Origin IGS: tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta .........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 taatgttctgtaatttttgtaaagagctcaagcttatacacaccaatttttagttaatgcaaagacatatagtaacaggtatagctttggcattgatgatagagcaattaatgaatatataatatccttataaagaaaaattgattttacccggtcagttacagtaaactatatacaacttatatagaagcggttatttcgatacttttattgctgaaatacaaattgaatagtaaggttgatgctcaaaatttattgggaaaataaaatgctgaaaaaaattaattacaaattactatattgtcctaacattcgctttaacgccggcagcaggtgcaagtcttattgagatttaaaacaatattagatacatagtcttggaggttaaaatataaa Mask Tandem Repeat Region ================================================ tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Find is-nt database================================================ Query_seq: TDE1765:TDE1766|TDE1765:TDE1766:hypothetical protein:hypothetical protein:<-<-:1811969..1812364 396 tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1765:TDE1766|TDE1765:TDE1766:hypothetical protein:hypothetical protein:<-<-:1811969..1812364 396 tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1765:TDE1766|TDE1765:TDE1766:hypothetical protein:hypothetical protein:<-<-:1811969..1812364 396 tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 111 End: 200 .............................................................................................................. M N F F Q H F I F P I N F E H Q P Y Y S I C I S A I K V S K .................................................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 256 End: 360 ............................................................................................................................................................................................................................................................... M F L Y K D I I Y S L I A L S S M P K L Y L L L Y V F A L T K N W C V .................................... Protein_Len: 39 Strand: - Start: 51 End: 167 .................................................. Y S K C R S G A N F R I N P C Y L L K Y N I K K L M K N E W Y I K L M L R V M ..................................................................................................................................................................................................................................... tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta 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================================================ tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 59 HP_score: -4.7 Tail_Score: -3.84825 Start: 210 End: 228 Full_Region: TCGAAATAACCGCTT CTATATA AGTTG TATATAG TTTACTGTAACTGAC .................................................................................................................................................................................................................CTATATAAGTTGTATATAG........................................................................................................................................................................ Find igs database================================================ Query_seq: TDE1765:TDE1766|TDE1765:TDE1766:hypothetical protein:hypothetical protein:<-<-:1811969..1812364 396 tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Intra-Species Hit: Count: 1 Min: 1 Max: 396 Len: 396 Subject: NC_002967_TDE1765_TDE1766|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1811969,1812364]|396 HSP 1 e-value: 0.0 bit: 743.0 Len: 396 Query Start:1 Query End:396 Subject Strand: POSITIVE Subject Start: 1 Subject End: 396 tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaannnnnnncagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta tttatattttaacctccaagactatgtatctaatattgttttaaatctcaataagacttgcacctgctgccggcgttaaagcgaatgttaggacaatatagtaatttgtaattaatttttttcagcattttattttcccaataaattttgagcatcaaccttactattcaatttgtatttcagcaataaaagtatcgaaataaccgcttctatataagttgtatatagtttactgtaactgaccgggtaaaatcaatttttctttataaggatattatatattcattaattgctctatcatcaatgccaaagctatacctgttactatatgtctttgcattaactaaaaattggtgtgtataagcttgagctctttacaaaaattacagaacatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAUUUUAACCUCCAAGACUAUGUAUCUAAUAUUGUUUUAAAUCUCAAUAAGACUUGCACCUGCUGCCGGCGUUAAAGCGAAUGUUAGGACAAUAUAGUAAUUUGUAAUUAAUUUUUUUCAGCAUUUUAUUUUCCCAAUAAAUUUUGAGCAUCAACCUUACUAUUCAAUUUGUAUUUCAGCAAUAAAAGUAUCGAAAUAACCGCUUCUAUAUAAGUUGUAUAUAGUUUACUGUAACUGACCGGGUAAAAUCAAUUUUUCUUUAUAAGGAUAUUAUAUAUUCAUUAAUUGCUCUAUCAUCAAUGCCAAAGCUAUACCUGUUACUAUAUGUCUUUGCAUUAACUAAAAAUUGGUGUGUAUAAGCUUGAGCUCUUUACAAAAAUUACAGAACAUUA ....................(((((((.((((((((((((((((..........(.((.(((.....))).))).))))))).)))))))))...)))))))..(((((((((........................(((((.......(((((...((((.......((((((((((...(((.....................)))...))))))))))..(((((....))))).......)))).....................((((((...))))))......))))).......(((((.(((((((((........)))).).)))))))))........)))))..((((..(((....)))...))))..)))))))))...... (-63.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGUUCUGUAAUUUUUGUAAAGAGCUCAAGCUUAUACACACCAAUUUUUAGUUAAUGCAAAGACAUAUAGUAACAGGUAUAGCUUUGGCAUUGAUGAUAGAGCAAUUAAUGAAUAUAUAAUAUCCUUAUAAAGAAAAAUUGAUUUUACCCGGUCAGUUACAGUAAACUAUAUACAACUUAUAUAGAAGCGGUUAUUUCGAUACUUUUAUUGCUGAAAUACAAAUUGAAUAGUAAGGUUGAUGCUCAAAAUUUAUUGGGAAAAUAAAAUGCUGAAAAAAAUUAAUUACAAAUUACUAUAUUGUCCUAACAUUCGCUUUAACGCCGGCAGCAGGUGCAAGUCUUAUUGAGAUUUAAAACAAUAUUAGAUACAUAGUCUUGGAGGUUAAAAUAUAAA ...((((((((......((((..((((....)))).))))............((((((((((((..((((........))))..)))).)))))))).)))))))).........(((((..((.((((...((((..((((((((((...(((.((((...((((..(((((((.....)))))))...(((.....))).))))...)))))))..............(((((..(((....(((((......)))))..)))....)))))...))))))))))........(((((((((.................((((.......)))).(((((((...)))))))...)))))).)))........)))).)))).))..))))).. (-70.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 935 100 51 191 142 NC_002967:TDE1765|5end_hypothetical_protein_1811878..1812108_NEGATIVE 393 93 51 176 134 NC_002967:TDE0276|5end_HD_domain_protein_308029..308259_NEGATIVE 356 92 57 194 159 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 350 204 161 175 132 NC_002967:TDE0441|5end_hypothetical_protein_496645..496875_NEGATIVE 332 94 51 187 144 NC_002967:TDE1825|5end_hypothetical_protein_1858344..1858574_NEGATIVE 309 92 62 178 133 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 308 93 57 208 176 NC_002967:TDE2390|5end_hypothetical_protein_2420558..2420788_NEGATIVE 302 95 55 120 71 NC_002967:TDE1824|5end_hypothetical_protein_1857011..1857241_POSITIVE 302 77 33 153 90 NC_002967:TDE0782|5end_50S_ribosomal_protein_L6_812970..813200_POSITIVE 299 96 57 66 21 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 295 110 63 86 39 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 291 95 58 194 137 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 288 92 58 188 151 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 286 103 67 147 114 NC_002967:TDE1047|5end_30S_ribosomal_protein_S12_1074097..1074327_POSITIVE 283 92 57 164 129 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 283 92 57 189 154 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 283 92 57 187 152 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 283 92 57 224 189 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 278 92 58 167 129 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 278 92 58 204 166 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 93 51 96 54 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 356 92 57 81 46 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 350 204 161 131 88 NC_002967:TDE0442|3end_hypothetical_protein_496689..496839_NEGATIVE 343 97 52 85 23 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 310 91 58 94 43 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 306 97 52 101 28 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 304 74 31 66 24 NC_002967:TDE0266|3end_hypothetical_protein_297767..297917_NEGATIVE 302 77 33 142 79 NC_002967:TDE0781|3end_30S_ribosomal_protein_S8_813039..813189_POSITIVE 291 95 58 83 26 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 288 92 58 48 11 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 288 92 58 48 11 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 287 92 58 112 57 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 286 103 67 46 13 NC_002967:TDE1046|3end_hypothetical_protein_1074076..1074226_POSITIVE 283 92 57 61 26 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 283 92 57 68 33 NC_002967:TDE1836|3end_hypothetical_protein_1868514..1868664_NEGATIVE 283 92 57 64 29 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 283 92 57 64 29 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 283 92 57 69 34 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 283 92 57 61 26 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 278 82 54 150 118 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE