Origin IGS: tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtggcgttgtggaaaaatatttacacttttataaccttctttccgccaataaaacatagagcagacttgtgtctaaagtagacgaaaatagaagctgatgtatttgctttataggcttgcataaaggcggaagcgcaagactgacacatacagacataatagaaaaaggtggtgtatcattgtttgatacaccacctttttactttctcaaatcatcaactaacctaaataatttactctctaataataactaatcaactatttttttacttacgtgaactgcttgtgctata Mask Tandem Repeat Region ================================================ tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Find is-nt database================================================ Query_seq: PI1868:PI1869|PI1868:PI1869:hypothetical protein:hypothetical protein:->->:1814976..1815270 295 tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1868:PI1869|PI1868:PI1869:hypothetical protein:hypothetical protein:->->:1814976..1815270 295 tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1868:PI1869|PI1868:PI1869:hypothetical protein:hypothetical protein:->->:1814976..1815270 295 tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 134 End: 262 ..................................................................................................................................... M M S V C V S L A L P P L C K P I K Q I H Q L L F S S T L D T S L L Y V L L A E R R L ................................. Protein_Len: 42 Strand: + Start: 145 End: 270 ................................................................................................................................................ M C Q S C A S A F M Q A Y K A N T S A S I F V Y F R H K S A L C F I G G K K V I K V ......................... Protein_Len: 50 Strand: - Start: 43 End: 192 .......................................... N N N S L L N N L N T S S K L F Y F P P T D F L S V G G K E I I D T H T L R A S G G K H L G I F C M ....................................................................................................... tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta 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: 81 Start: 61 End: 90 ............................................................TTTCTCAAATCATCAACTAACCTAAATAAT............................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.2 Tail_Score: -5.1764 Start: 98 End: 126 Full_Region: TTGAGAAAGTAAAAA GGTGGTGTATCA AACAA TGATACACCACC TTTTTCTATTATGTC .................................................................................................GGTGGTGTATCAAACAATGATACACCACC......................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.2 Tail_Score: -5.04601 Start: 98 End: 126 Full_Region: gacataatagaaaaa ggtggtgtatca ttgtt tgatacaccacc tttttactttctcaa .................................................................................................ggtggtgtatcattgtttgatacaccacc......................................................................................................................................................................... Find igs database================================================ Query_seq: PI1868:PI1869|PI1868:PI1869:hypothetical protein:hypothetical protein:->->:1814976..1815270 295 tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Intra-Species Hit: Count: 1 Min: 1 Max: 295 Len: 295 Subject: pint_PI1868_PI1869|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1814976,1815270]|295 HSP 1 e-value: 1.0E-153 bit: 543.0 Len: 295 Query Start:1 Query End:295 Subject Strand: POSITIVE Subject Start: 1 Subject End: 295 tatagcacaagcagttcacgtaagtnnnnnnntagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta tatagcacaagcagttcacgtaagtaaaaaaatagttgattagttattattagagagtaaattatttaggttagttgatgatttgagaaagtaaaaaggtggtgtatcaaacaatgatacaccacctttttctattatgtctgtatgtgtcagtcttgcgcttccgcctttatgcaagcctataaagcaaatacatcagcttctattttcgtctactttagacacaagtctgctctatgttttattggcggaaagaaggttataaaagtgtaaatatttttccacaacgccacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAGCACAAGCAGUUCACGUAAGUAAAAAAAUAGUUGAUUAGUUAUUAUUAGAGAGUAAAUUAUUUAGGUUAGUUGAUGAUUUGAGAAAGUAAAAAGGUGGUGUAUCAAACAAUGAUACACCACCUUUUUCUAUUAUGUCUGUAUGUGUCAGUCUUGCGCUUCCGCCUUUAUGCAAGCCUAUAAAGCAAAUACAUCAGCUUCUAUUUUCGUCUACUUUAGACACAAGUCUGCUCUAUGUUUUAUUGGCGGAAAGAAGGUUAUAAAAGUGUAAAUAUUUUUCCACAACGCCACUA (((((....(((((...((....))....((((((((.(((..(((....)))..))).)))))))).((..(((((((((((((....((.(((((((((((((((((.....))))))))))))))))))).....(..((((((((..(((.....)))..)))....)))))..)........))))).)))))))).))......(((((...)))))......))))))))))......(((((((((((...(((((....)))))...))))))).....))))... (-73.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGGCGUUGUGGAAAAAUAUUUACACUUUUAUAACCUUCUUUCCGCCAAUAAAACAUAGAGCAGACUUGUGUCUAAAGUAGACGAAAAUAGAAGCUGAUGUAUUUGCUUUAUAGGCUUGCAUAAAGGCGGAAGCGCAAGACUGACACAUACAGACAUAAUAGAAAAAGGUGGUGUAUCAUUGUUUGAUACACCACCUUUUUACUUUCUCAAAUCAUCAACUAACCUAAAUAAUUUACUCUCUAAUAAUAACUAAUCAACUAUUUUUUUACUUACGUGAACUGCUUGUGCUAUA ..(((((...(((((((........................)))))))............((((((..(..(((...(((((((..(((((((.((.(((((.(((((.....(((.(((((......((....))))))).)))...................(((((((((((((((((.....))))))))))))))))).......)))))))))).))..........(((........))).............)))))))))))))))))..).))))))..))))). (-72.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 287 247 93 55 pint:PI0024|5end_hypothetical_protein_28378..28608_POSITIVE 337 179 138 230 188 pint:PI0601|5end_hypothetical_protein_548758..548988_POSITIVE 327 179 138 61 25 pint:PI1173|5end_transcription_regulatory_protein,_LacI_family_1095051..1095281_POSITIVE 322 290 245 226 180 pint:PI1206|5end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1124698..1124928_POSITIVE 322 166 122 210 155 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 317 287 247 230 191 pint:PI2089|5end_conserved_hypothetical_protein_2046200..2046430_POSITIVE 316 189 146 215 168 pint:PI1604|5end_hypothetical_protein_1534017..1534247_POSITIVE 305 168 123 112 62 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 304 290 247 117 76 pint:PI0561|5end_hypothetical_protein_508952..509182_POSITIVE 303 188 141 57 4 pint:PI0700|5end_UDP-glucose_4-epimerase_637299..637529_POSITIVE 302 200 154 84 24 pint:PI0019|5end_conserved_hypothetical_protein_23742..23972_POSITIVE 301 140 96 105 71 pint:PI2166|5end_hypothetical_protein_2111394..2111624_POSITIVE 300 190 141 171 118 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 298 132 95 61 26 pint:PI1717|5end_major_outer_membrane_protein_1632666..1632896_POSITIVE 294 189 141 74 30 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 293 168 122 50 1 pint:PI1715|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1631639..1631869_POSITIVE 292 170 125 219 185 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 292 287 247 157 118 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 290 287 241 93 48 pint:PI2046|5end_hypothetical_protein_1999030..1999260_POSITIVE 287 185 141 83 36 pint:PI0316|5end_conserved_hypothetical_protein_298379..298609_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 290 245 83 37 pint:PI1204|3end_hypothetical_protein_1124635..1124785_POSITIVE 316 189 146 123 76 pint:PI1603|3end_hypothetical_protein_1534005..1534155_POSITIVE 311 189 141 104 49 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 310 180 132 150 100 pint:PI0163|3end_conserved_hypothetical_protein_158410..158560_POSITIVE 308 277 238 151 112 pint:PI1702|3end_hypothetical_protein_1620867..1621017_POSITIVE 300 190 141 60 7 pint:PI0529|3end_hypothetical_protein_483741..483891_POSITIVE 298 190 145 124 80 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE 292 170 125 102 68 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 292 287 247 42 3 pint:PI0095|3end_hypothetical_protein_91850..92000_POSITIVE 287 168 122 151 114 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 284 269 230 80 44 pint:PI1970|3end_hypothetical_protein_1927882..1928032_POSITIVE 282 170 129 149 111 pint:PI2155|3end_hypothetical_protein_2101052..2101202_POSITIVE 282 167 127 145 99 pint:PI1830|3end_conserved_hypothetical_protein_1770361..1770511_POSITIVE 282 187 147 73 23 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 281 176 137 63 18 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 280 253 212 121 82 pint:PI1746|3end_hypothetical_protein_1667606..1667756_POSITIVE 279 170 127 138 95 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 272 290 241 56 2 pint:PI0820|3end_hypothetical_protein_759980..760130_POSITIVE 271 200 156 141 102 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 268 261 228 133 95 pint:PI1921|3end_conserved_hypothetical_protein_1865100..1865250_POSITIVE