Origin IGS: tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgattgtttgtaaaaaagttgtgttgtttgctctttggagtacgctcttttggaaatagacggttcagatacaaggagttaggcgaaaataaagcagaggcgtatctatgatacgttgagcatttatttttggcgtgcgacgcagtagatgagctgtatattttcagaaaattcgggggggggggggtactatacagtattttgctactctttgtctagtaggttttgagaaaaaatttaattttttttctaccggaataacattttgtatcatagctaatattatagtgcaaaatagcggagctgtcaaggttatatgtttcgatattttaactgcgggatattccgcaatttgtggtaccaaagatgtgtacaagctatgtagacataaagttggaaagggcttataatgtgctctaaattatatttaggagaaataaa Mask Tandem Repeat Region ================================================ tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Find is-nt database================================================ Query_seq: TDE2140:TDE2141|TDE2140:TDE2141:protease II:hypothetical protein:<-<-:2175231..2175672 442 tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2140:TDE2141|TDE2140:TDE2141:protease II:hypothetical protein:<-<-:2175231..2175672 442 tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2140:TDE2141|TDE2140:TDE2141:protease II:hypothetical protein:<-<-:2175231..2175672 442 tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 4 End: 126 ... M S P K Y N L E H I I S P F Q L Y V Y I A C T H L W Y H K L R N I P Q L K Y R N I ............................................................................................................................................................................................................................................................................................................................ Protein_Len: 36 Strand: + Start: 116 End: 223 ................................................................................................................... M E T Y N L D S S A I L H Y N I S Y D T K C Y S G R K K I K F F L K T Y ........................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 66 End: 275 ................................................................. M Y T S L V P Q I A E Y P A V K I S K H I T L T A P L F C T I I L A M I Q N V I P V E K K L N F F S K P T R Q R V A K Y ....................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 242 End: 442 ................................................................................................................................................................................................................................................. M L Y S T P P P P N F L K I Y S S S T A S H A K N K C S T Y H R Y A S A L F S P N S L Y L N R L F P K E R T P K S K Q H Protein_Len: 35 Strand: - Start: 334 End: 438 ............................................................................................................................................................................................................................................................................................................................................. L Y A E A K N E G L E K Y R F R R N G F S R V G F L L C C L K K V F M .... Protein_Len: 60 Strand: - Start: 35 End: 271 .................................. A S Y G A T L I D F C I V K V A G S N Q V I I N A I I C F T I G T S F F N F K K E F G V L C L T A F Y Q I T G G G G R M ........................................................................................................................................................................... tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa 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: 94 Start: 131 End: 160 ..................................................................................................................................CTTGACAGCTCCGCTATTTTGCACTATAAT.......................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 31 End: 60 ..............................GTAGACATAAAGTTGGAAAGGGCTTATAAT.............................................................................................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -2.6 Tail_Score: -3.44848 Start: 54 End: 74 Full_Region: CCCTTTCCAACTTTA TGTCTACA TAGCT TGTACACA TCTTTGGTACCACAA .....................................................TGTCTACATAGCTTGTACACA................................................................................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE2140:TDE2141|TDE2140:TDE2141:protease II:hypothetical protein:<-<-:2175231..2175672 442 tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagtacccccccccccccgaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Intra-Species Hit: Count: 1 Min: 1 Max: 442 Len: 442 Subject: NC_002967_TDE2140_TDE2141|protease II:hypothetical protein|NEGATIVE:NEGATIVE|[2175231,2175672]|442 HSP 1 e-value: 1.0E-127 bit: 456.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagnnnnnnnnttaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagta............................................................................................................................................................................................ tttatttctcctaaatataatttagagcacattataagccctttccaactttatgtctacatagcttgtacacatctttggtaccacaaattgcggaatatcccgcagttaaaatatcgaaacatataaccttgacagctccgctattttgcactataatattagctatgatacaaaatgttattccggtagaaaaaaaattaaattttttctcaaaacctactagacaaagagtagcaaaatactgtatagta............................................................................................................................................................................................ HSP 2 e-value: 2.0E-94 bit: 347.0 Len: 175 Query Start:268 Query End:442 Subject Strand: POSITIVE Subject Start: 268 Subject End: 442 ...........................................................................................................................................................................................................................................................................gaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa ...........................................................................................................................................................................................................................................................................gaattttctgaaaatatacagctcatctactgcgtcgcacgccaaaaataaatgctcaacgtatcatagatacgcctctgctttattttcgcctaactccttgtatctgaaccgtctatttccaaaagagcgtactccaaagagcaaacaacacaacttttttacaaacaatcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUUCUCCUAAAUAUAAUUUAGAGCACAUUAUAAGCCCUUUCCAACUUUAUGUCUACAUAGCUUGUACACAUCUUUGGUACCACAAAUUGCGGAAUAUCCCGCAGUUAAAAUAUCGAAACAUAUAACCUUGACAGCUCCGCUAUUUUGCACUAUAAUAUUAGCUAUGAUACAAAAUGUUAUUCCGGUAGAAAAAAAAUUAAAUUUUUUCUCAAAACCUACUAGACAAAGAGUAGCAAAAUACUGUAUAGUACCCCCCCCCCCCCGAAUUUUCUGAAAAUAUACAGCUCAUCUACUGCGUCGCACGCCAAAAAUAAAUGCUCAACGUAUCAUAGAUACGCCUCUGCUUUAUUUUCGCCUAACUCCUUGUAUCUGAACCGUCUAUUUCCAAAAGAGCGUACUCCAAAGAGCAAACAACACAACUUUUUUACAAACAAUCAA ..........((((((...)))))).((....(((((((............((((....)))))))))))....(((((((.......((((((((......))))))))...........................((((.((((..(((.....)))...))))...(((((((...((((...(((((((..........................(((((........))))).......(((((((..............................)))))))....)))))))........((..((((((((.((....((((((...)))))).....)))))))))).)).))))...)))))))....................)))).....))))))))).............................. (-72.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUUGUUUGUAAAAAAGUUGUGUUGUUUGCUCUUUGGAGUACGCUCUUUUGGAAAUAGACGGUUCAGAUACAAGGAGUUAGGCGAAAAUAAAGCAGAGGCGUAUCUAUGAUACGUUGAGCAUUUAUUUUUGGCGUGCGACGCAGUAGAUGAGCUGUAUAUUUUCAGAAAAUUCGGGGGGGGGGGGGUACUAUACAGUAUUUUGCUACUCUUUGUCUAGUAGGUUUUGAGAAAAAAUUUAAUUUUUUUUCUACCGGAAUAACAUUUUGUAUCAUAGCUAAUAUUAUAGUGCAAAAUAGCGGAGCUGUCAAGGUUAUAUGUUUCGAUAUUUUAACUGCGGGAUAUUCCGCAAUUUGUGGUACCAAAGAUGUGUACAAGCUAUGUAGACAUAAAGUUGGAAAGGGCUUAUAAUGUGCUCUAAAUUAUAUUUAGGAGAAAUAAA ........................((((((.((((((((((((((...(((((((((((.((((((((..(((..(..((..(.((((((((((((...((((((((...))))))))..)).)))))))))).)..))..)...)))..)))))))).)))))))))))....(((((((((.((((((((....)))))))).)).)))))))....(((((((((((((((((((...)))))))))).((((.((....(((((((((.((((......)))).))))))))).((((((.((((..(((((.((((....))))..)))))....))))))))))...)).)))).((((..((((.((((.....)))).))))....))))..)))))))))..))))))))))..........)))))))))). (-124.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 906 110 61 201 152 NC_002967:TDE2140|5end_protease_II_2175140..2175370_NEGATIVE 588 390 341 206 157 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 381 350 301 228 179 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 375 268 253 82 67 NC_002967:TDE0612|5end_hypothetical_protein_647471..647701_NEGATIVE 375 268 253 164 149 NC_002967:TDE0611|5end_hypothetical_protein_647389..647619_NEGATIVE 317 380 332 129 64 NC_002967:TDE2261|5end_hypothetical_protein_2298013..2298243_NEGATIVE 317 389 344 144 83 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 316 390 341 219 160 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 309 390 342 152 103 NC_002967:TDE2205|5end_enoate_reductase,_putative_2244755..2244985_NEGATIVE 308 389 341 64 15 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 308 105 63 96 60 NC_002967:TDE1362|5end_hypothetical_protein_1400992..1401222_POSITIVE 306 390 346 49 6 NC_002967:TDE1748|5end_GTP-binding_protein,_GTP1/Obg_family_1803080..1803310_NEGATIVE 301 276 237 190 147 NC_002967:TDE2211|5end_hypothetical_protein_2251316..2251546_NEGATIVE 298 49 5 202 145 NC_002967:TDE2105|5end_hypothetical_protein_2131484..2131714_NEGATIVE 291 405 364 64 17 NC_002967:TDE2629|5end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2669329..2669559_POSITIVE 289 277 231 195 131 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 285 363 323 125 78 NC_002967:TDE2649|5end_ABC_transporter,_ATP-binding_protein_2688648..2688878_NEGATIVE 281 306 265 53 9 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 276 310 284 34 8 NC_002967:TDE1050|5end_hypothetical_protein_1077387..1077617_POSITIVE 275 375 331 114 61 NC_002967:TDE0674|5end_hypothetical_protein_713161..713391_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 446 270 222 52 8 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 371 370 322 110 57 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 317 380 332 109 44 NC_002967:TDE2262|3end_peptidase,_U32_family_2298033..2298183_NEGATIVE 317 389 344 144 83 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 310 398 364 40 3 NC_002967:TDE0820|3end_transcriptional_regulator,_TetR_family_843714..843864_NEGATIVE 308 389 341 71 22 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 308 105 63 130 94 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 305 300 256 62 13 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 300 348 301 73 11 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 285 363 323 107 60 NC_002967:TDE2650|3end_transcriptional_regulator,_putative_2688666..2688816_NEGATIVE 280 328 288 99 51 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 279 377 335 123 66 NC_002967:TDE0109|3end_phenylalanyl-tRNA_synthetase_alpha_subunit_128833..128983_NEGATIVE 278 120 78 53 11 NC_002967:TDE0709|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_744481..744631_NEGATIVE 274 109 62 63 12 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 271 405 368 118 78 NC_002967:TDE1079|3end_DNA-binding_protein/PTS_system,_IIA_component_1111805..1111955_POSITIVE 270 389 341 105 43 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 270 310 262 44 3 NC_002967:TDE0295|3end_DNA_gyrase,_A_subunit_324220..324370_NEGATIVE 266 65 27 128 87 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 266 314 272 127 78 NC_002967:TDE1067|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1094544..1094694_NEGATIVE 265 390 341 84 33 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE