Origin IGS: accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttagtttaatttctattgctacaaaagtacattttttttcttagaaatcggcatattttaggtattgacatactttttttgttgcatttttatattgcatagccctttcagtaagcttaaaaagtgttgcaataatcttataatcagacgttttgtgcttgtcttatgtcgcaacagagtattttaataaaatgatagaaaacttgtatttttaaataattaattctatttttgtcttagaaacacaaattaagtacactgaaatagataacgacttaaacaactatcggt Mask Tandem Repeat Region ================================================ accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Find is-nt database================================================ Query_seq: PI1565:PI1566|PI1565:PI1566:conserved hypothetical protein; possible surface antigen:predicted TPR-repeat-containing protein:->->:1487418..1487709 292 accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1565:PI1566|PI1565:PI1566:conserved hypothetical protein; possible surface antigen:predicted TPR-repeat-containing protein:->->:1487418..1487709 292 accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1565:PI1566|PI1565:PI1566:conserved hypothetical protein; possible surface antigen:predicted TPR-repeat-containing protein:->->:1487418..1487709 292 accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 115 End: 231 .................................................................................................................. M L R H K T S T K R L I I R L L Q H F L S L L K G L C N I K M Q Q K K Y V N T ............................................................. Protein_Len: 31 Strand: + Start: 156 End: 248 ........................................................................................................................................................... M I A T L F K L T E R A M Q Y K N A T K K V C Q Y L K Y A D F ............................................ Protein_Len: 40 Strand: - Start: 108 End: 227 ........................................................................................................... F V R N R C L V L V F R R I I L N N C C K K L K S F P S H L I F I C C F F Y T M ................................................................. accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag 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: 83 Start: 199 End: 228 ......................................................................................................................................................................................................ATTGACATACTTTTTTTGTTGCATTTTTAT................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -3.0 Tail_Score: -5.83226 Start: 219 End: 230 Full_Region: atcggcatattttag gtat tgac atac tttttttgttgcatt ..........................................................................................................................................................................................................................gtattgacatac.............................................................. Find igs database================================================ Query_seq: PI1565:PI1566|PI1565:PI1566:conserved hypothetical protein; possible surface antigen:predicted TPR-repeat-containing protein:->->:1487418..1487709 292 accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: pint_PI1565_PI1566|conserved hypothetical protein; possible surface antigen:predicted TPR-repeat-containing protein|POSITIVE:POSITIVE|[1487418,1487709]|292 HSP 1 e-value: 1.0E-137 bit: 490.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacnnnnnnngtatgtcaatacctaaaatatgccgatttctaagnnnnnnnntgtacttttgtagcaatagaaattaaactaag accgatagttgtttaagtcgttatctatttcagtgtacttaatttgtgtttctaagacaaaaatagaattaattatttaaaaatacaagttttctatcattttattaaaatactctgttgcgacataagacaagcacaaaacgtctgattataagattattgcaacactttttaagcttactgaaagggctatgcaatataaaaatgcaacaaaaaaagtatgtcaatacctaaaatatgccgatttctaagaaaaaaaatgtacttttgtagcaatagaaattaaactaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGAUAGUUGUUUAAGUCGUUAUCUAUUUCAGUGUACUUAAUUUGUGUUUCUAAGACAAAAAUAGAAUUAAUUAUUUAAAAAUACAAGUUUUCUAUCAUUUUAUUAAAAUACUCUGUUGCGACAUAAGACAAGCACAAAACGUCUGAUUAUAAGAUUAUUGCAACACUUUUUAAGCUUACUGAAAGGGCUAUGCAAUAUAAAAAUGCAACAAAAAAAGUAUGUCAAUACCUAAAAUAUGCCGAUUUCUAAGAAAAAAAAUGUACUUUUGUAGCAAUAGAAAUUAAACUAAG ...(((((((((((((((.(((((((((((...(((.((((...........))))))).)))))))..)))).))))))....)))).....)))))...............((((((((.(((.(((....(((......((((.......))))...))).(((.(((((...((((..((((.(((..((((.........)))).........((((....)))).........)))..))))))))..))))).))).))).))).))))))))............ (-48.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAGUUUAAUUUCUAUUGCUACAAAAGUACAUUUUUUUUCUUAGAAAUCGGCAUAUUUUAGGUAUUGACAUACUUUUUUUGUUGCAUUUUUAUAUUGCAUAGCCCUUUCAGUAAGCUUAAAAAGUGUUGCAAUAAUCUUAUAAUCAGACGUUUUGUGCUUGUCUUAUGUCGCAACAGAGUAUUUUAAUAAAAUGAUAGAAAACUUGUAUUUUUAAAUAAUUAAUUCUAUUUUUGUCUUAGAAACACAAAUUAAGUACACUGAAAUAGAUAACGACUUAAACAACUAUCGGU ....((((((..((.........(((((((((..(((((((((((((.........)))))))((((((.((((((....((((((.......(((((((..((..(((.((....)).)))..))..)))))))...........(((((.........)))))......)))))))))))).)))))).......))))))..)))))))))...........((((((((((((((((.........))))).)))..))))))))....)).)))))).......... (-48.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 190 141 142 92 pint:PI1643|5end_conserved_hypothetical_protein_1560936..1561166_POSITIVE 284 196 155 181 139 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 269 190 142 125 80 pint:PI1415|5end_cation_transporting_ATPase/E1-E2_ATPase_1333939..1334169_POSITIVE 269 190 142 99 54 pint:PI1414|5end_conserved_hypothetical_protein_1333913..1334143_POSITIVE 255 200 151 208 154 pint:PI1001|5end_hypothetical_protein_923510..923740_POSITIVE 252 210 161 192 128 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 249 50 1 130 87 pint:PI0599|5end_hypothetical_protein_547376..547606_POSITIVE 241 42 1 99 63 pint:PI0110|5end_ABC_transport_system,_ATP-binding_protein_107136..107366_POSITIVE 238 146 110 197 147 pint:PI0984|5end_hypothetical_protein_909936..910166_POSITIVE 238 46 1 228 193 pint:PI0600|5end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_547482..547712_POSITIVE 237 230 186 132 68 pint:PI0106|5end_ABC_transport_system,_ATP-binding/permease_101381..101611_POSITIVE 235 189 145 133 86 pint:PI1676|5end_phosphatidate_cytidylyltransferase_1590896..1591126_POSITIVE 234 147 111 73 44 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 229 146 109 230 191 pint:PI0148|5end_mannose-1-phosphate_guanylyltransferase_141423..141653_POSITIVE 228 208 161 223 175 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 223 190 142 195 161 pint:PI0393|5end_conserved_hypothetical_protein_358696..358926_POSITIVE 223 165 121 196 147 pint:PI0269|5end_conserved_hypothetical_protein_259835..260065_POSITIVE 222 190 142 165 123 pint:PI1806|5end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1740777..1741007_POSITIVE 222 50 8 173 129 pint:PI1333|5end_conserved_hypothetical_protein_1250777..1251007_POSITIVE 222 197 160 39 1 pint:PI0855|5end_hypothetical_protein_789094..789324_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 190 142 65 20 pint:PI1413|3end_hypothetical_protein_1333959..1334109_POSITIVE 241 42 1 66 30 pint:PI0109|3end_hypothetical_protein_107183..107333_POSITIVE 237 230 186 124 60 pint:PI0105|3end_possible_sulfatase_101453..101603_POSITIVE 231 180 131 102 52 pint:PI0118|3end_hypothetical_protein_111640..111790_POSITIVE 224 197 151 107 59 pint:PI1012|3end_DNA-binding_protein,_histone-like_family_933544..933694_POSITIVE 224 190 142 148 84 pint:PI0646|3end_hypothetical_protein_587205..587355_POSITIVE 223 165 121 71 22 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 221 210 161 70 26 pint:PI0345|3end_conserved_hypothetical_protein_320809..320959_POSITIVE 219 149 111 147 109 pint:PI2080|3end_hypothetical_protein_2038298..2038448_POSITIVE 218 168 124 146 94 pint:PI0919|3end_conserved_hypothetical_protein_849719..849869_POSITIVE 216 35 3 46 22 pint:PI1126|3end_methionyl-tRNA_formyltransferase_1052652..1052802_POSITIVE 215 186 141 150 106 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE 215 46 4 83 50 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 213 154 116 134 91 pint:PI1225|3end_hypothetical_protein_1147933..1148083_POSITIVE 213 38 11 76 45 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 212 167 134 59 21 pint:PI0240|3end_conserved_hypothetical_protein_239342..239492_POSITIVE 211 214 178 45 16 pint:PI1687|3end_ribosome_recycling_factor_1602902..1603052_POSITIVE 211 88 43 75 35 pint:PI0500|3end_mobilizable_transposon,_tnpC_protein_461407..461557_POSITIVE 210 49 3 75 18 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE 206 280 237 49 9 pint:PI2033|3end_hypothetical_protein_1987666..1987816_POSITIVE