Origin IGS: tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaagcaaaactaaataagcaacacttgttagggaatgtattagaattgcgaacggagagatgataaatggcaatagacggtgcaaaaattataggcagtgacgatgggtatgataatgattactgaatggatagaaagaataaagcgaaaacacaattgtaaagcacattttgggagtgatagttttcaaatgaaagactgtatcatagctccggtccacctgattccggaggagatttatgataatcaagagtttgatttctatgtcaaaacaaaatatgatgtttacctgctccgtattataaataatgaagctaagtgcgggattatttatccggcaaaacttagcggtattatatatatcataagcaatttacctattagcaaaaacaatataaccgaatctattcaaaaaactctaaatcgattagaggaatatggctttccaaatttaaagaactcaaaatgcaacatcgcatttcaaatagagtgataaa Mask Tandem Repeat Region ================================================ tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Find is-nt database================================================ Query_seq: TDE0500:TDE0501|TDE0500:TDE0501:hypothetical protein:hypothetical protein:<-<-:553777..554274 498 tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0500:TDE0501|TDE0500:TDE0501:hypothetical protein:hypothetical protein:<-<-:553777..554274 498 tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0500:TDE0501|TDE0500:TDE0501:hypothetical protein:hypothetical protein:<-<-:553777..554274 498 tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 125 End: 406 ............................................................................................................................ M A Y D I Y N T A K F C R I N N P A L S F I I Y N T E Q V N I I F C F D I E I K L L I I I N L L R N Q V D R S Y D T V F ............................................................................................ Protein_Len: 38 Strand: + Start: 342 End: 455 ..................................................................................................................................................................................................................................................................................................................................................... M C F R F I L S I H S V I I I I P I V T A Y N F C T V Y C H L S S L R S Q F ........................................... Protein_Len: 33 Strand: + Start: 400 End: 498 ............................................................................................................................................................................................................................................................................................................................................................................................................... M P I I F A P S I A I Y H L S V R N S N T F P N K C C L F S F A Y Protein_Len: 60 Strand: - Start: 8 End: 400 ....... K T K V Y F D F E Q N D Y I E E P I L H V P A I I C D K M Q F S D S G F H A K C N H K R K I R E I W E T I M I M G M T M .................................................................................................. Protein_Len: 31 Strand: - Start: 3 End: 95 .. I V R N S I R H Q M K L E K F K S L W I G R I S K S N K S Y M ................................................................................................................................................................................................................................................................................................................................................................................................................... tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac 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: 83 Start: 381 End: 410 ............................................................................................................................................................................................................................................................................................................................................................................................ATTATCATACCCATCGTCACTGCCTATAAT........................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 215 End: 244 ......................................................................................................................................................................................................................TTTGATTTCTATGTCAAAACAAAATATGAT.............................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -5.2 Tail_Score: -5.10497 Start: 65 End: 81 Full_Region: TGGAAAGCCATATTC CTCTAA TCGAT TTAGAG TTTTTTGAATAGATT ................................................................CTCTAATCGATTTAGAG................................................................................................................................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: TDE0500:TDE0501|TDE0500:TDE0501:hypothetical protein:hypothetical protein:<-<-:553777..554274 498 tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Intra-Species Hit: Count: 1 Min: 1 Max: 498 Len: 498 Subject: NC_002967_TDE0500_TDE0501|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[553777,554274]|498 HSP 1 e-value: 0.0 bit: 987.0 Len: 498 Query Start:1 Query End:498 Subject Strand: POSITIVE Subject Start: 1 Subject End: 498 tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac tttatcactctatttgaaatgcgatgttgcattttgagttctttaaatttggaaagccatattcctctaatcgatttagagttttttgaatagattcggttatattgtttttgctaataggtaaattgcttatgatatatataataccgctaagttttgccggataaataatcccgcacttagcttcattatttataatacggagcaggtaaacatcatattttgttttgacatagaaatcaaactcttgattatcataaatctcctccggaatcaggtggaccggagctatgatacagtctttcatttgaaaactatcactcccaaaatgtgctttacaattgtgttttcgctttattctttctatccattcagtaatcattatcatacccatcgtcactgcctataatttttgcaccgtctattgccatttatcatctctccgttcgcaattctaatacattccctaacaagtgttgcttatttagttttgcttac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCACUCUAUUUGAAAUGCGAUGUUGCAUUUUGAGUUCUUUAAAUUUGGAAAGCCAUAUUCCUCUAAUCGAUUUAGAGUUUUUUGAAUAGAUUCGGUUAUAUUGUUUUUGCUAAUAGGUAAAUUGCUUAUGAUAUAUAUAAUACCGCUAAGUUUUGCCGGAUAAAUAAUCCCGCACUUAGCUUCAUUAUUUAUAAUACGGAGCAGGUAAACAUCAUAUUUUGUUUUGACAUAGAAAUCAAACUCUUGAUUAUCAUAAAUCUCCUCCGGAAUCAGGUGGACCGGAGCUAUGAUACAGUCUUUCAUUUGAAAACUAUCACUCCCAAAAUGUGCUUUACAAUUGUGUUUUCGCUUUAUUCUUUCUAUCCAUUCAGUAAUCAUUAUCAUACCCAUCGUCACUGCCUAUAAUUUUUGCACCGUCUAUUGCCAUUUAUCAUCUCUCCGUUCGCAAUUCUAAUACAUUCCCUAACAAGUGUUGCUUAUUUAGUUUUGCUUAC ........((((((..(((...(((((.((.(((..((((.....))))..))).)).))))).((((((.....))))))..)))..))))))..(((.......((....)).....(((((((.((......((((.(((((...(((((((...((.((((.....)))).)))))))))...))))).))))..((((.(((.(((((...(((((((((......(((((.((((((....))))))............((((((..((.....)))))))))))))....(((.((((....)))))))........))))))))).)))))....(((....)))............................................................))).)))).....)).)))))))......)))...((((..((((.(((((........))))).......))))..)))).... (-94.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAGCAAAACUAAAUAAGCAACACUUGUUAGGGAAUGUAUUAGAAUUGCGAACGGAGAGAUGAUAAAUGGCAAUAGACGGUGCAAAAAUUAUAGGCAGUGACGAUGGGUAUGAUAAUGAUUACUGAAUGGAUAGAAAGAAUAAAGCGAAAACACAAUUGUAAAGCACAUUUUGGGAGUGAUAGUUUUCAAAUGAAAGACUGUAUCAUAGCUCCGGUCCACCUGAUUCCGGAGGAGAUUUAUGAUAAUCAAGAGUUUGAUUUCUAUGUCAAAACAAAAUAUGAUGUUUACCUGCUCCGUAUUAUAAAUAAUGAAGCUAAGUGCGGGAUUAUUUAUCCGGCAAAACUUAGCGGUAUUAUAUAUAUCAUAAGCAAUUUACCUAUUAGCAAAAACAAUAUAACCGAAUCUAUUCAAAAAACUCUAAAUCGAUUAGAGGAAUAUGGCUUUCCAAAUUUAAAGAACUCAAAAUGCAACAUCGCAUUUCAAAUAGAGUGAUAAA ....((............))..(((((.....(((((((....((.(((((...((((((.(.(((....(.((((((((((((...........))..((..((((((((((...((((.......((((((((...(((((..((....(((....)))...))..((((((....(((((....((((((....((...((((((((((((((...........)))))).....)))))))).))....))))))......)))))...))))))....)))))..))).)))))..((((.((((((..(((((((((.((((.....)))).))...)))))))..)))))).))))))))...))...))))))))..))...........))))..)))))))......((((((.....))))))...))).))))))).........(....)....)))))..))))))))).....)))))..... (-108.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 805 100 51 191 142 NC_002967:TDE0500|5end_hypothetical_protein_553686..553916_NEGATIVE 766 450 401 110 61 NC_002967:TDE0536|5end_hypothetical_protein_578864..579094_NEGATIVE 362 294 253 140 91 NC_002967:TDE1909|5end_conserved_hypothetical_protein_TIGR00159_1926872..1927102_NEGATIVE 358 185 142 226 182 NC_002967:TDE0255|5end_ABC_transporter,_ATP-binding_protein_290742..290972_NEGATIVE 303 301 261 89 47 NC_002967:TDE0142|5end_hypothetical_protein_164074..164304_NEGATIVE 301 429 390 71 32 NC_002967:TDE0530|5end_hypothetical_protein_574363..574593_POSITIVE 301 423 387 160 123 NC_002967:TDE0069|5end_conserved_hypothetical_protein_TIGR00238_76551..76781_POSITIVE 295 305 264 135 97 NC_002967:TDE0809|5end_hypothetical_protein_830785..831015_NEGATIVE 292 428 381 136 74 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 289 304 261 67 20 NC_002967:TDE0464|5end_NifU_domain_protein_518175..518405_NEGATIVE 286 308 261 158 100 NC_002967:TDE1454|5end_sugar_transporter_1501438..1501668_POSITIVE 285 429 390 52 6 NC_002967:TDE2344|5end_undecaprenyl_diphosphate_synthase_2381945..2382175_NEGATIVE 285 291 263 48 16 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 284 449 407 116 58 NC_002967:TDE0254|5end_hypothetical_protein_288654..288884_POSITIVE 283 430 389 87 50 NC_002967:TDE2371|5end_iron-sulfur_cluster-binding_protein_2403583..2403813_POSITIVE 281 288 251 217 180 NC_002967:TDE0722|5end_lipoprotein,_putative_758519..758749_POSITIVE 280 208 173 48 9 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 279 468 421 126 82 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 279 301 264 209 171 NC_002967:TDE1907|5end_holo-(acyl-carrier-protein)_synthase_1925097..1925327_NEGATIVE 274 100 55 180 132 NC_002967:TDE0445|5end_amino_acid_permease_499744..499974_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 294 253 136 87 NC_002967:TDE1910|3end_1-deoxy-D-xylulose-5-phosphate_synthase_1926876..1927026_NEGATIVE 349 301 261 73 21 NC_002967:TDE0950|3end_hypothetical_protein_974166..974316_NEGATIVE 308 287 259 33 4 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 301 423 387 141 104 NC_002967:TDE0068|3end_succinyl-diaminopimelate_desuccinylase_76612..76762_POSITIVE 295 305 264 108 70 NC_002967:TDE0810|3end_hypothetical_protein_830812..830962_NEGATIVE 292 428 381 134 72 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 286 302 268 60 23 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 285 429 390 51 5 NC_002967:TDE2345|3end_ribosome_recycling_factor_2381946..2382096_NEGATIVE 284 449 407 107 49 NC_002967:TDE0253|3end_hypothetical_protein_288725..288875_POSITIVE 283 304 267 101 59 NC_002967:TDE0626|3end_hypothetical_protein_659684..659834_POSITIVE 281 290 256 81 39 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 279 450 402 44 6 NC_002967:TDE2370|3end_hypothetical_protein_2403607..2403757_POSITIVE 274 100 55 127 79 NC_002967:TDE0444|3end_glutamine_amidotransferase_class-I_domain_protein_499771..499921_POSITIVE 273 395 352 109 65 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 269 296 259 47 1 NC_002967:TDE2715|3end_hypothetical_protein_2772936..2773086_POSITIVE 269 304 266 65 31 NC_002967:TDE1276|3end_hypothetical_protein_1310527..1310677_NEGATIVE 268 290 246 113 61 NC_002967:TDE0381|3end_hypothetical_protein_434461..434611_POSITIVE 267 305 261 151 106 NC_002967:TDE0941|3end_NLP/P60_family_protein_963623..963773_NEGATIVE 267 294 255 88 50 NC_002967:TDE0844|3end_pyruvate_phosphate_dikinase,_putative_867773..867923_POSITIVE 265 438 393 126 71 NC_002967:TDE0361|3end_transporter,_putative_407442..407592_POSITIVE