AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1075540


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 8 sgRNAs with CRISPR-Local

Find 147 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATAATAACAGTGAAAC+TGG 0.302635 7_2:+73877454 None:intergenic
GACAGCTAAGGGACATCAAA+TGG 0.370557 7_2:-73877339 Msa1075540:three_prime_UTR
TTGTGGATCAAGATATATAA+AGG 0.417254 7_2:-73877499 Msa1075540:CDS
TGCATATGCTTCAGATCTAA+AGG 0.484832 7_2:-73879071 Msa1075540:intron
AATAACAGTGAAACTGGATC+TGG 0.488205 7_2:+73877460 None:intergenic
TTTAATCATATGACAGCTAA+GGG 0.492921 7_2:-73877350 Msa1075540:three_prime_UTR
ACAGCTAAGGGACATCAAAT+GGG 0.523896 7_2:-73877338 Msa1075540:three_prime_UTR
TAATGTATCTTGATCTATTG+TGG 0.554912 7_2:-73877516 Msa1075540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATTTTTTATTTTTATTTA+GGG - chr7_2:73877436-73877455 Msa1075540:exon 0.0%
!!! TAATTTTTTATTTTTATTTA+GGG - chr7_2:73877436-73877455 Msa1075540:exon 0.0%
!!! TAATTTGTTAATATTTTCCT+TGG - chr7_2:73877944-73877963 Msa1075540:intron 15.0%
!! AATTACTAAAAAGATTAGTA+AGG + chr7_2:73878122-73878141 None:intergenic 15.0%
!!! TTACTAATCTTTTTAGTAAT+TGG - chr7_2:73878121-73878140 Msa1075540:intron 15.0%
!!! ACTGTATTAAGTTTTTTATT+AGG - chr7_2:73879034-73879053 Msa1075540:intron 15.0%
!!! TAATTTGTTAATATTTTCCT+TGG - chr7_2:73877944-73877963 Msa1075540:intron 15.0%
!! AATTACTAAAAAGATTAGTA+AGG + chr7_2:73878122-73878141 None:intergenic 15.0%
!!! TTACTAATCTTTTTAGTAAT+TGG - chr7_2:73878121-73878140 Msa1075540:intron 15.0%
!!! ACTGTATTAAGTTTTTTATT+AGG - chr7_2:73879034-73879053 Msa1075540:intron 15.0%
!!! TTACAGTAATCATTTTGTAA+GGG - chr7_2:73877634-73877653 Msa1075540:intron 20.0%
!!! TCGTTTAAATTCTAAAACAT+GGG + chr7_2:73877870-73877889 None:intergenic 20.0%
!! GAAAAAGATTAATATAACCA+AGG + chr7_2:73877964-73877983 None:intergenic 20.0%
!!! AATCTTTTTAGTAATTGGTT+TGG - chr7_2:73878126-73878145 Msa1075540:intron 20.0%
!! GAGTTTATTATTAATTGCTA+TGG - chr7_2:73878167-73878186 Msa1075540:intron 20.0%
!! CAAATAAACAATGAATTCAA+AGG + chr7_2:73878384-73878403 None:intergenic 20.0%
!!! TTGTTTATTTCTTATCCTAA+TGG - chr7_2:73878401-73878420 Msa1075540:intron 20.0%
!! AAAATAAATAACAGACCATT+AGG + chr7_2:73878419-73878438 None:intergenic 20.0%
!!! ATTTTGTTTTTTTAGACACA+TGG - chr7_2:73878434-73878453 Msa1075540:intron 20.0%
!!! AAAAACTACCTTTATCTTTT+TGG + chr7_2:73878741-73878760 None:intergenic 20.0%
!!! TGCTATATTGTTATATTTTG+TGG - chr7_2:73878853-73878872 Msa1075540:intron 20.0%
!!! ATTTTCTGTATTTTTTTCAC+AGG - chr7_2:73878902-73878921 Msa1075540:intron 20.0%
!!! TTACAGTAATCATTTTGTAA+GGG - chr7_2:73877634-73877653 Msa1075540:intron 20.0%
!!! TCGTTTAAATTCTAAAACAT+GGG + chr7_2:73877870-73877889 None:intergenic 20.0%
!! GAAAAAGATTAATATAACCA+AGG + chr7_2:73877964-73877983 None:intergenic 20.0%
!!! AATCTTTTTAGTAATTGGTT+TGG - chr7_2:73878126-73878145 Msa1075540:intron 20.0%
!! GAGTTTATTATTAATTGCTA+TGG - chr7_2:73878167-73878186 Msa1075540:intron 20.0%
!! CAAATAAACAATGAATTCAA+AGG + chr7_2:73878384-73878403 None:intergenic 20.0%
!!! TTGTTTATTTCTTATCCTAA+TGG - chr7_2:73878401-73878420 Msa1075540:intron 20.0%
!! AAAATAAATAACAGACCATT+AGG + chr7_2:73878419-73878438 None:intergenic 20.0%
!!! ATTTTGTTTTTTTAGACACA+TGG - chr7_2:73878434-73878453 Msa1075540:intron 20.0%
!!! AAAAACTACCTTTATCTTTT+TGG + chr7_2:73878741-73878760 None:intergenic 20.0%
!!! TGCTATATTGTTATATTTTG+TGG - chr7_2:73878853-73878872 Msa1075540:intron 20.0%
!!! ATTTTCTGTATTTTTTTCAC+AGG - chr7_2:73878902-73878921 Msa1075540:intron 20.0%
! TGCATATGCTTCAAATTTAA+AGG - chr7_2:73877516-73877535 Msa1075540:CDS 25.0%
! TTAACCAAAACAGCAATTAA+AGG + chr7_2:73877612-73877631 None:intergenic 25.0%
!! GTTACAGTAATCATTTTGTA+AGG - chr7_2:73877633-73877652 Msa1075540:intron 25.0%
!!! GTCGTTTAAATTCTAAAACA+TGG + chr7_2:73877871-73877890 None:intergenic 25.0%
! CAAAATATGCATCAAAAACA+TGG + chr7_2:73878230-73878249 None:intergenic 25.0%
! GCAACTTGAATTGAAATTTA+AGG + chr7_2:73878489-73878508 None:intergenic 25.0%
! TGATATGTCCAAAAAGATAA+AGG - chr7_2:73878730-73878749 Msa1075540:intron 25.0%
! TAATGTATCTTGATCTATTG+TGG - chr7_2:73878943-73878962 Msa1075540:intron 25.0%
! TTGTGGATCAAGATATATAA+AGG - chr7_2:73878960-73878979 Msa1075540:intron 25.0%
! GAAAATAATAACAGTGAAAC+TGG + chr7_2:73879008-73879027 None:intergenic 25.0%
!! TTTTAATCATATGACAGCTA+AGG - chr7_2:73879108-73879127 Msa1075540:CDS 25.0%
! TTTAATCATATGACAGCTAA+GGG - chr7_2:73879109-73879128 Msa1075540:CDS 25.0%
! TGCATATGCTTCAAATTTAA+AGG - chr7_2:73877516-73877535 Msa1075540:CDS 25.0%
! TTAACCAAAACAGCAATTAA+AGG + chr7_2:73877612-73877631 None:intergenic 25.0%
!! GTTACAGTAATCATTTTGTA+AGG - chr7_2:73877633-73877652 Msa1075540:intron 25.0%
!!! GTCGTTTAAATTCTAAAACA+TGG + chr7_2:73877871-73877890 None:intergenic 25.0%
! CAAAATATGCATCAAAAACA+TGG + chr7_2:73878230-73878249 None:intergenic 25.0%
! GCAACTTGAATTGAAATTTA+AGG + chr7_2:73878489-73878508 None:intergenic 25.0%
! TGATATGTCCAAAAAGATAA+AGG - chr7_2:73878730-73878749 Msa1075540:intron 25.0%
! TAATGTATCTTGATCTATTG+TGG - chr7_2:73878943-73878962 Msa1075540:intron 25.0%
! TTGTGGATCAAGATATATAA+AGG - chr7_2:73878960-73878979 Msa1075540:intron 25.0%
! GAAAATAATAACAGTGAAAC+TGG + chr7_2:73879008-73879027 None:intergenic 25.0%
!! TTTTAATCATATGACAGCTA+AGG - chr7_2:73879108-73879127 Msa1075540:CDS 25.0%
! TTTAATCATATGACAGCTAA+GGG - chr7_2:73879109-73879128 Msa1075540:CDS 25.0%
! AGTAATCATTTTGTAAGGGT+GGG - chr7_2:73877638-73877657 Msa1075540:intron 30.0%
AGTCAGAAACACTAAATCAA+AGG + chr7_2:73877737-73877756 None:intergenic 30.0%
AGATATGTGCATCAAAAACA+TGG + chr7_2:73878263-73878282 None:intergenic 30.0%
!!! TTTTTTAGACACATGGAAAG+TGG - chr7_2:73878441-73878460 Msa1075540:intron 30.0%
AGTGAAACAGAAGTTACAAA+AGG + chr7_2:73878655-73878674 None:intergenic 30.0%
TGTTTAAGCATGTTGTTAGT+TGG + chr7_2:73878705-73878724 None:intergenic 30.0%
! AGTAATCATTTTGTAAGGGT+GGG - chr7_2:73877638-73877657 Msa1075540:intron 30.0%
AGTCAGAAACACTAAATCAA+AGG + chr7_2:73877737-73877756 None:intergenic 30.0%
AGATATGTGCATCAAAAACA+TGG + chr7_2:73878263-73878282 None:intergenic 30.0%
!!! TTTTTTAGACACATGGAAAG+TGG - chr7_2:73878441-73878460 Msa1075540:intron 30.0%
AGTGAAACAGAAGTTACAAA+AGG + chr7_2:73878655-73878674 None:intergenic 30.0%
TGTTTAAGCATGTTGTTAGT+TGG + chr7_2:73878705-73878724 None:intergenic 30.0%
TGCATATGCTTCAGATCTAA+AGG - chr7_2:73877388-73877407 Msa1075540:three_prime_UTR 35.0%
! GAAACAAAAACAAAAGCACG+TGG + chr7_2:73877477-73877496 None:intergenic 35.0%
!! GTTGTTGTTTCATGATGCAT+CGG - chr7_2:73877562-73877581 Msa1075540:intron 35.0%
AAACAGCAATTAAAGGCCAA+TGG + chr7_2:73877605-73877624 None:intergenic 35.0%
!!! TTGGCCTTTAATTGCTGTTT+TGG - chr7_2:73877605-73877624 Msa1075540:intron 35.0%
! CAGTAATCATTTTGTAAGGG+TGG - chr7_2:73877637-73877656 Msa1075540:intron 35.0%
! GTAATCATTTTGTAAGGGTG+GGG - chr7_2:73877639-73877658 Msa1075540:intron 35.0%
ACATTAACCAAATAGTTCCC+AGG + chr7_2:73877694-73877713 None:intergenic 35.0%
! TGCATCTGCTGAAGATTTTA+AGG - chr7_2:73877829-73877848 Msa1075540:intron 35.0%
! GCATATTTTCCAGATTCAAG+AGG - chr7_2:73878039-73878058 Msa1075540:intron 35.0%
CCAATATTACCTCTTGAATC+TGG + chr7_2:73878051-73878070 None:intergenic 35.0%
CCAGATTCAAGAGGTAATAT+TGG - chr7_2:73878048-73878067 Msa1075540:intron 35.0%
CAAAGTATGCATCAAAGACA+TGG + chr7_2:73878323-73878342 None:intergenic 35.0%
AGGAAAATGATTCACACTAG+TGG + chr7_2:73878469-73878488 None:intergenic 35.0%
TAAGCATGTTGTTAGTTGGA+TGG + chr7_2:73878701-73878720 None:intergenic 35.0%
AATAACAGTGAAACTGGATC+TGG + chr7_2:73879002-73879021 None:intergenic 35.0%
TGCATATGCTTCAGATCTAA+AGG - chr7_2:73877388-73877407 Msa1075540:three_prime_UTR 35.0%
! GAAACAAAAACAAAAGCACG+TGG + chr7_2:73877477-73877496 None:intergenic 35.0%
!! GTTGTTGTTTCATGATGCAT+CGG - chr7_2:73877562-73877581 Msa1075540:intron 35.0%
AAACAGCAATTAAAGGCCAA+TGG + chr7_2:73877605-73877624 None:intergenic 35.0%
!!! TTGGCCTTTAATTGCTGTTT+TGG - chr7_2:73877605-73877624 Msa1075540:intron 35.0%
! CAGTAATCATTTTGTAAGGG+TGG - chr7_2:73877637-73877656 Msa1075540:intron 35.0%
! GTAATCATTTTGTAAGGGTG+GGG - chr7_2:73877639-73877658 Msa1075540:intron 35.0%
ACATTAACCAAATAGTTCCC+AGG + chr7_2:73877694-73877713 None:intergenic 35.0%
! TGCATCTGCTGAAGATTTTA+AGG - chr7_2:73877829-73877848 Msa1075540:intron 35.0%
! GCATATTTTCCAGATTCAAG+AGG - chr7_2:73878039-73878058 Msa1075540:intron 35.0%
CCAATATTACCTCTTGAATC+TGG + chr7_2:73878051-73878070 None:intergenic 35.0%
CCAGATTCAAGAGGTAATAT+TGG - chr7_2:73878048-73878067 Msa1075540:intron 35.0%
CAAAGTATGCATCAAAGACA+TGG + chr7_2:73878323-73878342 None:intergenic 35.0%
AGGAAAATGATTCACACTAG+TGG + chr7_2:73878469-73878488 None:intergenic 35.0%
TAAGCATGTTGTTAGTTGGA+TGG + chr7_2:73878701-73878720 None:intergenic 35.0%
AATAACAGTGAAACTGGATC+TGG + chr7_2:73879002-73879021 None:intergenic 35.0%
! TTTGAAGCATATGCAGAGCA+TGG + chr7_2:73877511-73877530 None:intergenic 40.0%
TGTTTCATGATTCACGTCTG+TGG - chr7_2:73877772-73877791 Msa1075540:intron 40.0%
AGTGGCTATCTTATCAGCTT+TGG - chr7_2:73878002-73878021 Msa1075540:intron 40.0%
GGACAAAAACAGAGAGAAAG+TGG + chr7_2:73878101-73878120 None:intergenic 40.0%
TGCTAGAACACAAGAAGTTG+AGG - chr7_2:73878506-73878525 Msa1075540:intron 40.0%
AAATGTCTCCAAGCCATTGA+AGG + chr7_2:73878612-73878631 None:intergenic 40.0%
ACAGCTAAGGGACATCAAAT+GGG - chr7_2:73879121-73879140 Msa1075540:CDS 40.0%
! TTTGAAGCATATGCAGAGCA+TGG + chr7_2:73877511-73877530 None:intergenic 40.0%
TGTTTCATGATTCACGTCTG+TGG - chr7_2:73877772-73877791 Msa1075540:intron 40.0%
AGTGGCTATCTTATCAGCTT+TGG - chr7_2:73878002-73878021 Msa1075540:intron 40.0%
GGACAAAAACAGAGAGAAAG+TGG + chr7_2:73878101-73878120 None:intergenic 40.0%
TGCTAGAACACAAGAAGTTG+AGG - chr7_2:73878506-73878525 Msa1075540:intron 40.0%
AAATGTCTCCAAGCCATTGA+AGG + chr7_2:73878612-73878631 None:intergenic 40.0%
! TCATTTTGTAAGGGTGGGGT+AGG - chr7_2:73877643-73877662 Msa1075540:intron 45.0%
!! TGTAGAGTTTTGTCCGTGAG+TGG - chr7_2:73877984-73878003 Msa1075540:intron 45.0%
GCTGATAAGATAGCCACTCA+CGG + chr7_2:73878000-73878019 None:intergenic 45.0%
GCTGAGTTAGTACATAGCCA+AGG - chr7_2:73878531-73878550 Msa1075540:intron 45.0%
AGCACTAACTCAGCATGTTC+AGG + chr7_2:73878558-73878577 None:intergenic 45.0%
CCATTGAAGGATGTCTAGCA+TGG + chr7_2:73878599-73878618 None:intergenic 45.0%
CCATGCTAGACATCCTTCAA+TGG - chr7_2:73878596-73878615 Msa1075540:intron 45.0%
CTAGACATCCTTCAATGGCT+TGG - chr7_2:73878601-73878620 Msa1075540:intron 45.0%
GACAGCTAAGGGACATCAAA+TGG - chr7_2:73879120-73879139 Msa1075540:CDS 45.0%
! TCATTTTGTAAGGGTGGGGT+AGG - chr7_2:73877643-73877662 Msa1075540:intron 45.0%
!! TGTAGAGTTTTGTCCGTGAG+TGG - chr7_2:73877984-73878003 Msa1075540:intron 45.0%
GCTGATAAGATAGCCACTCA+CGG + chr7_2:73878000-73878019 None:intergenic 45.0%
GCTGAGTTAGTACATAGCCA+AGG - chr7_2:73878531-73878550 Msa1075540:intron 45.0%
AGCACTAACTCAGCATGTTC+AGG + chr7_2:73878558-73878577 None:intergenic 45.0%
CCATTGAAGGATGTCTAGCA+TGG + chr7_2:73878599-73878618 None:intergenic 45.0%
CCATGCTAGACATCCTTCAA+TGG - chr7_2:73878596-73878615 Msa1075540:intron 45.0%
CTAGACATCCTTCAATGGCT+TGG - chr7_2:73878601-73878620 Msa1075540:intron 45.0%
GACAGCTAAGGGACATCAAA+TGG - chr7_2:73879120-73879139 Msa1075540:CDS 45.0%
!!! GTAATTTTTTATTTTTATTT+AGG - chr7_2:73877435-73877454 Msa1075540:exon 5.0%
!!! ATTTTTAAACTTATTTTTAT+TGG - chr7_2:73879066-73879085 Msa1075540:intron 5.0%
!!! GTAATTTTTTATTTTTATTT+AGG - chr7_2:73877435-73877454 Msa1075540:exon 5.0%
!!! ATTTTTAAACTTATTTTTAT+TGG - chr7_2:73879066-73879085 Msa1075540:intron 5.0%
TCTACTGTGTGCTCAGCCAT+TGG - chr7_2:73877586-73877605 Msa1075540:intron 50.0%
ACTCAGCATGTTCAGGTCCT+TGG + chr7_2:73878551-73878570 None:intergenic 50.0%
TCTACTGTGTGCTCAGCCAT+TGG - chr7_2:73877586-73877605 Msa1075540:intron 50.0%
ACTCAGCATGTTCAGGTCCT+TGG + chr7_2:73878551-73878570 None:intergenic 50.0%
TGCTTCTGTAATGCGCTGCC+TGG - chr7_2:73877673-73877692 Msa1075540:intron 55.0%
GCTTCTGTAATGCGCTGCCT+GGG - chr7_2:73877674-73877693 Msa1075540:intron 55.0%
TGCGCTGCCTGGGAACTATT+TGG - chr7_2:73877684-73877703 Msa1075540:intron 55.0%
TGCTTCTGTAATGCGCTGCC+TGG - chr7_2:73877673-73877692 Msa1075540:intron 55.0%
GCTTCTGTAATGCGCTGCCT+GGG - chr7_2:73877674-73877693 Msa1075540:intron 55.0%
TGCGCTGCCTGGGAACTATT+TGG - chr7_2:73877684-73877703 Msa1075540:intron 55.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 73877338 73879143 73877338 ID=Msa1075540;Name=Msa1075540
chr7_2 mRNA 73877338 73879143 73877338 ID=Msa1075540-mRNA-1;Parent=Msa1075540;Name=Msa1075540-mRNA-1;_AED=0.15;_eAED=0.36;_QI=0|0|0.25|0.5|0|0|4|112|64
chr7_2 exon 73877338 73877557 73877338 ID=Msa1075540-mRNA-1:exon:17228;Parent=Msa1075540-mRNA-1
chr7_2 exon 73878421 73878429 73878421 ID=Msa1075540-mRNA-1:exon:17227;Parent=Msa1075540-mRNA-1
chr7_2 exon 73878821 73878826 73878821 ID=Msa1075540-mRNA-1:exon:17226;Parent=Msa1075540-mRNA-1
chr7_2 exon 73879072 73879143 73879072 ID=Msa1075540-mRNA-1:exon:17225;Parent=Msa1075540-mRNA-1
chr7_2 CDS 73879072 73879143 73879072 ID=Msa1075540-mRNA-1:cds;Parent=Msa1075540-mRNA-1
chr7_2 CDS 73878821 73878826 73878821 ID=Msa1075540-mRNA-1:cds;Parent=Msa1075540-mRNA-1
chr7_2 CDS 73878421 73878429 73878421 ID=Msa1075540-mRNA-1:cds;Parent=Msa1075540-mRNA-1
chr7_2 CDS 73877450 73877557 73877450 ID=Msa1075540-mRNA-1:cds;Parent=Msa1075540-mRNA-1
chr7_2 three_prime_UTR 73877338 73877449 73877338 ID=Msa1075540-mRNA-1:three_prime_utr;Parent=Msa1075540-mRNA-1
Gene Sequence

>Msa1075540

AGTGTGAGTGACTCTTTTTATTTTTTGTTTCATGAATCACGTCTCTGCTCTGCATATGCTTCAGATCTAAAGGGTGGGATTCAAGAGGTTAACAATATTACTGTGATAATGTATCTTGATCTATTGTGGATCAAGATATATAAAGGAGTTATTATTATTTATCCAGATCCAGTTTCACTGTTATTATTTTCATGA

Protein sequence

>Msa1075540

SVSDSFYFLFHESRLCSAYASDLKGGIQEVNNITVIMYLDLLWIKIYKGVIIIYPDPVSLLLFS*