Origin IGS: cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag .........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 ctccttataatcttagattagaaaaaatcttttttcccgattagttacaatatacaatattctaaaatatagggcaagacggaaaatcgatttattcgtgcagagggtttaatactctgttgccgtgcaacgtacgataaaaattttttataacttattttcaaaattttcattgacttttttttcgattgcttgtattatgagactggacagtagtcatttttttaaggagcataccg Mask Tandem Repeat Region ================================================ cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag Find is-nt database================================================ Query_seq: TDE0237:TDE0238|TDE0237:TDE0238:HDIG domain protein:thioredoxin, selenocysteine-containing:<-->:271281..271519 239 cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0237:TDE0238|TDE0237:TDE0238:HDIG domain protein:thioredoxin, selenocysteine-containing:<-->:271281..271519 239 cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0237:TDE0238|TDE0237:TDE0238:HDIG domain protein:thioredoxin, selenocysteine-containing:<-->:271281..271519 239 cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 67 End: 192 .................................................................. M K I L K I S Y K K F L S Y V A R Q Q S I K P S A R I N R F S V L P Y I L E Y C I L ............................................... Protein_Len: 31 Strand: - Start: 131 End: 223 .................................................................................................................................. V R Q V F L D I K R R A R Y K L I N Y I T V L R S F L N K R M ................ Protein_Len: 38 Strand: - Start: 2 End: 115 . T H E K F F H S S D L R M I C A I S F F T L S F K S F L N Y F I K I T R Q M ............................................................................................................................ cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag 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: 88 Start: 39 End: 68 ......................................ATTGACTTTTTTTTCGATTGCTTGTATTAT........................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 162 End: 191 .................................................................................................................................................................CTTGCCCTATATTTTAGAATATTGTATATT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0237:TDE0238|TDE0237:TDE0238:HDIG domain protein:thioredoxin, selenocysteine-containing:<-->:271281..271519 239 cggtatgctccttaaaaaaatgactactgtccagtctcataatacaagcaatcgaaaaaaaagtcaatgaaaattttgaaaataagttataaaaaatttttatcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag Intra-Species Hit: Count: 1 Min: 21 Max: 239 Len: 219 Subject: NC_002967_TDE0237_TDE0238|HDIG domain protein:thioredoxin, selenocysteine-containing|NEGATIVE:POSITIVE|[271281, 271519]|239 HSP 1 e-value: 1.0E-72 bit: 274.0 Len: 138 Query Start:102 Query End:239 Subject Strand: POSITIVE Subject Start: 102 Subject End: 239 .....................................................................................................atcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag .....................................................................................................atcgtacgttgcacggcaacagagtattaaaccctctgcacgaataaatcgattttccgtcttgccctatattttagaatattgtatattgtaactaatcgggaaaaaagattttttctaatctaagattataaggag HSP 2 e-value: 1.0E-10 bit: 67.9 Len: 34 Query Start:21 Query End:54 Subject Strand: POSITIVE Subject Start: 21 Subject End: 54 ....................tgactactgtccagtctcataatacaagcaatcg......................................................................................................................................................................................... ....................tgactactgtccagtctcataatacaagcaatcg......................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACUACUGUCCAGUCUCAUAAUACAAGCAAUCGAAAAAAAAGUCAAUGAAAAUUUUGAAAAUAAGUUAUAAAAAAUUUUUAUCGUACGUUGCACGGCAACAGAGUAUUAAACCCUCUGCACGAAUAAAUCGAUUUUCCGUCUUGCCCUAUAUUUUAGAAUAUUGUAUAUUGUAACUAAUCGGGAAAAAAGAUUUUUUCUAAUCUAAGAUUAUAAGGAG .((((.......))))...((((((..(((((..........(((.(((((((((((...............))))))))))).).)))))))..(....)...))))))....((((....(((.(((((..(((((((..((((..(((((..((...))..)))))..)))).....)))))))...))))).)))(((((...)))))...)))) (-33.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUUAUAAUCUUAGAUUAGAAAAAAUCUUUUUUCCCGAUUAGUUACAAUAUACAAUAUUCUAAAAUAUAGGGCAAGACGGAAAAUCGAUUUAUUCGUGCAGAGGGUUUAAUACUCUGUUGCCGUGCAACGUACGAUAAAAAUUUUUUAUAACUUAUUUUCAAAAUUUUCAUUGACUUUUUUUUCGAUUGCUUGUAUUAUGAGACUGGACAGUAGUCA ...((((((((.(((((...((((((....)))))).......((........)).....)))))......((((((..(((((((..(((((..((((((..(((((.....)))))(((((...)))))))))))...)))))...............((((........))))....))))))).))))))..))))))))....(((....))). (-37.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 841 120 71 231 182 NC_002967:TDE0237|5end_HDIG_domain_protein_271190..271420_NEGATIVE 392 129 81 205 152 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 369 150 105 205 153 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 352 149 105 202 162 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 350 129 86 205 162 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 337 123 84 116 66 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 336 156 113 189 144 NC_002967:TDE2708|5end_hypothetical_protein_2761498..2761728_NEGATIVE 282 155 111 218 166 NC_002967:TDE1311|5end_ABC_transporter,_ATP-binding/permease_protein_1347371..1347601_POSITIVE 276 147 102 105 62 NC_002967:TDE1011|5end_hypothetical_protein_1038101..1038331_POSITIVE 275 152 113 80 35 NC_002967:TDE0614|5end_precorrin-4_C11-methyltransferase_647987..648217_POSITIVE 271 140 95 183 130 NC_002967:TDE1086|5end_conserved_hypothetical_protein_TIGR00255_1117786..1118016_POSITIVE 266 128 81 72 26 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 265 137 112 41 16 NC_002967:TDE1005|5end_hypothetical_protein_1030206..1030436_POSITIVE 263 123 83 201 160 NC_002967:TDE1343|5end_trypsin_domain/PDZ_domain_protein_1380546..1380776_POSITIVE 261 124 81 200 152 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 257 146 110 70 33 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 255 148 105 199 152 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 254 137 91 221 169 NC_002967:TDE0631|5end_sigma_factor_regulatory_protein,_putative_665295..665525_POSITIVE 254 101 78 64 35 NC_002967:TDE0610|5end_3-hydroxyacyl-CoA_dehydrogenase,_putative_647286..647516_NEGATIVE 250 158 114 225 167 NC_002967:TDE2004|5end_hypothetical_protein_2023622..2023852_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 654 129 84 71 26 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 479 130 83 113 66 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 466 129 83 65 19 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 464 129 81 147 95 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 436 148 105 50 18 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 430 129 86 89 47 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 418 128 84 57 21 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 410 130 83 57 9 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 392 129 81 135 82 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 352 149 105 65 25 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 350 129 86 135 92 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 337 123 84 77 27 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 282 155 111 107 55 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 276 147 102 95 52 NC_002967:TDE1010|3end_excinuclease_ABC,_A_subunit_1038171..1038321_POSITIVE 273 120 77 147 96 NC_002967:TDE2708|3end_hypothetical_protein_2755136..2755286_NEGATIVE 273 120 80 40 1 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 263 123 83 136 95 NC_002967:TDE1342|3end_hypothetical_protein_1380561..1380711_POSITIVE 254 101 78 71 42 NC_002967:TDE0611|3end_hypothetical_protein_647279..647429_NEGATIVE 241 151 114 147 108 NC_002967:TDE2041|3end_lipoprotein_releasing_system,_permease_protein,_putative_2070214..2070364_NEGATIVE 241 147 101 124 85 NC_002967:TDE0183|3end_ABC_transporter,_permease_protein_216783..216933_NEGATIVE