AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680030883.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680030883.01.T01 MTR_6g013820 100.000 117 0 0 1 117 1 117 1.51e-82 237
MsG0680030883.01.T01 MTR_7g012560 75.630 119 27 1 1 117 1 119 5.54e-60 180
MsG0680030883.01.T01 MTR_7g012560 78.218 101 20 1 1 99 1 101 1.26e-51 159
MsG0680030883.01.T01 MTR_7g027300 53.097 113 49 2 8 117 7 118 1.32e-34 115
MsG0680030883.01.T01 MTR_8g096380 48.718 117 56 2 4 117 3 118 1.96e-33 113
MsG0680030883.01.T01 MTR_7g027017 48.246 114 51 1 8 113 7 120 5.89e-33 117
MsG0680030883.01.T01 MTR_7g108180 41.322 121 66 4 1 117 1 120 1.02e-25 93.6
MsG0680030883.01.T01 MTR_8g096390 44.444 90 48 1 3 90 2 91 2.67e-23 87.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680030883.01.T01 AT3G01050 56.410 117 51 0 1 117 1 117 2.65e-46 145
MsG0680030883.01.T01 AT3G01050 56.410 117 51 0 1 117 1 117 2.65e-46 145
MsG0680030883.01.T01 AT3G01050 56.410 117 51 0 1 117 1 117 2.65e-46 145
MsG0680030883.01.T01 AT3G01050 56.410 117 51 0 1 117 1 117 2.65e-46 145
MsG0680030883.01.T01 AT3G01050 56.410 117 51 0 1 117 1 117 2.65e-46 145
MsG0680030883.01.T01 AT5G15460 61.864 118 42 1 1 115 1 118 9.02e-44 139
MsG0680030883.01.T01 AT5G15460 61.864 118 42 1 1 115 1 118 9.02e-44 139
MsG0680030883.01.T01 AT5G15460 61.864 118 42 1 1 115 1 118 9.02e-44 139
MsG0680030883.01.T01 AT1G22050 52.941 119 54 1 1 117 1 119 4.72e-43 137
MsG0680030883.01.T01 AT1G77870 52.101 119 53 2 3 117 2 120 1.49e-36 121
MsG0680030883.01.T01 AT3G26980 47.458 118 58 2 4 117 3 120 1.12e-32 111
MsG0680030883.01.T01 AT4G24990 48.718 117 56 3 4 117 3 118 9.31e-32 108
MsG0680030883.01.T01 AT4G24990 48.718 117 56 3 4 117 3 118 9.31e-32 108
MsG0680030883.01.T01 AT5G15460 52.381 84 37 1 37 117 11 94 4.29e-19 76.3

Find 30 sgRNAs with CRISPR-Local

Find 109 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTGTGCAACCACCTAATT+TGG 0.182555 6:-11100906 MsG0680030883.01.T01:CDS
AAAATTTATCATGTTGAAAA+TGG 0.189098 6:+11102656 None:intergenic
TACAAACCTTTGTCCAAATT+AGG 0.290205 6:+11100893 None:intergenic
TTCCTCATACAAAAGTTCTT+TGG 0.321789 6:-11100377 MsG0680030883.01.T01:three_prime_UTR
ATCAATTAGAGATCAAATTT+CGG 0.354770 6:-11101931 MsG0680030883.01.T01:CDS
ATCACTCTCAATACCAAAAC+AGG 0.397259 6:+11102105 None:intergenic
AGAATCTGTTTCTCTGAGTA+TGG 0.409372 6:-11101966 MsG0680030883.01.T01:exon
CAAATTGTGCAAAGTCTTGA+AGG 0.410163 6:-11102053 MsG0680030883.01.T01:five_prime_UTR
CATGAGACATCATCAATCAT+TGG 0.416175 6:-11102579 MsG0680030883.01.T01:five_prime_UTR
AGTCCATTGTGTAATCTTCC+TGG 0.429392 6:-11100950 MsG0680030883.01.T01:CDS
TCTGTTTCTCTGAGTATGGC+TGG 0.457554 6:-11101962 MsG0680030883.01.T01:exon
TGGTATTGAGAGTGATTAAG+AGG 0.459258 6:-11102098 MsG0680030883.01.T01:five_prime_UTR
TTGAGCGATGGATCGGATAT+TGG 0.459581 6:-11101908 MsG0680030883.01.T01:CDS
TTCAGAAGAGACAGTGAAAG+TGG 0.471690 6:+11102605 None:intergenic
AAGAAAGTATTCTTACTCAA+TGG 0.476431 6:-11101844 MsG0680030883.01.T01:CDS
GATGTGAAGTTAATTTGTGC+TGG 0.476748 6:-11101013 MsG0680030883.01.T01:CDS
ATCAAATTTCGGTTGAGCGA+TGG 0.478567 6:-11101920 MsG0680030883.01.T01:CDS
AAGTCTTGAAGGAGAGACTT+TGG 0.493107 6:-11102042 MsG0680030883.01.T01:five_prime_UTR
ATTCTTACTCAATGGCCAAA+AGG 0.495557 6:-11101836 MsG0680030883.01.T01:intron
ATTTCGGTTGAGCGATGGAT+CGG 0.507983 6:-11101915 MsG0680030883.01.T01:CDS
AAAGAAATTTCCATTGTCTG+TGG 0.558395 6:-11100452 MsG0680030883.01.T01:three_prime_UTR
CTGTTTCTCTGAGTATGGCT+GGG 0.558929 6:-11101961 MsG0680030883.01.T01:exon
CAACCACCTAATTTGGACAA+AGG 0.572921 6:-11100899 MsG0680030883.01.T01:intron
GGAAAAGAAAACATCACTCA+AGG 0.582597 6:-11102558 MsG0680030883.01.T01:intron
AAACCTTTGTCCAAATTAGG+TGG 0.589222 6:+11100896 None:intergenic
AGCATTGTTGTAACTCCACC+AGG 0.610313 6:+11100932 None:intergenic
CCATTGTGTAATCTTCCTGG+TGG 0.622842 6:-11100947 MsG0680030883.01.T01:CDS
AAATTGTGTGAAGAAACAAC+TGG 0.625643 6:+11100291 None:intergenic
GGAGAACAACAAAACAGTAG+AGG 0.643312 6:-11100981 MsG0680030883.01.T01:CDS
CCACCAGGAAGATTACACAA+TGG 0.747125 6:+11100947 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTTATCATGTTGAAAA+TGG + Chr6:11100224-11100243 None:intergenic 15.0%
!! CATTCAAATGTTTATATTAA+TGG - Chr6:11101554-11101573 MsG0680030883.01.T01:intron 15.0%
!! TACACTATGAATAAATAAAT+TGG + Chr6:11100688-11100707 None:intergenic 15.0%
!!! AATGTTTTATTTATTTGGAT+TGG - Chr6:11100638-11100657 MsG0680030883.01.T01:intron 15.0%
!!! ATTTTTAGTTCATATAGTTT+TGG - Chr6:11102256-11102275 MsG0680030883.01.T01:intron 15.0%
!! AATTGAATTACATGGAAAAT+TGG - Chr6:11101423-11101442 MsG0680030883.01.T01:intron 20.0%
!! ATCAATTAGAGATCAAATTT+CGG - Chr6:11100946-11100965 MsG0680030883.01.T01:CDS 20.0%
!! ATTGAATTACATGGAAAATT+GGG - Chr6:11101424-11101443 MsG0680030883.01.T01:intron 20.0%
!! GTTAAATGAATTGAATTACA+TGG - Chr6:11101415-11101434 MsG0680030883.01.T01:intron 20.0%
!!! ACATTTTTAGACTTTATAGT+TGG + Chr6:11101754-11101773 None:intergenic 20.0%
!!! ATATTTCCTTTTTGAAGATA+AGG - Chr6:11101818-11101837 MsG0680030883.01.T01:intron 20.0%
!!! CATGTTTTAAAAGCTATTAT+TGG - Chr6:11102056-11102075 MsG0680030883.01.T01:five_prime_UTR 20.0%
!!! GTTATTTTCATAAACTATCT+TGG + Chr6:11101217-11101236 None:intergenic 20.0%
!!! TACATGATTTGTTAATTTAG+TGG - Chr6:11100519-11100538 MsG0680030883.01.T01:CDS 20.0%
!!! TGGTTGTTTAATCTTATTTA+GGG - Chr6:11101065-11101084 MsG0680030883.01.T01:intron 20.0%
!!! TTCATTTTTGTAATTGTCTA+TGG - Chr6:11102466-11102485 MsG0680030883.01.T01:intron 20.0%
!!! TTGGTTGTTTAATCTTATTT+AGG - Chr6:11101064-11101083 MsG0680030883.01.T01:intron 20.0%
!!! TTTAATTCTCATTGATTTTC+TGG - Chr6:11102286-11102305 MsG0680030883.01.T01:intron 20.0%
!!! TTTTACATGTAGTAATAGTA+AGG + Chr6:11102533-11102552 None:intergenic 20.0%
!!! TTTTCTCAGTTATGAATAAA+AGG + Chr6:11100868-11100887 None:intergenic 20.0%
!!! TTTTTTGTTCTTGTTATTGT+TGG - Chr6:11100346-11100365 MsG0680030883.01.T01:three_prime_UTR 20.0%
! AACAAACAAGTAATGATCAT+AGG + Chr6:11100478-11100497 None:intergenic 25.0%
! AATTTGTGCTGGAAAAATAT+TGG - Chr6:11101875-11101894 MsG0680030883.01.T01:CDS 25.0%
! ACTTATTTGAGCTTATTTAC+TGG - Chr6:11101101-11101120 MsG0680030883.01.T01:intron 25.0%
! GAAAATTGGGAATATTAATG+TGG - Chr6:11101437-11101456 MsG0680030883.01.T01:intron 25.0%
! TAATGGTTTAACATTGTATG+AGG - Chr6:11101571-11101590 MsG0680030883.01.T01:intron 25.0%
! TACTGCAAATTAATAAGAAC+TGG - Chr6:11101390-11101409 MsG0680030883.01.T01:intron 25.0%
! TATGATCATTACTTGTTTGT+TGG - Chr6:11100477-11100496 MsG0680030883.01.T01:three_prime_UTR 25.0%
! TGTTCATTTGAATATTGTGT+TGG - Chr6:11100388-11100407 MsG0680030883.01.T01:three_prime_UTR 25.0%
! TTCAATGTAATCACAATTGT+CGG - Chr6:11101669-11101688 MsG0680030883.01.T01:intron 25.0%
!! AATCTTATTTAGGGTTTGTT+TGG - Chr6:11101074-11101093 MsG0680030883.01.T01:intron 25.0%
!! TCATGTTCTCAGAATTTTAT+CGG + Chr6:11101644-11101663 None:intergenic 25.0%
!! TTCACATCTTTTACAGTTTT+TGG + Chr6:11101852-11101871 None:intergenic 25.0%
!! TTTTAACACACTATAATTGC+AGG + Chr6:11102091-11102110 None:intergenic 25.0%
!!! AAGAAAGTATTCTTACTCAA+TGG - Chr6:11101033-11101052 MsG0680030883.01.T01:CDS 25.0%
!!! CTTTTTGTAAGTTTGTTGAT+TGG - Chr6:11100435-11100454 MsG0680030883.01.T01:three_prime_UTR 25.0%
!!! TTTGAATATTGTGTTGGTTT+TGG - Chr6:11100394-11100413 MsG0680030883.01.T01:three_prime_UTR 25.0%
AAACTATCTTGGAGAGATTA+TGG + Chr6:11101206-11101225 None:intergenic 30.0%
AAAGAAATTTCCATTGTCTG+TGG - Chr6:11102425-11102444 MsG0680030883.01.T01:intron 30.0%
AAATACATTGTTACGAGAGT+TGG + Chr6:11102223-11102242 None:intergenic 30.0%
AAATTGTGTGAAGAAACAAC+TGG + Chr6:11102589-11102608 None:intergenic 30.0%
ATTGGTATCTTGGTATTCAT+AGG + Chr6:11101346-11101365 None:intergenic 30.0%
CATACTCCTTATCTTCAAAA+AGG + Chr6:11101827-11101846 None:intergenic 30.0%
GATGATTCCATTTAAGTGTA+TGG - Chr6:11101505-11101524 MsG0680030883.01.T01:intron 30.0%
GTTACAACCATACACTTAAA+TGG + Chr6:11101515-11101534 None:intergenic 30.0%
TACAAACCTTTGTCCAAATT+AGG + Chr6:11101987-11102006 None:intergenic 30.0%
TCATTACAACAGACACAAAT+TGG + Chr6:11101364-11101383 None:intergenic 30.0%
TTCCTCATACAAAAGTTCTT+TGG - Chr6:11102500-11102519 MsG0680030883.01.T01:intron 30.0%
! AAATCTGAAACAGTGAAGAA+AGG + Chr6:11100747-11100766 None:intergenic 30.0%
! AACCAAAGAACTTTTGTATG+AGG + Chr6:11102505-11102524 None:intergenic 30.0%
! AGATTAAACAACCAACCTTT+TGG + Chr6:11101059-11101078 None:intergenic 30.0%
!! CTTTTTGAAGATAAGGAGTA+TGG - Chr6:11101825-11101844 MsG0680030883.01.T01:intron 30.0%
!! TGGATGTATTGATTGATAGA+AGG - Chr6:11101457-11101476 MsG0680030883.01.T01:intron 30.0%
!! TTACTTTTAACCACAGACAA+TGG + Chr6:11102438-11102457 None:intergenic 30.0%
!!! TTATTTTTTTGAGGGAGCAA+AGG - Chr6:11102014-11102033 MsG0680030883.01.T01:five_prime_UTR 30.0%
AAACCTTTGTCCAAATTAGG+TGG + Chr6:11101984-11102003 None:intergenic 35.0%
AACTTTGTAACCTCAAGAGA+CGG - Chr6:11100551-11100570 MsG0680030883.01.T01:CDS 35.0%
AATTTGAATTCCGTCTCTTG+AGG + Chr6:11100564-11100583 None:intergenic 35.0%
ACAGACACAAATTGGTATCT+TGG + Chr6:11101356-11101375 None:intergenic 35.0%
ATCACTCTCAATACCAAAAC+AGG + Chr6:11100775-11100794 None:intergenic 35.0%
ATTCTTACTCAATGGCCAAA+AGG - Chr6:11101041-11101060 MsG0680030883.01.T01:CDS 35.0%
CAAATTGTGCAAAGTCTTGA+AGG - Chr6:11100824-11100843 MsG0680030883.01.T01:intron 35.0%
CATGAGACATCATCAATCAT+TGG - Chr6:11100298-11100317 MsG0680030883.01.T01:three_prime_UTR 35.0%
GGAAAAGAAAACATCACTCA+AGG - Chr6:11100319-11100338 MsG0680030883.01.T01:three_prime_UTR 35.0%
! AGAATCTGTTTCTCTGAGTA+TGG - Chr6:11100911-11100930 MsG0680030883.01.T01:CDS 35.0%
! TCAGATTTTGCATCCTGTTT+TGG - Chr6:11100759-11100778 MsG0680030883.01.T01:intron 35.0%
! TGGTATTGAGAGTGATTAAG+AGG - Chr6:11100779-11100798 MsG0680030883.01.T01:intron 35.0%
!! GATGTGAAGTTAATTTGTGC+TGG - Chr6:11101864-11101883 MsG0680030883.01.T01:CDS 35.0%
AAGTCTTGAAGGAGAGACTT+TGG - Chr6:11100835-11100854 MsG0680030883.01.T01:intron 40.0%
AGTCCATTGTGTAATCTTCC+TGG - Chr6:11101927-11101946 MsG0680030883.01.T01:CDS 40.0%
AGTTGTGCAACCACCTAATT+TGG - Chr6:11101971-11101990 MsG0680030883.01.T01:five_prime_UTR 40.0%
ATCAAATTTCGGTTGAGCGA+TGG - Chr6:11100957-11100976 MsG0680030883.01.T01:CDS 40.0%
ATTCCTAGAGTCGCTCATTT+GGG + Chr6:11102161-11102180 None:intergenic 40.0%
CAACCACCTAATTTGGACAA+AGG - Chr6:11101978-11101997 MsG0680030883.01.T01:five_prime_UTR 40.0%
GGAGAACAACAAAACAGTAG+AGG - Chr6:11101896-11101915 MsG0680030883.01.T01:CDS 40.0%
GTGTGTTAAAATGTGTGCGT+TGG - Chr6:11102100-11102119 MsG0680030883.01.T01:five_prime_UTR 40.0%
TCATAGGAAGACAGAAAGAG+AGG + Chr6:11101330-11101349 None:intergenic 40.0%
TTACTCAATGGCCAAAAGGT+TGG - Chr6:11101045-11101064 MsG0680030883.01.T01:CDS 40.0%
TTCAGAAGAGACAGTGAAAG+TGG + Chr6:11100275-11100294 None:intergenic 40.0%
! ACACCTTCAATCAGAAGTGT+CGG - Chr6:11101719-11101738 MsG0680030883.01.T01:intron 40.0%
! ACTTACTGGTTGTTTCACAC+GGG - Chr6:11102124-11102143 MsG0680030883.01.T01:intron 40.0%
! CACTTACTGGTTGTTTCACA+CGG - Chr6:11102123-11102142 MsG0680030883.01.T01:intron 40.0%
! GTAGCAGCAGCAAAACTTTT+CGG + Chr6:11100996-11101015 None:intergenic 40.0%
! TAGCAGCAGCAAAACTTTTC+GGG + Chr6:11100995-11101014 None:intergenic 40.0%
! TGGACAAATTTCCTCTGAGA+CGG + Chr6:11100597-11100616 None:intergenic 40.0%
AGCATTGTTGTAACTCCACC+AGG + Chr6:11101948-11101967 None:intergenic 45.0%
ATTTCGGTTGAGCGATGGAT+CGG - Chr6:11100962-11100981 MsG0680030883.01.T01:CDS 45.0%
CCACCAGGAAGATTACACAA+TGG + Chr6:11101933-11101952 None:intergenic 45.0%
CCATTGTGTAATCTTCCTGG+TGG - Chr6:11101930-11101949 MsG0680030883.01.T01:CDS 45.0%
GAACCGACACTTCTGATTGA+AGG + Chr6:11101725-11101744 None:intergenic 45.0%
GATTCCTAGAGTCGCTCATT+TGG + Chr6:11102162-11102181 None:intergenic 45.0%
TTGAGCGATGGATCGGATAT+TGG - Chr6:11100969-11100988 MsG0680030883.01.T01:CDS 45.0%
! CTGTTTCTCTGAGTATGGCT+GGG - Chr6:11100916-11100935 MsG0680030883.01.T01:CDS 45.0%
! TCTGTTTCTCTGAGTATGGC+TGG - Chr6:11100915-11100934 MsG0680030883.01.T01:CDS 45.0%
! TTCTGATTGAAGGTGTGTCC+TGG + Chr6:11101715-11101734 None:intergenic 45.0%
!!! ATTTTTTTTTATTTTTTTGA+GGG - Chr6:11102006-11102025 MsG0680030883.01.T01:five_prime_UTR 5.0%
!!! TAAAATGATTTTATTTTTAA+TGG + Chr6:11100617-11100636 None:intergenic 5.0%
!!! TATTTTTTTTTATTTTTTTG+AGG - Chr6:11102005-11102024 MsG0680030883.01.T01:five_prime_UTR 5.0%
!!! TTTATAATGTTTTATTTATT+TGG - Chr6:11100633-11100652 MsG0680030883.01.T01:intron 5.0%
CAACCCAAATGAGCGACTCT+AGG - Chr6:11102155-11102174 MsG0680030883.01.T01:intron 50.0%
! ACTGGTTGTTTCACACGGGT+TGG - Chr6:11102128-11102147 MsG0680030883.01.T01:intron 50.0%
! ATGTGTGCGTTGGCACTTAC+TGG - Chr6:11102110-11102129 MsG0680030883.01.T01:five_prime_UTR 50.0%
CGACGTGTCAATGTCGTGTC+TGG + Chr6:11101618-11101637 None:intergenic 55.0%
!! CACAATTGTCGGTGCCGTGT+AGG - Chr6:11101680-11101699 MsG0680030883.01.T01:intron 55.0%
!! TTCCTCTGAGACCGTCTCAG+AGG - Chr6:11100583-11100602 MsG0680030883.01.T01:intron 55.0%
!! TTCCTCTGAGACGGTCTCAG+AGG + Chr6:11100588-11100607 None:intergenic 55.0%
CCTGGTGTCCGACACCTACA+CGG + Chr6:11101697-11101716 None:intergenic 60.0%
!! TGTCGGTGCCGTGTAGGTGT+CGG - Chr6:11101686-11101705 MsG0680030883.01.T01:intron 60.0%
!! CCGTGTAGGTGTCGGACACC+AGG - Chr6:11101694-11101713 MsG0680030883.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr6 gene 11100203 11102696 11100203 ID=MsG0680030883.01;Name=MsG0680030883.01
Chr6 mRNA 11100203 11102696 11100203 ID=MsG0680030883.01.T01;Parent=MsG0680030883.01;Name=MsG0680030883.01.T01;_AED=0.49;_eAED=0.49;_QI=305|1|1|1|0.66|0.5|4|313|117
Chr6 exon 11100203 11100571 11100203 ID=MsG0680030883.01.T01:exon:8258;Parent=MsG0680030883.01.T01
Chr6 exon 11100900 11101064 11100900 ID=MsG0680030883.01.T01:exon:8257;Parent=MsG0680030883.01.T01
Chr6 exon 11101837 11102136 11101837 ID=MsG0680030883.01.T01:exon:8256;Parent=MsG0680030883.01.T01
Chr6 exon 11102559 11102696 11102559 ID=MsG0680030883.01.T01:exon:8255;Parent=MsG0680030883.01.T01
Chr6 five_prime_UTR 11102559 11102696 11102559 ID=MsG0680030883.01.T01:five_prime_utr;Parent=MsG0680030883.01.T01
Chr6 five_prime_UTR 11101970 11102136 11101970 ID=MsG0680030883.01.T01:five_prime_utr;Parent=MsG0680030883.01.T01
Chr6 CDS 11101837 11101969 11101837 ID=MsG0680030883.01.T01:cds;Parent=MsG0680030883.01.T01
Chr6 CDS 11100900 11101064 11100900 ID=MsG0680030883.01.T01:cds;Parent=MsG0680030883.01.T01
Chr6 CDS 11100516 11100571 11100516 ID=MsG0680030883.01.T01:cds;Parent=MsG0680030883.01.T01
Chr6 three_prime_UTR 11100203 11100515 11100203 ID=MsG0680030883.01.T01:three_prime_utr;Parent=MsG0680030883.01.T01
Gene Sequence

>MsG0680030883.01.T01

ATGGCTGGGAAACAAGATCAATTAGAGATCAAATTTCGGTTGAGCGATGGATCGGATATTGGCCCGAAAAGTTTTGCTGCTGCTACTAGTATTGCAACTTTGAAAGAAAGTATTCTTACTCAATGGCCAAAAGATAAGGAGTATGGTCCAAAAACTGTAAAAGATGTGAAGTTAATTTGTGCTGGAAAAATATTGGAGAACAACAAAACAGTAGAGGAATGTCAGAGTCCATTGTGTAATCTTCCTGGTGGAGTTACAACAATGCTTGTAGTTGTGCAACCACCTAATTTGGACAAAGATAAGAAAGTAGCAGATGAAGCAATGCAAAGCAAATGTGTTTGTGTTATATTATAG
Protein sequence

>MsG0680030883.01.T01

MAGKQDQLEIKFRLSDGSDIGPKSFAAATSIATLKESILTQWPKDKEYGPKTVKDVKLICAGKILENNKTVEECQSPLCNLPGGVTTMLVVVQPPNLDKDKKVADEAMQSKCVCVIL*