AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0918390


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0918390 MtrunA17_Chr6g0471211 100.000 109 0 0 1 109 1 109 2.28e-63 187
Msa0918390 MtrunA17_Chr1g0203261 87.500 72 9 0 3 74 4 75 2.14e-26 94.0
Msa0918390 MtrunA17_Chr8g0387471 50.704 71 34 1 4 74 3 72 2.94e-17 71.6
Msa0918390 MtrunA17_Chr6g0469651 50.000 70 34 1 3 72 2 70 6.95e-16 68.2
Msa0918390 MtrunA17_Chr7g0233191 48.684 76 38 1 4 79 3 77 8.05e-16 67.4
Msa0918390 MtrunA17_Chr7g0248671 53.731 67 30 1 4 70 3 68 1.35e-15 68.6
Msa0918390 MtrunA17_Chr7g0233201 47.368 76 39 1 4 79 3 77 2.40e-15 66.2
Msa0918390 MtrunA17_Chr7g0233251 50.000 74 36 1 4 77 3 75 2.67e-15 66.2
Msa0918390 MtrunA17_Chr7g0233181 47.368 76 39 1 4 79 3 77 1.31e-14 64.3
Msa0918390 MtrunA17_Chr6g0469541 45.333 75 40 1 4 78 3 76 2.92e-14 63.5
Msa0918390 MtrunA17_Chr7g0233211 46.053 76 40 1 4 79 3 77 3.47e-14 63.2
Msa0918390 MtrunA17_Chr7g0233231 46.053 76 40 1 4 79 3 77 3.62e-14 63.2
Msa0918390 MtrunA17_Chr1g0202561 49.296 71 35 1 4 74 3 72 6.30e-14 63.2
Msa0918390 MtrunA17_Chr6g0469591 49.275 69 34 1 4 72 3 70 8.12e-14 62.8
Msa0918390 MtrunA17_Chr1g0202541 49.296 71 35 1 4 74 3 72 8.43e-14 62.8
Msa0918390 MtrunA17_Chr6g0469571 49.275 69 34 1 4 72 3 70 9.05e-14 62.4
Msa0918390 MtrunA17_Chr6g0469671 46.575 73 38 1 3 75 2 73 1.03e-13 62.0
Msa0918390 MtrunA17_Chr6g0469551 47.826 69 35 1 4 72 3 70 2.03e-13 61.6
Msa0918390 MtrunA17_Chr6g0469681 43.836 73 40 1 3 75 2 73 9.22e-13 60.1
Msa0918390 MtrunA17_Chr1g0202501 49.315 73 36 1 3 75 2 73 2.19e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0918390 AT5G23760.1 86.667 75 10 0 1 75 1 75 4.91e-28 98.6
Msa0918390 AT5G23760.2 84.375 64 10 0 12 75 1 64 1.83e-20 79.0
Msa0918390 AT1G01490.1 52.857 70 31 2 4 72 3 71 1.49e-15 68.6
Msa0918390 AT1G01490.2 52.857 70 31 2 4 72 3 71 1.49e-15 68.6
Msa0918390 AT1G01490.4 50.685 73 34 2 1 72 27 98 1.63e-15 69.3
Msa0918390 AT5G52740.1 48.571 70 33 2 3 72 2 68 8.89e-11 55.1

Find 15 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGCAGAAGGTTGTGTTAA+AGG 0.208879 6_2:+46093469 Msa0918390:intron
GAAAGAAGAGAAGAAATAAA+AGG 0.242019 6_2:+46093894 Msa0918390:exon
GAGCCATTTGAAGAGTTATA+TGG 0.314224 6_2:-46093234 None:intergenic
TACAGAAAGTAAATACTAAA+AGG 0.321970 6_2:-46094068 None:intergenic
GAGCAAAAGTTGACAGTGAT+TGG 0.365516 6_2:+46093700 Msa0918390:CDS
AGAAAAGAAAGAAGAGAAGA+AGG 0.371134 6_2:+46093816 Msa0918390:CDS
GTTGACAGTGATTGGTTCAA+TGG 0.405513 6_2:+46093708 Msa0918390:CDS
AGAGAAGAAAGAAGAGAAGA+AGG 0.411074 6_2:+46093864 Msa0918390:CDS
CCCTTTACCCACTACTATAT+AGG 0.419555 6_2:+46093153 None:intergenic
GAAGCAGCTGCAGATATCTA+TGG 0.439199 6_2:+46093533 Msa0918390:CDS
ACTCCATATAACTCTTCAAA+TGG 0.490526 6_2:+46093231 Msa0918390:exon
GAAGAAAGAAGAGAAGAAGG+AGG 0.516884 6_2:+46093867 Msa0918390:CDS
TATAACTCTTCAAATGGCTC+AGG 0.518462 6_2:+46093237 Msa0918390:exon
AAAGTTGATATTGTATCTGT+TGG 0.520457 6_2:+46093769 Msa0918390:CDS
GAAAACAAGAAATAAAATGA+AGG 0.568256 6_2:-46093206 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTAAATTAAATAGGAT+AGG - chr6_2:46093280-46093299 None:intergenic 10.0%
!!! AATGTTATTTAATAAATCAA+AGG + chr6_2:46093612-46093631 Msa0918390:intron 10.0%
!! ATAATCAATATAGAAAAATA+TGG - chr6_2:46093999-46094018 None:intergenic 10.0%
!! AAAATTAAATTAAATAGGAT+AGG - chr6_2:46093280-46093299 None:intergenic 10.0%
!!! AATGTTATTTAATAAATCAA+AGG + chr6_2:46093612-46093631 Msa0918390:intron 10.0%
!! ATAATCAATATAGAAAAATA+TGG - chr6_2:46093999-46094018 None:intergenic 10.0%
!! CGAACAAAATTAAATTAAAT+AGG - chr6_2:46093285-46093304 None:intergenic 15.0%
!!! ATTTAATTTAATTTTGTTCG+TGG + chr6_2:46093285-46093304 Msa0918390:intron 15.0%
!!! AACTTGTCTATAATTTTTTT+TGG + chr6_2:46094042-46094061 Msa0918390:three_prime_UTR 15.0%
!! CGAACAAAATTAAATTAAAT+AGG - chr6_2:46093285-46093304 None:intergenic 15.0%
!!! ATTTAATTTAATTTTGTTCG+TGG + chr6_2:46093285-46093304 Msa0918390:intron 15.0%
!!! AACTTGTCTATAATTTTTTT+TGG + chr6_2:46094042-46094061 Msa0918390:three_prime_UTR 15.0%
!! GAAAACAAGAAATAAAATGA+AGG - chr6_2:46093209-46093228 None:intergenic 20.0%
!! AGAGAATGGAAAAAAAAAAA+TGG - chr6_2:46093427-46093446 None:intergenic 20.0%
!! TACAGAAAGTAAATACTAAA+AGG - chr6_2:46094071-46094090 None:intergenic 20.0%
!! GAAAACAAGAAATAAAATGA+AGG - chr6_2:46093209-46093228 None:intergenic 20.0%
!! AGAGAATGGAAAAAAAAAAA+TGG - chr6_2:46093427-46093446 None:intergenic 20.0%
!! TACAGAAAGTAAATACTAAA+AGG - chr6_2:46094071-46094090 None:intergenic 20.0%
! ACATATATAGCTAAATCATG+AGG - chr6_2:46093351-46093370 None:intergenic 25.0%
!!! AAAGTTGATATTGTATCTGT+TGG + chr6_2:46093769-46093788 Msa0918390:CDS 25.0%
! AGAGAAAAAAGAAGAGAAAA+AGG + chr6_2:46093840-46093859 Msa0918390:CDS 25.0%
! GAAAGAAGAGAAGAAATAAA+AGG + chr6_2:46093894-46093913 Msa0918390:exon 25.0%
! ACATATATAGCTAAATCATG+AGG - chr6_2:46093351-46093370 None:intergenic 25.0%
!!! AAAGTTGATATTGTATCTGT+TGG + chr6_2:46093769-46093788 Msa0918390:CDS 25.0%
! AGAGAAAAAAGAAGAGAAAA+AGG + chr6_2:46093840-46093859 Msa0918390:CDS 25.0%
! GAAAGAAGAGAAGAAATAAA+AGG + chr6_2:46093894-46093913 Msa0918390:exon 25.0%
ACTCCATATAACTCTTCAAA+TGG + chr6_2:46093231-46093250 Msa0918390:exon 30.0%
AATAGGATAGGATAAGAAAG+AGG - chr6_2:46093268-46093287 None:intergenic 30.0%
ACACAGGAAATCTAATAGAT+TGG - chr6_2:46093324-46093343 None:intergenic 30.0%
TAAATCATGAGGATTTACAC+AGG - chr6_2:46093340-46093359 None:intergenic 30.0%
CCAATGAAAGAATAAGAGAA+TGG - chr6_2:46093441-46093460 None:intergenic 30.0%
CCATTCTCTTATTCTTTCAT+TGG + chr6_2:46093438-46093457 Msa0918390:intron 30.0%
!! TGTTGTGGATTTTGATGTAT+AGG + chr6_2:46093649-46093668 Msa0918390:intron 30.0%
AGAAAAGAAAGAAGAGAAGA+AGG + chr6_2:46093816-46093835 Msa0918390:CDS 30.0%
ACTCCATATAACTCTTCAAA+TGG + chr6_2:46093231-46093250 Msa0918390:exon 30.0%
AATAGGATAGGATAAGAAAG+AGG - chr6_2:46093268-46093287 None:intergenic 30.0%
ACACAGGAAATCTAATAGAT+TGG - chr6_2:46093324-46093343 None:intergenic 30.0%
TAAATCATGAGGATTTACAC+AGG - chr6_2:46093340-46093359 None:intergenic 30.0%
CCAATGAAAGAATAAGAGAA+TGG - chr6_2:46093441-46093460 None:intergenic 30.0%
CCATTCTCTTATTCTTTCAT+TGG + chr6_2:46093438-46093457 Msa0918390:intron 30.0%
!! TGTTGTGGATTTTGATGTAT+AGG + chr6_2:46093649-46093668 Msa0918390:intron 30.0%
AGAAAAGAAAGAAGAGAAGA+AGG + chr6_2:46093816-46093835 Msa0918390:CDS 30.0%
!! AAGGCTAGAGAATTTTGATG+AGG - chr6_2:46093190-46093209 None:intergenic 35.0%
GAGCCATTTGAAGAGTTATA+TGG - chr6_2:46093237-46093256 None:intergenic 35.0%
TATAACTCTTCAAATGGCTC+AGG + chr6_2:46093237-46093256 Msa0918390:exon 35.0%
TTGGATTGATTGAAAGCAGA+AGG + chr6_2:46093457-46093476 Msa0918390:intron 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG + chr6_2:46093469-46093488 Msa0918390:intron 35.0%
GCTGATCTATTGAATTGTTG+TGG + chr6_2:46093634-46093653 Msa0918390:intron 35.0%
GTGAAGAAGCTGAAAAAAGT+AGG + chr6_2:46093745-46093764 Msa0918390:CDS 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG - chr6_2:46093796-46093815 None:intergenic 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG + chr6_2:46093864-46093883 Msa0918390:CDS 35.0%
!! AAGGCTAGAGAATTTTGATG+AGG - chr6_2:46093190-46093209 None:intergenic 35.0%
GAGCCATTTGAAGAGTTATA+TGG - chr6_2:46093237-46093256 None:intergenic 35.0%
TATAACTCTTCAAATGGCTC+AGG + chr6_2:46093237-46093256 Msa0918390:exon 35.0%
TTGGATTGATTGAAAGCAGA+AGG + chr6_2:46093457-46093476 Msa0918390:intron 35.0%
AAAGCAGAAGGTTGTGTTAA+AGG + chr6_2:46093469-46093488 Msa0918390:intron 35.0%
GCTGATCTATTGAATTGTTG+TGG + chr6_2:46093634-46093653 Msa0918390:intron 35.0%
GTGAAGAAGCTGAAAAAAGT+AGG + chr6_2:46093745-46093764 Msa0918390:CDS 35.0%
! TCTTTCTTCTCTTCTTTTGC+AGG - chr6_2:46093796-46093815 None:intergenic 35.0%
AGAGAAGAAAGAAGAGAAGA+AGG + chr6_2:46093864-46093883 Msa0918390:CDS 35.0%
GAGCAAAAGTTGACAGTGAT+TGG + chr6_2:46093700-46093719 Msa0918390:CDS 40.0%
! GTTGACAGTGATTGGTTCAA+TGG + chr6_2:46093708-46093727 Msa0918390:CDS 40.0%
GAAGAAAGAAGAGAAGAAGG+AGG + chr6_2:46093867-46093886 Msa0918390:CDS 40.0%
! ACAAGTTTTGCAGCTTACAC+TGG - chr6_2:46094029-46094048 None:intergenic 40.0%
GAGCAAAAGTTGACAGTGAT+TGG + chr6_2:46093700-46093719 Msa0918390:CDS 40.0%
! GTTGACAGTGATTGGTTCAA+TGG + chr6_2:46093708-46093727 Msa0918390:CDS 40.0%
GAAGAAAGAAGAGAAGAAGG+AGG + chr6_2:46093867-46093886 Msa0918390:CDS 40.0%
! ACAAGTTTTGCAGCTTACAC+TGG - chr6_2:46094029-46094048 None:intergenic 40.0%
GAAGCAGCTGCAGATATCTA+TGG + chr6_2:46093533-46093552 Msa0918390:CDS 45.0%
GAAGCAGCTGCAGATATCTA+TGG + chr6_2:46093533-46093552 Msa0918390:CDS 45.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 46093168 46094116 46093168 ID=Msa0918390;Name=Msa0918390
chr6_2 mRNA 46093168 46094116 46093168 ID=Msa0918390-mRNA-1;Parent=Msa0918390;Name=Msa0918390-mRNA-1;_AED=0.15;_eAED=0.15;_QI=82|1|1|1|1|1|3|204|109
chr6_2 exon 46093168 46093258 46093168 ID=Msa0918390-mRNA-1:exon:7184;Parent=Msa0918390-mRNA-1
chr6_2 exon 46093476 46093554 46093476 ID=Msa0918390-mRNA-1:exon:7185;Parent=Msa0918390-mRNA-1
chr6_2 exon 46093671 46094116 46093671 ID=Msa0918390-mRNA-1:exon:7186;Parent=Msa0918390-mRNA-1
chr6_2 five_prime_UTR 46093168 46093249 46093168 ID=Msa0918390-mRNA-1:five_prime_utr;Parent=Msa0918390-mRNA-1
chr6_2 CDS 46093250 46093258 46093250 ID=Msa0918390-mRNA-1:cds;Parent=Msa0918390-mRNA-1
chr6_2 CDS 46093476 46093554 46093476 ID=Msa0918390-mRNA-1:cds;Parent=Msa0918390-mRNA-1
chr6_2 CDS 46093671 46093912 46093671 ID=Msa0918390-mRNA-1:cds;Parent=Msa0918390-mRNA-1
chr6_2 three_prime_UTR 46093913 46094116 46093913 ID=Msa0918390-mRNA-1:three_prime_utr;Parent=Msa0918390-mRNA-1
Gene Sequence

>Msa0918390

ATGGCTCAGAAGGTTGTGTTAAAGGTGTTAACTATGACTGATGACAAAACAAAGCAAAAAGCTATAGAAGCAGCTGCAGATATCTATGGTGTTGATTCAATTGTAGCAGATGTAAAAGAGCAAAAGTTGACAGTGATTGGTTCAATGGATACAGTGAAAATTGTGAAGAAGCTGAAAAAAGTAGGAAAAGTTGATATTGTATCTGTTGGTCCTGCAAAAGAAGAGAAGAAAGAAGAAAAGAAAGAAGAGAAGAAGGAAGAGAAAAAAGAAGAGAAAAAGGAAGAGAAGAAAGAAGAGAAGAAGGAGGAAAAGAAAGAAGAGAAGAAATAA

Protein sequence

>Msa0918390

MAQKVVLKVLTMTDDKTKQKAIEAAADIYGVDSIVADVKEQKLTVIGSMDTVKIVKKLKKVGKVDIVSVGPAKEEKKEEKKEEKKEEKKEEKKEEKKEEKKEEKKEEKK*