Origin IGS: ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggaatgcaaaggaatccgggggaaccgggtcgtaaaaaagcgcctgttcagctgttaatttgcaaagcaggcaagccggttaccggataggcaggcaacatgattgcagcttgcctgccgggtgtgtttacaggataacagaataatgcaataacataataacacaatgacacaagaataggataagatacgaacacacgggtatgtgcattcatggattgatcaatgtaccgatgcgtccatcacctgaccggttgattcatgtatccgtttatcggcagacagacaggctgaagcagccatacaatcatatgatcataacattacaaatccttttattatacaacag Mask Tandem Repeat Region ================================================ ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Find is-nt database================================================ Query_seq: PG1486:PG1487|PG1486:PG1487:conjugative transposon protein TraA:hypothetical protein:<-->:1561257..1561607 351 ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1486:PG1487|PG1486:PG1487:conjugative transposon protein TraA:hypothetical protein:<-->:1561257..1561607 351 ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1486:PG1487|PG1486:PG1487:conjugative transposon protein TraA:hypothetical protein:<-->:1561257..1561607 351 ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 131 End: 292 .................................................................................................................................. M H E C T Y P C V R I L S Y S C V I V L L C Y C I I L L S C K H T R Q A S C N H V A C L S G N R L A C F A N ........................................................... Protein_Len: 59 Strand: + Start: 123 End: 299 .......................................................................................................................... M D Q S M N A H T R V F V S Y P I L V S L C Y Y V I A L F C Y P V N T P G R Q A A I M L P A Y P V T G L P A L Q I N S .................................................... Protein_Len: 55 Strand: - Start: 3 End: 167 .. N Y L L L I Q L T I I M H N Y P Q K L R D T Q R Y V S V H I L R D P S P R M P V N I L G H I C M G T H E Y R M ........................................................................................................................................................................................ ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1486:PG1487|PG1486:PG1487:conjugative transposon protein TraA:hypothetical protein:<-->:1561257..1561607 351 ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Intra-Species Hit: Count: 1 Min: 1 Max: 351 Len: 351 Subject: NC_002950_PG1486_PG1487|conjugative transposon protein TraA:hypothetical protein|NEGATIVE:POSITIVE|[1561257,1561607]|351 HSP 1 e-value: 0.0 bit: 696.0 Len: 351 Query Start:1 Query End:351 Subject Strand: POSITIVE Subject Start: 1 Subject End: 351 ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt ctgttgtataataaaaggatttgtaatgttatgatcatatgattgtatggctgcttcagcctgtctgtctgccgataaacggatacatgaatcaaccggtcaggtgatggacgcatcggtacattgatcaatccatgaatgcacatacccgtgtgttcgtatcttatcctattcttgtgtcattgtgttattatgttattgcattattctgttatcctgtaaacacacccggcaggcaagctgcaatcatgttgcctgcctatccggtaaccggcttgcctgctttgcaaattaacagctgaacaggcgcttttttacgacccggttcccccggattcctttgcattcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUGUAUAAUAAAAGGAUUUGUAAUGUUAUGAUCAUAUGAUUGUAUGGCUGCUUCAGCCUGUCUGUCUGCCGAUAAACGGAUACAUGAAUCAACCGGUCAGGUGAUGGACGCAUCGGUACAUUGAUCAAUCCAUGAAUGCACAUACCCGUGUGUUCGUAUCUUAUCCUAUUCUUGUGUCAUUGUGUUAUUAUGUUAUUGCAUUAUUCUGUUAUCCUGUAAACACACCCGGCAGGCAAGCUGCAAUCAUGUUGCCUGCCUAUCCGGUAACCGGCUUGCCUGCUUUGCAAAUUAACAGCUGAACAGGCGCUUUUUUACGACCCGGUUCCCCCGGAUUCCUUUGCAUUCCUU ..............(((((..(((((..........((((((((((..(((((...))))).(..(((((((((.......((((((.((((.....(((.((((.((((((((((.((((((((.((......)).))))....)))).)))))))))))))).)))..)))).))))))..((((((..((((..((.(((......))).))..))))))))))..)))))))))..).)))))))))).........((((((.((((((..((((((.((.((.........)).)).))))))............))))))...))))))....))))).))))) (-102.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAAUGCAAAGGAAUCCGGGGGAACCGGGUCGUAAAAAAGCGCCUGUUCAGCUGUUAAUUUGCAAAGCAGGCAAGCCGGUUACCGGAUAGGCAGGCAACAUGAUUGCAGCUUGCCUGCCGGGUGUGUUUACAGGAUAACAGAAUAAUGCAAUAACAUAAUAACACAAUGACACAAGAAUAGGAUAAGAUACGAACACACGGGUAUGUGCAUUCAUGGAUUGAUCAAUGUACCGAUGCGUCCAUCACCUGACCGGUUGAUUCAUGUAUCCGUUUAUCGGCAGACAGACAGGCUGAAGCAGCCAUACAAUCAUAUGAUCAUAACAUUACAAAUCCUUUUAUUAUACAACAG ...(((((((.....(((((((....)).(.(((((........(((((((..((((((.((((..(((((.((...((((...))))...(((((((((..((....))..)))))))))..)).))))).)))).))))))....(((......)))..................)))))))......))))).)...)))))...)))))))..(((((((((((((....(((((((..((((((.....)).))))..))))))).((((.((....)).)))).(((((...))))).......))).))))))...........))))................ (-97.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1011 120 71 211 162 NC_002950:PG1486|5end_conjugative_transposon_protein_TraA_1561166..1561396_NEGATIVE 460 120 71 58 2 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 408 280 233 61 4 NC_002950:PG1560|5end_dTDP-glucose_4,6-dehydratase_1640131..1640361_NEGATIVE 392 275 240 70 33 NC_002950:PG0674|5end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724802..725032_NEGATIVE 389 267 229 224 178 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 388 287 242 171 113 NC_002950:PG1995|5end_hypothetical_protein_2085584..2085814_POSITIVE 386 280 232 68 25 NC_002950:PG0806|5end_oxidoreductase,_Gfo/Idh/MocA_family_863592..863822_NEGATIVE 378 275 232 73 26 NC_002950:PG1005|5end_lipoprotein,_putative_1063763..1063993_NEGATIVE 378 137 96 230 184 NC_002950:PG0305|5end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_340906..341136_POSITIVE 378 276 231 88 51 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 378 284 241 50 3 NC_002950:PG0034|5end_thioredoxin_42549..42779_NEGATIVE 377 280 233 61 2 NC_002950:PG1576|5end_L-aspartate_oxidase_1653016..1653246_POSITIVE 373 276 232 77 31 NC_002950:PG2218|5end_potassium_uptake_protein_TrkA_2331580..2331810_POSITIVE 372 89 45 92 40 NC_002950:PG0210|5end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_245969..246199_NEGATIVE 368 279 232 60 5 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 368 280 231 61 8 NC_002950:PG0802|5end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_859722..859952_NEGATIVE 367 279 231 58 20 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 367 280 231 45 2 NC_002950:PG0714|5end_copper_homeostasis_protein_CutC_768671..768901_NEGATIVE 364 299 252 202 143 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 356 280 231 179 123 NC_002950:PG0685|5end_ABC_transporter,_ATP-binding_protein_740116..740346_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 89 44 141 98 NC_002950:PG0344|3end_purple_acid_phosphatase_378543..378693_NEGATIVE 392 275 240 43 6 NC_002950:PG0675|3end_indolepyruvate_ferredoxin_oxidoreductase,_alpha_subunit_724829..724979_NEGATIVE 389 267 229 123 77 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 383 330 282 111 69 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 382 280 231 123 65 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 373 279 233 139 92 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 372 89 45 95 43 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 368 280 231 56 3 NC_002950:PG0803|3end_glucosamine-6-phosphate_deaminase_859727..859877_NEGATIVE 361 285 241 133 91 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 357 121 81 88 42 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE 356 280 231 86 30 NC_002950:PG0684|3end_ABC_transporter,_permease_protein,_putative_740103..740253_POSITIVE 355 280 238 54 3 NC_002950:PG1561|3end_dTDP-4-dehydrorhamnose_reductase_1640138..1640288_NEGATIVE 350 76 33 143 89 NC_002950:PG0363|3end_hypothetical_protein_398377..398527_POSITIVE 348 89 50 140 89 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 344 280 231 123 71 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 340 266 226 150 115 NC_002950:PG1470|3end_hypothetical_protein_1548431..1548581_POSITIVE 340 74 32 121 71 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 339 289 245 69 1 NC_002950:PG0903|3end_hypothetical_protein_969098..969248_NEGATIVE 338 280 240 96 55 NC_002950:PG2218|3end_potassium_uptake_protein_TrkA_2333000..2333150_POSITIVE 337 288 242 64 21 NC_002950:PG0632|3end_biopolymer_transport_protein_ExbD,_putative_685376..685526_POSITIVE