AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0113530

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 62 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.231913 1_3:-29470343 Msa0113530:intron
TCCTTTCGCTTCTCAGCTTA+CGG 0.302062 1_3:-29470199 Msa0113530:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 1_3:+29470404 None:intergenic
CTCTGTCTTAGCGCGGCTGC+TGG 0.312927 1_3:-29470504 Msa0113530:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 1_3:-29470231 Msa0113530:CDS
AAGAAACAATGACGGTATCT+AGG 0.347373 1_3:+29470457 None:intergenic
CCTTTCGCTTCTCAGCTTAC+GGG 0.354061 1_3:-29470198 Msa0113530:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 1_3:+29470531 None:intergenic
CAGAGGATGCAAGCGTTATC+CGG 0.442617 1_3:+29470522 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 1_3:+29470242 None:intergenic
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 1_3:-29470230 Msa0113530:CDS
GGTTGAGCCCTGGGATTTGA+CGG 0.472275 1_3:-29470588 None:intergenic
TCTCATGGAGAGTTTGATCC+TGG 0.473913 1_3:+29470039 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 1_3:+29470348 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 1_3:+29470087 None:intergenic
GCTGCCTCCCGTAGGAGTCT+GGG 0.490776 1_3:-29470342 Msa0113530:intron
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 1_3:+29470347 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 1_3:+29470218 None:intergenic
AACGCGTAAGAATCTGCCCT+TGG 0.504406 1_3:+29470141 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 1_3:+29470532 None:intergenic
TAGTGTTTCCAGTGGCGGAC+GGG 0.512766 1_3:+29470113 None:intergenic
GCCAGCGTTCATCCTGAGCC+AGG 0.514091 1_3:-29470057 Msa0113530:CDS
TAAGAATCTGCCCTTGGGAG+AGG 0.514923 1_3:+29470147 None:intergenic
GGAGAGTTTGATCCTGGCTC+AGG 0.515428 1_3:+29470045 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 1_3:-29470121 Msa0113530:CDS
ACGCGTAAGAATCTGCCCTT+GGG 0.539522 1_3:+29470142 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 1_3:+29470280 None:intergenic
AGAAACAATGACGGTATCTA+GGG 0.551942 1_3:+29470458 None:intergenic
CAGCAGCCGCGCTAAGACAG+AGG 0.557919 1_3:+29470505 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 1_3:+29470411 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 1_3:+29470219 None:intergenic
GTAGTGTTTCCAGTGGCGGA+CGG 0.565662 1_3:+29470112 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 1_3:+29470412 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 1_3:-29470227 Msa0113530:CDS
CGCAATGGGCGAAAGACTGA+CGG 0.572648 1_3:+29470379 None:intergenic
CCAGCTACTGATCACCGCCT+TGG 0.578071 1_3:-29470280 Msa0113530:CDS
ATTGGGCGTAAAACGTCTGT+AGG 0.583693 1_3:+29470549 None:intergenic
AGTGTGGTTGATCATCCTCT+CGG 0.585594 1_3:-29470304 Msa0113530:CDS
CTTTCGCTTCTCAGCTTACG+GGG 0.593788 1_3:-29470197 Msa0113530:intron
CTTTACACATGCAAGTCGAA+CGG 0.597034 1_3:+29470086 None:intergenic
CGTCAGTCTTTCGCCCATTG+CGG 0.602072 1_3:-29470378 Msa0113530:CDS
TCCTGGCTCAGGATGAACGC+TGG 0.603603 1_3:+29470056 None:intergenic
CGAAAGGAGGAATCCGCCCA+AGG 0.608783 1_3:+29470214 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 1_3:+29470217 None:intergenic
AGAGGATGATCAACCACACT+AGG 0.626241 1_3:+29470307 None:intergenic
GGGCGTAAAACGTCTGTAGG+TGG 0.627335 1_3:+29470552 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 1_3:+29470449 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 1_3:+29470247 None:intergenic
GGAAGTAGTGTTTCCAGTGG+CGG 0.647158 1_3:+29470108 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.647547 1_3:+29470397 None:intergenic
CCCGTAAGCTGAGAAGCGAA+AGG 0.647589 1_3:+29470198 None:intergenic
GACTTGTCTCAGTCCTAGTG+TGG 0.650592 1_3:-29470320 Msa0113530:CDS
TGGCTCAGGATGAACGCTGG+CGG 0.650788 1_3:+29470059 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 1_3:-29470427 Msa0113530:CDS
GTAAGCTGAGAAGCGAAAGG+AGG 0.682936 1_3:+29470201 None:intergenic
ACGGGAAGTAGTGTTTCCAG+TGG 0.695762 1_3:+29470105 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 1_3:+29470289 None:intergenic
TTGCATCCTCTGTCTTAGCG+CGG 0.711866 1_3:-29470511 Msa0113530:CDS
GGTGAGGTAATAGCTTACCA+AGG 0.724474 1_3:+29470263 None:intergenic
ACTGACGGAGCAATGCCGCG+TGG 0.732486 1_3:+29470394 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 1_3:+29470266 None:intergenic
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 1_3:+29470349 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AGAAACAATGACGGTATCTA+GGG + chr1_3:29470168-29470187 None:intergenic 35.0%
AAGAAACAATGACGGTATCT+AGG + chr1_3:29470169-29470188 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr1_3:29470094-29470113 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr1_3:29470177-29470196 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr1_3:29470196-29470215 Msa0113530:intron 40.0%
AGAGGAAAAACAGCTGGAAA+CGG + chr1_3:29470461-29470480 None:intergenic 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr1_3:29470539-29470558 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr1_3:29470540-29470559 None:intergenic 40.0%
ATTGGGCGTAAAACGTCTGT+AGG + chr1_3:29470077-29470096 None:intergenic 45.0%
! CGTTTTACGCCCAATCATTC+CGG - chr1_3:29470082-29470101 Msa0113530:CDS 45.0%
CAAGCGTTATCCGGAATGAT+TGG + chr1_3:29470095-29470114 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr1_3:29470173-29470192 Msa0113530:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr1_3:29470194-29470213 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr1_3:29470261-29470280 None:intergenic 45.0%
AGAGGATGATCAACCACACT+AGG + chr1_3:29470319-29470338 None:intergenic 45.0%
AGTGTGGTTGATCATCCTCT+CGG - chr1_3:29470319-29470338 Msa0113530:CDS 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr1_3:29470360-29470379 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr1_3:29470363-29470382 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr1_3:29470379-29470398 None:intergenic 45.0%
TCCTTTCGCTTCTCAGCTTA+CGG - chr1_3:29470424-29470443 Msa0113530:CDS 45.0%
!!! AGCTGTTTTTCCTCTCCCAA+GGG - chr1_3:29470466-29470485 Msa0113530:CDS 45.0%
CAGAGGATGCAAGCGTTATC+CGG + chr1_3:29470104-29470123 None:intergenic 50.0%
TTGCATCCTCTGTCTTAGCG+CGG - chr1_3:29470112-29470131 Msa0113530:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr1_3:29470262-29470281 None:intergenic 50.0%
AGACAAGTCCCAGACTCCTA+CGG + chr1_3:29470292-29470311 None:intergenic 50.0%
GACTTGTCTCAGTCCTAGTG+TGG - chr1_3:29470303-29470322 Msa0113530:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr1_3:29470384-29470403 None:intergenic 50.0%
GTAAGCTGAGAAGCGAAAGG+AGG + chr1_3:29470425-29470444 None:intergenic 50.0%
CCTTTCGCTTCTCAGCTTAC+GGG - chr1_3:29470425-29470444 Msa0113530:CDS 50.0%
CTTTCGCTTCTCAGCTTACG+GGG - chr1_3:29470426-29470445 Msa0113530:CDS 50.0%
CTTGGGAGAGGAAAAACAGC+TGG + chr1_3:29470467-29470486 None:intergenic 50.0%
!!! CAGCTGTTTTTCCTCTCCCA+AGG - chr1_3:29470465-29470484 Msa0113530:CDS 50.0%
TAAGAATCTGCCCTTGGGAG+AGG + chr1_3:29470479-29470498 None:intergenic 50.0%
ACGCGTAAGAATCTGCCCTT+GGG + chr1_3:29470484-29470503 None:intergenic 50.0%
AACGCGTAAGAATCTGCCCT+TGG + chr1_3:29470485-29470504 None:intergenic 50.0%
GGAAGTAGTGTTTCCAGTGG+CGG + chr1_3:29470518-29470537 None:intergenic 50.0%
ACGGGAAGTAGTGTTTCCAG+TGG + chr1_3:29470521-29470540 None:intergenic 50.0%
GGGCGTAAAACGTCTGTAGG+TGG + chr1_3:29470074-29470093 None:intergenic 55.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr1_3:29470214-29470233 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr1_3:29470215-29470234 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr1_3:29470214-29470233 Msa0113530:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr1_3:29470222-29470241 None:intergenic 55.0%
CGCAATGGGCGAAAGACTGA+CGG + chr1_3:29470247-29470266 None:intergenic 55.0%
CGTCAGTCTTTCGCCCATTG+CGG - chr1_3:29470245-29470264 Msa0113530:CDS 55.0%
GACAAGTCCCAGACTCCTAC+GGG + chr1_3:29470291-29470310 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr1_3:29470337-29470356 None:intergenic 55.0%
CCCGTAAGCTGAGAAGCGAA+AGG + chr1_3:29470428-29470447 None:intergenic 55.0%
!! TAGTGTTTCCAGTGGCGGAC+GGG + chr1_3:29470513-29470532 None:intergenic 55.0%
! GTAGTGTTTCCAGTGGCGGA+CGG + chr1_3:29470514-29470533 None:intergenic 55.0%
GGAGAGTTTGATCCTGGCTC+AGG + chr1_3:29470581-29470600 None:intergenic 55.0%
AAGTCCCAGACTCCTACGGG+AGG + chr1_3:29470288-29470307 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr1_3:29470346-29470365 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr1_3:29470343-29470362 Msa0113530:intron 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr1_3:29470408-29470427 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr1_3:29470409-29470428 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr1_3:29470412-29470431 None:intergenic 60.0%
TGGCTCAGGATGAACGCTGG+CGG + chr1_3:29470567-29470586 None:intergenic 60.0%
TCCTGGCTCAGGATGAACGC+TGG + chr1_3:29470570-29470589 None:intergenic 60.0%
CAGCAGCCGCGCTAAGACAG+AGG + chr1_3:29470121-29470140 None:intergenic 65.0%
CTCTGTCTTAGCGCGGCTGC+TGG - chr1_3:29470119-29470138 Msa0113530:CDS 65.0%
ACTGACGGAGCAATGCCGCG+TGG + chr1_3:29470232-29470251 None:intergenic 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr1_3:29470277-29470296 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr1_3:29470278-29470297 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr1_3:29470279-29470298 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr1_3:29470280-29470299 Msa0113530:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr1_3:29470281-29470300 Msa0113530:CDS 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr1_3:29470392-29470411 Msa0113530:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr1_3:29470393-29470412 Msa0113530:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr1_3:29470407-29470426 None:intergenic 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr1_3:29470502-29470521 Msa0113530:CDS 65.0%
GCCAGCGTTCATCCTGAGCC+AGG - chr1_3:29470566-29470585 Msa0113530:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr1_3:29470229-29470248 None:intergenic 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr1_3:29470273-29470292 Msa0113530:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr1_3:29470396-29470415 Msa0113530:CDS 75.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 29470044 29470601 29470044 ID=Msa0113530;Name=Msa0113530
chr1_3 mRNA 29470044 29470601 29470044 ID=Msa0113530-mRNA-1;Parent=Msa0113530;Name=Msa0113530-mRNA-1;_AED=0.15;_eAED=0.21;_QI=0|0|0|1|0|0|4|0|177
chr1_3 exon 29470464 29470601 29470464 ID=Msa0113530-mRNA-1:exon:9764;Parent=Msa0113530-mRNA-1
chr1_3 exon 29470355 29470450 29470355 ID=Msa0113530-mRNA-1:exon:9763;Parent=Msa0113530-mRNA-1
chr1_3 exon 29470198 29470350 29470198 ID=Msa0113530-mRNA-1:exon:9762;Parent=Msa0113530-mRNA-1
chr1_3 exon 29470044 29470187 29470044 ID=Msa0113530-mRNA-1:exon:9761;Parent=Msa0113530-mRNA-1
chr1_3 CDS 29470464 29470601 29470464 ID=Msa0113530-mRNA-1:cds;Parent=Msa0113530-mRNA-1
chr1_3 CDS 29470355 29470450 29470355 ID=Msa0113530-mRNA-1:cds;Parent=Msa0113530-mRNA-1
chr1_3 CDS 29470198 29470350 29470198 ID=Msa0113530-mRNA-1:cds;Parent=Msa0113530-mRNA-1
chr1_3 CDS 29470044 29470187 29470044 ID=Msa0113530-mRNA-1:cds;Parent=Msa0113530-mRNA-1
Gene Sequence

>Msa0113530

CTGGGATTTGACGGAAAACTTAAAAAGCCACCTACAGACGTTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTAGCGCGGCTGCTGGCACAGAGTTAGCTGATGCTTATTCCCTAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGTCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGACTTGTCTCAGTCCTAGTGTGGTTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTTCTCAGCTTACGGGCCGTTTCCAGCTGTTTTTCCTCTCCCAAGGGCAGATTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACTACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCCTGAGCCAGGATCAAACTCTCCA
Protein sequence

>Msa0113530

LGFDGKLKKPPTDVLRPIIPDNACILCLSAAAGTELADAYSLDTVIEKKFMTRRPFTSTRHCSVSLSPIAENSPLLPPESGTCLSPSVVDHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRFSAYGPFPAVFPLPRADSYALLTRPPLETLLPVRLACVKHAASVHPEPGSNSP