Origin IGS: gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaataaaattggaatacacctgcaaatgtcttgccctgtagaaaatatgcagattactgtgtcgcattgctaaaaatgtgagagaggggcatgtattaaaaattttagaacactgaaaaacaaaaaacaaac Mask Tandem Repeat Region ================================================ gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Find is-nt database================================================ Query_seq: TDE2544:TDE2545|TDE2544:TDE2545:hypothetical protein:hypothetical protein:<-<-:2571127..2571259 133 gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2544:TDE2545|TDE2544:TDE2545:hypothetical protein:hypothetical protein:<-<-:2571127..2571259 133 gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2544:TDE2545|TDE2544:TDE2545:hypothetical protein:hypothetical protein:<-<-:2571127..2571259 133 gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 3 End: 131 .. M F F V F Q C S K I F N T C P S L T F L A M R H S N L H I F Y R A R H L Q V Y S N F I .. gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac 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: 81 Start: 2 End: 31 .TTTGTTTTTTGTTTTTCAGTGTTCTAAAAT...................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: + Score: 83 Start: 96 End: 112 ...............................................................................................AGGGCAAGACATTTGCA..................... gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2544:TDE2545|TDE2544:TDE2545:hypothetical protein:hypothetical protein:<-<-:2571127..2571259 133 gtttgttttttgtttttcagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Intra-Species Hit: Count: 1 Min: 18 Max: 133 Len: 116 Subject: NC_002967_TDE2544_TDE2545|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2571127,2571259]|133 HSP 1 e-value: 9.0E-60 bit: 230.0 Len: 116 Query Start:18 Query End:133 Subject Strand: POSITIVE Subject Start: 18 Subject End: 133 .................cagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac .................cagtgttctaaaatttttaatacatgcccctctctcacatttttagcaatgcgacacagtaatctgcatattttctacagggcaagacatttgcaggtgtattccaattttattac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUGUUCUAAAAUUUUUAAUACAUGCCCCUCUCUCACAUUUUUAGCAAUGCGACACAGUAAUCUGCAUAUUUUCUACAGGGCAAGACAUUUGCAGGUGUAUUCCAAUUUUAUUAC ....((..(((((((...(((((((((((.....((.((((......)))).))..(((....))).............))))..(.(....))..)))))))..)))))))..)) (-15.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAUAAAAUUGGAAUACACCUGCAAAUGUCUUGCCCUGUAGAAAAUAUGCAGAUUACUGUGUCGCAUUGCUAAAAAUGUGAGAGAGGGGCAUGUAUUAAAAAUUUUAGAACACUG ((..(((((((..((((((..(((............(((((.......)))))....((.(.(((((((......))))))).).))..)))))))))...)))))))..)).... (-28.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 925 100 51 208 159 NC_002967:TDE2544|5end_hypothetical_protein_2571036..2571266_NEGATIVE 576 37 1 231 195 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 309 100 63 213 173 NC_002967:TDE2527|5end_hypothetical_protein_2556219..2556449_NEGATIVE 274 105 63 223 168 NC_002967:TDE1687|5end_hypothetical_protein_1744042..1744272_NEGATIVE 264 103 75 176 143 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 260 68 32 133 98 NC_002967:TDE0818|5end_ABC_transporter,_ATP-binding/permease_protein_841647..841877_NEGATIVE 255 101 66 54 15 NC_002967:TDE0585|5end_hypothetical_protein_625024..625254_NEGATIVE 254 100 51 58 5 NC_002967:TDE1827|5end_hydrolase,_carbon-nitrogen_family_1860830..1861060_NEGATIVE 254 100 51 58 5 NC_002967:TDE1793|5end_hydrolase,_carbon-nitrogen_family_1830844..1831074_NEGATIVE 254 83 46 109 74 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 250 108 62 73 12 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 249 106 63 194 153 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 249 95 53 195 154 NC_002967:TDE1634|5end_hypothetical_protein_1683063..1683293_NEGATIVE 246 100 55 146 105 NC_002967:TDE0034|5end_hypothetical_protein_41450..41680_NEGATIVE 244 97 52 58 16 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 242 95 52 195 153 NC_002967:TDE2105|5end_hypothetical_protein_2131484..2131714_NEGATIVE 242 106 62 185 144 NC_002967:TDE1681|5end_V-type_ATP_synthase_subunit_D_1733537..1733767_NEGATIVE 242 98 70 153 120 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 240 97 63 135 101 NC_002967:TDE0780|5end_ribosomal_protein_S14_812364..812594_POSITIVE 238 102 61 190 151 NC_002967:TDE0452|5end_hypothetical_protein_510143..510373_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 67 21 78 34 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 284 67 25 62 16 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 260 68 32 131 96 NC_002967:TDE0819|3end_ABC_transporter,_ATP-binding/permease_protein_841649..841799_NEGATIVE 249 106 63 139 98 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 244 97 52 44 2 NC_002967:TDE0907|3end_hypothetical_protein_925320..925470_POSITIVE 240 97 63 123 89 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 235 108 64 83 38 NC_002967:TDE0878|3end_hypothetical_protein_899929..900079_POSITIVE 234 67 23 53 12 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 233 67 26 114 84 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 232 100 51 139 82 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 231 103 84 25 6 NC_002967:TDE2009|3end_hypothetical_protein_2031247..2031397_POSITIVE 224 83 52 142 114 NC_002967:TDE1943|3end_30S_ribosomal_protein_S4_1959436..1959586_NEGATIVE 223 98 51 79 38 NC_002967:TDE1783|3end_hypothetical_protein_1823438..1823588_NEGATIVE 223 84 41 44 8 NC_002967:TDE0051|3end_alcohol_dehydrogenase,_iron-containing_60073..60223_NEGATIVE 220 68 24 80 19 NC_002967:TDE1003|3end_hypothetical_protein_1029325..1029475_POSITIVE 220 44 15 75 41 NC_002967:TDE0388|3end_hypothetical_protein_440050..440200_POSITIVE 219 98 59 88 42 NC_002967:TDE2152|3end_hypothetical_protein_2188804..2188954_NEGATIVE 217 73 31 85 43 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 216 100 53 151 98 NC_002967:TDE1027|3end_ribonuclease_III_1058382..1058532_POSITIVE 215 69 38 78 50 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE