Origin IGS: tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa .........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 tttaatttccttttcgtgtgctaggtctaacttctgatataccttcataagttagtttattacgctttaattgcccatcaagtaaagattcatataaagaatttcctgttctattaagagtcatattcaaaacgtttttgctcaaagttaggatcgtgtttgcttaacaaatctacgaaacgaaaaggtcaaggaaagcatcctaccctaaattctttatactata Mask Tandem Repeat Region ================================================ tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Find is-nt database================================================ Query_seq: SSA_0559:SSA_0560|SSA_0559:SSA_0560:hypothetical protein:hypothetical protein:->->:553180..553405 226 tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0559:SSA_0560|SSA_0559:SSA_0560:hypothetical protein:hypothetical protein:->->:553180..553405 226 tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0559:SSA_0560|SSA_0559:SSA_0560:hypothetical protein:hypothetical protein:->->:553180..553405 226 tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 73 End: 222 ........................................................................ M L T L S K N V L N M T L N R T G N S L Y E S L L D G Q L K R N K L T Y E G I S E V R P S T R K G N * .... tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa 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================================================ tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -3.5 Tail_Score: -2.5547 Start: 140 End: 162 Full_Region: agttagtttattacg ctttaattg cccat caagtaaag attcatataaagaat ...........................................................................................................................................ctttaattgcccatcaagtaaag................................................................ Find igs database================================================ Query_seq: SSA_0559:SSA_0560|SSA_0559:SSA_0560:hypothetical protein:hypothetical protein:->->:553180..553405 226 tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_009009_SSA_0559_SSA_0560|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[553180,553405]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa tatagtataaagaatttagggtaggatgctttccttgaccttttcgtttcgtagatttgttaagcaaacacgatcctaactttgagcaaaaacgttttgaatatgactcttaatagaacaggaaattctttatatgaatctttacttgatgggcaattaaagcgtaataaactaacttatgaaggtatatcagaagttagacctagcacacgaaaaggaaattaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAGUAUAAAGAAUUUAGGGUAGGAUGCUUUCCUUGACCUUUUCGUUUCGUAGAUUUGUUAAGCAAACACGAUCCUAACUUUGAGCAAAAACGUUUUGAAUAUGACUCUUAAUAGAACAGGAAAUUCUUUAUAUGAAUCUUUACUUGAUGGGCAAUUAAAGCGUAAUAAACUAACUUAUGAAGGUAUAUCAGAAGUUAGACCUAGCACACGAAAAGGAAAUUAAA ...............((((((.(((...))).))))))(((((((((.((((.(.((((.....)))))))))............((....(((((((((...((.(((.....((...((((..(((.......)))))))..))....))))).)))))))))......(((((((.(((.......))).))))))).....))..)))))))))........ (-41.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUUUCCUUUUCGUGUGCUAGGUCUAACUUCUGAUAUACCUUCAUAAGUUAGUUUAUUACGCUUUAAUUGCCCAUCAAGUAAAGAUUCAUAUAAAGAAUUUCCUGUUCUAUUAAGAGUCAUAUUCAAAACGUUUUUGCUCAAAGUUAGGAUCGUGUUUGCUUAACAAAUCUACGAAACGAAAAGGUCAAGGAAAGCAUCCUACCCUAAAUUCUUUAUACUAUA ........(((((((((...(((((((((((((.(((.......))).)))))))........((.......)).....((((((.(((((.((...(((((.....)))))..)).))))).........(((((((.((.....)).)))).)))..)))))).....))))).)..)))))))))...((((.....))))...................... (-40.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 75 32 181 137 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 257 64 21 42 1 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 255 60 18 221 183 NC_009009:SSA_0254|5end_hypothetical_protein_247492..247722_NEGATIVE 254 49 11 61 18 NC_009009:SSA_1440|5end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444721..1444951_NEGATIVE 254 80 34 210 164 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 253 60 25 124 95 NC_009009:SSA_2214|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215835..2216065_NEGATIVE 249 45 16 164 132 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 249 64 21 61 5 NC_009009:SSA_1360|5end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1376350..1376580_POSITIVE 248 156 119 172 135 NC_009009:SSA_1435|5end_hypothetical_protein_1442212..1442442_NEGATIVE 248 63 21 199 151 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 248 50 17 200 154 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 247 48 19 186 160 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 246 219 171 56 17 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 245 75 33 220 180 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 245 65 27 42 8 NC_009009:SSA_0079|5end_ROK_family_protein,_putative_82855..83085_POSITIVE 244 64 21 184 147 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 244 77 34 133 96 NC_009009:SSA_0119|5end_50S_ribosomal_protein_L5,_putative_113692..113922_POSITIVE 242 66 34 196 165 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 240 52 18 91 47 NC_009009:SSA_0684|5end_Fibril-like_structure_subunit_FibA,_putative_664992..665222_POSITIVE 239 78 33 172 122 NC_009009:SSA_1645|5end_hypothetical_protein_1646227..1646457_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 60 17 45 1 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE 292 67 23 144 99 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 283 53 28 26 1 NC_009009:SSA_0563|3end_Universal_stress_protein_family,_putative_554947..555097_NEGATIVE 275 60 12 150 103 NC_009009:SSA_2199|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2198679..2198829_NEGATIVE 274 49 7 74 31 NC_009009:SSA_1750|3end_Extracellular_nuclease,_putative_1735673..1735823_NEGATIVE 253 60 25 127 98 NC_009009:SSA_2215|3end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2215832..2215982_NEGATIVE 249 64 21 61 5 NC_009009:SSA_1359|3end_Arginine/histidine_ABC_transporter,_permease_component,_putative_1376430..1376580_POSITIVE 247 58 19 42 1 NC_009009:SSA_1950|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component,_putative_1944566..1944716_NEGATIVE 247 65 24 38 2 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 244 77 31 46 6 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 244 77 34 109 72 NC_009009:SSA_0118|3end_50S_ribosomal_protein_L24,_putative_113748..113898_POSITIVE 239 78 33 77 27 NC_009009:SSA_1646|3end_hypothetical_protein_1646322..1646472_NEGATIVE 239 58 11 91 47 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 236 58 11 108 55 NC_009009:SSA_1188|3end_Ribonuclease_HII,_putative_1216055..1216205_NEGATIVE 235 50 21 144 110 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 234 50 1 83 34 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 233 59 15 141 81 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 232 58 15 145 107 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 232 49 4 74 13 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 231 100 51 109 64 NC_009009:SSA_1242|3end_Dihydroorotate_dehydrogenase_B,_putative_1266448..1266598_NEGATIVE