Origin IGS: acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaggaaaataaagaattgagatcacataccgaatatattataaccgagaaacattctagtatatagaatattatggcaaagatatatctcactgatgagcattacttccaatgtgcaagtggactttttccagcacgt Mask Tandem Repeat Region ================================================ acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Find is-nt database================================================ Query_seq: PI1975:PI1976|PI1975:PI1976:conserved hypothetical protein:hypothetical protein:->->:1932994..1933132 139 acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1975:PI1976|PI1975:PI1976:conserved hypothetical protein:hypothetical protein:->->:1932994..1933132 139 acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1975:PI1976|PI1975:PI1976:conserved hypothetical protein:hypothetical protein:->->:1932994..1933132 139 acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 47 End: 139 .............................................. M R Y I F A I I F Y I L E C F S V I I Y S V C D L N S L F S L acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta 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: 82 Start: 95 End: 124 ..............................................................................................ATTGAGATCACATACCGAATATATTATAAC............... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 73 End: 102 ........................................................................CTATATACTAGAATGTTTCTCGGTTATAAT..................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -2.5 Tail_Score: -4.00468 Start: 69 End: 87 Full_Region: ATATCTTTGCCATAA TATTCTA TATAC TAGAATG TTTCTCGGTTATAAT ....................................................................TATTCTATATACTAGAATG.................................................... Find igs database================================================ Query_seq: PI1975:PI1976|PI1975:PI1976:conserved hypothetical protein:hypothetical protein:->->:1932994..1933132 139 acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: pint_PI1975_PI1976|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1932994,1933132]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta acgtgctggaaaaagtccacttgcacattggaagtaatgctcatcagtgagatatatctttgccataatattctatatactagaatgtttctcggttataatatattcggtatgtgatctcaattctttattttcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUGCUGGAAAAAGUCCACUUGCACAUUGGAAGUAAUGCUCAUCAGUGAGAUAUAUCUUUGCCAUAAUAUUCUAUAUACUAGAAUGUUUCUCGGUUAUAAUAUAUUCGGUAUGUGAUCUCAAUUCUUUAUUUUCCUUA ..((((((((.....))))...))))...((((((((..........((((((........(((..(((((((((.....)))))))))....)))....((((((...)))))).)))))).....)))))))).... (-26.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAAAAUAAAGAAUUGAGAUCACAUACCGAAUAUAUUAUAACCGAGAAACAUUCUAGUAUAUAGAAUAUUAUGGCAAAGAUAUAUCUCACUGAUGAGCAUUACUUCCAAUGUGCAAGUGGACUUUUUCCAGCACGU ...((((..........((((((......((((((((.(((((..(.(((.....))).)..))))).))))).))).........)))))).((((....)))).)))).((((((...((((.....)))))))))) (-22.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 44 2 199 151 pint:PI2121|5end_glucose_inhibited_division_protein_A_2069889..2070119_POSITIVE 300 44 2 54 6 pint:PI2122|5end_conserved_hypothetical_protein_2069744..2069974_POSITIVE 288 50 1 72 19 pint:PI1035|5end_queuine_tRNA-ribosyltransferase_(tRNA-guanine_transglycosylase)_953329..953559_POSITIVE 284 66 22 91 42 pint:PI1943|5end_hypothetical_protein_1901296..1901526_POSITIVE 275 50 2 97 46 pint:PI1609|5end_Na+/H+_anti-porter_1536058..1536288_POSITIVE 272 68 21 93 47 pint:PI0446|5end_DNA-directed_RNA_polymerase,_beta_subunit_413478..413708_POSITIVE 270 50 3 120 61 pint:PI0396|5end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_361993..362223_POSITIVE 267 47 3 208 168 pint:PI1667|5end_conserved_hypothetical_protein_1579763..1579993_POSITIVE 265 49 1 80 34 pint:PI0304|5end_hypothetical_protein_288582..288812_POSITIVE 257 74 33 46 2 pint:PI0971|5end_glycine_cleavage_system_T_protein_(aminomethyltransferase)_897847..898077_POSITIVE 252 65 23 39 5 pint:PI0833|5end_conserved_hypothetical_protein_770059..770289_POSITIVE 250 49 1 117 61 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 245 46 3 174 124 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 244 50 1 69 13 pint:PI1799|5end_30S_ribosomal_protein_S2_1732900..1733130_POSITIVE 244 52 13 96 53 pint:PI0750|5end_zinc_protease_677746..677976_POSITIVE 243 48 4 143 96 pint:PI2175|5end_RNA_polymerase_sigma-54_2115007..2115237_POSITIVE 243 46 5 41 1 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 242 58 11 102 54 pint:PI1725|5end_hypothetical_protein_1643024..1643254_POSITIVE 242 49 1 158 105 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 240 41 2 55 7 pint:PI2177|5end_phosphoribosylaminoimidazole_carboxylase_2117127..2117357_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 65 21 55 2 pint:PI0832|3end_sigma-54-dependent_transcriptional_regulator_770155..770305_POSITIVE 288 50 1 59 6 pint:PI1034|3end_conserved_hypothetical_protein;_possible_membrane_protein_953396..953546_POSITIVE 271 70 27 117 81 pint:PI1393|3end_aldose_1-epimerase_1313823..1313973_POSITIVE 269 49 2 133 89 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 244 50 2 74 28 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 234 46 1 58 7 pint:PI0964|3end_conserved_hypothetical_protein_894187..894337_POSITIVE 231 50 1 134 84 pint:PI1798|3end__elongation_factor_Ts_1732824..1732974_POSITIVE 231 57 16 145 92 pint:PI0419|3end_conserved_hypothetical_protein_387461..387611_POSITIVE 229 63 23 66 37 pint:PI1738|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_1660112..1660262_POSITIVE 229 40 1 73 31 pint:PI0157|3end_hypothetical_protein_151387..151537_POSITIVE 226 50 4 94 38 pint:PI0576|3end_helicase,_UvrD/Rep_521724..521874_POSITIVE 223 67 21 116 75 pint:PI0321|3end_conserved_hypothetical_protein_303286..303436_POSITIVE 222 49 2 55 9 pint:PI2176|3end_conserved_hypothetical_protein_2117178..2117328_POSITIVE 222 50 3 136 91 pint:PI1607|3end_ABC-related_lipoprotein_releasing_system,_ATP-binding_protein_1535834..1535984_POSITIVE 221 49 3 53 7 pint:PI2044|3end_hypothetical_protein_1997351..1997501_POSITIVE 220 49 2 150 94 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 220 64 21 111 66 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 219 50 1 123 61 pint:PI0924|3end_possible_glycosyl_hydrolase_855953..856103_POSITIVE 217 50 1 137 71 pint:PI0769|3end_phosphomannomutase_706172..706322_POSITIVE 216 50 1 149 94 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE