Origin IGS: tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtaaaataaggcacatcattattttcgtttttcggcaaaaagtaaaataaggcacatcattattttcgtttttcggcaaaaagtaagaaaaaataatttca Mask Tandem Repeat Region ================================================ tgaaattattttttcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Find is-nt database================================================ Query_seq: TF2056:TF2057|TF2056:TF2057:conserved hypothetical protein:hypothetical protein:->->:2222131..2222234 104 tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2056:TF2057|TF2056:TF2057:conserved hypothetical protein:hypothetical protein:->->:2222131..2222234 104 tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2056:TF2057|TF2056:TF2057:conserved hypothetical protein:hypothetical protein:->->:2222131..2222234 104 tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 5 End: 103 .... M I F S Y F L P K N E N N D V P Y F T F C R K T K I M M C L I L L . tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt 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================================================ tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2056:TF2057|TF2056:TF2057:conserved hypothetical protein:hypothetical protein:->->:2222131..2222234 104 tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: tfor_TF2056_TF2057|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2222131,2222234]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt tgaaattattttttcttactttttgccgaaaaacgaaaataatgatgtgccttattttactttttgccgaaaaacgaaaataatgatgtgccttattttacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAUUAUUUUUUCUUACUUUUUGCCGAAAAACGAAAAUAAUGAUGUGCCUUAUUUUACUUUUUGCCGAAAAACGAAAAUAAUGAUGUGCCUUAUUUUACUUU ....(((((((((((....((((((.((((((...(((((((.(.....).)))))))..)))))).))))))..))))).))))))................. (-12.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUAAAAUAAGGCACAUCAUUAUUUUCGUUUUUCGGCAAAAAGUAAAAUAAGGCACAUCAUUAUUUUCGUUUUUCGGCAAAAAGUAAGAAAAAAUAAUUUCA ........................(((((..((((..((..((((.(((((((.........)))))))...))))..))..))))...))))).......... ( -8.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 69 25 180 133 tfor:TF2636|5end_glutaminase_2806096..2806326_POSITIVE 239 70 21 204 149 tfor:TF2686|5end_ABC_transporter,_ATP-binding_protein_2862741..2862971_POSITIVE 230 49 10 108 69 tfor:TF1725|5end_hypothetical_protein_1851808..1852038_POSITIVE 228 69 24 125 70 tfor:TF0181|5end_ATP-dependent_DNA_helicase_192408..192638_POSITIVE 225 69 27 71 29 tfor:TF0766|5end_hypothetical_protein_811934..812164_POSITIVE 224 70 25 223 176 tfor:TF2388|5end_outer_membrane_protein,_TonB_dependent_receptor_2556000..2556230_POSITIVE 219 76 44 67 28 tfor:TF1237|5end_possible_L-fuculose_kinase_1322041..1322271_POSITIVE 218 70 24 48 3 tfor:TF0100|5end_conserved_hypothetical_protein_111135..111365_POSITIVE 215 69 24 209 169 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 214 70 21 207 150 tfor:TF1878|5end_ABC_transporter,_permease_component_2030561..2030791_POSITIVE 214 70 21 58 1 tfor:TF1877|5end_hypothetical_protein_2030412..2030642_POSITIVE 214 69 26 164 103 tfor:TF1822|5end_outer_membrane_lipoprotein_silC_precursor_1967599..1967829_POSITIVE 206 67 23 90 33 tfor:TF1828|5end_hypothetical_protein_1977049..1977279_POSITIVE 206 70 21 54 14 tfor:TF0336|5end_Xaa-Pro_aminopeptidase_360613..360843_POSITIVE 205 58 20 215 172 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 202 67 21 214 164 tfor:TF1837|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1985480..1985710_POSITIVE 201 68 21 212 164 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 200 70 24 61 14 tfor:TF1289|5end_ribosomal_protein_L11_methyltransferase_1370302..1370532_POSITIVE 200 93 54 150 95 tfor:TF0502|5end_acetylglutamate_kinase_527620..527850_POSITIVE 199 50 1 189 132 tfor:TF0782|5end_ThiJ/PfpI_family_protein_835976..836206_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 69 25 105 58 tfor:TF2635|3end_ABC_transporter,_ATP-binding_protein/permease_component_2806101..2806251_POSITIVE 239 70 21 108 53 tfor:TF2685|3end_iron-regulated_ABC-type_transporter_membrane_component_2862725..2862875_POSITIVE 236 68 21 151 95 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 233 52 20 134 101 tfor:TF0070|3end_possible_regulatory_element_77735..77885_POSITIVE 230 49 10 99 60 tfor:TF1724|3end_nitroreductase_family_protein_1851879..1852029_POSITIVE 228 69 24 117 62 tfor:TF0180|3end_carboxynorspermidine_decarboxylase_192480..192630_POSITIVE 225 69 27 71 29 tfor:TF0765|3end_conserved_hypothetical_protein_812014..812164_POSITIVE 219 76 44 52 13 tfor:TF1236|3end_L-rhamnose_isomerase_1322106..1322256_POSITIVE 217 70 27 87 38 tfor:TF2288|3end_hypothetical_protein_2442598..2442748_POSITIVE 214 69 26 130 69 tfor:TF1821|3end_cation_efflux_system_protein_1967645..1967795_POSITIVE 206 70 21 72 32 tfor:TF0337|3end_hypothetical_protein_360711..360861_POSITIVE 206 85 48 44 3 tfor:TF0181|3end_ATP-dependent_DNA_helicase_194863..195013_POSITIVE 205 58 20 100 57 tfor:TF1475|3end_glucose-6-phosphate_1-dehydrogenase_1569688..1569838_POSITIVE 203 76 31 72 17 tfor:TF0833|3end_conserved_hypothetical_protein_889052..889202_POSITIVE 199 70 27 104 60 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 199 50 1 137 80 tfor:TF0781|3end_serine_protease_inhibitor_836004..836154_POSITIVE 199 49 8 72 29 tfor:TF0077|3end_hypothetical_protein_84491..84641_POSITIVE 194 90 41 63 16 tfor:TF3026|3end_conserved_hypothetical_protein_3250254..3250404_POSITIVE 194 51 26 67 39 tfor:TF1506|3end_outer_membrane_receptor,_TonB-dependent_1614637..1614787_POSITIVE 192 76 34 116 78 tfor:TF2400|3end_conserved_hypothetical_protein_2573249..2573399_POSITIVE