Origin IGS: atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt .........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 aacaatgaaaacaagaaaatttctcctcatttttatcaccctctatacgatcttattcctaggtagaggcttgcagttgattgggataaattggttgatttaaccagtttatttccttttatttatcttgggaatcttagcttatcgtgaagaattaaaggagcagctggccttgattctgaccaagaagaaggaatttctaaaaacgatctccttgtat Mask Tandem Repeat Region ================================================ atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Find is-nt database================================================ Query_seq: SSA_2252:SSA_2253|SSA_2252:SSA_2253:hypothetical protein:3-Methyladenine DNA glycosylase I, constitutive, putative:<-<-:2248740..2248959 220 atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2252:SSA_2253|SSA_2252:SSA_2253:hypothetical protein:3-Methyladenine DNA glycosylase I, constitutive, putative:<-<-:2248740..2248959 220 atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2252:SSA_2253|SSA_2252:SSA_2253:hypothetical protein:3-Methyladenine DNA glycosylase I, constitutive, putative:<-<-:2248740..2248959 220 atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 121 End: 216 ........................................................................................................................ I L W N I G I L Q L G R G L F L I T Y L T I F I L L F K R T K M .... Protein_Len: 32 Strand: - Start: 1 End: 96 Y L S I T K L F E K K K T L I L A L Q E K L E E R Y A L I G L M ............................................................................................................................ atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt 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================================================ atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -5.5 Tail_Score: -5.10033 Start: 105 End: 138 Full_Region: ggcttgcagttgatt gggataaattggttg att taaccagtttatttcc ttttatttatcttgg ........................................................................................................gggataaattggttgatttaaccagtttatttcc.................................................................................. TransTerm Strand: - Conf: 79 HP_score: -7.3 Tail_Score: -4.39227 Start: 110 End: 134 Full_Region: tgcagttgattggga taaattggttg att taaccagttta tttccttttatttat .............................................................................................................taaattggttgatttaaccagttta...................................................................................... Find igs database================================================ Query_seq: SSA_2252:SSA_2253|SSA_2252:SSA_2253:hypothetical protein:3-Methyladenine DNA glycosylase I, constitutive, putative:<-<-:2248740..2248959 220 atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Intra-Species Hit: Count: 1 Min: 1 Max: 220 Len: 220 Subject: NC_009009_SSA_2252_SSA_2253|hypothetical protein:3-Methyladenine DNA glycosylase I, constitutive, putative|NEGATIVE:NEGATIVE|[2248740,2248959]|220 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt atacaaggagatcgtttttagaaattccttcttcttggtcagaatcaaggccagctgctcctttaattcttcacgataagctaagattcccaagataaataaaaggaaataaactggttaaatcaaccaatttatcccaatcaactgcaagcctctacctaggaataagatcgtatagagggtgataaaaatgaggagaaattttcttgttttcattgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACAAGGAGAUCGUUUUUAGAAAUUCCUUCUUCUUGGUCAGAAUCAAGGCCAGCUGCUCCUUUAAUUCUUCACGAUAAGCUAAGAUUCCCAAGAUAAAUAAAAGGAAAUAAACUGGUUAAAUCAACCAAUUUAUCCCAAUCAACUGCAAGCCUCUACCUAGGAAUAAGAUCGUAUAGAGGGUGAUAAAAAUGAGGAGAAAUUUUCUUGUUUUCAUUGUU ..((((((((((((((((((......((((((...(((((.......((((..((...((((((.(((..((.....................))..))).)))))).(((((.(((((.....))))).)))))...........))..))))...(....).....)))))...))))))...))))))))).......))))))))).......... (-43.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUGAAAACAAGAAAAUUUCUCCUCAUUUUUAUCACCCUCUAUACGAUCUUAUUCCUAGGUAGAGGCUUGCAGUUGAUUGGGAUAAAUUGGUUGAUUUAACCAGUUUAUUUCCUUUUAUUUAUCUUGGGAAUCUUAGCUUAUCGUGAAGAAUUAAAGGAGCAGCUGGCCUUGAUUCUGACCAAGAAGAAGGAAUUUCUAAAAACGAUCUCCUUGUAU ..........(((((........................(((((((..((......))....))))))).........(((((.(((((((((((((...)))))))))))))(((((((.....(((((((((((((((((..((.(..........).))..))))))....)))))...)))))))))))))...........)))))..))))).. (-49.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 919 80 31 171 122 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 397 62 25 53 13 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 357 85 45 61 16 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 354 186 141 73 24 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 346 63 27 227 188 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 336 163 136 43 14 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 333 64 30 231 197 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 332 69 29 145 97 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 326 61 24 227 188 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 325 67 33 40 3 NC_009009:SSA_1467|5end_Chorismate_synthase,_putative_1474293..1474523_NEGATIVE 324 77 31 107 43 NC_009009:SSA_0418|5end_AraC-type_DNA-binding_domain-containing_protein,_putative_415256..415486_POSITIVE 322 179 135 231 192 NC_009009:SSA_0571|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_565381..565611_POSITIVE 321 64 22 35 4 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 315 75 32 66 18 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 311 52 12 98 58 NC_009009:SSA_2256|5end_hypothetical_protein_2250604..2250834_POSITIVE 310 79 33 72 19 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 310 59 12 78 30 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 306 79 32 66 5 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 303 70 27 84 31 NC_009009:SSA_1335|5end_Ankyrin_repeat_protein,_putative_1349663..1349893_NEGATIVE 300 61 24 77 43 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 85 45 59 14 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 354 186 141 80 31 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 348 62 29 37 2 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 321 64 22 42 11 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 316 60 13 53 14 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 315 75 32 53 5 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 315 60 11 151 106 NC_009009:SSA_1382|3end_hypothetical_protein_1399797..1399947_NEGATIVE 311 52 12 144 104 NC_009009:SSA_2255|3end_Transcriptional_regulator,_XRE_family,_putative_2250730..2250880_POSITIVE 310 59 12 74 26 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 306 66 28 131 84 NC_009009:SSA_0684|3end_Fibril-like_structure_subunit_FibA,_putative_668893..669043_POSITIVE 304 61 29 148 110 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 303 75 31 141 106 NC_009009:SSA_1693|3end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1685105..1685255_NEGATIVE 298 57 31 132 100 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 291 90 41 62 9 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 291 76 31 67 26 NC_009009:SSA_1154|3end_hypothetical_protein_1183331..1183481_POSITIVE 291 59 11 146 86 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 290 90 45 62 18 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 288 62 25 133 97 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 286 82 41 127 87 NC_009009:SSA_1549|3end_hypothetical_protein_1551816..1551966_NEGATIVE 286 59 17 133 90 NC_009009:SSA_0530|3end_Ethanolamine_utilization_protein_(transporter),_putative_527417..527567_POSITIVE