Origin IGS: tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc .........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 gaatatacaatctcctttcgtaagacatcggtctgatcagatagtctaacaactatctaggacctcaggtggagcagagaagaaggtcgcaaacaaatattttacttccttatcctaaactccattttttaactcgagtatttcataatgttattataaataatttttaaagcgctttcaatattgtttgaaatttagattttagtttccgaattttccagaaaaacaggaattcctgaaagtactttcaggaattcgttttgtaggaaagccatttaaggagcaagcaaacttctaaaaagattctcatttctatgctccctcaggcaagtaaaaagggctagacaaaggcctagccccaaagggggacgaata Mask Tandem Repeat Region ================================================ tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Find is-nt database================================================ Query_seq: SSA_0070:SSA_0071|SSA_0070:SSA_0071:Acetylxylan esterase, putative:N-acetylmannosamine-6-p hosphate 2-epimerase 1, putative:->->:74975..75349 375 tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0070:SSA_0071|SSA_0070:SSA_0071:Acetylxylan esterase, putative:N-acetylmannosamine-6-p hosphate 2-epimerase 1, putative:->->:74975..75349 375 tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0070:SSA_0071|SSA_0070:SSA_0071:Acetylxylan esterase, putative:N-acetylmannosamine-6-p hosphate 2-epimerase 1, putative:->->:74975..75349 375 tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 2 End: 97 . M R P P L G L G L C L A L F T C L R E H R N E N L F R S L L A P ...................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: - Start: 209 End: 307 ................................................................................................................................................................................................................ F N N I I V N H F V R T L F H L K P Y P L L I N T Q S R R R Q E M .................................................................... tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 194 End: 223 .................................................................................................................................................................................................ATTGAAAGCGCTTTAAAAATTATTTATAAT........................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 219 End: 248 ..........................................................................................................................................................................................................................TTTAACTCGAGTATTTCATAATGTTATTAT............................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -8.3 Tail_Score: -4.84017 Start: 116 End: 149 Full_Region: ATGGCTTTCCTACAA AACGAATTCCTGAAA GTAC TTTCAGGAATTCCTG TTTTTCTGGAAAATT ...................................................................................................................AACGAATTCCTGAAAGTACTTTCAGGAATTCCTG.................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 89 HP_score: -10.9 Tail_Score: -4.03995 Start: 118 End: 147 Full_Region: GGCTTTCCTACAAAA CGAATTCCTGAAA GTAC TTTCAGGAATTCC TGTTTTTCTGGAAAA .....................................................................................................................CGAATTCCTGAAAGTACTTTCAGGAATTCC.................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 95 HP_score: -10.9 Tail_Score: -4.36914 Start: 118 End: 147 Full_Region: ttttccagaaaaaca ggaattcctgaaa gtac tttcaggaattcg ttttgtaggaaagcc .....................................................................................................................ggaattcctgaaagtactttcaggaattcg.................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -14.4 Tail_Score: -3.01915 Start: 119 End: 146 Full_Region: GCTTTCCTACAAAAC GAATTCCTGAAA GTAC TTTCAGGAATTC CTGTTTTTCTGGAAA ......................................................................................................................GAATTCCTGAAAGTACTTTCAGGAATTC..................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.4 Tail_Score: -3.21934 Start: 119 End: 146 Full_Region: tttccagaaaaacag gaattcctgaaa gtac tttcaggaattc gttttgtaggaaagc ......................................................................................................................gaattcctgaaagtactttcaggaattc..................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 52 HP_score: -2.8 Tail_Score: -3.97356 Start: 183 End: 200 Full_Region: taatttttaaagcgc tttcaa tattgt ttgaaa tttagattttagttt ......................................................................................................................................................................................tttcaatattgtttgaaa............................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0070:SSA_0071|SSA_0070:SSA_0071:Acetylxylan esterase, putative:N-acetylmannosamine-6-p hosphate 2-epimerase 1, putative:->->:74975..75349 375 tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc Intra-Species Hit: Count: 1 Min: 1 Max: 375 Len: 375 Subject: NC_009009_SSA_0070_SSA_0071|Acetylxylan esterase, putative:N-acetylmannosamine-6-p hosphate 2-epimerase 1, putative|POSITIVE:POSITIVE|[74975,75349]|375 HSP 1 e-value: 0.0 bit: 743.0 Len: 375 Query Start:1 Query End:375 Subject Strand: POSITIVE Subject Start: 1 Subject End: 375 tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc tattcgtccccctttggggctaggcctttgtctagccctttttacttgcctgagggagcatagaaatgagaatctttttagaagtttgcttgctccttaaatggctttcctacaaaacgaattcctgaaagtactttcaggaattcctgtttttctggaaaattcggaaactaaaatctaaatttcaaacaatattgaaagcgctttaaaaattatttataataacattatgaaatactcgagttaaaaaatggagtttaggataaggaagtaaaatatttgtttgcgaccttcttctctgctccacctgaggtcctagatagttgttagactatctgatcagaccgatgtcttacgaaaggagattgtatattc HSP 2 e-value: 9.0E-7 bit: 56.0 Len: 28 Query Start:119 Query End:146 Subject Strand: NEGATIVE Subject Start: 119 Subject End: 146 ......................................................................................................................gaattcctgaaagtactttcaggaattc..................................................................................................................................................................................................................................... ......................................................................................................................gaattcctgaaagtactttcaggaattc..................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCGUCCCCCUUUGGGGCUAGGCCUUUGUCUAGCCCUUUUUACUUGCCUGAGGGAGCAUAGAAAUGAGAAUCUUUUUAGAAGUUUGCUUGCUCCUUAAAUGGCUUUCCUACAAAACGAAUUCCUGAAAGUACUUUCAGGAAUUCCUGUUUUUCUGGAAAAUUCGGAAACUAAAAUCUAAAUUUCAAACAAUAUUGAAAGCGCUUUAAAAAUUAUUUAUAAUAACAUUAUGAAAUACUCGAGUUAAAAAAUGGAGUUUAGGAUAAGGAAGUAAAAUAUUUGUUUGCGACCUUCUUCUCUGCUCCACCUGAGGUCCUAGAUAGUUGUUAGACUAUCUGAUCAGACCGAUGUCUUACGAAAGGAGAUUGUAUAUUC ...............((((((((((....))))))))))........(((..((((((((..(((.(((((....)))))....)))...))))))))....)))..(((...(((((((((((((((((....))))))))))))..)))))...))).(((((((...............((((((......))))))...............((((((((...))))))))....)))))))......((((((..((((.((((..(((((.......)))))..)))).))))..)))))).....((((.(((((((((....)))))))))....))))...(((((.(....))))))......... (-105.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUAUACAAUCUCCUUUCGUAAGACAUCGGUCUGAUCAGAUAGUCUAACAACUAUCUAGGACCUCAGGUGGAGCAGAGAAGAAGGUCGCAAACAAAUAUUUUACUUCCUUAUCCUAAACUCCAUUUUUUAACUCGAGUAUUUCAUAAUGUUAUUAUAAAUAAUUUUUAAAGCGCUUUCAAUAUUGUUUGAAAUUUAGAUUUUAGUUUCCGAAUUUUCCAGAAAAACAGGAAUUCCUGAAAGUACUUUCAGGAAUUCGUUUUGUAGGAAAGCCAUUUAAGGAGCAAGCAAACUUCUAAAAAGAUUCUCAUUUCUAUGCUCCCUCAGGCAAGUAAAAAGGGCUAGACAAAGGCCUAGCCCCAAAGGGGGACGAAUA ..........((((((((.((........(((((....(((((((......))))))).)))))...((.((((((.((((((..(((.(((((((......................((((.............))))......(((.(((((.....)))))..)))..............)))))))...((((((..((.((((.(....(((((...(((((..((((((((((((....)))))))))))))))))...))))).((......)).).)))).))..))))))..)))..))..)))).)))))).))..)).........(((((((........)))))))..))))))))...... (-92.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 54 12 193 145 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 394 50 10 141 99 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 378 60 13 202 141 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 362 129 84 51 7 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 353 60 16 163 121 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 338 50 2 199 141 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 334 48 1 168 93 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 334 59 16 186 132 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 333 59 15 56 7 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 328 50 10 70 17 NC_009009:SSA_2182|5end_hypothetical_protein_2181020..2181250_NEGATIVE 323 338 291 154 101 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 321 49 4 184 124 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 321 59 11 147 98 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 318 39 1 227 185 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 317 55 11 48 2 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 311 331 293 59 24 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 310 59 16 159 122 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 310 90 43 173 125 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 309 60 11 195 143 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 308 50 5 49 3 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 350 301 113 62 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 355 59 11 66 8 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 344 368 326 147 105 NC_009009:SSA_1428|3end_hypothetical_protein_1435638..1435788_NEGATIVE 342 46 3 74 18 NC_009009:SSA_1047|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1062845..1062995_POSITIVE 321 49 4 106 46 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 321 59 11 150 101 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 313 299 252 86 49 NC_009009:SSA_0903|3end_NAD(P)H_dehydrogenase_(quinone),_putative_893813..893963_POSITIVE 309 60 11 140 88 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 307 51 11 151 116 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 303 50 1 151 92 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 303 58 11 131 82 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 299 59 12 123 68 NC_009009:SSA_2088|3end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2092766..2092916_NEGATIVE 297 330 281 94 29 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 296 81 44 59 13 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 292 32 1 70 32 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 291 43 5 147 96 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 290 56 16 146 87 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 288 56 12 76 30 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 288 50 4 100 35 NC_009009:SSA_0248|3end_hypothetical_protein_241844..241994_POSITIVE 287 320 274 115 64 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE