Origin IGS: tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttgatacttttaatatggtagtattattagtctttgaaactaatctatctattttattacgtgctcttttgataaggacacttgcatacaagtacatctttaaaagacatacttgtatgtagatacgatttattaatatcgtttttcctcttcattatacatttactttcta Mask Tandem Repeat Region ================================================ tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Find is-nt database================================================ Query_seq: PI1349:PI1350|PI1349:PI1350:polysaccharide export protein:conserved hypothetical protein:->->:1265781..1265956 176 tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1349:PI1350|PI1349:PI1350:polysaccharide export protein:conserved hypothetical protein:->->:1265781..1265956 176 tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1349:PI1350|PI1349:PI1350:polysaccharide export protein:conserved hypothetical protein:->->:1265781..1265956 176 tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 15 End: 113 .............. M M K R K N D I N K S Y L H T S M S F K D V L V C K C P Y Q K S T ............................................................... Protein_Len: 47 Strand: + Start: 34 End: 174 ................................. M L I N R I Y I Q V C L L K M Y L Y A S V L I K R A R N K I D R L V S K T N N T T I L K V S N .. Protein_Len: 35 Strand: - Start: 54 End: 158 ..................................................... M C T H R K F I Y K Y A L T R I L L A R L L I S L N T E F V L L V V M .................. Protein_Len: 30 Strand: - Start: 2 End: 91 . S L L H I I F L F F S I L L D Y R C V L I D K L S T S T H M ..................................................................................... tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta 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================================================ tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -8.3 Tail_Score: -2.96274 Start: 51 End: 92 Full_Region: ATTAATAAATCGTAT CTACATACAAGTATGTCTT TTA AAGATGTACTTGTATGCAAG TGTCCTTATCAAAAG ..................................................CTACATACAAGTATGTCTTTTAAAGATGTACTTGTATGCAAG.................................................................................... Find igs database================================================ Query_seq: PI1349:PI1350|PI1349:PI1350:polysaccharide export protein:conserved hypothetical protein:->->:1265781..1265956 176 tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: pint_PI1349_PI1350|polysaccharide export protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1265781,1265956]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta tagaaagtaaatgtataatgaagaggaaaaacgatattaataaatcgtatctacatacaagtatgtcttttaaagatgtacttgtatgcaagtgtccttatcaaaagagcacgtaataaaatagatagattagtttcaaagactaataatactaccatattaaaagtatcaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAGUAAAUGUAUAAUGAAGAGGAAAAACGAUAUUAAUAAAUCGUAUCUACAUACAAGUAUGUCUUUUAAAGAUGUACUUGUAUGCAAGUGUCCUUAUCAAAAGAGCACGUAAUAAAAUAGAUAGAUUAGUUUCAAAGACUAAUAAUACUACCAUAUUAAAAGUAUCAAAUUA ..................(((.(((((...(((((........))))).....(((((((((((((((.....)))))))))))))))......))))).)))...((..((.(((((...(((....(((((((.....)))))))....)))...)))))...)).))...... (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUGAUACUUUUAAUAUGGUAGUAUUAUUAGUCUUUGAAACUAAUCUAUCUAUUUUAUUACGUGCUCUUUUGAUAAGGACACUUGCAUACAAGUACAUCUUUAAAAGACAUACUUGUAUGUAGAUACGAUUUAUUAAUAUCGUUUUUCCUCUUCAUUAUACAUUUACUUUCUA ......(((((...(((((..((((....((((((.......))))))....))))..))))).))).))...(((..((((...(((((((((((((..(((.....)))..)))))))))))))..(((((........)))))...))))..))).................. (-36.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 232 129 82 104 44 pint:PI1287|5end_ATP_synthase,_A_subunit_1201224..1201454_POSITIVE 225 116 79 188 149 pint:PI0021|5end_orotate_phosphoribosyltransferase_24939..25169_POSITIVE 218 115 71 60 10 pint:PI0009|5end_NAD-dependent_epimerase/dehydratase_family_protein_9653..9883_POSITIVE 217 88 44 132 87 pint:PI1828|5end_peptidase,_M23/M37_family,_C-terminal_1768419..1768649_POSITIVE 213 97 51 188 129 pint:PI1901|5end_hemolysin_A_1843932..1844162_POSITIVE 212 115 71 158 113 pint:PI1374|5end_tetraacyldisaccharide_4'-kinase_1294725..1294955_POSITIVE 211 33 4 132 104 pint:PI0765|5end_conserved_hypothetical_protein;_possible_surface_protein_699753..699983_POSITIVE 209 89 46 59 5 pint:PI0315|5end_conserved_hypothetical_protein_296679..296909_POSITIVE 207 110 62 180 141 pint:PI0362|5end_hypothetical_protein_333397..333627_POSITIVE 206 115 77 65 20 pint:PI1852|5end_conserved_hypothetical_protein_1797952..1798182_POSITIVE 201 118 74 49 3 pint:PI2016|5end_ribosomal_large_subunit_pseudouridine_synthase_D_1973768..1973998_POSITIVE 199 110 62 89 38 pint:PI1322|5end_nucleoside_permease_1240324..1240554_POSITIVE 199 129 81 95 56 pint:PI0850|5end_conserved_hypothetical_protein_783231..783461_POSITIVE 199 129 81 57 18 pint:PI0849|5end_hypothetical_protein_783193..783423_POSITIVE 196 150 102 100 45 pint:PI1786|5end_hypothetical_protein_1718124..1718354_POSITIVE 196 100 58 95 64 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 193 114 75 220 188 pint:PI0697|5end_5'-nucleotidase_family_protein_633560..633790_POSITIVE 193 110 64 95 56 pint:PI0095|5end_hypothetical_protein_91444..91674_POSITIVE 190 112 76 139 107 pint:PI1931|5end_alpha_glycan_phosphorylase,_maltodextrin_phosphorylase_1875456..1875686_POSITIVE 190 114 73 157 127 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 88 54 37 3 pint:PI1349|3end_polysaccharide_export_protein_1265720..1265870_POSITIVE 279 99 60 110 68 pint:PI1007|3end_conserved_hypothetical_protein_928571..928721_POSITIVE 225 116 79 124 85 pint:PI0020|3end_conserved_hypothetical_protein_24955..25105_POSITIVE 224 110 67 121 68 pint:PI0422|3end_conserved_hypothetical_protein_388025..388175_POSITIVE 217 129 84 43 1 pint:PI1286|3end_ATP_synthase,_C_subunit_1201243..1201393_POSITIVE 214 100 57 61 31 pint:PI0932|3end_conserved_hypothetical_protein;_possible_hemin_receptor_865364..865514_POSITIVE 213 97 51 125 66 pint:PI1900|3end_conserved_hypothetical_protein_1843949..1844099_POSITIVE 212 114 72 132 87 pint:PI1552|3end_transcriptional_regulator,_LuxR_family_1469404..1469554_POSITIVE 207 124 87 145 92 pint:PI1512|3end_hypothetical_protein_1429893..1430043_POSITIVE 207 110 62 129 90 pint:PI0361|3end_hypothetical_protein_333426..333576_POSITIVE 199 110 62 86 35 pint:PI1321|3end_conserved_hypothetical_protein_1240401..1240551_POSITIVE 194 115 81 122 87 pint:PI1606|3end_conserved_hypothetical_protein_1535565..1535715_POSITIVE 194 113 75 145 100 pint:PI1378|3end_GTP-binding_protein_lepA_1301651..1301801_POSITIVE 193 110 64 108 69 pint:PI0093|3end_riboflavin_biosynthesis_protein_91537..91687_POSITIVE 190 114 73 148 118 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 188 115 75 91 46 pint:PI1977|3end_hypothetical_protein_1934619..1934769_POSITIVE 188 115 75 91 46 pint:PI1975|3end_conserved_hypothetical_protein_1932933..1933083_POSITIVE 188 98 61 48 16 pint:PI1758|3end_hypothetical_protein_1684057..1684207_POSITIVE 187 118 76 136 90 pint:PI1553|3end_hypothetical_protein_1470170..1470320_POSITIVE 185 129 81 69 18 pint:PI0041|3end_hypothetical_protein_42023..42173_POSITIVE