Origin IGS: tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt .........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 acatactaatgcgatgaaacccctaaagtttccgttggtaaatagtttttgtttcataacacaatgatattagtgaataaatgatttaagcgtcttagtgtgtcgcaaaaataacgtttatttcgttaatttgcaaactttcttacatatttcttttacattttagcttacttattgcgcatttcggcaacaaaagaatacaagataaaggtttttca Mask Tandem Repeat Region ================================================ tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Find is-nt database================================================ Query_seq: PI0211:PI0212|PI0211:PI0212:hypothetical protein:surface protein/internalin-related protein:->->:204339..204556 218 tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0211:PI0212|PI0211:PI0212:hypothetical protein:surface protein/internalin-related protein:->->:204339..204556 218 tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0211:PI0212|PI0211:PI0212:hypothetical protein:surface protein/internalin-related protein:->->:204339..204556 218 tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 S F G K D Q I R K N G F H A I L L S F H L L F I Y S L K C I L S I F T M .............................................................................................................. tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt 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: 84 Start: 82 End: 111 .................................................................................TTTGCAAATTAACGAAATAAACGTTATTTT........................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -2.3 Tail_Score: -4.56775 Start: 91 End: 107 Full_Region: AGAAAGTTTGCAAAT TAACG AAATAAA CGTTA TTTTTGCGACACACT ..........................................................................................TAACGAAATAAACGTTA............................................................................................................... TransTerm Strand: - Conf: 39 HP_score: -2.3 Tail_Score: -2.75562 Start: 91 End: 107 Full_Region: agtgtgtcgcaaaaa taacg tttattt cgtta atttgcaaactttct ..........................................................................................taacgtttatttcgtta............................................................................................................... Find igs database================================================ Query_seq: PI0211:PI0212|PI0211:PI0212:hypothetical protein:surface protein/internalin-related protein:->->:204339..204556 218 tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: pint_PI0211_PI0212|hypothetical protein:surface protein/internalin-related protein|POSITIVE:POSITIVE|[204339,204556]|218 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt tgaaaaacctttatcttgtattcttttgttgccgaaatgcgcaataagtaagctaaaatgtaaaagaaatatgtaagaaagtttgcaaattaacgaaataaacgttatttttgcgacacactaagacgcttaaatcatttattcactaatatcattgtgttatgaaacaaaaactatttaccaacggaaactttaggggtttcatcgcattagtatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAACCUUUAUCUUGUAUUCUUUUGUUGCCGAAAUGCGCAAUAAGUAAGCUAAAAUGUAAAAGAAAUAUGUAAGAAAGUUUGCAAAUUAACGAAAUAAACGUUAUUUUUGCGACACACUAAGACGCUUAAAUCAUUUAUUCACUAAUAUCAUUGUGUUAUGAAACAAAAACUAUUUACCAACGGAAACUUUAGGGGUUUCAUCGCAUUAGUAUGU (((((..(((.....((((......(((((((........))))))).(((((....(((((.......)))))......(((((((((.(((((.......)))))..))))))).))........)))))..((((.....(((..........)))..)))).))))...............(....)...)))..)))))..((((....)))) (-33.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUACUAAUGCGAUGAAACCCCUAAAGUUUCCGUUGGUAAAUAGUUUUUGUUUCAUAACACAAUGAUAUUAGUGAAUAAAUGAUUUAAGCGUCUUAGUGUGUCGCAAAAAUAACGUUUAUUUCGUUAAUUUGCAAACUUUCUUACAUAUUUCUUUUACAUUUUAGCUUACUUAUUGCGCAUUUCGGCAACAAAAGAAUACAAGAUAAAGGUUUUUCA ...((((((((....(((((.......)))))))))))))....(((.((((........)))).)))....(..(((.(((((..(((((((.....((.....))......)))))))..))))).)))..).((((((..(......((((((.........((.........)).......(....).))))))......)..))))))..... (-34.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 73 34 143 108 pint:PI0408|5end_hypothetical_protein_374154..374384_POSITIVE 265 70 28 72 26 pint:PI1156|5end_possible_glycerate_kinase_family_protein_1080583..1080813_POSITIVE 262 159 113 123 76 pint:PI0906|5end_hypothetical_protein_835653..835883_POSITIVE 261 68 23 117 67 pint:PI1034|5end_conserved_hypothetical_protein;_possible_membrane_protein_952093..952323_POSITIVE 257 120 72 159 110 pint:PI1753|5end_conserved_hypothetical_protein_1680291..1680521_POSITIVE 254 129 82 148 102 pint:PI0022|5end_hypothetical_protein_25641..25871_POSITIVE 253 117 73 136 91 pint:PI1246|5end_conserved_hypothetical_protein;_possible_lipoprotein_1169392..1169622_POSITIVE 239 55 11 97 38 pint:PI1439|5end_hypothetical_protein_1360009..1360239_POSITIVE 236 114 80 131 97 pint:PI1088|5end_conserved_hypothetical_protein_1011606..1011836_POSITIVE 234 56 15 86 50 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 232 50 14 78 30 pint:PI1836|5end_conserved_hypothetical_protein_1777308..1777538_POSITIVE 230 59 11 137 88 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 230 69 21 83 22 pint:PI0227|5end_ABC_transporter,_ATP-binding/permease_protein_223810..224040_POSITIVE 228 118 71 148 99 pint:PI1192|5end_carboxynorspermidine_decarboxylase_1111113..1111343_POSITIVE 228 160 111 200 144 pint:PI0453|5end_conserved_hypothetical_protein_426797..427027_POSITIVE 226 44 8 176 130 pint:PI0833|5end_conserved_hypothetical_protein_770059..770289_POSITIVE 226 130 83 159 116 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 222 53 11 209 169 pint:PI1832|5end_conserved_hypothetical_protein_1773161..1773391_POSITIVE 222 128 82 135 97 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 221 55 12 66 20 pint:PI0706|5end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_642226..642456_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 73 34 56 21 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 261 68 23 57 7 pint:PI1033|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_952113..952263_POSITIVE 259 118 78 126 87 pint:PI0181|3end_conserved_hypothetical_protein_173940..174090_POSITIVE 257 120 72 68 19 pint:PI1751|3end_desulfoferrodoxin_1680280..1680430_POSITIVE 254 129 82 75 29 pint:PI0021|3end_orotate_phosphoribosyltransferase_25648..25798_POSITIVE 244 58 11 151 106 pint:PI1190|3end_conserved_hypothetical_protein_1109319..1109469_POSITIVE 235 53 16 34 1 pint:PI0324|3end_conserved_hypothetical_protein_305680..305830_POSITIVE 234 56 15 77 41 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 230 59 11 147 98 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 230 69 21 77 16 pint:PI0226|3end_ABC_transporter,_ATP-binding_/_permease_protein_223884..224034_POSITIVE 229 203 161 125 83 pint:PI0963|3end_hypothetical_protein_893637..893787_POSITIVE 228 160 111 114 58 pint:PI0452|3end_conserved_hypothetical_protein;_possible_surface_antigen_426791..426941_POSITIVE 224 43 9 143 114 pint:PI0745|3end_conserved_hypothetical_protein_675670..675820_POSITIVE 222 53 11 135 95 pint:PI1831|3end_conserved_hypothetical_protein_1773167..1773317_POSITIVE 213 168 127 87 53 pint:PI0568|3end_hypothetical_protein_513131..513281_POSITIVE 210 209 162 59 4 pint:PI0646|3end_hypothetical_protein_587205..587355_POSITIVE 210 207 185 120 95 pint:PI0047|3end_phosphomethylpyrimidine_kinase_46781..46931_POSITIVE 210 47 10 140 98 pint:PI0035|3end_NAD-dependent_protein_deacetylase,_SIR2_family_38642..38792_POSITIVE 209 55 23 57 23 pint:PI0206|3end_TPR-repeat-containing_protein_199856..200006_POSITIVE 208 44 9 120 82 pint:PI0136|3end_surface_antigen_BspA_128084..128234_POSITIVE