Origin IGS: caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta .........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 taagcgaaatacagctaacaaatatagaaataaaacttattaagtattgttatggctctttgaaagaaacgaaaactttcaaagagccatatttttttataataactatttgttgtgttgtcgaaattcggcgaaagataaatcccatagtcgaatccgtctgaatagaaagtactcttttgtctgccacttgtttttctttctcttacaccttgttatatatagggaaatgagataataaagctgtaaaaatatttcacaagaatatctactacttaactcgctcgttgtcaatgatttacaaaacctg Mask Tandem Repeat Region ================================================ caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Find is-nt database================================================ Query_seq: PI1155:PI1156|PI1155:PI1156:hypothetical protein:possible glycerate kinase family protein:->->:1080413..1080722 310 caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1155:PI1156|PI1155:PI1156:hypothetical protein:possible glycerate kinase family protein:->->:1080413..1080722 310 caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1155:PI1156|PI1155:PI1156:hypothetical protein:possible glycerate kinase family protein:->->:1080413..1080722 310 caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 17 End: 202 ................ M T T S E L S S R Y S C E I F L Q L Y Y L I S L Y I T R C K R K K N K W Q T K E Y F L F R R I R L W D L S F A E F R Q H ............................................................................................................ Protein_Len: 46 Strand: + Start: 121 End: 258 ........................................................................................................................ M A D K R V L S I Q T D S T M G F I F R R I S T T Q Q I V I I K K Y G S L K V F V S F K E P .................................................... Protein_Len: 42 Strand: + Start: 168 End: 293 ....................................................................................................................................................................... M Y L S P N F D N T T N S Y Y K K I W L F E S F R F F Q R A I T I L N K F Y F Y I C ................. Protein_Len: 51 Strand: - Start: 150 End: 302 ..................................................................................................................................................... V S E V I P N I K R R I E V V C C I T I I F F Y P E K F T K T E K L S G Y C Y K I L K I E I N T L Q M ........ Protein_Len: 60 Strand: - Start: 76 End: 264 ........................................................................... R Y I V L H L L F F F L H C V F S Y K R N L R I R S H S K D K A S N R C C L L Y N N Y F F I A R Q F N E N R E F L W L M .............................................. caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta 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================================================ caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.8 Tail_Score: -5.67063 Start: 220 End: 260 Full_Region: cttattaagtattgt tatggctctttgaaag aaacgaaaa ctttcaaagagccata tttttttataataac ...........................................................................................................................................................................................................................tatggctctttgaaagaaacgaaaactttcaaagagccata.................................................. Find igs database================================================ Query_seq: PI1155:PI1156|PI1155:PI1156:hypothetical protein:possible glycerate kinase family protein:->->:1080413..1080722 310 caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: pint_PI1155_PI1156|hypothetical protein:possible glycerate kinase family protein|POSITIVE:POSITIVE|[1080413,1080722]|310 HSP 1 e-value: 1.0E-162 bit: 573.0 Len: 310 Query Start:1 Query End:310 Subject Strand: POSITIVE Subject Start: 1 Subject End: 310 caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattatnnnnnnntatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta caggttttgtaaatcattgacaacgagcgagttaagtagtagatattcttgtgaaatatttttacagctttattatctcatttccctatatataacaaggtgtaagagaaagaaaaacaagtggcagacaaaagagtactttctattcagacggattcgactatgggatttatctttcgccgaatttcgacaacacaacaaatagttattataaaaaaatatggctctttgaaagttttcgtttctttcaaagagccataacaatacttaataagttttatttctatatttgttagctgtatttcgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGUUUUGUAAAUCAUUGACAACGAGCGAGUUAAGUAGUAGAUAUUCUUGUGAAAUAUUUUUACAGCUUUAUUAUCUCAUUUCCCUAUAUAUAACAAGGUGUAAGAGAAAGAAAAACAAGUGGCAGACAAAAGAGUACUUUCUAUUCAGACGGAUUCGACUAUGGGAUUUAUCUUUCGCCGAAUUUCGACAACACAACAAAUAGUUAUUAUAAAAAAAUAUGGCUCUUUGAAAGUUUUCGUUUCUUUCAAAGAGCCAUAACAAUACUUAAUAAGUUUUAUUUCUAUAUUUGUUAGCUGUAUUUCGCUUA ...(((.((.....))..)))...((((((.....(((((((.((((.(((((.....((((((((.((((.((((...............)))).))))))))))))...((((......((((........(((((.....))))).((..(((((.......)))))..))....))))..)))).....)))))..)))).))))))).......((((((((((((((((.........))))))))))))))))..((((((((((((((...........)))))))))..))))))))))). (-65.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCGAAAUACAGCUAACAAAUAUAGAAAUAAAACUUAUUAAGUAUUGUUAUGGCUCUUUGAAAGAAACGAAAACUUUCAAAGAGCCAUAUUUUUUUAUAAUAACUAUUUGUUGUGUUGUCGAAAUUCGGCGAAAGAUAAAUCCCAUAGUCGAAUCCGUCUGAAUAGAAAGUACUCUUUUGUCUGCCACUUGUUUUUCUUUCUCUUACACCUUGUUAUAUAUAGGGAAAUGAGAUAAUAAAGCUGUAAAAAUAUUUCACAAGAAUAUCUACUACUUAACUCGCUCGUUGUCAAUGAUUUACAAAACCUG ..(((((...((((((((((((((.....((((.(((.....))).))))((((((((((((((((.........))))))))))))))))...............))))))))).))))).(((((..(((((((((((..((...(((.((....)).)))....))...)).)))))))))....((..(((((....((((.....((((((.....))))))....))))....))))).))......)))))......................)))))......................... (-67.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 70 25 188 143 pint:PI0851|5end_hypothetical_protein_784310..784540_POSITIVE 382 260 222 146 108 pint:PI1155|5end_hypothetical_protein_1080084..1080314_POSITIVE 356 50 2 50 2 pint:PI0689|5end_hypothetical_protein_625624..625854_POSITIVE 316 70 27 170 127 pint:PI2128|5end_hypothetical_protein_2076512..2076742_POSITIVE 305 90 41 144 91 pint:PI1339|5end_hypothetical_protein_1256671..1256901_POSITIVE 295 50 2 141 93 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 290 70 25 161 116 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 281 180 132 91 41 pint:PI2077|5end_hypothetical_protein_2035892..2036122_POSITIVE 279 89 45 190 144 pint:PI1168|5end_hypothetical_protein_1089696..1089926_POSITIVE 279 89 45 182 136 pint:PI1167|5end_hypothetical_protein_1089688..1089918_POSITIVE 275 90 52 41 1 pint:PI1340|5end_hypothetical_protein_1256568..1256798_POSITIVE 274 160 111 109 60 pint:PI0267|5end_conjugative_transposon_protein,_TraQ_258786..259016_POSITIVE 271 66 26 157 117 pint:PI1601|5end_hypothetical_protein_1530282..1530512_POSITIVE 271 189 142 78 28 pint:PI0297|5end_hypothetical_protein_277747..277977_POSITIVE 270 167 121 54 6 pint:PI1247|5end_conserved_hypothetical_protein_1171630..1171860_POSITIVE 269 184 146 215 174 pint:PI0871|5end_hypothetical_protein_806834..807064_POSITIVE 268 69 22 131 85 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 268 197 154 230 183 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 268 181 147 71 40 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 265 47 2 126 81 pint:PI2144|5end_hypothetical_protein_2091954..2092184_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 260 222 66 28 pint:PI1154|3end_conserved_hypothetical_protein;_possible_periplasmic_solute-binding_protein_1080084..1080234_POSITIVE 356 50 2 96 48 pint:PI0688|3end_hypothetical_protein_625750..625900_POSITIVE 353 50 2 92 44 pint:PI1051|3end_hypothetical_protein_970228..970378_POSITIVE 337 69 23 63 18 pint:PI1117|3end_glycosyl_transferase,_family_2_1042279..1042429_POSITIVE 295 50 2 56 8 pint:PI1566|3end_predicted_TPR-repeat-containing_protein_1489224..1489374_POSITIVE 287 50 2 76 28 pint:PI1391|3end_hypothetical_protein_1311694..1311844_POSITIVE 279 89 45 50 4 pint:PI1165|3end_hypothetical_protein_1089636..1089786_POSITIVE 275 139 101 140 100 pint:PI0491|3end_hypothetical_protein_451227..451377_POSITIVE 271 66 26 70 30 pint:PI1600|3end_conserved_hypothetical_protein_1530275..1530425_POSITIVE 271 189 142 75 25 pint:PI0296|3end_hypothetical_protein_277824..277974_POSITIVE 268 69 22 84 38 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 268 181 147 84 53 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 266 158 118 43 1 pint:PI1966|3end_conserved_hypothetical_protein_1924091..1924241_POSITIVE 265 47 2 66 21 pint:PI2143|3end_DNA_mismatch_repair_protein_2091974..2092124_POSITIVE 261 129 82 121 59 pint:PI1198|3end_acetyltransferase_1115219..1115369_POSITIVE 260 74 31 46 3 pint:PI0770|3end_hypothetical_protein_706354..706504_POSITIVE 260 70 22 66 17 pint:PI0051|3end_hypothetical_protein_53388..53538_POSITIVE 257 39 3 148 108 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 254 78 31 69 19 pint:PI2172|3end_hypothetical_protein_2113991..2114141_POSITIVE 249 192 152 144 105 pint:PI2077|3end_hypothetical_protein_2036070..2036220_POSITIVE