AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0898670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0898670 MtrunA17_Chr6g0484301 93.443 61 4 0 1 61 623 683 4.13e-34 121
Msa0898670 MtrunA17_Chr1g0212431 49.296 71 36 0 1 71 664 734 3.13e-17 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0898670 AT1G48840.1 56.522 69 30 0 2 70 621 689 8.56e-21 84.3
Msa0898670 AT3G18350.3 57.143 63 27 0 2 64 622 684 4.05e-19 79.7
Msa0898670 AT3G18350.1 57.143 63 27 0 2 64 622 684 4.05e-19 79.7
Msa0898670 AT3G18350.2 57.143 63 27 0 2 64 622 684 4.05e-19 79.7
Msa0898670 AT5G23390.1 55.556 54 24 0 18 71 676 729 1.13e-12 61.2

Find 21 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGATGGGAAAGGAGATTT+AGG 0.206881 6_1:+93116606 Msa0898670:CDS
TTATCTCTTTCAAGTTTAAC+AGG 0.295578 6_1:-93116656 None:intergenic
TCTATCAGCAGGATTGGTTT+TGG 0.305817 6_1:+93116499 Msa0898670:CDS
ACCTCCTAGGAAAGCTAGCC+CGG 0.419218 6_1:+93116583 Msa0898670:CDS
GAGATGGGAAAGGAGATTTA+GGG 0.437744 6_1:+93116607 Msa0898670:CDS
TGGTCTTCTATCAGCAGGAT+TGG 0.442451 6_1:+93116493 Msa0898670:CDS
GGAAAGCTAGCCCGGAGAGA+TGG 0.469553 6_1:+93116591 Msa0898670:CDS
AATCTCCTTTCCCATCTCTC+CGG 0.472573 6_1:-93116602 None:intergenic
GAAAGCTAGCCCGGAGAGAT+GGG 0.495678 6_1:+93116592 Msa0898670:CDS
TCAAGTTTAACAGGAGCAGC+TGG 0.495682 6_1:-93116647 None:intergenic
AGAAGAACTAGGTATTTAGT+AGG 0.496508 6_1:-93116530 None:intergenic
TAAACTTGAAAGAGATAAAG+AGG 0.498380 6_1:+93116661 Msa0898670:CDS
ATCTCCTTTCCCATCTCTCC+GGG 0.499030 6_1:-93116601 None:intergenic
GCACTTGGTCTTCTATCAGC+AGG 0.502073 6_1:+93116488 Msa0898670:CDS
CTCTCCGGGCTAGCTTTCCT+AGG 0.503547 6_1:-93116587 None:intergenic
TTACAATGTATTCACCTCCT+AGG 0.511457 6_1:+93116570 Msa0898670:CDS
GGGAAAGGAGATTTAGGGAA+TGG 0.584698 6_1:+93116612 Msa0898670:CDS
TCAAGAACACTAGAAGAACT+AGG 0.597331 6_1:-93116541 None:intergenic
AAAGGAGATTTAGGGAATGG+TGG 0.611191 6_1:+93116615 Msa0898670:CDS
GCTACAGAGAAGATGGCACT+TGG 0.618726 6_1:+93116473 None:intergenic
CTAGCCCGGAGAGATGGGAA+AGG 0.646632 6_1:+93116597 Msa0898670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATCTCTTTCAAGTTTAAC+AGG - chr6_1:93116659-93116678 None:intergenic 25.0%
! TAAACTTGAAAGAGATAAAG+AGG + chr6_1:93116661-93116680 Msa0898670:CDS 25.0%
AGAAGAACTAGGTATTTAGT+AGG - chr6_1:93116533-93116552 None:intergenic 30.0%
TCAAGAACACTAGAAGAACT+AGG - chr6_1:93116544-93116563 None:intergenic 35.0%
TTACAATGTATTCACCTCCT+AGG + chr6_1:93116570-93116589 Msa0898670:CDS 35.0%
!!! TCTATCAGCAGGATTGGTTT+TGG + chr6_1:93116499-93116518 Msa0898670:CDS 40.0%
AGAGATGGGAAAGGAGATTT+AGG + chr6_1:93116606-93116625 Msa0898670:CDS 40.0%
GAGATGGGAAAGGAGATTTA+GGG + chr6_1:93116607-93116626 Msa0898670:CDS 40.0%
AAAGGAGATTTAGGGAATGG+TGG + chr6_1:93116615-93116634 Msa0898670:CDS 40.0%
TGGTCTTCTATCAGCAGGAT+TGG + chr6_1:93116493-93116512 Msa0898670:CDS 45.0%
AATCTCCTTTCCCATCTCTC+CGG - chr6_1:93116605-93116624 None:intergenic 45.0%
GGGAAAGGAGATTTAGGGAA+TGG + chr6_1:93116612-93116631 Msa0898670:CDS 45.0%
TCAAGTTTAACAGGAGCAGC+TGG - chr6_1:93116650-93116669 None:intergenic 45.0%
! GCACTTGGTCTTCTATCAGC+AGG + chr6_1:93116488-93116507 Msa0898670:CDS 50.0%
ATCTCCTTTCCCATCTCTCC+GGG - chr6_1:93116604-93116623 None:intergenic 50.0%
ACCTCCTAGGAAAGCTAGCC+CGG + chr6_1:93116583-93116602 Msa0898670:CDS 55.0%
GAAAGCTAGCCCGGAGAGAT+GGG + chr6_1:93116592-93116611 Msa0898670:CDS 55.0%
!! TCCGGGCTAGCTTTCCTAGG+AGG - chr6_1:93116587-93116606 None:intergenic 60.0%
!! CTCTCCGGGCTAGCTTTCCT+AGG - chr6_1:93116590-93116609 None:intergenic 60.0%
GGAAAGCTAGCCCGGAGAGA+TGG + chr6_1:93116591-93116610 Msa0898670:CDS 60.0%
CTAGCCCGGAGAGATGGGAA+AGG + chr6_1:93116597-93116616 Msa0898670:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 93116485 93116700 93116485 ID=Msa0898670;Name=Msa0898670
chr6_1 mRNA 93116485 93116700 93116485 ID=Msa0898670-mRNA-1;Parent=Msa0898670;Name=Msa0898670-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|71
chr6_1 exon 93116485 93116700 93116485 ID=Msa0898670-mRNA-1:exon:15727;Parent=Msa0898670-mRNA-1
chr6_1 CDS 93116485 93116700 93116485 ID=Msa0898670-mRNA-1:cds;Parent=Msa0898670-mRNA-1
Gene Sequence

>Msa0898670

ATGGCACTTGGTCTTCTATCAGCAGGATTGGTTTTGGCTTTCTTACCTACTAAATACCTAGTTCTTCTAGTGTTCTTGAACACATTTACAATGTATTCACCTCCTAGGAAAGCTAGCCCGGAGAGATGGGAAAGGAGATTTAGGGAATGGTGGTTCAGCATACCAGCTGCTCCTGTTAAACTTGAAAGAGATAAAGAGGACAAGAAGAAAAAGTGA

Protein sequence

>Msa0898670

MALGLLSAGLVLAFLPTKYLVLLVFLNTFTMYSPPRKASPERWERRFREWWFSIPAAPVKLERDKEDKKKK*