Origin IGS: atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa .........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 ttcttaataaaatagaaaatttcgggatgcactcccgattttttacttgaagtagggaatgttttagtaagacatttctatactgtgatttattttctgcttgcttcttttagataaaatctaaaaaagaagcaggatagaaaaccaggtaaattgacacttaaaaacttcaccaaaatattagcaatttatctaaggaggaaat Mask Tandem Repeat Region ================================================ atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Find is-nt database================================================ Query_seq: SSA_1548:SSA_1549|SSA_1548:SSA_1549:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:hypothetical protein:<-<-:1551701..1551905 205 atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1548:SSA_1549|SSA_1548:SSA_1549:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:hypothetical protein:<-<-:1551701..1551905 205 atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1548:SSA_1549|SSA_1548:SSA_1549:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:hypothetical protein:<-<-:1551701..1551905 205 atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 18 End: 113 ................. M A N I L V K F L S V N L P G F L S C F F F R F Y L K E A S R K ............................................................................................ Protein_Len: 32 Strand: - Start: 92 End: 187 ........................................................................................... R F S A L L F Y I V T Y F H R V L V N G V E L L F D P T C G S M .................. atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa 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: 24 End: 53 .......................ATTGACACTTAAAAACTTCACCAAAATATT........................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1548:SSA_1549|SSA_1548:SSA_1549:NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:hypothetical protein:<-<-:1551701..1551905 205 atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_009009_SSA_1548_SSA_1549|NTP pyrophosphohydrolases including oxidative damage repair enzymes, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1551701,1551905]|205 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa atttcctccttagataaattgctaatattttggtgaagtttttaagtgtcaatttacctggttttctatcctgcttcttttttagattttatctaaaagaagcaagcagaaaataaatcacagtatagaaatgtcttactaaaacattccctacttcaagtaaaaaatcgggagtgcatcccgaaattttctattttattaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCCUCCUUAGAUAAAUUGCUAAUAUUUUGGUGAAGUUUUUAAGUGUCAAUUUACCUGGUUUUCUAUCCUGCUUCUUUUUUAGAUUUUAUCUAAAAGAAGCAAGCAGAAAAUAAAUCACAGUAUAGAAAUGUCUUACUAAAACAUUCCCUACUUCAAGUAAAAAAUCGGGAGUGCAUCCCGAAAUUUUCUAUUUUAUUAAGAA ........(((.((((((.........(((((.((((((.....(((((...........(((((((..(.(((((((((..(((((...)))))))))))))).).))))))).......((((.(((....)))))))...)))))....))))))..)))))..((((((.....))))))..........))))))))).. (-41.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUAAUAAAAUAGAAAAUUUCGGGAUGCACUCCCGAUUUUUUACUUGAAGUAGGGAAUGUUUUAGUAAGACAUUUCUAUACUGUGAUUUAUUUUCUGCUUGCUUCUUUUAGAUAAAAUCUAAAAAAGAAGCAGGAUAGAAAACCAGGUAAAUUGACACUUAAAAACUUCACCAAAAUAUUAGCAAUUUAUCUAAGGAGGAAAU (((((((((((....((((..((((((.....))))))..))))...((((((.((((((((((.....))))))))))....((((((((((((((((((((((((((((((((...)))))..))))))))))).)))))).....))))))).))).......))))))...............))))).))))))...... (-53.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 799 80 31 171 122 NC_009009:SSA_1548|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1551610..1551840_NEGATIVE 304 110 67 160 119 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 278 80 31 164 122 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 265 86 47 151 117 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 261 58 18 217 182 NC_009009:SSA_0920|5end_hypothetical_protein_930896..931126_POSITIVE 260 79 46 105 60 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 255 49 1 139 90 NC_009009:SSA_0246|5end_Conserved_uncharacterized_protein_239703..239933_POSITIVE 251 78 46 226 192 NC_009009:SSA_1291|5end_hypothetical_protein_1311102..1311332_NEGATIVE 242 125 83 53 6 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 239 188 146 157 113 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 238 109 62 216 145 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 237 100 59 151 113 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 237 184 144 215 174 NC_009009:SSA_1314|5end_Fe-S-cluster_oxidoreductase,_putative_1331240..1331470_NEGATIVE 237 79 31 119 69 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 236 109 66 177 137 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 234 77 32 77 17 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 233 62 30 54 24 NC_009009:SSA_1589|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1592608..1592838_NEGATIVE 231 76 31 162 122 NC_009009:SSA_0317|5end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311259..311489_POSITIVE 228 113 71 201 145 NC_009009:SSA_0924|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_933738..933968_POSITIVE 226 85 58 107 75 NC_009009:SSA_1456|5end_hypothetical_protein_1462349..1462579_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 110 67 64 23 NC_009009:SSA_1671|3end_hypothetical_protein_1670337..1670487_POSITIVE 265 86 47 95 61 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 253 78 31 115 66 NC_009009:SSA_1583|3end_6-O-methylguanine-DNA_methyltransferase,_putative_1585523..1585673_NEGATIVE 237 184 144 47 6 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 236 109 66 72 32 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 236 180 134 78 37 NC_009009:SSA_1711|3end_Endonuclease_III,_putative_1699007..1699157_NEGATIVE 230 107 69 61 18 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 228 113 71 81 25 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 224 103 62 143 104 NC_009009:SSA_0441|3end_hypothetical_protein_442175..442325_POSITIVE 223 184 146 34 3 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 218 115 71 76 28 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 217 80 32 121 65 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 216 77 31 108 51 NC_009009:SSA_1902|3end_tRNA_(guanine-N(7)-)-methyltransferase,_putative_1896753..1896903_NEGATIVE 216 76 33 92 54 NC_009009:SSA_0123|3end_50S_ribosomal_protein_L18P,_putative_116484..116634_POSITIVE 214 75 37 130 87 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 213 86 49 147 111 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 213 109 68 138 82 NC_009009:SSA_2099|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103621..2103771_NEGATIVE 210 70 21 59 3 NC_009009:SSA_2061|3end_Peptide_deformylase,_putative_2063259..2063409_POSITIVE 209 78 33 124 82 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 209 77 47 150 117 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE