Origin IGS: tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agatactattttttgttttgtaaagattaatatgtatactttgtaaaaaaacagaaaagaaagtgtgccttgtatcttaattcttccggcacgccttgaagaaactgtctcaataaacagctattgatatggctcttattttacttccagcta Mask Tandem Repeat Region ================================================ tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Find is-nt database================================================ Query_seq: TF2727:TF2728|TF2727:TF2728:outer membrane protein, possibly involved in nutrient binding:outer membrane protein, TonB dependent receptor:->->:2904595..2904747 153 tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2727:TF2728|TF2727:TF2728:outer membrane protein, possibly involved in nutrient binding:outer membrane protein, TonB dependent receptor:->->:2904595..2904747 153 tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2727:TF2728|TF2727:TF2728:outer membrane protein, possibly involved in nutrient binding:outer membrane protein, TonB dependent receptor:->->:2904595..2904747 153 tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 26 End: 124 ......................... M N S C L L R Q F L Q G V P E E L R Y K A H F L F C F F T K Y T Y ............................. Protein_Len: 40 Strand: + Start: 34 End: 153 ................................. M F I E T V S S R R A G R I K I Q G T L S F L F F Y K V Y I L I F T K Q K I V S tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct 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================================================ tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2727:TF2728|TF2727:TF2728:outer membrane protein, possibly involved in nutrient binding:outer membrane protein, TonB dependent receptor:->->:2904595..2904747 153 tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: tfor_TF2727_TF2728|outer membrane protein, possibly involved in nutrient binding:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[2904595,2904747]|153 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgnnnnnnnacaaagtatacatattaatctttacaaaacaaaaaatagtatct tagctggaagtaaaataagagccatatcaatagctgtttattgagacagtttcttcaaggcgtgccggaagaattaagatacaaggcacactttcttttctgtttttttacaaagtatacatattaatctttacaaaacaaaaaatagtatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUGGAAGUAAAAUAAGAGCCAUAUCAAUAGCUGUUUAUUGAGACAGUUUCUUCAAGGCGUGCCGGAAGAAUUAAGAUACAAGGCACACUUUCUUUUCUGUUUUUUUACAAAGUAUACAUAUUAAUCUUUACAAAACAAAAAAUAGUAUCU .....((((((.......(.(((.((((....(((((((....)))))))((((((..((....)).))))))....))))...))).)))))))....(((((((((......(((..............))).....)))))))))..... (-25.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUACUAUUUUUUGUUUUGUAAAGAUUAAUAUGUAUACUUUGUAAAAAAACAGAAAAGAAAGUGUGCCUUGUAUCUUAAUUCUUCCGGCACGCCUUGAAGAAACUGUCUCAAUAAACAGCUAUUGAUAUGGCUCUUAUUUUACUUCCAGCUA ..(((((.(((((((((((.(((((((........)).)))))....)))))))))))...)))))(((..(((((....((((((.((....))..)))))).((((........)))).....)))))))).................... (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 78 32 72 22 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 328 100 58 166 126 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 322 68 21 63 16 tfor:TF1321|5end_conserved_hypothetical_protein_1401565..1401795_POSITIVE 315 67 21 183 139 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 299 72 33 198 157 tfor:TF0091|5end_outer_membrane_protein_97701..97931_POSITIVE 295 108 63 172 123 tfor:TF3002|5end_helicase-related_protein_3217756..3217986_POSITIVE 295 108 63 117 68 tfor:TF2111|5end_RNA_polymerase_sigma-54_factor_2280506..2280736_POSITIVE 295 108 63 186 137 tfor:TF0717|5end_signal_recognition_particle_767654..767884_POSITIVE 291 91 54 63 21 tfor:TF0882|5end_hypothetical_protein_935919..936149_POSITIVE 288 90 41 217 167 tfor:TF0381|5end_cell_cycle_protein_401632..401862_POSITIVE 286 103 61 80 39 tfor:TF2603|5end_transcriptional_regulator,_AraC_family_2776578..2776808_POSITIVE 282 67 21 198 151 tfor:TF0088|5end_ABC_transporter,_permease_component_94299..94529_POSITIVE 281 96 52 150 100 tfor:TF2205|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2379055..2379285_POSITIVE 281 71 33 154 111 tfor:TF1774|5end_arylsulfatase_precursor_1911426..1911656_POSITIVE 280 90 53 48 9 tfor:TF0231|5end_conserved_hypothetical_protein_257804..258034_POSITIVE 276 68 27 129 88 tfor:TF0257|5end_hypothetical_protein_287610..287840_POSITIVE 275 71 33 224 185 tfor:TF2226|5end_CTn_excision_protein_2395529..2395759_POSITIVE 271 72 31 158 110 tfor:TF1916|5end_conserved_hypothetical_protein;_possible_ATPase_2068530..2068760_POSITIVE 269 76 33 60 13 tfor:TF0397|5end_ferredoxin-like_protein_417596..417826_POSITIVE 268 90 47 142 92 tfor:TF0491|5end_conserved_hypothetical_protein_513827..514057_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 78 32 72 22 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 306 98 51 89 33 tfor:TF0535|3end_surface_antigen_BspA_561701..561851_POSITIVE 305 68 35 127 89 tfor:TF2419|3end_conserved_hypothetical_protein;_possible_DNA_uptake-related_protein_2599175..2599325_POSITIVE 301 68 25 43 3 tfor:TF1320|3end_beta-galactosidase_1401625..1401775_POSITIVE 295 108 63 57 8 tfor:TF2110|3end_transposase_2280526..2280676_POSITIVE 294 98 51 113 68 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 291 91 54 57 15 tfor:TF0881|3end_conserved_hypothetical_protein_935993..936143_POSITIVE 288 90 41 138 88 tfor:TF0380|3end_conserved_hypothetical_protein_401633..401783_POSITIVE 281 96 52 137 87 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 281 71 33 53 10 tfor:TF1773|3end_hypothetical_protein_1911405..1911555_POSITIVE 275 90 60 27 1 tfor:TF0177|3end_hypothetical_protein_187154..187304_POSITIVE 269 76 33 60 13 tfor:TF0396|3end_conserved_hypothetical_protein_417676..417826_POSITIVE 268 90 47 139 89 tfor:TF0490|3end_conserved_hypothetical_protein_513904..514054_POSITIVE 268 68 21 84 51 tfor:TF0329|3end_membrane-bound_lytic_murein_transglycosylase_D_356240..356390_POSITIVE 262 69 27 149 102 tfor:TF1915|3end_NAD-dependent_protein_deacetylase,_SIR2_family_2068489..2068639_POSITIVE 261 75 33 50 2 tfor:TF2239|3end_hypothetical_protein_2414790..2414940_POSITIVE 260 69 24 76 20 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 259 70 31 132 93 tfor:TF1467|3end_conserved_hypothetical_protein_1557837..1557987_POSITIVE 258 67 21 52 4 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 257 67 34 147 124 tfor:TF2267|3end_lysozyme-related_protein_2435473..2435623_POSITIVE