Origin IGS: taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat .........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 ataccaaggcgactgacgggttgcacggaagaacgaatcgttgctgcttttcttaaccgtcagcttgctgatgaacaaaagcagaaggaaataaacgagtatggttccaataataatcattgcacaataaaaagaagaaaataagttggtattttagttggtatataaaaccttttttgtaactttgctaacataaatcaagccacgatggtggcactttatggaatgcaataatacgttaataaaacgataagagcataaaacaatgctatgacacacactttttcagctcgttgaaagtatttatctactttcacgagctgattttttattctta Mask Tandem Repeat Region ================================================ taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Find is-nt database================================================ Query_seq: PI0943:PI0945|PI0943:PI0945:conserved hypothetical protein:sodium:solute symporter family protein:->->:876052..876388 337 taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0943:PI0945|PI0943:PI0945:conserved hypothetical protein:sodium:solute symporter family protein:->->:876052..876388 337 taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0943:PI0945|PI0943:PI0945:conserved hypothetical protein:sodium:solute symporter family protein:->->:876052..876388 337 taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 6 End: 116 ..... M K N Q L V K V D K Y F Q R A E K V C V I A L F Y A L I V L L T Y Y C I P ............................................................................................................................................................................................................................. Protein_Len: 41 Strand: + Start: 59 End: 181 .......................................................... M C H S I V L C S Y R F I N V L L H S I K C H H R G L I Y V S K V T K K V L Y T N ............................................................................................................................................................ Protein_Len: 37 Strand: + Start: 172 End: 282 ........................................................................................................................................................................... M Y Q L K Y Q L I F F F L L C N D Y Y W N H T R L F P S A F V H Q Q A D G ....................................................... Protein_Len: 40 Strand: + Start: 218 End: 337 ......................................................................................................................................................................................................................... M I I I G T I L V Y F L L L L F I S K L T V K K S S N D S F F R A T R Q S P W Y Protein_Len: 47 Strand: - Start: 197 End: 337 .................................................................................................................................................................................................... K R R K I T C H N N N S G Y E N I E K Q K Q E D A L Q R N L F A A V I R E E T C G T L R R P M taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat 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================================================ taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -10.1 Tail_Score: -3.54636 Start: 17 End: 49 Full_Region: acacacactttttca gctcgttgaaagta tttatc tactttcacgagc tgattttttattctt ................gctcgttgaaagtatttatctactttcacgagc................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 75 HP_score: -8.1 Tail_Score: -3.69341 Start: 123 End: 136 Full_Region: TGCATTCCATAAAGT GCCAC CATC GTGGC TTGATTTATGTTAGC ..........................................................................................................................GCCACCATCGTGGC......................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0943:PI0945|PI0943:PI0945:conserved hypothetical protein:sodium:solute symporter family protein:->->:876052..876388 337 taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Intra-Species Hit: Count: 1 Min: 1 Max: 337 Len: 337 Subject: pint_PI0943_PI0945|conserved hypothetical protein:sodium:solute symporter family protein|POSITIVE:POSITIVE|[876052,876388]|337 HSP 1 e-value: 0.0 bit: 668.0 Len: 337 Query Start:1 Query End:337 Subject Strand: POSITIVE Subject Start: 1 Subject End: 337 taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat taagaataaaaaatcagctcgtgaaagtagataaatactttcaacgagctgaaaaagtgtgtgtcatagcattgttttatgctcttatcgttttattaacgtattattgcattccataaagtgccaccatcgtggcttgatttatgttagcaaagttacaaaaaaggttttatataccaactaaaataccaacttattttcttctttttattgtgcaatgattattattggaaccatactcgtttatttccttctgcttttgttcatcagcaagctgacggttaagaaaagcagcaacgattcgttcttccgtgcaacccgtcagtcgccttggtat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAUAAAAAAUCAGCUCGUGAAAGUAGAUAAAUACUUUCAACGAGCUGAAAAAGUGUGUGUCAUAGCAUUGUUUUAUGCUCUUAUCGUUUUAUUAACGUAUUAUUGCAUUCCAUAAAGUGCCACCAUCGUGGCUUGAUUUAUGUUAGCAAAGUUACAAAAAAGGUUUUAUAUACCAACUAAAAUACCAACUUAUUUUCUUCUUUUUAUUGUGCAAUGAUUAUUAUUGGAACCAUACUCGUUUAUUUCCUUCUGCUUUUGUUCAUCAGCAAGCUGACGGUUAAGAAAAGCAGCAACGAUUCGUUCUUCCGUGCAACCCGUCAGUCGCCUUGGUAU ...((((((((..((((((((((((((((......))))))).)))))))))....(.(((((....(((((......)))))......((((((.(((...((((((((((..((((((..(((((....)))))....))))))...................(((.......)))..................................))))))))))..))).))))))))))).)................))))))))....((..((((((((....(.....).(((..((........))..)))...)))))))).))........ (-81.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACCAAGGCGACUGACGGGUUGCACGGAAGAACGAAUCGUUGCUGCUUUUCUUAACCGUCAGCUUGCUGAUGAACAAAAGCAGAAGGAAAUAAACGAGUAUGGUUCCAAUAAUAAUCAUUGCACAAUAAAAAGAAGAAAAUAAGUUGGUAUUUUAGUUGGUAUAUAAAACCUUUUUUGUAACUUUGCUAACAUAAAUCAAGCCACGAUGGUGGCACUUUAUGGAAUGCAAUAAUACGUUAAUAAAACGAUAAGAGCAUAAAACAAUGCUAUGACACACACUUUUUCAGCUCGUUGAAAGUAUUUAUCUACUUUCACGAGCUGAUUUUUUAUUCUUA ...((...((((((....))))))..))..((((.(.(((((.((((((((.((...((((((....)))))))).)))))))).........)))))...).))))........................(((((.((((...(((.((((((((((((((((((((((....)))))))....))))))).........(((((....)))))......)))))))).......((((.....)))).....(((((......)))))..)))..........(((((((((.(((((((......))))))))))))))))..)))).))))). (-86.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 320 274 90 45 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 338 136 99 169 138 pint:PI0310|5end_outer_membrane_protein_291657..291887_POSITIVE 333 330 293 59 12 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 331 170 122 104 67 pint:PI2107|5end_hypothetical_protein_2059704..2059934_POSITIVE 331 170 122 61 24 pint:PI2108|5end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2059661..2059891_POSITIVE 329 288 243 231 190 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 322 330 283 99 49 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 316 310 263 171 115 pint:PI1627|5end_hypothetical_protein_1550445..1550675_POSITIVE 309 320 272 158 105 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 306 166 121 197 154 pint:PI2175|5end_RNA_polymerase_sigma-54_2115007..2115237_POSITIVE 300 312 274 141 104 pint:PI1618|5end_hypothetical_protein_1542670..1542900_POSITIVE 297 330 298 88 50 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 290 329 290 47 11 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 289 330 291 209 171 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 287 329 291 73 34 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 283 327 289 56 13 pint:PI0850|5end_conserved_hypothetical_protein_783231..783461_POSITIVE 281 324 288 125 82 pint:PI0707|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_643358..643588_POSITIVE 281 280 234 146 88 pint:PI0477|5end_30S_ribosomal_protein_S5_440392..440622_POSITIVE 280 320 272 197 134 pint:PI1003|5end_conserved_hypothetical_protein_924694..924924_POSITIVE 278 329 291 59 16 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 406 52 14 77 39 pint:PI0943|3end_conserved_hypothetical_protein_875991..876141_POSITIVE 341 320 274 90 45 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 338 136 99 34 3 pint:PI0308|3end_conserved_hypothetical_protein_291602..291752_POSITIVE 333 330 293 63 16 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 329 288 243 57 16 pint:PI0126|3end_conserved_hypothetical_protein_118589..118739_POSITIVE 320 88 41 80 20 pint:PI1222|3end_hypothetical_protein_1143378..1143528_POSITIVE 316 330 281 117 68 pint:PI0810|3end_hypothetical_protein_747026..747176_POSITIVE 306 166 121 79 36 pint:PI2174|3end_hypothetical_protein_2114969..2115119_POSITIVE 300 312 274 60 23 pint:PI1616|3end_hypothetical_protein_1542669..1542819_POSITIVE 290 299 256 85 41 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 289 300 251 145 96 pint:PI1367|3end_redox-sensitive_transcriptional_activator,__OxyR_1287863..1288013_POSITIVE 288 330 291 78 38 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 287 307 261 70 19 pint:PI0425|3end_hypothetical_protein_389722..389872_POSITIVE 285 330 287 41 1 pint:PI1848|3end_hypothetical_protein_1795015..1795165_POSITIVE 282 329 284 136 85 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 281 324 288 81 38 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 281 280 234 136 78 pint:PI0476|3end_50S_ribosomal_protein_L18_440462..440612_POSITIVE 280 273 234 116 78 pint:PI1704|3end_50S_ribosomal_protein_L32_1621680..1621830_POSITIVE 280 320 272 97 34 pint:PI1002|3end_metal_dependent_hydrolase_924674..924824_POSITIVE 278 329 284 147 94 pint:PI1153|3end_histidine_kinase_sensor_protein_1078638..1078788_POSITIVE