Origin IGS: taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaaaaggctttctatttaggtagaaaacaatagcttaggtaatcttctatctcaaacaaaacagcctctgcactaaatgtgcagaggctgttttgcttttttgtttctctta Mask Tandem Repeat Region ================================================ taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta Find is-nt database================================================ Query_seq: PI1587:PI1588|PI1587:PI1588:conserved hypothetical protein; possible permease:DNA polymerase III, epsilon chain:->->:1516327..1516441 115 taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1587:PI1588|PI1587:PI1588:conserved hypothetical protein; possible permease:DNA polymerase III, epsilon chain:->->:1516327..1516441 115 taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1587:PI1588|PI1587:PI1588:conserved hypothetical protein; possible permease:DNA polymerase III, epsilon chain:->->:1516327..1516441 115 taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta Predict ORF larger than 30AA ================================================ taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta 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================================================ taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -21.4 Tail_Score: -5.7827 Start: 17 End: 57 Full_Region: aatcttctatctcaa acaaaacagcctctgcac taaat gtgcagaggctgttttgc ttttttgtttctctt ................acaaaacagcctctgcactaaatgtgcagaggctgttttgc.......................................................... TransTerm Strand: - Conf: 100 HP_score: -24.9 Tail_Score: -4.03302 Start: 18 End: 56 Full_Region: atcttctatctcaaa caaaacagcctctgcac taaat gtgcagaggctgttttg cttttttgtttctct .................caaaacagcctctgcactaaatgtgcagaggctgttttg........................................................... Find igs database================================================ Query_seq: PI1587:PI1588|PI1587:PI1588:conserved hypothetical protein; possible permease:DNA polymerase III, epsilon chain:->->:1516327..1516441 115 taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagccttttttta Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: pint_PI1587_PI1588|conserved hypothetical protein; possible permease:DNA polymerase III, epsilon chain|POSITIVE:POSITIVE|[1516327,1516441]|115 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagcc........ taagagaaacaaaaaagcaaaacagcctctgcacatttagtgcagaggctgttttgtttgagatagaagattacctaagctattgttttctacctaaatagaaagcc........ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAGAAACAAAAAAGCAAAACAGCCUCUGCACAUUUAGUGCAGAGGCUGUUUUGUUUGAGAUAGAAGAUUACCUAAGCUAUUGUUUUCUACCUAAAUAGAAAGCC ..............((((((((((((((((((((.....))))))))))))))))))))..(((((.((.....))...)))))((((((((......)))))))). (-42.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUUUCUAUUUAGGUAGAAAACAAUAGCUUAGGUAAUCUUCUAUCUCAAACAAAACAGCCUCUGCACUAAAUGUGCAGAGGCUGUUUUGCUUUUUUGUUUCUCUUA ...........((((.(((((.(((.(((..(((((......))))).....((((((((((((((((.....)))))))))))))))))))...)))))))))))) (-39.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 521 58 16 181 140 pint:PI0654|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_596283..596513_POSITIVE 462 69 21 176 125 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 392 57 14 193 151 pint:PI0638|5end_hypothetical_protein_582218..582448_POSITIVE 392 57 14 92 50 pint:PI0637|5end_hypothetical_protein_582117..582347_POSITIVE 370 69 21 137 76 pint:PI1340|5end_hypothetical_protein_1256568..1256798_POSITIVE 338 57 21 218 179 pint:PI1339|5end_hypothetical_protein_1256671..1256901_POSITIVE 304 60 13 183 125 pint:PI1813|5end_hypothetical_protein_1752878..1753108_POSITIVE 297 70 24 183 123 pint:PI2097|5end_conserved_hypothetical_protein_2050912..2051142_POSITIVE 284 58 16 180 142 pint:PI1806|5end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1740777..1741007_POSITIVE 282 80 39 207 167 pint:PI0019|5end_conserved_hypothetical_protein_23742..23972_POSITIVE 273 85 41 47 10 pint:PI1799|5end_30S_ribosomal_protein_S2_1732900..1733130_POSITIVE 273 70 23 103 56 pint:PI0861|5end_glucosamine--fructose-6-phosphate_aminotransferase_(glutamine-fructose-6-phosphate_transaminase_(isomerizing))_796346..796576_POSITIVE 270 60 23 176 136 pint:PI1651|5end_hypothetical_protein_1563845..1564075_POSITIVE 268 55 14 58 24 pint:PI1744|5end_chromosome_partitioning_protein_1665635..1665865_POSITIVE 267 57 19 77 29 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 266 49 17 217 191 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 261 67 25 72 21 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 257 50 3 48 6 pint:PI1874|5end_hypothetical_protein_1818437..1818667_POSITIVE 257 80 31 212 165 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 257 60 16 208 157 pint:PI0269|5end_conserved_hypothetical_protein_259835..260065_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 649 59 15 76 32 pint:PI1587|3end_conserved_hypothetical_protein;_possible_permease_1516266..1516416_POSITIVE 521 58 16 54 13 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 392 57 14 108 66 pint:PI0636|3end_hypothetical_protein_582213..582363_POSITIVE 370 69 21 83 22 pint:PI1338|3end_phosphoserine_phosphatase_1256594..1256744_POSITIVE 321 64 24 66 11 pint:PI1689|3end_conserved_hypothetical_protein_1605202..1605352_POSITIVE 310 49 4 73 30 pint:PI0141|3end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_133308..133458_POSITIVE 304 60 13 79 21 pint:PI1812|3end_possible_alpha-amylase_1752854..1753004_POSITIVE 297 70 24 75 15 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 282 80 39 74 34 pint:PI0018|3end_hypothetical_protein_23689..23839_POSITIVE 273 65 24 78 28 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 261 70 24 105 58 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 257 80 31 101 54 pint:PI1436|3end_hypothetical_protein_1356232..1356382_POSITIVE 257 60 16 83 32 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 256 48 2 148 101 pint:PI1198|3end_acetyltransferase_1115219..1115369_POSITIVE 255 56 17 111 73 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 253 59 26 101 57 pint:PI0098|3end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_95532..95682_POSITIVE 251 68 21 52 1 pint:PI1722|3end_possible_peptidyl-prolyl_cis-trans_isomerase_1640995..1641145_POSITIVE 245 51 25 147 112 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 245 80 40 66 26 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 243 59 23 151 112 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE