Origin IGS: aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataactcctttcataggatactggtttctaattaaaacctaaactatatatgttttctattgataaattcaaagggggatttgaattccaccccccttgaacaaatttt Mask Tandem Repeat Region ================================================ aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Find is-nt database================================================ Query_seq: SMT_1142:SMT_1143|SMT_1142:SMT_1143:K02027 multiple sugar transport system substrate-binding protein:K02025 multiple sugar transport system permease protein:->->:1086958..1087067 110 aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1142:SMT_1143|SMT_1142:SMT_1143:K02027 multiple sugar transport system substrate-binding protein:K02025 multiple sugar transport system permease protein:->->:1086958..1087067 110 aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1142:SMT_1143|SMT_1142:SMT_1143:K02027 multiple sugar transport system substrate-binding protein:K02025 multiple sugar transport system permease protein:->->:1086958..1087067 110 aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Predict ORF larger than 30AA ================================================ aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt 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: 50 End: 79 .................................................ATAGAAAACATATATAGTTTAGGTTTTAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1142:SMT_1143|SMT_1142:SMT_1143:K02027 multiple sugar transport system substrate-binding protein:K02025 multiple sugar transport system permease protein:->->:1086958..1087067 110 aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: smit_SMT_1142_SMT_1143|K02027 multiple sugar transport system substrate-binding protein:K02025 multiple sugar transport system permease protein|POSITIVE:POSITIVE|[1086958,1087067]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt aaaatttgttcaaggggggtggaattcaaatccccctttgaatttatcaatagaaaacatatatagtttaggttttaattagaaaccagtatcctatgaaaggagttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUGUUCAAGGGGGGUGGAAUUCAAAUCCCCCUUUGAAUUUAUCAAUAGAAAACAUAUAUAGUUUAGGUUUUAAUUAGAAACCAGUAUCCUAUGAAAGGAGUUAUU ...((..((((((((((((..(....)....))))))))))))..)).......................((((((.....))))))....((((.....))))...... (-27.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAACUCCUUUCAUAGGAUACUGGUUUCUAAUUAAAACCUAAACUAUAUAUGUUUUCUAUUGAUAAAUUCAAAGGGGGAUUUGAAUUCCACCCCCCUUGAACAAAUUUU ...........((((((((.((.(((((.......)))))............)).))))).)))....(((((.(((((............))))).)))))........ (-19.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 41 11 214 181 smit:SMT_2113|5end_peptidyl-tRNA_hydrolase_2001191..2001421_NEGATIVE 266 40 1 179 142 smit:SMT_1247|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1207409..1207639_POSITIVE 261 36 2 231 184 smit:SMT_1120|5end_hypothetical_protein_1057063..1057293_NEGATIVE 232 41 11 75 45 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 229 42 8 214 174 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 228 34 10 54 37 smit:SMT_1528|5end_K03310_alanine_or_glycine:cation_symporter,_AGCS_family_1512667..1512897_NEGATIVE 223 45 2 59 17 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 219 56 13 52 4 smit:SMT_117|5end_K02025_multiple_sugar_transport_system_permease_protein_68487..68717_POSITIVE 218 48 3 198 156 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 212 46 12 157 129 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 208 41 13 95 65 smit:SMT_2161|5end_DNA_mismatch_repair_protein_2034946..2035176_POSITIVE 207 49 7 205 161 smit:SMT_1879|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836806..1837036_NEGATIVE 207 41 9 164 131 smit:SMT_992|5end_hypothetical_protein_934882..935112_NEGATIVE 206 35 15 160 145 smit:SMT_2053|5end_hypothetical_membrane_associated_protein_1964422..1964652_NEGATIVE 205 37 3 193 155 smit:SMT_2042|5end_K04077_chaperonin_GroEL_(Hsp60)_1953889..1954119_NEGATIVE 200 59 13 214 168 smit:SMT_240|5end_glutamate_synthase_small_subunit,_putative_177875..178105_POSITIVE 199 48 11 197 165 smit:SMT_308|5end_trans-2-enoyl-ACP_reductase_II_249439..249669_POSITIVE 198 107 69 101 68 smit:SMT_1792|5end_K03307_solute:Na+_symporter,_SSS_family_1767774..1768004_NEGATIVE 198 107 69 101 68 smit:SMT_1175|5end_K03307_solute:Na+_symporter,_SSS_family_1127660..1127890_NEGATIVE 198 41 10 163 133 smit:SMT_955|5end_acyltransferase_family_protein_904096..904326_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 42 6 82 41 smit:SMT_1142|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1086897..1087047_POSITIVE 218 48 3 95 53 smit:SMT_1531|3end_hypothetical_protein_1515449..1515599_NEGATIVE 212 46 12 101 73 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 212 46 12 101 73 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 205 37 3 69 31 smit:SMT_2043|3end_putative_mucus_binding_protein_1954013..1954163_NEGATIVE 203 46 7 97 53 smit:SMT_625|3end_50S_ribosomal_protein_L27_530400..530550_POSITIVE 200 59 13 47 1 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 199 48 11 79 47 smit:SMT_307|3end_K02078_acyl_carrier_protein_249401..249551_POSITIVE 198 107 69 99 66 smit:SMT_1176|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1127662..1127812_NEGATIVE 196 46 5 97 59 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 195 58 15 48 3 smit:SMT_328|3end_23S_rRNA_methyltransferase_264863..265013_POSITIVE 194 40 13 138 107 smit:SMT_1539|3end_sensor_histidine_kinase,_putative_1523315..1523465_NEGATIVE 193 33 5 90 59 smit:SMT_1542|3end_phosphomevalonate_kinase_1526077..1526227_NEGATIVE 192 39 12 81 49 smit:SMT_1779|3end_hypothetical_protein_1755093..1755243_NEGATIVE 191 41 11 71 38 smit:SMT_92|3end_GTP-binding_protein,_probable_translation_factor_24052..24202_POSITIVE 190 48 14 150 116 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 190 40 12 74 42 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 189 43 13 86 49 smit:SMT_1371|3end_hypothetical_protein_1350579..1350729_NEGATIVE 187 34 1 140 112 smit:SMT_638|3end_hypothetical_protein_543180..543330_NEGATIVE 187 107 64 80 29 smit:SMT_112|3end_hypothetical_protein_predicted_by_Glimmer/Critica_61378..61528_NEGATIVE