AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0739260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0739260 MtrunA17_Chr3g0133461 40.722 194 66 4 1 145 1096 1289 3.57e-32 120
Msa0739260 MtrunA17_Chr5g0438991 49.660 147 64 2 2 145 781 920 1.56e-31 118
Msa0739260 MtrunA17_Chr3g0138411 42.703 185 65 5 2 145 968 1152 4.99e-31 116
Msa0739260 MtrunA17_Chr6g0456861 47.097 155 58 7 2 145 584 725 5.03e-25 99.8
Msa0739260 MtrunA17_Chr5g0401991 38.211 123 62 4 1 117 106 220 1.36e-12 62.8
Msa0739260 MtrunA17_Chr6g0456851 77.778 36 8 0 1 36 819 854 7.14e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGATTCAACTTGTGTTGA+TGG 0.297810 5_1:+57414905 None:intergenic
ATGCAAAATTCGAGTGAATT+GGG 0.338777 5_1:-57414638 Msa0739260:CDS
AATGCAAAATTCGAGTGAAT+TGG 0.339185 5_1:-57414639 Msa0739260:CDS
CGTGGCGGGAAATGATTCTT+CGG 0.388636 5_1:+57415040 None:intergenic
TAATTGTTGTCCAGAATATA+AGG 0.425089 5_1:-57414944 Msa0739260:intron
ATCTCAATGCCGCGCAACTA+AGG 0.439497 5_1:-57414722 Msa0739260:CDS
GTGGCGGGAAATGATTCTTC+GGG 0.461758 5_1:+57415041 None:intergenic
ATCATATTGTTGATTGTTGA+AGG 0.465768 5_1:+57415117 None:intergenic
TGAGGAATACTTGGCGTGGC+GGG 0.467670 5_1:+57415026 None:intergenic
TAGTATTCTTTAGATGATAG+AGG 0.468348 5_1:+57414995 None:intergenic
CATATTGTTGATTGTTGAAG+GGG 0.483680 5_1:+57415119 None:intergenic
AACTGTGTTCTTACCAGCAC+CGG 0.522248 5_1:+57414865 None:intergenic
TCATATTGTTGATTGTTGAA+GGG 0.530915 5_1:+57415118 None:intergenic
TTTCAAATAATGCATTCTCA+AGG 0.532999 5_1:+57415089 None:intergenic
GATCATCATTGAGGAATACT+TGG 0.535043 5_1:+57415017 None:intergenic
TGCAAAATTCGAGTGAATTG+GGG 0.567604 5_1:-57414637 Msa0739260:CDS
ATGGTTCAGCCTTAGTTGCG+CGG 0.575355 5_1:+57414713 None:intergenic
ATGATAGAGGATCATCATTG+AGG 0.612365 5_1:+57415008 None:intergenic
GAACAGTATGGACGAGAGCA+TGG 0.616911 5_1:+57414694 None:intergenic
TTGAGGAATACTTGGCGTGG+CGG 0.621925 5_1:+57415025 None:intergenic
TCATTGAGGAATACTTGGCG+TGG 0.692050 5_1:+57415022 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTCATTAATTGTTTGCTA+CGG - chr5_1:57414924-57414943 Msa0739260:CDS 20.0%
!! TCATATTGTTGATTGTTGAA+GGG + chr5_1:57414633-57414652 None:intergenic 25.0%
!! ATCATATTGTTGATTGTTGA+AGG + chr5_1:57414634-57414653 None:intergenic 25.0%
! TTTCAAATAATGCATTCTCA+AGG + chr5_1:57414662-57414681 None:intergenic 25.0%
! TAGTATTCTTTAGATGATAG+AGG + chr5_1:57414756-57414775 None:intergenic 25.0%
! TAATTGTTGTCCAGAATATA+AGG - chr5_1:57414804-57414823 Msa0739260:intron 25.0%
!!! TTTTTGATTTGAGAACAGTA+TGG + chr5_1:57415069-57415088 None:intergenic 25.0%
! CATATTGTTGATTGTTGAAG+GGG + chr5_1:57414632-57414651 None:intergenic 30.0%
AGACGAGTTAAATCAAAAAC+CGG - chr5_1:57414864-57414883 Msa0739260:CDS 30.0%
AATGCAAAATTCGAGTGAAT+TGG - chr5_1:57415109-57415128 Msa0739260:CDS 30.0%
ATGCAAAATTCGAGTGAATT+GGG - chr5_1:57415110-57415129 Msa0739260:CDS 30.0%
GATCATCATTGAGGAATACT+TGG + chr5_1:57414734-57414753 None:intergenic 35.0%
ATGATAGAGGATCATCATTG+AGG + chr5_1:57414743-57414762 None:intergenic 35.0%
GTATCTCTCTCCTTATATTC+TGG + chr5_1:57414817-57414836 None:intergenic 35.0%
CTTGATTCAACTTGTGTTGA+TGG + chr5_1:57414846-57414865 None:intergenic 35.0%
TTATATTCCCTACACACAGA+TGG - chr5_1:57414976-57414995 Msa0739260:intron 35.0%
TGCAAAATTCGAGTGAATTG+GGG - chr5_1:57415111-57415130 Msa0739260:CDS 35.0%
GTTAAATCAAAAACCGGTGC+TGG - chr5_1:57414870-57414889 Msa0739260:CDS 40.0%
TCATTGAGGAATACTTGGCG+TGG + chr5_1:57414729-57414748 None:intergenic 45.0%
AACTGTGTTCTTACCAGCAC+CGG + chr5_1:57414886-57414905 None:intergenic 45.0%
CAGTTCACCATCTGTGTGTA+GGG + chr5_1:57414986-57415005 None:intergenic 45.0%
! GTGGCGGGAAATGATTCTTC+GGG + chr5_1:57414710-57414729 None:intergenic 50.0%
! CGTGGCGGGAAATGATTCTT+CGG + chr5_1:57414711-57414730 None:intergenic 50.0%
TTGAGGAATACTTGGCGTGG+CGG + chr5_1:57414726-57414745 None:intergenic 50.0%
GCAGTTCACCATCTGTGTGT+AGG + chr5_1:57414987-57415006 None:intergenic 50.0%
ATCTCAATGCCGCGCAACTA+AGG - chr5_1:57415026-57415045 Msa0739260:CDS 50.0%
ATGGTTCAGCCTTAGTTGCG+CGG + chr5_1:57415038-57415057 None:intergenic 50.0%
GAACAGTATGGACGAGAGCA+TGG + chr5_1:57415057-57415076 None:intergenic 50.0%
TGAGGAATACTTGGCGTGGC+GGG + chr5_1:57414725-57414744 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 57414615 57415155 57414615 ID=Msa0739260;Name=Msa0739260
chr5_1 mRNA 57414615 57415155 57414615 ID=Msa0739260-mRNA-1;Parent=Msa0739260;Name=Msa0739260-mRNA-1;_AED=0.46;_eAED=0.54;_QI=0|0|0|1|0|0|3|0|146
chr5_1 exon 57414984 57415155 57414984 ID=Msa0739260-mRNA-1:exon:16347;Parent=Msa0739260-mRNA-1
chr5_1 exon 57414848 57414952 57414848 ID=Msa0739260-mRNA-1:exon:16346;Parent=Msa0739260-mRNA-1
chr5_1 exon 57414615 57414775 57414615 ID=Msa0739260-mRNA-1:exon:16345;Parent=Msa0739260-mRNA-1
chr5_1 CDS 57414984 57415155 57414984 ID=Msa0739260-mRNA-1:cds;Parent=Msa0739260-mRNA-1
chr5_1 CDS 57414848 57414952 57414848 ID=Msa0739260-mRNA-1:cds;Parent=Msa0739260-mRNA-1
chr5_1 CDS 57414615 57414775 57414615 ID=Msa0739260-mRNA-1:cds;Parent=Msa0739260-mRNA-1
Gene Sequence

>Msa0739260

TTTGTGATTGATATCCCCTTCAACAATCAACAATATGATATCATCCTTGAGAATGCATTATTTGAAAATAGAAATAACTTTCTGAGCTTCTGCCCGAAGAATCATTTCCCGCCACGCCAAGTATTCCTCAATGATGATCCTCTATCATCTAAAGAATACTATTCTGCAGACAAATATAAGGAGAGAGATACTGATTGCCATCAACACAAGTTGAATCAAGACGAGTTAAATCAAAAACCGGTGCTGGTAAGAACACAGTTATCTCTCGAGCTTTATAATGGTGAACTGCTGAACATTTTGAAGCATGCATCTCAATGCCGCGCAACTAAGGCTGAACCATGCTCTCGTCCATACTGTTCTCAAATCAAAAAGTTGTTCTCTCATGCTAGTAAATGCAAAATTCGAGTGAATTGGGGCTGCCAGCACCGAAAAAGATAC
Protein sequence

>Msa0739260

FVIDIPFNNQQYDIILENALFENRNNFLSFCPKNHFPPRQVFLNDDPLSSKEYYSADKYKERDTDCHQHKLNQDELNQKPVLVRTQLSLELYNGELLNILKHASQCRATKAEPCSRPYCSQIKKLFSHASKCKIRVNWGCQHRKRY