Origin IGS: agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggcaagagattaaaaaaatttcactccaaaggttagaaagaactctaacttttggagtttttttatatcaattcttgctgattttgactctttttccgaataataaggtaaggaggtttct Mask Tandem Repeat Region ================================================ agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct Find is-nt database================================================ Query_seq: SSA_1218:SSA_1219|SSA_1218:SSA_1219:DNA repair protein radC, putative:Sortase, putative:<-<-:1240550..1240671 122 agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1218:SSA_1219|SSA_1218:SSA_1219:DNA repair protein radC, putative:Sortase, putative:<-<-:1240550..1240671 122 agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1218:SSA_1219|SSA_1218:SSA_1219:DNA repair protein radC, putative:Sortase, putative:<-<-:1240550..1240671 122 agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 3 End: 113 .. F R R V K N N P F L T L I L L F Q Y L F V G F T L T R E L R Q L S I K K M ......... agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct 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================================================ agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1218:SSA_1219|SSA_1218:SSA_1219:DNA repair protein radC, putative:Sortase, putative:<-<-:1240550..1240671 122 agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaatttttttaatctcttgcct Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: NC_009009_SSA_1218_SSA_1219|DNA repair protein radC, putative:Sortase, putative|NEGATIVE:NEGATIVE|[1240550,1240671]|122 HSP 1 e-value: 2.0E-39 bit: 163.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatatnnnnnnnctccaaaagttagagttctttctaacctttggagtgaaa................... agaaacctccttaccttattattcggaaaaagagtcaaaatcagcaagaattgatataaaaaaactccaaaagttagagttctttctaacctttggagtgaaa................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAACCUCCUUACCUUAUUAUUCGGAAAAAGAGUCAAAAUCAGCAAGAAUUGAUAUAAAAAAACUCCAAAAGUUAGAGUUCUUUCUAACCUUUGGAGUGAAA .......(((..............)))......(((((..((.....)).)))))........((((((((.(((((((....))))))).)))))))).... (-20.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCACUCCAAAGGUUAGAAAGAACUCUAACUUUUGGAGUUUUUUUAUAUCAAUUCUUGCUGAUUUUGACUCUUUUUCCGAAUAAUAAGGUAAGGAGGUUUCU ....(((((((((((((((......))))))))))))))).........((((.((.....))..))))((((((..((.........)).))))))...... (-28.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 50 1 141 92 NC_009009:SSA_1218|5end_DNA_repair_protein_radC,_putative_1240459..1240689_NEGATIVE 352 50 6 135 96 NC_009009:SSA_0184|5end_Competence_protein_ComYA,_putative_188156..188386_POSITIVE 323 28 1 45 20 NC_009009:SSA_2246|5end_Competence-damage_protein,_putative_2242496..2242726_NEGATIVE 314 100 57 139 93 NC_009009:SSA_1361|5end_ORFA,_transposon_ISSsa2_1377168..1377398_POSITIVE 314 100 57 139 93 NC_009009:SSA_0573|5end_hypothetical_protein_568732..568962_NEGATIVE 314 100 57 139 93 NC_009009:SSA_0265|5end_ORFA,_transposon_ISSsa1_259391..259621_POSITIVE 262 57 23 207 174 NC_009009:SSA_0293|5end_hypothetical_protein_287613..287843_NEGATIVE 242 45 7 120 80 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 240 54 24 196 165 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 232 40 6 132 99 NC_009009:SSA_0214|5end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210215..210445_POSITIVE 231 58 11 147 96 NC_009009:SSA_1185|5end_DNA_processing_Smf_protein,_putative_1214532..1214762_NEGATIVE 224 50 8 227 167 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 214 47 8 152 117 NC_009009:SSA_1848|5end_Methionyl-tRNA_formyltransferase,_putative_1843178..1843408_NEGATIVE 212 46 6 90 48 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 210 50 8 144 105 NC_009009:SSA_2167|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2167371..2167601_NEGATIVE 205 55 28 182 147 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 204 100 65 135 98 NC_009009:SSA_1925|5end_Seryl-tRNA_synthetase,_putative_1913508..1913738_POSITIVE 202 45 6 228 192 NC_009009:SSA_1789|5end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772856..1773086_NEGATIVE 202 100 73 159 132 NC_009009:SSA_0443|5end_Possible_ABC-type_efflux_pump_permease_component,_putative_442877..443107_POSITIVE 201 49 7 222 177 NC_009009:SSA_0381|5end_hypothetical_protein_372763..372993_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 100 53 64 17 NC_009009:SSA_0617|3end_Membrane_protease_subunits,_stomatin/prohibitin-like_protein_(SPFH_domain/band_7_family),_putative_611438..611588_POSITIVE 314 100 57 61 15 NC_009009:SSA_1360|3end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1377170..1377320_POSITIVE 314 100 57 70 24 NC_009009:SSA_0574|3end_YdjX_protein,_putative_568801..568951_NEGATIVE 296 100 64 44 5 NC_009009:SSA_0264|3end_PEP_phosphonomutase-like_protein,_putative_259376..259526_POSITIVE 262 57 23 48 15 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 257 50 6 72 33 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 242 45 7 148 108 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 221 48 8 145 100 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 214 47 8 68 33 NC_009009:SSA_1849|3end_Primosomal_protein_N',_putative_1843262..1843412_NEGATIVE 208 100 57 89 36 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 203 100 70 34 1 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE 199 45 6 134 86 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 195 99 51 78 41 NC_009009:SSA_1302|3end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1321762..1321912_NEGATIVE 194 49 6 132 85 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 193 45 3 133 93 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 190 35 7 58 22 NC_009009:SSA_0329|3end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_323815..323965_POSITIVE 184 48 5 83 43 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 184 98 55 114 65 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 183 89 51 88 46 NC_009009:SSA_1542|3end_Peptidase,_U32_family,_putative_1546825..1546975_NEGATIVE 183 68 25 63 8 NC_009009:SSA_1222|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1245038..1245188_NEGATIVE