Origin IGS: ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta .........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 taatgcacatttaacaatagtatgtaacttatgattatcagttttgttggatatgtgtagtttgattccgtaatcctccttcgtacggaatcggacttgcccgcgtaagcgggcttttttttataaacagccttttatagtttataaaccaaatattcactttaaaaaagccttaaaaaaagggccgtatttcctcacgtaaaaatctaacccaaatgatatgcgttactcaagtaaaaatctaaccgtag Mask Tandem Repeat Region ================================================ ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Find is-nt database================================================ Query_seq: TDE2588:TDE2589|TDE2588:TDE2589:integrase domain protein:putative aminopeptidase 1:-><-:2624839..2625089 251 ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2588:TDE2589|TDE2588:TDE2589:integrase domain protein:putative aminopeptidase 1:-><-:2624839..2625089 251 ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2588:TDE2589|TDE2588:TDE2589:integrase domain protein:putative aminopeptidase 1:-><-:2624839..2625089 251 ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 92 End: 211 ........................................................................................... M N I W F I N Y K R L F I K K S P L T R A S P I P Y E G G L R N Q T T H I Q Q N ........................................ ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta 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================================================ ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.8 Tail_Score: -5.93809 Start: 138 End: 153 Full_Region: tacggaatcggactt gcccgc gtaa gcgggc ttttttttataaaca .........................................................................................................................................gcccgcgtaagcgggc.................................................................................................. Find igs database================================================ Query_seq: TDE2588:TDE2589|TDE2588:TDE2589:integrase domain protein:putative aminopeptidase 1:-><-:2624839..2625089 251 ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Intra-Species Hit: Count: 1 Min: 1 Max: 251 Len: 251 Subject: NC_002967_TDE2588_TDE2589|integrase domain protein:putative aminopeptidase 1|POSITIVE:NEGATIVE|[2624839,2625089]|251 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 251 Query Start:1 Query End:251 Subject Strand: POSITIVE Subject Start: 1 Subject End: 251 ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggcccnnnnnnnaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttatnnnnnnnngcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta ctacggttagatttttacttgagtaacgcatatcatttgggttagatttttacgtgaggaaatacggccctttttttaaggcttttttaaagtgaatatttggtttataaactataaaaggctgtttataaaaaaaagcccgcttacgcgggcaagtccgattccgtacgaaggaggattacggaatcaaactacacatatccaacaaaactgataatcataagttacatactattgttaaatgtgcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUACGGUUAGAUUUUUACUUGAGUAACGCAUAUCAUUUGGGUUAGAUUUUUACGUGAGGAAAUACGGCCCUUUUUUUAAGGCUUUUUUAAAGUGAAUAUUUGGUUUAUAAACUAUAAAAGGCUGUUUAUAAAAAAAAGCCCGCUUACGCGGGCAAGUCCGAUUCCGUACGAAGGAGGAUUACGGAAUCAAACUACACAUAUCCAACAAAACUGAUAAUCAUAAGUUACAUACUAUUGUUAAAUGUGCAUUA ...(((((.....(((((((....((.((.........(((((..(((((..(....))))))..)))))..........)).))....)))))))...(((((((((((((...........))))))))).....((((((....)))))).(((..((((((((((....).....)))))))))..)))........))))...))))).((((((((....(((......)))....)))).)))) (-56.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGCACAUUUAACAAUAGUAUGUAACUUAUGAUUAUCAGUUUUGUUGGAUAUGUGUAGUUUGAUUCCGUAAUCCUCCUUCGUACGGAAUCGGACUUGCCCGCGUAAGCGGGCUUUUUUUUAUAAACAGCCUUUUAUAGUUUAUAAACCAAAUAUUCACUUUAAAAAAGCCUUAAAAAAAGGGCCGUAUUUCCUCACGUAAAAAUCUAACCCAAAUGAUAUGCGUUACUCAAGUAAAAAUCUAACCGUAG ((((((........((..(((.....)))..))..(((((.....((((((((((((.((((((((((((((...........)))))))))))))).((((((....)))))).....(((((((((...........))))))))).....................(((((......)))))..........))))))....)))))).....))))).))))))....................... (-60.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 184 141 51 1 NC_002967:TDE0874|5end_transcriptional_regulator,_putative_896939..897169_POSITIVE 341 177 137 186 122 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 338 185 142 155 120 NC_002967:TDE2725|5end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2783208..2783438_NEGATIVE 337 77 36 152 116 NC_002967:TDE2588|5end_integrase_domain_protein_2623496..2623726_POSITIVE 332 186 150 214 180 NC_002967:TDE1864|5end_crossover_junction_endodeoxyribonuclease_RuvC_1889108..1889338_NEGATIVE 331 176 135 109 58 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 322 167 122 100 49 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 321 178 133 140 102 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 316 175 139 36 7 NC_002967:TDE2633|5end_hypothetical_protein_2674359..2674589_POSITIVE 310 171 139 178 146 NC_002967:TDE0923|5end_ABC_transporter,_ATP-binding/permease_protein_945731..945961_NEGATIVE 309 167 135 79 38 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 308 172 136 69 19 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 306 174 137 68 30 NC_002967:TDE0360|5end_ABC_transporter,_ATP-binding/permease_protein_405844..406074_NEGATIVE 304 178 135 59 13 NC_002967:TDE0675|5end_hypothetical_protein_713994..714224_POSITIVE 301 167 131 81 29 NC_002967:TDE2554|5end_chaperonin,_33_kDa_family_2580745..2580975_POSITIVE 299 186 146 187 153 NC_002967:TDE1397|5end_flagellar_synthesis_regulator_FleN,_putative_1436014..1436244_POSITIVE 298 86 43 142 98 NC_002967:TDE2233|5end_iron_compound_ABC_transporter,_permease_protein,_putative_2272310..2272540_NEGATIVE 294 184 144 192 151 NC_002967:TDE2614|5end_ApbE_family_protein_2657133..2657363_NEGATIVE 293 176 140 231 193 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 293 180 141 203 141 NC_002967:TDE0273|5end_ABC_transporter,_ATP-binding/permease_protein_304633..304863_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 167 122 87 36 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 321 166 125 67 28 NC_002967:TDE1121|3end_hypothetical_protein_1152814..1152964_NEGATIVE 313 175 139 133 85 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 309 167 135 66 25 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 304 178 135 62 16 NC_002967:TDE0674|3end_hypothetical_protein_714077..714227_POSITIVE 298 86 43 142 98 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 298 177 137 61 13 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 293 167 140 43 17 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 292 186 148 75 37 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 291 90 42 86 35 NC_002967:TDE0448|3end_deoxyribose-phosphate_aldolase_506526..506676_POSITIVE 291 184 141 70 28 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 284 184 141 47 5 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 283 174 137 65 26 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 281 162 142 147 127 NC_002967:TDE2726|3end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2783201..2783351_NEGATIVE 278 170 137 89 47 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 276 177 132 81 41 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 275 180 139 53 23 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 275 188 147 79 29 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 275 188 147 37 2 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 270 163 136 92 58 NC_002967:TDE2428|3end_ribosomal_protein_L33_2456122..2456272_NEGATIVE