Origin IGS: ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa .........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 tttaaacattggaatatcaatttggaaaaagaaaacaattaaatgaaatctcaagatagaaactaatattaagccttgtcctcaaggctttttaatatttcccactataccttttattcccaaacttgaacaatagcttgcaatcatttttttaaaatagtatactagggctaagctatggaatcgtttgcatagaatcacgatgagtttaaaaagtgaaatctaggag Mask Tandem Repeat Region ================================================ ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Find is-nt database================================================ Query_seq: SSA_1457:SSA_1458|SSA_1457:SSA_1458:Neopullulanase, putative:hypothetical protein:<-<-:1464330..1464558 229 ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1457:SSA_1458|SSA_1457:SSA_1458:Neopullulanase, putative:hypothetical protein:<-<-:1464330..1464558 229 ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1457:SSA_1458|SSA_1457:SSA_1458:Neopullulanase, putative:hypothetical protein:<-<-:1464330..1464558 229 ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 8 End: 145 ....... M S L F K L I V I L C K R F H S L A L V Y Y F K K M I A S Y C S S L G I K G I V G N I K K P .................................................................................... ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa 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: 81 Start: 64 End: 93 ...............................................................CTTGCAATCATTTTTTTAAAATAGTATACT........................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -9.0 Tail_Score: -4.93696 Start: 142 End: 157 Full_Region: agaaactaatattaa gccttg tcct caaggc tttttaatatttccc .............................................................................................................................................gccttgtcctcaaggc........................................................................ Find igs database================================================ Query_seq: SSA_1457:SSA_1458|SSA_1457:SSA_1458:Neopullulanase, putative:hypothetical protein:<-<-:1464330..1464558 229 ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 229 Len: 229 Subject: NC_009009_SSA_1457_SSA_1458|Neopullulanase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1464330,1464558]|229 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttnnnnnnntgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa ctcctagatttcactttttaaactcatcgtgattctatgcaaacgattccatagcttagccctagtatactattttaaaaaaatgattgcaagctattgttcaagtttgggaataaaaggtatagtgggaaatattaaaaagccttgaggacaaggcttaatattagtttctatcttgagatttcatttaattgttttctttttccaaattgatattccaatgtttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUAGAUUUCACUUUUUAAACUCAUCGUGAUUCUAUGCAAACGAUUCCAUAGCUUAGCCCUAGUAUACUAUUUUAAAAAAAUGAUUGCAAGCUAUUGUUCAAGUUUGGGAAUAAAAGGUAUAGUGGGAAAUAUUAAAAAGCCUUGAGGACAAGGCUUAAUAUUAGUUUCUAUCUUGAGAUUUCAUUUAAUUGUUUUCUUUUUCCAAAUUGAUAUUCCAAUGUUUAAA ................(((((((...........((((((.....(((((..((((((((..((((.....(((..........))).....))))..))).)))))..))))).....))))))..((((........((((((((....))))))))..(((((((((.......((((...((......))...)))).....)))))))))))))...))))))) (-42.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAACAUUGGAAUAUCAAUUUGGAAAAAGAAAACAAUUAAAUGAAAUCUCAAGAUAGAAACUAAUAUUAAGCCUUGUCCUCAAGGCUUUUUAAUAUUUCCCACUAUACCUUUUAUUCCCAAACUUGAACAAUAGCUUGCAAUCAUUUUUUUAAAAUAGUAUACUAGGGCUAAGCUAUGGAAUCGUUUGCAUAGAAUCACGAUGAGUUUAAAAAGUGAAAUCUAGGAG ........(((((...(((((((((.(((((............(((....)))..((((.....((((((((((((((....)))))))...))))))).....))))..)))))....))))).))))..............(((((((((.....((((........))))..(((((.((....)).)))))...............)))))))))..)))))... (-38.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 889 70 21 161 112 NC_009009:SSA_1457|5end_Neopullulanase,_putative_1464239..1464469_NEGATIVE 284 184 141 47 5 NC_009009:SSA_0517|5end_Sensor_histidine_kinase,_putative_515060..515290_POSITIVE 269 199 151 179 136 NC_009009:SSA_0381|5end_hypothetical_protein_372763..372993_POSITIVE 268 61 23 174 130 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 264 159 122 202 164 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 264 134 93 56 9 NC_009009:SSA_1257|5end_hypothetical_protein_1283867..1284097_NEGATIVE 264 158 124 77 43 NC_009009:SSA_0801|5end_Mur_ligase_family_protein,_putative_784117..784347_NEGATIVE 261 185 141 173 120 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 260 69 28 44 1 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 258 97 51 141 90 NC_009009:SSA_1671|5end_hypothetical_protein_1669304..1669534_POSITIVE 258 61 23 134 98 NC_009009:SSA_1188|5end_Ribonuclease_HII,_putative_1216819..1217049_NEGATIVE 258 67 24 138 88 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 258 90 41 108 43 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 254 147 101 210 164 NC_009009:SSA_2288|5end_Cadmium_resistance_transporter,_putative_2290461..2290691_POSITIVE 254 167 122 61 19 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 253 55 17 218 185 NC_009009:SSA_0192|5end_Acetate_kinase,_putative_192909..193139_POSITIVE 250 49 2 83 32 NC_009009:SSA_2261|5end_Transcriptional_repressor_(arginine_synthesis),_putative_2258666..2258896_NEGATIVE 247 207 166 90 48 NC_009009:SSA_2245|5end_RecA_protein,_putative_2241109..2241339_NEGATIVE 246 64 29 46 1 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 243 67 23 131 87 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 181 141 86 47 NC_009009:SSA_2296|3end_Transcriptional_regulator,_XRE_family,_putative_2298549..2298699_NEGATIVE 284 184 141 47 5 NC_009009:SSA_0516|3end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_515140..515290_POSITIVE 264 134 93 65 18 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 258 61 23 147 111 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 258 67 24 123 73 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE 258 90 41 111 46 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 254 167 122 71 29 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 243 66 22 95 51 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 243 67 23 54 10 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 236 50 6 135 86 NC_009009:SSA_0151|3end_hypothetical_protein_145871..146021_POSITIVE 232 99 51 149 97 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 228 170 141 37 4 NC_009009:SSA_1431|3end_hypothetical_protein_1438047..1438197_NEGATIVE 228 64 22 131 83 NC_009009:SSA_1237|3end_Uracil-DNA_glycosylase,_putative_1261713..1261863_NEGATIVE 227 160 119 52 12 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 227 129 84 72 20 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 223 205 167 117 82 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 222 152 119 60 18 NC_009009:SSA_2338|3end_Conserved_uncharacterized_protein_2340392..2340542_POSITIVE 222 68 23 137 83 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 222 69 24 69 21 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 221 57 23 150 115 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE