Origin IGS: atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt .........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 aatttgttaaaaaataaataaagtaagggtttacaatctgcgattgatatgctataatgaaatcagaaattgaatagggtgagcgttactaagttggattaggcgtgaccgcaaataaattgagggaagatatagcctcggtttgtttgtggtctttttcttttgccagaaccctagaaaatgaagaggaggagat Mask Tandem Repeat Region ================================================ atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Find is-nt database================================================ Query_seq: SSA_1695:SSA_1696|SSA_1695:SSA_1696:Transcriptional antiterminator, BglG/SacY family (induction of sugar metabolism), putative:Tagatose 1,6-diphosphate aldolase 2, putative:<-<-:1688101..1688296 196 atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1695:SSA_1696|SSA_1695:SSA_1696:Transcriptional antiterminator, BglG/SacY family (induction of sugar metabolism), putative:Tagatose 1,6-diphosphate aldolase 2, putative:<-<-:1688101..1688296 196 atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1695:SSA_1696|SSA_1695:SSA_1696:Transcriptional antiterminator, BglG/SacY family (induction of sugar metabolism), putative:Tagatose 1,6-diphosphate aldolase 2, putative:<-<-:1688101..1688296 196 atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 1 End: 105 M S S S S F S R V L A K E K D H K Q T E A I S S L N L F A V T P N P T ........................................................................................... Protein_Len: 30 Strand: - Start: 3 End: 92 .. E E E E N E L T R A F S F S W L C V S A I D E R L K N A T M ........................................................................................................ atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt 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: 88 Start: 139 End: 168 ..........................................................................................................................................GTTTACAATCTGCGATTGATATGCTATAAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.1 Tail_Score: -5.45802 Start: 43 End: 90 Full_Region: agttggattaggcgt gaccgcaaataaattgagg gaagatatag cctcggtttgtttgtggtc tttttcttttgccag ..........................................gaccgcaaataaattgagggaagatatagcctcggtttgtttgtggtc.......................................................................................................... Find igs database================================================ Query_seq: SSA_1695:SSA_1696|SSA_1695:SSA_1696:Transcriptional antiterminator, BglG/SacY family (induction of sugar metabolism), putative:Tagatose 1,6-diphosphate aldolase 2, putative:<-<-:1688101..1688296 196 atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: NC_009009_SSA_1695_SSA_1696|Transcriptional antiterminator, BglG/SacY family (induction of sugar metabolism), putative:Tagatose 1,6-diphosphate aldolase 2, putative|NEGATIVE:NEGATIVE|[1688101,1688296]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt atctcctcctcttcattttctagggttctggcaaaagaaaaagaccacaaacaaaccgaggctatatcttccctcaatttatttgcggtcacgcctaatccaacttagtaacgctcaccctattcaatttctgatttcattatagcatatcaatcgcagattgtaaacccttactttatttattttttaacaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUCCUCCUCUUCAUUUUCUAGGGUUCUGGCAAAAGAAAAAGACCACAAACAAACCGAGGCUAUAUCUUCCCUCAAUUUAUUUGCGGUCACGCCUAAUCCAACUUAGUAACGCUCACCCUAUUCAAUUUCUGAUUUCAUUAUAGCAUAUCAAUCGCAGAUUGUAAACCCUUACUUUAUUUAUUUUUUAACAAAUU ....................((((((...(((..........((((.((((.(((..((((..........))))..))).)))).))))....((((......))))....))).))))))..((((((.(((((...............))))).))))))................................. (-29.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUGUUAAAAAAUAAAUAAAGUAAGGGUUUACAAUCUGCGAUUGAUAUGCUAUAAUGAAAUCAGAAAUUGAAUAGGGUGAGCGUUACUAAGUUGGAUUAGGCGUGACCGCAAAUAAAUUGAGGGAAGAUAUAGCCUCGGUUUGUUUGUGGUCUUUUUCUUUUGCCAGAACCCUAGAAAAUGAAGAGGAGGAGAU .(((((((....)))))))......(((((......(((((((..((.(((((....((....))..((((.(((..(((((...)))))..))).)))).)))))(((((((((((((((((((..........)))))))))))))))))))....))..))).)))))))))..................... (-49.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 957 120 71 211 162 NC_009009:SSA_1695|5end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1688010..1688240_NEGATIVE 327 100 56 224 181 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 322 179 136 175 127 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 314 47 1 145 98 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 293 96 57 106 62 NC_009009:SSA_2240|5end_Holliday_junction_resolvase,_putative_2237677..2237907_NEGATIVE 290 117 72 224 186 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 288 126 81 60 15 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 284 157 111 138 90 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 281 49 2 115 68 NC_009009:SSA_1134|5end_Xanthine_phosphoribosyltransferase,_putative_1159628..1159858_POSITIVE 281 121 82 170 125 NC_009009:SSA_0136|5end_ABC_transporter,_Zn_porter,_putative_131014..131244_POSITIVE 276 29 3 187 160 NC_009009:SSA_1376|5end_Transport_protein,_putative_1396111..1396341_NEGATIVE 275 120 71 204 156 NC_009009:SSA_1196|5end_Acetyltransferase,_GNAT_family,_putative_1222052..1222282_NEGATIVE 274 97 56 53 14 NC_009009:SSA_1380|5end_hypothetical_protein_1399131..1399361_NEGATIVE 270 115 72 68 19 NC_009009:SSA_0921|5end_Zn-dependeant_threonine_dehydrogenase,_putative_931047..931277_POSITIVE 268 90 43 156 106 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 267 96 52 57 11 NC_009009:SSA_0581|5end_Conserved_uncharacterized_protein_573329..573559_POSITIVE 265 35 2 127 96 NC_009009:SSA_1073|5end_Gamma-glutamyl_phosphate_reductase,_putative_1090886..1091116_POSITIVE 264 120 84 166 114 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 263 33 1 121 97 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 262 96 51 219 169 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 47 1 148 101 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 293 96 57 106 62 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 288 126 81 59 14 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 282 96 58 106 79 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 281 49 2 72 25 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 276 29 3 30 3 NC_009009:SSA_1377|3end_Asparaginyl-tRNA_synthetase,_putative_1396268..1396418_NEGATIVE 267 96 52 47 1 NC_009009:SSA_0580|3end_Isochorismatase_family_protein,_putative_573399..573549_POSITIVE 265 35 2 105 74 NC_009009:SSA_1072|3end_Glutamate_5-kinase,_putative_1090944..1091094_POSITIVE 264 120 84 101 49 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 263 33 1 121 97 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 261 110 61 133 94 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 255 160 114 56 14 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 255 160 114 151 109 NC_009009:SSA_1600|3end_hypothetical_protein_1606497..1606647_NEGATIVE 254 35 4 106 64 NC_009009:SSA_2047|3end_hypothetical_protein_2049735..2049885_NEGATIVE 253 145 111 63 29 NC_009009:SSA_1850|3end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1845710..1845860_NEGATIVE 253 158 111 151 95 NC_009009:SSA_1021|3end_Conserved_uncharacterized_protein_1037270..1037420_POSITIVE 251 32 1 132 93 NC_009009:SSA_1999|3end_hypothetical_protein_1996411..1996561_NEGATIVE 251 106 61 149 115 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 248 33 2 146 116 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 247 121 84 46 11 NC_009009:SSA_1937|3end_Malonyl-CoA:ACP_transacylase,_putative_1923851..1924001_NEGATIVE