Origin IGS: cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt .........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 acgataactccttatcaaatgtagaatagtgaaaagtcatccgaaaactggacaaaggcatcctttactctcagtctttcagatgattgcctgttttgaaacgcagatttttaaaatccgaccattcggtttgttttgttataaaaaataaagacctgcgccaaatagaaaacgtagtcttttagtccttgcctaaaataaaaagcaaagatagactaaataatgctaaaagctatgtcagcaccgtttagctactgcctgctgcttttagtttctaagttgtcctgactctgatgcttaagacaggccatttctctg Mask Tandem Repeat Region ================================================ cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Find is-nt database================================================ Query_seq: SSA_0345:SSA_0346|SSA_0345:SSA_0346:hypothetical protein:hypothetical protein:->->:339270..339587 318 cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0345:SSA_0346|SSA_0345:SSA_0346:hypothetical protein:hypothetical protein:->->:339270..339587 318 cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0345:SSA_0346|SSA_0345:SSA_0346:hypothetical protein:hypothetical protein:->->:339270..339587 318 cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 107 End: 205 .......................................................................................................... M F A F Y F R Q G L K D Y V F Y L A Q V F I F Y N K T N R M V G F ................................................................................................................. Protein_Len: 31 Strand: + Start: 153 End: 245 ........................................................................................................................................................ M W R R S L F F I T K Q T E W S D F K N L R F K T G N H L K D ......................................................................... Protein_Len: 45 Strand: - Start: 171 End: 305 .......................................................................................................................................................................... K K Y C F L G F P R I K F I Q T E F C A I M Q F V S L L P H R Q G T K P H S K V I R C K M ............. Protein_Len: 32 Strand: - Start: 137 End: 232 ........................................................................................................................................ F V V N E I Q R L D K N K I V F C V S H D S K L F R R K L V P M ...................................................................................... cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt 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================================================ cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -5.8 Tail_Score: -4.92812 Start: 190 End: 201 Full_Region: gcagatttttaaaat ccga ccat tcgg tttgttttgttataa .............................................................................................................................................................................................ccgaccattcgg..................................................................................................................... Find igs database================================================ Query_seq: SSA_0345:SSA_0346|SSA_0345:SSA_0346:hypothetical protein:hypothetical protein:->->:339270..339587 318 cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Intra-Species Hit: Count: 1 Min: 1 Max: 318 Len: 318 Subject: NC_009009_SSA_0345_SSA_0346|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[339270,339587]|318 HSP 1 e-value: 1.0E-180 bit: 630.0 Len: 318 Query Start:1 Query End:318 Subject Strand: POSITIVE Subject Start: 1 Subject End: 318 cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt cagagaaatggcctgtcttaagcatcagagtcaggacaacttagaaactaaaagcagcaggcagtagctaaacggtgctgacatagcttttagcattatttagtctatctttgctttttattttaggcaaggactaaaagactacgttttctatttggcgcaggtctttattttttataacaaaacaaaccgaatggtcggattttaaaaatctgcgtttcaaaacaggcaatcatctgaaagactgagagtaaaggatgcctttgtccagttttcggatgacttttcactattctacatttgataaggagttatcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAGAAAUGGCCUGUCUUAAGCAUCAGAGUCAGGACAACUUAGAAACUAAAAGCAGCAGGCAGUAGCUAAACGGUGCUGACAUAGCUUUUAGCAUUAUUUAGUCUAUCUUUGCUUUUUAUUUUAGGCAAGGACUAAAAGACUACGUUUUCUAUUUGGCGCAGGUCUUUAUUUUUUAUAACAAAACAAACCGAAUGGUCGGAUUUUAAAAAUCUGCGUUUCAAAACAGGCAAUCAUCUGAAAGACUGAGAGUAAAGGAUGCCUUUGUCCAGUUUUCGGAUGACUUUUCACUAUUCUACAUUUGAUAAGGAGUUAUCGU ..(((((...((((((.((((((..((((...((..(..(((((((...((((((((.((..((..((((((..(((((((........)))))))..))))))))..))))))))))..)))))))...)..)).(((((((.((((........))))..)))))))....................((((....))))..........)))).)))).)).))))))..(((((((((.(((((.((.((((((...)))))))))))))))))))))).)))))..............(((((....))))).. (-85.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAUAACUCCUUAUCAAAUGUAGAAUAGUGAAAAGUCAUCCGAAAACUGGACAAAGGCAUCCUUUACUCUCAGUCUUUCAGAUGAUUGCCUGUUUUGAAACGCAGAUUUUUAAAAUCCGACCAUUCGGUUUGUUUUGUUAUAAAAAAUAAAGACCUGCGCCAAAUAGAAAACGUAGUCUUUUAGUCCUUGCCUAAAAUAAAAAGCAAAGAUAGACUAAAUAAUGCUAAAAGCUAUGUCAGCACCGUUUAGCUACUGCCUGCUGCUUUUAGUUUCUAAGUUGUCCUGACUCUGAUGCUUAAGACAGGCCAUUUCUCUG ..(((((....))))).....((((..((((...(((((((.((((((((((.(((((...)))))..)).)))).)))).)))))))(((((((((((..(((((.((((((....((((....))))(((((......)))))...)))))).))))).....(((((....((((((....(((.((((............)))).)))))))))......(((((((((...((..(((..((......)))))..)).))))))))))))))....................)))))))))))))))..)))) (-76.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 239 191 170 121 NC_009009:SSA_0083|5end_hypothetical_protein_85437..85667_POSITIVE 360 297 256 51 2 NC_009009:SSA_1842|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_HTH_DNA-binding_domains),_putative_1836494..1836724_NEGATIVE 347 78 33 61 10 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 345 96 54 228 186 NC_009009:SSA_0332|5end_hypothetical_protein_325909..326139_POSITIVE 333 94 53 224 176 NC_009009:SSA_0142|5end_hypothetical_protein_137230..137460_POSITIVE 324 68 26 53 13 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 319 46 7 60 17 NC_009009:SSA_1198|5end_ATPase_(PilT_family),_putative_1223314..1223544_NEGATIVE 314 80 40 178 145 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 314 95 51 111 58 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 308 86 56 63 31 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 307 96 52 91 32 NC_009009:SSA_1578|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1581803..1582033_POSITIVE 305 95 52 78 27 NC_009009:SSA_0473|5end_Precorrin-6x_reductase,_putative_475502..475732_POSITIVE 304 109 61 58 8 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 303 263 227 59 22 NC_009009:SSA_0648|5end_hypothetical_protein_631468..631698_POSITIVE 301 93 57 52 17 NC_009009:SSA_1950|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component,_putative_1946527..1946757_NEGATIVE 300 94 58 50 7 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 300 97 53 226 175 NC_009009:SSA_0392|5end_hypothetical_protein_387876..388106_POSITIVE 297 74 32 136 96 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 296 89 53 47 5 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 294 97 53 211 163 NC_009009:SSA_1393|5end_hypothetical_protein_1408773..1409003_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 297 256 73 24 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 333 94 53 105 57 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 319 46 7 63 20 NC_009009:SSA_1199|3end_Phosphinothricin_acetyltransferase,_putative_1223311..1223461_NEGATIVE 314 80 40 80 47 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 314 95 51 85 32 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 308 86 56 48 16 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 305 95 54 151 116 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 305 95 52 81 30 NC_009009:SSA_0472|3end_Precorrin-3B_C17-methyltransferase,_putative_475585..475735_POSITIVE 300 97 53 71 20 NC_009009:SSA_0391|3end_Pyruvate_oxidase,_putative_387801..387951_POSITIVE 297 74 32 143 103 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 295 95 53 51 7 NC_009009:SSA_1565|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1568608..1568758_NEGATIVE 292 68 21 88 38 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 291 97 53 81 39 NC_009009:SSA_0772|3end_Histidine-containing_phosphocarrier_protein_of_the_PTS,_putative_752681..752831_POSITIVE 287 289 241 103 43 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 283 95 55 83 50 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 282 65 21 76 22 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 278 89 48 86 48 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 278 94 55 144 109 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 276 258 213 56 14 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 273 83 41 56 12 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE