Origin IGS: ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa .........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 ttgaactccaactataactttatcttataagaagatactaatagaaaaaaaaagggtcaaggggttttataaaatcatagtggaaaatttgcaaaatattgcggtattagaggttaccacatataaaaaacgccggttattcccgcataagaataaccggcattaaaaagttcaaggtttcttatttttgactgacccattttgcgaatccggcttttctaagtagaccgaaaccagacc Mask Tandem Repeat Region ================================================ ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Find is-nt database================================================ Query_seq: TDE0626:TDE0627|TDE0626:TDE0627:hypothetical protein:co-chaperone protein GrpE:->->:659745..659984 240 ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0626:TDE0627|TDE0626:TDE0627:hypothetical protein:co-chaperone protein GrpE:->->:659745..659984 240 ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0626:TDE0627|TDE0626:TDE0627:hypothetical protein:co-chaperone protein GrpE:->->:659745..659984 240 ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 32 End: 124 ............................... M R K M G Q S K I R N L E L F N A G Y S Y A G I T G V F Y M W .................................................................................................................... Protein_Len: 50 Strand: - Start: 78 End: 227 ............................................................................. H R N N K H P F L R R K K Y T T V E L V A I N Q L N E V I I K Y F G K V R K K E I L I K K Y S L T M ............. ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa 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: 83 Start: 180 End: 209 ...................................................................................................................................................................................CTTGACCCTTTTTTTTTCTATTAGTATCTT............................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 146 End: 175 .................................................................................................................................................TTTGCAAATTTTCCACTATGATTTTATAAA................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.4 Tail_Score: -5.43414 Start: 79 End: 110 Full_Region: CCTTGAACTTTTTAA TGCCGGTTATTCTT ATGC GGGAATAACCGGCG TTTTTTATATGTGGT ..............................................................................TGCCGGTTATTCTTATGCGGGAATAACCGGCG.................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -13.7 Tail_Score: -3.84422 Start: 80 End: 109 Full_Region: CTTGAACTTTTTAAT GCCGGTTATTCTT ATGC GGGAATAACCGGC GTTTTTTATATGTGG ...............................................................................GCCGGTTATTCTTATGCGGGAATAACCGGC................................................................................................................................... Find igs database================================================ Query_seq: TDE0626:TDE0627|TDE0626:TDE0627:hypothetical protein:co-chaperone protein GrpE:->->:659745..659984 240 ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: NC_002967_TDE0626_TDE0627|hypothetical protein:co-chaperone protein GrpE|POSITIVE:POSITIVE|[659745,659984]|240 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 240 Query Start:1 Query End:240 Subject Strand: POSITIVE Subject Start: 1 Subject End: 240 ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgacccnnnnnnnnnctattagtatcttcttataagataaagttatagttggagttcaa ggtctggtttcggtctacttagaaaagccggattcgcaaaatgggtcagtcaaaaataagaaaccttgaactttttaatgccggttattcttatgcgggaataaccggcgttttttatatgtggtaacctctaataccgcaatattttgcaaattttccactatgattttataaaaccccttgaccctttttttttctattagtatcttcttataagataaagttatagttggagttcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCUGGUUUCGGUCUACUUAGAAAAGCCGGAUUCGCAAAAUGGGUCAGUCAAAAAUAAGAAACCUUGAACUUUUUAAUGCCGGUUAUUCUUAUGCGGGAAUAACCGGCGUUUUUUAUAUGUGGUAACCUCUAAUACCGCAAUAUUUUGCAAAUUUUCCACUAUGAUUUUAUAAAACCCCUUGACCCUUUUUUUUUCUAUUAGUAUCUUCUUAUAAGAUAAAGUUAUAGUUGGAGUUCAA .(((((((((...(((....))).)))))))))..(((((((((((...((........)).)))...........(((((((((((((((......))))))))))))))).......(((((((........))))))).)))))))).....(((((((((((((((((..........((..((..(.......)..))..))..........)))))))))))).)))))..... (-65.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAACUCCAACUAUAACUUUAUCUUAUAAGAAGAUACUAAUAGAAAAAAAAAGGGUCAAGGGGUUUUAUAAAAUCAUAGUGGAAAAUUUGCAAAAUAUUGCGGUAUUAGAGGUUACCACAUAUAAAAAACGCCGGUUAUUCCCGCAUAAGAAUAACCGGCAUUAAAAAGUUCAAGGUUUCUUAUUUUUGACUGACCCAUUUUGCGAAUCCGGCUUUUCUAAGUAGACCGAAACCAGACC ...........((((.....((((((.....))))))...))))..........((((....((((((.............(((...((((((((((..((.((((........)))).))..........(((((((((((........)))))))))))..............((((..(((....)))..)))).))))))))))))).((((....)))).....)))))).)))) (-54.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 98 52 56 6 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 357 50 2 137 92 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 310 116 71 129 84 NC_002967:TDE2501|5end_response_regulator_2524773..2525003_POSITIVE 308 112 77 210 172 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 290 110 64 220 163 NC_002967:TDE2522|5end_ABC_transporter,_ATP-binding_protein_2548098..2548328_POSITIVE 290 120 71 59 6 NC_002967:TDE0859|5end_hypothetical_protein_880100..880330_POSITIVE 289 139 93 47 18 NC_002967:TDE1549|5end_recombination_protein_RecR_1592140..1592370_POSITIVE 281 111 80 209 173 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 280 127 82 75 7 NC_002967:TDE0591|5end_acetyl-CoA_carboxylase,_biotin_carboxylase_631352..631582_NEGATIVE 279 130 81 204 160 NC_002967:TDE0532|5end_TPR_domain_protein_575570..575800_POSITIVE 272 109 65 140 98 NC_002967:TDE2565|5end_hypothetical_protein_2591273..2591503_NEGATIVE 270 108 63 219 161 NC_002967:TDE1284|5end_methyl-accepting_chemotaxis_protein,_putative_1318720..1318950_POSITIVE 269 110 64 143 95 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 268 214 177 197 161 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 267 119 78 67 20 NC_002967:TDE1483|5end_hypothetical_protein_1528763..1528993_POSITIVE 267 138 92 111 51 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 266 110 65 70 24 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 265 132 92 56 15 NC_002967:TDE1100|5end_acetyltransferase,_GNAT_family_1134672..1134902_NEGATIVE 263 129 81 224 173 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 262 140 94 72 7 NC_002967:TDE2037|5end_ATP:guanido_phosphotransferase_domain_protein_2067720..2067950_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 128 91 102 66 NC_002967:TDE2734|3end_hypothetical_protein_2789861..2790011_POSITIVE 295 84 42 71 30 NC_002967:TDE2338|3end_hypothetical_protein_2374624..2374774_NEGATIVE 292 127 81 143 99 NC_002967:TDE0871|3end_hypothetical_protein_894657..894807_NEGATIVE 283 126 81 57 5 NC_002967:TDE0858|3end_hypothetical_protein_880170..880320_POSITIVE 282 128 81 134 85 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 281 111 80 137 101 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 276 139 94 29 1 NC_002967:TDE1548|3end_conserved_hypothetical_protein_TIGR00103_1592202..1592352_POSITIVE 272 109 65 81 39 NC_002967:TDE2566|3end_hypothetical_protein_2591332..2591482_NEGATIVE 272 109 64 75 34 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 267 138 92 97 37 NC_002967:TDE0907|3end_hypothetical_protein_925320..925470_POSITIVE 265 107 66 137 101 NC_002967:TDE2709|3end_BNR_domain_protein_2761694..2761844_NEGATIVE 265 132 92 65 24 NC_002967:TDE1101|3end_acetyltransferase,_GNAT_family_1134663..1134813_NEGATIVE 263 129 81 53 2 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 262 140 94 88 23 NC_002967:TDE2038|3end_UVR_domain_protein_2067704..2067854_NEGATIVE 260 140 93 97 58 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 259 109 64 86 41 NC_002967:TDE2004|3end_hypothetical_protein_2023845..2023995_POSITIVE 258 138 94 77 35 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 254 150 105 69 25 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 252 126 82 102 65 NC_002967:TDE1162|3end_ParB-like_nuclease_domain_protein_1196056..1196206_NEGATIVE 252 47 8 45 9 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE