Origin IGS: taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct .........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 agctgttttttctatatctttattaatgggtacaaaaatacaacaaaaaaagaaatcatcgaatgatcagatatctcaaaacagtattttttaacattaccacccgaaaaaccttttatttttttgcatttttgaattatcgacaacctttttaaataaacaatgcaaacccttttccgtatttcggtta Mask Tandem Repeat Region ================================================ taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct Find is-nt database================================================ Query_seq: TF3115:TF3116|TF3115:TF3116:possible sugar kinase:conserved hypothetical protein:->->:3352086..3352275 190 taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3115:TF3116|TF3115:TF3116:possible sugar kinase:conserved hypothetical protein:->->:3352086..3352275 190 taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3115:TF3116|TF3115:TF3116:possible sugar kinase:conserved hypothetical protein:->->:3352086..3352275 190 taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 9 End: 176 ........ M R K R V C I V Y L K R L S I I Q K C K K I K G F S G G N V K K Y C F E I S D H S M I S F F V V F L Y P L I K I .............. Protein_Len: 30 Strand: - Start: 39 End: 128 ...................................... F P Q R Y N L F A F F Y F T K R T T I N F F V T K L Y R I M .............................................................. taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct 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================================================ taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -4.0 Tail_Score: -5.33131 Start: 125 End: 135 Full_Region: TTTTGAGATATCTGA TCAT TCG ATGA TTTCTTTTTTTGTTG ............................................................................................................................TCATTCGATGA....................................................... Find igs database================================================ Query_seq: TF3115:TF3116|TF3115:TF3116:possible sugar kinase:conserved hypothetical protein:->->:3352086..3352275 190 taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattcaaaaatgcaaaaaaataaaaggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: tfor_TF3115_TF3116|possible sugar kinase:conserved hypothetical protein|POSITIVE:POSITIVE|[3352086,3352275]|190 HSP 1 e-value: 3.0E-45 bit: 182.0 Len: 113 Query Start:78 Query End:190 Subject Strand: POSITIVE Subject Start: 78 Subject End: 190 .............................................................................ggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttcnnnnnnngttgtatttttgtacccattaataaagatatagaaaaaacagct .............................................................................ggtttttcgggtggtaatgttaaaaaatactgttttgagatatctgatcattcgatgatttctttttttgttgtatttttgtacccattaataaagatatagaaaaaacagct HSP 2 e-value: 2.0E-24 bit: 113.0 Len: 57 Query Start:1 Query End:57 Subject Strand: POSITIVE Subject Start: 1 Subject End: 57 taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattc..................................................................................................................................... taaccgaaatacggaaaagggtttgcattgtttatttaaaaaggttgtcgataattc..................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCGAAAUACGGAAAAGGGUUUGCAUUGUUUAUUUAAAAAGGUUGUCGAUAAUUCAAAAAUGCAAAAAAAUAAAAGGUUUUUCGGGUGGUAAUGUUAAAAAAUACUGUUUUGAGAUAUCUGAUCAUUCGAUGAUUUCUUUUUUUGUUGUAUUUUUGUACCCAUUAAUAAAGAUAUAGAAAAAACAGCU ...(((.....)))....((((....((((...((((....))))...))))....(((((((((((...((.((((((..(((((((((((.(((((..(((((...)))))..)))))...))))))))).))..)))))).)).))))))))))).))))........................... (-35.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGUUUUUUCUAUAUCUUUAUUAAUGGGUACAAAAAUACAACAAAAAAAGAAAUCAUCGAAUGAUCAGAUAUCUCAAAACAGUAUUUUUUAACAUUACCACCCGAAAAACCUUUUAUUUUUUUGCAUUUUUGAAUUAUCGACAACCUUUUUAAAUAAACAAUGCAAACCCUUUUCCGUAUUUCGGUUA .((((((((....(((((((((((....(((.......................)))....)))))..))))))...))))))))..................((((((.((..........((((((((((((((..............)))))).....)))))))).........)).))))))... (-24.25) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 178 135 167 124 tfor:TF0703|5end_conserved_hypothetical_protein_747252..747482_POSITIVE 262 149 108 168 118 tfor:TF2940|5end_50S_ribosomal_protein_L11_3141367..3141597_POSITIVE 256 119 77 98 58 tfor:TF0585|5end_conserved_hypothetical_protein_614782..615012_POSITIVE 242 87 42 221 181 tfor:TF1894|5end_hypothetical_protein_2046739..2046969_POSITIVE 242 25 3 86 57 tfor:TF0320|5end_dihydroorotase_346062..346292_POSITIVE 241 166 121 136 81 tfor:TF2344|5end_ATP/GTP_binding_protein_2507422..2507652_POSITIVE 240 148 105 52 4 tfor:TF0159|5end_conserved_hypothetical_protein_169756..169986_POSITIVE 238 50 3 211 173 tfor:TF3042|5end_ferrous_iron_transport_protein_B_3269362..3269592_POSITIVE 238 47 4 52 8 tfor:TF1411|5end_conserved_hypothetical_protein_1490275..1490505_POSITIVE 235 150 106 114 61 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 235 150 106 63 10 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 230 149 107 80 46 tfor:TF1148|5end_para-aminobenzoate_synthase_component_I_1228219..1228449_POSITIVE 226 114 78 224 195 tfor:TF2602|5end_tRNA-(5-methylaminomethyl-2-thiouridylate)_methyltransferase_2775086..2775316_POSITIVE 225 158 122 143 106 tfor:TF0593|5end_membrane-associated_phospholipid_phosphatase_626393..626623_POSITIVE 224 90 41 152 106 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 223 149 107 78 22 tfor:TF2752|5end_endonuclease_III_2936781..2937011_POSITIVE 223 57 18 211 171 tfor:TF1002|5end_replicative_DNA_helicase_1056620..1056850_POSITIVE 221 49 18 181 150 tfor:TF2547|5end_hypothetical_protein_2730664..2730894_POSITIVE 219 174 131 231 188 tfor:TF2732|5end_thioredoxin_M_2911767..2911997_POSITIVE 219 36 4 201 165 tfor:TF1986|5end_hypothetical_protein_2137021..2137251_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 125 85 71 31 tfor:TF1071|3end_hypothetical_protein_1141687..1141837_POSITIVE 274 178 135 63 20 tfor:TF0702|3end_possible_peptidyl-prolyl_isomerase_747228..747378_POSITIVE 262 149 108 103 53 tfor:TF2939|3end_transcription_antiterminator_3141382..3141532_POSITIVE 247 100 63 68 31 tfor:TF1991|3end_hypothetical_protein_2143584..2143734_POSITIVE 241 166 121 136 81 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 236 147 107 143 88 tfor:TF1547|3end_conserved_hypothetical_protein_1652471..1652621_POSITIVE 235 150 106 82 29 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 231 180 131 77 27 tfor:TF2731|3end_Fe2+/Zn2+_uptake_regulation_protein_2911686..2911836_POSITIVE 227 50 4 115 56 tfor:TF1962|3end_TatD-related_deoxyribonuclease,_Mg-dependent_DNase_2113297..2113447_POSITIVE 225 158 122 121 84 tfor:TF0592|3end_epimerase/reductase_626451..626601_POSITIVE 224 90 41 149 103 tfor:TF1047|3end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1109318..1109468_POSITIVE 223 57 18 111 71 tfor:TF1001|3end_penicillin-binding_protein_1A_1056600..1056750_POSITIVE 221 49 18 40 9 tfor:TF2546|3end_S-adenosylmethionine_synthetase_2730603..2730753_POSITIVE 217 163 127 40 1 tfor:TF2671|3end_dipeptidyl_peptidase_IV_(DPP_IV)_N-terminal_region_2846163..2846313_POSITIVE 217 32 4 67 33 tfor:TF2639|3end_hypothetical_protein_2809333..2809483_POSITIVE 214 160 121 150 98 tfor:TF2554|3end_50S_ribosomal_protein_L23_2736396..2736546_POSITIVE 212 151 120 31 2 tfor:TF2751|3end_phenylalanyl-tRNA_synthetase,_alpha_subunit_2936815..2936965_POSITIVE 211 177 137 92 49 tfor:TF1053|3end_outer_membrane_receptor,_TonB-linked_1119650..1119800_POSITIVE 207 119 78 134 88 tfor:TF0476|3end_conserved_hypothetical_protein_495545..495695_POSITIVE 207 139 116 57 31 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE