Origin IGS: ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttatttcactcctctactgaaatagacttatgattaacagtatagtttcttatagtatcagaataacacctgatttacatatatccttctctcttggatttccaatgagtgaagttttaaaaataaaactccactcattattgag Mask Tandem Repeat Region ================================================ ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Find is-nt database================================================ Query_seq: TDE1956:TDE1957|TDE1956:TDE1957:hypothetical protein:hypothetical protein:->->:1971443..1971588 146 ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1956:TDE1957|TDE1956:TDE1957:hypothetical protein:hypothetical protein:->->:1971443..1971588 146 ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1956:TDE1957|TDE1956:TDE1957:hypothetical protein:hypothetical protein:->->:1971443..1971588 146 ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 3 End: 116 .. L L S H L K I K L V E S M P F G L S F S I H L D P T I R I S Y S V I S N I M .............................. ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -6.8 Tail_Score: -4.11216 Start: 32 End: 60 Full_Region: tgatttacatatatc cttctctcttgg attt ccaatgagtgaag ttttaaaaataaaac ...............................cttctctcttggatttccaatgagtgaag...................................................................................... Find igs database================================================ Query_seq: TDE1956:TDE1957|TDE1956:TDE1957:hypothetical protein:hypothetical protein:->->:1971443..1971588 146 ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002967_TDE1956_TDE1957|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1971443,1971588]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa ctcaataatgagtggagttttatttttaaaacttcactcattggaaatccaagagagaaggatatatgtaaatcaggtgttattctgatactataagaaactatactgttaatcataagtctatttcagtagaggagtgaaataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAAUAAUGAGUGGAGUUUUAUUUUUAAAACUUCACUCAUUGGAAAUCCAAGAGAGAAGGAUAUAUGUAAAUCAGGUGUUAUUCUGAUACUAUAAGAAACUAUACUGUUAAUCAUAAGUCUAUUUCAGUAGAGGAGUGAAAUAAA (((..(((((((((((((((((....)))))))))))))))))...........((((.((((.((((.......(((((..((((.........))))...)))))......)))).)))).))))....)))............ (-39.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUUCACUCCUCUACUGAAAUAGACUUAUGAUUAACAGUAUAGUUUCUUAUAGUAUCAGAAUAACACCUGAUUUACAUAUAUCCUUCUCUCUUGGAUUUCCAAUGAGUGAAGUUUUAAAAAUAAAACUCCACUCAUUAUUGAG (((((((((.........)))))))))..(((((..(((......)))..)))))..(((((........)))))........((((.........))))....((((((((.(((((((....))))))).))))))))...... (-28.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 60 14 50 8 NC_002967:TDE0126|5end_hypothetical_protein_145637..145867_NEGATIVE 244 59 11 227 187 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 233 87 41 165 115 NC_002967:TDE1452|5end_hypothetical_protein_1498891..1499121_POSITIVE 224 132 101 139 101 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 219 100 62 121 90 NC_002967:TDE1899|5end_hypothetical_protein_1921088..1921318_NEGATIVE 219 60 12 126 72 NC_002967:TDE0112|5end_hypothetical_protein_132044..132274_POSITIVE 217 91 54 40 6 NC_002967:TDE0364|5end_ABC_transporter,_ATP-binding_protein_411605..411835_NEGATIVE 215 75 34 45 3 NC_002967:TDE1046|5end_hypothetical_protein_1073646..1073876_POSITIVE 214 49 9 71 29 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 211 135 107 225 195 NC_002967:TDE2072|5end_hypothetical_protein_2098813..2099043_POSITIVE 205 80 49 162 129 NC_002967:TDE1538|5end_DNA_ligase,_NAD-dependent_1581568..1581798_POSITIVE 203 72 31 68 27 NC_002967:TDE0461|5end_hypothetical_protein_515863..516093_POSITIVE 202 51 22 86 57 NC_002967:TDE0082|5end_transcriptional_regulator,_MerR_family_94251..94481_NEGATIVE 201 44 1 105 65 NC_002967:TDE2048|5end_hypothetical_protein_2076411..2076641_POSITIVE 201 59 11 162 111 NC_002967:TDE1756|5end_hypothetical_protein_1807810..1808040_NEGATIVE 199 49 1 75 20 NC_002967:TDE1390|5end_hypothetical_protein_1429692..1429922_POSITIVE 199 88 41 48 5 NC_002967:TDE0953|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_976863..977093_POSITIVE 198 59 12 112 57 NC_002967:TDE1603|5end_ABC_transporter,_ATP-binding_protein_1654856..1655086_NEGATIVE 198 120 73 175 126 NC_002967:TDE0078|5end_glycine_reductase_complex_selenoprotein_GrdB1_90076..90306_NEGATIVE 196 79 36 166 120 NC_002967:TDE0710|5end_hypothetical_protein_745432..745662_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 42 2 84 46 NC_002967:TDE1956|3end_hypothetical_protein_1971382..1971532_POSITIVE 224 132 101 146 108 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 219 60 12 116 62 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 215 75 34 58 16 NC_002967:TDE1045|3end_hypothetical_protein_1073739..1073889_POSITIVE 214 49 9 51 9 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE 202 51 22 83 54 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 199 49 1 78 23 NC_002967:TDE1389|3end_hypothetical_protein_1429775..1429925_POSITIVE 199 88 41 51 8 NC_002967:TDE0952|3end_ABC_transporter,_ATP-binding_protein_976946..977096_POSITIVE 199 55 11 62 19 NC_002967:TDE0464|3end_NifU_domain_protein_517948..518098_NEGATIVE 198 59 12 121 66 NC_002967:TDE1604|3end_ABC_transporter,_permease_protein,_putative_1654847..1654997_NEGATIVE 196 139 103 89 49 NC_002967:TDE0171|3end_nuclease_SbcCD,_C_subunit,_putative_203137..203287_POSITIVE 195 90 48 150 106 NC_002967:TDE2006|3end_hypothetical_protein_2026870..2027020_POSITIVE 195 58 16 122 73 NC_002967:TDE1117|3end_hypothetical_protein_1149871..1150021_POSITIVE 192 55 24 35 3 NC_002967:TDE1415|3end_nucleotidyl_transferase/aminotransferase,_class_V_1459871..1460021_POSITIVE 191 92 54 104 64 NC_002967:TDE2016|3end_hypothetical_protein_2037824..2037974_NEGATIVE 185 89 48 63 11 NC_002967:TDE1983|3end_hypothetical_protein_1993376..1993526_NEGATIVE 185 77 39 87 46 NC_002967:TDE1961|3end_PIN_domain_protein_1974550..1974700_NEGATIVE 182 112 73 117 68 NC_002967:TDE1129|3end_lipoprotein,_putative_1162523..1162673_POSITIVE 179 111 73 149 107 NC_002967:TDE0079|3end_DNA-binding_protein_90095..90245_NEGATIVE 177 63 29 90 56 NC_002967:TDE2446|3end_malate_dehydrogenase_2474774..2474924_NEGATIVE