Origin IGS: attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatcataaccgctaaattcccaatttaagaagctcaaaccgcgactttagcatcctttagtacttccccttctttgtattatcatcctttcttttagaacagttcattttgaatttaaaaaattaaaatctattgaatttatttcagctaaaagtgaaaataatctgaataaatttttggaaaaacaagggggttcttaggggcggatgcactaagcggaattttggttatcaaagcggacaggatgtccgcctgtataagctgtacgagttttttgcgtaagcaaaaacactcgaagatgaaaaatgtactttggatgtacatttttcatcggtcataggggaggctaacaaccaacgaagtttcgaggtcaagaaatcttttatccgaaaaaatgccttagccttgaagctccgccggctatacatcccctaat Mask Tandem Repeat Region ================================================ attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Find is-nt database================================================ Query_seq: TDE2265:TDE2266|TDE2265:TDE2266:hypothetical protein:reverse transcriptase family protein:-><-:2302695..2303131 437 attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2265:TDE2266|TDE2265:TDE2266:hypothetical protein:reverse transcriptase family protein:-><-:2302695..2303131 437 attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2265:TDE2266|TDE2265:TDE2266:hypothetical protein:reverse transcriptase family protein:-><-:2302695..2303131 437 attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 9 End: 203 ........ M Y S R R S F K A K A F F R I K D F L T S K L R W L L A S P M T D E K C T S K V H F S S S S V F A Y A K N S Y S L Y R R .......................................................................................................................................................................................................................................... Protein_Len: 39 Strand: + Start: 106 End: 222 ......................................................................................................... M K N V H P K Y I F H L R V F L L T Q K T R T A Y T G G H P V R F D N Q N S A ....................................................................................................................................................................................................................... Protein_Len: 58 Strand: + Start: 113 End: 286 ................................................................................................................ M Y I Q S T F F I F E C F C L R K K L V Q L I Q A D I L S A L I T K I P L S A S A P K N P L V F P K I Y S D Y F H F ....................................................................................................................................................... Protein_Len: 40 Strand: - Start: 240 End: 359 ............................................................................................................................................................................................................................................... S G G Q K E L F K N L N N E S K A S I F E I S K L K K F E F H V T R F S L I I M .............................................................................. Protein_Len: 37 Strand: - Start: 158 End: 268 ............................................................................................................................................................. A F F E Y L K Y L R V D Q G S Q Y G F N R K T C G G R L V G K N K W F N M ......................................................................................................................................................................... Protein_Len: 55 Strand: - Start: 100 End: 264 ................................................................................................... S R H F I Y M W L V N K M K S H K Q K R L F S T C S I C A S M R D A K I V L I G S L A D A G L F G R T K G F M ............................................................................................................................................................................. Protein_Len: 41 Strand: - Start: 5 End: 124 .... * P I Y L R R L K L A L A N K R I F S K K V E F S R Q N N A E G I V S S F H V D M ......................................................................................................................................................................................................................................................................................................................... attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa 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: 81 Start: 352 End: 381 ...............................................................................................................................................................................................................................................................................................................................................................TTTAGTACTTCCCCTTCTTTGTATTATCAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 56 HP_score: -4.7 Tail_Score: -3.54158 Start: 21 End: 79 Full_Region: GGGATGTATAGCCGG CGGAGCTTCAAGGCTAAGGCATTTTTT CGGAT AAAAGATTTCTTGACCTCGAAACTTCG TTGGTTGTTAGCCTC ....................CGGAGCTTCAAGGCTAAGGCATTTTTTCGGATAAAAGATTTCTTGACCTCGAAACTTCG...................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 83 HP_score: -11.4 Tail_Score: -3.12892 Start: 107 End: 137 Full_Region: CTCCCCTATGACCGA TGAAAAATGTACAT CCA AAGTACATTTTTCA TCTTCGAGTGTTTTT ..........................................................................................................TGAAAAATGTACATCCAAAGTACATTTTTCA............................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 71 HP_score: -3.7 Tail_Score: -4.87626 Start: 114 End: 130 Full_Region: ATGACCGATGAAAAA TGTACAT CCA AAGTACA TTTTTCATCTTCGAG .................................................................................................................TGTACATCCAAAGTACA................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 90 HP_score: -12.3 Tail_Score: -3.72695 Start: 185 End: 201 Full_Region: GTACAGCTTATACAG GCGGACA TCC TGTCCGC TTTGATAACCAAAAT ........................................................................................................................................................................................GCGGACATCCTGTCCGC............................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE2265:TDE2266|TDE2265:TDE2266:hypothetical protein:reverse transcriptase family protein:-><-:2302695..2303131 437 attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaaaatttattcagattattttcacttttagctgaaataaattcaatagattttaattttttaaattcaaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Intra-Species Hit: Count: 1 Min: 1 Max: 437 Len: 437 Subject: NC_002967_TDE2265_TDE2266|hypothetical protein:reverse transcriptase family protein|POSITIVE:NEGATIVE|[2302695,2303131]|437 HSP 1 e-value: 1.0E-145 bit: 517.0 Len: 261 Query Start:1 Query End:261 Subject Strand: POSITIVE Subject Start: 1 Subject End: 261 attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaa................................................................................................................................................................................ attaggggatgtatagccggcggagcttcaaggctaaggcattttttcggataaaagatttcttgacctcgaaacttcgttggttgttagcctcccctatgaccgatgaaaaatgtacatccaaagtacatttttcatcttcgagtgtttttgcttacgcaaaaaactcgtacagcttatacaggcggacatcctgtccgctttgataaccaaaattccgcttagtgcatccgcccctaagaacccccttgtttttccaaa................................................................................................................................................................................ HSP 2 e-value: 3.0E-56 bit: 220.0 Len: 111 Query Start:327 Query End:437 Subject Strand: POSITIVE Subject Start: 327 Subject End: 437 ......................................................................................................................................................................................................................................................................................................................................aaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa ......................................................................................................................................................................................................................................................................................................................................aaaatgaactgttctaaaagaaaggatgataatacaaagaaggggaagtactaaaggatgctaaagtcgcggtttgagcttcttaaattgggaatttagcggttatgataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAGGGGAUGUAUAGCCGGCGGAGCUUCAAGGCUAAGGCAUUUUUUCGGAUAAAAGAUUUCUUGACCUCGAAACUUCGUUGGUUGUUAGCCUCCCCUAUGACCGAUGAAAAAUGUACAUCCAAAGUACAUUUUUCAUCUUCGAGUGUUUUUGCUUACGCAAAAAACUCGUACAGCUUAUACAGGCGGACAUCCUGUCCGCUUUGAUAACCAAAAUUCCGCUUAGUGCAUCCGCCCCUAAGAACCCCCUUGUUUUUCCAAAAAUUUAUUCAGAUUAUUUUCACUUUUAGCUGAAAUAAAUUCAAUAGAUUUUAAUUUUUUAAAUUCAAAAUGAACUGUUCUAAAAGAAAGGAUGAUAAUACAAAGAAGGGGAAGUACUAAAGGAUGCUAAAGUCGCGGUUUGAGCUUCUUAAAUUGGGAAUUUAGCGGUUAUGAUAA ..(((((((.(((((((((((((((.(((.(((.(((((.(((((((.....))))))).))))).))).))).)))))))))))))..)).))))))).....((((((((((((((.......))))))))))))))..(((((.(((((((....))))))))))))............((((((((.....))))))))..((((((.....(((..(((((((.....(((((((((((......))))))................((((((((..(((((((.((((.....))))...((.(((((....))))).)).............)))))))..))))))))..........)))))..))))))).))).((((((.((.(((((((((...))))))))).)).))))))))))))..... (-139.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCAUAACCGCUAAAUUCCCAAUUUAAGAAGCUCAAACCGCGACUUUAGCAUCCUUUAGUACUUCCCCUUCUUUGUAUUAUCAUCCUUUCUUUUAGAACAGUUCAUUUUGAAUUUAAAAAAUUAAAAUCUAUUGAAUUUAUUUCAGCUAAAAGUGAAAAUAAUCUGAAUAAAUUUUUGGAAAAACAAGGGGGUUCUUAGGGGCGGAUGCACUAAGCGGAAUUUUGGUUAUCAAAGCGGACAGGAUGUCCGCCUGUAUAAGCUGUACGAGUUUUUUGCGUAAGCAAAAACACUCGAAGAUGAAAAAUGUACUUUGGAUGUACAUUUUUCAUCGGUCAUAGGGGAGGCUAACAACCAACGAAGUUUCGAGGUCAAGAAAUCUUUUAUCCGAAAAAAUGCCUUAGCCUUGAAGCUCCGCCGGCUAUACAUCCCCUAAU .....(((((((..((((((((.....(((..((.......))..)))..(((((((((.......(((((...((((.((.(((....((..((((((....((((((((((.(((((....))))).))..(((((.....)))))...)))))))).....))))))..))....))).)).))))))))).......))).)))))).....).))))))))))))))....((((((.....))))))..............((((((((((((....))))))).)))))..((((((((((((((.......)))))))))))))).....(((((((.........((..((.((((((((((..(((..((.((((.....)))).))..)))..)))))))))).))..)).......))))))).. (-126.63) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 627 49 1 98 45 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 563 146 101 171 127 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 532 104 66 181 143 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 519 34 2 168 135 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 496 188 141 48 2 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 491 146 103 177 134 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 484 146 103 213 171 NC_002967:TDE2339|5end_leucyl-tRNA_synthetase_2374845..2375075_POSITIVE 457 146 102 229 185 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 436 78 31 192 143 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 431 57 15 58 1 NC_002967:TDE2107|5end_dihydroorotase,_putative_2132874..2133104_NEGATIVE 411 146 103 197 155 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 395 260 220 203 165 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 394 50 9 88 45 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 384 103 67 51 8 NC_002967:TDE2310|5end_hypothetical_protein_2348042..2348272_POSITIVE 384 95 57 226 179 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 381 70 21 189 134 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 373 118 75 199 147 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 370 146 104 117 75 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 360 50 4 212 165 NC_002967:TDE0884|5end_tRNA_(guanine-N(1)-)-methyltransferase_902221..902451_POSITIVE 354 200 153 65 15 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 576 50 3 68 16 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 548 38 5 151 119 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 542 160 111 142 95 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 444 100 54 77 31 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 419 228 183 54 10 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 418 200 151 53 7 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 416 39 11 83 53 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 394 146 103 97 55 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 381 70 21 135 80 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 358 255 219 36 1 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 350 227 184 82 27 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 342 49 2 136 91 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 341 160 114 86 45 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 333 200 153 76 28 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 333 99 67 88 58 NC_002967:TDE2135|3end_hypothetical_protein_2165418..2165568_POSITIVE 328 258 215 53 4 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 328 145 105 95 54 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 325 260 217 84 41 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 324 200 152 61 14 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 319 105 67 49 10 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE