Origin IGS: aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt .........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 aattaagcctcgctaataatttttttaaagaagaaaaatttttcccctttcataattattgtagagattatttaaagttaatagcaaaaattttaaaaaagaattaaattttattgataatttaaccgcagcggacgcaaagagtttttaaggcagaattgtttttattaacaagcaggactttctaatcaaaaatatggcaaacaaaactctaatgcgggtatttacatgtttt Mask Tandem Repeat Region ================================================ aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Find is-nt database================================================ Query_seq: TDE1343:TDE1344|TDE1343:TDE1344:trypsin domain/PDZ domain protein:hypothetical protein:->->:1382297..1382531 235 aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1343:TDE1344|TDE1343:TDE1344:trypsin domain/PDZ domain protein:hypothetical protein:->->:1382297..1382531 235 aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1343:TDE1344|TDE1343:TDE1344:trypsin domain/PDZ domain protein:hypothetical protein:->->:1382297..1382531 235 aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Predict ORF larger than 30AA ================================================ aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt 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================================================ aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1343:TDE1344|TDE1343:TDE1344:trypsin domain/PDZ domain protein:hypothetical protein:->->:1382297..1382531 235 aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcggttaaattatcaataaaatttaattcttttttaaaatttttgctattaactttaaataatctctacaataattatgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Intra-Species Hit: Count: 1 Min: 1 Max: 235 Len: 235 Subject: NC_002967_TDE1343_TDE1344|trypsin domain/PDZ domain protein:hypothetical protein|POSITIVE:POSITIVE|[1382297,1382531]|235 HSP 1 e-value: 6.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcgg............................................................................................................................. aaaacatgtaaatacccgcattagagttttgtttgccatatttttgattagaaagtcctgcttgttaataaaaacaattctgccttaaaaactctttgcgtccgctgcgg............................................................................................................................. HSP 2 e-value: 9.0E-9 bit: 61.9 Len: 52 Query Start:184 Query End:235 Subject Strand: POSITIVE Subject Start: 184 Subject End: 235 .......................................................................................................................................................................................tgaaaggggaaaaatttttcttctttnnnnnnnttattagcgaggcttaatt .......................................................................................................................................................................................tgaaaggggaaaaatttttcttctttaaaaaaattattagcgaggcttaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACAUGUAAAUACCCGCAUUAGAGUUUUGUUUGCCAUAUUUUUGAUUAGAAAGUCCUGCUUGUUAAUAAAAACAAUUCUGCCUUAAAAACUCUUUGCGUCCGCUGCGGUUAAAUUAUCAAUAAAAUUUAAUUCUUUUUUAAAAUUUUUGCUAUUAACUUUAAAUAAUCUCUACAAUAAUUAUGAAAGGGGAAAAAUUUUUCUUCUUUAAAAAAAUUAUUAGCGAGGCUUAAUU .......(((((....((((..((((((((....((...(((.((.(((((.(((.....))).)))))...)).)))...))....)))))))).))))........(((((((((........))))))))).............))))).............(((((((...(((((((.(.((((((((((....))))))))))...).)))))))...)))).)))... (-36.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAGCCUCGCUAAUAAUUUUUUUAAAGAAGAAAAAUUUUUCCCCUUUCAUAAUUAUUGUAGAGAUUAUUUAAAGUUAAUAGCAAAAAUUUUAAAAAAGAAUUAAAUUUUAUUGAUAAUUUAACCGCAGCGGACGCAAAGAGUUUUUAAGGCAGAAUUGUUUUUAUUAACAAGCAGGACUUUCUAAUCAAAAAUAUGGCAAACAAAACUCUAAUGCGGGUAUUUACAUGUUUU ........(((..((((((((.....((((..((((....))))..))))...))))))))..)))..........((((((((....((((((.....)))))).....)))))))).......(((((((....))..((((((((....((.....(((((((((((..(((.....)))..)))).)))))))..))....))))))))..)))))............... (-36.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 584 197 151 124 78 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 559 230 181 215 165 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 484 140 94 201 156 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 418 209 163 208 163 NC_002967:TDE0861|5end_tyrosyl-tRNA_synthetase_883098..883328_NEGATIVE 380 120 84 79 44 NC_002967:TDE1059|5end_hypothetical_protein_1086605..1086835_NEGATIVE 355 209 173 57 22 NC_002967:TDE2099|5end_hypothetical_protein_2125027..2125257_POSITIVE 351 136 92 229 185 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 328 116 82 116 80 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 328 116 82 116 80 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 313 115 90 28 3 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 294 117 75 141 103 NC_002967:TDE0912|5end_hypothetical_protein_931350..931580_POSITIVE 285 64 21 208 162 NC_002967:TDE0886|5end_hypothetical_protein_903341..903571_POSITIVE 281 110 93 231 214 NC_002967:TDE1906|5end_hypothetical_protein_1923883..1924113_POSITIVE 277 110 61 115 54 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 275 192 151 212 171 NC_002967:TDE0670|5end_ATP-dependent_protease_La_707938..708168_POSITIVE 266 58 14 226 183 NC_002967:TDE1017|5end_exodeoxyribonuclease_VII,_large_subunit_1047935..1048165_POSITIVE 265 113 77 53 7 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 263 60 16 73 37 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 255 112 80 34 1 NC_002967:TDE2307|5end_seryl-tRNA_synthetase_2345503..2345733_NEGATIVE 254 118 93 213 188 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 455 140 91 111 63 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 437 112 76 51 19 NC_002967:TDE2159|3end_hypothetical_protein_2193874..2194024_POSITIVE 374 114 80 94 53 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 335 126 82 74 28 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 328 116 82 54 18 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 294 117 75 40 2 NC_002967:TDE0911|3end_type_II_restriction_endonuclease_TdeIII_931329..931479_POSITIVE 287 110 77 117 86 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 282 110 69 137 96 NC_002967:TDE2329|3end_hypothetical_protein_2366347..2366497_NEGATIVE 264 87 52 33 1 NC_002967:TDE0903|3end_ATP-dependent_DNA_helicase_PcrA_922296..922446_POSITIVE 262 110 70 78 33 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 255 112 97 135 117 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE 252 120 73 59 3 NC_002967:TDE2503|3end_hypothetical_protein_2529079..2529229_POSITIVE 250 112 81 151 117 NC_002967:TDE2051|3end_hypothetical_protein_2079990..2080140_NEGATIVE 249 123 92 35 6 NC_002967:TDE0957|3end_glycerophosphoryl_diester_phosphodiesterase_family_protein_981075..981225_POSITIVE 244 63 24 87 49 NC_002967:TDE1734|3end_exodeoxyribonuclease_III_1789463..1789613_POSITIVE 244 110 81 145 119 NC_002967:TDE0408|3end_oxidoreductase,_NAD-binding_460536..460686_NEGATIVE 243 109 63 119 76 NC_002967:TDE0895|3end_transcriptional_regulator,_AraC_family_911227..911377_NEGATIVE 242 112 78 148 114 NC_002967:TDE1616|3end_glycerate_dehydrogenase_1663755..1663905_NEGATIVE 241 60 12 100 51 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 240 100 57 120 66 NC_002967:TDE0798|3end_transporter,_putative_821229..821379_NEGATIVE