Origin IGS: caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatgatcatataatatccggctacaagtttagaacatattttccatgtatgcaaattttccaagttaaaaaaatgaccaacaacaactttagttaacttttttattacatatcctcatcccgaacaatatcactgagccgggacctg Mask Tandem Repeat Region ================================================ caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Find is-nt database================================================ Query_seq: TF1090:TF1091|TF1090:TF1091:hypothetical protein:conserved hypothetical protein:->->:1159421..1159568 148 caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1090:TF1091|TF1090:TF1091:hypothetical protein:conserved hypothetical protein:->->:1159421..1159568 148 caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1090:TF1091|TF1090:TF1091:hypothetical protein:conserved hypothetical protein:->->:1159421..1159568 148 caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 43 End: 147 .......................................... M K K L T K V V V G H F F N L E N L H T W K I C S K L V A G Y Y M I I . caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat 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================================================ caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1090:TF1091|TF1090:TF1091:hypothetical protein:conserved hypothetical protein:->->:1159421..1159568 148 caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: tfor_TF1090_TF1091|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1159421,1159568]|148 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcannnnnnnaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat caggtcccggctcagtgatattgttcgggatgaggatatgtaataaaaaagttaactaaagttgttgttggtcatttttttaacttggaaaatttgcatacatggaaaatatgttctaaacttgtagccggatattatatgatcatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGUCCCGGCUCAGUGAUAUUGUUCGGGAUGAGGAUAUGUAAUAAAAAAGUUAACUAAAGUUGUUGUUGGUCAUUUUUUUAACUUGGAAAAUUUGCAUACAUGGAAAAUAUGUUCUAAACUUGUAGCCGGAUAUUAUAUGAUCAUAU ........((.(((...(((.(((((((.(..((..(((((((.....(((((((..(((((.(........)))))).))))))).......)))))))..(((((......)))))..))..)..))))))).))).))))).... (-27.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGAUCAUAUAAUAUCCGGCUACAAGUUUAGAACAUAUUUUCCAUGUAUGCAAAUUUUCCAAGUUAAAAAAAUGACCAACAACAACUUUAGUUAACUUUUUUAUUACAUAUCCUCAUCCCGAACAAUAUCACUGAGCCGGGACCUG ................(((((((...(((......(((((.......)))))..........(((((((..(((((........))..)))..)))))))................................))).)))))))..... (-18.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 35 1 127 96 tfor:TF0480|5end_ornithine_carbamoyltransferase_498550..498780_POSITIVE 299 35 2 76 37 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 295 34 1 49 8 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 282 36 1 57 13 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 281 42 3 142 102 tfor:TF2460|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2636757..2636987_POSITIVE 279 37 3 69 27 tfor:TF1200|5end_conserved_hypothetical_protein_1282717..1282947_POSITIVE 278 45 8 179 139 tfor:TF0623|5end_type_II_DNA_modification_enzyme;_methyltransferase_656810..657040_POSITIVE 274 34 1 28 2 tfor:TF2643|5end_possible_O-antigen_transporter_2811744..2811974_POSITIVE 269 35 3 113 77 tfor:TF2345|5end_dGTP_triphosphohydrolase_2508372..2508602_POSITIVE 269 42 1 204 173 tfor:TF1945|5end_glycerate_dehydrogenase_2093229..2093459_POSITIVE 267 33 1 57 25 tfor:TF2399|5end_precorrin-2_methyltransferase_2571250..2571480_POSITIVE 266 34 1 212 181 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 265 132 95 163 126 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 265 28 1 168 136 tfor:TF0719|5end_hypothetical_protein_769798..770028_POSITIVE 264 28 5 147 122 tfor:TF1810|5end_conserved_hypothetical_protein;_possible_membrane_protein_1950490..1950720_POSITIVE 262 28 1 37 13 tfor:TF1936|5end_conserved_hypothetical_protein_2083984..2084214_POSITIVE 261 33 4 221 177 tfor:TF2314|5end_conserved_hypothetical_protein_2473530..2473760_POSITIVE 261 35 4 184 161 tfor:TF1887|5end_hypothetical_protein_2040301..2040531_POSITIVE 261 36 1 59 13 tfor:TF0349|5end_hypothetical_protein_370367..370597_POSITIVE 260 36 1 113 75 tfor:TF1049|5end_cobyrinic_acid_a,c-diamide_synthase_1110140..1110370_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 36 1 52 8 tfor:TF0358|3end_hypothetical_protein_376304..376454_POSITIVE 309 40 1 140 103 tfor:TF0436|3end_conserved_hyothetical_protein_460828..460978_POSITIVE 305 35 1 124 93 tfor:TF0478|3end_conserved_hypothetical_protein_498627..498777_POSITIVE 294 50 1 79 12 tfor:TF2170|3end_hypothetical_protein_2345070..2345220_POSITIVE 282 36 1 57 13 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 279 37 3 69 27 tfor:TF1199|3end_dephospho-CoA_kinase_1282797..1282947_POSITIVE 278 42 1 67 13 tfor:TF0368|3end_hypothetical_protein_385834..385984_POSITIVE 274 34 1 31 5 tfor:TF2642|3end_acetylornithine_deacetylase_2811827..2811977_POSITIVE 269 35 3 95 59 tfor:TF2344|3end_ATP/GTP_binding_protein_2508434..2508584_POSITIVE 266 70 26 130 87 tfor:TF1015|3end_conserved_hypothetical_protein_1074115..1074265_POSITIVE 264 28 5 137 112 tfor:TF1808|3end_DNA_processing_protein_subunit_A_1950560..1950710_POSITIVE 262 28 1 52 28 tfor:TF1934|3end_hypothetical_protein_2084079..2084229_POSITIVE 261 35 4 144 121 tfor:TF1886|3end_auxin-regulated_protein_2040341..2040491_POSITIVE 261 36 1 59 13 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 260 36 1 110 72 tfor:TF1048|3end_permease_1110217..1110367_POSITIVE 260 40 3 48 19 tfor:TF0038|3end_conserved_hypothetical_protein_41213..41363_POSITIVE 259 45 7 141 105 tfor:TF0944|3end_TonB-dependent_receptor_988399..988549_POSITIVE 259 50 1 80 11 tfor:TF0342|3end_hypothetical_protein_366643..366793_POSITIVE 254 45 1 79 17 tfor:TF2426|3end_conserved_hypothetical_protein;_possible_TonB_receptor_2605931..2606081_POSITIVE 254 40 1 40 8 tfor:TF1649|3end_hypothetical_protein_1760119..1760269_POSITIVE