Origin IGS: ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atattgaattatttataaaatatgtgtataattaaagatatgtaaaagttttaggaggatagaaagaaatggttagaaaactaaaaggaacaaaaacagcaggaggaaaccaagctgatattgttaaacaagcacaagtaatgcaacaacag Mask Tandem Repeat Region ================================================ ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Find is-nt database================================================ Query_seq: FN1270:FN1271|FN1270:FN1271:Hypothetical cytosolic protein:Protease IV:<-<-:1926683..1926834 152 ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1270:FN1271|FN1270:FN1271:Hypothetical cytosolic protein:Protease IV:<-<-:1926683..1926834 152 ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1270:FN1271|FN1270:FN1271:Hypothetical cytosolic protein:Protease IV:<-<-:1926683..1926834 152 ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 11 End: 118 .......... M T C A C L T I S A W F P P A V F V P F S F L T I S F Y P P K T F T Y L .................................. ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 121 End: 150 ........................................................................................................................ATTGAATTATTTATAAAATATGTGTATAAT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1270:FN1271|FN1270:FN1271:Hypothetical cytosolic protein:Protease IV:<-<-:1926683..1926834 152 ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_003454_FN1270_FN1271|Hypothetical cytosolic protein:Protease IV|NEGATIVE:NEGATIVE|[1926683,1926834]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat ctgttgttgcattacttgtgcttgtttaacaatatcagcttggtttcctcctgctgtttttgttccttttagttttctaaccatttctttctatcctcctaaaacttttacatatctttaattatacacatattttataaataattcaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUGUUGCAUUACUUGUGCUUGUUUAACAAUAUCAGCUUGGUUUCCUCCUGCUGUUUUUGUUCCUUUUAGUUUUCUAACCAUUUCUUUCUAUCCUCCUAAAACUUUUACAUAUCUUUAAUUAUACACAUAUUUUAUAAAUAAUUCAAUAU ....(((((.((((.(((((.......(((((...((((..((......)).))))...)))))....((((....)))).......................................................))))).)))).))))). (-16.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUGAAUUAUUUAUAAAAUAUGUGUAUAAUUAAAGAUAUGUAAAAGUUUUAGGAGGAUAGAAAGAAAUGGUUAGAAAACUAAAAGGAACAAAAACAGCAGGAGGAAACCAAGCUGAUAUUGUUAAACAAGCACAAGUAAUGCAACAACAG ...(((.((((((.........(((((.....................((((((.....(((..(....)..))).....))))))..(((((...((((..(.(....))..))))...)))))......))))))))))).)))...... (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 840 50 1 141 92 NC_003454:FN1270|5end_Hypothetical_cytosolic_protein_1926592..1926822_NEGATIVE 338 78 36 101 52 NC_003454:FN1170|5end_Pyruvate-flavodoxin_oxidoreductase_1832273..1832503_NEGATIVE 334 100 54 102 64 NC_003454:FN0664|5end_2-nitropropane_dioxygenase_1319758..1319988_POSITIVE 303 65 30 87 46 NC_003454:FN0226|5end_4-hydroxythreonine-4-phosphate_dehydrogenase_854089..854319_NEGATIVE 299 60 18 112 66 NC_003454:FN1605|5end_Adenylosuccinate_synthetase_115276..115506_NEGATIVE 292 49 27 26 4 NC_003454:FN1427|5end_Phenazine_biosynthesis_protein_phzF_2095802..2096032_POSITIVE 292 89 48 226 174 NC_003454:FN1726|5end_Na+_driven_multidrug_efflux_pump_226059..226289_NEGATIVE 288 100 51 101 43 NC_003454:FN1159|5end_fructose_1,6-bisphosphatase_II_1814731..1814961_POSITIVE 281 79 36 193 137 NC_003454:FN1506|5end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_10871..11101_POSITIVE 279 100 51 163 118 NC_003454:FN0994|5end_hypothetical_protein_1649223..1649453_POSITIVE 273 110 61 118 62 NC_003454:FN1540|5end_Iron-sulfur_cluster-binding_protein_53055..53285_POSITIVE 271 76 37 172 129 NC_003454:FN0365|5end_ATP_synthase_protein_I,_sodium_ion_specific_994859..995089_NEGATIVE 270 109 65 146 105 NC_003454:FN1155|5end_Cell_division_protein_ftsI_1809442..1809672_POSITIVE 270 99 53 100 39 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 267 49 1 80 22 NC_003454:FN1619|5end_Hypothetical_cytosolic_protein_127644..127874_NEGATIVE 264 66 26 64 18 NC_003454:FN1298|5end_Adenylate_kinase_1955626..1955856_NEGATIVE 263 117 74 130 80 NC_003454:FN0699|5end_Protein_translocase_subunit_secD_1357051..1357281_POSITIVE 263 57 16 231 183 NC_003454:FN0515|5end_Acriflavin_resistance_protein_D_1167006..1167236_NEGATIVE 262 100 51 108 46 NC_003454:FN0208|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_834968..835198_POSITIVE 260 88 43 71 30 NC_003454:FN0083|5end_Ethanolamine_utilization_protein_eutM_precursor_721180..721410_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 100 54 61 23 NC_003454:FN0663|3end_hypothetical_protein_1319797..1319947_POSITIVE 303 65 30 62 21 NC_003454:FN0227|3end_hypothetical_protein_854114..854264_NEGATIVE 299 60 18 102 56 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 288 100 51 104 46 NC_003454:FN1158|3end_hypothetical_protein_1814814..1814964_POSITIVE 279 100 51 68 23 NC_003454:FN0993|3end_Trk_system_potassium_uptake_protein_trkG_1649208..1649358_POSITIVE 273 110 61 75 19 NC_003454:FN1539|3end_Iron-sulfur_cluster-binding_protein_53092..53242_POSITIVE 270 109 65 126 85 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 263 117 74 106 56 NC_003454:FN0698|3end_DNA_integration/recombination/invertion_protein_1357107..1357257_POSITIVE 262 100 51 86 24 NC_003454:FN0207|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_alpha-subunit_835026..835176_POSITIVE 257 107 61 92 51 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE 256 120 71 109 56 NC_003454:FN1627|3end_SSU_ribosomal_protein_S5P_133062..133212_NEGATIVE 254 79 38 68 23 NC_003454:FN1020|3end_3-hydroxybutyryl-CoA_dehydratase_1673800..1673950_NEGATIVE 254 99 51 105 54 NC_003454:FN1611|3end_Competence_protein_120597..120747_NEGATIVE 251 103 67 81 48 NC_003454:FN0326|3end_LSU_ribosomal_protein_L35P_961299..961449_NEGATIVE 249 99 65 71 36 NC_003454:FN0752|3end_Proline_iminopeptidase_1410721..1410871_NEGATIVE 249 111 74 99 60 NC_003454:FN0465|3end_hypothetical_protein_1111358..1111508_POSITIVE 249 100 55 92 43 NC_003454:FN0297|3end_ATPase_associated_with_chromosome_architecture/replication_931201..931351_POSITIVE 246 78 37 148 94 NC_003454:FN1735|3end_V-type_ATP_synthase_subunit_A_234251..234401_NEGATIVE 242 120 71 122 75 NC_003454:FN0595|3end_UDP-N-acetylglucosamine_acyltransferase_1250081..1250231_POSITIVE 241 100 55 101 48 NC_003454:FN1553|3end_Transporter_67150..67300_NEGATIVE