Origin IGS: cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attggaaacgcccttgttcactttcagtcccttatagcaatcatcattttcgggatgatgaagtagttcgtccatagttattgttctgtttatcagatctgcggcaatctcgcttgcagtaccgcttggcagcagctctacggggaaaag Mask Tandem Repeat Region ================================================ cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Find is-nt database================================================ Query_seq: PG0320:PG0321|PG0320:PG0321:hypothetical protein:arginine/ornithine transport system ATPase:->->:354638..354787 150 cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0320:PG0321|PG0320:PG0321:hypothetical protein:arginine/ornithine transport system ATPase:->->:354638..354787 150 cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0320:PG0321|PG0320:PG0321:hypothetical protein:arginine/ornithine transport system ATPase:->->:354638..354787 150 cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 16 End: 150 ............... M L P S G T A S E I A A D L I N R T I T M D E L L H H P E N D D C Y K G L K V N K G V S N cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat 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================================================ cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -4.1 Tail_Score: -3.25942 Start: 90 End: 110 Full_Region: TATGGACGAACTACT TCATCAT CCCGAAA ATGATGA TTGCTATAAGGGACT .........................................................................................TCATCATCCCGAAAATGATGA........................................ Find igs database================================================ Query_seq: PG0320:PG0321|PG0320:PG0321:hypothetical protein:arginine/ornithine transport system ATPase:->->:354638..354787 150 cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_002950_PG0320_PG0321|hypothetical protein:arginine/ornithine transport system ATPase|POSITIVE:POSITIVE|[354638,354787]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat cttttccccgtagagctgctgccaagcggtactgcaagcgagattgccgcagatctgataaacagaacaataactatggacgaactacttcatcatcccgaaaatgatgattgctataagggactgaaagtgaacaagggcgtttccaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCCCCGUAGAGCUGCUGCCAAGCGGUACUGCAAGCGAGAUUGCCGCAGAUCUGAUAAACAGAACAAUAACUAUGGACGAACUACUUCAUCAUCCCGAAAAUGAUGAUUGCUAUAAGGGACUGAAAGUGAACAAGGGCGUUUCCAAU .........((((.((((((....)))))).))))..(((.......)))...((((.....))))..........((((((..((..(((((((((((....................)))).)))...))))..))..))..)))).. (-35.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGGAAACGCCCUUGUUCACUUUCAGUCCCUUAUAGCAAUCAUCAUUUUCGGGAUGAUGAAGUAGUUCGUCCAUAGUUAUUGUUCUGUUUAUCAGAUCUGCGGCAAUCUCGCUUGCAGUACCGCUUGGCAGCAGCUCUACGGGGAAAAG ...(....)..................(((((((.(((..((((((((.....))))))))....(((.(.(((.(((......((((.....)))).(((((((......)).)))))....)))))))))).))).)).))))).... (-35.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 49 2 196 144 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 415 55 12 216 174 NC_002950:PG0488|5end_Holliday_junction_DNA_helicase_RuvB_528169..528399_POSITIVE 401 48 8 187 124 NC_002950:PG0515|5end_hypothetical_protein_557958..558188_NEGATIVE 395 49 8 55 6 NC_002950:PG0740|5end_NLP/P60_family_protein_787836..788066_POSITIVE 390 53 12 50 1 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 381 49 1 69 5 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 375 48 9 51 1 NC_002950:PG2069|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2164798..2165028_POSITIVE 368 59 14 178 139 NC_002950:PG0423|5end_hypothetical_protein_462251..462481_POSITIVE 366 60 15 135 77 NC_002950:PG0458|5end_ISPg5,_transposase_Orf2_501463..501693_NEGATIVE 362 50 8 49 1 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 361 56 12 200 152 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 359 42 6 193 149 NC_002950:PG1641|5end_phosphotyrosine_protein_phosphatase_1721763..1721993_NEGATIVE 356 58 18 45 3 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 349 50 8 206 168 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 347 59 14 196 145 NC_002950:PG1180|5end_hypothetical_protein_1263615..1263845_NEGATIVE 345 57 13 61 7 NC_002950:PG0189|5end_hypothetical_protein_225291..225521_POSITIVE 344 50 9 186 150 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 341 68 21 145 83 NC_002950:PG2128|5end_ISPg5,_transposase_Orf2_2234805..2235035_NEGATIVE 341 68 21 145 83 NC_002950:PG2057|5end_ISPg5,_transposase_Orf2_2155947..2156177_NEGATIVE 341 68 21 145 83 NC_002950:PG1710|5end_ISPg5,_transposase_Orf2_1795357..1795587_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 49 1 80 17 NC_002950:PG0739|3end_ribonuclease_Z_787941..788091_POSITIVE 404 49 9 141 105 NC_002950:PG0363|3end_hypothetical_protein_398377..398527_POSITIVE 390 53 12 63 14 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 388 50 1 125 70 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 382 50 6 149 98 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 381 49 1 72 8 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 369 50 11 128 92 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 366 60 15 81 23 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 363 49 11 55 21 NC_002950:PG0754|3end_DNA_topoisomerase_I_803389..803539_POSITIVE 362 48 16 45 9 NC_002950:PG2068|3end_glycerol-3-phosphate_cytidylyltransferase_2164872..2165022_POSITIVE 358 59 15 140 90 NC_002950:PG0965|3end_phosphatidylserine_decarboxylase_1025111..1025261_NEGATIVE 346 50 1 151 88 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 346 49 8 137 83 NC_002950:PG0809|3end_hypothetical_protein_865064..865214_NEGATIVE 345 49 3 151 94 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 345 57 13 74 20 NC_002950:PG0188|3end_lipoprotein,_putative_225384..225534_POSITIVE 342 47 5 148 97 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 342 47 5 148 97 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 342 54 12 62 13 NC_002950:PG0381|3end_cell_volume_regulation_protein_CvrA_411185..411335_NEGATIVE 341 68 21 91 29 NC_002950:PG2129|3end_ISPg5,_transposase_Orf1_2234859..2235009_NEGATIVE 341 68 21 91 29 NC_002950:PG2058|3end_ISPg5,_transposase_Orf1_2156001..2156151_NEGATIVE