Origin IGS: taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat .........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 attctaattattctaaataattcagcagcaaagatataaataattgcctatactattgaactttcttctttaaaaagtctaaaactatctttcttattcttacattttatttataaaataaagagattgtatttctttttaacatcgacaagggcaacgaagatttagtttcgttgcccttgattctttgtttatatattcttattttgtgttttctta Mask Tandem Repeat Region ================================================ taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Find is-nt database================================================ Query_seq: PI0620:PI0621|PI0620:PI0621:hypothetical protein:conserved hypothetical protein:->->:570691..570909 219 taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0620:PI0621|PI0620:PI0621:hypothetical protein:conserved hypothetical protein:->->:570691..570909 219 taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0620:PI0621|PI0620:PI0621:hypothetical protein:conserved hypothetical protein:->->:570691..570909 219 taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 15 End: 110 .............. M R I Y K Q R I K G N E T K S S L P L S M L K R N T I S L F Y K ............................................................................................................. Protein_Len: 42 Strand: - Start: 55 End: 180 ...................................................... I K T A R T S T L F F Y L R K I K Y I F H L F L F S L K L S K L S S L E I T Y A I M ....................................... Protein_Len: 31 Strand: - Start: 2 End: 94 . L F C L I L I Y L C L I L P L S V L D E N G K D I N F L F V M ............................................................................................................................. taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat 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: 81 Start: 12 End: 41 ...........CTTGATTCTTTGTTTATATATTCTTATTTT.................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -7.4 Tail_Score: -4.68132 Start: 34 End: 73 Full_Region: tttctttttaacatc gacaagggcaacgaag atttag tttcgttgcccttgattc tttgtttatatattc .................................gacaagggcaacgaagatttagtttcgttgcccttgattc.................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -12.7 Tail_Score: -4.41158 Start: 37 End: 72 Full_Region: ttctttttaacatcg acaagggcaacgaag atttag tttcgttgcccttga ttctttgtttatata ....................................acaagggcaacgaagatttagtttcgttgcccttga................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.2 Tail_Score: -3.23068 Start: 38 End: 71 Full_Region: tctttttaacatcga caagggcaacgaag atttag tttcgttgcccttg attctttgtttatat .....................................caagggcaacgaagatttagtttcgttgcccttg.................................................................................................................................................... TransTerm Strand: + Conf: 93 HP_score: -11.4 Tail_Score: -3.42503 Start: 41 End: 68 Full_Region: TAAACAAAGAATCAA GGGCAACGAA ACTAAATC TTCGTTGCCC TTGTCGATGTTAAAA ........................................GGGCAACGAAACTAAATCTTCGTTGCCC....................................................................................................................................................... Find igs database================================================ Query_seq: PI0620:PI0621|PI0620:PI0621:hypothetical protein:conserved hypothetical protein:->->:570691..570909 219 taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Intra-Species Hit: Count: 1 Min: 1 Max: 219 Len: 219 Subject: pint_PI0620_PI0621|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[570691,570909]|219 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat taagaaaacacaaaataagaatatataaacaaagaatcaagggcaacgaaactaaatcttcgttgcccttgtcgatgttaaaaagaaatacaatctctttattttataaataaaatgtaagaataagaaagatagttttagactttttaaagaagaaagttcaatagtataggcaattatttatatctttgctgctgaattatttagaataattagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAAACACAAAAUAAGAAUAUAUAAACAAAGAAUCAAGGGCAACGAAACUAAAUCUUCGUUGCCCUUGUCGAUGUUAAAAAGAAAUACAAUCUCUUUAUUUUAUAAAUAAAAUGUAAGAAUAAGAAAGAUAGUUUUAGACUUUUUAAAGAAGAAAGUUCAAUAGUAUAGGCAAUUAUUUAUAUCUUUGCUGCUGAAUUAUUUAGAAUAAUUAGAAU ...........................((((..((..(((((((((((((........)))))))))))))))..))))..............(((..((((((..(((((((...........................((((((((.....))))))))...((((...(((((..((....))..)))))))))..)))))))))))))..))).. (-42.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUAAUUAUUCUAAAUAAUUCAGCAGCAAAGAUAUAAAUAAUUGCCUAUACUAUUGAACUUUCUUCUUUAAAAAGUCUAAAACUAUCUUUCUUAUUCUUACAUUUUAUUUAUAAAAUAAAGAGAUUGUAUUUCUUUUUAACAUCGACAAGGGCAACGAAGAUUUAGUUUCGUUGCCCUUGAUUCUUUGUUUAUAUAUUCUUAUUUUGUGUUUUCUUA .......................((((.(((((((((((((((..........................((((((((...((.((.((((((.(((((..................))))))))))).)).)).))))))))......((((((((((((((......)))))))))))))).....)))))))))).......)))))))))...... (-39.38) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 438 70 29 156 117 pint:PI0625|5end_possible_membrane_transport_protein_573104..573334_POSITIVE 393 71 38 214 181 pint:PI0623|5end_hypothetical_protein_572167..572397_POSITIVE 291 75 31 212 166 pint:PI0300|5end_transposase_285163..285393_POSITIVE 280 77 33 76 31 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 278 73 31 119 68 pint:PI0223|5end_topoisomerase_IA_218377..218607_POSITIVE 273 72 37 106 60 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 270 100 53 205 146 pint:PI2134|5end_hypothetical_protein_2082269..2082499_POSITIVE 268 78 32 146 102 pint:PI1815|5end_polyphosphate-selective_porin_O_1753384..1753614_POSITIVE 264 207 171 195 157 pint:PI1344|5end_hypothetical_protein_1258551..1258781_POSITIVE 247 77 39 173 125 pint:PI0897|5end_ferredoxin,_4Fe-4S_828227..828457_POSITIVE 243 158 127 91 60 pint:PI0518|5end_5'-nucleotidase_precursor_477076..477306_POSITIVE 240 75 42 200 154 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 240 103 61 143 93 pint:PI0419|5end_conserved_hypothetical_protein_386701..386931_POSITIVE 240 103 61 108 58 pint:PI0418|5end_hypothetical_protein_386666..386896_POSITIVE 238 82 46 43 1 pint:PI1852|5end_conserved_hypothetical_protein_1797952..1798182_POSITIVE 238 78 43 221 186 pint:PI0207|5end_conserved_hypothetical_protein_199797..200027_POSITIVE 236 79 38 151 104 pint:PI1398|5end_probable_imidazolonepropionase_1319429..1319659_POSITIVE 235 75 34 54 10 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 234 70 36 190 160 pint:PI0781|5end_UDP-glucose/GDP-mannose_dehydrogenase_family;_probable__UDP-glucose_6-dehydrogenase_719260..719490_POSITIVE 234 77 41 38 1 pint:PI0577|5end_conserved_hypothetical_protein_521811..522041_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 438 70 29 52 13 pint:PI0623|3end_hypothetical_protein_573080..573230_POSITIVE 393 71 38 54 21 pint:PI0622|3end_hypothetical_protein_572087..572237_POSITIVE 393 79 38 63 20 pint:PI0620|3end_hypothetical_protein_570630..570780_POSITIVE 291 75 31 55 9 pint:PI0299|3end_hypothetical_protein_285086..285236_POSITIVE 278 73 31 104 53 pint:PI0222|3end_conserved_hypothetical_protein_218442..218592_POSITIVE 267 67 40 95 68 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE 264 207 171 103 65 pint:PI1343|3end_conserved_hypothetical_protein_1258539..1258689_POSITIVE 247 77 39 142 94 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 241 79 41 58 11 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 240 103 61 92 42 pint:PI0417|3end_hypothetical_protein_386730..386880_POSITIVE 240 103 61 69 19 pint:PI0416|3end_hypothetical_protein_386707..386857_POSITIVE 236 79 38 73 26 pint:PI1397|3end_histidine_ammonia-lyase_1319431..1319581_POSITIVE 235 75 34 58 14 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 230 77 33 150 100 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE 226 80 39 70 22 pint:PI0932|3end_conserved_hypothetical_protein;_possible_hemin_receptor_865364..865514_POSITIVE 221 77 42 127 96 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 219 90 41 127 94 pint:PI1942|3end_hypothetical_protein_1901269..1901419_POSITIVE 218 49 2 79 34 pint:PI0842|3end_5-formyltetrahydrofolate_cyclo-ligase_776191..776341_POSITIVE 215 74 32 136 106 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 214 79 42 146 112 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE