Origin IGS: tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tggggcgtatctatggaatccccgttagtgtttttattttttctcctatcgcaagtaatacaaagggtttcgcagtggttgcaagatttttctattttcattctatccatatttattgcgtactttgtatattcctttgcttactttgcgattaaaacctttcaccgcaagaggtggtcgctatgaaatca Mask Tandem Repeat Region ================================================ tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Find is-nt database================================================ Query_seq: TF2609:TF2610|TF2609:TF2610:dipeptidase, pathogenicity island-encoded protein D:nitroreductase:->->:2786325..2786515 191 tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2609:TF2610|TF2609:TF2610:dipeptidase, pathogenicity island-encoded protein D:nitroreductase:->->:2786325..2786515 191 tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2609:TF2610|TF2609:TF2610:dipeptidase, pathogenicity island-encoded protein D:nitroreductase:->->:2786325..2786515 191 tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 76 End: 189 ........................................................................... M N M D R M K I E K S C N H C E T L C I T C D R R K N K N T N G D S I D T P .. Protein_Len: 48 Strand: - Start: 40 End: 183 ....................................... D C L L C L F I C L V C Y I H I S H F Y F F R A V V A F G K T N S A I P S F I F V S V P I G Y M ........ Protein_Len: 57 Strand: - Start: 9 End: 179 ........ L S W R K R H F T K I A F Y A F S Y V F Y A I F I S L I F I S F D Q L W Q S V R Q I V Q S L L F F L F V L P S E M ............ Protein_Len: 35 Strand: - Start: 2 End: 106 . I E Y R G G R A T F P K L R L T L L P I Y L T R L L Y P Y F S F L F M ..................................................................................... tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca 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================================================ tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2609:TF2610|TF2609:TF2610:dipeptidase, pathogenicity island-encoded protein D:nitroreductase:->->:2786325..2786515 191 tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: tfor_TF2609_TF2610|dipeptidase, pathogenicity island-encoded protein D:nitroreductase|POSITIVE:POSITIVE|[2786325,2786515]|191 HSP 1 e-value: 7.0E-83 bit: 307.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagnnnnnnnnnnnncactaacggggattccatagatacgcccca tgatttcatagcgaccacctcttgcggtgaaaggttttaatcgcaaagtaagcaaaggaatatacaaagtacgcaataaatatggatagaatgaaaatagaaaaatcttgcaaccactgcgaaaccctttgtattacttgcgataggagaaaaaataaaaacactaacggggattccatagatacgcccca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUCAUAGCGACCACCUCUUGCGGUGAAAGGUUUUAAUCGCAAAGUAAGCAAAGGAAUAUACAAAGUACGCAAUAAAUAUGGAUAGAAUGAAAAUAGAAAAAUCUUGCAACCACUGCGAAACCCUUUGUAUUACUUGCGAUAGGAGAAAAAAUAAAAACACUAACGGGGAUUCCAUAGAUACGCCCCA ...((((((.((((.......)))).))))))..(((..(((((((.(((((((((((................................((....)).........(((((.....)))))...))))))).)))))))))))..)))...................((((..((....))....)))). (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGGGCGUAUCUAUGGAAUCCCCGUUAGUGUUUUUAUUUUUUCUCCUAUCGCAAGUAAUACAAAGGGUUUCGCAGUGGUUGCAAGAUUUUUCUAUUUUCAUUCUAUCCAUAUUUAUUGCGUACUUUGUAUAUUCCUUUGCUUACUUUGCGAUUAAAACCUUUCACCGCAAGAGGUGGUCGCUAUGAAAUCA .((((....((....))..))))..(((((.................(((((((((((..(((((((....((((.((((((((...............................))))).)))))))....))))))).)))).))))))).........(((((......))))).)))))........ (-40.48) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 59 11 63 22 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 354 46 10 113 69 tfor:TF1312|5end_hypothetical_protein_1388465..1388695_POSITIVE 354 46 10 113 69 tfor:TF1311|5end_hypothetical_protein_1388242..1388472_POSITIVE 333 46 10 113 69 tfor:TF1310|5end_hypothetical_protein_1388019..1388249_POSITIVE 333 150 107 41 1 tfor:TF1259|5end_hypothetical_protein_1338549..1338779_POSITIVE 324 49 1 173 116 tfor:TF3110|5end_conserved_hypothetical_protein_with_helicase_domain_3342714..3342944_POSITIVE 321 58 11 71 19 tfor:TF1592|5end_hypothetical_protein_1708325..1708555_POSITIVE 321 58 11 71 19 tfor:TF1590|5end_hypothetical_protein_1705811..1706041_POSITIVE 321 69 22 43 1 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 306 57 12 118 67 tfor:TF0947|5end_extracellular_protease_990627..990857_POSITIVE 304 44 10 207 172 tfor:TF2206|5end_conserved_hypothetical_protein;_possible_sugar_phosphate_isomerase/epimerase_2379969..2380199_POSITIVE 294 53 11 229 184 tfor:TF2777|5end_hypothetical_protein_2961595..2961825_POSITIVE 294 53 11 104 59 tfor:TF2776|5end_hypothetical_protein_2961470..2961700_POSITIVE 289 190 142 127 72 tfor:TF2712|5end_glycosyltransferase_2885918..2886148_POSITIVE 282 70 21 201 143 tfor:TF3146|5end_GTP-binding_protein_Obg_3381852..3382082_POSITIVE 276 59 11 147 78 tfor:TF3038|5end_conserved_hypothetical_protein_3264331..3264561_POSITIVE 269 43 7 180 140 tfor:TF2466|5end_pyruvate_kinase_2644385..2644615_POSITIVE 264 143 106 70 30 tfor:TF0379|5end_conserved_hypothetical_protein,_nif3_family_399458..399688_POSITIVE 263 88 41 204 153 tfor:TF0291|5end_triose-phosphate_isomerase_319299..319529_POSITIVE 261 53 19 37 4 tfor:TF1217|5end_hypothetical_protein_1303825..1304055_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 46 10 126 82 tfor:TF1311|3end_hypothetical_protein_1388558..1388708_POSITIVE 354 46 10 126 82 tfor:TF1310|3end_hypothetical_protein_1388335..1388485_POSITIVE 333 46 10 126 82 tfor:TF1312|3end_hypothetical_protein_1388781..1388931_POSITIVE 306 57 12 109 58 tfor:TF0946|3end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_990698..990848_POSITIVE 295 56 11 151 104 tfor:TF0343|3end_hypothetical_protein_366923..367073_POSITIVE 290 110 70 93 44 tfor:TF1303|3end_conserved_hypothetical_protein_1384698..1384848_POSITIVE 289 190 142 134 79 tfor:TF2711|3end_hemolysis_secretion_protein_2886005..2886155_POSITIVE 288 54 17 101 69 tfor:TF3141|3end_NADH:_ubiquinone_oxidoreductase,_subunit_A_3376267..3376417_POSITIVE 287 47 7 55 7 tfor:TF2613|3end_conserved_hypothetical_protein_2789798..2789948_POSITIVE 282 70 21 91 33 tfor:TF3145|3end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381822..3381972_POSITIVE 266 50 6 61 11 tfor:TF0356|3end_transposase_element_374096..374246_POSITIVE 264 143 106 52 12 tfor:TF0378|3end_aspartyl-tRNA_synthetase_399520..399670_POSITIVE 263 147 110 66 21 tfor:TF0323|3end_NAD-dependent_epimerase/dehydratase_family_protein_351053..351203_POSITIVE 261 53 19 34 1 tfor:TF1216|3end_possible_ECF-family_RNA_polymerase_sigma_factor_1303902..1304052_POSITIVE 258 69 21 49 6 tfor:TF0181|3end_ATP-dependent_DNA_helicase_194863..195013_POSITIVE 254 34 7 59 28 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 251 190 141 51 3 tfor:TF2973|3end_transposase_3180181..3180331_POSITIVE 251 150 110 60 9 tfor:TF2434|3end_conserved_hypothetical_protein_2614363..2614513_POSITIVE 251 190 141 72 24 tfor:TF1772|3end_ISPg4-related_transposase_(IS5_family)_1909660..1909810_POSITIVE 249 44 11 54 14 tfor:TF2322|3end_conserved_hypothetical_protein;_possible_lipoprotein_2483785..2483935_POSITIVE