Origin IGS: gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaattttgatttcttcctccatatgctagagtttgatatcaaattttagtgtcatcttaaagtagtcatattttgtcagtcttcttttttctgaattattgaaattgattagaacctctactattttattgatatgagctagtttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta .........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 tagaaaaagttggagtactgagctccaactttttctattatgtgactgaaagtcacataataaactagctcatatcaataaaatagtagaggttctaatcaatttcaataattcagaaaaaagaagactgacaaaatatgactactttaagatgacactaaaatttgatatcaaactctagcatatggaggaagaaatcaaaattaatggataggtgattacggatataaagttataagacttgaaactttatttcatagac Mask Tandem Repeat Region ================================================ gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaattttgatttcttcctccatatgctagagtttgatatcaaattttagtgtcatcttaaagtagtcatattttgtcagtcttcttttttctgaattattgaaattgattagaacctctactattttattgatatgagctagtttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta Find is-nt database================================================ Query_seq: SMT_1777:SMT_1778|SMT_1777:SMT_1778:hypothetical protein:ATP-dependent RNA helicase:-><-:1753439..1753700 262 gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaattttgatttcttcctccatatgctagagtttgatatcaaattttagtgtcatcttaaagtagtcatattttgtcagtcttcttttttctgaattattgaaattgattagaacctctactattttattgatatgagctagtttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1777:SMT_1778|SMT_1777:SMT_1778:hypothetical protein:ATP-dependent RNA helicase:-><-:1753439..1753700 262 gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaattttgatttcttcctccatatgctagagtttgatatcaaattttagtgtcatcttaaagtagtcatattttgtcagtcttcttttttctgaattattgaaattgattagaacctctactattttattgatatgagctagtttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1777:SMT_1778|SMT_1777:SMT_1778:hypothetical protein:ATP-dependent RNA helicase:-><-:1753439..1753700 262 gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaattttgatttcttcctccatatgctagagtttgatatcaaattttagtgtcatcttaaagtagtcatattttgtcagtcttcttttttctgaattattgaaattgattagaacctctactattttattgatatgagctagtttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 61 Max: 198 Len: 138 Subject: UniRef90_Q9FDV4 Cluster: SrtI; n=8; Streptococcus pyogenes|Rep: SrtI - Streptococcus pyogenes HSP 1 e-value: 6.0E-6 bit: 52.0 Len: 138 Query Start:61 Query End:198 Subject Strand: null Subject Start: 15 Subject End: 62 ............................................................ L A H I N K I V E V L I N F N N S - - E K R R L T K Y D Y F K M T L K F D I K L * H M E E E I K ................................................................ ............................................................ I A H L N K V A E V L L N L N N N D I E N R R L A R Y D Y A K M N L T A A I K I E E V E K E I E ................................................................ gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 85 End: 189 .................................................................................... L K I D F K L T M K F Y D Y K T L R R K E S N N F N I L V E V I K N M ......................................................................... gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta 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: 81 Start: 154 End: 183 .........................................................................................................................................................ATTGAAATTGATTAGAACCTCTACTATTTT............................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1777:SMT_1778|SMT_1777:SMT_1778:hypothetical protein:ATP-dependent RNA helicase:-><-:1753439..1753700 262 gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: smit_SMT_1777_SMT_1778|hypothetical protein:ATP-dependent RNA helicase|POSITIVE:NEGATIVE|[1753439,1753700]|262 HSP 1 e-value: 2.0E-28 bit: 127.0 Len: 64 Query Start:199 Query End:262 Subject Strand: POSITIVE Subject Start: 199 Subject End: 262 ......................................................................................................................................................................................................tttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta ......................................................................................................................................................................................................tttattatgtgactttcagtcacataatagaaaaagttggagctcagtactccaactttttcta HSP 2 e-value: 5.0E-26 bit: 119.0 Len: 60 Query Start:1 Query End:60 Subject Strand: POSITIVE Subject Start: 1 Subject End: 60 gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaat.......................................................................................................................................................................................................... gtctatgaaataaagtttcaagtcttataactttatatccgtaatcacctatccattaat.......................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUAUGAAAUAAAGUUUCAAGUCUUAUAACUUUAUAUCCGUAAUCACCUAUCCAUUAAUUUUGAUUUCUUCCUCCAUAUGCUAGAGUUUGAUAUCAAAUUUUAGUGUCAUCUUAAAGUAGUCAUAUUUUGUCAGUCUUCUUUUUUCUGAAUUAUUGAAAUUGAUUAGAACCUCUACUAUUUUAUUGAUAUGAGCUAGUUUAUUAUGUGACUUUCAGUCACAUAAUAGAAAAAGUUGGAGCUCAGUACUCCAACUUUUUCUA (..((((..((((((((...........))))))))...))))..)......................((..(((.....(((((((((((....)))))))))))((((...(((((((((....((((((((((.(((................)))))))).))))).....))))))))).))))..)))..))..(((((((((((.....)))))))))))(((((((((((((.......))))))))))))).. (-60.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAAGUUGGAGUACUGAGCUCCAACUUUUUCUAUUAUGUGACUGAAAGUCACAUAAUAAACUAGCUCAUAUCAAUAAAAUAGUAGAGGUUCUAAUCAAUUUCAAUAAUUCAGAAAAAAGAAGACUGACAAAAUAUGACUACUUUAAGAUGACACUAAAAUUUGAUAUCAAACUCUAGCAUAUGGAGGAAGAAAUCAAAAUUAAUGGAUAGGUGAUUACGGAUAUAAAGUUAUAAGACUUGAAACUUUAUUUCAUAGAC ((((((((((((((((.....)))))))))))))))).((((((((.....)))))))).((((.(((.((((((.............((((((......))))))......((((...........))))....))))))))).)))).(((.((.(((((.((((((.((...(((((.....)))))...)).)))))).))......))))).)))...((.((((((((.((.....)).)))))))).))...... (-60.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 467 170 126 170 127 smit:SMT_733|5end_hypothetical_protein_639798..640028_NEGATIVE 286 77 33 184 146 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 267 109 61 82 35 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 265 240 192 57 20 smit:SMT_1828|5end_PTS_system,_galactose-specific_IIC_component_1797668..1797898_POSITIVE 260 220 171 160 98 smit:SMT_1833|5end_tagatose_1,6-diphosphate_aldolase_1801369..1801599_POSITIVE 260 148 104 227 192 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 253 89 43 74 28 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 248 55 14 194 148 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 248 152 114 201 153 smit:SMT_403|5end_two-component_sensor_kinase_YesM_331580..331810_POSITIVE 244 99 52 226 180 smit:SMT_455|5end_cation_transport_ATPase_391670..391900_POSITIVE 243 139 91 95 58 smit:SMT_1958|5end_tryptophan_synthase,_beta_subunit_1890980..1891210_POSITIVE 239 260 229 158 127 smit:SMT_1338|5end_K05832_putative_ABC_transport_system_permease_protein_1313675..1313905_NEGATIVE 235 77 31 139 93 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 233 257 211 158 106 smit:SMT_924|5end_primosomal_protein_N'_879903..880133_NEGATIVE 228 120 73 222 172 smit:SMT_439|5end_hypothetical_protein_predicted_by_Glimmer/Critica_379387..379617_POSITIVE 225 150 107 62 13 smit:SMT_783|5end_K03710_GntR_family_transcriptional_regulator_694611..694841_POSITIVE 224 74 31 106 71 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 224 74 31 106 71 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 224 90 44 113 77 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 223 100 52 122 73 smit:SMT_1740|5end_choline_binding_protein_PcpA_1722354..1722584_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 89 43 62 16 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 239 260 229 82 51 smit:SMT_1339|3end_hypothetical_protein_1313751..1313901_NEGATIVE 235 77 31 146 100 smit:SMT_974|3end_DNA-binding_response_regulator_922170..922320_NEGATIVE 233 257 211 92 40 smit:SMT_925|3end_DNA-directed_RNA_polymerase_omega_chain_879969..880119_NEGATIVE 232 258 223 71 37 smit:SMT_246|3end_alcohol_dehydrogenase_182198..182348_NEGATIVE 228 120 73 132 82 smit:SMT_438|3end_hypothetical_protein_predicted_by_Glimmer/Critica_379377..379527_POSITIVE 224 74 31 106 71 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 224 74 31 106 71 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 221 85 44 138 90 smit:SMT_1960|3end_UDP-galactopyranose_mutase_1894094..1894244_POSITIVE 217 89 44 133 95 smit:SMT_1043|3end_chaperonin_GroEL_985110..985260_NEGATIVE 215 240 195 141 91 smit:SMT_1572|3end_excinuclease_ABC_subunit_B_1566470..1566620_POSITIVE 215 112 71 126 95 smit:SMT_1564|3end_transcriptional_antiterminator,_BglG_family_1557697..1557847_POSITIVE 214 108 63 101 48 smit:SMT_800|3end_glycyl-tRNA_synthetase_beta_chain_707596..707746_NEGATIVE 213 140 94 149 107 smit:SMT_1139|3end_rRNA_(guanine-N1-)-methyltransferase_1080683..1080833_POSITIVE 210 146 105 92 53 smit:SMT_1422|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1407357..1407507_NEGATIVE 210 147 108 82 44 smit:SMT_487|3end_transcriptional_regulator,_TetR_family_423017..423167_POSITIVE 208 150 104 118 56 smit:SMT_935|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_888749..888899_POSITIVE 207 198 152 98 47 smit:SMT_1361|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1338730..1338880_NEGATIVE 205 238 195 68 24 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 204 92 53 121 72 smit:SMT_1915|3end_pyridoxine_biosynthesis_protein_1860618..1860768_POSITIVE