Origin IGS: tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca .........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 tgctatccaccctaaaaaataaattaaaagtcctaaaataatcaatggaggaagtatcttaaaagtattttcaattccaaaacctgctactaatataaaaaataatattagtaaaggtactaacataacttccactaaatcacctctttactttatatattaagtaaattctcacattataaattttaaatcttattttaatttttataaaatctactactaattataccatatacaaagttttttttacaaataaaaaaagactatcacaaataaaaatgtataaaaaataatttattactttgcaatagtctttaataaaattttttatttaata Mask Tandem Repeat Region ================================================ tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca Find is-nt database================================================ Query_seq: FN1989:FN1990|FN1989:FN1990:Sodium-dependent tyrosine transporter:Tetratricopeptide repeat protein:->->:493888..494224 337 tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1989:FN1990|FN1989:FN1990:Sodium-dependent tyrosine transporter:Tetratricopeptide repeat protein:->->:493888..494224 337 tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1989:FN1990|FN1989:FN1990:Sodium-dependent tyrosine transporter:Tetratricopeptide repeat protein:->->:493888..494224 337 tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 7 End: 111 ...... M K N F I K D Y C K V I N Y F L Y I F I C D S L F L F V K K T L Y M V .................................................................................................................................................................................................................................. Protein_Len: 45 Strand: + Start: 203 End: 337 .......................................................................................................................................................................................................... M E V M L V P L L I L F F I L V A G F G I E N T F K I L P P L I I L G L L I Y F L G W I A Protein_Len: 46 Strand: - Start: 178 End: 315 ................................................................................................................................................................................. Y I F Y L P S K T S T I N T G K S I N N K I N T A P K P I S F V K L I S G G N I I K P S K M ...................... Protein_Len: 36 Strand: - Start: 48 End: 155 ............................................... K K Y M K I Q S L R K K N T F F V K Y I T Y N T T S K I F I L I L N L M ...................................................................................................................................................................................... tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca 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: 86 End: 115 .....................................................................................TTGTAAAAAAAACTTTGTATATGGTATAAT.............................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 125 End: 154 ............................................................................................................................TTTTAAATCTTATTTTAATTTTTATAAAAT....................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 126 End: 155 .............................................................................................................................TTTTATAAAAATTAAAATAAGATTTAAAAT...................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1989:FN1990|FN1989:FN1990:Sodium-dependent tyrosine transporter:Tetratricopeptide repeat protein:->->:493888..494224 337 tattaaataaaaaattttattaaagactattgcaaagtaataaattattttttatacatttttatttgtgatagtctttttttatttgtaaaaaaaactttgtatatggtataattagtagtagattttataaaaattaaaataagatttaaaatttataatgtgagaatttacttaatatataaagtaaagaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca Intra-Species Hit: Count: 1 Min: 98 Max: 337 Len: 240 Subject: NC_003454_FN1989_FN1990|Sodium-dependent tyrosine transporter:Tetratricopeptide repeat protein|POSITIVE:POSITIVE|[493888,494224]|337 HSP 1 e-value: 3.0E-77 bit: 289.0 Len: 146 Query Start:192 Query End:337 Subject Strand: POSITIVE Subject Start: 192 Subject End: 337 ...............................................................................................................................................................................................gaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca ...............................................................................................................................................................................................gaggtgatttagtggaagttatgttagtacctttactaatattattttttatattagtagcaggttttggaattgaaaatacttttaagatacttcctccattgattattttaggacttttaatttattttttagggtggatagca HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 27 Query Start:98 Query End:124 Subject Strand: POSITIVE Subject Start: 98 Subject End: 124 .................................................................................................ctttgtatatggtataattagtagtag..................................................................................................................................................................................................................... .................................................................................................ctttgtatatggtataattagtagtag..................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUGUAUAUGGUAUAAUUAGUAGUAGAUUUUAUAAAAAUUAAAAUAAGAUUUAAAAUUUAUAAUGUGAGAAUUUACUUAAUAUAUAAAGUAAAGAGGUGAUUUAGUGGAAGUUAUGUUAGUACCUUUACUAAUAUUAUUUUUUAUAUUAGUAGCAGGUUUUGGAAUUGAAAAUACUUUUAAGAUACUUCCUCCAUUGAUUAUUUUAGGACUUUUAAUUUAUUUUUUAGGGUGGAUAGCA ((((((((((((((.((((.((.((((((((((...................)))))))))).)).....))))))))..))))))))))....(((((((((..(.((((((....((((.((((((((((((((........)))))))))).)))).))))..((((((....))))))...)))))).)....)))))))))..........((((((((....)))))))).... (-41.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUAUCCACCCUAAAAAAUAAAUUAAAAGUCCUAAAAUAAUCAAUGGAGGAAGUAUCUUAAAAGUAUUUUCAAUUCCAAAACCUGCUACUAAUAUAAAAAAUAAUAUUAGUAAAGGUACUAACAUAACUUCCACUAAAUCACCUCUUUACUUUAUAUAUUAAGUAAAUUCUCACAUUAUAAAUUUUAAAUCUUAUUUUAAUUUUUAUAAAAUCUACUACUAAUUAUACCAUAUACAAAG ............................................((((.((((((.........(......).........((((..(((((((((........))))))))).)))).........)))))).............(((((((........)))))))........(((((((..(((((......)))))..)))))))..................))))........ (-32.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 200 156 50 5 NC_003454:FN0671|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326616..1326846_POSITIVE 270 196 155 170 132 NC_003454:FN1026|5end_tRNA_pseudouridine_synthase_A_1680823..1681053_NEGATIVE 260 219 181 202 148 NC_003454:FN0036|5end_Hypothetical_membrane-spanning_Protein_677609..677839_NEGATIVE 256 230 185 153 94 NC_003454:FN1978|5end_Cell_division_protein_ftsH_479479..479709_POSITIVE 251 239 192 130 87 NC_003454:FN1607|5end_Cytidylate_kinase_117893..118123_NEGATIVE 217 170 122 59 1 NC_003454:FN1941|5end_ClpB_protein_441279..441509_POSITIVE 213 237 191 45 1 NC_003454:FN1598|5end_hypothetical_protein_108152..108382_NEGATIVE 212 148 102 114 69 NC_003454:FN0666|5end_hypothetical_protein_1321599..1321829_POSITIVE 210 115 76 231 184 NC_003454:FN0348|5end_nicotinate_phosphoribosyltransferase_981723..981953_NEGATIVE 209 156 116 90 49 NC_003454:FN1293|5end_hypothetical_protein_1952147..1952377_NEGATIVE 205 155 115 132 91 NC_003454:FN1736|5end_V-type_sodium_ATP_synthase_subunit_A_236021..236251_NEGATIVE 198 215 175 128 78 NC_003454:FN1628|5end_LSU_ribosomal_protein_L18P_133948..134178_NEGATIVE 196 123 87 211 178 NC_003454:FN1408|5end_Aminoacyl-histidine_dipeptidase_2067395..2067625_POSITIVE 196 240 191 129 86 NC_003454:FN0559|5end_Phosphoglucomutase_1211316..1211546_POSITIVE 196 207 176 114 76 NC_003454:FN0449|5end_hypothetical_protein_1092683..1092913_POSITIVE 196 230 183 174 123 NC_003454:FN0425|5end_Hypothetical_cytosolic_protein_1068030..1068260_POSITIVE 195 240 192 71 25 NC_003454:FN0006|5end_tRNA_modification_GTPase_644505..644735_POSITIVE 194 239 191 147 105 NC_003454:FN1475|5end_N-acetylneuraminate_lyase_2157785..2158015_POSITIVE 194 229 184 138 95 NC_003454:FN1237|5end_Choline_kinase_1895057..1895287_NEGATIVE 194 230 187 140 98 NC_003454:FN1700|5end_hypothetical_protein_195799..196029_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 200 156 53 8 NC_003454:FN0670|3end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326699..1326849_POSITIVE 251 239 192 114 71 NC_003454:FN1608|3end_Ribosomal_protein_L11_methyltransferase_117909..118059_NEGATIVE 244 225 185 137 97 NC_003454:FN1977|3end_Cell_cycle_protein_MesJ_479562..479712_POSITIVE 237 181 150 55 24 NC_003454:FN1934|3end_hypothetical_protein_434266..434416_NEGATIVE 225 128 82 87 36 NC_003454:FN0905|3end_hypothetical_protein_1563781..1563931_NEGATIVE 222 128 81 82 31 NC_003454:FN1987|3end_Transcriptional_regulator,_GntR_family_490018..490168_NEGATIVE 221 240 202 84 40 NC_003454:FN2085|3end_hypothetical_protein_596560..596710_NEGATIVE 212 148 102 61 16 NC_003454:FN0665|3end_N-acetylmuramoyl-L-alanine_amidase_1321626..1321776_POSITIVE 205 155 115 114 73 NC_003454:FN1737|3end_V-type_ATP_synthase_subunit_F_236039..236189_NEGATIVE 200 129 81 86 41 NC_003454:FN0683|3end_hypothetical_protein_1338514..1338664_NEGATIVE 198 215 175 101 51 NC_003454:FN1629|3end_50S_ribosomal_protein_L6_133975..134125_NEGATIVE 196 123 87 127 94 NC_003454:FN1407|3end_Glutamate_formiminotransferase_2067391..2067541_POSITIVE 196 240 191 145 102 NC_003454:FN0558|3end_TraT_complement_resistance_protein_precursor_1211412..1211562_POSITIVE 196 207 176 98 60 NC_003454:FN0448|3end_DNA-repair_protein_1092747..1092897_POSITIVE 196 164 123 151 116 NC_003454:FN0335|3end_Outer_membrane_porin_F_969157..969307_NEGATIVE 195 240 194 133 88 NC_003454:FN1236|3end_Choline_transport_protein_1892512..1892662_NEGATIVE 195 240 192 65 19 NC_003454:FN0005|3end_Jag_protein_644579..644729_POSITIVE 194 239 191 125 83 NC_003454:FN1474|3end_N-acetylmannosamine_kinase_2157843..2157993_POSITIVE 194 229 184 146 102 NC_003454:FN0016|3end_hypothetical_protein_654366..654516_POSITIVE 194 230 187 150 108 NC_003454:FN1701|3end_ABC_transporter_ATP-binding_protein_195789..195939_NEGATIVE