Origin IGS: taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attctttaaatatttaaagggttgtgtcgaaatttaagactccaacacaacccttagtgaacatcttgttaaataaactaatgcgtgttaaatcgagtaaaggatttttatttcagccaaaacataatttttatcacgcaggattcattataacattttgtgtgttggaatta Mask Tandem Repeat Region ================================================ taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Find is-nt database================================================ Query_seq: PI1554:PI1555|PI1554:PI1555:hypothetical protein:conserved hypothetical protein:->->:1470544..1470716 173 taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1554:PI1555|PI1554:PI1555:hypothetical protein:conserved hypothetical protein:->->:1470544..1470716 173 taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1554:PI1555|PI1554:PI1555:hypothetical protein:conserved hypothetical protein:->->:1470544..1470716 173 taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: - Start: 1 End: 150 L E L V C F T I I F G A H Y F N H K P Q F L F G K S S K V R M L K N L L I N V L P Q T P T K F K S M ....................... taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat 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================================================ taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.3 Tail_Score: -3.81137 Start: 121 End: 155 Full_Region: CAAGATGTTCACTAA GGGTTGTGTTGGAGT CTTAA ATTTCGACACAACCC TTTAAATATTTAAAG ........................................................................................................................GGGTTGTGTTGGAGTCTTAAATTTCGACACAACCC.................. Find igs database================================================ Query_seq: PI1554:PI1555|PI1554:PI1555:hypothetical protein:conserved hypothetical protein:->->:1470544..1470716 173 taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: pint_PI1554_PI1555|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1470544,1470716]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat taattccaacacacaaaatgttataatgaatcctgcgtgataaaaattatgttttggctgaaataaaaatcctttactcgatttaacacgcattagtttatttaacaagatgttcactaagggttgtgttggagtcttaaatttcgacacaaccctttaaatatttaaagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCCAACACACAAAAUGUUAUAAUGAAUCCUGCGUGAUAAAAAUUAUGUUUUGGCUGAAAUAAAAAUCCUUUACUCGAUUUAACACGCAUUAGUUUAUUUAACAAGAUGUUCACUAAGGGUUGUGUUGGAGUCUUAAAUUUCGACACAACCCUUUAAAUAUUUAAAGAAU ..((((............(((((.(((((((..((((((..........((((((....)))))).(((((........)))))..))))))...))))))))))))(((((((....(((((((((((((((((.....)))))))))))))))))..)))))))...)))) (-44.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUUUAAAUAUUUAAAGGGUUGUGUCGAAAUUUAAGACUCCAACACAACCCUUAGUGAACAUCUUGUUAAAUAAACUAAUGCGUGUUAAAUCGAGUAAAGGAUUUUUAUUUCAGCCAAAACAUAAUUUUUAUCACGCAGGAUUCAUUAUAACAUUUUGUGUGUUGGAAUUA ((((((((........(((((((((((.(.............).)))))))))))....(((((...((((.......))))..)))))........))))))))...................(((((((...((((((((((..........))))))))))..))))))) (-33.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 156 111 138 98 pint:PI2157|5end_xanthosine_triphosphate_pyrophosphatase,_HAM1_family_2103736..2103966_POSITIVE 253 127 88 159 125 pint:PI2069|5end_ISPg3-related_transposase,_C-terminal_fragment_2028985..2029215_POSITIVE 253 127 88 159 125 pint:PI2070|5end_ISPg3-related_transposase,_N-terminal_fragment_2028985..2029215_POSITIVE 248 158 121 85 48 pint:PI1267|5end_probable_integrase_1186105..1186335_POSITIVE 241 149 104 61 12 pint:PI0480|5end_preprotein_translocase,_SecY_subunit_441576..441806_POSITIVE 227 149 109 90 56 pint:PI1765|5end_fructanase,_glycoside_hydrolase_family_1691281..1691511_POSITIVE 223 126 88 45 5 pint:PI1684|5end_dimethyladenosine_transferase_1601073..1601303_POSITIVE 222 60 32 102 66 pint:PI0290|5end_conserved_hypothetical_protein_273245..273475_POSITIVE 220 132 95 152 116 pint:PI2022|5end_hypothetical_protein_1978631..1978861_POSITIVE 220 132 95 106 70 pint:PI2023|5end_hypothetical_protein_1978585..1978815_POSITIVE 220 150 106 85 43 pint:PI1160|5end_possible_phosphatidylinositol-4-phosphate_5-kinase_1084756..1084986_POSITIVE 219 149 115 81 44 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 214 38 8 69 43 pint:PI1914|5end_RNA_polymerase,_ECF-type_sigma_factor_1858025..1858255_POSITIVE 211 148 108 79 34 pint:PI1796|5end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_protein_1730452..1730682_POSITIVE 211 167 121 115 77 pint:PI1603|5end_hypothetical_protein_1533779..1534009_POSITIVE 210 59 18 227 182 pint:PI0805|5end_conserved_hypothetical_protein_742729..742959_POSITIVE 208 139 92 179 126 pint:PI1960|5end_hypothetical_protein_1918013..1918243_POSITIVE 206 158 117 64 19 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 206 155 115 62 18 pint:PI0246|5end_conserved_hypothetical_protein_244166..244396_POSITIVE 205 150 108 151 101 pint:PI1269|5end_conserved_hypothetical_protein;_possible_peptidase_1188147..1188377_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 159 119 54 18 pint:PI0647|3end_potassium_uptake_protein_589276..589426_POSITIVE 241 149 104 53 4 pint:PI0479|3end_50S_ribosomal_protein_L15_441648..441798_POSITIVE 238 148 107 48 9 pint:PI0662|3end_conserved_hypothetical_protein_605213..605363_POSITIVE 220 132 95 72 36 pint:PI2021|3end_DNA_repair_protein_1978631..1978781_POSITIVE 220 159 122 131 96 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 219 155 122 121 93 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 211 167 121 75 37 pint:PI1602|3end_conserved_hypothetical_protein;_possible_internalin-related_protein_1533819..1533969_POSITIVE 210 160 116 50 12 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 209 157 119 99 58 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 209 159 113 100 42 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 208 139 92 56 3 pint:PI1959|3end_hypothetical_protein_1917970..1918120_POSITIVE 207 158 120 56 24 pint:PI2056|3end_conserved_hypothetical_protein_2014428..2014578_POSITIVE 206 155 115 74 30 pint:PI0245|3end_possible_mobilization_protein_244258..244408_POSITIVE 205 60 12 86 42 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 203 147 109 38 5 pint:PI0219|3end_conserved_hypothetical_protein_212037..212187_POSITIVE 202 158 111 112 59 pint:PI0398|3end_hypothetical_protein_363541..363691_POSITIVE 197 134 108 34 1 pint:PI1581|3end_cell_shape-determining_protein_1509383..1509533_POSITIVE 197 158 111 78 31 pint:PI0745|3end_conserved_hypothetical_protein_675670..675820_POSITIVE 195 139 105 42 1 pint:PI0550|3end_possible_glycosyl_hydrolase_502475..502625_POSITIVE 194 149 106 130 96 pint:PI0897|3end_ferredoxin,_4Fe-4S_828537..828687_POSITIVE