Origin IGS: attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat .........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 ataaaattgcctaacacccgcttcaacctgacattgcctttgcggcaatgcaggttaagcggaagttagacggatgccttcggcacgatgaactgtaactttgaaaaacaggatatggtctttgtaaactaaagcttaaaactcaaattaattgcttatttttactaaaaatgccgtattttattgtaataacagcttgataattatacgcataatgcgtataat Mask Tandem Repeat Region ================================================ attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Find is-nt database================================================ Query_seq: TDE1838:TDE1839|TDE1838:TDE1839:hypothetical protein:hypothetical protein:<-<-:1870256..1870480 225 attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1838:TDE1839|TDE1838:TDE1839:hypothetical protein:hypothetical protein:<-<-:1870256..1870480 225 attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1838:TDE1839|TDE1838:TDE1839:hypothetical protein:hypothetical protein:<-<-:1870256..1870480 225 attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Predict ORF larger than 30AA ================================================ attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat 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: 91 Start: 1 End: 30 CTTGATAATTATACGCATAATGCGTATAAT................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.2 Tail_Score: -3.06009 Start: 163 End: 209 Full_Region: GGCATCCGTCTAACT TCCGCTTAACCTGCATTGCC GCAAA GGCAATGTCAGGTTGAAGCGGG TGTTAGGCAATTTTA ..................................................................................................................................................................TCCGCTTAACCTGCATTGCCGCAAAGGCAATGTCAGGTTGAAGCGGG................ Find igs database================================================ Query_seq: TDE1838:TDE1839|TDE1838:TDE1839:hypothetical protein:hypothetical protein:<-<-:1870256..1870480 225 attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Intra-Species Hit: Count: 3 Min: 1 Max: 225 Len: 225 Subject: NC_002967_TDE1838_TDE1839|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1870256,1870480]|225 HSP 1 e-value: 1.0E-124 bit: 446.0 Len: 225 Query Start:1 Query End:225 Subject Strand: POSITIVE Subject Start: 1 Subject End: 225 attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat attatacgcattatgcgtataattatcaagctgttattacaataaaatacggcatttttagtaaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgccgcaaaggcaatgtcaggttgaagcgggtgttaggcaattttat Subject: NC_002967_TDE1830_TDE1831|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1863846,1864504]|659 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 149 Query Start:67 Query End:215 Subject Strand: POSITIVE Subject Start: 483 Subject End: 633 ..................................................................ataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccgaaggcatccgtctaacttccgcttaacctgcattgc--cgcaaaggcaatgtcaggttgaagcgggtgttag.......... ..................................................................ataagctattaattttggttttatgctttaatttataaaaaatacaccctatttttcaaagttacagtttatcgtgccgaaggcatcggtctaacattcgcttaacctgctttgcggctcgtccgcaatgtcaggttgaagcgggtgttag.......... Subject: NC_002967_TDE1784_TDE1785|transcriptional activator, AraC family:hypothetical protein|NEGATIVE:POSITIVE|[1824514,1825131]|618 HSP 1 e-value: 1.0E-17 bit: 91.7 Len: 117 Query Start:63 Query End:179 Subject Strand: POSITIVE Subject Start: 324 Subject End: 440 ..............................................................aaaaataagcaattaatttgagttttaagctttagtttacaaagaccatatcctgtttttcaaagttacagttcatcgtgccg-aaggcatccgtctaacttccgcttaacctgcatt.............................................. ..............................................................aaaactaagctattaatttgtgttttaagctttaatttataaaaat-ataccacatttttcaaagttacagtttatcgtgccgtaaggcatctgtctaactaccgcttaacctgcatt.............................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUACGCAUUAUGCGUAUAAUUAUCAAGCUGUUAUUACAAUAAAAUACGGCAUUUUUAGUAAAAAUAAGCAAUUAAUUUGAGUUUUAAGCUUUAGUUUACAAAGACCAUAUCCUGUUUUUCAAAGUUACAGUUCAUCGUGCCGAAGGCAUCCGUCUAACUUCCGCUUAACCUGCAUUGCCGCAAAGGCAAUGUCAGGUUGAAGCGGGUGUUAGGCAAUUUUAU (((((((((.....)))))))))......(((((....)).........((((((.....(((((...((((..((((........))))))))...)))))............((((...........))))......))))))..)))....(((((((.((((((((((((((((((((.....))))))).))))))).)))))).)))))))........ (-71.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAUUGCCUAACACCCGCUUCAACCUGACAUUGCCUUUGCGGCAAUGCAGGUUAAGCGGAAGUUAGACGGAUGCCUUCGGCACGAUGAACUGUAACUUUGAAAAACAGGAUAUGGUCUUUGUAAACUAAAGCUUAAAACUCAAAUUAAUUGCUUAUUUUUACUAAAAAUGCCGUAUUUUAUUGUAAUAACAGCUUGAUAAUUAUACGCAUAAUGCGUAUAAU ......(((.(((((..((((((.((((((.(((((((.....)))))))))))))))))))..))))).))).((((...))))..((.((((((....(((...((.((((((((((.((((((((...((((..................))))...)))))...))).)))))))))).)).)))..)))).)).)).(((((((((.....))))))))) (-64.77) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 997 210 163 172 125 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 789 140 91 231 182 NC_002967:TDE1838|5end_hypothetical_protein_1870165..1870395_NEGATIVE 764 160 111 230 180 NC_002967:TDE1842|5end_hypothetical_protein_1872005..1872235_NEGATIVE 764 160 111 230 180 NC_002967:TDE1802|5end_hypothetical_protein_1838108..1838338_NEGATIVE 735 218 171 194 144 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 734 210 163 196 146 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 721 210 161 182 130 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 721 210 161 168 116 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 718 217 171 222 173 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 705 210 161 175 123 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 699 210 161 177 123 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 686 217 171 185 136 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 686 217 171 207 158 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 685 210 165 215 167 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 685 210 163 198 148 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 685 210 165 180 132 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 685 210 165 177 129 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 668 217 171 206 158 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 664 218 171 193 143 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 646 210 165 229 181 NC_002967:TDE1813|5end_hypothetical_protein_1848249..1848479_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 948 210 165 89 44 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 757 179 131 55 6 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 742 210 161 84 32 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 735 218 171 83 33 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 721 210 161 78 26 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 721 210 161 75 23 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 707 220 171 101 47 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 693 210 161 78 26 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 692 210 163 73 23 NC_002967:TDE0097|3end_hypothetical_protein_114801..114951_POSITIVE 686 217 171 79 30 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 686 217 171 86 37 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 686 217 171 79 30 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 686 217 171 78 29 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 685 210 165 75 27 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 685 210 163 75 25 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 685 210 165 80 32 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 684 216 171 81 33 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 681 210 165 106 58 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 668 217 171 66 18 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 668 217 171 66 18 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE