Origin IGS: aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat .........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 atatattgagtataaattatctatgtatcagcgtcaagagagggagtattaaggccggaacaaagagtccgagcaaaatacctgccgcaataccgatgccaagtttgggtaaaagcccgatatttttttcccctttgcacgttctaacaggtttaaaacgatttgtccataagctttaaaagggcttcaaaatttttcatagtagacaaatgagttctcacgctcaattgactaaaatcgcttttttatgtacaataataaattgaggatatt Mask Tandem Repeat Region ================================================ aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Find is-nt database================================================ Query_seq: TDE2696:TDE2697|TDE2696:TDE2697:TPR domain protein:3-oxo-5-alpha-steroid 4-dehydrogenase family protein:<-->:2740127..2740399 273 aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2696:TDE2697|TDE2696:TDE2697:TPR domain protein:3-oxo-5-alpha-steroid 4-dehydrogenase family protein:<-->:2740127..2740399 273 aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2696:TDE2697|TDE2696:TDE2697:TPR domain protein:3-oxo-5-alpha-steroid 4-dehydrogenase family protein:<-->:2740127..2740399 273 aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 112 End: 222 ............................................................................................................... M V L N L L E R A K G K K I S G F Y P N L A S V L R Q V F C S D S L F R P ................................................... Protein_Len: 39 Strand: + Start: 134 End: 250 ..................................................................................................................................... M Q R G K K Y R A F T Q T W H R Y C G R Y F A R T L C S G L N T P S L D A D T ....................... Protein_Len: 34 Strand: + Start: 153 End: 254 ........................................................................................................................................................ M G L L P K L G I G I A A G I L L G L F V P A L I L P L L T L I H R ................... Protein_Len: 43 Strand: - Start: 130 End: 258 ................................................................................................................................. F T C L P F F Y R A K V W V Q C R Y Q P L Y K A R V R Q E P R L V G E R S A S V Y I M ............... Protein_Len: 58 Strand: - Start: 98 End: 271 ................................................................................................. L K H V F R K L G T L V H L P S F F I P S K G L S P M P I A A P I K S P S K T G A K I S G R K V S I C L Y N I S L M .. aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat 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: 87 Start: 18 End: 47 .................ATTGACTAAAATCGCTTTTTTATGTACAAT.................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 236 End: 265 ...........................................................................................................................................................................................................................................CTTGACGCTGATACATAGATAATTTATACT........ 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: 84 Start: 172 End: 188 ...........................................................................................................................................................................TTGGCATCGGTATTGCG..................................................................................... PromScan Matrix: RpoN Strand: + Score: 82 Start: 186 End: 202 .........................................................................................................................................................................................GCGGCAGGTATTTTGCT....................................................................... aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -2.6 Tail_Score: -2.95102 Start: 114 End: 134 Full_Region: tttttcccctttgca cgttctaa caggt ttaaaacg atttgtccataagct .................................................................................................................cgttctaacaggtttaaaacg........................................................................................................................................... Find igs database================================================ Query_seq: TDE2696:TDE2697|TDE2696:TDE2697:TPR domain protein:3-oxo-5-alpha-steroid 4-dehydrogenase family protein:<-->:2740127..2740399 273 aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Intra-Species Hit: Count: 1 Min: 1 Max: 273 Len: 273 Subject: NC_002967_TDE2696_TDE2697|TPR domain protein:3-oxo-5-alpha-steroid 4-dehydrogenase family protein|NEGATIVE:POSITIVE|[2740127,2740399]|273 HSP 1 e-value: 1.0E-140 bit: 500.0 Len: 273 Query Start:1 Query End:273 Subject Strand: POSITIVE Subject Start: 1 Subject End: 273 aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggnnnnnnntatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat aatatcctcaatttattattgtacataaaaaagcgattttagtcaattgagcgtgagaactcatttgtctactatgaaaaattttgaagcccttttaaagcttatggacaaatcgttttaaacctgttagaacgtgcaaaggggaaaaaaatatcgggcttttacccaaacttggcatcggtattgcggcaggtattttgctcggactctttgttccggccttaatactccctctcttgacgctgatacatagataatttatactcaatatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCCUCAAUUUAUUAUUGUACAUAAAAAAGCGAUUUUAGUCAAUUGAGCGUGAGAACUCAUUUGUCUACUAUGAAAAAUUUUGAAGCCCUUUUAAAGCUUAUGGACAAAUCGUUUUAAACCUGUUAGAACGUGCAAAGGGGAAAAAAAUAUCGGGCUUUUACCCAAACUUGGCAUCGGUAUUGCGGCAGGUAUUUUGCUCGGACUCUUUGUUCCGGCCUUAAUACUCCCUCUCUUGACGCUGAUACAUAGAUAAUUUAUACUCAAUAUAU ................(((((...((((((((((((((((((.(((.(((((....)..)))).))).)))((((((....((((((((...)))))))).))))))..)))))))))).....((((((..(((.((((((((.....(((((((((((.............))).))))))))......((((((..(((.((((.....)))).)))...)))))).))))).)))))))))))).........)))))...)))))... (-55.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUUGAGUAUAAAUUAUCUAUGUAUCAGCGUCAAGAGAGGGAGUAUUAAGGCCGGAACAAAGAGUCCGAGCAAAAUACCUGCCGCAAUACCGAUGCCAAGUUUGGGUAAAAGCCCGAUAUUUUUUUCCCCUUUGCACGUUCUAACAGGUUUAAAACGAUUUGUCCAUAAGCUUUAAAAGGGCUUCAAAAUUUUUCAUAGUAGACAAAUGAGUUCUCACGCUCAAUUGACUAAAAUCGCUUUUUUAUGUACAAUAAUAAAUUGAGGAUAUU ...(((((..((((((.......(((...(((((..((((.(((((((((...((((((........)))).))..))))).....(((.......))).....((((((....))))))........))))))))..)))))...))).........((((((......((((((.....))))))...............(((.(((.(((((......))))).))).)))))))))....))))))..)))))................ (-53.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 810 80 31 171 122 NC_002967:TDE2696|5end_TPR_domain_protein_2740036..2740266_NEGATIVE 367 245 201 200 145 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 348 218 171 65 23 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 346 200 154 148 84 NC_002967:TDE0834|5end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854863..855093_NEGATIVE 343 220 172 66 16 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 337 210 165 205 142 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 335 245 203 51 1 NC_002967:TDE2564|5end_PemK_family_protein_2589975..2590205_POSITIVE 333 219 171 70 16 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 329 241 201 51 9 NC_002967:TDE2310|5end_hypothetical_protein_2348042..2348272_POSITIVE 328 217 177 124 74 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 328 206 161 211 165 NC_002967:TDE0475|5end_ABC_transporter,_ATP-binding_protein_532208..532438_NEGATIVE 323 219 172 180 140 NC_002967:TDE1783|5end_hypothetical_protein_1823605..1823835_NEGATIVE 321 245 204 191 152 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 318 227 184 183 151 NC_002967:TDE0211|5end_ABC_transporter,_permease_protein,_cysTW_family_247286..247516_NEGATIVE 316 223 181 73 32 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 312 190 153 193 143 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 312 219 175 156 103 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 310 209 172 158 130 NC_002967:TDE1233|5end_hypothetical_protein_1267203..1267433_POSITIVE 309 220 183 41 6 NC_002967:TDE1541|5end_metallo-beta-lactamase_family_protein_1584898..1585128_POSITIVE 309 200 155 74 18 NC_002967:TDE0872|5end_recA_protein_894841..895071_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 244 217 35 10 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 351 245 202 64 13 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 346 200 154 144 80 NC_002967:TDE0835|3end_NADH-ubiquinone_oxidoreductase_854867..855017_NEGATIVE 332 219 172 55 1 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 323 191 154 119 78 NC_002967:TDE0012|3end_carbon_starvation_protein_CstA,_putative_17702..17852_POSITIVE 321 245 204 59 20 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 312 219 175 128 75 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 309 218 171 115 57 NC_002967:TDE0113|3end_Tpl_protein_133609..133759_POSITIVE 308 220 171 79 34 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 307 249 201 145 101 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 306 198 156 89 30 NC_002967:TDE1623|3end_hypothetical_protein_1671018..1671168_NEGATIVE 305 200 155 82 24 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 304 218 184 42 2 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 302 219 172 110 64 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 302 220 177 99 48 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 301 220 173 89 28 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 297 218 171 52 4 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 297 219 171 90 21 NC_002967:TDE0845|3end_conserved_hypothetical_protein_TIGR00266_868549..868699_POSITIVE 297 218 172 132 87 NC_002967:TDE0035|3end_acetyltransferase,_GNAT_family_41580..41730_NEGATIVE 295 249 203 150 104 NC_002967:TDE0387|3end_(R)-hydroxyglutaryl-CoA_dehydratase_activator_439256..439406_POSITIVE