Origin IGS: ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgcattttctcactttcgttttttttgtatttatattataatagttgtcaaacatattttctaacacaattatcttaataaattgtactattctacgaaagagtgtcccc Mask Tandem Repeat Region ================================================ ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Find is-nt database================================================ Query_seq: SSA_0382:SSA_0383|SSA_0382:SSA_0383:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:Beta-glucosidase, putative:<-->:374563..374673 111 ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0382:SSA_0383|SSA_0382:SSA_0383:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:Beta-glucosidase, putative:<-->:374563..374673 111 ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0382:SSA_0383|SSA_0382:SSA_0383:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:Beta-glucosidase, putative:<-->:374563..374673 111 ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 20 End: 109 ................... M V Q F I K I I V L E N M F D N Y Y N I N T K K T K V R K C .. ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa 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: 83 Start: 47 End: 76 ..............................................TTAGAAAATATGTTTGACAACTATTATAAT................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 69 End: 98 ....................................................................CTTTCGTTTTTTTTGTATTTATATTATAAT............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0382:SSA_0383|SSA_0382:SSA_0383:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:Beta-glucosidase, putative:<-->:374563..374673 111 ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_009009_SSA_0382_SSA_0383|Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:Beta-glucosidase, putative|NEGATIVE:POSITIVE|[374563,374673]|111 HSP 1 e-value: 1.0E-42 bit: 172.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacnnnnnnnncgaaagtgagaaaatgcaa ggggacactctttcgtagaatagtacaatttattaagataattgtgttagaaaatatgtttgacaactattataatataaatacaaaaaaaacgaaagtgagaaaatgcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGACACUCUUUCGUAGAAUAGUACAAUUUAUUAAGAUAAUUGUGUUAGAAAAUAUGUUUGACAACUAUUAUAAUAUAAAUACAAAAAAAACGAAAGUGAGAAAAUGCAA (....).(.(((((((...........((((((....(((((..(((((((.......)))))))...)))))...)))))).........))))))).)........... (-16.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCAUUUUCUCACUUUCGUUUUUUUUGUAUUUAUAUUAUAAUAGUUGUCAAACAUAUUUUCUAACACAAUUAUCUUAAUAAAUUGUACUAUUCUACGAAAGAGUGUCCCC .............(((((((.......((((...(((((..((((((((.................))))))))..)))))....))))......)))))))......... (-17.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 776 50 1 141 92 NC_009009:SSA_0382|5end_Transcriptional_regulator,_AraC_family_(arabinose-binding/dimerisation),_putative_374472..374702_NEGATIVE 237 36 1 135 93 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 198 108 63 189 134 NC_009009:SSA_1210|5end_GTP_pyrophosphokinase,_putative_1234655..1234885_NEGATIVE 195 69 37 158 121 NC_009009:SSA_0991|5end_Deoxyribonuclease,_putative_993342..993572_NEGATIVE 187 40 1 200 156 NC_009009:SSA_1283|5end_Nitroreductase,_putative_1304336..1304566_NEGATIVE 186 35 2 90 53 NC_009009:SSA_1365|5end_FmtA-like_protein,_putative_1382299..1382529_NEGATIVE 180 110 83 141 111 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 172 21 1 220 195 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 168 23 1 78 48 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 167 39 7 155 120 NC_009009:SSA_1079|5end_hypothetical_protein_1096385..1096615_POSITIVE 166 70 34 147 112 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 164 82 45 146 111 NC_009009:SSA_2128|5end_hypothetical_protein_2132092..2132322_NEGATIVE 164 39 5 126 97 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 161 34 2 185 155 NC_009009:SSA_1871|5end_Penicillin-binding_protein_2X,_putative_1868873..1869103_NEGATIVE 159 77 34 64 29 NC_009009:SSA_0745|5end_hypothetical_protein_727035..727265_NEGATIVE 158 69 24 195 146 NC_009009:SSA_2258|5end_hypothetical_protein_2254699..2254929_NEGATIVE 158 23 4 22 3 NC_009009:SSA_0141|5end_Copper_chaperone,_putative_136893..137123_POSITIVE 155 64 24 152 110 NC_009009:SSA_1808|5end_hypothetical_protein_1792209..1792439_NEGATIVE 154 44 1 172 122 NC_009009:SSA_0779|5end_Glycogen_phosphorylase,_putative_762209..762439_POSITIVE 154 48 6 205 152 NC_009009:SSA_0466|5end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469884..470114_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 187 40 1 90 46 NC_009009:SSA_1284|3end_hypothetical_protein_1304446..1304596_NEGATIVE 186 35 2 93 56 NC_009009:SSA_1366|3end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1382296..1382446_NEGATIVE 168 23 1 72 42 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 167 39 7 141 106 NC_009009:SSA_1078|3end_hypothetical_protein_1096451..1096601_POSITIVE 164 39 5 126 97 NC_009009:SSA_1516|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1522129..1522279_NEGATIVE 159 40 9 112 79 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 155 64 24 134 92 NC_009009:SSA_1809|3end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1792227..1792377_NEGATIVE 153 24 4 33 13 NC_009009:SSA_2333|3end_Integral_membrane_protein,_putative_2335216..2335366_NEGATIVE 153 45 6 128 92 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 148 45 10 74 43 NC_009009:SSA_0993|3end_hypothetical_protein_994758..994908_POSITIVE 146 68 21 110 61 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE 140 32 10 124 99 NC_009009:SSA_1998|3end_Trigger_factor,_putative_1995048..1995198_NEGATIVE 139 26 3 41 11 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 138 32 1 100 70 NC_009009:SSA_2059|3end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2060494..2060644_NEGATIVE 138 45 1 113 62 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 136 48 9 142 98 NC_009009:SSA_1450|3end_hypothetical_protein_1452405..1452555_NEGATIVE 135 48 6 126 85 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 135 45 1 91 57 NC_009009:SSA_1091|3end_Thymidylate_synthase,_putative_1109554..1109704_POSITIVE 133 34 1 74 45 NC_009009:SSA_1748|3end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1733543..1733693_NEGATIVE 130 49 6 54 5 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE