AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0013590

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0013590 MtrunA17_Chr6g0476171 84.158 101 14 2 10 110 147 245 1.32e-55 174
Msa0013590 MtrunA17_Chr1g0163111 43.182 88 46 3 24 110 144 228 3.46e-17 75.1
Msa0013590 MtrunA17_Chr1g0163131 39.130 92 54 1 19 110 217 306 5.04e-15 70.1
Msa0013590 MtrunA17_Chr1g0163151 37.634 93 54 2 18 110 133 221 1.99e-14 67.4
Msa0013590 MtrunA17_Chr1g0163201 38.318 107 54 3 5 109 295 391 2.92e-14 68.6
Msa0013590 MtrunA17_Chr1g0163181 36.559 93 55 2 18 110 341 429 9.95e-13 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTCAAAATCATGTGTTTA+AGG 0.174852 1_1:-21028965 Msa0013590:CDS
TATAATCAATACCTCGATTA+TGG 0.200198 1_1:-21029069 Msa0013590:CDS
GTTCAAAATCATGTGTTTAA+GGG 0.356485 1_1:-21028964 Msa0013590:CDS
AAGAGGCATAATATATTTAG+TGG 0.396534 1_1:-21029144 Msa0013590:CDS
ATAATCAATACCTCGATTAT+GGG 0.406179 1_1:-21029068 Msa0013590:CDS
ATTCAGTTGAGTTGAGAGTA+GGG 0.424365 1_1:-21029119 Msa0013590:CDS
CTTAACACCGGCATATGTTC+CGG 0.456767 1_1:-21028729 Msa0013590:three_prime_UTR
AGCAAGTTGGCTACTGTTCG+TGG 0.458444 1_1:+21028900 None:intergenic
TGAGAGTAGGGGAAGGAACA+TGG 0.483751 1_1:-21029107 Msa0013590:CDS
AATTCAGTTGAGTTGAGAGT+AGG 0.486713 1_1:-21029120 Msa0013590:CDS
GATTATGGGTGGTGCACTAA+AGG 0.488630 1_1:-21029054 Msa0013590:CDS
AATGTATATTTCTAACAGCT+TGG 0.489472 1_1:-21028644 Msa0013590:three_prime_UTR
AGAGAATGCAATGTGAAGAT+TGG 0.489972 1_1:-21029015 Msa0013590:CDS
TTCAGTTGAGTTGAGAGTAG+GGG 0.498731 1_1:-21029118 Msa0013590:CDS
GAATTTACATGAGATGTTGA+AGG 0.505102 1_1:-21029301 Msa0013590:CDS
TAGAAAAGGTAGATCGAAAA+CGG 0.516702 1_1:+21028799 None:intergenic
GGACTGTTCCGCAATAGAAA+AGG 0.518937 1_1:+21028785 None:intergenic
ATATGAAAGTGAAAGTAGAA+TGG 0.522726 1_1:+21028931 None:intergenic
GCGTACTCTGCAAGAGGAGG+AGG 0.523009 1_1:+21028677 None:intergenic
TGCCTCTTCAACAACTCACT+TGG 0.544194 1_1:+21029159 None:intergenic
TCGAAAACGGTGGTTGGAGA+TGG 0.549714 1_1:+21028812 None:intergenic
AAGTCATTTGAAAAGCAAGT+TGG 0.561426 1_1:+21028887 None:intergenic
GGTAGATCGAAAACGGTGGT+TGG 0.562097 1_1:+21028806 None:intergenic
TTTCTAACAGCTTGGTGTGG+CGG 0.581096 1_1:-21028636 Msa0013590:three_prime_UTR
AACATCTCATGTAAATTCGT+CGG 0.582408 1_1:+21029306 None:intergenic
CACTCATGGAGATATTGCTA+AGG 0.584920 1_1:+21028764 None:intergenic
ATGGGTGGTGCACTAAAGGT+TGG 0.586410 1_1:-21029050 Msa0013590:CDS
TACCAAGTGAGTTGTTGAAG+AGG 0.607188 1_1:-21029161 Msa0013590:CDS
GATGATGCCGGAACATATGC+CGG 0.624918 1_1:+21028722 None:intergenic
GGAAGGAACATGGTTTGTAG+AGG 0.629163 1_1:-21029097 Msa0013590:CDS
ATCAATACCTCGATTATGGG+TGG 0.629307 1_1:-21029065 Msa0013590:CDS
AAGATTGCGTACTCTGCAAG+AGG 0.629509 1_1:+21028671 None:intergenic
GCTTCAATATGAGATGATGC+CGG 0.636447 1_1:+21028710 None:intergenic
GTTGAGTTGAGAGTAGGGGA+AGG 0.642747 1_1:-21029114 Msa0013590:CDS
ATTGCGTACTCTGCAAGAGG+AGG 0.645506 1_1:+21028674 None:intergenic
ATATTTCTAACAGCTTGGTG+TGG 0.672707 1_1:-21028639 Msa0013590:three_prime_UTR
CGGAAAATATCTCTTAACAC+CGG 0.676621 1_1:-21028741 Msa0013590:three_prime_UTR
TAGCAATATCTCCATGAGTG+CGG 0.682668 1_1:-21028761 Msa0013590:three_prime_UTR
TAGTGCACCACCCATAATCG+AGG 0.702613 1_1:+21029058 None:intergenic
AAAAGGTAGATCGAAAACGG+TGG 0.728352 1_1:+21028802 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATAACATCATTAGACA+AGG - chr1_1:21028658-21028677 Msa0013590:three_prime_UTR 20.0%
!!! TTTTATAACATCATTAGACA+AGG - chr1_1:21028658-21028677 Msa0013590:three_prime_UTR 20.0%
!! AAGAGGCATAATATATTTAG+TGG - chr1_1:21028791-21028810 Msa0013590:three_prime_UTR 25.0%
! TATAATCAATACCTCGATTA+TGG - chr1_1:21028866-21028885 Msa0013590:CDS 25.0%
! ATAATCAATACCTCGATTAT+GGG - chr1_1:21028867-21028886 Msa0013590:CDS 25.0%
! TGTTCAAAATCATGTGTTTA+AGG - chr1_1:21028970-21028989 Msa0013590:CDS 25.0%
! GTTCAAAATCATGTGTTTAA+GGG - chr1_1:21028971-21028990 Msa0013590:CDS 25.0%
! ATATGAAAGTGAAAGTAGAA+TGG + chr1_1:21029007-21029026 None:intergenic 25.0%
!! AATGTATATTTCTAACAGCT+TGG - chr1_1:21029291-21029310 Msa0013590:CDS 25.0%
!! AAGAGGCATAATATATTTAG+TGG - chr1_1:21028791-21028810 Msa0013590:three_prime_UTR 25.0%
! TATAATCAATACCTCGATTA+TGG - chr1_1:21028866-21028885 Msa0013590:CDS 25.0%
! ATAATCAATACCTCGATTAT+GGG - chr1_1:21028867-21028886 Msa0013590:CDS 25.0%
! TGTTCAAAATCATGTGTTTA+AGG - chr1_1:21028970-21028989 Msa0013590:CDS 25.0%
! GTTCAAAATCATGTGTTTAA+GGG - chr1_1:21028971-21028990 Msa0013590:CDS 25.0%
! ATATGAAAGTGAAAGTAGAA+TGG + chr1_1:21029007-21029026 None:intergenic 25.0%
!! AATGTATATTTCTAACAGCT+TGG - chr1_1:21029291-21029310 Msa0013590:CDS 25.0%
AACATCTCATGTAAATTCGT+CGG + chr1_1:21028632-21028651 None:intergenic 30.0%
GAATTTACATGAGATGTTGA+AGG - chr1_1:21028634-21028653 Msa0013590:three_prime_UTR 30.0%
CAAACACATAGCTATATACA+TGG + chr1_1:21028708-21028727 None:intergenic 30.0%
AAGTCATTTGAAAAGCAAGT+TGG + chr1_1:21029051-21029070 None:intergenic 30.0%
! GACTTATTTCCAATGCTTTT+TGG - chr1_1:21029066-21029085 Msa0013590:CDS 30.0%
!! TATTTCCAATGCTTTTTGGT+CGG - chr1_1:21029070-21029089 Msa0013590:CDS 30.0%
TAGAAAAGGTAGATCGAAAA+CGG + chr1_1:21029139-21029158 None:intergenic 30.0%
AACATCTCATGTAAATTCGT+CGG + chr1_1:21028632-21028651 None:intergenic 30.0%
GAATTTACATGAGATGTTGA+AGG - chr1_1:21028634-21028653 Msa0013590:three_prime_UTR 30.0%
CAAACACATAGCTATATACA+TGG + chr1_1:21028708-21028727 None:intergenic 30.0%
AAGTCATTTGAAAAGCAAGT+TGG + chr1_1:21029051-21029070 None:intergenic 30.0%
! GACTTATTTCCAATGCTTTT+TGG - chr1_1:21029066-21029085 Msa0013590:CDS 30.0%
!! TATTTCCAATGCTTTTTGGT+CGG - chr1_1:21029070-21029089 Msa0013590:CDS 30.0%
TAGAAAAGGTAGATCGAAAA+CGG + chr1_1:21029139-21029158 None:intergenic 30.0%
TCTGTTCTTAAATATGCAGC+TGG - chr1_1:21028745-21028764 Msa0013590:three_prime_UTR 35.0%
!! AATTCAGTTGAGTTGAGAGT+AGG - chr1_1:21028815-21028834 Msa0013590:three_prime_UTR 35.0%
!! ATTCAGTTGAGTTGAGAGTA+GGG - chr1_1:21028816-21028835 Msa0013590:three_prime_UTR 35.0%
AGAGAATGCAATGTGAAGAT+TGG - chr1_1:21028920-21028939 Msa0013590:CDS 35.0%
! TAAAACCGACCAAAAAGCAT+TGG + chr1_1:21029078-21029097 None:intergenic 35.0%
! TCGATCTACCTTTTCTATTG+CGG - chr1_1:21029142-21029161 Msa0013590:CDS 35.0%
CGGAAAATATCTCTTAACAC+CGG - chr1_1:21029194-21029213 Msa0013590:intron 35.0%
! ATATTTCTAACAGCTTGGTG+TGG - chr1_1:21029296-21029315 Msa0013590:CDS 35.0%
!!! CGACTCTTGTTCTGATTTTT+TGG - chr1_1:21029323-21029342 Msa0013590:CDS 35.0%
!!! CTCTTGTTCTGATTTTTTGG+TGG - chr1_1:21029326-21029345 Msa0013590:CDS 35.0%
TCTGTTCTTAAATATGCAGC+TGG - chr1_1:21028745-21028764 Msa0013590:three_prime_UTR 35.0%
!! AATTCAGTTGAGTTGAGAGT+AGG - chr1_1:21028815-21028834 Msa0013590:three_prime_UTR 35.0%
!! ATTCAGTTGAGTTGAGAGTA+GGG - chr1_1:21028816-21028835 Msa0013590:three_prime_UTR 35.0%
AGAGAATGCAATGTGAAGAT+TGG - chr1_1:21028920-21028939 Msa0013590:CDS 35.0%
! TAAAACCGACCAAAAAGCAT+TGG + chr1_1:21029078-21029097 None:intergenic 35.0%
! TCGATCTACCTTTTCTATTG+CGG - chr1_1:21029142-21029161 Msa0013590:CDS 35.0%
CGGAAAATATCTCTTAACAC+CGG - chr1_1:21029194-21029213 Msa0013590:intron 35.0%
! ATATTTCTAACAGCTTGGTG+TGG - chr1_1:21029296-21029315 Msa0013590:CDS 35.0%
!!! CGACTCTTGTTCTGATTTTT+TGG - chr1_1:21029323-21029342 Msa0013590:CDS 35.0%
!!! CTCTTGTTCTGATTTTTTGG+TGG - chr1_1:21029326-21029345 Msa0013590:CDS 35.0%
TACCAAGTGAGTTGTTGAAG+AGG - chr1_1:21028774-21028793 Msa0013590:three_prime_UTR 40.0%
!! TTCAGTTGAGTTGAGAGTAG+GGG - chr1_1:21028817-21028836 Msa0013590:three_prime_UTR 40.0%
ATCAATACCTCGATTATGGG+TGG - chr1_1:21028870-21028889 Msa0013590:CDS 40.0%
AAAAGGTAGATCGAAAACGG+TGG + chr1_1:21029136-21029155 None:intergenic 40.0%
CACTCATGGAGATATTGCTA+AGG + chr1_1:21029174-21029193 None:intergenic 40.0%
TAGCAATATCTCCATGAGTG+CGG - chr1_1:21029174-21029193 Msa0013590:CDS 40.0%
! AGAGATATTTTCCGCACTCA+TGG + chr1_1:21029188-21029207 None:intergenic 40.0%
GCTTCAATATGAGATGATGC+CGG + chr1_1:21029228-21029247 None:intergenic 40.0%
TACCAAGTGAGTTGTTGAAG+AGG - chr1_1:21028774-21028793 Msa0013590:three_prime_UTR 40.0%
!! TTCAGTTGAGTTGAGAGTAG+GGG - chr1_1:21028817-21028836 Msa0013590:three_prime_UTR 40.0%
ATCAATACCTCGATTATGGG+TGG - chr1_1:21028870-21028889 Msa0013590:CDS 40.0%
AAAAGGTAGATCGAAAACGG+TGG + chr1_1:21029136-21029155 None:intergenic 40.0%
CACTCATGGAGATATTGCTA+AGG + chr1_1:21029174-21029193 None:intergenic 40.0%
TAGCAATATCTCCATGAGTG+CGG - chr1_1:21029174-21029193 Msa0013590:CDS 40.0%
! AGAGATATTTTCCGCACTCA+TGG + chr1_1:21029188-21029207 None:intergenic 40.0%
GCTTCAATATGAGATGATGC+CGG + chr1_1:21029228-21029247 None:intergenic 40.0%
TGCCTCTTCAACAACTCACT+TGG + chr1_1:21028779-21028798 None:intergenic 45.0%
! GGAAGGAACATGGTTTGTAG+AGG - chr1_1:21028838-21028857 Msa0013590:exon 45.0%
GATTATGGGTGGTGCACTAA+AGG - chr1_1:21028881-21028900 Msa0013590:CDS 45.0%
GGACTGTTCCGCAATAGAAA+AGG + chr1_1:21029153-21029172 None:intergenic 45.0%
CTTAACACCGGCATATGTTC+CGG - chr1_1:21029206-21029225 Msa0013590:intron 45.0%
AAGATTGCGTACTCTGCAAG+AGG + chr1_1:21029267-21029286 None:intergenic 45.0%
!! TTTCTAACAGCTTGGTGTGG+CGG - chr1_1:21029299-21029318 Msa0013590:CDS 45.0%
TGCCTCTTCAACAACTCACT+TGG + chr1_1:21028779-21028798 None:intergenic 45.0%
! GGAAGGAACATGGTTTGTAG+AGG - chr1_1:21028838-21028857 Msa0013590:exon 45.0%
GATTATGGGTGGTGCACTAA+AGG - chr1_1:21028881-21028900 Msa0013590:CDS 45.0%
GGACTGTTCCGCAATAGAAA+AGG + chr1_1:21029153-21029172 None:intergenic 45.0%
CTTAACACCGGCATATGTTC+CGG - chr1_1:21029206-21029225 Msa0013590:intron 45.0%
AAGATTGCGTACTCTGCAAG+AGG + chr1_1:21029267-21029286 None:intergenic 45.0%
!! TTTCTAACAGCTTGGTGTGG+CGG - chr1_1:21029299-21029318 Msa0013590:CDS 45.0%
!! GTTGAGTTGAGAGTAGGGGA+AGG - chr1_1:21028821-21028840 Msa0013590:three_prime_UTR 50.0%
TGAGAGTAGGGGAAGGAACA+TGG - chr1_1:21028828-21028847 Msa0013590:three_prime_UTR 50.0%
TAGTGCACCACCCATAATCG+AGG + chr1_1:21028880-21028899 None:intergenic 50.0%
ATGGGTGGTGCACTAAAGGT+TGG - chr1_1:21028885-21028904 Msa0013590:CDS 50.0%
! AGCAAGTTGGCTACTGTTCG+TGG + chr1_1:21029038-21029057 None:intergenic 50.0%
TCGAAAACGGTGGTTGGAGA+TGG + chr1_1:21029126-21029145 None:intergenic 50.0%
GGTAGATCGAAAACGGTGGT+TGG + chr1_1:21029132-21029151 None:intergenic 50.0%
GATGATGCCGGAACATATGC+CGG + chr1_1:21029216-21029235 None:intergenic 50.0%
ATTGCGTACTCTGCAAGAGG+AGG + chr1_1:21029264-21029283 None:intergenic 50.0%
!! GTTGAGTTGAGAGTAGGGGA+AGG - chr1_1:21028821-21028840 Msa0013590:three_prime_UTR 50.0%
TGAGAGTAGGGGAAGGAACA+TGG - chr1_1:21028828-21028847 Msa0013590:three_prime_UTR 50.0%
TAGTGCACCACCCATAATCG+AGG + chr1_1:21028880-21028899 None:intergenic 50.0%
ATGGGTGGTGCACTAAAGGT+TGG - chr1_1:21028885-21028904 Msa0013590:CDS 50.0%
! AGCAAGTTGGCTACTGTTCG+TGG + chr1_1:21029038-21029057 None:intergenic 50.0%
TCGAAAACGGTGGTTGGAGA+TGG + chr1_1:21029126-21029145 None:intergenic 50.0%
GGTAGATCGAAAACGGTGGT+TGG + chr1_1:21029132-21029151 None:intergenic 50.0%
GATGATGCCGGAACATATGC+CGG + chr1_1:21029216-21029235 None:intergenic 50.0%
ATTGCGTACTCTGCAAGAGG+AGG + chr1_1:21029264-21029283 None:intergenic 50.0%
GCGTACTCTGCAAGAGGAGG+AGG + chr1_1:21029261-21029280 None:intergenic 60.0%
GCGTACTCTGCAAGAGGAGG+AGG + chr1_1:21029261-21029280 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 21028590 21029367 21028590 ID=Msa0013590;Name=Msa0013590
chr1_1 mRNA 21028590 21029367 21028590 ID=Msa0013590-mRNA-1;Parent=Msa0013590;Name=Msa0013590-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|1|0.5|1|0|0|2|259|144
chr1_1 exon 21028590 21029193 21028590 ID=Msa0013590-mRNA-1:exon:7503;Parent=Msa0013590-mRNA-1
chr1_1 exon 21029278 21029367 21029278 ID=Msa0013590-mRNA-1:exon:7502;Parent=Msa0013590-mRNA-1
chr1_1 CDS 21029278 21029367 21029278 ID=Msa0013590-mRNA-1:cds;Parent=Msa0013590-mRNA-1
chr1_1 CDS 21028849 21029193 21028849 ID=Msa0013590-mRNA-1:cds;Parent=Msa0013590-mRNA-1
chr1_1 three_prime_UTR 21028590 21028848 21028590 ID=Msa0013590-mRNA-1:three_prime_utr;Parent=Msa0013590-mRNA-1
Gene Sequence

>Msa0013590

ATGTTTTCTTTGTTGTTAATTACTACAGATTCTGTAAGTCCGACGAATTTACATGAGATGTTGAAGGTTTTTATAACATCATTAGACAAGCTGGTCGTACTACCAAGTGAGTTGTTGAAGAGGCATAATATATTTAGTGGAAATTCAGTTGAGTTGAGAGTAGGGGAAGGAACATGGTTTGTAGAGGTGAATTATAATCAATACCTCGATTATGGGTGGTGCACTAAAGGTTGGCACGAATTTGTGAGAGAATGCAATGTGAAGATTGGAGACACTTGTTTGTTTGAGATGATTGATGTTCAAAATCATGTGTTTAAGGGTTCAATTATTCCATTCTACTTTCACTTTCATATGTTGAATTCCACGAACAGTAGCCAACTTGCTTTTCAAATGACTTATTTCCAATGCTTTTTGGTCGGTTTTACTAATATCTAA
Protein sequence

>Msa0013590

MFSLLLITTDSVSPTNLHEMLKVFITSLDKLVVLPSELLKRHNIFSGNSVELRVGEGTWFVEVNYNQYLDYGWCTKGWHEFVRECNVKIGDTCLFEMIDVQNHVFKGSIIPFYFHFHMLNSTNSSQLAFQMTYFQCFLVGFTNI*