Origin IGS: cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccgtcacggatggcggcagttccacgctcgcaagttttagcctgcggctaaaacttgaagattaaaaatgtacaagaatgtacattcataaacggacacggatgtccgtggttccaaacttccaagagttttagacgcaagtctaaaactctaagattaaaaatgtactcagg Mask Tandem Repeat Region ================================================ cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Find is-nt database================================================ Query_seq: TDE2133:TDE2134|TDE2133:TDE2134:cobalt transport protein, putative:hypothetical protein:<-->:2164414..2164586 173 cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2133:TDE2134|TDE2133:TDE2134:cobalt transport protein, putative:hypothetical protein:<-->:2164414..2164586 173 cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2133:TDE2134|TDE2133:TDE2134:cobalt transport protein, putative:hypothetical protein:<-->:2164414..2164586 173 cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 10 End: 123 ......... M F N L R V L D L R L K L L E V W N H G H P C P F M N V H S C T F L I F K F .................................................. Protein_Len: 39 Strand: - Start: 3 End: 119 .. S Y M K L R L T K S K R R F S K S T Q F W P C G H G N I F T C E Q V N K I K M ...................................................... cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg 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================================================ cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 79 HP_score: -9.0 Tail_Score: -3.9534 Start: 66 End: 81 Full_Region: GGAAGTTTGGAACCA CGGACA TCCG TGTCCG TTTATGAATGTACAT .................................................................CGGACATCCGTGTCCG............................................................................................ TransTerm Strand: + Conf: 79 HP_score: -6.2 Tail_Score: -4.87626 Start: 90 End: 105 Full_Region: GTGTCCGTTTATGAA TGTACA TTCT TGTACA TTTTTAATCTTCAAG .........................................................................................TGTACATTCTTGTACA.................................................................... Find igs database================================================ Query_seq: TDE2133:TDE2134|TDE2133:TDE2134:cobalt transport protein, putative:hypothetical protein:<-->:2164414..2164586 173 cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_002967_TDE2133_TDE2134|cobalt transport protein, putative:hypothetical protein|NEGATIVE:POSITIVE|[2164414,2164586]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg cctgagtacatttttaatcttagagttttagacttgcgtctaaaactcttggaagtttggaaccacggacatccgtgtccgtttatgaatgtacattcttgtacatttttaatcttcaagttttagccgcaggctaaaacttgcgagcgtggaactgccgccatccgtgacgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUGAGUACAUUUUUAAUCUUAGAGUUUUAGACUUGCGUCUAAAACUCUUGGAAGUUUGGAACCACGGACAUCCGUGUCCGUUUAUGAAUGUACAUUCUUGUACAUUUUUAAUCUUCAAGUUUUAGCCGCAGGCUAAAACUUGCGAGCGUGGAACUGCCGCCAUCCGUGACGG .................(((.((((((((((((....)))))))))))).))).(((((((...(((((((....)))))))(((.(((((((((....))))))))).))).(((((((((((((((...)))))))))))).))).((((.....))))..)))).))).. (-61.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGUCACGGAUGGCGGCAGUUCCACGCUCGCAAGUUUUAGCCUGCGGCUAAAACUUGAAGAUUAAAAAUGUACAAGAAUGUACAUUCAUAAACGGACACGGAUGUCCGUGGUUCCAAACUUCCAAGAGUUUUAGACGCAAGUCUAAAACUCUAAGAUUAAAAAUGUACUCAGG ((((((....)))))).....((.......((((((((((((...))))))))))))......................(((((((..(((..((((((((....)))))..))).........((((((((((((....))))))))))))....)))..)))))))...)) (-60.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 966 80 31 171 122 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 769 66 21 139 94 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 696 60 11 231 183 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 503 44 1 231 189 NC_002967:TDE2339|5end_leucyl-tRNA_synthetase_2374845..2375075_POSITIVE 501 160 114 228 182 NC_002967:TDE2489|5end_peptide_chain_release_factor_1_2512476..2512706_NEGATIVE 399 68 21 231 189 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 397 167 128 182 142 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 371 81 42 182 150 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 370 169 129 217 175 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 365 166 127 194 155 NC_002967:TDE2623|5end_hypothetical_protein_2664324..2664554_NEGATIVE 358 170 125 68 13 NC_002967:TDE2047|5end_hypothetical_protein_2076351..2076581_NEGATIVE 351 158 112 177 125 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 349 160 112 54 2 NC_002967:TDE1246|5end_lipoprotein,_putative_1279039..1279269_POSITIVE 349 170 125 65 6 NC_002967:TDE0571|5end_hypothetical_protein_601135..601365_POSITIVE 349 170 124 77 21 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 342 68 22 187 122 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 340 166 124 49 2 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 339 69 22 165 99 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 330 163 125 74 36 NC_002967:TDE0087|5end_Trk_system_potassium_uptake_protein_TrkA_103939..104169_POSITIVE 328 159 113 187 140 NC_002967:TDE1689|5end_ABC_transporter,_ATP-binding_protein_1746565..1746795_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 79 31 69 21 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 774 66 21 137 92 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 651 98 52 65 21 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 442 130 90 86 45 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 416 120 73 128 79 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 397 167 128 50 10 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 362 89 42 61 18 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 353 69 22 72 24 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 351 158 112 66 14 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 324 54 12 59 10 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 317 167 123 134 74 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 314 167 126 78 32 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE 312 153 118 62 23 NC_002967:TDE2642|3end_hypothetical_protein_2682111..2682261_NEGATIVE 310 170 127 66 23 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 306 168 126 64 18 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 306 149 104 126 78 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 304 170 148 133 109 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 303 168 126 149 96 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 303 167 126 83 36 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 301 170 126 115 75 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE