Origin IGS: tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttttcttaaaatgaaaaactaaataacctttaaatgaaactgctgtgatgtccattattgtcgaatgagcctttatggagctcatgagacactaatggctatcaagcagtttttatatattaaaaaaatttata Mask Tandem Repeat Region ================================================ tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Find is-nt database================================================ Query_seq: FN1259:FN1260|FN1259:FN1260:Uracil-DNA glycosylase:Sensory Transduction Protein Kinase:-><-:1915817..1915952 136 tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1259:FN1260|FN1259:FN1260:Uracil-DNA glycosylase:Sensory Transduction Protein Kinase:-><-:1915817..1915952 136 tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1259:FN1260|FN1259:FN1260:Uracil-DNA glycosylase:Sensory Transduction Protein Kinase:-><-:1915817..1915952 136 tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Predict ORF larger than 30AA ================================================ tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1259:FN1260|FN1259:FN1260:Uracil-DNA glycosylase:Sensory Transduction Protein Kinase:-><-:1915817..1915952 136 tataaatttttttaatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Intra-Species Hit: Count: 1 Min: 14 Max: 136 Len: 123 Subject: NC_003454_FN1259_FN1260|Uracil-DNA glycosylase:Sensory Transduction Protein Kinase|POSITIVE:NEGATIVE|[1915817,1915952]|136 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:14 Query End:136 Subject Strand: POSITIVE Subject Start: 14 Subject End: 136 .............aatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat .............aatatataaaaactgcttgatagccattagtgtctcatgagctccataaaggctcattcgacaataatggacatcacagcagtttcatttaaaggttatttagtttttcattttaagaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUAUAAAAACUGCUUGAUAGCCAUUAGUGUCUCAUGAGCUCCAUAAAGGCUCAUUCGACAAUAAUGGACAUCACAGCAGUUUCAUUUAAAGGUUAUUUAGUUUUUCAUUUUAAGAAAAAU .........((((((((((((..((((((.((((..(((((((.......)))))))..)))).))))))..)))).)))))))).................(((((((.......))))))) (-37.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCUUAAAAUGAAAAACUAAAUAACCUUUAAAUGAAACUGCUGUGAUGUCCAUUAUUGUCGAAUGAGCCUUUAUGGAGCUCAUGAGACACUAAUGGCUAUCAAGCAGUUUUUAUAUAUU .((((((.......)))))).................(((((((((.(((((.((((((.((((..((((((((....)).))))))..)))).)))))).))))))))))))))........ (-41.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 70 21 171 122 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 304 79 31 214 167 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 262 47 11 131 90 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 250 54 13 82 43 NC_003454:FN1227|5end_hypothetical_protein_1885707..1885937_NEGATIVE 244 118 73 169 127 NC_003454:FN0609|5end_SsrA-binding_protein_1264261..1264491_POSITIVE 242 53 14 228 192 NC_003454:FN0481|5end_hypothetical_protein_1127777..1128007_POSITIVE 238 56 17 156 119 NC_003454:FN0812|5end_Hypothetical_cytosolic_protein_1471051..1471281_POSITIVE 232 70 24 221 176 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 230 73 34 124 87 NC_003454:FN1404|5end_Imidazolonepropionase_2063066..2063296_POSITIVE 229 55 12 186 146 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 229 55 12 82 42 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 222 46 6 167 123 NC_003454:FN0354|5end_Hypothetical_membrane-spanning_protein_985292..985522_POSITIVE 220 63 21 66 20 NC_003454:FN2101|5end_Transporter_610246..610476_POSITIVE 219 55 13 36 1 NC_003454:FN0174|5end_Enoyl-[acyl-carrier-protein]_reductase_799427..799657_POSITIVE 218 74 35 178 134 NC_003454:FN0930|5end_Glycerol-3-phosphate_cytidylyltransferase_1583964..1584194_NEGATIVE 218 54 26 52 17 NC_003454:FN1797|5end_Spermidine/putrescine_transport_ATP-binding_protein_potA_278821..279051_POSITIVE 217 58 15 77 33 NC_003454:FN1620|5end_30S_ribosomal_protein_S2_127896..128126_POSITIVE 216 85 41 51 9 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 211 60 11 218 171 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 209 84 42 56 16 NC_003454:FN0668|5end_High-affinity_zinc_uptake_system_protein_znuA_precursor_1323969..1324199_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 70 21 69 20 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 345 90 41 75 27 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 304 79 31 81 34 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 276 70 24 54 8 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 268 90 48 89 37 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 238 56 17 133 96 NC_003454:FN0811|3end_hypothetical_protein_1471108..1471258_POSITIVE 237 90 48 68 14 NC_003454:FN0371|3end_hypothetical_protein_1000840..1000990_POSITIVE 230 73 34 111 74 NC_003454:FN1403|3end_Histidine_permease_2063133..2063283_POSITIVE 228 117 73 151 110 NC_003454:FN0608|3end_Exoribonuclease_II_1264324..1264474_POSITIVE 227 59 14 46 2 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 220 63 21 56 10 NC_003454:FN2100|3end_hypothetical_protein_610316..610466_POSITIVE 215 120 76 106 69 NC_003454:FN0701|3end_Methyltransferase_1360894..1361044_POSITIVE 205 49 20 113 81 NC_003454:FN0503|3end_Transcriptional_regulatory_protein,_LYSR_family_1152664..1152814_NEGATIVE 204 50 1 84 27 NC_003454:FN1200|3end_hypothetical_protein_1860227..1860377_NEGATIVE 204 88 42 146 106 NC_003454:FN1788|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_270233..270383_POSITIVE 202 53 18 98 55 NC_003454:FN1267|3end_hypothetical_protein_1923054..1923204_NEGATIVE 201 89 47 150 108 NC_003454:FN0904|3end_NAD(FAD)-utilizing_dehydrogenase_1563760..1563910_POSITIVE 197 114 71 103 61 NC_003454:FN0556|3end_hypothetical_protein_1208380..1208530_NEGATIVE 196 59 15 140 107 NC_003454:FN1628|3end_LSU_ribosomal_protein_L18P_133580..133730_NEGATIVE 191 80 31 135 79 NC_003454:FN1317|3end_RNA_polymerase_sigma_factor_1970273..1970423_NEGATIVE