AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene019999

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene019999.t1 MTR_3g070120 30.667 150 94 3 33 175 154 300 5.63e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGATGTTTGCTTCTTTA+AGG 0.138534 6.1:-12234023 None:intergenic
CTTAGATTTCAAATCCAATT+TGG 0.142363 6.1:+12234099 MS.gene019999:CDS
TTTACCTTTCTCACAAGATT+TGG 0.226819 6.1:+12234308 MS.gene019999:CDS
GAAGAGGGTTTCTCTTGTTT+TGG 0.245975 6.1:-12233998 None:intergenic
CTAAGAAGCTATTGAGAATA+AGG 0.252389 6.1:-12234081 None:intergenic
TTTCTAAGCTGCCCTGGTTT+AGG 0.266726 6.1:-12234187 None:intergenic
GGAGCGTGCTCGGTTAATTA+AGG 0.286151 6.1:+12234417 MS.gene019999:CDS
TCAAGAGCCGGAATTGGATT+TGG 0.301896 6.1:+12234396 MS.gene019999:CDS
TTACCTTTCTCACAAGATTT+GGG 0.302378 6.1:+12234309 MS.gene019999:CDS
TCCTTCACAGAGTTATAAAA+AGG 0.345114 6.1:-12234148 None:intergenic
TTAGATTTCAAATCCAATTT+GGG 0.355655 6.1:+12234100 MS.gene019999:CDS
GAAAGTTCAAGAGCCGGAAT+TGG 0.391991 6.1:+12234390 MS.gene019999:CDS
GGCAGCTTAGAAAGAGGATC+TGG 0.431103 6.1:+12234197 MS.gene019999:CDS
GCACGCTCCAAATCCAATTC+CGG 0.451517 6.1:-12234403 None:intergenic
GTCCCCAAATCTTGTGAGAA+AGG 0.458776 6.1:-12234312 None:intergenic
TCAAGATCATTATAGAATCT+AGG 0.460182 6.1:-12234274 None:intergenic
AATAAGGATTTCGTCATTGA+AGG 0.472722 6.1:-12234065 None:intergenic
ATCCTCTTTCTAAGCTGCCC+TGG 0.488059 6.1:-12234193 None:intergenic
ACAAGAGTTGACTGAGGAAT+CGG 0.492745 6.1:+12234333 MS.gene019999:CDS
AATTGGATTTGGAGCGTGCT+CGG 0.504506 6.1:+12234407 MS.gene019999:CDS
ATATGAGAACATGAAGAAAG+AGG 0.508111 6.1:+12234234 MS.gene019999:CDS
GTTGACTGAGGAATCGGATC+GGG 0.509055 6.1:+12234339 MS.gene019999:CDS
GTCATTTCTAAGTTATTGCA+AGG 0.515777 6.1:+12234451 MS.gene019999:CDS
ATTCTATAATGATCTTGAGC+AGG 0.520209 6.1:+12234279 MS.gene019999:CDS
GGAATCGGATCGGGTAGAGT+TGG 0.557159 6.1:+12234348 MS.gene019999:CDS
GGAATTGAAAGTTCAAGAGC+CGG 0.565005 6.1:+12234384 MS.gene019999:CDS
TGCTTCTTTAAGGAAGAAGA+GGG 0.572401 6.1:-12234013 None:intergenic
CTTAGTGTGAAACCTAAACC+AGG 0.573643 6.1:+12234175 MS.gene019999:CDS
TACCTTTCTCACAAGATTTG+GGG 0.576919 6.1:+12234310 MS.gene019999:CDS
AACCAGGGCAGCTTAGAAAG+AGG 0.584962 6.1:+12234191 MS.gene019999:CDS
GGGTAGAGTTGGATGAAATG+TGG 0.588939 6.1:+12234359 MS.gene019999:CDS
TTGCTTCTTTAAGGAAGAAG+AGG 0.590446 6.1:-12234014 None:intergenic
GATTTCGTCATTGAAGGTGA+AGG 0.598033 6.1:-12234059 None:intergenic
AGAGTTGGATGAAATGTGGA+AGG 0.601030 6.1:+12234363 MS.gene019999:CDS
AGTTGACTGAGGAATCGGAT+CGG 0.641138 6.1:+12234338 MS.gene019999:CDS
AGATCATTATAGAATCTAGG+AGG 0.675424 6.1:-12234271 None:intergenic
TTGGGGACAAGAGTTGACTG+AGG 0.693465 6.1:+12234327 MS.gene019999:CDS
TTAGTGTGAAACCTAAACCA+GGG 0.734419 6.1:+12234176 MS.gene019999:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGATTTCAAATCCAATTT+GGG + chr6.1:12234100-12234119 MS.gene019999:CDS 20.0%
! CTTAGATTTCAAATCCAATT+TGG + chr6.1:12234099-12234118 MS.gene019999:CDS 25.0%
! TCAAGATCATTATAGAATCT+AGG - chr6.1:12234277-12234296 None:intergenic 25.0%
!!! TTTCTCTTGTTTTGGATTTT+GGG - chr6.1:12233993-12234012 None:intergenic 25.0%
AATAAGGATTTCGTCATTGA+AGG - chr6.1:12234068-12234087 None:intergenic 30.0%
AGATCATTATAGAATCTAGG+AGG - chr6.1:12234274-12234293 None:intergenic 30.0%
ATATGAGAACATGAAGAAAG+AGG + chr6.1:12234234-12234253 MS.gene019999:CDS 30.0%
ATTCTATAATGATCTTGAGC+AGG + chr6.1:12234279-12234298 MS.gene019999:CDS 30.0%
CTAAGAAGCTATTGAGAATA+AGG - chr6.1:12234084-12234103 None:intergenic 30.0%
GTCATTTCTAAGTTATTGCA+AGG + chr6.1:12234451-12234470 MS.gene019999:CDS 30.0%
GTTTGATGTTTGCTTCTTTA+AGG - chr6.1:12234026-12234045 None:intergenic 30.0%
TCCTTCACAGAGTTATAAAA+AGG - chr6.1:12234151-12234170 None:intergenic 30.0%
TTACCTTTCTCACAAGATTT+GGG + chr6.1:12234309-12234328 MS.gene019999:CDS 30.0%
TTTACCTTTCTCACAAGATT+TGG + chr6.1:12234308-12234327 MS.gene019999:CDS 30.0%
! AGAATCTAGGAGGAAATTTT+TGG - chr6.1:12234264-12234283 None:intergenic 30.0%
! TCCTTTTTATAACTCTGTGA+AGG + chr6.1:12234147-12234166 MS.gene019999:CDS 30.0%
!!! GTTTCTCTTGTTTTGGATTT+TGG - chr6.1:12233994-12234013 None:intergenic 30.0%
TACCTTTCTCACAAGATTTG+GGG + chr6.1:12234310-12234329 MS.gene019999:CDS 35.0%
TTAGTGTGAAACCTAAACCA+GGG + chr6.1:12234176-12234195 MS.gene019999:CDS 35.0%
! TGCTTCTTTAAGGAAGAAGA+GGG - chr6.1:12234016-12234035 None:intergenic 35.0%
! TTGCTTCTTTAAGGAAGAAG+AGG - chr6.1:12234017-12234036 None:intergenic 35.0%
!! CATTGCATTTTGACCCAAAT+TGG - chr6.1:12234116-12234135 None:intergenic 35.0%
ACAAGAGTTGACTGAGGAAT+CGG + chr6.1:12234333-12234352 MS.gene019999:CDS 40.0%
AGAGTTGGATGAAATGTGGA+AGG + chr6.1:12234363-12234382 MS.gene019999:CDS 40.0%
CTTAGTGTGAAACCTAAACC+AGG + chr6.1:12234175-12234194 MS.gene019999:CDS 40.0%
GATTTCGTCATTGAAGGTGA+AGG - chr6.1:12234062-12234081 None:intergenic 40.0%
GGAATTGAAAGTTCAAGAGC+CGG + chr6.1:12234384-12234403 MS.gene019999:CDS 40.0%
!! GAAGAGGGTTTCTCTTGTTT+TGG - chr6.1:12234001-12234020 None:intergenic 40.0%
AGTTGACTGAGGAATCGGAT+CGG + chr6.1:12234338-12234357 MS.gene019999:CDS 45.0%
GAAAGTTCAAGAGCCGGAAT+TGG + chr6.1:12234390-12234409 MS.gene019999:CDS 45.0%
GGGTAGAGTTGGATGAAATG+TGG + chr6.1:12234359-12234378 MS.gene019999:CDS 45.0%
GTCCCCAAATCTTGTGAGAA+AGG - chr6.1:12234315-12234334 None:intergenic 45.0%
TCAAGAGCCGGAATTGGATT+TGG + chr6.1:12234396-12234415 MS.gene019999:CDS 45.0%
TTTCTAAGCTGCCCTGGTTT+AGG - chr6.1:12234190-12234209 None:intergenic 45.0%
! AATTGGATTTGGAGCGTGCT+CGG + chr6.1:12234407-12234426 MS.gene019999:CDS 45.0%
AACCAGGGCAGCTTAGAAAG+AGG + chr6.1:12234191-12234210 MS.gene019999:CDS 50.0%
ATCCTCTTTCTAAGCTGCCC+TGG - chr6.1:12234196-12234215 None:intergenic 50.0%
GCACGCTCCAAATCCAATTC+CGG - chr6.1:12234406-12234425 None:intergenic 50.0%
GGAGCGTGCTCGGTTAATTA+AGG + chr6.1:12234417-12234436 MS.gene019999:CDS 50.0%
GGCAGCTTAGAAAGAGGATC+TGG + chr6.1:12234197-12234216 MS.gene019999:CDS 50.0%
GTTGACTGAGGAATCGGATC+GGG + chr6.1:12234339-12234358 MS.gene019999:CDS 50.0%
TTGGGGACAAGAGTTGACTG+AGG + chr6.1:12234327-12234346 MS.gene019999:CDS 50.0%
GGAATCGGATCGGGTAGAGT+TGG + chr6.1:12234348-12234367 MS.gene019999:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 12233956 12234489 12233956 ID=MS.gene019999
chr6.1 mRNA 12233956 12234489 12233956 ID=MS.gene019999.t1;Parent=MS.gene019999
chr6.1 exon 12233956 12234489 12233956 ID=MS.gene019999.t1.exon1;Parent=MS.gene019999.t1
chr6.1 CDS 12233956 12234489 12233956 ID=cds.MS.gene019999.t1;Parent=MS.gene019999.t1
Gene Sequence

>MS.gene019999

ATGGCAAAGAAATCAAGTTGTTCTTCTTCGTCATCCCAAAATCCAAAACAAGAGAAACCCTCTTCTTCCTTAAAGAAGCAAACATCAAACTCACGTAAGAAAACCTTCACCTTCAATGACGAAATCCTTATTCTCAATAGCTTCTTAGATTTCAAATCCAATTTGGGTCAAAATGCAATGACAAATTACACTCCTTTTTATAACTCTGTGAAGGATTTGCTTAGTGTGAAACCTAAACCAGGGCAGCTTAGAAAGAGGATCTGGAAGTTGAAACAAAAATATGAGAACATGAAGAAAGAGGAAAACCAAAAATTTCCTCCTAGATTCTATAATGATCTTGAGCAGGAAATAATTTACCTTTCTCACAAGATTTGGGGACAAGAGTTGACTGAGGAATCGGATCGGGTAGAGTTGGATGAAATGTGGAAGGAATTGAAAGTTCAAGAGCCGGAATTGGATTTGGAGCGTGCTCGGTTAATTAAGGACTCGATTGACGTCATTTCTAAGTTATTGCAAGGATCATCTTCGTCTTAG
Protein sequence

>MS.gene019999.t1

MAKKSSCSSSSSQNPKQEKPSSSLKKQTSNSRKKTFTFNDEILILNSFLDFKSNLGQNAMTNYTPFYNSVKDLLSVKPKPGQLRKRIWKLKQKYENMKKEENQKFPPRFYNDLEQEIIYLSHKIWGQELTEESDRVELDEMWKELKVQEPELDLERARLIKDSIDVISKLLQGSSSS