Origin IGS: cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta .........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 taacgatgggtgagctttcgtaaagggtgatgaatcataatgggtgagcggcttcgttgcttacccattcttacacacctgaagagggtgtgcccaaacatagcgttttgacacatcctcttttcctgtagtgcaaatcgtctcttcacagtagtgtgaaatgattggcagttgaaaagttgaaaag Mask Tandem Repeat Region ================================================ cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Find is-nt database================================================ Query_seq: TF1504:TF1505|TF1504:TF1505:conserved hypothetical protein:conserved hypothetical protein:->->:1610726..1610912 187 cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1504:TF1505|TF1504:TF1505:conserved hypothetical protein:conserved hypothetical protein:->->:1610726..1610912 187 cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1504:TF1505|TF1504:TF1505:conserved hypothetical protein:conserved hypothetical protein:->->:1610726..1610912 187 cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 17 End: 124 ................ M P I I S H Y C E E T I C T T G K E D V S K R Y V W A H P L Q V C K N G ............................................................... Protein_Len: 49 Strand: + Start: 39 End: 185 ...................................... M K R R F A L Q E K R M C Q N A M F G H T L F R C V R M G K Q R S R S P I M I H H P L R K L T H R .. cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta 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================================================ cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -10.2 Tail_Score: -4.371 Start: 68 End: 104 Full_Region: tcttacacacctgaa gagggtgtgcccaaac atagc gttttgacacatcctc ttttcctgtagtgca ...................................................................gagggtgtgcccaaacatagcgttttgacacatcctc................................................................................... TransTerm Strand: - Conf: 87 HP_score: -11.6 Tail_Score: -3.62046 Start: 121 End: 147 Full_Region: ggtgatgaatcataa tgggtgagcggc ttc gttgcttaccca ttcttacacacctga ........................................................................................................................tgggtgagcggcttcgttgcttaccca........................................ Find igs database================================================ Query_seq: TF1504:TF1505|TF1504:TF1505:conserved hypothetical protein:conserved hypothetical protein:->->:1610726..1610912 187 cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: tfor_TF1504_TF1505|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1610726,1610912]|187 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta cttttcaacttttcaactgccaatcatttcacactactgtgaagagacgatttgcactacaggaaaagaggatgtgtcaaaacgctatgtttgggcacaccctcttcaggtgtgtaagaatgggtaagcaacgaagccgctcacccattatgattcatcaccctttacgaaagctcacccatcgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCAACUUUUCAACUGCCAAUCAUUUCACACUACUGUGAAGAGACGAUUUGCACUACAGGAAAAGAGGAUGUGUCAAAACGCUAUGUUUGGGCACACCCUCUUCAGGUGUGUAAGAAUGGGUAAGCAACGAAGCCGCUCACCCAUUAUGAUUCAUCACCCUUUACGAAAGCUCACCCAUCGUUA .........(((((...(((.((((.((((.(((....)))..)))).)))).)))....(((..((((((.((((((.((((.....)))).)))))).))))))..((((.((...(((((((.(((.........))).)))))))...)).))))..)))....))))).............. (-51.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGAUGGGUGAGCUUUCGUAAAGGGUGAUGAAUCAUAAUGGGUGAGCGGCUUCGUUGCUUACCCAUUCUUACACACCUGAAGAGGGUGUGCCCAAACAUAGCGUUUUGACACAUCCUCUUUUCCUGUAGUGCAAAUCGUCUCUUCACAGUAGUGUGAAAUGAUUGGCAGUUGAAAAGUUGAAAAG ((((.(((((..............(((((.((......((((((((((((((...))))))))))))))....)))))))((((((((((((.(.((((.....)))).).)))))))))))).)))))..(((.((((((...((((((....)))))))))))).)))........))))..... (-61.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 742 118 73 174 129 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 736 117 73 182 137 tfor:TF2536|5end_subtilisin-like_serine_protease_2719286..2719516_POSITIVE 591 119 73 178 129 tfor:TF0792|5end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_846454..846684_POSITIVE 553 106 61 227 183 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 454 130 81 200 148 tfor:TF0146|5end_glutamine-dependent_NAD(+)_synthetase_154855..155085_POSITIVE 451 106 66 201 161 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 440 105 67 155 114 tfor:TF1284|5end_glyceraldehyde_3-phosphate_dehydrogenase_1367939..1368169_POSITIVE 438 106 61 148 103 tfor:TF0107|5end_ion_channel_protein_113913..114143_POSITIVE 407 101 64 151 114 tfor:TF1024|5end_50S_ribosomal_protein_L19_1081948..1082178_POSITIVE 407 101 64 159 122 tfor:TF0702|5end_possible_peptidyl-prolyl_isomerase_744977..745207_POSITIVE 406 110 64 206 161 tfor:TF2289|5end_secretion_protein,_possible_HlyD_family_2442725..2442955_POSITIVE 405 147 103 225 177 tfor:TF0091|5end_outer_membrane_protein_97701..97931_POSITIVE 396 106 65 203 161 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 395 106 62 149 99 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 389 105 61 229 181 tfor:TF1454|5end_sugar_phosphate_epimerase/isomerase_1539696..1539926_POSITIVE 367 105 61 162 119 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 364 106 68 192 155 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 363 106 68 199 160 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 362 129 83 225 173 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 354 103 61 167 127 tfor:TF0216|5end_50S_ribosomal_protein_L20_242476..242706_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 553 106 61 46 2 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 451 106 66 55 15 tfor:TF2319|3end_acyl_carrier_protein_2476588..2476738_POSITIVE 438 106 61 62 17 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 408 106 68 112 74 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 396 106 65 48 6 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 389 105 61 110 62 tfor:TF1452|3end_conserved_hypothetical_protein;_possible_transglutaminase-like_enzyme_1539657..1539807_POSITIVE 388 106 61 56 11 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 377 104 64 49 9 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 365 166 124 79 38 tfor:TF0795|3end_hypothetical_protein_853199..853349_POSITIVE 363 106 68 60 21 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 358 110 61 69 20 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 342 107 61 64 19 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 339 169 124 84 42 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 328 140 91 66 20 tfor:TF2153|3end_6-phosphofructokinase_2329172..2329322_POSITIVE 319 110 71 135 95 tfor:TF2873|3end_conserved_hypothetical_protein_3064966..3065116_POSITIVE 318 104 68 64 28 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 312 105 67 60 22 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE 298 111 73 49 3 tfor:TF2348|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2513252..2513402_POSITIVE 297 169 123 147 101 tfor:TF2721|3end_conserved_hypothetical_protein_2896956..2897106_POSITIVE 295 139 95 74 35 tfor:TF0121|3end_hypothetical_protein_133217..133367_POSITIVE