Origin IGS: tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatttctctcttattctatttgtttctcctattatatcatgcctcttcatcattgaaaagtggacttcacaagactatactattcccaaatgtatcaaaaaaccttgcaactaggttacaaggttaatgaca Mask Tandem Repeat Region ================================================ tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Find is-nt database================================================ Query_seq: SMT_1386:SMT_1387|SMT_1386:SMT_1387:phosphoenolpyruvate-protein phosphotransferase:hypothetical protein:->->:1364671..1364802 132 tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1386:SMT_1387|SMT_1386:SMT_1387:phosphoenolpyruvate-protein phosphotransferase:hypothetical protein:->->:1364671..1364802 132 tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1386:SMT_1387|SMT_1386:SMT_1387:phosphoenolpyruvate-protein phosphotransferase:hypothetical protein:->->:1364671..1364802 132 tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 22 End: 120 ..................... N C P K K I C K P I T Y D Q S T W K E I I F L C S I I P S V F L M ............ Protein_Len: 41 Strand: - Start: 9 End: 131 ........ G Q L R T A L N K S V N P F L I T K H L G S K L S S S A H Y L L L F L Y F L L S M . tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc 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: 83 Start: 52 End: 81 ...................................................ATTGAAAAGTGGACTTCACAAGACTATACT................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 73 End: 102 ........................................................................CTTTTCAATGATGAAGAGGCATGATATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1386:SMT_1387|SMT_1386:SMT_1387:phosphoenolpyruvate-protein phosphotransferase:hypothetical protein:->->:1364671..1364802 132 tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: smit_SMT_1386_SMT_1387|phosphoenolpyruvate-protein phosphotransferase:hypothetical protein|POSITIVE:POSITIVE|[1364671,1364802]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc tgtcattaaccttgtaacctagttgcaaggttttttgatacatttgggaatagtatagtcttgtgaagtccacttttcaatgatgaagaggcatgatataataggagaaacaaatagaataagagagaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCAUUAACCUUGUAACCUAGUUGCAAGGUUUUUUGAUACAUUUGGGAAUAGUAUAGUCUUGUGAAGUCCACUUUUCAAUGAUGAAGAGGCAUGAUAUAAUAGGAGAAACAAAUAGAAUAAGAGAGAAAUC (((((..(((((((((((...)))))))))))...)))))..................((((((...(((..(((((((....)))))))....)))...))))))..................((....)) (-28.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUCUCUCUUAUUCUAUUUGUUUCUCCUAUUAUAUCAUGCCUCUUCAUCAUUGAAAAGUGGACUUCACAAGACUAUACUAUUCCCAAAUGUAUCAAAAAACCUUGCAACUAGGUUACAAGGUUAAUGACA ................((((((.......................((((....))))..(((.....)))................))))))..(((...(((((((.(((...))).)))))))..))).. (-14.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 110 66 185 130 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 276 96 58 93 45 smit:SMT_1844|5end_hypothetical_protein_1808587..1808817_POSITIVE 274 70 31 225 187 smit:SMT_1001|5end_aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_A_942161..942391_POSITIVE 268 78 31 102 44 smit:SMT_442|5end_transcriptional_regulator,_putative_381652..381882_POSITIVE 248 48 10 36 4 smit:SMT_1065|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1004341..1004571_POSITIVE 248 88 41 99 58 smit:SMT_993|5end_hypothetical_protein_935476..935706_NEGATIVE 247 99 61 118 76 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 246 108 68 56 20 smit:SMT_1717|5end_DNA-3-methyladenine_glycosylase_I_1704274..1704504_NEGATIVE 246 89 43 230 177 smit:SMT_747|5end_transcriptional_regulator,_LytR_family_652653..652883_NEGATIVE 243 50 10 218 178 smit:SMT_1749|5end_anthranilate_synthase_component_II_1727434..1727664_POSITIVE 242 98 51 166 126 smit:SMT_435|5end_orotate_phosphoribosyltransferase_376842..377072_POSITIVE 240 50 12 152 112 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 240 105 62 118 81 smit:SMT_379|5end_acetyltransferase,_GNAT_family_316095..316325_POSITIVE 231 92 51 51 13 smit:SMT_369|5end_hypothetical_cytosolic_protein_304012..304242_POSITIVE 227 97 54 202 158 smit:SMT_1164|5end_hypothetical_protein_1110115..1110345_POSITIVE 223 63 23 210 172 smit:SMT_1323|5end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1292187..1292417_POSITIVE 222 60 19 61 13 smit:SMT_1957|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1890645..1890875_POSITIVE 222 70 22 229 188 smit:SMT_1004|5end_thioredoxin_945430..945660_POSITIVE 220 96 51 199 135 smit:SMT_2093|5end_hypothetical_protein_LOC618557_1988441..1988671_POSITIVE 220 126 81 149 106 smit:SMT_1018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_954564..954794_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 79 42 93 45 smit:SMT_928|3end_hypothetical_protein_882859..883009_NEGATIVE 283 40 1 90 51 smit:SMT_1386|3end_phosphoenolpyruvate-protein_phosphotransferase_1364610..1364760_POSITIVE 248 48 10 34 2 smit:SMT_1064|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1004419..1004569_POSITIVE 248 88 41 99 58 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 246 108 68 46 10 smit:SMT_1718|3end_Holliday_junction_DNA_helicase_RuvA_1704284..1704434_NEGATIVE 245 66 21 112 75 smit:SMT_1420|3end_K02004_1404594..1404744_NEGATIVE 242 98 51 132 92 smit:SMT_434|3end_orotidine_5'-phosphate_decarboxylase_376888..377038_POSITIVE 240 50 12 67 27 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 231 40 2 136 94 smit:SMT_1581|3end_transcriptional_regulator,_biotin_repressor_family_1573120..1573270_NEGATIVE 229 80 33 83 29 smit:SMT_1253|3end_beta-galactosidase_1212912..1213062_NEGATIVE 218 39 1 86 50 smit:SMT_1408|3end_GTP-binding_protein_1386296..1386446_NEGATIVE 218 53 13 136 101 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE 213 109 66 149 110 smit:SMT_350|3end_immunity_protein_BlpL_290348..290498_POSITIVE 211 94 59 91 56 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 211 94 59 91 56 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 210 47 2 149 85 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 209 95 51 82 47 smit:SMT_1571|3end_CAAX_amino_terminal_protease_family_protein_1564405..1564555_POSITIVE 209 49 1 77 29 smit:SMT_1106|3end_ribonuclease_P_protein_component_1047601..1047751_NEGATIVE 208 109 66 149 110 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 206 97 58 97 52 smit:SMT_1818|3end_tryptophan_synthase,_alpha_subunit_1793037..1793187_POSITIVE