Origin IGS: tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggaatgccttcctcttcattccttcgtatgcgctaccgaacagccctcttgaaatgtgctgatatgatggttggggacagttagagaaggaattcttca Mask Tandem Repeat Region ================================================ tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Find is-nt database================================================ Query_seq: TF0610:TF0612|TF0610:TF0612:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:conserved hypothetical protein:->->:644104..644205 102 tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0610:TF0612|TF0610:TF0612:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:conserved hypothetical protein:->->:644104..644205 102 tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0610:TF0612|TF0610:TF0612:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:conserved hypothetical protein:->->:644104..644205 102 tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Predict ORF larger than 30AA ================================================ tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta 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================================================ tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0610:TF0612|TF0610:TF0612:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:conserved hypothetical protein:->->:644104..644205 102 tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: tfor_TF0610_TF0612|conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:conserved hypothetical protein|POSITIVE:POSITIVE|[644104,644205]|102 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta tgaagaattccttctctaactgtccccaaccatcatatcagcacatttcaagagggctgttcggtagcgcatacgaaggaatgaagaggaaggcattcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAGAAUUCCUUCUCUAACUGUCCCCAACCAUCAUAUCAGCACAUUUCAAGAGGGCUGUUCGGUAGCGCAUACGAAGGAAUGAAGAGGAAGGCAUUCCUUA ......((((((((.....(((................)))............(.((((.....)))).)....))))))))...((((((....)))))). (-20.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAAUGCCUUCCUCUUCAUUCCUUCGUAUGCGCUACCGAACAGCCCUCUUGAAAUGUGCUGAUAUGAUGGUUGGGGACAGUUAGAGAAGGAAUUCUUCA ..((((((.((((((((((((..((.((((((((((...(((.........)))....))))..)))))).)).))))))......).))))).)))))).. (-24.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 80 38 55 18 tfor:TF1868|5end_conserved_hypothetical_protein;_possible_transposase_2022598..2022828_POSITIVE 371 99 52 79 17 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 363 93 52 80 26 tfor:TF2244|5end_possible_mobilization_protein_2419425..2419655_POSITIVE 358 100 70 26 1 tfor:TF1415|5end_outer_membrane_protein,_TonB_dependent_receptor_1494268..1494498_POSITIVE 340 95 52 56 2 tfor:TF1844|5end_hypothetical_protein_1996389..1996619_POSITIVE 336 83 41 104 59 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 333 70 23 212 143 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 333 100 63 77 26 tfor:TF2371|5end_conserved_hypothetical_protein_2536974..2537204_POSITIVE 333 94 53 78 28 tfor:TF2048|5end_conserved_hypothetical_protein_2210643..2210873_POSITIVE 331 90 43 227 168 tfor:TF2524|5end_conserved_hypothetical_protein;_possible_endonuclease/exonuclease/phosphatase_family_protein_2702910..2703140_POSITIVE 330 95 54 61 16 tfor:TF1468|5end_beta-galactosidase_1557785..1558015_POSITIVE 329 94 56 110 67 tfor:TF2878|5end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3067304..3067534_POSITIVE 328 95 52 88 29 tfor:TF0697|5end_glycerol-3-phosphate_cytidyltransferase_740667..740897_POSITIVE 327 94 51 60 10 tfor:TF2369|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_2534554..2534784_POSITIVE 327 98 51 46 1 tfor:TF2309|5end_cysteinyl-tRNA_synthetase_2468892..2469122_POSITIVE 325 92 57 187 149 tfor:TF0325|5end_LysM_domain_protein_351917..352147_POSITIVE 322 94 51 69 18 tfor:TF1138|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1213863..1214093_POSITIVE 321 100 51 109 56 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 319 90 41 226 171 tfor:TF0555|5end_Bacteroides_aerotolerance_protein,_BatB_587048..587278_POSITIVE 318 95 51 140 90 tfor:TF0267|5end_conserved_hypothetical_protein_295803..296033_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 76 38 115 79 tfor:TF0279|3end_conserved_hypothetical_protein_308679..308829_POSITIVE 333 100 63 67 16 tfor:TF2370|3end_tRNA_delta-2_isopentenylpyrophosphate_transferase_2537044..2537194_POSITIVE 331 89 52 96 62 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE 328 95 52 82 23 tfor:TF0696|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_740741..740891_POSITIVE 321 100 51 119 66 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 310 96 53 64 17 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 310 70 21 48 9 tfor:TF1605|3end_outer_membrane_protein,_TonB_dependent_receptor_1722414..1722564_POSITIVE 309 85 43 149 94 tfor:TF2523|3end_NAD(P)H-flavin_oxidoreductase_2702916..2703066_POSITIVE 309 94 53 60 14 tfor:TF1936|3end_conserved_hypothetical_protein_2084549..2084699_POSITIVE 308 100 53 79 36 tfor:TF1903|3end_hypothetical_protein_2057627..2057777_POSITIVE 307 59 12 71 17 tfor:TF1067|3end_conserved_hypothetical_protein_1138116..1138266_POSITIVE 306 100 51 148 94 tfor:TF2208|3end_conserved_hypothetical_protein_2383988..2384138_POSITIVE 305 65 23 147 103 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 305 80 31 120 61 tfor:TF0573|3end_DNA_polymerase_III,_delta_subunit_604852..605002_POSITIVE 304 98 56 144 93 tfor:TF3102|3end_hypothetical_protein_3332969..3333119_POSITIVE 302 93 54 45 7 tfor:TF2243|3end_possible_mobilization_protein_2419470..2419620_POSITIVE 302 80 40 72 31 tfor:TF1755|3end_periplasmic_protease_1892867..1893017_POSITIVE 300 64 26 150 105 tfor:TF0793|3end_conserved_hypothetical_protein;_possible_AAA_superfamily_ATPase_851291..851441_POSITIVE 297 100 51 138 84 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 296 70 22 46 3 tfor:TF2129|3end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2306569..2306719_POSITIVE