Origin IGS: tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacctgctcttcggtttctgcagagcaaggacctgctattatgataggttggttttctttatgtggaagttctaacggttgtagttctaattccattataataatatgttgtccgttatatttttgaacta Mask Tandem Repeat Region ================================================ tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Find is-nt database================================================ Query_seq: PI1401:PI1402|PI1401:PI1402:TPR-repeat-containing protein:3-deoxy-7-phosphoheptulonate synthase:->->:1322944..1323074 131 tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1401:PI1402|PI1401:PI1402:TPR-repeat-containing protein:3-deoxy-7-phosphoheptulonate synthase:->->:1322944..1323074 131 tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1401:PI1402|PI1401:PI1402:TPR-repeat-containing protein:3-deoxy-7-phosphoheptulonate synthase:->->:1322944..1323074 131 tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 27 End: 131 .......................... M I I M E L E L Q P L E L P H K E N Q P I I I A G P C S A E T E E Q V tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta 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================================================ tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1401:PI1402|PI1401:PI1402:TPR-repeat-containing protein:3-deoxy-7-phosphoheptulonate synthase:->->:1322944..1323074 131 tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: pint_PI1401_PI1402|TPR-repeat-containing protein:3-deoxy-7-phosphoheptulonate synthase|POSITIVE:POSITIVE|[1322944,1323074]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta tagttcaaaaatataacggacaacatattattataatggaattagaactacaaccgttagaacttccacataaagaaaaccaacctatcataatagcaggtccttgctctgcagaaaccgaagagcaggta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUCAAAAAUAUAACGGACAACAUAUUAUUAUAAUGGAAUUAGAACUACAACCGUUAGAACUUCCACAUAAAGAAAACCAACCUAUCAUAAUAGCAGGUCCUUGCUCUGCAGAAACCGAAGAGCAGGUA .................((((....((((((.(((.(((((((..(((.......)))..)).)))))......(.....)....))).))))))....)))).((((((...(....)..)))))).... (-20.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCUGCUCUUCGGUUUCUGCAGAGCAAGGACCUGCUAUUAUGAUAGGUUGGUUUUCUUUAUGUGGAAGUUCUAACGGUUGUAGUUCUAAUUCCAUUAUAAUAAUAUGUUGUCCGUUAUAUUUUUGAACUA ....((((((.(((...))).)))))).(((..((..((((..((..(((((.(((((......)))))..))))).))..))))..))..)))....(((.((((((........)))))).)))..... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 127 84 132 93 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 301 129 94 231 198 pint:PI1484|5end_conserved_hypothetical_protein_1404619..1404849_POSITIVE 287 126 96 186 154 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 282 128 96 39 8 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 282 124 84 69 30 pint:PI1945|5end_ribonuclease_HII_1901932..1902162_POSITIVE 276 120 84 99 55 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 273 130 84 172 127 pint:PI2167|5end_hypothetical_protein_2111590..2111820_POSITIVE 270 130 81 74 13 pint:PI0633|5end_possible_preprotein_translocase,_YajC_subunit_579671..579901_POSITIVE 269 129 92 53 11 pint:PI1864|5end_chromate_transport_protein_1810318..1810548_POSITIVE 266 130 84 212 170 pint:PI0546|5end_hypothetical_protein_497799..498029_POSITIVE 265 127 86 196 147 pint:PI1675|5end_TonB-dependent_outer_membrane_receptor_1588107..1588337_POSITIVE 264 127 85 105 55 pint:PI1097|5end_acetyltransferase,_GNAT_family_1021443..1021673_POSITIVE 261 129 89 49 9 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 258 130 96 146 111 pint:PI1188|5end_hypothetical_protein_1108639..1108869_POSITIVE 258 126 81 57 8 pint:PI0697|5end_5'-nucleotidase_family_protein_633560..633790_POSITIVE 257 128 98 223 187 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 256 129 88 211 167 pint:PI2171|5end_conserved_hypothetical_protein_2112735..2112965_POSITIVE 256 124 85 163 126 pint:PI0359|5end_hypothetical_protein_328339..328569_POSITIVE 254 130 91 162 113 pint:PI1187|5end_conserved_hypothetical_protein_1106692..1106922_POSITIVE 252 129 85 180 127 pint:PI0222|5end_conserved_hypothetical_protein_217808..218038_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 130 96 61 25 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 303 127 84 41 2 pint:PI1008|3end_cytochrome_c_nitrite_reductase,_small_subunit_929331..929481_POSITIVE 293 130 84 110 68 pint:PI0343|3end_hypothetical_protein_317920..318070_POSITIVE 282 124 84 47 8 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 276 120 84 151 107 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 269 129 92 47 5 pint:PI1863|3end_phosphoribosylformylglycinamidine_synthase_1810392..1810542_POSITIVE 264 127 85 72 22 pint:PI1096|3end_glycosyltransferase_1021490..1021640_POSITIVE 263 130 100 31 2 pint:PI1979|3end_conserved_hypothetical_protein_1937327..1937477_POSITIVE 252 129 85 88 35 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 248 130 85 115 83 pint:PI1983|3end_possible_xylanase_1940004..1940154_POSITIVE 247 108 63 149 104 pint:PI0799|3end_alpha-amylase_family_protein_738854..739004_POSITIVE 246 130 95 61 23 pint:PI0076|3end_conserved_hypothetical_protein_76192..76342_POSITIVE 241 130 96 83 35 pint:PI1390|3end_hypothetical_protein_1311329..1311479_POSITIVE 237 129 96 142 93 pint:PI1988|3end_conserved_hypothetical_protein_1944068..1944218_POSITIVE 237 130 107 122 100 pint:PI0572|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_517589..517739_POSITIVE 237 57 14 110 69 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 236 130 89 72 30 pint:PI0904|3end_conserved_hypothetical_protein_834295..834445_POSITIVE 236 129 93 68 37 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 234 129 98 46 10 pint:PI1361|3end_CTP_synthase_(UTP-ammonia_lyase)_1279893..1280043_POSITIVE 234 128 83 70 26 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE