Origin IGS: tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agccttctttttcagaaacaataataaggtaacaacaattcaaacaagtattataaaaaggggaaattggcaaaacaaccctttcccctcttaaacattttga Mask Tandem Repeat Region ================================================ tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Find is-nt database================================================ Query_seq: PG0991:PG0992|PG0991:PG0992:translation initiation factor IF-3:threonyl-tRNA synthetase:<-<-:1052130..1052232 103 tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0991:PG0992|PG0991:PG0992:translation initiation factor IF-3:threonyl-tRNA synthetase:<-<-:1052130..1052232 103 tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0991:PG0992|PG0991:PG0992:translation initiation factor IF-3:threonyl-tRNA synthetase:<-<-:1052130..1052232 103 tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Predict ORF larger than 30AA ================================================ tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct 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: 82 Start: 25 End: 54 ........................GTTGTTTTGCCAATTTCCCCTTTTTATAAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0991:PG0992|PG0991:PG0992:translation initiation factor IF-3:threonyl-tRNA synthetase:<-<-:1052130..1052232 103 tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_002950_PG0991_PG0992|translation initiation factor IF-3:threonyl-tRNA synthetase|NEGATIVE:NEGATIVE|[1052130,1052232]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct tcaaaatgtttaagaggggaaagggttgttttgccaatttcccctttttataatacttgtttgaattgttgttaccttattattgtttctgaaaaagaaggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAAUGUUUAAGAGGGGAAAGGGUUGUUUUGCCAAUUUCCCCUUUUUAUAAUACUUGUUUGAAUUGUUGUUACCUUAUUAUUGUUUCUGAAAAAGAAGGCU (((((.((((.(((((((((((.(((......)))..)))))))))))...))))....))))).....................(((((.....)))))... (-23.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUUCUUUUUCAGAAACAAUAAUAAGGUAACAACAAUUCAAACAAGUAUUAUAAAAAGGGGAAAUUGGCAAAACAACCCUUUCCCCUCUUAAACAUUUUGA ...........((((((...((((((..((.............))...))))))....(((((((((((......)))...))))))))........)))))) (-16.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 821 60 11 151 102 NC_002950:PG0991|5end_translation_initiation_factor_IF-3_1052039..1052269_NEGATIVE 286 41 16 76 47 NC_002950:PG1288|5end_GDP-mannose_4,6-dehydratase_1365963..1366193_POSITIVE 275 49 6 77 44 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 265 35 13 131 109 NC_002950:PG0398|5end_recF_protein_435710..435940_NEGATIVE 264 35 13 220 187 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 263 49 7 207 156 NC_002950:PG2089|5end_hypothetical_protein_2188640..2188870_POSITIVE 261 54 14 64 26 NC_002950:PG2215|5end_mannose-1-phosphate_guanylyltransferase_2327695..2327925_NEGATIVE 261 49 13 43 5 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 259 44 1 162 108 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 253 47 2 139 76 NC_002950:PG2076|5end_hypothetical_protein_2176445..2176675_POSITIVE 253 47 2 139 76 NC_002950:PG1267|5end_hypothetical_protein_1346966..1347196_POSITIVE 245 49 16 61 25 NC_002950:PG0484|5end_hypothetical_protein_524858..525088_NEGATIVE 244 49 7 56 9 NC_002950:PG1055|5end_thiol_protease_1122647..1122877_NEGATIVE 243 47 2 139 76 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 243 47 2 139 76 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 242 70 21 129 69 NC_002950:PG0745|5end_lactoylglutathione_lyase,_putative_792380..792610_NEGATIVE 239 41 9 208 171 NC_002950:PG1385|5end_TPR_domain_protein_1466335..1466565_NEGATIVE 238 35 1 160 125 NC_002950:PG1775|5end_grpE_protein_1864844..1865074_POSITIVE 238 63 22 211 180 NC_002950:PG0706|5end_hypothetical_protein_760350..760580_POSITIVE 236 44 8 147 110 NC_002950:PG2094|5end_hypothetical_protein_2197868..2198098_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 47 14 79 48 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 293 45 12 62 29 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 272 49 5 58 8 NC_002950:PG1659|3end_hypothetical_protein_1743355..1743505_NEGATIVE 265 35 13 134 112 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE 263 49 7 150 99 NC_002950:PG2088|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_2188663..2188813_POSITIVE 246 48 13 107 65 NC_002950:PG1128|3end_exodeoxyribonuclease_VII_large_subunit_1205199..1205349_POSITIVE 239 60 12 98 36 NC_002950:PG0561|3end_peptidase,_M20/M25/M40_family_617700..617850_NEGATIVE 238 49 12 70 24 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 238 48 13 70 35 NC_002950:PG0232|3end_zinc_carboxypeptidase,_putative_267458..267608_NEGATIVE 235 47 15 109 77 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 235 48 13 107 68 NC_002950:PG0097|3end_hypothetical_protein_115056..115206_NEGATIVE 234 45 13 102 68 NC_002950:PG0060|3end_hypothetical_protein_72178..72328_POSITIVE 232 45 13 126 93 NC_002950:PG0215|3end_hypothetical_protein_252028..252178_POSITIVE 227 69 23 49 1 NC_002950:PG1727|3end_yitL_protein_1817652..1817802_POSITIVE 226 46 12 116 67 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 224 44 2 74 44 NC_002950:PG1887|3end_rhodanese-like_domain_protein_1985679..1985829_POSITIVE 224 44 1 63 6 NC_002950:PG1083|3end_hypothetical_protein_1150893..1151043_NEGATIVE 223 54 12 57 2 NC_002950:PG1280|3end_hypothetical_protein_1358801..1358951_POSITIVE 222 46 13 37 2 NC_002950:PG1898|3end_transporter,_putative_1996727..1996877_NEGATIVE 222 49 23 35 1 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE