Origin IGS: tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatcaggtcaaactgaaaaacggaacaccattaaaagtaattctaagcggttataaagtattaaagagatagttataatagatatgtgcggctattaccccttatacaagcgtaaacattttttatattttgcgttcgcttttgttatgattatttaacttatttgttcttgacaaataagaggtatgactgtatctttgcatcgtggttttttcataatagtattagatttaaggttaacaaagtgggttagaggctgtcgtgagatagcctttaatttttttatatctgtttca Mask Tandem Repeat Region ================================================ tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Find is-nt database================================================ Query_seq: TF1810:TF1811|TF1810:TF1811:conserved hypothetical protein; possible membrane protein:hypothetical protein:->->:1952367..1952662 296 tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1810:TF1811|TF1810:TF1811:conserved hypothetical protein; possible membrane protein:hypothetical protein:->->:1952367..1952662 296 tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1810:TF1811|TF1810:TF1811:conserved hypothetical protein; possible membrane protein:hypothetical protein:->->:1952367..1952662 296 tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 11 End: 139 .......... M K K L K A I S R Q P L T H F V N L K S N T I M K K P R C K D T V I P L I C Q E Q I S ............................................................................................................................................................. Protein_Len: 32 Strand: - Start: 142 End: 237 ............................................................................................................................................. I I M V F A F A F Y L F H K R K Y L P Y Y G C M D I I V I E K M ........................................................... Protein_Len: 42 Strand: - Start: 47 End: 172 .............................................. G V K N V K F R I S N H F F W S A F I C D Y R K N T L F L Y T L Y D Y C F R V C F M ............................................................................................................................ Protein_Len: 40 Strand: - Start: 1 End: 120 S V S I F F N F A I E R C G R V W K T L R L D L V I I F F G R H L S V T M G R M ................................................................................................................................................................................ tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata 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: 85 Start: 99 End: 128 ..................................................................................................CTTGACAAATAAGAGGTATGACTGTATCTT........................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 218 End: 247 .........................................................................................................................................................................................................................GTTATAAAGTATTAAAGAGATAGTTATAAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.0 Tail_Score: -5.77988 Start: 20 End: 47 Full_Region: ggttaacaaagtggg ttagaggctgtc gtga gatagcctttaa tttttttatatctgt ...................ttagaggctgtcgtgagatagcctttaa......................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF1810:TF1811|TF1810:TF1811:conserved hypothetical protein; possible membrane protein:hypothetical protein:->->:1952367..1952662 296 tgaaacagatataaaaaaattaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Intra-Species Hit: Count: 1 Min: 20 Max: 296 Len: 277 Subject: tfor_TF1810_TF1811|conserved hypothetical protein; possible membrane protein:hypothetical protein|POSITIVE:POSITIVE|[1952367,1952662]|296 HSP 1 e-value: 1.0E-155 bit: 549.0 Len: 277 Query Start:20 Query End:296 Subject Strand: POSITIVE Subject Start: 20 Subject End: 296 ...................ttaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata ...................ttaaaggctatctcacgacagcctctaacccactttgttaaccttaaatctaatactattatgaaaaaaccacgatgcaaagatacagtcatacctcttatttgtcaagaacaaataagttaaataatcataacaaaagcgaacgcaaaatataaaaaatgtttacgcttgtataaggggtaatagccgcacatatctattataactatctctttaatactttataaccgcttagaattacttttaatggtgttccgtttttcagtttgacctgata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAGGCUAUCUCACGACAGCCUCUAACCCACUUUGUUAACCUUAAAUCUAAUACUAUUAUGAAAAAACCACGAUGCAAAGAUACAGUCAUACCUCUUAUUUGUCAAGAACAAAUAAGUUAAAUAAUCAUAACAAAAGCGAACGCAAAAUAUAAAAAAUGUUUACGCUUGUAUAAGGGGUAAUAGCCGCACAUAUCUAUUAUAACUAUCUCUUUAAUACUUUAUAACCGCUUAGAAUUACUUUUAAUGGUGUUCCGUUUUUCAGUUUGACCUGAUA (((.(((((.((....)).))))).)))....((((((..............(((....)))..............))))))...((((((.((..(((((((((.....)))))))))...............((((((((((((...((.(((((....((((.((...(((((((.(((((((..........)))))))................)))))))...)).)))).....))))))).))))).)))))))..)).))).)))... (-44.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCAGGUCAAACUGAAAAACGGAACACCAUUAAAAGUAAUUCUAAGCGGUUAUAAAGUAUUAAAGAGAUAGUUAUAAUAGAUAUGUGCGGCUAUUACCCCUUAUACAAGCGUAAACAUUUUUUAUAUUUUGCGUUCGCUUUUGUUAUGAUUAUUUAACUUAUUUGUUCUUGACAAAUAAGAGGUAUGACUGUAUCUUUGCAUCGUGGUUUUUUCAUAAUAGUAUUAGAUUUAAGGUUAACAAAGUGGGUUAGAGGCUGUCGUGAGAUAGCCUUUAA ..((((......))))...........(((((.....((((..((.(((((((((...........((((((((((((((((...(((.((......)).........((((((((............))))))))))).))))))))))))))))..((((((((((...))))))))))...))))))))).(((.(((((..(((.....)))..)).)))..)))..))..))))....)))))..(((((((((((....))))))))))). (-69.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 191 160 50 14 tfor:TF1518|5end_peroxiredoxin_1627036..1627266_POSITIVE 268 199 161 175 136 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 257 190 156 101 53 tfor:TF2690|5end_possible_permease_2865466..2865696_POSITIVE 253 180 138 50 5 tfor:TF3065|5end_enolase_3291055..3291285_POSITIVE 250 191 162 230 202 tfor:TF1077|5end_conserved_hypothetical_protein_1146382..1146612_POSITIVE 246 189 162 94 68 tfor:TF1604|5end_possible_anti-sigma_factor_1717811..1718041_POSITIVE 245 197 167 215 184 tfor:TF1705|5end_conserved_hypothetical_protein;_possible_DNA_helicase_1827214..1827444_POSITIVE 244 197 158 64 25 tfor:TF1215|5end_haloacid_dehalogenase-like_hydrolase_1302510..1302740_POSITIVE 243 193 159 58 27 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 243 44 6 66 32 tfor:TF2576|5end_translation_initiation_factor_IF-1_2745912..2746142_POSITIVE 242 50 3 195 149 tfor:TF1245|5end_LemA_protein_1328822..1329052_POSITIVE 240 97 56 178 131 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 240 48 1 127 66 tfor:TF1317|5end_hypothetical_protein_1391378..1391608_POSITIVE 239 190 144 176 117 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 239 194 160 145 109 tfor:TF2051|5end_hypothetical_protein_2215183..2215413_POSITIVE 238 200 158 214 160 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 238 37 4 211 177 tfor:TF0932|5end_hypothitical_protein_972167..972397_POSITIVE 237 198 166 42 13 tfor:TF2768|5end_ferredoxin_oxidoreductase,_beta_subunit_2954076..2954306_POSITIVE 237 108 75 167 134 tfor:TF0105|5end_DNA-binding_stress_protein,_Dps_family_113354..113584_POSITIVE 236 262 228 89 56 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 50 5 81 25 tfor:TF0383|3end_alkyl_hydroperoxide_reductase,_subunit_C_406056..406206_POSITIVE 321 85 50 31 1 tfor:TF0787|3end_possible_inorganic_polyphosphate;_ATP-NAD_kinase_840344..840494_POSITIVE 290 32 5 148 109 tfor:TF0384|3end_conserved_hypothetical_protein_406140..406290_POSITIVE 269 188 141 81 28 tfor:TF2161|3end_conserved_hypothetical_protein_2338362..2338512_POSITIVE 257 190 156 88 40 tfor:TF2689|3end_hypothetical_protein_2865533..2865683_POSITIVE 257 34 5 53 15 tfor:TF0428|3end_methylmalonyl-CoA_mutase,_beta_subunit_450033..450183_POSITIVE 247 26 5 138 110 tfor:TF2047|3end_hypothetical_protein_2210298..2210448_POSITIVE 246 189 162 49 23 tfor:TF1603|3end_RNA_polymerase_ECF-type_sigma_factor_1717846..1717996_POSITIVE 243 44 6 59 25 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 242 198 166 140 104 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 242 50 3 106 60 tfor:TF1244|3end_hypothetical_protein_1328813..1328963_POSITIVE 240 97 56 146 99 tfor:TF2127|3end_hypothetical_protein_2304306..2304456_POSITIVE 239 195 177 67 45 tfor:TF1755|3end_periplasmic_protease_1892867..1893017_POSITIVE 237 198 166 37 8 tfor:TF2767|3end_2-oxoglutarate_synthase,_alpha_subunit_2954151..2954301_POSITIVE 237 108 75 41 8 tfor:TF0104|3end_redox-sensitive_transcriptional_activator,_OxyR_113308..113458_POSITIVE 236 50 9 63 22 tfor:TF2985|3end_glycosyltransferase_protein_3201646..3201796_POSITIVE 236 262 228 78 45 tfor:TF0764|3end_conserved_hypothetical_protein;_possible_exopolyphosphatase-related_protein_811371..811521_POSITIVE 235 39 16 147 119 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 231 46 4 52 7 tfor:TF2304|3end_OmpA_family_protein_2461415..2461565_POSITIVE 230 59 16 88 44 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE