Origin IGS: tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg .........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 cacccgcttcaacctgacattgcggacaagccgcaaatgcaggttaagcgaatgttagacggatgccttacggcacgataaactgtaactttgaaaaataggatatatttttataaattaaagtttaaagccccaattaatgggttaggttactctgagcaagagtgtcttttattataatggctatttgaga Mask Tandem Repeat Region ================================================ tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Find is-nt database================================================ Query_seq: TDE1842:TDE1843|TDE1842:TDE1843:hypothetical protein:hypothetical protein:<-<-:1872096..1872288 193 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1842:TDE1843|TDE1842:TDE1843:hypothetical protein:hypothetical protein:<-<-:1872096..1872288 193 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1842:TDE1843|TDE1842:TDE1843:hypothetical protein:hypothetical protein:<-<-:1872096..1872288 193 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 90 End: 182 ......................................................................................... M L F F K V T V Y R A V R H P S N I R L T C I C G L S A M S G ........... tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg 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: 84 Start: 75 End: 104 ..........................................................................TTTGAAAAATAGGATATATTTTTATAAATT......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1842:TDE1843|TDE1842:TDE1843:hypothetical protein:hypothetical protein:<-<-:1872096..1872288 193 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Intra-Species Hit: Count: 7 Min: 1 Max: 193 Len: 193 Subject: NC_002967_TDE1842_TDE1843|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1872096,1872288]|193 HSP 1 e-value: 1.0E-105 bit: 383.0 Len: 193 Query Start:1 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 193 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Subject: NC_002967_TDE1802_TDE1803|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1838199,1838484]|286 HSP 1 e-value: 1.0E-78 bit: 293.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttg................................. tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttg................................. Subject: NC_002967_TDE1784_TDE1785|transcriptional activator, AraC family:hypothetical protein|NEGATIVE:POSITIVE|[1824514,1825131]|618 HSP 1 e-value: 7.0E-46 bit: 184.0 Len: 125 Query Start:65 Query End:189 Subject Strand: POSITIVE Subject Start: 347 Subject End: 471 ................................................................tttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcg.... ................................................................tttaagctttaatttataaaaatataccacatttttcaaagttacagtttatcgtgccgtaaggcatctgtctaactaccgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcg.... 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: 140 Query Start:54 Query End:193 Subject Strand: POSITIVE Subject Start: 457 Subject End: 596 .....................................................ttaattggggctttaaactttaatttataaaaatatatcctattttt-caaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg .....................................................ttaatttgggctttacgctttaatttacaaaaacacaccctattttttcaaagttacagtttatcgtgccg-aaggcatcggtctaacattcgcttgacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg Subject: NC_002967_TDE1830_TDE1831|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1863846,1864504]|659 HSP 1 e-value: 2.0E-40 bit: 167.0 Len: 123 Query Start:71 Query End:193 Subject Strand: POSITIVE Subject Start: 508 Subject End: 629 ......................................................................ctttaatttataaaaa-tatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg ......................................................................ctttaatttataaaaaatacaccctatttttcaaagttacagtttatcgtgccg-aaggcatcggtctaacattcgcttaacctgc-tttgcggctcgtccgcaatgtcaggttgaagcgggtg Subject: NC_002967_TDE1786_TDE1787|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1826239,1826467]|229 HSP 1 e-value: 4.0E-38 bit: 159.0 Len: 100 Query Start:94 Query End:193 Subject Strand: POSITIVE Subject Start: 113 Subject End: 211 .............................................................................................tatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcgggtg .............................................................................................tatttttcaaaattacagtttatcgtgccg-aaggcatcggtctaacattcgcttaacctgcatttgcggctcgtccgcaatgtcaggttgaagcgggtg Subject: NC_002967_TDE1788_TDE1789|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1827006,1827427]|422 HSP 1 e-value: 2.0E-31 bit: 137.0 Len: 136 Query Start:54 Query End:189 Subject Strand: POSITIVE Subject Start: 274 Subject End: 409 .....................................................ttaattggggctttaaactttaatttataaaaatatatcctattttt-caaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcg.... .....................................................ttaatttgggttttatgctttaatttacaaaaacacaccctattttttcaaagttacagttcatcgtgccg-aaggcgtgcgcttaacattcgcttaacctgcatttgcggcttgtccgcaatgtcaggttgaagcg.... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCAAAUAGCCAUUAUAAUAAAAGACACUCUUGCUCAGAGUAACCUAACCCAUUAAUUGGGGCUUUAAACUUUAAUUUAUAAAAAUAUAUCCUAUUUUUCAAAGUUACAGUUUAUCGUGCCGUAAGGCAUCCGUCUAACAUUCGCUUAACCUGCAUUUGCGGCUUGUCCGCAAUGUCAGGUUGAAGCGGGUG .......................(((((((((.....))))).......((((.....))))....((((((.((((((..(((((((.....)))))))..)))))).))))))..(((((....)))))..))))..(((((((((((((((((((.((((.....)))))))).))))))).)))))))) (-58.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACCCGCUUCAACCUGACAUUGCGGACAAGCCGCAAAUGCAGGUUAAGCGAAUGUUAGACGGAUGCCUUACGGCACGAUAAACUGUAACUUUGAAAAAUAGGAUAUAUUUUUAUAAAUUAAAGUUUAAAGCCCCAAUUAAUGGGUUAGGUUACUCUGAGCAAGAGUGUCUUUUAUUAUAAUGGCUAUUUGAGA ....(((((.((((((.((((((((.....)))).))))))))))))))).........((((((((....(((....((((((.(((.(((((((((((.....))))))).))))))).))))))..))).......((((...(((.((((((.....)))))).)))...))))...))).)))))... (-52.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1013 190 141 176 127 NC_002967:TDE1836|5end_hypothetical_protein_1869443..1869673_NEGATIVE 1013 190 141 213 164 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 1013 190 141 178 129 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 1013 190 141 175 126 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 1013 190 141 213 164 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 1013 190 141 184 135 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 1010 190 141 194 145 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 967 190 141 180 129 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 967 190 141 166 115 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 964 190 141 198 149 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 961 190 141 173 124 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 961 190 141 196 147 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 957 190 141 197 149 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 936 190 141 227 178 NC_002967:TDE1790|5end_hypothetical_protein_1828007..1828237_NEGATIVE 932 190 141 227 178 NC_002967:TDE1813|5end_hypothetical_protein_1848249..1848479_NEGATIVE 932 190 141 183 134 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 920 190 142 173 125 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 894 188 141 231 184 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 868 140 91 231 182 NC_002967:TDE1842|5end_hypothetical_protein_1872005..1872235_NEGATIVE 868 140 91 231 182 NC_002967:TDE1802|5end_hypothetical_protein_1838108..1838338_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1013 190 141 77 28 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 1013 190 141 73 24 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 1013 190 141 78 29 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 1013 190 141 69 20 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 1013 190 141 87 38 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE 1013 190 141 73 24 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 994 190 141 82 33 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 991 190 141 71 22 NC_002967:TDE0097|3end_hypothetical_protein_114801..114951_POSITIVE 986 190 141 87 38 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 980 189 141 77 29 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 967 190 141 76 25 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 967 190 141 73 22 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 964 190 141 77 28 NC_002967:TDE1836|3end_hypothetical_protein_1868514..1868664_NEGATIVE 964 190 141 73 24 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 964 190 141 78 29 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 962 190 141 104 55 NC_002967:TDE1815|3end_hypothetical_protein_1849458..1849608_NEGATIVE 961 190 141 70 21 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 961 190 141 73 24 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 961 190 141 70 21 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 957 190 141 57 9 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE