Origin IGS: gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctgagagttttgctcgtagatagaaagtttgagactggttgaaccagtcttttcgtgttataatattcagacaagattgaacggagaaagtgtttcactcatc Mask Tandem Repeat Region ================================================ gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Find is-nt database================================================ Query_seq: SSA_1423:SSA_1424|SSA_1423:SSA_1424:Single-stranded DNA-specific exonuclease, 5'-3', putative:Hydrolase, putative:<-<-:1433874..1433978 105 gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1423:SSA_1424|SSA_1423:SSA_1424:Single-stranded DNA-specific exonuclease, 5'-3', putative:Hydrolase, putative:<-<-:1433874..1433978 105 gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1423:SSA_1424|SSA_1423:SSA_1424:Single-stranded DNA-specific exonuclease, 5'-3', putative:Hydrolase, putative:<-<-:1433874..1433978 105 gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 6 End: 104 ..... M K H F L R S I L S E Y Y N T K R L V Q P V S N F L S T S K T L R . gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga 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================================================ gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1423:SSA_1424|SSA_1423:SSA_1424:Single-stranded DNA-specific exonuclease, 5'-3', putative:Hydrolase, putative:<-<-:1433874..1433978 105 gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_009009_SSA_1423_SSA_1424|Single-stranded DNA-specific exonuclease, 5'-3', putative:Hydrolase, putative|NEGATIVE:NEGATIVE|[1433874,1433978]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga gatgagtgaaacactttctccgttcaatcttgtctgaatattataacacgaaaagactggttcaaccagtctcaaactttctatctacgagcaaaactctcagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAGUGAAACACUUUCUCCGUUCAAUCUUGUCUGAAUAUUAUAACACGAAAAGACUGGUUCAACCAGUCUCAAACUUUCUAUCUACGAGCAAAACUCUCAGGA ((.(((((((.....)))...((((..((......))............(((((((((((.....))))))).....)))).......))))...)))))).... (-19.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUGAGAGUUUUGCUCGUAGAUAGAAAGUUUGAGACUGGUUGAACCAGUCUUUUCGUGUUAUAAUAUUCAGACAAGAUUGAACGGAGAAAGUGUUUCACUCAUC ..(((((((.....)))....((((...(...((((((((.....))))))))..)...)))).....))))....((.((((((.......)).)))).))... (-21.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 850 100 51 191 142 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 315 56 11 185 137 NC_009009:SSA_2174|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2172689..2172919_NEGATIVE 258 69 23 150 102 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 250 90 49 163 113 NC_009009:SSA_2006|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme,_putative_2007215..2007445_NEGATIVE 250 86 49 178 149 NC_009009:SSA_1598|5end_hypothetical_protein_1605238..1605468_NEGATIVE 246 98 52 83 31 NC_009009:SSA_0054|5end_Phosphotransferase_system_sugar-specific_EIIB_component,_putative_58532..58762_POSITIVE 245 50 1 70 33 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 244 84 48 186 149 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 242 68 22 51 3 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 239 100 52 68 8 NC_009009:SSA_2304|5end_Conserved_uncharacterized_protein_2306270..2306500_NEGATIVE 236 39 1 176 143 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 235 60 11 68 21 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 234 85 47 209 168 NC_009009:SSA_1626|5end_DNA_translocase_ftsK,_putative_1629377..1629607_NEGATIVE 231 60 20 117 64 NC_009009:SSA_0998|5end_hypothetical_protein_998487..998717_POSITIVE 230 100 56 59 11 NC_009009:SSA_1936|5end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923838..1924068_NEGATIVE 225 76 51 40 15 NC_009009:SSA_0314|5end_Nucleoside-diphosphate-sugar_epimerase,_putative_310019..310249_NEGATIVE 223 95 52 231 198 NC_009009:SSA_0734|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_716895..717125_POSITIVE 223 92 54 103 63 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 222 60 15 141 94 NC_009009:SSA_0195|5end_hypothetical_protein_195113..195343_POSITIVE 222 98 55 208 158 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 69 23 71 23 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 249 81 41 133 91 NC_009009:SSA_0402|3end_Histidine_kinase,_putative_400099..400249_POSITIVE 246 98 52 86 34 NC_009009:SSA_0053|3end_Beta-galactosidase,_putative_58615..58765_POSITIVE 244 84 48 90 53 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 235 60 11 71 24 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 234 85 47 78 37 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 231 60 20 79 26 NC_009009:SSA_0997|3end_DNA-directed_DNA_polymerase_III_chain,_putative_998529..998679_POSITIVE 223 92 54 77 37 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 221 59 14 140 83 NC_009009:SSA_0298|3end_Malate_permease,_putative_292447..292597_POSITIVE 220 56 11 69 29 NC_009009:SSA_1850|3end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1845710..1845860_NEGATIVE 218 100 55 136 82 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 215 86 46 96 64 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 214 92 51 48 5 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 212 100 53 74 22 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 210 58 12 57 5 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 208 100 66 46 21 NC_009009:SSA_1937|3end_Malonyl-CoA:ACP_transacylase,_putative_1923851..1924001_NEGATIVE 208 84 54 135 104 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 207 43 16 37 14 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 206 100 67 148 100 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 205 93 55 84 35 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE