AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025091

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025091.t1 MTR_2g038720 86.842 114 15 0 1 114 72 185 1.25e-58 182
MS.gene025091.t1 MTR_4g126350 51.685 89 29 4 35 114 124 207 3.31e-18 78.2
MS.gene025091.t1 MTR_1g016170 64.103 39 14 0 76 114 170 208 6.90e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025091.t1 AT4G26150 40.789 76 43 1 39 114 147 220 3.81e-11 58.9
MS.gene025091.t1 AT5G56860 75.000 32 7 1 84 114 220 251 7.16e-11 58.2

Find 21 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCAAACAACAACACTGTT+AGG 0.256322 2.2:-48859415 MS.gene025091:CDS
TTAATCATTCTCTTCTTTGA+TGG 0.270861 2.2:+48859542 None:intergenic
TCCTCAGTTCTTACTAGATT+TGG 0.275505 2.2:+48859455 None:intergenic
GGATCATCAAGAAGTGAAAA+AGG 0.339108 2.2:-48859639 MS.gene025091:CDS
CTCTGGAGAAGTGGACCAAC+TGG 0.407869 2.2:-48859359 MS.gene025091:CDS
TTGTAACTTCTGGTGAATCA+TGG 0.418749 2.2:-48859661 MS.gene025091:CDS
CAAAGAAGAGAATGATTAAG+AGG 0.444414 2.2:-48859538 MS.gene025091:CDS
TTCAAACAACAACACTGTTA+GGG 0.464863 2.2:-48859414 MS.gene025091:CDS
GAGAATGATTAAGAGGATGA+TGG 0.470043 2.2:-48859531 MS.gene025091:CDS
GAGGATGATGGAAGATCAAA+GGG 0.487515 2.2:-48859519 MS.gene025091:CDS
TGTAACTTCTGGTGAATCAT+GGG 0.493931 2.2:-48859660 MS.gene025091:CDS
TTGGTCCACTTCTCCAGAGA+GGG 0.496789 2.2:+48859363 None:intergenic
ACACAACTAAGACCCCTCTC+TGG 0.508622 2.2:-48859376 MS.gene025091:CDS
AGAGGATGATGGAAGATCAA+AGG 0.536944 2.2:-48859520 MS.gene025091:CDS
AAGACCCCTCTCTGGAGAAG+TGG 0.553472 2.2:-48859368 MS.gene025091:CDS
AAGTGGACCAACTGGTCCCA+AGG 0.591915 2.2:-48859351 None:intergenic
AGAGAGGGGTCTTAGTTGTG+TGG 0.598153 2.2:+48859378 None:intergenic
ATATGTACCTTGGGACCAGT+TGG 0.609719 2.2:+48859344 None:intergenic
TGGTCCACTTCTCCAGAGAG+GGG 0.626088 2.2:+48859364 None:intergenic
GTTGGTCCACTTCTCCAGAG+AGG 0.682429 2.2:+48859362 None:intergenic
ACCAAATCTAGTAAGAACTG+AGG 0.700207 2.2:-48859456 MS.gene025091:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAAAAAGGATGAAAAAGAT+TGG - chr2.2:48859398-48859417 MS.gene025091:CDS 25.0%
! TTAATCATTCTCTTCTTTGA+TGG + chr2.2:48859484-48859503 None:intergenic 25.0%
!! GTTAAGAATTTTGTAACTTC+TGG - chr2.2:48859352-48859371 MS.gene025091:CDS 25.0%
CAAAGAAGAGAATGATTAAG+AGG - chr2.2:48859485-48859504 MS.gene025091:CDS 30.0%
TTCAAACAACAACACTGTTA+GGG - chr2.2:48859609-48859628 MS.gene025091:CDS 30.0%
TTTCAAACAACAACACTGTT+AGG - chr2.2:48859608-48859627 MS.gene025091:CDS 30.0%
! AGACGAGTATGAAAGTTTTA+TGG - chr2.2:48859429-48859448 MS.gene025091:CDS 30.0%
ACCAAATCTAGTAAGAACTG+AGG - chr2.2:48859567-48859586 MS.gene025091:CDS 35.0%
GAGAATGATTAAGAGGATGA+TGG - chr2.2:48859492-48859511 MS.gene025091:CDS 35.0%
GGATCATCAAGAAGTGAAAA+AGG - chr2.2:48859384-48859403 MS.gene025091:CDS 35.0%
TCCTCAGTTCTTACTAGATT+TGG + chr2.2:48859571-48859590 None:intergenic 35.0%
TGTAACTTCTGGTGAATCAT+GGG - chr2.2:48859363-48859382 MS.gene025091:CDS 35.0%
TTGTAACTTCTGGTGAATCA+TGG - chr2.2:48859362-48859381 MS.gene025091:CDS 35.0%
!! GTATGAAAGTTTTATGGCTG+AGG - chr2.2:48859435-48859454 MS.gene025091:CDS 35.0%
!! AGAGGATGATGGAAGATCAA+AGG - chr2.2:48859503-48859522 MS.gene025091:CDS 40.0%
!! GAGGATGATGGAAGATCAAA+GGG - chr2.2:48859504-48859523 MS.gene025091:CDS 40.0%
ACACAACTAAGACCCCTCTC+TGG - chr2.2:48859647-48859666 MS.gene025091:CDS 50.0%
AGAGAGGGGTCTTAGTTGTG+TGG + chr2.2:48859648-48859667 None:intergenic 50.0%
TTGGTCCACTTCTCCAGAGA+GGG + chr2.2:48859663-48859682 None:intergenic 50.0%
AAGTGGACCAACTGGTCCCA+AGG - chr2.2:48859672-48859691 MS.gene025091:CDS 55.0%
GTTGGTCCACTTCTCCAGAG+AGG + chr2.2:48859664-48859683 None:intergenic 55.0%
TGGTCCACTTCTCCAGAGAG+GGG + chr2.2:48859662-48859681 None:intergenic 55.0%
! AAGACCCCTCTCTGGAGAAG+TGG - chr2.2:48859655-48859674 MS.gene025091:CDS 55.0%
! CTCTGGAGAAGTGGACCAAC+TGG - chr2.2:48859664-48859683 MS.gene025091:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 48859352 48859693 48859352 ID=MS.gene025091
chr2.2 mRNA 48859352 48859693 48859352 ID=MS.gene025091.t1;Parent=MS.gene025091
chr2.2 exon 48859352 48859693 48859352 ID=MS.gene025091.t1.exon1;Parent=MS.gene025091.t1
chr2.2 CDS 48859352 48859693 48859352 ID=cds.MS.gene025091.t1;Parent=MS.gene025091.t1
Gene Sequence

>MS.gene025091

GTTAAGAATTTTGTAACTTCTGGTGAATCATGGGATCATCAAGAAGTGAAAAAGGATGAAAAAGATTGGAAGAAAGAAGACGAGTATGAAAGTTTTATGGCTGAGGATAGAACTTCAATGAAGTTGATGCCATCAAAGAAGAGAATGATTAAGAGGATGATGGAAGATCAAAGGGCTTCTGAGCAAGAATTTGAGAAACAAATTAAGCAATTATCACCAAATCTAGTAAGAACTGAGGATAGTAGCAACAACAATTTTTCAAACAACAACACTGTTAGGGTTTGTACTGACTGCCACACAACTAAGACCCCTCTCTGGAGAAGTGGACCAACTGGTCCCAAG
Protein sequence

>MS.gene025091.t1

VKNFVTSGESWDHQEVKKDEKDWKKEDEYESFMAEDRTSMKLMPSKKRMIKRMMEDQRASEQEFEKQIKQLSPNLVRTEDSSNNNFSNNNTVRVCTDCHTTKTPLWRSGPTGPK