Origin IGS: aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctttcctccgtataaagtttccttactattctactagtttttggcctattcgtcaaccgctccacgcccgattctcaaagaaaagcctctggggtggcttgggtatcattatagaaagaaaaaggtaagcaccgtcttctacttacctttcataattt Mask Tandem Repeat Region ================================================ aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Find is-nt database================================================ Query_seq: SMT_355:SMT_356|SMT_355:SMT_356:hypothetical protein:hypothetical protein:->->:292374..292533 160 aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_355:SMT_356|SMT_355:SMT_356:hypothetical protein:hypothetical protein:->->:292374..292533 160 aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_355:SMT_356|SMT_355:SMT_356:hypothetical protein:hypothetical protein:->->:292374..292533 160 aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 34 End: 147 ................................. R K R E I I I G L G G W L S K K S F R A H L P Q R I P W F S T S Y Y P F K M ............. Protein_Len: 39 Strand: - Start: 2 End: 118 . I I F P L Y F V T S V K K K R Y H Y G L W G L P K E K L I P R P A T S S Y A M .......................................... aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa 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: 87 Start: 102 End: 131 .....................................................................................................GTTGACGAATAGGCCAAAAACTAGTAGAAT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -3.7 Tail_Score: -4.87803 Start: 61 End: 74 Full_Region: TATAATGATACCCAA GCCAC CCCA GAGGC TTTTCTTTGAGAATC ............................................................GCCACCCCAGAGGC...................................................................................... Find igs database================================================ Query_seq: SMT_355:SMT_356|SMT_355:SMT_356:hypothetical protein:hypothetical protein:->->:292374..292533 160 aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: smit_SMT_355_SMT_356|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[292374,292533]|160 HSP 1 e-value: 6.0E-86 bit: 317.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa aaattatgaaaggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Inter-species Hit: Count: 2 Min: 1 Max: 160 Len: 160 Subject: NC_008533_SPD_0475_SPD_0476|CAAX amino terminal protease family protein:phosphotransferase enzyme family protein|POSITIVE:POSITIVE|[485448,485607]|160 HSP 1 e-value: 2.0E-55 bit: 216.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aaattatgaaa-ggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa aaattatgaaaaggtaagcagaagacggtgcttacctttttcaagctataatgatacccaagccaatccagaggcttttctttgagaatcggg-ttagagtggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Subject: NC_003098_spr0474_spr0475|ABC transporter ATP binding protein - unknown substrate:hypothetical protein|POSITIVE:POSITIVE|[477918,478077]|160 HSP 1 e-value: 2.0E-55 bit: 216.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aaattatgaaa-ggtaagtagaagacggtgcttacctttttctttctataatgatacccaagccaccccagaggcttttctttgagaatcgggcgtggagcggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa aaattatgaaaaggtaagcagaagacggtgcttacctttttcaagctataatgatacccaagccaatccagaggcttttctttgagaatcggg-ttagagtggttgacgaataggccaaaaactagtagaatagtaaggaaactttatacggaggaaagaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAUGAAAGGUAAGUAGAAGACGGUGCUUACCUUUUUCUUUCUAUAAUGAUACCCAAGCCACCCCAGAGGCUUUUCUUUGAGAAUCGGGCGUGGAGCGGUUGACGAAUAGGCCAAAAACUAGUAGAAUAGUAAGGAAACUUUAUACGGAGGAAAGAA .......((((((((((((........))))))))))))(((((((........(((....(((((((.((..(((......)))..))))).))))...)))...........((....((((......))))(((....))).....)).))))))). (-42.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUCCUCCGUAUAAAGUUUCCUUACUAUUCUACUAGUUUUUGGCCUAUUCGUCAACCGCUCCACGCCCGAUUCUCAAAGAAAAGCCUCUGGGGUGGCUUGGGUAUCAUUAUAGAAAGAAAAAGGUAAGCACCGUCUUCUACUUACCUUUCAUAAUUU .((((((....(((.(((((......))).)).))).(((..(((((......)))))..)))(((.(((....(((((.((......)).))))).))).)))...........)))))).(((((((((............)))))))))........ (-30.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 108 64 208 146 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 371 108 64 129 67 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 338 108 64 114 52 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 338 108 64 208 146 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 338 108 64 208 146 smit:SMT_1690|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1674779..1675009_NEGATIVE 338 108 64 208 146 smit:SMT_779|5end_ribonuclease_BN,_putative_688530..688760_NEGATIVE 338 108 64 208 146 smit:SMT_388|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_321172..321402_POSITIVE 338 108 64 182 120 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 336 109 64 173 133 smit:SMT_1245|5end_SOS_responce_UmuC_protein_1205120..1205350_POSITIVE 328 115 72 74 25 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 327 99 56 124 87 smit:SMT_1393|5end_hypothetical_protein_1369106..1369336_POSITIVE 320 109 68 48 4 smit:SMT_1015|5end_galactose_operon_repressor_951938..952168_POSITIVE 314 102 61 207 150 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 313 115 71 182 131 smit:SMT_568|5end_hypothetical_protein_485674..485904_POSITIVE 310 116 72 224 185 smit:SMT_142|5end_hypothetical_protein_95088..95318_NEGATIVE 308 138 91 74 18 smit:SMT_1248|5end_Na+/H+_antiporter_1210529..1210759_NEGATIVE 308 110 61 160 87 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 308 119 88 73 39 smit:SMT_318|5end_hypothetical_protein_258282..258512_NEGATIVE 305 130 89 157 110 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 300 108 69 77 39 smit:SMT_1639|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1625819..1626049_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 108 64 79 17 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 338 108 64 74 12 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 336 109 64 122 82 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 328 108 61 63 24 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 328 108 61 63 24 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE 328 115 72 61 12 smit:SMT_220|3end_Hypothetical_zinc_metalloprotease_153086..153236_POSITIVE 327 99 56 124 87 smit:SMT_1392|3end_dihydroxyacetone_kinase_1369186..1369336_POSITIVE 311 49 1 95 46 smit:SMT_1847|3end_hypothetical_protein_1812697..1812847_POSITIVE 308 138 91 62 6 smit:SMT_1249|3end_hypothetical_protein_1210541..1210691_NEGATIVE 308 119 88 51 17 smit:SMT_319|3end_K02356_elongation_factor_EF-P_258304..258454_NEGATIVE 298 97 55 145 106 smit:SMT_302|3end_K07444_putative_N6-adenine-specific_DNA_methylase_245319..245469_POSITIVE 297 114 71 150 109 smit:SMT_1044|3end_chaperonin_GroEL_(HSP60_family)_986038..986188_NEGATIVE 293 108 61 64 25 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 287 94 51 57 10 smit:SMT_2074|3end_dTDP-glucose_4,6-dehydratase_1977802..1977952_POSITIVE 282 102 62 149 111 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 280 110 61 61 10 smit:SMT_304|3end_hypothetical_protein_247583..247733_POSITIVE 276 108 61 61 22 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 275 61 23 112 71 smit:SMT_1047|3end_chaperonin,_10_kDa_987920..988070_NEGATIVE 275 61 23 112 71 smit:SMT_1045|3end_cochaperonin_GroES_987451..987601_NEGATIVE 272 108 61 63 24 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE