AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1087070


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 40 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGCCTTTCGGCCTGATCTT+AGG 0.275595 7_2:-87699002 Msa1087070:CDS
CGCGCGGGTACTTCGTTCTA+AGG 0.329525 7_2:-87698855 None:intergenic
TCGTCCACGGAGGGTGAGTC+AGG 0.342961 7_2:+87698978 None:intergenic
ACCTAGCCTCCTCCGTCCCT+CGG 0.407009 7_2:-87699072 Msa1087070:intron
AACGAAGTACCCGCGCGAGC+AGG 0.426901 7_2:+87698861 None:intergenic
ATTCCTGTACTACCCCTTGT+TGG 0.431214 7_2:+87699047 None:intergenic
CCCTTGTTGGTCCCGAGGGA+CGG 0.434382 7_2:+87699060 None:intergenic
GTGAGTCAGGGCCTAAGATC+AGG 0.453368 7_2:+87698991 None:intergenic
AGGCGTAGTCGATGGACAAC+AGG 0.473069 7_2:+87699019 None:intergenic
TACATGGTCTTACGACTTTG+CGG 0.476001 7_2:-87699440 Msa1087070:CDS
TGTCCATCGACTACGCCTTT+CGG 0.477754 7_2:-87699014 Msa1087070:CDS
TCCAATGCCCCGAAAACCTA+AGG 0.481914 7_2:+87698940 None:intergenic
CCTAGCCTCCTCCGTCCCTC+GGG 0.487169 7_2:-87699071 Msa1087070:intron
TCCGTCCCTCGGGACCAACA+AGG 0.498430 7_2:-87699061 Msa1087070:CDS
TTCGTCCAACCCTGCTCGCG+CGG 0.503688 7_2:-87698871 Msa1087070:CDS
AACCTTGCGGAGGAACCCTT+AGG 0.515988 7_2:-87698956 Msa1087070:CDS
CCGTCCCTCGGGACCAACAA+GGG 0.520911 7_2:-87699060 Msa1087070:CDS
TTGGTCCCGAGGGACGGAGG+AGG 0.522310 7_2:+87699066 None:intergenic
TCGTCCAACCCTGCTCGCGC+GGG 0.525250 7_2:-87698870 Msa1087070:CDS
AGTACCCGCGCGAGCAGGGT+TGG 0.535281 7_2:+87698866 None:intergenic
CTACCCCTTGTTGGTCCCGA+GGG 0.555675 7_2:+87699056 None:intergenic
AACCTAAGGGTTCCTCCGCA+AGG 0.559471 7_2:+87698954 None:intergenic
ACGAAGTACCCGCGCGAGCA+GGG 0.565436 7_2:+87698862 None:intergenic
GGACCAACAAGGGGTAGTAC+AGG 0.569765 7_2:-87699050 Msa1087070:CDS
AGGCCGAAAGGCGTAGTCGA+TGG 0.572797 7_2:+87699011 None:intergenic
TCCTCCGCAAGGTTCGTCCA+CGG 0.575439 7_2:+87698965 None:intergenic
CCGCAAGGTTCGTCCACGGA+GGG 0.579950 7_2:+87698969 None:intergenic
CGTCCACGGAGGGTGAGTCA+GGG 0.596173 7_2:+87698979 None:intergenic
TTGTTGGTCCCGAGGGACGG+AGG 0.609698 7_2:+87699063 None:intergenic
GGCTTGAGTAACGCAAACAT+TGG 0.611831 7_2:+87698911 None:intergenic
CGTCCCTCGGGACCAACAAG+GGG 0.613145 7_2:-87699059 Msa1087070:CDS
ACTACCCCTTGTTGGTCCCG+AGG 0.625318 7_2:+87699055 None:intergenic
GCGAGCAGGGTTGGACGAAG+CGG 0.626879 7_2:+87698875 None:intergenic
GGGCCTAAGATCAGGCCGAA+AGG 0.628716 7_2:+87698999 None:intergenic
CCAATGCCCCGAAAACCTAA+GGG 0.629622 7_2:+87698941 None:intergenic
CCCTCCGTGGACGAACCTTG+CGG 0.633512 7_2:-87698969 Msa1087070:CDS
TCCGCAAGGTTCGTCCACGG+AGG 0.633907 7_2:+87698968 None:intergenic
CGAAGCGGAAGCGAGAATGT+CGG 0.648690 7_2:+87698890 None:intergenic
AGGCCCTGACTCACCCTCCG+TGG 0.655611 7_2:-87698982 Msa1087070:CDS
TCCGTGGACGAACCTTGCGG+AGG 0.674144 7_2:-87698966 Msa1087070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTTTTTCAGGGTAAGAAG+GGG + chr7_2:87699159-87699178 None:intergenic 35.0%
!!! CTGTTTTTTCAGGGTAAGAA+GGG + chr7_2:87699160-87699179 None:intergenic 35.0%
CTTCTTACCCTGAAAAAACA+GGG - chr7_2:87699159-87699178 Msa1087070:intron 35.0%
TTCTTACCCTGAAAAAACAG+GGG - chr7_2:87699160-87699179 Msa1087070:intron 35.0%
TTGAACCGATAACCATCTTT+CGG - chr7_2:87699196-87699215 Msa1087070:intron 35.0%
CGACTGTTTACCAAAAACAC+AGG + chr7_2:87698883-87698902 None:intergenic 40.0%
! ACAACTCTCTCTAAGGAACT+CGG + chr7_2:87698976-87698995 None:intergenic 40.0%
! TACAGGTACCCTTTTGTTGA+AGG - chr7_2:87699044-87699063 Msa1087070:CDS 40.0%
TCGAACGACCTTCAACAAAA+GGG + chr7_2:87699055-87699074 None:intergenic 40.0%
!!! CCTGTTTTTTCAGGGTAAGA+AGG + chr7_2:87699161-87699180 None:intergenic 40.0%
CCTTCTTACCCTGAAAAAAC+AGG - chr7_2:87699158-87699177 Msa1087070:intron 40.0%
!! GTTATCGGTTCAAGAACACA+AGG + chr7_2:87699189-87699208 None:intergenic 40.0%
GTTAGCCGAAAGATGGTTAT+CGG + chr7_2:87699204-87699223 None:intergenic 40.0%
! TTTGCGGAGACCTGTGTTTT+TGG - chr7_2:87698870-87698889 Msa1087070:CDS 45.0%
!!! GTTTTTGGTAAACAGTCGCC+CGG - chr7_2:87698885-87698904 Msa1087070:CDS 45.0%
!! TTTTTGGTAAACAGTCGCCC+GGG - chr7_2:87698886-87698905 Msa1087070:CDS 45.0%
CAAAATAGCCCCGTAACTTC+GGG + chr7_2:87698953-87698972 None:intergenic 45.0%
GCAAAATAGCCCCGTAACTT+CGG + chr7_2:87698954-87698973 None:intergenic 45.0%
GGTAGGTAGAGAATACCTAG+GGG + chr7_2:87699005-87699024 None:intergenic 45.0%
GGGTAGGTAGAGAATACCTA+GGG + chr7_2:87699006-87699025 None:intergenic 45.0%
TGGGTAGGTAGAGAATACCT+AGG + chr7_2:87699007-87699026 None:intergenic 45.0%
CTCGAACGACCTTCAACAAA+AGG + chr7_2:87699056-87699075 None:intergenic 45.0%
GTAATTGATGCCATACTCCC+AGG + chr7_2:87699084-87699103 None:intergenic 45.0%
!!! AGGTGACCCCTGTTTTTTCA+GGG + chr7_2:87699169-87699188 None:intergenic 45.0%
!!! AAGGTGACCCCTGTTTTTTC+AGG + chr7_2:87699170-87699189 None:intergenic 45.0%
ATTCCTGTACTACCCCTTGT+TGG + chr7_2:87699250-87699269 None:intergenic 45.0%
GGCTTGAGTAACGCAAACAT+TGG + chr7_2:87699386-87699405 None:intergenic 45.0%
! AAGGTCGTTCGAGCTTTTCC+TGG - chr7_2:87699063-87699082 Msa1087070:CDS 50.0%
! AGGTCGTTCGAGCTTTTCCT+GGG - chr7_2:87699064-87699083 Msa1087070:CDS 50.0%
! TCGAGCTTTTCCTGGGAGTA+TGG - chr7_2:87699071-87699090 Msa1087070:intron 50.0%
GGCATCAATTACTTCAGCGC+CGG - chr7_2:87699092-87699111 Msa1087070:intron 50.0%
AGAGAAAATGCCTCCAGCCA+AGG + chr7_2:87699135-87699154 None:intergenic 50.0%
! AGGCTAGGTTAGCCGAAAGA+TGG + chr7_2:87699211-87699230 None:intergenic 50.0%
! TGTCCATCGACTACGCCTTT+CGG - chr7_2:87699280-87699299 Msa1087070:intron 50.0%
! CGGAGGAACCCTTAGGTTTT+CGG - chr7_2:87699345-87699364 Msa1087070:intron 50.0%
! GGAGGAACCCTTAGGTTTTC+GGG - chr7_2:87699346-87699365 Msa1087070:intron 50.0%
! GAGGAACCCTTAGGTTTTCG+GGG - chr7_2:87699347-87699366 Msa1087070:intron 50.0%
CCAATGCCCCGAAAACCTAA+GGG + chr7_2:87699356-87699375 None:intergenic 50.0%
TCCAATGCCCCGAAAACCTA+AGG + chr7_2:87699357-87699376 None:intergenic 50.0%
!! AAGGGGTGCCTCCTCACAAA+GGG + chr7_2:87698928-87698947 None:intergenic 55.0%
CACCCCTTCTCCCGAAGTTA+CGG - chr7_2:87698940-87698959 Msa1087070:CDS 55.0%
ACCCCTTCTCCCGAAGTTAC+GGG - chr7_2:87698941-87698960 Msa1087070:CDS 55.0%
GCGCGAGACAACTCTCTCTA+AGG + chr7_2:87698983-87699002 None:intergenic 55.0%
CTCTACCTACCCACCTGTGT+CGG - chr7_2:87699014-87699033 Msa1087070:CDS 55.0%
!! CTACCCACCTGTGTCGGTTT+CGG - chr7_2:87699020-87699039 Msa1087070:CDS 55.0%
!! TACCCACCTGTGTCGGTTTC+GGG - chr7_2:87699021-87699040 Msa1087070:CDS 55.0%
TACCCGAAACCGACACAGGT+GGG + chr7_2:87699026-87699045 None:intergenic 55.0%
GGACCAACAAGGGGTAGTAC+AGG - chr7_2:87699244-87699263 Msa1087070:intron 55.0%
AGGCGTAGTCGATGGACAAC+AGG + chr7_2:87699278-87699297 None:intergenic 55.0%
ACGCCTTTCGGCCTGATCTT+AGG - chr7_2:87699292-87699311 Msa1087070:intron 55.0%
GTGAGTCAGGGCCTAAGATC+AGG + chr7_2:87699306-87699325 None:intergenic 55.0%
AACCTTGCGGAGGAACCCTT+AGG - chr7_2:87699338-87699357 Msa1087070:intron 55.0%
AACCTAAGGGTTCCTCCGCA+AGG + chr7_2:87699343-87699362 None:intergenic 55.0%
!! CCCTTAGGTTTTCGGGGCAT+TGG - chr7_2:87699353-87699372 Msa1087070:intron 55.0%
CGAAGCGGAAGCGAGAATGT+CGG + chr7_2:87699407-87699426 None:intergenic 55.0%
TCACTGCGACCCCCTTTGTG+AGG - chr7_2:87698914-87698933 Msa1087070:CDS 60.0%
!! AGGGGTGCCTCCTCACAAAG+GGG + chr7_2:87698927-87698946 None:intergenic 60.0%
!! GAAGGGGTGCCTCCTCACAA+AGG + chr7_2:87698929-87698948 None:intergenic 60.0%
CCCCGTAACTTCGGGAGAAG+GGG + chr7_2:87698945-87698964 None:intergenic 60.0%
CCCCTTCTCCCGAAGTTACG+GGG - chr7_2:87698942-87698961 Msa1087070:CDS 60.0%
GCCCCGTAACTTCGGGAGAA+GGG + chr7_2:87698946-87698965 None:intergenic 60.0%
AGCCCCGTAACTTCGGGAGA+AGG + chr7_2:87698947-87698966 None:intergenic 60.0%
CGAAACCGACACAGGTGGGT+AGG + chr7_2:87699022-87699041 None:intergenic 60.0%
GTACCCGAAACCGACACAGG+TGG + chr7_2:87699027-87699046 None:intergenic 60.0%
CCTGTACCCGAAACCGACAC+AGG + chr7_2:87699030-87699049 None:intergenic 60.0%
!! CCTGTGTCGGTTTCGGGTAC+AGG - chr7_2:87699027-87699046 Msa1087070:CDS 60.0%
AGCGCCTGGTACTCGAACCT+TGG - chr7_2:87699115-87699134 Msa1087070:intron 60.0%
CCAGCCAAGGTTCGAGTACC+AGG + chr7_2:87699122-87699141 None:intergenic 60.0%
CCTGGTACTCGAACCTTGGC+TGG - chr7_2:87699119-87699138 Msa1087070:intron 60.0%
GGTACTCGAACCTTGGCTGG+AGG - chr7_2:87699122-87699141 Msa1087070:intron 60.0%
CTACCCCTTGTTGGTCCCGA+GGG + chr7_2:87699241-87699260 None:intergenic 60.0%
ACTACCCCTTGTTGGTCCCG+AGG + chr7_2:87699242-87699261 None:intergenic 60.0%
! AGGCCGAAAGGCGTAGTCGA+TGG + chr7_2:87699286-87699305 None:intergenic 60.0%
GGGCCTAAGATCAGGCCGAA+AGG + chr7_2:87699298-87699317 None:intergenic 60.0%
TCCTCCGCAAGGTTCGTCCA+CGG + chr7_2:87699332-87699351 None:intergenic 60.0%
CAAAGGGGGTCGCAGTGACC+AGG + chr7_2:87698912-87698931 None:intergenic 65.0%
CTGCGACCCCCTTTGTGAGG+AGG - chr7_2:87698917-87698936 Msa1087070:CDS 65.0%
! GGGGTGCCTCCTCACAAAGG+GGG + chr7_2:87698926-87698945 None:intergenic 65.0%
GAGAGTTGTCTCGCGCCCCT+AGG - chr7_2:87698987-87699006 Msa1087070:CDS 65.0%
GGTTCGAGTACCAGGCGCTC+CGG + chr7_2:87699114-87699133 None:intergenic 65.0%
ACCTAGCCTCCTCCGTCCCT+CGG - chr7_2:87699222-87699241 Msa1087070:intron 65.0%
TTGTTGGTCCCGAGGGACGG+AGG + chr7_2:87699234-87699253 None:intergenic 65.0%
TCCGTCCCTCGGGACCAACA+AGG - chr7_2:87699233-87699252 Msa1087070:intron 65.0%
CCCTTGTTGGTCCCGAGGGA+CGG + chr7_2:87699237-87699256 None:intergenic 65.0%
CCGTCCCTCGGGACCAACAA+GGG - chr7_2:87699234-87699253 Msa1087070:intron 65.0%
CGTCCCTCGGGACCAACAAG+GGG - chr7_2:87699235-87699254 Msa1087070:intron 65.0%
CGTCCACGGAGGGTGAGTCA+GGG + chr7_2:87699318-87699337 None:intergenic 65.0%
TCGTCCACGGAGGGTGAGTC+AGG + chr7_2:87699319-87699338 None:intergenic 65.0%
CCGCAAGGTTCGTCCACGGA+GGG + chr7_2:87699328-87699347 None:intergenic 65.0%
CCCTCCGTGGACGAACCTTG+CGG - chr7_2:87699325-87699344 Msa1087070:intron 65.0%
TCCGCAAGGTTCGTCCACGG+AGG + chr7_2:87699329-87699348 None:intergenic 65.0%
TCCGTGGACGAACCTTGCGG+AGG - chr7_2:87699328-87699347 Msa1087070:intron 65.0%
GCGAGCAGGGTTGGACGAAG+CGG + chr7_2:87699422-87699441 None:intergenic 65.0%
TTCGTCCAACCCTGCTCGCG+CGG - chr7_2:87699423-87699442 Msa1087070:intron 65.0%
! ACGAAGTACCCGCGCGAGCA+GGG + chr7_2:87699435-87699454 None:intergenic 65.0%
! AACGAAGTACCCGCGCGAGC+AGG + chr7_2:87699436-87699455 None:intergenic 65.0%
GGTAAACAGTCGCCCGGGCC+TGG - chr7_2:87698891-87698910 Msa1087070:CDS 70.0%
! TACTTCAGCGCCGGAGCGCC+TGG - chr7_2:87699101-87699120 Msa1087070:intron 70.0%
CCTAGCCTCCTCCGTCCCTC+GGG - chr7_2:87699223-87699242 Msa1087070:intron 70.0%
TTGGTCCCGAGGGACGGAGG+AGG + chr7_2:87699231-87699250 None:intergenic 70.0%
AGGCCCTGACTCACCCTCCG+TGG - chr7_2:87699312-87699331 Msa1087070:intron 70.0%
TCGTCCAACCCTGCTCGCGC+GGG - chr7_2:87699424-87699443 Msa1087070:intron 70.0%
AGTACCCGCGCGAGCAGGGT+TGG + chr7_2:87699431-87699450 None:intergenic 70.0%
GGGTCGCAGTGACCAGGCCC+GGG + chr7_2:87698906-87698925 None:intergenic 75.0%
GGGGTCGCAGTGACCAGGCC+CGG + chr7_2:87698907-87698926 None:intergenic 75.0%
CCCGAGGGACGGAGGAGGCT+AGG + chr7_2:87699226-87699245 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87698857 87699459 87698857 ID=Msa1087070;Name=Msa1087070
chr7_2 mRNA 87698857 87699459 87698857 ID=Msa1087070-mRNA-1;Parent=Msa1087070;Name=Msa1087070-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0|0|1|0|0|2|0|85
chr7_2 exon 87699434 87699459 87699434 ID=Msa1087070-mRNA-1:exon:24009;Parent=Msa1087070-mRNA-1
chr7_2 exon 87698857 87699088 87698857 ID=Msa1087070-mRNA-1:exon:24008;Parent=Msa1087070-mRNA-1
chr7_2 CDS 87699434 87699459 87699434 ID=Msa1087070-mRNA-1:cds;Parent=Msa1087070-mRNA-1
chr7_2 CDS 87698857 87699088 87698857 ID=Msa1087070-mRNA-1:cds;Parent=Msa1087070-mRNA-1
Gene Sequence

>Msa1087070

ATGGTCTTACGACTTTGCGGAGACCTCCTCCTCCGTCCCTCGGGACCAACAAGGGGTAGTACAGGAATATTCACCTGTTGTCCATCGACTACGCCTTTCGGCCTGATCTTAGGCCCTGACTCACCCTCCGTGGACGAACCTTGCGGAGGAACCCTTAGGTTTTCGGGGCATTGGATTCTCACCAATGTTTGCGTTACTCAAGCCGACATTCTCGCTTCCGCTTCGTCCAACCCTGCTCGCGCGGGTACTTCGTTCTAA

Protein sequence

>Msa1087070

MVLRLCGDLLLRPSGPTRGSTGIFTCCPSTTPFGLILGPDSPSVDEPCGGTLRFSGHWILTNVCVTQADILASASSNPARAGTSF*