AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0483980

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 70 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCACGCCTCCGTTACCTTT+TGG 0.196515 3_4:-1060687 Msa0483980:CDS
CTGTTCCCTGGGATTGGCTT+TGG 0.228349 3_4:+1060503 None:intergenic
CAGCTCACGTACCGCTTTAA+TGG 0.245260 3_4:-1060982 Msa0483980:CDS
TGTTCCCTGGGATTGGCTTT+GGG 0.270024 3_4:+1060504 None:intergenic
TCTCAGGTAGACAGTTTCTA+TGG 0.287253 3_4:+1060652 None:intergenic
GGCAAAGAAGGCCTCCTTCC+GGG 0.289862 3_4:+1060552 None:intergenic
AGGGAACAGTGAAGCTTCAT+AGG 0.345840 3_4:-1060489 None:intergenic
TCCTCGGGCCAGACGGAGAT+TGG 0.349112 3_4:+1060716 None:intergenic
TCCCGTCGATGTGAGCTCTT+GGG 0.355274 3_4:-1060888 Msa0483980:CDS
GCTTCACTGTTCCCTGGGAT+TGG 0.355814 3_4:+1060497 None:intergenic
AGGCAAAGAAGGCCTCCTTC+CGG 0.382980 3_4:+1060551 None:intergenic
AAAGTTACTCTAGGGATAAC+AGG 0.383241 3_4:+1060856 None:intergenic
CATTAAAGCGGTACGTGAGC+TGG 0.384796 3_4:+1060983 None:intergenic
TTCCCGTCGATGTGAGCTCT+TGG 0.386490 3_4:-1060889 Msa0483980:CDS
AGCTCACGTACCGCTTTAAT+GGG 0.395506 3_4:-1060981 Msa0483980:CDS
CCCTTCTGCCTTTGCACTCG+AGG 0.411231 3_4:-1060740 Msa0483980:CDS
CTCACATCGACGGGAAGGTT+TGG 0.420533 3_4:+1060896 None:intergenic
TGTAGTATGTTCCAAGGGTT+GGG 0.424624 3_4:+1060951 None:intergenic
CTGTAGTATGTTCCAAGGGT+TGG 0.452990 3_4:+1060950 None:intergenic
ACAGACCAAGGGACAGTCTC+AGG 0.456050 3_4:+1060636 None:intergenic
CAGAACGTCGTGAGACAGTT+CGG 0.457061 3_4:+1061009 None:intergenic
CCTTCTGCCTTTGCACTCGA+GGG 0.461384 3_4:-1060739 Msa0483980:CDS
AAAAGCCCAAAGCCAATCCC+AGG 0.461472 3_4:-1060509 Msa0483980:CDS
GACTGTCCCTTGGTCTGTAC+TGG 0.464231 3_4:-1060631 Msa0483980:CDS
CCCCAAGAGCTCACATCGAC+GGG 0.472021 3_4:+1060887 None:intergenic
ATGAAGCTTCACTGTTCCCT+GGG 0.472889 3_4:+1060492 None:intergenic
TATGAAGCTTCACTGTTCCC+TGG 0.477188 3_4:+1060491 None:intergenic
CTCGAGGGCCAATCTCCGTC+TGG 0.480699 3_4:-1060724 Msa0483980:CDS
GCCTTCCACCTAAGCTGCGC+AGG 0.489457 3_4:-1060532 Msa0483980:CDS
GCAAAGAAGGCCTCCTTCCG+GGG 0.489774 3_4:+1060553 None:intergenic
GATGTCGGCTCTTCGCCACC+TGG 0.508239 3_4:+1060925 None:intergenic
TCCTGCGCAGCTTAGGTGGA+AGG 0.508478 3_4:+1060531 None:intergenic
CTCAGGTAGACAGTTTCTAT+GGG 0.510655 3_4:+1060653 None:intergenic
CCCTCGAGTGCAAAGGCAGA+AGG 0.511073 3_4:+1060739 None:intergenic
GAGGCGTGCAAAGGTTTCCT+CGG 0.526013 3_4:+1060700 None:intergenic
AGGCGTGCAAAGGTTTCCTC+GGG 0.527025 3_4:+1060701 None:intergenic
CCAGAGTGGTATCTCACTGA+TGG 0.527423 3_4:-1060584 Msa0483980:CDS
CCCGTCGATGTGAGCTCTTG+GGG 0.534121 3_4:-1060887 Msa0483980:CDS
CCTTGGTCTGTACTGGCACA+AGG 0.538614 3_4:-1060624 Msa0483980:CDS
ATTAAAGCGGTACGTGAGCT+GGG 0.539036 3_4:+1060984 None:intergenic
CAAAGAAGGCCTCCTTCCGG+GGG 0.541469 3_4:+1060554 None:intergenic
AAGGTTTGGCACCTCGATGT+CGG 0.545826 3_4:+1060910 None:intergenic
TGGGCGAACAGCCCAACCCT+TGG 0.548090 3_4:-1060962 Msa0483980:CDS
GCTTAGGTGGAAGGCAAAGA+AGG 0.550243 3_4:+1060540 None:intergenic
TCCCCAAGAGCTCACATCGA+CGG 0.555494 3_4:+1060886 None:intergenic
GCCAATCTCCGTCTGGCCCG+AGG 0.562208 3_4:-1060717 Msa0483980:CDS
TGGAGCTGTAGTATGTTCCA+AGG 0.564153 3_4:+1060945 None:intergenic
TTGGAACATACTACAGCTCC+AGG 0.579135 3_4:-1060943 Msa0483980:CDS
GTCTACCTGAGACTGTCCCT+TGG 0.586612 3_4:-1060641 Msa0483980:CDS
GGGAACAGTGAAGCTTCATA+GGG 0.591786 3_4:-1060488 None:intergenic
AAGGTAACGGAGGCGTGCAA+AGG 0.595805 3_4:+1060691 None:intergenic
CCTCGAGTGCAAAGGCAGAA+GGG 0.595841 3_4:+1060740 None:intergenic
AAAGGTTTCCTCGGGCCAGA+CGG 0.597813 3_4:+1060709 None:intergenic
TGGGGCGTAGGCCTCCCAAA+AGG 0.606913 3_4:+1060672 None:intergenic
AAGAGCTCACATCGACGGGA+AGG 0.613365 3_4:+1060891 None:intergenic
AAAGCCCAAAGCCAATCCCA+GGG 0.619579 3_4:-1060508 Msa0483980:CDS
GGGCTGTTCGCCCATTAAAG+CGG 0.619701 3_4:+1060971 None:intergenic
AGACAGTTTCTATGGGGCGT+AGG 0.622986 3_4:+1060660 None:intergenic
GTAGGCCTCCCAAAAGGTAA+CGG 0.632223 3_4:+1060678 None:intergenic
GGAGCTGTAGTATGTTCCAA+GGG 0.640199 3_4:+1060946 None:intergenic
CCTTGTGCCAGTACAGACCA+AGG 0.645647 3_4:+1060624 None:intergenic
AGATTGGCCCTCGAGTGCAA+AGG 0.670375 3_4:+1060732 None:intergenic
CCATCAGTGAGATACCACTC+TGG 0.671241 3_4:+1060584 None:intergenic
AAAGAAGGCCTCCTTCCGGG+GGG 0.675250 3_4:+1060555 None:intergenic
GAATTCTAGCTCTTCCAGAG+TGG 0.675255 3_4:-1060598 Msa0483980:CDS
GGCCTCCCAAAAGGTAACGG+AGG 0.683463 3_4:+1060681 None:intergenic
CTTGTGCCAGTACAGACCAA+GGG 0.693537 3_4:+1060625 None:intergenic
GTGGCGAAGAGCCGACATCG+AGG 0.704477 3_4:-1060921 Msa0483980:CDS
TCAGGTAGACAGTTTCTATG+GGG 0.720720 3_4:+1060654 None:intergenic
GAACATACTACAGCTCCAGG+TGG 0.771466 3_4:-1060940 Msa0483980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACGGATAAAAGTTACTCTA+GGG + chr3_4:1060659-1060678 None:intergenic 30.0%
! AAAGTTACTCTAGGGATAAC+AGG + chr3_4:1060651-1060670 None:intergenic 35.0%
CAACGGATAAAAGTTACTCT+AGG + chr3_4:1060660-1060679 None:intergenic 35.0%
TGTAGTATGTTCCAAGGGTT+GGG + chr3_4:1060556-1060575 None:intergenic 40.0%
! AACTTTTATCCGTTGAGCGA+CGG - chr3_4:1060665-1060684 Msa0483980:CDS 40.0%
TCAGGTAGACAGTTTCTATG+GGG + chr3_4:1060853-1060872 None:intergenic 40.0%
CTCAGGTAGACAGTTTCTAT+GGG + chr3_4:1060854-1060873 None:intergenic 40.0%
TCTCAGGTAGACAGTTTCTA+TGG + chr3_4:1060855-1060874 None:intergenic 40.0%
ATTAAAGCGGTACGTGAGCT+GGG + chr3_4:1060523-1060542 None:intergenic 45.0%
AGCTCACGTACCGCTTTAAT+GGG - chr3_4:1060523-1060542 Msa0483980:CDS 45.0%
CTGTAGTATGTTCCAAGGGT+TGG + chr3_4:1060557-1060576 None:intergenic 45.0%
GGAGCTGTAGTATGTTCCAA+GGG + chr3_4:1060561-1060580 None:intergenic 45.0%
TGGAGCTGTAGTATGTTCCA+AGG + chr3_4:1060562-1060581 None:intergenic 45.0%
TTGGAACATACTACAGCTCC+AGG - chr3_4:1060561-1060580 Msa0483980:CDS 45.0%
!! GAATTCTAGCTCTTCCAGAG+TGG - chr3_4:1060906-1060925 Msa0483980:CDS 45.0%
ATGAAGCTTCACTGTTCCCT+GGG + chr3_4:1061015-1061034 None:intergenic 45.0%
TATGAAGCTTCACTGTTCCC+TGG + chr3_4:1061016-1061035 None:intergenic 45.0%
CAGAACGTCGTGAGACAGTT+CGG + chr3_4:1060498-1060517 None:intergenic 50.0%
CATTAAAGCGGTACGTGAGC+TGG + chr3_4:1060524-1060543 None:intergenic 50.0%
CAGCTCACGTACCGCTTTAA+TGG - chr3_4:1060522-1060541 Msa0483980:CDS 50.0%
GAACATACTACAGCTCCAGG+TGG - chr3_4:1060564-1060583 Msa0483980:CDS 50.0%
AAGGTTTGGCACCTCGATGT+CGG + chr3_4:1060597-1060616 None:intergenic 50.0%
GTAGGCCTCCCAAAAGGTAA+CGG + chr3_4:1060829-1060848 None:intergenic 50.0%
AGACAGTTTCTATGGGGCGT+AGG + chr3_4:1060847-1060866 None:intergenic 50.0%
CTTGTGCCAGTACAGACCAA+GGG + chr3_4:1060882-1060901 None:intergenic 50.0%
CCATCAGTGAGATACCACTC+TGG + chr3_4:1060923-1060942 None:intergenic 50.0%
CCAGAGTGGTATCTCACTGA+TGG - chr3_4:1060920-1060939 Msa0483980:CDS 50.0%
GCTTAGGTGGAAGGCAAAGA+AGG + chr3_4:1060967-1060986 None:intergenic 50.0%
AAAAGCCCAAAGCCAATCCC+AGG - chr3_4:1060995-1061014 Msa0483980:CDS 50.0%
AAAGCCCAAAGCCAATCCCA+GGG - chr3_4:1060996-1061015 Msa0483980:CDS 50.0%
!! TGTTCCCTGGGATTGGCTTT+GGG + chr3_4:1061003-1061022 None:intergenic 50.0%
GGGCTGTTCGCCCATTAAAG+CGG + chr3_4:1060536-1060555 None:intergenic 55.0%
CTCACATCGACGGGAAGGTT+TGG + chr3_4:1060611-1060630 None:intergenic 55.0%
AAGAGCTCACATCGACGGGA+AGG + chr3_4:1060616-1060635 None:intergenic 55.0%
TTCCCGTCGATGTGAGCTCT+TGG - chr3_4:1060615-1060634 Msa0483980:CDS 55.0%
TCCCGTCGATGTGAGCTCTT+GGG - chr3_4:1060616-1060635 Msa0483980:CDS 55.0%
TCCCCAAGAGCTCACATCGA+CGG + chr3_4:1060621-1060640 None:intergenic 55.0%
AGTCGGCCTTAGTGATCCGA+CGG + chr3_4:1060706-1060725 None:intergenic 55.0%
CCTCGAGTGCAAAGGCAGAA+GGG + chr3_4:1060767-1060786 None:intergenic 55.0%
CCTTCTGCCTTTGCACTCGA+GGG - chr3_4:1060765-1060784 Msa0483980:intron 55.0%
! AGATTGGCCCTCGAGTGCAA+AGG + chr3_4:1060775-1060794 None:intergenic 55.0%
AAAGGTTTCCTCGGGCCAGA+CGG + chr3_4:1060798-1060817 None:intergenic 55.0%
AGGCGTGCAAAGGTTTCCTC+GGG + chr3_4:1060806-1060825 None:intergenic 55.0%
GAGGCGTGCAAAGGTTTCCT+CGG + chr3_4:1060807-1060826 None:intergenic 55.0%
!! AAGGTAACGGAGGCGTGCAA+AGG + chr3_4:1060816-1060835 None:intergenic 55.0%
! TGCACGCCTCCGTTACCTTT+TGG - chr3_4:1060817-1060836 Msa0483980:intron 55.0%
! GCACGCCTCCGTTACCTTTT+GGG - chr3_4:1060818-1060837 Msa0483980:intron 55.0%
GTCTACCTGAGACTGTCCCT+TGG - chr3_4:1060863-1060882 Msa0483980:intron 55.0%
ACAGACCAAGGGACAGTCTC+AGG + chr3_4:1060871-1060890 None:intergenic 55.0%
GACTGTCCCTTGGTCTGTAC+TGG - chr3_4:1060873-1060892 Msa0483980:CDS 55.0%
CCTTGTGCCAGTACAGACCA+AGG + chr3_4:1060883-1060902 None:intergenic 55.0%
! CCTTGGTCTGTACTGGCACA+AGG - chr3_4:1060880-1060899 Msa0483980:CDS 55.0%
AGGCAAAGAAGGCCTCCTTC+CGG + chr3_4:1060956-1060975 None:intergenic 55.0%
! CTTTTCCTGCGCAGCTTAGG+TGG + chr3_4:1060980-1060999 None:intergenic 55.0%
!! CTGTTCCCTGGGATTGGCTT+TGG + chr3_4:1061004-1061023 None:intergenic 55.0%
GCTTCACTGTTCCCTGGGAT+TGG + chr3_4:1061010-1061029 None:intergenic 55.0%
CCCCAAGAGCTCACATCGAC+GGG + chr3_4:1060620-1060639 None:intergenic 60.0%
CCCGTCGATGTGAGCTCTTG+GGG - chr3_4:1060617-1060636 Msa0483980:CDS 60.0%
TCGGCACCGTCGGATCACTA+AGG - chr3_4:1060697-1060716 Msa0483980:CDS 60.0%
CGTCGAGCAGGGACGAAAGT+CGG + chr3_4:1060723-1060742 None:intergenic 60.0%
CGACTTTCGTCCCTGCTCGA+CGG - chr3_4:1060721-1060740 Msa0483980:CDS 60.0%
GACTTTCGTCCCTGCTCGAC+GGG - chr3_4:1060722-1060741 Msa0483980:CDS 60.0%
CCCTTCTGCCTTTGCACTCG+AGG - chr3_4:1060764-1060783 Msa0483980:intron 60.0%
CCCTCGAGTGCAAAGGCAGA+AGG + chr3_4:1060768-1060787 None:intergenic 60.0%
! CGCCTCCGTTACCTTTTGGG+AGG - chr3_4:1060821-1060840 Msa0483980:intron 60.0%
! GGCCTCCCAAAAGGTAACGG+AGG + chr3_4:1060826-1060845 None:intergenic 60.0%
AAAGAAGGCCTCCTTCCGGG+GGG + chr3_4:1060952-1060971 None:intergenic 60.0%
CAAAGAAGGCCTCCTTCCGG+GGG + chr3_4:1060953-1060972 None:intergenic 60.0%
GCAAAGAAGGCCTCCTTCCG+GGG + chr3_4:1060954-1060973 None:intergenic 60.0%
GGCAAAGAAGGCCTCCTTCC+GGG + chr3_4:1060955-1060974 None:intergenic 60.0%
TCCTGCGCAGCTTAGGTGGA+AGG + chr3_4:1060976-1060995 None:intergenic 60.0%
! GGGCTTTTCCTGCGCAGCTT+AGG + chr3_4:1060983-1061002 None:intergenic 60.0%
TGGGCGAACAGCCCAACCCT+TGG - chr3_4:1060542-1060561 Msa0483980:CDS 65.0%
!! GATGTCGGCTCTTCGCCACC+TGG + chr3_4:1060582-1060601 None:intergenic 65.0%
GTGGCGAAGAGCCGACATCG+AGG - chr3_4:1060583-1060602 Msa0483980:CDS 65.0%
GTGGAAGGGCCGTCGCTCAA+CGG + chr3_4:1060677-1060696 None:intergenic 65.0%
TGAGCGACGGCCCTTCCACT+CGG - chr3_4:1060678-1060697 Msa0483980:CDS 65.0%
! TCCGACGGTGCCGAGTGGAA+GGG + chr3_4:1060691-1060710 None:intergenic 65.0%
! ATCCGACGGTGCCGAGTGGA+AGG + chr3_4:1060692-1060711 None:intergenic 65.0%
! AGTGATCCGACGGTGCCGAG+TGG + chr3_4:1060696-1060715 None:intergenic 65.0%
TTTCGTCCCTGCTCGACGGG+TGG - chr3_4:1060725-1060744 Msa0483980:CDS 65.0%
TTCGTCCCTGCTCGACGGGT+GGG - chr3_4:1060726-1060745 Msa0483980:CDS 65.0%
CAAGACCCACCCGTCGAGCA+GGG + chr3_4:1060734-1060753 None:intergenic 65.0%
CTCGAGGGCCAATCTCCGTC+TGG - chr3_4:1060780-1060799 Msa0483980:intron 65.0%
TCCTCGGGCCAGACGGAGAT+TGG + chr3_4:1060791-1060810 None:intergenic 65.0%
TGGGGCGTAGGCCTCCCAAA+AGG + chr3_4:1060835-1060854 None:intergenic 65.0%
GCCTTCCACCTAAGCTGCGC+AGG - chr3_4:1060972-1060991 Msa0483980:CDS 65.0%
GCCCTTCCACTCGGCACCGT+CGG - chr3_4:1060687-1060706 Msa0483980:CDS 70.0%
GCAAGACCCACCCGTCGAGC+AGG + chr3_4:1060735-1060754 None:intergenic 70.0%
GCCAATCTCCGTCTGGCCCG+AGG - chr3_4:1060787-1060806 Msa0483980:intron 70.0%
CACTGATGGCTCGAGCCCCC+CGG - chr3_4:1060934-1060953 Msa0483980:CDS 70.0%
GATGGCTCGAGCCCCCCGGA+AGG - chr3_4:1060938-1060957 Msa0483980:CDS 75.0%
! GGCTCGAGCCCCCCGGAAGG+AGG - chr3_4:1060941-1060960 Msa0483980:CDS 80.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 1060490 1061036 1060490 ID=Msa0483980;Name=Msa0483980
chr3_4 mRNA 1060490 1061036 1060490 ID=Msa0483980-mRNA-1;Parent=Msa0483980;Name=Msa0483980-mRNA-1;_AED=0.45;_eAED=0.61;_QI=0|0|0|1|1|1|2|0|150
chr3_4 exon 1060864 1061036 1060864 ID=Msa0483980-mRNA-1:exon:301;Parent=Msa0483980-mRNA-1
chr3_4 exon 1060490 1060769 1060490 ID=Msa0483980-mRNA-1:exon:300;Parent=Msa0483980-mRNA-1
chr3_4 CDS 1060864 1061036 1060864 ID=Msa0483980-mRNA-1:cds;Parent=Msa0483980-mRNA-1
chr3_4 CDS 1060490 1060769 1060490 ID=Msa0483980-mRNA-1:cds;Parent=Msa0483980-mRNA-1
Gene Sequence

>Msa0483980

ATGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCACGTACCGCTTTAATGGGCGAACAGCCCAACCCTTGGAACATACTACAGCTCCAGGTGGCGAAGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGAGCTCTTGGGGAAGATCAGCCTGTTATCCCTAGATCAAGCTCCCTTCTGCCTTTGCACTCGAGGGCCAATCTCCGTCTGGCCCGAGGAAACCTTTGCACGCCTCCGTTACCTTTTGGGAGGCCTACGCCCCATAGAAACTGTCTACCTGAGACTGTCCCTTGGTCTGTACTGGCACAAGGTTAGAATTCTAGCTCTTCCAGAGTGGTATCTCACTGATGGCTCGAGCCCCCCGGAAGGAGGCCTTCTTTGCCTTCCACCTAAGCTGCGCAGGAAAAGCCCAAAGCCAATCCCAGGGAACAGTGAAGCTTCATAG
Protein sequence

>Msa0483980

MDRTVSRRSEPSSRTALMGEQPNPWNILQLQVAKSRHRGAKPSRRCELLGKISLLSLDQAPFCLCTRGPISVWPEETFARLRYLLGGLRPIETVYLRLSLGLYWHKVRILALPEWYLTDGSSPPEGGLLCLPPKLRRKSPKPIPGNSEAS*