Origin IGS: agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttcctccttgtaaacaaattagactatatgtctaaaaatggattttttatcttgtaatttagattttttaatgtataatctattatatcaaaattttagacaatatgtttaaaaaaggagaaact Mask Tandem Repeat Region ================================================ agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Find is-nt database================================================ Query_seq: SMT_81:SMT_82|SMT_81:SMT_82:K01421 putative membrane protein:transcriptional regulator, TetR family:<-->:13721..13847 127 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_81:SMT_82|SMT_81:SMT_82:K01421 putative membrane protein:transcriptional regulator, TetR family:<-->:13721..13847 127 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_81:SMT_82|SMT_81:SMT_82:K01421 putative membrane protein:transcriptional regulator, TetR family:<-->:13721..13847 127 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Predict ORF larger than 30AA ================================================ agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 34 End: 63 .................................TTTGATATAATAGATTATACATTAAAAAAT................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 40 End: 69 .......................................ATTTAGATTTTTTAATGTATAATCTATTAT.......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 63 HP_score: -5.2 Tail_Score: -4.41348 Start: 91 End: 107 Full_Region: ATAAAAAATCCATTT TTAGAC ATATA GTCTAA TTTGTTTACAAGGAG ..........................................................................................TTAGACATATAGTCTAA.................... Find igs database================================================ Query_seq: SMT_81:SMT_82|SMT_81:SMT_82:K01421 putative membrane protein:transcriptional regulator, TetR family:<-->:13721..13847 127 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: smit_SMT_81_SMT_82|K01421 putative membrane protein:transcriptional regulator, TetR family|NEGATIVE:POSITIVE|[13721,13847]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat Inter-species Hit: Count: 3 Min: 1 Max: 127 Len: 127 Subject: NC_008533_SPD_2058_SPD_2060|ABC transporter, permease protein, putative:transcriptional regulator, TetR family protein|POSITIVE:POSITIVE|[2038146,2039956]|1811 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1685 Subject End: 1811 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatctatttttagacatatagtctaatttgtttacaaggaggaaat Subject: NC_003098_spr2039_spr2040|Conserved hypothetical protein, truncation:hypothetical protein|NEGATIVE:POSITIVE|[2032279,2032456]|178 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 52 Subject End: 178 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatctatttttagacatatagtctaatttgtttacaaggaggaaat Subject: NC_003028_SP_2233_SP_2234|hypothetical protein:transcriptional regulator, TetR family|NEGATIVE:POSITIVE|[2154702,2154879]|178 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 52 Subject End: 178 agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatccatttttagacatatagtctaatttgtttacaaggaggaaat agtttctccttttttaaacatattgtctaaaattttgatataatagattatacattaaaaaatctaaattacaagataaaaaatctatttttagacatatagtctaatttgtttacaaggaggaaat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUCUCCUUUUUUAAACAUAUUGUCUAAAAUUUUGAUAUAAUAGAUUAUACAUUAAAAAAUCUAAAUUACAAGAUAAAAAAUCCAUUUUUAGACAUAUAGUCUAAUUUGUUUACAAGGAGGAAAU ..(((((((((...((((((...........((((((.((...((((((...........))))))...)))))))).............((((((.....))))))..)))))).))))))))).. (-24.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCCUCCUUGUAAACAAAUUAGACUAUAUGUCUAAAAAUGGAUUUUUUAUCUUGUAAUUUAGAUUUUUUAAUGUAUAAUCUAUUAUAUCAAAAUUUUAGACAAUAUGUUUAAAAAAGGAGAAACU .....((((((.((((((..((((((.....)))))).((((((((...(((.(((.((........)).))).))).)))))))).....................))))))...))))))..... (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 686 120 71 211 162 smit:SMT_81|5end_K01421_putative_membrane_protein_13630..13860_NEGATIVE 194 46 3 197 150 smit:SMT_1803|5end_K03693_penicillin_binding_protein_1776804..1777034_POSITIVE 187 47 2 144 93 smit:SMT_1004|5end_thioredoxin_945430..945660_POSITIVE 179 120 75 113 70 smit:SMT_143|5end_hypothetical_protein_95323..95553_NEGATIVE 178 114 74 104 70 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 177 105 71 60 27 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 176 49 3 143 98 smit:SMT_1802|5end_tyrosyl-tRNA_synthetase_1776712..1776942_NEGATIVE 176 118 85 189 162 smit:SMT_426|5end_hypothetical_protein_368344..368574_POSITIVE 173 46 3 213 161 smit:SMT_1820|5end_cation_transporter_CorA_family_1793600..1793830_POSITIVE 173 104 67 108 71 smit:SMT_826|5end_hypothetical_protein_750022..750252_NEGATIVE 172 32 1 118 93 smit:SMT_630|5end_phosphoserine_phosphatase_535459..535689_POSITIVE 165 47 5 141 97 smit:SMT_1055|5end_transcriptional_regulator,_GntR_family_994752..994982_NEGATIVE 163 59 18 195 149 smit:SMT_552|5end_DNA_polymerase_III,_gamma_and_tau_subunits_469445..469675_POSITIVE 161 117 72 65 24 smit:SMT_824|5end_asparaginyl-tRNA_synthetase_748393..748623_NEGATIVE 160 117 71 133 88 smit:SMT_239|5end_hypothetical_protein_177103..177333_POSITIVE 154 105 85 98 77 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 154 28 2 83 52 smit:SMT_1854|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1818375..1818605_POSITIVE 154 120 84 143 98 smit:SMT_838|5end_cation_efflux_family_protein_782924..783154_POSITIVE 149 120 84 164 137 smit:SMT_1778|5end_ATP-dependent_RNA_helicase_1754954..1755184_NEGATIVE 148 41 5 168 132 smit:SMT_1513|5end_hypothetical_protein_1495582..1495812_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 194 104 74 70 39 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 187 47 2 128 77 smit:SMT_1003|3end_hypothetical_protein_945494..945644_POSITIVE 173 46 3 88 36 smit:SMT_1819|3end_K03442_small_conductance_mechanosensitive_ion_channel,_MscS_family_1793555..1793705_POSITIVE 172 32 1 59 34 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 162 46 2 118 79 smit:SMT_483|3end_transcriptional_activator_TipA,_putative_419647..419797_POSITIVE 161 117 72 42 1 smit:SMT_825|3end_aspartate_aminotransferase_748416..748566_NEGATIVE 149 116 84 132 103 smit:SMT_425|3end_hypothetical_cytosolic_protein_368424..368574_POSITIVE 147 36 5 43 14 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 146 78 31 55 9 smit:SMT_1656|3end_glutamine_ABC_transporter_ATP-binding_protein_1645172..1645322_NEGATIVE 146 44 3 120 83 smit:SMT_277|3end_capsular_polysaccharide_biosynthesis_homolog_YwqC_220333..220483_POSITIVE 143 46 22 52 30 smit:SMT_888|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_836333..836483_POSITIVE 142 27 1 123 93 smit:SMT_522|3end_K02003_447500..447650_POSITIVE 142 16 1 62 47 smit:SMT_390|3end_PTS_system,_galactitol-specific_IIB_component,_putative_322679..322829_POSITIVE 141 103 62 145 101 smit:SMT_922|3end_RNA-binding_protein_875253..875403_NEGATIVE 140 120 86 67 33 smit:SMT_1531|3end_hypothetical_protein_1515449..1515599_NEGATIVE 140 37 1 98 70 smit:SMT_178|3end_50S_ribosomal_protein_L29_119447..119597_POSITIVE 139 104 75 39 11 smit:SMT_2034|3end_hydrolase,_haloacid_dehalogenase-like_family_1947257..1947407_POSITIVE 139 42 1 150 109 smit:SMT_1456|3end_pyrimidine-nucleoside_phosphorylase_1438555..1438705_NEGATIVE 138 120 88 148 106 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 138 40 6 145 103 smit:SMT_1089|3end_hypothetical_protein_1024343..1024493_NEGATIVE