AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0923790


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 46 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGTGTAGGCTTGGCTTTC+TGG 0.089164 6_2:-64565918 Msa0923790:five_prime_UTR
ATAGAAATTATTTGTCTCTA+AGG 0.241880 6_2:-64565388 Msa0923790:exon
TGTTTAGGCTGTTGAAGGTT+GGG 0.310010 6_2:-64565523 Msa0923790:intron
TGTTGGTTTGTTTGTGCTCA+TGG 0.333097 6_2:-64567528 Msa0923790:intron
ACTTATTTATATTTAGTAAT+GGG 0.349767 6_2:+64565287 None:intergenic
TAAAGTCAGGAGATGAATTA+TGG 0.353844 6_2:-64565479 Msa0923790:CDS
CCATACTTAGGTGGCTCATT+TGG 0.362701 6_2:-64565674 Msa0923790:CDS
ACTTGATGCAAGACATGCTT+TGG 0.365400 6_2:+64565150 None:intergenic
CTGGATTAGCATGGCACCTT+GGG 0.371240 6_2:-64565899 Msa0923790:intron
TGCAAGACATGCTTTGGAAT+TGG 0.380086 6_2:+64565156 None:intergenic
CCAAATGAGCCACCTAAGTA+TGG 0.382983 6_2:+64565674 None:intergenic
GTTTAGGCTGTTGAAGGTTG+GGG 0.389434 6_2:-64565522 Msa0923790:intron
TATCTTGTTTAGGCTGTTGA+AGG 0.389713 6_2:-64565528 Msa0923790:intron
TTGTTTAGGCTGTTGAAGGT+TGG 0.438805 6_2:-64565524 Msa0923790:intron
GACTTATTTATATTTAGTAA+TGG 0.441698 6_2:+64565286 None:intergenic
ACAAATAGAGTGTTTGTTGT+TGG 0.465701 6_2:+64566165 None:intergenic
TTGGATGTTGCAGAAAGAAA+AGG 0.471032 6_2:+64565090 None:intergenic
GGATTCACGAAAACAGCAAA+TGG 0.474560 6_2:-64565441 Msa0923790:CDS
TCTGGATTAGCATGGCACCT+TGG 0.479623 6_2:-64565900 Msa0923790:exon
GAAGCTGCATGAAAAGTAAG+AGG 0.486955 6_2:+64565237 None:intergenic
GACAAAGAATGGTGTAGGCT+TGG 0.487669 6_2:-64565926 Msa0923790:five_prime_UTR
TAAACTCAATGGACAAAGAA+TGG 0.488753 6_2:-64565937 Msa0923790:five_prime_UTR
GCAAAAGCAGGGTTAAAGTC+AGG 0.500832 6_2:-64565492 Msa0923790:CDS
CTTGGCTTTCTGGATTAGCA+TGG 0.510281 6_2:-64565908 Msa0923790:exon
TTATATTTAGTAATGGGTGT+TGG 0.513099 6_2:+64565293 None:intergenic
GGGTGTTGGTGTGTCTGTAG+TGG 0.521988 6_2:+64565307 None:intergenic
TACTAAATATAAATAAGTCG+TGG 0.532381 6_2:-64565282 Msa0923790:three_prime_UTR
GTGAATCCAAGCTTATCTGC+TGG 0.535393 6_2:+64565456 None:intergenic
TTATGGCCAGCAGATAAGCT+TGG 0.539708 6_2:-64565462 Msa0923790:CDS
GTGTGTCTGTAGTGGAGACT+TGG 0.541704 6_2:+64565315 None:intergenic
TGTTGTTGGTGTAGAAAATG+AGG 0.543974 6_2:+64566179 None:intergenic
TTTAGGCTGTTGAAGGTTGG+GGG 0.552652 6_2:-64565521 Msa0923790:intron
CTATGGCAGGTACCATACTT+AGG 0.555359 6_2:-64565686 Msa0923790:intron
ACTAAATATAAATAAGTCGT+GGG 0.563621 6_2:-64565281 Msa0923790:three_prime_UTR
CACTCACAGCAGGTTTCTCA+AGG 0.568836 6_2:+64565639 None:intergenic
CAATGGACAAAGAATGGTGT+AGG 0.571360 6_2:-64565931 Msa0923790:five_prime_UTR
TTGGAGATAGAACAGTTGAA+AGG 0.580481 6_2:+64565175 None:intergenic
TTGAAGACGACATAGCTGTA+AGG 0.582330 6_2:-64566213 Msa0923790:five_prime_UTR
GAGGAATTAATATAGCAAGT+AGG 0.597914 6_2:+64565256 None:intergenic
AAGTGATTTGGTGTGTGAGT+GGG 0.605770 6_2:+64567883 None:intergenic
GGTGTAGAAAATGAGGATGC+AGG 0.627573 6_2:+64566186 None:intergenic
TCACAAGAAAATGCATGACC+TGG 0.631525 6_2:+64565120 None:intergenic
GAAGTGATTTGGTGTGTGAG+TGG 0.631848 6_2:+64567882 None:intergenic
TCACAATCGCTGATTCGATG+AGG 0.682337 6_2:-64567422 Msa0923790:intron
TGGCAGGTACCATACTTAGG+TGG 0.694561 6_2:-64565683 Msa0923790:intron
GATGAAGCAGATCTGATGAG+CGG 0.792182 6_2:+64567482 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTTATTTATATTTAGTAAT+GGG + chr6_2:64567723-64567742 None:intergenic 10.0%
!!! TAATTTCAAGTTTTTTTTGT+TGG - chr6_2:64566019-64566038 Msa0923790:intron 15.0%
!!! AATATTCAACAACATTTTTA+TGG + chr6_2:64566183-64566202 None:intergenic 15.0%
!!! GGAAACAAAATTATAAATTT+TGG - chr6_2:64566331-64566350 Msa0923790:intron 15.0%
!! TAATAAATTTATCATGTATG+AGG + chr6_2:64567407-64567426 None:intergenic 15.0%
!! GACTTATTTATATTTAGTAA+TGG + chr6_2:64567724-64567743 None:intergenic 15.0%
!!! GAATTATGATGTTTTAAGTT+TGG - chr6_2:64565661-64565680 Msa0923790:CDS 20.0%
!!! TTTTTTTGTTGGTTTATTTG+TGG - chr6_2:64566030-64566049 Msa0923790:intron 20.0%
!!! AATTTTGGAATAGTAAACAT+AGG - chr6_2:64566346-64566365 Msa0923790:intron 20.0%
!!! ATTTTGGAATAGTAAACATA+GGG - chr6_2:64566347-64566366 Msa0923790:intron 20.0%
!!! TTCTTTTTTAGTAAACTCAA+TGG - chr6_2:64567059-64567078 Msa0923790:intron 20.0%
!! TAAGCATGTAAATTTGTATA+AGG + chr6_2:64567239-64567258 None:intergenic 20.0%
!! TACAAATTTACATGCTTATA+TGG - chr6_2:64567241-64567260 Msa0923790:intron 20.0%
!!! AAACTCAATAACTTTTATCA+TGG + chr6_2:64567295-64567314 None:intergenic 20.0%
!! TTATTGAGTTTAATTCACTA+TGG - chr6_2:64567304-64567323 Msa0923790:intron 20.0%
!!! ATTGATTCTAACTATAAAAG+TGG + chr6_2:64567431-64567450 None:intergenic 20.0%
!!! ACTTTTATAGTTAGAATCAA+TGG - chr6_2:64567430-64567449 Msa0923790:five_prime_UTR 20.0%
!! ATAGAAATTATTTGTCTCTA+AGG - chr6_2:64567619-64567638 Msa0923790:intron 20.0%
!! TACTAAATATAAATAAGTCG+TGG - chr6_2:64567725-64567744 Msa0923790:intron 20.0%
!! ACTAAATATAAATAAGTCGT+GGG - chr6_2:64567726-64567745 Msa0923790:intron 20.0%
!!! TGATGCAATTGACATTTTTT+AGG - chr6_2:64565332-64565351 Msa0923790:three_prime_UTR 25.0%
!!! GTTGTTTTTGTTTGTTTTGT+TGG - chr6_2:64565462-64565481 Msa0923790:CDS 25.0%
!!! ATGTGATGTTTAAGTTTTGT+TGG - chr6_2:64565817-64565836 Msa0923790:intron 25.0%
!! ATGAGAATAAGATGATTTGT+AGG - chr6_2:64565856-64565875 Msa0923790:intron 25.0%
! TAATCAAAATGCAGTAACAT+GGG + chr6_2:64566151-64566170 None:intergenic 25.0%
!!! TTACTGCATTTTGATTAGTT+TGG - chr6_2:64566154-64566173 Msa0923790:intron 25.0%
! TGTTACTGAAAAATAAACTG+TGG - chr6_2:64566279-64566298 Msa0923790:intron 25.0%
! GTTACTGAAAAATAAACTGT+GGG - chr6_2:64566280-64566299 Msa0923790:intron 25.0%
! ACTAATCAAAAGCTATACTA+AGG + chr6_2:64566476-64566495 None:intergenic 25.0%
!!! CTACTTTGAGGAAATATTTT+TGG + chr6_2:64566504-64566523 None:intergenic 25.0%
! AAGCACAAACATACATATAT+TGG + chr6_2:64566590-64566609 None:intergenic 25.0%
! TCTTTAATGCTCATATTGTT+AGG - chr6_2:64566609-64566628 Msa0923790:intron 25.0%
! CAGCTTGAAGTATAAATTTA+TGG + chr6_2:64566736-64566755 None:intergenic 25.0%
! TCTGTTGAAGATAAAATACA+AGG + chr6_2:64566883-64566902 None:intergenic 25.0%
! ACAATGAGAAAACTATTCTA+GGG + chr6_2:64566907-64566926 None:intergenic 25.0%
! TACAATGAGAAAACTATTCT+AGG + chr6_2:64566908-64566927 None:intergenic 25.0%
! CTAGTTATCTAACAAGTAAA+AGG + chr6_2:64567005-64567024 None:intergenic 25.0%
!! ACTTGTTAGATAACTAGATA+TGG - chr6_2:64567008-64567027 Msa0923790:intron 25.0%
!! TTATCAATTTTACTTACCCA+AGG + chr6_2:64567127-64567146 None:intergenic 25.0%
! AGATAGATAATTGCAATATC+AGG + chr6_2:64567464-64567483 None:intergenic 25.0%
!! TGCAATTATCTATCTTGTTT+AGG - chr6_2:64567469-64567488 Msa0923790:five_prime_UTR 25.0%
!!! TTATATTTAGTAATGGGTGT+TGG + chr6_2:64567717-64567736 None:intergenic 25.0%
! GATTTTCAGATGAAGTGATT+TGG + chr6_2:64565139-64565158 None:intergenic 30.0%
AGAGCAAAATAAATACGCAA+AGG + chr6_2:64565278-64565297 None:intergenic 30.0%
GATTTGTAGGTTAATCTGAT+TGG - chr6_2:64565869-64565888 Msa0923790:intron 30.0%
TTTGTGGATGATTTATCTAC+CGG - chr6_2:64566046-64566065 Msa0923790:intron 30.0%
CTAATCAAAATGCAGTAACA+TGG + chr6_2:64566152-64566171 None:intergenic 30.0%
AAAATTTGTGCACAGTAGTA+TGG - chr6_2:64566246-64566265 Msa0923790:intron 30.0%
AGCTTTCATTGATCATTAGA+TGG - chr6_2:64566310-64566329 Msa0923790:intron 30.0%
! AATCCAAAGTGTTTGTTAAG+TGG - chr6_2:64566563-64566582 Msa0923790:intron 30.0%
!! ACAAATAGAGTGTTTGTTGT+TGG + chr6_2:64566845-64566864 None:intergenic 30.0%
CAACAAACACTCTATTTGTA+TGG - chr6_2:64566846-64566865 Msa0923790:intron 30.0%
TAAACTCAATGGACAAAGAA+TGG - chr6_2:64567070-64567089 Msa0923790:intron 30.0%
ATAGTTAGAATCAATGGTCT+TGG - chr6_2:64567436-64567455 Msa0923790:five_prime_UTR 30.0%
TAAAGTCAGGAGATGAATTA+TGG - chr6_2:64567528-64567547 Msa0923790:intron 30.0%
GAGGAATTAATATAGCAAGT+AGG + chr6_2:64567754-64567773 None:intergenic 30.0%
!!! CCTTCAGTTTTTTCATTACA+CGG - chr6_2:64567803-64567822 Msa0923790:five_prime_UTR 30.0%
! CACTTTTCTTCACGAATTTG+CGG - chr6_2:64565240-64565259 Msa0923790:three_prime_UTR 35.0%
TCCTCAAAGTAGATCTTCAT+TGG - chr6_2:64566512-64566531 Msa0923790:intron 35.0%
TCCAATGAAGATCTACTTTG+AGG + chr6_2:64566516-64566535 None:intergenic 35.0%
!! GGAGTAGCTTTTGATTAGTT+TGG - chr6_2:64566533-64566552 Msa0923790:intron 35.0%
TGTTGTTGGTGTAGAAAATG+AGG + chr6_2:64566831-64566850 None:intergenic 35.0%
TGAGTTTAATTCACTATGGC+AGG - chr6_2:64567308-64567327 Msa0923790:intron 35.0%
! TATCTTGTTTAGGCTGTTGA+AGG - chr6_2:64567479-64567498 Msa0923790:five_prime_UTR 35.0%
CCGTGTAATGAAAAAACTGA+AGG + chr6_2:64567806-64567825 None:intergenic 35.0%
TTGGAGATAGAACAGTTGAA+AGG + chr6_2:64567835-64567854 None:intergenic 35.0%
!! AAGTGATTTGGTGTGTGAGT+GGG + chr6_2:64565127-64565146 None:intergenic 40.0%
!! TGTTGGTTTGTTTGTGCTCA+TGG - chr6_2:64565479-64565498 Msa0923790:CDS 40.0%
AACTTGGATCGCAAGAGATA+CGG + chr6_2:64566100-64566119 None:intergenic 40.0%
CACGACAAAGTGAACAAACT+TGG + chr6_2:64566116-64566135 None:intergenic 40.0%
GGTCCACTTAACAAACACTT+TGG + chr6_2:64566569-64566588 None:intergenic 40.0%
TTGAAGACGACATAGCTGTA+AGG - chr6_2:64566794-64566813 Msa0923790:intron 40.0%
CAATGGACAAAGAATGGTGT+AGG - chr6_2:64567076-64567095 Msa0923790:intron 40.0%
ATTAATCTACCACTCACAGC+AGG + chr6_2:64567381-64567400 None:intergenic 40.0%
TTGTTTAGGCTGTTGAAGGT+TGG - chr6_2:64567483-64567502 Msa0923790:five_prime_UTR 40.0%
TGTTTAGGCTGTTGAAGGTT+GGG - chr6_2:64567484-64567503 Msa0923790:five_prime_UTR 40.0%
GGATTCACGAAAACAGCAAA+TGG - chr6_2:64567566-64567585 Msa0923790:intron 40.0%
GAAGCTGCATGAAAAGTAAG+AGG + chr6_2:64567773-64567792 None:intergenic 40.0%
!! TGCAAGACATGCTTTGGAAT+TGG + chr6_2:64567854-64567873 None:intergenic 40.0%
ACTTGATGCAAGACATGCTT+TGG + chr6_2:64567860-64567879 None:intergenic 40.0%
! TTGCATCAAGTCTTTTCACC+AGG - chr6_2:64567869-64567888 Msa0923790:five_prime_UTR 40.0%
TCACAAGAAAATGCATGACC+TGG + chr6_2:64567890-64567909 None:intergenic 40.0%
!! GAAGTGATTTGGTGTGTGAG+TGG + chr6_2:64565128-64565147 None:intergenic 45.0%
GATGAAGCAGATCTGATGAG+CGG + chr6_2:64565528-64565547 None:intergenic 45.0%
!! TCACAATCGCTGATTCGATG+AGG - chr6_2:64565585-64565604 Msa0923790:intron 45.0%
GCAAATGCTCAGTGAAGTAC+CGG + chr6_2:64566068-64566087 None:intergenic 45.0%
CCACAATCGATACACGTGAA+CGG + chr6_2:64566221-64566240 None:intergenic 45.0%
GGTGTAGAAAATGAGGATGC+AGG + chr6_2:64566824-64566843 None:intergenic 45.0%
GACAAAGAATGGTGTAGGCT+TGG - chr6_2:64567081-64567100 Msa0923790:intron 45.0%
!! CTTGGCTTTCTGGATTAGCA+TGG - chr6_2:64567099-64567118 Msa0923790:intron 45.0%
CTATGGCAGGTACCATACTT+AGG - chr6_2:64567321-64567340 Msa0923790:intron 45.0%
CCAAATGAGCCACCTAAGTA+TGG + chr6_2:64567336-64567355 None:intergenic 45.0%
CCATACTTAGGTGGCTCATT+TGG - chr6_2:64567333-64567352 Msa0923790:intron 45.0%
GTTTAGGCTGTTGAAGGTTG+GGG - chr6_2:64567485-64567504 Msa0923790:five_prime_UTR 45.0%
TTTAGGCTGTTGAAGGTTGG+GGG - chr6_2:64567486-64567505 Msa0923790:five_prime_UTR 45.0%
GCAAAAGCAGGGTTAAAGTC+AGG - chr6_2:64567515-64567534 Msa0923790:five_prime_UTR 45.0%
TTATGGCCAGCAGATAAGCT+TGG - chr6_2:64567545-64567564 Msa0923790:intron 45.0%
GTGAATCCAAGCTTATCTGC+TGG + chr6_2:64567554-64567573 None:intergenic 45.0%
!!! TACTAATTTTATTATTTAAT+TGG - chr6_2:64566690-64566709 Msa0923790:intron 5.0%
!! CCGTTCACGTGTATCGATTG+TGG - chr6_2:64566218-64566237 Msa0923790:intron 50.0%
! ATGGTGTAGGCTTGGCTTTC+TGG - chr6_2:64567089-64567108 Msa0923790:intron 50.0%
!! TCTGGATTAGCATGGCACCT+TGG - chr6_2:64567107-64567126 Msa0923790:intron 50.0%
!! CTGGATTAGCATGGCACCTT+GGG - chr6_2:64567108-64567127 Msa0923790:intron 50.0%
TGGCAGGTACCATACTTAGG+TGG - chr6_2:64567324-64567343 Msa0923790:intron 50.0%
CACTCACAGCAGGTTTCTCA+AGG + chr6_2:64567371-64567390 None:intergenic 50.0%
CTTGAGAAACCTGCTGTGAG+TGG - chr6_2:64567369-64567388 Msa0923790:intron 50.0%
! GTGTGTCTGTAGTGGAGACT+TGG + chr6_2:64567695-64567714 None:intergenic 50.0%
TGGGGGAATGCAGCAAAAGC+AGG - chr6_2:64567503-64567522 Msa0923790:five_prime_UTR 55.0%
GGGGGAATGCAGCAAAAGCA+GGG - chr6_2:64567504-64567523 Msa0923790:five_prime_UTR 55.0%
!! GGGTGTTGGTGTGTCTGTAG+TGG + chr6_2:64567703-64567722 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 64565103 64567926 64565103 ID=Msa0923790;Name=Msa0923790
chr6_2 mRNA 64565103 64567926 64565103 ID=Msa0923790-mRNA-1;Parent=Msa0923790;Name=Msa0923790-mRNA-1;_AED=0.01;_eAED=0.01;_QI=381|1|1|1|0.4|0.33|6|304|65
chr6_2 exon 64565103 64565538 64565103 ID=Msa0923790-mRNA-1:exon:10156;Parent=Msa0923790-mRNA-1
chr6_2 exon 64565646 64565699 64565646 ID=Msa0923790-mRNA-1:exon:10155;Parent=Msa0923790-mRNA-1
chr6_2 exon 64565900 64565959 64565900 ID=Msa0923790-mRNA-1:exon:10154;Parent=Msa0923790-mRNA-1
chr6_2 exon 64566167 64566235 64566167 ID=Msa0923790-mRNA-1:exon:10153;Parent=Msa0923790-mRNA-1
chr6_2 exon 64567423 64567536 64567423 ID=Msa0923790-mRNA-1:exon:10152;Parent=Msa0923790-mRNA-1
chr6_2 exon 64567777 64567926 64567777 ID=Msa0923790-mRNA-1:exon:10151;Parent=Msa0923790-mRNA-1
chr6_2 five_prime_UTR 64567777 64567926 64567777 ID=Msa0923790-mRNA-1:five_prime_utr;Parent=Msa0923790-mRNA-1
chr6_2 five_prime_UTR 64567423 64567536 64567423 ID=Msa0923790-mRNA-1:five_prime_utr;Parent=Msa0923790-mRNA-1
chr6_2 five_prime_UTR 64566167 64566235 64566167 ID=Msa0923790-mRNA-1:five_prime_utr;Parent=Msa0923790-mRNA-1
chr6_2 five_prime_UTR 64565912 64565959 64565912 ID=Msa0923790-mRNA-1:five_prime_utr;Parent=Msa0923790-mRNA-1
chr6_2 CDS 64565900 64565911 64565900 ID=Msa0923790-mRNA-1:cds;Parent=Msa0923790-mRNA-1
chr6_2 CDS 64565646 64565699 64565646 ID=Msa0923790-mRNA-1:cds;Parent=Msa0923790-mRNA-1
chr6_2 CDS 64565407 64565538 64565407 ID=Msa0923790-mRNA-1:cds;Parent=Msa0923790-mRNA-1
chr6_2 three_prime_UTR 64565103 64565406 64565103 ID=Msa0923790-mRNA-1:three_prime_utr;Parent=Msa0923790-mRNA-1
Gene Sequence

>Msa0923790

ATGGCACCTTGGGTACCATACTTAGGTGGCTCATTTGGCATTATCTATATCCTTGAGAAACCTGCTGCTGTTGAAGGTTGGGGGAATGCAGCAAAAGCAGGGTTAAAGTCAGGAGATGAATTATGGCCAGCAGATAAGCTTGGATTCACGAAAACAGCAAATGGTTTTGTCTCTAAAGTTTCTATAGAAGAGAAATAG

Protein sequence

>Msa0923790

MAPWVPYLGGSFGIIYILEKPAAVEGWGNAAKAGLKSGDELWPADKLGFTKTANGFVSKVSIEEK*