Origin IGS: aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atctttctaaaaaccacttggatttttagaagtttctgtacaagaccggccggctcttaaaaagaatcggccggttttttatattaaagccatgtaaatcgtatagttgattatataatttgcatgatttttgttt Mask Tandem Repeat Region ================================================ aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Find is-nt database================================================ Query_seq: TDE2445:TDE2446|TDE2445:TDE2446:DNA-binding protein:malate dehydrogenase:-><-:2474728..2474863 136 aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2445:TDE2446|TDE2445:TDE2446:DNA-binding protein:malate dehydrogenase:-><-:2474728..2474863 136 aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2445:TDE2446|TDE2445:TDE2446:DNA-binding protein:malate dehydrogenase:-><-:2474728..2474863 136 aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Predict ORF larger than 30AA ================================================ aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat 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================================================ aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.7 Tail_Score: -3.29461 Start: 61 End: 93 Full_Region: GGCTTTAATATAAAA AACCGGCCGATTCTT TTT AAGAGCCGGCCGGTC TTGTACAGAAACTTC ............................................................AACCGGCCGATTCTTTTTAAGAGCCGGCCGGTC........................................... TransTerm Strand: - Conf: 100 HP_score: -15.3 Tail_Score: -5.47159 Start: 63 End: 91 Full_Region: agtttctgtacaaga ccggccggctctt aaa aagaatcggccgg ttttttatattaaag ..............................................................ccggccggctcttaaaaagaatcggccgg............................................. Find igs database================================================ Query_seq: TDE2445:TDE2446|TDE2445:TDE2446:DNA-binding protein:malate dehydrogenase:-><-:2474728..2474863 136 aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_002967_TDE2445_TDE2446|DNA-binding protein:malate dehydrogenase|POSITIVE:NEGATIVE|[2474728,2474863]|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 aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat aaacaaaaatcatgcaaattatataatcaactatacgatttacatggctttaatataaaaaaccggccgattctttttaagagccggccggtcttgtacagaaacttctaaaaatccaagtggtttttagaaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAAAAAUCAUGCAAAUUAUAUAAUCAACUAUACGAUUUACAUGGCUUUAAUAUAAAAAACCGGCCGAUUCUUUUUAAGAGCCGGCCGGUCUUGUACAGAAACUUCUAAAAAUCCAAGUGGUUUUUAGAAAGAU .....(((..((((.((((..((((......))))..)))).))))..)))..(((((...((((((((..(((.....)))..)))))))).))))).......(((((((((((.....))))))))))).... (-38.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUCUAAAAACCACUUGGAUUUUUAGAAGUUUCUGUACAAGACCGGCCGGCUCUUAAAAAGAAUCGGCCGGUUUUUUAUAUUAAAGCCAUGUAAAUCGUAUAGUUGAUUAUAUAAUUUGCAUGAUUUUUGUUU ...((((((((((((....)).))))))))))....((((.(((((((((((..(((.....)))..))))))))))).)))).......(((((((((..(((((....)))))..))))))))).......... (-46.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 102 63 72 27 NC_002967:TDE1371|5end_RNB-like_family_protein_1415169..1415399_NEGATIVE 341 87 42 137 88 NC_002967:TDE1379|5end_hypothetical_protein_1420658..1420888_NEGATIVE 331 106 61 210 170 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 319 88 44 214 166 NC_002967:TDE1633|5end_citrate_lyase_acyl_carrier_protein_1682691..1682921_NEGATIVE 311 98 62 205 175 NC_002967:TDE1592|5end_ABC_transporter,_ATP-binding_protein_1639491..1639721_POSITIVE 311 95 63 141 105 NC_002967:TDE0790|5end_30S_ribosomal_protein_S11_816951..817181_POSITIVE 308 109 64 102 43 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 307 92 64 196 168 NC_002967:TDE1332|5end_hflK_protein,_putative_1368042..1368272_POSITIVE 302 95 64 37 4 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 301 97 63 80 40 NC_002967:TDE0924|5end_ABC_transporter,_ATP-binding/permease_protein_947634..947864_NEGATIVE 299 97 54 188 139 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 293 106 64 133 86 NC_002967:TDE1681|5end_V-type_ATP_synthase_subunit_D_1733537..1733767_NEGATIVE 290 95 52 197 145 NC_002967:TDE0866|5end_hypothetical_protein_887614..887844_POSITIVE 287 97 66 47 9 NC_002967:TDE0138|5end_alkyldihydroxyacetonephosphate_synthase,_putative_158221..158451_POSITIVE 286 106 65 84 35 NC_002967:TDE1105|5end_ribosome-binding_factor_A_1138199..1138429_NEGATIVE 282 96 64 54 22 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 280 126 84 231 202 NC_002967:TDE2609|5end_MiaB-like_tRNA_modifying_enzyme_YliG,_TIGR01125_2650421..2650651_POSITIVE 280 86 43 196 152 NC_002967:TDE1941|5end_hypothetical_protein_1959285..1959515_NEGATIVE 279 96 58 211 158 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 278 96 63 231 197 NC_002967:TDE2528|5end_hypothetical_protein_2556912..2557142_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 95 57 77 38 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 368 96 57 53 21 NC_002967:TDE0680|3end_protein-export_membrane_protein_SecF_717613..717763_NEGATIVE 343 92 63 72 44 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 341 87 42 62 13 NC_002967:TDE1380|3end_hypothetical_protein_1420733..1420883_NEGATIVE 331 106 61 44 4 NC_002967:TDE1809|3end_hypothetical_protein_1845215..1845365_NEGATIVE 329 95 54 126 77 NC_002967:TDE2187|3end_ParB-like_nuclease_domain_protein_2221147..2221297_NEGATIVE 320 92 64 29 1 NC_002967:TDE2445|3end_DNA-binding_protein_2474667..2474817_POSITIVE 319 88 44 120 72 NC_002967:TDE1634|3end_hypothetical_protein_1682785..1682935_NEGATIVE 311 98 62 150 120 NC_002967:TDE1591|3end_inorganic_polyphosphate/ATP-NAD_kinase,_putative_1639516..1639666_POSITIVE 311 95 63 117 81 NC_002967:TDE0789|3end_30S_ribosomal_protein_S13_817007..817157_POSITIVE 307 92 64 148 120 NC_002967:TDE1331|3end_anaerobic_ribonucleoside_triphosphate_reductase_1368074..1368224_POSITIVE 303 98 57 66 26 NC_002967:TDE0009|3end_hypothetical_protein_13724..13874_NEGATIVE 302 95 64 35 2 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 293 106 64 122 75 NC_002967:TDE1682|3end_V-type_ATP_synthase_subunit_B_1733548..1733698_NEGATIVE 290 95 52 102 50 NC_002967:TDE0865|3end_hypothetical_protein_887599..887749_POSITIVE 286 106 65 91 42 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 281 89 66 151 127 NC_002967:TDE2553|3end_lysyl-tRNA_synthetase_2579047..2579197_NEGATIVE 280 86 43 45 1 NC_002967:TDE1943|3end_30S_ribosomal_protein_S4_1959436..1959586_NEGATIVE 278 108 66 123 80 NC_002967:TDE0485|3end_hypothetical_protein_542006..542156_NEGATIVE 277 106 61 58 2 NC_002967:TDE0445|3end_amino_acid_permease_501104..501254_POSITIVE