AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0405460


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 3_2:-40194032 Msa0405460:CDS
CGCGCGGGTACTTCGTTCTA+AGG 0.329525 3_2:-40193885 None:intergenic
TCGTCCACGGAGGGTGAGTC+AGG 0.342961 3_2:+40194008 None:intergenic
TGTCCATCGACTACGCCTTT+CGG 0.385423 3_2:-40194044 Msa0405460:CDS
ACCTAGCCTCCTCCGTCCCT+TGG 0.385958 3_2:-40194102 Msa0405460:intron
AACGAAGTACCCGCGCGAGC+AGG 0.426901 3_2:+40193891 None:intergenic
ATTCCTGTACTACCCCTTGT+TGG 0.431214 3_2:+40194077 None:intergenic
CCTAGCCTCCTCCGTCCCTT+GGG 0.441437 3_2:-40194101 Msa0405460:intron
AGGCGTAGTCGATGGACAAT+AGG 0.452831 3_2:+40194049 None:intergenic
GTGAGTCAGGGCCTAAGATC+AGG 0.453368 3_2:+40194021 None:intergenic
TACATGGTCTTACGACTTTG+CGG 0.476001 3_2:-40194470 Msa0405460:CDS
TCCAATGCCCCGAAAACCTA+AGG 0.481914 3_2:+40193970 None:intergenic
TTCGTCCAACCCTGCTCGCG+CGG 0.503688 3_2:-40193901 Msa0405460:CDS
TCCGTCCCTTGGGACCAACA+AGG 0.511589 3_2:-40194091 Msa0405460:CDS
AACCTTGCGGAGGAACCCTT+AGG 0.515988 3_2:-40193986 Msa0405460:CDS
TCGTCCAACCCTGCTCGCGC+GGG 0.525250 3_2:-40193900 Msa0405460:CDS
AGTACCCGCGCGAGCAGGGT+TGG 0.535281 3_2:+40193896 None:intergenic
ACTACCCCTTGTTGGTCCCA+AGG 0.547694 3_2:+40194085 None:intergenic
CTACCCCTTGTTGGTCCCAA+GGG 0.553353 3_2:+40194086 None:intergenic
CCCTTGTTGGTCCCAAGGGA+CGG 0.554740 3_2:+40194090 None:intergenic
CCGTCCCTTGGGACCAACAA+GGG 0.556978 3_2:-40194090 Msa0405460:CDS
GGACCAACAAGGGGTAGTAC+AGG 0.557987 3_2:-40194080 Msa0405460:CDS
AACCTAAGGGTTCCTCCGCA+AGG 0.559471 3_2:+40193984 None:intergenic
ACGAAGTACCCGCGCGAGCA+GGG 0.565436 3_2:+40193892 None:intergenic
AGGCCGAAAGGCGTAGTCGA+TGG 0.572797 3_2:+40194041 None:intergenic
TTGGTCCCAAGGGACGGAGG+AGG 0.573760 3_2:+40194096 None:intergenic
TCCTCCGCAAGGTTCGTCCA+CGG 0.575439 3_2:+40193995 None:intergenic
CCGCAAGGTTCGTCCACGGA+GGG 0.579950 3_2:+40193999 None:intergenic
CGTCCACGGAGGGTGAGTCA+GGG 0.596173 3_2:+40194009 None:intergenic
GGCTTGAGTAACGCAAACAT+TGG 0.611831 3_2:+40193941 None:intergenic
GCGAGCAGGGTTGGACGAAG+CGG 0.626879 3_2:+40193905 None:intergenic
GGGCCTAAGATCAGGCCGAA+AGG 0.628716 3_2:+40194029 None:intergenic
CCAATGCCCCGAAAACCTAA+GGG 0.629622 3_2:+40193971 None:intergenic
CCCTCCGTGGACGAACCTTG+CGG 0.633512 3_2:-40193999 Msa0405460:CDS
TCCGCAAGGTTCGTCCACGG+AGG 0.633907 3_2:+40193998 None:intergenic
CGTCCCTTGGGACCAACAAG+GGG 0.639779 3_2:-40194089 Msa0405460:CDS
TTGTTGGTCCCAAGGGACGG+AGG 0.644787 3_2:+40194093 None:intergenic
CGAAGCGGAAGCGAGAATGT+CGG 0.648690 3_2:+40193920 None:intergenic
AGGCCCTGACTCACCCTCCG+TGG 0.655611 3_2:-40194012 Msa0405460:CDS
TCCGTGGACGAACCTTGCGG+AGG 0.674144 3_2:-40193996 Msa0405460:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTTTTTCAGGGTAAGAAG+GGG + chr3_2:40194189-40194208 None:intergenic 35.0%
!!! CTGTTTTTTCAGGGTAAGAA+GGG + chr3_2:40194190-40194209 None:intergenic 35.0%
CTTCTTACCCTGAAAAAACA+GGG - chr3_2:40194189-40194208 Msa0405460:intron 35.0%
TTCTTACCCTGAAAAAACAG+GGG - chr3_2:40194190-40194209 Msa0405460:intron 35.0%
TTGAACCGATAACCATCTTT+CGG - chr3_2:40194226-40194245 Msa0405460:intron 35.0%
CGACTGTTTACCAAAAACAC+AGG + chr3_2:40193913-40193932 None:intergenic 40.0%
! ACAACTCTCTCTAAGGAACT+CGG + chr3_2:40194006-40194025 None:intergenic 40.0%
! TACAGGTACCCTTTTGTTGA+AGG - chr3_2:40194074-40194093 Msa0405460:CDS 40.0%
TCGAACGACCTTCAACAAAA+GGG + chr3_2:40194085-40194104 None:intergenic 40.0%
!!! CCTGTTTTTTCAGGGTAAGA+AGG + chr3_2:40194191-40194210 None:intergenic 40.0%
CCTTCTTACCCTGAAAAAAC+AGG - chr3_2:40194188-40194207 Msa0405460:intron 40.0%
!! GTTATCGGTTCAAGAACACA+AGG + chr3_2:40194219-40194238 None:intergenic 40.0%
GTTAGCCGAAAGATGGTTAT+CGG + chr3_2:40194234-40194253 None:intergenic 40.0%
! TTTGCGGAGACCTGTGTTTT+TGG - chr3_2:40193900-40193919 Msa0405460:CDS 45.0%
!!! GTTTTTGGTAAACAGTCGCC+CGG - chr3_2:40193915-40193934 Msa0405460:CDS 45.0%
!! TTTTTGGTAAACAGTCGCCC+GGG - chr3_2:40193916-40193935 Msa0405460:CDS 45.0%
CAAAATAGCCCCGTAACTTC+GGG + chr3_2:40193983-40194002 None:intergenic 45.0%
GCAAAATAGCCCCGTAACTT+CGG + chr3_2:40193984-40194003 None:intergenic 45.0%
GGTAGGTAGAGAATACCTAG+GGG + chr3_2:40194035-40194054 None:intergenic 45.0%
GGGTAGGTAGAGAATACCTA+GGG + chr3_2:40194036-40194055 None:intergenic 45.0%
TGGGTAGGTAGAGAATACCT+AGG + chr3_2:40194037-40194056 None:intergenic 45.0%
CTCGAACGACCTTCAACAAA+AGG + chr3_2:40194086-40194105 None:intergenic 45.0%
GTAATTGATGCCATACTCCC+AGG + chr3_2:40194114-40194133 None:intergenic 45.0%
!!! AGGTGACCCCTGTTTTTTCA+GGG + chr3_2:40194199-40194218 None:intergenic 45.0%
!!! AAGGTGACCCCTGTTTTTTC+AGG + chr3_2:40194200-40194219 None:intergenic 45.0%
ATTCCTGTACTACCCCTTGT+TGG + chr3_2:40194280-40194299 None:intergenic 45.0%
GGCTTGAGTAACGCAAACAT+TGG + chr3_2:40194416-40194435 None:intergenic 45.0%
! AAGGTCGTTCGAGCTTTTCC+TGG - chr3_2:40194093-40194112 Msa0405460:CDS 50.0%
! AGGTCGTTCGAGCTTTTCCT+GGG - chr3_2:40194094-40194113 Msa0405460:CDS 50.0%
! TCGAGCTTTTCCTGGGAGTA+TGG - chr3_2:40194101-40194120 Msa0405460:intron 50.0%
GGCATCAATTACTTCAGCGC+CGG - chr3_2:40194122-40194141 Msa0405460:intron 50.0%
AGAGAAAATGCCTCCAGCCA+AGG + chr3_2:40194165-40194184 None:intergenic 50.0%
! AGGCTAGGTTAGCCGAAAGA+TGG + chr3_2:40194241-40194260 None:intergenic 50.0%
AGGCGTAGTCGATGGACAAT+AGG + chr3_2:40194308-40194327 None:intergenic 50.0%
! TGTCCATCGACTACGCCTTT+CGG - chr3_2:40194310-40194329 Msa0405460:intron 50.0%
! CGGAGGAACCCTTAGGTTTT+CGG - chr3_2:40194375-40194394 Msa0405460:intron 50.0%
! GGAGGAACCCTTAGGTTTTC+GGG - chr3_2:40194376-40194395 Msa0405460:intron 50.0%
! GAGGAACCCTTAGGTTTTCG+GGG - chr3_2:40194377-40194396 Msa0405460:intron 50.0%
CCAATGCCCCGAAAACCTAA+GGG + chr3_2:40194386-40194405 None:intergenic 50.0%
TCCAATGCCCCGAAAACCTA+AGG + chr3_2:40194387-40194406 None:intergenic 50.0%
!! AAGGGGTGCCTCCTCACAAA+GGG + chr3_2:40193958-40193977 None:intergenic 55.0%
CACCCCTTCTCCCGAAGTTA+CGG - chr3_2:40193970-40193989 Msa0405460:CDS 55.0%
ACCCCTTCTCCCGAAGTTAC+GGG - chr3_2:40193971-40193990 Msa0405460:CDS 55.0%
GCGCGAGACAACTCTCTCTA+AGG + chr3_2:40194013-40194032 None:intergenic 55.0%
CTCTACCTACCCACCTGTGT+CGG - chr3_2:40194044-40194063 Msa0405460:CDS 55.0%
!! CTACCCACCTGTGTCGGTTT+CGG - chr3_2:40194050-40194069 Msa0405460:CDS 55.0%
!! TACCCACCTGTGTCGGTTTC+GGG - chr3_2:40194051-40194070 Msa0405460:CDS 55.0%
TACCCGAAACCGACACAGGT+GGG + chr3_2:40194056-40194075 None:intergenic 55.0%
CTACCCCTTGTTGGTCCCAA+GGG + chr3_2:40194271-40194290 None:intergenic 55.0%
ACTACCCCTTGTTGGTCCCA+AGG + chr3_2:40194272-40194291 None:intergenic 55.0%
GGACCAACAAGGGGTAGTAC+AGG - chr3_2:40194274-40194293 Msa0405460:intron 55.0%
ACGCCTTTCGGCCTGATCTT+AGG - chr3_2:40194322-40194341 Msa0405460:intron 55.0%
GTGAGTCAGGGCCTAAGATC+AGG + chr3_2:40194336-40194355 None:intergenic 55.0%
AACCTTGCGGAGGAACCCTT+AGG - chr3_2:40194368-40194387 Msa0405460:intron 55.0%
AACCTAAGGGTTCCTCCGCA+AGG + chr3_2:40194373-40194392 None:intergenic 55.0%
!! CCCTTAGGTTTTCGGGGCAT+TGG - chr3_2:40194383-40194402 Msa0405460:intron 55.0%
CGAAGCGGAAGCGAGAATGT+CGG + chr3_2:40194437-40194456 None:intergenic 55.0%
TCACTGCGACCCCCTTTGTG+AGG - chr3_2:40193944-40193963 Msa0405460:CDS 60.0%
!! AGGGGTGCCTCCTCACAAAG+GGG + chr3_2:40193957-40193976 None:intergenic 60.0%
!! GAAGGGGTGCCTCCTCACAA+AGG + chr3_2:40193959-40193978 None:intergenic 60.0%
CCCCGTAACTTCGGGAGAAG+GGG + chr3_2:40193975-40193994 None:intergenic 60.0%
CCCCTTCTCCCGAAGTTACG+GGG - chr3_2:40193972-40193991 Msa0405460:CDS 60.0%
GCCCCGTAACTTCGGGAGAA+GGG + chr3_2:40193976-40193995 None:intergenic 60.0%
AGCCCCGTAACTTCGGGAGA+AGG + chr3_2:40193977-40193996 None:intergenic 60.0%
CGAAACCGACACAGGTGGGT+AGG + chr3_2:40194052-40194071 None:intergenic 60.0%
GTACCCGAAACCGACACAGG+TGG + chr3_2:40194057-40194076 None:intergenic 60.0%
CCTGTACCCGAAACCGACAC+AGG + chr3_2:40194060-40194079 None:intergenic 60.0%
!! CCTGTGTCGGTTTCGGGTAC+AGG - chr3_2:40194057-40194076 Msa0405460:CDS 60.0%
AGCGCCTGGTACTCGAACCT+TGG - chr3_2:40194145-40194164 Msa0405460:intron 60.0%
CCAGCCAAGGTTCGAGTACC+AGG + chr3_2:40194152-40194171 None:intergenic 60.0%
CCTGGTACTCGAACCTTGGC+TGG - chr3_2:40194149-40194168 Msa0405460:intron 60.0%
GGTACTCGAACCTTGGCTGG+AGG - chr3_2:40194152-40194171 Msa0405460:intron 60.0%
TTGTTGGTCCCAAGGGACGG+AGG + chr3_2:40194264-40194283 None:intergenic 60.0%
TCCGTCCCTTGGGACCAACA+AGG - chr3_2:40194263-40194282 Msa0405460:intron 60.0%
CCCTTGTTGGTCCCAAGGGA+CGG + chr3_2:40194267-40194286 None:intergenic 60.0%
CCGTCCCTTGGGACCAACAA+GGG - chr3_2:40194264-40194283 Msa0405460:intron 60.0%
CGTCCCTTGGGACCAACAAG+GGG - chr3_2:40194265-40194284 Msa0405460:intron 60.0%
! AGGCCGAAAGGCGTAGTCGA+TGG + chr3_2:40194316-40194335 None:intergenic 60.0%
GGGCCTAAGATCAGGCCGAA+AGG + chr3_2:40194328-40194347 None:intergenic 60.0%
TCCTCCGCAAGGTTCGTCCA+CGG + chr3_2:40194362-40194381 None:intergenic 60.0%
CAAAGGGGGTCGCAGTGACC+AGG + chr3_2:40193942-40193961 None:intergenic 65.0%
CTGCGACCCCCTTTGTGAGG+AGG - chr3_2:40193947-40193966 Msa0405460:CDS 65.0%
! GGGGTGCCTCCTCACAAAGG+GGG + chr3_2:40193956-40193975 None:intergenic 65.0%
GAGAGTTGTCTCGCGCCCCT+AGG - chr3_2:40194017-40194036 Msa0405460:CDS 65.0%
GGTTCGAGTACCAGGCGCTC+CGG + chr3_2:40194144-40194163 None:intergenic 65.0%
ACCTAGCCTCCTCCGTCCCT+TGG - chr3_2:40194252-40194271 Msa0405460:intron 65.0%
CCTAGCCTCCTCCGTCCCTT+GGG - chr3_2:40194253-40194272 Msa0405460:intron 65.0%
TTGGTCCCAAGGGACGGAGG+AGG + chr3_2:40194261-40194280 None:intergenic 65.0%
CGTCCACGGAGGGTGAGTCA+GGG + chr3_2:40194348-40194367 None:intergenic 65.0%
TCGTCCACGGAGGGTGAGTC+AGG + chr3_2:40194349-40194368 None:intergenic 65.0%
CCGCAAGGTTCGTCCACGGA+GGG + chr3_2:40194358-40194377 None:intergenic 65.0%
CCCTCCGTGGACGAACCTTG+CGG - chr3_2:40194355-40194374 Msa0405460:intron 65.0%
TCCGCAAGGTTCGTCCACGG+AGG + chr3_2:40194359-40194378 None:intergenic 65.0%
TCCGTGGACGAACCTTGCGG+AGG - chr3_2:40194358-40194377 Msa0405460:intron 65.0%
GCGAGCAGGGTTGGACGAAG+CGG + chr3_2:40194452-40194471 None:intergenic 65.0%
TTCGTCCAACCCTGCTCGCG+CGG - chr3_2:40194453-40194472 Msa0405460:intron 65.0%
! ACGAAGTACCCGCGCGAGCA+GGG + chr3_2:40194465-40194484 None:intergenic 65.0%
! AACGAAGTACCCGCGCGAGC+AGG + chr3_2:40194466-40194485 None:intergenic 65.0%
GGTAAACAGTCGCCCGGGCC+TGG - chr3_2:40193921-40193940 Msa0405460:CDS 70.0%
! TACTTCAGCGCCGGAGCGCC+TGG - chr3_2:40194131-40194150 Msa0405460:intron 70.0%
CCCAAGGGACGGAGGAGGCT+AGG + chr3_2:40194256-40194275 None:intergenic 70.0%
AGGCCCTGACTCACCCTCCG+TGG - chr3_2:40194342-40194361 Msa0405460:intron 70.0%
TCGTCCAACCCTGCTCGCGC+GGG - chr3_2:40194454-40194473 Msa0405460:intron 70.0%
AGTACCCGCGCGAGCAGGGT+TGG + chr3_2:40194461-40194480 None:intergenic 70.0%
GGGTCGCAGTGACCAGGCCC+GGG + chr3_2:40193936-40193955 None:intergenic 75.0%
GGGGTCGCAGTGACCAGGCC+CGG + chr3_2:40193937-40193956 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 40193887 40194489 40193887 ID=Msa0405460;Name=Msa0405460
chr3_2 mRNA 40193887 40194489 40193887 ID=Msa0405460-mRNA-1;Parent=Msa0405460;Name=Msa0405460-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0|0|1|0|0|2|0|85
chr3_2 exon 40194464 40194489 40194464 ID=Msa0405460-mRNA-1:exon:7818;Parent=Msa0405460-mRNA-1
chr3_2 exon 40193887 40194118 40193887 ID=Msa0405460-mRNA-1:exon:7817;Parent=Msa0405460-mRNA-1
chr3_2 CDS 40194464 40194489 40194464 ID=Msa0405460-mRNA-1:cds;Parent=Msa0405460-mRNA-1
chr3_2 CDS 40193887 40194118 40193887 ID=Msa0405460-mRNA-1:cds;Parent=Msa0405460-mRNA-1
Gene Sequence

>Msa0405460

ATGGTCTTACGACTTTGCGGAGACCTCCTCCTCCGTCCCTTGGGACCAACAAGGGGTAGTACAGGAATATTCACCTATTGTCCATCGACTACGCCTTTCGGCCTGATCTTAGGCCCTGACTCACCCTCCGTGGACGAACCTTGCGGAGGAACCCTTAGGTTTTCGGGGCATTGGATTCTCACCAATGTTTGCGTTACTCAAGCCGACATTCTCGCTTCCGCTTCGTCCAACCCTGCTCGCGCGGGTACTTCGTTCTAA

Protein sequence

>Msa0405460

MVLRLCGDLLLRPLGPTRGSTGIFTYCPSTTPFGLILGPDSPSVDEPCGGTLRFSGHWILTNVCVTQADILASASSNPARAGTSF*