Origin IGS: acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacattgaaatttaatgaattacatttatctactgaattactagcagagattgaaaaagctggctttgtagaagcgagtcctattcaagagcaaacaattccacttgct .........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.........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 agcaagtggaattgtttgctcttgaataggactcgcttctacaaagccagctttttcaatctctgctagtaattcagtagataaatgtaattcattaaatttcaatgttcttcttctttctaaaggcggtgcgaagccaccttataaggcttttgatactcaactatcgaaacataccaagtgcttttctcttgctaaatctcgattttctgagagtattcgctcttctcttcataaatatggtctctcaagtctaggcactaaaaaagcgccgactcggtcgctagttcccactgaatagaaaaactgtatttctgcaactaatctagtataccacaaaagcacctaaaaagatagaacttgactgtaaaatattttattagagatttcttttgtaaaaaatgaaaacttgaaaatcattttcaaaagcattataatctacaaagaagaaaggaggcaggt Mask Tandem Repeat Region ================================================ acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacattgaaatttaatgaattacatttatctactgaattactagcagagattgaaaaagctggctttgtagaagcgagtcctattcaagagcaaacaattccacttgct Find is-nt database================================================ Query_seq: SSA_0705:SSA_0706|SSA_0705:SSA_0706:hypothetical protein:RNA helicase, putative:<-->:691041..691502 462 acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacattgaaatttaatgaattacatttatctactgaattactagcagagattgaaaaagctggctttgtagaagcgagtcctattcaagagcaaacaattccacttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0705:SSA_0706|SSA_0705:SSA_0706:hypothetical protein:RNA helicase, putative:<-->:691041..691502 462 acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacattgaaatttaatgaattacatttatctactgaattactagcagagattgaaaaagctggctttgtagaagcgagtcctattcaagagcaaacaattccacttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0705:SSA_0706|SSA_0705:SSA_0706:hypothetical protein:RNA helicase, putative:<-->:691041..691502 462 acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacattgaaatttaatgaattacatttatctactgaattactagcagagattgaaaaagctggctttgtagaagcgagtcctattcaagagcaaacaattccacttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 358 Max: 462 Len: 105 Subject: UniRef90_P0A4D7 Cluster: Probable ATP-dependent RNA helicase exp9; n=3; Streptococcus pneumoniae|Rep: Probable ATP-dependent RNA helicase exp9 - Streptococcus pneumoniae HSP 1 e-value: 2.0E-9 bit: 63.5 Len: 105 Query Start:358 Query End:462 Subject Strand: null Subject Start: 1 Subject End: 35 ..................................................................................................................................................................................................................................................................................................................................................................... L K F N E L H L S T E L L A E I E K A G F V E A S P I Q E Q T I P L A ..................................................................................................................................................................................................................................................................................................................................................................... M K F N E L N L S A D L L A E I E K A G F V E A S P I Q E Q T I P L A Subject: UniRef90_Q93HQ5 Cluster: Putative ATP-dependent RNA helicase; n=1; Streptococcus sobrinus|Rep: Putative ATP-dependent RNA helicase - Streptococcus sobrinus HSP 1 e-value: 5.0E-6 bit: 52.4 Len: 105 Query Start:358 Query End:462 Subject Strand: null Subject Start: 1 Subject End: 35 ..................................................................................................................................................................................................................................................................................................................................................................... L K F N E L H L S T E L L A E I E K A G F V E A S P I Q E Q T I P L A ..................................................................................................................................................................................................................................................................................................................................................................... M K F T E L H L A E D I L Q A V E K A G F V E P S P I Q E L T I P L A Subject: UniRef90_Q3CZJ4 Cluster: ATP-dependent RNA helicase, DEAD/DEAH box family; n=8; Streptococcus agalactiae|Rep: ATP-dependent RNA helicase, DEAD/DEAH box family - Streptococcus agalactiae H36B HSP 1 e-value: 5.0E-6 bit: 52.4 Len: 105 Query Start:358 Query End:462 Subject Strand: null Subject Start: 1 Subject End: 35 ..................................................................................................................................................................................................................................................................................................................................................................... L K F N E L H L S T E L L A E I E K A G F V E A S P I Q E Q T I P L A ..................................................................................................................................................................................................................................................................................................................................................................... M K F T E L N L S Q D I L S A V E K A G F V E P S P I Q E M T I P L A acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 25 End: 114 ........................ M I M L L K M I F K F S F F T K E I S N K I F Y S Q V L S F ............................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 37 Strand: + Start: 118 End: 228 ..................................................................................................................... M L L W Y T R L V A E I Q F F Y S V G T S D R V G A F L V P R L E R P Y L .......................................................................................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 358 End: 462 ..................................................................................................................................................................................................................................................................................................................................................................... M K F N E L H L S T E L L A E I E K A G F V E A S P I Q E Q T I P L A Protein_Len: 52 Strand: - Start: 209 End: 364 ................................................................................................................................................................................................................ V Q S V M N I F L L A F V R L F D L N L L L F A S P I N R Y N L I L L R I L H S R V A K L F F F F M S M .................................................................................................. Protein_Len: 60 Strand: - Start: 165 End: 437 .................................................................................................................................................................... R S K A L S F C K T H K S L Q T D F A K Y P P K A G G K S L L L V N F N L S N C K D V S N S A S I S F A P K T S A L G M ......................... acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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: 89 Start: 25 End: 54 ........................CTTGAAAATCATTTTCAAAAGCATTATAAT........................................................................................................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -6.8 Tail_Score: -5.1675 Start: 179 End: 194 Full_Region: ATTCAGTGGGAACTA GCGACCG AGT CGGCGC TTTTTTAGTGCCTAG ..................................................................................................................................................................................GCGACCGAGTCGGCGC............................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 39 HP_score: -2.2 Tail_Score: -2.56391 Start: 269 End: 285 Full_Region: AAAATCGAGATTTAG CAAGAG AAAAG CACTTG GTATGTTTCGATAGT ............................................................................................................................................................................................................................................................................CAAGAGAAAAGCACTTG................................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_0705:SSA_0706|SSA_0705:SSA_0706:hypothetical protein:RNA helicase, putative:<-->:691041..691502 462 acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 357 Len: 357 Subject: NC_009009_SSA_0705_SSA_0706|hypothetical protein:RNA helicase, putative|NEGATIVE:POSITIVE|[691041,691502]|462 HSP 1 e-value: 0.0 bit: 708.0 Len: 357 Query Start:1 Query End:357 Subject Strand: POSITIVE Subject Start: 1 Subject End: 357 acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaaca......................................................................................................... acctgcctcctttcttctttgtagattataatgcttttgaaaatgattttcaagttttcattttttacaaaagaaatctctaataaaatattttacagtcaagttctatctttttaggtgcttttgtggtatactagattagttgcagaaatacagtttttctattcagtgggaactagcgaccgagtcggcgcttttttagtgcctagacttgagagaccatatttatgaagagaagagcgaatactctcagaaaatcgagatttagcaagagaaaagcacttggtatgtttcgatagttgagtatcaaaagccttataaggtggcttcgcaccgcctttagaaagaagaagaaca......................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUGCCUCCUUUCUUCUUUGUAGAUUAUAAUGCUUUUGAAAAUGAUUUUCAAGUUUUCAUUUUUUACAAAAGAAAUCUCUAAUAAAAUAUUUUACAGUCAAGUUCUAUCUUUUUAGGUGCUUUUGUGGUAUACUAGAUUAGUUGCAGAAAUACAGUUUUUCUAUUCAGUGGGAACUAGCGACCGAGUCGGCGCUUUUUUAGUGCCUAGACUUGAGAGACCAUAUUUAUGAAGAGAAGAGCGAAUACUCUCAGAAAAUCGAGAUUUAGCAAGAGAAAAGCACUUGGUAUGUUUCGAUAGUUGAGUAUCAAAAGCCUUAUAAGGUGGCUUCGCACCGCCUUUAGAAAGAAGAAGAACA ..........((((((((((.(((..(((((.((((((((............(((.(((............(((....))).....................(((((.((((((((........((((((...........(((((.((((.......)))).....(((....))).)))))((((((((((((.....))))))..))))))....))))))....)))))))))))))))).)))(((((...((((((((.((.((((.(.....).)))).)).))))))))..)))))..)))))))).))))).(((((.......))))).))).)))))))))).... (-90.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUUCUUCUUUCUAAAGGCGGUGCGAAGCCACCUUAUAAGGCUUUUGAUACUCAACUAUCGAAACAUACCAAGUGCUUUUCUCUUGCUAAAUCUCGAUUUUCUGAGAGUAUUCGCUCUUCUCUUCAUAAAUAUGGUCUCUCAAGUCUAGGCACUAAAAAAGCGCCGACUCGGUCGCUAGUUCCCACUGAAUAGAAAAACUGUAUUUCUGCAACUAAUCUAGUAUACCACAAAAGCACCUAAAAAGAUAGAACUUGACUGUAAAAUAUUUUAUUAGAGAUUUCUUUUGUAAAAAAUGAAAACUUGAAAAUCAUUUUCAAAAGCAUUAUAAUCUACAAAGAAGAAAGGAGGCAGGU ...(((((((((((((..(((.(((.....))).)))(((((.((((((((..................((.((((.(.....).)))).))......(((((((.((((((....))))))((((....((((((...(..((((((((((((.((.....)).))).....(((.(((((.......((..((((((.......))))))))......)))))..)))...................))).))))))..)....))))))....)))).((((((((....)))).))))....)))))))....)))))))).)))))...........)))))))))).))). (-74.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 50 1 141 92 NC_009009:SSA_0705|5end_hypothetical_protein_690950..691180_NEGATIVE 403 347 303 52 2 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 363 215 180 214 180 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 357 208 161 193 140 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 331 160 115 59 11 NC_009009:SSA_1639|5end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1642031..1642261_NEGATIVE 319 207 169 215 169 NC_009009:SSA_1508|5end_ABC-type_lipopolysaccharide_transport_system,_permease_component,_putative_1513250..1513480_NEGATIVE 317 219 171 206 156 NC_009009:SSA_0055|5end_PTS_system,_IIC_component,_putative_59034..59264_POSITIVE 315 230 183 70 12 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 308 196 154 208 165 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 308 199 153 143 88 NC_009009:SSA_0679|5end_DNA_repair_and_genetic_recombination,_putative_660714..660944_POSITIVE 300 220 179 124 85 NC_009009:SSA_2112|5end_hypothetical_protein_2116091..2116321_NEGATIVE 300 220 179 203 164 NC_009009:SSA_2111|5end_30S_ribosomal_protein_S12,_putative_2116012..2116242_NEGATIVE 300 200 160 142 111 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 298 205 161 152 109 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 297 215 177 63 25 NC_009009:SSA_1357|5end_hypothetical_protein_1373024..1373254_NEGATIVE 295 203 165 209 162 NC_009009:SSA_1678|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1672181..1672411_NEGATIVE 295 214 178 50 1 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 294 275 233 195 153 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 294 210 166 177 137 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 293 206 169 89 45 NC_009009:SSA_1000|5end_Galactose_operon_transcriptional_repressor,_LacI_family,_putative_1000734..1000964_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 230 183 68 10 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 308 199 153 134 79 NC_009009:SSA_0678|3end_Transcriptional_regulator,_ArgR_family,_putative_660785..660935_POSITIVE 306 214 177 57 7 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 305 200 151 84 23 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 294 210 166 136 96 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 294 200 154 150 112 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 282 339 291 143 94 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 281 250 203 78 30 NC_009009:SSA_0433|3end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435028..435178_NEGATIVE 280 207 162 145 103 NC_009009:SSA_1582|3end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1585443..1585593_POSITIVE 279 203 164 73 32 NC_009009:SSA_1931|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta,_putative_1918544..1918694_NEGATIVE 275 269 229 40 7 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 275 341 311 124 98 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 273 344 305 133 89 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 272 217 178 127 94 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 272 208 168 73 26 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 271 195 156 71 35 NC_009009:SSA_1590|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1593342..1593492_POSITIVE 271 337 292 78 35 NC_009009:SSA_0917|3end_Cobalamin-independent_methionine_synthase_II,_putative_929087..929237_NEGATIVE 270 220 175 67 18 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 269 213 171 143 110 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE 269 224 181 74 26 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE