Origin IGS: taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga .........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 tcgtctaacttctttatattaaagtgttttatacgcatcttgtttcacgtgaaacaaagatgctgtttcgtagccctttgctctcttaaatgtagttttaagcggatagctcaattacttttagacagcgagaaccgaaagacggcagtgctgtgtctttcggttcgcttgtattttccgcctcttgcaaaggataggaatctctattctacaaagcaaaagcacttgttttgtgagatggaaataactatgctgcaagatagcaaggtttgttttgctggatagagtagggcttctatgaaagggaacgaagcaccgttctactctcaacgttgctta Mask Tandem Repeat Region ================================================ taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Find is-nt database================================================ Query_seq: PI2123:PI2124|PI2123:PI2124:adenine phosphoribosyltransferase:excinuclease ABC, subunit C:->->:2072385..2072723 339 taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2123:PI2124|PI2123:PI2124:adenine phosphoribosyltransferase:excinuclease ABC, subunit C:->->:2072385..2072723 339 taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2123:PI2124|PI2123:PI2124:adenine phosphoribosyltransferase:excinuclease ABC, subunit C:->->:2072385..2072723 339 taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 41 End: 133 ........................................ M E A L L Y P A K Q T L L S C S I V I S I S Q N K C F C F V E .............................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 10 End: 216 ......... M R V E R C F V P F H R S P T L S S K T N L A I L Q H S Y F H L T K Q V L L L C R I E I P I L C K R R K I Q A N R K T Q ........................................................................................................................... Protein_Len: 30 Strand: + Start: 150 End: 239 ..................................................................................................................................................... M Q E A E N T S E P K D T A L P S F G S R C L K V I E L S A .................................................................................................... Protein_Len: 31 Strand: + Start: 226 End: 318 ................................................................................................................................................................................................................................. M S Y P L K T T F K R A K G Y E T A S L F H V K Q D A Y K T L ..................... Protein_Len: 60 Strand: - Start: 58 End: 324 ......................................................... D K A L P P F Y L R V S L C L V A T K R N E S D L L L Q A I R K F S C K L S C L A V F C C R Q K V H F L I R I F C K L M ............... taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga 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================================================ taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -4.7 Tail_Score: -2.63631 Start: 19 End: 34 Full_Region: ggcttctatgaaagg gaacg aagcac cgttc tactctcaacgttgc ..................gaacgaagcaccgttc................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -11.9 Tail_Score: -3.95836 Start: 172 End: 210 Full_Region: ttacttttagacagc gagaaccgaaagacggca gtgc tgtgtctttcggttcgc ttgtattttccgcct ...........................................................................................................................................................................gagaaccgaaagacggcagtgctgtgtctttcggttcgc................................................................................................................................. TransTerm Strand: - Conf: 78 HP_score: -9.8 Tail_Score: -3.45592 Start: 277 End: 305 Full_Region: taaagtgttttatac gcatcttgtttc acgt gaaacaaagatgc tgtttcgtagccctt ....................................................................................................................................................................................................................................................................................gcatcttgtttcacgtgaaacaaagatgc.................................. Find igs database================================================ Query_seq: PI2123:PI2124|PI2123:PI2124:adenine phosphoribosyltransferase:excinuclease ABC, subunit C:->->:2072385..2072723 339 taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Intra-Species Hit: Count: 1 Min: 1 Max: 339 Len: 339 Subject: pint_PI2123_PI2124|adenine phosphoribosyltransferase:excinuclease ABC, subunit C|POSITIVE:POSITIVE|[2072385,2072723]|339 HSP 1 e-value: 0.0 bit: 672.0 Len: 339 Query Start:1 Query End:339 Subject Strand: POSITIVE Subject Start: 1 Subject End: 339 taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga taagcaacgttgagagtagaacggtgcttcgttccctttcatagaagccctactctatccagcaaaacaaaccttgctatcttgcagcatagttatttccatctcacaaaacaagtgcttttgctttgtagaatagagattcctatcctttgcaagaggcggaaaatacaagcgaaccgaaagacacagcactgccgtctttcggttctcgctgtctaaaagtaattgagctatccgcttaaaactacatttaagagagcaaagggctacgaaacagcatctttgtttcacgtgaaacaagatgcgtataaaacactttaatataaagaagttagacga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAACGUUGAGAGUAGAACGGUGCUUCGUUCCCUUUCAUAGAAGCCCUACUCUAUCCAGCAAAACAAACCUUGCUAUCUUGCAGCAUAGUUAUUUCCAUCUCACAAAACAAGUGCUUUUGCUUUGUAGAAUAGAGAUUCCUAUCCUUUGCAAGAGGCGGAAAAUACAAGCGAACCGAAAGACACAGCACUGCCGUCUUUCGGUUCUCGCUGUCUAAAAGUAAUUGAGCUAUCCGCUUAAAACUACAUUUAAGAGAGCAAAGGGCUACGAAACAGCAUCUUUGUUUCACGUGAAACAAGAUGCGUAUAAAACACUUUAAUAUAAAGAAGUUAGACGA .......(((((((((..((((((....)))))).)))))...(.((((((......(((.((((........))))..((((((((.((((..(((((..(((.(((((.((((....)))).))))))))...)))))..))))...))))))))...)))..........((((((((((((.((....))..))))))))))))..(((.(((.((((((.((((((.....))))))...))).))).))).)))..)))))).)..(((.(((((((.(((((....))))))))))))..........(((((...)))))..))).)))). (-102.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUCUAACUUCUUUAUAUUAAAGUGUUUUAUACGCAUCUUGUUUCACGUGAAACAAAGAUGCUGUUUCGUAGCCCUUUGCUCUCUUAAAUGUAGUUUUAAGCGGAUAGCUCAAUUACUUUUAGACAGCGAGAACCGAAAGACGGCAGUGCUGUGUCUUUCGGUUCGCUUGUAUUUUCCGCCUCUUGCAAAGGAUAGGAAUCUCUAUUCUACAAAGCAAAAGCACUUGUUUUGUGAGAUGGAAAUAACUAUGCUGCAAGAUAGCAAGGUUUGUUUUGCUGGAUAGAGUAGGGCUUCUAUGAAAGGGAACGAAGCACCGUUCUACUCUCAACGUUGCUUA .........................(((((....((((((((((((....))))).)))))))..((((((((((((..(((((..((((.((((((...(((.....))).)))))).))))..(((((((((((((((((((.((....))))))))))))))).............((.(((((((..(.((((..((.(((((..((((((((((......))))))))))..))))).))..)))).))))))))..))..........))))))...)))))))))))...)))))).))))).(((((.((((........)))).))))). (-109.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 237 191 100 65 pint:PI0791|5end_conserved_hypothetical_protein_728361..728591_POSITIVE 361 219 173 106 49 pint:PI1586|5end_possible_HesA/MoeB/ThiF_family_protein_1514372..1514602_POSITIVE 351 198 153 187 139 pint:PI0404|5end_integrase_371295..371525_POSITIVE 330 230 185 42 4 pint:PI0314|5end_conserved_hypothetical_protein_295552..295782_POSITIVE 320 217 172 157 104 pint:PI1618|5end_hypothetical_protein_1542670..1542900_POSITIVE 316 99 60 50 4 pint:PI0307|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290042..290272_POSITIVE 315 269 226 57 20 pint:PI1362|5end_60Kd_inner_membrane_protein_1279820..1280050_POSITIVE 315 238 196 229 196 pint:PI1229|5end_conserved_hypothetical_protein_1151260..1151490_POSITIVE 310 215 171 110 57 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 310 217 172 135 87 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 309 240 191 89 52 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 309 240 192 61 4 pint:PI0146|5end_transcription_elongation_factor_140338..140568_POSITIVE 307 190 142 47 2 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 307 220 172 87 38 pint:PI0064|5end_hypothetical_protein_63622..63852_POSITIVE 306 219 172 56 17 pint:PI0812|5end_conserved_hypothetical_protein;_possible_ferredoxin_750185..750415_POSITIVE 305 214 172 43 3 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 301 77 31 177 135 pint:PI1010|5end_conserved_hypothetical_protein_930922..931152_POSITIVE 300 210 171 39 5 pint:PI1447|5end_probable_OPT_oligopeptide_transporter_protein_1369972..1370202_POSITIVE 299 60 20 115 68 pint:PI0762|5end_mannose-6-phosphate_isomerase,_class_I_696420..696650_POSITIVE 298 158 111 66 1 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 218 171 140 83 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 363 237 191 44 9 pint:PI0789|3end_NAD-utilizing_dehydrogenase_728385..728535_POSITIVE 320 217 172 76 23 pint:PI1616|3end_hypothetical_protein_1542669..1542819_POSITIVE 316 218 171 78 34 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 315 269 226 50 13 pint:PI1361|3end_CTP_synthase_(UTP-ammonia_lyase)_1279893..1280043_POSITIVE 310 215 171 120 67 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 307 60 15 151 97 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 305 216 176 99 40 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 304 214 173 150 103 pint:PI1979|3end_conserved_hypothetical_protein_1937327..1937477_POSITIVE 301 87 48 70 35 pint:PI1610|3end_Na+/H+_anti-porter_1538002..1538152_POSITIVE 295 218 186 85 53 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 294 160 115 82 28 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 293 218 185 127 95 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 290 225 185 40 9 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 286 200 157 97 39 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE 280 218 171 143 94 pint:PI1180|3end_ferric_uptake_regulation_protein_1102409..1102559_POSITIVE 278 43 4 133 88 pint:PI1856|3end_nicotinate-nucleotide_adenylyltransferase_1803885..1804035_POSITIVE 278 48 3 86 24 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 276 48 4 98 45 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 275 228 189 151 105 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE