Origin IGS: tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatattttgaactgttatactacatcaaaaaagtttgggaatatataatttagcttttaatgaggattaacttctgtaaaaagcaggagttagtcctttttatttgacaaaaatcttgcaaaatattttaaaaagcaaattaataaaaaattattggtacttaaataaaaatggttgattttaacagaaaaagggtgtagaatattagaaataatttatttataaaaaaagtataaagggggattttatgaaagcaaagattttattatgctcaatgttaata Mask Tandem Repeat Region ================================================ tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta Find is-nt database================================================ Query_seq: FN2052:FN2053|FN2052:FN2053:hypothetical protein:Serine/threonine sodium symporter:<-<-:561034..561317 284 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2052:FN2053|FN2052:FN2053:hypothetical protein:Serine/threonine sodium symporter:<-<-:561034..561317 284 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2052:FN2053|FN2052:FN2053:hypothetical protein:Serine/threonine sodium symporter:<-<-:561034..561317 284 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 69 End: 191 .................................................................... M I S N I L H P F S V K I N H F Y L S T N N F L L I C F L K Y F A R F L S N K K D ............................................................................................. tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta 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: 81 End: 110 ................................................................................GTTGATTTTAACAGAAAAAGGGTGTAGAAT.............................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.0 Tail_Score: -5.27335 Start: 188 End: 220 Full_Region: tttagcttttaatga ggattaacttctgt aaaaa gcaggagttagtcc tttttatttgacaaa ...........................................................................................................................................................................................ggattaacttctgtaaaaagcaggagttagtcc................................................................ Find igs database================================================ Query_seq: FN2052:FN2053|FN2052:FN2053:hypothetical protein:Serine/threonine sodium symporter:<-<-:561034..561317 284 tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccctttttctgttaaaatcaaccatttttatttaagtaccaataattttttattaatttgctttttaaaatattttgcaagatttttgtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta Intra-Species Hit: Count: 1 Min: 1 Max: 284 Len: 284 Subject: NC_003454_FN2052_FN2053|hypothetical protein:Serine/threonine sodium symporter|NEGATIVE:NEGATIVE|[561034,561317]|284 HSP 1 e-value: 3.0E-55 bit: 216.0 Len: 109 Query Start:176 Query End:284 Subject Strand: POSITIVE Subject Start: 176 Subject End: 284 ...............................................................................................................................................................................gtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta ...............................................................................................................................................................................gtcaaataaaaaggactaactcctgctttttacagaagttaatcctcattaaaagctaaattatatattcccaaacttttttgatgtagtataacagttcaaaatatta HSP 2 e-value: 6.0E-32 bit: 139.0 Len: 91 Query Start:1 Query End:91 Subject Strand: POSITIVE Subject Start: 1 Subject End: 91 tattaacattgagcataataaaatctttgctttcataaaatccccctttatacnnnnnnnataaataaattatttctaatattctacaccc................................................................................................................................................................................................. tattaacattgagcataataaaatctttgctttcataaaatccccctttatactttttttataaataaattatttctaatattctacaccc................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAACAUUGAGCAUAAUAAAAUCUUUGCUUUCAUAAAAUCCCCCUUUAUACUUUUUUUAUAAAUAAAUUAUUUCUAAUAUUCUACACCCUUUUUCUGUUAAAAUCAACCAUUUUUAUUUAAGUACCAAUAAUUUUUUAUUAAUUUGCUUUUUAAAAUAUUUUGCAAGAUUUUUGUCAAAUAAAAAGGACUAACUCCUGCUUUUUACAGAAGUUAAUCCUCAUUAAAAGCUAAAUUAUAUAUUCCCAAACUUUUUUGAUGUAGUAUAACAGUUCAAAAUAUUA ........((((((................................((((((.......))))))..............(((.(((((............(((((........))))).......................((((((((((((.....(((((.(((((...))))).)))))...((((.(((((.(((.......))).))))).))))....)))))).)))))).....................))))).)))...))))))....... (-32.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUUUUGAACUGUUAUACUACAUCAAAAAAGUUUGGGAAUAUAUAAUUUAGCUUUUAAUGAGGAUUAACUUCUGUAAAAAGCAGGAGUUAGUCCUUUUUAUUUGACAAAAAUCUUGCAAAAUAUUUUAAAAAGCAAAUUAAUAAAAAAUUAUUGGUACUUAAAUAAAAAUGGUUGAUUUUAACAGAAAAAGGGUGUAGAAUAUUAGAAAUAAUUUAUUUAUAAAAAAAGUAUAAAGGGGGAUUUUAUGAAAGCAAAGAUUUUAUUAUGCUCAAUGUUAAUA (((((((.....(((.(((.(((((((......(((((((.............((((((...((((((((((((((((.....))))))))))))))))....((((.(((.....)))))))........))))))..((((((((....)))))))).))))))).......((((....))))........))))))).))).))).....................(((((((...((((((((.((....)))))))))).))))))).)))))))... (-57.40) 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:FN2063|5end_hypothetical_protein_575019..575249_NEGATIVE 720 50 1 141 92 NC_003454:FN2052|5end_hypothetical_protein_560943..561173_NEGATIVE 635 49 1 140 92 NC_003454:FN0249|5end_hypothetical_protein_872823..873053_POSITIVE 377 220 174 155 107 NC_003454:FN1997|5end_Transcriptional_regulator_499758..499988_POSITIVE 297 227 182 164 120 NC_003454:FN1343|5end_seC-independent_protein_TATD_1997232..1997462_NEGATIVE 294 226 183 208 165 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 274 220 171 197 149 NC_003454:FN0496|5end_hypothetical_protein_1140910..1141140_POSITIVE 274 218 183 231 196 NC_003454:FN1844|5end_Ketoacyl_reductase_hetN_333593..333823_POSITIVE 261 62 28 117 82 NC_003454:FN0978|5end_NA+/H+_antiporter_NHAC_1631965..1632195_NEGATIVE 261 130 82 174 116 NC_003454:FN0285|5end_RNA_binding_protein_914171..914401_NEGATIVE 260 66 22 126 86 NC_003454:FN0801|5end_Amino_acid_transport_ATP-binding_protein_1461433..1461663_NEGATIVE 250 55 11 115 74 NC_003454:FN0972|5end_Cobyrinic_acid_a,c-diamide_synthase_1625607..1625837_NEGATIVE 248 52 16 106 67 NC_003454:FN0897|5end_Hypothetical_cytosolic_protein_1555833..1556063_POSITIVE 248 267 223 161 110 NC_003454:FN0215|5end_MGTC/SAPB_Family_membrane_protein_839974..840204_NEGATIVE 248 47 12 102 62 NC_003454:FN1613|5end_hypothetical_protein_123486..123716_NEGATIVE 246 56 20 117 76 NC_003454:FN0371|5end_hypothetical_protein_999993..1000223_POSITIVE 240 232 196 83 44 NC_003454:FN0977|5end_Cobyric_acid_synthase_1630580..1630810_NEGATIVE 226 49 8 106 66 NC_003454:FN0718|5end_hypothetical_protein_1375616..1375846_POSITIVE 224 117 73 214 166 NC_003454:FN1915|5end_Anti-sigma_B_factor_412320..412550_NEGATIVE 222 222 188 102 64 NC_003454:FN1286|5end_30S_ribosomal_protein_S13_1944074..1944304_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 517 221 184 57 20 NC_003454:FN1801|3end_Sodium/glutamate_symport_carrier_protein_282636..282786_NEGATIVE 480 238 192 52 5 NC_003454:FN0209|3end_Hypothetical_cytosolic_protein_836800..836950_POSITIVE 469 238 193 47 1 NC_003454:FN0842|3end_hypothetical_protein_1502822..1502972_NEGATIVE 469 238 193 47 1 NC_003454:FN1890|3end_hypothetical_protein_373045..373195_NEGATIVE 377 220 174 59 11 NC_003454:FN1996|3end_Transporter_499742..499892_POSITIVE 375 221 183 74 40 NC_003454:FN0723|3end_hypothetical_protein_1383464..1383614_POSITIVE 334 221 184 76 39 NC_003454:FN1235|3end_Ankyrin_repeat_proteins_1892428..1892578_POSITIVE 294 226 183 68 25 NC_003454:FN0865|3end_hypothetical_protein_1523040..1523190_NEGATIVE 275 238 193 42 1 NC_003454:FN1843|3end_Surface_antigen_333468..333618_POSITIVE 274 220 171 62 14 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 260 66 22 133 93 NC_003454:FN0802|3end_Amino_acid_transport_system_permease_protein_1461426..1461576_NEGATIVE 250 55 11 96 55 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 248 47 12 79 39 NC_003454:FN1614|3end_MG(2+)_chelatase_family_protein_123509..123659_NEGATIVE 226 49 8 83 43 NC_003454:FN0717|3end_Ribosomal_small_subunit_pseudouridine_synthase_A_1375673..1375823_POSITIVE 224 117 73 128 80 NC_003454:FN1916|3end_hypothetical_protein_412406..412556_NEGATIVE 222 96 54 109 68 NC_003454:FN0582|3end_Lipoprotein_releasing_system_ATP-binding_protein_lolD_1239027..1239177_POSITIVE 221 51 26 91 62 NC_003454:FN0021|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_660854..661004_POSITIVE 217 250 207 129 84 NC_003454:FN1752|3end_Regulatory_protein_TENI_248591..248741_NEGATIVE 216 117 76 44 4 NC_003454:FN0795|3end_CBS_domain_containing_protein_1453076..1453226_POSITIVE 215 100 53 150 110 NC_003454:FN0195|3end_Dipeptide_transport_ATP-binding_protein_dppD_822407..822557_POSITIVE