AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354410


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 tig0014543:+267155 Msa1354410:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0014543:-267042 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0014543:+266957 Msa1354410:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0014543:-267094 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0014543:+267299 Msa1354410:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0014543:+267267 Msa1354410:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0014543:+266994 Msa1354410:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0014543:+267300 Msa1354410:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0014543:-266967 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0014543:+267340 Msa1354410:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0014543:-266976 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0014543:+266910 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0014543:-267339 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0014543:-267256 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0014543:+267345 Msa1354410:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0014543:+267268 Msa1354410:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0014543:+267156 Msa1354410:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0014543:-266918 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0014543:-267351 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0014543:-267150 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0014543:-267333 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0014543:-267411 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0014543:+267104 Msa1354410:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0014543:-267151 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0014543:-267041 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0014543:-267357 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0014543:-267280 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0014543:-267385 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0014543:-266966 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0014543:-267405 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0014543:+267377 Msa1354410:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0014543:-267386 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0014543:-267356 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0014543:+267341 Msa1354410:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0014543:-267119 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0014543:-267218 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0014543:-267004 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0014543:-267353 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0014543:-267300 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0014543:-267192 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0014543:-267352 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0014543:-267087 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0014543:-267279 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0014543:-266917 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0014543:-267086 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0014543:+267271 Msa1354410:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0014543:+267301 Msa1354410:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0014543:+267218 Msa1354410:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0014543:+267120 Msa1354410:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0014543:-266946 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0014543:+267194 Msa1354410:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0014543:-267284 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0014543:-267412 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0014543:-267442 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0014543:-267191 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0014543:-267309 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0014543:-267028 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0014543:-267393 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0014543:-267281 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0014543:-267390 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0014543:-267049 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0014543:-267179 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0014543:-266949 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0014543:-267101 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0014543:-267251 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0014543:-266993 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0014543:-267439 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0014543:+267071 Msa1354410:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0014543:-267297 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0014543:+267178 Msa1354410:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0014543:-267040 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0014543:-267209 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0014543:-267104 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0014543:-267235 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0014543:-267232 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0014543:+266987 Msa1354410:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0014543:-267149 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - tig0014543:267044-267063 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - tig0014543:266969-266988 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - tig0014543:267043-267062 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - tig0014543:267045-267064 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - tig0014543:267052-267071 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + tig0014543:267071-267090 Msa1354410:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - tig0014543:267414-267433 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - tig0014543:267415-267434 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - tig0014543:266970-266989 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - tig0014543:267031-267050 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + tig0014543:267048-267067 Msa1354410:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - tig0014543:267069-267088 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - tig0014543:267136-267155 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - tig0014543:267235-267254 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - tig0014543:267238-267257 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - tig0014543:267254-267273 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - tig0014543:266952-266971 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + tig0014543:266957-266976 Msa1354410:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - tig0014543:266979-266998 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + tig0014543:266987-267006 Msa1354410:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - tig0014543:267137-267156 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - tig0014543:267194-267213 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + tig0014543:267194-267213 Msa1354410:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - tig0014543:267259-267278 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + tig0014543:267299-267318 Msa1354410:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - tig0014543:267312-267331 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - tig0014543:267336-267355 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - tig0014543:267089-267108 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - tig0014543:267090-267109 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + tig0014543:267089-267108 Msa1354410:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - tig0014543:267097-267116 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - tig0014543:267167-267186 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - tig0014543:267195-267214 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - tig0014543:267212-267231 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - tig0014543:267300-267319 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + tig0014543:267300-267319 Msa1354410:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + tig0014543:267301-267320 Msa1354410:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + tig0014543:267341-267360 Msa1354410:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - tig0014543:267354-267373 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - tig0014543:267355-267374 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - tig0014543:267359-267378 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - tig0014543:267360-267379 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - tig0014543:267393-267412 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - tig0014543:267396-267415 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - tig0014543:267408-267427 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - tig0014543:266949-266968 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - tig0014543:267007-267026 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - tig0014543:267122-267141 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + tig0014543:267120-267139 Msa1354410:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - tig0014543:267166-267185 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + tig0014543:267178-267197 Msa1354410:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - tig0014543:267182-267201 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - tig0014543:267221-267240 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + tig0014543:267218-267237 Msa1354410:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - tig0014543:267283-267302 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - tig0014543:267284-267303 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - tig0014543:267287-267306 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - tig0014543:267303-267322 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - tig0014543:267342-267361 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + tig0014543:267340-267359 Msa1354410:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - tig0014543:267356-267375 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - tig0014543:267388-267407 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - tig0014543:267389-267408 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - tig0014543:266996-267015 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + tig0014543:266994-267013 Msa1354410:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - tig0014543:267152-267171 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - tig0014543:267153-267172 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - tig0014543:267154-267173 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + tig0014543:267155-267174 Msa1354410:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + tig0014543:267156-267175 Msa1354410:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - tig0014543:267163-267182 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + tig0014543:267267-267286 Msa1354410:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + tig0014543:267268-267287 Msa1354410:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - tig0014543:267282-267301 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + tig0014543:267345-267364 Msa1354410:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + tig0014543:267377-267396 Msa1354410:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - tig0014543:267104-267123 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - tig0014543:267107-267126 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + tig0014543:267104-267123 Msa1354410:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + tig0014543:267148-267167 Msa1354410:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + tig0014543:267271-267290 Msa1354410:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 266919 267454 266919 ID=Msa1354410;Name=Msa1354410
tig0014543 mRNA 266919 267454 266919 ID=Msa1354410-mRNA-1;Parent=Msa1354410;Name=Msa1354410-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0014543 exon 266919 267056 266919 ID=Msa1354410-mRNA-1:exon:9121;Parent=Msa1354410-mRNA-1
tig0014543 exon 267070 267165 267070 ID=Msa1354410-mRNA-1:exon:9122;Parent=Msa1354410-mRNA-1
tig0014543 exon 267170 267454 267170 ID=Msa1354410-mRNA-1:exon:9123;Parent=Msa1354410-mRNA-1
tig0014543 CDS 266919 267056 266919 ID=Msa1354410-mRNA-1:cds;Parent=Msa1354410-mRNA-1
tig0014543 CDS 267070 267165 267070 ID=Msa1354410-mRNA-1:cds;Parent=Msa1354410-mRNA-1
tig0014543 CDS 267170 267454 267170 ID=Msa1354410-mRNA-1:cds;Parent=Msa1354410-mRNA-1
Gene Sequence

>Msa1354410

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1354410

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS