Origin IGS: tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatatattattttaaagtataacattgtaaataaagatttacaactacatttttaagaaaaaagctattgtaaaataaattacaatagcctttaaaatttattttcattttaaata Mask Tandem Repeat Region ================================================ tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Find is-nt database================================================ Query_seq: FN0461:FN0462|FN0461:FN0462:Probable sigma(54) modulation protein:DNA mismatch repair protein mutL:->->:1107208..1107323 116 tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0461:FN0462|FN0461:FN0462:Probable sigma(54) modulation protein:DNA mismatch repair protein mutL:->->:1107208..1107323 116 tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0461:FN0462|FN0461:FN0462:Probable sigma(54) modulation protein:DNA mismatch repair protein mutL:->->:1107208..1107323 116 tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 9 End: 107 ........ M K I N F K G Y C N L F Y N S F F L K N V V V N L Y L Q C Y T L K ......... tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt 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: 82 Start: 72 End: 101 .......................................................................GTTGTAAATCTTTATTTACAATGTTATACT............... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -9.2 Tail_Score: -2.858 Start: 28 End: 53 Full_Region: atttttaagaaaaaa gctattgtaa aataaa ttacaatagc ctttaaaatttattt ...........................gctattgtaaaataaattacaatagc............................................................... Find igs database================================================ Query_seq: FN0461:FN0462|FN0461:FN0462:Probable sigma(54) modulation protein:DNA mismatch repair protein mutL:->->:1107208..1107323 116 tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_003454_FN0461_FN0462|Probable sigma(54) modulation protein:DNA mismatch repair protein mutL|POSITIVE:POSITIVE|[1107208,1107323]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt tatttaaaatgaaaataaattttaaaggctattgtaatttattttacaatagcttttttcttaaaaatgtagttgtaaatctttatttacaatgttatactttaaaataatatatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUAAAAUGAAAAUAAAUUUUAAAGGCUAUUGUAAUUUAUUUUACAAUAGCUUUUUUCUUAAAAAUGUAGUUGUAAAUCUUUAUUUACAAUGUUAUACUUUAAAAUAAUAUAUU ..................(((((((((((((((((((......))))))))))..................(((((((((....)))))))))......)))))))))........ (-23.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUAUUAUUUUAAAGUAUAACAUUGUAAAUAAAGAUUUACAACUACAUUUUUAAGAAAAAAGCUAUUGUAAAAUAAAUUACAAUAGCCUUUAAAAUUUAUUUUCAUUUUAAAUA .........((((((((.......((((((((....))))))))......)))))))).....((((((((((......)))))))))).((((((((........)))))))).. (-20.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 54 24 227 195 NC_003454:FN0165|5end_hypothetical_protein_793491..793721_POSITIVE 279 59 15 225 183 NC_003454:FN0093|5end_Thioredoxin_729169..729399_POSITIVE 256 62 25 221 181 NC_003454:FN1488|5end_Methenyltetrahydrofolate_cyclohydrolase_2170886..2171116_NEGATIVE 230 57 12 213 172 NC_003454:FN2010|5end_Transcriptional_regulator,_MarR_family_510302..510532_NEGATIVE 222 86 49 183 147 NC_003454:FN0012|5end_DNA_topology_modulation_protein_FLAR-related_protein_652114..652344_NEGATIVE 217 61 23 162 118 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 211 85 41 80 32 NC_003454:FN1524|5end_Dipeptide_transport_ATP-binding_protein_dppD_29799..30029_POSITIVE 196 54 17 198 156 NC_003454:FN0799|5end_Isoamylase_1459826..1460056_NEGATIVE 192 59 24 73 25 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 191 62 26 217 175 NC_003454:FN1949|5end_Xaa-Pro_dipeptidase_454922..455152_NEGATIVE 190 57 17 183 135 NC_003454:FN1257|5end_C4-dicarboxylate_transporter_small_subunit_1913664..1913894_NEGATIVE 186 65 27 146 107 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 186 86 42 75 34 NC_003454:FN0161|5end_RNA-directed_DNA_polymerase_788763..788993_POSITIVE 184 95 51 94 38 NC_003454:FN1051|5end_hypothetical_protein_1699781..1700011_POSITIVE 184 52 20 231 199 NC_003454:FN0903|5end_Polysialic_acid_capsule_expression_protein_kpsF_1561116..1561346_POSITIVE 184 62 21 168 134 NC_003454:FN0369|5end_Ribosomal-protein-alanine_acetyltransferase_998895..999125_NEGATIVE 179 70 25 116 65 NC_003454:FN0426|5end_Orotidine_5'-phosphate_decarboxylase_1068720..1068950_POSITIVE 177 70 46 78 48 NC_003454:FN0915|5end_PTS_system,_N-acetylglucosamine-specific_IIA_component_1572037..1572267_NEGATIVE 176 89 47 173 126 NC_003454:FN1736|5end_V-type_sodium_ATP_synthase_subunit_A_236021..236251_NEGATIVE 172 62 25 110 71 NC_003454:FN1075|5end_hypothetical_protein_1722042..1722272_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 58 25 86 52 NC_003454:FN1080|3end_Export_ABC_transporter_1727308..1727458_POSITIVE 280 68 24 86 31 NC_003454:FN0662|3end_Formiminoglutamase_1319188..1319338_POSITIVE 279 59 15 82 40 NC_003454:FN0092|3end_NADPH-dependent_butanol_dehydrogenase_729106..729256_POSITIVE 256 63 23 93 52 NC_003454:FN1277|3end_Aminoacyl-histidine_dipeptidase_1935294..1935444_NEGATIVE 254 57 24 67 34 NC_003454:FN0461|3end_Probable_sigma(54)_modulation_protein_1107147..1107297_POSITIVE 246 58 15 85 41 NC_003454:FN1081|3end_hypothetical_protein_1727325..1727475_NEGATIVE 242 61 26 88 48 NC_003454:FN0514|3end_hypothetical_protein_1163912..1164062_POSITIVE 236 63 26 90 48 NC_003454:FN0515|3end_Acriflavin_resistance_protein_D_1163938..1164088_NEGATIVE 234 62 24 86 44 NC_003454:FN1043|3end_hypothetical_protein_1694450..1694600_POSITIVE 230 57 12 82 41 NC_003454:FN2011|3end_Valyl-tRNA_synthetase_510433..510583_NEGATIVE 227 56 24 86 49 NC_003454:FN1266|3end_UTP--glucose-1-phosphate_uridylyltransferase_1922158..1922308_NEGATIVE 217 61 23 85 41 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 214 62 26 68 35 NC_003454:FN1985|3end_Inner_membrane_protein_487273..487423_NEGATIVE 212 61 24 102 62 NC_003454:FN1497|3end_Multidrug_resistance_protein_2_1014..1164_NEGATIVE 211 85 41 68 20 NC_003454:FN1523|3end_Dipeptide-binding_protein_29867..30017_POSITIVE 202 61 24 88 56 NC_003454:FN0039|3end_DNA_primase_(bacterial_type)_and_small_primase-like_proteins_678661..678811_NEGATIVE 200 56 17 79 38 NC_003454:FN1006|3end_Acetyltransferase_1660998..1661148_NEGATIVE 196 54 17 77 35 NC_003454:FN0800|3end_Amino_acid-binding_protein_1459947..1460097_NEGATIVE 191 62 26 76 34 NC_003454:FN1950|3end_Serine_protease_455063..455213_NEGATIVE 190 57 17 55 7 NC_003454:FN1258|3end_C4-dicarboxylate-binding_protein_1913792..1913942_NEGATIVE