Origin IGS: atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatggtacgataccatcttctttcttttgattgatagtaatgtctttttaatttcataatagataattgttttggttttacatttattttaatgctgatttaattcagacttgtgattttattgcaaaattagacaatagcttttctatttaattttaatatcataaaaaggttaaacaaagaataataaaaacgtaaaattgctatattggcactttgttgtgcatgcaaaaaactgtcaaaaataaaaaataagtagcattatgtagttgtataaatagctgataaacaaatgtttgctaatttaagatacattatttacaaaattgagtaatctttttaatataaaatttgtatatttgtcaaacaactaatgggaagcatatat Mask Tandem Repeat Region ================================================ atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt Find is-nt database================================================ Query_seq: PI2049:PI2050|PI2049:PI2050:possible transcriptional regulator, AraC family:hypothetical protein:->->:2003764..2004151 388 atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2049:PI2050|PI2049:PI2050:possible transcriptional regulator, AraC family:hypothetical protein:->->:2003764..2004151 388 atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2049:PI2050|PI2049:PI2050:possible transcriptional regulator, AraC family:hypothetical protein:->->:2003764..2004151 388 atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 143 End: 256 .............................................................................................................................................. M F D S F L H A Q Q S A N I A I L R F Y Y S L F N L F M I L K L N R K A I V .................................................................................................................................... Protein_Len: 33 Strand: + Start: 290 End: 388 ................................................................................................................................................................................................................................................................................................. M S I K I N V K P K Q L S I M K L K R H Y Y Q S K E R R W Y R T I atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt 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: 83 Start: 43 End: 72 ..........................................ATTTACAAAATTGAGTAATCTTTTTAATAT............................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2049:PI2050|PI2049:PI2050:possible transcriptional regulator, AraC family:hypothetical protein:->->:2003764..2004151 388 atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctacttattttttatttttgacagttttttgcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctgaattaaatcagcattaaaataaatgtaaaaccaaaacaattatctattatgaaattaaaaagacattactatcaatcaaaagaaagaagatggtatcgtaccatt Intra-Species Hit: Count: 1 Min: 1 Max: 388 Len: 388 Subject: pint_PI2049_PI2050|possible transcriptional regulator, AraC family:hypothetical protein|POSITIVE:POSITIVE|[2003764,2004151]|388 HSP 1 e-value: 3.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctactta............................................................................................................................................................................................................................................................ atatatgcttcccattagttgtttgacaaatatacaaattttatattaaaaagattactcaattttgtaaataatgtatcttaaattagcaaacatttgtttatcagctatttatacaactacataatgctactta............................................................................................................................................................................................................................................................ HSP 2 e-value: 5.0E-64 bit: 246.0 Len: 124 Query Start:160 Query End:283 Subject Strand: POSITIVE Subject Start: 160 Subject End: 283 ...............................................................................................................................................................gcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctg......................................................................................................... ...............................................................................................................................................................gcatgcacaacaaagtgccaatatagcaattttacgtttttattattctttgtttaacctttttatgatattaaaattaaatagaaaagctattgtctaattttgcaataaaatcacaagtctg......................................................................................................... HSP 3 e-value: 3.0E-16 bit: 87.7 Len: 44 Query Start:345 Query End:388 Subject Strand: POSITIVE Subject Start: 345 Subject End: 388 ........................................................................................................................................................................................................................................................................................................................................................gacattactatcaatcaaaagaaagaagatggtatcgtaccatt ........................................................................................................................................................................................................................................................................................................................................................gacattactatcaatcaaaagaaagaagatggtatcgtaccatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUGCUUCCCAUUAGUUGUUUGACAAAUAUACAAAUUUUAUAUUAAAAAGAUUACUCAAUUUUGUAAAUAAUGUAUCUUAAAUUAGCAAACAUUUGUUUAUCAGCUAUUUAUACAACUACAUAAUGCUACUUAUUUUUUAUUUUUGACAGUUUUUUGCAUGCACAACAAAGUGCCAAUAUAGCAAUUUUACGUUUUUAUUAUUCUUUGUUUAACCUUUUUAUGAUAUUAAAAUUAAAUAGAAAAGCUAUUGUCUAAUUUUGCAAUAAAAUCACAAGUCUGAAUUAAAUCAGCAUUAAAAUAAAUGUAAAACCAAAACAAUUAUCUAUUAUGAAAUUAAAAAGACAUUACUAUCAAUCAAAAGAAAGAAGAUGGUAUCGUACCAUU .(((((.........(((((((.(((.....(((((...((((((......((....))......))))))...))))).......((((((((....))))....)))).))).)))))))..(((((((..(((.(((..((((.(((...(((.(((((.((((......)))).....(((((((.....(((((........(((((((((...(((((......))))))))))))))))))).)))).)))....))))).))).))).))))..))).)))...)))))))......)))))...................................((..(((((((..((........)).)))))))..))...... (-49.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGUACGAUACCAUCUUCUUUCUUUUGAUUGAUAGUAAUGUCUUUUUAAUUUCAUAAUAGAUAAUUGUUUUGGUUUUACAUUUAUUUUAAUGCUGAUUUAAUUCAGACUUGUGAUUUUAUUGCAAAAUUAGACAAUAGCUUUUCUAUUUAAUUUUAAUAUCAUAAAAAGGUUAAACAAAGAAUAAUAAAAACGUAAAAUUGCUAUAUUGGCACUUUGUUGUGCAUGCAAAAAACUGUCAAAAAUAAAAAAUAAGUAGCAUUAUGUAGUUGUAUAAAUAGCUGAUAAACAAAUGUUUGCUAAUUUAAGAUACAUUAUUUACAAAAUUGAGUAAUCUUUUUAAUAUAAAAUUUGUAUAUUUGUCAAACAACUAAUGGGAAGCAUAUAU .((((((...))))))((((((....(((.(((((((...(((((...(((..((((((.((((((.(((.........))).)))))).....((((......))))..))))))..)))..........)))))..........(((..(((((((.(((..(((((((((((..(((......((((..((((((...((((((....((((......))))..(((......)))................))))))))))))..)))).((((((((.((((......)))).))).)))))...................)))..))))))))))))))))))))).)))...))))))).))).....))))))....... (-63.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 210 161 121 69 pint:PI1720|5end_conserved_hypothetical_protein_1636146..1636376_POSITIVE 265 185 152 139 101 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 248 200 152 85 32 pint:PI1844|5end_hypothetical_protein_1790092..1790322_POSITIVE 248 169 127 133 90 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 245 195 152 104 60 pint:PI1763|5end_two-component_system_sensor_histidine_kinase/response_regulator_1685877..1686107_POSITIVE 238 179 132 156 107 pint:PI2034|5end_conserved_hypothetical_protein_1987573..1987803_POSITIVE 231 218 175 222 170 pint:PI0027|5end_aminopeptidase_C_30468..30698_POSITIVE 224 218 174 185 141 pint:PI1614|5end_hypothetical_protein_1540801..1541031_POSITIVE 223 177 135 183 138 pint:PI1698|5end_subtilisin-like_serine_protease_1613830..1614060_POSITIVE 223 188 143 113 73 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 222 269 238 130 105 pint:PI1071|5end_DNA_topoisomerase_III_988290..988520_POSITIVE 222 178 132 68 34 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 219 39 5 139 106 pint:PI0810|5end_hypothetical_protein_746743..746973_POSITIVE 219 39 5 134 101 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 219 195 157 171 133 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 214 186 148 60 24 pint:PI1090|5end_tRNA_uracil_5-methyltransferase_1014366..1014596_POSITIVE 213 200 153 149 109 pint:PI1633|5end_hypothetical_protein_1552504..1552734_POSITIVE 213 200 153 69 29 pint:PI1631|5end_hypothetical_protein_1552424..1552654_POSITIVE 213 187 146 162 121 pint:PI1030|5end_biotin_carboxyl_carrier_protein_947846..948076_POSITIVE 213 159 119 212 166 pint:PI1023|5end_hypothetical_protein_939936..940166_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 210 161 102 50 pint:PI1719|3end_conserved_hypothetical_protein_1636207..1636357_POSITIVE 248 169 127 128 85 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 238 196 152 131 90 pint:PI2093|3end_hypothetical_protein_2049440..2049590_POSITIVE 238 196 152 97 56 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 223 188 143 42 2 pint:PI1467|3end_conserved_hypothetical_protein_1393909..1394059_POSITIVE 222 269 238 61 36 pint:PI1070|3end_peptidoglycan-associated_lipoprotein_988301..988451_POSITIVE 219 177 136 140 77 pint:PI0943|3end_conserved_hypothetical_protein_875991..876141_POSITIVE 213 200 153 59 19 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 212 180 134 120 70 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 209 298 252 141 99 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE 208 165 135 149 117 pint:PI1697|3end_conserved_hypothetical_protein_1613889..1614039_POSITIVE 207 194 160 133 97 pint:PI0105|3end_possible_sulfatase_101453..101603_POSITIVE 206 189 147 144 97 pint:PI1089|3end_conserved_hypothetical_protein_1014040..1014190_POSITIVE 206 166 126 49 18 pint:PI1000|3end_conserved_hypothetical_protein_923672..923822_POSITIVE 206 212 175 107 61 pint:PI0297|3end_hypothetical_protein_277916..278066_POSITIVE 204 336 292 89 45 pint:PI0934|3end_hypothetical_protein_866132..866282_POSITIVE 203 220 172 59 12 pint:PI0276|3end_anti-restriction_protein_265021..265171_POSITIVE 201 180 141 71 24 pint:PI0401|3end_conserved_hypothetical_protein_367107..367257_POSITIVE 197 164 128 141 111 pint:PI2119|3end_conserved_hypothetical_protein;_possible_cytochrome_B_subunit_2068758..2068908_POSITIVE 194 39 5 73 30 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE