Origin IGS: agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa .........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 ttctgctcctttctttttaaaaaccgaccagacggtttttttattttataaactcagtataacagacacagaaaactttgtccagtattttttcaaaaaagattatttttagtcaatgaaaatcatcagccaacttagaaactcgtcacaagcaactctctcatactaaaaactatatctaaaaaagctcggtaatgaaccaagcctttatct Mask Tandem Repeat Region ================================================ agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Find is-nt database================================================ Query_seq: SSA_0343:SSA_0345|SSA_0343:SSA_0345:DNA-damage-inducible protein P, putative:hypothetical protein:->->:338730..338942 213 agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0343:SSA_0345|SSA_0343:SSA_0345:DNA-damage-inducible protein P, putative:hypothetical protein:->->:338730..338942 213 agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0343:SSA_0345|SSA_0343:SSA_0345:DNA-damage-inducible protein P, putative:hypothetical protein:->->:338730..338942 213 agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Predict ORF larger than 30AA ================================================ agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa 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: 85 Start: 129 End: 158 ................................................................................................................................CTGGACAAAGTTTTCTGTGTCTGTTATACT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0343:SSA_0345|SSA_0343:SSA_0345:DNA-damage-inducible protein P, putative:hypothetical protein:->->:338730..338942 213 agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Intra-Species Hit: Count: 1 Min: 1 Max: 213 Len: 213 Subject: NC_009009_SSA_0343_SSA_0345|DNA-damage-inducible protein P, putative:hypothetical protein|POSITIVE:POSITIVE|[338730,338942]|213 HSP 1 e-value: 1.0E-105 bit: 381.0 Len: 213 Query Start:1 Query End:213 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaatnnnnnnnccgtctggtcggtttttaaaaagaaaggagcagaa agataaaggcttggttcattaccgagcttttttagatatagtttttagtatgagagagttgcttgtgacgagtttctaagttggctgatgattttcattgactaaaaataatcttttttgaaaaaatactggacaaagttttctgtgtctgttatactgagtttataaaataaaaaaaccgtctggtcggtttttaaaaagaaaggagcagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUAAAGGCUUGGUUCAUUACCGAGCUUUUUUAGAUAUAGUUUUUAGUAUGAGAGAGUUGCUUGUGACGAGUUUCUAAGUUGGCUGAUGAUUUUCAUUGACUAAAAAUAAUCUUUUUUGAAAAAAUACUGGACAAAGUUUUCUGUGUCUGUUAUACUGAGUUUAUAAAAUAAAAAAACCGUCUGGUCGGUUUUUAAAAAGAAAGGAGCAGAA ....(((((((((((.....))))))))))).........(((((((((...(((((.((((....).))).))))).........((((.....)))).)))))))))..((((((((......(((..(((((.((....)).)))))..)))..................((((((((......))))))))....))))))))...... (-46.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGCUCCUUUCUUUUUAAAAACCGACCAGACGGUUUUUUUAUUUUAUAAACUCAGUAUAACAGACACAGAAAACUUUGUCCAGUAUUUUUUCAAAAAAGAUUAUUUUUAGUCAAUGAAAAUCAUCAGCCAACUUAGAAACUCGUCACAAGCAACUCUCUCAUACUAAAAACUAUAUCUAAAAAAGCUCGGUAAUGAACCAAGCCUUUAUCU ...((((...........((((((((......))))))))............((.(((......((((.((....)).))))..................(((.(((((((.....))))))).))).....))).))............))))............................(((.(((.(((.....))).))).))).... (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 100 55 190 130 NC_009009:SSA_0690|5end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_674432..674662_POSITIVE 309 189 143 168 114 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 305 160 130 51 10 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 303 99 56 92 52 NC_009009:SSA_1992|5end_Fructose-bisphosphate_aldolase,_putative_1989972..1990202_NEGATIVE 298 42 8 207 170 NC_009009:SSA_0602|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_589918..590148_POSITIVE 294 77 31 181 133 NC_009009:SSA_0201|5end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_199825..200055_POSITIVE 285 67 21 162 114 NC_009009:SSA_1791|5end_Acylphosphatase,_putative_1773676..1773906_POSITIVE 272 97 51 206 158 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 269 104 62 157 111 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 258 80 47 202 168 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 258 145 111 61 33 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 256 209 178 196 166 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 252 160 128 54 20 NC_009009:SSA_2263|5end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2261176..2261406_NEGATIVE 250 89 41 134 76 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 248 90 43 184 123 NC_009009:SSA_1788|5end_Integral_membrane_protein,_possible_receptor,_putative_1772339..1772569_NEGATIVE 247 88 44 158 111 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 245 100 57 87 29 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 244 103 69 38 1 NC_009009:SSA_0822|5end_Large_conductance_mechano-sensitive_ion_channel,_putative_801972..802202_NEGATIVE 243 37 7 84 48 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 241 70 21 60 3 NC_009009:SSA_1563|5end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1567256..1567486_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 97 53 127 93 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 315 100 55 86 26 NC_009009:SSA_0689|3end_Penicillin-binding_protein_2B,_putative_674408..674558_POSITIVE 309 189 143 83 29 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 294 77 31 86 38 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 259 68 22 121 75 NC_009009:SSA_0629|3end_hypothetical_protein_619586..619736_POSITIVE 258 145 111 64 36 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 248 103 61 56 4 NC_009009:SSA_1341|3end_Carbamoyl-phosphate_synthase_large_chain,_putative_1356648..1356798_NEGATIVE 248 90 51 126 95 NC_009009:SSA_0898|3end_hypothetical_protein_889768..889918_NEGATIVE 241 190 145 134 94 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE 241 88 42 151 98 NC_009009:SSA_1053|3end_Pyruvate_phosphate_dikinase,_putative_1067447..1067597_NEGATIVE 239 90 43 150 103 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 237 49 7 73 33 NC_009009:SSA_1961|3end_Amino_acid_ABC_transporter,_amino_acid-binding_protein/permease_protein,_putative_1960193..1960343_POSITIVE 237 207 169 69 27 NC_009009:SSA_1692|3end_Phospho-B-galactosidase_LacG,_putative_1683600..1683750_NEGATIVE 237 31 5 86 60 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 235 70 22 50 1 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE 234 37 3 90 50 NC_009009:SSA_0471|3end_CbiG_protein,_putative_474783..474933_POSITIVE 234 107 65 118 70 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 233 97 51 73 21 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 232 70 21 73 36 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 231 159 112 105 66 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE