Origin IGS: agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtcatcccctcattgattgtattataccacaacttcctcaattttgtaagagctgtttttttatttaaccgcaaagatgctaagggcgcaaaggaaatttaaggatgttttgataacgcattct Mask Tandem Repeat Region ================================================ agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Find is-nt database================================================ Query_seq: TDE0974:TDE0975|TDE0974:TDE0975:hypothetical protein:hypothetical protein:->->:998936..999060 125 agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0974:TDE0975|TDE0974:TDE0975:hypothetical protein:hypothetical protein:->->:998936..999060 125 agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0974:TDE0975|TDE0974:TDE0975:hypothetical protein:hypothetical protein:->->:998936..999060 125 agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 27 End: 125 .......................... M S F A P L A S L R L N K K T A L T K L R K L W Y N T I N E G M T Protein_Len: 32 Strand: - Start: 26 End: 121 ......................... I E K A G K A D K R N F L F V A R V F N L F N H Y L V I L S P M .... agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact 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: 86 Start: 75 End: 104 ..........................................................................CTTACAAAATTGAGGAAGTTGTGGTATAAT..................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0974:TDE0975|TDE0974:TDE0975:hypothetical protein:hypothetical protein:->->:998936..999060 125 agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_002967_TDE0974_TDE0975|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[998936,999060]|125 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaatnnnnnnncagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact agaatgcgttatcaaaacatccttaaatttcctttgcgcccttagcatctttgcggttaaataaaaaaacagctcttacaaaattgaggaagttgtggtataatacaatcaatgaggggatgact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUGCGUUAUCAAAACAUCCUUAAAUUUCCUUUGCGCCCUUAGCAUCUUUGCGGUUAAAUAAAAAAACAGCUCUUACAAAAUUGAGGAAGUUGUGGUAUAAUACAAUCAAUGAGGGGAUGACU .......((((((......((((((........(((..((....(((....)))..............(((((((((.((....))))).))))))))..))).........)))))))))))). (-21.13) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCAUCCCCUCAUUGAUUGUAUUAUACCACAACUUCCUCAAUUUUGUAAGAGCUGUUUUUUUAUUUAACCGCAAAGAUGCUAAGGGCGCAAAGGAAAUUUAAGGAUGUUUUGAUAACGCAUUCU ...............((.((..((((..((.(((.((((.((((((.(..(.(((.((....(((((........)))))..)).))).)..).))))))..)))).))).))))))..)).)). (-17.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 431 119 72 164 120 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 362 75 32 151 108 NC_002967:TDE0161|5end_hypothetical_protein_187829..188059_NEGATIVE 354 58 18 176 130 NC_002967:TDE0770|5end_50S_ribosomal_protein_L2_807952..808182_POSITIVE 329 58 17 195 158 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 320 62 25 208 172 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 301 75 32 41 7 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 299 58 19 85 41 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 291 80 35 223 173 NC_002967:TDE2679|5end_hypothetical_protein_2719518..2719748_POSITIVE 291 77 36 224 184 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 287 66 28 136 96 NC_002967:TDE2156|5end_translation_initiation_factor_IF-3_2190719..2190949_NEGATIVE 285 50 7 203 159 NC_002967:TDE1641|5end_ribose_5-phosphate_isomerase_A_1691877..1692107_POSITIVE 281 55 17 214 166 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 280 73 32 133 94 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 280 62 25 75 40 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 272 56 15 85 35 NC_002967:TDE2182|5end_hypothetical_protein_2215035..2215265_NEGATIVE 268 77 32 186 136 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 263 56 30 43 15 NC_002967:TDE0597|5end_hypothetical_protein_637212..637442_NEGATIVE 257 56 32 69 46 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 255 58 18 122 61 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 254 75 31 73 25 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 58 14 81 36 NC_002967:TDE1642|3end_hypothetical_protein_1692771..1692921_NEGATIVE 354 58 18 142 96 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 329 58 17 83 46 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 326 86 44 71 32 NC_002967:TDE1012|3end_tex_protein,_putative_1043926..1044076_POSITIVE 304 74 32 76 42 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 299 58 19 88 44 NC_002967:TDE1260|3end_cholinephosphate_cytidylyltransferase/choline_kinase_1295676..1295826_POSITIVE 298 60 20 135 81 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 296 58 18 128 85 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 280 73 32 71 32 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 254 75 31 109 61 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 253 59 30 50 11 NC_002967:TDE1150|3end_hypothetical_protein_1187401..1187551_NEGATIVE 249 58 20 80 45 NC_002967:TDE0050|3end_RNA_methyltransferase,_TrmH_family_59283..59433_NEGATIVE 243 56 18 137 96 NC_002967:TDE1199|3end_cell_division_protein_FtsL,_putative_1231705..1231855_POSITIVE 242 58 19 51 11 NC_002967:TDE2159|3end_hypothetical_protein_2193874..2194024_POSITIVE 236 58 12 57 23 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 232 64 22 90 59 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 232 58 18 109 76 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 232 76 34 120 76 NC_002967:TDE1620|3end_hypothetical_protein_1666959..1667109_NEGATIVE 231 58 28 48 17 NC_002967:TDE2731|3end_TIM-barrel_protein,_putative,_NifR3_family_2788453..2788603_POSITIVE 231 44 1 151 101 NC_002967:TDE1886|3end_MiaB-like_tRNA_modifying_enzyme_1907082..1907232_NEGATIVE