Origin IGS: aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgttaatattaagttatataaataaaataaaagtgtctaacacgcagttcaagactgacaaaacccgctctgaagatcggccggttaaacgcctgtacgttttgcagcttaactgcacgttagatggacgcttcgcgctgaagacaatatcacagggagaaatt Mask Tandem Repeat Region ================================================ aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Find is-nt database================================================ Query_seq: TDE1808:TDE1809|TDE1808:TDE1809:hypothetical protein:hypothetical protein:<-<-:1845140..1845304 165 aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1808:TDE1809|TDE1808:TDE1809:hypothetical protein:hypothetical protein:<-<-:1845140..1845304 165 aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1808:TDE1809|TDE1808:TDE1809:hypothetical protein:hypothetical protein:<-<-:1845140..1845304 165 aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 2 End: 148 . M S P C D I V F S A K R P S N V Q L S C K T Y R R L T G R S S E R V L S V L N C V L D T F I L F I ................. Protein_Len: 32 Strand: + Start: 58 End: 153 ......................................................... M Q N V Q A F N R P I F R A G F V S L E L R V R H F Y F I Y I T ............ Protein_Len: 55 Strand: - Start: 1 End: 165 I E G Q S I T K L A F R G D L T C N L Q L V Y L R K V P R D E S R T K D T K F Q T N S V K I K N I Y S L I L M aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa 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================================================ aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -5.4 Tail_Score: -5.3689 Start: 122 End: 132 Full_Region: TCAGTCTTGAACTGC GTGT TAG ACAC TTTTATTTTATTTAT .........................................................................................................................GTGTTAGACAC................................. Find igs database================================================ Query_seq: TDE1808:TDE1809|TDE1808:TDE1809:hypothetical protein:hypothetical protein:<-<-:1845140..1845304 165 aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Intra-Species Hit: Count: 2 Min: 1 Max: 165 Len: 165 Subject: NC_002967_TDE1808_TDE1809|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1845140,1845304]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa aatttctccctgtgatattgtcttcagcgcgaagcgtccatctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Subject: NC_002967_TDE1828_TDE1829|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1861843,1862456]|614 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 124 Query Start:42 Query End:165 Subject Strand: POSITIVE Subject Start: 421 Subject End: 544 .........................................ctaacgtgcagttaagctgcaaaacgtacaggcgtttaaccggccgatcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa .........................................ctaacatgcagttaagctgcaaaacgtaccggcgtctagccggccgctcttcagagcgggttttgtcagtcttgaactgcgtgttagacacttttattttatttatataacttaatattaacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCUCCCUGUGAUAUUGUCUUCAGCGCGAAGCGUCCAUCUAACGUGCAGUUAAGCUGCAAAACGUACAGGCGUUUAACCGGCCGAUCUUCAGAGCGGGUUUUGUCAGUCUUGAACUGCGUGUUAGACACUUUUAUUUUAUUUAUAUAACUUAAUAUUAACAA ..........((((((((((......((((...))))...((((((((((((((((((((((((((.....((.......))..(((.((....)).))))))))).))).)))).)))))))))))))........................))))))).))). (-40.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUAAUAUUAAGUUAUAUAAAUAAAAUAAAAGUGUCUAACACGCAGUUCAAGACUGACAAAACCCGCUCUGAAGAUCGGCCGGUUAAACGCCUGUACGUUUUGCAGCUUAACUGCACGUUAGAUGGACGCUUCGCGCUGAAGACAAUAUCACAGGGAGAAAUU (((((.((((......)))).))))).........(((((((..((((((.(((.(((.(((((((((.((....)).)))..(((.....))).....))))))))))))))))))..)))))))......(((.(.(((..((.....)).))).).)))... (-37.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1023 130 81 221 172 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 578 69 21 146 98 NC_002967:TDE1816|5end_hypothetical_protein_1851673..1851903_NEGATIVE 477 63 21 144 102 NC_002967:TDE1825|5end_hypothetical_protein_1858344..1858574_NEGATIVE 381 149 105 201 158 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 372 100 56 154 95 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 372 126 81 60 15 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 360 69 27 226 182 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 360 67 25 169 123 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 358 126 81 52 6 NC_002967:TDE0163|5end_flavodoxin_193383..193613_NEGATIVE 351 116 73 219 174 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 351 100 57 203 165 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 349 109 62 173 118 NC_002967:TDE1129|5end_lipoprotein,_putative_1161730..1161960_POSITIVE 347 62 21 139 96 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 341 62 25 164 123 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 339 140 93 127 84 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 335 70 25 196 148 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 332 106 69 68 35 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 330 125 81 154 112 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 326 114 72 190 136 NC_002967:TDE2607|5end_hypothetical_protein_2648586..2648816_POSITIVE 320 87 41 61 10 NC_002967:TDE2572|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598738..2598968_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 578 69 21 53 5 NC_002967:TDE1817|3end_hypothetical_protein_1851766..1851916_NEGATIVE 371 100 51 61 6 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 369 126 81 147 107 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 364 67 22 59 9 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 360 69 27 64 20 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 349 109 62 148 93 NC_002967:TDE1128|3end_hypothetical_protein_1161785..1161935_POSITIVE 348 110 79 55 15 NC_002967:TDE2446|3end_malate_dehydrogenase_2474774..2474924_NEGATIVE 339 140 93 106 63 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 334 100 51 132 89 NC_002967:TDE1336|3end_hypothetical_protein_1373780..1373930_POSITIVE 331 100 51 70 27 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 326 114 72 75 21 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 326 101 66 150 109 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 325 119 71 88 28 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 322 129 87 147 100 NC_002967:TDE2759|3end_hypothetical_protein_2815101..2815251_POSITIVE 321 107 67 51 13 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 314 100 56 90 42 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 313 128 82 149 99 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 313 130 81 79 23 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 313 130 81 79 23 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 312 58 13 106 53 NC_002967:TDE0161|3end_hypothetical_protein_187725..187875_NEGATIVE