AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1019380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1019380 MtrunA17_Chr7g0235021 93.478 138 9 0 1 138 192 329 3.15e-90 265
Msa1019380 MtrunA17_Chr4g0015051 67.883 137 44 0 1 137 193 329 2.40e-63 196
Msa1019380 MtrunA17_Chr4g0015091 67.153 137 45 0 1 137 192 328 7.37e-63 195
Msa1019380 MtrunA17_Chr4g0014931 66.423 137 46 0 1 137 193 329 9.78e-60 187
Msa1019380 MtrunA17_Chr4g0014971 65.693 137 47 0 1 137 193 329 4.86e-59 185
Msa1019380 MtrunA17_Chr4g0014691 63.504 137 50 0 1 137 192 328 8.70e-59 184
Msa1019380 MtrunA17_Chr4g0014541 63.504 137 50 0 1 137 192 328 1.10e-58 184
Msa1019380 MtrunA17_Chr4g0014951 64.964 137 48 0 1 137 193 329 3.89e-57 180
Msa1019380 MtrunA17_Chr4g0015001 62.774 137 51 0 1 137 94 230 5.76e-57 177
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1019380 AT4G13010.1 73.723 137 36 0 1 137 192 328 6.99e-70 213

Find 29 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCCTTAGCTAGAGGAAATT+TGG 0.203726 7_1:-40989483 None:intergenic
AGTATTGATGGTCATGCAAC+TGG 0.350063 7_1:+40989524 Msa1019380:CDS
CTCTTTAATTCCACACCAAT+TGG 0.361493 7_1:-40989203 None:intergenic
TTACCATTCGTGTTCAAGTT+AGG 0.361630 7_1:-40989293 None:intergenic
AACTGAAGATCCTTACCCTT+TGG 0.395500 7_1:-40989413 None:intergenic
GTGGAATTAAAGAGTCCTTC+TGG 0.426954 7_1:+40989212 Msa1019380:CDS
GCTTCTAATTCCAAAGGGTA+AGG 0.460785 7_1:+40989403 Msa1019380:CDS
GGTTGGTCTAAGAGTATTGA+TGG 0.460981 7_1:+40989512 Msa1019380:CDS
ATTGACTATAAGACACCAAT+TGG 0.468885 7_1:+40989188 Msa1019380:CDS
ATGGAAATCGTCAAAAGCTT+AGG 0.472847 7_1:+40989152 Msa1019380:CDS
CCCTTTGGAATTAGAAGCAA+AGG 0.479238 7_1:-40989398 None:intergenic
CTTGTTGATTTGATTAAGCA+AGG 0.495471 7_1:+40989437 Msa1019380:CDS
GCCTTTGCTTCTAATTCCAA+AGG 0.500098 7_1:+40989397 Msa1019380:CDS
CACAAGTTGTTTCTTCGAGA+AGG 0.501978 7_1:-40989375 None:intergenic
CCTCTAGCTAAGGCTGAAGA+TGG 0.513384 7_1:+40989491 Msa1019380:CDS
CTCCAAATTTCCTCTAGCTA+AGG 0.534188 7_1:+40989481 Msa1019380:CDS
CCTTTGCTTCTAATTCCAAA+GGG 0.536074 7_1:+40989398 Msa1019380:CDS
GAGCCTAACTTGAACACGAA+TGG 0.537643 7_1:+40989290 Msa1019380:CDS
TAGCTAAGGCTGAAGATGGT+TGG 0.558067 7_1:+40989495 Msa1019380:CDS
GCATCATATTTCTTACCAGA+AGG 0.581763 7_1:-40989227 None:intergenic
GTCAACATTGAAGTAGAGCT+AGG 0.594837 7_1:-40989332 None:intergenic
TAACTTGAACACGAATGGTA+AGG 0.595964 7_1:+40989295 Msa1019380:CDS
CAAAAGCTTAGGAGCTGATG+AGG 0.597537 7_1:+40989163 Msa1019380:CDS
ATTGTGCAACGGATATTGCA+TGG 0.613154 7_1:+40989258 Msa1019380:CDS
CCATCTTCAGCCTTAGCTAG+AGG 0.614800 7_1:-40989491 None:intergenic
TGGTAAGAAATATGATGCAG+TGG 0.629719 7_1:+40989232 Msa1019380:CDS
CTATAAGACACCAATTGGTG+TGG 0.632516 7_1:+40989193 Msa1019380:CDS
GTATTGATGGTCATGCAACT+GGG 0.661439 7_1:+40989525 Msa1019380:CDS
TGCAGTGGTTCATTGTGCAA+CGG 0.675224 7_1:+40989247 Msa1019380:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATTGACTATAAGACACCAAT+TGG + chr7_1:40989188-40989207 Msa1019380:CDS 30.0%
!! CTTGTTGATTTGATTAAGCA+AGG + chr7_1:40989437-40989456 Msa1019380:CDS 30.0%
ATGGAAATCGTCAAAAGCTT+AGG + chr7_1:40989152-40989171 Msa1019380:CDS 35.0%
CTCTTTAATTCCACACCAAT+TGG - chr7_1:40989206-40989225 None:intergenic 35.0%
GCATCATATTTCTTACCAGA+AGG - chr7_1:40989230-40989249 None:intergenic 35.0%
TGGTAAGAAATATGATGCAG+TGG + chr7_1:40989232-40989251 Msa1019380:CDS 35.0%
! TTACCATTCGTGTTCAAGTT+AGG - chr7_1:40989296-40989315 None:intergenic 35.0%
TAACTTGAACACGAATGGTA+AGG + chr7_1:40989295-40989314 Msa1019380:CDS 35.0%
CCTTTGCTTCTAATTCCAAA+GGG + chr7_1:40989398-40989417 Msa1019380:CDS 35.0%
CTATAAGACACCAATTGGTG+TGG + chr7_1:40989193-40989212 Msa1019380:CDS 40.0%
GTGGAATTAAAGAGTCCTTC+TGG + chr7_1:40989212-40989231 Msa1019380:CDS 40.0%
ATTGTGCAACGGATATTGCA+TGG + chr7_1:40989258-40989277 Msa1019380:CDS 40.0%
GTCAACATTGAAGTAGAGCT+AGG - chr7_1:40989335-40989354 None:intergenic 40.0%
!! CACAAGTTGTTTCTTCGAGA+AGG - chr7_1:40989378-40989397 None:intergenic 40.0%
GCCTTTGCTTCTAATTCCAA+AGG + chr7_1:40989397-40989416 Msa1019380:CDS 40.0%
!! CCCTTTGGAATTAGAAGCAA+AGG - chr7_1:40989401-40989420 None:intergenic 40.0%
GCTTCTAATTCCAAAGGGTA+AGG + chr7_1:40989403-40989422 Msa1019380:CDS 40.0%
AACTGAAGATCCTTACCCTT+TGG - chr7_1:40989416-40989435 None:intergenic 40.0%
CTCCAAATTTCCTCTAGCTA+AGG + chr7_1:40989481-40989500 Msa1019380:CDS 40.0%
AGCCTTAGCTAGAGGAAATT+TGG - chr7_1:40989486-40989505 None:intergenic 40.0%
!! GGTTGGTCTAAGAGTATTGA+TGG + chr7_1:40989512-40989531 Msa1019380:CDS 40.0%
!! AGTATTGATGGTCATGCAAC+TGG + chr7_1:40989524-40989543 Msa1019380:CDS 40.0%
! GTATTGATGGTCATGCAACT+GGG + chr7_1:40989525-40989544 Msa1019380:CDS 40.0%
CAAAAGCTTAGGAGCTGATG+AGG + chr7_1:40989163-40989182 Msa1019380:CDS 45.0%
TGCAGTGGTTCATTGTGCAA+CGG + chr7_1:40989247-40989266 Msa1019380:CDS 45.0%
GAGCCTAACTTGAACACGAA+TGG + chr7_1:40989290-40989309 Msa1019380:CDS 45.0%
TAGCTAAGGCTGAAGATGGT+TGG + chr7_1:40989495-40989514 Msa1019380:CDS 45.0%
CCATCTTCAGCCTTAGCTAG+AGG - chr7_1:40989494-40989513 None:intergenic 50.0%
CCTCTAGCTAAGGCTGAAGA+TGG + chr7_1:40989491-40989510 Msa1019380:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 40989152 40989568 40989152 ID=Msa1019380;Name=Msa1019380
chr7_1 mRNA 40989152 40989568 40989152 ID=Msa1019380-mRNA-1;Parent=Msa1019380;Name=Msa1019380-mRNA-1;_AED=0.40;_eAED=0.41;_QI=0|-1|0|1|-1|1|1|0|138
chr7_1 exon 40989152 40989568 40989152 ID=Msa1019380-mRNA-1:exon:7956;Parent=Msa1019380-mRNA-1
chr7_1 CDS 40989152 40989568 40989152 ID=Msa1019380-mRNA-1:cds;Parent=Msa1019380-mRNA-1
Gene Sequence

>Msa1019380

ATGGAAATCGTCAAAAGCTTAGGAGCTGATGAGGTAATTGACTATAAGACACCAATTGGTGTGGAATTAAAGAGTCCTTCTGGTAAGAAATATGATGCAGTGGTTCATTGTGCAACGGATATTGCATGGTCAGTTTTTGAGCCTAACTTGAACACGAATGGTAAGGTTGTAGATATAACTCCTAGCTCTACTTCAATGTTGACATTTGCTCTTACTAAAATTACCTTCTCGAAGAAACAACTTGTGCCTTTGCTTCTAATTCCAAAGGGTAAGGATCTTCAGTTTCTTGTTGATTTGATTAAGCAAGGAAAGATTAAAACAGTTATAGACTCCAAATTTCCTCTAGCTAAGGCTGAAGATGGTTGGTCTAAGAGTATTGATGGTCATGCAACTGGGAAGATCATTTTTGAGTTTTGA

Protein sequence

>Msa1019380

MEIVKSLGADEVIDYKTPIGVELKSPSGKKYDAVVHCATDIAWSVFEPNLNTNGKVVDITPSSTSMLTFALTKITFSKKQLVPLLLIPKGKDLQFLVDLIKQGKIKTVIDSKFPLAKAEDGWSKSIDGHATGKIIFEF*