Origin IGS: tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat .........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 attttctttataggaaagagatacaagaaaactacagcaaactactattcttaccacttttaccaaacaatacagcaactacaacagtggaaaggacataataaagccgagtacaaaagtaattcttgcaatgcttttccttcaaaatggcaatgctactatataataatgtaaaagaaaaagcaataaaagaagaaacatttgcattattatacatattacaaatacatatttattcctatatttgcgagtataatatagaaagcttagacaagtcaagcaaatcctaatagtaaagaaattccatcttaagacaatagaaacaataaagcctccaagcgattttgaaatcagcaaggaggcattacgatatcgcaataacagtatatagcaaaaatgaaatgttaatttttagaatctaaaatca Mask Tandem Repeat Region ================================================ tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Find is-nt database================================================ Query_seq: PI0663:PI0664|PI0663:PI0664:possible transcriptional regulator:dihydroorotate dehydrogenase, electron transfer subunit:->->:606604..607030 427 tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0663:PI0664|PI0663:PI0664:possible transcriptional regulator:dihydroorotate dehydrogenase, electron transfer subunit:->->:606604..607030 427 tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0663:PI0664|PI0663:PI0664:possible transcriptional regulator:dihydroorotate dehydrogenase, electron transfer subunit:->->:606604..607030 427 tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 41 End: 283 ........................................ M L L L R Y R N A S L L I S K S L G G F I V S I V L R W N F F T I R I C L T C L S F L Y Y T R K Y R N K Y V F V I C I I ................................................................................................................................................ Protein_Len: 60 Strand: + Start: 196 End: 393 ................................................................................................................................................................................................... M C I C N M Y N N A N V S S F I A F S F T L L Y S S I A I L K E K H C K N Y F C T R L Y Y V L S T V V V A V L F G K S G .................................. Protein_Len: 39 Strand: - Start: 265 End: 381 ........................................................................................................................................................................................................................................................................ I T A N G N Q L F L M A L I V K T S P K I I D K G S N Y N S Y Q K T F T T L M .............................................. Protein_Len: 57 Strand: - Start: 257 End: 427 ................................................................................................................................................................................................................................................................ M I I Y Y C Q W K S P F A N C S N S K Y E A K N H G K W Q Q L Q Q I T Q Y F H Y S Y Y N A T T K K Y R K G I F F M Protein_Len: 54 Strand: - Start: 141 End: 302 ............................................................................................................................................ S K S S K D L S E I N Y E C I Y S Y I H I Q L I Y L L A F T E E K I A K E K V N N Y L L M A M K F S F C Q M ............................................................................................................................. Protein_Len: 35 Strand: - Start: 40 End: 144 ....................................... I S N N R Y R L A E K S I E F D S P P K I T E I T K L H F K K V I L M ........................................................................................................................................................................................................................................................................................... tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat 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: 81 Start: 241 End: 270 ................................................................................................................................................................................................................................................ATTGCTTTTTCTTTTACATTATTATATAGT............................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -7.0 Tail_Score: -4.66814 Start: 65 End: 97 Full_Region: TTGCGATATCGTAAT GCCTCCTTGCTGATT TCAA AATCGCTTGGAGGC TTTATTGTTTCTATT ................................................................GCCTCCTTGCTGATTTCAAAATCGCTTGGAGGC.......................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0663:PI0664|PI0663:PI0664:possible transcriptional regulator:dihydroorotate dehydrogenase, electron transfer subunit:->->:606604..607030 427 tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 427 Len: 427 Subject: pint_PI0663_PI0664|possible transcriptional regulator:dihydroorotate dehydrogenase, electron transfer subunit|POSITIVE:POSITIVE|[606604,607030]|427 HSP 1 e-value: 0.0 bit: 846.0 Len: 427 Query Start:1 Query End:427 Subject Strand: POSITIVE Subject Start: 1 Subject End: 427 tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat tgattttagattctaaaaattaacatttcatttttgctatatactgttattgcgatatcgtaatgcctccttgctgatttcaaaatcgcttggaggctttattgtttctattgtcttaagatggaatttctttactattaggatttgcttgacttgtctaagctttctatattatactcgcaaatataggaataaatatgtatttgtaatatgtataataatgcaaatgtttcttcttttattgctttttcttttacattattatatagtagcattgccattttgaaggaaaagcattgcaagaattacttttgtactcggctttattatgtcctttccactgttgtagttgctgtattgtttggtaaaagtggtaagaatagtagtttgctgtagttttcttgtatctctttcctataaagaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUAGAUUCUAAAAAUUAACAUUUCAUUUUUGCUAUAUACUGUUAUUGCGAUAUCGUAAUGCCUCCUUGCUGAUUUCAAAAUCGCUUGGAGGCUUUAUUGUUUCUAUUGUCUUAAGAUGGAAUUUCUUUACUAUUAGGAUUUGCUUGACUUGUCUAAGCUUUCUAUAUUAUACUCGCAAAUAUAGGAAUAAAUAUGUAUUUGUAAUAUGUAUAAUAAUGCAAAUGUUUCUUCUUUUAUUGCUUUUUCUUUUACAUUAUUAUAUAGUAGCAUUGCCAUUUUGAAGGAAAAGCAUUGCAAGAAUUACUUUUGUACUCGGCUUUAUUAUGUCCUUUCCACUGUUGUAGUUGCUGUAUUGUUUGGUAAAAGUGGUAAGAAUAGUAGUUUGCUGUAGUUUUCUUGUAUCUCUUUCCUAUAAAGAAAAU .(((..((((..(....................((((.(((......))).))))....((((.((((((..((.((((....))))))..)))))).)))).)..))))..)))...........((((((((....(((((...((((((....)).))))......((((((((..(((((((((..........))))))))).....))))))))..((((((....((..((((((..(((((.((...(((.....((((((((((((.((......(((((((((((..(((((((.....)))))))....)))))......)))))).....)).)).)))))))))))))..)).)))))..))))))..))..)))))).....................))))))))))))).. (-97.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCUUUAUAGGAAAGAGAUACAAGAAAACUACAGCAAACUACUAUUCUUACCACUUUUACCAAACAAUACAGCAACUACAACAGUGGAAAGGACAUAAUAAAGCCGAGUACAAAAGUAAUUCUUGCAAUGCUUUUCCUUCAAAAUGGCAAUGCUACUAUAUAAUAAUGUAAAAGAAAAAGCAAUAAAAGAAGAAACAUUUGCAUUAUUAUACAUAUUACAAAUACAUAUUUAUUCCUAUAUUUGCGAGUAUAAUAUAGAAAGCUUAGACAAGUCAAGCAAAUCCUAAUAGUAAAGAAAUUCCAUCUUAAGACAAUAGAAACAAUAAAGCCUCCAAGCGAUUUUGAAAUCAGCAAGGAGGCAUUACGAUAUCGCAAUAACAGUAUAUAGCAAAAAUGAAAUGUUAAUUUUUAGAAUCUAAAAUCA ..((((..((((((((..(((((.......(((.(.((.........(((((.(((((...........................))))).))))).........)).))))......(((((....(((.((((.............)))).))).....((((((((((((((........(.......)........))))))))))))))...))))).......))))).)))))))).((((((..............((((.((....))))))...........((((..........(((.........))).........((((((..((((((....)))).))..)))))).))))....))))))....................)))).......((((((...))))))... (-69.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 100 52 65 8 pint:PI1532|5end_uridylate_kinase_1451644..1451874_POSITIVE 326 75 32 177 132 pint:PI0025|5end_two_component_system_sensor_histidine_kinase_28682..28912_POSITIVE 323 360 311 187 127 pint:PI2005|5end_potassium_uptake_protein_1962950..1963180_POSITIVE 297 168 121 126 75 pint:PI0727|5end_integrase_659261..659491_POSITIVE 297 110 66 224 174 pint:PI0028|5end_aminopeptidase_31559..31789_POSITIVE 296 304 266 61 13 pint:PI0595|5end_conserved_hypothetical_protein_545571..545801_POSITIVE 293 100 51 57 12 pint:PI1707|5end_GTP-binding_protein_1623795..1624025_POSITIVE 293 380 331 204 153 pint:PI0656|5end_peptidase_T_(tripeptide_aminopeptidase)_599833..600063_POSITIVE 291 94 51 103 56 pint:PI1824|5end_ThiJ/PfpI_family_protein_1764479..1764709_POSITIVE 289 367 321 163 109 pint:PI2055|5end_hypothetical_protein_2012999..2013229_POSITIVE 288 100 52 126 88 pint:PI0546|5end_hypothetical_protein_497799..498029_POSITIVE 281 97 51 227 180 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 280 107 66 166 122 pint:PI0610|5end_conserved_hypothetical_protein_557403..557633_POSITIVE 279 97 52 220 172 pint:PI2109|5end_surface_antigen_BspA_2060553..2060783_POSITIVE 278 360 318 52 9 pint:PI1503|5end_30S_ribosomal_protein_S15_1423428..1423658_POSITIVE 277 354 317 154 115 pint:PI1668|5end_conserved_hypothetical_protein_1580692..1580922_POSITIVE 276 94 54 227 193 pint:PI0251|5end_hypothetical_protein_247551..247781_POSITIVE 275 72 31 55 6 pint:PI1369|5end_alkyl_hydroperoxide_reductase,_subunit__C_1289780..1290010_POSITIVE 275 76 52 53 23 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 274 159 111 90 45 pint:PI0297|5end_hypothetical_protein_277747..277977_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 100 52 75 18 pint:PI1531|3end_biotin--acetyl-CoA-carboxylase_ligase_1451734..1451884_POSITIVE 300 99 51 126 95 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 288 100 52 114 76 pint:PI0545|3end_sugar_kinase_497867..498017_POSITIVE 277 356 318 150 111 pint:PI0414|3end_hypothetical_protein_385210..385360_POSITIVE 275 76 52 34 4 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE 274 98 58 100 53 pint:PI0655|3end_Na+/H+_anitporter_599541..599691_POSITIVE 274 159 111 87 42 pint:PI0296|3end_hypothetical_protein_277824..277974_POSITIVE 272 168 141 38 8 pint:PI0726|3end_hypothetical_protein_659253..659403_POSITIVE 269 110 61 88 33 pint:PI1048|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_967193..967343_POSITIVE 268 252 220 89 56 pint:PI2054|3end_hypothetical_protein_2013076..2013226_POSITIVE 264 403 361 88 51 pint:PI0916|3end_hypothetical_protein_845915..846065_POSITIVE 263 349 315 96 61 pint:PI0150|3end_hypothetical_protein_143833..143983_POSITIVE 262 365 326 71 17 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 262 349 305 150 112 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 259 367 321 144 100 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 259 91 51 124 83 pint:PI0396|3end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_362396..362546_POSITIVE 259 73 35 136 92 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 258 95 53 46 5 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 258 109 66 104 56 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 257 99 51 62 17 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE