Origin IGS: aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgcctaaaattctcctataattatagtctattaaaaataccccctatttgtcaagcgtggacgtaaaatctcacagtgtctattttatattagatttaaggtgaggcaaatccggcactatacgaataaatgatactgtgatataatggactaaaaataggagctgttt Mask Tandem Repeat Region ================================================ aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Find is-nt database================================================ Query_seq: TDE1965:TDE1966|TDE1965:TDE1966:sodium/hydrogen exchanger family protein:trypsin domain/PDZ domain protein:<-->:1980242..1980412 171 aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1965:TDE1966|TDE1965:TDE1966:sodium/hydrogen exchanger family protein:trypsin domain/PDZ domain protein:<-->:1980242..1980412 171 aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1965:TDE1966|TDE1965:TDE1966:sodium/hydrogen exchanger family protein:trypsin domain/PDZ domain protein:<-->:1980242..1980412 171 aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Predict ORF larger than 30AA ================================================ aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt 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: 23 End: 52 ......................CTATACGAATAAATGATACTGTGATATAAT....................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1965:TDE1966|TDE1965:TDE1966:sodium/hydrogen exchanger family protein:trypsin domain/PDZ domain protein:<-->:1980242..1980412 171 aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: NC_002967_TDE1965_TDE1966|sodium/hydrogen exchanger family protein:trypsin domain/PDZ domain protein|NEGATIVE:POSITIVE|[1980242,1980412]|171 HSP 1 e-value: 2.0E-92 bit: 339.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt aaacagctcctatttttagtccattatatcacagtatcatttattcgtatagtgccggatttgcctcaccttaaatctaatataaaatagacactgtgagattttacgtccacgcttgacaaatagggggtatttttaatagactataattataggagaattttaggcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAGCUCCUAUUUUUAGUCCAUUAUAUCACAGUAUCAUUUAUUCGUAUAGUGCCGGAUUUGCCUCACCUUAAAUCUAAUAUAAAAUAGACACUGUGAGAUUUUACGUCCACGCUUGACAAAUAGGGGGUAUUUUUAAUAGACUAUAAUUAUAGGAGAAUUUUAGGCAUU ......(((((((...(((((.((((......((((((.((((((.((..((((..((((.((.(((((......((((........))))....)))))....)).)))).))))..)).)))))).))))))..)))).))))).....)))))))............. (-35.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGCCUAAAAUUCUCCUAUAAUUAUAGUCUAUUAAAAAUACCCCCUAUUUGUCAAGCGUGGACGUAAAAUCUCACAGUGUCUAUUUUAUAUUAGAUUUAAGGUGAGGCAAAUCCGGCACUAUACGAAUAAAUGAUACUGUGAUAUAAUGGACUAAAAAUAGGAGCUGUUU ........((((.(((((((..((.((((((((((................(((.......)))........((((((((((...(((((....(...((.((((.((.....))..)))).)))..))))).))))))))))..)))))))))).)))))))))..)))) (-38.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 879 70 21 161 112 NC_002967:TDE1965|5end_sodium/hydrogen_exchanger_family_protein_1980151..1980381_NEGATIVE 308 129 89 147 109 NC_002967:TDE1964|5end_Na/Pi_cotransporter_family_protein_1978780..1979010_NEGATIVE 273 59 18 65 28 NC_002967:TDE2110|5end_orotidine_5'-phosphate_decarboxylase_2135329..2135559_POSITIVE 267 94 51 167 121 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 257 64 37 39 6 NC_002967:TDE1270|5end_hypothetical_protein_1305011..1305241_NEGATIVE 256 123 95 175 145 NC_002967:TDE1481|5end_hypothetical_protein_1525657..1525887_POSITIVE 248 78 34 147 88 NC_002967:TDE1913|5end_hypothetical_protein_1929810..1930040_POSITIVE 246 66 34 44 15 NC_002967:TDE2291|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2328090..2328320_POSITIVE 244 120 76 157 111 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 239 70 34 182 149 NC_002967:TDE0766|5end_30S_ribosomal_protein_S10_805984..806214_POSITIVE 237 70 32 147 116 NC_002967:TDE1248|5end_hypothetical_protein_1282596..1282826_POSITIVE 235 86 41 219 171 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 233 169 125 49 7 NC_002967:TDE2569|5end_3-deoxy-7-phosphoheptulonate_synthase_2596308..2596538_POSITIVE 229 72 35 182 144 NC_002967:TDE1952|5end_hypothetical_protein_1969046..1969276_NEGATIVE 229 84 45 110 63 NC_002967:TDE1922|5end_hypothetical_protein_1941485..1941715_NEGATIVE 229 75 34 108 69 NC_002967:TDE0556|5end_hypothetical_protein_592092..592322_NEGATIVE 228 49 5 140 95 NC_002967:TDE1106|5end_translation_initiation_factor_IF-2_1140882..1141112_NEGATIVE 226 130 92 199 162 NC_002967:TDE2177|5end_hypothetical_protein_2206524..2206754_NEGATIVE 226 108 61 213 168 NC_002967:TDE1114|5end_transcriptional_regulator,_TetR_family_1148905..1149135_NEGATIVE 226 74 34 204 145 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 129 99 32 1 NC_002967:TDE1965|3end_sodium/hydrogen_exchanger_family_protein_1978895..1979045_NEGATIVE 278 69 31 94 44 NC_002967:TDE2490|3end_primosomal_protein_N'_2512703..2512853_NEGATIVE 248 78 34 145 86 NC_002967:TDE1912|3end_redox-sensing_transcriptional_repressor_Rex_1929888..1930038_POSITIVE 246 66 34 57 28 NC_002967:TDE2290|3end_transcriptional_regulator,_putative_2328183..2328333_POSITIVE 239 70 34 117 84 NC_002967:TDE0765|3end_translation_elongation_factor_Tu_805999..806149_POSITIVE 237 71 31 109 63 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 233 169 125 46 4 NC_002967:TDE2568|3end_thiamine_biosynthesis_protein_ThiI_2596385..2596535_POSITIVE 229 78 53 96 71 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 229 84 45 82 35 NC_002967:TDE1923|3end_hypothetical_protein_1941513..1941663_NEGATIVE 229 75 34 54 15 NC_002967:TDE0557|3end_hypothetical_protein_592146..592296_NEGATIVE 228 49 5 132 87 NC_002967:TDE1107|3end_transcription_elongation_factor_NusA_1140890..1141040_NEGATIVE 226 130 92 40 3 NC_002967:TDE2178|3end_hypothetical_protein_2206683..2206833_NEGATIVE 226 108 61 80 35 NC_002967:TDE1115|3end_DNA-binding_protein,_putative_1149038..1149188_NEGATIVE 220 72 41 134 91 NC_002967:TDE2089|3end_signal_recognition_particle_protein_2116232..2116382_NEGATIVE 220 59 13 128 76 NC_002967:TDE1654|3end_ATP-dependent_helicase_HrpA,_putative_1704911..1705061_POSITIVE 220 64 31 141 105 NC_002967:TDE1484|3end_hypothetical_protein_1529744..1529894_POSITIVE 220 75 32 151 108 NC_002967:TDE0826|3end_hypothetical_protein_847860..848010_POSITIVE 217 72 35 48 11 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 213 158 114 99 54 NC_002967:TDE0814|3end_transcriptional_regulator,_putative_835709..835859_NEGATIVE 213 137 94 139 98 NC_002967:TDE0749|3end_cobalamin_biosynthesis_protein_CobN,_putative_784473..784623_NEGATIVE