Origin IGS: acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaccgtagacacacaaaggggagatggggtacaattcgtcactccatcatcccctgcgaattgtgcgttacatttaaaaagcatttctaaaaatcctacaagttttttatagcgctcaaatagcgt Mask Tandem Repeat Region ================================================ acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Find is-nt database================================================ Query_seq: TDE2169:TDE2170|TDE2169:TDE2170:hypothetical protein:hypothetical protein:-><-:2201570..2201695 126 acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2169:TDE2170|TDE2169:TDE2170:hypothetical protein:hypothetical protein:-><-:2201570..2201695 126 acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2169:TDE2170|TDE2169:TDE2170:hypothetical protein:hypothetical protein:-><-:2201570..2201695 126 acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Predict ORF larger than 30AA ================================================ acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt 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================================================ acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -7.4 Tail_Score: -4.17296 Start: 73 End: 109 Full_Region: AACGCACAATTCGCA GGGGATGATGGAGTGACG AAT TGTACCCCATCTCCCC TTTGTGTGTCTACGG ........................................................................GGGGATGATGGAGTGACGAATTGTACCCCATCTCCCC................. Find igs database================================================ Query_seq: TDE2169:TDE2170|TDE2169:TDE2170:hypothetical protein:hypothetical protein:-><-:2201570..2201695 126 acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002967_TDE2169_TDE2170|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2201570,2201695]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt acgctatttgagcgctataaaaaacttgtaggatttttagaaatgctttttaaatgtaacgcacaattcgcaggggatgatggagtgacgaattgtaccccatctcccctttgtgtgtctacggtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUAUUUGAGCGCUAUAAAAAACUUGUAGGAUUUUUAGAAAUGCUUUUUAAAUGUAACGCACAAUUCGCAGGGGAUGAUGGAGUGACGAAUUGUACCCCAUCUCCCCUUUGUGUGUCUACGGUU .((((.....))))((((((.....))))))....(((((((.....))))))).(((((((((((.....((((((.(((((.(((........))).))))))))))))))))))).))).... (-37.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCGUAGACACACAAAGGGGAGAUGGGGUACAAUUCGUCACUCCAUCAUCCCCUGCGAAUUGUGCGUUACAUUUAAAAAGCAUUUCUAAAAAUCCUACAAGUUUUUUAUAGCGCUCAAAUAGCGU ....((.(((.(((((((((((((((((((((.....)).)))))))).)))))).....))))).)))))...((((((((...................))))))))..(((((.....))))) (-37.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 519 108 61 231 177 NC_002967:TDE2177|5end_hypothetical_protein_2206524..2206754_NEGATIVE 352 119 71 111 52 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 325 106 61 187 143 NC_002967:TDE1192|5end_hypothetical_protein_1219332..1219562_POSITIVE 322 110 61 73 9 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 285 118 74 70 17 NC_002967:TDE2236|5end_methylaspartate_mutase,_E_subunit_2276117..2276347_NEGATIVE 285 113 81 231 190 NC_002967:TDE0075|5end_sorbitol_dehydrogenase,_putative_86573..86803_NEGATIVE 281 108 61 189 128 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 265 106 67 94 50 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 264 104 65 195 147 NC_002967:TDE1026|5end_acyl_carrier_protein_1057302..1057532_POSITIVE 264 110 63 54 6 NC_002967:TDE0703|5end_transcriptional_regulator,_AbrB_family_738190..738420_NEGATIVE 262 90 41 56 4 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 261 119 74 169 115 NC_002967:TDE2630|5end_peptide_ABC_transporter,_permease_protein,_putative_2670879..2671109_POSITIVE 259 114 72 219 155 NC_002967:TDE1018|5end_hypothetical_protein_1049227..1049457_POSITIVE 258 119 72 187 134 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 258 77 34 67 27 NC_002967:TDE0759|5end_hypothetical_protein_799499..799729_NEGATIVE 257 119 96 89 67 NC_002967:TDE0612|5end_hypothetical_protein_647471..647701_NEGATIVE 257 119 96 171 149 NC_002967:TDE0611|5end_hypothetical_protein_647389..647619_NEGATIVE 255 109 67 68 23 NC_002967:TDE2240|5end_hypothetical_protein_2278422..2278652_NEGATIVE 255 103 67 226 184 NC_002967:TDE0756|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_796859..797089_NEGATIVE 253 87 43 169 129 NC_002967:TDE2681|5end_hypothetical_protein_2721407..2721637_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 648 118 72 82 36 NC_002967:TDE2178|3end_hypothetical_protein_2206683..2206833_NEGATIVE 309 114 81 147 109 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 301 119 79 92 53 NC_002967:TDE0578|3end_hypothetical_protein_609677..609827_POSITIVE 280 110 61 65 15 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 278 111 72 85 40 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 265 106 67 100 56 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 261 52 12 93 52 NC_002967:TDE2206|3end_hypothetical_protein_2244921..2245071_NEGATIVE 259 114 72 123 59 NC_002967:TDE1017|3end_exodeoxyribonuclease_VII,_large_subunit_1049211..1049361_POSITIVE 254 100 61 151 105 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 254 110 66 114 41 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 250 118 73 55 15 NC_002967:TDE0114|3end_iron-dependent_transcriptional_regulator_133581..133731_NEGATIVE 249 108 69 43 12 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 243 108 61 51 7 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 242 114 72 90 38 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 242 120 72 42 4 NC_002967:TDE0437|3end_PBS_lyase_HEAT-like_repeat_domain_protein_492136..492286_NEGATIVE 241 112 74 90 53 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 235 110 61 83 21 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 235 119 96 43 16 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 227 46 3 48 4 NC_002967:TDE1072|3end_lipoprotein,_putative_1103436..1103586_POSITIVE 225 120 71 68 28 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE