Origin IGS: gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt .........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 aaaacagtactcctaataagtgatgacactgttacggcttcacttataagtatagagcagccctgcttatttgtcaaggaagatttatagtattttctttacataaatttacaattttatttatttttaataaccgtagcgaacgccaagcattgagctaacgctcaacttcgcaaagggaaaagattattaagaaaaaccgtaggtttgtcttaatgacaatccatacctctaaatcaggggagatttttaagaggggagctaaaaaatgttcccctcttaaatggcgttttgaaaagatgaggggttataggggagaagaaaaacttttgctccatcaaaagtttgtcttttccc Mask Tandem Repeat Region ================================================ gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Find is-nt database================================================ Query_seq: TDE0715:TDE0716|TDE0715:TDE0716:hypothetical protein:CAAX amino terminal protease family protein:->->:750611..750967 357 gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0715:TDE0716|TDE0715:TDE0716:hypothetical protein:CAAX amino terminal protease family protein:->->:750611..750967 357 gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0715:TDE0716|TDE0715:TDE0716:hypothetical protein:CAAX amino terminal protease family protein:->->:750611..750967 357 gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 17 End: 118 ................ M M E Q K F F F S P I T P H L F K T P F K R G T F F S S P L K N L P ............................................................................................................................................................................................................................................... Protein_Len: 47 Strand: + Start: 57 End: 197 ........................................................ M F S K R H L R G E H F L A P L L K I S P D L E V W I V I K T N L R F F L I I F S L C E V E R ................................................................................................................................................................ Protein_Len: 32 Strand: - Start: 200 End: 295 ....................................................................................................................................................................................................... S L A Q R E S R N N F I F L I T F K H L S F V I F R G Q C I L M .............................................................. Protein_Len: 57 Strand: - Start: 2 End: 172 . S F V F K Q H L L L K E E G R Y G R M K E F R W K L P S C K K A G R K F I E G S K S T H I T M L V F R R N K K I M ......................................................................................................................................................................................... gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt 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: 89 Start: 280 End: 309 .......................................................................................................................................................................................................................................................................................CTTGACAAATAAGCAGGGCTGCTCTATACT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 57 HP_score: -3.3 Tail_Score: -4.08767 Start: 69 End: 114 Full_Region: cctctaaatcagggg agatttttaagaggggagc taaaaaat gttcccctcttaaatggcg ttttgaaaagatgag ....................................................................agatttttaagaggggagctaaaaaatgttcccctcttaaatggcg................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 67 HP_score: -8.3 Tail_Score: -3.09681 Start: 79 End: 104 Full_Region: aggggagatttttaa gaggggagc taaaaaat gttcccctc ttaaatggcgttttg ..............................................................................gaggggagctaaaaaatgttcccctc............................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 72 HP_score: -7.9 Tail_Score: -3.78026 Start: 139 End: 171 Full_Region: TAGAGGTATGGATTG TCATTAAGACAAACC TAC GGTTTTTCTTAATAA TCTTTTCCCTTTGCG ..........................................................................................................................................TCATTAAGACAAACCTACGGTTTTTCTTAATAA.......................................................................................................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -9.6 Tail_Score: -2.96755 Start: 142 End: 168 Full_Region: AGGTATGGATTGTCA TTAAGACAAACC TAC GGTTTTTCTTAA TAATCTTTTCCCTTT .............................................................................................................................................TTAAGACAAACCTACGGTTTTTCTTAA............................................................................................................................................................................................. TransTerm Strand: + Conf: 48 HP_score: -2.6 Tail_Score: -3.63694 Start: 179 End: 224 Full_Region: CTTAATAATCTTTTC CCTTTGCGAAGTTGAGCGTT AGCTC AATGCTTGGCGTTCGCTACGG TTATTAAAAATAAAT ..................................................................................................................................................................................CCTTTGCGAAGTTGAGCGTTAGCTCAATGCTTGGCGTTCGCTACGG..................................................................................................................................... Find igs database================================================ Query_seq: TDE0715:TDE0716|TDE0715:TDE0716:hypothetical protein:CAAX amino terminal protease family protein:->->:750611..750967 357 gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttattaaaaataaataaaattgtaaatttatgtaaagaaaatactataaatcttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Intra-Species Hit: Count: 5 Min: 1 Max: 357 Len: 357 Subject: NC_002967_TDE0715_TDE0716|hypothetical protein:CAAX amino terminal protease family protein|POSITIVE:POSITIVE|[750611,750967]|357 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttat................................................................................................................................. gggaaaagacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgaagttgagcgttagctcaatgcttggcgttcgctacggttat................................................................................................................................. HSP 2 e-value: 5.0E-39 bit: 163.0 Len: 82 Query Start:276 Query End:357 Subject Strand: POSITIVE Subject Start: 276 Subject End: 357 ...................................................................................................................................................................................................................................................................................cttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt ...................................................................................................................................................................................................................................................................................cttccttgacaaataagcagggctgctctatacttataagtgaagccgtaacagtgtcatcacttattaggagtactgtttt Subject: NC_002967_TDE0722_TDE0723|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[759925,760443]|519 HSP 1 e-value: 4.0E-92 bit: 339.0 Len: 179 Query Start:8 Query End:186 Subject Strand: POSITIVE Subject Start: 8 Subject End: 186 .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcg........................................................................................................................................................................... .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaacattttttagctcccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcg........................................................................................................................................................................... Subject: NC_002967_TDE0724_TDE0725|hypothetical protein:exopolysaccharide biosynthesis protein|POSITIVE:POSITIVE|[763298,763604]|307 HSP 1 e-value: 3.0E-74 bit: 280.0 Len: 171 Query Start:8 Query End:178 Subject Strand: POSITIVE Subject Start: 8 Subject End: 180 .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaaga-ggggaacattttttag-ctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttc................................................................................................................................................................................... .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttc................................................................................................................................................................................... Subject: NC_002967_TDE0723_TDE0724|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[761722,761992]|271 HSP 1 e-value: 4.0E-64 bit: 246.0 Len: 162 Query Start:21 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 ....................tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg-aacattttttagct-cccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctt............................................................................................................................................................................... ....................tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagtta-aggtgtggattatcattaagacaaacctacggtttttcttaataatcttttccctt............................................................................................................................................................................... Subject: NC_002967_TDE0969_TDE0970|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[994636,994908]|273 HSP 1 e-value: 3.0E-40 bit: 167.0 Len: 100 Query Start:86 Query End:185 Subject Strand: POSITIVE Subject Start: 170 Subject End: 269 .....................................................................................acattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgc............................................................................................................................................................................ .....................................................................................acattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgc............................................................................................................................................................................ HSP 2 e-value: 5.0E-36 bit: 153.0 Len: 77 Query Start:8 Query End:84 Subject Strand: POSITIVE Subject Start: 8 Subject End: 84 .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg................................................................................................................................................................................................................................................................................. .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAAAGACAAACUUUUGAUGGAGCAAAAGUUUUUCUUCUCCCCUAUAACCCCUCAUCUUUUCAAAACGCCAUUUAAGAGGGGAACAUUUUUUAGCUCCCCUCUUAAAAAUCUCCCCUGAUUUAGAGGUAUGGAUUGUCAUUAAGACAAACCUACGGUUUUUCUUAAUAAUCUUUUCCCUUUGCGAAGUUGAGCGUUAGCUCAAUGCUUGGCGUUCGCUACGGUUAUUAAAAAUAAAUAAAAUUGUAAAUUUAUGUAAAGAAAAUACUAUAAAUCUUCCUUGACAAAUAAGCAGGGCUGCUCUAUACUUAUAAGUGAAGCCGUAACAGUGUCAUCACUUAUUAGGAGUACUGUUUU ((((.((((.(((((((((......))))))))).)))).))))....................(((((....((((((((((((.(........).))))))))))))......(((((.((((...((..(((.....(((((((.(((((...))))).)))))))..(((((..((...(((((((..((((((.....))))))..)).)))))...)).........((((((..........))))))..)))))...............)))...))...))))))))).((((((......((((((((.(((......).))..))))))))..))))))..))))) (-96.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACAGUACUCCUAAUAAGUGAUGACACUGUUACGGCUUCACUUAUAAGUAUAGAGCAGCCCUGCUUAUUUGUCAAGGAAGAUUUAUAGUAUUUUCUUUACAUAAAUUUACAAUUUUAUUUAUUUUUAAUAACCGUAGCGAACGCCAAGCAUUGAGCUAACGCUCAACUUCGCAAAGGGAAAAGAUUAUUAAGAAAAACCGUAGGUUUGUCUUAAUGACAAUCCAUACCUCUAAAUCAGGGGAGAUUUUUAAGAGGGGAGCUAAAAAAUGUUCCCCUCUUAAAUGGCGUUUUGAAAAGAUGAGGGGUUAUAGGGGAGAAGAAAAACUUUUGCUCCAUCAAAAGUUUGUCUUUUCCC ........((((((....((((....))))(((((((........(((((((..(((((....)))))...(((.(((((((((.......))))))))))))..............))))))).........))))))).((((((..((.((((((....))))))....))....(((...(.(((((((((.(((((...))))).))))))))))..)))...(((((.....))))).....((((((((((((((........)))))))))))))).))))))...........)))))).....(((((((((.(((((((((......))))))))).))))))))) (-113.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 737 227 181 113 67 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 737 227 181 113 67 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 590 218 179 228 190 NC_002967:TDE0977|5end_hypothetical_protein_1000415..1000645_POSITIVE 584 219 179 217 180 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 544 214 180 231 197 NC_002967:TDE2315|5end_conserved_hypothetical_protein_TIGR00044_2352272..2352502_POSITIVE 436 71 34 213 170 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 430 227 181 175 130 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 404 220 172 209 166 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 393 79 34 226 179 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 387 220 173 53 1 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 381 83 41 200 160 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 368 210 163 72 20 NC_002967:TDE0598|5end_3-oxoacyl-(acyl-carrier-protein)_reductase_638101..638331_NEGATIVE 367 73 31 180 137 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 359 85 41 118 76 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 359 85 41 97 55 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 359 85 41 219 177 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 358 84 41 208 169 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 356 249 202 53 1 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 346 135 100 149 120 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 341 224 190 115 81 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 737 227 181 51 5 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 737 227 181 61 15 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 663 227 181 85 39 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 476 205 162 150 114 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 404 220 172 47 4 NC_002967:TDE1827|3end_hydrolase,_carbon-nitrogen_family_1859943..1860093_NEGATIVE 402 47 1 93 47 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 402 47 1 93 47 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 402 47 1 93 47 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 380 47 1 113 67 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 363 50 1 143 94 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 349 230 186 50 2 NC_002967:TDE0829|3end_putative_aminopeptidase_2_850185..850335_NEGATIVE 346 135 100 62 33 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 335 46 1 51 7 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 333 47 1 93 47 NC_002967:TDE0715|3end_hypothetical_protein_750550..750700_POSITIVE 319 226 182 111 60 NC_002967:TDE1385|3end_hypothetical_protein_1424793..1424943_NEGATIVE 318 84 41 68 29 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 315 64 24 108 69 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 310 224 193 78 46 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 306 209 170 90 43 NC_002967:TDE2785|3end_hypothetical_protein_2838601..2838751_NEGATIVE 305 219 172 134 89 NC_002967:TDE0781|3end_30S_ribosomal_protein_S8_813039..813189_POSITIVE