AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0596810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0596810 MtrunA17_Chr4g0019551 54.386 114 31 1 1 93 1 114 5.80e-31 110
Msa0596810 MtrunA17_Chr4g0019481 48.182 110 36 2 1 89 1 110 1.22e-23 91.3
Msa0596810 MtrunA17_Chr4g0019471 43.548 124 35 2 1 89 1 124 1.33e-21 86.3
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 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCGAATCTAATATTAAATT+TGG 0.129441 4_2:+28294367 None:intergenic
AAATAATTTACAAGATGATA+TGG 0.212103 4_2:-28294140 Msa0596810:CDS
GGTGGTTGAGGATGGTTATT+TGG 0.221703 4_2:+28294328 None:intergenic
TGTGGTTGAGGCTGGTTATT+TGG 0.223810 4_2:+28294307 None:intergenic
GCTTTCTGATAAGTGCTTCT+TGG 0.258496 4_2:+28294038 None:intergenic
TGCCATTTCCTCTTGCTTCC+TGG 0.265597 4_2:+28293970 None:intergenic
GGAGGCTGGCTCAAGTTAAT+TGG 0.275027 4_2:+28294238 None:intergenic
AGGTTCAAAGCTCGAACATT+AGG 0.361025 4_2:+28294217 None:intergenic
TGACTCGTATGCACAATAGA+AGG 0.372588 4_2:+28294187 None:intergenic
TATCAGAAAGCAAGAAGCTT+TGG 0.383471 4_2:-28294026 Msa0596810:CDS
GGCTGGTTATTTGGTGGTTG+AGG 0.391961 4_2:+28294316 None:intergenic
GGTTATTTGGTGGTTGAGGA+TGG 0.406136 4_2:+28294320 None:intergenic
TACCAGGAAGCAAGAGGAAA+TGG 0.421313 4_2:-28293972 Msa0596810:CDS
GGATGGTTATTTGGTGGTAG+AGG 0.431093 4_2:+28294337 None:intergenic
AAGTGAAGATGGAGCAGAAA+AGG 0.463976 4_2:-28294072 Msa0596810:CDS
AAGTTAATTGGCTGCACATG+TGG 0.509287 4_2:+28294250 None:intergenic
AATAATTTACAAGATGATAT+GGG 0.509595 4_2:-28294139 Msa0596810:CDS
GTTGCTTCTTCATCATCTCA+AGG 0.532802 4_2:+28293855 None:intergenic
GGTTGAGGCTGGTTATTTGG+TGG 0.533930 4_2:+28294310 None:intergenic
GACTCGTATGCACAATAGAA+GGG 0.537355 4_2:+28294188 None:intergenic
GAGAATGCAACAACAACACT+TGG 0.542875 4_2:-28293999 Msa0596810:CDS
GAGCAATCTAAGACAAATGC+TGG 0.544449 4_2:-28293890 Msa0596810:CDS
AACATGCACTGCTAAAACAT+GGG 0.552835 4_2:+28294405 None:intergenic
AAGCTCGAACATTAGGAGGC+TGG 0.553043 4_2:+28294224 None:intergenic
ACTGCATAAGAATTCTAGCT+TGG 0.557073 4_2:+28294453 None:intergenic
GGTTGAGGATGGTTATTTGG+TGG 0.557091 4_2:+28294331 None:intergenic
TAACATGCACTGCTAAAACA+TGG 0.569150 4_2:+28294404 None:intergenic
TCAACTGTTAGAAGTGAAGA+TGG 0.576254 4_2:-28294083 Msa0596810:CDS
TTCAAAGCTCGAACATTAGG+AGG 0.585789 4_2:+28294220 None:intergenic
ACTGCTAAAACATGGGGAGA+TGG 0.597465 4_2:+28294412 None:intergenic
GGAAACTACCAGGAAGCAAG+AGG 0.631081 4_2:-28293978 Msa0596810:CDS
GAAACAACATGAGGAGACAA+TGG 0.637862 4_2:-28293915 Msa0596810:CDS
AACAACACTTGGAAACTACC+AGG 0.641183 4_2:-28293988 Msa0596810:CDS
ACTCGTATGCACAATAGAAG+GGG 0.645441 4_2:+28294189 None:intergenic
CTCGTATGCACAATAGAAGG+GGG 0.684292 4_2:+28294190 None:intergenic
TTAATTGGCTGCACATGTGG+AGG 0.687081 4_2:+28294253 None:intergenic
ACATGCACTGCTAAAACATG+GGG 0.693010 4_2:+28294406 None:intergenic
AAACATGCAGAAACAACATG+AGG 0.696986 4_2:-28293924 Msa0596810:CDS
TGTGGAGGTGATGCATTGTG+TGG 0.709748 4_2:+28294268 None:intergenic
GCATACGAGTCAAGATCCTG+AGG 0.710797 4_2:-28294176 Msa0596810:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAATTTACAAGATGATA+TGG - chr4_2:28294161-28294180 Msa0596810:CDS 15.0%
!! AATAATTTACAAGATGATAT+GGG - chr4_2:28294162-28294181 Msa0596810:CDS 15.0%
!! CTCGAATCTAATATTAAATT+TGG + chr4_2:28293937-28293956 None:intergenic 20.0%
! TTTTGAACGATAATAACCTC+AGG + chr4_2:28294144-28294163 None:intergenic 30.0%
! ACTGCATAAGAATTCTAGCT+TGG + chr4_2:28293851-28293870 None:intergenic 35.0%
AACATGCACTGCTAAAACAT+GGG + chr4_2:28293899-28293918 None:intergenic 35.0%
TAACATGCACTGCTAAAACA+TGG + chr4_2:28293900-28293919 None:intergenic 35.0%
TCAACTGTTAGAAGTGAAGA+TGG - chr4_2:28294218-28294237 Msa0596810:CDS 35.0%
TATCAGAAAGCAAGAAGCTT+TGG - chr4_2:28294275-28294294 Msa0596810:CDS 35.0%
AAACATGCAGAAACAACATG+AGG - chr4_2:28294377-28294396 Msa0596810:CDS 35.0%
ACATGCACTGCTAAAACATG+GGG + chr4_2:28293898-28293917 None:intergenic 40.0%
! TGTGTTGCATTTTGTGGTTG+AGG + chr4_2:28294009-28294028 None:intergenic 40.0%
AAGTTAATTGGCTGCACATG+TGG + chr4_2:28294054-28294073 None:intergenic 40.0%
TTCAAAGCTCGAACATTAGG+AGG + chr4_2:28294084-28294103 None:intergenic 40.0%
AGGTTCAAAGCTCGAACATT+AGG + chr4_2:28294087-28294106 None:intergenic 40.0%
ACTCGTATGCACAATAGAAG+GGG + chr4_2:28294115-28294134 None:intergenic 40.0%
GACTCGTATGCACAATAGAA+GGG + chr4_2:28294116-28294135 None:intergenic 40.0%
TGACTCGTATGCACAATAGA+AGG + chr4_2:28294117-28294136 None:intergenic 40.0%
AAGTGAAGATGGAGCAGAAA+AGG - chr4_2:28294229-28294248 Msa0596810:CDS 40.0%
GCTTTCTGATAAGTGCTTCT+TGG + chr4_2:28294266-28294285 None:intergenic 40.0%
GAGAATGCAACAACAACACT+TGG - chr4_2:28294302-28294321 Msa0596810:CDS 40.0%
AACAACACTTGGAAACTACC+AGG - chr4_2:28294313-28294332 Msa0596810:CDS 40.0%
GAAACAACATGAGGAGACAA+TGG - chr4_2:28294386-28294405 Msa0596810:CDS 40.0%
! GAGCAATCTAAGACAAATGC+TGG - chr4_2:28294411-28294430 Msa0596810:CDS 40.0%
GTTGCTTCTTCATCATCTCA+AGG + chr4_2:28294449-28294468 None:intergenic 40.0%
ACTGCTAAAACATGGGGAGA+TGG + chr4_2:28293892-28293911 None:intergenic 45.0%
! GGATGGTTATTTGGTGGTAG+AGG + chr4_2:28293967-28293986 None:intergenic 45.0%
GGTTGAGGATGGTTATTTGG+TGG + chr4_2:28293973-28293992 None:intergenic 45.0%
GGTGGTTGAGGATGGTTATT+TGG + chr4_2:28293976-28293995 None:intergenic 45.0%
! GGTTATTTGGTGGTTGAGGA+TGG + chr4_2:28293984-28294003 None:intergenic 45.0%
! TGTGGTTGAGGCTGGTTATT+TGG + chr4_2:28293997-28294016 None:intergenic 45.0%
! TTGCATTTTGTGGTTGAGGC+TGG + chr4_2:28294005-28294024 None:intergenic 45.0%
! GGTCGATGTGTTGCATTTTG+TGG + chr4_2:28294015-28294034 None:intergenic 45.0%
TTAATTGGCTGCACATGTGG+AGG + chr4_2:28294051-28294070 None:intergenic 45.0%
GCACAATAGAAGGGGGATTA+AGG + chr4_2:28294107-28294126 None:intergenic 45.0%
CTCGTATGCACAATAGAAGG+GGG + chr4_2:28294114-28294133 None:intergenic 45.0%
TACCAGGAAGCAAGAGGAAA+TGG - chr4_2:28294329-28294348 Msa0596810:CDS 45.0%
! GGCTGGTTATTTGGTGGTTG+AGG + chr4_2:28293988-28294007 None:intergenic 50.0%
! GGTTGAGGCTGGTTATTTGG+TGG + chr4_2:28293994-28294013 None:intergenic 50.0%
TGTGGAGGTGATGCATTGTG+TGG + chr4_2:28294036-28294055 None:intergenic 50.0%
! GGAGGCTGGCTCAAGTTAAT+TGG + chr4_2:28294066-28294085 None:intergenic 50.0%
AAGCTCGAACATTAGGAGGC+TGG + chr4_2:28294080-28294099 None:intergenic 50.0%
GCATACGAGTCAAGATCCTG+AGG - chr4_2:28294125-28294144 Msa0596810:CDS 50.0%
GGAAACTACCAGGAAGCAAG+AGG - chr4_2:28294323-28294342 Msa0596810:CDS 50.0%
! TGCCATTTCCTCTTGCTTCC+TGG + chr4_2:28294334-28294353 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 28293844 28294479 28293844 ID=Msa0596810;Name=Msa0596810
chr4_2 mRNA 28293844 28294479 28293844 ID=Msa0596810-mRNA-1;Parent=Msa0596810;Name=Msa0596810-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|-1|0|1|-1|1|1|0|211
chr4_2 exon 28293844 28294479 28293844 ID=Msa0596810-mRNA-1:exon:7290;Parent=Msa0596810-mRNA-1
chr4_2 CDS 28293844 28294479 28293844 ID=Msa0596810-mRNA-1:cds;Parent=Msa0596810-mRNA-1
Gene Sequence

>Msa0596810

ATGACCAAGCTAGAATTCTTATGCAGTGATTGTGACGCAAAGTTTCCATCTCCCCATGTTTTAGCAGTGCATGTTATCGAACAACATCATCCAAATTTAATATTAGATTCGAGTGCAAATCCTCTACCACCAAATAACCATCCTCAACCACCAAATAACCAGCCTCAACCACAAAATGCAACACATCGACCACACAATGCATCACCTCCACATGTGCAGCCAATTAACTTGAGCCAGCCTCCTAATGTTCGAGCTTTGAACCTTAATCCCCCTTCTATTGTGCATACGAGTCAAGATCCTGAGGTTATTATCGTTCAAAATAATTTACAAGATGATATGGGAAATCAGAAGCTGACAACAGAAGTTGTGCAAGCTCAACTGTTAGAAGTGAAGATGGAGCAGAAAAGGCAGAATGATATCCAAGAAGCACTTATCAGAAAGCAAGAAGCTTTGGAAAAGAGAATGCAACAACAACACTTGGAAACTACCAGGAAGCAAGAGGAAATGGCAAAGAAGCAAGAAGAACTTGAAAGAAACATGCAGAAACAACATGAGGAGACAATGGCTGAGCAATCTAAGACAAATGCTGGCATTGCTGCTATCCTTGAGATGATGAAGAAGCAACAACAACCTTAA
Protein sequence

>Msa0596810

MTKLEFLCSDCDAKFPSPHVLAVHVIEQHHPNLILDSSANPLPPNNHPQPPNNQPQPQNATHRPHNASPPHVQPINLSQPPNVRALNLNPPSIVHTSQDPEVIIVQNNLQDDMGNQKLTTEVVQAQLLEVKMEQKRQNDIQEALIRKQEALEKRMQQQHLETTRKQEEMAKKQEELERNMQKQHEETMAEQSKTNAGIAAILEMMKKQQQP*