Origin IGS: tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta .........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.........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 taatggcaaaatctatctgcacgcataacaaaacgggccaaaacatagtggatttgcagagataagagcgtacctacgctgcgtatgaccatcattatttgtccaatacaacaactgtaagtagtcagattgtggttctgaatgtcgtggttccaatccgctgatgacaacttttaatataagaaaagagggtatatcgaaaccttgcgtttcaatataccctcttttcttttgcgcattaactgttcacaagccatatcaaggcactataaaaacatcaacaaggaagtgctaaagtaaagcgttaatcacgaaataaagaccaatggattatcgcaaaaccatctcgaaaatgtgaaaaaagaataaaaaacaagtgcagtttatagcttctcttgctctgttctgaaaaatattagtacattagcaaacgactatcataaactatgattacgagaaccaaacatttaagattcatcataagaaaccaaataattaccttttaatcattacatttattacattatgagaaaaaactatgtacgattagcccta Mask Tandem Repeat Region ================================================ tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta Find is-nt database================================================ Query_seq: PI0184:PI0185|PI0184:PI0185:possible fibronectin type III domain protein:conserved hypothetical protein:->->:176577..177131 555 tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0184:PI0185|PI0184:PI0185:possible fibronectin type III domain protein:conserved hypothetical protein:->->:176577..177131 555 tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0184:PI0185|PI0184:PI0185:possible fibronectin type III domain protein:conserved hypothetical protein:->->:176577..177131 555 tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 340 End: 540 ................................................................................................................................................................................................................................................................................................................................................... M E T Q G F D I P S F L I L K V V I S G L E P R H S E P Q S D Y L Q L L Y W T N N D G H T Q R R Y A L I S A N P L C F G ............... Protein_Len: 56 Strand: + Start: 386 End: 553 ................................................................................................................................................................................................................................................................................................................................................................................................. M S S A D W N H D I Q N H N L T T Y S C C I G Q I M M V I R S V G T L L S L Q I H Y V L A R F V M R A D R F C H .. Protein_Len: 44 Strand: - Start: 264 End: 395 ....................................................................................................................................................................................................................................................................... C K R T S T K I T G Q Y P K H V T L A C F F L P Y I S V C P K S I G E K R I N F T T M M ................................................................................................................................................................ Protein_Len: 34 Strand: - Start: 259 End: 360 .................................................................................................................................................................................................................................................................. K L V E K N I N K Y H R S I A Q S C N I R L L F S P I N F R L T E M ................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 30 End: 119 ............................. L T I F T I I L L Y N N P K K H H I K F T Q N E Y D Y N I M .................................................................................................................................................................................................................................................................................................................................................................................................................................................... tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta 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================================================ tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -23.5 Tail_Score: -3.67498 Start: 327 End: 373 Full_Region: AGTTAATGCGCAAAA GAAAAGAGGGTATATTGAAAC GCAAG GTTTCGATATACCCTCTTTTC TTATATTAAAAGTTG ......................................................................................................................................................................................................................................................................................................................................GAAAAGAGGGTATATTGAAACGCAAGGTTTCGATATACCCTCTTTTC...................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -21.3 Tail_Score: -4.1466 Start: 327 End: 373 Full_Region: caacttttaatataa gaaaagagggtatatcgaaac cttgc gtttcaatataccctcttttc ttttgcgcattaact ......................................................................................................................................................................................................................................................................................................................................gaaaagagggtatatcgaaaccttgcgtttcaatataccctcttttc...................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -17.6 Tail_Score: -4.90381 Start: 332 End: 368 Full_Region: ATGCGCAAAAGAAAA GAGGGTATATTGAAAC GCAAG GTTTCGATATACCCTC TTTTCTTATATTAAA ...........................................................................................................................................................................................................................................................................................................................................GAGGGTATATTGAAACGCAAGGTTTCGATATACCCTC........................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -15.4 Tail_Score: -5.08255 Start: 332 End: 368 Full_Region: tttaatataagaaaa gagggtatatcgaaac cttgc gtttcaatataccctc ttttcttttgcgcat ...........................................................................................................................................................................................................................................................................................................................................gagggtatatcgaaaccttgcgtttcaatataccctc........................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0184:PI0185|PI0184:PI0185:possible fibronectin type III domain protein:conserved hypothetical protein:->->:176577..177131 555 tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttgttttttattcttttttcacattttcgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta Intra-Species Hit: Count: 1 Min: 1 Max: 555 Len: 555 Subject: pint_PI0184_PI0185|possible fibronectin type III domain protein:conserved hypothetical protein|POSITIVE:POSITIVE|[176577,177131]|555 HSP 1 e-value: 0.0 bit: 692.0 Len: 349 Query Start:207 Query End:555 Subject Strand: POSITIVE Subject Start: 207 Subject End: 555 ..............................................................................................................................................................................................................cgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta ..............................................................................................................................................................................................................cgagatggttttgcgataatccattggtctttatttcgtgattaacgctttactttagcacttccttgttgatgtttttatagtgccttgatatggcttgtgaacagttaatgcgcaaaagaaaagagggtatattgaaacgcaaggtttcgatataccctcttttcttatattaaaagttgtcatcagcggattggaaccacgacattcagaaccacaatctgactacttacagttgttgtattggacaaataatgatggtcatacgcagcgtaggtacgctcttatctctgcaaatccactatgttttggcccgttttgttatgcgtgcagatagattttgccatta HSP 2 e-value: 2.0E-98 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttg..................................................................................................................................................................................................................................................................................................................................................................................... tagggctaatcgtacatagttttttctcataatgtaataaatgtaatgattaaaaggtaattatttggtttcttatgatgaatcttaaatgtttggttctcgtaatcatagtttatgatagtcgtttgctaatgtactaatatttttcagaacagagcaagagaagctataaactgcacttg..................................................................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGCUAAUCGUACAUAGUUUUUUCUCAUAAUGUAAUAAAUGUAAUGAUUAAAAGGUAAUUAUUUGGUUUCUUAUGAUGAAUCUUAAAUGUUUGGUUCUCGUAAUCAUAGUUUAUGAUAGUCGUUUGCUAAUGUACUAAUAUUUUUCAGAACAGAGCAAGAGAAGCUAUAAACUGCACUUGUUUUUUAUUCUUUUUUCACAUUUUCGAGAUGGUUUUGCGAUAAUCCAUUGGUCUUUAUUUCGUGAUUAACGCUUUACUUUAGCACUUCCUUGUUGAUGUUUUUAUAGUGCCUUGAUAUGGCUUGUGAACAGUUAAUGCGCAAAAGAAAAGAGGGUAUAUUGAAACGCAAGGUUUCGAUAUACCCUCUUUUCUUAUAUUAAAAGUUGUCAUCAGCGGAUUGGAACCACGACAUUCAGAACCACAAUCUGACUACUUACAGUUGUUGUAUUGGACAAAUAAUGAUGGUCAUACGCAGCGUAGGUACGCUCUUAUCUCUGCAAAUCCACUAUGUUUUGGCCCGUUUUGUUAUGCGUGCAGAUAGAUUUUGCCAUUA ..(((((((....((((((.....((((..(((((...(((.(.(((((..((.((((..............((((((.(((((..........)))))))))))...(((((((((....((.((((((..(((.((.(......).)).))).)))))).))...))))))))).)))).))..)))))).)))...)))))...)))).((.((((((((((.....((((((..((.(((((......(((.......)))..(((((((((((((((((((..((((.(((((.((.........))))))).))))..(((((((((((((((((((((((.....)))))))))))))))))))))))....))))))....)))))))))...)))).))))).))..)).)))).........(((((((.(((((.((((.(..((........))..))))))))))))))))).....)))))...))))).)).)))))).)))))))............(.(((((.....)))))).... (-146.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGCAAAAUCUAUCUGCACGCAUAACAAAACGGGCCAAAACAUAGUGGAUUUGCAGAGAUAAGAGCGUACCUACGCUGCGUAUGACCAUCAUUAUUUGUCCAAUACAACAACUGUAAGUAGUCAGAUUGUGGUUCUGAAUGUCGUGGUUCCAAUCCGCUGAUGACAACUUUUAAUAUAAGAAAAGAGGGUAUAUCGAAACCUUGCGUUUCAAUAUACCCUCUUUUCUUUUGCGCAUUAACUGUUCACAAGCCAUAUCAAGGCACUAUAAAAACAUCAACAAGGAAGUGCUAAAGUAAAGCGUUAAUCACGAAAUAAAGACCAAUGGAUUAUCGCAAAACCAUCUCGAAAAUGUGAAAAAAGAAUAAAAAACAAGUGCAGUUUAUAGCUUCUCUUGCUCUGUUCUGAAAAAUAUUAGUACAUUAGCAAACGACUAUCAUAAACUAUGAUUACGAGAACCAAACAUUUAAGAUUCAUCAUAAGAAACCAAAUAAUUACCUUUUAAUCAUUACAUUUAUUACAUUAUGAGAAAAAACUAUGUACGAUUAGCCCUA .....(((.........)))..............((((....(((((((((.(((((..((((((((.((((((......).)))))....)).))))))(((((.....(((((((........))).))))(((.((.....((((((((....(((..(((((..(((..(((((..(((((((((((((((((.(((((.....))))).)))))))))))))))))......)))))..))).....(((.......)))..........)))))....)))...(((.......)))...)))))))).....)))))..)))))....))))).)).(((((..(((((((.(((..................(((((((....((..(((((.(((.((((......)))).)))..)))))..)).....))))))).((((((.(((.......(......).(((.......))).............))).)))))).....))).))))))).)))))....))))))).......)))).. (-121.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 526 481 107 43 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 346 373 331 154 114 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 333 368 321 83 25 pint:PI0606|5end_naphthoate_synthase_552956..553186_POSITIVE 325 375 331 159 117 pint:PI0184|5end_possible_fibronectin_type_III_domain_protein_174355..174585_POSITIVE 325 375 331 151 109 pint:PI0183|5end_hypothetical_protein_174347..174577_POSITIVE 315 360 311 201 154 pint:PI1776|5end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1708623..1708853_POSITIVE 312 506 463 152 96 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 309 342 301 63 27 pint:PI1969|5end_hypothetical_protein_1925496..1925726_POSITIVE 309 438 393 80 41 pint:PI0244|5end_possible_mobilization_protein_C_240752..240982_POSITIVE 306 507 463 77 31 pint:PI0660|5end_conserved_hypothetical_protein_603438..603668_POSITIVE 303 510 461 111 62 pint:PI1003|5end_conserved_hypothetical_protein_924694..924924_POSITIVE 303 520 474 226 184 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 301 506 473 42 4 pint:PI0937|5end_hypothetical_protein_869235..869465_POSITIVE 300 370 326 117 73 pint:PI2082|5end_hypothetical_protein_2039878..2040108_POSITIVE 293 526 482 122 70 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 293 539 492 107 51 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 288 518 474 79 34 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 288 495 452 144 94 pint:PI0020|5end_conserved_hypothetical_protein_24525..24755_POSITIVE 286 539 491 79 19 pint:PI0902|5end_hypothetical_protein_832291..832521_POSITIVE 282 535 494 135 86 pint:PI2065|5end_hypothetical_protein_2026877..2027107_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 369 367 321 51 7 pint:PI0647|3end_potassium_uptake_protein_589276..589426_POSITIVE 346 373 331 108 68 pint:PI1462|3end_hypothetical_protein_1385383..1385533_POSITIVE 337 296 252 148 94 pint:PI0444|3end_50S_ribosomal_protein_L7/L12_413390..413540_POSITIVE 337 296 252 117 63 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 333 368 321 73 15 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 326 519 473 148 96 pint:PI0330|3end_hypothetical_protein_312545..312695_POSITIVE 318 537 491 83 34 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 309 342 301 51 15 pint:PI1968|3end_hypothetical_protein_1925564..1925714_POSITIVE 293 440 392 113 64 pint:PI0425|3end_hypothetical_protein_389722..389872_POSITIVE 290 338 291 120 78 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 287 537 496 142 110 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 284 256 213 90 43 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 284 322 287 124 89 pint:PI0652|3end_conserved_hypothetical_protein_595792..595942_POSITIVE 284 336 291 95 45 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 277 380 331 68 22 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE 270 499 451 141 85 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 268 505 472 79 46 pint:PI0753|3end_hypothetical_protein_683851..684001_POSITIVE 268 507 463 63 2 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 267 246 202 96 36 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 267 519 475 135 96 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE