Origin IGS: gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacttttattataccacaagactccagtcagggacgaactaaatagtcccccctttttctttggaaaagaaaactgagacagttctgcctcagttttgcgtattcagtttgtattcatgaaagcatattaccagatgatgaactacttccatcaatctaggcaaaatggcttc Mask Tandem Repeat Region ================================================ gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Find is-nt database================================================ Query_seq: SSA_0789:SSA_0790|SSA_0789:SSA_0790:Proton-translocating ATPase, F1 sector, epsilon subunit, putative:hypothetical protein:->->:773014..773186 173 gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0789:SSA_0790|SSA_0789:SSA_0790:Proton-translocating ATPase, F1 sector, epsilon subunit, putative:hypothetical protein:->->:773014..773186 173 gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0789:SSA_0790|SSA_0789:SSA_0790:Proton-translocating ATPase, F1 sector, epsilon subunit, putative:hypothetical protein:->->:773014..773186 173 gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 71 End: 172 ...................................................................... M R K T E A E L S Q F S F P K K K G G L F S S S L T G V L W Y N K S . gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt 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================================================ gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 79 HP_score: -8.7 Tail_Score: -4.07568 Start: 76 End: 105 Full_Region: TACAAACTGAATACG CAAAACTGAGGCA GAAC TGTCTCAGTTTTC TTTTCCAAAGAAAAA ...........................................................................CAAAACTGAGGCAGAACTGTCTCAGTTTTC.................................................................... TransTerm Strand: + Conf: 90 HP_score: -8.6 Tail_Score: -5.07652 Start: 81 End: 100 Full_Region: ACTGAATACGCAAAA CTGAGGCA GAAC TGTCTCAG TTTTCTTTTCCAAAG ................................................................................CTGAGGCAGAACTGTCTCAG......................................................................... TransTerm Strand: - Conf: 71 HP_score: -6.4 Tail_Score: -4.28656 Start: 81 End: 100 Full_Region: ctttggaaaagaaaa ctgagaca gttc tgcctcag ttttgcgtattcagt ................................................................................ctgagacagttctgcctcag......................................................................... Find igs database================================================ Query_seq: SSA_0789:SSA_0790|SSA_0789:SSA_0790:Proton-translocating ATPase, F1 sector, epsilon subunit, putative:hypothetical protein:->->:773014..773186 173 gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: NC_009009_SSA_0789_SSA_0790|Proton-translocating ATPase, F1 sector, epsilon subunit, putative:hypothetical protein|POSITIVE:POSITIVE|[773014,773186]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt gaagccattttgcctagattgatggaagtagttcatcatctggtaatatgctttcatgaatacaaactgaatacgcaaaactgaggcagaactgtctcagttttcttttccaaagaaaaaggggggactatttagttcgtccctgactggagtcttgtggtataataaaagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGCCAUUUUGCCUAGAUUGAUGGAAGUAGUUCAUCAUCUGGUAAUAUGCUUUCAUGAAUACAAACUGAAUACGCAAAACUGAGGCAGAACUGUCUCAGUUUUCUUUUCCAAAGAAAAAGGGGGGACUAUUUAGUUCGUCCCUGACUGGAGUCUUGUGGUAUAAUAAAAGUU ((((.(((.(((((.((((.((((((.....))))))))))))))).))).)))).....(((((.........(.((((((((((((....)))))))))))))..(((((.......((((((((((....))))).)))))...)))))..))))).............. (-51.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUUUAUUAUACCACAAGACUCCAGUCAGGGACGAACUAAAUAGUCCCCCCUUUUUCUUUGGAAAAGAAAACUGAGACAGUUCUGCCUCAGUUUUGCGUAUUCAGUUUGUAUUCAUGAAAGCAUAUUACCAGAUGAUGAACUACUUCCAUCAAUCUAGGCAAAAUGGCUUC ..(((((((.((((.....(((....))).(((((..........)))))..........(((((...((((((((((.((....)).))))))))).)...)))))...))))..)))))))(((.((.((((((((((.........)))).)))).)).)).)))..... (-37.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 60 12 206 160 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 320 163 121 68 14 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 309 160 125 178 136 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 304 160 117 77 32 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 298 158 114 118 68 NC_009009:SSA_0800|5end_Glutamine_amidotransferase,_putative_782774..783004_NEGATIVE 296 148 101 163 108 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 295 130 81 184 138 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 286 157 120 177 133 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 281 127 95 119 86 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 278 58 13 61 19 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 275 117 75 204 156 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 273 52 12 214 168 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 272 129 84 97 55 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 271 150 104 62 10 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 267 113 74 200 157 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 264 50 4 82 30 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 259 160 122 62 10 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 258 160 118 185 139 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 257 130 82 133 70 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 256 44 2 62 18 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 126 81 116 68 NC_009009:SSA_0743|3end_Transcriptional_repressor_(arginine_synthesis),_putative_725289..725439_NEGATIVE 322 60 12 81 35 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 320 163 121 68 14 NC_009009:SSA_0996|3end_cGMP-specific_phosphodiesterase,_putative_996859..997009_POSITIVE 306 111 75 96 61 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 304 160 117 90 45 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE 298 158 114 118 68 NC_009009:SSA_0801|3end_Mur_ligase_family_protein,_putative_782774..782924_NEGATIVE 298 98 53 147 109 NC_009009:SSA_0051|3end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55644..55794_POSITIVE 296 148 101 87 32 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 281 148 101 48 8 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 275 117 75 73 25 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 266 148 109 71 32 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 258 40 3 99 54 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 257 165 121 138 84 NC_009009:SSA_1215|3end_hypothetical_protein_1238247..1238397_POSITIVE 257 130 82 133 70 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 256 44 2 52 8 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 254 160 119 77 24 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 251 150 105 63 3 NC_009009:SSA_2021|3end_hypothetical_protein_2022500..2022650_NEGATIVE 251 159 119 150 116 NC_009009:SSA_1276|3end_Conserved_uncharacterized_protein_1298156..1298306_NEGATIVE 251 150 103 137 83 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 250 46 1 112 53 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE