AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0789870

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0789870 MtrunA17_Chr1g0195851 90.206 194 11 2 1 186 1 194 3.89e-118 332
Msa0789870 MtrunA17_Chr2g0296321 69.231 130 36 2 24 153 56 181 2.28e-59 186
Msa0789870 MtrunA17_Chr4g0067091 79.412 102 21 0 24 125 12 113 1.08e-58 182
Msa0789870 MtrunA17_Chr1g0191981 74.000 100 26 0 34 133 4 103 5.00e-53 165
Msa0789870 MtrunA17_Chr4g0076321 63.866 119 39 2 35 153 20 134 3.49e-52 163
Msa0789870 MtrunA17_Chr2g0290491 69.725 109 27 1 33 135 16 124 9.86e-52 163
Msa0789870 MtrunA17_Chr8g0384451 72.277 101 28 0 33 133 39 139 1.30e-51 164
Msa0789870 MtrunA17_Chr3g0102351 71.875 96 27 0 33 128 26 121 1.67e-50 161
Msa0789870 MtrunA17_Chr7g0263601 62.963 108 40 0 32 139 24 131 3.93e-50 159
Msa0789870 MtrunA17_Chr5g0446491 71.875 96 27 0 33 128 22 117 9.87e-50 159
Msa0789870 MtrunA17_Chr8g0382931 71.429 98 28 0 33 130 27 124 4.75e-49 157
Msa0789870 MtrunA17_Chr1g0185911 70.526 95 28 0 33 127 28 122 1.95e-48 155
Msa0789870 MtrunA17_Chr4g0076381 63.462 104 37 1 26 128 49 152 3.60e-48 157
Msa0789870 MtrunA17_Chr1g0165041 56.604 106 46 0 32 137 4 109 1.18e-42 141
Msa0789870 MtrunA17_Chr1g0159271 43.956 91 51 0 48 138 1 91 1.39e-22 87.4
Msa0789870 MtrunA17_Chr5g0446601 44.565 92 51 0 31 122 21 112 3.07e-21 86.3
Msa0789870 MtrunA17_Chr1g0159291 40.000 80 48 0 39 118 7 86 1.57e-18 76.3
Msa0789870 MtrunA17_Chr2g0307551 37.179 78 49 0 35 112 12 89 2.86e-17 75.1
Msa0789870 MtrunA17_Chr1g0158951 46.875 64 34 0 64 127 19 82 2.97e-16 70.9
Msa0789870 MtrunA17_Chr4g0062271 32.051 78 53 0 35 112 12 89 2.95e-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
Msa0789870 AT2G47810.1 77.451 102 23 0 31 132 48 149 3.82e-58 180
Msa0789870 AT5G47640.1 66.379 116 36 1 33 145 26 141 1.56e-53 169
Msa0789870 AT1G09030.1 56.738 141 56 1 32 172 1 136 1.35e-52 165
Msa0789870 AT4G14540.1 75.000 96 24 0 33 128 20 115 5.37e-52 164
Msa0789870 AT2G38880.3 65.179 112 37 1 32 143 19 128 1.70e-51 162
Msa0789870 AT2G38880.2 65.179 112 37 1 32 143 19 128 1.85e-51 162
Msa0789870 AT2G38880.1 65.179 112 37 1 32 143 19 128 1.85e-51 162
Msa0789870 AT2G38880.5 65.179 112 37 1 32 143 19 128 1.85e-51 162
Msa0789870 AT2G13570.1 73.267 101 27 0 33 133 35 135 2.53e-51 164
Msa0789870 AT2G38880.7 65.179 112 35 1 32 143 19 126 1.96e-50 159
Msa0789870 AT3G53340.5 50.000 150 67 2 32 181 27 168 2.95e-50 160
Msa0789870 AT3G53340.1 50.000 150 67 2 32 181 27 168 2.95e-50 160
Msa0789870 AT2G37060.2 64.486 107 38 0 32 138 28 134 1.34e-49 158
Msa0789870 AT2G37060.3 64.486 107 38 0 32 138 28 134 1.34e-49 158
Msa0789870 AT2G37060.1 64.486 107 38 0 32 138 28 134 1.34e-49 158
Msa0789870 AT2G38880.4 73.118 93 25 0 32 124 19 111 2.29e-49 155
Msa0789870 AT2G38880.11 73.118 93 25 0 32 124 19 111 6.05e-49 156
Msa0789870 AT2G38880.8 73.118 93 25 0 32 124 19 111 6.05e-49 156
Msa0789870 AT3G53340.4 72.043 93 26 0 32 124 27 119 6.61e-49 155
Msa0789870 AT2G38880.9 73.118 93 25 0 32 124 19 111 8.84e-49 155
Msa0789870 AT2G38880.10 73.118 93 25 0 32 124 19 111 8.84e-49 155
Msa0789870 AT2G38880.6 73.118 93 25 0 32 124 19 111 8.84e-49 155
Msa0789870 AT3G53340.3 69.697 99 29 1 32 130 27 124 8.87e-49 155
Msa0789870 AT3G53340.2 69.697 99 29 1 32 130 27 124 8.87e-49 155
Msa0789870 AT5G47670.2 57.273 110 47 0 32 141 27 136 1.66e-46 152
Msa0789870 AT5G47670.1 56.757 111 48 0 31 141 55 165 4.99e-46 151
Msa0789870 AT5G47670.3 56.757 111 48 0 31 141 55 165 4.99e-46 151
Msa0789870 AT1G21970.1 50.862 116 57 0 19 134 44 159 1.42e-41 140
Msa0789870 AT5G23090.4 32.432 111 72 2 35 142 12 122 1.55e-17 75.9
Msa0789870 AT5G23090.5 38.462 78 48 0 35 112 12 89 1.28e-16 73.6
Msa0789870 AT5G23090.2 38.462 78 48 0 35 112 12 89 1.28e-16 73.6
Msa0789870 AT5G23090.1 38.462 78 48 0 35 112 12 89 1.28e-16 73.6
Msa0789870 AT5G08190.2 32.292 96 63 1 35 128 12 107 4.99e-16 72.0
Msa0789870 AT5G08190.1 34.615 78 51 0 35 112 12 89 6.74e-15 69.3

Find 34 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCTTCTATGTTCAATAAT+AGG 0.214525 5_3:+517034 Msa0789870:CDS
GATGATGTTTGTTGGGCTTT+GGG 0.221205 5_3:+516811 Msa0789870:CDS
TGATGTTGTTACCCTTATTT+TGG 0.229982 5_3:-516915 None:intergenic
TGATGATGTTTGTTGGGCTT+TGG 0.269661 5_3:+516810 Msa0789870:CDS
GGAAAGAGGGAACCAAAATA+AGG 0.312778 5_3:+516903 Msa0789870:CDS
TGTTGGGCTTTGGGGACACT+AGG 0.347462 5_3:+516820 Msa0789870:CDS
AAAGGTATTTGTATAAGTAT+AGG 0.352771 5_3:+516869 Msa0789870:CDS
TTTGTATAAGTATAGGGAAT+TGG 0.359649 5_3:+516876 Msa0789870:CDS
GAAGCAACATTCACTTTCCT+TGG 0.401544 5_3:-517012 None:intergenic
ATCCGACCAACATTAGCTAT+TGG 0.403010 5_3:-516643 None:intergenic
AAGGTATTTGTATAAGTATA+GGG 0.417767 5_3:+516870 Msa0789870:CDS
GAATGGTGATGATGTTTGTT+GGG 0.429389 5_3:+516804 Msa0789870:CDS
GAAACATATGATTATGAAGA+TGG 0.453321 5_3:+516976 Msa0789870:CDS
ACATGGGTGATAACAACAAA+GGG 0.487792 5_3:+516524 None:intergenic
GAAAGAGGGAACCAAAATAA+GGG 0.501997 5_3:+516904 Msa0789870:CDS
GTTGGGCTTTGGGGACACTA+GGG 0.503961 5_3:+516821 Msa0789870:CDS
ATGATGTTTGTTGGGCTTTG+GGG 0.505210 5_3:+516812 Msa0789870:CDS
TGAATGGTGATGATGTTTGT+TGG 0.510123 5_3:+516803 Msa0789870:CDS
CTCTGAGACACACTCTTGCA+TGG 0.513185 5_3:-516719 None:intergenic
GAGAAGCGCAAGACAGTGAA+TGG 0.520201 5_3:+516787 Msa0789870:CDS
AGGGAATTGGATGCGGAAAG+AGG 0.523773 5_3:+516889 Msa0789870:CDS
TTGCTTCCAATAGCTAATGT+TGG 0.538809 5_3:+516637 Msa0789870:CDS
TTCAAAATCCCCTTGACTGA+AGG 0.540445 5_3:-517065 None:intergenic
GGGAATTGGATGCGGAAAGA+GGG 0.541973 5_3:+516890 Msa0789870:CDS
CCTATTATTGAACATAGAAG+AGG 0.550260 5_3:-517034 None:intergenic
TAAGTATAGGGAATTGGATG+CGG 0.557603 5_3:+516882 Msa0789870:CDS
ATTACGCTGAGCCACTCAAA+AGG 0.563009 5_3:+516851 Msa0789870:CDS
GAACAGTGACCTTCAGTCAA+GGG 0.574883 5_3:+517056 Msa0789870:CDS
TTCCAATAGCTAATGTTGGT+CGG 0.585707 5_3:+516641 Msa0789870:CDS
ATGGTAAGTCACAAACTCCA+AGG 0.613914 5_3:+516995 Msa0789870:CDS
AACAGTGACCTTCAGTCAAG+GGG 0.614235 5_3:+517057 Msa0789870:CDS
AACATGGGTGATAACAACAA+AGG 0.619511 5_3:+516523 None:intergenic
GGAACAGTGACCTTCAGTCA+AGG 0.622121 5_3:+517055 Msa0789870:CDS
AGCATCTGACAAGTGTCACA+AGG 0.642405 5_3:+516765 Msa0789870:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAGGTATTTGTATAAGTAT+AGG + chr5_3:516869-516888 Msa0789870:CDS 20.0%
!!! AAGGTATTTGTATAAGTATA+GGG + chr5_3:516870-516889 Msa0789870:CDS 20.0%
!!! TCTTTAGAGATTTTTGCATT+TGG - chr5_3:516688-516707 None:intergenic 25.0%
!! TTATACAAATACCTTTTGAG+TGG - chr5_3:516865-516884 None:intergenic 25.0%
! TTTGTATAAGTATAGGGAAT+TGG + chr5_3:516876-516895 Msa0789870:CDS 25.0%
! GAAACATATGATTATGAAGA+TGG + chr5_3:516976-516995 Msa0789870:CDS 25.0%
! TTAGAGATTTTTGCATTTGG+TGG - chr5_3:516685-516704 None:intergenic 30.0%
!!! GAGTTTGTTAGTTTTGTAAC+TGG + chr5_3:516739-516758 Msa0789870:CDS 30.0%
!! TGATGTTGTTACCCTTATTT+TGG - chr5_3:516918-516937 None:intergenic 30.0%
CCTATTATTGAACATAGAAG+AGG - chr5_3:517037-517056 None:intergenic 30.0%
CCTCTTCTATGTTCAATAAT+AGG + chr5_3:517034-517053 Msa0789870:CDS 30.0%
TTGCTTCCAATAGCTAATGT+TGG + chr5_3:516637-516656 Msa0789870:CDS 35.0%
TTCCAATAGCTAATGTTGGT+CGG + chr5_3:516641-516660 Msa0789870:CDS 35.0%
! TGAATGGTGATGATGTTTGT+TGG + chr5_3:516803-516822 Msa0789870:CDS 35.0%
! GAATGGTGATGATGTTTGTT+GGG + chr5_3:516804-516823 Msa0789870:CDS 35.0%
TAAGTATAGGGAATTGGATG+CGG + chr5_3:516882-516901 Msa0789870:CDS 35.0%
GAAAGAGGGAACCAAAATAA+GGG + chr5_3:516904-516923 Msa0789870:CDS 35.0%
ATCCGACCAACATTAGCTAT+TGG - chr5_3:516646-516665 None:intergenic 40.0%
! TGATGATGTTTGTTGGGCTT+TGG + chr5_3:516810-516829 Msa0789870:CDS 40.0%
! GATGATGTTTGTTGGGCTTT+GGG + chr5_3:516811-516830 Msa0789870:CDS 40.0%
! ATGATGTTTGTTGGGCTTTG+GGG + chr5_3:516812-516831 Msa0789870:CDS 40.0%
GGAAAGAGGGAACCAAAATA+AGG + chr5_3:516903-516922 Msa0789870:CDS 40.0%
ATGGTAAGTCACAAACTCCA+AGG + chr5_3:516995-517014 Msa0789870:CDS 40.0%
GAAGCAACATTCACTTTCCT+TGG - chr5_3:517015-517034 None:intergenic 40.0%
AGCATCTGACAAGTGTCACA+AGG + chr5_3:516765-516784 Msa0789870:CDS 45.0%
ATTACGCTGAGCCACTCAAA+AGG + chr5_3:516851-516870 Msa0789870:CDS 45.0%
GAACAGTGACCTTCAGTCAA+GGG + chr5_3:517056-517075 Msa0789870:CDS 45.0%
AACAGTGACCTTCAGTCAAG+GGG + chr5_3:517057-517076 Msa0789870:CDS 45.0%
!! CTCTGAGACACACTCTTGCA+TGG - chr5_3:516722-516741 None:intergenic 50.0%
! GAGAAGCGCAAGACAGTGAA+TGG + chr5_3:516787-516806 Msa0789870:CDS 50.0%
AGGGAATTGGATGCGGAAAG+AGG + chr5_3:516889-516908 Msa0789870:CDS 50.0%
GGGAATTGGATGCGGAAAGA+GGG + chr5_3:516890-516909 Msa0789870:CDS 50.0%
GGAACAGTGACCTTCAGTCA+AGG + chr5_3:517055-517074 Msa0789870:CDS 50.0%
!! TGTTGGGCTTTGGGGACACT+AGG + chr5_3:516820-516839 Msa0789870:CDS 55.0%
!! GTTGGGCTTTGGGGACACTA+GGG + chr5_3:516821-516840 Msa0789870:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 516526 517086 516526 ID=Msa0789870;Name=Msa0789870
chr5_3 mRNA 516526 517086 516526 ID=Msa0789870-mRNA-1;Parent=Msa0789870;Name=Msa0789870-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|186
chr5_3 exon 516526 517086 516526 ID=Msa0789870-mRNA-1:exon:107;Parent=Msa0789870-mRNA-1
chr5_3 CDS 516526 517086 516526 ID=Msa0789870-mRNA-1:cds;Parent=Msa0789870-mRNA-1
Gene Sequence

>Msa0789870

ATGGGTGATAACAACAAAGGGAAACTAGTCTCAGATAGAGAAGTCTTTAAGTACAACACAAATCTCACATCTCATGAGCAAGATCATGAAGTAATCAAAGAGCAAGATCGTTTGCTTCCAATAGCTAATGTTGGTCGGATCATGAAACAAATCTTGCCACCAAATGCAAAAATCTCTAAAGATGCTAAAGAAACCATGCAAGAGTGTGTCTCAGAGTTTGTTAGTTTTGTAACTGGTGAAGCATCTGACAAGTGTCACAAGGAGAAGCGCAAGACAGTGAATGGTGATGATGTTTGTTGGGCTTTGGGGACACTAGGGTTTGATGATTACGCTGAGCCACTCAAAAGGTATTTGTATAAGTATAGGGAATTGGATGCGGAAAGAGGGAACCAAAATAAGGGTAACAACATCAACAACAACAACAGTGATGAAATTGAAAACAATATTAATGAAACATATGATTATGAAGATGGTAAGTCACAAACTCCAAGGAAAGTGAATGTTGCTTCCTCTTCTATGTTCAATAATAGGAACAGTGACCTTCAGTCAAGGGGATTTTGA
Protein sequence

>Msa0789870

MGDNNKGKLVSDREVFKYNTNLTSHEQDHEVIKEQDRLLPIANVGRIMKQILPPNAKISKDAKETMQECVSEFVSFVTGEASDKCHKEKRKTVNGDDVCWALGTLGFDDYAEPLKRYLYKYRELDAERGNQNKGNNINNNNSDEIENNINETYDYEDGKSQTPRKVNVASSSMFNNRNSDLQSRGF*