Origin IGS: aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat .........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 atgaatttctgtgcccgctttaatatgtaaataaaacgaatcatttcataggaagcagtcccataaaaatccggctaattctttttacaggattagccgaaaagttttagcagttaaaagattaaggcaaaacagcaaacagttttccctcacgcaatagtcttgttgttcttcataaaatcaaatttgactttttacctcccttatgttaaaatacactt Mask Tandem Repeat Region ================================================ aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Find is-nt database================================================ Query_seq: TDE0804:TDE0805|TDE0804:TDE0805:hypothetical protein:hypothetical protein:<-->:828090..828310 221 aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0804:TDE0805|TDE0804:TDE0805:hypothetical protein:hypothetical protein:<-->:828090..828310 221 aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0804:TDE0805|TDE0804:TDE0805:hypothetical protein:hypothetical protein:<-->:828090..828310 221 aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. H I K V Y P L Y F T L N S K I F F L L V I A H P F V T Q Q K A K M ........................................................................................................................ aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat 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: 90 Start: 7 End: 36 ......TTTGACTTTTTACCTCCCTTATGTTAAAAT......................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -8.1 Tail_Score: -4.84359 Start: 121 End: 152 Full_Region: TAACTGCTAAAACTT TTCGGCTAATCCT GTAAAA AGAATTAGCCGGA TTTTTATGGGACTGC ........................................................................................................................TTCGGCTAATCCTGTAAAAAGAATTAGCCGGA..................................................................... TransTerm Strand: + Conf: 69 HP_score: -8.5 Tail_Score: -2.69598 Start: 123 End: 150 Full_Region: ACTGCTAAAACTTTT CGGCTAATCCT GTAAAA AGAATTAGCCG GATTTTTATGGGACT ..........................................................................................................................CGGCTAATCCTGTAAAAAGAATTAGCCG....................................................................... TransTerm Strand: + Conf: 50 HP_score: -4.4 Tail_Score: -2.99031 Start: 154 End: 178 Full_Region: AAGAATTAGCCGGAT TTTTATGGGA CTGCT TCCTATGAAA TGATTCGTTTTATTT .........................................................................................................................................................TTTTATGGGACTGCTTCCTATGAAA........................................... Find igs database================================================ Query_seq: TDE0804:TDE0805|TDE0804:TDE0805:hypothetical protein:hypothetical protein:<-->:828090..828310 221 aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Intra-Species Hit: Count: 1 Min: 1 Max: 221 Len: 221 Subject: NC_002967_TDE0804_TDE0805|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[828090,828310]|221 HSP 1 e-value: 1.0E-122 bit: 438.0 Len: 221 Query Start:1 Query End:221 Subject Strand: POSITIVE Subject Start: 1 Subject End: 221 aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat aagtgtattttaacataagggaggtaaaaagtcaaatttgattttatgaagaacaacaagactattgcgtgagggaaaactgtttgctgttttgccttaatcttttaactgctaaaacttttcggctaatcctgtaaaaagaattagccggatttttatgggactgcttcctatgaaatgattcgttttatttacatattaaagcgggcacagaaattcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUGUAUUUUAACAUAAGGGAGGUAAAAAGUCAAAUUUGAUUUUAUGAAGAACAACAAGACUAUUGCGUGAGGGAAAACUGUUUGCUGUUUUGCCUUAAUCUUUUAACUGCUAAAACUUUUCGGCUAAUCCUGUAAAAAGAAUUAGCCGGAUUUUUAUGGGACUGCUUCCUAUGAAAUGAUUCGUUUUAUUUACAUAUUAAAGCGGGCACAGAAAUUCAU ..((((.((((((..(((((((.((((..((((....(((.((((....)))))))...)))).)))).(((((.(((((........))))).))))).))))))).....((((((..((((((((((.((......)).)))))))))).((((((((((.....))))))))))......))))))........))))))...)))).......... (-51.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAAUUUCUGUGCCCGCUUUAAUAUGUAAAUAAAACGAAUCAUUUCAUAGGAAGCAGUCCCAUAAAAAUCCGGCUAAUUCUUUUUACAGGAUUAGCCGAAAAGUUUUAGCAGUUAAAAGAUUAAGGCAAAACAGCAAACAGUUUUCCCUCACGCAAUAGUCUUGUUGUUCUUCAUAAAAUCAAAUUUGACUUUUUACCUCCCUUAUGUUAAAAUACACUU (((((...........((((((((...(((.((((((.............(((.....)))..........(((((((((((......)))))))))))....))))))....)))....))))))))..((((((((((.(((...........))).)).)))))))).))))).........((((((................))))))........ (-39.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 100 51 191 142 NC_002967:TDE0804|5end_hypothetical_protein_827999..828229_NEGATIVE 355 98 61 88 42 NC_002967:TDE2095|5end_hypothetical_protein_2121749..2121979_POSITIVE 315 109 61 107 51 NC_002967:TDE0128|5end_HAMP_domain/GGDEF_domain/EAL_domain_protein_146240..146470_POSITIVE 300 176 131 157 116 NC_002967:TDE0145|5end_thiamine_ABC_transporter,_ATP-binding_protein_166700..166930_POSITIVE 288 113 73 195 157 NC_002967:TDE1018|5end_hypothetical_protein_1049227..1049457_POSITIVE 269 171 131 167 124 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 265 174 143 140 112 NC_002967:TDE0746|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_782109..782339_NEGATIVE 263 134 92 170 130 NC_002967:TDE2283|5end_permease,_putative_2320917..2321147_NEGATIVE 261 167 122 79 30 NC_002967:TDE1371|5end_RNB-like_family_protein_1415169..1415399_NEGATIVE 260 127 94 156 115 NC_002967:TDE2182|5end_hypothetical_protein_2215035..2215265_NEGATIVE 256 120 71 83 36 NC_002967:TDE1248|5end_hypothetical_protein_1282596..1282826_POSITIVE 254 170 129 219 179 NC_002967:TDE0497|5end_hypothetical_protein_551880..552110_NEGATIVE 250 126 83 177 139 NC_002967:TDE0628|5end_molecular_chaperone_DnaK_660609..660839_POSITIVE 249 169 128 61 20 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 249 190 141 203 158 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 247 169 122 202 146 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 245 171 131 140 101 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 245 160 112 96 43 NC_002967:TDE0791|5end_DNA-directed_RNA_polymerase_alpha_subunit_817342..817572_POSITIVE 244 128 81 145 101 NC_002967:TDE2261|5end_hypothetical_protein_2298013..2298243_NEGATIVE 244 98 57 138 89 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 176 131 146 105 NC_002967:TDE0144|3end_thiamine_ABC_transporter,_permease_protein_166769..166919_POSITIVE 288 113 73 99 61 NC_002967:TDE1017|3end_exodeoxyribonuclease_VII,_large_subunit_1049211..1049361_POSITIVE 269 171 131 112 69 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 257 174 142 94 61 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 255 102 65 41 2 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 250 125 82 110 70 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 249 127 85 51 6 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 249 190 141 51 6 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE 247 112 71 105 58 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 247 169 122 130 74 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 245 160 112 85 32 NC_002967:TDE0790|3end_30S_ribosomal_protein_S11_817411..817561_POSITIVE 244 128 81 125 81 NC_002967:TDE2262|3end_peptidase,_U32_family_2298033..2298183_NEGATIVE 243 98 61 140 108 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 242 173 138 87 57 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 241 172 143 151 125 NC_002967:TDE0747|3end_iron_compound_ABC_transporter,_permease_protein,_putative_782096..782246_NEGATIVE 240 169 130 83 38 NC_002967:TDE2566|3end_hypothetical_protein_2591332..2591482_NEGATIVE 239 188 147 54 6 NC_002967:TDE0674|3end_hypothetical_protein_714077..714227_POSITIVE 238 152 119 151 122 NC_002967:TDE0994|3end_hypothetical_protein_1022447..1022597_POSITIVE 237 106 67 67 15 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 237 159 123 36 1 NC_002967:TDE2445|3end_DNA-binding_protein_2474667..2474817_POSITIVE