Origin IGS: taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattacaattgttttatgttactaatcgaacgcaaatatacgaatatttcgtagtattggcacgaaaatgatgttaaaaaatgttgttggttgatgtttttttcgtatcgcccgtgaagaagtta Mask Tandem Repeat Region ================================================ taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Find is-nt database================================================ Query_seq: TF1352:TF1353|TF1352:TF1353:polysaccharide deacetylase-like protein:conserved hypothetical protein; possible penicillinase repressor:->->:1432923..1433047 125 taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1352:TF1353|TF1352:TF1353:polysaccharide deacetylase-like protein:conserved hypothetical protein; possible penicillinase repressor:->->:1432923..1433047 125 taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1352:TF1353|TF1352:TF1353:polysaccharide deacetylase-like protein:conserved hypothetical protein; possible penicillinase repressor:->->:1432923..1433047 125 taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 31 End: 120 .............................. M N Q Q H F L T S F S C Q Y Y E I F V Y L R S I S N I K Q L * ..... taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc 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================================================ taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1352:TF1353|TF1352:TF1353:polysaccharide deacetylase-like protein:conserved hypothetical protein; possible penicillinase repressor:->->:1432923..1433047 125 taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: tfor_TF1352_TF1353|polysaccharide deacetylase-like protein:conserved hypothetical protein; possible penicillinase repressor|POSITIVE:POSITIVE|[1432923,1433047]|125 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 taacttcttcacgggcgatacgnnnnnnncatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc taacttcttcacgggcgatacgaaaaaaacatcaaccaacaacattttttaacatcattttcgtgccaatactacgaaatattcgtatatttgcgttcgattagtaacataaaacaattgtaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUCUUCACGGGCGAUACGAAAAAAACAUCAACCAACAACAUUUUUUAACAUCAUUUUCGUGCCAAUACUACGAAAUAUUCGUAUAUUUGCGUUCGAUUAGUAACAUAAAACAAUUGUAAUC ...........((((((.((((((((...............................))))))))..((((.(((((.....)))))))))..)))))).......................... (-14.38) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUACAAUUGUUUUAUGUUACUAAUCGAACGCAAAUAUACGAAUAUUUCGUAGUAUUGGCACGAAAAUGAUGUUAAAAAAUGUUGUUGGUUGAUGUUUUUUUCGUAUCGCCCGUGAAGAAGUUA (((((.(((........)))..)))))...(((.....(((((.....))))).....((((((((((.((((((((..(((...)))..)))))))).)))))))...))).)))......... (-21.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 95 57 86 44 tfor:TF2367|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_2532002..2532232_POSITIVE 284 95 59 158 123 tfor:TF1928|5end_conserved_hypothetical_protein_2075529..2075759_POSITIVE 271 99 58 153 117 tfor:TF2042|5end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2201647..2201877_POSITIVE 271 102 71 141 109 tfor:TF0766|5end_hypothetical_protein_811934..812164_POSITIVE 256 108 61 49 7 tfor:TF0601|5end_aminomethyltransferase_(glycine_cleavage_system_T_protein)_631081..631311_POSITIVE 251 100 54 221 183 tfor:TF2053|5end_glycosyltransferase_2217102..2217332_POSITIVE 250 109 63 185 132 tfor:TF0036|5end_beta-hexosaminidase_precursor_35821..36051_POSITIVE 243 99 62 151 114 tfor:TF2409|5end_hypothetical_protein_2582972..2583202_POSITIVE 238 104 61 216 173 tfor:TF1435|5end_acetate_coenzyme_A_transferase_1519574..1519804_POSITIVE 238 100 61 208 170 tfor:TF0623|5end_type_II_DNA_modification_enzyme;_methyltransferase_656810..657040_POSITIVE 238 100 61 48 10 tfor:TF0622|5end_hypothetical_protein_656650..656880_POSITIVE 237 99 51 146 107 tfor:TF0288|5end_conserved_hypothetical_protein_317474..317704_POSITIVE 231 99 61 113 80 tfor:TF1174|5end_ABC_transporter,_permease_component_1256584..1256814_POSITIVE 228 109 62 96 45 tfor:TF0371|5end_beta-mannosidase_precursor_386763..386993_POSITIVE 221 99 55 190 148 tfor:TF0674|5end_transposase_fragment_717199..717429_POSITIVE 221 110 61 147 99 tfor:TF0225|5end_iron-containing_alcohol_dehydrogenase_251477..251707_POSITIVE 220 100 57 158 113 tfor:TF1250|5end_possible_cation_efflux_pump_1332324..1332554_POSITIVE 220 88 47 154 102 tfor:TF0156|5end_conserved_hypothetical_protein_164973..165203_POSITIVE 219 100 61 120 82 tfor:TF0884|5end_hypothetical_protein_937603..937833_POSITIVE 219 106 61 195 150 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 95 59 151 116 tfor:TF1927|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075602..2075752_POSITIVE 282 56 13 124 70 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 271 99 58 79 43 tfor:TF2041|3end_conserved_hypothetical_protein_2201653..2201803_POSITIVE 271 102 71 141 109 tfor:TF0765|3end_conserved_hypothetical_protein_812014..812164_POSITIVE 270 71 32 69 28 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 259 108 61 87 28 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 256 108 61 49 7 tfor:TF0600|3end_oxidoreductase/dehydrogenase_631161..631311_POSITIVE 243 99 62 71 34 tfor:TF2408|3end_conserved_hypothetical_protein;_possible_sugar_transferase_2582972..2583122_POSITIVE 240 108 62 104 59 tfor:TF2152|3end_uronate_isomerase_2328061..2328211_POSITIVE 238 100 61 48 10 tfor:TF0621|3end_phosphate_starvation-inducible_protein,_PhoH_656730..656880_POSITIVE 237 99 51 59 20 tfor:TF0287|3end_peptidase,_M23_family_317467..317617_POSITIVE 231 99 61 100 67 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 229 68 28 52 6 tfor:TF2285|3end_hypothetical_protein_2441024..2441174_POSITIVE 225 100 51 151 106 tfor:TF1434|3end_transketolase_1519595..1519745_POSITIVE 221 110 61 137 89 tfor:TF0224|3end_N-acetylglucosamine-6-phosphate_deacetylase_251547..251697_POSITIVE 220 100 57 110 65 tfor:TF1249|3end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1332356..1332506_POSITIVE 218 99 54 113 73 tfor:TF2857|3end_conserved_hypothetical_protein_3044379..3044529_POSITIVE 218 120 75 58 5 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 218 108 63 87 24 tfor:TF2001|3end_conserved_hypothetical_protein_2155931..2156081_POSITIVE 217 109 64 86 29 tfor:TF0793|3end_conserved_hypothetical_protein;_possible_AAA_superfamily_ATPase_851291..851441_POSITIVE