Origin IGS: aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagccgacagttgcccatttaattggttataacaaataagaaacaatacaatcttcgcaaaatatggcagaagaattagatatgaaacgcataccgcaacacattgccatcatt Mask Tandem Repeat Region ================================================ aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Find is-nt database================================================ Query_seq: PI0125:PI0126|PI0125:PI0126:undecaprenyl pyrophosphate synthase:conserved hypothetical protein:->->:117951..118064 114 aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0125:PI0126|PI0125:PI0126:undecaprenyl pyrophosphate synthase:conserved hypothetical protein:->->:117951..118064 114 aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0125:PI0126|PI0125:PI0126:undecaprenyl pyrophosphate synthase:conserved hypothetical protein:->->:117951..118064 114 aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Predict ORF larger than 30AA ================================================ aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta 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================================================ aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0125:PI0126|PI0125:PI0126:undecaprenyl pyrophosphate synthase:conserved hypothetical protein:->->:117951..118064 114 aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: pint_PI0125_PI0126|undecaprenyl pyrophosphate synthase:conserved hypothetical protein|POSITIVE:POSITIVE|[117951,118064]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta aatgatggcaatgtgttgcggtatgcgtttcatatctaattcttctgccatattttgcgaagattgtattgtttcttatttgttataaccaattaaatgggcaactgtcggcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUGGCAAUGUGUUGCGGUAUGCGUUUCAUAUCUAAUUCUUCUGCCAUAUUUUGCGAAGAUUGUAUUGUUUCUUAUUUGUUAUAACCAAUUAAAUGGGCAACUGUCGGCUA ....((((((..(.((((.((((((.....)))))))))).)...)))))).....((...(((......(((.((((((((...........)))))))).))).))).)).. (-19.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCCGACAGUUGCCCAUUUAAUUGGUUAUAACAAAUAAGAAACAAUACAAUCUUCGCAAAAUAUGGCAGAAGAAUUAGAUAUGAAACGCAUACCGCAACACAUUGCCAUCAUU .........(((((...((((.(((.......))).))))...........(((((((........)).)))))......((((.....))))..))))).............. (-14.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 49 2 194 134 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 308 45 1 116 74 pint:PI2049|5end_possible_transcriptional_regulator,_AraC_family_2002502..2002732_POSITIVE 305 58 13 193 141 pint:PI1646|5end_hypothetical_protein_1561954..1562184_POSITIVE 298 48 7 85 54 pint:PI0616|5end_electron_transfer_flavoprotein,_beta-subunit_565560..565790_POSITIVE 296 60 12 228 185 pint:PI0706|5end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_642226..642456_POSITIVE 296 60 11 72 16 pint:PI0587|5end_conserved_hypothetical_protein_534416..534646_POSITIVE 290 59 11 98 45 pint:PI2102|5end_DNA_topoisomerase_IV,_subunit_B_2055706..2055936_POSITIVE 286 59 14 182 142 pint:PI0596|5end_hypothetical_protein_546400..546630_POSITIVE 285 50 3 49 10 pint:PI1430|5end_subtilisin-like_serine_proteinase_1349598..1349828_POSITIVE 285 58 18 201 173 pint:PI0495|5end_conserved_hypothetical_protein_454872..455102_POSITIVE 285 58 18 192 164 pint:PI0494|5end_hypothetical_protein_454863..455093_POSITIVE 284 49 1 183 126 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 276 48 6 105 61 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 275 50 3 181 132 pint:PI2158|5end_glycosyl_transferase,_group_2_family_protein_2104392..2104622_POSITIVE 271 50 3 152 108 pint:PI2065|5end_hypothetical_protein_2026877..2027107_POSITIVE 269 60 12 100 50 pint:PI1828|5end_peptidase,_M23/M37_family,_C-terminal_1768419..1768649_POSITIVE 269 48 5 53 3 pint:PI0042|5end_hypothetical_protein_42981..43211_POSITIVE 267 58 14 79 37 pint:PI1628|5end_hypothetical_protein_1551082..1551312_POSITIVE 266 47 3 50 13 pint:PI1937|5end_hypothetical_protein_1889411..1889641_POSITIVE 266 74 40 110 79 pint:PI0966|5end_possible_glycosyl_hydrolase_894407..894637_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 45 1 100 58 pint:PI2048|3end_possible_two-component_system_sensor_histidine_kinase_2002566..2002716_POSITIVE 290 59 11 62 9 pint:PI2101|3end_conserved_hypothetical_protein_2055750..2055900_POSITIVE 289 59 19 123 86 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 287 59 11 104 57 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE 286 59 14 108 68 pint:PI0595|3end_conserved_hypothetical_protein_546406..546556_POSITIVE 284 49 1 144 87 pint:PI0170|3end_hypothetical_protein_163891..164041_POSITIVE 269 32 5 135 106 pint:PI0692|3end_iron_compound_ABC_transporter,_permease_protein_628269..628419_POSITIVE 269 48 5 148 98 pint:PI0043|3end_thiamine_phosphate_pyrophosphorylase_43156..43306_POSITIVE 267 58 14 74 32 pint:PI1627|3end_hypothetical_protein_1551157..1551307_POSITIVE 266 47 3 47 10 pint:PI1936|3end_conserved_hypothetical_protein;_possible_serine-type_protease_1889488..1889638_POSITIVE 266 50 6 145 102 pint:PI0601|3end_hypothetical_protein_549020..549170_POSITIVE 259 59 13 144 91 pint:PI0309|3end_hypothetical_protein_291729..291879_POSITIVE 251 50 4 151 88 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 247 51 15 111 73 pint:PI0875|3end_conserved_hypothetical_protein_811437..811587_POSITIVE 247 50 5 140 91 pint:PI0788|3end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726789..726939_POSITIVE 243 59 11 131 77 pint:PI1835|3end_L-asparaginase_I_1777276..1777426_POSITIVE 242 60 16 44 2 pint:PI0888|3end_hypothetical_protein_818613..818763_POSITIVE 241 53 11 116 76 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 239 59 16 147 104 pint:PI1713|3end_ABC_transporter,_ATP-binding_protein_1630192..1630342_POSITIVE 237 60 17 127 77 pint:PI0284|3end_flavoprotein_A_270157..270307_POSITIVE