AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1025620

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1025620 MtrunA17_Chr5g0393501 36.000 100 61 1 10 106 143 242 2.80e-13 63.5
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
CACAGTGCATGTACAAAATC+AGG 0.330296 7_1:+56399169 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.332982 7_1:-56399743 None:intergenic
TAGGGACTACCTCATACTTT+TGG 0.338565 7_1:+56399714 Msa1025620:intron
CGATTGTTCTACGAGTTTAG+TGG 0.409935 7_1:+56399426 Msa1025620:five_prime_UTR
ATCTACTTCCACCATGGTAC+TGG 0.424919 7_1:-56399467 None:intergenic
TCCGAACATCACATTTGGTA+TGG 0.428251 7_1:-56399829 None:intergenic
ACCTTTGAAGTTCCTATCGT+TGG 0.439777 7_1:+56399576 Msa1025620:CDS
CCTCTTCCGAACATCACATT+TGG 0.453517 7_1:-56399834 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.472065 7_1:-56399828 None:intergenic
TGCCGCACTCATTGAATGAT+AGG 0.473193 7_1:-56399538 None:intergenic
GTCATGTGTTTATCAAAGCT+TGG 0.475616 7_1:-56399952 None:intergenic
CCCATACCAAATGTGATGTT+CGG 0.477035 7_1:+56399828 Msa1025620:CDS
GAGCAATGACACTTGCTAGA+TGG 0.483539 7_1:+56399327 Msa1025620:five_prime_UTR
AGGAATTTGCCAAAAGTATG+AGG 0.497368 7_1:-56399723 None:intergenic
TTCTATATAAATAAGATGAA+CGG 0.497916 7_1:+56399219 Msa1025620:five_prime_UTR
TGAATATTTCTACGAGCTAC+CGG 0.507354 7_1:+56399305 Msa1025620:five_prime_UTR
CTGCCTAACTTCTAGGATGT+CGG 0.510869 7_1:+56399258 Msa1025620:five_prime_UTR
GGCCGTTGTTGACAGATGGT+TGG 0.512157 7_1:+56399394 Msa1025620:five_prime_UTR
TTGTGTTGCCAATGGTATTG+AGG 0.514824 7_1:+56399869 Msa1025620:CDS
AAATATTCAGCAACGAAGAA+TGG 0.515537 7_1:-56399291 None:intergenic
TCTCCGACATCCTAGAAGTT+AGG 0.520587 7_1:-56399261 None:intergenic
CCAAATGTGATGTTCGGAAG+AGG 0.546565 7_1:+56399834 Msa1025620:CDS
TCTAGCAAGTGTCATTGCTC+CGG 0.553561 7_1:-56399324 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 7_1:-56399801 None:intergenic
TTTCAAGTGCAAGTGTGTCA+TGG 0.557143 7_1:+56399908 Msa1025620:CDS
TGTCGGCCGTTGTTGACAGA+TGG 0.563208 7_1:+56399390 Msa1025620:five_prime_UTR
CACGATTACTTAATGTTGTG+CGG 0.568757 7_1:+56399759 Msa1025620:CDS
GTCTCCGGCCTCAATACCAT+TGG 0.575295 7_1:-56399877 None:intergenic
CGAACATCACATTTGGTATG+GGG 0.588480 7_1:-56399827 None:intergenic
TGACACTTGCTAGATGGTGA+TGG 0.594754 7_1:+56399333 Msa1025620:five_prime_UTR
GTTGCCAATGGTATTGAGGC+CGG 0.597504 7_1:+56399873 Msa1025620:CDS
TCCAACGATAGGAACTTCAA+AGG 0.611311 7_1:-56399577 None:intergenic
GACACTTGCTAGATGGTGAT+GGG 0.615365 7_1:+56399334 Msa1025620:five_prime_UTR
ATGTGATGTTCGGAAGAGGT+TGG 0.615603 7_1:+56399838 Msa1025620:CDS
GCCGCACTCATTGAATGATA+GGG 0.616026 7_1:-56399537 None:intergenic
TCGATCGACGAAATCACCTA+AGG 0.628108 7_1:+56399602 Msa1025620:CDS
ACCCTATCATTCAATGAGTG+CGG 0.636716 7_1:+56399536 Msa1025620:exon
GTCGATCGATATCCAACGAT+AGG 0.637968 7_1:-56399588 None:intergenic
GTCGCTTTCCAGTACCATGG+TGG 0.664216 7_1:+56399459 Msa1025620:five_prime_UTR
GCACTCATTGAATGATAGGG+TGG 0.666571 7_1:-56399534 None:intergenic
TTTGAAATCTACTTCCACCA+TGG 0.675135 7_1:-56399473 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 7_1:-56399396 None:intergenic
ATTGTCGCTTTCCAGTACCA+TGG 0.681766 7_1:+56399456 Msa1025620:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTTTTTCTTTTTTTTA+GGG + chr7_1:56399696-56399715 Msa1025620:intron 10.0%
!!! AGTTTTTTTTCTTTTTTTTA+GGG + chr7_1:56399696-56399715 Msa1025620:intron 10.0%
!! TTCTATATAAATAAGATGAA+CGG + chr7_1:56399219-56399238 Msa1025620:five_prime_UTR 15.0%
!! TTAGATATATGCTATAATAA+AGG + chr7_1:56399654-56399673 Msa1025620:intron 15.0%
!!! CAGTTTTTTTTCTTTTTTTT+AGG + chr7_1:56399695-56399714 Msa1025620:intron 15.0%
!! TTCTATATAAATAAGATGAA+CGG + chr7_1:56399219-56399238 Msa1025620:five_prime_UTR 15.0%
!! TTAGATATATGCTATAATAA+AGG + chr7_1:56399654-56399673 Msa1025620:intron 15.0%
!!! CAGTTTTTTTTCTTTTTTTT+AGG + chr7_1:56399695-56399714 Msa1025620:intron 15.0%
!! AAAAAACAATAAACAACCTT+AGG - chr7_1:56399621-56399640 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+AGG - chr7_1:56399621-56399640 None:intergenic 20.0%
!! TTTTCAACAAATCAGTTTGT+CGG + chr7_1:56399373-56399392 Msa1025620:five_prime_UTR 25.0%
!! TTTTCAACAAATCAGTTTGT+CGG + chr7_1:56399373-56399392 Msa1025620:five_prime_UTR 25.0%
AGTTAGGCAGAAAAAGTTTA+CGG - chr7_1:56399248-56399267 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG - chr7_1:56399294-56399313 None:intergenic 30.0%
AGTTAGGCAGAAAAAGTTTA+CGG - chr7_1:56399248-56399267 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG - chr7_1:56399294-56399313 None:intergenic 30.0%
!! ACTTTTTCTGCCTAACTTCT+AGG + chr7_1:56399251-56399270 Msa1025620:five_prime_UTR 35.0%
! TGAATATTTCTACGAGCTAC+CGG + chr7_1:56399305-56399324 Msa1025620:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+TGG - chr7_1:56399476-56399495 None:intergenic 35.0%
! AGGAATTTGCCAAAAGTATG+AGG - chr7_1:56399726-56399745 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr7_1:56399746-56399765 None:intergenic 35.0%
CACGATTACTTAATGTTGTG+CGG + chr7_1:56399759-56399778 Msa1025620:CDS 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr7_1:56399804-56399823 None:intergenic 35.0%
CTTGAAAAATAACACGTCTC+CGG - chr7_1:56399895-56399914 None:intergenic 35.0%
!! ACTTTTTCTGCCTAACTTCT+AGG + chr7_1:56399251-56399270 Msa1025620:five_prime_UTR 35.0%
! TGAATATTTCTACGAGCTAC+CGG + chr7_1:56399305-56399324 Msa1025620:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+TGG - chr7_1:56399476-56399495 None:intergenic 35.0%
! AGGAATTTGCCAAAAGTATG+AGG - chr7_1:56399726-56399745 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr7_1:56399746-56399765 None:intergenic 35.0%
CACGATTACTTAATGTTGTG+CGG + chr7_1:56399759-56399778 Msa1025620:CDS 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr7_1:56399804-56399823 None:intergenic 35.0%
CTTGAAAAATAACACGTCTC+CGG - chr7_1:56399895-56399914 None:intergenic 35.0%
CGATTGTTCTACGAGTTTAG+TGG + chr7_1:56399426-56399445 Msa1025620:five_prime_UTR 40.0%
ACCCTATCATTCAATGAGTG+CGG + chr7_1:56399536-56399555 Msa1025620:exon 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + chr7_1:56399576-56399595 Msa1025620:CDS 40.0%
TCCAACGATAGGAACTTCAA+AGG - chr7_1:56399580-56399599 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + chr7_1:56399714-56399733 Msa1025620:intron 40.0%
CGAACATCACATTTGGTATG+GGG - chr7_1:56399830-56399849 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr7_1:56399831-56399850 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr7_1:56399828-56399847 Msa1025620:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr7_1:56399832-56399851 None:intergenic 40.0%
! ACGAGTTTTTGTGTTGCCAA+TGG + chr7_1:56399861-56399880 Msa1025620:CDS 40.0%
TTGTGTTGCCAATGGTATTG+AGG + chr7_1:56399869-56399888 Msa1025620:CDS 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG + chr7_1:56399908-56399927 Msa1025620:CDS 40.0%
CGATTGTTCTACGAGTTTAG+TGG + chr7_1:56399426-56399445 Msa1025620:five_prime_UTR 40.0%
ACCCTATCATTCAATGAGTG+CGG + chr7_1:56399536-56399555 Msa1025620:exon 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + chr7_1:56399576-56399595 Msa1025620:CDS 40.0%
TCCAACGATAGGAACTTCAA+AGG - chr7_1:56399580-56399599 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + chr7_1:56399714-56399733 Msa1025620:intron 40.0%
CGAACATCACATTTGGTATG+GGG - chr7_1:56399830-56399849 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr7_1:56399831-56399850 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr7_1:56399828-56399847 Msa1025620:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr7_1:56399832-56399851 None:intergenic 40.0%
! ACGAGTTTTTGTGTTGCCAA+TGG + chr7_1:56399861-56399880 Msa1025620:CDS 40.0%
TTGTGTTGCCAATGGTATTG+AGG + chr7_1:56399869-56399888 Msa1025620:CDS 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG + chr7_1:56399908-56399927 Msa1025620:CDS 40.0%
!! CTGCCTAACTTCTAGGATGT+CGG + chr7_1:56399258-56399277 Msa1025620:five_prime_UTR 45.0%
TCTCCGACATCCTAGAAGTT+AGG - chr7_1:56399264-56399283 None:intergenic 45.0%
! TCTAGCAAGTGTCATTGCTC+CGG - chr7_1:56399327-56399346 None:intergenic 45.0%
! GAGCAATGACACTTGCTAGA+TGG + chr7_1:56399327-56399346 Msa1025620:five_prime_UTR 45.0%
! TGACACTTGCTAGATGGTGA+TGG + chr7_1:56399333-56399352 Msa1025620:five_prime_UTR 45.0%
! GACACTTGCTAGATGGTGAT+GGG + chr7_1:56399334-56399353 Msa1025620:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr7_1:56399399-56399418 None:intergenic 45.0%
!! ATTGTCGCTTTCCAGTACCA+TGG + chr7_1:56399456-56399475 Msa1025620:five_prime_UTR 45.0%
ATCTACTTCCACCATGGTAC+TGG - chr7_1:56399470-56399489 None:intergenic 45.0%
GCACTCATTGAATGATAGGG+TGG - chr7_1:56399537-56399556 None:intergenic 45.0%
GCCGCACTCATTGAATGATA+GGG - chr7_1:56399540-56399559 None:intergenic 45.0%
TGCCGCACTCATTGAATGAT+AGG - chr7_1:56399541-56399560 None:intergenic 45.0%
GTCGATCGATATCCAACGAT+AGG - chr7_1:56399591-56399610 None:intergenic 45.0%
TCGATCGACGAAATCACCTA+AGG + chr7_1:56399602-56399621 Msa1025620:CDS 45.0%
CCTCTTCCGAACATCACATT+TGG - chr7_1:56399837-56399856 None:intergenic 45.0%
CCAAATGTGATGTTCGGAAG+AGG + chr7_1:56399834-56399853 Msa1025620:CDS 45.0%
ATGTGATGTTCGGAAGAGGT+TGG + chr7_1:56399838-56399857 Msa1025620:CDS 45.0%
!! CTGCCTAACTTCTAGGATGT+CGG + chr7_1:56399258-56399277 Msa1025620:five_prime_UTR 45.0%
TCTCCGACATCCTAGAAGTT+AGG - chr7_1:56399264-56399283 None:intergenic 45.0%
! TCTAGCAAGTGTCATTGCTC+CGG - chr7_1:56399327-56399346 None:intergenic 45.0%
! GAGCAATGACACTTGCTAGA+TGG + chr7_1:56399327-56399346 Msa1025620:five_prime_UTR 45.0%
! TGACACTTGCTAGATGGTGA+TGG + chr7_1:56399333-56399352 Msa1025620:five_prime_UTR 45.0%
! GACACTTGCTAGATGGTGAT+GGG + chr7_1:56399334-56399353 Msa1025620:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr7_1:56399399-56399418 None:intergenic 45.0%
!! ATTGTCGCTTTCCAGTACCA+TGG + chr7_1:56399456-56399475 Msa1025620:five_prime_UTR 45.0%
ATCTACTTCCACCATGGTAC+TGG - chr7_1:56399470-56399489 None:intergenic 45.0%
GCACTCATTGAATGATAGGG+TGG - chr7_1:56399537-56399556 None:intergenic 45.0%
GCCGCACTCATTGAATGATA+GGG - chr7_1:56399540-56399559 None:intergenic 45.0%
TGCCGCACTCATTGAATGAT+AGG - chr7_1:56399541-56399560 None:intergenic 45.0%
GTCGATCGATATCCAACGAT+AGG - chr7_1:56399591-56399610 None:intergenic 45.0%
TCGATCGACGAAATCACCTA+AGG + chr7_1:56399602-56399621 Msa1025620:CDS 45.0%
CCTCTTCCGAACATCACATT+TGG - chr7_1:56399837-56399856 None:intergenic 45.0%
CCAAATGTGATGTTCGGAAG+AGG + chr7_1:56399834-56399853 Msa1025620:CDS 45.0%
ATGTGATGTTCGGAAGAGGT+TGG + chr7_1:56399838-56399857 Msa1025620:CDS 45.0%
! GTTGCCAATGGTATTGAGGC+CGG + chr7_1:56399873-56399892 Msa1025620:CDS 50.0%
! GTTGCCAATGGTATTGAGGC+CGG + chr7_1:56399873-56399892 Msa1025620:CDS 50.0%
TGTCGGCCGTTGTTGACAGA+TGG + chr7_1:56399390-56399409 Msa1025620:five_prime_UTR 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr7_1:56399394-56399413 Msa1025620:five_prime_UTR 55.0%
! GTCGCTTTCCAGTACCATGG+TGG + chr7_1:56399459-56399478 Msa1025620:five_prime_UTR 55.0%
GTCTCCGGCCTCAATACCAT+TGG - chr7_1:56399880-56399899 None:intergenic 55.0%
TGTCGGCCGTTGTTGACAGA+TGG + chr7_1:56399390-56399409 Msa1025620:five_prime_UTR 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr7_1:56399394-56399413 Msa1025620:five_prime_UTR 55.0%
! GTCGCTTTCCAGTACCATGG+TGG + chr7_1:56399459-56399478 Msa1025620:five_prime_UTR 55.0%
GTCTCCGGCCTCAATACCAT+TGG - chr7_1:56399880-56399899 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 56399173 56399962 56399173 ID=Msa1025620;Name=Msa1025620
chr7_1 mRNA 56399173 56399962 56399173 ID=Msa1025620-mRNA-1;Parent=Msa1025620;Name=Msa1025620-mRNA-1;_AED=0.10;_eAED=0.10;_QI=376|1|0.5|1|1|1|2|0|106
chr7_1 exon 56399173 56399623 56399173 ID=Msa1025620-mRNA-1:exon:11293;Parent=Msa1025620-mRNA-1
chr7_1 exon 56399717 56399962 56399717 ID=Msa1025620-mRNA-1:exon:11294;Parent=Msa1025620-mRNA-1
chr7_1 five_prime_UTR 56399173 56399548 56399173 ID=Msa1025620-mRNA-1:five_prime_utr;Parent=Msa1025620-mRNA-1
chr7_1 CDS 56399549 56399623 56399549 ID=Msa1025620-mRNA-1:cds;Parent=Msa1025620-mRNA-1
chr7_1 CDS 56399717 56399962 56399717 ID=Msa1025620-mRNA-1:cds;Parent=Msa1025620-mRNA-1
Gene Sequence

>Msa1025620

ATGAGTGCGGCAACATCGTTTTATTGTACCTTTGAAGTTCCTATCGTTGGATATCGATCGACGAAATCACCTAAGGGACTACCTCATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACTTAATGTTGTGCGGAACTTATGACAGTATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAGAGGTTGGACGAGTTTTTGTGTTGCCAATGGTATTGAGGCCGGAGACGTGTTATTTTTCAAGTGCAAGTGTGTCATGGACAAAAAATATGTTATCGTATCCAAGCTTTGA
Protein sequence

>Msa1025620

MSAATSFYCTFEVPIVGYRSTKSPKGLPHTFGKFLRVKHHDYLMLCGTYDSIIPVRLKYTDDPIPNVMFGRGWTSFCVANGIEAGDVLFFKCKCVMDKKYVIVSKL*