AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0534050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0534050 MtrunA17_Chr4g0007651 88.636 220 18 2 1 213 1 220 7.15e-129 362
Msa0534050 MtrunA17_Chr5g0405871 60.638 188 38 3 26 213 4 155 4.18e-66 200
Msa0534050 MtrunA17_Chr5g0405891 60.106 188 39 3 26 213 4 155 1.11e-65 199
Msa0534050 MtrunA17_Chr4g0014211 56.383 188 47 2 26 213 11 163 3.29e-65 198
Msa0534050 MtrunA17_Chr3g0139751 53.723 188 53 2 26 213 5 158 1.79e-64 196
Msa0534050 MtrunA17_Chr7g0221641 57.979 188 43 3 26 213 5 156 1.92e-62 191
Msa0534050 MtrunA17_Chr7g0259271 59.574 188 40 3 26 213 5 156 2.49e-62 191
Msa0534050 MtrunA17_Chr7g0259261 58.511 188 42 3 26 213 5 156 2.94e-62 191
Msa0534050 MtrunA17_Chr4g0014231 56.085 189 46 4 26 213 23 175 3.57e-62 191
Msa0534050 MtrunA17_Chr7g0259231 53.723 188 53 3 26 213 6 159 1.63e-60 186
Msa0534050 MtrunA17_Chr4g0014271 53.439 189 46 3 26 213 6 153 1.46e-58 181
Msa0534050 MtrunA17_Chr5g0438791 51.337 187 56 2 26 212 4 155 5.72e-58 180
Msa0534050 MtrunA17_Chr8g0362291 50.000 188 59 2 26 213 4 156 2.33e-57 178
Msa0534050 MtrunA17_Chr8g0361911 53.723 188 52 3 26 213 5 157 7.91e-57 177
Msa0534050 MtrunA17_Chr4g0014241 52.660 188 48 1 26 213 4 150 3.21e-56 175
Msa0534050 MtrunA17_Chr4g0014261 49.733 187 53 1 27 213 7 152 2.23e-55 173
Msa0534050 MtrunA17_Chr7g0221621 54.787 188 49 3 26 213 5 156 2.99e-55 173
Msa0534050 MtrunA17_Chr4g0015171 48.168 191 63 3 23 213 6 160 3.58e-55 173
Msa0534050 MtrunA17_Chr7g0259371 51.064 188 55 4 27 213 7 158 1.20e-54 171
Msa0534050 MtrunA17_Chr4g0015151 48.691 191 62 3 23 213 6 160 1.60e-53 169
Msa0534050 MtrunA17_Chr4g0007851 78.689 122 19 1 99 213 29 150 5.03e-52 164
Msa0534050 MtrunA17_Chr7g0259381 46.809 188 49 4 27 213 7 144 5.64e-46 149
Msa0534050 MtrunA17_Chr4g0009571 42.268 194 73 4 20 213 1 155 8.20e-41 136
Msa0534050 MtrunA17_Chr7g0259441 52.632 152 63 5 27 171 7 156 4.12e-38 130
Msa0534050 MtrunA17_Chr1g0202631 63.441 93 34 0 121 213 204 296 1.34e-35 127
Msa0534050 MtrunA17_Chr7g0259421 45.109 184 83 6 27 193 7 189 3.77e-34 120
Msa0534050 MtrunA17_Chr8g0381421 45.912 159 33 2 55 213 1 106 1.18e-33 116
Msa0534050 MtrunA17_Chr7g0259411 44.624 186 83 7 26 193 5 188 2.12e-30 110
Msa0534050 MtrunA17_Chr5g0436881 63.636 77 26 1 26 102 34 108 1.53e-27 101
Msa0534050 MtrunA17_Chr7g0214701 38.333 180 66 5 20 199 1 135 4.24e-26 98.2
Msa0534050 MtrunA17_Chr4g0067031 37.989 179 70 3 26 203 238 376 7.08e-26 102
Msa0534050 MtrunA17_Chr4g0015161 46.324 136 29 4 55 190 9 100 1.16e-24 93.2
Msa0534050 MtrunA17_Chr4g0014221 40.441 136 32 2 78 213 1 87 1.95e-24 92.4
Msa0534050 MtrunA17_Chr7g0259391 72.727 55 14 1 27 81 7 60 1.46e-19 79.0
Msa0534050 MtrunA17_Chr2g0310471 30.645 186 83 5 29 212 37 178 3.92e-18 79.0
Msa0534050 MtrunA17_Chr1g0211011 30.978 184 77 5 35 203 7 155 3.99e-18 77.8
Msa0534050 MtrunA17_Chr4g0074721 39.073 151 41 3 26 175 4 104 1.47e-17 75.1
Msa0534050 MtrunA17_Chr4g0071681 64.583 48 16 1 151 197 2 49 9.62e-15 65.9
Msa0534050 MtrunA17_Chr8g0361921 56.667 60 25 1 153 211 19 78 5.84e-14 64.7
Msa0534050 MtrunA17_Chr5g0447291 28.342 187 87 3 26 212 3 142 5.85e-14 66.6
Msa0534050 MtrunA17_Chr4g0014291 56.604 53 22 1 157 208 3 55 6.74e-14 63.9
Msa0534050 MtrunA17_Chr8g0335731 29.851 134 54 2 71 204 58 151 7.19e-12 62.0
Msa0534050 MtrunA17_Chr8g0335691 29.851 134 54 2 71 204 58 151 2.01e-11 62.0
Msa0534050 MtrunA17_Chr1g0167301 28.994 169 80 4 35 203 7 135 3.95e-11 61.2
Msa0534050 MtrunA17_Chr8g0392111 60.377 53 17 2 27 79 7 55 5.19e-11 56.6
Msa0534050 MtrunA17_Chr4g0014281 50.000 54 27 0 151 204 1 54 7.85e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0534050 AT1G20140.1 55.080 187 55 3 27 213 6 163 1.02e-61 190
Msa0534050 AT2G25700.1 52.941 187 59 2 27 213 6 163 1.10e-61 190
Msa0534050 AT1G75950.1 55.319 188 54 2 26 213 3 160 1.17e-61 190
Msa0534050 AT5G42190.1 57.754 187 59 3 27 213 5 171 6.42e-61 188
Msa0534050 AT4G34210.1 50.532 188 55 4 26 213 3 152 2.77e-57 178
Msa0534050 AT4G34470.1 50.000 188 56 4 26 213 3 152 3.60e-56 176
Msa0534050 AT3G60010.1 49.474 190 57 3 26 213 2 154 4.07e-51 162
Msa0534050 AT3G21850.1 45.789 190 62 4 26 213 3 153 8.10e-49 157
Msa0534050 AT2G03160.1 45.833 192 96 4 26 213 3 190 9.73e-46 150
Msa0534050 AT3G21860.1 44.444 189 65 4 26 213 3 152 3.71e-45 147
Msa0534050 AT2G03170.1 44.444 189 62 4 26 213 3 149 5.06e-45 147
Msa0534050 AT2G03190.1 42.857 189 83 4 26 213 3 167 5.26e-44 145
Msa0534050 AT3G21830.1 44.444 189 65 4 26 213 3 152 9.05e-43 141
Msa0534050 AT3G60020.1 42.564 195 64 5 25 213 1 153 2.01e-41 138
Msa0534050 AT3G25650.1 46.114 193 71 6 26 213 3 167 2.38e-41 139
Msa0534050 AT2G20160.1 41.489 188 68 3 26 212 3 149 2.08e-39 133
Msa0534050 AT1G10230.1 41.053 190 77 3 24 212 1 156 6.24e-37 127
Msa0534050 AT3G21840.1 43.226 155 48 4 26 179 3 118 1.88e-26 99.0

Find 46 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCAGAAGATGATCAAAT+TGG 0.232473 4_1:+9416838 Msa0534050:CDS
TGGTCTTGTGTATCGTAAAA+AGG 0.317649 4_1:+9417105 Msa0534050:CDS
CGTTCGGGCTGCGAATTACT+TGG 0.322167 4_1:+9417261 Msa0534050:CDS
TCGCTGGTTACGTTTGAGAT+AGG 0.345572 4_1:-9416998 None:intergenic
TACGCTGTTTGAACTCGTTC+GGG 0.347745 4_1:+9417246 Msa0534050:CDS
CTTGGATATTAAGAGCTTGC+TGG 0.358500 4_1:+9417279 Msa0534050:CDS
TTACGCTGTTTGAACTCGTT+CGG 0.374750 4_1:+9417245 Msa0534050:CDS
CGCTGGTTACGTTTGAGATA+GGG 0.415779 4_1:-9416997 None:intergenic
ACTTCTTTCTCTGCAGCCTT+AGG 0.416639 4_1:-9417166 None:intergenic
GGAGGATGAGCTTGAAAAGT+GGG 0.450380 4_1:+9417195 Msa0534050:CDS
TGTCGCCGTCGGAACTTACC+AGG 0.452533 4_1:-9416889 None:intergenic
GTGGGATGCTGAATTTGTTA+AGG 0.456238 4_1:+9417213 Msa0534050:CDS
TGCAGAGAAAGAAGTGAGTA+AGG 0.462604 4_1:+9417174 Msa0534050:CDS
CTTACTTGTAACACTGTAGC+TGG 0.467258 4_1:+9417304 Msa0534050:CDS
CGAATCTCCTCCTCTTCCTC+TGG 0.468986 4_1:-9417391 None:intergenic
AAGCAGAAGATGATCAAATT+GGG 0.495026 4_1:+9416839 Msa0534050:CDS
TGATTTCTCTCCAGAGGAAG+AGG 0.500085 4_1:+9417381 Msa0534050:CDS
AGGAGGATGAGCTTGAAAAG+TGG 0.500528 4_1:+9417194 Msa0534050:CDS
GACATCGGAGCAGATTCGTC+AGG 0.503138 4_1:+9417342 Msa0534050:CDS
TTGCTGAAGAAGAAAAGCCT+TGG 0.514532 4_1:+9417074 Msa0534050:CDS
TGTTTGTGATTCTAATGCTA+CGG 0.515837 4_1:-9416930 None:intergenic
GATTCGTAAGGAAAATCAAT+GGG 0.519861 4_1:+9417408 Msa0534050:CDS
TACGGCTTCGTCGATTTCGA+AGG 0.534173 4_1:-9416912 None:intergenic
AGATTCGTAAGGAAAATCAA+TGG 0.541072 4_1:+9417407 Msa0534050:CDS
GACAATTGTGTGGACGACAC+TGG 0.541258 4_1:+9416971 Msa0534050:CDS
AACCAGCGAGATTCTAGCTA+TGG 0.559406 4_1:+9417012 Msa0534050:CDS
TACCATAGCTAGAATCTCGC+TGG 0.560708 4_1:-9417014 None:intergenic
AGTACCGATGAAAAGAAATC+CGG 0.566724 4_1:+9417133 Msa0534050:CDS
ATCCGGTGAAGATGTTCCTA+AGG 0.572791 4_1:+9417150 Msa0534050:CDS
GGAAGAGGAGGAGATTCGTA+AGG 0.588394 4_1:+9417396 Msa0534050:CDS
TTACTTGTAACACTGTAGCT+GGG 0.593910 4_1:+9417305 Msa0534050:CDS
ATCACCCTGGTAAGTTCCGA+CGG 0.598983 4_1:+9416884 Msa0534050:CDS
AGCCTTAGGAACATCTTCAC+CGG 0.599023 4_1:-9417152 None:intergenic
TGCGAATGATTTCTCTCCAG+AGG 0.601037 4_1:+9417375 Msa0534050:CDS
TTTCTCTCCAGAGGAAGAGG+AGG 0.615178 4_1:+9417384 Msa0534050:CDS
GAAAAGCCTTGGAAGTCGGA+TGG 0.616563 4_1:+9417085 Msa0534050:CDS
ACAAGACCATCCGACTTCCA+AGG 0.617828 4_1:-9417091 None:intergenic
AGAAGAAAAGCCTTGGAAGT+CGG 0.624063 4_1:+9417081 Msa0534050:CDS
GATTTCGAAGGTGTCGCCGT+CGG 0.632222 4_1:-9416900 None:intergenic
AGAGAAAGAAGTGAGTAAGG+AGG 0.638426 4_1:+9417177 Msa0534050:CDS
CATGATCGAGGACAATTGTG+TGG 0.656095 4_1:+9416961 Msa0534050:CDS
AACAATCAAGTACATGATCG+AGG 0.662172 4_1:+9416949 Msa0534050:CDS
GATTATACGTGGTAAGACAT+CGG 0.685652 4_1:+9417327 Msa0534050:CDS
GTCGCCGTCGGAACTTACCA+GGG 0.695762 4_1:-9416888 None:intergenic
ACAATCAAAGAAGATCACCC+TGG 0.725005 4_1:+9416871 Msa0534050:CDS
ACTGTAGCTGGGATTATACG+TGG 0.729556 4_1:+9417316 Msa0534050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAAGCAGAAGATGATCAAAT+TGG + chr4_1:9416838-9416857 Msa0534050:CDS 30.0%
AAGCAGAAGATGATCAAATT+GGG + chr4_1:9416839-9416858 Msa0534050:CDS 30.0%
TGTTTGTGATTCTAATGCTA+CGG - chr4_1:9416933-9416952 None:intergenic 30.0%
AGATTCGTAAGGAAAATCAA+TGG + chr4_1:9417407-9417426 Msa0534050:CDS 30.0%
GATTCGTAAGGAAAATCAAT+GGG + chr4_1:9417408-9417427 Msa0534050:CDS 30.0%
AACAATCAAGTACATGATCG+AGG + chr4_1:9416949-9416968 Msa0534050:CDS 35.0%
!! TGGTCTTGTGTATCGTAAAA+AGG + chr4_1:9417105-9417124 Msa0534050:CDS 35.0%
!! AGTACCGATGAAAAGAAATC+CGG + chr4_1:9417133-9417152 Msa0534050:CDS 35.0%
! TTCACCGGATTTCTTTTCAT+CGG - chr4_1:9417140-9417159 None:intergenic 35.0%
TTACTTGTAACACTGTAGCT+GGG + chr4_1:9417305-9417324 Msa0534050:CDS 35.0%
GATTATACGTGGTAAGACAT+CGG + chr4_1:9417327-9417346 Msa0534050:CDS 35.0%
ACAATCAAAGAAGATCACCC+TGG + chr4_1:9416871-9416890 Msa0534050:CDS 40.0%
TTGCTGAAGAAGAAAAGCCT+TGG + chr4_1:9417074-9417093 Msa0534050:CDS 40.0%
AGAAGAAAAGCCTTGGAAGT+CGG + chr4_1:9417081-9417100 Msa0534050:CDS 40.0%
TGCAGAGAAAGAAGTGAGTA+AGG + chr4_1:9417174-9417193 Msa0534050:CDS 40.0%
AGAGAAAGAAGTGAGTAAGG+AGG + chr4_1:9417177-9417196 Msa0534050:CDS 40.0%
!! GTGGGATGCTGAATTTGTTA+AGG + chr4_1:9417213-9417232 Msa0534050:CDS 40.0%
TTACGCTGTTTGAACTCGTT+CGG + chr4_1:9417245-9417264 Msa0534050:CDS 40.0%
CTTGGATATTAAGAGCTTGC+TGG + chr4_1:9417279-9417298 Msa0534050:CDS 40.0%
CTTACTTGTAACACTGTAGC+TGG + chr4_1:9417304-9417323 Msa0534050:CDS 40.0%
CATGATCGAGGACAATTGTG+TGG + chr4_1:9416961-9416980 Msa0534050:CDS 45.0%
! CGCTGGTTACGTTTGAGATA+GGG - chr4_1:9417000-9417019 None:intergenic 45.0%
! TCGCTGGTTACGTTTGAGAT+AGG - chr4_1:9417001-9417020 None:intergenic 45.0%
! AACCAGCGAGATTCTAGCTA+TGG + chr4_1:9417012-9417031 Msa0534050:CDS 45.0%
TACCATAGCTAGAATCTCGC+TGG - chr4_1:9417017-9417036 None:intergenic 45.0%
ATCCGGTGAAGATGTTCCTA+AGG + chr4_1:9417150-9417169 Msa0534050:CDS 45.0%
AGCCTTAGGAACATCTTCAC+CGG - chr4_1:9417155-9417174 None:intergenic 45.0%
ACTTCTTTCTCTGCAGCCTT+AGG - chr4_1:9417169-9417188 None:intergenic 45.0%
AGGAGGATGAGCTTGAAAAG+TGG + chr4_1:9417194-9417213 Msa0534050:CDS 45.0%
GGAGGATGAGCTTGAAAAGT+GGG + chr4_1:9417195-9417214 Msa0534050:CDS 45.0%
TACGCTGTTTGAACTCGTTC+GGG + chr4_1:9417246-9417265 Msa0534050:CDS 45.0%
ACTGTAGCTGGGATTATACG+TGG + chr4_1:9417316-9417335 Msa0534050:CDS 45.0%
TGCGAATGATTTCTCTCCAG+AGG + chr4_1:9417375-9417394 Msa0534050:CDS 45.0%
TGATTTCTCTCCAGAGGAAG+AGG + chr4_1:9417381-9417400 Msa0534050:CDS 45.0%
ATCACCCTGGTAAGTTCCGA+CGG + chr4_1:9416884-9416903 Msa0534050:CDS 50.0%
!! TACGGCTTCGTCGATTTCGA+AGG - chr4_1:9416915-9416934 None:intergenic 50.0%
GACAATTGTGTGGACGACAC+TGG + chr4_1:9416971-9416990 Msa0534050:CDS 50.0%
GAAAAGCCTTGGAAGTCGGA+TGG + chr4_1:9417085-9417104 Msa0534050:CDS 50.0%
ACAAGACCATCCGACTTCCA+AGG - chr4_1:9417094-9417113 None:intergenic 50.0%
TTTCTCTCCAGAGGAAGAGG+AGG + chr4_1:9417384-9417403 Msa0534050:CDS 50.0%
GGAAGAGGAGGAGATTCGTA+AGG + chr4_1:9417396-9417415 Msa0534050:CDS 50.0%
!! GATTTCGAAGGTGTCGCCGT+CGG - chr4_1:9416903-9416922 None:intergenic 55.0%
CGTTCGGGCTGCGAATTACT+TGG + chr4_1:9417261-9417280 Msa0534050:CDS 55.0%
GACATCGGAGCAGATTCGTC+AGG + chr4_1:9417342-9417361 Msa0534050:CDS 55.0%
CGAATCTCCTCCTCTTCCTC+TGG - chr4_1:9417394-9417413 None:intergenic 55.0%
GTCGCCGTCGGAACTTACCA+GGG - chr4_1:9416891-9416910 None:intergenic 60.0%
TGTCGCCGTCGGAACTTACC+AGG - chr4_1:9416892-9416911 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 9416800 9417441 9416800 ID=Msa0534050;Name=Msa0534050
chr4_1 mRNA 9416800 9417441 9416800 ID=Msa0534050-mRNA-1;Parent=Msa0534050;Name=Msa0534050-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|213
chr4_1 exon 9416800 9417441 9416800 ID=Msa0534050-mRNA-1:exon:3056;Parent=Msa0534050-mRNA-1
chr4_1 CDS 9416800 9417441 9416800 ID=Msa0534050-mRNA-1:cds;Parent=Msa0534050-mRNA-1
Gene Sequence

>Msa0534050

ATGGCATCATCATCATCATCGACAAAGAAGATCACTCAAAAGCAGAAGATGATCAAATTGGGTAAGCAACAACAATCAAAGAAGATCACCCTGGTAAGTTCCGACGGCGACACCTTCGAAATCGACGAAGCCGTAGCATTAGAATCACAAACAATCAAGTACATGATCGAGGACAATTGTGTGGACGACACTGGAATCCCTATCTCAAACGTAACCAGCGAGATTCTAGCTATGGTAATTGAATATTGCAAGAAACATGTTGAAGCTGCTGCGTTTGCTGAAGAAGAAAAGCCTTGGAAGTCGGATGGTCTTGTGTATCGTAAAAAGGTTCTGAGTACCGATGAAAAGAAATCCGGTGAAGATGTTCCTAAGGCTGCAGAGAAAGAAGTGAGTAAGGAGGATGAGCTTGAAAAGTGGGATGCTGAATTTGTTAAGGTTGATAATATTACGCTGTTTGAACTCGTTCGGGCTGCGAATTACTTGGATATTAAGAGCTTGCTGGAGCTTACTTGTAACACTGTAGCTGGGATTATACGTGGTAAGACATCGGAGCAGATTCGTCAGGCTTTTAAGATTGCGAATGATTTCTCTCCAGAGGAAGAGGAGGAGATTCGTAAGGAAAATCAATGGGCTTTTGAATGA

Protein sequence

>Msa0534050

MASSSSSTKKITQKQKMIKLGKQQQSKKITLVSSDGDTFEIDEAVALESQTIKYMIEDNCVDDTGIPISNVTSEILAMVIEYCKKHVEAAAFAEEEKPWKSDGLVYRKKVLSTDEKKSGEDVPKAAEKEVSKEDELEKWDAEFVKVDNITLFELVRAANYLDIKSLLELTCNTVAGIIRGKTSEQIRQAFKIANDFSPEEEEEIRKENQWAFE*