AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0936690

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936690 MtrunA17_Chr6g0452771 93.258 89 6 0 1 89 396 484 2.01e-56 180
Msa0936690 MtrunA17_Chr6g0454331 85.227 88 13 0 1 88 395 482 1.13e-49 162
Msa0936690 MtrunA17_Chr6g0454171 82.022 89 16 0 1 89 226 314 3.67e-49 157
Msa0936690 MtrunA17_Chr6g0454141 82.955 88 15 0 1 88 396 483 1.60e-48 159
Msa0936690 MtrunA17_Chr8g0336331 84.091 88 14 0 1 88 393 480 2.26e-47 156
Msa0936690 MtrunA17_Chr6g0454201 84.091 88 14 0 1 88 397 484 2.98e-47 156
Msa0936690 MtrunA17_Chr6g0454151 82.022 89 16 0 1 89 394 482 1.09e-46 155
Msa0936690 MtrunA17_Chr6g0454291 80.460 87 17 0 1 87 393 479 1.04e-45 152
Msa0936690 MtrunA17_Chr5g0427561 79.545 88 18 0 1 88 1 88 1.15e-44 139
Msa0936690 MtrunA17_Chr7g0217881 77.528 89 20 0 1 89 378 466 1.92e-44 148
Msa0936690 MtrunA17_Chr6g0454271 77.273 88 20 0 1 88 203 290 4.18e-44 144
Msa0936690 MtrunA17_Chr6g0454351 77.528 89 20 0 1 89 381 469 4.20e-44 147
Msa0936690 MtrunA17_Chr3g0078841 77.273 88 20 0 1 88 394 481 6.17e-44 147
Msa0936690 MtrunA17_Chr6g0454341 77.273 88 20 0 1 88 394 481 7.15e-44 147
Msa0936690 MtrunA17_Chr6g0454361 76.404 89 21 0 1 89 397 485 2.24e-43 146
Msa0936690 MtrunA17_Chr6g0454301 80.460 87 17 0 1 87 647 733 2.95e-43 148
Msa0936690 MtrunA17_Chr6g0454301 72.093 86 24 0 1 86 146 231 2.11e-39 137
Msa0936690 MtrunA17_Chr6g0454261 78.409 88 19 0 1 88 396 483 3.52e-43 145
Msa0936690 MtrunA17_Chr6g0454191 77.273 88 20 0 1 88 397 484 4.28e-43 145
Msa0936690 MtrunA17_Chr8g0355011 76.136 88 21 0 1 88 278 365 4.83e-43 143
Msa0936690 MtrunA17_Chr6g0454221 78.313 83 18 0 1 83 147 229 1.90e-42 140
Msa0936690 MtrunA17_Chr6g0454401 76.136 88 21 0 1 88 397 484 2.37e-42 143
Msa0936690 MtrunA17_Chr8g0359821 76.136 88 21 0 1 88 394 481 5.51e-42 142
Msa0936690 MtrunA17_Chr5g0423981 70.787 89 26 0 1 89 361 449 7.23e-42 141
Msa0936690 MtrunA17_Chr6g0454371 75.000 88 22 0 1 88 87 174 1.83e-41 133
Msa0936690 MtrunA17_Chr6g0453961 69.663 89 27 0 1 89 406 494 6.82e-41 139
Msa0936690 MtrunA17_Chr6g0454211 73.864 88 23 0 1 88 683 770 1.01e-40 141
Msa0936690 MtrunA17_Chr6g0454131 71.591 88 25 0 1 88 395 482 1.47e-40 139
Msa0936690 MtrunA17_Chr6g0454181 72.727 88 24 0 1 88 396 483 2.52e-40 138
Msa0936690 MtrunA17_Chr6g0454121 71.591 88 25 0 1 88 395 482 4.78e-40 137
Msa0936690 MtrunA17_Chr6g0453951 69.663 89 27 0 1 89 443 531 2.63e-39 135
Msa0936690 MtrunA17_Chr6g0454231 72.093 86 23 1 1 85 134 219 2.92e-35 124
Msa0936690 MtrunA17_Chr6g0454321 69.620 79 24 0 1 79 394 472 8.62e-34 121
Msa0936690 MtrunA17_Chr3g0118721 54.762 84 38 0 2 85 207 290 1.25e-27 101
Msa0936690 MtrunA17_Chr3g0118671 53.571 84 39 0 2 85 391 474 1.30e-27 103
Msa0936690 MtrunA17_Chr3g0118751 53.571 84 39 0 2 85 362 445 3.07e-27 102
Msa0936690 MtrunA17_Chr3g0118771 53.571 84 39 0 2 85 406 489 5.02e-27 102
Msa0936690 MtrunA17_Chr3g0118711 52.381 84 40 0 2 85 398 481 6.46e-27 102
Msa0936690 MtrunA17_Chr3g0118691 51.190 84 41 0 2 85 400 483 1.76e-25 97.8
Msa0936690 MtrunA17_Chr2g0278711 54.023 87 39 1 1 86 392 478 4.69e-25 96.7
Msa0936690 MtrunA17_Chr3g0118701 50.000 84 42 0 2 85 400 483 1.34e-24 95.5
Msa0936690 MtrunA17_Chr5g0426431 48.864 88 43 2 1 87 394 480 3.57e-22 88.6
Msa0936690 MtrunA17_Chr5g0426401 50.000 88 40 3 1 86 227 312 4.32e-22 87.0
Msa0936690 MtrunA17_Chr4g0050341 48.148 81 42 0 1 81 407 487 6.51e-22 87.8
Msa0936690 MtrunA17_Chr8g0336261 76.471 51 12 0 1 51 87 137 1.07e-21 82.4
Msa0936690 MtrunA17_Chr3g0092641 45.977 87 45 2 1 86 394 479 1.78e-20 84.0
Msa0936690 MtrunA17_Chr3g0112771 41.176 85 50 0 1 85 368 452 9.41e-20 81.6
Msa0936690 MtrunA17_Chr6g0454241 78.049 41 9 0 44 84 1 41 4.16e-16 66.6
Msa0936690 MtrunA17_Chr4g0032331 36.842 76 48 0 1 76 368 443 2.75e-15 69.3
Msa0936690 MtrunA17_Chr5g0412101 36.905 84 52 1 1 84 388 470 4.26e-13 62.8
Msa0936690 MtrunA17_Chr5g0412131 36.905 84 52 1 1 84 387 469 5.44e-13 62.8
Msa0936690 MtrunA17_Chr3g0118661 45.783 83 45 0 1 83 396 478 1.62e-12 61.2
Msa0936690 MtrunA17_Chr3g0112761 31.395 86 58 1 1 85 365 450 2.36e-12 60.8
Msa0936690 MtrunA17_Chr4g0072771 37.647 85 52 1 1 84 381 465 4.92e-12 60.1
Msa0936690 MtrunA17_Chr5g0412111 32.143 84 56 1 1 84 379 461 4.08e-11 57.4
Msa0936690 MtrunA17_Chr6g0462571 34.524 84 51 1 1 80 374 457 9.66e-11 56.2
Msa0936690 MtrunA17_Chr3g0098111 31.111 90 56 1 1 84 380 469 9.95e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936690 AT1G22400.1 50.562 89 43 1 1 88 397 485 5.37e-24 94.4
Msa0936690 AT1G78270.1 50.000 86 42 1 1 85 396 481 6.11e-24 94.0
Msa0936690 AT1G22380.1 48.276 87 44 1 1 86 396 482 1.35e-23 93.2
Msa0936690 AT1G22340.1 48.864 88 44 1 1 87 397 484 4.24e-23 91.7
Msa0936690 AT1G22360.1 46.067 89 47 1 1 88 393 481 3.10e-20 83.6
Msa0936690 AT1G22370.2 52.809 89 41 1 1 88 391 479 2.49e-17 75.5
Msa0936690 AT5G59590.1 36.905 84 53 0 1 84 366 449 2.92e-17 75.1
Msa0936690 AT1G22370.1 52.809 89 41 1 1 88 221 309 2.42e-16 72.0
Msa0936690 AT3G11340.1 35.294 85 55 0 1 85 361 445 3.48e-16 72.0
Msa0936690 AT3G46660.1 35.366 82 53 0 1 82 372 453 1.66e-14 67.4
Msa0936690 AT3G46720.1 37.805 82 51 0 1 82 357 438 2.47e-14 67.0
Msa0936690 AT3G46670.1 34.146 82 54 0 1 82 365 446 2.92e-14 66.6
Msa0936690 AT5G59580.1 29.213 89 63 0 1 89 364 452 5.62e-14 65.9
Msa0936690 AT5G38010.1 35.802 81 52 0 1 81 370 450 8.07e-14 65.5
Msa0936690 AT5G05860.1 32.558 86 58 0 1 86 364 449 9.61e-14 65.1
Msa0936690 AT5G05870.1 30.952 84 58 0 1 84 371 454 1.02e-13 65.1
Msa0936690 AT3G46680.1 35.366 82 53 0 1 82 366 447 1.05e-13 65.1
Msa0936690 AT5G38040.1 33.333 81 54 0 1 81 366 446 4.58e-13 63.2
Msa0936690 AT5G17040.2 36.047 86 54 1 1 85 253 338 5.72e-13 62.8
Msa0936690 AT5G05880.1 30.952 84 58 0 1 84 365 448 5.96e-13 62.8
Msa0936690 AT5G17040.1 36.047 86 54 1 1 85 355 440 6.43e-13 62.8
Msa0936690 AT2G26480.1 28.736 87 62 0 1 87 362 448 2.60e-12 61.2
Msa0936690 AT5G17050.1 41.379 87 46 2 1 82 372 458 3.05e-12 60.8
Msa0936690 AT1G30530.1 36.047 86 54 1 1 85 366 451 5.73e-12 60.1
Msa0936690 AT1G22360.2 37.079 89 43 2 1 88 393 469 7.64e-12 59.7
Msa0936690 AT5G05890.1 30.952 84 58 0 1 84 369 452 1.12e-11 59.3
Msa0936690 AT3G55700.1 33.721 86 55 2 1 85 367 451 1.91e-11 58.5
Msa0936690 AT3G55710.1 34.884 86 54 2 1 85 371 455 2.39e-11 58.5
Msa0936690 AT3G46700.1 30.952 84 58 0 1 84 361 444 2.78e-11 58.2
Msa0936690 AT3G46690.1 38.272 81 50 0 1 81 366 446 3.59e-11 57.8

Find 23 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATCCCAATCTTCCATTCT+TGG 0.164386 6_3:+7534074 None:intergenic
TGGCAAATAATTCTACTGTT+AGG 0.360863 6_3:+7534094 None:intergenic
GAATTGATGGTGGGAGATAA+AGG 0.366402 6_3:-7534004 Msa0936690:CDS
ATTTGCCAAGAATGGAAGAT+TGG 0.375696 6_3:-7534079 Msa0936690:CDS
GTAGAATTATTTGCCAAGAA+TGG 0.382761 6_3:-7534087 Msa0936690:CDS
GCAGATGAGGACACAAGATT+TGG 0.413358 6_3:-7533941 Msa0936690:CDS
TTTGCCAAGAATGGAAGATT+GGG 0.444354 6_3:-7534078 Msa0936690:CDS
TGCCTTCTTCTTCAACTCCA+TGG 0.445104 6_3:+7533961 None:intergenic
GAAACTGATTAATGAATTGA+TGG 0.464761 6_3:-7534017 Msa0936690:CDS
TACCTCTTCTCTCTTTACAT+TGG 0.485576 6_3:+7534042 None:intergenic
AGGAAAGAAGATGAGGCAAA+AGG 0.504752 6_3:-7533984 Msa0936690:CDS
GATGAGGACACAAGATTTGG+TGG 0.524837 6_3:-7533938 Msa0936690:CDS
GAAGATGAGGCAAAAGGCCA+TGG 0.548548 6_3:-7533978 Msa0936690:CDS
GGCCATGGAGTTGAAGAAGA+AGG 0.559979 6_3:-7533963 Msa0936690:CDS
GTTGAAGAAGAAGGCAGATG+AGG 0.560190 6_3:-7533954 Msa0936690:CDS
TGGTTGTTCATATATGAACT+TGG 0.560604 6_3:-7533918 Msa0936690:CDS
GAGATAAAGGAAAGAAGATG+AGG 0.578725 6_3:-7533991 Msa0936690:CDS
CCAAGAATGGAAGATTGGGA+TGG 0.581034 6_3:-7534074 Msa0936690:CDS
ACTGATTAATGAATTGATGG+TGG 0.584937 6_3:-7534014 Msa0936690:CDS
CTGATTAATGAATTGATGGT+GGG 0.598725 6_3:-7534013 Msa0936690:CDS
CCGGAGTGCCAATGTTGTGT+AGG 0.599133 6_3:-7534138 None:intergenic
TACCAATGTAAAGAGAGAAG+AGG 0.629268 6_3:-7534044 Msa0936690:CDS
CTTGGACAAAGTGATCAATG+AGG 0.725106 6_3:-7533900 Msa0936690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GAAACTGATTAATGAATTGA+TGG - chr6_3:7533990-7534009 Msa0936690:CDS 25.0%
TGGCAAATAATTCTACTGTT+AGG + chr6_3:7533916-7533935 None:intergenic 30.0%
GTAGAATTATTTGCCAAGAA+TGG - chr6_3:7533920-7533939 Msa0936690:CDS 30.0%
ACTGATTAATGAATTGATGG+TGG - chr6_3:7533993-7534012 Msa0936690:CDS 30.0%
! CTGATTAATGAATTGATGGT+GGG - chr6_3:7533994-7534013 Msa0936690:CDS 30.0%
TGGTTGTTCATATATGAACT+TGG - chr6_3:7534089-7534108 Msa0936690:CDS 30.0%
GGTAGTTGATCAGCAAAAAA+TGG + chr6_3:7533895-7533914 None:intergenic 35.0%
ATTTGCCAAGAATGGAAGAT+TGG - chr6_3:7533928-7533947 Msa0936690:CDS 35.0%
TTTGCCAAGAATGGAAGATT+GGG - chr6_3:7533929-7533948 Msa0936690:CDS 35.0%
TACCAATGTAAAGAGAGAAG+AGG - chr6_3:7533963-7533982 Msa0936690:CDS 35.0%
TACCTCTTCTCTCTTTACAT+TGG + chr6_3:7533968-7533987 None:intergenic 35.0%
GAGATAAAGGAAAGAAGATG+AGG - chr6_3:7534016-7534035 Msa0936690:CDS 35.0%
!! GAATTGATGGTGGGAGATAA+AGG - chr6_3:7534003-7534022 Msa0936690:CDS 40.0%
AGGAAAGAAGATGAGGCAAA+AGG - chr6_3:7534023-7534042 Msa0936690:CDS 40.0%
CTTGGACAAAGTGATCAATG+AGG - chr6_3:7534107-7534126 Msa0936690:CDS 40.0%
CCATCCCAATCTTCCATTCT+TGG + chr6_3:7533936-7533955 None:intergenic 45.0%
CCAAGAATGGAAGATTGGGA+TGG - chr6_3:7533933-7533952 Msa0936690:CDS 45.0%
TGCCTTCTTCTTCAACTCCA+TGG + chr6_3:7534049-7534068 None:intergenic 45.0%
GTTGAAGAAGAAGGCAGATG+AGG - chr6_3:7534053-7534072 Msa0936690:CDS 45.0%
GCAGATGAGGACACAAGATT+TGG - chr6_3:7534066-7534085 Msa0936690:CDS 45.0%
GATGAGGACACAAGATTTGG+TGG - chr6_3:7534069-7534088 Msa0936690:CDS 45.0%
GAAGATGAGGCAAAAGGCCA+TGG - chr6_3:7534029-7534048 Msa0936690:CDS 50.0%
GGCCATGGAGTTGAAGAAGA+AGG - chr6_3:7534044-7534063 Msa0936690:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 7533880 7534149 7533880 ID=Msa0936690;Name=Msa0936690
chr6_3 mRNA 7533880 7534149 7533880 ID=Msa0936690-mRNA-1;Parent=Msa0936690;Name=Msa0936690-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|-1|0|1|-1|1|1|0|89
chr6_3 exon 7533880 7534149 7533880 ID=Msa0936690-mRNA-1:exon:2515;Parent=Msa0936690-mRNA-1
chr6_3 CDS 7533880 7534149 7533880 ID=Msa0936690-mRNA-1:cds;Parent=Msa0936690-mRNA-1
Gene Sequence

>Msa0936690

ATGTTGTGTAGGCCATTTTTTGCTGATCAACTACCTAACAGTAGAATTATTTGCCAAGAATGGAAGATTGGGATGGAAATTGATACCAATGTAAAGAGAGAAGAGGTAGAGAAACTGATTAATGAATTGATGGTGGGAGATAAAGGAAAGAAGATGAGGCAAAAGGCCATGGAGTTGAAGAAGAAGGCAGATGAGGACACAAGATTTGGTGGTTGTTCATATATGAACTTGGACAAAGTGATCAATGAGGTCTTGCTTAAACAATATTAG
Protein sequence

>Msa0936690

MLCRPFFADQLPNSRIICQEWKIGMEIDTNVKREEVEKLINELMVGDKGKKMRQKAMELKKKADEDTRFGGCSYMNLDKVINEVLLKQY*