Origin IGS: atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacctgaattgcaagtacacccaaacgcagcatgccgtggaacatttgtcctatccggcacggttcgtgttcaagattctgctacttgggatatggtatcttagtgtcaaaaacgatcaaataaagtcataaccatataggatgaagat Mask Tandem Repeat Region ================================================ atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Find is-nt database================================================ Query_seq: TF1228:TF1229|TF1228:TF1229:conserved hypothetical protein:hypothetical protein:->->:1314609..1314758 150 atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1228:TF1229|TF1228:TF1229:conserved hypothetical protein:hypothetical protein:->->:1314609..1314758 150 atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1228:TF1229|TF1228:TF1229:conserved hypothetical protein:hypothetical protein:->->:1314609..1314758 150 atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 49 End: 141 ................................................ S V M D W T A S D Q V R V T G S L V F T G R C A A N P H V Q M ......... Protein_Len: 38 Strand: - Start: 29 End: 142 ............................ K I T K S V L I G Y G L Y C F R S C S G H R I P C I N W P M S R K P T S A M ........ Protein_Len: 42 Strand: - Start: 21 End: 146 .................... S K I Q D N K V S L Y W I G L L L I K F V F R A P Y S L H E V A H Q T Q T Y K C N M .... atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta 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================================================ atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1228:TF1229|TF1228:TF1229:conserved hypothetical protein:hypothetical protein:->->:1314609..1314758 150 atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: tfor_TF1228_TF1229|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1314609,1314758]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta atcttcatcctatatggttatgactttatttgatcgtttttgacactaagataccatatcccaagtagcagaatcttgaacacgaaccgtgccggataggacaaatgttccacggcatgctgcgtttgggtgtacttgcaattcaggtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUCAUCCUAUAUGGUUAUGACUUUAUUUGAUCGUUUUUGACACUAAGAUACCAUAUCCCAAGUAGCAGAAUCUUGAACACGAACCGUGCCGGAUAGGACAAAUGUUCCACGGCAUGCUGCGUUUGGGUGUACUUGCAAUUCAGGUUA ........(((.((((((.....(((....((.(((....)))))..)))..))))))...((((((.((....((..(((.((...(((((((....((((....))))..))))))).)).)))..))))))))))......)))... (-33.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCUGAAUUGCAAGUACACCCAAACGCAGCAUGCCGUGGAACAUUUGUCCUAUCCGGCACGGUUCGUGUUCAAGAUUCUGCUACUUGGGAUAUGGUAUCUUAGUGUCAAAAACGAUCAAAUAAAGUCAUAACCAUAUAGGAUGAAGAU ...((((.............(((((..((((..(((((.(((.(....))))....)))))....((........))..))))...))))).((((((..(((..((((......)).))....))).....))))))))))........ (-28.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 130 87 226 180 tfor:TF0620|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_654711..654941_POSITIVE 396 140 91 209 165 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 384 139 92 119 67 tfor:TF0122|5end_hypothetical_protein_133162..133392_POSITIVE 374 130 83 82 16 tfor:TF2341|5end_hypothetical_protein_2505735..2505965_POSITIVE 374 122 81 67 19 tfor:TF2290|5end_ABC_transporter,_ATP-binding/permease_component_2443942..2444172_POSITIVE 361 130 83 124 79 tfor:TF2008|5end_DNA_polymerase_I_2159302..2159532_POSITIVE 356 139 91 62 5 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 355 139 91 81 33 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 353 140 93 214 159 tfor:TF0225|5end_iron-containing_alcohol_dehydrogenase_251477..251707_POSITIVE 349 139 92 187 122 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 347 118 74 217 158 tfor:TF1246|5end_protease,_with_chaperone_function_1329390..1329620_POSITIVE 347 130 87 49 3 tfor:TF0946|5end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_989482..989712_POSITIVE 344 123 83 204 160 tfor:TF2886|5end_RNA_methylase_SpoU_family_3075651..3075881_POSITIVE 344 129 81 117 45 tfor:TF0480|5end_ornithine_carbamoyltransferase_498550..498780_POSITIVE 343 124 81 201 160 tfor:TF2390|5end_conserved_hypothetical_protein_2560509..2560739_POSITIVE 341 124 82 60 9 tfor:TF0301|5end_outer_membrane_protein,_TonB_dependent_receptor_325457..325687_POSITIVE 340 127 82 224 180 tfor:TF2392|5end_alpha-galactosidase_2563384..2563614_POSITIVE 339 129 83 50 9 tfor:TF2174|5end_possible_endopeptidase_precursor_2346292..2346522_POSITIVE 338 134 93 181 145 tfor:TF2085|5end_D-alanyl-D-alanine_carboxypeptidase_2252043..2252273_POSITIVE 337 100 53 105 53 tfor:TF0874|5end_transposase_925685..925915_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 139 92 94 42 tfor:TF0121|3end_hypothetical_protein_133217..133367_POSITIVE 374 122 81 49 1 tfor:TF2289|3end_secretion_protein,_possible_HlyD_family_2444004..2444154_POSITIVE 361 130 83 69 24 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 356 140 91 60 11 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 355 139 91 78 30 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 344 129 81 114 42 tfor:TF0478|3end_conserved_hypothetical_protein_498627..498777_POSITIVE 341 124 82 64 13 tfor:TF0300|3end_hypothetical_protein_325541..325691_POSITIVE 338 134 93 99 63 tfor:TF2083|3end_conserved_hypothetical_protein_2252041..2252191_POSITIVE 334 128 88 41 2 tfor:TF0496|3end_conserved_hypothetical_protein_523869..524019_POSITIVE 333 122 84 51 3 tfor:TF0835|3end_conserved_hypothetical_protein_889366..889516_POSITIVE 328 130 83 64 18 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 326 130 83 63 1 tfor:TF0276|3end_hypothetical_protein_300982..301132_POSITIVE 322 126 83 59 24 tfor:TF0372|3end_transcriptional_regulator_391118..391268_POSITIVE 321 138 91 151 92 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE 321 139 94 50 1 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 321 138 91 52 1 tfor:TF0418|3end_possible_methyl-accepting_chemotaxis_protein_435326..435476_POSITIVE 320 92 51 128 90 tfor:TF0302|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_329611..329761_POSITIVE 318 140 92 147 96 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 317 130 87 129 68 tfor:TF3086|3end_conserved_hypothetical_protein_3319949..3320099_POSITIVE 312 128 86 74 17 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE