Origin IGS: tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa .........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 tttcttcatatctttttattatttaatggtttgcaaactaccccctatttaaatggggtatttgagtgattggaatgcaaaaataaataaatgtattgataaaaccactattgtttaagatttttttgtacctttgccgcactttttacaaataggggtacttgctaaaccccctttaacaaaacaagaca Mask Tandem Repeat Region ================================================ tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Find is-nt database================================================ Query_seq: PI0641:PI0642|PI0641:PI0642:conserved hypothetical protein:thioredoxin family protein:->->:584621..584811 191 tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0641:PI0642|PI0641:PI0642:conserved hypothetical protein:thioredoxin family protein:->->:584621..584811 191 tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0641:PI0642|PI0641:PI0642:conserved hypothetical protein:thioredoxin family protein:->->:584621..584811 191 tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 50 End: 151 ................................................. M R Q R Y K K I L N N S G F I N T F I Y F C I P I T Q I P H L N R G ........................................ tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa 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================================================ tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0641:PI0642|PI0641:PI0642:conserved hypothetical protein:thioredoxin family protein:->->:584621..584811 191 tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: pint_PI0641_PI0642|conserved hypothetical protein:thioredoxin family protein|POSITIVE:POSITIVE|[584621,584811]|191 HSP 1 e-value: 8.0E-92 bit: 337.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacnnnnnnntcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa tgtcttgttttgttaaagggggtttagcaagtacccctatttgtaaaaagtgcggcaaaggtacaaaaaaatcttaaacaatagtggttttatcaatacatttatttatttttgcattccaatcactcaaataccccatttaaatagggggtagtttgcaaaccattaaataataaaaagatatgaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUUGUUUUGUUAAAGGGGGUUUAGCAAGUACCCCUAUUUGUAAAAAGUGCGGCAAAGGUACAAAAAAAUCUUAAACAAUAGUGGUUUUAUCAAUACAUUUAUUUAUUUUUGCAUUCCAAUCACUCAAAUACCCCAUUUAAAUAGGGGGUAGUUUGCAAACCAUUAAAUAAUAAAAAGAUAUGAAGAAA ((((((..(((((((.....(((((.(((((..((((((((((.....((((.((..(((((........))))).......(((((((..(((((...............))).))...)))))))......)).))))))))))))))....))))))))))......)))))))))))))........ (-38.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUCAUAUCUUUUUAUUAUUUAAUGGUUUGCAAACUACCCCCUAUUUAAAUGGGGUAUUUGAGUGAUUGGAAUGCAAAAAUAAAUAAAUGUAUUGAUAAAACCACUAUUGUUUAAGAUUUUUUUGUACCUUUGCCGCACUUUUUACAAAUAGGGGUACUUGCUAAACCCCCUUUAACAAAACAAGACA ..((((..((((......(((((((....((((((...((((((..........))))))((..(....)..)).))))))..))))))).......)))).........(((((.(((.....((((((................))))))..(((((.........)))))))).)))))...)))).. (-31.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 91 52 136 96 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 275 63 22 196 145 pint:PI0737|5end_hypothetical_protein_671182..671412_POSITIVE 263 57 11 166 124 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 262 55 16 207 167 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 260 82 49 66 39 pint:PI1153|5end_histidine_kinase_sensor_protein_1077116..1077346_POSITIVE 259 44 7 68 26 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 246 60 15 194 149 pint:PI1229|5end_conserved_hypothetical_protein_1151260..1151490_POSITIVE 246 60 17 53 16 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 239 56 18 194 148 pint:PI1785|5end_conserved_hypothetical_protein_1717122..1717352_POSITIVE 236 160 112 178 133 pint:PI1488|5end_hypothetical_protein_1406994..1407224_POSITIVE 235 62 26 45 3 pint:PI1587|5end_conserved_hypothetical_protein;_possible_permease_1515284..1515514_POSITIVE 234 60 11 175 135 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 231 67 21 92 41 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 227 43 4 167 133 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 223 65 21 75 14 pint:PI1073|5end_hemogluttinin_A-related_protein_(HagA)_990593..990823_POSITIVE 222 169 135 145 115 pint:PI1478|5end_hypothetical_protein_1401873..1402103_POSITIVE 220 56 20 77 28 pint:PI0324|5end_conserved_hypothetical_protein_303735..303965_POSITIVE 220 190 143 114 59 pint:PI0032|5end_hypothetical_protein_36085..36315_POSITIVE 219 55 14 225 171 pint:PI0991|5end_conserved_hypothetical_protein_915309..915539_POSITIVE 219 44 6 222 181 pint:PI0776|5end_predicted_TPR-repeat-containing_protein_712077..712307_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 57 11 151 109 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 259 44 7 112 70 pint:PI1869|3end_hypothetical_protein_1815426..1815576_POSITIVE 258 57 17 82 40 pint:PI0297|3end_hypothetical_protein_277916..278066_POSITIVE 249 57 16 87 38 pint:PI1020|3end_hypothetical_protein_938779..938929_POSITIVE 248 59 11 101 45 pint:PI0060|3end_long-chain-fatty-acid--CoA_ligase_(acyl-CoA_synthetase)_60166..60316_POSITIVE 246 60 17 53 16 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 243 60 18 127 73 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 237 82 51 26 1 pint:PI1152|3end_response_regulator/transcriptional_regulator_RprY_1077156..1077306_POSITIVE 235 122 88 145 105 pint:PI1308|3end_hypothetical_protein_1223717..1223867_POSITIVE 234 56 11 99 49 pint:PI1623|3end_hypothetical_protein_1549261..1549411_POSITIVE 230 153 128 52 28 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 230 65 22 132 86 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 227 43 4 135 101 pint:PI1810|3end_outer_membrane_protein_1749566..1749716_POSITIVE 222 169 135 75 45 pint:PI1477|3end_TonB-dependent_outer_membrane_receptor_1401883..1402033_POSITIVE 220 56 20 74 25 pint:PI0322|3end_hypothetical_protein_303812..303962_POSITIVE 220 190 143 80 25 pint:PI0031|3end_peptidylprolyl_isomerase_36131..36281_POSITIVE 219 55 14 104 50 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 217 160 111 50 10 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE 217 58 15 79 27 pint:PI0545|3end_sugar_kinase_497867..498017_POSITIVE 216 60 17 104 52 pint:PI2123|3end_adenine_phosphoribosyltransferase_2072324..2072474_POSITIVE