Origin IGS: aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctttaaatatctcaataatttaaaaaaaagtcaatcggaaaagcgattattaaatgccaatcttttttttcaaattttgctatctattacaaacaatttctataataattatgaaagggggaattttttttaaaaaaaaattattagcgaggcttagtt Mask Tandem Repeat Region ================================================ aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Find is-nt database================================================ Query_seq: TDE0669:TDE0670|TDE0669:TDE0670:hypothetical protein:ATP-dependent protease La:<-->:707918..708077 160 aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0669:TDE0670|TDE0669:TDE0670:hypothetical protein:ATP-dependent protease La:<-->:707918..708077 160 aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0669:TDE0670|TDE0669:TDE0670:hypothetical protein:ATP-dependent protease La:<-->:707918..708077 160 aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 2 End: 106 . S L R A L L K K K F F I G G K M I I I S I T Q L L Y C F K F F F I P M ...................................................... aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga 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: 82 Start: 125 End: 154 ............................................................................................................................ATTGACTTTTTTTTAAATTATTGAGATATT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.0 Tail_Score: -3.04477 Start: 111 End: 128 Full_Region: AAGATTGGCATTTAA TAATCG CTTTTC CGATTG ACTTTTTTTTAAATT ..............................................................................................................TAATCGCTTTTCCGATTG................................ Find igs database================================================ Query_seq: TDE0669:TDE0670|TDE0669:TDE0670:hypothetical protein:ATP-dependent protease La:<-->:707918..708077 160 aactaagcctcgctaataatttttttttaaaaaaaattccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Intra-Species Hit: Count: 1 Min: 37 Max: 160 Len: 124 Subject: NC_002967_TDE0669_TDE0670|hypothetical protein:ATP-dependent protease La|NEGATIVE:POSITIVE|[707918,708077]|160 HSP 1 e-value: 8.0E-36 bit: 151.0 Len: 124 Query Start:37 Query End:160 Subject Strand: POSITIVE Subject Start: 37 Subject End: 160 ....................................ttccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgnnnnnnnngattggcatttaataatcgcttttccgattgacnnnnnnnnaaattattgagatatttaaaga ....................................ttccccctttcataattattatagaaattgtttgtaatagatagcaaaatttgaaaaaaaagattggcatttaataatcgcttttccgattgacttttttttaaattattgagatatttaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCCCCUUUCAUAAUUAUUAUAGAAAUUGUUUGUAAUAGAUAGCAAAAUUUGAAAAAAAAGAUUGGCAUUUAAUAAUCGCUUUUCCGAUUGACUUUUUUUUAAAUUAUUGAGAUAUUUAAAGA .......(((((...((((((((((.....)))))))))).......(((((((((((((.((((((..................))))))...)))))))))))))..))))).......... (-17.87) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUAAAUAUCUCAAUAAUUUAAAAAAAAGUCAAUCGGAAAAGCGAUUAUUAAAUGCCAAUCUUUUUUUUCAAAUUUUGCUAUCUAUUACAAACAAUUUCUAUAAUAAUUAUGAAAGGGGGAA ..........((((...((((((((((((((..(((((......))))).............))))))))).)))))....................((((.(((.....)))))))..)))). (-10.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 713 90 41 217 168 NC_002967:TDE0669|5end_hypothetical_protein_707827..708057_NEGATIVE 623 50 1 181 132 NC_002967:TDE0007|5end_hypothetical_protein_9874..10104_POSITIVE 565 50 4 180 134 NC_002967:TDE2707|5end_hypothetical_protein_2753947..2754177_POSITIVE 535 50 4 179 133 NC_002967:TDE2719|5end_hypothetical_protein_2776045..2776275_POSITIVE 528 50 4 180 134 NC_002967:TDE0862|5end_hypothetical_protein_883192..883422_POSITIVE 465 50 1 180 131 NC_002967:TDE0165|5end_hypothetical_protein_194122..194352_POSITIVE 378 50 4 180 133 NC_002967:TDE2098|5end_hypothetical_protein_2125085..2125315_NEGATIVE 358 50 1 177 127 NC_002967:TDE0049|5end_hypothetical_protein_59089..59319_NEGATIVE 328 50 1 178 129 NC_002967:TDE2136|5end_hypothetical_protein_2165659..2165889_NEGATIVE 322 49 4 178 133 NC_002967:TDE1691|5end_hypothetical_protein_1748273..1748503_NEGATIVE 319 49 4 180 135 NC_002967:TDE1344|5end_hypothetical_protein_1382392..1382622_POSITIVE 309 50 1 183 134 NC_002967:TDE0403|5end_hypothetical_protein_454433..454663_POSITIVE 267 59 11 191 143 NC_002967:TDE1976|5end_hypothetical_protein_1989115..1989345_POSITIVE 253 119 80 166 124 NC_002967:TDE0065|5end_hypothetical_protein_73346..73576_NEGATIVE 227 74 36 131 95 NC_002967:TDE2519|5end_hypothetical_protein_2546449..2546679_NEGATIVE 226 44 1 220 176 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 226 100 60 44 2 NC_002967:TDE0105|5end_MTA/SAH_nucleosidase_125454..125684_NEGATIVE 225 114 71 129 91 NC_002967:TDE0867|5end_hypothetical_protein_888542..888772_POSITIVE 222 89 62 181 155 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 221 88 43 213 170 NC_002967:TDE1002|5end_hypothetical_protein_1029137..1029367_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 59 11 52 4 NC_002967:TDE1975|3end_hypothetical_protein_1989056..1989206_POSITIVE 227 74 36 62 26 NC_002967:TDE2520|3end_hypothetical_protein_2546518..2546668_NEGATIVE 225 114 71 136 98 NC_002967:TDE0866|3end_hypothetical_protein_888629..888779_POSITIVE 221 88 43 74 31 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 221 90 44 59 21 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 210 97 58 132 97 NC_002967:TDE2701|3end_hypothetical_protein_2745861..2746011_POSITIVE 210 97 58 39 4 NC_002967:TDE2700|3end_citrate_carrier_protein,_CCS_family_2745768..2745918_POSITIVE 203 96 66 47 20 NC_002967:TDE2040|3end_lipoprotein_releasing_system,_ATP-binding_protein_2069541..2069691_NEGATIVE 203 99 61 57 26 NC_002967:TDE0784|3end_ribosomal_protein_S5_814492..814642_POSITIVE 188 114 82 37 10 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 188 90 44 59 21 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 188 113 82 149 118 NC_002967:TDE0856|3end_L-fuculose_phosphate_aldolase,_putative_878378..878528_POSITIVE 187 62 21 146 107 NC_002967:TDE1694|3end_hypothetical_protein_1749223..1749373_NEGATIVE 185 117 76 128 76 NC_002967:TDE2193|3end_deoxycytidylate_deaminase,_putative_2229263..2229413_NEGATIVE 185 100 66 131 99 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 184 96 60 151 112 NC_002967:TDE1343|3end_trypsin_domain/PDZ_domain_protein_1382236..1382386_POSITIVE 184 100 73 133 111 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE 182 60 11 75 25 NC_002967:TDE2237|3end_hypothetical_protein_2276298..2276448_NEGATIVE 182 68 21 95 50 NC_002967:TDE0557|3end_hypothetical_protein_592146..592296_NEGATIVE 175 25 2 38 12 NC_002967:TDE0737|3end_hypothetical_protein_775408..775558_NEGATIVE