AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1116630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1116630 MtrunA17_Chr7g0259101 97.927 193 4 0 1 193 201 393 3.14e-138 391
Msa1116630 MtrunA17_Chr7g0259101 93.814 194 11 1 1 193 1 194 4.30e-131 373
Msa1116630 MtrunA17_Chr7g0259091 94.845 194 9 1 1 193 1 194 2.36e-135 376
Msa1116630 MtrunA17_Chr7g0259071 76.166 193 44 1 1 193 1 191 6.38e-108 307
Msa1116630 MtrunA17_Chr7g0259121 58.523 176 66 4 23 193 20 193 1.75e-70 213
Msa1116630 MtrunA17_Chr1g0175911 50.769 195 91 4 1 193 1 192 1.07e-61 190
Msa1116630 MtrunA17_Chr4g0005081 50.000 166 81 2 29 193 33 197 7.59e-58 180
Msa1116630 MtrunA17_Chr4g0005071 47.541 183 94 2 12 193 15 196 3.46e-57 178
Msa1116630 MtrunA17_Chr4g0005031 44.974 189 98 3 6 193 38 221 8.67e-54 171
Msa1116630 MtrunA17_Chr3g0136641 48.128 187 92 5 9 193 5 188 2.02e-52 166
Msa1116630 MtrunA17_Chr4g0005041 48.214 168 81 4 29 193 34 198 2.22e-52 166
Msa1116630 MtrunA17_Chr4g0005011 48.795 166 81 3 29 193 35 197 1.08e-51 164
Msa1116630 MtrunA17_Chr4g0037481 52.941 153 70 2 42 193 41 192 1.27e-51 164
Msa1116630 MtrunA17_Chr3g0136631 45.745 188 96 5 9 193 5 189 1.37e-50 161
Msa1116630 MtrunA17_Chr7g0243501 50.000 168 80 3 28 193 27 192 1.26e-48 156
Msa1116630 MtrunA17_Chr4g0005111 42.857 175 97 3 19 193 19 190 1.36e-46 151
Msa1116630 MtrunA17_Chr5g0446751 46.667 180 86 5 19 193 15 189 7.47e-45 147
Msa1116630 MtrunA17_Chr1g0177051 45.732 164 83 4 33 192 24 185 1.80e-43 143
Msa1116630 MtrunA17_Chr4g0005131 39.205 176 104 3 19 193 18 191 4.83e-43 142
Msa1116630 MtrunA17_Chr4g0040551 42.268 194 102 6 1 193 1 185 1.13e-41 139
Msa1116630 MtrunA17_Chr3g0090231 42.268 194 102 6 1 193 1 185 3.17e-41 137
Msa1116630 MtrunA17_Chr3g0085311 47.651 149 75 2 44 192 43 188 4.97e-40 134
Msa1116630 MtrunA17_Chr3g0085291 47.651 149 73 2 44 192 43 186 1.42e-39 133
Msa1116630 MtrunA17_Chr3g0085301 44.966 149 79 2 44 192 48 193 4.25e-38 130
Msa1116630 MtrunA17_Chr3g0085321 43.709 151 82 2 42 192 41 188 5.95e-37 127
Msa1116630 MtrunA17_Chr4g0005091 36.047 172 94 2 22 193 20 175 3.79e-34 119
Msa1116630 MtrunA17_Chr4g0068381 39.735 151 90 1 43 193 31 180 2.35e-29 107
Msa1116630 MtrunA17_Chr4g0068391 39.735 151 90 1 43 193 31 180 3.38e-29 106
Msa1116630 MtrunA17_Chr4g0024951 31.507 146 99 1 43 188 29 173 4.39e-21 85.9
Msa1116630 MtrunA17_Chr4g0024961 32.215 149 100 1 40 188 26 173 6.21e-21 85.1
Msa1116630 MtrunA17_Chr1g0169511 40.000 95 55 2 77 171 133 225 1.52e-13 67.0
Msa1116630 MtrunA17_Chr1g0169281 38.947 95 56 2 77 171 139 231 1.63e-13 67.0
Msa1116630 MtrunA17_Chr1g0169291 40.000 95 55 2 77 171 133 225 2.13e-13 66.6
Msa1116630 MtrunA17_Chr4g0030731 37.383 107 66 1 70 176 177 282 3.45e-12 63.5
Msa1116630 MtrunA17_Chr4g0030681 37.383 107 66 1 70 176 178 283 3.53e-12 63.5
Msa1116630 MtrunA17_Chr1g0212861 33.846 130 78 4 70 192 225 353 1.43e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1116630 AT5G42500.1 50.898 167 78 3 26 192 23 185 9.49e-55 172
Msa1116630 AT5G42510.1 48.810 168 82 3 25 192 19 182 6.03e-52 165
Msa1116630 AT1G65870.1 53.548 155 67 3 40 192 38 189 6.78e-52 165
Msa1116630 AT1G22900.1 47.727 176 88 3 17 192 22 193 3.06e-50 161
Msa1116630 AT1G55210.1 41.848 184 101 4 12 193 8 187 3.09e-49 158
Msa1116630 AT1G55210.2 41.848 184 101 4 12 193 8 187 3.09e-49 158
Msa1116630 AT1G58170.1 43.386 189 101 2 5 193 3 185 3.38e-49 158
Msa1116630 AT3G13650.1 40.761 184 105 2 10 193 7 186 4.57e-49 158
Msa1116630 AT5G49040.1 40.107 187 108 3 10 193 6 191 4.84e-48 155
Msa1116630 AT4G38700.1 41.885 191 103 5 8 193 3 190 5.35e-44 145
Msa1116630 AT2G21100.1 42.188 192 106 2 1 192 1 187 7.09e-44 144
Msa1116630 AT2G21100.2 42.188 192 106 2 1 192 1 187 7.09e-44 144
Msa1116630 AT3G13662.1 47.651 149 70 3 32 180 32 172 4.59e-43 142
Msa1116630 AT2G21110.1 44.371 151 79 2 47 193 37 186 9.22e-43 142
Msa1116630 AT5G49030.3 40.606 165 94 3 10 171 6 169 1.20e-37 138
Msa1116630 AT3G58090.1 54.206 107 48 1 86 192 166 271 2.96e-34 122
Msa1116630 AT3G13660.1 44.538 119 65 1 75 193 8 125 6.01e-33 115
Msa1116630 AT4G23690.1 34.586 133 75 5 42 168 36 162 1.56e-13 66.2
Msa1116630 AT4G11210.1 30.968 155 99 5 26 179 22 169 7.42e-12 61.6

Find 53 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACGGATGGACAATTTAA+TGG 0.266137 7_3:-64363893 Msa1116630:CDS
CTTGGTAACCTAACTAATAA+TGG 0.304647 7_3:+64363696 None:intergenic
TGGAAGCACACTTAGCATAT+TGG 0.308313 7_3:-64363873 Msa1116630:CDS
CTTGAAAACCCAGCATTGTT+GGG 0.345342 7_3:+64364164 None:intergenic
ATGGATGACCCTTTGACGGC+TGG 0.362400 7_3:-64364013 Msa1116630:CDS
ACAATGGCCATTTCTCTAAC+AGG 0.363166 7_3:+64363827 None:intergenic
ACAAATACCATGCTAGGTTT+TGG 0.370876 7_3:+64364091 None:intergenic
GGAAGCACACTTAGCATATT+GGG 0.389276 7_3:-64363872 Msa1116630:CDS
TCTTGAAAACCCAGCATTGT+TGG 0.400814 7_3:+64364163 None:intergenic
ATGGCCATTGTTGGTGGGAC+TGG 0.413384 7_3:-64363815 Msa1116630:CDS
TACTTTCACGACATTGTGTC+AGG 0.427188 7_3:-64364115 Msa1116630:CDS
AAGCCTATCCCCAACAATGC+TGG 0.431336 7_3:-64364173 Msa1116630:CDS
TATTCCGTTGATTACACTAA+AGG 0.444889 7_3:-64363752 Msa1116630:CDS
GAGTGAACCTGTTAGAGAAA+TGG 0.463422 7_3:-64363834 Msa1116630:CDS
ATATTATAGAGAGGAAAGTA+AGG 0.472220 7_3:+64364224 None:intergenic
TGGATGACCCTTTGACGGCT+GGG 0.473571 7_3:-64364012 Msa1116630:CDS
TTCTATATCACAAGAGGAGA+TGG 0.477985 7_3:-64363942 Msa1116630:CDS
GGCGATGGATGACCCTTTGA+CGG 0.482950 7_3:-64364017 Msa1116630:CDS
TTTATAGTAATTAGTGGCAG+TGG 0.489871 7_3:+64364195 None:intergenic
GTAATTAGTGGCAGTGGCAA+GGG 0.501581 7_3:+64364201 None:intergenic
TGAATCAAAACTTGTGGGTA+AGG 0.505874 7_3:-64363981 Msa1116630:CDS
AGCCTATCCCCAACAATGCT+GGG 0.510899 7_3:-64364172 Msa1116630:CDS
GGTGATGACCATGGCATTCA+CGG 0.512137 7_3:-64363909 Msa1116630:CDS
GTATTTGTAGCTGAGCCTAA+TGG 0.523113 7_3:-64364076 Msa1116630:CDS
ATCGCCACAACTGTCCCAAA+TGG 0.528212 7_3:+64364034 None:intergenic
AGAGGAGATGGGACTAATGA+TGG 0.528699 7_3:-64363930 Msa1116630:CDS
ATTTGGGACAGTTGTGGCGA+TGG 0.529221 7_3:-64364032 Msa1116630:CDS
AGTAATTAGTGGCAGTGGCA+AGG 0.543512 7_3:+64364200 None:intergenic
GTTAGAGAAATGGCCATTGT+TGG 0.545345 7_3:-64363824 Msa1116630:CDS
TTTCGTACGTGGGTATGCTC+AGG 0.546620 7_3:-64363783 Msa1116630:CDS
AAACTTGTGGGTAAGGCTCA+AGG 0.547993 7_3:-64363974 Msa1116630:CDS
TCAGCTACAAATACCATGCT+AGG 0.557255 7_3:+64364085 None:intergenic
TTACACTTCTATATCACAAG+AGG 0.558364 7_3:-64363948 Msa1116630:CDS
TTGAAAACCCAGCATTGTTG+GGG 0.562104 7_3:+64364165 None:intergenic
GAACGTGAATCAAAACTTGT+GGG 0.564741 7_3:-64363986 Msa1116630:CDS
AGAGAAATGGCCATTGTTGG+TGG 0.569066 7_3:-64363821 Msa1116630:CDS
GTTCAAAGAAATGAGAATTG+TGG 0.571264 7_3:+64364246 None:intergenic
AGCTCCAGTCCCACCAACAA+TGG 0.574074 7_3:+64363811 None:intergenic
ATGACCATGGCATTCACGGA+TGG 0.585239 7_3:-64363905 Msa1116630:CDS
CACTAAAGGAGATGCCATTG+TGG 0.590470 7_3:-64363738 Msa1116630:CDS
TCTATATCACAAGAGGAGAT+GGG 0.592301 7_3:-64363941 Msa1116630:CDS
ATCTCCTTTAGTGTAATCAA+CGG 0.597699 7_3:+64363748 None:intergenic
GAGAAATGGCCATTGTTGGT+GGG 0.599344 7_3:-64363820 Msa1116630:CDS
TTGTCCATCCGTGAATGCCA+TGG 0.606931 7_3:+64363901 None:intergenic
AACCCAGCATTGTTGGGGAT+AGG 0.607331 7_3:+64364170 None:intergenic
GTTGCCATTTGGGACAGTTG+TGG 0.614741 7_3:-64364038 Msa1116630:CDS
CGAACGTGAATCAAAACTTG+TGG 0.618950 7_3:-64363987 Msa1116630:CDS
GTCAGGACCAAAACCTAGCA+TGG 0.622028 7_3:-64364098 Msa1116630:CDS
TGTAGCTGAGCCTAATGGCA+AGG 0.630219 7_3:-64364071 Msa1116630:CDS
TGTCGTGAAAGTAAAAGTGA+AGG 0.637192 7_3:+64364125 None:intergenic
TGGCAAGGGATATTATAGAG+AGG 0.685595 7_3:+64364215 None:intergenic
AAATATGTCATATTCCACAA+TGG 0.686079 7_3:+64363724 None:intergenic
ACTAATGATGGTGATGACCA+TGG 0.702330 7_3:-64363918 Msa1116630:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATTATAGAGAGGAAAGTA+AGG + chr7_3:64363756-64363775 None:intergenic 25.0%
!! TAGGCTTTTATAGTAATTAG+TGG + chr7_3:64363791-64363810 None:intergenic 25.0%
! AAATATGTCATATTCCACAA+TGG + chr7_3:64364256-64364275 None:intergenic 25.0%
GTTCAAAGAAATGAGAATTG+TGG + chr7_3:64363734-64363753 None:intergenic 30.0%
TTTATAGTAATTAGTGGCAG+TGG + chr7_3:64363785-64363804 None:intergenic 30.0%
! TAAAAAATGCGTTGCCATTT+GGG - chr7_3:64363929-64363948 Msa1116630:CDS 30.0%
TTACACTTCTATATCACAAG+AGG - chr7_3:64364029-64364048 Msa1116630:CDS 30.0%
! TATTCCGTTGATTACACTAA+AGG - chr7_3:64364225-64364244 Msa1116630:CDS 30.0%
ATCTCCTTTAGTGTAATCAA+CGG + chr7_3:64364232-64364251 None:intergenic 30.0%
TGTCGTGAAAGTAAAAGTGA+AGG + chr7_3:64363855-64363874 None:intergenic 35.0%
! ACAAATACCATGCTAGGTTT+TGG + chr7_3:64363889-64363908 None:intergenic 35.0%
!!! GCATTTTTTACCTTGCCATT+AGG + chr7_3:64363919-64363938 None:intergenic 35.0%
GTAAAAAATGCGTTGCCATT+TGG - chr7_3:64363928-64363947 Msa1116630:CDS 35.0%
!!! ACAAGTTTTGATTCACGTTC+GGG + chr7_3:64363991-64364010 None:intergenic 35.0%
!!! CACAAGTTTTGATTCACGTT+CGG + chr7_3:64363992-64364011 None:intergenic 35.0%
GAACGTGAATCAAAACTTGT+GGG - chr7_3:64363991-64364010 Msa1116630:CDS 35.0%
TGAATCAAAACTTGTGGGTA+AGG - chr7_3:64363996-64364015 Msa1116630:CDS 35.0%
TTCTATATCACAAGAGGAGA+TGG - chr7_3:64364035-64364054 Msa1116630:CDS 35.0%
TCTATATCACAAGAGGAGAT+GGG - chr7_3:64364036-64364055 Msa1116630:CDS 35.0%
TTCACGGATGGACAATTTAA+TGG - chr7_3:64364084-64364103 Msa1116630:CDS 35.0%
TGGCAAGGGATATTATAGAG+AGG + chr7_3:64363765-64363784 None:intergenic 40.0%
TTGAAAACCCAGCATTGTTG+GGG + chr7_3:64363815-64363834 None:intergenic 40.0%
CTTGAAAACCCAGCATTGTT+GGG + chr7_3:64363816-64363835 None:intergenic 40.0%
TCTTGAAAACCCAGCATTGT+TGG + chr7_3:64363817-64363836 None:intergenic 40.0%
TACTTTCACGACATTGTGTC+AGG - chr7_3:64363862-64363881 Msa1116630:CDS 40.0%
TCAGCTACAAATACCATGCT+AGG + chr7_3:64363895-64363914 None:intergenic 40.0%
GTATTTGTAGCTGAGCCTAA+TGG - chr7_3:64363901-64363920 Msa1116630:CDS 40.0%
CGAACGTGAATCAAAACTTG+TGG - chr7_3:64363990-64364009 Msa1116630:CDS 40.0%
! ACTAATGATGGTGATGACCA+TGG - chr7_3:64364059-64364078 Msa1116630:CDS 40.0%
! TGGAAGCACACTTAGCATAT+TGG - chr7_3:64364104-64364123 Msa1116630:CDS 40.0%
! GGAAGCACACTTAGCATATT+GGG - chr7_3:64364105-64364124 Msa1116630:CDS 40.0%
GAGTGAACCTGTTAGAGAAA+TGG - chr7_3:64364143-64364162 Msa1116630:CDS 40.0%
ACAATGGCCATTTCTCTAAC+AGG + chr7_3:64364153-64364172 None:intergenic 40.0%
GTTAGAGAAATGGCCATTGT+TGG - chr7_3:64364153-64364172 Msa1116630:CDS 40.0%
GTAATTAGTGGCAGTGGCAA+GGG + chr7_3:64363779-64363798 None:intergenic 45.0%
AGTAATTAGTGGCAGTGGCA+AGG + chr7_3:64363780-64363799 None:intergenic 45.0%
AAACTTGTGGGTAAGGCTCA+AGG - chr7_3:64364003-64364022 Msa1116630:CDS 45.0%
AGAGGAGATGGGACTAATGA+TGG - chr7_3:64364047-64364066 Msa1116630:CDS 45.0%
AGAGAAATGGCCATTGTTGG+TGG - chr7_3:64364156-64364175 Msa1116630:CDS 45.0%
GAGAAATGGCCATTGTTGGT+GGG - chr7_3:64364157-64364176 Msa1116630:CDS 45.0%
! GAGCTTTTCGTTTCGTACGT+GGG - chr7_3:64364184-64364203 Msa1116630:CDS 45.0%
CACTAAAGGAGATGCCATTG+TGG - chr7_3:64364239-64364258 Msa1116630:CDS 45.0%
AAGCCTATCCCCAACAATGC+TGG - chr7_3:64363804-64363823 Msa1116630:CDS 50.0%
AGCCTATCCCCAACAATGCT+GGG - chr7_3:64363805-64363824 Msa1116630:CDS 50.0%
AACCCAGCATTGTTGGGGAT+AGG + chr7_3:64363810-64363829 None:intergenic 50.0%
GTCAGGACCAAAACCTAGCA+TGG - chr7_3:64363879-64363898 Msa1116630:CDS 50.0%
TGTAGCTGAGCCTAATGGCA+AGG - chr7_3:64363906-64363925 Msa1116630:CDS 50.0%
! GTTGCCATTTGGGACAGTTG+TGG - chr7_3:64363939-64363958 Msa1116630:CDS 50.0%
ATCGCCACAACTGTCCCAAA+TGG + chr7_3:64363946-64363965 None:intergenic 50.0%
! ATTTGGGACAGTTGTGGCGA+TGG - chr7_3:64363945-64363964 Msa1116630:CDS 50.0%
GGTGATGACCATGGCATTCA+CGG - chr7_3:64364068-64364087 Msa1116630:CDS 50.0%
ATGACCATGGCATTCACGGA+TGG - chr7_3:64364072-64364091 Msa1116630:CDS 50.0%
TTGTCCATCCGTGAATGCCA+TGG + chr7_3:64364079-64364098 None:intergenic 50.0%
! GGAGCTTTTCGTTTCGTACG+TGG - chr7_3:64364183-64364202 Msa1116630:CDS 50.0%
TTTCGTACGTGGGTATGCTC+AGG - chr7_3:64364194-64364213 Msa1116630:CDS 50.0%
GGCGATGGATGACCCTTTGA+CGG - chr7_3:64363960-64363979 Msa1116630:CDS 55.0%
ATGGATGACCCTTTGACGGC+TGG - chr7_3:64363964-64363983 Msa1116630:CDS 55.0%
TGGATGACCCTTTGACGGCT+GGG - chr7_3:64363965-64363984 Msa1116630:CDS 55.0%
! ATGGCCATTGTTGGTGGGAC+TGG - chr7_3:64364162-64364181 Msa1116630:CDS 55.0%
AGCTCCAGTCCCACCAACAA+TGG + chr7_3:64364169-64364188 None:intergenic 55.0%
GTTCGGGCCCAGCCGTCAAA+GGG + chr7_3:64363975-64363994 None:intergenic 65.0%
CGTTCGGGCCCAGCCGTCAA+AGG + chr7_3:64363976-64363995 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 64363709 64364290 64363709 ID=Msa1116630;Name=Msa1116630
chr7_3 mRNA 64363709 64364290 64363709 ID=Msa1116630-mRNA-1;Parent=Msa1116630;Name=Msa1116630-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|-1|0|1|-1|1|1|0|193
chr7_3 exon 64363709 64364290 64363709 ID=Msa1116630-mRNA-1:exon:15240;Parent=Msa1116630-mRNA-1
chr7_3 CDS 64363709 64364290 64363709 ID=Msa1116630-mRNA-1:cds;Parent=Msa1116630-mRNA-1
Gene Sequence

>Msa1116630

ATGGCAAAATTCTCATCATGCTCCACAATTCTCATTTCTTTGAACCTTACTTTCCTCTCTATAATATCCCTTGCCACTGCCACTAATTACTATAAAAGCCTATCCCCAACAATGCTGGGTTTTCAAGAAGAGAAATTCACTCACCTTCACTTTTACTTTCACGACATTGTGTCAGGACCAAAACCTAGCATGGTATTTGTAGCTGAGCCTAATGGCAAGGTAAAAAATGCGTTGCCATTTGGGACAGTTGTGGCGATGGATGACCCTTTGACGGCTGGGCCCGAACGTGAATCAAAACTTGTGGGTAAGGCTCAAGGAATTTACACTTCTATATCACAAGAGGAGATGGGACTAATGATGGTGATGACCATGGCATTCACGGATGGACAATTTAATGGAAGCACACTTAGCATATTGGGTAGAAACATGATCATGAGTGAACCTGTTAGAGAAATGGCCATTGTTGGTGGGACTGGAGCTTTTCGTTTCGTACGTGGGTATGCTCAGGCTAAGTTTTATTCCGTTGATTACACTAAAGGAGATGCCATTGTGGAATATGACATATTTGTGTTCCATTATTAG
Protein sequence

>Msa1116630

MAKFSSCSTILISLNLTFLSIISLATATNYYKSLSPTMLGFQEEKFTHLHFYFHDIVSGPKPSMVFVAEPNGKVKNALPFGTVVAMDDPLTAGPERESKLVGKAQGIYTSISQEEMGLMMVMTMAFTDGQFNGSTLSILGRNMIMSEPVREMAIVGGTGAFRFVRGYAQAKFYSVDYTKGDAIVEYDIFVFHY*