AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0724650

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 43 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGGACTACCTCATACTTT+TGG 0.338565 5_1:+23478814 Msa0724650:intron
AATCGTGATGTTTCACTCTA+AGG 0.341127 5_1:-23478843 None:intergenic
CACAGTGCAAGTACAAAATC+AGG 0.370709 5_1:+23478266 None:intergenic
AAGTTAACGGAATAAGTTTA+CGG 0.387813 5_1:-23478342 None:intergenic
CGATTGTTCTACGAGTTTAG+TGG 0.409935 5_1:+23478536 Msa0724650:five_prime_UTR
TCCGAACATCACATTTGGTA+TGG 0.417548 5_1:-23478929 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 5_1:-23478577 None:intergenic
ACCTTTGAAGTTCCTATCGT+TGG 0.439777 5_1:+23478686 Msa0724650:five_prime_UTR
CCGAACATCACATTTGGTAT+GGG 0.451435 5_1:-23478928 None:intergenic
TGCCGCACTAATTGAATGAT+AGG 0.456891 5_1:-23478648 None:intergenic
TTGTGTTGCCAATGGTATTG+AGG 0.460704 5_1:+23478969 Msa0724650:CDS
ACTAACTGATTTGTTGAAAA+CGG 0.466471 5_1:-23478480 None:intergenic
GTCGCTTTCCAGTACCTTGG+TGG 0.467027 5_1:+23478569 Msa0724650:five_prime_UTR
CCAAATGTGATGTTCGGAAA+AGG 0.475440 5_1:+23478934 Msa0724650:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 5_1:+23478928 Msa0724650:CDS
GAGCAATGACACTTGCTAGA+TGG 0.477492 5_1:+23478437 Msa0724650:five_prime_UTR
GTCATGTGTTTATCAACGCT+TGG 0.483566 5_1:-23479052 None:intergenic
TGTGTTGCCAATGGTATTGA+GGG 0.494690 5_1:+23478970 Msa0724650:CDS
AGGAATTTGCCAAAAGTATG+AGG 0.497368 5_1:-23478823 None:intergenic
TTCTATATAAATAAGATGAA+CGG 0.497916 5_1:+23478316 Msa0724650:five_prime_UTR
TTTCAAGTGCAAGTACATCA+TGG 0.507590 5_1:+23479008 Msa0724650:CDS
CTGCCTAACTTCTAGGATGT+CGG 0.510869 5_1:+23478368 Msa0724650:five_prime_UTR
AAATATTCAGCAACGAAGAA+TGG 0.515537 5_1:-23478401 None:intergenic
TCTCCGACATCCTAGAAGTT+AGG 0.520587 5_1:-23478371 None:intergenic
TCTAGCAAGTGTCATTGCTC+TGG 0.521579 5_1:-23478434 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.526348 5_1:-23478883 None:intergenic
GGCTGTTGTTGACAGATGGT+TGG 0.547496 5_1:+23478504 Msa0724650:five_prime_UTR
CGAACATCACATTTGGTATG+GGG 0.552019 5_1:-23478927 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 5_1:-23478901 None:intergenic
GTCTCCGCCCTCAATACCAT+TGG 0.575295 5_1:-23478977 None:intergenic
AGTCGGCTGTTGTTGACAGA+TGG 0.580790 5_1:+23478500 Msa0724650:five_prime_UTR
ATCGTCGCTTTCCAGTACCT+TGG 0.585632 5_1:+23478566 Msa0724650:five_prime_UTR
TGACACTTGCTAGATGGTGA+TGG 0.594754 5_1:+23478443 Msa0724650:five_prime_UTR
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 5_1:+23478938 Msa0724650:CDS
TCCAACGATAGGAACTTCAA+AGG 0.611311 5_1:-23478687 None:intergenic
GACACTTGCTAGATGGTGAT+GGG 0.615365 5_1:+23478444 Msa0724650:five_prime_UTR
TCGATCGACGAAATCACCTA+AGG 0.628108 5_1:+23478712 Msa0724650:five_prime_UTR
GCCGCACTAATTGAATGATA+GGG 0.635015 5_1:-23478647 None:intergenic
GTCGATCGATATCCAACGAT+AGG 0.637968 5_1:-23478698 None:intergenic
ACCCTATCATTCAATTAGTG+CGG 0.638071 5_1:+23478646 Msa0724650:five_prime_UTR
GCACTAATTGAATGATAGGG+TGG 0.666571 5_1:-23478644 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 5_1:-23478583 None:intergenic
GTTGCCAATGGTATTGAGGG+CGG 0.712333 5_1:+23478973 Msa0724650:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTATATAAATAAGATGAA+CGG + chr5_1:23478316-23478335 Msa0724650:five_prime_UTR 15.0%
!! TTAGAAATATGCTATAATAA+AGG + chr5_1:23478764-23478783 Msa0724650:intron 15.0%
!!! TGTCATTAACATTTTTTTTA+GGG + chr5_1:23478796-23478815 Msa0724650:intron 15.0%
!! TTCTATATAAATAAGATGAA+CGG + chr5_1:23478316-23478335 Msa0724650:five_prime_UTR 15.0%
!! TTAGAAATATGCTATAATAA+AGG + chr5_1:23478764-23478783 Msa0724650:intron 15.0%
!!! TGTCATTAACATTTTTTTTA+GGG + chr5_1:23478796-23478815 Msa0724650:intron 15.0%
!! AAAAAACAATAAACAACCTT+AGG - chr5_1:23478731-23478750 None:intergenic 20.0%
!!! CTGTCATTAACATTTTTTTT+AGG + chr5_1:23478795-23478814 Msa0724650:intron 20.0%
!! AAAAAACAATAAACAACCTT+AGG - chr5_1:23478731-23478750 None:intergenic 20.0%
!!! CTGTCATTAACATTTTTTTT+AGG + chr5_1:23478795-23478814 Msa0724650:intron 20.0%
! AAGTTAACGGAATAAGTTTA+CGG - chr5_1:23478345-23478364 None:intergenic 25.0%
!!! ACTAACTGATTTGTTGAAAA+CGG - chr5_1:23478483-23478502 None:intergenic 25.0%
!! TTTTCAACAAATCAGTTAGT+CGG + chr5_1:23478483-23478502 Msa0724650:five_prime_UTR 25.0%
! AAGTTAACGGAATAAGTTTA+CGG - chr5_1:23478345-23478364 None:intergenic 25.0%
!!! ACTAACTGATTTGTTGAAAA+CGG - chr5_1:23478483-23478502 None:intergenic 25.0%
!! TTTTCAACAAATCAGTTAGT+CGG + chr5_1:23478483-23478502 Msa0724650:five_prime_UTR 25.0%
AGTTAGGCAGAAAAAGTTAA+CGG - chr5_1:23478358-23478377 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG - chr5_1:23478404-23478423 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr5_1:23478886-23478905 None:intergenic 30.0%
AGTTAGGCAGAAAAAGTTAA+CGG - chr5_1:23478358-23478377 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG - chr5_1:23478404-23478423 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr5_1:23478886-23478905 None:intergenic 30.0%
!! ACTTTTTCTGCCTAACTTCT+AGG + chr5_1:23478361-23478380 Msa0724650:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr5_1:23478586-23478605 None:intergenic 35.0%
ACCCTATCATTCAATTAGTG+CGG + chr5_1:23478646-23478665 Msa0724650:five_prime_UTR 35.0%
! AGGAATTTGCCAAAAGTATG+AGG - chr5_1:23478826-23478845 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr5_1:23478846-23478865 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr5_1:23478904-23478923 None:intergenic 35.0%
! TTTCAAGTGCAAGTACATCA+TGG + chr5_1:23479008-23479027 Msa0724650:CDS 35.0%
!! ACTTTTTCTGCCTAACTTCT+AGG + chr5_1:23478361-23478380 Msa0724650:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr5_1:23478586-23478605 None:intergenic 35.0%
ACCCTATCATTCAATTAGTG+CGG + chr5_1:23478646-23478665 Msa0724650:five_prime_UTR 35.0%
! AGGAATTTGCCAAAAGTATG+AGG - chr5_1:23478826-23478845 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr5_1:23478846-23478865 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr5_1:23478904-23478923 None:intergenic 35.0%
! TTTCAAGTGCAAGTACATCA+TGG + chr5_1:23479008-23479027 Msa0724650:CDS 35.0%
CGATTGTTCTACGAGTTTAG+TGG + chr5_1:23478536-23478555 Msa0724650:five_prime_UTR 40.0%
GCACTAATTGAATGATAGGG+TGG - chr5_1:23478647-23478666 None:intergenic 40.0%
GCCGCACTAATTGAATGATA+GGG - chr5_1:23478650-23478669 None:intergenic 40.0%
TGCCGCACTAATTGAATGAT+AGG - chr5_1:23478651-23478670 None:intergenic 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + chr5_1:23478686-23478705 Msa0724650:five_prime_UTR 40.0%
TCCAACGATAGGAACTTCAA+AGG - chr5_1:23478690-23478709 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + chr5_1:23478814-23478833 Msa0724650:intron 40.0%
CGAACATCACATTTGGTATG+GGG - chr5_1:23478930-23478949 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr5_1:23478931-23478950 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr5_1:23478928-23478947 Msa0724650:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr5_1:23478932-23478951 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr5_1:23478937-23478956 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr5_1:23478934-23478953 Msa0724650:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr5_1:23478938-23478957 Msa0724650:CDS 40.0%
! ACGAGTTTTTGTGTTGCCAA+TGG + chr5_1:23478961-23478980 Msa0724650:CDS 40.0%
TTGTGTTGCCAATGGTATTG+AGG + chr5_1:23478969-23478988 Msa0724650:CDS 40.0%
! TGTGTTGCCAATGGTATTGA+GGG + chr5_1:23478970-23478989 Msa0724650:CDS 40.0%
CGATTGTTCTACGAGTTTAG+TGG + chr5_1:23478536-23478555 Msa0724650:five_prime_UTR 40.0%
GCACTAATTGAATGATAGGG+TGG - chr5_1:23478647-23478666 None:intergenic 40.0%
GCCGCACTAATTGAATGATA+GGG - chr5_1:23478650-23478669 None:intergenic 40.0%
TGCCGCACTAATTGAATGAT+AGG - chr5_1:23478651-23478670 None:intergenic 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + chr5_1:23478686-23478705 Msa0724650:five_prime_UTR 40.0%
TCCAACGATAGGAACTTCAA+AGG - chr5_1:23478690-23478709 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + chr5_1:23478814-23478833 Msa0724650:intron 40.0%
CGAACATCACATTTGGTATG+GGG - chr5_1:23478930-23478949 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr5_1:23478931-23478950 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr5_1:23478928-23478947 Msa0724650:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr5_1:23478932-23478951 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr5_1:23478937-23478956 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr5_1:23478934-23478953 Msa0724650:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr5_1:23478938-23478957 Msa0724650:CDS 40.0%
! ACGAGTTTTTGTGTTGCCAA+TGG + chr5_1:23478961-23478980 Msa0724650:CDS 40.0%
TTGTGTTGCCAATGGTATTG+AGG + chr5_1:23478969-23478988 Msa0724650:CDS 40.0%
! TGTGTTGCCAATGGTATTGA+GGG + chr5_1:23478970-23478989 Msa0724650:CDS 40.0%
!! CTGCCTAACTTCTAGGATGT+CGG + chr5_1:23478368-23478387 Msa0724650:five_prime_UTR 45.0%
TCTCCGACATCCTAGAAGTT+AGG - chr5_1:23478374-23478393 None:intergenic 45.0%
! TCTAGCAAGTGTCATTGCTC+TGG - chr5_1:23478437-23478456 None:intergenic 45.0%
! GAGCAATGACACTTGCTAGA+TGG + chr5_1:23478437-23478456 Msa0724650:five_prime_UTR 45.0%
! TGACACTTGCTAGATGGTGA+TGG + chr5_1:23478443-23478462 Msa0724650:five_prime_UTR 45.0%
! GACACTTGCTAGATGGTGAT+GGG + chr5_1:23478444-23478463 Msa0724650:five_prime_UTR 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr5_1:23478580-23478599 None:intergenic 45.0%
GTCGATCGATATCCAACGAT+AGG - chr5_1:23478701-23478720 None:intergenic 45.0%
TCGATCGACGAAATCACCTA+AGG + chr5_1:23478712-23478731 Msa0724650:five_prime_UTR 45.0%
!! CTGCCTAACTTCTAGGATGT+CGG + chr5_1:23478368-23478387 Msa0724650:five_prime_UTR 45.0%
TCTCCGACATCCTAGAAGTT+AGG - chr5_1:23478374-23478393 None:intergenic 45.0%
! TCTAGCAAGTGTCATTGCTC+TGG - chr5_1:23478437-23478456 None:intergenic 45.0%
! GAGCAATGACACTTGCTAGA+TGG + chr5_1:23478437-23478456 Msa0724650:five_prime_UTR 45.0%
! TGACACTTGCTAGATGGTGA+TGG + chr5_1:23478443-23478462 Msa0724650:five_prime_UTR 45.0%
! GACACTTGCTAGATGGTGAT+GGG + chr5_1:23478444-23478463 Msa0724650:five_prime_UTR 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr5_1:23478580-23478599 None:intergenic 45.0%
GTCGATCGATATCCAACGAT+AGG - chr5_1:23478701-23478720 None:intergenic 45.0%
TCGATCGACGAAATCACCTA+AGG + chr5_1:23478712-23478731 Msa0724650:five_prime_UTR 45.0%
AGTCGGCTGTTGTTGACAGA+TGG + chr5_1:23478500-23478519 Msa0724650:five_prime_UTR 50.0%
GGCTGTTGTTGACAGATGGT+TGG + chr5_1:23478504-23478523 Msa0724650:five_prime_UTR 50.0%
! ATCGTCGCTTTCCAGTACCT+TGG + chr5_1:23478566-23478585 Msa0724650:five_prime_UTR 50.0%
! GTTGCCAATGGTATTGAGGG+CGG + chr5_1:23478973-23478992 Msa0724650:CDS 50.0%
AGTCGGCTGTTGTTGACAGA+TGG + chr5_1:23478500-23478519 Msa0724650:five_prime_UTR 50.0%
GGCTGTTGTTGACAGATGGT+TGG + chr5_1:23478504-23478523 Msa0724650:five_prime_UTR 50.0%
! ATCGTCGCTTTCCAGTACCT+TGG + chr5_1:23478566-23478585 Msa0724650:five_prime_UTR 50.0%
! GTTGCCAATGGTATTGAGGG+CGG + chr5_1:23478973-23478992 Msa0724650:CDS 50.0%
! GTCGCTTTCCAGTACCTTGG+TGG + chr5_1:23478569-23478588 Msa0724650:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr5_1:23478980-23478999 None:intergenic 55.0%
! GTCGCTTTCCAGTACCTTGG+TGG + chr5_1:23478569-23478588 Msa0724650:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr5_1:23478980-23478999 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 23478270 23479062 23478270 ID=Msa0724650;Name=Msa0724650
chr5_1 mRNA 23478270 23479062 23478270 ID=Msa0724650-mRNA-1;Parent=Msa0724650;Name=Msa0724650-mRNA-1;_AED=0.04;_eAED=0.04;_QI=518|1|0.5|1|1|1|2|0|63
chr5_1 exon 23478270 23478733 23478270 ID=Msa0724650-mRNA-1:exon:8706;Parent=Msa0724650-mRNA-1
chr5_1 exon 23478817 23479062 23478817 ID=Msa0724650-mRNA-1:exon:8707;Parent=Msa0724650-mRNA-1
chr5_1 five_prime_UTR 23478270 23478733 23478270 ID=Msa0724650-mRNA-1:five_prime_utr;Parent=Msa0724650-mRNA-1
chr5_1 five_prime_UTR 23478817 23478870 23478817 ID=Msa0724650-mRNA-1:five_prime_utr;Parent=Msa0724650-mRNA-1
chr5_1 CDS 23478871 23479062 23478871 ID=Msa0724650-mRNA-1:cds;Parent=Msa0724650-mRNA-1
Gene Sequence

>Msa0724650

ATGTTGTGCAGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGTTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTACATCATGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0724650

MLCRPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCVANGIEGGDVLIFKCKYIMDKKYVIVSKR*