Origin IGS: tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc .........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 gccgtaaaacggttgatatttgtgtggaaacatgctaatactataccgtaatgaaagacaaataccccgacagcagttacaatcattctcacagtacaccacgcgcacaagagcgaatcccgtccttcgtgcgcttttttacattaccccgtttaataaaaccgcaacgctcgcagagcgttgagctccgctcaacttcgcagaggattattaaggatgtccttacaaagattccattaaaaccgccacggatggcggtggttaagaccgctcggcagttaaattaaaaa Mask Tandem Repeat Region ================================================ tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Find is-nt database================================================ Query_seq: TDE2516:TDE2517|TDE2516:TDE2517:hypothetical protein:DNA repair protein RadA:-><-:2542254..2542543 290 tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2516:TDE2517|TDE2516:TDE2517:hypothetical protein:DNA repair protein RadA:-><-:2542254..2542543 290 tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2516:TDE2517|TDE2516:TDE2517:hypothetical protein:DNA repair protein RadA:-><-:2542254..2542543 290 tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 38 End: 199 ..................................... M R G G F N G I F V R T S L I I L C E V E R S S T L C E R C G F I K R G N V K K R T K D G I R S C A R G V L ........................................................................................... Protein_Len: 36 Strand: + Start: 181 End: 288 .................................................................................................................................................................................... M C A W C T V R M I V T A V G V F V F H Y G I V L A C F H T N I N R F T .. Protein_Len: 36 Strand: + Start: 183 End: 290 ...................................................................................................................................................................................... M R V V Y C E N D C N C C R G I C L S L R Y S I S M F P H K Y Q P F Y G Protein_Len: 54 Strand: - Start: 110 End: 271 ............................................................................................................. R E A L T A T K N F P T I Y F L A R L V P N A R T R T T Y Q S F S Q L Q Q R P I Q R E N R Y L I L M N G C M ................... Protein_Len: 60 Strand: - Start: 7 End: 240 ...... K T L V D K I I R Q S T S R L E V S Q S R Q P K I L R P L T F F R V F S P I R E Q A R P T S H S H N Y S S D P Y K D K M .................................................. tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc 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================================================ tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -10.4 Tail_Score: -2.71144 Start: 33 End: 48 Full_Region: aagattccattaaaa ccgcca cgga tggcgg tggttaagaccgctc ................................ccgccacggatggcgg.................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 84 HP_score: -8.5 Tail_Score: -4.63218 Start: 105 End: 129 Full_Region: GCGAAGTTGAGCGGA GCTCAACGCTC TGC GAGCGTTGCGG TTTTATTAAACGGGG ........................................................................................................GCTCAACGCTCTGCGAGCGTTGCGG................................................................................................................................................................. TransTerm Strand: + Conf: 82 HP_score: -12.0 Tail_Score: -3.3761 Start: 106 End: 128 Full_Region: CGAAGTTGAGCGGAG CTCAACGCTC TGC GAGCGTTGCG GTTTTATTAAACGGG .........................................................................................................CTCAACGCTCTGCGAGCGTTGCG.................................................................................................................................................................. TransTerm Strand: - Conf: 87 HP_score: -7.3 Tail_Score: -5.15969 Start: 157 End: 188 Full_Region: ctcacagtacaccac gcgcacaagagcg aatcc cgtccttcgtgcgc ttttttacattaccc ............................................................................................................................................................gcgcacaagagcgaatcccgtccttcgtgcgc...................................................................................................... Find igs database================================================ Query_seq: TDE2516:TDE2517|TDE2516:TDE2517:hypothetical protein:DNA repair protein RadA:-><-:2542254..2542543 290 tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Intra-Species Hit: Count: 2 Min: 1 Max: 290 Len: 290 Subject: NC_002967_TDE2516_TDE2517|hypothetical protein:DNA repair protein RadA|POSITIVE:NEGATIVE|[2542254,2542543]|290 HSP 1 e-value: 1.0E-163 bit: 575.0 Len: 290 Query Start:1 Query End:290 Subject Strand: POSITIVE Subject Start: 1 Subject End: 290 tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc tttttaatttaactgccgagcggtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaacgctctgcgagcgttgcggttttattaaacggggtaatgtaaaaaagcgcacgaaggacgggattcgctcttgtgcgcgtggtgtactgtgagaatgattgtaactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaaccgttttacggc Subject: NC_002967_TDE1055_TDE1056|MATE efflux family protein:hypothetical protein|NEGATIVE:POSITIVE|[1084422,1085349]|928 HSP 1 e-value: 8.0E-22 bit: 105.0 Len: 89 Query Start:23 Query End:111 Subject Strand: NEGATIVE Subject Start: 229 Subject End: 317 ......................gtcttaaccaccgccatccgtggcggttttaatggaatctttgtaaggacatccttaataatcctctgcgaagttgagcggagctcaac................................................................................................................................................................................... ......................gtcttaaccaccgccatccgtggcggttttaagggagtctttgtaatgacatccttaataagcctctggtaaattgagcaaagctcaac................................................................................................................................................................................... HSP 2 e-value: 3.0E-12 bit: 73.8 Len: 69 Query Start:212 Query End:280 Subject Strand: NEGATIVE Subject Start: 140 Subject End: 207 ...................................................................................................................................................................................................................taactgctgtcggggtatttgtctttcattacggtatagtattagcatgtttccacacaaatatcaacc.......... ...................................................................................................................................................................................................................taactgctgtcggtgtgtttgtctatcattacggtacagtgtaa-catgtttccacacaaatatcaacc.......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAAUUUAACUGCCGAGCGGUCUUAACCACCGCCAUCCGUGGCGGUUUUAAUGGAAUCUUUGUAAGGACAUCCUUAAUAAUCCUCUGCGAAGUUGAGCGGAGCUCAACGCUCUGCGAGCGUUGCGGUUUUAUUAAACGGGGUAAUGUAAAAAAGCGCACGAAGGACGGGAUUCGCUCUUGUGCGCGUGGUGUACUGUGAGAAUGAUUGUAACUGCUGUCGGGGUAUUUGUCUUUCAUUACGGUAUAGUAUUAGCAUGUUUCCACACAAAUAUCAACCGUUUUACGGC ..............((((((((((.......(((((((....)))))))((((((((((((....(((((....)))))......((((((........))))))..((((((((...)))))))).))))))))))))..(((..((((......((((((((..(.((.....)))..)))))))).((.(((((((((((((.(((....(((.(....).)))....))).))).)))))))))).))...))))...)))............))))))...)))) (-94.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGUAAAACGGUUGAUAUUUGUGUGGAAACAUGCUAAUACUAUACCGUAAUGAAAGACAAAUACCCCGACAGCAGUUACAAUCAUUCUCACAGUACACCACGCGCACAAGAGCGAAUCCCGUCCUUCGUGCGCUUUUUUACAUUACCCCGUUUAAUAAAACCGCAACGCUCGCAGAGCGUUGAGCUCCGCUCAACUUCGCAGAGGAUUAUUAAGGAUGUCCUUACAAAGAUUCCAUUAAAACCGCCACGGAUGGCGGUGGUUAAGACCGCUCGGCAGUUAAAUUAAAAA ((((....(((((...((((.(((((....))))).))))....)))))......................(((.(((..((((.(((((...(((......(((((((((..((.....))..))).)))))).....))).....................((...((((...))))(((((((...)))))))...)).)))))....(((((....)))))....))))...((((.(((((((....)))))))..))))))).))))))).............. (-78.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 110 61 205 156 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 720 130 89 111 69 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 720 130 89 111 69 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 709 126 81 231 186 NC_002967:TDE0977|5end_hypothetical_protein_1000415..1000645_POSITIVE 559 34 1 231 198 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 511 150 111 231 190 NC_002967:TDE2734|5end_hypothetical_protein_2789071..2789301_POSITIVE 499 119 89 231 200 NC_002967:TDE2315|5end_conserved_hypothetical_protein_TIGR00044_2352272..2352502_POSITIVE 441 258 211 208 162 NC_002967:TDE2313|5end_hypothetical_protein_2352010..2352240_NEGATIVE 441 129 86 215 162 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 433 57 11 225 185 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 404 130 89 173 132 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 390 119 72 119 61 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 390 250 201 102 49 NC_002967:TDE0742|5end_hypothetical_protein_778635..778865_NEGATIVE 380 129 84 195 150 NC_002967:TDE2628|5end_hypothetical_protein_2669068..2669298_POSITIVE 380 130 82 183 120 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 370 133 100 61 12 NC_002967:TDE2495|5end_hypothetical_protein_2521053..2521283_NEGATIVE 370 132 92 166 125 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 368 129 87 187 132 NC_002967:TDE1613|5end_hypothetical_protein_1661625..1661855_POSITIVE 366 49 11 218 164 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 362 78 31 81 31 NC_002967:TDE1397|5end_flagellar_synthesis_regulator_FleN,_putative_1436014..1436244_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 110 61 150 101 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 720 130 89 49 7 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 720 130 89 59 17 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 620 130 82 83 35 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 461 67 22 58 15 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 459 128 88 139 95 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 435 150 101 51 1 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 408 66 27 67 27 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 382 130 81 91 30 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 381 60 22 81 49 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 371 129 84 67 10 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 370 59 15 87 52 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 362 78 31 114 64 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 357 200 156 76 26 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 355 130 88 149 97 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 353 53 12 67 22 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 349 146 106 49 14 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 348 129 85 112 68 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 348 129 85 112 68 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 347 58 12 97 32 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE