Origin IGS: aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgttttcctccgttaagtttattaggttagacattgtagcattatttaggaaaaaagtaaagaataaataatatagaaaatagctcattacattccaaatttttatcttaaaatttggaatgtaactcacttattttctaaaacaaattattataaaaggggagagtaaatt Mask Tandem Repeat Region ================================================ aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Find is-nt database================================================ Query_seq: FN1614:FN1615|FN1614:FN1615:MG(2+) chelatase family protein:Integral membrane protein:<-->:125093..125264 172 aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1614:FN1615|FN1614:FN1615:MG(2+) chelatase family protein:Integral membrane protein:<-->:125093..125264 172 aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1614:FN1615|FN1614:FN1615:MG(2+) chelatase family protein:Integral membrane protein:<-->:125093..125264 172 aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 43 End: 171 .......................................... M S Y I P N F K I K I W N V M S Y F L Y Y L F F T F F L N N A T M S N L I N L T E E N . aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg 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: 85 Start: 111 End: 140 ..............................................................................................................CTTTACTTTTTTCCTAAATAATGCTACAAT................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 74 End: 103 .........................................................................TTTGGAATGTAATGAGCTATTTTCTATATT..................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 60 HP_score: -3.9 Tail_Score: -4.37092 Start: 40 End: 92 Full_Region: aaataatatagaaaa tagctcattacattccaaatttt tatctt aaaatttggaatgtaactcactta ttttctaaaacaaat .......................................tagctcattacattccaaatttttatcttaaaatttggaatgtaactcactta................................................................................ TransTerm Strand: + Conf: 68 HP_score: -4.7 Tail_Score: -4.74989 Start: 41 End: 92 Full_Region: TTTGTTTTAGAAAAT AAGTGAGTTACATTCCAAATTTT AAGATA AAAATTTGGAATGTAATGAGCTA TTTTCTATATTATTT ........................................AAGTGAGTTACATTCCAAATTTTAAGATAAAAATTTGGAATGTAATGAGCTA................................................................................ TransTerm Strand: + Conf: 71 HP_score: -7.3 Tail_Score: -3.95858 Start: 43 End: 90 Full_Region: TGTTTTAGAAAATAA GTGAGTTACATTCCAAATTTT AAGATA AAAATTTGGAATGTAATGAGC TATTTTCTATATTAT ..........................................GTGAGTTACATTCCAAATTTTAAGATAAAAATTTGGAATGTAATGAGC.................................................................................. TransTerm Strand: - Conf: 66 HP_score: -6.9 Tail_Score: -3.18115 Start: 44 End: 88 Full_Region: aatatagaaaatagc tcattacattccaaatttt tatctt aaaatttggaatgtaactca cttattttctaaaac ...........................................tcattacattccaaatttttatcttaaaatttggaatgtaactca.................................................................................... TransTerm Strand: - Conf: 84 HP_score: -11.1 Tail_Score: -2.78052 Start: 47 End: 86 Full_Region: tatagaaaatagctc attacattccaaatttt tatctt aaaatttggaatgtaac tcacttattttctaa ..............................................attacattccaaatttttatcttaaaatttggaatgtaac...................................................................................... TransTerm Strand: + Conf: 72 HP_score: -8.7 Tail_Score: -2.81187 Start: 53 End: 80 Full_Region: AATAAGTGAGTTACA TTCCAAATTTT AAGATA AAAATTTGGAA TGTAATGAGCTATTT ....................................................TTCCAAATTTTAAGATAAAAATTTGGAA............................................................................................ Find igs database================================================ Query_seq: FN1614:FN1615|FN1614:FN1615:MG(2+) chelatase family protein:Integral membrane protein:<-->:125093..125264 172 aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_003454_FN1614_FN1615|MG(2+) chelatase family protein:Integral membrane protein|NEGATIVE:POSITIVE|[125093,125264]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg aatttactctccccttttataataatttgttttagaaaataagtgagttacattccaaattttaagataaaaatttggaatgtaatgagctattttctatattatttattctttacttttttcctaaataatgctacaatgtctaacctaataaacttaacggaggaaaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUACUCUCCCCUUUUAUAAUAAUUUGUUUUAGAAAAUAAGUGAGUUACAUUCCAAAUUUUAAGAUAAAAAUUUGGAAUGUAAUGAGCUAUUUUCUAUAUUAUUUAUUCUUUACUUUUUUCCUAAAUAAUGCUACAAUGUCUAACCUAAUAAACUUAACGGAGGAAAACG .......(((((....................(((((((((.((..(((((((((((((((((......)))))))))))))))))..)))))))))))(((((((((................)))))))))............................)))))...... (-37.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUUCCUCCGUUAAGUUUAUUAGGUUAGACAUUGUAGCAUUAUUUAGGAAAAAAGUAAAGAAUAAAUAAUAUAGAAAAUAGCUCAUUACAUUCCAAAUUUUUAUCUUAAAAUUUGGAAUGUAACUCACUUAUUUUCUAAAACAAAUUAUUAUAAAAGGGGAGAGUAAAUU ..((((((((..(((.(((((......))))).((((...((((((((................)))))))).((((((((((....((((((((((((((((......)))))))))))))))).....))))))))))..)))).......)))..))))))))...... (-40.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 705 90 41 181 132 NC_003454:FN1614|5end_MG(2+)_chelatase_family_protein_125002..125232_NEGATIVE 497 90 41 185 138 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 432 90 41 227 175 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 426 90 41 214 162 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 424 90 41 201 149 NC_003454:FN1819|5end_Export_ABC_transporter_307519..307749_POSITIVE 417 90 41 231 184 NC_003454:FN0484|5end_Lipase_1129470..1129700_POSITIVE 396 90 41 189 142 NC_003454:FN0085|5end_Ethanolamine_utilization_cobalamin_adenosyltransferase_723270..723500_POSITIVE 371 90 41 182 130 NC_003454:FN2095|5end_General_secretion_pathway_protein_E_606080..606310_NEGATIVE 370 90 41 196 144 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 354 73 33 181 142 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 354 90 41 201 149 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 333 80 34 210 161 NC_003454:FN1459|5end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase_2141360..2141590_NEGATIVE 331 78 33 167 126 NC_003454:FN0670|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1325702..1325932_POSITIVE 323 57 11 148 98 NC_003454:FN1822|5end_Flavodoxin_311148..311378_POSITIVE 323 75 32 49 3 NC_003454:FN1821|5end_Hypothetical_cytosolic_protein_311031..311261_POSITIVE 287 90 41 187 140 NC_003454:FN1810|5end_Manganese_transport_system_membrane_protein_mntB_291953..292183_NEGATIVE 259 80 34 196 146 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 252 109 69 190 151 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 252 90 41 231 180 NC_003454:FN0358|5end_ATP_synthase_subunit_B_989674..989904_NEGATIVE 251 90 41 209 162 NC_003454:FN2036|5end_DNA-directed_RNA_polymerase_beta_chain_546371..546601_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 78 33 79 38 NC_003454:FN0669|3end_High-affinity_zinc_uptake_system_ATP-binding_protein_znuC_1325694..1325844_POSITIVE 323 57 11 129 79 NC_003454:FN1821|3end_Hypothetical_cytosolic_protein_311209..311359_POSITIVE 256 123 86 108 64 NC_003454:FN0331|3end_hypothetical_protein_966168..966318_POSITIVE 252 109 69 71 32 NC_003454:FN1069|3end_DNA_topoisomerase_I_1717082..1717232_POSITIVE 246 117 82 118 83 NC_003454:FN1732|3end_hypothetical_protein_231281..231431_NEGATIVE 245 64 33 43 13 NC_003454:FN1919|3end_Methyltransferase_415133..415283_NEGATIVE 243 108 62 87 47 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 243 115 71 93 55 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE 233 73 33 108 68 NC_003454:FN0797|3end_hypothetical_protein_1455668..1455818_NEGATIVE 230 85 47 43 5 NC_003454:FN0368|3end_adenylosuccinate_lyase_997038..997188_NEGATIVE 228 148 105 130 77 NC_003454:FN1012|3end_HPr_kinase/phosphorylase_1665680..1665830_NEGATIVE 227 107 62 91 51 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 226 113 71 112 58 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 225 104 71 88 58 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 224 125 82 133 78 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 220 102 62 62 23 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 218 55 13 67 23 NC_003454:FN0598|3end_Phospholipid-lipopolysaccharide_ABC_transporter_1253712..1253862_POSITIVE 218 108 62 86 46 NC_003454:FN1820|3end_Export_ABC_transporter_311016..311166_POSITIVE 217 136 95 128 89 NC_003454:FN0671|3end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1327538..1327688_POSITIVE 216 101 62 95 61 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE