Origin IGS: ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca .........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 tgatattaatgtgtttacctattgcataatatatatataataagtatattattgatttacagaagatatgactctgaaagttatagttaaaaatccgaaactattattaacaaaacattcttaatttctggatacaaaaggtagttgcggagtaaatgaacataatcagtattataaaacaggagacaaaa Mask Tandem Repeat Region ================================================ ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca Find is-nt database================================================ Query_seq: TDE0373:TDE0374|TDE0373:TDE0374:ABC transporter, ATP-binding/permease protein:glycosyl transferase, group 1 family protein:<-<-:427813..428003 191 ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0373:TDE0374|TDE0373:TDE0374:ABC transporter, ATP-binding/permease protein:glycosyl transferase, group 1 family protein:<-<-:427813..428003 191 ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0373:TDE0374|TDE0373:TDE0374:ABC transporter, ATP-binding/permease protein:glycosyl transferase, group 1 family protein:<-<-:427813..428003 191 ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 10 End: 102 ......... M F Y N T D Y V H L L R N Y L L Y P E I K N V L L I I V S D F ......................................................................................... Protein_Len: 31 Strand: + Start: 98 End: 190 ................................................................................................. M F N Y N F Q S H I F C K S I I Y L L Y I Y Y A I G K H I N I . ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca 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================================================ ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0373:TDE0374|TDE0373:TDE0374:ABC transporter, ATP-binding/permease protein:glycosyl transferase, group 1 family protein:<-<-:427813..428003 191 ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaataatatacttattatatatatattatgcaataggtaaacacattaatatca Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_002967_TDE0373_TDE0374|ABC transporter, ATP-binding/permease protein:glycosyl transferase, group 1 family protein|NEGATIVE:NEGATIVE|[427813,428003]|191 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaata................................................. ttttgtctcctgttttataatactgattatgttcatttactccgcaactaccttttgtatccagaaattaagaatgttttgttaataatagtttcggatttttaactataactttcagagtcatatcttctgtaaatcaata................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUCUCCUGUUUUAUAAUACUGAUUAUGUUCAUUUACUCCGCAACUACCUUUUGUAUCCAGAAAUUAAGAAUGUUUUGUUAAUAAUAGUUUCGGAUUUUUAACUAUAACUUUCAGAGUCAUAUCUUCUGUAAAUCAAUA ...((.(((.((..(((((....(((......))).....((((.(((((...((((....)))).(((((.((....)).)))))..))))).))))........)))))....))))).))................... (-16.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUGAUUUACAGAAGAUAUGACUCUGAAAGUUAUAGUUAAAAAUCCGAAACUAUUAUUAACAAAACAUUCUUAAUUUCUGGAUACAAAAGGUAGUUGCGGAGUAAAUGAACAUAAUCAGUAUUAUAAAACAGGAGACAAAA ((((((((.........(((((((.....)))))))(((.....((((.(((((((.............(((........))).......))))))).)))).......)))..))))))))..........(....).... (-20.25) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 788 70 21 161 112 NC_002967:TDE0373|5end_ABC_transporter,_ATP-binding/permease_protein_427722..427952_NEGATIVE 323 59 11 114 59 NC_002967:TDE1151|5end_hypothetical_protein_1188534..1188764_NEGATIVE 258 130 96 228 195 NC_002967:TDE2682|5end_hypothetical_protein_2723358..2723588_NEGATIVE 257 62 27 138 101 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 252 60 11 140 91 NC_002967:TDE1822|5end_hypothetical_protein_1855922..1856152_NEGATIVE 247 131 92 86 49 NC_002967:TDE0592|5end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631938..632168_NEGATIVE 243 60 29 119 84 NC_002967:TDE2650|5end_transcriptional_regulator,_putative_2689031..2689261_NEGATIVE 233 46 6 142 104 NC_002967:TDE1572|5end_hypothetical_protein_1620863..1621093_POSITIVE 232 116 74 190 136 NC_002967:TDE0721|5end_hypothetical_protein_756751..756981_POSITIVE 217 45 1 63 19 NC_002967:TDE0543|5end_hypothetical_protein_583126..583356_POSITIVE 217 83 41 88 48 NC_002967:TDE0492|5end_sensor_histidine_kinase/response_regulator_547468..547698_POSITIVE 215 46 2 156 94 NC_002967:TDE2345|5end_ribosome_recycling_factor_2382503..2382733_NEGATIVE 213 64 25 87 53 NC_002967:TDE2156|5end_translation_initiation_factor_IF-3_2190719..2190949_NEGATIVE 213 62 30 122 83 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 210 46 7 141 97 NC_002967:TDE0382|5end_hypothetical_protein_434393..434623_POSITIVE 209 63 27 139 105 NC_002967:TDE1599|5end_ABC_transporter,_ATP-binding/permease_protein_1650644..1650874_NEGATIVE 209 50 2 151 93 NC_002967:TDE1067|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1095701..1095931_NEGATIVE 208 136 91 107 59 NC_002967:TDE2225|5end_thioesterase_family_protein_2264868..2265098_POSITIVE 207 133 92 117 72 NC_002967:TDE1122|5end_anti-anti-sigma_factor_1153711..1153941_NEGATIVE 207 47 7 141 96 NC_002967:TDE1106|5end_translation_initiation_factor_IF-2_1140882..1141112_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 59 11 121 66 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE 233 46 6 45 7 NC_002967:TDE1571|3end_hypothetical_protein_1620846..1620996_POSITIVE 223 119 71 142 80 NC_002967:TDE2750|3end_GTP-binding_protein_HflX,_truncation_2807288..2807438_POSITIVE 217 83 41 88 48 NC_002967:TDE0491|3end_hypothetical_protein_547548..547698_POSITIVE 215 46 2 72 10 NC_002967:TDE2346|3end_elongation_factor_Ts_2382587..2382737_NEGATIVE 213 62 30 120 81 NC_002967:TDE0349|3end_phosphoenolpyruvate_synthase,_putative_393650..393800_POSITIVE 210 46 7 129 85 NC_002967:TDE0381|3end_hypothetical_protein_434461..434611_POSITIVE 209 63 27 138 104 NC_002967:TDE1600|3end_ABC_transporter,_ATP-binding/permease_protein_1650645..1650795_NEGATIVE 208 136 91 110 62 NC_002967:TDE2224|3end_hypothetical_protein_2264951..2265101_POSITIVE 207 133 92 91 46 NC_002967:TDE1123|3end_sigma_factor_regulatory_protein,_putative_1153737..1153887_NEGATIVE 207 47 7 133 88 NC_002967:TDE1107|3end_transcription_elongation_factor_NusA_1140890..1141040_NEGATIVE 206 64 23 89 49 NC_002967:TDE1151|3end_hypothetical_protein_1188268..1188418_NEGATIVE 204 63 23 113 79 NC_002967:TDE2425|3end_50S_ribosomal_protein_L11_2454719..2454869_NEGATIVE 197 67 27 125 85 NC_002967:TDE2406|3end_TldD/PmbA_family_protein_2432047..2432197_NEGATIVE 197 57 21 104 66 NC_002967:TDE2175|3end_hypothetical_protein_2204138..2204288_NEGATIVE 196 55 23 151 120 NC_002967:TDE0354|3end_general_stress_protein_14_399001..399151_POSITIVE 195 49 2 57 8 NC_002967:TDE2562|3end_cation_ABC_transporter,_permease_protein,_putative_2589788..2589938_POSITIVE 194 82 47 133 99 NC_002967:TDE2588|3end_integrase_domain_protein_2624778..2624928_POSITIVE 192 87 42 68 23 NC_002967:TDE1741|3end_penicillin-binding_protein_1795412..1795562_POSITIVE 192 58 13 101 56 NC_002967:TDE0267|3end_HAM1_protein_298563..298713_NEGATIVE