AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354770


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 tig0014543:-500843 Msa1354770:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0014543:+500956 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0014543:-501041 Msa1354770:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0014543:+500904 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0014543:-500699 Msa1354770:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0014543:-500731 Msa1354770:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0014543:-501004 Msa1354770:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0014543:-500698 Msa1354770:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0014543:+501031 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0014543:-500658 Msa1354770:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0014543:+501022 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0014543:-501088 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0014543:+500659 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0014543:+500742 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0014543:-500653 Msa1354770:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0014543:-500730 Msa1354770:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0014543:-500842 Msa1354770:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0014543:+501080 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0014543:+500647 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0014543:+500848 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0014543:+500665 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0014543:+500587 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0014543:-500894 Msa1354770:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0014543:+500847 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0014543:+500957 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0014543:+500641 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0014543:+500718 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0014543:+500613 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0014543:+501032 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0014543:+500593 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0014543:-500621 Msa1354770:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0014543:+500612 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0014543:+500642 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0014543:-500657 Msa1354770:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0014543:+500879 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0014543:+500780 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0014543:+500994 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0014543:+500645 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0014543:+500698 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0014543:+500806 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0014543:+500646 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0014543:+500911 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0014543:+500719 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0014543:+501081 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0014543:+500912 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0014543:-500727 Msa1354770:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0014543:-500697 Msa1354770:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0014543:-500780 Msa1354770:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0014543:-500878 Msa1354770:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0014543:+501052 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0014543:-500804 Msa1354770:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0014543:+500714 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0014543:+500586 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0014543:+500556 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0014543:+500807 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0014543:+500689 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0014543:+500970 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0014543:+500605 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0014543:+500717 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0014543:+500608 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0014543:+500949 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0014543:+500819 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0014543:+501049 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0014543:+500897 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0014543:+500747 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0014543:+501005 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0014543:+500559 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0014543:-500927 Msa1354770:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0014543:+500701 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0014543:-500820 Msa1354770:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0014543:+500958 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0014543:+500789 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0014543:+500894 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0014543:+500763 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0014543:+500766 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0014543:-501011 Msa1354770:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0014543:+500849 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + tig0014543:500691-500710 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + tig0014543:500616-500635 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + tig0014543:500690-500709 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + tig0014543:500692-500711 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + tig0014543:500699-500718 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - tig0014543:500718-500737 Msa1354770:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + tig0014543:501061-501080 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + tig0014543:501062-501081 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + tig0014543:500617-500636 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + tig0014543:500678-500697 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - tig0014543:500695-500714 Msa1354770:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + tig0014543:500716-500735 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + tig0014543:500783-500802 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + tig0014543:500882-500901 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + tig0014543:500885-500904 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + tig0014543:500901-500920 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + tig0014543:500599-500618 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - tig0014543:500604-500623 Msa1354770:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + tig0014543:500626-500645 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - tig0014543:500634-500653 Msa1354770:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + tig0014543:500784-500803 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + tig0014543:500841-500860 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - tig0014543:500841-500860 Msa1354770:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + tig0014543:500906-500925 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - tig0014543:500946-500965 Msa1354770:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + tig0014543:500959-500978 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + tig0014543:500983-501002 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + tig0014543:500736-500755 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + tig0014543:500737-500756 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - tig0014543:500736-500755 Msa1354770:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + tig0014543:500744-500763 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + tig0014543:500814-500833 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + tig0014543:500842-500861 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + tig0014543:500859-500878 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + tig0014543:500947-500966 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - tig0014543:500947-500966 Msa1354770:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - tig0014543:500948-500967 Msa1354770:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - tig0014543:500988-501007 Msa1354770:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + tig0014543:501001-501020 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + tig0014543:501002-501021 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + tig0014543:501006-501025 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + tig0014543:501007-501026 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + tig0014543:501040-501059 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + tig0014543:501043-501062 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + tig0014543:501055-501074 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + tig0014543:500596-500615 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + tig0014543:500654-500673 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + tig0014543:500769-500788 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - tig0014543:500767-500786 Msa1354770:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + tig0014543:500813-500832 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - tig0014543:500825-500844 Msa1354770:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + tig0014543:500829-500848 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + tig0014543:500868-500887 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - tig0014543:500865-500884 Msa1354770:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + tig0014543:500930-500949 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + tig0014543:500931-500950 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + tig0014543:500934-500953 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + tig0014543:500950-500969 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + tig0014543:500989-501008 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - tig0014543:500987-501006 Msa1354770:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + tig0014543:501003-501022 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + tig0014543:501035-501054 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + tig0014543:501036-501055 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + tig0014543:500643-500662 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - tig0014543:500641-500660 Msa1354770:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + tig0014543:500799-500818 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + tig0014543:500800-500819 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + tig0014543:500801-500820 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - tig0014543:500802-500821 Msa1354770:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - tig0014543:500803-500822 Msa1354770:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + tig0014543:500810-500829 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - tig0014543:500914-500933 Msa1354770:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - tig0014543:500915-500934 Msa1354770:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + tig0014543:500929-500948 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - tig0014543:500992-501011 Msa1354770:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - tig0014543:501024-501043 Msa1354770:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + tig0014543:500751-500770 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + tig0014543:500754-500773 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - tig0014543:500751-500770 Msa1354770:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - tig0014543:500795-500814 Msa1354770:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - tig0014543:500918-500937 Msa1354770:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 500566 501101 500566 ID=Msa1354770;Name=Msa1354770
tig0014543 mRNA 500566 501101 500566 ID=Msa1354770-mRNA-1;Parent=Msa1354770;Name=Msa1354770-mRNA-1;_AED=0.42;_eAED=0.45;_QI=0|0|0|1|0|0|3|0|173
tig0014543 exon 500964 501101 500964 ID=Msa1354770-mRNA-1:exon:9251;Parent=Msa1354770-mRNA-1
tig0014543 exon 500855 500950 500855 ID=Msa1354770-mRNA-1:exon:9250;Parent=Msa1354770-mRNA-1
tig0014543 exon 500566 500850 500566 ID=Msa1354770-mRNA-1:exon:9249;Parent=Msa1354770-mRNA-1
tig0014543 CDS 500964 501101 500964 ID=Msa1354770-mRNA-1:cds;Parent=Msa1354770-mRNA-1
tig0014543 CDS 500855 500950 500855 ID=Msa1354770-mRNA-1:cds;Parent=Msa1354770-mRNA-1
tig0014543 CDS 500566 500850 500566 ID=Msa1354770-mRNA-1:cds;Parent=Msa1354770-mRNA-1
Gene Sequence

>Msa1354770

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1354770

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS