Origin IGS: taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggaagaatacaagacgatgattataagagcgtgatttatcacgctcttatcattaagtttcccttttaaaattactgttatttgctttgcagggtattagaataatgtgggtaaaagctgtgtaacagaattcggacgcacgttatta Mask Tandem Repeat Region ================================================ taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Find is-nt database================================================ Query_seq: PI0019:PI0020|PI0019:PI0020:conserved hypothetical protein:conserved hypothetical protein:->->:24515..24664 150 taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0019:PI0020|PI0019:PI0020:conserved hypothetical protein:conserved hypothetical protein:->->:24515..24664 150 taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0019:PI0020|PI0019:PI0020:conserved hypothetical protein:conserved hypothetical protein:->->:24515..24664 150 taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Predict ORF larger than 30AA ================================================ taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta 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================================================ taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -12.2 Tail_Score: -3.4529 Start: 103 End: 122 Full_Region: GAAACTTAATGATAA GAGCGTGA TAAA TCACGCTC TTATAATCATCGTCT ......................................................................................................GAGCGTGATAAATCACGCTC............................ Find igs database================================================ Query_seq: PI0019:PI0020|PI0019:PI0020:conserved hypothetical protein:conserved hypothetical protein:->->:24515..24664 150 taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: pint_PI0019_PI0020|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[24515,24664]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta taataacgtgcgtccgaattctgttacacagcttttacccacattattctaataccctgcaaagcaaataacagtaattttaaaagggaaacttaatgataagagcgtgataaatcacgctcttataatcatcgtcttgtattcttccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAACGUGCGUCCGAAUUCUGUUACACAGCUUUUACCCACAUUAUUCUAAUACCCUGCAAAGCAAAUAACAGUAAUUUUAAAAGGGAAACUUAAUGAUAAGAGCGUGAUAAAUCACGCUCUUAUAAUCAUCGUCUUGUAUUCUUCCUA .(((((.(((.((..(((..(((.....)))..))))).))).))))).........(((((..(...................(((....)))....((((((((((((....)))))))))))).......)..)))))......... (-33.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAAGAAUACAAGACGAUGAUUAUAAGAGCGUGAUUUAUCACGCUCUUAUCAUUAAGUUUCCCUUUUAAAAUUACUGUUAUUUGCUUUGCAGGGUAUUAGAAUAAUGUGGGUAAAAGCUGUGUAACAGAAUUCGGACGCACGUUAUUA .......(((((.((((..((((.((((((((((((....)))))))))))).)))).))))..............((((..........)))).)))))..(((((((((.((.....(((.....))).......)).))))))))). (-40.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 145 103 188 146 pint:PI0902|5end_hypothetical_protein_832291..832521_POSITIVE 316 149 103 206 158 pint:PI0866|5end_hypothetical_protein_803776..804006_POSITIVE 315 48 5 159 113 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 289 150 103 211 166 pint:PI1041|5end_hypothetical_protein_960443..960673_POSITIVE 288 126 92 124 90 pint:PI0118|5end_hypothetical_protein_111321..111551_POSITIVE 285 48 11 152 109 pint:PI1735|5end_conserved_hypothetical_protein_1653428..1653658_POSITIVE 277 140 98 193 152 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 263 60 11 128 74 pint:PI0616|5end_electron_transfer_flavoprotein,_beta-subunit_565560..565790_POSITIVE 259 58 14 187 131 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 259 58 14 75 19 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 256 57 26 152 125 pint:PI0799|5end_alpha-amylase_family_protein_737083..737313_POSITIVE 250 128 88 223 183 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 249 140 93 167 124 pint:PI1209|5end_phosphate_starvation-inducible_protein,_phoH_family_1127959..1128189_POSITIVE 236 129 85 142 96 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 233 42 6 158 124 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 233 42 6 55 21 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 230 121 85 170 126 pint:PI2112|5end_phosphopantetheine_adenylyltransferase_2063194..2063424_POSITIVE 227 140 91 104 48 pint:PI1928|5end_conserved_hypothetical_protein_1871996..1872226_POSITIVE 227 50 7 193 150 pint:PI0449|5end_hypothetical_protein_422952..423182_POSITIVE 226 42 5 55 15 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 128 98 75 45 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 331 149 103 75 28 pint:PI2088|3end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_2045815..2045965_POSITIVE 298 39 5 139 103 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 288 126 92 37 3 pint:PI0117|3end_ribonuclease_HI_111314..111464_POSITIVE 267 150 103 67 17 pint:PI0962|3end_phosphoglycerate_mutase_892702..892852_POSITIVE 262 43 7 99 66 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 256 126 84 91 44 pint:PI1820|3end_hypothetical_protein_1760377..1760527_POSITIVE 250 64 21 118 81 pint:PI0215|3end_hypothetical_protein_209004..209154_POSITIVE 241 66 21 104 35 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 233 69 21 119 60 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 227 140 91 74 18 pint:PI1927|3end_hypothetical_protein_1872046..1872196_POSITIVE 226 42 5 65 25 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 223 119 87 39 6 pint:PI0932|3end_conserved_hypothetical_protein;_possible_hemin_receptor_865364..865514_POSITIVE 222 146 101 146 97 pint:PI1565|3end_conserved_hypothetical_protein;_possible_surface_antigen_1487357..1487507_POSITIVE 220 124 92 115 88 pint:PI1679|3end_hypothetical_protein_1594964..1595114_POSITIVE 219 64 22 47 8 pint:PI0660|3end_conserved_hypothetical_protein_603997..604147_POSITIVE 215 119 85 64 35 pint:PI2149|3end_3-oxoacyl-acyl-carrier-protein_synthase_2096793..2096943_POSITIVE 215 140 92 128 89 pint:PI2018|3end_50S_ribosomal_protein_L34_1975989..1976139_POSITIVE 215 127 85 81 26 pint:PI1222|3end_hypothetical_protein_1143378..1143528_POSITIVE 213 120 77 148 100 pint:PI1252|3end_hypothetical_protein_1175440..1175590_POSITIVE