AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1139680


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
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 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGATTGACTTTCAAATTC+AGG 0.203905 7_4:+10319637 Msa1139680:CDS
CAAGCAAACCGCTGGGAAAA+AGG 0.236819 7_4:+10320375 Msa1139680:CDS
TTTCCCAGCGGTTTGCTTGC+TGG 0.271941 7_4:-10320371 None:intergenic
GATGCGATCACCATTGAGTT+TGG 0.333702 7_4:+10320422 Msa1139680:CDS
CAACTTCATTTCGATTGAAA+TGG 0.342258 7_4:-10319691 None:intergenic
TCAAAATTTGCAAACATTGT+TGG 0.359181 7_4:+10319611 Msa1139680:CDS
GTCTTGACGCAAACCATCTT+CGG 0.403361 7_4:-10320467 None:intergenic
AAGATTGACTTTCAAATTCA+GGG 0.407038 7_4:+10319638 Msa1139680:CDS
TATGATCTTGCTTGATGATA+AGG 0.427105 7_4:+10319724 Msa1139680:CDS
TCATTTCGATTGAAATGGTC+CGG 0.432290 7_4:-10319686 None:intergenic
AGTTGAGAGTGTCGAAGGGC+TGG 0.461148 7_4:+10320400 Msa1139680:CDS
AGCCCTTCGACACTCTCAAC+TGG 0.469743 7_4:-10320398 None:intergenic
TACTCCAGCAAGCAAACCGC+TGG 0.499519 7_4:+10320367 Msa1139680:CDS
GATTTGTAGGAAAAGCTTCA+AGG 0.518503 7_4:+10319585 None:intergenic
CATTTCAATCGAAATGAAGT+TGG 0.522888 7_4:+10319692 Msa1139680:CDS
AGGGTCGTGTGATTAATCTC+TGG 0.540420 7_4:+10319657 Msa1139680:CDS
TGCTACTAAAGAGCCGAAGA+TGG 0.543874 7_4:+10320454 Msa1139680:CDS
ATCACCATTGAGTTTGGAGA+AGG 0.557143 7_4:+10320428 Msa1139680:CDS
AGAGCCTTCTCCAAACTCAA+TGG 0.564999 7_4:-10320432 None:intergenic
AGGCCAGTTGAGAGTGTCGA+AGG 0.575521 7_4:+10320395 Msa1139680:CDS
GGAGGTGATTCGAGCAACAA+CGG 0.610800 7_4:+10320323 Msa1139680:CDS
ACTCCAGCAAGCAAACCGCT+GGG 0.632167 7_4:+10320368 Msa1139680:CDS
GATTAATCTCTGGACTACTC+CGG 0.641375 7_4:+10319667 Msa1139680:CDS
GGCCAGTTGAGAGTGTCGAA+GGG 0.650645 7_4:+10320396 Msa1139680:CDS
TGATTCGAGCAACAACGGAG+AGG 0.708178 7_4:+10320328 Msa1139680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTAAGTATAATAATGAA+AGG + chr7_4:10319863-10319882 Msa1139680:intron 15.0%
!!! TAAGAAATTATTAGTCTATT+CGG + chr7_4:10319951-10319970 Msa1139680:intron 15.0%
!!! GTTTTAAGTATAATAATGAA+AGG + chr7_4:10319863-10319882 Msa1139680:intron 15.0%
!!! TAAGAAATTATTAGTCTATT+CGG + chr7_4:10319951-10319970 Msa1139680:intron 15.0%
!!! AATTTATGAGTTTTTTCAGT+TGG + chr7_4:10319748-10319767 Msa1139680:intron 20.0%
!!! TTCTGTTTTAATGCAATAAT+AGG + chr7_4:10319785-10319804 Msa1139680:intron 20.0%
!!! GTTATGCTTCATTATAATTT+TGG + chr7_4:10320289-10320308 Msa1139680:intron 20.0%
!!! AATTTATGAGTTTTTTCAGT+TGG + chr7_4:10319748-10319767 Msa1139680:intron 20.0%
!!! TTCTGTTTTAATGCAATAAT+AGG + chr7_4:10319785-10319804 Msa1139680:intron 20.0%
!!! GTTATGCTTCATTATAATTT+TGG + chr7_4:10320289-10320308 Msa1139680:intron 20.0%
! TCAAAATTTGCAAACATTGT+TGG + chr7_4:10319611-10319630 Msa1139680:CDS 25.0%
!! AAAGATTGACTTTCAAATTC+AGG + chr7_4:10319637-10319656 Msa1139680:CDS 25.0%
!! AAGATTGACTTTCAAATTCA+GGG + chr7_4:10319638-10319657 Msa1139680:CDS 25.0%
!!! CATTTTATTTATGCAGAACT+AGG + chr7_4:10320058-10320077 Msa1139680:intron 25.0%
!! TCATTTGTATTCGTTCTTTT+TGG - chr7_4:10320105-10320124 None:intergenic 25.0%
!! ATGCTTCATTATAATTTTGG+AGG + chr7_4:10320292-10320311 Msa1139680:intron 25.0%
! TCAAAATTTGCAAACATTGT+TGG + chr7_4:10319611-10319630 Msa1139680:CDS 25.0%
!! AAAGATTGACTTTCAAATTC+AGG + chr7_4:10319637-10319656 Msa1139680:CDS 25.0%
!! AAGATTGACTTTCAAATTCA+GGG + chr7_4:10319638-10319657 Msa1139680:CDS 25.0%
!!! CATTTTATTTATGCAGAACT+AGG + chr7_4:10320058-10320077 Msa1139680:intron 25.0%
!! TCATTTGTATTCGTTCTTTT+TGG - chr7_4:10320105-10320124 None:intergenic 25.0%
!! ATGCTTCATTATAATTTTGG+AGG + chr7_4:10320292-10320311 Msa1139680:intron 25.0%
CAACTTCATTTCGATTGAAA+TGG - chr7_4:10319694-10319713 None:intergenic 30.0%
CATTTCAATCGAAATGAAGT+TGG + chr7_4:10319692-10319711 Msa1139680:CDS 30.0%
! TATGATCTTGCTTGATGATA+AGG + chr7_4:10319724-10319743 Msa1139680:CDS 30.0%
! AGCTGTTAGGTATCATTTTA+GGG - chr7_4:10320212-10320231 None:intergenic 30.0%
!!! TCAAATCTTTTAGAGCTGTT+AGG - chr7_4:10320225-10320244 None:intergenic 30.0%
CAACTTCATTTCGATTGAAA+TGG - chr7_4:10319694-10319713 None:intergenic 30.0%
CATTTCAATCGAAATGAAGT+TGG + chr7_4:10319692-10319711 Msa1139680:CDS 30.0%
! TATGATCTTGCTTGATGATA+AGG + chr7_4:10319724-10319743 Msa1139680:CDS 30.0%
! AGCTGTTAGGTATCATTTTA+GGG - chr7_4:10320212-10320231 None:intergenic 30.0%
!!! TCAAATCTTTTAGAGCTGTT+AGG - chr7_4:10320225-10320244 None:intergenic 30.0%
TCATTTCGATTGAAATGGTC+CGG - chr7_4:10319689-10319708 None:intergenic 35.0%
!!! TGTTTTAATAGCATGCACTG+TGG + chr7_4:10319841-10319860 Msa1139680:intron 35.0%
ATGAAAGGCCTGTAAAAATG+CGG + chr7_4:10319878-10319897 Msa1139680:intron 35.0%
! GATAGAAACCGCATTTTTAC+AGG - chr7_4:10319889-10319908 None:intergenic 35.0%
! AATTATTAGTCTATTCGGCG+TGG + chr7_4:10319956-10319975 Msa1139680:intron 35.0%
TAGTTATTACAGCAGCAGTT+AGG - chr7_4:10320170-10320189 None:intergenic 35.0%
AACTAAAATGCCATAGCAGA+TGG + chr7_4:10320185-10320204 Msa1139680:intron 35.0%
! GCTGTTAGGTATCATTTTAG+GGG - chr7_4:10320211-10320230 None:intergenic 35.0%
! GAGCTGTTAGGTATCATTTT+AGG - chr7_4:10320213-10320232 None:intergenic 35.0%
!! ATAATTTTGGAGGCTCTTGA+AGG + chr7_4:10320302-10320321 Msa1139680:intron 35.0%
TCATTTCGATTGAAATGGTC+CGG - chr7_4:10319689-10319708 None:intergenic 35.0%
!!! TGTTTTAATAGCATGCACTG+TGG + chr7_4:10319841-10319860 Msa1139680:intron 35.0%
ATGAAAGGCCTGTAAAAATG+CGG + chr7_4:10319878-10319897 Msa1139680:intron 35.0%
! GATAGAAACCGCATTTTTAC+AGG - chr7_4:10319889-10319908 None:intergenic 35.0%
! AATTATTAGTCTATTCGGCG+TGG + chr7_4:10319956-10319975 Msa1139680:intron 35.0%
TAGTTATTACAGCAGCAGTT+AGG - chr7_4:10320170-10320189 None:intergenic 35.0%
AACTAAAATGCCATAGCAGA+TGG + chr7_4:10320185-10320204 Msa1139680:intron 35.0%
! GCTGTTAGGTATCATTTTAG+GGG - chr7_4:10320211-10320230 None:intergenic 35.0%
! GAGCTGTTAGGTATCATTTT+AGG - chr7_4:10320213-10320232 None:intergenic 35.0%
!! ATAATTTTGGAGGCTCTTGA+AGG + chr7_4:10320302-10320321 Msa1139680:intron 35.0%
GATTAATCTCTGGACTACTC+CGG + chr7_4:10319667-10319686 Msa1139680:CDS 40.0%
TTTCAGTTGGCAGTATGCAT+AGG + chr7_4:10319761-10319780 Msa1139680:intron 40.0%
!! TCGTTCTTTTTGGCATTCTG+TGG - chr7_4:10320095-10320114 None:intergenic 40.0%
TTATTACAGCAGCAGTTAGG+TGG - chr7_4:10320167-10320186 None:intergenic 40.0%
ATCACCATTGAGTTTGGAGA+AGG + chr7_4:10320428-10320447 Msa1139680:CDS 40.0%
GATTAATCTCTGGACTACTC+CGG + chr7_4:10319667-10319686 Msa1139680:CDS 40.0%
TTTCAGTTGGCAGTATGCAT+AGG + chr7_4:10319761-10319780 Msa1139680:intron 40.0%
!! TCGTTCTTTTTGGCATTCTG+TGG - chr7_4:10320095-10320114 None:intergenic 40.0%
TTATTACAGCAGCAGTTAGG+TGG - chr7_4:10320167-10320186 None:intergenic 40.0%
ATCACCATTGAGTTTGGAGA+AGG + chr7_4:10320428-10320447 Msa1139680:CDS 40.0%
AGGGTCGTGTGATTAATCTC+TGG + chr7_4:10319657-10319676 Msa1139680:CDS 45.0%
!! ATTTTAGGGGCCATCTGCTA+TGG - chr7_4:10320198-10320217 None:intergenic 45.0%
!! ATTTTGGAGGCTCTTGAAGG+AGG + chr7_4:10320305-10320324 Msa1139680:intron 45.0%
GATGCGATCACCATTGAGTT+TGG + chr7_4:10320422-10320441 Msa1139680:CDS 45.0%
AGAGCCTTCTCCAAACTCAA+TGG - chr7_4:10320435-10320454 None:intergenic 45.0%
TGCTACTAAAGAGCCGAAGA+TGG + chr7_4:10320454-10320473 Msa1139680:CDS 45.0%
GTCTTGACGCAAACCATCTT+CGG - chr7_4:10320470-10320489 None:intergenic 45.0%
AGGGTCGTGTGATTAATCTC+TGG + chr7_4:10319657-10319676 Msa1139680:CDS 45.0%
!! ATTTTAGGGGCCATCTGCTA+TGG - chr7_4:10320198-10320217 None:intergenic 45.0%
!! ATTTTGGAGGCTCTTGAAGG+AGG + chr7_4:10320305-10320324 Msa1139680:intron 45.0%
GATGCGATCACCATTGAGTT+TGG + chr7_4:10320422-10320441 Msa1139680:CDS 45.0%
AGAGCCTTCTCCAAACTCAA+TGG - chr7_4:10320435-10320454 None:intergenic 45.0%
TGCTACTAAAGAGCCGAAGA+TGG + chr7_4:10320454-10320473 Msa1139680:CDS 45.0%
GTCTTGACGCAAACCATCTT+CGG - chr7_4:10320470-10320489 None:intergenic 45.0%
ACAAATGAGCCGCACAAACG+CGG + chr7_4:10320117-10320136 Msa1139680:intron 50.0%
! AAGCTGTTTCCGCGTTTGTG+CGG - chr7_4:10320129-10320148 None:intergenic 50.0%
GGAGGTGATTCGAGCAACAA+CGG + chr7_4:10320323-10320342 Msa1139680:CDS 50.0%
TGATTCGAGCAACAACGGAG+AGG + chr7_4:10320328-10320347 Msa1139680:CDS 50.0%
CAAGCAAACCGCTGGGAAAA+AGG + chr7_4:10320375-10320394 Msa1139680:CDS 50.0%
!!! TCAACTGGCCTTTTTCCCAG+CGG - chr7_4:10320386-10320405 None:intergenic 50.0%
ACAAATGAGCCGCACAAACG+CGG + chr7_4:10320117-10320136 Msa1139680:intron 50.0%
! AAGCTGTTTCCGCGTTTGTG+CGG - chr7_4:10320129-10320148 None:intergenic 50.0%
GGAGGTGATTCGAGCAACAA+CGG + chr7_4:10320323-10320342 Msa1139680:CDS 50.0%
TGATTCGAGCAACAACGGAG+AGG + chr7_4:10320328-10320347 Msa1139680:CDS 50.0%
CAAGCAAACCGCTGGGAAAA+AGG + chr7_4:10320375-10320394 Msa1139680:CDS 50.0%
!!! TCAACTGGCCTTTTTCCCAG+CGG - chr7_4:10320386-10320405 None:intergenic 50.0%
GCACAAACGCGGAAACAGCT+TGG + chr7_4:10320128-10320147 Msa1139680:intron 55.0%
TACTCCAGCAAGCAAACCGC+TGG + chr7_4:10320367-10320386 Msa1139680:CDS 55.0%
ACTCCAGCAAGCAAACCGCT+GGG + chr7_4:10320368-10320387 Msa1139680:CDS 55.0%
! TTTCCCAGCGGTTTGCTTGC+TGG - chr7_4:10320374-10320393 None:intergenic 55.0%
!! AGGCCAGTTGAGAGTGTCGA+AGG + chr7_4:10320395-10320414 Msa1139680:CDS 55.0%
!! GGCCAGTTGAGAGTGTCGAA+GGG + chr7_4:10320396-10320415 Msa1139680:CDS 55.0%
AGCCCTTCGACACTCTCAAC+TGG - chr7_4:10320401-10320420 None:intergenic 55.0%
!! AGTTGAGAGTGTCGAAGGGC+TGG + chr7_4:10320400-10320419 Msa1139680:CDS 55.0%
GCACAAACGCGGAAACAGCT+TGG + chr7_4:10320128-10320147 Msa1139680:intron 55.0%
TACTCCAGCAAGCAAACCGC+TGG + chr7_4:10320367-10320386 Msa1139680:CDS 55.0%
ACTCCAGCAAGCAAACCGCT+GGG + chr7_4:10320368-10320387 Msa1139680:CDS 55.0%
! TTTCCCAGCGGTTTGCTTGC+TGG - chr7_4:10320374-10320393 None:intergenic 55.0%
!! AGGCCAGTTGAGAGTGTCGA+AGG + chr7_4:10320395-10320414 Msa1139680:CDS 55.0%
!! GGCCAGTTGAGAGTGTCGAA+GGG + chr7_4:10320396-10320415 Msa1139680:CDS 55.0%
AGCCCTTCGACACTCTCAAC+TGG - chr7_4:10320401-10320420 None:intergenic 55.0%
!! AGTTGAGAGTGTCGAAGGGC+TGG + chr7_4:10320400-10320419 Msa1139680:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 10319596 10320505 10319596 ID=Msa1139680;Name=Msa1139680
chr7_4 mRNA 10319596 10320505 10319596 ID=Msa1139680-mRNA-1;Parent=Msa1139680;Name=Msa1139680-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|0|0|1|1|0.5|2|0|113
chr7_4 exon 10319596 10319745 10319596 ID=Msa1139680-mRNA-1:exon:2542;Parent=Msa1139680-mRNA-1
chr7_4 exon 10320314 10320505 10320314 ID=Msa1139680-mRNA-1:exon:2543;Parent=Msa1139680-mRNA-1
chr7_4 CDS 10319596 10319745 10319596 ID=Msa1139680-mRNA-1:cds;Parent=Msa1139680-mRNA-1
chr7_4 CDS 10320314 10320505 10320314 ID=Msa1139680-mRNA-1:cds;Parent=Msa1139680-mRNA-1
Gene Sequence

>Msa1139680

AAAGCTTCAAGGATCTCAAAATTTGCAAACATTGTTGGCAGAAAGATTGACTTTCAAATTCAGGGTCGTGTGATTAATCTCTGGACTACTCCGGACCATTTCAATCGAAATGAAGTTGGCAGTATGCATATGATCTTGCTTGATGATAAGGCTCTTGAAGGAGGTGATTCGAGCAACAACGGAGAGGCTGTTGCAGCAACTGATACTCCAGCAAGCAAACCGCTGGGAAAAAGGCCAGTTGAGAGTGTCGAAGGGCTGGATGCGATCACCATTGAGTTTGGAGAAGGCTCTGCTACTAAAGAGCCGAAGATGGTTTGCGTCAAGACTGAAGATTTGAACTGA

Protein sequence

>Msa1139680

KASRISKFANIVGRKIDFQIQGRVINLWTTPDHFNRNEVGSMHMILLDDKALEGGDSSNNGEAVAATDTPASKPLGKRPVESVEGLDAITIEFGEGSATKEPKMVCVKTEDLN*