Origin IGS: ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat .........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 atgtgaagttagtaatattccattttatcatctgttaaactgtcgggttaaatgtatacaaaacatagagttggtagataacttttttaaagcatgatgaatataattgatatacataaaacgaaaccatccaattcaaatggatggttttctcttttttcaaaagtttttgttatactagatttatccctttaatacactgtattcagtcaatgattggtcgtaccattgagtgaaatatttcctaaacttagaattgaagtaagctctgaagtggttgaaggtattaaagtaaatggacgcttacaatttgtagttgagaatggtctgtatatcatagattagaaagaaaatagaa Mask Tandem Repeat Region ================================================ ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Find is-nt database================================================ Query_seq: SSA_1287:SSA_1288|SSA_1287:SSA_1288:hypothetical protein:hypothetical protein:<-<-:1306828..1307185 358 ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1287:SSA_1288|SSA_1287:SSA_1288:hypothetical protein:hypothetical protein:<-<-:1306828..1307185 358 ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1287:SSA_1288|SSA_1287:SSA_1288:hypothetical protein:hypothetical protein:<-<-:1306828..1307185 358 ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 21 End: 146 .................... M I Y R P F S T T N C K R P F T L I P S T T S E L T S I L S L G N I S L N G T T N H .................................................................................................................................................................................................................... Protein_Len: 37 Strand: + Start: 62 End: 172 ............................................................. M Y F N T F N H F R A Y F N S K F R K Y F T Q W Y D Q S L T E Y S V L K G .......................................................................................................................................................................................... Protein_Len: 42 Strand: + Start: 196 End: 321 ................................................................................................................................................................................................... M K K E K T I H L N W M V S F Y V Y Q L Y S S C F K K V I Y Q L Y V L Y T F N P T V ..................................... Protein_Len: 35 Strand: + Start: 224 End: 328 ............................................................................................................................................................................................................................... M G W F R F M Y I N Y I H H A L K K L S T N S M F C I H L T R Q F N R .............................. Protein_Len: 33 Strand: - Start: 167 End: 265 ...................................................................................................................................................................... L S L D L I V F V K S F L S F W G N S N S P K T K H I D I I N M M ............................................................................................. Protein_Len: 35 Strand: - Start: 126 End: 230 ............................................................................................................................. E I T R G I M S Q I C H I L P I F R T Y C F S K F F S F V M W K F Q M ................................................................................................................................ Protein_Len: 42 Strand: - Start: 17 End: 142 ................ D I I Y L G N E V V F Q L R G N V K I G E V V E S S V E I R L K P F I E S L P V V M ........................................................................................................................................................................................................................ ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat 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: 81 Start: 102 End: 131 .....................................................................................................ATTGAGTGAAATATTTCCTAAACTTAGAAT................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -4.9 Tail_Score: -5.22006 Start: 193 End: 205 Full_Region: aatggatggttttct ctttt ttc aaaag tttttgttatactag ................................................................................................................................................................................................cttttttcaaaag......................................................................................................................................................... TransTerm Strand: + Conf: 81 HP_score: -8.3 Tail_Score: -4.31065 Start: 212 End: 232 Full_Region: TGAAAAAAGAGAAAA CCATCCATT TGA ATTGGATGG TTTCGTTTTATGTAT ...................................................................................................................................................................................................................CCATCCATTTGAATTGGATGG.............................................................................................................................. TransTerm Strand: - Conf: 93 HP_score: -8.3 Tail_Score: -5.06052 Start: 212 End: 232 Full_Region: atacataaaacgaaa ccatccaat tca aatggatgg ttttctcttttttca ...................................................................................................................................................................................................................ccatccaattcaaatggatgg.............................................................................................................................. Find igs database================================================ Query_seq: SSA_1287:SSA_1288|SSA_1287:SSA_1288:hypothetical protein:hypothetical protein:<-<-:1306828..1307185 358 ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Intra-Species Hit: Count: 2 Min: 1 Max: 358 Len: 358 Subject: NC_009009_SSA_1287_SSA_1288|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1306828,1307185]|358 HSP 1 e-value: 0.0 bit: 710.0 Len: 358 Query Start:1 Query End:358 Subject Strand: POSITIVE Subject Start: 1 Subject End: 358 ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat ttctattttctttctaatctatgatatacagaccattctcaactacaaattgtaagcgtccatttactttaataccttcaaccacttcagagcttacttcaattctaagtttaggaaatatttcactcaatggtacgaccaatcattgactgaatacagtgtattaaagggataaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactctatgttttgtatacatttaacccgacagtttaacagatgataaaatggaatattactaacttcacat Subject: NC_009009_SSA_1285_SSA_1286|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1305560,1305848]|289 HSP 1 e-value: 6.0E-57 bit: 222.0 Len: 120 Query Start:174 Query End:293 Subject Strand: POSITIVE Subject Start: 83 Subject End: 202 .............................................................................................................................................................................aaatctagtataacaaaaacttttgaaaaaagagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagttatctaccaactcta................................................................. .............................................................................................................................................................................aaatctagtataacaaaaacttttgaaaaatgagaaaaccatccatttgaattggatggtttcgttttatgtatatcaattatattcatcatgctttaaaaaagctatctaccaactcta................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAUUUUCUUUCUAAUCUAUGAUAUACAGACCAUUCUCAACUACAAAUUGUAAGCGUCCAUUUACUUUAAUACCUUCAACCACUUCAGAGCUUACUUCAAUUCUAAGUUUAGGAAAUAUUUCACUCAAUGGUACGACCAAUCAUUGACUGAAUACAGUGUAUUAAAGGGAUAAAUCUAGUAUAACAAAAACUUUUGAAAAAAGAGAAAACCAUCCAUUUGAAUUGGAUGGUUUCGUUUUAUGUAUAUCAAUUAUAUUCAUCAUGCUUUAAAAAAGUUAUCUACCAACUCUAUGUUUUGUAUACAUUUAACCCGACAGUUUAACAGAUGAUAAAAUGGAAUAUUACUAACUUCACAU (((((((((...(((......((.((((((((...........(((.....)))...((((.....(((((((((((........(((.(((((((.........))))))).))).....((((.((((((((.......)))))))).))))...)).)))))))))))))...))).))))).)).(((((.(((..........((((((((((.......)))))))))).(((..(((((((.(((.............((((.....))))........(((.....)))))))))))))..))).))).)))))...)))....)))))))))................. (-64.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUGAAGUUAGUAAUAUUCCAUUUUAUCAUCUGUUAAACUGUCGGGUUAAAUGUAUACAAAACAUAGAGUUGGUAGAUAACUUUUUUAAAGCAUGAUGAAUAUAAUUGAUAUACAUAAAACGAAACCAUCCAAUUCAAAUGGAUGGUUUUCUCUUUUUUCAAAAGUUUUUGUUAUACUAGAUUUAUCCCUUUAAUACACUGUAUUCAGUCAAUGAUUGGUCGUACCAUUGAGUGAAAUAUUUCCUAAACUUAGAAUUGAAGUAAGCUCUGAAGUGGUUGAAGGUAUUAAAGUAAAUGGACGCUUACAAUUUGUAGUUGAGAAUGGUCUGUAUAUCAUAGAUUAGAAAGAAAAUAGAA (((((..((((((.(((((((((((((......((((..((..(((.((..((((.......)))).)).)))..)).)))).....))))..)))..)))))).)))))).))))).....(((((((((((.......))))))))))).(((.(((((..((((.((..((.((((......((.((((((((.((((...((((.((((((...........)))))).)))).(((((((((....)))....))))))........)))))))))))).))...))))))..)).)))).((((.....))))....((((((((.....))))))))....))))).))). (-70.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 100 51 191 142 NC_009009:SSA_1287|5end_hypothetical_protein_1306737..1306967_NEGATIVE 639 230 181 230 181 NC_009009:SSA_1285|5end_hypothetical_protein_1305469..1305699_NEGATIVE 279 124 82 127 79 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 268 116 76 176 126 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 267 45 1 197 156 NC_009009:SSA_0247|5end_hypothetical_protein_240032..240262_POSITIVE 263 100 57 216 186 NC_009009:SSA_0870|5end_Cell_division_protein_FtsE,_putative_862936..863166_POSITIVE 257 117 78 192 141 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 233 88 50 116 71 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 229 231 212 22 4 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 227 100 54 213 168 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 226 98 51 55 4 NC_009009:SSA_0159|5end_hypothetical_protein_155000..155230_POSITIVE 224 185 142 216 178 NC_009009:SSA_2193|5end_ADP-ribose_pyrophosphatase,_putative_2194793..2195023_NEGATIVE 224 96 55 68 26 NC_009009:SSA_2034|5end_50S_ribosomal_protein_L13,_putative_2039244..2039474_NEGATIVE 224 161 126 67 32 NC_009009:SSA_0909|5end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_920887..921117_POSITIVE 222 87 41 194 143 NC_009009:SSA_1759|5end_hypothetical_protein_1746969..1747199_NEGATIVE 219 101 61 47 4 NC_009009:SSA_0108|5end_50S_ribosomal_protein_L4,_putative_108816..109046_POSITIVE 217 95 56 60 15 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 216 61 31 23 1 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 215 326 281 182 125 NC_009009:SSA_2379|5end_Signal_transduction_protein_with_a_C-terminal_ATPase/histidine_kinase_domain,_putative_2385233..2385463_NEGATIVE 215 156 113 56 10 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 235 193 68 25 NC_009009:SSA_1289|3end_hypothetical_protein_1307909..1308059_NEGATIVE 235 100 51 135 83 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 233 88 50 97 52 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 232 167 136 56 21 NC_009009:SSA_2080|3end_hypothetical_protein_2084598..2084748_NEGATIVE 229 231 212 20 2 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 224 128 83 90 50 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE 218 115 72 133 77 NC_009009:SSA_1774|3end_RRNA_methylase,_putative_1760489..1760639_NEGATIVE 216 118 75 73 33 NC_009009:SSA_0549|3end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_545651..545801_POSITIVE 214 111 76 86 49 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 214 98 67 82 51 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 213 246 202 51 8 NC_009009:SSA_1812|3end_Modification_methylase,_putative_1797108..1797258_NEGATIVE 213 244 202 77 37 NC_009009:SSA_0572|3end_Dehydrogenase,_putative_568552..568702_POSITIVE 212 330 289 128 79 NC_009009:SSA_1809|3end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1792227..1792377_NEGATIVE 212 93 58 126 85 NC_009009:SSA_0939|3end_Inositol_monophosphatase_(Mg++_dependent),_putative_947705..947855_POSITIVE 212 99 51 120 67 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 210 118 77 143 97 NC_009009:SSA_2393|3end_Transcriptional_regulator,_XRE_family,_putative_204339..204489_POSITIVE 210 98 58 49 3 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 209 100 60 103 70 NC_009009:SSA_0530|3end_Ethanolamine_utilization_protein_(transporter),_putative_527417..527567_POSITIVE 208 162 121 146 112 NC_009009:SSA_2114|3end_Transcriptional_repressor_of_purine_operon,_putative_2116714..2116864_NEGATIVE 208 87 41 139 89 NC_009009:SSA_1940|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1926155..1926305_NEGATIVE