Origin IGS: tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt .........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 aagaatattttatacatttataaagttttatgcaagaccgatgaaaaatgtacatccgtgtacatttttcatcttagagttttgctaaagcaaaactctcgaagtatggaaccaccgccttccatggcggttgggggtgtacatccttgtatatttttcatcttcaagttttagcctgctgca Mask Tandem Repeat Region ================================================ tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Find is-nt database================================================ Query_seq: TDE1094:TDE1095|TDE1094:TDE1095:hypothetical protein:alanine racemase:->->:1129783..1129965 183 tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1094:TDE1095|TDE1094:TDE1095:hypothetical protein:alanine racemase:->->:1129783..1129965 183 tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1094:TDE1095|TDE1094:TDE1095:hypothetical protein:alanine racemase:->->:1129783..1129965 183 tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 17 End: 112 ................ M K M K N I Q G C T P P T A M E G G G S I L R E F C F S K T L R ....................................................................... Protein_Len: 55 Strand: - Start: 13 End: 177 ............ F K F I F F I C P H V G G V A M S P P P E M S R S N Q K L L V R L H F I Y V S T C K E D T K C L V K Y I Y L M ...... tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt 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: 148 End: 177 ...................................................................................................................................................CTTGCATAAAACTTTATAAATGTATAAAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -10.1 Tail_Score: -3.09175 Start: 109 End: 146 Full_Region: CTTTAGCAAAACTCT AAGATGAAAAATGTACA CGGA TGTACATTTTTCATCGG TCTTGCATAAAACTT ............................................................................................................AAGATGAAAAATGTACACGGATGTACATTTTTCATCGG..................................... TransTerm Strand: - Conf: 93 HP_score: -13.9 Tail_Score: -3.15768 Start: 113 End: 142 Full_Region: tttatgcaagaccga tgaaaaatgtaca tccg tgtacatttttca tcttagagttttgct ................................................................................................................tgaaaaatgtacatccgtgtacatttttca......................................... TransTerm Strand: - Conf: 82 HP_score: -6.2 Tail_Score: -4.87626 Start: 120 End: 135 Full_Region: aagaccgatgaaaaa tgtaca tccg tgtaca tttttcatcttagag .......................................................................................................................tgtacatccgtgtaca................................................ Find igs database================================================ Query_seq: TDE1094:TDE1095|TDE1094:TDE1095:hypothetical protein:alanine racemase:->->:1129783..1129965 183 tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: NC_002967_TDE1094_TDE1095|hypothetical protein:alanine racemase|POSITIVE:POSITIVE|[1129783,1129965]|183 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt tgcagcaggctaaaacttgaagatgaaaaatatacaaggatgtacacccccaaccgccatggaaggcggtggttccatacttcgagagttttgctttagcaaaactctaagatgaaaaatgtacacggatgtacatttttcatcggtcttgcataaaactttataaatgtataaaatattctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGCAGGCUAAAACUUGAAGAUGAAAAAUAUACAAGGAUGUACACCCCCAACCGCCAUGGAAGGCGGUGGUUCCAUACUUCGAGAGUUUUGCUUUAGCAAAACUCUAAGAUGAAAAAUGUACACGGAUGUACAUUUUUCAUCGGUCUUGCAUAAAACUUUAUAAAUGUAUAAAAUAUUCUU ((((..((((........(((((((.......((((....)))).....(((.(((((......))))))))...))).)))).((((((((((....))))))))))..(((((((((((((((....))))))))))))))).))))))))......((((((....))))))........ (-58.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUAUUUUAUACAUUUAUAAAGUUUUAUGCAAGACCGAUGAAAAAUGUACAUCCGUGUACAUUUUUCAUCUUAGAGUUUUGCUAAAGCAAAACUCUCGAAGUAUGGAACCACCGCCUUCCAUGGCGGUUGGGGGUGUACAUCCUUGUAUAUUUUUCAUCUUCAAGUUUUAGCCUGCUGCA ...((.((((((((....)))))))).))..(((((((.(((((((((((((((....)))))))))))))))..((((((((((....)))))))))).((((.((((((((((((((......))))).)))..(((((((....))))))).))))))))))..))))).))........ (-64.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 790 90 41 128 78 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 662 93 55 160 123 NC_002967:TDE2312|5end_hypothetical_protein_2348451..2348681_POSITIVE 655 108 61 73 28 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 640 90 45 180 133 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 616 77 37 115 74 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 582 150 101 192 142 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 541 150 101 171 119 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 513 147 101 50 3 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 482 100 53 224 179 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 472 96 54 150 107 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 406 130 83 226 184 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 357 100 53 168 124 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 356 144 111 170 136 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 347 152 111 224 173 NC_002967:TDE2339|5end_leucyl-tRNA_synthetase_2374845..2375075_POSITIVE 332 72 39 231 202 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 330 98 52 56 15 NC_002967:TDE2298|5end_galactokinase,_putative_2338267..2338497_NEGATIVE 328 73 45 213 182 NC_002967:TDE0722|5end_lipoprotein,_putative_758519..758749_POSITIVE 324 84 48 62 22 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 324 100 52 69 10 NC_002967:TDE0181|5end_methyl-accepting_chemotaxis_protein_215077..215307_NEGATIVE 323 106 64 143 92 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 676 145 101 88 44 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 662 93 55 66 29 NC_002967:TDE2311|3end_hypothetical_protein_2348437..2348587_POSITIVE 655 108 61 91 46 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 520 139 91 151 101 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 482 76 36 69 13 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 472 149 101 92 43 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 456 147 104 91 48 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 387 100 54 122 70 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 381 100 52 90 38 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 381 140 91 82 31 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 381 69 37 47 13 NC_002967:TDE0562|3end_hypothetical_protein_595581..595731_POSITIVE 351 88 53 48 16 NC_002967:TDE2483|3end_hypothetical_protein_2505880..2506030_NEGATIVE 328 72 33 52 4 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 318 72 34 70 29 NC_002967:TDE0203|3end_hypothetical_protein_237058..237208_POSITIVE 305 90 43 139 85 NC_002967:TDE1907|3end_holo-(acyl-carrier-protein)_synthase_1924726..1924876_NEGATIVE 303 86 46 124 86 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 296 94 53 132 89 NC_002967:TDE2507|3end_hypothetical_protein_2531643..2531793_NEGATIVE 294 81 54 55 25 NC_002967:TDE2770|3end_flagellar_hook-length_control_protein_FliK_2823044..2823194_NEGATIVE 293 99 52 102 47 NC_002967:TDE1998|3end_phosphohexose_mutase_family_protein_2017143..2017293_POSITIVE 288 127 81 130 75 NC_002967:TDE1972|3end_hypothetical_protein_1987102..1987252_NEGATIVE