Origin IGS: aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc .........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 gattttattataccattatttcgctttctgacaatagaaaaggatagaatttatagcaggaaatgtctactcggatattggattcttcttcgtgtgaaatcagttctcatcagcagttttttcaaaaaaatctttgcaatatttgccaaaaacttgtaagatagaaaagatgaatcattaggaggttctt Mask Tandem Repeat Region ================================================ aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Find is-nt database================================================ Query_seq: SSA_1232:SSA_1233|SSA_1232:SSA_1233:Topoisomerase IV subunit B, putative:Membrane protein, YqiH family, putative:<-->:1256846..1257035 190 aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1232:SSA_1233|SSA_1232:SSA_1233:Topoisomerase IV subunit B, putative:Membrane protein, YqiH family, putative:<-->:1256846..1257035 190 aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1232:SSA_1233|SSA_1232:SSA_1233:Topoisomerase IV subunit B, putative:Membrane protein, YqiH family, putative:<-->:1256846..1257035 190 aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 42 End: 137 ......................................... M A N I A K I F L K K L L M R T D F T R R R I Q Y P S R H F L L ..................................................... Protein_Len: 31 Strand: + Start: 88 End: 180 ....................................................................................... M I S H E E E S N I R V D I S C Y K F Y P F L L S E S E I M V .......... Protein_Len: 50 Strand: - Start: 35 End: 184 .................................. L N K A F I A F I K K F F S S I L V S K V R L L I W Y G L L C K R S Y I R D K E I T L F R F L P I M ...... Protein_Len: 33 Strand: - Start: 30 End: 128 ............................. R V L K Q C I N C L N K Q F F Q Q H S S I E C S S S D L I R T S M .............................................................. aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc 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: 84 Start: 29 End: 58 ............................TTTGCAATATTTGCCAAAAACTTGTAAGAT.................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 121 End: 150 ........................................................................................................................GTAGACATTTCCTGCTATAAATTCTATCCT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -3.3 Tail_Score: -5.40072 Start: 40 End: 60 Full_Region: TTCTATCTTACAAGT TTTTGGCAA ATA TTGCAAAGA TTTTTTTGAAAAAAC .......................................TTTTGGCAAATATTGCAAAGA.................................................................................................................................. Find igs database================================================ Query_seq: SSA_1232:SSA_1233|SSA_1232:SSA_1233:Topoisomerase IV subunit B, putative:Membrane protein, YqiH family, putative:<-->:1256846..1257035 190 aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_009009_SSA_1232_SSA_1233|Topoisomerase IV subunit B, putative:Membrane protein, YqiH family, putative|NEGATIVE:POSITIVE|[1256846,1257035]|190 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagannnnnnngaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc aagaacctcctaatgattcatcttttctatcttacaagtttttggcaaatattgcaaagatttttttgaaaaaactgctgatgagaactgatttcacacgaagaagaatccaatatccgagtagacatttcctgctataaattctatccttttctattgtcagaaagcgaaataatggtataataaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAACCUCCUAAUGAUUCAUCUUUUCUAUCUUACAAGUUUUUGGCAAAUAUUGCAAAGAUUUUUUUGAAAAAACUGCUGAUGAGAACUGAUUUCACACGAAGAAGAAUCCAAUAUCCGAGUAGACAUUUCCUGCUAUAAAUUCUAUCCUUUUCUAUUGUCAGAAAGCGAAAUAAUGGUAUAAUAAAAUC ....(((.......(((((.(((((...........(((((((((((.......(((((....))))).......))))...)))))))..........))))).))))).........(((((.......)))))..........((.((((((......)))))).))......)))........... (-27.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUAUUAUACCAUUAUUUCGCUUUCUGACAAUAGAAAAGGAUAGAAUUUAUAGCAGGAAAUGUCUACUCGGAUAUUGGAUUCUUCUUCGUGUGAAAUCAGUUCUCAUCAGCAGUUUUUUCAAAAAAAUCUUUGCAAUAUUUGCCAAAAACUUGUAAGAUAGAAAAGAUGAAUCAUUAGGAGGUUCUU ......................(((((((((.....((..(((((.((.((((((..(((((..(((((.........)))))..)))))..)))))).)).)))))..))....((((((((......(((((.((((..(((....)))..))))))))).))))))))......))))))))).... (-30.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 855 120 71 211 162 NC_009009:SSA_1232|5end_Topoisomerase_IV_subunit_B,_putative_1256755..1256985_NEGATIVE 282 125 83 76 20 NC_009009:SSA_0397|5end_hypothetical_protein_394657..394887_NEGATIVE 280 168 126 175 129 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 261 67 21 141 97 NC_009009:SSA_1339|5end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1355424..1355654_NEGATIVE 259 120 71 183 140 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 256 155 134 108 87 NC_009009:SSA_0160|5end_hypothetical_protein_158735..158965_POSITIVE 253 138 98 158 124 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 250 50 7 125 86 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 249 47 7 217 177 NC_009009:SSA_0381|5end_hypothetical_protein_372763..372993_POSITIVE 248 49 1 123 68 NC_009009:SSA_0615|5end_RggD,_putative_609195..609425_NEGATIVE 247 137 100 78 40 NC_009009:SSA_0992|5end_hypothetical_protein_993486..993716_POSITIVE 247 112 73 227 179 NC_009009:SSA_0934|5end_HydD,_putative_943208..943438_POSITIVE 246 179 142 138 106 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 241 82 43 210 166 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 241 87 41 192 144 NC_009009:SSA_0937|5end_Arsenate_reductase,_glutaredoxin_family,_putative_946183..946413_POSITIVE 238 48 6 130 72 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 236 162 122 167 115 NC_009009:SSA_1221|5end_L-lactate_dehydrogenase,_putative_1243956..1244186_POSITIVE 235 136 102 204 171 NC_009009:SSA_1428|5end_hypothetical_protein_1436348..1436578_NEGATIVE 229 186 142 131 87 NC_009009:SSA_1211|5end_hypothetical_protein_1234695..1234925_POSITIVE 229 62 21 148 100 NC_009009:SSA_0655|5end_Cell_division_protein_FtsA,_putative_638784..639014_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 125 83 59 3 NC_009009:SSA_0398|3end_hypothetical_protein_394674..394824_NEGATIVE 268 177 131 55 12 NC_009009:SSA_0442|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_443030..443180_POSITIVE 261 67 21 131 87 NC_009009:SSA_1340|3end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1355434..1355584_NEGATIVE 254 126 83 65 26 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 250 50 7 109 70 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 246 179 142 129 97 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 246 119 75 126 74 NC_009009:SSA_0156|3end_ATPase_with_chaperone_activity,_ATP-binding_subunit,_putative_153322..153472_POSITIVE 241 87 41 80 32 NC_009009:SSA_0936|3end_FAD_synthase,_putative_946151..946301_POSITIVE 238 48 6 143 85 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 236 44 1 104 56 NC_009009:SSA_1724|3end_CBS_domain_protein,_putative_1709897..1710047_NEGATIVE 228 170 123 94 47 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 228 45 4 54 15 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 227 170 128 50 2 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 226 118 76 99 54 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 225 45 8 150 111 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 223 61 21 139 100 NC_009009:SSA_0560|3end_hypothetical_protein_553717..553867_POSITIVE 221 170 128 55 21 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 221 170 124 64 20 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 220 138 101 94 52 NC_009009:SSA_2339|3end_Microcin_C7_resistance_protein,_putative_2341489..2341639_POSITIVE 219 46 7 120 70 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE