AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1182950

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1182950 MtrunA17_Chr8g0336861 95.402 87 4 0 31 117 280 366 6.59e-54 172
Msa1182950 MtrunA17_Chr8g0336851 88.506 87 9 1 31 117 279 364 1.94e-48 158
Msa1182950 MtrunA17_Chr8g0336871 85.057 87 12 1 31 117 89 174 3.53e-47 149
Msa1182950 MtrunA17_Chr8g0336801 82.143 84 14 1 34 117 74 156 8.36e-45 142
Msa1182950 MtrunA17_Chr8g0336841 78.571 84 17 1 34 117 9 91 1.21e-44 140
Msa1182950 MtrunA17_Chr8g0336761 80.460 87 16 1 31 117 279 364 3.87e-44 147
Msa1182950 MtrunA17_Chr8g0336631 81.609 87 15 1 31 117 280 365 1.72e-43 145
Msa1182950 MtrunA17_Chr8g0336781 78.161 87 18 1 31 117 315 400 5.61e-43 144
Msa1182950 MtrunA17_Chr8g0348081 80.460 87 16 1 31 117 279 364 1.13e-42 143
Msa1182950 MtrunA17_Chr2g0311831 75.000 84 20 1 34 117 289 371 1.44e-40 138
Msa1182950 MtrunA17_Chr2g0311861 68.966 87 26 1 31 117 262 347 2.04e-38 132
Msa1182950 MtrunA17_Chr2g0311761 70.115 87 25 1 31 117 287 372 2.91e-38 132
Msa1182950 MtrunA17_Chr4g0066121 68.966 87 27 0 31 117 280 366 1.40e-35 124
Msa1182950 MtrunA17_Chr2g0311921 63.218 87 31 1 31 117 273 358 1.41e-35 124
Msa1182950 MtrunA17_Chr8g0336751 69.048 84 25 1 34 117 315 397 4.61e-35 124
Msa1182950 MtrunA17_Chr8g0354241 63.529 85 29 2 34 117 291 374 1.37e-29 109
Msa1182950 MtrunA17_Chr1g0167951 56.322 87 37 1 31 117 270 355 2.37e-29 108
Msa1182950 MtrunA17_Chr7g0236011 57.471 87 33 2 34 117 288 373 1.42e-28 106
Msa1182950 MtrunA17_Chr7g0235951 56.322 87 34 2 34 117 288 373 9.48e-28 104
Msa1182950 MtrunA17_Chr4g0066991 54.444 90 37 2 31 117 265 353 1.13e-27 103
Msa1182950 MtrunA17_Chr1g0167931 57.143 84 35 1 34 117 236 318 2.08e-27 102
Msa1182950 MtrunA17_Chr8g0335411 55.172 87 35 2 34 117 288 373 2.26e-27 103
Msa1182950 MtrunA17_Chr8g0354261 57.647 85 34 2 34 117 291 374 1.08e-26 101
Msa1182950 MtrunA17_Chr1g0167961 55.952 84 36 1 34 117 290 372 3.68e-26 100
Msa1182950 MtrunA17_Chr1g0187821 50.575 87 42 1 31 117 285 370 1.05e-25 99.0
Msa1182950 MtrunA17_Chr1g0187831 53.571 84 37 2 34 116 291 373 1.50e-25 98.6
Msa1182950 MtrunA17_Chr2g0311741 58.333 84 31 3 34 117 248 327 1.19e-24 95.5
Msa1182950 MtrunA17_Chr6g0472861 53.409 88 39 2 31 117 287 373 1.97e-24 95.5
Msa1182950 MtrunA17_Chr7g0235981 52.222 90 39 2 31 117 239 327 2.11e-24 94.7
Msa1182950 MtrunA17_Chr7g0225881 52.874 87 37 3 34 117 285 370 2.24e-23 92.4
Msa1182950 MtrunA17_Chr1g0187811 51.163 86 39 2 34 117 409 493 2.46e-23 93.2
Msa1182950 MtrunA17_Chr1g0184241 52.381 84 36 2 34 117 288 367 2.07e-22 89.7
Msa1182950 MtrunA17_Chr2g0311701 52.747 91 37 3 31 117 287 375 2.19e-22 90.1
Msa1182950 MtrunA17_Chr8g0364471 50.575 87 39 2 34 117 288 373 3.21e-22 89.4
Msa1182950 MtrunA17_Chr7g0247991 49.425 87 40 2 34 117 288 373 4.62e-22 89.0
Msa1182950 MtrunA17_Chr4g0055591 49.438 89 42 2 31 117 274 361 6.34e-22 88.6
Msa1182950 MtrunA17_Chr2g0311681 52.747 91 37 3 31 117 281 369 8.60e-21 85.5
Msa1182950 MtrunA17_Chr2g0311691 50.549 91 39 3 31 117 281 369 1.67e-20 84.7
Msa1182950 MtrunA17_Chr1g0167911 53.012 83 38 1 34 116 274 355 2.63e-20 84.0
Msa1182950 MtrunA17_Chr2g0311711 46.988 83 35 4 34 112 288 365 2.60e-15 70.5
Msa1182950 MtrunA17_Chr1g0161081 38.095 84 48 3 34 116 291 371 3.92e-13 64.3
Msa1182950 MtrunA17_Chr1g0161041 40.476 84 46 3 34 116 314 394 6.36e-13 63.5
Msa1182950 MtrunA17_Chr8g0375701 34.483 87 53 2 31 117 273 355 6.83e-13 63.5
Msa1182950 MtrunA17_Chr2g0314361 34.940 83 50 3 35 117 1 79 4.80e-12 57.4
Msa1182950 MtrunA17_Chr5g0412651 33.784 74 46 1 32 105 264 334 7.23e-12 60.5
Msa1182950 MtrunA17_Chr7g0266651 35.294 85 53 2 34 117 279 362 2.52e-11 58.9
Msa1182950 MtrunA17_Chr1g0161111 38.158 76 43 3 34 108 350 422 5.40e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1182950 AT1G06650.2 64.706 85 28 2 34 117 286 369 6.67e-34 120
Msa1182950 AT1G06620.1 62.069 87 32 1 31 117 280 365 7.55e-32 115
Msa1182950 AT1G04380.1 61.905 84 31 1 34 117 263 345 1.25e-31 114
Msa1182950 AT5G59530.1 63.095 84 30 1 34 117 282 364 8.04e-31 112
Msa1182950 AT5G59540.1 60.714 84 32 1 34 117 284 366 1.55e-30 112
Msa1182950 AT1G06645.1 59.091 88 34 2 31 117 293 379 1.39e-29 109
Msa1182950 AT1G06640.1 59.091 88 34 2 31 117 283 369 4.19e-28 105
Msa1182950 AT1G04350.1 61.176 85 31 2 34 117 277 360 1.50e-26 101
Msa1182950 AT5G43440.1 54.762 84 37 1 34 117 283 365 4.61e-24 94.7
Msa1182950 AT5G43450.1 57.143 84 35 1 34 117 280 362 2.27e-23 92.8
Msa1182950 AT2G30830.1 54.545 88 37 3 31 117 273 358 3.91e-23 92.0
Msa1182950 AT3G61400.1 52.273 88 39 2 31 117 285 370 5.38e-23 92.0
Msa1182950 AT2G30840.1 57.647 85 33 3 34 117 280 362 2.02e-21 87.4
Msa1182950 AT2G25450.1 53.488 86 36 3 34 117 276 359 2.31e-20 84.7
Msa1182950 AT1G03410.2 48.235 85 41 3 34 117 279 361 9.30e-20 82.8
Msa1182950 AT1G03410.1 48.235 85 41 3 34 117 316 398 1.16e-19 82.8
Msa1182950 AT2G30840.3 56.250 80 32 3 39 117 279 356 3.24e-18 78.6
Msa1182950 AT1G03400.2 49.425 87 41 3 32 117 295 379 4.87e-18 78.2
Msa1182950 AT1G03400.1 49.412 85 40 3 34 117 269 351 9.04e-18 77.4

Find 15 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAGTAGTTTCTTTGTATT+TGG 0.104565 8_1:+18112892 None:intergenic
TATTCTTGGACCAACTTTAT+TGG 0.191904 8_1:+18113003 None:intergenic
AATTTATGATGGTGTTGTTT+TGG 0.321555 8_1:-18113359 Msa1182950:intron
AAGCATGCAACAGATATTCT+TGG 0.361845 8_1:+18112989 None:intergenic
ACAGTAGTTTCTTTGTATTT+GGG 0.372639 8_1:+18112893 None:intergenic
AAAGCATCTTCAAAGCTCTA+TGG 0.389751 8_1:-18112950 Msa1182950:CDS
TCTGATAATAGTTCCTTCAT+TGG 0.398109 8_1:+18112926 None:intergenic
ATTGCACAAACTAGATTGTA+TGG 0.416113 8_1:+18113384 None:intergenic
GCCTACTACTTTCGAGCAAA+AGG 0.422708 8_1:-18112857 Msa1182950:CDS
TTTCGAGCAAAAGGAGTAGA+TGG 0.447527 8_1:-18112848 Msa1182950:CDS
TTGTGCAATCTAATTTATGA+TGG 0.517183 8_1:-18113370 Msa1182950:CDS
AAAGCTCTATGGACCAATGA+AGG 0.519376 8_1:-18112939 Msa1182950:CDS
AGAGTACTTGCCAATAAAGT+TGG 0.534486 8_1:-18113013 Msa1182950:CDS
TGAAGATGCTTTAAGTCCTG+TGG 0.560622 8_1:+18112961 None:intergenic
GTAGTTTCTTTGTATTTGGG+AGG 0.568718 8_1:+18112896 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAACAAATAATTAGCTAT+AGG + chr8_1:18113173-18113192 None:intergenic 20.0%
! TTGTGCAATCTAATTTATGA+TGG - chr8_1:18112883-18112902 Msa1182950:CDS 25.0%
!!! AATTTATGATGGTGTTGTTT+TGG - chr8_1:18112894-18112913 Msa1182950:CDS 25.0%
! ACAAATAATTAGCTATAGGA+AGG + chr8_1:18113169-18113188 None:intergenic 25.0%
! ACAGTAGTTTCTTTGTATTT+GGG + chr8_1:18113363-18113382 None:intergenic 25.0%
! AACAGTAGTTTCTTTGTATT+TGG + chr8_1:18113364-18113383 None:intergenic 25.0%
ATTGCACAAACTAGATTGTA+TGG + chr8_1:18112872-18112891 None:intergenic 30.0%
TATTCTTGGACCAACTTTAT+TGG + chr8_1:18113253-18113272 None:intergenic 30.0%
TCTGATAATAGTTCCTTCAT+TGG + chr8_1:18113330-18113349 None:intergenic 30.0%
TGCCTTATCTTCCATCTTAT+TGG - chr8_1:18112973-18112992 Msa1182950:CDS 35.0%
CTCCAATAAGATGGAAGATA+AGG + chr8_1:18112978-18112997 None:intergenic 35.0%
CTTATCTTCCATCTTATTGG+AGG - chr8_1:18112976-18112995 Msa1182950:CDS 35.0%
ACATAACACCTCCAATAAGA+TGG + chr8_1:18112987-18113006 None:intergenic 35.0%
! AGAGTACTTGCCAATAAAGT+TGG - chr8_1:18113240-18113259 Msa1182950:intron 35.0%
AAGCATGCAACAGATATTCT+TGG + chr8_1:18113267-18113286 None:intergenic 35.0%
! AAAGCATCTTCAAAGCTCTA+TGG - chr8_1:18113303-18113322 Msa1182950:intron 35.0%
GTAGTTTCTTTGTATTTGGG+AGG + chr8_1:18113360-18113379 None:intergenic 35.0%
GACACCAGAGCTACAAAAAT+AGG - chr8_1:18112841-18112860 Msa1182950:CDS 40.0%
!!! GTGTCCTATTTTTGTAGCTC+TGG + chr8_1:18112848-18112867 None:intergenic 40.0%
! AGTCTCCTGCATTTTCAACT+TGG - chr8_1:18112934-18112953 Msa1182950:CDS 40.0%
! TGAAGCCAAGTTGAAAATGC+AGG + chr8_1:18112942-18112961 None:intergenic 40.0%
AGATAGAACAGTGCCTAACT+TGG - chr8_1:18113133-18113152 Msa1182950:intron 40.0%
! TGAAGATGCTTTAAGTCCTG+TGG + chr8_1:18113295-18113314 None:intergenic 40.0%
AAAGCTCTATGGACCAATGA+AGG - chr8_1:18113314-18113333 Msa1182950:intron 40.0%
! TCCTTTTGCTCGAAAGTAGT+AGG + chr8_1:18113400-18113419 None:intergenic 40.0%
TTTCGAGCAAAAGGAGTAGA+TGG - chr8_1:18113405-18113424 Msa1182950:CDS 40.0%
AGGTGCAGATTCTCCAAGTT+AGG + chr8_1:18113149-18113168 None:intergenic 45.0%
!!! GTTGCATGCTTTTTCTCCAC+AGG - chr8_1:18113276-18113295 Msa1182950:intron 45.0%
GCCTACTACTTTCGAGCAAA+AGG - chr8_1:18113396-18113415 Msa1182950:CDS 45.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 18112817 18113458 18112817 ID=Msa1182950;Name=Msa1182950
chr8_1 mRNA 18112817 18113458 18112817 ID=Msa1182950-mRNA-1;Parent=Msa1182950;Name=Msa1182950-mRNA-1;_AED=0.58;_eAED=0.58;_QI=0|0|0|0.5|1|1|2|0|117
chr8_1 exon 18113360 18113458 18113360 ID=Msa1182950-mRNA-1:exon:6946;Parent=Msa1182950-mRNA-1
chr8_1 exon 18112817 18113071 18112817 ID=Msa1182950-mRNA-1:exon:6945;Parent=Msa1182950-mRNA-1
chr8_1 CDS 18113360 18113458 18113360 ID=Msa1182950-mRNA-1:cds;Parent=Msa1182950-mRNA-1
chr8_1 CDS 18112817 18113071 18112817 ID=Msa1182950-mRNA-1:cds;Parent=Msa1182950-mRNA-1
Gene Sequence

>Msa1182950

ATGTGTCATGCACTAAGCAAAACAGACACCAGAGCTACAAAAATAGGACACACCATACAATCTAGTTTGTGCAATCTAATTTATGATGGTGTTGTTTTGCTCATAACAAATGACAAATTCAAGAGTGTTGTACATAGAGTACTTGCCAATAAAGTTGGTCCAAGAATATCTGTTGCATGCTTTTTCTCCACAGGACTTAAAGCATCTTCAAAGCTCTATGGACCAATGAAGGAACTATTATCAGAAGACAATCCTCCCAAATACAAAGAAACTACTGTTGCTGATTATGTAGCCTACTACTTTCGAGCAAAAGGAGTAGATGGTACTTCTGCACTTGAACATTACAAAATTTGA
Protein sequence

>Msa1182950

MCHALSKTDTRATKIGHTIQSSLCNLIYDGVVLLITNDKFKSVVHRVLANKVGPRISVACFFSTGLKASSKLYGPMKELLSEDNPPKYKETTVADYVAYYFRAKGVDGTSALEHYKI*