Origin IGS: gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cattgcggacgagccgcaactgcaggttaagcgaatgttagacatatggataacgaaaaaaatatagtgtaaaactaattagatattttctatagtagatgtaaatgtctagtatagtaatgaaaataaatgtgaaggtaaaac Mask Tandem Repeat Region ================================================ gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Find is-nt database================================================ Query_seq: TDE1814:TDE1815|TDE1814:TDE1815:hypothetical protein:hypothetical protein:<-<-:1849404..1849547 144 gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1814:TDE1815|TDE1814:TDE1815:hypothetical protein:hypothetical protein:<-<-:1849404..1849547 144 gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1814:TDE1815|TDE1814:TDE1815:hypothetical protein:hypothetical protein:<-<-:1849404..1849547 144 gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Predict ORF larger than 30AA ================================================ gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg 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: 81 Start: 2 End: 31 .TTTTACCTTCACATTTATTTTCATTACTAT................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 39 HP_score: -2.0 Tail_Score: -2.80537 Start: 53 End: 65 Full_Region: CATTTACATCTACTA TAGA AAATA TCTA ATTAGTTTTACACTA ....................................................TAGAAAATATCTA............................................................................... Find igs database================================================ Query_seq: TDE1814:TDE1815|TDE1814:TDE1815:hypothetical protein:hypothetical protein:<-<-:1849404..1849547 144 gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Intra-Species Hit: Count: 2 Min: 1 Max: 144 Len: 144 Subject: NC_002967_TDE1814_TDE1815|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1849404,1849547]|144 HSP 1 e-value: 7.0E-64 bit: 244.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatannnnnnncgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg Subject: NC_002967_TDE1792_TDE1793|hypothetical protein:hydrolase, carbon-nitrogen family|NEGATIVE:NEGATIVE|[1829886,1830046]|161 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatannnnnnncgttatccatatgtctaacattcgcttaacctgcagttgcggctcgtccgcaatg gttttaccttcacatttattttcattactatactagacatttacatctactatagaaaatatctaattagttttacactatatttttttcgttatccatatgtctaacattcgcttaacctacacttgcggcttgtccgcaatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUACCUUCACAUUUAUUUUCAUUACUAUACUAGACAUUUACAUCUACUAUAGAAAAUAUCUAAUUAGUUUUACACUAUAUUUUUUUCGUUAUCCAUAUGUCUAACAUUCGCUUAACCUGCAGUUGCGGCUCGUCCGCAAUG .................................(((((((........((...((((((((......((((.....))))))))))))..)).......)))))))......((.......)).(((((((.....))))))). (-19.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUGCGGACGAGCCGCAACUGCAGGUUAAGCGAAUGUUAGACAUAUGGAUAACGAAAAAAAUAUAGUGUAAAACUAAUUAGAUAUUUUCUAUAGUAGAUGUAAAUGUCUAGUAUAGUAAUGAAAAUAAAUGUGAAGGUAAAAC ..((((((.....))))))((.((.(((.......(((((..(....)..))))).........((((.....))))......((((..(((((.(((((......))))).))))).))))......))).)).))....... (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 989 140 91 231 182 NC_002967:TDE1814|5end_hypothetical_protein_1849313..1849543_NEGATIVE 811 140 91 231 182 NC_002967:TDE1792|5end_hypothetical_protein_1829795..1830025_NEGATIVE 743 140 96 166 122 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 708 140 95 179 139 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 701 140 97 157 114 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 700 140 103 158 121 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 684 140 94 195 153 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 684 140 94 195 153 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 664 140 101 176 137 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 664 140 96 178 138 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 633 140 95 209 168 NC_002967:TDE1790|5end_hypothetical_protein_1828007..1828237_NEGATIVE 607 140 95 180 139 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 598 140 101 162 119 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 579 140 105 160 125 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 572 140 103 215 178 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 568 139 91 231 181 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 568 140 95 148 107 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 563 139 95 154 114 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 553 138 103 165 130 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 534 140 95 209 168 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 811 140 91 69 20 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 743 140 96 55 11 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 735 140 97 51 8 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 726 140 102 69 31 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 702 140 102 39 2 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 701 140 97 60 17 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 700 140 103 59 22 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 684 140 94 55 13 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 664 140 96 55 15 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 664 140 97 64 25 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 663 140 91 69 24 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 659 140 97 39 1 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 637 140 101 60 17 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 610 140 97 55 12 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 601 140 102 59 21 NC_002967:TDE1836|3end_hypothetical_protein_1868514..1868664_NEGATIVE 598 140 101 58 15 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 579 140 105 60 25 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 576 140 105 53 18 NC_002967:TDE0097|3end_hypothetical_protein_114801..114951_POSITIVE 572 140 103 52 15 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 568 140 95 55 14 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE