Origin IGS: tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agatatcctttttccacgattacttaatactttattctaccataatttctagcagttagcacgtttctcataaaaatgaaaaaagtctgacgattttgtcagaccaaaataatataaccttaaaaagagaagaacaattcttccctccatatatcatatca Mask Tandem Repeat Region ================================================ tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Find is-nt database================================================ Query_seq: SMT_496:SMT_497|SMT_496:SMT_497:superoxide dismutase, manganese-dependent:hypothetical protein:->->:431179..431339 161 tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_496:SMT_497|SMT_496:SMT_497:superoxide dismutase, manganese-dependent:hypothetical protein:->->:431179..431339 161 tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_496:SMT_497|SMT_496:SMT_497:superoxide dismutase, manganese-dependent:hypothetical protein:->->:431179..431339 161 tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 12 End: 110 ........... M E G R I V L L F L R L Y Y F G L T K S S D F F H F Y E K R A N C ................................................... tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct 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================================================ tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -7.9 Tail_Score: -5.56112 Start: 58 End: 77 Full_Region: GGTTATATTATTTTG GTCTGAC AAAATC GTCAGAC TTTTTTCATTTTTAT .........................................................GTCTGACAAAATCGTCAGAC.................................................................................... Find igs database================================================ Query_seq: SMT_496:SMT_497|SMT_496:SMT_497:superoxide dismutase, manganese-dependent:hypothetical protein:->->:431179..431339 161 tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagacttttttcatttttatgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: smit_SMT_496_SMT_497|superoxide dismutase, manganese-dependent:hypothetical protein|POSITIVE:POSITIVE|[431179,431339]|161 HSP 1 e-value: 2.0E-36 bit: 153.0 Len: 77 Query Start:1 Query End:77 Subject Strand: POSITIVE Subject Start: 1 Subject End: 77 tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagac.................................................................................... tgatatgatatatggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagac.................................................................................... HSP 2 e-value: 8.0E-33 bit: 141.0 Len: 71 Query Start:91 Query End:161 Subject Strand: POSITIVE Subject Start: 91 Subject End: 161 ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct Inter-species Hit: Count: 3 Min: 13 Max: 161 Len: 149 Subject: NC_008533_SPD_0667_SPD_0668|superoxide dismutase, manganese-dependent:hypothetical protein|POSITIVE:POSITIVE|[688178,688333]|156 HSP 1 e-value: 8.0E-33 bit: 141.0 Len: 71 Query Start:91 Query End:161 Subject Strand: POSITIVE Subject Start: 86 Subject End: 156 ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct HSP 2 e-value: 1.0E-19 bit: 97.6 Len: 65 Query Start:13 Query End:77 Subject Strand: POSITIVE Subject Start: 8 Subject End: 72 ............tggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagac.................................................................................... ............tggagggaagaattgttcttctcttttttaggttataagattctggtctgacaaaatcgtcagac.................................................................................... Subject: NC_003098_spr0674_spr0675|Manganese co-factored superoxide dismutase:hypothetical protein|POSITIVE:POSITIVE|[680647,680802]|156 HSP 1 e-value: 8.0E-33 bit: 141.0 Len: 71 Query Start:91 Query End:161 Subject Strand: POSITIVE Subject Start: 86 Subject End: 156 ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct HSP 2 e-value: 1.0E-19 bit: 97.6 Len: 65 Query Start:13 Query End:77 Subject Strand: POSITIVE Subject Start: 8 Subject End: 72 ............tggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagac.................................................................................... ............tggagggaagaattgttcttctcttttttaggttataagattctggtctgacaaaatcgtcagac.................................................................................... Subject: NC_003028_SP_0766_SP_0767|superoxide dismutase, manganese-dependent:hypothetical protein|POSITIVE:POSITIVE|[725986,726140]|155 HSP 1 e-value: 2.0E-30 bit: 133.0 Len: 71 Query Start:91 Query End:161 Subject Strand: POSITIVE Subject Start: 85 Subject End: 155 ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtggaaaaaggatatct ..........................................................................................atgagaaacgtgctaactgctagaaattatggtagaataaagtattaagtaatcgtgaaaaaaggatatct HSP 2 e-value: 3.0E-17 bit: 89.7 Len: 65 Query Start:13 Query End:77 Subject Strand: POSITIVE Subject Start: 8 Subject End: 71 ............tggagggaagaattgttcttctctttttaaggttatattattttggtctgacaaaatcgtcagac.................................................................................... ............tggagggaagaattgttcttctcttttt-aggttataagattctggtctgacaaaatcgtcagac.................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAGGGAAGAAUUGUUCUUCUCUUUUUAAGGUUAUAUUAUUUUGGUCUGACAAAAUCGUCAGACUUUUUUCAUUUUUAUGAGAAACGUGCUAACUGCUAGAAAUUAUGGUAGAAUAAAGUAUUAAGUAAUCGUGGAAAAAGGAUAUCU .((((((((((.....))))))))))....((((((..((((((((((((((......))))))).((((((((....))))))))........((((((.......))))))..)))))))....))))))................. (-36.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUAUCCUUUUUCCACGAUUACUUAAUACUUUAUUCUACCAUAAUUUCUAGCAGUUAGCACGUUUCUCAUAAAAAUGAAAAAAGUCUGACGAUUUUGUCAGACCAAAAUAAUAUAACCUUAAAAAGAGAAGAACAAUUCUUCCCUCCA .......((((((......................................((.....)).......((((....)))).....((((((((....)))))))).................)))))).(((((.....)))))...... (-17.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 44 1 98 55 smit:SMT_666|5end_GTP_pyrophosphokinase-like_protein_577400..577630_NEGATIVE 237 79 31 165 123 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 237 50 2 173 134 smit:SMT_922|5end_RNA-binding_protein_876566..876796_NEGATIVE 236 115 74 120 76 smit:SMT_554|5end_K09013_Fe-S_cluster_assembly_ATP-binding_protein_471425..471655_POSITIVE 233 112 77 166 138 smit:SMT_1337|5end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312812..1313042_NEGATIVE 233 90 41 117 71 smit:SMT_167|5end_acetyltransferase,_GNAT_family_113171..113401_POSITIVE 231 99 57 212 165 smit:SMT_850|5end_hypothetical_protein_797014..797244_NEGATIVE 229 98 58 121 89 smit:SMT_977|5end_conserved_hypothetical_protein,_Rrf2_family_protein_925689..925919_NEGATIVE 228 102 80 24 1 smit:SMT_1292|5end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1254179..1254409_POSITIVE 226 78 31 95 43 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 226 78 31 95 43 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 223 117 72 76 35 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 222 66 24 223 176 smit:SMT_1992|5end_carboxynorspermidine_decarboxylase_1919207..1919437_NEGATIVE 222 66 24 223 176 smit:SMT_1415|5end_carboxynorspermidine_decarboxylase_1399570..1399800_NEGATIVE 220 100 55 141 86 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 220 50 1 186 134 smit:SMT_1338|5end_K05832_putative_ABC_transport_system_permease_protein_1313675..1313905_NEGATIVE 219 98 54 82 37 smit:SMT_1831|5end_galactose-6-phosphate_isomerase_1799912..1800142_POSITIVE 218 78 31 95 43 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 212 115 77 61 21 smit:SMT_525|5end_30S_ribosomal_protein_S16_450875..451105_POSITIVE 212 115 77 43 3 smit:SMT_509|5end_30S_ribosomal_protein_S16_438746..438976_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 37 1 43 2 smit:SMT_1178|3end_choline_binding_protein_A_1135442..1135592_NEGATIVE 260 50 2 117 62 smit:SMT_1983|3end_glycerophosphoryl_diester_phosphodiesterase_1913455..1913605_NEGATIVE 233 90 41 73 27 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE 229 98 58 45 13 smit:SMT_978|3end_hypothetical_protein_925765..925915_NEGATIVE 228 102 80 61 38 smit:SMT_1291|3end_hypothetical_protein_1254296..1254446_POSITIVE 223 117 72 86 45 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 220 99 52 41 4 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 220 50 1 110 58 smit:SMT_1339|3end_hypothetical_protein_1313751..1313901_NEGATIVE 216 140 94 57 14 smit:SMT_891|3end_oxidoreductase,_putative_839132..839282_POSITIVE 210 67 21 110 74 smit:SMT_1572|3end_excinuclease_ABC_subunit_B_1566470..1566620_POSITIVE 210 41 16 58 34 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE 205 99 62 141 99 smit:SMT_1994|3end_phosphoglycerate_mutase_1920058..1920208_NEGATIVE 205 99 62 141 99 smit:SMT_201|3end_phosphoglycerate_mutase_132101..132251_POSITIVE 203 103 65 145 116 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 203 100 57 146 98 smit:SMT_1183|3end_K02795_PTS_system,_mannose-specific_IIC_component_1140629..1140779_NEGATIVE 202 127 81 82 28 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 200 92 55 129 89 smit:SMT_1968|3end_transcription-repair_coupling_factor_1899951..1900101_NEGATIVE 200 90 45 102 48 smit:SMT_1461|3end_putative_phosphate_ABC_transporter_(ATP-binding_protein)_1443207..1443357_POSITIVE 200 98 78 77 55 smit:SMT_1072|3end_Cof_family_protein_1010357..1010507_NEGATIVE 200 101 63 122 75 smit:SMT_319|3end_K02356_elongation_factor_EF-P_258304..258454_NEGATIVE