Origin IGS: acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaatctcctcttttagggttattatgttttttggattgaattgtctcaatccttaagacatccgctgaaaaatgtacatccttgtacatttttcagcttagagttttagacttgcgtctaaaactcttggaagt Mask Tandem Repeat Region ================================================ acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Find is-nt database================================================ Query_seq: TDE2548:TDE2549|TDE2548:TDE2549:hypothetical protein:methyl-accepting chemotaxis protein:<-->:2573289..2573424 136 acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2548:TDE2549|TDE2548:TDE2549:hypothetical protein:methyl-accepting chemotaxis protein:<-->:2573289..2573424 136 acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2548:TDE2549|TDE2548:TDE2549:hypothetical protein:methyl-accepting chemotaxis protein:<-->:2573289..2573424 136 acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 46 End: 132 ............................................. M Y K D V H F S A D V L R I E T I Q S K K H N N P K R G D * .... Protein_Len: 31 Strand: - Start: 3 End: 95 .. E L L K L R L D L V R L Q F I Y L S T C K E A S T K L I S V M ......................................... acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa 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================================================ acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 87 HP_score: -12.4 Tail_Score: -3.08867 Start: 35 End: 74 Full_Region: GCAAGTCTAAAACTC TAAGCTGAAAAATGTACA AGGA TGTACATTTTTCAGCGGA TGTCTTAAGGATTGA ..................................TAAGCTGAAAAATGTACAAGGATGTACATTTTTCAGCGGA.............................................................. TransTerm Strand: + Conf: 74 HP_score: -6.2 Tail_Score: -4.57837 Start: 47 End: 62 Full_Region: CTCTAAGCTGAAAAA TGTACA AGGA TGTACA TTTTTCAGCGGATGT ..............................................TGTACAAGGATGTACA.......................................................................... TransTerm Strand: - Conf: 77 HP_score: -6.2 Tail_Score: -4.66833 Start: 47 End: 62 Full_Region: acatccgctgaaaaa tgtaca tcct tgtaca tttttcagcttagag ..............................................tgtacatccttgtaca.......................................................................... Find igs database================================================ Query_seq: TDE2548:TDE2549|TDE2548:TDE2549:hypothetical protein:methyl-accepting chemotaxis protein:<-->:2573289..2573424 136 acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_002967_TDE2548_TDE2549|hypothetical protein:methyl-accepting chemotaxis protein|NEGATIVE:POSITIVE|[2573289,2573424]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa acttccaagagttttagacgcaagtctaaaactctaagctgaaaaatgtacaaggatgtacatttttcagcggatgtcttaaggattgagacaattcaatccaaaaaacataataaccctaaaagaggagattaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCCAAGAGUUUUAGACGCAAGUCUAAAACUCUAAGCUGAAAAAUGUACAAGGAUGUACAUUUUUCAGCGGAUGUCUUAAGGAUUGAGACAAUUCAAUCCAAAAAACAUAAUAACCCUAAAAGAGGAGAUUAAA ..((((.((((((((((((....))))))))))))..(((((((((((((((....)))))))))))))))..((((.((..((((((((....))))))))..)).))))...............))))...... (-54.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUCUCCUCUUUUAGGGUUAUUAUGUUUUUUGGAUUGAAUUGUCUCAAUCCUUAAGACAUCCGCUGAAAAAUGUACAUCCUUGUACAUUUUUCAGCUUAGAGUUUUAGACUUGCGUCUAAAACUCUUGGAAGU ..((((..(((......)))..)))).(((((..(((((((......)))))))..))))).((((((((((((((((((....)))))))))))))))..((((((((((((....)))))))))))).)))... (-54.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 834 80 31 171 122 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 727 50 1 217 168 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 619 50 3 164 111 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 565 72 31 47 6 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 492 120 71 66 19 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 411 76 31 103 52 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 406 71 31 222 185 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 371 130 82 175 130 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 358 59 20 228 191 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 355 78 31 197 144 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 316 80 31 118 69 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 294 35 8 140 113 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 293 41 8 124 95 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 287 71 37 216 183 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 264 73 31 210 174 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 253 120 71 202 161 NC_002967:TDE0398|5end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_447773..448003_POSITIVE 250 69 38 204 170 NC_002967:TDE2339|5end_leucyl-tRNA_synthetase_2374845..2375075_POSITIVE 246 69 37 168 132 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 242 69 40 162 133 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 237 78 35 199 145 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 727 50 1 65 16 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 698 50 1 66 17 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 668 80 31 103 48 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 508 73 31 88 46 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 442 66 22 151 108 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 393 119 71 134 75 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 338 79 32 46 1 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 316 80 31 136 87 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 294 35 8 39 12 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 294 35 8 120 93 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 281 73 38 79 45 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 273 69 23 61 21 NC_002967:TDE0547|3end_hypothetical_protein_585971..586121_NEGATIVE 257 71 37 122 85 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 254 97 54 85 43 NC_002967:TDE0471|3end_BNR_domain_protein_526657..526807_NEGATIVE 244 55 11 67 23 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 241 56 20 42 5 NC_002967:TDE2142|3end_methyl-accepting_chemotaxis_protein_2177987..2178137_POSITIVE 236 106 64 145 101 NC_002967:TDE1846|3end_hypothetical_protein_1875169..1875319_NEGATIVE 233 96 60 101 58 NC_002967:TDE2715|3end_hypothetical_protein_2772936..2773086_POSITIVE 230 48 7 69 32 NC_002967:TDE2620|3end_hypothetical_protein_2662037..2662187_POSITIVE 227 94 56 46 3 NC_002967:TDE2244|3end_hypothetical_protein_2284320..2284470_POSITIVE