Origin IGS: gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt .........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 aaggtggactttttctcaagtctctactaaactactatttctaaatmacaagtttattttagcaaacgcgttccaaattccccaaaacatattctattttaggtttgtgaaaatcacttttttatggtagaatgtaaaagaatgtatgtcattcggaataacaataaaatgaggtaaaaac Mask Tandem Repeat Region ================================================ gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Find is-nt database================================================ Query_seq: SMT_927:SMT_928|SMT_927:SMT_928:KH domain protein:hypothetical protein:<-<-:882768..882948 181 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_927:SMT_928|SMT_927:SMT_928:KH domain protein:hypothetical protein:<-<-:882768..882948 181 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_927:SMT_928|SMT_927:SMT_928:KH domain protein:hypothetical protein:<-<-:882768..882948 181 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Predict ORF larger than 30AA ================================================ gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt 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: 86 Start: 49 End: 78 ................................................TTTGTGAAAATCACTTTTTTATGGTAGAAT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -5.4 Tail_Score: -5.31275 Start: 65 End: 75 Full_Region: ttctattttaggttt gtga aaa tcac ttttttatggtagaa ................................................................gtgaaaatcac.......................................................................................................... Find igs database================================================ Query_seq: SMT_927:SMT_928|SMT_927:SMT_928:KH domain protein:hypothetical protein:<-<-:882768..882948 181 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: smit_SMT_927_SMT_928|KH domain protein:hypothetical protein|NEGATIVE:NEGATIVE|[882768,882948]|181 HSP 1 e-value: 1.0E-97 bit: 356.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaagtccacctt Inter-species Hit: Count: 3 Min: 1 Max: 173 Len: 173 Subject: NC_008533_SPD_1549_SPD_1550|KH domain protein:addiction module toxin, Txe/YoeB family protein|NEGATIVE:NEGATIVE|[1573791,1573980]|190 HSP 1 e-value: 3.0E-83 bit: 308.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaag........ gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacacatttgcaaaaataaacttgttgtttagaaatagtagtttagtagagacttgagaaaaag........ Subject: NC_003098_spr1584_spr1585|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1566260,1566449]|190 HSP 1 e-value: 3.0E-83 bit: 308.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaag........ gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacacatttgcaaaaataaacttgttgtttagaaatagtagtttagtagagacttgagaaaaag........ Subject: NC_003028_SP_1739_SP_1740|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1644846,1645044]|199 HSP 1 e-value: 2.0E-78 bit: 292.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 10 Subject End: 182 gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttggggaatttggaacgcgtttgctaaaataaacttgtkatttagaaatagtagtttagtagagacttgagaaaaag........ gtttttacctcattttattgttattccgaatgacatacattcttttacattctaccataaaaaagtgattttcacaaacctaaaatagaatatgttttgaggaatttggaacacatttaccaaaataaacttgttgtttagaaatagtagtttagtagagacttgagaaaaag........ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUACCUCAUUUUAUUGUUAUUCCGAAUGACAUACAUUCUUUUACAUUCUACCAUAAAAAAGUGAUUUUCACAAACCUAAAAUAGAAUAUGUUUUGGGGAAUUUGGAACGCGUUUGCUAAAAUAAACUUGUKAUUUAGAAAUAGUAGUUUAGUAGAGACUUGAGAAAAAG ........((((...........((((((((.................................(((.....)))...(((((((((.....)))))))))..))))))))...((((.(((...((((((......(((....))).)))))).))))))).))))...... (-30.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUCUCAAGUCUCUACUAAACUACUAUUUCUAAAUMACAAGUUUAUUUUAGCAAACGCGUUCCAAAUUCCCCAAAACAUAUUCUAUUUUAGGUUUGUGAAAAUCACUUUUUUAUGGUAGAAUGUAAAAGAAUGUAUGUCAUUCGGAAUAACAAUAAAAUGAGGUAAAAAC .(((((((((.........((((((.................)))))).............(((((..............(((((((((..((((...(((.....)))...))))..)))))))))....(((((.....))))))))))..........))))).)))).. (-27.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 812 120 71 211 162 smit:SMT_927|5end_KH_domain_protein_882677..882907_NEGATIVE 259 120 71 144 87 smit:SMT_217|5end_hypothetical_protein_149236..149466_POSITIVE 229 116 77 133 97 smit:SMT_526|5end_RNA_binding_protein_451149..451379_POSITIVE 227 66 28 114 83 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 226 79 34 129 73 smit:SMT_651|5end_DNA_ligase_561944..562174_NEGATIVE 221 47 5 143 96 smit:SMT_1513|5end_hypothetical_protein_1495582..1495812_NEGATIVE 208 121 104 21 1 smit:SMT_1914|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1859486..1859716_POSITIVE 201 118 75 65 17 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 200 114 74 150 102 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 200 142 101 76 35 smit:SMT_659|5end_hypothetical_protein_570545..570775_NEGATIVE 199 120 98 33 9 smit:SMT_1606|5end_glutamate_racemase_1595857..1596087_POSITIVE 198 116 93 159 136 smit:SMT_1610|5end_tyrosine_recombinase_1598565..1598795_POSITIVE 193 120 74 77 27 smit:SMT_123|5end_hypothetical_protein_75391..75621_POSITIVE 191 89 48 127 89 smit:SMT_1712|5end_excinuclease_ABC_subunit_A_1700351..1700581_NEGATIVE 190 127 89 78 42 smit:SMT_1791|5end_hypothetical_protein_1765907..1766137_POSITIVE 190 62 31 171 147 smit:SMT_829|5end_putative_mucus_binding_protein_764939..765169_NEGATIVE 187 121 85 189 153 smit:SMT_1524|5end_peptidase_T_1504564..1504794_POSITIVE 187 35 1 192 153 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 186 110 64 174 141 smit:SMT_1486|5end_hypothetical_protein_1465909..1466139_POSITIVE 186 120 71 209 163 smit:SMT_322|5end_hypothetical_protein_260193..260423_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 116 77 113 77 smit:SMT_525|3end_30S_ribosomal_protein_S16_451209..451359_POSITIVE 227 66 28 80 49 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 216 110 61 145 106 smit:SMT_1716|3end_hypothetical_protein_1703657..1703807_POSITIVE 200 142 101 83 42 smit:SMT_660|3end_two-component_sensor_histidine_kinase_570538..570688_NEGATIVE 190 62 31 46 22 smit:SMT_830|3end_hypothetical_protein_765064..765214_NEGATIVE 189 115 79 74 30 smit:SMT_1747|3end_anthranilate_synthase_component_I_1726832..1726982_POSITIVE 188 120 77 70 22 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 187 35 1 111 72 smit:SMT_1063|3end_preprotein_translocase_SecA_subunit_1003307..1003457_POSITIVE 185 68 23 71 11 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 185 68 23 71 11 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 185 68 23 71 11 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 185 68 23 71 11 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 182 118 79 147 117 smit:SMT_1861|3end_sucrose_operon_repressor_(SCR_operon_regulatory_protein)_1824098..1824248_POSITIVE 182 118 79 147 117 smit:SMT_1762|3end_sucrose_operon_repressor,_HTH_and_periplasmic_binding_domains_1738541..1738691_POSITIVE 182 122 84 90 51 smit:SMT_366|3end_hypothetical_protein_302398..302548_POSITIVE 181 55 12 138 93 smit:SMT_1715|3end_MccC_family_protein_1703288..1703438_POSITIVE 179 54 13 56 11 smit:SMT_1331|3end_hypothetical_protein_1306045..1306195_NEGATIVE 178 104 77 34 6 smit:SMT_862|3end_hypothetical_protein_predicted_by_Glimmer/Critica_809191..809341_POSITIVE 177 117 97 142 125 smit:SMT_466|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_404342..404492_POSITIVE 173 109 71 132 95 smit:SMT_1758|3end_hypothetical_protein_1735029..1735179_NEGATIVE