Origin IGS: tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctcttcctccttttattataccacagttttaaatctaggttttctagattctctggctctatctatttattcggaaaagagatgaaaaaacctgagaatcatctcaggcttggtca Mask Tandem Repeat Region ================================================ tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Find is-nt database================================================ Query_seq: SMT_107:SMT_108|SMT_107:SMT_108:ribose-phosphate pyrophosphokinase:hypothetical protein:->->:53511..53627 117 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_107:SMT_108|SMT_107:SMT_108:ribose-phosphate pyrophosphokinase:hypothetical protein:->->:53511..53627 117 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_107:SMT_108|SMT_107:SMT_108:ribose-phosphate pyrophosphokinase:hypothetical protein:->->:53511..53627 117 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Predict ORF larger than 30AA ================================================ tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg 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================================================ tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_107:SMT_108|SMT_107:SMT_108:ribose-phosphate pyrophosphokinase:hypothetical protein:->->:53511..53627 117 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: smit_SMT_107_SMT_108|ribose-phosphate pyrophosphokinase:hypothetical protein|POSITIVE:POSITIVE|[53511,53627]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaaggaggaagagg Inter-species Hit: Count: 2 Min: 1 Max: 106 Len: 106 Subject: NC_003028_SP_0027_SP_0029|ribose-phosphate pyrophosphokinase:hypothetical protein|POSITIVE:NEGATIVE|[29831,30371]|541 HSP 1 e-value: 5.0E-30 bit: 131.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaa........... tgaccaagcctgagatgattctcaggttttttcgtcttttttccgaataaatagatagtagcggtgaatctagtaaagctagatttaaaactgtgatataataaaa........... Subject: NC_008533_SPD_0033_SPD_0035|ribose-phosphate pyrophosphokinase:hypothetical protein|POSITIVE:NEGATIVE|[29603,30142]|540 HSP 1 e-value: 3.0E-25 bit: 115.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 tgaccaagcctgagatgattctcaggttttttcatctcttttccgaataaatagatagagccagagaatctagaaaacctagatttaaaactgtggtataataaaa........... tgaccaagcctgagatgattctcagg-tttttcgtcttttttccgaataaatagatagtagcggtgaatctagtaaagctagatttaaaactgtgatataataaaa........... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACCAAGCCUGAGAUGAUUCUCAGGUUUUUUCAUCUCUUUUCCGAAUAAAUAGAUAGAGCCAGAGAAUCUAGAAAACCUAGAUUUAAAACUGUGGUAUAAUAAAA (((..((((((((((....))))))))))..))).........................((((.(((((((((.....))))))).....)).))))......... (-28.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUAUACCACAGUUUUAAAUCUAGGUUUUCUAGAUUCUCUGGCUCUAUCUAUUUAUUCGGAAAAGAGAUGAAAAAACCUGAGAAUCAUCUCAGGCUUGGUCA .............(((.....(((((((.....)))))))..))).((((.(((........)))..))))..((..((.(((((((....))))))).))..)). (-23.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 596 86 41 171 126 smit:SMT_1218|5end_DNA_polymerase_I_1179357..1179587_NEGATIVE 311 44 1 61 19 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 293 60 17 167 123 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 282 44 1 227 182 smit:SMT_1865|5end_D-alanyl_carrier_protein_1827058..1827288_POSITIVE 282 44 1 230 185 smit:SMT_1312|5end_D-alanyl_carrier_protein_1277042..1277272_POSITIVE 280 50 4 68 19 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 278 70 24 55 1 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 278 70 24 134 80 smit:SMT_1209|5end_choline_binding_protein_PcpA_1170972..1171202_NEGATIVE 271 46 7 197 153 smit:SMT_1560|5end_DNA_polymerase_III_alpha_subunit_1548612..1548842_NEGATIVE 265 66 21 197 158 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 263 44 2 106 56 smit:SMT_770|5end_K02053_spermidine/putrescine_transport_system_permease_protein_681359..681589_NEGATIVE 262 50 3 138 92 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 257 47 1 110 57 smit:SMT_2076|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1978592..1978822_NEGATIVE 257 47 1 217 164 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 254 60 19 159 117 smit:SMT_1188|5end_hypothetical_protein_1146653..1146883_NEGATIVE 253 44 8 217 188 smit:SMT_772|5end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_683300..683530_NEGATIVE 250 47 9 68 32 smit:SMT_1396|5end_uracil-DNA_glycosylase_1372064..1372294_POSITIVE 250 97 54 176 122 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 250 97 54 80 26 smit:SMT_470|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_407303..407533_NEGATIVE 248 78 31 139 87 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 46 7 104 55 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 293 38 9 92 58 smit:SMT_298|3end_penicillin-binding_protein_1A_240719..240869_NEGATIVE 278 70 24 147 93 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 277 66 24 81 30 smit:SMT_594|3end_lysyl-tRNA_synthetase_510348..510498_NEGATIVE 277 46 1 107 57 smit:SMT_107|3end_ribose-phosphate_pyrophosphokinase_53450..53600_POSITIVE 271 46 7 63 19 smit:SMT_1561|3end_putative_mucus_binding_protein_1548746..1548896_NEGATIVE 265 66 21 82 43 smit:SMT_430|3end_hypothetical_protein_372164..372314_POSITIVE 263 44 2 109 59 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 262 50 3 59 13 smit:SMT_383|3end_cysteinyl-tRNA_synthetase_319407..319557_POSITIVE 254 60 19 149 107 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 253 44 8 57 28 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 250 97 54 67 13 smit:SMT_480|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416765..416915_NEGATIVE 247 47 1 111 55 smit:SMT_1372|3end_hypothetical_protein_1350803..1350953_NEGATIVE 238 37 6 87 54 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 234 97 51 105 67 smit:SMT_1106|3end_ribonuclease_P_protein_component_1047601..1047751_NEGATIVE 230 36 5 44 17 smit:SMT_1832|3end_tagatose-6-phosphate_kinase_1801447..1801597_POSITIVE 229 66 32 51 7 smit:SMT_1034|3end_K05896_segregation_and_condensation_protein_A_976768..976918_NEGATIVE 229 95 53 73 29 smit:SMT_819|3end_hypothetical_protein_predicted_by_Glimmer/Critica_729966..730116_NEGATIVE 227 36 2 78 41 smit:SMT_1583|3end_polysaccharide_transporter,_PST_family_1574609..1574759_POSITIVE 226 49 1 63 10 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE