Origin IGS: cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtctactccttttgtcgtatatagaaatagtatagcaaaaaatcccccaaaatgtctttgggggagaaggataagtcagtattttttagatgtctatcacttaaggataaaag Mask Tandem Repeat Region ================================================ cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Find is-nt database================================================ Query_seq: SSA_2050:SSA_2051|SSA_2050:SSA_2051:Arabinose efflux permease, putative:Oligoendopeptidase, putative:->->:2054757..2054870 114 cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2050:SSA_2051|SSA_2050:SSA_2051:Arabinose efflux permease, putative:Oligoendopeptidase, putative:->->:2054757..2054870 114 cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2050:SSA_2051|SSA_2050:SSA_2051:Arabinose efflux permease, putative:Oligoendopeptidase, putative:->->:2054757..2054870 114 cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Predict ORF larger than 30AA ================================================ cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact 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================================================ cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.8 Tail_Score: -5.23316 Start: 49 End: 71 Full_Region: ACTGACTTATCCTTC TCCCCCAAAG ACA TTTTGGGGGA TTTTTTGCTATACTA ................................................TCCCCCAAAGACATTTTGGGGGA........................................... Find igs database================================================ Query_seq: SSA_2050:SSA_2051|SSA_2050:SSA_2051:Arabinose efflux permease, putative:Oligoendopeptidase, putative:->->:2054757..2054870 114 cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_009009_SSA_2050_SSA_2051|Arabinose efflux permease, putative:Oligoendopeptidase, putative|POSITIVE:POSITIVE|[2054757,2054870]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact cttttatccttaagtgatagacatctaaaaaatactgacttatccttctcccccaaagacattttgggggattttttgctatactatttctatatacgacaaaaggagtagact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUAUCCUUAAGUGAUAGACAUCUAAAAAAUACUGACUUAUCCUUCUCCCCCAAAGACAUUUUGGGGGAUUUUUUGCUAUACUAUUUCUAUAUACGACAAAAGGAGUAGACU ..(((((((....).))))))...........................((((((((((...))))))))))............((((((((............))))))))... (-22.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUACUCCUUUUGUCGUAUAUAGAAAUAGUAUAGCAAAAAAUCCCCCAAAAUGUCUUUGGGGGAGAAGGAUAAGUCAGUAUUUUUUAGAUGUCUAUCACUUAAGGAUAAAAG .(.((..(((((((((..(((.((....)))))..)))))...(((((((((.....)))))))))..))))..)).)..(((((((.((.((.....)))).))))))).... (-27.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 76 35 50 7 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 284 88 44 212 151 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 274 79 47 230 191 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 269 110 67 207 165 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 267 56 16 106 65 NC_009009:SSA_2218|5end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219941..2220171_NEGATIVE 266 90 45 94 43 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 261 90 42 83 24 NC_009009:SSA_1829|5end_RNA_methyltransferase,_putative_1820329..1820559_NEGATIVE 259 80 35 80 22 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 258 80 36 44 3 NC_009009:SSA_0091|5end_V-type_sodium_ATPase,_subunit_A,_putative_91037..91267_POSITIVE 248 68 29 57 11 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 247 60 13 110 61 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 247 60 15 202 154 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 245 72 35 229 195 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 245 85 44 71 12 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 242 80 32 124 80 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 235 80 40 132 88 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 235 80 34 111 66 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 232 109 63 51 3 NC_009009:SSA_0158|5end_hypothetical_protein_153801..154031_POSITIVE 229 69 23 52 2 NC_009009:SSA_0081|5end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_85071..85301_NEGATIVE 228 82 41 141 98 NC_009009:SSA_0378|5end_TRZ/ATZ_family_hydrolase,_putative_367276..367506_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 76 35 84 41 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 274 79 47 111 72 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 267 56 16 80 39 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 266 90 45 101 50 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 263 90 42 80 34 NC_009009:SSA_0778|3end_Glycogen_synthase,_putative_762076..762226_POSITIVE 258 79 35 151 101 NC_009009:SSA_0301|3end_hypothetical_protein_294753..294903_POSITIVE 247 60 13 91 42 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 245 71 49 42 20 NC_009009:SSA_2050|3end_Arabinose_efflux_permease,_putative_2054696..2054846_POSITIVE 243 72 39 46 2 NC_009009:SSA_1708|3end_hypothetical_protein_1698194..1698344_NEGATIVE 242 80 32 68 24 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 237 80 32 124 72 NC_009009:SSA_0917|3end_Cobalamin-independent_methionine_synthase_II,_putative_929087..929237_NEGATIVE 237 73 35 47 2 NC_009009:SSA_0560|3end_hypothetical_protein_553717..553867_POSITIVE 235 80 40 130 86 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 235 80 34 148 103 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 223 109 62 47 2 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 217 80 47 55 31 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 215 70 36 113 81 NC_009009:SSA_2254|3end_Holliday_junction_DNA_helicase_ruvA,_putative_2249434..2249584_NEGATIVE 215 81 45 136 103 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 215 66 26 90 41 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 213 80 36 132 71 NC_009009:SSA_1655|3end_hypothetical_protein_1651391..1651541_NEGATIVE