AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene50780

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50780.t1 MTR_4g071590 97.080 137 4 0 1 137 119 255 3.67e-100 289
MS.gene50780.t1 MTR_4g471590 97.080 137 4 0 1 137 119 255 3.67e-100 289
MS.gene50780.t1 MTR_3g117380 55.696 158 47 5 2 137 117 273 5.18e-47 154
MS.gene50780.t1 MTR_5g021340 38.220 191 61 6 1 137 157 344 2.27e-29 110
MS.gene50780.t1 MTR_8g076340 42.236 161 64 6 1 137 107 262 1.49e-27 103
MS.gene50780.t1 MTR_3g109760 40.361 166 64 7 2 137 91 251 1.22e-26 101
MS.gene50780.t1 MTR_8g013950 38.415 164 68 7 2 136 110 269 3.51e-24 95.5
MS.gene50780.t1 MTR_1g006650 36.782 174 70 7 2 136 105 277 1.31e-23 94.0
MS.gene50780.t1 MTR_1g094930 84.091 44 7 0 93 136 147 190 1.55e-23 91.7
MS.gene50780.t1 MTR_1g094930 84.091 44 7 0 93 136 242 285 2.87e-23 92.8
MS.gene50780.t1 MTR_6g032830 86.364 44 6 0 93 136 192 235 3.30e-23 91.7
MS.gene50780.t1 MTR_7g085410 86.364 44 6 0 93 136 188 231 6.69e-23 90.9
MS.gene50780.t1 MTR_2g094600 60.000 65 24 1 72 136 197 259 5.37e-22 89.0
MS.gene50780.t1 MTR_1g116010 79.545 44 9 0 93 136 164 207 6.46e-21 85.1
MS.gene50780.t1 MTR_4g058910 77.778 45 10 0 93 137 314 358 8.33e-21 87.0
MS.gene50780.t1 MTR_1g046680 81.818 44 8 0 93 136 172 215 1.42e-20 84.3
MS.gene50780.t1 MTR_5g007600 42.373 118 52 3 29 136 191 302 6.09e-19 81.3
MS.gene50780.t1 MTR_5g007600 60.000 60 22 1 77 136 143 200 2.93e-17 76.6
MS.gene50780.t1 MTR_7g446110 60.870 46 18 0 92 137 186 231 2.07e-15 70.5
MS.gene50780.t1 MTR_7g445980 53.448 58 26 1 80 136 20 77 1.17e-14 65.5
MS.gene50780.t1 MTR_7g445950 28.030 132 91 1 4 135 35 162 3.39e-14 66.2
MS.gene50780.t1 MTR_7g446070 58.140 43 18 0 93 135 132 174 4.01e-13 63.5
MS.gene50780.t1 MTR_5g020230 43.103 58 33 0 68 125 97 154 3.30e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50780.t1 AT4G36240 50.336 149 50 6 3 137 70 208 6.42e-36 124
MS.gene50780.t1 AT4G34680 48.571 140 55 6 2 136 96 223 3.49e-32 115
MS.gene50780.t1 AT4G34680 48.571 140 55 6 2 136 96 223 3.49e-32 115
MS.gene50780.t1 AT2G45050 41.250 160 60 4 1 136 73 222 5.32e-29 106
MS.gene50780.t1 AT5G66320 36.735 196 56 5 1 137 107 293 1.07e-28 107
MS.gene50780.t1 AT5G66320 36.735 196 56 5 1 137 107 293 1.07e-28 107
MS.gene50780.t1 AT3G60530 46.528 144 56 6 1 136 71 201 2.46e-28 104
MS.gene50780.t1 AT5G25830 39.267 191 60 11 1 137 75 263 2.41e-26 100
MS.gene50780.t1 AT4G32890 36.686 169 70 6 2 136 75 240 4.80e-25 97.4
MS.gene50780.t1 AT3G51080 86.667 45 6 0 93 137 221 265 1.53e-23 93.2
MS.gene50780.t1 AT3G54810 84.091 44 7 0 93 136 229 272 2.48e-22 90.1
MS.gene50780.t1 AT3G54810 84.091 44 7 0 93 136 229 272 2.48e-22 90.1
MS.gene50780.t1 AT3G24050 66.667 60 19 1 78 136 178 237 2.58e-21 86.7
MS.gene50780.t1 AT1G08010 79.545 44 9 0 93 136 220 263 1.36e-20 85.5
MS.gene50780.t1 AT1G08010 79.545 44 9 0 93 136 220 263 1.36e-20 85.5
MS.gene50780.t1 AT1G08010 79.545 44 9 0 93 136 220 263 1.36e-20 85.5
MS.gene50780.t1 AT1G08000 79.545 44 9 0 93 136 218 261 3.45e-19 81.6
MS.gene50780.t1 AT1G08000 79.545 44 9 0 93 136 218 261 3.45e-19 81.6
MS.gene50780.t1 AT3G45170 63.043 46 17 0 92 137 114 159 1.82e-16 72.8
MS.gene50780.t1 AT2G28340 69.767 43 13 0 95 137 193 235 2.50e-16 73.6

Find 53 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTTGTCTTGGTTGTTCT+AGG 0.195513 4.1:+31410833 None:intergenic
AGCCCCACCCGTTTGGGCTT+CGG 0.226880 4.1:+31410745 None:intergenic
GCCCCACCCGTTTGGGCTTC+GGG 0.232140 4.1:+31410746 None:intergenic
GGCCGATGATGTTGCGGATT+TGG 0.241470 4.1:-31410990 MS.gene50780:CDS
GGTTCGGCCCGGGCCTGAAC+TGG 0.312951 4.1:+31410914 None:intergenic
GAAACTGAGCCCCACCCGTT+TGG 0.331959 4.1:+31410738 None:intergenic
TCTTTGCTGAAAAGAGTATA+GGG 0.337151 4.1:+31410783 None:intergenic
AAACTGAGCCCCACCCGTTT+GGG 0.350163 4.1:+31410739 None:intergenic
CTCTCTATTGTATCCAGTTC+AGG 0.364580 4.1:-31410927 MS.gene50780:CDS
GCATTGGTTGGGCCCGGTCT+AGG 0.372639 4.1:+31410887 None:intergenic
ACAGTTGGGCCTTCTTGTCT+TGG 0.379924 4.1:+31410823 None:intergenic
GTTGGGCCCGGTCTAGGTTC+CGG 0.399228 4.1:+31410893 None:intergenic
AGTTCAGGCCCGGGCCGAAC+CGG 0.407384 4.1:-31410912 MS.gene50780:CDS
GTCTAGGTTCCGGTTCGGCC+CGG 0.414385 4.1:+31410903 None:intergenic
GGCCGAACCGGAACCTAGAC+CGG 0.414860 4.1:-31410900 MS.gene50780:CDS
TTCTTTGCTGAAAAGAGTAT+AGG 0.416988 4.1:+31410782 None:intergenic
TATGTAACGCTTGTGGTGTT+CGG 0.433641 4.1:-31410643 MS.gene50780:CDS
TATTGTATCCAGTTCAGGCC+CGG 0.446736 4.1:-31410922 MS.gene50780:CDS
GGAATGGGTGTCTCACTTTG+TGG 0.449579 4.1:-31410969 MS.gene50780:CDS
TCTAGGTTCCGGTTCGGCCC+GGG 0.468440 4.1:+31410904 None:intergenic
TTCTGCGGATTATAGAGAGC+TGG 0.472534 4.1:+31410858 None:intergenic
ATGATGTTGCGGATTTGGAA+TGG 0.479723 4.1:-31410985 MS.gene50780:CDS
CAGTGGAGAGCTGGTCCGCT+TGG 0.483307 4.1:-31410677 MS.gene50780:CDS
TGTGGTGTTCGGTTTAAGTC+CGG 0.492368 4.1:-31410632 MS.gene50780:CDS
GGATACAATAGAGAGAGTTC+TGG 0.493646 4.1:+31410935 None:intergenic
GCCCGAAGCCCAAACGGGTG+GGG 0.493923 4.1:-31410747 MS.gene50780:CDS
AAAATCCACACGTTACAGTT+GGG 0.498357 4.1:+31410809 None:intergenic
TGATGTTGCGGATTTGGAAT+GGG 0.501793 4.1:-31410984 MS.gene50780:CDS
GCCCGGTCTAGGTTCCGGTT+CGG 0.510484 4.1:+31410898 None:intergenic
AGCTGGGAATAAGCATTGGT+TGG 0.510903 4.1:+31410875 None:intergenic
TTCTCAGGCCGATGATGTTG+CGG 0.519029 4.1:-31410996 None:intergenic
GCTGGGAATAAGCATTGGTT+GGG 0.531676 4.1:+31410876 None:intergenic
AAAACGCCACAGTGGAGAGC+TGG 0.532352 4.1:-31410686 MS.gene50780:CDS
TGCATGCAGGTCTATACTCC+GGG 0.538197 4.1:+31410600 None:intergenic
TTCCAAATCCGCAACATCAT+CGG 0.540001 4.1:+31410988 None:intergenic
AGCCCGAAGCCCAAACGGGT+GGG 0.541657 4.1:-31410748 MS.gene50780:CDS
GAATAAGCATTGGTTGGGCC+CGG 0.542060 4.1:+31410881 None:intergenic
ATTGTATCCAGTTCAGGCCC+GGG 0.543140 4.1:-31410921 MS.gene50780:CDS
AGAGAGCTGGGAATAAGCAT+TGG 0.549150 4.1:+31410871 None:intergenic
GCCGAACCGGAACCTAGACC+GGG 0.552879 4.1:-31410899 MS.gene50780:CDS
TCTGCGGATTATAGAGAGCT+GGG 0.553907 4.1:+31410859 None:intergenic
AAAACGTCGGACTTGCATGC+AGG 0.554590 4.1:+31410587 None:intergenic
AAGCCCGAAGCCCAAACGGG+TGG 0.557944 4.1:-31410749 MS.gene50780:CDS
CTAGAACAACCAAGACAAGA+AGG 0.581886 4.1:-31410832 MS.gene50780:CDS
TTGCATGCAGGTCTATACTC+CGG 0.584277 4.1:+31410599 None:intergenic
ATACTCCGGGAAAAGCCGAC+CGG 0.594686 4.1:+31410613 None:intergenic
TGGTTGTTCTAGGCTTTCTG+CGG 0.603627 4.1:+31410843 None:intergenic
GTGTTCGGTTTAAGTCCGGT+CGG 0.631814 4.1:-31410628 MS.gene50780:CDS
GAAGGCCCAACTGTAACGTG+TGG 0.654146 4.1:-31410814 MS.gene50780:CDS
AAAACACTATGTAACGCTTG+TGG 0.656575 4.1:-31410650 MS.gene50780:CDS
AGCGGACCAGCTCTCCACTG+TGG 0.697012 4.1:+31410680 None:intergenic
ATGTTCAGAAAACGCCACAG+TGG 0.715931 4.1:-31410694 MS.gene50780:CDS
GTGGGGCTCAGTTTCAACGA+CGG 0.724625 4.1:-31410730 MS.gene50780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCTTTGCTGAAAAGAGTATA+GGG + chr4.1:31410808-31410827 None:intergenic 30.0%
! TTCTTTGCTGAAAAGAGTAT+AGG + chr4.1:31410809-31410828 None:intergenic 30.0%
AAAAATCCACACGTTACAGT+TGG + chr4.1:31410783-31410802 None:intergenic 35.0%
AAAACACTATGTAACGCTTG+TGG - chr4.1:31410938-31410957 MS.gene50780:CDS 35.0%
AAAATCCACACGTTACAGTT+GGG + chr4.1:31410782-31410801 None:intergenic 35.0%
! CAAGCGTTACATAGTGTTTT+CGG + chr4.1:31410938-31410957 None:intergenic 35.0%
ATGATGTTGCGGATTTGGAA+TGG - chr4.1:31410603-31410622 MS.gene50780:CDS 40.0%
CTAGAACAACCAAGACAAGA+AGG - chr4.1:31410756-31410775 MS.gene50780:CDS 40.0%
CTCTCTATTGTATCCAGTTC+AGG - chr4.1:31410661-31410680 MS.gene50780:CDS 40.0%
CTTCTTGTCTTGGTTGTTCT+AGG + chr4.1:31410758-31410777 None:intergenic 40.0%
GGATACAATAGAGAGAGTTC+TGG + chr4.1:31410656-31410675 None:intergenic 40.0%
TATGTAACGCTTGTGGTGTT+CGG - chr4.1:31410945-31410964 MS.gene50780:CDS 40.0%
TTCCAAATCCGCAACATCAT+CGG + chr4.1:31410603-31410622 None:intergenic 40.0%
! TCTTTTCAGCAAAGAAGCAG+AGG - chr4.1:31410813-31410832 MS.gene50780:CDS 40.0%
! TGATGTTGCGGATTTGGAAT+GGG - chr4.1:31410604-31410623 MS.gene50780:CDS 40.0%
AGAGAGCTGGGAATAAGCAT+TGG + chr4.1:31410720-31410739 None:intergenic 45.0%
ATGTTCAGAAAACGCCACAG+TGG - chr4.1:31410894-31410913 MS.gene50780:CDS 45.0%
TATTGTATCCAGTTCAGGCC+CGG - chr4.1:31410666-31410685 MS.gene50780:CDS 45.0%
TGTGGTGTTCGGTTTAAGTC+CGG - chr4.1:31410956-31410975 MS.gene50780:CDS 45.0%
TTGCATGCAGGTCTATACTC+CGG + chr4.1:31410992-31411011 None:intergenic 45.0%
! ACTGTGGCGTTTTCTGAACA+TGG + chr4.1:31410895-31410914 None:intergenic 45.0%
! CATAGTGTTTTCGGTCCAAG+CGG + chr4.1:31410929-31410948 None:intergenic 45.0%
! TCTGCGGATTATAGAGAGCT+GGG + chr4.1:31410732-31410751 None:intergenic 45.0%
! TGGTTGTTCTAGGCTTTCTG+CGG + chr4.1:31410748-31410767 None:intergenic 45.0%
! TTCTGCGGATTATAGAGAGC+TGG + chr4.1:31410733-31410752 None:intergenic 45.0%
!! AGCTGGGAATAAGCATTGGT+TGG + chr4.1:31410716-31410735 None:intergenic 45.0%
!! GCTGGGAATAAGCATTGGTT+GGG + chr4.1:31410715-31410734 None:intergenic 45.0%
AAAAAGCCCGAAGCCCAAAC+GGG - chr4.1:31410836-31410855 MS.gene50780:CDS 50.0%
ACAGTTGGGCCTTCTTGTCT+TGG + chr4.1:31410768-31410787 None:intergenic 50.0%
ATTGTATCCAGTTCAGGCCC+GGG - chr4.1:31410667-31410686 MS.gene50780:CDS 50.0%
GAAAAAGCCCGAAGCCCAAA+CGG - chr4.1:31410835-31410854 MS.gene50780:CDS 50.0%
GGAATGGGTGTCTCACTTTG+TGG - chr4.1:31410619-31410638 MS.gene50780:CDS 50.0%
GTGTTCGGTTTAAGTCCGGT+CGG - chr4.1:31410960-31410979 MS.gene50780:CDS 50.0%
TGCATGCAGGTCTATACTCC+GGG + chr4.1:31410991-31411010 None:intergenic 50.0%
! GCGTTTTCTGAACATGGCAG+TGG + chr4.1:31410889-31410908 None:intergenic 50.0%
!! GAATAAGCATTGGTTGGGCC+CGG + chr4.1:31410710-31410729 None:intergenic 50.0%
AAAACGCCACAGTGGAGAGC+TGG - chr4.1:31410902-31410921 MS.gene50780:CDS 55.0%
AAACTGAGCCCCACCCGTTT+GGG + chr4.1:31410852-31410871 None:intergenic 55.0%
ATACTCCGGGAAAAGCCGAC+CGG + chr4.1:31410978-31410997 None:intergenic 55.0%
GAAGGCCCAACTGTAACGTG+TGG - chr4.1:31410774-31410793 MS.gene50780:CDS 55.0%
GTGGGGCTCAGTTTCAACGA+CGG - chr4.1:31410858-31410877 MS.gene50780:CDS 55.0%
!! TAAGTCCGGTCGGCTTTTCC+CGG - chr4.1:31410970-31410989 MS.gene50780:CDS 55.0%
GAAACTGAGCCCCACCCGTT+TGG + chr4.1:31410853-31410872 None:intergenic 60.0%
AAGCCCGAAGCCCAAACGGG+TGG - chr4.1:31410839-31410858 MS.gene50780:CDS 65.0%
AGCCCCACCCGTTTGGGCTT+CGG + chr4.1:31410846-31410865 None:intergenic 65.0%
AGCCCGAAGCCCAAACGGGT+GGG - chr4.1:31410840-31410859 MS.gene50780:CDS 65.0%
AGCGGACCAGCTCTCCACTG+TGG + chr4.1:31410911-31410930 None:intergenic 65.0%
CAGTGGAGAGCTGGTCCGCT+TGG - chr4.1:31410911-31410930 MS.gene50780:CDS 65.0%
GCCCGGTCTAGGTTCCGGTT+CGG + chr4.1:31410693-31410712 None:intergenic 65.0%
GCCGAACCGGAACCTAGACC+GGG - chr4.1:31410689-31410708 MS.gene50780:CDS 65.0%
GGCCGAACCGGAACCTAGAC+CGG - chr4.1:31410688-31410707 MS.gene50780:CDS 65.0%
GTTGGGCCCGGTCTAGGTTC+CGG + chr4.1:31410698-31410717 None:intergenic 65.0%
!! GCATTGGTTGGGCCCGGTCT+AGG + chr4.1:31410704-31410723 None:intergenic 65.0%
!! GTCTAGGTTCCGGTTCGGCC+CGG + chr4.1:31410688-31410707 None:intergenic 65.0%
!! TCTAGGTTCCGGTTCGGCCC+GGG + chr4.1:31410687-31410706 None:intergenic 65.0%
AGTTCAGGCCCGGGCCGAAC+CGG - chr4.1:31410676-31410695 MS.gene50780:CDS 70.0%
GCCCCACCCGTTTGGGCTTC+GGG + chr4.1:31410845-31410864 None:intergenic 70.0%
GCCCGAAGCCCAAACGGGTG+GGG - chr4.1:31410841-31410860 MS.gene50780:CDS 70.0%
GGTTCGGCCCGGGCCTGAAC+TGG + chr4.1:31410677-31410696 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 31410599 31411011 31410599 ID=MS.gene50780
chr4.1 mRNA 31410599 31411011 31410599 ID=MS.gene50780.t1;Parent=MS.gene50780
chr4.1 exon 31410599 31411011 31410599 ID=MS.gene50780.t1.exon1;Parent=MS.gene50780.t1
chr4.1 CDS 31410599 31411011 31410599 ID=cds.MS.gene50780.t1;Parent=MS.gene50780.t1
Gene Sequence

>MS.gene50780

GCCGATGATGTTGCGGATTTGGAATGGGTGTCTCACTTTGTGGACGATTCTGTACCAGAACTCTCTCTATTGTATCCAGTTCAGGCCCGGGCCGAACCGGAACCTAGACCGGGCCCAACCAATGCTTATTCCCAGCTCTCTATAATCCGCAGAAAGCCTAGAACAACCAAGACAAGAAGGCCCAACTGTAACGTGTGGATTTTTAACCCTATACTCTTTTCAGCAAAGAAGCAGAGGAAAAAGCCCGAAGCCCAAACGGGTGGGGCTCAGTTTCAACGACGGTGCAGCCACTGCCATGTTCAGAAAACGCCACAGTGGAGAGCTGGTCCGCTTGGACCGAAAACACTATGTAACGCTTGTGGTGTTCGGTTTAAGTCCGGTCGGCTTTTCCCGGAGTATAGACCTGCATGCAA
Protein sequence

>MS.gene50780.t1

ADDVADLEWVSHFVDDSVPELSLLYPVQARAEPEPRPGPTNAYSQLSIIRRKPRTTKTRRPNCNVWIFNPILFSAKKQRKKPEAQTGGAQFQRRCSHCHVQKTPQWRAGPLGPKTLCNACGVRFKSGRLFPEYRPAC