AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0221820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0221820 MtrunA17_Chr2g0326411 98.551 207 3 0 1 207 87 293 2.16e-147 411
Msa0221820 MtrunA17_Chr4g0029441 68.500 200 55 3 1 199 91 283 2.40e-86 256
Msa0221820 MtrunA17_Chr4g0029501 67.327 202 58 3 1 200 91 286 1.01e-85 255
Msa0221820 MtrunA17_Chr4g0026611 67.500 200 62 1 1 200 95 291 5.60e-82 245
Msa0221820 MtrunA17_Chr2g0284411 53.571 196 79 3 1 195 86 270 1.00e-61 193
Msa0221820 MtrunA17_Chr2g0284431 52.217 203 85 3 1 202 107 298 2.23e-61 193
Msa0221820 MtrunA17_Chr2g0284451 46.635 208 100 3 1 202 89 291 2.67e-56 180
Msa0221820 MtrunA17_Chr8g0379611 62.308 130 49 0 1 130 95 224 4.63e-53 172
Msa0221820 MtrunA17_Chr2g0326421 50.877 171 84 0 1 171 87 257 8.06e-52 168
Msa0221820 MtrunA17_Chr8g0379621 60.902 133 48 3 1 130 111 242 1.94e-48 160
Msa0221820 MtrunA17_Chr8g0379631 60.902 133 48 3 1 130 111 242 1.94e-48 160
Msa0221820 MtrunA17_Chr4g0029431 59.231 130 53 0 1 130 85 214 3.35e-48 159
Msa0221820 MtrunA17_Chr4g0029331 50.314 159 63 2 1 159 80 222 4.81e-45 150
Msa0221820 MtrunA17_Chr2g0326431 53.846 130 59 1 1 130 59 187 8.84e-45 149
Msa0221820 MtrunA17_Chr7g0263981 46.875 128 66 2 1 127 58 184 5.01e-32 116
Msa0221820 MtrunA17_Chr2g0325021 37.662 154 89 1 19 165 73 226 9.06e-25 97.4
Msa0221820 MtrunA17_Chr7g0246041 37.037 135 85 0 21 155 217 351 4.37e-17 78.6
Msa0221820 MtrunA17_Chr5g0448001 33.333 141 86 4 21 158 85 220 3.06e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0221820 AT5G60490.1 50.000 130 63 2 1 129 57 185 3.62e-36 127
Msa0221820 AT5G03170.1 44.295 149 74 2 1 148 54 194 1.05e-35 126
Msa0221820 AT5G44130.1 35.165 182 101 3 1 180 54 220 6.13e-25 98.2
Msa0221820 AT2G20520.1 40.000 150 82 4 1 147 56 200 3.46e-22 90.9
Msa0221820 AT1G03870.1 34.637 179 106 4 1 173 57 230 5.25e-22 90.5
Msa0221820 AT3G46550.1 33.333 120 75 4 18 132 239 358 1.79e-11 62.8
Msa0221820 AT3G60900.1 28.777 139 93 1 21 159 223 355 9.93e-11 60.8

Find 47 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCCAGCAAGTGTTCTTAC+AGG 0.276561 2_1:+70628138 None:intergenic
ATAAATAGCAAGATGTTTAT+CGG 0.320043 2_1:+70628017 None:intergenic
GAAAATTGTTGCTGAGGTTC+CGG 0.329669 2_1:-70627950 Msa0221820:CDS
TGTTGCTGAGGTTCCGGCTT+TGG 0.331915 2_1:-70627944 Msa0221820:CDS
AGTGTTAACACCACGATTAA+TGG 0.347939 2_1:-70628051 Msa0221820:CDS
CATCTTGCTATTTATAAAGT+TGG 0.349855 2_1:-70628009 Msa0221820:CDS
AACCCTGTAAGAACACTTGC+TGG 0.390538 2_1:-70628141 Msa0221820:CDS
GAACTTAACGTGATTAGTTA+TGG 0.403328 2_1:-70628099 Msa0221820:CDS
AGTTGGGTGGCACTTGTTGT+TGG 0.447115 2_1:-70627787 Msa0221820:CDS
TTCTGAGAAGGCGGAATCGT+CGG 0.454414 2_1:+70628272 None:intergenic
TCTGAGAAGGCGGAATCGTC+GGG 0.465451 2_1:+70628273 None:intergenic
GCTGGTGCAGGCGCCAAAGC+CGG 0.482022 2_1:+70627931 None:intergenic
GCCTTAGCATCAGCAATAGC+TGG 0.484689 2_1:+70627913 None:intergenic
GGAAATGTGAACATTTCAAC+GGG 0.489369 2_1:-70628075 Msa0221820:CDS
ACCAGCTATTGCTGATGCTA+AGG 0.493657 2_1:-70627914 Msa0221820:CDS
GATTGACATGAGTGGAAGTT+GGG 0.497150 2_1:-70627803 Msa0221820:CDS
TTAGGAGCTGTGAGTTGAGC+TGG 0.506453 2_1:+70628328 None:intergenic
GCCTTCTCAGAACTCAAACC+AGG 0.511146 2_1:-70628261 Msa0221820:CDS
AGCAAGTGTTCTTACAGGGT+TGG 0.512112 2_1:+70628143 None:intergenic
GTTGAATCTTCAGATGATGA+TGG 0.519092 2_1:+70627868 None:intergenic
GGATTGACATGAGTGGAAGT+TGG 0.523635 2_1:-70627804 Msa0221820:CDS
GCATCAGCAATAGCTGGTGC+AGG 0.524825 2_1:+70627919 None:intergenic
TGCTAAGAAAATTGTTGCTG+AGG 0.530469 2_1:-70627956 Msa0221820:CDS
ACACTTGCTGGAAACAAACC+TGG 0.537319 2_1:-70628129 Msa0221820:CDS
GTTGTTGGAATTGTCTTCGT+GGG 0.546805 2_1:-70627772 Msa0221820:CDS
TTAGCAGGAGAAAATTCTGA+TGG 0.547442 2_1:+70627973 None:intergenic
GAGAGTGAGTTGAGGAACCC+TGG 0.549587 2_1:+70628243 None:intergenic
TGCGAGGATCGTTAAGCCGC+CGG 0.550833 2_1:+70628296 None:intergenic
CAGCTCCTAACCATAAAATC+CGG 0.551779 2_1:-70628315 Msa0221820:CDS
TTCCAGCAAGTGTTCTTACA+GGG 0.554792 2_1:+70628139 None:intergenic
TGAAGATTCAACAACGTCGC+AGG 0.554836 2_1:-70627857 Msa0221820:CDS
CCCTGGTTTGAGTTCTGAGA+AGG 0.557457 2_1:+70628260 None:intergenic
TGTTGTTGGAATTGTCTTCG+TGG 0.560250 2_1:-70627773 Msa0221820:CDS
CTTAACGTGATTAGTTATGG+TGG 0.562819 2_1:-70628096 Msa0221820:CDS
AGGCGGAATCGTCGGGTGCG+AGG 0.569498 2_1:+70628280 None:intergenic
CTGTGACTTCTAGTGCTATG+AGG 0.580983 2_1:-70627825 Msa0221820:CDS
CCTTCTCAGAACTCAAACCA+GGG 0.601582 2_1:-70628260 Msa0221820:CDS
TGGAAATGTGAACATTTCAA+CGG 0.610164 2_1:-70628076 Msa0221820:CDS
TTTCATTGGAGAGTGAGTTG+AGG 0.614496 2_1:+70628235 None:intergenic
GTTGGAATTGTCTTCGTGGG+AGG 0.620149 2_1:-70627769 Msa0221820:CDS
TGGTTTGAGTTCTGAGAAGG+CGG 0.623094 2_1:+70628263 None:intergenic
ATACAAAATCAGAAATAACA+TGG 0.635906 2_1:+70628190 None:intergenic
ATAGCACTAGAAGTCACAGC+AGG 0.654697 2_1:+70627829 None:intergenic
ATATATGATTCCATTAATCG+TGG 0.660112 2_1:+70628041 None:intergenic
CTCCTAACCATAAAATCCGG+CGG 0.662023 2_1:-70628312 Msa0221820:CDS
TGACATGAGTGGAAGTTGGG+TGG 0.700477 2_1:-70627800 Msa0221820:CDS
GCTATGAGGATTGACATGAG+TGG 0.716443 2_1:-70627811 Msa0221820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGTTCAAGTTTTTTTTCAT+TGG + chr2_1:70627883-70627902 None:intergenic 20.0%
!! ATACAAAATCAGAAATAACA+TGG + chr2_1:70627914-70627933 None:intergenic 20.0%
!! ATAAATAGCAAGATGTTTAT+CGG + chr2_1:70628087-70628106 None:intergenic 20.0%
! ATATATGATTCCATTAATCG+TGG + chr2_1:70628063-70628082 None:intergenic 25.0%
!!! CATCTTGCTATTTATAAAGT+TGG - chr2_1:70628092-70628111 Msa0221820:CDS 25.0%
! GAACTTAACGTGATTAGTTA+TGG - chr2_1:70628002-70628021 Msa0221820:CDS 30.0%
TGGAAATGTGAACATTTCAA+CGG - chr2_1:70628025-70628044 Msa0221820:CDS 30.0%
!! GATGATGGTTTTTCTTTTTC+AGG + chr2_1:70628221-70628240 None:intergenic 30.0%
! ACGTTAAGTTCAACTTTTCC+AGG + chr2_1:70627993-70628012 None:intergenic 35.0%
! CTTAACGTGATTAGTTATGG+TGG - chr2_1:70628005-70628024 Msa0221820:CDS 35.0%
GGAAATGTGAACATTTCAAC+GGG - chr2_1:70628026-70628045 Msa0221820:CDS 35.0%
AGTGTTAACACCACGATTAA+TGG - chr2_1:70628050-70628069 Msa0221820:CDS 35.0%
TTAGCAGGAGAAAATTCTGA+TGG + chr2_1:70628131-70628150 None:intergenic 35.0%
! TCAGCAACAATTTTCTTAGC+AGG + chr2_1:70628146-70628165 None:intergenic 35.0%
TGCTAAGAAAATTGTTGCTG+AGG - chr2_1:70628145-70628164 Msa0221820:CDS 35.0%
GTTGAATCTTCAGATGATGA+TGG + chr2_1:70628236-70628255 None:intergenic 35.0%
CAGCTCCTAACCATAAAATC+CGG - chr2_1:70627786-70627805 Msa0221820:CDS 40.0%
TTTCATTGGAGAGTGAGTTG+AGG + chr2_1:70627869-70627888 None:intergenic 40.0%
TTCCAGCAAGTGTTCTTACA+GGG + chr2_1:70627965-70627984 None:intergenic 40.0%
TTTCCAGCAAGTGTTCTTAC+AGG + chr2_1:70627966-70627985 None:intergenic 40.0%
GAAAATTGTTGCTGAGGTTC+CGG - chr2_1:70628151-70628170 Msa0221820:CDS 40.0%
!!! GGTTTTTCTTTTTCAGGCGT+CGG + chr2_1:70628215-70628234 None:intergenic 40.0%
GATTGACATGAGTGGAAGTT+GGG - chr2_1:70628298-70628317 Msa0221820:CDS 40.0%
TGTTGTTGGAATTGTCTTCG+TGG - chr2_1:70628328-70628347 Msa0221820:CDS 40.0%
GTTGTTGGAATTGTCTTCGT+GGG - chr2_1:70628329-70628348 Msa0221820:CDS 40.0%
CTCCTAACCATAAAATCCGG+CGG - chr2_1:70627789-70627808 Msa0221820:CDS 45.0%
!! TGGTTTGAGTTCTGAGAAGG+CGG + chr2_1:70627841-70627860 None:intergenic 45.0%
CCTTCTCAGAACTCAAACCA+GGG - chr2_1:70627841-70627860 Msa0221820:CDS 45.0%
AGCAAGTGTTCTTACAGGGT+TGG + chr2_1:70627961-70627980 None:intergenic 45.0%
AACCCTGTAAGAACACTTGC+TGG - chr2_1:70627960-70627979 Msa0221820:CDS 45.0%
! ACACTTGCTGGAAACAAACC+TGG - chr2_1:70627972-70627991 Msa0221820:CDS 45.0%
ACCAGCTATTGCTGATGCTA+AGG - chr2_1:70628187-70628206 Msa0221820:CDS 45.0%
TGAAGATTCAACAACGTCGC+AGG - chr2_1:70628244-70628263 Msa0221820:CDS 45.0%
ATAGCACTAGAAGTCACAGC+AGG + chr2_1:70628275-70628294 None:intergenic 45.0%
CTGTGACTTCTAGTGCTATG+AGG - chr2_1:70628276-70628295 Msa0221820:CDS 45.0%
GCTATGAGGATTGACATGAG+TGG - chr2_1:70628290-70628309 Msa0221820:CDS 45.0%
GGATTGACATGAGTGGAAGT+TGG - chr2_1:70628297-70628316 Msa0221820:CDS 45.0%
! TTAGGAGCTGTGAGTTGAGC+TGG + chr2_1:70627776-70627795 None:intergenic 50.0%
! AGCCGCCGGATTTTATGGTT+AGG + chr2_1:70627794-70627813 None:intergenic 50.0%
! CGTTAAGCCGCCGGATTTTA+TGG + chr2_1:70627799-70627818 None:intergenic 50.0%
! TTCTGAGAAGGCGGAATCGT+CGG + chr2_1:70627832-70627851 None:intergenic 50.0%
GCCTTCTCAGAACTCAAACC+AGG - chr2_1:70627840-70627859 Msa0221820:CDS 50.0%
!! CCCTGGTTTGAGTTCTGAGA+AGG + chr2_1:70627844-70627863 None:intergenic 50.0%
GCCTTAGCATCAGCAATAGC+TGG + chr2_1:70628191-70628210 None:intergenic 50.0%
TGACATGAGTGGAAGTTGGG+TGG - chr2_1:70628301-70628320 Msa0221820:CDS 50.0%
!! AGTTGGGTGGCACTTGTTGT+TGG - chr2_1:70628314-70628333 Msa0221820:CDS 50.0%
GTTGGAATTGTCTTCGTGGG+AGG - chr2_1:70628332-70628351 Msa0221820:CDS 50.0%
TCTGAGAAGGCGGAATCGTC+GGG + chr2_1:70627831-70627850 None:intergenic 55.0%
! GAGAGTGAGTTGAGGAACCC+TGG + chr2_1:70627861-70627880 None:intergenic 55.0%
TGTTGCTGAGGTTCCGGCTT+TGG - chr2_1:70628157-70628176 Msa0221820:CDS 55.0%
GCATCAGCAATAGCTGGTGC+AGG + chr2_1:70628185-70628204 None:intergenic 55.0%
TGCGAGGATCGTTAAGCCGC+CGG + chr2_1:70627808-70627827 None:intergenic 60.0%
AGGCGGAATCGTCGGGTGCG+AGG + chr2_1:70627824-70627843 None:intergenic 70.0%
GCTGGTGCAGGCGCCAAAGC+CGG + chr2_1:70628173-70628192 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 70627750 70628373 70627750 ID=Msa0221820;Name=Msa0221820
chr2_1 mRNA 70627750 70628373 70627750 ID=Msa0221820-mRNA-1;Parent=Msa0221820;Name=Msa0221820-mRNA-1;_AED=0.32;_eAED=0.32;_QI=0|-1|0|1|-1|1|1|0|207
chr2_1 exon 70627750 70628373 70627750 ID=Msa0221820-mRNA-1:exon:20266;Parent=Msa0221820-mRNA-1
chr2_1 CDS 70627750 70628373 70627750 ID=Msa0221820-mRNA-1:cds;Parent=Msa0221820-mRNA-1
Gene Sequence

>Msa0221820

ATGAAAACAACTCAACTAATCAGCCAGCTCAACTCACAGCTCCTAACCATAAAATCCGGCGGCTTAACGATCCTCGCACCCGACGATTCCGCCTTCTCAGAACTCAAACCAGGGTTCCTCAACTCACTCTCCAATGAAAAAAAACTTGAACTACTTCAATTCCATGTTATTTCTGATTTTGTATCTAGCTCAAACTTTGATACTTTAACCAACCCTGTAAGAACACTTGCTGGAAACAAACCTGGAAAAGTTGAACTTAACGTGATTAGTTATGGTGGAAATGTGAACATTTCAACGGGAAGTGTTAACACCACGATTAATGGAATCATATATACCGATAAACATCTTGCTATTTATAAAGTTGGTAAAGTGCTTATTCCATCAGAATTTTCTCCTGCTAAGAAAATTGTTGCTGAGGTTCCGGCTTTGGCGCCTGCACCAGCTATTGCTGATGCTAAGGCGCCGACGCCTGAAAAAGAAAAACCATCATCATCTGAAGATTCAACAACGTCGCAGGTTGTTCCTGCTGTGACTTCTAGTGCTATGAGGATTGACATGAGTGGAAGTTGGGTGGCACTTGTTGTTGGAATTGTCTTCGTGGGAGGTTTTTACAACAAAAACTAA
Protein sequence

>Msa0221820

MKTTQLISQLNSQLLTIKSGGLTILAPDDSAFSELKPGFLNSLSNEKKLELLQFHVISDFVSSSNFDTLTNPVRTLAGNKPGKVELNVISYGGNVNISTGSVNTTINGIIYTDKHLAIYKVGKVLIPSEFSPAKKIVAEVPALAPAPAIADAKAPTPEKEKPSSSEDSTTSQVVPAVTSSAMRIDMSGSWVALVVGIVFVGGFYNKN*