Origin IGS: aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catatacatacgacaaggcgacgttaacgtggtttgaaaagattttcgaagagtataagtctctacataacaaaacgcatattaccaaggtttttctattcctgataatatgcgttttttgattgtaaatatttt Mask Tandem Repeat Region ================================================ aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Find is-nt database================================================ Query_seq: SMT_130:SMT_131|SMT_130:SMT_131:capsular polysaccharide biosynthesis protein:phosphatase, putative:-><-:82986..83120 135 aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_130:SMT_131|SMT_130:SMT_131:capsular polysaccharide biosynthesis protein:phosphatase, putative:-><-:82986..83120 135 aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_130:SMT_131|SMT_130:SMT_131:capsular polysaccharide biosynthesis protein:phosphatase, putative:-><-:82986..83120 135 aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 6 End: 134 ..... M Y N Q K T H I I R N R K T L V I C V L L C R D L Y S S K I F S N H V N V A L S Y V Y . aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg 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================================================ aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 62 HP_score: -6.3 Tail_Score: -3.494 Start: 17 End: 65 Full_Region: AAATATTTACAATCA AAAAACGCATATTATCAGG AATAGAAAAAC CTTGGTAATATGCGTTTTG TTATGTAGAGACTTA ................AAAAACGCATATTATCAGGAATAGAAAAACCTTGGTAATATGCGTTTTG...................................................................... TransTerm Strand: + Conf: 80 HP_score: -6.2 Tail_Score: -4.84311 Start: 22 End: 60 Full_Region: TTTACAATCAAAAAA CGCATATTATCAGG AATAGAAAAAC CTTGGTAATATGCG TTTTGTTATGTAGAG .....................CGCATATTATCAGGAATAGAAAAACCTTGGTAATATGCG........................................................................... TransTerm Strand: - Conf: 74 HP_score: -3.9 Tail_Score: -5.32944 Start: 22 End: 60 Full_Region: ctctacataacaaaa cgcatattaccaaggtt tttct attcctgataatatgcg ttttttgattgtaaa .....................cgcatattaccaaggtttttctattcctgataatatgcg........................................................................... Find igs database================================================ Query_seq: SMT_130:SMT_131|SMT_130:SMT_131:capsular polysaccharide biosynthesis protein:phosphatase, putative:-><-:82986..83120 135 aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: smit_SMT_130_SMT_131|capsular polysaccharide biosynthesis protein:phosphatase, putative|POSITIVE:NEGATIVE|[82986,83120]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg aaaatatttacaatcaaaaaacgcatattatcaggaatagaaaaaccttggtaatatgcgttttgttatgtagagacttatactcttcgaaaatcttttcaaaccacgttaacgtcgccttgtcgtatgtatatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUUUACAAUCAAAAAACGCAUAUUAUCAGGAAUAGAAAAACCUUGGUAAUAUGCGUUUUGUUAUGUAGAGACUUAUACUCUUCGAAAAUCUUUUCAAACCACGUUAACGUCGCCUUGUCGUAUGUAUAUG ......((((((.....((((((((((((((((((...........))))))))))))))))))....))))))....(((((.....((((....))))...........(((.(.....).)))..))))).. (-31.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUACAUACGACAAGGCGACGUUAACGUGGUUUGAAAAGAUUUUCGAAGAGUAUAAGUCUCUACAUAACAAAACGCAUAUUACCAAGGUUUUUCUAUUCCUGAUAAUAUGCGUUUUUUGAUUGUAAAUAUUUU ..(((((..........((.(((....))).))((((((....))))))...)))))......((((..(.(((((((((((((...(((..(....)..)))..))))))))))))).)...))))........ (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 736 128 81 200 153 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 724 127 81 218 171 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 724 127 81 188 141 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 648 127 81 153 106 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 648 127 81 153 106 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 648 127 81 153 106 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 600 127 81 171 124 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 513 127 98 155 126 smit:SMT_604|5end_DNA_polymerase_III,_epsilon_chain_518693..518923_POSITIVE 493 122 81 173 124 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 492 111 77 196 162 smit:SMT_1592|5end_putative_hemolysin_1579655..1579885_POSITIVE 466 114 80 231 197 smit:SMT_496|5end_superoxide_dismutase,_manganese-dependent_430433..430663_POSITIVE 435 115 77 231 193 smit:SMT_957|5end_UDP-glucose_4-epimerase_905003..905233_NEGATIVE 435 115 77 231 193 smit:SMT_950|5end_UDP-glucose_4-epimerase_898696..898926_NEGATIVE 411 120 78 215 165 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 406 127 81 200 158 smit:SMT_1026|5end_sucrose_phosphorylase_962324..962554_NEGATIVE 379 109 68 226 188 smit:SMT_826|5end_hypothetical_protein_750022..750252_NEGATIVE 336 104 69 193 155 smit:SMT_741|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_645618..645848_NEGATIVE 278 127 93 121 90 smit:SMT_1539|5end_sensor_histidine_kinase,_putative_1524310..1524540_NEGATIVE 270 129 83 154 105 smit:SMT_478|5end_hypothetical_protein_predicted_by_Glimmer/Critica_414644..414874_POSITIVE 245 79 32 200 153 smit:SMT_577|5end_transcriptional_regulator,_LysR_family_495324..495554_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 710 130 81 150 101 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE 498 70 21 77 28 smit:SMT_779|3end_ribonuclease_BN,_putative_687883..688033_NEGATIVE 493 122 81 77 28 smit:SMT_1782|3end_hypothetical_protein_1759740..1759890_POSITIVE 483 127 84 141 98 smit:SMT_1911|3end_hypothetical_protein_1857840..1857990_POSITIVE 483 127 84 141 98 smit:SMT_867|3end_hypothetical_protein_816542..816692_POSITIVE 453 127 91 38 1 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 453 127 91 38 1 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 453 127 91 38 1 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 444 127 87 35 1 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 361 70 21 87 35 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 344 64 21 73 30 smit:SMT_130|3end_capsular_polysaccharide_biosynthesis_protein_82925..83075_POSITIVE 334 127 93 35 1 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE 334 67 21 68 24 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 311 70 21 62 14 smit:SMT_1615|3end_K02016_iron_complex_transport_system_substrate-binding_protein_1601734..1601884_NEGATIVE 282 120 76 130 84 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 278 127 93 124 93 smit:SMT_1540|3end_hypothetical_protein_1524307..1524457_NEGATIVE 276 125 85 67 30 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 267 69 21 65 17 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 264 120 80 42 3 smit:SMT_742|3end_hypothetical_protein_645784..645934_NEGATIVE 248 64 21 59 18 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE