AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1297160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATACCTTTGTGAAGATAAA+AGG 0.212182 8_3:+57078889 None:intergenic
GTGATCTCATCCAGGATGAT+AGG 0.356626 8_3:+57078172 None:intergenic
CCAGGATGATAGGGTGGATA+GGG 0.403549 8_3:+57078182 None:intergenic
ATGTTGAAGGAGGCAAGAAC+TGG 0.403774 8_3:-57078285 Msa1297160:CDS
TAAGGACGGGAAGGAACATT+TGG 0.428961 8_3:-57078687 Msa1297160:CDS
TCTTATAAAATCATCATGAT+AGG 0.434799 8_3:+57078110 None:intergenic
GCAAGAGGTGTGATGGCAGC+AGG 0.439246 8_3:+57078241 None:intergenic
AAATGTTCCTTCCCGTCCTT+AGG 0.450368 8_3:+57078689 None:intergenic
TGATGGCAGCAGGGGTAAGT+TGG 0.456592 8_3:+57078251 None:intergenic
CATACTACCTCTGCTAAGAT+TGG 0.469905 8_3:-57078217 Msa1297160:CDS
CCCTATCCACCCTATCATCC+TGG 0.477480 8_3:-57078182 Msa1297160:CDS
ACCATGTTGCAGAATGTTGA+AGG 0.481802 8_3:-57078298 Msa1297160:CDS
TAAGATAGTAACATATCCTA+AGG 0.501123 8_3:-57078705 Msa1297160:intron
ATTCTGCAACATGGTGGAAG+GGG 0.513075 8_3:+57078306 None:intergenic
TTGCAGGAGTGATCTCATCC+AGG 0.524797 8_3:+57078164 None:intergenic
TGTCTTTGAACAACAAGTGC+AGG 0.532648 8_3:-57078923 Msa1297160:CDS
AAAATCATCATGATAGGAAG+AGG 0.535692 8_3:+57078116 None:intergenic
ACATTCTGCAACATGGTGGA+AGG 0.539324 8_3:+57078304 None:intergenic
TGATCTCATCCAGGATGATA+GGG 0.550931 8_3:+57078173 None:intergenic
TAGTAACATATCCTAAGGAC+GGG 0.551671 8_3:-57078700 Msa1297160:CDS
TCCTTCAACATTCTGCAACA+TGG 0.556193 8_3:+57078297 None:intergenic
CATTCTGCAACATGGTGGAA+GGG 0.560478 8_3:+57078305 None:intergenic
AGTATGAGCAAGAGGTGTGA+TGG 0.566077 8_3:+57078234 None:intergenic
GATGGTCATTGTTGATGCTA+AGG 0.581330 8_3:-57078663 Msa1297160:intron
TCCAGGATGATAGGGTGGAT+AGG 0.585429 8_3:+57078181 None:intergenic
CAAGAGGTGTGATGGCAGCA+GGG 0.589536 8_3:+57078242 None:intergenic
GCAGAGGTAGTATGAGCAAG+AGG 0.599567 8_3:+57078226 None:intergenic
ATAGTAACATATCCTAAGGA+CGG 0.602531 8_3:-57078701 Msa1297160:CDS
CGGGAAGGAACATTTGGAGA+TGG 0.612772 8_3:-57078681 Msa1297160:CDS
TGTTGAAGGAGGCAAGAACT+GGG 0.613431 8_3:-57078284 Msa1297160:CDS
AACATATCCTAAGGACGGGA+AGG 0.619664 8_3:-57078696 Msa1297160:CDS
CAGGATGATAGGGTGGATAG+GGG 0.620934 8_3:+57078183 None:intergenic
AAGAGGTGTGATGGCAGCAG+GGG 0.623171 8_3:+57078243 None:intergenic
TTCAACATTCTGCAACATGG+TGG 0.658953 8_3:+57078300 None:intergenic
TCTCATCCAGGATGATAGGG+TGG 0.663515 8_3:+57078176 None:intergenic
ACTTGAACCAATCTTAGCAG+AGG 0.665354 8_3:+57078210 None:intergenic
ATGTTGCAGAATGTTGAAGG+AGG 0.685850 8_3:-57078295 Msa1297160:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAACTTATAACATGTTAAA+TGG - chr8_3:57078340-57078359 Msa1297160:intron 20.0%
!! ATGTTATTATGCAGTTATTT+AGG + chr8_3:57078387-57078406 None:intergenic 20.0%
!! TAAAAAAAAATAGCAGTTGA+TGG + chr8_3:57078425-57078444 None:intergenic 20.0%
!! ACATATGTTTAAACATATCA+AGG + chr8_3:57078759-57078778 None:intergenic 20.0%
!! CAAACTTATAACATGTTAAA+TGG - chr8_3:57078340-57078359 Msa1297160:intron 20.0%
!! ATGTTATTATGCAGTTATTT+AGG + chr8_3:57078387-57078406 None:intergenic 20.0%
!! TAAAAAAAAATAGCAGTTGA+TGG + chr8_3:57078425-57078444 None:intergenic 20.0%
!! ACATATGTTTAAACATATCA+AGG + chr8_3:57078759-57078778 None:intergenic 20.0%
!! AATTTGTAGTGTTTTCAACT+AGG - chr8_3:57078135-57078154 Msa1297160:CDS 25.0%
!! TTTAGGATATGTACATATGA+AGG + chr8_3:57078370-57078389 None:intergenic 25.0%
! TAAGATAGTAACATATCCTA+AGG - chr8_3:57078443-57078462 Msa1297160:intron 25.0%
! AAGATGTCATAAATTAGTCA+AGG + chr8_3:57078546-57078565 None:intergenic 25.0%
! TCAATTAAGATGATCTACAT+TGG - chr8_3:57078716-57078735 Msa1297160:intron 25.0%
!! AAAAAACTCTTACTCTAAGA+TGG - chr8_3:57079005-57079024 Msa1297160:intron 25.0%
!! AATTTGTAGTGTTTTCAACT+AGG - chr8_3:57078135-57078154 Msa1297160:CDS 25.0%
!! TTTAGGATATGTACATATGA+AGG + chr8_3:57078370-57078389 None:intergenic 25.0%
! TAAGATAGTAACATATCCTA+AGG - chr8_3:57078443-57078462 Msa1297160:intron 25.0%
! AAGATGTCATAAATTAGTCA+AGG + chr8_3:57078546-57078565 None:intergenic 25.0%
! TCAATTAAGATGATCTACAT+TGG - chr8_3:57078716-57078735 Msa1297160:intron 25.0%
!! AAAAAACTCTTACTCTAAGA+TGG - chr8_3:57079005-57079024 Msa1297160:intron 25.0%
! TACTCCTTTTATCTTCACAA+AGG - chr8_3:57078255-57078274 Msa1297160:CDS 30.0%
CATACCTTTGTGAAGATAAA+AGG + chr8_3:57078262-57078281 None:intergenic 30.0%
ATAGTAACATATCCTAAGGA+CGG - chr8_3:57078447-57078466 Msa1297160:intron 30.0%
TCAAGGAAATAATCAGTTGT+AGG + chr8_3:57078529-57078548 None:intergenic 30.0%
TGTGTGTTTGTTTGCTTATT+AGG - chr8_3:57078569-57078588 Msa1297160:intron 30.0%
GTGTGTTTGTTTGCTTATTA+GGG - chr8_3:57078570-57078589 Msa1297160:intron 30.0%
AGATGACAATGCTATGATTT+AGG - chr8_3:57078638-57078657 Msa1297160:intron 30.0%
! TATGATTTAGGACACAAATG+TGG - chr8_3:57078650-57078669 Msa1297160:intron 30.0%
! CTACATTGGTTATTTATCTG+TGG - chr8_3:57078730-57078749 Msa1297160:intron 30.0%
!!! TTAGAGTAAGAGTTTTTTGC+AGG + chr8_3:57079003-57079022 None:intergenic 30.0%
! TACTCCTTTTATCTTCACAA+AGG - chr8_3:57078255-57078274 Msa1297160:CDS 30.0%
CATACCTTTGTGAAGATAAA+AGG + chr8_3:57078262-57078281 None:intergenic 30.0%
ATAGTAACATATCCTAAGGA+CGG - chr8_3:57078447-57078466 Msa1297160:intron 30.0%
TCAAGGAAATAATCAGTTGT+AGG + chr8_3:57078529-57078548 None:intergenic 30.0%
TGTGTGTTTGTTTGCTTATT+AGG - chr8_3:57078569-57078588 Msa1297160:intron 30.0%
GTGTGTTTGTTTGCTTATTA+GGG - chr8_3:57078570-57078589 Msa1297160:intron 30.0%
AGATGACAATGCTATGATTT+AGG - chr8_3:57078638-57078657 Msa1297160:intron 30.0%
! TATGATTTAGGACACAAATG+TGG - chr8_3:57078650-57078669 Msa1297160:intron 30.0%
! CTACATTGGTTATTTATCTG+TGG - chr8_3:57078730-57078749 Msa1297160:intron 30.0%
!!! TTAGAGTAAGAGTTTTTTGC+AGG + chr8_3:57079003-57079022 None:intergenic 30.0%
!! CAGTTGATGGATATGTACTT+AGG + chr8_3:57078412-57078431 None:intergenic 35.0%
TAGTAACATATCCTAAGGAC+GGG - chr8_3:57078448-57078467 Msa1297160:intron 35.0%
ATCATAGCATTGTCATCTTG+TGG + chr8_3:57078636-57078655 None:intergenic 35.0%
TAAGAACATGATCTGTCACT+TGG - chr8_3:57078808-57078827 Msa1297160:intron 35.0%
!! CAGTTGATGGATATGTACTT+AGG + chr8_3:57078412-57078431 None:intergenic 35.0%
TAGTAACATATCCTAAGGAC+GGG - chr8_3:57078448-57078467 Msa1297160:intron 35.0%
ATCATAGCATTGTCATCTTG+TGG + chr8_3:57078636-57078655 None:intergenic 35.0%
TAAGAACATGATCTGTCACT+TGG - chr8_3:57078808-57078827 Msa1297160:intron 35.0%
TGTCTTTGAACAACAAGTGC+AGG - chr8_3:57078225-57078244 Msa1297160:CDS 40.0%
GATGGTCATTGTTGATGCTA+AGG - chr8_3:57078485-57078504 Msa1297160:intron 40.0%
TTCAACATTCTGCAACATGG+TGG + chr8_3:57078851-57078870 None:intergenic 40.0%
ACCATGTTGCAGAATGTTGA+AGG - chr8_3:57078850-57078869 Msa1297160:intron 40.0%
TCCTTCAACATTCTGCAACA+TGG + chr8_3:57078854-57078873 None:intergenic 40.0%
ATGTTGCAGAATGTTGAAGG+AGG - chr8_3:57078853-57078872 Msa1297160:intron 40.0%
CATACTACCTCTGCTAAGAT+TGG - chr8_3:57078931-57078950 Msa1297160:CDS 40.0%
ACTTGAACCAATCTTAGCAG+AGG + chr8_3:57078941-57078960 None:intergenic 40.0%
TGATCTCATCCAGGATGATA+GGG + chr8_3:57078978-57078997 None:intergenic 40.0%
TGTCTTTGAACAACAAGTGC+AGG - chr8_3:57078225-57078244 Msa1297160:CDS 40.0%
GATGGTCATTGTTGATGCTA+AGG - chr8_3:57078485-57078504 Msa1297160:intron 40.0%
TTCAACATTCTGCAACATGG+TGG + chr8_3:57078851-57078870 None:intergenic 40.0%
ACCATGTTGCAGAATGTTGA+AGG - chr8_3:57078850-57078869 Msa1297160:intron 40.0%
TCCTTCAACATTCTGCAACA+TGG + chr8_3:57078854-57078873 None:intergenic 40.0%
ATGTTGCAGAATGTTGAAGG+AGG - chr8_3:57078853-57078872 Msa1297160:intron 40.0%
CATACTACCTCTGCTAAGAT+TGG - chr8_3:57078931-57078950 Msa1297160:CDS 40.0%
ACTTGAACCAATCTTAGCAG+AGG + chr8_3:57078941-57078960 None:intergenic 40.0%
TGATCTCATCCAGGATGATA+GGG + chr8_3:57078978-57078997 None:intergenic 40.0%
AACATATCCTAAGGACGGGA+AGG - chr8_3:57078452-57078471 Msa1297160:intron 45.0%
AAATGTTCCTTCCCGTCCTT+AGG + chr8_3:57078462-57078481 None:intergenic 45.0%
TAAGGACGGGAAGGAACATT+TGG - chr8_3:57078461-57078480 Msa1297160:intron 45.0%
! ATTCTGCAACATGGTGGAAG+GGG + chr8_3:57078845-57078864 None:intergenic 45.0%
! CATTCTGCAACATGGTGGAA+GGG + chr8_3:57078846-57078865 None:intergenic 45.0%
! ACATTCTGCAACATGGTGGA+AGG + chr8_3:57078847-57078866 None:intergenic 45.0%
ATGTTGAAGGAGGCAAGAAC+TGG - chr8_3:57078863-57078882 Msa1297160:intron 45.0%
TGTTGAAGGAGGCAAGAACT+GGG - chr8_3:57078864-57078883 Msa1297160:intron 45.0%
! AGTATGAGCAAGAGGTGTGA+TGG + chr8_3:57078917-57078936 None:intergenic 45.0%
GTGATCTCATCCAGGATGAT+AGG + chr8_3:57078979-57078998 None:intergenic 45.0%
AACATATCCTAAGGACGGGA+AGG - chr8_3:57078452-57078471 Msa1297160:intron 45.0%
AAATGTTCCTTCCCGTCCTT+AGG + chr8_3:57078462-57078481 None:intergenic 45.0%
TAAGGACGGGAAGGAACATT+TGG - chr8_3:57078461-57078480 Msa1297160:intron 45.0%
! ATTCTGCAACATGGTGGAAG+GGG + chr8_3:57078845-57078864 None:intergenic 45.0%
! CATTCTGCAACATGGTGGAA+GGG + chr8_3:57078846-57078865 None:intergenic 45.0%
! ACATTCTGCAACATGGTGGA+AGG + chr8_3:57078847-57078866 None:intergenic 45.0%
ATGTTGAAGGAGGCAAGAAC+TGG - chr8_3:57078863-57078882 Msa1297160:intron 45.0%
TGTTGAAGGAGGCAAGAACT+GGG - chr8_3:57078864-57078883 Msa1297160:intron 45.0%
! AGTATGAGCAAGAGGTGTGA+TGG + chr8_3:57078917-57078936 None:intergenic 45.0%
GTGATCTCATCCAGGATGAT+AGG + chr8_3:57078979-57078998 None:intergenic 45.0%
CGGGAAGGAACATTTGGAGA+TGG - chr8_3:57078467-57078486 Msa1297160:intron 50.0%
AAGTTGCAGATGCAGCACAC+TGG + chr8_3:57078783-57078802 None:intergenic 50.0%
GCAGAGGTAGTATGAGCAAG+AGG + chr8_3:57078925-57078944 None:intergenic 50.0%
CAGGATGATAGGGTGGATAG+GGG + chr8_3:57078968-57078987 None:intergenic 50.0%
CCAGGATGATAGGGTGGATA+GGG + chr8_3:57078969-57078988 None:intergenic 50.0%
TCCAGGATGATAGGGTGGAT+AGG + chr8_3:57078970-57078989 None:intergenic 50.0%
TCTCATCCAGGATGATAGGG+TGG + chr8_3:57078975-57078994 None:intergenic 50.0%
TTGCAGGAGTGATCTCATCC+AGG + chr8_3:57078987-57079006 None:intergenic 50.0%
CGGGAAGGAACATTTGGAGA+TGG - chr8_3:57078467-57078486 Msa1297160:intron 50.0%
AAGTTGCAGATGCAGCACAC+TGG + chr8_3:57078783-57078802 None:intergenic 50.0%
GCAGAGGTAGTATGAGCAAG+AGG + chr8_3:57078925-57078944 None:intergenic 50.0%
CAGGATGATAGGGTGGATAG+GGG + chr8_3:57078968-57078987 None:intergenic 50.0%
CCAGGATGATAGGGTGGATA+GGG + chr8_3:57078969-57078988 None:intergenic 50.0%
TCCAGGATGATAGGGTGGAT+AGG + chr8_3:57078970-57078989 None:intergenic 50.0%
TCTCATCCAGGATGATAGGG+TGG + chr8_3:57078975-57078994 None:intergenic 50.0%
TTGCAGGAGTGATCTCATCC+AGG + chr8_3:57078987-57079006 None:intergenic 50.0%
TGATGGCAGCAGGGGTAAGT+TGG + chr8_3:57078900-57078919 None:intergenic 55.0%
! AAGAGGTGTGATGGCAGCAG+GGG + chr8_3:57078908-57078927 None:intergenic 55.0%
! CAAGAGGTGTGATGGCAGCA+GGG + chr8_3:57078909-57078928 None:intergenic 55.0%
CCCTATCCACCCTATCATCC+TGG - chr8_3:57078966-57078985 Msa1297160:intron 55.0%
TGATGGCAGCAGGGGTAAGT+TGG + chr8_3:57078900-57078919 None:intergenic 55.0%
! AAGAGGTGTGATGGCAGCAG+GGG + chr8_3:57078908-57078927 None:intergenic 55.0%
! CAAGAGGTGTGATGGCAGCA+GGG + chr8_3:57078909-57078928 None:intergenic 55.0%
CCCTATCCACCCTATCATCC+TGG - chr8_3:57078966-57078985 Msa1297160:intron 55.0%
! GCAAGAGGTGTGATGGCAGC+AGG + chr8_3:57078910-57078929 None:intergenic 60.0%
! GCAAGAGGTGTGATGGCAGC+AGG + chr8_3:57078910-57078929 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 57078123 57079047 57078123 ID=Msa1297160;Name=Msa1297160
chr8_3 mRNA 57078123 57079047 57078123 ID=Msa1297160-mRNA-1;Parent=Msa1297160;Name=Msa1297160-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|0|0|1|1|1|4|0|112
chr8_3 exon 57079043 57079047 57079043 ID=Msa1297160-mRNA-1:exon:16384;Parent=Msa1297160-mRNA-1
chr8_3 exon 57078894 57078954 57078894 ID=Msa1297160-mRNA-1:exon:16383;Parent=Msa1297160-mRNA-1
chr8_3 exon 57078664 57078723 57078664 ID=Msa1297160-mRNA-1:exon:16382;Parent=Msa1297160-mRNA-1
chr8_3 exon 57078123 57078335 57078123 ID=Msa1297160-mRNA-1:exon:16381;Parent=Msa1297160-mRNA-1
chr8_3 CDS 57079043 57079047 57079043 ID=Msa1297160-mRNA-1:cds;Parent=Msa1297160-mRNA-1
chr8_3 CDS 57078894 57078954 57078894 ID=Msa1297160-mRNA-1:cds;Parent=Msa1297160-mRNA-1
chr8_3 CDS 57078664 57078723 57078664 ID=Msa1297160-mRNA-1:cds;Parent=Msa1297160-mRNA-1
chr8_3 CDS 57078123 57078335 57078123 ID=Msa1297160-mRNA-1:cds;Parent=Msa1297160-mRNA-1
Gene Sequence

>Msa1297160

ATGATAAAAATTGATGTCTTTGAACAACAAGTGCAGGTAAATGATACTCCTTTTATCTTCACAAAGATAGTAACATATCCTAAGGACGGGAAGGAACATTTGGAGATGGTCATTGTTGATGCTAAGATGCAAACCCCTTCCACCATGTTGCAGAATGTTGAAGGAGGCAAGAACTGGGACTCACTCAGCCAACTTACCCCTGCTGCCATCACACCTCTTGCTCATACTACCTCTGCTAAGATTGGTTCAAGTGCTACCCCTATCCACCCTATCATCCTGGATGAGATCACTCCTGCAAAAAACTCTTACTCTAAGATGGTTAACCTCTTCCTATCATGA

Protein sequence

>Msa1297160

MIKIDVFEQQVQVNDTPFIFTKIVTYPKDGKEHLEMVIVDAKMQTPSTMLQNVEGGKNWDSLSQLTPAAITPLAHTTSAKIGSSATPIHPIILDEITPAKNSYSKMVNLFLS*