AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1087060


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 7_2:-87694254 Msa1087060:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 7_2:+87694367 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 7_2:-87694452 Msa1087060:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 7_2:+87694315 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 7_2:-87694110 Msa1087060:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 7_2:-87694142 Msa1087060:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 7_2:-87694415 Msa1087060:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 7_2:-87694109 Msa1087060:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 7_2:+87694442 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 7_2:-87694069 Msa1087060:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 7_2:+87694433 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 7_2:-87694499 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 7_2:+87694070 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 7_2:+87694153 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 7_2:-87694064 Msa1087060:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 7_2:-87694141 Msa1087060:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 7_2:-87694253 Msa1087060:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 7_2:+87694491 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 7_2:+87694058 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 7_2:+87694259 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 7_2:+87694076 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 7_2:+87693998 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 7_2:-87694305 Msa1087060:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 7_2:+87694258 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 7_2:+87694368 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 7_2:+87694052 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 7_2:+87694129 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 7_2:+87694024 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 7_2:+87694443 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 7_2:+87694004 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 7_2:-87694032 Msa1087060:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 7_2:+87694023 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 7_2:+87694053 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 7_2:-87694068 Msa1087060:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 7_2:+87694290 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 7_2:+87694191 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 7_2:+87694405 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 7_2:+87694056 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 7_2:+87694109 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 7_2:+87694217 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 7_2:+87694057 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 7_2:+87694322 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 7_2:+87694130 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 7_2:+87694492 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 7_2:+87694323 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 7_2:-87694138 Msa1087060:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 7_2:-87694108 Msa1087060:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 7_2:-87694191 Msa1087060:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 7_2:-87694289 Msa1087060:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 7_2:+87694463 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 7_2:-87694215 Msa1087060:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 7_2:+87694125 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 7_2:+87693997 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 7_2:+87693967 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 7_2:+87694218 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 7_2:+87694100 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 7_2:+87694381 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 7_2:+87694016 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 7_2:+87694128 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 7_2:+87694019 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 7_2:+87694360 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 7_2:+87694230 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 7_2:+87694460 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 7_2:+87694308 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 7_2:+87694158 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 7_2:+87694416 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 7_2:+87693970 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 7_2:-87694338 Msa1087060:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 7_2:+87694112 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 7_2:-87694231 Msa1087060:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 7_2:+87694369 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 7_2:+87694200 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 7_2:+87694305 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 7_2:+87694174 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 7_2:+87694177 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 7_2:-87694422 Msa1087060:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 7_2:+87694260 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr7_2:87694102-87694121 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr7_2:87694027-87694046 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr7_2:87694101-87694120 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr7_2:87694103-87694122 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr7_2:87694110-87694129 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr7_2:87694129-87694148 Msa1087060:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr7_2:87694472-87694491 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr7_2:87694473-87694492 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr7_2:87694028-87694047 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr7_2:87694089-87694108 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr7_2:87694106-87694125 Msa1087060:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr7_2:87694127-87694146 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr7_2:87694194-87694213 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr7_2:87694293-87694312 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr7_2:87694296-87694315 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr7_2:87694312-87694331 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr7_2:87694010-87694029 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr7_2:87694015-87694034 Msa1087060:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr7_2:87694037-87694056 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr7_2:87694045-87694064 Msa1087060:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr7_2:87694195-87694214 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr7_2:87694252-87694271 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr7_2:87694252-87694271 Msa1087060:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr7_2:87694317-87694336 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr7_2:87694357-87694376 Msa1087060:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr7_2:87694370-87694389 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr7_2:87694394-87694413 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr7_2:87694147-87694166 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr7_2:87694148-87694167 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr7_2:87694147-87694166 Msa1087060:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr7_2:87694155-87694174 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr7_2:87694225-87694244 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr7_2:87694253-87694272 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr7_2:87694270-87694289 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr7_2:87694358-87694377 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr7_2:87694358-87694377 Msa1087060:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr7_2:87694359-87694378 Msa1087060:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr7_2:87694399-87694418 Msa1087060:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr7_2:87694412-87694431 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr7_2:87694413-87694432 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr7_2:87694417-87694436 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr7_2:87694418-87694437 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr7_2:87694451-87694470 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr7_2:87694454-87694473 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr7_2:87694466-87694485 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr7_2:87694007-87694026 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr7_2:87694065-87694084 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr7_2:87694180-87694199 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr7_2:87694178-87694197 Msa1087060:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr7_2:87694224-87694243 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr7_2:87694236-87694255 Msa1087060:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr7_2:87694240-87694259 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr7_2:87694279-87694298 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr7_2:87694276-87694295 Msa1087060:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr7_2:87694341-87694360 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr7_2:87694342-87694361 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr7_2:87694345-87694364 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr7_2:87694361-87694380 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr7_2:87694400-87694419 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr7_2:87694398-87694417 Msa1087060:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr7_2:87694414-87694433 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr7_2:87694446-87694465 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr7_2:87694447-87694466 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr7_2:87694054-87694073 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr7_2:87694052-87694071 Msa1087060:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr7_2:87694210-87694229 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr7_2:87694211-87694230 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr7_2:87694212-87694231 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr7_2:87694213-87694232 Msa1087060:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr7_2:87694214-87694233 Msa1087060:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr7_2:87694221-87694240 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr7_2:87694325-87694344 Msa1087060:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr7_2:87694326-87694345 Msa1087060:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr7_2:87694340-87694359 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr7_2:87694403-87694422 Msa1087060:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr7_2:87694435-87694454 Msa1087060:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr7_2:87694162-87694181 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr7_2:87694165-87694184 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr7_2:87694162-87694181 Msa1087060:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr7_2:87694206-87694225 Msa1087060:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr7_2:87694329-87694348 Msa1087060:CDS 75.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87693977 87694512 87693977 ID=Msa1087060;Name=Msa1087060
chr7_2 mRNA 87693977 87694512 87693977 ID=Msa1087060-mRNA-1;Parent=Msa1087060;Name=Msa1087060-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr7_2 exon 87694375 87694512 87694375 ID=Msa1087060-mRNA-1:exon:24002;Parent=Msa1087060-mRNA-1
chr7_2 exon 87694266 87694361 87694266 ID=Msa1087060-mRNA-1:exon:24001;Parent=Msa1087060-mRNA-1
chr7_2 exon 87693977 87694261 87693977 ID=Msa1087060-mRNA-1:exon:24000;Parent=Msa1087060-mRNA-1
chr7_2 CDS 87694375 87694512 87694375 ID=Msa1087060-mRNA-1:cds;Parent=Msa1087060-mRNA-1
chr7_2 CDS 87694266 87694361 87694266 ID=Msa1087060-mRNA-1:cds;Parent=Msa1087060-mRNA-1
chr7_2 CDS 87693977 87694261 87693977 ID=Msa1087060-mRNA-1:cds;Parent=Msa1087060-mRNA-1
Gene Sequence

>Msa1087060

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1087060

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS