Origin IGS: ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctatcatctccttaataattatgataataacatattttagacagtgtactctttttttgaaaagaataaaaatatataaaatttatattaaaatgactttcatttatttaaaaaattaatattttagaaaaatactgaaatataaagtttttttagttattatttaaatagctattttaagaatattttgaaaaaaataagaaatatgttattataaagacacgctattataatttacataagaaaagtacaggaggaaaa Mask Tandem Repeat Region ================================================ ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga Find is-nt database================================================ Query_seq: FN0997:FN0998|FN0997:FN0998:hypothetical protein:Dipeptide-binding protein:<-->:1652125..1652386 262 ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0997:FN0998|FN0997:FN0998:hypothetical protein:Dipeptide-binding protein:<-->:1652125..1652386 262 ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0997:FN0998|FN0997:FN0998:hypothetical protein:Dipeptide-binding protein:<-->:1652125..1652386 262 ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 155 End: 247 .......................................................................................................................................................... M N E S H F N I N F I Y F Y S F Q K K S T L S K I C Y Y H N Y ............... Protein_Len: 38 Strand: - Start: 146 End: 259 ................................................................................................................................................. N K L Y I F T M K I Y I K Y I K I R K L F L T C Q R F Y T I I M I I L S I M ... ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga 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: 83 Start: 99 End: 128 ..................................................................................................ACTGAAATATAAAGTTTTTTTAGTTATTAT...................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 199 End: 228 ......................................................................................................................................................................................................TTTTCAAAAAAAGAGTACACTGTCTAAAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -3.4 Tail_Score: -4.16146 Start: 88 End: 108 Full_Region: aatataaagtttttt tagttatt attta aatagcta ttttaagaatatttt .......................................................................................tagttattatttaaatagcta.......................................................................................................................................................... Find igs database================================================ Query_seq: FN0997:FN0998|FN0997:FN0998:hypothetical protein:Dipeptide-binding protein:<-->:1652125..1652386 262 ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataactaaaaaaactttatatttcagtatttttctaaaatattaattttttaaataaatgaaagtcattttaatataaattttatatatttttattcttttcaaaaaaagagtacactgtctaaaatatgttattatcataattattaaggagatgataga Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: NC_003454_FN0997_FN0998|hypothetical protein:Dipeptide-binding protein|NEGATIVE:POSITIVE|[1652125,1652386]|262 HSP 1 e-value: 2.0E-41 bit: 170.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttannnnnnncaaaatattcttaaaatagctatttaaataataact........................................................................................................................................................... ttttcctcctgtacttttcttatgtaaattataatagcgtgtctttataataacatatttcttatttttttcaaaatattcttaaaatagctatttaaataataact........................................................................................................................................................... HSP 2 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:211 Query End:262 Subject Strand: POSITIVE Subject Start: 211 Subject End: 262 ..................................................................................................................................................................................................................gagtacactgtctaaaatatgttattatcataattattaaggagatgataga ..................................................................................................................................................................................................................gagtacactgtctaaaatatgttattatcataattattaaggagatgataga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCUCCUGUACUUUUCUUAUGUAAAUUAUAAUAGCGUGUCUUUAUAAUAACAUAUUUCUUAUUUUUUUCAAAAUAUUCUUAAAAUAGCUAUUUAAAUAAUAACUAAAAAAACUUUAUAUUUCAGUAUUUUUCUAAAAUAUUAAUUUUUUAAAUAAAUGAAAGUCAUUUUAAUAUAAAUUUUAUAUAUUUUUAUUCUUUUCAAAAAAAGAGUACACUGUCUAAAAUAUGUUAUUAUCAUAAUUAUUAAGGAGAUGAUAGA .....(((((..........(((((...........))))).....((((((((((((((............(((((((...((((.(((.((((.....)))).))).......((((((((..(((..(((((.......((((....))))......)))))..)))..)))))))).)))).)))))))(((((((((....))))))))).........))))))))))))))...........)))))........ (-33.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUCAUCUCCUUAAUAAUUAUGAUAAUAACAUAUUUUAGACAGUGUACUCUUUUUUUGAAAAGAAUAAAAAUAUAUAAAAUUUAUAUUAAAAUGACUUUCAUUUAUUUAAAAAAUUAAUAUUUUAGAAAAAUACUGAAAUAUAAAGUUUUUUUAGUUAUUAUUUAAAUAGCUAUUUUAAGAAUAUUUUGAAAAAAAUAAGAAAUAUGUUAUUAUAAAGACACGCUAUUAUAAUUUACAUAAGAAAAGUACAGGAGGAAAA .......((((((((....((((((((((((((((((((.((.(((....((((((....)))))).....((((((.......))))))......))).)).....(((((((.....(((((((((.......)))))))))...((((((.((((((((.....))))))))....)))))).)))))))........)))))))))))))))..((.....))...........)))))......)).)))))).... (-42.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 720 50 1 141 92 NC_003454:FN0997|5end_hypothetical_protein_1652034..1652264_NEGATIVE 288 48 3 137 94 NC_003454:FN1348|5end_ABC_transporter_ATP-binding_protein_2001141..2001371_NEGATIVE 264 48 3 141 103 NC_003454:FN0592|5end_ATP-dependent_DNA_helicase_pcrA_1245712..1245942_POSITIVE 223 50 1 178 129 NC_003454:FN1155|5end_Cell_division_protein_ftsI_1809442..1809672_POSITIVE 220 22 1 116 93 NC_003454:FN1605|5end_Adenylosuccinate_synthetase_115276..115506_NEGATIVE 208 72 32 187 142 NC_003454:FN0860|5end_hypothetical_protein_1521563..1521793_NEGATIVE 201 80 40 113 76 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 201 235 194 216 177 NC_003454:FN0587|5end_Hypothetical_membrane-spanning_protein_1242139..1242369_NEGATIVE 200 152 114 79 36 NC_003454:FN1401|5end_urocanate_hydratase_2058592..2058822_POSITIVE 200 48 5 167 124 NC_003454:FN0389|5end_hypothetical_protein_1027561..1027791_POSITIVE 194 43 5 62 24 NC_003454:FN1506|5end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_10871..11101_POSITIVE 193 170 123 120 66 NC_003454:FN1752|5end_Regulatory_protein_TENI_249211..249441_NEGATIVE 191 46 6 86 31 NC_003454:FN1373|5end_EBSC_protein_2021486..2021716_NEGATIVE 191 33 1 120 91 NC_003454:FN0315|5end_Transcriptional_regulator,_AraC_family_951934..952164_POSITIVE 190 92 55 138 101 NC_003454:FN1251|5end_High-affinity_iron_permease_1908008..1908238_POSITIVE 190 50 6 42 1 NC_003454:FN0443|5end_hypothetical_protein_1082680..1082910_POSITIVE 189 30 1 122 97 NC_003454:FN0720|5end_elongation_factor_P_1376976..1377206_POSITIVE 189 26 1 124 98 NC_003454:FN0321|5end_heat_shock_protein_90_957634..957864_POSITIVE 186 244 207 229 191 NC_003454:FN1147|5end_hypothetical_protein_1797829..1798059_NEGATIVE 185 256 214 208 167 NC_003454:FN1383|5end_DNA_polymerase_III_alpha_subunit_2037856..2038086_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 48 3 128 85 NC_003454:FN1349|3end_ABC_transporter_permease_protein_2001150..2001300_NEGATIVE 220 22 1 106 83 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 203 72 35 139 102 NC_003454:FN0666|3end_hypothetical_protein_1322296..1322446_POSITIVE 201 80 40 146 109 NC_003454:FN1438|3end_hypothetical_protein_2106541..2106691_POSITIVE 199 44 1 151 109 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 194 43 5 60 22 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE 193 170 123 117 63 NC_003454:FN1753|3end_thiamine_biosynthesis_protein_ThiH_249214..249364_NEGATIVE 191 46 6 74 19 NC_003454:FN1374|3end_Transcriptional_regulator_2021498..2021648_NEGATIVE 191 33 1 37 8 NC_003454:FN0314|3end_Caffeoyl-CoA_O-methyltransferase_951931..952081_POSITIVE 189 30 1 122 97 NC_003454:FN0719|3end_Hypothetical_cytosolic_protein_1377056..1377206_POSITIVE 185 45 1 125 74 NC_003454:FN2124|3end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633251..633401_NEGATIVE 183 91 51 113 64 NC_003454:FN0629|3end_PTS_system,_IID_component_1288267..1288417_NEGATIVE 178 240 198 96 54 NC_003454:FN1843|3end_Surface_antigen_333468..333618_POSITIVE 177 48 4 94 40 NC_003454:FN1205|3end_Protease_1863879..1864029_NEGATIVE 177 43 1 58 10 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 174 72 31 89 49 NC_003454:FN0949|3end_DNA_helicase_1602482..1602632_NEGATIVE 174 21 1 125 107 NC_003454:FN0521|3end_DNA_integration/recombination/invertion_protein_1172288..1172438_NEGATIVE 173 49 1 145 94 NC_003454:FN1732|3end_hypothetical_protein_231281..231431_NEGATIVE 172 152 126 62 33 NC_003454:FN0680|3end_Ribulose-phosphate_3-epimerase_1336182..1336332_POSITIVE 170 80 31 119 59 NC_003454:FN1465|3end_Permease_2148941..2149091_POSITIVE