Origin IGS: tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg .........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 cacccgcttcaacgctgacatttgttttgtcacgaaagttgcttgagcggtcgctgctagcgcagctcccttttttatgcaactttcgtgccaactttgctgccgctatgtgcgtcagcaaaggcacaaatgcaggttaagcggcagttagacggatgccttacggcacgataaactgtaactttgaaaaataggatatatttttataaattaaagtttaaagccccaattaatgggttaggttactctgagcaagagtgtcttttattataatggctatttgaga Mask Tandem Repeat Region ================================================ tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Find is-nt database================================================ Query_seq: TDE1802:TDE1803|TDE1802:TDE1803:hypothetical protein:hypothetical protein:<-<-:1838199..1838484 286 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1802:TDE1803|TDE1802:TDE1803:hypothetical protein:hypothetical protein:<-<-:1838199..1838484 286 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1802:TDE1803|TDE1802:TDE1803:hypothetical protein:hypothetical protein:<-<-:1838199..1838484 286 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 90 End: 209 ......................................................................................... M L F F K V T V Y R A V R H P S N C R L T C I C A F A D A H S G S K V G T K V A ............................................................................. Protein_Len: 42 Strand: + Start: 160 End: 285 ............................................................................................................................................................... M P L L T H I A A A K L A R K L H K K G S C A S S D R S S N F R D K T N V S V E A G . Protein_Len: 41 Strand: - Start: 150 End: 272 ..................................................................................................................................................... G A N T G K S V C M A A A F N A R F N C L F P L Q A L L S R E L L K R S L V F T M .............. tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg 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================================================ PromScan Matrix: RpoN Strand: + Score: 95 Start: 193 End: 209 ................................................................................................................................................................................................TTGGCACGAAAGTTGCA............................................................................. PromScan Matrix: RpoN Strand: - Score: 86 Start: 244 End: 260 ...................................................................................................................................................................................................................................................TTGTCACGAAAGTTGCT.......................... tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.3 Tail_Score: -3.05384 Start: 155 End: 204 Full_Region: CTGCCGCTTAACCTG CATTTGTGCCTTTGCTGACGC ACATA GCGGCAGCAAAGTTGGCACGAAAG TTGCATAAAAAAGGG ..........................................................................................................................................................CATTTGTGCCTTTGCTGACGCACATAGCGGCAGCAAAGTTGGCACGAAAG.................................................................................. TransTerm Strand: - Conf: 85 HP_score: -5.7 Tail_Score: -5.25803 Start: 217 End: 238 Full_Region: gaaagttgcttgagc ggtcgctgc tagc gcagctccc ttttttatgcaactt ........................................................................................................................................................................................................................ggtcgctgctagcgcagctccc................................................ Find igs database================================================ Query_seq: TDE1802:TDE1803|TDE1802:TDE1803:hypothetical protein:hypothetical protein:<-<-:1838199..1838484 286 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Intra-Species Hit: Count: 4 Min: 1 Max: 286 Len: 286 Subject: NC_002967_TDE1802_TDE1803|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1838199,1838484]|286 HSP 1 e-value: 1.0E-161 bit: 567.0 Len: 286 Query Start:1 Query End:286 Subject Strand: POSITIVE Subject Start: 1 Subject End: 286 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttgtgcctttgctgacgcacatagcggcagcaaagttggcacgaaagttgcataaaaaagggagctgcgctagcagcgaccgctcaagcaactttcgtgacaaaacaaatgtcagcgttgaagcgggtg Subject: NC_002967_TDE1842_TDE1843|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1872096,1872288]|193 HSP 1 e-value: 2.0E-78 bit: 293.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttg.............................................................................................................................. tctcaaatagccattataataaaagacactcttgctcagagtaacctaacccattaattggggctttaaactttaatttataaaaatatatcctatttttcaaagttacagtttatcgtgccgtaaggcatccgtctaacattcgcttaacctgcatttg.............................................................................................................................. Subject: NC_002967_TDE1809_TDE1810|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1845404,1846013]|610 HSP 1 e-value: 2.0E-16 bit: 87.7 Len: 107 Query Start:54 Query End:160 Subject Strand: POSITIVE Subject Start: 457 Subject End: 563 .....................................................ttaattggggctttaaactttaatttataaaaatatatcctatttt-tcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttg.............................................................................................................................. .....................................................ttaatttgggctttacgctttaatttacaaaaacacaccctattttttcaaagttacagtttatcgtgccg-aaggcatcggtctaacattcgcttgacctgcatttg.............................................................................................................................. Subject: NC_002967_TDE1788_TDE1789|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1827006,1827427]|422 HSP 1 e-value: 7.0E-7 bit: 56.0 Len: 107 Query Start:54 Query End:160 Subject Strand: POSITIVE Subject Start: 274 Subject End: 380 .....................................................ttaattggggctttaaactttaatttataaaaatatatcctatttt-tcaaagttacagtttatcgtgccgtaaggcatccgtctaactgccgcttaacctgcatttg.............................................................................................................................. .....................................................ttaatttgggttttatgctttaatttacaaaaacacaccctattttttcaaagttacagttcatcgtgccg-aaggcgtgcgcttaacattcgcttaacctgcatttg.............................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCAAAUAGCCAUUAUAAUAAAAGACACUCUUGCUCAGAGUAACCUAACCCAUUAAUUGGGGCUUUAAACUUUAAUUUAUAAAAAUAUAUCCUAUUUUUCAAAGUUACAGUUUAUCGUGCCGUAAGGCAUCCGUCUAACUGCCGCUUAACCUGCAUUUGUGCCUUUGCUGACGCACAUAGCGGCAGCAAAGUUGGCACGAAAGUUGCAUAAAAAAGGGAGCUGCGCUAGCAGCGACCGCUCAAGCAACUUUCGUGACAAAACAAAUGUCAGCGUUGAAGCGGGUG .......................(((((((((.....))))).......((((.....))))....((((((.((((((..(((((((.....)))))))..)))))).))))))..(((((....)))))..)))).....(((((((((((((((((((..((((((((.(((.....))).))))))))(((.((((((((((((........((..(((((....)))))..))......)))))))))))).))).))))))).))).)))).)))))... (-101.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACCCGCUUCAACGCUGACAUUUGUUUUGUCACGAAAGUUGCUUGAGCGGUCGCUGCUAGCGCAGCUCCCUUUUUUAUGCAACUUUCGUGCCAACUUUGCUGCCGCUAUGUGCGUCAGCAAAGGCACAAAUGCAGGUUAAGCGGCAGUUAGACGGAUGCCUUACGGCACGAUAAACUGUAACUUUGAAAAAUAGGAUAUAUUUUUAUAAAUUAAAGUUUAAAGCCCCAAUUAAUGGGUUAGGUUACUCUGAGCAAGAGUGUCUUUUAUUAUAAUGGCUAUUUGAGA ...((((((.(((.(((.(((((((.(((.((((((((((((..(((.((..(((((....)))))..)).)))....)))))))))))).)))((((((((.(((.....))).))))))))..)))))))))))))))))))(((((...((..((((....))))))...))))).((((((((...((((((.....))))))...))))))))...((((.....((((((...(((.((((((.....)))))).)))))))))....))))........ (-98.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 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 782 270 221 96 45 NC_002967:TDE0587|5end_hypothetical_protein_625749..625979_POSITIVE 750 227 181 60 12 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 750 227 181 217 169 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 636 176 131 149 107 NC_002967:TDE1795|5end_funZ_protein,_putative_1834673..1834903_NEGATIVE 626 200 151 202 153 NC_002967:TDE1769|5end_hypothetical_protein_1814377..1814607_NEGATIVE 613 160 118 145 103 NC_002967:TDE1811|5end_hypothetical_protein_1847483..1847713_NEGATIVE 596 160 116 143 99 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 587 169 121 195 143 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 587 169 121 195 143 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 537 156 119 143 107 NC_002967:TDE1825|5end_hypothetical_protein_1858344..1858574_NEGATIVE 529 169 121 176 126 NC_002967:TDE1823|5end_hypothetical_protein_1856990..1857220_NEGATIVE 522 169 136 159 126 NC_002967:TDE1793|5end_hydrolase,_carbon-nitrogen_family_1830844..1831074_NEGATIVE 517 124 82 231 189 NC_002967:TDE1773|5end_hypothetical_protein_1817101..1817331_NEGATIVE 517 169 121 146 105 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 507 160 111 220 167 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 503 176 136 163 126 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 480 166 121 168 116 NC_002967:TDE0262|5end_hypothetical_protein_296300..296530_NEGATIVE 475 160 118 143 102 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 849 160 111 57 8 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 727 280 231 84 35 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 714 190 141 134 85 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 704 158 114 44 3 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 636 176 131 56 14 NC_002967:TDE1796|3end_hypothetical_protein_1834766..1834916_NEGATIVE 630 160 118 46 5 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 613 160 118 48 6 NC_002967:TDE1812|3end_hypothetical_protein_1847580..1847730_NEGATIVE 611 280 233 73 27 NC_002967:TDE1771|3end_hypothetical_protein_1814579..1814729_NEGATIVE 587 169 121 55 3 NC_002967:TDE1832|3end_hypothetical_protein_1865172..1865322_NEGATIVE 586 169 121 51 1 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 583 160 117 43 1 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 566 160 112 48 1 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 503 176 136 59 22 NC_002967:TDE1828|3end_hypothetical_protein_1860934..1861084_NEGATIVE 480 166 121 68 16 NC_002967:TDE0263|3end_spermidine_N1-acetyltransferase,_putative_296400..296550_NEGATIVE 473 176 132 56 15 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 472 160 116 47 3 NC_002967:TDE1837|3end_hypothetical_protein_1869542..1869692_NEGATIVE 467 169 121 52 2 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 461 169 121 52 1 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE 449 176 132 56 11 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 437 176 134 70 31 NC_002967:TDE1780|3end_hypothetical_protein_1822183..1822333_NEGATIVE