Origin IGS: aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgtttcaccgagtcatccacataggcaaaggctaggtaagaaatggcnnnnnttaattaattaannnnntcaaccaaggagagactgtccttgatgtagggtgtggttatgggcct Mask Tandem Repeat Region ================================================ aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Find is-nt database================================================ Query_seq: SMT_1457:SMT_1458|SMT_1457:SMT_1458:16S rRNA m(2)G 1207 methyltransferase:K02040 phosphate transport system substrate-binding protein:<-->:1440300..1440416 117 aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1457:SMT_1458|SMT_1457:SMT_1458:16S rRNA m(2)G 1207 methyltransferase:K02040 phosphate transport system substrate-binding protein:<-->:1440300..1440416 117 aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1457:SMT_1458|SMT_1457:SMT_1458:16S rRNA m(2)G 1207 methyltransferase:K02040 phosphate transport system substrate-binding protein:<-->:1440300..1440416 117 aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Predict ORF larger than 30AA ================================================ aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc 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================================================ aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1457:SMT_1458|SMT_1457:SMT_1458:16S rRNA m(2)G 1207 methyltransferase:K02040 phosphate transport system substrate-binding protein:<-->:1440300..1440416 117 aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: smit_SMT_1457_SMT_1458|16S rRNA m(2)G 1207 methyltransferase:K02040 phosphate transport system substrate-binding protein|NEGATIVE:POSITIVE|[1440300,1440416]|117 HSP 1 e-value: 2.0E-42 bit: 172.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc aggcccataaccacaccctacatcaaggacagtctctccttggttgannnnnttaattaattaannnnngccatttcttacctagcctttgcctatgtggatgactcggtgaaacgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCCCAUAACCACACCCUACAUCAAGGACAGUCUCUCCUUGGUUGANNNNNUUAAUUAAUUAANNNNNGCCAUUUCUUACCUAGCCUUUGCCUAUGUGGAUGACUCGGUGAAACGC .(((.................((((((((.......)))))))).........(((....)))......))).....(((((.(((.((..(....)..)).).)).)))))..... (-18.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUUUCACCGAGUCAUCCACAUAGGCAAAGGCUAGGUAAGAAAUGGCNNNNNUUAAUUAAUUAANNNNNUCAACCAAGGAGAGACUGUCCUUGAUGUAGGGUGUGGUUAUGGGCCU .(((((((((.((((..((.....))....)))).)))..)))))).............................((((((.......)))))).....((((.(......).)))) (-21.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 940 47 1 138 92 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 307 42 2 225 173 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 296 110 74 71 28 smit:SMT_984|5end_transcriptional_regulator_Spx_930898..931128_NEGATIVE 283 44 1 67 23 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 282 43 2 186 130 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 275 42 11 43 4 smit:SMT_453|5end_CopAB_ATPase_metal-fist_type_repressor_390883..391113_POSITIVE 273 45 1 223 168 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 273 45 2 185 144 smit:SMT_1426|5end_K03095_SprT-like_protein_1411313..1411543_NEGATIVE 272 44 1 64 22 smit:SMT_1329|5end_GTP-binding_protein_CgtA_1305788..1306018_NEGATIVE 266 46 2 42 3 smit:SMT_895|5end_cysteinyl-tRNA_synthetase_843037..843267_NEGATIVE 266 46 2 42 3 smit:SMT_383|5end_cysteinyl-tRNA_synthetase_318689..318919_POSITIVE 260 45 1 106 41 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 259 35 1 229 179 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 256 42 1 49 2 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 245 43 16 84 56 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 244 47 1 83 45 smit:SMT_1606|5end_glutamate_racemase_1595857..1596087_POSITIVE 243 109 70 154 126 smit:SMT_669|5end_ribose-phosphate_pyrophosphokinase_578160..578390_POSITIVE 241 104 70 136 96 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 241 105 71 194 153 smit:SMT_314|5end_biotin_carboxylase_254277..254507_POSITIVE 240 109 71 39 4 smit:SMT_497|5end_hypothetical_protein_431200..431430_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 44 2 49 6 smit:SMT_1650|3end_ribonuclease_III_1637087..1637237_POSITIVE 287 110 73 138 93 smit:SMT_377|3end_hypothetical_protein_315848..315998_POSITIVE 273 45 1 113 58 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 250 110 74 134 100 smit:SMT_1580|3end_MutT/NUDIX_family_protein_1573153..1573303_POSITIVE 245 43 16 87 59 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 243 98 81 91 72 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 243 109 70 42 14 smit:SMT_667|3end_hypothetical_protein_578128..578278_POSITIVE 241 104 70 134 94 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 234 109 77 66 32 smit:SMT_625|3end_50S_ribosomal_protein_L27_530400..530550_POSITIVE 228 100 53 133 91 smit:SMT_608|3end_laminin-binding_surface_protein_521187..521337_POSITIVE 226 105 71 120 86 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 222 43 5 143 99 smit:SMT_2042|3end_K04077_chaperonin_GroEL_(Hsp60)_1952960..1953110_NEGATIVE 222 43 1 70 9 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 219 46 1 150 95 smit:SMT_1998|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1922640..1922790_POSITIVE 219 107 70 119 85 smit:SMT_1064|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1004419..1004569_POSITIVE 215 44 5 112 76 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 214 107 73 38 1 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE 214 101 71 128 99 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 214 101 71 128 99 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 213 110 73 62 13 smit:SMT_1795|3end_DNA_polymerase_III,_delta_subunit_1769185..1769335_NEGATIVE