Origin IGS: acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact .........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 agttttcctccaaagattgaatttttagcactctaaactatcgagtgctaatctatagttattattttatcacttggtcagaaatagtcaagaaaaaaaccggctagatgaaagaaaaattttattttttcttcacttggtcctaaactcaaaaaaacaagtccgagctaaaatcctctcagacttgtctttagggggaatgt Mask Tandem Repeat Region ================================================ acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Find is-nt database================================================ Query_seq: SSA_0224:SSA_0225|SSA_0224:SSA_0225:hypothetical protein:10 kDa chaperonin:->->:218579..218781 203 acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0224:SSA_0225|SSA_0224:SSA_0225:hypothetical protein:10 kDa chaperonin:->->:218579..218781 203 acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0224:SSA_0225|SSA_0224:SSA_0225:hypothetical protein:10 kDa chaperonin:->->:218579..218781 203 acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: - Start: 2 End: 130 . M G G L S L D S L I K A R V Q K K S N L V L H L F F L I K R E D L R N K E Q S N R V M ......................................................................... acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact 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================================================ acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 51 HP_score: -3.6 Tail_Score: -3.34715 Start: 17 End: 46 Full_Region: ctaaactcaaaaaaa caagtccgag ctaaaatcct ctcagacttg tctttagggggaatg ................caagtccgagctaaaatcctctcagacttg............................................................................................................................................................. TransTerm Strand: + Conf: 51 HP_score: -2.8 Tail_Score: -3.83205 Start: 73 End: 90 Full_Region: TTAGGACCAAGTGAA GAAAAA ATAAAA TTTTTC TTTCATCTAGCCGGT ........................................................................GAAAAAATAAAATTTTTC................................................................................................................. TransTerm Strand: - Conf: 45 HP_score: -2.8 Tail_Score: -3.21695 Start: 73 End: 90 Full_Region: accggctagatgaaa gaaaaa ttttat tttttc ttcacttggtcctaa ........................................................................gaaaaattttattttttc................................................................................................................. Find igs database================================================ Query_seq: SSA_0224:SSA_0225|SSA_0224:SSA_0225:hypothetical protein:10 kDa chaperonin:->->:218579..218781 203 acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_009009_SSA_0224_SSA_0225|hypothetical protein:10 kDa chaperonin|POSITIVE:POSITIVE|[218579,218781]|203 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 acattccccctaaagacaagtctgagaggattttagctcggacttgnnnnnnngagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggnnnnnnncttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact acattccccctaaagacaagtctgagaggattttagctcggacttgtttttttgagtttaggaccaagtgaagaaaaaataaaatttttctttcatctagccggtttttttcttgactatttctgaccaagtgataaaataataactatagattagcactcgatagtttagagtgctaaaaattcaatctttggaggaaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUCCCCCUAAAGACAAGUCUGAGAGGAUUUUAGCUCGGACUUGUUUUUUUGAGUUUAGGACCAAGUGAAGAAAAAAUAAAAUUUUUCUUUCAUCUAGCCGGUUUUUUUCUUGACUAUUUCUGACCAAGUGAUAAAAUAAUAACUAUAGAUUAGCACUCGAUAGUUUAGAGUGCUAAAAAUUCAAUCUUUGGAGGAAAACU ...((((.((.(((((((((((((((..(....)..)))))))))))))))((((((((.((.....(((((((((((......)))))).)))))....)).(((((...((((............))))....)))))............(((((((((.........))))))))))))))))).....)).)))).... (-52.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUCCUCCAAAGAUUGAAUUUUUAGCACUCUAAACUAUCGAGUGCUAAUCUAUAGUUAUUAUUUUAUCACUUGGUCAGAAAUAGUCAAGAAAAAAACCGGCUAGAUGAAAGAAAAAUUUUAUUUUUUCUUCACUUGGUCCUAAACUCAAAAAAACAAGUCCGAGCUAAAAUCCUCUCAGACUUGUCUUUAGGGGGAAUGU ....(((((((((((.((((....(((((((((.........))))))))).....................(((((..(....)..))))).........((((((.((((.((((((......)))))))))).))))))......))))....(((((((.(((..........))).))))))))))).)))))))... (-53.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 124 84 118 69 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 304 54 17 162 109 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 303 135 104 60 27 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 298 50 3 81 35 NC_009009:SSA_1006|5end_Dextransucrase,_putative_1007076..1007306_POSITIVE 295 186 151 154 122 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 287 55 12 156 107 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 286 45 11 231 194 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 282 62 21 231 177 NC_009009:SSA_1339|5end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1355424..1355654_NEGATIVE 278 176 145 164 124 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 273 45 5 185 139 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 267 50 1 179 125 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 265 49 2 191 138 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 265 132 91 206 151 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 260 50 2 74 28 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 252 129 88 65 24 NC_009009:SSA_0866|5end_Cation-transporting_ATPase,_E1-E_2_family,_putative_856983..857213_POSITIVE 252 136 100 77 36 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 250 66 22 80 25 NC_009009:SSA_0734|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_716895..717125_POSITIVE 250 40 3 37 7 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 249 60 12 211 159 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 249 43 4 63 26 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 51 12 79 40 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 316 74 35 51 4 NC_009009:SSA_1523|3end_Glutathione_peroxidase,_putative_1532620..1532770_POSITIVE 312 60 11 90 30 NC_009009:SSA_0955|3end_Aminopeptidase_N,_putative_961139..961289_POSITIVE 287 55 12 110 61 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 282 119 84 149 106 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 281 190 150 79 40 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 273 45 5 54 8 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 265 49 2 86 33 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 262 44 10 71 33 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 258 51 11 109 74 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 255 48 2 139 81 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 255 69 22 113 51 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 253 70 21 84 29 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 253 60 11 73 33 NC_009009:SSA_0080|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_84194..84344_POSITIVE 252 70 21 141 95 NC_009009:SSA_2024|3end_hypothetical_protein_2029105..2029255_NEGATIVE 252 58 13 90 38 NC_009009:SSA_1571|3end_Threonyl-tRNA_synthetase,_putative_1573211..1573361_NEGATIVE 251 58 12 118 76 NC_009009:SSA_0729|3end_hypothetical_protein_714677..714827_POSITIVE 250 40 3 33 3 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 249 43 4 72 35 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 247 54 13 72 39 NC_009009:SSA_1399|3end_hypothetical_protein_1411659..1411809_NEGATIVE