AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0783370

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 44 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCTTTCTCTAAAATTTA+AGG 0.102108 5_2:+67317640 Msa0783370:three_prime_UTR
TGTTATGATGCTTTATTATA+TGG 0.233517 5_2:+67317550 Msa0783370:three_prime_UTR
GCGAAATATGGAAGCTATAA+AGG 0.241421 5_2:+67317190 Msa0783370:CDS
AAACAAAATATTAATCAAAT+AGG 0.303510 5_2:-67316345 None:intergenic
GAAGTAAATGATGCGAAATA+TGG 0.348096 5_2:+67317178 Msa0783370:CDS
GTTGTTGCGGTAATACTAAT+AGG 0.359838 5_2:+67316474 Msa0783370:CDS
CCTCCTAGTAATTGTCTCTA+TGG 0.370084 5_2:+67316452 Msa0783370:CDS
ACCACGACCACGTCCACGTC+CGG 0.405196 5_2:-67317260 None:intergenic
GGCTATCCTGGTCGTGGTGG+TGG 0.418069 5_2:+67317214 Msa0783370:CDS
TAACCATTACCTCGGCAAAC+TGG 0.421810 5_2:-67316404 None:intergenic
CGAAATATGGAAGCTATAAA+GGG 0.431637 5_2:+67317191 Msa0783370:CDS
ATGCTAGTGTACTAGTGTTA+AGG 0.443736 5_2:+67317576 Msa0783370:three_prime_UTR
CCCGGACGTGGACGTGGTCG+TGG 0.455650 5_2:+67317259 Msa0783370:CDS
TATCCAGTTTGCCGAGGTAA+TGG 0.460407 5_2:+67316401 Msa0783370:CDS
TATCATGGTGGTCGTTATCC+CGG 0.474111 5_2:+67317241 Msa0783370:CDS
CGTGGTGGTGGTAATTATCA+TGG 0.484305 5_2:+67317226 Msa0783370:CDS
CGTGGACGTGGTCGTGGTAA+CGG 0.488326 5_2:+67317265 Msa0783370:CDS
GCACCTATCGCAACAGCCAC+AGG 0.500058 5_2:-67317314 None:intergenic
AGACAATTACTAGGAGGAGC+TGG 0.500224 5_2:-67316446 None:intergenic
GATAGGTGCTGCGCATATGC+TGG 0.500265 5_2:+67317328 Msa0783370:three_prime_UTR
CAACCATAGAGACAATTACT+AGG 0.500395 5_2:-67316455 None:intergenic
AACGGTGGTCGGCATGGATG+AGG 0.508381 5_2:+67317283 Msa0783370:CDS
CGTGGTAACGGTGGTCGGCA+TGG 0.511616 5_2:+67317277 Msa0783370:CDS
CGTTATCCCGGACGTGGACG+TGG 0.516758 5_2:+67317253 Msa0783370:CDS
TAAACTATGTTGTACTAGCA+TGG 0.548137 5_2:+67317437 Msa0783370:three_prime_UTR
CACCTATCGCAACAGCCACA+GGG 0.552098 5_2:-67317313 None:intergenic
GATAAATGCTGCTCATATGC+TGG 0.553499 5_2:+67316518 Msa0783370:CDS
CCACGACCACGTCCACGTCC+GGG 0.559671 5_2:-67317259 None:intergenic
GCCCCTGTGGCTGTTGCGAT+AGG 0.571660 5_2:+67317311 Msa0783370:three_prime_UTR
AATTGTCTCTATGGTTGTTG+CGG 0.579189 5_2:+67316461 Msa0783370:CDS
GGTGGTCGTTATCCCGGACG+TGG 0.585858 5_2:+67317247 Msa0783370:CDS
GTGGTCGTGGTAACGGTGGT+CGG 0.590329 5_2:+67317272 Msa0783370:CDS
TAATTACCACCACCACGACC+AGG 0.617550 5_2:-67317220 None:intergenic
TACTGCGGTAACCATTACCT+CGG 0.640257 5_2:-67316412 None:intergenic
TATGTGTGATGATGTTGATG+AGG 0.644218 5_2:+67317505 Msa0783370:three_prime_UTR
GGATGAGGTTATTGCCCCTG+TGG 0.654495 5_2:+67317298 Msa0783370:exon
GAAATATGGAAGCTATAAAG+GGG 0.661164 5_2:+67317192 Msa0783370:CDS
CCATAGAGACAATTACTAGG+AGG 0.673027 5_2:-67316452 None:intergenic
ACCTATCGCAACAGCCACAG+GGG 0.675647 5_2:-67317312 None:intergenic
GTAAGCTATCCAGTTTGCCG+AGG 0.679091 5_2:+67316395 Msa0783370:CDS
GGACGTGGTCGTGGTAACGG+TGG 0.686498 5_2:+67317268 Msa0783370:CDS
AAATATGGAAGCTATAAAGG+GGG 0.706345 5_2:+67317193 Msa0783370:CDS
GGTGGTGGTAATTATCATGG+TGG 0.730386 5_2:+67317229 Msa0783370:CDS
CTGGAAGACAAGTACTACTG+CGG 0.736775 5_2:-67316427 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACAAAATATTAATCAAAT+AGG - chr5_2:67316348-67316367 None:intergenic 10.0%
!!! AAAAATATTTTAGCATAAAA+TGG + chr5_2:67317032-67317051 Msa0783370:intron 10.0%
!! AAACAAAATATTAATCAAAT+AGG - chr5_2:67316348-67316367 None:intergenic 10.0%
!!! AAAAATATTTTAGCATAAAA+TGG + chr5_2:67317032-67317051 Msa0783370:intron 10.0%
!!! TTTGATTAATATTTTGTTTG+CGG + chr5_2:67316349-67316368 Msa0783370:CDS 15.0%
!! ATCTAAAAAAAAAGTTTCAA+AGG + chr5_2:67317055-67317074 Msa0783370:intron 15.0%
!!! TTTGATTAATATTTTGTTTG+CGG + chr5_2:67316349-67316368 Msa0783370:CDS 15.0%
!! ATCTAAAAAAAAAGTTTCAA+AGG + chr5_2:67317055-67317074 Msa0783370:intron 15.0%
!! TTATGACATATCTATACTAT+TGG - chr5_2:67316869-67316888 None:intergenic 20.0%
!!! TGTTATGATGCTTTATTATA+TGG + chr5_2:67317550-67317569 Msa0783370:three_prime_UTR 20.0%
!! TTATGACATATCTATACTAT+TGG - chr5_2:67316869-67316888 None:intergenic 20.0%
!!! TGTTATGATGCTTTATTATA+TGG + chr5_2:67317550-67317569 Msa0783370:three_prime_UTR 20.0%
! TAAATTAAATGTTTGTGACG+AGG + chr5_2:67316702-67316721 Msa0783370:intron 25.0%
! AAATTAAATGTTTGTGACGA+GGG + chr5_2:67316703-67316722 Msa0783370:intron 25.0%
! TAGTATAGATATGTCATAAG+TGG + chr5_2:67316870-67316889 Msa0783370:intron 25.0%
! TTTACAAATACATTGTGCAA+AGG - chr5_2:67316948-67316967 None:intergenic 25.0%
!! AGTCTCTCCTTTTAAATTTA+TGG + chr5_2:67316980-67316999 Msa0783370:intron 25.0%
! CCTCAATCCATAAATTTAAA+AGG - chr5_2:67316990-67317009 None:intergenic 25.0%
!!! CCTTTTAAATTTATGGATTG+AGG + chr5_2:67316987-67317006 Msa0783370:intron 25.0%
! TTGAGGTTTCTAACAAAATT+TGG + chr5_2:67317004-67317023 Msa0783370:intron 25.0%
! TAAATTAAATGTTTGTGACG+AGG + chr5_2:67316702-67316721 Msa0783370:intron 25.0%
! AAATTAAATGTTTGTGACGA+GGG + chr5_2:67316703-67316722 Msa0783370:intron 25.0%
! TAGTATAGATATGTCATAAG+TGG + chr5_2:67316870-67316889 Msa0783370:intron 25.0%
! TTTACAAATACATTGTGCAA+AGG - chr5_2:67316948-67316967 None:intergenic 25.0%
!! AGTCTCTCCTTTTAAATTTA+TGG + chr5_2:67316980-67316999 Msa0783370:intron 25.0%
! CCTCAATCCATAAATTTAAA+AGG - chr5_2:67316990-67317009 None:intergenic 25.0%
!!! CCTTTTAAATTTATGGATTG+AGG + chr5_2:67316987-67317006 Msa0783370:intron 25.0%
! TTGAGGTTTCTAACAAAATT+TGG + chr5_2:67317004-67317023 Msa0783370:intron 25.0%
AATACACAGCAACCAAATTT+CGG - chr5_2:67316837-67316856 None:intergenic 30.0%
TTTCTATAATGTGTTTGCAG+AGG + chr5_2:67317138-67317157 Msa0783370:intron 30.0%
GAAGTAAATGATGCGAAATA+TGG + chr5_2:67317178-67317197 Msa0783370:CDS 30.0%
CGAAATATGGAAGCTATAAA+GGG + chr5_2:67317191-67317210 Msa0783370:CDS 30.0%
GAAATATGGAAGCTATAAAG+GGG + chr5_2:67317192-67317211 Msa0783370:CDS 30.0%
AAATATGGAAGCTATAAAGG+GGG + chr5_2:67317193-67317212 Msa0783370:CDS 30.0%
TAAACTATGTTGTACTAGCA+TGG + chr5_2:67317437-67317456 Msa0783370:three_prime_UTR 30.0%
AATACACAGCAACCAAATTT+CGG - chr5_2:67316837-67316856 None:intergenic 30.0%
TTTCTATAATGTGTTTGCAG+AGG + chr5_2:67317138-67317157 Msa0783370:intron 30.0%
GAAGTAAATGATGCGAAATA+TGG + chr5_2:67317178-67317197 Msa0783370:CDS 30.0%
CGAAATATGGAAGCTATAAA+GGG + chr5_2:67317191-67317210 Msa0783370:CDS 30.0%
GAAATATGGAAGCTATAAAG+GGG + chr5_2:67317192-67317211 Msa0783370:CDS 30.0%
AAATATGGAAGCTATAAAGG+GGG + chr5_2:67317193-67317212 Msa0783370:CDS 30.0%
TAAACTATGTTGTACTAGCA+TGG + chr5_2:67317437-67317456 Msa0783370:three_prime_UTR 30.0%
CAACCATAGAGACAATTACT+AGG - chr5_2:67316458-67316477 None:intergenic 35.0%
AATTGTCTCTATGGTTGTTG+CGG + chr5_2:67316461-67316480 Msa0783370:CDS 35.0%
GTTGTTGCGGTAATACTAAT+AGG + chr5_2:67316474-67316493 Msa0783370:CDS 35.0%
TAATACTGTACTGTGTTCAC+AGG + chr5_2:67316640-67316659 Msa0783370:intron 35.0%
GAAAATTCACACACACAAGT+CGG - chr5_2:67316737-67316756 None:intergenic 35.0%
TGGATAGAAAGTCCGAAATT+TGG + chr5_2:67316822-67316841 Msa0783370:intron 35.0%
GCGAAATATGGAAGCTATAA+AGG + chr5_2:67317190-67317209 Msa0783370:CDS 35.0%
! TATGTGTGATGATGTTGATG+AGG + chr5_2:67317505-67317524 Msa0783370:three_prime_UTR 35.0%
ATGCTAGTGTACTAGTGTTA+AGG + chr5_2:67317576-67317595 Msa0783370:three_prime_UTR 35.0%
CAACCATAGAGACAATTACT+AGG - chr5_2:67316458-67316477 None:intergenic 35.0%
AATTGTCTCTATGGTTGTTG+CGG + chr5_2:67316461-67316480 Msa0783370:CDS 35.0%
GTTGTTGCGGTAATACTAAT+AGG + chr5_2:67316474-67316493 Msa0783370:CDS 35.0%
TAATACTGTACTGTGTTCAC+AGG + chr5_2:67316640-67316659 Msa0783370:intron 35.0%
GAAAATTCACACACACAAGT+CGG - chr5_2:67316737-67316756 None:intergenic 35.0%
TGGATAGAAAGTCCGAAATT+TGG + chr5_2:67316822-67316841 Msa0783370:intron 35.0%
GCGAAATATGGAAGCTATAA+AGG + chr5_2:67317190-67317209 Msa0783370:CDS 35.0%
! TATGTGTGATGATGTTGATG+AGG + chr5_2:67317505-67317524 Msa0783370:three_prime_UTR 35.0%
ATGCTAGTGTACTAGTGTTA+AGG + chr5_2:67317576-67317595 Msa0783370:three_prime_UTR 35.0%
CCATAGAGACAATTACTAGG+AGG - chr5_2:67316455-67316474 None:intergenic 40.0%
CCTCCTAGTAATTGTCTCTA+TGG + chr5_2:67316452-67316471 Msa0783370:CDS 40.0%
GATAAATGCTGCTCATATGC+TGG + chr5_2:67316518-67316537 Msa0783370:CDS 40.0%
CCATAGAGACAATTACTAGG+AGG - chr5_2:67316455-67316474 None:intergenic 40.0%
CCTCCTAGTAATTGTCTCTA+TGG + chr5_2:67316452-67316471 Msa0783370:CDS 40.0%
GATAAATGCTGCTCATATGC+TGG + chr5_2:67316518-67316537 Msa0783370:CDS 40.0%
TATCCAGTTTGCCGAGGTAA+TGG + chr5_2:67316401-67316420 Msa0783370:CDS 45.0%
TAACCATTACCTCGGCAAAC+TGG - chr5_2:67316407-67316426 None:intergenic 45.0%
TACTGCGGTAACCATTACCT+CGG - chr5_2:67316415-67316434 None:intergenic 45.0%
CTGGAAGACAAGTACTACTG+CGG - chr5_2:67316430-67316449 None:intergenic 45.0%
AGACAATTACTAGGAGGAGC+TGG - chr5_2:67316449-67316468 None:intergenic 45.0%
AGGTCAAAGTCGTAGCTCAA+CGG + chr5_2:67316660-67316679 Msa0783370:intron 45.0%
! ATTGTGCGTTGATCACGAGA+TGG + chr5_2:67316802-67316821 Msa0783370:intron 45.0%
!! CGTGGTGGTGGTAATTATCA+TGG + chr5_2:67317226-67317245 Msa0783370:CDS 45.0%
! GGTGGTGGTAATTATCATGG+TGG + chr5_2:67317229-67317248 Msa0783370:CDS 45.0%
TATCATGGTGGTCGTTATCC+CGG + chr5_2:67317241-67317260 Msa0783370:CDS 45.0%
TATCCAGTTTGCCGAGGTAA+TGG + chr5_2:67316401-67316420 Msa0783370:CDS 45.0%
TAACCATTACCTCGGCAAAC+TGG - chr5_2:67316407-67316426 None:intergenic 45.0%
TACTGCGGTAACCATTACCT+CGG - chr5_2:67316415-67316434 None:intergenic 45.0%
CTGGAAGACAAGTACTACTG+CGG - chr5_2:67316430-67316449 None:intergenic 45.0%
AGACAATTACTAGGAGGAGC+TGG - chr5_2:67316449-67316468 None:intergenic 45.0%
AGGTCAAAGTCGTAGCTCAA+CGG + chr5_2:67316660-67316679 Msa0783370:intron 45.0%
! ATTGTGCGTTGATCACGAGA+TGG + chr5_2:67316802-67316821 Msa0783370:intron 45.0%
!! CGTGGTGGTGGTAATTATCA+TGG + chr5_2:67317226-67317245 Msa0783370:CDS 45.0%
! GGTGGTGGTAATTATCATGG+TGG + chr5_2:67317229-67317248 Msa0783370:CDS 45.0%
TATCATGGTGGTCGTTATCC+CGG + chr5_2:67317241-67317260 Msa0783370:CDS 45.0%
GTAAGCTATCCAGTTTGCCG+AGG + chr5_2:67316395-67316414 Msa0783370:CDS 50.0%
AGCTATAAAGGGGGCTATCC+TGG + chr5_2:67317202-67317221 Msa0783370:CDS 50.0%
TAATTACCACCACCACGACC+AGG - chr5_2:67317223-67317242 None:intergenic 50.0%
GTAAGCTATCCAGTTTGCCG+AGG + chr5_2:67316395-67316414 Msa0783370:CDS 50.0%
AGCTATAAAGGGGGCTATCC+TGG + chr5_2:67317202-67317221 Msa0783370:CDS 50.0%
TAATTACCACCACCACGACC+AGG - chr5_2:67317223-67317242 None:intergenic 50.0%
GGATGAGGTTATTGCCCCTG+TGG + chr5_2:67317298-67317317 Msa0783370:exon 55.0%
ACCTATCGCAACAGCCACAG+GGG - chr5_2:67317315-67317334 None:intergenic 55.0%
CACCTATCGCAACAGCCACA+GGG - chr5_2:67317316-67317335 None:intergenic 55.0%
! GATAGGTGCTGCGCATATGC+TGG + chr5_2:67317328-67317347 Msa0783370:three_prime_UTR 55.0%
GGATGAGGTTATTGCCCCTG+TGG + chr5_2:67317298-67317317 Msa0783370:exon 55.0%
ACCTATCGCAACAGCCACAG+GGG - chr5_2:67317315-67317334 None:intergenic 55.0%
CACCTATCGCAACAGCCACA+GGG - chr5_2:67317316-67317335 None:intergenic 55.0%
! GATAGGTGCTGCGCATATGC+TGG + chr5_2:67317328-67317347 Msa0783370:three_prime_UTR 55.0%
AAAGGGGGCTATCCTGGTCG+TGG + chr5_2:67317208-67317227 Msa0783370:CDS 60.0%
CGTGGACGTGGTCGTGGTAA+CGG + chr5_2:67317265-67317284 Msa0783370:CDS 60.0%
!! GTGGTCGTGGTAACGGTGGT+CGG + chr5_2:67317272-67317291 Msa0783370:CDS 60.0%
AACGGTGGTCGGCATGGATG+AGG + chr5_2:67317283-67317302 Msa0783370:CDS 60.0%
GCACCTATCGCAACAGCCAC+AGG - chr5_2:67317317-67317336 None:intergenic 60.0%
AAAGGGGGCTATCCTGGTCG+TGG + chr5_2:67317208-67317227 Msa0783370:CDS 60.0%
CGTGGACGTGGTCGTGGTAA+CGG + chr5_2:67317265-67317284 Msa0783370:CDS 60.0%
!! GTGGTCGTGGTAACGGTGGT+CGG + chr5_2:67317272-67317291 Msa0783370:CDS 60.0%
AACGGTGGTCGGCATGGATG+AGG + chr5_2:67317283-67317302 Msa0783370:CDS 60.0%
GCACCTATCGCAACAGCCAC+AGG - chr5_2:67317317-67317336 None:intergenic 60.0%
GGCTATCCTGGTCGTGGTGG+TGG + chr5_2:67317214-67317233 Msa0783370:CDS 65.0%
GGTGGTCGTTATCCCGGACG+TGG + chr5_2:67317247-67317266 Msa0783370:CDS 65.0%
CGTTATCCCGGACGTGGACG+TGG + chr5_2:67317253-67317272 Msa0783370:CDS 65.0%
ACCACGACCACGTCCACGTC+CGG - chr5_2:67317263-67317282 None:intergenic 65.0%
!! GGACGTGGTCGTGGTAACGG+TGG + chr5_2:67317268-67317287 Msa0783370:CDS 65.0%
!! CGTGGTAACGGTGGTCGGCA+TGG + chr5_2:67317277-67317296 Msa0783370:CDS 65.0%
GCCCCTGTGGCTGTTGCGAT+AGG + chr5_2:67317311-67317330 Msa0783370:three_prime_UTR 65.0%
GGCTATCCTGGTCGTGGTGG+TGG + chr5_2:67317214-67317233 Msa0783370:CDS 65.0%
GGTGGTCGTTATCCCGGACG+TGG + chr5_2:67317247-67317266 Msa0783370:CDS 65.0%
CGTTATCCCGGACGTGGACG+TGG + chr5_2:67317253-67317272 Msa0783370:CDS 65.0%
ACCACGACCACGTCCACGTC+CGG - chr5_2:67317263-67317282 None:intergenic 65.0%
!! GGACGTGGTCGTGGTAACGG+TGG + chr5_2:67317268-67317287 Msa0783370:CDS 65.0%
!! CGTGGTAACGGTGGTCGGCA+TGG + chr5_2:67317277-67317296 Msa0783370:CDS 65.0%
GCCCCTGTGGCTGTTGCGAT+AGG + chr5_2:67317311-67317330 Msa0783370:three_prime_UTR 65.0%
GGGGGCTATCCTGGTCGTGG+TGG + chr5_2:67317211-67317230 Msa0783370:CDS 70.0%
CCACGACCACGTCCACGTCC+GGG - chr5_2:67317262-67317281 None:intergenic 70.0%
GGGGGCTATCCTGGTCGTGG+TGG + chr5_2:67317211-67317230 Msa0783370:CDS 70.0%
CCACGACCACGTCCACGTCC+GGG - chr5_2:67317262-67317281 None:intergenic 70.0%
CCCGGACGTGGACGTGGTCG+TGG + chr5_2:67317259-67317278 Msa0783370:CDS 75.0%
CCCGGACGTGGACGTGGTCG+TGG + chr5_2:67317259-67317278 Msa0783370:CDS 75.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 67316296 67317661 67316296 ID=Msa0783370;Name=Msa0783370
chr5_2 mRNA 67316296 67317661 67316296 ID=Msa0783370-mRNA-1;Parent=Msa0783370;Name=Msa0783370-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|0|0.5|0.5|1|1|2|358|129
chr5_2 exon 67316296 67316539 67316296 ID=Msa0783370-mRNA-1:exon:20217;Parent=Msa0783370-mRNA-1
chr5_2 exon 67317158 67317661 67317158 ID=Msa0783370-mRNA-1:exon:20218;Parent=Msa0783370-mRNA-1
chr5_2 CDS 67316296 67316539 67316296 ID=Msa0783370-mRNA-1:cds;Parent=Msa0783370-mRNA-1
chr5_2 CDS 67317158 67317303 67317158 ID=Msa0783370-mRNA-1:cds;Parent=Msa0783370-mRNA-1
chr5_2 three_prime_UTR 67317304 67317661 67317304 ID=Msa0783370-mRNA-1:three_prime_utr;Parent=Msa0783370-mRNA-1
Gene Sequence

>Msa0783370

ATGAATTTTTACGTGTTAAAAATATACAAAATTGTTATAATATTTAATTCCTATTTGATTAATATTTTGTTTGCGGAAGTTGTTGAACAAATAAATAAAGTAAGCTATCCAGTTTGCCGAGGTAATGGTTACCGCAGTAGTACTTGTCTTCCAGCTCCTCCTAGTAATTGTCTCTATGGTTGTTGCGGTAATACTAATAGGATTAATAGATCACTGAACTGTGATAAATGCTGCTCATATGCTGAGGTTGTTGAACGAACAAATGAAGTAAATGATGCGAAATATGGAAGCTATAAAGGGGGCTATCCTGGTCGTGGTGGTGGTAATTATCATGGTGGTCGTTATCCCGGACGTGGACGTGGTCGTGGTAACGGTGGTCGGCATGGATGA
Protein sequence

>Msa0783370

MNFYVLKIYKIVIIFNSYLINILFAEVVEQINKVSYPVCRGNGYRSSTCLPAPPSNCLYGCCGNTNRINRSLNCDKCCSYAEVVERTNEVNDAKYGSYKGGYPGRGGGNYHGGRYPGRGRGRGNGGRHG*