Origin IGS: taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaggttataggaaagaagaaaaacgtaattacaaagtaaaaatgtaattacgttttttttattttataattgcgtttccacaaagccatagtaccgtttttaaaagctcaaaccttccaaacagcaagttgagagtgtagcggaaagaagctta Mask Tandem Repeat Region ================================================ taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Find is-nt database================================================ Query_seq: PI0011:PI0012|PI0011:PI0012:conserved hypothetical protein:conserved hypothetical protein:->->:13389..13545 157 taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0011:PI0012|PI0011:PI0012:conserved hypothetical protein:conserved hypothetical protein:->->:13389..13545 157 taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0011:PI0012|PI0011:PI0012:conserved hypothetical protein:conserved hypothetical protein:->->:13389..13545 157 taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Predict ORF larger than 30AA ================================================ taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 85 End: 114 ....................................................................................AATGTAATTACGTTTTTTTTATTTTATAAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -6.2 Tail_Score: -5.39905 Start: 103 End: 131 Full_Region: ATAAAATAAAAAAAA CGTAATTACA TTTTTACTT TGTAATTACG TTTTTCTTCTTTCCT ......................................................................................................CGTAATTACATTTTTACTTTGTAATTACG.......................... Find igs database================================================ Query_seq: PI0011:PI0012|PI0011:PI0012:conserved hypothetical protein:conserved hypothetical protein:->->:13389..13545 157 taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: pint_PI0011_PI0012|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[13389,13545]|157 HSP 1 e-value: 8.0E-70 bit: 264.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaatnnnnnnnncgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta taagcttctttccgctacactctcaacttgctgtttggaaggtttgagcttttaaaaacggtactatggctttgtggaaacgcaattataaaataaaaaaaacgtaattacatttttactttgtaattacgtttttcttctttcctataacctttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCUUCUUUCCGCUACACUCUCAACUUGCUGUUUGGAAGGUUUGAGCUUUUAAAAACGGUACUAUGGCUUUGUGGAAACGCAAUUAUAAAAUAAAAAAAACGUAAUUACAUUUUUACUUUGUAAUUACGUUUUUCUUCUUUCCUAUAACCUUUUA .(((((((((((((..((((.........).))).)))))))...))))))........(((..(((((..(((((....)))))............(((((((((((((((.........)))))))))))))))........))))))))..... (-38.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGGUUAUAGGAAAGAAGAAAAACGUAAUUACAAAGUAAAAAUGUAAUUACGUUUUUUUUAUUUUAUAAUUGCGUUUCCACAAAGCCAUAGUACCGUUUUUAAAAGCUCAAACCUUCCAAACAGCAAGUUGAGAGUGUAGCGGAAAGAAGCUUA .....((((((((((...((((((((((((((((((.........)))))))))))))))))).))))))))))..(((((......((....)).(((((.....(..(((((..(((.(.....).))))))))..)..)))))...)))))... (-35.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 48 2 227 186 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 325 48 2 52 11 pint:PI0716|5end_conserved_hypothetical_protein_652136..652366_POSITIVE 297 46 9 74 15 pint:PI0221|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_212356..212586_POSITIVE 284 43 4 79 31 pint:PI0424|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_388429..388659_POSITIVE 270 50 2 215 159 pint:PI1729|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1648416..1648646_POSITIVE 264 50 5 85 40 pint:PI2057|5end_conserved_hypothetical_protein;_possible_metal-dependent_membrane_protease_2014939..2015169_POSITIVE 258 50 4 67 20 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 255 78 31 191 150 pint:PI0278|5end_hypothetical_protein_265414..265644_POSITIVE 254 50 4 149 112 pint:PI1332|5end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1249374..1249604_POSITIVE 248 50 4 88 51 pint:PI0068|5end_arginine_repressor_66586..66816_POSITIVE 247 72 31 98 46 pint:PI0215|5end_hypothetical_protein_208823..209053_POSITIVE 246 49 1 172 114 pint:PI2138|5end_nicotinate_phosphoribosyltransferase_2083836..2084066_POSITIVE 246 48 7 139 84 pint:PI0762|5end_mannose-6-phosphate_isomerase,_class_I_696420..696650_POSITIVE 244 45 5 122 74 pint:PI0311|5end_hypothetical_protein_294721..294951_POSITIVE 241 49 4 100 46 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 240 50 3 84 25 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 240 68 27 218 172 pint:PI0304|5end_hypothetical_protein_288582..288812_POSITIVE 239 70 27 112 56 pint:PI0774|5end_phosphoserine_aminotransferase_(phosphoserine_transaminase)_709497..709727_POSITIVE 239 49 7 78 32 pint:PI0584|5end_hypothetical_protein_527352..527582_POSITIVE 238 37 4 139 110 pint:PI1735|5end_conserved_hypothetical_protein_1653428..1653658_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 46 3 76 17 pint:PI1939|3end_hypothetical_protein_1896666..1896816_POSITIVE 258 50 4 83 36 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 257 62 27 134 97 pint:PI0253|3end_conjugative_transposon_protein,_TraD_248973..249123_POSITIVE 251 84 58 118 95 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 246 49 1 63 5 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 240 50 3 88 29 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 238 47 4 146 98 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 238 45 7 80 41 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 237 49 12 100 67 pint:PI2123|3end_adenine_phosphoribosyltransferase_2072324..2072474_POSITIVE 237 50 13 104 62 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 236 50 5 149 103 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE 236 49 8 128 82 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 234 46 14 124 87 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 234 80 31 81 34 pint:PI0540|3end_conserved_hypothetical_protein_493865..494015_POSITIVE 232 70 22 73 21 pint:PI0927|3end_transglutaminase-related_protein_859696..859846_POSITIVE 230 70 21 142 92 pint:PI0110|3end_ABC_transport_system,_ATP-binding_protein_107920..108070_POSITIVE 229 83 47 136 95 pint:PI0265|3end_conjugative_transposon_protein,_TraO_257957..258107_POSITIVE 228 42 3 149 111 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 227 79 31 57 5 pint:PI1013|3end_probable_transcriptional_regulator_934368..934518_POSITIVE 226 49 12 133 83 pint:PI1662|3end_hypothetical_protein_1577241..1577391_POSITIVE