Origin IGS: ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta .........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 taaacaatgtttttgcataatattgttgaaaacaagtaaaacgcacttactcaaaacctcaatatttaccgaatagcctctatttactttgcaagcaaatcgcaaagtgaatagaggcattttttgtatcctctcatttcaacgcaaaaccttaacaaactttaaagagcctaatttattgtaagtgggctttttttcgtatttttgcatcgaa Mask Tandem Repeat Region ================================================ ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Find is-nt database================================================ Query_seq: PI1032:PI1033|PI1032:PI1033:methylmalonyl-CoA decarboxylase, alpha subunit:ATP-dependent RNA helicase, DEAD/DEAH box family:->->:950223..950436 214 ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1032:PI1033|PI1032:PI1033:methylmalonyl-CoA decarboxylase, alpha subunit:ATP-dependent RNA helicase, DEAD/DEAH box family:->->:950223..950436 214 ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1032:PI1033|PI1032:PI1033:methylmalonyl-CoA decarboxylase, alpha subunit:ATP-dependent RNA helicase, DEAD/DEAH box family:->->:950223..950436 214 ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 86 End: 214 ..................................................................................... M Q K M P L F T L R F A C K V N R G Y S V N I E V L S K C V L L V F N N I M Q K H C L Protein_Len: 31 Strand: - Start: 34 End: 126 ................................. L L N P E K F N T L T K R Q F S L I C F I G R N V K R N A Q M ........................................................................................ ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta 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================================================ ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.8 Tail_Score: -5.40625 Start: 96 End: 140 Full_Region: caatatttaccgaat agcctctatttactttgcaa gcaaa tcgcaaagtgaatagaggca ttttttgtatcctct ...............................................................................................agcctctatttactttgcaagcaaatcgcaaagtgaatagaggca.......................................................................... TransTerm Strand: + Conf: 100 HP_score: -17.3 Tail_Score: -3.10622 Start: 97 End: 139 Full_Region: GAGGATACAAAAAAT GCCTCTATTCACTTTGCGA TTTGC TTGCAAAGTAAATAGAGGC TATTCGGTAAATATT ................................................................................................GCCTCTATTCACTTTGCGATTTGCTTGCAAAGTAAATAGAGGC........................................................................... TransTerm Strand: - Conf: 100 HP_score: -17.3 Tail_Score: -3.82748 Start: 97 End: 139 Full_Region: aatatttaccgaata gcctctatttactttgcaa gcaaa tcgcaaagtgaatagaggc attttttgtatcctc ................................................................................................gcctctatttactttgcaagcaaatcgcaaagtgaatagaggc........................................................................... Find igs database================================================ Query_seq: PI1032:PI1033|PI1032:PI1033:methylmalonyl-CoA decarboxylase, alpha subunit:ATP-dependent RNA helicase, DEAD/DEAH box family:->->:950223..950436 214 ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Intra-Species Hit: Count: 1 Min: 1 Max: 214 Len: 214 Subject: pint_PI1032_PI1033|methylmalonyl-CoA decarboxylase, alpha subunit:ATP-dependent RNA helicase, DEAD/DEAH box family|POSITIVE:POSITIVE|[950223,950436]|214 HSP 1 e-value: 1.0E-105 bit: 383.0 Len: 214 Query Start:1 Query End:214 Subject Strand: POSITIVE Subject Start: 1 Subject End: 214 ttcgatgcaaaaatacgnnnnnnngcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta ttcgatgcaaaaatacgaaaaaaagcccacttacaataaattaggctctttaaagtttgttaaggttttgcgttgaaatgagaggatacaaaaaatgcctctattcactttgcgatttgcttgcaaagtaaatagaggctattcggtaaatattgaggttttgagtaagtgcgttttacttgttttcaacaatattatgcaaaaacattgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGAUGCAAAAAUACGAAAAAAAGCCCACUUACAAUAAAUUAGGCUCUUUAAAGUUUGUUAAGGUUUUGCGUUGAAAUGAGAGGAUACAAAAAAUGCCUCUAUUCACUUUGCGAUUUGCUUGCAAAGUAAAUAGAGGCUAUUCGGUAAAUAUUGAGGUUUUGAGUAAGUGCGUUUUACUUGUUUUCAACAAUAUUAUGCAAAAACAUUGUUUA ((((((((((((..((((((((.((((................)))).)))....))))).....))))))))))))...(((.(((.........(((((((((.(((((((((.....))))))))).)))))))))......((((((((((..(...((((((((.....))))))))....)..))))))).)))......))).))). (-55.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAUGUUUUUGCAUAAUAUUGUUGAAAACAAGUAAAACGCACUUACUCAAAACCUCAAUAUUUACCGAAUAGCCUCUAUUUACUUUGCAAGCAAAUCGCAAAGUGAAUAGAGGCAUUUUUUGUAUCCUCUCAUUUCAACGCAAAACCUUAACAAACUUUAAAGAGCCUAAUUUAUUGUAAGUGGGCUUUUUUUCGUAUUUUUGCAUCGAA .............((((.(((((.(((((((...(((((.......)))))...............(((.(((..(((((((((((((((((.........)))))))))))))))))...))).)))........)))))))....................((((((((((.((......)).))))))))))...)))))..))))..... (-51.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 130 89 52 8 pint:PI0308|5end_conserved_hypothetical_protein_290587..290817_POSITIVE 287 138 95 173 129 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 284 88 42 140 92 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 283 128 81 132 94 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 270 140 107 207 169 pint:PI0610|5end_conserved_hypothetical_protein_557403..557633_POSITIVE 263 159 111 86 28 pint:PI2142|5end_conserved_hypothetical_protein_2087606..2087836_POSITIVE 255 150 106 87 33 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 253 148 101 65 30 pint:PI1790|5end_hypothetical_protein_1722179..1722409_POSITIVE 253 158 111 199 163 pint:PI1303|5end_ISPg3-related_transposase_1215135..1215365_POSITIVE 250 125 94 75 41 pint:PI0368|5end_hypothetical_protein_339582..339812_POSITIVE 249 159 111 97 52 pint:PI0694|5end_Na+/dicarboxylate_or_sulfate_symporter_629745..629975_POSITIVE 247 147 102 190 138 pint:PI1698|5end_subtilisin-like_serine_protease_1613830..1614060_POSITIVE 245 138 96 43 2 pint:PI1616|5end_hypothetical_protein_1542173..1542403_POSITIVE 245 84 44 220 176 pint:PI0827|5end_hypothetical_protein_763991..764221_POSITIVE 245 174 135 193 145 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 243 200 155 89 50 pint:PI1738|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_1659343..1659573_POSITIVE 243 115 71 118 76 pint:PI0410|5end_glutamyl-tRNA_synthetase_(glutamate--tRNA_ligase)_375947..376177_POSITIVE 242 159 112 72 24 pint:PI1011|5end_cytochrome_c_biogenesis_protein_CycY_932115..932345_POSITIVE 242 146 105 210 165 pint:PI0907|5end_NAD-dependent_DNA_ligase_834887..835117_POSITIVE 242 139 97 54 18 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 130 89 52 8 pint:PI0307|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290667..290817_POSITIVE 275 183 145 145 109 pint:PI1654|3end_hypothetical_protein_1567958..1568108_POSITIVE 255 150 106 141 87 pint:PI0118|3end_hypothetical_protein_111640..111790_POSITIVE 253 158 111 151 115 pint:PI1302|3end_hypothetical_protein_1215167..1215317_POSITIVE 250 125 94 53 19 pint:PI0367|3end_hypothetical_protein_339640..339790_POSITIVE 246 155 111 77 34 pint:PI0764|3end_permease_699145..699295_POSITIVE 243 200 155 59 20 pint:PI1737|3end_glycyl-tRNA_synthetase_1659393..1659543_POSITIVE 243 115 71 60 18 pint:PI0409|3end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_375969..376119_POSITIVE 242 159 112 72 24 pint:PI1010|3end_conserved_hypothetical_protein_932195..932345_POSITIVE 242 139 97 51 15 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 241 87 42 101 53 pint:PI1296|3end_glycosyltransferase_1209889..1210039_POSITIVE 239 168 121 73 36 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE 238 140 96 109 62 pint:PI2088|3end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_2045815..2045965_POSITIVE 238 179 132 140 74 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 237 87 44 89 50 pint:PI1858|3end_conserved_hypothetical_protein_1805355..1805505_POSITIVE 235 147 112 79 41 pint:PI1990|3end_hypothetical_protein_1944766..1944916_POSITIVE 233 139 96 81 32 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 233 158 111 46 3 pint:PI0408|3end_hypothetical_protein_374728..374878_POSITIVE 231 128 94 127 90 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 231 124 81 131 86 pint:PI0413|3end_outer_membrane_protein_384019..384169_POSITIVE