AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016835.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016835.01.T01 MTR_3g096290 85.965 171 12 2 1 171 1 159 1.21e-97 279
MsG0380016835.01.T01 MTR_3g096290 85.366 123 12 1 1 123 9 125 2.72e-65 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016835.01.T01 AT1G74880 71.311 122 29 1 50 171 43 158 5.39e-60 184

Find 58 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCTTTACCGTCAATTATT+TGG 0.062226 3:-88452912 MsG0380016835.01.T01:three_prime_UTR
GGTTTCTTAGGAAGAGTCTT+AGG 0.205905 3:+88453889 None:intergenic
GTAGTCTAATCCTTTGTAAT+AGG 0.224129 3:+88453585 None:intergenic
CTGGAATAAACAGGTTTCTT+AGG 0.242562 3:+88453877 None:intergenic
TCATGGCCGAAAACATTATC+TGG 0.263318 3:+88452871 None:intergenic
ATTGTGTCTCTCTTAATTAA+TGG 0.294241 3:-88454118 MsG0380016835.01.T01:exon
ATCTTTACCGTCAATTATTT+GGG 0.313147 3:-88452911 MsG0380016835.01.T01:three_prime_UTR
CTTATCTCTAGTTGTATGTA+TGG 0.394151 3:-88454142 MsG0380016835.01.T01:five_prime_UTR
CTTGACTCACTGGAATAAAC+AGG 0.396415 3:+88453868 None:intergenic
GATATGCGTATATTTGAAAC+AGG 0.408664 3:-88453445 MsG0380016835.01.T01:CDS
CAAATAATTGACGGTAAAGA+TGG 0.409008 3:+88452913 None:intergenic
TCTTGAACTGCACGAATCAA+TGG 0.413571 3:+88454003 None:intergenic
GTTTCTTAGGAAGAGTCTTA+GGG 0.440236 3:+88453890 None:intergenic
TGCTTAATTCTCAGGTTGCA+TGG 0.442545 3:-88453232 MsG0380016835.01.T01:intron
GCAGTTCAAGACGGTGAACC+AGG 0.447486 3:-88453991 MsG0380016835.01.T01:CDS
TAGTCTAATCCTTTGTAATA+GGG 0.459657 3:+88453586 None:intergenic
GCATCAGAGCTCTTAGTTTG+TGG 0.477417 3:+88453955 None:intergenic
TCTTACAATACTAGACAAAC+AGG 0.486958 3:+88452979 None:intergenic
AAATAATTGACGGTAAAGAT+GGG 0.491445 3:+88452914 None:intergenic
TTTGAGAAATGGGAAAGAGA+AGG 0.496635 3:+88454060 None:intergenic
CTTGAACTGCACGAATCAAT+GGG 0.503362 3:+88454004 None:intergenic
GGAAGCCAAGCTGGAGCAGT+GGG 0.508111 3:+88453200 None:intergenic
AGGAAGAGTCTTAGGGGCAG+TGG 0.518025 3:+88453897 None:intergenic
ATGGGAAAGAGAAGGAAAGG+AGG 0.524817 3:+88454068 None:intergenic
GAAATGGGAAAGAGAAGGAA+AGG 0.530112 3:+88454065 None:intergenic
TAATTGTCCCAAATAATTGA+CGG 0.531007 3:+88452904 None:intergenic
GCTTAATTCTCAGGTTGCAT+GGG 0.543172 3:-88453231 MsG0380016835.01.T01:intron
TCCTACATACATGCTTATCA+AGG 0.544432 3:-88453180 MsG0380016835.01.T01:intron
AGGAAGCCAAGCTGGAGCAG+TGG 0.544685 3:+88453199 None:intergenic
GAGTCCCCACTGCTCCAGCT+TGG 0.545534 3:-88453205 MsG0380016835.01.T01:CDS
AATTTGTGGACAGTGAAGAA+AGG 0.549691 3:-88453768 MsG0380016835.01.T01:intron
AATTCTCAGGTTGCATGGGT+AGG 0.550094 3:-88453227 MsG0380016835.01.T01:intron
TTGACGGTAAAGATGGGGTA+TGG 0.550468 3:+88452920 None:intergenic
TCTAATCCTTTGTAATAGGG+TGG 0.556199 3:+88453589 None:intergenic
TGAAGAAAGGTCAGATTGTG+AGG 0.558487 3:-88453755 MsG0380016835.01.T01:CDS
ATGTATGTAGGAAGCCAAGC+TGG 0.563654 3:+88453191 None:intergenic
GGGCACCCACCCTATTACAA+AGG 0.572065 3:-88453595 MsG0380016835.01.T01:CDS
TCAGATTGTGAGGGTGGACA+AGG 0.576125 3:-88453745 MsG0380016835.01.T01:CDS
GAAAGGTCAGATTGTGAGGG+TGG 0.585375 3:-88453751 MsG0380016835.01.T01:CDS
CATGGCCGAAAACATTATCT+GGG 0.595369 3:+88452872 None:intergenic
CTAATCCTTTGTAATAGGGT+GGG 0.595783 3:+88453590 None:intergenic
CAGTTCAAGACGGTGAACCA+GGG 0.597426 3:-88453990 MsG0380016835.01.T01:CDS
AGCACTACTAGAGGAGGCTG+AGG 0.602396 3:+88453930 None:intergenic
ATGGGGTATGGTGTCTCTGA+TGG 0.613977 3:+88452932 None:intergenic
TTGATTCGTGCAGTTCAAGA+CGG 0.616062 3:-88454000 MsG0380016835.01.T01:CDS
TTTGTTTGTTTACCTCACCA+CGG 0.617430 3:+88453551 None:intergenic
AGTTCAAGACGGTGAACCAG+GGG 0.628235 3:-88453989 MsG0380016835.01.T01:CDS
ACCTTGATAAGCATGTATGT+AGG 0.632174 3:+88453179 None:intergenic
GAATCAATGGGAAAGAAGAA+CGG 0.633893 3:+88454016 None:intergenic
TTTCTTAGGAAGAGTCTTAG+GGG 0.641863 3:+88453891 None:intergenic
AATAATTGACGGTAAAGATG+GGG 0.654864 3:+88452915 None:intergenic
GAAGAAAGGTCAGATTGTGA+GGG 0.659835 3:-88453754 MsG0380016835.01.T01:CDS
AGACTGAGCACTACTAGAGG+AGG 0.683341 3:+88453924 None:intergenic
GACTACATTTACGAAGACCG+TGG 0.695548 3:-88453568 MsG0380016835.01.T01:CDS
TGAAGACTGAGCACTACTAG+AGG 0.698555 3:+88453921 None:intergenic
CATTTACGAAGACCGTGGTG+AGG 0.713150 3:-88453563 MsG0380016835.01.T01:intron
GTTCAAGACGGTGAACCAGG+GGG 0.724086 3:-88453988 MsG0380016835.01.T01:CDS
GAAGCCAAGCTGGAGCAGTG+GGG 0.758823 3:+88453201 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTTGTGTAAAAAAATTAT+TGG + Chr3:88453690-88453709 None:intergenic 15.0%
!!! ATTTTGTTTTCATAATCTTT+TGG + Chr3:88453512-88453531 None:intergenic 15.0%
!!! TATTCATTTTTGTTAATTTG+TGG - Chr3:88453253-88453272 MsG0380016835.01.T01:intron 15.0%
! AAATAATTGACGGTAAAGAT+GGG + Chr3:88454124-88454143 None:intergenic 25.0%
! AAATGTCAAACTGTATTTGT+AGG - Chr3:88453562-88453581 MsG0380016835.01.T01:intron 25.0%
! AGATACTGAAAAATTAACCT+TGG + Chr3:88453413-88453432 None:intergenic 25.0%
! ATCTTTACCGTCAATTATTT+GGG - Chr3:88454124-88454143 MsG0380016835.01.T01:five_prime_UTR 25.0%
! ATTGTGTCTCTCTTAATTAA+TGG - Chr3:88452917-88452936 MsG0380016835.01.T01:three_prime_UTR 25.0%
! ATTTCTCAAAAACTTTGACA+AGG - Chr3:88452988-88453007 MsG0380016835.01.T01:exon 25.0%
! TAATTGTCCCAAATAATTGA+CGG + Chr3:88454134-88454153 None:intergenic 25.0%
! TAGTCTAATCCTTTGTAATA+GGG + Chr3:88453452-88453471 None:intergenic 25.0%
!! GTTTTCTATGATTCCAATTA+TGG - Chr3:88453722-88453741 MsG0380016835.01.T01:CDS 25.0%
!!! ATTTTTCAGTATCTTTCTGT+TGG - Chr3:88453419-88453438 MsG0380016835.01.T01:CDS 25.0%
!!! TGTCAAAGTTTTTGAGAAAT+GGG + Chr3:88452988-88453007 None:intergenic 25.0%
!!! TTGTCAAAGTTTTTGAGAAA+TGG + Chr3:88452989-88453008 None:intergenic 25.0%
!!! TTTTTCAGTATCTTTCTGTT+GGG - Chr3:88453420-88453439 MsG0380016835.01.T01:CDS 25.0%
AATAATTGACGGTAAAGATG+GGG + Chr3:88454123-88454142 None:intergenic 30.0%
CAAATAATTGACGGTAAAGA+TGG + Chr3:88454125-88454144 None:intergenic 30.0%
CAACAAAAAAAGTAAGAGTG+AGG + Chr3:88453999-88454018 None:intergenic 30.0%
CATCTTTACCGTCAATTATT+TGG - Chr3:88454123-88454142 MsG0380016835.01.T01:five_prime_UTR 30.0%
CTTATCTCTAGTTGTATGTA+TGG - Chr3:88452893-88452912 MsG0380016835.01.T01:three_prime_UTR 30.0%
CTTCACAATGTTACCATAAT+TGG + Chr3:88453738-88453757 None:intergenic 30.0%
GTAGTCTAATCCTTTGTAAT+AGG + Chr3:88453453-88453472 None:intergenic 30.0%
TAATGCTTTACTTGTTCCAA+TGG - Chr3:88453878-88453897 MsG0380016835.01.T01:CDS 30.0%
TCTTACAATACTAGACAAAC+AGG + Chr3:88454059-88454078 None:intergenic 30.0%
! GATATGCGTATATTTGAAAC+AGG - Chr3:88453590-88453609 MsG0380016835.01.T01:CDS 30.0%
! TAAGAAGATGACTCTTTTGT+TGG + Chr3:88452877-88452896 None:intergenic 30.0%
AATTTGTGGACAGTGAAGAA+AGG - Chr3:88453267-88453286 MsG0380016835.01.T01:intron 35.0%
ACCTTGATAAGCATGTATGT+AGG + Chr3:88453859-88453878 None:intergenic 35.0%
CAAACTGTATTTGTAGGTCT+TGG - Chr3:88453568-88453587 MsG0380016835.01.T01:CDS 35.0%
CTAATCCTTTGTAATAGGGT+GGG + Chr3:88453448-88453467 None:intergenic 35.0%
CTGGAATAAACAGGTTTCTT+AGG + Chr3:88453161-88453180 None:intergenic 35.0%
GAATCAATGGGAAAGAAGAA+CGG + Chr3:88453022-88453041 None:intergenic 35.0%
GTTTCTTAGGAAGAGTCTTA+GGG + Chr3:88453148-88453167 None:intergenic 35.0%
TATTAGATTGTAGCAGCCAT+TGG + Chr3:88453897-88453916 None:intergenic 35.0%
TCCTACATACATGCTTATCA+AGG - Chr3:88453855-88453874 MsG0380016835.01.T01:intron 35.0%
TCTAATCCTTTGTAATAGGG+TGG + Chr3:88453449-88453468 None:intergenic 35.0%
TGTACCATTGCTTAATTCTC+AGG - Chr3:88453795-88453814 MsG0380016835.01.T01:intron 35.0%
TTTCTTAGGAAGAGTCTTAG+GGG + Chr3:88453147-88453166 None:intergenic 35.0%
TTTGAGAAATGGGAAAGAGA+AGG + Chr3:88452978-88452997 None:intergenic 35.0%
TTTGTTTGTTTACCTCACCA+CGG + Chr3:88453487-88453506 None:intergenic 35.0%
! TGCTACCCAGATAATGTTTT+CGG - Chr3:88454158-88454177 MsG0380016835.01.T01:five_prime_UTR 35.0%
CTTGAACTGCACGAATCAAT+GGG + Chr3:88453034-88453053 None:intergenic 40.0%
CTTGACTCACTGGAATAAAC+AGG + Chr3:88453170-88453189 None:intergenic 40.0%
GAAATGGGAAAGAGAAGGAA+AGG + Chr3:88452973-88452992 None:intergenic 40.0%
GAAGAAAGGTCAGATTGTGA+GGG - Chr3:88453281-88453300 MsG0380016835.01.T01:intron 40.0%
GCAACCTGAGAATTAAGCAA+TGG + Chr3:88453802-88453821 None:intergenic 40.0%
GGACTCAAATAACATGTCCA+AGG - Chr3:88453393-88453412 MsG0380016835.01.T01:intron 40.0%
GGTTTCTTAGGAAGAGTCTT+AGG + Chr3:88453149-88453168 None:intergenic 40.0%
TAGTTATGTCAGCTGTGAGT+AGG - Chr3:88453369-88453388 MsG0380016835.01.T01:intron 40.0%
TATTTGGTTGCTTGACTCAC+TGG + Chr3:88453180-88453199 None:intergenic 40.0%
TCTTGAACTGCACGAATCAA+TGG + Chr3:88453035-88453054 None:intergenic 40.0%
TGAAGAAAGGTCAGATTGTG+AGG - Chr3:88453280-88453299 MsG0380016835.01.T01:intron 40.0%
! GAAGATGACTCTTTTGTTGG+TGG + Chr3:88452874-88452893 None:intergenic 40.0%
! GCTTAATTCTCAGGTTGCAT+GGG - Chr3:88453804-88453823 MsG0380016835.01.T01:intron 40.0%
! TGCTTAATTCTCAGGTTGCA+TGG - Chr3:88453803-88453822 MsG0380016835.01.T01:intron 40.0%
! TTGATTCGTGCAGTTCAAGA+CGG - Chr3:88453035-88453054 MsG0380016835.01.T01:intron 40.0%
ATGGGAAAGAGAAGGAAAGG+AGG + Chr3:88452970-88452989 None:intergenic 45.0%
ATGTATGTAGGAAGCCAAGC+TGG + Chr3:88453847-88453866 None:intergenic 45.0%
GACTACATTTACGAAGACCG+TGG - Chr3:88453467-88453486 MsG0380016835.01.T01:intron 45.0%
TGAAGACTGAGCACTACTAG+AGG + Chr3:88453117-88453136 None:intergenic 45.0%
TTATGTCAGCTGTGAGTAGG+AGG - Chr3:88453372-88453391 MsG0380016835.01.T01:intron 45.0%
TTGACGGTAAAGATGGGGTA+TGG + Chr3:88454118-88454137 None:intergenic 45.0%
! AATTCTCAGGTTGCATGGGT+AGG - Chr3:88453808-88453827 MsG0380016835.01.T01:intron 45.0%
! GCATCAGAGCTCTTAGTTTG+TGG + Chr3:88453083-88453102 None:intergenic 45.0%
!! AATTCAAATAAATATTTATT+TGG + Chr3:88453196-88453215 None:intergenic 5.0%
AGACTGAGCACTACTAGAGG+AGG + Chr3:88453114-88453133 None:intergenic 50.0%
AGTTCAAGACGGTGAACCAG+GGG - Chr3:88453046-88453065 MsG0380016835.01.T01:intron 50.0%
ATGGGGTATGGTGTCTCTGA+TGG + Chr3:88454106-88454125 None:intergenic 50.0%
CAGTTCAAGACGGTGAACCA+GGG - Chr3:88453045-88453064 MsG0380016835.01.T01:intron 50.0%
CATTTACGAAGACCGTGGTG+AGG - Chr3:88453472-88453491 MsG0380016835.01.T01:intron 50.0%
GAAAGGTCAGATTGTGAGGG+TGG - Chr3:88453284-88453303 MsG0380016835.01.T01:intron 50.0%
GTCAGTAGTGTGTGTGCTGT+AGG - Chr3:88453637-88453656 MsG0380016835.01.T01:intron 50.0%
GTGCTGTAGGTGTGAACCAA+AGG - Chr3:88453650-88453669 MsG0380016835.01.T01:intron 50.0%
TCAGATTGTGAGGGTGGACA+AGG - Chr3:88453290-88453309 MsG0380016835.01.T01:intron 50.0%
AGCACTACTAGAGGAGGCTG+AGG + Chr3:88453108-88453127 None:intergenic 55.0%
AGGAAGAGTCTTAGGGGCAG+TGG + Chr3:88453141-88453160 None:intergenic 55.0%
GCAGTTCAAGACGGTGAACC+AGG - Chr3:88453044-88453063 MsG0380016835.01.T01:intron 55.0%
GGGCACCCACCCTATTACAA+AGG - Chr3:88453440-88453459 MsG0380016835.01.T01:CDS 55.0%
GTTCAAGACGGTGAACCAGG+GGG - Chr3:88453047-88453066 MsG0380016835.01.T01:intron 55.0%
AGGAAGCCAAGCTGGAGCAG+TGG + Chr3:88453839-88453858 None:intergenic 60.0%
GAAGCCAAGCTGGAGCAGTG+GGG + Chr3:88453837-88453856 None:intergenic 60.0%
GGAAGCCAAGCTGGAGCAGT+GGG + Chr3:88453838-88453857 None:intergenic 60.0%
GGCATGCTGTCAGCTGCCTT+TGG + Chr3:88453669-88453688 None:intergenic 60.0%
GAGTCCCCACTGCTCCAGCT+TGG - Chr3:88453830-88453849 MsG0380016835.01.T01:intron 65.0%
TGTGGCTGTGTACTGCCCCC+TGG + Chr3:88453065-88453084 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 88452874 88454183 88452874 ID=MsG0380016835.01;Name=MsG0380016835.01
Chr3 mRNA 88452874 88454183 88452874 ID=MsG0380016835.01.T01;Parent=MsG0380016835.01;Name=MsG0380016835.01.T01;_AED=0.34;_eAED=0.34;_QI=62|0.8|0.83|1|0.6|0.5|6|132|171
Chr3 exon 88452874 88453035 88452874 ID=MsG0380016835.01.T01:exon:30650;Parent=MsG0380016835.01.T01
Chr3 exon 88453181 88453240 88453181 ID=MsG0380016835.01.T01:exon:30649;Parent=MsG0380016835.01.T01
Chr3 exon 88453414 88453473 88453414 ID=MsG0380016835.01.T01:exon:30648;Parent=MsG0380016835.01.T01
Chr3 exon 88453564 88453629 88453564 ID=MsG0380016835.01.T01:exon:30647;Parent=MsG0380016835.01.T01
Chr3 exon 88453722 88453777 88453722 ID=MsG0380016835.01.T01:exon:30646;Parent=MsG0380016835.01.T01
Chr3 exon 88453878 88454183 88453878 ID=MsG0380016835.01.T01:exon:30645;Parent=MsG0380016835.01.T01
Chr3 five_prime_UTR 88454122 88454183 88454122 ID=MsG0380016835.01.T01:five_prime_utr;Parent=MsG0380016835.01.T01
Chr3 CDS 88453878 88454121 88453878 ID=MsG0380016835.01.T01:cds;Parent=MsG0380016835.01.T01
Chr3 CDS 88453722 88453777 88453722 ID=MsG0380016835.01.T01:cds;Parent=MsG0380016835.01.T01
Chr3 CDS 88453564 88453629 88453564 ID=MsG0380016835.01.T01:cds;Parent=MsG0380016835.01.T01
Chr3 CDS 88453414 88453473 88453414 ID=MsG0380016835.01.T01:cds;Parent=MsG0380016835.01.T01
Chr3 CDS 88453181 88453240 88453181 ID=MsG0380016835.01.T01:cds;Parent=MsG0380016835.01.T01
Chr3 CDS 88453006 88453035 88453006 ID=MsG0380016835.01.T01:cds;Parent=MsG0380016835.01.T01
Chr3 three_prime_UTR 88452874 88453005 88452874 ID=MsG0380016835.01.T01:three_prime_utr;Parent=MsG0380016835.01.T01
Gene Sequence

>MsG0380016835.01.T01

ATGGCTTTCTGTGTAACTCTCTGCTACTACACCTCCTTTCCTTCTCTTTCCCATTTCTCAAAAACTTTGACAAGGAAACATGTCCGTTCTTCTTTCCCATTGATTCGTGCAGTTCAAGACGGTGAACCAGGGGGCAGTACACAGCCACAAACTAAGAGCTCTGATGCTTCCTCAGCCTCCTCTAGTAGTGCTCAGTCTTCAACCACTGCCCCTAAGACTCTTCCTAAGAAACCTGTTTATTCCATGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCATCAATTATCTTTCTGTTGGGCACCCACCCTATTACAAAGGATTAGACTACATTTACGAAGACCGTGGTGAGGTCTTGGATATGCGTATATTTGAAACAGGAGAGCATGCACTTGTAAGTAACTTGTCAGTAGTTGCATGGGTAGGAGTCCCCACTGCTCCAGCTTGGCTTCCTACATACATGCTTATCAAGTCAGAGAAGCTCAATTATGAGAGACTATAA

Protein sequence

>MsG0380016835.01.T01

MAFCVTLCYYTSFPSLSHFSKTLTRKHVRSSFPLIRAVQDGEPGGSTQPQTKSSDASSASSSSAQSSTTAPKTLPKKPVYSMKKGQIVRVDKEKYLNSINYLSVGHPPYYKGLDYIYEDRGEVLDMRIFETGEHALVSNLSVVAWVGVPTAPAWLPTYMLIKSEKLNYERL*