Origin IGS: taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa .........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 tttcctcctatataatattttttattactaaaattttttccttgtaaaactagctttaataagattactgcaacctctattattgttgagagagcattggagctctcgaaacactaatgactgtcaagtaatcaaagcatagtattggattataaaaaatttaagcaataaaaaaggggacttgcaccccaagtctagttttttaaagatggttttgctagcacatctactta Mask Tandem Repeat Region ================================================ taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Find is-nt database================================================ Query_seq: FN1994:FN1995|FN1994:FN1995:hypothetical protein:hypothetical protein:->->:498152..498384 233 taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1994:FN1995|FN1994:FN1995:hypothetical protein:hypothetical protein:->->:498152..498384 233 taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1994:FN1995|FN1994:FN1995:hypothetical protein:hypothetical protein:->->:498152..498384 233 taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Predict ORF larger than 30AA ================================================ taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa 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================================================ taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -2.4 Tail_Score: -3.47915 Start: 29 End: 65 Full_Region: TAGCAAAACCATCTT TAAAAAACTAGACTTG GGGTG CAAGTCCCCTTTTTTA TTGCTTAAATTTTTT ............................TAAAAAACTAGACTTGGGGTGCAAGTCCCCTTTTTTA........................................................................................................................................................................ Find igs database================================================ Query_seq: FN1994:FN1995|FN1994:FN1995:hypothetical protein:hypothetical protein:->->:498152..498384 233 taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_003454_FN1994_FN1995|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[498152,498384]|233 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa taagtagatgtgctagcaaaaccatctttaaaaaactagacttggggtgcaagtccccttttttattgcttaaattttttataatccaatactatgctttgattacttgacagtcattagtgtttcgagagctccaatgctctctcaacaataatagaggttgcagtaatcttattaaagctagttttacaaggaaaaaattttagtaataaaaaatattatataggaggaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAGAUGUGCUAGCAAAACCAUCUUUAAAAAACUAGACUUGGGGUGCAAGUCCCCUUUUUUAUUGCUUAAAUUUUUUAUAAUCCAAUACUAUGCUUUGAUUACUUGACAGUCAUUAGUGUUUCGAGAGCUCCAAUGCUCUCUCAACAAUAAUAGAGGUUGCAGUAAUCUUAUUAAAGCUAGUUUUACAAGGAAAAAAUUUUAGUAAUAAAAAAUAUUAUAUAGGAGGAAA ..((((....)))).(((...(((..((((......))))..)))..)))...(((((((((((((((((.(((((((((..........((((.((((((((((((((((..((((((.((((..((((((......))))))..)))).)))).)).)))).))))))).....))))))))).........))))))))).))))))))))).........))).))).. (-59.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCCUCCUAUAUAAUAUUUUUUAUUACUAAAAUUUUUUCCUUGUAAAACUAGCUUUAAUAAGAUUACUGCAACCUCUAUUAUUGUUGAGAGAGCAUUGGAGCUCUCGAAACACUAAUGACUGUCAAGUAAUCAAAGCAUAGUAUUGGAUUAUAAAAAAUUUAAGCAAUAAAAAAGGGGACUUGCACCCCAAGUCUAGUUUUUUAAAGAUGGUUUUGCUAGCACAUCUACUUA .................(((((((((.((.(((((((((...(.(((.(((((((((.....(((((((...((...(((((.((((..((((((......))))))..)))).)))))...))..)))))))))))).)))).))).)....))))))))).)).)))))))))..(((((((.....)))))))..........((((((((.....))).)))))..... (-55.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 611 160 111 175 123 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 431 170 121 218 167 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 317 167 121 212 162 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 267 168 133 59 32 NC_003454:FN1744|5end_Transporter_242920..243150_NEGATIVE 259 88 49 54 15 NC_003454:FN1326|5end_Undecaprenyl_pyrophosphate_synthetase_1981890..1982120_NEGATIVE 259 45 1 52 6 NC_003454:FN1679|5end_LPS_biosynthesis_protein_WbpG_175711..175941_NEGATIVE 257 100 52 137 92 NC_003454:FN0417|5end_Type_III_restriction-modification_system_restriction_subunit_1055887..1056117_POSITIVE 254 138 110 70 42 NC_003454:FN0947|5end_hypothetical_protein_1600457..1600687_POSITIVE 253 48 8 195 157 NC_003454:FN0995|5end_hypothetical_protein_1649966..1650196_POSITIVE 248 129 89 158 115 NC_003454:FN1089|5end_hypothetical_protein_1733042..1733272_POSITIVE 247 150 101 214 163 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 246 67 25 110 59 NC_003454:FN1558|5end_30S_ribosomal_protein_S12_80518..80748_NEGATIVE 239 136 97 130 86 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 232 58 14 101 46 NC_003454:FN0776|5end_asparagine_synthetase_AsnA_1431944..1432174_POSITIVE 227 150 101 194 142 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 227 150 101 90 38 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 224 85 54 127 98 NC_003454:FN0972|5end_Cobyrinic_acid_a,c-diamide_synthase_1625607..1625837_NEGATIVE 223 148 121 231 203 NC_003454:FN1584|5end_Beta-lactamase_96158..96388_NEGATIVE 222 144 107 44 7 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 218 140 104 228 192 NC_003454:FN0481|5end_hypothetical_protein_1127777..1128007_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 611 160 111 73 21 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 431 170 121 85 34 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 421 168 121 66 17 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 317 167 121 78 28 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 264 150 103 50 1 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 257 100 52 127 82 NC_003454:FN0416|3end_Type_III_restriction-modification_system_methylation_subunit_1055957..1056107_POSITIVE 248 129 89 131 88 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 239 168 129 48 6 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 232 50 1 85 32 NC_003454:FN1904|3end_Transcriptional_regulator,_MarR_family_393633..393783_POSITIVE 230 145 102 130 90 NC_003454:FN0721|3end_hypothetical_protein_1377633..1377783_NEGATIVE 224 164 122 147 116 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 224 85 54 108 79 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 224 136 94 136 94 NC_003454:FN1752|3end_Regulatory_protein_TENI_248591..248741_NEGATIVE 218 168 135 26 1 NC_003454:FN1745|3end_Cystathionine_gamma-synthase_242953..243103_NEGATIVE 216 146 113 77 43 NC_003454:FN0535|3end_hypothetical_protein_1190009..1190159_POSITIVE 214 47 4 82 32 NC_003454:FN1587|3end_Acetyltransferase_99334..99484_POSITIVE 213 135 94 112 69 NC_003454:FN1337|3end_hypothetical_protein_1990288..1990438_NEGATIVE 210 50 14 61 19 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 209 59 27 81 48 NC_003454:FN1621|3end_elongation_factor_Ts_129655..129805_POSITIVE 208 86 43 127 94 NC_003454:FN1969|3end_Hemin_transport_system_permease_protein_hmuU_467186..467336_NEGATIVE