Origin IGS: gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtagtttattttgagggcagcgcgccttgattgggagataaactaaaagacagattatcagggcaaactgcagctcctatgctcataggggccgtttcttttgtaaggcggatatttttccgttagctaattatcttatttatatagaaaaggaaaaac Mask Tandem Repeat Region ================================================ gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Find is-nt database================================================ Query_seq: SSA_0770:SSA_0771|SSA_0770:SSA_0771:Ribonucleoside-diphosphate reductase, putative:Glutaredoxin-like protein, putative:<-<-:751502..751661 160 gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0770:SSA_0771|SSA_0770:SSA_0771:Ribonucleoside-diphosphate reductase, putative:Glutaredoxin-like protein, putative:<-<-:751502..751661 160 gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0770:SSA_0771|SSA_0770:SSA_0771:Ribonucleoside-diphosphate reductase, putative:Glutaredoxin-like protein, putative:<-<-:751502..751661 160 gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 47 End: 151 .............................................. M R L T K E T A P M S I G A A V C P D N L S F S L S P N Q G A L P S K ......... Protein_Len: 31 Strand: - Start: 37 End: 129 .................................... R F F I R R V F S V A G I L M P A A T Q G S L R D K L K D G M ............................... Protein_Len: 35 Strand: - Start: 2 End: 106 . K E K E I Y I L Y N A L P F I D A K C F F R G R H A Y S S C N A R I M ...................................................... gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca 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================================================ gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -7.4 Tail_Score: -4.77173 Start: 66 End: 89 Full_Region: tatcagggcaaactg cagctcctat gctc ataggggccg tttcttttgtaaggc .................................................................cagctcctatgctcataggggccg....................................................................... Find igs database================================================ Query_seq: SSA_0770:SSA_0771|SSA_0770:SSA_0771:Ribonucleoside-diphosphate reductase, putative:Glutaredoxin-like protein, putative:<-<-:751502..751661 160 gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: NC_009009_SSA_0770_SSA_0771|Ribonucleoside-diphosphate reductase, putative:Glutaredoxin-like protein, putative|NEGATIVE:NEGATIVE|[751502,751661]|160 HSP 1 e-value: 6.0E-86 bit: 317.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca gtttttccttttctatataaataagataattagctaacggaaaaatatccgccttacaaaagaaacggcccctatgagcataggagctgcagtttgccctgataatctgtcttttagtttatctcccaatcaaggcgcgctgccctcaaaataaactaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUCCUUUUCUAUAUAAAUAAGAUAAUUAGCUAACGGAAAAAUAUCCGCCUUACAAAAGAAACGGCCCCUAUGAGCAUAGGAGCUGCAGUUUGCCCUGAUAAUCUGUCUUUUAGUUUAUCUCCCAAUCAAGGCGCGCUGCCCUCAAAAUAAACUACA ((((((((((..(((...............)))..)).))))))))...((((((.((((.....((((.(((((....))))).))))...))))....(((((.(((.....))).)))))........))))))....................... (-31.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAGUUUAUUUUGAGGGCAGCGCGCCUUGAUUGGGAGAUAAACUAAAAGACAGAUUAUCAGGGCAAACUGCAGCUCCUAUGCUCAUAGGGGCCGUUUCUUUUGUAAGGCGGAUAUUUUUCCGUUAGCUAAUUAUCUUAUUUAUAUAGAAAAGGAAAAAC .(((((((.((((((.(((.....)))....((((........))))...........)))))).))))))).((((((((....))))))))..((((((((.((.((((((......))))))....(((......)))....)).)))))))).... (-39.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1020 100 51 191 142 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 374 117 74 207 153 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 334 79 31 189 149 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 333 126 86 40 5 NC_009009:SSA_0658|5end_Conserved_uncharacterized_protein_642126..642356_POSITIVE 332 108 66 74 37 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 326 103 61 69 33 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 319 100 51 143 96 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 310 150 106 53 1 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 306 99 51 78 28 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 306 128 82 67 17 NC_009009:SSA_0576|5end_Conserved_GTPase,_putative_570039..570269_POSITIVE 302 85 49 55 18 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 298 109 67 153 111 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 298 103 68 183 139 NC_009009:SSA_1324|5end_Ceramide_glucosyltransferase,_putative_1341618..1341848_NEGATIVE 297 100 51 194 140 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 296 100 53 38 2 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 296 142 107 222 185 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 293 99 52 153 98 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 293 77 32 76 16 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 292 147 101 60 8 NC_009009:SSA_1731|5end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716808..1717038_NEGATIVE 292 110 61 73 18 NC_009009:SSA_1640|5end_hypothetical_protein_1642530..1642760_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 102 61 150 111 NC_009009:SSA_1029|3end_hypothetical_protein_1046167..1046317_NEGATIVE 351 102 61 70 22 NC_009009:SSA_1397|3end_hypothetical_protein_1410995..1411145_POSITIVE 323 150 102 64 11 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 306 128 82 64 14 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 302 110 61 113 57 NC_009009:SSA_0714|3end_hypothetical_protein_700649..700799_POSITIVE 293 99 52 78 23 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 292 110 61 60 5 NC_009009:SSA_1641|3end_MutT/nudix_family_protein,_putative_1642543..1642693_NEGATIVE 292 150 106 129 76 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 290 100 51 72 18 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 287 95 51 90 50 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 286 97 52 80 29 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 283 147 107 145 99 NC_009009:SSA_0716|3end_Competence_protein,_putative_703710..703860_POSITIVE 281 126 81 82 42 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 281 96 51 67 4 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 279 145 102 150 97 NC_009009:SSA_1301|3end_Conserved_uncharacterized_protein,_possible_surface_protein_1319010..1319160_NEGATIVE 276 127 82 112 60 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 271 100 53 89 48 NC_009009:SSA_2183|3end_Glucose-6-phosphate_isomerase,_putative_2181155..2181305_NEGATIVE 271 97 51 75 28 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 270 120 77 51 3 NC_009009:SSA_1526|3end_hypothetical_protein_1534674..1534824_POSITIVE 270 108 65 107 58 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE