Origin IGS: attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa .........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 tttcacattctccaaaatcttatttaagcaaaaataatagcaaaaaattcaaaaaaaaacaatcggggaactgttggaaattcagcggtattaaatttgcaaatatttatttctcaaaaagattaatatgcgccccaacagttttttattaccttgacaatcaaaaagaaattgtatatactaaataaaatagcattgctattttttaatgggaggggcttttaaagctgatataaggagaat Mask Tandem Repeat Region ================================================ attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa Find is-nt database================================================ Query_seq: TDE0284:TDE0285|TDE0284:TDE0285:hypothetical protein:translation elongation factor G:<-->:313519..313761 243 attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0284:TDE0285|TDE0284:TDE0285:hypothetical protein:translation elongation factor G:<-->:313519..313761 243 attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0284:TDE0285|TDE0284:TDE0285:hypothetical protein:translation elongation factor G:<-->:313519..313761 243 attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 121 End: 210 ........................................................................................................................ D K Q S I F I Q L N L V A S N G V T G R N N K K S N K A I M ................................. Protein_Len: 32 Strand: - Start: 59 End: 154 .......................................................... K T Y V I E K Q N D L Y Y F V T P A C I L R K S F Y I N A F K M ......................................................................................... attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa 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: 85 Start: 62 End: 91 .............................................................CTTGACAATCAAAAAGAAATTGTATATACT........................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 181 End: 210 ....................................................................................................................................................................................ATTGTTTTTTTTTGAATTTTTTGCTATTAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -5.4 Tail_Score: -5.14563 Start: 43 End: 53 Full_Region: atatactaaataaaa tagc att gcta ttttttaatgggagg ..........................................tagcattgcta.............................................................................................................................................................................................. Find igs database================================================ Query_seq: TDE0284:TDE0285|TDE0284:TDE0285:hypothetical protein:translation elongation factor G:<-->:313519..313761 243 attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattgtttttttttgaattttttgctattatttttgcttaaataagattttggagaatgtgaaa Intra-Species Hit: Count: 1 Min: 1 Max: 243 Len: 243 Subject: NC_002967_TDE0284_TDE0285|hypothetical protein:translation elongation factor G|NEGATIVE:POSITIVE|[313519,313761]|243 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattg........................................................... attctccttatatcagctttaaaagcccctcccattaaaaaatagcaatgctattttatttagtatatacaatttctttttgattgtcaaggtaataaaaaactgttggggcgcatattaatctttttgagaaataaatatttgcaaatttaataccgctgaatttccaacagttccccgattg........................................................... HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 29 Query Start:215 Query End:243 Subject Strand: POSITIVE Subject Start: 215 Subject End: 243 ......................................................................................................................................................................................................................gcttaaataagattttggagaatgtgaaa ......................................................................................................................................................................................................................gcttaaataagattttggagaatgtgaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUCCUUAUAUCAGCUUUAAAAGCCCCUCCCAUUAAAAAAUAGCAAUGCUAUUUUAUUUAGUAUAUACAAUUUCUUUUUGAUUGUCAAGGUAAUAAAAAACUGUUGGGGCGCAUAUUAAUCUUUUUGAGAAAUAAAUAUUUGCAAAUUUAAUACCGCUGAAUUUCCAACAGUUCCCCGAUUGUUUUUUUUUGAAUUUUUUGCUAUUAUUUUUGCUUAAAUAAGAUUUUGGAGAAUGUGAAA (((((((....(((.(((.....)))..............(((((((((((((.......))))))..((((((.......)))))).....(((.(((((((.(((((((.((.((((..((.....))..)))).....(((.(((((((.......))))))).)))..)).))))))).))))))).))).......)))))))................)))...)))))))...... (-46.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCACAUUCUCCAAAAUCUUAUUUAAGCAAAAAUAAUAGCAAAAAAUUCAAAAAAAAACAAUCGGGGAACUGUUGGAAAUUCAGCGGUAUUAAAUUUGCAAAUAUUUAUUUCUCAAAAAGAUUAAUAUGCGCCCCAACAGUUUUUUAUUACCUUGACAAUCAAAAAGAAAUUGUAUAUACUAAAUAAAAUAGCAUUGCUAUUUUUUAAUGGGAGGGGCUUUUAAAGCUGAUAUAAGGAGAAU ......(((((((.......(((((......))))).((((...................((((.((((((((((((....))))))))..(((((........)))))..)))).....)))).......(((((.((((((((((......(((.....))).)))))))))).....(((...((((((((...))))))))....)))..))))).......))))......))))))) (-47.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 812 50 1 141 92 NC_002967:TDE0284|5end_hypothetical_protein_313428..313658_NEGATIVE 465 80 32 154 106 NC_002967:TDE0339|5end_transcriptional_regulator,_TetR_family_377871..378101_POSITIVE 423 90 41 201 155 NC_002967:TDE0258|5end_methlytransferase,_UbiE/COQ5_family_292884..293114_NEGATIVE 369 90 41 161 112 NC_002967:TDE0274|5end_ABC_transporter,_ATP-binding/permease_protein_306423..306653_NEGATIVE 302 185 156 37 13 NC_002967:TDE1595|5end_cobalamin_biosynthesis_protein_CbiD_1646039..1646269_NEGATIVE 284 46 7 143 98 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 279 34 16 67 48 NC_002967:TDE1039|5end_riboflavin_biosynthesis_protein,_putative_1067072..1067302_POSITIVE 269 178 139 165 133 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 265 116 71 228 184 NC_002967:TDE2303|5end_hypothetical_protein_2343055..2343285_POSITIVE 264 28 2 51 20 NC_002967:TDE1032|5end_hypothetical_protein_1060154..1060384_POSITIVE 261 117 71 94 51 NC_002967:TDE1711|5end_RelA/SpoT_domain_protein_1766718..1766948_NEGATIVE 252 178 136 215 170 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 251 190 143 188 143 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 248 187 144 143 94 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 246 193 155 213 176 NC_002967:TDE1734|5end_exodeoxyribonuclease_III_1788613..1788843_POSITIVE 245 189 141 112 73 NC_002967:TDE0900|5end_ABC_transporter,_ATP-binding_protein_917188..917418_POSITIVE 241 50 5 150 98 NC_002967:TDE1600|5end_ABC_transporter,_ATP-binding/permease_protein_1652396..1652626_NEGATIVE 239 218 171 129 89 NC_002967:TDE1134|5end_hypothetical_protein_1165187..1165417_NEGATIVE 233 180 134 188 140 NC_002967:TDE1804|5end_hypothetical_protein_1842022..1842252_NEGATIVE 233 218 174 81 32 NC_002967:TDE0982|5end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1006477..1006707_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 465 80 32 67 19 NC_002967:TDE0338|3end_methyl-accepting_chemotaxis_protein-like_protein_377864..378014_POSITIVE 382 35 3 118 88 NC_002967:TDE0339|3end_transcriptional_regulator,_TetR_family_378568..378718_POSITIVE 269 178 139 143 111 NC_002967:TDE1334|3end_hypothetical_protein_1370874..1371024_POSITIVE 259 115 72 106 63 NC_002967:TDE0319|3end_hypothetical_protein_352547..352697_POSITIVE 249 70 23 46 1 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 245 189 141 121 82 NC_002967:TDE0899|3end_ABC_transporter,_permease_protein,_putative_917277..917427_POSITIVE 239 218 171 124 84 NC_002967:TDE1135|3end_hypothetical_protein_1165192..1165342_NEGATIVE 233 218 174 59 10 NC_002967:TDE0981|3end_hypothetical_protein_1006535..1006685_POSITIVE 226 182 141 130 76 NC_002967:TDE2174|3end_hypothetical_protein_2203099..2203249_NEGATIVE 226 148 103 116 77 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 225 219 178 90 45 NC_002967:TDE2149|3end_transglycosylase,_SLT_family_2185965..2186115_NEGATIVE 224 160 111 86 16 NC_002967:TDE1496|3end_chromosome_partition_protein_SmC,_putative_1543307..1543457_POSITIVE 223 33 15 49 31 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 219 115 75 64 21 NC_002967:TDE1941|3end_hypothetical_protein_1956505..1956655_NEGATIVE 219 186 158 95 63 NC_002967:TDE1584|3end_lipoprotein,_putative_1632854..1633004_POSITIVE 217 186 141 65 22 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 216 198 152 75 26 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 216 45 1 136 67 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 215 189 142 150 102 NC_002967:TDE1983|3end_hypothetical_protein_1993376..1993526_NEGATIVE 215 160 111 70 15 NC_002967:TDE1563|3end_hypothetical_protein_1616513..1616663_POSITIVE