Origin IGS: gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atattttctcctaaaaaatgatatgctgtttataaaggaaaaatccattaattctgaataaggtcttcaccgtacagtaaaccggtcattccccgctcggggaaggggggcttccctgtacggggaatgaacccttcccttagcggggaaaatgcctttcctaaaacttc Mask Tandem Repeat Region ================================================ gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Find is-nt database================================================ Query_seq: TDE0944:TDE0945|TDE0944:TDE0945:hypothetical protein:hypothetical protein:->->:967098..967267 170 gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0944:TDE0945|TDE0944:TDE0945:hypothetical protein:hypothetical protein:->->:967098..967267 170 gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0944:TDE0945|TDE0944:TDE0945:hypothetical protein:hypothetical protein:->->:967098..967267 170 gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 3 End: 113 .. T K P F A N E G S L S P N M G R V P F G G K G S R P I V P K S Y P S S R M ......................................................... gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -11.2 Tail_Score: -3.83998 Start: 37 End: 89 Full_Region: TCCCCGCTAAGGGAA GGGTTCATTCCCCGTACAGGGAAG CCCCC CTTCCCCGAGCGGGGAATGACCGG TTTACTGTACGGTGA ....................................GGGTTCATTCCCCGTACAGGGAAGCCCCCCTTCCCCGAGCGGGGAATGACCGG................................................................................. TransTerm Strand: - Conf: 91 HP_score: -14.5 Tail_Score: -3.17075 Start: 37 End: 88 Full_Region: caccgtacagtaaac cggtcattccccgctcggggaag ggggg cttccctgtacggggaatgaaccc ttcccttagcgggga ....................................cggtcattccccgctcggggaaggggggcttccctgtacggggaatgaaccc.................................................................................. TransTerm Strand: + Conf: 90 HP_score: -14.7 Tail_Score: -2.90078 Start: 38 End: 88 Full_Region: CCCCGCTAAGGGAAG GGTTCATTCCCCGTACAGGGAAG CCCCC CTTCCCCGAGCGGGGAATGACCG GTTTACTGTACGGTG .....................................GGTTCATTCCCCGTACAGGGAAGCCCCCCTTCCCCGAGCGGGGAATGACCG.................................................................................. Find igs database================================================ Query_seq: TDE0944:TDE0945|TDE0944:TDE0945:hypothetical protein:hypothetical protein:->->:967098..967267 170 gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_002967_TDE0944_TDE0945|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[967098,967267]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat gaagttttaggaaaggcattttccccgctaagggaagggttcattccccgtacagggaagccccccttccccgagcggggaatgaccggtttactgtacggtgaagaccttattcagaattaatggatttttcctttataaacagcatatcattttttaggagaaaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUUUUAGGAAAGGCAUUUUCCCCGCUAAGGGAAGGGUUCAUUCCCCGUACAGGGAAGCCCCCCUUCCCCGAGCGGGGAAUGACCGGUUUACUGUACGGUGAAGACCUUAUUCAGAAUUAAUGGAUUUUUCCUUUAUAAACAGCAUAUCAUUUUUUAGGAGAAAAUAU ..((((((..(.(((((...(((((((((..((((((((....(((((......)))))....))))))))..)))))))))..((((..........))))...).)))).)..))))))......((((((((.......................)))))))).... (-59.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUUUCUCCUAAAAAAUGAUAUGCUGUUUAUAAAGGAAAAAUCCAUUAAUUCUGAAUAAGGUCUUCACCGUACAGUAAACCGGUCAUUCCCCGCUCGGGGAAGGGGGGCUUCCCUGUACGGGGAAUGAACCCUUCCCUUAGCGGGGAAAAUGCCUUUCCUAAAACUUC .......................((((((.......(((....)))...............(((....)))..))))))....(((..(((((((((.(((((((((...(((((((....)))))).)..))))))))).)))))))))...))).............. (-59.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 459 72 32 80 35 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 425 79 31 79 29 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 417 80 34 57 11 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 417 72 32 59 14 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 417 72 32 181 136 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 415 89 47 146 110 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 406 73 32 231 182 NC_002967:TDE2042|5end_hypothetical_protein_2072179..2072409_NEGATIVE 396 80 31 200 123 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 383 68 24 42 1 NC_002967:TDE0522|5end_hypothetical_protein_568499..568729_POSITIVE 382 76 32 156 110 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 374 79 35 173 127 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 369 93 54 176 122 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 365 76 32 220 152 NC_002967:TDE0979|5end_penicillin_binding_protein_1003946..1004176_NEGATIVE 361 72 31 67 6 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 359 87 48 46 5 NC_002967:TDE1337|5end_hypothetical_protein_1374806..1375036_NEGATIVE 357 79 33 164 125 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 355 103 71 95 54 NC_002967:TDE2493|5end_hypothetical_protein_2518364..2518594_NEGATIVE 352 70 23 184 123 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 351 68 21 125 83 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 347 89 48 114 58 NC_002967:TDE0974|5end_hypothetical_protein_998694..998924_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 602 80 32 68 20 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 425 79 31 66 16 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 423 78 31 132 75 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 417 80 34 52 6 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 394 89 47 54 1 NC_002967:TDE0562|3end_hypothetical_protein_595581..595731_POSITIVE 393 110 62 92 39 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 381 98 62 57 5 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 374 79 35 86 40 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 356 80 31 68 13 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 356 80 36 143 85 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 338 118 73 77 28 NC_002967:TDE0062|3end_PTS_system,_IIA_component_69661..69811_POSITIVE 334 80 31 55 1 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 329 90 49 59 6 NC_002967:TDE1386|3end_methyl-accepting_chemotaxis_protein_1426856..1427006_POSITIVE 323 81 46 77 45 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 322 58 14 118 69 NC_002967:TDE1947|3end_ABC_transporter,_permease_protein_1962517..1962667_NEGATIVE 321 76 31 52 6 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 320 80 31 69 18 NC_002967:TDE2119|3end_glycine_reductase_complex_selenoprotein_GrdB2_2151398..2151548_NEGATIVE 318 70 27 56 10 NC_002967:TDE0796|3end_histidinol_phosphate_phosphatase_HisJ_family_protein_820946..821096_POSITIVE 317 80 31 70 17 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 317 82 41 142 91 NC_002967:TDE1042|3end_deoxyuridine_5'triphosphate_nucleotidohydrolase_1071006..1071156_POSITIVE