Origin IGS: ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt .........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 actgtaaaaatatcatatatcaatgcagtatgaaaaagtgatatttaatgtcagccttttaagtttccttcaagttttttataagtctgtcttaagtttctgggattatactaataccatcaaaatagaaatgaggacagtccaatgacatctaaagttaccctaaatgataagcaagtattgacattctcacaggcgcaaaagtaagaaaggaagtaataaaaatcagtaacgtttaaaaagcagcagaagcccttaactaattttttcatataaatctcctaaaacaagtaaaaagaaattttgaggctctttgtcgctccaaaacaaagcagccttagactactcataaaagaaatcacctctgccagctggaaggcagaggtggttttgtggtctggatggaaatcaagg Mask Tandem Repeat Region ================================================ ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Find is-nt database================================================ Query_seq: SSA_1753:SSA_1754|SSA_1753:SSA_1754:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:hypothetical protein:-><-:1742801..1743214 414 ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1753:SSA_1754|SSA_1753:SSA_1754:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:hypothetical protein:-><-:1742801..1743214 414 ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1753:SSA_1754|SSA_1753:SSA_1754:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:hypothetical protein:-><-:1742801..1743214 414 ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 137 End: 292 ........................................................................................................................................ M Y M K K L V K G F C C F L N V T D F Y Y F L S Y F C A C E N V N T C L S F R V T L D V I G L S S F L F .......................................................................................................................... Protein_Len: 43 Strand: - Start: 270 End: 398 ............................................................................................................................................................................................................................................................................. Q V T R M E I K I T N T Y D W F S L V S K Y F V Q L F S L L S V N F I V K E Y Q M S M ................ Protein_Len: 38 Strand: - Start: 1 End: 114 R S K W G S W L V V E A K W S A S T I E K I L L R L S S Q K P A V F L R L M ............................................................................................................................................................................................................................................................................................................ ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt 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================================================ ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -8.5 Tail_Score: -4.44245 Start: 23 End: 60 Full_Region: TTCCATCCAGACCAC AAAACCACCTCTGCC TTCCAGCT GGCAGAGGTGATTTC TTTTATGAGTAGTCT ......................AAAACCACCTCTGCCTTCCAGCTGGCAGAGGTGATTTC.................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -11.5 Tail_Score: -4.51378 Start: 27 End: 56 Full_Region: tactcataaaagaaa tcacctctgcc agctggaa ggcagaggtgg ttttgtggtctggat ..........................tcacctctgccagctggaaggcagaggtgg...................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 91 HP_score: -12.8 Tail_Score: -3.30104 Start: 28 End: 55 Full_Region: actcataaaagaaat cacctctgcc agctggaa ggcagaggtg gttttgtggtctgga ...........................cacctctgccagctggaaggcagaggtg....................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 70 HP_score: -4.2 Tail_Score: -4.64861 Start: 69 End: 83 Full_Region: TGATTTCTTTTATGA GTAGTC TAA GGCTGC TTTGTTTTGGAGCGA ....................................................................GTAGTCTAAGGCTGC........................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1753:SSA_1754|SSA_1753:SSA_1754:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:hypothetical protein:-><-:1742801..1743214 414 ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Intra-Species Hit: Count: 1 Min: 1 Max: 414 Len: 414 Subject: NC_009009_SSA_1753_SSA_1754|Transcriptional regulator, GntR family (repressor of trehalose operon), putative:hypothetical protein|POSITIVE:NEGATIVE|[1742801,1743214]|414 HSP 1 e-value: 0.0 bit: 821.0 Len: 414 Query Start:1 Query End:414 Subject Strand: POSITIVE Subject Start: 1 Subject End: 414 ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt ccttgatttccatccagaccacaaaaccacctctgccttccagctggcagaggtgatttcttttatgagtagtctaaggctgctttgttttggagcgacaaagagcctcaaaatttctttttacttgttttaggagatttatatgaaaaaattagttaagggcttctgctgctttttaaacgttactgatttttattacttcctttcttacttttgcgcctgtgagaatgtcaatacttgcttatcatttagggtaactttagatgtcattggactgtcctcatttctattttgatggtattagtataatcccagaaacttaagacagacttataaaaaacttgaaggaaacttaaaaggctgacattaaatatcactttttcatactgcattgatatatgatatttttacagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUGAUUUCCAUCCAGACCACAAAACCACCUCUGCCUUCCAGCUGGCAGAGGUGAUUUCUUUUAUGAGUAGUCUAAGGCUGCUUUGUUUUGGAGCGACAAAGAGCCUCAAAAUUUCUUUUUACUUGUUUUAGGAGAUUUAUAUGAAAAAAUUAGUUAAGGGCUUCUGCUGCUUUUUAAACGUUACUGAUUUUUAUUACUUCCUUUCUUACUUUUGCGCCUGUGAGAAUGUCAAUACUUGCUUAUCAUUUAGGGUAACUUUAGAUGUCAUUGGACUGUCCUCAUUUCUAUUUUGAUGGUAUUAGUAUAAUCCCAGAAACUUAAGACAGACUUAUAAAAAACUUGAAGGAAACUUAAAAGGCUGACAUUAAAUAUCACUUUUUCAUACUGCAUUGAUAUAUGAUAUUUUUACAGU ..(((((((((.((.((..........((((((((((........)))))))))).....((((((((((.((((.(((((.(((((((.......))))))))))))..................(((((.((.((((.......((((((((((.((((((.......))))))........))))))))))..........(((((((..........))))))).....(((((((((.((((..(((((........((((((....))).))).....)))))...))))))))..))))))))))).)))))...))))..))))))))))..)).)).))))).))))...((((.....((((((((.....(((........)))....))))))))...)))) (-97.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUAAAAAUAUCAUAUAUCAAUGCAGUAUGAAAAAGUGAUAUUUAAUGUCAGCCUUUUAAGUUUCCUUCAAGUUUUUUAUAAGUCUGUCUUAAGUUUCUGGGAUUAUACUAAUACCAUCAAAAUAGAAAUGAGGACAGUCCAAUGACAUCUAAAGUUACCCUAAAUGAUAAGCAAGUAUUGACAUUCUCACAGGCGCAAAAGUAAGAAAGGAAGUAAUAAAAAUCAGUAACGUUUAAAAAGCAGCAGAAGCCCUUAACUAAUUUUUUCAUAUAAAUCUCCUAAAACAAGUAAAAAGAAAUUUUGAGGCUCUUUGUCGCUCCAAAACAAAGCAGCCUUAGACUACUCAUAAAAGAAAUCACCUCUGCCAGCUGGAAGGCAGAGGUGGUUUUGUGGUCUGGAUGGAAAUCAAGG ((((((...((((...))))...))))))(((((((((((((((...)))))......(((((....((((..((((((((...(.(((((((..(((((((.((((((....)))..)))....))))))).))))))).)..............(((((......((((.......((((..(.((((.((..........)).)))).)..))))......)))))))))...))))))))....))))..)))))...))))))))))........(((......................((((((((((((.........)))))).))))))(((((((........(((((((((((((((........)))))))))))))))))))))).(((....))).))) (-90.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 49 1 74 28 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 347 55 12 163 107 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 347 245 201 148 99 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 342 58 11 151 89 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 338 80 37 54 4 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 337 46 1 151 98 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 335 109 68 176 135 NC_009009:SSA_0621|5end_SOS_responce_UmuC_protein,_putative_613737..613967_NEGATIVE 329 80 31 86 43 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 323 53 13 158 109 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 323 74 31 89 41 NC_009009:SSA_0097|5end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_98148..98378_POSITIVE 318 227 183 196 143 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 317 80 32 63 11 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 314 60 14 61 7 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 313 80 34 88 38 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 312 56 30 163 131 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 311 55 18 229 184 NC_009009:SSA_2332|5end_D-alanyl_carrier_protein,_putative_2335196..2335426_NEGATIVE 310 44 2 68 36 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 310 75 34 108 56 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 309 77 33 227 181 NC_009009:SSA_2213|5end_Nucleotide_sugar_dehydratase,_putative_2215111..2215341_NEGATIVE 308 79 31 60 6 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 55 11 63 9 NC_009009:SSA_1753|3end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1742740..1742890_POSITIVE 357 350 302 72 24 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE 342 58 11 74 12 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 339 80 31 131 61 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE 337 46 1 117 64 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 328 57 13 144 109 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 326 246 201 135 84 NC_009009:SSA_1374|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1391359..1391509_NEGATIVE 314 41 1 149 105 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 313 80 34 69 19 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 309 54 13 139 97 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 309 53 30 150 120 NC_009009:SSA_1568|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571960..1572110_POSITIVE 306 84 41 92 34 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 301 78 34 77 31 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 298 49 2 111 74 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 297 45 9 136 97 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 295 241 201 151 106 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 294 48 1 56 11 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 293 46 1 142 102 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 293 69 23 86 42 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 292 58 11 127 80 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE