Origin IGS: aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agccattcctcattgattgtattataccatacttaccgcagttttaaaagagccgcttttcaatttttaattggtaatttgtaattgccaattacccattaactttatggtcagtggaaaagtcacacagactgtccttatgcttacatacatcccgatattagcgtatcgcactgcaagtgtaaaatcccctgccggaaccgatgaatccaaaaaaaagatgaggcgagaaatgtacaatgatgtacattcataagcgggtatacgaatt Mask Tandem Repeat Region ================================================ aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Find is-nt database================================================ Query_seq: TDE1937:TDE1938|TDE1937:TDE1938:hypothetical protein:hypothetical protein:->->:1953509..1953779 271 aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1937:TDE1938|TDE1937:TDE1938:hypothetical protein:hypothetical protein:->->:1953509..1953779 271 aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1937:TDE1938|TDE1937:TDE1938:hypothetical protein:hypothetical protein:->->:1953509..1953779 271 aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 18 End: 125 ................. M N V H H C T F L A S S F F W I H R F R Q G I L H L Q C D T L I S G C M .................................................................................................................................................. Protein_Len: 60 Strand: + Start: 2 End: 202 . M R I P A Y E C T S L Y I S R L I F F L D S S V P A G D F T L A V R Y A N I G M Y V S I R T V C V T F P L T I K L M G N ..................................................................... Protein_Len: 60 Strand: - Start: 19 End: 201 .................. H V D N Y M E R R M K K K S E D T G A P S K V S A T R Y A L I P I Y T L M L V T Q T V K G S V M F N I P L Q C N C I V M ...................................................................... aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct 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: 222 End: 251 .............................................................................................................................................................................................................................CTTTTAAAACTGCGGTAAGTATGGTATAAT.................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 85 End: 114 ....................................................................................TTTTACACTTGCAGTGCGATACGCTAATAT............................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1937:TDE1938|TDE1937:TDE1938:hypothetical protein:hypothetical protein:->->:1953509..1953779 271 aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Intra-Species Hit: Count: 1 Min: 1 Max: 271 Len: 271 Subject: NC_002967_TDE1937_TDE1938|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1953509,1953779]|271 HSP 1 e-value: 1.0E-137 bit: 490.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcnnnnnnnnggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct aattcgtatacccgcttatgaatgtacatcattgtacatttctcgcctcatcttttttttggattcatcggttccggcaggggattttacacttgcagtgcgatacgctaatatcgggatgtatgtaagcataaggacagtctgtgtgacttttccactgaccataaagttaatgggtaattggcaattacaaattaccaattaaaaattgaaaagcggctcttttaaaactgcggtaagtatggtataatacaatcaatgaggaatggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCGUAUACCCGCUUAUGAAUGUACAUCAUUGUACAUUUCUCGCCUCAUCUUUUUUUUGGAUUCAUCGGUUCCGGCAGGGGAUUUUACACUUGCAGUGCGAUACGCUAAUAUCGGGAUGUAUGUAAGCAUAAGGACAGUCUGUGUGACUUUUCCACUGACCAUAAAGUUAAUGGGUAAUUGGCAAUUACAAAUUACCAAUUAAAAAUUGAAAAGCGGCUCUUUUAAAACUGCGGUAAGUAUGGUAUAAUACAAUCAAUGAGGAAUGGCU ..(((((....((((....(((((((((....)))))))))...(((..((((.......))))...((((((..(((((((((..((((((..((....(((((......))))).....((((....))))......))..))))))...)))).))).))......(((((.(((((((..........))))))).))))).)))))).....)))............))))...((((......)))).....)))))........ (-60.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCAUUCCUCAUUGAUUGUAUUAUACCAUACUUACCGCAGUUUUAAAAGAGCCGCUUUUCAAUUUUUAAUUGGUAAUUUGUAAUUGCCAAUUACCCAUUAACUUUAUGGUCAGUGGAAAAGUCACACAGACUGUCCUUAUGCUUACAUACAUCCCGAUAUUAGCGUAUCGCACUGCAAGUGUAAAAUCCCCUGCCGGAACCGAUGAAUCCAAAAAAAAGAUGAGGCGAGAAAUGUACAAUGAUGUACAUUCAUAAGCGGGUAUACGAAUU ....((((..........((((......))))...((((............(((.(((((.......(((((((((((.....)))))))))))..((((.......(((.(((.(((..((((.....))))....((((((((.((.......((((((....))))))...)).))))))))..))).)))))).....)))).........)))))....)))..(((.((((((....)))))))))....))))......)))). (-57.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 85 43 55 23 NC_002967:TDE2564|5end_PemK_family_protein_2589975..2590205_POSITIVE 342 88 46 147 100 NC_002967:TDE0834|5end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854863..855093_NEGATIVE 339 159 113 117 69 NC_002967:TDE0704|5end_SPFH_domain/Band_7_family_protein_739346..739576_NEGATIVE 333 142 101 215 169 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 333 142 101 184 138 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 315 108 69 44 10 NC_002967:TDE0593|5end_internalin-related_protein_633936..634166_NEGATIVE 314 41 2 199 162 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 311 78 31 159 112 NC_002967:TDE1783|5end_hypothetical_protein_1823605..1823835_NEGATIVE 310 107 61 227 172 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 309 119 73 225 167 NC_002967:TDE0738|5end_hypothetical_protein_775934..776164_NEGATIVE 305 51 21 217 182 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 303 89 42 180 117 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 303 118 72 99 31 NC_002967:TDE1079|5end_DNA-binding_protein/PTS_system,_IIA_component_1111120..1111350_POSITIVE 300 84 41 55 13 NC_002967:TDE2176|5end_site-specific_recombinase,_putative_2206239..2206469_NEGATIVE 299 78 31 159 112 NC_002967:TDE0059|5end_hypothetical_protein_67294..67524_POSITIVE 298 199 170 150 119 NC_002967:TDE1148|5end_hypothetical_protein_1186357..1186587_NEGATIVE 298 98 53 119 66 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 296 118 71 166 104 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 294 82 43 71 15 NC_002967:TDE2451|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2479832..2480062_POSITIVE 294 118 76 202 168 NC_002967:TDE1392|5end_hypothetical_protein_1432002..1432232_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 85 43 68 36 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 342 88 46 143 96 NC_002967:TDE0835|3end_NADH-ubiquinone_oxidoreductase_854867..855017_NEGATIVE 339 159 113 124 76 NC_002967:TDE0705|3end_SPFH_domain/Band_7_family_protein_739339..739489_NEGATIVE 311 54 12 92 55 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 308 55 12 138 90 NC_002967:TDE0145|3end_thiamine_ABC_transporter,_ATP-binding_protein_167412..167562_POSITIVE 298 199 170 81 50 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 298 98 53 94 41 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE 295 60 12 151 104 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 294 45 12 126 87 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 292 118 71 83 32 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 288 82 43 45 2 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 284 97 61 151 111 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 279 108 61 67 16 NC_002967:TDE0040|3end_AMP-binding_protein_45776..45926_NEGATIVE 275 85 49 132 100 NC_002967:TDE2088|3end_C4_zinc_finger_domain_protein,_DksA/TraR_family_2116183..2116333_POSITIVE 275 90 45 147 100 NC_002967:TDE0136|3end_hypothetical_protein_156723..156873_POSITIVE 274 108 68 129 95 NC_002967:TDE1964|3end_Na/Pi_cotransporter_family_protein_1977131..1977281_NEGATIVE 274 107 63 151 114 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 272 82 41 129 82 NC_002967:TDE1889|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_1909500..1909650_NEGATIVE 271 82 55 136 107 NC_002967:TDE0941|3end_NLP/P60_family_protein_963623..963773_NEGATIVE 270 88 41 147 102 NC_002967:TDE2329|3end_hypothetical_protein_2366347..2366497_NEGATIVE