Origin IGS: tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatcaattattaatgcaattttaataagaaggatctcaaatcccaacaccttcttccacctcgcccatcgaaagatcacacaggtttgcaatcagcccccaaacgatcccttttattctccatctcttactatca Mask Tandem Repeat Region ================================================ tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Find is-nt database================================================ Query_seq: TF2757:TF2758|TF2757:TF2758:hypothetical protein:hypothetical protein:->->:2942396..2942531 136 tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2757:TF2758|TF2757:TF2758:hypothetical protein:hypothetical protein:->->:2942396..2942531 136 tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2757:TF2758|TF2757:TF2758:hypothetical protein:hypothetical protein:->->:2942396..2942531 136 tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 45 End: 134 ............................................ M Q T C V I F R W A R W K K V L G F E I L L I K I A L I I D .. Protein_Len: 45 Strand: - Start: 2 End: 136 . I T L S P S Y F P D N P P Q N C V Q T I K R H A L H F F T N P N S I R R I L I A N I I S M Protein_Len: 32 Strand: - Start: 1 End: 96 S L L L H L I F P I T Q P S I A F R H S R E I P S T S S P T P M ........................................ tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat 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: 84 Start: 89 End: 118 ........................................................................................GTTGGGATTTGAGATCCTTCTTATTAAAAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2757:TF2758|TF2757:TF2758:hypothetical protein:hypothetical protein:->->:2942396..2942531 136 tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: tfor_TF2757_TF2758|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2942396,2942531]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat tgatagtaagagatggagaataaaagggatcgtttgggggctgattgcaaacctgtgtgatctttcgatgggcgaggtggaagaaggtgttgggatttgagatccttcttattaaaattgcattaataattgatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAGUAAGAGAUGGAGAAUAAAAGGGAUCGUUUGGGGGCUGAUUGCAAACCUGUGUGAUCUUUCGAUGGGCGAGGUGGAAGAAGGUGUUGGGAUUUGAGAUCCUUCUUAUUAAAAUUGCAUUAAUAAUUGAUAU .........................(((((((..((((.((.....))...))))..)))))))(((((..((((..(..((((((((.(..(...)..).).)))))))....)..)))).......)))))... (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCAAUUAUUAAUGCAAUUUUAAUAAGAAGGAUCUCAAAUCCCAACACCUUCUUCCACCUCGCCCAUCGAAAGAUCACACAGGUUUGCAAUCAGCCCCCAAACGAUCCCUUUUAUUCUCCAUCUCUUACUAUCA .......................(((((((.(((((......................((((.....(((....))).....))))..((.....))........))))).))))))).................. (-17.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 80 32 171 114 tfor:TF1247|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330387..1330617_POSITIVE 418 99 53 86 28 tfor:TF1832|5end_3-isopropylmalate_dehydratase,_small_subunit_1980832..1981062_POSITIVE 415 89 41 208 161 tfor:TF1974|5end_glyoxalase_I_related_protein_(lactoylglutathione_lyase)_2120950..2121180_POSITIVE 415 80 35 155 113 tfor:TF1243|5end_periplasmic_protease_1327243..1327473_POSITIVE 398 100 54 231 174 tfor:TF0704|5end_TPR-repeat-containing_protein_747888..748118_POSITIVE 376 79 32 105 58 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 373 79 33 156 104 tfor:TF0281|5end_hypothetical_protein_308909..309139_POSITIVE 373 79 33 54 2 tfor:TF0280|5end_hypothetical_protein_308807..309037_POSITIVE 364 95 52 127 74 tfor:TF1401|5end_Holliday_junction_DNA_helicase_1476502..1476732_POSITIVE 360 79 38 52 5 tfor:TF0236|5end_multidrug_resistance_protein_261779..262009_POSITIVE 356 80 31 164 111 tfor:TF1934|5end_hypothetical_protein_2083787..2084017_POSITIVE 351 100 52 104 44 tfor:TF3146|5end_GTP-binding_protein_Obg_3381852..3382082_POSITIVE 346 77 31 212 158 tfor:TF0904|5end_conserved_hypothetical_protein_948435..948665_POSITIVE 345 80 33 59 1 tfor:TF0710|5end_two_component_system_histidine_kinase_757250..757480_POSITIVE 344 73 32 170 131 tfor:TF1042|5end_possible_surface_antigen_with_leucine-rich_repeat_1102957..1103187_POSITIVE 343 100 53 229 187 tfor:TF1964|5end_MotA/TolQ/ExbB_proton_channel_family_2113560..2113790_POSITIVE 338 100 52 186 129 tfor:TF2666|5end_hypothetical_protein_2841818..2842048_POSITIVE 337 67 26 72 32 tfor:TF0613|5end_conserved_hypothetical_protein_646070..646300_POSITIVE 333 77 34 77 36 tfor:TF2643|5end_possible_O-antigen_transporter_2811744..2811974_POSITIVE 333 80 35 180 140 tfor:TF1295|5end_conserved_hypothetical_protein_1375854..1376084_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 80 32 133 76 tfor:TF1246|3end_protease,_with_chaperone_function_1330429..1330579_POSITIVE 418 99 53 77 19 tfor:TF1831|3end_conserved_hypothetical_protein_1980903..1981053_POSITIVE 379 80 31 101 43 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 366 98 59 89 43 tfor:TF1273|3end_hypothetical_protein_1357462..1357612_POSITIVE 364 95 52 118 65 tfor:TF1400|3end_polysaccharide_biosynthesis_protein;_membrane_protein_1476573..1476723_POSITIVE 363 79 31 110 49 tfor:TF0616|3end_conserved_hypothetical_protein_650658..650808_POSITIVE 338 100 52 139 82 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 338 100 52 139 82 tfor:TF2438|3end_hypothetical_protein_2616157..2616307_POSITIVE 338 100 52 139 82 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 338 100 52 139 82 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 337 67 26 59 19 tfor:TF0612|3end_conserved_hypothetical_protein_646137..646287_POSITIVE 333 77 34 80 39 tfor:TF2642|3end_acetylornithine_deacetylase_2811827..2811977_POSITIVE 329 98 52 131 62 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 323 88 44 151 105 tfor:TF2093|3end_conserved_hypothetical_protein_2262402..2262552_POSITIVE 321 79 32 135 93 tfor:TF1788|3end_conserved_hypothetical_protein_1930119..1930269_POSITIVE 320 56 13 150 91 tfor:TF1507|3end_outer_membrane_receptor,_TonB-dependent_1616268..1616418_POSITIVE 319 57 13 138 95 tfor:TF1041|3end_dihydroorotate_dehydrogenase,_catalytic_subunit_1103020..1103170_POSITIVE 319 95 52 69 27 tfor:TF0752|3end_nucleotide-binding_protein;_MAF-like_protein_801713..801863_POSITIVE 316 79 34 125 75 tfor:TF3004|3end_phosphoribosylformylglycinamidine_(FGAM)_synthase_3224576..3224726_POSITIVE 315 95 51 76 27 tfor:TF1519|3end_hypothetical_protein_1628022..1628172_POSITIVE