Origin IGS: tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa .........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 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaactaaagtgtaatgctattgcttttagagattttcataaacaagagcaacttccagcannnnnttaattaattaannnnnccgtttgcaacaactttcaaccagaaaatcaatctacgcgaggtttctgcgccaggttcttactgggaagatggaaa Mask Tandem Repeat Region ================================================ tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Find is-nt database================================================ Query_seq: SMT_1993:SMT_1994|SMT_1993:SMT_1994:hypothetical protein:phosphoglycerate mutase:<-<-:1919891..1920147 257 tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1993:SMT_1994|SMT_1993:SMT_1994:hypothetical protein:phosphoglycerate mutase:<-<-:1919891..1920147 257 tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1993:SMT_1994|SMT_1993:SMT_1994:hypothetical protein:phosphoglycerate mutase:<-<-:1919891..1920147 257 tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 140 End: 229 ........................................................................................................................................... M A L H F S F P H Q K Q P K G L L R L F F L I L I F L L D S ............................ tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa 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================================================ tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.2 Tail_Score: -5.77677 Start: 173 End: 196 Full_Region: TTTCCCCATCAAAAA CAGCCGAA AGGATTAC TTCGGCTG TTTTTTCTTATTTTG ............................................................................................................................................................................CAGCCGAAAGGATTACTTCGGCTG............................................................. TransTerm Strand: - Conf: 89 HP_score: -8.9 Tail_Score: -4.72272 Start: 173 End: 196 Full_Region: caaaataagaaaaaa cagccgaag taatcc tttcggctg tttttgatggggaaa ............................................................................................................................................................................cagccgaagtaatcctttcggctg............................................................. Find igs database================================================ Query_seq: SMT_1993:SMT_1994|SMT_1993:SMT_1994:hypothetical protein:phosphoglycerate mutase:<-<-:1919891..1920147 257 tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Intra-Species Hit: Count: 3 Min: 1 Max: 257 Len: 257 Subject: smit_SMT_1993_SMT_1994|hypothetical protein:phosphoglycerate mutase|NEGATIVE:NEGATIVE|[1919891,1920147]|257 HSP 1 e-value: 1.0E-122 bit: 438.0 Len: 257 Query Start:1 Query End:257 Subject Strand: POSITIVE Subject Start: 1 Subject End: 257 tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacnnnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa tttccatcttcccagtaagaacctggcgcagaaacctcgcgtagattgattttctggttgaaagttgttgcaaacggnnnnnttaattaattaannnnntgctggaagttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Subject: smit_SMT_201_SMT_202|phosphoglycerate mutase:K02011 iron(III) transport system permease protein|POSITIVE:NEGATIVE|[132162,132262]|101 HSP 1 e-value: 2.0E-50 bit: 200.0 Len: 101 Query Start:157 Query End:257 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 101 ............................................................................................................................................................ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa ............................................................................................................................................................ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Subject: smit_SMT_2061_SMT_2062|K02011 iron(III) transport system permease protein:phosphoglycerate mutase|POSITIVE:NEGATIVE|[1970863,1971002]|140 HSP 1 e-value: 3.0E-49 bit: 196.0 Len: 101 Query Start:157 Query End:257 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ............................................................................................................................................................ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa ............................................................................................................................................................ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaa Inter-species Hit: Count: 1 Min: 109 Max: 255 Len: 147 Subject: NC_003028_SP_0240_SP_0242|phosphoglycerate mutase family protein:ABC transporter, ATP-binding protein|POSITIVE:NEGATIVE|[210650,212386]|1737 HSP 1 e-value: 4.0E-45 bit: 182.0 Len: 147 Query Start:109 Query End:255 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 150 ............................................................................................................ttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccccatcaaaaacagccgaaagga-ttacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagact.. ............................................................................................................ttgctcttgtttatgaaaatctctaaaagcaatagcattacactttagttttccacatcaaaaacagccgaaaggagtgccctcggctgttttttcttatcttgatattcttatcaaatccctagctcatggcaagcaagtctagact.. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUCUUGUUUAUGAAAAUCUCUAAAAGCAAUAGCAUUACACUUUAGUUUUCCCCAUCAAAAACAGCCGAAAGGAUUACUUCGGCUGUUUUUUCUUAUUUUGAUAUUCCUACUAGAUUCCUAGUUCAUUGCAAGCAAGUCUAGACU .((((.((((((..((.....))...)))))).))))......((((((.......((((((((((((((((.(.....)))))))))).........)))))))......))))))...((((....(((....)))..))))... (-33.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUAGACUUGCUUGCAAUGAACUAGGAAUCUAGUAGGAAUAUCAAAAUAAGAAAAAACAGCCGAAGUAAUCCUUUCGGCUGUUUUUGAUGGGGAAAACUAAAGUGUAAUGCUAUUGCUUUUAGAGAUUUUCAUAAACAAGAGCAA ..........(((((.......(((((....)))))..(((.(((.........((((((((((((((......))))))))))))))...........((((((.(((((...))))))))))).))).)))........))))). (-36.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 32 1 231 200 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 292 111 73 201 163 smit:SMT_309|5end_acyl-carrier-protein_S-malonyltransferase_250406..250636_POSITIVE 274 90 43 47 1 smit:SMT_297|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_238547..238777_POSITIVE 263 85 55 132 105 smit:SMT_1681|5end_D-alanine-activating_enzyme_1664184..1664414_POSITIVE 263 124 81 114 61 smit:SMT_600|5end_ADP-ribose_pyrophosphatase_516307..516537_POSITIVE 259 99 56 218 178 smit:SMT_786|5end_hypothetical_protein_697964..698194_NEGATIVE 259 86 56 178 149 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 255 97 54 104 62 smit:SMT_920|5end_serine/threonine_protein_kinase_874501..874731_NEGATIVE 251 90 55 59 20 smit:SMT_1254|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1220882..1221112_NEGATIVE 247 120 80 111 77 smit:SMT_1276|5end_rod_shape-determining_protein_MreD_1239412..1239642_POSITIVE 246 140 91 147 98 smit:SMT_1857|5end_hypothetical_protein_1820931..1821161_POSITIVE 246 140 91 147 98 smit:SMT_834|5end_hypothetical_protein_777112..777342_NEGATIVE 245 85 43 169 117 smit:SMT_553|5end_hypothetical_protein_471128..471358_POSITIVE 244 87 48 124 70 smit:SMT_1675|5end_adenylosuccinate_synthetase_1661147..1661377_NEGATIVE 232 88 55 36 9 smit:SMT_619|5end_riboflavin_kinase_/_FMN_adenylyltransferase_527812..528042_POSITIVE 231 86 45 65 19 smit:SMT_1933|5end_K02006_cobalt_transport_system_ATP-binding_protein_1872222..1872452_NEGATIVE 231 127 81 149 99 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 228 117 72 112 60 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 228 117 72 112 60 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 228 91 51 139 104 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 794 110 61 51 2 smit:SMT_201|3end_phosphoglycerate_mutase_132101..132251_POSITIVE 665 140 99 42 1 smit:SMT_2062|3end_phosphoglycerate_mutase_1970913..1971063_NEGATIVE 315 93 60 79 46 smit:SMT_2061|3end_K02011_iron(III)_transport_system_permease_protein_1970802..1970952_POSITIVE 315 93 60 79 46 smit:SMT_202|3end_K02011_iron(III)_transport_system_permease_protein_132173..132323_NEGATIVE 263 85 55 41 14 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 263 124 81 104 51 smit:SMT_599|3end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_516377..516527_POSITIVE 259 99 56 94 54 smit:SMT_787|3end_K02440_glycerol_uptake_facilitator_protein_698088..698238_NEGATIVE 255 97 54 107 65 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 247 120 80 111 77 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 246 140 91 135 86 smit:SMT_1856|3end_polypeptide_deformylase_1820999..1821149_POSITIVE 246 140 91 135 86 smit:SMT_835|3end_polypeptide_deformylase_777124..777274_NEGATIVE 245 85 43 141 89 smit:SMT_552|3end_DNA_polymerase_III,_gamma_and_tau_subunits_471180..471330_POSITIVE 234 98 58 77 32 smit:SMT_320|3end_alcohol_dehydrogenase,_zinc-containing_259241..259391_NEGATIVE 228 117 72 112 60 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 228 117 72 112 60 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 228 91 51 83 48 smit:SMT_877|3end_hypothetical_protein_823558..823708_NEGATIVE 228 75 35 113 66 smit:SMT_630|3end_phosphoserine_phosphatase_536183..536333_POSITIVE 226 133 91 142 104 smit:SMT_660|3end_two-component_sensor_histidine_kinase_570538..570688_NEGATIVE 226 102 61 97 57 smit:SMT_142|3end_hypothetical_protein_93409..93559_NEGATIVE 223 96 53 56 18 smit:SMT_1071|3end_hypothetical_protein_1010386..1010536_POSITIVE