AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480018626.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480018626.01.T01 MTR_4g015540 96.748 123 4 0 1 123 1 123 1.22e-82 238
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480018626.01.T01 AT2G38140 70.588 68 20 0 56 123 51 118 1.91e-25 93.2

Find 61 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAATATACTATTTGGATTT+TGG 0.107192 4:+7742638 MsG0480018626.01.T01:three_prime_UTR
TCCATTTGCAATATACTATT+TGG 0.117600 4:+7742631 MsG0480018626.01.T01:three_prime_UTR
ATCTTCAAGCTTCTCTTTCT+TGG 0.182199 4:-7742495 None:intergenic
CATGACCTTTCCAACAGTTT+TGG 0.247061 4:-7742980 None:intergenic
TCGCTTTCACCAACCCCTTC+TGG 0.306084 4:+7741774 MsG0480018626.01.T01:CDS
GTTCCCTTGTTCTTGTTCCT+TGG 0.334623 4:-7742437 None:intergenic
TTCTCTTTCTTGGTAGCATC+TGG 0.349140 4:-7742485 None:intergenic
GTTATCTATCCTCTCAGTTA+TGG 0.351088 4:+7741605 MsG0480018626.01.T01:exon
TCCAAATAGTATATTGCAAA+TGG 0.394156 4:-7742632 None:intergenic
GAAAGAGAAGCTTGAAGATA+AGG 0.394365 4:+7742499 MsG0480018626.01.T01:CDS
AAACGGTTCAGCCATTCGTT+TGG 0.400874 4:+7741923 MsG0480018626.01.T01:CDS
ACATAATAGAGACTAAAATA+AGG 0.408810 4:-7742691 None:intergenic
AACCAAACAAAAGTTTCCTA+TGG 0.418290 4:+7742920 MsG0480018626.01.T01:three_prime_UTR
ATAGTCAAGGTTTAAAATCC+TGG 0.418883 4:+7742759 MsG0480018626.01.T01:three_prime_UTR
TGTACTGTGGCAGAGGTGAT+AGG 0.433997 4:+7741885 MsG0480018626.01.T01:CDS
AGGAACAAGAACAAGGGAAC+AGG 0.442127 4:+7742440 MsG0480018626.01.T01:CDS
GCGTGGAGTTGAAGAGAGAG+TGG 0.442584 4:-7741663 None:intergenic
TATCGTATTGAGAGTGGGAT+TGG 0.471785 4:+7742726 MsG0480018626.01.T01:three_prime_UTR
GTGATAGCATCCAAAACTGT+TGG 0.474147 4:+7742970 MsG0480018626.01.T01:three_prime_UTR
CGTGGAGTTGAAGAGAGAGT+GGG 0.490020 4:-7741662 None:intergenic
GTAGGCAAATACTGCCAATT+CGG 0.492656 4:+7742802 MsG0480018626.01.T01:three_prime_UTR
TCTTTCTTGGTAGCATCTGG+TGG 0.499433 4:-7742482 None:intergenic
TGCTATATCGTATTGAGAGT+GGG 0.507195 4:+7742721 MsG0480018626.01.T01:three_prime_UTR
AGTTGAAGAGAGAGTGGGGA+AGG 0.510341 4:-7741657 None:intergenic
GATTGGTGAATGAAGAGATT+GGG 0.511184 4:-7741715 None:intergenic
AAAGGTGAGAAGAGGAAGCG+TGG 0.518100 4:-7741680 None:intergenic
ATTGGGATTGAGAGAAGGAA+AGG 0.519722 4:-7741698 None:intergenic
AGAGAAGGAAAGGTGAGAAG+AGG 0.519757 4:-7741688 None:intergenic
GGAAAACTGCTAAGGGGAAA+CGG 0.521583 4:+7741906 MsG0480018626.01.T01:CDS
AAATCAACTAACTAGAAAAG+AGG 0.524873 4:-7742550 None:intergenic
TGATTGGTGAATGAAGAGAT+TGG 0.533012 4:-7741716 None:intergenic
TTTGCAGTGTACTGTGGCAG+AGG 0.534962 4:+7741878 MsG0480018626.01.T01:intron
GTGGAGTTGAAGAGAGAGTG+GGG 0.546303 4:-7741661 None:intergenic
TGGAAACACTCTTATAGTCA+AGG 0.551542 4:+7742746 MsG0480018626.01.T01:three_prime_UTR
AGGTGATAGGAAAACTGCTA+AGG 0.552164 4:+7741898 MsG0480018626.01.T01:CDS
TCTGGTGGAGCATAAATCCT+TGG 0.553001 4:-7742467 None:intergenic
ACCAAACAAAAGTTTCCTAT+GGG 0.556263 4:+7742921 MsG0480018626.01.T01:three_prime_UTR
GGGACTGATGAAGTGATGAT+TGG 0.557778 4:-7741732 None:intergenic
CTACAACAGCACAAATCCTA+AGG 0.557797 4:-7742888 None:intergenic
ACAAGGTTGAAGAGAGGGTG+GGG 0.560540 4:-7741752 None:intergenic
AAGAGATTGGGATTGAGAGA+AGG 0.560973 4:-7741703 None:intergenic
AGCATCCAAAACTGTTGGAA+AGG 0.565573 4:+7742975 MsG0480018626.01.T01:three_prime_UTR
GGTGATAGGAAAACTGCTAA+GGG 0.567207 4:+7741899 MsG0480018626.01.T01:CDS
AATCAACTAACTAGAAAAGA+GGG 0.568120 4:-7742549 None:intergenic
ACATTACATTTCCAAACGAA+TGG 0.569487 4:-7741934 None:intergenic
AAGGCCAAGGAACAAGAACA+AGG 0.570532 4:+7742433 MsG0480018626.01.T01:CDS
TGTTGCAGTCGCAGAAGCAA+AGG 0.577430 4:-7743017 None:intergenic
TTGCTATATCGTATTGAGAG+TGG 0.577737 4:+7742720 MsG0480018626.01.T01:three_prime_UTR
CGACAAGGTTGAAGAGAGGG+TGG 0.579098 4:-7741754 None:intergenic
GGTGGAGCATAAATCCTTGG+TGG 0.582114 4:-7742464 None:intergenic
TATCCTCTCAGTTATGGCCA+TGG 0.592654 4:+7741611 MsG0480018626.01.T01:exon
TAGAAGCAGCGATGATGCCA+TGG 0.599730 4:-7741628 None:intergenic
GACAAGGTTGAAGAGAGGGT+GGG 0.607447 4:-7741753 None:intergenic
AAGCGACAAGGTTGAAGAGA+GGG 0.625118 4:-7741757 None:intergenic
AGGCCAAGGAACAAGAACAA+GGG 0.651122 4:+7742434 MsG0480018626.01.T01:CDS
AAAGCGACAAGGTTGAAGAG+AGG 0.661146 4:-7741758 None:intergenic
GATGTTATCAGGCAAGGCCA+AGG 0.662413 4:+7742420 MsG0480018626.01.T01:intron
AGGGGTTGGTGAAAGCGACA+AGG 0.666764 4:-7741769 None:intergenic
ATGCCATGGCCATAACTGAG+AGG 0.696408 4:-7741614 None:intergenic
ACAAGGGAACAGGACCACCA+AGG 0.709490 4:+7742450 MsG0480018626.01.T01:CDS
GTGATAGGAAAACTGCTAAG+GGG 0.715035 4:+7741900 MsG0480018626.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGTACATTAATTCATGTT+TGG + Chr4:7742092-7742111 MsG0480018626.01.T01:intron 20.0%
!! ACATAATAGAGACTAAAATA+AGG - Chr4:7742694-7742713 None:intergenic 20.0%
!! TAAAGAAAAAATTACCAGAA+GGG - Chr4:7741791-7741810 None:intergenic 20.0%
!! TTAAAGAAAAAATTACCAGA+AGG - Chr4:7741792-7741811 None:intergenic 20.0%
!! TTCAAAAGTGGTTATAAAAT+AGG + Chr4:7742246-7742265 MsG0480018626.01.T01:intron 20.0%
!!! ATGATGTATCCTTTTATAAA+AGG + Chr4:7742165-7742184 MsG0480018626.01.T01:intron 20.0%
!!! GATTTATAGTTTTTGACATA+TGG + Chr4:7742606-7742625 MsG0480018626.01.T01:three_prime_UTR 20.0%
!!! TGGAATTTTTGTTATGAATT+TGG + Chr4:7741817-7741836 MsG0480018626.01.T01:intron 20.0%
! AAAGAAAAAATTACCAGAAG+GGG - Chr4:7741790-7741809 None:intergenic 25.0%
! AAATCAACTAACTAGAAAAG+AGG - Chr4:7742553-7742572 None:intergenic 25.0%
! AATCAACTAACTAGAAAAGA+GGG - Chr4:7742552-7742571 None:intergenic 25.0%
! ACACTGCAAAAAAAATAAAC+TGG - Chr4:7741868-7741887 None:intergenic 25.0%
! ACAGTTTGAGAAAAAATTGT+AGG + Chr4:7742784-7742803 MsG0480018626.01.T01:three_prime_UTR 25.0%
! ATATGTTATGTGATGTTATC+AGG + Chr4:7742409-7742428 MsG0480018626.01.T01:intron 25.0%
! CACTGCAAAAAAAATAAACT+GGG - Chr4:7741867-7741886 None:intergenic 25.0%
! GAATTTATTGAGTGTATGTT+CGG + Chr4:7741998-7742017 MsG0480018626.01.T01:intron 25.0%
! TCCAAATAGTATATTGCAAA+TGG - Chr4:7742635-7742654 None:intergenic 25.0%
! TCCATTTGCAATATACTATT+TGG + Chr4:7742631-7742650 MsG0480018626.01.T01:three_prime_UTR 25.0%
!! GCAATATACTATTTGGATTT+TGG + Chr4:7742638-7742657 MsG0480018626.01.T01:three_prime_UTR 25.0%
!!! TGGTAGTTATTTTTCAAAAG+TGG + Chr4:7742234-7742253 MsG0480018626.01.T01:intron 25.0%
AACCAAACAAAAGTTTCCTA+TGG + Chr4:7742920-7742939 MsG0480018626.01.T01:three_prime_UTR 30.0%
ACATTACATTTCCAAACGAA+TGG - Chr4:7741937-7741956 None:intergenic 30.0%
ACCAAACAAAAGTTTCCTAT+GGG + Chr4:7742921-7742940 MsG0480018626.01.T01:three_prime_UTR 30.0%
CCAGAAACATATGAGTTAAA+TGG - Chr4:7742339-7742358 None:intergenic 30.0%
CCATTTAACTCATATGTTTC+TGG + Chr4:7742336-7742355 MsG0480018626.01.T01:intron 30.0%
GGTTATAAAATAGGCTTACA+TGG + Chr4:7742255-7742274 MsG0480018626.01.T01:intron 30.0%
! ATAGTCAAGGTTTAAAATCC+TGG + Chr4:7742759-7742778 MsG0480018626.01.T01:three_prime_UTR 30.0%
! GATGCGTATCCTTTTATAAA+AGG - Chr4:7742177-7742196 None:intergenic 30.0%
!! AAAATTTTAGTCCCTCTTCA+TGG - Chr4:7742384-7742403 None:intergenic 30.0%
!!! ATTTTTTTTGCAGTGTACTG+TGG + Chr4:7741872-7741891 MsG0480018626.01.T01:intron 30.0%
AAAAAATTACCAGAAGGGGT+TGG - Chr4:7741786-7741805 None:intergenic 35.0%
ATCTTCAAGCTTCTCTTTCT+TGG - Chr4:7742498-7742517 None:intergenic 35.0%
GAAAGAGAAGCTTGAAGATA+AGG + Chr4:7742499-7742518 MsG0480018626.01.T01:CDS 35.0%
GACAAAAATTGTGACCGAAT+TGG - Chr4:7742819-7742838 None:intergenic 35.0%
GATTGGTGAATGAAGAGATT+GGG - Chr4:7741718-7741737 None:intergenic 35.0%
GTTATCTATCCTCTCAGTTA+TGG + Chr4:7741605-7741624 MsG0480018626.01.T01:exon 35.0%
TATAAAAGGATACGCATCGT+CGG + Chr4:7742179-7742198 MsG0480018626.01.T01:intron 35.0%
TATTGAGTGTATGTTCGGTT+AGG + Chr4:7742003-7742022 MsG0480018626.01.T01:intron 35.0%
TCCTATGGGAAAAACTGATT+TGG + Chr4:7742935-7742954 MsG0480018626.01.T01:three_prime_UTR 35.0%
TGATTGGTGAATGAAGAGAT+TGG - Chr4:7741719-7741738 None:intergenic 35.0%
TGCTATATCGTATTGAGAGT+GGG + Chr4:7742721-7742740 MsG0480018626.01.T01:three_prime_UTR 35.0%
TGGAAACACTCTTATAGTCA+AGG + Chr4:7742746-7742765 MsG0480018626.01.T01:three_prime_UTR 35.0%
TTATGTGATGTTATCAGGCA+AGG + Chr4:7742414-7742433 MsG0480018626.01.T01:intron 35.0%
TTGCTATATCGTATTGAGAG+TGG + Chr4:7742720-7742739 MsG0480018626.01.T01:three_prime_UTR 35.0%
! AATTTTTGTCGCTATGTGGT+TGG + Chr4:7742829-7742848 MsG0480018626.01.T01:three_prime_UTR 35.0%
! ATTTTTGTCGCTATGTGGTT+GGG + Chr4:7742830-7742849 MsG0480018626.01.T01:three_prime_UTR 35.0%
! CCTATGGGAAAAACTGATTT+GGG + Chr4:7742936-7742955 MsG0480018626.01.T01:three_prime_UTR 35.0%
! TCACAATTTTTGTCGCTATG+TGG + Chr4:7742825-7742844 MsG0480018626.01.T01:three_prime_UTR 35.0%
! TCCCATAGGAAACTTTTGTT+TGG - Chr4:7742925-7742944 None:intergenic 35.0%
! TGTCATGGATTTTTCTCCTT+AGG + Chr4:7742872-7742891 MsG0480018626.01.T01:three_prime_UTR 35.0%
!! GAAAAACTGATTTGGGATGT+TGG + Chr4:7742943-7742962 MsG0480018626.01.T01:three_prime_UTR 35.0%
!!! TTTTTTCTCAAACTGTGACC+AGG - Chr4:7742780-7742799 None:intergenic 35.0%
AACTACCAAATGCTTCATGC+AGG - Chr4:7742222-7742241 None:intergenic 40.0%
AAGAGATTGGGATTGAGAGA+AGG - Chr4:7741706-7741725 None:intergenic 40.0%
AGCATCCAAAACTGTTGGAA+AGG + Chr4:7742975-7742994 MsG0480018626.01.T01:three_prime_UTR 40.0%
AGGTGATAGGAAAACTGCTA+AGG + Chr4:7741898-7741917 MsG0480018626.01.T01:CDS 40.0%
ATTGGGATTGAGAGAAGGAA+AGG - Chr4:7741701-7741720 None:intergenic 40.0%
CATCAAAAACCTCGATGTCA+TGG + Chr4:7742857-7742876 MsG0480018626.01.T01:three_prime_UTR 40.0%
CTACAACAGCACAAATCCTA+AGG - Chr4:7742891-7742910 None:intergenic 40.0%
GACTTTGTAGTCCATGAAGA+GGG + Chr4:7742370-7742389 MsG0480018626.01.T01:intron 40.0%
GAGAAAAATCCATGACATCG+AGG - Chr4:7742869-7742888 None:intergenic 40.0%
GGTGATAGGAAAACTGCTAA+GGG + Chr4:7741899-7741918 MsG0480018626.01.T01:CDS 40.0%
GTAGGCAAATACTGCCAATT+CGG + Chr4:7742802-7742821 MsG0480018626.01.T01:three_prime_UTR 40.0%
GTGATAGCATCCAAAACTGT+TGG + Chr4:7742970-7742989 MsG0480018626.01.T01:three_prime_UTR 40.0%
GTGATAGGAAAACTGCTAAG+GGG + Chr4:7741900-7741919 MsG0480018626.01.T01:CDS 40.0%
TATCGTATTGAGAGTGGGAT+TGG + Chr4:7742726-7742745 MsG0480018626.01.T01:three_prime_UTR 40.0%
! CATGACCTTTCCAACAGTTT+TGG - Chr4:7742983-7743002 None:intergenic 40.0%
! CCCAAATCAGTTTTTCCCAT+AGG - Chr4:7742939-7742958 None:intergenic 40.0%
! CTCTTCATGGACTACAAAGT+CGG - Chr4:7742371-7742390 None:intergenic 40.0%
! TTACACCTGCATGAAGCATT+TGG + Chr4:7742214-7742233 MsG0480018626.01.T01:intron 40.0%
! TTCTCTTTCTTGGTAGCATC+TGG - Chr4:7742488-7742507 None:intergenic 40.0%
! TTTTTGTCGCTATGTGGTTG+GGG + Chr4:7742831-7742850 MsG0480018626.01.T01:three_prime_UTR 40.0%
AAACGGTTCAGCCATTCGTT+TGG + Chr4:7741923-7741942 MsG0480018626.01.T01:CDS 45.0%
AAAGCGACAAGGTTGAAGAG+AGG - Chr4:7741761-7741780 None:intergenic 45.0%
AAGCGACAAGGTTGAAGAGA+GGG - Chr4:7741760-7741779 None:intergenic 45.0%
AAGGCCAAGGAACAAGAACA+AGG + Chr4:7742433-7742452 MsG0480018626.01.T01:CDS 45.0%
AGAGAAGGAAAGGTGAGAAG+AGG - Chr4:7741691-7741710 None:intergenic 45.0%
AGGAACAAGAACAAGGGAAC+AGG + Chr4:7742440-7742459 MsG0480018626.01.T01:CDS 45.0%
AGGCCAAGGAACAAGAACAA+GGG + Chr4:7742434-7742453 MsG0480018626.01.T01:CDS 45.0%
CGACTTTGTAGTCCATGAAG+AGG + Chr4:7742369-7742388 MsG0480018626.01.T01:intron 45.0%
GGAAAACTGCTAAGGGGAAA+CGG + Chr4:7741906-7741925 MsG0480018626.01.T01:CDS 45.0%
GGGACTGATGAAGTGATGAT+TGG - Chr4:7741735-7741754 None:intergenic 45.0%
GTTCCCTTGTTCTTGTTCCT+TGG - Chr4:7742440-7742459 None:intergenic 45.0%
TATCCTCTCAGTTATGGCCA+TGG + Chr4:7741611-7741630 MsG0480018626.01.T01:exon 45.0%
TCTGGTGGAGCATAAATCCT+TGG - Chr4:7742470-7742489 None:intergenic 45.0%
! TCTTTCTTGGTAGCATCTGG+TGG - Chr4:7742485-7742504 None:intergenic 45.0%
!!! TAATTTTTTCTTTAAAAAAA+TGG + Chr4:7741797-7741816 MsG0480018626.01.T01:intron 5.0%
AAAGGTGAGAAGAGGAAGCG+TGG - Chr4:7741683-7741702 None:intergenic 50.0%
ACAAGGTTGAAGAGAGGGTG+GGG - Chr4:7741755-7741774 None:intergenic 50.0%
AGTTGAAGAGAGAGTGGGGA+AGG - Chr4:7741660-7741679 None:intergenic 50.0%
ATGCCATGGCCATAACTGAG+AGG - Chr4:7741617-7741636 None:intergenic 50.0%
CGTGGAGTTGAAGAGAGAGT+GGG - Chr4:7741665-7741684 None:intergenic 50.0%
GACAAGGTTGAAGAGAGGGT+GGG - Chr4:7741756-7741775 None:intergenic 50.0%
GATGTTATCAGGCAAGGCCA+AGG + Chr4:7742420-7742439 MsG0480018626.01.T01:intron 50.0%
GGTGGAGCATAAATCCTTGG+TGG - Chr4:7742467-7742486 None:intergenic 50.0%
GTGGAGTTGAAGAGAGAGTG+GGG - Chr4:7741664-7741683 None:intergenic 50.0%
TAGAAGCAGCGATGATGCCA+TGG - Chr4:7741631-7741650 None:intergenic 50.0%
TGTACTGTGGCAGAGGTGAT+AGG + Chr4:7741885-7741904 MsG0480018626.01.T01:CDS 50.0%
TGTTGCAGTCGCAGAAGCAA+AGG - Chr4:7743020-7743039 None:intergenic 50.0%
TTTGCAGTGTACTGTGGCAG+AGG + Chr4:7741878-7741897 MsG0480018626.01.T01:intron 50.0%
ACAAGGGAACAGGACCACCA+AGG + Chr4:7742450-7742469 MsG0480018626.01.T01:CDS 55.0%
CGACAAGGTTGAAGAGAGGG+TGG - Chr4:7741757-7741776 None:intergenic 55.0%
GCGTGGAGTTGAAGAGAGAG+TGG - Chr4:7741666-7741685 None:intergenic 55.0%
TCGCTTTCACCAACCCCTTC+TGG + Chr4:7741774-7741793 MsG0480018626.01.T01:CDS 55.0%
!! AGGGGTTGGTGAAAGCGACA+AGG - Chr4:7741772-7741791 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
Chr4 gene 7741595 7743073 7741595 ID=MsG0480018626.01;Name=MsG0480018626.01
Chr4 mRNA 7741595 7743073 7741595 ID=MsG0480018626.01.T01;Parent=MsG0480018626.01;Name=MsG0480018626.01.T01;_AED=0.49;_eAED=0.49;_QI=29|1|1|1|0.5|0.66|3|508|123
Chr4 exon 7741595 7741795 7741595 ID=MsG0480018626.01.T01:exon:2468;Parent=MsG0480018626.01.T01
Chr4 exon 7741885 7741949 7741885 ID=MsG0480018626.01.T01:exon:2469;Parent=MsG0480018626.01.T01
Chr4 exon 7742431 7743073 7742431 ID=MsG0480018626.01.T01:exon:2470;Parent=MsG0480018626.01.T01
Chr4 five_prime_UTR 7741595 7741623 7741595 ID=MsG0480018626.01.T01:five_prime_utr;Parent=MsG0480018626.01.T01
Chr4 CDS 7741624 7741795 7741624 ID=MsG0480018626.01.T01:cds;Parent=MsG0480018626.01.T01
Chr4 CDS 7741885 7741949 7741885 ID=MsG0480018626.01.T01:cds;Parent=MsG0480018626.01.T01
Chr4 CDS 7742431 7742565 7742431 ID=MsG0480018626.01.T01:cds;Parent=MsG0480018626.01.T01
Chr4 three_prime_UTR 7742566 7743073 7742566 ID=MsG0480018626.01.T01:three_prime_utr;Parent=MsG0480018626.01.T01
Gene Sequence

>MsG0480018626.01.T01

ATGGCCATGGCATCATCGCTGCTTCTAGCATCACCTTCCCCACTCTCTCTTCAACTCCACGCTTCCTCTTCTCACCTTTCCTTCTCTCAATCCCAATCTCTTCATTCACCAATCATCACTTCATCAGTCCCCACCCTCTCTTCAACCTTGTCGCTTTCACCAACCCCTTCTGTGTACTGTGGCAGAGGTGATAGGAAAACTGCTAAGGGGAAACGGTTCAGCCATTCGTTTGGAAATGCAAGGCCAAGGAACAAGAACAAGGGAACAGGACCACCAAGGATTTATGCTCCACCAGATGCTACCAAGAAAGAGAAGCTTGAAGATAAGGAAGTGATTAAGATTGAAATTAATGAATCCCTCTTTTCTAGTTAG

Protein sequence

>MsG0480018626.01.T01

MAMASSLLLASPSPLSLQLHASSSHLSFSQSQSLHSPIITSSVPTLSSTLSLSPTPSVYCGRGDRKTAKGKRFSHSFGNARPRNKNKGTGPPRIYAPPDATKKEKLEDKEVIKIEINESLFSS*