0.271172 7:+60114630 MsG0780039223.01.T01:CDS
CTTATTTCACACAATTCTTC+TGG 0.312073 7:+60115020 MsG0780039223.01.T01:CDS
CCGTCGACTTATTGGGAAAT+AGG 0.326664 7:+60115269 MsG0780039223.01.T01:CDS
CCTTCTTTCTTTCTGGATCA+AGG 0.352139 7:+60114845 MsG0780039223.01.T01:CDS
TTAGCTAGGGCTCTTAGCTT+CGG 0.355237 7:+60114677 MsG0780039223.01.T01:CDS
TCCACCATAATATGTAATTT+GGG 0.358752 7:-60114634 None:intergenic
TCAATCAATCATGCCTCAAC+TGG 0.362896 7:+60114988 MsG0780039223.01.T01:CDS
TCCATCTCCATCATTGCATA+TGG 0.363127 7:-60115074 None:intergenic
CTGCGGGAGTGCACGGTGCC+CGG 0.369511 7:-60114607 None:intergenic
TGTAACGCCGTCGACTTATT+GGG 0.370689 7:+60115262 MsG0780039223.01.T01:CDS
GTCCCGCCGGTTCGTCTACC+CGG 0.377226 7:+60114588 MsG0780039223.01.T01:CDS
AACAGTTGGGGTCGTTGCTC+CGG 0.390741 7:-60115162 None:intergenic
TATAGAAAGTAAAGAGGAAA+AGG 0.408802 7:-60115048 None:intergenic
GGAACCAACTGGTTTCAAAC+CGG 0.414551 7:+60115128 MsG0780039223.01.T01:CDS
GAGCAACGACCCCAACTGTT+TGG 0.423750 7:+60115165 MsG0780039223.01.T01:CDS
AAGATATCTTCCAAACAGTT+GGG 0.426149 7:-60115175 None:intergenic
AAAGATATCTTCCAAACAGT+TGG 0.439827 7:-60115176 None:intergenic
TATATTCCCATATGCAATGA+TGG 0.445860 7:+60115067 MsG0780039223.01.T01:CDS
TAGCTAGGGCTCTTAGCTTC+GGG 0.446478 7:+60114678 MsG0780039223.01.T01:CDS
TCTCAAACTACGGAACCAAC+TGG 0.446986 7:+60115117 MsG0780039223.01.T01:CDS
ACTGTTGCGCTCACTTAGCT+AGG 0.457468 7:+60114663 MsG0780039223.01.T01:CDS
AGTCGACGGCGTTACACCAT+TGG 0.458129 7:-60115255 None:intergenic
TTGGAAGATATCTTTAGAAA+AGG 0.459172 7:+60115184 MsG0780039223.01.T01:CDS
TCAGCAGAATTCTCAAACTA+CGG 0.459270 7:+60115107 MsG0780039223.01.T01:CDS
CTCCGGACTCTCTTTCTGTC+CGG 0.474369 7:+60114949 MsG0780039223.01.T01:CDS
AACCGGCGGGACGTTGCCAT+TGG 0.497106 7:-60114577 None:intergenic
CTCCGGACAGAAAGAGAGTC+CGG 0.503283 7:-60114951 None:intergenic
CAATGATGGAGATGGAGTAC+TGG 0.504978 7:+60115081 MsG0780039223.01.T01:CDS
TGCGGGAGTGCACGGTGCCC+GGG 0.509029 7:-60114606 None:intergenic
CGGTGCCCGGGTAGACGAAC+CGG 0.516910 7:-60114594 None:intergenic
GGGGATGCTGCGGGAGTGCA+CGG 0.519944 7:-60114614 None:intergenic
ATGTAATTTGGGGATGCTGC+GGG 0.525841 7:-60114623 None:intergenic
CCATCTCCATCATTGCATAT+GGG 0.527434 7:-60115073 None:intergenic
GTCGACGGCGTTACACCATT+GGG 0.528355 7:-60115254 None:intergenic
GAATAAACTAGAGTACATAT+AGG 0.534335 7:-60115224 None:intergenic
AATTCCTTCTCTTGATATGG+AGG 0.535919 7:+60114803 MsG0780039223.01.T01:CDS
GAACCAACTGGTTTCAAACC+GGG 0.539035 7:+60115129 MsG0780039223.01.T01:CDS
CGGACTCTCTTTCTGTCCGG+AGG 0.547527 7:+60114952 MsG0780039223.01.T01:CDS
TCCTGTACAGGAAGGGCCAA+TGG 0.550957 7:+60114561 None:intergenic
GGCCAATGGCAACGTCCCGC+CGG 0.558527 7:+60114575 MsG0780039223.01.T01:CDS
CCCATATGCAATGATGGAGA+TGG 0.568071 7:+60115073 MsG0780039223.01.T01:CDS
TGGGAATATAGAAAGTAAAG+AGG 0.576408 7:-60115054 None:intergenic
TGATAAACAATGATTCCCTC+CGG 0.577024 7:-60114968 None:intergenic
TCCCGCCGGTTCGTCTACCC+GGG 0.583895 7:+60114589 MsG0780039223.01.T01:CDS
AATGATGGAGATGGAGTACT+GGG 0.586189 7:+60115082 MsG0780039223.01.T01:CDS
CCTTGATCCAGAAAGAAAGA+AGG 0.591712 7:-60114845 None:intergenic
AACCAACTGGTTTCAAACCG+GGG 0.592362 7:+60115130 MsG0780039223.01.T01:CDS
GGACTCTCTTTCTGTCCGGA+GGG 0.599190 7:+60114953 MsG0780039223.01.T01:CDS
CTGTTGCGCTCACTTAGCTA+GGG 0.608731 7:+60114664 MsG0780039223.01.T01:CDS
CCCCAAATTACATATTATGG+TGG 0.609418 7:+60114633 MsG0780039223.01.T01:CDS
AAAACCTCCATATCAAGAGA+AGG 0.610694 7:-60114807 None:intergenic
AGATATCTTCCAAACAGTTG+GGG 0.624749 7:-60115174 None:intergenic
TATGTAATTTGGGGATGCTG+CGG 0.628643 7:-60114624 None:intergenic
ACCAACTGGTTTCAAACCGG+GGG 0.641576 7:+60115131 MsG0780039223.01.T01:CDS
CCACCATAATATGTAATTTG+GGG 0.642068 7:-60114633 None:intergenic
TGCCCGGGTAGACGAACCGG+CGG 0.642757 7:-60114591 None:intergenic
GCCCGGGTAGACGAACCGGC+GGG 0.649133 7:-60114590 None:intergenic
CCTATTTCCCAATAAGTCGA+CGG 0.660244 7:-60115269 None:intergenic
GTTTATTCGAAGTATCCCAA+TGG 0.661630 7:+60115239 MsG0780039223.01.T01:CDS
AGAGTACATATAGGATACAC+CGG 0.680335 7:-60115215 None:intergenic
ATGATGGAGATGGAGTACTG+GGG 0.841918 7:+60115083 MsG0780039223.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTGGATTATTTTTCTTGA+GGG + Chr7:60114715-60114734 MsG0780039223.01.T01:intron 20.0%
!!! TTAAAAAATAAAGTGTTCAG+TGG + Chr7:60114778-60114797 MsG0780039223.01.T01:intron 20.0%
! AGAAAAATAATCCAAATCGA+AGG - Chr7:60114712-60114731 None:intergenic 25.0%
! GAATAAACTAGAGTACATAT+AGG - Chr7:60115227-60115246 None:intergenic 25.0%
! TATAGAAAGTAAAGAGGAAA+AGG - Chr7:60115051-60115070 None:intergenic 25.0%
! TCCACCATAATATGTAATTT+GGG - Chr7:60114637-60114656 None:intergenic 25.0%
!! TTGGAAGATATCTTTAGAAA+AGG + Chr7:60115184-60115203 MsG0780039223.01.T01:CDS 25.0%
!!! GATTTGGATTATTTTTCTTG+AGG + Chr7:60114714-60114733 MsG0780039223.01.T01:intron 25.0%
!!! TTTGGATTATTTTTCTTGAG+GGG + Chr7:60114716-60114735 MsG0780039223.01.T01:intron 25.0%
AAAGATATCTTCCAAACAGT+TGG - Chr7:60115179-60115198 None:intergenic 30.0%
AAGATATCTTCCAAACAGTT+GGG - Chr7:60115178-60115197 None:intergenic 30.0%
CATCCCCAAATTACATATTA+TGG + Chr7:60114630-60114649 MsG0780039223.01.T01:CDS 30.0%
CCACCATAATATGTAATTTG+GGG - Chr7:60114636-60114655 None:intergenic 30.0%
CTCCACCATAATATGTAATT+TGG - Chr7:60114638-60114657 None:intergenic 30.0%
CTTATTTCACACAATTCTTC+TGG + Chr7:60115020-60115039 MsG0780039223.01.T01:CDS 30.0%
TATATTCCCATATGCAATGA+TGG + Chr7:60115067-60115086 MsG0780039223.01.T01:CDS 30.0%
TGGGAATATAGAAAGTAAAG+AGG - Chr7:60115057-60115076 None:intergenic 30.0%
TTGACCAACAAATTATGCAT+GGG - Chr7:60114896-60114915 None:intergenic 30.0%
! GAATGAATTCTATTGAGTTG+TGG - Chr7:60114922-60114941 None:intergenic 30.0%
! TAAGTGAATTTTTCCAGTTG+AGG - Chr7:60115004-60115023 None:intergenic 30.0%
!! GAATTCATTCTTTAAGACTC+CGG + Chr7:60114932-60114951 MsG0780039223.01.T01:intron 30.0%
!! TTGGATTATTTTTCTTGAGG+GGG + Chr7:60114717-60114736 MsG0780039223.01.T01:intron 30.0%
!! TTTAGAAAAGGTTTTAGCAC+CGG + Chr7:60115196-60115215 MsG0780039223.01.T01:CDS 30.0%
AAAACCTCCATATCAAGAGA+AGG - Chr7:60114810-60114829 None:intergenic 35.0%
AATTCCTTCTCTTGATATGG+AGG + Chr7:60114803-60114822 MsG0780039223.01.T01:CDS 35.0%
AGAGTACATATAGGATACAC+CGG - Chr7:60115218-60115237 None:intergenic 35.0%
AGATATCTTCCAAACAGTTG+GGG - Chr7:60115177-60115196 None:intergenic 35.0%
CCCCAAATTACATATTATGG+TGG + Chr7:60114633-60114652 MsG0780039223.01.T01:CDS 35.0%
GACAATTCCTTCTCTTGATA+TGG + Chr7:60114800-60114819 MsG0780039223.01.T01:CDS 35.0%
GTTGACCAACAAATTATGCA+TGG - Chr7:60114897-60114916 None:intergenic 35.0%
TCAGCAGAATTCTCAAACTA+CGG + Chr7:60115107-60115126 MsG0780039223.01.T01:CDS 35.0%
TGATAAACAATGATTCCCTC+CGG - Chr7:60114971-60114990 None:intergenic 35.0%
! GTTTATTCGAAGTATCCCAA+TGG + Chr7:60115239-60115258 MsG0780039223.01.T01:CDS 35.0%
! TCTCTTGATATGGAGGTTTT+AGG + Chr7:60114810-60114829 MsG0780039223.01.T01:CDS 35.0%
! TTCTCCCATGCATAATTTGT+TGG + Chr7:60114889-60114908 MsG0780039223.01.T01:intron 35.0%
CCATCTCCATCATTGCATAT+GGG - Chr7:60115076-60115095 None:intergenic 40.0%
CCTATTTCCCAATAAGTCGA+CGG - Chr7:60115272-60115291 None:intergenic 40.0%
CCTTCTTTCTTTCTGGATCA+AGG + Chr7:60114845-60114864 MsG0780039223.01.T01:CDS 40.0%
CCTTGATCCAGAAAGAAAGA+AGG - Chr7:60114848-60114867 None:intergenic 40.0%
TATGTAATTTGGGGATGCTG+CGG - Chr7:60114627-60114646 None:intergenic 40.0%
TCAATCAATCATGCCTCAAC+TGG + Chr7:60114988-60115007 MsG0780039223.01.T01:CDS 40.0%
TCCATCTCCATCATTGCATA+TGG - Chr7:60115077-60115096 None:intergenic 40.0%
! AATGATGGAGATGGAGTACT+GGG + Chr7:60115082-60115101 MsG0780039223.01.T01:CDS 40.0%
!!! ATATGGAGGTTTTAGGTCTC+TGG + Chr7:60114817-60114836 MsG0780039223.01.T01:CDS 40.0%
ATGTAATTTGGGGATGCTGC+GGG - Chr7:60114626-60114645 None:intergenic 45.0%
GTCAGAAATCACTGTCTGTC+TGG + Chr7:60114749-60114768 MsG0780039223.01.T01:intron 45.0%
TCTCAAACTACGGAACCAAC+TGG + Chr7:60115117-60115136 MsG0780039223.01.T01:CDS 45.0%
TTAGCTAGGGCTCTTAGCTT+CGG + Chr7:60114677-60114696 MsG0780039223.01.T01:CDS 45.0%
! AACCAACTGGTTTCAAACCG+GGG + Chr7:60115130-60115149 MsG0780039223.01.T01:CDS 45.0%
! CAATGATGGAGATGGAGTAC+TGG + Chr7:60115081-60115100 MsG0780039223.01.T01:CDS 45.0%
! CCCATATGCAATGATGGAGA+TGG + Chr7:60115073-60115092 MsG0780039223.01.T01:CDS 45.0%
! GAACCAACTGGTTTCAAACC+GGG + Chr7:60115129-60115148 MsG0780039223.01.T01:CDS 45.0%
! GGAACCAACTGGTTTCAAAC+CGG + Chr7:60115128-60115147 MsG0780039223.01.T01:CDS 45.0%
!! ATGATGGAGATGGAGTACTG+GGG + Chr7:60115083-60115102 MsG0780039223.01.T01:CDS 45.0%
!! CCGTCGACTTATTGGGAAAT+AGG + Chr7:60115269-60115288 MsG0780039223.01.T01:CDS 45.0%
!! TGTAACGCCGTCGACTTATT+GGG + Chr7:60115262-60115281 MsG0780039223.01.T01:CDS 45.0%
ACTGTTGCGCTCACTTAGCT+AGG + Chr7:60114663-60114682 MsG0780039223.01.T01:CDS 50.0%
CAAACCGGGGGAACAAAATC+CGG + Chr7:60115143-60115162 MsG0780039223.01.T01:CDS 50.0%
CTGTTGCGCTCACTTAGCTA+GGG + Chr7:60114664-60114683 MsG0780039223.01.T01:CDS 50.0%
TAGCTAGGGCTCTTAGCTTC+GGG + Chr7:60114678-60114697 MsG0780039223.01.T01:CDS 50.0%
! ACCAACTGGTTTCAAACCGG+GGG + Chr7:60115131-60115150 MsG0780039223.01.T01:CDS 50.0%
!! GTGTAACGCCGTCGACTTAT+TGG + Chr7:60115261-60115280 MsG0780039223.01.T01:CDS 50.0%
!!! GAGGTTTTAGGTCTCTGGAG+GGG + Chr7:60114822-60114841 MsG0780039223.01.T01:CDS 50.0%
!!! GGAGGTTTTAGGTCTCTGGA+GGG + Chr7:60114821-60114840 MsG0780039223.01.T01:CDS 50.0%
!!! TGGAGGTTTTAGGTCTCTGG+AGG + Chr7:60114820-60114839 MsG0780039223.01.T01:CDS 50.0%
AACAGTTGGGGTCGTTGCTC+CGG - Chr7:60115165-60115184 None:intergenic 55.0%
AGTCGACGGCGTTACACCAT+TGG - Chr7:60115258-60115277 None:intergenic 55.0%
CTCCGGACAGAAAGAGAGTC+CGG - Chr7:60114954-60114973 None:intergenic 55.0%
CTCCGGACTCTCTTTCTGTC+CGG + Chr7:60114949-60114968 MsG0780039223.01.T01:CDS 55.0%
GAGCAACGACCCCAACTGTT+TGG + Chr7:60115165-60115184 MsG0780039223.01.T01:CDS 55.0%
GCTCTTAGCTTCGGGTGAGA+GGG + Chr7:60114686-60114705 MsG0780039223.01.T01:intron 55.0%
GGACTCTCTTTCTGTCCGGA+GGG + Chr7:60114953-60114972 MsG0780039223.01.T01:CDS 55.0%
GGAGGGGCCTTCTTTCTTTC+TGG + Chr7:60114838-60114857 MsG0780039223.01.T01:CDS 55.0%
GTCGACGGCGTTACACCATT+GGG - Chr7:60115257-60115276 None:intergenic 55.0%
! TCCCCCGGTTTGAAACCAGT+TGG - Chr7:60115135-60115154 None:intergenic 55.0%
! TGCTCCGGATTTTGTTCCCC+CGG - Chr7:60115150-60115169 None:intergenic 55.0%
CGGACTCTCTTTCTGTCCGG+AGG + Chr7:60114952-60114971 MsG0780039223.01.T01:CDS 60.0%
GGCTCTTAGCTTCGGGTGAG+AGG + Chr7:60114685-60114704 MsG0780039223.01.T01:intron 60.0%
GGGTGAGAGGGCCTTCGATT+TGG + Chr7:60114698-60114717 MsG0780039223.01.T01:intron 60.0%
AACCGGCGGGACGTTGCCAT+TGG - Chr7:60114580-60114599 None:intergenic 65.0%
CGGTGCCCGGGTAGACGAAC+CGG - Chr7:60114597-60114616 None:intergenic 70.0%
GGCCAATGGCAACGTCCCGC+CGG + Chr7:60114575-60114594 MsG0780039223.01.T01:CDS 70.0%
TGCCCGGGTAGACGAACCGG+CGG - Chr7:60114594-60114613 None:intergenic 70.0%
! GGGGATGCTGCGGGAGTGCA+CGG - Chr7:60114617-60114636 None:intergenic 70.0%
!! GTCCCGCCGGTTCGTCTACC+CGG + Chr7:60114588-60114607 MsG0780039223.01.T01:CDS 70.0%
!! TCCCGCCGGTTCGTCTACCC+GGG + Chr7:60114589-60114608 MsG0780039223.01.T01:CDS 70.0%
GCCCGGGTAGACGAACCGGC+GGG - Chr7:60114593-60114612 None:intergenic 75.0%
! CTGCGGGAGTGCACGGTGCC+CGG - Chr7:60114610-60114629 None:intergenic 75.0%
! TGCGGGAGTGCACGGTGCCC+GGG - Chr7:60114609-60114628 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
Chr7 gene 60114572 60115301 60114572 ID=MsG0780039223.01;Name=MsG0780039223.01
Chr7 mRNA 60114572 60115301 60114572 ID=MsG0780039223.01.T01;Parent=MsG0780039223.01;Name=MsG0780039223.01.T01;_AED=0.33;_eAED=0.93;_QI=0|0|0|1|0|0|3|0|185
Chr7 exon 60114572 60114699 60114572 ID=MsG0780039223.01.T01:exon:7245;Parent=MsG0780039223.01.T01
Chr7 exon 60114791 60114866 60114791 ID=MsG0780039223.01.T01:exon:7246;Parent=MsG0780039223.01.T01
Chr7 exon 60114948 60115301 60114948 ID=MsG0780039223.01.T01:exon:7247;Parent=MsG0780039223.01.T01
Chr7 CDS 60114572 60114699 60114572 ID=MsG0780039223.01.T01:cds;Parent=MsG0780039223.01.T01
Chr7 CDS 60114791 60114866 60114791 ID=MsG0780039223.01.T01:cds;Parent=MsG0780039223.01.T01
Chr7 CDS 60114948 60115301 60114948 ID=MsG0780039223.01.T01:cds;Parent=MsG0780039223.01.T01
Gene Sequence

>MsG0780039223.01.T01

AAGGGCCAATGGCAACGTCCCGCCGGTTCGTCTACCCGGGCACCGTGCACTCCCGCAGCATCCCCAAATTACATATTATGGTGGAGTCTAAACTGTTGCGCTCACTTAGCTAGGGCTCTTAGCTTCGGTGTTCAGTGGACAATTCCTTCTCTTGATATGGAGGTTTTAGGTCTCTGGAGGGGCCTTCTTTCTTTCTGGATCAAGACTCCGGACTCTCTTTCTGTCCGGAGGGAATCATTGTTTATCAATCAATCATGCCTCAACTGGAAAAATTCACTTATTTCACACAATTCTTCTGGTCATGCCTTTTCCTCTTTACTTTCTATATTCCCATATGCAATGATGGAGATGGAGTACTGGGGATCAGCAGAATTCTCAAACTACGGAACCAACTGGTTTCAAACCGGGGGAACAAAATCCGGAGCAACGACCCCAACTGTTTGGAAGATATCTTTAGAAAAGGTTTTAGCACCGGTGTATCCTATATGTACTCTAGTTTATTCGAAGTATCCCAATGGTGTAACGCCGTCGACTTATTGGGAAATAGGAGTAAAATAA
Protein sequence

>MsG0780039223.01.T01

KGQWQRPAGSSTRAPCTPAASPNYILWWSLNCCAHLARALSFGVQWTIPSLDMEVLGLWRGLLSFWIKTPDSLSVRRESLFINQSCLNWKNSLISHNSSGHAFSSLLSIFPYAMMEMEYWGSAEFSNYGTNWFQTGGTKSGATTPTVWKISLEKVLAPVYPICTLVYSKYPNGVTPSTYWEIGVK*