AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1312950

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 17 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAAACACCTTTGCTCTTAA+TGG 0.113419 8_4:+10446208 None:intergenic
ATTGATTTCATTAACTTTAA+AGG 0.177612 8_4:+10444909 None:intergenic
CCATGTTTATAAATATAATT+TGG 0.195747 8_4:-10444881 Msa1312950:three_prime_UTR
TCGAGTGTTACCTGCATCTT+TGG 0.257314 8_4:+10445022 None:intergenic
CTTGGCACTCCATAGTAAAA+TGG 0.313706 8_4:+10445094 None:intergenic
GCAAAGGTGTTTCATCTAAC+GGG 0.388326 8_4:-10446199 Msa1312950:CDS
TAGAGTCATGTGAGTAATCT+TGG 0.418763 8_4:+10445076 None:intergenic
CCAAATTATATTTATAAACA+TGG 0.485194 8_4:+10444881 None:intergenic
AGCAAAGGTGTTTCATCTAA+CGG 0.514730 8_4:-10446200 Msa1312950:CDS
ATGATTTGATTACAGTGTGA+AGG 0.537265 8_4:-10445142 Msa1312950:intron
TGCAATCAGTCCAAAGATGC+AGG 0.540241 8_4:-10445032 Msa1312950:CDS
GGTAATAATCCCTAAAACAA+GGG 0.558384 8_4:+10445115 None:intergenic
TGGTAATAATCCCTAAAACA+AGG 0.569912 8_4:+10445114 None:intergenic
ATTGAAGCCATTAAGAGCAA+AGG 0.590976 8_4:-10446215 Msa1312950:CDS
CTCACATGACTCTAGTGTGA+AGG 0.613928 8_4:-10445067 Msa1312950:CDS
CATGACTCTAGTGTGAAGGC+TGG 0.622131 8_4:-10445063 Msa1312950:CDS
CAAAGGTGTTTCATCTAACG+GGG 0.644795 8_4:-10446198 Msa1312950:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATAATAATATAAAATTGCT+TGG - chr8_4:10445275-10445294 Msa1312950:intron 10.0%
!! TATAATAATATAAAATTGCT+TGG - chr8_4:10445275-10445294 Msa1312950:intron 10.0%
!!! ATTGATTTCATTAACTTTAA+AGG + chr8_4:10446186-10446205 None:intergenic 15.0%
!! CCAAATTATATTTATAAACA+TGG + chr8_4:10446214-10446233 None:intergenic 15.0%
!! CCATGTTTATAAATATAATT+TGG - chr8_4:10446211-10446230 Msa1312950:CDS 15.0%
!!! ATTGATTTCATTAACTTTAA+AGG + chr8_4:10446186-10446205 None:intergenic 15.0%
!! CCAAATTATATTTATAAACA+TGG + chr8_4:10446214-10446233 None:intergenic 15.0%
!! CCATGTTTATAAATATAATT+TGG - chr8_4:10446211-10446230 Msa1312950:CDS 15.0%
!! AATATACAAGTAAACCTATA+TGG + chr8_4:10445007-10445026 None:intergenic 20.0%
!! TATAGGTTTACTTGTATATT+AGG - chr8_4:10445007-10445026 Msa1312950:three_prime_UTR 20.0%
!!! TATATTAGGTTTGTCTTATT+TGG + chr8_4:10445134-10445153 None:intergenic 20.0%
!! ATATTTCAACTATACAGTAA+AGG + chr8_4:10445184-10445203 None:intergenic 20.0%
!! TTATAGTTAGTGAATTTGAA+TGG - chr8_4:10445383-10445402 Msa1312950:intron 20.0%
!! TTCAACATTAAGATTGAATA+TGG + chr8_4:10445425-10445444 None:intergenic 20.0%
!! TTCAAAATCTATTTACCTTT+CGG - chr8_4:10445512-10445531 Msa1312950:intron 20.0%
!! TTTATTACCAAAATGATCAA+TGG + chr8_4:10445721-10445740 None:intergenic 20.0%
!! TTGAATATAACCAATAAGAA+CGG - chr8_4:10445859-10445878 Msa1312950:intron 20.0%
!!! TTTTTCAAACAAAGATTTGA+AGG + chr8_4:10446139-10446158 None:intergenic 20.0%
!! AATATACAAGTAAACCTATA+TGG + chr8_4:10445007-10445026 None:intergenic 20.0%
!! TATAGGTTTACTTGTATATT+AGG - chr8_4:10445007-10445026 Msa1312950:three_prime_UTR 20.0%
!!! TATATTAGGTTTGTCTTATT+TGG + chr8_4:10445134-10445153 None:intergenic 20.0%
!! ATATTTCAACTATACAGTAA+AGG + chr8_4:10445184-10445203 None:intergenic 20.0%
!! TTATAGTTAGTGAATTTGAA+TGG - chr8_4:10445383-10445402 Msa1312950:intron 20.0%
!! TTCAACATTAAGATTGAATA+TGG + chr8_4:10445425-10445444 None:intergenic 20.0%
!! TTCAAAATCTATTTACCTTT+CGG - chr8_4:10445512-10445531 Msa1312950:intron 20.0%
!! TTTATTACCAAAATGATCAA+TGG + chr8_4:10445721-10445740 None:intergenic 20.0%
!! TTGAATATAACCAATAAGAA+CGG - chr8_4:10445859-10445878 Msa1312950:intron 20.0%
!!! TTTTTCAAACAAAGATTTGA+AGG + chr8_4:10446139-10446158 None:intergenic 20.0%
! TTTCACTAAGCATACTTATT+TGG - chr8_4:10444941-10444960 Msa1312950:three_prime_UTR 25.0%
!!! GTCTTATTTGGTTTCATTTT+GGG + chr8_4:10445122-10445141 None:intergenic 25.0%
!!! TGTCTTATTTGGTTTCATTT+TGG + chr8_4:10445123-10445142 None:intergenic 25.0%
! CATGCATATTGCAATATATT+AGG + chr8_4:10445148-10445167 None:intergenic 25.0%
!! CAGATTTTATGACTTTAGTT+AGG + chr8_4:10445218-10445237 None:intergenic 25.0%
!! ATAGATTTTGAATAGACGTT+GGG + chr8_4:10445504-10445523 None:intergenic 25.0%
!! AATAGATTTTGAATAGACGT+TGG + chr8_4:10445505-10445524 None:intergenic 25.0%
!! GGATTATTACCATTTTACTA+TGG - chr8_4:10445989-10446008 Msa1312950:intron 25.0%
! TTTCACTAAGCATACTTATT+TGG - chr8_4:10444941-10444960 Msa1312950:three_prime_UTR 25.0%
!!! GTCTTATTTGGTTTCATTTT+GGG + chr8_4:10445122-10445141 None:intergenic 25.0%
!!! TGTCTTATTTGGTTTCATTT+TGG + chr8_4:10445123-10445142 None:intergenic 25.0%
! CATGCATATTGCAATATATT+AGG + chr8_4:10445148-10445167 None:intergenic 25.0%
!! CAGATTTTATGACTTTAGTT+AGG + chr8_4:10445218-10445237 None:intergenic 25.0%
!! ATAGATTTTGAATAGACGTT+GGG + chr8_4:10445504-10445523 None:intergenic 25.0%
!! AATAGATTTTGAATAGACGT+TGG + chr8_4:10445505-10445524 None:intergenic 25.0%
!! GGATTATTACCATTTTACTA+TGG - chr8_4:10445989-10446008 Msa1312950:intron 25.0%
! GAAATCTGGAATTTCATTTC+TGG - chr8_4:10445539-10445558 Msa1312950:intron 30.0%
TTGTTGCGAAATTTCTTCTA+AGG - chr8_4:10445582-10445601 Msa1312950:intron 30.0%
CAATATGTGGCTTAAAATCA+TGG - chr8_4:10445624-10445643 Msa1312950:intron 30.0%
! TCTCACCTTACAATCAATTT+TGG + chr8_4:10445697-10445716 None:intergenic 30.0%
ATATTAAAATCTTGCTGACG+TGG - chr8_4:10445802-10445821 Msa1312950:intron 30.0%
TTTATTTCAGCCGTTCTTAT+TGG + chr8_4:10445872-10445891 None:intergenic 30.0%
CACTGTAATCAAATCATTGA+AGG + chr8_4:10445947-10445966 None:intergenic 30.0%
ATGATTTGATTACAGTGTGA+AGG - chr8_4:10445950-10445969 Msa1312950:intron 30.0%
GGTAATAATCCCTAAAACAA+GGG + chr8_4:10445980-10445999 None:intergenic 30.0%
TGGTAATAATCCCTAAAACA+AGG + chr8_4:10445981-10446000 None:intergenic 30.0%
! GAAATCTGGAATTTCATTTC+TGG - chr8_4:10445539-10445558 Msa1312950:intron 30.0%
TTGTTGCGAAATTTCTTCTA+AGG - chr8_4:10445582-10445601 Msa1312950:intron 30.0%
CAATATGTGGCTTAAAATCA+TGG - chr8_4:10445624-10445643 Msa1312950:intron 30.0%
! TCTCACCTTACAATCAATTT+TGG + chr8_4:10445697-10445716 None:intergenic 30.0%
ATATTAAAATCTTGCTGACG+TGG - chr8_4:10445802-10445821 Msa1312950:intron 30.0%
TTTATTTCAGCCGTTCTTAT+TGG + chr8_4:10445872-10445891 None:intergenic 30.0%
CACTGTAATCAAATCATTGA+AGG + chr8_4:10445947-10445966 None:intergenic 30.0%
ATGATTTGATTACAGTGTGA+AGG - chr8_4:10445950-10445969 Msa1312950:intron 30.0%
GGTAATAATCCCTAAAACAA+GGG + chr8_4:10445980-10445999 None:intergenic 30.0%
TGGTAATAATCCCTAAAACA+AGG + chr8_4:10445981-10446000 None:intergenic 30.0%
ATTGAAGCCATTAAGAGCAA+AGG - chr8_4:10444877-10444896 Msa1312950:three_prime_UTR 35.0%
TGAAACACCTTTGCTCTTAA+TGG + chr8_4:10444887-10444906 None:intergenic 35.0%
!! AGCAAAGGTGTTTCATCTAA+CGG - chr8_4:10444892-10444911 Msa1312950:three_prime_UTR 35.0%
AAGTGTCACACTATCACATA+AGG + chr8_4:10445248-10445267 None:intergenic 35.0%
TATGTGATGCATGCAATATG+TGG - chr8_4:10445611-10445630 Msa1312950:intron 35.0%
!!! CAATTTTGGTGGTGATAAAC+TGG + chr8_4:10445683-10445702 None:intergenic 35.0%
CACCACCAAAATTGATTGTA+AGG - chr8_4:10445689-10445708 Msa1312950:intron 35.0%
! CACCTTACAATCAATTTTGG+TGG + chr8_4:10445694-10445713 None:intergenic 35.0%
! GTGAGAACCATTGATCATTT+TGG - chr8_4:10445711-10445730 Msa1312950:intron 35.0%
!!! TGAAGGTAAACCCTTGTTTT+AGG - chr8_4:10445967-10445986 Msa1312950:intron 35.0%
!!! GAAGGTAAACCCTTGTTTTA+GGG - chr8_4:10445968-10445987 Msa1312950:intron 35.0%
TAGAGTCATGTGAGTAATCT+TGG + chr8_4:10446019-10446038 None:intergenic 35.0%
ATTGAAGCCATTAAGAGCAA+AGG - chr8_4:10444877-10444896 Msa1312950:three_prime_UTR 35.0%
TGAAACACCTTTGCTCTTAA+TGG + chr8_4:10444887-10444906 None:intergenic 35.0%
!! AGCAAAGGTGTTTCATCTAA+CGG - chr8_4:10444892-10444911 Msa1312950:three_prime_UTR 35.0%
AAGTGTCACACTATCACATA+AGG + chr8_4:10445248-10445267 None:intergenic 35.0%
TATGTGATGCATGCAATATG+TGG - chr8_4:10445611-10445630 Msa1312950:intron 35.0%
!!! CAATTTTGGTGGTGATAAAC+TGG + chr8_4:10445683-10445702 None:intergenic 35.0%
CACCACCAAAATTGATTGTA+AGG - chr8_4:10445689-10445708 Msa1312950:intron 35.0%
! CACCTTACAATCAATTTTGG+TGG + chr8_4:10445694-10445713 None:intergenic 35.0%
! GTGAGAACCATTGATCATTT+TGG - chr8_4:10445711-10445730 Msa1312950:intron 35.0%
!!! TGAAGGTAAACCCTTGTTTT+AGG - chr8_4:10445967-10445986 Msa1312950:intron 35.0%
!!! GAAGGTAAACCCTTGTTTTA+GGG - chr8_4:10445968-10445987 Msa1312950:intron 35.0%
TAGAGTCATGTGAGTAATCT+TGG + chr8_4:10446019-10446038 None:intergenic 35.0%
!! GCAAAGGTGTTTCATCTAAC+GGG - chr8_4:10444893-10444912 Msa1312950:three_prime_UTR 40.0%
!! CAAAGGTGTTTCATCTAACG+GGG - chr8_4:10444894-10444913 Msa1312950:three_prime_UTR 40.0%
TCAGCATACAGAATAGGAGA+GGG + chr8_4:10444974-10444993 None:intergenic 40.0%
TACCTTTCGGAGTTGAAATC+TGG - chr8_4:10445525-10445544 Msa1312950:intron 40.0%
TTCCAGATTTCAACTCCGAA+AGG + chr8_4:10445530-10445549 None:intergenic 40.0%
CTTGGCACTCCATAGTAAAA+TGG + chr8_4:10446001-10446020 None:intergenic 40.0%
!! GCAAAGGTGTTTCATCTAAC+GGG - chr8_4:10444893-10444912 Msa1312950:three_prime_UTR 40.0%
!! CAAAGGTGTTTCATCTAACG+GGG - chr8_4:10444894-10444913 Msa1312950:three_prime_UTR 40.0%
TCAGCATACAGAATAGGAGA+GGG + chr8_4:10444974-10444993 None:intergenic 40.0%
TACCTTTCGGAGTTGAAATC+TGG - chr8_4:10445525-10445544 Msa1312950:intron 40.0%
TTCCAGATTTCAACTCCGAA+AGG + chr8_4:10445530-10445549 None:intergenic 40.0%
CTTGGCACTCCATAGTAAAA+TGG + chr8_4:10446001-10446020 None:intergenic 40.0%
! GGGCTGCTGAATTTTCTTTG+TGG - chr8_4:10444914-10444933 Msa1312950:three_prime_UTR 45.0%
GTCAGCATACAGAATAGGAG+AGG + chr8_4:10444975-10444994 None:intergenic 45.0%
GATGCGTCAGCATACAGAAT+AGG + chr8_4:10444980-10444999 None:intergenic 45.0%
CTGACGCATCATCTCCATAT+AGG - chr8_4:10444990-10445009 Msa1312950:three_prime_UTR 45.0%
CTCACATGACTCTAGTGTGA+AGG - chr8_4:10446025-10446044 Msa1312950:intron 45.0%
TGCAATCAGTCCAAAGATGC+AGG - chr8_4:10446060-10446079 Msa1312950:intron 45.0%
TCGAGTGTTACCTGCATCTT+TGG + chr8_4:10446073-10446092 None:intergenic 45.0%
! GGGCTGCTGAATTTTCTTTG+TGG - chr8_4:10444914-10444933 Msa1312950:three_prime_UTR 45.0%
GTCAGCATACAGAATAGGAG+AGG + chr8_4:10444975-10444994 None:intergenic 45.0%
GATGCGTCAGCATACAGAAT+AGG + chr8_4:10444980-10444999 None:intergenic 45.0%
CTGACGCATCATCTCCATAT+AGG - chr8_4:10444990-10445009 Msa1312950:three_prime_UTR 45.0%
CTCACATGACTCTAGTGTGA+AGG - chr8_4:10446025-10446044 Msa1312950:intron 45.0%
TGCAATCAGTCCAAAGATGC+AGG - chr8_4:10446060-10446079 Msa1312950:intron 45.0%
TCGAGTGTTACCTGCATCTT+TGG + chr8_4:10446073-10446092 None:intergenic 45.0%
CATGACTCTAGTGTGAAGGC+TGG - chr8_4:10446029-10446048 Msa1312950:intron 50.0%
CATGACTCTAGTGTGAAGGC+TGG - chr8_4:10446029-10446048 Msa1312950:intron 50.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 10444841 10446273 10444841 ID=Msa1312950;Name=Msa1312950
chr8_4 mRNA 10444841 10446273 10444841 ID=Msa1312950-mRNA-1;Parent=Msa1312950;Name=Msa1312950-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|1|1|2|188|71
chr8_4 exon 10444841 10445149 10444841 ID=Msa1312950-mRNA-1:exon:3906;Parent=Msa1312950-mRNA-1
chr8_4 exon 10446179 10446273 10446179 ID=Msa1312950-mRNA-1:exon:3905;Parent=Msa1312950-mRNA-1
chr8_4 CDS 10446179 10446273 10446179 ID=Msa1312950-mRNA-1:cds;Parent=Msa1312950-mRNA-1
chr8_4 CDS 10445029 10445149 10445029 ID=Msa1312950-mRNA-1:cds;Parent=Msa1312950-mRNA-1
chr8_4 three_prime_UTR 10444841 10445028 10444841 ID=Msa1312950-mRNA-1:three_prime_utr;Parent=Msa1312950-mRNA-1
Gene Sequence

>Msa1312950

ATGCAGGACAAATGTTTCGAAGTTGCAAAACGCATAATTGAAGCCATTAAGAGCAAAGGTGTTTCATCTAACGGGGCTGCTGAATTTTCTTTGTGTGTGAAGGTAAACCCTTGTTTTAGGGATTATTACCATTTTACTATGGAGTGCCAAGATTACTCACATGACTCTAGTGTGAAGGCTGGTATTTTGATGCAATCAGTCCAAAGATGCAGGTAA
Protein sequence

>Msa1312950

MQDKCFEVAKRIIEAIKSKGVSSNGAAEFSLCVKVNPCFRDYYHFTMECQDYSHDSSVKAGILMQSVQRCR*