AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1386190


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 28 sgRNAs with CRISPR-Local

Find 149 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTTGAACTATAGGTTAC+TGG 0.243175 tig0020787:-83660 Msa1386170:intron
GGAGCGGTCAACCCTAAAAT+TGG 0.256923 tig0020787:+84119 Msa1386190:three_prime_UTR
TTGTTAAGTCTACCAGCATT+TGG 0.414353 tig0020787:+84061 Msa1386190:three_prime_UTR
ACTATAGGTTACTGGTGAAC+TGG 0.433578 tig0020787:-83652 Msa1386170:intron
GACCGCTCCACTATACTATC+CGG 0.460670 tig0020787:-84105 Msa1386170:intron
AACCCTAAAATTGGGATAGC+AGG 0.468485 tig0020787:+84128 Msa1386190:three_prime_UTR
CCAGGAAAATGAACTTGTAA+TGG 0.483912 tig0020787:+83899 Msa1386190:three_prime_UTR
GAGCGGTCAACCCTAAAATT+GGG 0.489496 tig0020787:+84120 Msa1386190:three_prime_UTR
ACAAGGACAATAGTAACAAA+AGG 0.501137 tig0020787:-83769 Msa1386170:intron
GTCAATCCCGGATAGTATAG+TGG 0.518572 tig0020787:+84098 Msa1386190:three_prime_UTR
ATGATGTCATACTAAAATGA+TGG 0.523136 tig0020787:+84035 Msa1386190:three_prime_UTR
TTACACACATGGAATGCCAC+TGG 0.532703 tig0020787:-84010 Msa1386170:intron
TACACACATGGAATGCCACT+GGG 0.553219 tig0020787:-84009 Msa1386170:intron
TCCGCGCTTATAGATAAGCC+TGG 0.560356 tig0020787:-83828 Msa1386170:intron
GGAAGAAAAGTTGTCAATCC+CGG 0.564792 tig0020787:+84086 Msa1386190:three_prime_UTR
ACCGCTCCACTATACTATCC+GGG 0.568853 tig0020787:-84104 Msa1386170:intron
GAAGTGCATGATTATGCACC+AGG 0.576335 tig0020787:+83881 Msa1386190:three_prime_UTR
TAAGTCTACCAGCATTTGGA+AGG 0.592684 tig0020787:+84065 Msa1386190:three_prime_UTR
AGTTTGTACTTGCAATCACA+AGG 0.594194 tig0020787:-83786 Msa1386170:intron
CTAAAATTGGGATAGCAGGA+TGG 0.596596 tig0020787:+84132 Msa1386190:three_prime_UTR
AATATATGAACAAAATGAGA+AGG 0.597928 tig0020787:+83589 Msa1386190:CDS
AATATAAAATATTCAAATAG+CGG 0.599437 tig0020787:-84155 Msa1386170:intron
GCTGTGAATGTTGTGCAAGT+TGG 0.626120 tig0020787:-84284 Msa1386170:intron
TCCAGGCTTATCTATAAGCG+CGG 0.655504 tig0020787:+83827 Msa1386190:three_prime_UTR
AATGTACGATGATAAAACCT+CGG 0.669056 tig0020787:+83980 Msa1386190:three_prime_UTR
TCCCGGATAGTATAGTGGAG+CGG 0.701465 tig0020787:+84103 Msa1386190:three_prime_UTR
ATGCCACTGGGAGCATACCG+AGG 0.706367 tig0020787:-83997 Msa1386170:intron
AAACCTCGGTATGCTCCCAG+TGG 0.718705 tig0020787:+83994 Msa1386190:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATCAATTAAATTTGAAATT+TGG - tig0020787:81970-81989 Msa1386170:intron 10.0%
!!! ATTATTGTATTTTTTAAATC+TGG - tig0020787:82653-82672 Msa1386170:three_prime_UTR 10.0%
!! AATATAAAATATTCAAATAG+CGG - tig0020787:84158-84177 Msa1386170:intron 10.0%
!!! ATGTTTTTTGATTAAATTGT+TGG - tig0020787:81882-81901 Msa1386170:intron 15.0%
!!! CTTATTTTAACTGATAATTA+TGG - tig0020787:82391-82410 Msa1386170:three_prime_UTR 15.0%
!! TTAAATTAAGAGAAAGAAAA+AGG + tig0020787:82680-82699 Msa1386190:intron 15.0%
!! TTATTAAGAAATACTTCTAT+TGG + tig0020787:83376-83395 Msa1386190:intron 15.0%
!!! TATATAAGTTTGAATTTTTC+AGG + tig0020787:83432-83451 Msa1386190:intron 15.0%
!!! ATATAAGTTTGAATTTTTCA+GGG + tig0020787:83433-83452 Msa1386190:intron 15.0%
!! TATTATAGTAAGAAAAACAT+TGG + tig0020787:83617-83636 Msa1386190:three_prime_UTR 15.0%
!! TTGTGAATATTTACATATGA+TGG + tig0020787:81698-81717 Msa1386190:intron 20.0%
!! GTTACTTACATTATTATAGA+TGG - tig0020787:81787-81806 Msa1386170:intron 20.0%
!! CTTAATAACAAACAGTATAT+GGG - tig0020787:81833-81852 Msa1386170:intron 20.0%
!! ACTTAATAACAAACAGTATA+TGG - tig0020787:81834-81853 Msa1386170:intron 20.0%
!!! TACATATGTTTGCAAAATTT+TGG + tig0020787:81944-81963 Msa1386190:intron 20.0%
!! TTTCAAATATCAATGGAAAA+TGG - tig0020787:82343-82362 Msa1386170:three_prime_UTR 20.0%
!!! ACGTTTTTTTCAAATATCAA+TGG - tig0020787:82350-82369 Msa1386170:three_prime_UTR 20.0%
!! CTAATACTTAGTTAATTAGA+GGG + tig0020787:83044-83063 Msa1386190:intron 20.0%
!!! ATTTTGTTCATATATTTGTG+GGG - tig0020787:83585-83604 Msa1386170:intron 20.0%
!!! CATTTTGTTCATATATTTGT+GGG - tig0020787:83586-83605 Msa1386170:intron 20.0%
!!! TCATTTTGTTCATATATTTG+TGG - tig0020787:83587-83606 Msa1386170:intron 20.0%
!! AATATATGAACAAAATGAGA+AGG + tig0020787:83589-83608 Msa1386190:CDS 20.0%
!!! ACTTTTTTTCTTTGAACTAT+AGG - tig0020787:83670-83689 Msa1386170:intron 20.0%
!! AAAAAGTTGAAGTAGATAAA+TGG + tig0020787:83683-83702 Msa1386190:three_prime_UTR 20.0%
!! TTTTGCAAACATATGTATCT+AGG - tig0020787:81941-81960 Msa1386170:intron 25.0%
! GTAAGTATACTTCAATATGT+GGG - tig0020787:82537-82556 Msa1386170:three_prime_UTR 25.0%
! TGTAAGTATACTTCAATATG+TGG - tig0020787:82538-82557 Msa1386170:three_prime_UTR 25.0%
! GCTAATACTTAGTTAATTAG+AGG + tig0020787:83043-83062 Msa1386190:intron 25.0%
! AGTTAATTAGAGGGATATTT+AGG + tig0020787:83053-83072 Msa1386190:intron 25.0%
! TTATTGTTTGCTTATGACAT+AGG - tig0020787:83298-83317 Msa1386170:intron 25.0%
! CATAAGCAAACAATAATGTT+TGG + tig0020787:83302-83321 Msa1386190:intron 25.0%
! CAAACTTATATAAGAATGTG+CGG - tig0020787:83424-83443 Msa1386170:intron 25.0%
!!! TTTTTTTTAGTTGCTCTTCT+TGG - tig0020787:83544-83563 Msa1386170:intron 25.0%
! ATGATGTCATACTAAAATGA+TGG + tig0020787:84035-84054 Msa1386190:three_prime_UTR 25.0%
AGGTTATATCATCTCAGTAT+AGG - tig0020787:81921-81940 Msa1386170:intron 30.0%
ACTTACATGTCAAAATGTCA+AGG + tig0020787:82021-82040 Msa1386190:intron 30.0%
ATATATTGGGCCTTTACAAA+TGG + tig0020787:82125-82144 Msa1386190:intron 30.0%
GATAAACTAATGATGTCTAC+TGG + tig0020787:82161-82180 Msa1386190:intron 30.0%
TAACAACTAGCAATATCCAT+CGG + tig0020787:82193-82212 Msa1386190:intron 30.0%
TTACAGTACTAATTCACTCT+AGG + tig0020787:82553-82572 Msa1386190:intron 30.0%
! GCTACTATTGTTTGCTAAAT+AGG - tig0020787:82861-82880 Msa1386170:intron 30.0%
TTGTGTCTTTCTCTGTAATT+TGG - tig0020787:82902-82921 Msa1386170:intron 30.0%
! CATTTTCTGCTGAAAATTCT+CGG + tig0020787:82961-82980 Msa1386190:intron 30.0%
! CTATGACTAATGAGTTGAAA+GGG - tig0020787:82992-83011 Msa1386170:intron 30.0%
! TCTATGACTAATGAGTTGAA+AGG - tig0020787:82993-83012 Msa1386170:intron 30.0%
AAGTATTAGCTGATCGATAA+AGG - tig0020787:83033-83052 Msa1386170:intron 30.0%
TAATTAGAGGGATATTTAGG+AGG + tig0020787:83056-83075 Msa1386190:intron 30.0%
CTCTTTACACAAAATCAAGT+GGG - tig0020787:83138-83157 Msa1386170:intron 30.0%
TCTCTTTACACAAAATCAAG+TGG - tig0020787:83139-83158 Msa1386170:intron 30.0%
TGGATATAAATTATGTGCAG+TGG - tig0020787:83224-83243 Msa1386170:CDS 30.0%
!!! TTTGAATTTTTCAGGGACTT+GGG + tig0020787:83440-83459 Msa1386190:intron 30.0%
TTCTTTGAACTATAGGTTAC+TGG - tig0020787:83663-83682 Msa1386170:intron 30.0%
ACAAGGACAATAGTAACAAA+AGG - tig0020787:83772-83791 Msa1386170:intron 30.0%
!!! TAGATAAGCCTGGAATTTTT+TGG - tig0020787:83821-83840 Msa1386170:intron 30.0%
AATGTACGATGATAAAACCT+CGG + tig0020787:83980-83999 Msa1386190:three_prime_UTR 30.0%
!! TGACATCATTTTTACACACA+TGG - tig0020787:84024-84043 Msa1386170:intron 30.0%
! ATGATGGAACGAACAAAAAG+TGG + tig0020787:81714-81733 Msa1386190:intron 35.0%
TGATGGAACGAACAAAAAGT+GGG + tig0020787:81715-81734 Msa1386190:intron 35.0%
AAATGTGGGAGAGATCATTT+GGG - tig0020787:81747-81766 Msa1386170:intron 35.0%
TATGGGAATTGTTTGTCAAG+AGG - tig0020787:81816-81835 Msa1386170:intron 35.0%
CTCCATGTGCAGTATATATT+GGG + tig0020787:82112-82131 Msa1386190:intron 35.0%
! AGACATCATTAGTTTATCCC+AGG - tig0020787:82159-82178 Msa1386170:three_prime_UTR 35.0%
TGTCAAAACATAACAGACCT+TGG - tig0020787:82242-82261 Msa1386170:three_prime_UTR 35.0%
TAACTAGAGCAACTGGTAAT+TGG - tig0020787:82499-82518 Msa1386170:three_prime_UTR 35.0%
ATTACCAGTTGCTCTAGTTA+AGG + tig0020787:82499-82518 Msa1386190:intron 35.0%
ACTTCAATATGTGGGAACAA+AGG - tig0020787:82529-82548 Msa1386170:three_prime_UTR 35.0%
GAGAAAGAAAAAGGACAATG+AGG + tig0020787:82689-82708 Msa1386190:intron 35.0%
GAGAAAGACACAATGCAAAT+AGG + tig0020787:82909-82928 Msa1386190:intron 35.0%
! ACTAATGAGTTGAAAGGGAT+TGG - tig0020787:82987-83006 Msa1386170:intron 35.0%
! CGATAAAGGTTGTGATTTGT+TGG - tig0020787:83019-83038 Msa1386170:intron 35.0%
TTTACACAAAATCAAGTGGG+TGG - tig0020787:83135-83154 Msa1386170:intron 35.0%
CTTTAGTGGAATCACATTGA+TGG - tig0020787:83173-83192 Msa1386170:intron 35.0%
!! ATTCTGAGACACTACTTTAG+TGG - tig0020787:83187-83206 Msa1386170:intron 35.0%
TTCAGTAGCAACTTGTACAA+AGG + tig0020787:83264-83283 Msa1386190:intron 35.0%
!!! GTTTGAATTTTTCAGGGACT+TGG + tig0020787:83439-83458 Msa1386190:intron 35.0%
AGTTTGTACTTGCAATCACA+AGG - tig0020787:83789-83808 Msa1386170:intron 35.0%
CAAAGAGACCAAAAAATTCC+AGG + tig0020787:83810-83829 Msa1386190:three_prime_UTR 35.0%
! CCATTACAAGTTCATTTTCC+TGG - tig0020787:83902-83921 Msa1386170:intron 35.0%
CCAGGAAAATGAACTTGTAA+TGG + tig0020787:83899-83918 Msa1386190:three_prime_UTR 35.0%
TTGTTAAGTCTACCAGCATT+TGG + tig0020787:84061-84080 Msa1386190:three_prime_UTR 35.0%
! ATCCTGCTATCCCAATTTTA+GGG - tig0020787:84133-84152 Msa1386170:intron 35.0%
GAAATGTGGGAGAGATCATT+TGG - tig0020787:81748-81767 Msa1386170:intron 40.0%
TGCTCAAAGGTAGGAAATGT+GGG - tig0020787:81761-81780 Msa1386170:intron 40.0%
ATGCTCAAAGGTAGGAAATG+TGG - tig0020787:81762-81781 Msa1386170:intron 40.0%
ACATTTCCTACCTTTGAGCA+TGG + tig0020787:81761-81780 Msa1386190:intron 40.0%
TTATAGATGGCCATGCTCAA+AGG - tig0020787:81774-81793 Msa1386170:intron 40.0%
ATATATACTGCACATGGAGG+AGG - tig0020787:82111-82130 Msa1386170:intron 40.0%
CCAATATATACTGCACATGG+AGG - tig0020787:82114-82133 Msa1386170:intron 40.0%
CCTCCATGTGCAGTATATAT+TGG + tig0020787:82111-82130 Msa1386190:intron 40.0%
! ATCATTAGTTTATCCCAGGC+AGG - tig0020787:82155-82174 Msa1386170:three_prime_UTR 40.0%
TACAATGTACTCTGAACCGA+TGG - tig0020787:82212-82231 Msa1386170:three_prime_UTR 40.0%
GTACATTGTAGAGAGAACCA+AGG + tig0020787:82222-82241 Msa1386190:intron 40.0%
GAGCAATTTCATAATCCCCA+CGG - tig0020787:82464-82483 Msa1386170:three_prime_UTR 40.0%
ATGTCCTTAACTAGAGCAAC+TGG - tig0020787:82506-82525 Msa1386170:three_prime_UTR 40.0%
CATCTAGCATTTCTCCTGTT+AGG + tig0020787:82721-82740 Msa1386190:intron 40.0%
TCAGCAGCAGAAACTTATAC+TGG - tig0020787:82752-82771 Msa1386170:three_prime_UTR 40.0%
ACAAAATCAAGTGGGTGGAT+TGG - tig0020787:83130-83149 Msa1386170:intron 40.0%
GTACAAGTTGCTACTGAAGA+AGG - tig0020787:83262-83281 Msa1386170:CDS 40.0%
TTGCTTATGACATAGGTCGA+CGG - tig0020787:83291-83310 Msa1386170:intron 40.0%
ATAAGAATGTGCGGATCTGA+AGG - tig0020787:83415-83434 Msa1386170:intron 40.0%
ACTATAGGTTACTGGTGAAC+TGG - tig0020787:83655-83674 Msa1386170:intron 40.0%
TAAGTCTACCAGCATTTGGA+AGG + tig0020787:84065-84084 Msa1386190:three_prime_UTR 40.0%
! CTTTTCTTCCTTCCAAATGC+TGG - tig0020787:84076-84095 Msa1386170:intron 40.0%
GGAAGAAAAGTTGTCAATCC+CGG + tig0020787:84086-84105 Msa1386190:three_prime_UTR 40.0%
AACCCTAAAATTGGGATAGC+AGG + tig0020787:84128-84147 Msa1386190:three_prime_UTR 40.0%
! CATCCTGCTATCCCAATTTT+AGG - tig0020787:84134-84153 Msa1386170:intron 40.0%
CTAAAATTGGGATAGCAGGA+TGG + tig0020787:84132-84151 Msa1386190:three_prime_UTR 40.0%
GGCCCAATATATACTGCACA+TGG - tig0020787:82117-82136 Msa1386170:intron 45.0%
! GGCAGGTTAGCCATTTGTAA+AGG - tig0020787:82138-82157 Msa1386170:three_prime_UTR 45.0%
TTACAAATGGCTAACCTGCC+TGG + tig0020787:82138-82157 Msa1386190:intron 45.0%
TACAAATGGCTAACCTGCCT+GGG + tig0020787:82139-82158 Msa1386190:intron 45.0%
AGGAGAAATGCTAGATGTGC+AGG - tig0020787:82718-82737 Msa1386170:three_prime_UTR 45.0%
TTATACTGGTGGAGCCTAAC+AGG - tig0020787:82738-82757 Msa1386170:three_prime_UTR 45.0%
GCAGCAGAAACTTATACTGG+TGG - tig0020787:82749-82768 Msa1386170:three_prime_UTR 45.0%
TGATGGGACAATCAAGGTGT+GGG - tig0020787:82810-82829 Msa1386170:CDS 45.0%
! ATGATGGGACAATCAAGGTG+TGG - tig0020787:82811-82830 Msa1386170:CDS 45.0%
!! AAGCGATGATGGGACAATCA+AGG - tig0020787:82816-82835 Msa1386170:CDS 45.0%
TGTCTCAGAATCTTACCCCA+TGG + tig0020787:83196-83215 Msa1386190:intron 45.0%
ATTATGTGCAGTGGAGCCAT+GGG - tig0020787:83215-83234 Msa1386170:CDS 45.0%
AATTATGTGCAGTGGAGCCA+TGG - tig0020787:83216-83235 Msa1386170:CDS 45.0%
GAAGGAGAAAGCTCATGACA+TGG - tig0020787:83244-83263 Msa1386170:CDS 45.0%
TCCAGGCTTATCTATAAGCG+CGG + tig0020787:83827-83846 Msa1386190:three_prime_UTR 45.0%
GAAGTGCATGATTATGCACC+AGG + tig0020787:83881-83900 Msa1386190:three_prime_UTR 45.0%
TACACACATGGAATGCCACT+GGG - tig0020787:84012-84031 Msa1386170:intron 45.0%
TTACACACATGGAATGCCAC+TGG - tig0020787:84013-84032 Msa1386170:intron 45.0%
GTCAATCCCGGATAGTATAG+TGG + tig0020787:84098-84117 Msa1386190:three_prime_UTR 45.0%
GAGCGGTCAACCCTAAAATT+GGG + tig0020787:84120-84139 Msa1386190:three_prime_UTR 45.0%
GCTGTGAATGTTGTGCAAGT+TGG - tig0020787:84287-84306 Msa1386170:intron 45.0%
AGATGGCCATGCTCAAAGGT+AGG - tig0020787:81770-81789 Msa1386170:intron 50.0%
AATCCCCACGGCTTTCTGTT+GGG - tig0020787:82452-82471 Msa1386170:three_prime_UTR 50.0%
TAATCCCCACGGCTTTCTGT+TGG - tig0020787:82453-82472 Msa1386170:three_prime_UTR 50.0%
GACAATCAAGGTGTGGGATC+TGG - tig0020787:82804-82823 Msa1386170:CDS 50.0%
TAGCCTCTGCAAGCGATGAT+GGG - tig0020787:82826-82845 Msa1386170:CDS 50.0%
!! CTGACCGTGATTCTGAAGCA+CGG - tig0020787:83082-83101 Msa1386170:intron 50.0%
TTATGTGCAGTGGAGCCATG+GGG - tig0020787:83214-83233 Msa1386170:CDS 50.0%
TCCGCGCTTATAGATAAGCC+TGG - tig0020787:83831-83850 Msa1386170:intron 50.0%
! TCCCGGATAGTATAGTGGAG+CGG + tig0020787:84103-84122 Msa1386190:three_prime_UTR 50.0%
ACCGCTCCACTATACTATCC+GGG - tig0020787:84107-84126 Msa1386170:intron 50.0%
GACCGCTCCACTATACTATC+CGG - tig0020787:84108-84127 Msa1386170:intron 50.0%
GGAGCGGTCAACCCTAAAAT+TGG + tig0020787:84119-84138 Msa1386190:three_prime_UTR 50.0%
TACGACCCAACAGAAAGCCG+TGG + tig0020787:82444-82463 Msa1386190:intron 55.0%
ACGACCCAACAGAAAGCCGT+GGG + tig0020787:82445-82464 Msa1386190:intron 55.0%
TGTCCCATCATCGCTTGCAG+AGG + tig0020787:82820-82839 Msa1386190:intron 55.0%
CTAGCCTCTGCAAGCGATGA+TGG - tig0020787:82827-82846 Msa1386170:CDS 55.0%
GAGGCCGTGCTTCAGAATCA+CGG + tig0020787:83075-83094 Msa1386190:intron 55.0%
AAACCTCGGTATGCTCCCAG+TGG + tig0020787:83994-84013 Msa1386190:three_prime_UTR 55.0%
CGACCCAACAGAAAGCCGTG+GGG + tig0020787:82446-82465 Msa1386190:intron 60.0%
TCGCTTGCAGAGGCTAGCAG+TGG + tig0020787:82830-82849 Msa1386190:intron 60.0%
! ATGCCACTGGGAGCATACCG+AGG - tig0020787:84000-84019 Msa1386170:intron 60.0%
Chromosome Type Strat End Strand Name
tig0020787 gene 81691 84310 81691 ID=Msa1386190;Name=Msa1386190
tig0020787 mRNA 81691 84310 81691 ID=Msa1386190-mRNA-1;Parent=Msa1386190;Name=Msa1386190-mRNA-1;_AED=0.28;_eAED=0.30;_QI=0|0|0.33|1|0|0|3|694|59
tig0020787 exon 81691 81699 81691 ID=Msa1386190-mRNA-1:exon:10029;Parent=Msa1386190-mRNA-1
tig0020787 exon 82221 82228 82221 ID=Msa1386190-mRNA-1:exon:10030;Parent=Msa1386190-mRNA-1
tig0020787 exon 83454 84310 83454 ID=Msa1386190-mRNA-1:exon:10031;Parent=Msa1386190-mRNA-1
tig0020787 CDS 81691 81699 81691 ID=Msa1386190-mRNA-1:cds;Parent=Msa1386190-mRNA-1
tig0020787 CDS 82221 82228 82221 ID=Msa1386190-mRNA-1:cds;Parent=Msa1386190-mRNA-1
tig0020787 CDS 83454 83616 83454 ID=Msa1386190-mRNA-1:cds;Parent=Msa1386190-mRNA-1
tig0020787 three_prime_UTR 83617 84310 83617 ID=Msa1386190-mRNA-1:three_prime_utr;Parent=Msa1386190-mRNA-1
Gene Sequence

>Msa1386190

ATGGTAATTAGTACATTGGACTTGGGATTCGATGTAGATACAGATTTATCTCTAAATAACAACTGCACAAATGTTGATGTTCAAAACACTCAAGTTTTCAGACGCCAAGAAGAGCAACTAAAAAAAAGATCTGATTCAAATTCAACCCCACAAATATATGAACAAAATGAGAAGGAATAG

Protein sequence

>Msa1386190

MVISTLDLGFDVDTDLSLNNNCTNVDVQNTQVFRRQEEQLKKRSDSNSTPQIYEQNEKE*