Origin IGS: tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaataacattcatcattcaactaaaatgcgtaggctaaattcaggacaggacatctcccaaaactctcttcttcttgtcccaatctgtgtttaactgtgcttatcta Mask Tandem Repeat Region ================================================ tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Find is-nt database================================================ Query_seq: TF1547:TF1548|TF1547:TF1548:conserved hypothetical protein:thiophene and furan oxidation protein:->->:1652532..1652640 109 tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1547:TF1548|TF1547:TF1548:conserved hypothetical protein:thiophene and furan oxidation protein:->->:1652532..1652640 109 tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1547:TF1548|TF1547:TF1548:conserved hypothetical protein:thiophene and furan oxidation protein:->->:1652532..1652640 109 tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Predict ORF larger than 30AA ================================================ tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta 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================================================ tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1547:TF1548|TF1547:TF1548:conserved hypothetical protein:thiophene and furan oxidation protein:->->:1652532..1652640 109 tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: tfor_TF1547_TF1548|conserved hypothetical protein:thiophene and furan oxidation protein|POSITIVE:POSITIVE|[1652532,1652640]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta tagataagcacagttaaacacagattgggacaagaagaagagagttttgggagatgtcctgtcctgaatttagcctacgcattttagttgaatgatgaatgttatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUAAGCACAGUUAAACACAGAUUGGGACAAGAAGAAGAGAGUUUUGGGAGAUGUCCUGUCCUGAAUUUAGCCUACGCAUUUUAGUUGAAUGAUGAAUGUUAUUUUA ......((((..((((((..(((..(((((((....((((....))))......)))))))..)))..))))))...(((((((.....))))).))..))))...... (-18.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAACAUUCAUCAUUCAACUAAAAUGCGUAGGCUAAAUUCAGGACAGGACAUCUCCCAAAACUCUCUUCUUCUUGUCCCAAUCUGUGUUUAACUGUGCUUAUCUA .............................((((((..(((((.((((...(((((......................)))))...)))).))))).))))))....... (-16.55) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 77 34 170 121 tfor:TF1045|5end_conserved_hypothetical_protein_1107665..1107895_POSITIVE 306 99 55 101 52 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 296 96 57 153 113 tfor:TF1718|5end_conserved_hypothetical_protein_1840462..1840692_POSITIVE 295 69 21 96 43 tfor:TF1650|5end_integrase_1760039..1760269_POSITIVE 284 90 46 231 179 tfor:TF1175|5end_membrane-fusion_protein_1258140..1258370_POSITIVE 282 60 20 96 55 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 282 80 31 224 158 tfor:TF0049|5end_membrane-associated_HD_superfamily_hydrolase_55245..55475_POSITIVE 279 90 46 42 1 tfor:TF2611|5end_conserved_hypothetical_protein_2787204..2787434_POSITIVE 275 63 28 195 149 tfor:TF1796|5end_ABC_transporter,_ATP-binding_protein_1936492..1936722_POSITIVE 275 60 20 77 26 tfor:TF1629|5end_hypothetical_protein_1741563..1741793_POSITIVE 274 61 25 142 101 tfor:TF2636|5end_glutaminase_2806096..2806326_POSITIVE 274 80 31 195 142 tfor:TF2141|5end_conserved_hypothetical_protein_2316677..2316907_POSITIVE 273 78 40 214 174 tfor:TF0906|5end_conserved_hypothetical_protein_949675..949905_POSITIVE 271 53 21 87 54 tfor:TF1694|5end_conserved_hypothetical_protein_1812493..1812723_POSITIVE 267 79 49 32 6 tfor:TF2364|5end_conserved_hypothetical_protein;_possible_DNA_binding_protein,_excisionase_family_2530362..2530592_POSITIVE 267 83 41 230 190 tfor:TF0349|5end_hypothetical_protein_370367..370597_POSITIVE 266 76 33 125 78 tfor:TF1672|5end_ATP_synthase,_B_subunit_1786726..1786956_POSITIVE 265 99 54 114 75 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 265 80 33 223 163 tfor:TF2225|5end_CTn_excision_protein_2394935..2395165_POSITIVE 265 66 31 80 48 tfor:TF1828|5end_hypothetical_protein_1977049..1977279_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 96 57 105 65 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 295 69 21 96 43 tfor:TF1649|3end_hypothetical_protein_1760119..1760269_POSITIVE 282 60 20 105 64 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 275 63 28 99 53 tfor:TF1795|3end_conserved_hypothetical_protein_1936476..1936626_POSITIVE 274 61 25 67 26 tfor:TF2635|3end_ABC_transporter,_ATP-binding_protein/permease_component_2806101..2806251_POSITIVE 266 76 33 54 7 tfor:TF1671|3end_ATP_synthase,_delta_subunit_1786735..1786885_POSITIVE 265 99 54 102 63 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 259 65 23 140 93 tfor:TF2582|3end_ABC_transporter,_ATP-binding_protein_2750283..2750433_POSITIVE 259 60 11 59 4 tfor:TF2039|3end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199835..2199985_POSITIVE 258 90 41 119 75 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 257 81 41 113 75 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 257 81 41 144 106 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 255 79 34 151 93 tfor:TF2027|3end_conserved_hypothetical_protein_2184176..2184326_POSITIVE 255 66 22 138 94 tfor:TF1688|3end_conserved_hypothetical_protein;_possible_periplasmic_protein_1804882..1805032_POSITIVE 251 87 42 67 18 tfor:TF2019|3end_dipeptidyl_peptidase_VI_2176401..2176551_POSITIVE 250 60 11 132 84 tfor:TF2081|3end_phosphopantetheine_adenylyltransferase_2249031..2249181_POSITIVE 249 67 25 148 98 tfor:TF2328|3end_conserved_hypothetical_protein_2488349..2488499_POSITIVE 248 88 46 143 98 tfor:TF1738|3end_outer_membrane_protein_1866946..1867096_POSITIVE 248 65 21 105 50 tfor:TF1250|3end_possible_cation_efflux_pump_1333801..1333951_POSITIVE 246 67 21 113 57 tfor:TF0584|3end_phosphopantetheinyl_transferase_614455..614605_POSITIVE