Origin IGS: attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacattctaattatacatctttttttgtgaaaaatccagtccgaatatggagaaatttgagaagttcgatgtttaaccgcaaaggacgctaagaccgcgaagatgatatgtttttaat Mask Tandem Repeat Region ================================================ attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Find is-nt database================================================ Query_seq: TDE0161:TDE0162|TDE0161:TDE0162:hypothetical protein:hypothetical protein:<-->:187920..188037 118 attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0161:TDE0162|TDE0161:TDE0162:hypothetical protein:hypothetical protein:<-->:187920..188037 118 attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0161:TDE0162|TDE0161:TDE0162:hypothetical protein:hypothetical protein:<-->:187920..188037 118 attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 12 End: 116 ........... M I F A V L A S F A V K H R T S Q I S P Y S D W I F H K K R C I I R M .. attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt 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================================================ attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0161:TDE0162|TDE0161:TDE0162:hypothetical protein:hypothetical protein:<-->:187920..188037 118 attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002967_TDE0161_TDE0162|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[187920,188037]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacnnnnnnngatgtataattagaatgtt attaaaaacatatcatcttcgcggtcttagcgtcctttgcggttaaacatcgaacttctcaaatttctccatattcggactggatttttcacaaaaaaagatgtataattagaatgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAAACAUAUCAUCUUCGCGGUCUUAGCGUCCUUUGCGGUUAAACAUCGAACUUCUCAAAUUUCUCCAUAUUCGGACUGGAUUUUUCACAAAAAAAGAUGUAUAAUUAGAAUGUU ......(((((.((.....(((.......)))........(((((.(((((................(((......))).((((....)).))......))))).))))).))))))) (-15.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUUCUAAUUAUACAUCUUUUUUUGUGAAAAAUCCAGUCCGAAUAUGGAGAAAUUUGAGAAGUUCGAUGUUUAACCGCAAAGGACGCUAAGACCGCGAAGAUGAUAUGUUUUUAAU .......(((..(((.(((..((((((((.........((((.....(((..(((((((((...))))).))))..)))....))))........)))))))).))).)))..))).. (-19.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 941 60 11 151 102 NC_002967:TDE0161|5end_hypothetical_protein_187829..188059_NEGATIVE 498 70 21 231 181 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 401 60 15 96 42 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 363 70 22 197 136 NC_002967:TDE0961|5end_DnaJ_domain_protein_983519..983749_POSITIVE 335 44 8 195 158 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 329 77 31 62 18 NC_002967:TDE2298|5end_galactokinase,_putative_2338267..2338497_NEGATIVE 317 70 21 179 123 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 308 59 18 64 23 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 303 60 14 195 148 NC_002967:TDE0835|5end_NADH-ubiquinone_oxidoreductase_855526..855756_NEGATIVE 294 53 20 39 10 NC_002967:TDE0852|5end_50S_ribosomal_protein_L13_875019..875249_POSITIVE 290 60 17 45 4 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 288 59 17 87 46 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 282 42 15 231 204 NC_002967:TDE1906|5end_hypothetical_protein_1923883..1924113_POSITIVE 281 42 15 146 119 NC_002967:TDE2488|5end_modification_methylase,_HemK_family_2511384..2511614_NEGATIVE 278 47 13 110 69 NC_002967:TDE1927|5end_phenylalanyl-tRNA_synthetase_beta_subunit_1943984..1944214_POSITIVE 270 60 16 160 111 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 270 59 12 216 182 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 261 57 16 188 140 NC_002967:TDE2633|5end_hypothetical_protein_2674359..2674589_POSITIVE 260 70 21 99 55 NC_002967:TDE2763|5end_flagellar_motor_switch_protein_2818771..2819001_NEGATIVE 259 70 21 106 39 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 44 8 83 46 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 309 60 13 73 26 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 308 59 18 53 12 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 305 46 21 94 63 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 299 44 1 81 31 NC_002967:TDE1642|3end_hypothetical_protein_1692771..1692921_NEGATIVE 289 44 21 81 52 NC_002967:TDE1636|3end_surface_antigen,_putative_1683517..1683667_NEGATIVE 283 58 14 39 1 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 281 42 15 139 112 NC_002967:TDE2489|3end_peptide_chain_release_factor_1_2511391..2511541_NEGATIVE 263 59 22 142 102 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 262 70 24 109 51 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 260 70 21 84 40 NC_002967:TDE2764|3end_flagellar_protein_2818786..2818936_NEGATIVE 259 69 21 56 1 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 258 59 11 85 34 NC_002967:TDE2304|3end_hypothetical_protein_2343735..2343885_POSITIVE 257 44 12 48 14 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 257 63 21 151 103 NC_002967:TDE1549|3end_recombination_protein_RecR_1592807..1592957_POSITIVE 256 53 25 34 6 NC_002967:TDE2707|3end_hypothetical_protein_2754929..2755079_POSITIVE 255 78 32 143 99 NC_002967:TDE2434|3end_polysaccharide_deacetylase_family_protein_2463300..2463450_NEGATIVE 254 53 16 146 107 NC_002967:TDE0948|3end_hypothetical_protein_970959..971109_NEGATIVE 253 62 21 88 45 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 253 57 11 148 94 NC_002967:TDE0064|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_71335..71485_NEGATIVE