Origin IGS: aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccctgagagaggcaagacctctcttttttatgcagtttagacggtgtagggaacagaatggagaaaagaaccgaattggcttcattatttgttaaactgtatctagaaagggggacgtt Mask Tandem Repeat Region ================================================ aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Find is-nt database================================================ Query_seq: SMT_1091:SMT_1092|SMT_1091:SMT_1092:competence-specific global transcription modulator:transcription antitermination factor:<-<-:1033131..1033249 119 aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1091:SMT_1092|SMT_1091:SMT_1092:competence-specific global transcription modulator:transcription antitermination factor:<-<-:1033131..1033249 119 aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1091:SMT_1092|SMT_1091:SMT_1092:competence-specific global transcription modulator:transcription antitermination factor:<-<-:1033131..1033249 119 aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 28 End: 117 ........................... C I I F G I R N K E G N Q E R C R R F Q M F F L P R A E R M .. aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg 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================================================ aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1091:SMT_1092|SMT_1091:SMT_1092:competence-specific global transcription modulator:transcription antitermination factor:<-<-:1033131..1033249 119 aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Intra-Species Hit: Count: 2 Min: 1 Max: 119 Len: 119 Subject: smit_SMT_1091_SMT_1092|competence-specific global transcription modulator:transcription antitermination factor|NEGATIVE:NEGATIVE|[1033131,1033249]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctccattctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg Subject: smit_SMT_101_SMT_102|cell division protein:competence-specific global transcription modulator|POSITIVE:POSITIVE|[34128,34247]|120 HSP 1 e-value: 1.0E-9 bit: 63.9 Len: 119 Query Start:1 Query End:119 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 120 aacgtccccctttctagatacagtttaacaaataatgaagccaattcggttcttttctcc-attctgttccctacaccgtctaaactgcataaaaaagagaggtcttgcctctctcaggg aacgttcccctttctagatacagtctaacaaatcaagaacttaattgggaccatttcgcctattctgtctcctttaccgtctcaactgcacaaaaaagagaggtcacgcctctctcaggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGUCCCCCUUUCUAGAUACAGUUUAACAAAUAAUGAAGCCAAUUCGGUUCUUUUCUCCAUUCUGUUCCCUACACCGUCUAAACUGCAUAAAAAAGAGAGGUCUUGCCUCUCUCAGGG .......((((.........(((((((((.........((((.....)))).............(((.....)))..)).)))))))........(((((((.....))))))).)))) (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUGAGAGAGGCAAGACCUCUCUUUUUUAUGCAGUUUAGACGGUGUAGGGAACAGAAUGGAGAAAAGAACCGAAUUGGCUUCAUUAUUUGUUAAACUGUAUCUAGAAAGGGGGACGUU ((((.(((((((.....)))))))(((..(((((((((.(((((....(....)..(((((((..((........))..)))))))..))))))))))))))..)))..))))...... (-33.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 90 41 181 132 smit:SMT_1091|5end_competence-specific_global_transcription_modulator_1033040..1033270_NEGATIVE 603 110 61 202 153 smit:SMT_102|5end_competence-specific_global_transcription_modulator_34108..34338_POSITIVE 373 88 41 59 16 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 373 88 41 59 16 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 339 90 47 55 15 smit:SMT_498|5end_hypothetical_protein_431751..431981_POSITIVE 320 23 2 114 93 smit:SMT_2048|5end_competence-specific_global_transcription_modulator_1958278..1958508_NEGATIVE 319 90 49 175 137 smit:SMT_1753|5end_tryptophan_synthase_beta_chain_1730349..1730579_POSITIVE 305 109 75 38 3 smit:SMT_1913|5end_RBL02035_1858257..1858487_POSITIVE 305 109 75 38 3 smit:SMT_1765|5end_ABC_transporter_sugar_permease_1740847..1741077_POSITIVE 293 90 42 119 74 smit:SMT_499|5end_hypothetical_protein_432572..432802_POSITIVE 285 50 3 143 97 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 284 109 69 215 171 smit:SMT_755|5end_shikimate_5-dehydrogenase_659917..660147_NEGATIVE 276 80 40 201 160 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 272 83 48 111 78 smit:SMT_1501|5end_recombination_protein_1484401..1484631_POSITIVE 269 80 40 67 18 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 265 108 66 199 155 smit:SMT_1586|5end_K07177_PDZ_domain-containing_protein_1575714..1575944_POSITIVE 259 79 36 116 62 smit:SMT_815|5end_hypothetical_protein_724294..724524_NEGATIVE 253 110 64 154 103 smit:SMT_665|5end_NAD+_kinase_576745..576975_NEGATIVE 248 80 36 184 122 smit:SMT_1104|5end_K06346_spoIIIJ-associated_protein_1046784..1047014_NEGATIVE 247 104 64 126 78 smit:SMT_1007|5end_radical_SAM_domain_protein_947035..947265_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 603 110 61 81 32 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 373 88 41 62 19 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 305 109 75 36 1 smit:SMT_1764|3end_K02025_multiple_sugar_transport_system_permease_protein_1740925..1741075_POSITIVE 289 90 51 34 1 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 281 89 41 148 101 smit:SMT_812|3end_acetyltransferase,_GNAT_family_721664..721814_NEGATIVE 280 45 3 150 107 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 272 83 48 56 23 smit:SMT_1500|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1484426..1484576_POSITIVE 259 79 36 68 14 smit:SMT_816|3end_SWF/SNF_family_helicase_724342..724492_NEGATIVE 253 109 61 49 4 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 247 104 64 133 85 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 247 80 31 70 28 smit:SMT_363|3end_K02519_translation_initiation_factor_IF-2_300751..300901_POSITIVE 243 110 73 75 34 smit:SMT_1097|3end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1038697..1038847_NEGATIVE 240 109 65 133 88 smit:SMT_1891|3end_putative_dihydrolipoamide_S-acetyltransferase_1845019..1845169_POSITIVE 240 81 41 143 100 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE 238 80 39 135 72 smit:SMT_666|3end_GTP_pyrophosphokinase-like_protein_576729..576879_NEGATIVE 236 50 2 82 29 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 235 79 33 56 11 smit:SMT_1502|3end_pantothenate_kinase_1486927..1487077_POSITIVE 232 88 41 132 77 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 227 106 64 52 11 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 227 110 76 91 59 smit:SMT_1112|3end_K02248_competence_protein_ComGF_1051387..1051537_NEGATIVE