Origin IGS: tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa .........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 ttattttctcttgacttttcaaatatataatactataatattaaaaattaattataagttttaaattaggaggagaaagttatgctaaggagaagaatgataaggaaagtaaaaaattaattaaataaccttatctattttatattagcttaacttttgtatatctttttgatatttataactttaaagtttaacacagatagctagtatatctgtgttttttattttaaaatattttattttatggataaggaaattaaaaatacattttgtatttatatttccttttttattttatatttagggggttaga Mask Tandem Repeat Region ================================================ tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Find is-nt database================================================ Query_seq: FN0802:FN0803|FN0802:FN0803:Amino acid transport system permease protein:trifunctional thioredoxin/methionine sulfoxide reductase A/B protein:<-<-:1462227..1462539 313 tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0802:FN0803|FN0802:FN0803:Amino acid transport system permease protein:trifunctional thioredoxin/methionine sulfoxide reductase A/B protein:<-<-:1462227..1462539 313 tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0802:FN0803|FN0802:FN0803:Amino acid transport system permease protein:trifunctional thioredoxin/methionine sulfoxide reductase A/B protein:<-<-:1462227..1462539 313 tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 35 End: 127 .................................. M N T K C I F N F L I H K I K Y F K I K N T D I L A I C V K L .......................................................................................................................................................................................... Protein_Len: 34 Strand: - Start: 13 End: 114 ............ I Y F L F P F I F V F H I K L K R I W L I F Y K L I F F V S I S A M ....................................................................................................................................................................................................... Protein_Len: 34 Strand: - Start: 5 End: 103 .... * G G L Y L I F F S I Y I C F T N K I E K D M F Y F I K F Y F V C M .................................................................................................................................................................................................................. tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa 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: 89 Start: 275 End: 304 ..................................................................................................................................................................................................................................................................................CTTGACTTTTCAAATATATAATACTATAAT......... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 188 End: 217 ...........................................................................................................................................................................................ATTTAATTAATTTTTTACTTTCCTTATCAT................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -6.3 Tail_Score: -5.8901 Start: 29 End: 62 Full_Region: ttattttatggataa ggaaattaaaaataca ttt tgtatttatatttcc ttttttattttatat ............................ggaaattaaaaatacattttgtatttatatttcc........................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 90 HP_score: -6.4 Tail_Score: -5.79595 Start: 97 End: 119 Full_Region: aactttaaagtttaa cacagata gctagta tatctgtg ttttttattttaaaa ................................................................................................cacagatagctagtatatctgtg.................................................................................................................................................................................................. TransTerm Strand: + Conf: 42 HP_score: -3.2 Tail_Score: -3.12668 Start: 99 End: 117 Full_Region: TTAAAATAAAAAACA CAGATA TACTAGC TATCTG TGTTAAACTTTAAAG ..................................................................................................CAGATATACTAGCTATCTG.................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0802:FN0803|FN0802:FN0803:Amino acid transport system permease protein:trifunctional thioredoxin/methionine sulfoxide reductase A/B protein:<-<-:1462227..1462539 313 tctaaccccctaaatataaaataaaaaaggaaatataaatacaaaatgtatttttaatttccttatccataaaataaaatattttaaaataaaaaacacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Intra-Species Hit: Count: 1 Min: 97 Max: 313 Len: 217 Subject: NC_003454_FN0802_FN0803|Amino acid transport system permease protein:trifunctional thioredoxin/methionine sulfoxide reductase A/B protein|NEGATIVE:NEGATIVE|[1462227,1462539]|313 HSP 1 e-value: 1.0E-119 bit: 430.0 Len: 217 Query Start:97 Query End:313 Subject Strand: POSITIVE Subject Start: 97 Subject End: 313 ................................................................................................cacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa ................................................................................................cacagatatactagctatctgtgttaaactttaaagttataaatatcaaaaagatatacaaaagttaagctaatataaaatagataaggttatttaattaattttttactttccttatcattcttctccttagcataactttctcctcctaatttaaaacttataattaatttttaatattatagtattatatatttgaaaagtcaagagaaaataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACAGAUAUACUAGCUAUCUGUGUUAAACUUUAAAGUUAUAAAUAUCAAAAAGAUAUACAAAAGUUAAGCUAAUAUAAAAUAGAUAAGGUUAUUUAAUUAAUUUUUUACUUUCCUUAUCAUUCUUCUCCUUAGCAUAACUUUCUCCUCCUAAUUUAAAACUUAUAAUUAAUUUUUAAUAUUAUAGUAUUAUAUAUUUGAAAAGUCAAGAGAAAAUAA ..((((((((...(((((..((((((((..(((..((((((((((((.....)))))...(((((((.(((((.........(((((((.....(((........)))....)))))))..........))))).)))))))..................))))))))))..)))))))).)))))....))))))))................... (-35.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUUUCUCUUGACUUUUCAAAUAUAUAAUACUAUAAUAUUAAAAAUUAAUUAUAAGUUUUAAAUUAGGAGGAGAAAGUUAUGCUAAGGAGAAGAAUGAUAAGGAAAGUAAAAAAUUAAUUAAAUAACCUUAUCUAUUUUAUAUUAGCUUAACUUUUGUAUAUCUUUUUGAUAUUUAUAACUUUAAAGUUUAACACAGAUAGCUAGUAUAUCUGUG ............((((((.........(((((......)))))........((((((((.(((((..((((...((((((((.(((((..((((....(((((((....(((........))).....)))))))..))))...))))).)))))))).....))))))))).))))))))....))))))...((((((((.......)))))))) (-41.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 614 44 1 231 188 NC_003454:FN0802|5end_Amino_acid_transport_system_permease_protein_1462136..1462366_NEGATIVE 296 136 92 112 70 NC_003454:FN0257|5end_Transporter_882516..882746_POSITIVE 268 150 104 138 100 NC_003454:FN1155|5end_Cell_division_protein_ftsI_1809442..1809672_POSITIVE 266 129 85 118 77 NC_003454:FN1874|5end_Ribose_5-phosphate_isomerase_363902..364132_NEGATIVE 260 153 121 104 62 NC_003454:FN1335|5end_Protein_translocase_subunit_YajC_1989011..1989241_NEGATIVE 257 141 108 227 191 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 253 158 113 138 83 NC_003454:FN1713|5end_tRNA_(Uracil-5-)_-methyltransferase_207494..207724_POSITIVE 250 147 120 118 92 NC_003454:FN1829|5end_hypothetical_protein_318556..318786_NEGATIVE 246 147 107 217 183 NC_003454:FN0133|5end_hypothetical_protein_769121..769351_POSITIVE 244 150 101 102 52 NC_003454:FN0062|5end_Hypothetical_cytosolic_protein_698605..698835_POSITIVE 237 150 110 81 40 NC_003454:FN0197|5end_Methyltransferase_822664..822894_POSITIVE 236 150 117 106 74 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 236 150 110 104 69 NC_003454:FN1851|5end_Ribonuclease_PH_340179..340409_POSITIVE 235 154 113 151 113 NC_003454:FN1130|5end_Tetraacyldisaccharide_4'-kinase_1777840..1778070_POSITIVE 232 157 124 95 65 NC_003454:FN0268|5end_DNA_repair_protein_recN_894330..894560_POSITIVE 230 150 101 104 49 NC_003454:FN1309|5end_hypothetical_protein_1964856..1965086_POSITIVE 228 147 102 189 153 NC_003454:FN1210|5end_Metal_dependent_hydrolase_1870766..1870996_NEGATIVE 228 155 120 38 1 NC_003454:FN1919|5end_Methyltransferase_415882..416112_NEGATIVE 224 158 130 123 94 NC_003454:FN0877|5end_Sodium/proline_symporter_1538873..1539103_NEGATIVE 221 147 107 102 55 NC_003454:FN1698|5end_dTDP-4-dehydrorhamnose_reductase_194593..194823_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 150 104 118 80 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 266 129 85 114 73 NC_003454:FN1875|3end_Peptidyl-prolyl_cis-trans_isomerase_363906..364056_NEGATIVE 250 147 120 103 77 NC_003454:FN1830|3end_DNA_polymerase_III_subunits_gamma_and_tau_318571..318721_NEGATIVE 237 150 110 84 43 NC_003454:FN0196|3end_Transcriptional_regulator,_FUR_family_822747..822897_POSITIVE 236 150 117 104 72 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 236 150 110 59 24 NC_003454:FN1850|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_340214..340364_POSITIVE 235 154 113 96 58 NC_003454:FN1129|3end_Chromosome_partition_protein_smc_1777865..1778015_POSITIVE 232 157 124 116 86 NC_003454:FN0267|3end_ATP-NAD_kinase_894431..894581_POSITIVE 228 155 120 41 4 NC_003454:FN1920|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_415879..416029_NEGATIVE 221 147 107 92 45 NC_003454:FN1699|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_194603..194753_NEGATIVE 220 168 127 108 68 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 220 149 103 105 54 NC_003454:FN0326|3end_LSU_ribosomal_protein_L35P_961299..961449_NEGATIVE 219 170 130 64 24 NC_003454:FN1725|3end_Potassium_uptake_protein_KtrB_223325..223475_NEGATIVE 218 150 101 149 97 NC_003454:FN1326|3end_Undecaprenyl_pyrophosphate_synthetase_1981198..1981348_NEGATIVE 215 123 85 118 73 NC_003454:FN0331|3end_hypothetical_protein_966168..966318_POSITIVE 211 149 107 87 33 NC_003454:FN1485|3end_Transporter_2167351..2167501_NEGATIVE 206 155 111 91 52 NC_003454:FN0207|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_alpha-subunit_835026..835176_POSITIVE 204 130 81 104 46 NC_003454:FN1431|3end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2099326..2099476_NEGATIVE 203 48 1 87 32 NC_003454:FN0544|3end_ADP-heptose:LPS_heptosyltransferase_II_1198128..1198278_POSITIVE 202 141 101 132 86 NC_003454:FN1197|3end_hypothetical_protein_1857035..1857185_NEGATIVE