Origin IGS: gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcatttacctctatagtatattttacacatattattgtgtaaaatcaaggaggttgcttaataattcggcattaaatatttacttagctcaatatgattttttaaatcggc Mask Tandem Repeat Region ================================================ gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Find is-nt database================================================ Query_seq: TDE0877:TDE0878|TDE0877:TDE0878:hypothetical protein:hypothetical protein:->->:899680..899791 112 gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0877:TDE0878|TDE0877:TDE0878:hypothetical protein:hypothetical protein:->->:899680..899791 112 gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0877:TDE0878|TDE0877:TDE0878:hypothetical protein:hypothetical protein:->->:899680..899791 112 gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 2 End: 109 . R N L F D Y Q A L Y I N L A S N N L L R R S K V C Y Y T Y F I S Y L Y M ... gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct 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: 83 Start: 63 End: 92 ..............................................................CTTGATTTTACACAATAATATGTGTAAAAT.................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 68 End: 97 ...................................................................TTTTACACAATAATATGTGTAAAATATACT............... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 61 HP_score: -6.9 Tail_Score: -2.85668 Start: 68 End: 91 Full_Region: AAGCAACCTCCTTGA TTTTACACA ATAATA TGTGTAAAA TATACTATAGAGGTA ...................................................................TTTTACACAATAATATGTGTAAAA..................... Find igs database================================================ Query_seq: TDE0877:TDE0878|TDE0877:TDE0878:hypothetical protein:hypothetical protein:->->:899680..899791 112 gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE0877_TDE0878|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[899680,899791]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct gccgatttaaaaaatcatattgagctaagtaaatatttaatgccgaattattaagcaacctccttgattttacacaataatatgtgtaaaatatactatagaggtaaatgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGAUUUAAAAAAUCAUAUUGAGCUAAGUAAAUAUUUAAUGCCGAAUUAUUAAGCAACCUCCUUGAUUUUACACAAUAAUAUGUGUAAAAUAUACUAUAGAGGUAAAUGCU ...((((.....))))...(((.(((((((....)))))..))))).......(((((((((....((((((((((......))))))))))........)))))...)))) (-20.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAUUUACCUCUAUAGUAUAUUUUACACAUAUUAUUGUGUAAAAUCAAGGAGGUUGCUUAAUAAUUCGGCAUUAAAUAUUUACUUAGCUCAAUAUGAUUUUUUAAAUCGGC (((....((((((.......((((((((((......))))))))))...))))))((((.........))))...............))).....(((((.....))))).. (-20.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 46 3 51 3 NC_002967:TDE1943|5end_30S_ribosomal_protein_S4_1960056..1960286_NEGATIVE 229 68 41 102 74 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 219 68 41 106 80 NC_002967:TDE0225|5end_prevent-host-death_family_protein_256377..256607_NEGATIVE 218 87 42 217 170 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 215 70 22 115 70 NC_002967:TDE0705|5end_SPFH_domain/Band_7_family_protein_740268..740498_NEGATIVE 209 80 41 176 136 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 209 62 21 61 21 NC_002967:TDE0389|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_440008..440238_POSITIVE 207 65 33 106 72 NC_002967:TDE0255|5end_ABC_transporter,_ATP-binding_protein_290742..290972_NEGATIVE 206 67 24 106 57 NC_002967:TDE0031|5end_hypothetical_protein_39095..39325_NEGATIVE 204 69 41 193 163 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 204 69 41 83 53 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 198 44 9 213 172 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 198 80 41 128 95 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 196 71 41 163 131 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 195 64 41 176 152 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 194 67 22 104 58 NC_002967:TDE1301|5end_DNA_repair_protein_RecN_1339116..1339346_NEGATIVE 193 56 12 228 181 NC_002967:TDE1651|5end_BioY_family_protein_1698732..1698962_NEGATIVE 192 87 42 126 78 NC_002967:TDE0281|5end_hypothetical_protein_310490..310720_NEGATIVE 192 68 43 105 79 NC_002967:TDE0103|5end_aminotransferase,_class-V_123686..123916_NEGATIVE 191 75 50 116 83 NC_002967:TDE0704|5end_SPFH_domain/Band_7_family_protein_739346..739576_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 68 41 87 59 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 219 68 41 89 63 NC_002967:TDE0226|3end_hypothetical_protein_256394..256544_NEGATIVE 218 87 42 98 51 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 207 65 33 106 72 NC_002967:TDE0256|3end_hypothetical_protein_290742..290892_NEGATIVE 198 65 21 118 73 NC_002967:TDE2299|3end_apolipoprotein_N-acyltransferase_2339937..2340087_POSITIVE 196 65 41 82 57 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 196 71 41 36 4 NC_002967:TDE1654|3end_ATP-dependent_helicase_HrpA,_putative_1704911..1705061_POSITIVE 195 64 41 44 20 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 193 56 12 103 56 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE 193 56 20 140 98 NC_002967:TDE1091|3end_hypothetical_protein_1123017..1123167_NEGATIVE 192 68 43 108 82 NC_002967:TDE0104|3end_3-dehydroquinate_synthase_123683..123833_NEGATIVE 191 75 50 123 90 NC_002967:TDE0705|3end_SPFH_domain/Band_7_family_protein_739339..739489_NEGATIVE 191 70 41 96 67 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 190 66 24 89 53 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 187 64 41 87 63 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 187 64 41 78 54 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 187 80 41 99 61 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 186 65 41 89 64 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 185 88 58 143 119 NC_002967:TDE1648|3end_hypothetical_protein_1696486..1696636_NEGATIVE 184 59 16 132 78 NC_002967:TDE1679|3end_ATP_synthase_subunit_K_1730627..1730777_NEGATIVE