AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0744020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0744020 MtrunA17_Chr5g0447061 58.537 123 49 2 1 122 1 122 2.30e-49 153
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTATATTCCTTCTTGCTTC+TGG 0.212854 5_1:-64690535 None:intergenic
ATCAAGGAGGAGTTGGAAAT+TGG 0.290061 5_1:+64690422 Msa0744020:CDS
TTTGTTCCACCACAAAATTA+TGG 0.333981 5_1:+64690604 Msa0744020:CDS
TTTCTTTAGGCTATTACTCA+TGG 0.421485 5_1:+64690899 Msa0744020:intron
AAGAACCTGTGGTTTGTCTC+AGG 0.425780 5_1:-64690493 None:intergenic
CACCACAAAATTATGGAGCT+TGG 0.430852 5_1:+64690611 Msa0744020:CDS
TGTTGGTGCGGTAACGGTCT+CGG 0.455039 5_1:-64690995 None:intergenic
AATCACCAGGGAGCTCTTCA+AGG 0.457956 5_1:-64690573 None:intergenic
TTCTTTAGGCTATTACTCAT+GGG 0.494106 5_1:+64690900 Msa0744020:intron
CATATCTGTTGGTGCGGTAA+CGG 0.499015 5_1:-64691001 None:intergenic
ATGGCAAATCAAGGAGGAGT+TGG 0.501152 5_1:+64690415 Msa0744020:CDS
CTGAAACTCTCAAGAACCTG+TGG 0.518744 5_1:-64690504 None:intergenic
CTAGAGAGATTGTGTTGACG+AGG 0.558612 5_1:+64690958 Msa0744020:CDS
ACAAATTGCTCGAAATCACC+AGG 0.563161 5_1:-64690586 None:intergenic
AACCTGTGGTTTGTCTCAGG+TGG 0.578043 5_1:-64690490 None:intergenic
ACCGCACCAACAGATATGCT+TGG 0.580278 5_1:+64691006 Msa0744020:CDS
CACTACCTTGAAGAGCTCCC+TGG 0.582630 5_1:+64690568 Msa0744020:CDS
GTTCATCCAAGCATATCTGT+TGG 0.609345 5_1:-64691012 None:intergenic
TCCAAGCATATCTGTTGGTG+CGG 0.624491 5_1:-64691007 None:intergenic
TTTACGGCCGAAAATGGACG+CGG 0.649194 5_1:+64690931 Msa0744020:CDS
TGGAGCTTGGAGTAATGATG+AGG 0.655946 5_1:+64690624 Msa0744020:CDS
TTCCACCTGAGACAAACCAC+AGG 0.670730 5_1:+64690488 Msa0744020:CDS
TTCACAATGGCAAATCAAGG+AGG 0.686222 5_1:+64690409 None:intergenic
CAAATTGCTCGAAATCACCA+GGG 0.727892 5_1:-64690585 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTAATGAAAAATAACA+TGG - chr5_1:64690765-64690784 None:intergenic 10.0%
!!! AACATATTTTAATCAAGAAA+AGG - chr5_1:64690742-64690761 None:intergenic 15.0%
!!! TAATGTTTTCTATTTTCTTT+AGG + chr5_1:64690886-64690905 Msa0744020:intron 15.0%
!!! TCTTTGGTTTTTTTTTTTGA+AGG + chr5_1:64690687-64690706 Msa0744020:intron 20.0%
!!! AACATGTTTTAATCAAGAAA+AGG - chr5_1:64690843-64690862 None:intergenic 20.0%
! TCATTAAAACATGTGTTCTT+TGG + chr5_1:64690671-64690690 Msa0744020:intron 25.0%
! TCATTAAAATATGCGTTCTT+TGG + chr5_1:64690774-64690793 Msa0744020:intron 25.0%
! AAATTTTTCCAGAAGCAAGA+AGG + chr5_1:64690527-64690546 Msa0744020:CDS 30.0%
TTTGTTCCACCACAAAATTA+TGG + chr5_1:64690604-64690623 Msa0744020:CDS 30.0%
TTTCTTTAGGCTATTACTCA+TGG + chr5_1:64690899-64690918 Msa0744020:intron 30.0%
TTCTTTAGGCTATTACTCAT+GGG + chr5_1:64690900-64690919 Msa0744020:intron 30.0%
GTTATATTCCTTCTTGCTTC+TGG - chr5_1:64690538-64690557 None:intergenic 35.0%
!!! GTTCTTTGGTTTTTTGTCGA+AGG + chr5_1:64690788-64690807 Msa0744020:intron 35.0%
! CTCATGGGATTGAGATTTTA+CGG + chr5_1:64690915-64690934 Msa0744020:CDS 35.0%
ATCAAGGAGGAGTTGGAAAT+TGG + chr5_1:64690422-64690441 Msa0744020:CDS 40.0%
CAAATTGCTCGAAATCACCA+GGG - chr5_1:64690588-64690607 None:intergenic 40.0%
ACAAATTGCTCGAAATCACC+AGG - chr5_1:64690589-64690608 None:intergenic 40.0%
! CAAGCTCCATAATTTTGTGG+TGG - chr5_1:64690613-64690632 None:intergenic 40.0%
CACCACAAAATTATGGAGCT+TGG + chr5_1:64690611-64690630 Msa0744020:CDS 40.0%
! CTCCAAGCTCCATAATTTTG+TGG - chr5_1:64690616-64690635 None:intergenic 40.0%
! TGAGATTTTACGGCCGAAAA+TGG + chr5_1:64690925-64690944 Msa0744020:CDS 40.0%
! TAGAAATCCGCGTCCATTTT+CGG - chr5_1:64690941-64690960 None:intergenic 40.0%
GTTCATCCAAGCATATCTGT+TGG - chr5_1:64691015-64691034 None:intergenic 40.0%
ATGGCAAATCAAGGAGGAGT+TGG + chr5_1:64690415-64690434 Msa0744020:CDS 45.0%
! AAGAACCTGTGGTTTGTCTC+AGG - chr5_1:64690496-64690515 None:intergenic 45.0%
CTGAAACTCTCAAGAACCTG+TGG - chr5_1:64690507-64690526 None:intergenic 45.0%
TGGAGCTTGGAGTAATGATG+AGG + chr5_1:64690624-64690643 Msa0744020:CDS 45.0%
! CTAGAGAGATTGTGTTGACG+AGG + chr5_1:64690958-64690977 Msa0744020:CDS 45.0%
CATATCTGTTGGTGCGGTAA+CGG - chr5_1:64691004-64691023 None:intergenic 45.0%
TCCAAGCATATCTGTTGGTG+CGG - chr5_1:64691010-64691029 None:intergenic 45.0%
TTCCACCTGAGACAAACCAC+AGG + chr5_1:64690488-64690507 Msa0744020:CDS 50.0%
! AACCTGTGGTTTGTCTCAGG+TGG - chr5_1:64690493-64690512 None:intergenic 50.0%
AATCACCAGGGAGCTCTTCA+AGG - chr5_1:64690576-64690595 None:intergenic 50.0%
TTTACGGCCGAAAATGGACG+CGG + chr5_1:64690931-64690950 Msa0744020:CDS 50.0%
ACCGCACCAACAGATATGCT+TGG + chr5_1:64691006-64691025 Msa0744020:CDS 50.0%
CACTACCTTGAAGAGCTCCC+TGG + chr5_1:64690568-64690587 Msa0744020:CDS 55.0%
! TGTTGGTGCGGTAACGGTCT+CGG - chr5_1:64690998-64691017 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 64690415 64691040 64690415 ID=Msa0744020;Name=Msa0744020
chr5_1 mRNA 64690415 64691040 64690415 ID=Msa0744020-mRNA-1;Parent=Msa0744020;Name=Msa0744020-mRNA-1;_AED=0.00;_eAED=0.02;_QI=0|0|0|1|1|1|2|0|122
chr5_1 exon 64690415 64690650 64690415 ID=Msa0744020-mRNA-1:exon:19149;Parent=Msa0744020-mRNA-1
chr5_1 exon 64690908 64691040 64690908 ID=Msa0744020-mRNA-1:exon:19150;Parent=Msa0744020-mRNA-1
chr5_1 CDS 64690415 64690650 64690415 ID=Msa0744020-mRNA-1:cds;Parent=Msa0744020-mRNA-1
chr5_1 CDS 64690908 64691040 64690908 ID=Msa0744020-mRNA-1:cds;Parent=Msa0744020-mRNA-1
Gene Sequence

>Msa0744020

ATGGCAAATCAAGGAGGAGTTGGAAATTGGAACGTAGATGATACATTGATGCTTAGACAAGCAATGATAATATTTCCACCTGAGACAAACCACAGGTTCTTGAGAGTTTCAGAAATTTTTCCAGAAGCAAGAAGGAATATAACTCTTTTGCAACACTACCTTGAAGAGCTCCCTGGTGATTTCGAGCAATTTGTTCCACCACAAAATTATGGAGCTTGGAGTAATGATGAGGATCAGCTATTACTCATGGGATTGAGATTTTACGGCCGAAAATGGACGCGGATTTCTAGAGAGATTGTGTTGACGAGGAACGCATCGCAATGCCGAGACCGTTACCGCACCAACAGATATGCTTGGATGAACTTTTAG
Protein sequence

>Msa0744020

MANQGGVGNWNVDDTLMLRQAMIIFPPETNHRFLRVSEIFPEARRNITLLQHYLEELPGDFEQFVPPQNYGAWSNDEDQLLLMGLRFYGRKWTRISREIVLTRNASQCRDRYRTNRYAWMNF*