AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene026887

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026887.t1 MTR_6g081160 66.667 60 16 1 20 75 1 60 7.52e-18 80.5
MS.gene026887.t1 MTR_6g081160 56.250 64 23 2 114 172 1 64 1.30e-13 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 41 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATACAAGGTAGTTATAAT+AGG 0.224337 2.3:+21207314 MS.gene026887:CDS
AAATAATACTATGGCTAGTT+TGG 0.292025 2.3:+21207606 MS.gene026887:CDS
CATGATGAAGTTTCTGCTTA+AGG 0.329845 2.3:-21207546 None:intergenic
AATACAAGGAAATAATACTA+TGG 0.401260 2.3:+21207597 MS.gene026887:CDS
TTTAGCAAAATAAAAGCATT+GGG 0.424274 2.3:+21207502 MS.gene026887:CDS
AATACAAGGTAGTTATAATA+GGG 0.431054 2.3:+21207315 MS.gene026887:CDS
ACACATCAATGCAATGTTTG+TGG 0.441710 2.3:+21207472 MS.gene026887:CDS
TTTAGCAATGGAAAAGCATT+GGG 0.444822 2.3:+21207220 MS.gene026887:CDS
TGAGAAAACCTATGAAGATT+CGG 0.461549 2.3:+21207087 MS.gene026887:CDS
TTATTTCCTTGTATTGAGAA+AGG 0.466446 2.3:-21207589 None:intergenic
TATTTCCTTGTATTGAGAAA+GGG 0.470601 2.3:-21207588 None:intergenic
AGTCAGAAAAGAGGGTGAAA+AGG 0.473192 2.3:+21207668 MS.gene026887:CDS
ACACATCAGTGCAATGTTTG+TGG 0.475496 2.3:+21207190 MS.gene026887:CDS
ATTCGGAAAAGACGATGAAA+AGG 0.477110 2.3:+21207104 MS.gene026887:CDS
CACATCAGTGCAATGTTTGT+GGG 0.483344 2.3:+21207191 MS.gene026887:CDS
AGTCTGAAAAGAGGATAAAG+AGG 0.489348 2.3:+21207386 MS.gene026887:CDS
TTTGATAAAGATAGTAAGCA+TGG 0.491925 2.3:+21207343 MS.gene026887:CDS
GATACCCCTTTCTCAATACA+AGG 0.503509 2.3:+21207583 MS.gene026887:CDS
ACTTCATCATGATTCACAAA+AGG 0.507116 2.3:+21207558 MS.gene026887:CDS
AACTACCTTGTATTGAGAGA+GGG 0.509993 2.3:-21207306 None:intergenic
AATTAATCATCGTTCACAAA+AGG 0.518691 2.3:+21207276 MS.gene026887:CDS
GCTTAAGGAAGTGAGATCTT+CGG 0.523012 2.3:-21207531 None:intergenic
CAAACCCCTCTCTCAATACA+AGG 0.526964 2.3:+21207301 MS.gene026887:CDS
AGAATCTACACATCAGTGCT+AGG 0.545184 2.3:+21207747 MS.gene026887:CDS
TCTTAAGAAAGTGAGATCTC+CGG 0.549197 2.3:-21207249 None:intergenic
CCCGTGAAGAGTCTGAAAAG+AGG 0.549764 2.3:+21207377 MS.gene026887:CDS
ATTTCCTTGTATTGAGAAAG+GGG 0.553284 2.3:-21207587 None:intergenic
GAAAAGCATTGGGTGGTCAC+CGG 0.556634 2.3:+21207230 MS.gene026887:CDS
CTATGAAGAGTCAGAAAAGA+GGG 0.570873 2.3:+21207660 MS.gene026887:CDS
CCTATGAAGAGTCAGAAAAG+AGG 0.578028 2.3:+21207659 MS.gene026887:CDS
AAGCGATGAAGATGATGCTA+AGG 0.582770 2.3:+21207708 MS.gene026887:CDS
TGAAGATGATGCTAAGGATG+AGG 0.590398 2.3:+21207714 MS.gene026887:CDS
ACTACCTTGTATTGAGAGAG+GGG 0.593179 2.3:-21207305 None:intergenic
TAACTACCTTGTATTGAGAG+AGG 0.601425 2.3:-21207307 None:intergenic
AGCAAAATAAAAGCATTGGG+TGG 0.607881 2.3:+21207505 MS.gene026887:CDS
TAGTGATGAAGATGATGCTA+AGG 0.613974 2.3:+21207144 MS.gene026887:CDS
AGCAATGGAAAAGCATTGGG+TGG 0.615604 2.3:+21207223 MS.gene026887:CDS
AAGTGATGAAGATGATGCTA+AGG 0.616457 2.3:+21207426 MS.gene026887:CDS
ATGGATAAAGATCATAAGCA+TGG 0.623190 2.3:+21207061 MS.gene026887:CDS
TGAAGATGATGCTAAGGATG+AGG 0.644459 2.3:+21207150 MS.gene026887:CDS
AGATCATAAGCATGATCACG+AGG 0.690275 2.3:+21207633 MS.gene026887:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATACAAGGAAATAATACTA+TGG + chr2.3:21207597-21207616 MS.gene026887:CDS 20.0%
!! AATACAAGGTAGTTATAATA+GGG + chr2.3:21207315-21207334 MS.gene026887:CDS 20.0%
!!! TTTAGCAAAATAAAAGCATT+GGG + chr2.3:21207502-21207521 MS.gene026887:CDS 20.0%
!!! TTTTAGCAAAATAAAAGCAT+TGG + chr2.3:21207501-21207520 MS.gene026887:CDS 20.0%
! AATTAATCATCGTTCACAAA+AGG + chr2.3:21207276-21207295 MS.gene026887:CDS 25.0%
! CAATACAAGGTAGTTATAAT+AGG + chr2.3:21207314-21207333 MS.gene026887:CDS 25.0%
! TATTTCCTTGTATTGAGAAA+GGG - chr2.3:21207591-21207610 None:intergenic 25.0%
! TTATTTCCTTGTATTGAGAA+AGG - chr2.3:21207592-21207611 None:intergenic 25.0%
! TTTGATAAAGATAGTAAGCA+TGG + chr2.3:21207343-21207362 MS.gene026887:CDS 25.0%
!! AAATAATACTATGGCTAGTT+TGG + chr2.3:21207606-21207625 MS.gene026887:CDS 25.0%
ACTTCATCATGATTCACAAA+AGG + chr2.3:21207558-21207577 MS.gene026887:CDS 30.0%
ATGGATAAAGATCATAAGCA+TGG + chr2.3:21207061-21207080 MS.gene026887:CDS 30.0%
ATTTCCTTGTATTGAGAAAG+GGG - chr2.3:21207590-21207609 None:intergenic 30.0%
TGAGAAAACCTATGAAGATT+CGG + chr2.3:21207087-21207106 MS.gene026887:CDS 30.0%
!! TTTAGCAATGGAAAAGCATT+GGG + chr2.3:21207220-21207239 MS.gene026887:CDS 30.0%
!! TTTTAGCAATGGAAAAGCAT+TGG + chr2.3:21207219-21207238 MS.gene026887:CDS 30.0%
AACTACCTTGTATTGAGAGA+GGG - chr2.3:21207309-21207328 None:intergenic 35.0%
AAGTGATGAAGATGATGCTA+AGG + chr2.3:21207426-21207445 MS.gene026887:CDS 35.0%
ACACATCAATGCAATGTTTG+TGG + chr2.3:21207472-21207491 MS.gene026887:CDS 35.0%
AGTCTGAAAAGAGGATAAAG+AGG + chr2.3:21207386-21207405 MS.gene026887:CDS 35.0%
ATTCGGAAAAGACGATGAAA+AGG + chr2.3:21207104-21207123 MS.gene026887:CDS 35.0%
CATGATGAAGTTTCTGCTTA+AGG - chr2.3:21207549-21207568 None:intergenic 35.0%
CTATGAAGAGTCAGAAAAGA+GGG + chr2.3:21207660-21207679 MS.gene026887:CDS 35.0%
TAACTACCTTGTATTGAGAG+AGG - chr2.3:21207310-21207329 None:intergenic 35.0%
TAGTGATGAAGATGATGCTA+AGG + chr2.3:21207144-21207163 MS.gene026887:CDS 35.0%
TCTTAAGAAAGTGAGATCTC+CGG - chr2.3:21207252-21207271 None:intergenic 35.0%
! TGTGGGAAAACTTTTAGCAA+TGG + chr2.3:21207208-21207227 MS.gene026887:CDS 35.0%
!! AGCAAAATAAAAGCATTGGG+TGG + chr2.3:21207505-21207524 MS.gene026887:CDS 35.0%
AAGCGATGAAGATGATGCTA+AGG + chr2.3:21207708-21207727 MS.gene026887:CDS 40.0%
ACACATCAGTGCAATGTTTG+TGG + chr2.3:21207190-21207209 MS.gene026887:CDS 40.0%
ACTACCTTGTATTGAGAGAG+GGG - chr2.3:21207308-21207327 None:intergenic 40.0%
AGATCATAAGCATGATCACG+AGG + chr2.3:21207633-21207652 MS.gene026887:CDS 40.0%
AGTCAGAAAAGAGGGTGAAA+AGG + chr2.3:21207668-21207687 MS.gene026887:CDS 40.0%
CACATCAGTGCAATGTTTGT+GGG + chr2.3:21207191-21207210 MS.gene026887:CDS 40.0%
CCTATGAAGAGTCAGAAAAG+AGG + chr2.3:21207659-21207678 MS.gene026887:CDS 40.0%
GATACCCCTTTCTCAATACA+AGG + chr2.3:21207583-21207602 MS.gene026887:CDS 40.0%
GCTTAAGGAAGTGAGATCTT+CGG - chr2.3:21207534-21207553 None:intergenic 40.0%
TGAAGATGATGCTAAGGATG+AGG + chr2.3:21207150-21207169 MS.gene026887:CDS 40.0%
! CCTCTTTTCTGACTCTTCAT+AGG - chr2.3:21207662-21207681 None:intergenic 40.0%
! CGTCTTTTCCGAATCTTCAT+AGG - chr2.3:21207098-21207117 None:intergenic 40.0%
! TCCTCTTTTCAGACTCTTCA+CGG - chr2.3:21207381-21207400 None:intergenic 40.0%
CAAACCCCTCTCTCAATACA+AGG + chr2.3:21207301-21207320 MS.gene026887:CDS 45.0%
! CCTCTTTTCAGACTCTTCAC+GGG - chr2.3:21207380-21207399 None:intergenic 45.0%
!! AGCAATGGAAAAGCATTGGG+TGG + chr2.3:21207223-21207242 MS.gene026887:CDS 45.0%
CCCGTGAAGAGTCTGAAAAG+AGG + chr2.3:21207377-21207396 MS.gene026887:CDS 50.0%
!! GAAAAGCATTGGGTGGTCAC+CGG + chr2.3:21207230-21207249 MS.gene026887:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 21207061 21207768 21207061 ID=MS.gene026887
chr2.3 mRNA 21207061 21207768 21207061 ID=MS.gene026887.t1;Parent=MS.gene026887
chr2.3 exon 21207061 21207768 21207061 ID=MS.gene026887.t1.exon1;Parent=MS.gene026887.t1
chr2.3 CDS 21207061 21207768 21207061 ID=cds.MS.gene026887.t1;Parent=MS.gene026887.t1
Gene Sequence

>MS.gene026887

ATGGATAAAGATCATAAGCATGGTTATGAGAAAACCTATGAAGATTCGGAAAAGACGATGAAAAGGTCTTCATGTTCACTATCTAGTGATGAAGATGATGCTAAGGATGAGGTTTCTGTTCAAGAATCTACACATCAGTGCAATGTTTGTGGGAAAACTTTTAGCAATGGAAAAGCATTGGGTGGTCACCGGAGATCTCACTTTCTTAAGAAGAAAATTAATCATCGTTCACAAAAGGTACAAACCCCTCTCTCAATACAAGGTAGTTATAATAGGGCTAGTTTTGATAAAGATAGTAAGCATGGTTTTGAGAACACCCGTGAAGAGTCTGAAAAGAGGATAAAGAGGTCTTTTAGTTCTCTATCAAGTGATGAAGATGATGCTAAGGATGAGCTTTCTATTCAAGAAACTACACATCAATGCAATGTTTGTGGAAAAATTTTTAGCAAAATAAAAGCATTGGGTGGTCACCGAAGATCTCACTTCCTTAAGCAGAAACTTCATCATGATTCACAAAAGGTTGATACCCCTTTCTCAATACAAGGAAATAATACTATGGCTAGTTTGGATAAAGATCATAAGCATGATCACGAGGATACCTATGAAGAGTCAGAAAAGAGGGTGAAAAGGTCAGCTTGTTCTCTATCAAGCGATGAAGATGATGCTAAGGATGAGGTTTCTGTTCAAGAATCTACACATCAGTGCTAG
Protein sequence

>MS.gene026887.t1

MDKDHKHGYEKTYEDSEKTMKRSSCSLSSDEDDAKDEVSVQESTHQCNVCGKTFSNGKALGGHRRSHFLKKKINHRSQKVQTPLSIQGSYNRASFDKDSKHGFENTREESEKRIKRSFSSLSSDEDDAKDELSIQETTHQCNVCGKIFSKIKALGGHRRSHFLKQKLHHDSQKVDTPFSIQGNNTMASLDKDHKHDHEDTYEESEKRVKRSACSLSSDEDDAKDEVSVQESTHQC