AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1461010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1461010 MtrunA17_Chr8g0379061 96.277 188 4 1 1 188 55 239 5.21e-133 372
Msa1461010 MtrunA17_Chr2g0283861 72.093 172 42 2 5 172 2 171 1.05e-80 238
Msa1461010 MtrunA17_Chr4g0041141 72.848 151 32 1 16 157 2 152 1.23e-80 237
Msa1461010 MtrunA17_Chr2g0325831 83.333 126 21 0 32 157 21 146 2.04e-80 236
Msa1461010 MtrunA17_Chr2g0315791 79.021 143 30 0 31 173 30 172 7.40e-80 235
Msa1461010 MtrunA17_Chr5g0431211 70.896 134 39 0 33 166 36 169 6.08e-72 217
Msa1461010 MtrunA17_Chr4g0051251 73.134 134 36 0 31 164 43 176 1.61e-71 216
Msa1461010 MtrunA17_Chr1g0167411 70.400 125 37 0 34 158 65 189 2.93e-64 197
Msa1461010 MtrunA17_Chr7g0274631 68.382 136 36 4 32 163 25 157 5.39e-63 192
Msa1461010 MtrunA17_Chr1g0187671 72.180 133 37 0 32 164 51 183 1.01e-60 187
Msa1461010 MtrunA17_Chr3g0105921 67.143 140 46 0 34 173 42 181 2.74e-60 187
Msa1461010 MtrunA17_Chr7g0261381 71.970 132 37 0 33 164 63 194 2.18e-58 182
Msa1461010 MtrunA17_Chr1g0183761 71.756 131 37 0 34 164 45 175 1.09e-57 180
Msa1461010 MtrunA17_Chr1g0190231 68.000 125 40 0 34 158 40 164 1.04e-52 166
Msa1461010 MtrunA17_Chr1g0211641 67.500 40 13 0 33 72 70 109 1.15e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1461010 AT2G42610.1 80.576 139 27 0 33 171 24 162 1.31e-79 235
Msa1461010 AT2G42610.2 80.576 139 27 0 33 171 24 162 1.31e-79 235
Msa1461010 AT4G18610.1 75.862 145 31 2 17 157 17 161 7.69e-73 218
Msa1461010 AT1G78815.1 76.190 126 30 0 32 157 38 163 8.83e-71 213
Msa1461010 AT1G07090.1 62.987 154 51 1 33 180 30 183 4.55e-70 211
Msa1461010 AT1G16910.1 71.756 131 37 0 32 162 21 151 1.25e-67 204
Msa1461010 AT5G58500.1 69.925 133 39 1 33 164 18 150 1.81e-66 202
Msa1461010 AT3G04510.1 67.647 136 44 0 34 169 33 168 6.69e-59 183
Msa1461010 AT3G23290.2 74.803 127 32 0 32 158 46 172 2.19e-58 182
Msa1461010 AT2G31160.1 70.229 131 39 0 34 164 54 184 2.98e-58 182
Msa1461010 AT5G28490.1 70.229 131 39 0 33 163 24 154 2.83e-57 179

Find 49 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCGTTACCTTGATCAATT+TGG 0.179894 tig0041209:-14262 Msa1461010:CDS
ACTCTTGAGATATTGATTAA+AGG 0.209241 tig0041209:+14339 None:intergenic
CTTGAGTAGTCCCCTTAATT+TGG 0.223949 tig0041209:+13972 None:intergenic
GAAGAAAAGTTACCAAATTA+AGG 0.233605 tig0041209:-13984 Msa1461010:CDS
TTTCAAGGTTGCATCTTCTT+TGG 0.250614 tig0041209:-14223 Msa1461010:CDS
ATGATCATGATGATTGGATT+TGG 0.342921 tig0041209:+14420 None:intergenic
TGAGATTCATACCTGCTTAG+TGG 0.351076 tig0041209:+14382 None:intergenic
CTTGTCCTCTCAAGCAAGCT+TGG 0.355615 tig0041209:-14174 Msa1461010:CDS
CCTTTGCCGGAGGAGCTATT+CGG 0.365308 tig0041209:-14078 Msa1461010:CDS
CTTTGCCGGAGGAGCTATTC+GGG 0.390335 tig0041209:-14077 Msa1461010:CDS
TTGTCCTCTCAAGCAAGCTT+GGG 0.395914 tig0041209:-14173 Msa1461010:CDS
TCGGAGACTAACCCCTTTGC+CGG 0.402692 tig0041209:-14091 Msa1461010:CDS
AAGACTAAGGTTCACTTTCA+AGG 0.409691 tig0041209:-14238 Msa1461010:CDS
CAGTGTGATAGTGGAACTAT+TGG 0.409844 tig0041209:+14310 None:intergenic
CTGATGATGATCATGATGAT+TGG 0.424129 tig0041209:+14414 None:intergenic
TGATCAATTTGGAAAGACTA+AGG 0.447537 tig0041209:-14251 Msa1461010:CDS
AAGAAAAGTTACCAAATTAA+GGG 0.448633 tig0041209:-13983 Msa1461010:CDS
CGAATAGCTCCTCCGGCAAA+GGG 0.448939 tig0041209:+14079 None:intergenic
TAGTCTTTCCAAATTGATCA+AGG 0.467755 tig0041209:+14254 None:intergenic
CTTCCCCAAGCTTGCTTGAG+AGG 0.469362 tig0041209:+14169 None:intergenic
CGAAGAGAACGGTGGATCAT+CGG 0.469733 tig0041209:-14110 Msa1461010:CDS
CCGAATAGCTCCTCCGGCAA+AGG 0.494461 tig0041209:+14078 None:intergenic
GTAAACCCGAATAGCTCCTC+CGG 0.521395 tig0041209:+14072 None:intergenic
GGTTTACCTTCGTGAGGTGA+AGG 0.526981 tig0041209:-14056 Msa1461010:CDS
GGTGAAGGATAGTCAACAAA+AGG 0.534311 tig0041209:-14041 Msa1461010:CDS
AGAGGACAAGCACAAGGTGC+AGG 0.534757 tig0041209:+14187 None:intergenic
TTGAAGTTACAGTGTGATAG+TGG 0.540734 tig0041209:+14301 None:intergenic
GCACAAGGTGCAGGTGGGGT+AGG 0.548293 tig0041209:+14196 None:intergenic
GGGACTACTCAAGCAGATCA+AGG 0.562036 tig0041209:-13962 Msa1461010:CDS
AGCAACAACAGCCACTAAGC+AGG 0.566051 tig0041209:-14393 Msa1461010:CDS
GGACAAGCACAAGGTGCAGG+TGG 0.580568 tig0041209:+14190 None:intergenic
ACAAGCACAAGGTGCAGGTG+GGG 0.589736 tig0041209:+14192 None:intergenic
TGATCCACCGTTCTCTTCGT+AGG 0.593342 tig0041209:+14114 None:intergenic
GACAAGCACAAGGTGCAGGT+GGG 0.594234 tig0041209:+14191 None:intergenic
AGAAAAGTTACCAAATTAAG+GGG 0.595981 tig0041209:-13982 Msa1461010:CDS
TGTCCTCTCAAGCAAGCTTG+GGG 0.598885 tig0041209:-14172 Msa1461010:CDS
GGAAGTCTTGATGCACTCAT+CGG 0.605369 tig0041209:-14151 Msa1461010:CDS
TATTCGGGTTTACCTTCGTG+AGG 0.609132 tig0041209:-14062 Msa1461010:CDS
TGGATTTGGAAGAAGATGCG+AGG 0.617333 tig0041209:+14434 None:intergenic
GATAGTCAACAAAAGGCAAG+AGG 0.633743 tig0041209:-14034 Msa1461010:CDS
ATAGTCAACAAAAGGCAAGA+GGG 0.646981 tig0041209:-14033 Msa1461010:CDS
TCTCTTCGTAGGCAGCTCGA+AGG 0.651841 tig0041209:+14125 None:intergenic
GAGACTAACCCCTTTGCCGG+AGG 0.652127 tig0041209:-14088 Msa1461010:CDS
CGAGCTGCCTACGAAGAGAA+CGG 0.662041 tig0041209:-14121 Msa1461010:CDS
AACGAAGAAAATCAAGAACA+TGG 0.665632 tig0041209:+14278 None:intergenic
TGCTTGAGAGGACAAGCACA+AGG 0.677587 tig0041209:+14181 None:intergenic
GAATAGCTCCTCCGGCAAAG+GGG 0.699942 tig0041209:+14080 None:intergenic
GACTATCCTTCACCTCACGA+AGG 0.701737 tig0041209:+14050 None:intergenic
GCTGCCTACGAAGAGAACGG+TGG 0.715708 tig0041209:-14118 Msa1461010:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTTTTTCTTCTTCTTATAT+GGG + tig0041209:14395-14414 None:intergenic 20.0%
!!! TTCTTTTTCTTCTTCTTATA+TGG + tig0041209:14396-14415 None:intergenic 20.0%
!! AAGAAAAGTTACCAAATTAA+GGG - tig0041209:14417-14436 Msa1461010:CDS 20.0%
!! ACTCTTGAGATATTGATTAA+AGG + tig0041209:14064-14083 None:intergenic 25.0%
! GAAGAAAAGTTACCAAATTA+AGG - tig0041209:14416-14435 Msa1461010:CDS 25.0%
! AGAAAAGTTACCAAATTAAG+GGG - tig0041209:14418-14437 Msa1461010:CDS 25.0%
ATGATCATGATGATTGGATT+TGG + tig0041209:13983-14002 None:intergenic 30.0%
AACGAAGAAAATCAAGAACA+TGG + tig0041209:14125-14144 None:intergenic 30.0%
TAGTCTTTCCAAATTGATCA+AGG + tig0041209:14149-14168 None:intergenic 30.0%
TGATCAATTTGGAAAGACTA+AGG - tig0041209:14149-14168 Msa1461010:CDS 30.0%
! GAGAGAAGAGTTTTCGATTT+GGG + tig0041209:13947-13966 None:intergenic 35.0%
! CTGATGATGATCATGATGAT+TGG + tig0041209:13989-14008 None:intergenic 35.0%
GCAGGTATGAATCTCAAAAA+CGG - tig0041209:14025-14044 Msa1461010:CDS 35.0%
AATCTCAAAAACGGAGAGAT+TGG - tig0041209:14034-14053 Msa1461010:CDS 35.0%
TTGAAGTTACAGTGTGATAG+TGG + tig0041209:14102-14121 None:intergenic 35.0%
CTTCGTTACCTTGATCAATT+TGG - tig0041209:14138-14157 Msa1461010:CDS 35.0%
AAGACTAAGGTTCACTTTCA+AGG - tig0041209:14162-14181 Msa1461010:CDS 35.0%
TTTCAAGGTTGCATCTTCTT+TGG - tig0041209:14177-14196 Msa1461010:CDS 35.0%
ATAGTCAACAAAAGGCAAGA+GGG - tig0041209:14367-14386 Msa1461010:CDS 35.0%
! GGAGAGAAGAGTTTTCGATT+TGG + tig0041209:13948-13967 None:intergenic 40.0%
TGAGATTCATACCTGCTTAG+TGG + tig0041209:14021-14040 None:intergenic 40.0%
!! CAGTGTGATAGTGGAACTAT+TGG + tig0041209:14093-14112 None:intergenic 40.0%
GGTGAAGGATAGTCAACAAA+AGG - tig0041209:14359-14378 Msa1461010:CDS 40.0%
GATAGTCAACAAAAGGCAAG+AGG - tig0041209:14366-14385 Msa1461010:CDS 40.0%
CTTGAGTAGTCCCCTTAATT+TGG + tig0041209:14431-14450 None:intergenic 40.0%
TGGATTTGGAAGAAGATGCG+AGG + tig0041209:13969-13988 None:intergenic 45.0%
TTGTCCTCTCAAGCAAGCTT+GGG - tig0041209:14227-14246 Msa1461010:CDS 45.0%
GGAAGTCTTGATGCACTCAT+CGG - tig0041209:14249-14268 Msa1461010:CDS 45.0%
! TATTCGGGTTTACCTTCGTG+AGG - tig0041209:14338-14357 Msa1461010:CDS 45.0%
AGCAACAACAGCCACTAAGC+AGG - tig0041209:14007-14026 Msa1461010:CDS 50.0%
TGCTTGAGAGGACAAGCACA+AGG + tig0041209:14222-14241 None:intergenic 50.0%
CTTGTCCTCTCAAGCAAGCT+TGG - tig0041209:14226-14245 Msa1461010:CDS 50.0%
TGTCCTCTCAAGCAAGCTTG+GGG - tig0041209:14228-14247 Msa1461010:CDS 50.0%
TGATCCACCGTTCTCTTCGT+AGG + tig0041209:14289-14308 None:intergenic 50.0%
CGAAGAGAACGGTGGATCAT+CGG - tig0041209:14290-14309 Msa1461010:CDS 50.0%
GTAAACCCGAATAGCTCCTC+CGG + tig0041209:14331-14350 None:intergenic 50.0%
GGTTTACCTTCGTGAGGTGA+AGG - tig0041209:14344-14363 Msa1461010:CDS 50.0%
GACTATCCTTCACCTCACGA+AGG + tig0041209:14353-14372 None:intergenic 50.0%
GGGACTACTCAAGCAGATCA+AGG - tig0041209:14438-14457 Msa1461010:CDS 50.0%
ACAAGCACAAGGTGCAGGTG+GGG + tig0041209:14211-14230 None:intergenic 55.0%
GACAAGCACAAGGTGCAGGT+GGG + tig0041209:14212-14231 None:intergenic 55.0%
AGAGGACAAGCACAAGGTGC+AGG + tig0041209:14216-14235 None:intergenic 55.0%
! CTTCCCCAAGCTTGCTTGAG+AGG + tig0041209:14234-14253 None:intergenic 55.0%
TCTCTTCGTAGGCAGCTCGA+AGG + tig0041209:14278-14297 None:intergenic 55.0%
CGAGCTGCCTACGAAGAGAA+CGG - tig0041209:14279-14298 Msa1461010:CDS 55.0%
TCGGAGACTAACCCCTTTGC+CGG - tig0041209:14309-14328 Msa1461010:CDS 55.0%
GAATAGCTCCTCCGGCAAAG+GGG + tig0041209:14323-14342 None:intergenic 55.0%
CGAATAGCTCCTCCGGCAAA+GGG + tig0041209:14324-14343 None:intergenic 55.0%
CCTTTGCCGGAGGAGCTATT+CGG - tig0041209:14322-14341 Msa1461010:CDS 55.0%
CTTTGCCGGAGGAGCTATTC+GGG - tig0041209:14323-14342 Msa1461010:CDS 55.0%
GGACAAGCACAAGGTGCAGG+TGG + tig0041209:14213-14232 None:intergenic 60.0%
GCTGCCTACGAAGAGAACGG+TGG - tig0041209:14282-14301 Msa1461010:CDS 60.0%
GAGACTAACCCCTTTGCCGG+AGG - tig0041209:14312-14331 Msa1461010:CDS 60.0%
CCGAATAGCTCCTCCGGCAA+AGG + tig0041209:14325-14344 None:intergenic 60.0%
GCACAAGGTGCAGGTGGGGT+AGG + tig0041209:14207-14226 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0041209 gene 13928 14494 13928 ID=Msa1461010;Name=Msa1461010
tig0041209 mRNA 13928 14494 13928 ID=Msa1461010-mRNA-1;Parent=Msa1461010;Name=Msa1461010-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|188
tig0041209 exon 13928 14494 13928 ID=Msa1461010-mRNA-1:exon:22980;Parent=Msa1461010-mRNA-1
tig0041209 CDS 13928 14494 13928 ID=Msa1461010-mRNA-1:cds;Parent=Msa1461010-mRNA-1
Gene Sequence

>Msa1461010

ATGTCTTCTTCTTCTTCCCAAATCGAAAACTCTTCTCTCCTCGCATCTTCTTCCAAATCCAATCATCATGATCATCATCAGCAACAACAGCCACTAAGCAGGTATGAATCTCAAAAACGGAGAGATTGGAACACCTTTAATCAATATCTCAAGAGTCAAAATCCAATAGTTCCACTATCACACTGTAACTTCAACCATGTTCTTGATTTTCTTCGTTACCTTGATCAATTTGGAAAGACTAAGGTTCACTTTCAAGGTTGCATCTTCTTTGGACAACCTACCCCACCTGCACCTTGTGCTTGTCCTCTCAAGCAAGCTTGGGGAAGTCTTGATGCACTCATCGGACGCCTTCGAGCTGCCTACGAAGAGAACGGTGGATCATCGGAGACTAACCCCTTTGCCGGAGGAGCTATTCGGGTTTACCTTCGTGAGGTGAAGGATAGTCAACAAAAGGCAAGAGGGATCCCATATAAGAAGAAGAAAAAGAAGAAGAAAAGTTACCAAATTAAGGGGACTACTCAAGCAGATCAAGGTGCTTGTGTCAAGCAACAAGATTCTTATAATTGA
Protein sequence

>Msa1461010

MSSSSSQIENSSLLASSSKSNHHDHHQQQQPLSRYESQKRRDWNTFNQYLKSQNPIVPLSHCNFNHVLDFLRYLDQFGKTKVHFQGCIFFGQPTPPAPCACPLKQAWGSLDALIGRLRAAYEENGGSSETNPFAGGAIRVYLREVKDSQQKARGIPYKKKKKKKKSYQIKGTTQADQGACVKQQDSYN*