Origin IGS: tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta .........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 taagacagaaatggcttcaagacgcggtgttttgaagccattttttgtattttccaatttaataaaaggactatcaatgctcataatggatagcaataaaacttcgcccctattcatcattttataaacggaaaaccgattataaagttgtaaacatttttcgcaaataacactatcgtttaactatctcgttatcagcgca Mask Tandem Repeat Region ================================================ tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Find is-nt database================================================ Query_seq: PI1005:PI1006|PI1005:PI1006:hypothetical protein:conserved hypothetical protein:->->:926542..926743 202 tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1005:PI1006|PI1005:PI1006:hypothetical protein:conserved hypothetical protein:->->:926542..926743 202 tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1005:PI1006|PI1005:PI1006:hypothetical protein:conserved hypothetical protein:->->:926542..926743 202 tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 35 End: 202 .................................. M C E K C L Q L Y N R F S V Y K M M N R G E V L L L S I M S I D S P F I K L E N T K N G F K T P R L E A I S V L Protein_Len: 38 Strand: - Start: 79 End: 192 .............................................................................. L I I F L P S T K N S D M I L M S L G K I L N S F V F F P K L V G R R S A M .......... tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta 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: 82 Start: 35 End: 64 ..................................ATTTGCGAAAAATGTTTACAACTTTATAAT.......................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 125 End: 154 ............................................................................................................................ATTGATAGTCCTTTTATTAAATTGGAAAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1005:PI1006|PI1005:PI1006:hypothetical protein:conserved hypothetical protein:->->:926542..926743 202 tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: pint_PI1005_PI1006|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[926542,926743]|202 HSP 1 e-value: 1.0E-111 bit: 400.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta tgcgctgataacgagatagttaaacgatagtgttatttgcgaaaaatgtttacaactttataatcggttttccgtttataaaatgatgaataggggcgaagttttattgctatccattatgagcattgatagtccttttattaaattggaaaatacaaaaaatggcttcaaaacaccgcgtcttgaagccatttctgtctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCGCUGAUAACGAGAUAGUUAAACGAUAGUGUUAUUUGCGAAAAAUGUUUACAACUUUAUAAUCGGUUUUCCGUUUAUAAAAUGAUGAAUAGGGGCGAAGUUUUAUUGCUAUCCAUUAUGAGCAUUGAUAGUCCUUUUAUUAAAUUGGAAAAUACAAAAAAUGGCUUCAAAACACCGCGUCUUGAAGCCAUUUCUGUCUUA ...(((.((((.(.((((((.....(((((.....(((((......((((((((..(((((((.(((....))).))))))).)).))))))...)))))...)))))))))))).)))).)))...((((((((..((....))..))).........((((((((((((.((.....)).)))))))))))))))))... (-49.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACAGAAAUGGCUUCAAGACGCGGUGUUUUGAAGCCAUUUUUUGUAUUUUCCAAUUUAAUAAAAGGACUAUCAAUGCUCAUAAUGGAUAGCAAUAAAACUUCGCCCCUAUUCAUCAUUUUAUAAACGGAAAACCGAUUAUAAAGUUGUAAACAUUUUUCGCAAAUAACACUAUCGUUUAACUAUCUCGUUAUCAGCGCA ....(((((((((((((((((((.....)))))))))))).)))))))....(((............)))........(((.(((((((((((.....((((................(((((((((.(((....))).)))))))))((..((.....))..))............))))..))))).)))))).)))... (-45.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 50 1 125 76 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 450 59 13 162 116 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 359 59 14 149 105 pint:PI1129|5end_hypothetical_protein_1055377..1055607_POSITIVE 353 59 14 133 89 pint:PI0004|5end_hypothetical_protein_6199..6429_POSITIVE 343 50 3 161 114 pint:PI1679|5end_hypothetical_protein_1594744..1594974_POSITIVE 341 90 41 74 26 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 332 50 1 141 87 pint:PI2144|5end_hypothetical_protein_2091954..2092184_POSITIVE 328 197 165 157 121 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 326 50 1 62 8 pint:PI0689|5end_hypothetical_protein_625624..625854_POSITIVE 325 54 13 157 116 pint:PI1694|5end_hypothetical_protein_1609717..1609947_POSITIVE 305 50 1 125 71 pint:PI0200|5end_hypothetical_protein_191545..191775_POSITIVE 301 60 11 135 86 pint:PI1733|5end_hypothetical_protein_1652160..1652390_POSITIVE 301 88 41 122 75 pint:PI0928|5end_hypothetical_protein_859851..860081_POSITIVE 297 78 31 208 162 pint:PI0851|5end_hypothetical_protein_784310..784540_POSITIVE 296 50 1 114 60 pint:PI1057|5end_hypothetical_protein_977286..977516_POSITIVE 294 135 93 135 95 pint:PI1478|5end_hypothetical_protein_1401873..1402103_POSITIVE 285 134 91 115 71 pint:PI2065|5end_hypothetical_protein_2026877..2027107_POSITIVE 284 72 37 171 140 pint:PI1346|5end_hypothetical_protein_1260814..1261044_POSITIVE 284 50 1 125 76 pint:PI0182|5end_hypothetical_protein_174093..174323_POSITIVE 282 41 4 43 8 pint:PI1709|5end_ABC_transporter,_ATP-binding_protein_1625843..1626073_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 50 1 78 29 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 341 90 41 141 93 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 332 50 1 81 27 pint:PI2143|3end_DNA_mismatch_repair_protein_2091974..2092124_POSITIVE 331 80 31 63 18 pint:PI0770|3end_hypothetical_protein_706354..706504_POSITIVE 329 54 14 54 14 pint:PI2172|3end_hypothetical_protein_2113991..2114141_POSITIVE 326 50 1 108 54 pint:PI0688|3end_hypothetical_protein_625750..625900_POSITIVE 294 135 93 65 25 pint:PI1477|3end_TonB-dependent_outer_membrane_receptor_1401883..1402033_POSITIVE 285 134 91 149 105 pint:PI2064|3end_conserved_hypothetical_protein;_possible_type_I_restriction-modification_system,_S_subunit_2026991..2027141_POSITIVE 280 50 1 136 82 pint:PI0054|3end_hypothetical_protein_54829..54979_POSITIVE 268 135 96 117 85 pint:PI0747|3end_possible_mobilization_protein_676702..676852_POSITIVE 261 139 95 138 85 pint:PI0195|3end_epimerase/reductase_188202..188352_POSITIVE 250 50 4 102 56 pint:PI1051|3end_hypothetical_protein_970228..970378_POSITIVE 249 128 82 65 19 pint:PI0691|3end_hypothetical_protein_628369..628519_POSITIVE 247 200 153 81 34 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 247 127 84 143 110 pint:PI0540|3end_conserved_hypothetical_protein_493865..494015_POSITIVE 246 50 1 66 17 pint:PI1600|3end_conserved_hypothetical_protein_1530275..1530425_POSITIVE 246 50 6 48 4 pint:PI0412|3end_primosomal_protein_N',_replication_factor_Y_382152..382302_POSITIVE 245 101 62 58 10 pint:PI1879|3end_uracil_phosphoribosyltransferase_1821245..1821395_POSITIVE 245 129 90 44 11 pint:PI1820|3end_hypothetical_protein_1760377..1760527_POSITIVE 242 199 163 120 83 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE