Origin IGS: aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacaattaggaaaaagggtgcaagtaacattgtatccgaaactaaaaataaagagacggcataacaaatatgccgcctctttataatgtataaaggcacattgaaataaagtttattcattattaatt Mask Tandem Repeat Region ================================================ aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Find is-nt database================================================ Query_seq: PI0562:PI0563|PI0562:PI0563:conserved hypothetical protein:possible integral membrane protein:->->:510259..510387 129 aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0562:PI0563|PI0562:PI0563:conserved hypothetical protein:possible integral membrane protein:->->:510259..510387 129 aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0562:PI0563|PI0562:PI0563:conserved hypothetical protein:possible integral membrane protein:->->:510259..510387 129 aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 38 End: 127 ..................................... M H Y K E A A Y L L C R L F I F S F G Y N V T C T L F P N C .. Protein_Len: 41 Strand: + Start: 6 End: 128 ..... M M N K L Y F N V P L Y I I K R R H I C Y A V S L F L V S D T M L L A P F F L I V . aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta 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================================================ aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.7 Tail_Score: -4.99134 Start: 46 End: 80 Full_Region: TGCCTTTATACATTA TAAAGAGGCGGCATA TTTGT TATGCCGTCTCTTTA TTTTTAGTTTCGGAT .............................................TAAAGAGGCGGCATATTTGTTATGCCGTCTCTTTA................................................. TransTerm Strand: + Conf: 100 HP_score: -13.1 Tail_Score: -5.00388 Start: 50 End: 76 Full_Region: TTTATACATTATAAA GAGGCGGCATA TTTGT TATGCCGTCTC TTTATTTTTAGTTTC .................................................GAGGCGGCATATTTGTTATGCCGTCTC..................................................... TransTerm Strand: - Conf: 93 HP_score: -10.9 Tail_Score: -4.04318 Start: 50 End: 76 Full_Region: gaaactaaaaataaa gagacggcata acaaa tatgccgcctc tttataatgtataaa .................................................gagacggcataacaaatatgccgcctc..................................................... Find igs database================================================ Query_seq: PI0562:PI0563|PI0562:PI0563:conserved hypothetical protein:possible integral membrane protein:->->:510259..510387 129 aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: pint_PI0562_PI0563|conserved hypothetical protein:possible integral membrane protein|POSITIVE:POSITIVE|[510259,510387]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta aattaataatgaataaactttatttcaatgtgcctttatacattataaagaggcggcatatttgttatgccgtctctttatttttagtttcggatacaatgttacttgcaccctttttcctaattgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAUAAUGAAUAAACUUUAUUUCAAUGUGCCUUUAUACAUUAUAAAGAGGCGGCAUAUUUGUUAUGCCGUCUCUUUAUUUUUAGUUUCGGAUACAAUGUUACUUGCACCCUUUUUCCUAAUUGUUA ...(((((((....(((((.......((((((......)))))).(((((((((((((((.....))))))))))))))).....))))).(((.....(((.....))).......)))..))))))) (-31.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAUUAGGAAAAAGGGUGCAAGUAACAUUGUAUCCGAAACUAAAAAUAAAGAGACGGCAUAACAAAUAUGCCGCCUCUUUAUAAUGUAUAAAGGCACAUUGAAAUAAAGUUUAUUCAUUAUUAAUU ..........(((...((((((((......)))))))).(((((.....(((((((.(((((((.....))))))).)))))))((((((........))))))......))))).))).......... (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 74 51 204 178 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 289 75 52 126 103 pint:PI0701|5end_hypothetical_protein_638356..638586_POSITIVE 266 80 31 178 125 pint:PI0620|5end_hypothetical_protein_569729..569959_POSITIVE 262 55 11 145 89 pint:PI2057|5end_conserved_hypothetical_protein;_possible_metal-dependent_membrane_protease_2014939..2015169_POSITIVE 261 93 51 51 10 pint:PI0692|5end_iron_compound_ABC_transporter,_permease_protein_627350..627580_POSITIVE 260 79 35 152 111 pint:PI0765|5end_conserved_hypothetical_protein;_possible_surface_protein_699753..699983_POSITIVE 256 89 49 134 95 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 253 95 52 202 142 pint:PI1669|5end_hypothetical_protein_1581257..1581487_POSITIVE 252 76 31 179 140 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 251 71 31 55 15 pint:PI0945|5end_sodium:solute_symporter_family_protein_876249..876479_POSITIVE 247 98 52 114 74 pint:PI0977|5end_riboflavin_synthase,_alpha_subunit_904043..904273_POSITIVE 245 91 52 114 67 pint:PI0051|5end_hypothetical_protein_52607..52837_POSITIVE 243 78 31 72 16 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 242 57 31 57 35 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 238 94 51 195 157 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 238 108 64 204 156 pint:PI0220|5end_conserved_hypothetical_protein_211980..212210_POSITIVE 238 75 32 226 177 pint:PI0026|5end_two-component_system_response_regulator_29756..29986_POSITIVE 237 109 61 176 124 pint:PI0959|5end_uridine_kinase_890495..890725_POSITIVE 234 92 53 178 138 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 233 114 72 173 120 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 445 81 45 46 10 pint:PI0562|3end_conserved_hypothetical_protein_510198..510348_POSITIVE 289 75 52 103 80 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE 270 80 38 68 25 pint:PI1003|3end_conserved_hypothetical_protein_925718..925868_POSITIVE 264 74 49 138 114 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 258 97 51 43 3 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 249 97 51 100 51 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 245 91 52 142 95 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 245 91 52 98 51 pint:PI0050|3end_conserved_hypothetical_protein_52671..52821_POSITIVE 244 58 18 134 100 pint:PI2014|3end_conserved_hypothetical_protein_1972603..1972753_POSITIVE 242 57 31 54 32 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 239 74 38 141 103 pint:PI1838|3end_conserved_hypothetical_protein_1782028..1782178_POSITIVE 233 90 47 69 20 pint:PI0618|3end_acyl-CoA_dehydrogenase_family_protein_569213..569363_POSITIVE 232 78 31 64 17 pint:PI1101|3end_hypothetical_protein_1025315..1025465_POSITIVE 231 72 33 106 55 pint:PI1372|3end_thiamine_monophosphate_kinase_1293971..1294121_POSITIVE 230 58 18 151 117 pint:PI1771|3end_alpha-glucosidase_1702274..1702424_POSITIVE 230 72 52 22 1 pint:PI1632|3end_hypothetical_protein_1553222..1553372_POSITIVE 230 72 52 22 1 pint:PI0339|3end_hypothetical_protein_316138..316288_POSITIVE 230 85 45 88 35 pint:PI0141|3end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_133308..133458_POSITIVE 226 99 51 71 2 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 225 83 50 141 93 pint:PI1050|3end_conserved_hypothetical_protein_969698..969848_POSITIVE