Origin IGS: attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt .........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 aaactgttataataattaagggaatatgttgtaccgcatataggagagaaaattatggatggttggaaaaattttgttgttatgcttagtggttttttagttgctgtaattttaagtatatacctaagtaaataattatggtataatattgatatatatggtgggctgccaataaaagtagagaggttggaataat Mask Tandem Repeat Region ================================================ attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Find is-nt database================================================ Query_seq: TDE2026:TDE2027|TDE2026:TDE2027:hypothetical protein:hypothetical protein:<-->:2052593..2052788 196 attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2026:TDE2027|TDE2026:TDE2027:hypothetical protein:hypothetical protein:<-->:2052593..2052788 196 attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2026:TDE2027|TDE2026:TDE2027:hypothetical protein:hypothetical protein:<-->:2052593..2052788 196 attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 1 End: 108 M I P T S L L L L A A H H I Y Q Y Y T I I I Y L G I Y L K L Q Q L K N H ........................................................................................ Protein_Len: 57 Strand: + Start: 24 End: 194 ....................... M G S P P Y I S I L Y H N Y L L R Y I L K I T A T K K P L S I T T K F F Q P S I I F S P I C G T T Y S L N Y Y N S .. Protein_Len: 31 Strand: - Start: 65 End: 157 ................................................................ K S L Y I S L I V A V L F G S L M V V F N K W G D M I K E G M ....................................... attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2026:TDE2027|TDE2026:TDE2027:hypothetical protein:hypothetical protein:<-->:2052593..2052788 196 attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: NC_002967_TDE2026_TDE2027|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2052593,2052788]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt attattccaacctctctacttttattggcagcccaccatatatatcaatattataccataattatttacttaggtatatacttaaaattacagcaactaaaaaaccactaagcataacaacaaaatttttccaaccatccataattttctctcctatatgcggtacaacatattcccttaattattataacagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUCCAACCUCUCUACUUUUAUUGGCAGCCCACCAUAUAUAUCAAUAUUAUACCAUAAUUAUUUACUUAGGUAUAUACUUAAAAUUACAGCAACUAAAAAACCACUAAGCAUAACAACAAAAUUUUUCCAACCAUCCAUAAUUUUCUCUCCUAUAUGCGGUACAACAUAUUCCCUUAAUUAUUAUAACAGUUU ........................(((...(((...((((((.........((((((.(((........)))))))))..............((.................)).........................................)))))).))).)))............................ (-11.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUGUUAUAAUAAUUAAGGGAAUAUGUUGUACCGCAUAUAGGAGAGAAAAUUAUGGAUGGUUGGAAAAAUUUUGUUGUUAUGCUUAGUGGUUUUUUAGUUGCUGUAAUUUUAAGUAUAUACCUAAGUAAAUAAUUAUGGUAUAAUAUUGAUAUAUAUGGUGGGCUGCCAAUAAAAGUAGAGAGGUUGGAAUAAU .....(((((..(((((................(((((((((......((((((((((.(..(((((((((((..((......))..)))..))))))))..))))))))))).(((((((((((((........))).))))).)))))....))))).)))).((((........))))...)))))..))))) (-30.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 60 11 151 102 NC_002967:TDE2026|5end_hypothetical_protein_2052502..2052732_NEGATIVE 290 178 139 126 88 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 285 161 131 107 76 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 274 42 1 130 90 NC_002967:TDE0858|5end_hypothetical_protein_879518..879748_POSITIVE 270 169 126 124 74 NC_002967:TDE1128|5end_hypothetical_protein_1160536..1160766_POSITIVE 265 114 81 96 66 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 254 43 1 149 90 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 246 167 126 112 77 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 243 177 131 60 13 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 241 41 10 101 57 NC_002967:TDE1783|5end_hypothetical_protein_1823605..1823835_NEGATIVE 238 169 121 113 66 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 237 158 124 107 78 NC_002967:TDE0515|5end_hypothetical_protein_563783..564013_NEGATIVE 237 179 138 145 100 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 236 33 11 225 197 NC_002967:TDE1153|5end_hypothetical_protein_1190858..1191088_NEGATIVE 235 161 134 51 21 NC_002967:TDE0004|5end_hypothetical_protein_4243..4473_POSITIVE 234 176 136 128 89 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 231 48 12 81 37 NC_002967:TDE2770|5end_flagellar_hook-length_control_protein_FliK_2824417..2824647_NEGATIVE 230 167 131 125 78 NC_002967:TDE1238|5end_translocase_1270815..1271045_POSITIVE 230 47 6 65 25 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 228 47 5 212 164 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 161 131 87 56 NC_002967:TDE1897|3end_phosphoribosylglycinamide_formyltransferase_1917525..1917675_NEGATIVE 274 42 1 130 90 NC_002967:TDE0857|3end_lipoprotein,_putative_879598..879748_POSITIVE 259 179 136 51 4 NC_002967:TDE1127|3end_TPR_domain_protein_1160535..1160685_POSITIVE 254 43 1 149 90 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 247 178 147 34 1 NC_002967:TDE2426|3end_transcription_antitermination_protein_NusG_2455242..2455392_NEGATIVE 246 167 126 100 65 NC_002967:TDE1301|3end_DNA_repair_protein_RecN_1337431..1337581_NEGATIVE 241 41 10 125 81 NC_002967:TDE1784|3end_transcriptional_activator,_AraC_family_1823581..1823731_NEGATIVE 237 158 124 82 53 NC_002967:TDE0516|3end_hypothetical_protein_563808..563958_NEGATIVE 237 179 138 123 78 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 234 176 136 131 92 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 228 47 5 148 100 NC_002967:TDE0690|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_728078..728228_POSITIVE 225 179 154 102 76 NC_002967:TDE0953|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978007..978157_POSITIVE 222 156 131 64 42 NC_002967:TDE1955|3end_hypothetical_protein_1970190..1970340_NEGATIVE 218 167 133 46 3 NC_002967:TDE1237|3end_hypothetical_protein_1270816..1270966_POSITIVE 216 163 121 120 57 NC_002967:TDE1073|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1104635..1104785_POSITIVE 212 36 5 139 105 NC_002967:TDE0446|3end_fibronectin_type_III_domain_protein_502848..502998_POSITIVE 212 170 131 124 75 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE 211 47 11 128 83 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 209 176 134 121 81 NC_002967:TDE0058|3end_hypothetical_protein_67398..67548_POSITIVE 206 167 136 78 42 NC_002967:TDE2765|3end_flagellar_motor_protein_2819374..2819524_NEGATIVE