Origin IGS: tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taattatcgtatccaaccaaacaaaaacttattatcataactggtaataagttttttgtgtttatagcttggaggttaagaagaattttactaaatttgcagaca Mask Tandem Repeat Region ================================================ tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Find is-nt database================================================ Query_seq: PI1059:PI1060|PI1059:PI1060:conserved hypothetical protein:conserved hypothetical protein:->->:979235..979339 105 tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1059:PI1060|PI1059:PI1060:conserved hypothetical protein:conserved hypothetical protein:->->:979235..979339 105 tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1059:PI1060|PI1059:PI1060:conserved hypothetical protein:conserved hypothetical protein:->->:979235..979339 105 tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Predict ORF larger than 30AA ================================================ tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta 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================================================ tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -6.7 Tail_Score: -3.97368 Start: 46 End: 88 Full_Region: attatcgtatccaac caaacaaaaacttattatca taac tggtaataagttttttgtg tttatagcttggagg .............................................caaacaaaaacttattatcataactggtaataagttttttgtg................. TransTerm Strand: + Conf: 85 HP_score: -5.4 Tail_Score: -5.38326 Start: 55 End: 78 Full_Region: TATAAACACAAAAAA CTTATTACCA GTTA TGATAATAAG TTTTTGTTTGGTTGG ......................................................CTTATTACCAGTTATGATAATAAG........................... Find igs database================================================ Query_seq: PI1059:PI1060|PI1059:PI1060:conserved hypothetical protein:conserved hypothetical protein:->->:979235..979339 105 tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: pint_PI1059_PI1060|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[979235,979339]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta tgtctgcaaatttagtaaaattcttcttaacctccaagctataaacacaaaaaacttattaccagttatgataataagtttttgtttggttggatacgataatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUGCAAAUUUAGUAAAAUUCUUCUUAACCUCCAAGCUAUAAACACAAAAAACUUAUUACCAGUUAUGAUAAUAAGUUUUUGUUUGGUUGGAUACGAUAAUUA ((((....(((((....)))))........((.((((((..........((((((((((((.((....)).))))))))))))))))))..))....)))).... (-18.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAUCGUAUCCAACCAAACAAAAACUUAUUAUCAUAACUGGUAAUAAGUUUUUUGUGUUUAUAGCUUGGAGGUUAAGAAGAAUUUUACUAAAUUUGCAGACA ...........(((((.((((((((((((((((((((....))))))))))))))...)))))...).))))).(((.....((((((....))))))...))). (-20.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 40 1 85 41 pint:PI0593|5end_NAD-specific_glutamate_dehydrogenase_542967..543197_POSITIVE 219 35 5 189 163 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 200 50 1 178 129 pint:PI0218|5end_conserved_hypothetical_protein_210770..211000_POSITIVE 195 96 54 206 159 pint:PI1267|5end_probable_integrase_1186105..1186335_POSITIVE 189 93 60 112 77 pint:PI0571|5end_conserved_hypothetical_protein;_possible_permease_515161..515391_POSITIVE 186 67 21 139 82 pint:PI0475|5end_50S_ribosomal_protein_L6_439453..439683_POSITIVE 179 93 59 177 151 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 178 40 5 169 131 pint:PI1504|5end_non-specific_DNA-binding_protein_1424318..1424548_POSITIVE 178 64 30 57 24 pint:PI0788|5end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726152..726382_POSITIVE 178 99 78 119 96 pint:PI0052|5end_hypothetical_protein_52312..52542_POSITIVE 177 60 14 198 150 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 176 100 64 143 112 pint:PI0033|5end_peptidylprolyl_isomerase_36215..36445_POSITIVE 174 45 9 186 138 pint:PI1842|5end_conserved_hypothetical_protein_1787935..1788165_POSITIVE 174 98 54 167 118 pint:PI0713|5end_hypothetical_protein_650294..650524_POSITIVE 174 99 71 124 99 pint:PI0574|5end_hypothetical_protein_519260..519490_POSITIVE 173 49 30 24 3 pint:PI0653|5end_hypothetical_protein_596046..596276_POSITIVE 171 48 3 229 191 pint:PI0855|5end_hypothetical_protein_789094..789324_POSITIVE 170 99 63 79 44 pint:PI0007|5end_hypothetical_protein_6417..6647_POSITIVE 169 94 55 139 100 pint:PI2067|5end_hypothetical_protein_2027760..2027990_POSITIVE 168 42 6 125 79 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 95 53 98 61 pint:PI1102|3end_conserved_hypothetical_protein_1026247..1026397_POSITIVE 233 67 32 79 45 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 219 35 5 118 92 pint:PI1467|3end_conserved_hypothetical_protein_1393909..1394059_POSITIVE 219 49 5 134 92 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 200 50 1 122 73 pint:PI0217|3end_conserved_hypothetical_protein;_possible_lipoprotein_210794..210944_POSITIVE 195 94 51 58 9 pint:PI1059|3end_conserved_hypothetical_protein_979174..979324_POSITIVE 193 80 34 104 50 pint:PI0429|3end_hypothetical_protein_399602..399752_POSITIVE 187 92 69 59 37 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 186 67 21 121 64 pint:PI0474|3end_30S_ribosomal_protein_S8_439515..439665_POSITIVE 177 98 62 111 77 pint:PI0246|3end_conserved_hypothetical_protein_244599..244749_POSITIVE 176 100 64 102 71 pint:PI0032|3end_hypothetical_protein_36254..36404_POSITIVE 174 45 9 140 92 pint:PI1841|3end_conserved_hypothetical_protein_1787969..1788119_POSITIVE 174 98 54 150 101 pint:PI0712|3end_conserved_hypothetical_protein;_possible_xylanase_650357..650507_POSITIVE 166 93 56 124 81 pint:PI1420|3end_probable_membrane_protein_1340652..1340802_POSITIVE 163 93 53 115 77 pint:PI2072|3end_possible_ISmav2-related_transposase_2031470..2031620_POSITIVE 162 93 53 129 87 pint:PI1559|3end_hypothetical_protein_1476972..1477122_POSITIVE 159 98 64 136 96 pint:PI0148|3end_mannose-1-phosphate_guanylyltransferase_142594..142744_POSITIVE 158 42 6 75 33 pint:PI2177|3end_phosphoribosylaminoimidazole_carboxylase_2117710..2117860_POSITIVE 157 39 9 41 9 pint:PI1093|3end_conserved_hypothetical_protein_1019196..1019346_POSITIVE 157 40 3 91 56 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE