AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0405450


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 77 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 3_2:-40189317 Msa0405450:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 3_2:+40189430 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 3_2:-40189515 Msa0405450:CDS
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 3_2:-40189173 Msa0405450:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 3_2:-40189205 Msa0405450:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 3_2:-40189172 Msa0405450:CDS
CAATGCCGTGTGGAGGTAAA+AGG 0.348698 3_2:+40189378 None:intergenic
CAAGCGTTATCCGGAATGAT+TGG 0.365557 3_2:+40189505 None:intergenic
CTCTGTCTTACCGTGGCTGC+TGG 0.390939 3_2:-40189478 Msa0405450:CDS
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 3_2:-40189132 Msa0405450:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 3_2:+40189496 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 3_2:-40189562 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 3_2:+40189133 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 3_2:+40189216 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 3_2:-40189127 Msa0405450:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 3_2:-40189204 Msa0405450:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 3_2:-40189316 Msa0405450:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 3_2:+40189554 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 3_2:+40189121 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 3_2:+40189322 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 3_2:+40189139 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 3_2:+40189061 None:intergenic
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 3_2:+40189321 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 3_2:+40189431 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 3_2:+40189115 None:intergenic
CCACACGGCATTGCTCCGTC+AGG 0.499380 3_2:-40189368 Msa0405450:CDS
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 3_2:+40189192 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 3_2:+40189087 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 3_2:+40189506 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 3_2:+40189067 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 3_2:-40189095 Msa0405450:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 3_2:+40189086 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 3_2:+40189116 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 3_2:-40189131 Msa0405450:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 3_2:+40189353 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 3_2:+40189254 None:intergenic
TAACTCTGTGCCAGCAGCCA+CGG 0.546303 3_2:+40189468 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 3_2:+40189119 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 3_2:+40189172 None:intergenic
GTGTGGAGGTAAAAGGCCTA+CGG 0.556074 3_2:+40189385 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 3_2:+40189280 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 3_2:+40189120 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 3_2:+40189193 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 3_2:+40189555 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 3_2:-40189201 Msa0405450:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 3_2:-40189171 Msa0405450:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 3_2:-40189254 Msa0405450:CDS
TGTGGAGGTAAAAGGCCTAC+GGG 0.584049 3_2:+40189386 None:intergenic
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 3_2:-40189352 Msa0405450:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 3_2:+40189526 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 3_2:-40189278 Msa0405450:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 3_2:+40189188 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 3_2:+40189060 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 3_2:+40189030 None:intergenic
GACGGAGCAATGCCGTGTGG+AGG 0.608359 3_2:+40189371 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 3_2:+40189281 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 3_2:+40189163 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 3_2:+40189444 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 3_2:+40189079 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 3_2:+40189191 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 3_2:+40189082 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 3_2:+40189423 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 3_2:+40189293 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 3_2:+40189523 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 3_2:+40189221 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 3_2:+40189033 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 3_2:-40189401 Msa0405450:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 3_2:+40189175 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 3_2:-40189294 Msa0405450:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 3_2:+40189432 None:intergenic
CAGCAGCCACGGTAAGACAG+AGG 0.684983 3_2:+40189479 None:intergenic
TTGCATCCTCTGTCTTACCG+TGG 0.687884 3_2:-40189485 Msa0405450:CDS
CCTGACGGAGCAATGCCGTG+TGG 0.695031 3_2:+40189368 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 3_2:+40189263 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 3_2:+40189237 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 3_2:+40189240 None:intergenic
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 3_2:+40189323 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr3_2:40189165-40189184 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr3_2:40189090-40189109 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr3_2:40189164-40189183 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr3_2:40189166-40189185 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr3_2:40189173-40189192 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr3_2:40189192-40189211 Msa0405450:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr3_2:40189535-40189554 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr3_2:40189536-40189555 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr3_2:40189091-40189110 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr3_2:40189152-40189171 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr3_2:40189169-40189188 Msa0405450:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr3_2:40189190-40189209 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr3_2:40189257-40189276 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr3_2:40189356-40189375 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr3_2:40189359-40189378 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr3_2:40189375-40189394 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr3_2:40189073-40189092 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr3_2:40189078-40189097 Msa0405450:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr3_2:40189100-40189119 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+TGG - chr3_2:40189108-40189127 Msa0405450:CDS 50.0%
TGTGGAGGTAAAAGGCCTAC+GGG + chr3_2:40189210-40189229 None:intergenic 50.0%
GTGTGGAGGTAAAAGGCCTA+CGG + chr3_2:40189211-40189230 None:intergenic 50.0%
! GTAGGCCTTTTACCTCCACA+CGG - chr3_2:40189210-40189229 Msa0405450:CDS 50.0%
CAATGCCGTGTGGAGGTAAA+AGG + chr3_2:40189218-40189237 None:intergenic 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr3_2:40189258-40189277 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr3_2:40189315-40189334 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr3_2:40189315-40189334 Msa0405450:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr3_2:40189380-40189399 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr3_2:40189420-40189439 Msa0405450:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr3_2:40189433-40189452 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr3_2:40189457-40189476 None:intergenic 50.0%
TAACTCTGTGCCAGCAGCCA+CGG + chr3_2:40189128-40189147 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr3_2:40189288-40189307 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr3_2:40189316-40189335 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr3_2:40189333-40189352 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr3_2:40189421-40189440 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr3_2:40189421-40189440 Msa0405450:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr3_2:40189422-40189441 Msa0405450:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr3_2:40189462-40189481 Msa0405450:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr3_2:40189475-40189494 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr3_2:40189476-40189495 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr3_2:40189480-40189499 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr3_2:40189481-40189500 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr3_2:40189514-40189533 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr3_2:40189517-40189536 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr3_2:40189529-40189548 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr3_2:40189070-40189089 None:intergenic 60.0%
CAGCAGCCACGGTAAGACAG+AGG + chr3_2:40189117-40189136 None:intergenic 60.0%
CTCTGTCTTACCGTGGCTGC+TGG - chr3_2:40189115-40189134 Msa0405450:CDS 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr3_2:40189243-40189262 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr3_2:40189241-40189260 Msa0405450:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr3_2:40189287-40189306 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr3_2:40189299-40189318 Msa0405450:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr3_2:40189303-40189322 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr3_2:40189342-40189361 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr3_2:40189339-40189358 Msa0405450:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr3_2:40189404-40189423 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr3_2:40189405-40189424 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr3_2:40189408-40189427 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr3_2:40189424-40189443 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr3_2:40189463-40189482 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr3_2:40189461-40189480 Msa0405450:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr3_2:40189477-40189496 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr3_2:40189509-40189528 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr3_2:40189510-40189529 None:intergenic 60.0%
GACGGAGCAATGCCGTGTGG+AGG + chr3_2:40189225-40189244 None:intergenic 65.0%
CCTGACGGAGCAATGCCGTG+TGG + chr3_2:40189228-40189247 None:intergenic 65.0%
CCACACGGCATTGCTCCGTC+AGG - chr3_2:40189225-40189244 Msa0405450:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr3_2:40189273-40189292 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr3_2:40189274-40189293 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr3_2:40189275-40189294 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr3_2:40189276-40189295 Msa0405450:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr3_2:40189277-40189296 Msa0405450:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr3_2:40189284-40189303 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr3_2:40189388-40189407 Msa0405450:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr3_2:40189389-40189408 Msa0405450:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr3_2:40189403-40189422 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr3_2:40189466-40189485 Msa0405450:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr3_2:40189498-40189517 Msa0405450:CDS 65.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr3_2:40189269-40189288 Msa0405450:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr3_2:40189392-40189411 Msa0405450:CDS 75.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 40189040 40189575 40189040 ID=Msa0405450;Name=Msa0405450
chr3_2 mRNA 40189040 40189575 40189040 ID=Msa0405450-mRNA-1;Parent=Msa0405450;Name=Msa0405450-mRNA-1;_AED=0.20;_eAED=0.23;_QI=0|0|0|1|0.5|0|3|0|173
chr3_2 exon 40189438 40189575 40189438 ID=Msa0405450-mRNA-1:exon:7805;Parent=Msa0405450-mRNA-1
chr3_2 exon 40189329 40189424 40189329 ID=Msa0405450-mRNA-1:exon:7804;Parent=Msa0405450-mRNA-1
chr3_2 exon 40189040 40189324 40189040 ID=Msa0405450-mRNA-1:exon:7803;Parent=Msa0405450-mRNA-1
chr3_2 CDS 40189438 40189575 40189438 ID=Msa0405450-mRNA-1:cds;Parent=Msa0405450-mRNA-1
chr3_2 CDS 40189329 40189424 40189329 ID=Msa0405450-mRNA-1:cds;Parent=Msa0405450-mRNA-1
chr3_2 CDS 40189040 40189324 40189040 ID=Msa0405450-mRNA-1:cds;Parent=Msa0405450-mRNA-1
Gene Sequence

>Msa0405450

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGTGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACACGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0405450

LGFDGELKKPPTDALRPIIPDNACILCLTVAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS