Origin IGS: tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggcggggacgggtgaggggctccatgaaaccggcaaacagagcggaaaaagaacacgaaagggatgcgtcttcgtgtttgtttgagacgcatctctccctttatgtttacgaaccgtcccgtatcgtctattttttcaaaagcctca Mask Tandem Repeat Region ================================================ tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Find is-nt database================================================ Query_seq: TF3144:TF3145|TF3144:TF3145:phosphomannomutase/phosphoglucomutase:conserved hypothetical protein; possible GTP cyclohydrolase I family:->->:3381245..3381393 149 tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3144:TF3145|TF3144:TF3145:phosphomannomutase/phosphoglucomutase:conserved hypothetical protein; possible GTP cyclohydrolase I family:->->:3381245..3381393 149 tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3144:TF3145|TF3144:TF3145:phosphomannomutase/phosphoglucomutase:conserved hypothetical protein; possible GTP cyclohydrolase I family:->->:3381245..3381393 149 tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 17 End: 148 ................ M D D T G R F V N I K G E M R L K Q T R R R I P F V F F F R S V C R F H G A P H P S P P . Protein_Len: 45 Strand: - Start: 2 End: 136 . L S K F F Y V I R S P E Y V Y L S L H T E F L C S S A D R E H E K E A R N A P K M S G R M ............. tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta 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================================================ tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -3.5 Tail_Score: -2.87725 Start: 49 End: 91 Full_Region: GTTCGTAAACATAAA GGGAGAGATGCGTCT CAAACAAACACGA AGACGCATCCCTTTC GTGTTCTTTTTCCGC ................................................GGGAGAGATGCGTCTCAAACAAACACGAAGACGCATCCCTTTC.......................................................... Find igs database================================================ Query_seq: TF3144:TF3145|TF3144:TF3145:phosphomannomutase/phosphoglucomutase:conserved hypothetical protein; possible GTP cyclohydrolase I family:->->:3381245..3381393 149 tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: tfor_TF3144_TF3145|phosphomannomutase/phosphoglucomutase:conserved hypothetical protein; possible GTP cyclohydrolase I family|POSITIVE:POSITIVE|[3381245,3381393]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta tgaggcttttgaaaaaatagacgatacgggacggttcgtaaacataaagggagagatgcgtctcaaacaaacacgaagacgcatccctttcgtgttctttttccgctctgtttgccggtttcatggagcccctcacccgtccccgccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGCUUUUGAAAAAAUAGACGAUACGGGACGGUUCGUAAACAUAAAGGGAGAGAUGCGUCUCAAACAAACACGAAGACGCAUCCCUUUCGUGUUCUUUUUCCGCUCUGUUUGCCGGUUUCAUGGAGCCCCUCACCCGUCCCCGCCUA ..((((.(((....)))..........(((((((...(((((((....(..((.((((((((((..........).))))))))).))..)(((.........)))..))))))).(((((....)))))......))))))).)))). (-47.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGCGGGGACGGGUGAGGGGCUCCAUGAAACCGGCAAACAGAGCGGAAAAAGAACACGAAAGGGAUGCGUCUUCGUGUUUGUUUGAGACGCAUCUCUCCCUUUAUGUUUACGAACCGUCCCGUAUCGUCUAUUUUUUCAAAAGCCUCA (((((((((((((((((((((..........(((.(.......))))..............((((((((((((.((........)))))))))))))))))))))).........)))))))....))))))................. (-48.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 117 72 71 17 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 418 140 91 222 168 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 390 140 91 162 111 tfor:TF1090|5end_hypothetical_protein_1159032..1159262_POSITIVE 377 90 45 150 107 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 368 139 93 225 169 tfor:TF2327|5end_conserved_hypothetical_protein;_possible_lipoprotein_2485709..2485939_POSITIVE 350 140 91 67 18 tfor:TF2091|5end_3-oxoacyl-acyl-carrier-protein_synthase_2259690..2259920_POSITIVE 349 139 91 82 25 tfor:TF1071|5end_hypothetical_protein_1140969..1141199_POSITIVE 348 129 81 155 99 tfor:TF2395|5end_conserved_hypothetical_protein_2566532..2566762_POSITIVE 346 140 91 219 173 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 346 140 95 72 25 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 346 130 81 84 36 tfor:TF0886|5end_conjugative_transposon_protein_fragment_937914..938144_POSITIVE 343 140 95 65 18 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 342 131 93 172 136 tfor:TF2525|5end_conserved_hypothetical_protein_2704027..2704257_POSITIVE 339 120 72 221 179 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 336 130 81 195 131 tfor:TF2877|5end_regulatory_protein_3065601..3065831_POSITIVE 335 140 91 67 11 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 335 139 95 212 173 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 335 139 95 212 173 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 334 130 87 207 155 tfor:TF1234|5end_rhamnulose-1-phosphate_aldolase_1318875..1319105_POSITIVE 330 118 97 216 194 tfor:TF3065|5end_enolase_3291055..3291285_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 117 72 129 75 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 352 128 86 68 21 tfor:TF3013|3end_conserved_hypothetical_protein_3237539..3237689_POSITIVE 348 129 81 133 77 tfor:TF2394|3end_integrase/recombinase_XerD_2566590..2566740_POSITIVE 347 139 97 98 43 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 346 130 81 145 97 tfor:TF0885|3end_conjugative_transposon_protein_fragment_938055..938205_POSITIVE 345 139 104 46 7 tfor:TF1070|3end_hydrolase_1141013..1141163_POSITIVE 335 140 100 46 1 tfor:TF2089|3end_acyl_carrier_protein_2259749..2259899_POSITIVE 334 130 87 107 55 tfor:TF1233|3end_dihydrodipicolinate_synthase_1318855..1319005_POSITIVE 329 119 84 150 113 tfor:TF0179|3end_pyrophosphate-energized_proton_pump_190691..190841_POSITIVE 328 125 81 138 85 tfor:TF0441|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_3_465314..465464_POSITIVE 327 140 104 58 10 tfor:TF0095|3end_methyltransferase_106845..106995_POSITIVE 325 140 96 150 99 tfor:TF2551|3end_30S_ribosomal_protein_S10_2734815..2734965_POSITIVE 325 118 74 84 33 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 323 130 84 139 81 tfor:TF2635|3end_ABC_transporter,_ATP-binding_protein/permease_component_2806101..2806251_POSITIVE 323 129 86 45 2 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 322 133 91 137 93 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 321 118 77 148 102 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 317 118 73 82 34 tfor:TF1839|3end_conserved_hypothetical_protein_1989699..1989849_POSITIVE 316 130 86 64 20 tfor:TF0930|3end_conserved_hypothetical_protein;_possible_prophage_protein_969965..970115_POSITIVE 315 139 92 118 57 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE