Origin IGS: tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta .........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 taggaaaaggagggttacattgcatagagtgtatcggttcagggaacaaaccaaaagtactttataggtctactgtgttttgcctgttccttgttggtaaatatacagaagaactgcactactcattctcgcaggcagacgaggcgcagtccctgccatttcttctatcattgtaaaggggtacgatgacgtttttctcatttcacgtccatcgtaccccttgtaaaaattgcctattgggttttatctacccattgtattattatagaaagggaaatccttgcaagttttctgctacgcctcactactcattataatgaagcacagcactatgaggcattagttccccaaaaatca Mask Tandem Repeat Region ================================================ tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Find is-nt database================================================ Query_seq: PI0138:PI0140|PI0138:PI0140:hypothetical protein:conserved hypothetical protein:->->:131426..131782 357 tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0138:PI0140|PI0138:PI0140:hypothetical protein:conserved hypothetical protein:->->:131426..131782 357 tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0138:PI0140|PI0138:PI0140:hypothetical protein:conserved hypothetical protein:->->:131426..131782 357 tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 121 End: 285 ........................................................................................................................ M G N F Y K G Y D G R E M R K T S S Y P F T M I E E M A G T A P R L P A R M S S A V L L Y I Y Q Q G T G K T Q ........................................................................ Protein_Len: 50 Strand: - Start: 185 End: 334 ........................................................................................................................................................................................ L S L L F P L S Q A E D A Q S F S Y H L E E T Y K G V L F L C F V T S R Y L V K P K N G S G I C E M ....................... Protein_Len: 41 Strand: - Start: 172 End: 294 ........................................................................................................................................................................... R V G K C H Y F F H C P S R R T Q R R S H T T C N K Q I N V L L S C A F C L L G M ............................................................... Protein_Len: 41 Strand: - Start: 135 End: 257 ...................................................................................................................................... L P Y S P R S I L F V D D Y G K V I I S S I A P V A G R R G A L I L L A T R R Y M .................................................................................................... Protein_Len: 43 Strand: - Start: 44 End: 172 ........................................... L S Y H P T A S F K C P N G K R Y Y Y L P Y I F G L L C N K C P T R H V H F S F F T M ......................................................................................................................................................................................... Protein_Len: 49 Strand: - Start: 1 End: 147 S K Q P V L A E Y H Q A E N Y H T T L R L L F S A L I E R E I I I C H T S L V W Y A I K V L P V M .................................................................................................................................................................................................................. tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta 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================================================ tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.2 Tail_Score: -2.82834 Start: 74 End: 90 Full_Region: CGTAGCAGAAAACTT GCAAGG ATTTC CCTTTC TATAATAATACAATG .........................................................................GCAAGGATTTCCCTTTC........................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 80 HP_score: -10.1 Tail_Score: -3.62096 Start: 138 End: 180 Full_Region: AGGCAATTTTTACAA GGGGTACGATGGACGT GAAATGAGAAAA ACGTCATCGTACCCC TTTACAATGATAGAA .........................................................................................................................................GGGGTACGATGGACGTGAAATGAGAAAAACGTCATCGTACCCC................................................................................................................................................................................. TransTerm Strand: - Conf: 77 HP_score: -10.1 Tail_Score: -3.3344 Start: 138 End: 180 Full_Region: ttctatcattgtaaa ggggtacgatgacgt ttttctcatttc acgtccatcgtacccc ttgtaaaaattgcct .........................................................................................................................................ggggtacgatgacgtttttctcatttcacgtccatcgtacccc................................................................................................................................................................................. TransTerm Strand: - Conf: 46 HP_score: -3.8 Tail_Score: -2.75822 Start: 169 End: 190 Full_Region: ctgccatttcttcta tcattgta aagggg tacgatga cgtttttctcatttc ........................................................................................................................................................................tcattgtaaaggggtacgatga....................................................................................................................................................................... TransTerm Strand: + Conf: 45 HP_score: -2.1 Tail_Score: -3.34398 Start: 240 End: 254 Full_Region: TGCGAGAATGAGTAG TGCAG TTCTT CTGTA TATTTACCAACAAGG ...............................................................................................................................................................................................................................................TGCAGTTCTTCTGTA....................................................................................................... Find igs database================================================ Query_seq: PI0138:PI0140|PI0138:PI0140:hypothetical protein:conserved hypothetical protein:->->:131426..131782 357 tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Intra-Species Hit: Count: 1 Min: 1 Max: 357 Len: 357 Subject: pint_PI0138_PI0140|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[131426,131782]|357 HSP 1 e-value: 0.0 bit: 708.0 Len: 357 Query Start:1 Query End:357 Subject Strand: POSITIVE Subject Start: 1 Subject End: 357 tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta tgatttttggggaactaatgcctcatagtgctgtgcttcattataatgagtagtgaggcgtagcagaaaacttgcaaggatttccctttctataataatacaatgggtagataaaacccaataggcaatttttacaaggggtacgatggacgtgaaatgagaaaaacgtcatcgtacccctttacaatgatagaagaaatggcagggactgcgcctcgtctgcctgcgagaatgagtagtgcagttcttctgtatatttaccaacaaggaacaggcaaaacacagtagacctataaagtacttttggtttgttccctgaaccgatacactctatgcaatgtaaccctccttttccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUUGGGGAACUAAUGCCUCAUAGUGCUGUGCUUCAUUAUAAUGAGUAGUGAGGCGUAGCAGAAAACUUGCAAGGAUUUCCCUUUCUAUAAUAAUACAAUGGGUAGAUAAAACCCAAUAGGCAAUUUUUACAAGGGGUACGAUGGACGUGAAAUGAGAAAAACGUCAUCGUACCCCUUUACAAUGAUAGAAGAAAUGGCAGGGACUGCGCCUCGUCUGCCUGCGAGAAUGAGUAGUGCAGUUCUUCUGUAUAUUUACCAACAAGGAACAGGCAAAACACAGUAGACCUAUAAAGUACUUUUGGUUUGUUCCCUGAACCGAUACACUCUAUGCAAUGUAACCCUCCUUUUCCUA .......(((((((....(((((.((((((((((((((((((((.....))))))))))))))))..........((((.....)))).))))..........(((((.......)))))..)))))........(((((((((((((.((((............)))))))))))))))))((((.(((((((..((((((((((((((((((((((((((....).)).)))))..)))))))))..)))).))))).....((.(((((((((((((.((..((......))..))..)))).))))))))).))...........))))).)).))))........))))))) (-108.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAAAAGGAGGGUUACAUUGCAUAGAGUGUAUCGGUUCAGGGAACAAACCAAAAGUACUUUAUAGGUCUACUGUGUUUUGCCUGUUCCUUGUUGGUAAAUAUACAGAAGAACUGCACUACUCAUUCUCGCAGGCAGACGAGGCGCAGUCCCUGCCAUUUCUUCUAUCAUUGUAAAGGGGUACGAUGACGUUUUUCUCAUUUCACGUCCAUCGUACCCCUUGUAAAAAUUGCCUAUUGGGUUUUAUCUACCCAUUGUAUUAUUAUAGAAAGGGAAAUCCUUGCAAGUUUUCUGCUACGCCUCACUACUCAUUAUAAUGAAGCACAGCACUAUGAGGCAUUAGUUCCCCAAAAAUCA ..(((((.((((((....(((((...(((((...((((((.((.......))....................((((((((((((...........)))))).))))))..))))))...)))))..(((((........))))).))))))))).)).)))))(((((.......(((((((((((((((((............)))).)))))))))))))........(((....(((((.......)))))..))).....)))))..(((((......(((.......)))...((((((....((((....)))).((...))....)))))).....)))))......... (-100.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 242 201 214 156 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 405 244 201 229 185 pint:PI1689|5end_conserved_hypothetical_protein_1604310..1604540_POSITIVE 370 248 201 72 9 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 339 244 202 47 2 pint:PI1588|5end_DNA_polymerase_III,_epsilon_chain_1516302..1516532_POSITIVE 339 227 189 41 1 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 335 249 202 168 120 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 328 230 187 185 127 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 324 249 210 212 158 pint:PI1731|5end_formate--tetrahydrofolate_ligase_1650122..1650352_POSITIVE 324 249 210 204 150 pint:PI1730|5end_hypothetical_protein_1650114..1650344_POSITIVE 324 257 211 108 62 pint:PI0915|5end_hypothetical_protein_845183..845413_POSITIVE 322 245 201 77 36 pint:PI2170|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112238..2112468_POSITIVE 320 58 19 107 65 pint:PI1494|5end_conserved_hypothetical_protein_1413046..1413276_POSITIVE 320 248 205 220 178 pint:PI1098|5end_conserved_hypothetical_protein_1022261..1022491_POSITIVE 318 257 212 140 84 pint:PI0819|5end_hypothetical_protein_759414..759644_POSITIVE 317 245 203 65 12 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 317 219 171 82 20 pint:PI0065|5end_conserved_hypothetical_protein_64501..64731_POSITIVE 316 244 201 77 29 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 315 250 201 55 8 pint:PI0139|5end_pyridoxine_biosynthesis_protein_131835..132065_POSITIVE 314 235 200 91 55 pint:PI2112|5end_phosphopantetheine_adenylyltransferase_2063194..2063424_POSITIVE 314 218 184 209 170 pint:PI0200|5end_hypothetical_protein_191545..191775_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 245 207 151 109 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 357 244 202 60 10 pint:PI0947|3end_conserved_hypothetical_protein_880709..880859_POSITIVE 355 65 21 62 12 pint:PI0138|3end_hypothetical_protein_131365..131515_POSITIVE 333 259 212 133 85 pint:PI2113|3end_hypothetical_protein_2064278..2064428_POSITIVE 331 238 192 145 85 pint:PI1750|3end_sulfate_transporter_1673896..1674046_POSITIVE 326 227 200 117 84 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 324 249 205 129 80 pint:PI1395|3end_hypothetical_protein_1314407..1314557_POSITIVE 322 245 201 84 43 pint:PI2169|3end_hypothetical_protein_2112325..2112475_POSITIVE 314 235 200 75 39 pint:PI2111|3end_conserved_hypothetical_protein_2063258..2063408_POSITIVE 314 250 201 108 51 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 309 244 201 75 32 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 308 73 31 149 101 pint:PI2147|3end_GTP-binding_protein_2094407..2094557_POSITIVE 305 247 201 48 8 pint:PI1137|3end_hypothetical_protein_1064618..1064768_POSITIVE 303 244 204 127 91 pint:PI0785|3end_hypothetical_protein_724138..724288_POSITIVE 303 244 204 124 88 pint:PI0786|3end_conserved_hypothetical_protein;_possible_glycosyltransferase_724135..724285_POSITIVE 302 243 201 73 3 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 300 239 192 121 63 pint:PI1487|3end_hypothetical_protein_1407940..1408090_POSITIVE 296 244 204 87 35 pint:PI2014|3end_conserved_hypothetical_protein_1972603..1972753_POSITIVE 295 237 191 64 10 pint:PI1908|3end_transcriptional_regulator,_AraC_family_1853204..1853354_POSITIVE 295 232 192 57 18 pint:PI1792|3end_hypothetical_protein_1725143..1725293_POSITIVE