AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1366070


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 tig0018442:+237209 Msa1366070:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0018442:-237096 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0018442:+237011 Msa1366070:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0018442:-237148 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0018442:+237353 Msa1366070:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0018442:+237321 Msa1366070:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0018442:+237048 Msa1366070:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0018442:+237354 Msa1366070:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0018442:-237021 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0018442:+237394 Msa1366070:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0018442:-237030 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0018442:+236964 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0018442:-237393 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0018442:-237310 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0018442:+237399 Msa1366070:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0018442:+237322 Msa1366070:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0018442:+237210 Msa1366070:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0018442:-236972 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0018442:-237405 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0018442:-237204 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0018442:-237387 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0018442:-237465 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0018442:+237158 Msa1366070:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0018442:-237205 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0018442:-237095 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0018442:-237411 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0018442:-237334 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0018442:-237439 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0018442:-237020 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0018442:-237459 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0018442:+237431 Msa1366070:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0018442:-237440 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0018442:-237410 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0018442:+237395 Msa1366070:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0018442:-237173 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0018442:-237272 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0018442:-237058 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0018442:-237407 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0018442:-237354 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0018442:-237246 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0018442:-237406 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0018442:-237141 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0018442:-237333 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0018442:-236971 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0018442:-237140 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0018442:+237325 Msa1366070:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0018442:+237355 Msa1366070:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0018442:+237272 Msa1366070:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0018442:+237174 Msa1366070:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0018442:-237000 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0018442:+237248 Msa1366070:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0018442:-237338 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0018442:-237466 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0018442:-237496 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0018442:-237245 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0018442:-237363 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0018442:-237082 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0018442:-237447 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0018442:-237335 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0018442:-237444 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0018442:-237103 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0018442:-237233 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0018442:-237003 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0018442:-237155 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0018442:-237305 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0018442:-237047 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0018442:-237493 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0018442:+237125 Msa1366070:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0018442:-237351 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0018442:+237232 Msa1366070:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0018442:-237094 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0018442:-237263 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0018442:-237158 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0018442:-237289 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0018442:-237286 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0018442:+237041 Msa1366070:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0018442:-237203 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - tig0018442:237098-237117 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - tig0018442:237023-237042 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - tig0018442:237097-237116 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - tig0018442:237099-237118 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - tig0018442:237106-237125 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + tig0018442:237125-237144 Msa1366070:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - tig0018442:237468-237487 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - tig0018442:237469-237488 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - tig0018442:237024-237043 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - tig0018442:237085-237104 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + tig0018442:237102-237121 Msa1366070:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - tig0018442:237123-237142 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - tig0018442:237190-237209 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - tig0018442:237289-237308 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - tig0018442:237292-237311 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - tig0018442:237308-237327 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - tig0018442:237006-237025 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + tig0018442:237011-237030 Msa1366070:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - tig0018442:237033-237052 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + tig0018442:237041-237060 Msa1366070:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - tig0018442:237191-237210 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - tig0018442:237248-237267 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + tig0018442:237248-237267 Msa1366070:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - tig0018442:237313-237332 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + tig0018442:237353-237372 Msa1366070:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - tig0018442:237366-237385 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - tig0018442:237390-237409 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - tig0018442:237143-237162 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - tig0018442:237144-237163 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + tig0018442:237143-237162 Msa1366070:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - tig0018442:237151-237170 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - tig0018442:237221-237240 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - tig0018442:237249-237268 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - tig0018442:237266-237285 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - tig0018442:237354-237373 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + tig0018442:237354-237373 Msa1366070:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + tig0018442:237355-237374 Msa1366070:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + tig0018442:237395-237414 Msa1366070:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - tig0018442:237408-237427 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - tig0018442:237409-237428 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - tig0018442:237413-237432 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - tig0018442:237414-237433 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - tig0018442:237447-237466 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - tig0018442:237450-237469 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - tig0018442:237462-237481 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - tig0018442:237003-237022 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - tig0018442:237061-237080 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - tig0018442:237176-237195 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + tig0018442:237174-237193 Msa1366070:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - tig0018442:237220-237239 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + tig0018442:237232-237251 Msa1366070:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - tig0018442:237236-237255 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - tig0018442:237275-237294 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + tig0018442:237272-237291 Msa1366070:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - tig0018442:237337-237356 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - tig0018442:237338-237357 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - tig0018442:237341-237360 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - tig0018442:237357-237376 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - tig0018442:237396-237415 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + tig0018442:237394-237413 Msa1366070:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - tig0018442:237410-237429 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - tig0018442:237442-237461 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - tig0018442:237443-237462 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - tig0018442:237050-237069 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + tig0018442:237048-237067 Msa1366070:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - tig0018442:237206-237225 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - tig0018442:237207-237226 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - tig0018442:237208-237227 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + tig0018442:237209-237228 Msa1366070:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + tig0018442:237210-237229 Msa1366070:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - tig0018442:237217-237236 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + tig0018442:237321-237340 Msa1366070:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + tig0018442:237322-237341 Msa1366070:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - tig0018442:237336-237355 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + tig0018442:237399-237418 Msa1366070:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + tig0018442:237431-237450 Msa1366070:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - tig0018442:237158-237177 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - tig0018442:237161-237180 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + tig0018442:237158-237177 Msa1366070:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + tig0018442:237202-237221 Msa1366070:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + tig0018442:237325-237344 Msa1366070:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0018442 gene 236973 237508 236973 ID=Msa1366070;Name=Msa1366070
tig0018442 mRNA 236973 237508 236973 ID=Msa1366070-mRNA-1;Parent=Msa1366070;Name=Msa1366070-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0018442 exon 236973 237110 236973 ID=Msa1366070-mRNA-1:exon:14951;Parent=Msa1366070-mRNA-1
tig0018442 exon 237124 237219 237124 ID=Msa1366070-mRNA-1:exon:14952;Parent=Msa1366070-mRNA-1
tig0018442 exon 237224 237508 237224 ID=Msa1366070-mRNA-1:exon:14953;Parent=Msa1366070-mRNA-1
tig0018442 CDS 236973 237110 236973 ID=Msa1366070-mRNA-1:cds;Parent=Msa1366070-mRNA-1
tig0018442 CDS 237124 237219 237124 ID=Msa1366070-mRNA-1:cds;Parent=Msa1366070-mRNA-1
tig0018442 CDS 237224 237508 237224 ID=Msa1366070-mRNA-1:cds;Parent=Msa1366070-mRNA-1
Gene Sequence

>Msa1366070

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1366070

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS