Origin IGS: ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgataattcactttatgcattttatgcagtctgcataagtgcataaactgcataaaacagatatacatatggaaaagaaagaactaaacagaatcttgtcaaccaaggcaccggcaggagaacgg Mask Tandem Repeat Region ================================================ ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Find is-nt database================================================ Query_seq: PI2074:PI2075|PI2074:PI2075:conserved hypothetical protein:conserved hypothetical protein:->->:2034436..2034560 125 ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2074:PI2075|PI2074:PI2075:conserved hypothetical protein:conserved hypothetical protein:->->:2034436..2034560 125 ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2074:PI2075|PI2074:PI2075:conserved hypothetical protein:conserved hypothetical protein:->->:2034436..2034560 125 ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 9 End: 101 ........ M P V P W L T R F C L V L S F P Y V Y L F Y A V Y A L M Q T A ........................ Protein_Len: 32 Strand: + Start: 20 End: 115 ................... M V D K I L F S S F F S I C I S V L C S L C T Y A D C I K C I K .......... ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca 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================================================ ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2074:PI2075|PI2074:PI2075:conserved hypothetical protein:conserved hypothetical protein:->->:2034436..2034560 125 ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: pint_PI2074_PI2075|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2034436,2034560]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca ccgttctcctgccggtgccttggttgacaagattctgtttagttctttcttttccatatgtatatctgttttatgcagtttatgcacttatgcagactgcataaaatgcataaagtgaattatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGUUCUCCUGCCGGUGCCUUGGUUGACAAGAUUCUGUUUAGUUCUUUCUUUUCCAUAUGUAUAUCUGUUUUAUGCAGUUUAUGCACUUAUGCAGACUGCAUAAAAUGCAUAAAGUGAAUUAUCA ............(((...((((.....))))...)))..((((((...(((.....(((((......(((((((((((((..((((....))))))))))))))))))))))))).))))))... (-28.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAAUUCACUUUAUGCAUUUUAUGCAGUCUGCAUAAGUGCAUAAACUGCAUAAAACAGAUAUACAUAUGGAAAAGAAAGAACUAAACAGAAUCUUGUCAACCAAGGCACCGGCAGGAGAACGG ...........((((((((.((((((((.(.......).)))))))).)))))))).....................................(((((((............)))))))...... (-23.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 30 2 223 189 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 333 48 2 183 123 pint:PI2139|5end_cysteinyl-tRNA_synthetase_2085266..2085496_POSITIVE 329 40 10 88 61 pint:PI0020|5end_conserved_hypothetical_protein_24525..24755_POSITIVE 310 44 6 178 125 pint:PI1680|5end_conserved_hypothetical_protein_1595038..1595268_POSITIVE 303 47 8 73 29 pint:PI0772|5end_conserved_hypothetical_protein_707157..707387_POSITIVE 299 26 1 86 56 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 286 34 2 56 16 pint:PI0276|5end_anti-restriction_protein_264429..264659_POSITIVE 285 45 1 228 175 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 278 39 9 228 191 pint:PI2160|5end_hypothetical_protein_2107270..2107500_POSITIVE 278 26 1 138 101 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 277 40 2 88 39 pint:PI0249|5end_conserved_hypothetical_protein_246572..246802_POSITIVE 277 50 1 92 22 pint:PI0184|5end_possible_fibronectin_type_III_domain_protein_174355..174585_POSITIVE 277 50 1 84 14 pint:PI0183|5end_hypothetical_protein_174347..174577_POSITIVE 274 38 1 85 40 pint:PI0231|5end_transcriptional_regulator_229453..229683_POSITIVE 269 117 75 96 61 pint:PI1909|5end_DNA_gyrase,_B_subunit_1853223..1853453_POSITIVE 268 48 2 82 31 pint:PI0468|5end_50S_ribosomal_protein_L29_436905..437135_POSITIVE 266 55 16 110 65 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 265 50 1 72 31 pint:PI1503|5end_30S_ribosomal_protein_S15_1423428..1423658_POSITIVE 265 22 1 154 127 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 263 50 2 230 173 pint:PI1665|5end_thymidylate_synthase_1578086..1578316_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 46 2 137 82 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 283 40 1 111 67 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 277 40 2 83 34 pint:PI0248|3end_protein_associated_with_conjugate_transformation/chromosome_partioning_246647..246797_POSITIVE 270 100 59 133 92 pint:PI1011|3end_cytochrome_c_biogenesis_protein_CycY_932989..933139_POSITIVE 268 48 2 73 22 pint:PI0467|3end_50S_ribosomal_protein_L16_436976..437126_POSITIVE 265 50 1 48 7 pint:PI1502|3end_hypothetical_protein_1423484..1423634_POSITIVE 265 22 1 131 104 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 264 34 5 36 1 pint:PI0275|3end_hypothetical_protein_264489..264639_POSITIVE 260 49 7 151 96 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 255 57 13 114 74 pint:PI2067|3end_hypothetical_protein_2028337..2028487_POSITIVE 255 47 1 80 25 pint:PI0360|3end_conserved_hypothetical_protein_333472..333622_POSITIVE 254 109 67 143 97 pint:PI1861|3end_hypothetical_protein_1806114..1806264_POSITIVE 252 48 2 62 3 pint:PI1632|3end_hypothetical_protein_1553222..1553372_POSITIVE 252 48 2 62 3 pint:PI0339|3end_hypothetical_protein_316138..316288_POSITIVE 252 24 3 56 33 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 246 29 1 87 51 pint:PI0728|3end_integrase_661508..661658_POSITIVE 245 49 5 138 93 pint:PI1369|3end_alkyl_hydroperoxide_reductase,_subunit__C_1290423..1290573_POSITIVE 243 66 22 144 106 pint:PI1946|3end_hypothetical_protein_1903020..1903170_POSITIVE 243 94 53 95 46 pint:PI1171|3end_hypothetical_protein_1091836..1091986_POSITIVE 243 45 1 54 4 pint:PI0705|3end_conserved_hypothetical_protein;_possible_lipoprotein_642271..642421_POSITIVE