Origin IGS: tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actatcaacttcttctgacttaaacacttgctttttgccattcttgtaaatgtaaacaccttgagcagatgccattgtggcacagaaaagaaaagctaaggtgagggctgtggatataaaatgctttctca Mask Tandem Repeat Region ================================================ tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Find is-nt database================================================ Query_seq: PI0076:PI0077|PI0076:PI0077:conserved hypothetical protein:hypothetical protein:->->:76253..76383 131 tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0076:PI0077|PI0076:PI0077:conserved hypothetical protein:hypothetical protein:->->:76253..76383 131 tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0076:PI0077|PI0076:PI0077:conserved hypothetical protein:hypothetical protein:->->:76253..76383 131 tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 17 End: 109 ................ M H S P H L S F S F L C H N G I C S R C L H L Q E W Q K A S V ...................... Protein_Len: 39 Strand: + Start: 15 End: 131 .............. M S T A L T L A F L F C A T M A S A Q G V Y I Y K N G K K Q V F K S E E V D S tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt 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================================================ tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0076:PI0077|PI0076:PI0077:conserved hypothetical protein:hypothetical protein:->->:76253..76383 131 tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: pint_PI0076_PI0077|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[76253,76383]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt tgagaaagcattttatatccacagccctcaccttagcttttcttttctgtgccacaatggcatctgctcaaggtgtttacatttacaagaatggcaaaaagcaagtgtttaagtcagaagaagttgatagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAAGCAUUUUAUAUCCACAGCCCUCACCUUAGCUUUUCUUUUCUGUGCCACAAUGGCAUCUGCUCAAGGUGUUUACAUUUACAAGAAUGGCAAAAAGCAAGUGUUUAAGUCAGAAGAAGUUGAUAGU .....((((((((...............(((((((((...........(((((.....)))))..))).))))))....(((((....))))).........))))))))..(((((......)))))... (-23.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUCAACUUCUUCUGACUUAAACACUUGCUUUUUGCCAUUCUUGUAAAUGUAAACACCUUGAGCAGAUGCCAUUGUGGCACAGAAAAGAAAAGCUAAGGUGAGGGCUGUGGAUAUAAAAUGCUUUCUCA ..((((.((.((....))........((..((((..((..(((((.....(((...(((..((.((....))))..)))..)))...)))))..)).))))..))....)).))))............... (-23.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 69 23 130 83 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 337 96 53 96 43 pint:PI1359|5end_hypothetical_protein_1275473..1275703_POSITIVE 328 76 31 201 157 pint:PI0339|5end_hypothetical_protein_315735..315965_POSITIVE 319 70 26 175 133 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 312 67 24 188 120 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 305 76 36 191 150 pint:PI0877|5end_hypothetical_protein_811378..811608_POSITIVE 302 75 35 70 26 pint:PI1075|5end_pyruvate_phosphate_dikinase_995828..996058_POSITIVE 300 73 41 231 191 pint:PI2074|5end_conserved_hypothetical_protein_2033660..2033890_POSITIVE 288 69 26 191 149 pint:PI0809|5end_hypothetical_protein_746630..746860_POSITIVE 288 76 32 56 8 pint:PI0485|5end_30S_ribosomal_protein_S4_444450..444680_POSITIVE 280 77 31 198 146 pint:PI0764|5end_permease_697962..698192_POSITIVE 279 88 51 78 39 pint:PI1871|5end_glycosyl_transferase,_group_1_family_protein_1815788..1816018_POSITIVE 278 77 35 140 102 pint:PI1611|5end_aspartate-semialdehyde_dehydrogenase_1538156..1538386_POSITIVE 278 69 23 94 40 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 277 68 21 185 122 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 276 70 21 222 169 pint:PI2156|5end_conserved_hypothetical_protein;_possible_permease_2102796..2103026_POSITIVE 276 68 22 128 82 pint:PI1402|5end_3-deoxy-7-phosphoheptulonate_synthase_1322935..1323165_POSITIVE 274 68 21 140 76 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 274 89 46 173 126 pint:PI0425|5end_hypothetical_protein_389454..389684_POSITIVE 274 89 46 64 17 pint:PI0426|5end_conserved_hypothetical_protein_389345..389575_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 96 53 59 6 pint:PI1358|3end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1275516..1275666_POSITIVE 336 67 24 87 44 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 328 76 31 99 55 pint:PI0338|3end_hypothetical_protein_315713..315863_POSITIVE 309 76 31 127 82 pint:PI1827|3end_peptidase,_M23/M37_family,_N-terminal_1768602..1768752_POSITIVE 283 70 21 115 57 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 273 73 37 106 65 pint:PI1342|3end_conserved_hypothetical_protein_1257799..1257949_POSITIVE 271 67 21 120 58 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 270 81 47 150 107 pint:PI1717|3end_major_outer_membrane_protein_1633888..1634038_POSITIVE 268 76 31 134 89 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE 266 80 34 129 63 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 265 62 21 144 101 pint:PI1025|3end_tRNA_modification_GTPase_942232..942382_POSITIVE 264 78 35 136 87 pint:PI0391|3end_conserved_hypothetical_protein_358216..358366_POSITIVE 261 67 22 141 84 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 258 78 32 72 15 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 257 75 36 120 84 pint:PI0191|3end_O-methyltransferase_181785..181935_POSITIVE 256 70 23 77 35 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 253 78 41 33 1 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 252 99 51 144 82 pint:PI0294|3end_conserved_hypothetical_protein_276806..276956_POSITIVE 250 49 10 104 72 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 250 70 21 90 34 pint:PI0728|3end_integrase_661508..661658_POSITIVE