AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0759670

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0759670 MtrunA17_Chr1g0163091 57.000 100 42 1 22 120 1 100 1.68e-32 114
Msa0759670 MtrunA17_Chr1g0162151 60.000 100 39 1 22 120 1 100 4.92e-28 104
Msa0759670 MtrunA17_Chr1g0163181 36.290 124 72 3 14 135 172 290 4.17e-17 77.8
Msa0759670 MtrunA17_Chr1g0163201 36.697 109 66 2 15 120 158 266 2.89e-16 75.5
Msa0759670 MtrunA17_Chr1g0163251 34.307 137 72 2 15 133 155 291 4.13e-15 72.0
Msa0759670 MtrunA17_Chr1g0163231 40.741 108 56 4 18 120 156 260 2.98e-14 68.9
Msa0759670 MtrunA17_Chr1g0163261 34.426 122 71 4 6 120 145 264 4.19e-13 65.9
Msa0759670 MtrunA17_Chr1g0163151 40.741 81 47 1 41 120 15 95 1.35e-12 63.5
Msa0759670 MtrunA17_Chr1g0163111 39.506 81 48 1 41 120 12 92 2.04e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGTGAATGAAAATAATT+TGG 0.165152 5_2:+15423743 Msa0759670:CDS
AAAATGTGGATTCTCATTAT+TGG 0.208624 5_2:-15423535 None:intergenic
GACATATTTGTAAGTTTAAG+AGG 0.329147 5_2:+15423774 Msa0759670:CDS
TTTGTGAATGAAAATAATTT+GGG 0.371770 5_2:+15423744 Msa0759670:CDS
TTGATGAGACCGCAATGTTA+AGG 0.388649 5_2:+15423637 Msa0759670:CDS
GACAATATTGATTATGTCTC+AGG 0.404078 5_2:+15423444 Msa0759670:CDS
GACGTCAAATGAAAGCGGTT+TGG 0.425075 5_2:-15423804 None:intergenic
TGATGAGACCGCAATGTTAA+GGG 0.427460 5_2:+15423638 Msa0759670:CDS
ACAACAGAAGTGCCAACAAC+AGG 0.485674 5_2:-15423881 None:intergenic
GGGTTACCGCGGATAGAACT+TGG 0.487538 5_2:+15423658 Msa0759670:CDS
GTCAATTTAAATTCAAAATG+TGG 0.501305 5_2:-15423549 None:intergenic
CAAGGAAGACCTCCTGTTGT+TGG 0.509382 5_2:+15423869 Msa0759670:CDS
GGTCTTCCTTGCGACTTGCT+AGG 0.516614 5_2:-15423857 None:intergenic
CCTTGCGACTTGCTAGGACG+TGG 0.537594 5_2:-15423851 None:intergenic
GTCTCAGGTACTAACAAAAG+AGG 0.544808 5_2:+15423459 Msa0759670:CDS
GAGTTAGGATGCAAAAGAAA+CGG 0.563358 5_2:-15423587 None:intergenic
AGACGTTCTGTTGTGTACAC+TGG 0.626699 5_2:+15423711 Msa0759670:CDS
CGCGGTAACCCTTAACATTG+CGG 0.643043 5_2:-15423646 None:intergenic
ATAGAGACGTCAAATGAAAG+CGG 0.647337 5_2:-15423809 None:intergenic
ACAGAAGTGCCAACAACAGG+AGG 0.647911 5_2:-15423878 None:intergenic
CGCAATGTTAAGGGTTACCG+CGG 0.649941 5_2:+15423647 Msa0759670:CDS
CCACGTCCTAGCAAGTCGCA+AGG 0.653799 5_2:+15423851 Msa0759670:CDS
TAGGATGCAAAAGAAACGGT+CGG 0.670186 5_2:-15423583 None:intergenic
CATATTCCAAGTTCTATCCG+CGG 0.674605 5_2:-15423664 None:intergenic
GTTCTGTTGTGTACACTGGT+TGG 0.678655 5_2:+15423715 Msa0759670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTGTGAATGAAAATAATT+TGG + chr5_2:15423743-15423762 Msa0759670:CDS 15.0%
!! TTTGTGAATGAAAATAATTT+GGG + chr5_2:15423744-15423763 Msa0759670:CDS 15.0%
!! GTCAATTTAAATTCAAAATG+TGG - chr5_2:15423552-15423571 None:intergenic 20.0%
!!! TTTTGACAATGTTAAAAAGA+AGG + chr5_2:15423917-15423936 Msa0759670:CDS 20.0%
! AAAATGTGGATTCTCATTAT+TGG - chr5_2:15423538-15423557 None:intergenic 25.0%
! ATTCTCTTGAAAAATGAGTT+AGG - chr5_2:15423605-15423624 None:intergenic 25.0%
! GACATATTTGTAAGTTTAAG+AGG + chr5_2:15423774-15423793 Msa0759670:CDS 25.0%
! CAATGTTAAAAAGAAGGTAA+AGG + chr5_2:15423923-15423942 Msa0759670:CDS 25.0%
! GACAATATTGATTATGTCTC+AGG + chr5_2:15423444-15423463 Msa0759670:CDS 30.0%
GAGTTAGGATGCAAAAGAAA+CGG - chr5_2:15423590-15423609 None:intergenic 35.0%
ATAGAGACGTCAAATGAAAG+CGG - chr5_2:15423812-15423831 None:intergenic 35.0%
GTCTCAGGTACTAACAAAAG+AGG + chr5_2:15423459-15423478 Msa0759670:CDS 40.0%
TAGGATGCAAAAGAAACGGT+CGG - chr5_2:15423586-15423605 None:intergenic 40.0%
TTGATGAGACCGCAATGTTA+AGG + chr5_2:15423637-15423656 Msa0759670:CDS 40.0%
TGATGAGACCGCAATGTTAA+GGG + chr5_2:15423638-15423657 Msa0759670:CDS 40.0%
CATATTCCAAGTTCTATCCG+CGG - chr5_2:15423667-15423686 None:intergenic 40.0%
AGACGTTCTGTTGTGTACAC+TGG + chr5_2:15423711-15423730 Msa0759670:CDS 45.0%
GTTCTGTTGTGTACACTGGT+TGG + chr5_2:15423715-15423734 Msa0759670:CDS 45.0%
GACGTCAAATGAAAGCGGTT+TGG - chr5_2:15423807-15423826 None:intergenic 45.0%
!! ACAACAGAAGTGCCAACAAC+AGG - chr5_2:15423884-15423903 None:intergenic 45.0%
CGCGGTAACCCTTAACATTG+CGG - chr5_2:15423649-15423668 None:intergenic 50.0%
CGCAATGTTAAGGGTTACCG+CGG + chr5_2:15423647-15423666 Msa0759670:CDS 50.0%
CAAGGAAGACCTCCTGTTGT+TGG + chr5_2:15423869-15423888 Msa0759670:CDS 50.0%
!! ACAGAAGTGCCAACAACAGG+AGG - chr5_2:15423881-15423900 None:intergenic 50.0%
GGGTTACCGCGGATAGAACT+TGG + chr5_2:15423658-15423677 Msa0759670:CDS 55.0%
! GGTCTTCCTTGCGACTTGCT+AGG - chr5_2:15423860-15423879 None:intergenic 55.0%
!! CCTTGCGACTTGCTAGGACG+TGG - chr5_2:15423854-15423873 None:intergenic 60.0%
CCACGTCCTAGCAAGTCGCA+AGG + chr5_2:15423851-15423870 Msa0759670:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 15423420 15423953 15423420 ID=Msa0759670;Name=Msa0759670
chr5_2 mRNA 15423420 15423953 15423420 ID=Msa0759670-mRNA-1;Parent=Msa0759670;Name=Msa0759670-mRNA-1;_AED=0.23;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|177
chr5_2 exon 15423420 15423953 15423420 ID=Msa0759670-mRNA-1:exon:6999;Parent=Msa0759670-mRNA-1
chr5_2 CDS 15423420 15423953 15423420 ID=Msa0759670-mRNA-1:cds;Parent=Msa0759670-mRNA-1
Gene Sequence

>Msa0759670

ATGAATTGTAAACAAGATGAGAATGACAATATTGATTATGTCTCAGGTACTAACAAAAGAGGCATGACGAAAAAGACTAAGAGATGTTCAATAATTGCAACTGCTAATGTAAAATCCAATAATGAGAATCCACATTTTGAATTTAAATTGACACAAACTTACGCCGACCGTTTCTTTTGCATCCTAACTCATTTTTCAAGAGAATACTTGAATGAGTTTGATGAGACCGCAATGTTAAGGGTTACCGCGGATAGAACTTGGAATATGACTGTGAAGTTTGATTATTATCAAAGACGTTCTGTTGTGTACACTGGTTGGAAGTTATTTGTGAATGAAAATAATTTGGGAGTTGATGACATATTTGTAAGTTTAAGAGGAACAAATCCAAACCGCTTTCATTTGACGTCTCTATTTCTCGAGCTAGAGATGAACCACGTCCTAGCAAGTCGCAAGGAAGACCTCCTGTTGTTGGCACTTCTGTTGTTACTAGTTTTGAGTTTTGACAATGTTAAAAAGAAGGTAAAGGTTACATAA
Protein sequence

>Msa0759670

MNCKQDENDNIDYVSGTNKRGMTKKTKRCSIIATANVKSNNENPHFEFKLTQTYADRFFCILTHFSREYLNEFDETAMLRVTADRTWNMTVKFDYYQRRSVVYTGWKLFVNENNLGVDDIFVSLRGTNPNRFHLTSLFLELEMNHVLASRKEDLLLLALLLLLVLSFDNVKKKVKVT*