AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1259380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1259380 MtrunA17_Chr4g0055101 82.682 179 28 1 3 178 8 186 1.34e-88 257
Msa1259380 MtrunA17_Chr4g0059481 54.884 215 37 6 14 169 25 238 1.07e-60 188
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGAGCGGGAGGAAGAATT+TGG 0.312405 8_2:+61009201 Msa1259380:CDS
AAGCCATAATCTGCTGATTT+CGG 0.337263 8_2:-61008742 None:intergenic
GAACCGAAATCAGCAGATTA+TGG 0.378368 8_2:+61008739 Msa1259380:CDS
TAGAAATAGTGGAAATCATC+AGG 0.380708 8_2:-61009059 None:intergenic
TTTCATGAGCTCTGATAAAC+TGG 0.396861 8_2:+61008711 Msa1259380:CDS
TTGATTCATGCAGGAGGAAA+AGG 0.416587 8_2:+61009810 Msa1259380:intron
TCATGGTCTCCTCGATTGCT+TGG 0.435909 8_2:-61009657 None:intergenic
ACGACATGGACATTTCAAAC+TGG 0.436567 8_2:+61009326 Msa1259380:CDS
GATGATTTCCACTATTTCTA+CGG 0.471616 8_2:+61009062 Msa1259380:CDS
ATCTGAGGACATTTCAACCT+TGG 0.472960 8_2:+61009839 Msa1259380:CDS
TAATACTTCCGTAGAAATAG+TGG 0.477563 8_2:-61009070 None:intergenic
GGGGATACGTCGTTTGATCA+TGG 0.484883 8_2:-61009674 None:intergenic
TGATCAAACGACGTATCCCC+AGG 0.493648 8_2:+61009677 Msa1259380:CDS
GCAAATGATGATTCTGTTTG+TGG 0.499262 8_2:+61009906 Msa1259380:CDS
TGAGGACATTTCAACCTTGG+AGG 0.501246 8_2:+61009842 Msa1259380:CDS
TGGTCTCCTCGATTGCTTGG+AGG 0.502855 8_2:-61009654 None:intergenic
CCTTCAGAATCATCAAACTA+AGG 0.527809 8_2:-61009940 None:intergenic
AGAGGACAGCTATGATGAGC+GGG 0.527843 8_2:+61009188 Msa1259380:CDS
GCTCTTCTGATGTGCAGAAG+TGG 0.537271 8_2:+61009871 Msa1259380:CDS
TTGTATTTATCGGCTTTGGT+TGG 0.554582 8_2:-61009609 None:intergenic
ATAAATACAAAACTATCAGA+TGG 0.567313 8_2:+61009622 Msa1259380:CDS
GAGCTCTGATAAACTGGCGG+AGG 0.595057 8_2:+61008717 Msa1259380:CDS
TGTAGCTAAAACAAAAGAAG+AGG 0.595337 8_2:+61009170 Msa1259380:intron
ATTTCAAACTGGAAAATCGA+TGG 0.595540 8_2:+61009337 Msa1259380:CDS
TGACGCAGAAGAAGAATCTG+AGG 0.596338 8_2:+61008657 Msa1259380:CDS
AGAAGAGCTCAGCTCCTCCA+AGG 0.597915 8_2:-61009856 None:intergenic
AGAAATAGTGGAAATCATCA+GGG 0.608858 8_2:-61009058 None:intergenic
AGGAAAAGGCAAAGAATCTG+AGG 0.616583 8_2:+61009824 Msa1259380:CDS
TGAAGAAGAAATTGACGACA+TGG 0.621062 8_2:+61009312 Msa1259380:CDS
GATCAAACGACGTATCCCCA+GGG 0.643779 8_2:+61009678 Msa1259380:CDS
AAGAGGACAGCTATGATGAG+CGG 0.651595 8_2:+61009187 Msa1259380:CDS
TTTCATCCTCCAAGCAATCG+AGG 0.655223 8_2:+61009648 Msa1259380:CDS
AATGATGATTCTGTTTGTGG+TGG 0.665654 8_2:+61009909 Msa1259380:CDS
CATGAGCTCTGATAAACTGG+CGG 0.669381 8_2:+61008714 Msa1259380:CDS
GAAATAGTGGAAATCATCAG+GGG 0.685394 8_2:-61009057 None:intergenic
ATCAAACGACGTATCCCCAG+GGG 0.723149 8_2:+61009679 Msa1259380:CDS
AAAGAAGAATAATACCCCTG+GGG 0.748744 8_2:-61009693 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTGAATTTTATTTGAAA+CGG + chr8_2:61009434-61009453 Msa1259380:intron 10.0%
!!! AATTTGAATTTTATTTGAAA+CGG + chr8_2:61009434-61009453 Msa1259380:intron 10.0%
!!! ATTTGGTATTATTGTTTTTT+CGG + chr8_2:61009218-61009237 Msa1259380:intron 15.0%
!!! ATTTGGTATTATTGTTTTTT+CGG + chr8_2:61009218-61009237 Msa1259380:intron 15.0%
!! TGTTAATGTTTATAATGTGT+TGG + chr8_2:61009120-61009139 Msa1259380:intron 20.0%
!! GTTAATGTTTATAATGTGTT+GGG + chr8_2:61009121-61009140 Msa1259380:intron 20.0%
!!! TTATTGTTTTTTCGGATTTA+AGG + chr8_2:61009226-61009245 Msa1259380:intron 20.0%
!!! TCTGATAGTTTTGTATTTAT+CGG - chr8_2:61009622-61009641 None:intergenic 20.0%
!! ATAAATACAAAACTATCAGA+TGG + chr8_2:61009622-61009641 Msa1259380:CDS 20.0%
!! TGTTAATGTTTATAATGTGT+TGG + chr8_2:61009120-61009139 Msa1259380:intron 20.0%
!! GTTAATGTTTATAATGTGTT+GGG + chr8_2:61009121-61009140 Msa1259380:intron 20.0%
!!! TTATTGTTTTTTCGGATTTA+AGG + chr8_2:61009226-61009245 Msa1259380:intron 20.0%
!!! TCTGATAGTTTTGTATTTAT+CGG - chr8_2:61009622-61009641 None:intergenic 20.0%
!! ATAAATACAAAACTATCAGA+TGG + chr8_2:61009622-61009641 Msa1259380:CDS 20.0%
! ATTATTAGAAGATGAATTCG+AGG + chr8_2:61008880-61008899 Msa1259380:intron 25.0%
!!! ATTTTTGAATGTGTTGTTGT+TGG + chr8_2:61008950-61008969 Msa1259380:intron 25.0%
! AATAATTATTGATGCAGATG+AGG + chr8_2:61009585-61009604 Msa1259380:intron 25.0%
! ATTATTAGAAGATGAATTCG+AGG + chr8_2:61008880-61008899 Msa1259380:intron 25.0%
!!! ATTTTTGAATGTGTTGTTGT+TGG + chr8_2:61008950-61008969 Msa1259380:intron 25.0%
! AATAATTATTGATGCAGATG+AGG + chr8_2:61009585-61009604 Msa1259380:intron 25.0%
!! TTGATTGATGATGCAGTAAA+AGG + chr8_2:61008987-61009006 Msa1259380:intron 30.0%
! AGAAATAGTGGAAATCATCA+GGG - chr8_2:61009061-61009080 None:intergenic 30.0%
! TAGAAATAGTGGAAATCATC+AGG - chr8_2:61009062-61009081 None:intergenic 30.0%
!! GATGATTTCCACTATTTCTA+CGG + chr8_2:61009062-61009081 Msa1259380:CDS 30.0%
TAATACTTCCGTAGAAATAG+TGG - chr8_2:61009073-61009092 None:intergenic 30.0%
TGTAGCTAAAACAAAAGAAG+AGG + chr8_2:61009170-61009189 Msa1259380:intron 30.0%
! TCATTTGTTTAGAATGTGTC+TGG + chr8_2:61009257-61009276 Msa1259380:intron 30.0%
ATTTCAAACTGGAAAATCGA+TGG + chr8_2:61009337-61009356 Msa1259380:CDS 30.0%
! GAAACTCAAAGAGAGATTTT+TGG + chr8_2:61009456-61009475 Msa1259380:intron 30.0%
!!! AGTTTTGTATTTATCGGCTT+TGG - chr8_2:61009616-61009635 None:intergenic 30.0%
!! TTGATTGATGATGCAGTAAA+AGG + chr8_2:61008987-61009006 Msa1259380:intron 30.0%
! AGAAATAGTGGAAATCATCA+GGG - chr8_2:61009061-61009080 None:intergenic 30.0%
! TAGAAATAGTGGAAATCATC+AGG - chr8_2:61009062-61009081 None:intergenic 30.0%
!! GATGATTTCCACTATTTCTA+CGG + chr8_2:61009062-61009081 Msa1259380:CDS 30.0%
TAATACTTCCGTAGAAATAG+TGG - chr8_2:61009073-61009092 None:intergenic 30.0%
TGTAGCTAAAACAAAAGAAG+AGG + chr8_2:61009170-61009189 Msa1259380:intron 30.0%
! TCATTTGTTTAGAATGTGTC+TGG + chr8_2:61009257-61009276 Msa1259380:intron 30.0%
ATTTCAAACTGGAAAATCGA+TGG + chr8_2:61009337-61009356 Msa1259380:CDS 30.0%
! GAAACTCAAAGAGAGATTTT+TGG + chr8_2:61009456-61009475 Msa1259380:intron 30.0%
!!! AGTTTTGTATTTATCGGCTT+TGG - chr8_2:61009616-61009635 None:intergenic 30.0%
! TTTCATGAGCTCTGATAAAC+TGG + chr8_2:61008711-61008730 Msa1259380:CDS 35.0%
!! AAGCCATAATCTGCTGATTT+CGG - chr8_2:61008745-61008764 None:intergenic 35.0%
AGTATTACTACTCTTCTTGC+AGG + chr8_2:61008775-61008794 Msa1259380:intron 35.0%
! TCACTAGTTTAGAATGCGTT+GGG + chr8_2:61008822-61008841 Msa1259380:intron 35.0%
! ATCAGGGGTCATGTATTTTA+TGG - chr8_2:61009045-61009064 None:intergenic 35.0%
! GAAATAGTGGAAATCATCAG+GGG - chr8_2:61009060-61009079 None:intergenic 35.0%
TGAAGAAGAAATTGACGACA+TGG + chr8_2:61009312-61009331 Msa1259380:CDS 35.0%
! TGATTAGTTCAATTCAACCG+TGG + chr8_2:61009401-61009420 Msa1259380:intron 35.0%
! GATTAGTTCAATTCAACCGT+GGG + chr8_2:61009402-61009421 Msa1259380:intron 35.0%
TCAAATTAAAGACATGCCCA+CGG - chr8_2:61009421-61009440 None:intergenic 35.0%
!! TTGTATTTATCGGCTTTGGT+TGG - chr8_2:61009612-61009631 None:intergenic 35.0%
AAAGAAGAATAATACCCCTG+GGG - chr8_2:61009696-61009715 None:intergenic 35.0%
GAAAGAAGAATAATACCCCT+GGG - chr8_2:61009697-61009716 None:intergenic 35.0%
AGAAAGAAGAATAATACCCC+TGG - chr8_2:61009698-61009717 None:intergenic 35.0%
!! GCTTGATTATTGATTCATGC+AGG + chr8_2:61009801-61009820 Msa1259380:intron 35.0%
!! TGATTATTGATTCATGCAGG+AGG + chr8_2:61009804-61009823 Msa1259380:intron 35.0%
GCAAATGATGATTCTGTTTG+TGG + chr8_2:61009906-61009925 Msa1259380:CDS 35.0%
AATGATGATTCTGTTTGTGG+TGG + chr8_2:61009909-61009928 Msa1259380:CDS 35.0%
! TTTCATGAGCTCTGATAAAC+TGG + chr8_2:61008711-61008730 Msa1259380:CDS 35.0%
!! AAGCCATAATCTGCTGATTT+CGG - chr8_2:61008745-61008764 None:intergenic 35.0%
AGTATTACTACTCTTCTTGC+AGG + chr8_2:61008775-61008794 Msa1259380:intron 35.0%
! TCACTAGTTTAGAATGCGTT+GGG + chr8_2:61008822-61008841 Msa1259380:intron 35.0%
! ATCAGGGGTCATGTATTTTA+TGG - chr8_2:61009045-61009064 None:intergenic 35.0%
! GAAATAGTGGAAATCATCAG+GGG - chr8_2:61009060-61009079 None:intergenic 35.0%
TGAAGAAGAAATTGACGACA+TGG + chr8_2:61009312-61009331 Msa1259380:CDS 35.0%
! TGATTAGTTCAATTCAACCG+TGG + chr8_2:61009401-61009420 Msa1259380:intron 35.0%
! GATTAGTTCAATTCAACCGT+GGG + chr8_2:61009402-61009421 Msa1259380:intron 35.0%
TCAAATTAAAGACATGCCCA+CGG - chr8_2:61009421-61009440 None:intergenic 35.0%
!! TTGTATTTATCGGCTTTGGT+TGG - chr8_2:61009612-61009631 None:intergenic 35.0%
AAAGAAGAATAATACCCCTG+GGG - chr8_2:61009696-61009715 None:intergenic 35.0%
GAAAGAAGAATAATACCCCT+GGG - chr8_2:61009697-61009716 None:intergenic 35.0%
AGAAAGAAGAATAATACCCC+TGG - chr8_2:61009698-61009717 None:intergenic 35.0%
!! GCTTGATTATTGATTCATGC+AGG + chr8_2:61009801-61009820 Msa1259380:intron 35.0%
!! TGATTATTGATTCATGCAGG+AGG + chr8_2:61009804-61009823 Msa1259380:intron 35.0%
GCAAATGATGATTCTGTTTG+TGG + chr8_2:61009906-61009925 Msa1259380:CDS 35.0%
AATGATGATTCTGTTTGTGG+TGG + chr8_2:61009909-61009928 Msa1259380:CDS 35.0%
GAACCGAAATCAGCAGATTA+TGG + chr8_2:61008739-61008758 Msa1259380:CDS 40.0%
! GTCACTAGTTTAGAATGCGT+TGG + chr8_2:61008821-61008840 Msa1259380:intron 40.0%
ACGACATGGACATTTCAAAC+TGG + chr8_2:61009326-61009345 Msa1259380:CDS 40.0%
TTGATTCATGCAGGAGGAAA+AGG + chr8_2:61009810-61009829 Msa1259380:intron 40.0%
AGGAAAAGGCAAAGAATCTG+AGG + chr8_2:61009824-61009843 Msa1259380:CDS 40.0%
ATCTGAGGACATTTCAACCT+TGG + chr8_2:61009839-61009858 Msa1259380:CDS 40.0%
GAACCGAAATCAGCAGATTA+TGG + chr8_2:61008739-61008758 Msa1259380:CDS 40.0%
! GTCACTAGTTTAGAATGCGT+TGG + chr8_2:61008821-61008840 Msa1259380:intron 40.0%
ACGACATGGACATTTCAAAC+TGG + chr8_2:61009326-61009345 Msa1259380:CDS 40.0%
TTGATTCATGCAGGAGGAAA+AGG + chr8_2:61009810-61009829 Msa1259380:intron 40.0%
AGGAAAAGGCAAAGAATCTG+AGG + chr8_2:61009824-61009843 Msa1259380:CDS 40.0%
ATCTGAGGACATTTCAACCT+TGG + chr8_2:61009839-61009858 Msa1259380:CDS 40.0%
TGACGCAGAAGAAGAATCTG+AGG + chr8_2:61008657-61008676 Msa1259380:CDS 45.0%
! CATGAGCTCTGATAAACTGG+CGG + chr8_2:61008714-61008733 Msa1259380:CDS 45.0%
AAGAGGACAGCTATGATGAG+CGG + chr8_2:61009187-61009206 Msa1259380:CDS 45.0%
TTTCATCCTCCAAGCAATCG+AGG + chr8_2:61009648-61009667 Msa1259380:CDS 45.0%
TGAGGACATTTCAACCTTGG+AGG + chr8_2:61009842-61009861 Msa1259380:CDS 45.0%
TGACGCAGAAGAAGAATCTG+AGG + chr8_2:61008657-61008676 Msa1259380:CDS 45.0%
! CATGAGCTCTGATAAACTGG+CGG + chr8_2:61008714-61008733 Msa1259380:CDS 45.0%
AAGAGGACAGCTATGATGAG+CGG + chr8_2:61009187-61009206 Msa1259380:CDS 45.0%
TTTCATCCTCCAAGCAATCG+AGG + chr8_2:61009648-61009667 Msa1259380:CDS 45.0%
TGAGGACATTTCAACCTTGG+AGG + chr8_2:61009842-61009861 Msa1259380:CDS 45.0%
!! ATTATTATTATTATTATTGA+TGG + chr8_2:61009146-61009165 Msa1259380:intron 5.0%
!! ATTATTATTATTATTATTGA+TGG + chr8_2:61009146-61009165 Msa1259380:intron 5.0%
AGAGGACAGCTATGATGAGC+GGG + chr8_2:61009188-61009207 Msa1259380:CDS 50.0%
GATGAGCGGGAGGAAGAATT+TGG + chr8_2:61009201-61009220 Msa1259380:CDS 50.0%
TCATGGTCTCCTCGATTGCT+TGG - chr8_2:61009660-61009679 None:intergenic 50.0%
GGGGATACGTCGTTTGATCA+TGG - chr8_2:61009677-61009696 None:intergenic 50.0%
TGATCAAACGACGTATCCCC+AGG + chr8_2:61009677-61009696 Msa1259380:CDS 50.0%
GATCAAACGACGTATCCCCA+GGG + chr8_2:61009678-61009697 Msa1259380:CDS 50.0%
ATCAAACGACGTATCCCCAG+GGG + chr8_2:61009679-61009698 Msa1259380:CDS 50.0%
GCTCTTCTGATGTGCAGAAG+TGG + chr8_2:61009871-61009890 Msa1259380:CDS 50.0%
AGAGGACAGCTATGATGAGC+GGG + chr8_2:61009188-61009207 Msa1259380:CDS 50.0%
GATGAGCGGGAGGAAGAATT+TGG + chr8_2:61009201-61009220 Msa1259380:CDS 50.0%
TCATGGTCTCCTCGATTGCT+TGG - chr8_2:61009660-61009679 None:intergenic 50.0%
GGGGATACGTCGTTTGATCA+TGG - chr8_2:61009677-61009696 None:intergenic 50.0%
TGATCAAACGACGTATCCCC+AGG + chr8_2:61009677-61009696 Msa1259380:CDS 50.0%
GATCAAACGACGTATCCCCA+GGG + chr8_2:61009678-61009697 Msa1259380:CDS 50.0%
ATCAAACGACGTATCCCCAG+GGG + chr8_2:61009679-61009698 Msa1259380:CDS 50.0%
GCTCTTCTGATGTGCAGAAG+TGG + chr8_2:61009871-61009890 Msa1259380:CDS 50.0%
! GAGCTCTGATAAACTGGCGG+AGG + chr8_2:61008717-61008736 Msa1259380:CDS 55.0%
TGGTCTCCTCGATTGCTTGG+AGG - chr8_2:61009657-61009676 None:intergenic 55.0%
AGAAGAGCTCAGCTCCTCCA+AGG - chr8_2:61009859-61009878 None:intergenic 55.0%
! GAGCTCTGATAAACTGGCGG+AGG + chr8_2:61008717-61008736 Msa1259380:CDS 55.0%
TGGTCTCCTCGATTGCTTGG+AGG - chr8_2:61009657-61009676 None:intergenic 55.0%
AGAAGAGCTCAGCTCCTCCA+AGG - chr8_2:61009859-61009878 None:intergenic 55.0%
GGACAGCTATGATGAGCGGG+AGG + chr8_2:61009191-61009210 Msa1259380:CDS 60.0%
GGACAGCTATGATGAGCGGG+AGG + chr8_2:61009191-61009210 Msa1259380:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 61008649 61009950 61008649 ID=Msa1259380;Name=Msa1259380
chr8_2 mRNA 61008649 61009950 61008649 ID=Msa1259380-mRNA-1;Parent=Msa1259380;Name=Msa1259380-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0|0|0.83|1|1|6|0|178
chr8_2 exon 61008649 61008775 61008649 ID=Msa1259380-mRNA-1:exon:19183;Parent=Msa1259380-mRNA-1
chr8_2 exon 61009003 61009086 61009003 ID=Msa1259380-mRNA-1:exon:19184;Parent=Msa1259380-mRNA-1
chr8_2 exon 61009175 61009222 61009175 ID=Msa1259380-mRNA-1:exon:19185;Parent=Msa1259380-mRNA-1
chr8_2 exon 61009308 61009358 61009308 ID=Msa1259380-mRNA-1:exon:19186;Parent=Msa1259380-mRNA-1
chr8_2 exon 61009602 61009700 61009602 ID=Msa1259380-mRNA-1:exon:19187;Parent=Msa1259380-mRNA-1
chr8_2 exon 61009823 61009950 61009823 ID=Msa1259380-mRNA-1:exon:19188;Parent=Msa1259380-mRNA-1
chr8_2 CDS 61008649 61008775 61008649 ID=Msa1259380-mRNA-1:cds;Parent=Msa1259380-mRNA-1
chr8_2 CDS 61009003 61009086 61009003 ID=Msa1259380-mRNA-1:cds;Parent=Msa1259380-mRNA-1
chr8_2 CDS 61009175 61009222 61009175 ID=Msa1259380-mRNA-1:cds;Parent=Msa1259380-mRNA-1
chr8_2 CDS 61009308 61009358 61009308 ID=Msa1259380-mRNA-1:cds;Parent=Msa1259380-mRNA-1
chr8_2 CDS 61009602 61009700 61009602 ID=Msa1259380-mRNA-1:cds;Parent=Msa1259380-mRNA-1
chr8_2 CDS 61009823 61009950 61009823 ID=Msa1259380-mRNA-1:cds;Parent=Msa1259380-mRNA-1
Gene Sequence

>Msa1259380

ATGATTATTGACGCAGAAGAAGAATCTGAGGAAATTTCAAAGTCGAAAAAGAGAAAAGACGATTTCATGAGCTCTGATAAACTGGCGGAGGAACCGAAATCAGCAGATTATGGCTTTGATTATGAAATAAAAGGAGAATATTATGTGTTCAAAGACGAATCAAACTCCATAAAATACATGACCCCTGATGATTTCCACTATTTCTACGGAACTAAAACAAAAGAAGAGGACAGCTATGATGAGCGGGAGGAAGAATTTGTTGATGAAGAAGAAATTGACGACATGGACATTTCAAACTGGAAAATCGATGATGAGGACCAACCAAAGCCGATAAATACAAAACTATCAGATGGAGATTTCATCCTCCAAGCAATCGAGGAGACCATGATCAAACGACGTATCCCCAGGGGAGGAAAAGGCAAAGAATCTGAGGACATTTCAACCTTGGAGGAGCTGAGCTCTTCTGATGTGCAGAAGTGGAAATCAGCAGATGCAAATGATGATTCTGTTTGTGGTGGTGATTATGCCTTAGTTTGA

Protein sequence

>Msa1259380

MIIDAEEESEEISKSKKRKDDFMSSDKLAEEPKSADYGFDYEIKGEYYVFKDESNSIKYMTPDDFHYFYGTKTKEEDSYDEREEEFVDEEEIDDMDISNWKIDDEDQPKPINTKLSDGDFILQAIEETMIKRRIPRGGKGKESEDISTLEELSSSDVQKWKSADANDDSVCGGDYALV*