Origin IGS: tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatggacgataagctaacagaaaacgaagaagtacaggaagtggtggcaaagcccattttcactgtaagagaacgaaaaaaagaggagactgcagaggcaacaacattgtctgagcagtctgctgattctgtggctatggacggaactgaggttgagttagaggtagaaaagcctca Mask Tandem Repeat Region ================================================ tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Find is-nt database================================================ Query_seq: PI1896:PI1898|PI1896:PI1898:hypothetical protein:S-adenosyl-methyltransferase:->->:1841249..1841427 179 tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1896:PI1898|PI1896:PI1898:hypothetical protein:S-adenosyl-methyltransferase:->->:1841249..1841427 179 tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1896:PI1898|PI1896:PI1898:hypothetical protein:S-adenosyl-methyltransferase:->->:1841249..1841427 179 tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 51 End: 161 .................................................. M S R L L R Q C C C L C S L L F F S F S Y S E N G L C H H F L Y F F V F C .................. Protein_Len: 46 Strand: + Start: 40 End: 177 ....................................... M A T E S A D C S D N V V A S A V S S F F R S L T V K M G F A T T S C T S S F S V S L S S I .. Protein_Len: 58 Strand: - Start: 3 End: 176 .. P K E V E L E V E T G D M A V S D A S Q E S L T T A E A T E E K K R E R V T F I P K A V V E Q V E E N E T L K D D M ... tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta 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================================================ tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -2.6 Tail_Score: -5.69379 Start: 53 End: 95 Full_Region: CCATAGCCACAGAAT CAGCAGACTGCTCAGACAAT GTT GTTGCCTCTGCAGTCTCCTC TTTTTTTCGTTCTCT ....................................................CAGCAGACTGCTCAGACAATGTTGTTGCCTCTGCAGTCTCCTC.................................................................................... TransTerm Strand: + Conf: 70 HP_score: -5.2 Tail_Score: -4.46828 Start: 55 End: 93 Full_Region: ATAGCCACAGAATCA GCAGACTGCTCAGACAAT GTT GTTGCCTCTGCAGTCTCC TCTTTTTTTCGTTCT ......................................................GCAGACTGCTCAGACAATGTTGTTGCCTCTGCAGTCTCC...................................................................................... TransTerm Strand: - Conf: 54 HP_score: -6.7 Tail_Score: -2.90061 Start: 55 End: 93 Full_Region: agaacgaaaaaaaga ggagactgcagaggcaa caaca ttgtctgagcagtctgc tgattctgtggctat ......................................................ggagactgcagaggcaacaacattgtctgagcagtctgc...................................................................................... Find igs database================================================ Query_seq: PI1896:PI1898|PI1896:PI1898:hypothetical protein:S-adenosyl-methyltransferase:->->:1841249..1841427 179 tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: pint_PI1896_PI1898|hypothetical protein:S-adenosyl- methyltransferase|POSITIVE:POSITIVE|[1841249, 1841427]|179 HSP 1 e-value: 1.0E-84 bit: 313.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctcnnnnnnncgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta tgaggcttttctacctctaactcaacctcagttccgtccatagccacagaatcagcagactgctcagacaatgttgttgcctctgcagtctcctctttttttcgttctcttacagtgaaaatgggctttgccaccacttcctgtacttcttcgttttctgttagcttatcgtccattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGCUUUUCUACCUCUAACUCAACCUCAGUUCCGUCCAUAGCCACAGAAUCAGCAGACUGCUCAGACAAUGUUGUUGCCUCUGCAGUCUCCUCUUUUUUUCGUUCUCUUACAGUGAAAAUGGGCUUUGCCACCACUUCCUGUACUUCUUCGUUUUCUGUUAGCUUAUCGUCCAUUUA .((((........)))).................((.....(((.((((((..((.(((((((..((.((((...)))).))..))))))).))........((......(((((.(((....(((...))).....))))))))......))..))))))..)))...))........ (-36.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGGACGAUAAGCUAACAGAAAACGAAGAAGUACAGGAAGUGGUGGCAAAGCCCAUUUUCACUGUAAGAGAACGAAAAAAAGAGGAGACUGCAGAGGCAACAACAUUGUCUGAGCAGUCUGCUGAUUCUGUGGCUAUGGACGGAACUGAGGUUGAGUUAGAGGUAGAAAAGCCUCA .............(((((.(((((..((......(((((((((..(.(((...))))..)))).)))))......))........((.(((((((..((((((.....))))))..))))))).))..))))))))))...(((..(((....)))..))).(((((......))))). (-52.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 94 51 59 11 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 337 90 43 131 72 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 332 165 121 190 136 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 332 165 121 190 136 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 325 147 101 182 126 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 324 90 43 204 157 pint:PI0993|5end_probable_TPR-repeat-containing_protein_917175..917405_POSITIVE 318 87 41 226 184 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 316 167 122 144 79 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 312 64 21 73 25 pint:PI1586|5end_possible_HesA/MoeB/ThiF_family_protein_1514372..1514602_POSITIVE 312 98 54 147 94 pint:PI0064|5end_hypothetical_protein_63622..63852_POSITIVE 310 141 103 113 71 pint:PI0224|5end_conserved_hypothetical_protein_220541..220771_POSITIVE 306 116 72 203 138 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 305 167 122 81 41 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 304 70 25 60 8 pint:PI1592|5end_conserved_hypothetical_protein;_possible_permease_1519897..1520127_POSITIVE 299 79 39 181 139 pint:PI1806|5end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1740777..1741007_POSITIVE 294 75 42 225 192 pint:PI0086|5end_possible_uroporphyrinogen-III_synthase_84944..85174_POSITIVE 293 70 22 59 9 pint:PI2008|5end__ABC_transporter,_ATP-binding_protein_1967123..1967353_POSITIVE 293 86 41 179 135 pint:PI0960|5end_hypothetical_protein_891137..891367_POSITIVE 292 83 51 197 159 pint:PI2168|5end_hypothetical_protein_2111286..2111516_POSITIVE 292 100 52 56 6 pint:PI0358|5end_hypothetical_protein_327561..327791_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 167 123 138 83 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 332 165 121 55 1 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 332 165 121 85 31 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 332 165 121 55 1 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 320 81 45 151 107 pint:PI0088|3end_S-adenosylmethionine_synthetase_88032..88182_POSITIVE 315 148 101 146 103 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 312 98 54 65 12 pint:PI0063|3end_transcriptional_regulator,_GntR_family_63620..63770_POSITIVE 310 141 103 75 33 pint:PI0223|3end_topoisomerase_IA_220583..220733_POSITIVE 297 90 43 134 65 pint:PI0779|3end_predicted_TPR-repeat-containing_protein_715800..715950_POSITIVE 294 49 3 146 109 pint:PI0713|3end_hypothetical_protein_650529..650679_POSITIVE 292 69 29 72 22 pint:PI0156|3end_conserved_hypothetical_protein_150913..151063_POSITIVE 291 163 124 73 19 pint:PI0237|3end_predicted_two-component_system_sensor_histidine_kinase_237081..237231_POSITIVE 289 88 43 58 10 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 287 155 112 64 12 pint:PI0847|3end_thiamine_biosynthesis_lipoprotein,_ApbE_782232..782382_POSITIVE 285 96 53 140 82 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 283 158 112 148 91 pint:PI2091|3end_DNA_processing_protein_2049226..2049376_POSITIVE 281 115 77 76 43 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 279 85 42 134 85 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 279 117 75 150 91 pint:PI1229|3end_conserved_hypothetical_protein_1151669..1151819_POSITIVE 278 108 61 70 18 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE