Origin IGS: taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta .........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 taattttaaattttatgttgtgattagctttaaaattagtatctttgcattggcaaatacaactcaagtagattaaagtaatgaacatcagtattgttacgaaagcttagagagaaagaaaaatgcaagcaaaataaagttccactcgtcaagaatggaactttattgtttctaaaaggaggatta Mask Tandem Repeat Region ================================================ taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Find is-nt database================================================ Query_seq: PI1842:PI1843|PI1842:PI1843:conserved hypothetical protein:hypothetical protein:->->:1788378..1788563 186 taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1842:PI1843|PI1842:PI1843:conserved hypothetical protein:hypothetical protein:->->:1788378..1788563 186 taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1842:PI1843|PI1842:PI1843:conserved hypothetical protein:hypothetical protein:->->:1788378..1788563 186 taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 35 End: 148 .................................. M T S G T L F C L H F S F S L S F R N N T D V H Y F N L L E L Y L P M Q R Y ...................................... Protein_Len: 31 Strand: + Start: 93 End: 185 ............................................................................................ M L M F I T L I Y L S C I C Q C K D T N F K A N H N I K F K I . Protein_Len: 31 Strand: - Start: 1 End: 93 L G G K L F L L T G N K V L P V K N Q K C K E K E R L K R L M ............................................................................................. taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta 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================================================ taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -9.9 Tail_Score: -4.06419 Start: 22 End: 52 Full_Region: aaaatgcaagcaaaa taaagttccactc gtcaa gaatggaacttta ttgtttctaaaagga .....................taaagttccactcgtcaagaatggaacttta...................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -6.3 Tail_Score: -4.63048 Start: 26 End: 48 Full_Region: tgcaagcaaaataaa gttccactc gtcaa gaatggaac tttattgtttctaaa .........................gttccactcgtcaagaatggaac.......................................................................................................................................... Find igs database================================================ Query_seq: PI1842:PI1843|PI1842:PI1843:conserved hypothetical protein:hypothetical protein:->->:1788378..1788563 186 taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: pint_PI1842_PI1843|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1788378,1788563]|186 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 186 Query Start:1 Query End:186 Subject Strand: POSITIVE Subject Start: 1 Subject End: 186 taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta taatcctccttttagaaacaataaagttccattcttgacgagtggaactttattttgcttgcatttttctttctctctaagctttcgtaacaatactgatgttcattactttaatctacttgagttgtatttgccaatgcaaagatactaattttaaagctaatcacaacataaaatttaaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCCUCCUUUUAGAAACAAUAAAGUUCCAUUCUUGACGAGUGGAACUUUAUUUUGCUUGCAUUUUUCUUUCUCUCUAAGCUUUCGUAACAAUACUGAUGUUCAUUACUUUAAUCUACUUGAGUUGUAUUUGCCAAUGCAAAGAUACUAAUUUUAAAGCUAAUCACAACAUAAAAUUUAAAAUUA .........(((((((...(((((((((((((((.....)))))))))))))))..(((((................)))))................(((((.((((((((((........(((....(((((....)))))...)))....)))))).))))...)))))....)))))))... (-32.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUUAAAUUUUAUGUUGUGAUUAGCUUUAAAAUUAGUAUCUUUGCAUUGGCAAAUACAACUCAAGUAGAUUAAAGUAAUGAACAUCAGUAUUGUUACGAAAGCUUAGAGAGAAAGAAAAAUGCAAGCAAAAUAAAGUUCCACUCGUCAAGAAUGGAACUUUAUUGUUUCUAAAAGGAGGAUUA ........(((((((.((((....))))..))))))).((((..((((....))))))))..(((...((((.....((((..(((....)).)..))))....((((..................))))..((((((((((((.((.....)).))))))))))))...))))....)))..... (-36.37) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 70 26 81 29 pint:PI0476|5end_50S_ribosomal_protein_L18_440041..440271_POSITIVE 270 166 122 63 15 pint:PI2088|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_2044437..2044667_POSITIVE 258 148 114 81 50 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 253 78 36 62 26 pint:PI1504|5end_non-specific_DNA-binding_protein_1424318..1424548_POSITIVE 240 146 114 118 80 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 240 147 108 74 40 pint:PI1010|5end_conserved_hypothetical_protein_930922..931152_POSITIVE 236 65 27 203 172 pint:PI1105|5end_hypothetical_protein_1028923..1029153_POSITIVE 236 63 34 145 109 pint:PI0056|5end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_54967..55197_POSITIVE 234 87 47 75 42 pint:PI1747|5end_membrane-bound_lytic_murein_transglycosylase_D_1667483..1667713_POSITIVE 233 63 24 126 81 pint:PI1317|5end_surface_antigen_BspA_1232838..1233068_POSITIVE 233 76 31 191 138 pint:PI0743|5end_hypothetical_protein_672728..672958_POSITIVE 232 128 81 154 102 pint:PI0050|5end_conserved_hypothetical_protein_51539..51769_POSITIVE 231 99 51 227 171 pint:PI0874|5end_conserved_hypothetical_protein_808978..809208_POSITIVE 231 134 97 81 46 pint:PI0398|5end_hypothetical_protein_363378..363608_POSITIVE 231 62 26 67 27 pint:PI0314|5end_conserved_hypothetical_protein_295552..295782_POSITIVE 228 69 24 64 14 pint:PI0967|5end_conserved_hypothetical_protein_895424..895654_POSITIVE 228 77 32 63 12 pint:PI0593|5end_NAD-specific_glutamate_dehydrogenase_542967..543197_POSITIVE 227 88 43 153 108 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 224 61 26 73 38 pint:PI0730|5end_hypothetical_protein_661685..661915_POSITIVE 222 78 35 193 150 pint:PI1616|5end_hypothetical_protein_1542173..1542403_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 70 26 56 4 pint:PI0475|3end_50S_ribosomal_protein_L6_440096..440246_POSITIVE 325 54 20 71 37 pint:PI1842|3end_conserved_hypothetical_protein_1788317..1788467_POSITIVE 272 86 49 58 13 pint:PI1654|3end_hypothetical_protein_1567958..1568108_POSITIVE 242 83 41 88 45 pint:PI0262|3end_conserved_hypothetical_protein_255094..255244_POSITIVE 240 144 105 129 87 pint:PI1368|3end_enolase_(phosphopyruvate_hydratase)_1289507..1289657_POSITIVE 236 63 34 142 106 pint:PI0055|3end_hypothetical_protein_55044..55194_POSITIVE 234 87 47 118 85 pint:PI1746|3end_hypothetical_protein_1667606..1667756_POSITIVE 233 76 31 132 79 pint:PI0742|3end_hypothetical_protein_672749..672899_POSITIVE 231 99 51 125 69 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE 227 88 43 134 89 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE 224 61 26 73 38 pint:PI0729|3end_integrase_661765..661915_POSITIVE 222 59 14 65 13 pint:PI0822|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_762025..762175_POSITIVE 222 64 32 150 107 pint:PI0604|3end_O-succinylbenzoic_acid--CoA_ligase_551918..552068_POSITIVE 221 148 114 45 5 pint:PI1042|3end_hypothetical_protein_961696..961846_POSITIVE 221 148 104 81 42 pint:PI0417|3end_hypothetical_protein_386730..386880_POSITIVE 221 148 104 58 19 pint:PI0416|3end_hypothetical_protein_386707..386857_POSITIVE 219 70 37 117 83 pint:PI0378|3end_conserved_hypothetical_protein;_possible_helicase_349539..349689_POSITIVE 213 63 23 145 102 pint:PI1761|3end_hypothetical_protein_1684543..1684693_POSITIVE 212 72 32 128 85 pint:PI1513|3end_conserved_hypothetical_protein_1432502..1432652_POSITIVE 210 74 31 136 73 pint:PI1638|3end_conserved_hypothetical_protein_1556613..1556763_POSITIVE