AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001933

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001933 MtrunA17_Chr1g0169431 98.770 244 3 0 1 244 1 244 0.0 498
MsaG001933 MtrunA17_Chr5g0395391 71.489 235 52 3 1 235 12 231 9.78e-105 306
MsaG001933 MtrunA17_Chr5g0395391 76.147 109 26 0 136 244 234 342 1.01e-56 184
MsaG001933 MtrunA17_Chr8g0340401 47.340 188 84 7 63 241 114 295 3.01e-39 139
MsaG001933 MtrunA17_Chr8g0372291 72.000 75 21 0 170 244 216 290 4.03e-36 129
MsaG001933 MtrunA17_Chr2g0326771 46.584 161 54 4 99 236 129 280 1.67e-35 128
MsaG001933 MtrunA17_Chr1g0146231 43.810 210 71 7 63 241 110 303 4.66e-35 127
MsaG001933 MtrunA17_Chr3g0140331 44.554 202 69 8 63 241 141 322 6.76e-35 127
MsaG001933 MtrunA17_Chr3g0145121 36.260 262 122 9 6 241 42 284 8.94e-35 126
MsaG001933 MtrunA17_Chr4g0035891 50.000 140 44 5 124 239 141 278 2.17e-33 122
MsaG001933 MtrunA17_Chr5g0404981 71.233 73 21 0 172 244 300 372 2.53e-33 124
MsaG001933 MtrunA17_Chr6g0461591 76.471 68 16 0 171 238 191 258 5.42e-33 120
MsaG001933 MtrunA17_Chr7g0253101 74.648 71 18 0 166 236 182 252 6.59e-33 120
MsaG001933 MtrunA17_Chr1g0199671 70.130 77 21 1 160 236 232 306 2.18e-32 120
MsaG001933 MtrunA17_Chr4g0028961 74.627 67 17 0 172 238 232 298 3.01e-32 120
MsaG001933 MtrunA17_Chr1g0213161 71.642 67 19 0 170 236 150 216 1.36e-31 116
MsaG001933 MtrunA17_Chr7g0232671 55.224 67 28 1 172 238 187 251 3.82e-19 83.6
MsaG001933 MtrunA17_Chr7g0232701 47.126 87 44 2 149 233 48 134 4.18e-18 78.2
MsaG001933 MtrunA17_Chr7g0232681 46.739 92 45 3 149 238 107 196 1.90e-17 77.8
MsaG001933 MtrunA17_Chr7g0271861 54.762 42 19 0 166 207 16 57 9.49e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001933 AT3G24050.1 80.000 75 15 0 170 244 192 266 2.47e-40 140
MsaG001933 AT4G32890.1 39.636 275 98 11 7 241 20 266 6.46e-38 135
MsaG001933 AT4G36240.1 38.340 253 104 6 6 239 12 231 6.98e-36 127
MsaG001933 AT4G34680.1 46.479 142 63 3 111 242 112 250 4.91e-35 126
MsaG001933 AT4G34680.2 46.479 142 63 3 111 242 112 250 4.91e-35 126
MsaG001933 AT5G66320.2 79.412 68 14 0 172 239 249 316 8.80e-35 127
MsaG001933 AT5G66320.1 79.412 68 14 0 172 239 249 316 8.80e-35 127
MsaG001933 AT5G25830.1 77.143 70 16 0 172 241 219 288 1.23e-33 124
MsaG001933 AT3G51080.1 72.603 73 20 0 172 244 221 293 2.74e-33 122
MsaG001933 AT3G60530.1 75.362 69 17 0 171 239 157 225 2.88e-33 120
MsaG001933 AT1G08010.2 72.464 69 19 0 170 238 218 286 2.82e-32 120
MsaG001933 AT1G08010.1 72.464 69 19 0 170 238 218 286 2.82e-32 120
MsaG001933 AT1G08010.3 72.464 69 19 0 170 238 218 286 2.82e-32 120
MsaG001933 AT2G45050.1 75.000 68 17 0 172 239 179 246 3.84e-32 118
MsaG001933 AT1G08000.2 64.634 82 29 0 157 238 203 284 7.00e-32 119
MsaG001933 AT1G08000.1 64.634 82 29 0 157 238 203 284 7.00e-32 119
MsaG001933 AT3G54810.1 75.000 68 17 0 172 239 229 296 6.57e-31 117
MsaG001933 AT3G54810.2 75.000 68 17 0 172 239 229 296 6.57e-31 117
MsaG001933 AT3G45170.1 60.294 68 27 0 172 239 115 182 2.38e-27 104
MsaG001933 AT2G28340.1 66.667 63 21 0 174 236 193 255 9.81e-26 102

Find 86 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTTTCTCTTTGGAAGTTT+TGG 0.158917 1:+28844193 None:intergenic
CTTGTGCTGTTCTCGAGCTT+TGG 0.240759 1:+28844374 None:intergenic
TTGTGCTGTTCTCGAGCTTT+GGG 0.269770 1:+28844375 None:intergenic
GGTTTGTTTCACTTTCTCTT+TGG 0.274207 1:+28844184 None:intergenic
AGTGAAGGAAAGGCTTTCTT+AGG 0.280723 1:+28845075 None:intergenic
GTCCAACAAAGATGCATTTC+CGG 0.285678 1:-28844462 MsaT001933.1:CDS
GACATTTCCTCCCAATGGTT+GGG 0.293078 1:+28844162 None:intergenic
CTATTTGCAGGACGGTATTC+AGG 0.302785 1:+28844035 None:intergenic
CGAAAAGTTGGGCTATTTGC+AGG 0.311001 1:+28844023 None:intergenic
CATGCATTACAAAGTGTCTT+TGG 0.315428 1:+28844089 None:intergenic
CAAAGTGTCTTTGGACCATT+TGG 0.337970 1:+28844098 None:intergenic
GAAGGTGGATCACTGCATTC+TGG 0.356189 1:+28845048 None:intergenic
GTTGTTTCCACGGGAATTGT+AGG 0.366200 1:+28844222 None:intergenic
TGGTTCTGTGGACGACCTCT+TGG 0.388206 1:-28845139 MsaT001933.1:CDS
GATGAGGAAGCAGAAGGGAA+TGG 0.399465 1:-28843961 MsaT001933.1:CDS
TTTGTAATGCATGTGGGGTT+AGG 0.415099 1:-28844079 MsaT001933.1:CDS
ACTTACAGAAAGTGAATTGA+TGG 0.418526 1:+28844999 None:intergenic
CCACGGGAATTGTAGGTTTG+AGG 0.425374 1:+28844229 None:intergenic
AAGCAGAAGGGAATGGGAAC+GGG 0.428545 1:-28843954 MsaT001933.1:CDS
TGTGATTGTAGCCACTTAAG+AGG 0.429240 1:+28844315 None:intergenic
AGCCGGAAATGCATCTTTGT+TGG 0.438765 1:+28844460 None:intergenic
TGCATGTCACTGCGAAAAGT+TGG 0.440834 1:+28844011 None:intergenic
ACATTTCCTCCCAATGGTTG+GGG 0.449081 1:+28844163 None:intergenic
ATTTGATGCTTCAAAAGATC+CGG 0.450692 1:+28844404 None:intergenic
TGAGTTGTCCTGTATTCAAC+CGG 0.452850 1:-28844423 MsaT001933.1:CDS
CAAAAGATCCGGTTGAATAC+AGG 0.453486 1:+28844415 None:intergenic
TTCGCTCAATCCATTGGCCC+TGG 0.469600 1:-28845028 MsaT001933.1:CDS
GACTTGCTCCGAGCACGGAC+AGG 0.471642 1:+28844284 None:intergenic
CCAGGAGGAGGTTGCAGAAG+AGG 0.477241 1:-28844498 MsaT001933.1:intron
GTGGAGATGAGGAAGCAGAA+GGG 0.478182 1:-28843966 MsaT001933.1:CDS
TTGCAGAAGAGGAGCTTGAA+TGG 0.482772 1:-28844487 MsaT001933.1:CDS
ATGAGGAAGCAGAAGGGAAT+GGG 0.486460 1:-28843960 MsaT001933.1:CDS
GTGAAACAAACCCCAACCAT+TGG 0.493226 1:-28844173 MsaT001933.1:CDS
TTGGTACTCGGTTGTTTCCA+CGG 0.494137 1:+28844212 None:intergenic
AACAGCATTACCCTCTTAAG+TGG 0.500575 1:-28844326 MsaT001933.1:CDS
GCATGTCACTGCGAAAAGTT+GGG 0.502991 1:+28844012 None:intergenic
TGGTACTCGGTTGTTTCCAC+GGG 0.505676 1:+28844213 None:intergenic
CAATGGCGTGCAGGTCCAAA+TGG 0.508669 1:-28844113 MsaT001933.1:CDS
TGAAGTTCCCTGTCCGTGCT+CGG 0.508770 1:-28844292 MsaT001933.1:CDS
TTGGATTTCTCATCTGACAT+AGG 0.508816 1:-28845120 MsaT001933.1:CDS
AGTGGAGATGAGGAAGCAGA+AGG 0.514467 1:-28843967 MsaT001933.1:CDS
TTCTGGTTTGAGTGAAGGAA+AGG 0.515866 1:+28845065 None:intergenic
TGACATTTCCTCCCAATGGT+TGG 0.516568 1:+28844161 None:intergenic
TGTGGGGTTAGGTATAAGTC+TGG 0.520333 1:-28844068 MsaT001933.1:CDS
TCCACCTTCGCTCAATCCAT+TGG 0.521499 1:-28845034 MsaT001933.1:CDS
GATGGAGGCCCTTGGTTCTG+TGG 0.522422 1:-28845151 MsaT001933.1:CDS
TGAAACAAACCCCAACCATT+GGG 0.524385 1:-28844172 MsaT001933.1:CDS
GTGAATTGATGGGATCATCC+AGG 0.528433 1:+28845010 None:intergenic
ATGGGATCATCCAGGGCCAA+TGG 0.530010 1:+28845018 None:intergenic
CTGCATTCTGGTTTGAGTGA+AGG 0.532294 1:+28845060 None:intergenic
TCATCTCCACTACTTTCCTG+TGG 0.533667 1:+28843979 None:intergenic
TCTCGTAGCAAGCCTCGCCT+TGG 0.534627 1:-28844263 MsaT001933.1:CDS
GATACTCCACAATGGCGTGC+AGG 0.539263 1:-28844122 MsaT001933.1:CDS
TCAACAAACGTTTCAACAGC+CGG 0.539345 1:+28844443 None:intergenic
TTGAGGCATCAGCAAGGCCA+AGG 0.541565 1:+28844246 None:intergenic
GAAGCAGAAGGGAATGGGAA+CGG 0.544276 1:-28843955 MsaT001933.1:CDS
GCCAATGGATTGAGCGAAGG+TGG 0.546210 1:+28845033 None:intergenic
ACTTAAGAGGGTAATGCTGT+TGG 0.550014 1:+28844328 None:intergenic
CATCTCCACTACTTTCCTGT+GGG 0.557649 1:+28843980 None:intergenic
TTTGGACCTGCACGCCATTG+TGG 0.572595 1:+28844116 None:intergenic
ATGATGACATTTCCTCCCAA+TGG 0.580868 1:+28844157 None:intergenic
ACAGGAAAGTAGTGGAGATG+AGG 0.582547 1:-28843977 MsaT001933.1:CDS
TGTGCTGTTCTCGAGCTTTG+GGG 0.589584 1:+28844376 None:intergenic
TACGAGACTTGCTCCGAGCA+CGG 0.591265 1:+28844279 None:intergenic
ACTTGCTCCGAGCACGGACA+GGG 0.594538 1:+28844285 None:intergenic
TGAATTGATGGGATCATCCA+GGG 0.600445 1:+28845011 None:intergenic
GCATCAGCAAGGCCAAGGCG+AGG 0.601336 1:+28844251 None:intergenic
GACACTTTGTAATGCATGTG+GGG 0.601729 1:-28844084 MsaT001933.1:CDS
AAGACACTTTGTAATGCATG+TGG 0.602236 1:-28844086 MsaT001933.1:CDS
TAATTCCCACAGGAAAGTAG+TGG 0.604924 1:-28843985 MsaT001933.1:CDS
GAGGTCGTCCACAGAACCAA+GGG 0.608143 1:+28845143 None:intergenic
AGACACTTTGTAATGCATGT+GGG 0.608576 1:-28844085 MsaT001933.1:CDS
CTTACAGAAAGTGAATTGAT+GGG 0.611737 1:+28845000 None:intergenic
GTGATTGTAGCCACTTAAGA+GGG 0.622729 1:+28844316 None:intergenic
ACATGCATTCTAATTCCCAC+AGG 0.630282 1:-28843995 MsaT001933.1:CDS
AACAAACCCCAACCATTGGG+AGG 0.635541 1:-28844169 MsaT001933.1:CDS
AGGGCCAATGGATTGAGCGA+AGG 0.639769 1:+28845030 None:intergenic
AGAGGTCGTCCACAGAACCA+AGG 0.642044 1:+28845142 None:intergenic
GGGAGGAAATGTCATCATTG+TGG 0.646984 1:-28844152 MsaT001933.1:CDS
CCTCAAACCTACAATTCCCG+TGG 0.649034 1:-28844229 MsaT001933.1:CDS
GACGGTATTCAGGTACAAGT+CGG 0.649278 1:+28844045 None:intergenic
AAGTTGGGCTATTTGCAGGA+CGG 0.658089 1:+28844027 None:intergenic
TTTCTCATCTGACATAGGTG+AGG 0.665571 1:-28845115 MsaT001933.1:CDS
GTAGGTTTGAGGCATCAGCA+AGG 0.716777 1:+28844240 None:intergenic
TGTCAGATGAGAAATCCAAG+AGG 0.747403 1:+28845124 None:intergenic
GAGTTGATGATACTCCACAA+TGG 0.801331 1:-28844130 MsaT001933.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 28843950 28845172 28843950 ID=MsaG001933
Chr1 mRNA 28843950 28845172 28843950 ID=MsaT001933.1;Parent=MsaG001933
Chr1 exon 28843950 28844516 28843950 ID=MsaT001933.1.exon2;Parent=MsaT001933.1
Chr1 CDS 28843950 28844516 28843950 ID=cds.MsaT001933.1;Parent=MsaT001933.1
Chr1 exon 28845005 28845172 28845005 ID=MsaT001933.1.exon1;Parent=MsaT001933.1
Chr1 CDS 28845005 28845172 28845005 ID=cds.MsaT001933.1;Parent=MsaT001933.1
Gene Sequence

>MsaT001933.1

ATGGAGGCCCTTGGTTCTGTGGACGACCTCTTGGATTTCTCATCTGACATAGGTGAGGATGATGATGATGACAAACCTAAGAAAGCCTTTCCTTCACTCAAACCAGAATGCAGTGATCCACCTTCGCTCAATCCATTGGCCCTGGATGATCCCATCAATTCACTTTCTGAGGAGGTTGCAGAAGAGGAGCTTGAATGGCTGTCCAACAAAGATGCATTTCCGGCTGTTGAAACGTTTGTTGAGTTGTCCTGTATTCAACCGGATCTTTTGAAGCATCAAATGACATCCCCAAAGCTCGAGAACAGCACAAGCAGCAGCAACAGCAATAACAGTTCCAACAGCATTACCCTCTTAAGTGGCTACAATCACATGAAGTTCCCTGTCCGTGCTCGGAGCAAGTCTCGTAGCAAGCCTCGCCTTGGCCTTGCTGATGCCTCAAACCTACAATTCCCGTGGAAACAACCGAGTACCAAAACTTCCAAAGAGAAAGTGAAACAAACCCCAACCATTGGGAGGAAATGTCATCATTGTGGAGTTGATGATACTCCACAATGGCGTGCAGGTCCAAATGGTCCAAAGACACTTTGTAATGCATGTGGGGTTAGGTATAAGTCTGGCCGACTTGTACCTGAATACCGTCCTGCAAATAGCCCAACTTTTCGCAGTGACATGCATTCTAATTCCCACAGGAAAGTAGTGGAGATGAGGAAGCAGAAGGGAATGGGAACGGGTTGA
Protein sequence

>MsaT001933.1

MEALGSVDDLLDFSSDIGEDDDDDKPKKAFPSLKPECSDPPSLNPLALDDPINSLSEEVAEEELEWLSNKDAFPAVETFVELSCIQPDLLKHQMTSPKLENSTSSSNSNNSSNSITLLSGYNHMKFPVRARSKSRSKPRLGLADASNLQFPWKQPSTKTSKEKVKQTPTIGRKCHHCGVDDTPQWRAGPNGPKTLCNACGVRYKSGRLVPEYRPANSPTFRSDMHSNSHRKVVEMRKQKGMGTG*