AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG031999


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG031999 MtrunA17_Chr6g0463901 98.230 339 6 0 1 339 1 339 0.0 695
MsaG031999 MtrunA17_Chr2g0278581 84.179 335 53 0 1 335 1 335 0.0 596
MsaG031999 MtrunA17_Chr7g0241071 50.000 342 153 2 11 335 71 411 4.73e-114 337
MsaG031999 MtrunA17_Chr4g0049821 40.836 311 161 6 32 332 87 384 4.63e-73 231
MsaG031999 MtrunA17_Chr3g0113101 28.996 269 163 8 67 327 116 364 1.46e-19 88.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG031999 AT1G43670.1 85.251 339 50 0 1 339 1 339 0.0 613
MsaG031999 AT3G54050.2 50.292 342 150 3 11 335 79 417 1.50e-114 338
MsaG031999 AT3G54050.1 50.292 342 150 3 11 335 79 417 1.50e-114 338
MsaG031999 AT5G64380.1 40.836 311 165 7 32 332 89 390 3.52e-74 234
MsaG031999 AT3G55800.1 30.037 273 155 9 67 327 123 371 2.81e-20 91.3

Find 83 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATAGCTACCAAGAAATA+TGG 0.228525 6:+41967908 None:intergenic
ACCACTGGAAGTGGTGTTAA+TGG 0.234751 6:-41971013 MsaT031999.1:CDS
GAATAAATCTTGCCTTTCTT+TGG 0.239412 6:+41970227 None:intergenic
TTGCTGAATAACATTGTTCT+TGG 0.264261 6:-41974119 MsaT031999.1:CDS
CCTAACTCACCCTGACATTA+AGG 0.279021 6:-41970957 MsaT031999.1:intron
GAAAGATCTCCCATATTTCT+TGG 0.282491 6:-41967918 MsaT031999.1:CDS
GCAAAGCTCATTGGACTTGC+AGG 0.289654 6:-41972756 MsaT031999.1:CDS
CTTCCCAATGTCCTTCTTGA+TGG 0.290934 6:-41968906 MsaT031999.1:CDS
CCTTAATGTCAGGGTGAGTT+AGG 0.309718 6:+41970957 None:intergenic
GTAAAATCTCCACGTGATTC+AGG 0.312460 6:+41974146 None:intergenic
ATGCATTACCCTTTCCTTGC+CGG 0.313636 6:+41968859 None:intergenic
GCAAAGTCTCTAAGATATAT+TGG 0.314481 6:-41970034 MsaT031999.1:CDS
AATAAATCTTGCCTTTCTTT+GGG 0.339648 6:+41970228 None:intergenic
ATTCAACACAAAACGTGTTA+TGG 0.348871 6:+41974184 None:intergenic
GTTCATCGTACATTGCTATA+TGG 0.377460 6:-41969095 MsaT031999.1:CDS
TTCACCCTTGACCCTTCTCT+TGG 0.378219 6:-41970989 MsaT031999.1:CDS
AAAGAAAGGCAAGATTTATT+CGG 0.384048 6:-41970225 MsaT031999.1:CDS
CAGAATATTACCTTAATGTC+AGG 0.386263 6:+41970947 None:intergenic
ATGAAGGGAACGCCAAGAAC+TGG 0.409253 6:-41970199 MsaT031999.1:CDS
TGCAGGAGAGACCAATGTTC+AGG 0.427688 6:-41972739 MsaT031999.1:intron
AGCTTTGCAGAACACCTCAT+TGG 0.427984 6:+41972128 None:intergenic
CATCATCTATGATTGGTTCA+TGG 0.429120 6:+41971224 None:intergenic
TGCAGAACATCATCTATGAT+TGG 0.429779 6:+41971217 None:intergenic
ATGTTGGAAGAGCCGTCTAA+TGG 0.435353 6:+41971600 None:intergenic
AGTAGGACCATCCCAGTTCT+TGG 0.436119 6:+41970187 None:intergenic
AAGATTTATTCGGTGAATGA+AGG 0.437587 6:-41970215 MsaT031999.1:CDS
TTTGTCAGCAGGGTACAAAA+AGG 0.440471 6:+41969067 None:intergenic
ATCGATTGTGGTGTTTCCAT+TGG 0.440634 6:-41971579 MsaT031999.1:CDS
GCTGGTCTTGCAAAGCTCAT+TGG 0.453630 6:-41972765 MsaT031999.1:CDS
AATGTCCTTCTTGATGGAAC+AGG 0.459315 6:-41968900 MsaT031999.1:CDS
GGCTTTCACCGGCAAGGAAA+GGG 0.474657 6:-41968867 MsaT031999.1:intron
ATATATCTTAGAGACTTTGC+TGG 0.483827 6:+41970037 None:intergenic
TCATAGCTACCAAGAAATAT+GGG 0.491600 6:+41967909 None:intergenic
GCTGCCAACATGTTCTTCCC+TGG 0.493174 6:+41971193 None:intergenic
AGATGAGGATGCAATATTTG+TGG 0.495684 6:-41971981 MsaT031999.1:CDS
AACAATGTTATTCAGCAAGA+TGG 0.502314 6:+41974124 None:intergenic
GTTCCATCAAGAAGGACATT+GGG 0.503823 6:+41968903 None:intergenic
GATGGAACAGGCAGGAGGAC+AGG 0.504743 6:-41968888 MsaT031999.1:CDS
AGGCTTTCACCGGCAAGGAA+AGG 0.509795 6:-41968868 MsaT031999.1:CDS
GCAGCTGGTTATTGCATGTA+CGG 0.516581 6:-41971175 MsaT031999.1:CDS
AGGATAAACTCGCCAAGAGA+AGG 0.516852 6:+41970977 None:intergenic
AACAACTTTCCACGCTGCTT+AGG 0.518664 6:+41971956 None:intergenic
TAGATGATGTTCTGCAACCA+GGG 0.531413 6:-41971210 MsaT031999.1:CDS
GGGAAGAACATGTTGGCAGC+TGG 0.533032 6:-41971190 MsaT031999.1:CDS
TCTTTGCAGATCCCAAAGAA+AGG 0.537179 6:-41970239 MsaT031999.1:intron
TGTTCCATCAAGAAGGACAT+TGG 0.542151 6:+41968902 None:intergenic
GGGAACACTTACCTGAACAT+TGG 0.543127 6:+41972728 None:intergenic
ATAGATGATGTTCTGCAACC+AGG 0.548458 6:-41971211 MsaT031999.1:CDS
GCAGGAGGACAGGCTTTCAC+CGG 0.548518 6:-41968878 MsaT031999.1:CDS
AGATTTATTCGGTGAATGAA+GGG 0.550932 6:-41970214 MsaT031999.1:CDS
TTGCAGTTTGTGATAACCAC+TGG 0.553944 6:-41971028 MsaT031999.1:intron
TCCTGCCTGTTCCATCAAGA+AGG 0.554789 6:+41968895 None:intergenic
GGAAACACCACAATCGATGT+TGG 0.558592 6:+41971584 None:intergenic
TGAAGGGAACGCCAAGAACT+GGG 0.558723 6:-41970198 MsaT031999.1:CDS
TAGGGATCATACAGTTCCAA+TGG 0.562520 6:+41971563 None:intergenic
CAAAGCTCTTTATGCTGCAG+AGG 0.565129 6:-41967871 MsaT031999.1:CDS
TTTGCTGGTGAACCATCTGT+TGG 0.566108 6:+41970052 None:intergenic
CTTGGTTTCTGAAGAAGATG+AGG 0.575814 6:-41971996 MsaT031999.1:CDS
AGAATATTACCTTAATGTCA+GGG 0.576590 6:+41970948 None:intergenic
ATTCATACGTACGCGGCAGT+AGG 0.578888 6:+41970170 None:intergenic
TGCAAAGCTTTGATAAGCAG+TGG 0.580054 6:-41972114 MsaT031999.1:CDS
GGCTCTTCCAACATCGATTG+TGG 0.580554 6:-41971591 MsaT031999.1:CDS
ACTCGCCAAGAGAAGGGTCA+AGG 0.584729 6:+41970984 None:intergenic
ACCATTAACACCACTTCCAG+TGG 0.586134 6:+41971012 None:intergenic
GGATAAACTCGCCAAGAGAA+GGG 0.588099 6:+41970978 None:intergenic
AGTCTCTAAGATATATTGGA+AGG 0.589845 6:-41970030 MsaT031999.1:intron
TCCTTCTTGATGGAACAGGC+AGG 0.593282 6:-41968896 MsaT031999.1:CDS
CATGTACGGAAGCTCTTGCA+CGG 0.593772 6:-41971161 MsaT031999.1:intron
AAATGCAAGTATCCAACAGA+TGG 0.594501 6:-41970064 MsaT031999.1:CDS
GCTTGATGTTCTTTCCAATG+AGG 0.597378 6:-41972142 MsaT031999.1:CDS
CTCGCCAAGAGAAGGGTCAA+GGG 0.597914 6:+41970985 None:intergenic
TTTGTGATAACCACTGGAAG+TGG 0.598951 6:-41971022 MsaT031999.1:CDS
TGTTTGTTCTGCTGTTAACA+AGG 0.601443 6:-41974087 MsaT031999.1:intron
AGAGTCCAAATGGAAAACTT+CGG 0.610193 6:-41969043 MsaT031999.1:intron
AGGACAGGCTTTCACCGGCA+AGG 0.624102 6:-41968873 MsaT031999.1:CDS
GGGAACGCCAAGAACTGGGA+TGG 0.631401 6:-41970194 MsaT031999.1:CDS
TACGATGTGCATCTGCGCTG+TGG 0.637166 6:+41974219 None:intergenic
CATCGTACATTGCTATATGG+AGG 0.654004 6:-41969092 MsaT031999.1:CDS
GCAACCAGGGAAGAACATGT+TGG 0.656103 6:-41971197 MsaT031999.1:CDS
TGGTAGCTATGATGATATCG+AGG 0.676941 6:-41967898 MsaT031999.1:CDS
TTCTTGATGGAACAGGCAGG+AGG 0.688021 6:-41968893 MsaT031999.1:CDS
TCTAAGCATCCTGAATCACG+TGG 0.704682 6:-41974155 MsaT031999.1:CDS
TTTGTGGATCCTAAGCAGCG+TGG 0.736390 6:-41971965 MsaT031999.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 41967863 41974246 41967863 ID=MsaG031999
Chr6 mRNA 41967863 41974246 41967863 ID=MsaT031999.1;Parent=MsaG031999
Chr6 exon 41967863 41967970 41967863 ID=MsaT031999.1.exon12;Parent=MsaT031999.1
Chr6 CDS 41967863 41967970 41967863 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41968868 41968943 41968868 ID=MsaT031999.1.exon11;Parent=MsaT031999.1
Chr6 CDS 41968868 41968943 41968868 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41969044 41969130 41969044 ID=MsaT031999.1.exon10;Parent=MsaT031999.1
Chr6 CDS 41969044 41969130 41969044 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41970031 41970096 41970031 ID=MsaT031999.1.exon9;Parent=MsaT031999.1
Chr6 CDS 41970031 41970096 41970031 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41970182 41970252 41970182 ID=MsaT031999.1.exon8;Parent=MsaT031999.1
Chr6 CDS 41970182 41970252 41970182 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41970958 41971044 41970958 ID=MsaT031999.1.exon7;Parent=MsaT031999.1
Chr6 CDS 41970958 41971044 41970958 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41971162 41971275 41971162 ID=MsaT031999.1.exon6;Parent=MsaT031999.1
Chr6 CDS 41971162 41971275 41971162 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41971575 41971641 41971575 ID=MsaT031999.1.exon5;Parent=MsaT031999.1
Chr6 CDS 41971575 41971641 41971575 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41971962 41972023 41971962 ID=MsaT031999.1.exon4;Parent=MsaT031999.1
Chr6 CDS 41971962 41972023 41971962 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41972107 41972181 41972107 ID=MsaT031999.1.exon3;Parent=MsaT031999.1
Chr6 CDS 41972107 41972181 41972107 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41972740 41972787 41972740 ID=MsaT031999.1.exon2;Parent=MsaT031999.1
Chr6 CDS 41972740 41972787 41972740 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Chr6 exon 41974088 41974246 41974088 ID=MsaT031999.1.exon1;Parent=MsaT031999.1
Chr6 CDS 41974088 41974246 41974088 ID=cds.MsaT031999.1;Parent=MsaT031999.1
Gene Sequence

>MsaT031999.1

ATGGACCACAGCGCAGATGCACATCGTACAGACTTGATGACCATAACACGTTTTGTGTTGAATGAACAGTCTAAGCATCCTGAATCACGTGGAGATTTTACCATCTTGCTGAATAACATTGTTCTTGGTTGCAAATTTGTTTGTTCTGCTGTTAACAAGGCTGGTCTTGCAAAGCTCATTGGACTTGCAGGAGAGACCAATGTTCAGGGTGAAGAGCAGAAGAAGCTTGATGTTCTTTCCAATGAGGTGTTCTGCAAAGCTTTGATAAGCAGTGGCAGAACATGCATCTTGGTTTCTGAAGAAGATGAGGATGCAATATTTGTGGATCCTAAGCAGCGTGGAAAGTACTGTGTTGTTTTTGATCCATTAGACGGCTCTTCCAACATCGATTGTGGTGTTTCCATTGGAACTATTTTTGGGATTTATATGATGAAAGATAACCATGAACCAATCATAGATGATGTTCTGCAACCAGGGAAGAACATGTTGGCAGCTGGTTATTGCATGTACGGAAGCTCTTGCACGTTTGTGATAACCACTGGAAGTGGTGTTAATGGTTTCACCCTTGACCCTTCTCTTGGCGAGTTTATCCTAACTCACCCTGACATTAAGATCCCAAAGAAAGGCAAGATTTATTCGGTGAATGAAGGGAACGCCAAGAACTGGGATGGTCCTACTGCCGCTTATGTGGAGAAATGCAAGTATCCAACAGATGGTTCACCAGCAAAGTCTCTAAGATATATTGGAAGCATGGTAGCTGATGTTCATCGTACATTGCTATATGGAGGTACCTTTTTGTACCCTGCTGACAAAAAGAGTCCAAATGGAAAACTTCGTGTATTGTATGAAGTCTTCCCAATGTCCTTCTTGATGGAACAGGCAGGAGGACAGGCTTTCACCGGCAAGGAAAGGGCACTTGATTTAGTTCCAACAAAATTGCATGAAAGATCTCCCATATTTCTTGGTAGCTATGATGATATCGAGGAAATCAAAGCTCTTTATGCTGCAGAGGCTAAATAA

Protein sequence

>MsaT031999.1

MDHSADAHRTDLMTITRFVLNEQSKHPESRGDFTILLNNIVLGCKFVCSAVNKAGLAKLIGLAGETNVQGEEQKKLDVLSNEVFCKALISSGRTCILVSEEDEDAIFVDPKQRGKYCVVFDPLDGSSNIDCGVSIGTIFGIYMMKDNHEPIIDDVLQPGKNMLAAGYCMYGSSCTFVITTGSGVNGFTLDPSLGEFILTHPDIKIPKKGKIYSVNEGNAKNWDGPTAAYVEKCKYPTDGSPAKSLRYIGSMVADVHRTLLYGGTFLYPADKKSPNGKLRVLYEVFPMSFLMEQAGGQAFTGKERALDLVPTKLHERSPIFLGSYDDIEEIKALYAAEAK*