Origin IGS: tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agttgtctaaccttataaaaggtagttgtttagccggcaaagatacgtctttttttctttttcttgtgtttctttatccaaatcccggagaattgtcatacctttga Mask Tandem Repeat Region ================================================ tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Find is-nt database================================================ Query_seq: TF0964:TF0965|TF0964:TF0965:conserved hypothetical protein:glycogen synthase:->->:1013437..1013543 107 tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0964:TF0965|TF0964:TF0965:conserved hypothetical protein:glycogen synthase:->->:1013437..1013543 107 tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0964:TF0965|TF0964:TF0965:conserved hypothetical protein:glycogen synthase:->->:1013437..1013543 107 tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 4 End: 105 ... * L Y S L E G P N P Y L F V L F L F F S T D K G A L C S G K I L N S M .. tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 67 End: 96 ..................................................................TTTGCCGGCTAAACAACTACCTTTTATAAG........... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0964:TF0965|TF0964:TF0965:conserved hypothetical protein:glycogen synthase:->->:1013437..1013543 107 tcaaaggtatgacaattctccgggatttggataaagaaacacaagaaaaagaaaaaaagacgtatctttgccggctaaacaactaccttttataaggttagacaact Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: tfor_TF0964_TF0965|conserved hypothetical protein:glycogen synthase|POSITIVE:POSITIVE|[1013437,1013543]|107 HSP 1 e-value: 7.0E-20 bit: 97.6 Len: 49 Query Start:59 Query End:107 Subject Strand: POSITIVE Subject Start: 59 Subject End: 107 ..........................................................gacgtatctttgccggctaaacaactaccttttataaggttagacaact ..........................................................gacgtatctttgccggctaaacaactaccttttataaggttagacaact HSP 2 e-value: 2.0E-17 bit: 89.7 Len: 45 Query Start:1 Query End:45 Subject Strand: POSITIVE Subject Start: 1 Subject End: 45 tcaaaggtatgacaattctccgggatttggataaagaaacacaag.............................................................. tcaaaggtatgacaattctccgggatttggataaagaaacacaag.............................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAGGUAUGACAAUUCUCCGGGAUUUGGAUAAAGAAACACAAGAAAAAGAAAAAAAGACGUAUCUUUGCCGGCUAAACAACUACCUUUUAUAAGGUUAGACAACU .((((((((((.(((.((.....)).)))..........(....)...............))))))))))............(((((((....)))).)))...... (-14.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUGUCUAACCUUAUAAAAGGUAGUUGUUUAGCCGGCAAAGAUACGUCUUUUUUUCUUUUUCUUGUGUUUCUUUAUCCAAAUCCCGGAGAAUUGUCAUACCUUUGA .................(((((((.....((..((((.(((((....)))))...........(((..(......)..)))...))))..))......))))))).. (-15.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 75 48 140 114 tfor:TF0710|5end_two_component_system_histidine_kinase_757250..757480_POSITIVE 272 75 40 110 79 tfor:TF1619|5end_riboflavin_synthase,_beta_subunit_1733948..1734178_POSITIVE 271 100 58 98 51 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 258 87 56 67 27 tfor:TF0835|5end_conserved_hypothetical_protein_888933..889163_POSITIVE 255 98 54 201 162 tfor:TF1473|5end_hypothetical_protein_1566341..1566571_POSITIVE 239 98 59 61 30 tfor:TF2950|5end_chloromuconate_cycloisomerase_3157399..3157629_POSITIVE 236 41 3 196 163 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 233 44 6 160 123 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 233 50 2 140 96 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 228 48 2 197 143 tfor:TF2981|5end_conserved_hypothetical_protein_3195969..3196199_POSITIVE 228 94 68 153 131 tfor:TF2685|5end_iron-regulated_ABC-type_transporter_membrane_component_2861191..2861421_POSITIVE 226 87 59 135 103 tfor:TF1910|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_2064001..2064231_POSITIVE 223 100 61 51 7 tfor:TF3151|5end_glyoxalase_family_protein_3386221..3386451_POSITIVE 220 45 2 146 113 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 220 97 59 78 38 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 220 97 59 66 26 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 217 100 61 211 171 tfor:TF2802|5end_possible_outer_membrane_protein_2989842..2990072_POSITIVE 217 41 2 62 31 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 215 45 2 211 176 tfor:TF3091|5end_50S_ribosomal_protein_L13_3324213..3324443_POSITIVE 215 90 47 159 117 tfor:TF1339|5end_aspartate_1-decarboxylase_1420908..1421138_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 75 36 74 34 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 286 76 33 98 53 tfor:TF2109|3end_possible_metallo-beta-lactamase_family_protein_2278960..2279110_POSITIVE 283 75 48 51 25 tfor:TF0709|3end_preprotein_translocase,_subunit_SecA_757241..757391_POSITIVE 271 100 58 90 43 tfor:TF1328|3end_possible_cytidylyltransferase_1408650..1408800_POSITIVE 258 87 56 106 66 tfor:TF0833|3end_conserved_hypothetical_protein_889052..889202_POSITIVE 255 98 54 117 78 tfor:TF1472|3end_acyl-ACP_thioesterase_1566337..1566487_POSITIVE 251 75 47 134 99 tfor:TF2162|3end_thermolysin_precursor_2340713..2340863_POSITIVE 239 98 59 61 30 tfor:TF2949|3end_dihydroxynaphthoate_synthase_(naphthoate_synthase)_3157479..3157629_POSITIVE 228 94 68 148 126 tfor:TF2684|3end_conserved_hypothetical_protein;_possible_CvpA_family_protein_2861266..2861416_POSITIVE 226 87 59 129 97 tfor:TF1909|3end_cobalamin_(5`-phosphate)_synthase_2064075..2064225_POSITIVE 225 79 45 84 40 tfor:TF0697|3end_glycerol-3-phosphate_cytidyltransferase_741265..741415_POSITIVE 220 45 2 139 106 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 217 41 2 62 31 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 216 70 25 83 42 tfor:TF2971|3end_possible_transposase_3179354..3179504_POSITIVE 216 70 25 83 42 tfor:TF1770|3end_hypothetical_protein_1908812..1908962_POSITIVE 215 45 2 58 23 tfor:TF3089|3end_ISPg2_(PGIS2)_transposase_3324140..3324290_POSITIVE 215 90 47 86 44 tfor:TF1337|3end_multidrug_efflux_pump,_BexA_1420915..1421065_POSITIVE 215 75 40 53 21 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 214 81 61 106 84 tfor:TF2455|3end_conserved_hypothetical_protein;_possible_membrane_protein_2632437..2632587_POSITIVE 212 79 53 66 34 tfor:TF1436|3end_phosphoglycolate_phosphatase_1521867..1522017_POSITIVE