Origin IGS: tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaggtaatttcctccaaatttcattatatcatattattgtctaaagtgtacaaaaatgttggagtagaaaaagtgtctgaattagtcagaaaaattagaataatataagtggcttttaggtacaaaaagagaatatattaattacatagaaaatattgatttatatatcaaatagttgtagagtgagaactataaaatactatctaggagttcaca Mask Tandem Repeat Region ================================================ tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Find is-nt database================================================ Query_seq: SMT_830:SMT_831|SMT_830:SMT_831:hypothetical protein:transcriptional activator, putative:<-->:772714..772930 217 tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_830:SMT_831|SMT_830:SMT_831:hypothetical protein:transcriptional activator, putative:<-->:772714..772930 217 tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_830:SMT_831|SMT_830:SMT_831:hypothetical protein:transcriptional activator, putative:<-->:772714..772930 217 tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 83 End: 190 .................................................................................. M L F L Y L K A T Y I I L I F L T N S D T F S T P T F L Y T L D N N M I ........................... Protein_Len: 33 Strand: - Start: 112 End: 210 ............................................................................................................... I I R I K R V L E S V K E V G V N K Y V K S L L I I Y H F K S S M ....... tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac 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: 33 End: 62 ................................ATTGATTTATATATCAAATAGTTGTAGAGT........................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_830:SMT_831|SMT_830:SMT_831:hypothetical protein:transcriptional activator, putative:<-->:772714..772930 217 tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Intra-Species Hit: Count: 1 Min: 1 Max: 217 Len: 217 Subject: smit_SMT_830_SMT_831|hypothetical protein:transcriptional activator, putative|NEGATIVE:POSITIVE|[772714,772930]|217 HSP 1 e-value: 1.0E-120 bit: 430.0 Len: 217 Query Start:1 Query End:217 Subject Strand: POSITIVE Subject Start: 1 Subject End: 217 tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac tgtgaactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttctgactaattcagacactttttctactccaacatttttgtacactttagacaataatatgatataatgaaatttggaggaaattacctac Inter-species Hit: Count: 2 Min: 5 Max: 128 Len: 124 Subject: NC_008533_SPD_1376_SPD_1377|G5 domain family protein:hypothetical protein|NEGATIVE:POSITIVE|[1395452,1395666]|215 HSP 1 e-value: 2.0E-28 bit: 127.0 Len: 124 Query Start:5 Query End:128 Subject Strand: POSITIVE Subject Start: 5 Subject End: 128 ....aactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttc......................................................................................... ....aactcctagatagtattttatagtttacaatgtacaactatttgaggcattaatcaatattttctgaacaattaatatattctgtttttgcacttaaaagccacttatattattctaatttttc......................................................................................... Subject: NC_003098_spr1403_spr1404|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1387921,1388111]|191 HSP 1 e-value: 2.0E-28 bit: 127.0 Len: 124 Query Start:5 Query End:128 Subject Strand: POSITIVE Subject Start: 5 Subject End: 128 ....aactcctagatagtattttatagttctcactctacaactatttgatatataaatcaatattttctatgtaattaatatattctctttttgtacctaaaagccacttatattattctaatttttc......................................................................................... ....aactcctagatagtattttatagtttacaatgtacaactatttgaggcattaatcaatattttctgaacaattaatatattctgtttttgcacttaaaagccacttatattattctaatttttc......................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUCCUAGAUAGUAUUUUAUAGUUCUCACUCUACAACUAUUUGAUAUAUAAAUCAAUAUUUUCUAUGUAAUUAAUAUAUUCUCUUUUUGUACCUAAAAGCCACUUAUAUUAUUCUAAUUUUUC ......((((..(((((..((((((..........))))))..)))))........................(((((((....(((((.......))))).....))))))).))))....... (-11.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAUUAGAAUAAUAUAAGUGGCUUUUAGGUACAAAAAGAGAAUAUAUUAAUUACAUAGAAAAUAUUGAUUUAUAUAUCAAAUAGUUGUAGAGUGAGAACUAUAAAAUACUAUCUAGGAGUU ......................((((((((((((........((.(((((.(((((.(((.....)))))))).)))))))..((((((.(......).)))))).......)))))))))))) (-17.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 737 50 1 145 96 smit:SMT_830|5end_hypothetical_protein_772623..772853_NEGATIVE 240 45 4 220 182 smit:SMT_1981|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912261..1912491_POSITIVE 218 50 3 227 183 smit:SMT_1960|5end_UDP-galactopyranose_mutase_1892899..1893129_POSITIVE 218 50 3 227 183 smit:SMT_287|5end_UDP-galactopyranose_mutase_230082..230312_POSITIVE 213 117 78 188 148 smit:SMT_329|5end_hypothetical_protein_265240..265470_POSITIVE 211 32 2 89 50 smit:SMT_138|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_89262..89492_POSITIVE 201 110 79 131 96 smit:SMT_1014|5end_galactokinase_951823..952053_NEGATIVE 200 59 21 57 17 smit:SMT_809|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_719745..719975_NEGATIVE 199 44 5 74 31 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 194 89 62 104 73 smit:SMT_1899|5end_hypothetical_protein_1850018..1850248_POSITIVE 194 48 6 116 72 smit:SMT_322|5end_hypothetical_protein_260193..260423_POSITIVE 191 102 77 198 167 smit:SMT_878|5end_excinuclease_ABC,_subunit_C_826249..826479_NEGATIVE 189 110 78 127 92 smit:SMT_1026|5end_sucrose_phosphorylase_962324..962554_NEGATIVE 187 50 3 157 100 smit:SMT_1234|5end_cadmium_efflux_system_accessory_protein_1194932..1195162_POSITIVE 184 49 2 70 17 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 183 43 1 133 95 smit:SMT_911|5end_hypothetical_protein_862023..862253_POSITIVE 183 46 3 194 155 smit:SMT_690|5end_pyrimidine_regulatory_protein_602168..602398_NEGATIVE 180 69 23 211 163 smit:SMT_1500|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483384..1483614_POSITIVE 180 33 3 131 98 smit:SMT_451|5end_thiamine-phosphate_pyrophosphorylase_388935..389165_POSITIVE 178 68 26 92 41 smit:SMT_1845|5end_K01191_alpha-mannosidase_1809663..1809893_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 194 48 6 113 69 smit:SMT_321|3end_hypothetical_protein_260270..260420_POSITIVE 187 50 3 145 88 smit:SMT_1233|3end_cadmium_resistance_protein_1195000..1195150_POSITIVE 180 33 3 138 105 smit:SMT_450|3end_hydroxyethylthiazole_kinase_389022..389172_POSITIVE 173 39 9 50 23 smit:SMT_1302|3end_hypothetical_protein_1264649..1264799_POSITIVE 172 28 1 116 85 smit:SMT_1176|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1127662..1127812_NEGATIVE 172 34 5 107 75 smit:SMT_749|3end_shikimate_kinase_653495..653645_NEGATIVE 171 103 77 73 46 smit:SMT_1251|3end_hypothetical_protein_1211329..1211479_NEGATIVE 170 117 81 93 61 smit:SMT_1272|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237004..1237154_POSITIVE 168 103 61 143 104 smit:SMT_1684|3end_acetyltransferase,_GNAT_family_1667248..1667398_NEGATIVE 164 33 2 107 77 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 159 47 4 112 80 smit:SMT_1749|3end_anthranilate_synthase_component_II_1728080..1728230_POSITIVE 157 39 2 112 78 smit:SMT_902|3end_hypothetical_protein_851424..851574_NEGATIVE 156 47 9 48 11 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 153 111 78 128 92 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 152 43 16 140 106 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 151 69 31 96 59 smit:SMT_1266|3end_predicted_transcriptional_regulator_1231774..1231924_POSITIVE 150 39 12 106 78 smit:SMT_782|3end_GMP_synthase_692957..693107_NEGATIVE 150 33 3 88 60 smit:SMT_754|3end_3-dehydroquinate_synthase_657977..658127_NEGATIVE 150 45 3 106 57 smit:SMT_639|3end_6-phospho-beta-galactosidase_543479..543629_NEGATIVE 150 26 1 102 73 smit:SMT_612|3end_hypothetical_protein_predicted_by_Glimmer/Critica_523674..523824_POSITIVE