Origin IGS: atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta .........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 taatacttttgtaacgcacaacttactataatccaatataaaactgcggggacaacaatgctattatgctgttgtccccgctttttgttagatatattgacgagcgtaaatgctagctttttttagatattctagtattcttagattttatagaatctttagactaacagataggaaatcgctcttgttttgtaaatataattctgaaggaaaacggtaatttcgat Mask Tandem Repeat Region ================================================ atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Find is-nt database================================================ Query_seq: PI0689:PI0690|PI0689:PI0690:hypothetical protein:uracil permease:->->:625938..626164 227 atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0689:PI0690|PI0689:PI0690:hypothetical protein:uracil permease:->->:625938..626164 227 atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0689:PI0690|PI0689:PI0690:hypothetical protein:uracil permease:->->:625938..626164 227 atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 133 End: 225 .................................................................................................................................... M S N K K R G Q Q H N S I V V P A V L Y W I I V S C A L Q K Y .. Protein_Len: 32 Strand: - Start: 105 End: 200 ........................................................................................................ F F S A N V S T L I D L L F R P C C C L L M T T G A T K Y Q I M ........................... Protein_Len: 36 Strand: - Start: 11 End: 118 .......... R K G E S N Y K C F L L S K R D T L R F I R Y F R L I S S Y R F F A L M ............................................................................................................. atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta 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================================================ atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -5.7 Tail_Score: -4.7033 Start: 145 End: 184 Full_Region: AATATATCTAACAAA AAGCGGGGACAACAG CATAATAGCA TTGTTGTCCCCGCAG TTTTATATTGGATTA ................................................................................................................................................AAGCGGGGACAACAGCATAATAGCATTGTTGTCCCCGCAG........................................... TransTerm Strand: + Conf: 78 HP_score: -9.2 Tail_Score: -3.41114 Start: 146 End: 183 Full_Region: ATATATCTAACAAAA AGCGGGGACAACAG CATAATAGCA TTGTTGTCCCCGCA GTTTTATATTGGATT .................................................................................................................................................AGCGGGGACAACAGCATAATAGCATTGTTGTCCCCGCA............................................ TransTerm Strand: + Conf: 95 HP_score: -12.7 Tail_Score: -2.63584 Start: 147 End: 182 Full_Region: TATATCTAACAAAAA GCGGGGACAACAG CATAATAGCA TTGTTGTCCCCGC AGTTTTATATTGGAT ..................................................................................................................................................GCGGGGACAACAGCATAATAGCATTGTTGTCCCCGC............................................. TransTerm Strand: - Conf: 100 HP_score: -12.0 Tail_Score: -5.12068 Start: 147 End: 182 Full_Region: atccaatataaaact gcggggacaaca atgctattatgc tgttgtccccgc tttttgttagatata ..................................................................................................................................................gcggggacaacaatgctattatgctgttgtccccgc............................................. Find igs database================================================ Query_seq: PI0689:PI0690|PI0689:PI0690:hypothetical protein:uracil permease:->->:625938..626164 227 atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: pint_PI0689_PI0690|hypothetical protein:uracil permease|POSITIVE:POSITIVE|[625938,626164]|227 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctnnnnnnngctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta atcgaaattaccgttttccttcagaattatatttacaaaacaagagcgatttcctatctgttagtctaaagattctataaaatctaagaatactagaatatctaaaaaaagctagcatttacgctcgtcaatatatctaacaaaaagcggggacaacagcataatagcattgttgtccccgcagttttatattggattatagtaagttgtgcgttacaaaagtatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAAAUUACCGUUUUCCUUCAGAAUUAUAUUUACAAAACAAGAGCGAUUUCCUAUCUGUUAGUCUAAAGAUUCUAUAAAAUCUAAGAAUACUAGAAUAUCUAAAAAAAGCUAGCAUUUACGCUCGUCAAUAUAUCUAACAAAAAGCGGGGACAACAGCAUAAUAGCAUUGUUGUCCCCGCAGUUUUAUAUUGGAUUAUAGUAAGUUGUGCGUUACAAAAGUAUUA ...((((.......))))............((((((.......(((((......((..(((((((....(((((......)))))........(((.....)))......)))))))..))))))).((((((((...(((.....((((((((((((((......))..)))))))))))).))).))))))))......)))))).((((.........)))).. (-49.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUACUUUUGUAACGCACAACUUACUAUAAUCCAAUAUAAAACUGCGGGGACAACAAUGCUAUUAUGCUGUUGUCCCCGCUUUUUGUUAGAUAUAUUGACGAGCGUAAAUGCUAGCUUUUUUUAGAUAUUCUAGUAUUCUUAGAUUUUAUAGAAUCUUUAGACUAACAGAUAGGAAAUCGCUCUUGUUUUGUAAAUAUAAUUCUGAAGGAAAACGGUAAUUUCGAU .............((((.(...(((.((((.((....((((((..((((((((((((..((......)))))))))))))).))))))..)))))).))).).))))...((((...((((((((((...........(((.((((((....))))))..)))...((((((((((......))))).))))).........))))))))))...))))........ (-52.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 47 1 102 52 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 352 47 1 230 184 pint:PI1804|5end_hypothetical_protein_1738109..1738339_POSITIVE 352 50 3 181 134 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 345 47 1 138 92 pint:PI0037|5end_hypothetical_protein_39354..39584_POSITIVE 330 184 146 213 167 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 322 189 143 93 37 pint:PI0277|5end_hypothetical_protein_264980..265210_POSITIVE 319 190 146 193 126 pint:PI0533|5end_ABC_transporter,_permease_protein_487259..487489_POSITIVE 315 49 1 80 32 pint:PI1182|5end_hypothetical_protein_1104025..1104255_POSITIVE 305 185 148 73 33 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 302 48 1 88 41 pint:PI2141|5end_hypothetical_protein_2087169..2087399_POSITIVE 300 48 1 139 92 pint:PI0322|5end_hypothetical_protein_303508..303738_POSITIVE 300 160 114 125 79 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 300 160 114 51 5 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 299 206 164 78 42 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 294 48 1 118 71 pint:PI1786|5end_hypothetical_protein_1718124..1718354_POSITIVE 291 38 1 129 92 pint:PI0926|5end_hypothetical_protein_856824..857054_POSITIVE 274 170 122 170 122 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 270 187 142 214 171 pint:PI1898|5end_S-adenosyl-methyltransferase_1841288..1841518_POSITIVE 267 183 147 112 72 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 266 186 145 84 46 pint:PI1284|5end_ATP_synthase,_delta_subunit_1199800..1200030_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 47 1 87 42 pint:PI0574|3end_hypothetical_protein_519444..519594_POSITIVE 349 183 147 143 112 pint:PI0588|3end_hypothetical_protein_535425..535575_POSITIVE 349 183 147 65 34 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 324 185 147 146 112 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 305 185 148 64 24 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 300 160 114 125 79 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 299 206 164 61 25 pint:PI1830|3end_conserved_hypothetical_protein_1770361..1770511_POSITIVE 295 189 146 54 1 pint:PI0276|3end_anti-restriction_protein_265021..265171_POSITIVE 278 170 146 144 116 pint:PI0532|3end_ABC_transporter,_ATP-binding/permease_protein_487329..487479_POSITIVE 270 187 142 81 38 pint:PI1897|3end_conserved_hypothetical_protein_1841235..1841385_POSITIVE 266 186 145 68 30 pint:PI1283|3end_ATP_synthase,_alpha_subunit_1199864..1200014_POSITIVE 257 214 174 43 1 pint:PI1979|3end_conserved_hypothetical_protein_1937327..1937477_POSITIVE 255 183 146 104 59 pint:PI0947|3end_conserved_hypothetical_protein_880709..880859_POSITIVE 253 182 146 52 11 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 251 217 172 91 50 pint:PI0215|3end_hypothetical_protein_209004..209154_POSITIVE 246 47 1 102 56 pint:PI1520|3end_hypothetical_protein_1441370..1441520_POSITIVE 246 178 147 151 122 pint:PI0432|3end_hypothetical_protein_405037..405187_POSITIVE 246 168 121 76 16 pint:PI0120|3end_glutamate_racemase_112697..112847_POSITIVE 241 178 146 40 1 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 241 185 143 78 20 pint:PI0626|3end_penicillin-binding_protein,_D-alanyl-D-alanine_carboxypeptidase_575698..575848_POSITIVE