Origin IGS: taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg .........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 cgctcatttggcttaactaaaacgttcgcaaaggtacgttaattcatacattaatcaaaataaaatgggagtttttaaagattaaatcggggagggatattatatgttttttgactcaatctttagctgctcggactgatatgatatcatcttcagaaaaatatgacgtcatattcggacaaatatgacgtcatttctgagcaaatatgacgtcatattttttattcactctcgtgataaggtatcagcgtatatataaaaagttgcttggaaagaggttgaaagacaagaaaaaggagttagaagggaagtctatttcctctaactccttaacctttttcgtta Mask Tandem Repeat Region ================================================ taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Find is-nt database================================================ Query_seq: PI1444:PI1445|PI1444:PI1445:protease ClpB:hypothetical protein:->->:1368198..1368542 345 taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1444:PI1445|PI1444:PI1445:protease ClpB:hypothetical protein:->->:1368198..1368542 345 taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1444:PI1445|PI1444:PI1445:protease ClpB:hypothetical protein:->->:1368198..1368542 345 taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 161 End: 304 ................................................................................................................................................................ I Q G F I V D Y K E S S S I M D T R A A L S Q T L F C I I D R G S K I K L F E W K I K I L T H M ......................................... Protein_Len: 46 Strand: - Start: 2 End: 139 . V F F T L S N S S I S K G E L E K K K D K L R K G L L K K Y I R Q Y R I V L T F L F Y S T M .............................................................................................................................................................................................................. taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg 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================================================ taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -4.3 Tail_Score: -2.79809 Start: 20 End: 47 Full_Region: agacaagaaaaagga gttagaagggaa gtcta tttcctctaac tccttaacctttttc ...................gttagaagggaagtctatttcctctaac.......................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -13.6 Tail_Score: -4.84359 Start: 129 End: 184 Full_Region: AGAGTGAATAAAAAA TATGACGTCATATTTGCTCAGAAATG ACGT CATATTTGTCCGAATATGACGTCATA TTTTTCTGAAGATGA ................................................................................................................................TATGACGTCATATTTGCTCAGAAATGACGTCATATTTGTCCGAATATGACGTCATA................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -9.2 Tail_Score: -5.49234 Start: 129 End: 184 Full_Region: tcatcttcagaaaaa tatgacgtcatattcggacaaatatg acgt catttctgagcaaatatgacgtcata ttttttattcactct ................................................................................................................................tatgacgtcatattcggacaaatatgacgtcatttctgagcaaatatgacgtcata................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -12.4 Tail_Score: -3.86524 Start: 153 End: 182 Full_Region: atcttcagaaaaata tgacgtcatatt cggaca aatatgacgtca tttctgagcaaatat ........................................................................................................................................................tgacgtcatattcggacaaatatgacgtca................................................................................................................................................................... Find igs database================================================ Query_seq: PI1444:PI1445|PI1444:PI1445:protease ClpB:hypothetical protein:->->:1368198..1368542 345 taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Intra-Species Hit: Count: 1 Min: 1 Max: 345 Len: 345 Subject: pint_PI1444_PI1445|protease ClpB:hypothetical protein|POSITIVE:POSITIVE|[1368198,1368542]|345 HSP 1 e-value: 0.0 bit: 684.0 Len: 345 Query Start:1 Query End:345 Subject Strand: POSITIVE Subject Start: 1 Subject End: 345 taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg taacgaaaaaggttaaggagttagaggaaatagacttcccttctaactcctttttcttgtctttcaacctctttccaagcaactttttatatatacgctgataccttatcacgagagtgaataaaaaatatgacgtcatatttgctcagaaatgacgtcatatttgtccgaatatgacgtcatatttttctgaagatgatatcatatcagtccgagcagctaaagattgagtcaaaaaacatataatatccctccccgatttaatctttaaaaactcccattttattttgattaatgtatgaattaacgtacctttgcgaacgttttagttaagccaaatgagcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGAAAAAGGUUAAGGAGUUAGAGGAAAUAGACUUCCCUUCUAACUCCUUUUUCUUGUCUUUCAACCUCUUUCCAAGCAACUUUUUAUAUAUACGCUGAUACCUUAUCACGAGAGUGAAUAAAAAAUAUGACGUCAUAUUUGCUCAGAAAUGACGUCAUAUUUGUCCGAAUAUGACGUCAUAUUUUUCUGAAGAUGAUAUCAUAUCAGUCCGAGCAGCUAAAGAUUGAGUCAAAAAACAUAUAAUAUCCCUCCCCGAUUUAAUCUUUAAAAACUCCCAUUUUAUUUUGAUUAAUGUAUGAAUUAACGUACCUUUGCGAACGUUUUAGUUAAGCCAAAUGAGCG ....((((((((..(((((((((((((((......))))..)))))))))))..))))...))))...(((.......((.....(((((((((..(((((((.....((((....))))...(((((((((((((((((((((..((((.(((....))).))))..)))))))))))))))))))))...............)))))))..(((....(((((((((((((........................)))))))))))))....))).................)))))))))....((((....))))..............)).....))).. (-91.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUCAUUUGGCUUAACUAAAACGUUCGCAAAGGUACGUUAAUUCAUACAUUAAUCAAAAUAAAAUGGGAGUUUUUAAAGAUUAAAUCGGGGAGGGAUAUUAUAUGUUUUUUGACUCAAUCUUUAGCUGCUCGGACUGAUAUGAUAUCAUCUUCAGAAAAAUAUGACGUCAUAUUCGGACAAAUAUGACGUCAUUUCUGAGCAAAUAUGACGUCAUAUUUUUUAUUCACUCUCGUGAUAAGGUAUCAGCGUAUAUAUAAAAAGUUGCUUGGAAAGAGGUUGAAAGACAAGAAAAAGGAGUUAGAAGGGAAGUCUAUUUCCUCUAACUCCUUAACCUUUUUCGUUA .(((.....)))........(((((((.....)).)))))..........((((((.....(((((....)))))....))))))..((..(((((........(((((((..((((..(((..(((.(((((((((((.(((....)))..))))......(((((((((((((......))))))))))))).)))))))..(((((((((.(((((((....((((....)))).)))))))..)))).)))))........))).)))..)).))..))))))).....(((((((((((.(((((.....))))))))))))))))..)))))..))... (-98.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 566 180 131 182 133 pint:PI0163|5end_conserved_hypothetical_protein_157116..157346_POSITIVE 492 166 126 230 190 pint:PI0108|5end_L-lactate_permease_104892..105122_POSITIVE 471 180 131 157 108 pint:PI0063|5end_transcriptional_regulator,_GntR_family_63181..63411_POSITIVE 399 167 121 185 138 pint:PI0001|5end_possible_Ton-B_receptor_400..630_POSITIVE 369 179 134 53 5 pint:PI1043|5end_conserved_hypothetical_protein_960855..961085_POSITIVE 339 76 37 215 173 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 317 100 52 93 40 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 285 80 32 140 83 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 283 218 185 204 163 pint:PI0767|5end_possible_TonB-dependent_receptor_701915..702145_POSITIVE 282 151 111 141 96 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 282 151 111 96 51 pint:PI1065|5end_hypothetical_protein_983382..983612_POSITIVE 281 80 37 135 92 pint:PI1839|5end_hypothetical_protein_1782178..1782408_POSITIVE 279 158 116 186 146 pint:PI1534|5end_ATPase/GTPase_1453679..1453909_POSITIVE 267 324 308 40 24 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 255 50 4 133 87 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 255 56 11 152 107 pint:PI0199|5end_phosphate_acetyltransferase_189890..190120_POSITIVE 254 76 32 222 179 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 247 56 15 161 123 pint:PI1908|5end_transcriptional_regulator,_AraC_family_1852261..1852491_POSITIVE 245 231 192 215 183 pint:PI0320|5end_probable_cobalamin_adenosyltransferase_302027..302257_POSITIVE 244 120 71 187 133 pint:PI1120|5end_conserved_hypothetical_protein_1044870..1045100_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 58 15 82 39 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 297 84 46 116 64 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 285 90 46 137 90 pint:PI1550|3end_conserved_hypothetical_protein_1467703..1467853_POSITIVE 284 171 132 54 5 pint:PI0162|3end_ADP-ribosylglycohydrolase_(ADP-ribosyl-[dinitrogen_reductase]_hydrolase)_157001..157151_POSITIVE 267 324 308 44 28 pint:PI2012|3end_hypothetical_protein_1971555..1971705_POSITIVE 256 69 24 131 93 pint:PI0121|3end_outer_membrane_protein,_ompH_family_113208..113358_POSITIVE 251 190 169 24 3 pint:PI2006|3end_potassium_uptake_system_protein_1965846..1965996_POSITIVE 244 222 188 90 49 pint:PI0559|3end_conserved_hypothetical_protein_508740..508890_POSITIVE 243 181 141 72 34 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 241 214 183 40 8 pint:PI0942|3end_DNA-binding_protein_HU_874979..875129_POSITIVE 241 59 11 121 66 pint:PI0749|3end_hypothetical_protein_677469..677619_POSITIVE 240 57 15 62 16 pint:PI1027|3end_hypothetical_protein_943399..943549_POSITIVE 237 80 38 95 52 pint:PI0093|3end_riboflavin_biosynthesis_protein_91537..91687_POSITIVE 234 80 39 113 67 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 233 148 111 41 2 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 232 80 35 139 78 pint:PI1849|3end_conserved_hypothetical_protein;_possible_acyltransferase_family_protein_1796039..1796189_POSITIVE 229 68 26 112 67 pint:PI0945|3end_sodium:solute_symporter_family_protein_877624..877774_POSITIVE 228 87 50 118 77 pint:PI1165|3end_hypothetical_protein_1089636..1089786_POSITIVE 228 69 25 72 14 pint:PI0847|3end_thiamine_biosynthesis_lipoprotein,_ApbE_782232..782382_POSITIVE 226 80 35 144 94 pint:PI1667|3end_conserved_hypothetical_protein_1580772..1580922_POSITIVE