Origin IGS: gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caggattcgattataaaagcggtgtagaaaaactttctcgccgctttttattaaagggagcctctaaaaactgatgtttttagaggcttctaagtaaggatgaccggaaccagac Mask Tandem Repeat Region ================================================ gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Find is-nt database================================================ Query_seq: TDE2256:TDE2257|TDE2256:TDE2257:hypothetical protein:5'-nucleotidase family protein:<-<-:2293478..2293592 115 gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2256:TDE2257|TDE2256:TDE2257:hypothetical protein:5'-nucleotidase family protein:<-<-:2293478..2293592 115 gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2256:TDE2257|TDE2256:TDE2257:hypothetical protein:5'-nucleotidase family protein:<-<-:2293478..2293592 115 gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Predict ORF larger than 30AA ================================================ gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg 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================================================ gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -12.0 Tail_Score: -3.72576 Start: 25 End: 60 Full_Region: CGGTCATCCTTACTT AGAAGCCTCTAAAAAC ATCA GTTTTTAGAGGCTCCC TTTAATAAAAAGCGG ........................AGAAGCCTCTAAAAACATCAGTTTTTAGAGGCTCCC....................................................... TransTerm Strand: - Conf: 100 HP_score: -15.8 Tail_Score: -3.35996 Start: 29 End: 56 Full_Region: tttttattaaaggga gcctctaaaaac tgat gtttttagaggc ttctaagtaaggatg ............................gcctctaaaaactgatgtttttagaggc........................................................... TransTerm Strand: + Conf: 76 HP_score: -6.9 Tail_Score: -4.46926 Start: 72 End: 97 Full_Region: TCCCTTTAATAAAAA GCGGCGAGAAA GTT TTTCTACACCGC TTTTATAATCGAATC .......................................................................GCGGCGAGAAAGTTTTTCTACACCGC.................. Find igs database================================================ Query_seq: TDE2256:TDE2257|TDE2256:TDE2257:hypothetical protein:5'-nucleotidase family protein:<-<-:2293478..2293592 115 gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE2256_TDE2257|hypothetical protein:5'-nucleotidase family protein|NEGATIVE:NEGATIVE|[2293478,2293592]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg gtctggttccggtcatccttacttagaagcctctaaaaacatcagtttttagaggctccctttaataaaaagcggcgagaaagtttttctacaccgcttttataatcgaatcctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUGGUUCCGGUCAUCCUUACUUAGAAGCCUCUAAAAACAUCAGUUUUUAGAGGCUCCCUUUAAUAAAAAGCGGCGAGAAAGUUUUUCUACACCGCUUUUAUAAUCGAAUCCUG ....(((((.(((.........((((((((((((((((((....)))))))))))))...)))))..((((((((.(((((.....)))).).))))))))...))))))))... (-35.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGAUUCGAUUAUAAAAGCGGUGUAGAAAAACUUUCUCGCCGCUUUUUAUUAAAGGGAGCCUCUAAAAACUGAUGUUUUUAGAGGCUUCUAAGUAAGGAUGACCGGAACCAGAC ..((.((((.((((((((((((((.((((.....)))))))))))))).......((((((((((((((((....))))))))))))))))........)))).)))).)).... (-47.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 100 51 191 142 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 483 64 25 157 112 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 413 59 28 108 77 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 380 79 31 201 140 NC_002967:TDE1623|5end_hypothetical_protein_1671980..1672210_NEGATIVE 317 62 22 161 117 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 308 100 67 226 189 NC_002967:TDE0133|5end_transcriptional_regulator,_GntR_family_152373..152603_POSITIVE 304 55 23 149 116 NC_002967:TDE1715|5end_phosphoglycerate_kinase_1770762..1770992_NEGATIVE 300 62 24 152 113 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 292 81 42 49 3 NC_002967:TDE1984|5end_hypothetical_protein_1997565..1997795_NEGATIVE 276 65 23 173 128 NC_002967:TDE2693|5end_ankyrin_repeat_protein_2731133..2731363_POSITIVE 275 63 28 204 169 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 274 60 16 148 100 NC_002967:TDE0346|5end_protease_PrtB_387897..388127_NEGATIVE 266 43 5 55 14 NC_002967:TDE0942|5end_long-chain-fatty-acid--CoA_ligase,_putative_964132..964362_POSITIVE 265 96 54 162 120 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 261 100 68 223 195 NC_002967:TDE1711|5end_RelA/SpoT_domain_protein_1766718..1766948_NEGATIVE 258 99 56 154 100 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 256 99 51 112 67 NC_002967:TDE1740|5end_hypothetical_protein_1792785..1793015_NEGATIVE 254 96 53 221 182 NC_002967:TDE0890|5end_hypothetical_protein_905890..906120_POSITIVE 252 40 5 97 56 NC_002967:TDE1440|5end_glucose-1-phosphate_thymidylyltransferase_1485353..1485583_POSITIVE 249 100 56 150 98 NC_002967:TDE2692|5end_CTP_synthetase_2729421..2729651_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 483 64 25 112 67 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 413 59 28 70 39 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 380 79 31 110 49 NC_002967:TDE1624|3end_glycine_dehydrogenase_subunit_2_1672071..1672221_NEGATIVE 367 61 27 67 33 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 366 64 21 93 47 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 354 62 28 86 51 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 339 55 26 58 29 NC_002967:TDE2270|3end_methyl-accepting_chemotaxis_protein_2306280..2306430_NEGATIVE 338 61 28 87 51 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 317 62 22 75 31 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 308 100 67 69 32 NC_002967:TDE0132|3end_hypothetical_protein_152296..152446_POSITIVE 305 77 31 115 59 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 305 80 31 87 34 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 304 55 23 60 27 NC_002967:TDE1716|3end_glyoxalase_family_protein_1770851..1771001_NEGATIVE 292 81 42 59 13 NC_002967:TDE1985|3end_hypothetical_protein_1997555..1997705_NEGATIVE 285 80 40 49 9 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 276 65 23 71 26 NC_002967:TDE2692|3end_CTP_synthetase_2731111..2731261_POSITIVE 275 63 28 80 45 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 267 90 41 148 95 NC_002967:TDE0339|3end_transcriptional_regulator,_TetR_family_378568..378718_POSITIVE 265 61 31 84 53 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 265 96 54 151 109 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE