Origin IGS: gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc .........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.........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 gacatgcggatgtacctgaatgctgctaaagaatacatgtcttctttaacggcttgtcaggcttgcttgtactctaaggagaagattagttgatgggctgctggtctgcagtctctttcttcataatctcgcctccttaaagatatcaataatttgttcaaataaaaaagccacactcgcagcttgccatttgaacacctgtgaaatcagaattttttccaactggaaatactttctgattcgacattcatttgttcagcaaaaaaagacccttcaaacaagttcaaagcacaccaaaaagcgattctaataacaaaacatcctatgtagtcagttttgaaaaaatctttcttagtgttcttcaagccatagcccgaaaagtcataatattaccgatagtcataaatgtctaagctgtcacacaaaatctttcaaaataccaatcccatagcttcgtagattgtttttctgtattttggcactatctcttaagcagtctaagtctcagtaaagagtagaaagtcagttcttaaagatagaatgaagccgacaggcctcatacccaactgaaaagtaaaaatattaaattatagatttattataccattttatattcccttgtcaagaatttttgggcagaattgcaaggctttgatttgtatgggaaaaagttaataaattcctttgcatttgaggaatttatggtataatagggctagaaagaagcagaagcccgcaggcttttttatttaggaaaggatgaactc Mask Tandem Repeat Region ================================================ gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Find is-nt database================================================ Query_seq: SSA_2205:SSA_2207|SSA_2205:SSA_2207:Transcription antitermination factor NusG, putative:hypothetical protein:<-<-:2206191..2206957 767 gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2205:SSA_2207|SSA_2205:SSA_2207:Transcription antitermination factor NusG, putative:hypothetical protein:<-<-:2206191..2206957 767 gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2205:SSA_2207|SSA_2205:SSA_2207:Transcription antitermination factor NusG, putative:hypothetical protein:<-<-:2206191..2206957 767 gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 65 End: 166 ................................................................ M N S S N A K E F I N F F P Y K S K P C N S A Q K F L T R E Y K M V ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 52 Strand: + Start: 403 End: 558 .................................................................................................................................................................................................................................................................................................................................................................................................................. M K N T K K D F F K T D Y I G C F V I R I A F W C A L N L F E G S F F A E Q M N V E S E S I S S W K K F ................................................................................................................................................................................................................. Protein_Len: 39 Strand: + Start: 528 End: 644 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M R K Y F Q L E K I L I S Q V F K W Q A A S V A F L F E Q I I D I F K E A R L ........................................................................................................................... Protein_Len: 41 Strand: + Start: 586 End: 708 ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M R V W L F Y L N K L L I S L R R R D Y E E R D C R P A A H Q L I F S L E Y K Q A ........................................................... Protein_Len: 60 Strand: - Start: 461 End: 670 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Q L T K K Q Q V F S H R I L F Y K W N S F I R I E C T N L H C A A L T A K K N S C I I S I K L S A L N H L F L S C V L M ................................................................................................. Protein_Len: 35 Strand: - Start: 441 End: 545 ........................................................................................................................................................................................................................................................................................................................................................................................................................................................ M P H K T I L I A K Q H A K F K N S P D K K A S C I F T S D S L I E M .............................................................................................................................................................................................................................. Protein_Len: 55 Strand: - Start: 358 End: 522 ..................................................................................................................................................................................................................................................................................................................................................................... V N I V I P L I I V K R A I A Q L V S L F I K E F S V V Y S T K N N S D S K P T S Q V Q K F P R K K S F L H M ..................................................................................................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 96 End: 188 ............................................................................................... S K G M C I L A K C N Q G F I R S L P I Y F P I I F R Y N L M ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 38 Strand: - Start: 61 End: 174 ............................................................ V M F E E F A F S N I L K K G Y L D F G Q L E A W F N K V L S Y L I T Y Y M ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc 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: 82 Start: 355 End: 384 ..................................................................................................................................................................................................................................................................................................................................................................TTAGACATTTATGACTATCGGTAATATTAT............................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 51 HP_score: -3.9 Tail_Score: -3.45433 Start: 66 End: 92 Full_Region: AGCCCTATTATACCA TAAATTCCT CAAATGCAA AGGAATTTA TTAACTTTTTCCCAT .................................................................TAAATTCCTCAAATGCAAAGGAATTTA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 47 HP_score: -4.6 Tail_Score: -2.66435 Start: 66 End: 92 Full_Region: atgggaaaaagttaa taaattcctt tgcattt gaggaattta tggtataatagggct .................................................................taaattcctttgcatttgaggaattta................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 73 HP_score: -7.7 Tail_Score: -3.76232 Start: 209 End: 226 Full_Region: CTTTTCAGTTGGGTA TGAGGCC TGTC GGCTTCA TTCTATCTTTAAGAA ................................................................................................................................................................................................................TGAGGCCTGTCGGCTTCA............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 78 HP_score: -2.3 Tail_Score: -5.63517 Start: 585 End: 598 Full_Region: GTGTTCAAATGGCAA GCTGC GAGT GTGGC TTTTTTATTTGAACA ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCTGCGAGTGTGGC......................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2205:SSA_2207|SSA_2205:SSA_2207:Transcription antitermination factor NusG, putative:hypothetical protein:<-<-:2206191..2206957 767 gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Intra-Species Hit: Count: 2 Min: 1 Max: 767 Len: 767 Subject: NC_009009_SSA_2205_SSA_2207|Transcription antitermination factor NusG, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2206191,2206957]|767 HSP 1 e-value: 0.0 bit: 1479.0 Len: 767 Query Start:1 Query End:767 Subject Strand: POSITIVE Subject Start: 1 Subject End: 767 gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtcnnnnnnngctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc gagttcatcctttcctaaataaaaaagcctgcgggcttctgcttctttctagccctattataccataaattcctcaaatgcaaaggaatttattaactttttcccatacaaatcaaagccttgcaattctgcccaaaaattcttgacaagggaatataaaatggtataataaatctataatttaatatttttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtctttttttgctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggcttttttatttgaacaaattattgatatctttaaggaggcgagattatgaagaaagagactgcagaccagcagcccatcaactaatcttctccttagagtacaagcaagcctgacaagccgttaaagaagacatgtattctttagcagcattcaggtacatccgcatgtc Subject: NC_009009_SSA_0159_SSA_0160|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[157117,158874]|1758 HSP 1 e-value: 0.0 bit: 682.0 Len: 414 Query Start:191 Query End:604 Subject Strand: POSITIVE Subject Start: 90 Subject End: 502 ..............................................................................................................................................................................................ttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctactctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctatgggattggtattttgaaagattttgtgtgacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttttcaaaactgactacataggatgttttgttattagaatcgctttttggtgtgctttgaacttgtttgaagggtcnnnnnnngctgaacaaatgaatgtcgaatcagaaagtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctgcgagtgtggctttttt................................................................................................................................................................... ..............................................................................................................................................................................................ttacttttcagttgggtatgaggcctgtcggcttcattctatctttaagaactgactttctaatctttactgagacttagactgcttaagagatagtgccaaaatacagaaaaacaatctacgaagctaagggattggtattttgaaagattttatgtaacagcttagacatttatgactatcggtaatattatgacttttcgggctatggcttgaagaacactaagaaagattttctcaaaactgactacataggatgttttgttagtagaatcggtttttggtgtgctttgaacttgtttgagaggtc-ttttttgctgaacaaatgaatgtcgaatcagaaggtatttccagttggaaaaaattctgatttcacaggtgttcaaatggcaagctacgagtgtggctttttt................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUUCAUCCUUUCCUAAAUAAAAAAGCCUGCGGGCUUCUGCUUCUUUCUAGCCCUAUUAUACCAUAAAUUCCUCAAAUGCAAAGGAAUUUAUUAACUUUUUCCCAUACAAAUCAAAGCCUUGCAAUUCUGCCCAAAAAUUCUUGACAAGGGAAUAUAAAAUGGUAUAAUAAAUCUAUAAUUUAAUAUUUUUACUUUUCAGUUGGGUAUGAGGCCUGUCGGCUUCAUUCUAUCUUUAAGAACUGACUUUCUACUCUUUACUGAGACUUAGACUGCUUAAGAGAUAGUGCCAAAAUACAGAAAAACAAUCUACGAAGCUAUGGGAUUGGUAUUUUGAAAGAUUUUGUGUGACAGCUUAGACAUUUAUGACUAUCGGUAAUAUUAUGACUUUUCGGGCUAUGGCUUGAAGAACACUAAGAAAGAUUUUUUCAAAACUGACUACAUAGGAUGUUUUGUUAUUAGAAUCGCUUUUUGGUGUGCUUUGAACUUGUUUGAAGGGUCUUUUUUUGCUGAACAAAUGAAUGUCGAAUCAGAAAGUAUUUCCAGUUGGAAAAAAUUCUGAUUUCACAGGUGUUCAAAUGGCAAGCUGCGAGUGUGGCUUUUUUAUUUGAACAAAUUAUUGAUAUCUUUAAGGAGGCGAGAUUAUGAAGAAAGAGACUGCAGACCAGCAGCCCAUCAACUAAUCUUCUCCUUAGAGUACAAGCAAGCCUGACAAGCCGUUAAAGAAGACAUGUAUUCUUUAGCAGCAUUCAGGUACAUCCGCAUGUC ...((((.((..(((((.......(((((....)))))..(((((....(((...(((((((((((((((((((.........)))))))))........(((((.................(((....))).(((......)))....))))).......))))))))))...))).................(((((..((((..((((((((....)))))))).(((((((((((..((((.((((...........)))).))))....))).))))))))..))))......))))).........)))))..)))))..)).....)))).(((..((((.((..((((.(((((((((.....(((((((......((((((((((((...((.(..(((.((((((((((.((((((..((((((...((....))...)))))).....))))))..)))))))))).)))..).)).)))))))))))).....)))))))....))))))))).((((((((....(((((....)))))...))))))))...(((.(((((((((((.((((..(....)..))))..))))))))))).....)))....((((((((((..(((((((.(..((..(.(.((((......))))))..))..))))))))))))))))))...))))..((((((...((.(((((((((........))))))))).))..))))))...)))))).))) (-214.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAUGCGGAUGUACCUGAAUGCUGCUAAAGAAUACAUGUCUUCUUUAACGGCUUGUCAGGCUUGCUUGUACUCUAAGGAGAAGAUUAGUUGAUGGGCUGCUGGUCUGCAGUCUCUUUCUUCAUAAUCUCGCCUCCUUAAAGAUAUCAAUAAUUUGUUCAAAUAAAAAAGCCACACUCGCAGCUUGCCAUUUGAACACCUGUGAAAUCAGAAUUUUUUCCAACUGGAAAUACUUUCUGAUUCGACAUUCAUUUGUUCAGCAAAAAAAGACCCUUCAAACAAGUUCAAAGCACACCAAAAAGCGAUUCUAAUAACAAAACAUCCUAUGUAGUCAGUUUUGAAAAAAUCUUUCUUAGUGUUCUUCAAGCCAUAGCCCGAAAAGUCAUAAUAUUACCGAUAGUCAUAAAUGUCUAAGCUGUCACACAAAAUCUUUCAAAAUACCAAUCCCAUAGCUUCGUAGAUUGUUUUUCUGUAUUUUGGCACUAUCUCUUAAGCAGUCUAAGUCUCAGUAAAGAGUAGAAAGUCAGUUCUUAAAGAUAGAAUGAAGCCGACAGGCCUCAUACCCAACUGAAAAGUAAAAAUAUUAAAUUAUAGAUUUAUUAUACCAUUUUAUAUUCCCUUGUCAAGAAUUUUUGGGCAGAAUUGCAAGGCUUUGAUUUGUAUGGGAAAAAGUUAAUAAAUUCCUUUGCAUUUGAGGAAUUUAUGGUAUAAUAGGGCUAGAAAGAAGCAGAAGCCCGCAGGCUUUUUUAUUUAGGAAAGGAUGAACUC .(((((.((((((..((((..((((.(((((((........))))))).))))...))))((((((((((.((.(((((((.((((((...((.(((((((......)))))))...))....))))))...))))))).))...((.......(((((((((....((((..(....)..))))...)))))))))..(((..((((((((...(((((....)))))....))))))))..)))....((((.....))))....))........))))))...))))...........................))))))))))).................((((((((((....((((......((((((...................((((((.............)))))).................(((((..(((((((...(((.((.((((..((((((.((((((((((((((.((((((..((((..(((......))).))))..)......))))))))))).((((.(((....))).)))).....(((....)))....(((.((((((...)))))).))).................))))))))........))))))..))))..)).)))....)))))))........(((((((((((.......))))))))))))))))....))))))....)))).(((((((....)))))))....))))))))))........ (-188.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 902 80 31 171 122 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 371 720 671 137 87 NC_009009:SSA_1557|5end_SRPR,_signal_recognition_particle-docking_protein,_putative_1560040..1560270_NEGATIVE 361 680 634 206 155 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 355 698 651 53 4 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 342 700 653 220 177 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 342 65 26 184 139 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 333 56 22 42 2 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 332 60 14 51 4 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 321 672 632 231 188 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 319 50 7 188 138 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 319 50 1 88 35 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 314 55 11 153 95 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 312 350 303 225 176 NC_009009:SSA_1859|5end_Penicillin-binding_protein-like_factor_A/_recombinase,_putative_1853704..1853934_POSITIVE 308 746 702 64 23 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 307 49 5 68 12 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 307 49 5 203 147 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 307 430 384 140 94 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 307 628 581 231 182 NC_009009:SSA_0788|5end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_771037..771267_POSITIVE 306 747 701 71 22 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 306 710 661 72 12 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 389 237 191 146 96 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 371 720 671 133 83 NC_009009:SSA_1558|3end_Hydrolase,_HAD_superfamily_1560044..1560194_NEGATIVE 361 680 634 63 12 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 342 65 26 138 93 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 336 240 197 70 29 NC_009009:SSA_2380|3end_hypothetical_protein_2385665..2385815_NEGATIVE 336 677 636 51 1 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 333 56 22 52 12 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 332 60 14 51 4 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 319 50 7 57 7 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 319 50 1 95 42 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 314 55 11 78 20 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 308 746 702 51 10 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 307 49 5 68 12 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 307 430 384 107 61 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 306 710 661 72 12 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 305 676 631 74 24 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 304 229 194 143 109 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 302 699 653 129 72 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 302 708 665 43 1 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 299 45 4 133 90 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE