Origin IGS: aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta .........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 taataaattatgagaaaggatgtagttgatagatatactattgatgataagggaagatttataaaacaataaatcttcctcctgaagttatataagtgctttctatgcgagaagtaggactggtagtaaaggttaacctttcactgatggacactaaagcagtagagattagacctatatgaaactcttctccgaagaatggattgaaaattctagtctatcagaaaaactcagataaagtataccgacaaggaagaaattacaagcattggcttctatcatgataaggattgcaaggaagtaatcacggaatttatagaaagcggacagacgatttatgcaagggtaactactcgtggactcgatgacagcgatattgcactaatcgtgtgtggacatggcacggtgaaagaagaagatactagcattaatggcactgtatatgaaatttcgggagaaacggattcccatggaattgctatcttggaaatcagaaccgacacaggttggctgaaagaaaagcaatcggaaacatttgatatctttgtgctggaaggaggttgcaaagagtcggtgattatt Mask Tandem Repeat Region ================================================ aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Find is-nt database================================================ Query_seq: PI1962:PI1963|PI1962:PI1963:conserved hypothetical protein:hypothetical protein:->->:1920767..1921348 582 aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1962:PI1963|PI1962:PI1963:conserved hypothetical protein:hypothetical protein:->->:1920767..1921348 582 aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1962:PI1963|PI1962:PI1963:conserved hypothetical protein:hypothetical protein:->->:1920767..1921348 582 aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 43 End: 198 .......................................... M K C F R L L F F Q P T C V G S D F Q D S N S M G I R F S R N F I Y S A I N A S I F F F H R A M S T H D ................................................................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 2 End: 244 . M I T D S L Q P P S S T K I S N V S D C F S F S Q P V S V L I S K I A I P W E S V S P E I S Y T V P L M L V S S S F T V .................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 208 End: 405 ............................................................................................................................................................................................................... M A V I E S T S S Y P C I N R L S A F Y K F R D Y F L A I L I M I E A N A C N F F L V G I L Y L S F S D R L E F S I H S ................................................................................................................................................................................. Protein_Len: 50 Strand: + Start: 372 End: 521 ................................................................................................................................................................................................................................................................................................................................................................................... M F N P F F G E E F H I G L I S T A L V S I S E R L T F T T S P T S R I E S T Y I T S G G R F I V L ............................................................. Protein_Len: 31 Strand: - Start: 72 End: 164 ....................................................................... G V Q T P E S K W S L L E M P I R K E R F K M Y L A M L A L M .................................................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 1 End: 363 H G C V I L A I D S D D L G R T T V R A Y I T Q G S E I F E T I V E K C D K D H Y F G I S T I E E K D T Y K I Q T K R M ........................................................................................................................................................................................................................... aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta 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================================================ aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 63 HP_score: -6.6 Tail_Score: -3.42996 Start: 503 End: 532 Full_Region: TTATATAACTTCAGG AGGAAGATTTAT TGTTTT ATAAATCTTCCC TTATCATCAATAGTA ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGGAAGATTTATTGTTTTATAAATCTTCCC.................................................. TransTerm Strand: + Conf: 74 HP_score: -10.1 Tail_Score: -2.65476 Start: 504 End: 531 Full_Region: TATATAACTTCAGGA GGAAGATTTAT TGTTTT ATAAATCTTCC CTTATCATCAATAGT .......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GGAAGATTTATTGTTTTATAAATCTTCC................................................... TransTerm Strand: - Conf: 49 HP_score: -3.7 Tail_Score: -3.22223 Start: 508 End: 527 Full_Region: ttgatgataagggaa gatttat aaaaca ataaatc ttcctcctgaagtta ...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................gatttataaaacaataaatc....................................................... Find igs database================================================ Query_seq: PI1962:PI1963|PI1962:PI1963:conserved hypothetical protein:hypothetical protein:->->:1920767..1921348 582 aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Intra-Species Hit: Count: 1 Min: 1 Max: 582 Len: 582 Subject: pint_PI1962_PI1963|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1920767,1921348]|582 HSP 1 e-value: 0.0 bit: 1154.0 Len: 582 Query Start:1 Query End:582 Subject Strand: POSITIVE Subject Start: 1 Subject End: 582 aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta aataatcaccgactctttgcaacctccttccagcacaaagatatcaaatgtttccgattgcttttctttcagccaacctgtgtcggttctgatttccaagatagcaattccatgggaatccgtttctcccgaaatttcatatacagtgccattaatgctagtatcttcttctttcaccgtgccatgtccacacacgattagtgcaatatcgctgtcatcgagtccacgagtagttacccttgcataaatcgtctgtccgctttctataaattccgtgattacttccttgcaatccttatcatgatagaagccaatgcttgtaatttcttccttgtcggtatactttatctgagtttttctgatagactagaattttcaatccattcttcggagaagagtttcatataggtctaatctctactgctttagtgtccatcagtgaaaggttaacctttactaccagtcctacttctcgcatagaaagcacttatataacttcaggaggaagatttattgttttataaatcttcccttatcatcaatagtatatctatcaactacatcctttctcataatttatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUCACCGACUCUUUGCAACCUCCUUCCAGCACAAAGAUAUCAAAUGUUUCCGAUUGCUUUUCUUUCAGCCAACCUGUGUCGGUUCUGAUUUCCAAGAUAGCAAUUCCAUGGGAAUCCGUUUCUCCCGAAAUUUCAUAUACAGUGCCAUUAAUGCUAGUAUCUUCUUCUUUCACCGUGCCAUGUCCACACACGAUUAGUGCAAUAUCGCUGUCAUCGAGUCCACGAGUAGUUACCCUUGCAUAAAUCGUCUGUCCGCUUUCUAUAAAUUCCGUGAUUACUUCCUUGCAAUCCUUAUCAUGAUAGAAGCCAAUGCUUGUAAUUUCUUCCUUGUCGGUAUACUUUAUCUGAGUUUUUCUGAUAGACUAGAAUUUUCAAUCCAUUCUUCGGAGAAGAGUUUCAUAUAGGUCUAAUCUCUACUGCUUUAGUGUCCAUCAGUGAAAGGUUAACCUUUACUACCAGUCCUACUUCUCGCAUAGAAAGCACUUAUAUAACUUCAGGAGGAAGAUUUAUUGUUUUAUAAAUCUUCCCUUAUCAUCAAUAGUAUAUCUAUCAACUACAUCCUUUCUCAUAAUUUAUUA .......((((((...................((((....((((.((((......(((((((..((((((((..((((......)))))))).....)))).)))))))...(((((.........)))))..)))).))))...))))......(((.(((((...(((((.(((.........((..(((.((((((.((((((....((((.(.(((......)))))))).....)))))).)))))).)))..))..............(.((((.(......).)))))......))).)))))...))))).)))...........))))))..((((.....)))).....(((((((.............(((.(((....)))..(((((..((((((((((....((((.(((...((((..(...((((((.((....))))))))....)..).)))....))))))).)).)))))))))))))..)))(((((((((((......)))))))))))..................))))))).......................... (-115.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAUUAUGAGAAAGGAUGUAGUUGAUAGAUAUACUAUUGAUGAUAAGGGAAGAUUUAUAAAACAAUAAAUCUUCCUCCUGAAGUUAUAUAAGUGCUUUCUAUGCGAGAAGUAGGACUGGUAGUAAAGGUUAACCUUUCACUGAUGGACACUAAAGCAGUAGAGAUUAGACCUAUAUGAAACUCUUCUCCGAAGAAUGGAUUGAAAAUUCUAGUCUAUCAGAAAAACUCAGAUAAAGUAUACCGACAAGGAAGAAAUUACAAGCAUUGGCUUCUAUCAUGAUAAGGAUUGCAAGGAAGUAAUCACGGAAUUUAUAGAAAGCGGACAGACGAUUUAUGCAAGGGUAACUACUCGUGGACUCGAUGACAGCGAUAUUGCACUAAUCGUGUGUGGACAUGGCACGGUGAAAGAAGAAGAUACUAGCAUUAAUGGCACUGUAUAUGAAAUUUCGGGAGAAACGGAUUCCCAUGGAAUUGCUAUCUUGGAAAUCAGAACCGACACAGGUUGGCUGAAAGAAAAGCAAUCGGAAACAUUUGAUAUCUUUGUGCUGGAAGGAGGUUGCAAAGAGUCGGUGAUUAUU ..........(((...((((((..((..((((.....))))..)).....((((((((((((......))))))))))))((((((.(((((((((((((....((((....((((...(((((...(((((....)))))..(((((((((............((((..((............))..))))...(((((.........))))).)))))))))....)).)))........(((((....(.((....)).)..((....((((((((.........((((((......)))))).........)))).))))..(((.((((((..(((((((((....))))......(((.......)))..)))))..)))))).))).......)).)))))...........)))).))))....)))))).)))))))...)))))).......((((((...))))))..)))))).....)))..((((((...(((((.((........)))))))..............((((((((((.......)).))))))))))))))....... (-140.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 238 203 46 7 pint:PI1664|5end_conserved_hypothetical_protein_1577285..1577515_POSITIVE 358 238 203 46 7 pint:PI0370|5end_conserved_hypothetical_protein_340453..340683_POSITIVE 341 244 201 63 21 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 337 239 194 225 165 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 332 330 281 55 9 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 317 509 462 141 93 pint:PI1542|5end_mobilization_protein_1461728..1461958_POSITIVE 315 127 81 77 29 pint:PI1626|5end_hypothetical_protein_1550194..1550424_POSITIVE 309 99 51 173 120 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 307 213 171 199 135 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 305 260 211 118 65 pint:PI2057|5end_conserved_hypothetical_protein;_possible_metal-dependent_membrane_protease_2014939..2015169_POSITIVE 304 244 201 82 21 pint:PI1892|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1834217..1834447_POSITIVE 304 96 55 151 107 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 302 260 211 70 21 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 302 260 211 200 143 pint:PI1660|5end_hypothetical_protein_1574659..1574889_POSITIVE 299 277 233 49 3 pint:PI0571|5end_conserved_hypothetical_protein;_possible_permease_515161..515391_POSITIVE 299 260 212 230 186 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 296 219 176 56 10 pint:PI0796|5end_competence_protein_733324..733554_POSITIVE 295 224 181 139 94 pint:PI0702|5end_conserved_hypothetical_protein;_possible_tetracenomycin_C_synthesis_protein_homolog_638640..638870_POSITIVE 293 489 445 167 127 pint:PI2031|5end_hypothetical_protein_1986053..1986283_POSITIVE 292 228 185 69 16 pint:PI0620|5end_hypothetical_protein_569729..569959_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 244 211 39 6 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 317 509 462 104 56 pint:PI1540|3end_hypothetical_protein_1461771..1461921_POSITIVE 315 127 81 71 23 pint:PI1625|3end_conserved_hypothetical_protein;_possible_phage_transposase_1550268..1550418_POSITIVE 314 150 103 88 39 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 303 220 171 148 99 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE 302 260 211 61 12 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 301 89 41 141 90 pint:PI1514|3end_tRNA_nucleotidyltransferase/poly(A)_polymerase_1434072..1434222_POSITIVE 300 109 70 67 28 pint:PI1769|3end_hypothetical_protein_1696937..1697087_POSITIVE 300 291 252 78 27 pint:PI0343|3end_hypothetical_protein_317920..318070_POSITIVE 299 220 180 85 44 pint:PI0778|3end_hypothetical_protein_714885..715035_POSITIVE 289 300 251 133 64 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 287 220 176 142 107 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 285 259 212 43 9 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 283 244 201 67 14 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE 283 277 231 102 50 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 281 320 274 143 102 pint:PI1704|3end_50S_ribosomal_protein_L32_1621680..1621830_POSITIVE 281 228 183 118 73 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 278 216 177 62 31 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 278 230 181 77 30 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 277 220 174 115 59 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE