AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0883860

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0883860 MtrunA17_Chr1g0172971 77.273 132 15 1 1 132 1 117 2.45e-64 207
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAGAAGTAAATGAAGTTTA+AGG 0.128987 6_1:-35979988 None:intergenic
TCTGTTGTTGGCCTGTTGTT+AGG 0.292589 6_1:+35980192 None:intergenic
GGTAATTATGCATATAATAC+TGG 0.300165 6_1:-35980336 Msa0883860:CDS
TTACTTCTCGAAATGATCTA+AGG 0.311482 6_1:+35980001 None:intergenic
TCCATGATTCTTTATTGCTA+GGG 0.444266 6_1:+35980403 None:intergenic
TTCCATGATTCTTTATTGCT+AGG 0.445442 6_1:+35980402 None:intergenic
GAAAGGGTTGGTTGTAAAGC+TGG 0.447509 6_1:-35980123 Msa0883860:CDS
GTTTGCTTAATCCTAACAAC+AGG 0.484661 6_1:-35980203 Msa0883860:CDS
CCCCTAGCAATAAAGAATCA+TGG 0.497001 6_1:-35980404 Msa0883860:CDS
ATGTGCATAAGATATATAGA+TGG 0.503060 6_1:-35980071 Msa0883860:CDS
TTACAACCAACCCTTTCCTC+AGG 0.505082 6_1:+35980129 None:intergenic
AGCTGGAATATATTTGAAGC+TGG 0.507410 6_1:-35980106 Msa0883860:CDS
ACAAAACAAGAAATCTGATA+AGG 0.511435 6_1:-35980274 Msa0883860:CDS
CTAAGGTAACGTGAATGCTC+TGG 0.514487 6_1:+35980018 None:intergenic
ACCAGTGGACTGTCTGTTGT+TGG 0.515301 6_1:+35980180 None:intergenic
CGTTATGCTTGTAACAAACA+AGG 0.517293 6_1:-35980240 Msa0883860:CDS
GAATGCTCTGGTTTATGTAA+TGG 0.517705 6_1:+35980030 None:intergenic
TAACAAACAAGGTTTCAAGA+AGG 0.524869 6_1:-35980229 Msa0883860:CDS
CCATGATTCTTTATTGCTAG+GGG 0.537011 6_1:+35980404 None:intergenic
GAGAGTGGACATCTTAGTGT+TGG 0.544996 6_1:-35980513 Msa0883860:CDS
AACAAACAAGGTTTCAAGAA+GGG 0.554561 6_1:-35980228 Msa0883860:CDS
TAAGATATATAGATGGGATG+TGG 0.566406 6_1:-35980064 Msa0883860:CDS
TGTGCATAAGATATATAGAT+GGG 0.600057 6_1:-35980070 Msa0883860:CDS
TCACTGATTCATGCTGAGAG+TGG 0.606950 6_1:-35980483 Msa0883860:CDS
GCCAACAACAGACAGTCCAC+TGG 0.611268 6_1:-35980181 Msa0883860:CDS
ATATCAACTTCATCTGAGAG+TGG 0.614980 6_1:-35980528 Msa0883860:CDS
TTCACAAACTCAATAACCAG+TGG 0.633415 6_1:+35980165 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAGAGATTGAAGATTTTTA+TGG - chr6_1:35980170-35980189 Msa0883860:CDS 20.0%
!!! ATAATACTGGATTTTCTATT+AGG - chr6_1:35980204-35980223 Msa0883860:CDS 20.0%
! GGTAATTATGCATATAATAC+TGG - chr6_1:35980191-35980210 Msa0883860:CDS 25.0%
! ACAAAACAAGAAATCTGATA+AGG - chr6_1:35980253-35980272 Msa0883860:CDS 25.0%
! ATGTGCATAAGATATATAGA+TGG - chr6_1:35980456-35980475 Msa0883860:CDS 25.0%
! TGTGCATAAGATATATAGAT+GGG - chr6_1:35980457-35980476 Msa0883860:CDS 25.0%
TCCATGATTCTTTATTGCTA+GGG + chr6_1:35980127-35980146 None:intergenic 30.0%
TTCCATGATTCTTTATTGCT+AGG + chr6_1:35980128-35980147 None:intergenic 30.0%
TAACAAACAAGGTTTCAAGA+AGG - chr6_1:35980298-35980317 Msa0883860:CDS 30.0%
AACAAACAAGGTTTCAAGAA+GGG - chr6_1:35980299-35980318 Msa0883860:CDS 30.0%
TAAGATATATAGATGGGATG+TGG - chr6_1:35980463-35980482 Msa0883860:CDS 30.0%
TTACTTCTCGAAATGATCTA+AGG + chr6_1:35980529-35980548 None:intergenic 30.0%
ATATCAACTTCATCTGAGAG+TGG - chr6_1:35979999-35980018 Msa0883860:CDS 35.0%
CCATGATTCTTTATTGCTAG+GGG + chr6_1:35980126-35980145 None:intergenic 35.0%
CGTTATGCTTGTAACAAACA+AGG - chr6_1:35980287-35980306 Msa0883860:CDS 35.0%
GTTTGCTTAATCCTAACAAC+AGG - chr6_1:35980324-35980343 Msa0883860:CDS 35.0%
TTCACAAACTCAATAACCAG+TGG + chr6_1:35980365-35980384 None:intergenic 35.0%
GAAAGTGAAAGAAAAACCTG+AGG - chr6_1:35980382-35980401 Msa0883860:CDS 35.0%
TGAAAGAAAAACCTGAGGAA+AGG - chr6_1:35980387-35980406 Msa0883860:CDS 35.0%
GAAAGAAAAACCTGAGGAAA+GGG - chr6_1:35980388-35980407 Msa0883860:CDS 35.0%
! AGCTGGAATATATTTGAAGC+TGG - chr6_1:35980421-35980440 Msa0883860:CDS 35.0%
! GAATGCTCTGGTTTATGTAA+TGG + chr6_1:35980500-35980519 None:intergenic 35.0%
CCCCTAGCAATAAAGAATCA+TGG - chr6_1:35980123-35980142 Msa0883860:CDS 40.0%
GAGAGTGGACATCTTAGTGT+TGG - chr6_1:35980014-35980033 Msa0883860:CDS 45.0%
!! TCACTGATTCATGCTGAGAG+TGG - chr6_1:35980044-35980063 Msa0883860:CDS 45.0%
! TCTGTTGTTGGCCTGTTGTT+AGG + chr6_1:35980338-35980357 None:intergenic 45.0%
GAAAAACCTGAGGAAAGGGT+TGG - chr6_1:35980392-35980411 Msa0883860:CDS 45.0%
TTACAACCAACCCTTTCCTC+AGG + chr6_1:35980401-35980420 None:intergenic 45.0%
!! GAAAGGGTTGGTTGTAAAGC+TGG - chr6_1:35980404-35980423 Msa0883860:CDS 45.0%
CTAAGGTAACGTGAATGCTC+TGG + chr6_1:35980512-35980531 None:intergenic 45.0%
!! ACCAGTGGACTGTCTGTTGT+TGG + chr6_1:35980350-35980369 None:intergenic 50.0%
GCCAACAACAGACAGTCCAC+TGG - chr6_1:35980346-35980365 Msa0883860:CDS 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 35979990 35980559 35979990 ID=Msa0883860;Name=Msa0883860
chr6_1 mRNA 35979990 35980559 35979990 ID=Msa0883860-mRNA-1;Parent=Msa0883860;Name=Msa0883860-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|189
chr6_1 exon 35979990 35980559 35979990 ID=Msa0883860-mRNA-1:exon:8594;Parent=Msa0883860-mRNA-1
chr6_1 CDS 35979990 35980559 35979990 ID=Msa0883860-mRNA-1:cds;Parent=Msa0883860-mRNA-1
Gene Sequence

>Msa0883860

ATGGATTTGATATCAACTTCATCTGAGAGTGGACATCTTAGTGTTGGAAATTCATCACTGATTCATGCTGAGAGTGGACAACTGAGTATTGAAACTTCTTCAATGATTCATGCTGATAGTTCTCAATGTTACTCCCCTAGCAATAAAGAATCATGGAAGTCTTTAGTCTTTCATTCTATTAAAGAGATTGAAGATTTTTATGGTAATTATGCATATAATACTGGATTTTCTATTAGGACTATGTTGAAGTCGAAGAATAATTCACAAAACAAGAAATCTGATAAGGTACATTATGTGCGTTATGCTTGTAACAAACAAGGTTTCAAGAAGGGAAGTTTGCTTAATCCTAACAACAGGCCAACAACAGACAGTCCACTGGTTATTGAGTTTGTGAAAGTGAAAGAAAAACCTGAGGAAAGGGTTGGTTGTAAAGCTGGAATATATTTGAAGCTGGATGAAGTTTTGAATGTGCATAAGATATATAGATGGGATGTGGCTCACTGTCATCCATTACATAAACCAGAGCATTCACGTTACCTTAGATCATTTCGAGAAGTAAATGAAGTTTAA
Protein sequence

>Msa0883860

MDLISTSSESGHLSVGNSSLIHAESGQLSIETSSMIHADSSQCYSPSNKESWKSLVFHSIKEIEDFYGNYAYNTGFSIRTMLKSKNNSQNKKSDKVHYVRYACNKQGFKKGSLLNPNNRPTTDSPLVIEFVKVKEKPEERVGCKAGIYLKLDEVLNVHKIYRWDVAHCHPLHKPEHSRYLRSFREVNEV*