Origin IGS: aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat .........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 ataattcaatgcgtctaacacccgcttcaacctgacattgcggacgagccgcaaatgcaggttaagcgaatgttagaccgatgccttcggcacgataaactgtaattttgaaaaataaggtttataattttaatgaatatataatgtataaacatacttacgtttatagattgcgttaacaaccattatttttaagaataaggaaatatttttaaaggagtattgtatt Mask Tandem Repeat Region ================================================ aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Find is-nt database================================================ Query_seq: TDE1786:TDE1787|TDE1786:TDE1787:hypothetical protein:hypothetical protein:<-<-:1826239..1826467 229 aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1786:TDE1787|TDE1786:TDE1787:hypothetical protein:hypothetical protein:<-<-:1826239..1826467 229 aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1786:TDE1787|TDE1786:TDE1787:hypothetical protein:hypothetical protein:<-<-:1826239..1826467 229 aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 2 End: 97 . M Q Y S F K N I S L F L K I M V V N A I Y K R K Y V Y T L Y I H .................................................................................................................................... Protein_Len: 51 Strand: + Start: 48 End: 200 ............................................... M L T Q S I N V S M F I H Y I F I K I I N L I F Q N Y S L S C R R H R S N I R L T C I C G S S A M S G ............................. aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat 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: 82 Start: 102 End: 131 .....................................................................................................ACTGTAATTTTGAAAAATAAGGTTTATAAT.................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -8.9 Tail_Score: -3.03159 Start: 160 End: 209 Full_Region: GGCATCGGTCTAACA TTCGCTTAACCTGCATTTGCGG CTCGT CCGCAATGTCAGGTTGAAGCGGG TGTTAGACGCATTGA ...............................................................................................................................................................TTCGCTTAACCTGCATTTGCGGCTCGTCCGCAATGTCAGGTTGAAGCGGG.................... Find igs database================================================ Query_seq: TDE1786:TDE1787|TDE1786:TDE1787:hypothetical protein:hypothetical protein:<-<-:1826239..1826467 229 aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Intra-Species Hit: Count: 5 Min: 1 Max: 229 Len: 229 Subject: NC_002967_TDE1786_TDE1787|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1826239,1826467]|229 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat aatacaatactcctttaaaaatatttccttattcttaaaaataatggttgttaacgcaatctataaacgtaagtatgtttatacattatatattcattaaaattataaaccttatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacgcattgaattat Subject: NC_002967_TDE1830_TDE1831|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1863846,1864504]|659 HSP 1 e-value: 2.0E-46 bit: 186.0 Len: 106 Query Start:113 Query End:218 Subject Strand: POSITIVE Subject Start: 532 Subject End: 636 ................................................................................................................tatttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacg........... ................................................................................................................tatttttcaaagttacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgc-tttgcggctcgtccgcaatgtcaggttgaagcgggtgttagacg........... Subject: NC_002967_TDE1809_TDE1810|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1845404,1846013]|610 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 101 Query Start:115 Query End:215 Subject Strand: POSITIVE Subject Start: 500 Subject End: 600 ..................................................................................................................tttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttag.............. ..................................................................................................................tttttcaaagttacagtttatcgtgccgaaggcatcggtctaacattcgcttgacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtgttag.............. Subject: NC_002967_TDE1788_TDE1789|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1827006,1827427]|422 HSP 1 e-value: 4.0E-29 bit: 129.0 Len: 101 Query Start:115 Query End:215 Subject Strand: POSITIVE Subject Start: 317 Subject End: 417 ..................................................................................................................tttttcaaaattacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttag.............. ..................................................................................................................tttttcaaagttacagttcatcgtgccgaaggcgtgcgcttaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgagtgttag.............. Subject: NC_002967_TDE1784_TDE1785|transcriptional activator, AraC family:hypothetical protein|NEGATIVE:POSITIVE|[1824514,1825131]|618 HSP 1 e-value: 4.0E-29 bit: 129.0 Len: 104 Query Start:114 Query End:217 Subject Strand: POSITIVE Subject Start: 377 Subject End: 481 .................................................................................................................atttttcaaaattacagtttatcgtgccg-aaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtgttagac............ .................................................................................................................atttttcaaagttacagtttatcgtgccgtaaggcatctgtctaactaccgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgaatgttagac............ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACAAUACUCCUUUAAAAAUAUUUCCUUAUUCUUAAAAAUAAUGGUUGUUAACGCAAUCUAUAAACGUAAGUAUGUUUAUACAUUAUAUAUUCAUUAAAAUUAUAAACCUUAUUUUUCAAAAUUACAGUUUAUCGUGCCGAAGGCAUCGGUCUAACAUUCGCUUAACCUGCAUUUGCGGCUCGUCCGCAAUGUCAGGUUGAAGCGGGUGUUAGACGCAUUGAAUUAU .............(((((.((((......)))).)))))..(((((..(((......(((.(((((((((....))))))))).)))..)))..)))))..................(((((..............(((((...)))))..(((((((((((((((((((((((((.((((.....)))))))).))))))).))))))))))))))...))))).... (-59.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUUCAAUGCGUCUAACACCCGCUUCAACCUGACAUUGCGGACGAGCCGCAAAUGCAGGUUAAGCGAAUGUUAGACCGAUGCCUUCGGCACGAUAAACUGUAAUUUUGAAAAAUAAGGUUUAUAAUUUUAAUGAAUAUAUAAUGUAUAAACAUACUUACGUUUAUAGAUUGCGUUAACAACCAUUAUUUUUAAGAAUAAGGAAAUAUUUUUAAAGGAGUAUUGUAUU ...(((((..(.((((((((..(((((.((((((.((((((((.....)))).)))))))))))))))..)))))))))..((((...))))..(((((((...((((....))))..)))))))........)))))...((((.(((((((........))))))).)))).....((((..(((.((((((((((((......))))))))))))))).))))... (-61.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1064 210 161 178 129 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 1064 210 161 177 128 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 1064 210 161 186 137 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 1017 210 161 182 131 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 1008 210 161 199 151 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 988 210 161 215 166 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 988 210 161 180 131 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 988 210 161 215 166 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 987 210 161 229 180 NC_002967:TDE1790|5end_hypothetical_protein_1828007..1828237_NEGATIVE 973 210 161 198 148 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 946 210 161 196 146 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 941 210 161 168 117 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 939 210 161 200 151 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 936 218 171 183 136 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 907 210 161 229 180 NC_002967:TDE1813|5end_hypothetical_protein_1848249..1848479_NEGATIVE 907 210 161 185 136 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 869 210 161 175 125 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 833 210 161 177 124 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 826 200 153 225 178 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 789 189 141 231 180 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 1064 210 161 79 30 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 1064 210 161 80 31 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 1064 210 161 89 40 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 1064 210 161 75 26 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 1045 210 161 84 35 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 1017 210 161 78 27 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 1015 210 161 80 31 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 1013 210 161 106 57 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 1008 210 161 59 11 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 1008 210 161 59 11 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 989 210 161 78 27 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 988 210 161 89 40 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 988 210 161 75 26 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 973 210 161 75 25 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 961 210 161 89 40 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 958 210 161 80 31 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 956 210 161 84 34 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 941 210 161 75 24 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 939 210 161 79 30 NC_002967:TDE1836|3end_hypothetical_protein_1868514..1868664_NEGATIVE 939 210 161 75 26 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE