AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1088840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1088840 MtrunA17_Chr2g0330451 94.652 187 8 2 1 187 1 185 4.03e-94 271
Msa1088840 MtrunA17_Chr2g0330441 63.830 188 60 4 2 184 3 187 7.37e-77 228
Msa1088840 MtrunA17_Chr8g0341921 59.880 167 64 1 2 168 3 166 2.58e-60 186
Msa1088840 MtrunA17_Chr6g0488551 45.198 177 97 0 1 177 1 177 1.22e-54 172
Msa1088840 MtrunA17_Chr7g0260751 49.390 164 78 2 11 174 18 176 9.21e-52 164
Msa1088840 MtrunA17_Chr1g0184741 49.708 171 75 1 4 174 10 169 1.56e-43 143
Msa1088840 MtrunA17_Chr5g0437751 38.596 171 100 2 9 174 21 191 4.67e-34 120
Msa1088840 MtrunA17_Chr4g0005191 40.385 156 91 1 22 175 45 200 9.54e-34 119
Msa1088840 MtrunA17_Chr1g0190601 40.571 175 96 2 4 178 10 176 7.26e-31 111
Msa1088840 MtrunA17_Chr1g0187861 38.776 98 58 1 20 115 6 103 1.17e-18 79.3
Msa1088840 MtrunA17_Chr3g0106401 38.298 141 85 1 36 174 28 168 7.42e-14 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1088840 AT1G55190.1 57.865 178 75 0 1 178 1 178 2.19e-69 209
Msa1088840 AT3G13720.1 54.335 173 79 0 1 173 1 173 7.16e-61 187
Msa1088840 AT3G13710.1 49.468 188 90 1 1 183 1 188 1.28e-59 184
Msa1088840 AT1G17700.1 50.000 178 87 2 1 177 1 177 6.40e-49 157
Msa1088840 AT1G04260.1 41.667 156 91 0 20 175 4 159 6.26e-39 132
Msa1088840 AT4G29658.2 42.045 176 99 2 1 175 1 174 1.14e-37 129
Msa1088840 AT1G08770.1 42.763 152 85 1 24 173 35 186 4.41e-37 128
Msa1088840 AT2G38360.1 35.326 184 109 3 1 174 11 194 3.77e-36 125
Msa1088840 AT5G01640.1 36.095 169 105 2 12 178 31 198 1.70e-33 119
Msa1088840 AT3G56110.3 37.427 171 102 2 11 176 16 186 1.13e-31 114
Msa1088840 AT3G56110.1 37.427 171 102 2 11 176 16 186 1.13e-31 114
Msa1088840 AT3G56110.2 37.427 171 102 2 11 176 16 186 1.13e-31 114
Msa1088840 AT3G56110.4 37.427 171 102 2 11 176 16 186 1.13e-31 114
Msa1088840 AT2G40380.1 36.757 185 96 3 11 174 2 186 5.26e-30 109
Msa1088840 AT5G05380.1 37.097 186 105 2 1 174 2 187 7.65e-29 107
Msa1088840 AT5G07110.1 41.429 140 80 1 37 174 45 184 1.13e-28 106
Msa1088840 AT5G05380.4 37.097 186 105 2 1 174 45 230 1.80e-28 107
Msa1088840 AT5G05380.3 37.097 186 105 2 1 174 53 238 2.06e-28 107
Msa1088840 AT5G05380.2 37.097 186 105 2 1 174 69 254 3.42e-28 107
Msa1088840 AT5G56230.1 30.357 168 116 1 8 174 7 174 5.48e-28 103
Msa1088840 AT1G55640.1 33.974 156 102 1 20 174 21 176 8.20e-26 98.2
Msa1088840 AT4G29658.1 43.119 109 61 1 68 175 3 111 9.29e-18 75.9
Msa1088840 AT4G00005.1 32.673 101 66 1 58 156 1 101 9.64e-11 57.0

Find 52 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGAACCTCTTGTTATCTT+TGG 0.288928 7_3:+2197915 Msa1088840:CDS
GCCGGATTTGAGGCGGTCTT+TGG 0.291200 7_3:-2197664 None:intergenic
GGATGATGGCGTAGTTCATC+TGG 0.387307 7_3:-2197794 None:intergenic
CATCGTCTTCGTCGTTCTCA+TGG 0.412362 7_3:+2197863 Msa1088840:CDS
GCCAAAGACCGCCTCAAATC+CGG 0.414007 7_3:+2197663 Msa1088840:CDS
TCCTCTTCCTCAGTCTTCTC+TGG 0.414218 7_3:+2197826 Msa1088840:CDS
ATGAATTCGAGGTTTGTTGC+AGG 0.451398 7_3:-2197633 None:intergenic
ATTCTTATCGCCGTTGCGGT+TGG 0.459068 7_3:+2198023 Msa1088840:CDS
TTTCTTGATGAAGAAGAAGA+AGG 0.460660 7_3:+2198095 Msa1088840:CDS
GGAAATAGCTTCGTGGAAGT+TGG 0.470169 7_3:-2197745 None:intergenic
ACGAAGACGATGAGTGAGAT+TGG 0.473115 7_3:-2197852 None:intergenic
GACCGCCTCAAATCCGGCCT+CGG 0.475536 7_3:+2197669 Msa1088840:CDS
CGCCGTTGCGGTTGGTGTTG+TGG 0.480076 7_3:+2198031 Msa1088840:CDS
CATCTGGAAGAAAGAGATGT+TGG 0.482307 7_3:-2197778 None:intergenic
GATCAAGAAGCAGGAGCACC+AGG 0.485484 7_3:-2198134 None:intergenic
GCCTCGGAACTCGCCGTCCA+TGG 0.485626 7_3:+2197685 Msa1088840:CDS
GGTGGGGATGATGATGAGGT+TGG 0.487376 7_3:-2197612 None:intergenic
GTGGGGATGATGATGAGGTT+GGG 0.488965 7_3:-2197611 None:intergenic
GCCAGAGAAGACTGAGGAAG+AGG 0.489667 7_3:-2197827 None:intergenic
TGAGGAAGAGGATGATGAGA+AGG 0.491579 7_3:-2197815 None:intergenic
TGAAGGAACGGAGGTTGAAG+AGG 0.492601 7_3:-2197713 None:intergenic
GAATAACACGATCACTGATA+AGG 0.500904 7_3:-2197941 None:intergenic
TTCGAGGTTTGTTGCAGGTG+GGG 0.512536 7_3:-2197628 None:intergenic
CTTATGTTGATTCTCACCGT+TGG 0.515006 7_3:+2197969 Msa1088840:CDS
GAGTTCCGAGGCCGGATTTG+AGG 0.519741 7_3:-2197674 None:intergenic
TGGCGCGTGTGATGAATTCG+AGG 0.527660 7_3:-2197644 None:intergenic
AATTCGAGGTTTGTTGCAGG+TGG 0.530722 7_3:-2197630 None:intergenic
GAGGATGATGAGAAGGATGA+TGG 0.534139 7_3:-2197808 None:intergenic
GAAGTTGGATGGGAGGTTGA+AGG 0.541239 7_3:-2197730 None:intergenic
TTCATCAAGAAACAGATCAC+TGG 0.548790 7_3:-2198084 None:intergenic
AACCACAACACCAACCGCAA+CGG 0.551906 7_3:-2198033 None:intergenic
GAATTACAGGATCAAGAAGC+AGG 0.554856 7_3:-2198143 None:intergenic
ATAGCTTCGTGGAAGTTGGA+TGG 0.557067 7_3:-2197741 None:intergenic
TGCAGGTGGGGATGATGATG+AGG 0.565935 7_3:-2197616 None:intergenic
TGGACGGCGAGTTCCGAGGC+CGG 0.568393 7_3:-2197682 None:intergenic
TAGCTTCGTGGAAGTTGGAT+GGG 0.573483 7_3:-2197740 None:intergenic
ACAACAACGATGACAAACTA+CGG 0.574851 7_3:+2197582 None:intergenic
CAATATTCTTATCGCCGTTG+CGG 0.580821 7_3:+2198019 Msa1088840:CDS
ATTCGAGGTTTGTTGCAGGT+GGG 0.581531 7_3:-2197629 None:intergenic
TGGATGGGAGGTTGAAGGAA+CGG 0.585117 7_3:-2197725 None:intergenic
TGAAGAGGAGTTTCCATGGA+CGG 0.586287 7_3:-2197698 None:intergenic
TTCCGAGGCCGGATTTGAGG+CGG 0.588969 7_3:-2197671 None:intergenic
AGGTTGAAGAGGAGTTTCCA+TGG 0.595913 7_3:-2197702 None:intergenic
TCCATGGACGGCGAGTTCCG+AGG 0.598894 7_3:-2197686 None:intergenic
CTTCGTGGAAGTTGGATGGG+AGG 0.625803 7_3:-2197737 None:intergenic
TGATACGGGAAATAGCTTCG+TGG 0.625890 7_3:-2197752 None:intergenic
AGGCGACCAAAGATAACAAG+AGG 0.631850 7_3:-2197921 None:intergenic
AGCAAGCAAAAGCAATCCAA+CGG 0.634952 7_3:-2197985 None:intergenic
TCGTCGTTCTCATGGCTGCG+TGG 0.645538 7_3:+2197871 Msa1088840:CDS
ATGGGAGGTTGAAGGAACGG+AGG 0.651337 7_3:-2197722 None:intergenic
CAAGAAGCAGGAGCACCAGG+TGG 0.670977 7_3:-2198131 None:intergenic
TTGGATGCCAGAGAAGACTG+AGG 0.685064 7_3:-2197833 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGAGATGTTGGTTTTGATA+CGG - chr7_3:2197770-2197789 None:intergenic 30.0%
TTTCTTGATGAAGAAGAAGA+AGG + chr7_3:2198095-2198114 Msa1088840:CDS 30.0%
!!! AGAGATGTTGGTTTTGATAC+GGG - chr7_3:2197769-2197788 None:intergenic 35.0%
! GATGAACCTCTTGTTATCTT+TGG + chr7_3:2197915-2197934 Msa1088840:CDS 35.0%
GAATAACACGATCACTGATA+AGG - chr7_3:2197944-2197963 None:intergenic 35.0%
TTCATCAAGAAACAGATCAC+TGG - chr7_3:2198087-2198106 None:intergenic 35.0%
!! ATGAATTCGAGGTTTGTTGC+AGG - chr7_3:2197636-2197655 None:intergenic 40.0%
CATCTGGAAGAAAGAGATGT+TGG - chr7_3:2197781-2197800 None:intergenic 40.0%
!! CTTATGTTGATTCTCACCGT+TGG + chr7_3:2197969-2197988 Msa1088840:CDS 40.0%
AGCAAGCAAAAGCAATCCAA+CGG - chr7_3:2197988-2198007 None:intergenic 40.0%
CAATATTCTTATCGCCGTTG+CGG + chr7_3:2198019-2198038 Msa1088840:CDS 40.0%
!! ATTCGAGGTTTGTTGCAGGT+GGG - chr7_3:2197632-2197651 None:intergenic 45.0%
!! AATTCGAGGTTTGTTGCAGG+TGG - chr7_3:2197633-2197652 None:intergenic 45.0%
TGAAGAGGAGTTTCCATGGA+CGG - chr7_3:2197701-2197720 None:intergenic 45.0%
AGGTTGAAGAGGAGTTTCCA+TGG - chr7_3:2197705-2197724 None:intergenic 45.0%
TAGCTTCGTGGAAGTTGGAT+GGG - chr7_3:2197743-2197762 None:intergenic 45.0%
ATAGCTTCGTGGAAGTTGGA+TGG - chr7_3:2197744-2197763 None:intergenic 45.0%
GGAAATAGCTTCGTGGAAGT+TGG - chr7_3:2197748-2197767 None:intergenic 45.0%
TGATACGGGAAATAGCTTCG+TGG - chr7_3:2197755-2197774 None:intergenic 45.0%
GAGGATGATGAGAAGGATGA+TGG - chr7_3:2197811-2197830 None:intergenic 45.0%
TGAGGAAGAGGATGATGAGA+AGG - chr7_3:2197818-2197837 None:intergenic 45.0%
ACGAAGACGATGAGTGAGAT+TGG - chr7_3:2197855-2197874 None:intergenic 45.0%
AGGCGACCAAAGATAACAAG+AGG - chr7_3:2197924-2197943 None:intergenic 45.0%
!! GTTGGATTGCTTTTGCTTGC+TGG + chr7_3:2197987-2198006 Msa1088840:CDS 45.0%
! GTGGGGATGATGATGAGGTT+GGG - chr7_3:2197614-2197633 None:intergenic 50.0%
!! TTCGAGGTTTGTTGCAGGTG+GGG - chr7_3:2197631-2197650 None:intergenic 50.0%
TGAAGGAACGGAGGTTGAAG+AGG - chr7_3:2197716-2197735 None:intergenic 50.0%
TGGATGGGAGGTTGAAGGAA+CGG - chr7_3:2197728-2197747 None:intergenic 50.0%
GAAGTTGGATGGGAGGTTGA+AGG - chr7_3:2197733-2197752 None:intergenic 50.0%
! GGATGATGGCGTAGTTCATC+TGG - chr7_3:2197797-2197816 None:intergenic 50.0%
TCCTCTTCCTCAGTCTTCTC+TGG + chr7_3:2197826-2197845 Msa1088840:CDS 50.0%
TTGGATGCCAGAGAAGACTG+AGG - chr7_3:2197836-2197855 None:intergenic 50.0%
CATCGTCTTCGTCGTTCTCA+TGG + chr7_3:2197863-2197882 Msa1088840:CDS 50.0%
ATTCTTATCGCCGTTGCGGT+TGG + chr7_3:2198023-2198042 Msa1088840:CDS 50.0%
AACCACAACACCAACCGCAA+CGG - chr7_3:2198036-2198055 None:intergenic 50.0%
! GGACTTTCGTTTTCTCCACC+TGG + chr7_3:2198116-2198135 Msa1088840:CDS 50.0%
! GGTGGGGATGATGATGAGGT+TGG - chr7_3:2197615-2197634 None:intergenic 55.0%
! TGCAGGTGGGGATGATGATG+AGG - chr7_3:2197619-2197638 None:intergenic 55.0%
TGGCGCGTGTGATGAATTCG+AGG - chr7_3:2197647-2197666 None:intergenic 55.0%
GCCAAAGACCGCCTCAAATC+CGG + chr7_3:2197663-2197682 Msa1088840:CDS 55.0%
ATGGGAGGTTGAAGGAACGG+AGG - chr7_3:2197725-2197744 None:intergenic 55.0%
CTTCGTGGAAGTTGGATGGG+AGG - chr7_3:2197740-2197759 None:intergenic 55.0%
GCCAGAGAAGACTGAGGAAG+AGG - chr7_3:2197830-2197849 None:intergenic 55.0%
! GCCGGATTTGAGGCGGTCTT+TGG - chr7_3:2197667-2197686 None:intergenic 60.0%
TTCCGAGGCCGGATTTGAGG+CGG - chr7_3:2197674-2197693 None:intergenic 60.0%
GAGTTCCGAGGCCGGATTTG+AGG - chr7_3:2197677-2197696 None:intergenic 60.0%
TCGTCGTTCTCATGGCTGCG+TGG + chr7_3:2197871-2197890 Msa1088840:CDS 60.0%
!! CAAGAAGCAGGAGCACCAGG+TGG - chr7_3:2198134-2198153 None:intergenic 60.0%
GACCGCCTCAAATCCGGCCT+CGG + chr7_3:2197669-2197688 Msa1088840:CDS 65.0%
TCCATGGACGGCGAGTTCCG+AGG - chr7_3:2197689-2197708 None:intergenic 65.0%
!! CGCCGTTGCGGTTGGTGTTG+TGG + chr7_3:2198031-2198050 Msa1088840:CDS 65.0%
TGGACGGCGAGTTCCGAGGC+CGG - chr7_3:2197685-2197704 None:intergenic 70.0%
GCCTCGGAACTCGCCGTCCA+TGG + chr7_3:2197685-2197704 Msa1088840:CDS 70.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 2197591 2198154 2197591 ID=Msa1088840;Name=Msa1088840
chr7_3 mRNA 2197591 2198154 2197591 ID=Msa1088840-mRNA-1;Parent=Msa1088840;Name=Msa1088840-mRNA-1;_AED=0.23;_eAED=0.24;_QI=0|-1|0|1|-1|1|1|0|187
chr7_3 exon 2197591 2198154 2197591 ID=Msa1088840-mRNA-1:exon:881;Parent=Msa1088840-mRNA-1
chr7_3 CDS 2197591 2198154 2197591 ID=Msa1088840-mRNA-1:cds;Parent=Msa1088840-mRNA-1
Gene Sequence

>Msa1088840

ATGACAAACTACGGCACAATCCCAACCTCATCATCATCCCCACCTGCAACAAACCTCGAATTCATCACACGCGCCAAAGACCGCCTCAAATCCGGCCTCGGAACTCGCCGTCCATGGAAACTCCTCTTCAACCTCCGTTCCTTCAACCTCCCATCCAACTTCCACGAAGCTATTTCCCGTATCAAAACCAACATCTCTTTCTTCCAGATGAACTACGCCATCATCCTTCTCATCATCCTCTTCCTCAGTCTTCTCTGGCATCCAATCTCACTCATCGTCTTCGTCGTTCTCATGGCTGCGTGGTTGTTTCTCTACTTTCTTCGTGATGAACCTCTTGTTATCTTTGGTCGCCTTATCAGTGATCGTGTTATTCTTGTGCTTATGTTGATTCTCACCGTTGGATTGCTTTTGCTTGCTGGTGCGATTCTCAATATTCTTATCGCCGTTGCGGTTGGTGTTGTGGTTGTTCTTCTTCATGCTGCTTTTAGAAACACCAGTGATCTGTTTCTTGATGAAGAAGAAGAAGGACTTTCGTTTTCTCCACCTGGTGCTCCTGCTTCTTGA
Protein sequence

>Msa1088840

MTNYGTIPTSSSSPPATNLEFITRAKDRLKSGLGTRRPWKLLFNLRSFNLPSNFHEAISRIKTNISFFQMNYAIILLIILFLSLLWHPISLIVFVVLMAAWLFLYFLRDEPLVIFGRLISDRVILVLMLILTVGLLLLAGAILNILIAVAVGVVVVLLHAAFRNTSDLFLDEEEEGLSFSPPGAPAS*