Origin IGS: gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttaaagtctcttttcttattttttatttcggtgaaatagctaagctatttagcacatgttctattatagcagatttctggcaggtgtcaagaaaaaaacttgacagactataaaattcttaaaccttttagaaatttgttatatttttaaagaaaaatcagaaagagaatgtc Mask Tandem Repeat Region ================================================ gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Find is-nt database================================================ Query_seq: SMT_508:SMT_509|SMT_508:SMT_509:hypothetical protein:30S ribosomal protein S16:<-->:438711..438885 175 gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_508:SMT_509|SMT_508:SMT_509:hypothetical protein:30S ribosomal protein S16:<-->:438711..438885 175 gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_508:SMT_509|SMT_508:SMT_509:hypothetical protein:30S ribosomal protein S16:<-->:438711..438885 175 gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 64 End: 156 ............................................................... L R D L K K R S V Q W F D A I I S C T S F L K A I E G F Y F M ................... gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa 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================================================ gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -4.3 Tail_Score: -3.34715 Start: 121 End: 135 Full_Region: TATAATAGAACATGT GCTAA ATAGC TTAGC TATTTCACCGAAATA ........................................................................................................................GCTAAATAGCTTAGC........................................ Find igs database================================================ Query_seq: SMT_508:SMT_509|SMT_508:SMT_509:hypothetical protein:30S ribosomal protein S16:<-->:438711..438885 175 gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: smit_SMT_508_SMT_509|hypothetical protein:30S ribosomal protein S16|NEGATIVE:POSITIVE|[438711,438885]|175 HSP 1 e-value: 3.0E-82 bit: 305.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagnnnnnnncttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa gacattctctttctgatttttctttaaaaatataacaaatttctaaaaggtttaagaattttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaataagaaaagagactttaaaa Inter-species Hit: Count: 3 Min: 33 Max: 175 Len: 143 Subject: NC_008533_SPD_0673_SPD_0674|hypothetical protein:ribosomal protein S16|NEGATIVE:POSITIVE|[693148,694012]|865 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 143 Query Start:33 Query End:175 Subject Strand: POSITIVE Subject Start: 721 Subject End: 865 ................................taacaaatttctaaaaggtttaagaattttatagtctgtcaagnnnnnnncttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaat--aagaaaagagactttaaaa ................................taacaaatttctaaatactttaagaaatttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagctcagctatttcaccgaaataaaaaattaaagaaatgagactttaaaa Subject: NC_003098_spr0681_spr0682|hypothetical protein:30S ribosomal protein S16|NEGATIVE:POSITIVE|[685735,686481]|747 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 143 Query Start:33 Query End:175 Subject Strand: POSITIVE Subject Start: 603 Subject End: 747 ................................taacaaatttctaaaaggtttaagaattttatagtctgtcaagnnnnnnncttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaat--aagaaaagagactttaaaa ................................taacaaatttctaaatactttaagaaatttatagtctgtcaagtttttttcttgacacctgccagaaatctgctataatagaacatgtgctaaatagctcagctatttcaccgaaataaaaaattaaagaaatgagactttaaaa Subject: NC_003028_SP_0774_SP_0775|hypothetical protein:30S ribosomal protein S16|NEGATIVE:POSITIVE|[731629,731797]|169 HSP 1 e-value: 4.0E-41 bit: 168.0 Len: 143 Query Start:33 Query End:175 Subject Strand: POSITIVE Subject Start: 25 Subject End: 169 ................................taacaaatttctaaaaggtttaagaattttatagtctgtcaagnnnnnnncttgacacctgccagaaatctgctataatagaacatgtgctaaatagcttagctatttcaccgaaataaaaaat--aagaaaagagactttaaaa ................................taacaaatttctaaatactttaagaaatttatagtctgtcaagtttttttcttgacacatgccagaaatctgctataatagaacatgtgctaaatagctcagctatttcaccgaaataaaaaattaaagaaatgagactttaaaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAAUUUCUAAAAGGUUUAAGAAUUUUAUAGUCUGUCAAGUUUUUUUCUUGACACCUGCCAGAAAUCUGCUAUAAUAGAACAUGUGCUAAAUAGCUUAGCUAUUUCACCGAAAUAAAAAAUAAGAAAAGAGACUUUAAAA ..............(((((((.......((((((..(((((((.......))))))).....(((....)))))))))........(((..(((((((...)))))))))).....................))))))).... (-21.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAAGUCUCUUUUCUUAUUUUUUAUUUCGGUGAAAUAGCUAAGCUAUUUAGCACAUGUUCUAUUAUAGCAGAUUUCUGGCAGGUGUCAAGAAAAAAACUUGACAGACUAUAAAAUUCUUAAACCUUUUAGAAAUUUGUUA ................................(((.((((((...))))))...)))...........((((((((((((((.((((((((((.......))))))......(((.....))).)))).)))))))))))))) (-29.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 867 100 51 223 174 smit:SMT_508|5end_hypothetical_protein_438620..438850_NEGATIVE 285 82 42 224 174 smit:SMT_309|5end_acyl-carrier-protein_S-malonyltransferase_250406..250636_POSITIVE 283 87 48 221 184 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 280 99 51 68 20 smit:SMT_1793|5end_inosine-5'-monophosphate_dehydrogenase_1767985..1768215_POSITIVE 273 80 32 157 113 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 266 75 31 57 11 smit:SMT_549|5end_hypothetical_cytosolic_protein_467057..467287_POSITIVE 259 74 36 214 168 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 249 75 35 139 103 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 248 73 32 70 34 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 247 65 23 170 126 smit:SMT_1933|5end_K02006_cobalt_transport_system_ATP-binding_protein_1872222..1872452_NEGATIVE 247 79 35 201 148 smit:SMT_1104|5end_K06346_spoIIIJ-associated_protein_1046784..1047014_NEGATIVE 247 75 33 90 49 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 247 79 32 94 28 smit:SMT_453|5end_CopAB_ATPase_metal-fist_type_repressor_390883..391113_POSITIVE 246 80 33 204 159 smit:SMT_1857|5end_hypothetical_protein_1820931..1821161_POSITIVE 246 73 35 203 160 smit:SMT_1542|5end_phosphomevalonate_kinase_1527084..1527314_NEGATIVE 246 80 33 204 159 smit:SMT_834|5end_hypothetical_protein_777112..777342_NEGATIVE 242 50 3 137 98 smit:SMT_1294|5end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1255983..1256213_POSITIVE 241 66 34 65 35 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 240 80 33 83 31 smit:SMT_1830|5end_galactose-6-phosphate_isomerase_1799338..1799568_POSITIVE 238 76 38 91 60 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 73 32 117 77 smit:SMT_788|3end_hypothetical_protein_699153..699303_NEGATIVE 271 73 51 85 64 smit:SMT_1557|3end_hypothetical_protein_1543650..1543800_POSITIVE 243 75 36 151 107 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 242 50 3 137 98 smit:SMT_1293|3end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1256063..1256213_POSITIVE 240 80 33 84 30 smit:SMT_447|3end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386987..387137_POSITIVE 238 76 38 83 52 smit:SMT_2014|3end_tryptophan_synthase_beta_chain_1932727..1932877_POSITIVE 238 73 51 77 56 smit:SMT_1925|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867458..1867608_POSITIVE 237 72 33 70 22 smit:SMT_1907|3end_phosphate-binding_protein_1854604..1854754_POSITIVE 232 74 31 151 109 smit:SMT_1355|3end_conserved_hypothetical_protein_TIGR00043_1331982..1332132_NEGATIVE 231 90 51 60 31 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 231 112 85 132 103 smit:SMT_1883|3end_hypothetical_protein_1838034..1838184_NEGATIVE 227 66 31 147 106 smit:SMT_1367|3end_K02237_competence_protein_ComEA_1346872..1347022_NEGATIVE 225 62 34 81 53 smit:SMT_1427|3end_S1_RNA_binding_domain_protein_1411300..1411450_NEGATIVE 225 73 35 150 116 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 223 99 54 88 30 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 222 100 58 84 51 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 221 75 36 70 23 smit:SMT_1161|3end_K05837_rod_shape_determining_protein_RodA_1105185..1105335_NEGATIVE 220 110 64 124 78 smit:SMT_900|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_848367..848517_NEGATIVE 218 66 36 137 104 smit:SMT_662|3end_A/G-specific_adenine_glycosylase_572652..572802_NEGATIVE 216 75 31 131 69 smit:SMT_417|3end_short_chain_dehydrogenase_361208..361358_POSITIVE