Origin IGS: ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt .........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 acatttcccctaaatcagcggattccgccgccaactacactattaaactagttcataataatgcaaaaaaaaagccgttatgtcaagagaagtaaactataaaacagctttttaacggcatcatggtaaaattatcggcatttatacttggtttctgaatatgtcagaactcattgaaaaaaaactccttttatggtataaaataatatatcaagttgaaccaaaataagccgaaaataaggggggaggcccgctcaa Mask Tandem Repeat Region ================================================ ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Find is-nt database================================================ Query_seq: TDE1092:TDE1093|TDE1092:TDE1093:hypothetical protein:hypothetical protein:<-->:1127256..1127513 258 ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1092:TDE1093|TDE1092:TDE1093:hypothetical protein:hypothetical protein:<-->:1127256..1127513 258 ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1092:TDE1093|TDE1092:TDE1093:hypothetical protein:hypothetical protein:<-->:1127256..1127513 258 ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 167 End: 256 ...................................................................................................................................................................... K E Q C L P K K K A N N H V L K I T Y N A A S D A S K P S M .. Protein_Len: 32 Strand: - Start: 33 End: 128 ................................ K P E V Q Y I I K Y W L L L K K E I L E S M N L F W T Y I G I M .................................................................................................................................. ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt 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: 57 End: 86 ........................................................ATTGAAAAAAAACTCCTTTTATGGTATAAA............................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 172 End: 201 ...........................................................................................................................................................................CTTGACATAACGGCTTTTTTTTTGCATTAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1092:TDE1093|TDE1092:TDE1093:hypothetical protein:hypothetical protein:<-->:1127256..1127513 258 ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: NC_002967_TDE1092_TDE1093|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1127256,1127513]|258 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagnnnnnnnncaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggcnnnnnnnnngcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt ttgagcgggcctccccccttattttcggcttattttggttcaacttgatatattattttataccataaaaggagttttttttcaatgagttctgacatattcagaaaccaagtataaatgccgataattttaccatgatgccgttaaaaagctgttttatagtttacttctcttgacataacggctttttttttgcattattatgaactagtttaatagtgtagttggcggcggaatccgctgatttaggggaaatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAGCGGGCCUCCCCCCUUAUUUUCGGCUUAUUUUGGUUCAACUUGAUAUAUUAUUUUAUACCAUAAAAGGAGUUUUUUUUCAAUGAGUUCUGACAUAUUCAGAAACCAAGUAUAAAUGCCGAUAAUUUUACCAUGAUGCCGUUAAAAAGCUGUUUUAUAGUUUACUUCUCUUGACAUAACGGCUUUUUUUUUGCAUUAUUAUGAACUAGUUUAAUAGUGUAGUUGGCGGCGGAAUCCGCUGAUUUAGGGGAAAUGU ......(((...)))((((((...(((((..((((((...................(((((((.......((((.....))))..((..((((((.....))))))..)).))))))).((((((.........(((((((.(..(((((((((((.....(((..........)))..)))))))))))..).))))))).....((((......))))...))))))..))))))..)))))..))))))...... (-59.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUCCCCUAAAUCAGCGGAUUCCGCCGCCAACUACACUAUUAAACUAGUUCAUAAUAAUGCAAAAAAAAAGCCGUUAUGUCAAGAGAAGUAAACUAUAAAACAGCUUUUUAACGGCAUCAUGGUAAAAUUAUCGGCAUUUAUACUUGGUUUCUGAAUAUGUCAGAACUCAUUGAAAAAAAACUCCUUUUAUGGUAUAAAAUAAUAUAUCAAGUUGAACCAAAAUAAGCCGAAAAUAAGGGGGGAGGCCCGCUCAA ................(((((.((((.((.((......((((......)))).....................(((((.(((((..(((((((.............)))))))...))))).)))))...(((.(((((..((((..(((((((((((.....))))).........................(((((((......))))))).....)))))).))))))))).)))..))))))))..)))))... (-54.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 943 50 1 141 92 NC_002967:TDE1092|5end_hypothetical_protein_1127165..1127395_NEGATIVE 340 46 2 75 25 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 307 143 103 66 23 NC_002967:TDE0761|5end_protease_complex-associated_polypeptide_799969..800199_POSITIVE 286 40 2 129 91 NC_002967:TDE2693|5end_ankyrin_repeat_protein_2731133..2731363_POSITIVE 284 48 3 81 24 NC_002967:TDE1105|5end_ribosome-binding_factor_A_1138199..1138429_NEGATIVE 284 240 202 231 203 NC_002967:TDE0086|5end_hypothetical_protein_103876..104106_NEGATIVE 283 240 194 216 171 NC_002967:TDE2059|5end_hypothetical_protein_2086509..2086739_NEGATIVE 283 160 111 163 121 NC_002967:TDE1162|5end_ParB-like_nuclease_domain_protein_1197684..1197914_NEGATIVE 279 45 3 208 152 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 273 47 7 223 185 NC_002967:TDE2680|5end_hypothetical_protein_2721072..2721302_NEGATIVE 272 44 3 49 7 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 269 241 204 63 24 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 268 242 208 72 39 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 268 186 141 52 15 NC_002967:TDE0603|5end_hypothetical_protein_640888..641118_POSITIVE 267 29 6 49 20 NC_002967:TDE2564|5end_PemK_family_protein_2589975..2590205_POSITIVE 264 50 6 72 16 NC_002967:TDE2553|5end_lysyl-tRNA_synthetase_2580633..2580863_NEGATIVE 264 21 3 227 203 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 264 250 204 43 3 NC_002967:TDE0763|5end_hypothetical_protein_804338..804568_NEGATIVE 264 197 153 192 143 NC_002967:TDE0423|5end_hypothetical_protein_476601..476831_POSITIVE 262 37 5 41 12 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 46 2 78 28 NC_002967:TDE2551|3end_hypothetical_protein_2576212..2576362_NEGATIVE 299 47 4 49 11 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 284 48 3 88 31 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 284 46 8 114 67 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 283 250 202 95 45 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 283 160 111 147 105 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE 280 31 6 148 121 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 272 160 118 41 1 NC_002967:TDE0760|3end_hypothetical_protein_800013..800163_POSITIVE 269 241 204 57 18 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 267 29 6 62 33 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 264 244 207 125 93 NC_002967:TDE2407|3end_amidophosphoribosyltransferase_2433644..2433794_NEGATIVE 264 250 204 147 107 NC_002967:TDE0763|3end_hypothetical_protein_804234..804384_NEGATIVE 264 197 153 121 72 NC_002967:TDE0422|3end_bacteriocin-type_signal_domain_protein_476610..476760_POSITIVE 262 37 5 44 15 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 262 178 132 101 63 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 262 240 213 33 5 NC_002967:TDE0242|3end_hypothetical_protein_275314..275464_NEGATIVE 261 248 220 80 49 NC_002967:TDE0074|3end_amino_acid_permease_family_protein_84156..84306_NEGATIVE 259 43 3 63 14 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 258 250 216 68 35 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 256 49 7 87 46 NC_002967:TDE2408|3end_hypothetical_protein_2435217..2435367_NEGATIVE