AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1365880


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:+20185 Msa1365880:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0018442:-20072 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0018442:+19987 Msa1365880:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0018442:-20124 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0018442:+20329 Msa1365880:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0018442:+20297 Msa1365880:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0018442:+20024 Msa1365880:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0018442:+20330 Msa1365880:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0018442:-19997 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0018442:+20370 Msa1365880:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0018442:-20006 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0018442:+19940 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0018442:-20369 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0018442:-20286 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0018442:+20375 Msa1365880:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0018442:+20298 Msa1365880:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0018442:+20186 Msa1365880:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0018442:-19948 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0018442:-20381 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0018442:-20180 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0018442:-20363 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0018442:-20441 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0018442:+20134 Msa1365880:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0018442:-20181 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0018442:-20071 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0018442:-20387 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0018442:-20310 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0018442:-20415 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0018442:-19996 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0018442:-20435 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0018442:+20407 Msa1365880:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0018442:-20416 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0018442:-20386 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0018442:+20371 Msa1365880:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0018442:-20149 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0018442:-20248 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0018442:-20034 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0018442:-20383 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0018442:-20330 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0018442:-20222 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0018442:-20382 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0018442:-20117 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0018442:-20309 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0018442:-19947 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0018442:-20116 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0018442:+20301 Msa1365880:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0018442:+20331 Msa1365880:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0018442:+20248 Msa1365880:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0018442:+20150 Msa1365880:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0018442:-19976 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0018442:+20224 Msa1365880:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0018442:-20314 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0018442:-20442 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0018442:-20472 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0018442:-20221 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0018442:-20339 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0018442:-20058 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0018442:-20423 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0018442:-20311 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0018442:-20420 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0018442:-20079 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0018442:-20209 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0018442:-19979 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0018442:-20131 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0018442:-20281 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0018442:-20023 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0018442:-20469 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0018442:+20101 Msa1365880:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0018442:-20327 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0018442:+20208 Msa1365880:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0018442:-20070 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0018442:-20239 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0018442:-20134 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0018442:-20265 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0018442:-20262 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0018442:+20017 Msa1365880:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0018442:-20179 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - tig0018442:20074-20093 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - tig0018442:19999-20018 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - tig0018442:20073-20092 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - tig0018442:20075-20094 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - tig0018442:20082-20101 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + tig0018442:20101-20120 Msa1365880:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - tig0018442:20444-20463 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - tig0018442:20445-20464 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - tig0018442:20000-20019 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - tig0018442:20061-20080 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + tig0018442:20078-20097 Msa1365880:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - tig0018442:20099-20118 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - tig0018442:20166-20185 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - tig0018442:20265-20284 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - tig0018442:20268-20287 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - tig0018442:20284-20303 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - tig0018442:19982-20001 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + tig0018442:19987-20006 Msa1365880:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - tig0018442:20009-20028 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + tig0018442:20017-20036 Msa1365880:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - tig0018442:20167-20186 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - tig0018442:20224-20243 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + tig0018442:20224-20243 Msa1365880:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - tig0018442:20289-20308 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + tig0018442:20329-20348 Msa1365880:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - tig0018442:20342-20361 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - tig0018442:20366-20385 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - tig0018442:20119-20138 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - tig0018442:20120-20139 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + tig0018442:20119-20138 Msa1365880:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - tig0018442:20127-20146 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - tig0018442:20197-20216 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - tig0018442:20225-20244 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - tig0018442:20242-20261 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - tig0018442:20330-20349 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + tig0018442:20330-20349 Msa1365880:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + tig0018442:20331-20350 Msa1365880:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + tig0018442:20371-20390 Msa1365880:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - tig0018442:20384-20403 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - tig0018442:20385-20404 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - tig0018442:20389-20408 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - tig0018442:20390-20409 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - tig0018442:20423-20442 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - tig0018442:20426-20445 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - tig0018442:20438-20457 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - tig0018442:19979-19998 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - tig0018442:20037-20056 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - tig0018442:20152-20171 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + tig0018442:20150-20169 Msa1365880:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - tig0018442:20196-20215 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + tig0018442:20208-20227 Msa1365880:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - tig0018442:20212-20231 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - tig0018442:20251-20270 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + tig0018442:20248-20267 Msa1365880:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - tig0018442:20313-20332 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - tig0018442:20314-20333 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - tig0018442:20317-20336 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - tig0018442:20333-20352 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - tig0018442:20372-20391 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + tig0018442:20370-20389 Msa1365880:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - tig0018442:20386-20405 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - tig0018442:20418-20437 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - tig0018442:20419-20438 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - tig0018442:20026-20045 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + tig0018442:20024-20043 Msa1365880:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - tig0018442:20182-20201 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - tig0018442:20183-20202 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - tig0018442:20184-20203 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + tig0018442:20185-20204 Msa1365880:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + tig0018442:20186-20205 Msa1365880:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - tig0018442:20193-20212 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + tig0018442:20297-20316 Msa1365880:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + tig0018442:20298-20317 Msa1365880:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - tig0018442:20312-20331 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + tig0018442:20375-20394 Msa1365880:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + tig0018442:20407-20426 Msa1365880:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - tig0018442:20134-20153 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - tig0018442:20137-20156 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + tig0018442:20134-20153 Msa1365880:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + tig0018442:20178-20197 Msa1365880:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + tig0018442:20301-20320 Msa1365880:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0018442 gene 19949 20484 19949 ID=Msa1365880;Name=Msa1365880
tig0018442 mRNA 19949 20484 19949 ID=Msa1365880-mRNA-1;Parent=Msa1365880;Name=Msa1365880-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0018442 exon 19949 20086 19949 ID=Msa1365880-mRNA-1:exon:14900;Parent=Msa1365880-mRNA-1
tig0018442 exon 20100 20195 20100 ID=Msa1365880-mRNA-1:exon:14901;Parent=Msa1365880-mRNA-1
tig0018442 exon 20200 20484 20200 ID=Msa1365880-mRNA-1:exon:14902;Parent=Msa1365880-mRNA-1
tig0018442 CDS 19949 20086 19949 ID=Msa1365880-mRNA-1:cds;Parent=Msa1365880-mRNA-1
tig0018442 CDS 20100 20195 20100 ID=Msa1365880-mRNA-1:cds;Parent=Msa1365880-mRNA-1
tig0018442 CDS 20200 20484 20200 ID=Msa1365880-mRNA-1:cds;Parent=Msa1365880-mRNA-1
Gene Sequence

>Msa1365880

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1365880

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS