Origin IGS: accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcaatctactcctctgaaccagtatcggcatataaagaaaaagcattagagattttttaatttatgaaaggggtaaatttttagttgacgtaagccgaaaataaatgtattatagatggt Mask Tandem Repeat Region ================================================ accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Find is-nt database================================================ Query_seq: TDE2350:TDE2351|TDE2350:TDE2351:lipoprotein, putative:hypothetical protein:<-->:2386752..2386872 121 accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2350:TDE2351|TDE2350:TDE2351:lipoprotein, putative:hypothetical protein:<-->:2386752..2386872 121 accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2350:TDE2351|TDE2350:TDE2351:lipoprotein, putative:hypothetical protein:<-->:2386752..2386872 121 accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Predict ORF larger than 30AA ================================================ accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct 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: 86 Start: 8 End: 37 .......GTTGACGTAAGCCGAAAATAAATGTATTAT.................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2350:TDE2351|TDE2350:TDE2351:lipoprotein, putative:hypothetical protein:<-->:2386752..2386872 121 accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: NC_002967_TDE2350_TDE2351|lipoprotein, putative:hypothetical protein|NEGATIVE:POSITIVE|[2386752,2386872]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct accatctataatacatttattttcggcttacgtcaactaaaaatttacccctttcataaattaaaaaatctctaatgctttttctttatatgccgatactggttcagaggagtagattgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAUCUAUAAUACAUUUAUUUUCGGCUUACGUCAACUAAAAAUUUACCCCUUUCAUAAAUUAAAAAAUCUCUAAUGCUUUUUCUUUAUAUGCCGAUACUGGUUCAGAGGAGUAGAUUGCU ........................(((....))).......(((((((.(((((.(((((...(((((.(......).))))).)))))..((((....))))..))))).)))))))... (-13.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAUCUACUCCUCUGAACCAGUAUCGGCAUAUAAAGAAAAAGCAUUAGAGAUUUUUUAAUUUAUGAAAGGGGUAAAUUUUUAGUUGACGUAAGCCGAAAAUAAAUGUAUUAUAGAUGGU .((.(((((..(((((...((......))((((....((((((.(......).))))))....))))..)))))...(((((..(((......)))..)))))..........))))).)) (-16.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 120 71 211 162 NC_002967:TDE2350|5end_lipoprotein,_putative_2386661..2386891_NEGATIVE 267 117 76 112 74 NC_002967:TDE2087|5end_translation_initiation_factor_IF-1_2115686..2115916_NEGATIVE 252 110 64 55 11 NC_002967:TDE2122|5end_DHH_superfamily_protein_2155910..2156140_NEGATIVE 250 110 64 61 7 NC_002967:TDE2610|5end_hypothetical_protein_2651970..2652200_NEGATIVE 245 120 75 134 90 NC_002967:TDE0212|5end_hypothetical_protein_248235..248465_NEGATIVE 239 116 78 48 1 NC_002967:TDE1297|5end_LysM_domain/M23/M37_peptidase_domain_protein_1334782..1335012_NEGATIVE 236 103 67 152 106 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 232 120 72 70 34 NC_002967:TDE2206|5end_hypothetical_protein_2245364..2245594_NEGATIVE 227 120 90 52 16 NC_002967:TDE0382|5end_hypothetical_protein_434393..434623_POSITIVE 224 117 71 231 168 NC_002967:TDE0077|5end_glycine_reductase_complex_proprotein_GrdE1_88732..88962_NEGATIVE 223 120 91 212 185 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 223 116 88 47 18 NC_002967:TDE1423|5end_hypothetical_protein_1466786..1467016_POSITIVE 221 120 73 64 13 NC_002967:TDE0676|5end_hypothetical_protein_714860..715090_POSITIVE 221 117 77 207 162 NC_002967:TDE0444|5end_glutamine_amidotransferase_class-I_domain_protein_498966..499196_POSITIVE 216 53 13 56 18 NC_002967:TDE1521|5end_fumarate_hydratase_1567211..1567441_POSITIVE 215 120 85 64 32 NC_002967:TDE2101|5end_hypothetical_protein_2126619..2126849_NEGATIVE 214 118 73 105 51 NC_002967:TDE0871|5end_hypothetical_protein_894797..895027_NEGATIVE 213 120 77 202 156 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 212 120 81 202 160 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 212 103 70 40 8 NC_002967:TDE1173|5end_site-specific_recombinase,_phage_integrase_family_1202321..1202551_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 120 75 51 7 NC_002967:TDE0213|3end_TPR_domain_protein_248318..248468_NEGATIVE 239 116 78 48 1 NC_002967:TDE1298|3end_cyclic_nucleotide_binding_domain_protein_1334782..1334932_NEGATIVE 232 120 72 68 32 NC_002967:TDE2207|3end_hypothetical_protein_2245366..2245516_NEGATIVE 227 120 90 40 4 NC_002967:TDE0381|3end_hypothetical_protein_434461..434611_POSITIVE 223 118 74 65 26 NC_002967:TDE2556|3end_hypothetical_protein_2582316..2582466_NEGATIVE 223 116 88 31 2 NC_002967:TDE1422|3end_glycosyl_transferase,_group_2_family_protein_1466850..1467000_POSITIVE 221 120 73 55 4 NC_002967:TDE0675|3end_hypothetical_protein_714931..715081_POSITIVE 217 109 67 142 100 NC_002967:TDE1291|3end_HD_domain_protein_1328638..1328788_NEGATIVE 217 120 76 129 81 NC_002967:TDE0490|3end_hypothetical_protein_546272..546422_NEGATIVE 216 53 13 41 3 NC_002967:TDE1520|3end_fumarate_hydratase_1567276..1567426_POSITIVE 215 120 85 67 35 NC_002967:TDE2102|3end_hypothetical_protein_2126616..2126766_NEGATIVE 211 119 77 58 12 NC_002967:TDE0404|3end_hypothetical_protein_455359..455509_NEGATIVE 208 120 71 129 80 NC_002967:TDE1604|3end_ABC_transporter,_permease_protein,_putative_1654847..1654997_NEGATIVE 206 120 84 64 11 NC_002967:TDE2096|3end_hypothetical_protein_2124491..2124641_POSITIVE 206 113 71 78 29 NC_002967:TDE1880|3end_hypothetical_protein_1903058..1903208_POSITIVE 203 120 93 71 34 NC_002967:TDE2610|3end_hypothetical_protein_2651854..2652004_NEGATIVE 203 119 72 145 87 NC_002967:TDE1313|3end_signal_peptidase_I_1351266..1351416_POSITIVE 202 120 72 63 6 NC_002967:TDE1113|3end_hypothetical_protein_1147729..1147879_NEGATIVE 201 117 76 56 17 NC_002967:TDE2021|3end_hypothetical_protein_2044157..2044307_NEGATIVE 201 61 24 82 38 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE