AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1276600

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 10 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 8_3:-11389769 None:intergenic
CCAATATTACCTCTTGAATC+TGG 0.362334 8_3:-11388812 None:intergenic
GACAGCTAAGGGACATCAAA+TGG 0.370557 8_3:+11389884 Msa1276600:three_prime_UTR
TTGTGGATCAAGATATATAA+AGG 0.417254 8_3:+11389724 Msa1276600:CDS
TGCATATGCTTCAGATCTAA+AGG 0.484832 8_3:+11388152 Msa1276600:CDS
AATAACAGTGAAACTGGATC+TGG 0.488205 8_3:-11389763 None:intergenic
TTTAATCATATGACAGCTAA+GGG 0.492921 8_3:+11389873 Msa1276600:three_prime_UTR
ACAGCTAAGGGACATCAAAT+GGG 0.523896 8_3:+11389885 Msa1276600:three_prime_UTR
TAATGTATCTTGATCTATTG+TGG 0.554912 8_3:+11389707 Msa1276600:CDS
GCTGATAAGATAGCCACTCA+CGG 0.687098 8_3:-11388761 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATTTTTTATTTTTATTTA+GGG + chr8_3:11388200-11388219 Msa1276600:intron 0.0%
!!! TAATTTTTTATTTTTATTTA+GGG + chr8_3:11388200-11388219 Msa1276600:intron 0.0%
!!! TAATTTGTTAATATTTTCCT+TGG + chr8_3:11388708-11388727 Msa1276600:intron 15.0%
!!! ACTGTATTAAGTTTTTTATT+AGG + chr8_3:11389798-11389817 Msa1276600:three_prime_UTR 15.0%
!!! TAATTTGTTAATATTTTCCT+TGG + chr8_3:11388708-11388727 Msa1276600:intron 15.0%
!!! ACTGTATTAAGTTTTTTATT+AGG + chr8_3:11389798-11389817 Msa1276600:three_prime_UTR 15.0%
!!! TTCTTATTTTTGTTCGATTT+AGG + chr8_3:11388079-11388098 Msa1276600:CDS 20.0%
!!! TTACAGTAATCATTTTGTAA+GGG + chr8_3:11388398-11388417 Msa1276600:intron 20.0%
!!! TCCTTTAAATTCTAAAACAT+GGG - chr8_3:11388634-11388653 None:intergenic 20.0%
!! GAAAAAGATTAATATAACCA+AGG - chr8_3:11388728-11388747 None:intergenic 20.0%
!! AGTTACTAAAAAGATTAGTA+AGG - chr8_3:11388886-11388905 None:intergenic 20.0%
!!! TTACTAATCTTTTTAGTAAC+TGG + chr8_3:11388885-11388904 Msa1276600:intron 20.0%
!! GAGTTTATTATTAATTGCTA+TGG + chr8_3:11388931-11388950 Msa1276600:intron 20.0%
!! CAAATAAACAATGAATTCAA+AGG - chr8_3:11389148-11389167 None:intergenic 20.0%
!!! TTGTTTATTTCTTATCCTAA+TGG + chr8_3:11389165-11389184 Msa1276600:intron 20.0%
!! AAAATAAATAACAGACCATT+AGG - chr8_3:11389183-11389202 None:intergenic 20.0%
!!! ATTTTGTTTTTTTAGACACA+TGG + chr8_3:11389198-11389217 Msa1276600:intron 20.0%
!!! AAAAACTACCTTTATCTTTT+TGG - chr8_3:11389505-11389524 None:intergenic 20.0%
!!! TGCTATATTGTTATATTTTG+TGG + chr8_3:11389617-11389636 Msa1276600:intron 20.0%
!!! ATTTTCTGTATTTTTTTCAC+AGG + chr8_3:11389666-11389685 Msa1276600:intron 20.0%
!!! TTCTTATTTTTGTTCGATTT+AGG + chr8_3:11388079-11388098 Msa1276600:CDS 20.0%
!!! TTACAGTAATCATTTTGTAA+GGG + chr8_3:11388398-11388417 Msa1276600:intron 20.0%
!!! TCCTTTAAATTCTAAAACAT+GGG - chr8_3:11388634-11388653 None:intergenic 20.0%
!! GAAAAAGATTAATATAACCA+AGG - chr8_3:11388728-11388747 None:intergenic 20.0%
!! AGTTACTAAAAAGATTAGTA+AGG - chr8_3:11388886-11388905 None:intergenic 20.0%
!!! TTACTAATCTTTTTAGTAAC+TGG + chr8_3:11388885-11388904 Msa1276600:intron 20.0%
!! GAGTTTATTATTAATTGCTA+TGG + chr8_3:11388931-11388950 Msa1276600:intron 20.0%
!! CAAATAAACAATGAATTCAA+AGG - chr8_3:11389148-11389167 None:intergenic 20.0%
!!! TTGTTTATTTCTTATCCTAA+TGG + chr8_3:11389165-11389184 Msa1276600:intron 20.0%
!! AAAATAAATAACAGACCATT+AGG - chr8_3:11389183-11389202 None:intergenic 20.0%
!!! ATTTTGTTTTTTTAGACACA+TGG + chr8_3:11389198-11389217 Msa1276600:intron 20.0%
!!! AAAAACTACCTTTATCTTTT+TGG - chr8_3:11389505-11389524 None:intergenic 20.0%
!!! TGCTATATTGTTATATTTTG+TGG + chr8_3:11389617-11389636 Msa1276600:intron 20.0%
!!! ATTTTCTGTATTTTTTTCAC+AGG + chr8_3:11389666-11389685 Msa1276600:intron 20.0%
! TGCATATGCTTCAAATTTAA+AGG + chr8_3:11388280-11388299 Msa1276600:intron 25.0%
! TTAACCAAAACAGCAATTAA+AGG - chr8_3:11388376-11388395 None:intergenic 25.0%
!! GTTACAGTAATCATTTTGTA+AGG + chr8_3:11388397-11388416 Msa1276600:intron 25.0%
! AGTCAGAAACATTAAATCAA+AGG - chr8_3:11388501-11388520 None:intergenic 25.0%
!!! TCCCATGTTTTAGAATTTAA+AGG + chr8_3:11388630-11388649 Msa1276600:intron 25.0%
!!! GTCCTTTAAATTCTAAAACA+TGG - chr8_3:11388635-11388654 None:intergenic 25.0%
!!! AATCTTTTTAGTAACTGGTT+TGG + chr8_3:11388890-11388909 Msa1276600:intron 25.0%
! CAAAATATGCATCAAAAACA+TGG - chr8_3:11388994-11389013 None:intergenic 25.0%
! TGATATGTCCAAAAAGATAA+AGG + chr8_3:11389494-11389513 Msa1276600:intron 25.0%
! TAATGTATCTTGATCTATTG+TGG + chr8_3:11389707-11389726 Msa1276600:CDS 25.0%
! TTGTGGATCAAGATATATAA+AGG + chr8_3:11389724-11389743 Msa1276600:CDS 25.0%
! GAAAATAATAACAGTGAAAC+TGG - chr8_3:11389772-11389791 None:intergenic 25.0%
!! TTTTAATCATATGACAGCTA+AGG + chr8_3:11389872-11389891 Msa1276600:three_prime_UTR 25.0%
! TTTAATCATATGACAGCTAA+GGG + chr8_3:11389873-11389892 Msa1276600:three_prime_UTR 25.0%
! TGCATATGCTTCAAATTTAA+AGG + chr8_3:11388280-11388299 Msa1276600:intron 25.0%
! TTAACCAAAACAGCAATTAA+AGG - chr8_3:11388376-11388395 None:intergenic 25.0%
!! GTTACAGTAATCATTTTGTA+AGG + chr8_3:11388397-11388416 Msa1276600:intron 25.0%
! AGTCAGAAACATTAAATCAA+AGG - chr8_3:11388501-11388520 None:intergenic 25.0%
!!! TCCCATGTTTTAGAATTTAA+AGG + chr8_3:11388630-11388649 Msa1276600:intron 25.0%
!!! GTCCTTTAAATTCTAAAACA+TGG - chr8_3:11388635-11388654 None:intergenic 25.0%
!!! AATCTTTTTAGTAACTGGTT+TGG + chr8_3:11388890-11388909 Msa1276600:intron 25.0%
! CAAAATATGCATCAAAAACA+TGG - chr8_3:11388994-11389013 None:intergenic 25.0%
! TGATATGTCCAAAAAGATAA+AGG + chr8_3:11389494-11389513 Msa1276600:intron 25.0%
! TAATGTATCTTGATCTATTG+TGG + chr8_3:11389707-11389726 Msa1276600:CDS 25.0%
! TTGTGGATCAAGATATATAA+AGG + chr8_3:11389724-11389743 Msa1276600:CDS 25.0%
! GAAAATAATAACAGTGAAAC+TGG - chr8_3:11389772-11389791 None:intergenic 25.0%
!! TTTTAATCATATGACAGCTA+AGG + chr8_3:11389872-11389891 Msa1276600:three_prime_UTR 25.0%
! TTTAATCATATGACAGCTAA+GGG + chr8_3:11389873-11389892 Msa1276600:three_prime_UTR 25.0%
! AGTAATCATTTTGTAAGGGT+GGG + chr8_3:11388402-11388421 Msa1276600:intron 30.0%
!!! TTTTTTAGACACATGGAAAG+TGG + chr8_3:11389205-11389224 Msa1276600:intron 30.0%
GCAACTTGAATTGAAATTTG+AGG - chr8_3:11389253-11389272 None:intergenic 30.0%
AGTGAAACAGAAGTTACAAA+AGG - chr8_3:11389419-11389438 None:intergenic 30.0%
TGTTTAAGCATGTTGTTAGT+TGG - chr8_3:11389469-11389488 None:intergenic 30.0%
! AGTAATCATTTTGTAAGGGT+GGG + chr8_3:11388402-11388421 Msa1276600:intron 30.0%
!!! TTTTTTAGACACATGGAAAG+TGG + chr8_3:11389205-11389224 Msa1276600:intron 30.0%
GCAACTTGAATTGAAATTTG+AGG - chr8_3:11389253-11389272 None:intergenic 30.0%
AGTGAAACAGAAGTTACAAA+AGG - chr8_3:11389419-11389438 None:intergenic 30.0%
TGTTTAAGCATGTTGTTAGT+TGG - chr8_3:11389469-11389488 None:intergenic 30.0%
TGCATATGCTTCAGATCTAA+AGG + chr8_3:11388152-11388171 Msa1276600:CDS 35.0%
! GAAACAAAAACAAAAGCACG+TGG - chr8_3:11388241-11388260 None:intergenic 35.0%
!! GTTGTTGTTTCATGATGCAT+CGG + chr8_3:11388326-11388345 Msa1276600:intron 35.0%
AAACAGCAATTAAAGGCCAA+TGG - chr8_3:11388369-11388388 None:intergenic 35.0%
!!! TTGGCCTTTAATTGCTGTTT+TGG + chr8_3:11388369-11388388 Msa1276600:intron 35.0%
! CAGTAATCATTTTGTAAGGG+TGG + chr8_3:11388401-11388420 Msa1276600:intron 35.0%
! GTAATCATTTTGTAAGGGTG+GGG + chr8_3:11388403-11388422 Msa1276600:intron 35.0%
ACATTAACCAAATAGTTCCC+AGG - chr8_3:11388458-11388477 None:intergenic 35.0%
! TGCATCTGCTGAAGATTTTA+AGG + chr8_3:11388593-11388612 Msa1276600:intron 35.0%
! GCATATTTTCCAGATTCAAG+AGG + chr8_3:11388803-11388822 Msa1276600:CDS 35.0%
CCAATATTACCTCTTGAATC+TGG - chr8_3:11388815-11388834 None:intergenic 35.0%
CCAGATTCAAGAGGTAATAT+TGG + chr8_3:11388812-11388831 Msa1276600:intron 35.0%
GGAAAAAAACAGAGAGAAAG+TGG - chr8_3:11388865-11388884 None:intergenic 35.0%
AGCTATGTGCATCAAAAACA+TGG - chr8_3:11389027-11389046 None:intergenic 35.0%
AGGAAAATGATTCACACTAG+TGG - chr8_3:11389233-11389252 None:intergenic 35.0%
TAAGCATGTTGTTAGTTGGA+TGG - chr8_3:11389465-11389484 None:intergenic 35.0%
AATAACAGTGAAACTGGATC+TGG - chr8_3:11389766-11389785 None:intergenic 35.0%
TGCATATGCTTCAGATCTAA+AGG + chr8_3:11388152-11388171 Msa1276600:CDS 35.0%
! GAAACAAAAACAAAAGCACG+TGG - chr8_3:11388241-11388260 None:intergenic 35.0%
!! GTTGTTGTTTCATGATGCAT+CGG + chr8_3:11388326-11388345 Msa1276600:intron 35.0%
AAACAGCAATTAAAGGCCAA+TGG - chr8_3:11388369-11388388 None:intergenic 35.0%
!!! TTGGCCTTTAATTGCTGTTT+TGG + chr8_3:11388369-11388388 Msa1276600:intron 35.0%
! CAGTAATCATTTTGTAAGGG+TGG + chr8_3:11388401-11388420 Msa1276600:intron 35.0%
! GTAATCATTTTGTAAGGGTG+GGG + chr8_3:11388403-11388422 Msa1276600:intron 35.0%
ACATTAACCAAATAGTTCCC+AGG - chr8_3:11388458-11388477 None:intergenic 35.0%
! TGCATCTGCTGAAGATTTTA+AGG + chr8_3:11388593-11388612 Msa1276600:intron 35.0%
! GCATATTTTCCAGATTCAAG+AGG + chr8_3:11388803-11388822 Msa1276600:CDS 35.0%
CCAATATTACCTCTTGAATC+TGG - chr8_3:11388815-11388834 None:intergenic 35.0%
CCAGATTCAAGAGGTAATAT+TGG + chr8_3:11388812-11388831 Msa1276600:intron 35.0%
GGAAAAAAACAGAGAGAAAG+TGG - chr8_3:11388865-11388884 None:intergenic 35.0%
AGCTATGTGCATCAAAAACA+TGG - chr8_3:11389027-11389046 None:intergenic 35.0%
AGGAAAATGATTCACACTAG+TGG - chr8_3:11389233-11389252 None:intergenic 35.0%
TAAGCATGTTGTTAGTTGGA+TGG - chr8_3:11389465-11389484 None:intergenic 35.0%
AATAACAGTGAAACTGGATC+TGG - chr8_3:11389766-11389785 None:intergenic 35.0%
! TTTGAAGCATATGCAGAGCA+TGG - chr8_3:11388275-11388294 None:intergenic 40.0%
TGTTTCATGATTCACGTCTG+TGG + chr8_3:11388536-11388555 Msa1276600:intron 40.0%
TGCTAGAACACAAGAAGTTG+AGG + chr8_3:11389270-11389289 Msa1276600:intron 40.0%
AAATGTCTCCAAGCCATTGA+AGG - chr8_3:11389376-11389395 None:intergenic 40.0%
ACAGCTAAGGGACATCAAAT+GGG + chr8_3:11389885-11389904 Msa1276600:three_prime_UTR 40.0%
! TTTGAAGCATATGCAGAGCA+TGG - chr8_3:11388275-11388294 None:intergenic 40.0%
TGTTTCATGATTCACGTCTG+TGG + chr8_3:11388536-11388555 Msa1276600:intron 40.0%
TGCTAGAACACAAGAAGTTG+AGG + chr8_3:11389270-11389289 Msa1276600:intron 40.0%
AAATGTCTCCAAGCCATTGA+AGG - chr8_3:11389376-11389395 None:intergenic 40.0%
TCTACTGTGTGCTCAACCAT+TGG + chr8_3:11388350-11388369 Msa1276600:intron 45.0%
! TCATTTTGTAAGGGTGGGGT+AGG + chr8_3:11388407-11388426 Msa1276600:intron 45.0%
!! TGTAGAGTTTTGTCCGTGAG+TGG + chr8_3:11388748-11388767 Msa1276600:intron 45.0%
GCTGATAAGATAGCCACTCA+CGG - chr8_3:11388764-11388783 None:intergenic 45.0%
GCTGAGTTAGTACATAGCCA+AGG + chr8_3:11389295-11389314 Msa1276600:intron 45.0%
AGCACTAACTCAGCATGTTC+AGG - chr8_3:11389322-11389341 None:intergenic 45.0%
CCATTGAAGGATGTCTAGCA+TGG - chr8_3:11389363-11389382 None:intergenic 45.0%
CCATGCTAGACATCCTTCAA+TGG + chr8_3:11389360-11389379 Msa1276600:intron 45.0%
CTAGACATCCTTCAATGGCT+TGG + chr8_3:11389365-11389384 Msa1276600:intron 45.0%
GACAGCTAAGGGACATCAAA+TGG + chr8_3:11389884-11389903 Msa1276600:three_prime_UTR 45.0%
TCTACTGTGTGCTCAACCAT+TGG + chr8_3:11388350-11388369 Msa1276600:intron 45.0%
! TCATTTTGTAAGGGTGGGGT+AGG + chr8_3:11388407-11388426 Msa1276600:intron 45.0%
!! TGTAGAGTTTTGTCCGTGAG+TGG + chr8_3:11388748-11388767 Msa1276600:intron 45.0%
GCTGATAAGATAGCCACTCA+CGG - chr8_3:11388764-11388783 None:intergenic 45.0%
GCTGAGTTAGTACATAGCCA+AGG + chr8_3:11389295-11389314 Msa1276600:intron 45.0%
AGCACTAACTCAGCATGTTC+AGG - chr8_3:11389322-11389341 None:intergenic 45.0%
CCATTGAAGGATGTCTAGCA+TGG - chr8_3:11389363-11389382 None:intergenic 45.0%
CCATGCTAGACATCCTTCAA+TGG + chr8_3:11389360-11389379 Msa1276600:intron 45.0%
CTAGACATCCTTCAATGGCT+TGG + chr8_3:11389365-11389384 Msa1276600:intron 45.0%
GACAGCTAAGGGACATCAAA+TGG + chr8_3:11389884-11389903 Msa1276600:three_prime_UTR 45.0%
!!! GTAATTTTTTATTTTTATTT+AGG + chr8_3:11388199-11388218 Msa1276600:intron 5.0%
!!! ATTTTTAAACTTATTTTTAT+TGG + chr8_3:11389830-11389849 Msa1276600:three_prime_UTR 5.0%
!!! GTAATTTTTTATTTTTATTT+AGG + chr8_3:11388199-11388218 Msa1276600:intron 5.0%
!!! ATTTTTAAACTTATTTTTAT+TGG + chr8_3:11389830-11389849 Msa1276600:three_prime_UTR 5.0%
ACTCAGCATGTTCAGGTCCT+TGG - chr8_3:11389315-11389334 None:intergenic 50.0%
ACTCAGCATGTTCAGGTCCT+TGG - chr8_3:11389315-11389334 None:intergenic 50.0%
TGCTTCTGTAATGCGCTGCC+TGG + chr8_3:11388437-11388456 Msa1276600:intron 55.0%
GCTTCTGTAATGCGCTGCCT+GGG + chr8_3:11388438-11388457 Msa1276600:intron 55.0%
TGCGCTGCCTGGGAACTATT+TGG + chr8_3:11388448-11388467 Msa1276600:intron 55.0%
TGCTTCTGTAATGCGCTGCC+TGG + chr8_3:11388437-11388456 Msa1276600:intron 55.0%
GCTTCTGTAATGCGCTGCCT+GGG + chr8_3:11388438-11388457 Msa1276600:intron 55.0%
TGCGCTGCCTGGGAACTATT+TGG + chr8_3:11388448-11388467 Msa1276600:intron 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 11388069 11389907 11388069 ID=Msa1276600;Name=Msa1276600
chr8_3 mRNA 11388069 11389907 11388069 ID=Msa1276600-mRNA-1;Parent=Msa1276600;Name=Msa1276600-mRNA-1;_AED=0.25;_eAED=0.44;_QI=0|0|0.33|0.66|0|0.66|3|112|94
chr8_3 exon 11388069 11388173 11388069 ID=Msa1276600-mRNA-1:exon:4641;Parent=Msa1276600-mRNA-1
chr8_3 exon 11388753 11388824 11388753 ID=Msa1276600-mRNA-1:exon:4642;Parent=Msa1276600-mRNA-1
chr8_3 exon 11389688 11389907 11389688 ID=Msa1276600-mRNA-1:exon:4643;Parent=Msa1276600-mRNA-1
chr8_3 CDS 11388069 11388173 11388069 ID=Msa1276600-mRNA-1:cds;Parent=Msa1276600-mRNA-1
chr8_3 CDS 11388753 11388824 11388753 ID=Msa1276600-mRNA-1:cds;Parent=Msa1276600-mRNA-1
chr8_3 CDS 11389688 11389795 11389688 ID=Msa1276600-mRNA-1:cds;Parent=Msa1276600-mRNA-1
chr8_3 three_prime_UTR 11389796 11389907 11389796 ID=Msa1276600-mRNA-1:three_prime_utr;Parent=Msa1276600-mRNA-1
Gene Sequence

>Msa1276600

TTGTCATTTTTTCTTATTTTTGTTCGATTTAGGAGTGTGAGTGACTGTTTTTATTTTTTGTTTCATGAATCACGTCTCTGCTCTGCATATGCTTCAGATCTAAAGAGTTTTGTCCGTGAGTGGCTATCTTATCAGCTTTGTAAACTTCTATCTTTGCATATTTTCCAGATTCAAGAGGTTAACAATATTACTGTGATAATGTATCTTGATCTATTGTGGATCAAGATATATAAAGGAGTTATTATTATATATCCAGATCCAGTTTCACTGTTATTATTTTCATGA
Protein sequence

>Msa1276600

LSFFLIFVRFRSVSDCFYFLFHESRLCSAYASDLKSFVREWLSYQLCKLLSLHIFQIQEVNNITVIMYLDLLWIKIYKGVIIIYPDPVSLLLFS*