AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0867740

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0867740 MtrunA17_Chr4g0031671 99.324 148 1 0 1 148 1 148 3.04e-102 289
Msa0867740 MtrunA17_Chr4g0031631 99.324 148 1 0 1 148 1 148 3.04e-102 289
Msa0867740 MtrunA17_Chr4g0030941 99.324 148 1 0 1 148 1 148 3.04e-102 289
Msa0867740 MtrunA17_Chr4g0035061 99.324 148 1 0 1 148 1 148 6.48e-102 288
Msa0867740 MtrunA17_Chr4g0035631 99.324 148 1 0 1 148 1 148 6.48e-102 288
Msa0867740 MtrunA17_Chr4g0031061 98.649 148 2 0 1 148 1 148 2.95e-101 286
Msa0867740 MtrunA17_Chr4g0032321 98.649 148 2 0 1 148 1 148 2.95e-101 286
Msa0867740 MtrunA17_Chr4g0035071 97.973 148 3 0 1 148 1 148 3.19e-100 284
Msa0867740 MtrunA17_Chr4g0030981 98.649 148 1 1 1 148 1 147 8.74e-100 283
Msa0867740 MtrunA17_Chr4g0030951 99.306 144 1 0 5 148 4 147 3.68e-99 281
Msa0867740 MtrunA17_Chr4g0046191 93.919 148 4 1 1 148 1 143 6.30e-89 255
Msa0867740 MtrunA17_Chr1g0197451 88.514 148 6 3 1 148 1 137 1.28e-78 229
Msa0867740 MtrunA17_Chr1g0198251 87.838 148 7 3 1 148 1 137 6.33e-78 227
Msa0867740 MtrunA17_Chr1g0182361 92.793 111 4 1 38 148 30 136 2.58e-64 192
Msa0867740 MtrunA17_Chr7g0263031 92.793 111 5 1 38 148 31 138 4.76e-64 192
Msa0867740 MtrunA17_Chr2g0320511 61.798 89 34 0 59 147 136 224 3.67e-37 127
Msa0867740 MtrunA17_Chr8g0368781 68.817 93 21 3 15 107 4 88 2.70e-34 115
Msa0867740 MtrunA17_Chr4g0031051 90.196 51 5 0 86 136 1 51 3.98e-27 95.9
Msa0867740 MtrunA17_Chr7g0228831 92.500 40 3 0 57 96 42 81 7.48e-23 86.7
Msa0867740 MtrunA17_Chr4g0014401 36.792 106 63 2 31 132 5 110 1.32e-13 63.5
Msa0867740 MtrunA17_Chr4g0075141 36.905 84 52 1 64 146 34 117 5.80e-12 59.3
Msa0867740 MtrunA17_Chr4g0062361 33.010 103 61 4 33 134 4 99 2.76e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0867740 AT3G45980.1 88.742 151 13 2 1 148 1 150 1.47e-83 242
Msa0867740 AT2G28720.1 86.093 151 18 1 1 148 1 151 9.70e-81 235
Msa0867740 AT1G07790.1 86.928 153 10 3 1 148 1 148 7.69e-80 233
Msa0867740 AT5G59910.1 91.176 136 9 2 13 148 18 150 2.66e-77 226
Msa0867740 AT3G46030.1 94.444 126 6 1 23 148 21 145 8.66e-76 222
Msa0867740 AT2G37470.1 82.432 148 15 3 1 147 1 138 6.01e-71 210
Msa0867740 AT3G53650.1 81.208 149 16 3 1 148 1 138 4.61e-69 205
Msa0867740 AT5G22880.1 87.586 145 16 2 4 148 3 145 4.25e-67 200
Msa0867740 AT5G02570.1 79.730 148 14 1 1 148 1 132 9.71e-67 199
Msa0867740 AT3G09480.1 84.127 126 16 1 23 148 5 126 2.13e-62 187
Msa0867740 AT1G08170.1 61.176 85 33 0 61 145 151 235 2.98e-37 127

Find 46 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCTAAGAGCTTGTGAATT+TGG 0.203095 6_1:-813351 None:intergenic
GGTAGCTTCTTTCCAGCCTT+TGG 0.299167 6_1:-813017 None:intergenic
GCTTGTTCTGCCCGGTGAAT+TGG 0.304089 6_1:+813292 Msa0867740:CDS
GCTGGCTTCTTCTCTCCCTT+TGG 0.362568 6_1:-812930 None:intergenic
CTTGTTGTACCTAGCGAGTC+TGG 0.384866 6_1:-813228 None:intergenic
TCTGCGGGTTTCTTCTCTGC+TGG 0.399254 6_1:-812948 None:intergenic
GCCTTTGGCTTCTTCTCCGC+CGG 0.402654 6_1:-813002 None:intergenic
GCGGCTGAACCACCTTCCTT+TGG 0.410543 6_1:-813038 None:intergenic
GTGGATTTCTTCTCCTCTGC+GGG 0.431011 6_1:-812963 None:intergenic
TCTCTTCTTCTTCTTGTCTC+CGG 0.444808 6_1:-813060 None:intergenic
ACCCTCAGAAACAGCATGCT+TGG 0.462043 6_1:-813315 None:intergenic
TTGCTTGAGATACCAATGTC+CGG 0.465790 6_1:-813143 None:intergenic
AGCATGCTTGGCCAATTCAC+CGG 0.471051 6_1:-813303 None:intergenic
GGGAAATTCAGACCGCGGTC+AGG 0.471115 6_1:+813270 Msa0867740:CDS
TGTGAATTTGGTCACAGCCT+TGG 0.493306 6_1:-813339 None:intergenic
AATTCCTTCAATGGCGCCAA+AGG 0.495983 6_1:+812914 None:intergenic
GCGGAGAAGAAGCCAAAGGC+TGG 0.504484 6_1:+813005 Msa0867740:CDS
AAGGAAGGTGGTTCAGCCGC+CGG 0.504946 6_1:+813041 Msa0867740:CDS
TGCTTGAGATACCAATGTCC+GGG 0.518516 6_1:-813142 None:intergenic
GCATGCTTGGCCAATTCACC+GGG 0.525255 6_1:-813302 None:intergenic
TGGTATCTCAAGCAAAGCCA+TGG 0.533917 6_1:+813151 Msa0867740:CDS
GCCAAGCATGCTGTTTCTGA+GGG 0.538001 6_1:+813314 Msa0867740:CDS
GGCCAAGCATGCTGTTTCTG+AGG 0.538906 6_1:+813313 Msa0867740:CDS
CACAGTCGCTGAGAAAGCTC+CGG 0.552253 6_1:+812983 Msa0867740:CDS
GCGGTCAGGCTTGTTCTGCC+CGG 0.555879 6_1:+813284 Msa0867740:CDS
ATTCCTTCAATGGCGCCAAA+GGG 0.555903 6_1:+812915 None:intergenic
ATTTCCCTCGAAGTGATCGT+CGG 0.569915 6_1:-813254 None:intergenic
TGCTGTTTCTGAGGGTACCA+AGG 0.572597 6_1:+813322 Msa0867740:CDS
CTTCTTCTTCTTGTCTCCGG+CGG 0.574610 6_1:-813057 None:intergenic
AAACAAGTTCACCCGGACAT+TGG 0.574952 6_1:+813131 Msa0867740:CDS
AGAAGCCGACGATCACTTCG+AGG 0.586465 6_1:+813249 Msa0867740:CDS
AAGAATCTTCCAGACTCGCT+AGG 0.594905 6_1:+813219 Msa0867740:CDS
TGTGGATTTCTTCTCCTCTG+CGG 0.602479 6_1:-812964 None:intergenic
GGAAAGAAGCTACCAAAGGA+AGG 0.624050 6_1:+813026 Msa0867740:CDS
CGGAGCTTTCTCAGCGACTG+TGG 0.628186 6_1:-812982 None:intergenic
GGCTGGAAAGAAGCTACCAA+AGG 0.634160 6_1:+813022 Msa0867740:CDS
AGTTCTGAAACAAGTTCACC+CGG 0.635033 6_1:+813124 Msa0867740:CDS
AGTCGCTGAGAAAGCTCCGG+CGG 0.656886 6_1:+812986 Msa0867740:CDS
GGTATCTCAAGCAAAGCCAT+GGG 0.659631 6_1:+813152 Msa0867740:CDS
GAAGCCGACGATCACTTCGA+GGG 0.660226 6_1:+813250 Msa0867740:CDS
AAGAAGCTACCAAAGGAAGG+TGG 0.666846 6_1:+813029 Msa0867740:CDS
TCCGGCGGAGAAGAAGCCAA+AGG 0.682003 6_1:+813001 Msa0867740:CDS
GAAACTGTTCATGATACCCA+TGG 0.683953 6_1:-813168 None:intergenic
GGGCAGAACAAGCCTGACCG+CGG 0.695125 6_1:-813282 None:intergenic
AGCAGAGAAGAAACCCGCAG+AGG 0.698236 6_1:+812950 Msa0867740:CDS
TTCGAGGGAAATTCAGACCG+CGG 0.709650 6_1:+813265 Msa0867740:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCTCTTCTTCTTCTTGTCTC+CGG - chr6_1:813063-813082 None:intergenic 40.0%
!! AGTTCTGAAACAAGTTCACC+CGG + chr6_1:813124-813143 Msa0867740:CDS 40.0%
TTGCTTGAGATACCAATGTC+CGG - chr6_1:813146-813165 None:intergenic 40.0%
GAAACTGTTCATGATACCCA+TGG - chr6_1:813171-813190 None:intergenic 40.0%
TGTGGATTTCTTCTCCTCTG+CGG - chr6_1:812967-812986 None:intergenic 45.0%
GGAAAGAAGCTACCAAAGGA+AGG + chr6_1:813026-813045 Msa0867740:CDS 45.0%
AAGAAGCTACCAAAGGAAGG+TGG + chr6_1:813029-813048 Msa0867740:CDS 45.0%
AAACAAGTTCACCCGGACAT+TGG + chr6_1:813131-813150 Msa0867740:CDS 45.0%
TGCTTGAGATACCAATGTCC+GGG - chr6_1:813145-813164 None:intergenic 45.0%
TGGTATCTCAAGCAAAGCCA+TGG + chr6_1:813151-813170 Msa0867740:CDS 45.0%
GGTATCTCAAGCAAAGCCAT+GGG + chr6_1:813152-813171 Msa0867740:CDS 45.0%
AAGAATCTTCCAGACTCGCT+AGG + chr6_1:813219-813238 Msa0867740:CDS 45.0%
ATTTCCCTCGAAGTGATCGT+CGG - chr6_1:813257-813276 None:intergenic 45.0%
TGTGAATTTGGTCACAGCCT+TGG - chr6_1:813342-813361 None:intergenic 45.0%
GTGGATTTCTTCTCCTCTGC+GGG - chr6_1:812966-812985 None:intergenic 50.0%
GGTAGCTTCTTTCCAGCCTT+TGG - chr6_1:813020-813039 None:intergenic 50.0%
GGCTGGAAAGAAGCTACCAA+AGG + chr6_1:813022-813041 Msa0867740:CDS 50.0%
CTTCTTCTTCTTGTCTCCGG+CGG - chr6_1:813060-813079 None:intergenic 50.0%
! CTTGTTGTACCTAGCGAGTC+TGG - chr6_1:813231-813250 None:intergenic 50.0%
TTCGAGGGAAATTCAGACCG+CGG + chr6_1:813265-813284 Msa0867740:CDS 50.0%
AGCATGCTTGGCCAATTCAC+CGG - chr6_1:813306-813325 None:intergenic 50.0%
!! GCCAAGCATGCTGTTTCTGA+GGG + chr6_1:813314-813333 Msa0867740:CDS 50.0%
ACCCTCAGAAACAGCATGCT+TGG - chr6_1:813318-813337 None:intergenic 50.0%
!! TGCTGTTTCTGAGGGTACCA+AGG + chr6_1:813322-813341 Msa0867740:CDS 50.0%
! GCTGGCTTCTTCTCTCCCTT+TGG - chr6_1:812933-812952 None:intergenic 55.0%
TCTGCGGGTTTCTTCTCTGC+TGG - chr6_1:812951-812970 None:intergenic 55.0%
AGCAGAGAAGAAACCCGCAG+AGG + chr6_1:812950-812969 Msa0867740:CDS 55.0%
CACAGTCGCTGAGAAAGCTC+CGG + chr6_1:812983-813002 Msa0867740:CDS 55.0%
AGAAGCCGACGATCACTTCG+AGG + chr6_1:813249-813268 Msa0867740:CDS 55.0%
GAAGCCGACGATCACTTCGA+GGG + chr6_1:813250-813269 Msa0867740:CDS 55.0%
GCTTGTTCTGCCCGGTGAAT+TGG + chr6_1:813292-813311 Msa0867740:CDS 55.0%
GCATGCTTGGCCAATTCACC+GGG - chr6_1:813305-813324 None:intergenic 55.0%
!! GGCCAAGCATGCTGTTTCTG+AGG + chr6_1:813313-813332 Msa0867740:CDS 55.0%
CGGAGCTTTCTCAGCGACTG+TGG - chr6_1:812985-813004 None:intergenic 60.0%
AGTCGCTGAGAAAGCTCCGG+CGG + chr6_1:812986-813005 Msa0867740:CDS 60.0%
TCCGGCGGAGAAGAAGCCAA+AGG + chr6_1:813001-813020 Msa0867740:CDS 60.0%
! GCCTTTGGCTTCTTCTCCGC+CGG - chr6_1:813005-813024 None:intergenic 60.0%
GCGGAGAAGAAGCCAAAGGC+TGG + chr6_1:813005-813024 Msa0867740:CDS 60.0%
GCGGCTGAACCACCTTCCTT+TGG - chr6_1:813041-813060 None:intergenic 60.0%
AAGGAAGGTGGTTCAGCCGC+CGG + chr6_1:813041-813060 Msa0867740:CDS 60.0%
GGGAAATTCAGACCGCGGTC+AGG + chr6_1:813270-813289 Msa0867740:CDS 60.0%
GGGCAGAACAAGCCTGACCG+CGG - chr6_1:813285-813304 None:intergenic 65.0%
! GCGGTCAGGCTTGTTCTGCC+CGG + chr6_1:813284-813303 Msa0867740:CDS 65.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 812924 813370 812924 ID=Msa0867740;Name=Msa0867740
chr6_1 mRNA 812924 813370 812924 ID=Msa0867740-mRNA-1;Parent=Msa0867740;Name=Msa0867740-mRNA-1;_AED=0.21;_eAED=0.21;_QI=0|-1|0|1|-1|1|1|0|148
chr6_1 exon 812924 813370 812924 ID=Msa0867740-mRNA-1:exon:234;Parent=Msa0867740-mRNA-1
chr6_1 CDS 812924 813370 812924 ID=Msa0867740-mRNA-1:cds;Parent=Msa0867740-mRNA-1
Gene Sequence

>Msa0867740

ATGGCGCCAAAGGGAGAGAAGAAGCCAGCAGAGAAGAAACCCGCAGAGGAGAAGAAATCCACAGTCGCTGAGAAAGCTCCGGCGGAGAAGAAGCCAAAGGCTGGAAAGAAGCTACCAAAGGAAGGTGGTTCAGCCGCCGGAGACAAGAAGAAGAAGAGAAGCAAGAAGAGCGTTGAAACATACAAGATTTACATCTTCAAAGTTCTGAAACAAGTTCACCCGGACATTGGTATCTCAAGCAAAGCCATGGGTATCATGAACAGTTTCATCAACGACATCTTCGAGAAGCTCGCTCAAGAATCTTCCAGACTCGCTAGGTACAACAAGAAGCCGACGATCACTTCGAGGGAAATTCAGACCGCGGTCAGGCTTGTTCTGCCCGGTGAATTGGCCAAGCATGCTGTTTCTGAGGGTACCAAGGCTGTGACCAAATTCACAAGCTCTTAG
Protein sequence

>Msa0867740

MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGDKKKKRSKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS*