AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016555.01

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 19 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACCTTGTACTCGTTGTTGT+TGG 0.334917 3:+85091647 None:intergenic
TGATAAGACTATACAGGATT+AGG 0.384895 3:+85091721 None:intergenic
CATTTCCGCTATTCACTTCA+CGG 0.387492 3:-85091611 MsG0380016555.01.T01:CDS
CGTGAAGTGAATAGCGGAAA+TGG 0.421717 3:+85091612 None:intergenic
CGCTATTCACTTCACGGCTG+AGG 0.475002 3:-85091605 MsG0380016555.01.T01:CDS
GATGAGTGATAAGACTATAC+AGG 0.492066 3:+85091715 None:intergenic
CGCCAACAACAACGAGTACA+AGG 0.504228 3:-85091649 MsG0380016555.01.T01:CDS
TATCACCGCCGCCGTTCACC+TGG 0.508173 3:-85091548 MsG0380016555.01.T01:intron
ACTCACCAGGTGAACGGCGG+CGG 0.547947 3:+85091543 None:intergenic
GGCTGAGGACAAAACAAGAA+AGG 0.574993 3:-85091590 MsG0380016555.01.T01:CDS
AACGGCGGCGGTGATAGATA+CGG 0.601775 3:+85091555 None:intergenic
AGGATTAGGAATGACACCAT+TGG 0.622277 3:+85091735 None:intergenic
AATCAAACTCACCAGGTGAA+CGG 0.627191 3:+85091537 None:intergenic
GAAGTGAATAGCGGAAATGG+TGG 0.653706 3:+85091615 None:intergenic
CAACAACGAGTACAAGGTGA+GGG 0.655207 3:-85091643 MsG0380016555.01.T01:CDS
GGTGATAGATACGGTTGCAA+CGG 0.663678 3:+85091564 None:intergenic
ACAACAACGAGTACAAGGTG+AGG 0.663882 3:-85091644 MsG0380016555.01.T01:CDS
CTCAGCCGTGAAGTGAATAG+CGG 0.680943 3:+85091606 None:intergenic
CAAACTCACCAGGTGAACGG+CGG 0.716929 3:+85091540 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTATAATTTATCAATAT+TGG + Chr3:85090488-85090507 None:intergenic 10.0%
!!! ATATTGATAAATTATACTTT+TGG - Chr3:85090488-85090507 MsG0380016555.01.T01:intron 10.0%
!! CACTATAATAAAATAGAATT+GGG - Chr3:85090848-85090867 MsG0380016555.01.T01:intron 15.0%
!! TCACTATAATAAAATAGAAT+TGG - Chr3:85090847-85090866 MsG0380016555.01.T01:intron 15.0%
!! TTAGAATAAAAACATTTAGT+TGG - Chr3:85090173-85090192 MsG0380016555.01.T01:intron 15.0%
!!! AAAAATTAAGTTGTTTTGTA+AGG - Chr3:85091542-85091561 MsG0380016555.01.T01:intron 15.0%
!!! TTACAAAACAACTTAATTTT+TGG + Chr3:85091543-85091562 None:intergenic 15.0%
!!! TTATATAACTTTAAGGAATA+AGG + Chr3:85090200-85090219 None:intergenic 15.0%
!!! TTCTAATTTTTTCAAGATTA+AGG + Chr3:85090540-85090559 None:intergenic 15.0%
!!! TTTTTATTCTAACACAAAAA+TGG + Chr3:85090165-85090184 None:intergenic 15.0%
!!! ATAAGTTGAAGATGATTTAT+TGG - Chr3:85090925-85090944 MsG0380016555.01.T01:intron 20.0%
!!! GATCTTGTGTTTTTATAATA+GGG - Chr3:85091259-85091278 MsG0380016555.01.T01:intron 20.0%
! ACACTGTACAATCATTAAAA+TGG + Chr3:85091616-85091635 None:intergenic 25.0%
! AGTATGATATATCTAATGAG+AGG - Chr3:85090138-85090157 MsG0380016555.01.T01:intron 25.0%
! CTCATTAGATATATCATACT+CGG + Chr3:85090138-85090157 None:intergenic 25.0%
! GCACTTCTTATATAACTTTA+AGG + Chr3:85090207-85090226 None:intergenic 25.0%
! TTATTATCCTACATCTCATA+AGG + Chr3:85091064-85091083 None:intergenic 25.0%
! TTCGGTCAATAAATAATGTT+TGG - Chr3:85090249-85090268 MsG0380016555.01.T01:intron 25.0%
!! ATATCAATGCTCAAACATTT+TGG + Chr3:85091207-85091226 None:intergenic 25.0%
!!! AATTAAGTTGTTTTGTAAGG+TGG - Chr3:85091545-85091564 MsG0380016555.01.T01:intron 25.0%
!!! ATTAAGTTGTTTTGTAAGGT+GGG - Chr3:85091546-85091565 MsG0380016555.01.T01:intron 25.0%
!!! GGATCTTGTGTTTTTATAAT+AGG - Chr3:85091258-85091277 MsG0380016555.01.T01:intron 25.0%
AACATGCTAGCAAGTAAAAA+AGG + Chr3:85091399-85091418 None:intergenic 30.0%
AATATGAAATCAAACTCACC+AGG + Chr3:85089992-85090011 None:intergenic 30.0%
CAAATCATTATTCAGAGTCA+TGG + Chr3:85091448-85091467 None:intergenic 30.0%
CTAGCAAGTAAAAAAGGTAA+CGG + Chr3:85091393-85091412 None:intergenic 30.0%
TGATAAGACTATACAGGATT+AGG + Chr3:85089801-85089820 None:intergenic 30.0%
TTGCATTTGTATACGAAGAT+TGG - Chr3:85090795-85090814 MsG0380016555.01.T01:intron 30.0%
! CTAGTTAAGTTGTTACCATA+AGG - Chr3:85090881-85090900 MsG0380016555.01.T01:intron 30.0%
! TGAAGTCACTATTTTGTTCA+AGG - Chr3:85090304-85090323 MsG0380016555.01.T01:intron 30.0%
! TTATCAATATTGGTCTGCAT+AGG + Chr3:85090478-85090497 None:intergenic 30.0%
! TTGACTTCAAGTTTCTCAAA+TGG + Chr3:85090624-85090643 None:intergenic 30.0%
!! ATAATGTTTGGTCTTAGAGA+AGG - Chr3:85090261-85090280 MsG0380016555.01.T01:intron 30.0%
!! TAAAAAAGGTAACGGAATCA+TGG + Chr3:85091385-85091404 None:intergenic 30.0%
!! TATAAGAAGTGCTTGTTAAC+AGG - Chr3:85090215-85090234 MsG0380016555.01.T01:intron 30.0%
!! TTTTTACTTGCTAGCATGTT+AGG - Chr3:85091399-85091418 MsG0380016555.01.T01:intron 30.0%
AAATATTAAACAACCCCGTC+AGG + Chr3:85091297-85091316 None:intergenic 35.0%
AAGTTCCTTGAGATACCTTA+TGG + Chr3:85090899-85090918 None:intergenic 35.0%
AATGTGAGAGAAGCTCAAAT+TGG + Chr3:85091714-85091733 None:intergenic 35.0%
AATTTGAGCTTCTCTCACAT+TGG - Chr3:85091713-85091732 MsG0380016555.01.T01:CDS 35.0%
ACTTGGCAAACATAGAATAG+TGG + Chr3:85090019-85090038 None:intergenic 35.0%
ATGTGATCCTTATGAGATGT+AGG - Chr3:85091054-85091073 MsG0380016555.01.T01:intron 35.0%
ATTCTATGTTTGCCAAGTTC+TGG - Chr3:85090021-85090040 MsG0380016555.01.T01:intron 35.0%
CACAAGATCCCTATAATTAC+AGG + Chr3:85091248-85091267 None:intergenic 35.0%
CCTAAAAACATCCTCGTATT+GGG - Chr3:85091659-85091678 MsG0380016555.01.T01:CDS 35.0%
GATGAGTGATAAGACTATAC+AGG + Chr3:85089807-85089826 None:intergenic 35.0%
GCTCAAATTGGAATAGTTCT+AGG + Chr3:85091702-85091721 None:intergenic 35.0%
GCTGGAGATGTAAATAAGAA+TGG - Chr3:85091112-85091131 MsG0380016555.01.T01:intron 35.0%
GGAGATGTAAATAAGAATGG+TGG - Chr3:85091115-85091134 MsG0380016555.01.T01:intron 35.0%
GTCATGTGCCTGTAATTATA+GGG - Chr3:85091237-85091256 MsG0380016555.01.T01:intron 35.0%
TAAACTGTTGGGAAAACTCT+TGG + Chr3:85090702-85090721 None:intergenic 35.0%
TCATTATTCAGAGTCATGGT+TGG + Chr3:85091444-85091463 None:intergenic 35.0%
TTCTATGTTTGCCAAGTTCT+GGG - Chr3:85090022-85090041 MsG0380016555.01.T01:intron 35.0%
TTCTTCTGTGATCTGATGAA+TGG - Chr3:85090395-85090414 MsG0380016555.01.T01:intron 35.0%
! AGAGTTTTCCCAACAGTTTA+AGG - Chr3:85090702-85090721 MsG0380016555.01.T01:intron 35.0%
! CAACCAATCTTTTTCTCTCT+CGG - Chr3:85089827-85089846 MsG0380016555.01.T01:intron 35.0%
! TCTCGGTTCTTTTTGTCATT+TGG - Chr3:85089844-85089863 MsG0380016555.01.T01:intron 35.0%
! TGTTACCATAAGGTATCTCA+AGG - Chr3:85090891-85090910 MsG0380016555.01.T01:intron 35.0%
!! AAAAGGTACTTGCAAGTTAC+AGG - Chr3:85091146-85091165 MsG0380016555.01.T01:intron 35.0%
!! AAAGGTACTTGCAAGTTACA+GGG - Chr3:85091147-85091166 MsG0380016555.01.T01:intron 35.0%
!! AGTTCTAGGACAATGTAGTA+TGG + Chr3:85091688-85091707 None:intergenic 35.0%
!! CCAATACGAGGATGTTTTTA+GGG + Chr3:85091661-85091680 None:intergenic 35.0%
!! CTCGGTTCTTTTTGTCATTT+GGG - Chr3:85089845-85089864 MsG0380016555.01.T01:intron 35.0%
!! GAGCATTGATATCATACTTG+AGG - Chr3:85091215-85091234 MsG0380016555.01.T01:intron 35.0%
AATCAAACTCACCAGGTGAA+CGG + Chr3:85089985-85090004 None:intergenic 40.0%
AATGGAAGCAGAGACAGAAA+AGG + Chr3:85090361-85090380 None:intergenic 40.0%
ACCCAAAGTTATCTGAGAGT+CGG + Chr3:85090669-85090688 None:intergenic 40.0%
AGTAGAGTGAGACTCGTAAA+AGG + Chr3:85091324-85091343 None:intergenic 40.0%
ATGGAAGCAGAGACAGAAAA+GGG + Chr3:85090360-85090379 None:intergenic 40.0%
CAGACACTCCTTAAACTGTT+GGG + Chr3:85090713-85090732 None:intergenic 40.0%
CATCAGATCACAGAAGAACA+CGG + Chr3:85090393-85090412 None:intergenic 40.0%
CATTTCCGCTATTCACTTCA+CGG - Chr3:85089908-85089927 MsG0380016555.01.T01:intron 40.0%
CCCTAAAAACATCCTCGTAT+TGG - Chr3:85091658-85091677 MsG0380016555.01.T01:CDS 40.0%
CGAGAGAGAAAAAGATTGGT+TGG + Chr3:85089829-85089848 None:intergenic 40.0%
CTAATCCATAAGAGCTGAGT+TGG - Chr3:85091588-85091607 MsG0380016555.01.T01:CDS 40.0%
CTTATTTACATCTCCAGCGA+TGG + Chr3:85091110-85091129 None:intergenic 40.0%
GAACCGAGAGAGAAAAAGAT+TGG + Chr3:85089833-85089852 None:intergenic 40.0%
GAGTCTCACTCTACTCATAT+CGG - Chr3:85091329-85091348 MsG0380016555.01.T01:intron 40.0%
GGTCATGTGCCTGTAATTAT+AGG - Chr3:85091236-85091255 MsG0380016555.01.T01:intron 40.0%
TAGCATAACGCTGTCTCATT+TGG - Chr3:85091512-85091531 MsG0380016555.01.T01:intron 40.0%
TAGTATGGTAACCCAATACG+AGG + Chr3:85091673-85091692 None:intergenic 40.0%
TCAGACACTCCTTAAACTGT+TGG + Chr3:85090714-85090733 None:intergenic 40.0%
TCCGACTCTCAGATAACTTT+GGG - Chr3:85090665-85090684 MsG0380016555.01.T01:intron 40.0%
TGTGTGACTGTGTTCTAACT+AGG - Chr3:85090445-85090464 MsG0380016555.01.T01:intron 40.0%
! AAGTGCTTGTTAACAGGAAG+AGG - Chr3:85090221-85090240 MsG0380016555.01.T01:intron 40.0%
! AGTGCTTGTTAACAGGAAGA+GGG - Chr3:85090222-85090241 MsG0380016555.01.T01:intron 40.0%
! CAAGGAACAAACTTTTCCTC+TGG - Chr3:85090322-85090341 MsG0380016555.01.T01:intron 40.0%
! CCCAATACGAGGATGTTTTT+AGG + Chr3:85091662-85091681 None:intergenic 40.0%
! GAATGGTGGAGACGTATAAA+AGG - Chr3:85091129-85091148 MsG0380016555.01.T01:intron 40.0%
! GGCAAACATAGAATAGTGGA+AGG + Chr3:85090015-85090034 None:intergenic 40.0%
!! AAAGGTAACGGAATCATGGA+TGG + Chr3:85091381-85091400 None:intergenic 40.0%
!! TAACAGGAAGAGGGAGTATT+CGG - Chr3:85090231-85090250 MsG0380016555.01.T01:intron 40.0%
!! TCAGCTCTTATGGATTAGAG+TGG + Chr3:85091586-85091605 None:intergenic 40.0%
!! TTGGTCTTAGAGAAGGAAGA+TGG - Chr3:85090268-85090287 MsG0380016555.01.T01:intron 40.0%
ACAACAACGAGTACAAGGTG+AGG - Chr3:85089875-85089894 MsG0380016555.01.T01:intron 45.0%
CAACAACGAGTACAAGGTGA+GGG - Chr3:85089876-85089895 MsG0380016555.01.T01:intron 45.0%
CACCTTGTACTCGTTGTTGT+TGG + Chr3:85089875-85089894 None:intergenic 45.0%
CTCCGACTCTCAGATAACTT+TGG - Chr3:85090664-85090683 MsG0380016555.01.T01:intron 45.0%
GGCTGAGGACAAAACAAGAA+AGG - Chr3:85089929-85089948 MsG0380016555.01.T01:intron 45.0%
GGGTTTCTGCGAAGAGAAAA+TGG + Chr3:85091641-85091660 None:intergenic 45.0%
GGTGATAGATACGGTTGCAA+CGG + Chr3:85089958-85089977 None:intergenic 45.0%
TATTAAACAACCCCGTCAGG+TGG + Chr3:85091294-85091313 None:intergenic 45.0%
TCTGATGAATGGAGAGTGAG+CGG - Chr3:85090406-85090425 MsG0380016555.01.T01:intron 45.0%
TGGAAGCAGAGACAGAAAAG+GGG + Chr3:85090359-85090378 None:intergenic 45.0%
TGGATCCAACTCAGCTCTTA+TGG + Chr3:85091596-85091615 None:intergenic 45.0%
! CGTGAAGTGAATAGCGGAAA+TGG + Chr3:85089910-85089929 None:intergenic 45.0%
! GAAGTGAATAGCGGAAATGG+TGG + Chr3:85089907-85089926 None:intergenic 45.0%
AGAACACGGCATGATGGCAA+TGG + Chr3:85090379-85090398 None:intergenic 50.0%
AGGGGAAAATACTCTGCCAG+AGG + Chr3:85090341-85090360 None:intergenic 50.0%
CACAGAAGAACACGGCATGA+TGG + Chr3:85090385-85090404 None:intergenic 50.0%
CGCCAACAACAACGAGTACA+AGG - Chr3:85089870-85089889 MsG0380016555.01.T01:intron 50.0%
CTCAGCCGTGAAGTGAATAG+CGG + Chr3:85089916-85089935 None:intergenic 50.0%
!! GCAATGCTACTTTCCATCGC+TGG - Chr3:85091094-85091113 MsG0380016555.01.T01:intron 50.0%
AACGGCGGCGGTGATAGATA+CGG + Chr3:85089967-85089986 None:intergenic 55.0%
CAAACTCACCAGGTGAACGG+CGG + Chr3:85089982-85090001 None:intergenic 55.0%
CGCTATTCACTTCACGGCTG+AGG - Chr3:85089914-85089933 MsG0380016555.01.T01:intron 55.0%
GCTATCGAAGGCCCAGAACT+TGG + Chr3:85090036-85090055 None:intergenic 55.0%
GTGAAACCGCGAGCTATCGA+AGG + Chr3:85090048-85090067 None:intergenic 55.0%
! GACTTGTTTGCCACCTGACG+GGG - Chr3:85091281-85091300 MsG0380016555.01.T01:intron 55.0%
! GGACTTGTTTGCCACCTGAC+GGG - Chr3:85091280-85091299 MsG0380016555.01.T01:intron 55.0%
! GGGACTTGTTTGCCACCTGA+CGG - Chr3:85091279-85091298 MsG0380016555.01.T01:intron 55.0%
TCTGGGCCTTCGATAGCTCG+CGG - Chr3:85090039-85090058 MsG0380016555.01.T01:intron 60.0%
ACTCACCAGGTGAACGGCGG+CGG + Chr3:85089979-85089998 None:intergenic 65.0%
TATCACCGCCGCCGTTCACC+TGG - Chr3:85089971-85089990 MsG0380016555.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 85089786 85091755 85089786 ID=MsG0380016555.01;Name=MsG0380016555.01
Chr3 mRNA 85089786 85091755 85089786 ID=MsG0380016555.01.T01;Parent=MsG0380016555.01;Name=MsG0380016555.01.T01;_AED=0.40;_eAED=0.40;_QI=1|0.75|0.8|1|0.25|0.2|5|0|68
Chr3 exon 85089786 85089786 85089786 ID=MsG0380016555.01.T01:exon:14456;Parent=MsG0380016555.01.T01
Chr3 exon 85091549 85091755 85091549 ID=MsG0380016555.01.T01:exon:14455;Parent=MsG0380016555.01.T01
Chr3 five_prime_UTR 85091755 85091755 85091755 ID=MsG0380016555.01.T01:five_prime_utr;Parent=MsG0380016555.01.T01
Chr3 CDS 85091549 85091754 85091549 ID=MsG0380016555.01.T01:cds;Parent=MsG0380016555.01.T01
Chr3 CDS 85089786 85089786 85089786 ID=MsG0380016555.01.T01:cds;Parent=MsG0380016555.01.T01
Gene Sequence

>MsG0380016555.01.T01

ATGGTGTCATTCCTAATCCTGTATAGTCTTATCACTCATCCAACCAATCTTTTTCTCTCTCGGTTCTTTTTGTCATTTGGGAGCGCCAACAACAACGAGTACAAGGTGAGGGATAAGCCACCATTTCCGCTATTCACTTCACGGCTGAGGACAAAACAAGAAAGGCAACCGTTGCAACCGTATCTATCACCGCCGCCGTTCACCTGA
Protein sequence

>MsG0380016555.01.T01

MVSFLILYSLITHPTNLFLSRFFLSFGSANNNEYKVRDKPPFPLFTSRLRTKQERQPLQPYLSPPPFT*