Origin IGS: tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat .........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 atcggctcctaatttacaatcagggaagtataaaagaaaatcggtaaaaattcaagtagttcgctgaaaatcggacatccgtgtccgattttcagcttagagtttgtggcaagcgcaaactcttgaagttggaaccacggacatccatgtccgctattaatgtacatccgtgtacgattttcagtggggtaaga Mask Tandem Repeat Region ================================================ tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Find is-nt database================================================ Query_seq: TDE1611:TDE1612|TDE1611:TDE1612:hypothetical protein:phosphoribosyl transferase domain protein:->->:1660495..1660688 194 tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1611:TDE1612|TDE1611:TDE1612:hypothetical protein:phosphoribosyl transferase domain protein:->->:1660495..1660688 194 tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1611:TDE1612|TDE1611:TDE1612:hypothetical protein:phosphoribosyl transferase domain protein:->->:1660495..1660688 194 tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 11 End: 100 .......... M K I V H G C T L I A D M D V R G S N F K S L R L P Q T L S .............................................................................................. Protein_Len: 52 Strand: + Start: 28 End: 183 ........................... M Y I N S G H G C P W F Q L Q E F A L A T N S K L K I G H G C P I F S E L L E F L P I F F Y T S L I V N ........... Protein_Len: 38 Strand: - Start: 1 End: 114 R V G S F I T C P H V N I A S M S T R P E L K L L K R K G C V R L Q F D S M ................................................................................ tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat 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: 87 Start: 139 End: 168 ..........................................................................................................................................CTTGAATTTTTACCGATTTTCTTTTATACT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -11.7 Tail_Score: -2.86773 Start: 95 End: 136 Full_Region: CGCTTGCCACAAACT CTAAGCTGAAAATCGGACA CGGA TGTCCGATTTTCAGCGAAC TACTTGAATTTTTAC ..............................................................................................CTAAGCTGAAAATCGGACACGGATGTCCGATTTTCAGCGAAC.......................................................... TransTerm Strand: - Conf: 88 HP_score: -9.9 Tail_Score: -4.19506 Start: 107 End: 124 Full_Region: gtagttcgctgaaaa tcggaca tccg tgtccga ttttcagcttagagt ..........................................................................................................tcggacatccgtgtccga...................................................................... Find igs database================================================ Query_seq: TDE1611:TDE1612|TDE1611:TDE1612:hypothetical protein:phosphoribosyl transferase domain protein:->->:1660495..1660688 194 tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_002967_TDE1611_TDE1612|hypothetical protein:phosphoribosyl transferase domain protein|POSITIVE:POSITIVE|[1660495,1660688]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat tcttaccccactgaaaatcgtacacggatgtacattaatagcggacatggatgtccgtggttccaacttcaagagtttgcgcttgccacaaactctaagctgaaaatcggacacggatgtccgattttcagcgaactacttgaatttttaccgattttcttttatacttccctgattgtaaattaggagccgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUACCCCACUGAAAAUCGUACACGGAUGUACAUUAAUAGCGGACAUGGAUGUCCGUGGUUCCAACUUCAAGAGUUUGCGCUUGCCACAAACUCUAAGCUGAAAAUCGGACACGGAUGUCCGAUUUUCAGCGAACUACUUGAAUUUUUACCGAUUUUCUUUUAUACUUCCCUGAUUGUAAAUUAGGAGCCGAU ............((((((((..(((((((((.(((...........))).)))))))))........((((((((((((.(.....).))))))))..(((((((((((((((....)))))))))))))))........)))).......))))))))...........((((((.....))))))....... (-59.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGGCUCCUAAUUUACAAUCAGGGAAGUAUAAAAGAAAAUCGGUAAAAAUUCAAGUAGUUCGCUGAAAAUCGGACAUCCGUGUCCGAUUUUCAGCUUAGAGUUUGUGGCAAGCGCAAACUCUUGAAGUUGGAACCACGGACAUCCAUGUCCGCUAUUAAUGUACAUCCGUGUACGAUUUUCAGUGGGGUAAGA ....(((((...........((.(((.(((((..........(((..((.((((........(((((((((((((((....)))))))))))))))..((((((((((.....)))))))))))))).))...))).((((((....)))))).......))))).))).)).............))))).... (-66.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 679 70 21 213 162 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 594 86 42 48 1 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 502 70 22 180 132 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 494 82 42 112 68 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 469 76 42 231 195 NC_002967:TDE1891|5end_hypothetical_protein_1911206..1911436_POSITIVE 437 138 91 55 5 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 415 90 41 156 103 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 407 59 12 109 60 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 406 82 41 188 145 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 402 78 35 158 114 NC_002967:TDE2312|5end_hypothetical_protein_2348451..2348681_POSITIVE 372 85 41 54 3 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 369 128 97 34 3 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 368 86 42 65 22 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 354 86 41 224 182 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 339 97 52 65 19 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 326 130 81 202 151 NC_002967:TDE1383|5end_hypothetical_protein_1422301..1422531_POSITIVE 326 87 41 65 18 NC_002967:TDE0977|5end_hypothetical_protein_1000415..1000645_POSITIVE 320 81 42 202 159 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 320 142 101 178 134 NC_002967:TDE0803|5end_hypothetical_protein_825317..825547_POSITIVE 318 80 39 64 29 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 544 70 21 90 41 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 506 128 83 62 11 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 471 130 81 57 10 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 457 128 83 62 11 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 402 78 35 64 20 NC_002967:TDE2311|3end_hypothetical_protein_2348437..2348587_POSITIVE 370 99 57 53 6 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 368 86 42 83 40 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 348 99 51 54 1 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 348 56 11 102 56 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 331 57 12 99 56 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 326 87 41 68 21 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 321 130 81 124 63 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 320 117 78 42 4 NC_002967:TDE2142|3end_methyl-accepting_chemotaxis_protein_2177987..2178137_POSITIVE 307 133 93 41 1 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 291 50 3 102 62 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 286 58 11 74 28 NC_002967:TDE0471|3end_BNR_domain_protein_526657..526807_NEGATIVE 283 89 41 65 12 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 281 123 81 49 5 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 281 65 25 80 30 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 279 90 41 128 67 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE