Origin IGS: tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaattttccttaataattagtttgtagataatatagtatataacaaaaaaactaaaatttaaagttaaaactaaaaagaatgaaattgaggttttagctcaaaagctttacttttttataaaaatagtgtataataaaataaatcaattttagaaaggagaaagaaga Mask Tandem Repeat Region ================================================ tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt Find is-nt database================================================ Query_seq: FN1198:FN1199|FN1198:FN1199:Transporter:DNA polymerase IV:<-->:1859032..1859200 169 tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1198:FN1199|FN1198:FN1199:Transporter:DNA polymerase IV:<-->:1859032..1859200 169 tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1198:FN1199|FN1198:FN1199:Transporter:DNA polymerase IV:<-->:1859032..1859200 169 tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 19 End: 129 .................. F Q N I K N Y V I K I F F Y L K Q A L V E I E N K K T K V K F K L K K T M ........................................ tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt 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: 86 Start: 34 End: 63 .................................CTTTACTTTTTTATAAAAATAGTGTATAAT.......................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 105 End: 134 ........................................................................................................CTTTAAATTTTAGTTTTTTTGTTATATACT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1198:FN1199|FN1198:FN1199:Transporter:DNA polymerase IV:<-->:1859032..1859200 169 tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattctttttagttttaactttaaattttagtttttttgttatatactatattatctacaaactaattattaaggaaaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_003454_FN1198_FN1199|Transporter:DNA polymerase IV|NEGATIVE:POSITIVE|[1859032,1859200]|169 HSP 1 e-value: 1.0E-44 bit: 180.0 Len: 91 Query Start:1 Query End:91 Subject Strand: POSITIVE Subject Start: 1 Subject End: 91 tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattc.............................................................................. tcttctttctcctttctaaaattgatttattttattatacactatttttataaaaaagtaaagcttttgagctaaaacctcaatttcattc.............................................................................. HSP 2 e-value: 3.0E-17 bit: 89.7 Len: 45 Query Start:125 Query End:169 Subject Strand: POSITIVE Subject Start: 125 Subject End: 169 ............................................................................................................................gttatatactatattatctacaaactaattattaaggaaaatttt ............................................................................................................................gttatatactatattatctacaaactaattattaaggaaaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUCUUUCUCCUUUCUAAAAUUGAUUUAUUUUAUUAUACACUAUUUUUAUAAAAAAGUAAAGCUUUUGAGCUAAAACCUCAAUUUCAUUCUUUUUAGUUUUAACUUUAAAUUUUAGUUUUUUUGUUAUAUACUAUAUUAUCUACAAACUAAUUAUUAAGGAAAAUUUU .........(((((..(((((((((((((((((.(((((.........))))).))))))))....(((((.......)))))...........)))))))))...........(((((..(((((.(((........)))..)))))..)))))..)))))....... (-18.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUUCCUUAAUAAUUAGUUUGUAGAUAAUAUAGUAUAUAACAAAAAAACUAAAAUUUAAAGUUAAAACUAAAAAGAAUGAAAUUGAGGUUUUAGCUCAAAAGCUUUACUUUUUUAUAAAAAUAGUGUAUAAUAAAAUAAAUCAAUUUUAGAAAGGAGAAAGAAGA ....((((((((...((((.((((((..((.(((((.(((......((((((.((((.(((..((((((((((...((........))..))))))))))..)))..)))).))))))......))).))))).))...)))))).)))).....))))))))...... (-25.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 682 100 51 191 142 NC_003454:FN1198|5end_Transporter_1858941..1859171_NEGATIVE 239 48 3 227 176 NC_003454:FN1270|5end_Hypothetical_cytosolic_protein_1926592..1926822_NEGATIVE 232 103 61 231 173 NC_003454:FN1482|5end_Guanosine-3',5'-bis(Diphosphate)_3'-pyrophosphohydrolase_2165992..2166222_NEGATIVE 230 48 3 137 93 NC_003454:FN0150|5end_Acyl_carrier_protein_778453..778683_POSITIVE 224 110 62 124 83 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 224 48 10 97 60 NC_003454:FN0555|5end_Transcriptional_regulator,_MerR_family_1207653..1207883_POSITIVE 224 45 5 166 124 NC_003454:FN1679|5end_LPS_biosynthesis_protein_WbpG_175711..175941_NEGATIVE 214 124 81 73 37 NC_003454:FN1656|5end_SSU_ribosomal_protein_S18P_152760..152990_NEGATIVE 213 104 65 49 15 NC_003454:FN1464|5end_1-deoxy-D-xylulose-5-phosphate_synthase_2147705..2147935_NEGATIVE 209 109 62 109 68 NC_003454:FN1608|5end_Ribosomal_protein_L11_methyltransferase_118847..119077_NEGATIVE 209 110 64 159 114 NC_003454:FN1607|5end_Cytidylate_kinase_117893..118123_NEGATIVE 208 45 3 144 94 NC_003454:FN0701|5end_Methyltransferase_1359261..1359491_POSITIVE 207 157 116 199 159 NC_003454:FN0205|5end_Sodium/glutamate_symport_carrier_protein_831469..831699_POSITIVE 206 115 71 62 27 NC_003454:FN0200|5end_Biotin_carboxyl_carrier_protein_of_glutaconyl-COA_decarboxylase_826123..826353_POSITIVE 206 102 63 112 66 NC_003454:FN1847|5end_DTDP-4-dehydrorhamnose_3,5-epimerase_336142..336372_POSITIVE 203 129 83 148 90 NC_003454:FN1626|5end_LSU_ribosomal_protein_L30P_133049..133279_NEGATIVE 202 120 77 132 83 NC_003454:FN1401|5end_urocanate_hydratase_2058592..2058822_POSITIVE 199 49 6 143 95 NC_003454:FN0916|5end_hypothetical_protein_1572514..1572744_NEGATIVE 198 144 106 55 17 NC_003454:FN0512|5end_Flavoprotein_1162597..1162827_NEGATIVE 198 43 1 136 91 NC_003454:FN2045|5end_Ferric_uptake_regulation_protein_550802..551032_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 48 3 74 23 NC_003454:FN1271|3end_Protease_IV_1926745..1926895_NEGATIVE 230 48 3 69 25 NC_003454:FN0149|3end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_778465..778615_POSITIVE 209 109 62 134 93 NC_003454:FN1609|3end_hypothetical_protein_118822..118972_NEGATIVE 209 110 64 143 98 NC_003454:FN1608|3end_Ribosomal_protein_L11_methyltransferase_117909..118059_NEGATIVE 208 45 3 122 72 NC_003454:FN0700|3end_Protein_translocase_subunit_secF_1359319..1359469_POSITIVE 207 157 116 56 16 NC_003454:FN0204|3end_Glutaconyl-CoA_decarboxylase_A_subunit_831406..831556_POSITIVE 206 102 63 115 69 NC_003454:FN1846|3end_hypothetical_protein_336225..336375_POSITIVE 203 129 83 135 77 NC_003454:FN1627|3end_SSU_ribosomal_protein_S5P_133062..133212_NEGATIVE 201 89 41 113 66 NC_003454:FN0273|3end_Butyrate-acetoacetate_CoA-transferase_subunit_B_900162..900312_POSITIVE 191 130 81 85 36 NC_003454:FN1092|3end_hypothetical_protein_1738261..1738411_POSITIVE 190 120 76 66 17 NC_003454:FN0676|3end_10_kDa_chaperonin_GROES_1332108..1332258_NEGATIVE 189 87 41 86 42 NC_003454:FN1376|3end_oxaloacetate_decarboxylase_2025305..2025455_POSITIVE 189 59 12 102 50 NC_003454:FN0318|3end_CITX_protein_955285..955435_NEGATIVE 186 155 114 123 77 NC_003454:FN1345|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase_1998130..1998280_NEGATIVE 182 92 54 43 2 NC_003454:FN1639|3end_SSU_ribosomal_protein_S3P_137504..137654_NEGATIVE 181 130 84 145 99 NC_003454:FN0399|3end_Dipeptide_transport_ATP-binding_protein_dppD_1038733..1038883_POSITIVE 178 129 85 94 52 NC_003454:FN0901|3end_DNA_polymerase,_bacteriophage-type_1560639..1560789_POSITIVE 176 120 76 101 56 NC_003454:FN0916|3end_hypothetical_protein_1572065..1572215_NEGATIVE 176 103 61 63 12 NC_003454:FN1675|3end_Transposase_172206..172356_NEGATIVE 175 50 1 148 98 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE