Origin IGS: cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agttacttggttttcagcaacaagtgggttgtaagttccaactgtttcgatgaaacgtccgtcacgtggtgaacgtgannnnnttaattaattaannnnntggaggagatacatagaggggtcg Mask Tandem Repeat Region ================================================ cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Find is-nt database================================================ Query_seq: SMT_528:SMT_529|SMT_528:SMT_529:hypothetical protein predicted by Glimmer/Critica:30S ribosomal protein S16:->->:452193..452316 124 cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_528:SMT_529|SMT_528:SMT_529:hypothetical protein predicted by Glimmer/Critica:30S ribosomal protein S16:->->:452193..452316 124 cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_528:SMT_529|SMT_528:SMT_529:hypothetical protein predicted by Glimmer/Critica:30S ribosomal protein S16:->->:452193..452316 124 cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Predict ORF larger than 30AA ================================================ cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact 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================================================ cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_528:SMT_529|SMT_528:SMT_529:hypothetical protein predicted by Glimmer/Critica:30S ribosomal protein S16:->->:452193..452316 124 cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: smit_SMT_528_SMT_529|hypothetical protein predicted by Glimmer/Critica:30S ribosomal protein S16|POSITIVE:POSITIVE|[452193,452316]|124 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact cgacccctctatgtatctcctccannnnnttaattaattaannnnntcacgttcaccacgtgacggacgtttcatcgaaacagttggaacttacaacccacttgttgctgaaaaccaagtaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGACCCCUCUAUGUAUCUCCUCCANNNNNUUAAUUAAUUAANNNNNUCACGUUCACCACGUGACGGACGUUUCAUCGAAACAGUUGGAACUUACAACCCACUUGUUGCUGAAAACCAAGUAACU ...........((((..(((..(.......................((((((.....)))))).....(((((...))))).)..)))...))))........((((((........)))))). (-20.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUACUUGGUUUUCAGCAACAAGUGGGUUGUAAGUUCCAACUGUUUCGAUGAAACGUCCGUCACGUGGUGAACGUGANNNNNUUAAUUAAUUAANNNNNUGGAGGAGAUACAUAGAGGGGUCG .....(((.((((((.(((((......)))))....((((...(((((...))))).....((((((.....))))))......................)))).)))).))...)))...... (-21.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 92 52 204 168 smit:SMT_176|5end_30S_ribosomal_protein_S3_118081..118311_POSITIVE 257 101 63 229 182 smit:SMT_1566|5end_K03475_PTS_system,_unknown_pentitol_phosphotransferase_enzyme_IIC_component_1557918..1558148_POSITIVE 254 86 49 117 80 smit:SMT_1922|5end_exonuclease_RexA_1865998..1866228_NEGATIVE 252 89 49 104 59 smit:SMT_1849|5end_hypothetical_protein_1813074..1813304_POSITIVE 249 100 56 165 126 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 247 101 61 222 182 smit:SMT_1334|5end_hypothetical_protein_1309077..1309307_NEGATIVE 245 87 51 199 166 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 242 73 48 143 118 smit:SMT_2168|5end_threonyl-tRNA_synthetase_2040991..2041221_POSITIVE 242 107 63 183 135 smit:SMT_1250|5end_hypothetical_protein_1211345..1211575_NEGATIVE 241 110 66 175 141 smit:SMT_2119|5end_mercuric_reductase_2005583..2005813_POSITIVE 241 110 61 210 146 smit:SMT_844|5end_putative_phospho-sugar_mutase_791064..791294_NEGATIVE 238 88 50 228 187 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 238 109 61 185 143 smit:SMT_1426|5end_K03095_SprT-like_protein_1411313..1411543_NEGATIVE 237 98 54 64 25 smit:SMT_1796|5end_dihydroorotate_dehydrogenase_A_1770816..1771046_NEGATIVE 237 81 49 152 118 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 237 78 51 183 156 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 235 100 54 203 157 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 230 89 49 42 4 smit:SMT_1848|5end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1813014..1813244_NEGATIVE 229 110 63 204 162 smit:SMT_1165|5end_sensor_protein_CiaH_1111820..1112050_NEGATIVE 229 110 63 204 162 smit:SMT_539|5end_sensor_histidine_kinase_CiaH_455752..455982_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 110 65 86 34 smit:SMT_1146|3end_maltose_operon_transcriptional_repressor_1091202..1091352_POSITIVE 237 81 49 150 116 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 237 110 61 84 38 smit:SMT_419|3end_hypothetical_protein_predicted_by_Glimmer/Critica_362510..362660_POSITIVE 229 77 49 148 115 smit:SMT_1778|3end_ATP-dependent_RNA_helicase_1753611..1753761_NEGATIVE 228 67 49 143 122 smit:SMT_185|3end_50S_ribosomal_protein_L6_122619..122769_POSITIVE 225 96 59 87 52 smit:SMT_1185|3end_beta-galactosidase_1142034..1142184_NEGATIVE 225 89 47 66 12 smit:SMT_313|3end_3R-hydroxymyristoyl_ACP_dehydrase_254345..254495_POSITIVE 220 97 54 81 27 smit:SMT_1441|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1424887..1425037_NEGATIVE 220 98 57 54 14 smit:SMT_929|3end_hypothetical_protein_883202..883352_NEGATIVE 219 85 57 133 108 smit:SMT_947|3end_ferredoxin_896682..896832_POSITIVE 217 98 53 54 3 smit:SMT_1606|3end_glutamate_racemase_1596731..1596881_POSITIVE 216 93 58 93 52 smit:SMT_2121|3end_putative_mucus_binding_protein_2006525..2006675_NEGATIVE 215 86 53 80 49 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 213 110 68 149 92 smit:SMT_1539|3end_sensor_histidine_kinase,_putative_1523315..1523465_NEGATIVE 212 110 70 143 89 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 211 100 51 75 28 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 211 76 49 120 87 smit:SMT_619|3end_riboflavin_kinase_/_FMN_adenylyltransferase_528719..528869_POSITIVE 209 105 65 66 14 smit:SMT_1108|3end_acetate_kinase_1048122..1048272_NEGATIVE 208 100 55 40 3 smit:SMT_1827|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1797722..1797872_POSITIVE 208 88 49 51 2 smit:SMT_604|3end_DNA_polymerase_III,_epsilon_chain_519069..519219_POSITIVE