AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0172220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0172220 MtrunA17_Chr1g0191021 57.627 236 50 3 1 187 1 235 3.93e-72 223
Msa0172220 MtrunA17_Chr7g0273821 52.273 88 32 2 59 142 75 156 1.05e-20 88.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0172220 AT3G04930.2 40.708 113 49 5 48 142 73 185 5.25e-17 78.2
Msa0172220 AT3G04930.1 40.708 113 49 5 48 142 73 185 5.75e-17 78.2
Msa0172220 AT5G28040.2 44.231 104 47 5 48 141 69 171 4.71e-15 72.8
Msa0172220 AT5G28040.1 44.231 104 47 5 48 141 69 171 4.71e-15 72.8
Msa0172220 AT1G44810.1 47.170 53 28 0 90 142 115 167 6.83e-11 60.1

Find 38 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCCATTTGCTCCCATTT+TGG 0.158841 1_4:-57205179 None:intergenic
TCAGTCAAATGAGCTGAATT+AGG 0.184630 1_4:-57205581 None:intergenic
CTGAATTAGGGTTAGGGTTT+GGG 0.227113 1_4:-57205568 None:intergenic
GGTGGTGGGGATGGTGGCAG+TGG 0.280876 1_4:-57205096 None:intergenic
GGTGGGGATGGTGGCAGTGG+TGG 0.286773 1_4:-57205093 None:intergenic
ACGACTCCCTTGAACCAAAA+TGG 0.287269 1_4:+57205165 Msa0172220:CDS
CAGTCAAATGAGCTGAATTA+GGG 0.341975 1_4:-57205580 None:intergenic
TCTTCTTATCATAATGATAC+TGG 0.348077 1_4:+57205302 Msa0172220:CDS
GCTGAATTAGGGTTAGGGTT+TGG 0.352389 1_4:-57205569 None:intergenic
AAATGAGCTGAATTAGGGTT+AGG 0.355729 1_4:-57205575 None:intergenic
ATTTCCTCATATTCTTCAAC+AGG 0.386946 1_4:-57205542 None:intergenic
TTTGTTGTTGCAGCGGTGTT+TGG 0.389163 1_4:-57205134 None:intergenic
AACAATAATTCAACTCCAAT+TGG 0.392174 1_4:+57205515 Msa0172220:CDS
TCTTCAACAGGAACACCAAT+TGG 0.422470 1_4:-57205530 None:intergenic
TCAGCGTAATCGTCTTGATT+GGG 0.423484 1_4:-57204969 None:intergenic
GTCAGCGTAATCGTCTTGAT+TGG 0.437669 1_4:-57204970 None:intergenic
TTGACAAAGATTGTTCAGTT+TGG 0.444201 1_4:-57205064 None:intergenic
TGAACCAAAATGGGAGCAAA+TGG 0.444622 1_4:+57205175 Msa0172220:CDS
TAAGATGATGGTGGTGGGGA+TGG 0.445734 1_4:-57205105 None:intergenic
CGACTCCCTTGAACCAAAAT+GGG 0.455745 1_4:+57205166 Msa0172220:CDS
AATGAGCTGAATTAGGGTTA+GGG 0.478935 1_4:-57205574 None:intergenic
ATCGTTCTATGATCAAATTA+AGG 0.483787 1_4:+57205325 Msa0172220:CDS
CTTCTTTAGTCCAGAGACAT+TGG 0.490028 1_4:-57205229 None:intergenic
CTCGATTACAACGCCAATCG+TGG 0.500789 1_4:+57205278 Msa0172220:CDS
GATGATGGTGGTGGGGATGG+TGG 0.508919 1_4:-57205102 None:intergenic
CTCATGGCATTCTCTCGAAA+CGG 0.520102 1_4:+57204936 None:intergenic
AAGGCTAAGATGATGGTGGT+GGG 0.520564 1_4:-57205110 None:intergenic
TGTTCCTGTTGAAGAATATG+AGG 0.531946 1_4:+57205538 Msa0172220:CDS
GACGAGATTACGATCTTGCA+AGG 0.547606 1_4:+57205251 Msa0172220:CDS
TGTTGCAGCGGTGTTTGGTA+AGG 0.547867 1_4:-57205129 None:intergenic
TAAGGCTAAGATGATGGTGG+TGG 0.558629 1_4:-57205111 None:intergenic
GACGATTACGCTGACATCGA+AGG 0.560108 1_4:+57204978 Msa0172220:CDS
ATGATAAGAAGATCCACGAT+TGG 0.603760 1_4:-57205291 None:intergenic
CAGCGTAATCGTCTTGATTG+GGG 0.609306 1_4:-57204968 None:intergenic
GTTTGGTAAGGCTAAGATGA+TGG 0.620548 1_4:-57205117 None:intergenic
AGGCTAAGATGATGGTGGTG+GGG 0.634264 1_4:-57205109 None:intergenic
TGGTAAGGCTAAGATGATGG+TGG 0.656489 1_4:-57205114 None:intergenic
GACGATGTTTGTTGTTGCAG+CGG 0.668168 1_4:-57205141 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATCAAATTTCTGAAGAA+CGG - chr1_4:57205423-57205442 None:intergenic 20.0%
! TCTTCTTATCATAATGATAC+TGG + chr1_4:57205302-57205321 Msa0172220:CDS 25.0%
! ATCGTTCTATGATCAAATTA+AGG + chr1_4:57205325-57205344 Msa0172220:CDS 25.0%
!!! GTTCTTCAGAAATTTGATTT+TGG + chr1_4:57205422-57205441 Msa0172220:intron 25.0%
!!! TCAGAAATTTGATTTTGGTA+AGG + chr1_4:57205427-57205446 Msa0172220:intron 25.0%
!! GATTTTGTGTGAAATTTCAA+AGG - chr1_4:57205486-57205505 None:intergenic 25.0%
! AACAATAATTCAACTCCAAT+TGG + chr1_4:57205515-57205534 Msa0172220:CDS 25.0%
!! GTTTGGTAGTTTTTGATGTT+TGG - chr1_4:57205050-57205069 None:intergenic 30.0%
TTGACAAAGATTGTTCAGTT+TGG - chr1_4:57205067-57205086 None:intergenic 30.0%
ATTTCCTCATATTCTTCAAC+AGG - chr1_4:57205545-57205564 None:intergenic 30.0%
! GGTAGTTTTTGATGTTTGGT+TGG - chr1_4:57205046-57205065 None:intergenic 35.0%
ATGATAAGAAGATCCACGAT+TGG - chr1_4:57205294-57205313 None:intergenic 35.0%
TGTTCCTGTTGAAGAATATG+AGG + chr1_4:57205538-57205557 Msa0172220:CDS 35.0%
AATGAGCTGAATTAGGGTTA+GGG - chr1_4:57205577-57205596 None:intergenic 35.0%
AAATGAGCTGAATTAGGGTT+AGG - chr1_4:57205578-57205597 None:intergenic 35.0%
CAGTCAAATGAGCTGAATTA+GGG - chr1_4:57205583-57205602 None:intergenic 35.0%
TCAGTCAAATGAGCTGAATT+AGG - chr1_4:57205584-57205603 None:intergenic 35.0%
TCAGCGTAATCGTCTTGATT+GGG - chr1_4:57204972-57204991 None:intergenic 40.0%
GTTTGGTAAGGCTAAGATGA+TGG - chr1_4:57205120-57205139 None:intergenic 40.0%
!!! TTGCTCCCATTTTGGTTCAA+GGG - chr1_4:57205174-57205193 None:intergenic 40.0%
!!! TTTGCTCCCATTTTGGTTCA+AGG - chr1_4:57205175-57205194 None:intergenic 40.0%
TGAACCAAAATGGGAGCAAA+TGG + chr1_4:57205175-57205194 Msa0172220:CDS 40.0%
! TCTTCCATTTGCTCCCATTT+TGG - chr1_4:57205182-57205201 None:intergenic 40.0%
! AGAAGCTTTTCCAATGTCTC+TGG + chr1_4:57205219-57205238 Msa0172220:CDS 40.0%
CTTCTTTAGTCCAGAGACAT+TGG - chr1_4:57205232-57205251 None:intergenic 40.0%
! CTTATCAACAAGCTAGCTCT+TGG - chr1_4:57205372-57205391 None:intergenic 40.0%
!! AGCTTGTTGATAAGCTTCGA+AGG + chr1_4:57205378-57205397 Msa0172220:intron 40.0%
TCTTCAACAGGAACACCAAT+TGG - chr1_4:57205533-57205552 None:intergenic 40.0%
CTGAATTAGGGTTAGGGTTT+GGG - chr1_4:57205571-57205590 None:intergenic 40.0%
CAGCGTAATCGTCTTGATTG+GGG - chr1_4:57204971-57204990 None:intergenic 45.0%
GTCAGCGTAATCGTCTTGAT+TGG - chr1_4:57204973-57204992 None:intergenic 45.0%
!! AAGGCTAAGATGATGGTGGT+GGG - chr1_4:57205113-57205132 None:intergenic 45.0%
!! TAAGGCTAAGATGATGGTGG+TGG - chr1_4:57205114-57205133 None:intergenic 45.0%
! TGGTAAGGCTAAGATGATGG+TGG - chr1_4:57205117-57205136 None:intergenic 45.0%
!! TTTGTTGTTGCAGCGGTGTT+TGG - chr1_4:57205137-57205156 None:intergenic 45.0%
!! GACGATGTTTGTTGTTGCAG+CGG - chr1_4:57205144-57205163 None:intergenic 45.0%
ACGACTCCCTTGAACCAAAA+TGG + chr1_4:57205165-57205184 Msa0172220:CDS 45.0%
CGACTCCCTTGAACCAAAAT+GGG + chr1_4:57205166-57205185 Msa0172220:CDS 45.0%
GACGAGATTACGATCTTGCA+AGG + chr1_4:57205251-57205270 Msa0172220:CDS 45.0%
GCTGAATTAGGGTTAGGGTT+TGG - chr1_4:57205572-57205591 None:intergenic 45.0%
GACGATTACGCTGACATCGA+AGG + chr1_4:57204978-57204997 Msa0172220:CDS 50.0%
!! TAAGATGATGGTGGTGGGGA+TGG - chr1_4:57205108-57205127 None:intergenic 50.0%
!! AGGCTAAGATGATGGTGGTG+GGG - chr1_4:57205112-57205131 None:intergenic 50.0%
TGTTGCAGCGGTGTTTGGTA+AGG - chr1_4:57205132-57205151 None:intergenic 50.0%
CTCGATTACAACGCCAATCG+TGG + chr1_4:57205278-57205297 Msa0172220:CDS 50.0%
!! GATGATGGTGGTGGGGATGG+TGG - chr1_4:57205105-57205124 None:intergenic 60.0%
! GGTGGGGATGGTGGCAGTGG+TGG - chr1_4:57205096-57205115 None:intergenic 70.0%
!! GGTGGTGGGGATGGTGGCAG+TGG - chr1_4:57205099-57205118 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 57204939 57205646 57204939 ID=Msa0172220;Name=Msa0172220
chr1_4 mRNA 57204939 57205646 57204939 ID=Msa0172220-mRNA-1;Parent=Msa0172220;Name=Msa0172220-mRNA-1;_AED=0.36;_eAED=0.36;_QI=0|0|0|1|1|1|2|0|187
chr1_4 exon 57204939 57205364 57204939 ID=Msa0172220-mRNA-1:exon:17484;Parent=Msa0172220-mRNA-1
chr1_4 exon 57205509 57205646 57205509 ID=Msa0172220-mRNA-1:exon:17485;Parent=Msa0172220-mRNA-1
chr1_4 CDS 57204939 57205364 57204939 ID=Msa0172220-mRNA-1:cds;Parent=Msa0172220-mRNA-1
chr1_4 CDS 57205509 57205646 57205509 ID=Msa0172220-mRNA-1:cds;Parent=Msa0172220-mRNA-1
Gene Sequence

>Msa0172220

ATGGCATTCTCTCGAAACGGCATCGTTATCCCCAATCAAGACGATTACGCTGACATCGAAGGTGAAGACGATGACGAATTAGAAGAAGAAGACAACTATTTTGTCCAACCAAACATCAAAAACTACCAAACTGAACAATCTTTGTCAACATTCACCACCACTGCCACCATCCCCACCACCATCATCTTAGCCTTACCAAACACCGCTGCAACAACAAACATCGTCGACGACTCCCTTGAACCAAAATGGGAGCAAATGGAAGAGAAGAACAACGATTCACAGAAGCTTTTCCAATGTCTCTGGACTAAAGAAGACGAGATTACGATCTTGCAAGGTTTGCTCGATTACAACGCCAATCGTGGATCTTCTTATCATAATGATACTGGATCGTTCTATGATCAAATTAAGGCAAAGATTCAACTCAATAATTGTAACAATAATTCAACTCCAATTGGTGTTCCTGTTGAAGAATATGAGGAAATCATCCCAAACCCTAACCCTAATTCAGCTCATTTGACTGAGAAGAAAGTTGCGCAATCTCGTAAGAGATTGCGAGCATCTTAG
Protein sequence

>Msa0172220

MAFSRNGIVIPNQDDYADIEGEDDDELEEEDNYFVQPNIKNYQTEQSLSTFTTTATIPTTIILALPNTAATTNIVDDSLEPKWEQMEEKNNDSQKLFQCLWTKEDEITILQGLLDYNANRGSSYHNDTGSFYDQIKAKIQLNNCNNNSTPIGVPVEEYEEIIPNPNPNSAHLTEKKVAQSRKRLRAS*