Origin IGS: gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttagattagtccgttcgttattattatgatttggatagttcttacttatgacaaaaagcgataaccgactccttctccgagcttccggaaggggccgttttttgttgtaaactgcaaattaacgaaaaaagagcaagatacgctactttccaccacccctcaaaccc Mask Tandem Repeat Region ================================================ gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Find is-nt database================================================ Query_seq: PG1015:PG1017|PG1015:PG1017:hypothetical protein:pyruvate phosphate dikinase:<-->:1076111..1076277 167 gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1015:PG1017|PG1015:PG1017:hypothetical protein:pyruvate phosphate dikinase:<-->:1076111..1076277 167 gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1015:PG1017|PG1015:PG1017:hypothetical protein:pyruvate phosphate dikinase:<-->:1076111..1076277 167 gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 12 End: 119 ........... M V E S S V S C S F F V N L Q F T T K N G P F R K L G E G V G Y R F L S ................................................ Protein_Len: 35 Strand: - Start: 3 End: 107 .. N S P H H F T A Y R A R K E N I Q L K C C F V A G E P L E S F S D T M ............................................................ gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa 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================================================ gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 90 HP_score: -5.8 Tail_Score: -5.55769 Start: 71 End: 102 Full_Region: acaaaaagcgataac cgactccttctccga gct tccggaaggggccg ttttttgttgtaaac ......................................................................cgactccttctccgagcttccggaaggggccg................................................................. Find igs database================================================ Query_seq: PG1015:PG1017|PG1015:PG1017:hypothetical protein:pyruvate phosphate dikinase:<-->:1076111..1076277 167 gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_002950_PG1015_PG1017|hypothetical protein:pyruvate phosphate dikinase|NEGATIVE:POSITIVE|[1076111,1076277]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa gggtttgaggggtggtggaaagtagcgtatcttgctcttttttcgttaatttgcagtttacaacaaaaaacggccccttccggaagctcggagaaggagtcggttatcgctttttgtcataagtaagaactatccaaatcataataataacgaacggactaatctaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUUUGAGGGGUGGUGGAAAGUAGCGUAUCUUGCUCUUUUUUCGUUAAUUUGCAGUUUACAACAAAAAACGGCCCCUUCCGGAAGCUCGGAGAAGGAGUCGGUUAUCGCUUUUUGUCAUAAGUAAGAACUAUCCAAAUCAUAAUAAUAACGAACGGACUAAUCUAA .((((((.(((((.((.(((((.((((.....)))))))))...((......))...............)).))))).(((((....)))))...(((...((((...((((........))))...)))).)))...................))))))....... (-36.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGAUUAGUCCGUUCGUUAUUAUUAUGAUUUGGAUAGUUCUUACUUAUGACAAAAAGCGAUAACCGACUCCUUCUCCGAGCUUCCGGAAGGGGCCGUUUUUUGUUGUAAACUGCAAAUUAACGAAAAAAGAGCAAGAUACGCUACUUUCCACCACCCCUCAAACCC ..(((...(((((.((((.......))))..)))))...)))...(((..((((((((((......(.(((((..((((......))))))))))))))))))))..))).................(((((((.......))).)))).................. (-34.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1055 120 71 211 162 NC_002950:PG1015|5end_hypothetical_protein_1076020..1076250_NEGATIVE 400 120 71 52 4 NC_002950:PG1063|5end_transcriptional_regulator,_putative_1131056..1131286_POSITIVE 383 113 71 68 19 NC_002950:PG1288|5end_GDP-mannose_4,6-dehydratase_1365963..1366193_POSITIVE 373 120 71 63 7 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 371 115 71 145 102 NC_002950:PG1143|5end_sugar_dehydrogenase,_UDP-glucose/GDP-mannose_dehydrogenase_family_1227198..1227428_NEGATIVE 368 114 71 208 158 NC_002950:PG0531|5end_NAD(+)_synthetase_581139..581369_NEGATIVE 359 119 71 149 99 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 353 115 72 231 181 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 352 120 71 91 46 NC_002950:PG0144|5end_hypothetical_protein_167668..167898_NEGATIVE 348 113 86 29 1 NC_002950:PG0135|5end_dimethyladenosine_transferase_157943..158173_NEGATIVE 345 120 72 91 36 NC_002950:PG1728|5end_cytidine/deoxycytidylate_deaminase_family_protein_1817644..1817874_POSITIVE 344 109 71 101 55 NC_002950:PG2139|5end_hypothetical_protein_2245648..2245878_POSITIVE 344 116 74 199 152 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 343 120 82 216 172 NC_002950:PG0579|5end_cell_division_protein_FtsW,_putative_635844..636074_POSITIVE 342 112 71 179 123 NC_002950:PG1248|5end_hypothetical_protein_1326532..1326762_NEGATIVE 338 114 71 217 165 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 337 118 73 103 50 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 336 98 53 180 123 NC_002950:PG0401|5end_hypothetical_protein_439306..439536_NEGATIVE 334 120 71 210 139 NC_002950:PG1868|5end_hypothetical_protein_1965619..1965849_NEGATIVE 333 113 71 204 162 NC_002950:PG2110|5end_thiamine_biosynthesis_protein_ThiC_2221212..2221442_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 114 71 66 19 NC_002950:PG1755|3end_fructose-bisphosphate_aldolase_1842397..1842547_NEGATIVE 374 109 64 68 31 NC_002950:PG0052|3end_sensor_histidine_kinase_64686..64836_POSITIVE 368 114 71 98 48 NC_002950:PG0532|3end_hypothetical_protein_581249..581399_NEGATIVE 357 120 71 85 35 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 340 117 71 107 66 NC_002950:PG0627|3end_RNA-binding_protein_681142..681292_NEGATIVE 338 111 71 147 95 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE 337 118 73 90 37 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 335 116 72 106 31 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 333 113 71 134 92 NC_002950:PG2111|3end_thiS_protein_2221282..2221432_NEGATIVE 333 96 52 151 109 NC_002950:PG0822|3end_hypothetical_protein_880328..880478_NEGATIVE 332 116 72 103 61 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 332 103 74 68 42 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 325 109 73 84 46 NC_002950:PG1359|3end_hypothetical_protein_1437644..1437794_NEGATIVE 323 105 71 147 108 NC_002950:PG1249|3end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase,_putative_1326547..1326697_NEGATIVE 321 45 1 101 53 NC_002950:PG1556|3end_hypothetical_protein_1637001..1637151_POSITIVE 321 119 71 107 61 NC_002950:PG0626|3end_hypothetical_protein_680346..680496_POSITIVE 316 120 71 78 6 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 316 119 72 140 95 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 315 103 71 121 81 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 314 118 71 144 92 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE