Origin IGS: taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcccaacctatactcgtggttcctaaatctaatcctaatattcttttcatattaataaggttatttcgatattttgtgtaaagttacaaaaaatattttaattcggagaaaattaatttgaaaaaacttgcacgttatgtaataaacccttatctttgcattactaattttaaagtattcacaataaggatttttccgttgtgagaacattaggttgcctcgtccttataacggggctttttttatgtctgcattttagcttttgtgagcaatgtagtaggttcaatagattttttgtggctgcagaagggtaattctttatttttgaacttttgttaaaacgactccgaatttgttaaaatccaaagcctcaacttcggaattacgggcacttttctgcactttaaattatttatttgcaaataacgccatta Mask Tandem Repeat Region ================================================ taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Find is-nt database================================================ Query_seq: PI1839:PI1840|PI1839:PI1840:hypothetical protein:conserved hypothetical protein:->->:1782561..1782995 435 taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1839:PI1840|PI1839:PI1840:hypothetical protein:conserved hypothetical protein:->->:1782561..1782995 435 taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1839:PI1840|PI1839:PI1840:hypothetical protein:conserved hypothetical protein:->->:1782561..1782995 435 taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 83 End: 253 .................................................................................. M R S R F N K S S K I K N Y P S A A T K N L L N L L H C S Q K L K C R H K K S P V I R T R Q P N V L T T E K S L L ...................................................................................................................................................................................... Protein_Len: 49 Strand: + Start: 225 End: 371 ................................................................................................................................................................................................................................ M F S Q R K N P Y C E Y F K I S N A K I R V Y Y I T C K F F Q I N F L R I K I F F V T L H K I S K ................................................................ Protein_Len: 30 Strand: - Start: 234 End: 323 ......................................................................................................................................................................................................................................... L P F I R I T F V K F N T I C L Y P N I V Y R A L K K L N M ................................................................................................................ Protein_Len: 45 Strand: - Start: 124 End: 258 ........................................................................................................................... G E A A V F F R N F R S C Q E C F S F H L C L F L G T I L V L C G L T R V V S F D K N H M ................................................................................................................................................................................. taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 311 End: 340 ......................................................................................................................................................................................................................................................................................................................TTTTCAAATTAATTTTCTCCGAATTAAAAT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -6.1 Tail_Score: -5.76633 Start: 198 End: 218 Full_Region: tgagaacattaggtt gcctcgt ccttata acggggc tttttttatgtctgc .....................................................................................................................................................................................................gcctcgtccttataacggggc......................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1839:PI1840|PI1839:PI1840:hypothetical protein:conserved hypothetical protein:->->:1782561..1782995 435 taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Intra-Species Hit: Count: 1 Min: 1 Max: 435 Len: 435 Subject: pint_PI1839_PI1840|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1782561,1782995]|435 HSP 1 e-value: 0.0 bit: 821.0 Len: 435 Query Start:1 Query End:435 Subject Strand: POSITIVE Subject Start: 1 Subject End: 435 taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacatnnnnnnngccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct taatggcgttatttgcaaataaataatttaaagtgcagaaaagtgcccgtaattccgaagttgaggctttggattttaacaaattcggagtcgttttaacaaaagttcaaaaataaagaattacccttctgcagccacaaaaaatctattgaacctactacattgctcacaaaagctaaaatgcagacataaaaaaagccccgttataaggacgaggcaacctaatgttctcacaacggaaaaatccttattgtgaatactttaaaattagtaatgcaaagataagggtttattacataacgtgcaagttttttcaaattaattttctccgaattaaaatattttttgtaactttacacaaaatatcgaaataaccttattaatatgaaaagaatattaggattagatttaggaaccacgagtataggttgggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGCGUUAUUUGCAAAUAAAUAAUUUAAAGUGCAGAAAAGUGCCCGUAAUUCCGAAGUUGAGGCUUUGGAUUUUAACAAAUUCGGAGUCGUUUUAACAAAAGUUCAAAAAUAAAGAAUUACCCUUCUGCAGCCACAAAAAAUCUAUUGAACCUACUACAUUGCUCACAAAAGCUAAAAUGCAGACAUAAAAAAAGCCCCGUUAUAAGGACGAGGCAACCUAAUGUUCUCACAACGGAAAAAUCCUUAUUGUGAAUACUUUAAAAUUAGUAAUGCAAAGAUAAGGGUUUAUUACAUAACGUGCAAGUUUUUUCAAAUUAAUUUUCUCCGAAUUAAAAUAUUUUUUGUAACUUUACACAAAAUAUCGAAAUAACCUUAUUAAUAUGAAAAGAAUAUUAGGAUUAGAUUUAGGAACCACGAGUAUAGGUUGGGCU ...((((.(((((((....))))))).......(((((((........(((((((.........((((((((((((....)))))))))))).(((((((....))).)))).....)))))))..)))))))))))...........((.((((((......(((((......((......)).....((((....(((.((((.....)))).)))..(((((((((((..........(((((((((((.((..((((........))))...))..)))))))))))....((((........(((.((((...(((((((.....))))))).(((((((.((((....)))).))))))).)))).)))........))))...)))))))))))......))))........))))))))))).)).. (-89.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCCAACCUAUACUCGUGGUUCCUAAAUCUAAUCCUAAUAUUCUUUUCAUAUUAAUAAGGUUAUUUCGAUAUUUUGUGUAAAGUUACAAAAAAUAUUUUAAUUCGGAGAAAAUUAAUUUGAAAAAACUUGCACGUUAUGUAAUAAACCCUUAUCUUUGCAUUACUAAUUUUAAAGUAUUCACAAUAAGGAUUUUUCCGUUGUGAGAACAUUAGGUUGCCUCGUCCUUAUAACGGGGCUUUUUUUAUGUCUGCAUUUUAGCUUUUGUGAGCAAUGUAGUAGGUUCAAUAGAUUUUUUGUGGCUGCAGAAGGGUAAUUCUUUAUUUUUGAACUUUUGUUAAAACGACUCCGAAUUUGUUAAAAUCCAAAGCCUCAACUUCGGAAUUACGGGCACUUUUCUGCACUUUAAAUUAUUUAUUUGCAAAUAACGCCAUUA .((..........(((((((((((............((((((.......))))))...(((((.....((((((((.((((....)))).))))))))..(((((((((........((..((((...(((((.....)))))...(((((....((((((((((.((.((((......(((((((..(((....))))))))))((((........(((((((.......)))))))...........(((((((...((((....)))))))))))...))))..)))).))...)))).))))))))))).........))))..))...((((....))))))))))))).............))))).......)))))))))))........((((...(((.....)))..))))......))..... (-90.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 641 80 33 153 106 pint:PI1511|5end_hypothetical_protein_1429580..1429810_POSITIVE 641 80 33 102 55 pint:PI1512|5end_hypothetical_protein_1429529..1429759_POSITIVE 305 96 52 66 24 pint:PI2086|5end_signal_peptidase_I_2041835..2042065_POSITIVE 298 77 32 228 180 pint:PI0021|5end_orotate_phosphoribosyltransferase_24939..25169_POSITIVE 293 72 32 54 16 pint:PI1101|5end_hypothetical_protein_1024597..1024827_POSITIVE 293 71 33 194 155 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 292 88 41 66 10 pint:PI0964|5end_conserved_hypothetical_protein_893238..893468_POSITIVE 290 218 196 51 34 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 287 239 197 105 69 pint:PI0588|5end_hypothetical_protein_535016..535246_POSITIVE 281 96 55 92 58 pint:PI0717|5end_conserved_hypothetical_protein_652558..652788_POSITIVE 271 240 197 163 107 pint:PI0090|5end_amidophosphoribosyltransferase_88379..88609_POSITIVE 269 88 44 221 178 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 267 236 195 75 38 pint:PI1827|5end_peptidase,_M23/M37_family,_N-terminal_1768013..1768243_POSITIVE 266 246 202 82 16 pint:PI0610|5end_conserved_hypothetical_protein_557403..557633_POSITIVE 266 74 33 49 10 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 262 255 212 95 52 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 261 71 32 143 82 pint:PI1078|5end_conserved_hypothetical_protein_999500..999730_POSITIVE 259 232 200 46 8 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 255 312 275 212 175 pint:PI0329|5end_hypothetical_protein_310066..310296_POSITIVE 254 72 43 203 165 pint:PI1127|5end_chloride_channel_protein_1052612..1052842_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 81 41 65 25 pint:PI1399|3end_hypothetical_protein_1320844..1320994_POSITIVE 290 218 196 19 2 pint:PI1810|3end_outer_membrane_protein_1749566..1749716_POSITIVE 281 96 55 75 41 pint:PI0715|3end_hypothetical_protein_652621..652771_POSITIVE 281 96 55 59 25 pint:PI0716|3end_conserved_hypothetical_protein_652605..652755_POSITIVE 280 72 31 151 103 pint:PI0609|3end_conserved_hypothetical_protein_557018..557168_POSITIVE 273 77 34 77 42 pint:PI0215|3end_hypothetical_protein_209004..209154_POSITIVE 271 240 197 59 3 pint:PI0089|3end_hypothetical_protein_88355..88505_POSITIVE 266 74 33 83 44 pint:PI0157|3end_hypothetical_protein_151387..151537_POSITIVE 264 73 43 125 91 pint:PI0771|3end_conserved_hypothetical_protein_707107..707257_POSITIVE 261 71 32 132 71 pint:PI1077|3end_hypothetical_protein_999569..999719_POSITIVE 260 99 60 96 53 pint:PI1590|3end_transcriptional_regulator_1518498..1518648_POSITIVE 259 232 200 50 12 pint:PI2012|3end_hypothetical_protein_1971555..1971705_POSITIVE 255 238 198 130 85 pint:PI0537|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_492412..492562_POSITIVE 255 312 275 59 22 pint:PI0328|3end_conserved_hypothetical_protein_309993..310143_POSITIVE 254 71 33 88 50 pint:PI1892|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1835547..1835697_POSITIVE 251 67 25 151 100 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 250 78 32 149 90 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 249 220 171 77 26 pint:PI0058|3end_conserved_hypothetical_protein_57044..57194_POSITIVE 244 217 185 43 15 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 244 70 24 137 89 pint:PI0509|3end_conserved_hypothetical_protein_469187..469337_POSITIVE