Origin IGS: ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttacccctccttaagttttgtaagtaagtgattttactataaagaggtttaaaaatcaaggactgaagttttataaattgtaagagaggaatttaaccgcggtgcacgcaaagaccgcaaaggaatttttaagagtctttctccgtaaaagtgggggcgctcccctaa Mask Tandem Repeat Region ================================================ ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Find is-nt database================================================ Query_seq: TDE1344:TDE1345|TDE1344:TDE1345:hypothetical protein:DNA primase:->->:1383411..1383578 168 ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1344:TDE1345|TDE1344:TDE1345:hypothetical protein:DNA primase:->->:1383411..1383578 168 ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1344:TDE1345|TDE1344:TDE1345:hypothetical protein:DNA primase:->->:1383411..1383578 168 ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 77 End: 166 ............................................................................ M P L L Q F I K L Q S L I F K P L Y S K I T Y L Q N L R R G .. ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa 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: 86 Start: 109 End: 138 ............................................................................................................CTTGATTTTTAAACCTCTTTATAGTAAAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1344:TDE1345|TDE1344:TDE1345:hypothetical protein:DNA primase:->->:1383411..1383578 168 ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_002967_TDE1344_TDE1345|hypothetical protein:DNA primase|POSITIVE:POSITIVE|[1383411,1383578]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa ttaggggagcgcccccacttttacggagaaagactcttaaaaattcctttgcggtctttgcgtgcaccgcggttaaattcctctcttacaatttataaaacttcagtccttgatttttaaacctctttatagtaaaatcacttacttacaaaacttaaggaggggtaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGGGGAGCGCCCCCACUUUUACGGAGAAAGACUCUUAAAAAUUCCUUUGCGGUCUUUGCGUGCACCGCGGUUAAAUUCCUCUCUUACAAUUUAUAAAACUUCAGUCCUUGAUUUUUAAACCUCUUUAUAGUAAAAUCACUUACUUACAAAACUUAAGGAGGGGUAA ...((((.....))))..(((((.((((.....)))))))))......((((((((.......).)))))))....(((((((.((((.......(((((..((((...)))).)))))...........(((((......))))).........))))))))))).. (-32.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACCCCUCCUUAAGUUUUGUAAGUAAGUGAUUUUACUAUAAAGAGGUUUAAAAAUCAAGGACUGAAGUUUUAUAAAUUGUAAGAGAGGAAUUUAACCGCGGUGCACGCAAAGACCGCAAAGGAAUUUUUAAGAGUCUUUCUCCGUAAAAGUGGGGGCGCUCCCCUAA .....((((((((...(((((((((...((((((((((.......)))...)))))))...))).......))))))...)))).)))).........(((((..........)))))......(((((((.(((.....)))..)))))))(((((....))))).. (-35.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 526 88 41 218 172 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 396 74 31 212 167 NC_002967:TDE2734|5end_hypothetical_protein_2789071..2789301_POSITIVE 379 88 47 152 108 NC_002967:TDE0161|5end_hypothetical_protein_187829..188059_NEGATIVE 368 72 40 231 198 NC_002967:TDE1906|5end_hypothetical_protein_1923883..1924113_POSITIVE 339 89 43 72 33 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 334 74 39 72 33 NC_002967:TDE2282|5end_tRNA_synthetase,_class_II_family_protein_2319665..2319895_NEGATIVE 323 74 32 123 77 NC_002967:TDE2732|5end_hypothetical_protein_2788448..2788678_POSITIVE 320 90 45 178 139 NC_002967:TDE0407|5end_glutamate_synthase_(NADPH),_homotetrameric_460522..460752_NEGATIVE 313 72 36 62 17 NC_002967:TDE2484|5end_hypothetical_protein_2507720..2507950_NEGATIVE 305 83 51 227 196 NC_002967:TDE2143|5end_penicillin-binding_protein_2178107..2178337_POSITIVE 304 90 51 90 48 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 300 74 40 59 30 NC_002967:TDE2495|5end_hypothetical_protein_2521053..2521283_NEGATIVE 296 85 47 45 4 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 294 89 48 131 82 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 293 63 23 54 15 NC_002967:TDE0982|5end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1006477..1006707_POSITIVE 293 26 1 172 141 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 293 26 1 189 158 NC_002967:TDE0469|5end_hypothetical_protein_523987..524217_NEGATIVE 291 82 50 181 141 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 291 85 50 53 17 NC_002967:TDE0977|5end_hypothetical_protein_1000415..1000645_POSITIVE 290 86 41 216 166 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 89 43 88 49 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 334 74 39 58 19 NC_002967:TDE2283|3end_permease,_putative_2319679..2319829_NEGATIVE 323 74 32 48 2 NC_002967:TDE2731|3end_TIM-barrel_protein,_putative,_NifR3_family_2788453..2788603_POSITIVE 317 72 32 145 107 NC_002967:TDE0408|3end_oxidoreductase,_NAD-binding_460536..460686_NEGATIVE 304 74 31 81 37 NC_002967:TDE1642|3end_hypothetical_protein_1692771..1692921_NEGATIVE 303 74 35 51 12 NC_002967:TDE2159|3end_hypothetical_protein_2193874..2194024_POSITIVE 296 85 47 73 32 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 293 26 1 85 54 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 291 85 50 56 20 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 289 80 35 134 88 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 286 82 41 137 95 NC_002967:TDE0895|3end_transcriptional_regulator,_AraC_family_911227..911377_NEGATIVE 286 84 43 53 4 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE 284 72 36 131 90 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 283 76 46 94 56 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 281 49 2 135 82 NC_002967:TDE1280|3end_hypothetical_protein_1315750..1315900_NEGATIVE 280 90 45 95 53 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 278 85 45 79 33 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 277 69 25 57 14 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 275 80 31 141 85 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 273 108 64 106 65 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE