AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0867670


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 77 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 6_1:+760639 Msa0867670:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 6_1:-760526 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_1:+760441 Msa0867670:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_1:-760578 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 6_1:+760783 Msa0867670:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 6_1:+760751 Msa0867670:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_1:+760478 Msa0867670:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 6_1:+760784 Msa0867670:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_1:-760451 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 6_1:+760824 Msa0867670:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_1:-760460 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_1:+760394 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 6_1:-760823 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 6_1:-760740 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 6_1:+760829 Msa0867670:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 6_1:+760752 Msa0867670:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 6_1:+760640 Msa0867670:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_1:-760402 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 6_1:-760835 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 6_1:-760634 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 6_1:-760817 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 6_1:-760895 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_1:+760588 Msa0867670:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 6_1:-760635 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 6_1:-760525 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 6_1:-760841 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 6_1:-760764 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 6_1:-760869 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_1:-760450 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 6_1:-760889 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 6_1:+760861 Msa0867670:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 6_1:-760870 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 6_1:-760840 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 6_1:+760825 Msa0867670:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_1:-760603 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 6_1:-760702 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_1:-760488 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 6_1:-760837 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 6_1:-760784 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 6_1:-760676 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 6_1:-760836 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_1:-760571 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 6_1:-760763 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_1:-760401 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_1:-760570 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 6_1:+760755 Msa0867670:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 6_1:+760785 Msa0867670:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 6_1:+760702 Msa0867670:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 6_1:+760604 Msa0867670:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_1:-760430 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 6_1:+760678 Msa0867670:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 6_1:-760768 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 6_1:-760896 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 6_1:-760926 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 6_1:-760675 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 6_1:-760793 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 6_1:-760512 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 6_1:-760877 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 6_1:-760765 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 6_1:-760874 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_1:-760533 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 6_1:-760663 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_1:-760433 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_1:-760585 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 6_1:-760735 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_1:-760477 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 6_1:-760923 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_1:+760555 Msa0867670:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 6_1:-760781 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 6_1:+760662 Msa0867670:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 6_1:-760524 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 6_1:-760693 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_1:-760588 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 6_1:-760719 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 6_1:-760716 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_1:+760471 Msa0867670:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 6_1:-760633 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr6_1:760528-760547 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - chr6_1:760453-760472 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - chr6_1:760527-760546 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - chr6_1:760529-760548 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr6_1:760536-760555 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + chr6_1:760555-760574 Msa0867670:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - chr6_1:760898-760917 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - chr6_1:760899-760918 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - chr6_1:760454-760473 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr6_1:760515-760534 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr6_1:760532-760551 Msa0867670:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr6_1:760553-760572 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - chr6_1:760620-760639 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - chr6_1:760719-760738 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - chr6_1:760722-760741 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - chr6_1:760738-760757 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr6_1:760436-760455 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr6_1:760441-760460 Msa0867670:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr6_1:760463-760482 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + chr6_1:760471-760490 Msa0867670:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - chr6_1:760621-760640 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - chr6_1:760678-760697 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + chr6_1:760678-760697 Msa0867670:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - chr6_1:760743-760762 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + chr6_1:760783-760802 Msa0867670:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - chr6_1:760796-760815 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - chr6_1:760820-760839 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr6_1:760573-760592 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr6_1:760574-760593 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr6_1:760573-760592 Msa0867670:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr6_1:760581-760600 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - chr6_1:760651-760670 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - chr6_1:760679-760698 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - chr6_1:760696-760715 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - chr6_1:760784-760803 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + chr6_1:760784-760803 Msa0867670:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + chr6_1:760785-760804 Msa0867670:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + chr6_1:760825-760844 Msa0867670:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - chr6_1:760838-760857 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - chr6_1:760839-760858 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - chr6_1:760843-760862 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - chr6_1:760844-760863 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - chr6_1:760877-760896 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - chr6_1:760880-760899 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - chr6_1:760892-760911 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr6_1:760433-760452 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr6_1:760491-760510 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - chr6_1:760606-760625 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + chr6_1:760604-760623 Msa0867670:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - chr6_1:760650-760669 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + chr6_1:760662-760681 Msa0867670:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - chr6_1:760666-760685 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - chr6_1:760705-760724 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + chr6_1:760702-760721 Msa0867670:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - chr6_1:760767-760786 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - chr6_1:760768-760787 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - chr6_1:760771-760790 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - chr6_1:760787-760806 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - chr6_1:760826-760845 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + chr6_1:760824-760843 Msa0867670:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - chr6_1:760840-760859 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - chr6_1:760872-760891 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - chr6_1:760873-760892 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr6_1:760480-760499 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr6_1:760478-760497 Msa0867670:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - chr6_1:760636-760655 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - chr6_1:760637-760656 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - chr6_1:760638-760657 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + chr6_1:760639-760658 Msa0867670:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + chr6_1:760640-760659 Msa0867670:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - chr6_1:760647-760666 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + chr6_1:760751-760770 Msa0867670:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + chr6_1:760752-760771 Msa0867670:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - chr6_1:760766-760785 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + chr6_1:760829-760848 Msa0867670:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + chr6_1:760861-760880 Msa0867670:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - chr6_1:760588-760607 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr6_1:760591-760610 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + chr6_1:760588-760607 Msa0867670:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + chr6_1:760632-760651 Msa0867670:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + chr6_1:760755-760774 Msa0867670:CDS 75.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 760403 760938 760403 ID=Msa0867670;Name=Msa0867670
chr6_1 mRNA 760403 760938 760403 ID=Msa0867670-mRNA-1;Parent=Msa0867670;Name=Msa0867670-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
chr6_1 exon 760403 760540 760403 ID=Msa0867670-mRNA-1:exon:223;Parent=Msa0867670-mRNA-1
chr6_1 exon 760554 760649 760554 ID=Msa0867670-mRNA-1:exon:224;Parent=Msa0867670-mRNA-1
chr6_1 exon 760654 760938 760654 ID=Msa0867670-mRNA-1:exon:225;Parent=Msa0867670-mRNA-1
chr6_1 CDS 760403 760540 760403 ID=Msa0867670-mRNA-1:cds;Parent=Msa0867670-mRNA-1
chr6_1 CDS 760554 760649 760554 ID=Msa0867670-mRNA-1:cds;Parent=Msa0867670-mRNA-1
chr6_1 CDS 760654 760938 760654 ID=Msa0867670-mRNA-1:cds;Parent=Msa0867670-mRNA-1
Gene Sequence

>Msa0867670

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0867670

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS