Origin IGS: tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaagcctcctaaaaccgattatagcataagacgcatgattattcaatgttttgagaatagcagcagagtctattagacacaaaaaaacccgccttgcggcgggttttaaactatactaggtataga Mask Tandem Repeat Region ================================================ tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Find is-nt database================================================ Query_seq: TDE0405:TDE0406|TDE0405:TDE0406:major outer sheath protein:hypothetical protein:->->:457242..457369 128 tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0405:TDE0406|TDE0405:TDE0406:major outer sheath protein:hypothetical protein:->->:457242..457369 128 tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0405:TDE0406|TDE0405:TDE0406:major outer sheath protein:hypothetical protein:->->:457242..457369 128 tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Predict ORF larger than 30AA ================================================ tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa 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: 89 Start: 80 End: 109 ...............................................................................ATTGAATAATCATGCGTCTTATGCTATAAT................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 90 HP_score: -11.8 Tail_Score: -4.17657 Start: 24 End: 39 Full_Region: ttagacacaaaaaaa cccgcc ttgc ggcggg ttttaaactatacta .......................cccgccttgcggcggg......................................................................................... Find igs database================================================ Query_seq: TDE0405:TDE0406|TDE0405:TDE0406:major outer sheath protein:hypothetical protein:->->:457242..457369 128 tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_002967_TDE0405_TDE0406|major outer sheath protein:hypothetical protein|POSITIVE:POSITIVE|[457242,457369]|128 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tctatacctagtatagtttaaaacccgccgcaaggcgggnnnnnnngtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa tctatacctagtatagtttaaaacccgccgcaaggcgggtttttttgtgtctaatagactctgctgctattctcaaaacattgaataatcatgcgtcttatgctataatcggttttaggaggcttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUACCUAGUAUAGUUUAAAACCCGCCGCAAGGCGGGUUUUUUUGUGUCUAAUAGACUCUGCUGCUAUUCUCAAAACAUUGAAUAAUCAUGCGUCUUAUGCUAUAAUCGGUUUUAGGAGGCUUAAA (((((...((((((((...((((((((((....)))))))))).))))).)))))))).........(((((..........))))).....((.(((((.(((......)))..))))).))..... (-36.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAGCCUCCUAAAACCGAUUAUAGCAUAAGACGCAUGAUUAUUCAAUGUUUUGAGAAUAGCAGCAGAGUCUAUUAGACACAAAAAAACCCGCCUUGCGGCGGGUUUUAAACUAUACUAGGUAUAGA ..........(((..(((...(((((........((.((.((((((..........))))))))))...(((.....))).....((((((((((....))))))))))...)))))...))).))). (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 78 31 81 38 NC_002967:TDE1963|5end_selenocysteine-specific_translation_elongation_factor_1975289..1975519_POSITIVE 355 68 28 124 86 NC_002967:TDE2521|5end_hypothetical_protein_2548074..2548304_NEGATIVE 349 68 26 52 17 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 337 66 27 231 184 NC_002967:TDE0625|5end_ABC_transporter,_ATP-binding_protein_657253..657483_POSITIVE 325 66 22 102 55 NC_002967:TDE0759|5end_hypothetical_protein_799499..799729_NEGATIVE 315 67 26 132 89 NC_002967:TDE0912|5end_hypothetical_protein_931350..931580_POSITIVE 306 67 28 180 138 NC_002967:TDE0410|5end_peptidase,_M48_family_462053..462283_POSITIVE 294 67 23 221 170 NC_002967:TDE1818|5end_hypothetical_protein_1853791..1854021_NEGATIVE 292 61 24 161 106 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 288 70 24 96 56 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 287 50 5 102 61 NC_002967:TDE1401|5end_DedA_family_protein_1442365..1442595_POSITIVE 285 49 7 44 5 NC_002967:TDE0162|5end_hypothetical_protein_187898..188128_POSITIVE 282 48 7 127 82 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 280 43 22 62 34 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 279 68 27 169 125 NC_002967:TDE2744|5end_type_I_restriction-modification_system,_S_subunit_2799853..2800083_NEGATIVE 279 52 11 204 158 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 276 65 27 101 50 NC_002967:TDE0914|5end_hypothetical_protein_933195..933425_NEGATIVE 273 50 25 68 36 NC_002967:TDE1504|5end_ribosomal_protein_L31_1553350..1553580_POSITIVE 272 67 24 66 9 NC_002967:TDE0456|5end_pyridoxine_biosynthesis_protein_513384..513614_NEGATIVE 271 45 5 212 164 NC_002967:TDE2747|5end_type_I_restriction-modification_system,_R_subunit_2804942..2805172_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 43 1 71 33 NC_002967:TDE0405|3end_major_outer_sheath_protein_457181..457331_POSITIVE 321 67 25 75 25 NC_002967:TDE2715|3end_hypothetical_protein_2772936..2773086_POSITIVE 321 68 25 53 4 NC_002967:TDE2276|3end_hypothetical_protein_2311945..2312095_NEGATIVE 318 69 23 107 45 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 316 73 35 91 47 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 296 69 21 125 56 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 295 43 11 75 33 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 287 50 5 91 50 NC_002967:TDE1400|3end_NAD(+)_synthetase_1442434..1442584_POSITIVE 287 49 10 72 28 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 279 68 27 141 97 NC_002967:TDE2745|3end_fic_family_protein_2799881..2800031_NEGATIVE 278 40 3 40 1 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 278 52 24 98 68 NC_002967:TDE0794|3end_hypothetical_protein_819224..819374_NEGATIVE 277 70 25 89 41 NC_002967:TDE0649|3end_hypothetical_protein_684034..684184_NEGATIVE 276 67 24 108 62 NC_002967:TDE2204|3end_Na+/H+_antiporter_family_protein_2242550..2242700_POSITIVE 276 65 27 149 98 NC_002967:TDE0915|3end_hypothetical_protein_933147..933297_NEGATIVE 275 51 23 149 121 NC_002967:TDE0573|3end_hypothetical_protein_604910..605060_POSITIVE 273 69 23 59 15 NC_002967:TDE0095|3end_hypothetical_protein_112622..112772_POSITIVE 269 67 22 46 4 NC_002967:TDE1809|3end_hypothetical_protein_1845215..1845365_NEGATIVE 268 65 26 102 73 NC_002967:TDE1534|3end_hypothetical_protein_1578667..1578817_NEGATIVE 267 68 25 47 4 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE