Origin IGS: acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt .........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 aacagagctttttcgtaaattcagtttaaatttatacataatctgcatttattatcggcaaaaaagccctgtaggtcaataaaataaccgcgtttttatagatttagaatatttttcggcaataattgaatcaacaaacctccgcacgaataaaaaaccggcctaaattaagctttaactgcctaattatccggccggtttggtttaaaactaaaaagacaaaatcttttctaaattgaaatgt Mask Tandem Repeat Region ================================================ acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Find is-nt database================================================ Query_seq: TDE0445:TDE0446|TDE0445:TDE0446:amino acid permease:fibronectin type III domain protein:->->:501165..501408 244 acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0445:TDE0446|TDE0445:TDE0446:amino acid permease:fibronectin type III domain protein:->->:501165..501408 244 acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0445:TDE0446|TDE0445:TDE0446:amino acid permease:fibronectin type III domain protein:->->:501165..501408 244 acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 9 End: 119 ........ N L F S K T K K T K F W V P R I I L C N F S L K P R N K I R A S T Q Q N M ............................................................................................................................. acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt 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: 85 Start: 165 End: 194 ....................................................................................................................................................................ATTGACCTACAGGGCTTTTTTGCCGATAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -2.0 Tail_Score: -5.5112 Start: 47 End: 87 Full_Region: TAGTTTTAAACCAAA CCGGCCGGATAATTAGGC AGTTAAA GCTTAATTTAGGCCGG TTTTTTATTCGTGCG ..............................................CCGGCCGGATAATTAGGCAGTTAAAGCTTAATTTAGGCCGG............................................................................................................................................................. Find igs database================================================ Query_seq: TDE0445:TDE0446|TDE0445:TDE0446:amino acid permease:fibronectin type III domain protein:->->:501165..501408 244 acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: NC_002967_TDE0445_TDE0446|amino acid permease:fibronectin type III domain protein|POSITIVE:POSITIVE|[501165,501408]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt acatttcaatttagaaaagattttgtctttttagttttaaaccaaaccggccggataattaggcagttaaagcttaatttaggccggttttttattcgtgcggaggtttgttgattcaattattgccgaaaaatattctaaatctataaaaacgcggttattttattgacctacagggcttttttgccgataataaatgcagattatgtataaatttaaactgaatttacgaaaaagctctgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUCAAUUUAGAAAAGAUUUUGUCUUUUUAGUUUUAAACCAAACCGGCCGGAUAAUUAGGCAGUUAAAGCUUAAUUUAGGCCGGUUUUUUAUUCGUGCGGAGGUUUGUUGAUUCAAUUAUUGCCGAAAAAUAUUCUAAAUCUAUAAAAACGCGGUUAUUUUAUUGACCUACAGGGCUUUUUUGCCGAUAAUAAAUGCAGAUUAUGUAUAAAUUUAAACUGAAUUUACGAAAAAGCUCUGUU .............((((((((...)))))))).(((((.....(((((((((....((((((((.......))))))))..)))))))))....((((.((((..(((.(......))))..))))))))..................)))))..(((((......))))).((((((((((((((..........(((((.....)))))((((((.....)))))).)))))))))))))). (-61.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGAGCUUUUUCGUAAAUUCAGUUUAAAUUUAUACAUAAUCUGCAUUUAUUAUCGGCAAAAAAGCCCUGUAGGUCAAUAAAAUAACCGCGUUUUUAUAGAUUUAGAAUAUUUUUCGGCAAUAAUUGAAUCAACAAACCUCCGCACGAAUAAAAAACCGGCCUAAAUUAAGCUUUAACUGCCUAAUUAUCCGGCCGGUUUGGUUUAAAACUAAAAAGACAAAAUCUUUUCUAAAUUGAAAUGU .((((.((((((((((((((.(((.(((..........))).))).)))))....)))...)))))).)))).(((..........)))..((((((.(((.((((((......((((((.....(((......)))......)).))))....(((((((((..(((((.((.......)).)))))....)))))))))..)))))).))).)))))).......((((......))))... (-47.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 109 62 219 176 NC_002967:TDE0712|5end_hypothetical_protein_746963..747193_NEGATIVE 341 116 88 204 176 NC_002967:TDE2146|5end_hydrolase,_alpha/beta_fold_family_2183060..2183290_POSITIVE 314 86 41 68 28 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 314 128 82 216 164 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 311 84 41 83 38 NC_002967:TDE2414|5end_hypothetical_protein_2441620..2441850_NEGATIVE 306 87 49 207 165 NC_002967:TDE2089|5end_signal_recognition_particle_protein_2117563..2117793_NEGATIVE 301 106 61 126 82 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 296 128 82 146 94 NC_002967:TDE0574|5end_surface_protein,_putative_604925..605155_POSITIVE 292 128 94 203 166 NC_002967:TDE0738|5end_hypothetical_protein_775934..776164_NEGATIVE 290 90 47 226 172 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 289 128 84 146 100 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 288 109 61 226 173 NC_002967:TDE0204|5end_glutamyl-tRNA_synthetase_236968..237198_POSITIVE 287 110 62 211 159 NC_002967:TDE0214|5end_hypothetical_protein_250449..250679_NEGATIVE 282 89 44 147 94 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 281 107 61 152 97 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 279 108 70 130 94 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 277 90 42 231 179 NC_002967:TDE1437|5end_capsular_polysaccharide_biosynthesis_protein_1482232..1482462_POSITIVE 276 90 48 70 40 NC_002967:TDE0359|5end_ABC_transporter,_ATP-binding/permease_protein_404100..404330_NEGATIVE 274 128 89 154 112 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 273 189 145 84 35 NC_002967:TDE1604|5end_ABC_transporter,_permease_protein,_putative_1655533..1655763_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 403 90 44 47 1 NC_002967:TDE0445|3end_amino_acid_permease_501104..501254_POSITIVE 374 117 71 53 15 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 317 106 61 105 42 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 293 109 89 140 120 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 289 128 84 78 32 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 283 105 61 111 53 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 282 89 44 92 39 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 281 107 61 137 82 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 279 108 70 118 82 NC_002967:TDE2400|3end_50S_ribosomal_protein_L34_2426172..2426322_NEGATIVE 276 90 48 68 38 NC_002967:TDE0360|3end_ABC_transporter,_ATP-binding/permease_protein_404102..404252_NEGATIVE 275 109 61 70 17 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 273 189 145 84 35 NC_002967:TDE1605|3end_hypothetical_protein_1655533..1655683_NEGATIVE 269 128 83 52 5 NC_002967:TDE2247|3end_PemK_family_protein_2286771..2286921_POSITIVE 267 90 41 50 6 NC_002967:TDE1672|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_ClpP_1726965..1727115_POSITIVE 267 103 62 125 97 NC_002967:TDE1501|3end_pyruvate_phosphate_dikinase_1550922..1551072_POSITIVE 265 109 61 128 74 NC_002967:TDE0640|3end_methyl-accepting_chemotaxis_protein_674531..674681_NEGATIVE 263 109 92 34 17 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 261 128 81 133 64 NC_002967:TDE0040|3end_AMP-binding_protein_45776..45926_NEGATIVE 260 90 44 60 23 NC_002967:TDE1384|3end_cadmium-translocating_P-type_ATPase_1424776..1424926_POSITIVE 260 128 90 78 37 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE