Origin IGS: aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa .........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 ttattacctccataaaaaattatttcttcccaattattctactatatttactataacatttcaaatattttattttttctatataaaaatggtataatattttaaaaatagttaaagaggtttttggtataaatataaaatttaaaaataaggagtgataattatgcaaccaacaaaagaatggttagaaaaatgggaaaaagtaaaagataaattgcaacctaatagtaatcttgtaaattattttactttaaaagaaattgctggaaaagaattagatgtt Mask Tandem Repeat Region ================================================ aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa Find is-nt database================================================ Query_seq: FN0728:FN0729|FN0728:FN0729:hypothetical protein:Phosphoglycerate mutase:<-->:1386211..1386493 283 aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0728:FN0729|FN0728:FN0729:hypothetical protein:Phosphoglycerate mutase:<-->:1386211..1386493 283 aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0728:FN0729|FN0728:FN0729:hypothetical protein:Phosphoglycerate mutase:<-->:1386211..1386493 283 aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 115 End: 261 .................................................................................................................. M H N Y H S L F L N F I F I P K T S L T I F K I L Y H F Y I E K I K Y L K C Y S K Y S R I I G K K ...................... Protein_Len: 43 Strand: - Start: 1 End: 129 V D L E K G A I E K L T F Y N V L N S N P Q L K D K V K E W K E L W E K T P Q M I I M .......................................................................................................................................................... aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa 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: 219 End: 248 ..........................................................................................................................................................................................................................TTTGAAATGTTATAGTAAATATAGTAGAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0728:FN0729|FN0728:FN0729:hypothetical protein:Phosphoglycerate mutase:<-->:1386211..1386493 283 aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactccttatttttaaattttatatttataccaaaaacctctttaactatttttaaaatattataccatttttatatagaaaaaataaaatatttgaaatgttatagtaaatatagtagaataattgggaagaaataattttttatggaggtaataa Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_003454_FN0728_FN0729|hypothetical protein:Phosphoglycerate mutase|NEGATIVE:POSITIVE|[1386211,1386493]|283 HSP 1 e-value: 6.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactcc....................................................................................................................................................... aacatctaattcttttccagcaatttcttttaaagtaaaataatttacaagattactattaggttgcaatttatcttttactttttcccatttttctaaccattcttttgttggttgcataattatcactcc....................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUCUAAUUCUUUUCCAGCAAUUUCUUUUAAAGUAAAAUAAUUUACAAGAUUACUAUUAGGUUGCAAUUUAUCUUUUACUUUUUCCCAUUUUUCUAACCAUUCUUUUGUUGGUUGCAUAAUUAUCACUCC ......(((((.....(((((((...........(((((....))))).............(((((.((........................)).)))))......)))))))......)))))....... (-12.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGUGAUAAUUAUGCAACCAACAAAAGAAUGGUUAGAAAAAUGGGAAAAAGUAAAAGAUAAAUUGCAACCUAAUAGUAAUCUUGUAAAUUAUUUUACUUUAAAAGAAAUUGCUGGAAAAGAAUUAGAUGUU ..((..((........(((((.........))))).............(((((((..(((((.((((((.............)))))).)))))))))))).......))..)).................. (-15.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 748 130 81 221 172 NC_003454:FN0728|5end_hypothetical_protein_1386120..1386350_NEGATIVE 253 115 72 102 54 NC_003454:FN0950|5end_Precorrin-6X_reductase_1607775..1608005_NEGATIVE 248 130 82 169 122 NC_003454:FN0514|5end_hypothetical_protein_1163431..1163661_POSITIVE 239 120 71 149 98 NC_003454:FN0992|5end_ADP-heptose:LPS_heptosyltransferase_II_1646598..1646828_POSITIVE 239 121 88 161 126 NC_003454:FN0376|5end_Iron(III)-transport_ATP-binding_protein_sfuC_1006365..1006595_POSITIVE 239 114 76 64 20 NC_003454:FN1633|5end_LSU_ribosomal_protein_L24P_135939..136169_NEGATIVE 239 114 76 184 140 NC_003454:FN1632|5end_LSU_ribosomal_protein_L5P_135819..136049_NEGATIVE 237 105 61 53 6 NC_003454:FN1326|5end_Undecaprenyl_pyrophosphate_synthetase_1981890..1982120_NEGATIVE 228 119 71 77 28 NC_003454:FN0652|5end_Glyceraldehyde_3-phosphate_dehydrogenase_1310362..1310592_POSITIVE 228 129 81 57 7 NC_003454:FN0259|5end_Zinc-transporting_ATPase_886258..886488_NEGATIVE 225 129 83 99 47 NC_003454:FN0170|5end_GTP-binding_protein_795211..795441_POSITIVE 225 108 61 120 68 NC_003454:FN0092|5end_NADPH-dependent_butanol_dehydrogenase_727908..728138_POSITIVE 224 36 2 94 64 NC_003454:FN1330|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1984958..1985188_NEGATIVE 216 109 71 63 30 NC_003454:FN1517|5end_Leucyl-tRNA_synthetase_23455..23685_NEGATIVE 213 55 24 53 25 NC_003454:FN1731|5end_Anthranilate_synthase_component_II_231037..231267_NEGATIVE 212 95 59 204 159 NC_003454:FN1492|5end_DNA_repair_protein_recO_2173470..2173700_NEGATIVE 212 130 86 103 57 NC_003454:FN0677|5end_hypothetical_protein_1332641..1332871_POSITIVE 209 116 74 116 74 NC_003454:FN2039|5end_50S_ribosomal_protein_L1_548557..548787_NEGATIVE 207 119 75 146 85 NC_003454:FN1994|5end_hypothetical_protein_497577..497807_POSITIVE 204 110 69 206 159 NC_003454:FN1210|5end_Metal_dependent_hydrolase_1870766..1870996_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 115 72 130 82 NC_003454:FN0951|3end_Precorrin-3B_C17-methyltransferase_1607747..1607897_NEGATIVE 239 120 71 146 95 NC_003454:FN0991|3end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1646675..1646825_POSITIVE 239 121 88 147 112 NC_003454:FN0375|3end_Iron(III)-binding_protein_1006431..1006581_POSITIVE 228 129 81 54 4 NC_003454:FN0260|3end_Transcriptional_repressor_smtB_886261..886411_NEGATIVE 225 108 61 100 48 NC_003454:FN0091|3end_Phosphoserine_phosphatase_727968..728118_POSITIVE 224 36 2 137 107 NC_003454:FN1331|3end_Methyltransferase_1984915..1985065_NEGATIVE 220 110 69 40 1 NC_003454:FN0196|3end_Transcriptional_regulator,_FUR_family_822747..822897_POSITIVE 216 54 11 151 113 NC_003454:FN0310|3end_Iron(III)-transport_ATP-binding_protein_sfuC_946946..947096_POSITIVE 216 109 71 55 22 NC_003454:FN1518|3end_RNA_polymerase_sigma-70_factor_23463..23613_NEGATIVE 210 60 13 95 45 NC_003454:FN0401|3end_hypothetical_protein_1039905..1040055_NEGATIVE 209 116 74 55 13 NC_003454:FN2040|3end_LSU_ribosomal_protein_L11P_548618..548768_NEGATIVE 208 110 61 149 94 NC_003454:FN1871|3end_hypothetical_protein_362297..362447_NEGATIVE 207 119 75 139 78 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 203 108 61 114 63 NC_003454:FN0290|3end_Hemolysin_916814..916964_NEGATIVE 200 107 64 86 46 NC_003454:FN1632|3end_LSU_ribosomal_protein_L5P_135268..135418_NEGATIVE 199 130 87 138 104 NC_003454:FN0967|3end_CbiD_protein_1619923..1620073_NEGATIVE 197 87 59 147 119 NC_003454:FN0834|3end_hypothetical_protein_1498088..1498238_POSITIVE 197 87 43 83 30 NC_003454:FN0010|3end_nicotinate-nucleotide_pyrophosphorylase_651118..651268_POSITIVE 197 103 61 117 70 NC_003454:FN1790|3end_Cob(I)alamin_adenosyltransferase_272112..272262_POSITIVE 196 97 56 101 51 NC_003454:FN1350|3end_Integral_membrane_protein_2002359..2002509_NEGATIVE