AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene001242

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001242.t1 MTR_5g035980 96.026 302 8 2 1 302 151 448 0.0 588
MS.gene001242.t1 MTR_3g078380 58.140 301 92 8 9 302 141 414 2.36e-110 326
MS.gene001242.t1 MTR_4g106480 54.153 301 102 5 4 302 135 401 6.45e-107 317
MS.gene001242.t1 MTR_8g089650 52.759 290 94 7 16 299 178 430 4.94e-93 283
MS.gene001242.t1 MTR_4g104410 46.897 290 115 7 11 297 110 363 4.50e-74 232
MS.gene001242.t1 MTR_5g018520 40.956 293 138 5 6 298 163 420 1.19e-69 223
MS.gene001242.t1 MTR_1g021590 40.909 286 134 5 12 297 181 431 8.39e-67 216
MS.gene001242.t1 MTR_4g068457 40.702 285 138 6 14 297 202 456 1.97e-60 200
MS.gene001242.t1 MTR_4g068457 26.568 271 128 13 53 296 131 357 6.89e-12 66.2
MS.gene001242.t1 MTR_2g060070 36.735 294 140 11 6 297 132 381 5.24e-53 179
MS.gene001242.t1 MTR_2g101410 36.328 256 129 7 47 299 185 409 2.82e-39 143
MS.gene001242.t1 MTR_3g110185 35.986 289 141 7 14 299 164 411 6.72e-38 142
MS.gene001242.t1 MTR_2g086140 32.335 167 102 4 96 259 16 174 8.55e-14 72.4
MS.gene001242.t1 MTR_4g053675 30.539 167 109 3 96 259 16 178 9.91e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene001242.t1 AT1G24130 58.333 300 94 4 4 302 146 415 5.86e-112 330
MS.gene001242.t1 AT5G50120 51.536 293 108 6 11 300 126 387 1.50e-97 293
MS.gene001242.t1 AT1G24530 52.962 287 96 8 13 299 158 405 9.03e-91 276
MS.gene001242.t1 AT2G26490 39.661 295 143 5 8 302 164 423 1.71e-65 213
MS.gene001242.t1 AT3G50390 36.824 296 150 5 5 297 163 424 1.11e-61 202
MS.gene001242.t1 AT3G50390 25.267 281 120 11 53 296 101 328 9.66e-11 62.8
MS.gene001242.t1 AT3G18950 39.298 285 141 5 13 297 212 464 1.40e-59 197
MS.gene001242.t1 AT3G18950 28.571 259 140 10 53 288 141 377 2.37e-13 70.5
MS.gene001242.t1 AT1G49450 38.811 286 147 5 13 297 208 466 1.33e-58 195
MS.gene001242.t1 AT1G49450 29.057 265 128 10 53 296 137 362 1.50e-17 83.2
MS.gene001242.t1 AT4G34380 37.676 284 151 4 14 297 199 456 3.24e-58 194
MS.gene001242.t1 AT3G51930 37.627 295 153 9 5 297 129 394 8.40e-55 183
MS.gene001242.t1 AT1G47610 35.354 297 154 9 5 300 90 349 2.78e-52 175
MS.gene001242.t1 AT1G47610 24.906 265 138 8 53 297 27 250 5.30e-13 68.9
MS.gene001242.t1 AT1G21651 27.660 188 105 6 48 233 522 680 1.83e-12 68.2
MS.gene001242.t1 AT1G21650 28.342 187 103 6 49 233 523 680 2.55e-12 68.2
MS.gene001242.t1 AT3G44530 30.909 165 101 5 96 256 16 171 3.68e-11 64.3
MS.gene001242.t1 AT3G44530 30.909 165 101 5 96 256 16 171 3.88e-11 64.3
MS.gene001242.t1 AT5G16750 25.296 253 149 11 16 255 361 586 6.69e-11 63.5

Find 29 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGATAGAACATTCAAAATT+TGG 0.193532 5.2:+26526568 MS.gene001242:CDS
GCAATTGTTGTTTCATCTTC+TGG 0.218219 5.2:+26526651 MS.gene001242:CDS
TAGCCTTAGTATGCCCTCTT+AGG 0.234642 5.2:-26526968 None:intergenic
CTGATTATAGTGTTAGATTA+TGG 0.250597 5.2:+26527036 MS.gene001242:CDS
CTGATAGAAAGATCAAAATT+TGG 0.302795 5.2:+26526694 MS.gene001242:CDS
TCTCTTGCTGTTTCGAAAGA+TGG 0.341375 5.2:+26526522 MS.gene001242:CDS
TACTAAGGCTATATTGTGTT+TGG 0.351474 5.2:+26526980 MS.gene001242:CDS
TCTTCTGGCGTTGTTTATAC+AGG 0.352761 5.2:+26526666 MS.gene001242:CDS
AGCATTATTCGAAATTGTTC+CGG 0.359690 5.2:+26526900 MS.gene001242:CDS
TTGATTGTGATATCAAAGTT+TGG 0.373353 5.2:+26527222 MS.gene001242:CDS
AGACCCAGACGACGAAAATA+TGG 0.382173 5.2:+26526932 MS.gene001242:CDS
TTTGGTTGTGATGGATGATT+TGG 0.391313 5.2:+26526998 MS.gene001242:CDS
AGATGGATTGTTTCTTTACT+CGG 0.453556 5.2:+26526539 MS.gene001242:CDS
AGTGTTAGATTATGGAAAAG+AGG 0.466262 5.2:+26527044 MS.gene001242:CDS
TATATTGTGTTTGGTTGTGA+TGG 0.472582 5.2:+26526989 MS.gene001242:CDS
GTCTGGGTCTTGGTCTAGTC+CGG 0.475863 5.2:-26526919 None:intergenic
GTGCTAGTTGGTGCCCTAAG+AGG 0.492886 5.2:+26526954 MS.gene001242:CDS
TGTTTCTTTACTCGGCTTCG+TGG 0.493077 5.2:+26526547 MS.gene001242:CDS
AGCCTTAGTATGCCCTCTTA+GGG 0.526558 5.2:-26526967 None:intergenic
GTTTCTTTACTCGGCTTCGT+GGG 0.536613 5.2:+26526548 MS.gene001242:CDS
GCTTTAGCACTAAACAAAGA+TGG 0.541869 5.2:+26526819 MS.gene001242:CDS
ATGGATGATTTGGTGTGTAG+TGG 0.553153 5.2:+26527008 MS.gene001242:CDS
TGCTAGTTGGTGCCCTAAGA+GGG 0.557068 5.2:+26526955 MS.gene001242:CDS
ATAGCAGATGATTCCAAAAG+TGG 0.557521 5.2:+26527137 MS.gene001242:CDS
GACGAAAATATGGTGCTAGT+TGG 0.564621 5.2:+26526942 MS.gene001242:CDS
TGCCCTAAGAGGGCATACTA+AGG 0.569818 5.2:+26526965 MS.gene001242:CDS
AGTTCTTATCTTGTTTACAG+TGG 0.604622 5.2:+26527194 MS.gene001242:CDS
GGAGACATAAGAAGTATACA+TGG 0.631337 5.2:+26526475 MS.gene001242:CDS
GAGACATAAGAAGTATACAT+GGG 0.687899 5.2:+26526476 MS.gene001242:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAAAGAAAAAGCATTTTT+TGG + chr5.2:26526761-26526780 MS.gene001242:CDS 15.0%
!!! TGATAGATCAATTTTAGTTT+GGG + chr5.2:26526866-26526885 MS.gene001242:CDS 20.0%
! CTGATAGAAAGATCAAAATT+TGG + chr5.2:26526694-26526713 MS.gene001242:CDS 25.0%
! CTGATTATAGTGTTAGATTA+TGG + chr5.2:26527036-26527055 MS.gene001242:CDS 25.0%
! TAAAAAAGCTGTTAAGTGTT+TGG + chr5.2:26527112-26527131 MS.gene001242:CDS 25.0%
! TGAAAAAAGTTATGCATGTT+TGG + chr5.2:26527073-26527092 MS.gene001242:CDS 25.0%
! TTGATTGTGATATCAAAGTT+TGG + chr5.2:26527222-26527241 MS.gene001242:CDS 25.0%
!!! AAGAAAAAGCATTTTTTGGT+TGG + chr5.2:26526765-26526784 MS.gene001242:CDS 25.0%
!!! GTGATAGATCAATTTTAGTT+TGG + chr5.2:26526865-26526884 MS.gene001242:CDS 25.0%
AGCATTATTCGAAATTGTTC+CGG + chr5.2:26526900-26526919 MS.gene001242:CDS 30.0%
AGTGTTAGATTATGGAAAAG+AGG + chr5.2:26527044-26527063 MS.gene001242:CDS 30.0%
GAAAAACGATCATTGAATGT+TGG - chr5.2:26526420-26526439 None:intergenic 30.0%
GATTCCAAAAGTGGTAAAAA+TGG + chr5.2:26527146-26527165 MS.gene001242:CDS 30.0%
GGGATAGAACATTCAAAATT+TGG + chr5.2:26526568-26526587 MS.gene001242:CDS 30.0%
TACTAAGGCTATATTGTGTT+TGG + chr5.2:26526980-26526999 MS.gene001242:CDS 30.0%
TATATTGTGTTTGGTTGTGA+TGG + chr5.2:26526989-26527008 MS.gene001242:CDS 30.0%
! AGTTCTTATCTTGTTTACAG+TGG + chr5.2:26527194-26527213 MS.gene001242:CDS 30.0%
! GAGACATAAGAAGTATACAT+GGG + chr5.2:26526476-26526495 MS.gene001242:CDS 30.0%
! TCATTTTCTCATCTTCTTCA+TGG - chr5.2:26526731-26526750 None:intergenic 30.0%
!! AGATGGATTGTTTCTTTACT+CGG + chr5.2:26526539-26526558 MS.gene001242:CDS 30.0%
!! GATGGATCAGTTTTATATTC+AGG + chr5.2:26526837-26526856 MS.gene001242:CDS 30.0%
ATAGCAGATGATTCCAAAAG+TGG + chr5.2:26527137-26527156 MS.gene001242:CDS 35.0%
CAAAAGTGGTAAAAATGGTG+GGG + chr5.2:26527151-26527170 MS.gene001242:CDS 35.0%
CCAAAAGTGGTAAAAATGGT+GGG + chr5.2:26527150-26527169 MS.gene001242:CDS 35.0%
CGAAAAATTACGTTGAAGTC+AGG + chr5.2:26526454-26526473 MS.gene001242:CDS 35.0%
GCTTTAGCACTAAACAAAGA+TGG + chr5.2:26526819-26526838 MS.gene001242:CDS 35.0%
TCCAAAAGTGGTAAAAATGG+TGG + chr5.2:26527149-26527168 MS.gene001242:CDS 35.0%
! GGAGACATAAGAAGTATACA+TGG + chr5.2:26526475-26526494 MS.gene001242:CDS 35.0%
!! GCAATTGTTGTTTCATCTTC+TGG + chr5.2:26526651-26526670 MS.gene001242:CDS 35.0%
!! TTTGGTTGTGATGGATGATT+TGG + chr5.2:26526998-26527017 MS.gene001242:CDS 35.0%
TCTTCTGGCGTTGTTTATAC+AGG + chr5.2:26526666-26526685 MS.gene001242:CDS 40.0%
! GACGAAAATATGGTGCTAGT+TGG + chr5.2:26526942-26526961 MS.gene001242:CDS 40.0%
!! ATGGATGATTTGGTGTGTAG+TGG + chr5.2:26527008-26527027 MS.gene001242:CDS 40.0%
!! CCCACCATTTTTACCACTTT+TGG - chr5.2:26527153-26527172 None:intergenic 40.0%
!! GCATGTTTGGCTGTTTTACA+AGG + chr5.2:26527086-26527105 MS.gene001242:CDS 40.0%
!! TCTCTTGCTGTTTCGAAAGA+TGG + chr5.2:26526522-26526541 MS.gene001242:CDS 40.0%
AGACCCAGACGACGAAAATA+TGG + chr5.2:26526932-26526951 MS.gene001242:CDS 45.0%
AGCCTTAGTATGCCCTCTTA+GGG - chr5.2:26526970-26526989 None:intergenic 45.0%
GTTTCTTTACTCGGCTTCGT+GGG + chr5.2:26526548-26526567 MS.gene001242:CDS 45.0%
TGTTTCTTTACTCGGCTTCG+TGG + chr5.2:26526547-26526566 MS.gene001242:CDS 45.0%
! AGCACCATATTTTCGTCGTC+TGG - chr5.2:26526939-26526958 None:intergenic 45.0%
! GCACCATATTTTCGTCGTCT+GGG - chr5.2:26526938-26526957 None:intergenic 45.0%
! TAGCCTTAGTATGCCCTCTT+AGG - chr5.2:26526971-26526990 None:intergenic 45.0%
! TATTTTCGTCGTCTGGGTCT+TGG - chr5.2:26526932-26526951 None:intergenic 45.0%
!! GGGGTTGATGATGATGATGA+TGG + chr5.2:26527170-26527189 MS.gene001242:CDS 45.0%
! TGCCCTAAGAGGGCATACTA+AGG + chr5.2:26526965-26526984 MS.gene001242:CDS 50.0%
! TGCTAGTTGGTGCCCTAAGA+GGG + chr5.2:26526955-26526974 MS.gene001242:CDS 50.0%
GTCTGGGTCTTGGTCTAGTC+CGG - chr5.2:26526922-26526941 None:intergenic 55.0%
! GTGCTAGTTGGTGCCCTAAG+AGG + chr5.2:26526954-26526973 MS.gene001242:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 26526360 26527268 26526360 ID=MS.gene001242
chr5.2 mRNA 26526360 26527268 26526360 ID=MS.gene001242.t1;Parent=MS.gene001242
chr5.2 exon 26526360 26527268 26526360 ID=MS.gene001242.t1.exon1;Parent=MS.gene001242.t1
chr5.2 CDS 26526360 26527268 26526360 ID=cds.MS.gene001242.t1;Parent=MS.gene001242.t1
Gene Sequence

>MS.gene001242

ATGACTAGTAATAGTACTAATCAAGAACAGAAGTTGTTTAAGTGCATAGCAACACTTCCAACATTCAATGATCGTTTTTCGAAGCTTTTTTCATCGAAAAATTACGTTGAAGTCAGGAGACATAAGAAGTATACATGGGTGAATCATATTGACGCTGTTTCTTCTCTTGCTGTTTCGAAAGATGGATTGTTTCTTTACTCGGCTTCGTGGGATAGAACATTCAAAATTTGGAGAGTTTCTGATTTCAAGTGTTTAGAGTCAGTGAAAAATGCACATGAAGATGCAATCAATGCAATTGTTGTTTCATCTTCTGGCGTTGTTTATACAGGTTCAGCTGATAGAAAGATCAAAATTTGGAAGAAGAAAAACCATGAAGAAGATGAGAAAATGAAAAGTAAAAGTAAAAAGAAAAAGCATTTTTTGGTTGGAACATTAGAGAAGCATAAATCAGCTGTGAATGCTTTAGCACTAAACAAAGATGGATCAGTTTTATATTCAGGTGCATGTGATAGATCAATTTTAGTTTGGGAAAAAAGCAATAGCATTATTCGAAATTGTTCCGGACTAGACCAAGACCCAGACGACGAAAATATGGTGCTAGTTGGTGCCCTAAGAGGGCATACTAAGGCTATATTGTGTTTGGTTGTGATGGATGATTTGGTGTGTAGTGGATCAGCTGATTATAGTGTTAGATTATGGAAAAGAGGAATTGATGAAAAAAGTTATGCATGTTTGGCTGTTTTACAAGGTCATAAAAAAGCTGTTAAGTGTTTGGCTATAGCAGATGATTCCAAAAGTGGTAAAAATGGTGGGGTTGATGATGATGATGATGGTAGTTCTTATCTTGTTTACAGTGGTAGTCTTGATTGTGATATCAAAGTTTGGCAAATACGCGTTCCCTTGATTTGA
Protein sequence

>MS.gene001242.t1

MTSNSTNQEQKLFKCIATLPTFNDRFSKLFSSKNYVEVRRHKKYTWVNHIDAVSSLAVSKDGLFLYSASWDRTFKIWRVSDFKCLESVKNAHEDAINAIVVSSSGVVYTGSADRKIKIWKKKNHEEDEKMKSKSKKKKHFLVGTLEKHKSAVNALALNKDGSVLYSGACDRSILVWEKSNSIIRNCSGLDQDPDDENMVLVGALRGHTKAILCLVVMDDLVCSGSADYSVRLWKRGIDEKSYACLAVLQGHKKAVKCLAIADDSKSGKNGGVDDDDDGSSYLVYSGSLDCDIKVWQIRVPLI