Origin IGS: taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt .........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 acggttctccataatatatatattatatcgatatgatataaacattgtaagcaggtagtatagggctcccaaaatattgaaatcagttaccctctatatattgtattagataaatagttatatgctattacctacagtattaaaaaaagaagaccttgacagtacaaaaaaggcatggtacactaaaagctataataatttataggaggcttttta Mask Tandem Repeat Region ================================================ taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt Find is-nt database================================================ Query_seq: TDE0251:TDE0252|TDE0251:TDE0252:tryptophanase:hypothetical protein:<-->:286187..286402 216 taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0251:TDE0252|TDE0251:TDE0252:tryptophanase:hypothetical protein:<-->:286187..286402 216 taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0251:TDE0252|TDE0251:TDE0252:tryptophanase:hypothetical protein:<-->:286187..286402 216 taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 15 End: 107 .............. L N N Y S K T Y W A K K T S D L D E K K L V T P L L M Y S N M ............................................................................................................. taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt 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: 33 End: 62 ................................CTTGACAGTACAAAAAAGGCATGGTACACT.......................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 166 End: 195 .....................................................................................................................................................................CTTACAATGTTTATATCATATCGATATAAT..................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -4.7 Tail_Score: -3.13191 Start: 176 End: 194 Full_Region: ACCTGCTTACAATGT TTATATC ATATC GATATAA TATATATATTATGGA ...............................................................................................................................................................................TTATATCATATCGATATAA...................... Find igs database================================================ Query_seq: TDE0251:TDE0252|TDE0251:TDE0252:tryptophanase:hypothetical protein:<-->:286187..286402 216 taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtttatatcatatcgatataatatatatattatggagaaccgt Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_002967_TDE0251_TDE0252|tryptophanase:hypothetical protein|NEGATIVE:POSITIVE|[286187,286402]|216 HSP 1 e-value: 8.0E-83 bit: 307.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttcnnnnnnnaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtt........................................ taaaaagcctcctataaattattatagcttttagtgtaccatgccttttttgtactgtcaaggtcttctttttttaatactgtaggtaatagcatataactatttatctaatacaatatatagagggtaactgatttcaatattttgggagccctatactacctgcttacaatgtt........................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGCCUCCUAUAAAUUAUUAUAGCUUUUAGUGUACCAUGCCUUUUUUGUACUGUCAAGGUCUUCUUUUUUUAAUACUGUAGGUAAUAGCAUAUAACUAUUUAUCUAAUACAAUAUAUAGAGGGUAACUGAUUUCAAUAUUUUGGGAGCCCUAUACUACCUGCUUACAAUGUU ....((((...((((((....))))))....(((((((...((((((((.((((.(((.((((....))))...........((((((((((.......))).)))))))..))).)))).)))))))).....(..(((....)))..)....)))))))...))))........ (-29.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUUGUAAGCAGGUAGUAUAGGGCUCCCAAAAUAUUGAAAUCAGUUACCCUCUAUAUAUUGUAUUAGAUAAAUAGUUAUAUGCUAUUACCUACAGUAUUAAAAAAAGAAGACCUUGACAGUACAAAAAAGGCAUGGUACACUAAAAGCUAUAAUAAUUUAUAGGAGGCUUUUUA ...((((((.(..((((((((((((..........((((....))))..))).((((.((((......)))).))))...))))))))).).))))))........((((((.((((....((((............))))........((((((....)))))))))))))))). (-28.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 811 70 21 161 112 NC_002967:TDE0251|5end_tryptophanase_286096..286326_NEGATIVE 311 67 33 102 70 NC_002967:TDE0179|5end_hypothetical_protein_212881..213111_NEGATIVE 274 78 33 223 180 NC_002967:TDE2429|5end_hypothetical_protein_2458037..2458267_NEGATIVE 264 71 39 121 88 NC_002967:TDE2437|5end_cyclic_nucleotide_binding_domain_protein_2467957..2468187_NEGATIVE 261 155 118 189 153 NC_002967:TDE2488|5end_modification_methylase,_HemK_family_2511384..2511614_NEGATIVE 261 167 121 62 19 NC_002967:TDE1647|5end_DNA-binding_protein_1696502..1696732_NEGATIVE 261 66 26 60 20 NC_002967:TDE0999|5end_formate/nitrite_transporter_1025870..1026100_POSITIVE 260 89 44 160 113 NC_002967:TDE0784|5end_ribosomal_protein_S5_813891..814121_POSITIVE 260 64 30 164 130 NC_002967:TDE0274|5end_ABC_transporter,_ATP-binding/permease_protein_306423..306653_NEGATIVE 258 68 27 73 30 NC_002967:TDE2517|5end_DNA_repair_protein_RadA_2543842..2544072_NEGATIVE 257 73 33 105 55 NC_002967:TDE1677|5end_single-strand_binding_protein_1730189..1730419_NEGATIVE 254 67 26 99 57 NC_002967:TDE2660|5end_hypothetical_protein_2697517..2697747_NEGATIVE 249 168 127 72 39 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 248 71 38 112 72 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 246 159 117 180 139 NC_002967:TDE2397|5end_hypothetical_protein_2425564..2425794_NEGATIVE 245 64 21 61 12 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 244 160 117 201 150 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 241 70 21 86 23 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 240 69 25 231 191 NC_002967:TDE1626|5end_glycine_cleavage_system_H_protein_1675279..1675509_NEGATIVE 239 73 38 147 108 NC_002967:TDE0790|5end_30S_ribosomal_protein_S11_816951..817181_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 60 11 127 73 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 311 67 33 129 97 NC_002967:TDE0180|3end_hypothetical_protein_212854..213004_NEGATIVE 290 165 122 102 53 NC_002967:TDE0659|3end_hypothetical_protein_695690..695840_NEGATIVE 281 70 26 146 86 NC_002967:TDE0494|3end_hypothetical_protein_549559..549709_NEGATIVE 279 57 15 130 87 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 268 74 33 50 13 NC_002967:TDE0717|3end_hypothetical_protein_752380..752530_POSITIVE 264 71 39 113 80 NC_002967:TDE2438|3end_hypothetical_protein_2467965..2468115_NEGATIVE 261 167 121 78 35 NC_002967:TDE1648|3end_hypothetical_protein_1696486..1696636_NEGATIVE 260 89 44 151 104 NC_002967:TDE0783|3end_ribosomal_protein_L18_813962..814112_POSITIVE 257 73 33 92 42 NC_002967:TDE1678|3end_ribosomal_protein_S6_1730202..1730352_NEGATIVE 254 67 26 92 50 NC_002967:TDE2661|3end_hypothetical_protein_2697524..2697674_NEGATIVE 249 75 33 49 2 NC_002967:TDE2518|3end_nucleotide-binding_protein_2543875..2544025_NEGATIVE 249 168 127 72 39 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 245 64 21 97 48 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 239 73 38 123 84 NC_002967:TDE0789|3end_30S_ribosomal_protein_S13_817007..817157_POSITIVE 238 167 125 58 18 NC_002967:TDE1247|3end_hypothetical_protein_1282425..1282575_POSITIVE 237 170 140 71 42 NC_002967:TDE2656|3end_cobalt_chelatase_2693900..2694050_POSITIVE 236 164 122 121 79 NC_002967:TDE2523|3end_hypothetical_protein_2550515..2550665_POSITIVE 236 68 22 49 12 NC_002967:TDE1970|3end_sensory_box_histidine_kinase_1984497..1984647_NEGATIVE 236 169 122 93 51 NC_002967:TDE0326|3end_ATP-dependent_DNA_helicase_RecQ_358748..358898_NEGATIVE