Origin IGS: tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagcggctcttaactgccagattattccttctacatacctcgttctataagcaaaagctggtaaaagaaatgtaaacatttttcacaagcgtaaataccgtctaaccatctaattatca Mask Tandem Repeat Region ================================================ tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Find is-nt database================================================ Query_seq: PI0659:PI0660|PI0659:PI0660:hypothetical protein:conserved hypothetical protein:->->:603457..603577 121 tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0659:PI0660|PI0659:PI0660:hypothetical protein:conserved hypothetical protein:->->:603457..603577 121 tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0659:PI0660|PI0659:PI0660:hypothetical protein:conserved hypothetical protein:->->:603457..603577 121 tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Predict ORF larger than 30AA ================================================ tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta 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================================================ tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0659:PI0660|PI0659:PI0660:hypothetical protein:conserved hypothetical protein:->->:603457..603577 121 tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: pint_PI0659_PI0660|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[603457,603577]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta tgataattagatggttagacggtatttacgcttgtgaaaaatgtttacatttcttttaccagcttttgcttatagaacgaggtatgtagaaggaataatctggcagttaagagccgcttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAAUUAGAUGGUUAGACGGUAUUUACGCUUGUGAAAAAUGUUUACAUUUCUUUUACCAGCUUUUGCUUAUAGAACGAGGUAUGUAGAAGGAAUAAUCUGGCAGUUAAGAGCCGCUUUA ........((((...((((((...(((((....)))))...)))))).(((((((((((..(((((..(.....)...)))))..))))))))))).))))(((........)))...... (-22.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCGGCUCUUAACUGCCAGAUUAUUCCUUCUACAUACCUCGUUCUAUAAGCAAAAGCUGGUAAAAGAAAUGUAAACAUUUUUCACAAGCGUAAAUACCGUCUAACCAUCUAAUUAUCA ....((((........((((((............((.......))..............))))))..(((((((....)))))))..............)))).................. (-13.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 471 49 1 129 81 pint:PI0061|5end_hypothetical_protein_60500..60730_POSITIVE 461 49 1 129 84 pint:PI1733|5end_hypothetical_protein_1652160..1652390_POSITIVE 461 60 11 151 102 pint:PI0755|5end_hypothetical_protein_686691..686921_POSITIVE 441 49 1 129 81 pint:PI0200|5end_hypothetical_protein_191545..191775_POSITIVE 434 49 1 157 109 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 394 80 31 71 21 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 361 60 11 151 91 pint:PI0182|5end_hypothetical_protein_174093..174323_POSITIVE 352 49 1 129 81 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 345 55 11 45 1 pint:PI1281|5end_hypothetical_protein_1196645..1196875_POSITIVE 341 58 11 174 126 pint:PI1168|5end_hypothetical_protein_1089696..1089926_POSITIVE 341 58 11 166 118 pint:PI1167|5end_hypothetical_protein_1089688..1089918_POSITIVE 337 74 32 142 101 pint:PI1057|5end_hypothetical_protein_977286..977516_POSITIVE 335 54 11 191 141 pint:PI0841|5end_hypothetical_protein_775406..775636_POSITIVE 334 49 9 157 117 pint:PI1694|5end_hypothetical_protein_1609717..1609947_POSITIVE 324 49 1 88 40 pint:PI1922|5end_hypothetical_protein_1865219..1865449_POSITIVE 322 49 1 118 70 pint:PI0099|5end_hypothetical_protein_95530..95760_POSITIVE 321 79 31 122 70 pint:PI0928|5end_hypothetical_protein_859851..860081_POSITIVE 318 118 76 99 56 pint:PI0123|5end_outer_membrane_protein,_ompH_family_113906..114136_POSITIVE 317 49 1 66 18 pint:PI0689|5end_hypothetical_protein_625624..625854_POSITIVE 313 50 1 146 97 pint:PI1866|5end_hypothetical_protein_1811693..1811923_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 80 31 138 88 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 375 59 12 61 14 pint:PI1485|3end_hypothetical_protein_1405339..1405489_POSITIVE 352 49 1 82 34 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 351 50 1 62 13 pint:PI0051|3end_hypothetical_protein_53388..53538_POSITIVE 317 73 31 50 7 pint:PI1165|3end_hypothetical_protein_1089636..1089786_POSITIVE 317 49 1 112 64 pint:PI0688|3end_hypothetical_protein_625750..625900_POSITIVE 309 48 1 84 37 pint:PI2143|3end_DNA_mismatch_repair_protein_2091974..2092124_POSITIVE 309 49 1 70 22 pint:PI1600|3end_conserved_hypothetical_protein_1530275..1530425_POSITIVE 296 49 1 92 44 pint:PI1813|3end_hypothetical_protein_1753086..1753236_POSITIVE 296 60 19 57 10 pint:PI0098|3end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_95532..95682_POSITIVE 281 49 1 54 6 pint:PI2172|3end_hypothetical_protein_2113991..2114141_POSITIVE 273 83 44 129 87 pint:PI1603|3end_hypothetical_protein_1534005..1534155_POSITIVE 270 52 12 95 55 pint:PI1391|3end_hypothetical_protein_1311694..1311844_POSITIVE 268 94 51 124 79 pint:PI0251|3end_hypothetical_protein_247810..247960_POSITIVE 266 106 68 43 1 pint:PI1886|3end_cell_division_protein_1829158..1829308_POSITIVE 252 60 12 64 5 pint:PI1424|3end_probable_peptidase_family_M48_1344044..1344194_POSITIVE 248 69 30 110 73 pint:PI0757|3end_possible_hemagglutinin/protease_693741..693891_POSITIVE 247 119 77 56 14 pint:PI2019|3end_elongation_factor_P_1976774..1976924_POSITIVE 245 120 78 136 87 pint:PI2011|3end_hypothetical_protein_1970730..1970880_POSITIVE 245 70 23 89 38 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE