Origin IGS: atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttattcctaggtgaaacaaaatagcattttttataagtctttgtcaatattgtaagatttttacgtctttacgcttgcaaaattcataacttatgtgtataatggggtaactggaggaatat Mask Tandem Repeat Region ================================================ atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Find is-nt database================================================ Query_seq: TDE1480:TDE1481|TDE1480:TDE1481:hypothetical protein:hypothetical protein:<-->:1525672..1525796 125 atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1480:TDE1481|TDE1480:TDE1481:hypothetical protein:hypothetical protein:<-->:1525672..1525796 125 atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1480:TDE1481|TDE1480:TDE1481:hypothetical protein:hypothetical protein:<-->:1525672..1525796 125 atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Predict ORF larger than 30AA ================================================ atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa 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: 91 Start: 20 End: 49 ...................CTTGCAAAATTCATAACTTATGTGTATAAT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1480:TDE1481|TDE1480:TDE1481:hypothetical protein:hypothetical protein:<-->:1525672..1525796 125 atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_002967_TDE1480_TDE1481|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1525672,1525796]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa atattcctccagttaccccattatacacataagttatgaattttgcaagcgtaaagacgtaaaaatcttacaatattgacaaagacttataaaaaatgctattttgtttcacctaggaataaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUCCUCCAGUUACCCCAUUAUACACAUAAGUUAUGAAUUUUGCAAGCGUAAAGACGUAAAAAUCUUACAAUAUUGACAAAGACUUAUAAAAAAUGCUAUUUUGUUUCACCUAGGAAUAAAAA .(((((((..((......((..(((..(((...((((((.((((((((..((((.((........))))))....))).)))))..))))))...))).)))..))......))))))))).... (-14.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUUCCUAGGUGAAACAAAAUAGCAUUUUUUAUAAGUCUUUGUCAAUAUUGUAAGAUUUUUACGUCUUUACGCUUGCAAAAUUCAUAACUUAUGUGUAUAAUGGGGUAACUGGAGGAAUAU ....(((((((.(((.(..(......((((.....((((((...(((.(((.(((((((.......(((....)))))))))).))).)))))))))))))......)..).)))..))))))). (-20.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 811 50 1 141 92 NC_002967:TDE1480|5end_hypothetical_protein_1525581..1525811_NEGATIVE 256 72 42 168 140 NC_002967:TDE1966|5end_trypsin_domain/PDZ_domain_protein_1980273..1980503_POSITIVE 232 50 1 157 105 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 224 99 55 216 174 NC_002967:TDE1670|5end_transcriptional_regulator,_MarR_family_1724461..1724691_NEGATIVE 224 88 41 225 171 NC_002967:TDE1097|5end_acetyltransferase,_GNAT_family_1132766..1132996_NEGATIVE 221 58 16 138 104 NC_002967:TDE2426|5end_transcription_antitermination_protein_NusG_2455799..2456029_NEGATIVE 219 54 20 157 120 NC_002967:TDE0525|5end_hypothetical_protein_570550..570780_POSITIVE 218 63 27 52 14 NC_002967:TDE1991|5end_hypothetical_protein_2009398..2009628_NEGATIVE 218 59 19 55 8 NC_002967:TDE0989|5end_hypothetical_protein_1017132..1017362_POSITIVE 216 80 46 49 13 NC_002967:TDE1009|5end_methyl-accepting_chemotaxis_protein_1035096..1035326_NEGATIVE 210 50 1 154 99 NC_002967:TDE2670|5end_glycosyl_transferase,_group_4_family_protein_2708034..2708264_NEGATIVE 208 60 16 173 132 NC_002967:TDE1698|5end_serine/threonine_protein_phosphatase_family_protein_1757184..1757414_NEGATIVE 207 85 47 47 11 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 201 110 63 163 112 NC_002967:TDE1229|5end_hypothetical_protein_1262413..1262643_POSITIVE 199 90 41 122 80 NC_002967:TDE1922|5end_hypothetical_protein_1941485..1941715_NEGATIVE 198 80 31 130 70 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 198 80 31 130 70 NC_002967:TDE1793|5end_hydrolase,_carbon-nitrogen_family_1830844..1831074_NEGATIVE 196 49 5 152 96 NC_002967:TDE1927|5end_phenylalanyl-tRNA_synthetase_beta_subunit_1943984..1944214_POSITIVE 195 61 42 213 195 NC_002967:TDE2602|5end_outer_membrane_protein,_putative_2640956..2641186_POSITIVE 188 69 29 164 123 NC_002967:TDE1731|5end_hypothetical_protein_1786935..1787165_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 58 16 134 100 NC_002967:TDE2427|3end_preprotein_translocase,_SecE_subunit_2455803..2455953_NEGATIVE 219 54 20 79 42 NC_002967:TDE0524|3end_hypothetical_protein_570552..570702_POSITIVE 204 50 8 78 37 NC_002967:TDE2525|3end_hypothetical_protein_2551835..2551985_NEGATIVE 199 90 41 94 52 NC_002967:TDE1923|3end_hypothetical_protein_1941513..1941663_NEGATIVE 192 61 26 148 120 NC_002967:TDE2023|3end_TPR_domain_protein_2049505..2049655_NEGATIVE 185 50 2 76 24 NC_002967:TDE2243|3end_CutC_family_protein_2282214..2282364_NEGATIVE 183 85 42 64 20 NC_002967:TDE1170|3end_DNA-binding_protein_1200242..1200392_POSITIVE 182 49 6 111 64 NC_002967:TDE2737|3end_hypothetical_protein_2792690..2792840_POSITIVE 181 67 43 33 7 NC_002967:TDE0014|3end_hypothetical_protein_19487..19637_POSITIVE 179 59 17 55 17 NC_002967:TDE1988|3end_hypothetical_protein_2005590..2005740_POSITIVE 178 60 28 63 21 NC_002967:TDE2688|3end_hypothetical_protein_2728462..2728612_POSITIVE 178 48 9 74 34 NC_002967:TDE2687|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_2727196..2727346_NEGATIVE 177 68 23 122 81 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 176 59 13 129 91 NC_002967:TDE2454|3end_hypothetical_protein_2482351..2482501_NEGATIVE 176 27 1 97 71 NC_002967:TDE0002|3end_DNA_gyrase,_B_subunit_3540..3690_POSITIVE 173 35 5 133 101 NC_002967:TDE1917|3end_cytidylyltransferase_domain_protein_1934764..1934914_NEGATIVE 172 25 4 124 102 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 170 47 3 106 60 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 169 120 73 133 79 NC_002967:TDE2341|3end_membrane-associated_zinc_metalloprotease,_putative_2377866..2378016_NEGATIVE 167 65 29 135 93 NC_002967:TDE2201|3end_hypothetical_protein_2238492..2238642_NEGATIVE