AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1003970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1003970 MtrunA17_Chr7g0214511 84.324 185 15 3 1 179 1 177 1.63e-94 276
Msa1003970 MtrunA17_Chr1g0180581 58.434 166 39 7 14 179 9 144 1.45e-45 149
Msa1003970 MtrunA17_Chr1g0193731 49.727 183 46 9 1 178 1 142 1.02e-29 110
Msa1003970 MtrunA17_Chr1g0169561 44.366 142 50 7 55 179 83 212 2.42e-19 83.2
Msa1003970 MtrunA17_Chr1g0169521 42.336 137 53 4 59 179 86 212 5.18e-18 79.7
Msa1003970 MtrunA17_Chr1g0174001 54.930 71 20 5 117 179 12 78 9.62e-12 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGACGCGGCCGCCGTTTCT+TGG 0.252455 7_1:+1038479 None:intergenic
TTCTTGGTGTTGTAGAATAT+TGG 0.276502 7_1:+1038495 None:intergenic
AGTACTTTGAACAGTCAATT+TGG 0.281486 7_1:+1038523 None:intergenic
TTCTGTTCTTGGTAATCATA+AGG 0.363019 7_1:-1038697 Msa1003970:CDS
CATATATCTCGCGGGTTATG+AGG 0.375166 7_1:-1038396 None:intergenic
ATCGCTCCCTTCAAAATTCC+AGG 0.381362 7_1:-1038848 Msa1003970:CDS
CAAAGCATTGAATGGACATA+AGG 0.388435 7_1:-1038592 Msa1003970:CDS
GCATCATTAGTTGTTGAAGA+TGG 0.413813 7_1:+1038768 None:intergenic
ACTTCTAACAAAGCATTGAA+TGG 0.414800 7_1:-1038600 Msa1003970:CDS
GAAGATGGTGGTGCAGTTTG+TGG 0.454649 7_1:+1038558 None:intergenic
GAATAGGGTTTGAGTAATCA+AGG 0.456225 7_1:+1038808 None:intergenic
CATCATTAGTTGTTGAAGAT+GGG 0.456727 7_1:+1038769 None:intergenic
GTCAATTTGGCTCTGTTCAA+AGG 0.462178 7_1:+1038536 None:intergenic
AAAGCATTGAATGGACATAA+GGG 0.470952 7_1:-1038591 Msa1003970:CDS
TAATCAAGGAAACGGAAAGA+AGG 0.496330 7_1:+1038822 None:intergenic
TCTTCAACAACTAATGATGC+TGG 0.499426 7_1:-1038765 Msa1003970:CDS
GGAGCGATGATAAACATCAT+TGG 0.502169 7_1:+1038863 None:intergenic
CTCATGTGATGTTTGCAACA+AGG 0.516766 7_1:-1038628 Msa1003970:CDS
TGGCTCTGTTCAAAGGAAGA+TGG 0.523783 7_1:+1038543 None:intergenic
TTGGTGTTGTAGAATATTGG+CGG 0.527171 7_1:+1038498 None:intergenic
AAGATGGTGGTGCAGTTTGT+GGG 0.535375 7_1:+1038559 None:intergenic
GGCCGCGTCGAAGAAGAAGA+AGG 0.538757 7_1:-1038467 Msa1003970:CDS
GAAACGGAAAGAAGGGTACC+TGG 0.540917 7_1:+1038830 None:intergenic
GGTTTGAGTAATCAAGGAAA+CGG 0.550662 7_1:+1038814 None:intergenic
TTTGGTTCATGATCATGAGA+AGG 0.562074 7_1:+1038888 None:intergenic
TATTCTACAACACCAAGAAA+CGG 0.569291 7_1:-1038491 Msa1003970:CDS
ATATATCTCGCGGGTTATGA+GGG 0.574949 7_1:-1038395 None:intergenic
TCATGATCATGAGAAGGAGA+TGG 0.576941 7_1:+1038894 None:intergenic
CTTTGTTGCATATATCTCGC+GGG 0.577301 7_1:-1038404 Msa1003970:CDS
AATCAAGGAAACGGAAAGAA+GGG 0.583538 7_1:+1038823 None:intergenic
ACAACGTAAAGAAGATCGTA+TGG 0.588297 7_1:-1038731 Msa1003970:CDS
CTCCTTCTTCTTCTTCGACG+CGG 0.618622 7_1:+1038465 None:intergenic
ACTTTGTTGCATATATCTCG+CGG 0.646341 7_1:-1038405 Msa1003970:CDS
CTCTGTTCAAAGGAAGATGG+TGG 0.704608 7_1:+1038546 None:intergenic
TCTACAACACCAAGAAACGG+CGG 0.738098 7_1:-1038488 Msa1003970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTCTTATTCTGTTCT+TGG - chr7_1:1038608-1038627 Msa1003970:CDS 20.0%
!!! TGATAAACATCATTGGTTTT+TGG + chr7_1:1038449-1038468 None:intergenic 25.0%
!!! TTTTGAGTTCATTCTGAATA+GGG + chr7_1:1038526-1038545 None:intergenic 25.0%
!!! TTTTTGAGTTCATTCTGAAT+AGG + chr7_1:1038527-1038546 None:intergenic 25.0%
CATCATTAGTTGTTGAAGAT+GGG + chr7_1:1038550-1038569 None:intergenic 30.0%
! TTCTGTTCTTGGTAATCATA+AGG - chr7_1:1038619-1038638 Msa1003970:CDS 30.0%
!! ACTTCTAACAAAGCATTGAA+TGG - chr7_1:1038716-1038735 Msa1003970:CDS 30.0%
!! AAAGCATTGAATGGACATAA+GGG - chr7_1:1038725-1038744 Msa1003970:CDS 30.0%
AGTACTTTGAACAGTCAATT+TGG + chr7_1:1038796-1038815 None:intergenic 30.0%
!! TTCTTGGTGTTGTAGAATAT+TGG + chr7_1:1038824-1038843 None:intergenic 30.0%
TATTCTACAACACCAAGAAA+CGG - chr7_1:1038825-1038844 Msa1003970:CDS 30.0%
! TTTGGTTCATGATCATGAGA+AGG + chr7_1:1038431-1038450 None:intergenic 35.0%
AATCAAGGAAACGGAAAGAA+GGG + chr7_1:1038496-1038515 None:intergenic 35.0%
TAATCAAGGAAACGGAAAGA+AGG + chr7_1:1038497-1038516 None:intergenic 35.0%
GGTTTGAGTAATCAAGGAAA+CGG + chr7_1:1038505-1038524 None:intergenic 35.0%
GAATAGGGTTTGAGTAATCA+AGG + chr7_1:1038511-1038530 None:intergenic 35.0%
GCATCATTAGTTGTTGAAGA+TGG + chr7_1:1038551-1038570 None:intergenic 35.0%
TCTTCAACAACTAATGATGC+TGG - chr7_1:1038551-1038570 Msa1003970:CDS 35.0%
ACAACGTAAAGAAGATCGTA+TGG - chr7_1:1038585-1038604 Msa1003970:CDS 35.0%
!! CAAAGCATTGAATGGACATA+AGG - chr7_1:1038724-1038743 Msa1003970:CDS 35.0%
!! TTGGTGTTGTAGAATATTGG+CGG + chr7_1:1038821-1038840 None:intergenic 35.0%
ACTTTGTTGCATATATCTCG+CGG - chr7_1:1038911-1038930 Msa1003970:CDS 35.0%
TCATGATCATGAGAAGGAGA+TGG + chr7_1:1038425-1038444 None:intergenic 40.0%
GGAGCGATGATAAACATCAT+TGG + chr7_1:1038456-1038475 None:intergenic 40.0%
!! AGGGTACCTGGAATTTTGAA+GGG + chr7_1:1038477-1038496 None:intergenic 40.0%
!!! AAGGGTACCTGGAATTTTGA+AGG + chr7_1:1038478-1038497 None:intergenic 40.0%
CTCATGTGATGTTTGCAACA+AGG - chr7_1:1038688-1038707 Msa1003970:CDS 40.0%
!! GTCAATTTGGCTCTGTTCAA+AGG + chr7_1:1038783-1038802 None:intergenic 40.0%
CTTTGTTGCATATATCTCGC+GGG - chr7_1:1038912-1038931 Msa1003970:CDS 40.0%
ATCGCTCCCTTCAAAATTCC+AGG - chr7_1:1038468-1038487 Msa1003970:CDS 45.0%
! AAGATGGTGGTGCAGTTTGT+GGG + chr7_1:1038760-1038779 None:intergenic 45.0%
CTCTGTTCAAAGGAAGATGG+TGG + chr7_1:1038773-1038792 None:intergenic 45.0%
! TGGCTCTGTTCAAAGGAAGA+TGG + chr7_1:1038776-1038795 None:intergenic 45.0%
TCTACAACACCAAGAAACGG+CGG - chr7_1:1038828-1038847 Msa1003970:CDS 45.0%
!! GAAACGGAAAGAAGGGTACC+TGG + chr7_1:1038489-1038508 None:intergenic 50.0%
! GAAGATGGTGGTGCAGTTTG+TGG + chr7_1:1038761-1038780 None:intergenic 50.0%
CTCCTTCTTCTTCTTCGACG+CGG + chr7_1:1038854-1038873 None:intergenic 50.0%
GGCCGCGTCGAAGAAGAAGA+AGG - chr7_1:1038849-1038868 Msa1003970:CDS 60.0%
TCGACGCGGCCGCCGTTTCT+TGG + chr7_1:1038840-1038859 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 1038398 1038940 1038398 ID=Msa1003970;Name=Msa1003970
chr7_1 mRNA 1038398 1038940 1038398 ID=Msa1003970-mRNA-1;Parent=Msa1003970;Name=Msa1003970-mRNA-1;_AED=0.24;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|180
chr7_1 exon 1038398 1038940 1038398 ID=Msa1003970-mRNA-1:exon:516;Parent=Msa1003970-mRNA-1
chr7_1 CDS 1038398 1038940 1038398 ID=Msa1003970-mRNA-1:cds;Parent=Msa1003970-mRNA-1
Gene Sequence

>Msa1003970

ATGTATTCTTCTTCTTCTTCATCTCCATCTCCTTCTCATGATCATGAACCAAAAACCAATGATGTTTATCATCGCTCCCTTCAAAATTCCAGGTACCCTTCTTTCCGTTTCCTTGATTACTCAAACCCTATTCAGAATGAACTCAAAAACCCATCTTCAACAACTAATGATGCTGGAAAACAACAGAACAACGTAAAGAAGATCGTATGGTTTTTTTCTTATTCTGTTCTTGGTAATCATAAGGATGTTGAAAAACAGAACAAACATACATACTCATACTCATACTCATACTCATGTGATGTTTGCAACAAGGTTTTTACTTCTAACAAAGCATTGAATGGACATAAGGGTGTTATTCACCCACAAACTGCACCACCATCTTCCTTTGAACAGAGCCAAATTGACTGTTCAAAGTACTTGCCGCCAATATTCTACAACACCAAGAAACGGCGGCCGCGTCGAAGAAGAAGAAGGAGATATATGAACATTGATGATGATGTGATTGCTGCTGAAACTTTGTTGCATATATCTCGCGGGTTATGA
Protein sequence

>Msa1003970

MYSSSSSSPSPSHDHEPKTNDVYHRSLQNSRYPSFRFLDYSNPIQNELKNPSSTTNDAGKQQNNVKKIVWFFSYSVLGNHKDVEKQNKHTYSYSYSYSCDVCNKVFTSNKALNGHKGVIHPQTAPPSSFEQSQIDCSKYLPPIFYNTKKRRPRRRRRRRYMNIDDDVIAAETLLHISRGL*