AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene50449


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 65 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGCTTGATGCAGGATTT+TGG 0.284785 7.4:-16160355 None:intergenic
GCTTCATTCTCTGCTGCTAC+TGG 0.357062 7.4:+16160304 MS.gene50449:CDS
ATCAAGCTGAAAACACCTTA+TGG 0.387510 7.4:+16160367 MS.gene50449:CDS
ACGCGGCGGTCTCGTGCTTC+CGG 0.391950 7.4:-16159058 None:intergenic
TGAGAGAAGGAGGGAGAGAC+AGG 0.393153 7.4:+16160213 MS.gene50449:CDS
TTTGGAACTTTACTTCCATA+AGG 0.419855 7.4:-16160382 None:intergenic
GCTCGTGCGCGTCGTTCTCC+AGG 0.444790 7.4:+16159232 MS.gene50449:CDS
TTTAGGCGATTGAGAGAAGG+AGG 0.446441 7.4:+16160203 MS.gene50449:intron
TGCGCGTCGTTCTCCAGGTT+CGG 0.449151 7.4:+16159237 MS.gene50449:CDS
ATATCCTGCAACGGCGTCCT+CGG 0.451746 7.4:-16159340 None:intergenic
GTACCCGAGGACGCCGTTGC+AGG 0.452614 7.4:+16159336 MS.gene50449:CDS
ACTGAGGAAATTGAGCAAAC+TGG 0.455510 7.4:+16160238 MS.gene50449:CDS
CGATCTGAACCGGCGGTGAA+TGG 0.459393 7.4:-16159172 None:intergenic
ACGAGCAACTTCGCGACGTA+CGG 0.459911 7.4:-16159215 None:intergenic
TTCACGCTCAATTATATCAA+TGG 0.466579 7.4:-16160488 None:intergenic
CCACGGCGAGTGGTGGTTGG+AGG 0.472234 7.4:-16159268 None:intergenic
GCGGTGAATGGAGCGGGTGC+AGG 0.472928 7.4:-16159160 None:intergenic
TCTTGAATCACGGCGGAGAA+AGG 0.474672 7.4:-16159115 None:intergenic
ATCTTCTTCAATTCACCTCA+TGG 0.478558 7.4:-16160593 None:intergenic
AGTGAAGAACCGATCTGAAC+CGG 0.482402 7.4:-16159182 None:intergenic
GTGTTTAGGCGATTGAGAGA+AGG 0.495099 7.4:+16160200 MS.gene50449:intron
CAGAACATCAGAAAAGGGTT+AGG 0.496050 7.4:+16160560 MS.gene50449:CDS
CTTCCACGGCGAGTGGTGGT+TGG 0.501586 7.4:-16159271 None:intergenic
AAACTTCCTGCTGCTGAAGA+TGG 0.501739 7.4:+16160424 MS.gene50449:CDS
GATTCACCATCTTCAGCAGC+AGG 0.505435 7.4:-16160430 None:intergenic
TATCCTGCAACGGCGTCCTC+GGG 0.507871 7.4:-16159339 None:intergenic
GAACCGGCGGTGAATGGAGC+GGG 0.509648 7.4:-16159166 None:intergenic
TTCAGCTGGTTAGCATGAAC+TGG 0.509893 7.4:-16160265 None:intergenic
TCTTCTTCCACGGCGAGTGG+TGG 0.510955 7.4:-16159275 None:intergenic
AACGGCGAAGAGAGAGAAAG+AGG 0.513945 7.4:-16159026 None:intergenic
AAAAGCAGAACATCAGAAAA+GGG 0.528951 7.4:+16160555 MS.gene50449:CDS
GTAGCAGCAGAGAATGAAGC+TGG 0.533970 7.4:-16160301 None:intergenic
GATCAGAGAAAATGTTCAGC+TGG 0.541232 7.4:-16160279 None:intergenic
CGAGCAACTTCGCGACGTAC+GGG 0.553693 7.4:-16159214 None:intergenic
CGAGGAGTGTACTTCCGTCT+TGG 0.554998 7.4:+16159314 MS.gene50449:CDS
ACCACTCGCCGTGGAAGAAG+AGG 0.555978 7.4:+16159277 MS.gene50449:CDS
GCCTCTTCTTCCACGGCGAG+TGG 0.556257 7.4:-16159278 None:intergenic
CTTCGCCGTTCATACTATGC+CGG 0.566266 7.4:+16159039 MS.gene50449:CDS
AATTCACCTCATGGACATCA+AGG 0.566381 7.4:-16160584 None:intergenic
TTAGGCGATTGAGAGAAGGA+GGG 0.570115 7.4:+16160204 MS.gene50449:intron
CATTCACCGCCGGTTCAGAT+CGG 0.577297 7.4:+16159173 MS.gene50449:CDS
TGGAGCGGGTGCAGGTGTAA+CGG 0.585593 7.4:-16159152 None:intergenic
TGCTTCCGGCATAGTATGAA+CGG 0.594718 7.4:-16159044 None:intergenic
AATAGAGTATCAACGTCAAG+AGG 0.595739 7.4:-16159085 None:intergenic
GAATGCAATAACTTCTTCTG+AGG 0.598545 7.4:-16160466 None:intergenic
CGGCTCAGATTCTTGAATCA+CGG 0.600207 7.4:-16159125 None:intergenic
GAGGGAGAGACAGGGAACTG+AGG 0.604365 7.4:+16160222 MS.gene50449:CDS
CCTCCAACCACCACTCGCCG+TGG 0.618566 7.4:+16159268 MS.gene50449:CDS
TGAACCGGCGGTGAATGGAG+CGG 0.620027 7.4:-16159167 None:intergenic
GGCGTCCTCGGGTACCAAGA+CGG 0.620398 7.4:-16159328 None:intergenic
TACTTCCGTCTTGGTACCCG+AGG 0.623356 7.4:+16159323 MS.gene50449:CDS
GGTGCAGGTGTAACGGAGAG+CGG 0.629682 7.4:-16159145 None:intergenic
CACTCCTCGACGCAGTAGCA+CGG 0.633694 7.4:-16159300 None:intergenic
GAGAGAAGGAGGGAGAGACA+GGG 0.634717 7.4:+16160214 MS.gene50449:CDS
GCACCCGCTCCATTCACCGC+CGG 0.637803 7.4:+16159163 MS.gene50449:CDS
CAACGTCAAGAGGGATGACG+CGG 0.656599 7.4:-16159075 None:intergenic
ATAGAGTATCAACGTCAAGA+GGG 0.669159 7.4:-16159084 None:intergenic
TAGCACGGCCTCTTCTTCCA+CGG 0.680838 7.4:-16159285 None:intergenic
TCACGGCGGAGAAAGGTCGT+CGG 0.682516 7.4:-16159108 None:intergenic
ATAGCAGTGATATCCTGCAA+CGG 0.687557 7.4:-16159349 None:intergenic
GAGGCCGTGCTACTGCGTCG+AGG 0.702265 7.4:+16159296 MS.gene50449:CDS
CGTCAAGAGGGATGACGCGG+CGG 0.704648 7.4:-16159072 None:intergenic
GAAGAACCGATCTGAACCGG+CGG 0.705189 7.4:-16159179 None:intergenic
TTAGGACCTTGATGTCCATG+AGG 0.720116 7.4:+16160578 MS.gene50449:CDS
CTCAGATTCTTGAATCACGG+CGG 0.734730 7.4:-16159122 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAAAATAAACTAAAAAGC+AGG - chr7.4:16159501-16159520 None:intergenic 15.0%
!!! AGAGAAAATTTTCATTATAA+CGG + chr7.4:16159678-16159697 MS.gene50449:intron 15.0%
!!! GAATTTGATTTAAATTGAAT+TGG + chr7.4:16160042-16160061 MS.gene50449:intron 15.0%
!! ATTCTGTTAATATTGTGTTT+AGG + chr7.4:16160186-16160205 MS.gene50449:intron 20.0%
!! TCTCATCAAAATAGAAAAAA+CGG + chr7.4:16159407-16159426 MS.gene50449:intron 20.0%
!! TTTAAATTGAATTGGCATAA+CGG + chr7.4:16160050-16160069 MS.gene50449:intron 20.0%
!!! TTGATTTGAATTGGAAAAAA+CGG + chr7.4:16159747-16159766 MS.gene50449:intron 20.0%
! CATTTACTTTGCTAATATTC+TGG + chr7.4:16159644-16159663 MS.gene50449:intron 25.0%
! CCGAATAAAGATAAATAAAC+CGG - chr7.4:16159559-16159578 None:intergenic 25.0%
! CCGGTTTATTTATCTTTATT+CGG + chr7.4:16159556-16159575 MS.gene50449:intron 25.0%
!! AGAGAAATTTTTCTTCAGAA+CGG + chr7.4:16159977-16159996 MS.gene50449:intron 25.0%
!! GGTTTTCAATTTTATCTAGA+AGG + chr7.4:16159428-16159447 MS.gene50449:intron 25.0%
!!! GACTAGAATTTGATTTGAAT+TGG + chr7.4:16159738-16159757 MS.gene50449:intron 25.0%
AAAAAGCAGAACATCAGAAA+AGG + chr7.4:16160554-16160573 MS.gene50449:CDS 30.0%
AAAAGCAGAACATCAGAAAA+GGG + chr7.4:16160555-16160574 MS.gene50449:CDS 30.0%
TATATGCGATGCTGAATATT+CGG + chr7.4:16159517-16159536 MS.gene50449:intron 30.0%
TTCACGCTCAATTATATCAA+TGG - chr7.4:16160491-16160510 None:intergenic 30.0%
! GCAATGTCAATGATGATTTT+TGG - chr7.4:16160403-16160422 None:intergenic 30.0%
! TTTGGAACTTTACTTCCATA+AGG - chr7.4:16160385-16160404 None:intergenic 30.0%
!!! TTTCTGATGTTCTGCTTTTT+TGG - chr7.4:16160554-16160573 None:intergenic 30.0%
ATCAAGCTGAAAACACCTTA+TGG + chr7.4:16160367-16160386 MS.gene50449:CDS 35.0%
CGGAATGCTTAATTGAAAAC+CGG + chr7.4:16159537-16159556 MS.gene50449:intron 35.0%
GAATGCAATAACTTCTTCTG+AGG - chr7.4:16160469-16160488 None:intergenic 35.0%
! AATAGAGTATCAACGTCAAG+AGG - chr7.4:16159088-16159107 None:intergenic 35.0%
! ATAGAGTATCAACGTCAAGA+GGG - chr7.4:16159087-16159106 None:intergenic 35.0%
!! AGGATTTTGGTGATTTCTTG+TGG - chr7.4:16160345-16160364 None:intergenic 35.0%
ACTGAGGAAATTGAGCAAAC+TGG + chr7.4:16160238-16160257 MS.gene50449:CDS 40.0%
ATAGCAGTGATATCCTGCAA+CGG - chr7.4:16159352-16159371 None:intergenic 40.0%
CAGAACATCAGAAAAGGGTT+AGG + chr7.4:16160560-16160579 MS.gene50449:CDS 40.0%
GATCAGAGAAAATGTTCAGC+TGG - chr7.4:16160282-16160301 None:intergenic 40.0%
! TTCAGCTTGATGCAGGATTT+TGG - chr7.4:16160358-16160377 None:intergenic 40.0%
!!! TGTTCTGCTTTTTTGGCTGT+AGG - chr7.4:16160547-16160566 None:intergenic 40.0%
AAACTTCCTGCTGCTGAAGA+TGG + chr7.4:16160424-16160443 MS.gene50449:CDS 45.0%
AGTGAAGAACCGATCTGAAC+CGG - chr7.4:16159185-16159204 None:intergenic 45.0%
CGGCTCAGATTCTTGAATCA+CGG - chr7.4:16159128-16159147 None:intergenic 45.0%
CTCAGATTCTTGAATCACGG+CGG - chr7.4:16159125-16159144 None:intergenic 45.0%
GTGTTTAGGCGATTGAGAGA+AGG + chr7.4:16160200-16160219 MS.gene50449:intron 45.0%
TGCTTCCGGCATAGTATGAA+CGG - chr7.4:16159047-16159066 None:intergenic 45.0%
TTAGGACCTTGATGTCCATG+AGG + chr7.4:16160578-16160597 MS.gene50449:CDS 45.0%
TTAGGCGATTGAGAGAAGGA+GGG + chr7.4:16160204-16160223 MS.gene50449:intron 45.0%
TTCAGCTGGTTAGCATGAAC+TGG - chr7.4:16160268-16160287 None:intergenic 45.0%
TTTAGGCGATTGAGAGAAGG+AGG + chr7.4:16160203-16160222 MS.gene50449:intron 45.0%
! AGGTGTTTTCAGCTTGATGC+AGG - chr7.4:16160365-16160384 None:intergenic 45.0%
AACGGCGAAGAGAGAGAAAG+AGG - chr7.4:16159029-16159048 None:intergenic 50.0%
CTTCGCCGTTCATACTATGC+CGG + chr7.4:16159039-16159058 MS.gene50449:CDS 50.0%
GATTCACCATCTTCAGCAGC+AGG - chr7.4:16160433-16160452 None:intergenic 50.0%
GCTTCATTCTCTGCTGCTAC+TGG + chr7.4:16160304-16160323 MS.gene50449:CDS 50.0%
GTAGCAGCAGAGAATGAAGC+TGG - chr7.4:16160304-16160323 None:intergenic 50.0%
TCTTGAATCACGGCGGAGAA+AGG - chr7.4:16159118-16159137 None:intergenic 50.0%
!!! GGAGGAGTATTTTCCGAACC+TGG - chr7.4:16159253-16159272 None:intergenic 50.0%
ACGAGCAACTTCGCGACGTA+CGG - chr7.4:16159218-16159237 None:intergenic 55.0%
ATATCCTGCAACGGCGTCCT+CGG - chr7.4:16159343-16159362 None:intergenic 55.0%
CAACGTCAAGAGGGATGACG+CGG - chr7.4:16159078-16159097 None:intergenic 55.0%
GAAGAACCGATCTGAACCGG+CGG - chr7.4:16159182-16159201 None:intergenic 55.0%
GAGAGAAGGAGGGAGAGACA+GGG + chr7.4:16160214-16160233 MS.gene50449:CDS 55.0%
TACTTCCGTCTTGGTACCCG+AGG + chr7.4:16159323-16159342 MS.gene50449:CDS 55.0%
TAGCACGGCCTCTTCTTCCA+CGG - chr7.4:16159288-16159307 None:intergenic 55.0%
TGAGAGAAGGAGGGAGAGAC+AGG + chr7.4:16160213-16160232 MS.gene50449:CDS 55.0%
! CGAGGAGTGTACTTCCGTCT+TGG + chr7.4:16159314-16159333 MS.gene50449:CDS 55.0%
!! CATTCACCGCCGGTTCAGAT+CGG + chr7.4:16159173-16159192 MS.gene50449:CDS 55.0%
ACCACTCGCCGTGGAAGAAG+AGG + chr7.4:16159277-16159296 MS.gene50449:CDS 60.0%
CACTCCTCGACGCAGTAGCA+CGG - chr7.4:16159303-16159322 None:intergenic 60.0%
CGAGCAACTTCGCGACGTAC+GGG - chr7.4:16159217-16159236 None:intergenic 60.0%
CGATCTGAACCGGCGGTGAA+TGG - chr7.4:16159175-16159194 None:intergenic 60.0%
GAGGGAGAGACAGGGAACTG+AGG + chr7.4:16160222-16160241 MS.gene50449:CDS 60.0%
TATCCTGCAACGGCGTCCTC+GGG - chr7.4:16159342-16159361 None:intergenic 60.0%
TCACGGCGGAGAAAGGTCGT+CGG - chr7.4:16159111-16159130 None:intergenic 60.0%
TCTTCTTCCACGGCGAGTGG+TGG - chr7.4:16159278-16159297 None:intergenic 60.0%
TGAACCGGCGGTGAATGGAG+CGG - chr7.4:16159170-16159189 None:intergenic 60.0%
TGCGCGTCGTTCTCCAGGTT+CGG + chr7.4:16159237-16159256 MS.gene50449:CDS 60.0%
TGGAGCGGGTGCAGGTGTAA+CGG - chr7.4:16159155-16159174 None:intergenic 60.0%
! GGTGCAGGTGTAACGGAGAG+CGG - chr7.4:16159148-16159167 None:intergenic 60.0%
CGTCAAGAGGGATGACGCGG+CGG - chr7.4:16159075-16159094 None:intergenic 65.0%
CTTCCACGGCGAGTGGTGGT+TGG - chr7.4:16159274-16159293 None:intergenic 65.0%
GAACCGGCGGTGAATGGAGC+GGG - chr7.4:16159169-16159188 None:intergenic 65.0%
GCCTCTTCTTCCACGGCGAG+TGG - chr7.4:16159281-16159300 None:intergenic 65.0%
GGCGTCCTCGGGTACCAAGA+CGG - chr7.4:16159331-16159350 None:intergenic 65.0%
ACGCGGCGGTCTCGTGCTTC+CGG - chr7.4:16159061-16159080 None:intergenic 70.0%
CCACGGCGAGTGGTGGTTGG+AGG - chr7.4:16159271-16159290 None:intergenic 70.0%
CCTCCAACCACCACTCGCCG+TGG + chr7.4:16159268-16159287 MS.gene50449:CDS 70.0%
GCACCCGCTCCATTCACCGC+CGG + chr7.4:16159163-16159182 MS.gene50449:CDS 70.0%
GCGGTGAATGGAGCGGGTGC+AGG - chr7.4:16159163-16159182 None:intergenic 70.0%
GCTCGTGCGCGTCGTTCTCC+AGG + chr7.4:16159232-16159251 MS.gene50449:CDS 70.0%
GTACCCGAGGACGCCGTTGC+AGG + chr7.4:16159336-16159355 MS.gene50449:CDS 70.0%
! GAGGCCGTGCTACTGCGTCG+AGG + chr7.4:16159296-16159315 MS.gene50449:CDS 70.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 16159017 16160603 16159017 ID=MS.gene50449
chr7.4 mRNA 16159017 16160603 16159017 ID=MS.gene50449.t1;Parent=MS.gene50449
chr7.4 exon 16159017 16159378 16159017 ID=MS.gene50449.t1.exon1;Parent=MS.gene50449.t1
chr7.4 CDS 16159017 16159378 16159017 ID=cds.MS.gene50449.t1;Parent=MS.gene50449.t1
chr7.4 exon 16160208 16160603 16160208 ID=MS.gene50449.t1.exon2;Parent=MS.gene50449.t1
chr7.4 CDS 16160208 16160603 16160208 ID=cds.MS.gene50449.t1;Parent=MS.gene50449.t1
Gene Sequence

>MS.gene50449

TTTCTCACTCCTCTTTCTCTCTCTTCGCCGTTCATACTATGCCGGAAGCACGAGACCGCCGCGTCATCCCTCTTGACGTTGATACTCTATTCCGACGACCTTTCTCCGCCGTGATTCAAGAATCTGAGCCGCTCTCCGTTACACCTGCACCCGCTCCATTCACCGCCGGTTCAGATCGGTTCTTCACTGAAAGAACTCCCGTACGTCGCGAAGTTGCTCGTGCGCGTCGTTCTCCAGGTTCGGAAAATACTCCTCCAACCACCACTCGCCGTGGAAGAAGAGGCCGTGCTACTGCGTCGAGGAGTGTACTTCCGTCTTGGTACCCGAGGACGCCGTTGCAGGATATCACTGCTATTGTTCGAGTAAATCTCTGATTCTTTTCTCTTTCTCTCTCATCAAAATAGAAAAAACGGTTTTCAATTTTATCTAGAAGGTTCTTTGAATATTTTTAAATTTTAGTTTAATATTAATATAATGATATCCTGCTTTTTAGTTTATTTTATATGCGATGCTGAATATTCGGAATGCTTAATTGAAAACCGGTTTATTTATCTTTATTCGGTTGTTTTGATAATTTGTTATGTGATGCTTAATTGTCTGTGATGAGTTTATCTTTAATTTGATTTGCATTTACTTTGCTAATATTCTGGTTAGCAAATTGAGAGAAAATTTTCATTATAACGGTTTAGCTTTAATCTTAAACGTTCTTTTGAGATACTTTGACTAGAATTTGATTTGAATTGGAAAAAACGGTTAATCTTTAATTAATCTAGAACGTTCTTTTGTTTTTAATATATATTTTGAATTTGAATTTTGAACTTGATTTTAGTTTAATTATATTAAATTCTGTCACAATATTCTGTTGTTCATTTGTTATGTGATACTTAATTTTCTGTGTTTAGTTTACGTTTAATTTGAATTTGATTTGATTTTACTTTGTTAATACTGTTTATTGAATTGAGAGAAATTTTTCTTCAGAACGGTTTAACTTTAAGCATAACTTCTCTTTGAAGTGTATTTGACTAGAATTTGATTTAAATTGAATTGGCATAACGGCTGTTTGTTGAGTTCAATTTGAATTGAATATGAACTTTATCGTTGTTAATGTTCTGTTGATTTGTTATGTGATGATGAATTTTCTGTATGTTTAGTTCAATCTGACTAATTTGATTCTGTTAATATTGTGTTTAGGCGATTGAGAGAAGGAGGGAGAGACAGGGAACTGAGGAAATTGAGCAAACTGGAACACCAGTTCATGCTAACCAGCTGAACATTTTCTCTGATCCAGCTTCATTCTCTGCTGCTACTGGATCTTCTTCACGTATCCACAAGAAATCACCAAAATCCTGCATCAAGCTGAAAACACCTTATGGAAGTAAAGTTCCAAAAATCATCATTGACATTGCAAAACTTCCTGCTGCTGAAGATGGTGAATCAGAGCTTCTGACTCCTCAGAAGAAGTTATTGCATTCCATTGATATAATTGAGCGTGAAGTGAAGCAAGAGTTGATGAAACTCAAGAGAACTCCTACAGCCAAAAAAGCAGAACATCAGAAAAGGGTTAGGACCTTGATGTCCATGAGGTGA

Protein sequence

>MS.gene50449.t1

FLTPLSLSSPFILCRKHETAASSLLTLILYSDDLSPPUFKNLSRSPLHLHPLHSPPVQIGSSLKELPYVAKLLVRVVLQVRKILLQPPLAVEEEAVLLRRGVYFRLGTRGRRCRISLLLFERLREGGRDRELRKLSKLEHQFMLTSUTFSLIQLHSLLLLDLLHVSTRNHQNPASSUKHLMEVKFQKSSLTLQNFLLLKMVNQSFULLRRSYCIPLIULSVKUSKSUUNSRELLQPKKQNIRKGLGPUCPUG