Origin IGS: ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctccgtttgctctatgcccatcaagtgtatagagcttttttgtgtacaattcttcaattttagttcaatatcagaaaaaaagaaccttgcatagcaagattcttttagtgtctgacttaaataattgttcttctgggaactaaatcgaa Mask Tandem Repeat Region ================================================ ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Find is-nt database================================================ Query_seq: SMT_561:SMT_562|SMT_561:SMT_562:putative translation elongation factor EF-Tu:ATP-dependent RNA helicase, DEAD/DEAH box family:-><-:480748..480898 151 ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_561:SMT_562|SMT_561:SMT_562:putative translation elongation factor EF-Tu:ATP-dependent RNA helicase, DEAD/DEAH box family:-><-:480748..480898 151 ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_561:SMT_562|SMT_561:SMT_562:putative translation elongation factor EF-Tu:ATP-dependent RNA helicase, DEAD/DEAH box family:-><-:480748..480898 151 ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 10 End: 108 ......... N G S S C N N L D S V L L I K S H L T R K K Q Y Q V L I S S N Y M ........................................... ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct 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================================================ ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.5 Tail_Score: -5.70829 Start: 48 End: 68 Full_Region: AGTCAGACACTAAAA GAATCTTGC TAT GCAAGGTTC TTTTTTTCTGATATT ...............................................GAATCTTGCTATGCAAGGTTC................................................................................... TransTerm Strand: - Conf: 85 HP_score: -8.3 Tail_Score: -4.39568 Start: 48 End: 68 Full_Region: aatatcagaaaaaaa gaaccttgc ata gcaagattc ttttagtgtctgact ...............................................gaaccttgcatagcaagattc................................................................................... Find igs database================================================ Query_seq: SMT_561:SMT_562|SMT_561:SMT_562:putative translation elongation factor EF-Tu:ATP-dependent RNA helicase, DEAD/DEAH box family:-><-:480748..480898 151 ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: smit_SMT_561_SMT_562|putative translation elongation factor EF-Tu:ATP-dependent RNA helicase, DEAD/DEAH box family|POSITIVE:NEGATIVE|[480748,480898]|151 HSP 1 e-value: 5.0E-68 bit: 258.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttcnnnnnnnctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct ttcgatttagttcccagaagaacaattatttaagtcagacactaaaagaatcttgctatgcaaggttctttttttctgatattgaactaaaattgaagaattgtacacaaaaaagctctatacacttgatgggcatagagcaaacggagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGAUUUAGUUCCCAGAAGAACAAUUAUUUAAGUCAGACACUAAAAGAAUCUUGCUAUGCAAGGUUCUUUUUUUCUGAUAUUGAACUAAAAUUGAAGAAUUGUACACAAAAAAGCUCUAUACACUUGAUGGGCAUAGAGCAAACGGAGCU ........((((((.....(.((((((.(((((((((((....(((((((((((((...)))))))))))))..))))))............))))).)))))).)........(((((((.(.((....))).)))))))....)))))) (-41.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCCGUUUGCUCUAUGCCCAUCAAGUGUAUAGAGCUUUUUUGUGUACAAUUCUUCAAUUUUAGUUCAAUAUCAGAAAAAAAGAACCUUGCAUAGCAAGAUUCUUUUAGUGUCUGACUUAAAUAAUUGUUCUUCUGGGAACUAAAUCGAA ..........(((((((((.(.....).)))))))))..................((...((((((((....(((((..(((((((.(((((...))))).)))))))....)))))..............(....).))))))))..)). (-34.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 150 126 192 165 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 260 150 115 109 67 smit:SMT_463|5end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_401926..402156_POSITIVE 257 79 37 227 179 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 255 86 46 53 11 smit:SMT_1839|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1805999..1806229_NEGATIVE 253 138 97 134 94 smit:SMT_1095|5end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1036373..1036603_POSITIVE 251 50 4 71 31 smit:SMT_680|5end_choline_transport_protein_589962..590192_NEGATIVE 240 70 29 154 110 smit:SMT_1359|5end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1338003..1338233_NEGATIVE 238 149 110 124 90 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 238 40 1 158 117 smit:SMT_192|5end_translation_initiation_factor_IF-1_126500..126730_POSITIVE 233 150 102 219 171 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 232 140 93 189 152 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 230 147 114 193 154 smit:SMT_1586|5end_K07177_PDZ_domain-containing_protein_1575714..1575944_POSITIVE 229 78 50 209 178 smit:SMT_1112|5end_K02248_competence_protein_ComGF_1051848..1052078_NEGATIVE 224 147 125 183 160 smit:SMT_992|5end_hypothetical_protein_934882..935112_NEGATIVE 220 150 114 46 5 smit:SMT_134|5end_LysM_domain_protein_85427..85657_POSITIVE 219 68 32 173 137 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 217 133 94 141 94 smit:SMT_1162|5end_ATP-dependent_DNA_helicase_1108895..1109125_NEGATIVE 217 77 32 65 20 smit:SMT_121|5end_hypothetical_protein_73303..73533_POSITIVE 215 150 124 48 6 smit:SMT_1745|5end_UDP-glucose_4-epimerase_1725541..1725771_NEGATIVE 213 99 52 83 29 smit:SMT_1532|5end_hypothetical_protein_1516296..1516526_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 79 31 56 10 smit:SMT_561|3end_putative_translation_elongation_factor_EF-Tu_480687..480837_POSITIVE 255 86 46 45 3 smit:SMT_1840|3end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806007..1806157_NEGATIVE 252 72 33 87 48 smit:SMT_110|3end_alpha-L-fucosidase_59207..59357_POSITIVE 251 50 4 81 41 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 230 67 23 59 14 smit:SMT_262|3end_glutathione_peroxidase_201906..202056_NEGATIVE 229 40 2 41 1 smit:SMT_191|3end_adenylate_kinase_126463..126613_POSITIVE 222 89 41 151 105 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 212 142 116 131 103 smit:SMT_1116|3end_K02244_competence_protein_ComGB_1052798..1052948_NEGATIVE 210 150 101 135 70 smit:SMT_1388|3end_hypothetical_protein_1365833..1365983_POSITIVE 208 85 63 27 3 smit:SMT_1486|3end_hypothetical_protein_1466444..1466594_POSITIVE 208 75 53 144 122 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 205 150 108 144 106 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 205 78 33 67 32 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 204 79 33 148 79 smit:SMT_1421|3end_K02003_1406584..1406734_NEGATIVE 204 149 107 109 62 smit:SMT_144|3end_hypothetical_protein_predicted_by_Glimmer/Critica_95848..95998_POSITIVE 199 150 108 58 9 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 199 150 108 58 9 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE 198 69 23 60 15 smit:SMT_359|3end_transcription_termination-antitermination_factor_295686..295836_POSITIVE 197 139 94 78 27 smit:SMT_398|3end_hypothetical_protein_328279..328429_POSITIVE 196 98 53 146 95 smit:SMT_1520|3end_K02004_1499805..1499955_NEGATIVE