Origin IGS: ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attattcgtttttatttattaactttgcggtctaaaggcttctgtaggaagaacaagaaatttcagaagactttcaaagatttaagcaacaagagaaagag Mask Tandem Repeat Region ================================================ ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Find is-nt database================================================ Query_seq: PI0724:PI0725|PI0724:PI0725:DNA polymerase III, delta subunit:hypothetical protein:->->:658662..658762 101 ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0724:PI0725|PI0724:PI0725:DNA polymerase III, delta subunit:hypothetical protein:->->:658662..658762 101 ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0724:PI0725|PI0724:PI0725:DNA polymerase III, delta subunit:hypothetical protein:->->:658662..658762 101 ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. K R K N S L D K F T K Q F K K N K R C F G K S R L T L L Y F R I M ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat 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================================================ ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0724:PI0725|PI0724:PI0725:DNA polymerase III, delta subunit:hypothetical protein:->->:658662..658762 101 ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: pint_PI0724_PI0725|DNA polymerase III, delta subunit:hypothetical protein|POSITIVE:POSITIVE|[658662,658762]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat ctctttctcttgttgcttaaatctttgaaagtcttctgaaatttcttgttcttcctacagaagcctttagaccgcaaagttaataaataaaaacgaataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUUCUCUUGUUGCUUAAAUCUUUGAAAGUCUUCUGAAAUUUCUUGUUCUUCCUACAGAAGCCUUUAGACCGCAAAGUUAAUAAAUAAAAACGAAUAAU .........(((((........(((((...((((...((..(((((.((.......)))))))..)).))))..)))))............)))))..... (-11.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUCGUUUUUAUUUAUUAACUUUGCGGUCUAAAGGCUUCUGUAGGAAGAACAAGAAAUUUCAGAAGACUUUCAAAGAUUUAAGCAACAAGAGAAAGAG ........................((((.((((((((.((((((...................)))))).))))...))))....))))............ (-12.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 79 37 73 24 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 264 70 22 101 59 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 261 82 45 220 174 pint:PI1772|5end_pullulanase_1702257..1702487_POSITIVE 258 50 2 148 103 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 249 65 25 43 4 pint:PI1045|5end_cytidine/deoxycytidylate_deaminase_family_protein_965104..965334_POSITIVE 243 50 1 139 94 pint:PI2005|5end_potassium_uptake_protein_1962950..1963180_POSITIVE 238 74 37 182 138 pint:PI1787|5end_conserved_hypothetical_protein_1718414..1718644_POSITIVE 238 46 1 183 132 pint:PI1216|5end_probable_phosphohydrolase_1134814..1135044_POSITIVE 234 48 1 188 140 pint:PI0764|5end_permease_697962..698192_POSITIVE 224 78 48 159 121 pint:PI2167|5end_hypothetical_protein_2111590..2111820_POSITIVE 224 67 25 72 33 pint:PI0095|5end_hypothetical_protein_91444..91674_POSITIVE 222 77 56 39 22 pint:PI1160|5end_possible_phosphatidylinositol-4-phosphate_5-kinase_1084756..1084986_POSITIVE 221 73 33 186 148 pint:PI0857|5end_hypothetical_protein_790697..790927_POSITIVE 218 50 3 162 108 pint:PI0730|5end_hypothetical_protein_661685..661915_POSITIVE 218 56 13 137 102 pint:PI0528|5end_hypothetical_protein_482791..483021_POSITIVE 217 81 45 190 156 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 216 76 31 227 179 pint:PI1420|5end_probable_membrane_protein_1340123..1340353_POSITIVE 215 80 45 203 162 pint:PI1777|5end_conserved_hypothetical_protein_1709402..1709632_POSITIVE 214 72 34 39 5 pint:PI1880|5end_phosphoenolpyruvate_carboxykinase_(ATP)_1821667..1821897_POSITIVE 214 80 32 68 31 pint:PI1665|5end_thymidylate_synthase_1578086..1578316_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 75 38 133 96 pint:PI0121|3end_outer_membrane_protein,_ompH_family_113208..113358_POSITIVE 265 79 37 150 101 pint:PI0783|3end_hypothetical_protein_723397..723547_POSITIVE 265 79 37 56 7 pint:PI0784|3end_possible_amidase_enhancer_precursor_723303..723453_POSITIVE 264 70 22 98 56 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 243 50 1 113 68 pint:PI2004|3end_1-deoxy-D-xylulose_5-phosphate_synthase_1963004..1963154_POSITIVE 238 74 37 68 24 pint:PI1786|3end_hypothetical_protein_1718380..1718530_POSITIVE 234 41 1 126 77 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE 234 48 1 148 100 pint:PI0763|3end_thymidine_kinase_698002..698152_POSITIVE 228 69 21 140 92 pint:PI1771|3end_alpha-glucosidase_1702274..1702424_POSITIVE 228 78 33 80 26 pint:PI0974|3end_hypothetical_protein_899591..899741_POSITIVE 224 67 25 85 46 pint:PI0093|3end_riboflavin_biosynthesis_protein_91537..91687_POSITIVE 218 75 32 121 72 pint:PI0770|3end_hypothetical_protein_706354..706504_POSITIVE 215 80 45 146 105 pint:PI1776|3end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1709425..1709575_POSITIVE 211 50 1 82 31 pint:PI0195|3end_epimerase/reductase_188202..188352_POSITIVE 210 80 31 80 27 pint:PI0987|3end_hypothetical_protein_912284..912434_POSITIVE 209 85 45 123 76 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 209 59 14 114 62 pint:PI0661|3end_hypothetical_protein_604215..604365_POSITIVE 208 53 11 107 65 pint:PI1847|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1793849..1793999_POSITIVE 206 63 23 151 117 pint:PI1496|3end_nucleoside_phosphorylase_1417816..1417966_POSITIVE 206 50 4 80 30 pint:PI0146|3end_transcription_elongation_factor_140885..141035_POSITIVE