AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0048100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0048100 MtrunA17_Chr4g0014841 90.435 115 11 0 1 115 249 363 4.24e-69 216
Msa0048100 MtrunA17_Chr4g0014801 82.759 116 18 1 1 114 249 364 6.33e-63 200
Msa0048100 MtrunA17_Chr4g0014781 82.906 117 18 1 1 115 249 365 3.31e-62 198
Msa0048100 MtrunA17_Chr4g0014791 79.661 118 18 3 1 115 249 363 7.66e-57 184
Msa0048100 MtrunA17_Chr4g0014861 76.068 117 25 2 1 114 125 241 2.75e-56 180
Msa0048100 MtrunA17_Chr4g0014871 72.650 117 29 2 1 114 250 366 2.89e-53 174
Msa0048100 MtrunA17_Chr3g0077151 57.895 114 44 2 1 113 245 355 4.83e-37 131
Msa0048100 MtrunA17_Chr2g0276751 35.593 118 72 1 1 114 265 382 1.80e-19 82.4
Msa0048100 MtrunA17_Chr3g0082631 36.090 133 64 3 1 112 137 269 1.59e-18 79.3
Msa0048100 MtrunA17_Chr7g0217461 33.594 128 67 5 3 113 255 381 6.01e-18 77.8
Msa0048100 MtrunA17_Chr1g0166771 33.858 127 71 3 1 115 221 346 1.28e-17 77.0
Msa0048100 MtrunA17_Chr4g0056431 37.121 132 61 4 1 111 255 385 2.07e-17 76.3
Msa0048100 MtrunA17_Chr1g0166791 34.400 125 69 3 3 115 256 379 4.76e-17 75.5
Msa0048100 MtrunA17_Chr1g0157611 33.333 129 66 4 3 113 243 369 1.26e-16 74.3
Msa0048100 MtrunA17_Chr1g0166731 36.290 124 67 4 1 113 152 274 1.27e-16 73.9
Msa0048100 MtrunA17_Chr7g0261811 34.454 119 68 2 3 111 260 378 3.33e-16 72.8
Msa0048100 MtrunA17_Chr1g0166711 35.484 124 68 4 1 113 255 377 5.19e-16 72.4
Msa0048100 MtrunA17_Chr1g0166741 32.283 127 73 3 1 115 257 382 6.17e-16 72.0
Msa0048100 MtrunA17_Chr7g0261831 32.500 120 70 2 3 111 3 122 3.34e-15 68.2
Msa0048100 MtrunA17_Chr5g0400371 37.634 93 48 3 31 114 381 472 4.87e-15 69.7
Msa0048100 MtrunA17_Chr4g0054891 37.634 93 48 3 31 114 379 470 7.53e-15 68.9
Msa0048100 MtrunA17_Chr7g0261661 31.933 119 71 1 3 111 146 264 2.45e-14 67.8
Msa0048100 MtrunA17_Chr7g0218851 30.894 123 70 5 3 111 279 400 3.85e-14 67.0
Msa0048100 MtrunA17_Chr3g0104011 31.250 128 71 4 1 111 248 375 4.01e-14 67.0
Msa0048100 MtrunA17_Chr4g0008651 37.143 105 60 2 16 115 285 388 5.19e-14 66.6
Msa0048100 MtrunA17_Chr8g0353031 31.387 137 71 4 1 114 228 364 5.22e-14 66.6
Msa0048100 MtrunA17_Chr1g0187241 33.333 123 69 3 1 111 256 377 6.55e-14 66.2
Msa0048100 MtrunA17_Chr7g0261881 31.092 119 72 2 3 111 260 378 9.21e-14 65.9
Msa0048100 MtrunA17_Chr7g0261771 33.333 123 72 2 3 115 264 386 1.19e-13 65.9
Msa0048100 MtrunA17_Chr7g0214461 30.894 123 70 4 3 111 309 430 1.99e-13 65.1
Msa0048100 MtrunA17_Chr7g0241741 31.496 127 71 4 1 111 247 373 2.03e-13 65.1
Msa0048100 MtrunA17_Chr4g0063591 36.275 102 52 3 20 111 275 373 2.05e-13 65.1
Msa0048100 MtrunA17_Chr1g0213711 30.952 126 71 3 1 111 249 373 2.40e-13 64.7
Msa0048100 MtrunA17_Chr7g0261791 31.707 123 74 1 3 115 263 385 2.82e-13 64.7
Msa0048100 MtrunA17_Chr4g0005901 31.373 102 62 2 18 111 282 383 3.37e-13 64.3
Msa0048100 MtrunA17_Chr6g0451841 40.000 65 39 0 49 113 284 348 7.86e-13 63.2
Msa0048100 MtrunA17_Chr3g0112611 37.143 105 59 2 16 115 282 384 8.18e-13 63.2
Msa0048100 MtrunA17_Chr8g0375311 44.262 61 33 1 54 114 337 396 8.66e-13 63.2
Msa0048100 MtrunA17_Chr8g0375361 34.021 97 56 2 24 113 299 394 4.18e-12 61.2
Msa0048100 MtrunA17_Chr8g0375291 45.000 60 32 1 54 113 337 395 5.87e-12 60.8
Msa0048100 MtrunA17_Chr5g0399071 35.385 130 64 4 1 111 254 382 7.34e-12 60.5
Msa0048100 MtrunA17_Chr4g0060071 40.000 80 45 2 32 111 32 108 8.06e-12 60.1
Msa0048100 MtrunA17_Chr8g0375331 45.000 60 32 1 54 113 321 379 9.41e-12 60.1
Msa0048100 MtrunA17_Chr1g0157601 31.008 129 69 4 3 113 242 368 1.13e-11 60.1
Msa0048100 MtrunA17_Chr3g0142101 32.222 90 58 1 25 111 297 386 1.18e-11 60.1
Msa0048100 MtrunA17_Chr5g0399061 34.848 132 67 4 1 113 255 386 1.20e-11 60.1
Msa0048100 MtrunA17_Chr4g0011471 36.986 73 45 1 39 111 302 373 1.52e-11 59.7
Msa0048100 MtrunA17_Chr3g0112671 49.123 57 29 0 57 113 327 383 1.52e-11 59.7
Msa0048100 MtrunA17_Chr2g0284701 32.857 140 63 6 1 114 264 398 1.62e-11 59.7
Msa0048100 MtrunA17_Chr7g0261751 35.443 79 51 0 37 115 344 422 1.80e-11 59.3
Msa0048100 MtrunA17_Chr5g0415961 39.506 81 46 2 32 111 307 385 2.56e-11 58.9
Msa0048100 MtrunA17_Chr8g0379971 31.298 131 69 5 4 114 271 400 2.81e-11 58.9
Msa0048100 MtrunA17_Chr8g0375321 43.333 60 33 1 54 113 334 392 3.21e-11 58.9
Msa0048100 MtrunA17_Chr8g0375341 43.333 60 33 1 54 113 337 395 3.61e-11 58.5
Msa0048100 MtrunA17_Chr7g0240381 43.103 58 33 0 57 114 325 382 5.21e-11 58.2
Msa0048100 MtrunA17_Chr3g0112631 42.373 59 34 0 57 115 29 87 5.92e-11 57.8
Msa0048100 MtrunA17_Chr3g0114501 29.032 124 75 2 1 111 249 372 9.34e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0048100 AT1G72125.1 48.739 119 54 3 1 114 253 369 1.42e-29 111
Msa0048100 AT1G22540.1 54.783 115 45 3 1 113 255 364 1.04e-28 108
Msa0048100 AT1G72120.1 49.558 113 54 2 1 112 253 363 1.55e-27 105
Msa0048100 AT1G72140.1 48.214 112 45 2 1 112 265 363 1.74e-25 99.8
Msa0048100 AT1G72130.2 47.009 117 49 3 1 113 127 234 4.64e-25 97.8
Msa0048100 AT1G72130.3 47.009 117 49 3 1 113 127 234 4.64e-25 97.8
Msa0048100 AT1G72130.1 47.009 117 49 3 1 113 245 352 8.19e-25 97.8
Msa0048100 AT1G22550.1 44.737 114 60 2 1 114 262 372 2.83e-24 96.3
Msa0048100 AT1G22570.2 44.828 116 56 3 1 111 224 336 1.36e-21 88.6
Msa0048100 AT1G22570.1 44.828 116 56 3 1 111 261 373 1.39e-21 88.6
Msa0048100 AT3G54450.1 32.117 137 69 3 1 115 223 357 5.47e-17 75.5
Msa0048100 AT1G33440.1 34.646 127 67 3 1 114 264 387 1.97e-15 71.2
Msa0048100 AT1G59740.1 38.636 88 50 1 31 114 309 396 3.63e-15 70.5
Msa0048100 AT5G14940.1 46.377 69 36 1 45 113 288 355 6.45e-15 69.7
Msa0048100 AT1G62200.1 37.079 89 48 3 30 111 319 406 1.60e-14 68.6
Msa0048100 AT5G46050.2 32.787 122 70 2 1 111 143 263 1.71e-14 68.6
Msa0048100 AT1G32450.1 35.789 95 51 2 28 113 304 397 1.81e-14 68.6
Msa0048100 AT5G46050.1 32.520 123 71 2 1 112 255 376 1.91e-14 68.2
Msa0048100 AT5G46040.1 29.600 125 78 1 1 115 255 379 1.11e-13 66.2
Msa0048100 AT3G01350.1 46.575 73 36 2 46 115 292 364 1.38e-13 65.9
Msa0048100 AT1G62200.3 44.828 58 31 1 54 111 393 449 1.48e-13 65.9
Msa0048100 AT1G62200.2 44.828 58 31 1 54 111 379 435 1.55e-13 65.9
Msa0048100 AT4G21680.1 37.895 95 47 4 31 114 292 385 1.57e-13 65.9
Msa0048100 AT3G54140.1 33.333 105 61 3 16 111 271 375 4.83e-13 64.3
Msa0048100 AT3G54140.2 33.333 105 61 3 16 111 271 375 4.83e-13 64.3
Msa0048100 AT5G01180.2 44.828 58 32 0 54 111 318 375 1.17e-12 63.2
Msa0048100 AT5G01180.3 44.828 58 32 0 54 111 318 375 1.17e-12 63.2
Msa0048100 AT5G01180.1 44.828 58 32 0 54 111 318 375 1.17e-12 63.2
Msa0048100 AT5G19640.1 30.709 127 71 4 1 111 282 407 1.20e-12 63.2
Msa0048100 AT2G02020.1 44.828 58 31 1 54 111 300 356 3.55e-12 62.0
Msa0048100 AT2G37900.1 38.043 92 49 3 31 115 299 389 1.03e-11 60.5
Msa0048100 AT2G37900.2 38.043 92 49 3 31 115 220 310 1.16e-11 60.5
Msa0048100 AT2G40460.1 34.375 96 60 1 16 111 274 366 4.83e-11 58.5
Msa0048100 AT2G02040.1 41.667 60 34 1 54 113 336 394 4.93e-11 58.5
Msa0048100 AT3G25260.1 33.333 117 68 2 1 114 238 347 7.66e-11 58.2

Find 27 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGCTACAACTTTGGTTTA+TGG 0.167031 1_2:+161880 Msa0048100:CDS
TACTAAGGTTGGTTCCAATT+TGG 0.203651 1_2:+161860 Msa0048100:CDS
ACCAAAGTTGTAGCCCAAAT+TGG 0.299132 1_2:-161874 None:intergenic
TCCAATTTGGGCTACAACTT+TGG 0.299380 1_2:+161873 Msa0048100:CDS
ACTACAAGTCTCGTCTTCTT+TGG 0.301060 1_2:-161809 None:intergenic
ACTAAGGTTGGTTCCAATTT+GGG 0.303752 1_2:+161861 Msa0048100:CDS
ATGCAGAAAACAATAGTTCC+TGG 0.369097 1_2:+161952 Msa0048100:CDS
TTCAATATCCGCTGTTGATA+AGG 0.369755 1_2:-161441 None:intergenic
TCGTTGCAGCTGTAAGAAAT+TGG 0.371085 1_2:+161411 Msa0048100:CDS
CTGCATAGAACTCCCTTGCT+TGG 0.411271 1_2:-161935 None:intergenic
TCGTCTTCTTTGGATCCCTT+TGG 0.422330 1_2:-161799 None:intergenic
TCTACATTCTTCACCAAGCA+AGG 0.478008 1_2:+161922 Msa0048100:CDS
GTTATCGTTTGAAGAGAGGC+AGG 0.510826 1_2:-161988 None:intergenic
AAGAAGCAAAGGCAGTACTA+AGG 0.553947 1_2:+161845 Msa0048100:CDS
TTACAGCTGCAACGAATACA+CGG 0.559250 1_2:-161403 None:intergenic
CAGTGAGATCGAAGAAGCAA+AGG 0.559693 1_2:+161834 Msa0048100:CDS
AGCAAAGGCAGTACTAAGGT+TGG 0.564362 1_2:+161849 Msa0048100:CDS
CAAGGGCAGGTTCCTCAACA+TGG 0.573606 1_2:+161765 Msa0048100:intron
ACAGCGGATATTGAAGAGGA+TGG 0.580451 1_2:+161449 Msa0048100:CDS
ATTGGTTATCGTTTGAAGAG+AGG 0.586290 1_2:-161992 None:intergenic
CTACATTCTTCACCAAGCAA+GGG 0.587319 1_2:+161923 Msa0048100:CDS
ATGGCATTGCTAAAACCAAA+GGG 0.587457 1_2:+161784 Msa0048100:CDS
CATGGCATTGCTAAAACCAA+AGG 0.607241 1_2:+161783 Msa0048100:CDS
ATCAACAGCGGATATTGAAG+AGG 0.620450 1_2:+161445 Msa0048100:CDS
GCAGGAGGTATGTCGAAACC+AGG 0.642425 1_2:-161970 None:intergenic
ATCGTTTGAAGAGAGGCAGG+AGG 0.679134 1_2:-161985 None:intergenic
GCGAAACACCTTATCAACAG+CGG 0.714560 1_2:+161433 Msa0048100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTGATTGTATTTTCAACAA+GGG + chr1_2:161748-161767 Msa0048100:intron 20.0%
!! TGAATTGTTCAGATTTTTGA+CGG - chr1_2:161484-161503 None:intergenic 25.0%
! ACATTCTGTTTATTTCCATT+GGG - chr1_2:161703-161722 None:intergenic 25.0%
! TACATTCTGTTTATTTCCAT+TGG - chr1_2:161704-161723 None:intergenic 25.0%
!! CTTTGATTGTATTTTCAACA+AGG + chr1_2:161747-161766 Msa0048100:intron 25.0%
AAAATACATCAATGTCCCAA+TGG + chr1_2:161685-161704 Msa0048100:intron 30.0%
TTCAATATCCGCTGTTGATA+AGG - chr1_2:161444-161463 None:intergenic 35.0%
! ATTGTATTTTCAACAAGGGC+AGG + chr1_2:161752-161771 Msa0048100:intron 35.0%
ATGGCATTGCTAAAACCAAA+GGG + chr1_2:161784-161803 Msa0048100:CDS 35.0%
! TACTAAGGTTGGTTCCAATT+TGG + chr1_2:161860-161879 Msa0048100:CDS 35.0%
! ACTAAGGTTGGTTCCAATTT+GGG + chr1_2:161861-161880 Msa0048100:CDS 35.0%
ATGCAGAAAACAATAGTTCC+TGG + chr1_2:161952-161971 Msa0048100:CDS 35.0%
TTACAGCTGCAACGAATACA+CGG - chr1_2:161406-161425 None:intergenic 40.0%
TCGTTGCAGCTGTAAGAAAT+TGG + chr1_2:161411-161430 Msa0048100:CDS 40.0%
ATCAACAGCGGATATTGAAG+AGG + chr1_2:161445-161464 Msa0048100:CDS 40.0%
!! GTTTTAGCAATGCCATGTTG+AGG - chr1_2:161780-161799 None:intergenic 40.0%
CATGGCATTGCTAAAACCAA+AGG + chr1_2:161783-161802 Msa0048100:CDS 40.0%
ACTACAAGTCTCGTCTTCTT+TGG - chr1_2:161812-161831 None:intergenic 40.0%
AAGAAGCAAAGGCAGTACTA+AGG + chr1_2:161845-161864 Msa0048100:CDS 40.0%
TCCAATTTGGGCTACAACTT+TGG + chr1_2:161873-161892 Msa0048100:CDS 40.0%
ACCAAAGTTGTAGCCCAAAT+TGG - chr1_2:161877-161896 None:intergenic 40.0%
! TGGGCTACAACTTTGGTTTA+TGG + chr1_2:161880-161899 Msa0048100:CDS 40.0%
TCTACATTCTTCACCAAGCA+AGG + chr1_2:161922-161941 Msa0048100:CDS 40.0%
CTACATTCTTCACCAAGCAA+GGG + chr1_2:161923-161942 Msa0048100:CDS 40.0%
GCGAAACACCTTATCAACAG+CGG + chr1_2:161433-161452 Msa0048100:CDS 45.0%
ACAGCGGATATTGAAGAGGA+TGG + chr1_2:161449-161468 Msa0048100:CDS 45.0%
TCGTCTTCTTTGGATCCCTT+TGG - chr1_2:161802-161821 None:intergenic 45.0%
CAGTGAGATCGAAGAAGCAA+AGG + chr1_2:161834-161853 Msa0048100:CDS 45.0%
AGCAAAGGCAGTACTAAGGT+TGG + chr1_2:161849-161868 Msa0048100:CDS 45.0%
GTTATCGTTTGAAGAGAGGC+AGG - chr1_2:161991-162010 None:intergenic 45.0%
CTGCATAGAACTCCCTTGCT+TGG - chr1_2:161938-161957 None:intergenic 50.0%
ATCGTTTGAAGAGAGGCAGG+AGG - chr1_2:161988-162007 None:intergenic 50.0%
CAAGGGCAGGTTCCTCAACA+TGG + chr1_2:161765-161784 Msa0048100:intron 55.0%
! GCAGGAGGTATGTCGAAACC+AGG - chr1_2:161973-161992 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 161398 162011 161398 ID=Msa0048100;Name=Msa0048100
chr1_2 mRNA 161398 162011 161398 ID=Msa0048100-mRNA-1;Parent=Msa0048100;Name=Msa0048100-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|1|0|1|1|0.5|2|0|115
chr1_2 exon 161398 161504 161398 ID=Msa0048100-mRNA-1:exon:9;Parent=Msa0048100-mRNA-1
chr1_2 exon 161774 162011 161774 ID=Msa0048100-mRNA-1:exon:10;Parent=Msa0048100-mRNA-1
chr1_2 CDS 161398 161504 161398 ID=Msa0048100-mRNA-1:cds;Parent=Msa0048100-mRNA-1
chr1_2 CDS 161774 162011 161774 ID=Msa0048100-mRNA-1:cds;Parent=Msa0048100-mRNA-1
Gene Sequence

>Msa0048100

ATCGGCCGTGTATTCGTTGCAGCTGTAAGAAATTGGCGAAACACCTTATCAACAGCGGATATTGAAGAGGATGGACTACTTCGCCGTCAAAAATCTGAACAATTCAAGTTCCTCAACATGGCATTGCTAAAACCAAAGGGATCCAAAGAAGACGAGACTTGTAGTCACAGTGAGATCGAAGAAGCAAAGGCAGTACTAAGGTTGGTTCCAATTTGGGCTACAACTTTGGTTTATGGCATTGTCTTTGCTCAAGTTTCTACATTCTTCACCAAGCAAGGGAGTTCTATGCAGAAAACAATAGTTCCTGGTTTCGACATACCTCCTGCCTCTCTTCAAACGATAACC
Protein sequence

>Msa0048100

IGRVFVAAVRNWRNTLSTADIEEDGLLRRQKSEQFKFLNMALLKPKGSKEDETCSHSEIEEAKAVLRLVPIWATTLVYGIVFAQVSTFFTKQGSSMQKTIVPGFDIPPASLQTIT