Origin IGS: attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaaactccttagattattttatcactttttaaaatttatttccataaaaatatcctttattaacaacaatatatattcaaaatttttagagttgtagtttgataaaatgtacgagttttatttttacattagataacatatttcccctccttaatcttagctcattctagcatattttttaagaaaagaaaaatttttatttggtaattaaactataaaagttctaaatagttgattttattattgaaaatataaggattttagagagaaaaaattttagaaaaaattgctaaggattacttttattttttatttatataaaaatcttgacattttattgtataacatatatacttttagtgtatagatataatacaaaaaaggaagatatatatgaaaaaaaaagaactagagtattttataaataat Mask Tandem Repeat Region ================================================ attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Find is-nt database================================================ Query_seq: FN1663:FN1664|FN1663:FN1664:hypothetical protein:hypothetical protein:<-->:161825..162254 430 attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1663:FN1664|FN1663:FN1664:hypothetical protein:hypothetical protein:<-->:161825..162254 430 attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1663:FN1664|FN1663:FN1664:hypothetical protein:hypothetical protein:<-->:161825..162254 430 attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 5 End: 118 .... * K Y F V R T R K K E Y I D E K K T N Y R Y V L L I Y T I C Y F T L I K I Y M ........................................................................................................................................................................................................................................................................................................................ attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg 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: 88 Start: 75 End: 104 ..........................................................................CTTGACATTTTATTGTATAACATATATACT...................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 31 End: 60 ..............................TTTCATATATATCTTCCTTTTTTGTATTAT.................................................................................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 247 End: 276 ......................................................................................................................................................................................................................................................CTTAAAAAATATGCTAGAATGAGCTAAGAT.......................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 385 End: 414 ................................................................................................................................................................................................................................................................................................................................................................................................ATGGAAATAAATTTTAAAAAGTGATAAAAT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 54 HP_score: -2.9 Tail_Score: -4.39568 Start: 76 End: 90 Full_Region: tcttgacattttatt gtata acata tatac ttttagtgtatagat ...........................................................................gtataacatatatac.................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN1663:FN1664|FN1663:FN1664:hypothetical protein:hypothetical protein:<-->:161825..162254 430 attatttataaaatactctagttctttttttttcatatatatcttccttttttgtattatatctatacactaaaagtatatatgttatacaataaaatgtcaagatttttatataaataaaaaataaaagtaatccttagcaattttttctaaaattttttctctctaaaatccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Intra-Species Hit: Count: 1 Min: 173 Max: 430 Len: 258 Subject: NC_003454_FN1663_FN1664|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[161825,162254]|430 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 258 Query Start:173 Query End:430 Subject Strand: POSITIVE Subject Start: 173 Subject End: 430 ............................................................................................................................................................................ccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg ............................................................................................................................................................................ccttatattttcaataataaaatcaactatttagaacttttatagtttaattaccaaataaaaatttttcttttcttaaaaaatatgctagaatgagctaagattaaggaggggaaatatgttatctaatgtaaaaataaaactcgtacattttatcaaactacaactctaaaaattttgaatatatattgttgttaataaaggatatttttatggaaataaattttaaaaagtgataaaataatctaaggagttttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUAUAUUUUCAAUAAUAAAAUCAACUAUUUAGAACUUUUAUAGUUUAAUUACCAAAUAAAAAUUUUUCUUUUCUUAAAAAAUAUGCUAGAAUGAGCUAAGAUUAAGGAGGGGAAAUAUGUUAUCUAAUGUAAAAAUAAAACUCGUACAUUUUAUCAAACUACAACUCUAAAAAUUUUGAAUAUAUAUUGUUGUUAAUAAAGGAUAUUUUUAUGGAAAUAAAUUUUAAAAAGUGAUAAAAUAAUCUAAGGAGUUUUG ..(((((((....((((((..............(((((.....))))).................((((((((((((((.......(((......))).....))))))))))))))..))))))..)))))))...((((((((.(..(((((((((....(((((.......................)))))...(((((..((((((....))))))..))))).....)))))))))......).)))))))) (-37.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAACUCCUUAGAUUAUUUUAUCACUUUUUAAAAUUUAUUUCCAUAAAAAUAUCCUUUAUUAACAACAAUAUAUAUUCAAAAUUUUUAGAGUUGUAGUUUGAUAAAAUGUACGAGUUUUAUUUUUACAUUAGAUAACAUAUUUCCCCUCCUUAAUCUUAGCUCAUUCUAGCAUAUUUUUUAAGAAAAGAAAAAUUUUUAUUUGGUAAUUAAACUAUAAAAGUUCUAAAUAGUUGAUUUUAUUAUUGAAAAUAUAAGG .......(((((....((((((........))))))...............................(((((.....((((....(((((((((((((((((((...(((((.((((...)))).)))))(((((((.((.((((.....(((((...(((((......))).))....)))))....)))).))..)))))))...))))))))))))...)))))))...))))......)))))......))))) (-32.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 78 31 211 157 NC_003454:FN0306|5end_Iron(III)_dicitrate_transport_system_permease_protein_fecD_941100..941330_POSITIVE 231 165 122 64 12 NC_003454:FN1176|5end_Hypothetical_cytosolic_protein_1837826..1838056_NEGATIVE 198 110 65 145 93 NC_003454:FN2084|5end_Permease_595708..595938_POSITIVE 196 112 77 55 20 NC_003454:FN0141|5end_hypothetical_protein_773265..773495_NEGATIVE 193 155 111 95 48 NC_003454:FN1410|5end_Transporter_2069934..2070164_POSITIVE 193 48 3 204 164 NC_003454:FN0190|5end_Two-component_sensor_kinase_yesM_813975..814205_POSITIVE 189 77 31 124 81 NC_003454:FN1637|5end_LSU_ribosomal_protein_L29P_137070..137300_NEGATIVE 180 112 86 198 169 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 179 129 86 44 8 NC_003454:FN1154|5end_Ribonuclease_BN_1808232..1808462_POSITIVE 178 112 77 55 20 NC_003454:FN1356|5end_hypothetical_protein_2007922..2008152_POSITIVE 178 206 167 36 2 NC_003454:FN0747|5end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1406254..1406484_NEGATIVE 178 112 77 55 20 NC_003454:FN0510|5end_hypothetical_protein_1160326..1160556_NEGATIVE 178 116 78 212 180 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 177 110 64 40 2 NC_003454:FN0036|5end_Hypothetical_membrane-spanning_Protein_677609..677839_NEGATIVE 176 86 41 119 77 NC_003454:FN0633|5end_Replication_protein_1290928..1291158_POSITIVE 172 77 32 184 146 NC_003454:FN1002|5end_Adenosylmethionine-8-amino-7-oxononanoate_aminotransferase_1656738..1656968_POSITIVE 171 113 84 182 159 NC_003454:FN0072|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_711715..711945_POSITIVE 170 114 81 37 1 NC_003454:FN1509|5end_hypothetical_protein_14176..14406_NEGATIVE 169 214 183 136 104 NC_003454:FN0383|5end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1014148..1014378_POSITIVE 166 176 146 44 12 NC_003454:FN1800|5end_Peptidyl-prolyl_cis-trans_isomerase_281630..281860_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 165 122 101 49 NC_003454:FN1177|3end_hypothetical_protein_1837789..1837939_NEGATIVE 208 124 83 73 28 NC_003454:FN0144|3end_hypothetical_protein_774165..774315_NEGATIVE 196 112 77 117 82 NC_003454:FN0141|3end_hypothetical_protein_773203..773353_NEGATIVE 189 77 31 124 81 NC_003454:FN1638|3end_50S_ribosomal_protein_L16_137070..137220_NEGATIVE 179 124 85 51 4 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 179 114 76 114 72 NC_003454:FN1509|3end_hypothetical_protein_14099..14249_NEGATIVE 178 206 167 39 5 NC_003454:FN0748|3end_hypothetical_protein_1406251..1406401_NEGATIVE 177 110 64 40 2 NC_003454:FN0037|3end_hypothetical_protein_677609..677759_NEGATIVE 177 72 33 78 37 NC_003454:FN1923|3end_Adenine-specific_methyltransferase_419607..419757_NEGATIVE 174 117 80 37 1 NC_003454:FN0996|3end_Hypothetical_membrane-spanning_protein_1650673..1650823_NEGATIVE 172 77 32 116 78 NC_003454:FN1001|3end_Dethiobiotin_synthetase_1656750..1656900_POSITIVE 171 99 63 56 19 NC_003454:FN0129|3end_Urease_accessory_protein_ureG_758370..758520_POSITIVE 169 214 183 132 100 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 168 98 63 77 41 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 168 129 82 54 5 NC_003454:FN1797|3end_Spermidine/putrescine_transport_ATP-binding_protein_potA_280031..280181_POSITIVE 165 220 173 63 7 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 164 35 1 59 23 NC_003454:FN1252|3end_34_kDa_membrane_antigen_precursor_1910134..1910284_POSITIVE 164 172 144 101 72 NC_003454:FN0617|3end_DNA_polymerase_III,_beta_chain_1276602..1276752_NEGATIVE 164 195 153 58 20 NC_003454:FN0068|3end_Lipoprotein_signal_peptidase_707885..708035_POSITIVE 164 138 96 59 9 NC_003454:FN1798|3end_Spermidine/putrescine_transport_system_permease_protein_potB_280872..281022_POSITIVE