Origin IGS: cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca .........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 tgagtcaaagtttatatagagatttaaaattaagacttatgcaaatggtagcaaaattggaaactaaagaagtgttatttctaggatgtaaaatcattctgaatatgttcgcctctcaacattagataagatagctagtatttttggaaagtagttacaaatttcaatgttatacagagattacctaacgcccacttcaacgctgacaaaagggaccatgcccgtttgcagattaggcgaatgttagaacgacgccttacggtacgataaactgcaattttgaagaataggatgtattttttataaattaaagcttaaaactccgattaataacttaggttatgtgagtaaagttatgttttatttatagtggctatttggctaagtgaggaaatacg Mask Tandem Repeat Region ================================================ cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Find is-nt database================================================ Query_seq: TDE1773:TDE1774|TDE1773:TDE1774:hypothetical protein:hypothetical protein:<-<-:1817192..1817589 398 cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1773:TDE1774|TDE1773:TDE1774:hypothetical protein:hypothetical protein:<-<-:1817192..1817589 398 cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1773:TDE1774|TDE1773:TDE1774:hypothetical protein:hypothetical protein:<-<-:1817192..1817589 398 cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 91 End: 261 .......................................................................................... M Y K K Y I L F F K I A V Y R T V R R R S N I R L I C K R A W S L L S A L K W A L G N L C I T L K F V T T F Q K Y ......................................................................................................................................... Protein_Len: 33 Strand: + Start: 293 End: 391 .................................................................................................................................................................................................................................................................................................... M F R M I L H P R N N T S L V S N F A T I C I S L N F K S L Y K L ....... Protein_Len: 32 Strand: - Start: 132 End: 227 ................................................................................................................................... R V T L R R E L M R R I Q L R A H D R K D A N F H A N P L R Q M ........................................................................................................................................................................... cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca 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================================================ cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1773:TDE1774|TDE1773:TDE1774:hypothetical protein:hypothetical protein:<-<-:1817192..1817589 398 cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Intra-Species Hit: Count: 3 Min: 1 Max: 398 Len: 398 Subject: NC_002967_TDE1773_TDE1774|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1817192,1817589]|398 HSP 1 e-value: 0.0 bit: 789.0 Len: 398 Query Start:1 Query End:398 Subject Strand: POSITIVE Subject Start: 1 Subject End: 398 cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca cgtatttcctcacttagccaaatagccactataaataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgcaaacgggcatggtcccttttgtcagcgttgaagtgggcgttaggtaatctctgtataacattgaaatttgtaactactttccaaaaatactagctatcttatctaatgttgagaggcgaacatattcagaatgattttacatcctagaaataacacttctttagtttccaattttgctaccatttgcataagtcttaattttaaatctctatataaactttgactca Subject: NC_002967_TDE1830_TDE1831|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1863846,1864504]|659 HSP 1 e-value: 7.0E-20 bit: 99.6 Len: 138 Query Start:34 Query End:171 Subject Strand: POSITIVE Subject Start: 456 Subject End: 592 .................................aataaaacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggcgtcgttctaacattcgcctaatctgc................................................................................................................................................................................................................................... .................................aataaaacataactttatccaaagaacataagctattaattttggttttatgctttaatttataaaaaatacaccctatttttcaaagttacagtttatcgtgccg-aaggcatcggtctaacattcgcttaacctgc................................................................................................................................................................................................................................... Subject: NC_002967_TDE1784_TDE1785|transcriptional activator, AraC family:hypothetical protein|NEGATIVE:POSITIVE|[1824514,1825131]|618 HSP 1 e-value: 6.0E-11 bit: 69.9 Len: 107 Query Start:39 Query End:145 Subject Strand: POSITIVE Subject Start: 306 Subject End: 411 ......................................aacataactttactcacataacctaagttattaatcggagttttaagctttaatttataaaaaatacatcctattcttcaaaattgcagtttatcgtaccgtaaggc............................................................................................................................................................................................................................................................. ......................................aacaaaactttactcaaaaaaactaagctattaatttgtgttttaagctttaatttat-aaaaatataccacatttttcaaagttacagtttatcgtgccgtaaggc............................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUUUCCUCACUUAGCCAAAUAGCCACUAUAAAUAAAACAUAACUUUACUCACAUAACCUAAGUUAUUAAUCGGAGUUUUAAGCUUUAAUUUAUAAAAAAUACAUCCUAUUCUUCAAAAUUGCAGUUUAUCGUACCGUAAGGCGUCGUUCUAACAUUCGCCUAAUCUGCAAACGGGCAUGGUCCCUUUUGUCAGCGUUGAAGUGGGCGUUAGGUAAUCUCUGUAUAACAUUGAAAUUUGUAACUACUUUCCAAAAAUACUAGCUAUCUUAUCUAAUGUUGAGAGGCGAACAUAUUCAGAAUGAUUUUACAUCCUAGAAAUAACACUUCUUUAGUUUCCAAUUUUGCUACCAUUUGCAUAAGUCUUAAUUUUAAAUCUCUAUAUAAACUUUGACUCA ...........(((((((......(((..(((((((.....(((((((..............))))))).....(((((.....))))).)))))))........................((((((...........((.(((((..((....))...))))).))))))))...))).((((..(..(((..(((...((((((....(((((.((((((((.((((((........))).....................(((.(((((........)))))))).....))).))))..))))......)))))......))))))....)))..)))....)..))))...)).))))).................................. (-58.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUCAAAGUUUAUAUAGAGAUUUAAAAUUAAGACUUAUGCAAAUGGUAGCAAAAUUGGAAACUAAAGAAGUGUUAUUUCUAGGAUGUAAAAUCAUUCUGAAUAUGUUCGCCUCUCAACAUUAGAUAAGAUAGCUAGUAUUUUUGGAAAGUAGUUACAAAUUUCAAUGUUAUACAGAGAUUACCUAACGCCCACUUCAACGCUGACAAAAGGGACCAUGCCCGUUUGCAGAUUAGGCGAAUGUUAGAACGACGCCUUACGGUACGAUAAACUGCAAUUUUGAAGAAUAGGAUGUAUUUUUUAUAAAUUAAAGCUUAAAACUCCGAUUAAUAACUUAGGUUAUGUGAGUAAAGUUAUGUUUUAUUUAUAGUGGCUAUUUGGCUAAGUGAGGAAAUACG ((((((..(((((.((........)))))))..)))))).((....(((((((.....(....)........)))))))..(((((((......))))))).........)).(((((...((((...(((((((((.(((((((.((((((((((...((((((..((.....)))))))).......(((..........(((.((((.(((......))).)))))))...(((((..(((....))).)))))...)))......))))))..)))).)))))))............(((((((.(((((.(((.((((......(((((....)))))..))))....))).)))))))))))).)))))))))..)))).)))))....... (-79.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 50 1 141 92 NC_002967:TDE1773|5end_hypothetical_protein_1817101..1817331_NEGATIVE 600 179 132 150 102 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 543 208 161 178 132 NC_002967:TDE1825|5end_hypothetical_protein_1858344..1858574_NEGATIVE 541 180 134 153 102 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 521 208 161 188 141 NC_002967:TDE0262|5end_hypothetical_protein_296300..296530_NEGATIVE 517 150 101 226 176 NC_002967:TDE1842|5end_hypothetical_protein_1872005..1872235_NEGATIVE 517 179 137 149 106 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 517 208 161 176 128 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 517 150 101 226 176 NC_002967:TDE1802|5end_hypothetical_protein_1838108..1838338_NEGATIVE 517 179 134 207 161 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 485 177 132 170 120 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 480 179 133 231 183 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 467 200 151 179 130 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 466 179 132 172 120 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 465 179 134 201 151 NC_002967:TDE1813|5end_hypothetical_protein_1848249..1848479_NEGATIVE 453 179 133 147 103 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 453 179 134 168 123 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 449 208 161 167 118 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 442 215 173 175 133 NC_002967:TDE0276|5end_HD_domain_protein_308029..308259_NEGATIVE 440 179 137 224 179 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 638 170 122 51 3 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 600 179 132 51 3 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 522 179 131 52 4 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 521 208 161 88 41 NC_002967:TDE0263|3end_spermidine_N1-acetyltransferase,_putative_296400..296550_NEGATIVE 517 179 137 52 9 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 511 179 133 47 1 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 507 179 137 43 1 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 497 180 133 70 21 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 493 180 131 56 2 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 468 179 137 44 1 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 467 200 151 66 17 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 449 208 161 74 25 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 442 215 173 95 53 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 437 179 137 44 2 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 435 223 191 103 71 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 433 216 191 96 71 NC_002967:TDE1794|3end_hypothetical_protein_1831015..1831165_NEGATIVE 426 208 161 74 28 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 426 208 161 77 31 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 426 208 161 105 59 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 426 208 161 48 2 NC_002967:TDE1814|3end_hypothetical_protein_1848429..1848579_NEGATIVE