AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0217090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0217090 MtrunA17_Chr2g0318901 93.548 93 6 0 1 93 181 273 7.03e-62 189
Msa0217090 MtrunA17_Chr2g0318871 88.172 93 11 0 1 93 181 273 8.19e-58 178
Msa0217090 MtrunA17_Chr2g0318931 77.108 83 17 1 1 81 190 272 4.35e-42 138
Msa0217090 MtrunA17_Chr8g0355841 57.955 88 37 0 1 88 431 518 4.67e-38 132
Msa0217090 MtrunA17_Chr8g0355831 62.500 80 30 0 1 80 273 352 5.70e-37 127
Msa0217090 MtrunA17_Chr8g0355321 60.000 80 32 0 1 80 224 303 1.58e-36 125
Msa0217090 MtrunA17_Chr8g0355311 58.824 85 35 0 1 85 112 196 3.10e-36 121
Msa0217090 MtrunA17_Chr8g0355871 59.494 79 32 0 1 79 144 222 8.59e-36 121
Msa0217090 MtrunA17_Chr8g0355331 53.488 86 40 0 1 86 343 428 1.74e-35 124
Msa0217090 MtrunA17_Chr8g0355861 57.500 80 34 0 1 80 182 261 3.11e-34 118
Msa0217090 MtrunA17_Chr1g0168781 59.524 84 34 0 1 84 181 264 7.40e-34 117
Msa0217090 MtrunA17_Chr1g0147331 44.304 79 43 1 1 78 245 323 3.75e-21 85.1
Msa0217090 MtrunA17_Chr1g0146631 44.304 79 43 1 1 78 245 323 3.82e-21 85.1
Msa0217090 MtrunA17_Chr1g0147261 41.026 78 45 1 1 77 220 297 5.96e-21 84.0
Msa0217090 MtrunA17_Chr3g0139431 46.341 82 41 2 1 79 240 321 1.25e-20 83.6
Msa0217090 MtrunA17_Chr1g0147271 43.038 79 44 1 1 78 305 383 3.36e-20 82.8
Msa0217090 MtrunA17_Chr1g0147301 40.506 79 46 1 1 78 205 283 1.28e-19 80.5
Msa0217090 MtrunA17_Chr1g0147241 39.744 78 46 1 1 77 233 310 6.13e-19 79.0
Msa0217090 MtrunA17_Chr1g0147311 40.506 79 46 1 1 78 276 354 1.39e-18 78.2
Msa0217090 MtrunA17_Chr1g0147251 39.744 78 46 1 1 77 163 240 2.84e-18 76.3
Msa0217090 MtrunA17_Chr1g0147291 40.506 79 46 1 1 78 187 265 3.61e-18 76.3
Msa0217090 MtrunA17_Chr1g0147321 39.744 78 46 1 1 77 158 235 1.42e-17 74.3
Msa0217090 MtrunA17_Chr3g0144411 38.750 80 47 2 2 79 459 538 1.75e-14 67.0
Msa0217090 MtrunA17_Chr3g0144421 36.250 80 49 2 2 79 223 302 5.56e-14 65.5
Msa0217090 MtrunA17_Chr4g0034821 37.805 82 49 2 2 81 212 293 6.58e-14 65.1
Msa0217090 MtrunA17_Chr3g0138231 37.805 82 49 2 2 81 187 268 7.27e-14 64.7
Msa0217090 MtrunA17_Chr3g0144451 36.585 82 50 2 2 81 196 277 3.84e-13 62.8
Msa0217090 MtrunA17_Chr4g0034691 36.585 82 48 4 2 79 627 708 6.19e-12 59.7
Msa0217090 MtrunA17_Chr4g0034731 39.024 82 46 4 2 79 351 432 9.10e-12 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0217090 AT5G25610.1 41.026 78 45 1 1 77 312 389 1.80e-17 75.9
Msa0217090 AT1G49320.1 41.250 80 44 3 2 78 199 278 7.77e-13 62.4

Find 18 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACAATAAAATACAACCTTT+TGG 0.266567 2_1:-63607112 None:intergenic
TTGTCATTTCCTAGGAAATA+AGG 0.268344 2_1:+63607289 Msa0217090:CDS
TGGTGCCAATGTTGCTGTTT+AGG 0.323507 2_1:+63607352 Msa0217090:CDS
ATAAAATAGCCTTATTTCCT+AGG 0.361639 2_1:-63607298 None:intergenic
GCATTGTCCAAACCTAAATT+AGG 0.363667 2_1:-63607326 None:intergenic
GTTTGTCATGCTGATACTTC+AGG 0.375794 2_1:+63607209 Msa0217090:CDS
AAACCTGTTTGTCATTTCCT+AGG 0.419287 2_1:+63607281 Msa0217090:CDS
ATGGGTACCTAATTTAGGTT+TGG 0.424424 2_1:+63607319 Msa0217090:CDS
AGAAAGCAGTGATGTGTCAT+AGG 0.434072 2_1:+63607081 None:intergenic
TTTCCTAGGAAATGACAAAC+AGG 0.459958 2_1:-63607284 None:intergenic
GTTCCATCATTTGCCACCAA+TGG 0.478916 2_1:-63607167 None:intergenic
TTAGGTTTGGACAATGCCTA+TGG 0.494021 2_1:+63607332 Msa0217090:CDS
GTTCCATTGGTGGCAAATGA+TGG 0.508291 2_1:+63607164 Msa0217090:CDS
TCATAGGTTGAATTTCCAAA+AGG 0.512621 2_1:+63607097 Msa0217090:CDS
CAGATTATGAAAGCTGATCC+AGG 0.521758 2_1:+63607254 Msa0217090:CDS
AACAGCAACATTGGCACCAT+AGG 0.567015 2_1:-63607348 None:intergenic
TGACAAACAGGTTTACTACC+TGG 0.588938 2_1:-63607272 None:intergenic
GTACACCTAAACAGCAACAT+TGG 0.590624 2_1:-63607357 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTGTCATGAAATTCA+TGG + chr2_1:63607125-63607144 Msa0217090:CDS 20.0%
!! GACAATAAAATACAACCTTT+TGG - chr2_1:63607115-63607134 None:intergenic 25.0%
!!! ATAAAATAGCCTTATTTCCT+AGG - chr2_1:63607301-63607320 None:intergenic 25.0%
!!! TAGGAAATAAGGCTATTTTA+TGG + chr2_1:63607300-63607319 Msa0217090:CDS 25.0%
!!! AGGAAATAAGGCTATTTTAT+GGG + chr2_1:63607301-63607320 Msa0217090:CDS 25.0%
!! ATTTTATGGGTACCTAATTT+AGG + chr2_1:63607314-63607333 Msa0217090:CDS 25.0%
! TCATAGGTTGAATTTCCAAA+AGG + chr2_1:63607097-63607116 Msa0217090:CDS 30.0%
! TTGTCATTTCCTAGGAAATA+AGG + chr2_1:63607289-63607308 Msa0217090:CDS 30.0%
! TCATGGAACAACAGCTTTTA+TGG + chr2_1:63607142-63607161 Msa0217090:CDS 35.0%
! AACAGCTTTTATGGTTCCAT+TGG + chr2_1:63607151-63607170 Msa0217090:CDS 35.0%
! AAACCTGTTTGTCATTTCCT+AGG + chr2_1:63607281-63607300 Msa0217090:CDS 35.0%
TTTCCTAGGAAATGACAAAC+AGG - chr2_1:63607287-63607306 None:intergenic 35.0%
! ATGGGTACCTAATTTAGGTT+TGG + chr2_1:63607319-63607338 Msa0217090:CDS 35.0%
GCATTGTCCAAACCTAAATT+AGG - chr2_1:63607329-63607348 None:intergenic 35.0%
! AGCTTTTATGGTTCCATTGG+TGG + chr2_1:63607154-63607173 Msa0217090:CDS 40.0%
GTTTGTCATGCTGATACTTC+AGG + chr2_1:63607209-63607228 Msa0217090:CDS 40.0%
CAGATTATGAAAGCTGATCC+AGG + chr2_1:63607254-63607273 Msa0217090:CDS 40.0%
TGACAAACAGGTTTACTACC+TGG - chr2_1:63607275-63607294 None:intergenic 40.0%
TTAGGTTTGGACAATGCCTA+TGG + chr2_1:63607332-63607351 Msa0217090:CDS 40.0%
! GTTCCATTGGTGGCAAATGA+TGG + chr2_1:63607164-63607183 Msa0217090:CDS 45.0%
GTTCCATCATTTGCCACCAA+TGG - chr2_1:63607170-63607189 None:intergenic 45.0%
AACAGCAACATTGGCACCAT+AGG - chr2_1:63607351-63607370 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 63607092 63607373 63607092 ID=Msa0217090;Name=Msa0217090
chr2_1 mRNA 63607092 63607373 63607092 ID=Msa0217090-mRNA-1;Parent=Msa0217090;Name=Msa0217090-mRNA-1;_AED=0.43;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|93
chr2_1 exon 63607092 63607373 63607092 ID=Msa0217090-mRNA-1:exon:17672;Parent=Msa0217090-mRNA-1
chr2_1 CDS 63607092 63607373 63607092 ID=Msa0217090-mRNA-1:cds;Parent=Msa0217090-mRNA-1
Gene Sequence

>Msa0217090

ATGTGTCATAGGTTGAATTTCCAAAAGGTTGTATTTTATTGTCATGAAATTCATGGAACAACAGCTTTTATGGTTCCATTGGTGGCAAATGATGGAACAAAAACTCAAGCACTAGCTGTTTGTCATGCTGATACTTCAGGCATGAATCAACATATGCTTCATCAGATTATGAAAGCTGATCCAGGTAGTAAACCTGTTTGTCATTTCCTAGGAAATAAGGCTATTTTATGGGTACCTAATTTAGGTTTGGACAATGCCTATGGTGCCAATGTTGCTGTTTAG
Protein sequence

>Msa0217090

MCHRLNFQKVVFYCHEIHGTTAFMVPLVANDGTKTQALAVCHADTSGMNQHMLHQIMKADPGSKPVCHFLGNKAILWVPNLGLDNAYGANVAV*