Origin IGS: aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt .........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 aatgatgagctcctttccgtccttggacagaaggaaacaaaatgagcaaatattgaacgctgagtatgctaaaaggcacaacaaagaaacagcgaaacaattctatgcaagacatgacctttatcgtcatatcatcatatttgtttcaatctgtcctttgatggccatcaatttggactattaaaatttttatcaagagtttttcttgatatattcagtataaggcataatgttcttttattttttacttctttttttacttcaataaactaatttgtaaaacgaagtgcaaaaaaaaactaggcgattcacctagttt Mask Tandem Repeat Region ================================================ aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt Find is-nt database================================================ Query_seq: SSA_2290:SSA_2291|SSA_2290:SSA_2291:hypothetical protein:hypothetical protein:->->:2293025..2293343 319 aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2290:SSA_2291|SSA_2290:SSA_2291:hypothetical protein:hypothetical protein:->->:2293025..2293343 319 aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2290:SSA_2291|SSA_2290:SSA_2291:hypothetical protein:hypothetical protein:->->:2293025..2293343 319 aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 54 End: 149 ..................................................... M E V K K E V K N K R T L C L I L N I S R K T L D K N F N S P N .......................................................................................................................................................................... Protein_Len: 43 Strand: + Start: 190 End: 318 ............................................................................................................................................................................................. M T I K V M S C I E L F R C F F V V P F S I L S V Q Y L L I L F P S V Q G R K G A H H . Protein_Len: 33 Strand: - Start: 162 End: 260 ................................................................................................................................................................. L V S Q F L Y S S I V I F T M D Q M S N N R Q K K T T G K L M S M ........................................................... Protein_Len: 60 Strand: - Start: 139 End: 318 .......................................................................................................................................... Y D L N I A M L P C I S V F I I I H R Y L D H R A Y F Q K A T E K N H R K A Y E A N L I Q E N Q K R R D L S P F S S M M . Protein_Len: 44 Strand: - Start: 50 End: 181 ................................................. N I S T F F S T F F L L V N H R I S F I D L F V R S L F K L L G F Q H G D F S L N F C M .......................................................................................................................................... aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt 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================================================ aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -4.4 Tail_Score: -2.50493 Start: 107 End: 131 Full_Region: ATGCCTTATACTGAA TATATCAAGA AAAAC TCTTGATAAA AATTTTAATAGTCCA ..........................................................................................................TATATCAAGAAAAACTCTTGATAAA............................................................................................................................................................................................ TransTerm Strand: + Conf: 49 HP_score: -4.2 Tail_Score: -3.08738 Start: 187 End: 209 Full_Region: TGAAACAAATATGAT GATATGAC GATAAAG GTCATGTC TTGCATAGAATTGTT ..........................................................................................................................................................................................GATATGACGATAAAGGTCATGTC.............................................................................................................. Find igs database================================================ Query_seq: SSA_2290:SSA_2291|SSA_2290:SSA_2291:hypothetical protein:hypothetical protein:->->:2293025..2293343 319 aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagtaaaaaaagaagtaaaaaataaaagaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt Intra-Species Hit: Count: 1 Min: 1 Max: 319 Len: 319 Subject: NC_009009_SSA_2290_SSA_2291|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2293025,2293343]|319 HSP 1 e-value: 1.0E-130 bit: 466.0 Len: 235 Query Start:85 Query End:319 Subject Strand: POSITIVE Subject Start: 85 Subject End: 319 ....................................................................................gaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt ....................................................................................gaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtccaaggacggaaaggagctcatcatt HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 61 Query Start:1 Query End:61 Subject Strand: POSITIVE Subject Start: 1 Subject End: 61 aaactaggtgaatcgcctagnnnnnnnnngcacttcgttttacaaattagtttattgaagt.................................................................................................................................................................................................................................................................. aaactaggtgaatcgcctagtttttttttgcacttcgttttacaaattagtttattgaagt.................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 2 Min: 85 Max: 319 Len: 235 Subject: NC_004368_gbs2066_gbs2067|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2140632,2140951]|320 HSP 1 e-value: 1.0E-112 bit: 404.0 Len: 235 Query Start:85 Query End:319 Subject Strand: POSITIVE Subject Start: 85 Subject End: 320 ....................................................................................gaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtcc-aaggacggaaaggagctcatcatt ....................................................................................gaacattacgccttatactgaatatatcaagaaaaactcttgatataaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgacatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttggtatactcagcgttcaatatttgctcattttgtttccttctgtccaaaggacagaaaggagctcatcatt Subject: NC_007432_SAK_2053_SAK_2054|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2046655,2046974]|320 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 235 Query Start:85 Query End:319 Subject Strand: POSITIVE Subject Start: 85 Subject End: 320 ....................................................................................gaacattatgccttatactgaatatatcaagaaaaactcttgataaaaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgatatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttagcatactcagcgttcaatatttgctcattttgtttccttctgtcc-aaggacggaaaggagctcatcatt ....................................................................................gaacattactccttatactgaatatatcaagaaaaactcttgatataaattttaatagtccaaattgatggccatcaaaggacagattgaaacaaatatgatgacatgacgataaaggtcatgtcttgcatagaattgtttcgctgtttctttgttgtgccttttggtatactcagcgttcaatatttgctcattttgtttccttctgtccaaaggacagaaaggagctcatcatt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACAUUAUGCCUUAUACUGAAUAUAUCAAGAAAAACUCUUGAUAAAAAUUUUAAUAGUCCAAAUUGAUGGCCAUCAAAGGACAGAUUGAAACAAAUAUGAUGAUAUGACGAUAAAGGUCAUGUCUUGCAUAGAAUUGUUUCGCUGUUUCUUUGUUGUGCCUUUUAGCAUACUCAGCGUUCAAUAUUUGCUCAUUUUGUUUCCUUCUGUCCAAGGACGGAAAGGAGCUCAUCAUU ..........((((..........((((((((.....))))))))............((((...(((((....))))).(((((((..((((((((.((((.((((((((.......))))))))..(((....((((...(((((......(((((.......)))))....)))))..))))...)))))))))))))))..)))))))..))))...))))........... (-68.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUGAGCUCCUUUCCGUCCUUGGACAGAAGGAAACAAAAUGAGCAAAUAUUGAACGCUGAGUAUGCUAAAAGGCACAACAAAGAAACAGCGAAACAAUUCUAUGCAAGACAUGACCUUUAUCGUCAUAUCAUCAUAUUUGUUUCAAUCUGUCCUUUGAUGGCCAUCAAUUUGGACUAUUAAAAUUUUUAUCAAGAGUUUUUCUUGAUAUAUUCAGUAUAAGGCAUAAUGUUC ......((((......((......(((((((..(((((((((((((((...((((..(((((....((((....))))(......)...)))))...))))....)))..((.(((((.......))))).)).)))).))))))))..))))))).((((((((((......))).)))))))......(((((((((...)))))))))............))......)))) (-59.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 229 188 123 85 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 318 230 196 33 1 NC_009009:SSA_1342|5end_Carbamoyl-phosphate_synthase_small_chain,_putative_1361017..1361247_NEGATIVE 298 230 181 215 171 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 298 156 118 55 15 NC_009009:SSA_0095|5end_Threonine_synthase,_putative_96555..96785_POSITIVE 294 208 161 225 181 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 293 228 188 224 191 NC_009009:SSA_0993|5end_hypothetical_protein_994064..994294_POSITIVE 286 214 173 195 146 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 283 182 143 52 13 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 282 182 143 221 161 NC_009009:SSA_0635|5end_Indole-3-glycerol_phosphate_synthase,_putative_624388..624618_POSITIVE 281 159 111 82 36 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 280 219 172 118 53 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 275 210 166 68 30 NC_009009:SSA_0461|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_463059..463289_POSITIVE 273 219 173 208 156 NC_009009:SSA_0926|5end_Histone_acetyltransferase_HPA2,_putative_935465..935695_POSITIVE 273 179 135 51 2 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 269 189 144 159 110 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 269 184 143 56 10 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 268 178 140 47 13 NC_009009:SSA_2190|5end_33_kDa_chaperonin,_putative_2191166..2191396_POSITIVE 268 182 141 57 18 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 267 215 173 231 193 NC_009009:SSA_1339|5end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1355424..1355654_NEGATIVE 263 179 132 192 151 NC_009009:SSA_1868|5end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863902..1864132_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 190 144 126 78 NC_009009:SSA_0513|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_512237..512387_POSITIVE 361 229 188 126 88 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 321 220 171 80 6 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 300 177 138 135 102 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 280 219 172 131 66 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 275 169 122 121 81 NC_009009:SSA_1005|3end_Sugar_ABC_transporter,_permease_protein,_putative_1006941..1007091_POSITIVE 275 210 166 75 37 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 269 189 144 101 52 NC_009009:SSA_2237|3end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2235508..2235658_NEGATIVE 269 189 143 53 16 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 262 219 176 148 101 NC_009009:SSA_2183|3end_Glucose-6-phosphate_isomerase,_putative_2181155..2181305_NEGATIVE 261 153 123 141 110 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 261 181 141 54 15 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 260 220 172 87 37 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 258 190 141 97 50 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 256 229 184 117 80 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 254 219 175 151 115 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 254 225 191 143 101 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 253 207 165 91 30 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 251 169 124 49 4 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 251 178 131 147 104 NC_009009:SSA_1655|3end_hypothetical_protein_1651391..1651541_NEGATIVE