Origin IGS: gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttatcaagatatttattattaattcctcaaatctttatcttatagaaattgtttgtaatagatagtaaaattctgcacttgaaatcggcaggaaaatatgataaaatcgccgtcttgagcaataggtcttaaagc Mask Tandem Repeat Region ================================================ gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Find is-nt database================================================ Query_seq: TDE1990:TDE1991|TDE1990:TDE1991:ATP-dependent helicase, DinG family:hypothetical protein:<-<-:2008587..2008723 137 gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1990:TDE1991|TDE1990:TDE1991:ATP-dependent helicase, DinG family:hypothetical protein:<-<-:2008587..2008723 137 gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1990:TDE1991|TDE1990:TDE1991:ATP-dependent helicase, DinG family:hypothetical protein:<-<-:2008587..2008723 137 gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 14 End: 106 ............. M L K T A I L S Y F P A D F K C R I L L S I T N N F Y K I K I ............................... gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac 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: 86 Start: 29 End: 58 ............................CTTGAAATCGGCAGGAAAATATGATAAAAT............................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 65 End: 94 ................................................................ATAGAAATTGTTTGTAATAGATAGTAAAAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1990:TDE1991|TDE1990:TDE1991:ATP-dependent helicase, DinG family:hypothetical protein:<-<-:2008587..2008723 137 gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_002967_TDE1990_TDE1991|ATP-dependent helicase, DinG family:hypothetical protein|NEGATIVE:NEGATIVE|[2008587,2008723]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac gctttaagacctattgctcaagacggcgattttatcatattttcctgccgatttcaagtgcagaattttactatctattacaaacaatttctataagataaagatttgaggaattaataataaatatcttgataaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUAAGACCUAUUGCUCAAGACGGCGAUUUUAUCAUAUUUUCCUGCCGAUUUCAAGUGCAGAAUUUUACUAUCUAUUACAAACAAUUUCUAUAAGAUAAAGAUUUGAGGAAUUAAUAAUAAAUAUCUUGAUAAAC ............((((((......))))))(((((((.......(((((........).))))......................(((((((...((((....)))).)))))))..............))))))). (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAUCAAGAUAUUUAUUAUUAAUUCCUCAAAUCUUUAUCUUAUAGAAAUUGUUUGUAAUAGAUAGUAAAAUUCUGCACUUGAAAUCGGCAGGAAAAUAUGAUAAAAUCGCCGUCUUGAGCAAUAGGUCUUAAAGC .....(((((((.(((((((((.(((...(((((..((.((.....))))..))))).))).))))))))).((((((.(........)))))))..................)))))))................. (-20.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 896 50 1 141 92 NC_002967:TDE1990|5end_ATP-dependent_helicase,_DinG_family_2008496..2008726_NEGATIVE 343 52 12 110 61 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 305 50 1 103 54 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 305 115 71 217 172 NC_002967:TDE0670|5end_ATP-dependent_protease_La_707938..708168_POSITIVE 304 47 2 103 51 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 297 69 25 48 2 NC_002967:TDE1896|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1917505..1917735_NEGATIVE 292 55 11 152 99 NC_002967:TDE2266|5end_reverse_transcriptase_family_protein_2304028..2304258_NEGATIVE 289 90 62 231 203 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 287 64 23 192 160 NC_002967:TDE1448|5end_glutamate_racemase,_putative_1493535..1493765_POSITIVE 281 49 1 102 65 NC_002967:TDE2085|5end_uridylate_kinase_2114182..2114412_POSITIVE 281 50 1 59 13 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 276 98 52 219 170 NC_002967:TDE1787|5end_hypothetical_protein_1826635..1826865_NEGATIVE 276 80 32 177 125 NC_002967:TDE1663|5end_OmpA_family_protein_1717319..1717549_POSITIVE 268 49 1 88 24 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 266 98 52 219 170 NC_002967:TDE1840|5end_hypothetical_protein_1871581..1871811_NEGATIVE 266 98 52 219 170 NC_002967:TDE1800|5end_hypothetical_protein_1837684..1837914_NEGATIVE 265 50 11 108 72 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 261 53 13 192 152 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 258 48 1 64 27 NC_002967:TDE2243|5end_CutC_family_protein_2282954..2283184_NEGATIVE 256 60 15 123 71 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 49 1 69 32 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 276 80 32 93 41 NC_002967:TDE1662|3end_replicative_DNA_helicase_1717315..1717465_POSITIVE 268 49 1 74 10 NC_002967:TDE1144|3end_hypothetical_protein_1181848..1181998_NEGATIVE 264 45 1 151 110 NC_002967:TDE1614|3end_hypothetical_protein_1662295..1662445_NEGATIVE 253 48 7 143 95 NC_002967:TDE0736|3end_hypothetical_protein_775000..775150_NEGATIVE 248 61 24 114 78 NC_002967:TDE1177|3end_flavodoxin_family_protein_1206594..1206744_NEGATIVE 247 69 22 57 18 NC_002967:TDE0533|3end_hypothetical_protein_576577..576727_POSITIVE 244 49 18 79 50 NC_002967:TDE0777|3end_50S_ribosomal_protein_L14_811557..811707_POSITIVE 243 49 2 84 25 NC_002967:TDE1449|3end_GTPase_YjeQ_1495379..1495529_POSITIVE 242 68 23 115 66 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE 238 46 1 149 97 NC_002967:TDE2243|3end_CutC_family_protein_2282214..2282364_NEGATIVE 236 47 1 124 88 NC_002967:TDE1433|3end_glycosyl_transferase,_group_2_family_protein_1478302..1478452_POSITIVE 235 27 1 111 83 NC_002967:TDE0096|3end_NADH_oxidase_114137..114287_POSITIVE 234 49 3 109 49 NC_002967:TDE1414|3end_phosphonopyruvate_decarboxylase,_putative_1458028..1458178_POSITIVE 234 58 11 59 7 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 234 73 35 50 5 NC_002967:TDE0213|3end_TPR_domain_protein_248318..248468_NEGATIVE 231 50 1 146 95 NC_002967:TDE0786|3end_ribosomal_protein_L15_815134..815284_POSITIVE 231 63 30 119 86 NC_002967:TDE0345|3end_methyl-accepting_chemotaxis_protein_DmcB_385744..385894_NEGATIVE 231 32 1 143 99 NC_002967:TDE0339|3end_transcriptional_regulator,_TetR_family_378568..378718_POSITIVE 228 50 20 70 41 NC_002967:TDE0933|3end_acetate_kinase_959336..959486_POSITIVE