AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1235060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1235060 MtrunA17_Chr8g0336861 95.402 87 4 0 31 117 280 366 6.59e-54 172
Msa1235060 MtrunA17_Chr8g0336851 88.506 87 9 1 31 117 279 364 1.94e-48 158
Msa1235060 MtrunA17_Chr8g0336871 85.057 87 12 1 31 117 89 174 3.53e-47 149
Msa1235060 MtrunA17_Chr8g0336801 82.143 84 14 1 34 117 74 156 8.36e-45 142
Msa1235060 MtrunA17_Chr8g0336841 78.571 84 17 1 34 117 9 91 1.21e-44 140
Msa1235060 MtrunA17_Chr8g0336761 80.460 87 16 1 31 117 279 364 3.87e-44 147
Msa1235060 MtrunA17_Chr8g0336631 81.609 87 15 1 31 117 280 365 1.72e-43 145
Msa1235060 MtrunA17_Chr8g0336781 78.161 87 18 1 31 117 315 400 5.61e-43 144
Msa1235060 MtrunA17_Chr8g0348081 80.460 87 16 1 31 117 279 364 1.13e-42 143
Msa1235060 MtrunA17_Chr2g0311831 75.000 84 20 1 34 117 289 371 1.44e-40 138
Msa1235060 MtrunA17_Chr2g0311861 68.966 87 26 1 31 117 262 347 2.04e-38 132
Msa1235060 MtrunA17_Chr2g0311761 70.115 87 25 1 31 117 287 372 2.91e-38 132
Msa1235060 MtrunA17_Chr4g0066121 68.966 87 27 0 31 117 280 366 1.40e-35 124
Msa1235060 MtrunA17_Chr2g0311921 63.218 87 31 1 31 117 273 358 1.41e-35 124
Msa1235060 MtrunA17_Chr8g0336751 69.048 84 25 1 34 117 315 397 4.61e-35 124
Msa1235060 MtrunA17_Chr8g0354241 63.529 85 29 2 34 117 291 374 1.37e-29 109
Msa1235060 MtrunA17_Chr1g0167951 56.322 87 37 1 31 117 270 355 2.37e-29 108
Msa1235060 MtrunA17_Chr7g0236011 57.471 87 33 2 34 117 288 373 1.42e-28 106
Msa1235060 MtrunA17_Chr7g0235951 56.322 87 34 2 34 117 288 373 9.48e-28 104
Msa1235060 MtrunA17_Chr4g0066991 54.444 90 37 2 31 117 265 353 1.13e-27 103
Msa1235060 MtrunA17_Chr1g0167931 57.143 84 35 1 34 117 236 318 2.08e-27 102
Msa1235060 MtrunA17_Chr8g0335411 55.172 87 35 2 34 117 288 373 2.26e-27 103
Msa1235060 MtrunA17_Chr8g0354261 57.647 85 34 2 34 117 291 374 1.08e-26 101
Msa1235060 MtrunA17_Chr1g0167961 55.952 84 36 1 34 117 290 372 3.68e-26 100
Msa1235060 MtrunA17_Chr1g0187821 50.575 87 42 1 31 117 285 370 1.05e-25 99.0
Msa1235060 MtrunA17_Chr1g0187831 53.571 84 37 2 34 116 291 373 1.50e-25 98.6
Msa1235060 MtrunA17_Chr2g0311741 58.333 84 31 3 34 117 248 327 1.19e-24 95.5
Msa1235060 MtrunA17_Chr6g0472861 53.409 88 39 2 31 117 287 373 1.97e-24 95.5
Msa1235060 MtrunA17_Chr7g0235981 52.222 90 39 2 31 117 239 327 2.11e-24 94.7
Msa1235060 MtrunA17_Chr7g0225881 52.874 87 37 3 34 117 285 370 2.24e-23 92.4
Msa1235060 MtrunA17_Chr1g0187811 51.163 86 39 2 34 117 409 493 2.46e-23 93.2
Msa1235060 MtrunA17_Chr1g0184241 52.381 84 36 2 34 117 288 367 2.07e-22 89.7
Msa1235060 MtrunA17_Chr2g0311701 52.747 91 37 3 31 117 287 375 2.19e-22 90.1
Msa1235060 MtrunA17_Chr8g0364471 50.575 87 39 2 34 117 288 373 3.21e-22 89.4
Msa1235060 MtrunA17_Chr7g0247991 49.425 87 40 2 34 117 288 373 4.62e-22 89.0
Msa1235060 MtrunA17_Chr4g0055591 49.438 89 42 2 31 117 274 361 6.34e-22 88.6
Msa1235060 MtrunA17_Chr2g0311681 52.747 91 37 3 31 117 281 369 8.60e-21 85.5
Msa1235060 MtrunA17_Chr2g0311691 50.549 91 39 3 31 117 281 369 1.67e-20 84.7
Msa1235060 MtrunA17_Chr1g0167911 53.012 83 38 1 34 116 274 355 2.63e-20 84.0
Msa1235060 MtrunA17_Chr2g0311711 46.988 83 35 4 34 112 288 365 2.60e-15 70.5
Msa1235060 MtrunA17_Chr1g0161081 38.095 84 48 3 34 116 291 371 3.92e-13 64.3
Msa1235060 MtrunA17_Chr1g0161041 40.476 84 46 3 34 116 314 394 6.36e-13 63.5
Msa1235060 MtrunA17_Chr8g0375701 34.483 87 53 2 31 117 273 355 6.83e-13 63.5
Msa1235060 MtrunA17_Chr2g0314361 34.940 83 50 3 35 117 1 79 4.80e-12 57.4
Msa1235060 MtrunA17_Chr5g0412651 33.784 74 46 1 32 105 264 334 7.23e-12 60.5
Msa1235060 MtrunA17_Chr7g0266651 35.294 85 53 2 34 117 279 362 2.52e-11 58.9
Msa1235060 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
Msa1235060 AT1G06650.2 64.706 85 28 2 34 117 286 369 6.67e-34 120
Msa1235060 AT1G06620.1 62.069 87 32 1 31 117 280 365 7.55e-32 115
Msa1235060 AT1G04380.1 61.905 84 31 1 34 117 263 345 1.25e-31 114
Msa1235060 AT5G59530.1 63.095 84 30 1 34 117 282 364 8.04e-31 112
Msa1235060 AT5G59540.1 60.714 84 32 1 34 117 284 366 1.55e-30 112
Msa1235060 AT1G06645.1 59.091 88 34 2 31 117 293 379 1.39e-29 109
Msa1235060 AT1G06640.1 59.091 88 34 2 31 117 283 369 4.19e-28 105
Msa1235060 AT1G04350.1 61.176 85 31 2 34 117 277 360 1.50e-26 101
Msa1235060 AT5G43440.1 54.762 84 37 1 34 117 283 365 4.61e-24 94.7
Msa1235060 AT5G43450.1 57.143 84 35 1 34 117 280 362 2.27e-23 92.8
Msa1235060 AT2G30830.1 54.545 88 37 3 31 117 273 358 3.91e-23 92.0
Msa1235060 AT3G61400.1 52.273 88 39 2 31 117 285 370 5.38e-23 92.0
Msa1235060 AT2G30840.1 57.647 85 33 3 34 117 280 362 2.02e-21 87.4
Msa1235060 AT2G25450.1 53.488 86 36 3 34 117 276 359 2.31e-20 84.7
Msa1235060 AT1G03410.2 48.235 85 41 3 34 117 279 361 9.30e-20 82.8
Msa1235060 AT1G03410.1 48.235 85 41 3 34 117 316 398 1.16e-19 82.8
Msa1235060 AT2G30840.3 56.250 80 32 3 39 117 279 356 3.24e-18 78.6
Msa1235060 AT1G03400.2 49.425 87 41 3 32 117 295 379 4.87e-18 78.2
Msa1235060 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_2:-12868436 None:intergenic
TATTCTTGGACCAACTTTAT+TGG 0.191904 8_2:-12868325 None:intergenic
AATTTATGATGGTGTTGTTT+TGG 0.321555 8_2:+12867969 Msa1235060:CDS
AAGCATGCAACAGATATTCT+TGG 0.361845 8_2:-12868339 None:intergenic
ACAGTAGTTTCTTTGTATTT+GGG 0.372639 8_2:-12868435 None:intergenic
AAAGCATCTTCAAAGCTCTA+TGG 0.389751 8_2:+12868378 Msa1235060:CDS
TCTGATAATAGTTCCTTCAT+TGG 0.398109 8_2:-12868402 None:intergenic
ATTGCACAAACTAGATTGTA+TGG 0.416113 8_2:-12867944 None:intergenic
GCCTACTACTTTCGAGCAAA+AGG 0.422708 8_2:+12868471 Msa1235060:CDS
TTTCGAGCAAAAGGAGTAGA+TGG 0.447527 8_2:+12868480 Msa1235060:CDS
TTGTGCAATCTAATTTATGA+TGG 0.517183 8_2:+12867958 Msa1235060:CDS
AAAGCTCTATGGACCAATGA+AGG 0.519376 8_2:+12868389 Msa1235060:CDS
AGAGTACTTGCCAATAAAGT+TGG 0.534486 8_2:+12868315 Msa1235060:CDS
TGAAGATGCTTTAAGTCCTG+TGG 0.560622 8_2:-12868367 None:intergenic
GTAGTTTCTTTGTATTTGGG+AGG 0.568718 8_2:-12868432 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAACAAATAATTAGCTAT+AGG - chr8_2:12868248-12868267 None:intergenic 20.0%
! TTGTGCAATCTAATTTATGA+TGG + chr8_2:12867958-12867977 Msa1235060:CDS 25.0%
!!! AATTTATGATGGTGTTGTTT+TGG + chr8_2:12867969-12867988 Msa1235060:CDS 25.0%
! ACAAATAATTAGCTATAGGA+AGG - chr8_2:12868244-12868263 None:intergenic 25.0%
! ACAGTAGTTTCTTTGTATTT+GGG - chr8_2:12868438-12868457 None:intergenic 25.0%
! AACAGTAGTTTCTTTGTATT+TGG - chr8_2:12868439-12868458 None:intergenic 25.0%
ATTGCACAAACTAGATTGTA+TGG - chr8_2:12867947-12867966 None:intergenic 30.0%
TATTCTTGGACCAACTTTAT+TGG - chr8_2:12868328-12868347 None:intergenic 30.0%
TCTGATAATAGTTCCTTCAT+TGG - chr8_2:12868405-12868424 None:intergenic 30.0%
TGCCTTATCTTCCATCTTAT+TGG + chr8_2:12868048-12868067 Msa1235060:intron 35.0%
CTCCAATAAGATGGAAGATA+AGG - chr8_2:12868053-12868072 None:intergenic 35.0%
CTTATCTTCCATCTTATTGG+AGG + chr8_2:12868051-12868070 Msa1235060:intron 35.0%
ACATAACACCTCCAATAAGA+TGG - chr8_2:12868062-12868081 None:intergenic 35.0%
! AGAGTACTTGCCAATAAAGT+TGG + chr8_2:12868315-12868334 Msa1235060:CDS 35.0%
AAGCATGCAACAGATATTCT+TGG - chr8_2:12868342-12868361 None:intergenic 35.0%
! AAAGCATCTTCAAAGCTCTA+TGG + chr8_2:12868378-12868397 Msa1235060:CDS 35.0%
GTAGTTTCTTTGTATTTGGG+AGG - chr8_2:12868435-12868454 None:intergenic 35.0%
GACACCAGAGCTACAAAAAT+AGG + chr8_2:12867916-12867935 Msa1235060:CDS 40.0%
!!! GTGTCCTATTTTTGTAGCTC+TGG - chr8_2:12867923-12867942 None:intergenic 40.0%
! AGTCTCCTGCATTTTCAACT+TGG + chr8_2:12868009-12868028 Msa1235060:intron 40.0%
! TGAAGCCAAGTTGAAAATGC+AGG - chr8_2:12868017-12868036 None:intergenic 40.0%
AGATAGAACAGTGCCTAACT+TGG + chr8_2:12868208-12868227 Msa1235060:intron 40.0%
! TGAAGATGCTTTAAGTCCTG+TGG - chr8_2:12868370-12868389 None:intergenic 40.0%
AAAGCTCTATGGACCAATGA+AGG + chr8_2:12868389-12868408 Msa1235060:CDS 40.0%
! TCCTTTTGCTCGAAAGTAGT+AGG - chr8_2:12868475-12868494 None:intergenic 40.0%
TTTCGAGCAAAAGGAGTAGA+TGG + chr8_2:12868480-12868499 Msa1235060:CDS 40.0%
AGGTGCAGATTCTCCAAGTT+AGG - chr8_2:12868224-12868243 None:intergenic 45.0%
!!! GTTGCATGCTTTTTCTCCAC+AGG + chr8_2:12868351-12868370 Msa1235060:CDS 45.0%
GCCTACTACTTTCGAGCAAA+AGG + chr8_2:12868471-12868490 Msa1235060:CDS 45.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 12867892 12868533 12867892 ID=Msa1235060;Name=Msa1235060
chr8_2 mRNA 12867892 12868533 12867892 ID=Msa1235060-mRNA-1;Parent=Msa1235060;Name=Msa1235060-mRNA-1;_AED=0.61;_eAED=0.61;_QI=0|0|0|0.5|1|1|2|0|117
chr8_2 exon 12867892 12867990 12867892 ID=Msa1235060-mRNA-1:exon:4994;Parent=Msa1235060-mRNA-1
chr8_2 exon 12868279 12868533 12868279 ID=Msa1235060-mRNA-1:exon:4995;Parent=Msa1235060-mRNA-1
chr8_2 CDS 12867892 12867990 12867892 ID=Msa1235060-mRNA-1:cds;Parent=Msa1235060-mRNA-1
chr8_2 CDS 12868279 12868533 12868279 ID=Msa1235060-mRNA-1:cds;Parent=Msa1235060-mRNA-1
Gene Sequence

>Msa1235060

ATGTGTCATGCACTAAGCAAAACAGACACCAGAGCTACAAAAATAGGACACACCATACAATCTAGTTTGTGCAATCTAATTTATGATGGTGTTGTTTTGCTCATAACAAATGACAAATTCAAGAGTGTTGTACATAGAGTACTTGCCAATAAAGTTGGTCCAAGAATATCTGTTGCATGCTTTTTCTCCACAGGACTTAAAGCATCTTCAAAGCTCTATGGACCAATGAAGGAACTATTATCAGAAGACAATCCTCCCAAATACAAAGAAACTACTGTTGCTGATTATGTAGCCTACTACTTTCGAGCAAAAGGAGTAGATGGTACTTCTGCACTTGAACATTACAAAATTTGA
Protein sequence

>Msa1235060

MCHALSKTDTRATKIGHTIQSSLCNLIYDGVVLLITNDKFKSVVHRVLANKVGPRISVACFFSTGLKASSKLYGPMKELLSEDNPPKYKETTVADYVAYYFRAKGVDGTSALEHYKI*