Origin IGS: aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat .........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 ataaacactcctcaatctttatcagtttcattatatagtataaactattttaccaaaagcaaaaacccgccttaaacgggcgggttgtggtgaagaaagtgatgaacctcctccttgataaattgacaataagcgtagacaaggtagcaagtagatgccacacctaaaagggcgacaaacaactcaaataaggcagacatagtcatggcgaacctcctctccttatcaggcaaaaatgcagatacgcttcccagcttaggcagtctgattgtttccgttttattttcctttccgacttacccaagtgagttcatcaccattataccaaaatacgaaagcggatacaatagtggtaaatcatggagcattctgttttagtttatattctcatattttcaacttataaatcttccagtcaattctataagtttttatttatgctcttctcttgatgatagcgttttaatatagtataatataagtccgaaattcattttaacaaaggagatatt Mask Tandem Repeat Region ================================================ aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Find is-nt database================================================ Query_seq: SSA_0243:SSA_0244|SSA_0243:SSA_0244:Cyclo-nucleotide phosphodiesterase, putative:hypothetical protein:<-->:238326..238837 512 aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0243:SSA_0244|SSA_0243:SSA_0244:Cyclo-nucleotide phosphodiesterase, putative:hypothetical protein:<-->:238326..238837 512 aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0243:SSA_0244|SSA_0243:SSA_0244:Cyclo-nucleotide phosphodiesterase, putative:hypothetical protein:<-->:238326..238837 512 aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 209 End: 307 ................................................................................................................................................................................................................ M G K S E R K I K R K Q S D C L S W E A Y L H F C L I R R G G S P ............................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 244 End: 438 ................................................................................................................................................................................................................................................... M R L P K L G S V S A F L P D K E R R F A M T M S A L F E L F V A L L G V A S T C Y L V Y A Y C Q F I K E E V H H F L H .......................................................................... Protein_Len: 37 Strand: + Start: 350 End: 460 ............................................................................................................................................................................................................................................................................................................................................................. M W H L L A T L S T L I V N L S R R R F I T F F T T T R P F K A G F C F W .................................................... Protein_Len: 41 Strand: + Start: 357 End: 479 .................................................................................................................................................................................................................................................................................................................................................................... M Y L L P C L R L L S I Y Q G G G S S L S S P Q P A R L R R V F A F G K I V Y T I ................................. Protein_Len: 59 Strand: - Start: 138 End: 314 ......................................................................................................................................... F L I S W S K G S N Y G S E Y K P I I T I F E S P Y T P F S F L V S V I L S G L S P L T D A N K G S L S L L N A M V M ...................................................................................................................................................................................................... Protein_Len: 45 Strand: - Start: 110 End: 244 ............................................................................................................. L N F I H S Y L S F C F A G H N V V I T D A K T N Q Y L P S S S V Q T L R F P F Y F P F M ............................................................................................................................................................................................................................................................................ Protein_Len: 31 Strand: - Start: 64 End: 156 ............................................................... S F L M F L F K Y F Q S S S K Y T S F I L I Y V L V S H E M M .................................................................................................................................................................................................................................................................................................................................................................... aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat 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: 86 Start: 36 End: 65 ...................................CTTGATGATAGCGTTTTAATATAGTATAAT............................................................................................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 165 End: 194 ....................................................................................................................................................................ATTGTATCCGCTTTCGTATTTTGGTATAAT.............................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -3.4 Tail_Score: -2.71261 Start: 352 End: 369 Full_Region: GTCGCCCTTTTAGGT GTGGCA TCTACT TGCTAC CTTGTCTACGCTTAT ...............................................................................................................................................................................................................................................................................................................................................................GTGGCATCTACTTGCTAC............................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -8.8 Tail_Score: -5.1166 Start: 429 End: 447 Full_Region: CTTTCTTCACCACAA CCCGCC CGTTTAA GGCGGG TTTTTGCTTTTGGTA ............................................................................................................................................................................................................................................................................................................................................................................................................................................CCCGCCCGTTTAAGGCGGG................................................................. TransTerm Strand: - Conf: 76 HP_score: -9.5 Tail_Score: -3.40403 Start: 429 End: 447 Full_Region: taccaaaagcaaaaa cccgcct taaac gggcggg ttgtggtgaagaaag ............................................................................................................................................................................................................................................................................................................................................................................................................................................cccgccttaaacgggcggg................................................................. Find igs database================================================ Query_seq: SSA_0243:SSA_0244|SSA_0243:SSA_0244:Cyclo-nucleotide phosphodiesterase, putative:hypothetical protein:<-->:238326..238837 512 aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Intra-Species Hit: Count: 1 Min: 1 Max: 512 Len: 512 Subject: NC_009009_SSA_0243_SSA_0244|Cyclo-nucleotide phosphodiesterase, putative:hypothetical protein|NEGATIVE:POSITIVE|[238326,238837]|512 HSP 1 e-value: 0.0 bit: 1015.0 Len: 512 Query Start:1 Query End:512 Subject Strand: POSITIVE Subject Start: 1 Subject End: 512 aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat aatatctcctttgttaaaatgaatttcggacttatattatactatattaaaacgctatcatcaagagaagagcataaataaaaacttatagaattgactggaagatttataagttgaaaatatgagaatataaactaaaacagaatgctccatgatttaccactattgtatccgctttcgtattttggtataatggtgatgaactcacttgggtaagtcggaaaggaaaataaaacggaaacaatcagactgcctaagctgggaagcgtatctgcatttttgcctgataaggagaggaggttcgccatgactatgtctgccttatttgagttgtttgtcgcccttttaggtgtggcatctacttgctaccttgtctacgcttattgtcaatttatcaaggaggaggttcatcactttcttcaccacaacccgcccgtttaaggcgggtttttgcttttggtaaaatagtttatactatataatgaaactgataaagattgaggagtgtttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCUCCUUUGUUAAAAUGAAUUUCGGACUUAUAUUAUACUAUAUUAAAACGCUAUCAUCAAGAGAAGAGCAUAAAUAAAAACUUAUAGAAUUGACUGGAAGAUUUAUAAGUUGAAAAUAUGAGAAUAUAAACUAAAACAGAAUGCUCCAUGAUUUACCACUAUUGUAUCCGCUUUCGUAUUUUGGUAUAAUGGUGAUGAACUCACUUGGGUAAGUCGGAAAGGAAAAUAAAACGGAAACAAUCAGACUGCCUAAGCUGGGAAGCGUAUCUGCAUUUUUGCCUGAUAAGGAGAGGAGGUUCGCCAUGACUAUGUCUGCCUUAUUUGAGUUGUUUGUCGCCCUUUUAGGUGUGGCAUCUACUUGCUACCUUGUCUACGCUUAUUGUCAAUUUAUCAAGGAGGAGGUUCAUCACUUUCUUCACCACAACCCGCCCGUUUAAGGCGGGUUUUUGCUUUUGGUAAAAUAGUUUAUACUAUAUAAUGAAACUGAUAAAGAUUGAGGAGUGUUUAU ((((.((((((.(((...((.(.(((((..((((((((...............(((.((.....))....))).........((((((((((.((.......)).))))))))))...))))))))..(((((((((...(((((((((((..((((((.((((((((((((..............)))))))))))).)))).)).((((((((.(((.((.(......).....(....)..)).)))))))))))...)).))))).))))...(((((((.(((((((.((((.((....))..(((...)))..))))....((((....((((((((.....)).))))))...))))....)))))))...((..................(((((((((.....))))))))).....((((((((.......))))))))...))....))))))))))))))))........))))).).))...))).))))))))))... (-128.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAACACUCCUCAAUCUUUAUCAGUUUCAUUAUAUAGUAUAAACUAUUUUACCAAAAGCAAAAACCCGCCUUAAACGGGCGGGUUGUGGUGAAGAAAGUGAUGAACCUCCUCCUUGAUAAAUUGACAAUAAGCGUAGACAAGGUAGCAAGUAGAUGCCACACCUAAAAGGGCGACAAACAACUCAAAUAAGGCAGACAUAGUCAUGGCGAACCUCCUCUCCUUAUCAGGCAAAAAUGCAGAUACGCUUCCCAGCUUAGGCAGUCUGAUUGUUUCCGUUUUAUUUUCCUUUCCGACUUACCCAAGUGAGUUCAUCACCAUUAUACCAAAAUACGAAAGCGGAUACAAUAGUGGUAAAUCAUGGAGCAUUCUGUUUUAGUUUAUAUUCUCAUAUUUUCAACUUAUAAAUCUUCCAGUCAAUUCUAUAAGUUUUUAUUUAUGCUCUUCUCUUGAUGAUAGCGUUUUAAUAUAGUAUAAUAUAAGUCCGAAAUUCAUUUUAACAAAGGAGAUAUU .................(((((((.((((.....(((((....))))).((((((........(((((((((.....))))))))).)))))).)))).)))))))....((((((..((((.(((..((((((..(((((..((.((.....(.((((.(........))))).).........(((((((((.((.(((((((.(((...(((........((((..(((....))).)))).(((....)))..)))..)))))))))).)).)))))))))(((.....(((((((....)))))))....((((((((.........(....)........)))))))).......)))))))..)))))..))))))..........((((.(((((((...(((..((......))..)))....((((.(((((..((.......)).)))))...))))........)))))))..)))).))).))))...))))))..... (-110.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 768 100 51 191 142 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 377 450 404 226 183 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 370 280 242 182 135 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 334 277 231 217 170 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 331 309 261 204 141 NC_009009:SSA_1850|5end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1846024..1846254_NEGATIVE 330 468 429 47 5 NC_009009:SSA_2116|5end_Cmp-binding-factor_1,_putative_2118566..2118796_NEGATIVE 329 390 341 176 113 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 320 358 317 52 8 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 318 360 313 212 161 NC_009009:SSA_1198|5end_ATPase_(PilT_family),_putative_1223314..1223544_NEGATIVE 313 380 331 44 2 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 312 390 342 162 102 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 311 284 241 208 168 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 309 460 413 215 166 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 307 299 251 51 5 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 307 460 414 153 103 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 307 190 148 114 66 NC_009009:SSA_2183|5end_Glucose-6-phosphate_isomerase,_putative_2182537..2182767_NEGATIVE 307 487 443 158 114 NC_009009:SSA_0745|5end_hypothetical_protein_727035..727265_NEGATIVE 303 307 261 173 112 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 303 340 292 72 19 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 302 456 421 85 32 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 450 404 128 85 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 347 344 301 42 4 NC_009009:SSA_0248|3end_hypothetical_protein_241844..241994_POSITIVE 335 427 382 136 94 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 330 468 429 57 15 NC_009009:SSA_2117|3end_DNA_recombination_protein_RmuC,_putative_2118556..2118706_NEGATIVE 315 459 420 60 17 NC_009009:SSA_1990|3end_Zn-porter_lipoprotein,_putative_1985402..1985552_NEGATIVE 313 380 331 44 2 NC_009009:SSA_0996|3end_cGMP-specific_phosphodiesterase,_putative_996859..997009_POSITIVE 312 390 342 128 68 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 309 436 391 127 87 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 309 460 413 151 102 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 307 460 414 146 96 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 307 288 241 129 88 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 306 292 260 148 114 NC_009009:SSA_1851|3end_Guanylate_kinase,_putative_1846050..1846200_NEGATIVE 303 444 401 148 108 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 300 360 311 130 85 NC_009009:SSA_1338|3end_hypothetical_protein_1351200..1351350_NEGATIVE 300 319 271 151 113 NC_009009:SSA_1028|3end_Transcriptional_repressor,_XRE_family,_putative_1045290..1045440_NEGATIVE 295 379 331 144 91 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 293 379 332 53 6 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 293 286 243 140 93 NC_009009:SSA_0655|3end_Cell_division_protein_FtsA,_putative_640222..640372_POSITIVE 292 463 429 44 4 NC_009009:SSA_0557|3end_hypothetical_protein_552393..552543_POSITIVE 291 459 413 137 81 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE