Origin IGS: aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt .........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 aaattttaacttcgctaaacagagtgtctataagaatgggagcaaagataatctttccgcccgaaacattgttcaatgagcttcgctcgactataacttcgattcattgacgaagaaggagaccgggggagcttttgtcgcttttatacttgattggtcgttaaggttcgtttttctgatgaaggtcaattgattcatcgtctttttatttcttgttattctccagccttctatttattttgtaaacataggatagcccgtctgaaaattacaggggatcgcgcagaaaggcataactttgcgagcatcgaatcaataaaaaataaacccgatactatactt Mask Tandem Repeat Region ================================================ aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Find is-nt database================================================ Query_seq: PG1595:PG1596|PG1595:PG1596:ribulose-phosphate 3-epimerase:isoleucyl-tRNA synthetase, putative:<-->:1674341..1674682 342 aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1595:PG1596|PG1595:PG1596:ribulose-phosphate 3-epimerase:isoleucyl-tRNA synthetase, putative:<-->:1674341..1674682 342 aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1595:PG1596|PG1595:PG1596:ribulose-phosphate 3-epimerase:isoleucyl-tRNA synthetase, putative:<-->:1674341..1674682 342 aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 5 End: 109 .... M V S G L F F I D S M L A K L C L S A R S P V I F R R A I L C L Q N K ......................................................................................................................................................................................................................................... Protein_Len: 47 Strand: + Start: 109 End: 249 ............................................................................................................ M E G W R I T R N K K T M N Q L T F I R K T N L N D Q S S I K A T K A P P V S F F V N E S K L ............................................................................................. Protein_Len: 30 Strand: + Start: 236 End: 325 ........................................................................................................................................................................................................................................... M N R S Y S R A K L I E Q C F G R K D Y L C S H S Y R H S V ................. Protein_Len: 34 Strand: + Start: 240 End: 341 ............................................................................................................................................................................................................................................... M E V I V E R S S L N N V S G G K I I F A P I L I D T L F S E V K I . Protein_Len: 35 Strand: - Start: 236 End: 340 ........................................................................................................................................................................................................................................... H I S T I T S R L E N F L T E P P F I I K A G M R I S V R N L S T L M .. Protein_Len: 60 Strand: - Start: 1 End: 189 D P K N K I S E I S A F N H R E A R D G T I K L R A I R H K C F L Y F A P S Y C S I F L R H I L Q G E D S F R V K V V M ......................................................................................................................................................... aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt 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================================================ aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1595:PG1596|PG1595:PG1596:ribulose-phosphate 3-epimerase:isoleucyl-tRNA synthetase, putative:<-->:1674341..1674682 342 aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Intra-Species Hit: Count: 1 Min: 1 Max: 342 Len: 342 Subject: NC_002950_PG1595_PG1596|ribulose-phosphate 3-epimerase:isoleucyl-tRNA synthetase, putative|NEGATIVE:POSITIVE|[1674341,1674682]|342 HSP 1 e-value: 0.0 bit: 678.0 Len: 342 Query Start:1 Query End:342 Subject Strand: POSITIVE Subject Start: 1 Subject End: 342 aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt aagtatagtatcgggtttattttttattgattcgatgctcgcaaagttatgcctttctgcgcgatcccctgtaattttcagacgggctatcctatgtttacaaaataaatagaaggctggagaataacaagaaataaaaagacgatgaatcaattgaccttcatcagaaaaacgaaccttaacgaccaatcaagtataaaagcgacaaaagctcccccggtctccttcttcgtcaatgaatcgaagttatagtcgagcgaagctcattgaacaatgtttcgggcggaaagattatctttgctcccattcttatagacactctgtttagcgaagttaaaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUAGUAUCGGGUUUAUUUUUUAUUGAUUCGAUGCUCGCAAAGUUAUGCCUUUCUGCGCGAUCCCCUGUAAUUUUCAGACGGGCUAUCCUAUGUUUACAAAAUAAAUAGAAGGCUGGAGAAUAACAAGAAAUAAAAAGACGAUGAAUCAAUUGACCUUCAUCAGAAAAACGAACCUUAACGACCAAUCAAGUAUAAAAGCGACAAAAGCUCCCCCGGUCUCCUUCUUCGUCAAUGAAUCGAAGUUAUAGUCGAGCGAAGCUCAUUGAACAAUGUUUCGGGCGGAAAGAUUAUCUUUGCUCCCAUUCUUAUAGACACUCUGUUUAGCGAAGUUAAAAUUU ......(((((((((((.((.....)).))))))))))).((((((.((...((((((((.(((..(.((((((((((....(.((((.((...((((((.....)))))))).)))).)....................(((((.(((......((((.............((........))................(((.......))).....))))...))).)))))........))))))))))..((((...))))..........)..))).))))))))..)).)))))).....(((...(((((.....)))))..))).......... (-72.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUAACUUCGCUAAACAGAGUGUCUAUAAGAAUGGGAGCAAAGAUAAUCUUUCCGCCCGAAACAUUGUUCAAUGAGCUUCGCUCGACUAUAACUUCGAUUCAUUGACGAAGAAGGAGACCGGGGGAGCUUUUGUCGCUUUUAUACUUGAUUGGUCGUUAAGGUUCGUUUUUCUGAUGAAGGUCAAUUGAUUCAUCGUCUUUUUAUUUCUUGUUAUUCUCCAGCCUUCUAUUUAUUUUGUAAACAUAGGAUAGCCCGUCUGAAAAUUACAGGGGAUCGCGCAGAAAGGCAUAACUUUGCGAGCAUCGAAUCAAUAAAAAAUAAACCCGAUACUAUACUU ......................((((((..((((.((((((((...(((((...((((.((((.....((((.(((((((......((((........)))))))))))))))....(....)))))))))...))))))))))))).))))..((.((((.((((((.(((((((((((((..(((....))))))))........((..(((((.(((.((..((...((((((....((....))..))))))...))..)).))).)))))..)).....))))))))..)))))))))).)).......................))))))...... (-75.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 971 90 41 181 132 NC_002950:PG1595|5end_ribulose-phosphate_3-epimerase_1674250..1674480_NEGATIVE 443 284 241 88 31 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 369 60 11 139 91 NC_002950:PG1474|5end_conjugative_transposon_protein_TraO_1550816..1551046_NEGATIVE 352 254 211 111 68 NC_002950:PG1850|5end_hypothetical_protein_1949957..1950187_NEGATIVE 341 267 225 91 50 NC_002950:PG0039|5end_hypothetical_protein_47637..47867_POSITIVE 338 228 181 134 74 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 335 234 191 130 89 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 333 330 282 204 162 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 331 96 52 47 11 NC_002950:PG0469|5end_hypothetical_protein_511658..511888_NEGATIVE 328 63 28 40 7 NC_002950:PG1747|5end_ribose_5-phosphate_isomerase_B,_putative_1832815..1833045_NEGATIVE 326 96 54 140 96 NC_002950:PG0942|5end_ISPg5,_transposase_Orf1_1002063..1002293_POSITIVE 325 247 201 73 20 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 324 317 271 51 7 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 322 80 32 90 42 NC_002950:PG1095|5end_RNA_methyltransferase,_TrmA_family_1160225..1160455_POSITIVE 321 100 51 219 168 NC_002950:PG1081|5end_acetate_kinase_1149627..1149857_NEGATIVE 321 259 211 88 39 NC_002950:PG0802|5end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_859722..859952_NEGATIVE 320 87 51 206 179 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 317 70 26 182 141 NC_002950:PG2061|5end_dihydrofolate_reductase_2158422..2158652_POSITIVE 316 236 191 119 73 NC_002950:PG1763|5end_ribonuclease_III_1851712..1851942_NEGATIVE 315 259 211 193 155 NC_002950:PG0451|5end_CBS_domain_protein_491519..491749_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 87 45 135 93 NC_002950:PG1614|3end_succinate_dehydrogenase_1693800..1693950_NEGATIVE 369 60 11 145 97 NC_002950:PG1475|3end_conjugative_transposon_protein_TraN_1550810..1550960_NEGATIVE 352 254 211 114 71 NC_002950:PG1851|3end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1949954..1950104_NEGATIVE 348 260 211 101 41 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 338 228 181 141 81 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 327 86 41 75 26 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 325 247 201 69 16 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 324 317 271 64 20 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 321 259 211 83 34 NC_002950:PG0803|3end_glucosamine-6-phosphate_deaminase_859727..859877_NEGATIVE 318 285 245 122 89 NC_002950:PG2009|3end_DNA_repair_protein_RecO,_putative_2099131..2099281_POSITIVE 317 70 26 136 95 NC_002950:PG2060|3end_thymidylate_synthase_2158456..2158606_POSITIVE 307 235 201 55 14 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 304 70 30 48 4 NC_002950:PG2068|3end_glycerol-3-phosphate_cytidylyltransferase_2164872..2165022_POSITIVE 303 286 251 143 107 NC_002950:PG0558|3end_purine_nucleoside_phosphorylase_615510..615660_NEGATIVE 299 78 32 91 38 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 299 245 202 79 39 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 298 260 213 74 36 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 297 236 199 35 1 NC_002950:PG1764|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_1851796..1851946_NEGATIVE 296 62 30 148 112 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 296 87 41 76 21 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE