AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1223300

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1223300 MtrunA17_Chr4g0074791 92.308 104 2 1 1 104 252 349 1.41e-60 194
Msa1223300 MtrunA17_Chr4g0074811 79.808 104 15 1 1 104 247 344 1.75e-52 173
Msa1223300 MtrunA17_Chr3g0098951 69.231 104 26 1 1 104 240 337 1.12e-43 150
Msa1223300 MtrunA17_Chr1g0157131 69.231 104 26 1 1 104 230 327 1.85e-43 149
Msa1223300 MtrunA17_Chr5g0444171 66.346 104 29 1 1 104 248 345 2.25e-42 147
Msa1223300 MtrunA17_Chr5g0444191 64.706 102 30 1 1 102 64 159 7.18e-41 135
Msa1223300 MtrunA17_Chr5g0397101 50.350 143 57 3 2 141 224 355 6.06e-39 137
Msa1223300 MtrunA17_Chr8g0387671 62.136 103 33 1 2 104 223 319 1.75e-38 136
Msa1223300 MtrunA17_Chr3g0131181 60.577 104 35 1 1 104 185 282 3.59e-38 135
Msa1223300 MtrunA17_Chr1g0176421 57.692 104 38 1 1 104 317 414 7.86e-38 135
Msa1223300 MtrunA17_Chr1g0173541 58.824 102 36 1 3 104 210 305 9.12e-38 134
Msa1223300 MtrunA17_Chr0c02g0489761 57.692 104 38 1 1 104 234 331 9.86e-38 134
Msa1223300 MtrunA17_Chr7g0242561 61.765 102 33 1 3 104 214 309 2.13e-37 133
Msa1223300 MtrunA17_Chr1g0170281 61.000 100 33 1 5 104 278 371 2.15e-37 134
Msa1223300 MtrunA17_Chr4g0059951 60.784 102 34 1 3 104 231 326 2.83e-37 133
Msa1223300 MtrunA17_Chr1g0200601 57.692 104 38 1 1 104 186 283 2.83e-37 132
Msa1223300 MtrunA17_Chr5g0441691 58.824 102 36 1 3 104 226 321 3.18e-37 132
Msa1223300 MtrunA17_Chr7g0257751 57.843 102 37 1 3 104 216 311 4.04e-37 132
Msa1223300 MtrunA17_Chr5g0448721 55.769 104 40 1 1 104 252 349 7.17e-36 129
Msa1223300 MtrunA17_Chr1g0176751 59.223 103 36 1 2 104 281 377 1.82e-35 128
Msa1223300 MtrunA17_Chr7g0267751 55.882 102 39 1 3 104 293 388 2.19e-34 125
Msa1223300 MtrunA17_Chr8g0385341 59.804 102 35 1 3 104 188 283 1.20e-33 122
Msa1223300 MtrunA17_Chr4g0033371 53.333 105 43 1 3 107 230 328 9.52e-33 120
Msa1223300 MtrunA17_Chr7g0267771 51.961 102 43 1 3 104 246 341 6.88e-32 117
Msa1223300 MtrunA17_Chr8g0374701 49.020 102 46 1 4 105 291 386 4.49e-29 110
Msa1223300 MtrunA17_Chr4g0045261 50.495 101 44 1 4 104 300 394 1.56e-28 109
Msa1223300 MtrunA17_Chr5g0402551 48.515 101 46 1 4 104 297 391 1.65e-28 109
Msa1223300 MtrunA17_Chr7g0256001 50.495 101 44 1 4 104 304 398 1.94e-27 106
Msa1223300 MtrunA17_Chr5g0405421 47.115 104 49 1 1 104 257 354 8.72e-27 104
Msa1223300 MtrunA17_Chr3g0127571 43.548 124 59 2 4 127 301 413 1.70e-26 103
Msa1223300 MtrunA17_Chr7g0276111 42.105 133 66 2 4 136 307 428 3.24e-26 102
Msa1223300 MtrunA17_Chr1g0203881 47.475 99 46 1 6 104 202 294 2.75e-24 97.1
Msa1223300 MtrunA17_Chr1g0190131 39.604 101 54 2 6 105 166 260 1.40e-19 82.0
Msa1223300 MtrunA17_Chr3g0132591 40.404 99 53 1 6 104 263 355 5.81e-18 79.0
Msa1223300 MtrunA17_Chr8g0355131 40.196 102 50 3 6 104 208 301 2.78e-15 71.6
Msa1223300 MtrunA17_Chr7g0274941 38.532 109 53 3 1 104 170 269 2.07e-14 68.2
Msa1223300 MtrunA17_Chr6g0478601 36.000 100 48 4 7 101 301 389 2.47e-12 63.2
Msa1223300 MtrunA17_Chr5g0441011 40.000 100 46 6 8 104 175 263 1.56e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1223300 AT4G04720.2 69.231 104 26 1 1 104 236 333 6.47e-46 156
Msa1223300 AT4G04720.1 69.231 104 26 1 1 104 236 333 6.47e-46 156
Msa1223300 AT1G50700.3 68.269 104 27 1 1 104 229 326 3.85e-45 153
Msa1223300 AT1G50700.1 68.269 104 27 1 1 104 229 326 7.44e-45 153
Msa1223300 AT1G50700.2 68.269 104 27 1 1 104 229 326 1.05e-44 153
Msa1223300 AT3G20410.2 67.308 104 28 1 1 104 247 344 1.35e-43 150
Msa1223300 AT3G20410.1 67.308 104 28 1 1 104 247 344 1.35e-43 150
Msa1223300 AT4G21940.3 66.346 104 29 1 1 104 258 355 1.83e-43 149
Msa1223300 AT4G21940.1 66.346 104 29 1 1 104 258 355 4.11e-43 149
Msa1223300 AT4G21940.2 66.346 104 29 1 1 104 258 355 4.45e-43 149
Msa1223300 AT1G61950.1 67.308 104 28 1 1 104 255 352 1.53e-42 147
Msa1223300 AT1G76040.3 63.462 104 32 1 1 104 268 365 3.18e-41 143
Msa1223300 AT1G76040.1 63.462 104 32 1 1 104 30 127 4.36e-41 139
Msa1223300 AT1G76040.4 63.462 104 32 1 1 104 30 127 4.36e-41 139
Msa1223300 AT1G76040.2 63.462 104 32 1 1 104 268 365 5.96e-41 143
Msa1223300 AT4G04740.4 66.346 104 29 1 1 104 225 322 7.25e-41 142
Msa1223300 AT4G04740.6 66.346 104 29 1 1 104 225 322 7.25e-41 142
Msa1223300 AT4G04740.5 66.346 104 29 1 1 104 225 322 7.25e-41 142
Msa1223300 AT4G04740.3 66.346 104 29 1 1 104 225 322 7.25e-41 142
Msa1223300 AT4G04740.1 66.346 104 29 1 1 104 225 322 7.25e-41 142
Msa1223300 AT4G04740.7 66.346 104 29 1 1 104 225 322 7.25e-41 142
Msa1223300 AT4G04740.2 66.346 104 29 1 1 104 225 322 1.79e-40 142
Msa1223300 AT5G12480.2 59.804 102 35 1 3 104 123 218 3.88e-38 134
Msa1223300 AT2G41860.1 59.804 102 35 1 3 104 212 307 4.04e-38 135
Msa1223300 AT2G41860.2 59.804 102 35 1 3 104 212 307 4.04e-38 135
Msa1223300 AT5G04870.1 60.194 103 35 1 2 104 307 403 4.34e-38 136
Msa1223300 AT5G12480.1 59.804 102 35 1 3 104 217 312 1.20e-37 134
Msa1223300 AT3G10660.2 58.654 104 37 1 1 104 342 439 1.33e-37 135
Msa1223300 AT3G10660.1 58.654 104 37 1 1 104 342 439 1.33e-37 135
Msa1223300 AT5G12180.1 58.654 104 37 1 1 104 229 326 2.16e-37 133
Msa1223300 AT3G51850.2 58.824 102 36 1 3 104 212 307 4.26e-37 132
Msa1223300 AT4G23650.1 58.824 102 36 1 3 104 236 331 4.47e-37 132
Msa1223300 AT3G51850.1 58.824 102 36 1 3 104 212 307 5.32e-37 132
Msa1223300 AT5G19360.1 56.731 104 39 1 1 104 224 321 1.56e-36 131
Msa1223300 AT4G35310.2 55.769 104 40 1 1 104 253 350 3.08e-36 130
Msa1223300 AT4G35310.1 55.769 104 40 1 1 104 253 350 3.08e-36 130
Msa1223300 AT2G38910.1 55.769 104 40 1 1 104 290 387 3.12e-36 130
Msa1223300 AT5G19450.2 56.190 105 40 1 3 107 215 313 3.99e-36 130
Msa1223300 AT5G19450.1 56.190 105 40 1 3 107 215 313 3.99e-36 130
Msa1223300 AT2G17290.1 55.769 104 40 1 1 104 241 338 6.37e-36 129
Msa1223300 AT2G17290.2 55.769 104 40 1 1 104 241 338 6.37e-36 129
Msa1223300 AT3G51850.3 58.824 102 36 1 3 104 212 307 8.39e-36 127
Msa1223300 AT3G57530.1 55.882 102 39 1 3 104 221 316 3.20e-35 127
Msa1223300 AT4G38230.4 54.808 104 41 1 1 104 180 277 6.15e-35 126
Msa1223300 AT4G38230.3 54.808 104 41 1 1 104 180 277 6.15e-35 126
Msa1223300 AT4G38230.2 54.808 104 41 1 1 104 210 307 8.24e-35 126
Msa1223300 AT2G35890.2 53.922 102 41 1 3 104 290 385 1.16e-34 126
Msa1223300 AT2G35890.1 53.922 102 41 1 3 104 290 385 1.16e-34 126
Msa1223300 AT5G23580.1 56.863 102 38 1 3 104 180 275 1.31e-34 125
Msa1223300 AT3G57530.2 55.882 102 39 1 3 104 221 316 2.78e-34 124
Msa1223300 AT1G18890.1 56.311 103 39 1 3 105 221 317 5.08e-34 124
Msa1223300 AT4G38230.1 54.808 104 41 1 1 104 36 133 1.01e-33 120
Msa1223300 AT1G74740.1 56.863 102 38 1 3 104 217 312 3.50e-33 122
Msa1223300 AT1G35670.1 59.000 100 35 1 5 104 186 279 1.77e-32 120
Msa1223300 AT4G09570.1 58.000 100 36 1 5 104 185 278 7.11e-32 118
Msa1223300 AT2G31500.1 52.941 102 42 1 3 104 224 319 7.72e-32 119
Msa1223300 AT3G50530.1 49.505 101 45 1 4 104 311 405 3.35e-28 108
Msa1223300 AT3G50530.2 49.505 101 45 1 4 104 342 436 3.53e-28 108
Msa1223300 AT3G19100.1 50.495 101 44 1 4 104 307 401 7.76e-28 107
Msa1223300 AT4G04710.1 55.238 105 46 1 1 104 196 300 3.62e-27 105
Msa1223300 AT4G04710.4 55.238 105 46 1 1 104 196 300 3.81e-27 105
Msa1223300 AT4G04700.1 50.476 105 46 1 1 105 188 286 4.55e-27 105
Msa1223300 AT2G17890.1 48.077 104 48 1 1 104 266 363 4.81e-27 105
Msa1223300 AT5G66210.6 48.077 104 48 1 1 104 220 317 8.75e-27 103
Msa1223300 AT5G66210.4 48.077 104 48 1 1 104 220 317 8.75e-27 103
Msa1223300 AT5G66210.5 48.077 104 48 1 1 104 220 317 1.15e-26 103
Msa1223300 AT5G66210.3 48.077 104 48 1 1 104 220 317 1.25e-26 103
Msa1223300 AT2G41140.1 49.505 101 45 1 4 104 286 380 1.27e-26 104
Msa1223300 AT5G66210.1 48.077 104 48 1 1 104 220 317 1.46e-26 103
Msa1223300 AT5G66210.2 48.077 104 48 1 1 104 220 317 1.46e-26 103
Msa1223300 AT1G49580.1 47.525 101 47 1 4 104 313 407 1.53e-26 103
Msa1223300 AT4G04710.3 55.769 104 34 2 1 104 182 273 4.75e-26 102
Msa1223300 AT4G04710.2 55.769 104 34 2 1 104 196 287 4.97e-26 102
Msa1223300 AT3G56760.1 48.515 101 46 1 4 104 287 381 6.42e-26 102
Msa1223300 AT4G36070.1 45.714 105 51 1 3 107 231 329 1.41e-25 101
Msa1223300 AT4G36070.2 45.714 105 51 1 3 107 231 329 1.50e-25 101
Msa1223300 AT5G24430.1 47.059 102 48 1 4 105 306 401 1.95e-25 100
Msa1223300 AT3G49370.1 48.039 102 47 1 4 105 305 400 4.37e-25 99.8
Msa1223300 AT2G46700.1 48.515 101 46 1 4 104 306 400 7.34e-25 99.4
Msa1223300 AT2G46700.2 48.515 101 46 1 4 104 125 219 1.37e-24 97.8
Msa1223300 AT2G46700.3 48.515 101 46 1 4 104 125 219 1.37e-24 97.8
Msa1223300 AT4G04695.1 46.667 105 50 1 1 105 188 286 1.43e-24 98.2
Msa1223300 AT1G12580.1 43.689 103 52 1 7 109 206 302 3.03e-24 97.4
Msa1223300 AT1G08650.2 35.652 115 60 3 6 119 175 276 2.66e-20 84.3
Msa1223300 AT1G08650.1 39.000 100 54 2 6 104 175 268 8.94e-20 83.2
Msa1223300 AT1G12680.1 41.414 99 52 1 6 104 258 350 7.63e-19 82.0
Msa1223300 AT3G04530.1 38.835 103 56 2 6 107 171 267 9.73e-19 80.1
Msa1223300 AT1G45160.1 36.893 103 49 4 1 98 850 941 7.26e-14 67.8
Msa1223300 AT1G45160.2 36.893 103 49 4 1 98 850 941 7.27e-14 67.8
Msa1223300 AT5G62310.1 38.776 98 44 4 6 98 943 1029 8.11e-13 65.1
Msa1223300 AT4G30960.1 35.897 117 52 6 8 119 185 283 6.78e-12 62.0
Msa1223300 AT5G10930.1 34.188 117 54 6 8 119 174 272 1.43e-11 61.2
Msa1223300 AT3G17850.1 36.000 100 48 4 7 101 1072 1160 1.54e-11 61.2
Msa1223300 AT2G45490.1 34.000 100 57 3 6 104 177 268 3.07e-11 59.7
Msa1223300 AT3G29160.1 39.796 98 47 3 8 103 179 266 8.04e-11 58.9
Msa1223300 AT3G29160.2 39.796 98 47 3 8 103 179 266 8.04e-11 58.9

Find 26 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGAAGTAATTCTCTTCTT+TGG 0.235983 8_1:-87767606 None:intergenic
TTGATCTCACCAGGTGAAAA+AGG 0.312768 8_1:-87767388 None:intergenic
AGGAAAGATTTATAATGATA+TGG 0.314241 8_1:+87767255 None:intergenic
GTAATTCTCTTCTTTGGATC+TGG 0.367241 8_1:-87767600 None:intergenic
TTAGCACTGTCTGATATTGA+TGG 0.374689 8_1:-87767552 None:intergenic
GTCAAGTTCACCCTCCAATA+TGG 0.379689 8_1:-87767511 None:intergenic
TTCTTTGCGGAAACTGATAA+GGG 0.386631 8_1:+87767477 Msa1223300:CDS
TTTCTTTGCGGAAACTGATA+AGG 0.390885 8_1:+87767476 Msa1223300:CDS
ATATTGTATATTCTACTTAG+TGG 0.404672 8_1:+87767358 Msa1223300:CDS
GGGACTATTGAATGCCATAT+TGG 0.419498 8_1:+87767497 Msa1223300:CDS
ATTACAATTGAAGTTATTTG+AGG 0.434291 8_1:-87767672 None:intergenic
ACGGAAAAGAAATAGACATT+TGG 0.440116 8_1:+87767323 Msa1223300:CDS
GAAATAGACATTTGGAGTGC+AGG 0.459846 8_1:+87767331 Msa1223300:CDS
ATTACTTCTAAACAAGTCCT+TGG 0.468958 8_1:+87767618 Msa1223300:CDS
ATTGATTAATTAATTAACAT+TGG 0.470291 8_1:-87767742 None:intergenic
TATAATGATATGGTAGGCAG+TGG 0.546112 8_1:+87767265 Msa1223300:CDS
GAGGTACTGCTTCGTAGTTA+CGG 0.557778 8_1:+87767304 Msa1223300:CDS
AAGATTTATAATGATATGGT+AGG 0.572498 8_1:+87767259 Msa1223300:CDS
AAAACAGTAGACTAGTACCA+AGG 0.575859 8_1:-87767635 None:intergenic
ACTATTGAATGCCATATTGG+AGG 0.579173 8_1:+87767500 Msa1223300:CDS
TAACTACGAAGCAGTACCTC+AGG 0.582907 8_1:-87767301 None:intergenic
CTGTCTGATATTGATGGCCA+TGG 0.583090 8_1:-87767546 None:intergenic
TTGTATATTCTACTTAGTGG+TGG 0.589937 8_1:+87767361 Msa1223300:CDS
CTATTGAATGCCATATTGGA+GGG 0.590578 8_1:+87767501 Msa1223300:CDS
TGGTTGCTATGTTGCTCCTG+AGG 0.592718 8_1:+87767285 Msa1223300:CDS
TTGACTTAGTGAGTGAGCCA+TGG 0.629803 8_1:+87767529 Msa1223300:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTTGTATAAATAGCAA+TGG - chr8_1:87767722-87767741 None:intergenic 15.0%
!! AAGATTTATAATGATATGGT+AGG + chr8_1:87767259-87767278 Msa1223300:CDS 20.0%
!! ATATTGTATATTCTACTTAG+TGG + chr8_1:87767358-87767377 Msa1223300:CDS 20.0%
!! AAAATTAACACTTCTATGAT+AGG + chr8_1:87767447-87767466 Msa1223300:intron 20.0%
!! AAATTAACACTTCTATGATA+GGG + chr8_1:87767448-87767467 Msa1223300:intron 20.0%
!! ATTACAATTGAAGTTATTTG+AGG - chr8_1:87767675-87767694 None:intergenic 20.0%
! CAACTTGTAATTTCAAAATG+TGG + chr8_1:87767408-87767427 Msa1223300:intron 25.0%
! TTAGAAGTAATTCTCTTCTT+TGG - chr8_1:87767609-87767628 None:intergenic 25.0%
!!! CTAGTCTACTGTTTTTAATT+TGG + chr8_1:87767643-87767662 Msa1223300:CDS 25.0%
ACGGAAAAGAAATAGACATT+TGG + chr8_1:87767323-87767342 Msa1223300:CDS 30.0%
TTGTATATTCTACTTAGTGG+TGG + chr8_1:87767361-87767380 Msa1223300:CDS 30.0%
! GATAGGGTTAATTTTCTTTG+CGG + chr8_1:87767464-87767483 Msa1223300:intron 30.0%
ATTACTTCTAAACAAGTCCT+TGG + chr8_1:87767618-87767637 Msa1223300:CDS 30.0%
TATAATGATATGGTAGGCAG+TGG + chr8_1:87767265-87767284 Msa1223300:CDS 35.0%
!! AATTACAAGTTGATCTCACC+AGG - chr8_1:87767400-87767419 None:intergenic 35.0%
TTTCTTTGCGGAAACTGATA+AGG + chr8_1:87767476-87767495 Msa1223300:CDS 35.0%
TTCTTTGCGGAAACTGATAA+GGG + chr8_1:87767477-87767496 Msa1223300:CDS 35.0%
ACTATTGAATGCCATATTGG+AGG + chr8_1:87767500-87767519 Msa1223300:CDS 35.0%
CTATTGAATGCCATATTGGA+GGG + chr8_1:87767501-87767520 Msa1223300:CDS 35.0%
TTAGCACTGTCTGATATTGA+TGG - chr8_1:87767555-87767574 None:intergenic 35.0%
GTAATTCTCTTCTTTGGATC+TGG - chr8_1:87767603-87767622 None:intergenic 35.0%
AAAACAGTAGACTAGTACCA+AGG - chr8_1:87767638-87767657 None:intergenic 35.0%
! GAAATAGACATTTGGAGTGC+AGG + chr8_1:87767331-87767350 Msa1223300:CDS 40.0%
TTGATCTCACCAGGTGAAAA+AGG - chr8_1:87767391-87767410 None:intergenic 40.0%
GGGACTATTGAATGCCATAT+TGG + chr8_1:87767497-87767516 Msa1223300:CDS 40.0%
TAACTACGAAGCAGTACCTC+AGG - chr8_1:87767304-87767323 None:intergenic 45.0%
!! GAGGTACTGCTTCGTAGTTA+CGG + chr8_1:87767304-87767323 Msa1223300:CDS 45.0%
ATCTCACCAGGTGAAAAAGG+CGG - chr8_1:87767388-87767407 None:intergenic 45.0%
GTCAAGTTCACCCTCCAATA+TGG - chr8_1:87767514-87767533 None:intergenic 45.0%
TTGACTTAGTGAGTGAGCCA+TGG + chr8_1:87767529-87767548 Msa1223300:CDS 45.0%
! CTGTCTGATATTGATGGCCA+TGG - chr8_1:87767549-87767568 None:intergenic 45.0%
TGGTTGCTATGTTGCTCCTG+AGG + chr8_1:87767285-87767304 Msa1223300:CDS 50.0%
!! GGTGGACCGCCTTTTTCACC+TGG + chr8_1:87767379-87767398 Msa1223300:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 87767259 87767755 87767259 ID=Msa1223300;Name=Msa1223300
chr8_1 mRNA 87767259 87767755 87767259 ID=Msa1223300-mRNA-1;Parent=Msa1223300;Name=Msa1223300-mRNA-1;_AED=0.47;_eAED=0.49;_QI=0|0|0|1|1|1|2|0|142
chr8_1 exon 87767259 87767400 87767259 ID=Msa1223300-mRNA-1:exon:31839;Parent=Msa1223300-mRNA-1
chr8_1 exon 87767469 87767755 87767469 ID=Msa1223300-mRNA-1:exon:31840;Parent=Msa1223300-mRNA-1
chr8_1 CDS 87767259 87767400 87767259 ID=Msa1223300-mRNA-1:cds;Parent=Msa1223300-mRNA-1
chr8_1 CDS 87767469 87767755 87767469 ID=Msa1223300-mRNA-1:cds;Parent=Msa1223300-mRNA-1
Gene Sequence

>Msa1223300

AAGATTTATAATGATATGGTAGGCAGTGGTTGCTATGTTGCTCCTGAGGTACTGCTTCGTAGTTACGGAAAAGAAATAGACATTTGGAGTGCAGGCATCATATTGTATATTCTACTTAGTGGTGGACCGCCTTTTTCACCTGGGTTAATTTTCTTTGCGGAAACTGATAAGGGACTATTGAATGCCATATTGGAGGGTGAACTTGACTTAGTGAGTGAGCCATGGCCATCAATATCAGACAGTGCTAAAGATCTAGTCAAGAAGATGCTAACACCAGATCCAAAGAAGAGAATTACTTCTAAACAAGTCCTTGGTACTAGTCTACTGTTTTTAATTTGGCTCAATCCTCAAATAACTTCAATTGTAATAGTTCTTTTAATAAAGTTAAAGCACCATTGCTATTTATACAAAATAACCAATGTTAATTAA
Protein sequence

>Msa1223300

KIYNDMVGSGCYVAPEVLLRSYGKEIDIWSAGIILYILLSGGPPFSPGLIFFAETDKGLLNAILEGELDLVSEPWPSISDSAKDLVKKMLTPDPKKRITSKQVLGTSLLFLIWLNPQITSIVIVLLIKLKHHCYLYKITNVN*