AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1095650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1095650 MtrunA17_Chr7g0223171 95.918 49 2 0 1 49 1 49 6.60e-30 99.0
Msa1095650 MtrunA17_Chr8g0376211 85.714 49 7 0 1 49 1 49 1.55e-27 92.8
Msa1095650 MtrunA17_Chr8g0376251 85.714 49 7 0 1 49 1 49 1.55e-27 92.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1095650 AT1G06515.1 66.038 53 14 1 1 49 1 53 1.30e-18 70.9
Msa1095650 AT1G06515.2 66.038 53 14 1 1 49 1 53 1.30e-18 70.9
Msa1095650 AT2G30942.1 62.264 53 16 1 1 49 1 53 3.48e-17 67.4

Find 18 sgRNAs with CRISPR-Local

Find 147 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTAACTATTACAGATATTT+TGG 0.137656 7_3:+18652754 Msa1095650:intron
CACCTTTACAATGTTACTTT+TGG 0.153503 7_3:+18652432 Msa1095650:CDS
TTCTCATTCATCTCTTTGTT+TGG 0.259859 7_3:+18652846 Msa1095650:three_prime_UTR
TGAACTACCTCTTGAAGAAC+TGG 0.347949 7_3:-18652814 None:intergenic
GGCTTTATATGCTGGATTGG+TGG 0.387109 7_3:+18652454 Msa1095650:CDS
CAGTTGTGGAAGTCATGAAT+TGG 0.399034 7_3:+18652394 Msa1095650:intron
TCATTCATCTCTTTGTTTGG+TGG 0.404736 7_3:+18652849 Msa1095650:three_prime_UTR
TTGGGCTTTATATGCTGGAT+TGG 0.428670 7_3:+18652451 Msa1095650:CDS
GCTTTATATGCTGGATTGGT+GGG 0.445941 7_3:+18652455 Msa1095650:CDS
CATGAATTGGGTTCAGCAAA+AGG 0.457099 7_3:+18652407 Msa1095650:exon
AAATCTCATGCGATCGCACC+AGG 0.500256 7_3:+18649880 Msa1095650:five_prime_UTR
GCCCAAAAGTAACATTGTAA+AGG 0.523226 7_3:-18652434 None:intergenic
AGTTGTGGAAGTCATGAATT+GGG 0.531926 7_3:+18652395 Msa1095650:intron
AAACAAAGAGATGAATGAGA+AGG 0.565845 7_3:-18652844 None:intergenic
AACAAAGAGATGAATGAGAA+GGG 0.571582 7_3:-18652843 None:intergenic
CAAAAGTAACATTGTAAAGG+TGG 0.589878 7_3:-18652431 None:intergenic
ACATTACCCAGTTCTTCAAG+AGG 0.625963 7_3:+18652807 Msa1095650:CDS
GAACTACCTCTTGAAGAACT+GGG 0.674773 7_3:-18652813 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAAAAAAAAATAAAAA+AGG - chr7_3:18650187-18650206 None:intergenic 0.0%
!!! TTTATTTCTTTTATGTTATT+TGG + chr7_3:18650200-18650219 Msa1095650:intron 10.0%
!! TAAAATACAAATACTTAATG+AGG - chr7_3:18651268-18651287 None:intergenic 15.0%
!!! TTGTGTAATCTTTAATTTTT+AGG + chr7_3:18652142-18652161 Msa1095650:intron 15.0%
!!! ACTGCAAAAAATATATTTTT+GGG - chr7_3:18652378-18652397 None:intergenic 15.0%
!!! AACTGCAAAAAATATATTTT+TGG - chr7_3:18652379-18652398 None:intergenic 15.0%
!!! ATTATTTGTTGTTTTGTTGA+TGG - chr7_3:18649688-18649707 None:intergenic 20.0%
!! AATGTTTGTTTGATACAAAA+TGG + chr7_3:18650086-18650105 Msa1095650:intron 20.0%
!! GAAAACTTTGATTCTTAAAA+AGG - chr7_3:18650292-18650311 None:intergenic 20.0%
!! ACAAATTACAGAATGAAAAA+TGG + chr7_3:18650469-18650488 Msa1095650:intron 20.0%
!!! TTTAAAACTATTGTTTTTGC+AGG - chr7_3:18650613-18650632 None:intergenic 20.0%
!! GAAAATATCACATCTAATAA+GGG - chr7_3:18650858-18650877 None:intergenic 20.0%
!! AGAAAATATCACATCTAATA+AGG - chr7_3:18650859-18650878 None:intergenic 20.0%
!!! ATAGTTTTTGGAATTTAAGT+TGG + chr7_3:18650971-18650990 Msa1095650:intron 20.0%
!!! TAGTTTTTGGAATTTAAGTT+GGG + chr7_3:18650972-18650991 Msa1095650:intron 20.0%
!! GAGTAATGAACATAATTAAA+AGG - chr7_3:18651127-18651146 None:intergenic 20.0%
!!! TTACTCTTTGATTTTGTAAT+TGG + chr7_3:18651141-18651160 Msa1095650:intron 20.0%
!! TTGCATTTCTATATATATAC+TGG + chr7_3:18652314-18652333 Msa1095650:intron 20.0%
!!! CTGCAAAAAATATATTTTTG+GGG - chr7_3:18652377-18652396 None:intergenic 20.0%
!!! AAATATATTTTTTGCAGTTG+TGG + chr7_3:18652380-18652399 Msa1095650:intron 20.0%
!! ACCATGTTAGTTATTTATAT+AGG + chr7_3:18652578-18652597 Msa1095650:intron 20.0%
!! CCATGTTAGTTATTTATATA+GGG + chr7_3:18652579-18652598 Msa1095650:intron 20.0%
!! CAAAATATCTGTAATAGTTA+AGG - chr7_3:18652756-18652775 None:intergenic 20.0%
!!! CTTAACTATTACAGATATTT+TGG + chr7_3:18652754-18652773 Msa1095650:intron 20.0%
! TCCAAAAAATGTTGAATGAT+CGG - chr7_3:18649854-18649873 None:intergenic 25.0%
! GAAATGAAGTCATATATGTT+TGG + chr7_3:18650579-18650598 Msa1095650:intron 25.0%
! AGAAAATGATATGTTTGTGT+CGG + chr7_3:18650830-18650849 Msa1095650:intron 25.0%
!!! TTGTAATTGTTTCTACTAAC+TGG - chr7_3:18650938-18650957 None:intergenic 25.0%
! ATTAAGACTTCTTTCTGAAT+TGG + chr7_3:18651081-18651100 Msa1095650:intron 25.0%
! TGAATTGGTATTAATTTAGC+TGG + chr7_3:18651096-18651115 Msa1095650:intron 25.0%
! AATATGACATGTCTTTAAGT+CGG + chr7_3:18651376-18651395 Msa1095650:intron 25.0%
!! GAATGTATTGTTTTCAGATT+CGG - chr7_3:18651447-18651466 None:intergenic 25.0%
! TTTAACATAACTAGCGTATT+TGG + chr7_3:18651531-18651550 Msa1095650:intron 25.0%
! CAGTTTCAACAATTCTTTAT+TGG - chr7_3:18651605-18651624 None:intergenic 25.0%
! TGCTATTGAGAATTCAAATT+AGG + chr7_3:18651802-18651821 Msa1095650:intron 25.0%
! GGGTCATAATCTTAATATAA+AGG - chr7_3:18652357-18652376 None:intergenic 25.0%
!!! ACCTTTACAATGTTACTTTT+GGG + chr7_3:18652433-18652452 Msa1095650:CDS 25.0%
!!! ACATTTTAAGATAACTACGA+AGG - chr7_3:18652551-18652570 None:intergenic 25.0%
! CCCTATATAAATAACTAACA+TGG - chr7_3:18652582-18652601 None:intergenic 25.0%
!! GATCTTTCTTTTTCACTTCA+CGG + chr7_3:18649758-18649777 Msa1095650:five_prime_UTR 30.0%
!! ATCTTTCTTTTTCACTTCAC+GGG + chr7_3:18649759-18649778 Msa1095650:five_prime_UTR 30.0%
!!! ACCGATCATTCAACATTTTT+TGG + chr7_3:18649850-18649869 Msa1095650:five_prime_UTR 30.0%
! ATCAACTGAATTTTCAACGA+AGG + chr7_3:18650035-18650054 Msa1095650:intron 30.0%
! TCAACTGAATTTTCAACGAA+GGG + chr7_3:18650036-18650055 Msa1095650:intron 30.0%
! TCAAAGTGTTCTAATCTTGA+AGG + chr7_3:18650253-18650272 Msa1095650:intron 30.0%
AACCCAACATAAACAATGAT+TGG + chr7_3:18650631-18650650 Msa1095650:intron 30.0%
CTCCAATCATTGTTTATGTT+GGG - chr7_3:18650636-18650655 None:intergenic 30.0%
ACTGAATGAAAGGTCAAAAT+AGG - chr7_3:18650715-18650734 None:intergenic 30.0%
TGTCTTAATAAGTGCATGTT+TGG - chr7_3:18650742-18650761 None:intergenic 30.0%
TAGCTGATTACATGGATAAT+GGG - chr7_3:18650791-18650810 None:intergenic 30.0%
TTCTTTACTAGCTGATTACA+TGG - chr7_3:18650799-18650818 None:intergenic 30.0%
! AGATGTGATATTTTCTTAGC+TGG + chr7_3:18650863-18650882 Msa1095650:intron 30.0%
GAAACAATTACAAGCATCAA+AGG + chr7_3:18650945-18650964 Msa1095650:intron 30.0%
TATTATCTCCAAAATTGTCG+TGG + chr7_3:18651028-18651047 Msa1095650:intron 30.0%
AAAACATTATTCCACTCGTT+AGG - chr7_3:18651237-18651256 None:intergenic 30.0%
ATATGACATGTCTTTAAGTC+GGG + chr7_3:18651377-18651396 Msa1095650:intron 30.0%
AACAATACATTCAAGAGCTT+AGG + chr7_3:18651455-18651474 Msa1095650:intron 30.0%
GATCCATAATTTGATTGAAG+CGG + chr7_3:18651579-18651598 Msa1095650:intron 30.0%
! ACATCAAATGTGCTTAGTTT+TGG + chr7_3:18651752-18651771 Msa1095650:intron 30.0%
!!! ATGGTTTTTTTCCATTAGTC+AGG - chr7_3:18651976-18651995 None:intergenic 30.0%
TGACGAATGAGGAATAATTA+TGG - chr7_3:18651995-18652014 None:intergenic 30.0%
TTGTATCCATCATTAATGCA+TGG + chr7_3:18652194-18652213 Msa1095650:intron 30.0%
CAAAAGTAACATTGTAAAGG+TGG - chr7_3:18652434-18652453 None:intergenic 30.0%
!!! CACCTTTACAATGTTACTTT+TGG + chr7_3:18652432-18652451 Msa1095650:CDS 30.0%
TGTAGGAGAAAGTGAAATAA+AGG - chr7_3:18652500-18652519 None:intergenic 30.0%
AACAAAGAGATGAATGAGAA+GGG - chr7_3:18652846-18652865 None:intergenic 30.0%
AAACAAAGAGATGAATGAGA+AGG - chr7_3:18652847-18652866 None:intergenic 30.0%
TTCTCATTCATCTCTTTGTT+TGG + chr7_3:18652846-18652865 Msa1095650:three_prime_UTR 30.0%
!! TCTTTCTTTTTCACTTCACG+GGG + chr7_3:18649760-18649779 Msa1095650:five_prime_UTR 35.0%
CCATATGATTGTTTCAGTCA+GGG - chr7_3:18650373-18650392 None:intergenic 35.0%
ATCCTCCAATATCTAGGAAA+GGG - chr7_3:18650440-18650459 None:intergenic 35.0%
AATCCTCCAATATCTAGGAA+AGG - chr7_3:18650441-18650460 None:intergenic 35.0%
GTCTTAATCCTCCAATATCT+AGG - chr7_3:18650446-18650465 None:intergenic 35.0%
!! AAACAGAAGTGTCTGTATGT+GGG + chr7_3:18650506-18650525 Msa1095650:intron 35.0%
CCTCCAATCATTGTTTATGT+TGG - chr7_3:18650637-18650656 None:intergenic 35.0%
CCAACATAAACAATGATTGG+AGG + chr7_3:18650634-18650653 Msa1095650:intron 35.0%
CTAGCTGATTACATGGATAA+TGG - chr7_3:18650792-18650811 None:intergenic 35.0%
!! CATCAAAGGTGCATAGTTTT+TGG + chr7_3:18650959-18650978 Msa1095650:intron 35.0%
! GCTTTTTGTCAGTCATTGTT+TGG - chr7_3:18651004-18651023 None:intergenic 35.0%
! TACACAATCCACGACAATTT+TGG - chr7_3:18651039-18651058 None:intergenic 35.0%
TAGGCATAAGCTGTAAAGTA+TGG - chr7_3:18651218-18651237 None:intergenic 35.0%
ACATTCAAGAGCTTAGGATT+TGG + chr7_3:18651461-18651480 Msa1095650:intron 35.0%
TGGTTTATGTCAAATCAGCA+AGG + chr7_3:18651551-18651570 Msa1095650:intron 35.0%
!! GAGCAATGATTTGTTTGTGT+TGG + chr7_3:18651624-18651643 Msa1095650:intron 35.0%
CAATGCCACATCAAATAAGA+GGG - chr7_3:18651650-18651669 None:intergenic 35.0%
ACAATGCCACATCAAATAAG+AGG - chr7_3:18651651-18651670 None:intergenic 35.0%
!!! TTAGTTTTGGAGTTCAAGTC+TGG + chr7_3:18651765-18651784 Msa1095650:intron 35.0%
AATTATTCCTCATTCGTCAG+TGG + chr7_3:18651996-18652015 Msa1095650:intron 35.0%
ATTATTCCTCATTCGTCAGT+GGG + chr7_3:18651997-18652016 Msa1095650:intron 35.0%
AGTTGTGGAAGTCATGAATT+GGG + chr7_3:18652395-18652414 Msa1095650:intron 35.0%
GCCCAAAAGTAACATTGTAA+AGG - chr7_3:18652437-18652456 None:intergenic 35.0%
!! TACTTTTGGGCTTTATATGC+TGG + chr7_3:18652446-18652465 Msa1095650:CDS 35.0%
GAAGGAGACAAAATCTATGT+AGG - chr7_3:18652517-18652536 None:intergenic 35.0%
! TACTGATGTGTTTTGTAGTG+CGG + chr7_3:18652783-18652802 Msa1095650:CDS 35.0%
! TCATTCATCTCTTTGTTTGG+TGG + chr7_3:18652849-18652868 Msa1095650:three_prime_UTR 35.0%
GATACAAAATGGTCGCATAG+CGG + chr7_3:18650097-18650116 Msa1095650:intron 40.0%
AAAAGGAAAGTGATCGCAGT+GGG - chr7_3:18650170-18650189 None:intergenic 40.0%
AAAAAGGAAAGTGATCGCAG+TGG - chr7_3:18650171-18650190 None:intergenic 40.0%
CCCTGACTGAAACAATCATA+TGG + chr7_3:18650370-18650389 Msa1095650:intron 40.0%
GCCATATGATTGTTTCAGTC+AGG - chr7_3:18650374-18650393 None:intergenic 40.0%
TCCTCCAATATCTAGGAAAG+GGG - chr7_3:18650439-18650458 None:intergenic 40.0%
!! GAAACAGAAGTGTCTGTATG+TGG + chr7_3:18650505-18650524 Msa1095650:intron 40.0%
GTTTGGATGCACTGAATGAA+AGG - chr7_3:18650725-18650744 None:intergenic 40.0%
!! ACATGGATAATGGGAGAATG+AGG - chr7_3:18650782-18650801 None:intergenic 40.0%
ATTTAAGTGAGCAGCAGCTT+AGG - chr7_3:18651183-18651202 None:intergenic 40.0%
TAACAGCGATTCATACACTC+CGG + chr7_3:18651286-18651305 Msa1095650:intron 40.0%
TTTCAGATTCGGATGCATGA+TGG - chr7_3:18651436-18651455 None:intergenic 40.0%
TGGCCGCTTCAATCAAATTA+TGG - chr7_3:18651585-18651604 None:intergenic 40.0%
! TGATTTGCGATTCACTTAGC+TGG + chr7_3:18651834-18651853 Msa1095650:intron 40.0%
CAGGCATAAGCTGTAAAGTA+TGG - chr7_3:18651957-18651976 None:intergenic 40.0%
TACAGCTTATGCCTGACTAA+TGG + chr7_3:18651962-18651981 Msa1095650:intron 40.0%
AGTCTACCACAGATGGTTAT+TGG + chr7_3:18652070-18652089 Msa1095650:intron 40.0%
CTCAAGCCATGCATTAATGA+TGG - chr7_3:18652203-18652222 None:intergenic 40.0%
CATCATTAATGCATGGCTTG+AGG + chr7_3:18652201-18652220 Msa1095650:intron 40.0%
CAGTTGTGGAAGTCATGAAT+TGG + chr7_3:18652394-18652413 Msa1095650:intron 40.0%
CATGAATTGGGTTCAGCAAA+AGG + chr7_3:18652407-18652426 Msa1095650:exon 40.0%
! TTGGGCTTTATATGCTGGAT+TGG + chr7_3:18652451-18652470 Msa1095650:CDS 40.0%
!! GCTTTATATGCTGGATTGGT+GGG + chr7_3:18652455-18652474 Msa1095650:CDS 40.0%
ACGAAGGAAAAGACATCTGA+AGG - chr7_3:18652535-18652554 None:intergenic 40.0%
ACATTACCCAGTTCTTCAAG+AGG + chr7_3:18652807-18652826 Msa1095650:CDS 40.0%
GAACTACCTCTTGAAGAACT+GGG - chr7_3:18652816-18652835 None:intergenic 40.0%
TGAACTACCTCTTGAAGAAC+TGG - chr7_3:18652817-18652836 None:intergenic 40.0%
GCGTTAGACTCCGAATCTAA+AGG + chr7_3:18650130-18650149 Msa1095650:intron 45.0%
ACTCCGAATCTAAAGGTCGT+GGG + chr7_3:18650137-18650156 Msa1095650:intron 45.0%
GAACCCACGACCTTTAGATT+CGG - chr7_3:18650143-18650162 None:intergenic 45.0%
! GGAAAGGGGCTCTAGTAATT+TGG - chr7_3:18650425-18650444 None:intergenic 45.0%
AGAGCCCCTTTCCTAGATAT+TGG + chr7_3:18650432-18650451 Msa1095650:intron 45.0%
TACAGCTTATGCCTAACGAG+TGG + chr7_3:18651223-18651242 Msa1095650:intron 45.0%
AGTCTGCCACAGATGGTTAT+TGG + chr7_3:18651325-18651344 Msa1095650:intron 45.0%
GACACACCAATAACCATCTG+TGG - chr7_3:18651334-18651353 None:intergenic 45.0%
! GTTGGCCCTCTTATTTGATG+TGG + chr7_3:18651642-18651661 Msa1095650:intron 45.0%
TGATGTGGCATTGTCTTGAC+TGG + chr7_3:18651657-18651676 Msa1095650:intron 45.0%
CAAATACCCACTGACGAATG+AGG - chr7_3:18652006-18652025 None:intergenic 45.0%
GGCAATAGTCTCGGAGTATA+TGG - chr7_3:18652044-18652063 None:intergenic 45.0%
ACTTGCTCAGGCAATAGTCT+CGG - chr7_3:18652053-18652072 None:intergenic 45.0%
GACACACCAATAACCATCTG+TGG - chr7_3:18651334-18651353 None:intergenic 45.0%
! GGCTTTATATGCTGGATTGG+TGG + chr7_3:18652454-18652473 Msa1095650:CDS 45.0%
AAATCTCATGCGATCGCACC+AGG + chr7_3:18649880-18649899 Msa1095650:five_prime_UTR 50.0%
! AAAATGGTCGCATAGCGGAG+TGG + chr7_3:18650102-18650121 Msa1095650:intron 50.0%
GACTCCGAATCTAAAGGTCG+TGG + chr7_3:18650136-18650155 Msa1095650:intron 50.0%
GCCCCTTTCCTAGATATTGG+AGG + chr7_3:18650435-18650454 Msa1095650:intron 50.0%
! ACTTGCTAAGGCAACAGAGC+CGG - chr7_3:18651308-18651327 None:intergenic 50.0%
!! CATCTGTGGCAGACTTGCTA+AGG - chr7_3:18651320-18651339 None:intergenic 50.0%
CTTAGCAAGTCTGCCACAGA+TGG + chr7_3:18651318-18651337 Msa1095650:intron 50.0%
! CATCTGTGGTAGACTTGCTC+AGG - chr7_3:18652065-18652084 None:intergenic 50.0%
CTGAGCAAGTCTACCACAGA+TGG + chr7_3:18652063-18652082 Msa1095650:intron 50.0%
TGATCGCGTGCGTGCGTACC+TGG - chr7_3:18649901-18649920 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 18649683 18652876 18649683 ID=Msa1095650;Name=Msa1095650
chr7_3 mRNA 18649683 18652876 18649683 ID=Msa1095650-mRNA-1;Parent=Msa1095650;Name=Msa1095650-mRNA-1;_AED=0.37;_eAED=0.37;_QI=230|1|0.66|1|0|0|3|44|49
chr7_3 exon 18649683 18649901 18649683 ID=Msa1095650-mRNA-1:exon:4025;Parent=Msa1095650-mRNA-1
chr7_3 exon 18652397 18652492 18652397 ID=Msa1095650-mRNA-1:exon:4026;Parent=Msa1095650-mRNA-1
chr7_3 exon 18652768 18652876 18652768 ID=Msa1095650-mRNA-1:exon:4027;Parent=Msa1095650-mRNA-1
chr7_3 five_prime_UTR 18649683 18649901 18649683 ID=Msa1095650-mRNA-1:five_prime_utr;Parent=Msa1095650-mRNA-1
chr7_3 five_prime_UTR 18652397 18652407 18652397 ID=Msa1095650-mRNA-1:five_prime_utr;Parent=Msa1095650-mRNA-1
chr7_3 CDS 18652408 18652492 18652408 ID=Msa1095650-mRNA-1:cds;Parent=Msa1095650-mRNA-1
chr7_3 CDS 18652768 18652832 18652768 ID=Msa1095650-mRNA-1:cds;Parent=Msa1095650-mRNA-1
chr7_3 three_prime_UTR 18652833 18652876 18652833 ID=Msa1095650-mRNA-1:three_prime_utr;Parent=Msa1095650-mRNA-1
Gene Sequence

>Msa1095650

ATGAATTGGGTTCAGCAAAAGGTCCACCTTTACAATGTTACTTTTGGGCTTTATATGCTGGATTGGTGGGAGCGTTGCTCATTCAATATTTTGGTGATTGTACTGATGTGTTTTGTAGTGCGGTACATTACCCAGTTCTTCAAGAGGTAG

Protein sequence

>Msa1095650

MNWVQQKVHLYNVTFGLYMLDWWERCSFNILVIVLMCFVVRYITQFFKR*